BLASTP 2.2.26 [Sep-21-2011]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.


Reference for compositional score matrix adjustment: Altschul, Stephen F., 
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.

Query= psy13846
         (1423 letters)

Database: nr 
           23,463,169 sequences; 8,064,228,071 total letters

Searching..................................................done



>gi|441657982|ref|XP_003274523.2| PREDICTED: DNA-directed RNA polymerase III subunit RPC1 [Nomascus
           leucogenys]
          Length = 1275

 Score =  537 bits (1384), Expect = e-149,   Method: Compositional matrix adjust.
 Identities = 282/569 (49%), Positives = 365/569 (64%), Gaps = 65/569 (11%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD Q  P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNQHAPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYFR VI ILQ ICK  TC  ++L +E+   F   L+ P L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFRAVIGILQMICK--TCCHIMLSQEEKKQFLDYLKRPGLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K ++C HCG  NG VKKCGLLKI HEKYK   K  D IV + L  +  A++ 
Sbjct: 144 KKISDKCRKKNICHHCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPIVSNFLQSFETAIEH 203

Query: 271 NPEIE----------------------AHKKFGLIQTLNPLEVLQL--------FEAIPL 300
           N E+E                      +     +I+   P +VL L        F    +
Sbjct: 204 NKEVEPLLGRAQVSLRIDRVSPCWPGSSRSPDRVIRPPQPPKVLGLQVNNANINFLRKLV 263

Query: 301 EDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKS---------DNDVVLFNRQP 351
           ++ P +   A   +     + R L   N  R  +  +LK          D DVVLFNRQP
Sbjct: 264 QNGPEVHPGANFIQQRHTQMKRFLKYGN--REKMAQELKYGDIVERHLIDGDVVLFNRQP 321

Query: 352 SLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKL 411
           SLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA+AEAL      
Sbjct: 322 SLHKLSIMAHLARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEAKAEAL------ 375

Query: 412 SIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLI 471
                   VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++
Sbjct: 376 --------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASIL 427

Query: 472 ADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYT 531
                  G  ++   R   P + ++   +WTGKQIFS+IL+P+ D PV ANL+TKG+ Y 
Sbjct: 428 V------GKDEKIKVRLPPPTI-LKPVTLWTGKQIFSVILRPSNDNPVRANLRTKGKQYC 480

Query: 532 A-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSR 590
              E+ C  DSYV ++NSEL++GSMDK TLGSG K N+FYILLRD+G++ A  AM RL+R
Sbjct: 481 GKGEDLCANDSYVTIQNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQNEAADAMSRLAR 540

Query: 591 MTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
           +   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 541 LAPVYLSNRGFSIGIGDVTPGQGLLKAKY 569



 Score =  271 bits (694), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 190/509 (37%), Positives = 265/509 (52%), Gaps = 97/509 (19%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A     S+P+LS  E++  +   +   EFL    ++F+++IKKF
Sbjct: 769  GKDEPLEFKRVLDNIKAVFPCPSEPALSKNELILTTESIMKKSEFLC-CQDSFLQEIKKF 827

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 828  IKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQVEKFLETCRDKYMRAQ 881

Query: 1115 IEP--------ATAVGALAAQ----------------SIGEPGTQMTLKTFH-------- 1142
            +EP        A ++G    Q                ++G P  +  +            
Sbjct: 882  MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 941

Query: 1143 ----------------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                                    GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 942  AQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1001

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGV-- 1235
            +++RY  C  + R   G + V G + + + P+++SKS    + Q +K+ LP V  + +  
Sbjct: 1002 ETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVKQQSLLM 1061

Query: 1236 QGINRAVIHEEDVE-GVTKYKLLVE-GDNLRDVMATYGVKGVKCSSNNTYEVY------- 1286
            +  +  V++ E V   +   KL V+ GD      A   V   + S ++ Y V        
Sbjct: 1062 ETQHLPVVNAETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDL 1121

Query: 1287 -------------------KTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTS 1327
                               KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT 
Sbjct: 1122 PKVKQQSLLMETQHLPVVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTY 1181

Query: 1328 KGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVG 1387
            KGEVLGITR GLAKMKESVL LASFE T+DHLFDAA++GQ D + GVSECIIMG+PMN+G
Sbjct: 1182 KGEVLGITRFGLAKMKESVLMLASFEKTADHLFDAAYFGQKDSVCGVSECIIMGIPMNIG 1241

Query: 1388 TGLIKLLQAVPRS-EPVPRTLLFDNPEFH 1415
            TGL KLL    R   P  R L+FD  EFH
Sbjct: 1242 TGLFKLLHKADRDPNPPKRPLIFDTNEFH 1270



 Score =  200 bits (509), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 125/267 (46%), Positives = 165/267 (61%), Gaps = 33/267 (12%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LDKD D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 921  GVPRIKEIINASKAISTPIITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 980

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  C  + R   G + V G + + + P+++SKS  
Sbjct: 981  CFILVKLSLERIRLLRLEVNAETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSM 1040

Query: 882  SKMYQ-MKQLLPSVVIKGV--QGINRAVIHEEDVE-GVTKYKLLVE-GDNLRDVMATYGV 936
              + Q +K+ LP V  + +  +  +  V++ E V   +   KL V+ GD      A   V
Sbjct: 1041 YYVLQFLKEDLPKVKQQSLLMETQHLPVVNAETVRYSICTSKLRVKPGDVAVHGEAVVCV 1100

Query: 937  KGVKCSSNNTYEVY--------------------------KTLGIEAARSTIMTEIKLVM 970
               + S ++ Y V                           KTLGIEAAR+TI+ EI+  M
Sbjct: 1101 TPRENSKSSMYYVLQFLKEDLPKVKQQSLLMETQHLPVVEKTLGIEAARTTIINEIQYTM 1160

Query: 971  ENHGMSIDFRHPMLVADLMTSKGEVLG 997
             NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1161 VNHGMSIDRRHVMLLSDLMTYKGEVLG 1187



 Score =  116 bits (291), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 685 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 744



 Score = 82.0 bits (201), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1211 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPNPPKRPLIFDTNEFH 1270

Query: 727  FPQV 730
             P V
Sbjct: 1271 IPLV 1274



 Score = 74.7 bits (182), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 376 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 430


>gi|449269147|gb|EMC79953.1| DNA-directed RNA polymerase III subunit RPC1, partial [Columba livia]
          Length = 1375

 Score =  419 bits (1076), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 239/479 (49%), Positives = 305/479 (63%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A    RS+P+LS  E++  S   +   EFL    ++F+++IKKF
Sbjct: 899  GKDEPLEFKRVLDNIRAVYPCRSEPALSKNELVLTSESIMKKNEFLC-CRDSFLQEIKKF 957

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       Q+L   D+I       P       E CR+KY+RAQ
Sbjct: 958  IKGVSEKIKKTRDKYGINDNGTTEPQVLYQLDRI------TPTQLEKFLETCRDKYMRAQ 1011

Query: 1115 IEPATAVGALAAQSIGEPGTQMTLKTFH-------------------------------- 1142
            +EP +AVGAL AQSIGEPGTQMTLKTFH                                
Sbjct: 1012 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1071

Query: 1143 ----------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                      FA            GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1072 AQLDKDDDPDFARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1131

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  CI + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1132 ETVRYSICISKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQSLKEELPKVVVQGIPE 1191

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG K SSNNTYEV KTLGIEAAR+T
Sbjct: 1192 VSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTKTSSNNTYEVEKTLGIEAARTT 1251

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1252 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1311

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL-QAVPRSEPVPRTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL +A   S P  R L+FDN EFH
Sbjct: 1312 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADKESTPPRRPLVFDNNEFH 1370



 Score =  351 bits (900), Expect = 2e-93,   Method: Compositional matrix adjust.
 Identities = 170/280 (60%), Positives = 208/280 (74%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 441 DGDIVLFNRQPSLHKLSIMAHIARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 500

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 501 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 546

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++       G  ++   R   P + ++   +WTGKQ+FSLILKP+ DCPV 
Sbjct: 547 AKACQIIASILV------GKDEKIKVRLPPPAI-LKPVTLWTGKQVFSLILKPSDDCPVK 599

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C+ DSYV ++NSEL++GSMDK TLGSG K N+FYILLRD+G+ 
Sbjct: 600 ANLRTKGKQYCGKGEDLCYNDSYVTIQNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQV 659

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 660 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 699



 Score =  295 bits (755), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 143/254 (56%), Positives = 180/254 (70%), Gaps = 5/254 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD    P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 11  EEMRQQAHIQVVSKNLYSQDNHHAPLQYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 70

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYF+ VI ILQ ICK  +C R++L  E+   F   L+ P L+YL ++ LK
Sbjct: 71  IDLELPCFHVGYFKAVIGILQMICK--SCCRIMLSVEEKKQFLDYLKRPGLTYLQKRGLK 128

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KK+ E  +K + CP+CG  NG VKKCGLLKI HEKYK   K  D +V   L  +  A++ 
Sbjct: 129 KKVSEKCRKKNTCPYCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPMVSTFLQSFETAIEH 188

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP EDIPLLLMN E  KPSDLILTRLLVPP C
Sbjct: 189 NKEVEPL--LGRAQENLNPLVVLNLFKRIPAEDIPLLLMNPEAGKPSDLILTRLLVPPLC 246

Query: 330 IRPSVISDLKSDND 343
           IRPSV+SDLKS  +
Sbjct: 247 IRPSVVSDLKSGTN 260



 Score =  292 bits (748), Expect = 9e-76,   Method: Compositional matrix adjust.
 Identities = 149/237 (62%), Positives = 187/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LDKD D D+AR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1051 GVPRIKEIINASKAISTPIITAQLDKDDDPDFARLVKGRIEKTLLGEISEYIEEVFLPDD 1110

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  CI + R   G + V G + + + P+++SKS  
Sbjct: 1111 CFILVKLSLERIRLLRLEVNAETVRYSICISKLRVKPGDVAVHGEAVVCVTPRENSKSSM 1170

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG K
Sbjct: 1171 YYVLQSLKEELPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTK 1230

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             SSNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1231 TSSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1287



 Score =  116 bits (291), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 815 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 874



 Score = 84.0 bits (206), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 40/64 (62%), Positives = 47/64 (73%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL-QAVPRSEPVPRTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL +A   S P  R L+FDN EFH
Sbjct: 1311 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADKESTPPRRPLVFDNNEFH 1370

Query: 727  FPQV 730
             P V
Sbjct: 1371 IPLV 1374



 Score = 74.7 bits (182), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 506 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 560


>gi|57529842|ref|NP_001006500.1| DNA-directed RNA polymerase III subunit RPC1 [Gallus gallus]
 gi|75571385|sp|Q5ZL98.1|RPC1_CHICK RecName: Full=DNA-directed RNA polymerase III subunit RPC1; Short=RNA
            polymerase III subunit C1; AltName: Full=DNA-directed RNA
            polymerase III subunit A
 gi|53130332|emb|CAG31495.1| hypothetical protein RCJMB04_7b9 [Gallus gallus]
          Length = 1390

 Score =  417 bits (1071), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 238/479 (49%), Positives = 305/479 (63%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A    RS+P+LS  E++  S   +   EFL    ++F+++IKKF
Sbjct: 914  GKDEPLEFKRVLDNIRAVYPCRSEPALSKNELVLTSESIMKKNEFLC-CRDSFLQEIKKF 972

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 973  IKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQLEKFLETCRDKYMRAQ 1026

Query: 1115 IEPATAVGALAAQSIGEPGTQMTLKTFH-------------------------------- 1142
            +EP +AVGAL AQSIGEPGTQMTLKTFH                                
Sbjct: 1027 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1086

Query: 1143 ----------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                      FA            GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1087 AQLDKDDDPDFARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1146

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  CI + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1147 ETVRYSICISKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQSLKEELPKVVVQGIPE 1206

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG K SSNNTYEV KTLGIEAAR+T
Sbjct: 1207 VSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTKTSSNNTYEVEKTLGIEAARTT 1266

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1267 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1326

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL-QAVPRSEPVPRTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL +A   S P  R L+FDN EFH
Sbjct: 1327 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADKESTPPRRPLIFDNNEFH 1385



 Score =  348 bits (894), Expect = 1e-92,   Method: Compositional matrix adjust.
 Identities = 169/280 (60%), Positives = 207/280 (73%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDIVLFNRQPSLHKLSIMAHIARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++       G  ++   R   P + ++   +WTGKQ+FS ILKP+ DCPV 
Sbjct: 562 AKACQIIASILV------GKDEKIKVRLPPPAI-LKPVTLWTGKQVFSSILKPSDDCPVK 614

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C+ DSYV ++NSEL++GSMDK TLGSG K N+FYILLRD+G+ 
Sbjct: 615 ANLRTKGKQYCGKGEDLCYNDSYVTIQNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQV 674

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 675 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 714



 Score =  297 bits (761), Expect = 3e-77,   Method: Compositional matrix adjust.
 Identities = 145/251 (57%), Positives = 179/251 (71%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD    P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNHHAPLQYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYF+ VI ILQ ICK  TC R++L  E+   F   L+ P L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFKAVIGILQMICK--TCCRIMLSVEEKKQFLDYLKRPGLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KK+ E  +K + CP+CG  NG VKKCGLLKI HEKYK   K  D IV   L  +  A++ 
Sbjct: 144 KKVSEKCRKKNTCPYCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPIVSTFLQSFETAIEH 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP EDIPLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NKEVEPL--LGRAQENLNPLVVLNLFKRIPAEDIPLLLMNPEAGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 262 IRPSVVSDLKS 272



 Score =  292 bits (747), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 149/237 (62%), Positives = 187/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LDKD D D+AR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1066 GVPRIKEIINASKAISTPIITAQLDKDDDPDFARLVKGRIEKTLLGEISEYIEEVFLPDD 1125

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  CI + R   G + V G + + + P+++SKS  
Sbjct: 1126 CFILVKLSLERIRLLRLEVNAETVRYSICISKLRVKPGDVAVHGEAVVCVTPRENSKSSM 1185

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG K
Sbjct: 1186 YYVLQSLKEELPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTK 1245

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             SSNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1246 TSSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1302



 Score =  116 bits (291), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 830 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 889



 Score = 84.0 bits (206), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 40/64 (62%), Positives = 47/64 (73%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL-QAVPRSEPVPRTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL +A   S P  R L+FDN EFH
Sbjct: 1326 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADKESTPPRRPLIFDNNEFH 1385

Query: 727  FPQV 730
             P V
Sbjct: 1386 IPIV 1389



 Score = 74.7 bits (182), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 521 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 575


>gi|345489196|ref|XP_001602571.2| PREDICTED: DNA-directed RNA polymerase III subunit RPC1-like [Nasonia
            vitripennis]
          Length = 1355

 Score =  417 bits (1071), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 231/481 (48%), Positives = 305/481 (63%), Gaps = 77/481 (16%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   PV+ KR+LDD+ ++++  ++  L    I+  ++  LDS++F    S+ F +++ +F
Sbjct: 885  GKDCPVDYKRVLDDVKSRSTHITEDPLDGPGIMKATSLLLDSEDF-ACLSDEFKQELAQF 943

Query: 1057 LEEFSKK-ESVTSH-QDKVSQPLREQI----LSHQDKIGHGRESNPFPSACKAEACREKY 1110
            L+  + K   V  H +   +QP+ + I    +S   +  H               C+EKY
Sbjct: 944  LKAVAIKIARVRQHIKSNDNQPVYKYIERLTVSQLAEFIH--------------TCKEKY 989

Query: 1111 VRAQIEPATAVGALAAQSIGEPGTQMTLKTFH---------------------------- 1142
            ++A+IEP TAVGALAAQSIGEPGTQMTLKTFH                            
Sbjct: 990  MKAKIEPGTAVGALAAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIINANPKIST 1049

Query: 1143 --------------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHL 1176
                          FA            GE+ EYIEEV++PDD F+L+K+D+DR++LL L
Sbjct: 1050 PIITAALENDTDPEFARRVKGRIEKTTLGEITEYIEEVYLPDDCFLLLKIDIDRVKLLKL 1109

Query: 1177 EVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKG 1234
            EVD++SIRY  C  + +    ++ + G S + + P     + +  + Q+K  +P+V++KG
Sbjct: 1110 EVDVNSIRYSLCTSKLKLNPKNVVIQGDSIITIYPSKQKHNLSVTLTQLKDSIPNVIVKG 1169

Query: 1235 VQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAA 1294
            +  ++RAVIH +D  G T+YKL VEGDN+RDVMAT GVKG K +SNNT EV+KTLGIEAA
Sbjct: 1170 IASVSRAVIHNDDSSGKTRYKLFVEGDNMRDVMATLGVKGPKTTSNNTIEVFKTLGIEAA 1229

Query: 1295 RSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFEN 1354
            R+TIMTEIKLVMENHGMSID RHPMLVADLMTS+GEVLGITR GLAKMKESVLNLASFE 
Sbjct: 1230 RATIMTEIKLVMENHGMSIDRRHPMLVADLMTSRGEVLGITRQGLAKMKESVLNLASFEK 1289

Query: 1355 TSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEF 1414
            T+DHLFDAA+YGQ D ISGVSE IIMG+P+ VGTG+ KLL    +     RTLLFD+P  
Sbjct: 1290 TADHLFDAAYYGQKDAISGVSESIIMGIPVPVGTGIFKLLHKSEKDPLKTRTLLFDSPNH 1349

Query: 1415 H 1415
            H
Sbjct: 1350 H 1350



 Score =  397 bits (1019), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 190/276 (68%), Positives = 217/276 (78%), Gaps = 21/276 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH+AKVL +RTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 428 DGDVVLFNRQPSLHKLSIMAHKAKVLENRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 487

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL              VLM NKSNLVTPRNGELLIAATQDFITGGYLLTQK+ F N+
Sbjct: 488 RAEAL--------------VLMGNKSNLVTPRNGELLIAATQDFITGGYLLTQKDTFLNK 533

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           +Q  ++ S L+A       I       +      ++ A++WTGKQIFS+IL+PN  CPV 
Sbjct: 534 SQVSQLISCLLAGEDTTMQI-------TLPKPAILKPAIMWTGKQIFSVILRPNEKCPVK 586

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           ANLKTKGRAYT+NEE C  DSYVI+RNS+LLAGSMDKSTLGSG K N+FYILLRD+GEDV
Sbjct: 587 ANLKTKGRAYTSNEELCINDSYVIIRNSQLLAGSMDKSTLGSGAKQNIFYILLRDWGEDV 646

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           A   MWRL+R+ S++LMNRGFSIGIGDVTPG   ++
Sbjct: 647 AALVMWRLARIASYFLMNRGFSIGIGDVTPGHSLLR 682



 Score =  306 bits (784), Expect = 6e-80,   Method: Compositional matrix adjust.
 Identities = 147/236 (62%), Positives = 189/236 (80%), Gaps = 2/236 (0%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA+  ISTPIITA L+ DTD ++AR VKGR+E+TTLGE+ EYIEEV++PDD
Sbjct: 1033 GVPRIKEIINANPKISTPIITAALENDTDPEFARRVKGRIEKTTLGEITEYIEEVYLPDD 1092

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             F+L+K+D+DR++LL LEVD++SIRY  C  + +    ++ + G S + + P     + +
Sbjct: 1093 CFLLLKIDIDRVKLLKLEVDVNSIRYSLCTSKLKLNPKNVVIQGDSIITIYPSKQKHNLS 1152

Query: 882  SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
              + Q+K  +P+V++KG+  ++RAVIH +D  G T+YKL VEGDN+RDVMAT GVKG K 
Sbjct: 1153 VTLTQLKDSIPNVIVKGIASVSRAVIHNDDSSGKTRYKLFVEGDNMRDVMATLGVKGPKT 1212

Query: 942  SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +SNNT EV+KTLGIEAAR+TIMTEIKLVMENHGMSID RHPMLVADLMTS+GEVLG
Sbjct: 1213 TSNNTIEVFKTLGIEAARATIMTEIKLVMENHGMSIDRRHPMLVADLMTSRGEVLG 1268



 Score =  254 bits (648), Expect = 3e-64,   Method: Compositional matrix adjust.
 Identities = 130/246 (52%), Positives = 170/246 (69%), Gaps = 13/246 (5%)

Query: 120 LLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTC 179
           LLD R+GT      C+TC + L++C+GHFGY+DL LPVFH+GYFR  I ILQSICK   C
Sbjct: 27  LLDSRLGTCSNANKCSTCNKPLNECIGHFGYLDLELPVFHVGYFRSTIGILQSICKK--C 84

Query: 180 ARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLL 239
           ++V+L  +    +  ++ NP LSYL RK+L+K+ILE  KK + C +CGE+NG VKK GLL
Sbjct: 85  SQVMLNPKDKKMYLDRVLNPNLSYLSRKALRKQILEKAKKCTTCHYCGELNGTVKKAGLL 144

Query: 240 KISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIP 299
           KI HEKYKN+ K  D IV+  LAEY++ V+ N E+E+  + GLI  LNPLEV+ L E IP
Sbjct: 145 KIVHEKYKNK-KPSDPIVQTKLAEYHKVVEDNKELESILQSGLISILNPLEVIGLLERIP 203

Query: 300 LEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKS----DN------DVVLFNR 349
             DIPLLLMN + S P DLILTR+ VPP  IRPS++SDLK+    DN      +++L N 
Sbjct: 204 ERDIPLLLMNPQCSVPRDLILTRIPVPPISIRPSIVSDLKAGTNEDNLTMKLSEILLINE 263

Query: 350 QPSLHK 355
              +H+
Sbjct: 264 AIQIHR 269



 Score =  120 bits (301), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 53/63 (84%), Positives = 59/63 (93%)

Query: 608 VTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           V   +GFV+NSF+SGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC+ Y
Sbjct: 798 VPAAKGFVENSFYSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCLHY 857

Query: 668 DMS 670
           D++
Sbjct: 858 DLT 860



 Score = 88.6 bits (218), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 41/54 (75%), Positives = 47/54 (87%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           VLM NKSNLVTPRNGELLIAATQDFITGGYLLTQK+ F N++Q  ++ S L+AG
Sbjct: 493 VLMGNKSNLVTPRNGELLIAATQDFITGGYLLTQKDTFLNKSQVSQLISCLLAG 546



 Score = 73.9 bits (180), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 35/59 (59%), Positives = 41/59 (69%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFH 726
            D  FDAA+YGQ D ISGVSE IIMG+P+ VGTG+ KLL    +     RTLLFD+P  H
Sbjct: 1292 DHLFDAAYYGQKDAISGVSESIIMGIPVPVGTGIFKLLHKSEKDPLKTRTLLFDSPNHH 1350


>gi|326923517|ref|XP_003207982.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1-like, partial
            [Meleagris gallopavo]
          Length = 641

 Score =  416 bits (1070), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 238/482 (49%), Positives = 307/482 (63%), Gaps = 73/482 (15%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A    RS+P+LS  E++  S   +   EFL    ++F+++IKKF
Sbjct: 165  GKDEPLEFKRVLDNIRAVYPCRSEPALSKNELVLTSESIMKKNEFLC-CRDSFLQEIKKF 223

Query: 1057 LEEFSKKESVTS-----HQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYV 1111
            ++  S+K   T      + +  ++P   ++L   D+I       P       E CR+KY+
Sbjct: 224  IKGVSEKIKKTRDKYGINDNGTTEP---RVLYQLDRI------TPTQLEKFLETCRDKYM 274

Query: 1112 RAQIEPATAVGALAAQSIGEPGTQMTLKTFH----------------------------- 1142
            RAQ+EP +AVGAL AQSIGEPGTQMTLKTFH                             
Sbjct: 275  RAQMEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTP 334

Query: 1143 -------------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLE 1177
                         FA            GE+ EYIEEVF+PDD FIL+KL ++RIRLL LE
Sbjct: 335  IITAQLDKDDDPDFARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLE 394

Query: 1178 VDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKG 1234
            V+ +++RY  CI + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G
Sbjct: 395  VNAETVRYSICISKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQSLKEELPKVVVQG 454

Query: 1235 VQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAA 1294
            +  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG K SSNNTYEV KTLGIEAA
Sbjct: 455  IPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTKTSSNNTYEVEKTLGIEAA 514

Query: 1295 RSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFEN 1354
            R+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE 
Sbjct: 515  RTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEK 574

Query: 1355 TSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL-QAVPRSEPVPRTLLFDNPE 1413
            T+DHLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL +A   S P  R L+FDN +
Sbjct: 575  TADHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADKESTPPRRPLVFDNND 634

Query: 1414 FH 1415
            FH
Sbjct: 635  FH 636



 Score =  293 bits (749), Expect = 6e-76,   Method: Compositional matrix adjust.
 Identities = 149/237 (62%), Positives = 187/237 (78%), Gaps = 3/237 (1%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
           GVPRIKEIINAS+ ISTPIITA LDKD D D+AR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 317 GVPRIKEIINASKAISTPIITAQLDKDDDPDFARLVKGRIEKTLLGEISEYIEEVFLPDD 376

Query: 824 SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
            FIL+KL ++RIRLL LEV+ +++RY  CI + R   G + V G + + + P+++SKS  
Sbjct: 377 CFILVKLSLERIRLLRLEVNAETVRYSICISKLRVKPGDVAVHGEAVVCVTPRENSKSSM 436

Query: 882 SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
             + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG K
Sbjct: 437 YYVLQSLKEELPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTK 496

Query: 941 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            SSNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 497 TSSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 553



 Score =  117 bits (292), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 81  AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 140



 Score = 82.8 bits (203), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 39/64 (60%), Positives = 47/64 (73%), Gaps = 1/64 (1%)

Query: 668 DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL-QAVPRSEPVPRTLLFDNPEFH 726
           D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL +A   S P  R L+FDN +FH
Sbjct: 577 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADKESTPPRRPLVFDNNDFH 636

Query: 727 FPQV 730
            P V
Sbjct: 637 IPIV 640


>gi|449504974|ref|XP_004174828.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1 isoform 2
            [Taeniopygia guttata]
          Length = 1369

 Score =  415 bits (1066), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 236/479 (49%), Positives = 305/479 (63%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A    RS+P+LS  E++  S   +   EFL    ++F+++IKKF
Sbjct: 893  GKDEPLEFKRVLDNIRAVYPCRSEPALSKNELVLTSESIMKKNEFLC-CQDSFLQEIKKF 951

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 952  IKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQLEKFLETCRDKYMRAQ 1005

Query: 1115 IEPATAVGALAAQSIGEPGTQMTLKTFH-------------------------------- 1142
            +EP +AVGAL AQSIGEPGTQMTLKTFH                                
Sbjct: 1006 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1065

Query: 1143 ----------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                      FA            GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1066 AQLDKDDDPDFARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1125

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C+ + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1126 ETVRYSICVSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQSLKEELPKVVVQGIPE 1185

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG K SSNNTYEV KTLGIEAAR+T
Sbjct: 1186 VSRAVIHVDEQSGKEKYKLLVEGDNLRAVMATHGVKGTKTSSNNTYEVEKTLGIEAARTT 1245

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1246 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1305

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL-QAVPRSEPVPRTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL +A   S P  R L+FD+ EFH
Sbjct: 1306 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHRADKESTPPRRPLIFDHNEFH 1364



 Score =  351 bits (901), Expect = 2e-93,   Method: Compositional matrix adjust.
 Identities = 170/280 (60%), Positives = 208/280 (74%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 435 DGDIVLFNRQPSLHKLSIMAHIARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 494

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 495 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 540

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++       G  ++   R   P + ++   +WTGKQ+FSLILKP+ DCPV 
Sbjct: 541 AKACQIIASILV------GKDEKIKVRLPPPAI-LKPVTLWTGKQVFSLILKPSDDCPVK 593

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C+ DSYV ++NSEL++GSMDK TLGSG K N+FYILLRD+G+ 
Sbjct: 594 ANLRTKGKQYCGKGEDLCYNDSYVTIQNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQV 653

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 654 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 693



 Score =  297 bits (761), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 143/254 (56%), Positives = 183/254 (72%), Gaps = 5/254 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD   +P+ +G+LD RMGT++K+  C TCG++L+DC+GH+GY
Sbjct: 5   EEMRQQAHIQVVSKNLYSQDNHHSPLQYGVLDHRMGTSEKDRPCETCGKSLADCLGHYGY 64

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYF+ VI ILQ ICK  TC R++L  E+   F   L+ P L+YL ++ LK
Sbjct: 65  IDLELPCFHVGYFKAVIGILQMICK--TCCRIMLSVEEKKQFLDYLKRPGLAYLQKRGLK 122

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KK+ E  +K + CP+CG  NG VKKCGLLKI HEKYK   K  D IV   L  +  A+++
Sbjct: 123 KKVSEKCRKKTTCPYCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPIVSTFLQSFETAIEY 182

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP+EDIPLLLMN +  KPSDLILTRLLVPP C
Sbjct: 183 NKEVEPL--LGRAQENLNPLVVLNLFKRIPVEDIPLLLMNPQAGKPSDLILTRLLVPPLC 240

Query: 330 IRPSVISDLKSDND 343
           IRPSV+SDLKS  +
Sbjct: 241 IRPSVVSDLKSGTN 254



 Score =  292 bits (747), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 148/237 (62%), Positives = 187/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LDKD D D+AR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1045 GVPRIKEIINASKAISTPIITAQLDKDDDPDFARLVKGRIEKTLLGEISEYIEEVFLPDD 1104

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  C+ + R   G + V G + + + P+++SKS  
Sbjct: 1105 CFILVKLSLERIRLLRLEVNAETVRYSICVSKLRVKPGDVAVHGEAVVCVTPRENSKSSM 1164

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG K
Sbjct: 1165 YYVLQSLKEELPKVVVQGIPEVSRAVIHVDEQSGKEKYKLLVEGDNLRAVMATHGVKGTK 1224

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             SSNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1225 TSSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1281



 Score =  116 bits (291), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 52/64 (81%), Positives = 58/64 (90%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 809 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 868

Query: 671 FDAA 674
             ++
Sbjct: 869 VRSS 872



 Score = 81.6 bits (200), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 39/64 (60%), Positives = 47/64 (73%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL-QAVPRSEPVPRTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL +A   S P  R L+FD+ EFH
Sbjct: 1305 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHRADKESTPPRRPLIFDHNEFH 1364

Query: 727  FPQV 730
             P V
Sbjct: 1365 IPIV 1368



 Score = 74.7 bits (182), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 500 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 554


>gi|224052370|ref|XP_002195476.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1 isoform 1
            [Taeniopygia guttata]
          Length = 1390

 Score =  415 bits (1066), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 236/479 (49%), Positives = 305/479 (63%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A    RS+P+LS  E++  S   +   EFL    ++F+++IKKF
Sbjct: 914  GKDEPLEFKRVLDNIRAVYPCRSEPALSKNELVLTSESIMKKNEFLC-CQDSFLQEIKKF 972

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 973  IKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQLEKFLETCRDKYMRAQ 1026

Query: 1115 IEPATAVGALAAQSIGEPGTQMTLKTFH-------------------------------- 1142
            +EP +AVGAL AQSIGEPGTQMTLKTFH                                
Sbjct: 1027 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1086

Query: 1143 ----------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                      FA            GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1087 AQLDKDDDPDFARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1146

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C+ + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1147 ETVRYSICVSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQSLKEELPKVVVQGIPE 1206

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG K SSNNTYEV KTLGIEAAR+T
Sbjct: 1207 VSRAVIHVDEQSGKEKYKLLVEGDNLRAVMATHGVKGTKTSSNNTYEVEKTLGIEAARTT 1266

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1267 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1326

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL-QAVPRSEPVPRTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL +A   S P  R L+FD+ EFH
Sbjct: 1327 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHRADKESTPPRRPLIFDHNEFH 1385



 Score =  351 bits (900), Expect = 2e-93,   Method: Compositional matrix adjust.
 Identities = 170/280 (60%), Positives = 208/280 (74%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDIVLFNRQPSLHKLSIMAHIARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++       G  ++   R   P + ++   +WTGKQ+FSLILKP+ DCPV 
Sbjct: 562 AKACQIIASILV------GKDEKIKVRLPPPAI-LKPVTLWTGKQVFSLILKPSDDCPVK 614

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C+ DSYV ++NSEL++GSMDK TLGSG K N+FYILLRD+G+ 
Sbjct: 615 ANLRTKGKQYCGKGEDLCYNDSYVTIQNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQV 674

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 675 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 714



 Score =  297 bits (761), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 143/251 (56%), Positives = 182/251 (72%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD   +P+ +G+LD RMGT++K+  C TCG++L+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNHHSPLQYGVLDHRMGTSEKDRPCETCGKSLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYF+ VI ILQ ICK  TC R++L  E+   F   L+ P L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFKAVIGILQMICK--TCCRIMLSVEEKKQFLDYLKRPGLAYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KK+ E  +K + CP+CG  NG VKKCGLLKI HEKYK   K  D IV   L  +  A+++
Sbjct: 144 KKVSEKCRKKTTCPYCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPIVSTFLQSFETAIEY 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP+EDIPLLLMN +  KPSDLILTRLLVPP C
Sbjct: 204 NKEVEPL--LGRAQENLNPLVVLNLFKRIPVEDIPLLLMNPQAGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 262 IRPSVVSDLKS 272



 Score =  292 bits (747), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 148/237 (62%), Positives = 187/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LDKD D D+AR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1066 GVPRIKEIINASKAISTPIITAQLDKDDDPDFARLVKGRIEKTLLGEISEYIEEVFLPDD 1125

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  C+ + R   G + V G + + + P+++SKS  
Sbjct: 1126 CFILVKLSLERIRLLRLEVNAETVRYSICVSKLRVKPGDVAVHGEAVVCVTPRENSKSSM 1185

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG K
Sbjct: 1186 YYVLQSLKEELPKVVVQGIPEVSRAVIHVDEQSGKEKYKLLVEGDNLRAVMATHGVKGTK 1245

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             SSNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1246 TSSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1302



 Score =  116 bits (291), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 830 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 889



 Score = 81.6 bits (200), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 39/64 (60%), Positives = 47/64 (73%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL-QAVPRSEPVPRTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL +A   S P  R L+FD+ EFH
Sbjct: 1326 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHRADKESTPPRRPLIFDHNEFH 1385

Query: 727  FPQV 730
             P V
Sbjct: 1386 IPIV 1389



 Score = 74.7 bits (182), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 521 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 575


>gi|451770412|ref|NP_001263425.1| DNA-directed RNA polymerase III subunit RPC1 [Danio rerio]
          Length = 1390

 Score =  414 bits (1064), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 233/479 (48%), Positives = 304/479 (63%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A  S   +P+LS  E+L  S+  +  K+FL    + F+ +I+KF
Sbjct: 914  GKDEPLEFKRVLDNIRAVYSCTGEPALSRNELLLTSDSIMKRKDFLC-CKDTFLEEIRKF 972

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 973  IKTVSEKVKKTRDKYGINDNGTTEPKVLYQLDRI------TPTQLEKFLETCRDKYMRAQ 1026

Query: 1115 IEPATAVGALAAQSIGEPGTQMTLKTFH-------------------------------- 1142
            +EP +AVGAL AQSIGEPGTQMTLKTFH                                
Sbjct: 1027 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKNISTPIIS 1086

Query: 1143 ----------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                      FA            GE+ EYIEEVF+PDD+FIL+KL +DRIRLL LEV+ 
Sbjct: 1087 ANLDTNDDPDFARLVKGRIEKTLLGEISEYIEEVFLPDDTFILVKLSLDRIRLLRLEVNA 1146

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C  + R   G + V G + + + P+++SKS    + Q +KQ LP VV++G+  
Sbjct: 1147 ETVRYSICTSKLRVKPGDVQVHGEAVVCVSPRENSKSSMYYVLQSLKQDLPKVVVQGIPE 1206

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  K+KLLVEGDN+R VMAT+GV G K +SNNTYEV KTLGIEAARST
Sbjct: 1207 VSRAVIHIDEQSGKQKFKLLVEGDNMRSVMATHGVNGSKTTSNNTYEVEKTLGIEAARST 1266

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML+ADLM+ KGE+LGITR GLAKMKESVL LASFE T+D
Sbjct: 1267 IINEIQYTMVNHGMSIDRRHVMLLADLMSYKGEILGITRFGLAKMKESVLMLASFEKTAD 1326

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPR-SEPVPRTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R ++P  R LLFD+P+FH
Sbjct: 1327 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHRSNREADPPRRPLLFDSPDFH 1385



 Score =  343 bits (881), Expect = 3e-91,   Method: Compositional matrix adjust.
 Identities = 167/277 (60%), Positives = 204/277 (73%), Gaps = 22/277 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDIVLFNRQPSLHKLSIMAHIARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +  +I ++++       G  ++      +P + ++   +WTGKQIFSLILKP++ CPV 
Sbjct: 562 TKACQIVASILV------GKDEKIKISLPHPAI-LKPIRLWTGKQIFSLILKPSKSCPVM 614

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DS+V++ NSEL+ GSMDK TLGSG K N+FYILLRD+G+ 
Sbjct: 615 ANLRTKGKQYCGKGEDLCANDSFVVIHNSELMCGSMDKGTLGSGSKNNIFYILLRDWGQQ 674

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++
Sbjct: 675 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLK 711



 Score =  286 bits (733), Expect = 5e-74,   Method: Compositional matrix adjust.
 Identities = 144/237 (60%), Positives = 186/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+NISTPII+A LD + D D+AR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1066 GVPRIKEIINASKNISTPIISANLDTNDDPDFARLVKGRIEKTLLGEISEYIEEVFLPDD 1125

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
            +FIL+KL +DRIRLL LEV+ +++RY  C  + R   G + V G + + + P+++SKS  
Sbjct: 1126 TFILVKLSLDRIRLLRLEVNAETVRYSICTSKLRVKPGDVQVHGEAVVCVSPRENSKSSM 1185

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +KQ LP VV++G+  ++RAVIH ++  G  K+KLLVEGDN+R VMAT+GV G K
Sbjct: 1186 YYVLQSLKQDLPKVVVQGIPEVSRAVIHIDEQSGKQKFKLLVEGDNMRSVMATHGVNGSK 1245

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNTYEV KTLGIEAARSTI+ EI+  M NHGMSID RH ML+ADLM+ KGE+LG
Sbjct: 1246 TTSNNTYEVEKTLGIEAARSTIINEIQYTMVNHGMSIDRRHVMLLADLMSYKGEILG 1302



 Score =  286 bits (731), Expect = 7e-74,   Method: Compositional matrix adjust.
 Identities = 138/250 (55%), Positives = 181/250 (72%), Gaps = 3/250 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           ++++QQ+HIQ+VSKNLY QD    P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EQMRQQAHIQVVSKNLYSQDTSHKPLQYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           +DL LP FHIGYF+ ++ ILQ ICK  TC+ +LL +E+   F   LR P L+YL ++ LK
Sbjct: 86  LDLELPCFHIGYFKAIVGILQMICK--TCSHILLTKEEKLQFLDYLRRPGLAYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K +VC +C   NG VKKCGLLKI HEKYK+  K  D  V D L  ++ A++ 
Sbjct: 144 KKISDKCRKKTVCLNCNAFNGSVKKCGLLKIIHEKYKSTKKVVDPAVSDFLQSFDVAIEH 203

Query: 271 NPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCI 330
           N E+E+       + LNPL VL LF  IP +D+PLLLMN E  KP+DLILTRLLVPP CI
Sbjct: 204 NKEVESLLTRAQ-ENLNPLVVLNLFRRIPDKDVPLLLMNPESGKPADLILTRLLVPPLCI 262

Query: 331 RPSVISDLKS 340
           RPSV+SDLKS
Sbjct: 263 RPSVVSDLKS 272



 Score =  115 bits (287), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 51/60 (85%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV +SF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 830 AKGFVADSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 889



 Score = 85.1 bits (209), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 38/62 (61%), Positives = 47/62 (75%), Gaps = 1/62 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPR-SEPVPRTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R ++P  R LLFD+P+FH
Sbjct: 1326 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHRSNREADPPRRPLLFDSPDFH 1385

Query: 727  FP 728
             P
Sbjct: 1386 IP 1387



 Score = 73.2 bits (178), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 32/55 (58%), Positives = 43/55 (78%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R +  +I ++++ G+
Sbjct: 521 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRTKACQIVASILVGK 575


>gi|345309868|ref|XP_001514706.2| PREDICTED: DNA-directed RNA polymerase III subunit RPC1
            [Ornithorhynchus anatinus]
          Length = 1489

 Score =  410 bits (1054), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 233/479 (48%), Positives = 302/479 (63%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A    +S+P+LS  E++  +   +   EFL    ++F+++IKKF
Sbjct: 1013 GKDEPLEFKRVLDNIKAVFPCQSEPALSKNELVLTTESIMKKNEFLC-CQDSFLQEIKKF 1071

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 1072 IKVVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQLEKFLETCRDKYMRAQ 1125

Query: 1115 IEPATAVGALAAQSIGEPGTQMTLKTFH-------------------------------- 1142
            +EP +AVGAL AQSIGEPGTQMTLKTFH                                
Sbjct: 1126 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1185

Query: 1143 ----------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                      FA            GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1186 AQLDSDDDSDFARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1245

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C+ + R   G + V G + L + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1246 ETVRYSICMSKLRVKPGDVAVHGEAVLCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPE 1305

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG K +SNNTYEV KTLGIEAAR+T
Sbjct: 1306 VSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTKTTSNNTYEVEKTLGIEAARTT 1365

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1366 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1425

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1426 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPNPPERPLVFDTSEFH 1484



 Score =  342 bits (878), Expect = 8e-91,   Method: Compositional matrix adjust.
 Identities = 169/280 (60%), Positives = 206/280 (73%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 555 DGDVVLFNRQPSLHKLSIMAHLARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 614

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 615 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 660

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+T +I ++++       G  ++   R   P + ++   +WTGKQ+FSLIL+P+   PV 
Sbjct: 661 AKTCQIIASILV------GKDEKIKVRLPPPTI-LKPVTLWTGKQVFSLILRPSDASPVR 713

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DSYV ++NSEL++GSMDK TLGSG K N+FYILLRD+G+ 
Sbjct: 714 ANLRTKGKQYCGRGEDLCVNDSYVTIQNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQL 773

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 774 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 813



 Score =  290 bits (741), Expect = 6e-75,   Method: Compositional matrix adjust.
 Identities = 147/237 (62%), Positives = 186/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LD D D D+AR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1165 GVPRIKEIINASKAISTPIITAQLDSDDDSDFARLVKGRIEKTLLGEISEYIEEVFLPDD 1224

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  C+ + R   G + V G + L + P+++SKS  
Sbjct: 1225 CFILVKLSLERIRLLRLEVNAETVRYSICMSKLRVKPGDVAVHGEAVLCVTPRENSKSSM 1284

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG K
Sbjct: 1285 YYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTK 1344

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1345 TTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1401



 Score =  286 bits (732), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 143/254 (56%), Positives = 181/254 (71%), Gaps = 5/254 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD   +P+ HG+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 125 EEMRQQAHIQVVSKNLYSQDNHHSPLLHGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 184

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYF+ VI +LQ ICK  TC  ++L  E+   F   L+ P L+YL ++ LK
Sbjct: 185 IDLELPCFHVGYFKAVIGVLQMICK--TCCHIMLSSEERKQFLDYLKRPGLTYLQKRGLK 242

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KK+ +  KK + C HCG  NG VKKCGLLKI HEKYK   K  D +V + L  +  A+++
Sbjct: 243 KKVSDKCKKKNTCHHCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPVVSNFLQSFETAIEY 302

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP EDIPLLLMN E  KPSDLILTRLLVPP C
Sbjct: 303 NKEVEP--LLGRAQENLNPLVVLNLFKRIPAEDIPLLLMNPEAGKPSDLILTRLLVPPLC 360

Query: 330 IRPSVISDLKSDND 343
           IRPSV+SDLKS  +
Sbjct: 361 IRPSVVSDLKSGTN 374



 Score =  116 bits (290), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 929 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 988



 Score = 81.6 bits (200), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1425 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPNPPERPLVFDTSEFH 1484

Query: 727  FPQV 730
             P V
Sbjct: 1485 IPIV 1488



 Score = 76.3 bits (186), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 34/55 (61%), Positives = 45/55 (81%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+T +I ++++ G+
Sbjct: 620 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKTCQIIASILVGK 674


>gi|410895601|ref|XP_003961288.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1-like
            [Takifugu rubripes]
          Length = 1390

 Score =  409 bits (1052), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 233/484 (48%), Positives = 304/484 (62%), Gaps = 77/484 (15%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A  +   +P+LS  E++  ++      +FL    ++F+ +IKKF
Sbjct: 914  GKDEPLEFKRVLDNIRAVYTCSDEPALSQNELVLTADAITKRADFLC-CRDSFLEEIKKF 972

Query: 1057 LEEFSKKESVTSHQDK-------VSQPLREQILSHQDKIGHGRESNPFPSACKAEACREK 1109
            ++ FS  E +   +DK        S+P   ++L   D+I       P       E CR+K
Sbjct: 973  VKGFS--ERIKKTRDKYGINDNGTSEP---KVLYQLDRI------TPTQLERFLETCRDK 1021

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFH--------------------------- 1142
            Y+RAQ+EP +AVGAL AQSIGEPGTQMTLKTFH                           
Sbjct: 1022 YMRAQMEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKNIS 1081

Query: 1143 ---------------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLH 1175
                           FA            GE+ EYIEEVF+PDD FIL+KL ++RIRLL 
Sbjct: 1082 TPIITAHLDVEDDADFARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLR 1141

Query: 1176 LEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVI 1232
            LEV+ +++RY  C+ + R   G + V G + + + P+++SKS    + Q +K+ LP VV+
Sbjct: 1142 LEVNAETVRYSICMSKLRVKPGDIAVHGEAVVCVSPRENSKSSMYYVLQSLKEDLPKVVV 1201

Query: 1233 KGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIE 1292
            +G+  + RAVIH ++  G  KYKLLVEGDNLR VMAT+GV G + +SNNT+EV KTLGIE
Sbjct: 1202 QGIPEVARAVIHIDEQSGRNKYKLLVEGDNLRAVMATHGVNGSRTTSNNTFEVEKTLGIE 1261

Query: 1293 AARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASF 1352
            AARSTI+ EI+  M NHGMSID RH ML+ADLM+ KGE+LGITR GLAKMKESVL LASF
Sbjct: 1262 AARSTIINEIQYTMVNHGMSIDRRHVMLLADLMSYKGEILGITRFGLAKMKESVLMLASF 1321

Query: 1353 ENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL-QAVPRSEPVPRTLLFDN 1411
            E T+DHLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL +A     P  R LLFDN
Sbjct: 1322 EKTADHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKAEKEPSPAKRPLLFDN 1381

Query: 1412 PEFH 1415
            P+FH
Sbjct: 1382 PDFH 1385



 Score =  348 bits (892), Expect = 2e-92,   Method: Compositional matrix adjust.
 Identities = 167/277 (60%), Positives = 205/277 (74%), Gaps = 22/277 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDIVLFNRQPSLHKLSIMAHIARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           +++ +I ++++    +   I       S      ++   +WTGKQIFS+ILKP+++CPVN
Sbjct: 562 SKSCQIVASILVGKDEKVRI-------SLPRPAIMKPMALWTGKQIFSVILKPSKECPVN 614

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ CH DS+V++ NSEL+ GSMDK TLGSG K N+FYILLRD+G+ 
Sbjct: 615 ANLRTKGKQYCGKGEDLCHNDSFVVIHNSELMCGSMDKGTLGSGSKNNIFYILLRDWGQL 674

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
            A  AM RL+R+   YL NRGFSIGIGDVTPGQ  ++
Sbjct: 675 EAANAMSRLARLAPVYLSNRGFSIGIGDVTPGQSLLK 711



 Score =  286 bits (731), Expect = 9e-74,   Method: Compositional matrix adjust.
 Identities = 143/237 (60%), Positives = 186/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+NISTPIITA+LD + D D+AR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1066 GVPRIKEIINASKNISTPIITAHLDVEDDADFARLVKGRIEKTLLGEISEYIEEVFLPDD 1125

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  C+ + R   G + V G + + + P+++SKS  
Sbjct: 1126 CFILVKLSLERIRLLRLEVNAETVRYSICMSKLRVKPGDIAVHGEAVVCVSPRENSKSSM 1185

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  + RAVIH ++  G  KYKLLVEGDNLR VMAT+GV G +
Sbjct: 1186 YYVLQSLKEDLPKVVVQGIPEVARAVIHIDEQSGRNKYKLLVEGDNLRAVMATHGVNGSR 1245

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNT+EV KTLGIEAARSTI+ EI+  M NHGMSID RH ML+ADLM+ KGE+LG
Sbjct: 1246 TTSNNTFEVEKTLGIEAARSTIINEIQYTMVNHGMSIDRRHVMLLADLMSYKGEILG 1302



 Score =  281 bits (718), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 137/250 (54%), Positives = 177/250 (70%), Gaps = 3/250 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           ++++QQ+HIQ+VSKNLY QD   TP+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EQMRQQAHIQVVSKNLYSQDTSHTPLAYGVLDHRMGTSEKDRPCLTCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           +DL LP FHIGYF+ +I ILQ ICK  TC+ ++L  E+   F  +L+ P L+YL ++ LK
Sbjct: 86  LDLELPCFHIGYFKAIIGILQMICK--TCSSIMLNREEKLQFMDQLKRPTLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI E  +K +VC +C   NG VKKCGLLKI HEKYK   K  D  V D L  ++ A++ 
Sbjct: 144 KKISEKCRKRTVCLNCSAFNGPVKKCGLLKIIHEKYKTNKKVVDPFVSDFLQSFDIAIEH 203

Query: 271 NPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCI 330
           N  +E        + LNPL V  LF+ I  EDIPLLLMN E   P+DLILTRLLVPP CI
Sbjct: 204 NKVLEPLLSRAQ-ENLNPLVVRNLFKRISREDIPLLLMNPEAGTPADLILTRLLVPPLCI 262

Query: 331 RPSVISDLKS 340
           RPSV+SDLKS
Sbjct: 263 RPSVVSDLKS 272



 Score =  117 bits (292), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 830 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 889



 Score = 87.4 bits (215), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 39/62 (62%), Positives = 46/62 (74%), Gaps = 1/62 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL-QAVPRSEPVPRTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL +A     P  R LLFDNP+FH
Sbjct: 1326 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKAEKEPSPAKRPLLFDNPDFH 1385

Query: 727  FP 728
             P
Sbjct: 1386 IP 1387



 Score = 74.3 bits (181), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 32/55 (58%), Positives = 45/55 (81%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R+++ +I ++++ G+
Sbjct: 521 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRSKSCQIVASILVGK 575


>gi|383861274|ref|XP_003706111.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1-like
            [Megachile rotundata]
          Length = 2015

 Score =  409 bits (1051), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 203/296 (68%), Positives = 229/296 (77%), Gaps = 24/296 (8%)

Query: 341  DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
            D+DVVLFNRQPSLHKLSIMAH+AKVL HRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 1090 DDDVVLFNRQPSLHKLSIMAHKAKVLEHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 1149

Query: 401  RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
            RAEAL              VLM NKSNLVTPRNGELLIAATQDFITGGYLLTQK+ F N+
Sbjct: 1150 RAEAL--------------VLMGNKSNLVTPRNGELLIAATQDFITGGYLLTQKDMFLNK 1195

Query: 461  AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +Q  ++A  L+A      G+    S     P + ++  V+WTGKQIFSLILKPN+ C + 
Sbjct: 1196 SQASQLAGCLLA------GLDIAMSIDLPEPAI-LKPTVLWTGKQIFSLILKPNKMCNIR 1248

Query: 521  ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            ANLKTKGRAYT NEE C  DSYVI+RNSELLAGSMDKSTLGSG K N+FYILLRD+GED+
Sbjct: 1249 ANLKTKGRAYTTNEELCINDSYVIIRNSELLAGSMDKSTLGSGSKQNIFYILLRDWGEDI 1308

Query: 581  AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFV---QNSFFSGLTPTEFFFHTM 633
            A TAMWRL+RM SF+LMNRGFSIGIGDVTPGQG +   Q    +G +    + H M
Sbjct: 1309 ATTAMWRLARMASFFLMNRGFSIGIGDVTPGQGLLKAKQELLHAGYSKCTEYIHQM 1364



 Score =  363 bits (933), Expect = 3e-97,   Method: Compositional matrix adjust.
 Identities = 210/462 (45%), Positives = 279/462 (60%), Gaps = 75/462 (16%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   PV+ KR+LD + AK+  +++ SL    ++  +NE L S+E+ +  S+ F +++  F
Sbjct: 1547 GKDCPVDYKRVLDHVRAKSPCKNEQSLDGPSVITATNELLSSEEY-ECLSKEFKQELATF 1605

Query: 1057 LEEFSKKESVTSHQDKVSQPLREQI----LSHQDKIGHGRESNPFPSACKAEACREKYVR 1112
            L+  ++K +   H    + P+  Q+    +S   +  H               C+EKY+R
Sbjct: 1606 LKSIARKIARLRHNAPSNIPVILQLERLTVSQLVEFIH--------------ICKEKYMR 1651

Query: 1113 AQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYIEEVFVPD 1158
            A+IEP TAVGALAAQSIGEPGTQMTLKTFHFAG              E+     ++  P 
Sbjct: 1652 AKIEPGTAVGALAAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIINANPKISTPI 1711

Query: 1159 DSFIL------------------------------IKLDMDRIRLLHLEVD--------- 1179
             +  L                              + L  D   L+ L++D         
Sbjct: 1712 ITAALENDVDPEYARRVKGRIEKTTLGEVTEYIDEVYLPDDCFLLIKLDIDRIKLLKLEV 1771

Query: 1180 -IDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQ 1236
             ++SIRY  C  + +     + V G S + + P  +  S N  + Q+K+ +P++V+KG+ 
Sbjct: 1772 DVNSIRYSICTSKLKLNPKLVNVRGDSIITVSPNKNKYSINYALTQLKETIPNIVVKGLP 1831

Query: 1237 GINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARS 1296
             ++RAVIH +D  G T+YKL VEGDN+R+VMAT GV G K +SNNT EV+KTLGIEAAR+
Sbjct: 1832 SVSRAVIHNDDSSGKTRYKLFVEGDNMREVMATLGVSGKKTTSNNTIEVFKTLGIEAARA 1891

Query: 1297 TIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTS 1356
            TIMTEIKLVMENHGMSID RHPMLVADLMTS+GEVLGITR GLAKMKESVLNLASFE T+
Sbjct: 1892 TIMTEIKLVMENHGMSIDRRHPMLVADLMTSRGEVLGITRQGLAKMKESVLNLASFEKTA 1951

Query: 1357 DHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 1398
            DHLFDAA+YGQ D I GVSE IIMG+P+ +GTG+ KLL   P
Sbjct: 1952 DHLFDAAYYGQKDVICGVSESIIMGIPVPLGTGIFKLLHKYP 1993



 Score =  306 bits (785), Expect = 4e-80,   Method: Compositional matrix adjust.
 Identities = 151/236 (63%), Positives = 188/236 (79%), Gaps = 2/236 (0%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA+  ISTPIITA L+ D D +YAR VKGR+E+TTLGEV EYI+EV++PDD
Sbjct: 1693 GVPRIKEIINANPKISTPIITAALENDVDPEYARRVKGRIEKTTLGEVTEYIDEVYLPDD 1752

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             F+LIKLD+DRI+LL LEVD++SIRY  C  + +     + V G S + + P  +  S N
Sbjct: 1753 CFLLIKLDIDRIKLLKLEVDVNSIRYSICTSKLKLNPKLVNVRGDSIITVSPNKNKYSIN 1812

Query: 882  SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
              + Q+K+ +P++V+KG+  ++RAVIH +D  G T+YKL VEGDN+R+VMAT GV G K 
Sbjct: 1813 YALTQLKETIPNIVVKGLPSVSRAVIHNDDSSGKTRYKLFVEGDNMREVMATLGVSGKKT 1872

Query: 942  SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +SNNT EV+KTLGIEAAR+TIMTEIKLVMENHGMSID RHPMLVADLMTS+GEVLG
Sbjct: 1873 TSNNTIEVFKTLGIEAARATIMTEIKLVMENHGMSIDRRHPMLVADLMTSRGEVLG 1928



 Score =  298 bits (762), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 156/322 (48%), Positives = 211/322 (65%), Gaps = 22/322 (6%)

Query: 87  VTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVG 146
           V     +++Q+H+ +V+KNLY QD + TP+P+G+LDRRMGT     NC +CG++L++C+G
Sbjct: 653 VDSRHNMERQAHMHVVAKNLYNQDVEHTPVPYGVLDRRMGTCNNTTNCASCGKSLNECIG 712

Query: 147 HFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVR 206
           HFGYIDL LPVFH+GYFR +I ILQSICKN  CA V+L E     +  ++ NP L YL R
Sbjct: 713 HFGYIDLELPVFHVGYFRSIIGILQSICKN--CAHVMLSEADKKHYLTRVLNPNLGYLTR 770

Query: 207 KSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNE 266
           K+L+K+ILE  KK +VC +CG++NG VKK GLLKI HEKYK + KK DAIV+  LAEYN 
Sbjct: 771 KALRKQILEKAKKTTVCQNCGDLNGTVKKAGLLKIVHEKYKAK-KKIDAIVQQKLAEYNN 829

Query: 267 AVKFNPEIEAHKKFGLIQTLNPLE---VLQLFEAIPLEDIPLLLMNAELSKPSDLILTRL 323
            ++ N  +E   + GL+  LNPLE   V  + E IP  DIPLL+MN E + P DLILTR+
Sbjct: 830 VLEDNKALEGILQNGLVNILNPLEVKVVQSILEKIPESDIPLLMMNPECALPKDLILTRI 889

Query: 324 LVPPNCIRPSVISDLKSD----------NDVVLFNRQPSLHKLSIMAHRAKV-LPHRTFR 372
            VPP CIRPSV+SDLK+           +++V  N     H+ S     AKV + +  + 
Sbjct: 890 PVPPICIRPSVVSDLKAGTTEDHLTMKLSEIVFINDVIQKHRQS----GAKVQMYNEDWE 945

Query: 373 FNECVCTPY-NADFDGDEMNVH 393
           F +  C  Y N++  G  +N+ 
Sbjct: 946 FLQLHCALYINSEMSGIPLNMQ 967



 Score =  121 bits (303), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 53/63 (84%), Positives = 59/63 (93%)

Query: 608  VTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
            +   +GFV+NSF+SGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC+ Y
Sbjct: 1460 IPAAKGFVENSFYSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCLHY 1519

Query: 668  DMS 670
            DM+
Sbjct: 1520 DMT 1522



 Score = 89.0 bits (219), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 41/54 (75%), Positives = 47/54 (87%)

Query: 21   VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
            VLM NKSNLVTPRNGELLIAATQDFITGGYLLTQK+ F N++Q  ++A  L+AG
Sbjct: 1155 VLMGNKSNLVTPRNGELLIAATQDFITGGYLLTQKDMFLNKSQASQLAGCLLAG 1208



 Score = 59.3 bits (142), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/42 (61%), Positives = 31/42 (73%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 709
            D  FDAA+YGQ D I GVSE IIMG+P+ +GTG+ KLL   P
Sbjct: 1952 DHLFDAAYYGQKDVICGVSESIIMGIPVPLGTGIFKLLHKYP 1993


>gi|317419477|emb|CBN81514.1| DNA-directed RNA polymerase III subunit RPC1 [Dicentrarchus labrax]
          Length = 1390

 Score =  408 bits (1048), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 232/484 (47%), Positives = 303/484 (62%), Gaps = 77/484 (15%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A  +   +P+LS  E++  ++  +   +FL    ++F+ +IKKF
Sbjct: 914  GKDEPLEFKRVLDNIRAVYTCPYEPALSQNELVLTADAIMKRADFLC-CRDSFLEEIKKF 972

Query: 1057 LEEFSKKESVTSHQDK-------VSQPLREQILSHQDKIGHGRESNPFPSACKAEACREK 1109
            ++  S  E +   +DK        S+P   ++L   D+I       P       E CR+K
Sbjct: 973  IKSVS--ERIKKTRDKYGINDNGTSEP---KVLYQLDRI------TPTQLEKYLETCRDK 1021

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFH--------------------------- 1142
            Y+RAQ+EP +AVGAL AQSIGEPGTQMTLKTFH                           
Sbjct: 1022 YMRAQMEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKNIS 1081

Query: 1143 ---------------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLH 1175
                           FA            GE+ EYIEEVF+PDD FIL+KL ++RIRLL 
Sbjct: 1082 TPIITANLDVEDDADFARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLR 1141

Query: 1176 LEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVI 1232
            LEV+ +++RY  C+ + R   G + V G + + + P+++SKS    + Q +K+ LP VV+
Sbjct: 1142 LEVNAETVRYSICMSKLRVKPGDIAVHGEAVVCVSPRENSKSSMYYVLQSLKEELPKVVV 1201

Query: 1233 KGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIE 1292
            +G+  + RAVIH ++  G  KYKLLVEGDNLR VMAT+GV G + +SNNTYEV KTLGIE
Sbjct: 1202 QGIPEVARAVIHIDEQSGKNKYKLLVEGDNLRAVMATHGVNGSRTTSNNTYEVEKTLGIE 1261

Query: 1293 AARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASF 1352
            AARSTI+ EI+  M NHGMSID RH ML+ADLM+ KGE+LGITR GLAKMKESVL LASF
Sbjct: 1262 AARSTIINEIQYTMVNHGMSIDRRHVMLLADLMSYKGEILGITRFGLAKMKESVLMLASF 1321

Query: 1353 ENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDN 1411
            E T+DHLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    +   PV R LLFDN
Sbjct: 1322 EKTADHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADKDPSPVKRPLLFDN 1381

Query: 1412 PEFH 1415
             +FH
Sbjct: 1382 ADFH 1385



 Score =  343 bits (881), Expect = 3e-91,   Method: Compositional matrix adjust.
 Identities = 169/278 (60%), Positives = 206/278 (74%), Gaps = 24/278 (8%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIMAH AKV PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDIVLFNRQPSLHKLSIMAHIAKVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRI-ASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           ++  +I AS L+     I   + R       P + ++   +WTGKQIFS+ILKP+++CPV
Sbjct: 562 SKACQIVASILVGKDEKIRVTLPR-------PAI-MKPMALWTGKQIFSVILKPSKECPV 613

Query: 520 NANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            ANL+TKG+ Y    E+ C+ DS+V++ NSEL+ GS+DK TLGSG K N+FYILLRD+G+
Sbjct: 614 KANLRTKGKQYCGKGEDLCYNDSFVVIHNSELMCGSLDKGTLGSGSKNNIFYILLRDWGQ 673

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
             A  AM RL+R+   +L NRGFSIGIGDVTPGQG ++
Sbjct: 674 LEAANAMSRLARLAPVFLSNRGFSIGIGDVTPGQGLLK 711



 Score =  285 bits (730), Expect = 9e-74,   Method: Compositional matrix adjust.
 Identities = 144/237 (60%), Positives = 185/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+NISTPIITA LD + D D+AR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1066 GVPRIKEIINASKNISTPIITANLDVEDDADFARLVKGRIEKTLLGEISEYIEEVFLPDD 1125

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  C+ + R   G + V G + + + P+++SKS  
Sbjct: 1126 CFILVKLSLERIRLLRLEVNAETVRYSICMSKLRVKPGDIAVHGEAVVCVSPRENSKSSM 1185

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  + RAVIH ++  G  KYKLLVEGDNLR VMAT+GV G +
Sbjct: 1186 YYVLQSLKEELPKVVVQGIPEVARAVIHIDEQSGKNKYKLLVEGDNLRAVMATHGVNGSR 1245

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNTYEV KTLGIEAARSTI+ EI+  M NHGMSID RH ML+ADLM+ KGE+LG
Sbjct: 1246 TTSNNTYEVEKTLGIEAARSTIINEIQYTMVNHGMSIDRRHVMLLADLMSYKGEILG 1302



 Score =  283 bits (724), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 135/250 (54%), Positives = 180/250 (72%), Gaps = 3/250 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           ++++QQ+HIQ+VSKNLY QD + TP+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EQMRQQAHIQVVSKNLYSQDTKHTPLSYGVLDHRMGTSEKDRPCLTCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           +DL LP FH+GYF+ +I ILQ ICK  TC+ ++L +E    F   L+ P L+YL ++ LK
Sbjct: 86  LDLELPCFHVGYFKAIIGILQMICK--TCSSIMLTKEDKLQFMDHLKRPNLAYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K ++C +C   NG VKKCGLLKI HEKYK   K  D  V D +  ++ A++ 
Sbjct: 144 KKISDKCRKRTICLNCSAFNGPVKKCGLLKIIHEKYKTTKKVVDPFVSDFMQSFDIAIEH 203

Query: 271 NPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCI 330
           N  +E        + LNPL VL +F+ IP EDIPLLLMN E  KP+DLILTRLLVPP CI
Sbjct: 204 NKMVEPLLTRAQ-ENLNPLVVLNMFKRIPQEDIPLLLMNPEAGKPADLILTRLLVPPLCI 262

Query: 331 RPSVISDLKS 340
           RPSV+SDLKS
Sbjct: 263 RPSVVSDLKS 272



 Score =  115 bits (287), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 51/60 (85%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV +SF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 830 AKGFVADSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 889



 Score = 85.5 bits (210), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 46/64 (71%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    +   PV R LLFDN +FH
Sbjct: 1326 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADKDPSPVKRPLLFDNADFH 1385

Query: 727  FPQV 730
             P +
Sbjct: 1386 IPLI 1389



 Score = 73.9 bits (180), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 32/55 (58%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R++  +I ++++ G+
Sbjct: 521 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRSKACQIVASILVGK 575


>gi|348508629|ref|XP_003441856.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1-like
            [Oreochromis niloticus]
          Length = 1390

 Score =  406 bits (1044), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 231/484 (47%), Positives = 302/484 (62%), Gaps = 77/484 (15%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A  +   +P+LS  E++  ++  +   +FL    ++F+ +IKKF
Sbjct: 914  GKDEPLEFKRVLDNIRAVYTCPDEPALSQNELVLTADAIMKRADFLC-CRDSFLEEIKKF 972

Query: 1057 LEEFSKKESVTSHQDK-------VSQPLREQILSHQDKIGHGRESNPFPSACKAEACREK 1109
            ++  S  E +   +DK        S+P   ++L   D++       P       E CR+K
Sbjct: 973  IKSVS--ERIKKTRDKYGINDNGTSEP---KVLYQLDRV------TPTQLEKFLETCRDK 1021

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFH--------------------------- 1142
            Y+RAQ+EP +AVGAL AQSIGEPGTQMTLKTFH                           
Sbjct: 1022 YMRAQMEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKNIS 1081

Query: 1143 ---------------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLH 1175
                           FA            GE+ EYIEEVF+PDD FIL+KL ++RIRLL 
Sbjct: 1082 TPIITAHLDVEDDADFARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLR 1141

Query: 1176 LEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVI 1232
            LEV+ +++RY  C+ + R     + V G + + + P+++SKS    + Q +K  LP VV+
Sbjct: 1142 LEVNAETVRYSICMSKLRVKPADIAVHGEAVVCVSPRENSKSSMYYVLQSLKGELPKVVV 1201

Query: 1233 KGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIE 1292
            +G+  + RAVIH ++    +KYKLLVEGDNLR VMAT+GV G + +SNNTYEV KTLGIE
Sbjct: 1202 QGIPEVARAVIHIDEQSSKSKYKLLVEGDNLRAVMATHGVNGSRTTSNNTYEVEKTLGIE 1261

Query: 1293 AARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASF 1352
            AARSTI+ EI+  M NHGMSID RH ML+ADLM+ KGE+LGITR GLAKMKESVL LASF
Sbjct: 1262 AARSTIINEIQYTMVNHGMSIDRRHVMLLADLMSYKGEILGITRFGLAKMKESVLMLASF 1321

Query: 1353 ENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDN 1411
            E T+DHLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   PV R LLFDN
Sbjct: 1322 EKTADHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPSPVKRPLLFDN 1381

Query: 1412 PEFH 1415
            P+FH
Sbjct: 1382 PDFH 1385



 Score =  352 bits (904), Expect = 7e-94,   Method: Compositional matrix adjust.
 Identities = 169/277 (61%), Positives = 207/277 (74%), Gaps = 22/277 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDIVLFNRQPSLHKLSIMAHIARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              +LM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------ILMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           ++  +I ++++       G  +R       P + ++   +WTGKQIFSLILKP+++CPVN
Sbjct: 562 SKACQIVASILV------GKDERVRISLPRPAI-IKPMALWTGKQIFSLILKPSKECPVN 614

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ CH DS+V++ NSEL+ GSMDK TLGSG K N+FYILLRD+G+ 
Sbjct: 615 ANLRTKGKQYCGKGEDLCHNDSFVVIHNSELMCGSMDKGTLGSGSKNNIFYILLRDWGQL 674

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++
Sbjct: 675 EAANAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLK 711



 Score =  286 bits (733), Expect = 4e-74,   Method: Compositional matrix adjust.
 Identities = 139/250 (55%), Positives = 181/250 (72%), Gaps = 3/250 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           ++++QQ+HIQ+VSKNLY QD + TP+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EQMRQQAHIQVVSKNLYSQDTKHTPLAYGVLDHRMGTSEKDRPCLTCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           +DL LP FH+GYF+  I ILQ ICK  TC+R++L +E+   F   L+ P L+YL ++ LK
Sbjct: 86  LDLELPCFHVGYFKATIGILQMICK--TCSRIMLTKEEKLQFMDYLKRPNLAYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K +VC +C   NG VKKCGLLKI HEKYK   K  DA V D L  ++ A++ 
Sbjct: 144 KKISDKCRKRTVCLNCSAFNGPVKKCGLLKIIHEKYKTTKKVVDAFVSDFLQSFDIAIEH 203

Query: 271 NPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCI 330
           N  +E        + LNPL VL LF  IP EDIPLLLMN E  KP+DLI+TRLLVPP CI
Sbjct: 204 NKLVEPLLTRAQ-ENLNPLVVLNLFRRIPEEDIPLLLMNPEAGKPADLIITRLLVPPLCI 262

Query: 331 RPSVISDLKS 340
           RPSV+SDLKS
Sbjct: 263 RPSVVSDLKS 272



 Score =  281 bits (720), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 142/237 (59%), Positives = 184/237 (77%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+NISTPIITA+LD + D D+AR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1066 GVPRIKEIINASKNISTPIITAHLDVEDDADFARLVKGRIEKTLLGEISEYIEEVFLPDD 1125

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  C+ + R     + V G + + + P+++SKS  
Sbjct: 1126 CFILVKLSLERIRLLRLEVNAETVRYSICMSKLRVKPADIAVHGEAVVCVSPRENSKSSM 1185

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K  LP VV++G+  + RAVIH ++    +KYKLLVEGDNLR VMAT+GV G +
Sbjct: 1186 YYVLQSLKGELPKVVVQGIPEVARAVIHIDEQSSKSKYKLLVEGDNLRAVMATHGVNGSR 1245

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNTYEV KTLGIEAARSTI+ EI+  M NHGMSID RH ML+ADLM+ KGE+LG
Sbjct: 1246 TTSNNTYEVEKTLGIEAARSTIINEIQYTMVNHGMSIDRRHVMLLADLMSYKGEILG 1302



 Score =  115 bits (287), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 51/60 (85%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV +SF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 830 AKGFVADSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 889



 Score = 90.1 bits (222), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 40/64 (62%), Positives = 47/64 (73%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   PV R LLFDNP+FH
Sbjct: 1326 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPSPVKRPLLFDNPDFH 1385

Query: 727  FPQV 730
             P +
Sbjct: 1386 LPLI 1389



 Score = 73.2 bits (178), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 31/55 (56%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           +LM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R++  +I ++++ G+
Sbjct: 521 ILMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRSKACQIVASILVGK 575


>gi|340711859|ref|XP_003394485.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1-like
           [Bombus terrestris]
          Length = 1385

 Score =  405 bits (1040), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 196/276 (71%), Positives = 222/276 (80%), Gaps = 21/276 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+DVVLFNRQPSLHKLSIMAH+AKVL HRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DDDVVLFNRQPSLHKLSIMAHKAKVLDHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL              +LM NKSNLVTPRNGELLIAATQDFITGGYLLTQK+ F N+
Sbjct: 516 RAEAL--------------ILMGNKSNLVTPRNGELLIAATQDFITGGYLLTQKDMFLNK 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           AQ  ++A  L+A   DI   I      S      ++ +++WTGKQIFSLILKPN  C + 
Sbjct: 562 AQASQLAGCLLAG-PDIAMSI------SLPEPAILKPSMLWTGKQIFSLILKPNSTCNIK 614

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           ANLKTKGRAYT+N+E C  DSYVI+RNSELLAG+MDKSTLGSG K N+FYILLRD+GED+
Sbjct: 615 ANLKTKGRAYTSNQELCINDSYVIIRNSELLAGTMDKSTLGSGSKQNIFYILLRDWGEDI 674

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           A  AMWRL+RM SF+LMNRGFSIGIGDVTPGQG ++
Sbjct: 675 ATIAMWRLARMASFFLMNRGFSIGIGDVTPGQGLLK 710



 Score =  375 bits (964), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 220/482 (45%), Positives = 289/482 (59%), Gaps = 75/482 (15%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   PV+ KR+LD + AK+  +++  L   +++  +NE L SK+  +  SE F +++  F
Sbjct: 913  GKDCPVDYKRVLDHVTAKSPCKNEEPLDGPDLIKATNELLGSKD-CECLSEEFKQELSTF 971

Query: 1057 LEEFSKKESVTSHQDKVSQPLREQI----LSHQDKIGHGRESNPFPSACKAEACREKYVR 1112
            L+  ++K     +    + P+  Q+    +S   +  H               C+EKY++
Sbjct: 972  LKGVARKIIHLRYNAPSNIPVIFQLERLTVSQLVEFIH--------------TCKEKYMK 1017

Query: 1113 AQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYIEEVFVPD 1158
            A+IEP TAVGALAAQSIGEPGTQMTLKTFHFAG              E+     ++  P 
Sbjct: 1018 AKIEPGTAVGALAAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIINANPKISTPI 1077

Query: 1159 DSFIL------------------------------IKLDMDRIRLLHLEVD--------- 1179
             S  L                              + L  D   L+ L++D         
Sbjct: 1078 ISAALENDVDPEYARRVKGRIEKTTLGEVTEYIEEVYLPDDCFLLVKLDIDRIKLLKLEV 1137

Query: 1180 -IDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQ 1236
             ++SIRY  C  + R     + V G S + + P  S  S N  + Q+K+ +P++VIKG+ 
Sbjct: 1138 DVNSIRYSICTSKLRLNPKLVNVRGDSIITVNPSKSKYSINYALTQLKETIPNIVIKGLP 1197

Query: 1237 GINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARS 1296
             ++RAVIH +D  G T+YKL VEG+N+R+VMAT GV G K +SNNT EV+KTLGIEAAR+
Sbjct: 1198 SVSRAVIHNDDSSGKTRYKLFVEGNNMREVMATLGVLGRKTTSNNTIEVFKTLGIEAARA 1257

Query: 1297 TIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTS 1356
            TIMTEIKLVMENHGMSID RHPMLVADLMTS+GEVLGITR GLAKMKESVLNLASFE TS
Sbjct: 1258 TIMTEIKLVMENHGMSIDRRHPMLVADLMTSRGEVLGITRQGLAKMKESVLNLASFEKTS 1317

Query: 1357 DHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHT 1416
            DHLFDAA+YGQ D I GVSE IIMG+P+ VGTG+ KLL    + EP  + L+FD+P+F  
Sbjct: 1318 DHLFDAAYYGQKDVICGVSESIIMGIPVPVGTGIFKLLHKADKDEPRIKELIFDDPQFKK 1377

Query: 1417 NT 1418
             T
Sbjct: 1378 TT 1379



 Score =  306 bits (783), Expect = 7e-80,   Method: Compositional matrix adjust.
 Identities = 152/236 (64%), Positives = 188/236 (79%), Gaps = 2/236 (0%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA+  ISTPII+A L+ D D +YAR VKGR+E+TTLGEV EYIEEV++PDD
Sbjct: 1059 GVPRIKEIINANPKISTPIISAALENDVDPEYARRVKGRIEKTTLGEVTEYIEEVYLPDD 1118

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             F+L+KLD+DRI+LL LEVD++SIRY  C  + R     + V G S + + P  S  S N
Sbjct: 1119 CFLLVKLDIDRIKLLKLEVDVNSIRYSICTSKLRLNPKLVNVRGDSIITVNPSKSKYSIN 1178

Query: 882  SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
              + Q+K+ +P++VIKG+  ++RAVIH +D  G T+YKL VEG+N+R+VMAT GV G K 
Sbjct: 1179 YALTQLKETIPNIVIKGLPSVSRAVIHNDDSSGKTRYKLFVEGNNMREVMATLGVLGRKT 1238

Query: 942  SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +SNNT EV+KTLGIEAAR+TIMTEIKLVMENHGMSID RHPMLVADLMTS+GEVLG
Sbjct: 1239 TSNNTIEVFKTLGIEAARATIMTEIKLVMENHGMSIDRRHPMLVADLMTSRGEVLG 1294



 Score =  302 bits (774), Expect = 9e-79,   Method: Compositional matrix adjust.
 Identities = 156/319 (48%), Positives = 213/319 (66%), Gaps = 19/319 (5%)

Query: 87  VTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVG 146
           V     +++Q+HI +V+KNLY QD + TP+P+G+LDR+MGT     NC +CG++L++C+G
Sbjct: 22  VDSRHNMERQAHIHVVAKNLYNQDVEHTPVPYGVLDRKMGTCNNITNCVSCGKSLNECIG 81

Query: 147 HFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVR 206
           HFGYIDL LPVFH+GYFR +I ILQSICKN  C+RV+L E     + A++ NP L YL R
Sbjct: 82  HFGYIDLELPVFHVGYFRSIIGILQSICKN--CSRVMLSEADKKHYLARVLNPNLGYLTR 139

Query: 207 KSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNE 266
           K+L+K+IL+  KK +VC +C ++NG VKK GLLKI HEKYK + KK DAIV+  LAEYN 
Sbjct: 140 KALRKQILDKAKKTTVCQYCRDLNGTVKKAGLLKIVHEKYKGK-KKIDAIVQQKLAEYNN 198

Query: 267 AVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVP 326
            ++ N  +E   + GL+  LNPLEV  + E IP  DIPLLLMN+E + P DLILTR+ VP
Sbjct: 199 VLEDNKALEGVLQSGLVNVLNPLEVQSILEKIPESDIPLLLMNSECALPKDLILTRIPVP 258

Query: 327 PNCIRPSVISDLKSD----------NDVVLFNRQPSLHKLSIMAHRAKV-LPHRTFRFNE 375
           P CIRPSV+SDLK+           +++V  N     H+ S     AKV + +  + F +
Sbjct: 259 PICIRPSVVSDLKAGTTEDHLTMKLSEIVFINDVIQKHRQS----GAKVQMYNEDWEFLQ 314

Query: 376 CVCTPY-NADFDGDEMNVH 393
             C  Y N++  G  +N+ 
Sbjct: 315 LHCALYINSEMSGIPLNMQ 333



 Score =  121 bits (303), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 53/63 (84%), Positives = 59/63 (93%)

Query: 608 VTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           +   +GFV+NSF+SGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC+ Y
Sbjct: 826 IPAAKGFVENSFYSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCLHY 885

Query: 668 DMS 670
           DM+
Sbjct: 886 DMT 888



 Score = 89.7 bits (221), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 41/54 (75%), Positives = 47/54 (87%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           +LM NKSNLVTPRNGELLIAATQDFITGGYLLTQK+ F N+AQ  ++A  L+AG
Sbjct: 521 ILMGNKSNLVTPRNGELLIAATQDFITGGYLLTQKDMFLNKAQASQLAGCLLAG 574



 Score = 74.7 bits (182), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 33/58 (56%), Positives = 42/58 (72%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEF 725
            D  FDAA+YGQ D I GVSE IIMG+P+ VGTG+ KLL    + EP  + L+FD+P+F
Sbjct: 1318 DHLFDAAYYGQKDVICGVSESIIMGIPVPVGTGIFKLLHKADKDEPRIKELIFDDPQF 1375


>gi|350402598|ref|XP_003486538.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1-like
           [Bombus impatiens]
          Length = 1385

 Score =  404 bits (1039), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 196/276 (71%), Positives = 222/276 (80%), Gaps = 21/276 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+DVVLFNRQPSLHKLSIMAH+AKVL HRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DDDVVLFNRQPSLHKLSIMAHKAKVLDHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL              +LM NKSNLVTPRNGELLIAATQDFITGGYLLTQK+ F N+
Sbjct: 516 RAEAL--------------ILMGNKSNLVTPRNGELLIAATQDFITGGYLLTQKDMFLNK 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           AQ  ++A  L+A   DI       S     P +  + +++WTGKQIFSLILKPN  C + 
Sbjct: 562 AQASQLAGCLLAG-PDIA-----MSITLPEPAIL-KPSMLWTGKQIFSLILKPNSTCNIK 614

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           ANLKTKGRAYT+N+E C  DSYVI+RNSELLAG+MDKSTLGSG K N+FYILLRD+GED+
Sbjct: 615 ANLKTKGRAYTSNQELCINDSYVIIRNSELLAGTMDKSTLGSGSKQNIFYILLRDWGEDI 674

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           A  AMWRL+RM SF+LMNRGFSIGIGDVTPGQG ++
Sbjct: 675 ATIAMWRLARMASFFLMNRGFSIGIGDVTPGQGLLK 710



 Score =  375 bits (964), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 219/479 (45%), Positives = 290/479 (60%), Gaps = 75/479 (15%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   PV+ KR+LD + AK+S +++  L   +++  +NE + SK+  +  SE F +++  F
Sbjct: 913  GKDCPVDYKRVLDHVTAKSSCKNEEPLDGPDLIKATNELVGSKD-CECLSEEFKQELSTF 971

Query: 1057 LEEFSKKESVTSHQDKVSQPLREQI----LSHQDKIGHGRESNPFPSACKAEACREKYVR 1112
            L+  ++K     +    + P+  Q+    +S   +  H               C+EKY++
Sbjct: 972  LKGVARKIIHLRYNAPSNIPVIFQLERITVSQLVEFIH--------------TCKEKYMK 1017

Query: 1113 AQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYIEEVFVPD 1158
            A+IEP TAVGALAAQSIGEPGTQMTLKTFHFAG              E+     ++  P 
Sbjct: 1018 AKIEPGTAVGALAAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIINANPKISTPI 1077

Query: 1159 DSFIL------------------------------IKLDMDRIRLLHLEVD--------- 1179
             S  L                              + L  D   L+ L++D         
Sbjct: 1078 ISAALENDVDPEYARRVKGRIEKTTLGEVTEYIEEVYLPDDCFLLVKLDIDRIKLLKLEV 1137

Query: 1180 -IDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQ 1236
             ++SIRY  C  + R     + V G S + + P  S  S N  + Q+K+ +P++VIKG+ 
Sbjct: 1138 DVNSIRYSICTSKLRLNPKLVNVRGDSIITVNPSKSKYSINYALTQLKETIPNIVIKGLP 1197

Query: 1237 GINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARS 1296
             ++RAVIH +D  G T+YKL VEG+N+R+VMAT GV G K +SNNT EV+KTLGIEAAR+
Sbjct: 1198 SVSRAVIHNDDSSGKTRYKLFVEGNNMREVMATLGVLGRKTTSNNTIEVFKTLGIEAARA 1257

Query: 1297 TIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTS 1356
            TIMTEIKLVMENHGMSID RHPMLVADLMTS+GEVLGITR GLAKMKESVLNLASFE TS
Sbjct: 1258 TIMTEIKLVMENHGMSIDRRHPMLVADLMTSRGEVLGITRQGLAKMKESVLNLASFEKTS 1317

Query: 1357 DHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFH 1415
            DHLFDAA+YGQ D I GVSE IIMG+P+ VGTG+ KLL    + EP  + L+FD+P+F+
Sbjct: 1318 DHLFDAAYYGQKDVICGVSESIIMGIPVPVGTGIFKLLHKADKDEPRIKELIFDDPQFN 1376



 Score =  306 bits (783), Expect = 7e-80,   Method: Compositional matrix adjust.
 Identities = 152/236 (64%), Positives = 188/236 (79%), Gaps = 2/236 (0%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA+  ISTPII+A L+ D D +YAR VKGR+E+TTLGEV EYIEEV++PDD
Sbjct: 1059 GVPRIKEIINANPKISTPIISAALENDVDPEYARRVKGRIEKTTLGEVTEYIEEVYLPDD 1118

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             F+L+KLD+DRI+LL LEVD++SIRY  C  + R     + V G S + + P  S  S N
Sbjct: 1119 CFLLVKLDIDRIKLLKLEVDVNSIRYSICTSKLRLNPKLVNVRGDSIITVNPSKSKYSIN 1178

Query: 882  SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
              + Q+K+ +P++VIKG+  ++RAVIH +D  G T+YKL VEG+N+R+VMAT GV G K 
Sbjct: 1179 YALTQLKETIPNIVIKGLPSVSRAVIHNDDSSGKTRYKLFVEGNNMREVMATLGVLGRKT 1238

Query: 942  SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +SNNT EV+KTLGIEAAR+TIMTEIKLVMENHGMSID RHPMLVADLMTS+GEVLG
Sbjct: 1239 TSNNTIEVFKTLGIEAARATIMTEIKLVMENHGMSIDRRHPMLVADLMTSRGEVLG 1294



 Score =  303 bits (777), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 157/319 (49%), Positives = 212/319 (66%), Gaps = 19/319 (5%)

Query: 87  VTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVG 146
           V     +++Q+HI IV+KNLY QD + TP+P+G+LDR+MGT     NC +CG++L++C+G
Sbjct: 22  VDSRHNMERQAHIHIVAKNLYNQDVEHTPVPYGVLDRKMGTCNNTTNCISCGKSLNECIG 81

Query: 147 HFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVR 206
           HFGYIDL LPVFH+GYFR +I ILQ+ICKN  C+ V+L E     + A++ NP L YL R
Sbjct: 82  HFGYIDLELPVFHVGYFRSIIGILQTICKN--CSHVMLSEADKKHYLARVLNPNLGYLTR 139

Query: 207 KSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNE 266
           K+L+K+IL+  KK +VC HC ++NG VKK GLLKI HEKYK + KK DAIV+  LAEYN 
Sbjct: 140 KALRKQILDKAKKTTVCQHCRDLNGTVKKAGLLKIVHEKYKGK-KKIDAIVQQKLAEYNN 198

Query: 267 AVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVP 326
            ++ N  +E   + GLI  LNPLEV  + E IP  DIPLLLMN+E + P DLILTR+ VP
Sbjct: 199 VLEDNKALEGVLQTGLISVLNPLEVQSILEKIPESDIPLLLMNSEYALPKDLILTRIPVP 258

Query: 327 PNCIRPSVISDLKSD----------NDVVLFNRQPSLHKLSIMAHRAKV-LPHRTFRFNE 375
           P CIRPSV+SDLK+           +++V  N     H+ S     AKV + +  + F +
Sbjct: 259 PICIRPSVVSDLKAGTTEDHLTMKLSEIVFINDVIQKHRQS----GAKVQMYNEDWEFLQ 314

Query: 376 CVCTPY-NADFDGDEMNVH 393
             C  Y N++  G  +N+ 
Sbjct: 315 LHCALYINSEMSGIPLNMQ 333



 Score =  121 bits (303), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 53/63 (84%), Positives = 59/63 (93%)

Query: 608 VTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           +   +GFV+NSF+SGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC+ Y
Sbjct: 826 IPAAKGFVENSFYSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCLHY 885

Query: 668 DMS 670
           DM+
Sbjct: 886 DMT 888



 Score = 89.7 bits (221), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 41/54 (75%), Positives = 47/54 (87%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           +LM NKSNLVTPRNGELLIAATQDFITGGYLLTQK+ F N+AQ  ++A  L+AG
Sbjct: 521 ILMGNKSNLVTPRNGELLIAATQDFITGGYLLTQKDMFLNKAQASQLAGCLLAG 574



 Score = 75.1 bits (183), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 33/59 (55%), Positives = 43/59 (72%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFH 726
            D  FDAA+YGQ D I GVSE IIMG+P+ VGTG+ KLL    + EP  + L+FD+P+F+
Sbjct: 1318 DHLFDAAYYGQKDVICGVSESIIMGIPVPVGTGIFKLLHKADKDEPRIKELIFDDPQFN 1376


>gi|328790760|ref|XP_003251457.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1-like,
           partial [Apis mellifera]
          Length = 1374

 Score =  403 bits (1036), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 196/276 (71%), Positives = 218/276 (78%), Gaps = 21/276 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+DVVLFNRQPSLHKLSIMAH+AK+L HRTFRFNECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 456 DDDVVLFNRQPSLHKLSIMAHKAKILDHRTFRFNECVCTPYNADFDGDEMNLHVPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL              VLM NKSNLVTPRNGELLIAATQDFITGGYLLTQK+ F N+
Sbjct: 516 RAEAL--------------VLMGNKSNLVTPRNGELLIAATQDFITGGYLLTQKDMFLNK 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q  ++A  L+A   DI       S     P +  +   +WTGKQIFSLILKPN  C + 
Sbjct: 562 TQASQLAGCLLAG-PDIA-----MSINLPEPAIL-KPTTLWTGKQIFSLILKPNNTCNIK 614

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           ANLKTKGRAYT NEE C  DSYVI+RNSELLAGSMDKSTLGSG K N+FYILLRD+GED+
Sbjct: 615 ANLKTKGRAYTTNEELCINDSYVIIRNSELLAGSMDKSTLGSGSKQNIFYILLRDWGEDI 674

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           A  AMWRL+RM SF+LMNRGFSIGIGDVTPGQG ++
Sbjct: 675 ATIAMWRLARMASFFLMNRGFSIGIGDVTPGQGLLK 710



 Score =  385 bits (989), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 225/476 (47%), Positives = 291/476 (61%), Gaps = 77/476 (16%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   PV+ KR+LD + AK+  +++ SL    ++  +NE L+S+E+ +  SE F +++  F
Sbjct: 913  GKDCPVDYKRILDHVRAKSPCKNEESLDGHSVIKATNELLNSEEY-ECLSEEFKQELSTF 971

Query: 1057 LEEFSKKESVTSHQDKVSQPLREQI----LSHQDKIGHGRESNPFPSACKAEACREKYVR 1112
            L+  ++K +   H   ++ P+  Q+    +S   +  H               C+EKY+R
Sbjct: 972  LKSVARKIARLRHNAALNVPVILQLERLTVSQLVEFIH--------------TCKEKYMR 1017

Query: 1113 AQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYIEEVFVPD 1158
            A+IEP TAVGALAAQSIGEPGTQMTLKTFHFAG              E+     ++  P 
Sbjct: 1018 AKIEPGTAVGALAAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIINASPKISTPI 1077

Query: 1159 DSFILIKLDMD-----RIR------------------------LLHLEVDID-------- 1181
             +  LI  D D     R++                         L +++DID        
Sbjct: 1078 ITAALIN-DADPEYARRVKGRIEKTTLGEVTEYIEEVYLPDDCFLLIKIDIDRIKLLKLE 1136

Query: 1182 ----SIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGV 1235
                SIRY  C  + R     + V G S + + P  +  S N  + Q+K+L+P++VIKG+
Sbjct: 1137 VDVNSIRYSICTSKLRLNPKLVNVRGDSIITVNPSKNKYSLNYALTQLKELIPNIVIKGL 1196

Query: 1236 QGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAAR 1295
              ++RAVIH +D  G  KYKL VEGDN+RDVMAT GV G K +SNNT EV+KTLGIEAAR
Sbjct: 1197 PSVSRAVIHNDDSCGKKKYKLFVEGDNMRDVMATLGVLGKKTTSNNTIEVFKTLGIEAAR 1256

Query: 1296 STIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENT 1355
            +TIMTEIKLVMENHGMSID RHPMLVADLMTS+GEVLGITR GLAKMKESVLNLASFE T
Sbjct: 1257 ATIMTEIKLVMENHGMSIDRRHPMLVADLMTSRGEVLGITRQGLAKMKESVLNLASFEKT 1316

Query: 1356 SDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDN 1411
            SDHLFDAA+YGQ D I GVSE IIMG+P+ VGTG+ KLL    + EP  R L+FD+
Sbjct: 1317 SDHLFDAAYYGQKDVICGVSESIIMGIPVPVGTGIFKLLHKADKDEPKKRDLIFDD 1372



 Score =  309 bits (791), Expect = 9e-81,   Method: Compositional matrix adjust.
 Identities = 156/236 (66%), Positives = 187/236 (79%), Gaps = 2/236 (0%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS  ISTPIITA L  D D +YAR VKGR+E+TTLGEV EYIEEV++PDD
Sbjct: 1059 GVPRIKEIINASPKISTPIITAALINDADPEYARRVKGRIEKTTLGEVTEYIEEVYLPDD 1118

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             F+LIK+D+DRI+LL LEVD++SIRY  C  + R     + V G S + + P  +  S N
Sbjct: 1119 CFLLIKIDIDRIKLLKLEVDVNSIRYSICTSKLRLNPKLVNVRGDSIITVNPSKNKYSLN 1178

Query: 882  SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
              + Q+K+L+P++VIKG+  ++RAVIH +D  G  KYKL VEGDN+RDVMAT GV G K 
Sbjct: 1179 YALTQLKELIPNIVIKGLPSVSRAVIHNDDSCGKKKYKLFVEGDNMRDVMATLGVLGKKT 1238

Query: 942  SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +SNNT EV+KTLGIEAAR+TIMTEIKLVMENHGMSID RHPMLVADLMTS+GEVLG
Sbjct: 1239 TSNNTIEVFKTLGIEAARATIMTEIKLVMENHGMSIDRRHPMLVADLMTSRGEVLG 1294



 Score =  297 bits (760), Expect = 4e-77,   Method: Compositional matrix adjust.
 Identities = 139/254 (54%), Positives = 184/254 (72%), Gaps = 3/254 (1%)

Query: 87  VTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVG 146
           V     +++Q+H+ +V+KNLY QD + TP+P+G+LDRRMGT     NC +CG+ L++C+G
Sbjct: 22  VDSRHNMERQAHMHVVAKNLYNQDVEHTPVPYGVLDRRMGTCNNTTNCASCGKTLNECIG 81

Query: 147 HFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVR 206
           HFGYIDL LPVFH+GYFR +I ILQ+ICKN  C+ V+L E     +  ++ NP L YL R
Sbjct: 82  HFGYIDLELPVFHVGYFRSIIGILQTICKN--CSHVMLSEIDKKHYLTRVLNPNLGYLTR 139

Query: 207 KSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNE 266
           K+L+K+IL+  KK SVC +CG++NG VKK GLLKI HEKYK + KK D IV+  LAEYN 
Sbjct: 140 KALRKQILDKAKKTSVCQNCGDLNGTVKKAGLLKIVHEKYKAK-KKVDVIVQQKLAEYNN 198

Query: 267 AVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVP 326
            ++ N  +E   + GL+  LNPLEV  + E IP  DIPLL+MN E + P DLILTR+ VP
Sbjct: 199 VLEENKALEGILQSGLVNVLNPLEVQSILEKIPENDIPLLMMNTECALPKDLILTRIPVP 258

Query: 327 PNCIRPSVISDLKS 340
           P CIRPSV+SD+K+
Sbjct: 259 PICIRPSVVSDIKA 272



 Score =  121 bits (303), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 53/63 (84%), Positives = 59/63 (93%)

Query: 608 VTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           +   +GFV+NSF+SGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC+ Y
Sbjct: 826 IPAAKGFVENSFYSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCLHY 885

Query: 668 DMS 670
           DM+
Sbjct: 886 DMT 888



 Score = 88.6 bits (218), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 41/54 (75%), Positives = 46/54 (85%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           VLM NKSNLVTPRNGELLIAATQDFITGGYLLTQK+ F N+ Q  ++A  L+AG
Sbjct: 521 VLMGNKSNLVTPRNGELLIAATQDFITGGYLLTQKDMFLNKTQASQLAGCLLAG 574



 Score = 70.9 bits (172), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 32/55 (58%), Positives = 39/55 (70%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDN 722
            D  FDAA+YGQ D I GVSE IIMG+P+ VGTG+ KLL    + EP  R L+FD+
Sbjct: 1318 DHLFDAAYYGQKDVICGVSESIIMGIPVPVGTGIFKLLHKADKDEPKKRDLIFDD 1372


>gi|156717272|ref|NP_001096178.1| polymerase (RNA) III (DNA directed) polypeptide A, 155kDa [Xenopus
            (Silurana) tropicalis]
 gi|134025743|gb|AAI35597.1| polr3a protein [Xenopus (Silurana) tropicalis]
          Length = 1390

 Score =  402 bits (1032), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 230/484 (47%), Positives = 301/484 (62%), Gaps = 77/484 (15%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+L+++ A      +P+LS  E++  S   +   EFL    ++++++IKKF
Sbjct: 913  GKDEPLEFKRVLENVKAVYPCSEEPALSKNELILTSESIMKKTEFLC-CQDSYLQEIKKF 971

Query: 1057 LEEFSKKESVTSHQDK-------VSQPLREQILSHQDKIGHGRESNPFPSACKAEACREK 1109
            +   S  E +   +DK        ++P   ++L   D+I       P       E CR+K
Sbjct: 972  VTGVS--ERIKKTRDKYGINDNGTTEP---RVLYQLDRI------TPTQLEKFLETCRDK 1020

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFH--------------------------- 1142
            Y+RAQ+EP +AVGAL AQSIGEPGTQMTLKTFH                           
Sbjct: 1021 YMRAQMEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKNIS 1080

Query: 1143 ---------------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLH 1175
                           FA            GE+ EYIEEVF+PDD F+L+KL ++RIRLL 
Sbjct: 1081 TPIITAHLDIDDDADFARLVKGRIEKTLLGEISEYIEEVFLPDDCFLLVKLSLERIRLLR 1140

Query: 1176 LEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVI 1232
            LEV+ +++RY  C+ + R   G + V G + L + P+++SKS    + Q +K+ LP VV+
Sbjct: 1141 LEVNAETVRYSICMSKLRVKPGDIAVHGEAVLCVTPRENSKSSMYYVLQSLKEDLPKVVV 1200

Query: 1233 KGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIE 1292
            +G+  + RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIE
Sbjct: 1201 QGIPEVARAVIHIDEQSGKEKYKLLVEGDNLRSVMATHGVKGSRTTSNNTYEVEKTLGIE 1260

Query: 1293 AARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASF 1352
            AARSTI+ EI+  M NHGMSID RH ML+ADLMT KGEVLGITR GLAKMKESVL LASF
Sbjct: 1261 AARSTIINEIQYTMVNHGMSIDRRHVMLLADLMTYKGEVLGITRFGLAKMKESVLMLASF 1320

Query: 1353 ENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP-RTLLFDN 1411
            E T+DHLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    +    P R L+FD+
Sbjct: 1321 EKTADHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADKDPSPPRRPLIFDH 1380

Query: 1412 PEFH 1415
             +FH
Sbjct: 1381 EDFH 1384



 Score =  339 bits (870), Expect = 6e-90,   Method: Compositional matrix adjust.
 Identities = 165/277 (59%), Positives = 203/277 (73%), Gaps = 22/277 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 455 DGDIVLFNRQPSLHKLSIMAHIARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 514

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEA               VLM  K+NLVTPRNGE LIAA QDF+T  YLLT K+ FF+R
Sbjct: 515 KAEAY--------------VLMGTKANLVTPRNGEPLIAAIQDFLTAAYLLTLKDTFFDR 560

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++       G  ++   R   P + ++   +WTGKQ+FSLIL+P+ D PV 
Sbjct: 561 AKACQIIASILV------GKDEKIKVRLPPPAI-LKPVTLWTGKQVFSLILQPSHDNPVR 613

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ CH DSYV ++NSEL+ GS+DK TLGSG K N+FYILLRD+G+ 
Sbjct: 614 ANLRTKGKQYCGKGEDLCHNDSYVTIQNSELMCGSLDKGTLGSGSKNNIFYILLRDWGQV 673

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
            A  AM RL+R+   +L NRGFSIGIGDVTPGQG ++
Sbjct: 674 EAADAMSRLARLAPVFLSNRGFSIGIGDVTPGQGLLK 710



 Score =  293 bits (749), Expect = 7e-76,   Method: Compositional matrix adjust.
 Identities = 148/237 (62%), Positives = 187/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+NISTPIITA+LD D D D+AR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1065 GVPRIKEIINASKNISTPIITAHLDIDDDADFARLVKGRIEKTLLGEISEYIEEVFLPDD 1124

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             F+L+KL ++RIRLL LEV+ +++RY  C+ + R   G + V G + L + P+++SKS  
Sbjct: 1125 CFLLVKLSLERIRLLRLEVNAETVRYSICMSKLRVKPGDIAVHGEAVLCVTPRENSKSSM 1184

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  + RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG +
Sbjct: 1185 YYVLQSLKEDLPKVVVQGIPEVARAVIHIDEQSGKEKYKLLVEGDNLRSVMATHGVKGSR 1244

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNTYEV KTLGIEAARSTI+ EI+  M NHGMSID RH ML+ADLMT KGEVLG
Sbjct: 1245 TTSNNTYEVEKTLGIEAARSTIINEIQYTMVNHGMSIDRRHVMLLADLMTYKGEVLG 1301



 Score =  290 bits (743), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 144/255 (56%), Positives = 183/255 (71%), Gaps = 5/255 (1%)

Query: 87  VTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVG 146
           V   ++++QQ+HIQIVSK+LY QD   TP+  G+LD RMGT++K+ +C TCG+NL++C+G
Sbjct: 21  VKSAEQMRQQAHIQIVSKSLYSQDNNHTPLAFGVLDHRMGTSEKDRHCQTCGKNLAECLG 80

Query: 147 HFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVR 206
           H+GY+DL LP FH+GYF+ VI ILQ ICK  TC+R+LL  E+   F   L+ P L+YL +
Sbjct: 81  HYGYLDLELPCFHVGYFKAVIGILQMICK--TCSRILLNAEERKQFLDFLKRPGLTYLQK 138

Query: 207 KSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNE 266
           + LKKKI +  +K +VC +CG  NG VKKCGLLKI HEKYK   K  D +V   L  ++ 
Sbjct: 139 RGLKKKISDKCRKKTVCLYCGAYNGSVKKCGLLKIIHEKYKTTKKVVDPMVSHFLQSFDT 198

Query: 267 AVKFNPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLV 325
           A++ N E+E+    G  Q  LNPL VL L   IP EDIPLLLMN E  KPSDLILTRLLV
Sbjct: 199 AIEHNKEVES--LLGRAQENLNPLIVLNLLRQIPAEDIPLLLMNPEAGKPSDLILTRLLV 256

Query: 326 PPNCIRPSVISDLKS 340
           PP CIRPSV+SDLKS
Sbjct: 257 PPLCIRPSVVSDLKS 271



 Score =  116 bits (291), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 829 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 888



 Score = 79.0 bits (193), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 35/62 (56%), Positives = 44/62 (70%), Gaps = 1/62 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP-RTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    +    P R L+FD+ +FH
Sbjct: 1325 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADKDPSPPRRPLIFDHEDFH 1384

Query: 727  FP 728
             P
Sbjct: 1385 HP 1386



 Score = 72.4 bits (176), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 32/55 (58%), Positives = 43/55 (78%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+T  YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 520 VLMGTKANLVTPRNGEPLIAAIQDFLTAAYLLTLKDTFFDRAKACQIIASILVGK 574


>gi|432923404|ref|XP_004080458.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1-like [Oryzias
            latipes]
          Length = 1390

 Score =  402 bits (1032), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 228/484 (47%), Positives = 302/484 (62%), Gaps = 77/484 (15%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A  +   +P+LS  +++  S+  +   +F+    ++F+ +IKKF
Sbjct: 914  GKDEPLEFKRVLDNIRAVYTCPDEPALSQNKLVLTSDAIMKRADFMC-CRDSFLEEIKKF 972

Query: 1057 LEEFSKKESVTSHQDK-------VSQPLREQILSHQDKIGHGRESNPFPSACKAEACREK 1109
            +   S  E +   +DK        S+P   ++L   D+I       P       E CR+K
Sbjct: 973  IRSMS--ERIKKTRDKYGINDNGTSEP---KVLYQLDRI------TPTQLEKFLETCRDK 1021

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFH--------------------------- 1142
            Y+RAQ+EP +AVGAL AQSIGEPGTQMTLKTFH                           
Sbjct: 1022 YMRAQMEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKNIS 1081

Query: 1143 ---------------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLH 1175
                           FA            GE+ EYIEEVF+PDD FIL+KL ++RIRLL 
Sbjct: 1082 TPIITAQLDVEDDADFARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLR 1141

Query: 1176 LEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVI 1232
            LEV+ +++RY  C+ + R   G + V G + + + P++++KS    + Q +K+ LP VV+
Sbjct: 1142 LEVNAETVRYSICMSKLRVKPGDIAVHGEAVVCVSPRENNKSSMYYVLQSLKEDLPKVVV 1201

Query: 1233 KGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIE 1292
            +G+  + RAVIH ++  G  KYKLLVEGDN+R VMAT+GV G + +SNNTYEV KTLGIE
Sbjct: 1202 QGIPEVARAVIHIDEQSGKNKYKLLVEGDNMRAVMATHGVNGSRTTSNNTYEVEKTLGIE 1261

Query: 1293 AARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASF 1352
            AARSTI+ EI+  M NHGMSID RH ML+ADLM+ KGE+LGITR GLAKMKESVL LASF
Sbjct: 1262 AARSTIINEIQYTMVNHGMSIDRRHVMLLADLMSYKGEILGITRFGLAKMKESVLMLASF 1321

Query: 1353 ENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDN 1411
            E T+DHLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    +   PV R LLFD+
Sbjct: 1322 EKTADHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADKDPTPVTRPLLFDH 1381

Query: 1412 PEFH 1415
             +FH
Sbjct: 1382 KDFH 1385



 Score =  345 bits (884), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 165/277 (59%), Positives = 203/277 (73%), Gaps = 22/277 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDVVLFNRQPSLHKLSIMAHIARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              +LM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------ILMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           ++  +I ++++    +   I       S      ++   +WTGKQIFS+IL+P++DCPV 
Sbjct: 562 SKACQIVASILVGKDEKVRI-------SLPHPAILKPMALWTGKQIFSMILRPSKDCPVK 614

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C+ DS+V++ NSEL+ GSMDK TLGSG K N+FYILLRD+G+ 
Sbjct: 615 ANLRTKGKQYCGKGEDLCYNDSFVVIHNSELMCGSMDKGTLGSGSKNNIFYILLRDWGQL 674

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
            A  AM RL+R+   YL NRGFSIGIGDVTPG G ++
Sbjct: 675 EAANAMSRLARLAPVYLSNRGFSIGIGDVTPGHGLLK 711



 Score =  290 bits (742), Expect = 4e-75,   Method: Compositional matrix adjust.
 Identities = 140/250 (56%), Positives = 181/250 (72%), Gaps = 3/250 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           ++++QQ+HIQ+VSKNLY QD + TP+PHG+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EQMRQQAHIQVVSKNLYSQDTKHTPLPHGVLDHRMGTSEKDRPCLTCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           +DL LP FH+GYF+ VI ILQ ICK  TC+ ++L +E+   F   L+ P L+YL ++ LK
Sbjct: 86  LDLELPCFHVGYFKAVIGILQMICK--TCSSIMLTKEEKLQFLDLLKRPNLAYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI E  +K +VC +C   NG VKKCGLLKI HEKYK   K  D  V + +  ++ A++ 
Sbjct: 144 KKISEKCRKRTVCLNCSAFNGTVKKCGLLKIIHEKYKTTKKVVDPFVSEFMQSFDTAIEH 203

Query: 271 NPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCI 330
           N  IE        + LNPL VL LF  IP EDIPLLLMN E  KP+DLI+TRLLVPP CI
Sbjct: 204 NKLIEPLLNRAQ-ENLNPLVVLNLFRRIPDEDIPLLLMNPEAGKPADLIITRLLVPPLCI 262

Query: 331 RPSVISDLKS 340
           RPSV+SDLKS
Sbjct: 263 RPSVVSDLKS 272



 Score =  283 bits (725), Expect = 4e-73,   Method: Compositional matrix adjust.
 Identities = 142/237 (59%), Positives = 185/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+NISTPIITA LD + D D+AR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1066 GVPRIKEIINASKNISTPIITAQLDVEDDADFARLVKGRIEKTLLGEISEYIEEVFLPDD 1125

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  C+ + R   G + V G + + + P++++KS  
Sbjct: 1126 CFILVKLSLERIRLLRLEVNAETVRYSICMSKLRVKPGDIAVHGEAVVCVSPRENNKSSM 1185

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  + RAVIH ++  G  KYKLLVEGDN+R VMAT+GV G +
Sbjct: 1186 YYVLQSLKEDLPKVVVQGIPEVARAVIHIDEQSGKNKYKLLVEGDNMRAVMATHGVNGSR 1245

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNTYEV KTLGIEAARSTI+ EI+  M NHGMSID RH ML+ADLM+ KGE+LG
Sbjct: 1246 TTSNNTYEVEKTLGIEAARSTIINEIQYTMVNHGMSIDRRHVMLLADLMSYKGEILG 1302



 Score =  115 bits (287), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 51/65 (78%), Positives = 58/65 (89%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV +SF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 830 AKGFVADSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 889

Query: 671 FDAAF 675
             ++ 
Sbjct: 890 VRSSM 894



 Score = 82.4 bits (202), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 37/62 (59%), Positives = 45/62 (72%), Gaps = 1/62 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    +   PV R LLFD+ +FH
Sbjct: 1326 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADKDPTPVTRPLLFDHKDFH 1385

Query: 727  FP 728
             P
Sbjct: 1386 IP 1387



 Score = 73.2 bits (178), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 31/55 (56%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           +LM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R++  +I ++++ G+
Sbjct: 521 ILMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRSKACQIVASILVGK 575


>gi|380025198|ref|XP_003696364.1| PREDICTED: LOW QUALITY PROTEIN: DNA-directed RNA polymerase III
            subunit RPC1-like, partial [Apis florea]
          Length = 1994

 Score =  398 bits (1022), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 195/276 (70%), Positives = 218/276 (78%), Gaps = 21/276 (7%)

Query: 341  DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
            D+DVVLFNRQPSLHKLSIMAH+AK+L HRTFRFNECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 1084 DDDVVLFNRQPSLHKLSIMAHKAKILDHRTFRFNECVCTPYNADFDGDEMNLHVPQTEEA 1143

Query: 401  RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
            RAEAL              VLM NKSNLVTPRNGELLIAATQDFITGGYLLTQK+ F N+
Sbjct: 1144 RAEAL--------------VLMGNKSNLVTPRNGELLIAATQDFITGGYLLTQKDMFLNK 1189

Query: 461  AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
             Q  ++A  L+A   DI       S     P + ++   +WTGKQ FSLILKPN  C + 
Sbjct: 1190 TQASQLAGCLLAG-PDIT-----MSINLPEPAI-LKPTTLWTGKQXFSLILKPNNTCNIK 1242

Query: 521  ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            ANLKTKGRAYT NEE C  DSYVI+RNSELLAGSMDKSTLGSG K N+FYILLRD+GED+
Sbjct: 1243 ANLKTKGRAYTTNEELCINDSYVIIRNSELLAGSMDKSTLGSGSKQNIFYILLRDWGEDI 1302

Query: 581  AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
            A  AMWRL+RM SF+LMNRGFSIGIGDVTPGQG ++
Sbjct: 1303 ATIAMWRLARMASFFLMNRGFSIGIGDVTPGQGLLK 1338



 Score =  373 bits (958), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 220/463 (47%), Positives = 283/463 (61%), Gaps = 77/463 (16%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   PV+ KR+LD + AK+  +++ SL    ++  +NE L+S+E+ +  SE F +++  F
Sbjct: 1541 GKDCPVDYKRILDHVRAKSPCKNEESLDGHSVIKATNELLNSEEY-ECLSEEFKQELSTF 1599

Query: 1057 LEEFSKKESVTSHQDKVSQPLREQI----LSHQDKIGHGRESNPFPSACKAEACREKYVR 1112
            L+  ++K +   H   ++ P+  Q+    +S   +  H               C+EKY+R
Sbjct: 1600 LKTVARKIARLRHNAILNVPVILQLERLTVSQLVEFIH--------------TCKEKYMR 1645

Query: 1113 AQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYIEEVFVPD 1158
            A+IEP TAVGALAAQSIGEPGTQMTLKTFHFAG              E+     ++  P 
Sbjct: 1646 AKIEPGTAVGALAAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIINASPKISTPI 1705

Query: 1159 DSFILIKLDMD-----RIR------------------------LLHLEVDID-------- 1181
             +  LI  D D     R++                         L +++DID        
Sbjct: 1706 ITAALIN-DADPEYARRVKGRIEKTILGEVTEYIEEVYLPDDCFLLIKIDIDRIKLLKLE 1764

Query: 1182 ----SIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGV 1235
                SIRY  C  + R     + V G S + + P  +  S N  + Q+K+L+P++VIKG+
Sbjct: 1765 VDVNSIRYSICTSKLRLNPKLVNVRGDSIITVNPSKNKYSLNYALTQLKELIPNIVIKGL 1824

Query: 1236 QGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAAR 1295
              ++RAVIH +D  G  KYKL VEGDN+RDVMAT GV G K +SNNT EV+KTLGIEAAR
Sbjct: 1825 PSVSRAVIHNDDSCGKKKYKLFVEGDNMRDVMATLGVLGKKTTSNNTIEVFKTLGIEAAR 1884

Query: 1296 STIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENT 1355
            +TIMTEIKLVMENHGMSID RHPMLVADLMTS+GEVLGITR GLAKMKESVLNLASFE T
Sbjct: 1885 ATIMTEIKLVMENHGMSIDRRHPMLVADLMTSRGEVLGITRQGLAKMKESVLNLASFEKT 1944

Query: 1356 SDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 1398
            SDHLFDAA+YGQ D I GVSE IIMG+P+ VGTG+ KLL   P
Sbjct: 1945 SDHLFDAAYYGQKDVICGVSESIIMGIPVPVGTGIFKLLHKYP 1987



 Score =  307 bits (786), Expect = 4e-80,   Method: Compositional matrix adjust.
 Identities = 155/236 (65%), Positives = 186/236 (78%), Gaps = 2/236 (0%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS  ISTPIITA L  D D +YAR VKGR+E+T LGEV EYIEEV++PDD
Sbjct: 1687 GVPRIKEIINASPKISTPIITAALINDADPEYARRVKGRIEKTILGEVTEYIEEVYLPDD 1746

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             F+LIK+D+DRI+LL LEVD++SIRY  C  + R     + V G S + + P  +  S N
Sbjct: 1747 CFLLIKIDIDRIKLLKLEVDVNSIRYSICTSKLRLNPKLVNVRGDSIITVNPSKNKYSLN 1806

Query: 882  SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
              + Q+K+L+P++VIKG+  ++RAVIH +D  G  KYKL VEGDN+RDVMAT GV G K 
Sbjct: 1807 YALTQLKELIPNIVIKGLPSVSRAVIHNDDSCGKKKYKLFVEGDNMRDVMATLGVLGKKT 1866

Query: 942  SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +SNNT EV+KTLGIEAAR+TIMTEIKLVMENHGMSID RHPMLVADLMTS+GEVLG
Sbjct: 1867 TSNNTIEVFKTLGIEAARATIMTEIKLVMENHGMSIDRRHPMLVADLMTSRGEVLG 1922



 Score =  296 bits (758), Expect = 6e-77,   Method: Compositional matrix adjust.
 Identities = 138/254 (54%), Positives = 184/254 (72%), Gaps = 3/254 (1%)

Query: 87  VTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVG 146
           V     +++Q+H+ +V+KNLY QD + TP+P+G+LDR+MGT     NC +CG+ L++C+G
Sbjct: 650 VDSRHNMERQAHMHVVAKNLYNQDVEHTPVPYGVLDRKMGTCNNTTNCASCGKTLNECIG 709

Query: 147 HFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVR 206
           HFGYIDL LPVFH+GYFR +I ILQ+ICKN  C+ V+L E     +  ++ NP L YL R
Sbjct: 710 HFGYIDLELPVFHVGYFRSIIGILQTICKN--CSHVMLSEIDKKHYLTRVLNPNLGYLTR 767

Query: 207 KSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNE 266
           K+L+K+IL+  KK SVC +CG++NG VKK GLLKI HEKYK + KK D IV+  LAEYN 
Sbjct: 768 KALRKQILDKAKKTSVCQNCGDLNGTVKKAGLLKIVHEKYKAK-KKVDVIVQQKLAEYNN 826

Query: 267 AVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVP 326
            ++ N  +E   + GL+  LNPLEV  + E IP  DIPLL+MN E + P DLILTR+ VP
Sbjct: 827 VLEENKALEGILQSGLVNVLNPLEVQSILEKIPENDIPLLMMNTECALPKDLILTRIPVP 886

Query: 327 PNCIRPSVISDLKS 340
           P CIRPSV+SD+K+
Sbjct: 887 PICIRPSVVSDIKA 900



 Score =  121 bits (303), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 53/63 (84%), Positives = 59/63 (93%)

Query: 608  VTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
            +   +GFV+NSF+SGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC+ Y
Sbjct: 1454 IPAAKGFVENSFYSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCLHY 1513

Query: 668  DMS 670
            DM+
Sbjct: 1514 DMT 1516



 Score = 88.2 bits (217), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 41/54 (75%), Positives = 46/54 (85%)

Query: 21   VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
            VLM NKSNLVTPRNGELLIAATQDFITGGYLLTQK+ F N+ Q  ++A  L+AG
Sbjct: 1149 VLMGNKSNLVTPRNGELLIAATQDFITGGYLLTQKDMFLNKTQASQLAGCLLAG 1202



 Score = 60.5 bits (145), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 27/42 (64%), Positives = 31/42 (73%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 709
            D  FDAA+YGQ D I GVSE IIMG+P+ VGTG+ KLL   P
Sbjct: 1946 DHLFDAAYYGQKDVICGVSESIIMGIPVPVGTGIFKLLHKYP 1987


>gi|47216067|emb|CAG04806.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 1319

 Score =  381 bits (978), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 227/493 (46%), Positives = 291/493 (59%), Gaps = 110/493 (22%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFL----------QDT- 1045
            G   P+E KR+LD+I A  +   +P+LS  E++  ++  +   +FL           DT 
Sbjct: 858  GKDEPLEFKRVLDNIRAVYACSDEPALSQNELVLTADAIMKRTDFLCCRDSFLEELTDTG 917

Query: 1046 SENFVRDIKKFLEEFSKKESVTSHQDK-------VSQPLREQILSHQDKIGHGRESNPFP 1098
            SE ++ +IKKF++ FS  E +   +DK        S+P   ++L   D+I       P  
Sbjct: 918  SEKYLEEIKKFVKSFS--ERIKKTRDKYGINDNGTSEP---KVLYQLDRI------TPTQ 966

Query: 1099 SACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFH---------------- 1142
                 E CR+KY+RAQ+EP +AVGAL AQSIGEPGTQMTLKTFH                
Sbjct: 967  LEKFLETCRDKYMRAQMEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRI 1026

Query: 1143 --------------------------FA------------GEVCEYIEEVFVPDDSFILI 1164
                                      FA            GE+ EYIEEVF+PDD FIL+
Sbjct: 1027 KEIINASKNISTPIITAHLDVEDDADFARLVKGRIEKTLLGEISEYIEEVFLPDDCFILV 1086

Query: 1165 KLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-M 1223
            KL ++RIRLL LE                         + + + P+++SKS    + Q +
Sbjct: 1087 KLSLERIRLLRLE-------------------------AVVCVSPRENSKSSMYYVLQSL 1121

Query: 1224 KQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTY 1283
            K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDN+R VMAT+GVKG + +SNNTY
Sbjct: 1122 KEELPKVVVQGIPEVSRAVIHIDEQSGRNKYKLLVEGDNMRAVMATHGVKGSRTTSNNTY 1181

Query: 1284 EVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMK 1343
            EV KTLGIEAARSTI+ EI+  M NHGMSID RH ML+ADLM+ KGE+LGITR GLAKMK
Sbjct: 1182 EVEKTLGIEAARSTIINEIQYTMVNHGMSIDRRHVMLLADLMSYKGEILGITRFGLAKMK 1241

Query: 1344 ESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EP 1402
            ESVL LASFE T+DHLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    +   P
Sbjct: 1242 ESVLMLASFEKTADHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADKDPSP 1301

Query: 1403 VPRTLLFDNPEFH 1415
              R LLFDN  FH
Sbjct: 1302 AKRPLLFDNAAFH 1314



 Score =  353 bits (906), Expect = 4e-94,   Method: Compositional matrix adjust.
 Identities = 169/277 (61%), Positives = 206/277 (74%), Gaps = 22/277 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 400 DGDIVLFNRQPSLHKLSIMAHIARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 459

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              +LM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 460 KAEAL--------------ILMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 505

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           ++  +I ++++    +   I       S+     ++   +WTGKQIFS+ILKP++DCPVN
Sbjct: 506 SKACQIVASILVGKDEKVRI-------SFPRPAIMKPMALWTGKQIFSVILKPSKDCPVN 558

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANLKTKG+ Y    E+ CH DS+V++ NSEL+ GSMDK TLGSG K N+FYILLRD+G+ 
Sbjct: 559 ANLKTKGKQYCGKGEDLCHNDSFVVIHNSELMCGSMDKGTLGSGSKNNIFYILLRDWGQL 618

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++
Sbjct: 619 EAANAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLK 655



 Score =  261 bits (668), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 136/235 (57%), Positives = 173/235 (73%), Gaps = 26/235 (11%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+NISTPIITA+LD + D D+AR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1022 GVPRIKEIINASKNISTPIITAHLDVEDDADFARLVKGRIEKTLLGEISEYIEEVFLPDD 1081

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSK 883
             FIL+KL ++RIRLL LE                         + + + P+++SKS    
Sbjct: 1082 CFILVKLSLERIRLLRLE-------------------------AVVCVSPRENSKSSMYY 1116

Query: 884  MYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCS 942
            + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDN+R VMAT+GVKG + +
Sbjct: 1117 VLQSLKEELPKVVVQGIPEVSRAVIHIDEQSGRNKYKLLVEGDNMRAVMATHGVKGSRTT 1176

Query: 943  SNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            SNNTYEV KTLGIEAARSTI+ EI+  M NHGMSID RH ML+ADLM+ KGE+LG
Sbjct: 1177 SNNTYEVEKTLGIEAARSTIINEIQYTMVNHGMSIDRRHVMLLADLMSYKGEILG 1231



 Score =  196 bits (498), Expect = 9e-47,   Method: Compositional matrix adjust.
 Identities = 110/250 (44%), Positives = 142/250 (56%), Gaps = 59/250 (23%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           ++++QQ+HIQ+VSKNLY QD   TP+ +G+LD RMGT++K+  C TCG+ L+DC+GH+GY
Sbjct: 26  EQMRQQAHIQVVSKNLYSQDTAHTPLAYGVLDHRMGTSEKDRPCLTCGKTLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           +DL LP FHIGYF+ +I ILQ+                                  + +K
Sbjct: 86  LDLELPCFHIGYFKAIIGILQA----------------------------------RPVK 111

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           K              CG          LLKI HEKYK   K  D  V + L  ++ A++ 
Sbjct: 112 K--------------CG----------LLKIIHEKYKTTKKVVDPFVSEFLQSFDIAIEH 147

Query: 271 NPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCI 330
           N  +E        + LNPL VL LF+ I  EDIPLLLMN E   P+DLILTRLLVPP CI
Sbjct: 148 NKVLEPLLSRAQ-ENLNPLVVLNLFKRISREDIPLLLMNPEAGIPADLILTRLLVPPLCI 206

Query: 331 RPSVISDLKS 340
           RPSV+SDLKS
Sbjct: 207 RPSVVSDLKS 216



 Score =  116 bits (291), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 774 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 833



 Score = 82.4 bits (202), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 37/62 (59%), Positives = 43/62 (69%), Gaps = 1/62 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    +   P  R LLFDN  FH
Sbjct: 1255 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADKDPSPAKRPLLFDNAAFH 1314

Query: 727  FP 728
             P
Sbjct: 1315 IP 1316



 Score = 73.2 bits (178), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 31/55 (56%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           +LM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R++  +I ++++ G+
Sbjct: 465 ILMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRSKACQIVASILVGK 519


>gi|221043166|dbj|BAH13260.1| unnamed protein product [Homo sapiens]
          Length = 1369

 Score =  380 bits (975), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 215/458 (46%), Positives = 288/458 (62%), Gaps = 46/458 (10%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A     S+P+LS  E++  +   +   EFL    ++F+++IKKF
Sbjct: 914  GKDEPLEFKRVLDNIKAVFPCPSEPALSKNELILTTESIMKKSEFLC-CQDSFLQEIKKF 972

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 973  IKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQVEKFLETCRDKYMRAQ 1026

Query: 1115 IEPATAVGALAAQ---SIGEPGTQMTLKTFH----------------------------- 1142
            +EP +AVGAL  Q   ++G P  +  +                                 
Sbjct: 1027 MEPGSAVGALCTQMNITLGVPRIKEIINASKAISTPIITAQLDKDDDADYARLVKGRIEK 1086

Query: 1143 -FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTV 1199
               GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ +++RY  C  + R   G + V
Sbjct: 1087 TLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNAETVRYSICTSKLRVKPGDVAV 1146

Query: 1200 SGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLV 1258
             G + + + P+++SKS    + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLV
Sbjct: 1147 HGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLV 1206

Query: 1259 EGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHP 1318
            EGDNLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH 
Sbjct: 1207 EGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHV 1266

Query: 1319 MLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECI 1378
            ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+DHLFDAA++GQ D + GVSECI
Sbjct: 1267 MLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTADHLFDAAYFGQKDSVCGVSECI 1326

Query: 1379 IMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 1415
            IMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1327 IMGIPMNIGTGLFKLLHKADRDPNPPKRPLIFDTNEFH 1364



 Score =  346 bits (887), Expect = 7e-92,   Method: Compositional matrix adjust.
 Identities = 169/280 (60%), Positives = 207/280 (73%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDVVLFNRQPSLHKLSIMAHLARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++       G  ++   R   P + ++   +WTGKQIFS+IL+P+ D PV 
Sbjct: 562 AKACQIIASILV------GKDEKIKVRLPPPTI-LKPVTLWTGKQIFSVILRPSDDNPVR 614

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DSYV ++NSEL++GSMDK TLGSG K N+FYILLRD+G++
Sbjct: 615 ANLRTKGKQYCGKGEDLCANDSYVTIQNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQN 674

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 675 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 714



 Score =  298 bits (764), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 145/251 (57%), Positives = 181/251 (72%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD Q  P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNQHAPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYFR VI ILQ ICK  TC  ++L +E+   F   L+ P L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFRAVIGILQMICK--TCCHIMLSQEEKKQFLDYLKRPGLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K ++C HCG  NG VKKCGLLKI HEKYK   K  D IV + L  +  A++ 
Sbjct: 144 KKISDKCRKKNICHHCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPIVSNFLQSFETAIEH 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP ED+PLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NKEVEPL--LGRAQENLNPLVVLNLFKRIPAEDVPLLLMNPEAGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 262 IRPSVVSDLKS 272



 Score =  290 bits (742), Expect = 4e-75,   Method: Compositional matrix adjust.
 Identities = 147/237 (62%), Positives = 186/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LDKD D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1045 GVPRIKEIINASKAISTPIITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 1104

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  C  + R   G + V G + + + P+++SKS  
Sbjct: 1105 CFILVKLSLERIRLLRLEVNAETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSM 1164

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG +
Sbjct: 1165 YYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTR 1224

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1225 TTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1281



 Score =  116 bits (291), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 830 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 889



 Score = 82.0 bits (201), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1305 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPNPPKRPLIFDTNEFH 1364

Query: 727  FPQV 730
             P V
Sbjct: 1365 IPLV 1368



 Score = 74.7 bits (182), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 521 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 575


>gi|307196534|gb|EFN78064.1| DNA-directed RNA polymerase III subunit RPC1 [Harpegnathos
           saltator]
          Length = 1334

 Score =  375 bits (963), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 179/276 (64%), Positives = 208/276 (75%), Gaps = 21/276 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+D+VLFNRQPSLHKLSIMAHRAK+L HRTFRFNECVC PYNADFDGDEMN+HLPQTEEA
Sbjct: 431 DDDIVLFNRQPSLHKLSIMAHRAKILNHRTFRFNECVCNPYNADFDGDEMNLHLPQTEEA 490

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL              VLM NKSNLVTPRNGELLIAATQDFIT  YLLT+KN F   
Sbjct: 491 RAEAL--------------VLMGNKSNLVTPRNGELLIAATQDFITSSYLLTRKNTFLTE 536

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           AQ + +A+ L+ D  ++  +       +  P   ++    WTGKQIF LI++PN +CPV 
Sbjct: 537 AQAVLLANCLMNDADNLVSV-------TLPPPAIIKPIKAWTGKQIFGLIMRPNEECPVK 589

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           ANL+TKG+AYT  EE C  DSYV++RNSELLAGSMDK TLGSG K ++FYILL D+GEDV
Sbjct: 590 ANLRTKGKAYTNGEEMCIEDSYVLIRNSELLAGSMDKVTLGSGTKQSIFYILLCDWGEDV 649

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           A  AMWRL+R+ S Y+ N GFSIGI DVTPG G +Q
Sbjct: 650 ATLAMWRLARLASCYITNAGFSIGISDVTPGHGLLQ 685



 Score =  363 bits (932), Expect = 4e-97,   Method: Compositional matrix adjust.
 Identities = 218/483 (45%), Positives = 279/483 (57%), Gaps = 82/483 (16%)

Query: 1001 PVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEF 1060
            P++ +R+L+ + AK+  + +  L   +I   + +     E      E    D+  FLE  
Sbjct: 862  PLDYQRVLEHVKAKSPHKEEIPLDGADITDTAFQWFADSERFSSVEEELKDDLLVFLEWV 921

Query: 1061 SKK-----ESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQI 1115
              +     +++  H     QP R  I   ++ I                 C EKY+RA+I
Sbjct: 922  GDRITHYRQNILCHSPVALQPGRFTISQLEEFI---------------HTCNEKYMRARI 966

Query: 1116 EPATAVGALAAQSIGEPGTQMTLK------------------------------------ 1139
            EP TAVGALAAQSIGEPGTQMTLK                                    
Sbjct: 967  EPGTAVGALAAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIINASLKISTPVITA 1026

Query: 1140 ------TFHFA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDID 1181
                  +F  A             +V EYIEEV + DD F+LIKLD D I+ L LEVD++
Sbjct: 1027 PLMNDTSFEIAMRVKGRIEKTTLKDVVEYIEEVCLFDDHFLLIKLDTDLIKSLKLEVDVN 1086

Query: 1182 SIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGIN 1239
            SI Y  C  +    + ++   G S + ++P  S +  N+++ Q+K+ LP+V+IKG+  + 
Sbjct: 1087 SICYSICTSKLHLTAKNVLAKGDSIITIQP--SKQKSNNELTQLKENLPNVIIKGLPSVA 1144

Query: 1240 RAVI-HEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTI 1298
            R VI   ED +G  KYKL VEGDNLR+VMAT G+   K +SNNT EVYK LGIEAAR+TI
Sbjct: 1145 RVVIDSHEDTDGKMKYKLFVEGDNLREVMATTGILSKKTTSNNTMEVYKALGIEAARTTI 1204

Query: 1299 MTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDH 1358
            MTEI+ VMENH +SID RH MLVADLMTS+GEVLGITR GLAKMKESVLNLASFE T+DH
Sbjct: 1205 MTEIESVMENHAISIDHRHLMLVADLMTSRGEVLGITRQGLAKMKESVLNLASFEKTADH 1264

Query: 1359 LFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP---RSEPVPRTLLFDNPEFH 1415
            LFDAA+YGQ+D I GVSE IIMG+P+ VGTGL  LL   P   + EP  RT LFD+P+FH
Sbjct: 1265 LFDAAYYGQSDTICGVSESIIMGIPIPVGTGLFTLLHKYPFPDKDEPQKRTPLFDDPQFH 1324

Query: 1416 TNT 1418
              T
Sbjct: 1325 KKT 1327



 Score =  292 bits (748), Expect = 8e-76,   Method: Compositional matrix adjust.
 Identities = 159/313 (50%), Positives = 202/313 (64%), Gaps = 21/313 (6%)

Query: 95  QQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLP 154
           QQ+HI +V+KNLY QD   TP+P+G LD RMGT      C TC   L+DC GHFGYIDL 
Sbjct: 3   QQAHIHVVAKNLYNQDSNHTPVPYGALDDRMGTCSNTKKCGTCEGKLNDCAGHFGYIDLE 62

Query: 155 LPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKIL 214
           LPVFH+GYFR +I+ILQ+ICK   CA V+L  E    +  K+ NP L YL RK+L+K+IL
Sbjct: 63  LPVFHVGYFRAIISILQTICKK--CAHVMLSPEDKNYYLLKVLNPNLGYLARKALRKQIL 120

Query: 215 ETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEI 274
           E  KK ++C +C EING VKK G+LKI HEKYKN+ K+++ I E LL++Y   V+ N EI
Sbjct: 121 EKAKKTTICQNCKEINGTVKKAGMLKIVHEKYKNKKKQENIIEEKLLSDYRYVVEHNKEI 180

Query: 275 EA-HKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPS 333
           ++  +  GL+ TLNP+ VL+LFE IP+ DIPLLLMN E + P DLILTR+ VPP CIRPS
Sbjct: 181 KSILQSSGLVFTLNPILVLELFERIPVCDIPLLLMNREHTLPQDLILTRIPVPPICIRPS 240

Query: 334 VISDLKSDNDVVLFNRQPSLHKLS--------IMAHR---AKV-LPHRTFRFNECVCTPY 381
           V SDLKS       N  P   KLS        I  H     KV + H  + F +  C  Y
Sbjct: 241 VASDLKSGT-----NEDPLTMKLSEIIFINNVIQKHMQSGVKVQMYHEDWEFLQLHCALY 295

Query: 382 -NADFDGDEMNVH 393
            N++  G  +N+ 
Sbjct: 296 INSEMSGIPLNMQ 308



 Score =  254 bits (648), Expect = 3e-64,   Method: Compositional matrix adjust.
 Identities = 138/237 (58%), Positives = 173/237 (72%), Gaps = 5/237 (2%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS  ISTP+ITA L  DT  + A  VKGR+E+TTL +V EYIEEV + DD
Sbjct: 1005 GVPRIKEIINASLKISTPVITAPLMNDTSFEIAMRVKGRIEKTTLKDVVEYIEEVCLFDD 1064

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             F+LIKLD D I+ L LEVD++SI Y  C  +    + ++   G S + ++P  S +  N
Sbjct: 1065 HFLLIKLDTDLIKSLKLEVDVNSICYSICTSKLHLTAKNVLAKGDSIITIQP--SKQKSN 1122

Query: 882  SKMYQMKQLLPSVVIKGVQGINRAVI-HEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
            +++ Q+K+ LP+V+IKG+  + R VI   ED +G  KYKL VEGDNLR+VMAT G+   K
Sbjct: 1123 NELTQLKENLPNVIIKGLPSVARVVIDSHEDTDGKMKYKLFVEGDNLREVMATTGILSKK 1182

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNT EVYK LGIEAAR+TIMTEI+ VMENH +SID RH MLVADLMTS+GEVLG
Sbjct: 1183 TTSNNTMEVYKALGIEAARTTIMTEIESVMENHAISIDHRHLMLVADLMTSRGEVLG 1239



 Score = 78.2 bits (191), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 37/62 (59%), Positives = 44/62 (70%), Gaps = 3/62 (4%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP---RSEPVPRTLLFDNPE 724
            D  FDAA+YGQ+D I GVSE IIMG+P+ VGTGL  LL   P   + EP  RT LFD+P+
Sbjct: 1263 DHLFDAAYYGQSDTICGVSESIIMGIPIPVGTGLFTLLHKYPFPDKDEPQKRTPLFDDPQ 1322

Query: 725  FH 726
            FH
Sbjct: 1323 FH 1324



 Score = 77.8 bits (190), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 37/52 (71%), Positives = 42/52 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLI 72
           VLM NKSNLVTPRNGELLIAATQDFIT  YLLT+KN F   AQ + +A+ L+
Sbjct: 496 VLMGNKSNLVTPRNGELLIAATQDFITSSYLLTRKNTFLTEAQAVLLANCLM 547


>gi|443729218|gb|ELU15202.1| hypothetical protein CAPTEDRAFT_219447 [Capitella teleta]
          Length = 1381

 Score =  374 bits (960), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 224/480 (46%), Positives = 288/480 (60%), Gaps = 71/480 (14%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   PV+ KR+++     +  + D +L+  ++  +    LD +EF +D S +F  ++ +F
Sbjct: 907  GKDKPVDFKRIMEHTQCLHPCQKDRNLNGDQLEKIVKAALDLEEF-RDCSGDFRDELLEF 965

Query: 1057 LEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIE 1116
            + EF  +   T ++ K+ Q    ++L HQ K     +   F        CR K++RA+IE
Sbjct: 966  VAEFRLQLDTTHNKYKMEQADSPEVL-HQLKRVTATQVKEF-----LVCCRNKFMRAKIE 1019

Query: 1117 PATAVGALAAQSIGEPGTQMTLKTFH---------------------------------- 1142
            P TAVGA+AAQSIGEPGTQMTLKTFH                                  
Sbjct: 1020 PGTAVGAVAAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIINASKNISTPIITAH 1079

Query: 1143 --------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDS 1182
                    FA            GEV EYIEEVF+PDD F+LIKLD+DRIRLL LEV  DS
Sbjct: 1080 LENDLDPEFARVVKGRIEKTLLGEVSEYIEEVFLPDDCFLLIKLDLDRIRLLKLEVTSDS 1139

Query: 1183 IRYCIERTRGISGHLTVSGHS--FLILKPKDSSKSFNSKMY----QMKQLLPSVVIKGVQ 1236
            I+  I   +     + V  HS   L + P +S+KS    MY    Q+KQ LP V+IKG+ 
Sbjct: 1140 IKESILTAKLKLKPMNVRVHSNAILCVAPTESAKS---SMYYVLQQLKQDLPKVIIKGIT 1196

Query: 1237 GINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARS 1296
             + RAVIH ++ +G + YKLLVEG+NL+ V+AT GVK     SNNTYE  KTLGIEAARS
Sbjct: 1197 SVQRAVIHVDEAKGDSCYKLLVEGNNLQSVIATPGVKANDTKSNNTYEAEKTLGIEAARS 1256

Query: 1297 TIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTS 1356
            TI+ E+   M NHGM+ID RH ML+ADLMT +GEVLGITR GLAKMKESVL LASFE T+
Sbjct: 1257 TIINEVVYTMVNHGMNIDIRHIMLLADLMTCRGEVLGITRFGLAKMKESVLMLASFEKTA 1316

Query: 1357 DHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 1415
            DHL++A+++GQ D I GVSECIIMG+PM++GTGL KLL    +   P  R LLFD  EFH
Sbjct: 1317 DHLYEASYHGQKDAICGVSECIIMGIPMSIGTGLFKLLHKAEKDVSPSRRPLLFDKNEFH 1376



 Score =  340 bits (873), Expect = 3e-90,   Method: Compositional matrix adjust.
 Identities = 162/276 (58%), Positives = 203/276 (73%), Gaps = 21/276 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI A  AKV+PHRTFRFNEC C P+NADFDGDEMN+HLPQTEEA
Sbjct: 450 DRDIVLFNRQPSLHKLSIQAFYAKVMPHRTFRFNECCCNPFNADFDGDEMNLHLPQTEEA 509

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEA+              VLM +KSN+VTPRNGE LIAA QDFITGGYLLTQK+ FF+R
Sbjct: 510 KAEAI--------------VLMGSKSNIVTPRNGEPLIAAIQDFITGGYLLTQKDVFFDR 555

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  ++AS +++        + R +     P    +   +W+GKQIFSLIL+P++   V 
Sbjct: 556 AKACQLASAILSQ-------MDRSTKVELPPPCIFKPLKMWSGKQIFSLILRPHQSSNVK 608

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            NL+TKG+ YT +E+ C +DS+V++ NS+LLAG MDK TLGSG K NVFY+LLRD+GE+ 
Sbjct: 609 INLRTKGKNYTKDEDLCIKDSFVVVHNSDLLAGCMDKGTLGSGSKNNVFYLLLRDYGEEA 668

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           A  ++ RL+R+   YL NRGFSIGIGDVTPG G +Q
Sbjct: 669 AAVSLSRLARLCPAYLSNRGFSIGIGDVTPGLGLLQ 704



 Score =  290 bits (741), Expect = 6e-75,   Method: Compositional matrix adjust.
 Identities = 148/277 (53%), Positives = 196/277 (70%), Gaps = 14/277 (5%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D+++Q  HIQ+VSKNLY QD  R P+ HG      GT++K+ +C TCG+NL++CVGH+GY
Sbjct: 26  DQMRQLGHIQVVSKNLYSQDGGRKPVSHG------GTSEKDNSCETCGKNLAECVGHYGY 79

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           +DL LPVFHIGYFR  + ILQ+ICK  TC+RVLL  E+   F   L+ P +SYL +K L+
Sbjct: 80  VDLELPVFHIGYFRATVVILQNICK--TCSRVLLQPEQKKQFFESLKRPNMSYLQKKGLR 137

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI E  KK S+CP+CG ING VKKCGLLKI HE+YK+  KK+DA++ DL+ E+  A+++
Sbjct: 138 KKIGEKCKKTSICPYCGSINGTVKKCGLLKIVHERYKHNKKKEDAVMSDLVIEFETAMEY 197

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N EIE     G  Q  LNPL V  LF+ I  EDIPLLLM+A+  +P +LILTR++VPP C
Sbjct: 198 NKEIEP--LLGKTQEMLNPLIVHNLFKNICEEDIPLLLMSADSCRPEELILTRIIVPPLC 255

Query: 330 IRPSVISDLKS---DNDVVLFNRQPSLHKLSIMAHRA 363
           IRPSVISDLK+   ++D+ +   +       I+ HRA
Sbjct: 256 IRPSVISDLKAGTNEDDITMKMTEILFLNDVIVKHRA 292



 Score =  271 bits (692), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 145/240 (60%), Positives = 178/240 (74%), Gaps = 9/240 (3%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+NISTPIITA+L+ D D ++AR+VKGR+E+T LGEV EYIEEVF+PDD
Sbjct: 1057 GVPRIKEIINASKNISTPIITAHLENDLDPEFARVVKGRIEKTLLGEVSEYIEEVFLPDD 1116

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHS--FLILKPKDSSKSFN 881
             F+LIKLD+DRIRLL LEV  DSI+  I   +     + V  HS   L + P +S+KS  
Sbjct: 1117 CFLLIKLDLDRIRLLKLEVTSDSIKESILTAKLKLKPMNVRVHSNAILCVAPTESAKS-- 1174

Query: 882  SKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVK 937
              MY    Q+KQ LP V+IKG+  + RAVIH ++ +G + YKLLVEG+NL+ V+AT GVK
Sbjct: 1175 -SMYYVLQQLKQDLPKVIIKGITSVQRAVIHVDEAKGDSCYKLLVEGNNLQSVIATPGVK 1233

Query: 938  GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
                 SNNTYE  KTLGIEAARSTI+ E+   M NHGM+ID RH ML+ADLMT +GEVLG
Sbjct: 1234 ANDTKSNNTYEAEKTLGIEAARSTIINEVVYTMVNHGMNIDIRHIMLLADLMTCRGEVLG 1293



 Score =  119 bits (298), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 53/60 (88%), Positives = 57/60 (95%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 823 ARGFVSNSFYSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 882



 Score = 80.5 bits (197), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 36/53 (67%), Positives = 46/53 (86%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIA 73
           VLM +KSN+VTPRNGE LIAA QDFITGGYLLTQK+ FF+RA+  ++AS +++
Sbjct: 515 VLMGSKSNIVTPRNGEPLIAAIQDFITGGYLLTQKDVFFDRAKACQLASAILS 567



 Score = 72.8 bits (177), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 33/63 (52%), Positives = 43/63 (68%), Gaps = 1/63 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
            D  ++A+++GQ D I GVSECIIMG+PM++GTGL KLL    +   P  R LLFD  EFH
Sbjct: 1317 DHLYEASYHGQKDAICGVSECIIMGIPMSIGTGLFKLLHKAEKDVSPSRRPLLFDKNEFH 1376

Query: 727  FPQ 729
              +
Sbjct: 1377 LSE 1379


>gi|395501590|ref|XP_003755175.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1 [Sarcophilus
            harrisii]
          Length = 1390

 Score =  373 bits (957), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 219/479 (45%), Positives = 290/479 (60%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A    +S+P+LS  E++  +   +   EFL    ++F+++IKKF
Sbjct: 914  GKDEPLEFKRVLDNIKAVFPCQSEPALSKNELVLTTESIMKRNEFLC-CQDSFLQEIKKF 972

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 973  IKVVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQIEKFLETCRDKYMRAQ 1026

Query: 1115 IEPATAVGAL---------------------------------------AAQSIGEPGTQ 1135
            +EP +AVGAL                                       A+++I  P   
Sbjct: 1027 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1086

Query: 1136 MTLKTFHFA---------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
              L   + A               GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1087 AQLDKDNDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1146

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C  + R   G + V G + L + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1147 ETVRYSICTSKLRVKPGDVAVHGEAVLCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPE 1206

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            + RAVIH ++  G  KYKLLVEGDNLR VMAT+GV+G K +SNNTYEV KTLGIEAARST
Sbjct: 1207 VARAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVQGTKTTSNNTYEVEKTLGIEAARST 1266

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1267 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1326

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1327 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPNPPKRPLIFDTNEFH 1385



 Score =  341 bits (875), Expect = 1e-90,   Method: Compositional matrix adjust.
 Identities = 168/280 (60%), Positives = 206/280 (73%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDVVLFNRQPSLHKLSIMAHLARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++       G  ++   R   P + ++   +WTGKQ+FSLIL+P+ + PV 
Sbjct: 562 AKACQIIASILV------GKDEKIKVRLPPPAI-LKPVTLWTGKQVFSLILQPSDENPVR 614

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DSYV ++NSEL++GSMDK TLGSG K N+FYILLRD+G+ 
Sbjct: 615 ANLRTKGKQYCGRGEDLCVNDSYVTIQNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQI 674

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 675 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 714



 Score =  291 bits (746), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 149/237 (62%), Positives = 185/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LDKD D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1066 GVPRIKEIINASKAISTPIITAQLDKDNDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 1125

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  C  + R   G + V G + L + P+++SKS  
Sbjct: 1126 CFILVKLSLERIRLLRLEVNAETVRYSICTSKLRVKPGDVAVHGEAVLCVTPRENSKSSM 1185

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  + RAVIH ++  G  KYKLLVEGDNLR VMAT+GV+G K
Sbjct: 1186 YYVLQFLKEDLPKVVVQGIPEVARAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVQGTK 1245

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNTYEV KTLGIEAARSTI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1246 TTSNNTYEVEKTLGIEAARSTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1302



 Score =  283 bits (723), Expect = 6e-73,   Method: Compositional matrix adjust.
 Identities = 142/251 (56%), Positives = 181/251 (72%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD   +P+ +G+LD RMGT++K+  C TCG+NL++C+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNHHSPLLYGVLDHRMGTSEKDRPCETCGKNLAECLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYF+ VI +LQ ICK  TC  ++L +E+   F   L+ P L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFKAVIGVLQMICK--TCCHIMLSQEERKQFLDYLKRPGLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  KK + C HCG  NG VKKCGLLKI HEKYK   K  D +V + L  +  A+++
Sbjct: 144 KKISDKCKKKNTCHHCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPVVSNFLQSFETAIEY 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP EDIPLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NKEVEP--LLGRAQENLNPLVVLNLFKRIPAEDIPLLLMNPEAGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 262 IRPSVVSDLKS 272



 Score =  116 bits (291), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 830 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 889



 Score = 82.0 bits (201), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1326 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPNPPKRPLIFDTNEFH 1385

Query: 727  FPQV 730
             P V
Sbjct: 1386 IPLV 1389



 Score = 74.3 bits (181), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 521 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 575


>gi|242015075|ref|XP_002428200.1| DNA-directed RNA polymerase III largest subunit, putative [Pediculus
            humanus corporis]
 gi|212512752|gb|EEB15462.1| DNA-directed RNA polymerase III largest subunit, putative [Pediculus
            humanus corporis]
          Length = 1364

 Score =  371 bits (952), Expect = 2e-99,   Method: Compositional matrix adjust.
 Identities = 218/454 (48%), Positives = 282/454 (62%), Gaps = 63/454 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   PV  +R LD I AK   R + +L +  +   ++E L+++EF     + F  D+K F
Sbjct: 914  GKDCPVNFQRTLDHIRAKYPYREEEALDSISVEKATDELLNTEEF-GVCDDVFKFDLKNF 972

Query: 1057 LEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKA-EACREKYVRAQI 1115
            +    +K ++T  +   +    E+ LS   K     E        +  + CR+KY+RA++
Sbjct: 973  MSGIVRKMALTRQKFGYN----ERNLSDIPKAIIQIERLTVSQIVEFFQICRKKYLRAKV 1028

Query: 1116 EPATAVGALAAQSIGEPGTQMTLKTFH--------------------------------- 1142
            E  TAVGALAAQSIGEPGTQMTLKTFH                                 
Sbjct: 1029 EAGTAVGALAAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIINASKKISTPIITA 1088

Query: 1143 ---------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDID 1181
                     FA            GE+ EYIEEVF+PDD FI++KLD+DRI+LL LEVD +
Sbjct: 1089 YLENDSDAEFARRVKGRIEKTTLGEISEYIEEVFLPDDFFIIVKLDVDRIKLLKLEVDAN 1148

Query: 1182 SIRYCIERTRGISGHLTVSGHSFLILKP--KDSSKSFNSKMYQMKQLLPSVVIKGVQGIN 1239
            SI+Y +   R +  ++ V   + L + P    ++   N  +  +K+ LP++VIKG+  +N
Sbjct: 1149 SIKYTLCTAR-LKVNVEVVSDTILKVTPIKTKNADRINYVLQSLKKSLPNIVIKGLSAVN 1207

Query: 1240 RAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIM 1299
            RAVIH +D +G TKYKL VEG NL +VMAT GV G K +SNN +EV+  LGIEAAR TI+
Sbjct: 1208 RAVIHHDDSKGGTKYKLFVEGYNLGEVMATNGVLGTKTTSNNIFEVFTYLGIEAARQTII 1267

Query: 1300 TEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHL 1359
            +EIK+VMENHGMSID RH ML+ADLMTS+GEVLGITRHGL KMKESVLNLASFE T+DHL
Sbjct: 1268 SEIKMVMENHGMSIDRRHIMLLADLMTSRGEVLGITRHGLVKMKESVLNLASFERTADHL 1327

Query: 1360 FDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            FDAA+YGQTD I+GVSE IIMGLP++VGTGL KL
Sbjct: 1328 FDAAYYGQTDAITGVSESIIMGLPVSVGTGLFKL 1361



 Score =  365 bits (937), Expect = 1e-97,   Method: Compositional matrix adjust.
 Identities = 174/276 (63%), Positives = 208/276 (75%), Gaps = 21/276 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+D+VLFNRQPSLHKLSIMAHRAKVL HRTFRFNECVCTPYNADFDGDEMN+HLPQT EA
Sbjct: 457 DDDIVLFNRQPSLHKLSIMAHRAKVLKHRTFRFNECVCTPYNADFDGDEMNLHLPQTLEA 516

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM+NK+NL TPRNGELLIAATQDFITG YLLTQKN FF +
Sbjct: 517 KAEAL--------------VLMSNKANLATPRNGELLIAATQDFITGAYLLTQKNTFFTQ 562

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+   + + ++A       I          P   ++   +WT KQIFS+ILKPN+ C + 
Sbjct: 563 AKANWLLACILAGKDANLHI-------DLPPPAIIKPMRLWTAKQIFSVILKPNKKCKIV 615

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            NL+TKG+AYT+ EE C  DS+V++RNS LLAG+MDK TLGSG K N+ YILLRD+GED 
Sbjct: 616 CNLRTKGKAYTSREEMCVNDSFVLIRNSVLLAGTMDKGTLGSGSKDNILYILLRDWGEDA 675

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           A T MWRL+R+ S++LMNRGFSIG+GDVTPG G ++
Sbjct: 676 AATVMWRLARIASWFLMNRGFSIGLGDVTPGVGLLR 711



 Score =  294 bits (753), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 136/248 (54%), Positives = 182/248 (73%), Gaps = 2/248 (0%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           +QQQ+HI +V KNLY QD  RTP+ +G+LDR+MGTN K+A CTTC + L+DC+GHFGYI+
Sbjct: 28  IQQQAHIHVVGKNLYNQDAPRTPVAYGVLDRQMGTNTKDATCTTCNKGLADCIGHFGYIN 87

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKK 212
           L LPVFHIGYFR VI ILQ+ICK  TC++VLL E+    +R +L+NP   YL RK+L+K+
Sbjct: 88  LELPVFHIGYFRSVIMILQTICK--TCSKVLLPEDLKKTYRLRLQNPKFLYLARKALRKQ 145

Query: 213 ILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNP 272
           I E  KK+S+CP+C  +NGVVKKCGLLK+ HEK++      DA++   +  YN  ++++ 
Sbjct: 146 IHEKAKKISICPYCQSLNGVVKKCGLLKLVHEKFRGSKSTTDALMAKHIQAYNNVLEYDR 205

Query: 273 EIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRP 332
           E+E+    G+   L PL+VL L E IP +D+ LL MN  +  P DL+LTRL VPP C+RP
Sbjct: 206 ELESVIASGVAFILTPLDVLNLLERIPEDDVCLLCMNPAMVHPRDLMLTRLPVPPLCVRP 265

Query: 333 SVISDLKS 340
           SVIS+LKS
Sbjct: 266 SVISELKS 273



 Score =  282 bits (721), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 143/236 (60%), Positives = 184/236 (77%), Gaps = 3/236 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITAYL+ D+D ++AR VKGR+E+TTLGE+ EYIEEVF+PDD
Sbjct: 1067 GVPRIKEIINASKKISTPIITAYLENDSDAEFARRVKGRIEKTTLGEISEYIEEVFLPDD 1126

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKP--KDSSKSFN 881
             FI++KLD+DRI+LL LEVD +SI+Y +   R +  ++ V   + L + P    ++   N
Sbjct: 1127 FFIIVKLDVDRIKLLKLEVDANSIKYTLCTAR-LKVNVEVVSDTILKVTPIKTKNADRIN 1185

Query: 882  SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
              +  +K+ LP++VIKG+  +NRAVIH +D +G TKYKL VEG NL +VMAT GV G K 
Sbjct: 1186 YVLQSLKKSLPNIVIKGLSAVNRAVIHHDDSKGGTKYKLFVEGYNLGEVMATNGVLGTKT 1245

Query: 942  SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +SNN +EV+  LGIEAAR TI++EIK+VMENHGMSID RH ML+ADLMTS+GEVLG
Sbjct: 1246 TSNNIFEVFTYLGIEAARQTIISEIKMVMENHGMSIDRRHIMLLADLMTSRGEVLG 1301



 Score =  120 bits (302), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 53/63 (84%), Positives = 59/63 (93%)

Query: 608 VTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           +   +GFV+NSF+S LTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVK+LEDLCVQY
Sbjct: 827 IPAAKGFVENSFYSSLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKALEDLCVQY 886

Query: 668 DMS 670
           DM+
Sbjct: 887 DMT 889



 Score = 82.0 bits (201), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 37/55 (67%), Positives = 46/55 (83%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM+NK+NL TPRNGELLIAATQDFITG YLLTQKN FF +A+   + + ++AG+
Sbjct: 522 VLMSNKANLATPRNGELLIAATQDFITGAYLLTQKNTFFTQAKANWLLACILAGK 576



 Score = 62.0 bits (149), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/37 (75%), Positives = 32/37 (86%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 704
            D  FDAA+YGQTD I+GVSE IIMGLP++VGTGL KL
Sbjct: 1325 DHLFDAAYYGQTDAITGVSESIIMGLPVSVGTGLFKL 1361


>gi|241633681|ref|XP_002408700.1| DNA-directed RNA polymerase II largest subunit, putative [Ixodes
           scapularis]
 gi|215501234|gb|EEC10728.1| DNA-directed RNA polymerase II largest subunit, putative [Ixodes
           scapularis]
          Length = 1394

 Score =  371 bits (952), Expect = 2e-99,   Method: Compositional matrix adjust.
 Identities = 180/289 (62%), Positives = 218/289 (75%), Gaps = 24/289 (8%)

Query: 330 IRPS-VISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGD 388
           +RP  V+     D DVVLFNRQPSLHKLSIMAH AKVLPHRTFRFNECVCTPYNADFDGD
Sbjct: 444 LRPGDVVERHLRDGDVVLFNRQPSLHKLSIMAHLAKVLPHRTFRFNECVCTPYNADFDGD 503

Query: 389 EMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGG 448
           EMN+HLPQTEEARAEAL              VLM  ++NLVTPRNGE LIAA QDFITGG
Sbjct: 504 EMNLHLPQTEEARAEAL--------------VLMGTRANLVTPRNGEPLIAAIQDFITGG 549

Query: 449 YLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAV-IWTGKQIF 507
           YLLTQ++ FF+RA+  ++A+ ++A         K  S     P   +R  V +WTGKQIF
Sbjct: 550 YLLTQRDVFFDRAKAAQLAAYMLAG--------KDVSISVELPPPAIRKPVCLWTGKQIF 601

Query: 508 SLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKAN 567
           SLI++P+R CPV A+L+ KG++YT+ EE C  D+YV++RNSELL+G+MDK T+GSG K N
Sbjct: 602 SLIIRPSRSCPVLASLRAKGKSYTSGEEMCANDAYVLIRNSELLSGTMDKGTMGSGSKNN 661

Query: 568 VFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           +FYILLRD+G+  A  AMWRL+R+ SFY+ NRGFSIGIGDVTPG G ++
Sbjct: 662 IFYILLRDYGDQYAADAMWRLARIASFYMQNRGFSIGIGDVTPGAGLLK 710



 Score =  326 bits (835), Expect = 8e-86,   Method: Compositional matrix adjust.
 Identities = 204/485 (42%), Positives = 275/485 (56%), Gaps = 72/485 (14%)

Query: 1000 TPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEE 1059
            TPV+  R+++   A+   R +  L    IL +  E L  K + +   E+F   + KF+  
Sbjct: 917  TPVDFGRVMELTRARKPCRGEKPLDQDAILRIGEEVLGGKSY-EGCGESFREALSKFVHG 975

Query: 1060 FSKKESVTS--HQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEP 1117
            ++ K + T   H    S   R  +L   D++   +  + F +      CREKY RA +EP
Sbjct: 976  YAAKVASTRARHGLDGSGDARPLVLWQLDRLTASQLRSFFAT------CREKYFRAVMEP 1029

Query: 1118 ATAVGAL---------------------------------------AAQSIGEPGTQMTL 1138
            ATAVGA+                                       A+++I  P     L
Sbjct: 1030 ATAVGAVCAQSIGEPATQMTLKTFHFAGVASMNITQGVPRIKEIINASKNISTPIITAAL 1089

Query: 1139 KTFHFA---------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSI 1183
                 A               GEV EY+EEVF+PD+ F+LIKLD+DRIRLL LEV+ D++
Sbjct: 1090 AVNQDAEYARRVKGRIEKTTLGEVSEYLEEVFLPDECFVLIKLDLDRIRLLQLEVNADTV 1149

Query: 1184 RYCIERTR-GISGH-LTVSGHSFLILKPKDSSK-SFNSKMYQMKQLLPSVVIKGVQGINR 1240
             Y I  ++  I G  L+V G + + ++P +++K S    +  +K+ LPSVVIKG+   +R
Sbjct: 1150 CYSIATSKLRIKGQNLSVVGSAVITVRPTETAKMSLYYALQTLKEQLPSVVIKGIPSTSR 1209

Query: 1241 AVIHEEDVEG-VTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIM 1299
            AVIH +D  G  T Y        LR+VMATYGV G + SSNNT EV K LGIEAAR+TI+
Sbjct: 1210 AVIHADDTVGPTTTYPAAGGRGRLREVMATYGVLGTRTSSNNTSEVEKCLGIEAARATII 1269

Query: 1300 TEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHL 1359
             EI + ME+HG+S+D RH ML+ADLMT +GEVLGITRHGLA+MKES L LASFE T+DHL
Sbjct: 1270 REIGVTMESHGISVDRRHLMLLADLMTFRGEVLGITRHGLARMKESALMLASFERTADHL 1329

Query: 1360 FDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV---PRSEPVPRTLLFDNPEFHT 1416
            FDAA+YGQ D I+GVSE II+G+PM +GTG   ++  V   P +E  PR L+FD  EFH 
Sbjct: 1330 FDAAYYGQVDEITGVSESIILGVPMGIGTGFFDMVHRVDWRPLAE--PRRLVFDRDEFHL 1387

Query: 1417 NTLAA 1421
            N  AA
Sbjct: 1388 NVAAA 1392



 Score =  271 bits (693), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 131/259 (50%), Positives = 179/259 (69%), Gaps = 4/259 (1%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G +   D +QQ SH+  VSKNLY +D     +P+G+LD ++GT+QK+  C TCG+ L+DC
Sbjct: 21  GVLNSHD-IQQLSHVHCVSKNLYQRDSLHKAVPYGVLDNKLGTSQKDKKCETCGKGLADC 79

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
           +GH+G +DL LPVFH+GYFR   NIL  +CK  TCARVL+  ++  GF   L+ P LSYL
Sbjct: 80  IGHYGLVDLELPVFHVGYFRATQNILHCVCK--TCARVLVPPQERQGFLDALQRPTLSYL 137

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEY 264
            +K+L KKI+E  +K S C  CG  NG VKKCGLLK+ HE++K  TKK DA++ + L ++
Sbjct: 138 QKKALHKKIIERCRKQSACHFCGARNGQVKKCGLLKLVHERFKA-TKKNDAMLAEFLEDF 196

Query: 265 NEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLL 324
           +EA  +NPE+++         LNPL VL LF  I  ED+PLL+MN +  +P DLILTR+ 
Sbjct: 197 DEARGYNPELDSVMGKVTSDILNPLVVLHLFRRILDEDVPLLVMNPKCGRPEDLILTRIP 256

Query: 325 VPPNCIRPSVISDLKSDND 343
           VPP CIRPSV+S+LK+  +
Sbjct: 257 VPPLCIRPSVVSELKAGTN 275



 Score =  256 bits (654), Expect = 6e-65,   Method: Compositional matrix adjust.
 Identities = 138/238 (57%), Positives = 178/238 (74%), Gaps = 4/238 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+NISTPIITA L  + D +YAR VKGR+E+TTLGEV EY+EEVF+PD+
Sbjct: 1066 GVPRIKEIINASKNISTPIITAALAVNQDAEYARRVKGRIEKTTLGEVSEYLEEVFLPDE 1125

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTR-GISG-HLTVSGHSFLILKPKDSSK-SF 880
             F+LIKLD+DRIRLL LEV+ D++ Y I  ++  I G +L+V G + + ++P +++K S 
Sbjct: 1126 CFVLIKLDLDRIRLLQLEVNADTVCYSIATSKLRIKGQNLSVVGSAVITVRPTETAKMSL 1185

Query: 881  NSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEG-VTKYKLLVEGDNLRDVMATYGVKGV 939
               +  +K+ LPSVVIKG+   +RAVIH +D  G  T Y        LR+VMATYGV G 
Sbjct: 1186 YYALQTLKEQLPSVVIKGIPSTSRAVIHADDTVGPTTTYPAAGGRGRLREVMATYGVLGT 1245

Query: 940  KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            + SSNNT EV K LGIEAAR+TI+ EI + ME+HG+S+D RH ML+ADLMT +GEVLG
Sbjct: 1246 RTSSNNTSEVEKCLGIEAARATIIREIGVTMESHGISVDRRHLMLLADLMTFRGEVLG 1303



 Score =  118 bits (296), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 55/65 (84%), Positives = 60/65 (92%), Gaps = 1/65 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D TP  +GFV++SF+SGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 
Sbjct: 824 DRTPQARGFVEDSFYSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCS 883

Query: 666 QYDMS 670
            YDM+
Sbjct: 884 HYDMT 888



 Score = 82.0 bits (201), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 36/57 (63%), Positives = 48/57 (84%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKV 77
           VLM  ++NLVTPRNGE LIAA QDFITGGYLLTQ++ FF+RA+  ++A+ ++AG+ V
Sbjct: 521 VLMGTRANLVTPRNGEPLIAAIQDFITGGYLLTQRDVFFDRAKAAQLAAYMLAGKDV 577



 Score = 67.0 bits (162), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 33/63 (52%), Positives = 42/63 (66%), Gaps = 5/63 (7%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV---PRSEPVPRTLLFDNPE 724
            D  FDAA+YGQ D I+GVSE II+G+PM +GTG   ++  V   P +E  PR L+FD  E
Sbjct: 1327 DHLFDAAYYGQVDEITGVSESIILGVPMGIGTGFFDMVHRVDWRPLAE--PRRLVFDRDE 1384

Query: 725  FHF 727
            FH 
Sbjct: 1385 FHL 1387


>gi|426255838|ref|XP_004021555.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1 [Ovis aries]
          Length = 1390

 Score =  370 bits (951), Expect = 2e-99,   Method: Compositional matrix adjust.
 Identities = 218/482 (45%), Positives = 291/482 (60%), Gaps = 73/482 (15%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A    RS+P+LS  E+L  +   +   EFL    ++F+++IKKF
Sbjct: 914  GKDEPLEFKRVLDNIKAVFPCRSEPALSKNELLLSAESIMKKNEFLC-CQDSFLQEIKKF 972

Query: 1057 LEEFSKKESVTS-----HQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYV 1111
            ++E S+K   T      + +  ++P   ++L   D+I       P       E CR+KY+
Sbjct: 973  IKEVSEKIKKTRDKYGINDNGTTEP---RVLYQLDRI------TPTQIEKFLETCRDKYM 1023

Query: 1112 RAQIEP--------ATAVGALAAQ----------------SIGEPGTQMTLKTFH----- 1142
            RAQ+EP        A ++G    Q                ++G P  +  +         
Sbjct: 1024 RAQMEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTP 1083

Query: 1143 -------------------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLE 1177
                                       GE+ EYIEEVF+PDD FIL+KL ++RIRLL LE
Sbjct: 1084 IITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLE 1143

Query: 1178 VDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKG 1234
            V+ +++RY  C+ R R   G + V G + L + P+++SKS    + Q +K+ LP VV++G
Sbjct: 1144 VNAETVRYSICMSRLRVKPGDVAVHGEAVLCVTPRENSKSSMYYVLQFLKEDLPKVVVQG 1203

Query: 1235 VQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAA 1294
            +  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIEAA
Sbjct: 1204 IPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAA 1263

Query: 1295 RSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFEN 1354
            R+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE 
Sbjct: 1264 RTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEK 1323

Query: 1355 TSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP-RTLLFDNPE 1413
            T+DHLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R    P R L+FD  E
Sbjct: 1324 TADHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKAHRDPSPPRRPLIFDTNE 1383

Query: 1414 FH 1415
            FH
Sbjct: 1384 FH 1385



 Score =  344 bits (882), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 169/277 (61%), Positives = 206/277 (74%), Gaps = 22/277 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDVVLFNRQPSLHKLSIMAHLARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++       G  ++   R   P + ++   +WTGKQIFS+IL+P+ D PV 
Sbjct: 562 AKACQIIASILV------GKDEKIKVRLPPPTI-LKPVTLWTGKQIFSVILRPSDDNPVR 614

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DSYV ++NSEL++GSMDK TLGSG K N+FYILLRD+G++
Sbjct: 615 ANLRTKGKQYCGRGEDLCVNDSYVTIQNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQN 674

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++
Sbjct: 675 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLK 711



 Score =  296 bits (757), Expect = 8e-77,   Method: Compositional matrix adjust.
 Identities = 145/251 (57%), Positives = 178/251 (70%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD    P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNNHAPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYFR VI ILQ ICK  TC  ++L +E+   F   L+ P L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFRAVIGILQMICK--TCCHIMLSQEEKKQFLDYLKRPGLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K + C HCG  NG VKKCGLLKI HEKYK   K  D IV   L  +  A++ 
Sbjct: 144 KKISDKCRKKNTCHHCGAFNGTVKKCGLLKIIHEKYKTNKKVMDPIVSSFLQSFETAIEH 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP EDIPLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NKEVEP--LLGKAQENLNPLVVLNLFKRIPAEDIPLLLMNPEAGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 262 IRPSVVSDLKS 272



 Score =  293 bits (751), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 149/237 (62%), Positives = 187/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LDKD D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1066 GVPRIKEIINASKAISTPIITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 1125

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  C+ R R   G + V G + L + P+++SKS  
Sbjct: 1126 CFILVKLSLERIRLLRLEVNAETVRYSICMSRLRVKPGDVAVHGEAVLCVTPRENSKSSM 1185

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG +
Sbjct: 1186 YYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTR 1245

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1246 TTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1302



 Score =  116 bits (291), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 830 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 889



 Score = 81.6 bits (200), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP-RTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R    P R L+FD  EFH
Sbjct: 1326 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKAHRDPSPPRRPLIFDTNEFH 1385

Query: 727  FPQV 730
             P V
Sbjct: 1386 IPLV 1389



 Score = 74.7 bits (182), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 521 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 575


>gi|357609436|gb|EHJ66444.1| hypothetical protein KGM_02886 [Danaus plexippus]
          Length = 1072

 Score =  369 bits (948), Expect = 5e-99,   Method: Compositional matrix adjust.
 Identities = 175/276 (63%), Positives = 209/276 (75%), Gaps = 21/276 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIM HRA+V P RTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 144 DGDVVLFNRQPSLHKLSIMCHRARVQPQRTFRFNECVCTPYNADFDGDEMNMHLPQTEEA 203

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL              +LM NKSNLVTPRNGELLIAATQDFITGGYL+TQ+++FF  
Sbjct: 204 RAEAL--------------ILMGNKSNLVTPRNGELLIAATQDFITGGYLITQRDSFFTL 249

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +  ++ + L+A       +          P   ++  ++WTGKQIFSLI+KPN+ C V 
Sbjct: 250 PEARQLVACLLAGPDSTMRV-------DMPPPAILKPRMLWTGKQIFSLIMKPNKRCEVK 302

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           ANL+TKG+ YT N++ C +DSYVI+RNSEL+ GSMDKSTLGSG K +VFYILLRD+GE+ 
Sbjct: 303 ANLETKGKNYTGNQDMCVQDSYVIIRNSELICGSMDKSTLGSGTKNSVFYILLRDWGEEY 362

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           AV  MWRL+RM S+Y+MNRGFS GI DVTPG   ++
Sbjct: 363 AVRGMWRLARMASYYMMNRGFSFGIIDVTPGNKLIE 398



 Score =  324 bits (831), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 198/490 (40%), Positives = 273/490 (55%), Gaps = 94/490 (19%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   PV+L R+L  + A   ++ +  L  + I+  + ETL   +F +     F  ++ +F
Sbjct: 601  GRDRPVDLTRVLRHVRASCRTQDEEPLDGEGIVVAAEETLALDDF-KTCPPEFKAELLEF 659

Query: 1057 LEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAE------------ 1104
            L+  + K           + LRE            R ++  P A + E            
Sbjct: 660  LKGTAAK----------VRSLRE------------RYASAGPVALQLERLTLTQLVRFIR 697

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFH---------------------- 1142
             C EKY R+ IEP TAVGALAAQSIGEPGTQMTLKTFH                      
Sbjct: 698  VCHEKYQRSIIEPGTAVGALAAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRVKEIINA 757

Query: 1143 --------------------FA------------GEVCEYIEEVFVPDDSFILIKLDMDR 1170
                                FA            GE+  YI+EV++P + F+L++LD +R
Sbjct: 758  SKNISTPIITAELMEPTDQEFARRVKGRVEKTTLGEITTYIDEVYLPHECFLLVRLDAER 817

Query: 1171 IRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKS--FNSKMYQMKQL 1226
            IRLL LEVD+ SI Y  C  + +   G++       + +  + S      N  + Q+ + 
Sbjct: 818  IRLLCLEVDVHSIVYSICTSKLKLKPGNVQAVSEWAIKVHAEASKHGGWLNVALQQLARQ 877

Query: 1227 LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVY 1286
            LPSVV+KG+  ++RAVI  +D   V +YKL VEGD LR+VMATYG+ G + +SNN  EV+
Sbjct: 878  LPSVVVKGLSKVSRAVIACDDTGPVNRYKLCVEGDGLREVMATYGIDGRRTTSNNILEVF 937

Query: 1287 KTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESV 1346
             TLGIEAA  TIM+E++ VM  HGM++D RH  L+A  M ++GEVLGITR+GLA+MKESV
Sbjct: 938  HTLGIEAAAGTIMSEVEAVMAGHGMAVDGRHVALLAAQMCARGEVLGITRYGLARMKESV 997

Query: 1347 LNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPR- 1405
            LNLASFE T+DHLFDAA+YGQ D I GVSECII+G+P  +GTG+++LL     +    + 
Sbjct: 998  LNLASFEKTADHLFDAAYYGQRDRIEGVSECIILGVPAGIGTGVLQLLHKHDHTTSQQQH 1057

Query: 1406 TLLFDNPEFH 1415
             LLFD+P++H
Sbjct: 1058 KLLFDDPKYH 1067



 Score =  237 bits (604), Expect = 4e-59,   Method: Compositional matrix adjust.
 Identities = 122/238 (51%), Positives = 168/238 (70%), Gaps = 4/238 (1%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
           GVPR+KEIINAS+NISTPIITA L + TD ++AR VKGR+E+TTLGE+  YI+EV++P +
Sbjct: 747 GVPRVKEIINASKNISTPIITAELMEPTDQEFARRVKGRVEKTTLGEITTYIDEVYLPHE 806

Query: 824 SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKS-- 879
            F+L++LD +RIRLL LEVD+ SI Y  C  + +   G++       + +  + S     
Sbjct: 807 CFLLVRLDAERIRLLCLEVDVHSIVYSICTSKLKLKPGNVQAVSEWAIKVHAEASKHGGW 866

Query: 880 FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
            N  + Q+ + LPSVV+KG+  ++RAVI  +D   V +YKL VEGD LR+VMATYG+ G 
Sbjct: 867 LNVALQQLARQLPSVVVKGLSKVSRAVIACDDTGPVNRYKLCVEGDGLREVMATYGIDGR 926

Query: 940 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
           + +SNN  EV+ TLGIEAA  TIM+E++ VM  HGM++D RH  L+A  M ++GEVLG
Sbjct: 927 RTTSNNILEVFHTLGIEAAAGTIMSEVEAVMAGHGMAVDGRHVALLAAQMCARGEVLG 984



 Score =  115 bits (287), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 52/67 (77%), Positives = 59/67 (88%)

Query: 608 VTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           +   +GFV+NSF+SGLTPTEFFFHTMGGREGLVDTAVKTAETGY+QRRLVKSLEDL + Y
Sbjct: 514 IPAARGFVENSFYSGLTPTEFFFHTMGGREGLVDTAVKTAETGYLQRRLVKSLEDLVLHY 573

Query: 668 DMSFDAA 674
           DM+   A
Sbjct: 574 DMTVRNA 580



 Score = 82.0 bits (201), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 36/54 (66%), Positives = 46/54 (85%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           +LM NKSNLVTPRNGELLIAATQDFITGGYL+TQ+++FF   +  ++ + L+AG
Sbjct: 209 ILMGNKSNLVTPRNGELLIAATQDFITGGYLITQRDSFFTLPEARQLVACLLAG 262



 Score = 65.5 bits (158), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 30/60 (50%), Positives = 42/60 (70%), Gaps = 1/60 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPR-TLLFDNPEFH 726
            D  FDAA+YGQ D I GVSECII+G+P  +GTG+++LL     +    +  LLFD+P++H
Sbjct: 1008 DHLFDAAYYGQRDRIEGVSECIILGVPAGIGTGVLQLLHKHDHTTSQQQHKLLFDDPKYH 1067


>gi|139948582|ref|NP_001077219.1| DNA-directed RNA polymerase III subunit RPC1 [Bos taurus]
 gi|187611407|sp|A4IF62.1|RPC1_BOVIN RecName: Full=DNA-directed RNA polymerase III subunit RPC1; Short=RNA
            polymerase III subunit C1; AltName: Full=DNA-directed RNA
            polymerase III subunit A
 gi|134024541|gb|AAI34423.1| POLR3A protein [Bos taurus]
 gi|296472154|tpg|DAA14269.1| TPA: polymerase (RNA) III (DNA directed) polypeptide A, 155kDa [Bos
            taurus]
          Length = 1390

 Score =  369 bits (946), Expect = 1e-98,   Method: Compositional matrix adjust.
 Identities = 215/479 (44%), Positives = 289/479 (60%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A    RS+P+LS  E+L  +   +   EFL    ++F+++IKKF
Sbjct: 914  GKDEPLEFKRVLDNIKAVFPCRSEPALSKNELLLSAESIMKKNEFLC-CQDSFLQEIKKF 972

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++E S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 973  IKEVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQIEKFLETCRDKYMRAQ 1026

Query: 1115 IEP--------ATAVGALAAQ----------------SIGEPGTQMTLKTFH-------- 1142
            +EP        A ++G    Q                ++G P  +  +            
Sbjct: 1027 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1086

Query: 1143 ----------------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                                    GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1087 AQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1146

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C+ + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1147 ETVRYSICMSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPE 1206

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+T
Sbjct: 1207 VSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAARTT 1266

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1267 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1326

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP-RTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R    P R L+FD  EFH
Sbjct: 1327 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKANRDPSPPRRPLIFDTNEFH 1385



 Score =  345 bits (885), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 169/280 (60%), Positives = 207/280 (73%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDVVLFNRQPSLHKLSIMAHLARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++       G  ++   R   P + ++   +WTGKQIFS+IL+P+ D PV 
Sbjct: 562 AKACQIIASILV------GKDEKIKVRLPPPTI-LKPVTLWTGKQIFSVILRPSDDNPVR 614

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DSYV ++NSEL++GSMDK TLGSG K N+FYILLRD+G++
Sbjct: 615 ANLRTKGKQYCGRGEDLCVNDSYVTIQNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQN 674

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 675 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 714



 Score =  296 bits (758), Expect = 6e-77,   Method: Compositional matrix adjust.
 Identities = 145/251 (57%), Positives = 179/251 (71%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD   +P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNNHSPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYFR VI ILQ ICK  TC  ++L +E+   F   L+ P L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFRAVIGILQMICK--TCCHIMLSQEEKKQFLDYLKRPGLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K + C HCG  NG VKKCGLLKI HEKYK   K  D IV   L  +  A++ 
Sbjct: 144 KKISDKCRKKNTCHHCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPIVSSFLQSFETAIEH 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP EDIPLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NKEVEPL--LGKAQENLNPLVVLNLFKRIPAEDIPLLLMNPEAGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 262 IRPSVVSDLKS 272



 Score =  291 bits (745), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 147/237 (62%), Positives = 187/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LDKD D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1066 GVPRIKEIINASKAISTPIITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 1125

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  C+ + R   G + V G + + + P+++SKS  
Sbjct: 1126 CFILVKLSLERIRLLRLEVNAETVRYSICMSKLRVKPGDVAVHGEAVVCVTPRENSKSSM 1185

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG +
Sbjct: 1186 YYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTR 1245

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1246 TTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1302



 Score =  116 bits (291), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 830 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 889



 Score = 81.6 bits (200), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP-RTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R    P R L+FD  EFH
Sbjct: 1326 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKANRDPSPPRRPLIFDTNEFH 1385

Query: 727  FPQV 730
             P V
Sbjct: 1386 IPLV 1389



 Score = 74.7 bits (182), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 521 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 575


>gi|397483770|ref|XP_003813067.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1 [Pan
           paniscus]
          Length = 1267

 Score =  366 bits (940), Expect = 4e-98,   Method: Compositional matrix adjust.
 Identities = 186/338 (55%), Positives = 235/338 (69%), Gaps = 27/338 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDVVLFNRQPSLHKLSIMAHLARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++       G  ++   R   P + ++   +WTGKQIFS+IL+P+ D PV 
Sbjct: 562 AKACQIIASILV------GKDEKIKVRLPPPTI-LKPVTLWTGKQIFSVILRPSDDNPVR 614

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DSYV ++NSEL++GSMDK TLGSG K N+FYILLRD+G++
Sbjct: 615 ANLRTKGKQYCGKGEDLCANDSYVTIQNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQN 674

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF---FSGLTPTEFFFHTMGGR 636
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +    +G    + +   +   
Sbjct: 675 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKYELLNAGYKKCDEYIEALNTG 734

Query: 637 EGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAA 674
           +          ET  ++RRLVKSLEDLC QYD++  ++
Sbjct: 735 KLQQQPGCTAEET--LERRLVKSLEDLCSQYDLTVRSS 770



 Score =  362 bits (928), Expect = 1e-96,   Method: Compositional matrix adjust.
 Identities = 212/479 (44%), Positives = 286/479 (59%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A     S+P+LS  E++  +   +   EFL    ++F+++IKKF
Sbjct: 791  GKDEPLEFKRVLDNIKAVFPCPSEPALSKNELILTTESIMKKSEFLC-CQDSFLQEIKKF 849

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 850  IKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQVEKFLETCRDKYMRAQ 903

Query: 1115 IEP--------ATAVGALAAQ----------------SIGEPGTQMTLKTFH-------- 1142
            +EP        A ++G    Q                ++G P  +  +            
Sbjct: 904  MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 963

Query: 1143 ----------------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                                    GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 964  AQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1023

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C  + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1024 ETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPE 1083

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+T
Sbjct: 1084 VSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAARTT 1143

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1144 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1203

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1204 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPNPPKRPLIFDTNEFH 1262



 Score =  298 bits (764), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 145/251 (57%), Positives = 181/251 (72%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD Q  P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNQHAPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYFR VI ILQ ICK  TC  ++L +E+   F   L+ P L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFRAVIGILQMICK--TCCHIMLSQEEKKQFLDYLKRPGLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K ++C HCG  NG VKKCGLLKI HEKYK   K  D IV + L  +  A++ 
Sbjct: 144 KKISDKCRKKNICHHCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPIVSNFLQSFETAIEH 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP ED+PLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NKEVEPL--LGRAQENLNPLVVLNLFKRIPAEDVPLLLMNPEAGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 262 IRPSVVSDLKS 272



 Score =  290 bits (741), Expect = 5e-75,   Method: Compositional matrix adjust.
 Identities = 147/237 (62%), Positives = 186/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LDKD D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 943  GVPRIKEIINASKAISTPIITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 1002

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  C  + R   G + V G + + + P+++SKS  
Sbjct: 1003 CFILVKLSLERIRLLRLEVNAETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSM 1062

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG +
Sbjct: 1063 YYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTR 1122

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1123 TTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1179



 Score = 82.0 bits (201), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1203 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPNPPKRPLIFDTNEFH 1262

Query: 727  FPQV 730
             P V
Sbjct: 1263 IPLV 1266



 Score = 74.7 bits (182), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 521 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 575


>gi|321475339|gb|EFX86302.1| hypothetical protein DAPPUDRAFT_45101 [Daphnia pulex]
          Length = 1389

 Score =  366 bits (939), Expect = 6e-98,   Method: Compositional matrix adjust.
 Identities = 175/290 (60%), Positives = 218/290 (75%), Gaps = 22/290 (7%)

Query: 328 NCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDG 387
           N  R  +I     D D+VLFNRQPSLHKLSIM HRAK+LPH TFR NECVCTPYNADFDG
Sbjct: 446 NLKRGDLIERHMMDEDIVLFNRQPSLHKLSIMCHRAKILPHLTFRLNECVCTPYNADFDG 505

Query: 388 DEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITG 447
           DEMN+HLPQTEEARAEAL              +LM NKSNLVTPRNGELLIAA QDFITG
Sbjct: 506 DEMNLHLPQTEEARAEAL--------------ILMGNKSNLVTPRNGELLIAAIQDFITG 551

Query: 448 GYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIF 507
            YLLT K+AFF+RA+T ++ ++++A   ++  +IK        P    + A +W+GKQIF
Sbjct: 552 AYLLTLKDAFFDRAKTCQMVASMLAG-DEVNMVIK------LPPPCIQKPAAMWSGKQIF 604

Query: 508 SLILKPNRDCPVNANLKTKGRAYT-ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKA 566
           SLIL+PN   P+  NL+TKG+ Y+  NEEFC  D ++++RNSE+LAG +DKST+GSG K 
Sbjct: 605 SLILRPNPGNPIKVNLRTKGKEYSKKNEEFCVNDGFLLVRNSEVLAGCVDKSTIGSGSKI 664

Query: 567 NVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           N+FY+LLRD+GED A+ AMW+L R+ S+Y+MNRGFSIGIGDVTPG+  ++
Sbjct: 665 NIFYVLLRDYGEDFAIQAMWKLCRVASYYMMNRGFSIGIGDVTPGKTLLK 714



 Score =  320 bits (820), Expect = 4e-84,   Method: Compositional matrix adjust.
 Identities = 198/473 (41%), Positives = 269/473 (56%), Gaps = 66/473 (13%)

Query: 1001 PVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEF 1060
            PV+ +R LD I A +    +  L   E+    N  +++    +    +F  +++ F+E  
Sbjct: 921  PVDFQRTLDHIKAASPYPDEEPLDDNELEHAFNTIMETD--FKTLGIDFKHELRVFVESQ 978

Query: 1061 SKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATA 1120
             K+        ++       +  H ++I  G+        C  +  +EKY RA+IEP TA
Sbjct: 979  VKRIKSVREIYQMDSRALHPVEKHLERITVGQ----LVEFC--DFAKEKYERAKIEPGTA 1032

Query: 1121 VGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYIEEVFVPDDSFILIK- 1165
            VGAL AQSIGEPGTQMTLKTFHFAG              E+    + +  P  S  L+K 
Sbjct: 1033 VGALCAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIINASKAISTPVISTQLLKD 1092

Query: 1166 ---------------------------------------LDMDRIRLLHLEVDIDSIR-- 1184
                                                   LDM+RIRLL LEVD  SIR  
Sbjct: 1093 DDPEYARRVKGRIEKTTLGEVTEYFEEVYLPDGCYMLIKLDMNRIRLLKLEVDASSIRLS 1152

Query: 1185 YCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQGINRAVI 1243
             C  + +     + V   S + +KP  ++KS    + Q +K+ LP VVIKG+  ++RAVI
Sbjct: 1153 LCTGKLKIKPNFVAVVSESIITVKPAPNAKSSTYHVMQHLKEELPKVVIKGLPTVSRAVI 1212

Query: 1244 HEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIK 1303
            + ++     +Y LLVEG+N+R+VMATYGV+G   +SNN  EV  TLGIEAA++TI  EIK
Sbjct: 1213 NIDETRKPPRYYLLVEGNNMREVMATYGVQGSSTTSNNILEVSSTLGIEAAKATIAKEIK 1272

Query: 1304 LVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAA 1363
              ME+HGMS+D RH  L++DLM+ +GE+LGITR+GL KMKESVL LASFE+TSDHLFDAA
Sbjct: 1273 FTMESHGMSVDRRHVALLSDLMSCRGEILGITRNGLNKMKESVLMLASFESTSDHLFDAA 1332

Query: 1364 FYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 1415
            +YGQ D ++GVSECIIMG+PM++GTG  KLL    +S  P  R L+FD PE+H
Sbjct: 1333 YYGQEDEVTGVSECIIMGIPMSIGTGAFKLLYKTGKSVPPKTRPLIFDVPEYH 1385



 Score =  284 bits (727), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 142/247 (57%), Positives = 175/247 (70%), Gaps = 10/247 (4%)

Query: 102 VSKNLYC-----QDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP 156
           VS+ LY      QD  R P+ +G+LDR+MGT+ K+A C TCG+ L DCVGHFGYIDL LP
Sbjct: 37  VSEKLYLENSSNQDSSRIPMQYGMLDRKMGTSVKDALCGTCGKGLEDCVGHFGYIDLELP 96

Query: 157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILET 216
           VFH+GYF+  IN+LQ+ICK  TC+ V+L E+    +RAKLRNP L YL +K ++K+I E 
Sbjct: 97  VFHVGYFKATINVLQTICK--TCSHVMLTEKMKKIYRAKLRNPNLPYLRKKVIRKQIQEL 154

Query: 217 TKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEA 276
            KKV  CPHC E+NGVVKKCG+LKISHEK++N    K  I+E  LA Y+ AV+FN EIE 
Sbjct: 155 CKKVKRCPHCDEMNGVVKKCGMLKISHEKFRN---VKKPIIEKELAAYDNAVQFNKEIEP 211

Query: 277 HKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVIS 336
                LI+ LNP+EVL L E IP E I  LLMN E   P D+ILTR+ VPP CIRPSV+S
Sbjct: 212 MLSSALIKMLNPIEVLHLLERIPDEHIQFLLMNPEHGHPKDMILTRVPVPPVCIRPSVVS 271

Query: 337 DLKSDND 343
           D KS  +
Sbjct: 272 DFKSGTN 278



 Score =  249 bits (635), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 130/237 (54%), Positives = 172/237 (72%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+I+  L KD D +YAR VKGR+E+TTLGEV EY EEV++PD 
Sbjct: 1066 GVPRIKEIINASKAISTPVISTQLLKDDDPEYARRVKGRIEKTTLGEVTEYFEEVYLPDG 1125

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             ++LIKLDM+RIRLL LEVD  SIR   C  + +     + V   S + +KP  ++KS  
Sbjct: 1126 CYMLIKLDMNRIRLLKLEVDASSIRLSLCTGKLKIKPNFVAVVSESIITVKPAPNAKSST 1185

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VVIKG+  ++RAVI+ ++     +Y LLVEG+N+R+VMATYGV+G  
Sbjct: 1186 YHVMQHLKEELPKVVIKGLPTVSRAVINIDETRKPPRYYLLVEGNNMREVMATYGVQGSS 1245

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNN  EV  TLGIEAA++TI  EIK  ME+HGMS+D RH  L++DLM+ +GE+LG
Sbjct: 1246 TTSNNILEVSSTLGIEAAKATIAKEIKFTMESHGMSVDRRHVALLSDLMSCRGEILG 1302



 Score =  117 bits (292), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 51/61 (83%), Positives = 56/61 (91%)

Query: 608 VTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           +   +GFV NSF+SGLTPTEFFFHTMGGREGLVDTAVKTA+TGYMQRRL+KSLEDLC QY
Sbjct: 830 IPAAKGFVSNSFYSGLTPTEFFFHTMGGREGLVDTAVKTADTGYMQRRLIKSLEDLCCQY 889

Query: 668 D 668
           D
Sbjct: 890 D 890



 Score = 86.7 bits (213), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 39/57 (68%), Positives = 50/57 (87%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKV 77
           +LM NKSNLVTPRNGELLIAA QDFITG YLLT K+AFF+RA+T ++ ++++AG +V
Sbjct: 524 ILMGNKSNLVTPRNGELLIAAIQDFITGAYLLTLKDAFFDRAKTCQMVASMLAGDEV 580



 Score = 79.7 bits (195), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 37/64 (57%), Positives = 46/64 (71%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
            D  FDAA+YGQ D ++GVSECIIMG+PM++GTG  KLL    +S  P  R L+FD PE+H
Sbjct: 1326 DHLFDAAYYGQEDEVTGVSECIIMGIPMSIGTGAFKLLYKTGKSVPPKTRPLIFDVPEYH 1385

Query: 727  FPQV 730
             P V
Sbjct: 1386 VPMV 1389


>gi|348576170|ref|XP_003473860.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1-like [Cavia
            porcellus]
          Length = 1390

 Score =  365 bits (936), Expect = 1e-97,   Method: Compositional matrix adjust.
 Identities = 218/479 (45%), Positives = 286/479 (59%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A     S+P+LS  E LALS E +  K       ++F+++IKKF
Sbjct: 914  GKDEPLEFKRVLDNIRAVYPCPSEPALSKNE-LALSTEAIMKKNEFLCCQDSFLQEIKKF 972

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 973  IKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQLEKFLETCRDKYMRAQ 1026

Query: 1115 IEP--------ATAVGALAAQ----------------SIGEPGTQMTLKTFH-------- 1142
            +EP        A ++G    Q                ++G P  +  +            
Sbjct: 1027 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1086

Query: 1143 ----------------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                                    GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1087 AQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1146

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +S+RY  C  + R   G + V G + + + P++SSKS    + Q +K+ LP VV++G+  
Sbjct: 1147 ESVRYSICTSKLRVKPGDVAVHGEAVVCVTPRESSKSSMYYVLQFLKEELPKVVVQGIPE 1206

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG + SSNNTYEV KTLGIEAAR+T
Sbjct: 1207 VSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTRTSSNNTYEVEKTLGIEAARTT 1266

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1267 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1326

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1327 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKANRDPNPPRRPLVFDTNEFH 1385



 Score =  345 bits (885), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 169/280 (60%), Positives = 207/280 (73%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDVVLFNRQPSLHKLSIMAHLARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++       G  ++   R  +P + ++   +WTGKQIFS+IL+P+ D PV 
Sbjct: 562 AKACQIIASILV------GKDEKVKVRLPHPAI-LKPVTLWTGKQIFSVILRPSDDNPVR 614

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DSYV ++NSEL+ GSMDK TLGSG K N+FYILLRD+G++
Sbjct: 615 ANLRTKGKQYCGKGEDLCVNDSYVTIQNSELMCGSMDKGTLGSGSKNNIFYILLRDWGQN 674

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 675 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 714



 Score =  296 bits (759), Expect = 4e-77,   Method: Compositional matrix adjust.
 Identities = 144/251 (57%), Positives = 178/251 (70%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD    P+ HG+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNSHAPLLHGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYFR VI +LQ ICK  TC  +LL  E+   F   L+ P L+YL ++ L+
Sbjct: 86  IDLELPCFHVGYFRAVIGVLQMICK--TCCHILLSREERQQFLDHLKRPGLTYLQKRGLR 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KK+ +  +K SVC HCG  NG VKKCGLLKI HEKYK   K  D +V   L  +  A++ 
Sbjct: 144 KKVSDKCRKKSVCHHCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPMVSSFLQSFETAIEH 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP ED+PLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NKEVEP--LLGRAQENLNPLIVLNLFKRIPAEDVPLLLMNPEAGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 262 IRPSVVSDLKS 272



 Score =  294 bits (752), Expect = 3e-76,   Method: Compositional matrix adjust.
 Identities = 150/237 (63%), Positives = 186/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LDKD D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1066 GVPRIKEIINASKAISTPIITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 1125

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +S+RY  C  + R   G + V G + + + P++SSKS  
Sbjct: 1126 CFILVKLSLERIRLLRLEVNAESVRYSICTSKLRVKPGDVAVHGEAVVCVTPRESSKSSM 1185

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG +
Sbjct: 1186 YYVLQFLKEELPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTR 1245

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             SSNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1246 TSSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1302



 Score =  116 bits (291), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 830 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 889



 Score = 81.3 bits (199), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1326 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKANRDPNPPRRPLVFDTNEFH 1385

Query: 727  FPQV 730
             P V
Sbjct: 1386 IPLV 1389



 Score = 74.7 bits (182), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 521 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 575


>gi|321451320|gb|EFX63013.1| hypothetical protein DAPPUDRAFT_67470 [Daphnia pulex]
          Length = 1391

 Score =  365 bits (936), Expect = 1e-97,   Method: Compositional matrix adjust.
 Identities = 175/290 (60%), Positives = 217/290 (74%), Gaps = 22/290 (7%)

Query: 328 NCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDG 387
           N  R  VI     D D+VLFNRQPSLHKLSIM HRAK+LPHRTFRFNECVCTPYNADFDG
Sbjct: 447 NLKRGDVIERHMMDEDIVLFNRQPSLHKLSIMCHRAKILPHRTFRFNECVCTPYNADFDG 506

Query: 388 DEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITG 447
           DEM +H PQTEEARAEAL              +LM NKSNLVTPRNGELLIAA QDFITG
Sbjct: 507 DEMTLHFPQTEEARAEAL--------------ILMTNKSNLVTPRNGELLIAAIQDFITG 552

Query: 448 GYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIF 507
            YLLT K+AFF+RA+T ++ ++++A   ++  +IK        P    + A +W+GKQIF
Sbjct: 553 AYLLTLKDAFFDRAKTCQMVASMLAG-DEVNMVIK------LPPPCIQKPAALWSGKQIF 605

Query: 508 SLILKPNRDCPVNANLKTKGRAYT-ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKA 566
           SLIL+PN    +  NL+TKG+ Y+  NEEFC  D ++++RNSE+LAG +DKST+GSG K 
Sbjct: 606 SLILRPNPGDRIKVNLRTKGKEYSKKNEEFCVNDGFLLVRNSEVLAGCVDKSTIGSGSKI 665

Query: 567 NVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           N+FY+LLRD+GED A+ AMW+L R+ S+Y+MNRGFSIGIGDVTPG+  ++
Sbjct: 666 NIFYVLLRDYGEDFAIQAMWKLGRVASYYMMNRGFSIGIGDVTPGKTLLK 715



 Score =  301 bits (770), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 147/255 (57%), Positives = 187/255 (73%), Gaps = 11/255 (4%)

Query: 92  RVQQQSHIQIVSKNLYC------QDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCV 145
           ++QQ SHIQIVS+ LY       QD  RTP+P+G+LDR+MGT+ K+A C TCG+ + +CV
Sbjct: 27  QIQQNSHIQIVSEKLYLENSSSNQDSSRTPVPNGMLDRKMGTSVKDALCATCGKGVENCV 86

Query: 146 GHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLV 205
           GHFGYIDL LPVFH+GYF+  IN+LQ+ICK  TC+ VLL E+    +RAKLR   L YL 
Sbjct: 87  GHFGYIDLELPVFHVGYFKATINVLQTICK--TCSHVLLPEKIRNIYRAKLRKQNLPYLR 144

Query: 206 RKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYN 265
           +++L+K+I E  K+V  CPHC E+NGVVKKCG+LKISHEK++N    K  I+E  L  Y+
Sbjct: 145 KQALRKQIQELCKEVKRCPHCDELNGVVKKCGMLKISHEKFRN---AKKPIIEAELVAYD 201

Query: 266 EAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLV 325
            AV+FN EIE      LI+ LNP+EV+ LFE IP ED+  +LMN+E   P D+ILTRL V
Sbjct: 202 NAVQFNKEIEPMLSSALIKMLNPIEVMHLFERIPDEDVQYILMNSEHGHPKDMILTRLPV 261

Query: 326 PPNCIRPSVISDLKS 340
           PP CIRPSV+SDLKS
Sbjct: 262 PPACIRPSVMSDLKS 276



 Score =  295 bits (754), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 188/483 (38%), Positives = 265/483 (54%), Gaps = 85/483 (17%)

Query: 1001 PVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEF 1060
            PV+ +R  + + A +    +  L   E+    +  +++  F +   ++   +++ F+E  
Sbjct: 922  PVDFQRGFEHVKAASPFPDEEPLDDIELKGAFDAIMETHTF-KKLGDDIKHELRVFVESQ 980

Query: 1061 SKK----ESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIE 1116
             K+      +  +  + S P+ +    H ++I  G+        C  +  +EKY RA+IE
Sbjct: 981  VKRIKSVRDIYKNDARASNPVEK----HLERITVGQ----LVEFC--DFAKEKYERAKIE 1030

Query: 1117 PATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYIEEVFVPDDSFI 1162
            P TAVGAL AQSI EP T+MTLK F  AG              E+    + +  P  S  
Sbjct: 1031 PGTAVGALCAQSIAEPCTKMTLKPFQLAGVASMNTTQGVHRLIEIINASKAISTPVISTQ 1090

Query: 1163 LIK----------------------------------------LDMDRIRLLHLEVDIDS 1182
            L+K                                        LDM+RIRLL LEVD  S
Sbjct: 1091 LLKDDDPEYARRVKGRIEKTTLGEVTQFFEEVYLPSGCFVKIKLDMNRIRLLKLEVDASS 1150

Query: 1183 IRYCIERTRGISGHLTVSGHSFLIL---------KPKDSSKSFNSKMYQMKQLLPSVVIK 1233
            IR  +      +G L ++  + L+          KP   S  ++   + M + LP VVIK
Sbjct: 1151 IRSSL-----CTGKLKLNPSTVLVFNEKVIYIQCKPTTKSSRYHVLQHVMNE-LPKVVIK 1204

Query: 1234 GVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEA 1293
            G+  ++R VI+ +D     ++ LLVEG+N+R+VMATYGV+G   +SNN  EV+ TLGIEA
Sbjct: 1205 GLTDVSRVVINIDDRRNPPRHSLLVEGNNMREVMATYGVQGSSTTSNNILEVFSTLGIEA 1264

Query: 1294 ARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFE 1353
            A+S I  EIK  ME+HGMS+D RH  L++DLM+ +GE+LGITRHGLAKMK+SVL LASFE
Sbjct: 1265 AKSMIAKEIKFTMESHGMSVDRRHVALLSDLMSCRGEILGITRHGLAKMKQSVLMLASFE 1324

Query: 1354 NTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNP 1412
            +TSDHLFDAA+YGQ D ++GVSECIIMG+PM +GTG  KLL    +S  P  R L+FD P
Sbjct: 1325 STSDHLFDAAYYGQEDEVTGVSECIIMGVPMAIGTGAFKLLYKTGKSVPPKTRPLIFDVP 1384

Query: 1413 EFH 1415
            E+H
Sbjct: 1385 EYH 1387



 Score =  225 bits (574), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 121/243 (49%), Positives = 165/243 (67%), Gaps = 15/243 (6%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GV R+ EIINAS+ ISTP+I+  L KD D +YAR VKGR+E+TTLGEV ++ EEV++P  
Sbjct: 1068 GVHRLIEIINASKAISTPVISTQLLKDDDPEYARRVKGRIEKTTLGEVTQFFEEVYLPSG 1127

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLIL---------KPK 874
             F+ IKLDM+RIRLL LEVD  SIR  +      +G L ++  + L+          KP 
Sbjct: 1128 CFVKIKLDMNRIRLLKLEVDASSIRSSL-----CTGKLKLNPSTVLVFNEKVIYIQCKPT 1182

Query: 875  DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATY 934
              S  ++   + M +L P VVIKG+  ++R VI+ +D     ++ LLVEG+N+R+VMATY
Sbjct: 1183 TKSSRYHVLQHVMNEL-PKVVIKGLTDVSRVVINIDDRRNPPRHSLLVEGNNMREVMATY 1241

Query: 935  GVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGE 994
            GV+G   +SNN  EV+ TLGIEAA+S I  EIK  ME+HGMS+D RH  L++DLM+ +GE
Sbjct: 1242 GVQGSSTTSNNILEVFSTLGIEAAKSMIAKEIKFTMESHGMSVDRRHVALLSDLMSCRGE 1301

Query: 995  VLG 997
            +LG
Sbjct: 1302 ILG 1304



 Score =  102 bits (253), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 45/61 (73%), Positives = 50/61 (81%)

Query: 608 VTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           +   +GFV NSF+SGL+PTE FFH M GREGLVDTAVKTAE  YMQRRL+K LEDLC QY
Sbjct: 831 IPAAKGFVSNSFYSGLSPTELFFHAMSGREGLVDTAVKTAEPMYMQRRLIKFLEDLCCQY 890

Query: 668 D 668
           D
Sbjct: 891 D 891



 Score = 86.3 bits (212), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 39/57 (68%), Positives = 50/57 (87%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKV 77
           +LM NKSNLVTPRNGELLIAA QDFITG YLLT K+AFF+RA+T ++ ++++AG +V
Sbjct: 525 ILMTNKSNLVTPRNGELLIAAIQDFITGAYLLTLKDAFFDRAKTCQMVASMLAGDEV 581



 Score = 78.6 bits (192), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 37/64 (57%), Positives = 45/64 (70%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
            D  FDAA+YGQ D ++GVSECIIMG+PM +GTG  KLL    +S  P  R L+FD PE+H
Sbjct: 1328 DHLFDAAYYGQEDEVTGVSECIIMGVPMAIGTGAFKLLYKTGKSVPPKTRPLIFDVPEYH 1387

Query: 727  FPQV 730
             P V
Sbjct: 1388 VPMV 1391


>gi|321458572|gb|EFX69638.1| hypothetical protein DAPPUDRAFT_62003 [Daphnia pulex]
          Length = 1238

 Score =  365 bits (936), Expect = 1e-97,   Method: Compositional matrix adjust.
 Identities = 175/290 (60%), Positives = 217/290 (74%), Gaps = 22/290 (7%)

Query: 328 NCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDG 387
           N  R  VI     D D+VLFNRQPSLHKLSIM HRAK+LPHRTFRFNECVCTPYNADFDG
Sbjct: 294 NLKRGDVIERHMMDEDIVLFNRQPSLHKLSIMCHRAKILPHRTFRFNECVCTPYNADFDG 353

Query: 388 DEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITG 447
           DEM +H PQTEEARAEAL              +LM NKSNLVTPRNGELLIAA QDFITG
Sbjct: 354 DEMTLHFPQTEEARAEAL--------------ILMTNKSNLVTPRNGELLIAAIQDFITG 399

Query: 448 GYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIF 507
            YLLT K+AFF+RA+T ++ ++++A   ++  +IK        P    + A +W+GKQIF
Sbjct: 400 AYLLTLKDAFFDRAKTCQMVASMLAG-DEVNMVIK------LPPPCIQKPAALWSGKQIF 452

Query: 508 SLILKPNRDCPVNANLKTKGRAYT-ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKA 566
           SLIL+PN    +  NL+TKG+ Y+  NEEFC  D ++++RNSE+LAG +DKST+GSG K 
Sbjct: 453 SLILRPNPGDRIKVNLRTKGKEYSKKNEEFCVNDGFLLVRNSEVLAGCVDKSTIGSGSKI 512

Query: 567 NVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           N+FY+LLRD+GED A+ AMW+L R+ S+Y+MNRGFSIGIGDVTPG+  ++
Sbjct: 513 NIFYVLLRDYGEDFAIQAMWKLCRVASYYMMNRGFSIGIGDVTPGKTLLK 562



 Score =  310 bits (793), Expect = 5e-81,   Method: Compositional matrix adjust.
 Identities = 195/476 (40%), Positives = 264/476 (55%), Gaps = 71/476 (14%)

Query: 1001 PVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEF 1060
            PV+  R  + + A  S   +  L   E+    N  +D+  F +    +F  +++ F+E  
Sbjct: 769  PVDFHRGFEHVKAAFSFPDEEPLDDIELQQAFNTIMDTDSF-KMLGVDFQHELRVFVESQ 827

Query: 1061 SKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEAC---REKYVRAQIEP 1117
             K+        K+       +  H ++I  G+           E C   +EKY RA+IEP
Sbjct: 828  VKRIKKVRQLFKMEGRSLLTVEKHLERITVGQ---------LVEFCDFSKEKYERAKIEP 878

Query: 1118 ATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYIEEVFVPDDSFIL 1163
             TAVGAL AQSIGEPGTQMTLKTFHFAG              E+    + +  P  S  L
Sbjct: 879  GTAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIINASKAISTPVISTQL 938

Query: 1164 IK----------------------------------------LDMDRIRLLHLEVDIDSI 1183
            +K                                        LDM+RIRLL LEVD  SI
Sbjct: 939  LKDDDPEYARRVKGRIEKTTLGEVTEYFEEVYLPSGCFVKIKLDMNRIRLLKLEVDASSI 998

Query: 1184 R--YCIERTRGISGHLTVSGHSFLILKPKDSSK-SFNSKMYQMKQLLPSVVIKGVQGINR 1240
            +   C  + +     + V     + ++ K++SK S    M+  K+ LP+V+IKG   ++R
Sbjct: 999  QSSLCTGKLKLNPDTVLVLNEKVIAVQCKETSKISLYGVMHHFKKELPTVIIKGFDDVSR 1058

Query: 1241 AVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMT 1300
             +I  +D     +Y LLVEG+N+R+VMATYG++G   +SNN  EV+ TLGIEAA++TI  
Sbjct: 1059 VIIKMDDSRNTPRYSLLVEGNNMREVMATYGIQGSSTTSNNILEVFSTLGIEAAKATIAK 1118

Query: 1301 EIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLF 1360
            EI+  ME+HGMS+D RH  L++DLM+ +GE+LGITRHGLAKMK SVL LASFE TSDHLF
Sbjct: 1119 EIQSTMESHGMSVDRRHVALLSDLMSCRGEILGITRHGLAKMKSSVLMLASFERTSDHLF 1178

Query: 1361 DAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 1415
            DAA+YGQ D +SGVSE IIMG+PM +GTG  KLL    +S +P  R L+FD PE+H
Sbjct: 1179 DAAYYGQEDEVSGVSERIIMGVPMGIGTGSFKLLYKTGKSVQPKTRPLIFDVPEYH 1234



 Score =  239 bits (611), Expect = 7e-60,   Method: Compositional matrix adjust.
 Identities = 123/237 (51%), Positives = 168/237 (70%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+I+  L KD D +YAR VKGR+E+TTLGEV EY EEV++P  
Sbjct: 915  GVPRIKEIINASKAISTPVISTQLLKDDDPEYARRVKGRIEKTTLGEVTEYFEEVYLPSG 974

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIR--YCIERTRGISGHLTVSGHSFLILKPKDSSK-SF 880
             F+ IKLDM+RIRLL LEVD  SI+   C  + +     + V     + ++ K++SK S 
Sbjct: 975  CFVKIKLDMNRIRLLKLEVDASSIQSSLCTGKLKLNPDTVLVLNEKVIAVQCKETSKISL 1034

Query: 881  NSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
               M+  K+ LP+V+IKG   ++R +I  +D     +Y LLVEG+N+R+VMATYG++G  
Sbjct: 1035 YGVMHHFKKELPTVIIKGFDDVSRVIIKMDDSRNTPRYSLLVEGNNMREVMATYGIQGSS 1094

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNN  EV+ TLGIEAA++TI  EI+  ME+HGMS+D RH  L++DLM+ +GE+LG
Sbjct: 1095 TTSNNILEVFSTLGIEAAKATIAKEIQSTMESHGMSVDRRHVALLSDLMSCRGEILG 1151



 Score =  152 bits (384), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 75/126 (59%), Positives = 91/126 (72%), Gaps = 3/126 (2%)

Query: 215 ETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEI 274
           E  K+V  CPHC E+NGVVKKCG+LKISHEK++N    K  I+E  L  Y+ AV+FN EI
Sbjct: 1   ELCKEVKRCPHCDELNGVVKKCGMLKISHEKFRN---AKKPIIEAELVAYDNAVQFNKEI 57

Query: 275 EAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSV 334
           E      LI+ LNP+EV+ LFE IP ED+  +LMN+E   P D+ILTRL VPP CIRPSV
Sbjct: 58  EPMLSSALIKMLNPIEVMHLFERIPDEDVQYILMNSEHGHPKDMILTRLPVPPACIRPSV 117

Query: 335 ISDLKS 340
           +SDLKS
Sbjct: 118 MSDLKS 123



 Score = 97.8 bits (242), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 44/61 (72%), Positives = 49/61 (80%)

Query: 608 VTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           +   +GFV NSF+SGL+PTEFFF  M GREGLVDTAV TAE  YMQRRL+K LEDLC QY
Sbjct: 678 IPAAKGFVSNSFYSGLSPTEFFFLAMSGREGLVDTAVTTAEPMYMQRRLIKFLEDLCCQY 737

Query: 668 D 668
           D
Sbjct: 738 D 738



 Score = 86.3 bits (212), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 39/57 (68%), Positives = 50/57 (87%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKV 77
           +LM NKSNLVTPRNGELLIAA QDFITG YLLT K+AFF+RA+T ++ ++++AG +V
Sbjct: 372 ILMTNKSNLVTPRNGELLIAAIQDFITGAYLLTLKDAFFDRAKTCQMVASMLAGDEV 428



 Score = 75.9 bits (185), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 37/64 (57%), Positives = 45/64 (70%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
            D  FDAA+YGQ D +SGVSE IIMG+PM +GTG  KLL    +S +P  R L+FD PE+H
Sbjct: 1175 DHLFDAAYYGQEDEVSGVSERIIMGVPMGIGTGSFKLLYKTGKSVQPKTRPLIFDVPEYH 1234

Query: 727  FPQV 730
             P V
Sbjct: 1235 VPMV 1238


>gi|194042171|ref|XP_001929395.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1-like [Sus
            scrofa]
          Length = 1390

 Score =  364 bits (935), Expect = 2e-97,   Method: Compositional matrix adjust.
 Identities = 214/479 (44%), Positives = 288/479 (60%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A    +S+P+LS  E+L  +   +   EFL    ++F+++IKKF
Sbjct: 914  GKDEPLEFKRVLDNIKAVFPCQSEPALSKNELLLTTESIMKKNEFLC-CQDSFLQEIKKF 972

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 973  IKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQIEKFLETCRDKYMRAQ 1026

Query: 1115 IEP--------ATAVGALAAQ----------------SIGEPGTQMTLKTFH-------- 1142
            +EP        A ++G    Q                ++G P  +  +            
Sbjct: 1027 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1086

Query: 1143 ----------------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                                    GE+ EYIEEVF+PDD FILIKL ++RIRLL LEV+ 
Sbjct: 1087 AQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILIKLSLERIRLLRLEVNA 1146

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C+ + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1147 ETVRYSICMSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPE 1206

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+T
Sbjct: 1207 VSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTQTTSNNTYEVEKTLGIEAARTT 1266

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1267 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1326

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP-RTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R    P R L+FD  EFH
Sbjct: 1327 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKANRDPSPPRRPLIFDTDEFH 1385



 Score =  344 bits (882), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 168/280 (60%), Positives = 207/280 (73%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDVVLFNRQPSLHKLSIMAHLARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++       G  ++   R   P + ++   +WTGKQ+FS+IL+P+ D PV 
Sbjct: 562 AKACQIIASILV------GKDEKIKVRLPPPTI-LKPVTLWTGKQVFSVILRPSYDNPVR 614

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DSYV ++NSEL++GSMDK TLGSG K N+FYILLRD+G++
Sbjct: 615 ANLRTKGKQYCGKGEDLCVNDSYVTIQNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQN 674

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 675 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 714



 Score =  296 bits (758), Expect = 5e-77,   Method: Compositional matrix adjust.
 Identities = 145/251 (57%), Positives = 180/251 (71%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD   +P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNNHSPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYFR VI ILQ ICK  TC  ++L +E+   F   L+ P L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFRAVIGILQMICK--TCCHIMLSQEERKQFLDYLKRPGLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K + C HCG  NG VKKCGLLKI HEKYK   K  D IV + L  +  A++ 
Sbjct: 144 KKISDKCRKKNTCHHCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPIVSNFLQSFETAIEH 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP EDIPLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NKEVEPL--LGRAQENLNPLVVLNLFKRIPAEDIPLLLMNPEAGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 262 IRPSVVSDLKS 272



 Score =  291 bits (745), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 148/237 (62%), Positives = 187/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LDKD D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1066 GVPRIKEIINASKAISTPIITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 1125

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FILIKL ++RIRLL LEV+ +++RY  C+ + R   G + V G + + + P+++SKS  
Sbjct: 1126 CFILIKLSLERIRLLRLEVNAETVRYSICMSKLRVKPGDVAVHGEAVVCVTPRENSKSSM 1185

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG +
Sbjct: 1186 YYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTQ 1245

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1246 TTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1302



 Score =  116 bits (291), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 830 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 889



 Score = 82.0 bits (201), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP-RTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R    P R L+FD  EFH
Sbjct: 1326 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKANRDPSPPRRPLIFDTDEFH 1385

Query: 727  FPQV 730
             P V
Sbjct: 1386 IPLV 1389



 Score = 74.3 bits (181), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 521 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 575


>gi|149690349|ref|XP_001504046.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1 [Equus
            caballus]
          Length = 1390

 Score =  364 bits (935), Expect = 2e-97,   Method: Compositional matrix adjust.
 Identities = 213/479 (44%), Positives = 287/479 (59%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A    RS+P+LS  E++  +   +   EFL    ++F+++IKKF
Sbjct: 914  GKDEPLEFKRVLDNIKAVFPCRSEPALSKNELILTTESIMKKNEFLC-CQDSFLQEIKKF 972

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 973  IKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQIEKFLETCRDKYMRAQ 1026

Query: 1115 IEP--------ATAVGALAAQ----------------SIGEPGTQMTLKTFH-------- 1142
            +EP        A ++G    Q                ++G P  +  +            
Sbjct: 1027 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1086

Query: 1143 ----------------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                                    GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1087 AQLDRDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1146

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C  + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1147 ETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPE 1206

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+T
Sbjct: 1207 VSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAARTT 1266

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1267 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1326

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP-RTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R    P R L+FD  EFH
Sbjct: 1327 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKANRDPSPPRRPLIFDTNEFH 1385



 Score =  345 bits (886), Expect = 8e-92,   Method: Compositional matrix adjust.
 Identities = 168/280 (60%), Positives = 207/280 (73%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDVVLFNRQPSLHKLSIMAHLARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++       G  ++   R   P + ++   +WTGKQIFS++L+P+ D PV 
Sbjct: 562 AKACQIIASILV------GKDEKIKVRLPPPTI-LKPVTLWTGKQIFSVVLRPSDDSPVR 614

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DSYV ++NSEL++GSMDK TLGSG K N+FYILLRD+G++
Sbjct: 615 ANLRTKGKQYCGRGEDLCANDSYVTIQNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQN 674

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 675 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 714



 Score =  297 bits (760), Expect = 3e-77,   Method: Compositional matrix adjust.
 Identities = 144/254 (56%), Positives = 181/254 (71%), Gaps = 5/254 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD    P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNNHAPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYFR VI ILQ ICK  TC  ++L +E+   F   L+ P L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFRAVIGILQMICK--TCCHIMLSQEEKKQFLDYLKRPGLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K ++C HCG  NG VKKCGLLKI HEKYK   K  D IV + L  +  A++ 
Sbjct: 144 KKISDKCRKKNICQHCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPIVSNFLQSFETAIEH 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP ED+PLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NKEVEPL--LGRAQENLNPLVVLNLFKRIPAEDVPLLLMNPEAGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKSDND 343
           IRPSV+SDLKS  +
Sbjct: 262 IRPSVVSDLKSGTN 275



 Score =  269 bits (687), Expect = 9e-69,   Method: Compositional matrix adjust.
 Identities = 146/237 (61%), Positives = 186/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LD+D D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1066 GVPRIKEIINASKAISTPIITAQLDRDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 1125

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  C  + R   G + V G + + + P+++SKS  
Sbjct: 1126 CFILVKLSLERIRLLRLEVNAETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSM 1185

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG +
Sbjct: 1186 YYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTR 1245

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1246 TTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1302



 Score =  116 bits (291), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 52/64 (81%), Positives = 58/64 (90%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 830 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 889

Query: 671 FDAA 674
             ++
Sbjct: 890 VRSS 893



 Score = 81.6 bits (200), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP-RTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R    P R L+FD  EFH
Sbjct: 1326 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKANRDPSPPRRPLIFDTNEFH 1385

Query: 727  FPQV 730
             P V
Sbjct: 1386 IPLV 1389



 Score = 74.3 bits (181), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 521 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 575


>gi|126272809|ref|XP_001364762.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1 [Monodelphis
            domestica]
          Length = 1390

 Score =  363 bits (933), Expect = 3e-97,   Method: Compositional matrix adjust.
 Identities = 215/479 (44%), Positives = 286/479 (59%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A    +S+P+LS  E++  +   +   EFL    E+F+++IKKF
Sbjct: 914  GKDEPLEFKRVLDNIKAVFPCQSEPALSKNELVLTTESIMKRNEFLC-CQESFLQEIKKF 972

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 973  IKIVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQIEKFLETCRDKYMRAQ 1026

Query: 1115 IEP--------ATAVGALAAQ----------------SIGEPGTQMTLKTFH-------- 1142
            +EP        A ++G    Q                ++G P  +  +            
Sbjct: 1027 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1086

Query: 1143 ----------------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                                    GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1087 AQLDQDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1146

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C  + R   G + V G + L + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1147 ETVRYSICTSKLRVKPGDVAVHGEAVLCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPE 1206

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            + RAVIH ++  G  KYKLLVEGDNLR VMAT+GV+G K +SNNTYEV KTLGIEAARST
Sbjct: 1207 VARAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVQGTKTTSNNTYEVEKTLGIEAARST 1266

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1267 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1326

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1327 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPNPPRRPLIFDTNEFH 1385



 Score =  342 bits (877), Expect = 9e-91,   Method: Compositional matrix adjust.
 Identities = 168/280 (60%), Positives = 206/280 (73%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDVVLFNRQPSLHKLSIMAHLARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++       G  ++   R   P + ++   +WTGKQ+FSLIL+P+ + PV 
Sbjct: 562 AKACQIIASILV------GKDEKIKVRLPPPTI-LKPVTLWTGKQVFSLILQPSDENPVR 614

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DSYV ++NSEL++GSMDK TLGSG K N+FYILLRD+G+ 
Sbjct: 615 ANLRTKGKQYCGRGEDLCVNDSYVTIQNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQT 674

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 675 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 714



 Score =  280 bits (717), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 141/254 (55%), Positives = 182/254 (71%), Gaps = 5/254 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD   +P+ +G+LD RMGT++K+  C TCG+NL++C+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNHHSPLLYGVLDHRMGTSEKDRPCETCGKNLAECLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYF+ VI +LQ ICK  TC  ++L +E+   F   L+ P L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFKAVIGVLQMICK--TCCHIMLSQEERKQFLDYLKRPGLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  KK + C +CG  NG VKKCGLLKI HEKYK   K  D +V + L  +  A+++
Sbjct: 144 KKISDKCKKKNTCHYCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPVVSNFLQSFETAIEY 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP EDIPLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NKEVEP--LLGRAQENLNPLVVLNLFKRIPAEDIPLLLMNPEAGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKSDND 343
           IRPSV+SDLKS  +
Sbjct: 262 IRPSVVSDLKSGTN 275



 Score =  274 bits (700), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 148/237 (62%), Positives = 185/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LD+D D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1066 GVPRIKEIINASKAISTPIITAQLDQDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 1125

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  C  + R   G + V G + L + P+++SKS  
Sbjct: 1126 CFILVKLSLERIRLLRLEVNAETVRYSICTSKLRVKPGDVAVHGEAVLCVTPRENSKSSM 1185

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  + RAVIH ++  G  KYKLLVEGDNLR VMAT+GV+G K
Sbjct: 1186 YYVLQFLKEDLPKVVVQGIPEVARAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVQGTK 1245

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNTYEV KTLGIEAARSTI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1246 TTSNNTYEVEKTLGIEAARSTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1302



 Score =  116 bits (291), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 52/64 (81%), Positives = 58/64 (90%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 830 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 889

Query: 671 FDAA 674
             ++
Sbjct: 890 VRSS 893



 Score = 81.6 bits (200), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1326 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPNPPRRPLIFDTNEFH 1385

Query: 727  FPQV 730
             P V
Sbjct: 1386 IPLV 1389



 Score = 74.3 bits (181), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 521 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 575


>gi|351708991|gb|EHB11910.1| DNA-directed RNA polymerase III subunit RPC1 [Heterocephalus glaber]
          Length = 1392

 Score =  363 bits (932), Expect = 3e-97,   Method: Compositional matrix adjust.
 Identities = 216/479 (45%), Positives = 287/479 (59%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A     S+P+LS  + LALS+E +  K       ++F+++IKKF
Sbjct: 916  GKDEPLEFKRVLDNIRAVYPCPSEPALSKND-LALSSEAIMKKSEFLCCQDSFLQEIKKF 974

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 975  IKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQLEKFLETCRDKYMRAQ 1028

Query: 1115 IEP--------ATAVGALAAQ----------------SIGEPGTQMTLKTFH-------- 1142
            +EP        A ++G    Q                ++G P  +  +            
Sbjct: 1029 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1088

Query: 1143 ----------------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                                    GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1089 AQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1148

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +S+RY  C  + R   G + V G + + + P++SSKS    + Q +K+ LP VV++G+  
Sbjct: 1149 ESVRYSICTSKLRVKPGDVAVHGEAVVCITPRESSKSSMYYVLQFLKEDLPKVVVQGIPE 1208

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+T
Sbjct: 1209 VSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAARTT 1268

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1269 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1328

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1329 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKANRDPNPPQRPLIFDTNEFH 1387



 Score =  341 bits (875), Expect = 2e-90,   Method: Compositional matrix adjust.
 Identities = 169/282 (59%), Positives = 207/282 (73%), Gaps = 24/282 (8%)

Query: 341 DNDVVLFNRQPSLHKLSIMAH--RAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTE 398
           D DVVLFNRQPSLHKLSIMAH  R +V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTE
Sbjct: 456 DGDVVLFNRQPSLHKLSIMAHLVRVRVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTE 515

Query: 399 EARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFF 458
           EA+AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF
Sbjct: 516 EAKAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFF 561

Query: 459 NRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCP 518
           +RA+  +I ++++       G  ++   R  +P + ++   +WTGKQIFS+IL+P+ D P
Sbjct: 562 DRAKACQIIASILV------GKDEKVRVRLPHPAI-LKPVTLWTGKQIFSVILRPSDDNP 614

Query: 519 VNANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFG 577
           V ANL+TKG+ Y    E+ C  DSYV ++NSEL+ GSMDK TLGSG K N+FYILLRD+G
Sbjct: 615 VRANLRTKGKQYCGKGEDLCVNDSYVTIQNSELMCGSMDKGTLGSGSKNNIFYILLRDWG 674

Query: 578 EDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
           ++ A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 675 QNEAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 716



 Score =  294 bits (753), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 143/251 (56%), Positives = 179/251 (71%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD    P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNNHAPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYFR VI ILQ ICK  TC  +LL +E+   F   L+ P L+YL ++ L+
Sbjct: 86  IDLELPCFHVGYFRAVIGILQMICK--TCCHILLSKEEKQQFLDHLKRPGLTYLQKRGLR 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KK+ +  +K S+C HCG  NG VKKCGLLKI HEKYK   K  D +V   L  +  A++ 
Sbjct: 144 KKVSDKCRKKSLCHHCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPMVSSFLQSFETAIEH 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP ED+PLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NKEVEP--LLGRAQENLNPLIVLNLFKRIPTEDVPLLLMNPEAGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 262 IRPSVVSDLKS 272



 Score =  293 bits (749), Expect = 6e-76,   Method: Compositional matrix adjust.
 Identities = 149/237 (62%), Positives = 186/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LDKD D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1068 GVPRIKEIINASKAISTPIITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 1127

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +S+RY  C  + R   G + V G + + + P++SSKS  
Sbjct: 1128 CFILVKLSLERIRLLRLEVNAESVRYSICTSKLRVKPGDVAVHGEAVVCITPRESSKSSM 1187

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG +
Sbjct: 1188 YYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTR 1247

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1248 TTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1304



 Score =  116 bits (291), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 832 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 891



 Score = 81.6 bits (200), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1328 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKANRDPNPPQRPLIFDTNEFH 1387

Query: 727  FPQV 730
             P V
Sbjct: 1388 IPLV 1391



 Score = 74.7 bits (182), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 523 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 577


>gi|297686603|ref|XP_002820840.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1, partial
            [Pongo abelii]
          Length = 518

 Score =  363 bits (932), Expect = 4e-97,   Method: Compositional matrix adjust.
 Identities = 213/482 (44%), Positives = 288/482 (59%), Gaps = 73/482 (15%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A     S+P+LS  E++  +   +   EFL    ++F+++IKKF
Sbjct: 42   GKDEPLEFKRVLDNIKAVFPCPSEPALSKNELILTTESIMKKSEFLC-CQDSFLQEIKKF 100

Query: 1057 LEEFSKKESVTS-----HQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYV 1111
            ++  S+K   T      + +  ++P   ++L   D+I       P       E CR+KY+
Sbjct: 101  IKGVSEKIKKTRDKYGINDNGTTEP---RVLYQLDRI------TPTQVEKFLETCRDKYM 151

Query: 1112 RAQIEP--------ATAVGALAAQ----------------SIGEPGTQMTLKTFH----- 1142
            RAQ+EP        A ++G    Q                ++G P  +  +         
Sbjct: 152  RAQMEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTP 211

Query: 1143 -------------------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLE 1177
                                       GE+ EYIEEVF+PDD FIL+KL ++RIRLL LE
Sbjct: 212  IITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLE 271

Query: 1178 VDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKG 1234
            V+ +++RY  C  + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G
Sbjct: 272  VNAETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQG 331

Query: 1235 VQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAA 1294
            +  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIEAA
Sbjct: 332  IPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAA 391

Query: 1295 RSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFEN 1354
            R+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE 
Sbjct: 392  RTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEK 451

Query: 1355 TSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPE 1413
            T+DHLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  E
Sbjct: 452  TADHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPNPPKRPLIFDTNE 511

Query: 1414 FH 1415
            FH
Sbjct: 512  FH 513



 Score =  290 bits (743), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 147/237 (62%), Positives = 186/237 (78%), Gaps = 3/237 (1%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
           GVPRIKEIINAS+ ISTPIITA LDKD D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 194 GVPRIKEIINASKAISTPIITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 253

Query: 824 SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
            FIL+KL ++RIRLL LEV+ +++RY  C  + R   G + V G + + + P+++SKS  
Sbjct: 254 CFILVKLSLERIRLLRLEVNAETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSM 313

Query: 882 SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
             + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG +
Sbjct: 314 YYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTR 373

Query: 941 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 374 TTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 430



 Score = 82.4 bits (202), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668 DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
           D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 454 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPNPPKRPLIFDTNEFH 513

Query: 727 FPQV 730
            P V
Sbjct: 514 IPLV 517


>gi|410975432|ref|XP_003994136.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1 [Felis catus]
          Length = 1390

 Score =  363 bits (931), Expect = 5e-97,   Method: Compositional matrix adjust.
 Identities = 212/479 (44%), Positives = 288/479 (60%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A    +S+P+LS  E++  +   +   EFL    ++F+++IKKF
Sbjct: 914  GKDEPLEFKRVLDNIKAVFPCQSEPALSKNELVLTTESIMKKTEFLC-CQDSFLQEIKKF 972

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 973  IKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQIEKFLETCRDKYMRAQ 1026

Query: 1115 IEP--------ATAVGALAAQ----------------SIGEPGTQMTLKTFH-------- 1142
            +EP        A ++G    Q                ++G P  +  +            
Sbjct: 1027 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1086

Query: 1143 ----------------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                                    GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1087 AQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1146

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C+ + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1147 ETVRYSICMSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPE 1206

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+T
Sbjct: 1207 VSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAARTT 1266

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1267 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1326

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP-RTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R    P R L+FD  EFH
Sbjct: 1327 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPSPPRRPLIFDTNEFH 1385



 Score =  346 bits (887), Expect = 7e-92,   Method: Compositional matrix adjust.
 Identities = 170/280 (60%), Positives = 207/280 (73%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH AKV PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDVVLFNRQPSLHKLSIMAHLAKVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++       G  ++   R   P + ++   +WTGKQIFS+IL+P+ D PV 
Sbjct: 562 AKACQIIASILV------GKDEKIKVRLPPPTI-LKPVTLWTGKQIFSVILRPSDDNPVR 614

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DSYV ++NSEL++GSMDK TLGSG K N+FYILLRD+G++
Sbjct: 615 ANLRTKGKQYCGKGEDLCVNDSYVTIQNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQN 674

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 675 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 714



 Score =  294 bits (753), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 143/251 (56%), Positives = 180/251 (71%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD    P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNNHAPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYFR VI ILQ ICK  TC  ++L +E+   F   L+ P L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFRAVIGILQMICK--TCCHIMLSQEEKKQFLDYLKRPGLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K ++C +CG  NG VKKCGLLKI HEKYK   K  D IV + L  +  A++ 
Sbjct: 144 KKISDKCRKKNICHYCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPIVSNFLQSFETAIEH 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP ED+PLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NKEVEPL--LGRAQENLNPLVVLNLFKRIPAEDVPLLLMNPEAGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 262 IRPSVVSDLKS 272



 Score =  291 bits (744), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 147/237 (62%), Positives = 187/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LDKD D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1066 GVPRIKEIINASKAISTPIITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 1125

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  C+ + R   G + V G + + + P+++SKS  
Sbjct: 1126 CFILVKLSLERIRLLRLEVNAETVRYSICMSKLRVKPGDVAVHGEAVVCVTPRENSKSSM 1185

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG +
Sbjct: 1186 YYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTR 1245

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1246 TTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1302



 Score =  116 bits (291), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 830 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 889



 Score = 81.6 bits (200), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP-RTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R    P R L+FD  EFH
Sbjct: 1326 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPSPPRRPLIFDTNEFH 1385

Query: 727  FPQV 730
             P V
Sbjct: 1386 IPLV 1389



 Score = 74.7 bits (182), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 521 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 575


>gi|427798211|gb|JAA64557.1| Putative rna polymerase i large subunit, partial [Rhipicephalus
           pulchellus]
          Length = 1429

 Score =  362 bits (929), Expect = 8e-97,   Method: Compositional matrix adjust.
 Identities = 169/276 (61%), Positives = 207/276 (75%), Gaps = 21/276 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH AKVLPHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDVVLFNRQPSLHKLSIMAHVAKVLPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL              +LM  ++NLVTPRNGE LIAA QDFITGGYL+TQK+ F +R
Sbjct: 516 RAEAL--------------ILMGTRANLVTPRNGEPLIAAIQDFITGGYLITQKDVFLDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +  ++AS ++A       +          P   ++   +WTGKQIFSLI++P+R  PV 
Sbjct: 562 IKACQLASCMLAGKDTNMKV-------ELPPPAILKPVCLWTGKQIFSLIMRPSRSSPVM 614

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           A L+ KG++YT+ EE C  D+YV++RNSELL+G+MDK T+GSG K N+FYILLRD+G+  
Sbjct: 615 ACLRAKGKSYTSGEEMCVNDAYVLIRNSELLSGTMDKGTMGSGSKNNIFYILLRDYGDQY 674

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           A  AMWRL R+T++Y+ NRGFSIGIGDVTPG G ++
Sbjct: 675 AADAMWRLVRLTAYYIQNRGFSIGIGDVTPGAGLIK 710



 Score =  328 bits (842), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 211/515 (40%), Positives = 284/515 (55%), Gaps = 109/515 (21%)

Query: 1001 PVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEF 1060
            PV+  R+++   A+N+ R++P L    IL LS E L  ++ +    E+F  D++ FL  +
Sbjct: 918  PVDFGRVMEVTRARNTHRNEPPLDMDGILQLSKEILGGED-MSVCGESFRNDLEAFLTTY 976

Query: 1061 SKKESVTSHQDKVSQPLRE-QILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEP-- 1117
            +K  + T    KV +  R+  +L   +++   +  + F      + CREKY+R+ +EP  
Sbjct: 977  AKGVAETYTLYKVKE--RDIPVLKQLNRLTASQLRSFF------DTCREKYLRSVMEPAT 1028

Query: 1118 ------ATAVGALAAQ-------------------------------SIGEP---GTQMT 1137
                  A ++G  A Q                               +I  P      M 
Sbjct: 1029 AVGAVCAQSIGEPATQMTLKTFHFAGVASMNITQGVPRIKEIINASKNISTPIITAALMN 1088

Query: 1138 LKTFHFA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRY 1185
                 +A            GEV EY+EEVF+PDD F+L+KLD+DRIRLL LEV  D+IRY
Sbjct: 1089 DTDAEYARRVKGRIEKTLLGEVSEYLEEVFLPDDCFVLVKLDIDRIRLLQLEVTADTIRY 1148

Query: 1186 CIE----RTRGISGHLTVSGHSFLILKPKDSSK-----SFNSKMYQMKQL---------- 1226
             I     + R  +  +   G S L ++P  SSK     S  + M Q+ ++          
Sbjct: 1149 SISLYKTKLRIKNEDIKAIGTSLLTIRPNASSKTSLYYSLQNLMEQLPKIVIKGIPSSSR 1208

Query: 1227 -------------------------LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD 1261
                                     LP +VIKG+   +RAVIH +D  G T+Y+LLVEGD
Sbjct: 1209 AVIHADDSLGGTRYRLLXLQNLMEQLPKIVIKGIPSSSRAVIHADDSLGGTRYRLLVEGD 1268

Query: 1262 NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 1321
             LRDV+ATYGVKG+K SSNNT EV KTLGIEAAR+TI+ EI + M+NHG+S+D RH ML+
Sbjct: 1269 GLRDVIATYGVKGIKTSSNNTSEVEKTLGIEAARTTIIREIGVTMQNHGISVDRRHLMLL 1328

Query: 1322 ADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMG 1381
            ADLMT +GEVLGITRHGLA+MKES L LASFE T+DHLFDAA+YGQTD ISGVSE II+G
Sbjct: 1329 ADLMTFRGEVLGITRHGLARMKESALMLASFEKTADHLFDAAYYGQTDEISGVSESIILG 1388

Query: 1382 LPMNVGTGLIKLLQAVP-RSEPVPRTLLFDNPEFH 1415
            +PM +GTG   L+  V  +    PR L+FD  EFH
Sbjct: 1389 VPMAIGTGFFDLVHKVDWQPLAAPRKLIFDRSEFH 1423



 Score =  270 bits (691), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 150/278 (53%), Positives = 185/278 (66%), Gaps = 44/278 (15%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+NISTPIITA L  DTD +YAR VKGR+E+T LGEV EY+EEVF+PDD
Sbjct: 1063 GVPRIKEIINASKNISTPIITAALMNDTDAEYARRVKGRIEKTLLGEVSEYLEEVFLPDD 1122

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIE----RTRGISGHLTVSGHSFLILKPKDSSK- 878
             F+L+KLD+DRIRLL LEV  D+IRY I     + R  +  +   G S L ++P  SSK 
Sbjct: 1123 CFVLVKLDIDRIRLLQLEVTADTIRYSISLYKTKLRIKNEDIKAIGTSLLTIRPNASSKT 1182

Query: 879  ----SFNSKMYQMKQL-----------------------------------LPSVVIKGV 899
                S  + M Q+ ++                                   LP +VIKG+
Sbjct: 1183 SLYYSLQNLMEQLPKIVIKGIPSSSRAVIHADDSLGGTRYRLLXLQNLMEQLPKIVIKGI 1242

Query: 900  QGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAAR 959
               +RAVIH +D  G T+Y+LLVEGD LRDV+ATYGVKG+K SSNNT EV KTLGIEAAR
Sbjct: 1243 PSSSRAVIHADDSLGGTRYRLLVEGDGLRDVIATYGVKGIKTSSNNTSEVEKTLGIEAAR 1302

Query: 960  STIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +TI+ EI + M+NHG+S+D RH ML+ADLMT +GEVLG
Sbjct: 1303 TTIIREIGVTMQNHGISVDRRHLMLLADLMTFRGEVLG 1340



 Score =  257 bits (657), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 124/254 (48%), Positives = 170/254 (66%), Gaps = 3/254 (1%)

Query: 87  VTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVG 146
           V   + +QQ SH+  VSKNLY ++     +P+G+LD R+GT+QK+  C TCG+ L+DCVG
Sbjct: 22  VLNANDIQQNSHVHCVSKNLYQRESLHKSVPYGVLDNRLGTSQKDKKCETCGKGLTDCVG 81

Query: 147 HFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVR 206
           HFG + L +PVFH+GYF+ V NIL ++CK   CARV+L   + A F   ++ P+ S+L +
Sbjct: 82  HFGQVSLGMPVFHVGYFKAVYNILHTVCK--MCARVMLPPPERARFLDMVQRPSTSFLTK 139

Query: 207 KSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNE 266
           KSL KKI+E  +K + CP CG +NG VKKCGLLK  +E+YK   KK + +++DL  +Y E
Sbjct: 140 KSLHKKIVEICRKQASCPFCGVVNGQVKKCGLLKFVYERYKAH-KKNEGVIKDLQDDYQE 198

Query: 267 AVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVP 326
           A  +N EI++         LNPL V  L   IP ED+PLLLMN    +P DL+LT + VP
Sbjct: 199 ARSYNNEIDSVINKVTSDILNPLVVRDLLRRIPDEDVPLLLMNTRCGRPEDLVLTHIPVP 258

Query: 327 PNCIRPSVISDLKS 340
           P CIRPSV+S LK+
Sbjct: 259 PLCIRPSVVSALKA 272



 Score =  116 bits (290), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 54/65 (83%), Positives = 59/65 (90%), Gaps = 1/65 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV++SF+SGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 
Sbjct: 824 DRSPQARGFVEDSFYSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCC 883

Query: 666 QYDMS 670
            YD S
Sbjct: 884 HYDRS 888



 Score = 77.4 bits (189), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 45/55 (81%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           +LM  ++NLVTPRNGE LIAA QDFITGGYL+TQK+ F +R +  ++AS ++AG+
Sbjct: 521 ILMGTRANLVTPRNGEPLIAAIQDFITGGYLITQKDVFLDRIKACQLASCMLAGK 575



 Score = 70.1 bits (170), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 34/60 (56%), Positives = 41/60 (68%), Gaps = 1/60 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP-RSEPVPRTLLFDNPEFH 726
            D  FDAA+YGQTD ISGVSE II+G+PM +GTG   L+  V  +    PR L+FD  EFH
Sbjct: 1364 DHLFDAAYYGQTDEISGVSESIILGVPMAIGTGFFDLVHKVDWQPLAAPRKLIFDRSEFH 1423


>gi|296220277|ref|XP_002756253.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1 isoform 1
            [Callithrix jacchus]
          Length = 1390

 Score =  362 bits (929), Expect = 9e-97,   Method: Compositional matrix adjust.
 Identities = 212/479 (44%), Positives = 287/479 (59%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A     S+P+LS  E++  +   ++  EFL    ++F+++IKKF
Sbjct: 914  GKDEPLEFKRVLDNIKAVFPCPSEPALSKNELILTTESIMNKSEFLC-CQDSFLQEIKKF 972

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 973  IKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQVEKFLETCRDKYMRAQ 1026

Query: 1115 IEP--------ATAVGALAAQ----------------SIGEPGTQMTLKTFH-------- 1142
            +EP        A ++G    Q                ++G P  +  +            
Sbjct: 1027 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1086

Query: 1143 ----------------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                                    GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1087 AQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1146

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C  + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1147 ETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPE 1206

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+T
Sbjct: 1207 VSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAARTT 1266

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1267 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1326

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1327 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKANRDPNPPRRPLIFDTNEFH 1385



 Score =  345 bits (886), Expect = 8e-92,   Method: Compositional matrix adjust.
 Identities = 169/280 (60%), Positives = 207/280 (73%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDVVLFNRQPSLHKLSIMAHLARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++       G  ++   R   P + ++   +WTGKQIFS+IL+P+ D PV 
Sbjct: 562 AKACQIIASILV------GKDEKIKVRLPPPTI-LKPVTLWTGKQIFSVILRPSDDNPVR 614

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DSYV ++NSEL++GSMDK TLGSG K N+FYILLRD+G++
Sbjct: 615 ANLRTKGKQYCGKGEDLCANDSYVTIQNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQN 674

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 675 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 714



 Score =  299 bits (766), Expect = 7e-78,   Method: Compositional matrix adjust.
 Identities = 145/251 (57%), Positives = 182/251 (72%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD Q  P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNQHAPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYFR VI ILQ ICK  TC  ++L +E+   F   L+ P+L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFRAVIGILQMICK--TCCHIMLSQEEKKQFLDYLKRPSLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K ++C HCG  NG VKKCGLLKI HEKYK   K  D IV + L  +  A++ 
Sbjct: 144 KKISDKCRKKNICHHCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPIVSNFLQSFETAIEH 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP ED+PLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NKEVEP--LLGRAQENLNPLVVLNLFKRIPAEDVPLLLMNPEAGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 262 IRPSVVSDLKS 272



 Score =  290 bits (743), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 147/237 (62%), Positives = 186/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LDKD D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1066 GVPRIKEIINASKAISTPIITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 1125

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  C  + R   G + V G + + + P+++SKS  
Sbjct: 1126 CFILVKLSLERIRLLRLEVNAETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSM 1185

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG +
Sbjct: 1186 YYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTR 1245

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1246 TTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1302



 Score =  116 bits (291), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 830 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 889



 Score = 81.3 bits (199), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1326 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKANRDPNPPRRPLIFDTNEFH 1385

Query: 727  FPQV 730
             P V
Sbjct: 1386 IPLV 1389



 Score = 74.7 bits (182), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 521 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 575


>gi|297301053|ref|XP_002805710.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1-like [Macaca
            mulatta]
          Length = 1405

 Score =  362 bits (929), Expect = 9e-97,   Method: Compositional matrix adjust.
 Identities = 212/479 (44%), Positives = 286/479 (59%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A     S+P+LS  E++  +   +   EFL    ++F+++IKKF
Sbjct: 929  GKDEPLEFKRVLDNIKAVFPCPSEPALSKNELILTTESIMKKSEFLC-CQDSFLQEIKKF 987

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 988  IKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQVEKFLETCRDKYMRAQ 1041

Query: 1115 IEP--------ATAVGALAAQ----------------SIGEPGTQMTLKTFH-------- 1142
            +EP        A ++G    Q                ++G P  +  +            
Sbjct: 1042 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1101

Query: 1143 ----------------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                                    GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1102 AQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1161

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C  + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1162 ETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPE 1221

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+T
Sbjct: 1222 VSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAARTT 1281

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1282 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1341

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1342 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPNPPKRPLIFDTNEFH 1400



 Score =  324 bits (831), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 165/295 (55%), Positives = 203/295 (68%), Gaps = 37/295 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDVVLFNRQPSLHKLSIMAHLARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++       G  ++   R   P + ++   +WTGKQIFS+IL+P+ D PV 
Sbjct: 562 AKACQIIASILV------GKDEKIKVRLPPPTI-LKPVTLWTGKQIFSVILRPSDDNPVR 614

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DSYV ++NSEL++GSMDK TLGSG K N+FYILLRD+G++
Sbjct: 615 ANLRTKGKQYCGKGEDLCANDSYVTIQNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQN 674

Query: 580 VAVTAMWRLSRMTSFY---------------LMNRGFSIGIGDVTPGQGFVQNSF 619
            A    ++ S M  F                  NRGFSIGIGDVTPGQG ++  +
Sbjct: 675 EATGLDYKTSLMGCFQDTCGSTRVIQFSRITQSNRGFSIGIGDVTPGQGLLKAKY 729



 Score =  299 bits (766), Expect = 7e-78,   Method: Compositional matrix adjust.
 Identities = 145/251 (57%), Positives = 181/251 (72%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD Q  P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNQHAPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYFR VI ILQ ICK  TC  ++L +E+   F   L+ P L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFRAVIGILQMICK--TCCHIMLSQEEKKQFLDYLKRPGLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K ++C HCG  NG VKKCGLLKI HEKYK   K  D IV + L  +  A++ 
Sbjct: 144 KKISDKCRKKNICHHCGSFNGTVKKCGLLKIIHEKYKTNKKVVDPIVSNFLQSFETAIEH 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP ED+PLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NKEVEPL--LGRAQENLNPLVVLNLFKRIPAEDVPLLLMNPEAGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 262 IRPSVVSDLKS 272



 Score =  290 bits (742), Expect = 4e-75,   Method: Compositional matrix adjust.
 Identities = 147/237 (62%), Positives = 186/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LDKD D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1081 GVPRIKEIINASKAISTPIITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 1140

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  C  + R   G + V G + + + P+++SKS  
Sbjct: 1141 CFILVKLSLERIRLLRLEVNAETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSM 1200

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG +
Sbjct: 1201 YYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTR 1260

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1261 TTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1317



 Score =  116 bits (291), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 845 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 904



 Score = 82.0 bits (201), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1341 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPNPPKRPLIFDTNEFH 1400

Query: 727  FPQV 730
             P V
Sbjct: 1401 IPLV 1404



 Score = 74.7 bits (182), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 521 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 575


>gi|402880352|ref|XP_003903768.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1 [Papio
            anubis]
          Length = 1390

 Score =  362 bits (928), Expect = 1e-96,   Method: Compositional matrix adjust.
 Identities = 212/479 (44%), Positives = 286/479 (59%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A     S+P+LS  E++  +   +   EFL    ++F+++IKKF
Sbjct: 914  GKDEPLEFKRVLDNIKAVFPCPSEPALSKNELILTTESIMKKSEFLC-CQDSFLQEIKKF 972

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 973  IKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQVEKFLETCRDKYMRAQ 1026

Query: 1115 IEP--------ATAVGALAAQ----------------SIGEPGTQMTLKTFH-------- 1142
            +EP        A ++G    Q                ++G P  +  +            
Sbjct: 1027 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1086

Query: 1143 ----------------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                                    GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1087 AQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1146

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C  + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1147 ETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPE 1206

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+T
Sbjct: 1207 VSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAARTT 1266

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1267 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1326

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1327 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPNPPKRPLIFDTNEFH 1385



 Score =  346 bits (887), Expect = 7e-92,   Method: Compositional matrix adjust.
 Identities = 169/280 (60%), Positives = 207/280 (73%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDVVLFNRQPSLHKLSIMAHLARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++       G  ++   R   P + ++   +WTGKQIFS+IL+P+ D PV 
Sbjct: 562 AKACQIIASILV------GKDEKIKVRLPPPTI-LKPVTLWTGKQIFSVILRPSDDNPVR 614

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DSYV ++NSEL++GSMDK TLGSG K N+FYILLRD+G++
Sbjct: 615 ANLRTKGKQYCGKGEDLCANDSYVTIQNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQN 674

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 675 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 714



 Score =  299 bits (766), Expect = 6e-78,   Method: Compositional matrix adjust.
 Identities = 145/251 (57%), Positives = 182/251 (72%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD Q  P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNQHAPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYFR VI ILQ ICK  TC  ++L +E+   F   L+ P+L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFRAVIGILQMICK--TCCHIMLSQEEKKQFLDYLKRPSLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K ++C HCG  NG VKKCGLLKI HEKYK   K  D IV + L  +  A++ 
Sbjct: 144 KKISDKCRKKNICHHCGSFNGTVKKCGLLKIIHEKYKTNKKVVDPIVSNFLQSFETAIEH 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP ED+PLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NKEVEPL--LGRAQENLNPLVVLNLFKRIPAEDVPLLLMNPEAGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 262 IRPSVVSDLKS 272



 Score =  290 bits (742), Expect = 4e-75,   Method: Compositional matrix adjust.
 Identities = 147/237 (62%), Positives = 186/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LDKD D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1066 GVPRIKEIINASKAISTPIITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 1125

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  C  + R   G + V G + + + P+++SKS  
Sbjct: 1126 CFILVKLSLERIRLLRLEVNAETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSM 1185

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG +
Sbjct: 1186 YYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTR 1245

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1246 TTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1302



 Score =  116 bits (291), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 830 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 889



 Score = 82.0 bits (201), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1326 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPNPPKRPLIFDTNEFH 1385

Query: 727  FPQV 730
             P V
Sbjct: 1386 IPLV 1389



 Score = 74.7 bits (182), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 521 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 575


>gi|426365245|ref|XP_004049691.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1 [Gorilla
            gorilla gorilla]
          Length = 1334

 Score =  362 bits (928), Expect = 1e-96,   Method: Compositional matrix adjust.
 Identities = 212/479 (44%), Positives = 286/479 (59%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A     S+P+LS  E++  +   +   EFL    ++F+++IKKF
Sbjct: 858  GKDEPLEFKRVLDNIKAVFPCPSEPALSKNELILTTESIMKKSEFLC-CQDSFLQEIKKF 916

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 917  IKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQVEKFLETCRDKYMRAQ 970

Query: 1115 IEP--------ATAVGALAAQ----------------SIGEPGTQMTLKTFH-------- 1142
            +EP        A ++G    Q                ++G P  +  +            
Sbjct: 971  MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1030

Query: 1143 ----------------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                                    GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1031 AQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1090

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C  + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1091 ETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPE 1150

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+T
Sbjct: 1151 VSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAARTT 1210

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1211 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1270

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1271 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPNPPKRPLIFDTNEFH 1329



 Score =  298 bits (764), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 145/251 (57%), Positives = 181/251 (72%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD Q  P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 17  EEMRQQAHIQVVSKNLYSQDNQHAPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 76

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYFR VI ILQ ICK  TC  ++L +E+   F   L+ P L+YL ++ LK
Sbjct: 77  IDLELPCFHVGYFRAVIGILQMICK--TCCHIMLSQEEKKQFLDCLKRPGLTYLQKRGLK 134

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K ++C HCG  NG VKKCGLLKI HEKYK   K  D IV + L  +  A++ 
Sbjct: 135 KKISDKCRKKNICHHCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPIVSNFLQSFETAIEH 194

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP ED+PLLLMN E  KPSDLILTRLLVPP C
Sbjct: 195 NKEVEPL--LGRAQENLNPLVVLNLFKRIPAEDVPLLLMNPEAGKPSDLILTRLLVPPLC 252

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 253 IRPSVVSDLKS 263



 Score =  290 bits (742), Expect = 4e-75,   Method: Compositional matrix adjust.
 Identities = 147/237 (62%), Positives = 186/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LDKD D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1010 GVPRIKEIINASKAISTPIITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 1069

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  C  + R   G + V G + + + P+++SKS  
Sbjct: 1070 CFILVKLSLERIRLLRLEVNAETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSM 1129

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG +
Sbjct: 1130 YYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTR 1189

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1190 TTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1246



 Score =  237 bits (605), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 122/234 (52%), Positives = 159/234 (67%), Gaps = 14/234 (5%)

Query: 387 GDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFIT 446
           GD +  HL   +       PSLHKLSIMAH        K+NLVTPRNGE LIAA QDF+T
Sbjct: 438 GDIVERHLIDGDVVLFNRQPSLHKLSIMAH------LTKANLVTPRNGEPLIAAIQDFLT 491

Query: 447 GGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQI 506
           G YLLT K+ FF+RA+  +I ++++       G  ++   R   P + ++   +WTGKQI
Sbjct: 492 GAYLLTLKDTFFDRAKACQIIASILV------GKDEKIKVRLPPPTI-LKPVTLWTGKQI 544

Query: 507 FSLILKPNRDCPVNANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGK 565
           FS+IL+P+ D PV ANL+TKG+ Y    E+ C  DSYV ++NSEL++GSMDK TLGSG K
Sbjct: 545 FSVILRPSNDNPVRANLRTKGKQYCGKGEDLCANDSYVTIQNSELMSGSMDKGTLGSGSK 604

Query: 566 ANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            N+FYILLRD+G++ A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 605 NNIFYILLRDWGQNEAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 658



 Score =  116 bits (291), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 52/64 (81%), Positives = 58/64 (90%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 774 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 833

Query: 671 FDAA 674
             ++
Sbjct: 834 VRSS 837



 Score = 82.0 bits (201), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1270 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPNPPKRPLIFDTNEFH 1329

Query: 727  FPQV 730
             P V
Sbjct: 1330 IPLV 1333



 Score = 68.9 bits (167), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 30/50 (60%), Positives = 41/50 (82%)

Query: 26  KSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 470 KANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 519



 Score = 47.0 bits (110), Expect = 0.079,   Method: Compositional matrix adjust.
 Identities = 21/25 (84%), Positives = 21/25 (84%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKV 365
           D DVVLFNRQPSLHKLSIMAH  K 
Sbjct: 447 DGDVVLFNRQPSLHKLSIMAHLTKA 471


>gi|417406396|gb|JAA49858.1| Putative rna polymerase i large subunit [Desmodus rotundus]
          Length = 1390

 Score =  362 bits (928), Expect = 1e-96,   Method: Compositional matrix adjust.
 Identities = 211/479 (44%), Positives = 288/479 (60%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A    +S+P+LS  E++  +   +   EFL    ++F+++IKKF
Sbjct: 914  GKDEPLEFKRVLDNIKAVFPCQSEPALSKNELILTTESIMKKNEFLC-CQDSFLQEIKKF 972

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 973  IKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQIEKFLETCRDKYMRAQ 1026

Query: 1115 IEP--------ATAVGALAAQ----------------SIGEPGTQMTLKTFH-------- 1142
            +EP        A ++G    Q                ++G P  +  +            
Sbjct: 1027 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1086

Query: 1143 ----------------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                                    GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1087 AQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1146

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C+ + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1147 ETVRYSICMSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPE 1206

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+T
Sbjct: 1207 VSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAARTT 1266

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1267 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1326

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP-RTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    +    P R L+FD  EFH
Sbjct: 1327 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADKDPSPPRRPLIFDTNEFH 1385



 Score =  346 bits (888), Expect = 5e-92,   Method: Compositional matrix adjust.
 Identities = 170/280 (60%), Positives = 206/280 (73%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDVVLFNRQPSLHKLSIMAHLARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++       G  ++   R   P + ++   +WTGKQIFS+IL+P+ D PV 
Sbjct: 562 AKACQIIASILV------GKDEKIKVRLPPPTI-LKPVTLWTGKQIFSVILRPSDDSPVR 614

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DSYV ++NSEL+ GSMDK TLGSG K N+FYILLRD+G++
Sbjct: 615 ANLRTKGKQYCGKGEDLCVNDSYVTIQNSELMTGSMDKGTLGSGSKNNIFYILLRDWGQN 674

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RLSR+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 675 EAADAMSRLSRLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 714



 Score =  296 bits (759), Expect = 5e-77,   Method: Compositional matrix adjust.
 Identities = 143/251 (56%), Positives = 180/251 (71%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD    P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNNHAPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYFR VI ILQ ICK  TC  ++L +E+   F   L+ P L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFRAVIGILQMICK--TCCHIMLSQEEKKQFLDYLKRPGLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K ++C HCG  NG VKKCGLLKI HEKYK   K  D +V + L  +  A++ 
Sbjct: 144 KKISDKCRKKNICHHCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPVVSNFLQSFETAIEH 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP ED+PLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NKEVEPL--LGRAQENLNPLVVLNLFKQIPAEDVPLLLMNPEAGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 262 IRPSVVSDLKS 272



 Score =  291 bits (744), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 147/237 (62%), Positives = 187/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LDKD D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1066 GVPRIKEIINASKAISTPIITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 1125

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  C+ + R   G + V G + + + P+++SKS  
Sbjct: 1126 CFILVKLSLERIRLLRLEVNAETVRYSICMSKLRVKPGDVAVHGEAVVCVTPRENSKSSM 1185

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG +
Sbjct: 1186 YYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTR 1245

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1246 TTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1302



 Score =  116 bits (291), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 830 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 889



 Score = 80.5 bits (197), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 37/64 (57%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP-RTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    +    P R L+FD  EFH
Sbjct: 1326 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADKDPSPPRRPLIFDTNEFH 1385

Query: 727  FPQV 730
             P V
Sbjct: 1386 IPLV 1389



 Score = 74.7 bits (182), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 521 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 575


>gi|410044035|ref|XP_507865.4| PREDICTED: DNA-directed RNA polymerase III subunit RPC1 [Pan
            troglodytes]
          Length = 1380

 Score =  362 bits (928), Expect = 1e-96,   Method: Compositional matrix adjust.
 Identities = 212/479 (44%), Positives = 286/479 (59%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A     S+P+LS  E++  +   +   EFL    ++F+++IKKF
Sbjct: 904  GKDEPLEFKRVLDNIKAVFPCPSEPALSKNELILTTESIMKKSEFLC-CQDSFLQEIKKF 962

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 963  IKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQVEKFLETCRDKYMRAQ 1016

Query: 1115 IEP--------ATAVGALAAQ----------------SIGEPGTQMTLKTFH-------- 1142
            +EP        A ++G    Q                ++G P  +  +            
Sbjct: 1017 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1076

Query: 1143 ----------------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                                    GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1077 AQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1136

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C  + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1137 ETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPE 1196

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+T
Sbjct: 1197 VSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAARTT 1256

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1257 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1316

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1317 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPNPPKRPLIFDTNEFH 1375



 Score =  345 bits (886), Expect = 9e-92,   Method: Compositional matrix adjust.
 Identities = 169/280 (60%), Positives = 207/280 (73%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 446 DGDVVLFNRQPSLHKLSIMAHLARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 505

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 506 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 551

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++       G  ++   R   P + ++   +WTGKQIFS+IL+P+ D PV 
Sbjct: 552 AKACQIIASILV------GKDEKIKVRLPPPTI-LKPVTLWTGKQIFSVILRPSDDNPVR 604

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DSYV ++NSEL++GSMDK TLGSG K N+FYILLRD+G++
Sbjct: 605 ANLRTKGKQYCGKGEDLCANDSYVTIQNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQN 664

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 665 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 704



 Score =  290 bits (742), Expect = 4e-75,   Method: Compositional matrix adjust.
 Identities = 147/237 (62%), Positives = 186/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LDKD D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1056 GVPRIKEIINASKAISTPIITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 1115

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  C  + R   G + V G + + + P+++SKS  
Sbjct: 1116 CFILVKLSLERIRLLRLEVNAETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSM 1175

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG +
Sbjct: 1176 YYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTR 1235

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1236 TTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1292



 Score =  246 bits (627), Expect = 9e-62,   Method: Compositional matrix adjust.
 Identities = 131/260 (50%), Positives = 162/260 (62%), Gaps = 33/260 (12%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD Q  P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNQHAPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGF---------RAKLRNPAL 201
           IDL LP FH+GYFR VI ILQ ICK  TC  ++L +E+ + F           +  N   
Sbjct: 86  IDLELPCFHVGYFRAVIGILQMICK--TCCHIMLSQEEKSSFSNFINHTTTSGQSENIIF 143

Query: 202 SYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLL 261
            +LV K                     + G VKKCGLLKI HEKYK   K  D IV + L
Sbjct: 144 YFLVNKL-------------------TLIGTVKKCGLLKIIHEKYKTNKKVVDPIVSNFL 184

Query: 262 AEYNEAVKFNPEIEAHKKFGLIQT-LNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
             +  A++ N E+E     G  Q   NPL VL L   IP ED+PLLLMN E  KPSDLIL
Sbjct: 185 QSFETAIEHNKEVEP--LLGRAQVYWNPLVVLNLLNEIPAEDVPLLLMNPEAGKPSDLIL 242

Query: 321 TRLLVPPNCIRPSVISDLKS 340
           TRLLVPP CIRPSV+SDLKS
Sbjct: 243 TRLLVPPLCIRPSVVSDLKS 262



 Score =  116 bits (291), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 820 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 879



 Score = 82.0 bits (201), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1316 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPNPPKRPLIFDTNEFH 1375

Query: 727  FPQV 730
             P V
Sbjct: 1376 IPLV 1379



 Score = 74.7 bits (182), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 511 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 565


>gi|427788425|gb|JAA59664.1| Putative rna polymerase i large subunit [Rhipicephalus pulchellus]
          Length = 1390

 Score =  362 bits (928), Expect = 1e-96,   Method: Compositional matrix adjust.
 Identities = 169/276 (61%), Positives = 207/276 (75%), Gaps = 21/276 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH AKVLPHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDVVLFNRQPSLHKLSIMAHVAKVLPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL              +LM  ++NLVTPRNGE LIAA QDFITGGYL+TQK+ F +R
Sbjct: 516 RAEAL--------------ILMGTRANLVTPRNGEPLIAAIQDFITGGYLITQKDVFLDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +  ++AS ++A       +          P   ++   +WTGKQIFSLI++P+R  PV 
Sbjct: 562 IKACQLASCMLAGKDTNMKV-------ELPPPAILKPVCLWTGKQIFSLIMRPSRSSPVM 614

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           A L+ KG++YT+ EE C  D+YV++RNSELL+G+MDK T+GSG K N+FYILLRD+G+  
Sbjct: 615 ACLRAKGKSYTSGEEMCVNDAYVLIRNSELLSGTMDKGTMGSGSKNNIFYILLRDYGDQY 674

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           A  AMWRL R+T++Y+ NRGFSIGIGDVTPG G ++
Sbjct: 675 AADAMWRLVRLTAYYIQNRGFSIGIGDVTPGAGLIK 710



 Score =  342 bits (877), Expect = 1e-90,   Method: Compositional matrix adjust.
 Identities = 209/476 (43%), Positives = 281/476 (59%), Gaps = 70/476 (14%)

Query: 1001 PVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEF 1060
            PV+  R+++   A+N+ R++P L    IL LS E L  ++ +    E+F  D++ FL  +
Sbjct: 918  PVDFGRVMEVTRARNTHRNEPPLDMDGILQLSKEILGGED-MSVCGESFRNDLEAFLTTY 976

Query: 1061 SKKESVTSHQDKVSQPLRE-QILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEP-- 1117
            +K  + T    KV +  R+  +L   +++   +  + F      + CREKY+R+ +EP  
Sbjct: 977  AKGVAETYTLYKVKE--RDIPVLKQLNRLTASQLRSFF------DTCREKYLRSVMEPAT 1028

Query: 1118 ------ATAVGALAAQ-------------------------------SIGEP---GTQMT 1137
                  A ++G  A Q                               +I  P      M 
Sbjct: 1029 AVGAVCAQSIGEPATQMTLKTFHFAGVASMNITQGVPRIKEIINASKNISTPIITAALMN 1088

Query: 1138 LKTFHFA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRY 1185
                 +A            GEV EY+EEVF+PDD F+L+KLD+DRIRLL LEV  D+IRY
Sbjct: 1089 DTDAEYARRVKGRIEKTLLGEVSEYLEEVFLPDDCFVLVKLDIDRIRLLQLEVTADTIRY 1148

Query: 1186 CIE----RTRGISGHLTVSGHSFLILKPKDSSK-SFNSKMYQMKQLLPSVVIKGVQGINR 1240
             I     + R  +  +   G S L ++P  SSK S    +  + + LP +VIKG+   +R
Sbjct: 1149 SISLYKTKLRIKNEDIKAIGTSLLTIRPNASSKTSLYYSLQNLMEQLPKIVIKGIPSSSR 1208

Query: 1241 AVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMT 1300
            AVIH +D  G T+Y+LLVEGD LRDV+ATYGVKG+K SSNNT EV KTLGIEAAR+TI+ 
Sbjct: 1209 AVIHADDSLGGTRYRLLVEGDGLRDVIATYGVKGIKTSSNNTSEVEKTLGIEAARTTIIR 1268

Query: 1301 EIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLF 1360
            EI + M+NHG+S+D RH ML+ADLMT +GEVLGITRHGLA+MKES L LASFE T+DHLF
Sbjct: 1269 EIGVTMQNHGISVDRRHLMLLADLMTFRGEVLGITRHGLARMKESALMLASFEKTADHLF 1328

Query: 1361 DAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP-RSEPVPRTLLFDNPEFH 1415
            DAA+YGQTD ISGVSE II+G+PM +GTG   L+  V  +    PR L+FD  EFH
Sbjct: 1329 DAAYYGQTDEISGVSESIILGVPMAIGTGFFDLVHKVDWQPLAAPRKLIFDRSEFH 1384



 Score =  284 bits (726), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 148/239 (61%), Positives = 182/239 (76%), Gaps = 5/239 (2%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+NISTPIITA L  DTD +YAR VKGR+E+T LGEV EY+EEVF+PDD
Sbjct: 1063 GVPRIKEIINASKNISTPIITAALMNDTDAEYARRVKGRIEKTLLGEVSEYLEEVFLPDD 1122

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIE----RTRGISGHLTVSGHSFLILKPKDSSK- 878
             F+L+KLD+DRIRLL LEV  D+IRY I     + R  +  +   G S L ++P  SSK 
Sbjct: 1123 CFVLVKLDIDRIRLLQLEVTADTIRYSISLYKTKLRIKNEDIKAIGTSLLTIRPNASSKT 1182

Query: 879  SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 938
            S    +  + + LP +VIKG+   +RAVIH +D  G T+Y+LLVEGD LRDV+ATYGVKG
Sbjct: 1183 SLYYSLQNLMEQLPKIVIKGIPSSSRAVIHADDSLGGTRYRLLVEGDGLRDVIATYGVKG 1242

Query: 939  VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +K SSNNT EV KTLGIEAAR+TI+ EI + M+NHG+S+D RH ML+ADLMT +GEVLG
Sbjct: 1243 IKTSSNNTSEVEKTLGIEAARTTIIREIGVTMQNHGISVDRRHLMLLADLMTFRGEVLG 1301



 Score =  257 bits (656), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 124/254 (48%), Positives = 170/254 (66%), Gaps = 3/254 (1%)

Query: 87  VTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVG 146
           V   + +QQ SH+  VSKNLY ++     +P+G+LD R+GT+QK+  C TCG+ L+DCVG
Sbjct: 22  VLNANDIQQNSHVHCVSKNLYQRESLHKSVPYGVLDNRLGTSQKDKKCETCGKGLTDCVG 81

Query: 147 HFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVR 206
           HFG + L +PVFH+GYF+ V NIL ++CK   CARV+L   + A F   ++ P+ S+L +
Sbjct: 82  HFGQVSLGMPVFHVGYFKAVYNILHTVCK--MCARVMLPPPERARFLDMVQRPSTSFLTK 139

Query: 207 KSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNE 266
           KSL KKI+E  +K + CP CG +NG VKKCGLLK  +E+YK   KK + +++DL  +Y E
Sbjct: 140 KSLHKKIVEICRKQASCPFCGVVNGQVKKCGLLKFVYERYKAH-KKNEGVIKDLQDDYQE 198

Query: 267 AVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVP 326
           A  +N EI++         LNPL V  L   IP ED+PLLLMN    +P DL+LT + VP
Sbjct: 199 ARSYNNEIDSVINKVTSDILNPLVVRDLLRRIPDEDVPLLLMNTRCGRPEDLVLTHIPVP 258

Query: 327 PNCIRPSVISDLKS 340
           P CIRPSV+S LK+
Sbjct: 259 PLCIRPSVVSALKA 272



 Score =  116 bits (290), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 54/65 (83%), Positives = 59/65 (90%), Gaps = 1/65 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV++SF+SGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 
Sbjct: 824 DRSPQARGFVEDSFYSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCC 883

Query: 666 QYDMS 670
            YD S
Sbjct: 884 HYDRS 888



 Score = 77.4 bits (189), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 45/55 (81%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           +LM  ++NLVTPRNGE LIAA QDFITGGYL+TQK+ F +R +  ++AS ++AG+
Sbjct: 521 ILMGTRANLVTPRNGEPLIAAIQDFITGGYLITQKDVFLDRIKACQLASCMLAGK 575



 Score = 70.1 bits (170), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 34/60 (56%), Positives = 41/60 (68%), Gaps = 1/60 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP-RSEPVPRTLLFDNPEFH 726
            D  FDAA+YGQTD ISGVSE II+G+PM +GTG   L+  V  +    PR L+FD  EFH
Sbjct: 1325 DHLFDAAYYGQTDEISGVSESIILGVPMAIGTGFFDLVHKVDWQPLAAPRKLIFDRSEFH 1384


>gi|410216326|gb|JAA05382.1| polymerase (RNA) III (DNA directed) polypeptide A, 155kDa [Pan
            troglodytes]
 gi|410254866|gb|JAA15400.1| polymerase (RNA) III (DNA directed) polypeptide A, 155kDa [Pan
            troglodytes]
 gi|410296284|gb|JAA26742.1| polymerase (RNA) III (DNA directed) polypeptide A, 155kDa [Pan
            troglodytes]
 gi|410329457|gb|JAA33675.1| polymerase (RNA) III (DNA directed) polypeptide A, 155kDa [Pan
            troglodytes]
          Length = 1390

 Score =  362 bits (928), Expect = 1e-96,   Method: Compositional matrix adjust.
 Identities = 212/479 (44%), Positives = 286/479 (59%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A     S+P+LS  E++  +   +   EFL    ++F+++IKKF
Sbjct: 914  GKDEPLEFKRVLDNIKAVFPCPSEPALSKNELILTTESIMKKSEFLC-CQDSFLQEIKKF 972

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 973  IKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQVEKFLETCRDKYMRAQ 1026

Query: 1115 IEP--------ATAVGALAAQ----------------SIGEPGTQMTLKTFH-------- 1142
            +EP        A ++G    Q                ++G P  +  +            
Sbjct: 1027 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1086

Query: 1143 ----------------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                                    GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1087 AQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1146

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C  + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1147 ETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPE 1206

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+T
Sbjct: 1207 VSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAARTT 1266

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1267 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1326

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1327 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPNPPKRPLIFDTNEFH 1385



 Score =  345 bits (886), Expect = 8e-92,   Method: Compositional matrix adjust.
 Identities = 169/280 (60%), Positives = 207/280 (73%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDVVLFNRQPSLHKLSIMAHLARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++       G  ++   R   P + ++   +WTGKQIFS+IL+P+ D PV 
Sbjct: 562 AKACQIIASILV------GKDEKIKVRLPPPTI-LKPVTLWTGKQIFSVILRPSDDNPVR 614

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DSYV ++NSEL++GSMDK TLGSG K N+FYILLRD+G++
Sbjct: 615 ANLRTKGKQYCGKGEDLCANDSYVTIQNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQN 674

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 675 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 714



 Score =  299 bits (765), Expect = 9e-78,   Method: Compositional matrix adjust.
 Identities = 145/251 (57%), Positives = 181/251 (72%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD Q  P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNQHAPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYFR VI ILQ ICK  TC  ++L +E+   F   L+ P L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFRAVIGILQMICK--TCCHIMLSQEEKKQFLDYLKRPGLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K ++C HCG  NG VKKCGLLKI HEKYK   K  D IV + L  +  A++ 
Sbjct: 144 KKISDKCRKKNICHHCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPIVSNFLQSFETAIEH 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP ED+PLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NKEVEPL--LGRAQENLNPLVVLNLFKRIPAEDVPLLLMNPEAGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 262 IRPSVVSDLKS 272



 Score =  290 bits (742), Expect = 4e-75,   Method: Compositional matrix adjust.
 Identities = 147/237 (62%), Positives = 186/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LDKD D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1066 GVPRIKEIINASKAISTPIITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 1125

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  C  + R   G + V G + + + P+++SKS  
Sbjct: 1126 CFILVKLSLERIRLLRLEVNAETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSM 1185

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG +
Sbjct: 1186 YYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTR 1245

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1246 TTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1302



 Score =  116 bits (291), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 830 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 889



 Score = 82.0 bits (201), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1326 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPNPPKRPLIFDTNEFH 1385

Query: 727  FPQV 730
             P V
Sbjct: 1386 IPLV 1389



 Score = 74.7 bits (182), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 521 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 575


>gi|321473486|gb|EFX84453.1| hypothetical protein DAPPUDRAFT_209553 [Daphnia pulex]
          Length = 1387

 Score =  362 bits (928), Expect = 1e-96,   Method: Compositional matrix adjust.
 Identities = 171/277 (61%), Positives = 213/277 (76%), Gaps = 22/277 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIM HRAK+LPHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DEDIVLFNRQPSLHKLSIMCHRAKILPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA               +LM NK NLVTPRNGELLIAA QDFITG YLLT K+AFF+R
Sbjct: 516 RAEAW--------------ILMGNKYNLVTPRNGELLIAAIQDFITGAYLLTLKDAFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+T ++ ++++A   ++  +IK        P    + A +W+GKQIFSLIL+PN    + 
Sbjct: 562 AKTCQMVASMLAG-DEVNMVIK------LPPPCIQKPAALWSGKQIFSLILRPNPGDRIK 614

Query: 521 ANLKTKGRAYT-ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            NL+TKG+ Y+  NEEFC  D ++++RNSE+LAG +DKST+GSG K N+FY+LLRD+GED
Sbjct: 615 VNLRTKGKEYSKKNEEFCVNDGFLLVRNSEVLAGCVDKSTIGSGSKINIFYVLLRDYGED 674

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
            A+ AMW+L R+ S+Y+MNRGFSIGIGDVTPG+  ++
Sbjct: 675 FAIQAMWKLCRVASYYMMNRGFSIGIGDVTPGKTLLK 711



 Score =  333 bits (853), Expect = 6e-88,   Method: Compositional matrix adjust.
 Identities = 207/477 (43%), Positives = 274/477 (57%), Gaps = 73/477 (15%)

Query: 1001 PVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEF 1060
            PV+ +R LD I A +    +  L   E+    N  +D+  F +    +F  +++ FLE  
Sbjct: 918  PVDFQRALDHIKAASPYPDEDPLDDIELQQAFNTIMDTDSF-KTLGIDFKHELRVFLESQ 976

Query: 1061 SKK-ESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEAC---REKYVRAQIE 1116
             K+ +SV        +PL   +  H ++I  G+           E C   +EKY RA+IE
Sbjct: 977  VKRIKSVRKIFQMEGRPL-HPVEKHLERITVGQ---------LVEFCDFSKEKYERAKIE 1026

Query: 1117 PATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYIEEVFVPDDSFI 1162
            P TAVGAL AQSIGEPGTQMTLKTFHFAG              E+    + +  P  S  
Sbjct: 1027 PGTAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIINASKAISTPVISTQ 1086

Query: 1163 LIK----------------------------------------LDMDRIRLLHLEVDIDS 1182
            L+K                                        LDM+RIRLL LEVD  S
Sbjct: 1087 LLKDDDPEYARRVKGRIEKTTLGEVTEYFEEVYLPDDCFLLIKLDMNRIRLLKLEVDASS 1146

Query: 1183 IRY--CIERTRGISGHLTVSGHSFLILKPKDSSK-SFNSKMYQMKQLLPSVVIKGVQGIN 1239
            IR+  C  + +     + V   + + +KP  S+K S    M  +K+ LP VVIKG+  ++
Sbjct: 1147 IRWSLCTGKLKIKPNFVVVVSETIITVKPAPSAKSSMYHVMQHLKEELPKVVIKGLPTVS 1206

Query: 1240 RAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIM 1299
            RAVI+ +D     +Y LLVEGDN+R+VMATYGV+G   +SNN  EV+ TLGIEAA++TI 
Sbjct: 1207 RAVINIDDTRKPPRYYLLVEGDNMREVMATYGVQGSSTTSNNILEVFSTLGIEAAKATIA 1266

Query: 1300 TEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHL 1359
             EI+  ME+HGMS+D RH  L++DLM+ +GE+LGITR+GLAKMKESVL LASFE TSDHL
Sbjct: 1267 KEIQFTMESHGMSVDRRHVALLSDLMSCRGEILGITRNGLAKMKESVLMLASFERTSDHL 1326

Query: 1360 FDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPV-PRTLLFDNPEFH 1415
            FDAA+YGQ D ++GVSECIIMG+PM +GTG  KLL    + +P  P  L+FD PE+H
Sbjct: 1327 FDAAYYGQEDEVTGVSECIIMGIPMAIGTGAFKLLYKTGKKDPPKPVPLIFDVPEYH 1383



 Score =  295 bits (756), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 140/240 (58%), Positives = 180/240 (75%), Gaps = 3/240 (1%)

Query: 101 IVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHI 160
           +V+K LY +D  RTP+ +G+LDRRMG + K+A C TCG+ L +CVGHFGYIDL LPVFH+
Sbjct: 36  VVAKELYNRDSSRTPVQYGMLDRRMGMSVKDALCGTCGKGLDECVGHFGYIDLELPVFHV 95

Query: 161 GYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKV 220
           GYF+  I +LQ+ICK  TC+  LL ++    +RAKLRNP L YL +K+L+K+I E  KKV
Sbjct: 96  GYFKATITVLQTICK--TCSHALLNDKMRKIYRAKLRNPNLPYLTKKALRKQIQEVCKKV 153

Query: 221 SVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKF 280
           + CPHC +INGVVKKCG+LKISHEK+++  KK + I++  L  Y+ AV+FN EIE     
Sbjct: 154 TRCPHCNDINGVVKKCGMLKISHEKFRS-VKKDNTIIKAELVAYDNAVQFNKEIEPMLSC 212

Query: 281 GLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKS 340
           GLI+ LNP+EVL LFE IP ED+  LLMN +   P D+ILTR+ VPP CIRPSV+SDLKS
Sbjct: 213 GLIKMLNPIEVLHLFERIPDEDVQFLLMNPQHGHPKDMILTRVPVPPVCIRPSVVSDLKS 272



 Score =  259 bits (661), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 133/237 (56%), Positives = 174/237 (73%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+I+  L KD D +YAR VKGR+E+TTLGEV EY EEV++PDD
Sbjct: 1064 GVPRIKEIINASKAISTPVISTQLLKDDDPEYARRVKGRIEKTTLGEVTEYFEEVYLPDD 1123

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKS-F 880
             F+LIKLDM+RIRLL LEVD  SIR+  C  + +     + V   + + +KP  S+KS  
Sbjct: 1124 CFLLIKLDMNRIRLLKLEVDASSIRWSLCTGKLKIKPNFVVVVSETIITVKPAPSAKSSM 1183

Query: 881  NSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
               M  +K+ LP VVIKG+  ++RAVI+ +D     +Y LLVEGDN+R+VMATYGV+G  
Sbjct: 1184 YHVMQHLKEELPKVVIKGLPTVSRAVINIDDTRKPPRYYLLVEGDNMREVMATYGVQGSS 1243

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNN  EV+ TLGIEAA++TI  EI+  ME+HGMS+D RH  L++DLM+ +GE+LG
Sbjct: 1244 TTSNNILEVFSTLGIEAAKATIAKEIQFTMESHGMSVDRRHVALLSDLMSCRGEILG 1300



 Score =  118 bits (296), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 53/61 (86%), Positives = 56/61 (91%)

Query: 608 VTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           +   +GFV NSF+SGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC QY
Sbjct: 827 IPAAKGFVSNSFYSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCCQY 886

Query: 668 D 668
           D
Sbjct: 887 D 887



 Score = 85.1 bits (209), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 40/64 (62%), Positives = 51/64 (79%), Gaps = 1/64 (1%)

Query: 14  ATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIA 73
           A    W +LM NK NLVTPRNGELLIAA QDFITG YLLT K+AFF+RA+T ++ ++++A
Sbjct: 515 ARAEAW-ILMGNKYNLVTPRNGELLIAAIQDFITGAYLLTLKDAFFDRAKTCQMVASMLA 573

Query: 74  GRKV 77
           G +V
Sbjct: 574 GDEV 577



 Score = 78.6 bits (192), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 36/64 (56%), Positives = 45/64 (70%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPV-PRTLLFDNPEFH 726
            D  FDAA+YGQ D ++GVSECIIMG+PM +GTG  KLL    + +P  P  L+FD PE+H
Sbjct: 1324 DHLFDAAYYGQEDEVTGVSECIIMGIPMAIGTGAFKLLYKTGKKDPPKPVPLIFDVPEYH 1383

Query: 727  FPQV 730
             P V
Sbjct: 1384 VPMV 1387


>gi|403297971|ref|XP_003939815.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1 [Saimiri
            boliviensis boliviensis]
          Length = 1390

 Score =  362 bits (928), Expect = 1e-96,   Method: Compositional matrix adjust.
 Identities = 212/479 (44%), Positives = 286/479 (59%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A     S+P+LS  E++  +   +   EFL    ++F+++IKKF
Sbjct: 914  GKDEPLEFKRVLDNIKAVFPCPSEPALSKNELILTTESIMKKSEFLC-CQDSFLQEIKKF 972

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 973  IKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQVEKFLETCRDKYMRAQ 1026

Query: 1115 IEP--------ATAVGALAAQ----------------SIGEPGTQMTLKTFH-------- 1142
            +EP        A ++G    Q                ++G P  +  +            
Sbjct: 1027 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1086

Query: 1143 ----------------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                                    GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1087 AQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1146

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C  + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1147 ETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPE 1206

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+T
Sbjct: 1207 VSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAARTT 1266

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1267 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1326

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1327 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKANRDPNPPKRPLIFDTNEFH 1385



 Score =  345 bits (886), Expect = 8e-92,   Method: Compositional matrix adjust.
 Identities = 169/280 (60%), Positives = 207/280 (73%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDVVLFNRQPSLHKLSIMAHLARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++       G  ++   R   P + ++   +WTGKQIFS+IL+P+ D PV 
Sbjct: 562 AKACQIIASILV------GKDEKIKVRLPPPTI-LKPVTLWTGKQIFSVILRPSDDNPVR 614

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DSYV ++NSEL++GSMDK TLGSG K N+FYILLRD+G++
Sbjct: 615 ANLRTKGKQYCGKGEDLCANDSYVTIQNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQN 674

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 675 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 714



 Score =  299 bits (765), Expect = 9e-78,   Method: Compositional matrix adjust.
 Identities = 145/251 (57%), Positives = 181/251 (72%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD Q  P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNQHAPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYFR VI ILQ ICK  TC  ++L +E+   F   L+ P L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFRAVIGILQMICK--TCCHIMLSQEEKKQFLDYLKRPGLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K ++C HCG  NG VKKCGLLKI HEKYK   K  D IV + L  +  A++ 
Sbjct: 144 KKISDKCRKKNICHHCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPIVSNFLQSFETAIEH 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP ED+PLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NKEVEPL--LGRAQENLNPLVVLNLFKRIPAEDVPLLLMNPEAGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 262 IRPSVVSDLKS 272



 Score =  290 bits (742), Expect = 4e-75,   Method: Compositional matrix adjust.
 Identities = 147/237 (62%), Positives = 186/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LDKD D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1066 GVPRIKEIINASKAISTPIITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 1125

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  C  + R   G + V G + + + P+++SKS  
Sbjct: 1126 CFILVKLSLERIRLLRLEVNAETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSM 1185

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG +
Sbjct: 1186 YYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTR 1245

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1246 TTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1302



 Score =  116 bits (291), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 830 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 889



 Score = 81.6 bits (200), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1326 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKANRDPNPPKRPLIFDTNEFH 1385

Query: 727  FPQV 730
             P V
Sbjct: 1386 IPLV 1389



 Score = 74.7 bits (182), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 521 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 575


>gi|39725938|ref|NP_008986.2| DNA-directed RNA polymerase III subunit RPC1 [Homo sapiens]
 gi|206729892|sp|O14802.2|RPC1_HUMAN RecName: Full=DNA-directed RNA polymerase III subunit RPC1; Short=RNA
            polymerase III subunit C1; AltName: Full=DNA-directed RNA
            polymerase III largest subunit; AltName:
            Full=DNA-directed RNA polymerase III subunit A; AltName:
            Full=RNA polymerase III 155 kDa subunit; Short=RPC155;
            AltName: Full=RNA polymerase III subunit C160
 gi|26996801|gb|AAH41089.1| Polymerase (RNA) III (DNA directed) polypeptide A, 155kDa [Homo
            sapiens]
 gi|119575002|gb|EAW54617.1| polymerase (RNA) III (DNA directed) polypeptide A, 155kDa [Homo
            sapiens]
 gi|168277638|dbj|BAG10797.1| DNA-directed RNA polymerase III subunit RPC1 [synthetic construct]
          Length = 1390

 Score =  362 bits (928), Expect = 1e-96,   Method: Compositional matrix adjust.
 Identities = 212/479 (44%), Positives = 286/479 (59%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A     S+P+LS  E++  +   +   EFL    ++F+++IKKF
Sbjct: 914  GKDEPLEFKRVLDNIKAVFPCPSEPALSKNELILTTESIMKKSEFLC-CQDSFLQEIKKF 972

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 973  IKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQVEKFLETCRDKYMRAQ 1026

Query: 1115 IEP--------ATAVGALAAQ----------------SIGEPGTQMTLKTFH-------- 1142
            +EP        A ++G    Q                ++G P  +  +            
Sbjct: 1027 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1086

Query: 1143 ----------------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                                    GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1087 AQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1146

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C  + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1147 ETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPE 1206

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+T
Sbjct: 1207 VSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAARTT 1266

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1267 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1326

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1327 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPNPPKRPLIFDTNEFH 1385



 Score =  345 bits (886), Expect = 9e-92,   Method: Compositional matrix adjust.
 Identities = 169/280 (60%), Positives = 207/280 (73%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDVVLFNRQPSLHKLSIMAHLARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++       G  ++   R   P + ++   +WTGKQIFS+IL+P+ D PV 
Sbjct: 562 AKACQIIASILV------GKDEKIKVRLPPPTI-LKPVTLWTGKQIFSVILRPSDDNPVR 614

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DSYV ++NSEL++GSMDK TLGSG K N+FYILLRD+G++
Sbjct: 615 ANLRTKGKQYCGKGEDLCANDSYVTIQNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQN 674

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 675 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 714



 Score =  299 bits (765), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 145/251 (57%), Positives = 181/251 (72%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD Q  P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNQHAPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYFR VI ILQ ICK  TC  ++L +E+   F   L+ P L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFRAVIGILQMICK--TCCHIMLSQEEKKQFLDYLKRPGLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K ++C HCG  NG VKKCGLLKI HEKYK   K  D IV + L  +  A++ 
Sbjct: 144 KKISDKCRKKNICHHCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPIVSNFLQSFETAIEH 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP ED+PLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NKEVEPL--LGRAQENLNPLVVLNLFKRIPAEDVPLLLMNPEAGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 262 IRPSVVSDLKS 272



 Score =  290 bits (742), Expect = 4e-75,   Method: Compositional matrix adjust.
 Identities = 147/237 (62%), Positives = 186/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LDKD D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1066 GVPRIKEIINASKAISTPIITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 1125

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  C  + R   G + V G + + + P+++SKS  
Sbjct: 1126 CFILVKLSLERIRLLRLEVNAETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSM 1185

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG +
Sbjct: 1186 YYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTR 1245

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1246 TTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1302



 Score =  116 bits (291), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 830 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 889



 Score = 82.0 bits (201), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1326 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPNPPKRPLIFDTNEFH 1385

Query: 727  FPQV 730
             P V
Sbjct: 1386 IPLV 1389



 Score = 74.7 bits (182), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 521 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 575


>gi|355562468|gb|EHH19062.1| hypothetical protein EGK_19701 [Macaca mulatta]
 gi|355782811|gb|EHH64732.1| hypothetical protein EGM_18035 [Macaca fascicularis]
 gi|380809180|gb|AFE76465.1| DNA-directed RNA polymerase III subunit RPC1 [Macaca mulatta]
 gi|383415455|gb|AFH30941.1| DNA-directed RNA polymerase III subunit RPC1 [Macaca mulatta]
 gi|383415457|gb|AFH30942.1| DNA-directed RNA polymerase III subunit RPC1 [Macaca mulatta]
 gi|383415459|gb|AFH30943.1| DNA-directed RNA polymerase III subunit RPC1 [Macaca mulatta]
 gi|383415461|gb|AFH30944.1| DNA-directed RNA polymerase III subunit RPC1 [Macaca mulatta]
 gi|383415463|gb|AFH30945.1| DNA-directed RNA polymerase III subunit RPC1 [Macaca mulatta]
          Length = 1390

 Score =  361 bits (927), Expect = 1e-96,   Method: Compositional matrix adjust.
 Identities = 212/479 (44%), Positives = 286/479 (59%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A     S+P+LS  E++  +   +   EFL    ++F+++IKKF
Sbjct: 914  GKDEPLEFKRVLDNIKAVFPCPSEPALSKNELILTTESIMKKSEFLC-CQDSFLQEIKKF 972

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 973  IKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQVEKFLETCRDKYMRAQ 1026

Query: 1115 IEP--------ATAVGALAAQ----------------SIGEPGTQMTLKTFH-------- 1142
            +EP        A ++G    Q                ++G P  +  +            
Sbjct: 1027 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1086

Query: 1143 ----------------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                                    GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1087 AQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1146

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C  + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1147 ETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPE 1206

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+T
Sbjct: 1207 VSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAARTT 1266

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1267 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1326

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1327 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPNPPKRPLIFDTNEFH 1385



 Score =  345 bits (886), Expect = 8e-92,   Method: Compositional matrix adjust.
 Identities = 169/280 (60%), Positives = 207/280 (73%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDVVLFNRQPSLHKLSIMAHLARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++       G  ++   R   P + ++   +WTGKQIFS+IL+P+ D PV 
Sbjct: 562 AKACQIIASILV------GKDEKIKVRLPPPTI-LKPVTLWTGKQIFSVILRPSDDNPVR 614

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DSYV ++NSEL++GSMDK TLGSG K N+FYILLRD+G++
Sbjct: 615 ANLRTKGKQYCGKGEDLCANDSYVTIQNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQN 674

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 675 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 714



 Score =  299 bits (765), Expect = 8e-78,   Method: Compositional matrix adjust.
 Identities = 145/251 (57%), Positives = 181/251 (72%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD Q  P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNQHAPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYFR VI ILQ ICK  TC  ++L +E+   F   L+ P L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFRAVIGILQMICK--TCCHIMLSQEEKKQFLDYLKRPGLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K ++C HCG  NG VKKCGLLKI HEKYK   K  D IV + L  +  A++ 
Sbjct: 144 KKISDKCRKKNICHHCGSFNGTVKKCGLLKIIHEKYKTNKKVVDPIVSNFLQSFETAIEH 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP ED+PLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NKEVEPL--LGRAQENLNPLVVLNLFKRIPAEDVPLLLMNPEAGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 262 IRPSVVSDLKS 272



 Score =  290 bits (742), Expect = 4e-75,   Method: Compositional matrix adjust.
 Identities = 147/237 (62%), Positives = 186/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LDKD D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1066 GVPRIKEIINASKAISTPIITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 1125

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  C  + R   G + V G + + + P+++SKS  
Sbjct: 1126 CFILVKLSLERIRLLRLEVNAETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSM 1185

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG +
Sbjct: 1186 YYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTR 1245

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1246 TTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1302



 Score =  116 bits (291), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 830 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 889



 Score = 82.0 bits (201), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1326 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPNPPKRPLIFDTNEFH 1385

Query: 727  FPQV 730
             P V
Sbjct: 1386 IPLV 1389



 Score = 74.7 bits (182), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 521 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 575


>gi|321473720|gb|EFX84687.1| hypothetical protein DAPPUDRAFT_222950 [Daphnia pulex]
          Length = 1387

 Score =  361 bits (927), Expect = 1e-96,   Method: Compositional matrix adjust.
 Identities = 171/277 (61%), Positives = 213/277 (76%), Gaps = 22/277 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIM HRAK+LPHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DEDIVLFNRQPSLHKLSIMCHRAKILPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA               +LM NK NLVTPRNGELLIAA QDFITG YLLT K+AFF+R
Sbjct: 516 RAEAW--------------ILMGNKFNLVTPRNGELLIAAIQDFITGAYLLTLKDAFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+T ++ ++++A   ++  +IK        P    + A +W+GKQIFSLIL+PN    + 
Sbjct: 562 AKTCQMVASMLAG-DEVNMVIK------LPPPCIQKPAALWSGKQIFSLILRPNPGDRIK 614

Query: 521 ANLKTKGRAYT-ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            NL+TKG+ Y+  NEEFC  D ++++RNSE+LAG +DKST+GSG K N+FY+LLRD+GED
Sbjct: 615 VNLRTKGKEYSKKNEEFCVNDGFLLVRNSEVLAGCVDKSTIGSGSKINIFYVLLRDYGED 674

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
            A+ AMW+L R+ S+Y+MNRGFSIGIGDVTPG+  ++
Sbjct: 675 FAIQAMWKLCRVASYYMMNRGFSIGIGDVTPGKTLLK 711



 Score =  337 bits (865), Expect = 2e-89,   Method: Compositional matrix adjust.
 Identities = 209/480 (43%), Positives = 275/480 (57%), Gaps = 71/480 (14%)

Query: 1001 PVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEF 1060
            PV+ +R LD I A +    +  L   E+    N  +D+  F +    +F  +++ F+E  
Sbjct: 918  PVDFQRALDHIKAASPYPDEEPLDDIELQQAFNTIMDTDSF-KMLGVDFQHELRVFVESQ 976

Query: 1061 SKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEAC---REKYVRAQIEP 1117
             K+        K+      ++  H ++I  G+           E C   +EKY RA+IEP
Sbjct: 977  VKRIKKVRQLFKMEGRSLLRVEKHLERITVGQ---------LVEFCDFSKEKYERAKIEP 1027

Query: 1118 ATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYIEEVFVPDDSFIL 1163
             TAVGAL AQSIGEPGTQMTLKTFHFAG              E+    + +  P  S  L
Sbjct: 1028 GTAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIINASKAISTPVISTQL 1087

Query: 1164 IK----------------------------------------LDMDRIRLLHLEVDIDSI 1183
            +K                                        LDM+RIRLL LEVD +SI
Sbjct: 1088 LKDDDPEYARRVKGRIEKTTLGEVTEYFEEVYLPDDCFMLIKLDMNRIRLLKLEVDANSI 1147

Query: 1184 RY--CIERTRGISGHLTVSGHSFLILKPKDSSK-SFNSKMYQMKQLLPSVVIKGVQGINR 1240
            ++  C  + +     + V   + +I+KP  SSK S    M  +K+ LP VVIKG+  ++R
Sbjct: 1148 QWSLCTCKLKIKPSFIKVISETIVIVKPAPSSKSSMYHVMQHLKETLPRVVIKGLPTVSR 1207

Query: 1241 AVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMT 1300
            AVI+ +D     +Y LLVEGDN+R+VMATYGVKG   +SNN  EVY TLGIEAA++TI  
Sbjct: 1208 AVINIDDTRKPPRYYLLVEGDNMREVMATYGVKGTSTTSNNILEVYTTLGIEAAKATIAK 1267

Query: 1301 EIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLF 1360
            EI+  ME+HGMS+D RH  L++DLM+ +GE+LGITRHGLAKMKESVL LASFE TSDHLF
Sbjct: 1268 EIQYTMESHGMSVDRRHVALLSDLMSCRGEILGITRHGLAKMKESVLMLASFERTSDHLF 1327

Query: 1361 DAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFHTNTL 1419
            DA++YGQ D I+GVSECIIMG+PM++GTG  KLL    +S  P  R L+FD PE+H   L
Sbjct: 1328 DASYYGQEDEITGVSECIIMGIPMSIGTGAFKLLYKTGKSVPPKTRPLIFDLPEYHVPML 1387



 Score =  291 bits (745), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 151/304 (49%), Positives = 206/304 (67%), Gaps = 17/304 (5%)

Query: 101 IVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHI 160
           +V++NLY +D  RTP+ +G+LDRRMG + K+A C TCG+ L++CVGHFGYIDL LPVFH+
Sbjct: 36  VVAQNLYNRDAGRTPMQYGMLDRRMGMSVKDAICATCGKGLTECVGHFGYIDLELPVFHV 95

Query: 161 GYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKV 220
           GYF+ VI ILQ+ICK  +C+ V+L E+    +RAKL+ P + YL +K+L+K+I E  KKV
Sbjct: 96  GYFKAVITILQTICK--SCSHVMLNEKMRKIYRAKLKGPKIPYLNKKALRKQIQEACKKV 153

Query: 221 SVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKF 280
           + CP+C +ING+VKKCG+LKISHEK+++  KK + I+++ L  Y  AV+FN EIE     
Sbjct: 154 TRCPNCNDINGMVKKCGMLKISHEKFRS-IKKDNVILKNELVAYENAVQFNKEIEPMLSS 212

Query: 281 GLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKS 340
           GLI+ LNPLEVL LFE IP ED+  L+MN E   P D+ILTR+ VPP CIRPSV+SDLKS
Sbjct: 213 GLIKMLNPLEVLHLFERIPDEDVQFLVMNPEHGHPKDMILTRVPVPPVCIRPSVVSDLKS 272

Query: 341 D----------NDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPY-NADFDGDE 389
                       ++V  N     H+LS  A    +L    + F +  C  Y N++  G  
Sbjct: 273 GTNEDDLTMKLTEIVFLNDVIVKHRLS-GAKSQMIL--EDWDFLQLQCALYINSELSGIP 329

Query: 390 MNVH 393
           +N+ 
Sbjct: 330 LNMQ 333



 Score =  262 bits (670), Expect = 8e-67,   Method: Compositional matrix adjust.
 Identities = 136/237 (57%), Positives = 176/237 (74%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+I+  L KD D +YAR VKGR+E+TTLGEV EY EEV++PDD
Sbjct: 1064 GVPRIKEIINASKAISTPVISTQLLKDDDPEYARRVKGRIEKTTLGEVTEYFEEVYLPDD 1123

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKS-F 880
             F+LIKLDM+RIRLL LEVD +SI++  C  + +     + V   + +I+KP  SSKS  
Sbjct: 1124 CFMLIKLDMNRIRLLKLEVDANSIQWSLCTCKLKIKPSFIKVISETIVIVKPAPSSKSSM 1183

Query: 881  NSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
               M  +K+ LP VVIKG+  ++RAVI+ +D     +Y LLVEGDN+R+VMATYGVKG  
Sbjct: 1184 YHVMQHLKETLPRVVIKGLPTVSRAVINIDDTRKPPRYYLLVEGDNMREVMATYGVKGTS 1243

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNN  EVY TLGIEAA++TI  EI+  ME+HGMS+D RH  L++DLM+ +GE+LG
Sbjct: 1244 TTSNNILEVYTTLGIEAAKATIAKEIQYTMESHGMSVDRRHVALLSDLMSCRGEILG 1300



 Score =  118 bits (296), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 53/61 (86%), Positives = 56/61 (91%)

Query: 608 VTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           +   +GFV NSF+SGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC QY
Sbjct: 827 IPAAKGFVSNSFYSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCCQY 886

Query: 668 D 668
           D
Sbjct: 887 D 887



 Score = 84.7 bits (208), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 40/64 (62%), Positives = 51/64 (79%), Gaps = 1/64 (1%)

Query: 14  ATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIA 73
           A    W +LM NK NLVTPRNGELLIAA QDFITG YLLT K+AFF+RA+T ++ ++++A
Sbjct: 515 ARAEAW-ILMGNKFNLVTPRNGELLIAAIQDFITGAYLLTLKDAFFDRAKTCQMVASMLA 573

Query: 74  GRKV 77
           G +V
Sbjct: 574 GDEV 577



 Score = 77.4 bits (189), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 36/64 (56%), Positives = 46/64 (71%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
            D  FDA++YGQ D I+GVSECIIMG+PM++GTG  KLL    +S  P  R L+FD PE+H
Sbjct: 1324 DHLFDASYYGQEDEITGVSECIIMGIPMSIGTGAFKLLYKTGKSVPPKTRPLIFDLPEYH 1383

Query: 727  FPQV 730
             P +
Sbjct: 1384 VPML 1387


>gi|301765986|ref|XP_002918413.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1-like
            [Ailuropoda melanoleuca]
          Length = 1390

 Score =  361 bits (926), Expect = 2e-96,   Method: Compositional matrix adjust.
 Identities = 211/479 (44%), Positives = 287/479 (59%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A    +S+P+LS  E++  +   +   EFL    ++F+++IK F
Sbjct: 914  GKDEPLEFKRVLDNIKAVFPCQSEPALSKNELVLTTESIMKKTEFLC-CQDSFLQEIKNF 972

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 973  VKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQIEKFLETCRDKYMRAQ 1026

Query: 1115 IEP--------ATAVGALAAQ----------------SIGEPGTQMTLKTFH-------- 1142
            +EP        A ++G    Q                ++G P  +  +            
Sbjct: 1027 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1086

Query: 1143 ----------------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                                    GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1087 AQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1146

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C+ + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1147 ETVRYSICMSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPE 1206

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+T
Sbjct: 1207 VSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAARTT 1266

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1267 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1326

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP-RTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R    P R L+FD  EFH
Sbjct: 1327 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPSPPRRPLIFDTSEFH 1385



 Score =  345 bits (885), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 168/280 (60%), Positives = 203/280 (72%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH AKV PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDVVLFNRQPSLHKLSIMAHLAKVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++    +   +          P   ++   +WTGKQIFS+IL+P+ D PV 
Sbjct: 562 AKACQIIASILVGKDEKIKV-------HLPPPTILKPVTLWTGKQIFSVILRPSDDNPVR 614

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DSYV ++NSEL++GSMDK TLGSG K N+FYILLRD+G+ 
Sbjct: 615 ANLRTKGKQYCGKGEDLCVNDSYVTIQNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQS 674

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 675 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 714



 Score =  293 bits (751), Expect = 3e-76,   Method: Compositional matrix adjust.
 Identities = 143/251 (56%), Positives = 179/251 (71%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD    P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNNHAPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYFR VI ILQ ICK  TC  ++L  E+   F   L+ P L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFRAVIGILQMICK--TCCHIMLSHEEKKQFLDYLKRPGLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K ++C +CG  NG VKKCGLLKI HEKYK   K  D IV + L  +  A++ 
Sbjct: 144 KKISDKCRKKNICHYCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPIVSNFLQSFETAIEH 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP ED+PLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NKEVEP--LLGRAQENLNPLVVLNLFKRIPAEDVPLLLMNPEAGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 262 IRPSVVSDLKS 272



 Score =  291 bits (744), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 147/237 (62%), Positives = 187/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LDKD D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1066 GVPRIKEIINASKAISTPIITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 1125

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  C+ + R   G + V G + + + P+++SKS  
Sbjct: 1126 CFILVKLSLERIRLLRLEVNAETVRYSICMSKLRVKPGDVAVHGEAVVCVTPRENSKSSM 1185

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG +
Sbjct: 1186 YYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTR 1245

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1246 TTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1302



 Score =  116 bits (291), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 830 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 889



 Score = 82.4 bits (202), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP-RTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R    P R L+FD  EFH
Sbjct: 1326 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPSPPRRPLIFDTSEFH 1385

Query: 727  FPQV 730
             P V
Sbjct: 1386 IPLV 1389



 Score = 74.7 bits (182), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 521 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 575


>gi|332024635|gb|EGI64832.1| DNA-directed RNA polymerase III subunit RPC1 [Acromyrmex echinatior]
          Length = 1988

 Score =  361 bits (926), Expect = 2e-96,   Method: Compositional matrix adjust.
 Identities = 175/276 (63%), Positives = 207/276 (75%), Gaps = 22/276 (7%)

Query: 341  DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
            D+D+VLFNRQPSLHKLSIM HR KVL HRTFRFNECVC PYNADFDGDEMN+HLPQTEEA
Sbjct: 1067 DDDLVLFNRQPSLHKLSIMTHRTKVLEHRTFRFNECVCAPYNADFDGDEMNLHLPQTEEA 1126

Query: 401  RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
            RAEAL              VL+ANKSNLVTPRNG+LLIAATQDFITG YLLTQK+ F   
Sbjct: 1127 RAEAL--------------VLLANKSNLVTPRNGDLLIAATQDFITGAYLLTQKDTFLQI 1172

Query: 461  AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
             Q  R+A  L+A +     +       +  P   ++ A +WTGKQIFSLI++PN++C V 
Sbjct: 1173 EQA-RLALCLLAGSDASMKV-------TLPPPAIIKPARLWTGKQIFSLIIRPNKECSVK 1224

Query: 521  ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            ANLK KG+ YT  +EFC  DSYVI+RNSELLAG+MDKS LGSG K N+FYILLRD+GEDV
Sbjct: 1225 ANLKAKGKTYTNGKEFCINDSYVIIRNSELLAGTMDKSILGSGSKQNIFYILLRDWGEDV 1284

Query: 581  AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
            A  AMWRL+R+T+ +   RG S+GIGD+ P QG ++
Sbjct: 1285 ATAAMWRLTRITNHFNFERGISLGIGDLIPSQGLLR 1320



 Score =  310 bits (794), Expect = 4e-81,   Method: Compositional matrix adjust.
 Identities = 194/467 (41%), Positives = 270/467 (57%), Gaps = 83/467 (17%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   PV+ +R+ + + AK    ++  L    ++  + E L S+E+ +  SE F  ++  F
Sbjct: 1523 GKDCPVDYERVYEHVRAKMPYITEEPLDYASVINATKEMLRSEEY-ECLSEEFKDELTSF 1581

Query: 1057 LE-EFSKK-----ESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKY 1110
            L+ + ++K     +++ S+    SQ L    +S   +  H               C+EKY
Sbjct: 1582 LKLKVARKIAFYRQNIISNSSVTSQ-LERFTVSQLVEFIH--------------TCKEKY 1626

Query: 1111 VRAQI---------------EPAT----------AVGAL--------------AAQSIGE 1131
            +RA+I               EP T           V A+              A+  I  
Sbjct: 1627 MRAKIEPGTAVGALAAQSIGEPGTQMTLKTFHFAGVAAMNITQGVPRIKEIINASPKIST 1686

Query: 1132 PGTQMTL-----------------KTFHFAGEVCEYIEEVFVPDDSFILIKLDMDRIRLL 1174
            P    TL                 KT    G+V EYIEE+++PDD F++IKLD++RI++L
Sbjct: 1687 PIITATLINDANSEIAEQVKARIEKTT--LGDVSEYIEEIYLPDDHFLIIKLDINRIKML 1744

Query: 1175 HLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDS-SKSFNSKMYQMKQLLPSVV 1231
             LE+D++S+ Y  C  + +  S ++     S +I++P  S  K  N    Q+ + +P+V+
Sbjct: 1745 KLEIDVNSVCYKLCTSKLKLTSKNVEKVTDSVIIIRPNRSKDKDSNFPFRQLTEAIPNVI 1804

Query: 1232 IKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGI 1291
            IKG+  INR V+H E++   +K+ L VEGDN R+VMAT G+ G K  SNNT EV+KTLGI
Sbjct: 1805 IKGLPSINRVVVHNENLGSKSKFTLFVEGDNFREVMATRGILGEKTKSNNTIEVFKTLGI 1864

Query: 1292 EAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLAS 1351
            EAAR+TIM+EIK VMENHG+SID RH ML+ADLMTS+GEVLGITR GLAKMKESVLNLAS
Sbjct: 1865 EAARTTIMSEIKSVMENHGISIDCRHLMLLADLMTSRGEVLGITRQGLAKMKESVLNLAS 1924

Query: 1352 FENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 1398
            FE T+DHLFDAA+YGQ D ISGVSE IIMG+P+ +GTG+ KLL   P
Sbjct: 1925 FEKTADHLFDAAYYGQKDVISGVSESIIMGIPVPLGTGIFKLLHKYP 1971



 Score =  262 bits (670), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 133/237 (56%), Positives = 177/237 (74%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS  ISTPIITA L  D + + A  VK R+E+TTLG+V EYIEE+++PDD
Sbjct: 1670 GVPRIKEIINASPKISTPIITATLINDANSEIAEQVKARIEKTTLGDVSEYIEEIYLPDD 1729

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDS-SKSF 880
             F++IKLD++RI++L LE+D++S+ Y  C  + +  S ++     S +I++P  S  K  
Sbjct: 1730 HFLIIKLDINRIKMLKLEIDVNSVCYKLCTSKLKLTSKNVEKVTDSVIIIRPNRSKDKDS 1789

Query: 881  NSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
            N    Q+ + +P+V+IKG+  INR V+H E++   +K+ L VEGDN R+VMAT G+ G K
Sbjct: 1790 NFPFRQLTEAIPNVIIKGLPSINRVVVHNENLGSKSKFTLFVEGDNFREVMATRGILGEK 1849

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
              SNNT EV+KTLGIEAAR+TIM+EIK VMENHG+SID RH ML+ADLMTS+GEVLG
Sbjct: 1850 TKSNNTIEVFKTLGIEAARTTIMSEIKSVMENHGISIDCRHLMLLADLMTSRGEVLG 1906



 Score =  239 bits (610), Expect = 7e-60,   Method: Compositional matrix adjust.
 Identities = 120/252 (47%), Positives = 164/252 (65%), Gaps = 7/252 (2%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           +  Q+ ++++SKNLY +D + TP   G LDRRMG +     C TC + L+DCVGHFGY++
Sbjct: 637 INMQASVEMISKNLYNEDTKHTPALQGALDRRMGVSSTGVECETCNKKLNDCVGHFGYLN 696

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKK 212
           L LPVFH+GYF+ +I ILQ+ICK  +CA VLL   +   F   ++NP   YL+RK+L+KK
Sbjct: 697 LELPVFHVGYFKSIIQILQTICK--SCAHVLLTHGERKFFSRSIQNPKSGYLMRKALRKK 754

Query: 213 ILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNP 272
           ILE  +K +VCP+C   NG VKK G LKI HEKYKN  KK D I+++ L E    ++ + 
Sbjct: 755 ILEVARKKTVCPNCKSNNGPVKKAGFLKIVHEKYKN-LKKTDPIIQEKLTELTPKIERDT 813

Query: 273 E----IEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPN 328
           E    +E + +    + L P  V +LF  IP  DI  LLMN   + P DL+L R+ VPP 
Sbjct: 814 EFKNIVEQNYRCVFDKYLYPNVVQELFNRIPTGDICFLLMNPGCATPVDLVLRRIPVPPI 873

Query: 329 CIRPSVISDLKS 340
           CIRPS++SDLK+
Sbjct: 874 CIRPSILSDLKA 885



 Score =  109 bits (272), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 46/60 (76%), Positives = 53/60 (88%)

Query: 611  GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
             +GFV+NSF+SGL   EF+FH MGGREGL DTAVKTAETGYMQRRL+KSLEDLC+ YDM+
Sbjct: 1439 AKGFVENSFYSGLVSKEFYFHAMGGREGLTDTAVKTAETGYMQRRLIKSLEDLCIHYDMT 1498



 Score = 77.4 bits (189), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 39/54 (72%), Positives = 44/54 (81%), Gaps = 1/54 (1%)

Query: 21   VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
            VL+ANKSNLVTPRNG+LLIAATQDFITG YLLTQK+ F    Q  R+A  L+AG
Sbjct: 1132 VLLANKSNLVTPRNGDLLIAATQDFITGAYLLTQKDTFLQIEQA-RLALCLLAG 1184



 Score = 61.2 bits (147), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 27/42 (64%), Positives = 32/42 (76%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 709
            D  FDAA+YGQ D ISGVSE IIMG+P+ +GTG+ KLL   P
Sbjct: 1930 DHLFDAAYYGQKDVISGVSESIIMGIPVPLGTGIFKLLHKYP 1971


>gi|73953679|ref|XP_536399.2| PREDICTED: DNA-directed RNA polymerase III subunit RPC1 [Canis lupus
            familiaris]
          Length = 1390

 Score =  361 bits (926), Expect = 2e-96,   Method: Compositional matrix adjust.
 Identities = 211/479 (44%), Positives = 287/479 (59%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A    +S+P+LS  E++  +   +   EFL    ++F+++IK F
Sbjct: 914  GKDEPLEFKRVLDNIKAVFPCQSEPALSKNELVLTTESIMKKTEFLC-CQDSFLQEIKNF 972

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 973  VKGISEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQIEKFLETCRDKYMRAQ 1026

Query: 1115 IEP--------ATAVGALAAQ----------------SIGEPGTQMTLKTFH-------- 1142
            +EP        A ++G    Q                ++G P  +  +            
Sbjct: 1027 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1086

Query: 1143 ----------------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                                    GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1087 AQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1146

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C+ + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1147 ETVRYSICMSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPE 1206

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+T
Sbjct: 1207 VSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAARTT 1266

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1267 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1326

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP-RTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R    P R L+FD  EFH
Sbjct: 1327 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPSPPRRPLIFDTNEFH 1385



 Score =  345 bits (886), Expect = 9e-92,   Method: Compositional matrix adjust.
 Identities = 168/280 (60%), Positives = 204/280 (72%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH AKV PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDVVLFNRQPSLHKLSIMAHLAKVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++    +   +          P   ++   +WTGKQIFS+IL+P+ D PV 
Sbjct: 562 AKACQIIASILVGKDEKIKV-------HLPPPTILKPVTLWTGKQIFSVILRPSDDNPVR 614

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DSYV ++NSEL++GSMDK TLGSG K N+FYILLRD+G++
Sbjct: 615 ANLRTKGKQYCGKGEDLCVNDSYVTIQNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQN 674

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 675 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 714



 Score =  294 bits (753), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 143/251 (56%), Positives = 180/251 (71%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD    P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNNHAPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYFR VI ILQ ICK  TC  ++L +E+   F   L+ P L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFRAVIGILQMICK--TCCHIMLSQEEKKQFLDYLKRPGLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K ++C +CG  NG VKKCGLLKI HEKYK   K  D IV + L  +  A++ 
Sbjct: 144 KKISDKCRKKNICHYCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPIVSNFLQSFETAIEH 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP ED+PLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NKEVEPL--LGRAQENLNPLVVLNLFKRIPAEDVPLLLMNPEAGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 262 IRPSVVSDLKS 272



 Score =  291 bits (744), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 147/237 (62%), Positives = 187/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LDKD D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1066 GVPRIKEIINASKAISTPIITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 1125

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  C+ + R   G + V G + + + P+++SKS  
Sbjct: 1126 CFILVKLSLERIRLLRLEVNAETVRYSICMSKLRVKPGDVAVHGEAVVCVTPRENSKSSM 1185

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG +
Sbjct: 1186 YYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTR 1245

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1246 TTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1302



 Score =  116 bits (291), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 830 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 889



 Score = 82.0 bits (201), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP-RTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R    P R L+FD  EFH
Sbjct: 1326 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPSPPRRPLIFDTNEFH 1385

Query: 727  FPQV 730
             P V
Sbjct: 1386 IPLV 1389



 Score = 74.7 bits (182), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 521 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 575


>gi|281340311|gb|EFB15895.1| hypothetical protein PANDA_006866 [Ailuropoda melanoleuca]
          Length = 1375

 Score =  361 bits (926), Expect = 2e-96,   Method: Compositional matrix adjust.
 Identities = 211/479 (44%), Positives = 287/479 (59%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A    +S+P+LS  E++  +   +   EFL    ++F+++IK F
Sbjct: 899  GKDEPLEFKRVLDNIKAVFPCQSEPALSKNELVLTTESIMKKTEFLC-CQDSFLQEIKNF 957

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 958  VKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQIEKFLETCRDKYMRAQ 1011

Query: 1115 IEP--------ATAVGALAAQ----------------SIGEPGTQMTLKTFH-------- 1142
            +EP        A ++G    Q                ++G P  +  +            
Sbjct: 1012 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1071

Query: 1143 ----------------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                                    GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1072 AQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1131

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C+ + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1132 ETVRYSICMSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPE 1191

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+T
Sbjct: 1192 VSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAARTT 1251

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1252 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1311

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP-RTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R    P R L+FD  EFH
Sbjct: 1312 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPSPPRRPLIFDTSEFH 1370



 Score =  345 bits (884), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 168/280 (60%), Positives = 203/280 (72%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH AKV PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 441 DGDVVLFNRQPSLHKLSIMAHLAKVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 500

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 501 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 546

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++    +   +          P   ++   +WTGKQIFS+IL+P+ D PV 
Sbjct: 547 AKACQIIASILVGKDEKIKV-------HLPPPTILKPVTLWTGKQIFSVILRPSDDNPVR 599

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DSYV ++NSEL++GSMDK TLGSG K N+FYILLRD+G+ 
Sbjct: 600 ANLRTKGKQYCGKGEDLCVNDSYVTIQNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQS 659

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 660 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 699



 Score =  293 bits (750), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 143/251 (56%), Positives = 179/251 (71%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD    P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 11  EEMRQQAHIQVVSKNLYSQDNNHAPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 70

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYFR VI ILQ ICK  TC  ++L  E+   F   L+ P L+YL ++ LK
Sbjct: 71  IDLELPCFHVGYFRAVIGILQMICK--TCCHIMLSHEEKKQFLDYLKRPGLTYLQKRGLK 128

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K ++C +CG  NG VKKCGLLKI HEKYK   K  D IV + L  +  A++ 
Sbjct: 129 KKISDKCRKKNICHYCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPIVSNFLQSFETAIEH 188

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP ED+PLLLMN E  KPSDLILTRLLVPP C
Sbjct: 189 NKEVEP--LLGRAQENLNPLVVLNLFKRIPAEDVPLLLMNPEAGKPSDLILTRLLVPPLC 246

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 247 IRPSVVSDLKS 257



 Score =  290 bits (743), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 147/237 (62%), Positives = 187/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LDKD D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1051 GVPRIKEIINASKAISTPIITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 1110

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  C+ + R   G + V G + + + P+++SKS  
Sbjct: 1111 CFILVKLSLERIRLLRLEVNAETVRYSICMSKLRVKPGDVAVHGEAVVCVTPRENSKSSM 1170

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG +
Sbjct: 1171 YYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTR 1230

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1231 TTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1287



 Score =  116 bits (291), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 815 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 874



 Score = 82.4 bits (202), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP-RTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R    P R L+FD  EFH
Sbjct: 1311 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPSPPRRPLIFDTSEFH 1370

Query: 727  FPQV 730
             P V
Sbjct: 1371 IPLV 1374



 Score = 74.7 bits (182), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 506 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 560


>gi|444720682|gb|ELW61459.1| DNA-directed RNA polymerase III subunit RPC1 [Tupaia chinensis]
          Length = 1368

 Score =  360 bits (924), Expect = 3e-96,   Method: Compositional matrix adjust.
 Identities = 213/479 (44%), Positives = 286/479 (59%), Gaps = 73/479 (15%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I      +S+P+LS  E++  +   +   EFL    ++F+++IKKF
Sbjct: 898  GKDEPLEFKRVLDNI------KSEPALSKNELVVTTESIMKKNEFLC-CQDSFLQEIKKF 950

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 951  IKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQIEKFLETCRDKYMRAQ 1004

Query: 1115 IEP--------ATAVGALAAQ----------------SIGEPGTQMTLKTFH-------- 1142
            +EP        A ++G    Q                ++G P  +  +            
Sbjct: 1005 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1064

Query: 1143 ----------------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                                    GE+ EYIEEVF+PDD FILIKL ++RIRLL LEV+ 
Sbjct: 1065 AQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILIKLSLERIRLLRLEVNA 1124

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C  + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1125 ETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPE 1184

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG K +SNNTYEV KTLGIEAAR+T
Sbjct: 1185 VSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTKTTSNNTYEVEKTLGIEAARTT 1244

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1245 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1304

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1305 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKANRDPNPPKRPLIFDTNEFH 1363



 Score =  344 bits (883), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 167/280 (59%), Positives = 204/280 (72%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 440 DGDVVLFNRQPSLHKLSIMAHLARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 499

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 500 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 545

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++    +   +          P   ++   +WTGKQIFS+IL+P+ D PV 
Sbjct: 546 AKACQIIASILVGKDEKIKV-------CLPPPTILKPVTLWTGKQIFSVILRPSDDNPVR 598

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DSYV ++NSEL++GSMDK TLGSG K N+FYILLRD+G++
Sbjct: 599 ANLRTKGKQYCGKGEDLCVNDSYVTIQNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQN 658

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 659 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 698



 Score =  294 bits (752), Expect = 3e-76,   Method: Compositional matrix adjust.
 Identities = 143/251 (56%), Positives = 179/251 (71%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD    P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNNHAPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYF+ VI ILQ ICK  TC  ++L +E+   F   L+ P L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFKAVIGILQMICK--TCCHIMLSQEEKKQFLDYLKRPGLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K ++C HCG  NG VKKCGLLKI HEKYK   K  D IV   L  +  A++ 
Sbjct: 144 KKISDKCRKKNICHHCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPIVSHFLQSFETAIEH 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP ED+PLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NKEVEPL--LGKAQENLNPLIVLNLFKRIPAEDVPLLLMNPEAGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 262 IRPSVVSDLKS 272



 Score =  291 bits (746), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 149/237 (62%), Positives = 186/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LDKD D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1044 GVPRIKEIINASKAISTPIITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 1103

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FILIKL ++RIRLL LEV+ +++RY  C  + R   G + V G + + + P+++SKS  
Sbjct: 1104 CFILIKLSLERIRLLRLEVNAETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSM 1163

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG K
Sbjct: 1164 YYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTK 1223

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1224 TTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1280



 Score =  116 bits (291), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 814 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 873



 Score = 82.0 bits (201), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1304 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKANRDPNPPKRPLIFDTNEFH 1363

Query: 727  FPQV 730
             P V
Sbjct: 1364 IPLV 1367



 Score = 74.3 bits (181), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 505 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 559


>gi|91092426|ref|XP_968165.1| PREDICTED: similar to AGAP004703-PA [Tribolium castaneum]
 gi|270004743|gb|EFA01191.1| hypothetical protein TcasGA2_TC010518 [Tribolium castaneum]
          Length = 1390

 Score =  360 bits (923), Expect = 4e-96,   Method: Compositional matrix adjust.
 Identities = 169/277 (61%), Positives = 211/277 (76%), Gaps = 22/277 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           ++DVVLFNRQPSLHKLSIMAHR KV  HRTFRFNECVC PYNADFDGDEMN+HLPQTEEA
Sbjct: 466 NDDVVLFNRQPSLHKLSIMAHRTKVHQHRTFRFNECVCNPYNADFDGDEMNLHLPQTEEA 525

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              +LM NK+NLVTPRNGELLIAATQDF+TGGYLLT+K+ F + 
Sbjct: 526 KAEAL--------------ILMGNKNNLVTPRNGELLIAATQDFLTGGYLLTKKDTFLDL 571

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A   ++A+TL+A+      I              ++   +W+GKQI SLI +PN+ CPV 
Sbjct: 572 AHASQLAATLLAENDTNMQI-------DLPTPCILKPRRLWSGKQICSLIFRPNKKCPVK 624

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKA-NVFYILLRDFGED 579
           ANL+ KG+AYT N E C +DSYV++RNSEL+AG++DKS LGSGGK  N+FY++LRDFG +
Sbjct: 625 ANLEAKGKAYTKNRELCVKDSYVLIRNSELIAGTLDKSHLGSGGKGNNIFYVILRDFGSE 684

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
            A+ +MWRL+++TS+YLMN GFSIGIGDVTP +G ++
Sbjct: 685 YAIKSMWRLAKLTSYYLMNSGFSIGIGDVTPSKGLLR 721



 Score =  337 bits (863), Expect = 4e-89,   Method: Compositional matrix adjust.
 Identities = 209/484 (43%), Positives = 278/484 (57%), Gaps = 92/484 (19%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   PV+  R+L  + AK   R +  L++ +I   +   L++ + L + SE F  ++K F
Sbjct: 924  GKDCPVDFDRVLRHVQAKCPYRDETILNSVQIRRATKTFLET-DALNECSEEFKAELKNF 982

Query: 1057 LEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPS-ACKA-----EACREKY 1110
            +             DKV+  LR + +   +K G G+         C       + C  KY
Sbjct: 983  M-------------DKVA--LRVENI--YNKFGDGKVVKEIERLTCSQLVTFLQICGSKY 1025

Query: 1111 VRAQIEPATAVGALAAQSIGEPGTQMTLKTFH---------------------------- 1142
             R+ IEP TAVGALAAQSIGEPGTQMTLKTFH                            
Sbjct: 1026 TRSIIEPGTAVGALAAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIINASKDIST 1085

Query: 1143 --------------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHL 1176
                          FA            GEV  +I+E++   D F+LI+L+ DRI+LL L
Sbjct: 1086 PIITASLTNPRDIGFAREVKARIERTTLGEVATFIDEIYTQYDCFLLIQLNYDRIKLLKL 1145

Query: 1177 EVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKS--FNSKMYQMKQLLPSVVI 1232
            E++ +++RY  C  + +     + V   + + + P  S  +  FN  + ++K  LPSVV+
Sbjct: 1146 EINAETVRYSICTSKLKLKPNEVRVESETIITVSPSGSKHTHRFNFSLNELKAKLPSVVV 1205

Query: 1233 KGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIE 1292
            KG+  +NRAVI +E+  G T Y L VEGDNLR+V+ATYGV G K  SNN  EVY TLGIE
Sbjct: 1206 KGLPTVNRAVIAKEEKGGETLYNLCVEGDNLREVIATYGVLGTKTVSNNIMEVYHTLGIE 1265

Query: 1293 AARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASF 1352
            AAR TIM+EIK+VMENHGMS+D+RH ML+A  MT  GEVLGITR+GL+KMK+S+LNLASF
Sbjct: 1266 AARETIMSEIKMVMENHGMSVDYRHIMLLAAQMTHTGEVLGITRYGLSKMKQSILNLASF 1325

Query: 1353 ENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL------QAVPRSEPVPRT 1406
            E T+DHLFDAA+YGQ D I+GVSE IIMG+P  +GTG+ KLL      +  P SEP    
Sbjct: 1326 EKTADHLFDAAYYGQVDKINGVSENIIMGMPAPIGTGIFKLLHKPHHIEENPPSEP---- 1381

Query: 1407 LLFD 1410
            LLF+
Sbjct: 1382 LLFE 1385



 Score =  286 bits (732), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 143/292 (48%), Positives = 199/292 (68%), Gaps = 25/292 (8%)

Query: 87  VTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVG 146
           +   + +QQQSHI +V+KNLY QD QRTPIP+G+LD+R+GTN KE+ C TCG+N++ CVG
Sbjct: 22  IESAESMQQQSHIHVVAKNLYNQDVQRTPIPYGVLDKRLGTNSKESPCQTCGKNINSCVG 81

Query: 147 HFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVR 206
           HFGYIDL LPV+H+GYFR +I+ILQ+ICKN  CARVLL EE+   +R +L N  LSY+ +
Sbjct: 82  HFGYIDLELPVYHVGYFRSIISILQTICKN--CARVLLSEEEKNQYRIRLSNEHLSYMTK 139

Query: 207 KSLKKKILETTKKVSVCPHCGEINGVVKKC---------GLLKISHEKYKNRTKKKDAIV 257
           K+++KKI+E  +K++ CP+C E NG VKK           +LKI  E  KNR   K+ ++
Sbjct: 140 KAIRKKIIEKCRKLTKCPYCKESNGFVKKLTASKGSTGGSVLKIVCE--KNRGSDKETVL 197

Query: 258 EDLLAEYNEAVKFNPEIEAH--KKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKP 315
           ++ + ++N A+  NPEI+        + Q L P++VL+LFE IP  DIPLL M++  S+P
Sbjct: 198 KEHIEKFNSAIDVNPEIKNALTANSAVSQILTPIDVLKLFERIPQSDIPLLAMDSRRSQP 257

Query: 316 SDLILTRLLVPPNCIRPSVISDLKS----------DNDVVLFNRQPSLHKLS 357
            DLI TR+LVPP  IRPSV+SDLK+           ++++  N     HKLS
Sbjct: 258 KDLIFTRMLVPPVSIRPSVVSDLKAGTNEDDLTMRQSEIIFINDVIKKHKLS 309



 Score =  254 bits (650), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 131/238 (55%), Positives = 171/238 (71%), Gaps = 4/238 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS++ISTPIITA L    D+ +AR VK R+ERTTLGEV  +I+E++   D
Sbjct: 1069 GVPRIKEIINASKDISTPIITASLTNPRDIGFAREVKARIERTTLGEVATFIDEIYTQYD 1128

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKS-- 879
             F+LI+L+ DRI+LL LE++ +++RY  C  + +     + V   + + + P  S  +  
Sbjct: 1129 CFLLIQLNYDRIKLLKLEINAETVRYSICTSKLKLKPNEVRVESETIITVSPSGSKHTHR 1188

Query: 880  FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
            FN  + ++K  LPSVV+KG+  +NRAVI +E+  G T Y L VEGDNLR+V+ATYGV G 
Sbjct: 1189 FNFSLNELKAKLPSVVVKGLPTVNRAVIAKEEKGGETLYNLCVEGDNLREVIATYGVLGT 1248

Query: 940  KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            K  SNN  EVY TLGIEAAR TIM+EIK+VMENHGMS+D+RH ML+A  MT  GEVLG
Sbjct: 1249 KTVSNNIMEVYHTLGIEAARETIMSEIKMVMENHGMSVDYRHIMLLAAQMTHTGEVLG 1306



 Score =  115 bits (288), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 55/67 (82%), Positives = 59/67 (88%), Gaps = 1/67 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV+NSF++GLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDL V Y
Sbjct: 837 TPEAKGFVENSFYTGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLVVHY 896

Query: 668 DMSFDAA 674
           D S   A
Sbjct: 897 DGSVRNA 903



 Score = 80.5 bits (197), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 36/53 (67%), Positives = 46/53 (86%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIA 73
           +LM NK+NLVTPRNGELLIAATQDF+TGGYLLT+K+ F + A   ++A+TL+A
Sbjct: 531 ILMGNKNNLVTPRNGELLIAATQDFLTGGYLLTKKDTFLDLAHASQLAATLLA 583



 Score = 58.2 bits (139), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 32/60 (53%), Positives = 39/60 (65%), Gaps = 10/60 (16%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL------QAVPRSEPVPRTLLFD 721
            D  FDAA+YGQ D I+GVSE IIMG+P  +GTG+ KLL      +  P SEP    LLF+
Sbjct: 1330 DHLFDAAYYGQVDKINGVSENIIMGMPAPIGTGIFKLLHKPHHIEENPPSEP----LLFE 1385


>gi|307166498|gb|EFN60583.1| DNA-directed RNA polymerase III subunit RPC1 [Camponotus
           floridanus]
          Length = 1384

 Score =  360 bits (923), Expect = 5e-96,   Method: Compositional matrix adjust.
 Identities = 176/277 (63%), Positives = 208/277 (75%), Gaps = 24/277 (8%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND+VLFNRQPSLHKLSIMAHR KVL HRTFRFNEC C PYNADFDGDEMN+HLPQTEEA
Sbjct: 448 DNDLVLFNRQPSLHKLSIMAHRTKVLKHRTFRFNECCCAPYNADFDGDEMNLHLPQTEEA 507

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VL+ANKSNLVTPRNG+LLIAATQDFITGGYLLTQK+ FF+R
Sbjct: 508 KAEAL--------------VLLANKSNLVTPRNGDLLIAATQDFITGGYLLTQKDVFFDR 553

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPV-VFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q +++A   +A            S     P+   ++   +WTGKQIFSLI++P+ +CPV
Sbjct: 554 EQ-VKLALCFLAGADA--------SLTVTLPIPAILKPVKLWTGKQIFSLIIRPSPECPV 604

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            ANLKTKG+ YT  EEFC  DSYVI+RNSELLAG+MD STLGSG K N+FYILLRD+GED
Sbjct: 605 KANLKTKGKTYTTGEEFCINDSYVIIRNSELLAGAMDVSTLGSGSKQNIFYILLRDWGED 664

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
            A  +MWRL+R+T+ +  +RG SIG+ D+   QG VQ
Sbjct: 665 YATASMWRLTRLTNHFNFDRGISIGLSDLIASQGLVQ 701



 Score =  349 bits (895), Expect = 8e-93,   Method: Compositional matrix adjust.
 Identities = 201/463 (43%), Positives = 276/463 (59%), Gaps = 77/463 (16%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   PV+ KR+ D + AK   +++  L A  +++ + + L ++E+    SE F +++ +F
Sbjct: 904  GKDCPVDYKRVYDHVRAKLPYKNEEPLDAVSVMSATEDMLSTEEY-DCLSEEFKKELVEF 962

Query: 1057 LEEFSKK-----ESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYV 1111
            ++  ++K     +++ S    V Q L    +S   +  H               C+EKY+
Sbjct: 963  MKTVAQKIAHYRQNIKSKASVVLQ-LERLTVSQLVEFIH--------------TCKEKYM 1007

Query: 1112 RAQIEPATAVGALAAQSIGEPGTQMTLKTFH----------------------------- 1142
            RA IEP TAVGALAAQSIGEPGT MTLKTFH                             
Sbjct: 1008 RAVIEPGTAVGALAAQSIGEPGTSMTLKTFHFAGVASMNITQGVPRIKEIINASPKISTP 1067

Query: 1143 -----------FAG--------------EVCEYIEEVFVPDDSFILIKLDMDRIRLLHLE 1177
                       F G              E+ + IE+V+   D F+ IKL+M++I+LL LE
Sbjct: 1068 IITATLVDGTDFEGAERVKARIQKTTLKEIVDCIEQVYTRGDYFLKIKLNMEKIKLLKLE 1127

Query: 1178 VDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGV 1235
            V+++SI Y  C  + +    ++   G S +I++P    ++ N    ++   LP +V+KG+
Sbjct: 1128 VNVNSICYILCTSKLKLTPKNVRAIGDSVIIIQPTKQKENPNFPFRRLMDALPKIVVKGM 1187

Query: 1236 QGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAAR 1295
              ++R V+H+E   G TK+KL VEGDN R+VMATYGV G K +SNNT EV+KTLGIEAAR
Sbjct: 1188 PSVSRVVVHDETSNGKTKWKLFVEGDNFREVMATYGVHGEKTTSNNTLEVFKTLGIEAAR 1247

Query: 1296 STIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENT 1355
            +TIM EIK VMENHG+S+D RH +L+ADLMT +GEVLGITR GL KMKESVLNLASFE T
Sbjct: 1248 TTIMAEIKSVMENHGISVDRRHLILLADLMTCRGEVLGITRQGLDKMKESVLNLASFEKT 1307

Query: 1356 SDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 1398
            +DHLFD+A+YGQ D I GVSE IIMG+P+ VGTG+ KLLQ  P
Sbjct: 1308 ADHLFDSAYYGQRDAICGVSESIIMGIPIPVGTGMFKLLQKYP 1350



 Score =  252 bits (644), Expect = 9e-64,   Method: Compositional matrix adjust.
 Identities = 122/249 (48%), Positives = 172/249 (69%), Gaps = 7/249 (2%)

Query: 96  QSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPL 155
           QS +Q++++NLY +D +RTP  HG+LDRRMG +     CTTCG+ L DCVGHFGYIDL L
Sbjct: 31  QSSVQVITRNLYNEDTERTPFMHGILDRRMGVSSNGTECTTCGKILQDCVGHFGYIDLAL 90

Query: 156 PVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILE 215
           P+FH+G+FR +I ILQ ICKN  C+ +LL  E+   +  K++NP   YL+RK L+K+I E
Sbjct: 91  PIFHVGHFRSIIQILQMICKN--CSHILLTTEERNFYSQKIQNPNFGYLMRKGLRKQIWE 148

Query: 216 TTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPE-- 273
             KK ++CP+C E NG VKK G LKI +E++KN  KK D ++++ LAE    ++ + E  
Sbjct: 149 KAKKKTICPNCKENNGPVKKAGFLKIVYERHKN-LKKTDPLIQEKLAELGPLMEQDKELK 207

Query: 274 --IEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIR 331
             ++ + +    Q L P  VL+LF  IP  D+ LLLMN + + P+DLIL+R+ VPP CIR
Sbjct: 208 SIVDQNHRTVFDQCLFPNMVLELFTRIPASDVCLLLMNPKCAVPADLILSRIPVPPVCIR 267

Query: 332 PSVISDLKS 340
           PS +SD+K+
Sbjct: 268 PSTLSDIKA 276



 Score =  246 bits (628), Expect = 7e-62,   Method: Compositional matrix adjust.
 Identities = 126/236 (53%), Positives = 170/236 (72%), Gaps = 2/236 (0%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS  ISTPIITA L   TD + A  VK R+++TTL E+ + IE+V+   D
Sbjct: 1050 GVPRIKEIINASPKISTPIITATLVDGTDFEGAERVKARIQKTTLKEIVDCIEQVYTRGD 1109

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             F+ IKL+M++I+LL LEV+++SI Y  C  + +    ++   G S +I++P    ++ N
Sbjct: 1110 YFLKIKLNMEKIKLLKLEVNVNSICYILCTSKLKLTPKNVRAIGDSVIIIQPTKQKENPN 1169

Query: 882  SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
                ++   LP +V+KG+  ++R V+H+E   G TK+KL VEGDN R+VMATYGV G K 
Sbjct: 1170 FPFRRLMDALPKIVVKGMPSVSRVVVHDETSNGKTKWKLFVEGDNFREVMATYGVHGEKT 1229

Query: 942  SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +SNNT EV+KTLGIEAAR+TIM EIK VMENHG+S+D RH +L+ADLMT +GEVLG
Sbjct: 1230 TSNNTLEVFKTLGIEAARTTIMAEIKSVMENHGISVDRRHLILLADLMTCRGEVLG 1285



 Score =  107 bits (266), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 46/59 (77%), Positives = 53/59 (89%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
           +GFV+NSF+SGL   EF+FH MGGREGL DTAVKTA+TGYMQRRL+KSLEDLCV YDM+
Sbjct: 821 KGFVKNSFYSGLGSKEFYFHAMGGREGLTDTAVKTADTGYMQRRLIKSLEDLCVHYDMT 879



 Score = 83.6 bits (205), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 40/54 (74%), Positives = 48/54 (88%), Gaps = 1/54 (1%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           VL+ANKSNLVTPRNG+LLIAATQDFITGGYLLTQK+ FF+R Q +++A   +AG
Sbjct: 513 VLLANKSNLVTPRNGDLLIAATQDFITGGYLLTQKDVFFDREQ-VKLALCFLAG 565



 Score = 61.2 bits (147), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 27/42 (64%), Positives = 32/42 (76%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 709
            D  FD+A+YGQ D I GVSE IIMG+P+ VGTG+ KLLQ  P
Sbjct: 1309 DHLFDSAYYGQRDAICGVSESIIMGIPIPVGTGMFKLLQKYP 1350


>gi|291404119|ref|XP_002718445.1| PREDICTED: polymerase (RNA) III (DNA directed) polypeptide A, 155kDa
            [Oryctolagus cuniculus]
          Length = 1390

 Score =  360 bits (923), Expect = 5e-96,   Method: Compositional matrix adjust.
 Identities = 213/484 (44%), Positives = 289/484 (59%), Gaps = 77/484 (15%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A    +++P+LS  E++  S   +   EFL    ++F+++IKKF
Sbjct: 914  GKDEPLEFKRVLDNIRAVFPCQNEPALSKNELILTSEAIMKKNEFLC-CQDSFLQEIKKF 972

Query: 1057 LEEFSKKESVTSHQDK-------VSQPLREQILSHQDKIGHGRESNPFPSACKAEACREK 1109
            ++  S  E +   +DK        ++P   ++L   D+I       P       E CR+K
Sbjct: 973  IKGVS--ERIKKTRDKYGINDNGTTEP---RVLYQLDRI------TPTQIEKFLETCRDK 1021

Query: 1110 YVRAQIEP--------ATAVGALAAQ----------------SIGEPGTQMTLKTFH--- 1142
            Y+RAQ+EP        A ++G    Q                ++G P  +  +       
Sbjct: 1022 YMRAQMEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAIS 1081

Query: 1143 ---------------------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLH 1175
                                         GE+ EYIEEVF+PDD FIL+KL ++RIRLL 
Sbjct: 1082 TPIITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLR 1141

Query: 1176 LEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVI 1232
            LEV+ +++RY  C  + R   G + V G + + + P+++SKS    + Q +K+ LP VV+
Sbjct: 1142 LEVNAETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVVV 1201

Query: 1233 KGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIE 1292
            +G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GV+G + +SNNTYEV KTLGIE
Sbjct: 1202 QGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVRGTRTTSNNTYEVEKTLGIE 1261

Query: 1293 AARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASF 1352
            AAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASF
Sbjct: 1262 AARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASF 1321

Query: 1353 ENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDN 1411
            E T+DHLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD 
Sbjct: 1322 EKTADHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKANRDPNPPRRPLIFDT 1381

Query: 1412 PEFH 1415
             EFH
Sbjct: 1382 SEFH 1385



 Score =  345 bits (884), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 169/280 (60%), Positives = 207/280 (73%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDVVLFNRQPSLHKLSIMAHLARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++       G  ++   R   P + ++   +WTGKQIFS+IL+P+ D PV 
Sbjct: 562 AKACQIIASILV------GKDEKIKVRLPPPTI-LKPVTLWTGKQIFSVILRPSDDSPVR 614

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DSYV ++NSEL++GSMDK TLGSG K N+FYILLRD+G++
Sbjct: 615 ANLRTKGKQYCGKGEDLCVNDSYVTIQNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQN 674

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 675 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 714



 Score =  295 bits (756), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 146/251 (58%), Positives = 178/251 (70%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD    P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNNHAPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYFR VI ILQ ICK  TC  +LL  E+   F   L+ P L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFRAVIGILQMICK--TCCHILLSPEEKKQFLDYLKRPGLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI E  +K + C HCG +NG VKKCGLLKI HEKYK   K  D IV   L  +  A++ 
Sbjct: 144 KKISEKCRKKNACHHCGAVNGTVKKCGLLKIIHEKYKTNKKVVDPIVSTFLQSFETAIEH 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP ED+PLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NREVEP--LLGRAQENLNPLIVLNLFKRIPAEDVPLLLMNPEAGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 262 IRPSVVSDLKS 272



 Score =  288 bits (738), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 146/237 (61%), Positives = 186/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LDKD D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1066 GVPRIKEIINASKAISTPIITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 1125

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  C  + R   G + V G + + + P+++SKS  
Sbjct: 1126 CFILVKLSLERIRLLRLEVNAETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSM 1185

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GV+G +
Sbjct: 1186 YYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVRGTR 1245

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1246 TTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1302



 Score =  116 bits (291), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 830 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 889



 Score = 81.6 bits (200), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1326 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKANRDPNPPRRPLIFDTSEFH 1385

Query: 727  FPQV 730
             P V
Sbjct: 1386 IPLV 1389



 Score = 74.3 bits (181), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 521 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 575


>gi|432115682|gb|ELK36917.1| DNA-directed RNA polymerase III subunit RPC1 [Myotis davidii]
          Length = 951

 Score =  359 bits (921), Expect = 7e-96,   Method: Compositional matrix adjust.
 Identities = 215/479 (44%), Positives = 288/479 (60%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A    +S+P+LS  E L LS E++  K       ++F+++IK F
Sbjct: 475  GKDEPLEFKRVLDNIKAVFPCQSEPALSKNE-LVLSTESIMKKHEFLCCQDSFLQEIKNF 533

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 534  IKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQIEKFLETCRDKYMRAQ 587

Query: 1115 I---------------EPAT----------AVGAL--------------AAQSIGEPGTQ 1135
            +               EP T           V ++              A+++I  P   
Sbjct: 588  MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 647

Query: 1136 MTLKTFHFA---------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
              L     A               GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 648  AQLDKDEDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 707

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C+ + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 708  ETVRYSICMSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPE 767

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+T
Sbjct: 768  VSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAARTT 827

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 828  IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 887

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 888  HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKANRDPSPTRRPLIFDTKEFH 946



 Score =  346 bits (887), Expect = 6e-92,   Method: Compositional matrix adjust.
 Identities = 169/280 (60%), Positives = 207/280 (73%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 17  DGDVVLFNRQPSLHKLSIMAHLARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 76

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 77  KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 122

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++       G  ++   R   P + ++   +WTGKQIFS+IL+P+ D PV 
Sbjct: 123 AKACQIIASILV------GKDEKIKVRLPPPTI-LKPVTLWTGKQIFSVILRPSDDNPVR 175

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DSYV ++NSEL++GSMDK TLGSG K N+FYILLRD+G++
Sbjct: 176 ANLRTKGKQYCGKGEDLCINDSYVTIQNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQN 235

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 236 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 275



 Score =  291 bits (746), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 147/237 (62%), Positives = 187/237 (78%), Gaps = 3/237 (1%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
           GVPRIKEIINAS+ ISTPIITA LDKD D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 627 GVPRIKEIINASKAISTPIITAQLDKDEDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 686

Query: 824 SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
            FIL+KL ++RIRLL LEV+ +++RY  C+ + R   G + V G + + + P+++SKS  
Sbjct: 687 CFILVKLSLERIRLLRLEVNAETVRYSICMSKLRVKPGDVAVHGEAVVCVTPRENSKSSM 746

Query: 882 SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
             + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG +
Sbjct: 747 YYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTR 806

Query: 941 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 807 TTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 863



 Score =  116 bits (291), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 391 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 450



 Score = 82.4 bits (202), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668 DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
           D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 887 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKANRDPSPTRRPLIFDTKEFH 946

Query: 727 FPQV 730
            P V
Sbjct: 947 IPFV 950



 Score = 74.7 bits (182), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 82  VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 136


>gi|355712750|gb|AES04453.1| polymerase III polypeptide A, 155kDa [Mustela putorius furo]
          Length = 526

 Score =  358 bits (918), Expect = 2e-95,   Method: Compositional matrix adjust.
 Identities = 214/482 (44%), Positives = 290/482 (60%), Gaps = 73/482 (15%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A    +S+P+LS  E++  +   +   EFL    ++F+++IK F
Sbjct: 50   GKDEPLEFKRVLDNIKAVFPCQSEPALSKNELVLTTESIMKKTEFLC-CQDSFLQEIKNF 108

Query: 1057 LEEFSKKESVTS-----HQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYV 1111
            ++  S+K   T      + +  ++P   ++L   D+I       P       E CR+KY+
Sbjct: 109  IKGVSEKIKKTRDKYGINDNGTTEP---RVLYQLDRI------TPTQIEKFLETCRDKYM 159

Query: 1112 RAQI---------------EPAT----------AVGAL--------------AAQSIGEP 1132
            RAQ+               EP T           V ++              A+++I  P
Sbjct: 160  RAQMEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTP 219

Query: 1133 GTQMTLKTFHFA---------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLE 1177
                 L     A               GE+ EYIEEVF+PDD FIL+KL ++RIRLL LE
Sbjct: 220  IITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLE 279

Query: 1178 VDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKG 1234
            V+ +++RY  C+ + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G
Sbjct: 280  VNAETVRYSICMSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQG 339

Query: 1235 VQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAA 1294
            +  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIEAA
Sbjct: 340  IPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAA 399

Query: 1295 RSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFEN 1354
            R+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE 
Sbjct: 400  RTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEK 459

Query: 1355 TSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP-RTLLFDNPE 1413
            T+DHLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R    P R L+FD  E
Sbjct: 460  TADHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPSPPRRPLIFDTNE 519

Query: 1414 FH 1415
            FH
Sbjct: 520  FH 521



 Score =  291 bits (744), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 147/237 (62%), Positives = 187/237 (78%), Gaps = 3/237 (1%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
           GVPRIKEIINAS+ ISTPIITA LDKD D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 202 GVPRIKEIINASKAISTPIITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 261

Query: 824 SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
            FIL+KL ++RIRLL LEV+ +++RY  C+ + R   G + V G + + + P+++SKS  
Sbjct: 262 CFILVKLSLERIRLLRLEVNAETVRYSICMSKLRVKPGDVAVHGEAVVCVTPRENSKSSM 321

Query: 882 SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
             + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG +
Sbjct: 322 YYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTR 381

Query: 941 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 382 TTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 438



 Score = 82.0 bits (201), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668 DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP-RTLLFDNPEFH 726
           D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R    P R L+FD  EFH
Sbjct: 462 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPSPPRRPLIFDTNEFH 521

Query: 727 FPQV 730
            P V
Sbjct: 522 IPLV 525



 Score = 51.6 bits (122), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 22/25 (88%), Positives = 24/25 (96%)

Query: 646 TAETGYMQRRLVKSLEDLCVQYDMS 670
           TAETGYMQRRLVKSLEDLC QYD++
Sbjct: 1   TAETGYMQRRLVKSLEDLCSQYDLT 25


>gi|2460208|gb|AAB86536.1| RNA polymerase III largest subunit [Homo sapiens]
          Length = 1391

 Score =  357 bits (916), Expect = 3e-95,   Method: Compositional matrix adjust.
 Identities = 212/480 (44%), Positives = 286/480 (59%), Gaps = 68/480 (14%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A     S+P+LS  E++  +   +   EFL    ++F+++IKKF
Sbjct: 914  GKDEPLEFKRVLDNIKAVFPCPSEPALSKNELILTTESIMKKSEFLC-CQDSFLQEIKKF 972

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 973  IKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQVEKFLETCRDKYMRAQ 1026

Query: 1115 IEP--------ATAVGALAAQ----------------SIGEPGTQMTLKTFH-------- 1142
            +EP        A ++G    Q                ++G P  +  +            
Sbjct: 1027 MEPGSAVGALCAQSIGEPGTQMTLKTFHFGGVASMNITLGVPRIKEIINASKAISTPIIT 1086

Query: 1143 ----------------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                                    GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1087 AQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1146

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C  + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1147 ETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPE 1206

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+T
Sbjct: 1207 VSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAARTT 1266

Query: 1298 IMTEIKLVME-NHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTS 1356
            I+ EI+  M  NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+
Sbjct: 1267 IINEIQYTMVVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTA 1326

Query: 1357 DHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 1415
            DHLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1327 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPNPPKRPLIFDTNEFH 1386



 Score =  345 bits (886), Expect = 8e-92,   Method: Compositional matrix adjust.
 Identities = 169/280 (60%), Positives = 207/280 (73%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDVVLFNRQPSLHKLSIMAHLARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++       G  ++   R   P + ++   +WTGKQIFS+IL+P+ D PV 
Sbjct: 562 AKACQIIASILV------GKDEKIKVRLPPPTI-LKPVTLWTGKQIFSVILRPSDDNPVR 614

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DSYV ++NSEL++GSMDK TLGSG K N+FYILLRD+G++
Sbjct: 615 ANLRTKGKQYCGKGEDLCANDSYVTIQNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQN 674

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 675 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 714



 Score =  297 bits (761), Expect = 3e-77,   Method: Compositional matrix adjust.
 Identities = 144/251 (57%), Positives = 180/251 (71%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD Q  P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNQHAPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYFR VI ILQ ICK  TC  ++L +E+   F   L+ P L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFRAVIGILQMICK--TCCHIMLSQEEKKQFLDYLKRPGLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K ++C HCG  NG VKKCGLLKI HEKYK   K  D IV + L  +  A++ 
Sbjct: 144 KKISDKCRKKNICHHCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPIVSNFLQSFETAIEH 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP ED+PLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NKEVEPL--LGRAQENLNPLVVLNLFKRIPAEDVPLLLMNPEAGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKS 340
            RPSV+SDLKS
Sbjct: 262 FRPSVVSDLKS 272



 Score =  285 bits (730), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 147/238 (61%), Positives = 186/238 (78%), Gaps = 4/238 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LDKD D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1066 GVPRIKEIINASKAISTPIITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 1125

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  C  + R   G + V G + + + P+++SKS  
Sbjct: 1126 CFILVKLSLERIRLLRLEVNAETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSM 1185

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG +
Sbjct: 1186 YYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTR 1245

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVM-ENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNTYEV KTLGIEAAR+TI+ EI+  M  NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1246 TTSNNTYEVEKTLGIEAARTTIINEIQYTMVVNHGMSIDRRHVMLLSDLMTYKGEVLG 1303



 Score =  116 bits (291), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 830 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 889



 Score = 82.0 bits (201), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1327 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPNPPKRPLIFDTNEFH 1386

Query: 727  FPQV 730
             P V
Sbjct: 1387 IPLV 1390



 Score = 74.7 bits (182), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 521 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 575


>gi|124486963|ref|NP_001074716.1| DNA-directed RNA polymerase III subunit RPC1 [Mus musculus]
 gi|187956633|gb|AAI51169.1| Polymerase (RNA) III (DNA directed) polypeptide A [Mus musculus]
 gi|187956659|gb|AAI51170.1| Polymerase (RNA) III (DNA directed) polypeptide A [Mus musculus]
 gi|223462631|gb|AAI51003.1| Polymerase (RNA) III (DNA directed) polypeptide A [Mus musculus]
          Length = 1390

 Score =  355 bits (912), Expect = 8e-95,   Method: Compositional matrix adjust.
 Identities = 208/479 (43%), Positives = 286/479 (59%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A    +++P+LS  ++   +   +   EFL    ++F+++IK F
Sbjct: 914  GKDEPLEFKRVLDNIKAVYPCQTEPALSKNDLTLTAEAIMKKNEFLC-CQDSFLQEIKTF 972

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 973  IKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQIEKFLETCRDKYMRAQ 1026

Query: 1115 IEP--------ATAVGALAAQ----------------SIGEPGTQMTLKTFH-------- 1142
            +EP        A ++G    Q                ++G P  +  +            
Sbjct: 1027 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1086

Query: 1143 ----------------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                                    GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1087 AQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1146

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C  + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1147 ETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPE 1206

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  K+KLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+T
Sbjct: 1207 VSRAVIHIDEQSGKEKFKLLVEGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAARTT 1266

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1267 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1326

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R  +P  R L+FD  EFH
Sbjct: 1327 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKANRDPKPPRRPLIFDTHEFH 1385



 Score =  344 bits (883), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 169/280 (60%), Positives = 206/280 (73%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDVVLFNRQPSLHKLSIMAHLARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++       G  ++   R   P + ++   +WTGKQIFS+IL+P+ D PV 
Sbjct: 562 AKACQIIASILV------GKDEKIKVRLPPPTI-LKPVTLWTGKQIFSVILRPSDDNPVR 614

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DSYV ++NSEL+ GSMDK TLGSG K N+FYILLRD+G++
Sbjct: 615 ANLRTKGKQYCGKGEDLCVNDSYVTIQNSELMCGSMDKGTLGSGSKNNIFYILLRDWGQN 674

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 675 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 714



 Score =  293 bits (751), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 144/251 (57%), Positives = 179/251 (71%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD    P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNNHAPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYFR VI ILQ ICK  TC  ++L +E+   F   L+ P L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFRAVIGILQMICK--TCCHIMLSQEEKQQFLDFLKRPGLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K S C +CG  NG VKKCGLLKI HEKYK   K  D IV + L  +  A++ 
Sbjct: 144 KKISDKCRKKSTCHYCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPIVSNFLQSFETAIEH 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP ED+PLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NKEVEPL--LGRAQENLNPLVVLNLFKRIPAEDVPLLLMNPESGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 262 IRPSVVSDLKS 272



 Score =  288 bits (738), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 146/237 (61%), Positives = 186/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LDKD D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1066 GVPRIKEIINASKAISTPIITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 1125

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  C  + R   G + V G + + + P+++SKS  
Sbjct: 1126 CFILVKLSLERIRLLRLEVNAETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSM 1185

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  ++RAVIH ++  G  K+KLLVEGDNLR VMAT+GVKG +
Sbjct: 1186 YYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKFKLLVEGDNLRAVMATHGVKGTR 1245

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1246 TTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1302



 Score =  116 bits (291), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 830 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 889



 Score = 81.6 bits (200), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 45/64 (70%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R  +P  R L+FD  EFH
Sbjct: 1326 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKANRDPKPPRRPLIFDTHEFH 1385

Query: 727  FPQV 730
             P V
Sbjct: 1386 IPLV 1389



 Score = 74.7 bits (182), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 521 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 575


>gi|148669493|gb|EDL01440.1| mCG7865 [Mus musculus]
          Length = 1349

 Score =  355 bits (912), Expect = 8e-95,   Method: Compositional matrix adjust.
 Identities = 208/479 (43%), Positives = 286/479 (59%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A    +++P+LS  ++   +   +   EFL    ++F+++IK F
Sbjct: 873  GKDEPLEFKRVLDNIKAVYPCQTEPALSKNDLTLTAEAIMKKNEFLC-CQDSFLQEIKTF 931

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 932  IKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQIEKFLETCRDKYMRAQ 985

Query: 1115 IEP--------ATAVGALAAQ----------------SIGEPGTQMTLKTFH-------- 1142
            +EP        A ++G    Q                ++G P  +  +            
Sbjct: 986  MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1045

Query: 1143 ----------------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                                    GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1046 AQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1105

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C  + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1106 ETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPE 1165

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  K+KLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+T
Sbjct: 1166 VSRAVIHIDEQSGKEKFKLLVEGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAARTT 1225

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1226 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1285

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R  +P  R L+FD  EFH
Sbjct: 1286 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKANRDPKPPRRPLIFDTHEFH 1344



 Score =  293 bits (751), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 144/251 (57%), Positives = 179/251 (71%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD    P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNNHAPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYFR VI ILQ ICK  TC  ++L +E+   F   L+ P L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFRAVIGILQMICK--TCCHIMLSQEEKQQFLDFLKRPGLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K S C +CG  NG VKKCGLLKI HEKYK   K  D IV + L  +  A++ 
Sbjct: 144 KKISDKCRKKSTCHYCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPIVSNFLQSFETAIEH 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP ED+PLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NKEVEP--LLGRAQENLNPLVVLNLFKRIPAEDVPLLLMNPESGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 262 IRPSVVSDLKS 272



 Score =  288 bits (738), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 146/237 (61%), Positives = 186/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LDKD D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1025 GVPRIKEIINASKAISTPIITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 1084

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  C  + R   G + V G + + + P+++SKS  
Sbjct: 1085 CFILVKLSLERIRLLRLEVNAETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSM 1144

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  ++RAVIH ++  G  K+KLLVEGDNLR VMAT+GVKG +
Sbjct: 1145 YYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKFKLLVEGDNLRAVMATHGVKGTR 1204

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1205 TTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1261



 Score =  278 bits (710), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 146/279 (52%), Positives = 174/279 (62%), Gaps = 61/279 (21%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDVVLFNRQPSLHKLSIMAHLARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++       G  ++   R   P +     V W                   
Sbjct: 562 AKACQIIASILV------GKDEKIKVRLPPPTIL---KVCW------------------- 593

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
                                YV ++NSEL+ GSMDK TLGSG K N+FYILLRD+G++ 
Sbjct: 594 -------------------GQYVTIQNSELMCGSMDKGTLGSGSKNNIFYILLRDWGQNE 634

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
           A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 635 AADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 673



 Score =  116 bits (291), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 789 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 848



 Score = 81.6 bits (200), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 45/64 (70%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R  +P  R L+FD  EFH
Sbjct: 1285 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKANRDPKPPRRPLIFDTHEFH 1344

Query: 727  FPQV 730
             P V
Sbjct: 1345 IPLV 1348



 Score = 74.3 bits (181), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 521 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 575


>gi|395820429|ref|XP_003783569.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1 [Otolemur
            garnettii]
          Length = 1390

 Score =  354 bits (909), Expect = 2e-94,   Method: Compositional matrix adjust.
 Identities = 211/479 (44%), Positives = 285/479 (59%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A     S+ +LS  E++  +   +   EFL    ++F+++IKKF
Sbjct: 914  GKDEPLEFKRVLDNIKAVFPCPSERALSKNELILTTESIMKKNEFLC-CQDSFLQEIKKF 972

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 973  IKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQVEKFLETCRDKYMRAQ 1026

Query: 1115 IEP--------ATAVGALAAQ----------------SIGEPGTQMTLKTFH-------- 1142
            +EP        A ++G    Q                ++G P  +  +            
Sbjct: 1027 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1086

Query: 1143 ----------------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                                    GE+ EYIEEVF+PDD FILIKL ++RIRLL LEV+ 
Sbjct: 1087 AQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILIKLSLERIRLLRLEVNA 1146

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C+ + R   G + V G + + + P+++SKS    + Q +K+ L  VV++G+  
Sbjct: 1147 ETVRYSICMSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLLKVVVQGIPE 1206

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+T
Sbjct: 1207 VSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAARTT 1266

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1267 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1326

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1327 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKANRDPNPPRRPLIFDTNEFH 1385



 Score =  343 bits (880), Expect = 4e-91,   Method: Compositional matrix adjust.
 Identities = 169/280 (60%), Positives = 205/280 (73%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDVVLFNRQPSLHKLSIMAHLARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++       G  ++   R   P + ++   +WTGKQIFS+IL+P+ D PV 
Sbjct: 562 AKACQIIASILV------GKDEKIKVRLPPPTI-LKPVTLWTGKQIFSVILRPSDDNPVR 614

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DSYV ++NSEL+ GSMDK TLGSG K N+FYILLRD+G++
Sbjct: 615 ANLRTKGKQYCGKGEDLCVNDSYVTIQNSELMCGSMDKGTLGSGSKNNIFYILLRDWGQN 674

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG +   +
Sbjct: 675 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLTAKY 714



 Score =  300 bits (767), Expect = 5e-78,   Method: Compositional matrix adjust.
 Identities = 146/251 (58%), Positives = 181/251 (72%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD   TP+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNHHTPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYFR VI ILQ ICK  TC  ++L +E+   F   L+ P L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFRAVIGILQMICK--TCCHIMLSQEERKQFLDYLKRPGLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K S+C HCG  NG VKKCGLLKI HEKYK   K  D IV + L  +  A++ 
Sbjct: 144 KKISDKCRKKSICHHCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPIVSNFLQSFETAIEH 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP ED+PLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NKEVEP--LLGRAQENLNPLVVLNLFKRIPAEDVPLLLMNPEAGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 262 IRPSVVSDLKS 272



 Score =  287 bits (734), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 147/237 (62%), Positives = 186/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LDKD D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1066 GVPRIKEIINASKAISTPIITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 1125

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FILIKL ++RIRLL LEV+ +++RY  C+ + R   G + V G + + + P+++SKS  
Sbjct: 1126 CFILIKLSLERIRLLRLEVNAETVRYSICMSKLRVKPGDVAVHGEAVVCVTPRENSKSSM 1185

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ L  VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG +
Sbjct: 1186 YYVLQFLKEDLLKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTR 1245

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1246 TTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1302



 Score =  116 bits (291), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 830 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 889



 Score = 81.3 bits (199), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1326 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKANRDPNPPRRPLIFDTNEFH 1385

Query: 727  FPQV 730
             P V
Sbjct: 1386 IPLV 1389



 Score = 74.3 bits (181), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 521 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 575


>gi|109503668|ref|XP_001056048.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1 [Rattus
            norvegicus]
 gi|392353748|ref|XP_341389.5| PREDICTED: DNA-directed RNA polymerase III subunit RPC1 [Rattus
            norvegicus]
          Length = 1390

 Score =  353 bits (906), Expect = 4e-94,   Method: Compositional matrix adjust.
 Identities = 208/479 (43%), Positives = 285/479 (59%), Gaps = 67/479 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A    +S+ +LS  E+   +   +   EFL    ++F+++IK F
Sbjct: 914  GKDEPLEFKRVLDNIKAVYPCQSERALSKNELTLTTEAIMKKNEFLC-CQDSFLQEIKTF 972

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I   +           E CR+KY+RAQ
Sbjct: 973  IKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRITRTQIEKFL------ETCRDKYMRAQ 1026

Query: 1115 IEP--------ATAVGALAAQ----------------SIGEPGTQMTLKTFH-------- 1142
            +EP        A ++G    Q                ++G P  +  +            
Sbjct: 1027 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1086

Query: 1143 ----------------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                                    GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1087 AQLDMDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1146

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQG 1237
            +++RY  C  + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G+  
Sbjct: 1147 ETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPE 1206

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            ++RAVIH ++  G  K+KLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+T
Sbjct: 1207 VSRAVIHIDEQSGKEKFKLLVEGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAARTT 1266

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+D
Sbjct: 1267 IINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTAD 1326

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 1415
            HLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R  +P  R L+FD  EFH
Sbjct: 1327 HLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKANRDPKPPRRPLIFDTHEFH 1385



 Score =  346 bits (887), Expect = 7e-92,   Method: Compositional matrix adjust.
 Identities = 170/280 (60%), Positives = 206/280 (73%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH AKV PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDVVLFNRQPSLHKLSIMAHLAKVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++       G  ++   R   P + ++   +WTGKQIFS+IL+P+ D PV 
Sbjct: 562 AKACQIIASILV------GKDEKIKVRLPPPTI-LKPVTLWTGKQIFSVILRPSDDNPVR 614

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DSYV ++NSEL+ GSMDK TLGSG K N+FYILLRD+G++
Sbjct: 615 ANLRTKGKQYCGKGEDLCTNDSYVTIQNSELMCGSMDKGTLGSGSKNNIFYILLRDWGQN 674

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 675 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 714



 Score =  294 bits (753), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 144/251 (57%), Positives = 179/251 (71%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD    P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNNHAPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYFR VI ILQ ICK  TC  ++L +E+   F   L+ P L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFRAVIGILQMICK--TCCHIMLSQEEKQQFLDFLKRPGLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K S C +CG  NG VKKCGLLKI HEKYK   K  D IV + L  +  A++ 
Sbjct: 144 KKISDKCRKKSTCHYCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPIVSNFLQSFETAIEH 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP ED+PLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NKEVEPL--LGRAQENLNPLVVLNLFKRIPAEDVPLLLMNPEAGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 262 IRPSVVSDLKS 272



 Score =  286 bits (732), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 145/237 (61%), Positives = 185/237 (78%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LD D D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1066 GVPRIKEIINASKAISTPIITAQLDMDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 1125

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  C  + R   G + V G + + + P+++SKS  
Sbjct: 1126 CFILVKLSLERIRLLRLEVNAETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSM 1185

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  ++RAVIH ++  G  K+KLLVEGDNLR VMAT+GVKG +
Sbjct: 1186 YYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKFKLLVEGDNLRAVMATHGVKGTR 1245

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1246 TTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1302



 Score =  116 bits (291), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 830 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 889



 Score = 81.6 bits (200), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 45/64 (70%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R  +P  R L+FD  EFH
Sbjct: 1326 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKANRDPKPPRRPLIFDTHEFH 1385

Query: 727  FPQV 730
             P V
Sbjct: 1386 IPLV 1389



 Score = 74.7 bits (182), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 521 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 575


>gi|328710964|ref|XP_001945328.2| PREDICTED: DNA-directed RNA polymerase III subunit RPC1-like
           [Acyrthosiphon pisum]
          Length = 1366

 Score =  352 bits (904), Expect = 6e-94,   Method: Compositional matrix adjust.
 Identities = 173/297 (58%), Positives = 216/297 (72%), Gaps = 32/297 (10%)

Query: 331 RPSVISDLK---------SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPY 381
           RP++  DLK         SD D+VLFNRQPSLH+LSIM HRAKVL H T RFNECVCTPY
Sbjct: 441 RPAIAKDLKIGDIVERHLSDGDIVLFNRQPSLHRLSIMCHRAKVLEHNTLRFNECVCTPY 500

Query: 382 NADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAAT 441
           NADFDGDEMN+HLPQTEEARAEA               +LM NKSNLVTPRNG++LIAAT
Sbjct: 501 NADFDGDEMNLHLPQTEEARAEA--------------ALLMINKSNLVTPRNGDILIAAT 546

Query: 442 QDFITGGYLLTQKNAFFNRAQTMRIASTLIA-DTSDICGIIKRFSWRSWNPVVFVRTAVI 500
           QDFITG YLLT KN F N+  + R+   L++ D  +I   + R       P + ++   +
Sbjct: 547 QDFITGAYLLTHKNTFLNQRDSSRLIGWLMSGDDINIDLTLPR-------PAI-LKPHKL 598

Query: 501 WTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTL 560
           WTGKQI S+I++P++ C V ANL+ KG++YT +EEFC +DSYV ++NSELLAG+MDK+TL
Sbjct: 599 WTGKQILSIIMRPSKKCLVKANLRCKGKSYTRDEEFCFKDSYVYIKNSELLAGTMDKATL 658

Query: 561 GSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           GSG K+N+FY+LL D+G DV    MWRL+R+TS++LM RGFSIGIGDVTP    +Q+
Sbjct: 659 GSGSKSNIFYVLLADWGSDVCCKVMWRLTRLTSYFLMLRGFSIGIGDVTPSDDLLQS 715



 Score =  335 bits (858), Expect = 1e-88,   Method: Compositional matrix adjust.
 Identities = 199/462 (43%), Positives = 270/462 (58%), Gaps = 83/462 (17%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G+G PV+ KR+  ++ A      + +L ++EIL ++ + L S+ F Q+ +  F  +++ F
Sbjct: 917  GDGVPVDFKRVYFNVTANYPCTDECTLDSEEILKITEDVLLSENF-QNVNTIFTEELRNF 975

Query: 1057 LEEFS------KKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKY 1110
             +  +      +K+ +     K+ +    Q++                       C  KY
Sbjct: 976  GKNLANNMAELRKKWLNLEVSKIQRITSTQLIKFY------------------VTCLTKY 1017

Query: 1111 VRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYIEEVFV 1156
            + A IEP T VGA+AAQSIGEPGTQMTLKTFHFAG              E+    + +  
Sbjct: 1018 MAAVIEPGTPVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIINSSKNIST 1077

Query: 1157 P----------DDSF------------------------------ILIKLDMDRIRLLHL 1176
            P          D  F                              +LI +DM+RI+LL L
Sbjct: 1078 PIITAYLENDKDKEFARIVKARIEQTTLTEVCSFIDVVLDSAECYLLIHIDMNRIKLLQL 1137

Query: 1177 EVDIDSIRYCIERTRGI---SGHLTVSGHSFL-ILKPKDSSKSFNSKMYQMKQLLPSVVI 1232
            EV I++IR  I  T  I   +  + +   S + I  P   ++S N+ +    Q L  VVI
Sbjct: 1138 EVTIETIRDSILSTPRIGIKANQVNIDNESCVSISLPSKGTQSLNNWINIYSQNLQKVVI 1197

Query: 1233 KGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIE 1292
            KG+  ++RAVIHEED  G  +YKLLVEGDNLR+VMAT GV G +C+SNNT++V+  LGIE
Sbjct: 1198 KGISAVSRAVIHEEDDNGEIRYKLLVEGDNLREVMATPGVIGKRCTSNNTFQVWNALGIE 1257

Query: 1293 AARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASF 1352
            A+R+TI++EI  VM NHG+SID RHPML+ADLMTS+GE+LGITR GL+KMKESVLNLASF
Sbjct: 1258 ASRATIISEIDSVMGNHGISIDPRHPMLIADLMTSRGELLGITRFGLSKMKESVLNLASF 1317

Query: 1353 ENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            E TSDHLFDAA+YGQTD I+GVSE IIMG+P+N+GTG  KL+
Sbjct: 1318 EKTSDHLFDAAYYGQTDTINGVSESIIMGIPINLGTGFFKLI 1359



 Score =  269 bits (688), Expect = 7e-69,   Method: Compositional matrix adjust.
 Identities = 142/316 (44%), Positives = 198/316 (62%), Gaps = 13/316 (4%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYC---QDPQRTPIPHGLLDRRMGTNQKEANCTTCGQ 139
           I  TV     +Q++SH+ I ++NLY     +  RTP P+G+LD ++G NQK+A C TC +
Sbjct: 18  ISFTVDNPQDIQRKSHLCINTRNLYAINNNNASRTPHPYGVLDHKLGVNQKDATCMTCNK 77

Query: 140 NLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNP 199
            L+DC GH G+IDL LPVFH+G+F  VI ILQ+ICKNP CA+VLL EE    F  KLRN 
Sbjct: 78  GLNDCPGHLGFIDLQLPVFHVGFFSSVITILQTICKNPFCAKVLLNEEDRMFFYTKLRNK 137

Query: 200 ALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVED 259
            L+Y +RK + K++    KKV +CP C +I G VKK G+LKIS+++Y  R KK     E 
Sbjct: 138 NLTYTMRKKVFKEVHAKAKKVQICPFCSDIVGQVKKNGILKISYDRY--RYKKPGTEAES 195

Query: 260 LLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLI 319
            L   N+ VK+N E+E+ + +   + LNP EVL+L  +IP EDI LL MN E+S P  L+
Sbjct: 196 KLCALNDVVKYNKEVESMRNYLFNENLNPQEVLRLLLSIPYEDIILLGMNPEVSNPGWLL 255

Query: 320 LTRLLVPPNCIRPSVISDLKS---DNDVVLFNRQPSLHKLSIMAHRAK----VLPHRTFR 372
           +TR+LVPPNCIRPS +SD++S   ++D+ L   +       I+ H+       L H  + 
Sbjct: 256 MTRMLVPPNCIRPSAVSDIRSGTNEDDLTLKLSEVLFINDVIVKHKQSGAKPQLLHEDWE 315

Query: 373 FNECVCTPY-NADFDG 387
           + +  C  Y N+D  G
Sbjct: 316 YLQLHCALYINSDLSG 331



 Score =  259 bits (662), Expect = 8e-66,   Method: Compositional matrix adjust.
 Identities = 134/238 (56%), Positives = 177/238 (74%), Gaps = 4/238 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIIN+S+NISTPIITAYL+ D D ++ARIVK R+E+TTL EVC +I+ V    +
Sbjct: 1061 GVPRIKEIINSSKNISTPIITAYLENDKDKEFARIVKARIEQTTLTEVCSFIDVVLDSAE 1120

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFL-ILKPKDSSKS 879
             ++LI +DM+RI+LL LEV I++IR  I  T  I   +  + +   S + I  P   ++S
Sbjct: 1121 CYLLIHIDMNRIKLLQLEVTIETIRDSILSTPRIGIKANQVNIDNESCVSISLPSKGTQS 1180

Query: 880  FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
             N+ +    Q L  VVIKG+  ++RAVIHEED  G  +YKLLVEGDNLR+VMAT GV G 
Sbjct: 1181 LNNWINIYSQNLQKVVIKGISAVSRAVIHEEDDNGEIRYKLLVEGDNLREVMATPGVIGK 1240

Query: 940  KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +C+SNNT++V+  LGIEA+R+TI++EI  VM NHG+SID RHPML+ADLMTS+GE+LG
Sbjct: 1241 RCTSNNTFQVWNALGIEASRATIISEIDSVMGNHGISIDPRHPMLIADLMTSRGELLG 1298



 Score =  122 bits (305), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 57/68 (83%), Positives = 61/68 (89%), Gaps = 1/68 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV+NSF+SGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV Y
Sbjct: 830 TPEAKGFVENSFYSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVHY 889

Query: 668 DMSFDAAF 675
           D +   AF
Sbjct: 890 DNTVRNAF 897



 Score = 77.0 bits (188), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 35/57 (61%), Positives = 44/57 (77%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKV 77
           +LM NKSNLVTPRNG++LIAATQDFITG YLLT KN F N+  + R+   L++G  +
Sbjct: 525 LLMINKSNLVTPRNGDILIAATQDFITGAYLLTHKNTFLNQRDSSRLIGWLMSGDDI 581



 Score = 60.5 bits (145), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 26/38 (68%), Positives = 32/38 (84%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 705
            D  FDAA+YGQTD I+GVSE IIMG+P+N+GTG  KL+
Sbjct: 1322 DHLFDAAYYGQTDTINGVSESIIMGIPINLGTGFFKLI 1359


>gi|158298044|ref|XP_318130.4| AGAP004703-PA [Anopheles gambiae str. PEST]
 gi|157014619|gb|EAA13195.5| AGAP004703-PA [Anopheles gambiae str. PEST]
          Length = 1379

 Score =  352 bits (904), Expect = 6e-94,   Method: Compositional matrix adjust.
 Identities = 176/297 (59%), Positives = 213/297 (71%), Gaps = 34/297 (11%)

Query: 331 RPSVISDLKS---------DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPY 381
           R  V  DLK          D DVVLFNRQPSLHKLSIM H AKV P RTFRFNEC CTPY
Sbjct: 440 RDKVAQDLKCGDIVERHLIDGDVVLFNRQPSLHKLSIMCHVAKVQPQRTFRFNECACTPY 499

Query: 382 NADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAAT 441
           NADFDGDEMN+HLPQTEEARAEAL              VLM NKSNLVTPRNGELLIAAT
Sbjct: 500 NADFDGDEMNLHLPQTEEARAEAL--------------VLMGNKSNLVTPRNGELLIAAT 545

Query: 442 QDFITGGYLLTQKNAFFNRAQTMRIASTLIA--DTSDICGIIKRFSWRSWNPVVFVRTAV 499
           QDFITGGYLLTQK+ F    Q M++A+ +++  D++ +  + +        P + ++   
Sbjct: 546 QDFITGGYLLTQKDQFLTLEQVMQLAACMLSGPDSNMVIDLPR--------PAI-LKPRK 596

Query: 500 IWTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKST 559
           +WTGKQIFSLILKPN    VNANL TKGR YT + + C +DS+VI+RNS+LL G+MDK T
Sbjct: 597 LWTGKQIFSLILKPNSQSCVNANLYTKGRNYTRDNDMCVKDSWVIIRNSQLLCGAMDKGT 656

Query: 560 LGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           LGSG K  +FY++LRDFGE+ A+ +MWRL+RM S+++MN GFS GIGDVTP +  ++
Sbjct: 657 LGSGTKNCIFYVILRDFGEEYAIKSMWRLARMASYFMMNHGFSFGIGDVTPSRKLLE 713



 Score =  329 bits (843), Expect = 9e-87,   Method: Compositional matrix adjust.
 Identities = 195/464 (42%), Positives = 263/464 (56%), Gaps = 91/464 (19%)

Query: 1001 PVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEF 1060
            PV+++R    +      R +  L  +E+L+     L + +F  +  ++F ++   FLE+F
Sbjct: 920  PVDIERQFMHVRNMLPCRDEIPLRGEEVLSEGERILSTPQF-SNCRQDFRKECLDFLEKF 978

Query: 1061 SKK-----------ESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREK 1109
             ++             VT+   + +    E+ L                        R K
Sbjct: 979  GRRLCTLQRLYRNGPRVTTEVQRTTAGQLEEFLLQ---------------------VRNK 1017

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFH--------------------------- 1142
            Y +A  EP TAVGALAAQSIGEPGTQMTLKTFH                           
Sbjct: 1018 YNKAVTEPGTAVGALAAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIVEIINATKAIS 1077

Query: 1143 ---------------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLH 1175
                           FA            GE+  YIEEV+  ++ F+LIKLD+ RIR+L 
Sbjct: 1078 TPIITAEIENNTNMEFARKVKARIEKTTLGEISSYIEEVYKMNECFLLIKLDLGRIRVLG 1137

Query: 1176 LEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDS--SKSFNSKMYQMKQLLPSVV 1231
            LEV+ D+IRY  C  + +    ++ V G S +I++P  S  S S N+++ ++   +P+VV
Sbjct: 1138 LEVNADTIRYSICTSKLKLKQENVEVYGPSLIIIRPDSSKHSHSLNAELQRLITAIPNVV 1197

Query: 1232 IKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGI 1291
            + G+  ++RAVI  +D  G  KY+L VEG  LRDVM TYGV G +  SNN  EVY+TLGI
Sbjct: 1198 VAGLPQVSRAVIAVDDSRGTPKYRLCVEGCGLRDVMGTYGVIGNRTKSNNILEVYQTLGI 1257

Query: 1292 EAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLAS 1351
            EAAR+TIMTEI  VME HGMS+D RH ML++  MTS+GEVLGITRHGLAKM+ESV NLAS
Sbjct: 1258 EAARTTIMTEITEVMEGHGMSVDHRHIMLLSGQMTSRGEVLGITRHGLAKMRESVFNLAS 1317

Query: 1352 FENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 1395
            FE T+DHLFDAA+YGQTD + GVSE II+G+P ++GTGL KL+ 
Sbjct: 1318 FEKTADHLFDAAYYGQTDSVDGVSERIILGMPASIGTGLFKLIH 1361



 Score =  264 bits (674), Expect = 3e-67,   Method: Compositional matrix adjust.
 Identities = 131/253 (51%), Positives = 177/253 (69%), Gaps = 8/253 (3%)

Query: 92  RVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYI 151
           ++QQ++HI +V+KNLY Q+  RTP+ +G+LDRRMG +QK+A C TC + L+DCVGHFGYI
Sbjct: 27  QIQQEAHIHVVAKNLYNQNADRTPVAYGVLDRRMGVSQKDATCETCKKGLNDCVGHFGYI 86

Query: 152 DLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKK 211
           DL LPVFH+G+FR  I ILQSICK   C+RV+L EE+   F  +L NP LSYL +KS+  
Sbjct: 87  DLALPVFHVGHFRATITILQSICK--VCSRVMLKEEEKKNFSTRLVNPNLSYLAKKSIHS 144

Query: 212 KILETTKKVSVCPHCGEINGVVKKC-GLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           ++L+  KK + CP+C  +NG VKK  GL+KI HE ++ + K  D +V   L E   AV+ 
Sbjct: 145 QVLKKAKKNTKCPYCNSLNGPVKKGPGLMKIVHEPFRGK-KPSDPLVTHALHEMQAAVES 203

Query: 271 NPEIEAHKKFG---LIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPP 327
           N E+ A    G   L + LN +EVL LF  IP  D+PLL M +  S P+DLI+TR+ VPP
Sbjct: 204 NREL-AQTVVGPSSLSKELNAVEVLDLFRNIPKSDVPLLGMTSTYSNPADLIVTRVFVPP 262

Query: 328 NCIRPSVISDLKS 340
            CIRPSV+S++K+
Sbjct: 263 VCIRPSVVSEVKA 275



 Score =  250 bits (638), Expect = 5e-63,   Method: Compositional matrix adjust.
 Identities = 128/238 (53%), Positives = 175/238 (73%), Gaps = 4/238 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRI EIINA++ ISTPIITA ++ +T++++AR VK R+E+TTLGE+  YIEEV+  ++
Sbjct: 1062 GVPRIVEIINATKAISTPIITAEIENNTNMEFARKVKARIEKTTLGEISSYIEEVYKMNE 1121

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDS--SKS 879
             F+LIKLD+ RIR+L LEV+ D+IRY  C  + +    ++ V G S +I++P  S  S S
Sbjct: 1122 CFLLIKLDLGRIRVLGLEVNADTIRYSICTSKLKLKQENVEVYGPSLIIIRPDSSKHSHS 1181

Query: 880  FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
             N+++ ++   +P+VV+ G+  ++RAVI  +D  G  KY+L VEG  LRDVM TYGV G 
Sbjct: 1182 LNAELQRLITAIPNVVVAGLPQVSRAVIAVDDSRGTPKYRLCVEGCGLRDVMGTYGVIGN 1241

Query: 940  KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +  SNN  EVY+TLGIEAAR+TIMTEI  VME HGMS+D RH ML++  MTS+GEVLG
Sbjct: 1242 RTKSNNILEVYQTLGIEAARTTIMTEITEVMEGHGMSVDHRHIMLLSGQMTSRGEVLG 1299



 Score =  113 bits (282), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 51/61 (83%), Positives = 55/61 (90%)

Query: 608 VTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           +   +GFVQNSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGY+QRRLVK LEDL VQY
Sbjct: 829 IPAARGFVQNSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYLQRRLVKCLEDLVVQY 888

Query: 668 D 668
           D
Sbjct: 889 D 889



 Score = 85.1 bits (209), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 39/54 (72%), Positives = 46/54 (85%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           VLM NKSNLVTPRNGELLIAATQDFITGGYLLTQK+ F    Q M++A+ +++G
Sbjct: 524 VLMGNKSNLVTPRNGELLIAATQDFITGGYLLTQKDQFLTLEQVMQLAACMLSG 577



 Score = 57.0 bits (136), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 24/39 (61%), Positives = 31/39 (79%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  FDAA+YGQTD + GVSE II+G+P ++GTGL KL+ 
Sbjct: 1323 DHLFDAAYYGQTDSVDGVSERIILGMPASIGTGLFKLIH 1361


>gi|55778568|gb|AAH86344.1| Polr3a protein [Rattus norvegicus]
          Length = 491

 Score =  350 bits (898), Expect = 3e-93,   Method: Compositional matrix adjust.
 Identities = 211/482 (43%), Positives = 288/482 (59%), Gaps = 73/482 (15%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A    +S+ +LS  E+   +   +   EFL    ++F+++IK F
Sbjct: 15   GKDEPLEFKRVLDNIKAVYPCQSERALSKNELTLTTEAIMKKNEFLC-CQDSFLQEIKTF 73

Query: 1057 LEEFSKKESVTS-----HQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYV 1111
            ++  S+K   T      + +  ++P   ++L   D+I   +           E CR+KY+
Sbjct: 74   IKGVSEKIKKTRDKYGINDNGTTEP---RVLYQLDRITRTQIEKFL------ETCRDKYM 124

Query: 1112 RAQI---------------EPAT----------AVGAL--------------AAQSIGEP 1132
            RAQ+               EP T           V ++              A+++I  P
Sbjct: 125  RAQMEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTP 184

Query: 1133 GTQMTLKTFHFA---------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLE 1177
                 L     A               GE+ EYIEEVF+PDD FIL+KL ++RIRLL LE
Sbjct: 185  IITAQLDMDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLE 244

Query: 1178 VDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKG 1234
            V+ +++RY  C  + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G
Sbjct: 245  VNAETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQG 304

Query: 1235 VQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAA 1294
            +  ++RAVIH ++  G  K+KLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIEAA
Sbjct: 305  IPEVSRAVIHIDEQSGKEKFKLLVEGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAA 364

Query: 1295 RSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFEN 1354
            R+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE 
Sbjct: 365  RTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEK 424

Query: 1355 TSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPE 1413
            T+DHLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R  +P  R L+FD  E
Sbjct: 425  TADHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKANRDPKPPRRPLIFDTHE 484

Query: 1414 FH 1415
            FH
Sbjct: 485  FH 486



 Score =  286 bits (732), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 145/237 (61%), Positives = 185/237 (78%), Gaps = 3/237 (1%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
           GVPRIKEIINAS+ ISTPIITA LD D D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 167 GVPRIKEIINASKAISTPIITAQLDMDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 226

Query: 824 SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
            FIL+KL ++RIRLL LEV+ +++RY  C  + R   G + V G + + + P+++SKS  
Sbjct: 227 CFILVKLSLERIRLLRLEVNAETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSM 286

Query: 882 SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
             + Q +K+ LP VV++G+  ++RAVIH ++  G  K+KLLVEGDNLR VMAT+GVKG +
Sbjct: 287 YYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKFKLLVEGDNLRAVMATHGVKGTR 346

Query: 941 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 347 TTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 403



 Score = 82.4 bits (202), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 45/64 (70%), Gaps = 1/64 (1%)

Query: 668 DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
           D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R  +P  R L+FD  EFH
Sbjct: 427 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKANRDPKPPRRPLIFDTHEFH 486

Query: 727 FPQV 730
            P V
Sbjct: 487 IPLV 490


>gi|149015767|gb|EDL75115.1| similar to polymerase (RNA) III (DNA directed) (155kD) [Rattus
            norvegicus]
          Length = 745

 Score =  350 bits (898), Expect = 4e-93,   Method: Compositional matrix adjust.
 Identities = 213/484 (44%), Positives = 289/484 (59%), Gaps = 77/484 (15%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFL--QDTSENFVRDIK 1054
            G   P+E KR+LD+I A    +S+ +LS  E+   +   +   EFL  QD+   F+++IK
Sbjct: 269  GKDEPLEFKRVLDNIKAVYPCQSERALSKNELTLTTEAIMKKNEFLCCQDS---FLQEIK 325

Query: 1055 KFLEEFSKKESVTS-----HQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREK 1109
             F++  S+K   T      + +  ++P   ++L   D+I   +           E CR+K
Sbjct: 326  TFIKGVSEKIKKTRDKYGINDNGTTEP---RVLYQLDRITRTQIEKFL------ETCRDK 376

Query: 1110 YVRAQI---------------EPAT----------AVGAL--------------AAQSIG 1130
            Y+RAQ+               EP T           V ++              A+++I 
Sbjct: 377  YMRAQMEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAIS 436

Query: 1131 EPGTQMTLKTFHFA---------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLH 1175
             P     L     A               GE+ EYIEEVF+PDD FIL+KL ++RIRLL 
Sbjct: 437  TPIITAQLDMDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLR 496

Query: 1176 LEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVI 1232
            LEV+ +++RY  C  + R   G + V G + + + P+++SKS    + Q +K+ LP VV+
Sbjct: 497  LEVNAETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVVV 556

Query: 1233 KGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIE 1292
            +G+  ++RAVIH ++  G  K+KLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIE
Sbjct: 557  QGIPEVSRAVIHIDEQSGKEKFKLLVEGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGIE 616

Query: 1293 AARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASF 1352
            AAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASF
Sbjct: 617  AARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASF 676

Query: 1353 ENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDN 1411
            E T+DHLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R  +P  R L+FD 
Sbjct: 677  EKTADHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKANRDPKPPRRPLIFDT 736

Query: 1412 PEFH 1415
             EFH
Sbjct: 737  HEFH 740



 Score =  287 bits (734), Expect = 4e-74,   Method: Compositional matrix adjust.
 Identities = 145/237 (61%), Positives = 185/237 (78%), Gaps = 3/237 (1%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
           GVPRIKEIINAS+ ISTPIITA LD D D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 421 GVPRIKEIINASKAISTPIITAQLDMDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 480

Query: 824 SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
            FIL+KL ++RIRLL LEV+ +++RY  C  + R   G + V G + + + P+++SKS  
Sbjct: 481 CFILVKLSLERIRLLRLEVNAETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSM 540

Query: 882 SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
             + Q +K+ LP VV++G+  ++RAVIH ++  G  K+KLLVEGDNLR VMAT+GVKG +
Sbjct: 541 YYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKFKLLVEGDNLRAVMATHGVKGTR 600

Query: 941 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 601 TTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 657



 Score =  116 bits (291), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 185 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 244



 Score = 99.8 bits (247), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/69 (63%), Positives = 54/69 (78%)

Query: 551 LAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           + GSMDK TLGSG K N+FYILLRD+G++ A  AM RL+R+   YL NRGFSIGIGDVTP
Sbjct: 1   MCGSMDKGTLGSGSKNNIFYILLRDWGQNEAADAMSRLARLAPVYLSNRGFSIGIGDVTP 60

Query: 611 GQGFVQNSF 619
           GQG ++  +
Sbjct: 61  GQGLLKAKY 69



 Score = 82.0 bits (201), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 45/64 (70%), Gaps = 1/64 (1%)

Query: 668 DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
           D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R  +P  R L+FD  EFH
Sbjct: 681 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKANRDPKPPRRPLIFDTHEFH 740

Query: 727 FPQV 730
            P V
Sbjct: 741 IPLV 744


>gi|324500904|gb|ADY40409.1| DNA-directed RNA polymerase III subunit RPC1 [Ascaris suum]
          Length = 1405

 Score =  347 bits (890), Expect = 3e-92,   Method: Compositional matrix adjust.
 Identities = 166/276 (60%), Positives = 202/276 (73%), Gaps = 20/276 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DNDVVLFNRQPSLHK+SIM+HRAK++P RTFRFNEC CTPYNADFDGDEMN+H+PQT EA
Sbjct: 453 DNDVVLFNRQPSLHKISIMSHRAKIVPGRTFRFNECACTPYNADFDGDEMNLHVPQTYEA 512

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA               +LM  KSNL+TPR+GE LIAA QDFITGGYL+T K++FF R
Sbjct: 513 RAEA--------------SLLMGVKSNLITPRSGEPLIAAIQDFITGGYLMTHKDSFFPR 558

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           ++  R AS +I   +      K+ S     P    +   +WTGKQ+  LI++P+ D  V+
Sbjct: 559 SEVHRFASAIIDANA------KKQSRIRIPPPAIRKPVELWTGKQLVELIIRPDVDSKVS 612

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            NL TK ++YT NEEFC +DSYVI+RNS L+ G +DK+ LGSG K N+FYILLRDFGED 
Sbjct: 613 LNLTTKNKSYTGNEEFCVKDSYVIIRNSVLICGVLDKALLGSGSKTNIFYILLRDFGEDA 672

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           AV AMWRL+RM   YL NRGFSIGIGDV PG+G ++
Sbjct: 673 AVDAMWRLARMAPVYLTNRGFSIGIGDVRPGEGLLK 708



 Score =  268 bits (686), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 161/373 (43%), Positives = 218/373 (58%), Gaps = 65/373 (17%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCE 1149
            E C +K  RA  EP TAVGA+AA SIGEP TQMTLKTFHFAG              E+  
Sbjct: 1032 ELCNDKLKRAVTEPGTAVGAIAATSIGEPSTQMTLKTFHFAGVASMNITQGVPRIKEIIN 1091

Query: 1150 YIEEVFVP----------------------------------------DDSFILIKLDMD 1169
             ++ +  P                                        DD F+L+K++  
Sbjct: 1092 GVKLISTPIITAALSNEKDESLARRVKARIEKTTLGEICEYIEEVYLPDDCFVLVKINAK 1151

Query: 1170 RIRLLHLEVDIDSIRYCIERTRGIS----GHLTVSGHSFLILKPKDSSKSFNSKMYQMKQ 1225
            R+RLL LE+ + SI   I  T+         + + G + L+++P D +K   SKM  ++ 
Sbjct: 1152 RVRLLQLEITMGSIAQSICSTKLPVPVKLNQIRILGKTILVIRPPDLAKC--SKMMAIQY 1209

Query: 1226 L---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNT 1282
            L   L +VV+KG+ G+ R VI  ++ +G   YKLLVEG + + VMAT G+ G +   NN 
Sbjct: 1210 LKYNLTNVVVKGLPGVVRCVITADEKKG-DSYKLLVEGTDYQSVMATMGIDGRRTYFNNA 1268

Query: 1283 YEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKM 1342
              V + LGIEAAR++I++EI   ME+HG+ +D RH ML+AD+MT +GEVLGITR+GL KM
Sbjct: 1269 LTVAEVLGIEAARTSIISEILSTMESHGIGLDQRHVMLLADVMTYRGEVLGITRNGLVKM 1328

Query: 1343 KESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEP 1402
            KESVL LASFE T+DHL++AAF+ Q D I+GVSECIIMG PM +GTGL K+L    +   
Sbjct: 1329 KESVLLLASFEKTTDHLYEAAFFSQEDKIAGVSECIIMGTPMTIGTGLFKVLYNHGKPPN 1388

Query: 1403 V-PRTLLFDNPEF 1414
            V P+  +F+ PEF
Sbjct: 1389 VQPKLTIFETPEF 1401



 Score =  222 bits (565), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 124/292 (42%), Positives = 178/292 (60%), Gaps = 25/292 (8%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQR-TPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFG 149
           + ++Q +HI + +  LY + P R  P P G LD R+GT QK  +C TC QNL+DCVGHFG
Sbjct: 26  ETMRQVAHIPVFNNKLYDECPGRWIPAPFGPLDPRLGTCQKNTDCQTCKQNLTDCVGHFG 85

Query: 150 YIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSL 209
           Y+DL LPVFH+G+FR  I +LQ ICK+  C+ +LL  E+   F  ++ NP L YL RK+L
Sbjct: 86  YVDLALPVFHVGFFRLTIQMLQCICKH--CSGLLLSGEQRKAFLRQVNNPNLDYLRRKAL 143

Query: 210 KKKILETTKKVSVCPHCGEINGVVKKC--GLLKISHEKYKNRTKKKDAIVEDLLAEYNEA 267
            K+I+  +KK+++CPHCG  NGVVKK    +LKI+H          D I  D ++++  A
Sbjct: 144 HKRIVAASKKITICPHCGHKNGVVKKAVGAVLKIAH---------MDPIPADKISKFVCA 194

Query: 268 VKFNPEIEA---HKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMN--AELSKPSDLILTR 322
            + N E+       KF L   LNPLEV ++F  + LED+PLL++      + P D++ TR
Sbjct: 195 AQENKELSTLLPKVKFSL---LNPLEVQKIFSKVRLEDVPLLMIRPFGSHNHPVDVLFTR 251

Query: 323 LLVPPNCIRPSVISDLKS---DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTF 371
           L VPP CIRPSV+S++KS   ++D+ +   +  L    I  H+    P +T 
Sbjct: 252 LPVPPCCIRPSVVSEVKSGTTEDDITMKLSEIMLINDIIRKHKKDGAPAKTI 303



 Score =  212 bits (540), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 117/241 (48%), Positives = 163/241 (67%), Gaps = 10/241 (4%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIIN  + ISTPIITA L  + D   AR VK R+E+TTLGE+CEYIEEV++PDD
Sbjct: 1082 GVPRIKEIINGVKLISTPIITAALSNEKDESLARRVKARIEKTTLGEICEYIEEVYLPDD 1141

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS----GHLTVSGHSFLILKPKDSSKS 879
             F+L+K++  R+RLL LE+ + SI   I  T+         + + G + L+++P D +K 
Sbjct: 1142 CFVLVKINAKRVRLLQLEITMGSIAQSICSTKLPVPVKLNQIRILGKTILVIRPPDLAKC 1201

Query: 880  FNSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGV 936
              SKM  ++ L   L +VV+KG+ G+ R VI  ++ +G   YKLLVEG + + VMAT G+
Sbjct: 1202 --SKMMAIQYLKYNLTNVVVKGLPGVVRCVITADEKKG-DSYKLLVEGTDYQSVMATMGI 1258

Query: 937  KGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL 996
             G +   NN   V + LGIEAAR++I++EI   ME+HG+ +D RH ML+AD+MT +GEVL
Sbjct: 1259 DGRRTYFNNALTVAEVLGIEAARTSIISEILSTMESHGIGLDQRHVMLLADVMTYRGEVL 1318

Query: 997  G 997
            G
Sbjct: 1319 G 1319



 Score =  114 bits (286), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 53/61 (86%), Positives = 56/61 (91%), Gaps = 1/61 (1%)

Query: 609 TPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV+NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVK LEDLCV Y
Sbjct: 824 TPAAKGFVENSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKCLEDLCVNY 883

Query: 668 D 668
           D
Sbjct: 884 D 884



 Score = 75.1 bits (183), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 35/60 (58%), Positives = 44/60 (73%)

Query: 13  YATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLI 72
           Y  R    +LM  KSNL+TPR+GE LIAA QDFITGGYL+T K++FF R++  R AS +I
Sbjct: 510 YEARAEASLLMGVKSNLITPRSGEPLIAAIQDFITGGYLMTHKDSFFPRSEVHRFASAII 569



 Score = 62.8 bits (151), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 30/61 (49%), Positives = 40/61 (65%), Gaps = 1/61 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPV-PRTLLFDNPEFH 726
            D  ++AAF+ Q D I+GVSECIIMG PM +GTGL K+L    +   V P+  +F+ PEF 
Sbjct: 1343 DHLYEAAFFSQEDKIAGVSECIIMGTPMTIGTGLFKVLYNHGKPPNVQPKLTIFETPEFR 1402

Query: 727  F 727
             
Sbjct: 1403 L 1403


>gi|327276885|ref|XP_003223197.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1-like
           [Anolis carolinensis]
          Length = 1337

 Score =  347 bits (890), Expect = 3e-92,   Method: Compositional matrix adjust.
 Identities = 166/280 (59%), Positives = 203/280 (72%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDIVLFNRQPSLHKLSIMAHIARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+T +I ++++    +   +          P   ++   +WTGKQ+F +ILKP++ CPV 
Sbjct: 562 AKTCQIIASILVGKDEKIKV-------HLPPPAILKPVTLWTGKQVFGVILKPSKSCPVK 614

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DSYV + NSEL++GSMDK TLGSG K N+FYILLRD+G+ 
Sbjct: 615 ANLRTKGKQYCGKGEDLCTNDSYVTIHNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQV 674

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 675 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 714



 Score =  289 bits (740), Expect = 7e-75,   Method: Compositional matrix adjust.
 Identities = 173/395 (43%), Positives = 233/395 (58%), Gaps = 72/395 (18%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A   SRS+P+LS  E++  +   +   EFL    ++F+++IKKF
Sbjct: 914  GKDEPLEFKRVLDNIRAVYPSRSEPALSKNELMLTAESIMKKNEFLC-CQDSFLQEIKKF 972

Query: 1057 LEEFSKKESVTS-----HQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYV 1111
            ++  S+K   T      + +  ++P    +L   D+I       P       E CREKY+
Sbjct: 973  IKNMSEKIKKTRDKYGINDNGTTEPY---VLYQLDRI------TPTQLEKFLETCREKYM 1023

Query: 1112 RAQIEPATAVGALAAQSIGEPGTQMTLKTFH----------------------------- 1142
            RAQ+EP +AVGAL AQSIGEPGTQMTLKTFH                             
Sbjct: 1024 RAQMEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTP 1083

Query: 1143 -------------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLE 1177
                         FA            GE+ EYIEEVF+PDD FIL+KL ++RIRLL LE
Sbjct: 1084 IITAHLDTDDDPDFARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLE 1143

Query: 1178 VDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKG 1234
            V+ +++RY  C+ + R   G + V G + + + P++SSKS    + Q +K+ LP VV++G
Sbjct: 1144 VNAETVRYSICVSKLRVKPGDVAVHGEAVVCVTPRESSKSSMYYVLQSLKEELPKVVVQG 1203

Query: 1235 VQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAA 1294
            +  + RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG   +SNNTYEV KTLGIEA+
Sbjct: 1204 IPEVARAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTSTTSNNTYEVEKTLGIEAS 1263

Query: 1295 RSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 1329
            R+TI+ EI+  M NHGMSID RH ML++DLMT K 
Sbjct: 1264 RTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKA 1298



 Score =  279 bits (713), Expect = 9e-72,   Method: Compositional matrix adjust.
 Identities = 143/254 (56%), Positives = 182/254 (71%), Gaps = 5/254 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD   +P+ HG+LD RMGT++K+  C TCG+NL++C+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNNHSPLLHGVLDHRMGTSEKDRPCETCGKNLAECLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYF+ +I ILQ ICK  TC  ++L  E+   F   L+ P L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFKAIIGILQMICK--TCCHIMLTVEEQKQFLDYLKRPGLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KK+ E  +K + CPHCG  NG VKKCGLLKI HEKYK   K  D IV + +  ++ A++ 
Sbjct: 144 KKVSEKCRKKNTCPHCGAFNGTVKKCGLLKIIHEKYKTTKKIMDPIVSNFIQSFDTAIEH 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N EIE+    G  Q  LNPL VL L + IP EDIPLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NKEIES--LLGKAQENLNPLVVLNLLKRIPAEDIPLLLMNPESGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKSDND 343
           IRPSV+SDLKS  +
Sbjct: 262 IRPSVVSDLKSGTN 275



 Score =  277 bits (709), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 140/233 (60%), Positives = 180/233 (77%), Gaps = 3/233 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA+LD D D D+AR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1066 GVPRIKEIINASKAISTPIITAHLDTDDDPDFARLVKGRIEKTLLGEISEYIEEVFLPDD 1125

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  C+ + R   G + V G + + + P++SSKS  
Sbjct: 1126 CFILVKLSLERIRLLRLEVNAETVRYSICVSKLRVKPGDVAVHGEAVVCVTPRESSKSSM 1185

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + Q +K+ LP VV++G+  + RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG  
Sbjct: 1186 YYVLQSLKEELPKVVVQGIPEVARAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTS 1245

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
             +SNNTYEV KTLGIEA+R+TI+ EI+  M NHGMSID RH ML++DLMT K 
Sbjct: 1246 TTSNNTYEVEKTLGIEASRTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKA 1298



 Score =  116 bits (291), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 52/64 (81%), Positives = 58/64 (90%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 830 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 889

Query: 671 FDAA 674
             ++
Sbjct: 890 VRSS 893



 Score = 76.3 bits (186), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 34/55 (61%), Positives = 45/55 (81%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+T +I ++++ G+
Sbjct: 521 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKTCQIIASILVGK 575


>gi|344251250|gb|EGW07354.1| DNA-directed RNA polymerase III subunit RPC1 [Cricetulus griseus]
          Length = 1076

 Score =  345 bits (886), Expect = 8e-92,   Method: Compositional matrix adjust.
 Identities = 169/280 (60%), Positives = 207/280 (73%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 435 DGDVVLFNRQPSLHKLSIMAHLARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 494

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 495 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 540

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++       G  ++   R   P + ++   +WTGKQIFS+IL+P+ D PV 
Sbjct: 541 AKACQIIASILV------GKDEKIKVRLPPPTI-LKPVTLWTGKQIFSIILRPSDDSPVR 593

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DSYV ++NSEL++GSMDK TLGSG K N+FYILLRD+G++
Sbjct: 594 ANLRTKGKQYCGKGEDLCVNDSYVTIQNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQN 653

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 654 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 693



 Score =  293 bits (749), Expect = 6e-76,   Method: Compositional matrix adjust.
 Identities = 143/251 (56%), Positives = 179/251 (71%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD    P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 5   EEMRQQAHIQVVSKNLYSQDNNHAPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 64

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYFR VI ILQ ICK  TC  ++L +E+   F   L+ P L+YL ++ LK
Sbjct: 65  IDLELPCFHVGYFRAVIGILQMICK--TCCHIMLSQEEKQQFLDFLKRPGLTYLQKRGLK 122

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K S C +CG  NG VKKCGLLKI HEKYK   K  D +V + L  +  A++ 
Sbjct: 123 KKISDKCRKKSTCHYCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPVVSNFLQSFETAIEH 182

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP ED+PLLLMN E  KPSDLILTRLLVPP C
Sbjct: 183 NKEVEPL--LGRAQENLNPLVVLNLFKRIPAEDVPLLLMNPEAGKPSDLILTRLLVPPLC 240

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 241 IRPSVVSDLKS 251



 Score = 76.3 bits (186), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 35/46 (76%), Positives = 40/46 (86%)

Query: 1328 KGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISG 1373
            +GEVLGITR GLAKMKESVL LASFE T+DHLFDAA++GQ D + G
Sbjct: 1018 EGEVLGITRFGLAKMKESVLMLASFEKTADHLFDAAYFGQKDSVCG 1063



 Score = 74.7 bits (182), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 500 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 554


>gi|354482229|ref|XP_003503302.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1-like
           [Cricetulus griseus]
          Length = 1280

 Score =  345 bits (885), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 169/280 (60%), Positives = 207/280 (73%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDVVLFNRQPSLHKLSIMAHLARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++       G  ++   R   P + ++   +WTGKQIFS+IL+P+ D PV 
Sbjct: 562 AKACQIIASILV------GKDEKIKVRLPPPTI-LKPVTLWTGKQIFSIILRPSDDSPVR 614

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DSYV ++NSEL++GSMDK TLGSG K N+FYILLRD+G++
Sbjct: 615 ANLRTKGKQYCGKGEDLCVNDSYVTIQNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQN 674

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 675 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 714



 Score =  293 bits (751), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 143/251 (56%), Positives = 179/251 (71%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD    P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNNHAPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYFR VI ILQ ICK  TC  ++L +E+   F   L+ P L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFRAVIGILQMICK--TCCHIMLSQEEKQQFLDFLKRPGLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K S C +CG  NG VKKCGLLKI HEKYK   K  D +V + L  +  A++ 
Sbjct: 144 KKISDKCRKKSTCHYCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPVVSNFLQSFETAIEH 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP ED+PLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NKEVEPL--LGRAQENLNPLVVLNLFKRIPAEDVPLLLMNPEAGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 262 IRPSVVSDLKS 272



 Score =  170 bits (431), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 142/412 (34%), Positives = 209/412 (50%), Gaps = 53/412 (12%)

Query: 614  FVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDA 673
            FV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++  +
Sbjct: 833  FVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLTVRS 892

Query: 674  AFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVYYE 733
            +       I G             G GL        + EP+    + DN +  +P     
Sbjct: 893  STGDIIQFIYG-------------GDGLDPAAME-GKDEPLEFKRVLDNIKAVYPC---- 934

Query: 734  RRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINASRNISTPIITA---YLDKD 790
             + + ++        T  +    ++   QD    ++EI    + +S  I      Y   D
Sbjct: 935  -QSEPALSKNELTLTTEAIMKKNEFLCCQDSF--LQEIKTFIKGVSEKIKKTRDKYGIND 991

Query: 791  TDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDM----DRIRLLHLEVDIDS 846
                  R++  +L+R T  ++ +++E      D ++  KL +      + L    V+ ++
Sbjct: 992  NGTTEPRVLY-QLDRITPTQIEKFLETC---RDKYMRWKLTVVVRGAGMLLEKARVNAET 1047

Query: 847  IRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQ--- 900
            +RY  C  + R   G + V G + + + P+++SKS    + Q +K+ LP V  + V+   
Sbjct: 1048 VRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVNAETVRYSI 1107

Query: 901  -------GINRAVIHEEDVEGVT-----KYKLLVEGDNLR-DVMATYGVKGVKCS--SNN 945
                         +H E V  VT     K  +      L+ D+   +G    + S  + +
Sbjct: 1108 CTSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKDWGSSQKELSPLTPS 1167

Query: 946  TYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            + +V KTLGIEAAR+TI+ EI+  M NHGMSI+ RH ML++DLMT KGEVLG
Sbjct: 1168 SAQVEKTLGIEAARTTIINEIQYTMFNHGMSINRRHVMLLSDLMTYKGEVLG 1219



 Score =  166 bits (420), Expect = 9e-38,   Method: Compositional matrix adjust.
 Identities = 138/426 (32%), Positives = 204/426 (47%), Gaps = 79/426 (18%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A    +S+P+LS  E+   +   +   EFL    ++F+++IK F
Sbjct: 914  GKDEPLEFKRVLDNIKAVYPCQSEPALSKNELTLTTEAIMKKNEFLC-CQDSFLQEIKTF 972

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+R +
Sbjct: 973  IKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQIEKFLETCRDKYMRWK 1026

Query: 1115 I-----------EPATAVGALAAQSIGEPGTQMTLKTFHFAGE--VCEYIEEVFVPDDSF 1161
            +           E A         SI     ++        GE  VC    E       +
Sbjct: 1027 LTVVVRGAGMLLEKARVNAETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYY 1086

Query: 1162 ILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSK 1219
            +L  L  D  +     V+ +++RY  C  + R   G + V G + + + P+++SKS    
Sbjct: 1087 VLQFLKEDLPK-----VNAETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKS---S 1138

Query: 1220 MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCS- 1278
            MY + Q L                                     D+   +G    + S 
Sbjct: 1139 MYYVLQFLKE-----------------------------------DLPKDWGSSQKELSP 1163

Query: 1279 -SNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRH 1337
             + ++ +V KTLGIEAAR+TI+ EI+  M NHGMSI+ RH ML++DLMT KGEVLGITR 
Sbjct: 1164 LTPSSAQVEKTLGIEAARTTIINEIQYTMFNHGMSINRRHVMLLSDLMTYKGEVLGITRF 1223

Query: 1338 GLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ-A 1396
            GLAKMKESVL LASFE T+DHLFDAA++GQ D +     C++ G    + T  + LLQ  
Sbjct: 1224 GLAKMKESVLMLASFEKTADHLFDAAYFGQKDSV-----CVVFG----INTECVYLLQNQ 1274

Query: 1397 VPRSEP 1402
             P  EP
Sbjct: 1275 SPNIEP 1280



 Score = 74.7 bits (182), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 521 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 575


>gi|431904080|gb|ELK09502.1| DNA-directed RNA polymerase III subunit RPC1 [Pteropus alecto]
          Length = 1375

 Score =  345 bits (884), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 169/280 (60%), Positives = 207/280 (73%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDVVLFNRQPSLHKLSIMAHLARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++       G  ++   R   P + ++   +WTGKQIFS+IL+P+ D PV 
Sbjct: 562 AKACQIIASILV------GKDEKIKVRLPPPTI-LKPVTLWTGKQIFSVILRPSDDNPVR 614

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DSYV ++NSEL++GSMDK TLGSG K N+FYILLRD+G++
Sbjct: 615 ANLRTKGKQYCGKGEDLCINDSYVTIQNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQN 674

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 675 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 714



 Score =  322 bits (825), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 207/477 (43%), Positives = 279/477 (58%), Gaps = 78/477 (16%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A    +S+P+LS  E++  +   +   EFL    ++F+++IKKF
Sbjct: 914  GKDEPLEFKRVLDNIKAVFPCQSEPALSKNELILTTESIMKKNEFLC-CQDSFLQEIKKF 972

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 973  IKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQIEKFLETCRDKYMRAQ 1026

Query: 1115 IEP--------ATAVGALAAQ----------------SIGEPGTQMTLKTFH-------- 1142
            +EP        A ++G    Q                ++G P  +  +            
Sbjct: 1027 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1086

Query: 1143 ----------------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                                    GE+ EYIEEVF+PDD FIL+KL ++RIRLL LE+ +
Sbjct: 1087 AQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLELRV 1146

Query: 1181 DSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQGIN 1239
                          G + V G + + + P+++SKS    + Q +K+ LP VV++G+  ++
Sbjct: 1147 KP------------GDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPEVS 1194

Query: 1240 RAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIM 1299
            RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+TI+
Sbjct: 1195 RAVIHIDEQSG-KKYKLLVEGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAARTTII 1253

Query: 1300 TEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHL 1359
             EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+DHL
Sbjct: 1254 NEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTADHL 1313

Query: 1360 FDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP-RTLLFDNPEFH 1415
            FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R    P R L+FD  EFH
Sbjct: 1314 FDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPSPPRRPLIFDTNEFH 1370



 Score =  295 bits (756), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 143/251 (56%), Positives = 180/251 (71%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD    P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNNHAPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYFR VI ILQ ICK  TC  ++L +E+   F   L+ P L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFRAVIGILQMICK--TCCHIMLSQEEKKQFLDYLKRPGLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K ++C HCG  NG VKKCGLLKI HEKYK   K  D +V + L  +  A++ 
Sbjct: 144 KKISDKCRKKNICHHCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPMVSNFLQSFETAIEH 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP ED+PLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NKEVEPL--LGRAQENLNPLVVLNLFKRIPAEDVPLLLMNPEAGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 262 IRPSVVSDLKS 272



 Score =  249 bits (637), Expect = 6e-63,   Method: Compositional matrix adjust.
 Identities = 142/235 (60%), Positives = 178/235 (75%), Gaps = 14/235 (5%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LDKD D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1066 GVPRIKEIINASKAISTPIITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 1125

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSK 883
             FIL+KL ++RIRLL LE+ +              G + V G + + + P+++SKS    
Sbjct: 1126 CFILVKLSLERIRLLRLELRVK------------PGDVAVHGEAVVCVTPRENSKSSMYY 1173

Query: 884  MYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCS 942
            + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG + +
Sbjct: 1174 VLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSG-KKYKLLVEGDNLRAVMATHGVKGTRTT 1232

Query: 943  SNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1233 SNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1287



 Score =  116 bits (291), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 830 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 889



 Score = 81.6 bits (200), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP-RTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R    P R L+FD  EFH
Sbjct: 1311 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPSPPRRPLIFDTNEFH 1370

Query: 727  FPQV 730
             P V
Sbjct: 1371 IPLV 1374



 Score = 74.7 bits (182), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 521 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 575


>gi|20159751|gb|AAM12030.1| RNA polymerase III subunit RPC155-B [Homo sapiens]
          Length = 387

 Score =  344 bits (883), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 167/280 (59%), Positives = 204/280 (72%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 92  DGDVVLFNRQPSLHKLSIMAHLARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 151

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 152 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 197

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++    +   +          P   ++   +WTGKQIFS+IL+P+ D PV 
Sbjct: 198 AKACQIIASILVGKDEKIKV-------RLPPPTILKPVTLWTGKQIFSVILRPSDDNPVR 250

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DSYV ++NSEL++GSMDK TLGSG K N+FYILLRD+G++
Sbjct: 251 ANLRTKGKQYCGKGEDLCANDSYVTIQNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQN 310

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG ++  +
Sbjct: 311 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKY 350



 Score = 73.9 bits (180), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 157 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 211


>gi|344274310|ref|XP_003408960.1| PREDICTED: LOW QUALITY PROTEIN: DNA-directed RNA polymerase III
           subunit RPC1-like [Loxodonta africana]
          Length = 1392

 Score =  344 bits (882), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 169/280 (60%), Positives = 206/280 (73%), Gaps = 22/280 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDVVLFNRQPSLHKLSIMAHLARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++       G  ++   R   P + ++   +WTGKQIFS+IL+P+ D PV 
Sbjct: 562 AKACQIIASILV------GKDEKIKVRLPPPTI-LKPVTLWTGKQIFSVILRPSDDNPVR 614

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           ANL+TKG+ Y    E+ C  DSYV ++NSEL++GSMDK TLGSG K N+FYILLRD+G++
Sbjct: 615 ANLRTKGKQYCGKGEDLCVNDSYVTIQNSELMSGSMDKGTLGSGSKNNIFYILLRDWGQN 674

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
            A  AM RL+R+   YL NRGFSIGIGDVTPGQG +   +
Sbjct: 675 EAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLTAKY 714



 Score =  323 bits (829), Expect = 3e-85,   Method: Compositional matrix adjust.
 Identities = 205/481 (42%), Positives = 277/481 (57%), Gaps = 69/481 (14%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E KR+LD+I A     S+P+LS  E L L+ E++  K   +   ++F+++IKKF
Sbjct: 914  GKDEPLEFKRVLDNIKAVFPCPSEPALSRNE-LTLTMESIMQKSEFRCCQDSFLQEIKKF 972

Query: 1057 LEEFSKKESVTSHQDKVSQ--PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            ++  S+K   T  +  ++       ++L   D+I       P       E CR+KY+RAQ
Sbjct: 973  VKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRI------TPTQIEKFLETCRDKYMRAQ 1026

Query: 1115 IEP--------ATAVGALAAQ----------------SIGEPGTQMTLKTFH-------- 1142
            +EP        A ++G    Q                ++G P  +  +            
Sbjct: 1027 MEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIIT 1086

Query: 1143 ----------------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 1180
                                    GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ 
Sbjct: 1087 AQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNA 1146

Query: 1181 DSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQM-KQLLPSVVIKGVQG 1237
            +++RY  C  + R   G + V G + + + P+++SKS    + Q+ K+ LP VV++ +  
Sbjct: 1147 ETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQLLKEDLPKVVVQVIPE 1206

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRD-VMATYGVKGVKCSSNNT-YEVYKTLGIEAAR 1295
            ++RAVIH ++  G  KYKLLVEGD     VMAT GVKG +     T  EV KTLGIEAAR
Sbjct: 1207 VSRAVIHIDEQSGKEKYKLLVEGDKPGGPVMATTGVKGNRDHPPKTPLEVEKTLGIEAAR 1266

Query: 1296 STIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENT 1355
            +TI+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T
Sbjct: 1267 TTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKT 1326

Query: 1356 SDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEF 1414
            +DHLFDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EF
Sbjct: 1327 ADHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPNPPKRPLIFDTNEF 1386

Query: 1415 H 1415
            H
Sbjct: 1387 H 1387



 Score =  293 bits (749), Expect = 6e-76,   Method: Compositional matrix adjust.
 Identities = 142/251 (56%), Positives = 179/251 (71%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD    P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNNHAPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           +DL LP FH+GYFR VI ILQ ICK  TC  ++L +E+   F   L+ P L+YL ++ LK
Sbjct: 86  VDLELPCFHVGYFRAVIGILQMICK--TCCHIMLSQEEKKQFLDYLKRPGLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K ++C  CG  NG VKKCGLLKI HEKYK   K  D IV + L  +  A++ 
Sbjct: 144 KKISDKCRKKTICHQCGAFNGTVKKCGLLKIIHEKYKTNKKIVDPIVSNFLQSFETAIEH 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP ED+PLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NKEVEPL--LGRAQENLNPLVVLNLFKRIPAEDVPLLLMNPEAGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 262 IRPSVVSDLKS 272



 Score =  254 bits (649), Expect = 3e-64,   Method: Compositional matrix adjust.
 Identities = 139/239 (58%), Positives = 176/239 (73%), Gaps = 5/239 (2%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA LDKD D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 1066 GVPRIKEIINASKAISTPIITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDD 1125

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KL ++RIRLL LEV+ +++RY  C  + R   G + V G + + + P+++SKS  
Sbjct: 1126 CFILVKLSLERIRLLRLEVNAETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSM 1185

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRD-VMATYGVKGV 939
              + Q +K+ LP VV++ +  ++RAVIH ++  G  KYKLLVEGD     VMAT GVKG 
Sbjct: 1186 YYVLQLLKEDLPKVVVQVIPEVSRAVIHIDEQSGKEKYKLLVEGDKPGGPVMATTGVKGN 1245

Query: 940  KCSSNNT-YEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +     T  EV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 1246 RDHPPKTPLEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 1304



 Score =  116 bits (291), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC QYD++
Sbjct: 830 AKGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLT 889



 Score = 81.6 bits (200), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
            D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 1328 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPNPPKRPLIFDTNEFH 1387

Query: 727  FPQV 730
             P V
Sbjct: 1388 IPLV 1391



 Score = 74.7 bits (182), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 521 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 575


>gi|390334195|ref|XP_781681.2| PREDICTED: DNA-directed RNA polymerase III subunit RPC1-like,
           partial [Strongylocentrotus purpuratus]
          Length = 681

 Score =  343 bits (880), Expect = 4e-91,   Method: Compositional matrix adjust.
 Identities = 207/447 (46%), Positives = 263/447 (58%), Gaps = 66/447 (14%)

Query: 608 VTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           +   +GFV+NSF+SGLTP+EFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC  Y
Sbjct: 155 IPAAKGFVKNSFYSGLTPSEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSHY 214

Query: 668 DMSFDAAF-------YGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTL-- 718
           D +   +        YG      G+    + G    V   L ++LQ V    P  +    
Sbjct: 215 DQTVRNSMSDIIQFKYGD----DGLDPAAMEGKGKQVD--LPRVLQHVQNKYPSKKEYSL 268

Query: 719 -----------LFDNPEF-HFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQD--- 763
                      +  + EF    Q +    RDY  +   S++ +   +   + +   D   
Sbjct: 269 GSIDIRRMAGEILKSKEFAECSQEFKTTLRDYIDECCTSLQKSRRAYKIAEAQTEPDVLY 328

Query: 764 ---------------------------GVPRIKEIINASRNISTPIITAYLDKDTDLDYA 796
                                      GVPRIKEIINAS+NISTPIITA LD   D D+A
Sbjct: 329 QLHRFTSTQLHHFLTMCKTKHQRHITLGVPRIKEIINASKNISTPIITAELDIVNDADFA 388

Query: 797 RIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSI--RYCIERT 854
           R+VKGR+E+T LGEV EYIEEVF+PD+ F+LIKLD+DRIRLL LEV  +SI    C  + 
Sbjct: 389 RLVKGRIEKTLLGEVSEYIEEVFLPDNCFVLIKLDLDRIRLLKLEVSAESICMSICASKL 448

Query: 855 RGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ----MKQLLPSVVIKGVQGINRAVIHEE 910
           +   G L     + + ++P ++SKS    MY     +KQ + +VVI+G   ++RAVIH +
Sbjct: 449 KVKPGQLRAVAENLITVEPAETSKS---SMYYNLQFLKQSVANVVIQGSPNVSRAVIHID 505

Query: 911 DVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVM 970
           +  G  KYKLLVEGDNL+ V+AT GVKG   +SNNT E+ KTLGIEAAR  IM+EI+  M
Sbjct: 506 EKAGELKYKLLVEGDNLQGVIATRGVKGTHTTSNNTVEMEKTLGIEAARRCIMSEIEYTM 565

Query: 971 ENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +HGMSID RH ML+ DLMT K  VLG
Sbjct: 566 VSHGMSIDHRHVMLLGDLMTYKXXVLG 592



 Score =  320 bits (821), Expect = 3e-84,   Method: Compositional matrix adjust.
 Identities = 195/441 (44%), Positives = 265/441 (60%), Gaps = 29/441 (6%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G G  V+L R+L  +  K  S+ + SL + +I  ++ E L SKEF  + S+ F   ++ +
Sbjct: 242  GKGKQVDLPRVLQHVQNKYPSKKEYSLGSIDIRRMAGEILKSKEF-AECSQEFKTTLRDY 300

Query: 1057 LEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIE 1116
            ++E       +    K+++   E  + +Q       + + F + CK +   ++++   + 
Sbjct: 301  IDECCTSLQKSRRAYKIAEAQTEPDVLYQLHRFTSTQLHHFLTMCKTK--HQRHITLGV- 357

Query: 1117 PATAVGALAAQSIGEPGTQMTLKTFHFA---------------GEVCEYIEEVFVPDDSF 1161
            P       A+++I  P     L   + A               GEV EYIEEVF+PD+ F
Sbjct: 358  PRIKEIINASKNISTPIITAELDIVNDADFARLVKGRIEKTLLGEVSEYIEEVFLPDNCF 417

Query: 1162 ILIKLDMDRIRLLHLEVDIDSI--RYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSK 1219
            +LIKLD+DRIRLL LEV  +SI    C  + +   G L     + + ++P ++SKS    
Sbjct: 418  VLIKLDLDRIRLLKLEVSAESICMSICASKLKVKPGQLRAVAENLITVEPAETSKS---S 474

Query: 1220 MYQ----MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 1275
            MY     +KQ + +VVI+G   ++RAVIH ++  G  KYKLLVEGDNL+ V+AT GVKG 
Sbjct: 475  MYYNLQFLKQSVANVVIQGSPNVSRAVIHIDEKAGELKYKLLVEGDNLQGVIATRGVKGT 534

Query: 1276 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGIT 1335
              +SNNT E+ KTLGIEAAR  IM+EI+  M +HGMSID RH ML+ DLMT K  VLGIT
Sbjct: 535  HTTSNNTVEMEKTLGIEAARRCIMSEIEYTMVSHGMSIDHRHVMLLGDLMTYKXXVLGIT 594

Query: 1336 RHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 1395
            R GLA MKESVL LASFE TSDHLF+AA++GQ D I GVSECIIMG+PMNVGTG+ KLL 
Sbjct: 595  RFGLANMKESVLMLASFERTSDHLFEAAYFGQKDAICGVSECIIMGIPMNVGTGIFKLLH 654

Query: 1396 AVPRS-EPVPRTLLFDNPEFH 1415
               +   P  R LLFDNPE H
Sbjct: 655  KSDKPVHPPRRNLLFDNPELH 675



 Score = 84.0 bits (206), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 38/62 (61%), Positives = 44/62 (70%), Gaps = 1/62 (1%)

Query: 668 DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
           D  F+AA++GQ D I GVSECIIMG+PMNVGTG+ KLL    +   P  R LLFDNPE H
Sbjct: 616 DHLFEAAYFGQKDAICGVSECIIMGIPMNVGTGIFKLLHKSDKPVHPPRRNLLFDNPELH 675

Query: 727 FP 728
            P
Sbjct: 676 LP 677



 Score = 54.7 bits (130), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 23/39 (58%), Positives = 29/39 (74%)

Query: 578 EDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           E+ A  AM R++++   YL NRGFSIGIGDVTPG G +Q
Sbjct: 1   EEYAADAMSRMAKLCPAYLSNRGFSIGIGDVTPGAGLLQ 39


>gi|195432649|ref|XP_002064329.1| GK20105 [Drosophila willistoni]
 gi|194160414|gb|EDW75315.1| GK20105 [Drosophila willistoni]
          Length = 1381

 Score =  343 bits (879), Expect = 6e-91,   Method: Compositional matrix adjust.
 Identities = 159/277 (57%), Positives = 199/277 (71%), Gaps = 21/277 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+D+VLFNRQPSLHK+SIM HRAKV P RTFRFNEC CTPYNADFDGDEMN+HLPQTEEA
Sbjct: 455 DDDIVLFNRQPSLHKMSIMCHRAKVQPQRTFRFNECTCTPYNADFDGDEMNLHLPQTEEA 514

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+              +LM N+SNLVTP+NGE+LIAATQDFITGGYLLTQK  F  +
Sbjct: 515 RAEAI--------------ILMGNQSNLVTPKNGEILIAATQDFITGGYLLTQKEVFLTK 560

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            + M++A+  +++      I          P   ++   +WTGKQIFSL+++PN D P+ 
Sbjct: 561 EEAMQLAACFLSNDDSTMRI-------QMPPPAILKPRRLWTGKQIFSLLMRPNSDSPIL 613

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            N+  KGR Y  N + C+ DS+V +RNSEL+ G MDK+TLGSG K  +FY+LLRDFGE  
Sbjct: 614 LNMVCKGRNYAGNLDLCNNDSWVHIRNSELMCGVMDKATLGSGTKQCIFYLLLRDFGEAF 673

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           A  AMWRL+R+ SF++ NRGFS GI DVTP +  +Q+
Sbjct: 674 ATKAMWRLARIASFFIQNRGFSFGISDVTPSKKLLQH 710



 Score =  254 bits (650), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 131/256 (51%), Positives = 173/256 (67%), Gaps = 8/256 (3%)

Query: 87  VTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVG 146
           V+  D++QQ+S ++I+SKNLY    QR P+P+G+LDRRMG + K+A C TCGQ L++C+G
Sbjct: 22  VSGADQIQQESLVRIISKNLY--QAQRQPVPYGVLDRRMGISTKDAVCETCGQGLNECIG 79

Query: 147 HFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVR 206
           HFGY+DL LPVFHIG+FR  INILQ ICK  +CA V+L  E    F  KL NP  SYL +
Sbjct: 80  HFGYMDLALPVFHIGHFRSTINILQMICK--SCAHVMLKMEDRNIFEKKLHNPNFSYLGK 137

Query: 207 KSLKKKILETTKKVSVCPHCGEINGVVKKC-GLLKISHEKYKNRTKKKDAIVEDLLAEYN 265
           K+L  ++L   KKV+ CPHC   NG VKK  GLLKI H+ YK R  K DAI ++ L E  
Sbjct: 138 KALHAQMLAKAKKVTKCPHCAAPNGGVKKGPGLLKILHDPYKGR--KVDAIYKNTLEEML 195

Query: 266 EAVKFNPEIE-AHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLL 324
            + + N ++      +   + L PL VL LFE IP +D+PLL M +  + P  LI+TR+ 
Sbjct: 196 RSTELNRDLNLTLSNYSTAEELTPLMVLDLFEQIPQKDVPLLGMCSRGAHPKHLIVTRVF 255

Query: 325 VPPNCIRPSVISDLKS 340
           VPP CIRPSV+SD+K+
Sbjct: 256 VPPACIRPSVLSDVKA 271



 Score =  251 bits (642), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 172/473 (36%), Positives = 248/473 (52%), Gaps = 90/473 (19%)

Query: 1001 PVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEF 1060
            PV+L    D++ A+        LS+ EIL+     L   EF +  S+ F  D+ K L   
Sbjct: 916  PVDLVHQYDNLRAQKPRGEQKPLSSTEILSEVETILKQPEFAEARSD-FKADVNKHLNSV 974

Query: 1061 SKK-----ESVTSHQD---KVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVR 1112
            +K+     +   +H D   ++     EQ+L +  +I                   E+Y R
Sbjct: 975  AKRIEGIHKKYLAHGDLCHQIEAVSGEQLLEYLRRIN------------------ERYNR 1016

Query: 1113 AQIEPATAVGAL---------------------------------------AAQSIGEPG 1133
            A  EP TAVGA+                                       A ++I  P 
Sbjct: 1017 AVSEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIVEIINATKTISTPI 1076

Query: 1134 TQMTLK---TFHFA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEV 1178
                L+   +  +A            GE+  Y+E V       ++I +DM RI++L L +
Sbjct: 1077 ITAELRNNTSMEYARQVKARIEKTTLGELSSYVEVVCRAFSCHLVIGIDMARIKVLGLHI 1136

Query: 1179 DIDSIRYCI--ERTRGISGHLTVSGHSFLILKPKDSSKS--FNSKMYQMKQLLPSVVIKG 1234
            ++D+I   I   R R     + V+  S  I+   +++++   N+++ ++   + +VV+ G
Sbjct: 1137 NLDTIVASILKSRLRIKPNQVEVASKSSRIIVRVEATRTATINAELSRLAISIQNVVVAG 1196

Query: 1235 VQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAA 1294
            +  INRAVI  +D      YKL +EG  LR+V+ATYG+ G +  SNN  EV++TLGIEAA
Sbjct: 1197 LPNINRAVIAVDDTVQPHTYKLCIEGYGLREVIATYGIIGKRTRSNNICEVFQTLGIEAA 1256

Query: 1295 RSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFEN 1354
            R+ IM+EI  VME HGMS+D RH ML+A  MT++GEVLGITRHGLAKM+ESV NLASFE 
Sbjct: 1257 RTIIMSEITDVMEGHGMSVDSRHIMLLASQMTARGEVLGITRHGLAKMRESVFNLASFEK 1316

Query: 1355 TSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ-----AVPRSEP 1402
            T+DHLFDAA+YGQTD ++GVSE II+G+P  +GTG+ KLLQ      VP  EP
Sbjct: 1317 TADHLFDAAYYGQTDAVNGVSERIILGMPAGIGTGIFKLLQHHEDKEVPPIEP 1369



 Score =  201 bits (510), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 111/238 (46%), Positives = 160/238 (67%), Gaps = 4/238 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRI EIINA++ ISTPIITA L  +T ++YAR VK R+E+TTLGE+  Y+E V     
Sbjct: 1058 GVPRIVEIINATKTISTPIITAELRNNTSMEYARQVKARIEKTTLGELSSYVEVVCRAFS 1117

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCI--ERTRGISGHLTVSGHSFLILKPKDSSKS-- 879
              ++I +DM RI++L L +++D+I   I   R R     + V+  S  I+   +++++  
Sbjct: 1118 CHLVIGIDMARIKVLGLHINLDTIVASILKSRLRIKPNQVEVASKSSRIIVRVEATRTAT 1177

Query: 880  FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
             N+++ ++   + +VV+ G+  INRAVI  +D      YKL +EG  LR+V+ATYG+ G 
Sbjct: 1178 INAELSRLAISIQNVVVAGLPNINRAVIAVDDTVQPHTYKLCIEGYGLREVIATYGIIGK 1237

Query: 940  KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +  SNN  EV++TLGIEAAR+ IM+EI  VME HGMS+D RH ML+A  MT++GEVLG
Sbjct: 1238 RTRSNNICEVFQTLGIEAARTIIMSEITDVMEGHGMSVDSRHIMLLASQMTARGEVLG 1295



 Score =  114 bits (286), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 54/77 (70%), Positives = 59/77 (76%)

Query: 608 VTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           +   +GFVQNSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGY+QRRLVK LEDL V Y
Sbjct: 825 IPAARGFVQNSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYLQRRLVKCLEDLVVHY 884

Query: 668 DMSFDAAFYGQTDCISG 684
           D +   A     D I G
Sbjct: 885 DGTVRNAINEMVDTIYG 901



 Score = 77.8 bits (190), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 33/53 (62%), Positives = 44/53 (83%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIA 73
           +LM N+SNLVTP+NGE+LIAATQDFITGGYLLTQK  F  + + M++A+  ++
Sbjct: 520 ILMGNQSNLVTPKNGEILIAATQDFITGGYLLTQKEVFLTKEEAMQLAACFLS 572



 Score = 60.5 bits (145), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 29/51 (56%), Positives = 36/51 (70%), Gaps = 5/51 (9%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ-----AVPRSEP 713
            D  FDAA+YGQTD ++GVSE II+G+P  +GTG+ KLLQ      VP  EP
Sbjct: 1319 DHLFDAAYYGQTDAVNGVSERIILGMPAGIGTGIFKLLQHHEDKEVPPIEP 1369


>gi|384871708|gb|AFI25034.1| FI19733p1 [Drosophila melanogaster]
          Length = 1410

 Score =  342 bits (876), Expect = 1e-90,   Method: Compositional matrix adjust.
 Identities = 159/277 (57%), Positives = 198/277 (71%), Gaps = 21/277 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHK+SIM HRAKV P RTFRFNEC CTPYNADFDGDEMN+HLPQTEEA
Sbjct: 482 DGDIVLFNRQPSLHKMSIMCHRAKVQPQRTFRFNECACTPYNADFDGDEMNLHLPQTEEA 541

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL              +LM N+SNLVTP+NGE+LIAATQDFITGGYLLTQK  F  +
Sbjct: 542 RAEAL--------------ILMGNQSNLVTPKNGEILIAATQDFITGGYLLTQKEVFLTK 587

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            + M++A+  +A+      I          P   ++   +WTGKQ+FSL+++PN D  V 
Sbjct: 588 EEAMQLAACFLANEDSTMHI-------KLPPPALLKPRRLWTGKQMFSLLMRPNDDSQVR 640

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            N+  KGR YT N++ C  DS++ +RNSEL+ G MDK+T+GSG K  +FY+LLRDFGE  
Sbjct: 641 LNMVNKGRNYTRNKDLCSNDSWIHIRNSELMCGVMDKATMGSGTKQCIFYLLLRDFGESH 700

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           A  AMWRL+R+ S++L NRGFS GI DVTP +  +Q+
Sbjct: 701 ATKAMWRLARIASYFLQNRGFSFGISDVTPSKKLLQH 737



 Score =  296 bits (758), Expect = 5e-77,   Method: Compositional matrix adjust.
 Identities = 188/467 (40%), Positives = 261/467 (55%), Gaps = 78/467 (16%)

Query: 1001 PVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEF 1060
            PV+L    D++ A++    D  L+A+E+       L + EF  +  ++F  D++  +   
Sbjct: 943  PVDLVHQYDNLRAQHPQGKDRPLNAEEMSEALETLLRTPEF-AEARDDFKLDVRNHINTV 1001

Query: 1061 SKKESVTSHQDKVSQPLREQI--LSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPA 1118
            SK+      + +    L  QI  L+ +  +   R  N            ++Y RA  EP 
Sbjct: 1002 SKRIGQLQKRYEKCIDLCHQIECLTTEQLLQFVRRIN------------DRYNRAVTEPG 1049

Query: 1119 TAVGALAAQSIGEPGTQMTLKTFH------------------------------------ 1142
            TAVGA+AAQSIGEPGTQMTLKTFH                                    
Sbjct: 1050 TAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIVEIINATKTISTPIITAELE 1109

Query: 1143 ------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIR 1184
                  FA             E+  Y+E V  P   ++ I +DM RI+LL L +D+D+I 
Sbjct: 1110 NCHSMEFARQVKARIEKTTLAELSSYVEVVCGPYSCYLAIGVDMARIKLLGLHIDLDTIV 1169

Query: 1185 YCIERTR---GISGHLTVSGHSFLILKPKDSSKS-FNSKMYQMKQLLPSVVIKGVQGINR 1240
            + I ++R     +    V+  S ++++ + +  S  N+++ ++   L +VV+ G+  INR
Sbjct: 1170 FSILKSRMRVKPTQVEVVASQSRIVVRVEATRTSTINAELARLALSLQNVVVAGLPNINR 1229

Query: 1241 AVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMT 1300
            AVI  +D      YKL +EG  LRDV+ATYGV G +  SNN  E+Y+TLGIEAAR+ IM+
Sbjct: 1230 AVIAVDDARQPPTYKLCIEGYGLRDVIATYGVVGKRTRSNNICEIYQTLGIEAARTIIMS 1289

Query: 1301 EIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLF 1360
            EI  VME HGMS+D+RH ML+A  MT++GEVLGITRHGLAKM+ESV NLASFE T+DHLF
Sbjct: 1290 EITEVMEGHGMSVDWRHIMLLASQMTARGEVLGITRHGLAKMRESVFNLASFEKTADHLF 1349

Query: 1361 DAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ-----AVPRSEP 1402
            DAA+YGQTD I+GVSE II+G+P  +GTG+ KLLQ      VP  EP
Sbjct: 1350 DAAYYGQTDAINGVSERIILGMPACIGTGIFKLLQQHEDKQVPPIEP 1396



 Score =  242 bits (618), Expect = 9e-61,   Method: Compositional matrix adjust.
 Identities = 124/256 (48%), Positives = 169/256 (66%), Gaps = 8/256 (3%)

Query: 87  VTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVG 146
           ++  D +QQ++ ++I+SKNLY    QR P+P+G+LDRRMG + K+A C TCGQ L++C+G
Sbjct: 49  ISGADEIQQEALVRIISKNLY--QAQRQPVPYGVLDRRMGISTKDAMCETCGQGLNECIG 106

Query: 147 HFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVR 206
           HFGY+DL LPVFHIG+FR  INILQ ICK   CA V+L  E    +  KL NP  SYL +
Sbjct: 107 HFGYLDLALPVFHIGHFRSTINILQMICK--VCAHVMLKPEDRQLYEKKLHNPNFSYLGK 164

Query: 207 KSLKKKILETTKKVSVCPHCGEINGVVKKC-GLLKISHEKYKNRTKKKDAIVEDLLAEYN 265
           K+L  ++L   KKV+ CPHCG  NG VKK  GLLKI H+ YK R  K D++    + E  
Sbjct: 165 KALHVQMLAKAKKVTKCPHCGSPNGGVKKGPGLLKILHDPYKGR--KMDSLFTSNMNEML 222

Query: 266 EAVKFNPEIEAH-KKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLL 324
            + + N ++ +    +   + L PL VL LFE IP  D+ LL M +  + P  LI+TR+ 
Sbjct: 223 RSTQTNRDLNSTLGNYSTAEELTPLMVLDLFEQIPQRDVALLGMCSHDAHPKHLIVTRVF 282

Query: 325 VPPNCIRPSVISDLKS 340
           VPP CIRPSV+S++K+
Sbjct: 283 VPPACIRPSVLSEVKA 298



 Score =  210 bits (534), Expect = 5e-51,   Method: Compositional matrix adjust.
 Identities = 113/238 (47%), Positives = 162/238 (68%), Gaps = 4/238 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRI EIINA++ ISTPIITA L+    +++AR VK R+E+TTL E+  Y+E V  P  
Sbjct: 1085 GVPRIVEIINATKTISTPIITAELENCHSMEFARQVKARIEKTTLAELSSYVEVVCGPYS 1144

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTR---GISGHLTVSGHSFLILKPKDSSKS- 879
             ++ I +DM RI+LL L +D+D+I + I ++R     +    V+  S ++++ + +  S 
Sbjct: 1145 CYLAIGVDMARIKLLGLHIDLDTIVFSILKSRMRVKPTQVEVVASQSRIVVRVEATRTST 1204

Query: 880  FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
             N+++ ++   L +VV+ G+  INRAVI  +D      YKL +EG  LRDV+ATYGV G 
Sbjct: 1205 INAELARLALSLQNVVVAGLPNINRAVIAVDDARQPPTYKLCIEGYGLRDVIATYGVVGK 1264

Query: 940  KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +  SNN  E+Y+TLGIEAAR+ IM+EI  VME HGMS+D+RH ML+A  MT++GEVLG
Sbjct: 1265 RTRSNNICEIYQTLGIEAARTIIMSEITEVMEGHGMSVDWRHIMLLASQMTARGEVLG 1322



 Score =  115 bits (289), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 64/122 (52%), Positives = 73/122 (59%), Gaps = 14/122 (11%)

Query: 608 VTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           +   +GFVQNSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGY+QRRLVK LEDL V Y
Sbjct: 852 IPAARGFVQNSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYLQRRLVKCLEDLVVHY 911

Query: 668 DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHF 727
           D +   A     D I G             G GL  +     R++PV     +DN     
Sbjct: 912 DGTVRNAVNEMVDTIYG-------------GDGLDPVSMET-RNKPVDLVHQYDNLRAQH 957

Query: 728 PQ 729
           PQ
Sbjct: 958 PQ 959



 Score = 79.0 bits (193), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 34/53 (64%), Positives = 44/53 (83%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIA 73
           +LM N+SNLVTP+NGE+LIAATQDFITGGYLLTQK  F  + + M++A+  +A
Sbjct: 547 ILMGNQSNLVTPKNGEILIAATQDFITGGYLLTQKEVFLTKEEAMQLAACFLA 599



 Score = 60.1 bits (144), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 30/51 (58%), Positives = 36/51 (70%), Gaps = 5/51 (9%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ-----AVPRSEP 713
            D  FDAA+YGQTD I+GVSE II+G+P  +GTG+ KLLQ      VP  EP
Sbjct: 1346 DHLFDAAYYGQTDAINGVSERIILGMPACIGTGIFKLLQQHEDKQVPPIEP 1396


>gi|281360912|ref|NP_001096987.2| CG17209 [Drosophila melanogaster]
 gi|272506113|gb|ABW09418.2| CG17209 [Drosophila melanogaster]
          Length = 1383

 Score =  341 bits (875), Expect = 1e-90,   Method: Compositional matrix adjust.
 Identities = 159/277 (57%), Positives = 198/277 (71%), Gaps = 21/277 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHK+SIM HRAKV P RTFRFNEC CTPYNADFDGDEMN+HLPQTEEA
Sbjct: 455 DGDIVLFNRQPSLHKMSIMCHRAKVQPQRTFRFNECACTPYNADFDGDEMNLHLPQTEEA 514

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL              +LM N+SNLVTP+NGE+LIAATQDFITGGYLLTQK  F  +
Sbjct: 515 RAEAL--------------ILMGNQSNLVTPKNGEILIAATQDFITGGYLLTQKEVFLTK 560

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            + M++A+  +A+      I          P   ++   +WTGKQ+FSL+++PN D  V 
Sbjct: 561 EEAMQLAACFLANEDSTMHI-------KLPPPALLKPRRLWTGKQMFSLLMRPNDDSQVR 613

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            N+  KGR YT N++ C  DS++ +RNSEL+ G MDK+T+GSG K  +FY+LLRDFGE  
Sbjct: 614 LNMVNKGRNYTRNKDLCSNDSWIHIRNSELMCGVMDKATMGSGTKQCIFYLLLRDFGESH 673

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           A  AMWRL+R+ S++L NRGFS GI DVTP +  +Q+
Sbjct: 674 ATKAMWRLARIASYFLQNRGFSFGISDVTPSKKLLQH 710



 Score =  296 bits (758), Expect = 6e-77,   Method: Compositional matrix adjust.
 Identities = 188/467 (40%), Positives = 261/467 (55%), Gaps = 78/467 (16%)

Query: 1001 PVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEF 1060
            PV+L    D++ A++    D  L+A+E+       L + EF  +  ++F  D++  +   
Sbjct: 916  PVDLVHQYDNLRAQHPQGKDRPLNAEEMSEALETLLRTPEF-AEARDDFKLDVRNHINTV 974

Query: 1061 SKKESVTSHQDKVSQPLREQI--LSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPA 1118
            SK+      + +    L  QI  L+ +  +   R  N            ++Y RA  EP 
Sbjct: 975  SKRIGQLQKRYEKCIDLCHQIECLTTEQLLQFVRRIN------------DRYNRAVTEPG 1022

Query: 1119 TAVGALAAQSIGEPGTQMTLKTFH------------------------------------ 1142
            TAVGA+AAQSIGEPGTQMTLKTFH                                    
Sbjct: 1023 TAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIVEIINATKTISTPIITAELE 1082

Query: 1143 ------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIR 1184
                  FA             E+  Y+E V  P   ++ I +DM RI+LL L +D+D+I 
Sbjct: 1083 NCHSMEFARQVKARIEKTTLAELSSYVEVVCGPYSCYLAIGVDMARIKLLGLHIDLDTIV 1142

Query: 1185 YCIERTR---GISGHLTVSGHSFLILKPKDSSKS-FNSKMYQMKQLLPSVVIKGVQGINR 1240
            + I ++R     +    V+  S ++++ + +  S  N+++ ++   L +VV+ G+  INR
Sbjct: 1143 FSILKSRMRVKPTQVEVVASQSRIVVRVEATRTSTINAELARLALSLQNVVVAGLPNINR 1202

Query: 1241 AVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMT 1300
            AVI  +D      YKL +EG  LRDV+ATYGV G +  SNN  E+Y+TLGIEAAR+ IM+
Sbjct: 1203 AVIAVDDARQPPTYKLCIEGYGLRDVIATYGVVGKRTRSNNICEIYQTLGIEAARTIIMS 1262

Query: 1301 EIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLF 1360
            EI  VME HGMS+D+RH ML+A  MT++GEVLGITRHGLAKM+ESV NLASFE T+DHLF
Sbjct: 1263 EITEVMEGHGMSVDWRHIMLLASQMTARGEVLGITRHGLAKMRESVFNLASFEKTADHLF 1322

Query: 1361 DAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ-----AVPRSEP 1402
            DAA+YGQTD I+GVSE II+G+P  +GTG+ KLLQ      VP  EP
Sbjct: 1323 DAAYYGQTDAINGVSERIILGMPACIGTGIFKLLQQHEDKQVPPIEP 1369



 Score =  243 bits (619), Expect = 8e-61,   Method: Compositional matrix adjust.
 Identities = 124/256 (48%), Positives = 169/256 (66%), Gaps = 8/256 (3%)

Query: 87  VTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVG 146
           ++  D +QQ++ ++I+SKNLY    QR P+P+G+LDRRMG + K+A C TCGQ L++C+G
Sbjct: 22  ISGADEIQQEALVRIISKNLY--QAQRQPVPYGVLDRRMGISTKDAMCETCGQGLNECIG 79

Query: 147 HFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVR 206
           HFGY+DL LPVFHIG+FR  INILQ ICK   CA V+L  E    +  KL NP  SYL +
Sbjct: 80  HFGYLDLALPVFHIGHFRSTINILQMICK--VCAHVMLKPEDRQLYEKKLHNPNFSYLGK 137

Query: 207 KSLKKKILETTKKVSVCPHCGEINGVVKKC-GLLKISHEKYKNRTKKKDAIVEDLLAEYN 265
           K+L  ++L   KKV+ CPHCG  NG VKK  GLLKI H+ YK R  K D++    + E  
Sbjct: 138 KALHVQMLAKAKKVTKCPHCGSPNGGVKKGPGLLKILHDPYKGR--KMDSLFTSNMNEML 195

Query: 266 EAVKFNPEIEAH-KKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLL 324
            + + N ++ +    +   + L PL VL LFE IP  D+ LL M +  + P  LI+TR+ 
Sbjct: 196 RSTQTNRDLNSTLGNYSTAEELTPLMVLDLFEQIPQRDVALLGMCSHDAHPKHLIVTRVF 255

Query: 325 VPPNCIRPSVISDLKS 340
           VPP CIRPSV+S++K+
Sbjct: 256 VPPACIRPSVLSEVKA 271



 Score =  210 bits (534), Expect = 6e-51,   Method: Compositional matrix adjust.
 Identities = 113/238 (47%), Positives = 162/238 (68%), Gaps = 4/238 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRI EIINA++ ISTPIITA L+    +++AR VK R+E+TTL E+  Y+E V  P  
Sbjct: 1058 GVPRIVEIINATKTISTPIITAELENCHSMEFARQVKARIEKTTLAELSSYVEVVCGPYS 1117

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTR---GISGHLTVSGHSFLILKPKDSSKS- 879
             ++ I +DM RI+LL L +D+D+I + I ++R     +    V+  S ++++ + +  S 
Sbjct: 1118 CYLAIGVDMARIKLLGLHIDLDTIVFSILKSRMRVKPTQVEVVASQSRIVVRVEATRTST 1177

Query: 880  FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
             N+++ ++   L +VV+ G+  INRAVI  +D      YKL +EG  LRDV+ATYGV G 
Sbjct: 1178 INAELARLALSLQNVVVAGLPNINRAVIAVDDARQPPTYKLCIEGYGLRDVIATYGVVGK 1237

Query: 940  KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +  SNN  E+Y+TLGIEAAR+ IM+EI  VME HGMS+D+RH ML+A  MT++GEVLG
Sbjct: 1238 RTRSNNICEIYQTLGIEAARTIIMSEITEVMEGHGMSVDWRHIMLLASQMTARGEVLG 1295



 Score =  115 bits (289), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 64/122 (52%), Positives = 73/122 (59%), Gaps = 14/122 (11%)

Query: 608 VTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           +   +GFVQNSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGY+QRRLVK LEDL V Y
Sbjct: 825 IPAARGFVQNSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYLQRRLVKCLEDLVVHY 884

Query: 668 DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHF 727
           D +   A     D I G             G GL  +     R++PV     +DN     
Sbjct: 885 DGTVRNAVNEMVDTIYG-------------GDGLDPVSMET-RNKPVDLVHQYDNLRAQH 930

Query: 728 PQ 729
           PQ
Sbjct: 931 PQ 932



 Score = 79.0 bits (193), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 34/53 (64%), Positives = 44/53 (83%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIA 73
           +LM N+SNLVTP+NGE+LIAATQDFITGGYLLTQK  F  + + M++A+  +A
Sbjct: 520 ILMGNQSNLVTPKNGEILIAATQDFITGGYLLTQKEVFLTKEEAMQLAACFLA 572



 Score = 60.1 bits (144), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 30/51 (58%), Positives = 36/51 (70%), Gaps = 5/51 (9%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ-----AVPRSEP 713
            D  FDAA+YGQTD I+GVSE II+G+P  +GTG+ KLLQ      VP  EP
Sbjct: 1319 DHLFDAAYYGQTDAINGVSERIILGMPACIGTGIFKLLQQHEDKQVPPIEP 1369


>gi|312073209|ref|XP_003139417.1| RNA polymerase Rpb1 [Loa loa]
 gi|307765420|gb|EFO24654.1| RNA polymerase Rpb1 [Loa loa]
          Length = 1403

 Score =  341 bits (875), Expect = 1e-90,   Method: Compositional matrix adjust.
 Identities = 165/283 (58%), Positives = 202/283 (71%), Gaps = 20/283 (7%)

Query: 334 VISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVH 393
           VI     DND+VLFNRQPSLHK+SIM+HRAKV+P RTFRFNEC CTPYNADFDGDEMN+H
Sbjct: 446 VIERHLDDNDIVLFNRQPSLHKISIMSHRAKVVPGRTFRFNECACTPYNADFDGDEMNLH 505

Query: 394 LPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 453
           +PQT EARAEA               +LM  KSNL+TPR+GE LIAA QDFITG YLLT 
Sbjct: 506 VPQTYEARAEA--------------SLLMGVKSNLITPRSGEPLIAAIQDFITGTYLLTH 551

Query: 454 KNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKP 513
           K++FF R++  R A+ +I   S      K+       P   ++ A +WTGKQ+  LI++P
Sbjct: 552 KDSFFPRSEVHRFAAAIIDSNS------KKQQRIRIPPPAILKPAELWTGKQLAELIIRP 605

Query: 514 NRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILL 573
           + D  +N NL TK ++YT NEEFC +DSYVI+RNS LL G +DK+ LGSG K ++FYILL
Sbjct: 606 DVDSKINLNLTTKNKSYTGNEEFCVKDSYVIIRNSVLLCGVLDKALLGSGSKTSIFYILL 665

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           RDFGED A+ AMWRL RM S +L NRGFSIGIGDV P +  ++
Sbjct: 666 RDFGEDAAIDAMWRLGRMASVFLSNRGFSIGIGDVRPSKALLK 708



 Score =  269 bits (688), Expect = 8e-69,   Method: Compositional matrix adjust.
 Identities = 163/373 (43%), Positives = 221/373 (59%), Gaps = 67/373 (17%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYI 1151
            C  K+ RA  EP TAVGA+AA SIGEP TQMTLKTFHFAG              E+   +
Sbjct: 1032 CSRKFRRAICEPGTAVGAVAATSIGEPSTQMTLKTFHFAGVASMNITQGVPRIKEIINGV 1091

Query: 1152 EEVFVP----------------------------------------DDSFILIKLDMDRI 1171
            + +  P                                        DD FIL+K++  R+
Sbjct: 1092 KLISTPIITAALMNEKDEKLARRVKARIEKTTLGEICDYIEEVYLPDDCFILLKINAKRV 1151

Query: 1172 RLLHLEVDIDSIRYCIERTR-----GISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQL 1226
            RLL LE+ + SI   I  ++      IS  + + G + + ++P + +K   SKM  ++ L
Sbjct: 1152 RLLQLEITMSSIAQSICSSKLPVPVKIS-QIKILGKTIMTIRPPELAKC--SKMMAIQYL 1208

Query: 1227 ---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTY 1283
               + +VV+KG+ GI R VIH ++ +G   YKLLVEG + R+VMAT GV G +   NN  
Sbjct: 1209 KYNIGNVVVKGLPGIVRCVIHADEKKG-DSYKLLVEGIDYREVMATVGVDGRRTYFNNAL 1267

Query: 1284 EVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMK 1343
             V   LGIEAARS+I++EI   M +HG+ +D RH ML+ADLMT +GEVLGITR+GL KMK
Sbjct: 1268 TVADVLGIEAARSSIISEILSTMASHGIGLDQRHVMLLADLMTYRGEVLGITRNGLVKMK 1327

Query: 1344 ESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPV 1403
            ESVL LASFE T+DHLF+AAF+ Q D I GVSECII+G P+ +GTGL KLL+   +   +
Sbjct: 1328 ESVLLLASFEKTADHLFEAAFFSQEDKICGVSECIILGTPITIGTGLFKLLRNHGKQLTI 1387

Query: 1404 PR-TLLFDNPEFH 1415
            P+ + +F++PEF+
Sbjct: 1388 PKMSTIFESPEFN 1400



 Score =  221 bits (562), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 128/300 (42%), Positives = 184/300 (61%), Gaps = 25/300 (8%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQR-TPIPHGLLDRRMGTNQKEANCTTCGQNL 141
           ++ T    + ++Q +HI + +  LY + P R  PI HG LD R+GT QK+ +C TC QNL
Sbjct: 18  VQFTAGNAESMRQVAHIPVFNSKLYDESPGRWVPIAHGPLDPRLGTCQKQTDCQTCKQNL 77

Query: 142 SDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPAL 201
            DCVGHFGYIDL +PVFH+G+FR  I +LQ ICK   C+ +L+ +E+   F  ++ NP L
Sbjct: 78  VDCVGHFGYIDLAIPVFHVGFFRLTIQMLQCICK--FCSAMLITDEQKKAFLHQVNNPNL 135

Query: 202 SYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKC--GLLKISHEKYKNRTKKKDAIVED 259
            YL RK+L K+I+  +KK++VC  CG  NG+VKK    +LKI+H          + I  D
Sbjct: 136 DYLRRKALHKRIVAASKKITVCNRCGHKNGIVKKAVGAVLKIAH---------AEVIPAD 186

Query: 260 LLAEYNEAVKFNPEIE---AHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLM-NAELSK- 314
             +EY  A + N E++      KF L   L+PL+V  LF  I  EDIPLL++ +A+  K 
Sbjct: 187 NYSEYVYAAQENKELQNLLPKTKFTL---LDPLQVQVLFSKIEKEDIPLLMVRSADTPKH 243

Query: 315 PSDLILTRLLVPPNCIRPSVISDLKS---DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTF 371
           PSD+ILTR+ VPP CIRPSV+S++KS   ++D+ +   +  L    I  H+ +  P +T 
Sbjct: 244 PSDVILTRIPVPPCCIRPSVVSEVKSGTTEDDITMKLSEIMLINDVIKKHKKEGSPTKTI 303



 Score =  211 bits (536), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 120/242 (49%), Positives = 164/242 (67%), Gaps = 12/242 (4%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIIN  + ISTPIITA L  + D   AR VK R+E+TTLGE+C+YIEEV++PDD
Sbjct: 1080 GVPRIKEIINGVKLISTPIITAALMNEKDEKLARRVKARIEKTTLGEICDYIEEVYLPDD 1139

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTR-----GISGHLTVSGHSFLILKPKDSSK 878
             FIL+K++  R+RLL LE+ + SI   I  ++      IS  + + G + + ++P + +K
Sbjct: 1140 CFILLKINAKRVRLLQLEITMSSIAQSICSSKLPVPVKIS-QIKILGKTIMTIRPPELAK 1198

Query: 879  SFNSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYG 935
               SKM  ++ L   + +VV+KG+ GI R VIH ++ +G   YKLLVEG + R+VMAT G
Sbjct: 1199 C--SKMMAIQYLKYNIGNVVVKGLPGIVRCVIHADEKKG-DSYKLLVEGIDYREVMATVG 1255

Query: 936  VKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            V G +   NN   V   LGIEAARS+I++EI   M +HG+ +D RH ML+ADLMT +GEV
Sbjct: 1256 VDGRRTYFNNALTVADVLGIEAARSSIISEILSTMASHGIGLDQRHVMLLADLMTYRGEV 1315

Query: 996  LG 997
            LG
Sbjct: 1316 LG 1317



 Score =  116 bits (291), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 53/61 (86%), Positives = 57/61 (93%), Gaps = 1/61 (1%)

Query: 609 TPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV+NSF+SGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVK LEDLC+ Y
Sbjct: 824 TPAAKGFVENSFYSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKCLEDLCINY 883

Query: 668 D 668
           D
Sbjct: 884 D 884



 Score = 71.6 bits (174), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 34/60 (56%), Positives = 43/60 (71%)

Query: 13  YATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLI 72
           Y  R    +LM  KSNL+TPR+GE LIAA QDFITG YLLT K++FF R++  R A+ +I
Sbjct: 510 YEARAEASLLMGVKSNLITPRSGEPLIAAIQDFITGTYLLTHKDSFFPRSEVHRFAAAII 569



 Score = 63.5 bits (153), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 29/61 (47%), Positives = 43/61 (70%), Gaps = 1/61 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPR-TLLFDNPEFH 726
            D  F+AAF+ Q D I GVSECII+G P+ +GTGL KLL+   +   +P+ + +F++PEF+
Sbjct: 1341 DHLFEAAFFSQEDKICGVSECIILGTPITIGTGLFKLLRNHGKQLTIPKMSTIFESPEFN 1400

Query: 727  F 727
             
Sbjct: 1401 L 1401


>gi|195355413|ref|XP_002044186.1| GM22579 [Drosophila sechellia]
 gi|194129475|gb|EDW51518.1| GM22579 [Drosophila sechellia]
          Length = 1369

 Score =  340 bits (873), Expect = 3e-90,   Method: Compositional matrix adjust.
 Identities = 159/277 (57%), Positives = 198/277 (71%), Gaps = 21/277 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHK+SIM HRAKV P RTFRFNEC CTPYNADFDGDEMN+HLPQTEEA
Sbjct: 441 DEDIVLFNRQPSLHKMSIMCHRAKVQPQRTFRFNECACTPYNADFDGDEMNLHLPQTEEA 500

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL              +LM N+SNLVTP+NGE+LIAATQDFITGGYLLTQK  F  +
Sbjct: 501 RAEAL--------------ILMGNQSNLVTPKNGEILIAATQDFITGGYLLTQKEVFLTK 546

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            + M++A+  +A+      I          P   ++   +WTGKQ+FSL+++PN D  V 
Sbjct: 547 EEAMQLAACFLANEDSTMHI-------KLPPPALLKPRRLWTGKQMFSLLMRPNDDSQVR 599

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            N+  KGR YT N++ C  DS++ +RNSEL+ G MDK+T+GSG K  +FY+LLRDFGE  
Sbjct: 600 LNMVNKGRNYTGNKDLCSNDSWIHIRNSELMCGVMDKATMGSGTKQCIFYLLLRDFGELH 659

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           A  AMWRL+R+ S++L NRGFS GI DVTP +  +Q+
Sbjct: 660 ATKAMWRLARIASYFLQNRGFSFGISDVTPSKKLLQH 696



 Score =  295 bits (755), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 187/467 (40%), Positives = 261/467 (55%), Gaps = 78/467 (16%)

Query: 1001 PVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEF 1060
            PV+L    D++ A++    D  L+A+++       L + EF  +  ++F  D++  +   
Sbjct: 902  PVDLVHQYDNLRAQHPQGKDRPLNAEKMSEALETLLKTPEF-AEARDDFKLDVRNHINTV 960

Query: 1061 SKKESVTSHQDKVSQPLREQI--LSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPA 1118
            SK+      + +    L  QI  L+ +  +   R  N            ++Y RA  EP 
Sbjct: 961  SKRIGQLQKRYEKCINLCHQIECLTTEQLLQFVRRIN------------DRYNRAVTEPG 1008

Query: 1119 TAVGALAAQSIGEPGTQMTLKTFH------------------------------------ 1142
            TAVGA+AAQSIGEPGTQMTLKTFH                                    
Sbjct: 1009 TAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIVEIINATKTISTPIITAELE 1068

Query: 1143 ------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIR 1184
                  FA             E+  Y+E V  P   ++ I +DM RI+LL L +D+D+I 
Sbjct: 1069 NCHSMEFARQVKARIEKTTLAELSSYVEVVCGPYSCYLAIGVDMARIKLLGLHIDLDTIV 1128

Query: 1185 YCIERTR---GISGHLTVSGHSFLILKPKDSSKS-FNSKMYQMKQLLPSVVIKGVQGINR 1240
            + I ++R     +    V+  S ++++ + +  S  N+++ ++   L +VV+ G+  INR
Sbjct: 1129 FSILKSRMRVKPTQVEVVASQSRIVVRVEATRTSTINAELARLALCLQNVVVAGLPNINR 1188

Query: 1241 AVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMT 1300
            AVI  +D      YKL +EG  LRDV+ATYGV G +  SNN  E+Y+TLGIEAAR+ IM+
Sbjct: 1189 AVIAVDDARQPPTYKLCIEGYGLRDVIATYGVVGKRTRSNNICEIYQTLGIEAARTIIMS 1248

Query: 1301 EIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLF 1360
            EI  VME HGMS+D+RH ML+A  MT++GEVLGITRHGLAKM+ESV NLASFE T+DHLF
Sbjct: 1249 EITEVMEGHGMSVDWRHIMLLASQMTARGEVLGITRHGLAKMRESVFNLASFEKTADHLF 1308

Query: 1361 DAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ-----AVPRSEP 1402
            DAA+YGQTD I+GVSE II+G+P  +GTG+ KLLQ      VP  EP
Sbjct: 1309 DAAYYGQTDAINGVSERIILGMPACIGTGIFKLLQLHEDKQVPPIEP 1355



 Score =  241 bits (615), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 124/256 (48%), Positives = 168/256 (65%), Gaps = 8/256 (3%)

Query: 87  VTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVG 146
           ++  D +QQ++ ++I+SKNLY    QR P+P+G+LDRRMG + K+A C TCGQ L++C+G
Sbjct: 22  ISGADEIQQEALVRIISKNLY--QAQRQPVPYGVLDRRMGISTKDAMCDTCGQGLNECIG 79

Query: 147 HFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVR 206
           HFGY+DL LPVFHIG+FR  INILQ ICK   CA V+L  E    +  KL NP  SYL +
Sbjct: 80  HFGYLDLALPVFHIGHFRSTINILQMICK--VCAHVMLKPEDRQLYEKKLHNPNFSYLGK 137

Query: 207 KSLKKKILETTKKVSVCPHCGEINGVVKKC-GLLKISHEKYKNRTKKKDAIVEDLLAEYN 265
           K+L  ++L   KKV+ CPHCG  NG VKK  GLLKI H+ YK R  K D +    + E  
Sbjct: 138 KALHVQMLAKAKKVTKCPHCGSPNGGVKKGPGLLKILHDPYKGR--KMDLLFTSNMNEML 195

Query: 266 EAVKFNPEIEAH-KKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLL 324
            + + N ++ +    +   + L PL VL LFE IP  D+ LL M +  + P  LI+TR+ 
Sbjct: 196 HSTQANRDLNSTLGNYSTAEELTPLMVLDLFEQIPQRDVALLGMCSHDAHPKHLIVTRVF 255

Query: 325 VPPNCIRPSVISDLKS 340
           VPP CIRPSV+S++K+
Sbjct: 256 VPPACIRPSVLSEVKA 271



 Score =  211 bits (536), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 113/238 (47%), Positives = 162/238 (68%), Gaps = 4/238 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRI EIINA++ ISTPIITA L+    +++AR VK R+E+TTL E+  Y+E V  P  
Sbjct: 1044 GVPRIVEIINATKTISTPIITAELENCHSMEFARQVKARIEKTTLAELSSYVEVVCGPYS 1103

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTR---GISGHLTVSGHSFLILKPKDSSKS- 879
             ++ I +DM RI+LL L +D+D+I + I ++R     +    V+  S ++++ + +  S 
Sbjct: 1104 CYLAIGVDMARIKLLGLHIDLDTIVFSILKSRMRVKPTQVEVVASQSRIVVRVEATRTST 1163

Query: 880  FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
             N+++ ++   L +VV+ G+  INRAVI  +D      YKL +EG  LRDV+ATYGV G 
Sbjct: 1164 INAELARLALCLQNVVVAGLPNINRAVIAVDDARQPPTYKLCIEGYGLRDVIATYGVVGK 1223

Query: 940  KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +  SNN  E+Y+TLGIEAAR+ IM+EI  VME HGMS+D+RH ML+A  MT++GEVLG
Sbjct: 1224 RTRSNNICEIYQTLGIEAARTIIMSEITEVMEGHGMSVDWRHIMLLASQMTARGEVLG 1281



 Score =  115 bits (288), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 64/122 (52%), Positives = 73/122 (59%), Gaps = 14/122 (11%)

Query: 608 VTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           +   +GFVQNSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGY+QRRLVK LEDL V Y
Sbjct: 811 IPAARGFVQNSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYLQRRLVKCLEDLVVHY 870

Query: 668 DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHF 727
           D +   A     D I G             G GL  +     R++PV     +DN     
Sbjct: 871 DGTVRNAVNEMVDTIYG-------------GDGLDPVSMET-RNKPVDLVHQYDNLRAQH 916

Query: 728 PQ 729
           PQ
Sbjct: 917 PQ 918



 Score = 79.0 bits (193), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 34/53 (64%), Positives = 44/53 (83%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIA 73
           +LM N+SNLVTP+NGE+LIAATQDFITGGYLLTQK  F  + + M++A+  +A
Sbjct: 506 ILMGNQSNLVTPKNGEILIAATQDFITGGYLLTQKEVFLTKEEAMQLAACFLA 558



 Score = 60.1 bits (144), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 30/51 (58%), Positives = 36/51 (70%), Gaps = 5/51 (9%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ-----AVPRSEP 713
            D  FDAA+YGQTD I+GVSE II+G+P  +GTG+ KLLQ      VP  EP
Sbjct: 1305 DHLFDAAYYGQTDAINGVSERIILGMPACIGTGIFKLLQLHEDKQVPPIEP 1355


>gi|405974578|gb|EKC39212.1| DNA-directed RNA polymerase III subunit RPC1 [Crassostrea gigas]
          Length = 1368

 Score =  340 bits (871), Expect = 5e-90,   Method: Compositional matrix adjust.
 Identities = 210/481 (43%), Positives = 278/481 (57%), Gaps = 92/481 (19%)

Query: 997  GNGTPVELKRLLDDIIA--KNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIK 1054
            G   P++ KR+ D I A  ++S R +PSLS  ++ A  N TL    F +  S++F +D+ 
Sbjct: 911  GKDQPIDFKRVYDHIKANTRSSFREEPSLSGADLRAFVNTTLQENLF-KSFSDDFKKDLI 969

Query: 1055 KFLEEFSKKESVTSHQDKVSQPLREQ---ILSHQDKIGHGRESNPFPSACKAEACREKYV 1111
             F+++   +   T  +  +    R +   +L   ++I   +             CR+K++
Sbjct: 970  NFIDDVGSEIDKTRQKFGMMNAQRSELPPVLFELNRITTSQAKQFL------NICRDKFM 1023

Query: 1112 RAQIEPATAVGALAAQSIGEPGTQMTLKTFH----------------------------- 1142
            ++QIEP TAVGA+ AQSIGEPGTQMTLKTFH                             
Sbjct: 1024 KSQIEPGTAVGAVCAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIINASKNISTP 1083

Query: 1143 -------------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLE 1177
                         FA            GEV EYIEEVF+PDD FIL+KLDMDRIRLL LE
Sbjct: 1084 IITAELMVDSDPEFARVVKGRIEKTTLGEVSEYIEEVFLPDDCFILVKLDMDRIRLLKLE 1143

Query: 1178 VDIDSIR--YCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQM-KQLLPSVVIKG 1234
            V++DSIR   C  + R     + +   + L ++P+++SKS    + QM K+ LPSV+IKG
Sbjct: 1144 VNVDSIRESLCKSKLRVKPQDIQIHSSAVLSVRPRETSKSSLYYVLQMLKKELPSVMIKG 1203

Query: 1235 VQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAA 1294
            +Q + RAVIH ++ +G T YKLLVEGDNL  VMAT G+KG +  SNNT+ + +TLGIEAA
Sbjct: 1204 IQNVTRAVIHIDEKKGET-YKLLVEGDNLLAVMATPGIKGTRACSNNTFAMERTLGIEAA 1262

Query: 1295 RSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFEN 1354
            R+TIM E+   M +HGMSID RH ML+ADLMT KGEVLGITR GLAKMKESVL LASFE 
Sbjct: 1263 RTTIMNEVNFTMSSHGMSIDIRHVMLLADLMTFKGEVLGITRFGLAKMKESVLMLASFEK 1322

Query: 1355 TSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEF 1414
            T+DHLF+AA++GQ D I+                   K+  A PR     R L+FD P+F
Sbjct: 1323 TADHLFEAAYHGQRDTINAE-----------------KIDPAPPR-----RELIFDTPDF 1360

Query: 1415 H 1415
            H
Sbjct: 1361 H 1361



 Score =  338 bits (867), Expect = 1e-89,   Method: Compositional matrix adjust.
 Identities = 164/323 (50%), Positives = 218/323 (67%), Gaps = 26/323 (8%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND++LFNRQPSLHKLSI A  AKV+PHRTFRFNEC C P+NADFDGDEMN+HLPQTEEA
Sbjct: 454 DNDIILFNRQPSLHKLSIQAFYAKVMPHRTFRFNECCCNPFNADFDGDEMNLHLPQTEEA 513

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEA+               LM +KSN++TPRNGE LIAA QDFITGGYL+TQK+ F +R
Sbjct: 514 KAEAI--------------TLMGSKSNIITPRNGEPLIAAIQDFITGGYLITQKDVFLDR 559

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  ++ +++++       I          P   ++   +WTGKQIFS++L+PN++ PV 
Sbjct: 560 ARACQLIASMLSGRERTLKI-------DLPPPAIIKPIKLWTGKQIFSVLLRPNKNSPVR 612

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           ANL TKG+ Y+  E+ C  DS+V++RNSELL G+MDK TLG G K N+FY++LRDFGE  
Sbjct: 613 ANLWTKGKNYSGGEDLCINDSFVVIRNSELLCGAMDKGTLGGGSKNNIFYVILRDFGEQE 672

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ---NSFFSGLTPTEFFFHTMGGRE 637
           A  A+ RL+R+   YL +RGFSIGIGDVTPG G ++   N    G T  + F   +   E
Sbjct: 673 AADALSRLARLCPAYLSHRGFSIGIGDVTPGAGLIKAKNNLLEDGYTKCDSFIRDL--EE 730

Query: 638 GLVDTAVKTAETGYMQRRLVKSL 660
           G + T    +E   ++  +++ L
Sbjct: 731 GKLQTQPGCSEEETLEAMILREL 753



 Score =  281 bits (719), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 147/237 (62%), Positives = 184/237 (77%), Gaps = 4/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+NISTPIITA L  D+D ++AR+VKGR+E+TTLGEV EYIEEVF+PDD
Sbjct: 1066 GVPRIKEIINASKNISTPIITAELMVDSDPEFARVVKGRIEKTTLGEVSEYIEEVFLPDD 1125

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIR--YCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             FIL+KLDMDRIRLL LEV++DSIR   C  + R     + +   + L ++P+++SKS  
Sbjct: 1126 CFILVKLDMDRIRLLKLEVNVDSIRESLCKSKLRVKPQDIQIHSSAVLSVRPRETSKSSL 1185

Query: 882  SKMYQM-KQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
              + QM K+ LPSV+IKG+Q + RAVIH ++ +G T YKLLVEGDNL  VMAT G+KG +
Sbjct: 1186 YYVLQMLKKELPSVMIKGIQNVTRAVIHIDEKKGET-YKLLVEGDNLLAVMATPGIKGTR 1244

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
              SNNT+ + +TLGIEAAR+TIM E+   M +HGMSID RH ML+ADLMT KGEVLG
Sbjct: 1245 ACSNNTFAMERTLGIEAARTTIMNEVNFTMSSHGMSIDIRHVMLLADLMTFKGEVLG 1301



 Score =  275 bits (702), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 133/249 (53%), Positives = 176/249 (70%), Gaps = 5/249 (2%)

Query: 92  RVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYI 151
           ++QQ SH+ +VSKNLY QD  R P+P G LD +MGT+ KE +C TCG+ L+DC GH+GYI
Sbjct: 27  QMQQLSHLHVVSKNLYSQDGGRKPVPFGALDHKMGTSDKENSCETCGKGLADCTGHYGYI 86

Query: 152 DLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKK 211
           DL LP FHIGYFR  I +LQ ICK  TC++ LL  ++   F   ++ P L+YL RK LKK
Sbjct: 87  DLELPCFHIGYFRATIQLLQMICK--TCSQALLSPDQKKTFMENVKKP-LTYLQRKVLKK 143

Query: 212 KILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFN 271
           KI +  +K+SVC  CG  NG+VKKCGLLKI H+KYK R K  D ++E+ +  +  A++ N
Sbjct: 144 KIYDKCRKMSVCVSCGAYNGMVKKCGLLKIIHDKYKQR-KGTDPVIEEFMGSFEAAMEHN 202

Query: 272 PEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIR 331
            ++E        + LNP++V Q+F  IP E+IPLL+MN E+  P DLILTR+LVPP CIR
Sbjct: 203 KDLEPLLS-KTQEVLNPIKVQQIFLQIPEEEIPLLMMNPEVGSPKDLILTRILVPPICIR 261

Query: 332 PSVISDLKS 340
           PSV+SDLK+
Sbjct: 262 PSVVSDLKA 270



 Score =  115 bits (288), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 51/60 (85%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV+NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDLC  YD++
Sbjct: 827 ARGFVENSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSHYDLT 886



 Score = 77.0 bits (188), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 32/55 (58%), Positives = 47/55 (85%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRK 76
           LM +KSN++TPRNGE LIAA QDFITGGYL+TQK+ F +RA+  ++ +++++GR+
Sbjct: 520 LMGSKSNIITPRNGEPLIAAIQDFITGGYLITQKDVFLDRARACQLIASMLSGRE 574


>gi|162944844|gb|ABY20491.1| LD04803p [Drosophila melanogaster]
          Length = 1410

 Score =  339 bits (869), Expect = 8e-90,   Method: Compositional matrix adjust.
 Identities = 158/277 (57%), Positives = 197/277 (71%), Gaps = 21/277 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHK+SIM HRAKV P RTFRFNEC CTPYNADFDGDEMN+HLPQTEEA
Sbjct: 482 DGDIVLFNRQPSLHKMSIMCHRAKVQPQRTFRFNECACTPYNADFDGDEMNLHLPQTEEA 541

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL              +LM N+SNLVTP+NGE+LIAATQDFITGGYLLTQK  F  +
Sbjct: 542 RAEAL--------------ILMGNQSNLVTPKNGEILIAATQDFITGGYLLTQKEVFLTK 587

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            + M++A+  +A+      I          P   ++   +WTGKQ+FSL+++PN D  V 
Sbjct: 588 EEAMQLAACFLANEDSTMHI-------KLPPPALLKPRRLWTGKQMFSLLMRPNDDSQVR 640

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            N+  K R YT N++ C  DS++ +RNSEL+ G MDK+T+GSG K  +FY+LLRDFGE  
Sbjct: 641 LNMVNKSRNYTRNKDLCSNDSWIHIRNSELMCGVMDKATMGSGTKQCIFYLLLRDFGESH 700

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           A  AMWRL+R+ S++L NRGFS GI DVTP +  +Q+
Sbjct: 701 ATKAMWRLARIASYFLQNRGFSFGISDVTPSKKLLQH 737



 Score =  296 bits (758), Expect = 6e-77,   Method: Compositional matrix adjust.
 Identities = 187/467 (40%), Positives = 262/467 (56%), Gaps = 78/467 (16%)

Query: 1001 PVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEF 1060
            PV+L    D++ A++    D  L+A+E+       L + EF  +  ++F  D++  +   
Sbjct: 943  PVDLVHQYDNLRAQHPQGKDRPLNAEEMSEALETLLRTPEF-AEARDDFKLDVRNHINTV 1001

Query: 1061 SKKESVTSHQDKVSQPLREQI--LSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPA 1118
            SK+      + +    L  QI  L+ +  +   R  N            ++Y RA  EP 
Sbjct: 1002 SKRIGQLQKRYEKCIDLCHQIECLTTEQLLQFVRRIN------------DRYNRAVTEPG 1049

Query: 1119 TAVGALAAQSIGEPGTQMTLKTFH------------------------------------ 1142
            TAVGA+AAQSIGEPGTQMTLKTFH                                    
Sbjct: 1050 TAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIVEIINATKTISTPIITAELE 1109

Query: 1143 ------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIR 1184
                  FA             E+  Y+E V  P   ++ I +DM RI+LL L +D+D+I 
Sbjct: 1110 NCHSMEFARQVKARIEKTTLAELSSYVEVVCGPYSCYLAIGVDMARIKLLGLHIDLDTIV 1169

Query: 1185 YCIERTR---GISGHLTVSGHSFLILKPKDS-SKSFNSKMYQMKQLLPSVVIKGVQGINR 1240
            + I ++R     +    V+  S ++++ + + + + N+++ ++   L +VV+ G+  INR
Sbjct: 1170 FSILKSRMRVKPTQVEVVASQSRIVVRVEATRTSTINAELARLALSLQNVVVAGLPNINR 1229

Query: 1241 AVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMT 1300
            AVI  +D      YKL +EG  LRDV+ATYGV G +  SNN  E+Y+TLGIEAAR+ IM+
Sbjct: 1230 AVIAVDDARQPPTYKLCIEGYGLRDVIATYGVVGKRTRSNNICEIYQTLGIEAARTIIMS 1289

Query: 1301 EIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLF 1360
            EI  VME HGMS+D+RH ML+A  MT++GEVLGITRHGLAKM+ESV NLASFE T+DHLF
Sbjct: 1290 EITEVMEGHGMSVDWRHIMLLASQMTARGEVLGITRHGLAKMRESVFNLASFEKTADHLF 1349

Query: 1361 DAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ-----AVPRSEP 1402
            DAA+YGQTD I+GVSE II+G+P  +GTG+ KLLQ      VP  EP
Sbjct: 1350 DAAYYGQTDAINGVSERIILGMPACIGTGIFKLLQQHEDKQVPPIEP 1396



 Score =  242 bits (618), Expect = 9e-61,   Method: Compositional matrix adjust.
 Identities = 124/256 (48%), Positives = 169/256 (66%), Gaps = 8/256 (3%)

Query: 87  VTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVG 146
           ++  D +QQ++ ++I+SKNLY    QR P+P+G+LDRRMG + K+A C TCGQ L++C+G
Sbjct: 49  ISGADEIQQEALVRIISKNLY--QAQRQPVPYGVLDRRMGISTKDAMCETCGQGLNECIG 106

Query: 147 HFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVR 206
           HFGY+DL LPVFHIG+FR  INILQ ICK   CA V+L  E    +  KL NP  SYL +
Sbjct: 107 HFGYLDLALPVFHIGHFRSTINILQMICK--VCAHVMLKPEDRQLYEKKLHNPNFSYLGK 164

Query: 207 KSLKKKILETTKKVSVCPHCGEINGVVKKC-GLLKISHEKYKNRTKKKDAIVEDLLAEYN 265
           K+L  ++L   KKV+ CPHCG  NG VKK  GLLKI H+ YK R  K D++    + E  
Sbjct: 165 KALHVQMLAKAKKVTKCPHCGSPNGGVKKGPGLLKILHDPYKGR--KMDSLFTSNMNEML 222

Query: 266 EAVKFNPEIEAH-KKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLL 324
            + + N ++ +    +   + L PL VL LFE IP  D+ LL M +  + P  LI+TR+ 
Sbjct: 223 RSTQTNRDLNSTLGNYSTAEELTPLMVLDLFEQIPQRDVALLGMCSHDAHPKHLIVTRVF 282

Query: 325 VPPNCIRPSVISDLKS 340
           VPP CIRPSV+S++K+
Sbjct: 283 VPPACIRPSVLSEVKA 298



 Score =  210 bits (534), Expect = 5e-51,   Method: Compositional matrix adjust.
 Identities = 112/238 (47%), Positives = 163/238 (68%), Gaps = 4/238 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRI EIINA++ ISTPIITA L+    +++AR VK R+E+TTL E+  Y+E V  P  
Sbjct: 1085 GVPRIVEIINATKTISTPIITAELENCHSMEFARQVKARIEKTTLAELSSYVEVVCGPYS 1144

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTR---GISGHLTVSGHSFLILKPKDS-SKS 879
             ++ I +DM RI+LL L +D+D+I + I ++R     +    V+  S ++++ + + + +
Sbjct: 1145 CYLAIGVDMARIKLLGLHIDLDTIVFSILKSRMRVKPTQVEVVASQSRIVVRVEATRTST 1204

Query: 880  FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
             N+++ ++   L +VV+ G+  INRAVI  +D      YKL +EG  LRDV+ATYGV G 
Sbjct: 1205 INAELARLALSLQNVVVAGLPNINRAVIAVDDARQPPTYKLCIEGYGLRDVIATYGVVGK 1264

Query: 940  KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +  SNN  E+Y+TLGIEAAR+ IM+EI  VME HGMS+D+RH ML+A  MT++GEVLG
Sbjct: 1265 RTRSNNICEIYQTLGIEAARTIIMSEITEVMEGHGMSVDWRHIMLLASQMTARGEVLG 1322



 Score =  115 bits (289), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 64/122 (52%), Positives = 73/122 (59%), Gaps = 14/122 (11%)

Query: 608 VTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           +   +GFVQNSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGY+QRRLVK LEDL V Y
Sbjct: 852 IPAARGFVQNSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYLQRRLVKCLEDLVVHY 911

Query: 668 DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHF 727
           D +   A     D I G             G GL  +     R++PV     +DN     
Sbjct: 912 DGTVRNAVNEMVDTIYG-------------GDGLDPVSMET-RNKPVDLVHQYDNLRAQH 957

Query: 728 PQ 729
           PQ
Sbjct: 958 PQ 959



 Score = 79.0 bits (193), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 34/53 (64%), Positives = 44/53 (83%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIA 73
           +LM N+SNLVTP+NGE+LIAATQDFITGGYLLTQK  F  + + M++A+  +A
Sbjct: 547 ILMGNQSNLVTPKNGEILIAATQDFITGGYLLTQKEVFLTKEEAMQLAACFLA 599



 Score = 60.1 bits (144), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 30/51 (58%), Positives = 36/51 (70%), Gaps = 5/51 (9%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ-----AVPRSEP 713
            D  FDAA+YGQTD I+GVSE II+G+P  +GTG+ KLLQ      VP  EP
Sbjct: 1346 DHLFDAAYYGQTDAINGVSERIILGMPACIGTGIFKLLQQHEDKQVPPIEP 1396


>gi|195478969|ref|XP_002100717.1| GE17218 [Drosophila yakuba]
 gi|194188241|gb|EDX01825.1| GE17218 [Drosophila yakuba]
          Length = 1383

 Score =  338 bits (868), Expect = 1e-89,   Method: Compositional matrix adjust.
 Identities = 159/277 (57%), Positives = 197/277 (71%), Gaps = 21/277 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHK+SIM HRAKV P RTFRFNEC CTPYNADFDGDEMN+HLPQTEEA
Sbjct: 455 DGDIVLFNRQPSLHKMSIMCHRAKVQPQRTFRFNECACTPYNADFDGDEMNLHLPQTEEA 514

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL              +LM N+SNLVTP+NGE+LIAATQDFITGGYLLTQK  F  +
Sbjct: 515 RAEAL--------------ILMGNQSNLVTPKNGEILIAATQDFITGGYLLTQKEVFLTK 560

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            + M++A+  +A+      I          P   ++   +WTGKQ+FSL+++PN D  V 
Sbjct: 561 EEAMQLAACFLANEDSTMHI-------KLPPPALLKPRRLWTGKQMFSLLMRPNDDSHVR 613

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            N+  KGR YT N + C  DS++ +RNSEL+ G MDK+T+GSG K  +FY+LLRDFGE  
Sbjct: 614 LNMVNKGRNYTRNMDLCSNDSWIHIRNSELMCGVMDKATMGSGTKQCIFYLLLRDFGELH 673

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           A  AMWRL+R+ S++L NRGFS GI DVTP +  +Q+
Sbjct: 674 ATKAMWRLARIASYFLQNRGFSFGISDVTPSKKLLQH 710



 Score =  300 bits (767), Expect = 5e-78,   Method: Compositional matrix adjust.
 Identities = 189/465 (40%), Positives = 259/465 (55%), Gaps = 74/465 (15%)

Query: 1001 PVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEF 1060
            PV+L    D++ A++    D  L A+E+       L S EF  +  ++F  D++  +   
Sbjct: 916  PVDLVHQYDNLRAQHPQGKDRPLPAEELSEALETLLASPEF-AEARDDFKLDVRNHITTV 974

Query: 1061 SKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATA 1120
            SK+  +   Q +  + +    L HQ +     +   F          ++Y RA  EP TA
Sbjct: 975  SKR--IGQLQKRYEKYIN---LCHQIECLTAEQLLQF-----VRRINDRYNRAVTEPGTA 1024

Query: 1121 VGALAAQSIGEPGTQMTLKTFH-------------------------------------- 1142
            VGA+AAQSIGEPGTQMTLKTFH                                      
Sbjct: 1025 VGAIAAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIVEIINATKTISTPIITAELENC 1084

Query: 1143 ----FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYC 1186
                FA             E+  Y+E V  P   ++ I +DM RI+LL L +D+D+I + 
Sbjct: 1085 HSMEFARQVKARIEKTTLAELSSYVEVVCGPYSCYLAIGIDMARIKLLGLHIDLDTIVFS 1144

Query: 1187 IERTRGISGHLTVSG---HSFLILKPKDSSKS-FNSKMYQMKQLLPSVVIKGVQGINRAV 1242
            I ++R       V     HS ++++ + +  S  N+++ ++   L +VV+ G+  INRAV
Sbjct: 1145 ILKSRMRVKPTQVEAVVKHSRIVVRVEATRTSTINAELARLALSLQNVVVAGLPNINRAV 1204

Query: 1243 IHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEI 1302
            I  +D      YKL +EG  LRDV+ATYGV G +  SNN  E+Y+TLGIEAAR+ IM+EI
Sbjct: 1205 IAVDDARQPPTYKLCIEGYGLRDVIATYGVVGKRTRSNNICEIYQTLGIEAARTIIMSEI 1264

Query: 1303 KLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDA 1362
              VME HGMS+D+RH ML+A  MT++GEVLGITRHGLAKM+ESV NLASFE T+DHLFDA
Sbjct: 1265 TEVMEGHGMSVDWRHIMLLASQMTARGEVLGITRHGLAKMRESVFNLASFEKTADHLFDA 1324

Query: 1363 AFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ-----AVPRSEP 1402
            A+YGQTD I+GVSE II+G+P  +GTG+ KLLQ      VP  EP
Sbjct: 1325 AYYGQTDAINGVSERIILGMPAGIGTGIFKLLQHHEDKQVPPIEP 1369



 Score =  242 bits (618), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 124/256 (48%), Positives = 169/256 (66%), Gaps = 8/256 (3%)

Query: 87  VTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVG 146
           ++  D +QQ++ ++I+SKNLY    QR P+P+G+LDRRMG + K+A C TCGQ L++C+G
Sbjct: 22  ISGADEIQQEALVRIISKNLY--QAQRQPVPYGVLDRRMGISTKDAMCETCGQGLNECIG 79

Query: 147 HFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVR 206
           HFGY+DL LPVFHIG+FR  INILQ ICK   CA V+L  E    +  KL NP  SYL +
Sbjct: 80  HFGYLDLALPVFHIGHFRSTINILQMICK--ACAHVMLKPEDRQLYEKKLHNPNFSYLGK 137

Query: 207 KSLKKKILETTKKVSVCPHCGEINGVVKKC-GLLKISHEKYKNRTKKKDAIVEDLLAEYN 265
           K+L  ++L   KKV+ CPHCG  NG VKK  GLLKI H+ YK R  K D++    + E  
Sbjct: 138 KALHVQMLAKAKKVTKCPHCGSPNGGVKKGPGLLKILHDPYKGR--KVDSLFTSNMNEML 195

Query: 266 EAVKFNPEIEAH-KKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLL 324
            + + N ++ +    +   + L PL VL LFE IP  D+ LL M +  + P  LI+TR+ 
Sbjct: 196 RSTEANRDLNSTLGNYSTAEELTPLMVLDLFEQIPQRDVALLGMCSHDAHPKHLIVTRVF 255

Query: 325 VPPNCIRPSVISDLKS 340
           VPP CIRPSV+S++K+
Sbjct: 256 VPPACIRPSVLSEVKA 271



 Score =  212 bits (539), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 114/238 (47%), Positives = 161/238 (67%), Gaps = 4/238 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRI EIINA++ ISTPIITA L+    +++AR VK R+E+TTL E+  Y+E V  P  
Sbjct: 1058 GVPRIVEIINATKTISTPIITAELENCHSMEFARQVKARIEKTTLAELSSYVEVVCGPYS 1117

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSG---HSFLILKPKDSSKS- 879
             ++ I +DM RI+LL L +D+D+I + I ++R       V     HS ++++ + +  S 
Sbjct: 1118 CYLAIGIDMARIKLLGLHIDLDTIVFSILKSRMRVKPTQVEAVVKHSRIVVRVEATRTST 1177

Query: 880  FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
             N+++ ++   L +VV+ G+  INRAVI  +D      YKL +EG  LRDV+ATYGV G 
Sbjct: 1178 INAELARLALSLQNVVVAGLPNINRAVIAVDDARQPPTYKLCIEGYGLRDVIATYGVVGK 1237

Query: 940  KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +  SNN  E+Y+TLGIEAAR+ IM+EI  VME HGMS+D+RH ML+A  MT++GEVLG
Sbjct: 1238 RTRSNNICEIYQTLGIEAARTIIMSEITEVMEGHGMSVDWRHIMLLASQMTARGEVLG 1295



 Score =  115 bits (288), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 64/122 (52%), Positives = 73/122 (59%), Gaps = 14/122 (11%)

Query: 608 VTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           +   +GFVQNSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGY+QRRLVK LEDL V Y
Sbjct: 825 IPAARGFVQNSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYLQRRLVKCLEDLVVHY 884

Query: 668 DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHF 727
           D +   A     D I G             G GL  +     R++PV     +DN     
Sbjct: 885 DGTVRNAVNEMVDTIYG-------------GDGLDPVSMET-RNKPVDLVHQYDNLRAQH 930

Query: 728 PQ 729
           PQ
Sbjct: 931 PQ 932



 Score = 79.0 bits (193), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 34/53 (64%), Positives = 44/53 (83%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIA 73
           +LM N+SNLVTP+NGE+LIAATQDFITGGYLLTQK  F  + + M++A+  +A
Sbjct: 520 ILMGNQSNLVTPKNGEILIAATQDFITGGYLLTQKEVFLTKEEAMQLAACFLA 572



 Score = 61.2 bits (147), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 30/51 (58%), Positives = 36/51 (70%), Gaps = 5/51 (9%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ-----AVPRSEP 713
            D  FDAA+YGQTD I+GVSE II+G+P  +GTG+ KLLQ      VP  EP
Sbjct: 1319 DHLFDAAYYGQTDAINGVSERIILGMPAGIGTGIFKLLQHHEDKQVPPIEP 1369


>gi|194894264|ref|XP_001978037.1| GG17910 [Drosophila erecta]
 gi|190649686|gb|EDV46964.1| GG17910 [Drosophila erecta]
          Length = 1383

 Score =  337 bits (865), Expect = 2e-89,   Method: Compositional matrix adjust.
 Identities = 158/277 (57%), Positives = 197/277 (71%), Gaps = 21/277 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHK+SIM HRAKV P RTFRFNEC CTPYNADFDGDEMN+HLPQTEEA
Sbjct: 455 DGDIVLFNRQPSLHKMSIMCHRAKVQPQRTFRFNECACTPYNADFDGDEMNLHLPQTEEA 514

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL              +LM N+SNLVTP+NGE+LIAATQDFITGGYLLTQK  F  +
Sbjct: 515 RAEAL--------------ILMGNQSNLVTPKNGEILIAATQDFITGGYLLTQKEVFLTK 560

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            + M++A+  +++      I          P   ++   +WTGKQ+FSL+++PN D  V 
Sbjct: 561 EEAMQLAACFLSNEDSTMHI-------KLPPPALLKPRRLWTGKQMFSLLMRPNDDSHVR 613

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            N+  KGR YT N + C  DS++ +RNSEL+ G MDK+T+GSG K  +FY+LLRDFGE  
Sbjct: 614 LNMVNKGRNYTRNMDLCSNDSWIHIRNSELMCGVMDKATMGSGTKQCIFYLLLRDFGELH 673

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           A  AMWRL+R+ S++L NRGFS GI DVTP +  +Q+
Sbjct: 674 ATKAMWRLARIASYFLQNRGFSFGISDVTPSKKLLQH 710



 Score =  300 bits (769), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 188/465 (40%), Positives = 261/465 (56%), Gaps = 74/465 (15%)

Query: 1001 PVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEF 1060
            PV+L    D++ A++    D  L A+E+       L + EF  +  ++F  D++  +   
Sbjct: 916  PVDLVHQYDNLRAQHPQGKDRPLLAEELSEALETLLKTPEF-SEARDDFKLDVRNHINTV 974

Query: 1061 SKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATA 1120
            SK+  +   Q +  + +    L HQ +     +   F          ++Y RA  EP TA
Sbjct: 975  SKR--IGQLQKRYEKYIN---LCHQIECLTAEQLLQF-----VRRINDRYNRAVTEPGTA 1024

Query: 1121 VGALAAQSIGEPGTQMTLKTFH-------------------------------------- 1142
            VGA+AAQSIGEPGTQMTLKTFH                                      
Sbjct: 1025 VGAIAAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIVEIINATKTISTPIITAELENC 1084

Query: 1143 ----FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYC 1186
                FA             E+  Y+E V  P   ++ I +DM RI+LL L +D+D+I + 
Sbjct: 1085 HSMEFARQVKARIEKTTLAELSSYVEVVCGPYSCYLAIGIDMARIKLLGLHIDLDTIVFS 1144

Query: 1187 IERTR---GISGHLTVSGHSFLILKPKDSSKS-FNSKMYQMKQLLPSVVIKGVQGINRAV 1242
            I ++R     +    V+ HS ++++ + +  S  N+++ ++   L +VV+ G+  INRAV
Sbjct: 1145 ILKSRMRVKPTQVEAVASHSRIVVRVEATRTSTINAELARLALSLQNVVVAGLPNINRAV 1204

Query: 1243 IHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEI 1302
            I  +D      YKL +EG  LRDV+ATYGV G +  SNN  E+Y+TLGIEAAR+ IM+EI
Sbjct: 1205 IAVDDARQPPTYKLCIEGYGLRDVIATYGVVGKRTRSNNICEIYQTLGIEAARTIIMSEI 1264

Query: 1303 KLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDA 1362
              VME HGMS+D+RH ML+A  MT++GEVLGITRHGLAKM+ESV NLASFE T+DHLFDA
Sbjct: 1265 TEVMEGHGMSVDWRHIMLLASQMTARGEVLGITRHGLAKMRESVFNLASFEKTADHLFDA 1324

Query: 1363 AFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ-----AVPRSEP 1402
            A+YGQTD I+GVSE II+G+P  +GTG+ KLLQ      VP  EP
Sbjct: 1325 AYYGQTDAINGVSERIILGMPAGIGTGIFKLLQHHEDKQVPPIEP 1369



 Score =  246 bits (627), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 125/256 (48%), Positives = 171/256 (66%), Gaps = 8/256 (3%)

Query: 87  VTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVG 146
           ++  D +QQ++ ++I+SKNLY    QR P+P+G+LDRRMG + K+A C TCGQ L++C+G
Sbjct: 22  ISGADEIQQEALVRIISKNLY--QAQRQPVPYGVLDRRMGISTKDATCETCGQGLNECIG 79

Query: 147 HFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVR 206
           HFGY+DL LPVFHIG+FR  INILQ ICK  TCA V+L  E    +  KL NP  SYL +
Sbjct: 80  HFGYLDLALPVFHIGHFRSTINILQMICK--TCAHVMLKPEDRQLYEKKLHNPNFSYLGK 137

Query: 207 KSLKKKILETTKKVSVCPHCGEINGVVKKC-GLLKISHEKYKNRTKKKDAIVEDLLAEYN 265
           K+L  ++L   KKV+ CPHCG  NG VKK  GLLKI H+ YK R  K D++  + + E  
Sbjct: 138 KALHVQMLAKAKKVTKCPHCGSPNGGVKKGPGLLKILHDPYKGR--KVDSLFTNHINELL 195

Query: 266 EAVKFNPEIEAH-KKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLL 324
            + + N ++ +    +   + L PL VL LFE IP  D+ LL M +  + P  LI+TR+ 
Sbjct: 196 RSTEANRDLNSTLGNYSTAEELTPLMVLDLFEQIPQRDVALLGMCSHDAHPKHLIVTRVF 255

Query: 325 VPPNCIRPSVISDLKS 340
           VPP CIRPSV+S++K+
Sbjct: 256 VPPACIRPSVLSEVKA 271



 Score =  213 bits (543), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 114/238 (47%), Positives = 163/238 (68%), Gaps = 4/238 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRI EIINA++ ISTPIITA L+    +++AR VK R+E+TTL E+  Y+E V  P  
Sbjct: 1058 GVPRIVEIINATKTISTPIITAELENCHSMEFARQVKARIEKTTLAELSSYVEVVCGPYS 1117

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTR---GISGHLTVSGHSFLILKPKDSSKS- 879
             ++ I +DM RI+LL L +D+D+I + I ++R     +    V+ HS ++++ + +  S 
Sbjct: 1118 CYLAIGIDMARIKLLGLHIDLDTIVFSILKSRMRVKPTQVEAVASHSRIVVRVEATRTST 1177

Query: 880  FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
             N+++ ++   L +VV+ G+  INRAVI  +D      YKL +EG  LRDV+ATYGV G 
Sbjct: 1178 INAELARLALSLQNVVVAGLPNINRAVIAVDDARQPPTYKLCIEGYGLRDVIATYGVVGK 1237

Query: 940  KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +  SNN  E+Y+TLGIEAAR+ IM+EI  VME HGMS+D+RH ML+A  MT++GEVLG
Sbjct: 1238 RTRSNNICEIYQTLGIEAARTIIMSEITEVMEGHGMSVDWRHIMLLASQMTARGEVLG 1295



 Score =  115 bits (289), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 64/122 (52%), Positives = 73/122 (59%), Gaps = 14/122 (11%)

Query: 608 VTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           +   +GFVQNSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGY+QRRLVK LEDL V Y
Sbjct: 825 IPAARGFVQNSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYLQRRLVKCLEDLVVHY 884

Query: 668 DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHF 727
           D +   A     D I G             G GL  +     R++PV     +DN     
Sbjct: 885 DGTVRNAVNEMVDTIYG-------------GDGLDPVSMET-RNKPVDLVHQYDNLRAQH 930

Query: 728 PQ 729
           PQ
Sbjct: 931 PQ 932



 Score = 77.8 bits (190), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 33/53 (62%), Positives = 44/53 (83%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIA 73
           +LM N+SNLVTP+NGE+LIAATQDFITGGYLLTQK  F  + + M++A+  ++
Sbjct: 520 ILMGNQSNLVTPKNGEILIAATQDFITGGYLLTQKEVFLTKEEAMQLAACFLS 572



 Score = 61.2 bits (147), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 30/51 (58%), Positives = 36/51 (70%), Gaps = 5/51 (9%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ-----AVPRSEP 713
            D  FDAA+YGQTD I+GVSE II+G+P  +GTG+ KLLQ      VP  EP
Sbjct: 1319 DHLFDAAYYGQTDAINGVSERIILGMPAGIGTGIFKLLQHHEDKQVPPIEP 1369


>gi|402586876|gb|EJW80813.1| DNA-directed RNA polymerase, partial [Wuchereria bancrofti]
          Length = 735

 Score =  337 bits (864), Expect = 3e-89,   Method: Compositional matrix adjust.
 Identities = 162/276 (58%), Positives = 198/276 (71%), Gaps = 20/276 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DNDVVLFNRQPSLHK+SIM+HRAK++  RTFRFNEC CTPYNADFDGDEMN+H+PQT EA
Sbjct: 392 DNDVVLFNRQPSLHKISIMSHRAKIVRGRTFRFNECACTPYNADFDGDEMNLHVPQTYEA 451

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA               +LM  KSNL+TPR+GE LIAA QDFITG YLLT K++FF R
Sbjct: 452 RAEA--------------SLLMGVKSNLITPRSGEPLIAAIQDFITGTYLLTHKDSFFPR 497

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           ++  R A+ +I  +S      K+       P   ++   +WTGKQ+  LI++P+ D  +N
Sbjct: 498 SEVHRFAAAIIDSSS------KKQQRIQIPPPAILKPVELWTGKQLIELIIRPDVDSKIN 551

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            NL TK ++YT NEEFC +DSYVI+RNS LL G +DK+ LGSG K N+FYILLRDFGED 
Sbjct: 552 LNLTTKNKSYTGNEEFCVKDSYVIIRNSVLLCGVLDKALLGSGSKTNIFYILLRDFGEDA 611

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           AV AMWRL RM   +L NRGFSIGIGDV P +  ++
Sbjct: 612 AVDAMWRLGRMAPVFLSNRGFSIGIGDVRPSKALLK 647



 Score =  187 bits (476), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 112/256 (43%), Positives = 156/256 (60%), Gaps = 24/256 (9%)

Query: 126 GTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLG 185
           GT QK  +C TC QNL DCVGHFGYIDL +PVFH+G+FR  I +LQ ICK   C+ +L+ 
Sbjct: 1   GTCQKHTDCQTCKQNLVDCVGHFGYIDLAIPVFHVGFFRLTIQMLQCICK--FCSAMLIT 58

Query: 186 EEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKC--GLLKISH 243
            E+      ++ NP L YL RK+L K+I+  +KK++VC  CG  NG+VKK    +LKI+H
Sbjct: 59  GEQKKALLHQVNNPNLDYLRRKALHKRIVAASKKITVCNRCGHKNGIVKKAVGAVLKIAH 118

Query: 244 EKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIE---AHKKFGLIQTLNPLEVLQLFEAIPL 300
                     + I  D  +EY  A + N E++      KF L   L+PL+V  LF  I  
Sbjct: 119 A---------EVIPADNYSEYVYAAQENKELQNLLPKTKFTL---LDPLQVQILFNKIEK 166

Query: 301 EDIPLLLM-NAELSK-PSDLILTRLLVPPNCIRPSVISDLKS---DNDVVLFNRQPSLHK 355
           EDIPLL++ +A+  K PSD+ILTR+ VPP CIRPSV+S++KS   ++D+ +   +  L  
Sbjct: 167 EDIPLLMVRSADTPKHPSDVILTRIPVPPCCIRPSVVSEVKSGTTEDDITMKLSEIMLIN 226

Query: 356 LSIMAHRAKVLPHRTF 371
             I  H+ +  P +T 
Sbjct: 227 DVIEKHKREGSPTKTI 242



 Score = 71.6 bits (174), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 34/60 (56%), Positives = 43/60 (71%)

Query: 13  YATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLI 72
           Y  R    +LM  KSNL+TPR+GE LIAA QDFITG YLLT K++FF R++  R A+ +I
Sbjct: 449 YEARAEASLLMGVKSNLITPRSGEPLIAAIQDFITGTYLLTHKDSFFPRSEVHRFAAAII 508


>gi|195132669|ref|XP_002010765.1| GI21717 [Drosophila mojavensis]
 gi|193907553|gb|EDW06420.1| GI21717 [Drosophila mojavensis]
          Length = 1382

 Score =  337 bits (864), Expect = 3e-89,   Method: Compositional matrix adjust.
 Identities = 157/277 (56%), Positives = 197/277 (71%), Gaps = 21/277 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+D+VLFNRQPSLHK+SIM HRAKV P RTFRFNEC CTPYNADFDGDEMN+HLPQTEEA
Sbjct: 455 DDDIVLFNRQPSLHKMSIMCHRAKVQPQRTFRFNECACTPYNADFDGDEMNLHLPQTEEA 514

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL              +LM N+SNLVTP+NGE+LIAATQDFITGGYLLTQK  F  +
Sbjct: 515 RAEAL--------------ILMGNQSNLVTPKNGEILIAATQDFITGGYLLTQKEVFLTK 560

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            + M++A+  +A+      I          P    +   +WTGKQ+FSL+++PN D  V 
Sbjct: 561 EEAMQLAACFLANEDSTMRI-------QMPPPAIWKPRRLWTGKQLFSLLMRPNDDSIVR 613

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            N+  KGR Y+ N + C  DS++ +RNSEL+ G+MDK+T+GSG K  +FY+LLRDFGE  
Sbjct: 614 LNMVNKGRNYSGNMDLCVNDSWIHIRNSELMCGTMDKATMGSGTKQCIFYLLLRDFGEAF 673

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           A  AMWRL+R+ S+++ NRGFS GI DVTP    +Q+
Sbjct: 674 ATKAMWRLARIASYFIQNRGFSFGISDVTPSARLLQH 710



 Score =  291 bits (745), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 183/462 (39%), Positives = 247/462 (53%), Gaps = 86/462 (18%)

Query: 1001 PVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEF 1060
            PV+L    D++ A+        L A EIL+     L   EF  +   +F RD+   L   
Sbjct: 916  PVDLNHQYDNLRAQLPCGDQQPLEAGEILSTVESLLQLPEF-AEARADFKRDVTSHLNTV 974

Query: 1061 SKKESV------TSHQDKVSQP---LREQILSHQDKIGHGRESNPFPSACKAEACREKYV 1111
            +K+ S         H+D   Q     REQ+L    +I                   ++Y 
Sbjct: 975  TKRISKLQEKYGAEHKDLCKQIECISREQLLEFLRRIN------------------DRYN 1016

Query: 1112 RAQIEPATAVGALAAQSIGEPGTQMTLKTFH----------------------------- 1142
            RA  EP TAVGA+AAQSIGEPGTQMTLKTFH                             
Sbjct: 1017 RAVTEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIVEIINATKTISTP 1076

Query: 1143 -------------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLE 1177
                         FA            GE+  ++E V  P    ++I +D  RI++L L 
Sbjct: 1077 IITAELRNNTSMEFARQVKARIEKTTLGELSSFVELVCGPQSCHLVIGIDTARIKVLGLH 1136

Query: 1178 VDIDSIRYCIERTR----GISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIK 1233
            +D+DSI   I ++R        H        ++      + + N+++ ++   + +VV+ 
Sbjct: 1137 IDLDSIMCSILKSRLRIKANQLHAIPKKSRIIVRVEATRNATINAELARLATTIQNVVVA 1196

Query: 1234 GVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEA 1293
            G+  I RAVI  +D +    YKL +EG  LR+V+ATYGV G +  SNN  E+Y+TLGIEA
Sbjct: 1197 GLPNIARAVIAVDDAKQPPTYKLCIEGYGLREVIATYGVVGERTRSNNICEIYQTLGIEA 1256

Query: 1294 ARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFE 1353
            AR+ IM+EI  VME HGMS+D+RH ML+A  MT++GEVLGITRHGLAKM+ESV NLASFE
Sbjct: 1257 ARTIIMSEITDVMEGHGMSVDWRHIMLLASQMTARGEVLGITRHGLAKMRESVFNLASFE 1316

Query: 1354 NTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 1395
             T+DHLFDAA+YGQTD I+GVSE II+G+P  +GTG+ KLLQ
Sbjct: 1317 KTADHLFDAAYYGQTDAINGVSERIILGMPAGIGTGIFKLLQ 1358



 Score =  254 bits (650), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 131/256 (51%), Positives = 170/256 (66%), Gaps = 8/256 (3%)

Query: 87  VTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVG 146
           ++  D +QQ+S ++I+SKNLY    QR P+P+G+LDRRMG + K+A C TCGQ L++C+G
Sbjct: 22  ISGADEIQQESLVRIISKNLY--QAQRQPVPYGVLDRRMGISTKDAVCETCGQGLNECIG 79

Query: 147 HFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVR 206
           HFGY+DL LPVFHIG+FR  INILQ ICK  TCARV+L  E  A F  KL NP  SYL +
Sbjct: 80  HFGYLDLALPVFHIGHFRSTINILQMICK--TCARVMLKPEDRAVFEKKLHNPNFSYLGK 137

Query: 207 KSLKKKILETTKKVSVCPHCGEINGVVKKC-GLLKISHEKYKNRTKKKDAIVEDLLAEYN 265
           K+L  ++L   KKV+ CPHC   NG VKK  GLLKI H+ YK R  KKDA     + E  
Sbjct: 138 KALHSQMLAKAKKVTKCPHCNAANGGVKKGPGLLKILHDPYKGR--KKDATFTSHMEEML 195

Query: 266 EAVKFNPEIE-AHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLL 324
            + + N ++      +   + L PL VL LFE IP  DI LL M +  + P  LI+TR+ 
Sbjct: 196 RSTELNRDLNLTLSNYSAAEELTPLMVLDLFEQIPQSDIALLGMCSRGAHPKHLIVTRVF 255

Query: 325 VPPNCIRPSVISDLKS 340
           VPP CIRPSV+S++K+
Sbjct: 256 VPPACIRPSVLSEVKA 271



 Score =  204 bits (520), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 108/238 (45%), Positives = 156/238 (65%), Gaps = 4/238 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRI EIINA++ ISTPIITA L  +T +++AR VK R+E+TTLGE+  ++E V  P  
Sbjct: 1059 GVPRIVEIINATKTISTPIITAELRNNTSMEFARQVKARIEKTTLGELSSFVELVCGPQS 1118

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTR----GISGHLTVSGHSFLILKPKDSSKS 879
              ++I +D  RI++L L +D+DSI   I ++R        H        ++      + +
Sbjct: 1119 CHLVIGIDTARIKVLGLHIDLDSIMCSILKSRLRIKANQLHAIPKKSRIIVRVEATRNAT 1178

Query: 880  FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
             N+++ ++   + +VV+ G+  I RAVI  +D +    YKL +EG  LR+V+ATYGV G 
Sbjct: 1179 INAELARLATTIQNVVVAGLPNIARAVIAVDDAKQPPTYKLCIEGYGLREVIATYGVVGE 1238

Query: 940  KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +  SNN  E+Y+TLGIEAAR+ IM+EI  VME HGMS+D+RH ML+A  MT++GEVLG
Sbjct: 1239 RTRSNNICEIYQTLGIEAARTIIMSEITDVMEGHGMSVDWRHIMLLASQMTARGEVLG 1296



 Score =  114 bits (285), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 54/77 (70%), Positives = 59/77 (76%)

Query: 608 VTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           +   +GFVQNSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGY+QRRLVK LEDL V Y
Sbjct: 825 IPAARGFVQNSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYLQRRLVKCLEDLVVHY 884

Query: 668 DMSFDAAFYGQTDCISG 684
           D +   A     D I G
Sbjct: 885 DGTVRNAVNEMVDTIYG 901



 Score = 79.3 bits (194), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 35/60 (58%), Positives = 45/60 (75%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFFR 80
           +LM N+SNLVTP+NGE+LIAATQDFITGGYLLTQK  F  + + M++A+  +A      R
Sbjct: 520 ILMGNQSNLVTPKNGEILIAATQDFITGGYLLTQKEVFLTKEEAMQLAACFLANEDSTMR 579



 Score = 60.1 bits (144), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 26/39 (66%), Positives = 32/39 (82%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  FDAA+YGQTD I+GVSE II+G+P  +GTG+ KLLQ
Sbjct: 1320 DHLFDAAYYGQTDAINGVSERIILGMPAGIGTGIFKLLQ 1358


>gi|170584528|ref|XP_001897051.1| RNA polymerase Rpb1, domain 1 family protein [Brugia malayi]
 gi|158595586|gb|EDP34129.1| RNA polymerase Rpb1, domain 1 family protein [Brugia malayi]
          Length = 1404

 Score =  337 bits (864), Expect = 3e-89,   Method: Compositional matrix adjust.
 Identities = 162/276 (58%), Positives = 198/276 (71%), Gaps = 20/276 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DNDVVLFNRQPSLHK+SIM+HRAK++P RTFRFNEC CTPYNADFDGDEMN+H+PQT EA
Sbjct: 453 DNDVVLFNRQPSLHKISIMSHRAKIVPGRTFRFNECACTPYNADFDGDEMNLHVPQTYEA 512

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA               +LM  KSNL+TPR+GE LIAA QDFITG YLLT K++FF R
Sbjct: 513 RAEA--------------SLLMGVKSNLITPRSGEPLIAAIQDFITGTYLLTHKDSFFPR 558

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +  R A+ +I  +S      K+       P   ++   +WTGKQ+  LI++P+ D  ++
Sbjct: 559 LEVHRFAAAIIDSSS------KKQQRIRIPPPAILKPVELWTGKQLVELIIRPDVDSKIS 612

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            NL TK ++YT NEEFC +DSYVI+RNS LL G +DK+ LGSG K N+FYILLRDFGED 
Sbjct: 613 LNLTTKNKSYTGNEEFCVKDSYVIIRNSVLLCGVLDKALLGSGSKTNIFYILLRDFGEDA 672

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           AV AMWRL RM   +L NRGFSIGIGDV P +  ++
Sbjct: 673 AVDAMWRLGRMAPVFLSNRGFSIGIGDVRPSKTLLK 708



 Score =  266 bits (680), Expect = 7e-68,   Method: Compositional matrix adjust.
 Identities = 163/373 (43%), Positives = 220/373 (58%), Gaps = 67/373 (17%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYI 1151
            C  K+ RA  EP TAVGA+AA SIGEP TQMTLKTFHFAG              E+   +
Sbjct: 1033 CLRKFRRAICEPGTAVGAVAATSIGEPSTQMTLKTFHFAGVASMNITQGVPRIKEIINGV 1092

Query: 1152 EEVFVP----------------------------------------DDSFILIKLDMDRI 1171
            + +  P                                        DD FIL+K++  R+
Sbjct: 1093 KLISTPLITAALTNEKDEKLARRVKARIEKTTLGEICDYIEEVYLPDDCFILLKINAKRV 1152

Query: 1172 RLLHLEVDIDSIRYCIERTR-----GISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQL 1226
            RLL LE+ + SI   I  ++      IS  +T+ G + + ++P + +K   SKM  ++ L
Sbjct: 1153 RLLQLEITMSSIAQSICTSKLPVPVKIS-QITILGKTIMTIRPPELAKC--SKMMAIQYL 1209

Query: 1227 ---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTY 1283
               + +VV+KG+ GI R VIH ++ +G   YKLLVEG + R+VMAT GV G +   NN  
Sbjct: 1210 KYNIGNVVVKGLPGIVRCVIHADEKKG-DSYKLLVEGIDYREVMATLGVDGRRTYFNNAL 1268

Query: 1284 EVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMK 1343
             V   LGIEAARS+I++EI   M +HG+ +D RH ML+ADLMT +GEVLGITR+GL KMK
Sbjct: 1269 TVADVLGIEAARSSIISEILSTMASHGIGLDQRHVMLLADLMTYRGEVLGITRNGLVKMK 1328

Query: 1344 ESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPV 1403
            ESVL LASFE T+DHLF+AAF+ Q D I GVSECII+G P+ +GTGL KLL    +   +
Sbjct: 1329 ESVLLLASFEKTADHLFEAAFFSQEDKICGVSECIILGTPITIGTGLFKLLYDHGKQLTI 1388

Query: 1404 PR-TLLFDNPEFH 1415
             + + +F++PEF+
Sbjct: 1389 SKMSTIFESPEFN 1401



 Score =  218 bits (556), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 128/300 (42%), Positives = 183/300 (61%), Gaps = 25/300 (8%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQR-TPIPHGLLDRRMGTNQKEANCTTCGQNL 141
           ++ T    + ++Q +HI I +  LY ++P R  P+ HG LD R+GT QK  +C TC QNL
Sbjct: 18  VQFTAGNAESMRQVAHIPIFNSKLYDENPGRWIPVAHGPLDPRLGTCQKHTDCQTCKQNL 77

Query: 142 SDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPAL 201
            DCVGHFGYIDL +PVFH+G+FR  I +LQ ICK   C+ +L+  E+   F  ++ NP L
Sbjct: 78  VDCVGHFGYIDLAIPVFHVGFFRLTIQMLQCICK--FCSAMLITGEQKKAFLHQVNNPNL 135

Query: 202 SYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKC--GLLKISHEKYKNRTKKKDAIVED 259
            YL RK+L K+I+  +KK++VC  CG  NG+VKK    +LKI+H          + I  D
Sbjct: 136 DYLRRKALHKRIVAASKKITVCNRCGHKNGIVKKAVGAVLKIAH---------AEVIPAD 186

Query: 260 LLAEYNEAVKFNPEIE---AHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLM-NAELSK- 314
             +EY  A + N E++      KF L   L+PL+V  LF  I  EDIPLL++ +A+  K 
Sbjct: 187 NYSEYVYAAQENKELQNLLPKTKFTL---LDPLQVQILFNKIEKEDIPLLMVRSADTPKH 243

Query: 315 PSDLILTRLLVPPNCIRPSVISDLKS---DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTF 371
           PSD+ILTR+ VPP CIRPSV+S++KS   ++D+ +   +  L    I  H+ +  P +T 
Sbjct: 244 PSDVILTRIPVPPCCIRPSVVSEVKSGTTEDDITMKLSEIMLINDVIEKHKKEGSPTKTI 303



 Score =  212 bits (540), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 120/242 (49%), Positives = 165/242 (68%), Gaps = 12/242 (4%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIIN  + ISTP+ITA L  + D   AR VK R+E+TTLGE+C+YIEEV++PDD
Sbjct: 1081 GVPRIKEIINGVKLISTPLITAALTNEKDEKLARRVKARIEKTTLGEICDYIEEVYLPDD 1140

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTR-----GISGHLTVSGHSFLILKPKDSSK 878
             FIL+K++  R+RLL LE+ + SI   I  ++      IS  +T+ G + + ++P + +K
Sbjct: 1141 CFILLKINAKRVRLLQLEITMSSIAQSICTSKLPVPVKIS-QITILGKTIMTIRPPELAK 1199

Query: 879  SFNSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYG 935
               SKM  ++ L   + +VV+KG+ GI R VIH ++ +G   YKLLVEG + R+VMAT G
Sbjct: 1200 C--SKMMAIQYLKYNIGNVVVKGLPGIVRCVIHADEKKG-DSYKLLVEGIDYREVMATLG 1256

Query: 936  VKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            V G +   NN   V   LGIEAARS+I++EI   M +HG+ +D RH ML+ADLMT +GEV
Sbjct: 1257 VDGRRTYFNNALTVADVLGIEAARSSIISEILSTMASHGIGLDQRHVMLLADLMTYRGEV 1316

Query: 996  LG 997
            LG
Sbjct: 1317 LG 1318



 Score =  117 bits (293), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 54/61 (88%), Positives = 57/61 (93%), Gaps = 1/61 (1%)

Query: 609 TPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV+NSF+SGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVK LEDLCV Y
Sbjct: 824 TPAAKGFVENSFYSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKCLEDLCVNY 883

Query: 668 D 668
           D
Sbjct: 884 D 884



 Score = 70.5 bits (171), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 34/60 (56%), Positives = 42/60 (70%)

Query: 13  YATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLI 72
           Y  R    +LM  KSNL+TPR+GE LIAA QDFITG YLLT K++FF R +  R A+ +I
Sbjct: 510 YEARAEASLLMGVKSNLITPRSGEPLIAAIQDFITGTYLLTHKDSFFPRLEVHRFAAAII 569



 Score = 59.3 bits (142), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 28/61 (45%), Positives = 41/61 (67%), Gaps = 1/61 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPR-TLLFDNPEFH 726
            D  F+AAF+ Q D I GVSECII+G P+ +GTGL KLL    +   + + + +F++PEF+
Sbjct: 1342 DHLFEAAFFSQEDKICGVSECIILGTPITIGTGLFKLLYDHGKQLTISKMSTIFESPEFN 1401

Query: 727  F 727
             
Sbjct: 1402 L 1402


>gi|195399321|ref|XP_002058269.1| GJ15582 [Drosophila virilis]
 gi|194150693|gb|EDW66377.1| GJ15582 [Drosophila virilis]
          Length = 1044

 Score =  336 bits (862), Expect = 6e-89,   Method: Compositional matrix adjust.
 Identities = 156/277 (56%), Positives = 196/277 (70%), Gaps = 21/277 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+D+VLFNRQPSLHK+SIM HRAKV P RTFRFNEC CTPYNADFDGDEMN+HLPQTEEA
Sbjct: 455 DDDIVLFNRQPSLHKMSIMCHRAKVQPQRTFRFNECACTPYNADFDGDEMNLHLPQTEEA 514

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL              +LM N+SNLVTP+NGE+LIAATQDFITGGYLLTQK  F  +
Sbjct: 515 RAEAL--------------ILMGNQSNLVTPKNGEILIAATQDFITGGYLLTQKEVFLTK 560

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            + M++A+  +A+      I          P    +   +WTGKQ+FSL+++PN D  V 
Sbjct: 561 EEAMQLAACFLANEDSTMRI-------QMPPPAIWKPRRLWTGKQLFSLLMRPNDDSNVR 613

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            N+  KGR Y  N + C  DS++ +RNSEL+ G+MDK+T+GSG K  +FY+LLRDFGE  
Sbjct: 614 LNMVNKGRNYAGNMDLCANDSWIHIRNSELMCGTMDKATMGSGTKQCIFYLLLRDFGEAF 673

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           A  AMWRL+R+ S+++ NRGFS GI DVTP +  + +
Sbjct: 674 ATKAMWRLARIASYFIQNRGFSFGISDVTPSEKLLHH 710



 Score =  253 bits (645), Expect = 8e-64,   Method: Compositional matrix adjust.
 Identities = 129/260 (49%), Positives = 173/260 (66%), Gaps = 8/260 (3%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           ++  ++  D +QQ+S ++I+SKNLY    QR P+P+G+LDRRMG + K+A C TCGQ L+
Sbjct: 18  VQFGISGADEIQQESLVRIISKNLY--QAQRQPVPYGVLDRRMGISTKDALCETCGQGLN 75

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALS 202
           +C+GHFGY+DL LPVFHIG+FR  INILQ ICK  TCA V+L  E  A F  KL NP  S
Sbjct: 76  ECIGHFGYLDLALPVFHIGHFRSTINILQMICK--TCAHVMLKAEDRAVFEKKLHNPNFS 133

Query: 203 YLVRKSLKKKILETTKKVSVCPHCGEINGVVKKC-GLLKISHEKYKNRTKKKDAIVEDLL 261
           YL +K+L  ++L   KKV+ CPHCG  NG VKK  GLLKI H+ YK R  KKDA+    +
Sbjct: 134 YLGKKALHSQMLAKAKKVTKCPHCGAANGGVKKGPGLLKILHDPYKGR--KKDAVFTSHM 191

Query: 262 AEYNEAVKFNPEIE-AHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
            +   + + N ++      +   + L PL VL LFE IP  D+ LL M +  + P  LI+
Sbjct: 192 DQMLRSTELNRDLNLTLSNYSAAEELTPLMVLDLFEQIPQSDVALLGMCSRGAHPKHLIV 251

Query: 321 TRLLVPPNCIRPSVISDLKS 340
           TR+ VPP CIRPSV+S++K+
Sbjct: 252 TRVFVPPACIRPSVLSEVKA 271



 Score =  114 bits (286), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 70/163 (42%), Positives = 84/163 (51%), Gaps = 37/163 (22%)

Query: 608 VTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           +   +GFVQNSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGY+QRRLVK LEDL V Y
Sbjct: 825 IPAARGFVQNSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYLQRRLVKCLEDLVVHY 884

Query: 668 DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHF 727
           D +   A     D I G             G GL  +     R++PV     +DN     
Sbjct: 885 DGTVRNAINEMVDTIYG-------------GDGLDPVSMET-RNKPVDLNHQYDNLRAQL 930

Query: 728 PQV-----------------------YYERRRDYSVKVTASVK 747
           P V                       + E R D+ + +TA +K
Sbjct: 931 PCVEQQQPLEADEILGVAETLLKLPEFAEARLDFKLDITAHLK 973



 Score = 79.0 bits (193), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 35/60 (58%), Positives = 45/60 (75%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFFR 80
           +LM N+SNLVTP+NGE+LIAATQDFITGGYLLTQK  F  + + M++A+  +A      R
Sbjct: 520 ILMGNQSNLVTPKNGEILIAATQDFITGGYLLTQKEVFLTKEEAMQLAACFLANEDSTMR 579



 Score = 45.1 bits (105), Expect = 0.30,   Method: Compositional matrix adjust.
 Identities = 43/145 (29%), Positives = 62/145 (42%), Gaps = 29/145 (20%)

Query: 1001 PVELKRLLDDIIAK-NSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEE 1059
            PV+L    D++ A+         L A EIL ++   L   EF  +   +F  DI   L+ 
Sbjct: 916  PVDLNHQYDNLRAQLPCVEQQQPLEADEILGVAETLLKLPEF-AEARLDFKLDITAHLKN 974

Query: 1060 FSKKESVTSHQ---------DKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKY 1110
             +K+      Q         +++    REQ+L    +I                   ++Y
Sbjct: 975  IAKRIGQLQQQYGSKHRSLCNQIECLSREQLLEFLRRIN------------------DRY 1016

Query: 1111 VRAQIEPATAVGALAAQSIGEPGTQ 1135
             RA  EP TAVGA AAQ+IGE GTQ
Sbjct: 1017 NRAVSEPGTAVGANAAQTIGERGTQ 1041


>gi|157130170|ref|XP_001655623.1| DNA-directed RNA polymerase II largest subunit [Aedes aegypti]
 gi|108871980|gb|EAT36205.1| AAEL011692-PA [Aedes aegypti]
          Length = 1298

 Score =  336 bits (861), Expect = 6e-89,   Method: Compositional matrix adjust.
 Identities = 202/457 (44%), Positives = 266/457 (58%), Gaps = 77/457 (16%)

Query: 1001 PVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEF 1060
            PV++ R    + +    R++  LS  EIL ++ E L   +F   +  +F ++  +FL +F
Sbjct: 839  PVDIDRQFMHVRSVYPCRNEAPLSGNEILPVAEEILKKSDF-DGSRADFRKECLEFLSKF 897

Query: 1061 SKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEA----CREKYVRAQIE 1116
             ++       D++ +  R     H  K+    E     +  + EA     R KY +A  E
Sbjct: 898  GQR------LDQIQKRYR-----HCSKVSLEVERT---TRGQLEAFLTQVRNKYNKAITE 943

Query: 1117 PATAVGALAAQSIGEPGTQMTLKTFH---------------------------------- 1142
            P TAVGALAAQSIGEPGTQMTLKTFH                                  
Sbjct: 944  PGTAVGALAAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIVEIINATKAISTPIITAE 1003

Query: 1143 --------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDS 1182
                    FA            GE+  YIEE +  DD F+LIKLD+DRIR+L LEV+ ++
Sbjct: 1004 IEDNTSMEFARKVKARIEKTTLGEISSYIEEAYKSDDCFLLIKLDLDRIRVLGLEVNAET 1063

Query: 1183 IRY--CIERTRGISGHLTVSGHSFLILKPKDS--SKSFNSKMYQMKQLLPSVVIKGVQGI 1238
            IRY  C  + +    ++ V G S +I++P  S  S + N+++ ++   +P+VV+ G+  +
Sbjct: 1064 IRYSICTSKLKLKQENVEVYGPSLIIIRPDPSKHSHALNAELQRLLTAIPNVVVAGLPQV 1123

Query: 1239 NRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTI 1298
            +RAVI  +D  G   YKL VEG  LRDVMATYGV G +  SNN  EVY TLGIEAAR+TI
Sbjct: 1124 SRAVIAVDDSRGPPTYKLCVEGYGLRDVMATYGVVGARTKSNNILEVYVTLGIEAARTTI 1183

Query: 1299 MTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDH 1358
            M EI  VME HGMS+D RH ML+A  MTS+GEVLGITRHGLAKM+ESV NLASFE T+DH
Sbjct: 1184 MNEITDVMEGHGMSVDHRHIMLLASQMTSRGEVLGITRHGLAKMRESVFNLASFEKTADH 1243

Query: 1359 LFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 1395
            LFDAA+YGQTD I GVSE II+G+P  +GTGL KL+ 
Sbjct: 1244 LFDAAYYGQTDSIDGVSERIILGMPAAIGTGLFKLIH 1280



 Score =  333 bits (853), Expect = 6e-88,   Method: Compositional matrix adjust.
 Identities = 197/394 (50%), Positives = 232/394 (58%), Gaps = 80/394 (20%)

Query: 331 RPSVISDLKS---------DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPY 381
           R  V  DLK          D DVVLFNRQPSLHKLSIM H AKV P RTFRFNEC CTPY
Sbjct: 439 RDKVAQDLKCGDIVERHLMDGDVVLFNRQPSLHKLSIMCHVAKVQPQRTFRFNECACTPY 498

Query: 382 NADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAAT 441
           NADFDGDEMN+HLPQTEEARAEAL              VLM NKSNLVTPRNGELLIAAT
Sbjct: 499 NADFDGDEMNLHLPQTEEARAEAL--------------VLMGNKSNLVTPRNGELLIAAT 544

Query: 442 QDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIW 501
           QDFITGGYLLTQK+ F  R Q M++A+ +++      G           P + ++   +W
Sbjct: 545 QDFITGGYLLTQKDQFLTREQVMQLAACMLS------GPDANMEIDLPKPAI-IKPRKMW 597

Query: 502 TGKQIFSLILKPNRDCPVNANLKTK----GRAYTANEEFCHRDSYVILRNSELLAGSMDK 557
           TGKQIFSLILKPN+DC VNANL TK     R     ++    + Y   R  E +A  M K
Sbjct: 598 TGKQIFSLILKPNKDCIVNANLSTKDVTPSRKLLQEKQKLLENGYS--RCDEYIA-EMKK 654

Query: 558 STL----GSGGKANVFYILLRDFG--EDVAVTAMWRLSRMTSFYLM-----NRGFSIGIG 606
            TL    G   +  +  ++L++     ++A  A +R    T+  L+     ++G +I I 
Sbjct: 655 GTLQCQPGCTAEQTLEAVMLKELSSIRELAAKACFRELHPTNSALIMAQSGSKGSNINIS 714

Query: 607 D--------------------------------VTPGQGFVQNSFFSGLTPTEFFFHTMG 634
                                            +   +GFVQNSF+SGLTPTEFFFHTM 
Sbjct: 715 QMIACVGQQAINGKRVPNGFEDRALPHFEKFSKIPAARGFVQNSFYSGLTPTEFFFHTMA 774

Query: 635 GREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           GREGLVDTAVKTAETGY+QRRLVK LEDL VQYD
Sbjct: 775 GREGLVDTAVKTAETGYLQRRLVKCLEDLVVQYD 808



 Score =  270 bits (690), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 130/250 (52%), Positives = 180/250 (72%), Gaps = 5/250 (2%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           +QQ++H+ +V+KNLY QD  RTP+ +G+LDRRMG +QK+A C TC + L+DCVGHFGYID
Sbjct: 28  IQQEAHLHVVAKNLYNQDANRTPVTYGVLDRRMGVSQKDATCDTCKKGLNDCVGHFGYID 87

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKK 212
           L LPVFH+G+FR  I ILQSICK   C+RV+L E++   F A+L NP LSYL +KS+  +
Sbjct: 88  LALPVFHVGHFRATITILQSICK--VCSRVMLKEDEKKQFSARLMNPNLSYLAKKSIHSQ 145

Query: 213 ILETTKKVSVCPHCGEINGVVKK-CGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFN 271
           +L+  KK + CP+CG +NG VKK  GL+KI HE ++ + K  D +V + L     A++ N
Sbjct: 146 VLKKAKKNTKCPYCGSLNGPVKKGAGLMKIVHEPFRGK-KATDPLVTNALEVMMSAIEGN 204

Query: 272 PEI-EAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCI 330
            E+ +      L++ LNP+EVL LF+ IP  DIPLL M +  S P+DLI+TR+ VPP CI
Sbjct: 205 RELSQTIGPSSLMKELNPVEVLDLFKNIPKSDIPLLGMTSPESNPADLIVTRVFVPPVCI 264

Query: 331 RPSVISDLKS 340
           RPSV+S++K+
Sbjct: 265 RPSVVSEVKA 274



 Score =  251 bits (640), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 129/238 (54%), Positives = 172/238 (72%), Gaps = 4/238 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRI EIINA++ ISTPIITA ++ +T +++AR VK R+E+TTLGE+  YIEE +  DD
Sbjct: 981  GVPRIVEIINATKAISTPIITAEIEDNTSMEFARKVKARIEKTTLGEISSYIEEAYKSDD 1040

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDS--SKS 879
             F+LIKLD+DRIR+L LEV+ ++IRY  C  + +    ++ V G S +I++P  S  S +
Sbjct: 1041 CFLLIKLDLDRIRVLGLEVNAETIRYSICTSKLKLKQENVEVYGPSLIIIRPDPSKHSHA 1100

Query: 880  FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
             N+++ ++   +P+VV+ G+  ++RAVI  +D  G   YKL VEG  LRDVMATYGV G 
Sbjct: 1101 LNAELQRLLTAIPNVVVAGLPQVSRAVIAVDDSRGPPTYKLCVEGYGLRDVMATYGVVGA 1160

Query: 940  KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +  SNN  EVY TLGIEAAR+TIM EI  VME HGMS+D RH ML+A  MTS+GEVLG
Sbjct: 1161 RTKSNNILEVYVTLGIEAARTTIMNEITDVMEGHGMSVDHRHIMLLASQMTSRGEVLG 1218



 Score = 88.6 bits (218), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 40/54 (74%), Positives = 47/54 (87%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           VLM NKSNLVTPRNGELLIAATQDFITGGYLLTQK+ F  R Q M++A+ +++G
Sbjct: 523 VLMGNKSNLVTPRNGELLIAATQDFITGGYLLTQKDQFLTREQVMQLAACMLSG 576



 Score = 57.0 bits (136), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 25/39 (64%), Positives = 30/39 (76%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  FDAA+YGQTD I GVSE II+G+P  +GTGL KL+ 
Sbjct: 1242 DHLFDAAYYGQTDSIDGVSERIILGMPAAIGTGLFKLIH 1280


>gi|170039594|ref|XP_001847615.1| conserved hypothetical protein [Culex quinquefasciatus]
 gi|167863133|gb|EDS26516.1| conserved hypothetical protein [Culex quinquefasciatus]
          Length = 1303

 Score =  335 bits (859), Expect = 1e-88,   Method: Compositional matrix adjust.
 Identities = 199/397 (50%), Positives = 234/397 (58%), Gaps = 81/397 (20%)

Query: 331 RPSVISDLKS---------DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPY 381
           R  V  DLK          D DVVLFNRQPSLHKLSIM H AKV P RTFRFNEC CTPY
Sbjct: 439 RDKVAQDLKCGDIVERHLMDGDVVLFNRQPSLHKLSIMCHVAKVQPQRTFRFNECACTPY 498

Query: 382 NADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAAT 441
           NADFDGDEMN+HLPQTEEARAEAL              VLM NKSNLVTPRNGELLIAAT
Sbjct: 499 NADFDGDEMNLHLPQTEEARAEAL--------------VLMGNKSNLVTPRNGELLIAAT 544

Query: 442 QDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIW 501
           QDFITGGYLLTQK+ F  R Q M++A+ +++      G           P + ++   +W
Sbjct: 545 QDFITGGYLLTQKDQFLTREQVMQLAACMLS------GPDANMEIDLPKPAI-IKPRKLW 597

Query: 502 TGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCH--RDSYVILRNS-----ELLAGS 554
           TGKQIFSLILKPNR   VNANL TKGR YT  ++      +   +L N      E +A  
Sbjct: 598 TGKQIFSLILKPNRHSVVNANLSTKGRNYTTGKDIRKLLEEKQKLLENGYSRCDEYIA-E 656

Query: 555 MDKSTL----GSGGKANVFYILLRDFG--EDVAVTAMWRLSRMTSFYLM-----NRGFSI 603
           M K TL    G   +  +  ++L++     ++A  A +R    T+  L+     ++G +I
Sbjct: 657 MKKGTLQCQPGCTAEQTLEAVMLKELSSIRELAAKACFRELHPTNSALIMAQSGSKGSNI 716

Query: 604 GIGD--------------------------------VTPGQGFVQNSFFSGLTPTEFFFH 631
            I                                  +   +GFVQNSF+SGLTPTEFFFH
Sbjct: 717 NISQMIACVGQQAINGKRVPNGFEDRALPHFEKFSKIPAARGFVQNSFYSGLTPTEFFFH 776

Query: 632 TMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           TM GREGLVDTAVKTAETGY+QRRLVK LEDL VQYD
Sbjct: 777 TMAGREGLVDTAVKTAETGYLQRRLVKCLEDLVVQYD 813



 Score =  333 bits (853), Expect = 6e-88,   Method: Compositional matrix adjust.
 Identities = 198/453 (43%), Positives = 263/453 (58%), Gaps = 69/453 (15%)

Query: 1001 PVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEF 1060
            PV+++R    +      R +  L   EIL   ++ L + EF      +F ++  +FL++F
Sbjct: 844  PVDIERQFMHVRNMFPCRDEAPLRGAEILETGDKILQTAEF-DGCRADFRKECLEFLKKF 902

Query: 1061 SKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATA 1120
               E + S Q + +   +  +   +   G  ++             R+KY +A  EP TA
Sbjct: 903  G--ERLHSVQSRYNTDAKVSLEVERTTPGQLKKF--------LMQVRDKYNKAITEPGTA 952

Query: 1121 VGALAAQSIGEPGTQMTLKTFH-------------------------------------- 1142
            VGALAAQSIGEPGTQMTLKTFH                                      
Sbjct: 953  VGALAAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIVEIINATKAISTPIITAEIADN 1012

Query: 1143 ----FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRY- 1185
                FA            GE+  YIEEV+  DD F+LIKLD+DRIR+L LEV+ ++IRY 
Sbjct: 1013 TSMEFARKVKARIEKTTLGEISSYIEEVYKSDDCFLLIKLDLDRIRVLGLEVNAETIRYS 1072

Query: 1186 -CIERTRGISGHLTVSGHSFLILKPKDS--SKSFNSKMYQMKQLLPSVVIKGVQGINRAV 1242
             C  + +    ++ V G S +I++P  +  S + N+++ ++   +P+VV+ G+  ++RAV
Sbjct: 1073 ICTSKLKLKQENVEVYGPSLIIIRPDPTKHSHALNAELQRLLSAIPNVVVAGLPQVSRAV 1132

Query: 1243 IHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEI 1302
            I  +D  G   YKL VEG  LRDVMATYGV G +  SNN  EVY TLGIEAAR+TIM EI
Sbjct: 1133 IAVDDAHGPPTYKLCVEGYGLRDVMATYGVVGARTKSNNILEVYVTLGIEAARTTIMNEI 1192

Query: 1303 KLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDA 1362
              VME HGMS+D RH ML+A  MTS+GEVLGITRHGLAKM+ESV NLASFE T+DHLFDA
Sbjct: 1193 TDVMEGHGMSVDHRHIMLLASQMTSRGEVLGITRHGLAKMRESVFNLASFEKTADHLFDA 1252

Query: 1363 AFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 1395
            A+YGQTD I GVSE II+G+P  +GTGL KL+ 
Sbjct: 1253 AYYGQTDSIDGVSERIILGMPAAIGTGLFKLIH 1285



 Score =  269 bits (687), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 133/250 (53%), Positives = 179/250 (71%), Gaps = 5/250 (2%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           +QQ+SH+ +V+KNLY QD  RTP+ +G+LDRRMG +QK+A C TC + L+DCVGHFGYI+
Sbjct: 28  IQQESHLHVVAKNLYNQDANRTPVSYGVLDRRMGVSQKDATCDTCKKGLNDCVGHFGYIN 87

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKK 212
           L LPVFH+G+FR  I ILQSICK   C+RV+L E++   F A+L NP LSYL +KS+  +
Sbjct: 88  LALPVFHVGHFRATITILQSICK--ICSRVMLKEDEKKQFSARLTNPNLSYLAKKSIHSQ 145

Query: 213 ILETTKKVSVCPHCGEINGVVKK-CGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFN 271
           +L+  KK + CP CG +NG VKK  GL+KI HE ++ + K  D +V   L E   A++ N
Sbjct: 146 VLKKAKKNTKCPCCGCLNGPVKKGAGLMKIVHEPFRGK-KATDPLVTSALDEMLGAIEGN 204

Query: 272 PEI-EAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCI 330
            E+ +      LI+ LNPLEVL LF+ IP  DIPLL M +  S P+DLI+TR+ VPP CI
Sbjct: 205 RELSQTVGPSSLIKELNPLEVLDLFKNIPKSDIPLLGMTSPESNPADLIVTRVFVPPVCI 264

Query: 331 RPSVISDLKS 340
           RPSV+S++K+
Sbjct: 265 RPSVVSEVKA 274



 Score =  250 bits (639), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 129/238 (54%), Positives = 172/238 (72%), Gaps = 4/238 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRI EIINA++ ISTPIITA +  +T +++AR VK R+E+TTLGE+  YIEEV+  DD
Sbjct: 986  GVPRIVEIINATKAISTPIITAEIADNTSMEFARKVKARIEKTTLGEISSYIEEVYKSDD 1045

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDS--SKS 879
             F+LIKLD+DRIR+L LEV+ ++IRY  C  + +    ++ V G S +I++P  +  S +
Sbjct: 1046 CFLLIKLDLDRIRVLGLEVNAETIRYSICTSKLKLKQENVEVYGPSLIIIRPDPTKHSHA 1105

Query: 880  FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
             N+++ ++   +P+VV+ G+  ++RAVI  +D  G   YKL VEG  LRDVMATYGV G 
Sbjct: 1106 LNAELQRLLSAIPNVVVAGLPQVSRAVIAVDDAHGPPTYKLCVEGYGLRDVMATYGVVGA 1165

Query: 940  KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +  SNN  EVY TLGIEAAR+TIM EI  VME HGMS+D RH ML+A  MTS+GEVLG
Sbjct: 1166 RTKSNNILEVYVTLGIEAARTTIMNEITDVMEGHGMSVDHRHIMLLASQMTSRGEVLG 1223



 Score = 88.6 bits (218), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 40/54 (74%), Positives = 47/54 (87%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           VLM NKSNLVTPRNGELLIAATQDFITGGYLLTQK+ F  R Q M++A+ +++G
Sbjct: 523 VLMGNKSNLVTPRNGELLIAATQDFITGGYLLTQKDQFLTREQVMQLAACMLSG 576



 Score = 57.0 bits (136), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 25/39 (64%), Positives = 30/39 (76%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  FDAA+YGQTD I GVSE II+G+P  +GTGL KL+ 
Sbjct: 1247 DHLFDAAYYGQTDSIDGVSERIILGMPAAIGTGLFKLIH 1285


>gi|156370189|ref|XP_001628354.1| predicted protein [Nematostella vectensis]
 gi|156215328|gb|EDO36291.1| predicted protein [Nematostella vectensis]
          Length = 1398

 Score =  333 bits (855), Expect = 4e-88,   Method: Compositional matrix adjust.
 Identities = 165/323 (51%), Positives = 215/323 (66%), Gaps = 26/323 (8%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH A V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDVVLFNRQPSLHKLSIMAHLATVRPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL               LM  K+NLVTPRNGE LIAA QDFITG YLLT K+ F +R
Sbjct: 516 KAEAL--------------TLMGVKNNLVTPRNGEPLIAAIQDFITGAYLLTYKDVFLDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           +   ++ ++++A       I          P    +   +WTGKQ+FS++L+PN    V 
Sbjct: 562 SHIAQLCASILAGKDTGVDI-------ELPPPAIHKPCRLWTGKQVFSVLLRPNPKVKVR 614

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            NL+ +G+ YT+ E+ C  DS+V++ NS+L+ G++DK+ LGSG K +VFY+LLRDFG+ V
Sbjct: 615 MNLRARGKQYTSGEDLCVNDSFVVIHNSDLMCGALDKAVLGSGSKNSVFYVLLRDFGQQV 674

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ---NSFFSGLTPTEFFFHTMGGRE 637
           A  AMWR++R+  F+L NRGFSIGIGDVTPG G +Q   +   +G +  E + +    RE
Sbjct: 675 AADAMWRVARICPFFLSNRGFSIGIGDVTPGHGLLQAKEDLLSTGYSKCEDYINEF--RE 732

Query: 638 GLVDTAVKTAETGYMQRRLVKSL 660
           G + T    +    ++  ++K L
Sbjct: 733 GKLQTQPGCSAEDTLEAVILKEL 755



 Score =  306 bits (785), Expect = 4e-80,   Method: Compositional matrix adjust.
 Identities = 195/497 (39%), Positives = 269/497 (54%), Gaps = 87/497 (17%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P++  R+   I   +  R +  L++     ++   ++S EF +  S++F  +   F
Sbjct: 913  GKDKPLDFSRVFSHIQCNHVMREERPLTSSRAREIAKGIIESSEF-EMCSKDFKTETSDF 971

Query: 1057 LEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNP---FPSACKA-------EAC 1106
            +E  +KK               E+I +    + H   SN    + + C           C
Sbjct: 972  VENLAKK--------------IEKIHAQYGVVPHSITSNKIVDYVNRCTETQLKLFLSMC 1017

Query: 1107 REKYVRAQIEP--------ATAVGALAAQ----------------SIGEPGTQMTLKTFH 1142
            REKY+RA++EP        A ++G    Q                ++G P  +  +    
Sbjct: 1018 REKYLRARMEPGSAVGAICAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASR 1077

Query: 1143 ------------------------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIR 1172
                                            GEV EYIEEVF+PD+ ++LIKLD +RIR
Sbjct: 1078 KISTPIISAQLQDDRDQELARAVKGRIERTLLGEVTEYIEEVFLPDNCYLLIKLDTERIR 1137

Query: 1173 LLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFLILKPKDSSKS-FNSKMYQMKQLLP 1228
            LL LEVD D+I+  I  +R +      + V   + + + P +S+KS  +  M Q++  LP
Sbjct: 1138 LLKLEVDADTIQAAICSSRKLRLNQSQVRVHSSAVICVYPTESAKSSLHYVMQQLRSDLP 1197

Query: 1229 SVVIKGVQGINRAVIH---EEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEV 1285
             V+IKG + + RA+IH   E+   G   YKLLVEGD+L+ V++T GVKG   +SNNT EV
Sbjct: 1198 GVLIKGYKNVTRAIIHIDEEQSRGGEEHYKLLVEGDDLQAVISTMGVKGNGTTSNNTIEV 1257

Query: 1286 YKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKES 1345
             + LGIEAAR TIM EI   M+NHGMSID RH ML+A+LM  KGE+LGITRHGLAKMKES
Sbjct: 1258 ERVLGIEAARQTIMNEIIYTMKNHGMSIDVRHVMLLAELMAFKGEILGITRHGLAKMKES 1317

Query: 1346 VLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVP 1404
            VL LASFE T+DHLF+AA +G+ D I GVSECIIMG+PMN+GTG+ KLL    RS +P  
Sbjct: 1318 VLMLASFERTADHLFEAALHGRKDPIDGVSECIIMGMPMNIGTGMFKLLHKPTRSGDPSR 1377

Query: 1405 RTLLFDNPEFHTNTLAA 1421
            R L+FDN  FH   + A
Sbjct: 1378 RPLIFDNNNFHLPVVPA 1394



 Score =  249 bits (637), Expect = 6e-63,   Method: Compositional matrix adjust.
 Identities = 135/241 (56%), Positives = 171/241 (70%), Gaps = 7/241 (2%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINASR ISTPII+A L  D D + AR VKGR+ERT LGEV EYIEEVF+PD+
Sbjct: 1065 GVPRIKEIINASRKISTPIISAQLQDDRDQELARAVKGRIERTLLGEVTEYIEEVFLPDN 1124

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFLILKPKDSSK-S 879
             ++LIKLD +RIRLL LEVD D+I+  I  +R +      + V   + + + P +S+K S
Sbjct: 1125 CYLLIKLDTERIRLLKLEVDADTIQAAICSSRKLRLNQSQVRVHSSAVICVYPTESAKSS 1184

Query: 880  FNSKMYQMKQLLPSVVIKGVQGINRAVIH---EEDVEGVTKYKLLVEGDNLRDVMATYGV 936
             +  M Q++  LP V+IKG + + RA+IH   E+   G   YKLLVEGD+L+ V++T GV
Sbjct: 1185 LHYVMQQLRSDLPGVLIKGYKNVTRAIIHIDEEQSRGGEEHYKLLVEGDDLQAVISTMGV 1244

Query: 937  KGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL 996
            KG   +SNNT EV + LGIEAAR TIM EI   M+NHGMSID RH ML+A+LM  KGE+L
Sbjct: 1245 KGNGTTSNNTIEVERVLGIEAARQTIMNEIIYTMKNHGMSIDVRHVMLLAELMAFKGEIL 1304

Query: 997  G 997
            G
Sbjct: 1305 G 1305



 Score =  248 bits (632), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 141/311 (45%), Positives = 196/311 (63%), Gaps = 11/311 (3%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           +++QQ SH+Q +SKNLY QD  RTP+P+G+LD  MGT  K+  C TCG+ L+DCVGH+GY
Sbjct: 26  EQMQQYSHLQCISKNLYNQDNTRTPVPYGVLDPHMGTCSKDRMCETCGKGLADCVGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LPVFH+G+FR  I ILQ +CKN  C RVLL   +   F   L+ P +S L +K +K
Sbjct: 86  IDLELPVFHVGHFRSTIIILQCVCKN--CCRVLLPPAEKKQFLDTLKKPNISSLAKKGMK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI+E  KK+S CP+C ++NG V+K GL+KI HEKYK   K  D I+ D  + ++ A++ 
Sbjct: 144 KKIVEKCKKISHCPYCEDLNGFVRKVGLMKIVHEKYKTTRKIVDPIISDFQSSFDVALEN 203

Query: 271 NPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCI 330
           N E+         + LNPL VL +F+ IP +D PLL+ +  +S P DLI+ R+L PP CI
Sbjct: 204 NKELSPLLPKAQ-EVLNPLRVLDIFQQIPEQDYPLLMFSPGMSHPHDLIMRRILAPPVCI 262

Query: 331 RPSVISDLKS---DNDVVLFNRQPSLHKLSIMAHR---AKV-LPHRTFRFNECVCTPY-N 382
           RPSVIS+L S   ++DV +   +       I  HR   AKV +    + F +  C  Y N
Sbjct: 263 RPSVISELASGSNEDDVTMKLTEIVFLNDVIRKHRSVGAKVQMIMEDWDFLQLQCALYIN 322

Query: 383 ADFDGDEMNVH 393
           ++  G  +N+ 
Sbjct: 323 SEMSGIPLNMQ 333



 Score =  115 bits (288), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV+NSFFSGLTPTEFFFH MGGREGLVDTAVKTAETGYMQRRLVKSLEDL  QYD++
Sbjct: 829 AKGFVKNSFFSGLTPTEFFFHAMGGREGLVDTAVKTAETGYMQRRLVKSLEDLSTQYDIT 888



 Score = 78.2 bits (191), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 37/64 (57%), Positives = 45/64 (70%), Gaps = 1/64 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
            D  F+AA +G+ D I GVSECIIMG+PMN+GTG+ KLL    RS +P  R L+FDN  FH
Sbjct: 1329 DHLFEAALHGRKDPIDGVSECIIMGMPMNIGTGMFKLLHKPTRSGDPSRRPLIFDNNNFH 1388

Query: 727  FPQV 730
             P V
Sbjct: 1389 LPVV 1392



 Score = 70.1 bits (170), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 31/54 (57%), Positives = 42/54 (77%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           LM  K+NLVTPRNGE LIAA QDFITG YLLT K+ F +R+   ++ ++++AG+
Sbjct: 522 LMGVKNNLVTPRNGEPLIAAIQDFITGAYLLTYKDVFLDRSHIAQLCASILAGK 575


>gi|157126795|ref|XP_001660950.1| DNA-directed RNA polymerase II largest subunit [Aedes aegypti]
 gi|108873160|gb|EAT37385.1| AAEL010617-PA [Aedes aegypti]
          Length = 1298

 Score =  333 bits (853), Expect = 5e-88,   Method: Compositional matrix adjust.
 Identities = 200/457 (43%), Positives = 266/457 (58%), Gaps = 77/457 (16%)

Query: 1001 PVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEF 1060
            PV++ R    + +    R++  L+  EI+ ++ E L   +F   +  +F ++  +FL +F
Sbjct: 839  PVDIDRQFMHVRSVYPCRNEAPLNGNEIVPVAEEILKKSDF-DGSRADFRKECLEFLSKF 897

Query: 1061 SKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEA----CREKYVRAQIE 1116
             ++       D++ +  R     H  K+    E     +  + EA     R KY +A  E
Sbjct: 898  GQR------LDQIQKRYR-----HCSKVSLEVERT---TRGQLEAFLTQVRNKYNKAITE 943

Query: 1117 PATAVGALAAQSIGEPGTQMTLKTFH---------------------------------- 1142
            P TAVGALAAQSIGEPGTQMTLKTFH                                  
Sbjct: 944  PGTAVGALAAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIVEIINATKAISTPIITAE 1003

Query: 1143 --------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDS 1182
                    FA            GE+  YIEE +  DD F+LIKLD+DRIR+L LEV+ ++
Sbjct: 1004 IEDNTSMEFARKVKARIEKTTLGEISSYIEEAYKSDDCFLLIKLDLDRIRVLGLEVNAET 1063

Query: 1183 IRY--CIERTRGISGHLTVSGHSFLILKPKDS--SKSFNSKMYQMKQLLPSVVIKGVQGI 1238
            IRY  C  + +    ++ V G S +I++P  S  S + N+++ ++   +P+VV+ G+  +
Sbjct: 1064 IRYSICTSKLKLKQENVEVYGPSLIIIRPDPSKHSHALNAELQRLLTAIPNVVVAGLPQV 1123

Query: 1239 NRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTI 1298
            +RAVI  +D  G   YKL VEG  LRDVMATYGV G +  SNN  EVY TLGIEAAR+TI
Sbjct: 1124 SRAVIAVDDSRGPPTYKLCVEGYGLRDVMATYGVVGARTKSNNILEVYVTLGIEAARTTI 1183

Query: 1299 MTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDH 1358
            M EI  VME HGMS+D RH ML+A  MTS+GEVLGITRHGLAKM+ESV NLASFE T+DH
Sbjct: 1184 MNEITDVMEGHGMSVDHRHIMLLASQMTSRGEVLGITRHGLAKMRESVFNLASFEKTADH 1243

Query: 1359 LFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 1395
            LFDAA+YGQTD I GVSE II+G+P  +GTGL KL+ 
Sbjct: 1244 LFDAAYYGQTDSIDGVSERIILGMPAAIGTGLFKLIH 1280



 Score =  332 bits (851), Expect = 8e-88,   Method: Compositional matrix adjust.
 Identities = 197/394 (50%), Positives = 232/394 (58%), Gaps = 80/394 (20%)

Query: 331 RPSVISDLKS---------DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPY 381
           R  V  DLK          D DVVLFNRQPSLHKLSIM H AKV P RTFRFNEC CTPY
Sbjct: 439 RDKVAQDLKCGDIVERHLMDGDVVLFNRQPSLHKLSIMCHVAKVQPQRTFRFNECACTPY 498

Query: 382 NADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAAT 441
           NADFDGDEMN+HLPQTEEARAEAL              VLM NKSNLVTPRNGELLIAAT
Sbjct: 499 NADFDGDEMNLHLPQTEEARAEAL--------------VLMGNKSNLVTPRNGELLIAAT 544

Query: 442 QDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIW 501
           QDFITGGYLLTQK+ F  R Q M++A+ +++      G           P + ++   +W
Sbjct: 545 QDFITGGYLLTQKDQFLTREQVMQLAACMLS------GPDANMEIDLPKPAI-IKPRKMW 597

Query: 502 TGKQIFSLILKPNRDCPVNANLKTK----GRAYTANEEFCHRDSYVILRNSELLAGSMDK 557
           TGKQIFSLILKPN+DC VNANL TK     R     ++    + Y   R  E +A  M K
Sbjct: 598 TGKQIFSLILKPNKDCIVNANLSTKDVTPSRKLLQEKQKLLENGYS--RCDEYIA-EMKK 654

Query: 558 STL----GSGGKANVFYILLRDFG--EDVAVTAMWRLSRMTSFYLM-----NRGFSIGIG 606
            TL    G   +  +  ++L++     ++A  A +R    T+  L+     ++G +I I 
Sbjct: 655 GTLQCQPGCTAEQTLEAVMLKELSSIRELAAKACFRELHPTNSALIMAQSGSKGSNINIS 714

Query: 607 D--------------------------------VTPGQGFVQNSFFSGLTPTEFFFHTMG 634
                                            +   +GFVQNSF+SGLTPTEFFFHTM 
Sbjct: 715 QMIACVGQQAINGKRVPNGFEDRALPHFEKFSKIPAARGFVQNSFYSGLTPTEFFFHTMA 774

Query: 635 GREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           GREGLVDTAVKTAETGY+QRRLVK LEDL VQYD
Sbjct: 775 GREGLVDTAVKTAETGYLQRRLVKCLEDLVVQYD 808



 Score =  270 bits (689), Expect = 5e-69,   Method: Compositional matrix adjust.
 Identities = 130/250 (52%), Positives = 180/250 (72%), Gaps = 5/250 (2%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           +QQ++H+ +V+KNLY QD  RTP+ +G+LDRRMG +QK+A C TC + L+DCVGHFGYID
Sbjct: 28  IQQEAHLHVVAKNLYNQDANRTPVTYGVLDRRMGVSQKDATCDTCKKGLNDCVGHFGYID 87

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKK 212
           L LPVFH+G+FR  I ILQSICK   C+RV+L E++   F A+L NP LSYL +KS+  +
Sbjct: 88  LALPVFHVGHFRATITILQSICK--VCSRVMLKEDEKKQFSARLMNPNLSYLAKKSIHSQ 145

Query: 213 ILETTKKVSVCPHCGEINGVVKK-CGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFN 271
           +L+  KK + CP+CG +NG VKK  GL+KI HE ++ + K  D +V + L     A++ N
Sbjct: 146 VLKKAKKNTKCPYCGSLNGPVKKGAGLMKIVHEPFRGK-KATDPLVTNALEVMMSAIEGN 204

Query: 272 PEI-EAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCI 330
            E+ +      L++ LNP+EVL LF+ IP  DIPLL M +  S P+DLI+TR+ VPP CI
Sbjct: 205 RELSQTIGPSSLMKELNPVEVLDLFKNIPKSDIPLLGMTSPESNPADLIVTRVFVPPVCI 264

Query: 331 RPSVISDLKS 340
           RPSV+S++K+
Sbjct: 265 RPSVVSEVKA 274



 Score =  250 bits (639), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 129/238 (54%), Positives = 172/238 (72%), Gaps = 4/238 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRI EIINA++ ISTPIITA ++ +T +++AR VK R+E+TTLGE+  YIEE +  DD
Sbjct: 981  GVPRIVEIINATKAISTPIITAEIEDNTSMEFARKVKARIEKTTLGEISSYIEEAYKSDD 1040

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDS--SKS 879
             F+LIKLD+DRIR+L LEV+ ++IRY  C  + +    ++ V G S +I++P  S  S +
Sbjct: 1041 CFLLIKLDLDRIRVLGLEVNAETIRYSICTSKLKLKQENVEVYGPSLIIIRPDPSKHSHA 1100

Query: 880  FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
             N+++ ++   +P+VV+ G+  ++RAVI  +D  G   YKL VEG  LRDVMATYGV G 
Sbjct: 1101 LNAELQRLLTAIPNVVVAGLPQVSRAVIAVDDSRGPPTYKLCVEGYGLRDVMATYGVVGA 1160

Query: 940  KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +  SNN  EVY TLGIEAAR+TIM EI  VME HGMS+D RH ML+A  MTS+GEVLG
Sbjct: 1161 RTKSNNILEVYVTLGIEAARTTIMNEITDVMEGHGMSVDHRHIMLLASQMTSRGEVLG 1218



 Score = 88.6 bits (218), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 40/54 (74%), Positives = 47/54 (87%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           VLM NKSNLVTPRNGELLIAATQDFITGGYLLTQK+ F  R Q M++A+ +++G
Sbjct: 523 VLMGNKSNLVTPRNGELLIAATQDFITGGYLLTQKDQFLTREQVMQLAACMLSG 576



 Score = 57.0 bits (136), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 25/39 (64%), Positives = 30/39 (76%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  FDAA+YGQTD I GVSE II+G+P  +GTGL KL+ 
Sbjct: 1242 DHLFDAAYYGQTDSIDGVSERIILGMPAAIGTGLFKLIH 1280


>gi|341888769|gb|EGT44704.1| hypothetical protein CAEBREN_28388 [Caenorhabditis brenneri]
          Length = 1024

 Score =  333 bits (853), Expect = 6e-88,   Method: Compositional matrix adjust.
 Identities = 160/276 (57%), Positives = 199/276 (72%), Gaps = 20/276 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DNDVVLFNRQPSLHK+SIM+HRAKV+P RTFRFNEC CTPYNADFDGDEMN+HLPQT EA
Sbjct: 452 DNDVVLFNRQPSLHKISIMSHRAKVMPGRTFRFNECACTPYNADFDGDEMNLHLPQTYEA 511

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEA                LM  K+NL+TPR+GE L+AA QDFITGGYLLT K+ F  R
Sbjct: 512 KAEA--------------SELMNVKNNLITPRSGEPLVAAIQDFITGGYLLTHKDTFLPR 557

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  R A+ LI  ++      K+ +     P   +R   +WTGKQ+  LI++P++   V+
Sbjct: 558 AEVYRFAAALIDASA------KKQTKIRIPPPAILRPVELWTGKQLIELIIRPDKGSQVS 611

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            NL TK ++Y+ N EFC++DSYVI+RNS LLAG +DKS LGS  K N+FY+L+RD+GED 
Sbjct: 612 LNLTTKNKSYSGNLEFCNKDSYVIIRNSVLLAGCLDKSLLGSSSKVNIFYMLMRDYGEDA 671

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           AV AMWRL+RM   +L NRGFSIGIGDV P +  +Q
Sbjct: 672 AVDAMWRLARMAPVFLSNRGFSIGIGDVRPSEKLLQ 707



 Score =  189 bits (479), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 112/287 (39%), Positives = 161/287 (56%), Gaps = 20/287 (6%)

Query: 93  VQQQSHIQIVSKNLYCQD--PQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           ++Q +H+ + +  LY +D   +  P  +G LD +MG + K   C TCG  L+DCVGHFGY
Sbjct: 28  MRQTAHVPVFNNKLY-EDVGGKLQPAAYGPLDPKMGVSTKTGLCATCGLGLTDCVGHFGY 86

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
            DL +PVFHIG+F+  I +LQ ICKN  C+ +LL  E+   F  ++ NP + YL RK+L 
Sbjct: 87  FDLDVPVFHIGFFKLTIQLLQCICKN--CSSILLTAEQHRVFSRQVMNPNIDYLHRKALH 144

Query: 211 KKILETTKKVSVCPHCGEINGVVKKC--GLLKISHEKYKNRTKKKDAIVEDLLAEYNEAV 268
           K+I+   KK S C  CG  NG VKK    +LKI+             +  D L +Y    
Sbjct: 145 KRIVAACKKGSTCQQCGMKNGTVKKAVGTVLKIAFA---------SPVPADELGKYATMF 195

Query: 269 KFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLM-NAELSKPSDLILTRLLVPP 327
             N E+  H +      LNPL V +LF  I   DIP+L++ + E   P+DL+LTR+ VPP
Sbjct: 196 TVNQEVGEHVRKMKFTLLNPLFVQKLFANIKEADIPVLMVRSGEEKHPNDLLLTRMPVPP 255

Query: 328 NCIRPSVISDLKS---DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTF 371
            CIRPSV+S++KS   ++DV +   +  L    +  H+    P +T 
Sbjct: 256 VCIRPSVVSEVKSGTTEDDVTMKLMEIMLTNDVLKKHKRDGAPSKTL 302



 Score =  101 bits (251), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 48/54 (88%), Positives = 50/54 (92%), Gaps = 1/54 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLE 661
           TP  +GFV NSF+SGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVK LE
Sbjct: 823 TPEAKGFVANSFYSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKCLE 876



 Score = 69.3 bits (168), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 32/51 (62%), Positives = 39/51 (76%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLI 72
           LM  K+NL+TPR+GE L+AA QDFITGGYLLT K+ F  RA+  R A+ LI
Sbjct: 518 LMNVKNNLITPRSGEPLVAAIQDFITGGYLLTHKDTFLPRAEVYRFAAALI 568


>gi|195175545|ref|XP_002028504.1| GL19707 [Drosophila persimilis]
 gi|194104024|gb|EDW26067.1| GL19707 [Drosophila persimilis]
          Length = 968

 Score =  333 bits (853), Expect = 6e-88,   Method: Compositional matrix adjust.
 Identities = 157/277 (56%), Positives = 195/277 (70%), Gaps = 21/277 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND+VLFNRQPSLHK+SIM HRAKV P RTFRFNEC CTPYNADFDGDEMN+HLPQTEEA
Sbjct: 455 DNDIVLFNRQPSLHKMSIMCHRAKVQPQRTFRFNECACTPYNADFDGDEMNLHLPQTEEA 514

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL              +LM N+SNLVTP+NGE+LIAATQDFITGGYLLTQK  F  +
Sbjct: 515 RAEAL--------------ILMGNQSNLVTPKNGEILIAATQDFITGGYLLTQKEVFLTK 560

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            + M++A+  + +      I              ++   +WTGKQIFSL+++PN D  + 
Sbjct: 561 EEAMQLAACFLDNEDSTMNI-------QIPAPALLKPRRLWTGKQIFSLLMRPNSDSHIR 613

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            N+  KGR YT N + C  DS++ +RNSEL+ G MDK+T+GSG K  +FY+LLRDFGE  
Sbjct: 614 LNMVNKGRNYTKNMDLCINDSWIHIRNSELMCGVMDKATMGSGTKQCIFYLLLRDFGEAH 673

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           A  AMWRL+R+TS+++ N GFS GI DVTP Q  + +
Sbjct: 674 ATKAMWRLARITSYFIQNLGFSFGISDVTPSQKLLHH 710



 Score =  245 bits (625), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 126/260 (48%), Positives = 170/260 (65%), Gaps = 8/260 (3%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           ++  ++  D +QQ++ ++I SKNLY    QR P+P G+LDRRMG + K+A C TCG  L+
Sbjct: 18  VQFGISGADEIQQEALVRITSKNLY--QGQRQPVPSGVLDRRMGISTKDAVCETCGHGLN 75

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALS 202
           +C+GHFGY+DL LPVFHIG+FR  INILQ ICK  +CA+V+L  E    F  KL NP  S
Sbjct: 76  ECIGHFGYLDLALPVFHIGHFRATINILQMICK--SCAQVMLKFEDRLSFEKKLHNPNFS 133

Query: 203 YLVRKSLKKKILETTKKVSVCPHCGEINGVVKKC-GLLKISHEKYKNRTKKKDAIVEDLL 261
           YL +K+L  ++L   KKV+ CPHCG  NG VKK  GLLKI H+ YK R  K DA+    +
Sbjct: 134 YLGKKALHAQMLAKAKKVTKCPHCGTANGGVKKGPGLLKILHDPYKGR--KVDAVFTSNM 191

Query: 262 AEYNEAVKFNPEIE-AHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
            E   + +FN ++      +   + L PL VL LFE IP  D+ LL M +  + P  LI+
Sbjct: 192 DEMLRSTEFNRDLNLTLSNYSTAEELTPLMVLDLFEQIPQSDVALLGMCSRGAHPKHLIV 251

Query: 321 TRLLVPPNCIRPSVISDLKS 340
           TR+ VPP CIRPSV+S++K+
Sbjct: 252 TRVFVPPACIRPSVLSEVKA 271



 Score =  113 bits (283), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 54/77 (70%), Positives = 59/77 (76%)

Query: 608 VTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           +   +GFVQNSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGY+QRRLVK LEDL V Y
Sbjct: 825 IPAARGFVQNSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYLQRRLVKCLEDLVVHY 884

Query: 668 DMSFDAAFYGQTDCISG 684
           D +   A     D I G
Sbjct: 885 DGTVRNAVSEMVDTIYG 901



 Score = 77.0 bits (188), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 33/52 (63%), Positives = 43/52 (82%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLI 72
           +LM N+SNLVTP+NGE+LIAATQDFITGGYLLTQK  F  + + M++A+  +
Sbjct: 520 ILMGNQSNLVTPKNGEILIAATQDFITGGYLLTQKEVFLTKEEAMQLAACFL 571


>gi|20159759|gb|AAM12032.1| RNA polymerase III subunit RPC155-D [Homo sapiens]
          Length = 299

 Score =  333 bits (853), Expect = 6e-88,   Method: Compositional matrix adjust.
 Identities = 168/275 (61%), Positives = 210/275 (76%), Gaps = 4/275 (1%)

Query: 1145 GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGH 1202
            GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ +++RY  C  + R   G + V G 
Sbjct: 20   GEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNAETVRYSICTSKLRVKPGDVAVHGE 79

Query: 1203 SFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD 1261
            + + + P+++SKS    + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGD
Sbjct: 80   AVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGD 139

Query: 1262 NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 1321
            NLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML+
Sbjct: 140  NLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLL 199

Query: 1322 ADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMG 1381
            +DLMT KGEVLGITR GLAKMKESVL LASFE T+DHLFDAA++GQ D + GVSECIIMG
Sbjct: 200  SDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTADHLFDAAYFGQKDSVCGVSECIIMG 259

Query: 1382 LPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 1415
            +PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 260  IPMNIGTGLFKLLHKADRDPNPPKRPLIFDTNEFH 294



 Score =  245 bits (625), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 124/211 (58%), Positives = 162/211 (76%), Gaps = 3/211 (1%)

Query: 790 DTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRY 849
           D D DYAR+VKGR+E+T LGE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ +++RY
Sbjct: 1   DDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNAETVRY 60

Query: 850 --CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQGINRAV 906
             C  + R   G + V G + + + P+++SKS    + Q +K+ LP VV++G+  ++RAV
Sbjct: 61  SICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVVVQGIPEVSRAV 120

Query: 907 IHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEI 966
           IH ++  G  KYKLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+TI+ EI
Sbjct: 121 IHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAARTTIINEI 180

Query: 967 KLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
           +  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 181 QYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 211



 Score = 82.8 bits (203), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668 DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
           D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R   P  R L+FD  EFH
Sbjct: 235 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPNPPKRPLIFDTNEFH 294

Query: 727 FPQV 730
            P V
Sbjct: 295 IPLV 298


>gi|340379445|ref|XP_003388237.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1-like
           [Amphimedon queenslandica]
          Length = 1402

 Score =  331 bits (848), Expect = 2e-87,   Method: Compositional matrix adjust.
 Identities = 159/275 (57%), Positives = 196/275 (71%), Gaps = 21/275 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH  KV+PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 454 DGDVVLFNRQPSLHKLSIMAHFVKVMPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 513

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  KSNLVTPRNGE LIAA QDFI+  +LLTQK+ FF+R
Sbjct: 514 KAEAL--------------VLMGVKSNLVTPRNGEPLIAAIQDFISASFLLTQKDVFFDR 559

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           AQ  +I S ++++      I          P   ++   +WTGKQ+ S+++ PN+   V 
Sbjct: 560 AQFFQIVSAMLSNHDSNIKI-------DIPPPAIIKPVKLWTGKQVMSVLISPNKKSNVI 612

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            NL+ KG+ YT  E+ C  DS+V++ NS  L GS+DK+TLGSG K ++F++LLRD+GE  
Sbjct: 613 INLRAKGKQYTKGEDMCSNDSFVVIHNSSHLCGSLDKATLGSGSKNSIFFVLLRDYGEQE 672

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFV 615
           A   M RL+R+T +YL NRGFSIGIGDVTPG+G V
Sbjct: 673 AADCMSRLARLTPYYLSNRGFSIGIGDVTPGRGLV 707



 Score =  296 bits (757), Expect = 7e-77,   Method: Compositional matrix adjust.
 Identities = 198/493 (40%), Positives = 276/493 (55%), Gaps = 81/493 (16%)

Query: 997  GNGTPVELKRLLDDIIA----KNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRD 1052
            G   PV+   +L  +      K   +S+P+LS      L ++  D K F    ++ F  +
Sbjct: 911  GKDKPVDFTHVLHHVTVSYAMKFPCKSEPALSPLGFQKLFDQFCDYKRF-HLCNDTFKTE 969

Query: 1053 IKKFL-EEFSKKESVTSH---QDKVSQPLREQILSHQDKIGH--GR-ESNPFPSACKAEA 1105
            +K FL ++ SK + + S     D  S+      +++   + +  GR  S  F +    + 
Sbjct: 970  LKDFLAKKISKLQGLWSFFNITDTTSENSDNSDITYISPVLYQLGRITSTQFWTF--VDT 1027

Query: 1106 CREKYVRAQIEPATAVGAL---------------------------------------AA 1126
            C +K+++++IEP +AVGA+                                       AA
Sbjct: 1028 CIDKFLKSRIEPGSAVGAICAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINAA 1087

Query: 1127 QSIGEPGTQMTL-----------------KTFHFAGEVCEYIEEVFVPDDSFILIKLDMD 1169
            ++I  P    +L                 KT    GEV  YIEE +  D  F+ IKLD  
Sbjct: 1088 KTISTPIISTSLVIEDDPEAARLVKGRIEKTL--LGEVSRYIEEAYEVDGCFLCIKLDKR 1145

Query: 1170 RIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQL 1226
            RIRLL LE++ D ++  I    + +    H+++     L + P ++ K+  S+ Y M++L
Sbjct: 1146 RIRLLKLEINADIVQNSILNAPKLKLKPTHISIRDKWTLFIYPPETEKT--SEYYMMQKL 1203

Query: 1227 ---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTY 1283
               LP VVIKG+  ++RA+IH+++  G TKYKLLVEG NLR VMAT+GVKG   +SN+T 
Sbjct: 1204 KFALPRVVIKGINSVSRAIIHQDESNGKTKYKLLVEGLNLRAVMATHGVKGNSTTSNHTI 1263

Query: 1284 EVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMK 1343
            EV KTLGIEAAR TIM EI   M NHGM+ID RH ML+ADLMT KGEVLGITR GLAKMK
Sbjct: 1264 EVEKTLGIEAARQTIMNEIAYTMVNHGMNIDARHIMLLADLMTFKGEVLGITRFGLAKMK 1323

Query: 1344 ESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSE-P 1402
            ESVL LASFE TSDHLFDAAF+GQ+D ++GVS+CIIMG PM++GTG+ +LL    R+  P
Sbjct: 1324 ESVLMLASFEKTSDHLFDAAFHGQSDVVNGVSDCIIMGRPMSLGTGMFQLLFKPSRTPLP 1383

Query: 1403 VPRTLLFDNPEFH 1415
               +L+FD P+ H
Sbjct: 1384 TKTSLIFDTPDLH 1396



 Score =  245 bits (625), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 132/283 (46%), Positives = 178/283 (62%), Gaps = 8/283 (2%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           I+ ++   +++QQQ+H+ + +  LY QD  R P+P G+LD +MGTNQK++ C TC ++LS
Sbjct: 19  IQFSLFSPNKIQQQAHVHVFNSALYAQD-SRIPVPFGVLDNKMGTNQKDSVCKTCDKSLS 77

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALS 202
           DCVGH+GYIDL LPVFH+GYFR  I+ILQ ICK  TC+RVL+       +   L  P +S
Sbjct: 78  DCVGHYGYIDLQLPVFHVGYFRNTISILQVICK--TCSRVLVTGTDRQSYFDLLSRPFIS 135

Query: 203 YLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLA 262
            L +K++ KKI E  KK+S CPHC   NG VKKCG+ KI HEK + + KK  +       
Sbjct: 136 SLAKKTIFKKINEKCKKISTCPHCQSTNGSVKKCGVFKILHEKIR-KEKKFQSESSAFRE 194

Query: 263 EYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTR 322
            + EAV  N ++E +      + L PL+VL LF  IP EDI LL M     +P DLI+TR
Sbjct: 195 TFAEAVIHNRDLEQYLNKAQ-EILTPLKVLNLFRNIPDEDIVLLGMTLAAGRPEDLIVTR 253

Query: 323 LLVPPNCIRPSVISDLK---SDNDVVLFNRQPSLHKLSIMAHR 362
           LLVPP CIRPSV+SD +   +++DV +  R        I  HR
Sbjct: 254 LLVPPLCIRPSVVSDTQAGTTEDDVTIKLRDIIFANDVIHRHR 296



 Score =  238 bits (608), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 131/240 (54%), Positives = 169/240 (70%), Gaps = 8/240 (3%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ ISTPII+  L  + D + AR+VKGR+E+T LGEV  YIEE +  D 
Sbjct: 1076 GVPRIKEIINAAKTISTPIISTSLVIEDDPEAARLVKGRIEKTLLGEVSRYIEEAYEVDG 1135

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSGHSFLILKPKDSSKSF 880
             F+ IKLD  RIRLL LE++ D ++  I    + +    H+++     L + P ++ K+ 
Sbjct: 1136 CFLCIKLDKRRIRLLKLEINADIVQNSILNAPKLKLKPTHISIRDKWTLFIYPPETEKT- 1194

Query: 881  NSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVK 937
             S+ Y M++L   LP VVIKG+  ++RA+IH+++  G TKYKLLVEG NLR VMAT+GVK
Sbjct: 1195 -SEYYMMQKLKFALPRVVIKGINSVSRAIIHQDESNGKTKYKLLVEGLNLRAVMATHGVK 1253

Query: 938  GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            G   +SN+T EV KTLGIEAAR TIM EI   M NHGM+ID RH ML+ADLMT KGEVLG
Sbjct: 1254 GNSTTSNHTIEVEKTLGIEAARQTIMNEIAYTMVNHGMNIDARHIMLLADLMTFKGEVLG 1313



 Score =  114 bits (284), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 50/58 (86%), Positives = 54/58 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV+NSF++GL PTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC  YD
Sbjct: 827 AKGFVKNSFYTGLVPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCCHYD 884



 Score = 75.5 bits (184), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 33/63 (52%), Positives = 46/63 (73%), Gaps = 1/63 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSE-PVPRTLLFDNPEFH 726
            D  FDAAF+GQ+D ++GVS+CIIMG PM++GTG+ +LL    R+  P   +L+FD P+ H
Sbjct: 1337 DHLFDAAFHGQSDVVNGVSDCIIMGRPMSLGTGMFQLLFKPSRTPLPTKTSLIFDTPDLH 1396

Query: 727  FPQ 729
             PQ
Sbjct: 1397 LPQ 1399



 Score = 73.2 bits (178), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 34/53 (64%), Positives = 42/53 (79%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIA 73
           VLM  KSNLVTPRNGE LIAA QDFI+  +LLTQK+ FF+RAQ  +I S +++
Sbjct: 519 VLMGVKSNLVTPRNGEPLIAAIQDFISASFLLTQKDVFFDRAQFFQIVSAMLS 571


>gi|268535924|ref|XP_002633097.1| C. briggsae CBR-RPC-1 protein [Caenorhabditis briggsae]
          Length = 1402

 Score =  329 bits (844), Expect = 6e-87,   Method: Compositional matrix adjust.
 Identities = 159/276 (57%), Positives = 195/276 (70%), Gaps = 20/276 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DNDVVLFNRQPSLHK+SIM+HRAKV+P RTFRFNEC CTPYNADFDGDEMN+HLPQT EA
Sbjct: 452 DNDVVLFNRQPSLHKISIMSHRAKVMPGRTFRFNECACTPYNADFDGDEMNLHLPQTYEA 511

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEA                LM  K+NL+TPR+GE L+AA QDFITGGYLLT K+ F  R
Sbjct: 512 KAEA--------------SELMNVKNNLITPRSGEPLVAAIQDFITGGYLLTHKDTFLPR 557

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  R A+ LI  ++      K+ S     P    R   +WTGKQ+  LI++P++   V+
Sbjct: 558 AEVYRFAAALIDASA------KKQSKIRIPPPAIRRPVELWTGKQLIELIIRPDKGSQVS 611

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            NL  K ++Y+ N E C +DSYVI+RNS LLAG +DKS LGS  K N+FY+L+RD+GED 
Sbjct: 612 LNLTAKNKSYSGNLELCSKDSYVIIRNSVLLAGVLDKSLLGSSSKVNIFYMLMRDYGEDA 671

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           AV AMWRL+RM   +L NRGFSIGIGDV P +  +Q
Sbjct: 672 AVDAMWRLARMAPVFLSNRGFSIGIGDVRPSERLLQ 707



 Score =  265 bits (678), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 160/371 (43%), Positives = 212/371 (57%), Gaps = 61/371 (16%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCE 1149
            + C  K  RA  EP TAVGA+AA SIGEP TQMTLKTFHFAG              E+  
Sbjct: 1029 QLCYYKIARAITEPGTAVGAIAATSIGEPSTQMTLKTFHFAGVASMNITQGVPRIKEIIN 1088

Query: 1150 YIEEVFVP----------------------------------------DDSFILIKLDMD 1169
             ++ +  P                                        DD F+L+KL+  
Sbjct: 1089 AVKTISTPIITASLLDPYDESLARRVKARIEKTTLGEICDYIEEVYLPDDYFLLVKLNSK 1148

Query: 1170 RIRLLHLEVDIDSIRYCIERTR---GISGHLTVS-GHSFLILKPKDSSK-SFNSKMYQMK 1224
            RIRLL LEV ++SI Y I  ++    + G   +S G + + ++P  +SK S    M  +K
Sbjct: 1149 RIRLLQLEVSLESISYAIVTSKVCPMMRGCKIISHGKTMMAIRPPSTSKLSKTMTMQMLK 1208

Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYE 1284
              L +VV+KG+  +NR VIH ++ +G   Y LLVEG + R V+++ GV   K + NN   
Sbjct: 1209 YSLGNVVVKGISSVNRCVIHADEKKGDC-YSLLVEGTDFRSVLSSVGVDPKKTNFNNALV 1267

Query: 1285 VYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKE 1344
            V + LGIEAAR+ I+ EI   M+ HG+ +D RH ML+AD+MT +GEVLGITR+GL KMK+
Sbjct: 1268 VAEVLGIEAARTCIINEIIATMDAHGIGLDRRHVMLLADVMTYRGEVLGITRNGLVKMKD 1327

Query: 1345 SVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP 1404
            SVL LASFE T DHLF+AAF+ Q D I GVSECIIMG PM VGTG  KL+Q   +   + 
Sbjct: 1328 SVLLLASFEKTMDHLFEAAFFSQKDVIHGVSECIIMGTPMTVGTGTFKLMQKYEKKALLK 1387

Query: 1405 R-TLLFDNPEF 1414
            + T +F+ PE 
Sbjct: 1388 KNTPIFERPEL 1398



 Score =  213 bits (541), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 118/239 (49%), Positives = 161/239 (67%), Gaps = 6/239 (2%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA + ISTPIITA L    D   AR VK R+E+TTLGE+C+YIEEV++PDD
Sbjct: 1079 GVPRIKEIINAVKTISTPIITASLLDPYDESLARRVKARIEKTTLGEICDYIEEVYLPDD 1138

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTR---GISGHLTVS-GHSFLILKPKDSSK- 878
             F+L+KL+  RIRLL LEV ++SI Y I  ++    + G   +S G + + ++P  +SK 
Sbjct: 1139 YFLLVKLNSKRIRLLQLEVSLESISYAIVTSKVCPMMRGCKIISHGKTMMAIRPPSTSKL 1198

Query: 879  SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 938
            S    M  +K  L +VV+KG+  +NR VIH ++ +G   Y LLVEG + R V+++ GV  
Sbjct: 1199 SKTMTMQMLKYSLGNVVVKGISSVNRCVIHADEKKGDC-YSLLVEGTDFRSVLSSVGVDP 1257

Query: 939  VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             K + NN   V + LGIEAAR+ I+ EI   M+ HG+ +D RH ML+AD+MT +GEVLG
Sbjct: 1258 KKTNFNNALVVAEVLGIEAARTCIINEIIATMDAHGIGLDRRHVMLLADVMTYRGEVLG 1316



 Score =  193 bits (491), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 116/287 (40%), Positives = 161/287 (56%), Gaps = 20/287 (6%)

Query: 93  VQQQSHIQIVSKNLYCQD--PQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           ++Q +H+ I +  LY +D   +  P  +G LD RMG + K   C TCG  L+DCVGHFGY
Sbjct: 28  MRQTAHVPIFNNKLY-EDVGGKLQPASYGPLDPRMGVSTKTGICATCGLGLTDCVGHFGY 86

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
            DL +PVFHIG+F+  I +LQ ICKN  C+ +LL  E+   F  ++ NP + YL RK+L 
Sbjct: 87  FDLDVPVFHIGFFKLTIQLLQCICKN--CSSILLTPEQHRVFSRQVMNPNIDYLHRKALH 144

Query: 211 KKILETTKKVSVCPHCGEINGVVKKC--GLLKISHEKYKNRTKKKDAIVEDLLAEYNEAV 268
           K+I+   KK S C  CG  NG VKK    +LKI+             +  D L +Y    
Sbjct: 145 KRIVAACKKSSTCTQCGLKNGTVKKAVGAVLKIAFA---------SPVPADELGKYQTVF 195

Query: 269 KFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLM-NAELSKPSDLILTRLLVPP 327
             N EI  H K      LNPL V +LF  I   DIP+L++ + E   P+DL+LTR+ VPP
Sbjct: 196 NANQEIGDHVKKMKFTLLNPLFVQKLFANIKEADIPVLMVRSGEEKHPNDLLLTRMPVPP 255

Query: 328 NCIRPSVISDLKS---DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTF 371
            CIRPSV+S++KS   ++DV +   +  L    +  H+    P +T 
Sbjct: 256 VCIRPSVVSEVKSGTTEDDVTMKLMEIMLTNDVLKKHKRDGAPAKTL 302



 Score =  114 bits (286), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 53/61 (86%), Positives = 55/61 (90%), Gaps = 1/61 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV NSF+SGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVK LEDLC  Y
Sbjct: 823 TPEAKGFVANSFYSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKCLEDLCASY 882

Query: 668 D 668
           D
Sbjct: 883 D 883



 Score = 69.3 bits (168), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 32/51 (62%), Positives = 39/51 (76%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLI 72
           LM  K+NL+TPR+GE L+AA QDFITGGYLLT K+ F  RA+  R A+ LI
Sbjct: 518 LMNVKNNLITPRSGEPLVAAIQDFITGGYLLTHKDTFLPRAEVYRFAAALI 568



 Score = 62.0 bits (149), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 30/59 (50%), Positives = 38/59 (64%), Gaps = 1/59 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPR-TLLFDNPEF 725
            D  F+AAF+ Q D I GVSECIIMG PM VGTG  KL+Q   +   + + T +F+ PE 
Sbjct: 1340 DHLFEAAFFSQKDVIHGVSECIIMGTPMTVGTGTFKLMQKYEKKALLKKNTPIFERPEL 1398


>gi|25145495|ref|NP_501127.2| Protein RPC-1 [Caenorhabditis elegans]
 gi|351059526|emb|CCD66619.1| Protein RPC-1 [Caenorhabditis elegans]
          Length = 1400

 Score =  328 bits (841), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 158/276 (57%), Positives = 195/276 (70%), Gaps = 20/276 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DNDVVLFNRQPSLHK+SIM+HRAKV+P RTFRFNEC CTPYNADFDGDEMN+HLPQT EA
Sbjct: 452 DNDVVLFNRQPSLHKISIMSHRAKVMPGRTFRFNECACTPYNADFDGDEMNLHLPQTYEA 511

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEA                LM  K+NL+TPR+GE L+AA QDFITGGYLLT K+ F  R
Sbjct: 512 KAEA--------------SELMNVKNNLITPRSGEPLVAAIQDFITGGYLLTHKDTFLPR 557

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  R A+ LI  ++      K+ +     P    R   +WTGKQ+  LI++P++   V+
Sbjct: 558 AEVYRFAAALIDASA------KKQTKIRIPPPAIRRPVELWTGKQLIELIIRPDKGSDVS 611

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            NL  K ++YT N E C +DSYVI+RNS LLAG +DKS LGS  K N+FY+L+RD+GED 
Sbjct: 612 LNLTAKNKSYTGNLELCSKDSYVIIRNSVLLAGCLDKSLLGSSSKVNIFYMLMRDYGEDA 671

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           AV AMWRL+RM   +L NRGFSIGIGDV P +  ++
Sbjct: 672 AVDAMWRLARMAPVFLSNRGFSIGIGDVRPSEQLLR 707



 Score =  262 bits (670), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 158/353 (44%), Positives = 200/353 (56%), Gaps = 64/353 (18%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCE 1149
            E C  K  RA  EP TAVGA+AA SIGEP TQMTLKTFHFAG              E+  
Sbjct: 1029 ELCYYKVARAITEPGTAVGAIAATSIGEPSTQMTLKTFHFAGVASMNITQGVPRIKEIIN 1088

Query: 1150 YIEEVFVP----------------------------------------DDSFILIKLDMD 1169
             ++ +  P                                        DD F+L+KL+  
Sbjct: 1089 AVKTISTPIITAALLDPYDESLARRVKARIEKTTLGEICDYIEEVYLPDDYFLLVKLNSK 1148

Query: 1170 RIRLLHLEVDIDSIRYCIE------RTRGISGHLTVSGHSFLILKPKDSSK-SFNSKMYQ 1222
            RIRLL LEV ++SI Y I       + RG    +   G + + ++P  +SK S    M  
Sbjct: 1149 RIRLLQLEVCMESISYAIATSKVCPQMRGCK--IVAHGKTMMAIRPPSTSKLSKTMTMQI 1206

Query: 1223 MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNT 1282
            +K  L +VV+KG+  +NR VIH ++ +G   Y LLVEG + R V+++ GV   K + NN 
Sbjct: 1207 LKYSLANVVVKGIPSVNRCVIHADEKKG-DFYSLLVEGTDFRSVLSSVGVDPRKTNFNNA 1265

Query: 1283 YEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKM 1342
              V   LGIEAARS I+ EI   M+ HG+ +D RH ML+AD+MT +GEVLGITR+GL KM
Sbjct: 1266 LVVADVLGIEAARSCIINEIIATMDAHGIGLDRRHVMLLADVMTYRGEVLGITRNGLVKM 1325

Query: 1343 KESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 1395
            K+SVL LASFE T DHLF+AAF+ Q D I GVSECIIMG PM VGTG  KL+Q
Sbjct: 1326 KDSVLLLASFEKTMDHLFEAAFFSQRDVIHGVSECIIMGTPMTVGTGTFKLMQ 1378



 Score =  211 bits (538), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 119/241 (49%), Positives = 158/241 (65%), Gaps = 10/241 (4%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA + ISTPIITA L    D   AR VK R+E+TTLGE+C+YIEEV++PDD
Sbjct: 1079 GVPRIKEIINAVKTISTPIITAALLDPYDESLARRVKARIEKTTLGEICDYIEEVYLPDD 1138

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIE------RTRGISGHLTVSGHSFLILKPKDSS 877
             F+L+KL+  RIRLL LEV ++SI Y I       + RG    +   G + + ++P  +S
Sbjct: 1139 YFLLVKLNSKRIRLLQLEVCMESISYAIATSKVCPQMRGCK--IVAHGKTMMAIRPPSTS 1196

Query: 878  K-SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGV 936
            K S    M  +K  L +VV+KG+  +NR VIH ++ +G   Y LLVEG + R V+++ GV
Sbjct: 1197 KLSKTMTMQILKYSLANVVVKGIPSVNRCVIHADEKKG-DFYSLLVEGTDFRSVLSSVGV 1255

Query: 937  KGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL 996
               K + NN   V   LGIEAARS I+ EI   M+ HG+ +D RH ML+AD+MT +GEVL
Sbjct: 1256 DPRKTNFNNALVVADVLGIEAARSCIINEIIATMDAHGIGLDRRHVMLLADVMTYRGEVL 1315

Query: 997  G 997
            G
Sbjct: 1316 G 1316



 Score =  192 bits (488), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 112/286 (39%), Positives = 162/286 (56%), Gaps = 18/286 (6%)

Query: 93  VQQQSHIQIVSKNLYCQ-DPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYI 151
           ++Q +H+ I +  LY   + +  P  +G LD +MG + K   C+TCG  L+DCVGHFGY 
Sbjct: 28  MRQTAHVPIFNNKLYEDVEGKLQPANYGPLDPKMGVSTKTGTCSTCGLGLTDCVGHFGYF 87

Query: 152 DLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKK 211
           DL +PVFHIG+F+  I +LQ ICKN  C+ +LL  E+   F  ++ NP L YL RK+L K
Sbjct: 88  DLDVPVFHIGFFKLTIQLLQCICKN--CSSILLTPEQHRVFSRQVMNPNLDYLHRKALHK 145

Query: 212 KILETTKKVSVCPHCGEINGVVKKC--GLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVK 269
           +I+   KK S C HCG  NG VKK    +LKI+             +  D L ++     
Sbjct: 146 RIVAACKKGSTCSHCGLKNGTVKKAVGAVLKIAFA---------SPVSVDELGKFATMFS 196

Query: 270 FNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLM-NAELSKPSDLILTRLLVPPN 328
            N E+  H +      LNPL V +LF  I   DIP+L++ + E   P+DL+LTR+ VPP 
Sbjct: 197 SNQEVGDHVRKMKFTLLNPLFVQKLFSNIKEGDIPVLMVRSGEEKHPNDLLLTRMPVPPV 256

Query: 329 CIRPSVISDLK---SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTF 371
           CIRPSV+S++K   +++DV +   +  L    +  H+    P +T 
Sbjct: 257 CIRPSVVSEVKAGTTEDDVTMKLMEIMLTNDVLKKHKRDGAPSKTL 302



 Score =  114 bits (286), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 53/61 (86%), Positives = 55/61 (90%), Gaps = 1/61 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV NSF+SGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVK LEDLC  Y
Sbjct: 823 TPEAKGFVANSFYSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKCLEDLCASY 882

Query: 668 D 668
           D
Sbjct: 883 D 883



 Score = 69.3 bits (168), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 32/51 (62%), Positives = 39/51 (76%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLI 72
           LM  K+NL+TPR+GE L+AA QDFITGGYLLT K+ F  RA+  R A+ LI
Sbjct: 518 LMNVKNNLITPRSGEPLVAAIQDFITGGYLLTHKDTFLPRAEVYRFAAALI 568



 Score = 58.2 bits (139), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 26/39 (66%), Positives = 29/39 (74%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  F+AAF+ Q D I GVSECIIMG PM VGTG  KL+Q
Sbjct: 1340 DHLFEAAFFSQRDVIHGVSECIIMGTPMTVGTGTFKLMQ 1378


>gi|308449389|ref|XP_003087948.1| CRE-RPC-1 protein [Caenorhabditis remanei]
 gi|308250793|gb|EFO94745.1| CRE-RPC-1 protein [Caenorhabditis remanei]
          Length = 1027

 Score =  328 bits (840), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 156/276 (56%), Positives = 195/276 (70%), Gaps = 20/276 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DNDVVLFNRQPSLHK+SIM+HRAKV+P RTFRFNEC CTPYNADFDGDEMN+HLPQT EA
Sbjct: 53  DNDVVLFNRQPSLHKISIMSHRAKVMPGRTFRFNECACTPYNADFDGDEMNLHLPQTYEA 112

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEA                LM  K+NL+TPR+GE L+AA QDFITGGYLLT K+ F  R
Sbjct: 113 KAEA--------------SELMNVKNNLITPRSGEPLVAAIQDFITGGYLLTHKDTFLPR 158

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  R A+ LI  ++      K+ +     P    +   +WTGKQ+  LI++P++   ++
Sbjct: 159 AEVYRFAAALIDASA------KKQTKIRIPPPAIRKPVELWTGKQLIELIIRPDKGSQIS 212

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            NL  K ++Y+ N E C +DSYVI+RNS LLAG +DKS LGS  K N+FY+L+RD+GED 
Sbjct: 213 LNLTAKNKSYSGNLELCSKDSYVIIRNSVLLAGVLDKSLLGSSSKVNIFYMLMRDYGEDA 272

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           AV AMWRL+RM   +L NRGFSIGIGDV P +  +Q
Sbjct: 273 AVDAMWRLARMAPVFLSNRGFSIGIGDVRPSERLLQ 308



 Score =  263 bits (671), Expect = 6e-67,   Method: Compositional matrix adjust.
 Identities = 159/372 (42%), Positives = 209/372 (56%), Gaps = 65/372 (17%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCE 1149
            + C  K  RA  EP TAVGA+AA SIGEP TQMTLKTFHFAG              E+  
Sbjct: 654  QLCYYKVARAITEPGTAVGAIAATSIGEPSTQMTLKTFHFAGVASMNITQGVPRIKEIIN 713

Query: 1150 YIEEVFVP----------------------------------------DDSFILIKLDMD 1169
             ++ +  P                                        DD F+L+KL+  
Sbjct: 714  AVKTISTPIITAALLDPYDESLARRVKARIEKTTLGEICDYIEEVYLPDDYFLLVKLNSK 773

Query: 1170 RIRLLHLEVDIDSIRYCIERT------RGISGHLTVSGHSFLILKPKDSSK-SFNSKMYQ 1222
            RIRLL LEV ++SI + I  +      RG    +   G + + ++P  +SK S    M  
Sbjct: 774  RIRLLQLEVSLESIAFAISTSKVCPMMRGCK--IVAHGKTMMAIRPPSTSKLSKTMTMQM 831

Query: 1223 MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNT 1282
            +K  L +VVIKG+  +NR VIH ++ +G   Y LLVEG + R V+++ GV   K + NN 
Sbjct: 832  LKYSLGNVVIKGISSVNRCVIHADEKKG-DFYSLLVEGTDFRSVLSSVGVDPRKTNFNNA 890

Query: 1283 YEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKM 1342
              V + LGIEAAR+ I+ EI   M+ HG+ +D RH ML+AD+MT +GEVLGITR+GL KM
Sbjct: 891  LVVAEVLGIEAARTCIINEIIATMDAHGIGLDRRHVMLLADVMTYRGEVLGITRNGLVKM 950

Query: 1343 KESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEP 1402
            K+SVL LASFE T DHLF+AAF+ Q D I GVSECIIMG PM VGTG  KL+Q   +   
Sbjct: 951  KDSVLLLASFEKTMDHLFEAAFFSQRDVIHGVSECIIMGTPMTVGTGTFKLMQKHEKKAI 1010

Query: 1403 VPR-TLLFDNPE 1413
            + + + +F  PE
Sbjct: 1011 LKQNSPIFQRPE 1022



 Score =  213 bits (541), Expect = 9e-52,   Method: Compositional matrix adjust.
 Identities = 118/241 (48%), Positives = 159/241 (65%), Gaps = 10/241 (4%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
           GVPRIKEIINA + ISTPIITA L    D   AR VK R+E+TTLGE+C+YIEEV++PDD
Sbjct: 704 GVPRIKEIINAVKTISTPIITAALLDPYDESLARRVKARIEKTTLGEICDYIEEVYLPDD 763

Query: 824 SFILIKLDMDRIRLLHLEVDIDSIRYCIERT------RGISGHLTVSGHSFLILKPKDSS 877
            F+L+KL+  RIRLL LEV ++SI + I  +      RG    +   G + + ++P  +S
Sbjct: 764 YFLLVKLNSKRIRLLQLEVSLESIAFAISTSKVCPMMRGCK--IVAHGKTMMAIRPPSTS 821

Query: 878 K-SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGV 936
           K S    M  +K  L +VVIKG+  +NR VIH ++ +G   Y LLVEG + R V+++ GV
Sbjct: 822 KLSKTMTMQMLKYSLGNVVIKGISSVNRCVIHADEKKG-DFYSLLVEGTDFRSVLSSVGV 880

Query: 937 KGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL 996
              K + NN   V + LGIEAAR+ I+ EI   M+ HG+ +D RH ML+AD+MT +GEVL
Sbjct: 881 DPRKTNFNNALVVAEVLGIEAARTCIINEIIATMDAHGIGLDRRHVMLLADVMTYRGEVL 940

Query: 997 G 997
           G
Sbjct: 941 G 941



 Score =  115 bits (288), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 53/61 (86%), Positives = 55/61 (90%), Gaps = 1/61 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV NSF+SGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVK LEDLC  Y
Sbjct: 424 TPEAKGFVANSFYSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKCLEDLCASY 483

Query: 668 D 668
           D
Sbjct: 484 D 484



 Score = 69.3 bits (168), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 32/51 (62%), Positives = 39/51 (76%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLI 72
           LM  K+NL+TPR+GE L+AA QDFITGGYLLT K+ F  RA+  R A+ LI
Sbjct: 119 LMNVKNNLITPRSGEPLVAAIQDFITGGYLLTHKDTFLPRAEVYRFAAALI 169



 Score = 58.9 bits (141), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 29/58 (50%), Positives = 37/58 (63%), Gaps = 1/58 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPR-TLLFDNPE 724
            D  F+AAF+ Q D I GVSECIIMG PM VGTG  KL+Q   +   + + + +F  PE
Sbjct: 965  DHLFEAAFFSQRDVIHGVSECIIMGTPMTVGTGTFKLMQKHEKKAILKQNSPIFQRPE 1022


>gi|308491392|ref|XP_003107887.1| hypothetical protein CRE_12654 [Caenorhabditis remanei]
 gi|308249834|gb|EFO93786.1| hypothetical protein CRE_12654 [Caenorhabditis remanei]
          Length = 1406

 Score =  326 bits (836), Expect = 5e-86,   Method: Compositional matrix adjust.
 Identities = 156/276 (56%), Positives = 195/276 (70%), Gaps = 20/276 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DNDVVLFNRQPSLHK+SIM+HRAKV+P RTFRFNEC CTPYNADFDGDEMN+HLPQT EA
Sbjct: 457 DNDVVLFNRQPSLHKISIMSHRAKVMPGRTFRFNECACTPYNADFDGDEMNLHLPQTYEA 516

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEA                LM  K+NL+TPR+GE L+AA QDFITGGYLLT K+ F  R
Sbjct: 517 KAEA--------------SELMNVKNNLITPRSGEPLVAAIQDFITGGYLLTHKDTFLPR 562

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  R A+ LI  ++      K+ +     P    +   +WTGKQ+  LI++P++   ++
Sbjct: 563 AEVYRFAAALIDASA------KKQTKIRIPPPAIRKPVELWTGKQLIELIIRPDKGSQIS 616

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            NL  K ++Y+ N E C +DSYVI+RNS LLAG +DKS LGS  K N+FY+L+RD+GED 
Sbjct: 617 LNLTAKNKSYSGNLELCSKDSYVIIRNSVLLAGVLDKSLLGSSSKVNIFYMLMRDYGEDA 676

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           AV AMWRL+RM   +L NRGFSIGIGDV P +  +Q
Sbjct: 677 AVDAMWRLARMAPVFLSNRGFSIGIGDVRPSERLLQ 712



 Score =  262 bits (670), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 156/353 (44%), Positives = 201/353 (56%), Gaps = 64/353 (18%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCE 1149
            + C  K  RA  EP TAVGA+AA SIGEP TQMTLKTFHFAG              E+  
Sbjct: 1033 QLCYYKVARAITEPGTAVGAIAATSIGEPSTQMTLKTFHFAGVASMNITQGVPRIKEIIN 1092

Query: 1150 YIEEVFVP----------------------------------------DDSFILIKLDMD 1169
             ++ +  P                                        DD F+L+KL+  
Sbjct: 1093 AVKTISTPIITAALLDPYDESLARRVKARIEKTTLGEICDYIEEVYLPDDYFLLVKLNSK 1152

Query: 1170 RIRLLHLEVDIDSIRYCIERT------RGISGHLTVSGHSFLILKPKDSSK-SFNSKMYQ 1222
            RIRLL LEV ++SI + I  +      RG    +   G + + ++P  +SK S    M  
Sbjct: 1153 RIRLLQLEVSLESIAFAISTSKVCPMMRGCK--IVAHGKTMMAIRPPSTSKLSKTMTMQM 1210

Query: 1223 MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNT 1282
            +K  L +VVIKG+  +NR VIH ++ +G   Y LLVEG + R V+++ GV   K + NN 
Sbjct: 1211 LKYSLGNVVIKGISSVNRCVIHADEKKG-DFYSLLVEGTDFRSVLSSVGVDPRKTNFNNA 1269

Query: 1283 YEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKM 1342
              V + LGIEAAR+ I+ EI   M+ HG+ +D RH ML+AD+MT +GEVLGITR+GL KM
Sbjct: 1270 LVVAEVLGIEAARTCIINEIIATMDAHGIGLDRRHVMLLADVMTYRGEVLGITRNGLVKM 1329

Query: 1343 KESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 1395
            K+SVL LASFE T DHLF+AAF+ Q D I GVSECIIMG PM VGTG  KL+Q
Sbjct: 1330 KDSVLLLASFEKTMDHLFEAAFFSQRDVIHGVSECIIMGTPMTVGTGTFKLMQ 1382



 Score =  213 bits (541), Expect = 8e-52,   Method: Compositional matrix adjust.
 Identities = 118/241 (48%), Positives = 159/241 (65%), Gaps = 10/241 (4%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA + ISTPIITA L    D   AR VK R+E+TTLGE+C+YIEEV++PDD
Sbjct: 1083 GVPRIKEIINAVKTISTPIITAALLDPYDESLARRVKARIEKTTLGEICDYIEEVYLPDD 1142

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERT------RGISGHLTVSGHSFLILKPKDSS 877
             F+L+KL+  RIRLL LEV ++SI + I  +      RG    +   G + + ++P  +S
Sbjct: 1143 YFLLVKLNSKRIRLLQLEVSLESIAFAISTSKVCPMMRGCK--IVAHGKTMMAIRPPSTS 1200

Query: 878  K-SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGV 936
            K S    M  +K  L +VVIKG+  +NR VIH ++ +G   Y LLVEG + R V+++ GV
Sbjct: 1201 KLSKTMTMQMLKYSLGNVVIKGISSVNRCVIHADEKKG-DFYSLLVEGTDFRSVLSSVGV 1259

Query: 937  KGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL 996
               K + NN   V + LGIEAAR+ I+ EI   M+ HG+ +D RH ML+AD+MT +GEVL
Sbjct: 1260 DPRKTNFNNALVVAEVLGIEAARTCIINEIIATMDAHGIGLDRRHVMLLADVMTYRGEVL 1319

Query: 997  G 997
            G
Sbjct: 1320 G 1320



 Score =  189 bits (480), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 113/290 (38%), Positives = 160/290 (55%), Gaps = 21/290 (7%)

Query: 93  VQQQSHIQIVSKNLYCQD--PQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           ++Q +H+ I +  LY +D   +  P  +G LD RMG + K   C TCG  L+DCVGHFGY
Sbjct: 28  MRQTAHVPIFNNKLY-EDVGGKLQPANYGPLDPRMGVSTKTGTCATCGLGLTDCVGHFGY 86

Query: 151 IDLPLPVFHIGYFRCVINILQSICKN---PTCARVLLGEEKAAGFRAKLRNPALSYLVRK 207
            DL +PVFHIG+F+  I +LQ ICK      C+ +LL  E+   F  ++ NP + YL RK
Sbjct: 87  FDLDVPVFHIGFFKLTIQLLQCICKQRNFQNCSSILLNPEQHRVFSRQVMNPNIDYLHRK 146

Query: 208 SLKKKILETTKKVSVCPHCGEINGVVKKC--GLLKISHEKYKNRTKKKDAIVEDLLAEYN 265
           +L K+I+   KK S C  CG  NG VKK    +LKI+             +  D L +Y 
Sbjct: 147 ALHKRIVAACKKSSTCTQCGLKNGTVKKAVGTVLKIAFA---------SPVPADELGKYA 197

Query: 266 EAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLM-NAELSKPSDLILTRLL 324
                N E+  H K      LNPL V +LF  +   DIP+L++ + E   P+DL+LTR+ 
Sbjct: 198 TMFNANQEVGDHVKKMKFTLLNPLFVQKLFANVKQADIPVLMVRSGEEKHPNDLLLTRMP 257

Query: 325 VPPNCIRPSVISDLKS---DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTF 371
           VPP CIRPSV+S++KS   ++DV +   +  L    +  H+    P +T 
Sbjct: 258 VPPVCIRPSVVSEVKSGTTEDDVTMKLMEIMLTNDVLKKHKRDGAPSKTL 307



 Score =  114 bits (286), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 53/61 (86%), Positives = 55/61 (90%), Gaps = 1/61 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV NSF+SGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVK LEDLC  Y
Sbjct: 828 TPEAKGFVANSFYSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKCLEDLCASY 887

Query: 668 D 668
           D
Sbjct: 888 D 888



 Score = 69.3 bits (168), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 32/51 (62%), Positives = 39/51 (76%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLI 72
           LM  K+NL+TPR+GE L+AA QDFITGGYLLT K+ F  RA+  R A+ LI
Sbjct: 523 LMNVKNNLITPRSGEPLVAAIQDFITGGYLLTHKDTFLPRAEVYRFAAALI 573



 Score = 58.5 bits (140), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 26/39 (66%), Positives = 29/39 (74%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  F+AAF+ Q D I GVSECIIMG PM VGTG  KL+Q
Sbjct: 1344 DHLFEAAFFSQRDVIHGVSECIIMGTPMTVGTGTFKLMQ 1382


>gi|391343926|ref|XP_003746256.1| PREDICTED: LOW QUALITY PROTEIN: DNA-directed RNA polymerase III
           subunit RPC1-like [Metaseiulus occidentalis]
          Length = 1386

 Score =  324 bits (830), Expect = 3e-85,   Method: Compositional matrix adjust.
 Identities = 159/277 (57%), Positives = 198/277 (71%), Gaps = 22/277 (7%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D DVVLFNRQPSLHKLSIMAH+A VLPHRT RFNECVCTPYNADFDGDEMN+H+PQT E
Sbjct: 455 TDGDVVLFNRQPSLHKLSIMAHKAVVLPHRTLRFNECVCTPYNADFDGDEMNIHMPQTYE 514

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           ARAEA+              VLMA  +N+VTPRNGE LI A QDFITGGYLLT K+  F+
Sbjct: 515 ARAEAM--------------VLMATTANIVTPRNGEPLIGAIQDFITGGYLLTHKDEMFD 560

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           R     + S  +A   D+   ++       +P + ++  V+WTGKQIFSLILKP++   V
Sbjct: 561 RETACHLISQFVAG-RDVSTTVEL-----PHPAI-LKPKVLWTGKQIFSLILKPSKSSDV 613

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
             +L+ K +  T NE+ C  D+YVI+RNSELL G MDK T+GSG K ++FY+LLRD+   
Sbjct: 614 RIHLRAKNKNXTKNEDMCTNDNYVIMRNSELLCGRMDKGTMGSGSKNSIFYLLLRDYSAQ 673

Query: 580 VAVTAMWRLSRMTSFYLMN-RGFSIGIGDVTPGQGFV 615
            A  AMWRL+R+++F+L++ RGFSIGIGDVTPG   V
Sbjct: 674 HAADAMWRLARISAFFLLSTRGFSIGIGDVTPGASLV 710



 Score =  318 bits (816), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 199/486 (40%), Positives = 268/486 (55%), Gaps = 83/486 (17%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G  + V+  R+L+ + A N    + +     ++ LS + +   +F +     F+  + ++
Sbjct: 914  GKDSVVDFNRVLEMVKASNRYPDEIAEDPDTLIELSKQIVREPDFDRGVKRYFIDMLLEY 973

Query: 1057 LE-------EFSKKESVTSHQDKV-SQPLREQILSHQDKIGHGRESNPFPSACKAEACRE 1108
            +E       E  +K  VT    K+  +P R      +D I                  + 
Sbjct: 974  IERVAESNRESWRKLGVTKDSPKIFKEPWRLTKSHLRDFI---------------MTSKN 1018

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFH-------------------------- 1142
            KY++A++EPATA+GA+ AQSIGEP TQMTLKTFH                          
Sbjct: 1019 KYLKAKLEPATAIGAICAQSIGEPATQMTLKTFHFAGVASMNITQGVPRIKEIINASKAI 1078

Query: 1143 ----------------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLL 1174
                            FA            GE+ EY+EE++VPDD F++I+L +DRIRLL
Sbjct: 1079 ATPIITATLLDDSDPEFARRVKSRVEKTTLGEIAEYLEEIYVPDDVFVMIRLAIDRIRLL 1138

Query: 1175 HLEVDIDSIRYCIERTRGISGH-LTVSGHSFLILKPKDSSKSFN-SKMYQ-MKQLLPSVV 1231
             LEV   +IRY I   + I  + +TV  +S + ++   S+ + N S + Q +   LP VV
Sbjct: 1139 QLEVSAQTIRYAICLDKKIKPNDVTVHSNSVITVRASKSTSNQNLSHIIQDLMANLPKVV 1198

Query: 1232 IKGVQGINRAVIHEEDVEGVTK-YKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLG 1290
            +KGV    RAVIH +D       YKLLVE + L DV++TYGV+  KC  NN  EV + LG
Sbjct: 1199 VKGVAA--RAVIHCDDTTPEKPVYKLLVESNRLLDVLSTYGVRPEKCRCNNILEVSEVLG 1256

Query: 1291 IEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLA 1350
            IEAAR  I+TE++  ME HG+SID RH ML+ADLMT  GEV+GITRHGLAKMKES L LA
Sbjct: 1257 IEAARHQIITEMRETMEGHGISIDMRHLMLLADLMTRTGEVVGITRHGLAKMKESALMLA 1316

Query: 1351 SFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFD 1410
            SFE T+DHLFDAA+YGQ D ++GVSECII+G PM  GTG   L+   PR  P P  L+FD
Sbjct: 1317 SFEKTADHLFDAAYYGQRDDVTGVSECIILGKPMKQGTGFFNLVYDFPRQPPPPSDLIFD 1376

Query: 1411 NPEFHT 1416
             PE HT
Sbjct: 1377 VPELHT 1382



 Score =  226 bits (576), Expect = 7e-56,   Method: Compositional matrix adjust.
 Identities = 127/238 (53%), Positives = 167/238 (70%), Gaps = 6/238 (2%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ I+TPIITA L  D+D ++AR VK R+E+TTLGE+ EY+EE++VPDD
Sbjct: 1064 GVPRIKEIINASKAIATPIITATLLDDSDPEFARRVKSRVEKTTLGEIAEYLEEIYVPDD 1123

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGH-LTVSGHSFLILKPKDSSKSFN- 881
             F++I+L +DRIRLL LEV   +IRY I   + I  + +TV  +S + ++   S+ + N 
Sbjct: 1124 VFVMIRLAIDRIRLLQLEVSAQTIRYAICLDKKIKPNDVTVHSNSVITVRASKSTSNQNL 1183

Query: 882  SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTK-YKLLVEGDNLRDVMATYGVKGV 939
            S + Q +   LP VV+KGV    RAVIH +D       YKLLVE + L DV++TYGV+  
Sbjct: 1184 SHIIQDLMANLPKVVVKGVAA--RAVIHCDDTTPEKPVYKLLVESNRLLDVLSTYGVRPE 1241

Query: 940  KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            KC  NN  EV + LGIEAAR  I+TE++  ME HG+SID RH ML+ADLMT  GEV+G
Sbjct: 1242 KCRCNNILEVSEVLGIEAARHQIITEMRETMEGHGISIDMRHLMLLADLMTRTGEVVG 1299



 Score =  220 bits (560), Expect = 6e-54,   Method: Compositional matrix adjust.
 Identities = 121/276 (43%), Positives = 169/276 (61%), Gaps = 21/276 (7%)

Query: 74  GRKVFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQ--RTPIPHGLLDRRMGTNQKE 131
           G  V  R +  G +T  D +   SHI+ V+K+LY  D    R   P+G+LD ++GT+ + 
Sbjct: 10  GETVEVRQMAFGILTP-DEIGALSHIKCVNKSLYIADHSKGRQASPYGVLDPKLGTSSRA 68

Query: 132 ANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAG 191
             C TCG+ L++CVGHFGYIDL  PVFH G+FR  INILQ ICKN  CA +LL +E    
Sbjct: 69  GVCETCGKGLTECVGHFGYIDLECPVFHCGFFRECINILQCICKN--CAHILLPDEIKDK 126

Query: 192 FRAKLRNPALSYLVRKSLKKKILETTKKVS--VCPHCGEINGVVKKCGLLKISHEKYKNR 249
           +R ++++  L Y+ +K L  +ILE  +K+    CP C  +NG VKK G+LKI H++ +N+
Sbjct: 127 YRQRIQSRELDYVTKKHLHTEILEKCRKLQGKTCPKCQFVNGFVKKAGMLKIMHDRTRNK 186

Query: 250 TKKK-----DAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIP 304
            KK+     DA   DL A  +     + EIE          ++ ++ L LFE IP  D+P
Sbjct: 187 PKKRTKEEIDAEDSDLKAGKDGLPAPSTEIE---------LVDAMKCLHLFERIPEYDVP 237

Query: 305 LLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKS 340
           LL MNAE+ +P +LI TR+LVPP CIRPSV SD ++
Sbjct: 238 LLFMNAEIGRPENLIQTRVLVPPLCIRPSVASDFRA 273



 Score =  108 bits (271), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 48/60 (80%), Positives = 55/60 (91%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV++SFF+GLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRL+KSLED+ + YD S
Sbjct: 830 ARGFVEDSFFTGLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLIKSLEDMMLNYDSS 889



 Score = 77.8 bits (190), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 34/61 (55%), Positives = 40/61 (65%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHF 727
            D  FDAA+YGQ D ++GVSECII+G PM  GTG   L+   PR  P P  L+FD PE H 
Sbjct: 1323 DHLFDAAYYGQRDDVTGVSECIILGKPMKQGTGFFNLVYDFPRQPPPPSDLIFDVPELHT 1382

Query: 728  P 728
            P
Sbjct: 1383 P 1383



 Score = 75.5 bits (184), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 36/65 (55%), Positives = 42/65 (64%)

Query: 13  YATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLI 72
           Y  R    VLMA  +N+VTPRNGE LI A QDFITGGYLLT K+  F+R     + S  +
Sbjct: 513 YEARAEAMVLMATTANIVTPRNGEPLIGAIQDFITGGYLLTHKDEMFDRETACHLISQFV 572

Query: 73  AGRKV 77
           AGR V
Sbjct: 573 AGRDV 577


>gi|194758651|ref|XP_001961575.1| GF14868 [Drosophila ananassae]
 gi|190615272|gb|EDV30796.1| GF14868 [Drosophila ananassae]
          Length = 1301

 Score =  312 bits (799), Expect = 1e-81,   Method: Compositional matrix adjust.
 Identities = 177/391 (45%), Positives = 221/391 (56%), Gaps = 70/391 (17%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+D+VLFNRQPSLHK+SIM HRAKV P RTFRFNEC CTPYNADFDGDEMN+HLPQTEEA
Sbjct: 455 DDDIVLFNRQPSLHKMSIMCHRAKVQPQRTFRFNECACTPYNADFDGDEMNLHLPQTEEA 514

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL              +LM N+SNLVTP+NGE+LIAATQDFITGGYLLTQK  F  +
Sbjct: 515 RAEAL--------------ILMGNQSNLVTPKNGEILIAATQDFITGGYLLTQKEVFLTK 560

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            + M++A+  +A+      I          P   ++   +WTGKQ+FSL+++PN D   N
Sbjct: 561 EEAMQLAACFLANEDSTMHI-------EMPPPALLKPRRLWTGKQMFSLLMRPNHDSQ-N 612

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRN--------SELLAGSMDKSTLGSGGKANVFYIL 572
                     T ++       Y++ R          +L AG++ +   G   +  +  ++
Sbjct: 613 RGFSFGISDVTPSKRLLEHKEYLLQRGYAKCNEYIEKLKAGTL-QCQPGCTPEETLESVM 671

Query: 573 LRDFG---EDVAVTAMWRLSRMTSFYLM----NRGFSIGIGD------------------ 607
           LR+     E  A T    L    S  +M    ++G +I I                    
Sbjct: 672 LRELSGIREQAAKTCFAELHPTNSALIMALSGSKGSNINISQMIACVGQQAISGKRVPNG 731

Query: 608 --------------VTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQ 653
                         +   +GFVQNSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGY+Q
Sbjct: 732 FENRALPHFDRHSAIPAARGFVQNSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYLQ 791

Query: 654 RRLVKSLEDLCVQYDMSFDAAFYGQTDCISG 684
           RRLVK LEDL V YD +   A     D I G
Sbjct: 792 RRLVKCLEDLVVHYDGTVRNAVNEMVDTIYG 822



 Score =  305 bits (782), Expect = 8e-80,   Method: Compositional matrix adjust.
 Identities = 189/454 (41%), Positives = 256/454 (56%), Gaps = 72/454 (15%)

Query: 1001 PVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEF 1060
            PV+L    D++ A+      P L   EI   +     + EF  ++ E+F  D++K L+  
Sbjct: 837  PVDLVHQYDNLRAQIHPGQQPPLRGSEIPEAAESLFKTPEF-AESREDFKEDVRKHLKTV 895

Query: 1061 SKKESVTSHQDKVSQPLREQI--LSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPA 1118
            SK+ S+   +      L  QI  L+ +  +   R  N            ++Y RA  EP 
Sbjct: 896  SKRISLLQEKYDPYGNLCNQIECLTTEQLLEFLRRIN------------DRYNRAVTEPG 943

Query: 1119 TAVGALAAQSIGEPGTQMTLKTFH------------------------------------ 1142
            TAVGA+AAQSIGEPGTQMTLKTFH                                    
Sbjct: 944  TAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIVEIINATKTISTPIITAELQ 1003

Query: 1143 ------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIR 1184
                  FA            GE+  Y+E V  P   ++ I +DM RI+LL L +++D+I 
Sbjct: 1004 DNLSMEFARQVKARIEKTTLGELSSYVEVVCGPHCCYLAIGIDMSRIKLLGLHINLDTIV 1063

Query: 1185 YCI--ERTRGISGHLTVSGHSFLILKPKDS-SKSFNSKMYQMKQLLPSVVIKGVQGINRA 1241
              I   R R     + V+  S ++++ + + + + NS++ ++   L SVV+ G+  INRA
Sbjct: 1064 ASILKSRMRLKPAQVEVARDSRIVVRVEATKNATINSELARLALSLQSVVVAGLPNINRA 1123

Query: 1242 VIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTE 1301
            VI  +D      YKL +EG  LRDV+ATYGV GV   SNN  E+Y+TLGIEAAR+ IM+E
Sbjct: 1124 VIAVDDARQPATYKLCIEGYGLRDVIATYGVVGVHTRSNNICEIYQTLGIEAARTIIMSE 1183

Query: 1302 IKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFD 1361
            I  VME HGMS+D+RH ML+A  MT++GEVLGITRHGLAKM+ESV NLASFE T+DHLFD
Sbjct: 1184 ITEVMEGHGMSVDWRHIMLLASQMTARGEVLGITRHGLAKMRESVFNLASFEKTADHLFD 1243

Query: 1362 AAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 1395
            AA+YGQTD I+GVSE II+G+P  +GTG+ KLL 
Sbjct: 1244 AAYYGQTDAINGVSERIILGMPAGIGTGIFKLLH 1277



 Score =  250 bits (638), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 129/256 (50%), Positives = 171/256 (66%), Gaps = 8/256 (3%)

Query: 87  VTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVG 146
           ++  D +QQ+S ++I+SKNLY    QR P+P G+LDRRMG   K+A C TCGQ L++C+G
Sbjct: 22  ISAADEIQQESLVRIISKNLY--QAQRQPVPFGVLDRRMGIGTKDAMCETCGQGLNECIG 79

Query: 147 HFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVR 206
           HFGY+DL LPVFHIG+FR  INILQ ICK  TCA+V+L  E  A F  KL NP  SYL +
Sbjct: 80  HFGYLDLALPVFHIGHFRSTINILQMICK--TCAQVMLKTEDRAVFEKKLHNPNFSYLGK 137

Query: 207 KSLKKKILETTKKVSVCPHCGEINGVVKKC-GLLKISHEKYKNRTKKKDAIVEDLLAEYN 265
           K+L  ++L   KKV+ CPHCG  NG VKK  GLLKI H+ YK R  K D+   + + E  
Sbjct: 138 KALHVQMLAKAKKVTKCPHCGSPNGGVKKGPGLLKILHDPYKGR--KVDSAFTNNMNEML 195

Query: 266 EAVKFNPEIEAH-KKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLL 324
            + + N ++ A    +   + L PL VL LFE IP  D+ LL M +  + P +LI+TR+ 
Sbjct: 196 RSTEANRDLNATLSSYSTAEELTPLMVLDLFEQIPQSDVALLGMCSRGAHPKNLIVTRVF 255

Query: 325 VPPNCIRPSVISDLKS 340
           VPP CIRPSV+S++K+
Sbjct: 256 VPPACIRPSVLSEVKA 271



 Score =  216 bits (550), Expect = 7e-53,   Method: Compositional matrix adjust.
 Identities = 116/237 (48%), Positives = 162/237 (68%), Gaps = 3/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRI EIINA++ ISTPIITA L  +  +++AR VK R+E+TTLGE+  Y+E V  P  
Sbjct: 979  GVPRIVEIINATKTISTPIITAELQDNLSMEFARQVKARIEKTTLGELSSYVEVVCGPHC 1038

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCI--ERTRGISGHLTVSGHSFLILKPKDS-SKSF 880
             ++ I +DM RI+LL L +++D+I   I   R R     + V+  S ++++ + + + + 
Sbjct: 1039 CYLAIGIDMSRIKLLGLHINLDTIVASILKSRMRLKPAQVEVARDSRIVVRVEATKNATI 1098

Query: 881  NSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
            NS++ ++   L SVV+ G+  INRAVI  +D      YKL +EG  LRDV+ATYGV GV 
Sbjct: 1099 NSELARLALSLQSVVVAGLPNINRAVIAVDDARQPATYKLCIEGYGLRDVIATYGVVGVH 1158

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
              SNN  E+Y+TLGIEAAR+ IM+EI  VME HGMS+D+RH ML+A  MT++GEVLG
Sbjct: 1159 TRSNNICEIYQTLGIEAARTIIMSEITEVMEGHGMSVDWRHIMLLASQMTARGEVLG 1215



 Score = 79.0 bits (193), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 34/53 (64%), Positives = 44/53 (83%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIA 73
           +LM N+SNLVTP+NGE+LIAATQDFITGGYLLTQK  F  + + M++A+  +A
Sbjct: 520 ILMGNQSNLVTPKNGEILIAATQDFITGGYLLTQKEVFLTKEEAMQLAACFLA 572



 Score = 58.2 bits (139), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 25/39 (64%), Positives = 31/39 (79%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  FDAA+YGQTD I+GVSE II+G+P  +GTG+ KLL 
Sbjct: 1239 DHLFDAAYYGQTDAINGVSERIILGMPAGIGTGIFKLLH 1277


>gi|291233819|ref|XP_002736852.1| PREDICTED: polymerase (RNA) III (DNA directed) polypeptide A,
            155kDa-like [Saccoglossus kowalevskii]
          Length = 322

 Score =  306 bits (784), Expect = 5e-80,   Method: Compositional matrix adjust.
 Identities = 160/257 (62%), Positives = 191/257 (74%), Gaps = 3/257 (1%)

Query: 1145 GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCI--ERTRGISGHLTVSGH 1202
            GEV EYIEEVF+PD  FILIKL + RI++L LEV+ D++RY I   + R     + + G 
Sbjct: 65   GEVSEYIEEVFLPDQCFILIKLHLKRIKILKLEVNSDTVRYSILTAKLRIKPQEVVLHGD 124

Query: 1203 SFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD 1261
            S + + P +SSKS    + Q +K  L +VVI+GV  + RAVIH +D  GV KYKLLVEGD
Sbjct: 125  SVICVHPVESSKSSMYYVLQSLKDTLANVVIQGVPSVTRAVIHIDDKSGVEKYKLLVEGD 184

Query: 1262 NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 1321
            NLR V+AT GVKG   +SNNT EV KTLGIEAAR TI+ EI+  M +HGMSID RH ML+
Sbjct: 185  NLRAVIATRGVKGTHTTSNNTVEVEKTLGIEAARQTIINEIQYTMVSHGMSIDHRHMMLL 244

Query: 1322 ADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMG 1381
            ADLM  KGE+LGITR GLAKMKESVL LASFE T+DHLFDAA+YGQ D I+GVSECIIMG
Sbjct: 245  ADLMAYKGEILGITRFGLAKMKESVLMLASFEKTADHLFDAAYYGQKDAINGVSECIIMG 304

Query: 1382 LPMNVGTGLIKLLQAVP 1398
            +PM +GTGL KLL   P
Sbjct: 305  IPMTIGTGLFKLLHKYP 321



 Score =  265 bits (677), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 143/237 (60%), Positives = 175/237 (73%), Gaps = 3/237 (1%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
           GVPRIKEIINAS+NISTPII+A L+ D D + ARIVKGR+E+T LGEV EYIEEVF+PD 
Sbjct: 20  GVPRIKEIINASKNISTPIISASLEIDDDPEVARIVKGRIEKTLLGEVSEYIEEVFLPDQ 79

Query: 824 SFILIKLDMDRIRLLHLEVDIDSIRYCI--ERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
            FILIKL + RI++L LEV+ D++RY I   + R     + + G S + + P +SSKS  
Sbjct: 80  CFILIKLHLKRIKILKLEVNSDTVRYSILTAKLRIKPQEVVLHGDSVICVHPVESSKSSM 139

Query: 882 SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
             + Q +K  L +VVI+GV  + RAVIH +D  GV KYKLLVEGDNLR V+AT GVKG  
Sbjct: 140 YYVLQSLKDTLANVVIQGVPSVTRAVIHIDDKSGVEKYKLLVEGDNLRAVIATRGVKGTH 199

Query: 941 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +SNNT EV KTLGIEAAR TI+ EI+  M +HGMSID RH ML+ADLM  KGE+LG
Sbjct: 200 TTSNNTVEVEKTLGIEAARQTIINEIQYTMVSHGMSIDHRHMMLLADLMAYKGEILG 256



 Score = 68.9 bits (167), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 29/42 (69%), Positives = 33/42 (78%)

Query: 668 DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 709
           D  FDAA+YGQ D I+GVSECIIMG+PM +GTGL KLL   P
Sbjct: 280 DHLFDAAYYGQKDAINGVSECIIMGIPMTIGTGLFKLLHKYP 321


>gi|195048078|ref|XP_001992466.1| GH24768 [Drosophila grimshawi]
 gi|193893307|gb|EDV92173.1| GH24768 [Drosophila grimshawi]
          Length = 1303

 Score =  303 bits (775), Expect = 7e-79,   Method: Compositional matrix adjust.
 Identities = 175/396 (44%), Positives = 220/396 (55%), Gaps = 80/396 (20%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+D+VLFNRQPSLHK+SIM HRAKV P RTFRFNEC CTPYNADFDGDEMN+HLPQTEEA
Sbjct: 455 DDDIVLFNRQPSLHKMSIMCHRAKVQPQRTFRFNECACTPYNADFDGDEMNLHLPQTEEA 514

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL              +LM N+SNLVTP+NGE+LIAATQDFITGGYLLTQK  F  +
Sbjct: 515 RAEAL--------------ILMGNQSNLVTPKNGEILIAATQDFITGGYLLTQKEVFLTK 560

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              M++A+  +A       I          P    +   +WTGKQ+FSL+++PN D    
Sbjct: 561 EDAMQLAACFLASEDSTLRI-------QMPPPAIWKPRRLWTGKQMFSLLMRPNDDS--- 610

Query: 521 ANLKTKGRAY-----TANEEFCHRDSYVILRN--------SELLAGSMDKSTLGSGGKAN 567
              K +G ++     T + +       ++ R          +L +G++ +   G   +  
Sbjct: 611 ---KNRGFSFGISDVTPSAKLLQHKQVLLERGYAKCNEYIEKLKSGTL-QCQPGCTPEET 666

Query: 568 VFYILLRDFG---EDVAVTAMWRLSRMTSFYLM----NRGFSIGIGD------------- 607
           +  ++LR+     E  A T    L    S  +M    ++G +I I               
Sbjct: 667 LEAVMLRELSGIREQAAKTCFAELHPTNSALIMALSGSKGSNINISQMIACVGQQAVSGK 726

Query: 608 -------------------VTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAE 648
                              +   +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAE
Sbjct: 727 RVPNGFENRALPHFERHSAIPAARGFVGNSFYSGLTPTEFFFHTMAGREGLVDTAVKTAE 786

Query: 649 TGYMQRRLVKSLEDLCVQYDMSFDAAFYGQTDCISG 684
           TGY+QRRLVK LEDL V YD +   A     D I G
Sbjct: 787 TGYLQRRLVKCLEDLVVHYDGTVRNAINEMVDTIYG 822



 Score =  290 bits (743), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 183/453 (40%), Positives = 257/453 (56%), Gaps = 68/453 (15%)

Query: 1001 PVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEF 1060
            PV+L    D++ A+        L   EIL++++  L  KEF ++   +F  D+   L+  
Sbjct: 837  PVDLHHQYDNLRAQQPIGDQLPLQYDEILSVADWMLKQKEF-KEARADFKLDVTNHLKMV 895

Query: 1061 SKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATA 1120
            SK+  +   Q +  +  + Q+L +Q +     +   F          ++Y RA  EP TA
Sbjct: 896  SKR--IGQLQQRYGE--QHQVLCNQIESISQEQLLEF-----LRRINDRYNRAVTEPGTA 946

Query: 1121 VGALAAQSIGEPGTQMTLKTFH-------------------------------------- 1142
            VGA+AAQSIGEPGTQMTLKTFH                                      
Sbjct: 947  VGAIAAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIVEIINATKSISTPIITAELRNN 1006

Query: 1143 ----FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYC 1186
                FA            GE+  Y+E V  P    ++I +D  RI++L L +D+D+I   
Sbjct: 1007 KSMEFARQVKARIEKTTLGELSSYVELVCGPYSCHLVINIDAARIKVLGLYIDLDTIIAS 1066

Query: 1187 I--ERTRGISGHL-TVSGHSFLILKPKDS-SKSFNSKMYQMKQLLPSVVIKGVQGINRAV 1242
            I   R R   G +  +   S +I++ + + + + N+++ ++   + +VV+ G+  I RAV
Sbjct: 1067 ILKSRLRIKPGQVHAIPKKSRIIIRVESTKNATINAELARLAITIQNVVVGGLPNIARAV 1126

Query: 1243 IHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEI 1302
            I  +D +    YKL +EG  LRDV+ATYGV G K  SNN  E+Y+TLGIEAAR+ IM+EI
Sbjct: 1127 IAVDDAQQPPTYKLCIEGYGLRDVIATYGVIGEKTRSNNICEIYQTLGIEAARTVIMSEI 1186

Query: 1303 KLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDA 1362
              VME HGMS+D+RH ML+A  MT++GEVLGITRHGLAKM+ESV NLASFE T+DHLFDA
Sbjct: 1187 TDVMEGHGMSVDWRHIMLLASQMTARGEVLGITRHGLAKMRESVFNLASFEKTADHLFDA 1246

Query: 1363 AFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 1395
            A+YGQ D I+GVSE II+G+P  +GTG+ KLLQ
Sbjct: 1247 AYYGQMDAINGVSERIILGMPAGIGTGIFKLLQ 1279



 Score =  244 bits (624), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 126/256 (49%), Positives = 170/256 (66%), Gaps = 8/256 (3%)

Query: 87  VTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVG 146
           ++  D +QQ+S ++I+SKNLY    QR P+P+G+LDRRMG + K+A C TCGQ L++C+G
Sbjct: 22  ISGSDEIQQESLVRIISKNLY--QAQRQPVPYGVLDRRMGISTKDALCETCGQGLNECIG 79

Query: 147 HFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVR 206
           HFGY+DL LPVFHIG+FR  I+ILQ ICK  TCA V+L  E    F  KL NP  SYL +
Sbjct: 80  HFGYLDLALPVFHIGHFRSTISILQMICK--TCAHVMLKPEDRIVFEKKLHNPNFSYLGK 137

Query: 207 KSLKKKILETTKKVSVCPHCGEINGVVKKC-GLLKISHEKYKNRTKKKDAIVEDLLAEYN 265
           K+L  ++L   KKV+ CP+C   NG VKK  GLLKI H+ YK R  KKDA   + + E  
Sbjct: 138 KALHSQMLAKAKKVTKCPYCMASNGGVKKGPGLLKIQHDPYKGR--KKDAHFNNHMDEML 195

Query: 266 EAVKFNPEI-EAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLL 324
            + + N ++ +    +   + L PL VL LFE IP  D+ LL M +  + P  LI+TR+ 
Sbjct: 196 RSTELNRDLNQTLSNYSAAEELTPLMVLDLFEQIPQSDVALLGMCSRGAHPKHLIVTRVF 255

Query: 325 VPPNCIRPSVISDLKS 340
           VPP CIRPSV+S++K+
Sbjct: 256 VPPACIRPSVLSEVKA 271



 Score =  204 bits (519), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 112/238 (47%), Positives = 162/238 (68%), Gaps = 4/238 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRI EIINA+++ISTPIITA L  +  +++AR VK R+E+TTLGE+  Y+E V  P  
Sbjct: 980  GVPRIVEIINATKSISTPIITAELRNNKSMEFARQVKARIEKTTLGELSSYVELVCGPYS 1039

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCI--ERTRGISGHL-TVSGHSFLILKPKDS-SKS 879
              ++I +D  RI++L L +D+D+I   I   R R   G +  +   S +I++ + + + +
Sbjct: 1040 CHLVINIDAARIKVLGLYIDLDTIIASILKSRLRIKPGQVHAIPKKSRIIIRVESTKNAT 1099

Query: 880  FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
             N+++ ++   + +VV+ G+  I RAVI  +D +    YKL +EG  LRDV+ATYGV G 
Sbjct: 1100 INAELARLAITIQNVVVGGLPNIARAVIAVDDAQQPPTYKLCIEGYGLRDVIATYGVIGE 1159

Query: 940  KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            K  SNN  E+Y+TLGIEAAR+ IM+EI  VME HGMS+D+RH ML+A  MT++GEVLG
Sbjct: 1160 KTRSNNICEIYQTLGIEAARTVIMSEITDVMEGHGMSVDWRHIMLLASQMTARGEVLG 1217



 Score = 78.6 bits (192), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 35/60 (58%), Positives = 44/60 (73%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFFR 80
           +LM N+SNLVTP+NGE+LIAATQDFITGGYLLTQK  F  +   M++A+  +A      R
Sbjct: 520 ILMGNQSNLVTPKNGEILIAATQDFITGGYLLTQKEVFLTKEDAMQLAACFLASEDSTLR 579



 Score = 58.2 bits (139), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 25/39 (64%), Positives = 31/39 (79%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  FDAA+YGQ D I+GVSE II+G+P  +GTG+ KLLQ
Sbjct: 1241 DHLFDAAYYGQMDAINGVSERIILGMPAGIGTGIFKLLQ 1279


>gi|320170274|gb|EFW47173.1| polymerase III polypeptide A [Capsaspora owczarzaki ATCC 30864]
          Length = 1472

 Score =  301 bits (772), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 150/275 (54%), Positives = 190/275 (69%), Gaps = 25/275 (9%)

Query: 343 DVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARA 402
           D+ LFNRQPSLHKLSIM H  ++ P RTFRFNECVCTPYNADFDGDEMN+H+PQTEEARA
Sbjct: 505 DIALFNRQPSLHKLSIMCHFVRISPFRTFRFNECVCTPYNADFDGDEMNLHVPQTEEARA 564

Query: 403 EALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 462
           EA+              VLM  KSN++TPRNGE LIAA QDFITG YLL++K+ F +++ 
Sbjct: 565 EAM--------------VLMGVKSNMITPRNGEPLIAAIQDFITGAYLLSRKDLFLDQS- 609

Query: 463 TMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNAN 522
              + + L A  SD  GI          P   ++   +WTGKQ+FS++++PN+ C    N
Sbjct: 610 ---MFTQLCACMSD-AGI-----QIDIPPPAILKPVRLWTGKQLFSVLMRPNKQCKARMN 660

Query: 523 LKTKGRAYT-ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVA 581
           L+T  R Y+  +EE C  D +V +RNSELL+GSMDK+ LGSG K+ +FY+LLRDFGE  A
Sbjct: 661 LRTASRTYSKKDEEMCKNDGFVNIRNSELLSGSMDKALLGSGSKSTIFYVLLRDFGEQTA 720

Query: 582 VTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
             AM RL+++ S +L N GFSIGIGDVTP    +Q
Sbjct: 721 ADAMSRLAKLASRFLCNYGFSIGIGDVTPTLKLLQ 755



 Score =  252 bits (643), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 138/290 (47%), Positives = 191/290 (65%), Gaps = 21/290 (7%)

Query: 1145 GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSF 1204
            GE+ +++ E+F P  SF+ ++L   +IR L L++D + ++  +  ++    H  V+    
Sbjct: 1187 GEISDFMREIFTPHQSFLHVRLSRSQIRQLCLQIDAEQVKNALLASKPEQIH--VASPFD 1244

Query: 1205 LILKP---KDSS----KSFNSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKY 1254
            L +KP   KDSS    K  +S  + ++ L   + +V++ G+  + RAVI+++      KY
Sbjct: 1245 LCIKPPVEKDSSLSELKKLSSSFFSIQHLNHAIGNVIVSGISTVKRAVINQKTP---GKY 1301

Query: 1255 KLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSID 1314
             LLVEG NL  VM   GV  ++  SN+  E+  +LGIEAARSTIM EI+  M++HGMSID
Sbjct: 1302 NLLVEGTNLLAVMGIEGVDWMRTKSNHIMEMKDSLGIEAARSTIMNEIQYTMQSHGMSID 1361

Query: 1315 FRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGV 1374
             RH ML+ADLMTSKG+VLGITR G+AKMKESVL LASFE T+DHLFDA+ YGQTD + GV
Sbjct: 1362 TRHLMLLADLMTSKGDVLGITRFGIAKMKESVLMLASFEKTTDHLFDASLYGQTDSVRGV 1421

Query: 1375 SECIIMGLPMNVGTGLIKLLQA------VPRSEPVPRTLLFDNPEFHTNT 1418
            SECIIMG+PM +GTGL KLLQ         + +   R+ LFDNP+ HT +
Sbjct: 1422 SECIIMGIPMTIGTGLFKLLQRQAVGSNAVKKKLAQRSFLFDNPKLHTTS 1471



 Score =  221 bits (564), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 109/245 (44%), Positives = 157/245 (64%), Gaps = 4/245 (1%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           +Q+ SH+++V++ LY Q P R P PHG LD+R+GT+ K+  C TCG  ++ C GHFG + 
Sbjct: 27  MQRISHMRVVNRELY-QQPDRVPTPHGPLDKRLGTSMKQHTCETCGHPMTSCPGHFGDLQ 85

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKK 212
             LPVFH GYF+ +  +LQ+ICK  TC+RV+L  E+   F  +LRNP L  L ++++ KK
Sbjct: 86  FELPVFHYGYFKAITTVLQNICK--TCSRVMLPVEERLFFLQRLRNPLLEMLHKRAICKK 143

Query: 213 ILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNP 272
           + E  +++  CP+C   NG VKK   +K+SH+ Y+   K++     D L  + EAV  N 
Sbjct: 144 VNEKCRRLHNCPYCNAPNGPVKKVAFMKLSHDTYRMSEKQRSDDRVDFLNSFQEAVARNK 203

Query: 273 EIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRP 332
           ++       + + LNPL VL+LFEAIP ED+ LL ++    +P  LILTR+LVPP CIRP
Sbjct: 204 DLRPLLTKAMDE-LNPLRVLRLFEAIPNEDVELLGLDPLKGRPERLILTRMLVPPACIRP 262

Query: 333 SVISD 337
           SV  D
Sbjct: 263 SVAMD 267



 Score =  192 bits (489), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 113/244 (46%), Positives = 157/244 (64%), Gaps = 15/244 (6%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA L   +    ARIVKGR E T LGE+ +++ E+F P  
Sbjct: 1142 GVPRIKEIINASKVISTPIITAELLDQSKESIARIVKGRTESTRLGEISDFMREIFTPHQ 1201

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKP---KDSS--- 877
            SF+ ++L   +IR L L++D + ++  +  ++    H  V+    L +KP   KDSS   
Sbjct: 1202 SFLHVRLSRSQIRQLCLQIDAEQVKNALLASKPEQIH--VASPFDLCIKPPVEKDSSLSE 1259

Query: 878  -KSFNSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMAT 933
             K  +S  + ++ L   + +V++ G+  + RAVI+++      KY LLVEG NL  VM  
Sbjct: 1260 LKKLSSSFFSIQHLNHAIGNVIVSGISTVKRAVINQKTP---GKYNLLVEGTNLLAVMGI 1316

Query: 934  YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
             GV  ++  SN+  E+  +LGIEAARSTIM EI+  M++HGMSID RH ML+ADLMTSKG
Sbjct: 1317 EGVDWMRTKSNHIMEMKDSLGIEAARSTIMNEIQYTMQSHGMSIDTRHLMLLADLMTSKG 1376

Query: 994  EVLG 997
            +VLG
Sbjct: 1377 DVLG 1380



 Score =  113 bits (283), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 51/67 (76%), Positives = 59/67 (88%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV+NSFF+GL+PTEFFFHTMGGREGLVDTAVKTAETGYMQRRL+K+LEDL VQYD +
Sbjct: 874 AKGFVRNSFFTGLSPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLMKALEDLSVQYDST 933

Query: 671 FDAAFYG 677
              +  G
Sbjct: 934 VRDSIGG 940



 Score = 78.2 bits (191), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 63/176 (35%), Positives = 83/176 (47%), Gaps = 27/176 (15%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNET----LDSKEFLQDTSENFVRD 1052
            G+  PV+ KR+ + +   + + SD SL   EI   S++     L+ +  LQ      + D
Sbjct: 958  GSNKPVDFKRVFEHVRNNSPAGSDQSLFPYEITQFSHKVILLYLEERRALQRPGTRAMHD 1017

Query: 1053 --IKKFLEEF-----SKKESVTSHQDKVS------QPL-----REQILSHQDKIGHGRES 1094
              + +F EE      S  +S+ S +DK         PL     R   LS   ++      
Sbjct: 1018 EPVPQFYEELRGFLQSVADSLASMRDKRGLDPYSIGPLDKSDPRSVALSESARLQQSIVD 1077

Query: 1095 NPFPSACKA-----EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
                   K      E C  KY RA IE  TAVGA+ AQSIGEPGTQMTLKTFHFAG
Sbjct: 1078 KVAKYTSKQLEGFRELCVSKYKRATIEAGTAVGAVGAQSIGEPGTQMTLKTFHFAG 1133



 Score = 75.1 bits (183), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 35/65 (53%), Positives = 43/65 (66%), Gaps = 6/65 (9%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA------VPRSEPVPRTLLFD 721
            D  FDA+ YGQTD + GVSECIIMG+PM +GTGL KLLQ         + +   R+ LFD
Sbjct: 1404 DHLFDASLYGQTDSVRGVSECIIMGIPMTIGTGLFKLLQRQAVGSNAVKKKLAQRSFLFD 1463

Query: 722  NPEFH 726
            NP+ H
Sbjct: 1464 NPKLH 1468



 Score = 61.6 bits (148), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 27/51 (52%), Positives = 39/51 (76%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           VLM  KSN++TPRNGE LIAA QDFITG YLL++K+ F +++   ++ + +
Sbjct: 568 VLMGVKSNMITPRNGEPLIAAIQDFITGAYLLSRKDLFLDQSMFTQLCACM 618


>gi|195566972|ref|XP_002107049.1| GD17239 [Drosophila simulans]
 gi|194204446|gb|EDX18022.1| GD17239 [Drosophila simulans]
          Length = 723

 Score =  300 bits (769), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 187/465 (40%), Positives = 264/465 (56%), Gaps = 74/465 (15%)

Query: 1001 PVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEF 1060
            PV+L    D++ A++   +D  L+A+E+       L + EF  +  ++F  D++  +   
Sbjct: 256  PVDLVHQYDNLRAQHPQGTDRPLNAEEMSEALETLLKTPEF-AEARDDFKLDVRNHINTV 314

Query: 1061 SKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATA 1120
            SK+  +   Q +  + +    L HQ +     +   F          ++Y RA  EP TA
Sbjct: 315  SKR--IGQLQKRYEKCIN---LCHQIECLTTEQLLQF-----VRRINDRYNRAVTEPGTA 364

Query: 1121 VGALAAQSIGEPGTQMTLKTFH-------------------------------------- 1142
            VGA+AAQSIGEPGTQMTLKTFH                                      
Sbjct: 365  VGAIAAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIVEIINATKTISTPIITAELENC 424

Query: 1143 ----FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYC 1186
                FA             E+  Y+E V  P   ++ I +DM RI+LL L +D+D+I + 
Sbjct: 425  HSMEFARQVKARIEKTTLAELSSYVEVVCGPYSCYLAIGVDMARIKLLGLHIDLDTIVFS 484

Query: 1187 IERTR---GISGHLTVSGHSFLILKPKDS-SKSFNSKMYQMKQLLPSVVIKGVQGINRAV 1242
            I ++R     +   TV+  S ++++ + + + + N+++ ++   L +VV+ G+  INRAV
Sbjct: 485  ILKSRMRVKPTQVETVASQSRIVVRVEATRTSTINAELARLALCLQNVVVAGLPNINRAV 544

Query: 1243 IHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEI 1302
            I  +D      YKL +EG  LRDV+ATYGV G +  SNN  E+Y+TLGIEAAR+ IM+EI
Sbjct: 545  IAVDDARQPPTYKLCIEGYGLRDVIATYGVVGKRTRSNNICEIYQTLGIEAARTIIMSEI 604

Query: 1303 KLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDA 1362
              VME HGMS+D+RH ML+A  MT++GEVLGITRHGLAKM+ESV NLASFE T+DHLFDA
Sbjct: 605  TEVMEGHGMSVDWRHIMLLASQMTARGEVLGITRHGLAKMRESVFNLASFEKTADHLFDA 664

Query: 1363 AFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ-----AVPRSEP 1402
            A+YGQTD I+GVSE II+G+P  +GTG+ KLLQ      VP  EP
Sbjct: 665  AYYGQTDAINGVSERIILGMPACIGTGIFKLLQLHEDKQVPPIEP 709



 Score =  213 bits (542), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 113/238 (47%), Positives = 164/238 (68%), Gaps = 4/238 (1%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
           GVPRI EIINA++ ISTPIITA L+    +++AR VK R+E+TTL E+  Y+E V  P  
Sbjct: 398 GVPRIVEIINATKTISTPIITAELENCHSMEFARQVKARIEKTTLAELSSYVEVVCGPYS 457

Query: 824 SFILIKLDMDRIRLLHLEVDIDSIRYCIERTR---GISGHLTVSGHSFLILKPKDS-SKS 879
            ++ I +DM RI+LL L +D+D+I + I ++R     +   TV+  S ++++ + + + +
Sbjct: 458 CYLAIGVDMARIKLLGLHIDLDTIVFSILKSRMRVKPTQVETVASQSRIVVRVEATRTST 517

Query: 880 FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
            N+++ ++   L +VV+ G+  INRAVI  +D      YKL +EG  LRDV+ATYGV G 
Sbjct: 518 INAELARLALCLQNVVVAGLPNINRAVIAVDDARQPPTYKLCIEGYGLRDVIATYGVVGK 577

Query: 940 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
           +  SNN  E+Y+TLGIEAAR+ IM+EI  VME HGMS+D+RH ML+A  MT++GEVLG
Sbjct: 578 RTRSNNICEIYQTLGIEAARTIIMSEITEVMEGHGMSVDWRHIMLLASQMTARGEVLG 635



 Score =  115 bits (289), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 64/122 (52%), Positives = 73/122 (59%), Gaps = 14/122 (11%)

Query: 608 VTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           +   +GFVQNSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGY+QRRLVK LEDL V Y
Sbjct: 165 IPAARGFVQNSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYLQRRLVKCLEDLVVHY 224

Query: 668 DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHF 727
           D +   A     D I G             G GL  +     R++PV     +DN     
Sbjct: 225 DGTVRNAVNEMVDTIYG-------------GDGLDPVSMET-RNKPVDLVHQYDNLRAQH 270

Query: 728 PQ 729
           PQ
Sbjct: 271 PQ 272



 Score = 60.1 bits (144), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 30/51 (58%), Positives = 36/51 (70%), Gaps = 5/51 (9%)

Query: 668 DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ-----AVPRSEP 713
           D  FDAA+YGQTD I+GVSE II+G+P  +GTG+ KLLQ      VP  EP
Sbjct: 659 DHLFDAAYYGQTDAINGVSERIILGMPACIGTGIFKLLQLHEDKQVPPIEP 709



 Score = 43.5 bits (101), Expect = 0.87,   Method: Compositional matrix adjust.
 Identities = 16/33 (48%), Positives = 24/33 (72%)

Query: 585 MWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           +W L+ + S++L NRGFS GI DVTP +  +Q+
Sbjct: 18  IWLLNNIASYFLQNRGFSFGISDVTPSKKLLQH 50


>gi|440795844|gb|ELR16958.1| ferrochelatase [Acanthamoeba castellanii str. Neff]
          Length = 472

 Score =  299 bits (765), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 176/385 (45%), Positives = 231/385 (60%), Gaps = 69/385 (17%)

Query: 1093 ESNPFPSACKAEA----CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFH------ 1142
            +S+P  +  K +A    CR+K+ RA+IEP TAVGAL AQSIGEPGTQMTLKTFH      
Sbjct: 66   QSSPATAPTKLDAFLSLCRDKFKRAEIEPGTAVGALGAQSIGEPGTQMTLKTFHFAGVAS 125

Query: 1143 ------------------------------------FA------------GEVCEYIEEV 1154
                                                FA            GEV EYI+EV
Sbjct: 126  MNITLGVPRIKEIINASKNISTPIITAILSQDSDEKFARIVKGRIEKTTLGEVSEYIKEV 185

Query: 1155 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSGHSFLILKPKD 1211
            + P   +I +KLD D IR L LE++  S+   I    RT+  + H++ SG   L + P +
Sbjct: 186  YNPGGCYISVKLDKDAIRALQLEINSASVMRAILNSPRTKIKAEHVSTSGEWKLRVMPIE 245

Query: 1212 SSKSFNSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVM 1267
             S+    +MY     +K LLPSV+I+G+  ++RAVI+++      +Y LLVEG NL  VM
Sbjct: 246  RSRE---QMYFSLQTVKNLLPSVLIRGIPTVSRAVINKKGSGADARYNLLVEGYNLLSVM 302

Query: 1268 ATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTS 1327
            AT GV G + +SN+  EV  TLGIEAAR TIM EI+  M+ HGM+ID RH ML+ADLM  
Sbjct: 303  ATPGVVGSRTTSNHIIEVMTTLGIEAARVTIMNEIQYTMKEHGMNIDTRHVMLLADLMCF 362

Query: 1328 KGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVG 1387
            +GE+LGITRHG+ KM +SV+ LASFE T+DHLF+A+F+ + D I+GVSE IIMG+P+ VG
Sbjct: 363  RGEILGITRHGIDKMNDSVMMLASFEKTTDHLFNASFHARQDTITGVSESIIMGIPIAVG 422

Query: 1388 TGLIKLLQAVPRSEPVP-RTLLFDN 1411
            TGL KLL+  P  +  P R LL D+
Sbjct: 423  TGLFKLLRKTPSLDKEPKRGLLLDS 447



 Score =  233 bits (595), Expect = 5e-58,   Method: Compositional matrix adjust.
 Identities = 128/241 (53%), Positives = 168/241 (69%), Gaps = 10/241 (4%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
           GVPRIKEIINAS+NISTPIITA L +D+D  +ARIVKGR+E+TTLGEV EYI+EV+ P  
Sbjct: 131 GVPRIKEIINASKNISTPIITAILSQDSDEKFARIVKGRIEKTTLGEVSEYIKEVYNPGG 190

Query: 824 SFILIKLDMDRIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSGHSFLILKPKDSSKSF 880
            +I +KLD D IR L LE++  S+   I    RT+  + H++ SG   L + P + S+  
Sbjct: 191 CYISVKLDKDAIRALQLEINSASVMRAILNSPRTKIKAEHVSTSGEWKLRVMPIERSRE- 249

Query: 881 NSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGV 936
             +MY     +K LLPSV+I+G+  ++RAVI+++      +Y LLVEG NL  VMAT GV
Sbjct: 250 --QMYFSLQTVKNLLPSVLIRGIPTVSRAVINKKGSGADARYNLLVEGYNLLSVMATPGV 307

Query: 937 KGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL 996
            G + +SN+  EV  TLGIEAAR TIM EI+  M+ HGM+ID RH ML+ADLM  +GE+L
Sbjct: 308 VGSRTTSNHIIEVMTTLGIEAARVTIMNEIQYTMKEHGMNIDTRHVMLLADLMCFRGEIL 367

Query: 997 G 997
           G
Sbjct: 368 G 368



 Score = 58.9 bits (141), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 29/56 (51%), Positives = 39/56 (69%), Gaps = 1/56 (1%)

Query: 668 DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP-RTLLFDN 722
           D  F+A+F+ + D I+GVSE IIMG+P+ VGTGL KLL+  P  +  P R LL D+
Sbjct: 392 DHLFNASFHARQDTITGVSESIIMGIPIAVGTGLFKLLRKTPSLDKEPKRGLLLDS 447


>gi|449672715|ref|XP_002167919.2| PREDICTED: DNA-directed RNA polymerase III subunit RPC1-like, partial
            [Hydra magnipapillata]
          Length = 848

 Score =  298 bits (762), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 190/461 (41%), Positives = 258/461 (55%), Gaps = 82/461 (17%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P++++RL   +        + SL+ +EIL LS    +    +Q      ++D++ F
Sbjct: 383  GKDKPLDIERLFHHLRCTYPCNHEKSLNTEEILKLSENVYNESISVQKCGSLLIQDLRDF 442

Query: 1057 LEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIE 1116
             ++  K   ++             +LS++    H  E++   +      C ++Y+ A+ E
Sbjct: 443  FKKLVKNLKLSE----------SLLLSNRKGTAHIAETHVIKTI---NECAKRYLHARCE 489

Query: 1117 PATAVGALAAQSIGEPGTQMTLKTFHFAG------------------------------- 1145
            P TAVGAL AQSIGEPGTQMTLKTFHFAG                               
Sbjct: 490  PGTAVGALCAQSIGEPGTQMTLKTFHFAGVATMNITLGVPRIKEIINASKKISTPIITAP 549

Query: 1146 -EVCEYIE----------------------EVFVPDDSFILIKLDMDRIRLLHLEVDIDS 1182
             EV + IE                      EVF PD  ++LIK+D  RI LL LE+D ++
Sbjct: 550  LEVDDDIEYARSVKGRVEKTTLGEVCEYIEEVFTPDACYLLIKIDSQRINLLKLEIDANA 609

Query: 1183 IRY--CIE-RTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQL---LPSVVIKGVQ 1236
            I+Y  CI  + +     +++ G + L + P +++KS  S  Y M+ L   L  V++KG  
Sbjct: 610  IKYALCISPKLKLKPQFVSIHGKNVLTVHPIETAKS--SMYYIMQNLKCQLQHVLVKGYP 667

Query: 1237 GINRAVIHEEDVEGVTK--YKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAA 1294
             + RA+IH +D +  +K  YKLLVEGD+LR VM T G+K  +C+SNNT EV KTLGIEAA
Sbjct: 668  TVTRAIIHLDDEKKGSKNSYKLLVEGDDLRSVMGTRGIKASECTSNNTIEVEKTLGIEAA 727

Query: 1295 RSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFEN 1354
            R TIM EI   M++HGMSID RH ML+ADLMT +GEVLGITR GLAKMKESVL LASFE 
Sbjct: 728  RVTIMNEITYTMKSHGMSIDSRHVMLLADLMTFRGEVLGITRFGLAKMKESVLMLASFER 787

Query: 1355 TSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 1395
            T+DH      +      SGVSECIIMG+PMN+GTG+ KL+Q
Sbjct: 788  TADHXXXXXHFN-----SGVSECIIMGIPMNLGTGMFKLIQ 823



 Score =  254 bits (648), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 138/242 (57%), Positives = 177/242 (73%), Gaps = 10/242 (4%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
           GVPRIKEIINAS+ ISTPIITA L+ D D++YAR VKGR+E+TTLGEVCEYIEEVF PD 
Sbjct: 527 GVPRIKEIINASKKISTPIITAPLEVDDDIEYARSVKGRVEKTTLGEVCEYIEEVFTPDA 586

Query: 824 SFILIKLDMDRIRLLHLEVDIDSIRY--CIE-RTRGISGHLTVSGHSFLILKPKDSSKSF 880
            ++LIK+D  RI LL LE+D ++I+Y  CI  + +     +++ G + L + P +++KS 
Sbjct: 587 CYLLIKIDSQRINLLKLEIDANAIKYALCISPKLKLKPQFVSIHGKNVLTVHPIETAKS- 645

Query: 881 NSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTK--YKLLVEGDNLRDVMATYG 935
            S  Y M+ L   L  V++KG   + RA+IH +D +  +K  YKLLVEGD+LR VM T G
Sbjct: 646 -SMYYIMQNLKCQLQHVLVKGYPTVTRAIIHLDDEKKGSKNSYKLLVEGDDLRSVMGTRG 704

Query: 936 VKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
           +K  +C+SNNT EV KTLGIEAAR TIM EI   M++HGMSID RH ML+ADLMT +GEV
Sbjct: 705 IKASECTSNNTIEVEKTLGIEAARVTIMNEITYTMKSHGMSIDSRHVMLLADLMTFRGEV 764

Query: 996 LG 997
           LG
Sbjct: 765 LG 766



 Score =  159 bits (401), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 68/116 (58%), Positives = 90/116 (77%)

Query: 500 IWTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKST 559
           +WTGKQ+ S++L+PN       NL+TKG+ Y+ +EE C  DSYV+L NS+LLAG++DK+ 
Sbjct: 4   LWTGKQVISVMLRPNNLSSTLVNLRTKGKNYSKDEELCVNDSYVVLHNSDLLAGTLDKNI 63

Query: 560 LGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFV 615
           +GSG K  +FY+LLRDFGE  A  AMWRL+R+T ++LMN GFSIGIGDVTPGQ  +
Sbjct: 64  IGSGSKDTIFYVLLRDFGEQAAADAMWRLARITPWFLMNFGFSIGIGDVTPGQSLI 119



 Score =  113 bits (282), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 51/68 (75%), Positives = 58/68 (85%)

Query: 608 VTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           +   +GFV NSFFSG+TPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVKSLEDL +QY
Sbjct: 296 IPAAKGFVGNSFFSGMTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLSLQY 355

Query: 668 DMSFDAAF 675
           D +  ++ 
Sbjct: 356 DYTVRSSM 363



 Score = 47.4 bits (111), Expect = 0.069,   Method: Compositional matrix adjust.
 Identities = 19/24 (79%), Positives = 23/24 (95%)

Query: 683 SGVSECIIMGLPMNVGTGLIKLLQ 706
           SGVSECIIMG+PMN+GTG+ KL+Q
Sbjct: 800 SGVSECIIMGIPMNLGTGMFKLIQ 823


>gi|20159749|gb|AAM12029.1| RNA polymerase III subunit RPC155-A [Homo sapiens]
          Length = 374

 Score =  295 bits (754), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 145/251 (57%), Positives = 181/251 (72%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD Q  P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNQHAPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYFR VI ILQ ICK  TC  ++L +E+   F   L+ P L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFRAVIGILQMICK--TCCHIMLSQEEKKQFLDYLKRPGLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K ++C HCG  NG VKKCGLLKI HEKYK   K  D IV + L  +  A++ 
Sbjct: 144 KKISDKCRKKNICHHCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPIVSNFLQSFETAIEH 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP ED+PLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NKEVEP--LLGRAQENLNPLVVLNLFKRIPAEDVPLLLMNPEAGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 262 IRPSVVSDLKS 272


>gi|316997015|dbj|BAJ52635.1| RNA polymerase III largest subunit [Ephydatia fluviatilis]
          Length = 899

 Score =  294 bits (753), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 197/490 (40%), Positives = 264/490 (53%), Gaps = 91/490 (18%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   PVE  R+L  I AK   R++  LS  ++  L    L  K   Q  S+ F R +K+F
Sbjct: 408  GQDIPVEFPRVLQHIKAKFPCRNESPLSPSQLEFLCEMIL--KADFQFCSDEFKRGMKEF 465

Query: 1057 LEEFSK--KESVTSH--QDKVSQ----------------PLREQILSHQDKIGHGRESNP 1096
            L++ +K  ++    H  +D  +Q                P +  +L  QD+I   +  N 
Sbjct: 466  LDKVTKILQQGWNRHGLEDPFAQGKEKCGRAGELLSPVDPSKPSVLYEQDRITKTQLEN- 524

Query: 1097 FPSACKAEACREKYVRAQIEP--------ATAVGALAAQ----------------SIGEP 1132
                     C +KY+RA+ EP        A ++G    Q                ++G P
Sbjct: 525  -----FVNVCSDKYMRARTEPGTAVGAICAQSIGEPGTQMTLKTFHFAGVASMNITLGVP 579

Query: 1133 GTQMTLKTF------------------HFA------------GEVCEYIEEVFVPDDSFI 1162
              +  +                      FA            GEV  +IEEV+ PDD +I
Sbjct: 580  RIKEIINASKIISTPIITAPLDVDDDPEFARVVKGRIEKTLLGEVARFIEEVYEPDDCYI 639

Query: 1163 LIKLDMDRIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSGHSFLILKPKDSSKS-FNS 1218
             I LD +RIRLL LE+D  SI   +    + +    ++T+   + + + P D+SKS    
Sbjct: 640  RIVLDTNRIRLLKLEIDAYSIAASLCTAPKLKLKPPNVTIRSEATVHISPPDNSKSSLYY 699

Query: 1219 KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCS 1278
             M  +K  LP+VV+KG+  + RA+IH+++ +   KYKLLVEG NL+ V+ T GVKG    
Sbjct: 700  SMQFLKSQLPNVVVKGITSVTRAIIHKDEGKSGNKYKLLVEGMNLQAVIGTVGVKGPATK 759

Query: 1279 SNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHG 1338
            SN+T EV KTLGIEAAR TI+ EI   M +HGMSID RH ML+ADLMT KGEVLGITR G
Sbjct: 760  SNHTAEVEKTLGIEAARKTIIDEIAYTMSSHGMSIDVRHVMLLADLMTFKGEVLGITRFG 819

Query: 1339 LAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ--- 1395
            LAKM+ESVL LASFE T+DHLFDAAF+GQ D I+GVSECIIMG+PM++GTGL KLL    
Sbjct: 820  LAKMRESVLMLASFEKTADHLFDAAFHGQEDAINGVSECIIMGIPMSIGTGLFKLLHKSA 879

Query: 1396 --AVPRSEPV 1403
              AVPR  P+
Sbjct: 880  KPAVPRKRPL 889



 Score =  241 bits (614), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 131/238 (55%), Positives = 168/238 (70%), Gaps = 4/238 (1%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
           GVPRIKEIINAS+ ISTPIITA LD D D ++AR+VKGR+E+T LGEV  +IEEV+ PDD
Sbjct: 577 GVPRIKEIINASKIISTPIITAPLDVDDDPEFARVVKGRIEKTLLGEVARFIEEVYEPDD 636

Query: 824 SFILIKLDMDRIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSGHSFLILKPKDSSKS- 879
            +I I LD +RIRLL LE+D  SI   +    + +    ++T+   + + + P D+SKS 
Sbjct: 637 CYIRIVLDTNRIRLLKLEIDAYSIAASLCTAPKLKLKPPNVTIRSEATVHISPPDNSKSS 696

Query: 880 FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
               M  +K  LP+VV+KG+  + RA+IH+++ +   KYKLLVEG NL+ V+ T GVKG 
Sbjct: 697 LYYSMQFLKSQLPNVVVKGITSVTRAIIHKDEGKSGNKYKLLVEGMNLQAVIGTVGVKGP 756

Query: 940 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
              SN+T EV KTLGIEAAR TI+ EI   M +HGMSID RH ML+ADLMT KGEVLG
Sbjct: 757 ATKSNHTAEVEKTLGIEAARKTIIDEIAYTMSSHGMSIDVRHVMLLADLMTFKGEVLG 814



 Score =  221 bits (562), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 109/225 (48%), Positives = 147/225 (65%), Gaps = 21/225 (9%)

Query: 391 NVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYL 450
           N+HLPQTEEA+AEA+              VLM  KSNLVTPRNGE LIAA QDFIT  YL
Sbjct: 1   NLHLPQTEEAKAEAV--------------VLMGVKSNLVTPRNGEPLIAAIQDFITASYL 46

Query: 451 LTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLI 510
           LTQK+ FF+RA   ++ ++++     +  I          P    + A +WTGKQ+ SL+
Sbjct: 47  LTQKDVFFDRALFCQVVASMLHGKDTLLKI-------DIPPPAIWKPAKLWTGKQVISLL 99

Query: 511 LKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFY 570
           ++PN++  V  NL+ KG+ YT  E+ C  DS+V++ NS+ + G +DKS LGSG K N+FY
Sbjct: 100 IRPNQNSSVIMNLRAKGKQYTKGEDLCSCDSFVVIYNSQHMCGCLDKSALGSGSKTNIFY 159

Query: 571 ILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFV 615
           ILLRD+GE VA   M RL+R+  ++L NRGFS+GI DVTPG+  +
Sbjct: 160 ILLRDYGEQVAADCMSRLARLCPYFLTNRGFSMGISDVTPGKKLI 204



 Score =  113 bits (283), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 51/63 (80%), Positives = 58/63 (92%), Gaps = 1/63 (1%)

Query: 609 TPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           +PG +GFV+NSFF+GL P EFFFHT+GGREGLVDTAVKTAETGYMQRRLVKSLEDLC  Y
Sbjct: 321 SPGAKGFVENSFFTGLNPAEFFFHTVGGREGLVDTAVKTAETGYMQRRLVKSLEDLCSNY 380

Query: 668 DMS 670
           D++
Sbjct: 381 DLT 383



 Score = 74.3 bits (181), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 34/60 (56%), Positives = 44/60 (73%)

Query: 21 VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFFR 80
          VLM  KSNLVTPRNGE LIAA QDFIT  YLLTQK+ FF+RA   ++ ++++ G+    +
Sbjct: 16 VLMGVKSNLVTPRNGEPLIAAIQDFITASYLLTQKDVFFDRALFCQVVASMLHGKDTLLK 75



 Score = 69.7 bits (169), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 33/52 (63%), Positives = 39/52 (75%), Gaps = 5/52 (9%)

Query: 668 DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ-----AVPRSEPV 714
           D  FDAAF+GQ D I+GVSECIIMG+PM++GTGL KLL      AVPR  P+
Sbjct: 838 DHLFDAAFHGQEDAINGVSECIIMGIPMSIGTGLFKLLHKSAKPAVPRKRPL 889


>gi|326923515|ref|XP_003207981.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC1-like,
           partial [Meleagris gallopavo]
          Length = 429

 Score =  294 bits (752), Expect = 3e-76,   Method: Compositional matrix adjust.
 Identities = 145/251 (57%), Positives = 179/251 (71%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD    P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNHHAPLQYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYF+ VI ILQ ICK  TC R++L  E+   F   L+ P L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFKAVIGILQMICK--TCCRIMLSVEEKKQFLDYLKRPGLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KK+ E  +K + CP+CG  NG VKKCGLLKI HEKYK   K  D IV   L  +  A++ 
Sbjct: 144 KKVSEKCRKKNTCPYCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPIVSTFLQSFETAIEH 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP EDIPLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NKEVEP--LLGRAQENLNPLVVLNLFKRIPAEDIPLLLMNPEAGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 262 IRPSVVSDLKS 272


>gi|432115681|gb|ELK36916.1| DNA-directed RNA polymerase III subunit RPC1 [Myotis davidii]
          Length = 413

 Score =  293 bits (751), Expect = 3e-76,   Method: Compositional matrix adjust.
 Identities = 144/251 (57%), Positives = 180/251 (71%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD    P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNNHAPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYFR VI ILQ ICK  TC  ++L +E+   F   L+ P L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFRAVIGILQMICK--TCCHIMLSQEEKKQFLDYLKRPGLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K ++C HCG  NG VKKCGLLKI HEKYK   K  D IV + L  +  A++ 
Sbjct: 144 KKISDKCRKKNICHHCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPIVSNFLHSFETAIEH 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP ED+PLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NKEVEP--LLGRAQENLNPLVVLNLFKQIPAEDVPLLLMNPEAGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 262 IRPSVVSDLKS 272


>gi|301109379|ref|XP_002903770.1| DNA-directed RNA polymerase III largest subunit [Phytophthora
           infestans T30-4]
 gi|262096773|gb|EEY54825.1| DNA-directed RNA polymerase III largest subunit [Phytophthora
           infestans T30-4]
          Length = 1534

 Score =  291 bits (746), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 145/273 (53%), Positives = 180/273 (65%), Gaps = 25/273 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHK+SIM+HR KV+P RTFRFNECVC+PYNADFDGDEMN+HLPQTEEA
Sbjct: 470 DGDIVLFNRQPSLHKMSIMSHRVKVMPWRTFRFNECVCSPYNADFDGDEMNMHLPQTEEA 529

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EA+               LM  + NL+TPRNGE L+AATQDF+T  YLLTQKN FFNR
Sbjct: 530 RTEAI--------------TLMGVEQNLITPRNGEPLVAATQDFLTASYLLTQKNIFFNR 575

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q  ++ S +      I             P   V    +WTGKQ+ SL++KPN    V 
Sbjct: 576 EQFCQVISIMSDANEHI----------ELPPPAIVLPVRLWTGKQVISLLVKPNAQTKVL 625

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           ANL+ K R YT+N+  C +D YV  RNSEL+ G++ K TLG G K  +FY+L+RD G   
Sbjct: 626 ANLELKERNYTSNKFMCWKDGYVCFRNSELICGNLGKKTLGDGSKQGLFYVLIRDHGSHE 685

Query: 581 AVTAMWRLSRMTSFYLMN-RGFSIGIGDVTPGQ 612
           A   M RL+++ + +L N +GFSIGI DVTP +
Sbjct: 686 AARCMNRLAKLCARWLGNFKGFSIGIDDVTPSE 718



 Score =  249 bits (636), Expect = 7e-63,   Method: Compositional matrix adjust.
 Identities = 156/369 (42%), Positives = 204/369 (55%), Gaps = 78/369 (21%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGE---------------------- 1146
            KY RA +EP  AVGA+ AQSI EPGTQMTLKTFHFAG                       
Sbjct: 1155 KYNRAGMEPGEAVGAVGAQSISEPGTQMTLKTFHFAGVASMNVTLGVPRLKEIINASKII 1214

Query: 1147 ---------VCE-----------------------YIEEVFVPDDSFILIKLDMDRIRLL 1174
                     VC+                       +I+EVF  D +++ +KLD+  I  L
Sbjct: 1215 STPIITAALVCKTDERSARIVKGRIEKTTLGEIAVHIKEVFARDQAYLSVKLDLTAIEQL 1274

Query: 1175 HLEVDIDSIRYCIERTRGISG----HLTVSGHSFL---------ILKP------KDSSKS 1215
            HL +   S+R  I    G+       L    H  L         +L P      K  ++ 
Sbjct: 1275 HLNITARSVRNSILNAVGVGPRAVLRLLKEQHVLLNARCPDKLRLLAPPNYKGAKGETRG 1334

Query: 1216 FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYK---LLVEGDNLRDVMATYGV 1272
                +  +K  LP V+++G+  +NRAVI+ E+V+  +  K   LLVEG  L +VM   GV
Sbjct: 1335 AYFALQALKAELPGVIVQGIPTVNRAVINYEEVQDSSAAKSLHLLVEGYGLAEVMGIPGV 1394

Query: 1273 KGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL 1332
             G+  +SN+  EV KTLGIEAAR  I +E+  +M  +G+ ID RH ML++D+MT KGEVL
Sbjct: 1395 DGLHTTSNHIIEVEKTLGIEAARELISSEVNYIMSAYGIGIDRRHLMLLSDIMTFKGEVL 1454

Query: 1333 GITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIK 1392
            GITR G+AKMKESVL LASFE T+DHLFDAA + +TD I GVSECIIMG+P+ +GTG+ K
Sbjct: 1455 GITRFGIAKMKESVLMLASFEKTTDHLFDAAVHSRTDAIVGVSECIIMGIPIPLGTGIFK 1514

Query: 1393 LLQAV--PR 1399
            LL+ V  PR
Sbjct: 1515 LLRQVDKPR 1523



 Score =  194 bits (494), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 109/245 (44%), Positives = 148/245 (60%), Gaps = 8/245 (3%)

Query: 95  QQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLP 154
           + S +++ SK+L+ +   R P  +G+LD+R+G + K+  C TC   L+DCVGHFGYI L 
Sbjct: 45  RMSELRVQSKDLF-KVQTREPQGNGVLDKRLGVSNKKDTCETCHLKLADCVGHFGYIKLE 103

Query: 155 LPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKIL 214
           LPVFHIGYF+ +  ILQ+ICK   C+RVLL   +   F  ++R+P    L    L+KKI 
Sbjct: 104 LPVFHIGYFKAITEILQNICK--CCSRVLLPPTERELFLRRMRDPKADVLRLVGLRKKIA 161

Query: 215 ETTKKVSVCPHCGEINGVVKK--CGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNP 272
              KK   CPHC  ING V+K     LK+ HEKY  R K    +    +A++ EA   NP
Sbjct: 162 TLCKKTVKCPHCDAINGTVRKITSTTLKLVHEKY--RAKATHDLRNVFVAQFAEAQANNP 219

Query: 273 EIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRP 332
           EI AH      + L+PL V QLF+ IP +D  LL ++A+  +P  L+L  +LVPP CIRP
Sbjct: 220 EIGAHLPKAQ-EDLSPLVVQQLFKEIPDQDCELLWVDADGGRPEKLLLNSVLVPPVCIRP 278

Query: 333 SVISD 337
           SV  D
Sbjct: 279 SVAMD 283



 Score =  187 bits (474), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 113/256 (44%), Positives = 154/256 (60%), Gaps = 22/256 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPR+KEIINAS+ ISTPIITA L   TD   ARIVKGR+E+TTLGE+  +I+EVF  D 
Sbjct: 1200 GVPRLKEIINASKIISTPIITAALVCKTDERSARIVKGRIEKTTLGEIAVHIKEVFARDQ 1259

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISG----HLTVSGHSFL---------I 870
            +++ +KLD+  I  LHL +   S+R  I    G+       L    H  L         +
Sbjct: 1260 AYLSVKLDLTAIEQLHLNITARSVRNSILNAVGVGPRAVLRLLKEQHVLLNARCPDKLRL 1319

Query: 871  LKP------KDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYK---LL 921
            L P      K  ++     +  +K  LP V+++G+  +NRAVI+ E+V+  +  K   LL
Sbjct: 1320 LAPPNYKGAKGETRGAYFALQALKAELPGVIVQGIPTVNRAVINYEEVQDSSAAKSLHLL 1379

Query: 922  VEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRH 981
            VEG  L +VM   GV G+  +SN+  EV KTLGIEAAR  I +E+  +M  +G+ ID RH
Sbjct: 1380 VEGYGLAEVMGIPGVDGLHTTSNHIIEVEKTLGIEAARELISSEVNYIMSAYGIGIDRRH 1439

Query: 982  PMLVADLMTSKGEVLG 997
             ML++D+MT KGEVLG
Sbjct: 1440 LMLLSDIMTFKGEVLG 1455



 Score =  106 bits (265), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 48/60 (80%), Positives = 53/60 (88%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLT TEFFFHTMGGREGLVDTAVKTAETGYM RRL+K+LEDL  QYD +
Sbjct: 841 AKGFVANSFYSGLTATEFFFHTMGGREGLVDTAVKTAETGYMARRLMKALEDLSCQYDQT 900



 Score = 68.9 bits (167), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 31/50 (62%), Positives = 38/50 (76%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM  + NL+TPRNGE L+AATQDF+T  YLLTQKN FFNR Q  ++ S +
Sbjct: 536 LMGVEQNLITPRNGEPLVAATQDFLTASYLLTQKNIFFNREQFCQVISIM 585



 Score = 56.2 bits (134), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 27/45 (60%), Positives = 34/45 (75%), Gaps = 2/45 (4%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV--PR 710
            D  FDAA + +TD I GVSECIIMG+P+ +GTG+ KLL+ V  PR
Sbjct: 1479 DHLFDAAVHSRTDAIVGVSECIIMGIPIPLGTGIFKLLRQVDKPR 1523


>gi|302409260|ref|XP_003002464.1| DNA-directed RNA polymerase III subunit RPC1 [Verticillium
           albo-atrum VaMs.102]
 gi|261358497|gb|EEY20925.1| DNA-directed RNA polymerase III subunit RPC1 [Verticillium
           albo-atrum VaMs.102]
          Length = 1456

 Score =  291 bits (746), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 149/293 (50%), Positives = 188/293 (64%), Gaps = 37/293 (12%)

Query: 331 RPSVISDLK---------SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPY 381
           R  V  DLK          DND+VLFNRQPSLHKLSIM+H  KV P RTFR NECVCTPY
Sbjct: 447 RGQVARDLKVGDVVERHIEDNDIVLFNRQPSLHKLSIMSHLVKVRPWRTFRLNECVCTPY 506

Query: 382 NADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAAT 441
           NADFDGDEMN+H+PQTEEARAEA+               LM  K NL TP+NGE +IAAT
Sbjct: 507 NADFDGDEMNLHVPQTEEARAEAIN--------------LMGVKHNLATPKNGEPIIAAT 552

Query: 442 QDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIW 501
           QDFIT  YLL+ K+ FF+R     I   ++   + +             P   ++   +W
Sbjct: 553 QDFITAAYLLSGKDRFFDRKTFTYIVMHMMDGITHL----------DLPPPAILKPQALW 602

Query: 502 TGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFC----HRDSYVILRNSELLAGSMDK 557
           TGKQ+FS++L+PN++C V  NL  K R Y A    C      D+++++RNSE++ G MDK
Sbjct: 603 TGKQVFSMMLRPNKECQVKINLDAKCREYKAKPGQCPDMDPEDAWLVIRNSEVMCGRMDK 662

Query: 558 STLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           ST+G G K +VFY++LRDFG D AVTAM RL+++ +  L NRGFSIG+GDV P
Sbjct: 663 STVGGGKKDSVFYVILRDFGPDEAVTAMNRLAKLCARQLTNRGFSIGVGDVFP 715



 Score =  211 bits (537), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 149/379 (39%), Positives = 193/379 (50%), Gaps = 78/379 (20%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGE------------------- 1146
            C EKY +A +EP  AVGA+ AQSIGEPGTQMTLKTFHFAG                    
Sbjct: 1067 CLEKYKKAHVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIINAS 1126

Query: 1147 -----------------------VCEYIEEVFVPD------DSF------ILIKLDMDRI 1171
                                   V   IE+ +V D      D +      +++++DMD +
Sbjct: 1127 KLISTPVIKCPLVQNKEMRAARIVKARIEKTYVSDILSYIEDEWMANAGNVVLQIDMDAL 1186

Query: 1172 RLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSFLI------------LKPKDSSKSF 1216
              + L + I  +   I R R +    G L +      I             K K S +  
Sbjct: 1187 SDMQLGIGIHDVAEAICRHRKLKVQRGDLHIGQSRIEIRVRVDENAAAKRTKAKGSEEQA 1246

Query: 1217 N--SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 1274
            +   +   +++L+P V I G     RA+I   + +    + +LVEG  LR  M T GV G
Sbjct: 1247 DLLVRANYLRRLVPFVAISGYPDATRAIIQTSEHD---THTVLVEGYGLRACMNTEGVDG 1303

Query: 1275 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGI 1334
             K S+NN  E    LGIEAARSTI  EI  VM +  M ID RH  L+AD+MT KGEVLGI
Sbjct: 1304 TKTSTNNVMEARDILGIEAARSTIAHEIGEVMGD--MDIDPRHMQLLADVMTYKGEVLGI 1361

Query: 1335 TRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            TR GL+KM++SVL LASFE T DHLFDAA   +TD I GVSECIIMG  M VGTG   ++
Sbjct: 1362 TRFGLSKMRDSVLQLASFEKTPDHLFDAAAGMKTDKIEGVSECIIMGQTMTVGTGAFHVV 1421

Query: 1395 Q--AVPRSEPVPRTLLFDN 1411
            +  A+   +   R  LF++
Sbjct: 1422 RRLALQSGDISERPALFED 1440



 Score =  194 bits (494), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 112/285 (39%), Positives = 160/285 (56%), Gaps = 14/285 (4%)

Query: 67  IASTLIAGRKVFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMG 126
           + S L+      F+G+  G  + +D +  Q+ +++  + LY  D  R P  HG LD R+G
Sbjct: 9   VKSQLVDNLPKRFQGIKFGIQSNQD-IANQAVLEVSDRLLYDVDNNRAPFQHGPLDPRLG 67

Query: 127 TNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGE 186
           T+ K   C TC ++L +C GHFG++ LPLP FHIGY   V  ILQ ICK+  C+R+LL E
Sbjct: 68  TSSKIGKCDTCQESLQNCTGHFGHVRLPLPAFHIGYLGFVRTILQDICKD--CSRILLTE 125

Query: 187 EKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKY 246
            +   F  +LR P +  L R  + KKI E  +K   C +CG ING ++K G+LK+ H+K+
Sbjct: 126 PERRAFLKELRRPFIDNLRRTQICKKINEQCRKTKTCHYCGSINGQIRKVGVLKLVHDKF 185

Query: 247 ----KNRTKKK----DAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAI 298
               K+ + KK      IV D  A ++EA K NP+++ H +  + + LNPL VL LF+ I
Sbjct: 186 VAYNKSTSMKKVPPESKIVFD--ASFDEAKKQNPDLDKHLRKAM-EDLNPLRVLNLFKTI 242

Query: 299 PLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
              D  LL ++    +P   I   L  PP CIRPSV  D  S  D
Sbjct: 243 SPTDCELLGLDPVEGRPEMFIWQFLPAPPVCIRPSVAQDNASTED 287



 Score =  146 bits (368), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 102/275 (37%), Positives = 148/275 (53%), Gaps = 23/275 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+I   L ++ ++  ARIVK R+E+T + ++  YIE+ ++ + 
Sbjct: 1115 GVPRIKEIINASKLISTPVIKCPLVQNKEMRAARIVKARIEKTYVSDILSYIEDEWMANA 1174

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSFLI---------- 870
              +++++DMD +  + L + I  +   I R R +    G L +      I          
Sbjct: 1175 GNVVLQIDMDALSDMQLGIGIHDVAEAICRHRKLKVQRGDLHIGQSRIEIRVRVDENAAA 1234

Query: 871  --LKPKDSSKSFN--SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDN 926
               K K S +  +   +   +++L+P V I G     RA+I   + +    + +LVEG  
Sbjct: 1235 KRTKAKGSEEQADLLVRANYLRRLVPFVAISGYPDATRAIIQTSEHD---THTVLVEGYG 1291

Query: 927  LRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVA 986
            LR  M T GV G K S+NN  E    LGIEAARSTI  EI  VM +  M ID RH  L+A
Sbjct: 1292 LRACMNTEGVDGTKTSTNNVMEARDILGIEAARSTIAHEIGEVMGD--MDIDPRHMQLLA 1349

Query: 987  DLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDP 1021
            D+MT KGEVLG  T   L ++ D ++   S    P
Sbjct: 1350 DVMTYKGEVLGI-TRFGLSKMRDSVLQLASFEKTP 1383



 Score =  102 bits (253), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 46/59 (77%), Positives = 50/59 (84%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV NSF+SGL PTEF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL  +YD
Sbjct: 839 PSKGFVGNSFYSGLLPTEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSTRYD 897



 Score = 58.5 bits (140), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 28/53 (52%), Positives = 35/53 (66%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           LM  K NL TP+NGE +IAATQDFIT  YLL+ K+ FF+R     I   ++ G
Sbjct: 532 LMGVKHNLATPKNGEPIIAATQDFITAAYLLSGKDRFFDRKTFTYIVMHMMDG 584



 Score = 44.7 bits (104), Expect = 0.37,   Method: Compositional matrix adjust.
 Identities = 26/57 (45%), Positives = 34/57 (59%), Gaps = 2/57 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ--AVPRSEPVPRTLLFDN 722
            D  FDAA   +TD I GVSECIIMG  M VGTG   +++  A+   +   R  LF++
Sbjct: 1384 DHLFDAAAGMKTDKIEGVSECIIMGQTMTVGTGAFHVVRRLALQSGDISERPALFED 1440


>gi|346972060|gb|EGY15512.1| DNA-directed RNA polymerase III subunit RPC1 [Verticillium dahliae
           VdLs.17]
          Length = 1456

 Score =  291 bits (745), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 144/274 (52%), Positives = 183/274 (66%), Gaps = 28/274 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND+VLFNRQPSLHKLSIM+H  KV P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 466 DNDIVLFNRQPSLHKLSIMSHLVKVRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 525

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K NL TP+NGE +IAATQDFIT  YLL+ K+ FF+R
Sbjct: 526 RAEAIN--------------LMGVKHNLATPKNGEPIIAATQDFITAAYLLSGKDRFFDR 571

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                I   ++   + +             P   ++   +WTGKQ+FS++L+PN++C V 
Sbjct: 572 KTFTYIVMHMMDGITHL----------DLPPPAILKPQALWTGKQVFSMMLRPNKECQVK 621

Query: 521 ANLKTKGRAYTANEEFC----HRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL  K R Y A    C      D+++++RNSE++ G MDKST+G G K +VFY++LRDF
Sbjct: 622 INLDAKCREYKAKPGQCPDMDPEDAWLVIRNSEVMCGRMDKSTVGGGKKDSVFYVILRDF 681

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           G D AVTAM RL+++ +  L NRGFSIG+GDV P
Sbjct: 682 GPDEAVTAMNRLAKLCARQLTNRGFSIGVGDVFP 715



 Score =  211 bits (537), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 149/379 (39%), Positives = 193/379 (50%), Gaps = 78/379 (20%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGE------------------- 1146
            C EKY +A +EP  AVGA+ AQSIGEPGTQMTLKTFHFAG                    
Sbjct: 1067 CLEKYKKAHVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIINAS 1126

Query: 1147 -----------------------VCEYIEEVFVPD------DSF------ILIKLDMDRI 1171
                                   V   IE+ +V D      D +      +++++DMD +
Sbjct: 1127 KLISTPVIKCPLVQNKEMRAARIVKARIEKTYVSDILSYIEDEWMANAGNVVLQIDMDAL 1186

Query: 1172 RLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSFLI------------LKPKDSSKSF 1216
              + L + I  +   I R R +    G L +      I             K K S +  
Sbjct: 1187 SDMQLGIGIHDVAEAICRHRKLKVQRGDLHIGQSRIEIRVRVDENAAAKRTKAKGSEEQA 1246

Query: 1217 N--SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 1274
            +   +   +++L+P V I G     RA+I   + +    + +LVEG  LR  M T GV G
Sbjct: 1247 DLLVRANYLRRLVPFVAISGYPDATRAIIQTSEHD---THTVLVEGYGLRACMNTEGVDG 1303

Query: 1275 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGI 1334
             K S+NN  E    LGIEAARSTI  EI  VM +  M ID RH  L+AD+MT KGEVLGI
Sbjct: 1304 TKTSTNNVMEARDILGIEAARSTIAHEIGEVMGD--MDIDPRHMQLLADVMTYKGEVLGI 1361

Query: 1335 TRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            TR GL+KM++SVL LASFE T DHLFDAA   +TD I GVSECIIMG  M VGTG   ++
Sbjct: 1362 TRFGLSKMRDSVLQLASFEKTPDHLFDAAAGMKTDKIEGVSECIIMGQTMTVGTGAFHVV 1421

Query: 1395 Q--AVPRSEPVPRTLLFDN 1411
            +  A+   +   R  LF++
Sbjct: 1422 RRLALQSGDISERPALFED 1440



 Score =  194 bits (494), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 110/283 (38%), Positives = 156/283 (55%), Gaps = 10/283 (3%)

Query: 67  IASTLIAGRKVFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMG 126
           + S L+      F+G+  G  + +D +  Q+ +++  + LY  D  R P  HG LD R+G
Sbjct: 9   VKSQLVDNLPKRFQGIKFGIQSNQD-IANQAVLEVSDRLLYDVDNNRAPFQHGPLDPRLG 67

Query: 127 TNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGE 186
           T+ K   C TC ++L +C GHFG++ LPLP FHIGY   V  ILQ ICK+  C+R+LL E
Sbjct: 68  TSSKIGKCDTCQESLQNCTGHFGHVRLPLPAFHIGYLGFVRTILQDICKD--CSRILLTE 125

Query: 187 EKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEK- 245
            +   F  +LR P +  L R  + KKI E  +K   C +CG ING ++K G+LK+ H+K 
Sbjct: 126 PERRAFLKELRRPFIDNLRRTQICKKINEQCRKTKTCHYCGSINGQIRKVGVLKLVHDKF 185

Query: 246 --YKNRTKKKDAIVEDLL---AEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPL 300
             Y   T  K    E  +   A ++EA K NP+++ H +  + + LNPL VL LF+ I  
Sbjct: 186 VAYNKSTSMKKVPPESKIAFDASFDEAKKQNPDLDKHLRKAM-EDLNPLRVLNLFKTISP 244

Query: 301 EDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
            D  LL ++    +P   I   L  PP CIRPSV  D  S  D
Sbjct: 245 TDCELLGLDPVEGRPEMFIWQFLPAPPVCIRPSVAQDNASTED 287



 Score =  146 bits (368), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 102/275 (37%), Positives = 148/275 (53%), Gaps = 23/275 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+I   L ++ ++  ARIVK R+E+T + ++  YIE+ ++ + 
Sbjct: 1115 GVPRIKEIINASKLISTPVIKCPLVQNKEMRAARIVKARIEKTYVSDILSYIEDEWMANA 1174

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSFLI---------- 870
              +++++DMD +  + L + I  +   I R R +    G L +      I          
Sbjct: 1175 GNVVLQIDMDALSDMQLGIGIHDVAEAICRHRKLKVQRGDLHIGQSRIEIRVRVDENAAA 1234

Query: 871  --LKPKDSSKSFN--SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDN 926
               K K S +  +   +   +++L+P V I G     RA+I   + +    + +LVEG  
Sbjct: 1235 KRTKAKGSEEQADLLVRANYLRRLVPFVAISGYPDATRAIIQTSEHD---THTVLVEGYG 1291

Query: 927  LRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVA 986
            LR  M T GV G K S+NN  E    LGIEAARSTI  EI  VM +  M ID RH  L+A
Sbjct: 1292 LRACMNTEGVDGTKTSTNNVMEARDILGIEAARSTIAHEIGEVMGD--MDIDPRHMQLLA 1349

Query: 987  DLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDP 1021
            D+MT KGEVLG  T   L ++ D ++   S    P
Sbjct: 1350 DVMTYKGEVLGI-TRFGLSKMRDSVLQLASFEKTP 1383



 Score =  102 bits (253), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 46/59 (77%), Positives = 50/59 (84%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV NSF+SGL PTEF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL  +YD
Sbjct: 839 PSKGFVGNSFYSGLLPTEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSTRYD 897



 Score = 58.5 bits (140), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 28/53 (52%), Positives = 35/53 (66%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           LM  K NL TP+NGE +IAATQDFIT  YLL+ K+ FF+R     I   ++ G
Sbjct: 532 LMGVKHNLATPKNGEPIIAATQDFITAAYLLSGKDRFFDRKTFTYIVMHMMDG 584



 Score = 44.7 bits (104), Expect = 0.36,   Method: Compositional matrix adjust.
 Identities = 26/57 (45%), Positives = 34/57 (59%), Gaps = 2/57 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ--AVPRSEPVPRTLLFDN 722
            D  FDAA   +TD I GVSECIIMG  M VGTG   +++  A+   +   R  LF++
Sbjct: 1384 DHLFDAAAGMKTDKIEGVSECIIMGQTMTVGTGAFHVVRRLALQSGDISERPALFED 1440


>gi|31544947|gb|AAH53071.1| Polr3a protein [Mus musculus]
          Length = 649

 Score =  290 bits (743), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 144/251 (57%), Positives = 179/251 (71%), Gaps = 5/251 (1%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + ++QQ+HIQ+VSKNLY QD    P+ +G+LD RMGT++K+  C TCG+NL+DC+GH+GY
Sbjct: 26  EEMRQQAHIQVVSKNLYSQDNNHAPLLYGVLDHRMGTSEKDRPCETCGKNLADCLGHYGY 85

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL LP FH+GYFR VI ILQ ICK  TC  ++L +E+   F   L+ P L+YL ++ LK
Sbjct: 86  IDLELPCFHVGYFRAVIGILQMICK--TCCHIMLSQEEKQQFLDFLKRPGLTYLQKRGLK 143

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           KKI +  +K S C +CG  NG VKKCGLLKI HEKYK   K  D IV + L  +  A++ 
Sbjct: 144 KKISDKCRKKSTCHYCGAFNGTVKKCGLLKIIHEKYKTNKKVVDPIVSNFLQSFETAIEH 203

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           N E+E     G  Q  LNPL VL LF+ IP ED+PLLLMN E  KPSDLILTRLLVPP C
Sbjct: 204 NKEVEP--LLGRAQENLNPLVVLNLFKRIPAEDVPLLLMNPESGKPSDLILTRLLVPPLC 261

Query: 330 IRPSVISDLKS 340
           IRPSV+SDLKS
Sbjct: 262 IRPSVVSDLKS 272



 Score =  234 bits (598), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 117/202 (57%), Positives = 141/202 (69%), Gaps = 22/202 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH A+V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 456 DGDVVLFNRQPSLHKLSIMAHLARVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+R
Sbjct: 516 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I ++++    +   +          P   ++   +WTGKQIFS+IL+P+ D PV 
Sbjct: 562 AKACQIIASILVGKDEKIKV-------RLPPPTILKPVTLWTGKQIFSVILRPSDDNPVR 614

Query: 521 ANLKTKGRAYTAN-EEFCHRDS 541
           ANL+TKG+ Y    E+ C  DS
Sbjct: 615 ANLRTKGKQYCGKGEDLCVNDS 636



 Score = 74.7 bits (182), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 44/55 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM  K+NLVTPRNGE LIAA QDF+TG YLLT K+ FF+RA+  +I ++++ G+
Sbjct: 521 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGK 575


>gi|190347890|gb|EDK40245.2| DNA-directed RNA polymerase III largest subunit [Meyerozyma
           guilliermondii ATCC 6260]
          Length = 1379

 Score =  290 bits (742), Expect = 4e-75,   Method: Compositional matrix adjust.
 Identities = 145/276 (52%), Positives = 192/276 (69%), Gaps = 29/276 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH+LSI++H AK+ P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 395 DGDVVLFNRQPSLHRLSILSHYAKIRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 454

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL+TP++GE +IAATQDFITG YL++ K++F++R
Sbjct: 455 RAEAIN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFYDR 500

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A  +++ S +++D            +    P +F +  ++WTGKQ+FSL++KPN++  V 
Sbjct: 501 ATFIQLLS-MMSDAD--------LQFDLPPPTIF-KPVMLWTGKQVFSLLMKPNKNSNVI 550

Query: 521 ANLKTKGRAYTA-----NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL  K +A+T        E    D YVI+R S++L+G MDKSTLG G K +VFY +LRD
Sbjct: 551 VNLDAKNKAFTPPAPGYPNEMSPNDGYVIIRGSQVLSGVMDKSTLGDGKKHSVFYTILRD 610

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           FG D A  AM R++++ + YL NRGFSIGI DVTPG
Sbjct: 611 FGPDAAAEAMNRMAKLCARYLGNRGFSIGINDVTPG 646



 Score =  259 bits (663), Expect = 5e-66,   Method: Compositional matrix adjust.
 Identities = 168/450 (37%), Positives = 242/450 (53%), Gaps = 97/450 (21%)

Query: 1037 DSKEFL--QDTSENFVRDIKKFLEEFSKK----------ESVTSHQDKVSQPLREQILSH 1084
            DS+EF+   D    F + I++F+ E + +          +S  S       P++   ++ 
Sbjct: 916  DSEEFIDQNDAERAFYKSIREFVSEKASQLAEIRQSKNLKSGWSRPASKDDPVQLNAVNQ 975

Query: 1085 QDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFA 1144
              KI   +  N F      + C  KY RA++EP TAVGA+ AQSIGEPGTQMTLKTFHFA
Sbjct: 976  LSKISL-KAINKF-----LDQCIYKYSRAKVEPGTAVGAIGAQSIGEPGTQMTLKTFHFA 1029

Query: 1145 GEVC----------------------EYIEEVFVPDD----------------------- 1159
            G                           I  V V DD                       
Sbjct: 1030 GVASMNVTLGVPRIKEIINASKVISTPIINGVLVNDDDEIAARVVKGRIEKTLLEDVAFF 1089

Query: 1160 ---------SFILIKLDMDRIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSGHSFLIL 1207
                     +++ +K+D+D I  L LE+ I+SI + I    + + ++  ++++G   + +
Sbjct: 1090 IEDVYKDNLAYLSVKIDLDTIEKLQLELTIESIAHAIVTAPKLKIVASDVSIAGRDRINV 1149

Query: 1208 -------------------KPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDV 1248
                               +  DS+ S   +M Q+K+ LPSV IKG+  I+RAVI+ +D 
Sbjct: 1150 LVTLRETKADLLKNMADDYRASDSTNSLFFRMQQLKRALPSVCIKGLPEISRAVINIKD- 1208

Query: 1249 EGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMEN 1308
                K +LLVEG  L+ VM+T G+ G K ++N+  EV++ LGIEAAR++I+ EI   M  
Sbjct: 1209 --NGKKELLVEGYGLKQVMSTDGIIGTKTTTNHVLEVFEVLGIEAARASIIGEIDYTMSK 1266

Query: 1309 HGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQT 1368
            HGMS+D RH  L+ D+M+ KGEVLGITR GL+KM++SVL LASFE T+DHLFDAAFY + 
Sbjct: 1267 HGMSVDPRHIQLLGDVMSYKGEVLGITRFGLSKMRDSVLQLASFEKTTDHLFDAAFYMKK 1326

Query: 1369 DCISGVSECIIMGLPMNVGTGLIKLLQAVP 1398
            D I GVSECII+G  M++GTG  +L+++ P
Sbjct: 1327 DQIEGVSECIILGQTMSIGTGAFQLVKSSP 1356



 Score =  186 bits (472), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 108/256 (42%), Positives = 161/256 (62%), Gaps = 25/256 (9%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII   L  D D   AR+VKGR+E+T L +V  +IE+V+  + 
Sbjct: 1039 GVPRIKEIINASKVISTPIINGVLVNDDDEIAARVVKGRIEKTLLEDVAFFIEDVYKDNL 1098

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSGHSFLIL--------- 871
            +++ +K+D+D I  L LE+ I+SI + I    + + ++  ++++G   + +         
Sbjct: 1099 AYLSVKIDLDTIEKLQLELTIESIAHAIVTAPKLKIVASDVSIAGRDRINVLVTLRETKA 1158

Query: 872  ----------KPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLL 921
                      +  DS+ S   +M Q+K+ LPSV IKG+  I+RAVI+ +D     K +LL
Sbjct: 1159 DLLKNMADDYRASDSTNSLFFRMQQLKRALPSVCIKGLPEISRAVINIKD---NGKKELL 1215

Query: 922  VEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRH 981
            VEG  L+ VM+T G+ G K ++N+  EV++ LGIEAAR++I+ EI   M  HGMS+D RH
Sbjct: 1216 VEGYGLKQVMSTDGIIGTKTTTNHVLEVFEVLGIEAARASIIGEIDYTMSKHGMSVDPRH 1275

Query: 982  PMLVADLMTSKGEVLG 997
              L+ D+M+ KGEVLG
Sbjct: 1276 IQLLGDVMSYKGEVLG 1291



 Score =  134 bits (337), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 83/203 (40%), Positives = 110/203 (54%), Gaps = 10/203 (4%)

Query: 148 FGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRK 207
            G+I L LPVFH+GYFR VI++LQ ICK  +C+ VLL EE    F   LR P +  L R 
Sbjct: 11  LGHIRLALPVFHVGYFRAVISVLQCICK--SCSAVLLDEETKRKFLNDLRRPGIDNLRRM 68

Query: 208 SLKKKILETTKKVSVCPHCGEINGVVKKC------GLLKISHEKYKNRTKKKDAIVEDLL 261
              KK+++  KK   C  C  INGVVKK         LKI H+ ++   KK     +   
Sbjct: 69  KTLKKVVDQCKKQRRCLRCYHINGVVKKAASGSGPAALKIVHDTFRWVGKKSAPEKDAWD 128

Query: 262 AEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL-SKPSDLIL 320
            E++E    NPE+E   K  +   LNPL+VL LF+ I  +D  L  ++A    +P   I 
Sbjct: 129 QEFDEVFARNPEVEKFAK-RVHDDLNPLKVLNLFKQITPQDCELFGIDASRGGRPEMYIW 187

Query: 321 TRLLVPPNCIRPSVISDLKSDND 343
             L  PP CIRPSV+ D +S+ D
Sbjct: 188 RYLPAPPVCIRPSVMMDAQSNED 210



 Score =  101 bits (251), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 47/61 (77%), Positives = 52/61 (85%), Gaps = 1/61 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV+NSFFSGL+P EF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QY
Sbjct: 767 TPQSKGFVRNSFFSGLSPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSAQY 826

Query: 668 D 668
           D
Sbjct: 827 D 827



 Score = 61.6 bits (148), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 26/50 (52%), Positives = 41/50 (82%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM  K+NL+TP++GE +IAATQDFITG YL++ K++F++RA  +++ S +
Sbjct: 461 LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFYDRATFIQLLSMM 510



 Score = 52.4 bits (124), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 23/42 (54%), Positives = 31/42 (73%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 709
            D  FDAAFY + D I GVSECII+G  M++GTG  +L+++ P
Sbjct: 1315 DHLFDAAFYMKKDQIEGVSECIILGQTMSIGTGAFQLVKSSP 1356


>gi|429851154|gb|ELA26368.1| DNA-directed RNA polymerase iii largest [Colletotrichum
           gloeosporioides Nara gc5]
          Length = 1456

 Score =  290 bits (741), Expect = 5e-75,   Method: Compositional matrix adjust.
 Identities = 148/295 (50%), Positives = 186/295 (63%), Gaps = 37/295 (12%)

Query: 331 RPSVISDLK---------SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPY 381
           R  V  DLK          DND+VLFNRQPSLHKLSIM+H  KV P RTFR NECVC PY
Sbjct: 448 RNQVAQDLKIGDVVERHLEDNDIVLFNRQPSLHKLSIMSHLVKVRPWRTFRLNECVCGPY 507

Query: 382 NADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAAT 441
           NADFDGDEMN+H+PQTEEARAEA+               LM  K NL TP+NGE +IAAT
Sbjct: 508 NADFDGDEMNLHVPQTEEARAEAIN--------------LMGVKHNLATPKNGEPVIAAT 553

Query: 442 QDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIW 501
           QDFIT  YLL+ K+ FF+R     I   ++     +             P   ++   +W
Sbjct: 554 QDFITAAYLLSGKDRFFDRKTFTYICMHMMDGNVHL----------DLPPPAILKPQALW 603

Query: 502 TGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFC----HRDSYVILRNSELLAGSMDK 557
           TGKQ+FS++++PN+D PV  NL  K R Y A    C      D ++++RNSE++ G MDK
Sbjct: 604 TGKQVFSIMMRPNKDSPVKVNLDAKCREYKARPGQCPDMDPNDGWLVVRNSEVMCGRMDK 663

Query: 558 STLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
           ST+GSG K +VFY++LRDFG D AV  M RL+++ + +L NRGFSIG+GDV P Q
Sbjct: 664 STVGSGKKDSVFYVILRDFGPDAAVVTMNRLAKLCARHLTNRGFSIGVGDVFPTQ 718



 Score =  205 bits (521), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 137/362 (37%), Positives = 188/362 (51%), Gaps = 77/362 (21%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCE-- 1149
            C EKY +A +EP  AVGA+ AQSIGEPGTQMTLKTFHFAG              E+    
Sbjct: 1066 CLEKYKKAHVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIINAS 1125

Query: 1150 -------------------------------YIEEV--FVPDDSF-----ILIKLDMDRI 1171
                                           Y+E++  ++ D+ F     +++++DMD +
Sbjct: 1126 KTISTPVITCPLVQNRELTAARIVKARIEKTYVEDILSYIEDEWFADSGNVVLQVDMDAL 1185

Query: 1172 RLLHLEVDIDSI--RYCIERTRGIS--------GHLTV--------SGHSFLILKPKDSS 1213
              + L + +  +    C  +   IS        G + +        +    +  KP D  
Sbjct: 1186 SNMQLGIGLGDVAEAICKHKKMKISRQDMHIGPGRIEIRVRLDESAASKRSVKAKPVDEH 1245

Query: 1214 KSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVK 1273
                 +   +++ +P+V I G     RA+I   + E    + +LVEG  L+  M T GV+
Sbjct: 1246 GDLLVRANYLRRTIPTVSISGYPEATRAIIQTSEQE---THTVLVEGYGLQKCMNTEGVE 1302

Query: 1274 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 1333
            G +  SNN  E    LGIEAAR+TI  EI  VM +  M ID RH  L+AD+MT KGEVLG
Sbjct: 1303 GRRVKSNNVMECRDVLGIEAARTTIAHEIGEVMGD--MGIDPRHMQLLADVMTYKGEVLG 1360

Query: 1334 ITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            ITR GL+KM++SVL LASFE T DHLF+AA   +TD I GVSECIIMG  M+VGTG   +
Sbjct: 1361 ITRFGLSKMRDSVLQLASFEKTPDHLFEAAAGMKTDQIEGVSECIIMGQTMSVGTGAFHV 1420

Query: 1394 LQ 1395
            ++
Sbjct: 1421 VR 1422



 Score =  192 bits (489), Expect = 8e-46,   Method: Compositional matrix adjust.
 Identities = 107/283 (37%), Positives = 157/283 (55%), Gaps = 10/283 (3%)

Query: 67  IASTLIAGRKVFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMG 126
           + S L+      F+G+  G  + +D +  Q+ +++  + LY  +  R P  HG LD R+G
Sbjct: 10  VKSQLVDKLPKRFKGIKFGIQSNQD-IANQAVLEVSDRLLYDIEKNRAPYQHGPLDPRLG 68

Query: 127 TNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGE 186
           T+ K   C TC ++L +C GHFG++ LPLP FHIGY R V+ ILQ ICK+  C +VLL E
Sbjct: 69  TSSKTGKCATCQESLQNCTGHFGHVRLPLPAFHIGYLRFVMMILQDICKD--CGKVLLTE 126

Query: 187 EKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEK- 245
            +   F  +LR P L  L R  + K+I E  +KV  C +CG + G ++K G+LK++H+K 
Sbjct: 127 SEKRAFLKELRRPLLDNLRRSQICKRINEQCRKVKNCMYCGSVQGQIRKVGVLKLAHDKF 186

Query: 246 --YKNRTKKKDAIVEDLLA---EYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPL 300
             Y   T  K    E  +     ++EA K N E++ H +  + + +NPL VL LF+ I  
Sbjct: 187 VTYNKSTSAKKVPPESKIKFDESFSEARKNNAELDKHLRKAM-EDMNPLRVLNLFKMISP 245

Query: 301 EDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
            D  LL ++    +P   I   L  PP CIRPSV  D  S+ D
Sbjct: 246 TDCELLGLDPAEGRPEMFIWQFLPAPPVCIRPSVAQDNASNED 288



 Score =  145 bits (366), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 99/276 (35%), Positives = 147/276 (53%), Gaps = 24/276 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+IT  L ++ +L  ARIVK R+E+T + ++  YIE+ +  D 
Sbjct: 1114 GVPRIKEIINASKTISTPVITCPLVQNRELTAARIVKARIEKTYVEDILSYIEDEWFADS 1173

Query: 824  SFILIKLDMDRIRLLHLEVDIDSI--RYCIERTRGIS--------GHLTV--------SG 865
              +++++DMD +  + L + +  +    C  +   IS        G + +        + 
Sbjct: 1174 GNVVLQVDMDALSNMQLGIGLGDVAEAICKHKKMKISRQDMHIGPGRIEIRVRLDESAAS 1233

Query: 866  HSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD 925
               +  KP D       +   +++ +P+V I G     RA+I   + E    + +LVEG 
Sbjct: 1234 KRSVKAKPVDEHGDLLVRANYLRRTIPTVSISGYPEATRAIIQTSEQE---THTVLVEGY 1290

Query: 926  NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 985
             L+  M T GV+G +  SNN  E    LGIEAAR+TI  EI  VM +  M ID RH  L+
Sbjct: 1291 GLQKCMNTEGVEGRRVKSNNVMECRDVLGIEAARTTIAHEIGEVMGD--MGIDPRHMQLL 1348

Query: 986  ADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDP 1021
            AD+MT KGEVLG  T   L ++ D ++   S    P
Sbjct: 1349 ADVMTYKGEVLGI-TRFGLSKMRDSVLQLASFEKTP 1383



 Score =  104 bits (259), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 47/59 (79%), Positives = 50/59 (84%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV NSF+SGL PTEF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 840 PSKGFVANSFYSGLLPTEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSTQYD 898



 Score = 58.2 bits (139), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 28/53 (52%), Positives = 35/53 (66%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           LM  K NL TP+NGE +IAATQDFIT  YLL+ K+ FF+R     I   ++ G
Sbjct: 533 LMGVKHNLATPKNGEPVIAATQDFITAAYLLSGKDRFFDRKTFTYICMHMMDG 585



 Score = 42.7 bits (99), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 27/72 (37%), Positives = 40/72 (55%), Gaps = 2/72 (2%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ--AVPRSEPVPRTLLFDNPEF 725
            D  F+AA   +TD I GVSECIIMG  M+VGTG   +++  A+ + +   R   F++   
Sbjct: 1384 DHLFEAAAGMKTDQIEGVSECIIMGQTMSVGTGAFHVVRRLALEKGDVGQRKTTFEDAWA 1443

Query: 726  HFPQVYYERRRD 737
                V  + RR+
Sbjct: 1444 AQTAVKRKSRRN 1455


>gi|322704718|gb|EFY96310.1| DNA-directed RNA polymerase III [Metarhizium anisopliae ARSEF 23]
          Length = 1447

 Score =  290 bits (741), Expect = 6e-75,   Method: Compositional matrix adjust.
 Identities = 145/274 (52%), Positives = 181/274 (66%), Gaps = 28/274 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIM+H AK+ P RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 466 DGDVVLFNRQPSLHKLSIMSHLAKIRPWRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 525

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K NL TP+NGE +IAATQDFIT  +LL+ K+ FF+R
Sbjct: 526 RAEAIN--------------LMGVKYNLATPKNGEPIIAATQDFITAAFLLSSKDRFFDR 571

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                I   ++   + I             P   V    +WTGKQIFS++++PN+DC V 
Sbjct: 572 KSFSYICMHMMEQGTKI----------EIPPPAIVAPKALWTGKQIFSIMMRPNKDCSVK 621

Query: 521 ANLKTKGRAYTANEEFC----HRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL  K RAY A    C      D ++++RNSE++ G MDKST+GSG K ++FY++LRDF
Sbjct: 622 INLDAKCRAYKARPGQCPDMDPNDGWLVVRNSEVMCGRMDKSTVGSGKKDSIFYVILRDF 681

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           G D AV AM RL+++ +  L NRGFSIG+GDV P
Sbjct: 682 GPDEAVIAMNRLAKLCARALTNRGFSIGVGDVFP 715



 Score =  212 bits (540), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 176/508 (34%), Positives = 240/508 (47%), Gaps = 98/508 (19%)

Query: 970  MENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSR-SDPSLSAQEI 1028
            ME     ++F+     A+ +T   E     TP E++   D ++A    R     L+  E 
Sbjct: 922  MEGSAEPVNFKRTWSHAETLTWDNEEAAM-TPSEIRAFCDSMLAVERKRFPRHGLAYGEK 980

Query: 1029 LALSNET---LDSKE----FLQDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQI 1081
            L   + T   +D  E    FL+ T EN V  +   LE+  K        DK+   LR   
Sbjct: 981  LDYEDTTDYGIDEHEGARRFLK-TIENHVEGLASKLEKVRKLAGFDG--DKM---LRATA 1034

Query: 1082 LSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTF 1141
              H D+      +         + C EKY +A +EP  AVGA+ AQSIGEPGTQMTLKTF
Sbjct: 1035 QDHADRTAKVTATT---LRLFIKMCLEKYKKAHVEPGHAVGAVGAQSIGEPGTQMTLKTF 1091

Query: 1142 HFAG--------------EVCE---------------------------------YIEEV 1154
            HFAG              E+                                   YI +V
Sbjct: 1092 HFAGVAGMSITQGVPRIKEIINASKNISTPVITCPLMNDKQIEAARVVKGRIEKTYISDV 1151

Query: 1155 -------FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSF 1204
                   + PD+  +++++D   +  LHL + I  I   I + R +      L+V G   
Sbjct: 1152 LHFVEDEWRPDEGNVVLQIDRSALSDLHLGIGIYDIAESICKQRKLKIPREDLSVYGER- 1210

Query: 1205 LILKPKDSSKSFNSKMYQ-----------------MKQLLPSVVIKGVQGINRAVIHEED 1247
            ++++ +D+S     K  +                 +++ LP V I G     RA+I   +
Sbjct: 1211 IVIRVRDASDMPARKTTRTKPALEDSGDMLLRANFLRRALPHVPISGYSEATRAIIQTSE 1270

Query: 1248 VEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVME 1307
                  + +LVEG  LR+ M T GV G +  SNN  E    LGIEAARSTI  EI  VM 
Sbjct: 1271 ---QNTHTVLVEGYGLRECMTTEGVIGTQTRSNNVMECRDVLGIEAARSTIADEISQVMG 1327

Query: 1308 NHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQ 1367
            +  M ID RH  L+AD+MT KGEVLGITR GL+KM++SVL LASFE T DHLF+AA   +
Sbjct: 1328 D--MGIDPRHMQLLADVMTYKGEVLGITRFGLSKMRDSVLQLASFEKTPDHLFEAAAGMK 1385

Query: 1368 TDCISGVSECIIMGLPMNVGTGLIKLLQ 1395
            TD I GVSECIIMG  M VGTG  ++++
Sbjct: 1386 TDQIEGVSECIIMGQTMAVGTGAFQVVR 1413



 Score =  196 bits (498), Expect = 8e-47,   Method: Compositional matrix adjust.
 Identities = 106/271 (39%), Positives = 156/271 (57%), Gaps = 11/271 (4%)

Query: 79  FRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCG 138
           F+G+  G  + +D +  Q+ +++  + LY  +  R P  HG LD R+GT+ K   C TC 
Sbjct: 21  FKGIKFGIQSNQD-IANQAVLEVSDRLLYDIENNRAPYRHGPLDPRLGTSSKSGKCDTCH 79

Query: 139 QNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN 198
            +L +C+GHFG++ LPLP FHIGY R +++ILQ ICK+  C RVLL E +   F  +LR 
Sbjct: 80  DSLQNCIGHFGHVRLPLPAFHIGYLRFIMSILQEICKD--CGRVLLEEPERRSFLKELRR 137

Query: 199 PALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEK---YKNRTKKKDA 255
           P +  L R  + K+I E  +K   CP+CG +NG ++K G+LK++H+K   Y   T  K  
Sbjct: 138 P-MDNLRRTQICKRINEQCRKSKTCPYCGSVNGQIRKIGVLKLTHDKFSFYNKSTAAKKV 196

Query: 256 IVEDLLA---EYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL 312
             E  +     ++EA + NPE+E H +  + + LNPL VL LF+ I   D  LL ++   
Sbjct: 197 PPESKVKFDDSFSEAKRENPELEKHLRKAM-EDLNPLRVLNLFKMISPTDCELLGLDPAE 255

Query: 313 SKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
            +P   I   +  PP CIRPSV  D  S+ D
Sbjct: 256 GRPEMFIWQFVPAPPVCIRPSVAQDNASNED 286



 Score =  157 bits (396), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 105/278 (37%), Positives = 152/278 (54%), Gaps = 27/278 (9%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+NISTP+IT  L  D  ++ AR+VKGR+E+T + +V  ++E+ + PD+
Sbjct: 1104 GVPRIKEIINASKNISTPVITCPLMNDKQIEAARVVKGRIEKTYISDVLHFVEDEWRPDE 1163

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSFLILKPKDSSKSF 880
              +++++D   +  LHL + I  I   I + R +      L+V G   ++++ +D+S   
Sbjct: 1164 GNVVLQIDRSALSDLHLGIGIYDIAESICKQRKLKIPREDLSVYGER-IVIRVRDASDMP 1222

Query: 881  NSKMYQ-----------------MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVE 923
              K  +                 +++ LP V I G     RA+I   +      + +LVE
Sbjct: 1223 ARKTTRTKPALEDSGDMLLRANFLRRALPHVPISGYSEATRAIIQTSE---QNTHTVLVE 1279

Query: 924  GDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPM 983
            G  LR+ M T GV G +  SNN  E    LGIEAARSTI  EI  VM +  M ID RH  
Sbjct: 1280 GYGLRECMTTEGVIGTQTRSNNVMECRDVLGIEAARSTIADEISQVMGD--MGIDPRHMQ 1337

Query: 984  LVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDP 1021
            L+AD+MT KGEVLG  T   L ++ D ++   S    P
Sbjct: 1338 LLADVMTYKGEVLGI-TRFGLSKMRDSVLQLASFEKTP 1374



 Score =  101 bits (252), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 45/59 (76%), Positives = 51/59 (86%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSF++GL PTEF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 839 PSKGFVKNSFYTGLFPTEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSTQYD 897



 Score = 56.6 bits (135), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/40 (62%), Positives = 31/40 (77%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           LM  K NL TP+NGE +IAATQDFIT  +LL+ K+ FF+R
Sbjct: 532 LMGVKYNLATPKNGEPIIAATQDFITAAFLLSSKDRFFDR 571



 Score = 42.7 bits (99), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 21/39 (53%), Positives = 27/39 (69%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  F+AA   +TD I GVSECIIMG  M VGTG  ++++
Sbjct: 1375 DHLFEAAAGMKTDQIEGVSECIIMGQTMAVGTGAFQVVR 1413


>gi|322702047|gb|EFY93795.1| DNA-directed RNA polymerase III [Metarhizium acridum CQMa 102]
          Length = 1447

 Score =  289 bits (740), Expect = 7e-75,   Method: Compositional matrix adjust.
 Identities = 145/274 (52%), Positives = 181/274 (66%), Gaps = 28/274 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIM+H AK+ P RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 466 DGDVVLFNRQPSLHKLSIMSHLAKIRPWRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 525

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K NL TP+NGE +IAATQDFIT  +LL+ K+ FF+R
Sbjct: 526 RAEAIN--------------LMGVKYNLATPKNGEPIIAATQDFITAAFLLSSKDRFFDR 571

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                I   ++   + I             P   V    +WTGKQIFS++++PN+DC V 
Sbjct: 572 KSFSYICMHMMEQGTKI----------EIPPPAIVAPKALWTGKQIFSIMMRPNKDCSVK 621

Query: 521 ANLKTKGRAYTANEEFC----HRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL  K RAY A    C      D ++++RNSE++ G MDKST+GSG K ++FY++LRDF
Sbjct: 622 INLDAKCRAYKARPGQCPDMDPNDGWLVVRNSEVMCGRMDKSTVGSGKKDSIFYVILRDF 681

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           G D AV AM RL+++ +  L NRGFSIG+GDV P
Sbjct: 682 GPDEAVIAMNRLAKLCARALTNRGFSIGVGDVFP 715



 Score =  208 bits (529), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 174/508 (34%), Positives = 239/508 (47%), Gaps = 98/508 (19%)

Query: 970  MENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSR-SDPSLSAQEI 1028
            ME     ++F+     A+ +T   +     TP E++   D ++A    R     L+  E 
Sbjct: 922  MEGSAEPVNFKRTWSHAETLTWDNDEAAM-TPSEIRAFCDSMLAVERKRFPRHGLAYGEK 980

Query: 1029 LALSNET---LDSKE----FLQDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQI 1081
            L   + T   +D  E    FL+ T EN V  +   LE+  K        DK+   LR   
Sbjct: 981  LDYEDTTDYGIDEHEGARRFLK-TIENHVEGLASKLEKVRKLAGFDG--DKM---LRATA 1034

Query: 1082 LSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTF 1141
              H D+      +         + C EKY +A +EP  AVGA+ AQSIGEPGTQMTLKTF
Sbjct: 1035 QDHADRTAKVTATT---LRLFIKMCLEKYKKAHVEPGHAVGAVGAQSIGEPGTQMTLKTF 1091

Query: 1142 HFAG--------------EVCE---------------------------------YIEEV 1154
            HFAG              E+                                   YI +V
Sbjct: 1092 HFAGVAGMSITQGVPRIKEIINASKNISTPVITCPLMNDKQIEAARVVKGRIEKTYISDV 1151

Query: 1155 -------FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSF 1204
                   + P +  +++++D   +  LHL + I  I   I + R +      L+V G   
Sbjct: 1152 LHFVEDEWRPGEGNVVLQIDRSALSDLHLGIGIYDIAESICKQRKLKIPREDLSVYGER- 1210

Query: 1205 LILKPKDSSKSFNSKMYQ-----------------MKQLLPSVVIKGVQGINRAVIHEED 1247
            ++++ +D+S     K  +                 +++ LP V I G     RA+I   +
Sbjct: 1211 IVIRVRDASDMPARKTTRTKPALEDSGDMLLRANFLRRALPHVPISGYSEATRAIIQTSE 1270

Query: 1248 VEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVME 1307
                  + +LVEG  LR+ M T GV G K  SNN  E    LGIEAAR+TI  EI  VM 
Sbjct: 1271 ---QNTHTVLVEGYGLRECMTTEGVLGTKTRSNNVMECRDVLGIEAARTTIADEISQVMG 1327

Query: 1308 NHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQ 1367
            +  M ID RH  L+AD+MT KGEVLGITR GL+KM++SVL LASFE T DHLF+AA   +
Sbjct: 1328 D--MGIDPRHMQLLADVMTYKGEVLGITRFGLSKMRDSVLQLASFEKTPDHLFEAAAGMK 1385

Query: 1368 TDCISGVSECIIMGLPMNVGTGLIKLLQ 1395
            TD I GVSECIIMG  M VGTG  ++++
Sbjct: 1386 TDQIEGVSECIIMGQTMAVGTGAFQVVR 1413



 Score =  196 bits (497), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 106/271 (39%), Positives = 156/271 (57%), Gaps = 11/271 (4%)

Query: 79  FRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCG 138
           F+G+  G  + +D +  Q+ +++  + LY  +  R P  HG LD R+GT+ K   C TC 
Sbjct: 21  FKGIKFGIQSNQD-IANQAVLEVSDRLLYDIENNRAPYRHGPLDPRLGTSSKSGKCDTCH 79

Query: 139 QNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN 198
            +L +C+GHFG++ LPLP FHIGY R +++ILQ ICK+  C RVLL E +   F  +LR 
Sbjct: 80  DSLQNCIGHFGHVRLPLPAFHIGYLRFIMSILQEICKD--CGRVLLEEPERRSFLKELRR 137

Query: 199 PALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEK---YKNRTKKKDA 255
           P +  L R  + K+I E  +K   CP+CG +NG ++K G+LK++H+K   Y   T  K  
Sbjct: 138 P-MDNLRRTQICKRINEQCRKSRTCPYCGSVNGQIRKIGVLKLTHDKFSFYNKSTAAKKV 196

Query: 256 IVEDLLA---EYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL 312
             E  +     ++EA + NPE+E H +  + + LNPL VL LF+ I   D  LL ++   
Sbjct: 197 PPESKVKFDDSFSEAKRENPELEKHLRKAM-EDLNPLRVLNLFKMISPTDCELLGLDPAE 255

Query: 313 SKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
            +P   I   +  PP CIRPSV  D  S+ D
Sbjct: 256 GRPEMFIWQFVPAPPVCIRPSVAQDNASNED 286



 Score =  154 bits (389), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 104/278 (37%), Positives = 151/278 (54%), Gaps = 27/278 (9%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+NISTP+IT  L  D  ++ AR+VKGR+E+T + +V  ++E+ + P +
Sbjct: 1104 GVPRIKEIINASKNISTPVITCPLMNDKQIEAARVVKGRIEKTYISDVLHFVEDEWRPGE 1163

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSFLILKPKDSSKSF 880
              +++++D   +  LHL + I  I   I + R +      L+V G   ++++ +D+S   
Sbjct: 1164 GNVVLQIDRSALSDLHLGIGIYDIAESICKQRKLKIPREDLSVYGER-IVIRVRDASDMP 1222

Query: 881  NSKMYQ-----------------MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVE 923
              K  +                 +++ LP V I G     RA+I   +      + +LVE
Sbjct: 1223 ARKTTRTKPALEDSGDMLLRANFLRRALPHVPISGYSEATRAIIQTSE---QNTHTVLVE 1279

Query: 924  GDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPM 983
            G  LR+ M T GV G K  SNN  E    LGIEAAR+TI  EI  VM +  M ID RH  
Sbjct: 1280 GYGLRECMTTEGVLGTKTRSNNVMECRDVLGIEAARTTIADEISQVMGD--MGIDPRHMQ 1337

Query: 984  LVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDP 1021
            L+AD+MT KGEVLG  T   L ++ D ++   S    P
Sbjct: 1338 LLADVMTYKGEVLGI-TRFGLSKMRDSVLQLASFEKTP 1374



 Score =  101 bits (252), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 45/59 (76%), Positives = 51/59 (86%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSF++GL PTEF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 839 PSKGFVKNSFYTGLFPTEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSTQYD 897



 Score = 56.6 bits (135), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/40 (62%), Positives = 31/40 (77%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           LM  K NL TP+NGE +IAATQDFIT  +LL+ K+ FF+R
Sbjct: 532 LMGVKYNLATPKNGEPIIAATQDFITAAFLLSSKDRFFDR 571



 Score = 42.4 bits (98), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 21/39 (53%), Positives = 27/39 (69%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  F+AA   +TD I GVSECIIMG  M VGTG  ++++
Sbjct: 1375 DHLFEAAAGMKTDQIEGVSECIIMGQTMAVGTGAFQVVR 1413


>gi|348676845|gb|EGZ16662.1| hypothetical protein PHYSODRAFT_500633 [Phytophthora sojae]
          Length = 1532

 Score =  288 bits (737), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 145/274 (52%), Positives = 185/274 (67%), Gaps = 27/274 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHK+SIM+HR KV+P RTFRFNECVC+PYNADFDGDEMN+HLPQTEEA
Sbjct: 466 DGDIVLFNRQPSLHKMSIMSHRVKVMPWRTFRFNECVCSPYNADFDGDEMNMHLPQTEEA 525

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EA+               LM  + NL+TPRNGE L+AATQDF+T  YLLTQKN FFNR
Sbjct: 526 RTEAI--------------TLMGVEQNLITPRNGEPLVAATQDFLTASYLLTQKNIFFNR 571

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPV-VFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q  ++ S +++D ++   +          P+   V    +WTGKQ+ SL++KPN    V
Sbjct: 572 EQFCQVIS-IMSDANEHIEL----------PLPAIVLPVRLWTGKQVISLLVKPNSQTKV 620

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            ANL+ K R YT N+  C +D YV  RNSEL+ G++ K TLG G K  +FY+L+RD G  
Sbjct: 621 MANLELKERNYTNNKYMCWKDGYVCFRNSELICGNLGKKTLGDGSKQGLFYVLIRDHGSH 680

Query: 580 VAVTAMWRLSRMTSFYLMN-RGFSIGIGDVTPGQ 612
            A   M RL+++ + +L N +GFSIGI DVTP +
Sbjct: 681 EAARCMNRLAKLCARWLGNFKGFSIGIDDVTPSE 714



 Score =  251 bits (642), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 155/367 (42%), Positives = 203/367 (55%), Gaps = 76/367 (20%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGE---------------------- 1146
            KY RA +EP  AVGA+ AQSI EPGTQMTLKTFHFAG                       
Sbjct: 1152 KYNRAGMEPGEAVGAVGAQSISEPGTQMTLKTFHFAGVASMNVTLGVPRLKEIINASKVI 1211

Query: 1147 ---------VCE-----------------------YIEEVFVPDDSFILIKLDMDRIRLL 1174
                     VC+                       +I+EVF  D +++ +KLD+  I  L
Sbjct: 1212 STPIITAALVCKTDERSARIVKGRIEKTTLGEIAVHIKEVFARDQAYLSVKLDLTAIEQL 1271

Query: 1175 HLEVDIDSIRYCIERTRGISG----HLTVSGHSFL---------ILKP------KDSSKS 1215
            HL +   S+R  I    G+       L    H  L         +L P      K  S+ 
Sbjct: 1272 HLNITARSVRNSILNAVGVGPRGALRLLKEQHVLLNARCPDKLRLLAPPNYKGAKGDSRG 1331

Query: 1216 FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYK---LLVEGDNLRDVMATYGV 1272
                +  +K  LP V+++G+  +NRAVI+ E+V+  +  K   LLVEG  L +VM   GV
Sbjct: 1332 AYFALQALKAELPGVIVQGIPTVNRAVINYEEVQDASATKSLHLLVEGYGLAEVMGIPGV 1391

Query: 1273 KGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL 1332
             G+  +SN+  EV KTLGIEAAR  I +E+  +M  +G+ ID RH ML++D+MT KGEVL
Sbjct: 1392 DGLHTTSNHIIEVEKTLGIEAARELISSEVNYIMSAYGIGIDRRHLMLLSDIMTFKGEVL 1451

Query: 1333 GITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIK 1392
            GITR G+AKMKESVL LASFE T+DHLFDAA + +TD I GVSECIIMG+P+ +GTG+ K
Sbjct: 1452 GITRFGIAKMKESVLMLASFEKTTDHLFDAAVHSRTDAIVGVSECIIMGIPIPLGTGIFK 1511

Query: 1393 LLQAVPR 1399
            LL+ V +
Sbjct: 1512 LLRQVEK 1518



 Score =  197 bits (502), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 111/245 (45%), Positives = 149/245 (60%), Gaps = 8/245 (3%)

Query: 95  QQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLP 154
           Q S +++ SK+L+ +   R P   G+LD+R+G + K+  C TC   L+DCVGHFGYI L 
Sbjct: 41  QMSELRVHSKDLF-KVQTREPAADGVLDKRLGVSNKKDTCDTCHLKLADCVGHFGYIKLE 99

Query: 155 LPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKIL 214
           LPVFHIGYF+ +  ILQ+ICK  +C+RVLL   +   F  ++R+P    L    L+KKI 
Sbjct: 100 LPVFHIGYFKAITEILQNICK--SCSRVLLPPAERETFLRRMRDPRADVLRLVGLRKKIA 157

Query: 215 ETTKKVSVCPHCGEINGVVKK--CGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNP 272
              KK   CP+C  ING V+K     LK+ HEKY  R K    +    +A++ EA   NP
Sbjct: 158 ALCKKTIKCPYCDAINGSVRKITSTTLKLVHEKY--RAKATHDLRNVFVAQFAEAQANNP 215

Query: 273 EIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRP 332
           EI AH      + L+PL VLQLF+ IP +D  LL ++A+  +P  LIL  +LVPP CIRP
Sbjct: 216 EIGAHLPKAQ-EDLSPLVVLQLFKEIPDQDCELLWVDADNGRPERLILNSVLVPPVCIRP 274

Query: 333 SVISD 337
           SV  D
Sbjct: 275 SVAMD 279



 Score =  189 bits (479), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 114/256 (44%), Positives = 154/256 (60%), Gaps = 22/256 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPR+KEIINAS+ ISTPIITA L   TD   ARIVKGR+E+TTLGE+  +I+EVF  D 
Sbjct: 1197 GVPRLKEIINASKVISTPIITAALVCKTDERSARIVKGRIEKTTLGEIAVHIKEVFARDQ 1256

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISG----HLTVSGHSFL---------I 870
            +++ +KLD+  I  LHL +   S+R  I    G+       L    H  L         +
Sbjct: 1257 AYLSVKLDLTAIEQLHLNITARSVRNSILNAVGVGPRGALRLLKEQHVLLNARCPDKLRL 1316

Query: 871  LKP------KDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYK---LL 921
            L P      K  S+     +  +K  LP V+++G+  +NRAVI+ E+V+  +  K   LL
Sbjct: 1317 LAPPNYKGAKGDSRGAYFALQALKAELPGVIVQGIPTVNRAVINYEEVQDASATKSLHLL 1376

Query: 922  VEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRH 981
            VEG  L +VM   GV G+  +SN+  EV KTLGIEAAR  I +E+  +M  +G+ ID RH
Sbjct: 1377 VEGYGLAEVMGIPGVDGLHTTSNHIIEVEKTLGIEAARELISSEVNYIMSAYGIGIDRRH 1436

Query: 982  PMLVADLMTSKGEVLG 997
             ML++D+MT KGEVLG
Sbjct: 1437 LMLLSDIMTFKGEVLG 1452



 Score =  106 bits (265), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 48/60 (80%), Positives = 53/60 (88%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLT TEFFFHTMGGREGLVDTAVKTAETGYM RRL+K+LEDL  QYD +
Sbjct: 837 AKGFVANSFYSGLTATEFFFHTMGGREGLVDTAVKTAETGYMARRLMKALEDLSCQYDQT 896



 Score = 68.9 bits (167), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 31/50 (62%), Positives = 38/50 (76%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM  + NL+TPRNGE L+AATQDF+T  YLLTQKN FFNR Q  ++ S +
Sbjct: 532 LMGVEQNLITPRNGEPLVAATQDFLTASYLLTQKNIFFNREQFCQVISIM 581



 Score = 56.2 bits (134), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/43 (58%), Positives = 33/43 (76%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPR 710
            D  FDAA + +TD I GVSECIIMG+P+ +GTG+ KLL+ V +
Sbjct: 1476 DHLFDAAVHSRTDAIVGVSECIIMGIPIPLGTGIFKLLRQVEK 1518


>gi|302500232|ref|XP_003012110.1| hypothetical protein ARB_01618 [Arthroderma benhamiae CBS 112371]
 gi|291175666|gb|EFE31470.1| hypothetical protein ARB_01618 [Arthroderma benhamiae CBS 112371]
          Length = 1444

 Score =  288 bits (737), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 139/280 (49%), Positives = 185/280 (66%), Gaps = 28/280 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++H  KV PHRTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 470 DGDIVLFNRQPSLHKLSILSHFVKVRPHRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 529

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  KSNL TP+NGE +IAA QDFIT  YLL+ K+ FF+R
Sbjct: 530 RAEAME--------------LMGVKSNLATPKNGEPIIAAIQDFITAAYLLSSKDNFFDR 575

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
               +I  +++  ++       RF      P   ++  ++WTGKQ+FS++++PN+DCPV 
Sbjct: 576 KTFTQICLSMLDSST-------RF---ELPPPATIKPQMLWTGKQVFSVLMRPNKDCPVK 625

Query: 521 ANLKTKGRAYT----ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL    R          + C  D ++ +RNSE+L G  DKST+G+G K N+F+++ RDF
Sbjct: 626 VNLDAACRQLKLVKGQPRDLCENDGWLCIRNSEMLCGVADKSTIGAGKKDNIFFVIQRDF 685

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           G   A  AM RLS++++ +L N+GFSIGI DV PG+  V+
Sbjct: 686 GYAAAAEAMNRLSKLSARWLTNKGFSIGITDVYPGESLVK 725



 Score =  176 bits (446), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 102/267 (38%), Positives = 150/267 (56%), Gaps = 12/267 (4%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G ++ +D +  Q+H++I  + L+  D  R    +G +D R+G + K   C TCG +L +C
Sbjct: 30  GVLSNQD-IISQAHVEISDRKLFDLDNNRAVARNGPMDPRLGISNKSDTCETCGGDLQEC 88

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFGY+ L LP FH+GYF+  I ILQ ICK+  C+++LL E++   +  +LR P L  L
Sbjct: 89  NGHFGYVRLVLPAFHVGYFKRTIEILQDICKD--CSKILLPEDERRSYLKELRRPGLDNL 146

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKC--GLLKISHEKYK----NRTKKKDAIVE 258
            R  + K+I    +K  VC +C  ING VKK   G LKI H+K++    + + KK     
Sbjct: 147 RRMQINKRINVRCRKTPVCYYCNAINGTVKKASTGALKIVHDKFRAFNASLSAKKIPPPS 206

Query: 259 DLLAE--YNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPS 316
            L  +  + EA K NP+IE H +  +   LNPL VL+LF  I  ED  LL +N + ++P 
Sbjct: 207 KLAFDRSFEEAKKSNPDIEKHYR-RVFDDLNPLRVLKLFRRISNEDCELLSLNVDGARPE 265

Query: 317 DLILTRLLVPPNCIRPSVISDLKSDND 343
             +   +  PP  IRPSV  +  S  D
Sbjct: 266 YFLWQFIPAPPVPIRPSVGQEGASTED 292



 Score =  176 bits (445), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 151/489 (30%), Positives = 215/489 (43%), Gaps = 101/489 (20%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNE-----------------TLDSK 1039
             +  PV   R      +    + +  LSA EILAL  E                 TL  K
Sbjct: 927  ASAKPVHFDRTFTHAESTTYDKDEKGLSADEILALCEELIAPERKKLVRYDLLGNTLSYK 986

Query: 1040 ---EFLQDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNP 1096
               +F  D  E+  RD    +EE+   ++         +   +   +H  KI   R    
Sbjct: 987  AENDFATDQWES-NRDFLSSIEEYVAAKAAQLRPSDNEEGKEQMAFTHTSKIS-ARTLKA 1044

Query: 1097 FPSACKAEACREKYVRAQIEPA---TAVGALAAQSIGEPGTQMTLKTFHFAG-------- 1145
            F ++C      +KY+RA +EP     A+GA +    G   T  T      AG        
Sbjct: 1045 FITSC-----LDKYMRAHVEPGHSIGAIGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVP 1099

Query: 1146 -------------------------------------------EVCEYIEEVFVPDDSFI 1162
                                                       ++  YIEE      SFI
Sbjct: 1100 RIKEIINASKEISTPIITCELVNKTDMRIAEIVKGRVEKLFLKDIVYYIEENRSQTSSFI 1159

Query: 1163 LIKLDMDRIRLLHLEVDIDSIRYCIERTRGISG------------HLTVSGHSFLILKPK 1210
             IK+D   I+ L LE+ +  I   I++ +                H+ V   + +     
Sbjct: 1160 NIKVDFSTIKKLQLELTLRQILLAIKKHKAFKAADLTFRSFNSHIHIYVDEGASMAGVSV 1219

Query: 1211 DSSKSFNSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDV 1266
               K   S  Y     ++++LP++ + G     RAVI     E V    LLVEG  LR  
Sbjct: 1220 SEQKITGSDPYIRINYLRRILPNIQVFGYPDCTRAVIRVG--EKVATNILLVEGYGLRAC 1277

Query: 1267 MATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMT 1326
            M T G++G +  +N+  E+   LGIEAAR+TI+ EI  VM   GM+ID RH  L+AD+MT
Sbjct: 1278 MTTDGIEGHRTRTNHVMEMRDVLGIEAARTTIIDEISSVMS--GMAIDPRHMQLLADVMT 1335

Query: 1327 SKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNV 1386
             KGEVLGITR GLAK+++SVL LASFE T+DHLFDA   G+ D + GVSECIIMG  +++
Sbjct: 1336 YKGEVLGITRFGLAKIRDSVLQLASFEKTADHLFDAGGAGRRDTVQGVSECIIMGKTISL 1395

Query: 1387 GTGLIKLLQ 1395
            GTG +++++
Sbjct: 1396 GTGSMEVVR 1404



 Score =  151 bits (381), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 103/250 (41%), Positives = 137/250 (54%), Gaps = 20/250 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIIT  L   TD+  A IVKGR+E+  L ++  YIEE      
Sbjct: 1097 GVPRIKEIINASKEISTPIITCELVNKTDMRIAEIVKGRVEKLFLKDIVYYIEENRSQTS 1156

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISG------------HLTVSGHSFLIL 871
            SFI IK+D   I+ L LE+ +  I   I++ +                H+ V   + +  
Sbjct: 1157 SFINIKVDFSTIKKLQLELTLRQILLAIKKHKAFKAADLTFRSFNSHIHIYVDEGASMAG 1216

Query: 872  KPKDSSKSFNSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927
                  K   S  Y     ++++LP++ + G     RAVI     E V    LLVEG  L
Sbjct: 1217 VSVSEQKITGSDPYIRINYLRRILPNIQVFGYPDCTRAVIRVG--EKVATNILLVEGYGL 1274

Query: 928  RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 987
            R  M T G++G +  +N+  E+   LGIEAAR+TI+ EI  VM   GM+ID RH  L+AD
Sbjct: 1275 RACMTTDGIEGHRTRTNHVMEMRDVLGIEAARTTIIDEISSVMS--GMAIDPRHMQLLAD 1332

Query: 988  LMTSKGEVLG 997
            +MT KGEVLG
Sbjct: 1333 VMTYKGEVLG 1342



 Score =  103 bits (258), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 46/58 (79%), Positives = 51/58 (87%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV+NSFFSGLTPTEF FH M GREGL+DTAVKTAETGYM RRL+KSLEDL  +YD
Sbjct: 843 AKGFVRNSFFSGLTPTEFLFHAMSGREGLIDTAVKTAETGYMSRRLMKSLEDLSTRYD 900



 Score = 58.9 bits (141), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 27/51 (52%), Positives = 36/51 (70%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLI 72
           LM  KSNL TP+NGE +IAA QDFIT  YLL+ K+ FF+R    +I  +++
Sbjct: 536 LMGVKSNLATPKNGEPIIAAIQDFITAAYLLSSKDNFFDRKTFTQICLSML 586



 Score = 42.0 bits (97), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 18/39 (46%), Positives = 28/39 (71%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  FDA   G+ D + GVSECIIMG  +++GTG +++++
Sbjct: 1366 DHLFDAGGAGRRDTVQGVSECIIMGKTISLGTGSMEVVR 1404


>gi|327294643|ref|XP_003232017.1| DNA-directed RNA polymerase III largest subunit [Trichophyton
           rubrum CBS 118892]
 gi|326465962|gb|EGD91415.1| DNA-directed RNA polymerase III largest subunit [Trichophyton
           rubrum CBS 118892]
          Length = 1444

 Score =  288 bits (737), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 139/280 (49%), Positives = 185/280 (66%), Gaps = 28/280 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++H  KV PHRTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 470 DGDIVLFNRQPSLHKLSILSHFVKVRPHRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 529

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  KSNL TP+NGE +IAA QDFIT  YLL+ K+ FF+R
Sbjct: 530 RAEAME--------------LMGVKSNLATPKNGEPIIAAIQDFITAAYLLSSKDNFFDR 575

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
               +I  +++  ++       RF      P   ++  ++WTGKQ+FS++++PN+DCPV 
Sbjct: 576 KTFTQICLSMLDSST-------RF---ELPPPATIKPQMLWTGKQVFSVLMRPNKDCPVK 625

Query: 521 ANLKTKGRAYT----ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL    R          + C  D ++ +RNSE+L G  DKST+G+G K N+F+++ RDF
Sbjct: 626 VNLDAACRQLKLVKGQPRDLCENDGWLCIRNSEMLCGVADKSTIGAGKKDNIFFVIQRDF 685

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           G   A  AM RLS++++ +L N+GFSIGI DV PG+  V+
Sbjct: 686 GYAAAAEAMNRLSKLSARWLTNKGFSIGITDVYPGESLVR 725



 Score =  176 bits (446), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 102/267 (38%), Positives = 150/267 (56%), Gaps = 12/267 (4%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G ++ +D +  Q+H++I  + L+  D  R    +G +D R+G + K   C TCG +L +C
Sbjct: 30  GVLSNQD-IISQAHVEISDRKLFDLDNNRAVARNGPMDPRLGISNKSDTCETCGGDLQEC 88

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFGY+ L LP FH+GYF+  I ILQ ICK+  C+++LL E++   +  +LR P L  L
Sbjct: 89  NGHFGYVRLVLPAFHVGYFKRTIEILQDICKD--CSKILLPEDERRSYLKELRRPGLDNL 146

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKC--GLLKISHEKYK----NRTKKKDAIVE 258
            R  + K+I    +K  VC +C  ING VKK   G LKI H+K++    + + KK     
Sbjct: 147 RRMQINKRINVRCRKTPVCFYCNAINGTVKKASTGALKIVHDKFRAFNASLSAKKIPPPS 206

Query: 259 DLLAE--YNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPS 316
            L  +  + EA K NP+IE H +  +   LNPL VL+LF  I  ED  LL +N + ++P 
Sbjct: 207 KLAFDRSFEEAKKSNPDIEKHYR-RVFDDLNPLRVLKLFRRISNEDCELLSLNVDGARPE 265

Query: 317 DLILTRLLVPPNCIRPSVISDLKSDND 343
             +   +  PP  IRPSV  +  S  D
Sbjct: 266 YFLWQFIPAPPVPIRPSVGQEGASTED 292



 Score =  176 bits (445), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 151/489 (30%), Positives = 215/489 (43%), Gaps = 101/489 (20%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNE-----------------TLDSK 1039
             +  PV   R      +    + +  LSA EILAL  E                 TL  K
Sbjct: 927  ASAKPVHFDRTFTHAESTTYDKDEKGLSADEILALCEELIAPERKKLVRYDLLGNTLSYK 986

Query: 1040 ---EFLQDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNP 1096
               +F  D  E+  RD    +EE+   ++         +   +   +H  KI   R    
Sbjct: 987  AKNDFATDQWES-NRDFLSSIEEYVAAKATQLRPSDNEEGKEQMAFTHTSKIS-ARTLKA 1044

Query: 1097 FPSACKAEACREKYVRAQIEPA---TAVGALAAQSIGEPGTQMTLKTFHFAG-------- 1145
            F ++C      +KY+RA +EP     A+GA +    G   T  T      AG        
Sbjct: 1045 FITSC-----LDKYMRAHVEPGHSIGAIGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVP 1099

Query: 1146 -------------------------------------------EVCEYIEEVFVPDDSFI 1162
                                                       ++  YIEE      SFI
Sbjct: 1100 RIKEIINASKEISTPIITCELVNKTDMRIAEIVKGRVEKLFLKDIVYYIEENRSQTSSFI 1159

Query: 1163 LIKLDMDRIRLLHLEVDIDSIRYCIERTRGISG------------HLTVSGHSFLILKPK 1210
             IK+D   I+ L LE+ +  I   I++ +                H+ V   + +     
Sbjct: 1160 NIKVDFSTIKKLQLELTLRQILLAIKKHKAFKAADLTFRSFNSHIHIYVDEGASMAGVSV 1219

Query: 1211 DSSKSFNSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDV 1266
               K   S  Y     ++++LP++ + G     RAVI     E V    LLVEG  LR  
Sbjct: 1220 SEQKITGSDPYIRINYLRRILPNIQVFGYPDCTRAVIRVG--EKVATNILLVEGYGLRAC 1277

Query: 1267 MATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMT 1326
            M T G++G +  +N+  E+   LGIEAAR+TI+ EI  VM   GM+ID RH  L+AD+MT
Sbjct: 1278 MTTDGIEGHRTRTNHVMEMRDVLGIEAARTTIIDEISSVMS--GMAIDPRHMQLLADVMT 1335

Query: 1327 SKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNV 1386
             KGEVLGITR GLAK+++SVL LASFE T+DHLFDA   G+ D + GVSECIIMG  +++
Sbjct: 1336 YKGEVLGITRFGLAKIRDSVLQLASFEKTADHLFDAGGAGRRDTVQGVSECIIMGKTISL 1395

Query: 1387 GTGLIKLLQ 1395
            GTG +++++
Sbjct: 1396 GTGSMEVVR 1404



 Score =  151 bits (381), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 103/250 (41%), Positives = 137/250 (54%), Gaps = 20/250 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIIT  L   TD+  A IVKGR+E+  L ++  YIEE      
Sbjct: 1097 GVPRIKEIINASKEISTPIITCELVNKTDMRIAEIVKGRVEKLFLKDIVYYIEENRSQTS 1156

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISG------------HLTVSGHSFLIL 871
            SFI IK+D   I+ L LE+ +  I   I++ +                H+ V   + +  
Sbjct: 1157 SFINIKVDFSTIKKLQLELTLRQILLAIKKHKAFKAADLTFRSFNSHIHIYVDEGASMAG 1216

Query: 872  KPKDSSKSFNSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927
                  K   S  Y     ++++LP++ + G     RAVI     E V    LLVEG  L
Sbjct: 1217 VSVSEQKITGSDPYIRINYLRRILPNIQVFGYPDCTRAVIRVG--EKVATNILLVEGYGL 1274

Query: 928  RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 987
            R  M T G++G +  +N+  E+   LGIEAAR+TI+ EI  VM   GM+ID RH  L+AD
Sbjct: 1275 RACMTTDGIEGHRTRTNHVMEMRDVLGIEAARTTIIDEISSVMS--GMAIDPRHMQLLAD 1332

Query: 988  LMTSKGEVLG 997
            +MT KGEVLG
Sbjct: 1333 VMTYKGEVLG 1342



 Score =  103 bits (258), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 46/58 (79%), Positives = 51/58 (87%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV+NSFFSGLTPTEF FH M GREGL+DTAVKTAETGYM RRL+KSLEDL  +YD
Sbjct: 843 AKGFVRNSFFSGLTPTEFLFHAMSGREGLIDTAVKTAETGYMSRRLMKSLEDLSTRYD 900



 Score = 58.9 bits (141), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 27/51 (52%), Positives = 36/51 (70%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLI 72
           LM  KSNL TP+NGE +IAA QDFIT  YLL+ K+ FF+R    +I  +++
Sbjct: 536 LMGVKSNLATPKNGEPIIAAIQDFITAAYLLSSKDNFFDRKTFTQICLSML 586



 Score = 42.0 bits (97), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 18/39 (46%), Positives = 28/39 (71%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  FDA   G+ D + GVSECIIMG  +++GTG +++++
Sbjct: 1366 DHLFDAGGAGRRDTVQGVSECIIMGKTISLGTGSMEVVR 1404


>gi|326469885|gb|EGD93894.1| DNA-directed RNA polymerase III largest subunit [Trichophyton
           tonsurans CBS 112818]
          Length = 1444

 Score =  288 bits (737), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 139/280 (49%), Positives = 185/280 (66%), Gaps = 28/280 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++H  KV PHRTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 470 DGDIVLFNRQPSLHKLSILSHFVKVRPHRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 529

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  KSNL TP+NGE +IAA QDFIT  YLL+ K+ FF+R
Sbjct: 530 RAEAME--------------LMGVKSNLATPKNGEPIIAAIQDFITAAYLLSSKDNFFDR 575

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
               +I  +++  ++       RF      P   ++  ++WTGKQ+FS++++PN+DCPV 
Sbjct: 576 KTFTQICLSMLDSST-------RF---ELPPPATIKPQMLWTGKQVFSVLMRPNKDCPVK 625

Query: 521 ANLKTKGRAYT----ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL    R          + C  D ++ +RNSE+L G  DKST+G+G K N+F+++ RDF
Sbjct: 626 VNLDAACRQLKLVKGQPRDLCENDGWLCIRNSEMLCGVADKSTIGAGKKDNIFFVIQRDF 685

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           G   A  AM RLS++++ +L N+GFSIGI DV PG+  V+
Sbjct: 686 GYAAAAEAMNRLSKLSARWLTNKGFSIGITDVYPGESLVR 725



 Score =  176 bits (447), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 102/267 (38%), Positives = 150/267 (56%), Gaps = 12/267 (4%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G ++ +D +  Q+H++I  + L+  D  R    +G +D R+G + K   C TCG +L +C
Sbjct: 30  GVLSNQD-IISQAHVEISDRKLFDLDNNRAVARNGPMDPRLGISNKSDTCETCGGDLQEC 88

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFGY+ L LP FH+GYF+  I ILQ ICK+  C+++LL E++   +  +LR P L  L
Sbjct: 89  NGHFGYVRLVLPAFHVGYFKRTIEILQDICKD--CSKILLPEDERRSYLKELRRPGLDNL 146

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKC--GLLKISHEKYK----NRTKKKDAIVE 258
            R  + K+I    +K  VC +C  ING VKK   G LKI H+K++    + + KK     
Sbjct: 147 RRMQINKRINVRCRKTPVCYYCNAINGTVKKASTGALKIVHDKFRAFNASLSAKKIPPPS 206

Query: 259 DLLAE--YNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPS 316
            L  +  + EA K NP+IE H +  +   LNPL VL+LF  I  ED  LL +N + ++P 
Sbjct: 207 KLAFDRSFEEAKKANPDIEKHYR-RVFDDLNPLRVLKLFRRISNEDCELLSLNVDGARPE 265

Query: 317 DLILTRLLVPPNCIRPSVISDLKSDND 343
             +   +  PP  IRPSV  +  S  D
Sbjct: 266 YFLWQFIPAPPVPIRPSVGQEGASTED 292



 Score =  176 bits (445), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 151/489 (30%), Positives = 215/489 (43%), Gaps = 101/489 (20%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNE-----------------TLDSK 1039
             +  PV   R      +    + +  LSA EILAL  E                 TL  K
Sbjct: 927  ASAKPVHFDRTFTHAESTTYDKDEKGLSADEILALCEELIAPERKKLVRYDLLGNTLSYK 986

Query: 1040 ---EFLQDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNP 1096
               +F  D  E+  RD    +EE+   ++         +   +   +H  KI   R    
Sbjct: 987  AETDFATDQWES-NRDFLSSIEEYVAAKAAQLRPSDNEEGKEQMAFTHTSKIS-ARTLKA 1044

Query: 1097 FPSACKAEACREKYVRAQIEPA---TAVGALAAQSIGEPGTQMTLKTFHFAG-------- 1145
            F ++C      +KY+RA +EP     A+GA +    G   T  T      AG        
Sbjct: 1045 FITSC-----LDKYMRAHVEPGHSIGAIGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVP 1099

Query: 1146 -------------------------------------------EVCEYIEEVFVPDDSFI 1162
                                                       ++  YIEE      SFI
Sbjct: 1100 RIKEIINASKEISTPIITCELVNKTDMRIAEIVKGRVEKLFLKDIVYYIEENRSQTSSFI 1159

Query: 1163 LIKLDMDRIRLLHLEVDIDSIRYCIERTRGISG------------HLTVSGHSFLILKPK 1210
             IK+D   I+ L LE+ +  I   I++ +                H+ V   + +     
Sbjct: 1160 NIKVDFSTIKKLQLELTLRQILLAIKKHKAFKAADLTFRSFNSHIHIYVDEGASMAGVSV 1219

Query: 1211 DSSKSFNSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDV 1266
               K   S  Y     ++++LP++ + G     RAVI     E V    LLVEG  LR  
Sbjct: 1220 SEQKITGSDPYIRINYLRRILPNIQVFGYPDCTRAVIRVG--EKVATNILLVEGYGLRAC 1277

Query: 1267 MATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMT 1326
            M T G++G +  +N+  E+   LGIEAAR+TI+ EI  VM   GM+ID RH  L+AD+MT
Sbjct: 1278 MTTDGIEGHRTRTNHVMEMRDVLGIEAARTTIIDEISSVMS--GMAIDPRHMQLLADVMT 1335

Query: 1327 SKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNV 1386
             KGEVLGITR GLAK+++SVL LASFE T+DHLFDA   G+ D + GVSECIIMG  +++
Sbjct: 1336 YKGEVLGITRFGLAKIRDSVLQLASFEKTADHLFDAGGAGRRDTVQGVSECIIMGKTISL 1395

Query: 1387 GTGLIKLLQ 1395
            GTG +++++
Sbjct: 1396 GTGSMEVVR 1404



 Score =  151 bits (381), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 103/250 (41%), Positives = 137/250 (54%), Gaps = 20/250 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIIT  L   TD+  A IVKGR+E+  L ++  YIEE      
Sbjct: 1097 GVPRIKEIINASKEISTPIITCELVNKTDMRIAEIVKGRVEKLFLKDIVYYIEENRSQTS 1156

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISG------------HLTVSGHSFLIL 871
            SFI IK+D   I+ L LE+ +  I   I++ +                H+ V   + +  
Sbjct: 1157 SFINIKVDFSTIKKLQLELTLRQILLAIKKHKAFKAADLTFRSFNSHIHIYVDEGASMAG 1216

Query: 872  KPKDSSKSFNSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927
                  K   S  Y     ++++LP++ + G     RAVI     E V    LLVEG  L
Sbjct: 1217 VSVSEQKITGSDPYIRINYLRRILPNIQVFGYPDCTRAVIRVG--EKVATNILLVEGYGL 1274

Query: 928  RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 987
            R  M T G++G +  +N+  E+   LGIEAAR+TI+ EI  VM   GM+ID RH  L+AD
Sbjct: 1275 RACMTTDGIEGHRTRTNHVMEMRDVLGIEAARTTIIDEISSVMS--GMAIDPRHMQLLAD 1332

Query: 988  LMTSKGEVLG 997
            +MT KGEVLG
Sbjct: 1333 VMTYKGEVLG 1342



 Score =  103 bits (258), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 46/58 (79%), Positives = 51/58 (87%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV+NSFFSGLTPTEF FH M GREGL+DTAVKTAETGYM RRL+KSLEDL  +YD
Sbjct: 843 AKGFVRNSFFSGLTPTEFLFHAMSGREGLIDTAVKTAETGYMSRRLMKSLEDLSTRYD 900



 Score = 58.9 bits (141), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 27/51 (52%), Positives = 36/51 (70%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLI 72
           LM  KSNL TP+NGE +IAA QDFIT  YLL+ K+ FF+R    +I  +++
Sbjct: 536 LMGVKSNLATPKNGEPIIAAIQDFITAAYLLSSKDNFFDRKTFTQICLSML 586



 Score = 42.0 bits (97), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 18/39 (46%), Positives = 28/39 (71%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  FDA   G+ D + GVSECIIMG  +++GTG +++++
Sbjct: 1366 DHLFDAGGAGRRDTVQGVSECIIMGKTISLGTGSMEVVR 1404


>gi|380495147|emb|CCF32618.1| RNA polymerase Rpb1 [Colletotrichum higginsianum]
          Length = 1456

 Score =  288 bits (736), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 147/293 (50%), Positives = 185/293 (63%), Gaps = 37/293 (12%)

Query: 331 RPSVISDLK---------SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPY 381
           R  V  DLK          DND+VLFNRQPSLHKLSIM+H  KV P RTFR NECVC PY
Sbjct: 448 RNQVAQDLKIGDVVERHLEDNDIVLFNRQPSLHKLSIMSHLVKVRPWRTFRLNECVCGPY 507

Query: 382 NADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAAT 441
           NADFDGDEMN+H+PQTEEARAEA+               LM  K NL TP+NGE +IAAT
Sbjct: 508 NADFDGDEMNLHVPQTEEARAEAIN--------------LMGVKHNLATPKNGEPVIAAT 553

Query: 442 QDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIW 501
           QDFIT  YLL+ K+ FF+R     I   ++     +             P   ++   +W
Sbjct: 554 QDFITAAYLLSSKDNFFDRKTFTYICMHMMDGKVHL----------DLPPPAVLKPKALW 603

Query: 502 TGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFC----HRDSYVILRNSELLAGSMDK 557
           TGKQ+FS++++PN+D PV  NL  K R Y A    C      D+++++RNSE++ G MDK
Sbjct: 604 TGKQVFSMMMRPNKDSPVKINLDAKCREYKARAGQCPDMDPEDAWLVIRNSEVMCGVMDK 663

Query: 558 STLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           ST+G G K +VFY++LRDFG D AV  M RL+++ + +L NRGFSIGIGDV P
Sbjct: 664 STVGDGKKDSVFYVILRDFGPDAAVVTMNRLAKLCARHLTNRGFSIGIGDVFP 716



 Score =  201 bits (512), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 139/362 (38%), Positives = 185/362 (51%), Gaps = 77/362 (21%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGE------------------- 1146
            C EKY +A +EP  AVGA+ AQSIGEPGTQMTLKTFHFAG                    
Sbjct: 1066 CLEKYKKAHVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIINAS 1125

Query: 1147 -----------------------VCEYIEEVFVPD------DSF------ILIKLDMDRI 1171
                                   V   IE+ FV D      D +      +++K+DMD +
Sbjct: 1126 KVISTPVITCPLVQNREMTAARIVKARIEKTFVEDILSYIEDEWFAESGSVVLKVDMDAL 1185

Query: 1172 RLLHLEVDIDSIRYCIERTRGI----------SGHLTV--------SGHSFLILKPKDSS 1213
              + L + +  +   I + + +          +G + +        +    +  KP D  
Sbjct: 1186 SDMQLGITLGDVAEAICKHKKMKVSRSDMHIGAGRIEIRVRLDESAAAKRAIKAKPVDEL 1245

Query: 1214 KSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVK 1273
                 +   +++ +P+V I G     RA+I   + E    + +LVEG  L   M T GV+
Sbjct: 1246 GDLLVRANYLRRTIPTVAISGYPEATRAIIQTSEQE---THTVLVEGYGLLACMNTEGVE 1302

Query: 1274 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 1333
            G +  SNN  E    LGIEAARSTI  EI  VM +  M+ID RH  L+AD+MT KGEVLG
Sbjct: 1303 GRRVKSNNVMECRDVLGIEAARSTIAYEIGEVMGD--MNIDPRHMQLLADVMTYKGEVLG 1360

Query: 1334 ITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            ITR GL+KM++SVL LASFE T DHLF+AA   +TD I GVSECIIMG  M VGTG   +
Sbjct: 1361 ITRFGLSKMRDSVLQLASFEKTPDHLFEAAAGMKTDQIEGVSECIIMGQTMTVGTGAFHV 1420

Query: 1394 LQ 1395
            ++
Sbjct: 1421 VR 1422



 Score =  193 bits (490), Expect = 8e-46,   Method: Compositional matrix adjust.
 Identities = 107/283 (37%), Positives = 157/283 (55%), Gaps = 10/283 (3%)

Query: 67  IASTLIAGRKVFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMG 126
           + S L+      F+G+  G  + +D +  Q+ +++  + LY  +  R P  HG LD R+G
Sbjct: 10  VKSQLVDKLPKRFKGIKFGIQSNQD-IANQAVLEVSDRLLYDIEKNRAPYQHGPLDPRLG 68

Query: 127 TNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGE 186
           T+ K   C TC ++L +C GHFG++ LPLP FHIGY R V+ ILQ ICK+  C +VLL E
Sbjct: 69  TSSKTGKCATCQESLQNCTGHFGHVRLPLPAFHIGYLRFVMMILQDICKD--CGKVLLTE 126

Query: 187 EKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEK- 245
            +   F  +LR P L  L R  + K+I E  +KV  C +CG + G ++K G+LK++H+K 
Sbjct: 127 SEKRAFLKELRRPLLDNLRRSQICKRINEQCRKVKNCMYCGSVQGQIRKVGVLKLAHDKF 186

Query: 246 --YKNRTKKKDAIVEDLLA---EYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPL 300
             Y   T  K    E  +     ++EA K N E++ H +  + + +NPL VL LF+ I  
Sbjct: 187 VTYNKSTSAKKVPPESKIKFDESFSEARKNNAELDKHLRKAM-EDMNPLRVLNLFKMISP 245

Query: 301 EDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
            D  LL ++    +P   I   L  PP CIRPSV  D  S+ D
Sbjct: 246 TDCELLGLDPAEGRPEMFIWQFLPAPPVCIRPSVAQDNASNED 288



 Score =  139 bits (350), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 97/276 (35%), Positives = 148/276 (53%), Gaps = 24/276 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+IT  L ++ ++  ARIVK R+E+T + ++  YIE+ +  + 
Sbjct: 1114 GVPRIKEIINASKVISTPVITCPLVQNREMTAARIVKARIEKTFVEDILSYIEDEWFAES 1173

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI----------SGHLTV--------SG 865
              +++K+DMD +  + L + +  +   I + + +          +G + +        + 
Sbjct: 1174 GSVVLKVDMDALSDMQLGITLGDVAEAICKHKKMKVSRSDMHIGAGRIEIRVRLDESAAA 1233

Query: 866  HSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD 925
               +  KP D       +   +++ +P+V I G     RA+I   + E    + +LVEG 
Sbjct: 1234 KRAIKAKPVDELGDLLVRANYLRRTIPTVAISGYPEATRAIIQTSEQE---THTVLVEGY 1290

Query: 926  NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 985
             L   M T GV+G +  SNN  E    LGIEAARSTI  EI  VM +  M+ID RH  L+
Sbjct: 1291 GLLACMNTEGVEGRRVKSNNVMECRDVLGIEAARSTIAYEIGEVMGD--MNIDPRHMQLL 1348

Query: 986  ADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDP 1021
            AD+MT KGEVLG  T   L ++ D ++   S    P
Sbjct: 1349 ADVMTYKGEVLGI-TRFGLSKMRDSVLQLASFEKTP 1383



 Score =  105 bits (262), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 47/59 (79%), Positives = 51/59 (86%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSF+SGL PTEF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 840 PSKGFVENSFYSGLLPTEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSTQYD 898



 Score = 59.3 bits (142), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 28/54 (51%), Positives = 36/54 (66%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           LM  K NL TP+NGE +IAATQDFIT  YLL+ K+ FF+R     I   ++ G+
Sbjct: 533 LMGVKHNLATPKNGEPVIAATQDFITAAYLLSSKDNFFDRKTFTYICMHMMDGK 586



 Score = 42.4 bits (98), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 21/39 (53%), Positives = 26/39 (66%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  F+AA   +TD I GVSECIIMG  M VGTG   +++
Sbjct: 1384 DHLFEAAAGMKTDQIEGVSECIIMGQTMTVGTGAFHVVR 1422


>gi|146415288|ref|XP_001483614.1| DNA-directed RNA polymerase III largest subunit [Meyerozyma
           guilliermondii ATCC 6260]
          Length = 1379

 Score =  287 bits (734), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 144/276 (52%), Positives = 191/276 (69%), Gaps = 29/276 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH+LSI++H AK+ P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 395 DGDVVLFNRQPSLHRLSILSHYAKIRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 454

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL+TP++GE +IAATQDFITG YL++ K++F++R
Sbjct: 455 RAEAIN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFYDR 500

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A  +++ S +++D            +    P +F +  ++WTGKQ+FSL++KPN++  V 
Sbjct: 501 ATFIQLLS-MMSDAD--------LQFDLPPPTIF-KPVMLWTGKQVFSLLMKPNKNSNVI 550

Query: 521 ANLKTKGRAYTA-----NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL  K +A+T        E    D YVI+R S++L+G MDK TLG G K +VFY +LRD
Sbjct: 551 VNLDAKNKAFTPPAPGYPNEMSPNDGYVIIRGSQVLSGVMDKLTLGDGKKHSVFYTILRD 610

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           FG D A  AM R++++ + YL NRGFSIGI DVTPG
Sbjct: 611 FGPDAAAEAMNRMAKLCARYLGNRGFSIGINDVTPG 646



 Score =  259 bits (661), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 169/450 (37%), Positives = 246/450 (54%), Gaps = 97/450 (21%)

Query: 1037 DSKEFL--QDTSENFVRDIKKF-------LEEFSKKESVTSHQDKVSQ---PLREQILSH 1084
            DS+EF+   D    F + I++F       L E  + +++ S   + +    P++   ++ 
Sbjct: 916  DSEEFIDQNDAERAFYKSIREFVLEKASQLAEIRQSKNLKSGWSRPASKDDPVQLNAVNQ 975

Query: 1085 QDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFA 1144
              KI   +  N F      + C  KY RA++EP TAVGA+ AQSIGEPGTQMTLKTFHFA
Sbjct: 976  LSKISL-KAINKF-----LDQCIYKYSRAKVEPGTAVGAIGAQSIGEPGTQMTLKTFHFA 1029

Query: 1145 G--------------EVCE--------YIEEVFVPDD----------------------- 1159
            G              E+           I  V V DD                       
Sbjct: 1030 GVASMNVTLGVPRIKEIINASKVISTPIINGVLVNDDDEIAARVVKGRIEKTLLEDVAFF 1089

Query: 1160 ---------SFILIKLDMDRIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSGHSFLIL 1207
                     +++ +K+D+D I  L LE+ I+SI + I    + + ++  ++++G   + +
Sbjct: 1090 IEDVYKDNLAYLSVKIDLDTIEKLQLELTIESIAHAIVTAPKLKIVASDVSIAGRDRINV 1149

Query: 1208 -------------------KPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDV 1248
                               +  DS+ S   +M Q+K+ LPSV IKG+  I+RAVI+ +D 
Sbjct: 1150 LVTLRETKADLLKNMADDYRASDSTNSLFFRMQQLKRALPSVCIKGLPEISRAVINIKD- 1208

Query: 1249 EGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMEN 1308
                K +LLVEG  L+ VM+T G+ G K ++N+  EV++ LGIEAAR++I+ EI   M  
Sbjct: 1209 --NGKKELLVEGYGLKQVMSTDGIIGTKTTTNHVLEVFEVLGIEAARASIIGEIDYTMSK 1266

Query: 1309 HGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQT 1368
            HGMS+D RH  L+ D+M+ KGEVLGITR GL+KM++SVL LASFE T+DHLFDAAFY + 
Sbjct: 1267 HGMSVDPRHIQLLGDVMSYKGEVLGITRFGLSKMRDSVLQLASFEKTTDHLFDAAFYMKK 1326

Query: 1369 DCISGVSECIIMGLPMNVGTGLIKLLQAVP 1398
            D I GVSECII+G  M++GTG  +L+++ P
Sbjct: 1327 DQIEGVSECIILGQTMSIGTGAFQLVKSSP 1356



 Score =  186 bits (472), Expect = 9e-44,   Method: Compositional matrix adjust.
 Identities = 108/256 (42%), Positives = 161/256 (62%), Gaps = 25/256 (9%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII   L  D D   AR+VKGR+E+T L +V  +IE+V+  + 
Sbjct: 1039 GVPRIKEIINASKVISTPIINGVLVNDDDEIAARVVKGRIEKTLLEDVAFFIEDVYKDNL 1098

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSGHSFLIL--------- 871
            +++ +K+D+D I  L LE+ I+SI + I    + + ++  ++++G   + +         
Sbjct: 1099 AYLSVKIDLDTIEKLQLELTIESIAHAIVTAPKLKIVASDVSIAGRDRINVLVTLRETKA 1158

Query: 872  ----------KPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLL 921
                      +  DS+ S   +M Q+K+ LPSV IKG+  I+RAVI+ +D     K +LL
Sbjct: 1159 DLLKNMADDYRASDSTNSLFFRMQQLKRALPSVCIKGLPEISRAVINIKD---NGKKELL 1215

Query: 922  VEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRH 981
            VEG  L+ VM+T G+ G K ++N+  EV++ LGIEAAR++I+ EI   M  HGMS+D RH
Sbjct: 1216 VEGYGLKQVMSTDGIIGTKTTTNHVLEVFEVLGIEAARASIIGEIDYTMSKHGMSVDPRH 1275

Query: 982  PMLVADLMTSKGEVLG 997
              L+ D+M+ KGEVLG
Sbjct: 1276 IQLLGDVMSYKGEVLG 1291



 Score =  128 bits (322), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 82/203 (40%), Positives = 107/203 (52%), Gaps = 10/203 (4%)

Query: 148 FGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRK 207
            G+I L LPVFH+GYFR VI +LQ ICK   C+ VLL EE    F   LR P +  L R 
Sbjct: 11  LGHIRLALPVFHVGYFRAVILVLQCICK--LCSAVLLDEETKRKFLNDLRRPGIDNLRRM 68

Query: 208 SLKKKILETTKKVSVCPHCGEINGVVKKC------GLLKISHEKYKNRTKKKDAIVEDLL 261
              KK+++  KK   C  C  INGVVKK         LKI H+ ++   KK     +   
Sbjct: 69  KTLKKVVDQCKKQRRCLRCYHINGVVKKAASGSGPAALKIVHDTFRWVGKKSAPEKDAWD 128

Query: 262 AEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL-SKPSDLIL 320
            E++E    NPE+E   K  +   LNPL+VL LF+ I  +D  L  ++A    +P   I 
Sbjct: 129 QEFDEVFARNPEVEKFAK-RVHDDLNPLKVLNLFKQITPQDCELFGIDASRGGRPEMYIW 187

Query: 321 TRLLVPPNCIRPSVISDLKSDND 343
             L  PP CIRPSV+ D + + D
Sbjct: 188 RYLPAPPVCIRPSVMMDAQLNED 210



 Score =  101 bits (251), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 47/61 (77%), Positives = 52/61 (85%), Gaps = 1/61 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV+NSFFSGL+P EF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QY
Sbjct: 767 TPQSKGFVRNSFFSGLSPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSAQY 826

Query: 668 D 668
           D
Sbjct: 827 D 827



 Score = 61.6 bits (148), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 26/50 (52%), Positives = 41/50 (82%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM  K+NL+TP++GE +IAATQDFITG YL++ K++F++RA  +++ S +
Sbjct: 461 LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFYDRATFIQLLSMM 510



 Score = 52.4 bits (124), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 23/42 (54%), Positives = 31/42 (73%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 709
            D  FDAAFY + D I GVSECII+G  M++GTG  +L+++ P
Sbjct: 1315 DHLFDAAFYMKKDQIEGVSECIILGQTMSIGTGAFQLVKSSP 1356


>gi|365984467|ref|XP_003669066.1| hypothetical protein NDAI_0C01620 [Naumovozyma dairenensis CBS 421]
 gi|343767834|emb|CCD23823.1| hypothetical protein NDAI_0C01620 [Naumovozyma dairenensis CBS 421]
          Length = 1460

 Score =  287 bits (734), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 146/282 (51%), Positives = 187/282 (66%), Gaps = 30/282 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH+LSI++H AK+ P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 468 DGDVVLFNRQPSLHRLSILSHYAKIRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 527

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+R
Sbjct: 528 RAEAIN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDR 573

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A       TL    S +C    +F      P   ++   +WTGKQ+FSL++KPN+D PV 
Sbjct: 574 A-------TLTQLLSMMCDANLQF---DIPPPAIMKPHYLWTGKQLFSLLIKPNKDSPVV 623

Query: 521 ANLKTKGRAYTANE------EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLR 574
            NL  K + Y   +      E    D YVI+R S++L+G MDKS LG G K +VFY +LR
Sbjct: 624 INLDAKNKVYIPPKTKAYPNEMSRNDGYVIIRGSQILSGVMDKSVLGDGKKHSVFYTILR 683

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           D+G   A TAM R++++ + +L NRGFSIGI DVTP     Q
Sbjct: 684 DYGPQEAATAMNRMAKLCARFLGNRGFSIGISDVTPADDLKQ 725



 Score =  246 bits (627), Expect = 8e-62,   Method: Compositional matrix adjust.
 Identities = 156/377 (41%), Positives = 214/377 (56%), Gaps = 77/377 (20%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG----------------------- 1145
            KY +A++EP TAVGA+ AQSIGEPGTQMTLKTFHFAG                       
Sbjct: 1077 KYRKARVEPGTAVGAIGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIINASKVI 1136

Query: 1146 -------------------EVCEYIEEVFVPDDSF------------ILIKLDMDRIRLL 1174
                                V   IE+  + D ++            I +++D++ I  L
Sbjct: 1137 STPIINAVLVNENDERAARVVKGRIEKTLLSDVAYYIQDVYKDNLSFIQVRIDLNTIEKL 1196

Query: 1175 HLEVDIDSIRYCIERT---RGISGHLTVSGHSFLIL-------KPKDSSKSF-----NSK 1219
             LE+ I+ I   + R    + ++  + + G   + +       K K  S +      N+ 
Sbjct: 1197 QLELTIEDIAVALTRAPKLKILTSDVNIIGKDKIAINVFPEGYKAKSISTAAKEPTENAV 1256

Query: 1220 MYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 1276
             Y+M+ L   LPS+V+KG+  I RAVI+  D +G  K +LLVEG  LRDVM T GV G+K
Sbjct: 1257 FYRMQHLRRALPSIVVKGLPEIARAVINIRD-DG--KRELLVEGYGLRDVMCTDGVIGMK 1313

Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITR 1336
             ++N+  EV   LGIEAARS+I+ EI   M NHGMS+D RH  L+ D+MT KGEVLGITR
Sbjct: 1314 TTTNHILEVNTVLGIEAARSSIVGEIDYTMSNHGMSVDPRHIQLLGDVMTYKGEVLGITR 1373

Query: 1337 HGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA 1396
             GL+KM++SVL LASFE T+DHLFDAAFY + D + GVSECII+G  M++GTG  K+++ 
Sbjct: 1374 FGLSKMRDSVLQLASFEKTTDHLFDAAFYMKKDAVEGVSECIILGQTMSIGTGSFKVVKG 1433

Query: 1397 --VPRSEPVPRTLLFDN 1411
              + +    P+  LF+N
Sbjct: 1434 TEIAKESLKPKPTLFEN 1450



 Score =  184 bits (467), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 115/252 (45%), Positives = 159/252 (63%), Gaps = 21/252 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII A L  + D   AR+VKGR+E+T L +V  YI++V+  + 
Sbjct: 1122 GVPRIKEIINASKVISTPIINAVLVNENDERAARVVKGRIEKTLLSDVAYYIQDVYKDNL 1181

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERT---RGISGHLTVSGHSFLIL-------KP 873
            SFI +++D++ I  L LE+ I+ I   + R    + ++  + + G   + +       K 
Sbjct: 1182 SFIQVRIDLNTIEKLQLELTIEDIAVALTRAPKLKILTSDVNIIGKDKIAINVFPEGYKA 1241

Query: 874  KDSSKSF-----NSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD 925
            K  S +      N+  Y+M+ L   LPS+V+KG+  I RAVI+  D +G  K +LLVEG 
Sbjct: 1242 KSISTAAKEPTENAVFYRMQHLRRALPSIVVKGLPEIARAVINIRD-DG--KRELLVEGY 1298

Query: 926  NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 985
             LRDVM T GV G+K ++N+  EV   LGIEAARS+I+ EI   M NHGMS+D RH  L+
Sbjct: 1299 GLRDVMCTDGVIGMKTTTNHILEVNTVLGIEAARSSIVGEIDYTMSNHGMSVDPRHIQLL 1358

Query: 986  ADLMTSKGEVLG 997
             D+MT KGEVLG
Sbjct: 1359 GDVMTYKGEVLG 1370



 Score =  171 bits (433), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 97/248 (39%), Positives = 136/248 (54%), Gaps = 11/248 (4%)

Query: 96  QSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPL 155
           QS ++I S++L+  +  R P   G LD+RMG +     C TC  NL+ C GHFG+I L L
Sbjct: 29  QSEVEISSRDLFDLEKGREPKTGGALDKRMGVSSSSLECETCHGNLASCHGHFGHIKLAL 88

Query: 156 PVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILE 215
           PVFH+GYF+  I ILQ ICK  TC+ +LL ++    F  +LR P +  L R  + KK+L+
Sbjct: 89  PVFHVGYFKATIQILQGICK--TCSAILLSDKDRRQFLNELRRPGVDNLRRMGILKKVLD 146

Query: 216 TTKKVSVCPHCGEINGVV------KKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVK 269
             KK   C  CG +NGVV           LKI H+ ++   KK     +  + ++ E + 
Sbjct: 147 QCKKQRRCLQCGALNGVVKKAAAGAGSASLKIIHDNFRWVGKKSAPEKDKWVGDWKEVLS 206

Query: 270 FNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL--SKPSDLILTRLLVPP 327
            +PE+E   K      LNPL+ L LF+ I  ED  LL +N+ +   +P   I   L  PP
Sbjct: 207 HHPELERFVK-RCSDDLNPLKTLNLFKQIKPEDCELLGVNSTVKSGRPETYIWRYLPAPP 265

Query: 328 NCIRPSVI 335
            CIRPSV+
Sbjct: 266 VCIRPSVM 273



 Score =  102 bits (253), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 46/57 (80%), Positives = 50/57 (87%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NSFFSGLTP EF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 845 KGFVRNSFFSGLTPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSCQYD 901



 Score = 62.4 bits (150), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/50 (54%), Positives = 40/50 (80%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+RA   ++ S +
Sbjct: 534 LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDRATLTQLLSMM 583



 Score = 53.9 bits (128), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 25/57 (43%), Positives = 37/57 (64%), Gaps = 2/57 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA--VPRSEPVPRTLLFDN 722
            D  FDAAFY + D + GVSECII+G  M++GTG  K+++   + +    P+  LF+N
Sbjct: 1394 DHLFDAAFYMKKDAVEGVSECIILGQTMSIGTGSFKVVKGTEIAKESLKPKPTLFEN 1450


>gi|342886359|gb|EGU86224.1| hypothetical protein FOXB_03263 [Fusarium oxysporum Fo5176]
          Length = 1404

 Score =  287 bits (734), Expect = 4e-74,   Method: Compositional matrix adjust.
 Identities = 141/274 (51%), Positives = 182/274 (66%), Gaps = 28/274 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND+VLFNRQPSLHKLSIM+H AKV P RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 422 DNDIVLFNRQPSLHKLSIMSHLAKVRPWRTFRLNECVCGPYNADFDGDEMNLHVPQTEEA 481

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K NL TP+NGE +IAATQDFIT  +LL+ K+ FF+R
Sbjct: 482 RAEAIN--------------LMGIKHNLATPKNGEPVIAATQDFITAAFLLSSKDRFFDR 527

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                +   ++   + +             P   +    +WTGKQ+FS++++PN+D PV 
Sbjct: 528 KTFTYLCMHMMDGKTHL----------DMPPPAIIAPQSLWTGKQLFSMLMRPNKDSPVK 577

Query: 521 ANLKTKGRAYTANEEFC----HRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL  K RAY A    C      D ++++RNSE++ G MDKST+G+G K ++FY++LRDF
Sbjct: 578 VNLDAKCRAYKARPGQCPDMDPNDGWLVVRNSEVMCGRMDKSTVGTGKKDSIFYVILRDF 637

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           G D AV AM RL+++ +  L NRGFSIG+GDV P
Sbjct: 638 GPDEAVIAMNRLAKLCARQLTNRGFSIGVGDVFP 671



 Score =  164 bits (414), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 104/273 (38%), Positives = 151/273 (55%), Gaps = 25/273 (9%)

Query: 1143 FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTV 1199
            +  +V  ++E+ +   +  +++++D   +  +HL +    I   I + R +      L++
Sbjct: 1103 YISDVLRFVEDEWRTTEGNVVLQIDSAALSDMHLGIGPYDIAEAICKQRKLKVQRDDLSI 1162

Query: 1200 SGHSFLI-----LKPKDSSKSFNSKMYQ------------MKQLLPSVVIKGVQGINRAV 1242
             G   ++       P     +  SK               +++ LP+V I G     RA+
Sbjct: 1163 DGERIIVRVRDVTDPATKRTTARSKAAAAETGDMLLRANFLRRSLPNVPISGYPEATRAI 1222

Query: 1243 IHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEI 1302
            I   +    + + +LVEG  LR+ M T GV G K  +NN  E    LGIEAAR+TI  EI
Sbjct: 1223 IQTSEQ---STHTVLVEGYGLRECMTTEGVIGTKARTNNVMECRDVLGIEAARTTIADEI 1279

Query: 1303 KLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDA 1362
              VM +  M ID RH  L+AD+MT KGEVLGITR GL+KM++SVL LASFE T DHLF+A
Sbjct: 1280 GEVMGD--MGIDPRHMQLLADVMTYKGEVLGITRFGLSKMRDSVLQLASFEKTPDHLFEA 1337

Query: 1363 AFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 1395
            A   +TD I GVSECIIMG  M+VGTG  ++++
Sbjct: 1338 AAGMKTDQIEGVSECIIMGQTMSVGTGAFQVVR 1370



 Score =  142 bits (359), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 97/278 (34%), Positives = 147/278 (52%), Gaps = 26/278 (9%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+IT  L+ +  ++ AR+VKGR+E+T + +V  ++E+ +   +
Sbjct: 1060 GVPRIKEIINASKAISTPVITCPLENNEQIEAARVVKGRIEKTYISDVLRFVEDEWRTTE 1119

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSFL-----ILKPKD 875
              +++++D   +  +HL +    I   I + R +      L++ G   +     +  P  
Sbjct: 1120 GNVVLQIDSAALSDMHLGIGPYDIAEAICKQRKLKVQRDDLSIDGERIIVRVRDVTDPAT 1179

Query: 876  SSKSFNSKMYQ------------MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVE 923
               +  SK               +++ LP+V I G     RA+I   +    + + +LVE
Sbjct: 1180 KRTTARSKAAAAETGDMLLRANFLRRSLPNVPISGYPEATRAIIQTSE---QSTHTVLVE 1236

Query: 924  GDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPM 983
            G  LR+ M T GV G K  +NN  E    LGIEAAR+TI  EI  VM +  M ID RH  
Sbjct: 1237 GYGLRECMTTEGVIGTKARTNNVMECRDVLGIEAARTTIADEIGEVMGD--MGIDPRHMQ 1294

Query: 984  LVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDP 1021
            L+AD+MT KGEVLG  T   L ++ D ++   S    P
Sbjct: 1295 LLADVMTYKGEVLGI-TRFGLSKMRDSVLQLASFEKTP 1331



 Score =  120 bits (300), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 84/271 (30%), Positives = 123/271 (45%), Gaps = 56/271 (20%)

Query: 79  FRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCG 138
           F+G+  G  + +D +  Q+ +++  + LY  +  R P  HG LD R+             
Sbjct: 23  FKGIKFGIQSNQD-IANQAVLEVSDRLLYDIENNRAPYRHGPLDSRL------------- 68

Query: 139 QNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN 198
                                             ICK+  C RVLL E +   F  +LR 
Sbjct: 69  ---------------------------------EICKD--CGRVLLEEPERQQFLKELRR 93

Query: 199 PALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEK---YKNRTKKKDA 255
           P L  L R  + KKI E  +K+  CP+CG +NG ++K G+LK++H+K   Y   T  K  
Sbjct: 94  PFLDNLRRTQICKKINEQCRKIKTCPYCGSLNGQIRKIGVLKLAHDKFVAYNKSTAAKKV 153

Query: 256 IVEDLLA---EYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL 312
             E  +     +NEA + NPE++ H +  + + LNPL VL LF+ I   D  LL ++   
Sbjct: 154 PPESKIKFDNSFNEAKRENPELDKHLRKAM-EDLNPLRVLNLFKMISPTDCELLGLDPAE 212

Query: 313 SKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
            +P   I   L  PP CIRPSV  D  S+ D
Sbjct: 213 GRPEMFIWQFLPAPPVCIRPSVAQDNASNED 243



 Score =  103 bits (257), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 46/59 (77%), Positives = 51/59 (86%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSF++GL PTEF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 795 PSKGFVKNSFYTGLFPTEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSTQYD 853



 Score = 68.9 bits (167), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 30/40 (75%), Positives = 33/40 (82%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            C EKY +A +EP  AVGA+ A SIGEPGTQMTLKTFHFAG
Sbjct: 1012 CLEKYKKAHVEPGHAVGAVGAHSIGEPGTQMTLKTFHFAG 1051



 Score = 56.6 bits (135), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/40 (62%), Positives = 31/40 (77%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           LM  K NL TP+NGE +IAATQDFIT  +LL+ K+ FF+R
Sbjct: 488 LMGIKHNLATPKNGEPVIAATQDFITAAFLLSSKDRFFDR 527



 Score = 43.5 bits (101), Expect = 0.80,   Method: Compositional matrix adjust.
 Identities = 21/39 (53%), Positives = 28/39 (71%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  F+AA   +TD I GVSECIIMG  M+VGTG  ++++
Sbjct: 1332 DHLFEAAAGMKTDQIEGVSECIIMGQTMSVGTGAFQVVR 1370


>gi|46136689|ref|XP_390036.1| hypothetical protein FG09860.1 [Gibberella zeae PH-1]
          Length = 2443

 Score =  286 bits (732), Expect = 5e-74,   Method: Compositional matrix adjust.
 Identities = 141/280 (50%), Positives = 182/280 (65%), Gaps = 28/280 (10%)

Query: 341  DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
            DND+VLFNRQPSLHKLSIM+H AKV P RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 1461 DNDIVLFNRQPSLHKLSIMSHLAKVRPWRTFRLNECVCGPYNADFDGDEMNLHVPQTEEA 1520

Query: 401  RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
            RAEA+               LM  K NL TP+NGE +IAATQDFIT  YLL+ K+ FF+R
Sbjct: 1521 RAEAI--------------NLMGIKHNLATPKNGEPVIAATQDFITAAYLLSGKDRFFDR 1566

Query: 461  AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                 +   ++   + +             P   +    +WTGKQ+F ++++PN+D PV 
Sbjct: 1567 KTFTYLCMHMMDGKTHL----------DLPPPAIIAPQSLWTGKQLFGMLMRPNKDSPVK 1616

Query: 521  ANLKTKGRAYTANEEFC----HRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
             NL  K + Y A    C      D ++++RNSE++ G MDKST+G G K ++FY++LRDF
Sbjct: 1617 VNLDAKCKTYKARPGQCPDMDPNDGWLVVRNSEVMCGRMDKSTVGDGKKDSIFYVILRDF 1676

Query: 577  GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
            G D AVTAM RL+++ +  L N GFSIGIGDV P +  +Q
Sbjct: 1677 GPDEAVTAMNRLAKLCARQLTNHGFSIGIGDVFPPESLIQ 1716



 Score =  202 bits (513), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 105/257 (40%), Positives = 149/257 (57%), Gaps = 9/257 (3%)

Query: 93   VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
            +  Q+ +++  + LY  +  R P  HG LD R+GT+ K+  C+TC ++L DC GHFG++ 
Sbjct: 1029 IANQAVLEVSDRLLYDIENNRAPYRHGPLDSRLGTSSKQGRCSTCQESLKDCNGHFGHVR 1088

Query: 153  LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKK 212
            LPLP FH+GY R +++ILQ ICK+  C RVLL E     F   LR P L  L R  + K+
Sbjct: 1089 LPLPAFHVGYLRFIMSILQEICKD--CGRVLLDEPDRQQFLKDLRRPFLDNLRRTQICKR 1146

Query: 213  ILETTKKVSVCPHCGEINGVVKKCGLLKISHEK---YKNRTKKKDAIVEDLLA---EYNE 266
            I E  +KV  CP+CG +NG ++K G+LK++H+K   Y   T  K    E  +     +NE
Sbjct: 1147 INEQCRKVKTCPYCGSLNGQIRKIGVLKLAHDKFVAYNKSTSIKKTPPESKIKFDNSFNE 1206

Query: 267  AVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVP 326
            A + NPE++ H +  + + LNPL VL LF+ I   D  LL ++    +P   I   L  P
Sbjct: 1207 AKRENPELDKHLRKAM-EDLNPLRVLNLFKMISPTDCELLGLDPAEGRPEMFIWQFLPAP 1265

Query: 327  PNCIRPSVISDLKSDND 343
            P CIRPSV  D  S+ D
Sbjct: 1266 PVCIRPSVAQDNASNED 1282



 Score =  168 bits (425), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 97/191 (50%), Positives = 125/191 (65%), Gaps = 7/191 (3%)

Query: 1223 MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNT 1282
            +++ LP+V I G     RA+I   +      + +LVEG  LR+ M T GV G K SSNN 
Sbjct: 2242 LRRALPNVPISGYSEATRAIIQTSEQ---NTHTVLVEGYGLRECMTTEGVIGTKASSNNV 2298

Query: 1283 YEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKM 1342
             E    LGIEAAR+TI  EI  VM +  M+ID RH  L+AD+MT KGEVLGITR GL+KM
Sbjct: 2299 MECRDVLGIEAARTTIAVEIGSVMGD--MNIDPRHMQLLADVMTYKGEVLGITRFGLSKM 2356

Query: 1343 KESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ--AVPRS 1400
            ++SVL LASFE T DHLF+AA   +TD I GVSECIIMG  M+VGTG  ++++   +  S
Sbjct: 2357 RDSVLQLASFEKTPDHLFEAAAGMKTDQIEGVSECIIMGQTMSVGTGAFQVVRRLGIRDS 2416

Query: 1401 EPVPRTLLFDN 1411
            E   +  LF++
Sbjct: 2417 EVKKKLTLFED 2427



 Score =  146 bits (368), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 94/254 (37%), Positives = 139/254 (54%), Gaps = 25/254 (9%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+IT  L+ +  ++ AR+VKGR+E+T + ++  ++E+ +   +
Sbjct: 2099 GVPRIKEIINASKAISTPVITCPLENNEQIEAARVVKGRIEKTYISDILRFVEDEWRTTE 2158

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSFL-----ILKPKD 875
              +++++D   +  +HL +    I   I + R +      L++ G   +     I  P  
Sbjct: 2159 GNVVLQIDPTALSDMHLGIGPYDIAEAICKQRKLKVQRDDLSIDGDRIIVRVRDISDPAA 2218

Query: 876  SSKSFNSKMYQ------------MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVE 923
               +  SK               +++ LP+V I G     RA+I   +      + +LVE
Sbjct: 2219 KRTATRSKAAAAESGDMLLRANFLRRALPNVPISGYSEATRAIIQTSE---QNTHTVLVE 2275

Query: 924  GDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPM 983
            G  LR+ M T GV G K SSNN  E    LGIEAAR+TI  EI  VM +  M+ID RH  
Sbjct: 2276 GYGLRECMTTEGVIGTKASSNNVMECRDVLGIEAARTTIAVEIGSVMGD--MNIDPRHMQ 2333

Query: 984  LVADLMTSKGEVLG 997
            L+AD+MT KGEVLG
Sbjct: 2334 LLADVMTYKGEVLG 2347



 Score =  106 bits (265), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 47/59 (79%), Positives = 52/59 (88%)

Query: 610  PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            P +GFV+NSF+SGL+PTEF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 1834 PSKGFVKNSFYSGLSPTEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSTQYD 1892



 Score = 69.3 bits (168), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 30/40 (75%), Positives = 33/40 (82%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            C EKY +A +EP  AVGA+ A SIGEPGTQMTLKTFHFAG
Sbjct: 2051 CLEKYKKAHVEPGHAVGAVGAHSIGEPGTQMTLKTFHFAG 2090



 Score = 57.8 bits (138), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 26/40 (65%), Positives = 31/40 (77%)

Query: 22   LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
            LM  K NL TP+NGE +IAATQDFIT  YLL+ K+ FF+R
Sbjct: 1527 LMGIKHNLATPKNGEPVIAATQDFITAAYLLSGKDRFFDR 1566



 Score = 43.9 bits (102), Expect = 0.61,   Method: Compositional matrix adjust.
 Identities = 25/57 (43%), Positives = 36/57 (63%), Gaps = 2/57 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ--AVPRSEPVPRTLLFDN 722
            D  F+AA   +TD I GVSECIIMG  M+VGTG  ++++   +  SE   +  LF++
Sbjct: 2371 DHLFEAAAGMKTDQIEGVSECIIMGQTMSVGTGAFQVVRRLGIRDSEVKKKLTLFED 2427


>gi|302661310|ref|XP_003022324.1| hypothetical protein TRV_03535 [Trichophyton verrucosum HKI 0517]
 gi|291186264|gb|EFE41706.1| hypothetical protein TRV_03535 [Trichophyton verrucosum HKI 0517]
          Length = 1444

 Score =  286 bits (732), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 138/280 (49%), Positives = 185/280 (66%), Gaps = 28/280 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + D+VLFNRQPSLHKLSI++H  KV PHRTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 470 NGDIVLFNRQPSLHKLSILSHFVKVRPHRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 529

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  KSNL TP+NGE +IAA QDFIT  YLL+ K+ FF+R
Sbjct: 530 RAEAME--------------LMGVKSNLATPKNGEPIIAAIQDFITAAYLLSSKDNFFDR 575

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
               +I  +++  ++       RF      P   ++  ++WTGKQ+FS++++PN+DCPV 
Sbjct: 576 KTFTQICLSMLDSST-------RF---ELPPPATIKPQMLWTGKQVFSVLMRPNKDCPVK 625

Query: 521 ANLKTKGRAYT----ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL    R          + C  D ++ +RNSE+L G  DKST+G+G K N+F+++ RDF
Sbjct: 626 VNLDAACRQLKLVKGQPRDLCENDGWLCIRNSEMLCGVADKSTIGAGKKDNIFFVIQRDF 685

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           G   A  AM RLS++++ +L N+GFSIGI DV PG+  V+
Sbjct: 686 GYAAAAEAMNRLSKLSARWLTNKGFSIGITDVYPGESLVK 725



 Score =  176 bits (446), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 102/267 (38%), Positives = 150/267 (56%), Gaps = 12/267 (4%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G ++ +D +  Q+H++I  + L+  D  R    +G +D R+G + K   C TCG +L +C
Sbjct: 30  GVLSNQD-IISQAHVEISDRKLFDLDNNRAVARNGPMDPRLGISNKSDTCETCGGDLQEC 88

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFGY+ L LP FH+GYF+  I ILQ ICK+  C+++LL E++   +  +LR P L  L
Sbjct: 89  NGHFGYVRLVLPAFHVGYFKRTIEILQDICKD--CSKILLPEDERRSYLKELRRPGLDNL 146

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKC--GLLKISHEKYK----NRTKKKDAIVE 258
            R  + K+I    +K  VC +C  ING VKK   G LKI H+K++    + + KK     
Sbjct: 147 RRMQINKRINVRCRKTPVCYYCNAINGTVKKASTGALKIVHDKFRAFNASLSAKKIPPPS 206

Query: 259 DLLAE--YNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPS 316
            L  +  + EA K NP+IE H +  +   LNPL VL+LF  I  ED  LL +N + ++P 
Sbjct: 207 KLAFDRSFEEAKKSNPDIEKHYR-RVFDDLNPLRVLKLFRRISNEDCELLSLNVDGARPE 265

Query: 317 DLILTRLLVPPNCIRPSVISDLKSDND 343
             +   +  PP  IRPSV  +  S  D
Sbjct: 266 YFLWQFIPAPPVPIRPSVGQEGPSTED 292



 Score =  176 bits (445), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 151/489 (30%), Positives = 215/489 (43%), Gaps = 101/489 (20%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNE-----------------TLDSK 1039
             +  PV   R      +    + +  LSA EILAL  E                 TL  K
Sbjct: 927  ASAKPVHFDRTFTHAESTTYDKDEKGLSADEILALCEELIAPERKKLVRYDLLGNTLSYK 986

Query: 1040 ---EFLQDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNP 1096
               +F  D  E+  RD    +EE+   ++         +   +   +H  KI   R    
Sbjct: 987  AENDFATDQWES-NRDFLSSIEEYVAAKAAQLRPSDNEEGKEQMAFTHTSKIS-ARTLKA 1044

Query: 1097 FPSACKAEACREKYVRAQIEPA---TAVGALAAQSIGEPGTQMTLKTFHFAG-------- 1145
            F ++C      +KY+RA +EP     A+GA +    G   T  T      AG        
Sbjct: 1045 FITSC-----LDKYMRAHVEPGHSIGAIGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVP 1099

Query: 1146 -------------------------------------------EVCEYIEEVFVPDDSFI 1162
                                                       ++  YIEE      SFI
Sbjct: 1100 RIKEIINASKEISTPIITCELVNKTDMRIAEIVKGRVEKLFLKDIVYYIEENRSQTSSFI 1159

Query: 1163 LIKLDMDRIRLLHLEVDIDSIRYCIERTRGISG------------HLTVSGHSFLILKPK 1210
             IK+D   I+ L LE+ +  I   I++ +                H+ V   + +     
Sbjct: 1160 NIKVDFSTIKKLQLELTLRQILLAIKKHKAFKAADLTFRSFNSHIHIYVDEGASMAGVSV 1219

Query: 1211 DSSKSFNSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDV 1266
               K   S  Y     ++++LP++ + G     RAVI     E V    LLVEG  LR  
Sbjct: 1220 SEQKITGSDPYIRINYLRRILPNIQVFGYPDCTRAVIRVG--EKVATNILLVEGYGLRAC 1277

Query: 1267 MATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMT 1326
            M T G++G +  +N+  E+   LGIEAAR+TI+ EI  VM   GM+ID RH  L+AD+MT
Sbjct: 1278 MTTDGIEGHRTRTNHVMEMRDVLGIEAARTTIIDEISSVMS--GMAIDPRHMQLLADVMT 1335

Query: 1327 SKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNV 1386
             KGEVLGITR GLAK+++SVL LASFE T+DHLFDA   G+ D + GVSECIIMG  +++
Sbjct: 1336 YKGEVLGITRFGLAKIRDSVLQLASFEKTADHLFDAGGAGRRDTVQGVSECIIMGKTISL 1395

Query: 1387 GTGLIKLLQ 1395
            GTG +++++
Sbjct: 1396 GTGSMEVVR 1404



 Score =  151 bits (381), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 103/250 (41%), Positives = 137/250 (54%), Gaps = 20/250 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIIT  L   TD+  A IVKGR+E+  L ++  YIEE      
Sbjct: 1097 GVPRIKEIINASKEISTPIITCELVNKTDMRIAEIVKGRVEKLFLKDIVYYIEENRSQTS 1156

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISG------------HLTVSGHSFLIL 871
            SFI IK+D   I+ L LE+ +  I   I++ +                H+ V   + +  
Sbjct: 1157 SFINIKVDFSTIKKLQLELTLRQILLAIKKHKAFKAADLTFRSFNSHIHIYVDEGASMAG 1216

Query: 872  KPKDSSKSFNSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927
                  K   S  Y     ++++LP++ + G     RAVI     E V    LLVEG  L
Sbjct: 1217 VSVSEQKITGSDPYIRINYLRRILPNIQVFGYPDCTRAVIRVG--EKVATNILLVEGYGL 1274

Query: 928  RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 987
            R  M T G++G +  +N+  E+   LGIEAAR+TI+ EI  VM   GM+ID RH  L+AD
Sbjct: 1275 RACMTTDGIEGHRTRTNHVMEMRDVLGIEAARTTIIDEISSVMS--GMAIDPRHMQLLAD 1332

Query: 988  LMTSKGEVLG 997
            +MT KGEVLG
Sbjct: 1333 VMTYKGEVLG 1342



 Score =  104 bits (259), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 46/58 (79%), Positives = 51/58 (87%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV+NSFFSGLTPTEF FH M GREGL+DTAVKTAETGYM RRL+KSLEDL  +YD
Sbjct: 843 AKGFVRNSFFSGLTPTEFLFHAMSGREGLIDTAVKTAETGYMSRRLMKSLEDLSTRYD 900



 Score = 58.9 bits (141), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 27/51 (52%), Positives = 36/51 (70%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLI 72
           LM  KSNL TP+NGE +IAA QDFIT  YLL+ K+ FF+R    +I  +++
Sbjct: 536 LMGVKSNLATPKNGEPIIAAIQDFITAAYLLSSKDNFFDRKTFTQICLSML 586



 Score = 42.0 bits (97), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 18/39 (46%), Positives = 28/39 (71%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  FDA   G+ D + GVSECIIMG  +++GTG +++++
Sbjct: 1366 DHLFDAGGAGRRDTVQGVSECIIMGKTISLGTGSMEVVR 1404


>gi|302914119|ref|XP_003051073.1| hypothetical protein NECHADRAFT_41824 [Nectria haematococca mpVI
           77-13-4]
 gi|256732011|gb|EEU45360.1| hypothetical protein NECHADRAFT_41824 [Nectria haematococca mpVI
           77-13-4]
          Length = 1449

 Score =  286 bits (732), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 142/278 (51%), Positives = 182/278 (65%), Gaps = 28/278 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND+VLFNRQPSLHKLSIM+H AKV P RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 468 DNDIVLFNRQPSLHKLSIMSHLAKVRPWRTFRLNECVCGPYNADFDGDEMNLHVPQTEEA 527

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K NL TP+NGE +IAATQDFIT  +LL+ K+ FF+R
Sbjct: 528 RAEAIN--------------LMGIKHNLATPKNGEPVIAATQDFITAAFLLSSKDRFFDR 573

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                +   ++   + +             P   +    +WTGKQ+FS++++PN+D  V 
Sbjct: 574 KTFTYLCMHMMDGKTHL----------DMPPPAIIAPQALWTGKQLFSMLMRPNKDSKVK 623

Query: 521 ANLKTKGRAYTANEEFC----HRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL  K RAY A    C      D ++++RNSE++ G MDKST+GSG K ++FY++LRDF
Sbjct: 624 VNLDAKCRAYKARPGQCPDMDPNDGWLVVRNSEVMCGRMDKSTVGSGKKDSIFYVILRDF 683

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGF 614
           G D AV AM RL+++ +  L NRGFSIG+GDV P Q  
Sbjct: 684 GPDEAVIAMNRLAKLCARQLTNRGFSIGVGDVFPTQSL 721



 Score =  202 bits (515), Expect = 8e-49,   Method: Compositional matrix adjust.
 Identities = 142/364 (39%), Positives = 186/364 (51%), Gaps = 80/364 (21%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-------------------- 1145
            C +KY +A +EP  AVGA+ A SIGEPGTQMTLKTFHFAG                    
Sbjct: 1058 CLDKYKKAHVEPGHAVGAVGAHSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIINAS 1117

Query: 1146 ---------------EVCE------------YIEEV--FVPD-----DSFILIKLDMDRI 1171
                           E  E            YI +V  FV D     +  +++++D   +
Sbjct: 1118 KTISTPVITCPLENNEQIEAARVVKGRIEKTYISDVLRFVEDEWRTNEGNVVLQIDSTAL 1177

Query: 1172 RLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSFLILKPKDSSKSFNSKMYQMK---- 1224
              +HL +    I   I + R +      L++ G   +I++ +D S S      + K    
Sbjct: 1178 SDMHLGIGPYDIAEAICKQRKLKVQRDDLSIDGER-IIVRVRDVSDSTKRTTARSKAAAD 1236

Query: 1225 -------------QLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYG 1271
                         + LP+V I G     RA+I   +      + +LVEG  LR+ M T G
Sbjct: 1237 DTGDMLLRANFLRRALPTVPISGYSEATRAIIQTSE---QNTHTVLVEGYGLRECMTTEG 1293

Query: 1272 VKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 1331
            V G+K  SNN  E    LGIEAAR+TI  EI  VM +  M ID RH  L+AD+MT KGEV
Sbjct: 1294 VIGIKARSNNVMECRDVLGIEAARTTIAAEIGEVMGD--MGIDPRHMQLLADVMTYKGEV 1351

Query: 1332 LGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLI 1391
            LGITR GL+KM++SVL LASFE T DHLF+AA   +TD I GVSECIIMG  M VGTG  
Sbjct: 1352 LGITRFGLSKMRDSVLQLASFEKTPDHLFEAAAGMKTDQIEGVSECIIMGQTMRVGTGAF 1411

Query: 1392 KLLQ 1395
            ++++
Sbjct: 1412 QVVR 1415



 Score =  199 bits (505), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 108/271 (39%), Positives = 155/271 (57%), Gaps = 10/271 (3%)

Query: 79  FRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCG 138
           F+G+  G  + +D +  Q+ +++  + LY  +  R P  HG LD R+GT+ K   C TC 
Sbjct: 23  FKGIKFGIQSNQD-IANQAVLEVSDRLLYDIENNRAPYRHGPLDSRLGTSSKAGKCATCE 81

Query: 139 QNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN 198
            +LS+C GHFG++ LPLP FH+GY R +++ILQ ICK+  C RVLL E +   F  +LR 
Sbjct: 82  LSLSECNGHFGHVRLPLPAFHVGYLRFIMSILQEICKD--CGRVLLEEPERRQFLKELRR 139

Query: 199 PALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEK---YKNRTKKKDA 255
           P L  L R  + KKI    +K+  CP+CG ING ++K G+LK++H+K   Y   T  K  
Sbjct: 140 PFLDNLRRTQICKKINAECRKIKTCPYCGSINGQIRKIGVLKLAHDKFSFYNKSTSVKKV 199

Query: 256 IVEDLLA---EYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL 312
             E  +     + EA + NPE++ H +  + + LNPL VL LF+ I   D  LL ++   
Sbjct: 200 PPESKIKFDNSFTEAKRENPELDKHLRKAM-EDLNPLRVLNLFKMISPTDCELLGLDPAE 258

Query: 313 SKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
            +P   I   L  PP CIRPSV  D  S+ D
Sbjct: 259 GRPEMFIWQFLPAPPVCIRPSVAQDNASNED 289



 Score =  148 bits (374), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 99/278 (35%), Positives = 151/278 (54%), Gaps = 27/278 (9%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+IT  L+ +  ++ AR+VKGR+E+T + +V  ++E+ +  ++
Sbjct: 1106 GVPRIKEIINASKTISTPVITCPLENNEQIEAARVVKGRIEKTYISDVLRFVEDEWRTNE 1165

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSFLILKPKDSSKSF 880
              +++++D   +  +HL +    I   I + R +      L++ G   +I++ +D S S 
Sbjct: 1166 GNVVLQIDSTALSDMHLGIGPYDIAEAICKQRKLKVQRDDLSIDGER-IIVRVRDVSDST 1224

Query: 881  NSKMYQ-----------------MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVE 923
                 +                 +++ LP+V I G     RA+I   +      + +LVE
Sbjct: 1225 KRTTARSKAAADDTGDMLLRANFLRRALPTVPISGYSEATRAIIQTSE---QNTHTVLVE 1281

Query: 924  GDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPM 983
            G  LR+ M T GV G+K  SNN  E    LGIEAAR+TI  EI  VM +  M ID RH  
Sbjct: 1282 GYGLRECMTTEGVIGIKARSNNVMECRDVLGIEAARTTIAAEIGEVMGD--MGIDPRHMQ 1339

Query: 984  LVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDP 1021
            L+AD+MT KGEVLG  T   L ++ D ++   S    P
Sbjct: 1340 LLADVMTYKGEVLGI-TRFGLSKMRDSVLQLASFEKTP 1376



 Score =  103 bits (257), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 46/59 (77%), Positives = 51/59 (86%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSF++GL PTEF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 841 PSKGFVKNSFYTGLFPTEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSTQYD 899



 Score = 56.6 bits (135), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 26/54 (48%), Positives = 36/54 (66%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           LM  K NL TP+NGE +IAATQDFIT  +LL+ K+ FF+R     +   ++ G+
Sbjct: 534 LMGIKHNLATPKNGEPVIAATQDFITAAFLLSSKDRFFDRKTFTYLCMHMMDGK 587



 Score = 43.1 bits (100), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 21/39 (53%), Positives = 27/39 (69%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  F+AA   +TD I GVSECIIMG  M VGTG  ++++
Sbjct: 1377 DHLFEAAAGMKTDQIEGVSECIIMGQTMRVGTGAFQVVR 1415


>gi|402077501|gb|EJT72850.1| hypothetical protein GGTG_09702 [Gaeumannomyces graminis var.
           tritici R3-111a-1]
          Length = 1461

 Score =  286 bits (732), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 140/274 (51%), Positives = 180/274 (65%), Gaps = 27/274 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIM+H  KV P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 470 DGDIVLFNRQPSLHKLSIMSHLVKVRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 529

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K NL TP+NGE +IAATQDFIT  YLL+ K+ FF+R
Sbjct: 530 RAEAIN--------------LMGVKHNLATPKNGEPIIAATQDFITAAYLLSSKDNFFSR 575

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                +   ++ D  +         +    P   ++   +WTGKQIF+++++PN+  PV 
Sbjct: 576 KVFTYLCQHMMVDGKE---------YLELPPPAILKPCALWTGKQIFNVLMRPNKQSPVK 626

Query: 521 ANLKTKGRAYTAN----EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL  K R Y        + C  D ++I+RNSE++ G MDKS +G G K ++FY++LRDF
Sbjct: 627 VNLDAKCREYKVRPGEAPDLCPNDGWLIIRNSEIMCGVMDKSIVGGGKKDSIFYVILRDF 686

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           G D AVTAM RL+++ +  L NRGFSIG+GDV P
Sbjct: 687 GPDYAVTAMNRLAKLCARTLGNRGFSIGVGDVFP 720



 Score =  199 bits (506), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 116/273 (42%), Positives = 157/273 (57%), Gaps = 14/273 (5%)

Query: 79  FRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCG 138
           F+ L  G  + +D V Q   ++I  K LY  +  RTP  HG LD R+GT+ K A C TC 
Sbjct: 24  FKELKFGIQSNQDIVNQ-GVLEISEKQLYDIENNRTPSRHGPLDHRLGTSSKTAECQTCA 82

Query: 139 QNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN 198
           Q L +C GHFG++ LPLP FHIGY R V  ILQ+ICK+  CARVLL E +   F  +LR 
Sbjct: 83  QPLQNCSGHFGHVRLPLPAFHIGYLRFVQTILQNICKD--CARVLLTEPERRKFLTELRR 140

Query: 199 PALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKY-----KNRTKK- 252
           P +  L R  + KKI E  +KV +CP+C  +NG ++K G+LK++H+K+      N  KK 
Sbjct: 141 PGIDNLRRTGICKKINEQCRKVKICPYCDSVNGTIRKIGVLKLAHDKFVAFNKSNSAKKI 200

Query: 253 --KDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNA 310
             +  IV D    Y  A K  P++E H +  + + LNPL+VL LF+ I   D  LL ++ 
Sbjct: 201 PPESKIVFDNSFLY--AKKAVPDLEKHLRKAM-EDLNPLKVLTLFKMITPTDCELLGLDP 257

Query: 311 ELSKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
              +P   +   L  PP CIRPSV  D  S+ D
Sbjct: 258 SEGRPEMFLWQYLPAPPICIRPSVAQDNASNED 290



 Score =  169 bits (428), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 123/368 (33%), Positives = 180/368 (48%), Gaps = 81/368 (22%)

Query: 1106 CREKYVRAQIEPATAVGAL---------------------------------------AA 1126
            C+EK+ RA++EP  AVGA+                                       A+
Sbjct: 1070 CQEKHERAKVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIINAS 1129

Query: 1127 QSIGEPGTQMTLKTFH---------------FAGEVCEYIEEVFVPDDSFILIKLDMDRI 1171
            +SI  P     L                   +  +V  +IE+ +  D   ++++ DM  +
Sbjct: 1130 KSISTPVITCPLMNNKQIEAARVVKGRIEKTYISDVLRFIEDEWKADAGSVVLQFDMAVL 1189

Query: 1172 RLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSFLIL-------------------KP 1209
            + +HL + +  I   I + + +      L +   S  I+                     
Sbjct: 1190 QDMHLGIGMADIAESICKHKKLKLEPDDLRLGSSSIEIVVRNTWVDVAAAKKAARSRSAA 1249

Query: 1210 KDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMAT 1269
             + S     ++  ++++LP+V I G    +RA+I   +    +++ +LVEG  LR  M T
Sbjct: 1250 MEESPDLLLRVNHLRRMLPTVPISGYPEASRAIIQTSEK---SEHTVLVEGYGLRACMTT 1306

Query: 1270 YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 1329
             GV G K  SNN  E    LGIEAAR+TI TEI+ VM +  M ID RH  L+AD+MT KG
Sbjct: 1307 EGVIGTKTKSNNVMENRDVLGIEAARTTIATEIEAVMGD--MGIDPRHMQLLADVMTYKG 1364

Query: 1330 EVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
            +VLGITR GL+KM++SVL LASFE T DHLF AA   +TD I GVSECIIMG  M+VGTG
Sbjct: 1365 DVLGITRFGLSKMRDSVLQLASFEKTPDHLFAAAAGMKTDRIEGVSECIIMGQTMSVGTG 1424

Query: 1390 LIKLLQAV 1397
              ++++A+
Sbjct: 1425 ACQIVRAL 1432



 Score =  146 bits (369), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 99/280 (35%), Positives = 152/280 (54%), Gaps = 28/280 (10%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS++ISTP+IT  L  +  ++ AR+VKGR+E+T + +V  +IE+ +  D 
Sbjct: 1118 GVPRIKEIINASKSISTPVITCPLMNNKQIEAARVVKGRIEKTYISDVLRFIEDEWKADA 1177

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSFLIL--------- 871
              ++++ DM  ++ +HL + +  I   I + + +      L +   S  I+         
Sbjct: 1178 GSVVLQFDMAVLQDMHLGIGMADIAESICKHKKLKLEPDDLRLGSSSIEIVVRNTWVDVA 1237

Query: 872  ----------KPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLL 921
                         + S     ++  ++++LP+V I G    +RA+I   +    +++ +L
Sbjct: 1238 AAKKAARSRSAAMEESPDLLLRVNHLRRMLPTVPISGYPEASRAIIQTSE---KSEHTVL 1294

Query: 922  VEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRH 981
            VEG  LR  M T GV G K  SNN  E    LGIEAAR+TI TEI+ VM +  M ID RH
Sbjct: 1295 VEGYGLRACMTTEGVIGTKTKSNNVMENRDVLGIEAARTTIATEIEAVMGD--MGIDPRH 1352

Query: 982  PMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDP 1021
              L+AD+MT KG+VLG  T   L ++ D ++   S    P
Sbjct: 1353 MQLLADVMTYKGDVLGI-TRFGLSKMRDSVLQLASFEKTP 1391



 Score =  102 bits (254), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 46/59 (77%), Positives = 50/59 (84%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV NSF+SGL PTEF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 844 PSKGFVANSFYSGLLPTEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSTQYD 902



 Score = 58.2 bits (139), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 26/40 (65%), Positives = 31/40 (77%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           LM  K NL TP+NGE +IAATQDFIT  YLL+ K+ FF+R
Sbjct: 536 LMGVKHNLATPKNGEPIIAATQDFITAAYLLSSKDNFFSR 575



 Score = 43.5 bits (101), Expect = 0.81,   Method: Compositional matrix adjust.
 Identities = 22/41 (53%), Positives = 29/41 (70%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 708
            D  F AA   +TD I GVSECIIMG  M+VGTG  ++++A+
Sbjct: 1392 DHLFAAAAGMKTDRIEGVSECIIMGQTMSVGTGACQIVRAL 1432


>gi|325185155|emb|CCA19646.1| DNAdirected RNA polymerase III largest subunit puta [Albugo
           laibachii Nc14]
 gi|325188545|emb|CCA23078.1| RNA polymerase III putative [Albugo laibachii Nc14]
          Length = 1543

 Score =  286 bits (732), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 153/319 (47%), Positives = 196/319 (61%), Gaps = 43/319 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHK+SIMAHRAKV+P RTFRFNECVC+PYNADFDGDEMN+HLPQTEEA
Sbjct: 475 DGDVVLFNRQPSLHKMSIMAHRAKVMPWRTFRFNECVCSPYNADFDGDEMNMHLPQTEEA 534

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL               LM  + N++TPRNGE L+AATQDF+T  YLLTQKN FFNR
Sbjct: 535 RTEAL--------------TLMGVEHNMITPRNGEPLVAATQDFLTASYLLTQKNIFFNR 580

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q  ++ + +++D  +   I +        P + +    +WTGKQ+ SL++KPN    + 
Sbjct: 581 EQFCQMIA-IMSDAVEHIDIPE--------PAI-IHPLRLWTGKQVISLLIKPNDFSKIL 630

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            NL+ K R YT N   C++D YV  RNSEL+ G++ K TLG G K  +FY+L+RD G   
Sbjct: 631 VNLELKERNYTNNTYMCYKDGYVCFRNSELMCGNLCKKTLGDGSKQGLFYVLIRDHGSHE 690

Query: 581 AVTAMWRLSRMTSFYL-MNRGFSIGIGDVTPGQGFVQNSFFSGLTPTEFFFHTMGGREGL 639
           A   M RL+++ + +L  ++GFSIGI DVTP                    H MG +  L
Sbjct: 691 AARCMNRLAKLCARWLGGSKGFSIGIDDVTPS------------------VHLMGKKNEL 732

Query: 640 VDTAVKTAETGYMQRRLVK 658
           + +    A     Q RL K
Sbjct: 733 LQSGYNGANEAIEQYRLGK 751



 Score =  207 bits (527), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 125/276 (45%), Positives = 172/276 (62%), Gaps = 21/276 (7%)

Query: 1145 GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---------- 1194
            GE+  +I+EVF  D +++ + LD   I+ LHL +   ++R  I +  GI           
Sbjct: 1253 GEIAIHIKEVFARDQAYLSVGLDTHAIKQLHLNISAQTVRNSILKAVGIGPRSILRMLKE 1312

Query: 1195 GHLTVSGH---SFLILKPKDSSKSFNSKMY----QMKQLLPSVVIKGVQGINRAVIHEE- 1246
             H+ ++        IL P +   SF    Y     +K  LP+V+++G+  +NRAVI+ E 
Sbjct: 1313 QHVLLNARCPSKLRILAPSNQKTSFTRGAYFTMQALKAELPNVIVQGIPQVNRAVINYEE 1372

Query: 1247 ---DVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIK 1303
               D  GV  + LLVEG  L +VM   G+ G+   SN+  EV KTLGIEAAR  I +E+ 
Sbjct: 1373 GKTDSHGVRTHHLLVEGYGLAEVMGVPGIDGLNTRSNHIIEVEKTLGIEAARELISSEVS 1432

Query: 1304 LVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAA 1363
             +M  +G+ ID RH ML++D+MT KGEVLGITR G+AKMKESVL LASFE T+DHLFDAA
Sbjct: 1433 YIMSAYGIGIDRRHLMLLSDIMTFKGEVLGITRFGIAKMKESVLMLASFEKTTDHLFDAA 1492

Query: 1364 FYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPR 1399
             + +TD I GVSECIIMG+P+ +GTG+ KLL+ V +
Sbjct: 1493 VHSRTDAIVGVSECIIMGIPIPIGTGIFKLLRRVEK 1528



 Score =  202 bits (515), Expect = 8e-49,   Method: Compositional matrix adjust.
 Identities = 108/250 (43%), Positives = 149/250 (59%), Gaps = 8/250 (3%)

Query: 90  EDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFG 149
           E  + + S +++ S++L+     R P  +G+LD+R+G + K   C TC   LSDCVGHFG
Sbjct: 45  EVEMMRMSEMRVTSRDLFAVQ-SRDPAKNGVLDKRLGVSNKSDTCDTCSLRLSDCVGHFG 103

Query: 150 YIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSL 209
           YI L LPVFHIG+F+ ++ ILQ ICK   C+RVLL       F  ++R+P    L  K+L
Sbjct: 104 YIKLELPVFHIGFFKAILEILQMICKE--CSRVLLSPSDRESFLQRVRDPRADALRLKAL 161

Query: 210 KKKILETTKKVSVCPHCGEINGVVKKC--GLLKISHEKYKNRTKKKDAIVEDLLAEYNEA 267
           +KK+    K+V  CPHC  +NG V+K     LK+ HEK+  R K    +    +A++ EA
Sbjct: 162 RKKMATLCKRVVKCPHCQSVNGTVRKVNSSTLKLLHEKF--RAKSAQDLRNVFVAQFREA 219

Query: 268 VKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPP 327
              NPEI  H      Q L+P+ V +LFE IP +D  LL +++ L +P  LIL  LLVPP
Sbjct: 220 QTINPEIRQHLPKAQ-QDLSPVIVQELFERIPDQDCELLWIDSSLGRPEKLILNSLLVPP 278

Query: 328 NCIRPSVISD 337
            CIRPSV  D
Sbjct: 279 VCIRPSVAMD 288



 Score =  196 bits (499), Expect = 6e-47,   Method: Compositional matrix adjust.
 Identities = 113/255 (44%), Positives = 155/255 (60%), Gaps = 21/255 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPR+KEIINAS+NISTPIITA L   TD   ARIVKG++E+TTLGE+  +I+EVF  D 
Sbjct: 1208 GVPRLKEIINASKNISTPIITAALVNKTDERSARIVKGQIEKTTLGEIAIHIKEVFARDQ 1267

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS----------GHLTVSGH---SFLI 870
            +++ + LD   I+ LHL +   ++R  I +  GI            H+ ++        I
Sbjct: 1268 AYLSVGLDTHAIKQLHLNISAQTVRNSILKAVGIGPRSILRMLKEQHVLLNARCPSKLRI 1327

Query: 871  LKPKDSSKSFNSKMY----QMKQLLPSVVIKGVQGINRAVIHEE----DVEGVTKYKLLV 922
            L P +   SF    Y     +K  LP+V+++G+  +NRAVI+ E    D  GV  + LLV
Sbjct: 1328 LAPSNQKTSFTRGAYFTMQALKAELPNVIVQGIPQVNRAVINYEEGKTDSHGVRTHHLLV 1387

Query: 923  EGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHP 982
            EG  L +VM   G+ G+   SN+  EV KTLGIEAAR  I +E+  +M  +G+ ID RH 
Sbjct: 1388 EGYGLAEVMGVPGIDGLNTRSNHIIEVEKTLGIEAARELISSEVSYIMSAYGIGIDRRHL 1447

Query: 983  MLVADLMTSKGEVLG 997
            ML++D+MT KGEVLG
Sbjct: 1448 MLLSDIMTFKGEVLG 1462



 Score =  106 bits (265), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 48/58 (82%), Positives = 52/58 (89%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV NSF+SGLT TEFFFHTMGGREGLVDTAVKTAETGYM RRL+K+LEDL  QYD
Sbjct: 846 AKGFVANSFYSGLTATEFFFHTMGGREGLVDTAVKTAETGYMARRLMKALEDLSCQYD 903



 Score = 66.6 bits (161), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 29/42 (69%), Positives = 34/42 (80%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 63
           LM  + N++TPRNGE L+AATQDF+T  YLLTQKN FFNR Q
Sbjct: 541 LMGVEHNMITPRNGEPLVAATQDFLTASYLLTQKNIFFNREQ 582



 Score = 64.7 bits (156), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 53/180 (29%), Positives = 83/180 (46%), Gaps = 22/180 (12%)

Query: 983  MLVADLMTSKGEVLGNGTPVELKRLLDDII---AKNSSRSDPSLSAQEILALSNETLDSK 1039
            M+ A+LMT    +  +  P + K  + +++    KN S     +  +E    +++ +D  
Sbjct: 1025 MMEANLMTP-ATIKSSDQPPQKKVKISNLLHSEVKNESTGSILMKNEEDPIFNHDDIDVD 1083

Query: 1040 EFLQDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPS 1099
            +   +T++ F    ++  EE    +  T  ++K   P+  ++     K  +  ES     
Sbjct: 1084 DV--ETAKQFWAAHER--EELDTVDMCTWEKNKFKDPIARKLWIEMAKEQNTSESREAGC 1139

Query: 1100 ACKAEACR--------------EKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
                  CR               KY RA +EP  AVGA+ AQSI EPGTQMTLKTFHFAG
Sbjct: 1140 LISHNVCRITQLQIEKLLEVSLYKYHRACMEPGEAVGAIGAQSISEPGTQMTLKTFHFAG 1199


>gi|50293727|ref|XP_449275.1| hypothetical protein [Candida glabrata CBS 138]
 gi|49528588|emb|CAG62249.1| unnamed protein product [Candida glabrata]
          Length = 1459

 Score =  286 bits (731), Expect = 8e-74,   Method: Compositional matrix adjust.
 Identities = 143/282 (50%), Positives = 189/282 (67%), Gaps = 30/282 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH+LSI++H AK+ P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 468 DGDVVLFNRQPSLHRLSILSHYAKIRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 527

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF++
Sbjct: 528 RAEAIN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDK 573

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A   ++ S +++D S    I          P   ++   +WTGKQ+FSL++KPN++ PV 
Sbjct: 574 ASLTQLLS-MMSDGSLQFDI---------PPPAIMKPCYLWTGKQVFSLLIKPNKNSPVK 623

Query: 521 ANLKTKGRAYTANE------EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLR 574
            NL  K + Y   +      E    D +VI+R S++L+G MDKS LG G K +VFY +LR
Sbjct: 624 INLDAKNKVYIPPKQKHYPNEMSQNDGFVIVRGSQILSGVMDKSVLGDGKKHSVFYTILR 683

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           DFG   A +AM R++++ + YL NRGFSIGI DVTP     Q
Sbjct: 684 DFGPQEAASAMNRMAKLCARYLGNRGFSIGISDVTPADDLKQ 725



 Score =  219 bits (559), Expect = 7e-54,   Method: Compositional matrix adjust.
 Identities = 128/286 (44%), Positives = 183/286 (63%), Gaps = 23/286 (8%)

Query: 1146 EVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGH 1202
            +VC YI++V+  + +++ +K+D++ I  L LE+ I+ I   I R   +   +  +TV G 
Sbjct: 1167 DVCYYIQDVYKENMAYLQVKVDLNTIDKLQLELTIEDIAIAITRAPKLKIQTSDVTVLGK 1226

Query: 1203 SFLILK-------PKDSSKSF-----NSKMYQMKQL---LPSVVIKGVQGINRAVIHEED 1247
              + +         K SS S      N   Y+M+ L   LPS+++KG+  I RAVI+  D
Sbjct: 1227 DKIAINVLPEGFGSKTSSTSLKEPTENDVFYRMQTLRRALPSIMVKGLNDIARAVINIRD 1286

Query: 1248 VEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVME 1307
             +G  K +LLVEG  LRDVM T GV G K ++N+  E++  LGIEAAR++I+ EI   M 
Sbjct: 1287 -DG--KRELLVEGYGLRDVMCTDGVIGAKTATNHVLEIFNVLGIEAARASIIGEIDYTMS 1343

Query: 1308 NHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQ 1367
            NHGMS+D RH  L+ D+MT KGEVLGITR GL+KM++SVL LASFE T+DHLFDAAFY +
Sbjct: 1344 NHGMSVDPRHIQLLGDVMTFKGEVLGITRFGLSKMRDSVLQLASFEKTTDHLFDAAFYMK 1403

Query: 1368 TDCISGVSECIIMGLPMNVGTGLIKLLQA--VPRSEPVPRTLLFDN 1411
             D + GVSECII+G  M++GTG  K+++   +   E  P+  LF++
Sbjct: 1404 KDAVEGVSECIILGQTMSIGTGSFKVVKNTDIAEDELKPKRTLFES 1449



 Score =  189 bits (480), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 115/252 (45%), Positives = 159/252 (63%), Gaps = 21/252 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII A L  + D   AR+VKGR+E+T L +VC YI++V+  + 
Sbjct: 1121 GVPRIKEIINASKVISTPIINAVLVNNNDERAARVVKGRIEKTLLSDVCYYIQDVYKENM 1180

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFLILK-------P 873
            +++ +K+D++ I  L LE+ I+ I   I R   +   +  +TV G   + +         
Sbjct: 1181 AYLQVKVDLNTIDKLQLELTIEDIAIAITRAPKLKIQTSDVTVLGKDKIAINVLPEGFGS 1240

Query: 874  KDSSKSF-----NSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD 925
            K SS S      N   Y+M+ L   LPS+++KG+  I RAVI+  D +G  K +LLVEG 
Sbjct: 1241 KTSSTSLKEPTENDVFYRMQTLRRALPSIMVKGLNDIARAVINIRD-DG--KRELLVEGY 1297

Query: 926  NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 985
             LRDVM T GV G K ++N+  E++  LGIEAAR++I+ EI   M NHGMS+D RH  L+
Sbjct: 1298 GLRDVMCTDGVIGAKTATNHVLEIFNVLGIEAARASIIGEIDYTMSNHGMSVDPRHIQLL 1357

Query: 986  ADLMTSKGEVLG 997
             D+MT KGEVLG
Sbjct: 1358 GDVMTFKGEVLG 1369



 Score =  183 bits (465), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 103/248 (41%), Positives = 143/248 (57%), Gaps = 11/248 (4%)

Query: 96  QSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPL 155
           QS ++I S++L+  +  R+P   G LD RMG +     CTTC  NL+ C GHFG+I L L
Sbjct: 29  QSELEISSRDLFDLENNRSPKEGGALDPRMGVSASSMECTTCHGNLASCHGHFGHIKLAL 88

Query: 156 PVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILE 215
           PVFH+GYF+  I ILQ ICK  TC+ +LL E+    F ++LR P +  L R +L KK+L+
Sbjct: 89  PVFHVGYFKATIQILQGICK--TCSAILLSEQDKRHFLSELRRPGVDNLRRMALLKKVLD 146

Query: 216 TTKKVSVCPHCGEINGVVKKCGL------LKISHEKYKNRTKKKDAIVEDLLAEYNEAVK 269
             KK   C HCG +NGVVKK         LKI H+ ++   KK     +  + ++ E + 
Sbjct: 147 QCKKQRRCLHCGALNGVVKKAAAGAGTASLKIIHDTFRWVGKKSTPEKDKWIGDWKEVLS 206

Query: 270 FNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNA--ELSKPSDLILTRLLVPP 327
            NPE+E + K      LNPL+ L LF+ I  ED  LL ++A  +  +P   I   +  PP
Sbjct: 207 HNPELERYVKRA-TDDLNPLKTLNLFKQIASEDCELLGIDATNKAGRPETYIWRYIPAPP 265

Query: 328 NCIRPSVI 335
            CIRPSV+
Sbjct: 266 VCIRPSVM 273



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 45/57 (78%), Positives = 50/57 (87%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NSFFSGL+P EF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 845 KGFVRNSFFSGLSPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSCQYD 901



 Score = 62.4 bits (150), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/57 (49%), Positives = 42/57 (73%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVF 78
           LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF++A   ++ S +  G   F
Sbjct: 534 LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDKASLTQLLSMMSDGSLQF 590



 Score = 52.4 bits (124), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 25/57 (43%), Positives = 37/57 (64%), Gaps = 2/57 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA--VPRSEPVPRTLLFDN 722
            D  FDAAFY + D + GVSECII+G  M++GTG  K+++   +   E  P+  LF++
Sbjct: 1393 DHLFDAAFYMKKDAVEGVSECIILGQTMSIGTGSFKVVKNTDIAEDELKPKRTLFES 1449


>gi|302308245|ref|NP_985109.2| AER252Cp [Ashbya gossypii ATCC 10895]
 gi|299789362|gb|AAS52933.2| AER252Cp [Ashbya gossypii ATCC 10895]
 gi|374108334|gb|AEY97241.1| FAER252Cp [Ashbya gossypii FDAG1]
          Length = 1459

 Score =  286 bits (731), Expect = 9e-74,   Method: Compositional matrix adjust.
 Identities = 145/277 (52%), Positives = 188/277 (67%), Gaps = 30/277 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH+LSI++H AK+ P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 467 DGDVVLFNRQPSLHRLSILSHYAKIRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 526

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+R
Sbjct: 527 RAEAIN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDR 572

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A  +++ S +++D +    I          P   +R   +WTGKQ+FSL++KPN+  PV 
Sbjct: 573 ATFVQMLS-MMSDGNLQFDI---------PPPAIMRPHYLWTGKQLFSLLIKPNKKSPVI 622

Query: 521 ANLKTKGRAYTANE------EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLR 574
            NL  K + Y A +      E    D YV++R S +L+G MDKS LG G K +VFY +LR
Sbjct: 623 INLDAKNKVYIAPKNKAYPNEMSANDGYVVIRGSNILSGVMDKSVLGDGKKHSVFYTILR 682

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           DFG   A  AM R++++ + YL NRGFSIGI DVTPG
Sbjct: 683 DFGPQEATQAMNRMAKLCARYLGNRGFSIGISDVTPG 719



 Score =  249 bits (636), Expect = 9e-63,   Method: Compositional matrix adjust.
 Identities = 155/377 (41%), Positives = 211/377 (55%), Gaps = 77/377 (20%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCE----- 1149
            KY +A++EP TAVGA+ A SIGEPGTQMTLKTFHFAG              E+       
Sbjct: 1076 KYRKAKVEPGTAVGAIGAHSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIINASKVI 1135

Query: 1150 ---YIEEVFVPDD--------------------------------SFILIKLDMDRIRLL 1174
                I    V DD                                SF+ +K+D+  I  L
Sbjct: 1136 STPIINATLVNDDDERAARVVKGRVEKTLLSDVIFYIQDVYRDNMSFLQVKVDLATIEKL 1195

Query: 1175 HLEVDIDSIRYCIERTRGI---SGHLTVSGHSFL---ILKPKDSSKSFNS---------- 1218
             LE+ ++ I   I     +   +G +++ G + +   +    D +KS ++          
Sbjct: 1196 QLELTVEDIAIAITSAPKLKISTGDVSIVGRNKININVCNDLDKAKSISTLASEPHENDV 1255

Query: 1219 --KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 1276
              KM  +++ LP +V+KG+  I+RAVI+  D +G  K +LLVEG  LRDVM T GV G K
Sbjct: 1256 FFKMQHLRRALPGIVVKGLPDISRAVINIRD-DG--KRELLVEGYGLRDVMTTDGVVGYK 1312

Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITR 1336
              +N+  EVY  LGIEAAR++I+ EI   M NHGMS+D RH  L+ D+MT KGEVLGITR
Sbjct: 1313 TKTNHFLEVYDVLGIEAARTSIIDEIDYTMSNHGMSVDPRHIQLLGDVMTYKGEVLGITR 1372

Query: 1337 HGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA 1396
             GL+KM++SVL LASFE T+DHLFDAAFY + D + GVSECII+G  M +GTG  K+++ 
Sbjct: 1373 FGLSKMRDSVLQLASFEKTTDHLFDAAFYMKKDAVEGVSECIILGQTMTIGTGSFKVVKG 1432

Query: 1397 --VPRSEPVPRTLLFDN 1411
              +   +  P+  LF+N
Sbjct: 1433 TNISPDDLKPKPTLFEN 1449



 Score =  187 bits (475), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 113/252 (44%), Positives = 158/252 (62%), Gaps = 21/252 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII A L  D D   AR+VKGR+E+T L +V  YI++V+  + 
Sbjct: 1121 GVPRIKEIINASKVISTPIINATLVNDDDERAARVVKGRVEKTLLSDVIFYIQDVYRDNM 1180

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFL---ILKPKDSS 877
            SF+ +K+D+  I  L LE+ ++ I   I     +   +G +++ G + +   +    D +
Sbjct: 1181 SFLQVKVDLATIEKLQLELTVEDIAIAITSAPKLKISTGDVSIVGRNKININVCNDLDKA 1240

Query: 878  KSFNS------------KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD 925
            KS ++            KM  +++ LP +V+KG+  I+RAVI+  D +G  K +LLVEG 
Sbjct: 1241 KSISTLASEPHENDVFFKMQHLRRALPGIVVKGLPDISRAVINIRD-DG--KRELLVEGY 1297

Query: 926  NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 985
             LRDVM T GV G K  +N+  EVY  LGIEAAR++I+ EI   M NHGMS+D RH  L+
Sbjct: 1298 GLRDVMTTDGVVGYKTKTNHFLEVYDVLGIEAARTSIIDEIDYTMSNHGMSVDPRHIQLL 1357

Query: 986  ADLMTSKGEVLG 997
             D+MT KGEVLG
Sbjct: 1358 GDVMTYKGEVLG 1369



 Score =  185 bits (469), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 99/248 (39%), Positives = 146/248 (58%), Gaps = 11/248 (4%)

Query: 96  QSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPL 155
           QS ++I +++L+  +  R P   G LD RMG +  +A C+TC   L+ C GHFG+I L L
Sbjct: 29  QSEVEIFTRDLFDLEDGRAPKKGGALDSRMGVSSSQAECSTCHGTLASCHGHFGHIKLAL 88

Query: 156 PVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILE 215
           PVFH+GYF+  I ILQSICKN  CA++LL EE    F ++LR P +  L R +  KK+L+
Sbjct: 89  PVFHVGYFKATIQILQSICKN--CAKLLLNEEDKRQFLSELRRPGIDNLRRMATLKKVLD 146

Query: 216 TTKKVSVCPHCGEINGVV------KKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVK 269
             KK   C HCG +NGVV           LKI H+ ++   KK     +  + ++N+ ++
Sbjct: 147 QCKKQRRCLHCGMLNGVVKKAAAGSGSAALKIIHDTFRWVGKKSAPEKDKWIGDWNQVLQ 206

Query: 270 FNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL--SKPSDLILTRLLVPP 327
            +PE+E + K  + + LNPL+ L LF+ I  +D  LL +++ +   +P   I   L  PP
Sbjct: 207 HSPELERYMKRTM-ENLNPLKTLNLFKQISPQDCELLGIDSTVKAGRPETYIWRYLPAPP 265

Query: 328 NCIRPSVI 335
            CIRPSV+
Sbjct: 266 VCIRPSVM 273



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 45/57 (78%), Positives = 50/57 (87%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NSFFSGL+P EF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 844 KGFVRNSFFSGLSPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSCQYD 900



 Score = 63.5 bits (153), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 29/57 (50%), Positives = 43/57 (75%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVF 78
           LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+RA  +++ S +  G   F
Sbjct: 533 LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDRATFVQMLSMMSDGNLQF 589



 Score = 52.8 bits (125), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 25/57 (43%), Positives = 36/57 (63%), Gaps = 2/57 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA--VPRSEPVPRTLLFDN 722
            D  FDAAFY + D + GVSECII+G  M +GTG  K+++   +   +  P+  LF+N
Sbjct: 1393 DHLFDAAFYMKKDAVEGVSECIILGQTMTIGTGSFKVVKGTNISPDDLKPKPTLFEN 1449


>gi|344229980|gb|EGV61865.1| beta and beta-prime subunits of DNA dependent RNA-polymerase
           [Candida tenuis ATCC 10573]
          Length = 1453

 Score =  285 bits (730), Expect = 9e-74,   Method: Compositional matrix adjust.
 Identities = 144/276 (52%), Positives = 182/276 (65%), Gaps = 29/276 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH+LSI++H AK+ P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 465 DGDVVLFNRQPSLHRLSILSHYAKIRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 524

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL+TP++GE +IAATQDFITG YL+T K++FF R
Sbjct: 525 RAEAIN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLITHKDSFFER 570

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A   ++          +C +          P   ++   +WTGKQ+FSL++KPN+   V 
Sbjct: 571 ASVNQL----------LCMMSDANLQFDLPPPAIIKPVSLWTGKQVFSLLIKPNKASNVV 620

Query: 521 ANLKTKGRAYTANE-----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL  K + Y   E     E    D YVI+R S++L+G MDKSTLG G K +VFY +LRD
Sbjct: 621 INLDAKAKTYIPPERHFANEMSPNDGYVIIRGSQILSGVMDKSTLGDGKKHSVFYTILRD 680

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           +G   A  AM R+S++ + YL NRGFSIGI DVTPG
Sbjct: 681 YGPTEAAEAMNRMSKLCARYLGNRGFSIGINDVTPG 716



 Score =  255 bits (651), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 153/367 (41%), Positives = 207/367 (56%), Gaps = 80/367 (21%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCE-- 1149
            C  KY RA++EP TAVGA+ AQSIGEPGTQMTLKTFHFAG              E+    
Sbjct: 1063 CLYKYSRAKVEPGTAVGAIGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIINAS 1122

Query: 1150 ------YIEEVFVPDD--------------------------------SFILIKLDMDRI 1171
                   I  V V DD                                +++ +K+D+  I
Sbjct: 1123 KAISTPIINSVLVNDDDEIAARVVKGRIEKTLLKDVAFHIQDVYKNNMAYLSVKIDLKTI 1182

Query: 1172 RLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSFLIL--------------------K 1208
              L LE++IDSI   I     +     H++++G   + +                    K
Sbjct: 1183 EKLQLELNIDSIAQAIVNAPKLKIQPAHVSITGSDRINILVTLNDSKVESLAKSMNVDYK 1242

Query: 1209 PKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMA 1268
              D+S     +M  +K++LP + IKG+  I+RAVI+  D    +K +LLVEG  L++VM+
Sbjct: 1243 LSDASNVLFFRMQHLKRMLPEICIKGLPNISRAVINIRD---DSKKELLVEGYGLKEVMS 1299

Query: 1269 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK 1328
            T GV G K ++N+  EV++ LGIEAARS+I+ EI   M  HGMS+D RH  L+ D+MT K
Sbjct: 1300 TDGVVGTKTTTNHVLEVFEVLGIEAARSSIIGEIDYTMSKHGMSVDPRHIQLLGDVMTYK 1359

Query: 1329 GEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGT 1388
            GEVLGITR GL+KM++SVL LASFE T+DHLFDAAFY + D + GVSECII+G  M++GT
Sbjct: 1360 GEVLGITRFGLSKMRDSVLQLASFEKTTDHLFDAAFYMKNDKVEGVSECIILGQTMSIGT 1419

Query: 1389 GLIKLLQ 1395
            G  KL++
Sbjct: 1420 GAFKLVK 1426



 Score =  184 bits (467), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 108/257 (42%), Positives = 158/257 (61%), Gaps = 26/257 (10%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII + L  D D   AR+VKGR+E+T L +V  +I++V+  + 
Sbjct: 1111 GVPRIKEIINASKAISTPIINSVLVNDDDEIAARVVKGRIEKTLLKDVAFHIQDVYKNNM 1170

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSFLIL--------- 871
            +++ +K+D+  I  L LE++IDSI   I     +     H++++G   + +         
Sbjct: 1171 AYLSVKIDLKTIEKLQLELNIDSIAQAIVNAPKLKIQPAHVSITGSDRINILVTLNDSKV 1230

Query: 872  -----------KPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKL 920
                       K  D+S     +M  +K++LP + IKG+  I+RAVI+  D    +K +L
Sbjct: 1231 ESLAKSMNVDYKLSDASNVLFFRMQHLKRMLPEICIKGLPNISRAVINIRDD---SKKEL 1287

Query: 921  LVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFR 980
            LVEG  L++VM+T GV G K ++N+  EV++ LGIEAARS+I+ EI   M  HGMS+D R
Sbjct: 1288 LVEGYGLKEVMSTDGVVGTKTTTNHVLEVFEVLGIEAARSSIIGEIDYTMSKHGMSVDPR 1347

Query: 981  HPMLVADLMTSKGEVLG 997
            H  L+ D+MT KGEVLG
Sbjct: 1348 HIQLLGDVMTYKGEVLG 1364



 Score =  172 bits (435), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 97/255 (38%), Positives = 142/255 (55%), Gaps = 10/255 (3%)

Query: 96  QSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPL 155
           QS +++ +++LY  +  RT    G LD +MG +   + C+TC  NL+ C GHFG+I L L
Sbjct: 29  QSEVEVKTRDLYDLEKGRTVKEFGALDTKMGISANSSECSTCHGNLASCHGHFGHIRLAL 88

Query: 156 PVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILE 215
           PVFH+GYF+ +I ILQ ICKN  C  +LL E+    + A LR P +  L R  + K +++
Sbjct: 89  PVFHVGYFKAIIQILQCICKN--CGHILLDEQTKRKYLADLRRPYIDNLRRMKILKSVVD 146

Query: 216 TTKKVSVCPHCGEINGVVKKC------GLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVK 269
             KK   C  C  +NGVVKK         LKI H+ ++   KK     E   +E  + + 
Sbjct: 147 QCKKQRRCFKCTHVNGVVKKAASGAGPAALKIVHDTFRWVGKKPTPEKEVWDSEIEQVLT 206

Query: 270 FNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMN-AELSKPSDLILTRLLVPPN 328
            NPE+E   K  + + LNPL+VL LF+ I  ++  L  ++ +   +P   I   L  PP 
Sbjct: 207 RNPELEKFTK-RMYEDLNPLKVLHLFKQITPDECELFGLDPSRGGRPETYIWRYLPAPPV 265

Query: 329 CIRPSVISDLKSDND 343
           CIRPSV+ D +S+ D
Sbjct: 266 CIRPSVMMDAQSNED 280



 Score =  102 bits (253), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 48/61 (78%), Positives = 52/61 (85%), Gaps = 1/61 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV+NSFFSGLTP EF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QY
Sbjct: 837 TPQSKGFVRNSFFSGLTPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSSQY 896

Query: 668 D 668
           D
Sbjct: 897 D 897



 Score = 62.0 bits (149), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/41 (65%), Positives = 35/41 (85%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRA 62
           LM  K+NL+TP++GE +IAATQDFITG YL+T K++FF RA
Sbjct: 531 LMGVKNNLLTPKSGEPIIAATQDFITGSYLITHKDSFFERA 571



 Score = 50.8 bits (120), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 22/39 (56%), Positives = 29/39 (74%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  FDAAFY + D + GVSECII+G  M++GTG  KL++
Sbjct: 1388 DHLFDAAFYMKNDKVEGVSECIILGQTMSIGTGAFKLVK 1426


>gi|408390218|gb|EKJ69624.1| hypothetical protein FPSE_10220 [Fusarium pseudograminearum CS3096]
          Length = 1450

 Score =  285 bits (730), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 141/280 (50%), Positives = 182/280 (65%), Gaps = 28/280 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND+VLFNRQPSLHKLSIM+H AKV P RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 468 DNDIVLFNRQPSLHKLSIMSHLAKVRPWRTFRLNECVCGPYNADFDGDEMNLHVPQTEEA 527

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K NL TP+NGE +IAATQDFIT  YLL+ K+ FF+R
Sbjct: 528 RAEAIN--------------LMGIKHNLATPKNGEPVIAATQDFITAAYLLSGKDRFFDR 573

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                +   ++   + +             P   +    +WTGKQ+F ++++PN+D PV 
Sbjct: 574 KTFTYLCMHMMDGKTHL----------DLPPPAIIAPQSLWTGKQLFGMLMRPNKDSPVK 623

Query: 521 ANLKTKGRAYTANEEFC----HRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL  K + Y A    C      D ++++RNSE++ G MDKST+G G K ++FY++LRDF
Sbjct: 624 VNLDAKCKTYKARPGQCPDMDPNDGWLVVRNSEVMCGRMDKSTVGDGKKDSIFYVILRDF 683

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           G D AVTAM RL+++ +  L N GFSIGIGDV P +  +Q
Sbjct: 684 GPDEAVTAMNRLAKLCARQLTNHGFSIGIGDVFPPESLIQ 723



 Score =  204 bits (520), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 109/271 (40%), Positives = 157/271 (57%), Gaps = 10/271 (3%)

Query: 79  FRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCG 138
           F+G+  G  + +D +  Q+ +++  + LY  +  R P  HG LD R+GT+ K+  C+TC 
Sbjct: 23  FKGIKFGIQSNQD-IANQAVLEVSDRLLYDIENNRAPYRHGPLDSRLGTSSKQGRCSTCQ 81

Query: 139 QNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN 198
           ++L DC GHFG++ LPLP FH+GY R +++ILQ ICK+  C RVLL E     F   LR 
Sbjct: 82  ESLKDCNGHFGHVRLPLPAFHVGYLRFIMSILQEICKD--CGRVLLEEPDRQQFLKDLRR 139

Query: 199 PALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEK---YKNRTKKKDA 255
           P L  L R  + K+I E  +KV  CP+CG +NG ++K G+LK++H+K   Y   T  K  
Sbjct: 140 PFLDNLRRTQICKRINEQCRKVKTCPYCGSLNGQIRKIGVLKLAHDKFVAYNKSTSIKKT 199

Query: 256 IVEDLLA---EYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL 312
             E  +     +NEA + NPE++ H +  + + LNPL VL LF+ I   D  LL ++   
Sbjct: 200 PPESKIKFDNSFNEAKRENPELDKHLRKAM-EDLNPLRVLNLFKMISPTDCELLGLDPAE 258

Query: 313 SKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
            +P   I   L  PP CIRPSV  D  S+ D
Sbjct: 259 GRPEMFIWQFLPAPPVCIRPSVAQDNASNED 289



 Score =  166 bits (421), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 93/173 (53%), Positives = 117/173 (67%), Gaps = 5/173 (2%)

Query: 1223 MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNT 1282
            +++ LP+V I G     RA+I   +      + +LVEG  LR+ M T GV G K SSNN 
Sbjct: 1249 LRRALPNVPISGYSEATRAIIQTSEQ---NTHTVLVEGYGLRECMTTEGVIGTKASSNNV 1305

Query: 1283 YEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKM 1342
             E    LGIEAAR+TI  EI  VM +  M+ID RH  L+AD+MT KGEVLGITR GL+KM
Sbjct: 1306 MECRDVLGIEAARTTIAVEIGSVMGD--MNIDPRHMQLLADVMTYKGEVLGITRFGLSKM 1363

Query: 1343 KESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 1395
            ++SVL LASFE T DHLF+AA   +TD I GVSECIIMG  M+VGTG  ++++
Sbjct: 1364 RDSVLQLASFEKTPDHLFEAAAGMKTDQIEGVSECIIMGQTMSVGTGAFQVVR 1416



 Score =  144 bits (363), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 98/279 (35%), Positives = 150/279 (53%), Gaps = 28/279 (10%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+IT  L+ +  ++ AR+VKGR+E+T + ++  ++E+ +   +
Sbjct: 1106 GVPRIKEIINASKAISTPVITCPLENNEQIEAARVVKGRIEKTYISDILRFVEDEWRTTE 1165

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSFLILKPKDSSKSF 880
              +++++D   +  +HL +    I   I + R +      L++ G   +I++ +D S   
Sbjct: 1166 GNVVLQIDPTALSDMHLGIGPYDIAEAICKQRKLKVQRDDLSIDGDR-IIVRVRDISDPA 1224

Query: 881  NSKMYQ------------------MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLV 922
              +                     +++ LP+V I G     RA+I   +      + +LV
Sbjct: 1225 AKRTAARSKAAAAESGDMLLRANFLRRALPNVPISGYSEATRAIIQTSE---QNTHTVLV 1281

Query: 923  EGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHP 982
            EG  LR+ M T GV G K SSNN  E    LGIEAAR+TI  EI  VM +  M+ID RH 
Sbjct: 1282 EGYGLRECMTTEGVIGTKASSNNVMECRDVLGIEAARTTIAVEIGSVMGD--MNIDPRHM 1339

Query: 983  MLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDP 1021
             L+AD+MT KGEVLG  T   L ++ D ++   S    P
Sbjct: 1340 QLLADVMTYKGEVLGI-TRFGLSKMRDSVLQLASFEKTP 1377



 Score =  105 bits (263), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 47/59 (79%), Positives = 52/59 (88%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSF+SGL+PTEF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 841 PSKGFVKNSFYSGLSPTEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSTQYD 899



 Score = 69.3 bits (168), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 30/40 (75%), Positives = 33/40 (82%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            C EKY +A +EP  AVGA+ A SIGEPGTQMTLKTFHFAG
Sbjct: 1058 CLEKYKKAHVEPGHAVGAVGAHSIGEPGTQMTLKTFHFAG 1097



 Score = 57.8 bits (138), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 27/54 (50%), Positives = 36/54 (66%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           LM  K NL TP+NGE +IAATQDFIT  YLL+ K+ FF+R     +   ++ G+
Sbjct: 534 LMGIKHNLATPKNGEPVIAATQDFITAAYLLSGKDRFFDRKTFTYLCMHMMDGK 587



 Score = 43.5 bits (101), Expect = 0.94,   Method: Compositional matrix adjust.
 Identities = 21/39 (53%), Positives = 28/39 (71%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  F+AA   +TD I GVSECIIMG  M+VGTG  ++++
Sbjct: 1378 DHLFEAAAGMKTDQIEGVSECIIMGQTMSVGTGAFQVVR 1416


>gi|310799174|gb|EFQ34067.1| RNA polymerase Rpb1 [Glomerella graminicola M1.001]
          Length = 1342

 Score =  285 bits (729), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 140/280 (50%), Positives = 183/280 (65%), Gaps = 28/280 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND+VLFNRQPSLHKLSIM+H  KV P RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 353 DNDIVLFNRQPSLHKLSIMSHLVKVRPWRTFRLNECVCGPYNADFDGDEMNLHVPQTEEA 412

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K NL TP+NGE +IAATQDFIT  YLL+ K+ FF+R
Sbjct: 413 RAEAIN--------------LMGVKHNLATPKNGEPVIAATQDFITAAYLLSSKDNFFDR 458

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                I   ++     +             P   ++   +WTGKQ+F+++++PN++ PV 
Sbjct: 459 KTFTYICMHMMDGKVHL----------DLPPPAVLKPKALWTGKQVFNMMMRPNKESPVK 508

Query: 521 ANLKTKGRAYTANEEFC----HRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL  K R Y A    C      D+++++RNSE++ G MDKST+G G K +VFY++LRDF
Sbjct: 509 INLDAKCREYKARAGQCPDMDPEDAWLVIRNSEVMCGVMDKSTVGDGKKDSVFYVILRDF 568

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           G D AV  M RL+++ + +L NRGFSIGIGDV P +  ++
Sbjct: 569 GPDAAVATMNRLAKLCARHLTNRGFSIGIGDVFPTEKLLE 608



 Score =  203 bits (516), Expect = 6e-49,   Method: Compositional matrix adjust.
 Identities = 143/388 (36%), Positives = 194/388 (50%), Gaps = 79/388 (20%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGE------------------- 1146
            C EKY +A +EP  AVGA+ AQSIGEPGTQMTLKTFHFAG                    
Sbjct: 952  CLEKYKKAHVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIINAS 1011

Query: 1147 -----------------------VCEYIEEVFVPD------DSF------ILIKLDMDRI 1171
                                   V   IE+ FV D      D +      +++K+DMD +
Sbjct: 1012 KVISTPVITCPLVQNRELTAARIVKARIEKTFVEDILSYIEDEWFAESGNVVLKVDMDAL 1071

Query: 1172 RLLHLEVDIDSIRYCIERTRGI----------SGHLTV--------SGHSFLILKPKDSS 1213
              + L + +  +   I + + +          +G + +        +    +  KP D  
Sbjct: 1072 SDMQLGITLGDVAEAICKHKKMKVSRSDMHIGAGRIEIRVRLDESAAAKRAVKGKPVDDL 1131

Query: 1214 KSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVK 1273
                 +   +++ +P+V I G     RA+I   + E    + +LVEG  L   M T GV 
Sbjct: 1132 GDLLVRANYLRRTIPTVAISGYPLATRAIIQTSEQE---THTVLVEGYGLLSCMNTEGVD 1188

Query: 1274 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 1333
            G +  +NN  E    LGIEAARSTI  EI  VM +  M+ID RH  L+AD+MT KGEVLG
Sbjct: 1189 GRRVKTNNVMECRDVLGIEAARSTIAYEIGEVMGD--MNIDPRHMQLLADVMTYKGEVLG 1246

Query: 1334 ITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            ITR GL+KM++SVL LASFE T DHLF+AA   +TD I GVSECIIMG  M VGTG   +
Sbjct: 1247 ITRFGLSKMRDSVLQLASFEKTPDHLFEAAAGMKTDQIEGVSECIIMGQTMTVGTGAFHV 1306

Query: 1394 LQ--AVPRSEPVPRTLLFDNPEFHTNTL 1419
            ++  A+ + +   R   F++      TL
Sbjct: 1307 VRRLALEKGDVGQRKTAFEDAWAADTTL 1334



 Score =  140 bits (354), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 97/276 (35%), Positives = 147/276 (53%), Gaps = 24/276 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+IT  L ++ +L  ARIVK R+E+T + ++  YIE+ +  + 
Sbjct: 1000 GVPRIKEIINASKVISTPVITCPLVQNRELTAARIVKARIEKTFVEDILSYIEDEWFAES 1059

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI----------SGHLTV--------SG 865
              +++K+DMD +  + L + +  +   I + + +          +G + +        + 
Sbjct: 1060 GNVVLKVDMDALSDMQLGITLGDVAEAICKHKKMKVSRSDMHIGAGRIEIRVRLDESAAA 1119

Query: 866  HSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD 925
               +  KP D       +   +++ +P+V I G     RA+I   + E    + +LVEG 
Sbjct: 1120 KRAVKGKPVDDLGDLLVRANYLRRTIPTVAISGYPLATRAIIQTSEQE---THTVLVEGY 1176

Query: 926  NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 985
             L   M T GV G +  +NN  E    LGIEAARSTI  EI  VM +  M+ID RH  L+
Sbjct: 1177 GLLSCMNTEGVDGRRVKTNNVMECRDVLGIEAARSTIAYEIGEVMGD--MNIDPRHMQLL 1234

Query: 986  ADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDP 1021
            AD+MT KGEVLG  T   L ++ D ++   S    P
Sbjct: 1235 ADVMTYKGEVLGI-TRFGLSKMRDSVLQLASFEKTP 1269



 Score =  105 bits (263), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 47/59 (79%), Positives = 51/59 (86%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSF+SGL PTEF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 726 PSKGFVENSFYSGLLPTEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSTQYD 784



 Score =  103 bits (258), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 62/171 (36%), Positives = 90/171 (52%), Gaps = 7/171 (4%)

Query: 179 CARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGL 238
           C +VLL E +   F  +LR P L  L R  + K+I E  +KV  C +CG + G ++K G+
Sbjct: 5   CGKVLLTESERRAFLKELRRPLLDNLRRSQICKRINEQCRKVKNCMYCGSVQGQIRKVGV 64

Query: 239 LKISHEK---YKNRTKKKDAIVEDLLA---EYNEAVKFNPEIEAHKKFGLIQTLNPLEVL 292
           LK++H+K   Y   T  K    E  +     ++EA K N E++ H +  + + +NPL VL
Sbjct: 65  LKLAHDKFVTYNKSTSAKKVPPESKIKFDESFSEARKNNAELDKHLRKAM-EDMNPLRVL 123

Query: 293 QLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
            LF+ I   D  LL ++    +P   I   L  PP CIRPSV  D  S+ D
Sbjct: 124 NLFKMISPSDCELLGLDPAEGRPEMFIWQFLPAPPVCIRPSVAQDNASNED 174



 Score = 59.3 bits (142), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 28/54 (51%), Positives = 36/54 (66%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           LM  K NL TP+NGE +IAATQDFIT  YLL+ K+ FF+R     I   ++ G+
Sbjct: 419 LMGVKHNLATPKNGEPVIAATQDFITAAYLLSSKDNFFDRKTFTYICMHMMDGK 472



 Score = 42.4 bits (98), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 21/39 (53%), Positives = 26/39 (66%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  F+AA   +TD I GVSECIIMG  M VGTG   +++
Sbjct: 1270 DHLFEAAAGMKTDQIEGVSECIIMGQTMTVGTGAFHVVR 1308


>gi|363753734|ref|XP_003647083.1| hypothetical protein Ecym_5525 [Eremothecium cymbalariae
           DBVPG#7215]
 gi|356890719|gb|AET40266.1| hypothetical protein Ecym_5525 [Eremothecium cymbalariae
           DBVPG#7215]
          Length = 1459

 Score =  285 bits (728), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 144/278 (51%), Positives = 188/278 (67%), Gaps = 30/278 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH+LSI++H AK+ P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 467 DGDVVLFNRQPSLHRLSILSHYAKIRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 526

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL+TP++GE +I+ATQDFITG YL++ K++FF+R
Sbjct: 527 RAEAIN--------------LMGVKNNLLTPKSGEPIISATQDFITGSYLISHKDSFFDR 572

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A   ++ S ++AD +       +F      P   ++   +WTGKQ+FSL+++PN+  PV 
Sbjct: 573 ATFTQLLS-MMADAN------MQFDLP---PPAIIKPCYLWTGKQVFSLLIRPNKKSPVI 622

Query: 521 ANLKTKGRAY------TANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLR 574
            NL  K + Y      +   E    D YVI+R SE+L G MDKS LG G K +VFY +LR
Sbjct: 623 INLDAKNKVYLPPKNKSFPNEMSSNDGYVIIRGSEILCGVMDKSVLGDGKKHSVFYTILR 682

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
           DFG   A  AM R++++ + YL NRGFSIGI DVTPG+
Sbjct: 683 DFGPYEAAKAMNRMAKLCARYLGNRGFSIGINDVTPGK 720



 Score =  246 bits (627), Expect = 8e-62,   Method: Compositional matrix adjust.
 Identities = 155/380 (40%), Positives = 211/380 (55%), Gaps = 83/380 (21%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG----------------------- 1145
            KY +A++EP TAVGA+ A SIGEPGTQMTLKTFHFAG                       
Sbjct: 1076 KYHKAKVEPGTAVGAIGAHSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKVI 1135

Query: 1146 -------------------EVCEYIEEVFVPDDSF------------ILIKLDMDRIRLL 1174
                                V   IE+  + D  F            I +K+D+  I  L
Sbjct: 1136 STPIINALLVNDNDERAARVVKGRIEKTLLSDVVFYIQDVYRDNMSFIQVKVDLSTIEKL 1195

Query: 1175 HLEVDIDSIRYCIERTRGI---SGHLTVSGH-----------------SFLILKPKDSSK 1214
             LE+ I+ I   I R   +   +G +++ G                  S L+ +P ++  
Sbjct: 1196 QLELTIEDIAIAISRAPKLKISTGDVSIIGKNKINISVGNDLEKGKSISTLVSEPNENDV 1255

Query: 1215 SFNSKMYQMKQLLPSVVIKGVQGINRAVIH-EEDVEGVTKYKLLVEGDNLRDVMATYGVK 1273
             +  +M  +++ LP++V+KG+  I+RAVI+  ED     K +LLVEG  LRDVM T GV 
Sbjct: 1256 FY--RMQHLRRALPNIVVKGLPDISRAVINILED----GKRELLVEGYGLRDVMTTDGVI 1309

Query: 1274 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 1333
            G K  +N+  EV++ LGIEAAR++I+ EI   M NHGMS+D RH  L+ D+MT KGEVLG
Sbjct: 1310 GYKTKTNHFLEVFEVLGIEAARTSIIDEIDYTMSNHGMSVDPRHIQLLGDVMTYKGEVLG 1369

Query: 1334 ITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            ITR GL+KM++SVL LASFE T+DHLFDAAFY + D + GVSECII+G  M++GTG  K+
Sbjct: 1370 ITRFGLSKMRDSVLQLASFEKTTDHLFDAAFYMKKDAVEGVSECIILGQTMSIGTGSFKV 1429

Query: 1394 LQA--VPRSEPVPRTLLFDN 1411
            ++   +   E  P   LF+N
Sbjct: 1430 VRGTNISMDELKPNPTLFEN 1449



 Score =  196 bits (498), Expect = 8e-47,   Method: Compositional matrix adjust.
 Identities = 109/272 (40%), Positives = 160/272 (58%), Gaps = 14/272 (5%)

Query: 72  IAGRKVFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKE 131
           +A +K+  +GL    ++  D V Q S ++I +++L+  +  R P   G LD +MG +  +
Sbjct: 8   VAPKKI--KGLHFSALSASDIVAQ-SEVEIFTRDLFDLENGRAPKQGGALDSKMGVSSSQ 64

Query: 132 ANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAG 191
           A C+TC  NL+ C GHFG+I L LPVFHIGYF+  I ILQSICKN  CA +LL EE+   
Sbjct: 65  AECSTCHGNLASCHGHFGHIKLALPVFHIGYFKATIQILQSICKN--CAAILLSEEEKRQ 122

Query: 192 FRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKC------GLLKISHEK 245
           F A+LR P +  L R +  +K+L+  KK   C HCG +NGVVKK         LKI H+ 
Sbjct: 123 FLAELRRPGIDNLRRMATLRKVLDQCKKQRRCLHCGALNGVVKKAATGSGSAALKIIHDT 182

Query: 246 YKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPL 305
           ++   KK     E  + ++N+ ++ NPE+E + K  +   LNPL+ L LF+ +  +D  L
Sbjct: 183 FRWVGKKSAPEKEKWIGDWNQVLQHNPELERYMKRSM-DNLNPLKTLNLFKQVRAQDCEL 241

Query: 306 LLMNAEL--SKPSDLILTRLLVPPNCIRPSVI 335
           L +++ +   +P   I   L  PP CIRPSV+
Sbjct: 242 LGIDSTVKAGRPETYIWRYLPAPPVCIRPSVM 273



 Score =  188 bits (478), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 114/255 (44%), Positives = 159/255 (62%), Gaps = 27/255 (10%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII A L  D D   AR+VKGR+E+T L +V  YI++V+  + 
Sbjct: 1121 GVPRIKEIINASKVISTPIINALLVNDNDERAARVVKGRIEKTLLSDVVFYIQDVYRDNM 1180

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGH-------------- 866
            SFI +K+D+  I  L LE+ I+ I   I R   +   +G +++ G               
Sbjct: 1181 SFIQVKVDLSTIEKLQLELTIEDIAIAISRAPKLKISTGDVSIIGKNKINISVGNDLEKG 1240

Query: 867  ---SFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIH-EEDVEGVTKYKLLV 922
               S L+ +P ++   +  +M  +++ LP++V+KG+  I+RAVI+  ED     K +LLV
Sbjct: 1241 KSISTLVSEPNENDVFY--RMQHLRRALPNIVVKGLPDISRAVINILED----GKRELLV 1294

Query: 923  EGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHP 982
            EG  LRDVM T GV G K  +N+  EV++ LGIEAAR++I+ EI   M NHGMS+D RH 
Sbjct: 1295 EGYGLRDVMTTDGVIGYKTKTNHFLEVFEVLGIEAARTSIIDEIDYTMSNHGMSVDPRHI 1354

Query: 983  MLVADLMTSKGEVLG 997
             L+ D+MT KGEVLG
Sbjct: 1355 QLLGDVMTYKGEVLG 1369



 Score = 99.0 bits (245), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 46/61 (75%), Positives = 52/61 (85%), Gaps = 1/61 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV++SFFSGL+P EF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QY
Sbjct: 840 TPQSKGFVRSSFFSGLSPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSCQY 899

Query: 668 D 668
           D
Sbjct: 900 D 900



 Score = 60.5 bits (145), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 26/50 (52%), Positives = 40/50 (80%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM  K+NL+TP++GE +I+ATQDFITG YL++ K++FF+RA   ++ S +
Sbjct: 533 LMGVKNNLLTPKSGEPIISATQDFITGSYLISHKDSFFDRATFTQLLSMM 582



 Score = 53.5 bits (127), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 26/57 (45%), Positives = 36/57 (63%), Gaps = 2/57 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA--VPRSEPVPRTLLFDN 722
            D  FDAAFY + D + GVSECII+G  M++GTG  K+++   +   E  P   LF+N
Sbjct: 1393 DHLFDAAFYMKKDAVEGVSECIILGQTMSIGTGSFKVVRGTNISMDELKPNPTLFEN 1449


>gi|326479108|gb|EGE03118.1| DNA-directed RNA polymerase III largest subunit [Trichophyton
           equinum CBS 127.97]
          Length = 1427

 Score =  285 bits (728), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 138/280 (49%), Positives = 184/280 (65%), Gaps = 28/280 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++H  KV PHRTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 469 DGDIVLFNRQPSLHKLSILSHFVKVRPHRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 528

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  KSNL TP+NGE +IAA QDFIT  YLL+ K+ FF+R
Sbjct: 529 RAEAME--------------LMGVKSNLATPKNGEPIIAAIQDFITAAYLLSSKDNFFDR 574

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
               +I  +++  ++       RF      P   ++  ++WTGKQ+FS++++ N+DCPV 
Sbjct: 575 KTFTQICLSMLDSST-------RF---ELPPPATIKPQMLWTGKQVFSVLMRSNKDCPVK 624

Query: 521 ANLKTKGRAYT----ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL    R          + C  D ++ +RNSE+L G  DKST+G+G K N+F+++ RDF
Sbjct: 625 VNLDAACRQLKLVKGQPRDLCENDGWLCIRNSEMLCGVADKSTIGAGKKDNIFFVIQRDF 684

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           G   A  AM RLS++++ +L N+GFSIGI DV PG+  V+
Sbjct: 685 GYAAAAEAMNRLSKLSARWLTNKGFSIGITDVYPGESLVR 724



 Score =  176 bits (446), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 102/267 (38%), Positives = 150/267 (56%), Gaps = 12/267 (4%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G ++ +D +  Q+H++I  + L+  D  R    +G +D R+G + K   C TCG +L +C
Sbjct: 29  GVLSNQD-IISQAHVEISDRKLFDLDNNRAVARNGPMDPRLGISNKSDTCETCGGDLQEC 87

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFGY+ L LP FH+GYF+  I ILQ ICK+  C+++LL E++   +  +LR P L  L
Sbjct: 88  NGHFGYVRLVLPAFHVGYFKRTIEILQDICKD--CSKILLPEDERRSYLKELRRPGLDNL 145

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKC--GLLKISHEKYK----NRTKKKDAIVE 258
            R  + K+I    +K  VC +C  ING VKK   G LKI H+K++    + + KK     
Sbjct: 146 RRMQINKRINVRCRKTPVCYYCNAINGTVKKASTGALKIVHDKFRAFNASLSAKKIPPPS 205

Query: 259 DLLAE--YNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPS 316
            L  +  + EA K NP+IE H +  +   LNPL VL+LF  I  ED  LL +N + ++P 
Sbjct: 206 KLAFDRSFEEAKKANPDIEKHYR-RVFDDLNPLRVLKLFRRISNEDCELLSLNVDGARPE 264

Query: 317 DLILTRLLVPPNCIRPSVISDLKSDND 343
             +   +  PP  IRPSV  +  S  D
Sbjct: 265 YFLWQFIPAPPVPIRPSVGQEGASTED 291



 Score =  174 bits (440), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 110/269 (40%), Positives = 154/269 (57%), Gaps = 20/269 (7%)

Query: 1143 FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISG------- 1195
            F  ++  YIEE      SFI IK+D   I+ L LE+ +  I   I++ +           
Sbjct: 1123 FLKDIVYYIEENRSQTSSFINIKVDFSTIKKLQLELTLRQILLAIKKHKAFKAADLTFRS 1182

Query: 1196 -----HLTVSGHSFLILKPKDSSKSFNSKMY----QMKQLLPSVVIKGVQGINRAVIHEE 1246
                 H+ V   + +        K   S  Y     ++++LP++ + G     RAVI   
Sbjct: 1183 FNSHIHIYVDEGASMAGVSVSEQKITGSDPYIRINYLRRILPNIQVFGYPDCTRAVIRVG 1242

Query: 1247 DVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVM 1306
              E V    LLVEG  LR  M T G++G +  +N+  E+   LGIEAAR+TI+ EI  VM
Sbjct: 1243 --EKVATNILLVEGYGLRACMTTDGIEGHRTRTNHVMEMRDVLGIEAARTTIIDEISSVM 1300

Query: 1307 ENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYG 1366
               GM+ID RH  L+AD+MT KGEVLGITR GLAK+++SVL LASFE T+DHLFDA   G
Sbjct: 1301 S--GMAIDPRHMQLLADVMTYKGEVLGITRFGLAKIRDSVLQLASFEKTADHLFDAGGAG 1358

Query: 1367 QTDCISGVSECIIMGLPMNVGTGLIKLLQ 1395
            + D + GVSECIIMG  +++GTG +++++
Sbjct: 1359 RRDTVQGVSECIIMGKTISLGTGSMEVVR 1387



 Score =  151 bits (381), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 103/250 (41%), Positives = 137/250 (54%), Gaps = 20/250 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIIT  L   TD+  A IVKGR+E+  L ++  YIEE      
Sbjct: 1080 GVPRIKEIINASKEISTPIITCELVNKTDMRIAEIVKGRVEKLFLKDIVYYIEENRSQTS 1139

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISG------------HLTVSGHSFLIL 871
            SFI IK+D   I+ L LE+ +  I   I++ +                H+ V   + +  
Sbjct: 1140 SFINIKVDFSTIKKLQLELTLRQILLAIKKHKAFKAADLTFRSFNSHIHIYVDEGASMAG 1199

Query: 872  KPKDSSKSFNSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927
                  K   S  Y     ++++LP++ + G     RAVI     E V    LLVEG  L
Sbjct: 1200 VSVSEQKITGSDPYIRINYLRRILPNIQVFGYPDCTRAVIRVG--EKVATNILLVEGYGL 1257

Query: 928  RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 987
            R  M T G++G +  +N+  E+   LGIEAAR+TI+ EI  VM   GM+ID RH  L+AD
Sbjct: 1258 RACMTTDGIEGHRTRTNHVMEMRDVLGIEAARTTIIDEISSVMS--GMAIDPRHMQLLAD 1315

Query: 988  LMTSKGEVLG 997
            +MT KGEVLG
Sbjct: 1316 VMTYKGEVLG 1325



 Score =  103 bits (258), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 46/58 (79%), Positives = 51/58 (87%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV+NSFFSGLTPTEF FH M GREGL+DTAVKTAETGYM RRL+KSLEDL  +YD
Sbjct: 842 AKGFVRNSFFSGLTPTEFLFHAMSGREGLIDTAVKTAETGYMSRRLMKSLEDLSTRYD 899



 Score = 58.9 bits (141), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 28/57 (49%), Positives = 37/57 (64%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVF 78
           LM  KSNL TP+NGE +IAA QDFIT  YLL+ K+ FF+R    +I  +++     F
Sbjct: 535 LMGVKSNLATPKNGEPIIAAIQDFITAAYLLSSKDNFFDRKTFTQICLSMLDSSTRF 591



 Score = 42.0 bits (97), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 18/39 (46%), Positives = 28/39 (71%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  FDA   G+ D + GVSECIIMG  +++GTG +++++
Sbjct: 1349 DHLFDAGGAGRRDTVQGVSECIIMGKTISLGTGSMEVVR 1387


>gi|164657764|ref|XP_001730008.1| hypothetical protein MGL_2994 [Malassezia globosa CBS 7966]
 gi|159103902|gb|EDP42794.1| hypothetical protein MGL_2994 [Malassezia globosa CBS 7966]
          Length = 1376

 Score =  284 bits (727), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 140/277 (50%), Positives = 183/277 (66%), Gaps = 29/277 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIM HRAK+ P RTFR NECVC+PYNADFDGDEMN+H+PQTEEA
Sbjct: 433 DGDIVLFNRQPSLHKLSIMCHRAKIRPWRTFRLNECVCSPYNADFDGDEMNMHVPQTEEA 492

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL               LM  K NLVTPRNGE ++AATQDFIT  +LL+++  FF R
Sbjct: 493 RTEAL--------------TLMGVKHNLVTPRNGEPIVAATQDFITAAFLLSRRGRFFTR 538

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           AQ ++I S     +  I             P   ++   +WTGKQ+FS +++PN+  PV 
Sbjct: 539 AQFVQICSYFGDASLHI----------DLPPPAILKPVRLWTGKQLFSCMIRPNKQSPVL 588

Query: 521 ANLKTKGRAYTANE-----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL+ + R +         E    D Y++++NSE+L G MDK+T+G G K +VF ++LRD
Sbjct: 589 VNLEARCRTFEKPRDGHVNEMSPNDGYLVIQNSEVLCGVMDKATVGDGKKQSVFGVILRD 648

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
           +G D AV +M RL++  + +L N+GFS+GIGDVTPGQ
Sbjct: 649 YGPDAAVASMNRLAKTCARWLSNQGFSLGIGDVTPGQ 685



 Score =  228 bits (580), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 175/503 (34%), Positives = 237/503 (47%), Gaps = 80/503 (15%)

Query: 983  MLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFL 1042
             L  D      E+ GN  PVE  R      AK +      L   E++ L N  L    F 
Sbjct: 878  FLYGDDGLDPAELEGNALPVEYNRTFRHASAKTADVPSRYLLPYEVMDLVNHLLSQDRFE 937

Query: 1043 QDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQ----------ILSHQDKIGHGR 1092
            +  +  ++  +++F  E   K    + +     P  E+           L   D      
Sbjct: 938  RVCTSKYIDQVREFCYEQVAKRMAETREAYGMYPALERDGDWDVDTDLSLGADDAQRAVV 997

Query: 1093 ESNPFPSACKA----EACREKYVRAQIEPATAVGAL------------------------ 1124
            E+    S          C +KY+RA+IEP +AVGA+                        
Sbjct: 998  ENKVRVSEATILEFINLCWDKYMRAKIEPGSAVGAVGAQSIGEPGTQMTLKTFHFAGVAS 1057

Query: 1125 ---------------AAQSIGEPGTQMTLKTFH---------------FAGEVCEYIEEV 1154
                           AA+ I  P    TL +                 + G+V   IEE 
Sbjct: 1058 MNVTLGVPRIKEIINAAKVINTPIIAATLVSEKSEQAARIVKGRIEKTYLGDVASVIEEA 1117

Query: 1155 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSGHS---FLILK 1208
            +    ++I I +D   I+ L LEV +D I+  I    R +     + V  +     + + 
Sbjct: 1118 WSGTYTYIGIDIDTAAIQKLQLEVTLDDIKRAIVAMPRMKIKEERIIVLPNQDRLQIYIH 1177

Query: 1209 PKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMA 1268
            P +  K     + Q+K+ LP VVIKG+   +RAVI +E      + KLLVEG  LR+VM 
Sbjct: 1178 PDEKEKDVYYSLKQLKRQLPKVVIKGIPHASRAVISDEK----GQRKLLVEGYGLREVMT 1233

Query: 1269 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK 1328
            T GV G    +N+  E+ + LGIEAARS+I  EI   M +HGMSID RH ML+AD+MT K
Sbjct: 1234 TEGVVGTHTHTNHVMEMQQVLGIEAARSSIYREIDYTMASHGMSIDPRHVMLLADVMTYK 1293

Query: 1329 GEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLP-MNVG 1387
            GEVLGITR G+AKMK+SVL LASFE T+DHLFDAA +G++D ISGVSE IIMG P   VG
Sbjct: 1294 GEVLGITRFGVAKMKDSVLMLASFEKTTDHLFDAALFGKSDSISGVSESIIMGNPAQTVG 1353

Query: 1388 TGLIKLLQAVPRSEPVPRTLLFD 1410
            TG+  L+   P   P PR L+FD
Sbjct: 1354 TGMPALVSQKPTLAP-PRQLVFD 1375



 Score =  197 bits (500), Expect = 5e-47,   Method: Compositional matrix adjust.
 Identities = 104/248 (41%), Positives = 148/248 (59%), Gaps = 7/248 (2%)

Query: 97  SHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP 156
           + +++V++++Y   P R P   G+LDRRMG + K + C TCGQ ++DCVGH+GYI L LP
Sbjct: 10  AELEVVTRDIY-DLPNRDPRRGGVLDRRMGVSDKVSTCETCGQRMADCVGHYGYIKLVLP 68

Query: 157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILET 216
           VFH+G+F+ V++ILQ ICK  +CARVLL E     F  + R P L  L R    K +   
Sbjct: 69  VFHVGFFKHVVSILQMICK--SCARVLLEEPDRRRFLRRFRRPGLENLQRAQTFKAVNAA 126

Query: 217 TKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF-NPEIE 275
            +K+  CPHCG  NG VKK G+LKI HEK++ +  +++ +  +    ++ AV   N E+ 
Sbjct: 127 ARKMLYCPHCGSTNGTVKKAGVLKIVHEKFRQKKTEEEQL--EFRKTFSTAVSMGNGELA 184

Query: 276 AHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVI 335
            H      + LNPL VL LF  I  ED  LL +  +  +P + I   + VPP CIRPSV 
Sbjct: 185 PHLNKAQ-EDLNPLRVLDLFRRISDEDCELLALKPQFGRPEEYIWQYICVPPVCIRPSVA 243

Query: 336 SDLKSDND 343
            D  ++ D
Sbjct: 244 QDGATNED 251



 Score =  179 bits (455), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 110/240 (45%), Positives = 146/240 (60%), Gaps = 10/240 (4%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ I+TPII A L  +     ARIVKGR+E+T LG+V   IEE +    
Sbjct: 1063 GVPRIKEIINAAKVINTPIIAATLVSEKSEQAARIVKGRIEKTYLGDVASVIEEAWSGTY 1122

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSGHS---FLILKPKDSS 877
            ++I I +D   I+ L LEV +D I+  I    R +     + V  +     + + P +  
Sbjct: 1123 TYIGIDIDTAAIQKLQLEVTLDDIKRAIVAMPRMKIKEERIIVLPNQDRLQIYIHPDEKE 1182

Query: 878  KSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVK 937
            K     + Q+K+ LP VVIKG+   +RAVI +E      + KLLVEG  LR+VM T GV 
Sbjct: 1183 KDVYYSLKQLKRQLPKVVIKGIPHASRAVISDEK----GQRKLLVEGYGLREVMTTEGVV 1238

Query: 938  GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            G    +N+  E+ + LGIEAARS+I  EI   M +HGMSID RH ML+AD+MT KGEVLG
Sbjct: 1239 GTHTHTNHVMEMQQVLGIEAARSSIYREIDYTMASHGMSIDPRHVMLLADVMTYKGEVLG 1298



 Score =  105 bits (262), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 47/61 (77%), Positives = 52/61 (85%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV+NSFFSGL PTEF FH + GREGLVDTAVKTAETGYMQRRL+K+LEDL   YD 
Sbjct: 807 PSKGFVRNSFFSGLEPTEFLFHAISGREGLVDTAVKTAETGYMQRRLMKALEDLSTHYDF 866

Query: 670 S 670
           S
Sbjct: 867 S 867



 Score = 64.3 bits (155), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 29/48 (60%), Positives = 37/48 (77%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIAS 69
           LM  K NLVTPRNGE ++AATQDFIT  +LL+++  FF RAQ ++I S
Sbjct: 499 LMGVKHNLVTPRNGEPIVAATQDFITAAFLLSRRGRFFTRAQFVQICS 546



 Score = 55.1 bits (131), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 30/55 (54%), Positives = 36/55 (65%), Gaps = 2/55 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLP-MNVGTGLIKLLQAVPRSEPVPRTLLFD 721
            D  FDAA +G++D ISGVSE IIMG P   VGTG+  L+   P   P PR L+FD
Sbjct: 1322 DHLFDAALFGKSDSISGVSESIIMGNPAQTVGTGMPALVSQKPTLAP-PRQLVFD 1375


>gi|320581578|gb|EFW95798.1| DNA-directed RNA polymerase III subunit, putative [Ogataea
           parapolymorpha DL-1]
          Length = 1469

 Score =  284 bits (727), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 141/279 (50%), Positives = 189/279 (67%), Gaps = 29/279 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH+LSIM+H AK+ P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 466 DGDIVLFNRQPSLHRLSIMSHFAKIRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 525

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL+TP++GE +IAATQDFITG YL++ K++F++R
Sbjct: 526 RAEAMN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLISNKDSFYDR 571

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A   ++ + +++D +    I          P    + A +WTGKQ+FSL+++PNR   V 
Sbjct: 572 ATFTQMLA-MMSDGALHVDI---------PPPAIFKPAFMWTGKQLFSLLIRPNRQSKVV 621

Query: 521 ANLKTKGRAYTA-----NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL  K + +         E    D +V++RNS++L+G MDKSTLG G K +VFY +LRD
Sbjct: 622 INLDAKNKTFVPPPPGMPSEMSPNDGFVVIRNSQILSGVMDKSTLGDGKKHSVFYTILRD 681

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGF 614
           +G D A  AM R++++ + YL NRGFSIGI DVTPG+  
Sbjct: 682 YGADEAANAMNRMAKLCARYLGNRGFSIGINDVTPGENL 720



 Score =  231 bits (588), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 158/409 (38%), Positives = 216/409 (52%), Gaps = 99/409 (24%)

Query: 1073 VSQPLREQILSHQDKIGHG--RESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIG 1130
            VS P RE++++   K+     RE            C  KY++A++EP TAVGA+ A SIG
Sbjct: 1043 VSDPERERVVTQLAKVSESMIREF--------LRLCLHKYLKAKVEPGTAVGAIGAHSIG 1094

Query: 1131 EPGTQMTLKTFHFAG------------------------------------------EVC 1148
            EPGTQMTLKTFHFAG                                           V 
Sbjct: 1095 EPGTQMTLKTFHFAGVASMNVTLGVPRIKEIINASKVISTPIINAVLVNDEDERAARVVK 1154

Query: 1149 EYIEEVFVPDDSFIL------------IKLDMDRIRLLHLEVDIDSIRYCI------ERT 1190
              IE+  + D +F +            +K+D+  I  L LE+ ID I   I      + +
Sbjct: 1155 GRIEKTILEDVAFFIEDVYKENQAYLQVKIDLHTIERLQLELTIDQIASAIVDAPKLKIS 1214

Query: 1191 RG---ISGH------------------LTVSGHSFLILKPKDSSK-----SFNSKMYQMK 1224
            RG   I G                    T S     ++K  D  +     S   +M Q++
Sbjct: 1215 RGDVAIVGKNRIQVFVSETGNETGKTARTASSRESSVVKDADERERLERTSLFFRMQQLR 1274

Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYE 1284
            ++L  VV+KG+  I+RAVI+ +D +G  K +LLVEG  L+ VMAT GV   +  +N+  E
Sbjct: 1275 RVLTKVVVKGLPDISRAVINVKD-DG--KKELLVEGYGLKAVMATDGVVAHRTKTNHVLE 1331

Query: 1285 VYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKE 1344
            ++  LGIEAAR++I++EI   M +HGM++D RH  L+ D+MT KGEVLGITR GLAKM++
Sbjct: 1332 IFDVLGIEAARASIISEIDYTMGSHGMAVDPRHIQLLGDVMTYKGEVLGITRFGLAKMRD 1391

Query: 1345 SVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            SVL LASFE T+DHLFDAAFY + D + GVSE II+G  M++GTG  KL
Sbjct: 1392 SVLQLASFEKTTDHLFDAAFYMKKDLVEGVSERIILGQTMSIGTGAFKL 1440



 Score =  176 bits (445), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 105/263 (39%), Positives = 143/263 (54%), Gaps = 25/263 (9%)

Query: 96  QSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPL 155
           QS +++ ++NL+  D  R P+ +G LD +MG + K   C TC  NL+ C GHFG+I L L
Sbjct: 29  QSEVEVATRNLFDLDHGRAPVANGALDTKMGISSKSGECATCHGNLNTCHGHFGHIKLAL 88

Query: 156 PVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILE 215
           PVFH+GYF+ +I +LQ+ICK  TC+ VLL E     F   LR P L  L R  + KK+L+
Sbjct: 89  PVFHVGYFKSIIQVLQTICK--TCSAVLLDEASKRQFLNDLRRPGLDNLRRMKILKKLLD 146

Query: 216 TTKKVSVCPHCGEINGVVKK------CGLLKISHEKYKNRTKKK-------DAIVEDLLA 262
             KK   C  CG +NGVVKK         LKI H+ ++   KK        D   EDL  
Sbjct: 147 QAKKQRRCLRCGALNGVVKKAAAGAGPAALKIIHDTFRWVGKKGADEKLQWDEDFEDLFD 206

Query: 263 EYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTR 322
           E       NP++E   K      LNPL+VL LF+ +   D  LL ++       ++ L R
Sbjct: 207 E-------NPDLEKFFK-RCFDDLNPLKVLNLFKQVDTSDCELLGIDPSKGGRPEMYLWR 258

Query: 323 LL-VPPNCIRPSVI-SDLKSDND 343
            L  PP CIRPSV+ +D  + N+
Sbjct: 259 YLPAPPVCIRPSVVMTDTNTSNE 281



 Score =  170 bits (431), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 110/266 (41%), Positives = 158/266 (59%), Gaps = 35/266 (13%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII A L  D D   AR+VKGR+E+T L +V  +IE+V+  + 
Sbjct: 1118 GVPRIKEIINASKVISTPIINAVLVNDEDERAARVVKGRIEKTILEDVAFFIEDVYKENQ 1177

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCI------ERTRG---ISGH-------------- 860
            +++ +K+D+  I  L LE+ ID I   I      + +RG   I G               
Sbjct: 1178 AYLQVKIDLHTIERLQLELTIDQIASAIVDAPKLKISRGDVAIVGKNRIQVFVSETGNET 1237

Query: 861  ----LTVSGHSFLILKPKDSSK-----SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEED 911
                 T S     ++K  D  +     S   +M Q++++L  VV+KG+  I+RAVI+ +D
Sbjct: 1238 GKTARTASSRESSVVKDADERERLERTSLFFRMQQLRRVLTKVVVKGLPDISRAVINVKD 1297

Query: 912  VEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVME 971
             +G  K +LLVEG  L+ VMAT GV   +  +N+  E++  LGIEAAR++I++EI   M 
Sbjct: 1298 -DG--KKELLVEGYGLKAVMATDGVVAHRTKTNHVLEIFDVLGIEAARASIISEIDYTMG 1354

Query: 972  NHGMSIDFRHPMLVADLMTSKGEVLG 997
            +HGM++D RH  L+ D+MT KGEVLG
Sbjct: 1355 SHGMAVDPRHIQLLGDVMTYKGEVLG 1380



 Score = 95.1 bits (235), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 42/57 (73%), Positives = 48/57 (84%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NSFFSGL+P EF FH + GREGLVDTAVKTAETGY  RRL+KS+EDL   YD
Sbjct: 842 KGFVRNSFFSGLSPPEFLFHAISGREGLVDTAVKTAETGYTSRRLMKSMEDLSAGYD 898



 Score = 60.1 bits (144), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 26/53 (49%), Positives = 41/53 (77%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           LM  K+NL+TP++GE +IAATQDFITG YL++ K++F++RA   ++ + +  G
Sbjct: 532 LMGVKNNLLTPKSGEPIIAATQDFITGSYLISNKDSFYDRATFTQMLAMMSDG 584



 Score = 45.4 bits (106), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 21/37 (56%), Positives = 26/37 (70%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 704
            D  FDAAFY + D + GVSE II+G  M++GTG  KL
Sbjct: 1404 DHLFDAAFYMKKDLVEGVSERIILGQTMSIGTGAFKL 1440


>gi|294659690|ref|XP_462102.2| DEHA2G12980p [Debaryomyces hansenii CBS767]
 gi|218511816|sp|Q6BI69.2|RPC1_DEBHA RecName: Full=DNA-directed RNA polymerase III subunit RPC1;
           Short=RNA polymerase III subunit C1; AltName:
           Full=DNA-directed RNA polymerase III largest subunit
 gi|199434160|emb|CAG90588.2| DEHA2G12980p [Debaryomyces hansenii CBS767]
          Length = 1457

 Score =  284 bits (727), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 143/281 (50%), Positives = 187/281 (66%), Gaps = 29/281 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH+LSI++H AK+ P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 465 DGDIVLFNRQPSLHRLSILSHYAKIRPWRTFRLNECVCTPYNADFDGDEMNIHVPQTEEA 524

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+R
Sbjct: 525 RAEAIN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLVSHKDSFFDR 570

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A  +++   +    +DI   I         P    +  ++WTGKQ+FSL++KPN+   V 
Sbjct: 571 ASLVQLLCMM--SDADIQFDIP--------PPAIFKPVMLWTGKQVFSLLIKPNKKSNVV 620

Query: 521 ANLKTKGRAYTA-----NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL  K + YT        E    D +VI+R S++L+G MDKSTLG G K +VFY +LRD
Sbjct: 621 INLDAKNKTYTPPAKGFPNEMSPNDGFVIIRGSQILSGVMDKSTLGDGKKHSVFYTILRD 680

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           +G D A  AM R++++ + YL NRGFSIGI DV PG    Q
Sbjct: 681 YGPDEAANAMNRMAKLCARYLGNRGFSIGINDVIPGSDLKQ 721



 Score =  255 bits (652), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 159/372 (42%), Positives = 216/372 (58%), Gaps = 82/372 (22%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCE 1149
            E C  KY RA++EP TAVGA+ AQSIGEPGTQMTLKTFHFAG              E+  
Sbjct: 1064 EQCIYKYSRAKVEPGTAVGAIGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIIN 1123

Query: 1150 --------YIEEVFVPDD--------------------------------SFILIKLDMD 1169
                     I  V V DD                                +++ IK+D++
Sbjct: 1124 ASKVISTPIINSVLVNDDDEIAARVVKGRVEKTLLEDVAYFIEDVYKNNMAYLSIKIDLN 1183

Query: 1170 RIRLLHLEVDIDSIRYCIE---RTRGISGHLTVSGHSFL-----ILKPK----------- 1210
             I  L LE++I+SI + I    + + ++G ++V+G   +     + +PK           
Sbjct: 1184 TIEKLQLELNIESIAHSIANAPKLKILAGDVSVTGKDRINVLVTLREPKSINLMKNASAD 1243

Query: 1211 ----DSS--KSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLR 1264
                D+S   S   +M  +K+ LP + IKG+  I+RAVI+  D +G  K +LLVEG  L+
Sbjct: 1244 YKGTDASIVNSLFFRMQHLKRALPRICIKGLPDISRAVINIRD-DG--KKELLVEGYGLK 1300

Query: 1265 DVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADL 1324
            +VM+T GV G K S+N+  EV++ LGIEAAR++I+ EI   M  HGMS+D RH  L+ D+
Sbjct: 1301 EVMSTDGVVGTKTSTNHILEVFQVLGIEAARASIIGEIDYTMSKHGMSVDPRHIQLLGDV 1360

Query: 1325 MTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPM 1384
            MT KGEVLGITR GL+KM++SVL LASFE T+DHLFDA+FY + D I GVSECII+G  M
Sbjct: 1361 MTYKGEVLGITRFGLSKMRDSVLQLASFEKTTDHLFDASFYMKNDKIEGVSECIILGQTM 1420

Query: 1385 NVGTGLIKLLQA 1396
            N+GTG  KL+ +
Sbjct: 1421 NIGTGAFKLVNS 1432



 Score =  183 bits (464), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 113/259 (43%), Positives = 166/259 (64%), Gaps = 28/259 (10%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII + L  D D   AR+VKGR+E+T L +V  +IE+V+  + 
Sbjct: 1114 GVPRIKEIINASKVISTPIINSVLVNDDDEIAARVVKGRVEKTLLEDVAYFIEDVYKNNM 1173

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIE---RTRGISGHLTVSGHSFL-----ILKPK- 874
            +++ IK+D++ I  L LE++I+SI + I    + + ++G ++V+G   +     + +PK 
Sbjct: 1174 AYLSIKIDLNTIEKLQLELNIESIAHSIANAPKLKILAGDVSVTGKDRINVLVTLREPKS 1233

Query: 875  --------------DSS--KSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKY 918
                          D+S   S   +M  +K+ LP + IKG+  I+RAVI+  D +G  K 
Sbjct: 1234 INLMKNASADYKGTDASIVNSLFFRMQHLKRALPRICIKGLPDISRAVINIRD-DG--KK 1290

Query: 919  KLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSID 978
            +LLVEG  L++VM+T GV G K S+N+  EV++ LGIEAAR++I+ EI   M  HGMS+D
Sbjct: 1291 ELLVEGYGLKEVMSTDGVVGTKTSTNHILEVFQVLGIEAARASIIGEIDYTMSKHGMSVD 1350

Query: 979  FRHPMLVADLMTSKGEVLG 997
             RH  L+ D+MT KGEVLG
Sbjct: 1351 PRHIQLLGDVMTYKGEVLG 1369



 Score =  178 bits (451), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 106/272 (38%), Positives = 149/272 (54%), Gaps = 11/272 (4%)

Query: 79  FRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCG 138
            +G+  G ++ +D +  QS +++ +++LY  +  R P   G LD +MG +     C TC 
Sbjct: 13  IKGIEFGALSAKD-IIAQSEVEVHTRDLYDLEKGRIPKDGGALDTKMGISSNANECATCH 71

Query: 139 QNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN 198
            NL+ C GHFG+I L LPVFH+GYF+  I +LQ ICKN  C+ VLL E+    F   LR 
Sbjct: 72  GNLASCHGHFGHIKLALPVFHVGYFKATIQVLQCICKN--CSAVLLDEQTKRSFLNDLRR 129

Query: 199 PALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKC------GLLKISHEKYKNRTKK 252
           P +  L R  + KK+LE  KK   C +C  +NGVVKK         LKI H+ ++   KK
Sbjct: 130 PHIDNLRRMKILKKLLEQCKKQRRCLNCNHVNGVVKKAASGAGPAALKIVHDTFRWIGKK 189

Query: 253 KDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMN-AE 311
                +    E++E    NPE+E   K  +   LNPL+VL LF+ I   D  LL ++ A 
Sbjct: 190 ATPEKDLWDKEFDEVFSRNPELEKFVK-RIHDDLNPLKVLNLFKQISPSDCELLGIDSAR 248

Query: 312 LSKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
             +P   I   L  PP CIRPSV+ D +S+ D
Sbjct: 249 GGRPEMYIWRYLPAPPVCIRPSVMMDAQSNED 280



 Score =  101 bits (252), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 47/61 (77%), Positives = 53/61 (86%), Gaps = 1/61 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV+NSFFSGLTP EF FH++ GREGLVDTAVKTAETGYM RRL+KSL+DL  QY
Sbjct: 837 TPQSKGFVRNSFFSGLTPPEFLFHSISGREGLVDTAVKTAETGYMSRRLMKSLDDLSAQY 896

Query: 668 D 668
           D
Sbjct: 897 D 897



 Score = 61.6 bits (148), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 26/46 (56%), Positives = 39/46 (84%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRI 67
           LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+RA  +++
Sbjct: 531 LMGVKNNLLTPKSGEPIIAATQDFITGSYLVSHKDSFFDRASLVQL 576



 Score = 52.0 bits (123), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 23/40 (57%), Positives = 29/40 (72%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA 707
            D  FDA+FY + D I GVSECII+G  MN+GTG  KL+ +
Sbjct: 1393 DHLFDASFYMKNDKIEGVSECIILGQTMNIGTGAFKLVNS 1432


>gi|406607118|emb|CCH41506.1| DNA-directed RNA polymerase III subunit [Wickerhamomyces ciferrii]
          Length = 1457

 Score =  284 bits (726), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 144/276 (52%), Positives = 188/276 (68%), Gaps = 29/276 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH+LSI++H AK+ P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 467 DGDVVLFNRQPSLHRLSILSHYAKIRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 526

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+R
Sbjct: 527 RAEAIN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDR 572

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A   ++ S +     D+     +F      P    +   +WTGKQ+FSL++KPN+  PV 
Sbjct: 573 ATFTQLLSMM--SDGDL-----QF---DLPPPAIHKPVYMWTGKQVFSLLIKPNKKSPVV 622

Query: 521 ANLKTKGRAYTANE-----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL  K +A+T        E    D +VI+R S++L+G MDKSTLG G K +VFY +LRD
Sbjct: 623 INLDAKNKAFTPPAKGLPMEMSPNDGFVIIRGSQILSGVMDKSTLGDGKKHSVFYTILRD 682

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           +G   A TAM R++++ + +L NRGFSIGI DVTPG
Sbjct: 683 YGPKEAATAMNRMAKLCARFLGNRGFSIGISDVTPG 718



 Score =  253 bits (647), Expect = 5e-64,   Method: Compositional matrix adjust.
 Identities = 158/377 (41%), Positives = 208/377 (55%), Gaps = 77/377 (20%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEVC-------------------- 1148
            KY RAQ+EP TAVGA+AA SIGEPGTQMTLKTFHFAG                       
Sbjct: 1075 KYSRAQVEPGTAVGAIAAHSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIINASKVI 1134

Query: 1149 --EYIEEVFVPDD--------------------------------SFILIKLDMDRIRLL 1174
                I  V V DD                                S+I +K+D+  I  L
Sbjct: 1135 STPIINAVLVNDDDERAARVVKGRVEKTLLSDIVYYIQDVYKDDMSYIQVKVDLKTIEKL 1194

Query: 1175 HLEVDIDSIRYCIERTRGI---SGHLTVSGHSFL---ILKPKDSSKSFNS---------- 1218
             LE+ +D I   I R   +    G ++V G + +   +      +KS ++          
Sbjct: 1195 QLELTMDDIAVAISRAPKLKIPGGDVSVVGRNKININVFPEGARAKSVSTSAKEPLENEL 1254

Query: 1219 --KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 1276
              +M  +++ LP V +KG   I RAVI+  D +G  K +LLVEG  LRDVM T GV G K
Sbjct: 1255 FFRMQHLRRALPGVTVKGFPDIARAVINVRD-DG--KKELLVEGYGLRDVMCTDGVIGTK 1311

Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITR 1336
              +N+  EV++ LGIEAAR +I+ EI   M NHGMS+D RH  L+ D+M+ KGEVLGITR
Sbjct: 1312 TKTNHILEVWQVLGIEAARGSIINEIDYTMSNHGMSVDPRHIQLLGDVMSYKGEVLGITR 1371

Query: 1337 HGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA 1396
             GL+KM++SVL LASFE T+DHLFDA+FY ++D + GVSECII+G  M +GTG  KL++ 
Sbjct: 1372 FGLSKMRDSVLQLASFEKTTDHLFDASFYMKSDAVEGVSECIILGQTMAIGTGAFKLVKQ 1431

Query: 1397 VP--RSEPVPRTLLFDN 1411
             P   SE   +  LF++
Sbjct: 1432 TPIEDSELKQKDTLFED 1448



 Score =  187 bits (474), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 112/252 (44%), Positives = 154/252 (61%), Gaps = 21/252 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII A L  D D   AR+VKGR+E+T L ++  YI++V+  D 
Sbjct: 1120 GVPRIKEIINASKVISTPIINAVLVNDDDERAARVVKGRVEKTLLSDIVYYIQDVYKDDM 1179

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFL---ILKPKDSS 877
            S+I +K+D+  I  L LE+ +D I   I R   +    G ++V G + +   +      +
Sbjct: 1180 SYIQVKVDLKTIEKLQLELTMDDIAVAISRAPKLKIPGGDVSVVGRNKININVFPEGARA 1239

Query: 878  KSFNS------------KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD 925
            KS ++            +M  +++ LP V +KG   I RAVI+  D +G  K +LLVEG 
Sbjct: 1240 KSVSTSAKEPLENELFFRMQHLRRALPGVTVKGFPDIARAVINVRD-DG--KKELLVEGY 1296

Query: 926  NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 985
             LRDVM T GV G K  +N+  EV++ LGIEAAR +I+ EI   M NHGMS+D RH  L+
Sbjct: 1297 GLRDVMCTDGVIGTKTKTNHILEVWQVLGIEAARGSIINEIDYTMSNHGMSVDPRHIQLL 1356

Query: 986  ADLMTSKGEVLG 997
             D+M+ KGEVLG
Sbjct: 1357 GDVMSYKGEVLG 1368



 Score =  180 bits (456), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 105/273 (38%), Positives = 154/273 (56%), Gaps = 12/273 (4%)

Query: 79  FRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCG 138
            +G+  G ++++D V Q S +++ +++L+  +  R P  +G LD  MG +   + C+ C 
Sbjct: 13  IKGIEFGALSEKDIVAQ-SEVEVSTRDLFDLEEGRKPKKNGALDSHMGISSNSSECSVCK 71

Query: 139 QNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN 198
            NL+ C GHFG++ LPLPVFH+GYF+  I +LQSICK  +C  +LL EE    FR +LR 
Sbjct: 72  GNLATCHGHFGHLKLPLPVFHVGYFKATIQVLQSICK--SCGSMLLDEEAKRQFRLELRR 129

Query: 199 PALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGL------LKISHEKYKNRTKK 252
           P +  L R  + KKIL+  KK   C  CG +NGVVKK         LKI H+ ++   KK
Sbjct: 130 PGIDNLRRMGILKKILDQCKKQRRCLDCGAVNGVVKKAAAGSGTASLKIVHDTFRWIGKK 189

Query: 253 KDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNA-E 311
                 +   +   AV  NP+IE   K   +  LNPL+VL LF+ +  ED  L+ +++  
Sbjct: 190 PTIEKGEWDKDIETAVHNNPDIERFAKR-CMDDLNPLKVLNLFKQVKPEDCELMGIDSGR 248

Query: 312 LSKPSDLILTRLLVPPNCIRPSV-ISDLKSDND 343
             +P   I   L  PP CIRPSV +SD  + N+
Sbjct: 249 GGRPETYIWRYLPAPPVCIRPSVMMSDSPTSNE 281



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 45/57 (78%), Positives = 50/57 (87%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NSFFSGL+P EF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 843 KGFVRNSFFSGLSPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSCQYD 899



 Score = 62.8 bits (151), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 28/53 (52%), Positives = 41/53 (77%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+RA   ++ S +  G
Sbjct: 533 LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDRATFTQLLSMMSDG 585



 Score = 53.1 bits (126), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 26/57 (45%), Positives = 37/57 (64%), Gaps = 2/57 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP--RSEPVPRTLLFDN 722
            D  FDA+FY ++D + GVSECII+G  M +GTG  KL++  P   SE   +  LF++
Sbjct: 1392 DHLFDASFYMKSDAVEGVSECIILGQTMAIGTGAFKLVKQTPIEDSELKQKDTLFED 1448


>gi|50309797|ref|XP_454912.1| hypothetical protein [Kluyveromyces lactis NRRL Y-1140]
 gi|49644047|emb|CAG99999.1| KLLA0E21253p [Kluyveromyces lactis]
          Length = 1457

 Score =  284 bits (726), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 143/282 (50%), Positives = 189/282 (67%), Gaps = 30/282 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH+LSI++H AK+ P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 466 DGDVVLFNRQPSLHRLSILSHYAKIRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 525

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+R
Sbjct: 526 RAEAIN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDR 571

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           AQ  ++ S +++D++    I          P   ++   +WTGKQ+FSL++KP+R  PV 
Sbjct: 572 AQLTQLLS-MMSDSNLQFDI---------PPPSIMKPHYLWTGKQVFSLLIKPSRKSPVV 621

Query: 521 ANLKTKGRAYTA------NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLR 574
            NL  K + Y          E    D +V++R S +L+G MDKS LG G K +VFY +LR
Sbjct: 622 INLDAKNKVYLPPPKKEYPNEMSQNDGFVLIRGSNILSGVMDKSVLGDGKKHSVFYTILR 681

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           D+G + A  AM R++++ + YL NRGFSIGI DVTPG    Q
Sbjct: 682 DYGPNEAAQAMNRMAKLCARYLGNRGFSIGINDVTPGSDLKQ 723



 Score =  252 bits (644), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 157/376 (41%), Positives = 208/376 (55%), Gaps = 77/376 (20%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG----------------------- 1145
            KY RA++EP TAVGA+ AQSIGEPGTQMTLKTFHFAG                       
Sbjct: 1075 KYHRARVEPGTAVGAIGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIINASKVI 1134

Query: 1146 -------------------EVCEYIEEVFVPDDSFIL------------IKLDMDRIRLL 1174
                                V   +E+  + D SF +            IK+D + I  L
Sbjct: 1135 STPIINAVLVNDNDERAARVVKGRVEKTLLSDVSFYVQDIYRDNMAFLQIKIDSETIEKL 1194

Query: 1175 HLEVDIDSIRYCIERTRGI---SGHLTVSGHSFLILKPKDSSKSFNS------------- 1218
             LE+ ++ I   I +   +   +  +++ G   + +      KS  S             
Sbjct: 1195 QLELTLEDIVVAIAKAPKLKIGTNDISIIGKDKINIAVSSDGKSMKSISTAMKEPEPNEV 1254

Query: 1219 --KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 1276
              +M Q+++ LP +V+KG   I+RAVI+  D +G  K +LLVEG  LRDVM T GV G K
Sbjct: 1255 FYRMQQLRRALPHIVVKGFSDISRAVINIRD-DG--KRELLVEGYGLRDVMTTDGVIGSK 1311

Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITR 1336
              +N+  EVY  LGIEAARS I+ EI   M NHGMS+D RH  L+ D+MT KGEVLGITR
Sbjct: 1312 TKTNHILEVYDVLGIEAARSCIINEIDYTMSNHGMSVDPRHIQLLGDVMTYKGEVLGITR 1371

Query: 1337 HGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ- 1395
             GLAKM++SVL LASFE T+DHLFDAAFY + D + GVSECII+G  M++GTG  K+++ 
Sbjct: 1372 FGLAKMRDSVLQLASFEKTTDHLFDAAFYMKNDAVEGVSECIILGQTMSIGTGSFKVVKN 1431

Query: 1396 -AVPRSEPVPRTLLFD 1410
              V  ++  P+  LF+
Sbjct: 1432 TVVGENDLTPKPTLFE 1447



 Score =  186 bits (473), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 111/252 (44%), Positives = 153/252 (60%), Gaps = 21/252 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII A L  D D   AR+VKGR+E+T L +V  Y+++++  + 
Sbjct: 1120 GVPRIKEIINASKVISTPIINAVLVNDNDERAARVVKGRVEKTLLSDVSFYVQDIYRDNM 1179

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFLILKPKDSSKSF 880
            +F+ IK+D + I  L LE+ ++ I   I +   +   +  +++ G   + +      KS 
Sbjct: 1180 AFLQIKIDSETIEKLQLELTLEDIVVAIAKAPKLKIGTNDISIIGKDKINIAVSSDGKSM 1239

Query: 881  NS---------------KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD 925
             S               +M Q+++ LP +V+KG   I+RAVI+  D +G  K +LLVEG 
Sbjct: 1240 KSISTAMKEPEPNEVFYRMQQLRRALPHIVVKGFSDISRAVINIRD-DG--KRELLVEGY 1296

Query: 926  NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 985
             LRDVM T GV G K  +N+  EVY  LGIEAARS I+ EI   M NHGMS+D RH  L+
Sbjct: 1297 GLRDVMTTDGVIGSKTKTNHILEVYDVLGIEAARSCIINEIDYTMSNHGMSVDPRHIQLL 1356

Query: 986  ADLMTSKGEVLG 997
             D+MT KGEVLG
Sbjct: 1357 GDVMTYKGEVLG 1368



 Score =  180 bits (457), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 107/272 (39%), Positives = 154/272 (56%), Gaps = 14/272 (5%)

Query: 72  IAGRKVFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKE 131
           IA +K+  +G+    ++  D V Q S ++I +++L+  D  R+    G LD RMG +  +
Sbjct: 8   IAPKKI--KGISFSALSAADIVSQ-SEVEISTRDLFDLDNGRSAKEGGALDPRMGVSSSQ 64

Query: 132 ANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAG 191
           A CTTC  NL+ C GHFG+I L LPVFH+GYF+  I ILQS+CK   C  +LL EE    
Sbjct: 65  AECTTCHGNLASCHGHFGHIKLALPVFHVGYFKATIQILQSVCKG--CGALLLSEEDKRK 122

Query: 192 FRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVV------KKCGLLKISHEK 245
           F  +LR P +  L R ++ KKIL+  KK   C  CGE+NGVV           LKI H+ 
Sbjct: 123 FLTELRRPGMDNLRRMNILKKILDQCKKQRRCFECGELNGVVKKAAAGSGSAALKIIHDT 182

Query: 246 YKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPL 305
           ++   KK     E  + ++ + ++ NPE+E + K   +  LNPL+VL LF+ I   D  L
Sbjct: 183 FRWVGKKSAPEKEQWIGDWKQVLENNPELERYVK-RCMDDLNPLKVLNLFKQIKPNDCEL 241

Query: 306 LLMN--AELSKPSDLILTRLLVPPNCIRPSVI 335
           L ++  ++  +P   I   L  PP CIRPSV+
Sbjct: 242 LGIDSTSKSGRPETYIWRYLPAPPVCIRPSVM 273



 Score =  100 bits (250), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 47/61 (77%), Positives = 52/61 (85%), Gaps = 1/61 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV+NSFFSGL+P EF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QY
Sbjct: 839 TPQSKGFVRNSFFSGLSPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSCQY 898

Query: 668 D 668
           D
Sbjct: 899 D 899



 Score = 65.1 bits (157), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 28/50 (56%), Positives = 41/50 (82%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+RAQ  ++ S +
Sbjct: 532 LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDRAQLTQLLSMM 581



 Score = 52.8 bits (125), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 25/56 (44%), Positives = 37/56 (66%), Gaps = 2/56 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ--AVPRSEPVPRTLLFD 721
            D  FDAAFY + D + GVSECII+G  M++GTG  K+++   V  ++  P+  LF+
Sbjct: 1392 DHLFDAAFYMKNDAVEGVSECIILGQTMSIGTGSFKVVKNTVVGENDLTPKPTLFE 1447


>gi|315056651|ref|XP_003177700.1| DNA-directed RNA polymerase III subunit RPC1 [Arthroderma gypseum
           CBS 118893]
 gi|311339546|gb|EFQ98748.1| DNA-directed RNA polymerase III subunit RPC1 [Arthroderma gypseum
           CBS 118893]
          Length = 1429

 Score =  283 bits (725), Expect = 4e-73,   Method: Compositional matrix adjust.
 Identities = 138/280 (49%), Positives = 184/280 (65%), Gaps = 28/280 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++H  KV PHRTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 469 DGDIVLFNRQPSLHKLSILSHFVKVRPHRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 528

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  KSNL TP+NGE +IAA QDFIT  YLL+ K+ FF+R
Sbjct: 529 RAEAME--------------LMGVKSNLATPKNGEPIIAAIQDFITAAYLLSSKDNFFDR 574

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
               +I  +++  ++       RF      P   ++  ++WTGKQ+FS++++PN+D PV 
Sbjct: 575 KTFTQICLSMLDSST-------RF---ELPPPATIKPQMLWTGKQVFSVLMRPNKDSPVK 624

Query: 521 ANLKTKGRAYT----ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL    R          + C  D ++ +RNSE+L G  DKST+G+G K N+F+++ RDF
Sbjct: 625 VNLDAACRQLKLVKGQPRDLCENDGWLCIRNSEMLCGVADKSTIGAGKKDNIFFVIQRDF 684

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           G   A  AM RLS++++ +L N+GFSIGI DV PG+  V+
Sbjct: 685 GYAAAAEAMNRLSKLSARWLTNKGFSIGITDVYPGESLVR 724



 Score =  192 bits (488), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 132/345 (38%), Positives = 176/345 (51%), Gaps = 74/345 (21%)

Query: 1121 VGALAAQSIGEPGTQMTLKTFHFAGEV---------------------------CE---- 1149
            + A+ AQSIGEPGTQMTLKTFHFAG                             CE    
Sbjct: 1049 IRAIGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIINASKEISTPIITCELVNK 1108

Query: 1150 -----------------------YIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYC 1186
                                   YIEE      SFI IK+D   I+ L LE+ +  I   
Sbjct: 1109 TDMRIAEIVKGRVEKLFLKDIVYYIEENRSQTSSFINIKVDFSTIKKLQLELTLRQILLA 1168

Query: 1187 IERTRGISG------------HLTVSGHSFLILKPKDSSKSFNSKMY----QMKQLLPSV 1230
            I++ +                H+ V   + +        K   S  Y     ++++LP++
Sbjct: 1169 IKKHKAFKATDLTFRSFKSHIHIYVDEGASMAGVSVSEQKITGSDPYIRINYLRRILPNI 1228

Query: 1231 VIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLG 1290
             + G     RAVI     E V    LLVEG  LR  M T G++G +  +N+  E+   LG
Sbjct: 1229 QVFGYPDCTRAVIRVG--EKVATNILLVEGYGLRACMTTDGIEGHRTRTNHVMEMRDVLG 1286

Query: 1291 IEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLA 1350
            IEAAR+TI+ EI  VM   GM+ID RH  L+AD+MT KGEVLGITR GLAK+++SVL LA
Sbjct: 1287 IEAARTTIIDEISSVMS--GMAIDPRHMQLLADVMTYKGEVLGITRFGLAKIRDSVLQLA 1344

Query: 1351 SFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 1395
            SFE T+DHLFDA   G+ D + GVSECIIMG  +++GTG +++++
Sbjct: 1345 SFEKTADHLFDAGGAGRHDTVQGVSECIIMGKTISLGTGSMEVVR 1389



 Score =  176 bits (446), Expect = 9e-41,   Method: Compositional matrix adjust.
 Identities = 101/267 (37%), Positives = 150/267 (56%), Gaps = 12/267 (4%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G ++ +D +  Q+H++I  + L+  D  R    +G +D R+G + K   C TCG +L +C
Sbjct: 29  GVLSNQD-IISQAHVEISDRKLFDLDNNRAVARNGPMDPRLGISNKSDTCETCGGDLQEC 87

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFGY+ L LP FH+GYF+  I ILQ ICK+  C+++LL E++   +  +LR P L  L
Sbjct: 88  NGHFGYVRLVLPAFHVGYFKRTIEILQDICKD--CSKILLPEDERRSYLKELRRPGLDNL 145

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKC--GLLKISHEKYK----NRTKKKDAIVE 258
            R  + K+I    +K  +C +C  ING VKK   G LKI H+K++    + + KK     
Sbjct: 146 RRMQINKRINVRCRKTPICYYCNAINGTVKKASTGALKIVHDKFRAFNASLSAKKIPPPS 205

Query: 259 DLLAE--YNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPS 316
            L  +  + EA K NP+IE H +  +   LNPL VL+LF  I  ED  LL +N + ++P 
Sbjct: 206 KLAFDRSFEEAKKSNPDIEKHYR-RVFDDLNPLRVLKLFRRISNEDCELLSLNVDGARPE 264

Query: 317 DLILTRLLVPPNCIRPSVISDLKSDND 343
             +   +  PP  IRPSV  +  S  D
Sbjct: 265 YFLWQFIPAPPVPIRPSVGQEGASTED 291



 Score =  151 bits (381), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 103/250 (41%), Positives = 137/250 (54%), Gaps = 20/250 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIIT  L   TD+  A IVKGR+E+  L ++  YIEE      
Sbjct: 1082 GVPRIKEIINASKEISTPIITCELVNKTDMRIAEIVKGRVEKLFLKDIVYYIEENRSQTS 1141

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISG------------HLTVSGHSFLIL 871
            SFI IK+D   I+ L LE+ +  I   I++ +                H+ V   + +  
Sbjct: 1142 SFINIKVDFSTIKKLQLELTLRQILLAIKKHKAFKATDLTFRSFKSHIHIYVDEGASMAG 1201

Query: 872  KPKDSSKSFNSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927
                  K   S  Y     ++++LP++ + G     RAVI     E V    LLVEG  L
Sbjct: 1202 VSVSEQKITGSDPYIRINYLRRILPNIQVFGYPDCTRAVIRVG--EKVATNILLVEGYGL 1259

Query: 928  RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 987
            R  M T G++G +  +N+  E+   LGIEAAR+TI+ EI  VM   GM+ID RH  L+AD
Sbjct: 1260 RACMTTDGIEGHRTRTNHVMEMRDVLGIEAARTTIIDEISSVMS--GMAIDPRHMQLLAD 1317

Query: 988  LMTSKGEVLG 997
            +MT KGEVLG
Sbjct: 1318 VMTYKGEVLG 1327



 Score =  103 bits (258), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 46/58 (79%), Positives = 51/58 (87%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV+NSFFSGLTPTEF FH M GREGL+DTAVKTAETGYM RRL+KSLEDL  +YD
Sbjct: 842 AKGFVRNSFFSGLTPTEFLFHAMSGREGLIDTAVKTAETGYMSRRLMKSLEDLSTRYD 899



 Score = 58.9 bits (141), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 27/51 (52%), Positives = 36/51 (70%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLI 72
           LM  KSNL TP+NGE +IAA QDFIT  YLL+ K+ FF+R    +I  +++
Sbjct: 535 LMGVKSNLATPKNGEPIIAAIQDFITAAYLLSSKDNFFDRKTFTQICLSML 585



 Score = 41.6 bits (96), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 18/39 (46%), Positives = 28/39 (71%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  FDA   G+ D + GVSECIIMG  +++GTG +++++
Sbjct: 1351 DHLFDAGGAGRHDTVQGVSECIIMGKTISLGTGSMEVVR 1389


>gi|354544265|emb|CCE40988.1| hypothetical protein CPAR2_110260 [Candida parapsilosis]
          Length = 1446

 Score =  283 bits (723), Expect = 6e-73,   Method: Compositional matrix adjust.
 Identities = 145/281 (51%), Positives = 187/281 (66%), Gaps = 29/281 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH+LSI+AH AKV P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 470 DGDVVLFNRQPSLHRLSILAHYAKVRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 529

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+R
Sbjct: 530 RAEAIN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDR 575

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A  +++ S +    +DI   I         P   V+  ++WTGKQ+FSL++KPNR   V 
Sbjct: 576 ASLVQLLSMM--SDADIQFDIP--------PPTIVKPIMLWTGKQVFSLLIKPNRHSKVV 625

Query: 521 ANLKTKGRAYTA-----NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL  K + +         E    D +VI+R S++L+G MDKSTLG G K +VFY +LRD
Sbjct: 626 INLNAKNKTFHPPAKGLPSEMSPNDGFVIIRGSQILSGLMDKSTLGDGKKHSVFYTILRD 685

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           +G   A  AM R++++ + +L NRGFSIGI DVTP     Q
Sbjct: 686 YGPQEAAAAMNRMAKLCARFLGNRGFSIGINDVTPAHELKQ 726



 Score =  253 bits (646), Expect = 6e-64,   Method: Compositional matrix adjust.
 Identities = 180/506 (35%), Positives = 264/506 (52%), Gaps = 105/506 (20%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETL--------------DSKEFL 1042
            G+  PV   R  D       + +D  L   EI+ L+++TL               S++ L
Sbjct: 929  GDAKPVNFIRQWDHAYNITYNVNDKPLLPYEIVELADKTLKPLVDKVAVVGTESQSEDEL 988

Query: 1043 ---QDTSENFVRDIKKFLEEFSKK-------ESVTSHQDKVSQPLREQILSHQDKIGHGR 1092
               +D  + F   +++FL E ++K         + ++ +K+ +   ++IL  +D++    
Sbjct: 989  VDQKDAEKAFYESVREFLREKAEKLARLRESRGLKAYYNKIHE---DEILVDEDEVKLNA 1045

Query: 1093 ESNPFPSACKA-----EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-- 1145
             +     + +A     + C  KY RA++EP TAVGA+ AQSIGEPGTQMTLKTFHFAG  
Sbjct: 1046 VNQLMRISHRAAKEFMKQCLYKYSRAKVEPGTAVGAIGAQSIGEPGTQMTLKTFHFAGVA 1105

Query: 1146 ------------EVCE--------YIEEVFVPDD-------------------------- 1159
                        E+           I  V V DD                          
Sbjct: 1106 SMNVTLGVPRIKEIINASKTISTPIINAVLVNDDDEIAARVAKGRIEKTLLKDVAFYIED 1165

Query: 1160 ------SFILIKLDMDRIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSGHSFL----- 1205
                  +++ IK+D++ I  L LE+ I++I   I    + R     + ++  + +     
Sbjct: 1166 VYKDNMAYLAIKIDLETIDKLQLELTIENIAQAIFKAPKLRIAPSDVVITAKNRINVLCN 1225

Query: 1206 --------ILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLL 1257
                    +    DSS +   +M  +K++LP + IKG+  I RAVI+ +D +G  K +LL
Sbjct: 1226 VNESKSESLKSVGDSSNALFFRMQTLKRVLPDICIKGLPNIFRAVINIKD-DG--KKELL 1282

Query: 1258 VEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRH 1317
            VEG  L+DVM T G+ G K ++N+  EV + LGIEAAR +I+ EI+  M NHGMS+D RH
Sbjct: 1283 VEGYGLKDVMNTEGIVGTKTTTNHVLEVNEILGIEAARGSIIREIEYTMSNHGMSVDPRH 1342

Query: 1318 PMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSEC 1377
              L+ D+MT KGEVLGITR GL+KM++SVL LASFE T+DHLFDAAF+ + D I GVSEC
Sbjct: 1343 IQLLGDVMTYKGEVLGITRFGLSKMRDSVLQLASFEKTTDHLFDAAFFMKKDKIEGVSEC 1402

Query: 1378 IIMGLPMNVGTGLIKLLQAVPRSEPV 1403
            II+G  M VGTG  KL+++    E V
Sbjct: 1403 IILGQTMRVGTGAFKLVKSSNYDEKV 1428



 Score =  181 bits (459), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 109/250 (43%), Positives = 156/250 (62%), Gaps = 19/250 (7%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII A L  D D   AR+ KGR+E+T L +V  YIE+V+  + 
Sbjct: 1112 GVPRIKEIINASKTISTPIINAVLVNDDDEIAARVAKGRIEKTLLKDVAFYIEDVYKDNM 1171

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSGHSFL----------- 869
            +++ IK+D++ I  L LE+ I++I   I    + R     + ++  + +           
Sbjct: 1172 AYLAIKIDLETIDKLQLELTIENIAQAIFKAPKLRIAPSDVVITAKNRINVLCNVNESKS 1231

Query: 870  --ILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927
              +    DSS +   +M  +K++LP + IKG+  I RAVI+ +D +G  K +LLVEG  L
Sbjct: 1232 ESLKSVGDSSNALFFRMQTLKRVLPDICIKGLPNIFRAVINIKD-DG--KKELLVEGYGL 1288

Query: 928  RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 987
            +DVM T G+ G K ++N+  EV + LGIEAAR +I+ EI+  M NHGMS+D RH  L+ D
Sbjct: 1289 KDVMNTEGIVGTKTTTNHVLEVNEILGIEAARGSIIREIEYTMSNHGMSVDPRHIQLLGD 1348

Query: 988  LMTSKGEVLG 997
            +MT KGEVLG
Sbjct: 1349 VMTYKGEVLG 1358



 Score =  169 bits (429), Expect = 8e-39,   Method: Compositional matrix adjust.
 Identities = 100/256 (39%), Positives = 145/256 (56%), Gaps = 12/256 (4%)

Query: 96  QSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPL 155
           QS ++I++++LY  +  R P   G LD +MG +   + C TC  NL+ C GHFG+I L L
Sbjct: 30  QSEVEILTRDLYDLEKGRAPKEGGALDTKMGISSNSSECATCHGNLASCNGHFGHIRLAL 89

Query: 156 PVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILE 215
           PVFH+GYF+ VI++LQ +CKN  C  +LL  +    F ++LR P +  L R  + K+I +
Sbjct: 90  PVFHVGYFKAVISVLQCVCKN--CGAILLDPQAKRQFLSELRRPNIDNLKRMKILKRIND 147

Query: 216 TTKKVSVCPHCGEINGVVKKC------GLLKISHEKYKNRTKKKDAIVEDLLAEYNEAV- 268
             KK   C  C  +NGVVKK         LKI H+ ++    KKD   + L  E  + V 
Sbjct: 148 QCKKQRRCLKCNHVNGVVKKAASGAGPASLKIVHDTFR-WIGKKDTPEKTLWDEDLDLVF 206

Query: 269 KFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMN-AELSKPSDLILTRLLVPP 327
           + NP++E   K  + +  NPL+ L LF+ I  ED  LL M+ ++  +P   I   L  PP
Sbjct: 207 QRNPDLEKFAK-RIQEDFNPLKTLNLFKQIIPEDCELLGMDSSKGGRPETYIWRYLPAPP 265

Query: 328 NCIRPSVISDLKSDND 343
            CIRPSV+ D +S+ D
Sbjct: 266 VCIRPSVMMDAQSNED 281



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 47/61 (77%), Positives = 52/61 (85%), Gaps = 1/61 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV+NSFFSGL+P EF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QY
Sbjct: 842 TPQSKGFVRNSFFSGLSPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSSQY 901

Query: 668 D 668
           D
Sbjct: 902 D 902



 Score = 63.2 bits (152), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 27/50 (54%), Positives = 41/50 (82%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+RA  +++ S +
Sbjct: 536 LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDRASLVQLLSMM 585



 Score = 50.8 bits (120), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 25/47 (53%), Positives = 31/47 (65%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPV 714
            D  FDAAF+ + D I GVSECII+G  M VGTG  KL+++    E V
Sbjct: 1382 DHLFDAAFFMKKDKIEGVSECIILGQTMRVGTGAFKLVKSSNYDEKV 1428


>gi|440795837|gb|ELR16951.1| DNAdirected RNA polymerase subunit A [Acanthamoeba castellanii str.
           Neff]
          Length = 1230

 Score =  283 bits (723), Expect = 7e-73,   Method: Compositional matrix adjust.
 Identities = 138/273 (50%), Positives = 179/273 (65%), Gaps = 29/273 (10%)

Query: 343 DVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARA 402
           DVVLFNRQPSLH++SIM HR +V+P RTFRFNECVC PYNADFDGDEMNVH+PQTEEARA
Sbjct: 379 DVVLFNRQPSLHRISIMCHRVRVMPWRTFRFNECVCGPYNADFDGDEMNVHVPQTEEARA 438

Query: 403 EALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 462
           EA+               LMA   NL+TPRNGE L+AATQDF+T  YL+T+K+AFF+RA+
Sbjct: 439 EAM--------------TLMAVNQNLITPRNGEPLVAATQDFLTASYLVTRKDAFFDRAE 484

Query: 463 TMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNAN 522
             R+ S  +   + I             P   V+   +WTGKQ+F ++L+PN++  V  +
Sbjct: 485 FCRLCSFFVDADAKI----------DIPPPAIVKPMELWTGKQLFYILLRPNKNVDVCLS 534

Query: 523 LKTKGRAYTANEEF-----CHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFG 577
           ++ KGR YT    +     C +D YV+   SELL G MDK TLG G K N+F++L+RD+ 
Sbjct: 535 MEVKGREYTGKGSYEPLYMCRKDGYVVFHQSELLCGIMDKKTLGGGSKENIFHVLMRDYS 594

Query: 578 EDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
             VA   M RL++  + +L + GFSIGI DV P
Sbjct: 595 TIVAADRMSRLAKFCARWLADWGFSIGISDVMP 627



 Score =  192 bits (489), Expect = 9e-46,   Method: Compositional matrix adjust.
 Identities = 100/181 (55%), Positives = 130/181 (71%), Gaps = 1/181 (0%)

Query: 1232 IKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGI 1291
            I   + ++ AVI+++      +Y LLVEG NL  VMAT GV G + +SN+  EV  TLGI
Sbjct: 1024 IAHTKAVDGAVINKKGSGADARYNLLVEGYNLLSVMATPGVVGSRTTSNHIIEVMTTLGI 1083

Query: 1292 EAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLAS 1351
            EAAR TIM EI+  M+ HGM+ID RH ML+ADLM  +GE+LGITRHG+ KM +SV+ LAS
Sbjct: 1084 EAARVTIMNEIQYTMKEHGMNIDTRHVMLLADLMCFRGEILGITRHGIDKMNDSVMMLAS 1143

Query: 1352 FENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP-RTLLFD 1410
            FE T+DHLF+A+F+ + D I+GVSE IIMG+P+ VGTGL KLL+  P  +  P R LL D
Sbjct: 1144 FEKTTDHLFNASFHARQDTITGVSESIIMGIPIAVGTGLFKLLRKTPSLDKEPKRGLLLD 1203

Query: 1411 N 1411
            +
Sbjct: 1204 S 1204



 Score =  110 bits (276), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 50/58 (86%), Positives = 55/58 (94%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV+NSFF+GLT TEFFFHTMGGREGLVDTAVKTAETGYMQRRL+K+LEDL VQYD
Sbjct: 752 AKGFVKNSFFTGLTGTEFFFHTMGGREGLVDTAVKTAETGYMQRRLMKALEDLAVQYD 809



 Score =  103 bits (256), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 54/102 (52%), Positives = 70/102 (68%)

Query: 896  IKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGI 955
            I   + ++ AVI+++      +Y LLVEG NL  VMAT GV G + +SN+  EV  TLGI
Sbjct: 1024 IAHTKAVDGAVINKKGSGADARYNLLVEGYNLLSVMATPGVVGSRTTSNHIIEVMTTLGI 1083

Query: 956  EAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            EAAR TIM EI+  M+ HGM+ID RH ML+ADLM  +GE+LG
Sbjct: 1084 EAARVTIMNEIQYTMKEHGMNIDTRHVMLLADLMCFRGEILG 1125



 Score = 73.9 bits (180), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 34/67 (50%), Positives = 45/67 (67%), Gaps = 1/67 (1%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           +Q+ S IQ+VS  L+ Q P+R P+P+G LD RMG    +  C+TCGQ + +C GHFGYI 
Sbjct: 42  MQRLSEIQVVSHLLF-QLPKREPMPYGPLDPRMGVCNTKGICSTCGQKVQECAGHFGYIK 100

Query: 153 LPLPVFH 159
           L LP  H
Sbjct: 101 LALPDPH 107



 Score = 68.2 bits (165), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 30/51 (58%), Positives = 40/51 (78%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLI 72
           LMA   NL+TPRNGE L+AATQDF+T  YL+T+K+AFF+RA+  R+ S  +
Sbjct: 443 LMAVNQNLITPRNGEPLVAATQDFLTASYLVTRKDAFFDRAEFCRLCSFFV 493



 Score = 67.8 bits (164), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 43/120 (35%), Positives = 63/120 (52%), Gaps = 11/120 (9%)

Query: 221 SVCPHCGEINGVVKKCGLLKISHEKY-KNRTKKKDAIVEDL--LAEYNEAVKFNPEIEAH 277
            +C  CG+    V++C      H  Y K       A  +DL  L E++EAVK +  +  H
Sbjct: 80  GICSTCGQ---KVQECA----GHFGYIKLALPDPHAAADDLQFLGEFDEAVKLDESLAPH 132

Query: 278 KKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD 337
                   LNP+ ++ +F  IP ED+ L+ MN +++ P+ L+L  LLVPP  IRPSV  D
Sbjct: 133 LNKAQ-DDLNPIRIMNIFSRIPPEDLELMDMNGKIANPTHLVLQHLLVPPITIRPSVAMD 191



 Score = 57.4 bits (137), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 29/56 (51%), Positives = 39/56 (69%), Gaps = 1/56 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP-RTLLFDN 722
            D  F+A+F+ + D I+GVSE IIMG+P+ VGTGL KLL+  P  +  P R LL D+
Sbjct: 1149 DHLFNASFHARQDTITGVSESIIMGIPIAVGTGLFKLLRKTPSLDKEPKRGLLLDS 1204


>gi|366996196|ref|XP_003677861.1| hypothetical protein NCAS_0H02040 [Naumovozyma castellii CBS 4309]
 gi|342303731|emb|CCC71514.1| hypothetical protein NCAS_0H02040 [Naumovozyma castellii CBS 4309]
          Length = 1460

 Score =  282 bits (722), Expect = 8e-73,   Method: Compositional matrix adjust.
 Identities = 145/301 (48%), Positives = 191/301 (63%), Gaps = 30/301 (9%)

Query: 322 RLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPY 381
           R+ +  N     V+     D DVVLFNRQPSLH+LSI++H AK+ P RTFR NECVCTPY
Sbjct: 449 RIKLAKNLQHGDVVERHLEDGDVVLFNRQPSLHRLSILSHFAKIRPWRTFRLNECVCTPY 508

Query: 382 NADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAAT 441
           NADFDGDEMN+H+PQTEEARAEA+               LM  K+NL+TP++GE +IAAT
Sbjct: 509 NADFDGDEMNLHVPQTEEARAEAIN--------------LMGVKNNLLTPKSGEPIIAAT 554

Query: 442 QDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIW 501
           QDFITG YL++ K++FF+RA   ++ S +   T        RF      P   ++   +W
Sbjct: 555 QDFITGSYLISHKDSFFDRATLTQLLSMMSNGTL-------RF---DIPPPAIMKPYYMW 604

Query: 502 TGKQIFSLILKPNRDCPVNANLKTKGRAYTANE------EFCHRDSYVILRNSELLAGSM 555
           TGKQ+FSL+++PN++ PV  NL  K + +   +      E    D YV++R S +L+G M
Sbjct: 605 TGKQVFSLLIRPNKESPVVINLDAKNKVFMPPKYKDYPNEMSRNDGYVVIRGSNILSGVM 664

Query: 556 DKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFV 615
           DKS LG G K +VFY +LRD+G   A  AM R+S++ + YL NRGFSIGI DVTP     
Sbjct: 665 DKSVLGDGKKHSVFYTILRDYGPQEAANAMNRMSKLCARYLGNRGFSIGISDVTPADDLK 724

Query: 616 Q 616
           Q
Sbjct: 725 Q 725



 Score =  244 bits (622), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 155/376 (41%), Positives = 208/376 (55%), Gaps = 77/376 (20%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG----------------------- 1145
            KY +A++EP TAVGA+ AQSIGEPGTQMTLKTFHFAG                       
Sbjct: 1077 KYRKARVEPGTAVGAIGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIINASKVI 1136

Query: 1146 -------------------EVCEYIEEVFVPDDSF------------ILIKLDMDRIRLL 1174
                                V   IE+  + D ++            I +++D+  I  L
Sbjct: 1137 STPIINAVLVNENDERAARVVKGRIEKTLLSDIAYYIQDVYKDNLSFIQVRVDLGTIEKL 1196

Query: 1175 HLEVDIDSIRYCIERT---------------RGISGHLTVSGHSFLILKPKDSSKSFNSK 1219
             LE+ I+ I   I +                  I+ ++   G+    +       S N+ 
Sbjct: 1197 QLELTIEDIAVAITKAPKLKIQTSDVNILGKDKIAINVYPDGYKAKSISTMAKEPSNNAV 1256

Query: 1220 MYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 1276
             Y+M+ L   LPS+V+KG   I+RAVI+  D +G  K +LLVEG  LRDVM T GV G+K
Sbjct: 1257 FYRMQHLRRVLPSIVVKGFGDISRAVINIRD-DG--KRELLVEGYGLRDVMCTDGVIGMK 1313

Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITR 1336
             ++N+  EV   LGIEAARS+I+ EI   M NHGMS+D RH  L+ D+MT KGE+LGITR
Sbjct: 1314 TTTNHILEVNNVLGIEAARSSIIGEIDYTMSNHGMSVDPRHIQLLGDVMTYKGEILGITR 1373

Query: 1337 HGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA 1396
             GL+KM++SVL LASFE T+DHLFDAAFY + D + GVSECII+G  M++GTG  K+++ 
Sbjct: 1374 FGLSKMRDSVLQLASFEKTTDHLFDAAFYMKKDAVEGVSECIILGQTMSIGTGSFKVVKG 1433

Query: 1397 VPRSEP--VPRTLLFD 1410
               SE    P+  LF+
Sbjct: 1434 TNISEADLKPKPTLFE 1449



 Score =  183 bits (464), Expect = 8e-43,   Method: Compositional matrix adjust.
 Identities = 112/252 (44%), Positives = 154/252 (61%), Gaps = 21/252 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII A L  + D   AR+VKGR+E+T L ++  YI++V+  + 
Sbjct: 1122 GVPRIKEIINASKVISTPIINAVLVNENDERAARVVKGRIEKTLLSDIAYYIQDVYKDNL 1181

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERT---------------RGISGHLTVSGHSF 868
            SFI +++D+  I  L LE+ I+ I   I +                  I+ ++   G+  
Sbjct: 1182 SFIQVRVDLGTIEKLQLELTIEDIAVAITKAPKLKIQTSDVNILGKDKIAINVYPDGYKA 1241

Query: 869  LILKPKDSSKSFNSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD 925
              +       S N+  Y+M+ L   LPS+V+KG   I+RAVI+  D +G  K +LLVEG 
Sbjct: 1242 KSISTMAKEPSNNAVFYRMQHLRRVLPSIVVKGFGDISRAVINIRD-DG--KRELLVEGY 1298

Query: 926  NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 985
             LRDVM T GV G+K ++N+  EV   LGIEAARS+I+ EI   M NHGMS+D RH  L+
Sbjct: 1299 GLRDVMCTDGVIGMKTTTNHILEVNNVLGIEAARSSIIGEIDYTMSNHGMSVDPRHIQLL 1358

Query: 986  ADLMTSKGEVLG 997
             D+MT KGE+LG
Sbjct: 1359 GDVMTYKGEILG 1370



 Score =  170 bits (430), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 97/248 (39%), Positives = 138/248 (55%), Gaps = 11/248 (4%)

Query: 96  QSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPL 155
           QS I++ S++L+  +  R P   G LDR+MG +     C TC  NL+ C GHFG+I L L
Sbjct: 29  QSEIEVSSRDLFDLEKGREPKIGGALDRKMGVSSSSLECETCHGNLASCHGHFGHIKLAL 88

Query: 156 PVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILE 215
           PVFH+GYF+  I ILQ +CK  TC+ +LL ++    F  +LR P +  L R  + KK+L+
Sbjct: 89  PVFHVGYFKATIQILQGVCK--TCSAILLNDQDKRQFLTELRRPGVDNLRRMGILKKVLD 146

Query: 216 TTKKVSVCPHCGEINGVVKKCGL------LKISHEKYKNRTKKKDAIVEDLLAEYNEAVK 269
             KK   C  CG +NGVVKK         LKI H+ ++   KK     +  + ++ E + 
Sbjct: 147 QCKKQRRCLQCGALNGVVKKAAAGAGPASLKIIHDTFRWVGKKSAPEKDKWVGDWKEVLS 206

Query: 270 FNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL--SKPSDLILTRLLVPP 327
            +PE+E   K      LNPL+ L LF+ I  ED  LL +++ +   +P   I   L  PP
Sbjct: 207 HHPELERFMKR-CSDDLNPLKTLNLFKQIKPEDCELLGIDSTVKSGRPETYIWRYLPAPP 265

Query: 328 NCIRPSVI 335
            CIRPSV+
Sbjct: 266 VCIRPSVM 273



 Score =  102 bits (253), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 46/57 (80%), Positives = 50/57 (87%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NSFFSGLTP EF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 845 KGFVRNSFFSGLTPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSCQYD 901



 Score = 63.2 bits (152), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 28/53 (52%), Positives = 41/53 (77%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+RA   ++ S +  G
Sbjct: 534 LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDRATLTQLLSMMSNG 586



 Score = 52.8 bits (125), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 26/56 (46%), Positives = 36/56 (64%), Gaps = 2/56 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEP--VPRTLLFD 721
            D  FDAAFY + D + GVSECII+G  M++GTG  K+++    SE    P+  LF+
Sbjct: 1394 DHLFDAAFYMKKDAVEGVSECIILGQTMSIGTGSFKVVKGTNISEADLKPKPTLFE 1449


>gi|340519695|gb|EGR49933.1| predicted protein [Trichoderma reesei QM6a]
          Length = 1465

 Score =  282 bits (721), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 139/274 (50%), Positives = 183/274 (66%), Gaps = 28/274 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIM+H AK+ P RTFR NECVC PYNADFDGDEMN+H+PQ+EEA
Sbjct: 466 DGDVVLFNRQPSLHKLSIMSHLAKIRPWRTFRLNECVCGPYNADFDGDEMNLHVPQSEEA 525

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL TP+NGE +IAATQDFIT  YLL+ K+ F+NR
Sbjct: 526 RAEAI--------------TLMGVKNNLATPKNGEPIIAATQDFITASYLLSSKDRFYNR 571

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                I + ++   + I             P   ++   +WTGKQIF+++++PN+  PV 
Sbjct: 572 KAFTYICTHMVDGVTHI----------DLPPPSIIKPEALWTGKQIFNVLMRPNKQSPVL 621

Query: 521 ANLKTKGRAYTANEEFC----HRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL  + R Y+A    C      D+++++RNSE++ G MDKS +GSG K +VFYI+LRDF
Sbjct: 622 VNLDARCREYSARPGQCPDMDPNDAWLVIRNSEVMCGRMDKSIIGSGKKNSVFYIILRDF 681

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           G D AV AM RL+++ +  L N+GFS+G+GDV P
Sbjct: 682 GPDHAVYAMNRLTKLCARQLGNQGFSLGVGDVFP 715



 Score =  198 bits (503), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 109/271 (40%), Positives = 155/271 (57%), Gaps = 10/271 (3%)

Query: 79  FRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCG 138
           F+G+  G  + +D V Q   +++  + LY  D  R P+ +G LD RMGT+ K   C TC 
Sbjct: 22  FKGIKFGIQSNQDIVNQ-GVLEVSQRMLYDIDNNRAPLTNGALDIRMGTSSKSGKCGTCQ 80

Query: 139 QNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN 198
           + L  C+GHFG++ L LP FHIGY R +  ILQ++CK  TCA+VLL EE+   F   LR 
Sbjct: 81  EPLKFCIGHFGHVRLALPAFHIGYLRFIQTILQNVCK--TCAKVLLTEEERRSFLQDLRR 138

Query: 199 PALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEK---YKNRTKKKDA 255
           P L  + R  + K+I E  +K   CP+CGEING ++K G+LK++H+K   YK  T +K  
Sbjct: 139 PGLDNIRRTQICKRINEQCRKCRQCPYCGEINGQIRKVGVLKLTHDKFSAYKKSTSQKKL 198

Query: 256 IVEDLL---AEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL 312
             E  +   A ++EA K NP+++ H    + + LNPL VL  F+ I   D  LL ++   
Sbjct: 199 PPESKIAFDASFDEAKKLNPDLDKHLARAM-EDLNPLWVLNHFKMITATDCELLGLDPTE 257

Query: 313 SKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
            +P   I   +  PP CIRPSV  +  S  D
Sbjct: 258 GRPEMFIWQFVPAPPVCIRPSVAQEGASTED 288



 Score =  175 bits (443), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 117/292 (40%), Positives = 165/292 (56%), Gaps = 31/292 (10%)

Query: 1146 EVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLT-VS-GHS 1203
            +V + IE+ +V D   I++ +DM+ ++ +HL + I  I   I R + +    T VS G +
Sbjct: 1160 DVLKAIEDEWVSDRGTIVLYIDMEALQNMHLGIGIVDIAEAILRFKKLKIQPTDVSVGPN 1219

Query: 1204 FL----------------------ILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRA 1241
            ++                       L   + +  F  ++  ++++LP V I G     RA
Sbjct: 1220 YIKIYVLNSWVDPDAAKKRQRSQGSLTMTEEASDFLLRVNHLRRMLPKVPISGYNEATRA 1279

Query: 1242 VIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTE 1301
            +I   +     ++ +LVEG  LR  M T GV G K  SN+  E    LGIEAAR+TI+ E
Sbjct: 1280 IIQTSEQ---NEHTVLVEGYGLRACMTTEGVIGTKSRSNSVMEARDVLGIEAARTTIVDE 1336

Query: 1302 IKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFD 1361
            I  VM   GM ID RH  L+AD+MT KGEVLGITR GL+KM+ESVL LASFE T DHLF+
Sbjct: 1337 ISSVMA--GMDIDPRHIQLLADVMTFKGEVLGITRFGLSKMRESVLQLASFEKTPDHLFE 1394

Query: 1362 AAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA--VPRSEPVPRTLLFDN 1411
            AA   +TD I GVSECIIMG  M+VGTG  ++++   +   E  P+  LF++
Sbjct: 1395 AAAGMKTDRIEGVSECIIMGQTMSVGTGSFQVVRRLNIQEWEVKPKKTLFED 1446



 Score =  153 bits (386), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 103/258 (39%), Positives = 145/258 (56%), Gaps = 29/258 (11%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+NISTP+IT  L  D  ++ ARIVKGR+E+T + +V + IE+ +V D 
Sbjct: 1114 GVPRIKEIINASKNISTPVITCPLLNDKQIEAARIVKGRIEKTYVIDVLKAIEDEWVSDR 1173

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLT-VS-GHSFL------------ 869
              I++ +DM+ ++ +HL + I  I   I R + +    T VS G +++            
Sbjct: 1174 GTIVLYIDMEALQNMHLGIGIVDIAEAILRFKKLKIQPTDVSVGPNYIKIYVLNSWVDPD 1233

Query: 870  ----------ILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYK 919
                       L   + +  F  ++  ++++LP V I G     RA+I   +     ++ 
Sbjct: 1234 AAKKRQRSQGSLTMTEEASDFLLRVNHLRRMLPKVPISGYNEATRAIIQTSEQ---NEHT 1290

Query: 920  LLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDF 979
            +LVEG  LR  M T GV G K  SN+  E    LGIEAAR+TI+ EI  VM   GM ID 
Sbjct: 1291 VLVEGYGLRACMTTEGVIGTKSRSNSVMEARDVLGIEAARTTIVDEISSVMA--GMDIDP 1348

Query: 980  RHPMLVADLMTSKGEVLG 997
            RH  L+AD+MT KGEVLG
Sbjct: 1349 RHIQLLADVMTFKGEVLG 1366



 Score =  102 bits (254), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 45/57 (78%), Positives = 51/57 (89%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NSF+SGL PTEFFFH + GREGL+DTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 841 KGFVRNSFYSGLFPTEFFFHAISGREGLIDTAVKTAETGYMSRRLMKSLEDLSTQYD 897



 Score = 70.1 bits (170), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 30/40 (75%), Positives = 34/40 (85%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            C E+Y +A +EP  AVGA+ AQSIGEPGTQMTLKTFHFAG
Sbjct: 1066 CLERYHKAHVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAG 1105



 Score = 61.6 bits (148), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 28/53 (52%), Positives = 37/53 (69%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           LM  K+NL TP+NGE +IAATQDFIT  YLL+ K+ F+NR     I + ++ G
Sbjct: 532 LMGVKNNLATPKNGEPIIAATQDFITASYLLSSKDRFYNRKAFTYICTHMVDG 584



 Score = 47.8 bits (112), Expect = 0.051,   Method: Compositional matrix adjust.
 Identities = 28/71 (39%), Positives = 41/71 (57%), Gaps = 2/71 (2%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA--VPRSEPVPRTLLFDNPEF 725
            D  F+AA   +TD I GVSECIIMG  M+VGTG  ++++   +   E  P+  LF++   
Sbjct: 1390 DHLFEAAAGMKTDRIEGVSECIIMGQTMSVGTGSFQVVRRLNIQEWEVKPKKTLFEDAWT 1449

Query: 726  HFPQVYYERRR 736
               +   ERR+
Sbjct: 1450 ETVKAKKERRK 1460


>gi|342320897|gb|EGU12835.1| DNA-directed RNA polymerase [Rhodotorula glutinis ATCC 204091]
          Length = 1804

 Score =  282 bits (721), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 139/281 (49%), Positives = 189/281 (67%), Gaps = 33/281 (11%)

Query: 341  DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
            D+D+VLFNRQPSLH+LSI++HR KV P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 808  DDDIVLFNRQPSLHRLSILSHRVKVRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 867

Query: 401  RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
            R EA                LM  K NLVTPRNGE +IAATQDFITG YL+T+++ FFNR
Sbjct: 868  RTEAFQ--------------LMNIKRNLVTPRNGEPIIAATQDFITGCYLITRRDTFFNR 913

Query: 461  AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
             + +++ S L     +I             P   ++   +WTGKQ+F+++++PN+D PVN
Sbjct: 914  QEFVQMCSYLQDAELEI----------ELPPPTILKPERLWTGKQVFNVLMRPNKDSPVN 963

Query: 521  ANLKTKGRAY-TANEEF--------CHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYI 571
             NL+ K + +   + EF           D Y++++NSE+++G  DKST+G G K +VF +
Sbjct: 964  VNLECKNKTFGKPSTEFDMSYPNFMSVNDGYLVVQNSEIISGVFDKSTVGDGNKKSVFAV 1023

Query: 572  LLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
            + RDFGED A   M R++++ + +L N+GFSIGI DVTPG+
Sbjct: 1024 IQRDFGEDHAAKCMNRMAKLCARWLANKGFSIGISDVTPGE 1064



 Score =  212 bits (540), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 127/289 (43%), Positives = 181/289 (62%), Gaps = 14/289 (4%)

Query: 1134 TQMTLKTFHFAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIE---RT 1190
            T ++L+      ++   I  V+     ++ + +DM  IR L LEV +DSI   I    R 
Sbjct: 1512 TLVSLELTDLVVQIASVIAGVYSQGQMYVSVHIDMRAIRALQLEVTLDSIAASISSAPRL 1571

Query: 1191 RGISGHLTVSGHSFLIL-----KPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHE 1245
            +  S  +TV  H+  I        +D   ++   M+ ++++LPS+ +KGV G+ RAVI +
Sbjct: 1572 KIKSADITVKRHTDEIHIVAHHNGEDKMPAYRRLMW-LRRVLPSISVKGVPGLQRAVI-Q 1629

Query: 1246 EDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLV 1305
            ++ EG+ +  LLVEG+ LR+VM T GV G +  SN+  EV K LGIEAAR TI+ +I   
Sbjct: 1630 QNGEGIKE--LLVEGEGLREVMVTDGVIGTQTKSNHVMEVEKVLGIEAARKTIIDQIHYT 1687

Query: 1306 MENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFY 1365
            M++HG+ +D RH ML+ D+M  KGEVLGITR G++KMK+SVL LASFE T+DHLFDA+F 
Sbjct: 1688 MDSHGLGVDPRHLMLLGDVMCFKGEVLGITRFGVSKMKDSVLMLASFEKTTDHLFDASFN 1747

Query: 1366 GQTDCISGVSECIIMGLPM-NVGTGLIKLLQAVPRSEPVPRTLLFDNPE 1413
             + D I GVSECII+G P  NVGT +  L+   P+  P  +T LF+ PE
Sbjct: 1748 ARRDPIQGVSECIILGSPANNVGTAMPALVADKPKLPPRYQT-LFERPE 1795



 Score =  205 bits (521), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 124/357 (34%), Positives = 180/357 (50%), Gaps = 35/357 (9%)

Query: 9   LTLYYATRNCWQVLMAN------------KSNLVTPRNGELLIAATQDFITGGYLLTQKN 56
           L L +AT  CW   +A              ++L + R G++  A     + G   L +  
Sbjct: 286 LALVHAT--CWPAPIAEPLKYRQVARQAPSADLTSGRRGQVERAFAA-LLKGSMTLYRPR 342

Query: 57  AFFNRAQTMRIASTLIAGRKVFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPI 116
           A F R     ++ +    + + F      +V         S  +   ++LY    +R P+
Sbjct: 343 AAFERDADSTLSPSSTHSKHIQF------SVLSSREAVAISEFEANQRDLYTPGDRR-PV 395

Query: 117 PHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKN 176
            HG+LD+R+GT+ K   C TCG  L+DCVGH+ YI L LPVFHIGYF+ +++ILQ ICK 
Sbjct: 396 EHGVLDKRLGTSDKTGKCDTCGLGLADCVGHYAYIKLVLPVFHIGYFKHILSILQCICK- 454

Query: 177 PTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKC 236
            TC+R+LL   +   + A  R P L  L   +  K++    +K + CPHCG INGVVKK 
Sbjct: 455 -TCSRILLDSSQHRKYLALFRRPNLDSLTIAAYSKQLAALCRKCTTCPHCGAINGVVKKI 513

Query: 237 GLLKISHEKYKNRTKKKDAIVED----------LLAEYNEAVKFNPEIEAHKKFGLIQTL 286
           G ++I HEK++ R  KKDA   D              + EAVK +  +E H     I  L
Sbjct: 514 GTMRIGHEKWRGRNLKKDAGGRDGAEGKGNYTAWRESFAEAVKEDKMLEPHIDKA-IDDL 572

Query: 287 NPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
           NPL+VL LF  I   D  LL ++    +P + +   + VPP CIRPSV  +  ++ D
Sbjct: 573 NPLKVLTLFRKITSSDCELLGLDPTAGRPEEFLWQYISVPPVCIRPSVAQEAATNED 629



 Score =  176 bits (445), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 111/261 (42%), Positives = 155/261 (59%), Gaps = 31/261 (11%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEV------------ 811
            GVPRIKEIINA++ ISTPII+A L +D     ARIVKGR+E+T LG+V            
Sbjct: 1459 GVPRIKEIINAAKTISTPIISAKLFQDKLEQAARIVKGRVEKTYLGDVSHRLITLVSLEL 1518

Query: 812  -------CEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIE---RTRGISGHL 861
                      I  V+     ++ + +DM  IR L LEV +DSI   I    R +  S  +
Sbjct: 1519 TDLVVQIASVIAGVYSQGQMYVSVHIDMRAIRALQLEVTLDSIAASISSAPRLKIKSADI 1578

Query: 862  TVSGHSFLIL-----KPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVT 916
            TV  H+  I        +D   ++   M+ ++++LPS+ +KGV G+ RAVI +++ EG+ 
Sbjct: 1579 TVKRHTDEIHIVAHHNGEDKMPAYRRLMW-LRRVLPSISVKGVPGLQRAVI-QQNGEGIK 1636

Query: 917  KYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMS 976
            +  LLVEG+ LR+VM T GV G +  SN+  EV K LGIEAAR TI+ +I   M++HG+ 
Sbjct: 1637 E--LLVEGEGLREVMVTDGVIGTQTKSNHVMEVEKVLGIEAARKTIIDQIHYTMDSHGLG 1694

Query: 977  IDFRHPMLVADLMTSKGEVLG 997
            +D RH ML+ D+M  KGEVLG
Sbjct: 1695 VDPRHLMLLGDVMCFKGEVLG 1715



 Score = 97.1 bits (240), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 49/80 (61%), Positives = 56/80 (70%), Gaps = 1/80 (1%)

Query: 606  GDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
            G + P  +GFV NSF+SGL  TEF FH + GREGLVDTAVKTAETGYM RRL+K+LEDL 
Sbjct: 1181 GAIDPLAKGFVSNSFYSGLRATEFLFHAISGREGLVDTAVKTAETGYMARRLMKALEDLS 1240

Query: 665  VQYDMSFDAAFYGQTDCISG 684
             +YD S   A  G    I G
Sbjct: 1241 SRYDRSVRNATGGVVQFIYG 1260



 Score = 79.7 bits (195), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 46/130 (35%), Positives = 69/130 (53%), Gaps = 11/130 (8%)

Query: 1027 EILALSNETLDSKEFLQDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSHQD 1086
            EI  L  E   +  F    SE F+R++++F+++   +++    ++    P    +  +Q 
Sbjct: 1321 EINRLVAEKTATPYFTNSCSEEFLRELREFVDQQIAQQAAKYREEYGMPPALAPLKRNQS 1380

Query: 1087 KIGHGRESNPFPSACKAEA-----------CREKYVRAQIEPATAVGALAAQSIGEPGTQ 1135
            K G    +       K +            C  K+V+A+IEP +AVGA+ AQSIGEPGTQ
Sbjct: 1381 KFGKADAAMQAIVNNKTKVTVTQIEEFLQLCWTKFVKAKIEPGSAVGAIGAQSIGEPGTQ 1440

Query: 1136 MTLKTFHFAG 1145
            MTLKTFHFAG
Sbjct: 1441 MTLKTFHFAG 1450



 Score = 66.6 bits (161), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 31/50 (62%), Positives = 40/50 (80%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM  K NLVTPRNGE +IAATQDFITG YL+T+++ FFNR + +++ S L
Sbjct: 874 LMNIKRNLVTPRNGEPIIAATQDFITGCYLITRRDTFFNRQEFVQMCSYL 923



 Score = 49.7 bits (117), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 28/58 (48%), Positives = 36/58 (62%), Gaps = 2/58 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPM-NVGTGLIKLLQAVPRSEPVPRTLLFDNPE 724
            D  FDA+F  + D I GVSECII+G P  NVGT +  L+   P+  P  +T LF+ PE
Sbjct: 1739 DHLFDASFNARRDPIQGVSECIILGSPANNVGTAMPALVADKPKLPPRYQT-LFERPE 1795


>gi|281204162|gb|EFA78358.1| RNA polymerase III [Polysphondylium pallidum PN500]
          Length = 1393

 Score =  282 bits (721), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 138/270 (51%), Positives = 182/270 (67%), Gaps = 24/270 (8%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH+A+V+P RT RFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 450 DGDVVLFNRQPSLHKLSIMAHKARVMPWRTLRFNECVCTPYNADFDGDEMNLHLPQTEEA 509

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL              +LM   +NL+TPRNGE L+AATQDF+T  YL+++++AF++R
Sbjct: 510 RAEAL--------------ILMGVTNNLITPRNGEPLVAATQDFLTSSYLISRRDAFYDR 555

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +   +  T  AD          +      P   ++   +WTGKQ+F ++L+P+    V 
Sbjct: 556 TRFAYMC-THFADA---------YEHIDMPPPTILKPIELWTGKQLFEVLLRPSVKSHVL 605

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            N +TK R Y  N   C +D YV  RNSEL+ GS+DKS +G G K ++F+IL+RDF   +
Sbjct: 606 VNFETKSRTYEKNLYMCPKDGYVYFRNSELMCGSIDKSIIGGGNKNSLFHILMRDFTPAI 665

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           A  AM RL+++ + +L ++GFSIGI DV P
Sbjct: 666 AANAMTRLAKLCARFLGDQGFSIGIPDVKP 695



 Score =  238 bits (608), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 176/491 (35%), Positives = 247/491 (50%), Gaps = 90/491 (18%)

Query: 1001 PVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDT--------------- 1045
            PV+  R +  + +    R++ SL   +I  L    L S +F Q T               
Sbjct: 908  PVDFARAMMSVKSTKQCRNEESLRPYKIKLLLESQLKSSKFAQCTDLFKDEIRSFFYGKP 967

Query: 1046 -SENFVRDIKKFLEEFS-------KKESVTSHQDKVSQPLREQILSHQ-DKIGHGRESNP 1096
              E ++ ++ K  + F+         +++TS +D+    L      H  D+I    +S  
Sbjct: 968  KQEGYIEELLKLRKSFNLPSYEVDGDQTMTSVEDEPPARLTPDQFEHLVDQIHRITKSQ- 1026

Query: 1097 FPSACKAEACREKYVRAQIEPATAVGAL-------------------------------- 1124
                   E C +KY RA+IEP TAVGA+                                
Sbjct: 1027 --LELFLEICLDKYSRARIEPGTAVGAVGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVP 1084

Query: 1125 -------AAQSIGEPGTQMTLKTFH---------------FAGEVCEYIEEVFVPDDSFI 1162
                   AA++I  P    TL                     G+V  +I+EVF     +I
Sbjct: 1085 RIKEIINAAKTISTPIITATLNCDDDIRSARIVAGRIEKVTLGQVAIFIKEVFRNAGCYI 1144

Query: 1163 LIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFLILKPKDSSKSFNSK 1219
             IK+D   I    L++D +SIR  I  T+ +     H+  SG   + ++P D+S+     
Sbjct: 1145 TIKIDKKFIDSQQLDIDPESIRRAIIGTKILKLKEKHVIASGDDKIRVEPVDTSREMMLY 1204

Query: 1220 MYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCS 1278
              Q +K  LP+V+++G+  +NR VI E++     KYKLL+EG +L  VM T G+ G   +
Sbjct: 1205 NLQFLKNNLPNVIVRGISTVNRVVIDEKN----GKYKLLIEGYDLLHVMTTAGINGTHTN 1260

Query: 1279 SNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHG 1338
            SN+  EV K LGIEA R TI+ EI+++M NHGMSID RH ML+ADLM+ KGE+LGITR G
Sbjct: 1261 SNHMMEVEKYLGIEAVRQTIIDEIQMIMINHGMSIDSRHVMLLADLMSFKGEILGITRFG 1320

Query: 1339 LAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 1398
            +AKMKESVL LASFE T+DHLFDAA + + D I GVSECIIMG+P+ +GTGL KLL    
Sbjct: 1321 IAKMKESVLMLASFEKTTDHLFDAAVHRRQDDIVGVSECIIMGIPVPLGTGLFKLLYN-S 1379

Query: 1399 RSEPVPRTLLF 1409
            R   +PR  L 
Sbjct: 1380 RKTNLPRKSLL 1390



 Score =  226 bits (577), Expect = 6e-56,   Method: Compositional matrix adjust.
 Identities = 119/257 (46%), Positives = 159/257 (61%), Gaps = 7/257 (2%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G I+  +   D +   SH++I+++ L+ Q   R P+ +G LD R+GT+ K   C TCG +
Sbjct: 16  GHIQFGILSPDDMISLSHVEIINRELFDQS-NRGPMQYGCLDNRLGTSDKSIICKTCGLS 74

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
           + DCVGHFGYI L LPVFHIGYF+ + NILQ ICK   C+ +LL +EK   F  K+RN  
Sbjct: 75  IVDCVGHFGYIKLQLPVFHIGYFKNITNILQMICKG--CSAILLDDEKKTTFLRKIRNRK 132

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDL 260
           L  L R++L KKI    +K   CP C  + G VKK   LK+ HE+YK    K D  + D 
Sbjct: 133 LDVLQRRALLKKIYLECRKKKFCPRCNMVQGTVKKVSALKLVHERYKG---KNDEYIRDF 189

Query: 261 LAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
           L+ ++EA+K+N E++ H K    + LNPL  L LF+ I  +D  LL MN EL +P  LIL
Sbjct: 190 LSNFDEAIKYNSEMKGHIKKAQ-EDLNPLVALNLFKRITSQDTELLDMNPELGRPERLIL 248

Query: 321 TRLLVPPNCIRPSVISD 337
           T +LVPP CIRPSV  D
Sbjct: 249 THILVPPVCIRPSVPMD 265



 Score =  202 bits (514), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 115/238 (48%), Positives = 158/238 (66%), Gaps = 8/238 (3%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ ISTPIITA L+ D D+  ARIV GR+E+ TLG+V  +I+EVF    
Sbjct: 1082 GVPRIKEIINAAKTISTPIITATLNCDDDIRSARIVAGRIEKVTLGQVAIFIKEVFRNAG 1141

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFLILKPKDSSKSF 880
             +I IK+D   I    L++D +SIR  I  T+ +     H+  SG   + ++P D+S+  
Sbjct: 1142 CYITIKIDKKFIDSQQLDIDPESIRRAIIGTKILKLKEKHVIASGDDKIRVEPVDTSREM 1201

Query: 881  NSKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
                 Q +K  LP+V+++G+  +NR VI E++     KYKLL+EG +L  VM T G+ G 
Sbjct: 1202 MLYNLQFLKNNLPNVIVRGISTVNRVVIDEKN----GKYKLLIEGYDLLHVMTTAGINGT 1257

Query: 940  KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
              +SN+  EV K LGIEA R TI+ EI+++M NHGMSID RH ML+ADLM+ KGE+LG
Sbjct: 1258 HTNSNHMMEVEKYLGIEAVRQTIIDEIQMIMINHGMSIDSRHVMLLADLMSFKGEILG 1315



 Score =  112 bits (281), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 53/80 (66%), Positives = 61/80 (76%), Gaps = 7/80 (8%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV NSF++G+ PTEFFFHTMGGREGLVDTAVKTAETGYMQRRL+K+LEDL  QYD 
Sbjct: 819 PAKGFVANSFYTGMIPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLMKALEDLSTQYD- 877

Query: 670 SFDAAFYGQTDCISGVSECI 689
                 Y   D I G+ + I
Sbjct: 878 ------YTVRDSIGGIVQFI 891



 Score = 58.9 bits (141), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 23/43 (53%), Positives = 36/43 (83%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 63
           +LM   +NL+TPRNGE L+AATQDF+T  YL+++++AF++R +
Sbjct: 515 ILMGVTNNLITPRNGEPLVAATQDFLTSSYLISRRDAFYDRTR 557



 Score = 51.2 bits (121), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 28/53 (52%), Positives = 34/53 (64%), Gaps = 1/53 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLF 720
            D  FDAA + + D I GVSECIIMG+P+ +GTGL KLL    R   +PR  L 
Sbjct: 1339 DHLFDAAVHRRQDDIVGVSECIIMGIPVPLGTGLFKLLYN-SRKTNLPRKSLL 1390


>gi|367030511|ref|XP_003664539.1| hypothetical protein MYCTH_2307483 [Myceliophthora thermophila ATCC
           42464]
 gi|347011809|gb|AEO59294.1| hypothetical protein MYCTH_2307483 [Myceliophthora thermophila ATCC
           42464]
          Length = 1555

 Score =  281 bits (720), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 138/282 (48%), Positives = 185/282 (65%), Gaps = 29/282 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND+VLFNRQPSLHKLSIM+H  KV P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 470 DNDIVLFNRQPSLHKLSIMSHLVKVRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 529

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL+TP+NGE +IAATQDFIT  YLL+ K+ FF+R
Sbjct: 530 RAEAIN--------------LMGVKNNLITPKNGEPIIAATQDFITAAYLLSSKDRFFDR 575

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                I + ++   + +             P   ++   +WTGKQIF+++++PN++ PV 
Sbjct: 576 TSFTYICTQMLLGDTHL----------ELPPPAILKPRALWTGKQIFNVLMRPNKESPVL 625

Query: 521 ANLKTKGRAYTANE-----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL  K + Y   +     +    DS++++RNSE++ G MDKST+G G K +VFY++LRD
Sbjct: 626 VNLDAKNKVYKPKKDGQIPDMDIDDSFLVVRNSEVMCGRMDKSTVGGGKKNSVFYVILRD 685

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           FG D A  AM RL+++ +  L  RGFSIG+GDV P     ++
Sbjct: 686 FGPDHAAAAMNRLAKLCARTLTLRGFSIGVGDVWPSTSLTKH 727



 Score =  217 bits (553), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 147/400 (36%), Positives = 202/400 (50%), Gaps = 98/400 (24%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEV---------------- 1147
            + C  KY +A++EP  AVGA+ AQSIGEPGTQMTLKTFHFAG                  
Sbjct: 1127 QMCLHKYKKARVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIIN 1186

Query: 1148 -----------CE---------------------------YIEEVFVPDDSFILIKLDMD 1169
                       CE                           YI++ ++PD + I++++D+ 
Sbjct: 1187 ASKLISTPVITCELENKVDLKAARVVKGRIEKTYISDVISYIDDEWLPDVAKIVLQVDLQ 1246

Query: 1170 -------------------RIRLLHLEVDIDSIRYCIERTRGI----------------- 1193
                               R + L L+V+ D +R   +R   I                 
Sbjct: 1247 ALSDMQLGITMKDIADAIVRAKKLKLKVEPDDLRIGGDRVEVIIRNTWQDATAARKAARV 1306

Query: 1194 SGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTK 1253
                   GH F+     +S+  F  ++  +K++LP V I G    +RA+I   +     +
Sbjct: 1307 RAAAIEKGH-FISSTLDESAADFQLRVNFLKRMLPQVAISGYPEASRAIIQTSE---KNE 1362

Query: 1254 YKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSI 1313
            +K+LVEG  LR  M T GV G KC +N+  E    LGIEAAR+TI TEI  VM    M+I
Sbjct: 1363 HKVLVEGYGLRACMTTEGVIGTKCVTNSVMECRDVLGIEAARATIATEIGSVMRE--MNI 1420

Query: 1314 DFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISG 1373
            D RH  L+AD+MT KGE+LGITR GLAKM++SVL LASFE T DHLFDAA   + D I G
Sbjct: 1421 DPRHMELLADVMTYKGEILGITRFGLAKMRDSVLQLASFEKTPDHLFDAAAGMKKDRIQG 1480

Query: 1374 VSECIIMGLPMNVGTGLIKLLQ--AVPRSEPVPRTLLFDN 1411
            VSECIIMG  M++GTG  ++++   +   +  P+  LF++
Sbjct: 1481 VSECIIMGQSMSIGTGAFQVVRRLGIRDHQVAPKPTLFED 1520



 Score =  195 bits (495), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 108/264 (40%), Positives = 151/264 (57%), Gaps = 19/264 (7%)

Query: 96  QSHIQIVSKN--------LYCQDPQRTPIPHGLLDRRMGTN--QKEANCTTCGQNLSDCV 145
           QSH  IVS+         LY  + +RT  PHG LD R+GT+   +E+ C+TC   L +C 
Sbjct: 30  QSHQDIVSQGVLEVSDNLLYDVENRRTAFPHGPLDPRLGTSSTNRESKCSTCHLGLQECP 89

Query: 146 GHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLV 205
           GHFG++ LPLPVFHIGY + +   LQ+ICK+  CARVLL E +   F  +LR P +  L 
Sbjct: 90  GHFGHVRLPLPVFHIGYLKYIQATLQNICKD--CARVLLQEPERRQFLKELRRPGIDNLR 147

Query: 206 RKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEK---YKNRTKKKDAIVE---D 259
           R ++ KKI E  +K   CPHCG I GV++K  ++K+ H+K   Y   T +K    E   +
Sbjct: 148 RSAILKKINEQCRKARTCPHCGSIQGVIRKLSVMKLVHDKFSAYNKSTAQKKIPPESKVE 207

Query: 260 LLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLI 319
             A + +A K+ PE+E H K  + + LNPL VL LF+ I   D  LL ++    +P   +
Sbjct: 208 FDASFEQAKKYTPELEKHTKKAM-EDLNPLRVLNLFKQISPTDCELLGLDPSEGRPEMFL 266

Query: 320 LTRLLVPPNCIRPSVISDLKSDND 343
              +  PP CIRPSV  +  S+ D
Sbjct: 267 WQYVPAPPICIRPSVAQENASNED 290



 Score =  156 bits (395), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 103/270 (38%), Positives = 147/270 (54%), Gaps = 42/270 (15%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+IT  L+   DL  AR+VKGR+E+T + +V  YI++ ++PD 
Sbjct: 1177 GVPRIKEIINASKLISTPVITCELENKVDLKAARVVKGRIEKTYISDVISYIDDEWLPDV 1236

Query: 824  SFILIKLDMD-------------------RIRLLHLEVDIDSIRYCIERTRGI------- 857
            + I++++D+                    R + L L+V+ D +R   +R   I       
Sbjct: 1237 AKIVLQVDLQALSDMQLGITMKDIADAIVRAKKLKLKVEPDDLRIGGDRVEVIIRNTWQD 1296

Query: 858  ----------SGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVI 907
                             GH F+     +S+  F  ++  +K++LP V I G    +RA+I
Sbjct: 1297 ATAARKAARVRAAAIEKGH-FISSTLDESAADFQLRVNFLKRMLPQVAISGYPEASRAII 1355

Query: 908  HEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIK 967
               +     ++K+LVEG  LR  M T GV G KC +N+  E    LGIEAAR+TI TEI 
Sbjct: 1356 QTSEK---NEHKVLVEGYGLRACMTTEGVIGTKCVTNSVMECRDVLGIEAARATIATEIG 1412

Query: 968  LVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             VM    M+ID RH  L+AD+MT KGE+LG
Sbjct: 1413 SVMRE--MNIDPRHMELLADVMTYKGEILG 1440



 Score =  103 bits (257), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 45/59 (76%), Positives = 51/59 (86%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSF++GL PTEF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 844 PSKGFVRNSFYTGLVPTEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSTQYD 902



 Score = 63.2 bits (152), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 28/53 (52%), Positives = 38/53 (71%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           LM  K+NL+TP+NGE +IAATQDFIT  YLL+ K+ FF+R     I + ++ G
Sbjct: 536 LMGVKNNLITPKNGEPIIAATQDFITAAYLLSSKDRFFDRTSFTYICTQMLLG 588



 Score = 45.1 bits (105), Expect = 0.32,   Method: Compositional matrix adjust.
 Identities = 23/57 (40%), Positives = 35/57 (61%), Gaps = 2/57 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ--AVPRSEPVPRTLLFDN 722
            D  FDAA   + D I GVSECIIMG  M++GTG  ++++   +   +  P+  LF++
Sbjct: 1464 DHLFDAAAGMKKDRIQGVSECIIMGQSMSIGTGAFQVVRRLGIRDHQVAPKPTLFED 1520


>gi|255717220|ref|XP_002554891.1| KLTH0F16236p [Lachancea thermotolerans]
 gi|238936274|emb|CAR24454.1| KLTH0F16236p [Lachancea thermotolerans CBS 6340]
          Length = 1460

 Score =  281 bits (719), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 141/277 (50%), Positives = 190/277 (68%), Gaps = 30/277 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH+LSI++H AK+ P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 467 DGDVVLFNRQPSLHRLSILSHYAKIRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 526

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+R
Sbjct: 527 RAEAIN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFSR 572

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+ +++ S +++D +    I          P   ++   +WTGKQ+FSL+++PN++ PV 
Sbjct: 573 AEFVQLLS-MMSDGNLQFDI---------PPPSIMKPYYMWTGKQVFSLLIRPNKESPVV 622

Query: 521 ANLKTKGRAY------TANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLR 574
            NL  K + Y      +   E    D YV++R S++L+G MDKS LG G K +VFY +LR
Sbjct: 623 INLDAKNKVYIPPKDKSLPNEMSINDGYVVIRGSKILSGVMDKSVLGDGKKHSVFYTILR 682

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           DFG   A  AM R++++ + +L NRGFSIGI DVTPG
Sbjct: 683 DFGPQEAAFAMNRMAKLCARFLGNRGFSIGINDVTPG 719



 Score =  242 bits (618), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 184/531 (34%), Positives = 268/531 (50%), Gaps = 113/531 (21%)

Query: 973  HGMSIDFRH---PMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDPSLSAQEIL 1029
            H  ++ F H   P+L   +M     VL    P+E K +  D +    +  DPSL      
Sbjct: 940  HANNVTFNHVDKPLLPYQIMQQTNGVL---KPLEEKLVRYDNLG---NELDPSLQ----- 988

Query: 1030 ALSNETLDSKEFL-QDTSE-NFVRDIKKFL-EEFSKKESVTSHQ---DKVSQPLREQILS 1083
                   D  E++ QD +E NF + ++ ++ E+ S   ++ +H+   + + +P  E    
Sbjct: 989  -------DRVEYIDQDDAERNFYKSLRDYMYEKASHLANIRAHKGLKEFLDEPAAELQAM 1041

Query: 1084 HQDKIGHGRESNPFPSACKA---------EACREKYVRAQIEPATAVGALAAQSIGEPGT 1134
              D+             CK          E    KY +A++EP TAVGA+ A SIGEPGT
Sbjct: 1042 DLDEGAPASALASVDQLCKISSKLVLKFLEIAIFKYHKAKVEPGTAVGAVGAHSIGEPGT 1101

Query: 1135 QMTLKTFHFAG------------------------------------------EVCEYIE 1152
            QMTLKTFHFAG                                           V   IE
Sbjct: 1102 QMTLKTFHFAGVASMNVTLGVPRIKEIINASKVISTPIINAVLVNNNDERAARVVKGRIE 1161

Query: 1153 EVFVPDDSFIL------------IKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHL 1197
            +  + D +F +            +K+D+  I  L LE+ ++ I   I R   +   +  +
Sbjct: 1162 KTLLSDVAFYIQDVYKDNMSFLQVKVDLGTIEKLQLELTVEDIAVAITRAAKLKIAASDV 1221

Query: 1198 TVSGHSFL-------ILKPKDSSKSF-----NSKMYQMKQL---LPSVVIKGVQGINRAV 1242
            ++ G   +       + K K  S S      N   Y+M+ L   LP +V+KG+  I RAV
Sbjct: 1222 SIMGKDKVNINVYPEMAKLKSISTSAKEPVENELFYRMQHLRRALPGIVVKGLPDIARAV 1281

Query: 1243 IHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEI 1302
            I+ +D +G    +LLVEG  LR+VM T GV G+K  +N+  EV+  LGIEAAR++I+ EI
Sbjct: 1282 INIKD-DG--SRELLVEGYGLREVMTTDGVIGMKTKTNHILEVFSVLGIEAARTSIVGEI 1338

Query: 1303 KLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDA 1362
               M NHGMS+D RH  L+ D+MT KGE+LGITR GL+KM++SVL LASFE T+DHLFDA
Sbjct: 1339 DYTMSNHGMSVDPRHVQLLGDVMTYKGEILGITRFGLSKMRDSVLQLASFEKTTDHLFDA 1398

Query: 1363 AFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA--VPRSEPVPRTLLFDN 1411
            AFY + D + GVSECII+G  M++GTG  K+++   +  S+  P+  LF++
Sbjct: 1399 AFYMKKDAVEGVSECIILGQTMSIGTGAFKVVKGTDISESDLAPKPTLFES 1449



 Score =  183 bits (465), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 105/272 (38%), Positives = 155/272 (56%), Gaps = 14/272 (5%)

Query: 72  IAGRKVFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKE 131
           IA +++  +GL    ++  D V Q S ++I +++L+  +  R P   G LD RMG +  +
Sbjct: 8   IAPKRI--KGLEFSALSASDIVAQ-SKVEISTRDLFDLENGRKPKSGGALDTRMGVSSSQ 64

Query: 132 ANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAG 191
           A C+TC  NL+ C GHFG+I L LPVFH+GYF+  I +LQSICK  TCA +LL EE    
Sbjct: 65  AECSTCHGNLASCHGHFGHIKLSLPVFHVGYFKATIQVLQSICK--TCAALLLSEEDKHQ 122

Query: 192 FRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGL------LKISHEK 245
           F ++LR P +  L R  + KK+++  KK   C  CG +NGVVKK         LKI H+ 
Sbjct: 123 FLSELRRPGIDNLRRMGILKKVVDQCKKQRRCLRCGSLNGVVKKAAAGSGSASLKILHDT 182

Query: 246 YKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPL 305
           ++   KK     +  + ++   +  NPE+E + K   +  LNPL+ L LF+ +  ED  L
Sbjct: 183 FRWVGKKSAPEKDKWVGDWKTVLAHNPELERYVK-KCMDDLNPLKTLNLFKQVAPEDCEL 241

Query: 306 LLMNAEL--SKPSDLILTRLLVPPNCIRPSVI 335
           L +++ +   +P   I   L  PP CIRPSV+
Sbjct: 242 LGIDSTVKSGRPETYIWRYLPAPPVCIRPSVM 273



 Score =  179 bits (453), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 111/252 (44%), Positives = 156/252 (61%), Gaps = 21/252 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII A L  + D   AR+VKGR+E+T L +V  YI++V+  + 
Sbjct: 1121 GVPRIKEIINASKVISTPIINAVLVNNNDERAARVVKGRIEKTLLSDVAFYIQDVYKDNM 1180

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFL-------ILKP 873
            SF+ +K+D+  I  L LE+ ++ I   I R   +   +  +++ G   +       + K 
Sbjct: 1181 SFLQVKVDLGTIEKLQLELTVEDIAVAITRAAKLKIAASDVSIMGKDKVNINVYPEMAKL 1240

Query: 874  KDSSKSF-----NSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD 925
            K  S S      N   Y+M+ L   LP +V+KG+  I RAVI+ +D +G    +LLVEG 
Sbjct: 1241 KSISTSAKEPVENELFYRMQHLRRALPGIVVKGLPDIARAVINIKD-DG--SRELLVEGY 1297

Query: 926  NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 985
             LR+VM T GV G+K  +N+  EV+  LGIEAAR++I+ EI   M NHGMS+D RH  L+
Sbjct: 1298 GLREVMTTDGVIGMKTKTNHILEVFSVLGIEAARTSIVGEIDYTMSNHGMSVDPRHVQLL 1357

Query: 986  ADLMTSKGEVLG 997
             D+MT KGE+LG
Sbjct: 1358 GDVMTYKGEILG 1369



 Score =  100 bits (250), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 47/61 (77%), Positives = 52/61 (85%), Gaps = 1/61 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV+NSFFSGL+P EF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QY
Sbjct: 840 TPQSKGFVRNSFFSGLSPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSCQY 899

Query: 668 D 668
           D
Sbjct: 900 D 900



 Score = 64.7 bits (156), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 29/57 (50%), Positives = 44/57 (77%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVF 78
           LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+RA+ +++ S +  G   F
Sbjct: 533 LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFSRAEFVQLLSMMSDGNLQF 589



 Score = 54.7 bits (130), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 25/57 (43%), Positives = 38/57 (66%), Gaps = 2/57 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA--VPRSEPVPRTLLFDN 722
            D  FDAAFY + D + GVSECII+G  M++GTG  K+++   +  S+  P+  LF++
Sbjct: 1393 DHLFDAAFYMKKDAVEGVSECIILGQTMSIGTGAFKVVKGTDISESDLAPKPTLFES 1449


>gi|389626659|ref|XP_003710983.1| DNA-directed RNA polymerase III subunit RPC1 [Magnaporthe oryzae
           70-15]
 gi|351650512|gb|EHA58371.1| DNA-directed RNA polymerase III subunit RPC1 [Magnaporthe oryzae
           70-15]
 gi|440463479|gb|ELQ33059.1| DNA-directed RNA polymerase III subunit RPC1 [Magnaporthe oryzae
           Y34]
 gi|440481206|gb|ELQ61814.1| DNA-directed RNA polymerase III subunit RPC1 [Magnaporthe oryzae
           P131]
          Length = 1456

 Score =  281 bits (719), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 135/274 (49%), Positives = 177/274 (64%), Gaps = 27/274 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIM+H  KV P RTFR NEC CTPYNADFDGDEMN+H+PQTEEA
Sbjct: 469 DGDIVLFNRQPSLHKLSIMSHFVKVRPWRTFRLNECACTPYNADFDGDEMNLHVPQTEEA 528

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EA+               LM  K NL TP+NGE +IAATQDFIT  YL++ K+ F++R
Sbjct: 529 RTEAM--------------TLMGVKYNLATPKNGEPIIAATQDFITAAYLISLKDVFYDR 574

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                +   ++ D  D         +    P   ++   +WTGKQ+FS++L+PN++ PV 
Sbjct: 575 KTFTYVCQHMLMDGKD---------YLDLPPPAILKPRALWTGKQVFSMMLRPNKESPVK 625

Query: 521 ANLKTKGRAYTAN----EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL  K R Y        + C  D ++++RNSE++ G MDKS +G G K ++FY++LRDF
Sbjct: 626 INLDAKCREYKPRPGECPDMCPNDGWLVIRNSEVMCGKMDKSIVGGGKKDSIFYVILRDF 685

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           G D AV  M RL+++ +  L NRGFSIG+GDV P
Sbjct: 686 GPDHAVIVMSRLAKLCARTLGNRGFSIGVGDVFP 719



 Score =  201 bits (512), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 111/271 (40%), Positives = 159/271 (58%), Gaps = 10/271 (3%)

Query: 79  FRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCG 138
           F+ +  G  + +D V Q   ++I  K LY  +  RTP  HG LD R+GT+ K A C TC 
Sbjct: 23  FKEIKFGIQSNQDIVNQ-GVLEISEKQLYDVENNRTPSRHGPLDHRLGTSSKTAECQTCA 81

Query: 139 QNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN 198
           Q L +C GHFG++ LPLP FHIGY R +  ILQ+ICK+  CARVLL E +   F  +LR 
Sbjct: 82  QQLQNCNGHFGHVRLPLPAFHIGYLRFIQMILQNICKD--CARVLLTEPERRKFLLELRR 139

Query: 199 PALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKY----KNRTKKKD 254
           P +  L R  + KKI E  +KV +CP+C  +NG ++K G+LK++H+K+    K+   +K 
Sbjct: 140 PGIDNLRRTGICKKINEQCRKVKICPYCDSVNGTIRKIGVLKLAHDKFVTFNKSNALRKQ 199

Query: 255 AIVEDLLAE--YNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL 312
             V  ++ +  +N A K  PE++ H +  + + LNPL+VL LF+ I   D  LL ++   
Sbjct: 200 PPVSKIVFDNSFNYAKKSVPELDKHLRKAM-EDLNPLKVLTLFKMISPTDCELLGLDPSE 258

Query: 313 SKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
            +P   +   L  PP CIRPSV  D  S+ D
Sbjct: 259 GRPEMFLWQYLPAPPICIRPSVQQDTSSNED 289



 Score =  174 bits (441), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 115/297 (38%), Positives = 164/297 (55%), Gaps = 28/297 (9%)

Query: 1143 FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTV 1199
            +  +V  +IE+ +  D   +++++DM  ++ +HL + +  I   I + + +      L +
Sbjct: 1161 YVSDVLRFIEDEWKADTGSVVLQIDMGALQDMHLGIGLPEIAEAICKYKKLKIEPDDLRL 1220

Query: 1200 SGHSFLIL------------------KPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRA 1241
            S  S  I+                     + S     ++  ++++LP V I G     RA
Sbjct: 1221 SSDSVEIVVRNTWADTAAAKKAARSRTTTEDSPDLLLRVNHLRRVLPQVPISGYPEAARA 1280

Query: 1242 VIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTE 1301
            +I   +     ++K+LVEG  LR+ M T GV G    SNN  E    LGIEAARSTI TE
Sbjct: 1281 IIQTSEK---NEHKVLVEGYGLRECMTTEGVIGTSVISNNVMEARDILGIEAARSTIATE 1337

Query: 1302 IKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFD 1361
            I  VM +  M ID RH  L+AD+MT KG+VLGITR GL+KM++SVL LASFE T DHLF 
Sbjct: 1338 IGSVMGD--MGIDPRHMQLLADVMTYKGDVLGITRFGLSKMRDSVLQLASFEKTPDHLFA 1395

Query: 1362 AAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA--VPRSEPVPRTLLFDNPEFHT 1416
            AA   +TD I GVSECIIMG  M+VGTG  K+++A  +   +  PR  LF++    T
Sbjct: 1396 AAAGMKTDKIEGVSECIIMGQTMSVGTGASKIVRALNLKPDDCKPRPTLFEDAWSQT 1452



 Score =  148 bits (373), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 101/279 (36%), Positives = 150/279 (53%), Gaps = 27/279 (9%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+IT  L  +  ++ AR+VKGR+E+T + +V  +IE+ +  D 
Sbjct: 1118 GVPRIKEIINASKLISTPVITCPLQNNKQIEAARVVKGRIEKTYVSDVLRFIEDEWKADT 1177

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSFLIL--------- 871
              +++++DM  ++ +HL + +  I   I + + +      L +S  S  I+         
Sbjct: 1178 GSVVLQIDMGALQDMHLGIGLPEIAEAICKYKKLKIEPDDLRLSSDSVEIVVRNTWADTA 1237

Query: 872  ---------KPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLV 922
                        + S     ++  ++++LP V I G     RA+I   +     ++K+LV
Sbjct: 1238 AAKKAARSRTTTEDSPDLLLRVNHLRRVLPQVPISGYPEAARAIIQTSE---KNEHKVLV 1294

Query: 923  EGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHP 982
            EG  LR+ M T GV G    SNN  E    LGIEAARSTI TEI  VM +  M ID RH 
Sbjct: 1295 EGYGLRECMTTEGVIGTSVISNNVMEARDILGIEAARSTIATEIGSVMGD--MGIDPRHM 1352

Query: 983  MLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDP 1021
             L+AD+MT KG+VLG  T   L ++ D ++   S    P
Sbjct: 1353 QLLADVMTYKGDVLGI-TRFGLSKMRDSVLQLASFEKTP 1390



 Score =  102 bits (254), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 46/59 (77%), Positives = 50/59 (84%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV NSF+SGL PTEF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 843 PSKGFVANSFYSGLLPTEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSTQYD 901



 Score = 70.9 bits (172), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 31/40 (77%), Positives = 35/40 (87%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            C+EK+ RA+ EP  AVGA+ AQSIGEPGTQMTLKTFHFAG
Sbjct: 1070 CQEKHERAKTEPGHAVGAVGAQSIGEPGTQMTLKTFHFAG 1109



 Score = 55.5 bits (132), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/40 (60%), Positives = 31/40 (77%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           LM  K NL TP+NGE +IAATQDFIT  YL++ K+ F++R
Sbjct: 535 LMGVKYNLATPKNGEPIIAATQDFITAAYLISLKDVFYDR 574



 Score = 46.2 bits (108), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 27/57 (47%), Positives = 36/57 (63%), Gaps = 2/57 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA--VPRSEPVPRTLLFDN 722
            D  F AA   +TD I GVSECIIMG  M+VGTG  K+++A  +   +  PR  LF++
Sbjct: 1391 DHLFAAAAGMKTDKIEGVSECIIMGQTMSVGTGASKIVRALNLKPDDCKPRPTLFED 1447


>gi|448520288|ref|XP_003868270.1| Rpo31 protein [Candida orthopsilosis Co 90-125]
 gi|380352609|emb|CCG22836.1| Rpo31 protein [Candida orthopsilosis]
          Length = 1443

 Score =  281 bits (719), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 143/281 (50%), Positives = 187/281 (66%), Gaps = 29/281 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH+LSI+AH AKV P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 467 DGDVVLFNRQPSLHRLSILAHYAKVRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 526

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+R
Sbjct: 527 RAEAIN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDR 572

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A  +++ S +    +DI   I         P   ++  ++WTGKQ+FSL++KPNR   V 
Sbjct: 573 ASLVQLLSMM--SDADIQFDIP--------PPAIMKPVMLWTGKQVFSLLIKPNRQSKVV 622

Query: 521 ANLKTKGRAYTA-----NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL  K + +         E    D +V++R S++L+G MDKSTLG G K +VFY +LRD
Sbjct: 623 INLNAKNKTFHPPAKGLPSEMSPNDGFVLIRGSQILSGLMDKSTLGDGKKHSVFYTILRD 682

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           +G   A  AM R++++ + +L NRGFSIGI DVTP     Q
Sbjct: 683 YGPQEAAAAMNRMAKLCARFLGNRGFSIGINDVTPAHELKQ 723



 Score =  252 bits (643), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 173/439 (39%), Positives = 240/439 (54%), Gaps = 87/439 (19%)

Query: 1039 KEFLQDTSENFVR-DIKKFLEEFSKK---ESVTSHQDKVSQPLREQILSHQDKIGHGRES 1094
            +EFL+D +E   R    + L+ F  +   + +   +D+       Q+L    KI H R +
Sbjct: 1000 REFLRDKAETLARLRESRGLQAFYTRVNEDDIQLDEDEAKINAVNQLL----KISH-RAA 1054

Query: 1095 NPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------- 1145
              F      + C  KY RA++EP TAVGA+ AQSIGEPGTQMTLKTFHFAG         
Sbjct: 1055 KEF-----MKQCLYKYSRAKVEPGTAVGAIGAQSIGEPGTQMTLKTFHFAGVASMNVTLG 1109

Query: 1146 -----EVCE--------YIEEVFVPDD--------------------------------S 1160
                 E+           I  V V DD                                +
Sbjct: 1110 VPRIKEIINASKTISTPIINAVLVNDDDEIAARVAKGRIEKTLLKDVAFYIEDVYKDNMA 1169

Query: 1161 FILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSFLIL---------- 1207
            ++ IK+D++ I  L LE+ ID+I   I +   +      + ++G + + +          
Sbjct: 1170 YLAIKVDLETIDKLQLELTIDNIAQAICKAPKLKIAPSDVIITGKNRINVLCNVNESKSE 1229

Query: 1208 KPKDSSKSFNS---KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLR 1264
              K +S S N+   +M  +K++LP + IKG+  I RAVI+ +D +G  K +LLVEG  L+
Sbjct: 1230 SLKSASDSLNALFFRMQTLKRVLPDICIKGLPNIFRAVINIKD-DG--KKELLVEGYGLK 1286

Query: 1265 DVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADL 1324
            DVM T G+ G K ++N+  EV + LGIEAAR +I+ EI   M NHGMS+D RH  L+ D+
Sbjct: 1287 DVMNTEGIVGTKTTTNHVLEVNEILGIEAARGSIIREIDYTMSNHGMSVDPRHIQLLGDV 1346

Query: 1325 MTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPM 1384
            MT KGEVLGITR GL+KM++SVL LASFE T+DHLFDAAF+ + D I GVSECII+G  M
Sbjct: 1347 MTYKGEVLGITRFGLSKMRDSVLQLASFEKTTDHLFDAAFFMKKDKIEGVSECIILGKTM 1406

Query: 1385 NVGTGLIKLLQAVPRSEPV 1403
            +VGTG  KL+++    E V
Sbjct: 1407 SVGTGAFKLVKSSNYDENV 1425



 Score =  182 bits (463), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 111/250 (44%), Positives = 158/250 (63%), Gaps = 19/250 (7%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII A L  D D   AR+ KGR+E+T L +V  YIE+V+  + 
Sbjct: 1109 GVPRIKEIINASKTISTPIINAVLVNDDDEIAARVAKGRIEKTLLKDVAFYIEDVYKDNM 1168

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSFLIL--------- 871
            +++ IK+D++ I  L LE+ ID+I   I +   +      + ++G + + +         
Sbjct: 1169 AYLAIKVDLETIDKLQLELTIDNIAQAICKAPKLKIAPSDVIITGKNRINVLCNVNESKS 1228

Query: 872  -KPKDSSKSFNS---KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927
               K +S S N+   +M  +K++LP + IKG+  I RAVI+ +D +G  K +LLVEG  L
Sbjct: 1229 ESLKSASDSLNALFFRMQTLKRVLPDICIKGLPNIFRAVINIKD-DG--KKELLVEGYGL 1285

Query: 928  RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 987
            +DVM T G+ G K ++N+  EV + LGIEAAR +I+ EI   M NHGMS+D RH  L+ D
Sbjct: 1286 KDVMNTEGIVGTKTTTNHVLEVNEILGIEAARGSIIREIDYTMSNHGMSVDPRHIQLLGD 1345

Query: 988  LMTSKGEVLG 997
            +MT KGEVLG
Sbjct: 1346 VMTYKGEVLG 1355



 Score =  172 bits (435), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 104/259 (40%), Positives = 143/259 (55%), Gaps = 18/259 (6%)

Query: 96  QSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPL 155
           QS ++I +++LY  +  R P   G LD RMG +   + C TC  NL+ C GHFG+I L L
Sbjct: 30  QSEVEIQTRDLYDLEKGRVPKEGGALDTRMGISSNSSECATCHGNLASCNGHFGHIRLAL 89

Query: 156 PVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILE 215
           PVFH+GYF+ VI++LQ +CKN  C  +LL  +    F ++LR P +  L R  + KKI +
Sbjct: 90  PVFHVGYFKAVISVLQCVCKN--CGAILLEPQAKRQFLSELRRPNIDNLKRMKILKKIND 147

Query: 216 TTKKVSVCPHCGEINGVVKKC------GLLKISHEKY----KNRTKKKDAIVEDLLAEYN 265
             KK   C  C  +NGVVKK         LKI H+ +    K  T +K    EDL    +
Sbjct: 148 QCKKQRRCLKCNHVNGVVKKAASGAGPASLKIVHDTFRWIGKKDTPEKTVWDEDL----D 203

Query: 266 EAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNA-ELSKPSDLILTRLL 324
              K NP++E   K  + +  NPL+ L LF+ I  ED  LL M+A +  +P   I   L 
Sbjct: 204 LVFKRNPDLEKFAK-RIQEDFNPLKTLNLFKQIIPEDCELLGMDASKGGRPEMYIWRYLP 262

Query: 325 VPPNCIRPSVISDLKSDND 343
            PP CIRPSV+ D +S+ D
Sbjct: 263 APPVCIRPSVMMDAQSNED 281



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 47/61 (77%), Positives = 52/61 (85%), Gaps = 1/61 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV+NSFFSGL+P EF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QY
Sbjct: 839 TPQSKGFVRNSFFSGLSPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSSQY 898

Query: 668 D 668
           D
Sbjct: 899 D 899



 Score = 63.2 bits (152), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 27/50 (54%), Positives = 41/50 (82%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+RA  +++ S +
Sbjct: 533 LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDRASLVQLLSMM 582



 Score = 50.4 bits (119), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 25/47 (53%), Positives = 32/47 (68%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPV 714
            D  FDAAF+ + D I GVSECII+G  M+VGTG  KL+++    E V
Sbjct: 1379 DHLFDAAFFMKKDKIEGVSECIILGKTMSVGTGAFKLVKSSNYDENV 1425


>gi|358393275|gb|EHK42676.1| hypothetical protein TRIATDRAFT_86460 [Trichoderma atroviride IMI
           206040]
          Length = 1463

 Score =  281 bits (719), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 138/274 (50%), Positives = 183/274 (66%), Gaps = 28/274 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIM+H AK+ P RTFR NECVC PYNADFDGDEMN+H+PQ+EEA
Sbjct: 466 DGDIVLFNRQPSLHKLSIMSHFAKIRPWRTFRLNECVCGPYNADFDGDEMNLHVPQSEEA 525

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K NL TP+NGE +IAATQDFIT  YLL+ K+ F+NR
Sbjct: 526 RAEAM--------------TLMGVKHNLATPKNGEPIIAATQDFITASYLLSSKDRFYNR 571

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                I + ++    +I             P   ++   +WTGKQIF+++++PN++ PV 
Sbjct: 572 KAFTYICTHMMDGVVNI----------DLPPPSIIKPEALWTGKQIFNVLMRPNKESPVL 621

Query: 521 ANLKTKGRAYTANEEFC----HRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL  + R Y+A    C      D+++++RNSE++ G MDKS +GSG K +VFYI+LRDF
Sbjct: 622 VNLDARCREYSARPGQCPDMDPNDAWLVIRNSEVMCGRMDKSIIGSGKKNSVFYIILRDF 681

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           G D AV AM RL+++ +  L N+GFS+G+GDV P
Sbjct: 682 GPDHAVAAMNRLTKLCARALGNQGFSLGVGDVFP 715



 Score =  200 bits (509), Expect = 5e-48,   Method: Compositional matrix adjust.
 Identities = 110/271 (40%), Positives = 157/271 (57%), Gaps = 10/271 (3%)

Query: 79  FRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCG 138
           F+G+  G  + +D V Q   +++  + LY  D  R+P+ +G LD RMGT+ K   C TC 
Sbjct: 22  FKGIKFGIQSNQDIVNQ-GVLEVSQRMLYDIDNNRSPLTNGALDLRMGTSSKSGKCGTCQ 80

Query: 139 QNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN 198
           + L  C+GHFG++ L LP FHIGY R +  ILQ++CK  TCARVLL EE+   F   LR 
Sbjct: 81  EPLKFCIGHFGHVRLALPAFHIGYLRFIQTILQNVCK--TCARVLLTEEERRSFLHDLRR 138

Query: 199 PALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEK---YKNRTKKKDA 255
           P L  + R ++ K+I E  +K   CP+CGEING ++K G+LK++H+K   YK  T +K  
Sbjct: 139 PGLDNIRRTAVYKRINEQCRKCRTCPYCGEINGQIRKVGVLKLTHDKFSAYKKSTSQKKM 198

Query: 256 IVEDLL---AEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL 312
             E  +   A ++EA K NP+++ H    + + LNPL VL  F+ I   D  LL ++   
Sbjct: 199 PPESKIAFDASFDEAKKLNPDLDKHLVRAM-EDLNPLWVLNHFKMIGPTDCELLGLDPTE 257

Query: 313 SKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
            +P   I   +  PP CIRPSV  +  S  D
Sbjct: 258 GRPEMFIWQFVPAPPVCIRPSVAQEGASTED 288



 Score =  179 bits (453), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 114/295 (38%), Positives = 165/295 (55%), Gaps = 31/295 (10%)

Query: 1143 FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTV 1199
            F  +V + IE+ +V D   +++ +DM+ ++ +HL + +  I   I R + +      +++
Sbjct: 1157 FVIDVLKAIEDEWVTDRGTVILYIDMEALQSMHLGIGVVDIAEAILRFKKLKIQPSDISI 1216

Query: 1200 SGHSFLI---------------------LKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGI 1238
              +   I                     L   + +  F  ++  +++ LP + I G    
Sbjct: 1217 GPNYIKIFVLNSWVDPDAAKKRQRSGASLTMTEETSDFLLRVNHLRRTLPKIPISGYNEA 1276

Query: 1239 NRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTI 1298
             RA+I   +    +++ +LVEG  LR  M T GV G K SSN+  E    LGIEAAR+TI
Sbjct: 1277 TRAIIQTSEQ---SEHMVLVEGYGLRACMTTEGVIGTKASSNSVMEARDVLGIEAARTTI 1333

Query: 1299 MTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDH 1358
            + EI  VM   GM ID RH  L+AD+MT KGEVLGITR GL+KM+ESVL LASFE T DH
Sbjct: 1334 VVEISAVMA--GMDIDPRHIQLLADVMTFKGEVLGITRFGLSKMRESVLQLASFEKTPDH 1391

Query: 1359 LFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA--VPRSEPVPRTLLFDN 1411
            LFDAA   +TD I GVSECIIMG  M+VGTG  ++++   +   E  P+  LF++
Sbjct: 1392 LFDAAAKMKTDRIEGVSECIIMGQTMSVGTGSFQVVRRLNIQDWEVAPKKTLFED 1446



 Score =  153 bits (387), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 98/258 (37%), Positives = 144/258 (55%), Gaps = 29/258 (11%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+NISTP+IT  L  D  ++ ARIVKGR+E+T + +V + IE+ +V D 
Sbjct: 1114 GVPRIKEIINASKNISTPVITCPLLNDKQIEAARIVKGRIEKTFVIDVLKAIEDEWVTDR 1173

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSFLI---------- 870
              +++ +DM+ ++ +HL + +  I   I R + +      +++  +   I          
Sbjct: 1174 GTVILYIDMEALQSMHLGIGVVDIAEAILRFKKLKIQPSDISIGPNYIKIFVLNSWVDPD 1233

Query: 871  -----------LKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYK 919
                       L   + +  F  ++  +++ LP + I G     RA+I   +    +++ 
Sbjct: 1234 AAKKRQRSGASLTMTEETSDFLLRVNHLRRTLPKIPISGYNEATRAIIQTSEQ---SEHM 1290

Query: 920  LLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDF 979
            +LVEG  LR  M T GV G K SSN+  E    LGIEAAR+TI+ EI  VM   GM ID 
Sbjct: 1291 VLVEGYGLRACMTTEGVIGTKASSNSVMEARDVLGIEAARTTIVVEISAVMA--GMDIDP 1348

Query: 980  RHPMLVADLMTSKGEVLG 997
            RH  L+AD+MT KGEVLG
Sbjct: 1349 RHIQLLADVMTFKGEVLG 1366



 Score =  102 bits (254), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 45/57 (78%), Positives = 51/57 (89%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NSF+SGL PTEFFFH + GREGL+DTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 841 KGFVRNSFYSGLFPTEFFFHAISGREGLIDTAVKTAETGYMSRRLMKSLEDLSTQYD 897



 Score = 70.1 bits (170), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 30/40 (75%), Positives = 34/40 (85%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            C E+Y +A +EP  AVGA+ AQSIGEPGTQMTLKTFHFAG
Sbjct: 1066 CLERYHKAHVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAG 1105



 Score = 60.5 bits (145), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 28/53 (52%), Positives = 36/53 (67%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           LM  K NL TP+NGE +IAATQDFIT  YLL+ K+ F+NR     I + ++ G
Sbjct: 532 LMGVKHNLATPKNGEPIIAATQDFITASYLLSSKDRFYNRKAFTYICTHMMDG 584



 Score = 47.8 bits (112), Expect = 0.051,   Method: Compositional matrix adjust.
 Identities = 29/71 (40%), Positives = 40/71 (56%), Gaps = 2/71 (2%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA--VPRSEPVPRTLLFDNPEF 725
            D  FDAA   +TD I GVSECIIMG  M+VGTG  ++++   +   E  P+  LF++   
Sbjct: 1390 DHLFDAAAKMKTDRIEGVSECIIMGQTMSVGTGSFQVVRRLNIQDWEVAPKKTLFEDAWA 1449

Query: 726  HFPQVYYERRR 736
               +   E RR
Sbjct: 1450 ENLKAKKELRR 1460


>gi|150951372|ref|XP_001387687.2| DNA-directed RNA polymerase III subunit C1 (RPO31) [Scheffersomyces
           stipitis CBS 6054]
 gi|149388539|gb|EAZ63664.2| DNA-directed RNA polymerase III subunit C1 (RPO31) [Scheffersomyces
           stipitis CBS 6054]
          Length = 1448

 Score =  281 bits (719), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 142/276 (51%), Positives = 188/276 (68%), Gaps = 29/276 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH+LSI++H AK+ P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 466 DGDVVLFNRQPSLHRLSILSHYAKIRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 525

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+R
Sbjct: 526 RAEAIN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDR 571

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A  +++ S +    +D+   I         P    +  ++WTGKQ+FSL++KPN+   V 
Sbjct: 572 ASLVQLLSMM--SDADVQFDIP--------PPSIFKPVMLWTGKQVFSLLIKPNKKSNVV 621

Query: 521 ANLKTKGRAYTANE-----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL  K + +   E     E    D +VI+R S++LAG MDKS LG G K +VFY +LRD
Sbjct: 622 INLDAKCKTFIPPEKGLPSEMSPNDGFVIIRGSQVLAGVMDKSLLGDGKKHSVFYTILRD 681

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           +G + A TAM R++++ + +L NRGFSIGI DVTPG
Sbjct: 682 YGPEEAATAMNRMAKLCARFLGNRGFSIGINDVTPG 717



 Score =  256 bits (654), Expect = 7e-65,   Method: Compositional matrix adjust.
 Identities = 185/508 (36%), Positives = 256/508 (50%), Gaps = 117/508 (23%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVR--DIK 1054
            G+  PV  KR  D       +  D SL   EI+ L N  L+  E      +  +R  ++ 
Sbjct: 925  GDARPVNFKRQWDHAFNITFNIKDKSLLPYEIIDLVNSILEPLE------DRLIRYDNVG 978

Query: 1055 KFL--EEFSKKESVTSHQDKVS--QPLREQILSHQDKIGHGRESNPF------------- 1097
            K L  E+F K E +  +  + +  Q LR+ +    +++   RE                 
Sbjct: 979  KILPEEDFDKIEYIDQNDAERAYYQSLRDFVTDKAEQLAQIREHRGLRTFFTRPDSEDIL 1038

Query: 1098 ----PSACKA----------------EACREKYVRAQIEPATAVGALAAQSIGEPGTQMT 1137
                 SA  A                E    KY +A++EP TAVGA+ AQSIGEPGTQMT
Sbjct: 1039 FDSDESAVNAVDQLLKISSKTIEKFLEQSLYKYSKAKVEPGTAVGAIGAQSIGEPGTQMT 1098

Query: 1138 LKTFHFAG--------------EVCE--------YIEEVFVPDD---------------- 1159
            LKTFHFAG              E+           I  V V DD                
Sbjct: 1099 LKTFHFAGVASMNVTLGVPRIKEIINASKTISTPIINSVLVNDDDEIAARVVKGRVEKTL 1158

Query: 1160 ----------------SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTVS 1200
                            +++ IK+DM  I  L LE+ ID I   I     +    G ++VS
Sbjct: 1159 LKDVAFFIEDVYKNEMAYLSIKIDMSTIEKLQLELTIDDIVTAIHNAPKLKISPGDVSVS 1218

Query: 1201 GHSFL------------ILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDV 1248
            G   +             LK   ++     +M Q+++ LP++ IKG+  I RAVI+  D 
Sbjct: 1219 GKDRVNVLATLRESKADALKNGSNANELFFRMQQLRRSLPNICIKGLPNIMRAVINIRD- 1277

Query: 1249 EGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMEN 1308
            +G  K +LLVEG  L+DVM+T G+ G K ++N+  EV++ LGIEAAR++I+ EI   M N
Sbjct: 1278 DG--KKELLVEGYGLKDVMSTDGIVGTKTTTNHVLEVFEVLGIEAARASIIKEIDYTMSN 1335

Query: 1309 HGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQT 1368
            HGMS+D RH  L+ D+MT KGEVLGITR GL+KM++SVL LASFE T+DHLFDAAF+ ++
Sbjct: 1336 HGMSVDPRHIQLLGDVMTYKGEVLGITRFGLSKMRDSVLQLASFEKTTDHLFDAAFFMKS 1395

Query: 1369 DCISGVSECIIMGLPMNVGTGLIKLLQA 1396
            D I GVSECII+G  M++GTG  KL+++
Sbjct: 1396 DKIEGVSECIILGQSMSIGTGSFKLVKS 1423



 Score =  188 bits (478), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 112/249 (44%), Positives = 157/249 (63%), Gaps = 18/249 (7%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII + L  D D   AR+VKGR+E+T L +V  +IE+V+  + 
Sbjct: 1115 GVPRIKEIINASKTISTPIINSVLVNDDDEIAARVVKGRVEKTLLKDVAFFIEDVYKNEM 1174

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSFL----------- 869
            +++ IK+DM  I  L LE+ ID I   I     +    G ++VSG   +           
Sbjct: 1175 AYLSIKIDMSTIEKLQLELTIDDIVTAIHNAPKLKISPGDVSVSGKDRVNVLATLRESKA 1234

Query: 870  -ILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLR 928
              LK   ++     +M Q+++ LP++ IKG+  I RAVI+  D +G  K +LLVEG  L+
Sbjct: 1235 DALKNGSNANELFFRMQQLRRSLPNICIKGLPNIMRAVINIRD-DG--KKELLVEGYGLK 1291

Query: 929  DVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADL 988
            DVM+T G+ G K ++N+  EV++ LGIEAAR++I+ EI   M NHGMS+D RH  L+ D+
Sbjct: 1292 DVMSTDGIVGTKTTTNHVLEVFEVLGIEAARASIIKEIDYTMSNHGMSVDPRHIQLLGDV 1351

Query: 989  MTSKGEVLG 997
            MT KGEVLG
Sbjct: 1352 MTYKGEVLG 1360



 Score =  178 bits (451), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 106/272 (38%), Positives = 148/272 (54%), Gaps = 11/272 (4%)

Query: 79  FRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCG 138
            +GL    ++ +D V Q S +++ +++LY  +  RTP   G LD RMG +     C TC 
Sbjct: 13  IKGLEFSALSAKDIVAQ-SEVEVQTRDLYDLEKGRTPKVAGALDTRMGISSNSNECATCH 71

Query: 139 QNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN 198
            NL+ C GHFG+I L LPVFH+GYF+ +I +LQ ICKN  C+ VLL E     F + LR 
Sbjct: 72  GNLASCHGHFGHIRLALPVFHVGYFKSIIQVLQCICKN--CSAVLLDENTKRQFISDLRR 129

Query: 199 PALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKC------GLLKISHEKYKNRTKK 252
           P +  L R  + KK+L+  KK   C  C  +NGVVKK         LKI H+ ++   KK
Sbjct: 130 PNIDNLRRMKILKKVLDQCKKQRRCLKCNHVNGVVKKAASGAGPAALKIVHDTFRWIGKK 189

Query: 253 KDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMN-AE 311
                E    E+++ +  NPE+E   K  +   LNPL+ L LF+ I   D  L  ++ A 
Sbjct: 190 PTPEKEYWDKEFDQVLSRNPELEKFAK-RVYDDLNPLKTLNLFKQITPSDCELFGLDPAR 248

Query: 312 LSKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
             +P   I   L  PP CIRPSV+ D +S+ D
Sbjct: 249 GGRPEMYIWRYLPAPPVCIRPSVMMDSQSNED 280



 Score =  100 bits (249), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 47/61 (77%), Positives = 52/61 (85%), Gaps = 1/61 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV+NSF+SGLTP EF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QY
Sbjct: 838 TPQSKGFVRNSFYSGLTPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSSQY 897

Query: 668 D 668
           D
Sbjct: 898 D 898



 Score = 63.2 bits (152), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 27/50 (54%), Positives = 41/50 (82%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+RA  +++ S +
Sbjct: 532 LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDRASLVQLLSMM 581



 Score = 50.4 bits (119), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 22/40 (55%), Positives = 31/40 (77%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA 707
            D  FDAAF+ ++D I GVSECII+G  M++GTG  KL+++
Sbjct: 1384 DHLFDAAFFMKSDKIEGVSECIILGQSMSIGTGSFKLVKS 1423


>gi|358060144|dbj|GAA94203.1| hypothetical protein E5Q_00851 [Mixia osmundae IAM 14324]
          Length = 1436

 Score =  281 bits (718), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 140/276 (50%), Positives = 184/276 (66%), Gaps = 29/276 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+D+VLFNRQPSLHKLSIM+HR KV P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 480 DDDIVLFNRQPSLHKLSIMSHRVKVRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 539

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EA          AH    LM+ K NLVTPRNGE +IAATQDFITG +LL++++ F NR
Sbjct: 540 RTEA----------AH----LMSIKQNLVTPRNGEPIIAATQDFITGAFLLSRRDKFLNR 585

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I   L     D+             P   +R   +WTGKQ+FS++++P+    + 
Sbjct: 586 AEIGQILCYLTDAEGDL----------ELPPPTILRPKQLWTGKQVFSVLMRPSSRSSIC 635

Query: 521 ANLKTKGRAYTA-----NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL+ K R + A       +    D Y+++ NS ++ G++DK+T+G G K +VF +LLRD
Sbjct: 636 VNLEAKCRTFEAPPAGYAPDMSPNDGYLVIENSVIMCGALDKATVGDGKKNSVFGVLLRD 695

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           +G D A  AM RLS++ + +L N+GFSIGI DVTPG
Sbjct: 696 YGADAAAQAMNRLSKLCARWLTNQGFSIGISDVTPG 731



 Score =  233 bits (593), Expect = 9e-58,   Method: Compositional matrix adjust.
 Identities = 174/491 (35%), Positives = 244/491 (49%), Gaps = 97/491 (19%)

Query: 997  GNGTPVELKRLLDDIIAK-NSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKK 1055
            G+G+PVE  R    I A    +++   L    IL L++  L +  F      +F   IK 
Sbjct: 939  GDGSPVEFVRTWQHIRATVPHTKTSKPLMPYAILELTDRLLATDRFDMTRHSDFPAQIKA 998

Query: 1056 F------------------LEEFSKKESVTSHQD--KVSQPLREQILSHQDKIGHGRESN 1095
            F                  +E   K E      D   ++ P    ++  + K    + + 
Sbjct: 999  FVVKHIVAPAARFRRAYGMIEALEKHEEWDDETDLTGLAGPKAVHVVDQKTKTTEDQIAR 1058

Query: 1096 PFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEV-------- 1147
                      C EKY R+ +EP TAVGA+ AQSIGEPGTQMTLKTFHFAG          
Sbjct: 1059 FL------LLCWEKYARSMVEPGTAVGAIGAQSIGEPGTQMTLKTFHFAGVASMNVTLGV 1112

Query: 1148 -------------------CEYIEEVFVPDDSFILIKLDMDRIRL--------------- 1173
                                E + ++   + S  +IK  +++  L               
Sbjct: 1113 PRIKEIINASKVISTPIITAELLSDLAQSEASARVIKARIEKTYLGEIASQMAPTVTATQ 1172

Query: 1174 --LHLEVDIDSI-RYCIERT-RGISGHLTV--------------SGHSFLILKPKDSSKS 1215
              +++++D+D++ R  +E T   I+  +                SG   + L   D S+S
Sbjct: 1173 AYVNIQIDMDTVSRLQLEVTPHSIAASILAAKLKLGKGNVSASHSGRIRIYLPDDDGSES 1232

Query: 1216 FNSKMYQMK------QLLPSVVIKGVQGINRAVIHEEDVEGVTKYK-LLVEGDNLRDVMA 1268
             +S  +++       +LLP+VV+KGV   +RAVI  +  +G +K K LLVEG+ LR+VM 
Sbjct: 1233 TSSAPHKLDRLNTLCRLLPNVVVKGVGACSRAVIQVK--QGSSKEKHLLVEGNGLREVMT 1290

Query: 1269 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK 1328
            T GV G + +SN+  EV K LGIEAAR TI+ EI   M  HG+S+D RH  L+ D+MT K
Sbjct: 1291 TDGVDGRRVTSNHIMEVVKVLGIEAARQTIINEIGGTMGAHGLSVDPRHLGLLGDVMTCK 1350

Query: 1329 GEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPM-NVG 1387
            GEVLGITR G+AK+K+S L LASFE T+DHLFDAA Y + D I G+SE IIMGLP  N G
Sbjct: 1351 GEVLGITRFGVAKLKDSTLMLASFEKTTDHLFDAAVYSRQDDIDGISESIIMGLPANNCG 1410

Query: 1388 TGLIKLLQAVP 1398
            T L  ++   P
Sbjct: 1411 TSLPSVVSKRP 1421



 Score =  194 bits (494), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 103/232 (44%), Positives = 134/232 (57%), Gaps = 5/232 (2%)

Query: 112 QRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQ 171
           +R P P G+LDRR+G   K++NC TCG+   +CVGH+GYI L +P+FH GYFR  I ILQ
Sbjct: 77  EREPKPGGVLDRRLGIADKKSNCETCGERAKECVGHYGYIKLTVPLFHTGYFRKTIEILQ 136

Query: 172 SICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEING 231
            ICK   C+R LL +++      KLR P L    R    K+++ T KK   CPHCG ING
Sbjct: 137 VICK--VCSRTLLDDDQQRAALRKLRRPNLDNTQRDRFLKEVVATAKKALNCPHCGSING 194

Query: 232 VVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEV 291
            VKK G LKI HEKY  R +K     E     ++ A++   E++          LNPL  
Sbjct: 195 TVKKAGSLKIIHEKY--RARKMKPAREAFEQSFDHALQDTKELKGSISRAQ-DDLNPLRA 251

Query: 292 LQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
           L+LFE I   D  LL ++A +S+P   I   LLVPP  IRPSV  D  ++ D
Sbjct: 252 LKLFECITNPDCELLGLDATISRPETFIWQYLLVPPVTIRPSVQQDDATNED 303



 Score =  174 bits (440), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 114/247 (46%), Positives = 150/247 (60%), Gaps = 15/247 (6%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLD--YARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPRIKEIINAS+ ISTPIITA L  D       AR++K R+E+T LGE+   +      
Sbjct: 1111 GVPRIKEIINASKVISTPIITAELLSDLAQSEASARVIKARIEKTYLGEIASQMAPTVTA 1170

Query: 822  DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSG-HSFLI---LKPKDSS 877
              +++ I++DMD +  L LEV   SI   I   +   G   VS  HS  I   L   D S
Sbjct: 1171 TQAYVNIQIDMDTVSRLQLEVTPHSIAASILAAKLKLGKGNVSASHSGRIRIYLPDDDGS 1230

Query: 878  KSFNSKMYQMKQL------LPSVVIKGVQGINRAVIHEEDVEGVTKYK-LLVEGDNLRDV 930
            +S +S  +++ +L      LP+VV+KGV   +RAVI  +  +G +K K LLVEG+ LR+V
Sbjct: 1231 ESTSSAPHKLDRLNTLCRLLPNVVVKGVGACSRAVIQVK--QGSSKEKHLLVEGNGLREV 1288

Query: 931  MATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMT 990
            M T GV G + +SN+  EV K LGIEAAR TI+ EI   M  HG+S+D RH  L+ D+MT
Sbjct: 1289 MTTDGVDGRRVTSNHIMEVVKVLGIEAARQTIINEIGGTMGAHGLSVDPRHLGLLGDVMT 1348

Query: 991  SKGEVLG 997
             KGEVLG
Sbjct: 1349 CKGEVLG 1355



 Score =  107 bits (267), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 47/61 (77%), Positives = 55/61 (90%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV+NSF+SGLT TEFFFH + GREGLVDTAVKTAETGYMQRRL+K+LEDL  +YD+
Sbjct: 854 PSKGFVRNSFYSGLTATEFFFHAISGREGLVDTAVKTAETGYMQRRLMKALEDLSTRYDL 913

Query: 670 S 670
           S
Sbjct: 914 S 914



 Score = 65.1 bits (157), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 29/46 (63%), Positives = 38/46 (82%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRI 67
           LM+ K NLVTPRNGE +IAATQDFITG +LL++++ F NRA+  +I
Sbjct: 546 LMSIKQNLVTPRNGEPIIAATQDFITGAFLLSRRDKFLNRAEIGQI 591


>gi|116201487|ref|XP_001226555.1| hypothetical protein CHGG_08628 [Chaetomium globosum CBS 148.51]
 gi|88177146|gb|EAQ84614.1| hypothetical protein CHGG_08628 [Chaetomium globosum CBS 148.51]
          Length = 1290

 Score =  281 bits (718), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 138/275 (50%), Positives = 185/275 (67%), Gaps = 29/275 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DNDVVLFNRQPSLHKLSIM+H AK+ P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 340 DNDVVLFNRQPSLHKLSIMSHLAKIRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 399

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K NLVTP+NGE +IAATQDFIT  YLL+ K+ FF+R
Sbjct: 400 RAEAIN--------------LMGVKHNLVTPKNGEPIIAATQDFITAAYLLSSKDIFFDR 445

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A    + + ++   + +             P   ++   +WTGKQIF+++++PN++ PV 
Sbjct: 446 ASFTYVCTQMLLGDTHL----------ELPPPAIIKPRALWTGKQIFNVLMRPNKESPVL 495

Query: 521 ANLKTKGRAYTANE-----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL+ K + +   +     +    D+++++RNSE++ G MDK+T+G G K +VFY++LRD
Sbjct: 496 VNLEAKNKVFFKKKDGQIPDMDIDDAFLVVRNSEVMCGRMDKATVGGGKKNSVFYVILRD 555

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           FG D A  AM RLS++ +  L  RGFSIG+GDV P
Sbjct: 556 FGPDHAAVAMNRLSKLCARTLSLRGFSIGVGDVWP 590



 Score =  104 bits (260), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 72/240 (30%), Positives = 118/240 (49%), Gaps = 53/240 (22%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+I+  L+   D+  AR+VKGR+E+T + ++  ++++ ++PD 
Sbjct: 1047 GVPRIKEIINASKTISTPVISCELENRVDIKAARVVKGRIEKTYVSDIISFVDDEWLPDV 1106

Query: 824  SFILIKLDMD-------------------RIRLLHLEVDIDSIRYCIERTRGI------- 857
            + I++++D+                    R + L L+V+ + +R   +R   I       
Sbjct: 1107 AKIVLQVDLQALSDMQLGISMKDIADAIVRAKKLKLKVEPEDLRIGRDRVEVIVRNTWQD 1166

Query: 858  ----------------SGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQG 901
                             GH+  S          +S+  F  ++  +K++LP VVI G   
Sbjct: 1167 VTAARKAARVRAAAVEKGHIMSSALD-------ESAADFQLRVNFLKRMLPQVVISGYPD 1219

Query: 902  INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTY-EVYKTLGIEAARS 960
              RA+I  +D     ++ +LVEG  LR  M T GV G KC +N+   +    LGI   R+
Sbjct: 1220 AARAIIQTDD---KNEHMVLVEGYGLRACMTTEGVIGTKCVTNSVMRKCRDVLGIRGGRA 1276



 Score =  103 bits (256), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 45/59 (76%), Positives = 51/59 (86%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSF++GL PTEF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 714 PSKGFVRNSFYTGLVPTEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSTQYD 772



 Score = 69.7 bits (169), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 30/42 (71%), Positives = 35/42 (83%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            + C  KY +A++EP  AVGA+ AQSIGEPGTQMTLKTFHFAG
Sbjct: 997  QMCLHKYKKARVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAG 1038



 Score = 64.3 bits (155), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 33/82 (40%), Positives = 47/82 (57%), Gaps = 1/82 (1%)

Query: 262 AEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
           A +N+A K+ PE+E H +  + + LNPL+VL LF AI   D  LL ++    +P   +  
Sbjct: 80  ASFNQAKKYTPELEKHTRKAM-EDLNPLKVLNLFRAISQTDCELLGLDPSEGRPDMFLWQ 138

Query: 322 RLLVPPNCIRPSVISDLKSDND 343
            L  PP CIRPSV  +  S+ D
Sbjct: 139 YLPAPPICIRPSVAQENASNED 160



 Score = 64.3 bits (155), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 29/53 (54%), Positives = 38/53 (71%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           LM  K NLVTP+NGE +IAATQDFIT  YLL+ K+ FF+RA    + + ++ G
Sbjct: 406 LMGVKHNLVTPKNGEPIIAATQDFITAAYLLSSKDIFFDRASFTYVCTQMLLG 458



 Score = 50.8 bits (120), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 31/87 (35%), Positives = 47/87 (54%), Gaps = 4/87 (4%)

Query: 1211 DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATY 1270
            +S+  F  ++  +K++LP VVI G     RA+I  +D     ++ +LVEG  LR  M T 
Sbjct: 1193 ESAADFQLRVNFLKRMLPQVVISGYPDAARAIIQTDDK---NEHMVLVEGYGLRACMTTE 1249

Query: 1271 GVKGVKCSSNNTY-EVYKTLGIEAARS 1296
            GV G KC +N+   +    LGI   R+
Sbjct: 1250 GVIGTKCVTNSVMRKCRDVLGIRGGRA 1276


>gi|358385218|gb|EHK22815.1| hypothetical protein TRIVIDRAFT_28982 [Trichoderma virens Gv29-8]
          Length = 1465

 Score =  281 bits (718), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 138/274 (50%), Positives = 183/274 (66%), Gaps = 28/274 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIM+H AK+ P RTFR NECVC PYNADFDGDEMN+H+PQ+EEA
Sbjct: 466 DGDVVLFNRQPSLHKLSIMSHLAKIRPWRTFRLNECVCGPYNADFDGDEMNLHVPQSEEA 525

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL TP+NGE +IAATQDFIT  YLL+ K+ F+NR
Sbjct: 526 RAEAI--------------TLMGVKNNLATPKNGEPIIAATQDFITASYLLSSKDRFYNR 571

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                I + ++   + +             P   ++   +WTGKQIF+++++PN+  PV 
Sbjct: 572 KTFTYICTHMMDGVTHL----------DLPPPSIIKPEALWTGKQIFNVLMRPNKQSPVL 621

Query: 521 ANLKTKGRAYTANEEFC----HRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL  + R Y+A    C      D+++++RNSE++ G MDKS +GSG K +VFYI+LRDF
Sbjct: 622 VNLDARCREYSARPGQCPDMDPNDAWLVIRNSEVMCGRMDKSIIGSGKKNSVFYIILRDF 681

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           G D AV AM RL+++ +  L N+GFS+G+GDV P
Sbjct: 682 GPDHAVMAMNRLTKLCARQLGNQGFSLGVGDVFP 715



 Score =  199 bits (505), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 111/271 (40%), Positives = 156/271 (57%), Gaps = 10/271 (3%)

Query: 79  FRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCG 138
           F+G+  G  + +D V Q   +++  + LY  D  R+P+ +G LD RMGT+ K   C TC 
Sbjct: 22  FKGIKFGIQSNQDIVNQ-GVLEVSQRMLYDIDNNRSPLINGALDLRMGTSSKSGKCGTCQ 80

Query: 139 QNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN 198
           + L  C+GHFG++ L LP FHIGY R +  ILQ++CK  TCA+VLL EE+   F   LR 
Sbjct: 81  EPLKFCIGHFGHVRLALPAFHIGYLRFIQTILQNVCK--TCAKVLLTEEERRSFLQDLRR 138

Query: 199 PALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEK---YKNRTKKKDA 255
           P L  + R  + KKI E  +K   CP+CGEING ++K G+LK++H+K   YK  T +K  
Sbjct: 139 PGLDNIRRTQICKKINEQCRKCRQCPYCGEINGQIRKVGVLKLTHDKFSAYKKSTSQKKL 198

Query: 256 IVEDLL---AEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL 312
             E  L   A ++EA K NP+++ H    + + LNPL VL  F+ I   D  LL ++   
Sbjct: 199 PPESKLAFDASFDEAKKLNPDLDKHLVRAM-EDLNPLWVLNHFKMITPTDCELLGLDPSE 257

Query: 313 SKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
            +P   I   +  PP CIRPSV  +  S  D
Sbjct: 258 GRPEMFIWQFVPAPPVCIRPSVAQEGASTED 288



 Score =  174 bits (442), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 113/292 (38%), Positives = 161/292 (55%), Gaps = 31/292 (10%)

Query: 1146 EVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLT------- 1198
            +V + IE+ +V D   I++ +DM+ ++ +HL + +  I   I + + +    T       
Sbjct: 1160 DVLKAIEDEWVSDRGTIVLYIDMEALQNMHLGIGVVDIAEAILKFKKLKIQPTDISVGPN 1219

Query: 1199 -----------------VSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRA 1241
                                 S   L   + +  F  ++  ++++LP V I G     RA
Sbjct: 1220 YIKIYVLNSWVDPDAAKKRQRSLASLTLTEEAPDFLLRVNHLRRMLPKVPISGYNEATRA 1279

Query: 1242 VIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTE 1301
            +I   +    +++ +LVEG  LR  M T GV G K  SN+  E    LGIEAAR+TI+ E
Sbjct: 1280 IIQTSET---SEHTVLVEGYGLRACMTTEGVIGTKSRSNSVMEARDVLGIEAARTTIVDE 1336

Query: 1302 IKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFD 1361
            I  VM   GM ID RH  L+AD+MT KGEVLGITR GL+KM+ESVL LASFE T DHLF+
Sbjct: 1337 ISSVMA--GMDIDPRHIQLLADVMTFKGEVLGITRFGLSKMRESVLQLASFEKTPDHLFE 1394

Query: 1362 AAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA--VPRSEPVPRTLLFDN 1411
            AA   +TD I GVSECIIMG  M+VGTG  ++++   +   E  P+  LF++
Sbjct: 1395 AAAGMKTDRIEGVSECIIMGQTMSVGTGSFQVVRRLNIQEWEVKPKKTLFED 1446



 Score =  151 bits (382), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 98/258 (37%), Positives = 141/258 (54%), Gaps = 29/258 (11%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+NISTP+IT  L  D  ++ A+IVKGR+E+T + +V + IE+ +V D 
Sbjct: 1114 GVPRIKEIINASKNISTPVITCPLLNDKQIEAAKIVKGRIEKTYVIDVLKAIEDEWVSDR 1173

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLT--------------------- 862
              I++ +DM+ ++ +HL + +  I   I + + +    T                     
Sbjct: 1174 GTIVLYIDMEALQNMHLGIGVVDIAEAILKFKKLKIQPTDISVGPNYIKIYVLNSWVDPD 1233

Query: 863  ---VSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYK 919
                   S   L   + +  F  ++  ++++LP V I G     RA+I   +    +++ 
Sbjct: 1234 AAKKRQRSLASLTLTEEAPDFLLRVNHLRRMLPKVPISGYNEATRAIIQTSET---SEHT 1290

Query: 920  LLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDF 979
            +LVEG  LR  M T GV G K  SN+  E    LGIEAAR+TI+ EI  VM   GM ID 
Sbjct: 1291 VLVEGYGLRACMTTEGVIGTKSRSNSVMEARDVLGIEAARTTIVDEISSVMA--GMDIDP 1348

Query: 980  RHPMLVADLMTSKGEVLG 997
            RH  L+AD+MT KGEVLG
Sbjct: 1349 RHIQLLADVMTFKGEVLG 1366



 Score =  102 bits (253), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 45/57 (78%), Positives = 51/57 (89%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NSF+SGL PTEFFFH + GREGL+DTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 841 KGFVRNSFYSGLFPTEFFFHAISGREGLIDTAVKTAETGYMSRRLMKSLEDLSTQYD 897



 Score = 70.1 bits (170), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 30/40 (75%), Positives = 34/40 (85%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            C E+Y +A +EP  AVGA+ AQSIGEPGTQMTLKTFHFAG
Sbjct: 1066 CLERYHKAHVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAG 1105



 Score = 60.8 bits (146), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 28/53 (52%), Positives = 37/53 (69%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           LM  K+NL TP+NGE +IAATQDFIT  YLL+ K+ F+NR     I + ++ G
Sbjct: 532 LMGVKNNLATPKNGEPIIAATQDFITASYLLSSKDRFYNRKTFTYICTHMMDG 584



 Score = 47.4 bits (111), Expect = 0.054,   Method: Compositional matrix adjust.
 Identities = 28/71 (39%), Positives = 41/71 (57%), Gaps = 2/71 (2%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA--VPRSEPVPRTLLFDNPEF 725
            D  F+AA   +TD I GVSECIIMG  M+VGTG  ++++   +   E  P+  LF++   
Sbjct: 1390 DHLFEAAAGMKTDRIEGVSECIIMGQTMSVGTGSFQVVRRLNIQEWEVKPKKTLFEDAWA 1449

Query: 726  HFPQVYYERRR 736
               +   ERR+
Sbjct: 1450 ETVKAKKERRK 1460


>gi|171677863|ref|XP_001903882.1| hypothetical protein [Podospora anserina S mat+]
 gi|170937000|emb|CAP61658.1| unnamed protein product [Podospora anserina S mat+]
          Length = 1521

 Score =  281 bits (718), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 138/285 (48%), Positives = 186/285 (65%), Gaps = 30/285 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND+VLFNRQPSLHKLSIM+H AK+ P RTFR NECVC+PYNADFDGDEMN+H+PQTEEA
Sbjct: 478 DNDIVLFNRQPSLHKLSIMSHYAKIRPWRTFRLNECVCSPYNADFDGDEMNLHVPQTEEA 537

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL TP+NGE +IAATQDFIT  YLL+ K+ F++R
Sbjct: 538 RAEAIN--------------LMGVKNNLCTPKNGEPIIAATQDFITAAYLLSGKDRFYDR 583

Query: 461 AQTMRIAST-LIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           +    I +  L+ DT           +    P   ++   +WTGKQIF+++++PN++ PV
Sbjct: 584 SSFTYICTQMLLGDT-----------YLELPPPAILKPKALWTGKQIFNVMMRPNKESPV 632

Query: 520 NANLKTKGRAYTANE----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
             NL  K + Y        +    DS++++RNSE++ G MDKST+G G K +VFY++LRD
Sbjct: 633 LVNLDAKNKVYNKGNLQPPDMDIDDSFLVVRNSEVICGRMDKSTVGEGKKNSVFYVILRD 692

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSFF 620
           +G D A   M RL+++ +  L  RGFSIG+GDV P Q   ++   
Sbjct: 693 YGADYAAATMNRLAKLCARSLTLRGFSIGVGDVFPSQALTEHKLM 737



 Score =  165 bits (418), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 95/191 (49%), Positives = 127/191 (66%), Gaps = 5/191 (2%)

Query: 1206 ILKPKD-SSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLR 1264
            +  P D S+  F  ++  +K++LP V I G     RA+I+ +     + + +LVEG  LR
Sbjct: 1294 VANPGDESAADFQLRVNFLKRMLPEVPIAGHPETTRAIINVD--SKTSAHTVLVEGYGLR 1351

Query: 1265 DVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADL 1324
              M T GV G KC +N+  E    LGIEAAR+TI  EI+ VM +  M+ID RH  L+AD+
Sbjct: 1352 ACMTTEGVVGTKCLTNSVMECRDVLGIEAARTTIAFEIQQVMGD--MNIDPRHMELLADV 1409

Query: 1325 MTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPM 1384
            MT KG++LGITR GLAKM++SVL LASFE T DHLFDAA   +TD I GVSECIIMG  M
Sbjct: 1410 MTYKGDILGITRFGLAKMRDSVLQLASFEKTPDHLFDAAAGMKTDRILGVSECIIMGQTM 1469

Query: 1385 NVGTGLIKLLQ 1395
            ++GTG  ++++
Sbjct: 1470 SIGTGSFQVVR 1480



 Score =  147 bits (371), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 95/274 (34%), Positives = 145/274 (52%), Gaps = 14/274 (5%)

Query: 79  FRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRM-GTN--QKEANCT 135
           F+ L  G  + +D +  Q  +++    LY  +  R P  HG LD R+ GT+  + +A C 
Sbjct: 26  FKALKFGIQSTQD-ILNQGVLEVSDNLLYDVENNRAPFKHGPLDPRLQGTSSPKPDAKCH 84

Query: 136 TCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAK 195
           TC Q+L  C GHFG++ LPLPVFHIGY + +   LQ+ICK  +C+R+LL  E+   F   
Sbjct: 85  TCHQDLMGCPGHFGHVKLPLPVFHIGYLKYIQATLQNICK--SCSRILLTNEERRRFLRS 142

Query: 196 LRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEK---YKNRTKK 252
           LR      + R ++ K+I E  +KV  C HCG++ G ++K   +K+ H+K   Y   T +
Sbjct: 143 LRREQ-DNMARTAVLKRINEQCRKVRNCYHCGDLQGTIRKLSCMKLVHDKFVAYNKSTAQ 201

Query: 253 KDAIVEDLL---AEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMN 309
           K    E  +   A +  A     E+  H +  +   ++PL+VL LF+ I   D  LL ++
Sbjct: 202 KKVAPESKIEFDASFESAKAHFAELGKHTRRAM-DDMHPLKVLNLFKEINSVDCELLGLD 260

Query: 310 AELSKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
               +P   +   L  PP CIRPSV  +  S+ D
Sbjct: 261 PAEGRPEMFLWRYLPAPPLCIRPSVAQESASNED 294



 Score =  135 bits (340), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 98/294 (33%), Positives = 152/294 (51%), Gaps = 41/294 (13%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+IT  L+   D+  AR VK R+E+T + ++ +Y+++V++ D 
Sbjct: 1153 GVPRIKEIINASKTISTPVITCVLENTKDVSAARAVKHRIEKTYIKDILDYVDDVWLQDV 1212

Query: 824  SFILIKLDMDRIRLLH---------------------------LEVDIDSIRYCIERTRG 856
            + I+++L+ D +  L                            L+V+ + I   +  T  
Sbjct: 1213 AKIVLRLEKDGLENLEQIGITTTDIADAIVKAKKLKLKIEPEDLKVNKNVIEVLVHNTWQ 1272

Query: 857  ISGHLTVSG--------HSFLILKPKD-SSKSFNSKMYQMKQLLPSVVIKGVQGINRAVI 907
             +     +             +  P D S+  F  ++  +K++LP V I G     RA+I
Sbjct: 1273 DATAARKAARQRAAALEKGLTVANPGDESAADFQLRVNFLKRMLPEVPIAGHPETTRAII 1332

Query: 908  HEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIK 967
            + +     + + +LVEG  LR  M T GV G KC +N+  E    LGIEAAR+TI  EI+
Sbjct: 1333 NVD--SKTSAHTVLVEGYGLRACMTTEGVVGTKCLTNSVMECRDVLGIEAARTTIAFEIQ 1390

Query: 968  LVMENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDP 1021
             VM +  M+ID RH  L+AD+MT KG++LG  T   L ++ D ++   S    P
Sbjct: 1391 QVMGD--MNIDPRHMELLADVMTYKGDILGI-TRFGLAKMRDSVLQLASFEKTP 1441



 Score = 99.8 bits (247), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 44/58 (75%), Positives = 50/58 (86%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV+NSF++GL PTEF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 852 AKGFVKNSFYTGLHPTEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSTQYD 909



 Score = 74.7 bits (182), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/42 (78%), Positives = 36/42 (85%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            E C EKY +AQ+EP  AVGA+ AQSIGEPGTQMTLKTFHFAG
Sbjct: 1103 ELCLEKYKKAQVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAG 1144



 Score = 60.1 bits (144), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 27/53 (50%), Positives = 38/53 (71%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           LM  K+NL TP+NGE +IAATQDFIT  YLL+ K+ F++R+    I + ++ G
Sbjct: 544 LMGVKNNLCTPKNGEPIIAATQDFITAAYLLSGKDRFYDRSSFTYICTQMLLG 596



 Score = 43.1 bits (100), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 21/39 (53%), Positives = 28/39 (71%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  FDAA   +TD I GVSECIIMG  M++GTG  ++++
Sbjct: 1442 DHLFDAAAGMKTDRILGVSECIIMGQTMSIGTGSFQVVR 1480


>gi|296827068|ref|XP_002851111.1| DNA-directed RNA polymerase III largest subunit [Arthroderma otae
           CBS 113480]
 gi|238838665|gb|EEQ28327.1| DNA-directed RNA polymerase III largest subunit [Arthroderma otae
           CBS 113480]
          Length = 1443

 Score =  280 bits (717), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 134/280 (47%), Positives = 182/280 (65%), Gaps = 28/280 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++H  KV PHRTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 469 DGDIVLFNRQPSLHKLSILSHFVKVRPHRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 528

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R+EA+               LM  K+NL TP+NG  +IAA QDFIT  YLL+ K+ FF+R
Sbjct: 529 RSEAME--------------LMGVKNNLATPKNGAPIIAAIQDFITAAYLLSSKDNFFDR 574

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
               +I  +++  ++ +             P   ++  ++WTGKQ+FS++++PN+D PV 
Sbjct: 575 KTFTQICLSMLDSSTRL----------ELPPPATLKPQMLWTGKQVFSVLMRPNKDSPVK 624

Query: 521 ANLKTKGRAYT----ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL    R +        + C  D ++ +RNSE+L G  DKST+G G K N+F+++ RDF
Sbjct: 625 VNLDAACRQFKRVKDQPRDLCENDGWLCIRNSEMLCGVADKSTIGDGRKDNIFFVIQRDF 684

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           G   A  AM RLS++++ +L N+GFSIGI DV PG G V+
Sbjct: 685 GPAAAAEAMNRLSKLSARWLTNKGFSIGITDVYPGTGLVK 724



 Score =  221 bits (562), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 172/493 (34%), Positives = 238/493 (48%), Gaps = 109/493 (22%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSK----------------- 1039
             +  PV  +R      +    R+D  LSA EI+AL  E L  +                 
Sbjct: 926  ASAKPVHFERTFTHAESTTYDRNDRGLSADEIMALCEELLAPERKKLARFDLLGNTLPYT 985

Query: 1040 ---EFLQDTSENFVRDIKKFLEEF--SKKESVTSHQDKVSQPLREQILSHQDKIGHGRES 1094
               +F  D  E+  RD    +EEF  +K E + S   + S+   +   +H  K+   R  
Sbjct: 986  AENDFATDQWES-NRDFLSSIEEFVANKAEQLRSIDGEESKG--QMAFTHTGKLS-ARTL 1041

Query: 1095 NPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHF----------- 1143
              F ++C      +KY+RA +EP  ++GA+ AQSIGEPGTQMTLKTFHF           
Sbjct: 1042 KAFIASC-----LDKYMRAHVEPGHSIGAIGAQSIGEPGTQMTLKTFHFAGVAGMSITQG 1096

Query: 1144 ------------------------------AGEVCE-------------YIEEVFVPDDS 1160
                                          A E+ +             YIEE+     S
Sbjct: 1097 VPRIKEIINASKEISTPIITCELTNKTDMRAAEIVKGRIEKLFLKDIVYYIEEIRSESTS 1156

Query: 1161 FILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISG------------HLTV------SGH 1202
            FI IK+D   I  L LE+ +  I   I++ +                H+ V      +G 
Sbjct: 1157 FIKIKVDFSTIDKLQLEITLPQILLAIKKHKAFKAADLRFQTYHSHIHIYVDEGASMAGV 1216

Query: 1203 SFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDN 1262
            S   LK   S      ++  ++++LP++ + G     RAVI     E V    LLVEG  
Sbjct: 1217 SVSELKITGSDPYI--RINYLRRILPNIQVFGYPDCARAVIRVG--EKVATNILLVEGYG 1272

Query: 1263 LRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVA 1322
            LR  M T GV G +  +N+  E+   LGIEAAR+TI+ EI  VM   GMSID RH  L+A
Sbjct: 1273 LRACMTTDGVDGHRTRTNHIMEMRDVLGIEAARTTIIDEISSVMS--GMSIDPRHMQLLA 1330

Query: 1323 DLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGL 1382
            D+MT KGEVLGITR GLAK+++SVL LASFE T+DHLFDA   G+ D + GVSECIIMG 
Sbjct: 1331 DVMTYKGEVLGITRFGLAKIRDSVLQLASFEKTADHLFDAGGAGRRDAVQGVSECIIMGK 1390

Query: 1383 PMNVGTGLIKLLQ 1395
             +++GTG +++++
Sbjct: 1391 TISLGTGSMEVVR 1403



 Score =  176 bits (447), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 102/267 (38%), Positives = 150/267 (56%), Gaps = 12/267 (4%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G ++ +D +  Q+H++I  + L+  D  R    +G +D R+G + K   C TCG +L +C
Sbjct: 29  GVLSNQD-IISQAHVEISDRKLFDLDNNRAVARNGPMDPRLGISNKSDTCETCGGDLQEC 87

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFGY+ L LP FH+GYF+  I ILQ ICK+  C+++LL E++   +  +LR P L  L
Sbjct: 88  NGHFGYVRLVLPAFHVGYFKRTIEILQDICKD--CSKILLPEDERRSYLKELRRPGLDNL 145

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKC--GLLKISHEKYK----NRTKKKDAIVE 258
            R  + K+I    +K  VC +C  ING VKK   G LKI H+K++    + + KK     
Sbjct: 146 RRMQINKRINVRCRKTPVCYYCNAINGTVKKASTGALKIVHDKFRAFNASLSAKKIPPPS 205

Query: 259 DLLAE--YNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPS 316
            L  +  + EA K NP+IE H +  +   LNPL VL+LF  I  ED  LL +N + ++P 
Sbjct: 206 KLAFDRSFEEAKKSNPDIEKHYR-RVFDDLNPLRVLKLFRRISDEDCELLSLNVDEARPE 264

Query: 317 DLILTRLLVPPNCIRPSVISDLKSDND 343
             +   +  PP  IRPSV  +  S  D
Sbjct: 265 YFLWQFIPAPPVPIRPSVGQEGASTED 291



 Score =  154 bits (388), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 107/252 (42%), Positives = 139/252 (55%), Gaps = 24/252 (9%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIIT  L   TD+  A IVKGR+E+  L ++  YIEE+     
Sbjct: 1096 GVPRIKEIINASKEISTPIITCELTNKTDMRAAEIVKGRIEKLFLKDIVYYIEEIRSEST 1155

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISG------------HLTV------SG 865
            SFI IK+D   I  L LE+ +  I   I++ +                H+ V      +G
Sbjct: 1156 SFIKIKVDFSTIDKLQLEITLPQILLAIKKHKAFKAADLRFQTYHSHIHIYVDEGASMAG 1215

Query: 866  HSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD 925
             S   LK   S      ++  ++++LP++ + G     RAVI     E V    LLVEG 
Sbjct: 1216 VSVSELKITGSDPYI--RINYLRRILPNIQVFGYPDCARAVIRVG--EKVATNILLVEGY 1271

Query: 926  NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 985
             LR  M T GV G +  +N+  E+   LGIEAAR+TI+ EI  VM   GMSID RH  L+
Sbjct: 1272 GLRACMTTDGVDGHRTRTNHIMEMRDVLGIEAARTTIIDEISSVMS--GMSIDPRHMQLL 1329

Query: 986  ADLMTSKGEVLG 997
            AD+MT KGEVLG
Sbjct: 1330 ADVMTYKGEVLG 1341



 Score =  103 bits (258), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 46/58 (79%), Positives = 51/58 (87%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV+NSFFSGLTPTEF FH M GREGL+DTAVKTAETGYM RRL+KSLEDL  +YD
Sbjct: 842 AKGFVRNSFFSGLTPTEFLFHAMSGREGLIDTAVKTAETGYMSRRLMKSLEDLSTRYD 899



 Score = 55.5 bits (132), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 25/51 (49%), Positives = 35/51 (68%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLI 72
           LM  K+NL TP+NG  +IAA QDFIT  YLL+ K+ FF+R    +I  +++
Sbjct: 535 LMGVKNNLATPKNGAPIIAAIQDFITAAYLLSSKDNFFDRKTFTQICLSML 585



 Score = 42.4 bits (98), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 18/39 (46%), Positives = 28/39 (71%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  FDA   G+ D + GVSECIIMG  +++GTG +++++
Sbjct: 1365 DHLFDAGGAGRRDAVQGVSECIIMGKTISLGTGSMEVVR 1403


>gi|452844664|gb|EME46598.1| hypothetical protein DOTSEDRAFT_70566 [Dothistroma septosporum
           NZE10]
          Length = 1491

 Score =  280 bits (717), Expect = 4e-72,   Method: Compositional matrix adjust.
 Identities = 138/279 (49%), Positives = 186/279 (66%), Gaps = 26/279 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++HRAK+ P RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 476 DGDIVLFNRQPSLHKLSILSHRAKIRPWRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 535

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EA                LM  K NL TP+NG  +IAA QDFITG YL++QK+ FF+R
Sbjct: 536 RTEATE--------------LMGVKHNLATPKNGTPIIAAIQDFITGAYLISQKDLFFSR 581

Query: 461 AQTMRIASTL---IADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDC 517
            Q   + S +   +  T    G  K++      P ++ +   +WTGKQI++L++KP+RD 
Sbjct: 582 RQFTHVVSFMYNALEVTDPYTG--KKYPIEIPPPAIW-KPQTLWTGKQIWNLLMKPHRDY 638

Query: 518 PVNANLKTKGRAYTA------NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYI 571
           PVN NL+ K + +         ++    DSY+++RNSE + G+ DK+T+G G K +VFY+
Sbjct: 639 PVNVNLEAKLKQFAPPSRPGDADDMVDSDSYLVIRNSETMCGAFDKATIGDGKKTSVFYV 698

Query: 572 LLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           ++RDFG D A  AM RL+++++ +L  RGFSIGI DV P
Sbjct: 699 IMRDFGPDYAAAAMTRLAKLSARWLGERGFSIGISDVYP 737



 Score =  190 bits (483), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 155/494 (31%), Positives = 237/494 (47%), Gaps = 97/494 (19%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEF-LQDTSENFVR---- 1051
            G+  PV  +R     I    + S+ +L+  EIL L N TLD++   L   SE+  R    
Sbjct: 946  GSAKPVNFERTWMHAITSTWNNSERTLTMAEILELVNTTLDAERVKLIRVSEDGKRLEYT 1005

Query: 1052 ---DIKKFLEEFSKKESVTSHQDKVSQPL---REQILSHQDKIGHGRESNPFPSACKA-- 1103
               +++K L+   + E   +  D ++  +    ++++ +Q K+   ++      +     
Sbjct: 1006 YDWEVEKNLKLVDQSEYSRTFLDDIAGFIVGKADKMVKNQAKLEGSQDIFKITRSALDRF 1065

Query: 1104 -EACREKYVRAQIEPATAVGAL-------------------------------------- 1124
             + C  KY +++ E   AVGA+                                      
Sbjct: 1066 LQLCLRKYEKSKTEAGHAVGAVGAHSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEII 1125

Query: 1125 -AAQSIGEPGTQMTLKTFH---------------FAGEVCEYIEEVFVPDDSFILIKLDM 1168
             A++ I  P     L + +               + G++ +YIE+V+     +I ++++ 
Sbjct: 1126 NASKVISTPVINCALDSKYVDMAGRFVKALIEKTYLGDIVDYIEDVWHRGGCYINMRVNW 1185

Query: 1169 DRIRLLHLEVDIDSIRYCIERTRG---ISGHLTVSGHSFL---ILKPKDSSKS---FNSK 1219
            ++I  L L + +  +   I+RT+G   +       GH  +   I+ P   S++   F  K
Sbjct: 1186 EQIENLGLRISMWQLIDAIDRTKGFKAMGASAQAIGHHHIRVHIIPPDSGSRARGRFAGK 1245

Query: 1220 ---------------MYQMKQLLPSVVIKGVQGINRAVIHEEDVE---GVTKYKLLVEGD 1261
                           ++ +K+ LPSVV+KG     RA+I ++D +   G     +LVEG 
Sbjct: 1246 GKADASDGSEVMFMQLHSLKRRLPSVVVKGYPEAARAIIKKDDKKDETGKEPISVLVEGY 1305

Query: 1262 NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 1321
             L+  M T GV G K  SNN  E+   LGIEAAR TI+ EI  VM   GM ID RH  L+
Sbjct: 1306 GLKACMTTEGVNGYKTKSNNVMEMRDVLGIEAARKTIIDEISSVM--GGMDIDPRHMQLL 1363

Query: 1322 ADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMG 1381
            AD+MT KGEVLGITR GLAKM++SVL LASFE T DHLF+AA   + D I GVSECIIMG
Sbjct: 1364 ADVMTYKGEVLGITRFGLAKMRDSVLQLASFEKTPDHLFEAAAKMKKDDIEGVSECIIMG 1423

Query: 1382 LPMNVGTGLIKLLQ 1395
              M VGTG +K+++
Sbjct: 1424 QSMGVGTGAMKVVR 1437



 Score =  154 bits (389), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 108/285 (37%), Positives = 153/285 (53%), Gaps = 30/285 (10%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+I   LD        R VK  +E+T LG++ +YIE+V+    
Sbjct: 1117 GVPRIKEIINASKVISTPVINCALDSKYVDMAGRFVKALIEKTYLGDIVDYIEDVWHRGG 1176

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRG---ISGHLTVSGHSFL---ILKPKDSS 877
             +I ++++ ++I  L L + +  +   I+RT+G   +       GH  +   I+ P   S
Sbjct: 1177 CYINMRVNWEQIENLGLRISMWQLIDAIDRTKGFKAMGASAQAIGHHHIRVHIIPPDSGS 1236

Query: 878  KS---FNSK---------------MYQMKQLLPSVVIKGVQGINRAVIHEEDVE---GVT 916
            ++   F  K               ++ +K+ LPSVV+KG     RA+I ++D +   G  
Sbjct: 1237 RARGRFAGKGKADASDGSEVMFMQLHSLKRRLPSVVVKGYPEAARAIIKKDDKKDETGKE 1296

Query: 917  KYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMS 976
               +LVEG  L+  M T GV G K  SNN  E+   LGIEAAR TI+ EI  VM   GM 
Sbjct: 1297 PISVLVEGYGLKACMTTEGVNGYKTKSNNVMEMRDVLGIEAARKTIIDEISSVM--GGMD 1354

Query: 977  IDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDP 1021
            ID RH  L+AD+MT KGEVLG  T   L ++ D ++   S    P
Sbjct: 1355 IDPRHMQLLADVMTYKGEVLGI-TRFGLAKMRDSVLQLASFEKTP 1398



 Score =  154 bits (388), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 95/264 (35%), Positives = 137/264 (51%), Gaps = 16/264 (6%)

Query: 93  VQQQSHIQIVSKNLY--CQDPQ--RTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHF 148
           V  QS + +  +NLY     P   R    HG LD R+GT+ K   C+TC Q L +C GHF
Sbjct: 33  VVAQSVVAVKDRNLYDISDRPGGGRAITNHGPLDPRLGTSSKNGTCSTCQQGLKECNGHF 92

Query: 149 GYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKS 208
           G++ L LP FH GY + +I  L  +CK+  C++VLL E++   +  +LR P L  L +  
Sbjct: 93  GHVKLALPCFHYGYLKRIIEALNCVCKD--CSKVLLPEKEKRIYLKQLRRPGLDGLRKDV 150

Query: 209 LKKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKY------KNRTKKKDAIVEDL 260
           + KKI    +KV  CPHC   NG V+K     +K+ H KY        ++K+K A +   
Sbjct: 151 IIKKISGECRKVKRCPHCESYNGPVRKVAGHPIKMFHNKYAVYTNSNAKSKQKPADMMAF 210

Query: 261 LAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL-SKPSDLI 319
              + EA K   ++E H K      L PL VL + + +P  D+ LL M+ +   +P  +I
Sbjct: 211 EKTFEEASKAILDVERHMKRA-ADDLTPLRVLNILKKVPNVDVELLGMDPQSGGRPEYMI 269

Query: 320 LTRLLVPPNCIRPSVISDLKSDND 343
            T +  PP  IRPSV  +  S  D
Sbjct: 270 WTHIPAPPVAIRPSVAQEAASTED 293



 Score =  105 bits (261), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 47/59 (79%), Positives = 52/59 (88%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
           +GFV +SFFSGLTPTEF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD++
Sbjct: 863 KGFVADSFFSGLTPTEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSAQYDLT 921



 Score = 59.7 bits (143), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 27/48 (56%), Positives = 34/48 (70%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIAS 69
           LM  K NL TP+NG  +IAA QDFITG YL++QK+ FF+R Q   + S
Sbjct: 542 LMGVKHNLATPKNGTPIIAAIQDFITGAYLISQKDLFFSRRQFTHVVS 589



 Score = 43.1 bits (100), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 21/39 (53%), Positives = 27/39 (69%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  F+AA   + D I GVSECIIMG  M VGTG +K+++
Sbjct: 1399 DHLFEAAAKMKKDDIEGVSECIIMGQSMGVGTGAMKVVR 1437


>gi|156841103|ref|XP_001643927.1| hypothetical protein Kpol_1016p9 [Vanderwaltozyma polyspora DSM
           70294]
 gi|156114557|gb|EDO16069.1| hypothetical protein Kpol_1016p9 [Vanderwaltozyma polyspora DSM
           70294]
          Length = 1460

 Score =  280 bits (717), Expect = 4e-72,   Method: Compositional matrix adjust.
 Identities = 139/282 (49%), Positives = 187/282 (66%), Gaps = 30/282 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH+LSI++H AK+ P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 468 DGDIVLFNRQPSLHRLSILSHFAKIRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 527

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL+TP++GE +IAATQDFITG YL++ K+ F +R
Sbjct: 528 RAEAMN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDTFLDR 573

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A   ++ S +++D++    I          P   ++   +WTGKQ+FSL++KPN+D PV 
Sbjct: 574 ATFTQLLS-MMSDSNLQFDI---------PPPTIIKPYCLWTGKQLFSLLIKPNKDSPVV 623

Query: 521 ANLKTKGRAY------TANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLR 574
            NL  K + +      +   E    D +V++R S++L+G MDKS LG G K +VFY +LR
Sbjct: 624 INLDAKNKVFIPPKSKSLPNEMSQNDGFVVIRGSQILSGVMDKSVLGDGKKHSVFYTILR 683

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           D+G   A  AM R++++ + YL NRGFSIGI DVTP     Q
Sbjct: 684 DYGPQEAANAMNRMAKLCARYLGNRGFSIGISDVTPDNALKQ 725



 Score =  247 bits (631), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 191/532 (35%), Positives = 261/532 (49%), Gaps = 120/532 (22%)

Query: 994  EVLGNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLD---------------- 1037
            E+ GN  PV  KR  D  I      S   L    I+  +N+ L                 
Sbjct: 925  EMEGNAQPVNFKRSWDHAINITFDNSAQGLLPYAIINKTNDILAPFEERLIRYDNIGTLV 984

Query: 1038 ------SKEFLQ--DTSENFVRDIKKFLEEFSKKESVTS--HQDK-----VSQPLREQIL 1082
                    EF+   D+  NF   ++K+++E   K S+ +   +DK      S+P  E   
Sbjct: 985  KANDQAKDEFVDQLDSERNFYCSLRKYMQE---KASILASIRKDKGLKELSSEPGNEFKE 1041

Query: 1083 SHQDKIGHGRESNPFPSACKA---------EACREKYVRAQIEPATAVGALAAQSIGEPG 1133
               D+             CK          E    KY RA++EP TAVGA+ AQSIGEPG
Sbjct: 1042 MDLDEGESSEARFAVEKLCKITEKTVEKFLEIAMSKYRRARVEPGTAVGAIGAQSIGEPG 1101

Query: 1134 TQMTLKTFHFAG------------------------------------------EVCEYI 1151
            TQMTLKTFHFAG                                           V   I
Sbjct: 1102 TQMTLKTFHFAGVASMNVTLGVPRIKEIINASKVISTPIINAVLVNDNDKRAARVVKGRI 1161

Query: 1152 EEVFVPDDSFIL------------IKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLT- 1198
            E+  + D ++ +            +K+D+  I  L LE+ I+ I   + R   +    T 
Sbjct: 1162 EKTLLSDVAYYVQDVYKDNLSFLEVKIDLSTIDKLQLELTIEDIAVALTRAPKLKIQTTD 1221

Query: 1199 ---VSGHSFLI-LKPKDS-SKSFNSKM---------YQMKQL---LPSVVIKGVQGINRA 1241
               VS     I + P+ S +KS ++ M         Y+M+ L   LP +V+ G+  I RA
Sbjct: 1222 VQIVSKDKITISVYPEGSKAKSISTSMKEPSENDVFYRMQTLRRALPQIVVNGLPDIARA 1281

Query: 1242 VIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTE 1301
            VI+  D +G  K +LLVEG  LR+VM T GV G K ++N+  EV+  LGIEAARS+I+ E
Sbjct: 1282 VINIRD-DG--KRELLVEGYGLREVMCTDGVIGSKTTTNHVLEVFSVLGIEAARSSIIGE 1338

Query: 1302 IKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFD 1361
            I   M NHGMS+D RH  L+ D+MT KGEVLGITR GL+KM++SVL LASFE T+DHLFD
Sbjct: 1339 IDYTMSNHGMSVDPRHIQLLGDVMTYKGEVLGITRFGLSKMRDSVLQLASFEKTTDHLFD 1398

Query: 1362 AAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA--VPRSEPVPRTLLFDN 1411
            AAFY + D + GVSECII+G  M++GTG  K+L++  +   +  P+  LF+N
Sbjct: 1399 AAFYMKKDAVEGVSECIILGQTMSIGTGAFKILKSTEIKPDDLKPKRTLFEN 1450



 Score =  183 bits (464), Expect = 8e-43,   Method: Compositional matrix adjust.
 Identities = 116/252 (46%), Positives = 157/252 (62%), Gaps = 21/252 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII A L  D D   AR+VKGR+E+T L +V  Y+++V+  + 
Sbjct: 1122 GVPRIKEIINASKVISTPIINAVLVNDNDKRAARVVKGRIEKTLLSDVAYYVQDVYKDNL 1181

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLT----VSGHSFLI-LKPKDS-S 877
            SF+ +K+D+  I  L LE+ I+ I   + R   +    T    VS     I + P+ S +
Sbjct: 1182 SFLEVKIDLSTIDKLQLELTIEDIAVALTRAPKLKIQTTDVQIVSKDKITISVYPEGSKA 1241

Query: 878  KSFNSKM---------YQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD 925
            KS ++ M         Y+M+ L   LP +V+ G+  I RAVI+  D +G  K +LLVEG 
Sbjct: 1242 KSISTSMKEPSENDVFYRMQTLRRALPQIVVNGLPDIARAVINIRD-DG--KRELLVEGY 1298

Query: 926  NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 985
             LR+VM T GV G K ++N+  EV+  LGIEAARS+I+ EI   M NHGMS+D RH  L+
Sbjct: 1299 GLREVMCTDGVIGSKTTTNHVLEVFSVLGIEAARSSIIGEIDYTMSNHGMSVDPRHIQLL 1358

Query: 986  ADLMTSKGEVLG 997
             D+MT KGEVLG
Sbjct: 1359 GDVMTYKGEVLG 1370



 Score =  175 bits (443), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 96/248 (38%), Positives = 140/248 (56%), Gaps = 11/248 (4%)

Query: 96  QSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPL 155
           QS +++ +++L+  +  R P   G LD +MG +     CTTC  NL+ C GHFG+I L L
Sbjct: 29  QSEVEVSTRDLFDLENGRAPKIGGALDPKMGVSSSSMECTTCHGNLASCHGHFGHIKLAL 88

Query: 156 PVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILE 215
           PVFH+GYF+  I ILQ ICKN  C+ +LL +     F  +LR P +  L R ++ KKIL+
Sbjct: 89  PVFHVGYFKATIQILQGICKN--CSSILLNDTDRRDFLHELRRPGIDNLKRMAIIKKILD 146

Query: 216 TTKKVSVCPHCGEINGVVKKCGL------LKISHEKYKNRTKKKDAIVEDLLAEYNEAVK 269
             KK   C  CG +NGVVK+         LKI H+ ++   KK     ++ + ++ + + 
Sbjct: 147 QCKKQRRCLTCGALNGVVKRAAAGSGSASLKIIHDTFRWVGKKSSPEKDEWVGDWEKVLA 206

Query: 270 FNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL--SKPSDLILTRLLVPP 327
            NPE+E   K  +   LNPL+ L LF+ I  ED  LL +++ +   +P   I   L  PP
Sbjct: 207 NNPELERFAKRSM-DDLNPLKTLNLFKQIRPEDCELLGIDSTVKAGRPETYIWRYLPAPP 265

Query: 328 NCIRPSVI 335
            CIRPSV+
Sbjct: 266 VCIRPSVM 273



 Score =  101 bits (251), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 47/61 (77%), Positives = 52/61 (85%), Gaps = 1/61 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV+NSFFSGL+P EF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QY
Sbjct: 841 TPQSKGFVRNSFFSGLSPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSCQY 900

Query: 668 D 668
           D
Sbjct: 901 D 901



 Score = 59.3 bits (142), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/50 (52%), Positives = 38/50 (76%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM  K+NL+TP++GE +IAATQDFITG YL++ K+ F +RA   ++ S +
Sbjct: 534 LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDTFLDRATFTQLLSMM 583



 Score = 55.1 bits (131), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 26/57 (45%), Positives = 38/57 (66%), Gaps = 2/57 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA--VPRSEPVPRTLLFDN 722
            D  FDAAFY + D + GVSECII+G  M++GTG  K+L++  +   +  P+  LF+N
Sbjct: 1394 DHLFDAAFYMKKDAVEGVSECIILGQTMSIGTGAFKILKSTEIKPDDLKPKRTLFEN 1450


>gi|340939410|gb|EGS20032.1| RNA polymerase-like protein [Chaetomium thermophilum var.
           thermophilum DSM 1495]
          Length = 1541

 Score =  280 bits (716), Expect = 4e-72,   Method: Compositional matrix adjust.
 Identities = 135/275 (49%), Positives = 184/275 (66%), Gaps = 29/275 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND+VLFNRQPSLHKLSIM+H  KV P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 469 DNDIVLFNRQPSLHKLSIMSHLVKVRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 528

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K NL+TP+NGE +IAATQDFIT  YLL+ K+ FF+R
Sbjct: 529 RAEAIN--------------LMGVKHNLITPKNGEPIIAATQDFITAAYLLSSKDKFFDR 574

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                I + ++   + +             P   ++   +WTGKQIF+++++PN++CPV 
Sbjct: 575 ETFTYICTQMLLGETHL----------DLPPPAIMKPRCLWTGKQIFNVLMRPNKECPVL 624

Query: 521 ANLKTKGRAYTANE-----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL  K + ++  +     +    D+++++RNSE++ G MDK+T+G G K +VFY++LRD
Sbjct: 625 VNLDAKNKVFSKKKDGHPPDMDIDDAFLVVRNSEVMCGRMDKATVGGGKKNSVFYVILRD 684

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           +G D A  AM RL+++ +  L  RGFSIG+GDV P
Sbjct: 685 YGPDYAAAAMNRLAKLCARMLTLRGFSIGVGDVWP 719



 Score =  201 bits (510), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 114/290 (39%), Positives = 163/290 (56%), Gaps = 12/290 (4%)

Query: 62  AQTMRIASTLIAGRKVFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLL 121
           A T R    ++  R   F+ L  G  + +D V Q   +++    LY  +  RT  PHG L
Sbjct: 4   AVTRRRKEQVVDQRPKRFKALKFGIQSHQDIVSQ-GVLEVSDNLLYDVENNRTAFPHGPL 62

Query: 122 DRRMGTN--QKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTC 179
           D RMGT+   ++A C TC   L DC GHFG++ LPLPVFHIGY + +   LQ+ICK+  C
Sbjct: 63  DPRMGTSSTNRDAKCATCNMGLQDCPGHFGHVRLPLPVFHIGYLKYIQTTLQNICKD--C 120

Query: 180 ARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLL 239
           ARVLL E +   F  +LR P +  L R ++ KKI E  +KV  CP+CGEI GV++K  ++
Sbjct: 121 ARVLLTEPERRQFLKELRRPGIDNLRRAAILKKINEQCRKVKQCPYCGEIQGVIRKLSVM 180

Query: 240 KISHEKYK--NRTKKKDAIVEDLLAEYN----EAVKFNPEIEAHKKFGLIQTLNPLEVLQ 293
           K+ H+KY   N++  +  I  +   E++     A K+ PE+E H K  +   LNPL+VL 
Sbjct: 181 KLVHDKYAAYNKSTAQKKIAPESKVEFDASFENAKKYTPELEKHTKKAM-DDLNPLKVLN 239

Query: 294 LFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
           LF+ I   D  LL ++    +P   +   +  PP CIRPSV  +  S+ D
Sbjct: 240 LFKRISPTDCELLGLDPTEGRPEMFLWQYIPAPPICIRPSVAQENASNED 289



 Score =  178 bits (452), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 112/305 (36%), Positives = 168/305 (55%), Gaps = 41/305 (13%)

Query: 1143 FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI-------------------DSI 1183
            +  +V  YI++ ++PD + I++++D+  +  + L + I                   D +
Sbjct: 1210 YISDVISYIDDEWLPDVAKIVLQVDLQAVADMQLGITIKDIADAIVKNKKLKLKVEPDDL 1269

Query: 1184 RYCIERTRGI----------------SGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLL 1227
            R   +R   I                     +   + + L   +S   F  ++  +K++L
Sbjct: 1270 RVGHDRVEVIVRNTWTDATAARKAARQRAAAIEKGTAMPLTMDESVADFQLRVNFLKRML 1329

Query: 1228 PSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYK 1287
            P V I G    NRA+I  +D  G  ++ +LVEG  LR  M T GV G +C +N+  E   
Sbjct: 1330 PQVAISGYPEANRAIIQTDDKTG--EHAVLVEGYGLRQCMTTEGVIGTQCVTNSVMECRD 1387

Query: 1288 TLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVL 1347
             LGIEAAR+TI +EI+ VM++  M+ID RH  L+AD+MT KGE+LGITR GLAKM++SVL
Sbjct: 1388 VLGIEAARTTIASEIRSVMKD--MNIDPRHMELLADVMTYKGEILGITRFGLAKMRDSVL 1445

Query: 1348 NLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ--AVPRSEPVPR 1405
             LASFE T DHLFDAA   + D I GVSECIIMG  M++GTG  ++++   +   +  PR
Sbjct: 1446 QLASFEKTPDHLFDAAAGMKKDRILGVSECIIMGQSMSIGTGAFQVVRRLGIRDHQLAPR 1505

Query: 1406 TLLFD 1410
              +F+
Sbjct: 1506 ATVFE 1510



 Score =  154 bits (389), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 97/269 (36%), Positives = 147/269 (54%), Gaps = 39/269 (14%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+IT  L+   D+  AR+VK R+E+T + +V  YI++ ++PD 
Sbjct: 1167 GVPRIKEIINASKLISTPVITCKLENKVDIKAARVVKARIEKTYISDVISYIDDEWLPDV 1226

Query: 824  SFILIKLDMDRIRLLHLEVDI-------------------DSIRYCIERTRGI------- 857
            + I++++D+  +  + L + I                   D +R   +R   I       
Sbjct: 1227 AKIVLQVDLQAVADMQLGITIKDIADAIVKNKKLKLKVEPDDLRVGHDRVEVIVRNTWTD 1286

Query: 858  ---------SGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIH 908
                          +   + + L   +S   F  ++  +K++LP V I G    NRA+I 
Sbjct: 1287 ATAARKAARQRAAAIEKGTAMPLTMDESVADFQLRVNFLKRMLPQVAISGYPEANRAIIQ 1346

Query: 909  EEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKL 968
             +D  G  ++ +LVEG  LR  M T GV G +C +N+  E    LGIEAAR+TI +EI+ 
Sbjct: 1347 TDDKTG--EHAVLVEGYGLRQCMTTEGVIGTQCVTNSVMECRDVLGIEAARTTIASEIRS 1404

Query: 969  VMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            VM++  M+ID RH  L+AD+MT KGE+LG
Sbjct: 1405 VMKD--MNIDPRHMELLADVMTYKGEILG 1431



 Score =  103 bits (257), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 45/59 (76%), Positives = 52/59 (88%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSF++GLTP+EF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 843 PSKGFVRNSFYTGLTPSEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSTQYD 901



 Score = 69.7 bits (169), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 30/42 (71%), Positives = 35/42 (83%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            + C  KY +A++EP  AVGA+ AQSIGEPGTQMTLKTFHFAG
Sbjct: 1117 QMCLHKYKKARVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAG 1158



 Score = 62.4 bits (150), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/53 (52%), Positives = 37/53 (69%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           LM  K NL+TP+NGE +IAATQDFIT  YLL+ K+ FF+R     I + ++ G
Sbjct: 535 LMGVKHNLITPKNGEPIIAATQDFITAAYLLSSKDKFFDRETFTYICTQMLLG 587



 Score = 43.5 bits (101), Expect = 0.92,   Method: Compositional matrix adjust.
 Identities = 23/56 (41%), Positives = 34/56 (60%), Gaps = 2/56 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ--AVPRSEPVPRTLLFD 721
            D  FDAA   + D I GVSECIIMG  M++GTG  ++++   +   +  PR  +F+
Sbjct: 1455 DHLFDAAAGMKKDRILGVSECIIMGQSMSIGTGAFQVVRRLGIRDHQLAPRATVFE 1510


>gi|255938285|ref|XP_002559913.1| Pc13g15170 [Penicillium chrysogenum Wisconsin 54-1255]
 gi|211584533|emb|CAP92586.1| Pc13g15170 [Penicillium chrysogenum Wisconsin 54-1255]
          Length = 1448

 Score =  280 bits (716), Expect = 4e-72,   Method: Compositional matrix adjust.
 Identities = 138/282 (48%), Positives = 187/282 (66%), Gaps = 29/282 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++H AK+ PHRTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 470 DGDIVLFNRQPSLHKLSILSHFAKIRPHRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 529

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL TP+NGE +I+A QDFI+  Y+L+ K+ F++R
Sbjct: 530 RAEAME--------------LMGVKNNLATPKNGEPIISAIQDFISAAYVLSSKDNFYDR 575

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A   +I   ++       G   RF      P   ++  ++WTGKQ+F+++++PN+D PV 
Sbjct: 576 ASFTQICLYML-------GPETRF---DLPPPSILKPQMMWTGKQVFNILMRPNKDDPVM 625

Query: 521 ANLKTKGRAYT-----ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL    R +      + ++    D ++++RNSE++ G MDKST+GSG K NVFYILLRD
Sbjct: 626 VNLDAACREFKMPKDGSPKDLDPNDGWLVIRNSEVMCGVMDKSTIGSGKKDNVFYILLRD 685

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           FG   A   M RLS++++ +  N GFSIGIGDV P +  VQ+
Sbjct: 686 FGPPAAAEGMNRLSKLSARWFTNIGFSIGIGDVYPSEELVQS 727



 Score =  187 bits (476), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 107/267 (40%), Positives = 153/267 (57%), Gaps = 12/267 (4%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G +T +D V Q + +++  +  +  D  RT + +G LD RMG + K  +C TCG NL DC
Sbjct: 30  GVLTNDDIVGQ-AVVEVSDRKFFDLDQTRTVVSNGPLDPRMGISNKTDSCATCGNNLKDC 88

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFG++ L LP FH+GYF+ VI+ILQ ICK   C+ +LL E +   +  ++R P L  L
Sbjct: 89  NGHFGHVRLVLPSFHVGYFKRVISILQEICKE--CSNILLPEAERRTYLREMRRPGLDNL 146

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKYKN-----RTKKKDAIV 257
            R  + K+I E  +K   C +CG INGVVKK G   LKI+H+K++        KK+  I 
Sbjct: 147 RRTQIAKRINERCRKTRECTYCGAINGVVKKTGTSALKITHDKFRAFNASVSVKKQTPIS 206

Query: 258 EDLL-AEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPS 316
           +D+    + EA   NPE+E H K      +NPL VL+LF+ +   D  L+ MN + ++P 
Sbjct: 207 KDVFDNSFLEARGANPEVEKHFKKAQ-DDMNPLRVLKLFKKMSDSDCELIGMNPKEARPE 265

Query: 317 DLILTRLLVPPNCIRPSVISDLKSDND 343
             +   +  PP CIRPSV  D  S  D
Sbjct: 266 MFLWQFIPAPPVCIRPSVGQDGASTED 292



 Score =  187 bits (474), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 135/380 (35%), Positives = 194/380 (51%), Gaps = 77/380 (20%)

Query: 1105 ACREKYVRAQIEPATAVGAL---------------------------------------A 1125
            AC  KY RAQ+EP  AVGA+                                       A
Sbjct: 1054 ACLLKYKRAQVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIINA 1113

Query: 1126 AQSIGEP---------GTQMTLKTFH------FAGEVCEYIEEVFVPDDSFILIKLDMDR 1170
            ++ I  P         G+ +  +         F  +V   I EV+ PDD+++ + L+   
Sbjct: 1114 SREISTPVVACELVNRGSTIAARIVKGRIEKTFLQDVIHSITEVWSPDDAYLKVVLNWKT 1173

Query: 1171 IRLLHLEVDIDSIRYCIERTRGISG--------HLTVSGHSFL-------ILKPKDSSKS 1215
            I  L LE+    I   I+  +   G        H ++  H  L       + K + ++ S
Sbjct: 1174 IEDLALEITTPQIVEAIKTNKRFKGGDLKFSCKHGSIKVHMDLDPASKASLSKTEIAATS 1233

Query: 1216 FNS--KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVK 1273
             +   ++  +K++LP + I G     RA+I  +  E  T   LLVEG  LR+ M T GV 
Sbjct: 1234 IDPFLRLKHLKRILPHIQILGHPRAARAIIRTD--ETSTTNTLLVEGYGLRECMTTMGVD 1291

Query: 1274 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 1333
            G+   +NN  E  + LGIEAARSTI+ EI  VM++  M ID RH  L+AD+MT KGEVLG
Sbjct: 1292 GLHTRTNNIMEAREVLGIEAARSTIVVEISEVMKD--MDIDPRHMQLLADVMTYKGEVLG 1349

Query: 1334 ITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            ITR GLAKM++SVL LASFE T+DHLFDA   G+TD I GVSECIIMG  +++GTG +++
Sbjct: 1350 ITRFGLAKMRDSVLQLASFEKTADHLFDAGGLGRTDLIEGVSECIIMGKTVSLGTGAMEV 1409

Query: 1394 LQAVP--RSEPVPRTLLFDN 1411
            ++ +   + +  PR  +F++
Sbjct: 1410 VRKLNFYQGQIGPRKTVFED 1429



 Score =  153 bits (386), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 103/251 (41%), Positives = 141/251 (56%), Gaps = 21/251 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINASR ISTP++   L        ARIVKGR+E+T L +V   I EV+ PDD
Sbjct: 1103 GVPRIKEIINASREISTPVVACELVNRGSTIAARIVKGRIEKTFLQDVIHSITEVWSPDD 1162

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISG--------HLTVSGHSFL------ 869
            +++ + L+   I  L LE+    I   I+  +   G        H ++  H  L      
Sbjct: 1163 AYLKVVLNWKTIEDLALEITTPQIVEAIKTNKRFKGGDLKFSCKHGSIKVHMDLDPASKA 1222

Query: 870  -ILKPKDSSKSFNS--KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDN 926
             + K + ++ S +   ++  +K++LP + I G     RA+I  +  E  T   LLVEG  
Sbjct: 1223 SLSKTEIAATSIDPFLRLKHLKRILPHIQILGHPRAARAIIRTD--ETSTTNTLLVEGYG 1280

Query: 927  LRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVA 986
            LR+ M T GV G+   +NN  E  + LGIEAARSTI+ EI  VM++  M ID RH  L+A
Sbjct: 1281 LRECMTTMGVDGLHTRTNNIMEAREVLGIEAARSTIVVEISEVMKD--MDIDPRHMQLLA 1338

Query: 987  DLMTSKGEVLG 997
            D+MT KGEVLG
Sbjct: 1339 DVMTYKGEVLG 1349



 Score =  101 bits (251), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 46/59 (77%), Positives = 49/59 (83%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSFFSGL P EF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL   YD
Sbjct: 844 PSKGFVRNSFFSGLQPPEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSSMYD 902



 Score = 54.3 bits (129), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 24/57 (42%), Positives = 37/57 (64%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVF 78
           LM  K+NL TP+NGE +I+A QDFI+  Y+L+ K+ F++RA   +I   ++     F
Sbjct: 536 LMGVKNNLATPKNGEPIISAIQDFISAAYVLSSKDNFYDRASFTQICLYMLGPETRF 592



 Score = 46.2 bits (108), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 23/57 (40%), Positives = 38/57 (66%), Gaps = 2/57 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP--RSEPVPRTLLFDN 722
            D  FDA   G+TD I GVSECIIMG  +++GTG +++++ +   + +  PR  +F++
Sbjct: 1373 DHLFDAGGLGRTDLIEGVSECIIMGKTVSLGTGAMEVVRKLNFYQGQIGPRKTVFED 1429


>gi|345567741|gb|EGX50669.1| hypothetical protein AOL_s00075g95 [Arthrobotrys oligospora ATCC
           24927]
          Length = 1442

 Score =  280 bits (716), Expect = 4e-72,   Method: Compositional matrix adjust.
 Identities = 138/276 (50%), Positives = 180/276 (65%), Gaps = 28/276 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSI++H  KV P +TFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 467 DGDVVLFNRQPSLHKLSILSHYVKVRPWKTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 526

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EA+               LM  K+NL TPRNGE +IAA QDFIT  YLL+ K+ FF+R
Sbjct: 527 RTEAIN--------------LMGVKNNLCTPRNGEPIIAAIQDFITAAYLLSNKDNFFDR 572

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                +   ++     I             P   ++   +WTGKQ+FS+++KPN+   V 
Sbjct: 573 KSFATLCMFMVNGNEQI----------DLPPPAVIKPEAMWTGKQLFSVLIKPNKKSKVV 622

Query: 521 ANLKTKGRAYTA----NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL  K R + A      + C  D ++++R SE++ G MDKST+GSG K++VFY++LRD+
Sbjct: 623 LNLDAKCRDFKAVPGMAPDLCPNDGWLVIRGSEVMCGLMDKSTVGSGKKSSVFYVILRDY 682

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
           G D AV AM RL+++ + +L NRGFSIGI DV+PGQ
Sbjct: 683 GADEAVAAMNRLAKLCARWLGNRGFSIGINDVSPGQ 718



 Score =  251 bits (642), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 186/506 (36%), Positives = 246/506 (48%), Gaps = 94/506 (18%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEF------LQDTSE-NF 1049
            G+  PV L R  +         +DPSL   EI+A+  E LD  E       L  T E + 
Sbjct: 925  GDAKPVNLVRTYNHAENLTWDNNDPSLLPYEIIAMCRELLDFDELEAMLARLGPTDEIDS 984

Query: 1050 VRDIKKFLEEFSKKESVTSHQDKVSQPLR---EQILSHQDKIGHGRESNPFPSAC----- 1101
                ++ L  F K+ +V   + +    L    E + S +  +G+    N    A      
Sbjct: 985  KVAFRQSLYHFVKERAVECARIRERVGLMACLEPVDSDEYDMGYIDSLNATAKAIVDRVH 1044

Query: 1102 KAEA---------CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEV----- 1147
            K  A         C  KY R+++EP TAVGA+ AQSIGEPGTQMTLKTFHFAG       
Sbjct: 1045 KISARTLREFISQCMTKYSRSKVEPGTAVGAVGAQSIGEPGTQMTLKTFHFAGVASMNVT 1104

Query: 1148 ----------------------CE---------------------------YIEEVFVPD 1158
                                  CE                           YIE+V  PD
Sbjct: 1105 LGVPRIKEIINASKSISTPIIKCELVNKSDIRSARYVKGRIEKTYLEDIIFYIEDVCSPD 1164

Query: 1159 DSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSFLI--------- 1206
            DS+I IK+D   I  L LE+ I+ I   I R   +      L V+G    I         
Sbjct: 1165 DSYISIKIDEATIDKLGLELTIEDIMTAITRAPKLKIDKSQLKVTGSRIRIYVYELSERE 1224

Query: 1207 LKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDV 1266
            +K      S + ++  +K++LP VV+KG     RAVI  ++  G     L VEG  LR  
Sbjct: 1225 MKRSKEDLSVHQRIQALKRVLPRVVVKGYPEATRAVISTDESSG--NNTLCVEGYGLRQC 1282

Query: 1267 MATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMT 1326
            M T GV G K  +N+  E+   LGIEAAR TI+ EI   M  HGM +D RH  L+ D+MT
Sbjct: 1283 MNTDGVVGTKTKTNSVMEMRTVLGIEAARFTIIDEISFTMREHGMDVDPRHIQLLGDVMT 1342

Query: 1327 SKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNV 1386
             KGEVLGITR GLAKM++SVL LASFE T+DHLFDAAF+ + D I GVSECII+G  M +
Sbjct: 1343 YKGEVLGITRFGLAKMRDSVLQLASFEKTTDHLFDAAFHTKKDKIEGVSECIILGQSMGI 1402

Query: 1387 GTGLIKLLQ--AVPRSEPVPRTLLFD 1410
            GTG  ++++   +  ++  P+  LF+
Sbjct: 1403 GTGAFQVVRRLGMDAADLKPKRCLFE 1428



 Score =  176 bits (447), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 109/246 (44%), Positives = 141/246 (57%), Gaps = 14/246 (5%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS++ISTPII   L   +D+  AR VKGR+E+T L ++  YIE+V  PDD
Sbjct: 1106 GVPRIKEIINASKSISTPIIKCELVNKSDIRSARYVKGRIEKTYLEDIIFYIEDVCSPDD 1165

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFLI---------L 871
            S+I IK+D   I  L LE+ I+ I   I R   +      L V+G    I         +
Sbjct: 1166 SYISIKIDEATIDKLGLELTIEDIMTAITRAPKLKIDKSQLKVTGSRIRIYVYELSEREM 1225

Query: 872  KPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVM 931
            K      S + ++  +K++LP VV+KG     RAVI  ++  G     L VEG  LR  M
Sbjct: 1226 KRSKEDLSVHQRIQALKRVLPRVVVKGYPEATRAVISTDESSG--NNTLCVEGYGLRQCM 1283

Query: 932  ATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTS 991
             T GV G K  +N+  E+   LGIEAAR TI+ EI   M  HGM +D RH  L+ D+MT 
Sbjct: 1284 NTDGVVGTKTKTNSVMEMRTVLGIEAARFTIIDEISFTMREHGMDVDPRHIQLLGDVMTY 1343

Query: 992  KGEVLG 997
            KGEVLG
Sbjct: 1344 KGEVLG 1349



 Score =  171 bits (434), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 96/267 (35%), Positives = 149/267 (55%), Gaps = 15/267 (5%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G ++ +D V+Q + I++ +  L+  +  R P  +G+LD RMG + K   C TCG+NL  C
Sbjct: 31  GILSTQDMVKQ-AVIEVSTDRLF-NETGRQPTENGVLDPRMGISNKTDTCKTCGENLQAC 88

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFG++ L LP FHIGYF+ +I++LQ+ICK   C+ +LL       +  ++R P +  L
Sbjct: 89  NGHFGHVKLALPAFHIGYFKHIISVLQNICKE--CSAILLDSSMRRSYLKEIRKPGIDNL 146

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYK--------NRTKKKDAI 256
            R  + KKI E  +K   C  CG ING VKK G LK+ H+K++        ++   +  +
Sbjct: 147 RRVQICKKINEQCRKTKACFVCGAINGTVKKVGPLKVIHDKFRAFNSSNAASKVPPEAKV 206

Query: 257 VEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPS 316
           + D    + EA K N +++ H +  +   LNPL+VL LF+ +   D  LL M+    +P 
Sbjct: 207 IFD--KSFMEAKKTNQDLDKHIRKAM-DDLNPLKVLNLFKKVSPADCELLGMDPGQGRPE 263

Query: 317 DLILTRLLVPPNCIRPSVISDLKSDND 343
             +   +  PP CIRPSV  +  S+ D
Sbjct: 264 MFLWQYMPAPPVCIRPSVSQEDASNED 290



 Score =  107 bits (267), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 48/59 (81%), Positives = 52/59 (88%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSFFSGLTPTEF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 840 PSKGFVRNSFFSGLTPTEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSAQYD 898



 Score = 58.5 bits (140), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 27/53 (50%), Positives = 35/53 (66%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           LM  K+NL TPRNGE +IAA QDFIT  YLL+ K+ FF+R     +   ++ G
Sbjct: 533 LMGVKNNLCTPRNGEPIIAAIQDFITAAYLLSNKDNFFDRKSFATLCMFMVNG 585



 Score = 47.4 bits (111), Expect = 0.067,   Method: Compositional matrix adjust.
 Identities = 23/56 (41%), Positives = 36/56 (64%), Gaps = 2/56 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ--AVPRSEPVPRTLLFD 721
            D  FDAAF+ + D I GVSECII+G  M +GTG  ++++   +  ++  P+  LF+
Sbjct: 1373 DHLFDAAFHTKKDKIEGVSECIILGQSMGIGTGAFQVVRRLGMDAADLKPKRCLFE 1428


>gi|19112298|ref|NP_595506.1| DNA-directed RNA polymerase III complex large subunit Rpc1
           (predicted) [Schizosaccharomyces pombe 972h-]
 gi|9297042|sp|O94666.1|RPC1_SCHPO RecName: Full=DNA-directed RNA polymerase III subunit rpc1;
           Short=RNA polymerase III subunit C1; AltName:
           Full=DNA-directed RNA polymerase III largest subunit;
           AltName: Full=RPC158
 gi|4467280|emb|CAB37604.1| DNA-directed RNA polymerase III complex large subunit Rpc1
           (predicted) [Schizosaccharomyces pombe]
 gi|76782169|gb|ABA54855.1| RNA polymerase III largest subunit Rpc1 [Schizosaccharomyces pombe]
          Length = 1405

 Score =  280 bits (715), Expect = 5e-72,   Method: Compositional matrix adjust.
 Identities = 140/278 (50%), Positives = 182/278 (65%), Gaps = 28/278 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DNDVVLFNRQPSLHKLSIMAH  KV P RT RFNECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 450 DNDVVLFNRQPSLHKLSIMAHLVKVRPWRTLRFNECVCGPYNADFDGDEMNLHVPQTEEA 509

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           + EAL               LM  K+NLV+PRNGE +IAATQDFIT  YLL+ K+ F +R
Sbjct: 510 KTEALE--------------LMGIKNNLVSPRNGEPIIAATQDFITAAYLLSLKDTFLDR 555

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                I   ++  ++ I             P   ++   +WTGKQ+F++++KPNR   V 
Sbjct: 556 KSISNICCYMMDASTHI----------DLPPPAIIKPRCLWTGKQVFTVLMKPNRFSKVL 605

Query: 521 ANLKTKGRAY----TANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL  K R++    +   E C +D Y+++RNSE++AG +DKS +G G K ++FY++LRD+
Sbjct: 606 VNLDAKTRSFSRIKSKTPEMCPKDGYLMIRNSEIIAGVVDKSVVGDGKKDSLFYVILRDY 665

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGF 614
           G   A  A+ RLS+M + +L NRGFSIGI DV PG+  
Sbjct: 666 GALEAAEAITRLSKMCARFLGNRGFSIGIEDVQPGKSL 703



 Score =  268 bits (686), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 178/503 (35%), Positives = 253/503 (50%), Gaps = 83/503 (16%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G+G  VE KR     +  N  R D ++   EI+   N  LD  +FL + + +F+  I+ F
Sbjct: 908  GDGQAVEFKRTWIHSVNLNYDRHDSAMLPYEIIDYVNRALDDPKFLTNCNRDFIETIRTF 967

Query: 1057 -LEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAE----------- 1104
             +E  +K  +    +  ++  L E  +   D +  G E  P       E           
Sbjct: 968  VIENIAKYLASVRERRDLAPMLEEPDMDDLDDM-EGDEFAPVAKRKSVENIIRVTEKQLR 1026

Query: 1105 ----ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------- 1145
                 C EKY+RA++EP TAVGA+ AQSIGEPGTQMTLKTFHFAG               
Sbjct: 1027 SFVDRCWEKYMRAKVEPGTAVGAIGAQSIGEPGTQMTLKTFHFAGVAAQTTLGVPRIKEI 1086

Query: 1146 --------------------------------------EVCEYIEEVFVPDDSFILIKLD 1167
                                                  +V  YIEEV+ P  +++ I+++
Sbjct: 1087 INAAKTISTPIITGQLINDRDERSARVVKGRIEKTYLKDVTSYIEEVYGPVTTYLSIQVN 1146

Query: 1168 MDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSG-----HSFLILKPKDSSKSFNSK 1219
             D I  L L++ +  I   I  T  +   S  +TV+      H       K S      +
Sbjct: 1147 FDTISKLQLDITLADIAAAIWNTPKLKIPSQQVTVNNTLQQIHVHTSSDGKSSETEVYYR 1206

Query: 1220 MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSS 1279
            +   K++LP VV+ G+  INR+VI++E      K +L +EG  L+ VM T G+ G K S+
Sbjct: 1207 LQTYKRVLPDVVVAGIPTINRSVINQES----GKIELFMEGTGLQAVMNTEGIVGTKTST 1262

Query: 1280 NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGL 1339
            N+  E+   LGIEAAR +I++EI   M  HG+++D RH ML+ D+MT KGEVLGITR G+
Sbjct: 1263 NHVMEMKDVLGIEAARYSIISEIGYTMAKHGLTVDPRHIMLLGDVMTCKGEVLGITRFGV 1322

Query: 1340 AKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL-QAVP 1398
            AKMK+SVL LASFE T+DHLF+AA     D I G+SECI++G    +GT + +L+ +   
Sbjct: 1323 AKMKDSVLALASFEKTTDHLFNAAARFAKDSIEGISECIVLGKLAPIGTNVFQLIRRTEE 1382

Query: 1399 RSEPVPRTLLFDNPEFHTNTLAA 1421
              E  P+ LLFD P  H   + A
Sbjct: 1383 EEEQKPKELLFDTPSLHQLEITA 1405



 Score =  194 bits (494), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 101/245 (41%), Positives = 148/245 (60%), Gaps = 5/245 (2%)

Query: 99  IQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVF 158
           +++  ++LY     R+P  HG LD  MGT+ K+ NC TCG++++DC+GHFGY+ L LPVF
Sbjct: 32  VEVSRRDLYTMT-DRSPAEHGALDLHMGTSNKQINCATCGESMADCMGHFGYVKLALPVF 90

Query: 159 HIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTK 218
           HIGYF+  + ILQ+ICK+  C+ VLL +++   F   LR P +  L R  + K+I +  K
Sbjct: 91  HIGYFKATLTILQNICKD--CSSVLLSDQEKRQFLKDLRRPGIDNLRRSQICKRINDHCK 148

Query: 219 KVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHK 278
           K+  C  C  + GVVKK G LKI HE+++   K +D   E+    ++EA+K  PE++ H 
Sbjct: 149 KMRRCSKCDAMQGVVKKAGPLKIIHERFRYVRKSQDD-EENFRHSFDEALKTIPELKMHL 207

Query: 279 KFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDL 338
                  LNPL+VL LF+ I   D  LL M+ E  +P +L+   +  PP CIRPSV  + 
Sbjct: 208 SKAH-DDLNPLKVLNLFKQITPVDCELLGMDPEHGRPENLLWRYVPAPPVCIRPSVAQEG 266

Query: 339 KSDND 343
            +  D
Sbjct: 267 ATTED 271



 Score =  177 bits (450), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 104/242 (42%), Positives = 147/242 (60%), Gaps = 12/242 (4%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ ISTPIIT  L  D D   AR+VKGR+E+T L +V  YIEEV+ P  
Sbjct: 1079 GVPRIKEIINAAKTISTPIITGQLINDRDERSARVVKGRIEKTYLKDVTSYIEEVYGPVT 1138

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSG-----HSFLILKPKD 875
            +++ I+++ D I  L L++ +  I   I  T  +   S  +TV+      H       K 
Sbjct: 1139 TYLSIQVNFDTISKLQLDITLADIAAAIWNTPKLKIPSQQVTVNNTLQQIHVHTSSDGKS 1198

Query: 876  SSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYG 935
            S      ++   K++LP VV+ G+  INR+VI++E      K +L +EG  L+ VM T G
Sbjct: 1199 SETEVYYRLQTYKRVLPDVVVAGIPTINRSVINQES----GKIELFMEGTGLQAVMNTEG 1254

Query: 936  VKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            + G K S+N+  E+   LGIEAAR +I++EI   M  HG+++D RH ML+ D+MT KGEV
Sbjct: 1255 IVGTKTSTNHVMEMKDVLGIEAARYSIISEIGYTMAKHGLTVDPRHIMLLGDVMTCKGEV 1314

Query: 996  LG 997
            LG
Sbjct: 1315 LG 1316



 Score = 99.8 bits (247), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 45/58 (77%), Positives = 49/58 (84%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV NSF+SGLTPTEF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL   YD
Sbjct: 824 AKGFVSNSFYSGLTPTEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSSAYD 881



 Score = 58.2 bits (139), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 27/51 (52%), Positives = 35/51 (68%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLI 72
           LM  K+NLV+PRNGE +IAATQDFIT  YLL+ K+ F +R     I   ++
Sbjct: 516 LMGIKNNLVSPRNGEPIIAATQDFITAAYLLSLKDTFLDRKSISNICCYMM 566



 Score = 43.1 bits (100), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 23/60 (38%), Positives = 33/60 (55%), Gaps = 1/60 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL-QAVPRSEPVPRTLLFDNPEFH 726
            D  F+AA     D I G+SECI++G    +GT + +L+ +     E  P+ LLFD P  H
Sbjct: 1340 DHLFNAAARFAKDSIEGISECIVLGKLAPIGTNVFQLIRRTEEEEEQKPKELLFDTPSLH 1399


>gi|384497273|gb|EIE87764.1| hypothetical protein RO3G_12475 [Rhizopus delemar RA 99-880]
          Length = 1273

 Score =  280 bits (715), Expect = 6e-72,   Method: Compositional matrix adjust.
 Identities = 137/284 (48%), Positives = 188/284 (66%), Gaps = 28/284 (9%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           SDNDVVLFNRQPSLH+LSIMAH AKV+P RTFRFNECVC+PYNADFDGDEMN+HLPQT+E
Sbjct: 412 SDNDVVLFNRQPSLHRLSIMAHFAKVMPWRTFRFNECVCSPYNADFDGDEMNMHLPQTQE 471

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           A+AEA+               LM  K+NLVTPRNGE LIAATQDFIT  YLL+ K+ F+ 
Sbjct: 472 AKAEAME--------------LMGVKNNLVTPRNGEPLIAATQDFITASYLLSHKDTFYT 517

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           R +  +  S +      I             P V  +   +WTGKQ+F+++ +PN++  V
Sbjct: 518 RGEFAQACSMMCDADLKI----------DLPPPVIWKPQRLWTGKQVFNVLFRPNKESKV 567

Query: 520 NANLKTKGRAYTANE----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
             +++ K +++   E    + C  D +++++NSE++ G +DK+ +G G K +VFY++LRD
Sbjct: 568 LLSVEAKTKSFVKQEGRLPDMCPNDGWLVVQNSEIMCGLVDKAVVGDGNKNSVFYVILRD 627

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
           +G   A   M RL+++ + +L NRGFSIGI DVTPG+   +  F
Sbjct: 628 YGPIEAAKCMNRLAKLCARWLANRGFSIGISDVTPGERLSRIKF 671



 Score =  190 bits (483), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 111/231 (48%), Positives = 150/231 (64%), Gaps = 5/231 (2%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ ISTPIIT  L  + D+  AR+VKGR+E+TTLG+V  Y+EEV+ P++
Sbjct: 1042 GVPRIKEIINAAKVISTPIITCELHSNQDVRAARVVKGRVEKTTLGDVAVYMEEVYEPNE 1101

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS-GHLTVSGHSFLILKPKDSSKSFNS 882
            ++ILI++D+D I  L LE ++  I + I+    +  G L V      I++    +K   S
Sbjct: 1102 TYILIRIDLDAINRLQLETNLHQIAHAIKTAPKLKMGQLDVQTSRPDIIRVYVHAKQEES 1161

Query: 883  KMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
              Y +K L   L SVVI G+  + RAVI E+   G    +LLVEG  L DVM T G+ G 
Sbjct: 1162 MYYNLKALKRVLTSVVITGLPPVVRAVISEKQ-GGKGAKQLLVEGYGLLDVMTTDGIVGD 1220

Query: 940  KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMT 990
            K +SN+  EV   LGIEAARSTI+ EI + ME+HGM+ID RH  L+ D+MT
Sbjct: 1221 KTTSNHIMEVADVLGIEAARSTIINEITMTMESHGMTIDHRHVFLLGDIMT 1271



 Score =  187 bits (474), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 99/247 (40%), Positives = 141/247 (57%), Gaps = 16/247 (6%)

Query: 97  SHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP 156
           +  ++  ++LY +   R P+ +G+LD R+GT  K+A C TCGQ + +C GH+GYI L LP
Sbjct: 5   AEFEVTQRDLY-KPESRIPVKNGVLDLRLGTTLKDAFCETCGQKMQECAGHWGYIKLVLP 63

Query: 157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILET 216
           +FH+GYFR            PTC+RV+L E     +  +LR P L  L R  + K+I E 
Sbjct: 64  IFHVGYFR------------PTCSRVMLEEPDRRIYLRRLRAPGLDNLQRNRILKQIQEK 111

Query: 217 TKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEA 276
            KKV+ C HC  +NGVVKK G +KI+H+KY  R K+     E     ++ A    PE++ 
Sbjct: 112 CKKVTYCMHCNSVNGVVKKVGPMKITHDKY--RLKRVADEAEQFRKTFDAAAASMPELKP 169

Query: 277 HKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVIS 336
           H        LNPL VL+LF+ I  ED  LL ++ E  +P   I   L VPP C+RPSV+ 
Sbjct: 170 HINKAQ-DDLNPLRVLRLFQRISPEDCELLGLSEEHGRPEWYIWQYLPVPPACVRPSVVQ 228

Query: 337 DLKSDND 343
           +  + N+
Sbjct: 229 EDNTSNE 235



 Score =  175 bits (444), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 140/430 (32%), Positives = 201/430 (46%), Gaps = 77/430 (17%)

Query: 969  VMENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDPSLSAQEI 1028
            V  + G  + F +     D MT +GE    G PVE  R L  +        +  L   EI
Sbjct: 847  VRNSEGAMLQFFYGADGLDPMTIEGE----GVPVEFARNLRHVQEITPLNGERGLLPWEI 902

Query: 1029 LALSNETLDSKEFLQDTSENFVRDIKKFLEE-----FSKKESVTSHQDKVSQPLREQILS 1083
              ++ + + ++ + ++   +F+  + KF+EE      +K       Q  ++ P  + +  
Sbjct: 903  NYITQQEIQTEIWQKNCLPSFIDMVTKFVEEKIAGRLAKIRKAHGMQSGLAMPDEDYMDI 962

Query: 1084 HQDKIGHGRES----NPFPSACKA-----EACREKYVRAQIEPATAVGALAAQSIGEPGT 1134
              D+           N F    +        C  KY++A+IEP TAVGA+ A SIGEPGT
Sbjct: 963  DIDEDEDEAVKTVVRNLFTITERQLRDYLHVCVSKYMKAKIEPGTAVGAIGAHSIGEPGT 1022

Query: 1135 QMTLKTFHFAGEV---------------------------CE------------------ 1149
            QMTLKTFHFAG                             CE                  
Sbjct: 1023 QMTLKTFHFAGVASMNITLGVPRIKEIINAAKVISTPIITCELHSNQDVRAARVVKGRVE 1082

Query: 1150 ---------YIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS-GHLTV 1199
                     Y+EEV+ P++++ILI++D+D I  L LE ++  I + I+    +  G L V
Sbjct: 1083 KTTLGDVAVYMEEVYEPNETYILIRIDLDAINRLQLETNLHQIAHAIKTAPKLKMGQLDV 1142

Query: 1200 SGHSFLILKPKDSSKSFNSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKL 1256
                  I++    +K   S  Y +K L   L SVVI G+  + RAVI E+   G    +L
Sbjct: 1143 QTSRPDIIRVYVHAKQEESMYYNLKALKRVLTSVVITGLPPVVRAVISEKQ-GGKGAKQL 1201

Query: 1257 LVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFR 1316
            LVEG  L DVM T G+ G K +SN+  EV   LGIEAARSTI+ EI + ME+HGM+ID R
Sbjct: 1202 LVEGYGLLDVMTTDGIVGDKTTSNHIMEVADVLGIEAARSTIINEITMTMESHGMTIDHR 1261

Query: 1317 HPMLVADLMT 1326
            H  L+ D+MT
Sbjct: 1262 HVFLLGDIMT 1271



 Score =  101 bits (251), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 43/61 (70%), Positives = 52/61 (85%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV+NSF++GL+PTEF FH + GREGLVDTAVKTAETGYM RRL+K+ EDL   YD+
Sbjct: 786 PAKGFVRNSFYTGLSPTEFLFHAISGREGLVDTAVKTAETGYMARRLMKAFEDLTTHYDL 845

Query: 670 S 670
           S
Sbjct: 846 S 846



 Score = 62.8 bits (151), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 29/50 (58%), Positives = 36/50 (72%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM  K+NLVTPRNGE LIAATQDFIT  YLL+ K+ F+ R +  +  S +
Sbjct: 479 LMGVKNNLVTPRNGEPLIAATQDFITASYLLSHKDTFYTRGEFAQACSMM 528


>gi|328874135|gb|EGG22501.1| RNA polymerase III [Dictyostelium fasciculatum]
          Length = 1507

 Score =  280 bits (715), Expect = 6e-72,   Method: Compositional matrix adjust.
 Identities = 137/270 (50%), Positives = 185/270 (68%), Gaps = 24/270 (8%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DV+LFNRQPSLHKLSIM H+A+V+P RT RFNECVCTPYNADFDGDEMN+H PQTEEA
Sbjct: 540 DGDVMLFNRQPSLHKLSIMCHKARVMPWRTLRFNECVCTPYNADFDGDEMNIHCPQTEEA 599

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL              +LM   +NL+TPRNGE L+AATQDF+T  YL+++++AF++R
Sbjct: 600 RAEAL--------------ILMGVTNNLITPRNGEPLVAATQDFLTSSYLISRRDAFYDR 645

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  ++  T  AD  +   + +        P + V+   +WTGKQ+F ++L+P+    V 
Sbjct: 646 ARFTQMC-THFADAYEHIDLPQ--------PTI-VKPIELWTGKQLFEVLLRPSVKSHVL 695

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            N +T  R YT N   C RD YV  RNSEL+ GS+DKS +G G K ++F++L+RDF   +
Sbjct: 696 VNFETNSRTYTKNTYMCPRDGYVCFRNSELMCGSIDKSIIGGGNKDSLFHVLMRDFTPAI 755

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           A  AM RL+++ + +L ++GFSIGI DV P
Sbjct: 756 AANAMTRLAKLCARFLGDQGFSIGIPDVKP 785



 Score =  231 bits (588), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 144/367 (39%), Positives = 202/367 (55%), Gaps = 58/367 (15%)

Query: 1104 EACREKYVRAQIEPATAVGAL--------------------------------------- 1124
            + C +KY RA+IEP TAVGA+                                       
Sbjct: 1140 DICLDKYNRARIEPGTAVGAIGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIIN 1199

Query: 1125 AAQSIGEPGTQMTLKTFH---------------FAGEVCEYIEEVFVPDDSFILIKLDMD 1169
            A+++I  P    TL                     G++  YI+EVF     ++ +K+D  
Sbjct: 1200 ASKTISTPIITATLNCDDDIRAARIVTGRIEKTTLGQISVYIKEVFRSGGCYLSVKIDKH 1259

Query: 1170 RIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSFLILKPKDSSKSFNSKMYQMKQL 1226
             I  + +EV  +SI+  I  T+G+     ++   G    I  P+ + +     +  +K  
Sbjct: 1260 FIDSMQIEVSAESIKASILGTKGLKLKPANIETLGEKLRIKPPEHNRRLILYSLQFLKNN 1319

Query: 1227 LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVY 1286
            LP+V++ G+  +NR VI + + E   KY+LLVEG +L  VMAT G+KG    SN+  EV 
Sbjct: 1320 LPNVIVHGIPTVNRVVISKPN-EKEDKYQLLVEGYDLLKVMATPGIKGTHTCSNHIMEVE 1378

Query: 1287 KTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESV 1346
            K LGIEA RS I++EI+++M +HGMSID RH ML+ADLM  KGE+LGITR G+AKMKESV
Sbjct: 1379 KVLGIEAVRSIIISEIQMIMVSHGMSIDIRHIMLMADLMCFKGEILGITRFGIAKMKESV 1438

Query: 1347 LNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRT 1406
            L LASFE T+DHLFDAA + + D I GVSECIIMG+P+ +GTGL KLL    ++    ++
Sbjct: 1439 LMLASFEKTTDHLFDAAVHRRQDDIVGVSECIIMGIPVPLGTGLFKLLYTAKKTNLPRKS 1498

Query: 1407 LLFDNPE 1413
            LL  N +
Sbjct: 1499 LLLGNEQ 1505



 Score =  226 bits (576), Expect = 7e-56,   Method: Compositional matrix adjust.
 Identities = 117/253 (46%), Positives = 163/253 (64%), Gaps = 10/253 (3%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G ++ ED ++  SH+ I+++ L+ Q+ +R P+P+G LD ++GT+ K  NC TCG ++ DC
Sbjct: 113 GILSPEDMIRL-SHVHIINRELFSQE-KRAPMPYGCLDNKLGTSDKGVNCQTCGLSIVDC 170

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
           VGHFGYIDL LPVFHIGYF+ + NILQ ICKN  C+ VLL +E  A +  K+RN  L  L
Sbjct: 171 VGHFGYIDLQLPVFHIGYFKNITNILQMICKN--CSTVLLDDEPKATYLRKMRNRKLDVL 228

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEY 264
            R++L KK+    +K  +CP C  +NG VKK   LK+ HEKYK   + +     DL+ ++
Sbjct: 229 QRRALFKKVYTDCRKKKICPKCNSVNGPVKKVSALKLIHEKYKKEEEHR-----DLIEQF 283

Query: 265 NEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLL 324
            +A+K N E+  H K    + LNPL V  LF+ I  +D  LL M+ ++ +P  LILT LL
Sbjct: 284 EDALKANAEMRNHVKKAQ-EDLNPLVVFNLFKRISYQDTELLDMDPDVGRPERLILTHLL 342

Query: 325 VPPNCIRPSVISD 337
           VPP  IRPSV  D
Sbjct: 343 VPPVSIRPSVPMD 355



 Score =  201 bits (511), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 112/237 (47%), Positives = 156/237 (65%), Gaps = 4/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA L+ D D+  ARIV GR+E+TTLG++  YI+EVF    
Sbjct: 1190 GVPRIKEIINASKTISTPIITATLNCDDDIRAARIVTGRIEKTTLGQISVYIKEVFRSGG 1249

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSFLILKPKDSSKSF 880
             ++ +K+D   I  + +EV  +SI+  I  T+G+     ++   G    I  P+ + +  
Sbjct: 1250 CYLSVKIDKHFIDSMQIEVSAESIKASILGTKGLKLKPANIETLGEKLRIKPPEHNRRLI 1309

Query: 881  NSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
               +  +K  LP+V++ G+  +NR VI + + E   KY+LLVEG +L  VMAT G+KG  
Sbjct: 1310 LYSLQFLKNNLPNVIVHGIPTVNRVVISKPN-EKEDKYQLLVEGYDLLKVMATPGIKGTH 1368

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
              SN+  EV K LGIEA RS I++EI+++M +HGMSID RH ML+ADLM  KGE+LG
Sbjct: 1369 TCSNHIMEVEKVLGIEAVRSIIISEIQMIMVSHGMSIDIRHIMLMADLMCFKGEILG 1425



 Score =  107 bits (268), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 50/74 (67%), Positives = 58/74 (78%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF++G+ PTEFFFHTMGGREGLVDTAVKTAETGYMQRRL+K+LEDL  QYD +
Sbjct: 910 AKGFVGNSFYTGMIPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLMKALEDLSTQYDYT 969

Query: 671 FDAAFYGQTDCISG 684
              +  G    I G
Sbjct: 970 VRDSTGGIVQFIYG 983



 Score = 60.8 bits (146), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 24/49 (48%), Positives = 40/49 (81%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIAS 69
           +LM   +NL+TPRNGE L+AATQDF+T  YL+++++AF++RA+  ++ +
Sbjct: 605 ILMGVTNNLITPRNGEPLVAATQDFLTSSYLISRRDAFYDRARFTQMCT 653



 Score = 54.7 bits (130), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 27/57 (47%), Positives = 37/57 (64%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPE 724
            D  FDAA + + D I GVSECIIMG+P+ +GTGL KLL    ++    ++LL  N +
Sbjct: 1449 DHLFDAAVHRRQDDIVGVSECIIMGIPVPLGTGLFKLLYTAKKTNLPRKSLLLGNEQ 1505


>gi|412989108|emb|CCO15699.1| DNA-directed RNA polymerase III largest subunit [Bathycoccus
           prasinos]
          Length = 1499

 Score =  279 bits (714), Expect = 7e-72,   Method: Compositional matrix adjust.
 Identities = 140/271 (51%), Positives = 183/271 (67%), Gaps = 25/271 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHK+SIMAHRAKV+P RT RFNECVC PYNADFDGDEMN+HLPQTEEA
Sbjct: 479 DGDIVLFNRQPSLHKMSIMAHRAKVMPWRTLRFNECVCAPYNADFDGDEMNIHLPQTEEA 538

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM    NL TP+NGE+LIAATQDF+T  +LLT K  FF+R
Sbjct: 539 RAEAIS--------------LMGVTQNLCTPKNGEILIAATQDFLTASFLLTSKEVFFDR 584

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           +Q  ++A+ +    SD    I   S     P + V+   +WTGKQIFS++++P     + 
Sbjct: 585 SQFGQLAAYM----SDALESIDLPS-----PAI-VKPIEMWTGKQIFSVLIRPRMRDQIF 634

Query: 521 ANLKTKGRAYT-ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            NL+   +AYT  N++ C  D YV ++NSE+++G + K+TLG G K  +FY+L  D+G D
Sbjct: 635 VNLEVSEKAYTKVNQQMCSNDGYVCIQNSEIISGQLGKATLGGGNKTGLFYVLNSDYGAD 694

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           VA  AM RL+++ + ++  RGFSIGI DV P
Sbjct: 695 VAANAMNRLAKLAARWIGIRGFSIGIDDVKP 725



 Score =  238 bits (607), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 149/361 (41%), Positives = 205/361 (56%), Gaps = 69/361 (19%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCE 1149
            +AC +KY   +IEP TAVGA+ AQSIGEPGTQMTLKTFHFAG              E+  
Sbjct: 1071 KACVQKYKSKRIEPGTAVGAVGAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIIN 1130

Query: 1150 YIEEVFVP-------DDSFI----LIKLDMDRIRL------------------------- 1173
              + +  P        D  +    L+K  M++  L                         
Sbjct: 1131 ATKNISTPIITAKLISDKDVKAARLVKGRMEKTMLGEICETISVVLRPSGAYLEFVLDEK 1190

Query: 1174 ----LHLEVDIDSIRYCI---ERTRGISGHLTVSGHSFLILKPKD---SSKSFNSK---- 1219
                L L+V  +S R  I    + +    ++ ++G+  + + P D   SSK    K    
Sbjct: 1191 AIASLQLDVTAESAREAILAAPKLKLKDHNVVLAGNRAIHVIPPDEKASSKDPTGKRAII 1250

Query: 1220 --MYQMKQLLPSVVIKGVQGINRAVIHEEDV---EGVTKYKLLVEGDNLRDVMATYGVKG 1274
              +  ++  +P V+++G+  + RAVI++  +   +    + L+VEG NL DVM+  GV G
Sbjct: 1251 NVLQSLRTAVPKVIVRGLSSVTRAVINKGGMSSKDDKDSFNLIVEGTNLLDVMSIDGVVG 1310

Query: 1275 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGI 1334
             + ++N+  E  ++LGIEAARS ++ EI   M+ HGMSID RH ML+AD+MT KGEVLGI
Sbjct: 1311 EETTTNHIMEAERSLGIEAARSCVIKEINDTMKAHGMSIDSRHSMLLADVMTYKGEVLGI 1370

Query: 1335 TRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            TR G+AKMKESVL LASFE T+DHLF+AA  G+TD I GVSECIIMG+PM +GTG+ KL 
Sbjct: 1371 TRFGMAKMKESVLMLASFEKTTDHLFEAALRGRTDQIDGVSECIIMGVPMPIGTGMFKLK 1430

Query: 1395 Q 1395
            Q
Sbjct: 1431 Q 1431



 Score =  183 bits (465), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 107/249 (42%), Positives = 155/249 (62%), Gaps = 15/249 (6%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++NISTPIITA L  D D+  AR+VKGR+E+T LGE+CE I  V  P  
Sbjct: 1121 GVPRIKEIINATKNISTPIITAKLISDKDVKAARLVKGRMEKTMLGEICETISVVLRPSG 1180

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSGHSFLILKPKD---SS 877
            +++   LD   I  L L+V  +S R  I    + +    ++ ++G+  + + P D   SS
Sbjct: 1181 AYLEFVLDEKAIASLQLDVTAESAREAILAAPKLKLKDHNVVLAGNRAIHVIPPDEKASS 1240

Query: 878  KSFNSK------MYQMKQLLPSVVIKGVQGINRAVIHEEDV---EGVTKYKLLVEGDNLR 928
            K    K      +  ++  +P V+++G+  + RAVI++  +   +    + L+VEG NL 
Sbjct: 1241 KDPTGKRAIINVLQSLRTAVPKVIVRGLSSVTRAVINKGGMSSKDDKDSFNLIVEGTNLL 1300

Query: 929  DVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADL 988
            DVM+  GV G + ++N+  E  ++LGIEAARS ++ EI   M+ HGMSID RH ML+AD+
Sbjct: 1301 DVMSIDGVVGEETTTNHIMEAERSLGIEAARSCVIKEINDTMKAHGMSIDSRHSMLLADV 1360

Query: 989  MTSKGEVLG 997
            MT KGEVLG
Sbjct: 1361 MTYKGEVLG 1369



 Score =  162 bits (411), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 92/246 (37%), Positives = 140/246 (56%), Gaps = 18/246 (7%)

Query: 99  IQIVSKNLYCQDPQRTPIPHGLLDRRMGT-NQKEANCTTCGQNLSDCVGHFGYIDLPLPV 157
           + +  + LY    +R P+  G+LD R+GT N+ +  C TC   + DC GHFGY+ L LPV
Sbjct: 55  LHVTERTLYTPT-ERMPLEGGILDPRLGTTNKSQPECQTCKGKIMDCSGHFGYLKLELPV 113

Query: 158 FHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN-----PALSYLVRKSLKKK 212
           FH+GYF+ +++ LQ +CK  +C  +L+ EE+      KLR+       + +  R+ + KK
Sbjct: 114 FHVGYFKAIVHCLQCVCKECSC--LLMKEEEQEEMLTKLRSREKKIGGVDHAYRRVMFKK 171

Query: 213 ILETTKKVSVCPHCGEINGVVKKCGL-LKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFN 271
           +LE  K+  VC  C  +NG VK+ G  LKI HEKY +   ++    E     + EA+K N
Sbjct: 172 LLEKCKRTKVCFQCEAVNGPVKRAGQNLKIIHEKYTSNKAEQ----EKRERAFEEAMKHN 227

Query: 272 PEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIR 331
            ++  H        LNP+ VLQ+F+ I  +D+ LL +     +P ++++T L VPP CIR
Sbjct: 228 DQLRQHISRAQ-DDLNPIRVLQIFKRIAEKDLSLLDL---AQRPENMVITHLSVPPCCIR 283

Query: 332 PSVISD 337
           PSV  D
Sbjct: 284 PSVELD 289



 Score =  105 bits (262), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 49/64 (76%), Positives = 55/64 (85%), Gaps = 1/64 (1%)

Query: 606 GDVTPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           G+ TP  +GFV NSF+SGL PTEFFFHTM GREGLVDTAVKTAETGYM RRL+K+LEDL 
Sbjct: 844 GEKTPAAKGFVANSFYSGLLPTEFFFHTMAGREGLVDTAVKTAETGYMSRRLMKALEDLS 903

Query: 665 VQYD 668
           + YD
Sbjct: 904 LGYD 907



 Score = 61.2 bits (147), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 27/50 (54%), Positives = 37/50 (74%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM    NL TP+NGE+LIAATQDF+T  +LLT K  FF+R+Q  ++A+ +
Sbjct: 545 LMGVTQNLCTPKNGEILIAATQDFLTASFLLTSKEVFFDRSQFGQLAAYM 594



 Score = 56.2 bits (134), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/39 (64%), Positives = 30/39 (76%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  F+AA  G+TD I GVSECIIMG+PM +GTG+ KL Q
Sbjct: 1393 DHLFEAALRGRTDQIDGVSECIIMGVPMPIGTGMFKLKQ 1431


>gi|440634119|gb|ELR04038.1| hypothetical protein GMDG_06549 [Geomyces destructans 20631-21]
          Length = 1478

 Score =  279 bits (714), Expect = 7e-72,   Method: Compositional matrix adjust.
 Identities = 137/278 (49%), Positives = 179/278 (64%), Gaps = 28/278 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D++LFNRQPSLHKLSIM+H  KV P RTFRFNECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 474 DGDIILFNRQPSLHKLSIMSHYVKVRPWRTFRFNECVCGPYNADFDGDEMNIHVPQTEEA 533

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EA+               LM  K+NL TP++GE +I+ATQDFIT  YLL+ K  FF+R
Sbjct: 534 RTEAIN--------------LMGVKNNLCTPKSGEPIISATQDFITAAYLLSSKENFFDR 579

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                +   ++    DI             P   ++   +WTGKQ+FS++++PN+  PV 
Sbjct: 580 KTFAHLCMYMVDGKMDI----------DIPPPAIIKPEALWTGKQVFSVLMRPNKTSPVK 629

Query: 521 ANLKTKGRAYTA----NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL  K R Y A      +    D ++++RNSE++ G MDK+T+GSG K  +FY +LRDF
Sbjct: 630 VNLDAKCRDYKAVAGQAPDMDPNDGWLVVRNSEVMCGRMDKTTVGSGKKDCIFYTILRDF 689

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGF 614
           G D AV AM RL+++++ YL NRGFSIGI DV P +  
Sbjct: 690 GPDHAVLAMNRLAKLSARYLTNRGFSIGISDVYPSKSL 727



 Score =  204 bits (518), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 132/366 (36%), Positives = 186/366 (50%), Gaps = 80/366 (21%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG------------------ 1145
            E C  KY++A +EP  AVGA+ AQSIGEPGTQMTL+TFHFAG                  
Sbjct: 1075 ELCLTKYLKAHVEPGHAVGAVGAQSIGEPGTQMTLRTFHFAGVAGMSITQGVPRIKEIIN 1134

Query: 1146 ------------------------EVCEYIEEVFVPD------------DSFILIKLDMD 1169
                                     V   IE+ ++ D             + I + +D+ 
Sbjct: 1135 ASKLISTPVMTCPLENPHDIVAARVVKGRIEKTYISDCIRFVEDMWSAKSATICLSVDVQ 1194

Query: 1170 RIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFLIL-----------------KP 1209
             +  +HL++    I   I R + +   +  L + G    +                  K 
Sbjct: 1195 GVSEMHLDITTADIANAILRNKKLKIPNDALDIIGDDIFVRVAHGSNTGTFGRGGAAKKS 1254

Query: 1210 KDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMAT 1269
             D +     ++  +K+ +P++ + G     RA+I ++  E    + + VEG  LR  M T
Sbjct: 1255 TDEASDLLLRVNYLKRTIPTIPVSGYPEATRAIIQQDKGE----HTVHVEGYGLRACMTT 1310

Query: 1270 YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 1329
             GV G + ++N+  E  + LGIEAAR+TI  EI+ VM    M+ID RH  L+AD+MT KG
Sbjct: 1311 EGVIGTRVTTNSVVECNQVLGIEAARTTIANEIESVMSE--MNIDPRHMQLLADVMTYKG 1368

Query: 1330 EVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
            E+LGITR GL+KM++SVL LASFE T DHLFDAA   + D I GVSECIIMG  M+VGTG
Sbjct: 1369 EILGITRFGLSKMRDSVLQLASFEKTPDHLFDAAAGMKKDAIEGVSECIIMGQTMSVGTG 1428

Query: 1390 LIKLLQ 1395
              K+++
Sbjct: 1429 AFKVVR 1434



 Score =  189 bits (481), Expect = 9e-45,   Method: Compositional matrix adjust.
 Identities = 106/271 (39%), Positives = 148/271 (54%), Gaps = 10/271 (3%)

Query: 79  FRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCG 138
           F+ L  G  +  D V Q   +++  + LY  +  R P+P+G +D R+GT+ K   C TCG
Sbjct: 30  FKELKFGVQSTRDIVNQ-GVLEVSDRMLYDVEKNRKPVPNGAVDPRLGTSSKTGRCETCG 88

Query: 139 QNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN 198
           + L++C GHFG++ L LP FHIGY + VI ILQ ICK+  CARVLL E +   F  +LR 
Sbjct: 89  EGLNNCNGHFGHVRLALPAFHIGYLKLVIAILQEICKD--CARVLLTESERRQFLKELRR 146

Query: 199 PALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEK---YKNRTKKKDA 255
           P +  L R  + KKI    +K   CP+C  +NG ++K G+ K++H+K   Y   T  +  
Sbjct: 147 PNIDNLKRTQICKKINAQCRKAKTCPYCSAVNGQIRKTGVFKLTHDKFLAYNKSTAARKV 206

Query: 256 IVEDLLA---EYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL 312
           I  +  A    + EA K N E++ H K  +   LNPL VL LF  I   D  LL +N   
Sbjct: 207 IPPEKAAFDKSFVEAKKTNAELDKHLKKAM-DDLNPLRVLNLFRMITPTDCELLGINPSE 265

Query: 313 SKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
            +P   +   +  PP CIRPSV  D  S  D
Sbjct: 266 GRPEMFLWQYVPAPPICIRPSVAQDGASTED 296



 Score =  140 bits (353), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 91/278 (32%), Positives = 148/278 (53%), Gaps = 27/278 (9%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP++T  L+   D+  AR+VKGR+E+T + +   ++E+++    
Sbjct: 1125 GVPRIKEIINASKLISTPVMTCPLENPHDIVAARVVKGRIEKTYISDCIRFVEDMWSAKS 1184

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFLIL--------- 871
            + I + +D+  +  +HL++    I   I R + +   +  L + G    +          
Sbjct: 1185 ATICLSVDVQGVSEMHLDITTADIANAILRNKKLKIPNDALDIIGDDIFVRVAHGSNTGT 1244

Query: 872  --------KPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVE 923
                    K  D +     ++  +K+ +P++ + G     RA+I ++  E    + + VE
Sbjct: 1245 FGRGGAAKKSTDEASDLLLRVNYLKRTIPTIPVSGYPEATRAIIQQDKGE----HTVHVE 1300

Query: 924  GDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPM 983
            G  LR  M T GV G + ++N+  E  + LGIEAAR+TI  EI+ VM    M+ID RH  
Sbjct: 1301 GYGLRACMTTEGVIGTRVTTNSVVECNQVLGIEAARTTIANEIESVMSE--MNIDPRHMQ 1358

Query: 984  LVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDP 1021
            L+AD+MT KGE+LG  T   L ++ D ++   S    P
Sbjct: 1359 LLADVMTYKGEILGI-TRFGLSKMRDSVLQLASFEKTP 1395



 Score =  105 bits (263), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 47/59 (79%), Positives = 51/59 (86%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSFF GLTPTEF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 847 PSKGFVRNSFFGGLTPTEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSTQYD 905



 Score = 56.2 bits (134), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/54 (46%), Positives = 36/54 (66%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           LM  K+NL TP++GE +I+ATQDFIT  YLL+ K  FF+R     +   ++ G+
Sbjct: 540 LMGVKNNLCTPKSGEPIISATQDFITAAYLLSSKENFFDRKTFAHLCMYMVDGK 593



 Score = 45.4 bits (106), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 22/39 (56%), Positives = 27/39 (69%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  FDAA   + D I GVSECIIMG  M+VGTG  K+++
Sbjct: 1396 DHLFDAAAGMKKDAIEGVSECIIMGQTMSVGTGAFKVVR 1434


>gi|336466341|gb|EGO54506.1| DNA-directed RNA polymerase III largest subunit [Neurospora
           tetrasperma FGSC 2508]
 gi|350286795|gb|EGZ68042.1| DNA-directed RNA polymerase III largest subunit [Neurospora
           tetrasperma FGSC 2509]
          Length = 1475

 Score =  279 bits (714), Expect = 7e-72,   Method: Compositional matrix adjust.
 Identities = 137/281 (48%), Positives = 185/281 (65%), Gaps = 28/281 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIM+HRAKV P RTFR NECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 410 DGDIVLFNRQPSLHKLSIMSHRAKVRPWRTFRLNECVCTPYNADFDGDEMNLHLPQTEEA 469

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  ++NL+TP+NGE +IAATQDFIT  YLL+ K+ F +R
Sbjct: 470 RAEAIN--------------LMGVQNNLITPKNGEPIIAATQDFITAAYLLSSKDLFLDR 515

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                I + ++   + +             P   ++   +WTGKQIF+++++PN+  PV 
Sbjct: 516 KTFTYICTQMLLGETHL----------DLPPPTIIKPVELWTGKQIFNVLMRPNKQSPVL 565

Query: 521 ANLKTKGRAYTAN----EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL+ K + Y A      +    D Y+++RNSE++ G MDKST+G G K +VFY++LRD+
Sbjct: 566 VNLEAKNKVYKAKPGELPDMDIDDCYLVVRNSEVMCGRMDKSTVGGGKKNSVFYVILRDW 625

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           G + A  AM RL+++ +  L  RGFSIG+GDV P +   ++
Sbjct: 626 GPEHAAQAMNRLAKLCARTLTLRGFSIGVGDVYPSKDLTEH 666



 Score =  216 bits (551), Expect = 6e-53,   Method: Compositional matrix adjust.
 Identities = 154/439 (35%), Positives = 215/439 (48%), Gaps = 104/439 (23%)

Query: 1051 RDIKKFLEEFSKKESVTSHQD-KVSQPLREQIL-SHQDKIGHGRESN--PFPSACKAEAC 1106
            +D    L+EF+  E   +  D K+  P  E+I  +H D++    E+    F + C +   
Sbjct: 983  QDNADLLKEFAAWEKKQNGGDIKMLDPEEEEIQQAHVDRVAKVSEATLRKFMNLCLS--- 1039

Query: 1107 REKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEV------------------- 1147
              K+ +A++EP  AVGA+ AQSIGEPGTQMTLKTFHFAG                     
Sbjct: 1040 --KFDKAKVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIIGASK 1097

Query: 1148 --------CE---------------------------YIEEVFVPDDSFILIKLDMDRIR 1172
                    CE                           Y+E+V++PD + I++K+DM  + 
Sbjct: 1098 LISTPVISCELENNRDIKAARIVKGKIEKTYISDVITYVEDVWLPDVAKIVLKIDMQALS 1157

Query: 1173 LLHLEVDIDSIRYCI------------------------------------ERTRGISGH 1196
             + L + +  I   I                                    ++       
Sbjct: 1158 DMQLGIGLREIMVAIVKAKKLKLKVEMDDLKIGPDNTIEVIVSNDWKDLTAQKKAARVRA 1217

Query: 1197 LTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKL 1256
              +     L+    +++  F  ++  +K++LP+V I G     RA+I   +     ++K+
Sbjct: 1218 AAIEKGQLLLTTSDETAADFQLRVNFLKRMLPAVPISGYPEAFRAIIQSSE---SNEHKV 1274

Query: 1257 LVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFR 1316
            LVEG  LR  M T GV G KC SN+  E    LGIEAAR+TI  EI  VM +  M ID R
Sbjct: 1275 LVEGYGLRACMTTEGVIGTKCISNSIMECRDVLGIEAARTTIAKEIGSVMGD--MGIDPR 1332

Query: 1317 HPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSE 1376
            H  L+AD+MT KGE+LGITRHGLAKM++SVL LASFE T DHLFDAA   +TD I GVSE
Sbjct: 1333 HMDLLADVMTYKGEILGITRHGLAKMRDSVLQLASFERTPDHLFDAAAGMKTDRILGVSE 1392

Query: 1377 CIIMGLPMNVGTGLIKLLQ 1395
            CIIMG  M +GTG  ++++
Sbjct: 1393 CIIMGQTMKIGTGAFQVVR 1411



 Score =  191 bits (485), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 105/271 (38%), Positives = 153/271 (56%), Gaps = 10/271 (3%)

Query: 79  FRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCG 138
           FR L  G  + +D V Q   +++    LY  +  R   PHG LD R+GT+ K   C TC 
Sbjct: 21  FRALQFGVQSHQDIVNQ-GVLEVSDNLLYDVENGRRTFPHGPLDPRLGTSSKTGTCETCN 79

Query: 139 QNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN 198
             L  C GHFG++ LPLPVFHIGY + +   LQ+ICK  TC++VLL EE  A F   LR 
Sbjct: 80  LPLQSCAGHFGHVRLPLPVFHIGYLKYIQATLQNICK--TCSKVLLEEEPKAKFLKALRA 137

Query: 199 PALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKY----KNRTKKKD 254
           P +  L R ++ KKI +  +K   CP+CG+  GV++K  ++K++H+K+    K+  +KK 
Sbjct: 138 PGIDNLKRSAILKKINDECRKQKTCPYCGDTQGVIRKLSVMKLTHDKFSHFNKSTAQKKV 197

Query: 255 AIVEDLL--AEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL 312
             V      + + +A  F P++E H K  +   ++PL+VL+LF+ I  ED  LL +N   
Sbjct: 198 PPVAKAAFDSSFIQAKTFTPDLEKHSKKAM-DDMDPLKVLKLFKKITAEDCELLGLNPSE 256

Query: 313 SKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
            +P   +   L  PP CIRPSV  +  S+ D
Sbjct: 257 GRPEMFLWQYLPAPPICIRPSVQQEAASNED 287



 Score =  149 bits (375), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 95/270 (35%), Positives = 142/270 (52%), Gaps = 41/270 (15%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEII AS+ ISTP+I+  L+ + D+  ARIVKG++E+T + +V  Y+E+V++PD 
Sbjct: 1085 GVPRIKEIIGASKLISTPVISCELENNRDIKAARIVKGKIEKTYISDVITYVEDVWLPDV 1144

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCI-------------------------------- 851
            + I++K+DM  +  + L + +  I   I                                
Sbjct: 1145 AKIVLKIDMQALSDMQLGIGLREIMVAIVKAKKLKLKVEMDDLKIGPDNTIEVIVSNDWK 1204

Query: 852  ----ERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVI 907
                ++         +     L+    +++  F  ++  +K++LP+V I G     RA+I
Sbjct: 1205 DLTAQKKAARVRAAAIEKGQLLLTTSDETAADFQLRVNFLKRMLPAVPISGYPEAFRAII 1264

Query: 908  HEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIK 967
               +     ++K+LVEG  LR  M T GV G KC SN+  E    LGIEAAR+TI  EI 
Sbjct: 1265 QSSES---NEHKVLVEGYGLRACMTTEGVIGTKCISNSIMECRDVLGIEAARTTIAKEIG 1321

Query: 968  LVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             VM +  M ID RH  L+AD+MT KGE+LG
Sbjct: 1322 SVMGD--MGIDPRHMDLLADVMTYKGEILG 1349



 Score =  103 bits (256), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 45/59 (76%), Positives = 51/59 (86%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSF++GL PTEF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 783 PSKGFVRNSFYTGLVPTEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSTQYD 841



 Score = 58.9 bits (141), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/53 (49%), Positives = 37/53 (69%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           LM  ++NL+TP+NGE +IAATQDFIT  YLL+ K+ F +R     I + ++ G
Sbjct: 476 LMGVQNNLITPKNGEPIIAATQDFITAAYLLSSKDLFLDRKTFTYICTQMLLG 528



 Score = 43.1 bits (100), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 21/39 (53%), Positives = 27/39 (69%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  FDAA   +TD I GVSECIIMG  M +GTG  ++++
Sbjct: 1373 DHLFDAAAGMKTDRILGVSECIIMGQTMKIGTGAFQVVR 1411


>gi|367014307|ref|XP_003681653.1| hypothetical protein TDEL_0E01990 [Torulaspora delbrueckii]
 gi|359749314|emb|CCE92442.1| hypothetical protein TDEL_0E01990 [Torulaspora delbrueckii]
          Length = 1460

 Score =  279 bits (714), Expect = 8e-72,   Method: Compositional matrix adjust.
 Identities = 140/277 (50%), Positives = 186/277 (67%), Gaps = 30/277 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH+LSI++H AK+ P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 468 DGDVVLFNRQPSLHRLSILSHYAKIRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 527

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+R
Sbjct: 528 RAEAIN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDR 573

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
               ++ S +++D +          +    P + ++   +WTGKQ+FSL++KPN+  PV 
Sbjct: 574 GSLTQLLS-MMSDGN--------LQFDIPAPAI-MKPCYLWTGKQVFSLLIKPNKKSPVV 623

Query: 521 ANLKTKGRAY------TANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLR 574
            NL  K + +      +   E    D YVI+R SE+L+G MDKS LG G K +VFY +LR
Sbjct: 624 INLDAKNKVFIPPKSKSLPSEMSQNDGYVIIRGSEILSGVMDKSVLGDGKKHSVFYTILR 683

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           D+G   A  AM R++++ + YL NRGFSIGI DVTP 
Sbjct: 684 DYGPQEAANAMNRMAKLCARYLGNRGFSIGISDVTPA 720



 Score =  248 bits (634), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 156/381 (40%), Positives = 209/381 (54%), Gaps = 85/381 (22%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG----------------------- 1145
            KY RA++EP TAVGA+ AQSIGEPGTQMTLKTFHFAG                       
Sbjct: 1077 KYRRARVEPGTAVGAIGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIINASKVI 1136

Query: 1146 -------------------EVCEYIEEVFVPDDSFIL------------IKLDMDRIRLL 1174
                                V   IE+  + D +F +            +++D++ I  L
Sbjct: 1137 STPIINAVLVNDNDERAARVVKGRIEKTLLSDVAFYIQDVYQDNLSFMQVRIDLNTIDKL 1196

Query: 1175 HLEVDIDSIRYCIERTRGISGHLTVSGHSFLIL--------------KPKDSSKSFNS-- 1218
             LE+ I+ I   I R    +  L +      IL              K K  S S     
Sbjct: 1197 QLELTIEDIAVAITR----APKLKIQASDVTILDKDKIAINVFPEGYKAKSISTSAKEPH 1252

Query: 1219 ------KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGV 1272
                  +M Q+++ LP +V+KG+  I+RAVI+  D    TK +LLVEG  LRDVM+T GV
Sbjct: 1253 ENDVFFRMQQLRRSLPGIVVKGLPDISRAVINVRD---DTKRELLVEGYGLRDVMSTDGV 1309

Query: 1273 KGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL 1332
             G K ++N+  EV+  LGIEAAR++I+ EI   M NHGMS+D RH  L+ D+MT KGE+L
Sbjct: 1310 VGHKTATNHILEVFSVLGIEAARASIIGEIDYTMSNHGMSVDPRHIQLLGDVMTYKGEIL 1369

Query: 1333 GITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIK 1392
            GITR GL+KM++SVL LASFE T+DHLFDAAFY + D + GVSECII+G  M++GTG  K
Sbjct: 1370 GITRFGLSKMRDSVLQLASFEKTTDHLFDAAFYMKRDAVEGVSECIILGQTMSIGTGAFK 1429

Query: 1393 LLQAVPRSEP--VPRTLLFDN 1411
            +++     E    P+  LF++
Sbjct: 1430 VIKGTDLHEQDLRPKPTLFES 1450



 Score =  187 bits (475), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 114/256 (44%), Positives = 155/256 (60%), Gaps = 29/256 (11%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII A L  D D   AR+VKGR+E+T L +V  YI++V+  + 
Sbjct: 1122 GVPRIKEIINASKVISTPIINAVLVNDNDERAARVVKGRIEKTLLSDVAFYIQDVYQDNL 1181

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLIL------------ 871
            SF+ +++D++ I  L LE+ I+ I   I R    +  L +      IL            
Sbjct: 1182 SFMQVRIDLNTIDKLQLELTIEDIAVAITR----APKLKIQASDVTILDKDKIAINVFPE 1237

Query: 872  --KPKDSSKSFNS--------KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLL 921
              K K  S S           +M Q+++ LP +V+KG+  I+RAVI+  D    TK +LL
Sbjct: 1238 GYKAKSISTSAKEPHENDVFFRMQQLRRSLPGIVVKGLPDISRAVINVRDD---TKRELL 1294

Query: 922  VEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRH 981
            VEG  LRDVM+T GV G K ++N+  EV+  LGIEAAR++I+ EI   M NHGMS+D RH
Sbjct: 1295 VEGYGLRDVMSTDGVVGHKTATNHILEVFSVLGIEAARASIIGEIDYTMSNHGMSVDPRH 1354

Query: 982  PMLVADLMTSKGEVLG 997
              L+ D+MT KGE+LG
Sbjct: 1355 IQLLGDVMTYKGEILG 1370



 Score =  176 bits (447), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 97/248 (39%), Positives = 140/248 (56%), Gaps = 11/248 (4%)

Query: 96  QSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPL 155
           QS ++I +++L+  +  R P   G LD +MG +     CTTC  NL+ C GHFG+I L L
Sbjct: 29  QSEVEISTRDLFDLENGRAPRAGGALDPKMGVSSSSLECTTCHGNLASCHGHFGHIKLAL 88

Query: 156 PVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILE 215
           PVFH+GYF+  I ILQ ICKN  C+ VLL +     F ++LR P +  L R  +  K+L+
Sbjct: 89  PVFHVGYFKATIQILQGICKN--CSAVLLDDHDRRHFLSELRRPGVDNLRRMGILSKVLD 146

Query: 216 TTKKVSVCPHCGEINGVVKKCGL------LKISHEKYKNRTKKKDAIVEDLLAEYNEAVK 269
             KK   C  CG +NGVVKK         LKI H+ ++   KK     +  + +++E + 
Sbjct: 147 QCKKQRRCLQCGALNGVVKKAAAGSGSASLKIIHDTFRWAGKKSVPEKDKWVGDWDEVLS 206

Query: 270 FNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNA--ELSKPSDLILTRLLVPP 327
            NPE+E + K   +  LNPL+ L LF+ +  ED  LL +++  +  +P   I   L  PP
Sbjct: 207 HNPELERYVKR-CMDDLNPLKTLNLFKQLKPEDCELLGIDSSNKSGRPETYIWRYLPAPP 265

Query: 328 NCIRPSVI 335
            CIRPSV+
Sbjct: 266 VCIRPSVM 273



 Score =  102 bits (253), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 46/57 (80%), Positives = 50/57 (87%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NSFFSGLTP EF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 845 KGFVRNSFFSGLTPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSCQYD 901



 Score = 62.4 bits (150), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/57 (49%), Positives = 41/57 (71%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVF 78
           LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+R    ++ S +  G   F
Sbjct: 534 LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDRGSLTQLLSMMSDGNLQF 590



 Score = 51.6 bits (122), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 25/57 (43%), Positives = 36/57 (63%), Gaps = 2/57 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEP--VPRTLLFDN 722
            D  FDAAFY + D + GVSECII+G  M++GTG  K+++     E    P+  LF++
Sbjct: 1394 DHLFDAAFYMKRDAVEGVSECIILGQTMSIGTGAFKVIKGTDLHEQDLRPKPTLFES 1450


>gi|164426670|ref|XP_956571.2| DNA-directed RNA polymerase III largest subunit [Neurospora crassa
           OR74A]
 gi|157071429|gb|EAA27335.2| DNA-directed RNA polymerase III largest subunit [Neurospora crassa
           OR74A]
          Length = 1474

 Score =  279 bits (714), Expect = 8e-72,   Method: Compositional matrix adjust.
 Identities = 137/281 (48%), Positives = 185/281 (65%), Gaps = 28/281 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIM+HRAKV P RTFR NECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 409 DGDIVLFNRQPSLHKLSIMSHRAKVRPWRTFRLNECVCTPYNADFDGDEMNLHLPQTEEA 468

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  ++NL+TP+NGE +IAATQDFIT  YLL+ K+ F +R
Sbjct: 469 RAEAIN--------------LMGVQNNLITPKNGEPIIAATQDFITAAYLLSSKDLFLDR 514

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                I + ++   + +             P   ++   +WTGKQIF+++++PN+  PV 
Sbjct: 515 KTFTYICTQMLLGETHL----------DLPPPTIIKPVELWTGKQIFNVLMRPNKQSPVL 564

Query: 521 ANLKTKGRAYTAN----EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL+ K + Y A      +    D Y+++RNSE++ G MDKST+G G K +VFY++LRD+
Sbjct: 565 VNLEAKNKVYKAKPGELPDMDIDDCYLVVRNSEVMCGRMDKSTVGGGKKNSVFYVILRDW 624

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           G + A  AM RL+++ +  L  RGFSIG+GDV P +   ++
Sbjct: 625 GPEHAAQAMNRLAKLCARTLTLRGFSIGVGDVYPSKDLTEH 665



 Score =  216 bits (551), Expect = 6e-53,   Method: Compositional matrix adjust.
 Identities = 154/439 (35%), Positives = 215/439 (48%), Gaps = 104/439 (23%)

Query: 1051 RDIKKFLEEFSKKESVTSHQD-KVSQPLREQIL-SHQDKIGHGRESN--PFPSACKAEAC 1106
            +D    L+EF+  E   +  D K+  P  E+I  +H D++    E+    F + C +   
Sbjct: 982  QDNADLLKEFAAWEKKQNGGDIKMLDPEEEEIQQAHVDRVAKVSEATLRKFMNLCLS--- 1038

Query: 1107 REKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEV------------------- 1147
              K+ +A++EP  AVGA+ AQSIGEPGTQMTLKTFHFAG                     
Sbjct: 1039 --KFDKAKVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIIGASK 1096

Query: 1148 --------CE---------------------------YIEEVFVPDDSFILIKLDMDRIR 1172
                    CE                           Y+E+V++PD + I++K+DM  + 
Sbjct: 1097 LISTPVISCELENNRDIKAARIVKGKIEKTYISDVITYVEDVWLPDVAKIVLKIDMQALS 1156

Query: 1173 LLHLEVDIDSIRYCI------------------------------------ERTRGISGH 1196
             + L + +  I   I                                    ++       
Sbjct: 1157 DMQLGIGLREIMVAIVKAKKLKLKVEMDDLKIGPDNTIEVIVSNDWKDLTAQKKAARVRA 1216

Query: 1197 LTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKL 1256
              +     L+    +++  F  ++  +K++LP+V I G     RA+I   +     ++K+
Sbjct: 1217 AAIEKGQLLLTTSDETAADFQLRVNFLKRMLPAVPISGYPEAFRAIIQSSE---SNEHKV 1273

Query: 1257 LVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFR 1316
            LVEG  LR  M T GV G KC SN+  E    LGIEAAR+TI  EI  VM +  M ID R
Sbjct: 1274 LVEGYGLRACMTTEGVIGTKCISNSIMECRDVLGIEAARTTIAKEIGSVMGD--MGIDPR 1331

Query: 1317 HPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSE 1376
            H  L+AD+MT KGE+LGITRHGLAKM++SVL LASFE T DHLFDAA   +TD I GVSE
Sbjct: 1332 HMDLLADVMTYKGEILGITRHGLAKMRDSVLQLASFERTPDHLFDAAAGMKTDRILGVSE 1391

Query: 1377 CIIMGLPMNVGTGLIKLLQ 1395
            CIIMG  M +GTG  ++++
Sbjct: 1392 CIIMGQTMKIGTGAFQVVR 1410



 Score =  191 bits (485), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 105/271 (38%), Positives = 153/271 (56%), Gaps = 10/271 (3%)

Query: 79  FRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCG 138
           FR L  G  + +D V Q   +++    LY  +  R   PHG LD R+GT+ K   C TC 
Sbjct: 21  FRALQFGVQSHQDIVNQ-GVLEVSDNLLYDVENGRRTFPHGPLDPRLGTSSKTGTCETCN 79

Query: 139 QNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN 198
             L  C GHFG++ LPLPVFHIGY + +   LQ+ICK  TC++VLL EE  A F   LR 
Sbjct: 80  LPLQSCAGHFGHVRLPLPVFHIGYLKYIQATLQNICK--TCSKVLLEEEPKAKFLKALRA 137

Query: 199 PALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKY----KNRTKKKD 254
           P +  L R ++ KKI +  +K   CP+CG+  GV++K  ++K++H+K+    K+  +KK 
Sbjct: 138 PGIDNLKRSAILKKINDECRKQKTCPYCGDTQGVIRKLSVMKLTHDKFSHFNKSTAQKKV 197

Query: 255 AIVEDLL--AEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL 312
             V      + + +A  F P++E H K  +   ++PL+VL+LF+ I  ED  LL +N   
Sbjct: 198 PPVAKAAFDSSFIQAKTFTPDLEKHSKKAM-DDMDPLKVLKLFKKITAEDCELLGLNPSE 256

Query: 313 SKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
            +P   +   L  PP CIRPSV  +  S+ D
Sbjct: 257 GRPEMFLWQYLPAPPICIRPSVQQEAASNED 287



 Score =  149 bits (375), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 95/270 (35%), Positives = 142/270 (52%), Gaps = 41/270 (15%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEII AS+ ISTP+I+  L+ + D+  ARIVKG++E+T + +V  Y+E+V++PD 
Sbjct: 1084 GVPRIKEIIGASKLISTPVISCELENNRDIKAARIVKGKIEKTYISDVITYVEDVWLPDV 1143

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCI-------------------------------- 851
            + I++K+DM  +  + L + +  I   I                                
Sbjct: 1144 AKIVLKIDMQALSDMQLGIGLREIMVAIVKAKKLKLKVEMDDLKIGPDNTIEVIVSNDWK 1203

Query: 852  ----ERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVI 907
                ++         +     L+    +++  F  ++  +K++LP+V I G     RA+I
Sbjct: 1204 DLTAQKKAARVRAAAIEKGQLLLTTSDETAADFQLRVNFLKRMLPAVPISGYPEAFRAII 1263

Query: 908  HEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIK 967
               +     ++K+LVEG  LR  M T GV G KC SN+  E    LGIEAAR+TI  EI 
Sbjct: 1264 QSSES---NEHKVLVEGYGLRACMTTEGVIGTKCISNSIMECRDVLGIEAARTTIAKEIG 1320

Query: 968  LVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             VM +  M ID RH  L+AD+MT KGE+LG
Sbjct: 1321 SVMGD--MGIDPRHMDLLADVMTYKGEILG 1348



 Score =  103 bits (256), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 45/59 (76%), Positives = 51/59 (86%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSF++GL PTEF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 782 PSKGFVRNSFYTGLVPTEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSTQYD 840



 Score = 58.5 bits (140), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/53 (49%), Positives = 37/53 (69%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           LM  ++NL+TP+NGE +IAATQDFIT  YLL+ K+ F +R     I + ++ G
Sbjct: 475 LMGVQNNLITPKNGEPIIAATQDFITAAYLLSSKDLFLDRKTFTYICTQMLLG 527



 Score = 43.1 bits (100), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 21/39 (53%), Positives = 27/39 (69%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  FDAA   +TD I GVSECIIMG  M +GTG  ++++
Sbjct: 1372 DHLFDAAAGMKTDRILGVSECIIMGQTMKIGTGAFQVVR 1410


>gi|328354455|emb|CCA40852.1| DNA-directed RNA polymerase II subunit A [Komagataella pastoris CBS
           7435]
          Length = 1460

 Score =  279 bits (714), Expect = 8e-72,   Method: Compositional matrix adjust.
 Identities = 145/276 (52%), Positives = 187/276 (67%), Gaps = 29/276 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH+LSI++H AK+ P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 469 DGDVVLFNRQPSLHRLSILSHFAKIRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 528

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R+EA+               LM  K+NL+TP++GE +IAATQDFITG YL++ K+ FF+R
Sbjct: 529 RSEAMN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDTFFDR 574

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A  ++I    +A  SD    I+ F      P +F + A +WTGKQ+FSL++KPN    VN
Sbjct: 575 ASLVQI----LASMSD---GIEHFDLPP--PSIF-KPAYLWTGKQVFSLLIKPNAKSNVN 624

Query: 521 ANLKTKGRAYTA-----NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL  K + +         E    D +VI+R S++L+G MDKS LG G K +VFY +LRD
Sbjct: 625 INLDAKCKTFIPPPAGQPSEMSPNDGFVIVRGSKILSGVMDKSLLGDGKKHSVFYTILRD 684

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           +G   A  AM R++++ + YL NRGFSIGI DVTPG
Sbjct: 685 YGPHEAANAMNRMAKLCARYLGNRGFSIGINDVTPG 720



 Score =  248 bits (634), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 158/387 (40%), Positives = 213/387 (55%), Gaps = 82/387 (21%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCE 1149
            E    KY RA++EP TAVGA+ AQSIGEPGTQMTLKTFHFAG              E+  
Sbjct: 1067 ELSATKYNRAKVEPGTAVGAIGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIIN 1126

Query: 1150 YIEEVFVP---------DD-------------------------------SFILIKLDMD 1169
              + +  P         DD                               +++ +K+D++
Sbjct: 1127 ASKTISTPIINAVLVNEDDERAARVVKGRIEKTILQDVVYYIQDVYKENQAYLQVKVDLE 1186

Query: 1170 RIRLLHLEVDIDSIRYCIERTRG-------------------ISGHLTVSGHSFLILKPK 1210
             I  L LE++ID IR  I +                      +S  L  S       K  
Sbjct: 1187 TIERLQLELNIDEIRLAIVKAPKLKLALEDVIITGRNKISVCVSDALLDSISKTAAAKGI 1246

Query: 1211 DSSKSFNS----KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDV 1266
            D+S +  +    +M  +K++L  VV+KG+  I+RAVI+  D +G  K +LLVEG  L++V
Sbjct: 1247 DTSSTMANELFFRMQHLKRVLTKVVVKGLPDISRAVINIRD-DG--KKELLVEGYGLKEV 1303

Query: 1267 MATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMT 1326
            +AT GV G K  +N+  EVY+TLGIEAARS I+ EI   M  HGMS+D RH  L+ D+M+
Sbjct: 1304 IATDGVVGCKTKTNHVLEVYETLGIEAARSCIINEIDYTMSKHGMSVDPRHIQLLGDVMS 1363

Query: 1327 SKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNV 1386
             KGEVLGITR GLAKM++SVL LASFE T+DHLFDAAFY + D + GVSEC+I+G  M +
Sbjct: 1364 YKGEVLGITRFGLAKMRDSVLQLASFEKTTDHLFDAAFYMKKDLVEGVSECVILGQTMTI 1423

Query: 1387 GTGLIKLLQAVP--RSEPVPRTLLFDN 1411
            GTG  +L++     R + V +  LFD+
Sbjct: 1424 GTGAFQLVKKTETQRGQLVAKPTLFDD 1450



 Score =  183 bits (465), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 112/257 (43%), Positives = 157/257 (61%), Gaps = 26/257 (10%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII A L  + D   AR+VKGR+E+T L +V  YI++V+  + 
Sbjct: 1117 GVPRIKEIINASKTISTPIINAVLVNEDDERAARVVKGRIEKTILQDVVYYIQDVYKENQ 1176

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRG-------------------ISGHLTVS 864
            +++ +K+D++ I  L LE++ID IR  I +                      +S  L  S
Sbjct: 1177 AYLQVKVDLETIERLQLELNIDEIRLAIVKAPKLKLALEDVIITGRNKISVCVSDALLDS 1236

Query: 865  GHSFLILKPKDSSKSFNS----KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKL 920
                   K  D+S +  +    +M  +K++L  VV+KG+  I+RAVI+  D +G  K +L
Sbjct: 1237 ISKTAAAKGIDTSSTMANELFFRMQHLKRVLTKVVVKGLPDISRAVINIRD-DG--KKEL 1293

Query: 921  LVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFR 980
            LVEG  L++V+AT GV G K  +N+  EVY+TLGIEAARS I+ EI   M  HGMS+D R
Sbjct: 1294 LVEGYGLKEVIATDGVVGCKTKTNHVLEVYETLGIEAARSCIINEIDYTMSKHGMSVDPR 1353

Query: 981  HPMLVADLMTSKGEVLG 997
            H  L+ D+M+ KGEVLG
Sbjct: 1354 HIQLLGDVMSYKGEVLG 1370



 Score =  171 bits (434), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 101/269 (37%), Positives = 146/269 (54%), Gaps = 11/269 (4%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           +E      D++  QS +++ ++NL+  +  R P   G LD RMG + K   C TC  NL+
Sbjct: 16  LEFNALSSDQIIAQSEVEVNTRNLFNLEKGRAPAKDGALDTRMGVSSKSGECATCHGNLA 75

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALS 202
            C GHFG+I L LPVFH+GYF+ VI +LQ+ICK  +CA VLL E+        LR+P   
Sbjct: 76  TCHGHFGHIKLALPVFHVGYFKAVIQVLQTICK--SCASVLLDEKTKRKALEDLRSPNND 133

Query: 203 YLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGL------LKISHEKYKNRTKKKDAI 256
            L R  + K+ILE  KK   C  CG +NGVVKK         LK+ H+ ++   KK    
Sbjct: 134 NLRRMKIIKRILEQAKKQRRCLKCGALNGVVKKASAGAGPASLKVIHDTFRWIGKKPSQE 193

Query: 257 VEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPS 316
             +   +++  +  NP++E   K      LNPL+VL LF+ +   D  LL ++       
Sbjct: 194 KVEWYEDFDNLLINNPDLEKFLKRAY-DDLNPLKVLNLFKQVDPSDCELLGIDTTRGGRP 252

Query: 317 DLILTRLL-VPPNCIRPSVI-SDLKSDND 343
           ++ L R +  PP CIRPSV+ SD  + N+
Sbjct: 253 EMYLWRYVPAPPVCIRPSVLMSDSNTSNE 281



 Score = 99.4 bits (246), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 46/61 (75%), Positives = 51/61 (83%), Gaps = 1/61 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV+NSF+SGL P EF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QY
Sbjct: 841 TPQSKGFVRNSFYSGLNPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSAQY 900

Query: 668 D 668
           D
Sbjct: 901 D 901



 Score = 64.7 bits (156), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 29/57 (50%), Positives = 44/57 (77%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVF 78
           LM  K+NL+TP++GE +IAATQDFITG YL++ K+ FF+RA  ++I +++  G + F
Sbjct: 535 LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDTFFDRASLVQILASMSDGIEHF 591



 Score = 52.8 bits (125), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 25/57 (43%), Positives = 36/57 (63%), Gaps = 2/57 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP--RSEPVPRTLLFDN 722
            D  FDAAFY + D + GVSEC+I+G  M +GTG  +L++     R + V +  LFD+
Sbjct: 1394 DHLFDAAFYMKKDLVEGVSECVILGQTMTIGTGAFQLVKKTETQRGQLVAKPTLFDD 1450


>gi|254573222|ref|XP_002493720.1| RNA polymerase III subunit C160, part of core enzyme [Komagataella
           pastoris GS115]
 gi|238033519|emb|CAY71541.1| RNA polymerase III subunit C160, part of core enzyme [Komagataella
           pastoris GS115]
          Length = 1460

 Score =  279 bits (713), Expect = 9e-72,   Method: Compositional matrix adjust.
 Identities = 145/276 (52%), Positives = 187/276 (67%), Gaps = 29/276 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH+LSI++H AK+ P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 469 DGDVVLFNRQPSLHRLSILSHFAKIRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 528

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R+EA+               LM  K+NL+TP++GE +IAATQDFITG YL++ K+ FF+R
Sbjct: 529 RSEAMN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDTFFDR 574

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A  ++I    +A  SD    I+ F      P +F + A +WTGKQ+FSL++KPN    VN
Sbjct: 575 ASLVQI----LASMSD---GIEHFDLPP--PSIF-KPAYLWTGKQVFSLLIKPNAKSNVN 624

Query: 521 ANLKTKGRAYTA-----NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL  K + +         E    D +VI+R S++L+G MDKS LG G K +VFY +LRD
Sbjct: 625 INLDAKCKTFIPPPAGQPSEMSPNDGFVIVRGSKILSGVMDKSLLGDGKKHSVFYTILRD 684

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           +G   A  AM R++++ + YL NRGFSIGI DVTPG
Sbjct: 685 YGPHEAANAMNRMAKLCARYLGNRGFSIGINDVTPG 720



 Score =  248 bits (633), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 158/387 (40%), Positives = 213/387 (55%), Gaps = 82/387 (21%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCE 1149
            E    KY RA++EP TAVGA+ AQSIGEPGTQMTLKTFHFAG              E+  
Sbjct: 1067 ELSATKYNRAKVEPGTAVGAIGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIIN 1126

Query: 1150 YIEEVFVP---------DD-------------------------------SFILIKLDMD 1169
              + +  P         DD                               +++ +K+D++
Sbjct: 1127 ASKTISTPIINAVLVNEDDERAARVVKGRIEKTILQDVVYYIQDVYKENQAYLQVKVDLE 1186

Query: 1170 RIRLLHLEVDIDSIRYCIERTRG-------------------ISGHLTVSGHSFLILKPK 1210
             I  L LE++ID IR  I +                      +S  L  S       K  
Sbjct: 1187 TIERLQLELNIDEIRLAIVKAPKLKLALEDVIITGRNKISVCVSDALLDSISKTAAAKGI 1246

Query: 1211 DSSKSFNS----KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDV 1266
            D+S +  +    +M  +K++L  VV+KG+  I+RAVI+  D +G  K +LLVEG  L++V
Sbjct: 1247 DTSSTMANELFFRMQHLKRVLTKVVVKGLPDISRAVINIRD-DG--KKELLVEGYGLKEV 1303

Query: 1267 MATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMT 1326
            +AT GV G K  +N+  EVY+TLGIEAARS I+ EI   M  HGMS+D RH  L+ D+M+
Sbjct: 1304 IATDGVVGCKTKTNHVLEVYETLGIEAARSCIINEIDYTMSKHGMSVDPRHIQLLGDVMS 1363

Query: 1327 SKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNV 1386
             KGEVLGITR GLAKM++SVL LASFE T+DHLFDAAFY + D + GVSEC+I+G  M +
Sbjct: 1364 YKGEVLGITRFGLAKMRDSVLQLASFEKTTDHLFDAAFYMKKDLVEGVSECVILGQTMTI 1423

Query: 1387 GTGLIKLLQAVP--RSEPVPRTLLFDN 1411
            GTG  +L++     R + V +  LFD+
Sbjct: 1424 GTGAFQLVKKTETQRGQLVAKPTLFDD 1450



 Score =  183 bits (464), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 112/257 (43%), Positives = 157/257 (61%), Gaps = 26/257 (10%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII A L  + D   AR+VKGR+E+T L +V  YI++V+  + 
Sbjct: 1117 GVPRIKEIINASKTISTPIINAVLVNEDDERAARVVKGRIEKTILQDVVYYIQDVYKENQ 1176

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRG-------------------ISGHLTVS 864
            +++ +K+D++ I  L LE++ID IR  I +                      +S  L  S
Sbjct: 1177 AYLQVKVDLETIERLQLELNIDEIRLAIVKAPKLKLALEDVIITGRNKISVCVSDALLDS 1236

Query: 865  GHSFLILKPKDSSKSFNS----KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKL 920
                   K  D+S +  +    +M  +K++L  VV+KG+  I+RAVI+  D +G  K +L
Sbjct: 1237 ISKTAAAKGIDTSSTMANELFFRMQHLKRVLTKVVVKGLPDISRAVINIRD-DG--KKEL 1293

Query: 921  LVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFR 980
            LVEG  L++V+AT GV G K  +N+  EVY+TLGIEAARS I+ EI   M  HGMS+D R
Sbjct: 1294 LVEGYGLKEVIATDGVVGCKTKTNHVLEVYETLGIEAARSCIINEIDYTMSKHGMSVDPR 1353

Query: 981  HPMLVADLMTSKGEVLG 997
            H  L+ D+M+ KGEVLG
Sbjct: 1354 HIQLLGDVMSYKGEVLG 1370



 Score =  171 bits (434), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 101/269 (37%), Positives = 146/269 (54%), Gaps = 11/269 (4%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           +E      D++  QS +++ ++NL+  +  R P   G LD RMG + K   C TC  NL+
Sbjct: 16  LEFNALSSDQIIAQSEVEVNTRNLFNLEKGRAPAKDGALDTRMGVSSKSGECATCHGNLA 75

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALS 202
            C GHFG+I L LPVFH+GYF+ VI +LQ+ICK  +CA VLL E+        LR+P   
Sbjct: 76  TCHGHFGHIKLALPVFHVGYFKAVIQVLQTICK--SCASVLLDEKTKRKALEDLRSPNND 133

Query: 203 YLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGL------LKISHEKYKNRTKKKDAI 256
            L R  + K+ILE  KK   C  CG +NGVVKK         LK+ H+ ++   KK    
Sbjct: 134 NLRRMKIIKRILEQAKKQRRCLKCGALNGVVKKASAGAGPASLKVIHDTFRWIGKKPSQE 193

Query: 257 VEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPS 316
             +   +++  +  NP++E   K      LNPL+VL LF+ +   D  LL ++       
Sbjct: 194 KVEWYEDFDNLLINNPDLEKFLKRAY-DDLNPLKVLNLFKQVDPSDCELLGIDTTRGGRP 252

Query: 317 DLILTRLL-VPPNCIRPSVI-SDLKSDND 343
           ++ L R +  PP CIRPSV+ SD  + N+
Sbjct: 253 EMYLWRYVPAPPVCIRPSVLMSDSNTSNE 281



 Score = 99.4 bits (246), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 46/61 (75%), Positives = 51/61 (83%), Gaps = 1/61 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV+NSF+SGL P EF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QY
Sbjct: 841 TPQSKGFVRNSFYSGLNPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSAQY 900

Query: 668 D 668
           D
Sbjct: 901 D 901



 Score = 64.7 bits (156), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 29/57 (50%), Positives = 44/57 (77%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVF 78
           LM  K+NL+TP++GE +IAATQDFITG YL++ K+ FF+RA  ++I +++  G + F
Sbjct: 535 LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDTFFDRASLVQILASMSDGIEHF 591



 Score = 52.8 bits (125), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 25/57 (43%), Positives = 36/57 (63%), Gaps = 2/57 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP--RSEPVPRTLLFDN 722
            D  FDAAFY + D + GVSEC+I+G  M +GTG  +L++     R + V +  LFD+
Sbjct: 1394 DHLFDAAFYMKKDLVEGVSECVILGQTMTIGTGAFQLVKKTETQRGQLVAKPTLFDD 1450


>gi|350640058|gb|EHA28411.1| hypothetical protein ASPNIDRAFT_128642 [Aspergillus niger ATCC 1015]
          Length = 2063

 Score =  278 bits (712), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 138/282 (48%), Positives = 187/282 (66%), Gaps = 29/282 (10%)

Query: 341  DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
            D D+VLFNRQPSLHKLSI++H AKV PHRTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 1083 DGDIVLFNRQPSLHKLSILSHFAKVRPHRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 1142

Query: 401  RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
            RAEA+               LM  K+NL TP+NGE +I+A QDFI+  Y+L+ K+ FF+R
Sbjct: 1143 RAEAME--------------LMGVKNNLATPKNGEPIISAIQDFISAAYILSSKDNFFDR 1188

Query: 461  AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                +I   ++       G   RF      P   ++  ++WTGKQ+F+++++PN+D PV 
Sbjct: 1189 RSFTQICLYML-------GPQTRF---DLPPPAVLKPQMLWTGKQVFNILMRPNKDDPVL 1238

Query: 521  ANLKTKGRAYTANEEFCHR-----DSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
             NL    R + A ++   R     DS++++RNSE++ G MDKST+GSG K NVFYI+LRD
Sbjct: 1239 VNLDAACRQFKAPKDGTPRDLDPKDSWLVIRNSEVMCGVMDKSTIGSGKKDNVFYIMLRD 1298

Query: 576  FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
            +G   A   M RLSR+++ +  N GFSIGI DV P +  +++
Sbjct: 1299 YGPVAAAEGMNRLSRLSARWFTNMGFSIGITDVYPSEKLLRS 1340



 Score =  218 bits (555), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 170/508 (33%), Positives = 253/508 (49%), Gaps = 101/508 (19%)

Query: 968  LVMENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSS---RSDPSLS 1024
            L ME     + F    + A+  T K +   +  P E+  + +++++K  S   R D   +
Sbjct: 1538 LDMEGKAKPVHFDRTFIHAESTTYKNDER-SLLPAEIMEICEEMLSKERSKLVRKDLMGN 1596

Query: 1025 AQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSH 1084
                +  S+  +D  E  +D  E+  + +    ++   +       D+ SQ    + L+H
Sbjct: 1597 ELGYMDRSDHGVDQFESARDFLESIQQYVATKADKLISRGGDIDPNDERSQ----KGLNH 1652

Query: 1085 QDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFA 1144
              K+   R    F S+C       KY +AQ+E   AVGA+ AQSIGEPGTQMTLKTFHFA
Sbjct: 1653 TGKLTE-RTLRTFISSCLM-----KYKKAQVEAGHAVGAVGAQSIGEPGTQMTLKTFHFA 1706

Query: 1145 G---------------------------EVCE---------------------------Y 1150
            G                             CE                           Y
Sbjct: 1707 GVAGMSITQGVPRIKEIINASKEISTPVVACELVTKDNIIAARIVKGRIEKTYLRDIIHY 1766

Query: 1151 IEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIE----------RTRGISGHLTVS 1200
            + E +   +++I +K++   I+ L LE+ I++I   I+          + R    H+   
Sbjct: 1767 VRETWTGKEAYITVKINWKTIQDLALELKIENILSAIKNHKRFKADDLKFRCSRSHI--- 1823

Query: 1201 GHSFLILKPKDSSKSFNSK-------------MYQMKQLLPSVVIKGVQGINRAVIHEED 1247
             H ++ + P  S+K+  SK             +  +K++LP + + G     RA+I  + 
Sbjct: 1824 -HVYMDVDP--STKANLSKTEIAHTSADPFLRLKHLKRMLPDIQVLGHPQAFRAIIRTD- 1879

Query: 1248 VEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVME 1307
             E  T   LLVEG  LR+ M T GV G++ S+NN  E+   LGIEAAR+TI+ EI  VM+
Sbjct: 1880 -ETSTTNTLLVEGYGLRECMTTMGVDGLRTSTNNVMEMRDVLGIEAARTTIVQEISEVMK 1938

Query: 1308 NHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQ 1367
            +  M ID RH  L+AD+MT KGEVLGITR GLAKM++SVL LASFE T+DHLFDA   G+
Sbjct: 1939 D--MDIDPRHMQLLADVMTYKGEVLGITRFGLAKMRDSVLQLASFEKTADHLFDAGGAGR 1996

Query: 1368 TDCISGVSECIIMGLPMNVGTGLIKLLQ 1395
            +D I GVSECIIMG  +++GTG +++++
Sbjct: 1997 SDLIEGVSECIIMGKTVSLGTGAMEVVR 2024



 Score =  172 bits (436), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 99/267 (37%), Positives = 140/267 (52%), Gaps = 15/267 (5%)

Query: 87  VTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVG 146
           V   D +  Q  +++  +  +  D  R  + +G LD RMG + K ++C TCG  L  C G
Sbjct: 644 VLSNDDIVSQGVVEVSDRKFFDLDHDRAVVANGPLDARMGISNKTSSCQTCGGTLQICNG 703

Query: 147 HFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVR 206
           HFG++ L LP FH+GYF+ VI ILQ +CK   C+R+LL E     +  ++R P L  L R
Sbjct: 704 HFGHVRLVLPAFHVGYFKRVITILQEVCKE--CSRILLPEADRRAYLREMRRPGLDNLRR 761

Query: 207 KSLKKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKYK--------NRTKKKDAI 256
             + K+I E  +K   C  CG +NGVVKK G   LKI+H+K++         +      I
Sbjct: 762 GQIAKRINERCRKTRNCEACGAVNGVVKKAGTSALKITHDKFRAFNASTSVKKVPPPSKI 821

Query: 257 VEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPS 316
           V D    ++EA   N E+E H K      +N L VL LF+ I   D  LL +N + ++P 
Sbjct: 822 VFD--RSFDEARTSNAEVEKHYKKAQ-DDMNALRVLNLFKKISDTDCELLGLNPKEARPE 878

Query: 317 DLILTRLLVPPNCIRPSVISDLKSDND 343
             +   +  PP CIRPSV  D  S  D
Sbjct: 879 MFLWQFIPAPPVCIRPSVGQDAASTED 905



 Score =  152 bits (384), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 100/257 (38%), Positives = 148/257 (57%), Gaps = 33/257 (12%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP++   L    ++  ARIVKGR+E+T L ++  Y+ E +   +
Sbjct: 1716 GVPRIKEIINASKEISTPVVACELVTKDNIIAARIVKGRIEKTYLRDIIHYVRETWTGKE 1775

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIE----------RTRGISGHLTVSGHSFLILKP 873
            ++I +K++   I+ L LE+ I++I   I+          + R    H+    H ++ + P
Sbjct: 1776 AYITVKINWKTIQDLALELKIENILSAIKNHKRFKADDLKFRCSRSHI----HVYMDVDP 1831

Query: 874  KDSSKSFNSK-------------MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKL 920
              S+K+  SK             +  +K++LP + + G     RA+I  +  E  T   L
Sbjct: 1832 --STKANLSKTEIAHTSADPFLRLKHLKRMLPDIQVLGHPQAFRAIIRTD--ETSTTNTL 1887

Query: 921  LVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFR 980
            LVEG  LR+ M T GV G++ S+NN  E+   LGIEAAR+TI+ EI  VM++  M ID R
Sbjct: 1888 LVEGYGLRECMTTMGVDGLRTSTNNVMEMRDVLGIEAARTTIVQEISEVMKD--MDIDPR 1945

Query: 981  HPMLVADLMTSKGEVLG 997
            H  L+AD+MT KGEVLG
Sbjct: 1946 HMQLLADVMTYKGEVLG 1962



 Score =  104 bits (260), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 47/59 (79%), Positives = 51/59 (86%)

Query: 610  PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            P +GFV+NSFFSGL PTEF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL  +YD
Sbjct: 1457 PSKGFVRNSFFSGLEPTEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSTRYD 1515



 Score = 53.9 bits (128), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 24/57 (42%), Positives = 37/57 (64%)

Query: 22   LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVF 78
            LM  K+NL TP+NGE +I+A QDFI+  Y+L+ K+ FF+R    +I   ++  +  F
Sbjct: 1149 LMGVKNNLATPKNGEPIISAIQDFISAAYILSSKDNFFDRRSFTQICLYMLGPQTRF 1205



 Score = 43.9 bits (102), Expect = 0.69,   Method: Compositional matrix adjust.
 Identities = 19/39 (48%), Positives = 29/39 (74%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  FDA   G++D I GVSECIIMG  +++GTG +++++
Sbjct: 1986 DHLFDAGGAGRSDLIEGVSECIIMGKTVSLGTGAMEVVR 2024


>gi|255722720|ref|XP_002546294.1| DNA-directed RNA polymerase III largest subunit [Candida tropicalis
           MYA-3404]
 gi|240130811|gb|EER30373.1| DNA-directed RNA polymerase III largest subunit [Candida tropicalis
           MYA-3404]
          Length = 1159

 Score =  278 bits (712), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 142/281 (50%), Positives = 188/281 (66%), Gaps = 29/281 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH+LSI++H AKV P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 464 DGDVVLFNRQPSLHRLSILSHYAKVRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 523

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+R
Sbjct: 524 RAEAIN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDR 569

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A   ++ S +++D +          +    P +F +  ++WTGKQ+FSL++KPN+   V 
Sbjct: 570 ASLSQLLS-MMSDAN--------IQFDIPPPAIF-KPVMLWTGKQVFSLLIKPNKQSKVV 619

Query: 521 ANLKTKGRAYTA-----NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL  K + +         E    D +V++R S++L+G MDKSTLG G K +VFY +LRD
Sbjct: 620 INLDAKNKTFHPPAKGLPNEMSPNDGFVVIRGSQILSGLMDKSTLGDGKKHSVFYTILRD 679

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           +G   A  AM R+++M + YL NRGFSIGI DVTP     Q
Sbjct: 680 YGPQEAANAMNRMAKMCARYLGNRGFSIGINDVTPADELKQ 720



 Score =  179 bits (453), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 110/276 (39%), Positives = 153/276 (55%), Gaps = 19/276 (6%)

Query: 79  FRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCG 138
            +GL  G ++ +D V Q S ++I +++LY  +  RTP  HG LD RMG +     C+TC 
Sbjct: 13  IKGLEFGALSAKDIVAQ-SEVEIQTRDLYDLEKGRTPKEHGALDTRMGISSNAQECSTCH 71

Query: 139 QNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN 198
            NL+ C GHFG+I L LPVFH+GYF+ +I++LQ ICKN  CA VLL E     F   LR 
Sbjct: 72  GNLASCHGHFGHIRLALPVFHVGYFKSIISVLQCICKN--CAAVLLDEPTKRRFLNDLRR 129

Query: 199 PALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKC------GLLKISHEKY----KN 248
           P +  L R  + K+++E  KK   C  C  +NGVVKK         LKI H+ +    K 
Sbjct: 130 PNIDNLRRMKILKQVIEQCKKQRRCLKCNHVNGVVKKAASGAGPAALKIVHDTFRWIGKK 189

Query: 249 RTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLM 308
            T +K+A  +DL     +  + NPE+    K  +   LNPL+ L LF+ I   D  L  +
Sbjct: 190 DTPEKNAWDDDL----EKVFQRNPELSKFVK-RIHDDLNPLKTLNLFKQITPSDCELFGL 244

Query: 309 N-AELSKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
           + A+  +P   I   L  PP CIRPSV+ D +S+ D
Sbjct: 245 DPAKGGRPEMYIWRYLPAPPVCIRPSVMMDAQSNED 280



 Score =  102 bits (253), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 46/57 (80%), Positives = 50/57 (87%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NSFFSGLTP EF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 840 KGFVRNSFFSGLTPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSTQYD 896



 Score = 75.1 bits (183), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 33/42 (78%), Positives = 36/42 (85%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            E C  KY RA++EP TAVGA+ AQSIGEPGTQMTLKTFHFAG
Sbjct: 1036 EQCLYKYSRAKVEPGTAVGAIGAQSIGEPGTQMTLKTFHFAG 1077



 Score = 74.3 bits (181), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 38/72 (52%), Positives = 52/72 (72%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII + L  D D   AR+ KGR+E+T L +V  YIE+V+  + 
Sbjct: 1086 GVPRIKEIINASKVISTPIINSVLVNDEDEIAARVAKGRIEKTLLEDVAFYIEDVYKDNL 1145

Query: 824  SFILIKLDMDRI 835
             ++ IK+D++ I
Sbjct: 1146 CYLSIKIDLETI 1157



 Score = 62.4 bits (150), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/50 (54%), Positives = 40/50 (80%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+RA   ++ S +
Sbjct: 530 LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDRASLSQLLSMM 579


>gi|154270754|ref|XP_001536231.1| DNA-directed RNA polymerase III largest subunit [Ajellomyces
           capsulatus NAm1]
 gi|150409805|gb|EDN05245.1| DNA-directed RNA polymerase III largest subunit [Ajellomyces
           capsulatus NAm1]
          Length = 1439

 Score =  278 bits (712), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 140/281 (49%), Positives = 186/281 (66%), Gaps = 30/281 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++H AKV PHRTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 470 DGDIVLFNRQPSLHKLSILSHFAKVRPHRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 529

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K NL TP+NGE +I+A QDFIT  YLL+ K+ F++R
Sbjct: 530 RAEAME--------------LMGVKHNLATPKNGEPIISAIQDFITAAYLLSSKDVFYDR 575

Query: 461 AQTMRIASTLI-ADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
                I   ++ +DT        RF      P   ++  ++WTGKQ+F+++++PN+  PV
Sbjct: 576 KTFTHICLYMLESDT--------RF---DLPPPSVLKPQILWTGKQVFNVLMRPNKQSPV 624

Query: 520 NANLKTKGRAYTANE----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
             NL    R + A +    +    D ++ +RNSE++ G MDKST+GSG K +VFY++LRD
Sbjct: 625 LINLDAACREFKAPKGTPRDLDANDGWLCIRNSEIMCGVMDKSTIGSGKKDSVFYVMLRD 684

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           FG DVA   M RLSR+++ +L N GFSIGI DV PG+  ++
Sbjct: 685 FGPDVASEGMNRLSRLSARWLTNLGFSIGITDVYPGEKLLE 725



 Score =  227 bits (579), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 146/363 (40%), Positives = 195/363 (53%), Gaps = 74/363 (20%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEV----------------- 1147
            AC  KY RAQ+EP  AVGA+ AQSIGEPGTQMTLKTFHFAG                   
Sbjct: 1032 ACLTKYKRAQVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIINA 1091

Query: 1148 ----------CE---------------------------YIEEVFVPDDSFILIKLDMDR 1170
                      CE                           YIEE +  ++++I IK+D   
Sbjct: 1092 SKEISTPVITCELVNKQDLRAAQIVKGRVEKTFVRDIIYYIEEDWTGNEAYINIKIDFST 1151

Query: 1171 IRLLHLEVDIDSIRYCIE------------RTRGISGHLTVSGHSFLILKPKDSSKSFNS 1218
            I+ L LE+ +  I   I+            R+ G   H+ V   +      K    +  +
Sbjct: 1152 IQNLQLELTLQDILMAIKKHKRFKSADLKFRSFGSHIHIFVDQQTARTALSKAEEAATGA 1211

Query: 1219 KMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 1274
              Y     +K+L+P++ + G     RA+I  ++    T   LLVEG  LRD M T G+ G
Sbjct: 1212 DPYIRLKHLKRLIPNIQVIGHSQCARAIIRTDETN--TTNTLLVEGYGLRDCMTTDGING 1269

Query: 1275 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGI 1334
                +NN  E    LGIEAAR+TI+ EI  VM++  M+ID RH  L+AD+MT KGEVLGI
Sbjct: 1270 RHTRTNNIMETRAVLGIEAARTTIVDEIGEVMKD--MAIDPRHMQLLADVMTYKGEVLGI 1327

Query: 1335 TRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            TR GLAKM++SVL LASFE T+DHLFDA   G+TD I GVSECII+G  +++GTG ++++
Sbjct: 1328 TRFGLAKMRDSVLQLASFEKTADHLFDAGGAGRTDLIEGVSECIIVGKSVSLGTGAMEVV 1387

Query: 1395 QAV 1397
            +A+
Sbjct: 1388 RAL 1390



 Score =  184 bits (468), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 106/269 (39%), Positives = 147/269 (54%), Gaps = 16/269 (5%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G ++ +D V Q + +++  + L+  D  R   PHG LD RMG + K   C TCG  L  C
Sbjct: 30  GVLSTQDIVSQ-AVVEVSDRKLFDLDNDRAVAPHGPLDGRMGISSKSGTCDTCGGALQVC 88

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFG++ L LP FH+GYF+ VI+ILQ ICK   C+ +LL E +   F  +LR P +  L
Sbjct: 89  SGHFGHVKLVLPAFHVGYFKRVISILQEICKE--CSHILLPETERRAFLRELRRPGIDNL 146

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKYK--------NRTKKKD 254
            R  + KKI E  +K   C  C  +NGVVKK G   LKI+HEK++         +     
Sbjct: 147 RRMQIAKKINERCRKTRTCYKCNAVNGVVKKAGTSALKITHEKFRAFNASTSVKKIPPPS 206

Query: 255 AIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSK 314
            +V D    + EA K NP+I+ H K      L+PL VL+LF ++  ED  LL +N E ++
Sbjct: 207 KVVFD--KSFEEAKKSNPDIDKHFKKAH-DDLHPLRVLRLFRSVSNEDCELLSLNPEEAR 263

Query: 315 PSDLILTRLLVPPNCIRPSVISDLKSDND 343
           P   +   +  PP CIRPSV  +  S  D
Sbjct: 264 PEVFLWQYVPAPPVCIRPSVGQEAASTED 292



 Score =  156 bits (395), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 101/250 (40%), Positives = 142/250 (56%), Gaps = 20/250 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+IT  L    DL  A+IVKGR+E+T + ++  YIEE +  ++
Sbjct: 1081 GVPRIKEIINASKEISTPVITCELVNKQDLRAAQIVKGRVEKTFVRDIIYYIEEDWTGNE 1140

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIE------------RTRGISGHLTVSGHSFLIL 871
            ++I IK+D   I+ L LE+ +  I   I+            R+ G   H+ V   +    
Sbjct: 1141 AYINIKIDFSTIQNLQLELTLQDILMAIKKHKRFKSADLKFRSFGSHIHIFVDQQTARTA 1200

Query: 872  KPKDSSKSFNSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927
              K    +  +  Y     +K+L+P++ + G     RA+I  ++    T   LLVEG  L
Sbjct: 1201 LSKAEEAATGADPYIRLKHLKRLIPNIQVIGHSQCARAIIRTDETN--TTNTLLVEGYGL 1258

Query: 928  RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 987
            RD M T G+ G    +NN  E    LGIEAAR+TI+ EI  VM++  M+ID RH  L+AD
Sbjct: 1259 RDCMTTDGINGRHTRTNNIMETRAVLGIEAARTTIVDEIGEVMKD--MAIDPRHMQLLAD 1316

Query: 988  LMTSKGEVLG 997
            +MT KGEVLG
Sbjct: 1317 VMTYKGEVLG 1326



 Score =  105 bits (262), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 47/59 (79%), Positives = 52/59 (88%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSFFSGLTPTEF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  +YD
Sbjct: 843 PAKGFVRNSFFSGLTPTEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSTRYD 901



 Score = 54.3 bits (129), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 23/40 (57%), Positives = 30/40 (75%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           LM  K NL TP+NGE +I+A QDFIT  YLL+ K+ F++R
Sbjct: 536 LMGVKHNLATPKNGEPIISAIQDFITAAYLLSSKDVFYDR 575



 Score = 45.4 bits (106), Expect = 0.26,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 31/41 (75%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 708
            D  FDA   G+TD I GVSECII+G  +++GTG +++++A+
Sbjct: 1350 DHLFDAGGAGRTDLIEGVSECIIVGKSVSLGTGAMEVVRAL 1390


>gi|225554972|gb|EEH03266.1| DNA-directed RNA polymerase III largest subunit [Ajellomyces
           capsulatus G186AR]
          Length = 1456

 Score =  278 bits (712), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 140/281 (49%), Positives = 187/281 (66%), Gaps = 30/281 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++H AKV PHRTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 470 DGDIVLFNRQPSLHKLSILSHFAKVRPHRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 529

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL TP+NGE +I+A QDFIT  YLL+ K+ F++R
Sbjct: 530 RAEAME--------------LMGVKNNLATPKNGEPIISAIQDFITAAYLLSSKDIFYDR 575

Query: 461 AQTMRIASTLI-ADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
                I   ++ +DT        RF      P   ++  ++WTGKQ+F+++++PN+  PV
Sbjct: 576 KTFTHICLYMLESDT--------RF---DLPPPSVLKPQILWTGKQVFNVLMRPNKQSPV 624

Query: 520 NANLKTKGRAYTANE----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
             NL    R + A +    +    D ++ +RNSE++ G MDKST+GSG K +VFY++LRD
Sbjct: 625 LINLDAACREFKAPKGTPRDLDANDGWLCIRNSEIMCGVMDKSTIGSGKKDSVFYVMLRD 684

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           FG DVA   M RLSR+++ +L N GFSIGI DV PG+  ++
Sbjct: 685 FGPDVASEGMNRLSRLSARWLTNLGFSIGITDVYPGEKLLE 725



 Score =  227 bits (579), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 146/363 (40%), Positives = 195/363 (53%), Gaps = 74/363 (20%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEV----------------- 1147
            AC  KY RAQ+EP  AVGA+ AQSIGEPGTQMTLKTFHFAG                   
Sbjct: 1049 ACLTKYKRAQVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIINA 1108

Query: 1148 ----------CE---------------------------YIEEVFVPDDSFILIKLDMDR 1170
                      CE                           YIEE +  ++++I IK+D   
Sbjct: 1109 SKEISTPVITCELVNKQDLRAAQIVKGRVEKTFVRDIIYYIEEDWTGNEAYINIKIDFST 1168

Query: 1171 IRLLHLEVDIDSIRYCIE------------RTRGISGHLTVSGHSFLILKPKDSSKSFNS 1218
            I+ L LE+ +  I   I+            R+ G   H+ V   +      K    +  +
Sbjct: 1169 IQNLQLELTLQDILMAIKKHKRFKSADLKFRSFGSHIHIFVDQQTTRTALSKTEEAATGA 1228

Query: 1219 KMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 1274
              Y     +K+L+P++ + G     RA+I  ++    T   LLVEG  LRD M T G+ G
Sbjct: 1229 DPYIRLKHLKRLIPNIQVIGHPQCARAIIRTDETN--TTNTLLVEGYGLRDCMTTDGING 1286

Query: 1275 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGI 1334
                +NN  E    LGIEAAR+TI+ EI  VM++  M+ID RH  L+AD+MT KGEVLGI
Sbjct: 1287 RHTRTNNIMETRAVLGIEAARTTIVDEIGEVMKD--MAIDPRHMQLLADVMTYKGEVLGI 1344

Query: 1335 TRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            TR GLAKM++SVL LASFE T+DHLFDA   G+TD I GVSECII+G  +++GTG ++++
Sbjct: 1345 TRFGLAKMRDSVLQLASFEKTADHLFDAGGAGRTDLIEGVSECIIVGKSVSLGTGAMEVV 1404

Query: 1395 QAV 1397
            +A+
Sbjct: 1405 RAL 1407



 Score =  184 bits (467), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 106/269 (39%), Positives = 147/269 (54%), Gaps = 16/269 (5%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G ++ +D V Q + +++  + L+  D  R   PHG LD RMG + K   C TCG  L  C
Sbjct: 30  GVLSTQDIVSQ-AVVEVSDRKLFDLDNDRAVAPHGPLDGRMGISSKSGTCDTCGGALQVC 88

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFG++ L LP FH+GYF+ VI+ILQ ICK   C+ +LL E +   F  +LR P +  L
Sbjct: 89  SGHFGHVKLVLPAFHVGYFKRVISILQEICKE--CSHILLPETERRAFLRELRRPGIDNL 146

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKYK--------NRTKKKD 254
            R  + KKI E  +K   C  C  +NGVVKK G   LKI+HEK++         +     
Sbjct: 147 RRMQIAKKINERCRKTRTCYKCNAVNGVVKKAGTSALKITHEKFRAFNASASVKKIPPPS 206

Query: 255 AIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSK 314
            +V D    + EA K NP+I+ H K      L+PL VL+LF ++  ED  LL +N E ++
Sbjct: 207 KVVFD--KSFEEAKKSNPDIDKHFKKAH-DDLHPLRVLRLFRSVSNEDCELLSLNPEEAR 263

Query: 315 PSDLILTRLLVPPNCIRPSVISDLKSDND 343
           P   +   +  PP CIRPSV  +  S  D
Sbjct: 264 PEVFLWQYVPAPPVCIRPSVGQEAASTED 292



 Score =  156 bits (394), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 101/250 (40%), Positives = 142/250 (56%), Gaps = 20/250 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+IT  L    DL  A+IVKGR+E+T + ++  YIEE +  ++
Sbjct: 1098 GVPRIKEIINASKEISTPVITCELVNKQDLRAAQIVKGRVEKTFVRDIIYYIEEDWTGNE 1157

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIE------------RTRGISGHLTVSGHSFLIL 871
            ++I IK+D   I+ L LE+ +  I   I+            R+ G   H+ V   +    
Sbjct: 1158 AYINIKIDFSTIQNLQLELTLQDILMAIKKHKRFKSADLKFRSFGSHIHIFVDQQTTRTA 1217

Query: 872  KPKDSSKSFNSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927
              K    +  +  Y     +K+L+P++ + G     RA+I  ++    T   LLVEG  L
Sbjct: 1218 LSKTEEAATGADPYIRLKHLKRLIPNIQVIGHPQCARAIIRTDETN--TTNTLLVEGYGL 1275

Query: 928  RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 987
            RD M T G+ G    +NN  E    LGIEAAR+TI+ EI  VM++  M+ID RH  L+AD
Sbjct: 1276 RDCMTTDGINGRHTRTNNIMETRAVLGIEAARTTIVDEIGEVMKD--MAIDPRHMQLLAD 1333

Query: 988  LMTSKGEVLG 997
            +MT KGEVLG
Sbjct: 1334 VMTYKGEVLG 1343



 Score =  105 bits (262), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 47/59 (79%), Positives = 52/59 (88%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSFFSGLTPTEF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  +YD
Sbjct: 843 PAKGFVRNSFFSGLTPTEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSTRYD 901



 Score = 54.3 bits (129), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 23/40 (57%), Positives = 31/40 (77%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           LM  K+NL TP+NGE +I+A QDFIT  YLL+ K+ F++R
Sbjct: 536 LMGVKNNLATPKNGEPIISAIQDFITAAYLLSSKDIFYDR 575



 Score = 45.4 bits (106), Expect = 0.24,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 31/41 (75%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 708
            D  FDA   G+TD I GVSECII+G  +++GTG +++++A+
Sbjct: 1367 DHLFDAGGAGRTDLIEGVSECIIVGKSVSLGTGAMEVVRAL 1407


>gi|401623626|gb|EJS41719.1| rpo31p [Saccharomyces arboricola H-6]
          Length = 1460

 Score =  278 bits (712), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 140/282 (49%), Positives = 188/282 (66%), Gaps = 30/282 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH+LSI++H AK+ P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 468 DGDVVLFNRQPSLHRLSILSHYAKIRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 527

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL+TP++GE +IAATQDFITG YL++ K++F++R
Sbjct: 528 RAEAIN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFYDR 573

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A   ++ S +++D       +++F      P   ++   +WTGKQ+FSL++KPN + PV 
Sbjct: 574 ATLTQLLS-MMSDG------VEQF---DIPPPAIMKPYYLWTGKQVFSLLIKPNHNSPVV 623

Query: 521 ANLKTKGRAYTANE------EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLR 574
            NL  K + +   +      E    D +VI+R S +L+G MDKS LG G K +VFY +LR
Sbjct: 624 INLDAKNKVFVPPKSKSLPSEMSQNDGFVIIRGSNILSGVMDKSVLGDGKKHSVFYTILR 683

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           D+G   A  AM R+S++ + +L NRGFSIGI DVTP     Q
Sbjct: 684 DYGPQEAANAMNRMSKLCARFLGNRGFSIGINDVTPADDLKQ 725



 Score =  219 bits (557), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 128/286 (44%), Positives = 176/286 (61%), Gaps = 23/286 (8%)

Query: 1146 EVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRG------------- 1192
            +V  Y+++V+  + SFI +++D+  I  L LE+ I+ I   I R                
Sbjct: 1168 DVAYYVQDVYKDNLSFIQVRIDLATIDKLQLELTIEDIAVAITRASKLKIQASDVNIIGK 1227

Query: 1193 --ISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQL---LPSVVIKGVQGINRAVIHEED 1247
              I+ ++   G+    +       S N   Y+M+QL   +P VV+KG+  I+RAVI+  D
Sbjct: 1228 DRIAINVFPDGYKAKSISTSAKEPSENDVFYRMQQLRRAIPDVVVKGLPDISRAVINIRD 1287

Query: 1248 VEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVME 1307
                 K +LLVEG  LRDVM T GV G K ++N+  EV+  LGIEAAR +I+ EI   M 
Sbjct: 1288 N---GKRELLVEGYGLRDVMCTDGVIGSKTTTNHVLEVFSVLGIEAARYSIVREINYTMS 1344

Query: 1308 NHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQ 1367
            NHGMS+D RH  L+ D+MT KGEVLGITR GL+KM++SVL LASFE T+DHLFDAAFY +
Sbjct: 1345 NHGMSVDPRHIQLLGDVMTYKGEVLGITRFGLSKMRDSVLQLASFEKTTDHLFDAAFYMK 1404

Query: 1368 TDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEP--VPRTLLFDN 1411
             D + GVSECII+G  M++GTG  K+++    SE   VPR  LF++
Sbjct: 1405 KDAVEGVSECIILGQTMSIGTGSFKVVKGTNISENDLVPRPCLFES 1450



 Score =  186 bits (471), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 113/252 (44%), Positives = 151/252 (59%), Gaps = 21/252 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII A L  D D   AR+VKGR+E+T L +V  Y+++V+  + 
Sbjct: 1122 GVPRIKEIINASKVISTPIINAVLVNDNDERAARVVKGRVEKTLLSDVAYYVQDVYKDNL 1181

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRG---------------ISGHLTVSGHSF 868
            SFI +++D+  I  L LE+ I+ I   I R                  I+ ++   G+  
Sbjct: 1182 SFIQVRIDLATIDKLQLELTIEDIAVAITRASKLKIQASDVNIIGKDRIAINVFPDGYKA 1241

Query: 869  LILKPKDSSKSFNSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD 925
              +       S N   Y+M+QL   +P VV+KG+  I+RAVI+  D     K +LLVEG 
Sbjct: 1242 KSISTSAKEPSENDVFYRMQQLRRAIPDVVVKGLPDISRAVINIRDN---GKRELLVEGY 1298

Query: 926  NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 985
             LRDVM T GV G K ++N+  EV+  LGIEAAR +I+ EI   M NHGMS+D RH  L+
Sbjct: 1299 GLRDVMCTDGVIGSKTTTNHVLEVFSVLGIEAARYSIVREINYTMSNHGMSVDPRHIQLL 1358

Query: 986  ADLMTSKGEVLG 997
             D+MT KGEVLG
Sbjct: 1359 GDVMTYKGEVLG 1370



 Score =  179 bits (454), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 99/248 (39%), Positives = 139/248 (56%), Gaps = 11/248 (4%)

Query: 96  QSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPL 155
           QS +++ +++L+  +  R P  +G LD +MG +     CTTC  NL+ C GHFG++ L L
Sbjct: 29  QSEVEVSTRDLFDLEKDRAPKANGALDPKMGVSSSSLECTTCHGNLASCHGHFGHLKLAL 88

Query: 156 PVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILE 215
           PVFHIGYF+  I ILQ ICKN  C+ +LL E     F  +LR P +  L R  + KKIL+
Sbjct: 89  PVFHIGYFKATIQILQGICKN--CSSILLSETDKRQFLHELRRPGVDNLRRMGILKKILD 146

Query: 216 TTKKVSVCPHCGEINGVVKK------CGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVK 269
             KK   C HCG +NGVVKK         LKI H+ ++   KK     +  + E+ E + 
Sbjct: 147 QCKKQRRCLHCGALNGVVKKAAAGAGSAALKIIHDTFRWVGKKSAPEKDIWVGEWKEVLG 206

Query: 270 FNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL--SKPSDLILTRLLVPP 327
            NPE+E + K   +  LNPL+ L LF+ +   D  LL ++  +   +P   I   L  PP
Sbjct: 207 HNPELERYVK-RCMDDLNPLKTLNLFKQVKSADCELLGIDTTVPSGRPETYIWRYLPAPP 265

Query: 328 NCIRPSVI 335
            CIRPSV+
Sbjct: 266 VCIRPSVM 273



 Score =  100 bits (250), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 48/70 (68%), Positives = 55/70 (78%), Gaps = 1/70 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV+NSFFSGL+P EF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QY
Sbjct: 841 TPQSKGFVRNSFFSGLSPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSCQY 900

Query: 668 DMSFDAAFYG 677
           D +   +  G
Sbjct: 901 DNTVRTSANG 910



 Score = 68.9 bits (167), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 29/37 (78%), Positives = 34/37 (91%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            KY +A++EP TA+GA+ AQSIGEPGTQMTLKTFHFAG
Sbjct: 1077 KYRKARLEPGTAIGAIGAQSIGEPGTQMTLKTFHFAG 1113



 Score = 62.8 bits (151), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 28/57 (49%), Positives = 43/57 (75%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVF 78
           LM  K+NL+TP++GE +IAATQDFITG YL++ K++F++RA   ++ S +  G + F
Sbjct: 534 LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFYDRATLTQLLSMMSDGVEQF 590



 Score = 56.2 bits (134), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 28/57 (49%), Positives = 38/57 (66%), Gaps = 2/57 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEP--VPRTLLFDN 722
            D  FDAAFY + D + GVSECII+G  M++GTG  K+++    SE   VPR  LF++
Sbjct: 1394 DHLFDAAFYMKKDAVEGVSECIILGQTMSIGTGSFKVVKGTNISENDLVPRPCLFES 1450


>gi|260946503|ref|XP_002617549.1| DNA-directed RNA polymerase III largest subunit [Clavispora
           lusitaniae ATCC 42720]
 gi|238849403|gb|EEQ38867.1| DNA-directed RNA polymerase III largest subunit [Clavispora
           lusitaniae ATCC 42720]
          Length = 1491

 Score =  278 bits (712), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 138/276 (50%), Positives = 188/276 (68%), Gaps = 29/276 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH+LSI++H AK+ P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 500 DGDVVLFNRQPSLHRLSILSHYAKIRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 559

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+R
Sbjct: 560 RAEAIN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDR 605

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A  +++   +++D            +    P VF +  ++WTGKQ+FS++++PN+   V 
Sbjct: 606 ASLVQLL-CMMSDAD--------MQFDIPPPTVF-KPVMLWTGKQVFSMLIRPNKKSNVV 655

Query: 521 ANLKTKGRAYTA-----NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            N+  K + +         E    D +V++R S++L+G MDKSTLG G K +VFY +LRD
Sbjct: 656 INVDAKNKTFIPPPKHLPNEMSPNDGFVVIRGSQILSGVMDKSTLGDGKKHSVFYTILRD 715

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           +G D A  AM R++++ + YL NRGFSIGI DVTPG
Sbjct: 716 YGPDEAAKAMNRMAKLCARYLGNRGFSIGINDVTPG 751



 Score =  254 bits (648), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 159/384 (41%), Positives = 214/384 (55%), Gaps = 82/384 (21%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-------------------- 1145
            C  KY+RA++EP TAVGA+ A SIGEPGTQMTLKTFHFAG                    
Sbjct: 1102 CLYKYLRARVEPGTAVGAIGAHSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIINAA 1161

Query: 1146 -----------------EVCE-----YIEEVFVPDDSFIL------------IKLDMDRI 1171
                             EV        IE+  + D +F +            IK+D+  I
Sbjct: 1162 KVISTPIINTVLVNDEDEVAARVVKGRIEKTLLRDVAFFVEDVYKNDMAYLSIKIDLKTI 1221

Query: 1172 RLLHLEVDIDSIRYCIE---RTRGISGHLTVSGHSFLIL--------------------K 1208
              L LE+ +D+IR  I    + + ++  ++V G   + +                    K
Sbjct: 1222 EKLQLELTMDNIRQAIANAPKLKILNSEVSVYGKDRINVLVTLRESKSESLARTAASDYK 1281

Query: 1209 PKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMA 1268
              D + S   +M  +K+ LP VVIKG+  I+RAVI+  D    +K +LLVEG  L+DVM+
Sbjct: 1282 ASDVNNSLFFRMQHLKRALPDVVIKGLPNISRAVINIRD---DSKKELLVEGYGLKDVMS 1338

Query: 1269 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK 1328
            T G+ G K S+N+  EVY+ LGIEAAR++I+ EI   M  HGMS+D RH  L+ D+MT K
Sbjct: 1339 TDGIVGTKTSTNHVLEVYEVLGIEAARASIIGEIDYTMSKHGMSVDPRHIQLLGDVMTYK 1398

Query: 1329 GEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGT 1388
            GEVLGITR GL+KM++SVL LASFE T+DHLFDAAF+ + D I GVSECII+G  M++GT
Sbjct: 1399 GEVLGITRFGLSKMRDSVLQLASFEKTTDHLFDAAFFMKNDKIEGVSECIILGQTMSIGT 1458

Query: 1389 GLIKLLQAVPRSEP--VPRTLLFD 1410
            G  KL++     E    P+  LF+
Sbjct: 1459 GAFKLVKTSHFEEKHLKPKPCLFE 1482



 Score =  187 bits (475), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 111/257 (43%), Positives = 158/257 (61%), Gaps = 26/257 (10%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ ISTPII   L  D D   AR+VKGR+E+T L +V  ++E+V+  D 
Sbjct: 1150 GVPRIKEIINAAKVISTPIINTVLVNDEDEVAARVVKGRIEKTLLRDVAFFVEDVYKNDM 1209

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIE---RTRGISGHLTVSGHSFLIL--------- 871
            +++ IK+D+  I  L LE+ +D+IR  I    + + ++  ++V G   + +         
Sbjct: 1210 AYLSIKIDLKTIEKLQLELTMDNIRQAIANAPKLKILNSEVSVYGKDRINVLVTLRESKS 1269

Query: 872  -----------KPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKL 920
                       K  D + S   +M  +K+ LP VVIKG+  I+RAVI+  D    +K +L
Sbjct: 1270 ESLARTAASDYKASDVNNSLFFRMQHLKRALPDVVIKGLPNISRAVINIRDD---SKKEL 1326

Query: 921  LVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFR 980
            LVEG  L+DVM+T G+ G K S+N+  EVY+ LGIEAAR++I+ EI   M  HGMS+D R
Sbjct: 1327 LVEGYGLKDVMSTDGIVGTKTSTNHVLEVYEVLGIEAARASIIGEIDYTMSKHGMSVDPR 1386

Query: 981  HPMLVADLMTSKGEVLG 997
            H  L+ D+MT KGEVLG
Sbjct: 1387 HIQLLGDVMTYKGEVLG 1403



 Score =  179 bits (454), Expect = 9e-42,   Method: Compositional matrix adjust.
 Identities = 109/273 (39%), Positives = 154/273 (56%), Gaps = 13/273 (4%)

Query: 79  FRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCG 138
            +GL    ++  D V Q S ++I +++LY  +  R+    G LD +MGT+     C+TC 
Sbjct: 46  IKGLEFSALSARDIVAQ-SEVEITTRDLYDLEKGRSVREGGALDTKMGTSTNAVECSTCH 104

Query: 139 QNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN 198
            NL+ C GHFG++ L LPVFH+GYF+ +I++LQ ICKN  CA VLL E+    F + LR 
Sbjct: 105 GNLATCHGHFGHVRLALPVFHVGYFKAIISVLQCICKN--CAAVLLDEQTKRAFLSDLRR 162

Query: 199 PALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKC------GLLKISHEKYKNRTKK 252
           P +  L R  + KK++E  KK   C  C  +NGVVKK         LKI H+ ++    K
Sbjct: 163 PNIDNLRRMKVLKKVVEQCKKQRRCLKCHHVNGVVKKAASGAGPAALKILHDTFR-YVGK 221

Query: 253 KDAIVEDLL-AEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAE 311
           K A  +DL   E++E    NPE+E   K  + + LNPL+VL LF  I  +D  L  ++A 
Sbjct: 222 KSAPEKDLWDREFDEVFHRNPELEKFAK-RVHEDLNPLKVLNLFRQITPQDCELFGIDAA 280

Query: 312 L-SKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
              +P   I   L  PP CIRPSV+ D +S+ D
Sbjct: 281 RGGRPEMYIWRYLPAPPVCIRPSVMMDNQSNED 313



 Score = 98.6 bits (244), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 46/61 (75%), Positives = 51/61 (83%), Gaps = 1/61 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV+NSFFSGL+P EF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL   Y
Sbjct: 872 TPQSKGFVRNSFFSGLSPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSSSY 931

Query: 668 D 668
           D
Sbjct: 932 D 932



 Score = 62.0 bits (149), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 26/46 (56%), Positives = 39/46 (84%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRI 67
           LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+RA  +++
Sbjct: 566 LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDRASLVQL 611



 Score = 50.1 bits (118), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 26/56 (46%), Positives = 35/56 (62%), Gaps = 2/56 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEP--VPRTLLFD 721
            D  FDAAF+ + D I GVSECII+G  M++GTG  KL++     E    P+  LF+
Sbjct: 1427 DHLFDAAFFMKNDKIEGVSECIILGQTMSIGTGAFKLVKTSHFEEKHLKPKPCLFE 1482


>gi|145242160|ref|XP_001393726.1| DNA-directed RNA polymerase III subunit RPO31 [Aspergillus niger
           CBS 513.88]
 gi|134078271|emb|CAK96852.1| unnamed protein product [Aspergillus niger]
          Length = 1450

 Score =  278 bits (712), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 138/282 (48%), Positives = 187/282 (66%), Gaps = 29/282 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++H AKV PHRTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 470 DGDIVLFNRQPSLHKLSILSHFAKVRPHRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 529

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL TP+NGE +I+A QDFI+  Y+L+ K+ FF+R
Sbjct: 530 RAEAME--------------LMGVKNNLATPKNGEPIISAIQDFISAAYILSSKDNFFDR 575

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
               +I   ++       G   RF      P   ++  ++WTGKQ+F+++++PN+D PV 
Sbjct: 576 RSFTQICLYML-------GPQTRF---DLPPPAVLKPQMLWTGKQVFNILMRPNKDDPVL 625

Query: 521 ANLKTKGRAYTANEEFCHR-----DSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL    R + A ++   R     DS++++RNSE++ G MDKST+GSG K NVFYI+LRD
Sbjct: 626 VNLDAACRQFKAPKDGTPRDLDPKDSWLVIRNSEVMCGVMDKSTIGSGKKDNVFYIMLRD 685

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           +G   A   M RLSR+++ +  N GFSIGI DV P +  +++
Sbjct: 686 YGPVAAAEGMNRLSRLSARWFTNMGFSIGITDVYPSEKLLRS 727



 Score =  218 bits (556), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 170/508 (33%), Positives = 253/508 (49%), Gaps = 101/508 (19%)

Query: 968  LVMENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSS---RSDPSLS 1024
            L ME     + F    + A+  T K +   +  P E+  + +++++K  S   R D   +
Sbjct: 925  LDMEGKAKPVHFDRTFIHAESTTYKNDER-SLLPAEIMEICEEMLSKERSKLVRKDLMGN 983

Query: 1025 AQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSH 1084
                +  S+  +D  E  +D  E+  + +    ++   +       D+ SQ    + L+H
Sbjct: 984  ELGYMDRSDHGVDQFESARDFLESIQQYVATKADKLISRGGDIDPNDERSQ----KGLNH 1039

Query: 1085 QDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFA 1144
              K+   R    F S+C       KY +AQ+E   AVGA+ AQSIGEPGTQMTLKTFHFA
Sbjct: 1040 TGKLTE-RTLRTFISSCLM-----KYKKAQVEAGHAVGAVGAQSIGEPGTQMTLKTFHFA 1093

Query: 1145 G---------------------------EVCE---------------------------Y 1150
            G                             CE                           Y
Sbjct: 1094 GVAGMSITQGVPRIKEIINASKEISTPVVACELVTKDNIIAARIVKGRIEKTYLRDIIHY 1153

Query: 1151 IEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIE----------RTRGISGHLTVS 1200
            + E +   +++I +K++   I+ L LE+ I++I   I+          + R    H+   
Sbjct: 1154 VRETWTGKEAYITVKINWKTIQDLALELKIENILSAIKNHKRFKADDLKFRCSRSHI--- 1210

Query: 1201 GHSFLILKPKDSSKSFNSK-------------MYQMKQLLPSVVIKGVQGINRAVIHEED 1247
             H ++ + P  S+K+  SK             +  +K++LP + + G     RA+I  + 
Sbjct: 1211 -HVYMDVDP--STKANLSKTEIAHTSADPFLRLKHLKRMLPDIQVLGHPQAFRAIIRTD- 1266

Query: 1248 VEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVME 1307
             E  T   LLVEG  LR+ M T GV G++ S+NN  E+   LGIEAAR+TI+ EI  VM+
Sbjct: 1267 -ETSTTNTLLVEGYGLRECMTTMGVDGLRTSTNNVMEMRDVLGIEAARTTIVQEISEVMK 1325

Query: 1308 NHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQ 1367
            +  M ID RH  L+AD+MT KGEVLGITR GLAKM++SVL LASFE T+DHLFDA   G+
Sbjct: 1326 D--MDIDPRHMQLLADVMTYKGEVLGITRFGLAKMRDSVLQLASFEKTADHLFDAGGAGR 1383

Query: 1368 TDCISGVSECIIMGLPMNVGTGLIKLLQ 1395
            +D I GVSECIIMG  +++GTG +++++
Sbjct: 1384 SDLIEGVSECIIMGKTVSLGTGAMEVVR 1411



 Score =  172 bits (437), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 99/267 (37%), Positives = 140/267 (52%), Gaps = 15/267 (5%)

Query: 87  VTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVG 146
           V   D +  Q  +++  +  +  D  R  + +G LD RMG + K ++C TCG  L  C G
Sbjct: 31  VLSNDDIVSQGVVEVSDRKFFDLDHDRAVVANGPLDARMGISNKTSSCQTCGGTLQICNG 90

Query: 147 HFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVR 206
           HFG++ L LP FH+GYF+ VI ILQ +CK   C+R+LL E     +  ++R P L  L R
Sbjct: 91  HFGHVRLVLPAFHVGYFKRVITILQEVCKE--CSRILLPEADRRAYLREMRRPGLDNLRR 148

Query: 207 KSLKKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKYK--------NRTKKKDAI 256
             + K+I E  +K   C  CG +NGVVKK G   LKI+H+K++         +      I
Sbjct: 149 GQIAKRINERCRKTRNCEACGAVNGVVKKAGTSALKITHDKFRAFNASTSVKKVPPPSKI 208

Query: 257 VEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPS 316
           V D    ++EA   N E+E H K      +N L VL LF+ I   D  LL +N + ++P 
Sbjct: 209 VFD--RSFDEARTSNAEVEKHYKKAQ-DDMNALRVLNLFKKISDTDCELLGLNPKEARPE 265

Query: 317 DLILTRLLVPPNCIRPSVISDLKSDND 343
             +   +  PP CIRPSV  D  S  D
Sbjct: 266 MFLWQFIPAPPVCIRPSVGQDAASTED 292



 Score =  152 bits (384), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 100/257 (38%), Positives = 148/257 (57%), Gaps = 33/257 (12%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP++   L    ++  ARIVKGR+E+T L ++  Y+ E +   +
Sbjct: 1103 GVPRIKEIINASKEISTPVVACELVTKDNIIAARIVKGRIEKTYLRDIIHYVRETWTGKE 1162

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIE----------RTRGISGHLTVSGHSFLILKP 873
            ++I +K++   I+ L LE+ I++I   I+          + R    H+    H ++ + P
Sbjct: 1163 AYITVKINWKTIQDLALELKIENILSAIKNHKRFKADDLKFRCSRSHI----HVYMDVDP 1218

Query: 874  KDSSKSFNSK-------------MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKL 920
              S+K+  SK             +  +K++LP + + G     RA+I  +  E  T   L
Sbjct: 1219 --STKANLSKTEIAHTSADPFLRLKHLKRMLPDIQVLGHPQAFRAIIRTD--ETSTTNTL 1274

Query: 921  LVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFR 980
            LVEG  LR+ M T GV G++ S+NN  E+   LGIEAAR+TI+ EI  VM++  M ID R
Sbjct: 1275 LVEGYGLRECMTTMGVDGLRTSTNNVMEMRDVLGIEAARTTIVQEISEVMKD--MDIDPR 1332

Query: 981  HPMLVADLMTSKGEVLG 997
            H  L+AD+MT KGEVLG
Sbjct: 1333 HMQLLADVMTYKGEVLG 1349



 Score =  104 bits (260), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 47/59 (79%), Positives = 51/59 (86%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSFFSGL PTEF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL  +YD
Sbjct: 844 PSKGFVRNSFFSGLEPTEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSTRYD 902



 Score = 53.9 bits (128), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 24/57 (42%), Positives = 37/57 (64%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVF 78
           LM  K+NL TP+NGE +I+A QDFI+  Y+L+ K+ FF+R    +I   ++  +  F
Sbjct: 536 LMGVKNNLATPKNGEPIISAIQDFISAAYILSSKDNFFDRRSFTQICLYMLGPQTRF 592



 Score = 43.9 bits (102), Expect = 0.71,   Method: Compositional matrix adjust.
 Identities = 19/39 (48%), Positives = 29/39 (74%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  FDA   G++D I GVSECIIMG  +++GTG +++++
Sbjct: 1373 DHLFDAGGAGRSDLIEGVSECIIMGKTVSLGTGAMEVVR 1411


>gi|425778039|gb|EKV16185.1| DNA-directed RNA polymerase [Penicillium digitatum PHI26]
 gi|425781413|gb|EKV19382.1| DNA-directed RNA polymerase [Penicillium digitatum Pd1]
          Length = 2075

 Score =  278 bits (711), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 138/282 (48%), Positives = 184/282 (65%), Gaps = 29/282 (10%)

Query: 341  DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
            D D+VLFNRQPSLHKLSI++H AK+ PHRTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 1097 DGDIVLFNRQPSLHKLSILSHFAKIRPHRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 1156

Query: 401  RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
            RAEA+               LM  K+NL TP+NGE +I+A QDFI+  Y+L+ K+ FF+R
Sbjct: 1157 RAEAME--------------LMGVKNNLATPKNGEPIISAIQDFISAAYVLSSKDNFFDR 1202

Query: 461  AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            A   +I   ++       G   RF      P   ++  ++WTGKQ+F+++++PN   PV 
Sbjct: 1203 ASFTQICLYML-------GPETRF---DLPPPSVLKPQMMWTGKQVFNILMRPNSSDPVM 1252

Query: 521  ANLKTKGRAYTA-----NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
             NL    R +        ++    D ++++RNSE++ G MDKST+GSG K NVFYI+LRD
Sbjct: 1253 VNLDAACREFKMPKDGRPKDLDPNDGWLVIRNSEVMCGVMDKSTIGSGKKDNVFYIMLRD 1312

Query: 576  FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
            FG   A   M RLS++++ +  N GFSIGIGDV P  G VQ+
Sbjct: 1313 FGPPAAAEGMNRLSKLSARWFTNIGFSIGIGDVYPSAGLVQS 1354



 Score =  223 bits (568), Expect = 6e-55,   Method: Compositional matrix adjust.
 Identities = 147/380 (38%), Positives = 205/380 (53%), Gaps = 77/380 (20%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG------------------- 1145
            AC  KY +AQ+EP  AVGA+ AQSIGEPGTQMTLKTFHFAG                   
Sbjct: 1681 ACLLKYKKAQVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIINA 1740

Query: 1146 --------EVCEYIE---------------------------EVFVPDDSFILIKLDMDR 1170
                      CE +                            EV+ PD++++ + L+   
Sbjct: 1741 SKEISTPVVACELVNKESTIAARIVKGRIEKTFLSDVIRSITEVWSPDEAYLKVVLNWKT 1800

Query: 1171 IRLLHLEVDIDSIRYCIERTRGISG--------------HLTVSGHSFLIL-KPKDSSKS 1215
            I  L LE+    I   I+  +   G              H+ +   S   L K + ++ S
Sbjct: 1801 IEDLALEITTPQIVEAIKTNKRFKGSDLKFSCKQASIKVHMDLDPASKAGLSKTEIAATS 1860

Query: 1216 FNS--KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVK 1273
             +   ++  +K++LP++ I G     RA+I  +  E  T   LLVEG  LR+ M T GV 
Sbjct: 1861 VDPFLRLKHLKRILPNIQILGHPRATRAIIRTD--ETSTTNTLLVEGYGLRECMTTMGVD 1918

Query: 1274 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 1333
            G++  +NN  E  + LG+EAARSTI+ EI  VM++  M ID RH  L+AD+MT KGEVLG
Sbjct: 1919 GLRTRTNNIMEAREVLGVEAARSTIVVEISEVMKD--MDIDPRHMQLLADVMTYKGEVLG 1976

Query: 1334 ITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            ITR GLAKM++SVL LASFE T+DHLFDA   G+TD I GVSECIIMG  +++GTG +++
Sbjct: 1977 ITRFGLAKMRDSVLQLASFEKTADHLFDAGGLGRTDLIEGVSECIIMGKTVSLGTGAMEV 2036

Query: 1394 LQAVP--RSEPVPRTLLFDN 1411
            ++ +   + +  PR  +F++
Sbjct: 2037 VRKLNFYQGQIGPRKTVFED 2056



 Score =  187 bits (476), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 106/267 (39%), Positives = 153/267 (57%), Gaps = 12/267 (4%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G +T +D V Q + +++  +  +  D  RT + +G LD+RMG + K   C TCG NL DC
Sbjct: 657 GVLTNDDIVGQ-AVVEVSDRKFFDLDQTRTVVANGPLDQRMGISNKTDACATCGNNLKDC 715

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFG++ L LP FH+GYF+ VI+ILQ ICK   C+ +LL E +   +  ++R P L  L
Sbjct: 716 NGHFGHVRLILPSFHVGYFKRVISILQEICKE--CSNILLPEAERRSYLREMRRPGLDNL 773

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKYKN-----RTKKKDAIV 257
            R  + K+I E  +K   C +CG INGVVKK G   LKI+H+K++        KK+  I 
Sbjct: 774 RRTQIAKRINERCRKTRECTYCGAINGVVKKTGTSALKITHDKFRAFNVSVSVKKQTPIS 833

Query: 258 EDLL-AEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPS 316
           +D+    + EA   NP++E H K      +NPL VL+LF+ +   D  L+ MN + ++P 
Sbjct: 834 KDVFDNSFLEARGANPDVEKHFKKAQ-DDMNPLRVLKLFKKMSDSDCELIGMNPKEARPE 892

Query: 317 DLILTRLLVPPNCIRPSVISDLKSDND 343
             +   +  PP CIRPSV  D  S  D
Sbjct: 893 MFLWQFIPAPPVCIRPSVGQDGASTED 919



 Score =  150 bits (380), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 100/251 (39%), Positives = 142/251 (56%), Gaps = 21/251 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP++   L        ARIVKGR+E+T L +V   I EV+ PD+
Sbjct: 1730 GVPRIKEIINASKEISTPVVACELVNKESTIAARIVKGRIEKTFLSDVIRSITEVWSPDE 1789

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISG--------------HLTVSGHSFL 869
            +++ + L+   I  L LE+    I   I+  +   G              H+ +   S  
Sbjct: 1790 AYLKVVLNWKTIEDLALEITTPQIVEAIKTNKRFKGSDLKFSCKQASIKVHMDLDPASKA 1849

Query: 870  IL-KPKDSSKSFNS--KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDN 926
             L K + ++ S +   ++  +K++LP++ I G     RA+I  +  E  T   LLVEG  
Sbjct: 1850 GLSKTEIAATSVDPFLRLKHLKRILPNIQILGHPRATRAIIRTD--ETSTTNTLLVEGYG 1907

Query: 927  LRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVA 986
            LR+ M T GV G++  +NN  E  + LG+EAARSTI+ EI  VM++  M ID RH  L+A
Sbjct: 1908 LRECMTTMGVDGLRTRTNNIMEAREVLGVEAARSTIVVEISEVMKD--MDIDPRHMQLLA 1965

Query: 987  DLMTSKGEVLG 997
            D+MT KGEVLG
Sbjct: 1966 DVMTYKGEVLG 1976



 Score =  101 bits (251), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 46/59 (77%), Positives = 49/59 (83%)

Query: 610  PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            P +GFV+NSFFSGL P EF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL   YD
Sbjct: 1471 PSKGFVRNSFFSGLEPPEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSSMYD 1529



 Score = 55.5 bits (132), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/46 (52%), Positives = 34/46 (73%)

Query: 22   LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRI 67
            LM  K+NL TP+NGE +I+A QDFI+  Y+L+ K+ FF+RA   +I
Sbjct: 1163 LMGVKNNLATPKNGEPIISAIQDFISAAYVLSSKDNFFDRASFTQI 1208



 Score = 46.2 bits (108), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 23/57 (40%), Positives = 38/57 (66%), Gaps = 2/57 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP--RSEPVPRTLLFDN 722
            D  FDA   G+TD I GVSECIIMG  +++GTG +++++ +   + +  PR  +F++
Sbjct: 2000 DHLFDAGGLGRTDLIEGVSECIIMGKTVSLGTGAMEVVRKLNFYQGQIGPRKTVFED 2056


>gi|66818062|ref|XP_642724.1| RNA polymerase III, largest subunit [Dictyostelium discoideum AX4]
 gi|74860514|sp|Q86AQ5.1|RPC1_DICDI RecName: Full=DNA-directed RNA polymerase III subunit rpc1;
           Short=RNA polymerase III subunit C1; AltName:
           Full=DNA-directed RNA polymerase III subunit A
 gi|60470813|gb|EAL68785.1| RNA polymerase III, largest subunit [Dictyostelium discoideum AX4]
          Length = 1450

 Score =  278 bits (711), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 132/272 (48%), Positives = 183/272 (67%), Gaps = 24/272 (8%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D++LFNRQPSLHKLSIM+H+A+V+P RT RFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 448 DGDIMLFNRQPSLHKLSIMSHKARVMPWRTLRFNECVCTPYNADFDGDEMNIHLPQTEEA 507

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A +LM   +NL+TPRNGE L+AATQDF+T  YL+++++AF+ R
Sbjct: 508 RAE--------------ATILMGVTNNLITPRNGEPLVAATQDFLTASYLISRRDAFYER 553

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +   +  T  AD ++   +          P   ++   +WTGKQIF ++L+P+    V 
Sbjct: 554 YR-FALMCTHFADANEHIDL---------PPPAILKPVELWTGKQIFEVLLRPSVKSHVL 603

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            N +T+ R Y+ N   C +D YV  RNSEL+ GS+DKS +G G K ++F+IL+RDF   +
Sbjct: 604 CNFETRSRTYSKNLYMCPKDGYVYFRNSELMCGSIDKSIIGGGNKNSLFHILMRDFSPTI 663

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
           A   M RL+++ + +L ++GFSIGI D+ P +
Sbjct: 664 AANCMTRLAKLCARFLGDQGFSIGIPDIKPAE 695



 Score =  268 bits (686), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 159/366 (43%), Positives = 216/366 (59%), Gaps = 59/366 (16%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEV---------------- 1147
            + C +KY RA+IEP TAVGA+ AQSIGEPGTQMTLKTFHFAG                  
Sbjct: 1086 DICLDKYSRARIEPGTAVGAIGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIIN 1145

Query: 1148 ---------------CEY-----------------------IEEVFVPDDSFILIKLDMD 1169
                           C+Y                       I+EV      ++ IK+D +
Sbjct: 1146 AAKNISTPIITASLNCDYDIRSARIVAGRIEKTTLGHVATHIKEVVKRAGCYLSIKIDKN 1205

Query: 1170 RIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSG-HSFLILKPKDSSKSFNSKMYQMKQ 1225
             +  L LE++  +I   I  T+G+      +T +G +   I+ P +  +     +  +K 
Sbjct: 1206 FVDSLQLEINSKTISQSIASTKGLKLKPEQITTNGDYKLRIVPPANIREGSLYYLQFLKN 1265

Query: 1226 LLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEV 1285
             LP+V++KG+  +NR VI + D E   +Y+LLVEG +LR VMAT G+KG   +SN+  E 
Sbjct: 1266 NLPAVIVKGIPTVNRVVISKVD-EKQERYQLLVEGYDLRAVMATPGIKGTHTTSNHIMEC 1324

Query: 1286 YKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKES 1345
              TLGIE AR+TIM+EI ++M +HGMSID RH ML+ADLM+ KGE+LGITR G+AKMKES
Sbjct: 1325 ENTLGIETARNTIMSEIDMIMTSHGMSIDIRHVMLLADLMSFKGEILGITRFGIAKMKES 1384

Query: 1346 VLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPR 1405
            VL LASFE T+DHLFDAA + + D I GVSECIIMG+ + +GTGL KLL+   ++    +
Sbjct: 1385 VLMLASFEKTTDHLFDAAVHHRQDDIVGVSECIIMGVVIPLGTGLFKLLRKSNKNNLPKK 1444

Query: 1406 TLLFDN 1411
            +LL  +
Sbjct: 1445 SLLLQD 1450



 Score =  232 bits (592), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 120/257 (46%), Positives = 168/257 (65%), Gaps = 8/257 (3%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G I+  +  ED + + SH+QIV++ L+    +R P P+G+LD ++GT+ K+A CTTCG +
Sbjct: 15  GHIQFGLLSEDDIVRLSHVQIVNRELF-DLVKRKPTPYGVLDNKLGTSDKQAMCTTCGLS 73

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
           + DCVGHFGYI L LPVFHIGY + ++NILQ ICK  +C+ +LL EEK   +  K+RN  
Sbjct: 74  IVDCVGHFGYIKLQLPVFHIGYLKNIMNILQMICK--SCSTILLNEEKKQYYLRKMRNKK 131

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDL 260
           +  L RKSL KKI    +K   C  CG  NG++KK G  KI HEKYK +T+     ++D 
Sbjct: 132 MDNLQRKSLLKKIFLECRKTKECLKCGSTNGMIKKSGAFKIIHEKYKGKTES----LQDY 187

Query: 261 LAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
            A Y++A+K+NPE+++H K      LNPL  L LF+ I  +DI ++ M+  + +P  LIL
Sbjct: 188 YALYDDAIKYNPEMKSHIKKAQ-DDLNPLVALNLFKKISYQDIEIMNMDPVIGRPERLIL 246

Query: 321 TRLLVPPNCIRPSVISD 337
           T +LVPP  IRPSV  D
Sbjct: 247 TYMLVPPVSIRPSVPMD 263



 Score =  204 bits (520), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 114/238 (47%), Positives = 160/238 (67%), Gaps = 5/238 (2%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++NISTPIITA L+ D D+  ARIV GR+E+TTLG V  +I+EV     
Sbjct: 1136 GVPRIKEIINAAKNISTPIITASLNCDYDIRSARIVAGRIEKTTLGHVATHIKEVVKRAG 1195

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSG-HSFLILKPKDSSKS 879
             ++ IK+D + +  L LE++  +I   I  T+G+      +T +G +   I+ P +  + 
Sbjct: 1196 CYLSIKIDKNFVDSLQLEINSKTISQSIASTKGLKLKPEQITTNGDYKLRIVPPANIREG 1255

Query: 880  FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
                +  +K  LP+V++KG+  +NR VI + D E   +Y+LLVEG +LR VMAT G+KG 
Sbjct: 1256 SLYYLQFLKNNLPAVIVKGIPTVNRVVISKVD-EKQERYQLLVEGYDLRAVMATPGIKGT 1314

Query: 940  KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
              +SN+  E   TLGIE AR+TIM+EI ++M +HGMSID RH ML+ADLM+ KGE+LG
Sbjct: 1315 HTTSNHIMECENTLGIETARNTIMSEIDMIMTSHGMSIDIRHVMLLADLMSFKGEILG 1372



 Score =  108 bits (269), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 51/78 (65%), Positives = 59/78 (75%), Gaps = 7/78 (8%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSF 671
           +GFV NSF++G+ PTEFFFHTMGGREGLVDTAVKTAETGYMQRRL+K+LEDL   YD   
Sbjct: 819 KGFVSNSFYTGMIPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLMKALEDLSTHYD--- 875

Query: 672 DAAFYGQTDCISGVSECI 689
               Y   D I G+ + I
Sbjct: 876 ----YTVRDSIGGIVQFI 889



 Score = 58.2 bits (139), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 23/41 (56%), Positives = 34/41 (82%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           +LM   +NL+TPRNGE L+AATQDF+T  YL+++++AF+ R
Sbjct: 513 ILMGVTNNLITPRNGEPLVAATQDFLTASYLISRRDAFYER 553



 Score = 48.9 bits (115), Expect = 0.021,   Method: Compositional matrix adjust.
 Identities = 25/55 (45%), Positives = 36/55 (65%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDN 722
            D  FDAA + + D I GVSECIIMG+ + +GTGL KLL+   ++    ++LL  +
Sbjct: 1396 DHLFDAAVHHRQDDIVGVSECIIMGVVIPLGTGLFKLLRKSNKNNLPKKSLLLQD 1450


>gi|365763066|gb|EHN04597.1| Rpo31p [Saccharomyces cerevisiae x Saccharomyces kudriavzevii VIN7]
          Length = 1460

 Score =  278 bits (711), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 140/282 (49%), Positives = 188/282 (66%), Gaps = 30/282 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH+LSI++H AK+ P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 468 DGDVVLFNRQPSLHRLSILSHYAKIRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 527

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL+TP++GE +IAATQDFITG YL++ K++F++R
Sbjct: 528 RAEAIN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFYDR 573

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A   ++ S +++D       I+ F      P   ++   +WTGKQ+FSL++KPN + PV 
Sbjct: 574 ATLTQLLS-MMSDG------IEHF---DIPPPAIMKPYYLWTGKQVFSLLIKPNHNSPVV 623

Query: 521 ANLKTKGRAYTANE------EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLR 574
            NL  K + +   +      E    D +VI+R S++L+G MDKS LG G K +VFY +LR
Sbjct: 624 INLDAKNKVFVPPKSKSLPNEMSQNDGFVIIRGSQILSGVMDKSVLGDGKKHSVFYTILR 683

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           D+G   A  AM R++++ + +L NRGFSIGI DVTP     Q
Sbjct: 684 DYGPQEAANAMNRMAKLCARFLGNRGFSIGINDVTPADDLKQ 725



 Score =  248 bits (632), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 156/377 (41%), Positives = 209/377 (55%), Gaps = 77/377 (20%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG----------------------- 1145
            KY +A++EP TA+GA+ AQSIGEPGTQMTLKTFHFAG                       
Sbjct: 1077 KYRKARLEPGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIINASKVI 1136

Query: 1146 -------------------EVCEYIEEVFVPDDSF------------ILIKLDMDRIRLL 1174
                                V   +E+  + D +F            I +++D+  I  L
Sbjct: 1137 STPIINAVLVNDNDERAARVVKGRVEKTLLSDVAFYVQDVYKDNLSFIQVRIDLGTIDKL 1196

Query: 1175 HLEVDIDSIRYCIERTRG---------------ISGHLTVSGHSFLILKPKDSSKSFNSK 1219
             LE+ I+ I   I R                  I+ ++   G+    +       S N  
Sbjct: 1197 QLELTIEDIAVAITRASKLKIQASDVNIIGKDRIAINVFPEGYKAKSISTSAKEPSENDV 1256

Query: 1220 MYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 1276
             Y+M+QL   LP VV+KG+  I+RAVI+  D +G  K +LLVEG  LRDVM T GV G +
Sbjct: 1257 FYRMQQLRRALPDVVVKGLPDISRAVINIRD-DG--KRELLVEGYGLRDVMCTDGVIGSR 1313

Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITR 1336
             ++N+  EV+  LGIEAAR +I+ EI   M NHGMS+D RH  L+ D+MT KGEVLGITR
Sbjct: 1314 TTTNHVLEVFSVLGIEAARYSIIREINYTMSNHGMSVDPRHIQLLGDVMTYKGEVLGITR 1373

Query: 1337 HGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA 1396
             GL+KM++SVL LASFE T+DHLFDAAFY + D + GVSECII+G  M++GTG  K+++ 
Sbjct: 1374 FGLSKMRDSVLQLASFEKTTDHLFDAAFYMKKDAVEGVSECIILGQTMSIGTGSFKVVKG 1433

Query: 1397 VPRSEP--VPRTLLFDN 1411
               SE   VP+  LF++
Sbjct: 1434 TNISEKDLVPKRCLFES 1450



 Score =  186 bits (471), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 114/252 (45%), Positives = 153/252 (60%), Gaps = 21/252 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII A L  D D   AR+VKGR+E+T L +V  Y+++V+  + 
Sbjct: 1122 GVPRIKEIINASKVISTPIINAVLVNDNDERAARVVKGRVEKTLLSDVAFYVQDVYKDNL 1181

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRG---------------ISGHLTVSGHSF 868
            SFI +++D+  I  L LE+ I+ I   I R                  I+ ++   G+  
Sbjct: 1182 SFIQVRIDLGTIDKLQLELTIEDIAVAITRASKLKIQASDVNIIGKDRIAINVFPEGYKA 1241

Query: 869  LILKPKDSSKSFNSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD 925
              +       S N   Y+M+QL   LP VV+KG+  I+RAVI+  D +G  K +LLVEG 
Sbjct: 1242 KSISTSAKEPSENDVFYRMQQLRRALPDVVVKGLPDISRAVINIRD-DG--KRELLVEGY 1298

Query: 926  NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 985
             LRDVM T GV G + ++N+  EV+  LGIEAAR +I+ EI   M NHGMS+D RH  L+
Sbjct: 1299 GLRDVMCTDGVIGSRTTTNHVLEVFSVLGIEAARYSIIREINYTMSNHGMSVDPRHIQLL 1358

Query: 986  ADLMTSKGEVLG 997
             D+MT KGEVLG
Sbjct: 1359 GDVMTYKGEVLG 1370



 Score =  179 bits (453), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 100/248 (40%), Positives = 139/248 (56%), Gaps = 11/248 (4%)

Query: 96  QSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPL 155
           QS +++ +++L+  +  R P  +G LD +MG +     C TC  NL+ C GHFG++ L L
Sbjct: 29  QSEVEVSTRDLFDLEKDRAPKANGALDPKMGVSSSSLECATCHGNLASCHGHFGHLKLAL 88

Query: 156 PVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILE 215
           PVFHIGYF+  I ILQ ICKN  C+ +LL E     F  +LR P +  L R  + KKIL+
Sbjct: 89  PVFHIGYFKATIQILQGICKN--CSAILLSEIDKRQFLHELRRPGVDNLRRMGILKKILD 146

Query: 216 TTKKVSVCPHCGEINGVVKK------CGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVK 269
             KK   C HCG +NGVVKK         LKI H+ ++   KK     +  + E+ E + 
Sbjct: 147 QCKKQRRCLHCGALNGVVKKAAAGAGSAALKIIHDTFRWVGKKSAPEKDIWVGEWKEVLA 206

Query: 270 FNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL--SKPSDLILTRLLVPP 327
            NPE+E + K   +  LNPL+ L LF+ I   D  LL ++A +   +P   I   L  PP
Sbjct: 207 HNPELERYVKR-CMDDLNPLKTLNLFKQIKSADCELLGIDATVPSGRPETYIWRYLPAPP 265

Query: 328 NCIRPSVI 335
            CIRPSV+
Sbjct: 266 VCIRPSVM 273



 Score =  100 bits (250), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 46/66 (69%), Positives = 53/66 (80%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSF 671
           +GFV+NSFFSGL+P EF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD + 
Sbjct: 845 KGFVRNSFFSGLSPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSCQYDNTV 904

Query: 672 DAAFYG 677
             +  G
Sbjct: 905 RTSANG 910



 Score = 62.4 bits (150), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/57 (49%), Positives = 43/57 (75%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVF 78
           LM  K+NL+TP++GE +IAATQDFITG YL++ K++F++RA   ++ S +  G + F
Sbjct: 534 LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFYDRATLTQLLSMMSDGIEHF 590



 Score = 55.1 bits (131), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 27/57 (47%), Positives = 38/57 (66%), Gaps = 2/57 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEP--VPRTLLFDN 722
            D  FDAAFY + D + GVSECII+G  M++GTG  K+++    SE   VP+  LF++
Sbjct: 1394 DHLFDAAFYMKKDAVEGVSECIILGQTMSIGTGSFKVVKGTNISEKDLVPKRCLFES 1450


>gi|256272995|gb|EEU07959.1| Rpo31p [Saccharomyces cerevisiae JAY291]
 gi|349581277|dbj|GAA26435.1| K7_Rpo31p [Saccharomyces cerevisiae Kyokai no. 7]
          Length = 1460

 Score =  278 bits (711), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 140/282 (49%), Positives = 188/282 (66%), Gaps = 30/282 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH+LSI++H AK+ P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 468 DGDVVLFNRQPSLHRLSILSHYAKIRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 527

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL+TP++GE +IAATQDFITG YL++ K++F++R
Sbjct: 528 RAEAIN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFYDR 573

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A   ++ S +++D       I+ F      P   ++   +WTGKQ+FSL++KPN + PV 
Sbjct: 574 ATLTQLLS-MMSDG------IEHF---DIPPPAIMKPYYLWTGKQVFSLLIKPNHNSPVV 623

Query: 521 ANLKTKGRAYTANE------EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLR 574
            NL  K + +   +      E    D +VI+R S++L+G MDKS LG G K +VFY +LR
Sbjct: 624 INLDAKNKVFVPPKSKSLPNEMSQNDGFVIIRGSQILSGVMDKSVLGDGKKHSVFYTILR 683

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           D+G   A  AM R++++ + +L NRGFSIGI DVTP     Q
Sbjct: 684 DYGPQEAANAMNRMAKLCARFLGNRGFSIGINDVTPADDLKQ 725



 Score =  248 bits (632), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 156/377 (41%), Positives = 209/377 (55%), Gaps = 77/377 (20%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG----------------------- 1145
            KY +A++EP TA+GA+ AQSIGEPGTQMTLKTFHFAG                       
Sbjct: 1077 KYRKARLEPGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIINASKVI 1136

Query: 1146 -------------------EVCEYIEEVFVPDDSF------------ILIKLDMDRIRLL 1174
                                V   +E+  + D +F            I +++D+  I  L
Sbjct: 1137 STPIINAVLVNDNDERAARVVKGRVEKTLLSDVAFYVQDVYKDNLSFIQVRIDLGTIDKL 1196

Query: 1175 HLEVDIDSIRYCIERTRG---------------ISGHLTVSGHSFLILKPKDSSKSFNSK 1219
             LE+ I+ I   I R                  I+ ++   G+    +       S N  
Sbjct: 1197 QLELTIEDIAVAITRASKLKIQASDVNIIGKDRIAINVFPEGYKAKSISTSAKEPSENDV 1256

Query: 1220 MYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 1276
             Y+M+QL   LP VV+KG+  I+RAVI+  D +G  K +LLVEG  LRDVM T GV G +
Sbjct: 1257 FYRMQQLRRALPDVVVKGLPDISRAVINIRD-DG--KRELLVEGYGLRDVMCTDGVIGSR 1313

Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITR 1336
             ++N+  EV+  LGIEAAR +I+ EI   M NHGMS+D RH  L+ D+MT KGEVLGITR
Sbjct: 1314 TTTNHVLEVFSVLGIEAARYSIIREINYTMSNHGMSVDPRHIQLLGDVMTYKGEVLGITR 1373

Query: 1337 HGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA 1396
             GL+KM++SVL LASFE T+DHLFDAAFY + D + GVSECII+G  M++GTG  K+++ 
Sbjct: 1374 FGLSKMRDSVLQLASFEKTTDHLFDAAFYMKKDAVEGVSECIILGQTMSIGTGSFKVVKG 1433

Query: 1397 VPRSEP--VPRTLLFDN 1411
               SE   VP+  LF++
Sbjct: 1434 TNISEKDLVPKRCLFES 1450



 Score =  186 bits (472), Expect = 9e-44,   Method: Compositional matrix adjust.
 Identities = 114/252 (45%), Positives = 153/252 (60%), Gaps = 21/252 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII A L  D D   AR+VKGR+E+T L +V  Y+++V+  + 
Sbjct: 1122 GVPRIKEIINASKVISTPIINAVLVNDNDERAARVVKGRVEKTLLSDVAFYVQDVYKDNL 1181

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRG---------------ISGHLTVSGHSF 868
            SFI +++D+  I  L LE+ I+ I   I R                  I+ ++   G+  
Sbjct: 1182 SFIQVRIDLGTIDKLQLELTIEDIAVAITRASKLKIQASDVNIIGKDRIAINVFPEGYKA 1241

Query: 869  LILKPKDSSKSFNSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD 925
              +       S N   Y+M+QL   LP VV+KG+  I+RAVI+  D +G  K +LLVEG 
Sbjct: 1242 KSISTSAKEPSENDVFYRMQQLRRALPDVVVKGLPDISRAVINIRD-DG--KRELLVEGY 1298

Query: 926  NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 985
             LRDVM T GV G + ++N+  EV+  LGIEAAR +I+ EI   M NHGMS+D RH  L+
Sbjct: 1299 GLRDVMCTDGVIGSRTTTNHVLEVFSVLGIEAARYSIIREINYTMSNHGMSVDPRHIQLL 1358

Query: 986  ADLMTSKGEVLG 997
             D+MT KGEVLG
Sbjct: 1359 GDVMTYKGEVLG 1370



 Score =  179 bits (455), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 100/248 (40%), Positives = 139/248 (56%), Gaps = 11/248 (4%)

Query: 96  QSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPL 155
           QS +++ +++L+  +  R P  +G LD +MG +     C TC  NL+ C GHFG++ L L
Sbjct: 29  QSEVEVSTRDLFDLEKDRAPKANGALDPKMGVSSSSLECATCHGNLASCHGHFGHLKLAL 88

Query: 156 PVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILE 215
           PVFHIGYF+  I ILQ ICKN  C+ +LL E     F  +LR P +  L R  + KKIL+
Sbjct: 89  PVFHIGYFKATIQILQGICKN--CSAILLSETDKRQFLHELRRPGVDNLRRMGILKKILD 146

Query: 216 TTKKVSVCPHCGEINGVVKK------CGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVK 269
             KK   C HCG +NGVVKK         LKI H+ ++   KK     +  + E+ E + 
Sbjct: 147 QCKKQRRCLHCGALNGVVKKAAAGAGSAALKIIHDTFRWVGKKSAPEKDIWVGEWKEVLA 206

Query: 270 FNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL--SKPSDLILTRLLVPP 327
            NPE+E + K   +  LNPL+ L LF+ I   D  LL ++A +   +P   I   L  PP
Sbjct: 207 HNPELERYVKR-CMDDLNPLKTLNLFKQIKSADCELLGIDATVPSGRPETYIWRYLPAPP 265

Query: 328 NCIRPSVI 335
            CIRPSV+
Sbjct: 266 VCIRPSVM 273



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 46/66 (69%), Positives = 53/66 (80%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSF 671
           +GFV+NSFFSGL+P EF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD + 
Sbjct: 845 KGFVRNSFFSGLSPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSCQYDNTV 904

Query: 672 DAAFYG 677
             +  G
Sbjct: 905 RTSANG 910



 Score = 62.4 bits (150), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/57 (49%), Positives = 43/57 (75%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVF 78
           LM  K+NL+TP++GE +IAATQDFITG YL++ K++F++RA   ++ S +  G + F
Sbjct: 534 LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFYDRATLTQLLSMMSDGIEHF 590



 Score = 55.1 bits (131), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 27/57 (47%), Positives = 38/57 (66%), Gaps = 2/57 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEP--VPRTLLFDN 722
            D  FDAAFY + D + GVSECII+G  M++GTG  K+++    SE   VP+  LF++
Sbjct: 1394 DHLFDAAFYMKKDAVEGVSECIILGQTMSIGTGSFKVVKGTNISEKDLVPKRCLFES 1450


>gi|6324690|ref|NP_014759.1| Rpo31p [Saccharomyces cerevisiae S288c]
 gi|133356|sp|P04051.1|RPC1_YEAST RecName: Full=DNA-directed RNA polymerase III subunit RPC1;
           Short=RNA polymerase III subunit C1; AltName:
           Full=DNA-directed RNA polymerase III largest subunit;
           AltName: Full=RNA polymerase III subunit C160
 gi|4400|emb|CAA26905.1| RNA polymerase III largest subunit [Saccharomyces cerevisiae]
 gi|1050828|emb|CAA62123.1| ORF O3254 [Saccharomyces cerevisiae]
 gi|1164961|emb|CAA64036.1| YOR3254c [Saccharomyces cerevisiae]
 gi|1420309|emb|CAA99314.1| RPO31 [Saccharomyces cerevisiae]
 gi|151945738|gb|EDN63979.1| RNA polymerase C [Saccharomyces cerevisiae YJM789]
 gi|285814998|tpg|DAA10891.1| TPA: Rpo31p [Saccharomyces cerevisiae S288c]
 gi|392296445|gb|EIW07547.1| Rpo31p [Saccharomyces cerevisiae CEN.PK113-7D]
          Length = 1460

 Score =  278 bits (711), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 140/282 (49%), Positives = 188/282 (66%), Gaps = 30/282 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH+LSI++H AK+ P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 468 DGDVVLFNRQPSLHRLSILSHYAKIRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 527

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL+TP++GE +IAATQDFITG YL++ K++F++R
Sbjct: 528 RAEAIN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFYDR 573

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A   ++ S +++D       I+ F      P   ++   +WTGKQ+FSL++KPN + PV 
Sbjct: 574 ATLTQLLS-MMSDG------IEHF---DIPPPAIMKPYYLWTGKQVFSLLIKPNHNSPVV 623

Query: 521 ANLKTKGRAYTANE------EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLR 574
            NL  K + +   +      E    D +VI+R S++L+G MDKS LG G K +VFY +LR
Sbjct: 624 INLDAKNKVFVPPKSKSLPNEMSQNDGFVIIRGSQILSGVMDKSVLGDGKKHSVFYTILR 683

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           D+G   A  AM R++++ + +L NRGFSIGI DVTP     Q
Sbjct: 684 DYGPQEAANAMNRMAKLCARFLGNRGFSIGINDVTPADDLKQ 725



 Score =  248 bits (632), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 156/377 (41%), Positives = 209/377 (55%), Gaps = 77/377 (20%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG----------------------- 1145
            KY +A++EP TA+GA+ AQSIGEPGTQMTLKTFHFAG                       
Sbjct: 1077 KYRKARLEPGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIINASKVI 1136

Query: 1146 -------------------EVCEYIEEVFVPDDSF------------ILIKLDMDRIRLL 1174
                                V   +E+  + D +F            I +++D+  I  L
Sbjct: 1137 STPIINAVLVNDNDERAARVVKGRVEKTLLSDVAFYVQDVYKDNLSFIQVRIDLGTIDKL 1196

Query: 1175 HLEVDIDSIRYCIERTRG---------------ISGHLTVSGHSFLILKPKDSSKSFNSK 1219
             LE+ I+ I   I R                  I+ ++   G+    +       S N  
Sbjct: 1197 QLELTIEDIAVAITRASKLKIQASDVNIIGKDRIAINVFPEGYKAKSISTSAKEPSENDV 1256

Query: 1220 MYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 1276
             Y+M+QL   LP VV+KG+  I+RAVI+  D +G  K +LLVEG  LRDVM T GV G +
Sbjct: 1257 FYRMQQLRRALPDVVVKGLPDISRAVINIRD-DG--KRELLVEGYGLRDVMCTDGVIGSR 1313

Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITR 1336
             ++N+  EV+  LGIEAAR +I+ EI   M NHGMS+D RH  L+ D+MT KGEVLGITR
Sbjct: 1314 TTTNHVLEVFSVLGIEAARYSIIREINYTMSNHGMSVDPRHIQLLGDVMTYKGEVLGITR 1373

Query: 1337 HGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA 1396
             GL+KM++SVL LASFE T+DHLFDAAFY + D + GVSECII+G  M++GTG  K+++ 
Sbjct: 1374 FGLSKMRDSVLQLASFEKTTDHLFDAAFYMKKDAVEGVSECIILGQTMSIGTGSFKVVKG 1433

Query: 1397 VPRSEP--VPRTLLFDN 1411
               SE   VP+  LF++
Sbjct: 1434 TNISEKDLVPKRCLFES 1450



 Score =  186 bits (472), Expect = 9e-44,   Method: Compositional matrix adjust.
 Identities = 114/252 (45%), Positives = 153/252 (60%), Gaps = 21/252 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII A L  D D   AR+VKGR+E+T L +V  Y+++V+  + 
Sbjct: 1122 GVPRIKEIINASKVISTPIINAVLVNDNDERAARVVKGRVEKTLLSDVAFYVQDVYKDNL 1181

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRG---------------ISGHLTVSGHSF 868
            SFI +++D+  I  L LE+ I+ I   I R                  I+ ++   G+  
Sbjct: 1182 SFIQVRIDLGTIDKLQLELTIEDIAVAITRASKLKIQASDVNIIGKDRIAINVFPEGYKA 1241

Query: 869  LILKPKDSSKSFNSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD 925
              +       S N   Y+M+QL   LP VV+KG+  I+RAVI+  D +G  K +LLVEG 
Sbjct: 1242 KSISTSAKEPSENDVFYRMQQLRRALPDVVVKGLPDISRAVINIRD-DG--KRELLVEGY 1298

Query: 926  NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 985
             LRDVM T GV G + ++N+  EV+  LGIEAAR +I+ EI   M NHGMS+D RH  L+
Sbjct: 1299 GLRDVMCTDGVIGSRTTTNHVLEVFSVLGIEAARYSIIREINYTMSNHGMSVDPRHIQLL 1358

Query: 986  ADLMTSKGEVLG 997
             D+MT KGEVLG
Sbjct: 1359 GDVMTYKGEVLG 1370



 Score =  179 bits (455), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 100/248 (40%), Positives = 139/248 (56%), Gaps = 11/248 (4%)

Query: 96  QSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPL 155
           QS +++ +++L+  +  R P  +G LD +MG +     C TC  NL+ C GHFG++ L L
Sbjct: 29  QSEVEVSTRDLFDLEKDRAPKANGALDPKMGVSSSSLECATCHGNLASCHGHFGHLKLAL 88

Query: 156 PVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILE 215
           PVFHIGYF+  I ILQ ICKN  C+ +LL E     F  +LR P +  L R  + KKIL+
Sbjct: 89  PVFHIGYFKATIQILQGICKN--CSAILLSETDKRQFLHELRRPGVDNLRRMGILKKILD 146

Query: 216 TTKKVSVCPHCGEINGVVKK------CGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVK 269
             KK   C HCG +NGVVKK         LKI H+ ++   KK     +  + E+ E + 
Sbjct: 147 QCKKQRRCLHCGALNGVVKKAAAGAGSAALKIIHDTFRWVGKKSAPEKDIWVGEWKEVLA 206

Query: 270 FNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL--SKPSDLILTRLLVPP 327
            NPE+E + K   +  LNPL+ L LF+ I   D  LL ++A +   +P   I   L  PP
Sbjct: 207 HNPELERYVKR-CMDDLNPLKTLNLFKQIKSADCELLGIDATVPSGRPETYIWRYLPAPP 265

Query: 328 NCIRPSVI 335
            CIRPSV+
Sbjct: 266 VCIRPSVM 273



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 45/57 (78%), Positives = 50/57 (87%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NSFFSGL+P EF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 845 KGFVRNSFFSGLSPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSCQYD 901



 Score = 62.4 bits (150), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/57 (49%), Positives = 43/57 (75%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVF 78
           LM  K+NL+TP++GE +IAATQDFITG YL++ K++F++RA   ++ S +  G + F
Sbjct: 534 LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFYDRATLTQLLSMMSDGIEHF 590



 Score = 55.1 bits (131), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 27/57 (47%), Positives = 38/57 (66%), Gaps = 2/57 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEP--VPRTLLFDN 722
            D  FDAAFY + D + GVSECII+G  M++GTG  K+++    SE   VP+  LF++
Sbjct: 1394 DHLFDAAFYMKKDAVEGVSECIILGQTMSIGTGSFKVVKGTNISEKDLVPKRCLFES 1450


>gi|344305554|gb|EGW35786.1| DNA-directed RNA polymerase III subunit C1 [Spathaspora
           passalidarum NRRL Y-27907]
          Length = 1445

 Score =  278 bits (711), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 147/310 (47%), Positives = 202/310 (65%), Gaps = 29/310 (9%)

Query: 306 LLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKV 365
           ++   EL+K +     R ++  N     V+     D DVVLFNRQPSLH+LSI++H AK+
Sbjct: 430 IMKQNELAKRNLRFGNREILAKNLRIGDVVERHIEDGDVVLFNRQPSLHRLSILSHYAKI 489

Query: 366 LPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANK 425
            P RTFR NECVCTPYNADFDGDEMN+H+PQTEEARAEA+               LM  K
Sbjct: 490 RPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEARAEAIN--------------LMGVK 535

Query: 426 SNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFS 485
           +NL+TP++GE +IAATQDFITG YL++ K++FF+RA  +++ S +    +D+     +F 
Sbjct: 536 NNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDRASFVQLLSMM--SDADV-----QFD 588

Query: 486 WRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTA-----NEEFCHRD 540
                P +F +  ++WTGKQ+FSL++KPN+   V  NL  K + +         E    D
Sbjct: 589 LPP--PTIF-KPVMLWTGKQVFSLLIKPNKKSNVIINLDAKNKTFIPPAKGLPSEMSPND 645

Query: 541 SYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRG 600
            +VI+R S++L+G MDKSTLG G K +VFY +LRD+G   A +AM R++++ + YL NRG
Sbjct: 646 GFVIIRGSQILSGLMDKSTLGDGKKHSVFYTILRDYGPQEAASAMNRMAKLCARYLGNRG 705

Query: 601 FSIGIGDVTP 610
           FSIGI DVTP
Sbjct: 706 FSIGINDVTP 715



 Score =  267 bits (683), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 192/509 (37%), Positives = 273/509 (53%), Gaps = 91/509 (17%)

Query: 970  MENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDPSLSAQEIL 1029
            ME     ++F      A  +T  G+  G   P E+KRL+D I+    S+    L   + L
Sbjct: 922  MEGDAKPVNFNRQWDHAYNLTYDGDETGL-LPYEIKRLVDSILTPLESK----LIRYDNL 976

Query: 1030 A--LSNETLDSKEFL--QDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSH- 1084
               L++   D  E++   D    F + ++ FL + ++K +    + K  QP   +I S  
Sbjct: 977  GRELADADQDRIEYIDQNDAEREFYQSLRDFLGKKAEKLARL-REAKGLQPFFTKIESEM 1035

Query: 1085 ---QDKIGHGRESNPFPSACKA-----EACREKYVRAQIEPATAVGALAAQSIGEPGTQM 1136
               +D++     +     + K      E C  KY RA++EP TAVGA+ AQSIGEPGTQM
Sbjct: 1036 SVDEDEVKLNSINQLLKISSKTVEKFLEQCLYKYSRARVEPGTAVGAIGAQSIGEPGTQM 1095

Query: 1137 TLKTFHFAG--------------EVCE--------YIEEVFVPDD--------------- 1159
            TLKTFHFAG              E+           I  V V DD               
Sbjct: 1096 TLKTFHFAGVASMNVTLGVPRIKEIINASKTISTPIINAVLVNDDDEIAARVVKGRIEKT 1155

Query: 1160 -----------------SFILIKLDMDRIRLLHLEVDIDSIRYCIE---RTRGISGHLTV 1199
                             +++ IK+D++ I  L LE+ ID+I   I+   + +   G ++V
Sbjct: 1156 LLEDVAFFIEDVYKDNLAYLSIKIDLETIDKLQLELTIDNIVRAIQNAPKLKITPGDVSV 1215

Query: 1200 SGHSF--LILKPKDSSKSFNS----------KMYQMKQLLPSVVIKGVQGINRAVIHEED 1247
            SG     +++  K+ + S  S          +M Q+K+ LPS+ IKG+  I RAVI+  D
Sbjct: 1216 SGKDRVNVLVNLKEKTDSLKSQAETKNALFFRMQQLKRALPSICIKGLPNIFRAVINIRD 1275

Query: 1248 VEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVME 1307
                +K +LLVEG  L+DVM+T GV G K ++N+  EV++ LGIEAARS+I+ EI   M 
Sbjct: 1276 ---DSKKELLVEGYGLKDVMSTDGVVGTKTTTNHVLEVFEILGIEAARSSIIKEIDYTMS 1332

Query: 1308 NHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQ 1367
            NHGMS+D RH  L+ D+MT KGEVLGITR GL+KM++SVL LASFE T+DHLFDAAF+ +
Sbjct: 1333 NHGMSVDPRHIQLLGDVMTYKGEVLGITRFGLSKMRDSVLQLASFEKTTDHLFDAAFFMK 1392

Query: 1368 TDCISGVSECIIMGLPMNVGTGLIKLLQA 1396
             D I GVSECII+G  M++GTG  KL+++
Sbjct: 1393 NDKIEGVSECIILGQTMSIGTGSFKLVKS 1421



 Score =  195 bits (496), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 116/249 (46%), Positives = 163/249 (65%), Gaps = 18/249 (7%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII A L  D D   AR+VKGR+E+T L +V  +IE+V+  + 
Sbjct: 1113 GVPRIKEIINASKTISTPIINAVLVNDDDEIAARVVKGRIEKTLLEDVAFFIEDVYKDNL 1172

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIE---RTRGISGHLTVSGHSFL--ILKPKDSSK 878
            +++ IK+D++ I  L LE+ ID+I   I+   + +   G ++VSG   +  ++  K+ + 
Sbjct: 1173 AYLSIKIDLETIDKLQLELTIDNIVRAIQNAPKLKITPGDVSVSGKDRVNVLVNLKEKTD 1232

Query: 879  SFNS----------KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLR 928
            S  S          +M Q+K+ LPS+ IKG+  I RAVI+  D    +K +LLVEG  L+
Sbjct: 1233 SLKSQAETKNALFFRMQQLKRALPSICIKGLPNIFRAVINIRDD---SKKELLVEGYGLK 1289

Query: 929  DVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADL 988
            DVM+T GV G K ++N+  EV++ LGIEAARS+I+ EI   M NHGMS+D RH  L+ D+
Sbjct: 1290 DVMSTDGVVGTKTTTNHVLEVFEILGIEAARSSIIKEIDYTMSNHGMSVDPRHIQLLGDV 1349

Query: 989  MTSKGEVLG 997
            MT KGEVLG
Sbjct: 1350 MTYKGEVLG 1358



 Score =  177 bits (448), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 105/272 (38%), Positives = 150/272 (55%), Gaps = 11/272 (4%)

Query: 79  FRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCG 138
            +GL    ++ +D V Q S +++ +++LY  +  RTP   G LD RMG +   + C+TC 
Sbjct: 13  IKGLEFSALSAKDIVAQ-SEVEVQTRDLYDLEKGRTPKVQGALDTRMGISSNASECSTCH 71

Query: 139 QNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN 198
            NL+ C GHFG+I L LPVFH+GYF+ +I +LQ ICKN  C+ VLL E+    +   LR 
Sbjct: 72  GNLASCHGHFGHIRLALPVFHVGYFKSIIQVLQCICKN--CSAVLLDEQAKRTYLNDLRK 129

Query: 199 PALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKC------GLLKISHEKYKNRTKK 252
           P +  L R  + +K+L+  KK   C  C  +NGVVKK         LKI H+ ++   KK
Sbjct: 130 PNIDNLRRMKILRKVLDQCKKQRRCLKCNHVNGVVKKAASGAGPAALKIVHDTFRWIGKK 189

Query: 253 KDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMN-AE 311
                E    E+N     NPE+E   K  + + LNPL+ L LF+ I   D  L+ ++ A 
Sbjct: 190 PTPEKELWDQEFNLVFDRNPELERFAK-RVHEDLNPLKTLNLFKQISPSDCELIGIDSAR 248

Query: 312 LSKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
             +P   I   L  PP CIRPSV+ D +S+ D
Sbjct: 249 GGRPEMYIWRYLPAPPVCIRPSVMMDAQSNED 280



 Score =  101 bits (251), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 47/61 (77%), Positives = 52/61 (85%), Gaps = 1/61 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV+NSF+SGLTP EF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QY
Sbjct: 837 TPQSKGFVRNSFYSGLTPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSAQY 896

Query: 668 D 668
           D
Sbjct: 897 D 897



 Score = 62.8 bits (151), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 27/50 (54%), Positives = 41/50 (82%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+RA  +++ S +
Sbjct: 531 LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDRASFVQLLSMM 580



 Score = 50.1 bits (118), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 22/40 (55%), Positives = 30/40 (75%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA 707
            D  FDAAF+ + D I GVSECII+G  M++GTG  KL+++
Sbjct: 1382 DHLFDAAFFMKNDKIEGVSECIILGQTMSIGTGSFKLVKS 1421


>gi|190407445|gb|EDV10712.1| DNA-directed RNA polymerase III largest subunit [Saccharomyces
           cerevisiae RM11-1a]
 gi|207341165|gb|EDZ69295.1| YOR116Cp-like protein [Saccharomyces cerevisiae AWRI1631]
 gi|259149599|emb|CAY86403.1| Rpo31p [Saccharomyces cerevisiae EC1118]
 gi|323331486|gb|EGA72901.1| Rpo31p [Saccharomyces cerevisiae AWRI796]
 gi|323352093|gb|EGA84630.1| Rpo31p [Saccharomyces cerevisiae VL3]
          Length = 1460

 Score =  278 bits (711), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 140/282 (49%), Positives = 188/282 (66%), Gaps = 30/282 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH+LSI++H AK+ P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 468 DGDVVLFNRQPSLHRLSILSHYAKIRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 527

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL+TP++GE +IAATQDFITG YL++ K++F++R
Sbjct: 528 RAEAIN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFYDR 573

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A   ++ S +++D       I+ F      P   ++   +WTGKQ+FSL++KPN + PV 
Sbjct: 574 ATLTQLLS-MMSDG------IEHF---DIPPPAIMKPYYLWTGKQVFSLLIKPNHNSPVV 623

Query: 521 ANLKTKGRAYTANE------EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLR 574
            NL  K + +   +      E    D +VI+R S++L+G MDKS LG G K +VFY +LR
Sbjct: 624 INLDAKNKVFVPPKSKSLPNEMSQNDGFVIIRGSQILSGVMDKSVLGDGKKHSVFYTILR 683

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           D+G   A  AM R++++ + +L NRGFSIGI DVTP     Q
Sbjct: 684 DYGPQEAANAMNRMAKLCARFLGNRGFSIGINDVTPADDLKQ 725



 Score =  248 bits (632), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 156/377 (41%), Positives = 209/377 (55%), Gaps = 77/377 (20%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG----------------------- 1145
            KY +A++EP TA+GA+ AQSIGEPGTQMTLKTFHFAG                       
Sbjct: 1077 KYRKARLEPGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIINASKVI 1136

Query: 1146 -------------------EVCEYIEEVFVPDDSF------------ILIKLDMDRIRLL 1174
                                V   +E+  + D +F            I +++D+  I  L
Sbjct: 1137 STPIINAVLVNDNDERAARVVKGRVEKTLLSDVAFYVQDVYKDNLSFIQVRIDLGTIDKL 1196

Query: 1175 HLEVDIDSIRYCIERTRG---------------ISGHLTVSGHSFLILKPKDSSKSFNSK 1219
             LE+ I+ I   I R                  I+ ++   G+    +       S N  
Sbjct: 1197 QLELTIEDIAVAITRASKLKIQASDVNIIGKDRIAINVFPEGYKAKSISTSAKEPSENDV 1256

Query: 1220 MYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 1276
             Y+M+QL   LP VV+KG+  I+RAVI+  D +G  K +LLVEG  LRDVM T GV G +
Sbjct: 1257 FYRMQQLRRALPDVVVKGLPDISRAVINIRD-DG--KRELLVEGYGLRDVMCTDGVIGSR 1313

Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITR 1336
             ++N+  EV+  LGIEAAR +I+ EI   M NHGMS+D RH  L+ D+MT KGEVLGITR
Sbjct: 1314 TTTNHVLEVFSVLGIEAARYSIIREINYTMSNHGMSVDPRHIQLLGDVMTYKGEVLGITR 1373

Query: 1337 HGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA 1396
             GL+KM++SVL LASFE T+DHLFDAAFY + D + GVSECII+G  M++GTG  K+++ 
Sbjct: 1374 FGLSKMRDSVLQLASFEKTTDHLFDAAFYMKKDAVEGVSECIILGQTMSIGTGSFKVVKG 1433

Query: 1397 VPRSEP--VPRTLLFDN 1411
               SE   VP+  LF++
Sbjct: 1434 TNISEKDLVPKRCLFES 1450



 Score =  186 bits (472), Expect = 9e-44,   Method: Compositional matrix adjust.
 Identities = 114/252 (45%), Positives = 153/252 (60%), Gaps = 21/252 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII A L  D D   AR+VKGR+E+T L +V  Y+++V+  + 
Sbjct: 1122 GVPRIKEIINASKVISTPIINAVLVNDNDERAARVVKGRVEKTLLSDVAFYVQDVYKDNL 1181

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRG---------------ISGHLTVSGHSF 868
            SFI +++D+  I  L LE+ I+ I   I R                  I+ ++   G+  
Sbjct: 1182 SFIQVRIDLGTIDKLQLELTIEDIAVAITRASKLKIQASDVNIIGKDRIAINVFPEGYKA 1241

Query: 869  LILKPKDSSKSFNSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD 925
              +       S N   Y+M+QL   LP VV+KG+  I+RAVI+  D +G  K +LLVEG 
Sbjct: 1242 KSISTSAKEPSENDVFYRMQQLRRALPDVVVKGLPDISRAVINIRD-DG--KRELLVEGY 1298

Query: 926  NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 985
             LRDVM T GV G + ++N+  EV+  LGIEAAR +I+ EI   M NHGMS+D RH  L+
Sbjct: 1299 GLRDVMCTDGVIGSRTTTNHVLEVFSVLGIEAARYSIIREINYTMSNHGMSVDPRHIQLL 1358

Query: 986  ADLMTSKGEVLG 997
             D+MT KGEVLG
Sbjct: 1359 GDVMTYKGEVLG 1370



 Score =  179 bits (455), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 100/248 (40%), Positives = 139/248 (56%), Gaps = 11/248 (4%)

Query: 96  QSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPL 155
           QS +++ +++L+  +  R P  +G LD +MG +     C TC  NL+ C GHFG++ L L
Sbjct: 29  QSEVEVSTRDLFDLEKDRAPKANGALDPKMGVSSSSLECATCHGNLASCHGHFGHLKLAL 88

Query: 156 PVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILE 215
           PVFHIGYF+  I ILQ ICKN  C+ +LL E     F  +LR P +  L R  + KKIL+
Sbjct: 89  PVFHIGYFKATIQILQGICKN--CSAILLSETDKRQFLHELRRPGVDNLRRMGILKKILD 146

Query: 216 TTKKVSVCPHCGEINGVVKK------CGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVK 269
             KK   C HCG +NGVVKK         LKI H+ ++   KK     +  + E+ E + 
Sbjct: 147 QCKKQRRCLHCGALNGVVKKAAAGAGSAALKIIHDTFRWVGKKSAPEKDIWVGEWKEVLA 206

Query: 270 FNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL--SKPSDLILTRLLVPP 327
            NPE+E + K   +  LNPL+ L LF+ I   D  LL ++A +   +P   I   L  PP
Sbjct: 207 HNPELERYVKR-CMDDLNPLKTLNLFKQIKSADCELLGIDATVPSGRPETYIWRYLPAPP 265

Query: 328 NCIRPSVI 335
            CIRPSV+
Sbjct: 266 VCIRPSVM 273



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 46/66 (69%), Positives = 53/66 (80%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSF 671
           +GFV+NSFFSGL+P EF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD + 
Sbjct: 845 KGFVRNSFFSGLSPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSCQYDNTV 904

Query: 672 DAAFYG 677
             +  G
Sbjct: 905 RTSANG 910



 Score = 62.0 bits (149), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/57 (49%), Positives = 43/57 (75%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVF 78
           LM  K+NL+TP++GE +IAATQDFITG YL++ K++F++RA   ++ S +  G + F
Sbjct: 534 LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFYDRATLTQLLSMMSDGIEHF 590



 Score = 55.1 bits (131), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 27/57 (47%), Positives = 38/57 (66%), Gaps = 2/57 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEP--VPRTLLFDN 722
            D  FDAAFY + D + GVSECII+G  M++GTG  K+++    SE   VP+  LF++
Sbjct: 1394 DHLFDAAFYMKKDAVEGVSECIILGQTMSIGTGSFKVVKGTNISEKDLVPKRCLFES 1450


>gi|410079408|ref|XP_003957285.1| hypothetical protein KAFR_0D05030 [Kazachstania africana CBS 2517]
 gi|372463870|emb|CCF58150.1| hypothetical protein KAFR_0D05030 [Kazachstania africana CBS 2517]
          Length = 1462

 Score =  278 bits (711), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 144/296 (48%), Positives = 190/296 (64%), Gaps = 30/296 (10%)

Query: 322 RLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPY 381
           RL +  N     ++     D DVVLFNRQPSLH+LSI++H AK+ P RTFR NECVCTPY
Sbjct: 450 RLKLAKNLQYGDIVERHLEDGDVVLFNRQPSLHRLSILSHYAKIRPWRTFRLNECVCTPY 509

Query: 382 NADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAAT 441
           NADFDGDEMN+H+PQTEEARAEA+               LM  K+NL+TP++GE +IAAT
Sbjct: 510 NADFDGDEMNLHVPQTEEARAEAIN--------------LMGVKNNLLTPKSGEPIIAAT 555

Query: 442 QDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIW 501
           QDFITG YL++ K++FF+RA   ++ S +++D +    I          P   ++   +W
Sbjct: 556 QDFITGSYLISHKDSFFDRATFTQLLS-MMSDGNLQFDI---------PPPAIMKPYYLW 605

Query: 502 TGKQIFSLILKPNRDCPVNANLKTKGRAY------TANEEFCHRDSYVILRNSELLAGSM 555
           TGKQ+FSL++KPN   PV  NL  K + Y      +   E    D +VI+R S +L+G M
Sbjct: 606 TGKQLFSLLIKPNHKSPVVINLDAKNKVYIPPKSKSLPNEMSRNDGFVIIRGSNILSGVM 665

Query: 556 DKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           DKS LG G K +VFY +LRD+G   A  AM R+S++ + +L NRGFSIGI DVTP 
Sbjct: 666 DKSVLGDGKKHSVFYTILRDYGPQEAANAMNRMSKLCARFLGNRGFSIGISDVTPA 721



 Score =  242 bits (617), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 179/530 (33%), Positives = 267/530 (50%), Gaps = 116/530 (21%)

Query: 994  EVLGNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDI 1053
            E+ G+  PV   R  D  +    + ++  L   +++  +NE L+  E      +N   ++
Sbjct: 926  EMEGSAQPVNFNRSWDHALNITFNNNERGLLPYQVMKKTNEVLNPLEERLVRYDNLGNEV 985

Query: 1054 -KKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRES-----------------N 1095
             K+ L++    +   + +D   + LR  I S  D + H R+S                 +
Sbjct: 986  MKEDLDKLEYADQFDAERD-FYKTLRSYIQSKSDHLAHVRKSRGLLELLSEPGEELQSLH 1044

Query: 1096 PFPSA-----------CKA---------EACREKYVRAQIEPATAVGALAAQSIGEPGTQ 1135
            P   A           CK          E    KY +A++EP TAVGA+ AQSIGEPGTQ
Sbjct: 1045 PDERATDVSRSSVDQLCKITEKAVLKFLEIALSKYRKARVEPGTAVGAIGAQSIGEPGTQ 1104

Query: 1136 MTLKTFHFAG--------------EVCEYIEEVFVPDDSFILI----------------- 1164
            MTLKTFHFAG              E+    + +  P  + +L+                 
Sbjct: 1105 MTLKTFHFAGVASMNVTLGVPRIKEIINASKTISTPIINAVLVNNNDERAARVVKGRVEK 1164

Query: 1165 -----------------------KLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLT 1198
                                   ++D++ I  L LE+ I+ I   + +   +   +  ++
Sbjct: 1165 TMLSDVAYYIQDVYKDNLSFLQIRIDLNTIEKLQLELTIEDIAVALTKAPKLKIQASDVS 1224

Query: 1199 VSGHSFLILK--PKDS-SKSFNS------------KMYQMKQLLPSVVIKGVQGINRAVI 1243
            ++G   +I+   P+ S SKS ++            +M Q+++ LP +V+KG+  I RAVI
Sbjct: 1225 IAGDDKVIVNVFPEGSKSKSISTSAKDPSENDVFYRMQQLRRALPHIVVKGLPEIARAVI 1284

Query: 1244 HEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIK 1303
            +  D +G  K +LLVEG  LR+VM T GV G K  +N+  EV   LGIEAARS+I+ EI 
Sbjct: 1285 NIRD-DG--KRELLVEGYGLREVMCTDGVIGSKTVTNHVLEVSSVLGIEAARSSIIGEID 1341

Query: 1304 LVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAA 1363
              M NHGMS+D RH  L+ D+MT KGEVLGITR GL+KM++SVL LASFE T+DHLFDAA
Sbjct: 1342 YTMSNHGMSVDPRHIQLLGDVMTYKGEVLGITRFGLSKMRDSVLQLASFEKTTDHLFDAA 1401

Query: 1364 FYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA--VPRSEPVPRTLLFDN 1411
            FY + D + GVSECII+G  M++GTG  K+++   +   +  P+  LF++
Sbjct: 1402 FYMKKDNVEGVSECIILGQTMSIGTGSFKVVKGTDIKPEDLKPKPTLFES 1451



 Score =  185 bits (469), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 113/252 (44%), Positives = 161/252 (63%), Gaps = 21/252 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII A L  + D   AR+VKGR+E+T L +V  YI++V+  + 
Sbjct: 1123 GVPRIKEIINASKTISTPIINAVLVNNNDERAARVVKGRVEKTMLSDVAYYIQDVYKDNL 1182

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFLILK--PKDS-S 877
            SF+ I++D++ I  L LE+ I+ I   + +   +   +  ++++G   +I+   P+ S S
Sbjct: 1183 SFLQIRIDLNTIEKLQLELTIEDIAVALTKAPKLKIQASDVSIAGDDKVIVNVFPEGSKS 1242

Query: 878  KSFNS------------KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD 925
            KS ++            +M Q+++ LP +V+KG+  I RAVI+  D +G  K +LLVEG 
Sbjct: 1243 KSISTSAKDPSENDVFYRMQQLRRALPHIVVKGLPEIARAVINIRD-DG--KRELLVEGY 1299

Query: 926  NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 985
             LR+VM T GV G K  +N+  EV   LGIEAARS+I+ EI   M NHGMS+D RH  L+
Sbjct: 1300 GLREVMCTDGVIGSKTVTNHVLEVSSVLGIEAARSSIIGEIDYTMSNHGMSVDPRHIQLL 1359

Query: 986  ADLMTSKGEVLG 997
             D+MT KGEVLG
Sbjct: 1360 GDVMTYKGEVLG 1371



 Score =  171 bits (433), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 98/262 (37%), Positives = 144/262 (54%), Gaps = 12/262 (4%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           IE +      +  QS ++I S++L+  +  R    +G LD RMG +     C TC  NL+
Sbjct: 16  IEFSALSASDIVAQSEVEISSRDLFDLEQNRKQKENGALDPRMGVSSSSLTCETCHGNLA 75

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA-L 201
            C GHFG+I L LPVFH+GYF+  I ILQ+ICKN  C+ VLL +E    +  +LR    +
Sbjct: 76  SCHGHFGHIKLALPVFHVGYFKATIQILQAICKN--CSSVLLSDEDKKKYLHELRTSGRI 133

Query: 202 SYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGL------LKISHEKYKNRTKKKDA 255
             L +  + KK+++  KK   C HCG +NGVVKK         LKI H+ ++   KK   
Sbjct: 134 DNLKKMGILKKVMDQCKKQRRCLHCGALNGVVKKAAAGSGTASLKIIHDTFRWVGKKSTP 193

Query: 256 IVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL--S 313
             ++ + ++NE +  +PE+E   K      LNPL+ L LF+ +  ED  LL +++ +   
Sbjct: 194 EKDNWIGDWNEVLSHHPELERFVKR-CTDDLNPLKTLNLFKQVRPEDCELLGIDSTVKSG 252

Query: 314 KPSDLILTRLLVPPNCIRPSVI 335
           +P   I   L  PP CIRPSV+
Sbjct: 253 RPETYIWRYLPAPPVCIRPSVM 274



 Score =  102 bits (254), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 48/61 (78%), Positives = 52/61 (85%), Gaps = 1/61 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV+NSFFSGLTP EF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QY
Sbjct: 842 TPQSKGFVRNSFFSGLTPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSCQY 901

Query: 668 D 668
           D
Sbjct: 902 D 902



 Score = 63.5 bits (153), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 29/57 (50%), Positives = 42/57 (73%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVF 78
           LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+RA   ++ S +  G   F
Sbjct: 535 LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDRATFTQLLSMMSDGNLQF 591



 Score = 50.1 bits (118), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 24/57 (42%), Positives = 37/57 (64%), Gaps = 2/57 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA--VPRSEPVPRTLLFDN 722
            D  FDAAFY + D + GVSECII+G  M++GTG  K+++   +   +  P+  LF++
Sbjct: 1395 DHLFDAAFYMKKDNVEGVSECIILGQTMSIGTGSFKVVKGTDIKPEDLKPKPTLFES 1451


>gi|238504894|ref|XP_002383676.1| DNA-directed RNA polymerase III largest subunit, putative
           [Aspergillus flavus NRRL3357]
 gi|220689790|gb|EED46140.1| DNA-directed RNA polymerase III largest subunit, putative
           [Aspergillus flavus NRRL3357]
          Length = 1436

 Score =  278 bits (710), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 136/282 (48%), Positives = 185/282 (65%), Gaps = 29/282 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++H AKV PHRTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 470 DGDIVLFNRQPSLHKLSILSHFAKVRPHRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 529

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL TP+NGE +I+A QDFI+  Y+L+ K+ FF+R
Sbjct: 530 RAEAME--------------LMGVKNNLATPKNGEPIISAIQDFISAAYILSSKDNFFDR 575

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
               +I   ++       G   RF      P   ++  ++WTGKQ+F+++++PN+D PV 
Sbjct: 576 RSFTQICLYML-------GPETRF---DLPPPAVLKPQMLWTGKQVFNILMRPNKDDPVM 625

Query: 521 ANLKTKGRAYTA-----NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL    R Y        ++   +D ++++RNSE++ G MDK+T+GSG K NVFY++LRD
Sbjct: 626 VNLDAACREYKPPKDGRPKDLDPKDGWLVIRNSEVMCGVMDKATIGSGKKDNVFYVMLRD 685

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           FG   A   M RLSR+++ +  N GFSIGI DV P +  +Q+
Sbjct: 686 FGPPAAAEGMNRLSRLSARWFTNMGFSIGITDVYPSEKLLQS 727



 Score =  177 bits (448), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 102/267 (38%), Positives = 140/267 (52%), Gaps = 15/267 (5%)

Query: 87  VTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVG 146
           V   D +  Q  +++  +  +  D  R+ + HG LD RMG + K A+C TCG  L  C G
Sbjct: 31  VLSNDDIVSQGVVEVSDRKFFDLDRDRSVVAHGPLDSRMGVSSKTASCQTCGGALQVCNG 90

Query: 147 HFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVR 206
           HFG++ L LP FH+GYF+ VI ILQ ICK   C+ +LL E +   F  ++R P L  L R
Sbjct: 91  HFGHVKLVLPSFHVGYFKRVITILQEICKE--CSHILLPEGERRAFLREMRRPGLDNLRR 148

Query: 207 KSLKKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKYK--------NRTKKKDAI 256
             + K+I E  +K   C  CG  NGVVKK G   LKI+H+K++         +      I
Sbjct: 149 LQIAKRINERCRKTRNCDRCGATNGVVKKAGTSALKITHDKFRAFNASTSMKKIPPPSKI 208

Query: 257 VEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPS 316
           V D    + EA   NPE+E H K      +N L VL LF+ I   D  LL ++ + ++P 
Sbjct: 209 VFD--RSFEEARSHNPEVEKHHKKAQ-DDMNALRVLNLFKRISDTDCELLGLDPKEARPE 265

Query: 317 DLILTRLLVPPNCIRPSVISDLKSDND 343
             +   +  PP CIRPSV  D  S  D
Sbjct: 266 MFLWQYIPAPPVCIRPSVGQDASSTED 292



 Score =  175 bits (443), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 145/468 (30%), Positives = 231/468 (49%), Gaps = 97/468 (20%)

Query: 1001 PVELKRLLDDIIAKNSSRSDPSLSAQEILAL-------SNETLDSKEFLQDTSENFVRDI 1053
            P E+  + +++++K  ++    L  +++L +       SN  +D  E    ++ +F+  I
Sbjct: 957  PAEIMEVCEEMLSKERAK----LVRKDLLDVELGYMDRSNHGVDQFE----SARDFLESI 1008

Query: 1054 KKFLEEFSKKESVTSHQDKV--SQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYV 1111
            ++++   +K + + S    +  S    +Q L+H  K+   +    F SAC       KY 
Sbjct: 1009 QQYVS--TKADKLISRGGDIDPSDERSQQGLNHTGKLTE-KTLRTFISACLM-----KYK 1060

Query: 1112 RAQIEPATAVGAL---------------------------------------AAQSIGEP 1132
            +AQ+EP  AVGA+                                       A++ I  P
Sbjct: 1061 KAQVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIINASKEISTP 1120

Query: 1133 GTQMTLKTFH---------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLE 1177
                 L T                 +  ++  Y+ E +   +++I +K++   I+ L LE
Sbjct: 1121 VVSCELVTKDNVIAARIVKGRIEKTYLRDITHYVRETWTGKEAYITVKINWKTIQDLALE 1180

Query: 1178 VDIDSIRYCIERTRGISG----------HLTVSGHSFLILKPKDSSKSFNSKMYQMKQLL 1227
            + I  I   I+  R              H+    H ++  +   +S     ++  +K+LL
Sbjct: 1181 LKIQDILAAIKNHRRFKSDDLKFRCQRSHI----HIYMDTEIAATSADPFLRLKHLKRLL 1236

Query: 1228 PSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYK 1287
            P + + G     RA+I  +D    T   LLVEG  LR  M T GV G++ S+NN  E+ +
Sbjct: 1237 PDIQVLGHPQAYRAIIRTDDTS--TTNTLLVEGYGLRACMNTIGVDGLRTSTNNVMEMRE 1294

Query: 1288 TLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVL 1347
             LGIEAAR+TI+ EI  VM++  M ID RH  L+AD+MT KGEVLGITR GLAKM++SVL
Sbjct: 1295 VLGIEAARTTIVREISEVMKD--MDIDPRHMQLLADVMTYKGEVLGITRFGLAKMRDSVL 1352

Query: 1348 NLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 1395
             LASFE T+DHLFDA   G+TD + GVSECIIMG  +++GTG +++++
Sbjct: 1353 QLASFEKTADHLFDAGGAGRTDLVEGVSECIIMGKTVSLGTGAMEVVR 1400



 Score =  145 bits (367), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 97/244 (39%), Positives = 142/244 (58%), Gaps = 18/244 (7%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+++  L    ++  ARIVKGR+E+T L ++  Y+ E +   +
Sbjct: 1103 GVPRIKEIINASKEISTPVVSCELVTKDNVIAARIVKGRIEKTYLRDITHYVRETWTGKE 1162

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS----------GHLTVSGHSFLILKP 873
            ++I +K++   I+ L LE+ I  I   I+  R              H+    H ++  + 
Sbjct: 1163 AYITVKINWKTIQDLALELKIQDILAAIKNHRRFKSDDLKFRCQRSHI----HIYMDTEI 1218

Query: 874  KDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMAT 933
              +S     ++  +K+LLP + + G     RA+I  +D    T   LLVEG  LR  M T
Sbjct: 1219 AATSADPFLRLKHLKRLLPDIQVLGHPQAYRAIIRTDDTS--TTNTLLVEGYGLRACMNT 1276

Query: 934  YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
             GV G++ S+NN  E+ + LGIEAAR+TI+ EI  VM++  M ID RH  L+AD+MT KG
Sbjct: 1277 IGVDGLRTSTNNVMEMREVLGIEAARTTIVREISEVMKD--MDIDPRHMQLLADVMTYKG 1334

Query: 994  EVLG 997
            EVLG
Sbjct: 1335 EVLG 1338



 Score =  101 bits (252), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 46/59 (77%), Positives = 50/59 (84%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSFFSGL P EF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL  +YD
Sbjct: 844 PSKGFVRNSFFSGLEPYEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSSRYD 902



 Score = 53.5 bits (127), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 23/46 (50%), Positives = 33/46 (71%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRI 67
           LM  K+NL TP+NGE +I+A QDFI+  Y+L+ K+ FF+R    +I
Sbjct: 536 LMGVKNNLATPKNGEPIISAIQDFISAAYILSSKDNFFDRRSFTQI 581



 Score = 44.3 bits (103), Expect = 0.46,   Method: Compositional matrix adjust.
 Identities = 19/39 (48%), Positives = 29/39 (74%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  FDA   G+TD + GVSECIIMG  +++GTG +++++
Sbjct: 1362 DHLFDAGGAGRTDLVEGVSECIIMGKTVSLGTGAMEVVR 1400


>gi|330791878|ref|XP_003284018.1| RNA polymerase III, largest subunit [Dictyostelium purpureum]
 gi|325086064|gb|EGC39460.1| RNA polymerase III, largest subunit [Dictyostelium purpureum]
          Length = 1396

 Score =  278 bits (710), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 134/276 (48%), Positives = 184/276 (66%), Gaps = 24/276 (8%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D++LFNRQPSLHKLSIM+H+A+V+P RT RFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 444 DGDIMLFNRQPSLHKLSIMSHKARVMPWRTLRFNECVCTPYNADFDGDEMNIHLPQTEEA 503

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A +LM   +NL+TPRNGE L+AATQDF+T  YL+++++AF++R
Sbjct: 504 RAE--------------ATILMGVTNNLITPRNGEPLVAATQDFLTASYLISRRDAFYDR 549

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +   +  T  AD ++   +          P   ++   +WTGKQIF ++L+P+    V 
Sbjct: 550 YR-FTLMCTHFADANEHIDL---------PPPAILKPIELWTGKQIFEVLLRPSVKSHVL 599

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
              +TK R Y+ N   C +D YV  RNSEL+ GS+DKS +G G K ++F+IL+RDF   +
Sbjct: 600 CTFETKSRTYSKNLYMCPKDGYVYFRNSELMCGSIDKSIIGGGNKNSLFHILMRDFSPSI 659

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           A  +M RL+++ + +L ++GFSIGI DV P     Q
Sbjct: 660 AANSMTRLAKLCARFLGDQGFSIGIPDVQPAPDLDQ 695



 Score =  230 bits (586), Expect = 6e-57,   Method: Compositional matrix adjust.
 Identities = 130/271 (47%), Positives = 178/271 (65%), Gaps = 5/271 (1%)

Query: 1145 GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHL----TVS 1200
            G V E+I+EV      ++ IK+D   I  L LE++  +I   I  T+G+   +     +S
Sbjct: 1126 GHVAEHIKEVVKRGGCYLSIKIDKKFIDSLQLEINARTIAQSILSTKGLKLKVDQVSALS 1185

Query: 1201 GHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEG 1260
             +   I  P +  +     +  +K  LPSV++KG+  INR VI + D E   +Y+LLVEG
Sbjct: 1186 EYKLRITPPGNCREQTLYYLQSLKNNLPSVIVKGIPTINRVVISKID-EKQERYQLLVEG 1244

Query: 1261 DNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPML 1320
             +LR VMAT G+KG   +SN+  E   TLGIE AR+TIM+EI+++M +HGMSID RH ML
Sbjct: 1245 YDLRAVMATSGIKGTHTTSNHIMECENTLGIETARNTIMSEIQMIMTSHGMSIDVRHVML 1304

Query: 1321 VADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIM 1380
            +ADLM+ KGE+LGITR G+AKMKESVL LASFE T+DHLFDAA + + D I GVSECIIM
Sbjct: 1305 LADLMSFKGEILGITRFGIAKMKESVLMLASFEKTTDHLFDAAVHHRQDDIVGVSECIIM 1364

Query: 1381 GLPMNVGTGLIKLLQAVPRSEPVPRTLLFDN 1411
            G  + +GTGL KLL+   ++    ++LL D+
Sbjct: 1365 GSVIPLGTGLFKLLRKSNKNNLPKKSLLLDD 1395



 Score =  228 bits (581), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 119/257 (46%), Positives = 168/257 (65%), Gaps = 8/257 (3%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G I+  +  E+ + + SH+Q+V++ L+    +R P P+G+LD ++GT+ K+ NCTTCG +
Sbjct: 11  GHIQFGLLSEEDIVRLSHVQLVNRELF-DLLKRKPQPYGVLDNKLGTSDKQQNCTTCGLS 69

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
           + DCVGHFGYI L LPVFHIGY + ++NILQ ICKN  C+ +LL EEK + +  K+RN  
Sbjct: 70  IVDCVGHFGYIKLQLPVFHIGYLKNIMNILQMICKN--CSSILLDEEKKSTYLRKMRNKK 127

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDL 260
           L  L RKSL KKI    +K   C  C   NG+++K G  KI HEKYK + +     +++ 
Sbjct: 128 LDNLQRKSLLKKIFLDCRKTKECFKCKSTNGMIRKSGAFKIIHEKYKGKQEN----LQEY 183

Query: 261 LAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
            A Y+EAVK+NPE+++H K    + LNPL  L LF+ I  +DI ++ MN  + +P  LIL
Sbjct: 184 YALYDEAVKYNPEMKSHIKKAQ-EDLNPLVALNLFKKISYQDIEIMNMNPIVGRPERLIL 242

Query: 321 TRLLVPPNCIRPSVISD 337
           T +LVPP  IRPSV  D
Sbjct: 243 TYMLVPPVSIRPSVPMD 259



 Score =  207 bits (528), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 116/238 (48%), Positives = 158/238 (66%), Gaps = 5/238 (2%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIIN ++NISTPIITA L+ D D+  ARIV GR+E+TTLG V E+I+EV     
Sbjct: 1081 GVPRIKEIINGAKNISTPIITASLNCDNDIRSARIVAGRIEKTTLGHVAEHIKEVVKRGG 1140

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHL----TVSGHSFLILKPKDSSKS 879
             ++ IK+D   I  L LE++  +I   I  T+G+   +     +S +   I  P +  + 
Sbjct: 1141 CYLSIKIDKKFIDSLQLEINARTIAQSILSTKGLKLKVDQVSALSEYKLRITPPGNCREQ 1200

Query: 880  FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
                +  +K  LPSV++KG+  INR VI + D E   +Y+LLVEG +LR VMAT G+KG 
Sbjct: 1201 TLYYLQSLKNNLPSVIVKGIPTINRVVISKID-EKQERYQLLVEGYDLRAVMATSGIKGT 1259

Query: 940  KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
              +SN+  E   TLGIE AR+TIM+EI+++M +HGMSID RH ML+ADLM+ KGE+LG
Sbjct: 1260 HTTSNHIMECENTLGIETARNTIMSEIQMIMTSHGMSIDVRHVMLLADLMSFKGEILG 1317



 Score =  109 bits (272), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 48/67 (71%), Positives = 56/67 (83%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF++G+ PTEFFFHTMGGREGLVDTAVKTAETGYMQRRL+K+LEDL   YD +
Sbjct: 814 AKGFVSNSFYTGMIPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLMKALEDLSTHYDYT 873

Query: 671 FDAAFYG 677
              +F G
Sbjct: 874 VRDSFGG 880



 Score = 77.4 bits (189), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 53/122 (43%), Positives = 71/122 (58%), Gaps = 19/122 (15%)

Query: 1026 QEILALSNETLDSKEFLQDTSENFVRDIKKFLEEFSKKESVT--SHQDKVSQPLREQILS 1083
            +E++ L N+    KE+ +DT+ N    +++  EE S  E +   S+Q  V Q  R  I S
Sbjct: 968  EELIKLRNQ-FGLKEYTEDTA-NIEDALERENEELSIDERIARESNQQVVDQIHR--ITS 1023

Query: 1084 HQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHF 1143
             Q ++               + C +KY RA+IEP TAVGA+ AQSIGEPGTQMTLKTFHF
Sbjct: 1024 TQVELF-------------LDICLDKYNRAKIEPGTAVGAIGAQSIGEPGTQMTLKTFHF 1070

Query: 1144 AG 1145
            AG
Sbjct: 1071 AG 1072



 Score = 58.5 bits (140), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 23/41 (56%), Positives = 35/41 (85%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           +LM   +NL+TPRNGE L+AATQDF+T  YL+++++AF++R
Sbjct: 509 ILMGVTNNLITPRNGEPLVAATQDFLTASYLISRRDAFYDR 549



 Score = 50.1 bits (118), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 26/55 (47%), Positives = 36/55 (65%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDN 722
            D  FDAA + + D I GVSECIIMG  + +GTGL KLL+   ++    ++LL D+
Sbjct: 1341 DHLFDAAVHHRQDDIVGVSECIIMGSVIPLGTGLFKLLRKSNKNNLPKKSLLLDD 1395


>gi|367041111|ref|XP_003650936.1| hypothetical protein THITE_2110899 [Thielavia terrestris NRRL 8126]
 gi|346998197|gb|AEO64600.1| hypothetical protein THITE_2110899 [Thielavia terrestris NRRL 8126]
          Length = 1547

 Score =  278 bits (710), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 137/276 (49%), Positives = 185/276 (67%), Gaps = 31/276 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+D+VLFNRQPSLHKLSIM+H  KV P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 470 DDDIVLFNRQPSLHKLSIMSHLVKVRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 529

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K NL+TP+NGE +IAATQDFIT  +LL+ K+ FF+R
Sbjct: 530 RAEAIN--------------LMGVKHNLITPKNGEPIIAATQDFITAAFLLSSKDRFFDR 575

Query: 461 AQTMRIAST-LIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
                I +  L+ DT           +    P   ++   +WTGKQIF+++++PN++ PV
Sbjct: 576 TTFTYICTQMLLGDT-----------YLELPPPAIIKPRALWTGKQIFNVMMRPNKESPV 624

Query: 520 NANLKTKGRAYTANE-----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLR 574
             NL  K +A+   +     +    D+++++RNSE++ G MDKST+G G K +VFY++LR
Sbjct: 625 LVNLDAKNKAFQKKQDGEIPDMDIDDAFLVVRNSEVMCGRMDKSTVGGGKKNSVFYVILR 684

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           DFG + A  AM RL+++++  L  RGFSIG+GDV P
Sbjct: 685 DFGPEYAAAAMNRLAKLSARTLTLRGFSIGVGDVWP 720



 Score =  191 bits (484), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 106/264 (40%), Positives = 151/264 (57%), Gaps = 19/264 (7%)

Query: 96  QSHIQIVSKN--------LYCQDPQRTPIPHGLLDRRMGTN--QKEANCTTCGQNLSDCV 145
           QSH  IVS+         LY  + +RT  PHG LD R+GT+   +E  C+TC   L +C 
Sbjct: 30  QSHQDIVSQGVLEVSDNLLYDVENRRTAFPHGPLDPRLGTSSTNRENKCSTCHLGLQECP 89

Query: 146 GHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLV 205
           GHFG++ LPLPVFHIGY + +   LQ+ICK+  CARVLL E +   F  +LR P +  L 
Sbjct: 90  GHFGHVRLPLPVFHIGYLKYIQATLQNICKD--CARVLLQEPERRQFLKELRRPGIDNLR 147

Query: 206 RKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKY----KNRTKKKDAIVEDLL 261
           R ++ K+I E  +K   CP+CG I GV++K  ++K+ H+KY    K+  +KK A    L 
Sbjct: 148 RSAILKRINEQCRKAKTCPYCGSIQGVIRKLSVMKLVHDKYAAYNKSTAQKKIAPQSKLE 207

Query: 262 --AEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLI 319
             A + +A K+ PE+E H +  +   LNPL+VL LF+ I   D   L ++    +P   +
Sbjct: 208 FDASFEQAKKYTPELEKHTRKAM-DDLNPLKVLNLFKQISPSDCEFLGLDPAEGRPEMFL 266

Query: 320 LTRLLVPPNCIRPSVISDLKSDND 343
              +  PP CIRPSV  +  S+ D
Sbjct: 267 WQYVPAPPICIRPSVAQENASNED 290



 Score =  172 bits (436), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 108/288 (37%), Positives = 157/288 (54%), Gaps = 40/288 (13%)

Query: 1143 FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS-----GHL 1197
            +  +V  YI++ ++PD + I++++D+  +  + L +    I   I R + +        L
Sbjct: 1216 YISDVISYIDDEWLPDVAKIVLQVDVQALSDMQLGITTKDIADAIVRAKKLKLKVEPEDL 1275

Query: 1198 TVSGHSFLIL------------------------------KPKDSSKSFNSKMYQMKQLL 1227
             +S +   ++                                 +S+  F  ++  +K++L
Sbjct: 1276 RISANRVEVVVRNTWQDVTAARKAARARAAAIEKGQHVSSATDESAADFQLRVNFLKRML 1335

Query: 1228 PSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYK 1287
            P V I G     RA+I   D     ++++LVEG  LR  M T GV G +C +N+  E   
Sbjct: 1336 PHVAISGYPEAARAIIQTSDA---NEHEVLVEGYGLRACMTTEGVIGTQCVTNSVMECRD 1392

Query: 1288 TLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVL 1347
             LGIEAAR+TI  EI  VM +  MSID RH  L+AD+MT KGEVLGITR GLAKM++SVL
Sbjct: 1393 VLGIEAARTTIAKEIGQVMSS--MSIDPRHMELLADVMTYKGEVLGITRFGLAKMRDSVL 1450

Query: 1348 NLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 1395
             LASFE T DHLFDAA   + D I GVSECIIMG  M++GTG  ++++
Sbjct: 1451 QLASFEKTPDHLFDAAAGMKKDRIQGVSECIIMGQTMSIGTGAFQVVR 1498



 Score =  150 bits (379), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 97/269 (36%), Positives = 144/269 (53%), Gaps = 40/269 (14%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+IT  L+   D+  AR+VKGR+E+T + +V  YI++ ++PD 
Sbjct: 1173 GVPRIKEIINASKLISTPVITCKLENKWDIKAARVVKGRIEKTYISDVISYIDDEWLPDV 1232

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS-----GHLTVSGHSFLIL------- 871
            + I++++D+  +  + L +    I   I R + +        L +S +   ++       
Sbjct: 1233 AKIVLQVDVQALSDMQLGITTKDIADAIVRAKKLKLKVEPEDLRISANRVEVVVRNTWQD 1292

Query: 872  -----------------------KPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIH 908
                                      +S+  F  ++  +K++LP V I G     RA+I 
Sbjct: 1293 VTAARKAARARAAAIEKGQHVSSATDESAADFQLRVNFLKRMLPHVAISGYPEAARAIIQ 1352

Query: 909  EEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKL 968
              D     ++++LVEG  LR  M T GV G +C +N+  E    LGIEAAR+TI  EI  
Sbjct: 1353 TSDA---NEHEVLVEGYGLRACMTTEGVIGTQCVTNSVMECRDVLGIEAARTTIAKEIGQ 1409

Query: 969  VMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            VM +  MSID RH  L+AD+MT KGEVLG
Sbjct: 1410 VMSS--MSIDPRHMELLADVMTYKGEVLG 1436



 Score =  103 bits (257), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 45/59 (76%), Positives = 51/59 (86%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSF++GL PTEF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 844 PSKGFVRNSFYTGLVPTEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSAQYD 902



 Score = 72.0 bits (175), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 40/103 (38%), Positives = 58/103 (56%), Gaps = 13/103 (12%)

Query: 1043 QDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACK 1102
            +D SE  ++D+++ ++           +D+     R +  +H D++    E         
Sbjct: 1075 RDPSEYVLKDLRRKVD----------GEDEFGDAARAKAQAHVDRVAKVSERT---LRTF 1121

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
             + C  KY RA++EP  AVGA+ AQSIGEPGTQMTLKTFHFAG
Sbjct: 1122 IQMCLHKYRRARVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAG 1164



 Score = 60.8 bits (146), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 27/53 (50%), Positives = 37/53 (69%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           LM  K NL+TP+NGE +IAATQDFIT  +LL+ K+ FF+R     I + ++ G
Sbjct: 536 LMGVKHNLITPKNGEPIIAATQDFITAAFLLSSKDRFFDRTTFTYICTQMLLG 588



 Score = 43.1 bits (100), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 20/39 (51%), Positives = 27/39 (69%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  FDAA   + D I GVSECIIMG  M++GTG  ++++
Sbjct: 1460 DHLFDAAAGMKKDRIQGVSECIIMGQTMSIGTGAFQVVR 1498


>gi|169780898|ref|XP_001824913.1| DNA-directed RNA polymerase III subunit RPO31 [Aspergillus oryzae
           RIB40]
 gi|83773653|dbj|BAE63780.1| unnamed protein product [Aspergillus oryzae RIB40]
 gi|391867224|gb|EIT76474.1| RNA polymerase III, large subunit [Aspergillus oryzae 3.042]
          Length = 1447

 Score =  278 bits (710), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 136/282 (48%), Positives = 185/282 (65%), Gaps = 29/282 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++H AKV PHRTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 470 DGDIVLFNRQPSLHKLSILSHFAKVRPHRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 529

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL TP+NGE +I+A QDFI+  Y+L+ K+ FF+R
Sbjct: 530 RAEAME--------------LMGVKNNLATPKNGEPIISAIQDFISAAYILSSKDNFFDR 575

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
               +I   ++       G   RF      P   ++  ++WTGKQ+F+++++PN+D PV 
Sbjct: 576 RSFTQICLYML-------GPETRF---DLPPPAVLKPQMLWTGKQVFNILMRPNKDDPVM 625

Query: 521 ANLKTKGRAYTA-----NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL    R Y        ++   +D ++++RNSE++ G MDK+T+GSG K NVFY++LRD
Sbjct: 626 VNLDAACREYKPPKDGRPKDLDPKDGWLVIRNSEVMCGVMDKATIGSGKKDNVFYVMLRD 685

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           FG   A   M RLSR+++ +  N GFSIGI DV P +  +Q+
Sbjct: 686 FGPPAAAEGMNRLSRLSARWFTNMGFSIGITDVYPSEKLLQS 727



 Score =  213 bits (542), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 145/362 (40%), Positives = 195/362 (53%), Gaps = 75/362 (20%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEV----------------- 1147
            AC  KY +AQ+EP  AVGA+ AQSIGEPGTQMTLKTFHFAG                   
Sbjct: 1054 ACLMKYKKAQVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIINA 1113

Query: 1148 ----------CE---------------------------YIEEVFVPDDSFILIKLDMDR 1170
                      CE                           Y+ E +   +++I +K++   
Sbjct: 1114 SKEISTPVVSCELVTKDNVIAARIVKGRIEKTYLRDITHYVRETWTGKEAYITVKINWKT 1173

Query: 1171 IRLLHLEVDIDSIRYCIERTR--------------GISGHLTVSGHSFLILKPKD---SS 1213
            I+ L LE+ I  I   I+  R               I  ++ V   S L L   +   +S
Sbjct: 1174 IQDLALELKIQDILAAIKNHRRFKSDDLKFRCQRSHIHIYMDVDPASKLGLSKTEIAATS 1233

Query: 1214 KSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVK 1273
                 ++  +K+LLP + + G     RA+I  +D    T   LLVEG  LR  M T GV 
Sbjct: 1234 ADPFLRLKHLKRLLPDIQVLGHPQAYRAIIRTDDTS--TTNTLLVEGYGLRACMNTIGVD 1291

Query: 1274 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 1333
            G++ S+NN  E+ + LGIEAAR+TI+ EI  VM++  M ID RH  L+AD+MT KGEVLG
Sbjct: 1292 GLRTSTNNVMEMREVLGIEAARTTIVREISEVMKD--MDIDPRHMQLLADVMTYKGEVLG 1349

Query: 1334 ITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            ITR GLAKM++SVL LASFE T+DHLFDA   G+TD + GVSECIIMG  +++GTG +++
Sbjct: 1350 ITRFGLAKMRDSVLQLASFEKTADHLFDAGGAGRTDLVEGVSECIIMGKTVSLGTGAMEV 1409

Query: 1394 LQ 1395
            ++
Sbjct: 1410 VR 1411



 Score =  177 bits (448), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 102/267 (38%), Positives = 140/267 (52%), Gaps = 15/267 (5%)

Query: 87  VTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVG 146
           V   D +  Q  +++  +  +  D  R+ + HG LD RMG + K A+C TCG  L  C G
Sbjct: 31  VLSNDDIVSQGVVEVSDRKFFDLDRDRSVVAHGPLDSRMGVSSKTASCQTCGGALQVCNG 90

Query: 147 HFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVR 206
           HFG++ L LP FH+GYF+ VI ILQ ICK   C+ +LL E +   F  ++R P L  L R
Sbjct: 91  HFGHVKLVLPSFHVGYFKRVITILQEICKE--CSHILLPEGERRAFLREMRRPGLDNLRR 148

Query: 207 KSLKKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKYK--------NRTKKKDAI 256
             + K+I E  +K   C  CG  NGVVKK G   LKI+H+K++         +      I
Sbjct: 149 LQIAKRINERCRKTRNCDRCGATNGVVKKAGTSALKITHDKFRAFNASTSMKKIPPPSKI 208

Query: 257 VEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPS 316
           V D    + EA   NPE+E H K      +N L VL LF+ I   D  LL ++ + ++P 
Sbjct: 209 VFD--RSFEEARSHNPEVEKHHKKAQ-DDMNALRVLNLFKRISDTDCELLGLDPKEARPE 265

Query: 317 DLILTRLLVPPNCIRPSVISDLKSDND 343
             +   +  PP CIRPSV  D  S  D
Sbjct: 266 MFLWQYIPAPPVCIRPSVGQDASSTED 292



 Score =  143 bits (360), Expect = 9e-31,   Method: Compositional matrix adjust.
 Identities = 100/251 (39%), Positives = 144/251 (57%), Gaps = 21/251 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+++  L    ++  ARIVKGR+E+T L ++  Y+ E +   +
Sbjct: 1103 GVPRIKEIINASKEISTPVVSCELVTKDNVIAARIVKGRIEKTYLRDITHYVRETWTGKE 1162

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTR--------------GISGHLTVSGHSFL 869
            ++I +K++   I+ L LE+ I  I   I+  R               I  ++ V   S L
Sbjct: 1163 AYITVKINWKTIQDLALELKIQDILAAIKNHRRFKSDDLKFRCQRSHIHIYMDVDPASKL 1222

Query: 870  ILKPKD---SSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDN 926
             L   +   +S     ++  +K+LLP + + G     RA+I  +D    T   LLVEG  
Sbjct: 1223 GLSKTEIAATSADPFLRLKHLKRLLPDIQVLGHPQAYRAIIRTDDTS--TTNTLLVEGYG 1280

Query: 927  LRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVA 986
            LR  M T GV G++ S+NN  E+ + LGIEAAR+TI+ EI  VM++  M ID RH  L+A
Sbjct: 1281 LRACMNTIGVDGLRTSTNNVMEMREVLGIEAARTTIVREISEVMKD--MDIDPRHMQLLA 1338

Query: 987  DLMTSKGEVLG 997
            D+MT KGEVLG
Sbjct: 1339 DVMTYKGEVLG 1349



 Score =  101 bits (251), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 46/59 (77%), Positives = 50/59 (84%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSFFSGL P EF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL  +YD
Sbjct: 844 PSKGFVRNSFFSGLEPYEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSSRYD 902



 Score = 53.5 bits (127), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 23/46 (50%), Positives = 33/46 (71%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRI 67
           LM  K+NL TP+NGE +I+A QDFI+  Y+L+ K+ FF+R    +I
Sbjct: 536 LMGVKNNLATPKNGEPIISAIQDFISAAYILSSKDNFFDRRSFTQI 581



 Score = 44.3 bits (103), Expect = 0.47,   Method: Compositional matrix adjust.
 Identities = 19/39 (48%), Positives = 29/39 (74%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  FDA   G+TD + GVSECIIMG  +++GTG +++++
Sbjct: 1373 DHLFDAGGAGRTDLVEGVSECIIMGKTVSLGTGAMEVVR 1411


>gi|358371706|dbj|GAA88313.1| DNA-directed RNA polymerase III largest subunit [Aspergillus kawachii
            IFO 4308]
          Length = 2146

 Score =  277 bits (709), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 137/282 (48%), Positives = 187/282 (66%), Gaps = 29/282 (10%)

Query: 341  DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
            D D+VLFNRQPSLHKLSI++H AKV PHRTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 1166 DGDIVLFNRQPSLHKLSILSHFAKVRPHRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 1225

Query: 401  RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
            RAEA+               LM  K+NL TP+NGE +I+A QDFI+  Y+L+ K+ FF+R
Sbjct: 1226 RAEAME--------------LMGVKNNLATPKNGEPIISAIQDFISAAYILSSKDNFFDR 1271

Query: 461  AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                +I   ++       G   RF      P   ++  ++WTGKQ+F+++++PN+D PV 
Sbjct: 1272 RSFTQICLYML-------GPQTRF---DLPPPAVLKPQMLWTGKQVFNILMRPNKDDPVL 1321

Query: 521  ANLKTKGRAYTANEEFCHR-----DSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
             NL    R + A ++   R     D+++++RNSE++ G MDKST+GSG K NVFYI+LRD
Sbjct: 1322 VNLDAACREFKAPKDGTPRDLDPKDAWLVIRNSEVMCGVMDKSTIGSGKKDNVFYIMLRD 1381

Query: 576  FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
            +G   A   M RLSR+++ +  N GFSIGI DV P +  +++
Sbjct: 1382 YGPVAAAEGMNRLSRLSARWFTNMGFSIGITDVYPSEKLLRS 1423



 Score =  218 bits (556), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 170/508 (33%), Positives = 253/508 (49%), Gaps = 101/508 (19%)

Query: 968  LVMENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSS---RSDPSLS 1024
            L ME     + F    + A+  T K +   +  P E+  + +++++K  S   R D   +
Sbjct: 1621 LDMEGKAKPVHFDRTFIHAESTTYKNDER-SLLPAEIMEICEEMLSKERSKLVRKDLMGN 1679

Query: 1025 AQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSH 1084
                +  S+  +D  E  +D  E+  + +    ++   +       D+ SQ    + L+H
Sbjct: 1680 ELGYMDRSDHGVDQFESARDFLESIQQYVATKADKLISRGGDIDPNDERSQ----KGLNH 1735

Query: 1085 QDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFA 1144
              K+   R    F S+C       KY +AQ+E   AVGA+ AQSIGEPGTQMTLKTFHFA
Sbjct: 1736 TGKLTE-RTLRTFISSCLM-----KYKKAQVEAGHAVGAVGAQSIGEPGTQMTLKTFHFA 1789

Query: 1145 G---------------------------EVCE---------------------------Y 1150
            G                             CE                           Y
Sbjct: 1790 GVAGMSITQGVPRIKEIINASKEISTPVVACELVTKDNIIAARIVKGRIEKTYLRDIIHY 1849

Query: 1151 IEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIE----------RTRGISGHLTVS 1200
            + E +   +++I +K++   I+ L LE+ I++I   I+          + R    H+   
Sbjct: 1850 VRETWTGKEAYITVKINWKTIQDLALELKIENILSAIKNHKRFKADDLKFRCSRSHI--- 1906

Query: 1201 GHSFLILKPKDSSKSFNSK-------------MYQMKQLLPSVVIKGVQGINRAVIHEED 1247
             H ++ + P  S+K+  SK             +  +K++LP + + G     RA+I  + 
Sbjct: 1907 -HVYMDVDP--STKANLSKTEIAHTSADPFLRLKHLKRMLPDIQVLGHPQAFRAIIRTD- 1962

Query: 1248 VEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVME 1307
             E  T   LLVEG  LR+ M T GV G++ S+NN  E+   LGIEAAR+TI+ EI  VM+
Sbjct: 1963 -ETSTTNTLLVEGYGLRECMTTMGVDGLRTSTNNVMEMRDVLGIEAARTTIVQEISEVMK 2021

Query: 1308 NHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQ 1367
            +  M ID RH  L+AD+MT KGEVLGITR GLAKM++SVL LASFE T+DHLFDA   G+
Sbjct: 2022 D--MDIDPRHMQLLADVMTYKGEVLGITRFGLAKMRDSVLQLASFEKTADHLFDAGGAGR 2079

Query: 1368 TDCISGVSECIIMGLPMNVGTGLIKLLQ 1395
            +D I GVSECIIMG  +++GTG +++++
Sbjct: 2080 SDLIEGVSECIIMGKTVSLGTGAMEVVR 2107



 Score =  172 bits (435), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 99/267 (37%), Positives = 140/267 (52%), Gaps = 15/267 (5%)

Query: 87  VTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVG 146
           V   D +  Q  +++  +  +  D  R  + +G LD RMG + K ++C TCG  L  C G
Sbjct: 727 VLSNDDIVSQGVVEVSDRKFFDLDHDRAVVANGPLDARMGISNKTSSCQTCGGALQVCNG 786

Query: 147 HFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVR 206
           HFG++ L LP FH+GYF+ VI ILQ +CK   C+R+LL E     +  ++R P L  L R
Sbjct: 787 HFGHVRLVLPAFHVGYFKRVITILQEVCKE--CSRILLPEADRRAYLREMRRPGLDNLRR 844

Query: 207 KSLKKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKYK--------NRTKKKDAI 256
             + K+I E  +K   C  CG +NGVVKK G   LKI+H+K++         +      I
Sbjct: 845 GQIAKRINERCRKTRNCEACGAVNGVVKKAGTSALKITHDKFRAFNASTSVKKVPPPSKI 904

Query: 257 VEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPS 316
           V D    ++EA   N E+E H K      +N L VL LF+ I   D  LL +N + ++P 
Sbjct: 905 VFD--RSFDEARTSNAEVEKHYKKAQ-DDMNALRVLNLFKKISDTDCELLGLNPKEARPE 961

Query: 317 DLILTRLLVPPNCIRPSVISDLKSDND 343
             +   +  PP CIRPSV  D  S  D
Sbjct: 962 MFLWQFIPAPPVCIRPSVGQDAASTED 988



 Score =  152 bits (385), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 100/257 (38%), Positives = 148/257 (57%), Gaps = 33/257 (12%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP++   L    ++  ARIVKGR+E+T L ++  Y+ E +   +
Sbjct: 1799 GVPRIKEIINASKEISTPVVACELVTKDNIIAARIVKGRIEKTYLRDIIHYVRETWTGKE 1858

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIE----------RTRGISGHLTVSGHSFLILKP 873
            ++I +K++   I+ L LE+ I++I   I+          + R    H+    H ++ + P
Sbjct: 1859 AYITVKINWKTIQDLALELKIENILSAIKNHKRFKADDLKFRCSRSHI----HVYMDVDP 1914

Query: 874  KDSSKSFNSK-------------MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKL 920
              S+K+  SK             +  +K++LP + + G     RA+I  +  E  T   L
Sbjct: 1915 --STKANLSKTEIAHTSADPFLRLKHLKRMLPDIQVLGHPQAFRAIIRTD--ETSTTNTL 1970

Query: 921  LVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFR 980
            LVEG  LR+ M T GV G++ S+NN  E+   LGIEAAR+TI+ EI  VM++  M ID R
Sbjct: 1971 LVEGYGLRECMTTMGVDGLRTSTNNVMEMRDVLGIEAARTTIVQEISEVMKD--MDIDPR 2028

Query: 981  HPMLVADLMTSKGEVLG 997
            H  L+AD+MT KGEVLG
Sbjct: 2029 HMQLLADVMTYKGEVLG 2045



 Score =  104 bits (260), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 47/59 (79%), Positives = 51/59 (86%)

Query: 610  PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            P +GFV+NSFFSGL PTEF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL  +YD
Sbjct: 1540 PSKGFVRNSFFSGLEPTEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSTRYD 1598



 Score = 53.9 bits (128), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 24/57 (42%), Positives = 37/57 (64%)

Query: 22   LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVF 78
            LM  K+NL TP+NGE +I+A QDFI+  Y+L+ K+ FF+R    +I   ++  +  F
Sbjct: 1232 LMGVKNNLATPKNGEPIISAIQDFISAAYILSSKDNFFDRRSFTQICLYMLGPQTRF 1288



 Score = 43.9 bits (102), Expect = 0.71,   Method: Compositional matrix adjust.
 Identities = 19/39 (48%), Positives = 29/39 (74%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  FDA   G++D I GVSECIIMG  +++GTG +++++
Sbjct: 2069 DHLFDAGGAGRSDLIEGVSECIIMGKTVSLGTGAMEVVR 2107


>gi|241955144|ref|XP_002420293.1| DNA-directed RNA polymerase III subunit, putative [Candida
           dubliniensis CD36]
 gi|223643634|emb|CAX42517.1| DNA-directed RNA polymerase III subunit, putative [Candida
           dubliniensis CD36]
          Length = 1448

 Score =  277 bits (709), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 140/281 (49%), Positives = 188/281 (66%), Gaps = 29/281 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH+LSI++H AK+ P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 464 DGDVVLFNRQPSLHRLSILSHYAKIRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 523

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+R
Sbjct: 524 RAEAIN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDR 569

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A  +++ S +    +DI   I         P    +  ++WTGKQ+FSL++KPN+   V 
Sbjct: 570 ATLVQLLSMM--SDADIQFDIP--------PPTIFKPVMLWTGKQVFSLLIKPNKKSNVV 619

Query: 521 ANLKTKGRAYTANE-----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL  K + +   +     E    D +V++R S++L+G MDKSTLG G K +VFY +LRD
Sbjct: 620 INLDAKNKTFHPPKKGLPNEMSPNDGFVVIRGSKILSGLMDKSTLGDGKKHSVFYTILRD 679

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           +G + A  AM R++++ + +L NRGFSIGI DVTP     Q
Sbjct: 680 YGPEEAAAAMNRMAKLCARFLGNRGFSIGINDVTPADELKQ 720



 Score =  246 bits (629), Expect = 5e-62,   Method: Compositional matrix adjust.
 Identities = 164/432 (37%), Positives = 238/432 (55%), Gaps = 82/432 (18%)

Query: 1044 DTSENFVRDIKKFLEEFSKKESVTSHQDKV----SQPLREQILSHQDKIGHG---RESNP 1096
            D   +F + I+ F+ + S + +    +  +    + P  ++I+  +D++      + S  
Sbjct: 995  DGERDFYKSIRDFITKKSTRLARLREERGLKAYFTAPNEDEIVMDEDRVTSNAIDQLSKI 1054

Query: 1097 FPSACKA--EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------- 1145
              +A K   E C  KY RA++EP TAVGA+ AQSIGEPGTQMTLKTFHFAG         
Sbjct: 1055 SSNAVKTFLEQCLYKYSRARVEPGTAVGAIGAQSIGEPGTQMTLKTFHFAGVASMNVTLG 1114

Query: 1146 -----EVCE--------YIEEVFVPDD--------------------------------S 1160
                 E+           I  V V DD                                +
Sbjct: 1115 VPRIKEIINASKVISTPIINAVLVNDDDEIAARVAKGRIEKTLLEDVAFYIEDVYKDNLA 1174

Query: 1161 FILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGH---SFLILKPKDSSK 1214
            ++ IK+D++ I  L LE+++++I   I     +      ++V+G    + L+   +  ++
Sbjct: 1175 YLSIKVDLETIDKLQLELNLENIAVAIANAPKLKISQSDVSVTGKDRINVLVSIKETKTE 1234

Query: 1215 SFNS----------KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLR 1264
            S  +          +M  +K+ LP V IKG+  I RAVI+ +D +G  K +LLVEG  L+
Sbjct: 1235 SLRNTVDPKNALFFRMQHLKRALPGVCIKGLPNIFRAVINIKD-DG--KKELLVEGYGLK 1291

Query: 1265 DVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADL 1324
            DVM T G+ G K ++N+  EV + LGIEAAR +I+ EI   M NHGMS+D RH  L+ D+
Sbjct: 1292 DVMNTEGIVGTKTTTNHVLEVNQILGIEAARGSIIKEIDYTMSNHGMSVDPRHIQLLGDV 1351

Query: 1325 MTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPM 1384
            MT KGEVLGITR GL+KM++SVL LASFE T+DHLFDAAF+ + D I GVSECII+G  M
Sbjct: 1352 MTYKGEVLGITRFGLSKMRDSVLQLASFEKTTDHLFDAAFFMKNDKIEGVSECIILGQTM 1411

Query: 1385 NVGTGLIKLLQA 1396
            ++GTG  KL+++
Sbjct: 1412 SIGTGSFKLVKS 1423



 Score =  180 bits (456), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 108/272 (39%), Positives = 151/272 (55%), Gaps = 11/272 (4%)

Query: 79  FRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCG 138
            +GL  G ++ +D V Q S ++I +++LY  +  R P  HG LD +MG +     C+TC 
Sbjct: 13  IKGLEFGALSAKDIVAQ-SEVEIQTRDLYDLEKGRVPKEHGALDTKMGISSNAQECSTCH 71

Query: 139 QNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN 198
            NL+ C GHFG+I L LPVFH+GYF+ +I++LQ ICKN  CA VLL E+    +   LR 
Sbjct: 72  GNLASCHGHFGHIRLALPVFHVGYFKSIISVLQCICKN--CAAVLLDEQSKRQYLNDLRK 129

Query: 199 PALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKC------GLLKISHEKYKNRTKK 252
           P +  L R  + KKI+E  KK   C  C  INGVVKK         LKI H+ ++   KK
Sbjct: 130 PHIDNLRRMKIIKKIIEQCKKQRRCLKCNHINGVVKKAASGAGPAALKIVHDTFRWIGKK 189

Query: 253 KDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMN-AE 311
           +         E ++    NPE+E   K  +   LNPL+ L LF+ I  +D  L  ++ A+
Sbjct: 190 ETLEKTIWDEELDQVFIRNPELEKFAK-RIHDDLNPLKTLNLFKQITPQDCELFGLDPAK 248

Query: 312 LSKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
             +P   I   L  PP CIRPSV+ D +S+ D
Sbjct: 249 GGRPEMYIWRYLPAPPVCIRPSVMMDAQSNED 280



 Score =  177 bits (449), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 109/250 (43%), Positives = 157/250 (62%), Gaps = 19/250 (7%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII A L  D D   AR+ KGR+E+T L +V  YIE+V+  + 
Sbjct: 1114 GVPRIKEIINASKVISTPIINAVLVNDDDEIAARVAKGRIEKTLLEDVAFYIEDVYKDNL 1173

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGH---SFLILKPKDSS 877
            +++ IK+D++ I  L LE+++++I   I     +      ++V+G    + L+   +  +
Sbjct: 1174 AYLSIKVDLETIDKLQLELNLENIAVAIANAPKLKISQSDVSVTGKDRINVLVSIKETKT 1233

Query: 878  KSFNS----------KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927
            +S  +          +M  +K+ LP V IKG+  I RAVI+ +D +G  K +LLVEG  L
Sbjct: 1234 ESLRNTVDPKNALFFRMQHLKRALPGVCIKGLPNIFRAVINIKD-DG--KKELLVEGYGL 1290

Query: 928  RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 987
            +DVM T G+ G K ++N+  EV + LGIEAAR +I+ EI   M NHGMS+D RH  L+ D
Sbjct: 1291 KDVMNTEGIVGTKTTTNHVLEVNQILGIEAARGSIIKEIDYTMSNHGMSVDPRHIQLLGD 1350

Query: 988  LMTSKGEVLG 997
            +MT KGEVLG
Sbjct: 1351 VMTYKGEVLG 1360



 Score =  102 bits (253), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 48/61 (78%), Positives = 52/61 (85%), Gaps = 1/61 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV+NSFFSGLTP EF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QY
Sbjct: 836 TPQSKGFVRNSFFSGLTPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSSQY 895

Query: 668 D 668
           D
Sbjct: 896 D 896



 Score = 63.2 bits (152), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 27/50 (54%), Positives = 41/50 (82%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+RA  +++ S +
Sbjct: 530 LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDRATLVQLLSMM 579



 Score = 50.1 bits (118), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 22/40 (55%), Positives = 30/40 (75%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA 707
            D  FDAAF+ + D I GVSECII+G  M++GTG  KL+++
Sbjct: 1384 DHLFDAAFFMKNDKIEGVSECIILGQTMSIGTGSFKLVKS 1423


>gi|448112703|ref|XP_004202165.1| Piso0_001648 [Millerozyma farinosa CBS 7064]
 gi|359465154|emb|CCE88859.1| Piso0_001648 [Millerozyma farinosa CBS 7064]
          Length = 1454

 Score =  277 bits (708), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 138/281 (49%), Positives = 190/281 (67%), Gaps = 29/281 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH+LSI++H AKV P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 464 DGDVVLFNRQPSLHRLSILSHFAKVRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 523

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL+TP++GE +IAATQDFITG YL++ K++F++R
Sbjct: 524 RAEAMN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFYDR 569

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A  +++ S +++D +          +    P +F +  ++WTGKQIFSL+++PN++  V 
Sbjct: 570 AALVQMLS-MMSDAN--------VQYDIPPPAIF-KPVMLWTGKQIFSLLIRPNKNSKVL 619

Query: 521 ANLKTKGRAYTA-----NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL  K + +         E    D +V++R S++L+G MDKS LG G K +VFY +LRD
Sbjct: 620 INLDAKNKTFIPPLKGFPNEMSQNDGFVVIRGSQILSGVMDKSLLGDGKKHSVFYTILRD 679

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           +G D A  AM R++++ + ++ NRGFSIGI DV PG    Q
Sbjct: 680 YGPDEAANAMNRMAKLCARFMGNRGFSIGINDVIPGSELKQ 720



 Score =  249 bits (636), Expect = 8e-63,   Method: Compositional matrix adjust.
 Identities = 158/387 (40%), Positives = 217/387 (56%), Gaps = 82/387 (21%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCE 1149
            + C  KY RA++EP TAVGA+ A SIGEPGTQMTLKTFHFAG              E+  
Sbjct: 1063 DQCIYKYFRAKVEPGTAVGAIGAHSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIIN 1122

Query: 1150 --------YIEEVFVPDD--------------------------------SFILIKLDMD 1169
                     I  V V DD                                ++I IK+D++
Sbjct: 1123 ASKVISTPIINSVLVNDDDERAARVVKGRIEKTLLEDVAFYIEDVYKENMAYISIKVDLE 1182

Query: 1170 RIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFL--ILKPKDS------------ 1212
             I  L LE+ I+ I   I     +   +  + +SG   +  ++  KDS            
Sbjct: 1183 TIEKLQLELTIEQIARAIANAPKLKISAADVAISGKDKINVLVTLKDSKADNLMRNIAAD 1242

Query: 1213 --SKSFNSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDV 1266
              S   N+ ++     +K+ LP + + G+  I+RAVI+  D +G  K +LLVEG  L++V
Sbjct: 1243 YGSTDMNNSLFFRAQVLKRALPHICVNGLSDISRAVINIRD-DG--KKELLVEGYGLKNV 1299

Query: 1267 MATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMT 1326
            M+T GV G K ++N+  E+++ LGIEAAR++I+ EI   M NHGMS+D RH  L+ D+MT
Sbjct: 1300 MSTDGVVGTKTTTNHVLEIFEVLGIEAARASIIKEIDYTMTNHGMSVDPRHIQLLGDVMT 1359

Query: 1327 SKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNV 1386
             KGEVLGITR GL+KM++SVL LASFE T+DHLFDA+FY + D I GVSECII+G  MN+
Sbjct: 1360 YKGEVLGITRFGLSKMRDSVLQLASFEKTTDHLFDASFYMKEDKIEGVSECIILGQTMNI 1419

Query: 1387 GTGLIKLLQA--VPRSEPVPRTLLFDN 1411
            GTG  KL+++  V  S   P+  LF+N
Sbjct: 1420 GTGAFKLVKSFNVGESALKPKEALFEN 1446



 Score =  181 bits (460), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 108/272 (39%), Positives = 150/272 (55%), Gaps = 11/272 (4%)

Query: 79  FRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCG 138
            +G+  G ++  D +  QS +++ +++LY  +  RT    G LD RMG +   + C+TC 
Sbjct: 13  IKGVQFGALSASD-IIAQSEVEVQTRDLYDLEKGRTAKESGALDTRMGISSNSSECSTCH 71

Query: 139 QNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN 198
            NL+ C GHFG+I L LPVFH+GYF+ ++++LQSICKN  C  +LL E     F  +LR 
Sbjct: 72  GNLASCHGHFGHIRLALPVFHVGYFKNIMSVLQSICKN--CGAILLDETTRRSFLNELRR 129

Query: 199 PALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKC------GLLKISHEKYKNRTKK 252
           P L  L R  + K+ILE  KK   C  C  INGVVKK         LKI H+ ++   KK
Sbjct: 130 PNLDNLKRMKILKRILEQCKKQRRCVKCNHINGVVKKAASGSGPAALKIVHDTFRWIGKK 189

Query: 253 KDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMN-AE 311
                     E++E    NPE+E   K  +   LNPL+VL LF+ I   D  LL ++ A 
Sbjct: 190 PTPEKALWNEEFDEVFARNPELEKFSK-RVYDDLNPLKVLNLFKQIEPADCELLGIDPAR 248

Query: 312 LSKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
             +P   I   L  PP CIRPSV+ D +S+ D
Sbjct: 249 GGRPEMYIWRYLPAPPVCIRPSVMMDTQSNED 280



 Score =  177 bits (450), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 109/257 (42%), Positives = 159/257 (61%), Gaps = 26/257 (10%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII + L  D D   AR+VKGR+E+T L +V  YIE+V+  + 
Sbjct: 1113 GVPRIKEIINASKVISTPIINSVLVNDDDERAARVVKGRIEKTLLEDVAFYIEDVYKENM 1172

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFL--ILKPKDS-- 876
            ++I IK+D++ I  L LE+ I+ I   I     +   +  + +SG   +  ++  KDS  
Sbjct: 1173 AYISIKVDLETIEKLQLELTIEQIARAIANAPKLKISAADVAISGKDKINVLVTLKDSKA 1232

Query: 877  ------------SKSFNSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKL 920
                        S   N+ ++     +K+ LP + + G+  I+RAVI+  D +G  K +L
Sbjct: 1233 DNLMRNIAADYGSTDMNNSLFFRAQVLKRALPHICVNGLSDISRAVINIRD-DG--KKEL 1289

Query: 921  LVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFR 980
            LVEG  L++VM+T GV G K ++N+  E+++ LGIEAAR++I+ EI   M NHGMS+D R
Sbjct: 1290 LVEGYGLKNVMSTDGVVGTKTTTNHVLEIFEVLGIEAARASIIKEIDYTMTNHGMSVDPR 1349

Query: 981  HPMLVADLMTSKGEVLG 997
            H  L+ D+MT KGEVLG
Sbjct: 1350 HIQLLGDVMTYKGEVLG 1366



 Score =  103 bits (257), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 48/61 (78%), Positives = 53/61 (86%), Gaps = 1/61 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV+NSFFSGL+PTEF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QY
Sbjct: 836 TPQSKGFVRNSFFSGLSPTEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSTQY 895

Query: 668 D 668
           D
Sbjct: 896 D 896



 Score = 61.2 bits (147), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 26/50 (52%), Positives = 41/50 (82%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM  K+NL+TP++GE +IAATQDFITG YL++ K++F++RA  +++ S +
Sbjct: 530 LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFYDRAALVQMLSMM 579



 Score = 57.0 bits (136), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 29/57 (50%), Positives = 38/57 (66%), Gaps = 2/57 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA--VPRSEPVPRTLLFDN 722
            D  FDA+FY + D I GVSECII+G  MN+GTG  KL+++  V  S   P+  LF+N
Sbjct: 1390 DHLFDASFYMKEDKIEGVSECIILGQTMNIGTGAFKLVKSFNVGESALKPKEALFEN 1446


>gi|325091897|gb|EGC45207.1| DNA-directed RNA polymerase III [Ajellomyces capsulatus H88]
          Length = 1456

 Score =  277 bits (708), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 138/280 (49%), Positives = 185/280 (66%), Gaps = 28/280 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++H AKV PHRTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 470 DGDIVLFNRQPSLHKLSILSHFAKVRPHRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 529

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL TP+NGE +I+A QDFIT  YLL+ K+ F++R
Sbjct: 530 RAEAME--------------LMGVKNNLATPKNGEPIISAIQDFITAAYLLSSKDVFYDR 575

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                I   ++   SD        +     P   ++  ++WTGKQ+F+++++PN+  PV 
Sbjct: 576 KTFTHICLYMLE--SD--------TLFDLPPPSVLKPQILWTGKQVFNVLMRPNKQSPVL 625

Query: 521 ANLKTKGRAYTANE----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL    R + A +    +    D ++ +RNSE++ G MDKST+GSG K +VFY++LRDF
Sbjct: 626 INLDAACREFKAPKGTPRDLDANDGWLCIRNSEIMCGVMDKSTIGSGKKDSVFYVMLRDF 685

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           G DVA   M RLSR+++ +L N GFSIGI DV PG+  ++
Sbjct: 686 GPDVASEGMNRLSRLSARWLTNLGFSIGITDVYPGEKLLE 725



 Score =  227 bits (578), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 146/363 (40%), Positives = 195/363 (53%), Gaps = 74/363 (20%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEV----------------- 1147
            AC  KY RAQ+EP  AVGA+ AQSIGEPGTQMTLKTFHFAG                   
Sbjct: 1049 ACLTKYKRAQVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIINA 1108

Query: 1148 ----------CE---------------------------YIEEVFVPDDSFILIKLDMDR 1170
                      CE                           YIEE +  ++++I IK+D   
Sbjct: 1109 SKEISTPVITCELVNKQDLRAAQIVKGRVEKTFVRDIIYYIEEDWTGNEAYINIKIDFST 1168

Query: 1171 IRLLHLEVDIDSIRYCIE------------RTRGISGHLTVSGHSFLILKPKDSSKSFNS 1218
            I+ L LE+ +  I   I+            R+ G   H+ V   +      K    +  +
Sbjct: 1169 IQNLQLELTLQDILMAIKKHKRFKSADLKFRSFGSHIHIFVDQQTTRTALSKTEEAATGA 1228

Query: 1219 KMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 1274
              Y     +K+L+P++ + G     RA+I  ++    T   LLVEG  LRD M T G+ G
Sbjct: 1229 DPYIRLKHLKRLIPNIQVIGHPQCARAIIRTDETN--TTNTLLVEGYGLRDCMTTDGING 1286

Query: 1275 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGI 1334
                +NN  E    LGIEAAR+TI+ EI  VM++  M+ID RH  L+AD+MT KGEVLGI
Sbjct: 1287 HHTRTNNIMETRAVLGIEAARTTIVEEIGEVMKD--MAIDPRHMQLLADVMTYKGEVLGI 1344

Query: 1335 TRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            TR GLAKM++SVL LASFE T+DHLFDA   G+TD I GVSECII+G  +++GTG ++++
Sbjct: 1345 TRFGLAKMRDSVLQLASFEKTADHLFDAGGAGRTDLIEGVSECIIVGKSVSLGTGAMEVV 1404

Query: 1395 QAV 1397
            +A+
Sbjct: 1405 RAL 1407



 Score =  184 bits (468), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 106/269 (39%), Positives = 147/269 (54%), Gaps = 16/269 (5%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G ++ +D V Q + +++  + L+  D  R   PHG LD RMG + K   C TCG  L  C
Sbjct: 30  GVLSTQDIVSQ-AVVEVSDRKLFDLDNDRAVAPHGPLDGRMGISSKSGTCDTCGGALQVC 88

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFG++ L LP FH+GYF+ VI+ILQ ICK   C+ +LL E +   F  +LR P +  L
Sbjct: 89  SGHFGHVKLVLPAFHVGYFKRVISILQEICKE--CSHILLPETERRAFLRELRRPGIDNL 146

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKYK--------NRTKKKD 254
            R  + KKI E  +K   C  C  +NGVVKK G   LKI+HEK++         +     
Sbjct: 147 RRMQIAKKINERCRKTRTCYKCNAVNGVVKKAGTSALKITHEKFRAFNASTSVKKIPPPS 206

Query: 255 AIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSK 314
            +V D    + EA K NP+I+ H K      L+PL VL+LF ++  ED  LL +N E ++
Sbjct: 207 KVVFD--KSFEEAKKSNPDIDKHFKKAH-DDLHPLRVLRLFRSVSNEDCELLSLNPEEAR 263

Query: 315 PSDLILTRLLVPPNCIRPSVISDLKSDND 343
           P   +   +  PP CIRPSV  +  S  D
Sbjct: 264 PEVFLWQYVPAPPVCIRPSVGQEAASTED 292



 Score =  156 bits (394), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 101/250 (40%), Positives = 142/250 (56%), Gaps = 20/250 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+IT  L    DL  A+IVKGR+E+T + ++  YIEE +  ++
Sbjct: 1098 GVPRIKEIINASKEISTPVITCELVNKQDLRAAQIVKGRVEKTFVRDIIYYIEEDWTGNE 1157

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIE------------RTRGISGHLTVSGHSFLIL 871
            ++I IK+D   I+ L LE+ +  I   I+            R+ G   H+ V   +    
Sbjct: 1158 AYINIKIDFSTIQNLQLELTLQDILMAIKKHKRFKSADLKFRSFGSHIHIFVDQQTTRTA 1217

Query: 872  KPKDSSKSFNSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927
              K    +  +  Y     +K+L+P++ + G     RA+I  ++    T   LLVEG  L
Sbjct: 1218 LSKTEEAATGADPYIRLKHLKRLIPNIQVIGHPQCARAIIRTDETN--TTNTLLVEGYGL 1275

Query: 928  RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 987
            RD M T G+ G    +NN  E    LGIEAAR+TI+ EI  VM++  M+ID RH  L+AD
Sbjct: 1276 RDCMTTDGINGHHTRTNNIMETRAVLGIEAARTTIVEEIGEVMKD--MAIDPRHMQLLAD 1333

Query: 988  LMTSKGEVLG 997
            +MT KGEVLG
Sbjct: 1334 VMTYKGEVLG 1343



 Score =  105 bits (262), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 47/59 (79%), Positives = 52/59 (88%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSFFSGLTPTEF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  +YD
Sbjct: 843 PAKGFVRNSFFSGLTPTEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSTRYD 901



 Score = 55.1 bits (131), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 25/57 (43%), Positives = 36/57 (63%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVF 78
           LM  K+NL TP+NGE +I+A QDFIT  YLL+ K+ F++R     I   ++    +F
Sbjct: 536 LMGVKNNLATPKNGEPIISAIQDFITAAYLLSSKDVFYDRKTFTHICLYMLESDTLF 592



 Score = 45.4 bits (106), Expect = 0.25,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 31/41 (75%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 708
            D  FDA   G+TD I GVSECII+G  +++GTG +++++A+
Sbjct: 1367 DHLFDAGGAGRTDLIEGVSECIIVGKSVSLGTGAMEVVRAL 1407


>gi|121706250|ref|XP_001271388.1| DNA-directed RNA polymerase III largest subunit, putative
           [Aspergillus clavatus NRRL 1]
 gi|119399534|gb|EAW09962.1| DNA-directed RNA polymerase III largest subunit, putative
           [Aspergillus clavatus NRRL 1]
          Length = 1449

 Score =  277 bits (708), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 137/282 (48%), Positives = 185/282 (65%), Gaps = 29/282 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++H AKV PHRTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 470 DGDIVLFNRQPSLHKLSILSHFAKVRPHRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 529

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL TP+NGE +I+A QDFI+  Y+L+ K+ FF+R
Sbjct: 530 RAEAME--------------LMGVKNNLATPKNGEPIISAIQDFISAAYVLSSKDNFFDR 575

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
               +I   ++       G   RF      P   ++  ++WTGKQ+F+++++PN+D PV 
Sbjct: 576 RSFTQICLYML-------GPETRF---DLPPPSILKPQMMWTGKQVFNILMRPNKDDPVM 625

Query: 521 ANLKTKGRAYTA-----NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL    R Y        ++    D ++++RNSE++ G MDKST+GSG K NVFYI+LRD
Sbjct: 626 VNLDAACREYKPPKDGRPKDLDPNDGWLVIRNSEVMCGVMDKSTIGSGKKDNVFYIMLRD 685

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           +G   A   M RLS++++ +  N GFSIGI DV P +G V++
Sbjct: 686 YGPPAAAEGMNRLSKLSARWFTNMGFSIGITDVYPSEGLVRS 727



 Score =  182 bits (463), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 129/370 (34%), Positives = 187/370 (50%), Gaps = 87/370 (23%)

Query: 1105 ACREKYVRAQIEPATAVGAL---------------------------------------A 1125
            AC  KY RAQ+EP  AVGA+                                       A
Sbjct: 1054 ACLLKYKRAQVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIINA 1113

Query: 1126 AQSIGEPGTQMTLKTFH---------------FAGEVCEYIEEVFVPDDSFILIKLDMDR 1170
            +++I  P     L T                 F  ++  Y+ E +   +++I +K++ + 
Sbjct: 1114 SKAISTPVISCDLVTKDNVIAARIVKGRIEKTFLRDIIHYVRETWTGKEAYITVKINWET 1173

Query: 1171 IRLLHLEVDIDSIRYCIE----------RTRGISGHLTVSGHSFLILKPKDSSKSFNSK- 1219
            I+ L LE+ I  I   I+          + R    H+    H ++ + P  +SK+  SK 
Sbjct: 1174 IQNLALELKIHHIVAAIKNHKRFKADDLKFRSSRSHI----HIYMDVDP--ASKASLSKT 1227

Query: 1220 ------------MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVM 1267
                        +  +K++LP + + G    +RA+I  +D        LLVEG  L++ M
Sbjct: 1228 EVAATSSDPFLRLKHLKRMLPDIQVLGHPQASRAIIRTDDTSSTNT--LLVEGYGLKECM 1285

Query: 1268 ATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTS 1327
             T GV G+   SNN  E+ + LGIEAAR TI+ EI  VM++  M ID RH  L+AD+MT 
Sbjct: 1286 TTLGVNGLHTYSNNVMEMREVLGIEAARVTIIQEISEVMKD--MDIDPRHMQLLADVMTY 1343

Query: 1328 KGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVG 1387
            KGEVLGITR GLAKM++SVL LASFE T+DHLFDA   G+TD I GVSECIIMG  +++G
Sbjct: 1344 KGEVLGITRFGLAKMRDSVLQLASFEKTADHLFDAGGAGRTDLIEGVSECIIMGKTVSLG 1403

Query: 1388 TGLIKLLQAV 1397
            TG +++++ +
Sbjct: 1404 TGAMEVVRKM 1413



 Score =  182 bits (462), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 103/267 (38%), Positives = 144/267 (53%), Gaps = 15/267 (5%)

Query: 87  VTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVG 146
           V   D +  Q  +++  +  +  +  R  +PHG LD+RMG + K A C TCG +L  C G
Sbjct: 31  VLSNDDIVSQGVVEVSDRKFFNLEHDRAVVPHGPLDQRMGISSKTATCQTCGGSLQVCNG 90

Query: 147 HFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVR 206
           HFG++ L LP FH+GYF+ VI+ILQ ICK   C+R+LL E +   F  ++R P L  L R
Sbjct: 91  HFGHVRLVLPAFHVGYFKRVISILQEICKE--CSRILLPEAERRAFLREMRRPGLDNLRR 148

Query: 207 KSLKKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKYK--------NRTKKKDAI 256
             + K+I E  +K   C  CG +NGVVKK G   LKI+H+K++         +      I
Sbjct: 149 LQIAKRINERCRKTRTCETCGTVNGVVKKAGNSALKITHDKFRAFNASTSVKKVPPPSKI 208

Query: 257 VEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPS 316
           V D    ++EA   N E+E H K      +N L VL LF+ I   D  LL +N + ++P 
Sbjct: 209 VFD--RSFDEARNSNAEVEKHYKKAQ-DDMNALRVLNLFKKISDTDCELLGLNPKEARPE 265

Query: 317 DLILTRLLVPPNCIRPSVISDLKSDND 343
             +   +  PP CIRPSV  D  S  D
Sbjct: 266 MFLWQFIPAPPVCIRPSVGQDAASTED 292



 Score =  149 bits (377), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 99/257 (38%), Positives = 146/257 (56%), Gaps = 33/257 (12%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+I+  L    ++  ARIVKGR+E+T L ++  Y+ E +   +
Sbjct: 1103 GVPRIKEIINASKAISTPVISCDLVTKDNVIAARIVKGRIEKTFLRDIIHYVRETWTGKE 1162

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIE----------RTRGISGHLTVSGHSFLILKP 873
            ++I +K++ + I+ L LE+ I  I   I+          + R    H+    H ++ + P
Sbjct: 1163 AYITVKINWETIQNLALELKIHHIVAAIKNHKRFKADDLKFRSSRSHI----HIYMDVDP 1218

Query: 874  KDSSKSFNSK-------------MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKL 920
              +SK+  SK             +  +K++LP + + G    +RA+I  +D        L
Sbjct: 1219 --ASKASLSKTEVAATSSDPFLRLKHLKRMLPDIQVLGHPQASRAIIRTDDTSSTN--TL 1274

Query: 921  LVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFR 980
            LVEG  L++ M T GV G+   SNN  E+ + LGIEAAR TI+ EI  VM++  M ID R
Sbjct: 1275 LVEGYGLKECMTTLGVNGLHTYSNNVMEMREVLGIEAARVTIIQEISEVMKD--MDIDPR 1332

Query: 981  HPMLVADLMTSKGEVLG 997
            H  L+AD+MT KGEVLG
Sbjct: 1333 HMQLLADVMTYKGEVLG 1349



 Score =  104 bits (260), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 58/124 (46%), Positives = 72/124 (58%), Gaps = 18/124 (14%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV+NSFFSGL PTEF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL  +YD 
Sbjct: 844 PSKGFVRNSFFSGLEPTEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSSRYD- 902

Query: 670 SFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQ 729
                     D +   S+ I+       G  L+  +    +++PV     FD    H   
Sbjct: 903 ----------DTVRNSSDAIVQ---FQYGDDLLDPVDMEGKAKPVH----FDRTFIHSES 945

Query: 730 VYYE 733
           + Y+
Sbjct: 946 ITYD 949



 Score = 53.1 bits (126), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 23/46 (50%), Positives = 33/46 (71%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRI 67
           LM  K+NL TP+NGE +I+A QDFI+  Y+L+ K+ FF+R    +I
Sbjct: 536 LMGVKNNLATPKNGEPIISAIQDFISAAYVLSSKDNFFDRRSFTQI 581



 Score = 45.1 bits (105), Expect = 0.30,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 30/41 (73%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 708
            D  FDA   G+TD I GVSECIIMG  +++GTG +++++ +
Sbjct: 1373 DHLFDAGGAGRTDLIEGVSECIIMGKTVSLGTGAMEVVRKM 1413


>gi|240274343|gb|EER37860.1| DNA-directed RNA polymerase III largest subunit [Ajellomyces
           capsulatus H143]
          Length = 1333

 Score =  277 bits (708), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 138/280 (49%), Positives = 185/280 (66%), Gaps = 28/280 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++H AKV PHRTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 437 DGDIVLFNRQPSLHKLSILSHFAKVRPHRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 496

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL TP+NGE +I+A QDFIT  YLL+ K+ F++R
Sbjct: 497 RAEAME--------------LMGVKNNLATPKNGEPIISAIQDFITAAYLLSSKDVFYDR 542

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                I   ++   SD        +     P   ++  ++WTGKQ+F+++++PN+  PV 
Sbjct: 543 KTFTHICLYMLE--SD--------TLFDLPPPSVLKPQILWTGKQVFNVLMRPNKQSPVL 592

Query: 521 ANLKTKGRAYTANE----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL    R + A +    +    D ++ +RNSE++ G MDKST+GSG K +VFY++LRDF
Sbjct: 593 INLDAACREFKAPKGTPRDLDANDGWLCIRNSEIMCGVMDKSTIGSGKKDSVFYVMLRDF 652

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           G DVA   M RLSR+++ +L N GFSIGI DV PG+  ++
Sbjct: 653 GPDVASEGMNRLSRLSARWLTNLGFSIGITDVYPGEKLLE 692



 Score =  227 bits (578), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 146/363 (40%), Positives = 195/363 (53%), Gaps = 74/363 (20%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEV----------------- 1147
            AC  KY RAQ+EP  AVGA+ AQSIGEPGTQMTLKTFHFAG                   
Sbjct: 926  ACLTKYKRAQVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIINA 985

Query: 1148 ----------CE---------------------------YIEEVFVPDDSFILIKLDMDR 1170
                      CE                           YIEE +  ++++I IK+D   
Sbjct: 986  SKEISTPVITCELVNKQDLRAAQIVKGRVEKTFVRDIIYYIEEDWTGNEAYINIKIDFST 1045

Query: 1171 IRLLHLEVDIDSIRYCIE------------RTRGISGHLTVSGHSFLILKPKDSSKSFNS 1218
            I+ L LE+ +  I   I+            R+ G   H+ V   +      K    +  +
Sbjct: 1046 IQNLQLELTLQDILMAIKKHKRFKSADLKFRSFGSHIHIFVDQQTTRTALSKTEEAATGA 1105

Query: 1219 KMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 1274
              Y     +K+L+P++ + G     RA+I  ++    T   LLVEG  LRD M T G+ G
Sbjct: 1106 DPYIRLKHLKRLIPNIQVIGHPQCARAIIRTDETN--TTNTLLVEGYGLRDCMTTDGING 1163

Query: 1275 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGI 1334
                +NN  E    LGIEAAR+TI+ EI  VM++  M+ID RH  L+AD+MT KGEVLGI
Sbjct: 1164 HHTRTNNIMETRAVLGIEAARTTIVEEIGEVMKD--MAIDPRHMQLLADVMTYKGEVLGI 1221

Query: 1335 TRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            TR GLAKM++SVL LASFE T+DHLFDA   G+TD I GVSECII+G  +++GTG ++++
Sbjct: 1222 TRFGLAKMRDSVLQLASFEKTADHLFDAGGAGRTDLIEGVSECIIVGKSVSLGTGAMEVV 1281

Query: 1395 QAV 1397
            +A+
Sbjct: 1282 RAL 1284



 Score =  155 bits (392), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 101/250 (40%), Positives = 142/250 (56%), Gaps = 20/250 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+IT  L    DL  A+IVKGR+E+T + ++  YIEE +  ++
Sbjct: 975  GVPRIKEIINASKEISTPVITCELVNKQDLRAAQIVKGRVEKTFVRDIIYYIEEDWTGNE 1034

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIE------------RTRGISGHLTVSGHSFLIL 871
            ++I IK+D   I+ L LE+ +  I   I+            R+ G   H+ V   +    
Sbjct: 1035 AYINIKIDFSTIQNLQLELTLQDILMAIKKHKRFKSADLKFRSFGSHIHIFVDQQTTRTA 1094

Query: 872  KPKDSSKSFNSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927
              K    +  +  Y     +K+L+P++ + G     RA+I  ++    T   LLVEG  L
Sbjct: 1095 LSKTEEAATGADPYIRLKHLKRLIPNIQVIGHPQCARAIIRTDETN--TTNTLLVEGYGL 1152

Query: 928  RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 987
            RD M T G+ G    +NN  E    LGIEAAR+TI+ EI  VM++  M+ID RH  L+AD
Sbjct: 1153 RDCMTTDGINGHHTRTNNIMETRAVLGIEAARTTIVEEIGEVMKD--MAIDPRHMQLLAD 1210

Query: 988  LMTSKGEVLG 997
            +MT KGEVLG
Sbjct: 1211 VMTYKGEVLG 1220



 Score =  122 bits (306), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/269 (31%), Positives = 122/269 (45%), Gaps = 49/269 (18%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G ++ +D V Q + +++  + L+  D  R   PHG LD RMG + K   C TCG  L +C
Sbjct: 30  GVLSTQDIVSQ-AVVEVSDRKLFDLDNDRAVAPHGPLDGRMGISSKSGTCDTCGGALQEC 88

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
                                              + +LL E +   F  +LR P +  L
Sbjct: 89  -----------------------------------SHILLPETERRAFLRELRRPGIDNL 113

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKYK--------NRTKKKD 254
            R  + KKI E  +K   C  C  +NGVVKK G   LKI+HEK++         +     
Sbjct: 114 RRMQIAKKINERCRKTRTCYKCNAVNGVVKKAGTSALKITHEKFRAFNASTSVKKIPPPS 173

Query: 255 AIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSK 314
            +V D    + EA K NP+I+ H K      L+PL VL+LF ++  ED  LL +N E ++
Sbjct: 174 KVVFD--KSFEEAKKSNPDIDKHFKKAH-DDLHPLRVLRLFRSVSNEDCELLSLNPEEAR 230

Query: 315 PSDLILTRLLVPPNCIRPSVISDLKSDND 343
           P   +   +  PP CIRPSV  +  S  D
Sbjct: 231 PEVFLWQYVPAPPVCIRPSVGQEAASTED 259



 Score = 55.1 bits (131), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 25/57 (43%), Positives = 36/57 (63%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVF 78
           LM  K+NL TP+NGE +I+A QDFIT  YLL+ K+ F++R     I   ++    +F
Sbjct: 503 LMGVKNNLATPKNGEPIISAIQDFITAAYLLSSKDVFYDRKTFTHICLYMLESDTLF 559



 Score = 45.4 bits (106), Expect = 0.25,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 31/41 (75%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 708
            D  FDA   G+TD I GVSECII+G  +++GTG +++++A+
Sbjct: 1244 DHLFDAGGAGRTDLIEGVSECIIVGKSVSLGTGAMEVVRAL 1284


>gi|115390328|ref|XP_001212669.1| DNA-directed RNA polymerase III largest subunit [Aspergillus
           terreus NIH2624]
 gi|114195065|gb|EAU36765.1| DNA-directed RNA polymerase III largest subunit [Aspergillus
           terreus NIH2624]
          Length = 1450

 Score =  277 bits (708), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 136/282 (48%), Positives = 185/282 (65%), Gaps = 29/282 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++H AKV PHRTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 470 DGDIVLFNRQPSLHKLSILSHFAKVRPHRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 529

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL TP+NGE +I+A QDFI+  Y+L+ K+ FF+R
Sbjct: 530 RAEAME--------------LMGVKNNLATPKNGEPIISAIQDFISAAYILSSKDNFFDR 575

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
               ++   ++       G   RF      P   ++  ++WTGKQ+F+++++PN+D PV 
Sbjct: 576 RSFTQLCLYML-------GPETRF---DLPPPAVLKPQMLWTGKQVFNILMRPNKDDPVL 625

Query: 521 ANLKTKGRAYTA-----NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL    R +        ++   +D ++++RNSE++ G MDKST+GSG K NVFYI+LRD
Sbjct: 626 VNLDAACREFKQPKDGRPKDLDPKDGWLVIRNSEMMCGVMDKSTIGSGKKDNVFYIMLRD 685

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           +G   A   M RLSR+++ +  N GFSIGI DV P Q  +Q+
Sbjct: 686 YGPAAAAEGMNRLSRLSARWFTNMGFSIGITDVYPSQKLLQS 727



 Score =  226 bits (575), Expect = 9e-56,   Method: Compositional matrix adjust.
 Identities = 147/366 (40%), Positives = 198/366 (54%), Gaps = 79/366 (21%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG------------------- 1145
            AC  KY +AQ+EP  AVGA+ AQSIGEPGTQMTLKTFHFAG                   
Sbjct: 1054 ACLMKYKKAQVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIINA 1113

Query: 1146 --------EVCE---------------------------YIEEVFVPDDSFILIKLDMDR 1170
                      CE                           Y+ E +   ++FI +K++   
Sbjct: 1114 SKEISTPVVACELVTKDNIIAARIVKGRIEKTYLRDIIHYVRETWTGKEAFITVKINWKT 1173

Query: 1171 IRLLHLEVDIDSIRYCIERTRGISG------HLTVSGHSFLILKPKDSSKSFNSK----- 1219
            I+ L LE+ I++I   I+  +          H     H ++ L P  SSK+  SK     
Sbjct: 1174 IQDLALELKINNILAAIKNHKRFKADDLKFRHSRSHIHIYMDLDP--SSKASLSKTEIAA 1231

Query: 1220 --------MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYG 1271
                    +  +K++LP + + G     RA+I  +  E  T   LLVEG  LR+ M T G
Sbjct: 1232 TSADPFLRLKHLKRMLPDIQVLGHPQAYRAIIRTD--ETSTTNTLLVEGYGLRECMTTLG 1289

Query: 1272 VKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 1331
            V G+  S+NN  E+ + LGIEAAR TI+ EI  VM++  M ID RH  L+AD+MT KGEV
Sbjct: 1290 VDGLHTSTNNVMEMREVLGIEAARVTIVQEISEVMKD--MDIDPRHMQLLADVMTYKGEV 1347

Query: 1332 LGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLI 1391
            LGITR GLAKM++SVL LASFE T+DHLFDA   G++D I GVSECIIMG  +++GTG +
Sbjct: 1348 LGITRFGLAKMRDSVLQLASFEKTADHLFDAGGAGRSDMIEGVSECIIMGKTVSLGTGAM 1407

Query: 1392 KLLQAV 1397
            ++++ +
Sbjct: 1408 EVVRKM 1413



 Score =  185 bits (469), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 108/269 (40%), Positives = 144/269 (53%), Gaps = 19/269 (7%)

Query: 87  VTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVG 146
           V   D +  Q  +++  +  +  D  R  + HG LD RMG + K A C TCG +L  C G
Sbjct: 31  VLSHDDIVSQGVVEVSDRKFFDLDHDRAVVAHGPLDARMGISNKAATCQTCGLDLKACNG 90

Query: 147 HFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVR 206
           HFG++ L LP FH+GYF+ VI ILQ ICK   C+R+LL E +   +  ++R P L  L R
Sbjct: 91  HFGHVRLVLPAFHVGYFKRVITILQEICKE--CSRILLPEGERRSYLREMRRPGLDNLRR 148

Query: 207 KSLKKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKYK-----NRTKK-----KD 254
             + K++ E  KK   C  CG INGVVKK G   LKI+H+K++       TKK     K 
Sbjct: 149 LQIAKRVHERCKKTKTCEACGTINGVVKKAGTSALKITHDKFRAYNISTSTKKVLPPGKG 208

Query: 255 AIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSK 314
           A  + L+    EA + NPE+E H K      LN L VL LF+ I   D  LL +N   ++
Sbjct: 209 AFDDSLM----EARRHNPEVEKHHKKAQ-DDLNALRVLNLFKRISDTDCELLGLNPREAR 263

Query: 315 PSDLILTRLLVPPNCIRPSVISDLKSDND 343
           P   +   +  PP CIRPSV  D  S  D
Sbjct: 264 PEMFLWQFIPAPPVCIRPSVGQDAASTED 292



 Score =  155 bits (393), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 102/253 (40%), Positives = 145/253 (57%), Gaps = 25/253 (9%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP++   L    ++  ARIVKGR+E+T L ++  Y+ E +   +
Sbjct: 1103 GVPRIKEIINASKEISTPVVACELVTKDNIIAARIVKGRIEKTYLRDIIHYVRETWTGKE 1162

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISG------HLTVSGHSFLILKPKDSS 877
            +FI +K++   I+ L LE+ I++I   I+  +          H     H ++ L P  SS
Sbjct: 1163 AFITVKINWKTIQDLALELKINNILAAIKNHKRFKADDLKFRHSRSHIHIYMDLDP--SS 1220

Query: 878  KSFNSK-------------MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEG 924
            K+  SK             +  +K++LP + + G     RA+I  +  E  T   LLVEG
Sbjct: 1221 KASLSKTEIAATSADPFLRLKHLKRMLPDIQVLGHPQAYRAIIRTD--ETSTTNTLLVEG 1278

Query: 925  DNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPML 984
              LR+ M T GV G+  S+NN  E+ + LGIEAAR TI+ EI  VM++  M ID RH  L
Sbjct: 1279 YGLRECMTTLGVDGLHTSTNNVMEMREVLGIEAARVTIVQEISEVMKD--MDIDPRHMQL 1336

Query: 985  VADLMTSKGEVLG 997
            +AD+MT KGEVLG
Sbjct: 1337 LADVMTYKGEVLG 1349



 Score =  104 bits (259), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 47/59 (79%), Positives = 51/59 (86%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSFFSGL PTEF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL  +YD
Sbjct: 844 PSKGFVRNSFFSGLEPTEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSSKYD 902



 Score = 53.5 bits (127), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 22/40 (55%), Positives = 31/40 (77%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           LM  K+NL TP+NGE +I+A QDFI+  Y+L+ K+ FF+R
Sbjct: 536 LMGVKNNLATPKNGEPIISAIQDFISAAYILSSKDNFFDR 575



 Score = 43.9 bits (102), Expect = 0.71,   Method: Compositional matrix adjust.
 Identities = 19/41 (46%), Positives = 30/41 (73%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 708
            D  FDA   G++D I GVSECIIMG  +++GTG +++++ +
Sbjct: 1373 DHLFDAGGAGRSDMIEGVSECIIMGKTVSLGTGAMEVVRKM 1413


>gi|68481134|ref|XP_715482.1| hypothetical protein CaO19.10615 [Candida albicans SC5314]
 gi|46437106|gb|EAK96458.1| hypothetical protein CaO19.10615 [Candida albicans SC5314]
          Length = 1448

 Score =  276 bits (707), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 140/281 (49%), Positives = 187/281 (66%), Gaps = 29/281 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH+LSI++H AK+ P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 464 DGDVVLFNRQPSLHRLSILSHYAKIRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 523

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+R
Sbjct: 524 RAEAIN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDR 569

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A  +++ S +    +DI   I         P    +  ++WTGKQ+FSL++KPN+   V 
Sbjct: 570 ATLVQLLSMM--SDADIQFDIP--------PPTIFKPVMLWTGKQVFSLLIKPNKKSNVV 619

Query: 521 ANLKTKGRAYTANE-----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL  K + +   +     E    D +V++R S++L+G MDKSTLG G K +VFY +LRD
Sbjct: 620 INLDAKNKTFHPPKKGLPNEMSPNDGFVVIRGSKILSGLMDKSTLGDGKKHSVFYTILRD 679

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           +G   A  AM R++++ + +L NRGFSIGI DVTP     Q
Sbjct: 680 YGPQEAAAAMNRMAKLCARFLGNRGFSIGINDVTPADELKQ 720



 Score =  247 bits (630), Expect = 4e-62,   Method: Compositional matrix adjust.
 Identities = 163/432 (37%), Positives = 233/432 (53%), Gaps = 82/432 (18%)

Query: 1044 DTSENFVRDIKKFLEEFSKKESVTSHQDKV----SQPLREQILSHQDKIGHGRESNPFPS 1099
            D   +F + I+ FL + S + ++   +  +    + P  ++I+  +D +           
Sbjct: 995  DGERDFYKSIRDFLTKKSIRLALLREERGLKAYFTAPTEDEIVMDEDAVKVKAIDQLSKI 1054

Query: 1100 ACKA-----EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------- 1145
            + KA     E C  KY RA++EP TAVGA+ AQSIGEPGTQMTLKTFHFAG         
Sbjct: 1055 SSKAVKTFLEQCLYKYSRARVEPGTAVGAIGAQSIGEPGTQMTLKTFHFAGVASMNVTLG 1114

Query: 1146 -----EVCE--------YIEEVFVPDD--------------------------------S 1160
                 E+           I  V V DD                                +
Sbjct: 1115 VPRIKEIINASKVISTPIINAVLVNDDDEIAARVAKGRIEKTLLEDVAFYIEDVYKDNLA 1174

Query: 1161 FILIKLDMDRIRLLHLEVDIDSIRYCIE---RTRGISGHLTVSGHSFL------------ 1205
            ++ IK+D++ I  L LE+++++I   I    + +     ++V+G   +            
Sbjct: 1175 YLSIKIDLETIDKLQLELNLENIAVAIANAPKLKIAQSDVSVTGKDRINVLVNIKETKTE 1234

Query: 1206 -ILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLR 1264
             +    D   +   +M  +K+ LP V IKG+  I RAVI+ +D +G  K +LLVEG  L+
Sbjct: 1235 SLRNTVDPKNALFFRMQYLKRALPGVCIKGLPNIFRAVINIKD-DG--KKELLVEGYGLK 1291

Query: 1265 DVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADL 1324
            DVM T G+ G K ++N+  EV + LGIEAAR +I+ EI   M NHGMS+D RH  L+ D+
Sbjct: 1292 DVMNTEGIVGTKTTTNHVLEVNQILGIEAARGSIIKEIDYTMSNHGMSVDPRHIQLLGDV 1351

Query: 1325 MTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPM 1384
            MT KGEVLGITR GL+KM++SVL LASFE T+DHLFDAAF+ + D I GVSECII+G  M
Sbjct: 1352 MTYKGEVLGITRFGLSKMRDSVLQLASFEKTTDHLFDAAFFMKNDKIEGVSECIILGQTM 1411

Query: 1385 NVGTGLIKLLQA 1396
            ++GTG  KL+++
Sbjct: 1412 SIGTGSFKLVKS 1423



 Score =  178 bits (451), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 107/272 (39%), Positives = 151/272 (55%), Gaps = 11/272 (4%)

Query: 79  FRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCG 138
            +GL  G ++ +D V Q S ++I +++LY  +  R P  HG LD +MG +     C+TC 
Sbjct: 13  IKGLEFGALSAKDIVAQ-SEVEIQTRDLYDLEKGRVPKEHGALDTKMGISSNAQECSTCH 71

Query: 139 QNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN 198
            NL+ C GHFG+I L LPVFH+GYF+ +I++LQ ICK  +CA VLL E+    +   LR 
Sbjct: 72  GNLASCHGHFGHIRLALPVFHVGYFKSIISVLQCICK--SCAAVLLDEQSKRQYLNDLRK 129

Query: 199 PALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKC------GLLKISHEKYKNRTKK 252
           P +  L R  + KKI+E  KK   C  C  INGVVKK         LKI H+ ++   KK
Sbjct: 130 PHIDNLRRMKIIKKIIEQCKKQRRCLKCNHINGVVKKAASGAGPAALKIVHDTFRWIGKK 189

Query: 253 KDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMN-AE 311
           +         E ++    NPE+E   K  +   LNPL+ L LF+ I  +D  L  ++ A+
Sbjct: 190 ETLEKTIWDEELDQVFIRNPELEKFAK-RIHDDLNPLKTLNLFKQITPQDCELFGLDPAK 248

Query: 312 LSKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
             +P   I   L  PP CIRPSV+ D +S+ D
Sbjct: 249 GGRPEMYIWRYLPAPPVCIRPSVMMDSQSNED 280



 Score =  177 bits (449), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 108/250 (43%), Positives = 154/250 (61%), Gaps = 19/250 (7%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII A L  D D   AR+ KGR+E+T L +V  YIE+V+  + 
Sbjct: 1114 GVPRIKEIINASKVISTPIINAVLVNDDDEIAARVAKGRIEKTLLEDVAFYIEDVYKDNL 1173

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIE---RTRGISGHLTVSGHSFL----------- 869
            +++ IK+D++ I  L LE+++++I   I    + +     ++V+G   +           
Sbjct: 1174 AYLSIKIDLETIDKLQLELNLENIAVAIANAPKLKIAQSDVSVTGKDRINVLVNIKETKT 1233

Query: 870  --ILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927
              +    D   +   +M  +K+ LP V IKG+  I RAVI+ +D +G  K +LLVEG  L
Sbjct: 1234 ESLRNTVDPKNALFFRMQYLKRALPGVCIKGLPNIFRAVINIKD-DG--KKELLVEGYGL 1290

Query: 928  RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 987
            +DVM T G+ G K ++N+  EV + LGIEAAR +I+ EI   M NHGMS+D RH  L+ D
Sbjct: 1291 KDVMNTEGIVGTKTTTNHVLEVNQILGIEAARGSIIKEIDYTMSNHGMSVDPRHIQLLGD 1350

Query: 988  LMTSKGEVLG 997
            +MT KGEVLG
Sbjct: 1351 VMTYKGEVLG 1360



 Score =  102 bits (253), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 48/61 (78%), Positives = 52/61 (85%), Gaps = 1/61 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV+NSFFSGLTP EF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QY
Sbjct: 836 TPQSKGFVRNSFFSGLTPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSSQY 895

Query: 668 D 668
           D
Sbjct: 896 D 896



 Score = 63.2 bits (152), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 27/50 (54%), Positives = 41/50 (82%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+RA  +++ S +
Sbjct: 530 LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDRATLVQLLSMM 579



 Score = 49.7 bits (117), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 22/40 (55%), Positives = 30/40 (75%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA 707
            D  FDAAF+ + D I GVSECII+G  M++GTG  KL+++
Sbjct: 1384 DHLFDAAFFMKNDKIEGVSECIILGQTMSIGTGSFKLVKS 1423


>gi|406863545|gb|EKD16592.1| DNA-directed RNA polymerase III [Marssonina brunnea f. sp.
            'multigermtubi' MB_m1]
          Length = 1965

 Score =  276 bits (707), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 136/276 (49%), Positives = 178/276 (64%), Gaps = 28/276 (10%)

Query: 341  DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
            D D++LFNRQPSLHKLSIM+H AK+ P RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 959  DGDIILFNRQPSLHKLSIMSHYAKIRPWRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 1018

Query: 401  RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
            R EA+               LM  K+NL TP+NGE +I+ATQDFIT  YLL+ K  FF+R
Sbjct: 1019 RTEAIN--------------LMGVKNNLSTPKNGEPIISATQDFITAAYLLSSKENFFDR 1064

Query: 461  AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                 +   ++   + +             P   ++   +WTGKQ+FS +++PN+  PV 
Sbjct: 1065 KTFTNLCMYMVDGNTHL----------DVPPPAIIKPQALWTGKQVFSALMRPNKKSPVK 1114

Query: 521  ANLKTKGRAYTANEEFCH----RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
             NL  K R Y      C      D ++++RNSE++ G MDK+T+GSG K ++FYI+LRDF
Sbjct: 1115 VNLDAKCRDYQFVPGQCPDMDINDGWLVVRNSEVMCGRMDKTTVGSGKKDSIFYIILRDF 1174

Query: 577  GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
            G D AV AM RLS++++ YL N GFSIGI DV P +
Sbjct: 1175 GPDEAVLAMNRLSKISARYLTNMGFSIGISDVYPSK 1210



 Score =  212 bits (540), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 140/367 (38%), Positives = 190/367 (51%), Gaps = 79/367 (21%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGE------------------- 1146
            C  KY +A +EP  AVGA+ AQSIGEPGTQMTLKTFHFAG                    
Sbjct: 1560 CLSKYAKAHVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIINAS 1619

Query: 1147 -----------------------VCEYIEEVFVPD------------DSFILIKLDMDRI 1171
                                   V   IE+ ++ D             + + + +D+D +
Sbjct: 1620 KVISTPVISCPLENEREIQVARIVKARIEKTYISDVIRFIEDMWSAKAATLCLSVDLDYL 1679

Query: 1172 RLLHLEVDIDSIRY--CIERTRGISG-HLTVSGHSFLILKPKDSSKSFNSKMYQ------ 1222
              + L + ++ I    C+ +   I G  +TVS     +    +S  +  ++  +      
Sbjct: 1680 NEMQLGITVEDIAQTICMNKKLKIRGTDVTVSHECIFVNVTSESGGNLGARGAKNKAYVD 1739

Query: 1223 ------------MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATY 1270
                        +K+ LP++ I G     RA++   + E V  + +LVEG  LR  M T 
Sbjct: 1740 DGSSDVLLRVNFLKRTLPTITISGYPDATRAIVQVSEDETV--HTVLVEGYGLRACMTTE 1797

Query: 1271 GVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGE 1330
            GV G + +SN+  EV   LGIEAARSTI TEI  VM +  M ID RH  L+AD+MT KGE
Sbjct: 1798 GVVGRRVTSNSIMEVNTVLGIEAARSTIATEIGAVMGD--MGIDPRHMQLLADVMTYKGE 1855

Query: 1331 VLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGL 1390
            VLGITR GL+KM++SVL LASFE T DHLFDAA   +TD I GVSECIIMG  M+VGTG 
Sbjct: 1856 VLGITRFGLSKMRDSVLQLASFEKTPDHLFDAAAGMKTDLIEGVSECIIMGQTMSVGTGA 1915

Query: 1391 IKLLQAV 1397
             ++++ +
Sbjct: 1916 FQVVRKL 1922



 Score =  190 bits (482), Expect = 7e-45,   Method: Compositional matrix adjust.
 Identities = 107/262 (40%), Positives = 145/262 (55%), Gaps = 17/262 (6%)

Query: 96  QSHIQIVSKN--------LYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGH 147
           QS+ QIV++         LY  +  R P+P+G LD R+GT+ K   C TCG  L++C GH
Sbjct: 523 QSNTQIVNQAVLEVSNTLLYDVEKMRKPMPNGPLDPRLGTSSKNGTCGTCGDILANCNGH 582

Query: 148 FGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRK 207
           FG+I L LPVFHIGY +  +  LQ ICK   CARVLL + +   F  +LR P +  L R 
Sbjct: 583 FGHIRLALPVFHIGYLKLTMKFLQEICKE--CARVLLTDTERRSFLQRLRKPGIDNLERT 640

Query: 208 SLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYK---NRTKKKDAIVEDLLA-- 262
            + KKI E  +K   CP+C  +NG ++K G++K++H+KY+     T +K      LL   
Sbjct: 641 RICKKINEQCRKARTCPYCDAVNGQIRKVGIVKLAHDKYQAFNKSTAQKKVPPPSLLTYQ 700

Query: 263 -EYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
             + EA K NPE+E H K  +   LN L VL LF+ I   D  LL +N    +P   I  
Sbjct: 701 KSFEEAKKANPELEKHMKKAM-DDLNALRVLNLFKMITPSDCELLGLNPLEGRPEMFIWQ 759

Query: 322 RLLVPPNCIRPSVISDLKSDND 343
            +  PP CIRPSV  +  S  D
Sbjct: 760 FVPAPPICIRPSVAQENASTED 781



 Score =  150 bits (378), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 100/279 (35%), Positives = 153/279 (54%), Gaps = 26/279 (9%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+I+  L+ + ++  ARIVK R+E+T + +V  +IE+++    
Sbjct: 1608 GVPRIKEIINASKVISTPVISCPLENEREIQVARIVKARIEKTYISDVIRFIEDMWSAKA 1667

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISG-HLTVSGHSFLILKPKDSSKSF 880
            + + + +D+D +  + L + ++ I    C+ +   I G  +TVS     +    +S  + 
Sbjct: 1668 ATLCLSVDLDYLNEMQLGITVEDIAQTICMNKKLKIRGTDVTVSHECIFVNVTSESGGNL 1727

Query: 881  NSKMYQ------------------MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLV 922
             ++  +                  +K+ LP++ I G     RA++   + E V  + +LV
Sbjct: 1728 GARGAKNKAYVDDGSSDVLLRVNFLKRTLPTITISGYPDATRAIVQVSEDETV--HTVLV 1785

Query: 923  EGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHP 982
            EG  LR  M T GV G + +SN+  EV   LGIEAARSTI TEI  VM +  M ID RH 
Sbjct: 1786 EGYGLRACMTTEGVVGRRVTSNSIMEVNTVLGIEAARSTIATEIGAVMGD--MGIDPRHM 1843

Query: 983  MLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDP 1021
             L+AD+MT KGEVLG  T   L ++ D ++   S    P
Sbjct: 1844 QLLADVMTYKGEVLGI-TRFGLSKMRDSVLQLASFEKTP 1881



 Score =  103 bits (258), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 46/59 (77%), Positives = 51/59 (86%)

Query: 610  PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            P +GFV+NSFF+GL PTEF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 1332 PSKGFVRNSFFTGLRPTEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSTQYD 1390



 Score = 57.0 bits (136), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 26/53 (49%), Positives = 35/53 (66%)

Query: 22   LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
            LM  K+NL TP+NGE +I+ATQDFIT  YLL+ K  FF+R     +   ++ G
Sbjct: 1025 LMGVKNNLSTPKNGEPIISATQDFITAAYLLSSKENFFDRKTFTNLCMYMVDG 1077



 Score = 45.8 bits (107), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 22/41 (53%), Positives = 29/41 (70%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 708
            D  FDAA   +TD I GVSECIIMG  M+VGTG  ++++ +
Sbjct: 1882 DHLFDAAAGMKTDLIEGVSECIIMGQTMSVGTGAFQVVRKL 1922


>gi|238881190|gb|EEQ44828.1| DNA-directed RNA polymerase III largest subunit [Candida albicans
           WO-1]
          Length = 1448

 Score =  276 bits (707), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 140/281 (49%), Positives = 187/281 (66%), Gaps = 29/281 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH+LSI++H AK+ P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 464 DGDVVLFNRQPSLHRLSILSHYAKIRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 523

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+R
Sbjct: 524 RAEAIN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDR 569

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A  +++ S +    +DI   I         P    +  ++WTGKQ+FSL++KPN+   V 
Sbjct: 570 ATLVQLLSMM--SDADIQFDIP--------PPTIFKPVMLWTGKQVFSLLIKPNKKSNVV 619

Query: 521 ANLKTKGRAYTANE-----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL  K + +   +     E    D +V++R S++L+G MDKSTLG G K +VFY +LRD
Sbjct: 620 INLDAKNKTFHPPKKGLPNEMSPNDGFVVIRGSKILSGLMDKSTLGDGKKHSVFYTILRD 679

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           +G   A  AM R++++ + +L NRGFSIGI DVTP     Q
Sbjct: 680 YGPQEAAAAMNRMAKLCARFLGNRGFSIGINDVTPADELKQ 720



 Score =  246 bits (627), Expect = 8e-62,   Method: Compositional matrix adjust.
 Identities = 152/363 (41%), Positives = 206/363 (56%), Gaps = 73/363 (20%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCE 1149
            E C  KY RA++EP TAVGA+ AQSIGEPGTQMTLKTFHFAG              E+  
Sbjct: 1064 EQCLYKYSRARVEPGTAVGAIGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIIN 1123

Query: 1150 --------YIEEVFVPDD--------------------------------SFILIKLDMD 1169
                     I  V V DD                                +++ IK+D++
Sbjct: 1124 ASKVISTPIINAVLVNDDDEIAARVAKGRIEKTLLEDVAFYIEDVYKDNLAYLSIKIDLE 1183

Query: 1170 RIRLLHLEVDIDSIRYCIE---RTRGISGHLTVSGHSFL-------------ILKPKDSS 1213
             I  L LE+++++I   I    + +     ++V+G   +             +    D  
Sbjct: 1184 TIDKLQLELNLENIAVAIANAPKLKIAQSDVSVTGKDRINVLVNIKETKTESLRNTVDPK 1243

Query: 1214 KSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVK 1273
             +   +M  +K+ LP V IKG+  I RAVI+ +D +G  K +LLVEG  L+DVM T G+ 
Sbjct: 1244 NALFFRMQYLKRALPGVCIKGLPNIFRAVINIKD-DG--KKELLVEGYGLKDVMNTEGIV 1300

Query: 1274 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 1333
            G K ++N+  EV + LGIEAAR +I+ EI   M NHGMS+D RH  L+ D+MT KGEVLG
Sbjct: 1301 GTKTTTNHVLEVNQILGIEAARGSIIKEIDYTMSNHGMSVDPRHIQLLGDVMTYKGEVLG 1360

Query: 1334 ITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            ITR GL+KM++SVL LASFE T+DHLFDAAF+ + D I GVSECII+G  M++GTG  KL
Sbjct: 1361 ITRFGLSKMRDSVLQLASFEKTTDHLFDAAFFMKNDKIEGVSECIILGQTMSIGTGSFKL 1420

Query: 1394 LQA 1396
            +++
Sbjct: 1421 VKS 1423



 Score =  178 bits (452), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 107/272 (39%), Positives = 151/272 (55%), Gaps = 11/272 (4%)

Query: 79  FRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCG 138
            +GL  G ++ +D V Q S ++I +++LY  +  R P  HG LD +MG +     C+TC 
Sbjct: 13  IKGLEFGALSAKDIVAQ-SEVEIQTRDLYDLEKGRVPKEHGALDTKMGISSNAQECSTCH 71

Query: 139 QNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN 198
            NL+ C GHFG+I L LPVFH+GYF+ +I++LQ ICK  +CA VLL E+    +   LR 
Sbjct: 72  GNLASCHGHFGHIRLALPVFHVGYFKSIISVLQCICK--SCAAVLLDEQSKRQYLNDLRK 129

Query: 199 PALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKC------GLLKISHEKYKNRTKK 252
           P +  L R  + KKI+E  KK   C  C  INGVVKK         LKI H+ ++   KK
Sbjct: 130 PHIDNLRRMKIIKKIIEQCKKQRRCLKCNHINGVVKKAASGAGPAALKIVHDTFRWIGKK 189

Query: 253 KDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMN-AE 311
           +         E ++    NPE+E   K  +   LNPL+ L LF+ I  +D  L  ++ A+
Sbjct: 190 ETLEKTIWDEELDQVFIRNPELEKFAK-RIHDDLNPLKTLNLFKQITPQDCELFGLDPAK 248

Query: 312 LSKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
             +P   I   L  PP CIRPSV+ D +S+ D
Sbjct: 249 GGRPEMYIWRYLPAPPVCIRPSVMMDAQSNED 280



 Score =  177 bits (448), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 108/250 (43%), Positives = 154/250 (61%), Gaps = 19/250 (7%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII A L  D D   AR+ KGR+E+T L +V  YIE+V+  + 
Sbjct: 1114 GVPRIKEIINASKVISTPIINAVLVNDDDEIAARVAKGRIEKTLLEDVAFYIEDVYKDNL 1173

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIE---RTRGISGHLTVSGHSFL----------- 869
            +++ IK+D++ I  L LE+++++I   I    + +     ++V+G   +           
Sbjct: 1174 AYLSIKIDLETIDKLQLELNLENIAVAIANAPKLKIAQSDVSVTGKDRINVLVNIKETKT 1233

Query: 870  --ILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927
              +    D   +   +M  +K+ LP V IKG+  I RAVI+ +D +G  K +LLVEG  L
Sbjct: 1234 ESLRNTVDPKNALFFRMQYLKRALPGVCIKGLPNIFRAVINIKD-DG--KKELLVEGYGL 1290

Query: 928  RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 987
            +DVM T G+ G K ++N+  EV + LGIEAAR +I+ EI   M NHGMS+D RH  L+ D
Sbjct: 1291 KDVMNTEGIVGTKTTTNHVLEVNQILGIEAARGSIIKEIDYTMSNHGMSVDPRHIQLLGD 1350

Query: 988  LMTSKGEVLG 997
            +MT KGEVLG
Sbjct: 1351 VMTYKGEVLG 1360



 Score =  102 bits (253), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 48/61 (78%), Positives = 52/61 (85%), Gaps = 1/61 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV+NSFFSGLTP EF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QY
Sbjct: 836 TPQSKGFVRNSFFSGLTPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSSQY 895

Query: 668 D 668
           D
Sbjct: 896 D 896



 Score = 63.2 bits (152), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 27/50 (54%), Positives = 41/50 (82%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+RA  +++ S +
Sbjct: 530 LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDRATLVQLLSMM 579



 Score = 49.7 bits (117), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 22/40 (55%), Positives = 30/40 (75%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA 707
            D  FDAAF+ + D I GVSECII+G  M++GTG  KL+++
Sbjct: 1384 DHLFDAAFFMKNDKIEGVSECIILGQTMSIGTGSFKLVKS 1423


>gi|68481275|ref|XP_715412.1| hypothetical protein CaO19.3103 [Candida albicans SC5314]
 gi|46437034|gb|EAK96387.1| hypothetical protein CaO19.3103 [Candida albicans SC5314]
          Length = 1448

 Score =  276 bits (707), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 140/281 (49%), Positives = 187/281 (66%), Gaps = 29/281 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH+LSI++H AK+ P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 464 DGDVVLFNRQPSLHRLSILSHYAKIRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 523

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+R
Sbjct: 524 RAEAIN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDR 569

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A  +++ S +    +DI   I         P    +  ++WTGKQ+FSL++KPN+   V 
Sbjct: 570 ATLVQLLSMM--SDADIQFDIP--------PPTIFKPVMLWTGKQVFSLLIKPNKKSNVV 619

Query: 521 ANLKTKGRAYTANE-----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL  K + +   +     E    D +V++R S++L+G MDKSTLG G K +VFY +LRD
Sbjct: 620 INLDAKNKTFHPPKKGLPNEMSPNDGFVVIRGSKILSGLMDKSTLGDGKKHSVFYTILRD 679

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           +G   A  AM R++++ + +L NRGFSIGI DVTP     Q
Sbjct: 680 YGPQEAAAAMNRMAKLCARFLGNRGFSIGINDVTPADELKQ 720



 Score =  247 bits (630), Expect = 4e-62,   Method: Compositional matrix adjust.
 Identities = 163/432 (37%), Positives = 233/432 (53%), Gaps = 82/432 (18%)

Query: 1044 DTSENFVRDIKKFLEEFSKKESVTSHQDKV----SQPLREQILSHQDKIGHGRESNPFPS 1099
            D   +F + I+ FL + S + ++   +  +    + P  ++I+  +D +           
Sbjct: 995  DGERDFYKSIRDFLTKKSIRLALLREERGLKAYFTAPTEDEIVMDEDAVKVKAIDQLSKI 1054

Query: 1100 ACKA-----EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------- 1145
            + KA     E C  KY RA++EP TAVGA+ AQSIGEPGTQMTLKTFHFAG         
Sbjct: 1055 SSKAVKTFLEQCLYKYSRARVEPGTAVGAIGAQSIGEPGTQMTLKTFHFAGVASMNVTLG 1114

Query: 1146 -----EVCE--------YIEEVFVPDD--------------------------------S 1160
                 E+           I  V V DD                                +
Sbjct: 1115 VPRIKEIINASKVISTPIINAVLVNDDDEIAARVAKGRIEKTLLEDVAFYIEDVYKDNLA 1174

Query: 1161 FILIKLDMDRIRLLHLEVDIDSIRYCIE---RTRGISGHLTVSGHSFL------------ 1205
            ++ IK+D++ I  L LE+++++I   I    + +     ++V+G   +            
Sbjct: 1175 YLSIKIDLETIDKLQLELNLENIAVAIANAPKLKIAQSDVSVTGKDRINVLVNIKETKTE 1234

Query: 1206 -ILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLR 1264
             +    D   +   +M  +K+ LP V IKG+  I RAVI+ +D +G  K +LLVEG  L+
Sbjct: 1235 SLRNTVDPKNALFFRMQYLKRALPGVCIKGLPNIFRAVINIKD-DG--KKELLVEGYGLK 1291

Query: 1265 DVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADL 1324
            DVM T G+ G K ++N+  EV + LGIEAAR +I+ EI   M NHGMS+D RH  L+ D+
Sbjct: 1292 DVMNTEGIVGTKTTTNHVLEVNQILGIEAARGSIIKEIDYTMSNHGMSVDPRHIQLLGDV 1351

Query: 1325 MTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPM 1384
            MT KGEVLGITR GL+KM++SVL LASFE T+DHLFDAAF+ + D I GVSECII+G  M
Sbjct: 1352 MTYKGEVLGITRFGLSKMRDSVLQLASFEKTTDHLFDAAFFMKNDKIEGVSECIILGQTM 1411

Query: 1385 NVGTGLIKLLQA 1396
            ++GTG  KL+++
Sbjct: 1412 SIGTGSFKLVKS 1423



 Score =  177 bits (450), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 107/272 (39%), Positives = 151/272 (55%), Gaps = 11/272 (4%)

Query: 79  FRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCG 138
            +GL  G ++ +D V Q S ++I +++LY  +  R P  HG LD +MG +     C+TC 
Sbjct: 13  IKGLEFGALSAKDIVAQ-SEVEIQTRDLYDLEKGRVPKEHGALDTKMGISSNAQECSTCH 71

Query: 139 QNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN 198
            NL+ C GHFG+I L LPVFH+GYF+ +I++LQ ICK  +CA VLL E+    +   LR 
Sbjct: 72  GNLASCHGHFGHIRLALPVFHVGYFKSIISVLQCICK--SCAAVLLDEQSKRQYLNDLRK 129

Query: 199 PALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKC------GLLKISHEKYKNRTKK 252
           P +  L R  + KKI+E  KK   C  C  INGVVKK         LKI H+ ++   KK
Sbjct: 130 PHIDNLRRMKIIKKIIEQCKKQRRCLKCNHINGVVKKAASGAGPAALKIVHDTFRWIGKK 189

Query: 253 KDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMN-AE 311
           +         E ++    NPE+E   K  +   LNPL+ L LF+ I  +D  L  ++ A+
Sbjct: 190 ETLEKTIWDEELDQVFIRNPELEKFAK-RIHDDLNPLKTLNLFKQITPQDCELFGLDPAK 248

Query: 312 LSKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
             +P   I   L  PP CIRPSV+ D +S+ D
Sbjct: 249 GGRPEMYIWRYLPAPPVCIRPSVMMDSQSNED 280



 Score =  177 bits (448), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 108/250 (43%), Positives = 154/250 (61%), Gaps = 19/250 (7%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII A L  D D   AR+ KGR+E+T L +V  YIE+V+  + 
Sbjct: 1114 GVPRIKEIINASKVISTPIINAVLVNDDDEIAARVAKGRIEKTLLEDVAFYIEDVYKDNL 1173

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIE---RTRGISGHLTVSGHSFL----------- 869
            +++ IK+D++ I  L LE+++++I   I    + +     ++V+G   +           
Sbjct: 1174 AYLSIKIDLETIDKLQLELNLENIAVAIANAPKLKIAQSDVSVTGKDRINVLVNIKETKT 1233

Query: 870  --ILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927
              +    D   +   +M  +K+ LP V IKG+  I RAVI+ +D +G  K +LLVEG  L
Sbjct: 1234 ESLRNTVDPKNALFFRMQYLKRALPGVCIKGLPNIFRAVINIKD-DG--KKELLVEGYGL 1290

Query: 928  RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 987
            +DVM T G+ G K ++N+  EV + LGIEAAR +I+ EI   M NHGMS+D RH  L+ D
Sbjct: 1291 KDVMNTEGIVGTKTTTNHVLEVNQILGIEAARGSIIKEIDYTMSNHGMSVDPRHIQLLGD 1350

Query: 988  LMTSKGEVLG 997
            +MT KGEVLG
Sbjct: 1351 VMTYKGEVLG 1360



 Score =  102 bits (253), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 48/61 (78%), Positives = 52/61 (85%), Gaps = 1/61 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV+NSFFSGLTP EF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QY
Sbjct: 836 TPQSKGFVRNSFFSGLTPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSSQY 895

Query: 668 D 668
           D
Sbjct: 896 D 896



 Score = 62.8 bits (151), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 27/50 (54%), Positives = 41/50 (82%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+RA  +++ S +
Sbjct: 530 LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDRATLVQLLSMM 579



 Score = 49.7 bits (117), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 22/40 (55%), Positives = 30/40 (75%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA 707
            D  FDAAF+ + D I GVSECII+G  M++GTG  KL+++
Sbjct: 1384 DHLFDAAFFMKNDKIEGVSECIILGQTMSIGTGSFKLVKS 1423


>gi|303315581|ref|XP_003067798.1| DNA-directed RNA polymerase III largest subunit, putative
           [Coccidioides posadasii C735 delta SOWgp]
 gi|240107468|gb|EER25653.1| DNA-directed RNA polymerase III largest subunit, putative
           [Coccidioides posadasii C735 delta SOWgp]
          Length = 1444

 Score =  276 bits (707), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 137/281 (48%), Positives = 185/281 (65%), Gaps = 30/281 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++H  KV PHRTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 470 DGDIVLFNRQPSLHKLSILSHFVKVRPHRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 529

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL TP+NGE +IAA QDFIT  YLL+ K+ F++R
Sbjct: 530 RAEAME--------------LMGVKNNLATPKNGEPIIAAIQDFITAAYLLSSKDNFYDR 575

Query: 461 AQTMRIASTLIADTSDICG-IIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
                         + ICG +++  +     P   ++  ++WTGKQ+F+++++P+++ PV
Sbjct: 576 GS-----------FTQICGYMLQPGTKFDLPPPAVLKPQMLWTGKQVFNVLMRPSKESPV 624

Query: 520 NANLKTKGRAYTANE----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
             NL    R + A +    +    D ++ +RNSE++ G MDKST+GSG K +VFY++LRD
Sbjct: 625 LVNLDAACREFRAPKGTPRDLDPNDGWLCIRNSEIMCGVMDKSTIGSGKKDSVFYVMLRD 684

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           FG  VA  AM RLSR+++ +  N GFSIGI DV PG   +Q
Sbjct: 685 FGPQVAAEAMNRLSRLSARWFTNIGFSIGITDVYPGDSLLQ 725



 Score =  222 bits (566), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 144/363 (39%), Positives = 193/363 (53%), Gaps = 74/363 (20%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEV----------------- 1147
            +C  KY +AQ+EP  AVGA+ AQSIGEPGTQMTLKTFHFAG                   
Sbjct: 1052 SCLTKYKKAQVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIINA 1111

Query: 1148 ----------CE---------------------------YIEEVFVPDDSFILIKLDMDR 1170
                      CE                           YIEE +    ++I IK+D   
Sbjct: 1112 SKEISTPIITCELVNKEDVRAAQIVKGRVEKTFIKDIIYYIEEAWTGSVAYINIKIDFST 1171

Query: 1171 IRLLHLEVDIDSIRYCIE------------RTRGISGHLTVSGHSFLILKPKDSSKSFNS 1218
            I+ L LE+ +  I   I+            R+ G   H+ V   +      K    +  S
Sbjct: 1172 IQALQLELTLRDILNAIKKHKRFRSDDLKFRSFGSHIHIFVDQATTKTSLTKAEQAATGS 1231

Query: 1219 KMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 1274
              Y     +K+LLP++ + G    +RA+I  ++    T   LLVEG  LR  M T G+ G
Sbjct: 1232 DPYIRLKHLKRLLPTIQVLGHPQCSRAIIRTDETN--TTNTLLVEGYGLRACMTTDGIFG 1289

Query: 1275 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGI 1334
             +  +NN  E    LGIEAAR+TI+ EI  VM++  M ID RH  L+AD+MT KGEVLGI
Sbjct: 1290 TRTRTNNIMETKDVLGIEAARTTIVDEISDVMKD--MGIDPRHMQLLADVMTYKGEVLGI 1347

Query: 1335 TRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            TR GLAKM++SVL LASFE T+DHLFDA   G+TD + GVSECII+G  +++GTG ++++
Sbjct: 1348 TRFGLAKMRDSVLQLASFEKTADHLFDAGGAGRTDLVEGVSECIILGKSVSLGTGAMEMV 1407

Query: 1395 QAV 1397
            +A+
Sbjct: 1408 RAM 1410



 Score =  168 bits (426), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 103/268 (38%), Positives = 147/268 (54%), Gaps = 14/268 (5%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G +  +D V Q + +++  + L+  D  R    HG LD RMG + K   C TCG  L +C
Sbjct: 30  GVLASQDIVSQ-ALVEVSDRKLFDLDNDRAVARHGPLDGRMGISSKSGTCETCGGALQEC 88

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFG++ L LP FH+GYF+ VI ILQ ICK+  C+R+LL E +   F  ++R   +  L
Sbjct: 89  NGHFGHVRLVLPAFHVGYFKRVIGILQEICKD--CSRILLPENERRIFLKEMRRQGIDNL 146

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKYK----NRTKKKDAIVE 258
            R  + K+I +  +K   C  C  +NGVVKK G   LKI+H+K++    + + KK     
Sbjct: 147 RRMQINKRINDRCRKTRTCYVCHAVNGVVKKAGTSALKITHDKFRAFNASTSAKKVPPPS 206

Query: 259 DLLAE--YNEAVKFNPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKP 315
            L+ +  + EA + N +IE H  F  +Q  LNPL VL+LF  I  ED  LL +N E  +P
Sbjct: 207 KLVFDRSFEEAKRSNTDIEKH--FKKVQDDLNPLRVLKLFRRISDEDCELLGLNPEEVRP 264

Query: 316 SDLILTRLLVPPNCIRPSVISDLKSDND 343
              +   +  PP  IRPSV  +  S  D
Sbjct: 265 EMFLWQYIPAPPVSIRPSVGQEGASTED 292



 Score =  153 bits (386), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 102/250 (40%), Positives = 140/250 (56%), Gaps = 20/250 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIIT  L    D+  A+IVKGR+E+T + ++  YIEE +    
Sbjct: 1101 GVPRIKEIINASKEISTPIITCELVNKEDVRAAQIVKGRVEKTFIKDIIYYIEEAWTGSV 1160

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIE------------RTRGISGHLTVSGHSFLIL 871
            ++I IK+D   I+ L LE+ +  I   I+            R+ G   H+ V   +    
Sbjct: 1161 AYINIKIDFSTIQALQLELTLRDILNAIKKHKRFRSDDLKFRSFGSHIHIFVDQATTKTS 1220

Query: 872  KPKDSSKSFNSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927
              K    +  S  Y     +K+LLP++ + G    +RA+I  ++    T   LLVEG  L
Sbjct: 1221 LTKAEQAATGSDPYIRLKHLKRLLPTIQVLGHPQCSRAIIRTDETN--TTNTLLVEGYGL 1278

Query: 928  RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 987
            R  M T G+ G +  +NN  E    LGIEAAR+TI+ EI  VM++  M ID RH  L+AD
Sbjct: 1279 RACMTTDGIFGTRTRTNNIMETKDVLGIEAARTTIVDEISDVMKD--MGIDPRHMQLLAD 1336

Query: 988  LMTSKGEVLG 997
            +MT KGEVLG
Sbjct: 1337 VMTYKGEVLG 1346



 Score =  103 bits (256), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 45/59 (76%), Positives = 52/59 (88%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSFFSGL P+EFFFH + GREGL+DTAVKTAETGYM RRL+KSLEDL  +YD
Sbjct: 843 PAKGFVRNSFFSGLIPSEFFFHAISGREGLIDTAVKTAETGYMSRRLMKSLEDLSSRYD 901



 Score = 57.0 bits (136), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 25/51 (49%), Positives = 35/51 (68%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLI 72
           LM  K+NL TP+NGE +IAA QDFIT  YLL+ K+ F++R    +I   ++
Sbjct: 536 LMGVKNNLATPKNGEPIIAAIQDFITAAYLLSSKDNFYDRGSFTQICGYML 586



 Score = 45.4 bits (106), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 19/41 (46%), Positives = 31/41 (75%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 708
            D  FDA   G+TD + GVSECII+G  +++GTG +++++A+
Sbjct: 1370 DHLFDAGGAGRTDLVEGVSECIILGKSVSLGTGAMEMVRAM 1410


>gi|149234447|ref|XP_001523103.1| DNA-directed RNA polymerase III largest subunit [Lodderomyces
           elongisporus NRRL YB-4239]
 gi|146453212|gb|EDK47468.1| DNA-directed RNA polymerase III largest subunit [Lodderomyces
           elongisporus NRRL YB-4239]
          Length = 1450

 Score =  276 bits (707), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 142/281 (50%), Positives = 187/281 (66%), Gaps = 29/281 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH+LSI++H AK+ P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 470 DGDVVLFNRQPSLHRLSILSHYAKIRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 529

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL+TP++GE +IAATQDFITG YL++ K+ F +R
Sbjct: 530 RAEAIN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDTFLDR 575

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A  +++ S +    +DI   I         P    +  ++WTGKQ+FSL++KPN+   V 
Sbjct: 576 ASLVQLLSMM--SDADIHFDIP--------PPAIFKPVMLWTGKQVFSLLIKPNKQSKVI 625

Query: 521 ANLKTKGRA-YTANE----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL  K +  + A +    E    D YV++R S++L+G MDKSTLG G K +VFY++LRD
Sbjct: 626 INLNAKNKTCHPAPKGFPPEMSTNDGYVVIRGSQILSGLMDKSTLGDGKKDSVFYVILRD 685

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           +G   A  AM R++++ + YL NRGFSIGI DVTP     Q
Sbjct: 686 YGPHEAAAAMNRMAKLCARYLGNRGFSIGINDVTPATELRQ 726



 Score =  240 bits (613), Expect = 4e-60,   Method: Compositional matrix adjust.
 Identities = 177/509 (34%), Positives = 249/509 (48%), Gaps = 103/509 (20%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFL-------------- 1042
            G+  PV   R  D       S +D SL   +I+ +  +TL  +E                
Sbjct: 929  GDAKPVNFIRQWDHAYNLTFSANDKSLLPYQIMDVVEQTLRPREEALKTGDEEGKTEDQL 988

Query: 1043 ---QDTSENFVRDIKKFLEEFSKKESVTSHQ---------DKVSQPLREQIL----SHQD 1086
               +D    F R ++ F+ + +++ +    +         DK S    E +L    S  +
Sbjct: 989  VDQKDAQREFYRSVRDFMAQKAERLARLREERGLKPYFTFDKQSSDQDEMVLDEDASKVN 1048

Query: 1087 KIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG- 1145
             I    + +          C  KY RA++E  TAVGA+ AQSIGEPGTQMTLKTFHFAG 
Sbjct: 1049 AIDQLMKISKKTVKIFLTQCLYKYSRAKVEAGTAVGAIGAQSIGEPGTQMTLKTFHFAGV 1108

Query: 1146 -------------EVCE--------YIEEVFVPDDSFILIK------------------- 1165
                         E+           I  V V +D  I  +                   
Sbjct: 1109 ASMNVTLGVPRIKEIINASKTISTPIINAVLVNEDDEIAARVAKGRIEKTSLKDVSIYIE 1168

Query: 1166 -------------LDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFLILKP 1209
                         +D+D I  L LE+DI +I   I +   +      ++V G   +++  
Sbjct: 1169 DVYKDNLAFLSIKVDLDSIEKLQLELDISNIAEAICKAPKLKISQSDVSVMGKDRILVAC 1228

Query: 1210 K-------------DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKL 1256
            +             D   +   +M  +K++LP + IKG+  I RAVI+ +D     K +L
Sbjct: 1229 RVTESKTESLKSGEDQRNNLFFRMQLLKRVLPDICIKGLPNIFRAVINIKD---DNKKEL 1285

Query: 1257 LVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFR 1316
            LVEG  L+DVM T G+ G K ++N+  EV + LGIEAARS+I+ EI   M N+GMS+D R
Sbjct: 1286 LVEGYGLKDVMNTEGIVGTKTTTNHVLEVNEILGIEAARSSIIREIDYTMSNYGMSVDPR 1345

Query: 1317 HPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSE 1376
            H  L+ D+MT KGEVLGITR GL+KM++SVL LASFE T+DHLFDAAFY + D I GVSE
Sbjct: 1346 HIQLLGDVMTYKGEVLGITRFGLSKMRDSVLQLASFEKTTDHLFDAAFYMKRDKIEGVSE 1405

Query: 1377 CIIMGLPMNVGTGLIKLLQAVPRSEPVPR 1405
            CII+G  M +GTG  KL+++   S+ V R
Sbjct: 1406 CIILGQTMAIGTGAFKLVKSSNFSDKVLR 1434



 Score =  182 bits (462), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 109/250 (43%), Positives = 155/250 (62%), Gaps = 19/250 (7%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII A L  + D   AR+ KGR+E+T+L +V  YIE+V+  + 
Sbjct: 1116 GVPRIKEIINASKTISTPIINAVLVNEDDEIAARVAKGRIEKTSLKDVSIYIEDVYKDNL 1175

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFLILKPK------ 874
            +F+ IK+D+D I  L LE+DI +I   I +   +      ++V G   +++  +      
Sbjct: 1176 AFLSIKVDLDSIEKLQLELDISNIAEAICKAPKLKISQSDVSVMGKDRILVACRVTESKT 1235

Query: 875  -------DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927
                   D   +   +M  +K++LP + IKG+  I RAVI+ +D     K +LLVEG  L
Sbjct: 1236 ESLKSGEDQRNNLFFRMQLLKRVLPDICIKGLPNIFRAVINIKDD---NKKELLVEGYGL 1292

Query: 928  RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 987
            +DVM T G+ G K ++N+  EV + LGIEAARS+I+ EI   M N+GMS+D RH  L+ D
Sbjct: 1293 KDVMNTEGIVGTKTTTNHVLEVNEILGIEAARSSIIREIDYTMSNYGMSVDPRHIQLLGD 1352

Query: 988  LMTSKGEVLG 997
            +MT KGEVLG
Sbjct: 1353 VMTYKGEVLG 1362



 Score =  179 bits (453), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 103/268 (38%), Positives = 144/268 (53%), Gaps = 10/268 (3%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           +E +    D +  QS +++ +++LY  +  RT    G LD RMGT+     C+TC  NL+
Sbjct: 17  LEFSALSADDIVAQSEVEVQTRDLYDLEKGRTAKAGGALDPRMGTSSNAQECSTCHGNLA 76

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALS 202
            C GHFG+I L LPVFH+GYF+ +I +LQ ICKN  CA VLL E+    F  +LR P + 
Sbjct: 77  SCQGHFGHIKLALPVFHVGYFKAIITVLQCICKN--CAAVLLDEKNKRQFLNELRKPDID 134

Query: 203 YLVRKSLKKKILETTKKVSVCPHCGEINGVVKKC------GLLKISHEKYKNRTKKKDAI 256
            L R  + KK+ +  KK   C  C  +NGVVKK         LKI H+ ++   KK    
Sbjct: 135 NLKRMKILKKVSDQCKKQRRCLKCNHVNGVVKKAASGAGPAALKIVHDTFRWIGKKDTPE 194

Query: 257 VEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNA-ELSKP 315
            E+   E  +    NPE+E + K  + +  NPL+ L LF+ I   D  L  M+     +P
Sbjct: 195 KEEWDKEIEQVFMRNPELEKYAK-RITEDFNPLKTLNLFKQITPSDCELFGMDPLRGGRP 253

Query: 316 SDLILTRLLVPPNCIRPSVISDLKSDND 343
              I   L  PP CIRPSV+ D +S+ D
Sbjct: 254 EMYIWRYLPAPPVCIRPSVMMDAQSNED 281



 Score =  101 bits (251), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 47/61 (77%), Positives = 52/61 (85%), Gaps = 1/61 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV+NSFFSGL+P EF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QY
Sbjct: 842 TPQSKGFVRNSFFSGLSPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSAQY 901

Query: 668 D 668
           D
Sbjct: 902 D 902



 Score = 60.5 bits (145), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 26/50 (52%), Positives = 39/50 (78%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM  K+NL+TP++GE +IAATQDFITG YL++ K+ F +RA  +++ S +
Sbjct: 536 LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDTFLDRASLVQLLSMM 585



 Score = 52.0 bits (123), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 26/49 (53%), Positives = 33/49 (67%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPR 716
            D  FDAAFY + D I GVSECII+G  M +GTG  KL+++   S+ V R
Sbjct: 1386 DHLFDAAFYMKRDKIEGVSECIILGQTMAIGTGAFKLVKSSNFSDKVLR 1434


>gi|320035344|gb|EFW17285.1| DNA-directed RNA polymerase III largest subunit [Coccidioides
           posadasii str. Silveira]
          Length = 1444

 Score =  276 bits (706), Expect = 6e-71,   Method: Compositional matrix adjust.
 Identities = 137/281 (48%), Positives = 185/281 (65%), Gaps = 30/281 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++H  KV PHRTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 470 DGDIVLFNRQPSLHKLSILSHFVKVRPHRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 529

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL TP+NGE +IAA QDFIT  YLL+ K+ F++R
Sbjct: 530 RAEAME--------------LMGVKNNLATPKNGEPIIAAIQDFITAAYLLSSKDNFYDR 575

Query: 461 AQTMRIASTLIADTSDICG-IIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
                         + ICG +++  +     P   ++  ++WTGKQ+F+++++P+++ PV
Sbjct: 576 GS-----------FTQICGYMLQPGTKFDLPPPAVLKPQMLWTGKQVFNVLMRPSKESPV 624

Query: 520 NANLKTKGRAYTANE----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
             NL    R + A +    +    D ++ +RNSE++ G MDKST+GSG K +VFY++LRD
Sbjct: 625 LVNLDAACREFRAPKGTPRDLDPNDGWLCIRNSEIMCGVMDKSTIGSGKKDSVFYVMLRD 684

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           FG  VA  AM RLSR+++ +  N GFSIGI DV PG   +Q
Sbjct: 685 FGPQVAAEAMNRLSRLSARWFTNIGFSIGITDVYPGDSLLQ 725



 Score =  222 bits (566), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 144/363 (39%), Positives = 193/363 (53%), Gaps = 74/363 (20%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEV----------------- 1147
            +C  KY +AQ+EP  AVGA+ AQSIGEPGTQMTLKTFHFAG                   
Sbjct: 1052 SCLTKYKKAQVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIINA 1111

Query: 1148 ----------CE---------------------------YIEEVFVPDDSFILIKLDMDR 1170
                      CE                           YIEE +    ++I IK+D   
Sbjct: 1112 SKEISTPIITCELVNKEDVRAAQIVKGRVEKTFIKDIIYYIEEAWTGSVAYINIKIDFST 1171

Query: 1171 IRLLHLEVDIDSIRYCIE------------RTRGISGHLTVSGHSFLILKPKDSSKSFNS 1218
            I+ L LE+ +  I   I+            R+ G   H+ V   +      K    +  S
Sbjct: 1172 IQALQLELTLRDILNAIKKHKRFRSDDLKFRSFGSHIHIFVDQATTKTSLTKAEQAATGS 1231

Query: 1219 KMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 1274
              Y     +K+LLP++ + G    +RA+I  ++    T   LLVEG  LR  M T G+ G
Sbjct: 1232 DPYIRLKHLKRLLPTIQVLGHPQCSRAIIRTDETN--TTNTLLVEGYGLRACMTTDGIFG 1289

Query: 1275 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGI 1334
             +  +NN  E    LGIEAAR+TI+ EI  VM++  M ID RH  L+AD+MT KGEVLGI
Sbjct: 1290 TRTRTNNIMETKDVLGIEAARTTIVDEISDVMKD--MGIDPRHMQLLADVMTYKGEVLGI 1347

Query: 1335 TRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            TR GLAKM++SVL LASFE T+DHLFDA   G+TD + GVSECII+G  +++GTG ++++
Sbjct: 1348 TRFGLAKMRDSVLQLASFEKTADHLFDAGGAGRTDLVEGVSECIILGKSVSLGTGAMEMV 1407

Query: 1395 QAV 1397
            +A+
Sbjct: 1408 RAM 1410



 Score =  168 bits (426), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 103/268 (38%), Positives = 147/268 (54%), Gaps = 14/268 (5%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G +  +D V Q + +++  + L+  D  R    HG LD RMG + K   C TCG  L +C
Sbjct: 30  GVLASQDIVSQ-ALVEVSDRKLFDLDNDRAVARHGPLDGRMGISSKSGTCETCGGALQEC 88

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFG++ L LP FH+GYF+ VI ILQ ICK+  C+R+LL E +   F  ++R   +  L
Sbjct: 89  NGHFGHVRLVLPAFHVGYFKRVIGILQEICKD--CSRILLPENERRIFLKEMRRQGIDNL 146

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKYK----NRTKKKDAIVE 258
            R  + K+I +  +K   C  C  +NGVVKK G   LKI+H+K++    + + KK     
Sbjct: 147 RRMQINKRINDRCRKTRTCYVCHAVNGVVKKAGTSALKITHDKFRAFNASTSAKKVPPPS 206

Query: 259 DLLAE--YNEAVKFNPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKP 315
            L+ +  + EA + N +IE H  F  +Q  LNPL VL+LF  I  ED  LL +N E  +P
Sbjct: 207 KLVFDRSFEEAKRSNTDIEKH--FKKVQDDLNPLRVLKLFRRISDEDCELLGLNPEEVRP 264

Query: 316 SDLILTRLLVPPNCIRPSVISDLKSDND 343
              +   +  PP  IRPSV  +  S  D
Sbjct: 265 EMFLWQYIPAPPVSIRPSVGQEGASTED 292



 Score =  153 bits (386), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 102/250 (40%), Positives = 140/250 (56%), Gaps = 20/250 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIIT  L    D+  A+IVKGR+E+T + ++  YIEE +    
Sbjct: 1101 GVPRIKEIINASKEISTPIITCELVNKEDVRAAQIVKGRVEKTFIKDIIYYIEEAWTGSV 1160

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIE------------RTRGISGHLTVSGHSFLIL 871
            ++I IK+D   I+ L LE+ +  I   I+            R+ G   H+ V   +    
Sbjct: 1161 AYINIKIDFSTIQALQLELTLRDILNAIKKHKRFRSDDLKFRSFGSHIHIFVDQATTKTS 1220

Query: 872  KPKDSSKSFNSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927
              K    +  S  Y     +K+LLP++ + G    +RA+I  ++    T   LLVEG  L
Sbjct: 1221 LTKAEQAATGSDPYIRLKHLKRLLPTIQVLGHPQCSRAIIRTDETN--TTNTLLVEGYGL 1278

Query: 928  RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 987
            R  M T G+ G +  +NN  E    LGIEAAR+TI+ EI  VM++  M ID RH  L+AD
Sbjct: 1279 RACMTTDGIFGTRTRTNNIMETKDVLGIEAARTTIVDEISDVMKD--MGIDPRHMQLLAD 1336

Query: 988  LMTSKGEVLG 997
            +MT KGEVLG
Sbjct: 1337 VMTYKGEVLG 1346



 Score =  103 bits (256), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 45/59 (76%), Positives = 52/59 (88%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSFFSGL P+EFFFH + GREGL+DTAVKTAETGYM RRL+KSLEDL  +YD
Sbjct: 843 PAKGFVRNSFFSGLIPSEFFFHAISGREGLIDTAVKTAETGYMSRRLMKSLEDLSSRYD 901



 Score = 57.0 bits (136), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 25/51 (49%), Positives = 35/51 (68%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLI 72
           LM  K+NL TP+NGE +IAA QDFIT  YLL+ K+ F++R    +I   ++
Sbjct: 536 LMGVKNNLATPKNGEPIIAAIQDFITAAYLLSSKDNFYDRGSFTQICGYML 586



 Score = 45.4 bits (106), Expect = 0.22,   Method: Compositional matrix adjust.
 Identities = 19/41 (46%), Positives = 31/41 (75%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 708
            D  FDA   G+TD + GVSECII+G  +++GTG +++++A+
Sbjct: 1370 DHLFDAGGAGRTDLVEGVSECIILGKSVSLGTGAMEMVRAM 1410


>gi|330914134|ref|XP_003296505.1| hypothetical protein PTT_06631 [Pyrenophora teres f. teres 0-1]
 gi|311331266|gb|EFQ95369.1| hypothetical protein PTT_06631 [Pyrenophora teres f. teres 0-1]
          Length = 1472

 Score =  276 bits (706), Expect = 6e-71,   Method: Compositional matrix adjust.
 Identities = 138/279 (49%), Positives = 182/279 (65%), Gaps = 26/279 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++HRAK+ P RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 481 DGDIVLFNRQPSLHKLSILSHRAKIRPWRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 540

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EA                LM  K NL TP+NG  +IAA QDFIT  YLL+ KN FF+R
Sbjct: 541 RTEATE--------------LMGVKYNLATPKNGTPIIAAIQDFITAAYLLSNKNNFFDR 586

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
               +I + +            +       P V  +   +WTGKQ+F+L+++PN++C V 
Sbjct: 587 KTFCQIVNYMFNGEGAFDPDTGKKHPIDIPPPVVWKPQALWTGKQVFNLLMRPNKECRVL 646

Query: 521 ANLK--------TKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYIL 572
            NL+        T G+A   NE+    D+Y+++RNSE++ G MDK+T+G G K +VFY++
Sbjct: 647 INLEAACKQYKGTPGKAPDLNED----DAYLVIRNSEVMCGVMDKATVGDGKKDSVFYVM 702

Query: 573 LRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           +RDFG D AV  M RLS++++ +L N GFS+GI DVTPG
Sbjct: 703 MRDFGPDHAVQGMNRLSKLSARWLTNNGFSLGISDVTPG 741



 Score =  232 bits (591), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 172/510 (33%), Positives = 245/510 (48%), Gaps = 116/510 (22%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALS------------------------ 1032
            G   PV   R     +    + ++ SL+ QE+  ++                        
Sbjct: 949  GKAKPVHFDRTFSHAVTSTWNNAESSLTPQEVRDITEAKLNTERNRYPRYKLDGVTRLDY 1008

Query: 1033 ----NETLDSKEFLQD---TSENFVRDIKKFLEEFSKKESVT--SHQDKVSQPLREQILS 1083
                ++ +D KE L+D   T ++++ +  + LE+      V   S +D+   P   +  S
Sbjct: 1009 RDTTDDGIDQKESLRDFLDTVQDYIFNKAQKLEQTLTWLGVVQPSVKDRKQSPADAEKYS 1068

Query: 1084 HQDKIGHGRES--NPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTF 1141
              D I     S  + F + C       KY R++++P  AVGA+ AQSIGEPGTQMTLKTF
Sbjct: 1069 LSDGIAKISHSALDTFITLCLT-----KYHRSRVQPGHAVGAIGAQSIGEPGTQMTLKTF 1123

Query: 1142 HFAGEV---------------------------CE------------------------- 1149
            HFAG                             CE                         
Sbjct: 1124 HFAGVAGMSITQGVPRIKEIINASSTISTPVIDCELENKVSERVAREVKARVEKTYLRDV 1183

Query: 1150 --YIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTR----GISGHLTVSGHS 1203
              Y+E+V+ P+ +++ +++D D I+ L ++V    I   I   +    G +G     G  
Sbjct: 1184 IRYVEDVWHPEGAYVALRIDWDTIQKLFIDVKPHDIAAAINAHKPLKWGKAGAQVHIGQK 1243

Query: 1204 FLILKPKDSS-------------KSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEE---D 1247
             + +   D               K+F  ++ Q+K L+P VVIKG    +RAVI +E   +
Sbjct: 1244 LIRVDVPDPDATKKRPVKTSRNYKNFFERVQQVKALIPDVVIKGYPDCSRAVIKKETSPN 1303

Query: 1248 VEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVME 1307
             +G  + KLLVEG  LRD M T G+   K  SNN  EV   LGIEAAR+TI+ EI  VM 
Sbjct: 1304 AQGEYECKLLVEGYGLRDCMTTPGIVPYKTVSNNIMEVKTVLGIEAARATIVREIGSVMG 1363

Query: 1308 NHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQ 1367
            N  M ID RH  L+AD+MT KGEV GITR GL K ++SVL LASFE T DHLF+AA  G+
Sbjct: 1364 N--MDIDPRHMQLLADVMTFKGEVFGITRFGLQKTRDSVLQLASFEKTPDHLFEAAARGK 1421

Query: 1368 TDCISGVSECIIMGLPMNVGTGLIKLLQAV 1397
            TD I GVSECIIMG  + +GTG +++++ +
Sbjct: 1422 TDTIDGVSECIIMGQSVKLGTGSMQVVRPL 1451



 Score =  164 bits (415), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 106/254 (41%), Positives = 143/254 (56%), Gaps = 22/254 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS  ISTP+I   L+       AR VK R+E+T L +V  Y+E+V+ P+ 
Sbjct: 1136 GVPRIKEIINASSTISTPVIDCELENKVSERVAREVKARVEKTYLRDVIRYVEDVWHPEG 1195

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTR----GISGHLTVSGHSFLILKPKDSS-- 877
            +++ +++D D I+ L ++V    I   I   +    G +G     G   + +   D    
Sbjct: 1196 AYVALRIDWDTIQKLFIDVKPHDIAAAINAHKPLKWGKAGAQVHIGQKLIRVDVPDPDAT 1255

Query: 878  -----------KSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEE---DVEGVTKYKLLVE 923
                       K+F  ++ Q+K L+P VVIKG    +RAVI +E   + +G  + KLLVE
Sbjct: 1256 KKRPVKTSRNYKNFFERVQQVKALIPDVVIKGYPDCSRAVIKKETSPNAQGEYECKLLVE 1315

Query: 924  GDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPM 983
            G  LRD M T G+   K  SNN  EV   LGIEAAR+TI+ EI  VM N  M ID RH  
Sbjct: 1316 GYGLRDCMTTPGIVPYKTVSNNIMEVKTVLGIEAARATIVREIGSVMGN--MDIDPRHMQ 1373

Query: 984  LVADLMTSKGEVLG 997
            L+AD+MT KGEV G
Sbjct: 1374 LLADVMTFKGEVFG 1387



 Score =  153 bits (387), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 94/273 (34%), Positives = 146/273 (53%), Gaps = 16/273 (5%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQ----RTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G  + +D V Q + +++  +N+Y   P     RT   +G +D  MG + K+  C TCG+ 
Sbjct: 26  GIYSNQDIVNQ-AVLEVSDRNVYDLQPAANNTRTLTANGPMDTLMGISSKQGTCGTCGEG 84

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
           L  C GHFG+I L LP FH+GY + +I +L  ICK+  C+RVLL E +   +   +R P 
Sbjct: 85  LDKCNGHFGHIKLALPAFHVGYLKHIIEVLNCICKD--CSRVLLDEVERRRYLRSMRRPD 142

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKYK--NR----TKK 252
           +  L + ++ KKI++  +K   CP+C  + G V+K     LKI H +Y   NR    T+K
Sbjct: 143 MDTLRKGAVTKKIIDDCRKKKTCPYCNALQGTVRKVPGHPLKIIHNRYDAFNRSTAKTRK 202

Query: 253 KDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL 312
                 +    ++ A   NP+++ H K   +  ++PL  L LF+ I  ED  LL M  E 
Sbjct: 203 PPPGKLEFDQSFDTAKAANPDLDKHMKKA-VDDMHPLRTLNLFKKISPEDCELLAMVPED 261

Query: 313 SKPSDLILTRLLVPPNCIRPSVISDLKSDNDVV 345
           ++P  LI   + VPP  +RPSV+ +  +  D V
Sbjct: 262 ARPEMLIWEYMPVPPVALRPSVMQEGGATEDDV 294



 Score =  103 bits (258), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 47/57 (82%), Positives = 50/57 (87%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV NSFFSGLTP+EF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 866 KGFVSNSFFSGLTPSEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSAQYD 922



 Score = 59.3 bits (142), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 28/57 (49%), Positives = 35/57 (61%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVF 78
           LM  K NL TP+NG  +IAA QDFIT  YLL+ KN FF+R    +I + +  G   F
Sbjct: 547 LMGVKYNLATPKNGTPIIAAIQDFITAAYLLSNKNNFFDRKTFCQIVNYMFNGEGAF 603



 Score = 45.1 bits (105), Expect = 0.31,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 30/41 (73%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 708
            D  F+AA  G+TD I GVSECIIMG  + +GTG +++++ +
Sbjct: 1411 DHLFEAAARGKTDTIDGVSECIIMGQSVKLGTGSMQVVRPL 1451


>gi|258564805|ref|XP_002583147.1| DNA-directed RNA polymerase III largest subunit [Uncinocarpus
           reesii 1704]
 gi|237906848|gb|EEP81249.1| DNA-directed RNA polymerase III largest subunit [Uncinocarpus
           reesii 1704]
          Length = 1435

 Score =  276 bits (706), Expect = 7e-71,   Method: Compositional matrix adjust.
 Identities = 136/280 (48%), Positives = 183/280 (65%), Gaps = 28/280 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++H  KV PHRTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 470 DGDIVLFNRQPSLHKLSILSHFVKVRPHRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 529

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL TP+NGE +IAA QDFIT  YLL+ K+ F++R
Sbjct: 530 RAEAME--------------LMGVKNNLATPKNGEPIIAAIQDFITAAYLLSSKDNFYDR 575

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              +     ++   +               P   ++  ++WTGKQ+F+++++P++D PV 
Sbjct: 576 KTFLLYCGYMLEPGTKF----------DLPPPAVLKPQMLWTGKQVFNVMMRPSKDSPVL 625

Query: 521 ANLKTKGRAYTANE----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL    R ++A +    +    D ++ +RNSE++ G MDKST+GSG K +VFY++LRDF
Sbjct: 626 LNLDAACREFSAPKGTPRDLDADDGWLCIRNSEIMCGLMDKSTIGSGKKDSVFYVMLRDF 685

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           G  VA  AM RLSR+++ +L N GFSIGI DV PG   +Q
Sbjct: 686 GPRVAAEAMNRLSRLSARWLTNMGFSIGITDVYPGDALLQ 725



 Score =  222 bits (565), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 163/488 (33%), Positives = 237/488 (48%), Gaps = 104/488 (21%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSK--------------EFL 1042
            G   PV   R      A   S+ D  L   EI++L  + L ++              +++
Sbjct: 928  GKAKPVHFDRTFTHAEATTYSKDDQGLPCSEIMSLCRKLLSAERSKLNRFDLLGNGLDYM 987

Query: 1043 Q---------DTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRE 1093
                      +++ +F++ I+ ++   +K+    +  D +  P  +  +SH  K+   + 
Sbjct: 988  DRSDHGIDQLESNRDFLQSIEDYVWSKTKQLQPVTGTD-LDTPDGQMAISHTAKLS-AKT 1045

Query: 1094 SNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEV------ 1147
               F ++C       KY +AQ+EP  AVGA+ AQSIGEPGTQMTLKTFHFAG        
Sbjct: 1046 LTAFVTSCLT-----KYKKAQVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQ 1100

Query: 1148 ---------------------CE---------------------------YIEEVFVPDD 1159
                                 CE                           YIEE +    
Sbjct: 1101 GVPRIKEIINASKEISTPIITCELVNKEDLRAAQIVKGRVEKTFIKDIIYYIEEAWTGSV 1160

Query: 1160 SFILIKLDMDRIRLLHLEVDIDSIRYCIE------------RTRGISGHLTVSGHSFLIL 1207
            ++I IK+D   I+ L LE+ +  I   I+            R+ G   H+ V   +   L
Sbjct: 1161 AYINIKIDFSAIQALQLELTLRDILNAIKTHKRFKSDDLKFRSFGSHIHIFVDQTAAKTL 1220

Query: 1208 KPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVM 1267
               + + + +    ++K L     + G    +RAVI  ++    TK  LLVEG  LR  M
Sbjct: 1221 SKTEQTATGSDPYIRLKHL----KLLGYPQCSRAVIRTDETN--TKNTLLVEGYGLRACM 1274

Query: 1268 ATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTS 1327
             T G+ G +  +NN  E    LGIEAAR+TI+ EI  VM++  M ID RH  L+AD+MT 
Sbjct: 1275 TTDGIWGTRTRTNNIMETKDVLGIEAARTTIVDEISEVMKD--MRIDPRHMQLLADVMTY 1332

Query: 1328 KGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVG 1387
            KGEVLGITR GLAKM++SVL LASFE T+DHLFDA   G+TD + GVSECIIMG  +++G
Sbjct: 1333 KGEVLGITRFGLAKMRDSVLQLASFEKTADHLFDAGGAGRTDLVEGVSECIIMGKSVSLG 1392

Query: 1388 TGLIKLLQ 1395
            TG +++++
Sbjct: 1393 TGAMEIVR 1400



 Score =  178 bits (452), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 105/268 (39%), Positives = 149/268 (55%), Gaps = 14/268 (5%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G +  +D V Q +H+++  + L+  D  R    HG LD RMG + K   C TCG  L +C
Sbjct: 30  GVLASQDIVSQ-AHVEVSDRKLFDLDNDRAVARHGPLDGRMGISSKSGTCETCGGALQEC 88

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFG++ L LP FH+GYF+ VI+ILQ ICK+  C+R+LL E +   F   +R P +  L
Sbjct: 89  NGHFGHVRLVLPAFHVGYFKRVISILQEICKD--CSRILLPENERRSFLRDMRRPGIDNL 146

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKYK----NRTKKKDAIVE 258
            R  + K+I E  +K   C  C  +NGVVKK G   LKI+H+K++    + + KK     
Sbjct: 147 RRMQINKRINERCRKTRTCYTCNAVNGVVKKAGTSALKITHDKFRAFNASTSAKKIPPAS 206

Query: 259 DLLAE--YNEAVKFNPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKP 315
            L+ +  + EA + N +IE H  F  +Q  LNPL VL+LF  I  ED  LL +N +  +P
Sbjct: 207 KLVFDQSFEEAKRSNTDIEKH--FKKVQDDLNPLRVLKLFRRISNEDCELLGLNPKEVRP 264

Query: 316 SDLILTRLLVPPNCIRPSVISDLKSDND 343
              +   +  PP  IRPSV  +  S  D
Sbjct: 265 EMFLWQFIPAPPVSIRPSVGQEGASTED 292



 Score =  150 bits (379), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 101/246 (41%), Positives = 138/246 (56%), Gaps = 20/246 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIIT  L    DL  A+IVKGR+E+T + ++  YIEE +    
Sbjct: 1101 GVPRIKEIINASKEISTPIITCELVNKEDLRAAQIVKGRVEKTFIKDIIYYIEEAWTGSV 1160

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIE------------RTRGISGHLTVSGHSFLIL 871
            ++I IK+D   I+ L LE+ +  I   I+            R+ G   H+ V   +   L
Sbjct: 1161 AYINIKIDFSAIQALQLELTLRDILNAIKTHKRFKSDDLKFRSFGSHIHIFVDQTAAKTL 1220

Query: 872  KPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVM 931
               + + + +    ++K L     + G    +RAVI  ++    TK  LLVEG  LR  M
Sbjct: 1221 SKTEQTATGSDPYIRLKHL----KLLGYPQCSRAVIRTDETN--TKNTLLVEGYGLRACM 1274

Query: 932  ATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTS 991
             T G+ G +  +NN  E    LGIEAAR+TI+ EI  VM++  M ID RH  L+AD+MT 
Sbjct: 1275 TTDGIWGTRTRTNNIMETKDVLGIEAARTTIVDEISEVMKD--MRIDPRHMQLLADVMTY 1332

Query: 992  KGEVLG 997
            KGEVLG
Sbjct: 1333 KGEVLG 1338



 Score =  100 bits (249), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 44/58 (75%), Positives = 51/58 (87%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV+NSFFSGLTP+E FFH + GREGL+DTAVKTAETGYM RRL+KSLEDL  +YD
Sbjct: 844 AKGFVRNSFFSGLTPSELFFHAISGREGLIDTAVKTAETGYMSRRLMKSLEDLSCRYD 901



 Score = 55.5 bits (132), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/40 (60%), Positives = 31/40 (77%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           LM  K+NL TP+NGE +IAA QDFIT  YLL+ K+ F++R
Sbjct: 536 LMGVKNNLATPKNGEPIIAAIQDFITAAYLLSSKDNFYDR 575



 Score = 44.7 bits (104), Expect = 0.37,   Method: Compositional matrix adjust.
 Identities = 19/39 (48%), Positives = 29/39 (74%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  FDA   G+TD + GVSECIIMG  +++GTG +++++
Sbjct: 1362 DHLFDAGGAGRTDLVEGVSECIIMGKSVSLGTGAMEIVR 1400


>gi|239614510|gb|EEQ91497.1| DNA-directed RNA polymerase III largest subunit [Ajellomyces
           dermatitidis ER-3]
          Length = 1456

 Score =  276 bits (705), Expect = 7e-71,   Method: Compositional matrix adjust.
 Identities = 138/281 (49%), Positives = 185/281 (65%), Gaps = 30/281 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++H AKV PHRTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 470 DGDIVLFNRQPSLHKLSILSHFAKVRPHRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 529

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL TP+NGE +I+A QDFIT  Y+L+ K+ F++R
Sbjct: 530 RAEAME--------------LMGVKNNLATPKNGEPIISAIQDFITAAYMLSSKDVFYDR 575

Query: 461 AQTMRIASTLI-ADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
                I   ++ +DT        RF      P   ++  ++WTGKQIF+++++PN+  PV
Sbjct: 576 KAFTHICLYMLQSDT--------RF---DLPPPSVIKPQMLWTGKQIFNVLMRPNKQSPV 624

Query: 520 NANLKTKGRAYTANE----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
             NL    R + A +    +    D ++ +RNSE++ G MDKST+GSG K +VFY++LRD
Sbjct: 625 LVNLDAACRGFKAPKGTPRDLDANDGWLCIRNSEVMCGVMDKSTIGSGKKDSVFYVMLRD 684

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           FG +VA   M RLSR+++ +  N GFSIGI DV PG   ++
Sbjct: 685 FGPEVAAEGMNRLSRLSARWFTNMGFSIGITDVYPGDKLLE 725



 Score =  192 bits (488), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 132/363 (36%), Positives = 185/363 (50%), Gaps = 74/363 (20%)

Query: 1105 ACREKYVRAQIEPATAVGAL---------------------------------------A 1125
            AC  KY RAQ+EP  AVGA+                                       A
Sbjct: 1049 ACLTKYKRAQVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIINA 1108

Query: 1126 AQSIGEPGTQMTLKTFH---------------FAGEVCEYIEEVFVPDDSFILIKLDMDR 1170
            ++ I  P     L   H               F  ++  YIEE +  ++++I IK+D   
Sbjct: 1109 SKEISTPVITCELVNKHDLRAAQIVKGRVEKTFIRDIIYYIEEDWTGNEAYINIKIDFST 1168

Query: 1171 IRLLHLEVDIDSIRYCIE------------RTRGISGHLTVSGHSFLILKPKDSSKSFNS 1218
            I+ L LE+++  I   I+            R+ G   H+ V  H+      K    +  +
Sbjct: 1169 IQNLQLELNLQDILVAIKKHKRFKSADLKFRSFGSHIHIFVDQHATRTALSKTEEAATGA 1228

Query: 1219 KMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 1274
              Y     +K+L+P++ + G     RA+I  ++    T   LLVEG  LRD M T G+ G
Sbjct: 1229 DPYIRLKHLKRLIPNIQVIGHPQCARAIIRTDETN--TTNTLLVEGYGLRDCMTTDGING 1286

Query: 1275 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGI 1334
                +NN  E    LGIEAAR+TI+ EI  VM++  MSID RH  L+AD+MT KGEVLGI
Sbjct: 1287 HHTRTNNIMEARTVLGIEAARTTIVDEISEVMKD--MSIDPRHMQLLADVMTYKGEVLGI 1344

Query: 1335 TRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            TR GLAKM++SVL LASFE T+DHLFDA   G+TD I GVSECII+G  +++GTG ++++
Sbjct: 1345 TRFGLAKMRDSVLQLASFEKTADHLFDAGGAGRTDLIEGVSECIIVGKSVSLGTGAMEVV 1404

Query: 1395 QAV 1397
            +A+
Sbjct: 1405 RAL 1407



 Score =  182 bits (462), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 105/269 (39%), Positives = 147/269 (54%), Gaps = 16/269 (5%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G ++ +D V Q + +++  + L+  +  R   PHG LD RMG + K   C TCG  L  C
Sbjct: 30  GVLSTQDIVSQ-AVVEVSDRKLFDLENDRAVAPHGPLDGRMGISSKSGTCDTCGGALQVC 88

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFG++ L LP FH+GYF+ VI+ILQ ICK   C+ +LL E +   F  +LR P +  L
Sbjct: 89  SGHFGHVRLVLPAFHVGYFKRVISILQEICKE--CSHILLPENERRAFLRELRRPGIDNL 146

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKYK--------NRTKKKD 254
            R  + KKI E  +K   C  C  +NGVVKK G   LKI+HEK++         +     
Sbjct: 147 RRMQIAKKINERCRKTRTCYRCNAVNGVVKKAGTSALKITHEKFRAFNASSSVKKIPPPS 206

Query: 255 AIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSK 314
            +V D    + EA K NP+IE H K      L+PL VL+LF ++  +D  LL +N E ++
Sbjct: 207 KVVFD--QSFEEAKKSNPDIEKHFKKAH-DDLHPLRVLKLFRSVSDKDCELLGLNPEEAR 263

Query: 315 PSDLILTRLLVPPNCIRPSVISDLKSDND 343
           P   +   +  PP CIRPSV  +  S  D
Sbjct: 264 PEVFLWQYIPAPPVCIRPSVGQEAASTED 292



 Score =  160 bits (406), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 103/250 (41%), Positives = 144/250 (57%), Gaps = 20/250 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+IT  L    DL  A+IVKGR+E+T + ++  YIEE +  ++
Sbjct: 1098 GVPRIKEIINASKEISTPVITCELVNKHDLRAAQIVKGRVEKTFIRDIIYYIEEDWTGNE 1157

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIE------------RTRGISGHLTVSGHSFLIL 871
            ++I IK+D   I+ L LE+++  I   I+            R+ G   H+ V  H+    
Sbjct: 1158 AYINIKIDFSTIQNLQLELNLQDILVAIKKHKRFKSADLKFRSFGSHIHIFVDQHATRTA 1217

Query: 872  KPKDSSKSFNSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927
              K    +  +  Y     +K+L+P++ + G     RA+I  ++    T   LLVEG  L
Sbjct: 1218 LSKTEEAATGADPYIRLKHLKRLIPNIQVIGHPQCARAIIRTDETN--TTNTLLVEGYGL 1275

Query: 928  RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 987
            RD M T G+ G    +NN  E    LGIEAAR+TI+ EI  VM++  MSID RH  L+AD
Sbjct: 1276 RDCMTTDGINGHHTRTNNIMEARTVLGIEAARTTIVDEISEVMKD--MSIDPRHMQLLAD 1333

Query: 988  LMTSKGEVLG 997
            +MT KGEVLG
Sbjct: 1334 VMTYKGEVLG 1343



 Score =  104 bits (260), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 47/59 (79%), Positives = 52/59 (88%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSFFSGLTPTEF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  +YD
Sbjct: 843 PAKGFVRNSFFSGLTPTEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSSRYD 901



 Score = 53.9 bits (128), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 22/40 (55%), Positives = 31/40 (77%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           LM  K+NL TP+NGE +I+A QDFIT  Y+L+ K+ F++R
Sbjct: 536 LMGVKNNLATPKNGEPIISAIQDFITAAYMLSSKDVFYDR 575



 Score = 45.4 bits (106), Expect = 0.26,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 31/41 (75%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 708
            D  FDA   G+TD I GVSECII+G  +++GTG +++++A+
Sbjct: 1367 DHLFDAGGAGRTDLIEGVSECIIVGKSVSLGTGAMEVVRAL 1407


>gi|444314063|ref|XP_004177689.1| hypothetical protein TBLA_0A03720 [Tetrapisispora blattae CBS 6284]
 gi|387510728|emb|CCH58170.1| hypothetical protein TBLA_0A03720 [Tetrapisispora blattae CBS 6284]
          Length = 1458

 Score =  276 bits (705), Expect = 7e-71,   Method: Compositional matrix adjust.
 Identities = 138/276 (50%), Positives = 185/276 (67%), Gaps = 30/276 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH+LSI++H AK+ P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 467 DGDVVLFNRQPSLHRLSILSHYAKIRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 526

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+R
Sbjct: 527 RAEAIN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDR 572

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A   ++ S +       C    +F      P   ++   +WTGKQ+FSL++KPN + PV 
Sbjct: 573 ATFTQLLSMM-------CDGNLQFDIP---PPAIMKPCYLWTGKQLFSLLIKPNSNSPVV 622

Query: 521 ANLKTKGRAY------TANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLR 574
            N+  K + +      +   E    D +V++R S++L+G MDKS LG G K +VFY +LR
Sbjct: 623 INVDAKNKVFKPPKDKSLPSEMSPNDGFVVIRGSQILSGVMDKSVLGDGKKHSVFYTILR 682

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           D+G   A TAM R++++ + +L NRGFSIGI DVTP
Sbjct: 683 DYGPQEAATAMNRMAKLCARFLGNRGFSIGINDVTP 718



 Score =  242 bits (618), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 152/358 (42%), Positives = 201/358 (56%), Gaps = 74/358 (20%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG----------------------- 1145
            KY RA++EP TAVGA+ AQSIGEPGTQMTLKTFHFAG                       
Sbjct: 1076 KYRRARVEPGTAVGAIGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIINASKVI 1135

Query: 1146 -------------------EVCEYIEEVFVPD------------DSFILIKLDMDRIRLL 1174
                                V   IE+  + D            +S++ +K+D+  I  L
Sbjct: 1136 STPIINAVLVNENDERAARVVKGRIEKTLLSDVAYYIQDCYKDNNSYLEVKIDLGTIEKL 1195

Query: 1175 HLEVDIDSIRYCIERTRGIS---GHLTVSGHS--FLILKPKDSSKSF---------NSKM 1220
             LE+ +  I   I R   +    G +    +S   + ++P+ S             N+  
Sbjct: 1196 QLELTMSDIADAIARAPKLKIQFGDVVPESNSKIRISVRPEASVSKISASAKEPLENNVF 1255

Query: 1221 YQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 1277
            Y+M+ L   LPS+V+KG+  I RAVI+  D     K +LLVEG  LRDVM T GV G K 
Sbjct: 1256 YRMQHLRRALPSIVVKGLPDIARAVINIRD---NGKRELLVEGYGLRDVMCTDGVIGSKT 1312

Query: 1278 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRH 1337
            ++N+  EV   LGIEAAR++I+ EI   M NHGMS+D RH  L+ D+MT KGEVLGITR 
Sbjct: 1313 TTNHVLEVNSVLGIEAARASIIGEIDYTMSNHGMSVDPRHIQLLGDVMTYKGEVLGITRF 1372

Query: 1338 GLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 1395
            GL+KM++SVL LASFE T+DHLFDAAFY + D + GVSECII+G  M++GTG  K+++
Sbjct: 1373 GLSKMRDSVLQLASFEKTTDHLFDAAFYMKKDAVEGVSECIILGQTMSIGTGSFKVVK 1430



 Score =  187 bits (476), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 103/248 (41%), Positives = 142/248 (57%), Gaps = 11/248 (4%)

Query: 96  QSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPL 155
           QS + I +++LY  +  R P   G LD+RMG +     C TC  NL+ C GHFG+I L L
Sbjct: 29  QSEVAITTRDLYDLEHGRAPKKSGALDQRMGVSSSNLECETCHGNLASCHGHFGHIKLAL 88

Query: 156 PVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILE 215
           PVFH+GYF+  I ILQ+ICK  +CA VLL +E    F ++LR P +  L R  + KKIL+
Sbjct: 89  PVFHVGYFKATIQILQAICK--SCAAVLLSDEDKRNFLSELRRPGIDNLKRMGILKKILD 146

Query: 216 TTKKVSVCPHCGEINGVVKKCGL------LKISHEKYKNRTKKKDAIVEDLLAEYNEAVK 269
             KK   C HCG +NGVVKK         LKI H+ ++   KK+    +  + ++ E + 
Sbjct: 147 QCKKQRRCLHCGGLNGVVKKAAAGGGSASLKIIHDTFRWVGKKQTPEKDSWVGDWQEVLS 206

Query: 270 FNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMN--AELSKPSDLILTRLLVPP 327
            NPE+E   K  +   LNPL+ L LF+ I  ED  LL ++  ++  +P   I   L  PP
Sbjct: 207 HNPELERFVKRAM-DDLNPLKTLNLFKQIKPEDCELLGIDSTSKSGRPETYIWRYLPAPP 265

Query: 328 NCIRPSVI 335
            CIRPSV+
Sbjct: 266 VCIRPSVM 273



 Score =  179 bits (455), Expect = 7e-42,   Method: Compositional matrix adjust.
 Identities = 111/251 (44%), Positives = 153/251 (60%), Gaps = 20/251 (7%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII A L  + D   AR+VKGR+E+T L +V  YI++ +  ++
Sbjct: 1121 GVPRIKEIINASKVISTPIINAVLVNENDERAARVVKGRIEKTLLSDVAYYIQDCYKDNN 1180

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHS--FLILKPKDSSK 878
            S++ +K+D+  I  L LE+ +  I   I R   +    G +    +S   + ++P+ S  
Sbjct: 1181 SYLEVKIDLGTIEKLQLELTMSDIADAIARAPKLKIQFGDVVPESNSKIRISVRPEASVS 1240

Query: 879  SF---------NSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDN 926
                       N+  Y+M+ L   LPS+V+KG+  I RAVI+  D     K +LLVEG  
Sbjct: 1241 KISASAKEPLENNVFYRMQHLRRALPSIVVKGLPDIARAVINIRDN---GKRELLVEGYG 1297

Query: 927  LRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVA 986
            LRDVM T GV G K ++N+  EV   LGIEAAR++I+ EI   M NHGMS+D RH  L+ 
Sbjct: 1298 LRDVMCTDGVIGSKTTTNHVLEVNSVLGIEAARASIIGEIDYTMSNHGMSVDPRHIQLLG 1357

Query: 987  DLMTSKGEVLG 997
            D+MT KGEVLG
Sbjct: 1358 DVMTYKGEVLG 1368



 Score = 99.8 bits (247), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/57 (77%), Positives = 50/57 (87%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NSF+SGL+P EF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 844 KGFVRNSFYSGLSPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSCQYD 900



 Score = 63.5 bits (153), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 29/57 (50%), Positives = 42/57 (73%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVF 78
           LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+RA   ++ S +  G   F
Sbjct: 533 LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDRATFTQLLSMMCDGNLQF 589



 Score = 50.1 bits (118), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 21/39 (53%), Positives = 29/39 (74%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  FDAAFY + D + GVSECII+G  M++GTG  K+++
Sbjct: 1392 DHLFDAAFYMKKDAVEGVSECIILGQTMSIGTGSFKVVK 1430


>gi|67524109|ref|XP_660116.1| hypothetical protein AN2512.2 [Aspergillus nidulans FGSC A4]
 gi|40744841|gb|EAA63997.1| hypothetical protein AN2512.2 [Aspergillus nidulans FGSC A4]
          Length = 2092

 Score =  276 bits (705), Expect = 8e-71,   Method: Compositional matrix adjust.
 Identities = 140/282 (49%), Positives = 184/282 (65%), Gaps = 29/282 (10%)

Query: 341  DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
            D D+VLFNRQPSLHKLSI++H AKV PHRTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 1117 DGDIVLFNRQPSLHKLSILSHFAKVRPHRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 1176

Query: 401  RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
            RAEA+               LM  K+NL TP+NGE +I A QDFI+  YLL+ K+ FF+R
Sbjct: 1177 RAEAME--------------LMGVKNNLATPKNGEPIIGAIQDFISAAYLLSSKDNFFDR 1222

Query: 461  AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                +I   ++       G   RF      P VF +  ++WTGKQ+F+++++PN+D PV 
Sbjct: 1223 RSFTQICLYML-------GPQTRFDLPP--PAVF-KPQMLWTGKQVFNILMRPNKDDPVL 1272

Query: 521  ANLKTKGRAYTANE-----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
             NL    + +   +     +    DS++++RNSE++ G MDKST+GSG K NVFYI+LRD
Sbjct: 1273 VNLDAACKQFKPPKGNQPRDLDPNDSWLVVRNSEVMCGVMDKSTVGSGKKDNVFYIMLRD 1332

Query: 576  FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
            FG   A   M RLS++++ +  N GFSIGI DV P    VQ+
Sbjct: 1333 FGPAAAAEGMNRLSKLSARWFSNMGFSIGITDVYPSDRLVQS 1374



 Score =  224 bits (570), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 168/507 (33%), Positives = 251/507 (49%), Gaps = 103/507 (20%)

Query: 970  MENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDPSLSAQEIL 1029
            ME     + F    + A+  T K E   + +P E+  + +++++K  ++    L+  +++
Sbjct: 1574 MEGKAKPVHFDRTFIHAETTTYKNEER-SLSPAEIMEVCEEMLSKERAK----LARYDLM 1628

Query: 1030 ALSNETLDSKEFLQD---TSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQI---LS 1083
                + +D  +   D   ++ +F+  I+++++  +K + + S     S P  E+    L+
Sbjct: 1629 GAELDYMDRSDHGVDQFESARDFLDSIQQYVQ--TKADKLISRGGD-SDPSDERTIKGLN 1685

Query: 1084 HQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHF 1143
            H  K+   R    F + C       KY +AQ+EP  AVGA+ AQSIGEPGTQMTLKTFHF
Sbjct: 1686 HTGKLTE-RTLRTFIAECLM-----KYKKAQVEPGHAVGAVGAQSIGEPGTQMTLKTFHF 1739

Query: 1144 AGEV---------------------------CE--------------------------- 1149
            AG                             CE                           
Sbjct: 1740 AGVAGMSITQGVPRIKEIINASKEISTPVISCELVEKRNIVAARMAKGRIEKTFLRDIIH 1799

Query: 1150 YIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIE----------RTRGISGHLTV 1199
            Y+ E +   ++++ +K++ D I  L L++ +  IR  IE          + R    H+  
Sbjct: 1800 YVRETWTGKEAYLTVKINWDTISALELDLTVGKIRQAIENHRRFKSEDLKLRSTRSHI-- 1857

Query: 1200 SGHSFLILKPKDSSKSFNSKMYQMKQ-----------LLPSVVIKGVQGINRAVIHEEDV 1248
              H  + L P    K   +++                LLP + + G    NRA+I  +D 
Sbjct: 1858 --HIHIDLDPASKEKLSKTEIAATSSDPFLRLKALKRLLPDIQVLGHPQANRAIIRTDDK 1915

Query: 1249 EGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMEN 1308
                   LLVEG  LR  M T G+ G++  SNN  E  + LGIEAARSTI+ EI  VM++
Sbjct: 1916 SDTN--TLLVEGYGLRQCMNTVGIDGLRTRSNNVMETREVLGIEAARSTIIQEISEVMKD 1973

Query: 1309 HGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQT 1368
              M ID RH  L+AD+MT KGEVLGITR GLAKM++SVL LASFE T+DHLFDA   G+T
Sbjct: 1974 --MDIDPRHMQLLADVMTYKGEVLGITRFGLAKMRDSVLQLASFEKTADHLFDAGGAGRT 2031

Query: 1369 DCISGVSECIIMGLPMNVGTGLIKLLQ 1395
            D I GVSECIIMG  +++GTG +++++
Sbjct: 2032 DLIEGVSECIIMGKTVSLGTGAMEVVR 2058



 Score =  174 bits (441), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 101/267 (37%), Positives = 143/267 (53%), Gaps = 15/267 (5%)

Query: 87  VTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVG 146
           V   D +  Q  +++  +  +  +  R+ +P+G LD RMG + K + C TCG  L  C G
Sbjct: 678 VLSNDDIVSQGVVEVSDRKFFNLENDRSIVPNGPLDARMGISNKTSTCQTCGGALQVCNG 737

Query: 147 HFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVR 206
           HFG++ L LP FH+GYF+ VI+ILQ ICK   C+ +LL E +   F  ++R P L  L R
Sbjct: 738 HFGHVRLVLPAFHVGYFKRVISILQEICKE--CSHILLPEAERRAFLREMRRPRLDNLRR 795

Query: 207 KSLKKKILETTKKVSVCPHCGEINGVVKKCGL--LKISHEKYKNRTKKKDA--------I 256
             + K++ +  +K   C +CG +NGVVKK G   LKI+H+K++       A        I
Sbjct: 796 MQIAKRVNDRCRKTRTCENCGAVNGVVKKTGTSSLKITHDKFRAFNASTSAKKIPPPSKI 855

Query: 257 VEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPS 316
           V D   E  EA   NPE+E H K      LN L VL LF+ I   D  LL ++ + ++P 
Sbjct: 856 VFDRSLE--EARSSNPEVEKHHKKAQ-DDLNALRVLNLFKRISDSDCELLGLDPKEARPE 912

Query: 317 DLILTRLLVPPNCIRPSVISDLKSDND 343
             +   +  PP CIRPSV  D  S  D
Sbjct: 913 MFLWQFIPAPPVCIRPSVGQDASSTED 939



 Score =  150 bits (380), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 97/255 (38%), Positives = 139/255 (54%), Gaps = 29/255 (11%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+I+  L +  ++  AR+ KGR+E+T L ++  Y+ E +   +
Sbjct: 1750 GVPRIKEIINASKEISTPVISCELVEKRNIVAARMAKGRIEKTFLRDIIHYVRETWTGKE 1809

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIE----------RTRGISGHLTVSGHSFLILKP 873
            +++ +K++ D I  L L++ +  IR  IE          + R    H+    H  + L P
Sbjct: 1810 AYLTVKINWDTISALELDLTVGKIRQAIENHRRFKSEDLKLRSTRSHI----HIHIDLDP 1865

Query: 874  KDSSKSFNSKMYQMKQ-----------LLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLV 922
                K   +++                LLP + + G    NRA+I  +D        LLV
Sbjct: 1866 ASKEKLSKTEIAATSSDPFLRLKALKRLLPDIQVLGHPQANRAIIRTDDKSDTN--TLLV 1923

Query: 923  EGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHP 982
            EG  LR  M T G+ G++  SNN  E  + LGIEAARSTI+ EI  VM++  M ID RH 
Sbjct: 1924 EGYGLRQCMNTVGIDGLRTRSNNVMETREVLGIEAARSTIIQEISEVMKD--MDIDPRHM 1981

Query: 983  MLVADLMTSKGEVLG 997
             L+AD+MT KGEVLG
Sbjct: 1982 QLLADVMTYKGEVLG 1996



 Score =  100 bits (250), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 46/59 (77%), Positives = 49/59 (83%)

Query: 610  PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            P +GFV+NSFFSGL P EF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL   YD
Sbjct: 1491 PSKGFVRNSFFSGLLPYEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSTGYD 1549



 Score = 54.7 bits (130), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 25/57 (43%), Positives = 36/57 (63%)

Query: 22   LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVF 78
            LM  K+NL TP+NGE +I A QDFI+  YLL+ K+ FF+R    +I   ++  +  F
Sbjct: 1183 LMGVKNNLATPKNGEPIIGAIQDFISAAYLLSSKDNFFDRRSFTQICLYMLGPQTRF 1239



 Score = 45.1 bits (105), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 20/39 (51%), Positives = 29/39 (74%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  FDA   G+TD I GVSECIIMG  +++GTG +++++
Sbjct: 2020 DHLFDAGGAGRTDLIEGVSECIIMGKTVSLGTGAMEVVR 2058


>gi|261196045|ref|XP_002624426.1| DNA-directed RNA polymerase III [Ajellomyces dermatitidis SLH14081]
 gi|239587559|gb|EEQ70202.1| DNA-directed RNA polymerase III [Ajellomyces dermatitidis SLH14081]
          Length = 1456

 Score =  276 bits (705), Expect = 8e-71,   Method: Compositional matrix adjust.
 Identities = 138/281 (49%), Positives = 185/281 (65%), Gaps = 30/281 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++H AKV PHRTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 470 DGDIVLFNRQPSLHKLSILSHFAKVRPHRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 529

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL TP+NGE +I+A QDFIT  Y+L+ K+ F++R
Sbjct: 530 RAEAME--------------LMGVKNNLATPKNGEPIISAIQDFITAAYMLSSKDVFYDR 575

Query: 461 AQTMRIASTLI-ADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
                I   ++ +DT        RF      P   ++  ++WTGKQIF+++++PN+  PV
Sbjct: 576 KAFTHICLYMLQSDT--------RF---DLPPPSVIKPQMLWTGKQIFNVLMRPNKQSPV 624

Query: 520 NANLKTKGRAYTANE----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
             NL    R + A +    +    D ++ +RNSE++ G MDKST+GSG K +VFY++LRD
Sbjct: 625 LVNLDAACRGFKAPKGTPRDLDANDGWLCIRNSEVMCGVMDKSTIGSGKKDSVFYVMLRD 684

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           FG +VA   M RLSR+++ +  N GFSIGI DV PG   ++
Sbjct: 685 FGPEVAAEGMNRLSRLSARWFTNMGFSIGITDVYPGDKLLE 725



 Score =  192 bits (488), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 132/363 (36%), Positives = 185/363 (50%), Gaps = 74/363 (20%)

Query: 1105 ACREKYVRAQIEPATAVGAL---------------------------------------A 1125
            AC  KY RAQ+EP  AVGA+                                       A
Sbjct: 1049 ACLTKYKRAQVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIINA 1108

Query: 1126 AQSIGEPGTQMTLKTFH---------------FAGEVCEYIEEVFVPDDSFILIKLDMDR 1170
            ++ I  P     L   H               F  ++  YIEE +  ++++I IK+D   
Sbjct: 1109 SKEISTPVITCELVNKHDLRAAQIVKGRVEKTFIRDIIYYIEEDWTGNEAYINIKIDFST 1168

Query: 1171 IRLLHLEVDIDSIRYCIE------------RTRGISGHLTVSGHSFLILKPKDSSKSFNS 1218
            I+ L LE+++  I   I+            R+ G   H+ V  H+      K    +  +
Sbjct: 1169 IQNLQLELNLQDILVAIKKHKRFKSADLKFRSFGSHIHIFVDQHATRTALSKTEEAATGA 1228

Query: 1219 KMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 1274
              Y     +K+L+P++ + G     RA+I  ++    T   LLVEG  LRD M T G+ G
Sbjct: 1229 DPYIRLKHLKRLIPNIQVIGHPQCARAIIRTDETN--TTNTLLVEGYGLRDCMTTDGING 1286

Query: 1275 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGI 1334
                +NN  E    LGIEAAR+TI+ EI  VM++  MSID RH  L+AD+MT KGEVLGI
Sbjct: 1287 HHTRTNNIMEARTVLGIEAARTTIVDEISEVMKD--MSIDPRHMQLLADVMTYKGEVLGI 1344

Query: 1335 TRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            TR GLAKM++SVL LASFE T+DHLFDA   G+TD I GVSECII+G  +++GTG ++++
Sbjct: 1345 TRFGLAKMRDSVLQLASFEKTADHLFDAGGAGRTDLIEGVSECIIVGKSVSLGTGAMEVV 1404

Query: 1395 QAV 1397
            +A+
Sbjct: 1405 RAL 1407



 Score =  182 bits (462), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 105/269 (39%), Positives = 147/269 (54%), Gaps = 16/269 (5%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G ++ +D V Q + +++  + L+  +  R   PHG LD RMG + K   C TCG  L  C
Sbjct: 30  GVLSTQDIVSQ-AVVEVSDRKLFDLENDRAVAPHGPLDGRMGISSKSGTCDTCGGALQVC 88

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFG++ L LP FH+GYF+ VI+ILQ ICK   C+ +LL E +   F  +LR P +  L
Sbjct: 89  SGHFGHVRLVLPAFHVGYFKRVISILQEICKE--CSHILLPENERRAFLRELRRPGIDNL 146

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKYK--------NRTKKKD 254
            R  + KKI E  +K   C  C  +NGVVKK G   LKI+HEK++         +     
Sbjct: 147 RRMQIAKKINERCRKTRTCYRCNAVNGVVKKAGTSALKITHEKFRAFNASSSVKKIPPPS 206

Query: 255 AIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSK 314
            +V D    + EA K NP+IE H K      L+PL VL+LF ++  +D  LL +N E ++
Sbjct: 207 KVVFD--QSFEEAKKSNPDIEKHFKKAH-DDLHPLRVLKLFRSVSDKDCELLGLNPEEAR 263

Query: 315 PSDLILTRLLVPPNCIRPSVISDLKSDND 343
           P   +   +  PP CIRPSV  +  S  D
Sbjct: 264 PEVFLWQYIPAPPVCIRPSVGQEAASTED 292



 Score =  160 bits (406), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 103/250 (41%), Positives = 144/250 (57%), Gaps = 20/250 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+IT  L    DL  A+IVKGR+E+T + ++  YIEE +  ++
Sbjct: 1098 GVPRIKEIINASKEISTPVITCELVNKHDLRAAQIVKGRVEKTFIRDIIYYIEEDWTGNE 1157

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIE------------RTRGISGHLTVSGHSFLIL 871
            ++I IK+D   I+ L LE+++  I   I+            R+ G   H+ V  H+    
Sbjct: 1158 AYINIKIDFSTIQNLQLELNLQDILVAIKKHKRFKSADLKFRSFGSHIHIFVDQHATRTA 1217

Query: 872  KPKDSSKSFNSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927
              K    +  +  Y     +K+L+P++ + G     RA+I  ++    T   LLVEG  L
Sbjct: 1218 LSKTEEAATGADPYIRLKHLKRLIPNIQVIGHPQCARAIIRTDETN--TTNTLLVEGYGL 1275

Query: 928  RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 987
            RD M T G+ G    +NN  E    LGIEAAR+TI+ EI  VM++  MSID RH  L+AD
Sbjct: 1276 RDCMTTDGINGHHTRTNNIMEARTVLGIEAARTTIVDEISEVMKD--MSIDPRHMQLLAD 1333

Query: 988  LMTSKGEVLG 997
            +MT KGEVLG
Sbjct: 1334 VMTYKGEVLG 1343



 Score =  104 bits (260), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 47/59 (79%), Positives = 52/59 (88%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSFFSGLTPTEF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  +YD
Sbjct: 843 PAKGFVRNSFFSGLTPTEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSSRYD 901



 Score = 53.9 bits (128), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 22/40 (55%), Positives = 31/40 (77%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           LM  K+NL TP+NGE +I+A QDFIT  Y+L+ K+ F++R
Sbjct: 536 LMGVKNNLATPKNGEPIISAIQDFITAAYMLSSKDVFYDR 575



 Score = 45.1 bits (105), Expect = 0.27,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 31/41 (75%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 708
            D  FDA   G+TD I GVSECII+G  +++GTG +++++A+
Sbjct: 1367 DHLFDAGGAGRTDLIEGVSECIIVGKSVSLGTGAMEVVRAL 1407


>gi|328766444|gb|EGF76498.1| hypothetical protein BATDEDRAFT_14837 [Batrachochytrium
           dendrobatidis JAM81]
          Length = 1407

 Score =  276 bits (705), Expect = 9e-71,   Method: Compositional matrix adjust.
 Identities = 137/292 (46%), Positives = 187/292 (64%), Gaps = 45/292 (15%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+DVVLFNRQPSLHKLSIM+H  KV P RTFRFNECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 454 DDDVVLFNRQPSLHKLSIMSHFVKVRPWRTFRFNECVCTPYNADFDGDEMNLHVPQTEEA 513

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NLVTPRNGE LIAATQDFIT  YLL++K+ F++R
Sbjct: 514 RAEAME--------------LMGTKNNLVTPRNGEPLIAATQDFITASYLLSRKDVFYDR 559

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           +Q  +I S L     +I             P   ++   +WTGKQ+F ++L+P+++  + 
Sbjct: 560 SQFSQICSYLGDSLLNI----------DLPPPTILKPFALWTGKQVFGVMLRPSQESKII 609

Query: 521 ANLKTKGRAYTANEE---------------------FCHRDSYVILRNSELLAGSMDKST 559
            NL+TK R +  +++                     FC  D Y+   NSEL++G +DK+ 
Sbjct: 610 INLETKCRTFDKDQKDRHGIAFGKSKTQAGHLFHPSFCPNDGYLFFHNSELMSGVIDKAI 669

Query: 560 LGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           +G G K ++FY++LRD+G   A   M +++++++ +L N+GFSIGI DV PG
Sbjct: 670 IGDGNKKSMFYVVLRDYGPPAAADCMNKIAKLSARWLANQGFSIGINDVQPG 721



 Score =  263 bits (672), Expect = 5e-67,   Method: Compositional matrix adjust.
 Identities = 142/275 (51%), Positives = 195/275 (70%), Gaps = 7/275 (2%)

Query: 1146 EVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRG--ISGHLTVSGHS 1203
            ++ EYI+EV  P++  I+IK+D++ IR L LEV+ID+IR+ I R     IS  +T+S   
Sbjct: 1131 DITEYIQEVITPEEVCIVIKIDLETIRKLQLEVNIDTIRWAIIRAPKLKISDMVTISDR- 1189

Query: 1204 FLILKPKDSSKSFNSK--MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD 1261
              ++ P+  + S NS   M  +K+ LP VV+KG+  ++RAVI+  DV   +++ LLVEG 
Sbjct: 1190 LRVVVPRLKNDSINSYIIMQALKRALPKVVVKGLSTVSRAVIN--DVTEESRFNLLVEGY 1247

Query: 1262 NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 1321
             L++VM   GV G+  SSN+  E  KTLGIEAAR TI+ +I   M++HGM+ID RH ML+
Sbjct: 1248 GLKEVMGIDGVDGLNTSSNHVLECLKTLGIEAARQTIIDQILYTMKSHGMTIDRRHVMLL 1307

Query: 1322 ADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMG 1381
            ADLM+ KGEVLGITR G+AKMK+SVL LASFE T+DHLF+A+FY + D I GVSECIIMG
Sbjct: 1308 ADLMSFKGEVLGITRFGIAKMKDSVLMLASFEKTTDHLFEASFYSKHDKIQGVSECIIMG 1367

Query: 1382 LPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHT 1416
            +PM++GTGL KL+Q   +     + LLFD P+FH+
Sbjct: 1368 VPMSLGTGLFKLVQETNQFVKTKQPLLFDAPDFHS 1402



 Score =  210 bits (535), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 113/268 (42%), Positives = 160/268 (59%), Gaps = 6/268 (2%)

Query: 77  VFFRGLIEGTVTKEDRVQQQSHIQIVSKNLY-CQDPQRTPIPHGLLDRRMGTNQKEANCT 135
           VF R  I+  V      +Q S +++  ++LY      R P   G LDRR+GT  K   C 
Sbjct: 11  VFSRKRIDFGVLSAQDAKQLSILELHQRDLYDVSKNNRPPAKFGALDRRLGTADKSIPCE 70

Query: 136 TCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAK 195
           TCG+ + DCVGHFG I L LPVFHIGYF+ +I +LQ+ICK  +C+ VL+ E+    +  +
Sbjct: 71  TCGETMQDCVGHFGIIRLVLPVFHIGYFKLMITVLQNICK--SCSCVLIDEQTRRVYLKR 128

Query: 196 LRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDA 255
           LRNP L  + RK + K +    KK + CPHC  +NG+VKK G LKI HEK+K + K ++ 
Sbjct: 129 LRNPNLDGVRRKDILKNLNILCKKTARCPHCNSLNGMVKKVGALKIVHEKFKKKAKTEEE 188

Query: 256 IVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKP 315
             ++    +N A+K +P ++AH      + LNPL ++ LF+AI  +D  L+ +N ELS+P
Sbjct: 189 --DEFRKSFNHAIKLDPTLKAHISKAQ-EDLNPLVIMNLFQAISNDDCELMGLNPELSRP 245

Query: 316 SDLILTRLLVPPNCIRPSVISDLKSDND 343
              I + L VPP CIRPSV  +  S  D
Sbjct: 246 EQYIWSALPVPPVCIRPSVGQENSSTED 273



 Score =  201 bits (510), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 119/249 (47%), Positives = 164/249 (65%), Gaps = 18/249 (7%)

Query: 764  GVPRIKEIINASRNISTPIITAYL-----------DKDTDLDYARIVKGRLERTTLGEVC 812
            GVPRIKEIINAS+ ISTPII A L            +      +R+VKGR+E+T L ++ 
Sbjct: 1074 GVPRIKEIINASKTISTPIIDAKLAPMVGGYGGNQTRFAAEAASRVVKGRIEKTLLEDIT 1133

Query: 813  EYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRG--ISGHLTVSGHSFLI 870
            EYI+EV  P++  I+IK+D++ IR L LEV+ID+IR+ I R     IS  +T+S     +
Sbjct: 1134 EYIQEVITPEEVCIVIKIDLETIRKLQLEVNIDTIRWAIIRAPKLKISDMVTISDR-LRV 1192

Query: 871  LKPKDSSKSFNSK--MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLR 928
            + P+  + S NS   M  +K+ LP VV+KG+  ++RAVI+  DV   +++ LLVEG  L+
Sbjct: 1193 VVPRLKNDSINSYIIMQALKRALPKVVVKGLSTVSRAVIN--DVTEESRFNLLVEGYGLK 1250

Query: 929  DVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADL 988
            +VM   GV G+  SSN+  E  KTLGIEAAR TI+ +I   M++HGM+ID RH ML+ADL
Sbjct: 1251 EVMGIDGVDGLNTSSNHVLECLKTLGIEAARQTIIDQILYTMKSHGMTIDRRHVMLLADL 1310

Query: 989  MTSKGEVLG 997
            M+ KGEVLG
Sbjct: 1311 MSFKGEVLG 1319



 Score =  104 bits (260), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 46/61 (75%), Positives = 53/61 (86%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV NSF+SGL+PTEF FH + GREGLVDTAVKTAETGYMQRRL+K+LEDL   YD+
Sbjct: 844 PAKGFVGNSFYSGLSPTEFLFHAVSGREGLVDTAVKTAETGYMQRRLMKALEDLVCHYDL 903

Query: 670 S 670
           S
Sbjct: 904 S 904



 Score = 85.5 bits (210), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 62/186 (33%), Positives = 86/186 (46%), Gaps = 34/186 (18%)

Query: 969  VMENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDPSLSAQEI 1028
            V ++ G  + FR+     D       + G+  PVE  R L    A     +DP LS  + 
Sbjct: 905  VRDSGGGIVQFRY----GDDGLDPPNIEGSELPVEFSRNLMHSRALIPIENDPFLSRNQW 960

Query: 1029 LALSNETLDSKEFLQDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKI 1088
              +     + KEF    S  F+R +  FLE              V++P+           
Sbjct: 961  QKIIQVETNKKEFKTICSSEFIRALVAFLER---------ELGDVAKPV----------- 1000

Query: 1089 GHGRESNPFPSACKAEA---------CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLK 1139
             HGR+++ +       A         C+ KY+RA ++P TAVGA+ AQSIGEPGTQMTLK
Sbjct: 1001 -HGRDTDKYAIKNGVTATQLYHFINTCKTKYIRAVVQPGTAVGAVGAQSIGEPGTQMTLK 1059

Query: 1140 TFHFAG 1145
            TFHFAG
Sbjct: 1060 TFHFAG 1065



 Score = 72.0 bits (175), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 33/61 (54%), Positives = 43/61 (70%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHF 727
            D  F+A+FY + D I GVSECIIMG+PM++GTGL KL+Q   +     + LLFD P+FH 
Sbjct: 1343 DHLFEASFYSKHDKIQGVSECIIMGVPMSLGTGLFKLVQETNQFVKTKQPLLFDAPDFHS 1402

Query: 728  P 728
            P
Sbjct: 1403 P 1403



 Score = 68.9 bits (167), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 32/50 (64%), Positives = 40/50 (80%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM  K+NLVTPRNGE LIAATQDFIT  YLL++K+ F++R+Q  +I S L
Sbjct: 520 LMGTKNNLVTPRNGEPLIAATQDFITASYLLSRKDVFYDRSQFSQICSYL 569


>gi|327351527|gb|EGE80384.1| hypothetical protein BDDG_03325 [Ajellomyces dermatitidis ATCC
           18188]
          Length = 855

 Score =  275 bits (704), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 136/280 (48%), Positives = 183/280 (65%), Gaps = 28/280 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++H AKV PHRTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 470 DGDIVLFNRQPSLHKLSILSHFAKVRPHRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 529

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL TP+NGE +I+A QDFIT  Y+L+ K+ F++R
Sbjct: 530 RAEAME--------------LMGVKNNLATPKNGEPIISAIQDFITAAYMLSSKDVFYDR 575

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                I   ++   +       RF      P   ++  ++WTGKQIF+++++PN+  PV 
Sbjct: 576 KAFTHICLYMLQSDT-------RF---DLPPPSVIKPQMLWTGKQIFNVLMRPNKQSPVL 625

Query: 521 ANLKTKGRAYTANE----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL    R + A +    +    D ++ +RNSE++ G MDKST+GSG K +VFY++LRDF
Sbjct: 626 VNLDAACRGFKAPKGTPRDLDANDGWLCIRNSEVMCGVMDKSTIGSGKKDSVFYVMLRDF 685

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           G +VA   M RLSR+++ +  N GFSIGI DV PG   ++
Sbjct: 686 GPEVAAEGMNRLSRLSARWFTNMGFSIGITDVYPGDKLLE 725



 Score =  180 bits (457), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 105/269 (39%), Positives = 147/269 (54%), Gaps = 16/269 (5%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G ++ +D V Q + +++  + L+  +  R   PHG LD RMG + K   C TCG  L  C
Sbjct: 30  GVLSTQDIVSQ-AVVEVSDRKLFDLENDRAVAPHGPLDGRMGISSKSGTCDTCGGALQVC 88

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFG++ L LP FH+GYF+ VI+ILQ ICK   C+ +LL E +   F  +LR P +  L
Sbjct: 89  SGHFGHVRLVLPAFHVGYFKRVISILQEICKE--CSHILLPENERRAFLRELRRPGIDNL 146

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKYK--------NRTKKKD 254
            R  + KKI E  +K   C  C  +NGVVKK G   LKI+HEK++         +     
Sbjct: 147 RRMQIAKKINERCRKTRTCYRCNAVNGVVKKAGTSALKITHEKFRAFNASSSVKKIPPPS 206

Query: 255 AIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSK 314
            +V D    + EA K NP+IE H K      L+PL VL+LF ++  +D  LL +N E ++
Sbjct: 207 KVVFD--QSFEEAKKSNPDIEKHFKKAH-DDLHPLRVLKLFRSVSDKDCELLGLNPEEAR 263

Query: 315 PSDLILTRLLVPPNCIRPSVISDLKSDND 343
           P   +   +  PP CIRPSV  +  S  D
Sbjct: 264 PEVFLWQYIPAPPVCIRPSVGQEAASTED 292



 Score = 53.9 bits (128), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 22/40 (55%), Positives = 31/40 (77%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           LM  K+NL TP+NGE +I+A QDFIT  Y+L+ K+ F++R
Sbjct: 536 LMGVKNNLATPKNGEPIISAIQDFITAAYMLSSKDVFYDR 575


>gi|259487939|tpe|CBF87003.1| TPA: hypothetical protein similar to RNA polymerase III (Broad)
           [Aspergillus nidulans FGSC A4]
          Length = 1445

 Score =  275 bits (704), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 140/282 (49%), Positives = 184/282 (65%), Gaps = 29/282 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++H AKV PHRTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 470 DGDIVLFNRQPSLHKLSILSHFAKVRPHRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 529

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL TP+NGE +I A QDFI+  YLL+ K+ FF+R
Sbjct: 530 RAEAME--------------LMGVKNNLATPKNGEPIIGAIQDFISAAYLLSSKDNFFDR 575

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
               +I   ++       G   RF      P VF +  ++WTGKQ+F+++++PN+D PV 
Sbjct: 576 RSFTQICLYML-------GPQTRFDLPP--PAVF-KPQMLWTGKQVFNILMRPNKDDPVL 625

Query: 521 ANLKTKGRAYTANE-----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL    + +   +     +    DS++++RNSE++ G MDKST+GSG K NVFYI+LRD
Sbjct: 626 VNLDAACKQFKPPKGNQPRDLDPNDSWLVVRNSEVMCGVMDKSTVGSGKKDNVFYIMLRD 685

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           FG   A   M RLS++++ +  N GFSIGI DV P    VQ+
Sbjct: 686 FGPAAAAEGMNRLSKLSARWFSNMGFSIGITDVYPSDRLVQS 727



 Score =  224 bits (570), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 168/509 (33%), Positives = 252/509 (49%), Gaps = 103/509 (20%)

Query: 970  MENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDPSLSAQEIL 1029
            ME     + F    + A+  T K E   + +P E+  + +++++K  ++    L+  +++
Sbjct: 927  MEGKAKPVHFDRTFIHAETTTYKNEER-SLSPAEIMEVCEEMLSKERAK----LARYDLM 981

Query: 1030 ALSNETLDSKEFLQD---TSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQI---LS 1083
                + +D  +   D   ++ +F+  I+++++  +K + + S     S P  E+    L+
Sbjct: 982  GAELDYMDRSDHGVDQFESARDFLDSIQQYVQ--TKADKLISRGGD-SDPSDERTIKGLN 1038

Query: 1084 HQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHF 1143
            H  K+   R    F + C       KY +AQ+EP  AVGA+ AQSIGEPGTQMTLKTFHF
Sbjct: 1039 HTGKLTE-RTLRTFIAECLM-----KYKKAQVEPGHAVGAVGAQSIGEPGTQMTLKTFHF 1092

Query: 1144 AGEV---------------------------CE--------------------------- 1149
            AG                             CE                           
Sbjct: 1093 AGVAGMSITQGVPRIKEIINASKEISTPVISCELVEKRNIVAARMAKGRIEKTFLRDIIH 1152

Query: 1150 YIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIE----------RTRGISGHLTV 1199
            Y+ E +   ++++ +K++ D I  L L++ +  IR  IE          + R    H+  
Sbjct: 1153 YVRETWTGKEAYLTVKINWDTISALELDLTVGKIRQAIENHRRFKSEDLKLRSTRSHI-- 1210

Query: 1200 SGHSFLILKPKDSSKSFNSKMYQMKQ-----------LLPSVVIKGVQGINRAVIHEEDV 1248
              H  + L P    K   +++                LLP + + G    NRA+I  +D 
Sbjct: 1211 --HIHIDLDPASKEKLSKTEIAATSSDPFLRLKALKRLLPDIQVLGHPQANRAIIRTDDK 1268

Query: 1249 EGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMEN 1308
                   LLVEG  LR  M T G+ G++  SNN  E  + LGIEAARSTI+ EI  VM++
Sbjct: 1269 SDTN--TLLVEGYGLRQCMNTVGIDGLRTRSNNVMETREVLGIEAARSTIIQEISEVMKD 1326

Query: 1309 HGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQT 1368
              M ID RH  L+AD+MT KGEVLGITR GLAKM++SVL LASFE T+DHLFDA   G+T
Sbjct: 1327 --MDIDPRHMQLLADVMTYKGEVLGITRFGLAKMRDSVLQLASFEKTADHLFDAGGAGRT 1384

Query: 1369 DCISGVSECIIMGLPMNVGTGLIKLLQAV 1397
            D I GVSECIIMG  +++GTG +++++ +
Sbjct: 1385 DLIEGVSECIIMGKTVSLGTGAMEVVRKM 1413



 Score =  174 bits (441), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 102/267 (38%), Positives = 146/267 (54%), Gaps = 15/267 (5%)

Query: 87  VTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVG 146
           V   D +  Q  +++  +  +  +  R+ +P+G LD RMG + K + C TCG  L  C G
Sbjct: 31  VLSNDDIVSQGVVEVSDRKFFNLENDRSIVPNGPLDARMGISNKTSTCQTCGGALQVCNG 90

Query: 147 HFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVR 206
           HFG++ L LP FH+GYF+ VI+ILQ ICK   C+ +LL E +   F  ++R P L  L R
Sbjct: 91  HFGHVRLVLPAFHVGYFKRVISILQEICKE--CSHILLPEAERRAFLREMRRPRLDNLRR 148

Query: 207 KSLKKKILETTKKVSVCPHCGEINGVVKKCGL--LKISHEKYK----NRTKKK----DAI 256
             + K++ +  +K   C +CG +NGVVKK G   LKI+H+K++    + + KK      I
Sbjct: 149 MQIAKRVNDRCRKTRTCENCGAVNGVVKKTGTSSLKITHDKFRAFNASTSAKKIPPPSKI 208

Query: 257 VEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPS 316
           V D   E  EA   NPE+E H K      LN L VL LF+ I   D  LL ++ + ++P 
Sbjct: 209 VFDRSLE--EARSSNPEVEKHHKKAQ-DDLNALRVLNLFKRISDSDCELLGLDPKEARPE 265

Query: 317 DLILTRLLVPPNCIRPSVISDLKSDND 343
             +   +  PP CIRPSV  D  S  D
Sbjct: 266 MFLWQFIPAPPVCIRPSVGQDASSTED 292



 Score =  150 bits (379), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 97/255 (38%), Positives = 139/255 (54%), Gaps = 29/255 (11%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+I+  L +  ++  AR+ KGR+E+T L ++  Y+ E +   +
Sbjct: 1103 GVPRIKEIINASKEISTPVISCELVEKRNIVAARMAKGRIEKTFLRDIIHYVRETWTGKE 1162

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIE----------RTRGISGHLTVSGHSFLILKP 873
            +++ +K++ D I  L L++ +  IR  IE          + R    H+    H  + L P
Sbjct: 1163 AYLTVKINWDTISALELDLTVGKIRQAIENHRRFKSEDLKLRSTRSHI----HIHIDLDP 1218

Query: 874  KDSSKSFNSKMYQMKQ-----------LLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLV 922
                K   +++                LLP + + G    NRA+I  +D        LLV
Sbjct: 1219 ASKEKLSKTEIAATSSDPFLRLKALKRLLPDIQVLGHPQANRAIIRTDDKSDTN--TLLV 1276

Query: 923  EGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHP 982
            EG  LR  M T G+ G++  SNN  E  + LGIEAARSTI+ EI  VM++  M ID RH 
Sbjct: 1277 EGYGLRQCMNTVGIDGLRTRSNNVMETREVLGIEAARSTIIQEISEVMKD--MDIDPRHM 1334

Query: 983  MLVADLMTSKGEVLG 997
             L+AD+MT KGEVLG
Sbjct: 1335 QLLADVMTYKGEVLG 1349



 Score =  100 bits (250), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 46/59 (77%), Positives = 49/59 (83%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSFFSGL P EF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL   YD
Sbjct: 844 PSKGFVRNSFFSGLLPYEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSTGYD 902



 Score = 54.7 bits (130), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 25/57 (43%), Positives = 36/57 (63%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVF 78
           LM  K+NL TP+NGE +I A QDFI+  YLL+ K+ FF+R    +I   ++  +  F
Sbjct: 536 LMGVKNNLATPKNGEPIIGAIQDFISAAYLLSSKDNFFDRRSFTQICLYMLGPQTRF 592



 Score = 45.1 bits (105), Expect = 0.29,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 30/41 (73%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 708
            D  FDA   G+TD I GVSECIIMG  +++GTG +++++ +
Sbjct: 1373 DHLFDAGGAGRTDLIEGVSECIIMGKTVSLGTGAMEVVRKM 1413


>gi|213410469|ref|XP_002176004.1| DNA-directed RNA polymerase III complex large subunit Rpc1
           [Schizosaccharomyces japonicus yFS275]
 gi|212004051|gb|EEB09711.1| DNA-directed RNA polymerase III complex large subunit Rpc1
           [Schizosaccharomyces japonicus yFS275]
          Length = 1406

 Score =  275 bits (703), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 148/317 (46%), Positives = 189/317 (59%), Gaps = 46/317 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DNDVVLFNRQPSLHKLSIMAH  KV P RT RFNECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 450 DNDVVLFNRQPSLHKLSIMAHLVKVRPWRTLRFNECVCGPYNADFDGDEMNLHVPQTEEA 509

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL               LM  K+NLVTPRNGE +IAATQDFIT  YLL+ K+ F +R
Sbjct: 510 RTEALE--------------LMGIKNNLVTPRNGEPIIAATQDFITASYLLSLKDCFLDR 555

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                +   ++  +  I             P   ++   +WTGKQ+F ++++PN   PV 
Sbjct: 556 KTFCNLCCFMVDASVHI----------DIPPPAILKPRCLWTGKQLFGVLMRPNHLSPVM 605

Query: 521 ANLKTKGRAYTANE----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL    R+    +    E C  D Y++++NSELLAG +DKS +G G K ++FY++LRD+
Sbjct: 606 VNLAANTRSIAKGKCSPPEMCPNDGYLLIQNSELLAGVVDKSIVGDGKKNSLFYVILRDY 665

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSFFSGLTPTEFFFHTMGGR 636
           G   A   M RL+++ + YL NRGFSIGI DV PGQ                 +HT   +
Sbjct: 666 GPIEAAATMNRLAKLCARYLGNRGFSIGINDVQPGQR---------------LYHT---K 707

Query: 637 EGLVDTAVKTAETGYMQ 653
           E LV+ A   ++   MQ
Sbjct: 708 EALVEKAYSVSDDLIMQ 724



 Score =  257 bits (657), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 169/494 (34%), Positives = 249/494 (50%), Gaps = 82/494 (16%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G+GTPV  +R          +  D  L   +I+  +   L S++F  + +ENF+  ++ F
Sbjct: 908  GDGTPVAFERCWSHSSNITYNEDDSGLLPYKIIEETESILSSRKFTANCTENFIESVRTF 967

Query: 1057 LEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEA----------- 1105
            + E   K+      ++   P  E+            +  P  +    +            
Sbjct: 968  VIERLAKKLAQVRANRQLAPKLERPSEDDFDDFENDDFAPLAARKSVDNVLRVSKKQLYT 1027

Query: 1106 ----CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG---------------- 1145
                C EKY++A++EP TAVGA+ A SIGEPGTQMTLKTFHFAG                
Sbjct: 1028 FLQFCWEKYMKAKVEPGTAVGAVGAHSIGEPGTQMTLKTFHFAGVAAQTTLGVPRIKEII 1087

Query: 1146 -------------------------------------EVCEYIEEVFVPDDSFILIKLDM 1168
                                                 +V   +EE+F P +++I + ++ 
Sbjct: 1088 NAAKTISTPIIYGALVNDQDVRSARVVKGRIEKTYLKDVISSLEEIFGPTNTYISVHVNF 1147

Query: 1169 DRIRLLHLEV---DIDSIRYCIERTRGISGHLTV--SGHSFLILKPKDSSKSFNSKMY-- 1221
            D IR L L++   DI S  +   + +     +TV  S +   +    D+    NS +Y  
Sbjct: 1148 DTIRKLQLDLTLADIASAIWTAPKLKIPMQQVTVHDSANEIRVHVTPDTKDFENSSVYYR 1207

Query: 1222 --QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSS 1279
                K+ LP+VV+ G+   +RA+I +E      K +L+VEG  LR+VM T G+ G K  +
Sbjct: 1208 LQTYKRALPNVVVSGIPKTSRAIILQEG----EKKQLVVEGYGLREVMNTEGIVGSKTFT 1263

Query: 1280 NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGL 1339
            N+  E+   LGIEAAR +I+ EI   M NHG+++D RH ML+ D+MT KGEVLGITR G+
Sbjct: 1264 NHVMEMNAVLGIEAARQSIIYEIDSTMRNHGLTVDPRHIMLLGDVMTCKGEVLGITRFGV 1323

Query: 1340 AKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPR 1399
            AKMK+SVL+LASFE T+DHLFDAA     D I G+SECI++G    +GT + +L++    
Sbjct: 1324 AKMKDSVLSLASFEKTTDHLFDAAARFAKDSIEGISECIVLGKLAPIGTNVFQLIRTTEE 1383

Query: 1400 S-EPVPRTLLFDNP 1412
            S +  P+ LLFDNP
Sbjct: 1384 SHDQEPKKLLFDNP 1397



 Score =  191 bits (485), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 97/246 (39%), Positives = 150/246 (60%), Gaps = 7/246 (2%)

Query: 99  IQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVF 158
           +++ +++LY    +R P+ HG LDRRMGT  + A C TCG+ ++DC+GHFG++ L LPVF
Sbjct: 32  VEVSTRDLYTMT-ERKPVEHGALDRRMGTTDRNAVCATCGEGVADCIGHFGHVRLALPVF 90

Query: 159 HIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTK 218
           +IGYF+  + ILQ+ICK+  CA VL+ + +   F  +LR P +  L R  + K++ +  K
Sbjct: 91  NIGYFKTTLTILQNICKD--CATVLVSQREKQNFLKELRKPGIDNLRRTQICKRLNDACK 148

Query: 219 KVSVCPHCGEINGVVKKCGLLKISHEKYK-NRTKKKDAIVEDLLAEYNEAVKFNPEIEAH 277
           KV VCP+C +  GVVKK G LKI HE+++ NR  +++    +    +++A+K  P++  H
Sbjct: 149 KVRVCPYCNKTQGVVKKAGPLKIIHERFRFNRKMQEEG--GEFRQSFDQALKAMPDLRPH 206

Query: 278 KKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD 337
                   LNPL VL LF+ I   D  LL M+ E  +P +L+   +  PP  IRP+V  +
Sbjct: 207 LHKAH-DDLNPLRVLNLFKQITPMDCELLGMDPEKGRPENLLWQYMPAPPVTIRPTVAQE 265

Query: 338 LKSDND 343
             +  D
Sbjct: 266 GATTED 271



 Score =  174 bits (440), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 103/243 (42%), Positives = 149/243 (61%), Gaps = 13/243 (5%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ ISTPII   L  D D+  AR+VKGR+E+T L +V   +EE+F P +
Sbjct: 1079 GVPRIKEIINAAKTISTPIIYGALVNDQDVRSARVVKGRIEKTYLKDVISSLEEIFGPTN 1138

Query: 824  SFILIKLDMDRIRLLHLEV---DIDSIRYCIERTRGISGHLTV--SGHSFLILKPKDSSK 878
            ++I + ++ D IR L L++   DI S  +   + +     +TV  S +   +    D+  
Sbjct: 1139 TYISVHVNFDTIRKLQLDLTLADIASAIWTAPKLKIPMQQVTVHDSANEIRVHVTPDTKD 1198

Query: 879  SFNSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATY 934
              NS +Y      K+ LP+VV+ G+   +RA+I +E      K +L+VEG  LR+VM T 
Sbjct: 1199 FENSSVYYRLQTYKRALPNVVVSGIPKTSRAIILQEG----EKKQLVVEGYGLREVMNTE 1254

Query: 935  GVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGE 994
            G+ G K  +N+  E+   LGIEAAR +I+ EI   M NHG+++D RH ML+ D+MT KGE
Sbjct: 1255 GIVGSKTFTNHVMEMNAVLGIEAARQSIIYEIDSTMRNHGLTVDPRHIMLLGDVMTCKGE 1314

Query: 995  VLG 997
            VLG
Sbjct: 1315 VLG 1317



 Score = 98.6 bits (244), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 44/58 (75%), Positives = 49/58 (84%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV NSF++GLTPTEF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL   YD
Sbjct: 824 AKGFVSNSFYTGLTPTEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLTSAYD 881



 Score = 58.9 bits (141), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 27/40 (67%), Positives = 32/40 (80%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           LM  K+NLVTPRNGE +IAATQDFIT  YLL+ K+ F +R
Sbjct: 516 LMGIKNNLVTPRNGEPIIAATQDFITASYLLSLKDCFLDR 555



 Score = 48.1 bits (113), Expect = 0.040,   Method: Compositional matrix adjust.
 Identities = 29/75 (38%), Positives = 39/75 (52%), Gaps = 1/75 (1%)

Query: 657  VKSLEDLCVQYDMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVP 715
            V SL       D  FDAA     D I G+SECI++G    +GT + +L++    S +  P
Sbjct: 1330 VLSLASFEKTTDHLFDAAARFAKDSIEGISECIVLGKLAPIGTNVFQLIRTTEESHDQEP 1389

Query: 716  RTLLFDNPEFHFPQV 730
            + LLFDNP     QV
Sbjct: 1390 KKLLFDNPTLPSLQV 1404


>gi|254584114|ref|XP_002497625.1| ZYRO0F09856p [Zygosaccharomyces rouxii]
 gi|238940518|emb|CAR28692.1| ZYRO0F09856p [Zygosaccharomyces rouxii]
          Length = 1458

 Score =  275 bits (703), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 137/277 (49%), Positives = 184/277 (66%), Gaps = 30/277 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH+LSI++H AK+ P RTFR NECVCTPYNADFDGDEMN+H+PQ+EEA
Sbjct: 466 DGDVVLFNRQPSLHRLSILSHYAKIRPWRTFRLNECVCTPYNADFDGDEMNLHVPQSEEA 525

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  KSNL+TP++GE +IAATQDFITG YL++ K++FF++
Sbjct: 526 RAEAIN--------------LMGVKSNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDK 571

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
               ++ S +++D +    I     W+            +WTGKQIFSL+++PN+  PV 
Sbjct: 572 YDMTQLLS-MMSDGALQFDIPPPTIWKP---------CYLWTGKQIFSLLIRPNKKSPVV 621

Query: 521 ANLKTKGRAY------TANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLR 574
            NL  K + Y      +   E    D +V++R S++L+G MDKS LG G K +VFY +LR
Sbjct: 622 LNLDAKNKVYIPPKSKSLPNEMSQNDGFVLIRGSQILSGVMDKSVLGDGKKHSVFYTILR 681

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           D+G   A  AM R++++ + Y+ NRGFSIGI DVTP 
Sbjct: 682 DYGSQEAAEAMNRMAKLCARYVGNRGFSIGISDVTPA 718



 Score =  247 bits (631), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 153/377 (40%), Positives = 205/377 (54%), Gaps = 77/377 (20%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG----------------------- 1145
            KY RA++EP TAVGA+ AQSIGEPGTQMTLKTFHFAG                       
Sbjct: 1075 KYRRAKVEPGTAVGAIGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIINASKVI 1134

Query: 1146 -------------------EVCEYIEEVFVPDDSFIL------------IKLDMDRIRLL 1174
                                V   IE+  + D +F +            +++D+  I  L
Sbjct: 1135 STPIINAVLVNESDERAARVVKGRIEKTLLSDVAFYIQDVYRDNLSYLQVRVDLSTIDKL 1194

Query: 1175 HLEVDIDSIRYCIERTRGISGHLT------------------VSGHSFLILKPKDSSKSF 1216
             LE+ I+ I   + R   +    +                      S   L  + S    
Sbjct: 1195 QLELTIEDIAVAMTRAPKLKIQASDVHIVGKDKIAINVFPDGAKAKSISTLAKEPSENEV 1254

Query: 1217 NSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 1276
              +M Q+++ LP +V+KG+  I+RAVI+  D +G  K +LLVEG  LRDVM+T GV G K
Sbjct: 1255 FYRMQQLRRALPGIVVKGLSDISRAVINIRD-DG--KRELLVEGYGLRDVMSTDGVVGHK 1311

Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITR 1336
              +N+  EVY  LGIEAAR++I+ EI   M NHGMS+D RH  L+ D+MT KGE+LGITR
Sbjct: 1312 TVTNHILEVYSVLGIEAARASIVGEIDYTMSNHGMSVDPRHIQLLGDVMTYKGEILGITR 1371

Query: 1337 HGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA 1396
             GL+KM++SVL LASFE T+DHLFDAAFY + D + GVSECII+G  M +GTG  K+++ 
Sbjct: 1372 FGLSKMRDSVLQLASFEKTTDHLFDAAFYMKKDAVEGVSECIILGQTMAIGTGAFKVVKG 1431

Query: 1397 VPRSEPV--PRTLLFDN 1411
               SE    P+  LF++
Sbjct: 1432 TNVSEEQLKPKPTLFES 1448



 Score =  182 bits (463), Expect = 9e-43,   Method: Compositional matrix adjust.
 Identities = 108/252 (42%), Positives = 152/252 (60%), Gaps = 21/252 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII A L  ++D   AR+VKGR+E+T L +V  YI++V+  + 
Sbjct: 1120 GVPRIKEIINASKVISTPIINAVLVNESDERAARVVKGRIEKTLLSDVAFYIQDVYRDNL 1179

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLT------------------VSG 865
            S++ +++D+  I  L LE+ I+ I   + R   +    +                     
Sbjct: 1180 SYLQVRVDLSTIDKLQLELTIEDIAVAMTRAPKLKIQASDVHIVGKDKIAINVFPDGAKA 1239

Query: 866  HSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD 925
             S   L  + S      +M Q+++ LP +V+KG+  I+RAVI+  D +G  K +LLVEG 
Sbjct: 1240 KSISTLAKEPSENEVFYRMQQLRRALPGIVVKGLSDISRAVINIRD-DG--KRELLVEGY 1296

Query: 926  NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 985
             LRDVM+T GV G K  +N+  EVY  LGIEAAR++I+ EI   M NHGMS+D RH  L+
Sbjct: 1297 GLRDVMSTDGVVGHKTVTNHILEVYSVLGIEAARASIVGEIDYTMSNHGMSVDPRHIQLL 1356

Query: 986  ADLMTSKGEVLG 997
             D+MT KGE+LG
Sbjct: 1357 GDVMTYKGEILG 1368



 Score =  173 bits (438), Expect = 7e-40,   Method: Compositional matrix adjust.
 Identities = 95/248 (38%), Positives = 138/248 (55%), Gaps = 11/248 (4%)

Query: 96  QSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPL 155
           QS ++I +++L+  +  R P   G LD +MG +     C TC  NL+ C GHFG+I L L
Sbjct: 29  QSEVEISTRDLFDLENGRAPKTGGALDPKMGVSSSSMECQTCHGNLASCHGHFGHIKLAL 88

Query: 156 PVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILE 215
           PVFHIGYF+  I ILQ ICK   C+ +LL +     F ++LR P +  L R  + KK+L+
Sbjct: 89  PVFHIGYFKATIQILQGICKE--CSSILLEDTDKKHFLSELRRPGVDNLRRMGILKKVLD 146

Query: 216 TTKKVSVCPHCGEINGVVKKCGL------LKISHEKYKNRTKKKDAIVEDLLAEYNEAVK 269
             KK   C  CG +NGVVKK         LKI H+ ++   KK     E  + +++  + 
Sbjct: 147 QCKKQRRCLQCGALNGVVKKAAAGGGSASLKIIHDTFRWAGKKSVPEKEKWIGDWDSVLA 206

Query: 270 FNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL--SKPSDLILTRLLVPP 327
            +PE+E + K   +  LNPL+ L LF+ +  ED  LL +++ +   +P   I   L  PP
Sbjct: 207 HSPELERYVKR-CMDDLNPLKTLNLFKQVKPEDCELLGIDSTIKSGRPETYIWRYLPAPP 265

Query: 328 NCIRPSVI 335
            CIRPSV+
Sbjct: 266 VCIRPSVM 273



 Score = 97.8 bits (242), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 44/57 (77%), Positives = 49/57 (85%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NSFFSGLTP EF +H + GREGLVDTAVKTAETGYM RRL+KSLEDL   YD
Sbjct: 843 KGFVRNSFFSGLTPPEFLYHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSCLYD 899



 Score = 61.6 bits (148), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 28/57 (49%), Positives = 41/57 (71%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVF 78
           LM  KSNL+TP++GE +IAATQDFITG YL++ K++FF++    ++ S +  G   F
Sbjct: 532 LMGVKSNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDKYDMTQLLSMMSDGALQF 588



 Score = 52.8 bits (125), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 26/57 (45%), Positives = 36/57 (63%), Gaps = 2/57 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPV--PRTLLFDN 722
            D  FDAAFY + D + GVSECII+G  M +GTG  K+++    SE    P+  LF++
Sbjct: 1392 DHLFDAAFYMKKDAVEGVSECIILGQTMAIGTGAFKVVKGTNVSEEQLKPKPTLFES 1448


>gi|392869043|gb|EAS30407.2| DNA-directed RNA polymerase III largest subunit [Coccidioides
           immitis RS]
          Length = 1444

 Score =  275 bits (702), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 136/281 (48%), Positives = 184/281 (65%), Gaps = 30/281 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++H  KV PHRTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 470 DGDIVLFNRQPSLHKLSILSHFVKVRPHRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 529

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL TP+NGE +IAA QDFIT  YLL+ K+ F++R
Sbjct: 530 RAEAME--------------LMGVKNNLATPKNGEPIIAAIQDFITAAYLLSSKDNFYDR 575

Query: 461 AQTMRIASTLIADTSDICG-IIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
                         +  CG +++  +     P   ++  ++WTGKQ+F+++++P+++ PV
Sbjct: 576 GS-----------FTQTCGYMLQPGTKFDLPPPAVLKPQMLWTGKQVFNVLMRPSKESPV 624

Query: 520 NANLKTKGRAYTANE----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
             NL    R + A +    +    D ++ +RNSE++ G MDKST+GSG K +VFY++LRD
Sbjct: 625 LVNLDAACREFRAPKGTPRDLDPNDGWLCIRNSEIMCGVMDKSTIGSGKKDSVFYVMLRD 684

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           FG  VA  AM RLSR+++ +  N GFSIGI DV PG   +Q
Sbjct: 685 FGPQVAAEAMNRLSRLSARWFTNIGFSIGITDVYPGDSLLQ 725



 Score =  223 bits (567), Expect = 7e-55,   Method: Compositional matrix adjust.
 Identities = 144/363 (39%), Positives = 193/363 (53%), Gaps = 74/363 (20%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEV----------------- 1147
            +C  KY +AQ+EP  AVGA+ AQSIGEPGTQMTLKTFHFAG                   
Sbjct: 1052 SCLTKYKKAQVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIINA 1111

Query: 1148 ----------CE---------------------------YIEEVFVPDDSFILIKLDMDR 1170
                      CE                           YIEE +    ++I IK+D   
Sbjct: 1112 SKEISTPIITCELVNKEDVRAAQIVKGRVEKTFIKDIIYYIEEAWTSSVAYINIKIDFST 1171

Query: 1171 IRLLHLEVDIDSIRYCIE------------RTRGISGHLTVSGHSFLILKPKDSSKSFNS 1218
            I+ L LE+ +  I   I+            R+ G   H+ V   +      K    +  S
Sbjct: 1172 IQALQLELTLRDILNAIKKHKRFRSDDLKFRSFGSHIHIFVDQATTKTSLTKAEQAATGS 1231

Query: 1219 KMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 1274
              Y     +K+LLP++ + G    +RA+I  ++    T   LLVEG  LR  M T G+ G
Sbjct: 1232 DPYIRLKHLKRLLPTIQVLGHPQCSRAIIRTDETN--TTNTLLVEGYGLRACMTTDGIFG 1289

Query: 1275 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGI 1334
             +  +NN  E    LGIEAAR+TI+ EI  VM++  M ID RH  L+AD+MT KGEVLGI
Sbjct: 1290 TRTRTNNIMETKDVLGIEAARTTIVDEISDVMKD--MGIDPRHMQLLADVMTYKGEVLGI 1347

Query: 1335 TRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            TR GLAKM++SVL LASFE T+DHLFDA   G+TD + GVSECII+G  +++GTG ++++
Sbjct: 1348 TRFGLAKMRDSVLQLASFEKTADHLFDAGGAGRTDLVEGVSECIILGKSVSLGTGAMEMV 1407

Query: 1395 QAV 1397
            +A+
Sbjct: 1408 RAM 1410



 Score =  169 bits (427), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 103/268 (38%), Positives = 147/268 (54%), Gaps = 14/268 (5%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G +  +D V Q + +++  + L+  D  R    HG LD RMG + K   C TCG  L +C
Sbjct: 30  GVLASQDIVSQ-ALVEVSDRKLFDLDNDRAVARHGPLDGRMGISSKSGTCETCGGALQEC 88

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFG++ L LP FH+GYF+ VI ILQ ICK+  C+R+LL E +   F  ++R   +  L
Sbjct: 89  NGHFGHVRLVLPAFHVGYFKRVIGILQEICKD--CSRILLPENERRIFLKEMRRQGIDNL 146

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKYK----NRTKKKDAIVE 258
            R  + K+I +  +K   C  C  +NGVVKK G   LKI+H+K++    + + KK     
Sbjct: 147 RRMQINKRINDRCRKTRTCYVCHAVNGVVKKAGTSALKITHDKFRAFNASTSAKKVPPPS 206

Query: 259 DLLAE--YNEAVKFNPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKP 315
            L+ +  + EA + N +IE H  F  +Q  LNPL VL+LF  I  ED  LL +N E  +P
Sbjct: 207 KLVFDRSFEEAKRSNTDIEKH--FKKVQDDLNPLRVLKLFRRISDEDCELLGLNPEEVRP 264

Query: 316 SDLILTRLLVPPNCIRPSVISDLKSDND 343
              +   +  PP  IRPSV  +  S  D
Sbjct: 265 EMFLWQYIPAPPVSIRPSVGQEGASTED 292



 Score =  153 bits (387), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 102/250 (40%), Positives = 140/250 (56%), Gaps = 20/250 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIIT  L    D+  A+IVKGR+E+T + ++  YIEE +    
Sbjct: 1101 GVPRIKEIINASKEISTPIITCELVNKEDVRAAQIVKGRVEKTFIKDIIYYIEEAWTSSV 1160

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIE------------RTRGISGHLTVSGHSFLIL 871
            ++I IK+D   I+ L LE+ +  I   I+            R+ G   H+ V   +    
Sbjct: 1161 AYINIKIDFSTIQALQLELTLRDILNAIKKHKRFRSDDLKFRSFGSHIHIFVDQATTKTS 1220

Query: 872  KPKDSSKSFNSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927
              K    +  S  Y     +K+LLP++ + G    +RA+I  ++    T   LLVEG  L
Sbjct: 1221 LTKAEQAATGSDPYIRLKHLKRLLPTIQVLGHPQCSRAIIRTDETN--TTNTLLVEGYGL 1278

Query: 928  RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 987
            R  M T G+ G +  +NN  E    LGIEAAR+TI+ EI  VM++  M ID RH  L+AD
Sbjct: 1279 RACMTTDGIFGTRTRTNNIMETKDVLGIEAARTTIVDEISDVMKD--MGIDPRHMQLLAD 1336

Query: 988  LMTSKGEVLG 997
            +MT KGEVLG
Sbjct: 1337 VMTYKGEVLG 1346



 Score =  103 bits (256), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 45/59 (76%), Positives = 52/59 (88%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSFFSGL P+EFFFH + GREGL+DTAVKTAETGYM RRL+KSLEDL  +YD
Sbjct: 843 PAKGFVRNSFFSGLIPSEFFFHAISGREGLIDTAVKTAETGYMSRRLMKSLEDLSSRYD 901



 Score = 55.8 bits (133), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/41 (58%), Positives = 31/41 (75%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRA 62
           LM  K+NL TP+NGE +IAA QDFIT  YLL+ K+ F++R 
Sbjct: 536 LMGVKNNLATPKNGEPIIAAIQDFITAAYLLSSKDNFYDRG 576



 Score = 45.4 bits (106), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 19/41 (46%), Positives = 31/41 (75%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 708
            D  FDA   G+TD + GVSECII+G  +++GTG +++++A+
Sbjct: 1370 DHLFDAGGAGRTDLVEGVSECIILGKSVSLGTGAMEMVRAM 1410


>gi|378732247|gb|EHY58706.1| DNA-directed RNA polymerase III subunit C1 [Exophiala dermatitidis
           NIH/UT8656]
          Length = 1581

 Score =  275 bits (702), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 136/281 (48%), Positives = 182/281 (64%), Gaps = 30/281 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++H  KV PHRTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 469 DGDIVLFNRQPSLHKLSILSHFVKVRPHRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 528

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EA               +LM  K N+VTP+NGE +I+A QDFIT  +LL+  + FF++
Sbjct: 529 RTEAT--------------LLMGVKHNIVTPKNGEPIISAIQDFITASFLLSSLDQFFDK 574

Query: 461 AQTMRIASTLIADTSDIC-GIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
                   T +     +C G+++  +     P   ++   +WTGKQ+FS++L+PN+  PV
Sbjct: 575 -------KTFVT----MCIGMLEPDTKFELPPPAVIKPQTLWTGKQVFSVMLRPNKQSPV 623

Query: 520 NANLKTKGRAYTANEEFCHR----DSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
             NL    R ++      HR    DS++ +RNSE+L G MDK+T+GSG K +VFYIL RD
Sbjct: 624 TVNLDAASRDHSQYHPGLHRDLQDDSFLCIRNSEVLCGRMDKATVGSGKKNSVFYILYRD 683

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           FG D A   M RLS++ + +L N+GF++GI DVTP    V+
Sbjct: 684 FGPDAAAQGMNRLSKLCARWLGNQGFTVGISDVTPPDPLVK 724



 Score =  175 bits (443), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 104/267 (38%), Positives = 149/267 (55%), Gaps = 14/267 (5%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G ++ +D +  QS +++  + ++  D  RT   +G LDRRMG + K   C TCG+ L  C
Sbjct: 31  GVLSDQD-IINQSQVELADRRMFDLDKGRTYAEYGPLDRRMGVSGKRDICQTCGEQLQTC 89

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFG++ L LPVFH+GYF+ VI ILQSICK+  C+ +LL E     +   LR  A   L
Sbjct: 90  NGHFGHVKLVLPVFHVGYFKKVIQILQSICKD--CSAILLSEADRRKYHNALRRVANDSL 147

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKYK----NRTKKKDAIVE 258
            + ++ +K+ +  +K  VC  CG ING+V+K G   LKISH+K+K    +   KK    E
Sbjct: 148 RQAAIVRKVADQCRKTKVCFECGAINGLVRKAGTSALKISHDKFKAFNSSTAAKKQPPPE 207

Query: 259 --DLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPS 316
             +    +  A + N E+E H K  +   LNPL VL+LF  I   D  LL + +  +KP 
Sbjct: 208 KIEFDKSFETAKESNQELEKHLKKAM-DDLNPLRVLKLFRRIRRSDRELLGLRS--AKPE 264

Query: 317 DLILTRLLVPPNCIRPSVISDLKSDND 343
           D +   +  PP CIRPSV  +  S  D
Sbjct: 265 DFLWLYIPAPPVCIRPSVGQEGASTED 291



 Score =  149 bits (375), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 78/150 (52%), Positives = 107/150 (71%), Gaps = 2/150 (1%)

Query: 1246 EDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLV 1305
            +D + V  ++++VEG  LR  M T GV      +N+  E  + LGIEAARS I+ EI+ V
Sbjct: 1402 DDGKPVQMHRVMVEGYGLRYCMNTEGVDPYHTHTNSVIETLQVLGIEAARSKIILEIQEV 1461

Query: 1306 MENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFY 1365
            M++  +SID RH  L+AD+MT KGEVLGITR GLAKM++SVL LASFE T+DH+FDA   
Sbjct: 1462 MKS--LSIDPRHMSLLADVMTYKGEVLGITRFGLAKMRDSVLQLASFEKTADHVFDAGIA 1519

Query: 1366 GQTDCISGVSECIIMGLPMNVGTGLIKLLQ 1395
            G+ D I GVSE +I+G  M VGTG++++++
Sbjct: 1520 GKVDKIEGVSESVIVGKTMGVGTGMVEVVR 1549



 Score =  101 bits (251), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 45/59 (76%), Positives = 49/59 (83%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GF+ NSFFSGL P EF FH +GGR GLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 842 PSKGFISNSFFSGLLPYEFLFHAVGGRVGLVDTAVKTAETGYMSRRLMKSLEDLSTQYD 900



 Score = 73.2 bits (178), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 33/40 (82%), Positives = 35/40 (87%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            C EKY RA+ EPA AVGA+ AQSIGEPGTQMTLKTFHFAG
Sbjct: 1115 CLEKYERARTEPAHAVGAVGAQSIGEPGTQMTLKTFHFAG 1154



 Score = 72.8 bits (177), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 42/88 (47%), Positives = 58/88 (65%), Gaps = 2/88 (2%)

Query: 910  EDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLV 969
            +D + V  ++++VEG  LR  M T GV      +N+  E  + LGIEAARS I+ EI+ V
Sbjct: 1402 DDGKPVQMHRVMVEGYGLRYCMNTEGVDPYHTHTNSVIETLQVLGIEAARSKIILEIQEV 1461

Query: 970  MENHGMSIDFRHPMLVADLMTSKGEVLG 997
            M++  +SID RH  L+AD+MT KGEVLG
Sbjct: 1462 MKS--LSIDPRHMSLLADVMTYKGEVLG 1487



 Score = 72.4 bits (176), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 58/172 (33%), Positives = 90/172 (52%), Gaps = 24/172 (13%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDL----DYARIVKGRLERTTLGEVCEYIEEVF 819
            GVPRIKEIINAS++ISTP+IT  L++  DL      ARIVKGR+E   L ++  +I+   
Sbjct: 1163 GVPRIKEIINASKDISTPVITCRLERRRDLTIPESLARIVKGRIECLYLEDITSFIQISH 1222

Query: 820  VPDD-SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISG---HLTVSGHSFLIL---K 872
              D  S I++K+ +D I  L L++ +  I   I++ R +      + + G   L +    
Sbjct: 1223 SLDKPSCIVLKISLDTIIELGLDLTLTDICNAIQKHRQLKAAKLRIQIRGKDELKIHSDA 1282

Query: 873  PKDSSKSFNS-------------KMYQMKQLLPSVVIKGVQGINRAVIHEED 911
            P  S+K   +             ++  ++++LPSV I G     RAV+  ED
Sbjct: 1283 PIKSTKRGAAARIDEDGQTERLIRLQTLRRVLPSVHILGHPTATRAVVMAED 1334



 Score = 50.4 bits (119), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 21/41 (51%), Positives = 31/41 (75%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           +LM  K N+VTP+NGE +I+A QDFIT  +LL+  + FF++
Sbjct: 534 LLMGVKHNIVTPKNGEPIISAIQDFITASFLLSSLDQFFDK 574



 Score = 42.7 bits (99), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 18/39 (46%), Positives = 27/39 (69%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  FDA   G+ D I GVSE +I+G  M VGTG++++++
Sbjct: 1511 DHVFDAGIAGKVDKIEGVSESVIVGKTMGVGTGMVEVVR 1549


>gi|119191177|ref|XP_001246195.1| hypothetical protein CIMG_05636 [Coccidioides immitis RS]
          Length = 1430

 Score =  275 bits (702), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 136/281 (48%), Positives = 184/281 (65%), Gaps = 30/281 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++H  KV PHRTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 470 DGDIVLFNRQPSLHKLSILSHFVKVRPHRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 529

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL TP+NGE +IAA QDFIT  YLL+ K+ F++R
Sbjct: 530 RAEAME--------------LMGVKNNLATPKNGEPIIAAIQDFITAAYLLSSKDNFYDR 575

Query: 461 AQTMRIASTLIADTSDICG-IIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
                         +  CG +++  +     P   ++  ++WTGKQ+F+++++P+++ PV
Sbjct: 576 GS-----------FTQTCGYMLQPGTKFDLPPPAVLKPQMLWTGKQVFNVLMRPSKESPV 624

Query: 520 NANLKTKGRAYTANE----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
             NL    R + A +    +    D ++ +RNSE++ G MDKST+GSG K +VFY++LRD
Sbjct: 625 LVNLDAACREFRAPKGTPRDLDPNDGWLCIRNSEIMCGVMDKSTIGSGKKDSVFYVMLRD 684

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           FG  VA  AM RLSR+++ +  N GFSIGI DV PG   +Q
Sbjct: 685 FGPQVAAEAMNRLSRLSARWFTNIGFSIGITDVYPGDSLLQ 725



 Score =  197 bits (502), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 138/357 (38%), Positives = 178/357 (49%), Gaps = 75/357 (21%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEV----------------- 1147
            +C  KY +AQ+EP  AVGA+ AQSIGEPGTQMTLKTFHFAG                   
Sbjct: 1052 SCLTKYKKAQVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIINA 1111

Query: 1148 ----------CE---------------------------YIEEVFVPDDSFILIKLDMDR 1170
                      CE                           YIEE +    ++I IK+D   
Sbjct: 1112 SKEISTPIITCELVNKEDVRAAQIVKGRVEKTFIKDIIYYIEEAWTSSVAYINIKIDFST 1171

Query: 1171 IRLLHLEVDIDSIRYCIE------------RTRGISGHLTVSGHSFLILKPKDSSKSFNS 1218
            I+ L LE+ +  I   I+            R+ G   H+ V   +      K    +  S
Sbjct: 1172 IQALQLELTLRDILNAIKKHKRFRSDDLKFRSFGSHIHIFVDQATTKTSLTKAEQAATGS 1231

Query: 1219 KMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 1274
              Y     +K+LLP++ + G    +RA+I  ++    T   LLVEG  LR  M T G+ G
Sbjct: 1232 DPYIRLKHLKRLLPTIQVLGHPQCSRAIIRTDETN--TTNTLLVEGYGLRACMTTDGIFG 1289

Query: 1275 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGI 1334
             +  +NN  E    LGIEAAR+TI+ EI  VM++  M ID RH  L+AD+MT KGEVLGI
Sbjct: 1290 TRTRTNNIMETKDVLGIEAARTTIVDEISDVMKD--MGIDPRHMQLLADVMTYKGEVLGI 1347

Query: 1335 TRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLI 1391
            TR GLAKM++SVL LASFE T+DHLFDA   G+TD + G    + M   MN   G I
Sbjct: 1348 TRFGLAKMRDSVLQLASFEKTADHLFDAGGAGRTDLVEGTG-AMEMVRAMNFYEGQI 1403



 Score =  169 bits (427), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 103/268 (38%), Positives = 147/268 (54%), Gaps = 14/268 (5%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G +  +D V Q + +++  + L+  D  R    HG LD RMG + K   C TCG  L +C
Sbjct: 30  GVLASQDIVSQ-ALVEVSDRKLFDLDNDRAVARHGPLDGRMGISSKSGTCETCGGALQEC 88

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFG++ L LP FH+GYF+ VI ILQ ICK+  C+R+LL E +   F  ++R   +  L
Sbjct: 89  NGHFGHVRLVLPAFHVGYFKRVIGILQEICKD--CSRILLPENERRIFLKEMRRQGIDNL 146

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKYK----NRTKKKDAIVE 258
            R  + K+I +  +K   C  C  +NGVVKK G   LKI+H+K++    + + KK     
Sbjct: 147 RRMQINKRINDRCRKTRTCYVCHAVNGVVKKAGTSALKITHDKFRAFNASTSAKKVPPPS 206

Query: 259 DLLAE--YNEAVKFNPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKP 315
            L+ +  + EA + N +IE H  F  +Q  LNPL VL+LF  I  ED  LL +N E  +P
Sbjct: 207 KLVFDRSFEEAKRSNTDIEKH--FKKVQDDLNPLRVLKLFRRISDEDCELLGLNPEEVRP 264

Query: 316 SDLILTRLLVPPNCIRPSVISDLKSDND 343
              +   +  PP  IRPSV  +  S  D
Sbjct: 265 EMFLWQYIPAPPVSIRPSVGQEGASTED 292



 Score =  153 bits (387), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 102/250 (40%), Positives = 140/250 (56%), Gaps = 20/250 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIIT  L    D+  A+IVKGR+E+T + ++  YIEE +    
Sbjct: 1101 GVPRIKEIINASKEISTPIITCELVNKEDVRAAQIVKGRVEKTFIKDIIYYIEEAWTSSV 1160

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIE------------RTRGISGHLTVSGHSFLIL 871
            ++I IK+D   I+ L LE+ +  I   I+            R+ G   H+ V   +    
Sbjct: 1161 AYINIKIDFSTIQALQLELTLRDILNAIKKHKRFRSDDLKFRSFGSHIHIFVDQATTKTS 1220

Query: 872  KPKDSSKSFNSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927
              K    +  S  Y     +K+LLP++ + G    +RA+I  ++    T   LLVEG  L
Sbjct: 1221 LTKAEQAATGSDPYIRLKHLKRLLPTIQVLGHPQCSRAIIRTDETN--TTNTLLVEGYGL 1278

Query: 928  RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 987
            R  M T G+ G +  +NN  E    LGIEAAR+TI+ EI  VM++  M ID RH  L+AD
Sbjct: 1279 RACMTTDGIFGTRTRTNNIMETKDVLGIEAARTTIVDEISDVMKD--MGIDPRHMQLLAD 1336

Query: 988  LMTSKGEVLG 997
            +MT KGEVLG
Sbjct: 1337 VMTYKGEVLG 1346



 Score =  103 bits (256), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 45/59 (76%), Positives = 52/59 (88%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSFFSGL P+EFFFH + GREGL+DTAVKTAETGYM RRL+KSLEDL  +YD
Sbjct: 843 PAKGFVRNSFFSGLIPSEFFFHAISGREGLIDTAVKTAETGYMSRRLMKSLEDLSSRYD 901



 Score = 55.8 bits (133), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/41 (58%), Positives = 31/41 (75%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRA 62
           LM  K+NL TP+NGE +IAA QDFIT  YLL+ K+ F++R 
Sbjct: 536 LMGVKNNLATPKNGEPIIAAIQDFITAAYLLSSKDNFYDRG 576


>gi|189192955|ref|XP_001932816.1| DNA-directed RNA polymerase III subunit RPC1 [Pyrenophora
           tritici-repentis Pt-1C-BFP]
 gi|187978380|gb|EDU45006.1| DNA-directed RNA polymerase III subunit RPC1 [Pyrenophora
           tritici-repentis Pt-1C-BFP]
          Length = 1471

 Score =  274 bits (701), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 138/279 (49%), Positives = 180/279 (64%), Gaps = 26/279 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++HRAK+ P RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 480 DGDIVLFNRQPSLHKLSILSHRAKIRPWRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 539

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EA                LM  K NL TP+NG  +IAA QDFIT  YLL+ KN FF+R
Sbjct: 540 RTEATE--------------LMGVKYNLATPKNGTPIIAAIQDFITAAYLLSNKNNFFDR 585

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
               +I + +            +       P V  +   +WTGKQ+F+L+++PN+ C V 
Sbjct: 586 KTFCQIVNYMFNGEGAFDPDTGKKHPIDIPPPVIWKPQALWTGKQVFNLLMRPNKGCRVL 645

Query: 521 ANLK--------TKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYIL 572
            NL+        T G+A   NE     D+Y+++RNSE++ G MDK+T+G G K +VFY++
Sbjct: 646 INLEAACKQFKGTPGQAPDLNEN----DAYLVIRNSEVMCGVMDKATVGDGKKDSVFYVM 701

Query: 573 LRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           +RDFG D AV  M RLS++++ +L N GFS+GI DVTPG
Sbjct: 702 MRDFGPDHAVQGMNRLSKLSARWLTNNGFSLGISDVTPG 740



 Score =  236 bits (602), Expect = 7e-59,   Method: Compositional matrix adjust.
 Identities = 174/510 (34%), Positives = 246/510 (48%), Gaps = 116/510 (22%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILAL------------------------- 1031
            G   PV   R     +      ++ SL+ QE+  +                         
Sbjct: 948  GKAKPVHFDRTFSHAVTSTWDNAESSLTPQEVRDITESKLNTERNKYTRYKLDGVTQLDY 1007

Query: 1032 ---SNETLDSKEFLQD---TSENFVRDIKKFLEEFSKKESV--TSHQDKVSQPLREQILS 1083
               S++ +D  E L+D   T ++++    K LE+      V  TS +D    P   +  S
Sbjct: 1008 RDPSDDGIDQHESLRDFLDTVQDYIFKKAKKLEDTLTWLGVVQTSVEDGKQSPADAEKYS 1067

Query: 1084 HQDKIGHGRES--NPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTF 1141
              D I     S  + F + C +     KY R++++P  AVGA+ AQSIGEPGTQMTLKTF
Sbjct: 1068 LADGIAKISRSALDTFIALCWS-----KYHRSRVQPGHAVGAIGAQSIGEPGTQMTLKTF 1122

Query: 1142 HFAGEV---------------------------CE------------------------- 1149
            HFAG                             CE                         
Sbjct: 1123 HFAGVAGMSITQGVPRIKEIINASSTISTPVIDCELENKVSERVAREVKARIEKTYLRDV 1182

Query: 1150 --YIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTR----GISGHLTVSGHS 1203
              Y+E+V+ P+ +++ +++D D I+ L ++V    I+  I   +    G +G     G  
Sbjct: 1183 IRYVEDVWYPEGAYVAMRIDWDTIQKLFIDVKPHEIKAAISAHKPLKWGKAGAAVHVGQK 1242

Query: 1204 FLILKPKD-------------SSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEE---D 1247
            ++ ++  D             + KSF  ++ Q+K L+P VVIKG     RAVI +E   +
Sbjct: 1243 YIRVEVPDPDATKKRPAKTSRNHKSFFERVQQVKALIPDVVIKGYPDCTRAVIKKETSPN 1302

Query: 1248 VEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVME 1307
             +G  + KLLVEG  LR+ M T G+   K  SNN  EV   LGIEAAR+TI+ EI  VM 
Sbjct: 1303 AQGQYECKLLVEGYGLRNCMTTPGIVPYKTVSNNIMEVKTVLGIEAARATIVREIGSVMG 1362

Query: 1308 NHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQ 1367
            N  M ID RH  L+AD+MT KGEV GITR GL K ++SVL LASFE T DHLF+AA  G+
Sbjct: 1363 N--MDIDPRHMQLLADVMTFKGEVFGITRFGLQKTRDSVLQLASFEKTPDHLFEAAARGK 1420

Query: 1368 TDCISGVSECIIMGLPMNVGTGLIKLLQAV 1397
            TD I GVSECIIMG  + +GTG +++++ +
Sbjct: 1421 TDTIDGVSECIIMGQSVKLGTGSMQVVRPL 1450



 Score =  168 bits (426), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 106/254 (41%), Positives = 146/254 (57%), Gaps = 22/254 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS  ISTP+I   L+       AR VK R+E+T L +V  Y+E+V+ P+ 
Sbjct: 1135 GVPRIKEIINASSTISTPVIDCELENKVSERVAREVKARIEKTYLRDVIRYVEDVWYPEG 1194

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTR----GISGHLTVSGHSFLILKPKD---- 875
            +++ +++D D I+ L ++V    I+  I   +    G +G     G  ++ ++  D    
Sbjct: 1195 AYVAMRIDWDTIQKLFIDVKPHEIKAAISAHKPLKWGKAGAAVHVGQKYIRVEVPDPDAT 1254

Query: 876  ---------SSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEE---DVEGVTKYKLLVE 923
                     + KSF  ++ Q+K L+P VVIKG     RAVI +E   + +G  + KLLVE
Sbjct: 1255 KKRPAKTSRNHKSFFERVQQVKALIPDVVIKGYPDCTRAVIKKETSPNAQGQYECKLLVE 1314

Query: 924  GDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPM 983
            G  LR+ M T G+   K  SNN  EV   LGIEAAR+TI+ EI  VM N  M ID RH  
Sbjct: 1315 GYGLRNCMTTPGIVPYKTVSNNIMEVKTVLGIEAARATIVREIGSVMGN--MDIDPRHMQ 1372

Query: 984  LVADLMTSKGEVLG 997
            L+AD+MT KGEV G
Sbjct: 1373 LLADVMTFKGEVFG 1386



 Score =  159 bits (401), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 97/273 (35%), Positives = 147/273 (53%), Gaps = 16/273 (5%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDP----QRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G  + +D V Q + +++  +N+Y   P     RT   +G +D  MG + K+ NC TCG+ 
Sbjct: 26  GIYSNQDIVNQ-AVLEVSDRNVYDLQPGANNTRTLTSNGPMDIHMGISSKQGNCGTCGEG 84

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
           L  C GHFG+I L LP FH+GY + +I +L  ICK+  C+RVLL E +   +   +R P 
Sbjct: 85  LDKCNGHFGHIKLALPAFHVGYLKHIIEVLNCICKD--CSRVLLDEVERRRYLRSMRRPD 142

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKYK--NR----TKK 252
           +  L + ++ KKI+E  +K   CP+C  + G V+K     LKI H +Y   NR    TKK
Sbjct: 143 MDTLRKGAVTKKIIEDCRKKKTCPYCNALQGTVRKVPGHPLKIIHNRYDAFNRSTAKTKK 202

Query: 253 KDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL 312
                 +    ++ A   NP+++ H K   +  ++PL  L LF+ I  ED  LL M  E 
Sbjct: 203 PPPGKLEFDQSFDTAKSANPDVDKHVKKA-VDDMHPLRALNLFKKISPEDCELLAMVPED 261

Query: 313 SKPSDLILTRLLVPPNCIRPSVISDLKSDNDVV 345
           ++P  LI   + VPP  +RPSV+ +  +  D V
Sbjct: 262 ARPEMLIWEYMPVPPVALRPSVMQEGGATEDDV 294



 Score =  102 bits (253), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 46/57 (80%), Positives = 49/57 (85%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV NSFFSGLTP+EF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL   YD
Sbjct: 865 KGFVSNSFFSGLTPSEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSAHYD 921



 Score = 59.3 bits (142), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 28/57 (49%), Positives = 35/57 (61%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVF 78
           LM  K NL TP+NG  +IAA QDFIT  YLL+ KN FF+R    +I + +  G   F
Sbjct: 546 LMGVKYNLATPKNGTPIIAAIQDFITAAYLLSNKNNFFDRKTFCQIVNYMFNGEGAF 602



 Score = 45.1 bits (105), Expect = 0.31,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 30/41 (73%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 708
            D  F+AA  G+TD I GVSECIIMG  + +GTG +++++ +
Sbjct: 1410 DHLFEAAARGKTDTIDGVSECIIMGQSVKLGTGSMQVVRPL 1450


>gi|70998935|ref|XP_754189.1| DNA-directed RNA polymerase III largest subunit [Aspergillus
           fumigatus Af293]
 gi|66851826|gb|EAL92151.1| DNA-directed RNA polymerase III largest subunit, putative
           [Aspergillus fumigatus Af293]
 gi|159127207|gb|EDP52322.1| DNA-directed RNA polymerase III largest subunit, putative
           [Aspergillus fumigatus A1163]
          Length = 1453

 Score =  274 bits (700), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 135/282 (47%), Positives = 184/282 (65%), Gaps = 29/282 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++H AKV PHRTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 470 DGDIVLFNRQPSLHKLSILSHFAKVRPHRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 529

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL TP+NGE +I+A QDFI+  Y+L+ K+ FF+R
Sbjct: 530 RAEAME--------------LMGVKNNLATPKNGEPIISAIQDFISAAYILSSKDNFFDR 575

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
               +I   ++       G   RF      P   ++  ++WTGKQ+F+++++PN+D PV 
Sbjct: 576 RSFTQICLYML-------GPETRF---DLPPPAVLKPQMLWTGKQVFNILMRPNKDDPVL 625

Query: 521 ANLKTKGRAYTA-----NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL    R +        ++    D ++++RNSE++ G MDK+T+GSG K NVFYI+LRD
Sbjct: 626 VNLDAACREFKPPKDGRPKDLDPNDGWLVIRNSEVMCGVMDKATIGSGKKDNVFYIMLRD 685

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           FG   A   M RLS++++ +  N GFSIGI DV P +  V++
Sbjct: 686 FGPAAAAEGMNRLSKLSARWFTNMGFSIGITDVYPSESLVRS 727



 Score =  220 bits (561), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 142/370 (38%), Positives = 201/370 (54%), Gaps = 87/370 (23%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEY 1150
            +C  KY +AQ+EP  AVGA+ AQSIGEPGTQMTLKTFHFAG              E+   
Sbjct: 1054 SCLMKYKKAQVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIINA 1113

Query: 1151 IEEVFVP----------------------------------------DDSFILIKLDMDR 1170
             +E+  P                                         ++++ +K++ + 
Sbjct: 1114 SKEISTPVISCDLVTKDNVIAARIVKGRIEKTYLRDIIHYVREAWTGKEAYLTVKINWET 1173

Query: 1171 IRLLHLEVDIDSIRYCIE----------RTRGISGHLTVSGHSFLILKPKDSSKSFNSK- 1219
            I+ L LE+ I +I   I+          + R  + H+    H ++ + P  +SK+  SK 
Sbjct: 1174 IQNLALELKIRNIVDAIKNHKRFKADDLKFRSTNSHI----HIYMDIDP--ASKASLSKT 1227

Query: 1220 ------------MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVM 1267
                        +  +K++LP + + G    NRA+I  +D        LLVEG  L++ M
Sbjct: 1228 EIAATSADPFLRLKHLKRILPDIQVLGHPQANRAIIRTDDTSSTN--TLLVEGYGLKECM 1285

Query: 1268 ATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTS 1327
             T GV G++ S+NN  E+   LGIEAAR TI+ EI  VM++  M ID RH  L+AD+MT 
Sbjct: 1286 TTLGVNGLRTSTNNVMEMRDVLGIEAARVTIVQEISEVMKD--MGIDPRHMQLLADVMTY 1343

Query: 1328 KGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVG 1387
            KGEVLGITR GLAKM++SVL LASFE T+DHLFDA   G+TD I GVSECIIMG  +++G
Sbjct: 1344 KGEVLGITRFGLAKMRDSVLQLASFEKTADHLFDAGGAGRTDLIEGVSECIIMGKTVSLG 1403

Query: 1388 TGLIKLLQAV 1397
            TG +++++ +
Sbjct: 1404 TGAMEVVRKL 1413



 Score =  184 bits (467), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 103/267 (38%), Positives = 145/267 (54%), Gaps = 15/267 (5%)

Query: 87  VTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVG 146
           V   D +  Q+ +++  +  +  +  R  +PHG LD RMG + K A C TCG +L  C G
Sbjct: 31  VLSNDDIVSQAVVEVSDRKFFDLEHDRAVVPHGPLDGRMGISSKTATCQTCGGSLQVCNG 90

Query: 147 HFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVR 206
           HFG++ L LP FH+GYF+ VI+ILQ ICK   C+R+LL E +   F  ++R P L  L R
Sbjct: 91  HFGHVRLVLPAFHVGYFKRVISILQEICKE--CSRILLPEAERRAFLREMRRPGLDNLRR 148

Query: 207 KSLKKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKYK--------NRTKKKDAI 256
             + K++ E  +K   C  CG INGVVKK G   LKI+H+K++         +      I
Sbjct: 149 LQIAKRVNERCRKTRTCEACGAINGVVKKAGNSALKITHDKFRAFNVSTSVKKVPPPSKI 208

Query: 257 VEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPS 316
           V D    ++EA   NPE+E H K      +N L VL LF+ +   D  LL +N + ++P 
Sbjct: 209 VFD--RSFDEARTSNPEVEKHYKKAQ-DDMNALRVLNLFKKVSDTDCELLGLNPKEARPE 265

Query: 317 DLILTRLLVPPNCIRPSVISDLKSDND 343
             +   +  PP CIRPSV  D  S  D
Sbjct: 266 MFLWQFIPAPPVCIRPSVGQDAASTED 292



 Score =  154 bits (390), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 99/257 (38%), Positives = 149/257 (57%), Gaps = 33/257 (12%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+I+  L    ++  ARIVKGR+E+T L ++  Y+ E +   +
Sbjct: 1103 GVPRIKEIINASKEISTPVISCDLVTKDNVIAARIVKGRIEKTYLRDIIHYVREAWTGKE 1162

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIE----------RTRGISGHLTVSGHSFLILKP 873
            +++ +K++ + I+ L LE+ I +I   I+          + R  + H+    H ++ + P
Sbjct: 1163 AYLTVKINWETIQNLALELKIRNIVDAIKNHKRFKADDLKFRSTNSHI----HIYMDIDP 1218

Query: 874  KDSSKSFNSK-------------MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKL 920
              +SK+  SK             +  +K++LP + + G    NRA+I  +D        L
Sbjct: 1219 --ASKASLSKTEIAATSADPFLRLKHLKRILPDIQVLGHPQANRAIIRTDDTSSTN--TL 1274

Query: 921  LVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFR 980
            LVEG  L++ M T GV G++ S+NN  E+   LGIEAAR TI+ EI  VM++  M ID R
Sbjct: 1275 LVEGYGLKECMTTLGVNGLRTSTNNVMEMRDVLGIEAARVTIVQEISEVMKD--MGIDPR 1332

Query: 981  HPMLVADLMTSKGEVLG 997
            H  L+AD+MT KGEVLG
Sbjct: 1333 HMQLLADVMTYKGEVLG 1349



 Score =  103 bits (258), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 47/59 (79%), Positives = 51/59 (86%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSFFSGL PTEF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL  +YD
Sbjct: 844 PSKGFVRNSFFSGLLPTEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSSRYD 902



 Score = 53.5 bits (127), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 23/46 (50%), Positives = 33/46 (71%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRI 67
           LM  K+NL TP+NGE +I+A QDFI+  Y+L+ K+ FF+R    +I
Sbjct: 536 LMGVKNNLATPKNGEPIISAIQDFISAAYILSSKDNFFDRRSFTQI 581



 Score = 45.1 bits (105), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 30/41 (73%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 708
            D  FDA   G+TD I GVSECIIMG  +++GTG +++++ +
Sbjct: 1373 DHLFDAGGAGRTDLIEGVSECIIMGKTVSLGTGAMEVVRKL 1413


>gi|367004166|ref|XP_003686816.1| hypothetical protein TPHA_0H01760 [Tetrapisispora phaffii CBS 4417]
 gi|357525118|emb|CCE64382.1| hypothetical protein TPHA_0H01760 [Tetrapisispora phaffii CBS 4417]
          Length = 1459

 Score =  274 bits (700), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 141/279 (50%), Positives = 187/279 (67%), Gaps = 31/279 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVH-LPQTEE 399
           D D+VLFNRQPSLH+LSI++H AK+ P RTFR NECVCTPYNADFDGDEMN+    QTEE
Sbjct: 467 DGDIVLFNRQPSLHRLSILSHFAKIRPWRTFRLNECVCTPYNADFDGDEMNLLCYQQTEE 526

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           ARAEA+               LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+
Sbjct: 527 ARAEAIN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFD 572

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           RA   ++ S +++D +          +    P +F +   +WTGKQIFSL++KPN++ PV
Sbjct: 573 RATLTQLLS-MMSDAN--------LKFDIPPPAIF-KPQCLWTGKQIFSLLIKPNKESPV 622

Query: 520 NANLKTKGRAYTANE------EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILL 573
             NL  K + Y   +      E    D YVI+R SE+L+G MDKS LG G K +VFY +L
Sbjct: 623 VINLDAKNKVYIPPQNKSWPSEMSPNDGYVIIRGSEILSGVMDKSVLGDGKKHSVFYTIL 682

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
           RD+G   +  AM R++++ + YL NRGFSIGI DVTPG+
Sbjct: 683 RDYGPQESANAMNRMAKLCARYLGNRGFSIGISDVTPGE 721



 Score =  251 bits (641), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 173/456 (37%), Positives = 243/456 (53%), Gaps = 94/456 (20%)

Query: 1044 DTSENFVRDIKKFL----EEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNP--- 1096
            D   +F   I++++    E+ +K     S ++ +S+P  E  L H D       SN    
Sbjct: 999  DAKRDFYASIREYMVEKAEQLAKIRKARSLKELISEPAEE--LQHID-FDENIPSNVREV 1055

Query: 1097 FPSACKA---------EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-- 1145
                CK          E    KY RA++EP TAVGA+ AQSIGEPGTQMTLKTFHFAG  
Sbjct: 1056 VDKLCKISEANVKKFLEIAISKYHRAKVEPGTAVGAIGAQSIGEPGTQMTLKTFHFAGVA 1115

Query: 1146 ----------------------------------------EVCEYIEEVFVPDDSF---- 1161
                                                     V   IE+  + D ++    
Sbjct: 1116 SMNVTLGVPRIKEIINASKTISTPIIKAVLVNDSDRRAARVVKGRIEKTLLSDVAYYIED 1175

Query: 1162 --------ILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFLILKP- 1209
                    I IK+D+  I  L LE+ I+ I   I +   +   S ++ + G+  + +   
Sbjct: 1176 VYRDNRTFIRIKIDLSTIEKLQLELTIEDIAIAISKAPKLKIDSSNIHIVGNDKIAIDVF 1235

Query: 1210 KDSSKSFNS------------KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLL 1257
            +++SKS ++            KM  +++ LP VV+KG+  I+RAVI+ +D    +K +LL
Sbjct: 1236 EEASKSISTSLKESSENTVFYKMQTLRRALPDVVVKGLADISRAVINIKD---DSKTELL 1292

Query: 1258 VEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRH 1317
            VEG  LRDVM T GV G K S+N+  E++  LGIEAARS+I+ EI   M NHGMS+D RH
Sbjct: 1293 VEGYGLRDVMCTDGVIGTKTSTNHILEIFNVLGIEAARSSIVGEIDYTMSNHGMSVDPRH 1352

Query: 1318 PMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSEC 1377
              L+ D+MT KGEVLGITR GL+KM++SVL LASFE T+DHLFDAAFY + D + GVSEC
Sbjct: 1353 IQLLGDVMTFKGEVLGITRFGLSKMRDSVLQLASFEKTTDHLFDAAFYMKKDEVKGVSEC 1412

Query: 1378 IIMGLPMNVGTGLIKLLQ--AVPRSEPVPRTLLFDN 1411
            II+G  M++GTG   +++   V   +  P+  LF++
Sbjct: 1413 IILGQTMSIGTGSFNVVKHTVVSPEQVKPKRTLFES 1448



 Score =  197 bits (502), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 116/250 (46%), Positives = 162/250 (64%), Gaps = 19/250 (7%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII A L  D+D   AR+VKGR+E+T L +V  YIE+V+  + 
Sbjct: 1122 GVPRIKEIINASKTISTPIIKAVLVNDSDRRAARVVKGRIEKTLLSDVAYYIEDVYRDNR 1181

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFLILKP-KDSSKS 879
            +FI IK+D+  I  L LE+ I+ I   I +   +   S ++ + G+  + +   +++SKS
Sbjct: 1182 TFIRIKIDLSTIEKLQLELTIEDIAIAISKAPKLKIDSSNIHIVGNDKIAIDVFEEASKS 1241

Query: 880  FNS------------KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927
             ++            KM  +++ LP VV+KG+  I+RAVI+ +D    +K +LLVEG  L
Sbjct: 1242 ISTSLKESSENTVFYKMQTLRRALPDVVVKGLADISRAVINIKDD---SKTELLVEGYGL 1298

Query: 928  RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 987
            RDVM T GV G K S+N+  E++  LGIEAARS+I+ EI   M NHGMS+D RH  L+ D
Sbjct: 1299 RDVMCTDGVIGTKTSTNHILEIFNVLGIEAARSSIVGEIDYTMSNHGMSVDPRHIQLLGD 1358

Query: 988  LMTSKGEVLG 997
            +MT KGEVLG
Sbjct: 1359 VMTFKGEVLG 1368



 Score =  176 bits (447), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 97/248 (39%), Positives = 142/248 (57%), Gaps = 11/248 (4%)

Query: 96  QSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPL 155
           QS ++I +++L+  +  R PI  G LD +MG +     C+TC  NL+ C GHFG+I L L
Sbjct: 29  QSEVEISTRDLFDLENGRAPIEGGALDPKMGVSSSTLECSTCHGNLASCHGHFGHIKLSL 88

Query: 156 PVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILE 215
           PVFH+GYF+  I ILQ +CK  +C+ +LL +     F  +LR P +  L R S+ KKIL+
Sbjct: 89  PVFHVGYFKATIQILQGVCK--SCSAILLNDTDKRHFLHELRKPDIDNLKRMSILKKILD 146

Query: 216 TTKKVSVCPHCGEINGVVKKCGL------LKISHEKYKNRTKKKDAIVEDLLAEYNEAVK 269
             KK   C  CG++NGVVK+         LKI H+ ++   KK     +  + ++N+ + 
Sbjct: 147 QCKKQRRCLECGDLNGVVKRAATGSGSASLKIIHDTFRWVGKKNVPEKDKWIGDWNQVLT 206

Query: 270 FNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELS--KPSDLILTRLLVPP 327
            NPE+E   K      LNPL+ L LF+ I  ED  LL +++ ++  +P   I   L  PP
Sbjct: 207 NNPELEKFIK-RCTDDLNPLKTLNLFKQIKNEDCELLGIDSTVASGRPETYIWRYLPAPP 265

Query: 328 NCIRPSVI 335
            CIRPSV+
Sbjct: 266 VCIRPSVM 273



 Score =  101 bits (252), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 48/70 (68%), Positives = 55/70 (78%), Gaps = 1/70 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV+NSFF+GLTP EF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QY
Sbjct: 841 TPQSKGFVRNSFFTGLTPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSCQY 900

Query: 668 DMSFDAAFYG 677
           D +   +  G
Sbjct: 901 DNTIRTSSNG 910



 Score = 62.4 bits (150), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/50 (54%), Positives = 40/50 (80%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+RA   ++ S +
Sbjct: 534 LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDRATLTQLLSMM 583



 Score = 48.1 bits (113), Expect = 0.032,   Method: Compositional matrix adjust.
 Identities = 24/57 (42%), Positives = 36/57 (63%), Gaps = 2/57 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ--AVPRSEPVPRTLLFDN 722
            D  FDAAFY + D + GVSECII+G  M++GTG   +++   V   +  P+  LF++
Sbjct: 1392 DHLFDAAFYMKKDEVKGVSECIILGQTMSIGTGSFNVVKHTVVSPEQVKPKRTLFES 1448


>gi|403214358|emb|CCK68859.1| hypothetical protein KNAG_0B04240 [Kazachstania naganishii CBS
           8797]
          Length = 1455

 Score =  273 bits (699), Expect = 4e-70,   Method: Compositional matrix adjust.
 Identities = 138/276 (50%), Positives = 182/276 (65%), Gaps = 30/276 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH+LSI++H AK+ P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 468 DGDVVLFNRQPSLHRLSILSHYAKIRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 527

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+ 
Sbjct: 528 RAEAIN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDL 573

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
               ++ S +++D      I          P   ++   +WTGKQ+FSL+++PN+  PV 
Sbjct: 574 GSLTQLLS-MMSDAKLQFDI---------PPPAIMKPYYLWTGKQVFSLLIRPNKKSPVV 623

Query: 521 ANLKTKGRAYTANE------EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLR 574
            NL  K + Y   +      E    D +VI+R SE+L+G MDKS LG G K +VFY +LR
Sbjct: 624 INLDAKNKVYIPPKDKSFPNEMSINDGFVIIRGSEILSGVMDKSVLGDGKKHSVFYTILR 683

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           D+G   A   M R++++ + YL NRGFSIGI DVTP
Sbjct: 684 DYGPQEAANTMNRMAKLCARYLGNRGFSIGISDVTP 719



 Score =  236 bits (603), Expect = 5e-59,   Method: Compositional matrix adjust.
 Identities = 153/359 (42%), Positives = 198/359 (55%), Gaps = 75/359 (20%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG----------------------- 1145
            KY RA++EP TAVGA+ AQSIGEPGTQMTLKTFHFAG                       
Sbjct: 1072 KYHRAKVEPGTAVGAIGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIINASKVI 1131

Query: 1146 -------------------EVCEYIEEVFVPDDSFIL------------IKLDMDRIRLL 1174
                                V   IE+  + D +F +            I++D+  I  L
Sbjct: 1132 STPIINAVLVNEGDERAARVVKGRIEKTLLSDLAFYIQDVYRGNMSYLEIRVDLATIEKL 1191

Query: 1175 HLEVDIDSIRYCIERTRGI-------------SGHLTVSGHSFLILKPKDSSK--SFNSK 1219
             LE+ ++ I   + R   +               H+ V            S+K  S N  
Sbjct: 1192 QLELTMEDIAVALSRAPKLKIQTTDIHILGKDKIHVNVYPEGMKAKSISTSAKEPSENEV 1251

Query: 1220 MYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 1276
             Y+M+ L   LP VV+KG+  I+RAVI+  D +G  K +LLVEG  LR+VM T GV G K
Sbjct: 1252 FYKMQTLRRSLPDVVVKGLPDISRAVINIRD-DG--KRELLVEGYGLREVMCTDGVIGSK 1308

Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITR 1336
              +N+  EV   LGIEAAR++I+ EI   M NHGMS+D RH  L+ D+MT KGEVLGITR
Sbjct: 1309 TITNHVLEVNSVLGIEAARASIVGEIDYTMSNHGMSVDPRHIQLLGDVMTYKGEVLGITR 1368

Query: 1337 HGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 1395
             GL+KM++SVL LASFE T+DHLFDAAFY + D + GVSECII+G  M+VGTG  K+++
Sbjct: 1369 FGLSKMRDSVLQLASFEKTTDHLFDAAFYMKKDAVEGVSECIILGQTMSVGTGSFKVVK 1427



 Score =  172 bits (435), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 111/252 (44%), Positives = 151/252 (59%), Gaps = 21/252 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII A L  + D   AR+VKGR+E+T L ++  YI++V+  + 
Sbjct: 1117 GVPRIKEIINASKVISTPIINAVLVNEGDERAARVVKGRIEKTLLSDLAFYIQDVYRGNM 1176

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISG-------------HLTVSGHSFLI 870
            S++ I++D+  I  L LE+ ++ I   + R   +               H+ V       
Sbjct: 1177 SYLEIRVDLATIEKLQLELTMEDIAVALSRAPKLKIQTTDIHILGKDKIHVNVYPEGMKA 1236

Query: 871  LKPKDSSK--SFNSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD 925
                 S+K  S N   Y+M+ L   LP VV+KG+  I+RAVI+  D +G  K +LLVEG 
Sbjct: 1237 KSISTSAKEPSENEVFYKMQTLRRSLPDVVVKGLPDISRAVINIRD-DG--KRELLVEGY 1293

Query: 926  NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 985
             LR+VM T GV G K  +N+  EV   LGIEAAR++I+ EI   M NHGMS+D RH  L+
Sbjct: 1294 GLREVMCTDGVIGSKTITNHVLEVNSVLGIEAARASIVGEIDYTMSNHGMSVDPRHIQLL 1353

Query: 986  ADLMTSKGEVLG 997
             D+MT KGEVLG
Sbjct: 1354 GDVMTYKGEVLG 1365



 Score =  167 bits (423), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 100/260 (38%), Positives = 142/260 (54%), Gaps = 11/260 (4%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           IE +      +  QS ++I +++L+  +  R     G LDRRMG +     C TC  NL+
Sbjct: 16  IEFSALNAADIVAQSEVEITTRDLFDLEKGREQKTGGALDRRMGVSSSSQECMTCHGNLA 75

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALS 202
            C GHFG+I L LPVFH+GYF+  I ILQ ICK+  C+ VLL ++    F  +LR P + 
Sbjct: 76  SCHGHFGHIKLALPVFHVGYFKSTIQILQCICKD--CSAVLLSDKDRRDFLKELRRPGID 133

Query: 203 YLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGL------LKISHEKYKNRTKKKDAI 256
            L + S+ KK+++  KK   C  CG +NGVVKK         LKI H+ ++   KK    
Sbjct: 134 NLRKMSILKKVIDQCKKQRRCLKCGGLNGVVKKAAAGAGTASLKIIHDTFRWVGKKMVPE 193

Query: 257 VEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL--SK 314
            +  + E+NE +  +PE+E   K      LNPL+ L LF+ +  ED  LL +N+ +   +
Sbjct: 194 KDRWIGEWNEILTHHPELERFVKR-CSDDLNPLKTLTLFKQLKSEDCELLGINSTVRSGR 252

Query: 315 PSDLILTRLLVPPNCIRPSV 334
           P   I   L  PP CIRPSV
Sbjct: 253 PETYIWRYLPAPPVCIRPSV 272



 Score =  102 bits (253), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 48/61 (78%), Positives = 52/61 (85%), Gaps = 1/61 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV+NSFFSGLTP EF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QY
Sbjct: 841 TPQSKGFVRNSFFSGLTPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSCQY 900

Query: 668 D 668
           D
Sbjct: 901 D 901



 Score = 58.2 bits (139), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 25/50 (50%), Positives = 38/50 (76%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM  K+NL+TP++GE +IAATQDFITG YL++ K++FF+     ++ S +
Sbjct: 534 LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFFDLGSLTQLLSMM 583



 Score = 50.4 bits (119), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 22/39 (56%), Positives = 29/39 (74%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  FDAAFY + D + GVSECII+G  M+VGTG  K+++
Sbjct: 1389 DHLFDAAFYMKKDAVEGVSECIILGQTMSVGTGSFKVVK 1427


>gi|322702468|gb|EFY94113.1| DNA-directed RNA polymerase III largest subunit [Metarhizium
           anisopliae ARSEF 23]
          Length = 1364

 Score =  273 bits (699), Expect = 4e-70,   Method: Compositional matrix adjust.
 Identities = 138/294 (46%), Positives = 186/294 (63%), Gaps = 29/294 (9%)

Query: 321 TRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTP 380
           T L+    CI   V+     D D+VLFNRQPSLHKLSIM+H  KV P RTFR NECVC P
Sbjct: 363 TELIANKLCIG-DVVERHIEDGDIVLFNRQPSLHKLSIMSHFVKVRPWRTFRLNECVCNP 421

Query: 381 YNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAA 440
           YNADFDGDEMN+H+PQTEEAR EA+               LM  K NL+TP++GE +IAA
Sbjct: 422 YNADFDGDEMNLHVPQTEEARTEAMS--------------LMGVKHNLITPKSGEPIIAA 467

Query: 441 TQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVI 500
           TQDFIT  YLL+ K+ FF+R     I   ++   + +             P   +    +
Sbjct: 468 TQDFITAAYLLSYKDRFFDRKTFTTICIHMLDGGTQL----------DLPPPAIIVPKTL 517

Query: 501 WTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFC----HRDSYVILRNSELLAGSMD 556
           WTGKQIF+++++PN   PV  NL  + +++      C      D ++++RNS+++ G MD
Sbjct: 518 WTGKQIFNVLMRPNNRSPVMVNLDARCKSFVTRPGQCPDMDPNDGWLVVRNSQVMCGQMD 577

Query: 557 KSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           KST+GSG K ++FY++LRD+G D AV+AM RL+++ + YL NRGFSIG+GDV P
Sbjct: 578 KSTVGSGKKDSIFYVILRDYGPDEAVSAMNRLAKLCARYLTNRGFSIGVGDVYP 631



 Score =  149 bits (375), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 93/191 (48%), Positives = 122/191 (63%), Gaps = 8/191 (4%)

Query: 1208 KPKDSSKSFNSKMYQ---MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLR 1264
            K K +++ F   M +   +++ LPSV I G     RA+I  E  E  T Y++LVEG  LR
Sbjct: 1142 KNKSAAEGFRDMMLRANFLRRTLPSVPISGYPDATRALI--ETTEENT-YRVLVEGYGLR 1198

Query: 1265 DVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADL 1324
              MAT GV G +  +N+  E  + LGIEAAR+TI  EI  VM    M ID RH  L+AD+
Sbjct: 1199 ACMATEGVVGTQVRTNSVMECGQVLGIEAARTTIADEIAEVMGY--MGIDPRHMQLLADV 1256

Query: 1325 MTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPM 1384
            MT KGEVLGITR GL+K ++SVL+LASFE  +DHLFDA    + D I  VSE II+G  M
Sbjct: 1257 MTYKGEVLGITRFGLSKTRDSVLHLASFEKPADHLFDAVAGMKMDRIEEVSESIILGQAM 1316

Query: 1385 NVGTGLIKLLQ 1395
            +VGTG + +++
Sbjct: 1317 SVGTGGLDVVR 1327



 Score =  132 bits (333), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 97/251 (38%), Positives = 137/251 (54%), Gaps = 22/251 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRI EIINASR ISTP+IT  L     ++ A++VK R+E+T + ++  +IE  +    
Sbjct: 1020 GVPRINEIINASRAISTPVITCPLLNKWQIEAAKVVKARIEKTYVSDILCFIEVEWDCQS 1079

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSFLI-------LKP 873
              I++++D D +  +   V + ++   I   R +      +TV      +       L P
Sbjct: 1080 GHIVMQVDTDTLANMQAGVGVFNVAQAICDQRKLKVRPEDVTVDKDIIFVRIRETDDLPP 1139

Query: 874  KDSSKS----FNSKMYQ---MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDN 926
            +  +KS    F   M +   +++ LPSV I G     RA+I  E  E  T Y++LVEG  
Sbjct: 1140 RSKNKSAAEGFRDMMLRANFLRRTLPSVPISGYPDATRALI--ETTEENT-YRVLVEGYG 1196

Query: 927  LRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVA 986
            LR  MAT GV G +  +N+  E  + LGIEAAR+TI  EI  VM    M ID RH  L+A
Sbjct: 1197 LRACMATEGVVGTQVRTNSVMECGQVLGIEAARTTIADEIAEVMGY--MGIDPRHMQLLA 1254

Query: 987  DLMTSKGEVLG 997
            D+MT KGEVLG
Sbjct: 1255 DVMTYKGEVLG 1265



 Score =  108 bits (269), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 65/172 (37%), Positives = 89/172 (51%), Gaps = 7/172 (4%)

Query: 178 TCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCG 237
           TC+ VLL +     F  +LR P L  L R  + K+I E  +KV  CPHC  ING V+K G
Sbjct: 33  TCSHVLLQDNDRQTFLKELRRPHLDNLRRSQICKRINEQCRKVKSCPHCTSINGQVRKIG 92

Query: 238 LLKISHEKYKN-----RTKKKDAIVEDLLAE-YNEAVKFNPEIEAHKKFGLIQTLNPLEV 291
           +LK++H+K+ +       KK   + +    E +  A   NPE+  H     ++ LNPL V
Sbjct: 93  VLKLTHDKFSSYNKSTSVKKVPPVAKTQFDESFATARNGNPELSKHLHKA-VEDLNPLRV 151

Query: 292 LQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
           L LF+ I   D  LL +N    +P   I   L  PP CIRPS+  D  S+ D
Sbjct: 152 LGLFQRIGSVDCELLGLNPSDGRPEMFIWQYLPAPPVCIRPSIAQDNASNED 203



 Score =  102 bits (255), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 46/59 (77%), Positives = 52/59 (88%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSF+SGL PTEF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL V+YD
Sbjct: 755 PSKGFVKNSFYSGLLPTEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSVKYD 813



 Score = 72.4 bits (176), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 54/177 (30%), Positives = 76/177 (42%), Gaps = 33/177 (18%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILA------------------LSNETLDS 1038
            G GTPV+  R      +      +PSL   EI                    L NE LD 
Sbjct: 840  GAGTPVQFHRTWTHAESLTRDDDEPSLMPHEIGIICDSMLEPYRSRYVRKGLLHNEELDY 899

Query: 1039 KEFL------QDTSENFVRDIKKFLEEFS----KKESVTSHQDKVSQPLREQILSHQDKI 1088
            ++         ++   F++ IK +++  +    K   +  +Q     P RE    H D+ 
Sbjct: 900  EDDSDYGIDEHESGRKFLKSIKSYIDGLASRLRKVREIAGYQGNT--PSRETAQDHVDRT 957

Query: 1089 GHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
                 +           C +K+ +A +EP   VGA+ AQSIGEPGTQMTLKTFHFAG
Sbjct: 958  AKVAATT---LRLFIRLCLDKFTKAHVEPGHPVGAVGAQSIGEPGTQMTLKTFHFAG 1011



 Score = 57.4 bits (137), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 27/53 (50%), Positives = 36/53 (67%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           LM  K NL+TP++GE +IAATQDFIT  YLL+ K+ FF+R     I   ++ G
Sbjct: 448 LMGVKHNLITPKSGEPIIAATQDFITAAYLLSYKDRFFDRKTFTTICIHMLDG 500


>gi|147905844|ref|NP_001080302.1| polymerase (RNA) III (DNA directed) polypeptide A, 155kDa [Xenopus
           laevis]
 gi|28422598|gb|AAH44092.1| Rpc155-prov protein [Xenopus laevis]
          Length = 489

 Score =  273 bits (697), Expect = 7e-70,   Method: Compositional matrix adjust.
 Identities = 145/258 (56%), Positives = 184/258 (71%), Gaps = 5/258 (1%)

Query: 87  VTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVG 146
           V   ++++QQ+HIQIVSK+LY QD   TP+  G+LD RMGT++K+ NC TCG+NL++C+G
Sbjct: 21  VKSAEQMRQQAHIQIVSKSLYGQDNNHTPLAFGVLDHRMGTSEKDRNCQTCGKNLAECLG 80

Query: 147 HFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVR 206
           H+GY+DL LP FH+GYF+ VI ILQ ICK  TC+R+LL  E+   F   L+ P L+YL +
Sbjct: 81  HYGYLDLELPCFHVGYFKAVIGILQMICK--TCSRILLTAEERKQFLDFLKRPGLAYLQK 138

Query: 207 KSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNE 266
           + LKKKI +  +K +VC +CG  NG VKKCGLLKI HEKYK   K  D +V   L  ++ 
Sbjct: 139 RGLKKKISDKCRKKTVCLYCGAYNGPVKKCGLLKIFHEKYKTTKKVVDPMVSHFLQSFDT 198

Query: 267 AVKFNPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLV 325
           A++ N E+E+    G  Q  LNPL VL L   IP EDIPLLLMN E  KPSDLILTRLLV
Sbjct: 199 AIEHNKEVES--LLGRAQENLNPLVVLNLLRRIPAEDIPLLLMNPEAGKPSDLILTRLLV 256

Query: 326 PPNCIRPSVISDLKSDND 343
           PP CIRPSV+SDLKS  +
Sbjct: 257 PPLCIRPSVVSDLKSGTN 274



 Score = 45.4 bits (106), Expect = 0.26,   Method: Compositional matrix adjust.
 Identities = 19/21 (90%), Positives = 20/21 (95%)

Query: 341 DNDVVLFNRQPSLHKLSIMAH 361
           D D+VLFNRQPSLHKLSIMAH
Sbjct: 455 DGDIVLFNRQPSLHKLSIMAH 475


>gi|403159566|ref|XP_003320172.2| DNA-directed RNA polymerase III subunit C1 [Puccinia graminis f.
           sp. tritici CRL 75-36-700-3]
 gi|375168152|gb|EFP75753.2| DNA-directed RNA polymerase III subunit C1 [Puccinia graminis f.
           sp. tritici CRL 75-36-700-3]
          Length = 1419

 Score =  272 bits (696), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 138/277 (49%), Positives = 185/277 (66%), Gaps = 29/277 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIM+HRAK+ P RTFRFNECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 472 DGDVVLFNRQPSLHKLSIMSHRAKIRPWRTFRFNECVCTPYNADFDGDEMNLHVPQTEEA 531

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EA                LM  K NLVTPRNGE +IAATQDFIT  +LL++K+ F++R
Sbjct: 532 RTEATE--------------LMNIKYNLVTPRNGEPIIAATQDFITASFLLSRKDNFYDR 577

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q  +I   L   T  I             P V  +   +WTGKQ+F+++++PN+D PV 
Sbjct: 578 QQFSQILQYLSDATLHI----------DLPPPVIWKPVRLWTGKQVFNVLMRPNKDSPVK 627

Query: 521 ANLKTKGRAYT-ANEEF----CHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            N++ K   +  A  E+       D +++++NSE++ G +DK+ +G G K ++F ++  D
Sbjct: 628 VNVEAKCATHQKAAPEYLPDMSPNDGWLVIQNSEIMCGVVDKAIVGGGKKDSIFAVINCD 687

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
           FG D AV AM RL+++++ +L N GFSIG+GDVTPG+
Sbjct: 688 FGPDEAVKAMNRLAKVSARWLANMGFSIGVGDVTPGE 724



 Score =  213 bits (541), Expect = 8e-52,   Method: Compositional matrix adjust.
 Identities = 160/496 (32%), Positives = 225/496 (45%), Gaps = 90/496 (18%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G+G PVE  R      A  S      L   EI  L  + L    F    ++ F   +  F
Sbjct: 931  GDGEPVEFARTWRHTKATVSHLDGRGLHPYEITQLVTDGLAQPRFTTACTQRFRDSVLDF 990

Query: 1057 LEEFSKKESVTSHQDKVSQP---LREQILSHQDKIGHGRESNPFPSACKAEA-------- 1105
            + E   K +    Q     P   L      + D      E++      K +         
Sbjct: 991  MVERVVKPAANFRQSYGMYPALELEGDWDEYTDLSAGVSEASKKIVINKTQVTLKQIETF 1050

Query: 1106 ---CREKYVRAQIEPATAVGAL-------------------------------------- 1124
               C +KYV+A++EP TAVGA+                                      
Sbjct: 1051 LDHCWKKYVKAKVEPGTAVGAVGAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEII 1110

Query: 1125 -AAQSIGEPGTQMTLKTFH---------------FAGEVCEYIEEVFVPDDSFILIKLDM 1168
             A++ I  P     L   H               + G+V   IEE++  D  ++ I +DM
Sbjct: 1111 NASKLINGPIINAPLVANHNERSARIVKARLEKTYLGDVTSVIEEMYSNDSMYLGIHIDM 1170

Query: 1169 DRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSK-------------- 1214
            + ++ L LEV +DSI++ I      +  L ++     I+  K+  +              
Sbjct: 1171 ETVQRLQLEVTLDSIKWSIIN----APKLKITADQIQIIPRKNRIRVYVDTNLADGEKVL 1226

Query: 1215 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 1274
             F  K+  ++++LP VVIKG+    R VI++       +Y+LLVEG  L DVM T GV G
Sbjct: 1227 PFYQKLMFLRRVLPGVVIKGLPKAGRTVINKNSK---NEYELLVEGYGLLDVMTTDGVVG 1283

Query: 1275 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGI 1334
                 N+  E    LGIEAAR+ I+ EI   M++HG+ +D RH ML+ D+M  KGEVLGI
Sbjct: 1284 THTMPNHIMEAQSVLGIEAARNCIIKEISYTMDSHGLKVDPRHMMLLGDIMCYKGEVLGI 1343

Query: 1335 TRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMN-VGTGLIKL 1393
            TR G+AKMK+SVL LASFE T+DHLFDAA Y + D I GVSECIIMG P N +GT    L
Sbjct: 1344 TRFGIAKMKDSVLMLASFEKTTDHLFDAALYSKRDAIEGVSECIIMGNPANDIGTSAACL 1403

Query: 1394 LQAVPRSEPVPRTLLF 1409
            +  VP+  P  + L +
Sbjct: 1404 VSEVPKLPPRRKVLFY 1419



 Score =  191 bits (484), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 102/231 (44%), Positives = 133/231 (57%), Gaps = 5/231 (2%)

Query: 113 RTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQS 172
           + P   G+LD R+GT+ K   C TC   ++DCVGH+ YI L LPVFHIGYFR VI +LQ 
Sbjct: 61  KKPAKGGVLDSRLGTSDKSGICGTCNAKMADCVGHYSYIKLILPVFHIGYFRAVIQMLQD 120

Query: 173 ICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGV 232
           ICK  TCARVLL EE    +  K R P L  L R+ L K++    +K+  CP+CG  NG 
Sbjct: 121 ICK--TCARVLLSEEDRRLYLIKFRRPNLENLQRQHLAKQVNTACRKIITCPYCGATNGT 178

Query: 233 VKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVL 292
           VKK G L+I HEK+  R KKK   +      +  AVK   E+  H      + +NPL VL
Sbjct: 179 VKKVGALRIIHEKF--RAKKKADELAAFRDTFITAVKETKELGPHLHKAQ-EDMNPLRVL 235

Query: 293 QLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
            LF  I   D  LL ++ E+ +P + I   + VPP CIRPSV  +  ++ D
Sbjct: 236 NLFRRITPSDCELLGLDPEVGRPEEYIWQYIHVPPVCIRPSVAQEAATNED 286



 Score =  167 bits (424), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 102/248 (41%), Positives = 144/248 (58%), Gaps = 21/248 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ I+ PII A L  + +   ARIVK RLE+T LG+V   IEE++  D 
Sbjct: 1102 GVPRIKEIINASKLINGPIINAPLVANHNERSARIVKARLEKTYLGDVTSVIEEMYSNDS 1161

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSK----- 878
             ++ I +DM+ ++ L LEV +DSI++ I      +  L ++     I+  K+  +     
Sbjct: 1162 MYLGIHIDMETVQRLQLEVTLDSIKWSIIN----APKLKITADQIQIIPRKNRIRVYVDT 1217

Query: 879  ---------SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRD 929
                      F  K+  ++++LP VVIKG+    R VI++       +Y+LLVEG  L D
Sbjct: 1218 NLADGEKVLPFYQKLMFLRRVLPGVVIKGLPKAGRTVINKNS---KNEYELLVEGYGLLD 1274

Query: 930  VMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLM 989
            VM T GV G     N+  E    LGIEAAR+ I+ EI   M++HG+ +D RH ML+ D+M
Sbjct: 1275 VMTTDGVVGTHTMPNHIMEAQSVLGIEAARNCIIKEISYTMDSHGLKVDPRHMMLLGDIM 1334

Query: 990  TSKGEVLG 997
              KGEVLG
Sbjct: 1335 CYKGEVLG 1342



 Score = 99.0 bits (245), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 46/68 (67%), Positives = 53/68 (77%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV+NSF SGL  TEF FH + GREGLVDTAVKTAETGYMQRRL+K+LEDL  +YD 
Sbjct: 846 PAKGFVRNSFHSGLRATEFLFHAISGREGLVDTAVKTAETGYMQRRLMKALEDLATRYDD 905

Query: 670 SFDAAFYG 677
           S   +  G
Sbjct: 906 SVRNSVGG 913



 Score = 60.1 bits (144), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 29/50 (58%), Positives = 37/50 (74%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM  K NLVTPRNGE +IAATQDFIT  +LL++K+ F++R Q  +I   L
Sbjct: 538 LMNIKYNLVTPRNGEPIIAATQDFITASFLLSRKDNFYDRQQFSQILQYL 587



 Score = 51.6 bits (122), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 26/54 (48%), Positives = 32/54 (59%), Gaps = 1/54 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMN-VGTGLIKLLQAVPRSEPVPRTLLF 720
            D  FDAA Y + D I GVSECIIMG P N +GT    L+  VP+  P  + L +
Sbjct: 1366 DHLFDAALYSKRDAIEGVSECIIMGNPANDIGTSAACLVSEVPKLPPRRKVLFY 1419


>gi|448115320|ref|XP_004202788.1| Piso0_001648 [Millerozyma farinosa CBS 7064]
 gi|359383656|emb|CCE79572.1| Piso0_001648 [Millerozyma farinosa CBS 7064]
          Length = 1454

 Score =  272 bits (696), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 135/275 (49%), Positives = 187/275 (68%), Gaps = 29/275 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH+LSI++H AKV P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 464 DGDVVLFNRQPSLHRLSILSHFAKVRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 523

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL+TP++GE +IAATQDFITG YL++ K++F++R
Sbjct: 524 RAEAMN--------------LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFYDR 569

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A  +++ S +++D +          +    P +F +  ++WTGKQ+FSL+++PN+   V 
Sbjct: 570 AALVQMLS-MMSDAN--------VQYDIPPPAIF-KPVMLWTGKQLFSLLIRPNKKSKVL 619

Query: 521 ANLKTKGRAYTA-----NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL  K + +         E    D +V++R S++L+G MDKS LG G K +VFY +LRD
Sbjct: 620 INLDAKNKTFIPPLKGFPNEMSQNDGFVVIRGSQILSGVMDKSLLGDGKKHSVFYTILRD 679

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           +G D A  AM R++++ + ++ NRGFSIGI DV P
Sbjct: 680 YGPDEAANAMNRMAKLCARFMGNRGFSIGINDVIP 714



 Score =  252 bits (643), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 158/387 (40%), Positives = 215/387 (55%), Gaps = 82/387 (21%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCE 1149
            + C  KY RA++EP TAVGA+ A SIGEPGTQMTLKTFHFAG              E+  
Sbjct: 1063 DQCVYKYFRAKVEPGTAVGAIGAHSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIIN 1122

Query: 1150 --------YIEEVFVPDD--------------------------------SFILIKLDMD 1169
                     I  V V DD                                ++I IK+D+D
Sbjct: 1123 ASKVISTPIINSVLVNDDDERAARVVKGRIEKTLLEDVAFYIEDVYKENMAYISIKVDLD 1182

Query: 1170 RIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHS----FLILKPKDS---------- 1212
             I  L LE+ I+ I   I     +   +  + +SG       + LK   +          
Sbjct: 1183 TIEKLQLELTIEQIARAIANAPKLKISAADVAISGKDKINVLVTLKENKADNLMRNIAAD 1242

Query: 1213 --SKSFNSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDV 1266
              S   N+ ++     +K+ LP + + G+  I+RAVI+  D +G  K +LLVEG  L++V
Sbjct: 1243 YGSTDMNNSLFFRAQVLKRALPQICVNGLSDISRAVINIRD-DG--KKELLVEGYGLKNV 1299

Query: 1267 MATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMT 1326
            M+T GV G K ++N+  E+++ LGIEAAR++I+ EI   M NHGMS+D RH  L+ D+MT
Sbjct: 1300 MSTDGVVGTKTTTNHVLEIFQVLGIEAARASIIKEIDYTMTNHGMSVDPRHIQLLGDVMT 1359

Query: 1327 SKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNV 1386
             KGEVLGITR GL+KM++SVL LASFE T+DHLFDA+FY + D I GVSECII+G  MN+
Sbjct: 1360 YKGEVLGITRFGLSKMRDSVLQLASFEKTTDHLFDASFYMKEDKIEGVSECIILGQTMNI 1419

Query: 1387 GTGLIKLLQAVPRSEPV--PRTLLFDN 1411
            GTG  KL+++   SE    P+  LF+N
Sbjct: 1420 GTGAFKLVKSFNISESALKPKEALFEN 1446



 Score =  181 bits (460), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 108/272 (39%), Positives = 150/272 (55%), Gaps = 11/272 (4%)

Query: 79  FRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCG 138
            +G+  G ++  D +  QS +++ +++LY  +  RT    G LD RMG +   + C+TC 
Sbjct: 13  IKGVQFGALSASD-IIAQSEVEVQTRDLYDLEKGRTAKESGALDTRMGISSNSSECSTCH 71

Query: 139 QNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN 198
            NL+ C GHFG+I L LPVFH+GYF+ ++++LQSICKN  C  +LL E     F  +LR 
Sbjct: 72  GNLASCHGHFGHIRLALPVFHVGYFKNIMSVLQSICKN--CGAILLDETTRRSFLNELRR 129

Query: 199 PALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKC------GLLKISHEKYKNRTKK 252
           P L  L R  + K+ILE  KK   C  C  INGVVKK         LKI H+ ++   KK
Sbjct: 130 PNLDNLKRMKILKRILEQCKKQRRCVKCNHINGVVKKAASGSGPAALKIVHDTFRWIGKK 189

Query: 253 KDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMN-AE 311
                     E++E    NPE+E   K  +   LNPL+VL LF+ I   D  LL ++ A 
Sbjct: 190 PTPEKALWNEEFDEVFARNPELEKFSK-RVYDDLNPLKVLNLFKQIEPADCELLGIDPAR 248

Query: 312 LSKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
             +P   I   L  PP CIRPSV+ D +S+ D
Sbjct: 249 GGRPEMYIWRYLPAPPVCIRPSVMMDTQSNED 280



 Score =  179 bits (453), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 109/257 (42%), Positives = 157/257 (61%), Gaps = 26/257 (10%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII + L  D D   AR+VKGR+E+T L +V  YIE+V+  + 
Sbjct: 1113 GVPRIKEIINASKVISTPIINSVLVNDDDERAARVVKGRIEKTLLEDVAFYIEDVYKENM 1172

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHS----FLILKPKDS 876
            ++I IK+D+D I  L LE+ I+ I   I     +   +  + +SG       + LK   +
Sbjct: 1173 AYISIKVDLDTIEKLQLELTIEQIARAIANAPKLKISAADVAISGKDKINVLVTLKENKA 1232

Query: 877  ------------SKSFNSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKL 920
                        S   N+ ++     +K+ LP + + G+  I+RAVI+  D +G  K +L
Sbjct: 1233 DNLMRNIAADYGSTDMNNSLFFRAQVLKRALPQICVNGLSDISRAVINIRD-DG--KKEL 1289

Query: 921  LVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFR 980
            LVEG  L++VM+T GV G K ++N+  E+++ LGIEAAR++I+ EI   M NHGMS+D R
Sbjct: 1290 LVEGYGLKNVMSTDGVVGTKTTTNHVLEIFQVLGIEAARASIIKEIDYTMTNHGMSVDPR 1349

Query: 981  HPMLVADLMTSKGEVLG 997
            H  L+ D+MT KGEVLG
Sbjct: 1350 HIQLLGDVMTYKGEVLG 1366



 Score =  103 bits (258), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 48/61 (78%), Positives = 53/61 (86%), Gaps = 1/61 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV+NSFFSGL+PTEF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QY
Sbjct: 836 TPQSKGFVRNSFFSGLSPTEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSTQY 895

Query: 668 D 668
           D
Sbjct: 896 D 896



 Score = 61.2 bits (147), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 26/50 (52%), Positives = 41/50 (82%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM  K+NL+TP++GE +IAATQDFITG YL++ K++F++RA  +++ S +
Sbjct: 530 LMGVKNNLLTPKSGEPIIAATQDFITGSYLISHKDSFYDRAALVQMLSMM 579



 Score = 58.2 bits (139), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 29/57 (50%), Positives = 38/57 (66%), Gaps = 2/57 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPV--PRTLLFDN 722
            D  FDA+FY + D I GVSECII+G  MN+GTG  KL+++   SE    P+  LF+N
Sbjct: 1390 DHLFDASFYMKEDKIEGVSECIILGQTMNIGTGAFKLVKSFNISESALKPKEALFEN 1446


>gi|449296109|gb|EMC92129.1| hypothetical protein BAUCODRAFT_78328 [Baudoinia compniacensis UAMH
           10762]
          Length = 1477

 Score =  272 bits (695), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 133/285 (46%), Positives = 181/285 (63%), Gaps = 39/285 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++H+ KV P RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 482 DGDIVLFNRQPSLHKLSILSHKVKVRPWRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 541

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EA+               LM  K NL TP+NG  +IAA QDFITG YL++QK+ FF R
Sbjct: 542 RTEAIE--------------LMGVKHNLATPKNGTPIIAAIQDFITGSYLISQKDRFFTR 587

Query: 461 AQ----------TMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLI 510
            Q           M +   L  +  D+             P    +   +WTGKQ+++++
Sbjct: 588 RQFCQIVTFMFDGMHVDDPLTGEQRDV----------QIPPPAIFKPQSLWTGKQVWNVL 637

Query: 511 LKPNRDCPVNANLKTKGRAYTA-----NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGK 565
           +KP+   PVN NL  KG+ Y+A       +    DSY+++RNSE++ G+MDK+ +G G K
Sbjct: 638 MKPHPSYPVNVNLDAKGKQYSAPLGNTAPDLLPNDSYLVVRNSEVMCGTMDKAVIGDGKK 697

Query: 566 ANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
            ++FY+++RDFG + AV AM RL+++++ +L  +GFSIGI DV P
Sbjct: 698 DSIFYVIMRDFGPEYAVAAMNRLAKLSARWLTEQGFSIGISDVYP 742



 Score =  211 bits (536), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 129/362 (35%), Positives = 193/362 (53%), Gaps = 72/362 (19%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFH----------------------- 1142
            C  K+ ++++EP  AVGA+ AQSIGEPGTQMTLKTFH                       
Sbjct: 1079 CLRKFEKSKVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIINAS 1138

Query: 1143 ------------------FAG-------------EVCEYIEEVFVPDDSFILIKLDMDRI 1171
                               AG             ++  Y+E+V+     ++ +++D   +
Sbjct: 1139 RVISTPVITCALDSRYEELAGRFAKAIIQKTYLKDIVAYVEDVWFVGGCYLNMRIDWRTV 1198

Query: 1172 RLLHLEVDIDSIRYCIERTRG-----ISGHLTVSGHSFLILKPKDSSKSFNSK------- 1219
              L L + +  ++  +ER +G     +   +    H  +      +S++ N+        
Sbjct: 1199 EGLGLRIGMAEVKDAVERHKGFKTLNVEARVVGGCHLRVFCDTPSASQTKNAAVTDELFM 1258

Query: 1220 -MYQMKQLLPSVVIKGVQGINRAVIHEEDVE---GVTKYKLLVEGDNLRDVMATYGVKGV 1275
             + Q+K+ LP+VVI+G    +RA++ ++D     G     + VEG  L+  M T G+ G+
Sbjct: 1259 TIQQLKRRLPNVVIRGYPDAHRAILKKDDKPDRTGREPISVFVEGYGLKLCMTTPGIDGL 1318

Query: 1276 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGIT 1335
              ++N+  EV   LGIEAAR TI++EI  VM   GM ID RH  L+AD+MT +GEVLGIT
Sbjct: 1319 HTTTNSIMEVASVLGIEAARRTIISEISSVM--GGMDIDPRHMQLLADVMTYRGEVLGIT 1376

Query: 1336 RHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 1395
            R GL+KM++SVL LASFE T DHLFDAA  G+ D + GVSECIIMG P+ +GTG + +++
Sbjct: 1377 RFGLSKMRDSVLQLASFEKTPDHLFDAAVGGKRDEVKGVSECIIMGQPVRIGTGSVGIVR 1436

Query: 1396 AV 1397
             +
Sbjct: 1437 PL 1438



 Score =  152 bits (385), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 90/263 (34%), Positives = 142/263 (53%), Gaps = 18/263 (6%)

Query: 96  QSHIQIVSKNLYCQDPQRT-----PI-PHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFG 149
           QS + I  +NLY  +  R      P+  HG LD ++GT+ K + C TCG  L +C GHFG
Sbjct: 40  QSVVNINDRNLYDLEADRETGKGRPLTKHGPLDEKLGTSGKNSLCQTCGLGLKECNGHFG 99

Query: 150 YIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSL 209
           ++ L LP  H GY + ++++L  +CK   C+R+LL E++      +LR P L  L + +L
Sbjct: 100 HVKLTLPALHYGYMKKIVDVLSCVCKG--CSRILLPEKERRVALRQLRRPGLDSLRKAAL 157

Query: 210 KKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKYKN------RTKKKDAIVEDLL 261
            KKI    KK+ VCP C  +NG V++     +KI H ++        ++K+K   + +  
Sbjct: 158 CKKISADCKKIKVCPRCAGLNGPVRRQAHHPVKIMHHRFAKYTSSNAKSKQKPQAMVEFE 217

Query: 262 AEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMN-AELSKPSDLIL 320
             + EA K + +IE + +  L   L PL VL +F+ +P  D+ LL ++ +   +P  ++ 
Sbjct: 218 ESFTEAKKASADIERNMRRAL-DDLTPLRVLHIFKKMPDMDVELLGLDPSRGGRPEYMVW 276

Query: 321 TRLLVPPNCIRPSVISDLKSDND 343
           T +  PP  IRPSV  D  S  D
Sbjct: 277 THVPAPPVAIRPSVAQDAASTED 299



 Score =  144 bits (364), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 94/274 (34%), Positives = 149/274 (54%), Gaps = 19/274 (6%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINASR ISTP+IT  LD   +    R  K  +++T L ++  Y+E+V+    
Sbjct: 1127 GVPRIKEIINASRVISTPVITCALDSRYEELAGRFAKAIIQKTYLKDIVAYVEDVWFVGG 1186

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRG-----ISGHLTVSGHSFLILKPKDSSK 878
             ++ +++D   +  L L + +  ++  +ER +G     +   +    H  +      +S+
Sbjct: 1187 CYLNMRIDWRTVEGLGLRIGMAEVKDAVERHKGFKTLNVEARVVGGCHLRVFCDTPSASQ 1246

Query: 879  SFNSK--------MYQMKQLLPSVVIKGVQGINRAVIHEEDVE---GVTKYKLLVEGDNL 927
            + N+         + Q+K+ LP+VVI+G    +RA++ ++D     G     + VEG  L
Sbjct: 1247 TKNAAVTDELFMTIQQLKRRLPNVVIRGYPDAHRAILKKDDKPDRTGREPISVFVEGYGL 1306

Query: 928  RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 987
            +  M T G+ G+  ++N+  EV   LGIEAAR TI++EI  VM   GM ID RH  L+AD
Sbjct: 1307 KLCMTTPGIDGLHTTTNSIMEVASVLGIEAARRTIISEISSVM--GGMDIDPRHMQLLAD 1364

Query: 988  LMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDP 1021
            +MT +GEVLG  T   L ++ D ++   S    P
Sbjct: 1365 VMTYRGEVLGI-TRFGLSKMRDSVLQLASFEKTP 1397



 Score =  103 bits (256), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 47/59 (79%), Positives = 50/59 (84%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV NSFFSGL PTEF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL  +YD
Sbjct: 866 PAKGFVVNSFFSGLNPTEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSARYD 924



 Score = 61.2 bits (147), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 29/56 (51%), Positives = 37/56 (66%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKV 77
           LM  K NL TP+NG  +IAA QDFITG YL++QK+ FF R Q  +I + +  G  V
Sbjct: 548 LMGVKHNLATPKNGTPIIAAIQDFITGSYLISQKDRFFTRRQFCQIVTFMFDGMHV 603



 Score = 46.6 bits (109), Expect = 0.095,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 29/41 (70%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 708
            D  FDAA  G+ D + GVSECIIMG P+ +GTG + +++ +
Sbjct: 1398 DHLFDAAVGGKRDEVKGVSECIIMGQPVRIGTGSVGIVRPL 1438


>gi|119490427|ref|XP_001263030.1| DNA-directed RNA polymerase III largest subunit, putative
           [Neosartorya fischeri NRRL 181]
 gi|119411190|gb|EAW21133.1| DNA-directed RNA polymerase III largest subunit, putative
           [Neosartorya fischeri NRRL 181]
          Length = 1453

 Score =  271 bits (694), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 134/282 (47%), Positives = 184/282 (65%), Gaps = 29/282 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++H AKV PHRTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 470 DGDIVLFNRQPSLHKLSILSHFAKVRPHRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 529

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NL TP+NGE +I+A QDFI+  Y+L+ K+ FF+R
Sbjct: 530 RAEAME--------------LMGVKNNLATPKNGEPIISAIQDFISAAYILSSKDNFFDR 575

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
               +I   ++       G   RF      P   ++  ++WTGKQ+F+++++P++D PV 
Sbjct: 576 RSFTQICLYML-------GPETRF---DLPPPAVLKPQMLWTGKQVFNILMRPSKDDPVL 625

Query: 521 ANLKTKGRAYTA-----NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL    R +        ++    D ++++RNSE++ G MDK+T+GSG K NVFYI+LRD
Sbjct: 626 VNLDAACREFKPPKDGRPKDLDPNDGWLVIRNSEVMCGVMDKATIGSGKKDNVFYIMLRD 685

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           FG   A   M RLS++++ +  N GFSIGI DV P +  V++
Sbjct: 686 FGPAAAAEGMNRLSKLSARWFTNMGFSIGITDVYPSESLVRS 727



 Score =  218 bits (556), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 141/370 (38%), Positives = 201/370 (54%), Gaps = 87/370 (23%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEY 1150
            +C  KY +AQ+EP  AVGA+ AQSIGEPGTQMTLKTFHFAG              E+   
Sbjct: 1054 SCLMKYKKAQVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIINA 1113

Query: 1151 IEEVFVP----------------------------------------DDSFILIKLDMDR 1170
             +E+  P                                         ++++ +K++ + 
Sbjct: 1114 SKEISTPVISCDLVTKDNVIAARIVKGRIEKTYLRDIIHYVREAWTGKEAYLTVKINWET 1173

Query: 1171 IRLLHLEVDIDSIRYCIE----------RTRGISGHLTVSGHSFLILKPKDSSKSFNSK- 1219
            I+ L LE+ I +I   I+          + R  + H+    H ++ + P  +SK+  SK 
Sbjct: 1174 IQNLALELKIRNIVDAIKNHKRFKADDLKFRSTNSHI----HIYMDIDP--ASKASLSKT 1227

Query: 1220 ------------MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVM 1267
                        +  +K++LP + + G    +RA+I  +D        LLVEG  L++ M
Sbjct: 1228 EIAATSADPFLRLKHLKRILPDIQVLGHPQASRAIIRTDDTSSTN--TLLVEGYGLKECM 1285

Query: 1268 ATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTS 1327
             T GV G++ S+NN  E+   LGIEAAR TI+ EI  VM++  M ID RH  L+AD+MT 
Sbjct: 1286 TTLGVNGLRTSTNNVMEMRDVLGIEAARVTIVQEISEVMKD--MGIDPRHMQLLADVMTY 1343

Query: 1328 KGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVG 1387
            KGEVLGITR GLAKM++SVL LASFE T+DHLFDA   G+TD I GVSECIIMG  +++G
Sbjct: 1344 KGEVLGITRFGLAKMRDSVLQLASFEKTADHLFDAGGAGRTDLIEGVSECIIMGKTVSLG 1403

Query: 1388 TGLIKLLQAV 1397
            TG +++++ +
Sbjct: 1404 TGAMEVVRKL 1413



 Score =  181 bits (460), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 103/267 (38%), Positives = 144/267 (53%), Gaps = 15/267 (5%)

Query: 87  VTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVG 146
           V   D +  Q+ +++  +  +  +  R  +PHG LD RMG + K A C TCG +L  C G
Sbjct: 31  VLSNDDIVSQAVVEVSDRKFFDLEHDRAVVPHGPLDGRMGISSKTATCQTCGGSLQVCNG 90

Query: 147 HFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVR 206
           HFG++ L LP FH+GYF+ VI+ILQ ICK   C+R+LL E +   F  ++R P L  L R
Sbjct: 91  HFGHVRLVLPAFHVGYFKRVISILQEICKE--CSRILLPEAERRAFLREMRRPGLDNLRR 148

Query: 207 KSLKKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKYK--------NRTKKKDAI 256
             + K+I E  +K   C  CG INGVVKK G   LKI+H+K++         +      I
Sbjct: 149 LQIAKRINERCRKTRTCEACGAINGVVKKAGNSALKITHDKFRAFNVSTSVKKVPPPSKI 208

Query: 257 VEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPS 316
           V D    ++EA   N E+E H K      +N L VL LF+ +   D  LL +N + ++P 
Sbjct: 209 VFD--RSFDEARTSNAEVEKHYKKAQ-DDMNALRVLNLFKKVSDTDCELLGLNPKEARPE 265

Query: 317 DLILTRLLVPPNCIRPSVISDLKSDND 343
             +   +  PP CIRPSV  D  S  D
Sbjct: 266 MFLWQFIPAPPVCIRPSVGQDAASTED 292



 Score =  152 bits (385), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 98/257 (38%), Positives = 149/257 (57%), Gaps = 33/257 (12%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+I+  L    ++  ARIVKGR+E+T L ++  Y+ E +   +
Sbjct: 1103 GVPRIKEIINASKEISTPVISCDLVTKDNVIAARIVKGRIEKTYLRDIIHYVREAWTGKE 1162

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIE----------RTRGISGHLTVSGHSFLILKP 873
            +++ +K++ + I+ L LE+ I +I   I+          + R  + H+    H ++ + P
Sbjct: 1163 AYLTVKINWETIQNLALELKIRNIVDAIKNHKRFKADDLKFRSTNSHI----HIYMDIDP 1218

Query: 874  KDSSKSFNSK-------------MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKL 920
              +SK+  SK             +  +K++LP + + G    +RA+I  +D        L
Sbjct: 1219 --ASKASLSKTEIAATSADPFLRLKHLKRILPDIQVLGHPQASRAIIRTDDTSSTN--TL 1274

Query: 921  LVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFR 980
            LVEG  L++ M T GV G++ S+NN  E+   LGIEAAR TI+ EI  VM++  M ID R
Sbjct: 1275 LVEGYGLKECMTTLGVNGLRTSTNNVMEMRDVLGIEAARVTIVQEISEVMKD--MGIDPR 1332

Query: 981  HPMLVADLMTSKGEVLG 997
            H  L+AD+MT KGEVLG
Sbjct: 1333 HMQLLADVMTYKGEVLG 1349



 Score =  103 bits (258), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 47/59 (79%), Positives = 51/59 (86%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSFFSGL PTEF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL  +YD
Sbjct: 844 PSKGFVRNSFFSGLLPTEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSSRYD 902



 Score = 53.5 bits (127), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 23/46 (50%), Positives = 33/46 (71%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRI 67
           LM  K+NL TP+NGE +I+A QDFI+  Y+L+ K+ FF+R    +I
Sbjct: 536 LMGVKNNLATPKNGEPIISAIQDFISAAYILSSKDNFFDRRSFTQI 581



 Score = 45.1 bits (105), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 30/41 (73%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 708
            D  FDA   G+TD I GVSECIIMG  +++GTG +++++ +
Sbjct: 1373 DHLFDAGGAGRTDLIEGVSECIIMGKTVSLGTGAMEVVRKL 1413


>gi|451993939|gb|EMD86411.1| hypothetical protein COCHEDRAFT_1186563 [Cochliobolus
           heterostrophus C5]
          Length = 1473

 Score =  271 bits (693), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 134/276 (48%), Positives = 181/276 (65%), Gaps = 18/276 (6%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++HRAKV P RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 482 DGDIVLFNRQPSLHKLSILSHRAKVRPWRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 541

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EA                LM  K NL TP+NG  +IAA QDFIT  YLL+ KN FF+R
Sbjct: 542 RTEATE--------------LMGVKYNLATPKNGTPIIAAIQDFITAAYLLSNKNNFFDR 587

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
               +I + +            +       P V ++   +WTGKQ+F+L+++P + C V 
Sbjct: 588 RTFCQIVNYMFNGEGAFDPDTGKRHPIEIPPPVVLKPQALWTGKQVFNLLMRPYKKCRVL 647

Query: 521 ANLKTKGRAY--TANE--EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL+   + +  T ++  +    D+Y+++RNSE++ G MDK+T+G G K +VFY+++RDF
Sbjct: 648 VNLEAACKQFKNTPDQPPDLNENDAYLVIRNSEVMCGVMDKATVGDGKKDSVFYVMMRDF 707

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
           G D AV  M RLS++++ +L N GFS+GI DVTPG+
Sbjct: 708 GPDHAVQGMNRLSKLSARWLSNNGFSLGISDVTPGE 743



 Score =  222 bits (565), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 142/366 (38%), Positives = 196/366 (53%), Gaps = 76/366 (20%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGE------------------- 1146
            C  KY R++++P  AVGA+ AQSIGEPGTQMTLKTFHFAG                    
Sbjct: 1090 CLTKYHRSRVQPGHAVGAIGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIINAS 1149

Query: 1147 --------VCE---------------------------YIEEVFVPDDSFILIKLDMDRI 1171
                     CE                           Y+E+V+ P+ ++I +++D D I
Sbjct: 1150 STISTPVIACELSNKISESAARIVKARVEKTYLRDVISYVEDVWHPNGAYIAMRIDWDTI 1209

Query: 1172 RLLHLEVDIDSIRYCIERTR----GISGHLTVSGHSFLILKPKDSS-------------K 1214
              L ++V    I   I   +    G +G       S + ++  D +             K
Sbjct: 1210 NKLFVDVQPYEIAAAINAHKPLKWGKAGANVRISSSIIRVEVPDPNAAKKRPVKTTRNHK 1269

Query: 1215 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEE---DVEGVTKYKLLVEGDNLRDVMATYG 1271
             +  ++ Q+K L+P VVIKG    +RA+I +E   + +G  + +LLVEG  L+D M T G
Sbjct: 1270 EYFERVQQVKSLIPDVVIKGYPDCSRAIIKKESSPNAQGHYECQLLVEGYGLQDCMTTPG 1329

Query: 1272 VKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 1331
            ++     SN+  EV   LGIEAAR+TI+ EI  VM N  M ID RH  L+AD+MT KGEV
Sbjct: 1330 IEPYNTKSNHVMEVKTVLGIEAARATIVREIGDVMGN--MDIDPRHMQLLADVMTFKGEV 1387

Query: 1332 LGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLI 1391
             GITR GL K ++SVL LASFE T DHLF+AA  G+TD I GVSECIIMG  + +GTG +
Sbjct: 1388 FGITRFGLQKTRDSVLQLASFEKTPDHLFEAAARGKTDTIDGVSECIIMGQSVKLGTGAM 1447

Query: 1392 KLLQAV 1397
            ++++ +
Sbjct: 1448 QVVRPL 1453



 Score =  159 bits (403), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 96/273 (35%), Positives = 149/273 (54%), Gaps = 16/273 (5%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLY----CQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G  + +D V Q + +++  +N+Y      D  RT   +G +D RMG + K+  C TCG+ 
Sbjct: 26  GIYSNQDIVNQ-AVLEVSDRNVYDLQPAADNTRTLTANGPMDTRMGISSKQGTCATCGEG 84

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
           L  C GHFG+I L LP FH+GY + +I +L  ICK+  C+RVLL E +   +   +R P 
Sbjct: 85  LDTCNGHFGHIKLALPAFHVGYLKHIIEVLNCICKD--CSRVLLDEVERRRYLRSMRRPD 142

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKYK--NRTKKKDAI 256
           +  L + ++ K+ILE  +K   CP+C  + G V+K     LKI H +Y   NR+  K   
Sbjct: 143 MDTLRKGAVTKRILEDCRKKKTCPYCNGLQGTVRKVPGHPLKIIHNRYDAFNRSTAKTKK 202

Query: 257 VEDLLAEYNEAVK----FNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL 312
                 E++++ +     NP+++ H K   +  ++PL VL LF+ I  ED  LL M  E 
Sbjct: 203 APPGKIEFDQSFETSKSANPDLDKHLKKA-VDDMHPLRVLNLFKKISPEDCELLAMIPED 261

Query: 313 SKPSDLILTRLLVPPNCIRPSVISDLKSDNDVV 345
           ++P  LI   + VPP  +RPSV+ +  +  D V
Sbjct: 262 ARPEMLIWEYMPVPPVALRPSVMQEGGATEDDV 294



 Score =  157 bits (396), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 102/254 (40%), Positives = 143/254 (56%), Gaps = 22/254 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS  ISTP+I   L        ARIVK R+E+T L +V  Y+E+V+ P+ 
Sbjct: 1138 GVPRIKEIINASSTISTPVIACELSNKISESAARIVKARVEKTYLRDVISYVEDVWHPNG 1197

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTR----GISGHLTVSGHSFLILKPKDSS-- 877
            ++I +++D D I  L ++V    I   I   +    G +G       S + ++  D +  
Sbjct: 1198 AYIAMRIDWDTINKLFVDVQPYEIAAAINAHKPLKWGKAGANVRISSSIIRVEVPDPNAA 1257

Query: 878  -----------KSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEE---DVEGVTKYKLLVE 923
                       K +  ++ Q+K L+P VVIKG    +RA+I +E   + +G  + +LLVE
Sbjct: 1258 KKRPVKTTRNHKEYFERVQQVKSLIPDVVIKGYPDCSRAIIKKESSPNAQGHYECQLLVE 1317

Query: 924  GDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPM 983
            G  L+D M T G++     SN+  EV   LGIEAAR+TI+ EI  VM N  M ID RH  
Sbjct: 1318 GYGLQDCMTTPGIEPYNTKSNHVMEVKTVLGIEAARATIVREIGDVMGN--MDIDPRHMQ 1375

Query: 984  LVADLMTSKGEVLG 997
            L+AD+MT KGEV G
Sbjct: 1376 LLADVMTFKGEVFG 1389



 Score =  103 bits (258), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 47/57 (82%), Positives = 50/57 (87%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV NSFFSGLTP+EF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 867 KGFVSNSFFSGLTPSEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSAQYD 923



 Score = 58.9 bits (141), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 28/57 (49%), Positives = 35/57 (61%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVF 78
           LM  K NL TP+NG  +IAA QDFIT  YLL+ KN FF+R    +I + +  G   F
Sbjct: 548 LMGVKYNLATPKNGTPIIAAIQDFITAAYLLSNKNNFFDRRTFCQIVNYMFNGEGAF 604



 Score = 45.4 bits (106), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 30/41 (73%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 708
            D  F+AA  G+TD I GVSECIIMG  + +GTG +++++ +
Sbjct: 1413 DHLFEAAARGKTDTIDGVSECIIMGQSVKLGTGAMQVVRPL 1453


>gi|242807568|ref|XP_002484983.1| DNA-directed RNA polymerase III largest subunit, putative
           [Talaromyces stipitatus ATCC 10500]
 gi|218715608|gb|EED15030.1| DNA-directed RNA polymerase III largest subunit, putative
           [Talaromyces stipitatus ATCC 10500]
          Length = 1441

 Score =  271 bits (693), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 133/281 (47%), Positives = 182/281 (64%), Gaps = 29/281 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+ L+NRQPSLHKLSI++H  KV P+RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 470 DGDIALYNRQPSLHKLSILSHFVKVRPYRTFRMNECVCNPYNADFDGDEMNLHIPQTEEA 529

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R+EA+               LM  K+NLVTP+NGE +I A QDFI+  Y+L+ K+ FF+R
Sbjct: 530 RSEAME--------------LMGVKNNLVTPKNGEPIIGAIQDFISAAYMLSSKDNFFDR 575

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
               +I   ++       G   RF      P   ++  ++WTGKQ+F+++++PN+D PV 
Sbjct: 576 RSFTQICLYML-------GPETRF---DLPPPAILKPQMLWTGKQVFNILMRPNKDDPVK 625

Query: 521 ANLKTKGRAYTANEEFCHR-----DSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            N+    R + A ++   +     D ++++RNSE++ G MDKST+GSG K NVFYI+LRD
Sbjct: 626 VNIDAACREFKAPKDGQPKDLDPNDGWLVIRNSEIMCGVMDKSTIGSGKKDNVFYIMLRD 685

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           FG   A   M RLS++ + +  N GFSIGI DV P +  VQ
Sbjct: 686 FGPPAAAEGMNRLSKLCARWFTNVGFSIGITDVYPSEKLVQ 726



 Score =  221 bits (564), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 151/390 (38%), Positives = 211/390 (54%), Gaps = 81/390 (20%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCE 1149
            ++C  KY +A+IEP  AVGA+ AQSIGEPGTQMTLKTFHFAG              E+  
Sbjct: 1052 KSCLSKYEKAKIEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVGNLALTQGVPRIKEIIN 1111

Query: 1150 YIEEV---------FVPD-------------------------------DSFILIKLDMD 1169
              +E+          VPD                               + +I +KL+ D
Sbjct: 1112 ASKEISTPVITCHLAVPDKVHAARIAKGRIEKTFLRDIIHYIRESWSDKEGYITVKLNWD 1171

Query: 1170 RIRLLHLEVDIDSIRYCIERTRGISGH-LTVS---GHSFLILKPKDSSKSFNSK------ 1219
             I  L LE+ +  I+  I   R   G  L++     H  + +    SSK+  SK      
Sbjct: 1172 TIENLQLELSLPQIKEAIINHRRFKGKDLSIDVLRSHIKIRVDMDPSSKAGLSKTDIAAT 1231

Query: 1220 -------MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGV 1272
                   +  +K++LP + + G     RA+IH E   G+   KLLVEG  LR+ M T G+
Sbjct: 1232 SADPYLRLKHLKRMLPDIQVLGHPQARRAIIHSE--RGLN--KLLVEGYGLRECMNTDGI 1287

Query: 1273 KGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL 1332
            +GV+  +NN  E+   LGIEAAR TI+ E+  VM++  M ID RH  L+AD+MT+ GEVL
Sbjct: 1288 EGVRTKTNNVMEMRAVLGIEAARGTIINEMSEVMKD--MDIDPRHMHLLADIMTTTGEVL 1345

Query: 1333 GITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIK 1392
            GITR G+AKM++SVL LASFE T+DHLFDA   G+TD + GVSECIIMG  +++GTG ++
Sbjct: 1346 GITRFGMAKMRDSVLQLASFEKTADHLFDAGGTGRTDRVEGVSECIIMGKTVSLGTGAME 1405

Query: 1393 LLQAVPRSE--PVPRTLLFDNP--EFHTNT 1418
            +++ +   E    P+  +F++   E H  T
Sbjct: 1406 VVRKLNFYEGHTGPKKTVFEDAWSEVHRET 1435



 Score =  169 bits (428), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 100/267 (37%), Positives = 144/267 (53%), Gaps = 12/267 (4%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G ++  D V  Q+ +++  +  Y  +  R    +G LDRR+G + K   C TCG    DC
Sbjct: 29  GALSDND-VISQAVVEVSDRRFYDLERDRVVQENGPLDRRLGISGKMETCLTCGLGHKDC 87

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFG++ L LP FHIGYF+ VI ILQ ICK   C+ +LL E +   F  ++R P +  L
Sbjct: 88  NGHFGHVKLVLPAFHIGYFKRVIGILQVICKE--CSAILLPEAERRAFLKEMRRPRMDNL 145

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKYK----NRTKKKDAIVE 258
            R  + K+++E  KK   CP CG +NGVVKK G   LKI HEK++    +   KK A + 
Sbjct: 146 RRLQIAKRVVERCKKTRECPRCGAVNGVVKKAGTAALKIVHEKFRYYNQSTAMKKVAPIS 205

Query: 259 DLLAE--YNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPS 316
            ++ +    EA   NP+++   K      L+ L V+ LF+ I   D  LL ++    +P 
Sbjct: 206 KIVFDNSLTEARASNPDVDRFYKKAQ-DDLHALRVMNLFKKITNADCELLGLDPTEVRPE 264

Query: 317 DLILTRLLVPPNCIRPSVISDLKSDND 343
             +   +  PPNCIRPSV  D  S+ D
Sbjct: 265 TFLWQYIPAPPNCIRPSVSQDGASNED 291



 Score =  160 bits (406), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 107/266 (40%), Positives = 151/266 (56%), Gaps = 24/266 (9%)

Query: 749  TLELWNPGDYKLSQDGVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTL 808
            T      G+  L+Q GVPRIKEIINAS+ ISTP+IT +L     +  ARI KGR+E+T L
Sbjct: 1088 TFHFAGVGNLALTQ-GVPRIKEIINASKEISTPVITCHLAVPDKVHAARIAKGRIEKTFL 1146

Query: 809  GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGH-LTVS--- 864
             ++  YI E +   + +I +KL+ D I  L LE+ +  I+  I   R   G  L++    
Sbjct: 1147 RDIIHYIRESWSDKEGYITVKLNWDTIENLQLELSLPQIKEAIINHRRFKGKDLSIDVLR 1206

Query: 865  GHSFLILKPKDSSKSFNSK-------------MYQMKQLLPSVVIKGVQGINRAVIHEED 911
             H  + +    SSK+  SK             +  +K++LP + + G     RA+IH E 
Sbjct: 1207 SHIKIRVDMDPSSKAGLSKTDIAATSADPYLRLKHLKRMLPDIQVLGHPQARRAIIHSE- 1265

Query: 912  VEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVME 971
              G+   KLLVEG  LR+ M T G++GV+  +NN  E+   LGIEAAR TI+ E+  VM+
Sbjct: 1266 -RGLN--KLLVEGYGLRECMNTDGIEGVRTKTNNVMEMRAVLGIEAARGTIINEMSEVMK 1322

Query: 972  NHGMSIDFRHPMLVADLMTSKGEVLG 997
            +  M ID RH  L+AD+MT+ GEVLG
Sbjct: 1323 D--MDIDPRHMHLLADIMTTTGEVLG 1346



 Score =  105 bits (262), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 46/59 (77%), Positives = 52/59 (88%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSFFS L+PTEFFFH M GREGL+DTAVKTAETGYM RRL+KSLEDL  +YD
Sbjct: 844 PSKGFVRNSFFSSLSPTEFFFHAMSGREGLIDTAVKTAETGYMSRRLMKSLEDLSAKYD 902



 Score = 55.1 bits (131), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/46 (52%), Positives = 33/46 (71%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRI 67
           LM  K+NLVTP+NGE +I A QDFI+  Y+L+ K+ FF+R    +I
Sbjct: 536 LMGVKNNLVTPKNGEPIIGAIQDFISAAYMLSSKDNFFDRRSFTQI 581



 Score = 44.7 bits (104), Expect = 0.45,   Method: Compositional matrix adjust.
 Identities = 26/77 (33%), Positives = 41/77 (53%), Gaps = 7/77 (9%)

Query: 639  LVDTAVKTAETGYMQRRLVKSLEDLCVQY-------DMSFDAAFYGQTDCISGVSECIIM 691
            L D    T E   + R  +  + D  +Q        D  FDA   G+TD + GVSECIIM
Sbjct: 1334 LADIMTTTGEVLGITRFGMAKMRDSVLQLASFEKTADHLFDAGGTGRTDRVEGVSECIIM 1393

Query: 692  GLPMNVGTGLIKLLQAV 708
            G  +++GTG +++++ +
Sbjct: 1394 GKTVSLGTGAMEVVRKL 1410


>gi|396496347|ref|XP_003844722.1| similar to DNA-directed RNA polymerase iii largest subunit
           [Leptosphaeria maculans JN3]
 gi|312221303|emb|CBY01243.1| similar to DNA-directed RNA polymerase iii largest subunit
           [Leptosphaeria maculans JN3]
          Length = 1520

 Score =  271 bits (693), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 137/287 (47%), Positives = 182/287 (63%), Gaps = 32/287 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++HRAK+ P RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 532 DGDIVLFNRQPSLHKLSILSHRAKIRPWRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 591

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EA                LM  K NL TP+NG  +IAA QDFIT  YLL+ KN F++R
Sbjct: 592 RTEATE--------------LMGVKYNLATPKNGTPIIAAIQDFITAAYLLSNKNNFYDR 637

Query: 461 AQTMRIASTLI-------ADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKP 513
               +I + +         DT     I          P V  +   +WTGKQ+F+L+++P
Sbjct: 638 RTFCQIVNYMFNGDGAYDPDTGLTLPI-------EIPPPVVWKPQALWTGKQVFNLLMRP 690

Query: 514 NRDCPVNANLKTKGRAYT----ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVF 569
           N+   V  NL+   + +      + +    D+Y+++RNSE++ G MDK+T+G G K +VF
Sbjct: 691 NKASRVLVNLEAACKQFKNTPGQSPDLNENDAYLVIRNSEVMCGVMDKATVGDGKKDSVF 750

Query: 570 YILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           Y+++RDFG D AV  M RLSR+++ +L N GFS+GI DVTPG+  VQ
Sbjct: 751 YVMMRDFGPDHAVQGMNRLSRLSARWLTNNGFSLGISDVTPGEKLVQ 797



 Score =  219 bits (558), Expect = 9e-54,   Method: Compositional matrix adjust.
 Identities = 139/366 (37%), Positives = 195/366 (53%), Gaps = 76/366 (20%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEV------------------ 1147
            C  KY R++++P  AVGA+ AQSIGEPGTQMTLKTFHFAG                    
Sbjct: 1136 CLTKYHRSRVQPGHAVGAIGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIINAS 1195

Query: 1148 ---------CE---------------------------YIEEVFVPDDSFILIKLDMDRI 1171
                     CE                           Y+E+V+ P+ ++I +++D D  
Sbjct: 1196 STISTPVITCELSNKVSESAARMVKARVEKTYLRDIISYVEDVWHPNGAYIAMRIDWDTA 1255

Query: 1172 RLLHLEVDIDSIRYCIERTR----GISGHLTVSGHSFLILKPKDSS-------------K 1214
              L ++V    I   I + +    G +G      +S + ++  D +             K
Sbjct: 1256 NKLFIDVQPGEIIRAINKHKPLKWGKAGAAVRISNSLIRVEIPDPASAKKRPVKTTKNHK 1315

Query: 1215 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEE---DVEGVTKYKLLVEGDNLRDVMATYG 1271
             F  ++  +K L+P VVIKG     RA+I ++   + +G  + +LLVEG   R+ M T G
Sbjct: 1316 EFFERVQHVKALIPDVVIKGYPDCTRAIIKKDSSPNAQGEYECQLLVEGYGFRECMTTPG 1375

Query: 1272 VKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 1331
            ++  K  SN+  EV   LGIEAAR+TI+ EI  VM N  M ID RH  L+AD+MT KG+V
Sbjct: 1376 IEPYKTKSNHIMEVRTVLGIEAARATIVREIGDVMGN--MDIDPRHMQLLADVMTFKGDV 1433

Query: 1332 LGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLI 1391
             GITR GL K ++SVL LASFE T DHLF+AA  G+TD I GVSECIIMG  + +GTG +
Sbjct: 1434 YGITRFGLQKTRDSVLQLASFEKTPDHLFEAAARGKTDTIDGVSECIIMGQSVKLGTGAM 1493

Query: 1392 KLLQAV 1397
            ++++ +
Sbjct: 1494 QVVRPL 1499



 Score =  167 bits (424), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 100/273 (36%), Positives = 148/273 (54%), Gaps = 16/273 (5%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDP----QRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G  + +D V Q + +++  +N+Y   P    +RT   +G +D  MG + K   C TCG+ 
Sbjct: 76  GIYSNQDIVNQ-AVLEVSDRNVYDLAPAANNERTLTANGPMDIHMGISSKTGTCGTCGEG 134

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
           L  C GHFG+I L LP FH+GY + +I +L  ICK+  C+RVLL E +   +   +R P 
Sbjct: 135 LDKCNGHFGHIKLALPAFHVGYLKHIIEVLNCICKD--CSRVLLDETERRKYLRSMRRPD 192

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGL--LKISHEKYK--NRT----KK 252
           +  L R ++ KKILE  +K   CP+CG + G V+K     LKI H +Y   NR+    KK
Sbjct: 193 MDTLRRTAISKKILEDCRKKKTCPYCGALQGTVRKVPAHPLKIIHNRYDAYNRSTAKQKK 252

Query: 253 KDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL 312
             A   +    +  A   NP+++ H K   +  ++PL VL LF+ I  ED  LL M  E 
Sbjct: 253 APAGKIEFDQSFEAAKAANPDLDKHLKKA-VDDMHPLRVLNLFKKISPEDCELLAMIPED 311

Query: 313 SKPSDLILTRLLVPPNCIRPSVISDLKSDNDVV 345
           ++P  LI   + VPP  +RPSV+ +  +  D V
Sbjct: 312 ARPEMLIWEYMPVPPVALRPSVMQEGGATEDDV 344



 Score =  154 bits (390), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 98/254 (38%), Positives = 143/254 (56%), Gaps = 22/254 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS  ISTP+IT  L        AR+VK R+E+T L ++  Y+E+V+ P+ 
Sbjct: 1184 GVPRIKEIINASSTISTPVITCELSNKVSESAARMVKARVEKTYLRDIISYVEDVWHPNG 1243

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTR----GISGHLTVSGHSFLILKPKDSS-- 877
            ++I +++D D    L ++V    I   I + +    G +G      +S + ++  D +  
Sbjct: 1244 AYIAMRIDWDTANKLFIDVQPGEIIRAINKHKPLKWGKAGAAVRISNSLIRVEIPDPASA 1303

Query: 878  -----------KSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEE---DVEGVTKYKLLVE 923
                       K F  ++  +K L+P VVIKG     RA+I ++   + +G  + +LLVE
Sbjct: 1304 KKRPVKTTKNHKEFFERVQHVKALIPDVVIKGYPDCTRAIIKKDSSPNAQGEYECQLLVE 1363

Query: 924  GDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPM 983
            G   R+ M T G++  K  SN+  EV   LGIEAAR+TI+ EI  VM N  M ID RH  
Sbjct: 1364 GYGFRECMTTPGIEPYKTKSNHIMEVRTVLGIEAARATIVREIGDVMGN--MDIDPRHMQ 1421

Query: 984  LVADLMTSKGEVLG 997
            L+AD+MT KG+V G
Sbjct: 1422 LLADVMTFKGDVYG 1435



 Score =  104 bits (259), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 47/57 (82%), Positives = 50/57 (87%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV NSFFSGLTP+EF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 917 KGFVSNSFFSGLTPSEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSAQYD 973



 Score = 55.8 bits (133), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/57 (45%), Positives = 35/57 (61%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVF 78
           LM  K NL TP+NG  +IAA QDFIT  YLL+ KN F++R    +I + +  G   +
Sbjct: 598 LMGVKYNLATPKNGTPIIAAIQDFITAAYLLSNKNNFYDRRTFCQIVNYMFNGDGAY 654



 Score = 45.8 bits (107), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 30/41 (73%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 708
            D  F+AA  G+TD I GVSECIIMG  + +GTG +++++ +
Sbjct: 1459 DHLFEAAARGKTDTIDGVSECIIMGQSVKLGTGAMQVVRPL 1499


>gi|298709808|emb|CBJ31607.1| RNA polymerase III, largest subunit [Ectocarpus siliculosus]
          Length = 1518

 Score =  271 bits (692), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 137/272 (50%), Positives = 177/272 (65%), Gaps = 25/272 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHK+SIM+HRAK++P RTFRFNECVC+PYNADFDGDEMN+HLPQTEEA
Sbjct: 508 DGDVVLFNRQPSLHKMSIMSHRAKIMPWRTFRFNECVCSPYNADFDGDEMNMHLPQTEEA 567

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A  LMA   NLVTPRNGE L+AATQDF+T  YL+TQ++ FF+ 
Sbjct: 568 RAE--------------ASQLMAVPYNLVTPRNGEPLVAATQDFLTAAYLITQRDIFFDH 613

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
               ++AS +  D  +   I          P   ++   +WTGKQ  SL+++P+++  + 
Sbjct: 614 ETFCKVASYM-GDAGEHVDI---------PPPAIMKPVALWTGKQAMSLMVRPSKENKIL 663

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            N ++K + Y  N   C  D YV   NSEL+ G++ K TLG G K  +FY L+R+ G   
Sbjct: 664 VNFESKEKNYKGNRFLCPSDGYVCYHNSELMCGNLAKKTLGDGSKTGLFYTLIREHGPLE 723

Query: 581 AVTAMWRLSRMTSFYL-MNRGFSIGIGDVTPG 611
           A   M RL+++ + YL  +RGFSIGI DVTPG
Sbjct: 724 AARCMNRLAKVCARYLGGHRGFSIGIEDVTPG 755



 Score =  249 bits (637), Expect = 7e-63,   Method: Compositional matrix adjust.
 Identities = 182/541 (33%), Positives = 265/541 (48%), Gaps = 143/541 (26%)

Query: 999  GTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQ--DTSENFVRDIKKF 1056
            G PV+  +L+  + + N    + +LS +E+  L N  L  KEF Q     + +  ++K++
Sbjct: 979  GQPVDYAKLMTQVTSTNLFLHEKTLSPKELRQLCNRVLAGKEFQQILPQGQRWTEELKQY 1038

Query: 1057 LEEFSKKESVTSHQDKVSQPLREQILSHQDKIG-----------------------HGRE 1093
            L++      VT+ +  + + LR    +    +G                        G E
Sbjct: 1039 LQDL-----VTTRKG-LREGLRLPTEAPATAVGTAAWRAEKLGPAGSAKFKDWWEFAGIE 1092

Query: 1094 SNPFPS---------ACKAEA---------CREKYVRAQIEPATA----VGALAAQSIGE 1131
              P  S          C+  A         C +KY RA +EP  A    VGA+ AQSI E
Sbjct: 1093 GTPEESEAGELVVSNTCRVTASQAKEFLRRCLDKYKRALVEPGEASLSRVGAIGAQSISE 1152

Query: 1132 PGTQMTLKTFHFAG--------------EVCEYIEEVFVP--------DDS--------- 1160
            PGTQMTLKTFHFAG              E+    + +  P        DDS         
Sbjct: 1153 PGTQMTLKTFHFAGVASMNVTLGVPRLKEIINASKNISTPIITAKLVQDDSKTSARVVKA 1212

Query: 1161 -----------------------FILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGH- 1196
                                   FI IKLDM  ++ LHL++++ ++R+ I   +G  G  
Sbjct: 1213 KIEKTTLGQVAVYMKEVFSASECFIAIKLDMHAVQDLHLDINVHTVRHSI--LKGNFGET 1270

Query: 1197 --------------LTVSGHSFLILKPKDS-SKSFNSK----------MYQMKQLLPSVV 1231
                          ++  GH   ++ P+ S +KS  +           +  +K +LP V+
Sbjct: 1271 RPRVLRDLKPQNVVISGGGHKIKVMPPELSGAKSARAAETVRPKTFFVLQALKAVLPGVI 1330

Query: 1232 IKGVQGINRAVIH-EEDVEGVT-------KYKLLVEGDNLRDVMATYGVKGVKCSSNNTY 1283
            ++G+  +NRAVI+ +E+  G         +Y LLVEG  L  VM   G+ G +  SN+  
Sbjct: 1331 VQGIPSVNRAVINVQENSSGAASGAAPKERYHLLVEGYGLAAVMGAPGIDGTRTRSNHII 1390

Query: 1284 EVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMK 1343
            EV+ TLG+EAAR  I  EI  +M+ +G+SID RH +L+AD+MT KGEVLGITR G++KM+
Sbjct: 1391 EVFHTLGVEAARIIISEEITYIMKAYGISIDRRHLLLLADVMTFKGEVLGITRFGVSKMR 1450

Query: 1344 ESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPV 1403
            ESVL LASFE T+DHLFDA+ +G+ D I GVSECIIMG+P+ +GTGL KLL    + +P 
Sbjct: 1451 ESVLMLASFEKTTDHLFDASVHGRHDAIVGVSECIIMGIPIPLGTGLFKLLMNEDKIKPP 1510

Query: 1404 P 1404
            P
Sbjct: 1511 P 1511



 Score =  189 bits (481), Expect = 8e-45,   Method: Compositional matrix adjust.
 Identities = 111/268 (41%), Positives = 163/268 (60%), Gaps = 36/268 (13%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPR+KEIINAS+NISTPIITA L +D     AR+VK ++E+TTLG+V  Y++EVF   +
Sbjct: 1175 GVPRLKEIINASKNISTPIITAKLVQDDSKTSARVVKAKIEKTTLGQVAVYMKEVFSASE 1234

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGH---------------LTVSGHSF 868
             FI IKLDM  ++ LHL++++ ++R+ I   +G  G                ++  GH  
Sbjct: 1235 CFIAIKLDMHAVQDLHLDINVHTVRHSI--LKGNFGETRPRVLRDLKPQNVVISGGGHKI 1292

Query: 869  LILKPKDS-SKSFNSK----------MYQMKQLLPSVVIKGVQGINRAVIH-EEDVEGVT 916
             ++ P+ S +KS  +           +  +K +LP V+++G+  +NRAVI+ +E+  G  
Sbjct: 1293 KVMPPELSGAKSARAAETVRPKTFFVLQALKAVLPGVIVQGIPSVNRAVINVQENSSGAA 1352

Query: 917  -------KYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLV 969
                   +Y LLVEG  L  VM   G+ G +  SN+  EV+ TLG+EAAR  I  EI  +
Sbjct: 1353 SGAAPKERYHLLVEGYGLAAVMGAPGIDGTRTRSNHIIEVFHTLGVEAARIIISEEITYI 1412

Query: 970  MENHGMSIDFRHPMLVADLMTSKGEVLG 997
            M+ +G+SID RH +L+AD+MT KGEVLG
Sbjct: 1413 MKAYGISIDRRHLLLLADVMTFKGEVLG 1440



 Score =  181 bits (460), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 104/254 (40%), Positives = 151/254 (59%), Gaps = 12/254 (4%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + V++ S  Q+ S+ L+ + P+R   P+G LD R+G + K A C TC + L DC GH+G+
Sbjct: 73  EEVERMSEFQVWSRELF-KMPERIAAPNGCLDPRLGVSDKTAVCETCSKLLVDCAGHYGH 131

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNP-ALSYLVRKSL 209
           I L LPVFHIGYF+  + +LQ ICK  TC+RVLL +     +  ++RNP  +  L R +L
Sbjct: 132 IKLELPVFHIGYFKHTLTMLQCICK--TCSRVLLHDASRVKYLKRMRNPRGMGALERGNL 189

Query: 210 KKKILETTKKVSVCPH--CGEINGVVKKCG---LLKISHEKYKNRTKKKDAIVEDLLAEY 264
            KKI+   KK + C H  C  +NG VKK      LK+ H+++K   K    ++++L A+ 
Sbjct: 190 HKKIVTECKKSTSCFHESCYAVNGTVKKVTGSQTLKLVHDRFKG--KPPGNVLQELTADM 247

Query: 265 NEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLL 324
             A + N EI  H    + + L+ L VL LF+ +  ED  LL M+A + +P +LI+  LL
Sbjct: 248 KVAAQANREIPKHLGMAM-EDLSALRVLHLFQRMTDEDAELLWMDARVGRPENLIIENLL 306

Query: 325 VPPNCIRPSVISDL 338
           VPP  IRPSV  DL
Sbjct: 307 VPPVPIRPSVAMDL 320



 Score =  106 bits (265), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 48/58 (82%), Positives = 53/58 (91%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV NSF+SGLT TEFFFHTMGGREGLVDTAVKTAETGYM RRL+K+LEDL +QYD
Sbjct: 879 AKGFVANSFYSGLTATEFFFHTMGGREGLVDTAVKTAETGYMARRLMKALEDLSMQYD 936



 Score = 62.0 bits (149), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 28/50 (56%), Positives = 37/50 (74%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LMA   NLVTPRNGE L+AATQDF+T  YL+TQ++ FF+     ++AS +
Sbjct: 574 LMAVPYNLVTPRNGEPLVAATQDFLTAAYLITQRDIFFDHETFCKVASYM 623



 Score = 56.6 bits (135), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 26/48 (54%), Positives = 34/48 (70%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP 715
            D  FDA+ +G+ D I GVSECIIMG+P+ +GTGL KLL    + +P P
Sbjct: 1464 DHLFDASVHGRHDAIVGVSECIIMGIPIPLGTGLFKLLMNEDKIKPPP 1511


>gi|451856837|gb|EMD70128.1| hypothetical protein COCSADRAFT_177734 [Cochliobolus sativus
           ND90Pr]
          Length = 1473

 Score =  270 bits (691), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 137/277 (49%), Positives = 185/277 (66%), Gaps = 20/277 (7%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++HRAKV P RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 482 DGDIVLFNRQPSLHKLSILSHRAKVRPWRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 541

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EA                LM  K NL TP+NG  +IAA QDFIT  YLL+ KN FF+R
Sbjct: 542 RTEATE--------------LMGVKYNLATPKNGTPIIAAIQDFITAAYLLSNKNNFFDR 587

Query: 461 AQTMRIASTLI-ADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
               +I + +   + +      KR       PVV+ +   +WTGKQ+F+L+++P + C V
Sbjct: 588 RTFCQIVNYMFNGEGAFDPDTGKRHPIEIPPPVVW-KPQALWTGKQVFNLLMRPYKKCRV 646

Query: 520 NANLKTKGRAY--TANE--EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
             NL+   + +  T ++  +    D+Y+++RNSE++ G MDK+T+G G K +VFY+++RD
Sbjct: 647 LVNLEAACKQFKNTPDQPPDLNENDAYLVIRNSEVMCGVMDKATVGDGKKDSVFYVMMRD 706

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
           FG D AV  M RLS++++ +L N GFS+GI DVTPG+
Sbjct: 707 FGPDHAVQGMNRLSKLSARWLSNNGFSLGISDVTPGE 743



 Score =  221 bits (564), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 142/366 (38%), Positives = 196/366 (53%), Gaps = 76/366 (20%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGE------------------- 1146
            C  KY R++++P  AVGA+ AQSIGEPGTQMTLKTFHFAG                    
Sbjct: 1090 CLTKYHRSRVQPGHAVGAIGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIINAS 1149

Query: 1147 --------VCE---------------------------YIEEVFVPDDSFILIKLDMDRI 1171
                     CE                           Y+E+V+ P+ ++I +++D D I
Sbjct: 1150 STISTPVIACELSNKISESAARIVKARVEKTYLRDVISYVEDVWHPNGAYIAMRIDWDTI 1209

Query: 1172 RLLHLEVDIDSIRYCIERTR----GISGHLTVSGHSFLILKPKDSS-------------K 1214
              L ++V    I   I   +    G +G       S + ++  D +             K
Sbjct: 1210 NKLFVDVQPYEIAAAINAHKPLKWGKAGANVRISSSIIRVEVPDPNAAKKRPVKTTRNHK 1269

Query: 1215 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEE---DVEGVTKYKLLVEGDNLRDVMATYG 1271
             +  ++ Q+K L+P VVIKG    +RA+I +E   + +G  + +LLVEG  L+D M T G
Sbjct: 1270 EYFERVQQVKSLIPDVVIKGYPDCSRAIIKKESSPNAQGHYECQLLVEGYGLQDCMTTPG 1329

Query: 1272 VKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 1331
            ++     SN+  EV   LGIEAAR+TI+ EI  VM N  M ID RH  L+AD+MT KGEV
Sbjct: 1330 IEPYNTKSNHVMEVKTVLGIEAARATIVREIGDVMGN--MDIDPRHMQLLADVMTFKGEV 1387

Query: 1332 LGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLI 1391
             GITR GL K ++SVL LASFE T DHLF+AA  G+TD I GVSECIIMG  + +GTG +
Sbjct: 1388 FGITRFGLQKTRDSVLQLASFEKTPDHLFEAAARGKTDTIDGVSECIIMGQSVKLGTGAM 1447

Query: 1392 KLLQAV 1397
            ++++ +
Sbjct: 1448 QVVRPL 1453



 Score =  160 bits (404), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 97/273 (35%), Positives = 148/273 (54%), Gaps = 16/273 (5%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLY----CQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G  + +D V Q + +++  +N+Y      D  RT   +G +D RMG + K+  C TCG+ 
Sbjct: 26  GIYSNQDIVNQ-AVLEVSDRNVYDLQPAADNTRTLTANGPMDTRMGISSKQGTCATCGEG 84

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
           L  C GHFG+I L LP FH+GY + +I +L  ICK+  C+RVLL E +   +   +R P 
Sbjct: 85  LDTCNGHFGHIKLALPAFHVGYLKHIIEVLNCICKD--CSRVLLDEVERRRYLRSMRRPD 142

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKYK--NRTKKKDAI 256
           +  L + ++ K+ILE  +K   CP+C  + G V+K     LKI H +Y   NR+  K   
Sbjct: 143 MDTLRKGAVTKRILEDCRKKKTCPYCNGLQGTVRKVPGHPLKIIHNRYDAFNRSTAKTKK 202

Query: 257 VEDLLAEYNE----AVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL 312
                 E+++    A   NP+++ H K   +  ++PL VL LF+ I  ED  LL M  E 
Sbjct: 203 APPGKIEFDQSFETAKSANPDLDKHLKKA-VDDMHPLRVLNLFKKISPEDCELLAMIPED 261

Query: 313 SKPSDLILTRLLVPPNCIRPSVISDLKSDNDVV 345
           ++P  LI   + VPP  +RPSV+ +  +  D V
Sbjct: 262 ARPEMLIWEYMPVPPVALRPSVMQEGGATEDDV 294



 Score =  157 bits (396), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 102/254 (40%), Positives = 143/254 (56%), Gaps = 22/254 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS  ISTP+I   L        ARIVK R+E+T L +V  Y+E+V+ P+ 
Sbjct: 1138 GVPRIKEIINASSTISTPVIACELSNKISESAARIVKARVEKTYLRDVISYVEDVWHPNG 1197

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTR----GISGHLTVSGHSFLILKPKDSS-- 877
            ++I +++D D I  L ++V    I   I   +    G +G       S + ++  D +  
Sbjct: 1198 AYIAMRIDWDTINKLFVDVQPYEIAAAINAHKPLKWGKAGANVRISSSIIRVEVPDPNAA 1257

Query: 878  -----------KSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEE---DVEGVTKYKLLVE 923
                       K +  ++ Q+K L+P VVIKG    +RA+I +E   + +G  + +LLVE
Sbjct: 1258 KKRPVKTTRNHKEYFERVQQVKSLIPDVVIKGYPDCSRAIIKKESSPNAQGHYECQLLVE 1317

Query: 924  GDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPM 983
            G  L+D M T G++     SN+  EV   LGIEAAR+TI+ EI  VM N  M ID RH  
Sbjct: 1318 GYGLQDCMTTPGIEPYNTKSNHVMEVKTVLGIEAARATIVREIGDVMGN--MDIDPRHMQ 1375

Query: 984  LVADLMTSKGEVLG 997
            L+AD+MT KGEV G
Sbjct: 1376 LLADVMTFKGEVFG 1389



 Score =  103 bits (258), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 47/57 (82%), Positives = 50/57 (87%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV NSFFSGLTP+EF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 867 KGFVSNSFFSGLTPSEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSAQYD 923



 Score = 58.9 bits (141), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 28/57 (49%), Positives = 35/57 (61%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVF 78
           LM  K NL TP+NG  +IAA QDFIT  YLL+ KN FF+R    +I + +  G   F
Sbjct: 548 LMGVKYNLATPKNGTPIIAAIQDFITAAYLLSNKNNFFDRRTFCQIVNYMFNGEGAF 604



 Score = 45.4 bits (106), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 30/41 (73%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 708
            D  F+AA  G+TD I GVSECIIMG  + +GTG +++++ +
Sbjct: 1413 DHLFEAAARGKTDTIDGVSECIIMGQSVKLGTGAMQVVRPL 1453


>gi|156043073|ref|XP_001588093.1| conserved hypothetical protein [Sclerotinia sclerotiorum 1980]
 gi|154694927|gb|EDN94665.1| conserved hypothetical protein [Sclerotinia sclerotiorum 1980
           UF-70]
          Length = 1459

 Score =  270 bits (690), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 133/279 (47%), Positives = 178/279 (63%), Gaps = 31/279 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIM+H AK+ P RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 466 DGDIVLFNRQPSLHKLSIMSHYAKIRPWRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 525

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EA+               LM  K+NL TP+NGE +I+ATQDFIT  YLL+ K  FF+R
Sbjct: 526 RTEAIN--------------LMGVKNNLSTPKNGEPIISATQDFITAAYLLSSKENFFDR 571

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                I   ++     +             P   ++   +WTGKQ+FS++++PN+   + 
Sbjct: 572 KTFTNICMYMVDSNLHL----------QLPPPAILKPQALWTGKQVFSILMRPNKQDNIL 621

Query: 521 ANLKTKGRAYTAN-------EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILL 573
            N+  K R +  N        +    D ++++RNSE++ G MDKST+GSG K ++FY++L
Sbjct: 622 VNVDAKCRDFVPNMVPPGYANDMEANDGWLVIRNSEVMCGLMDKSTVGSGKKDSIFYVIL 681

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
           RD+G D AV AM RLS++++ YL N GFSIGI DV P +
Sbjct: 682 RDYGPDAAVVAMNRLSKLSARYLTNMGFSIGISDVYPSE 720



 Score =  209 bits (531), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 115/271 (42%), Positives = 158/271 (58%), Gaps = 10/271 (3%)

Query: 79  FRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCG 138
           F+ L  G ++ +D V Q   I++ +K LY  D  RTPIPHG LD R+GT+ K   C TC 
Sbjct: 22  FKELKFGILSNQDIVNQ-GVIEVSNKTLYNVDNGRTPIPHGPLDPRLGTSSKAGRCETCD 80

Query: 139 QNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN 198
           + L DC GHFG++ LPLP FHIGY + +I ILQ+ICK  TCARVLL + +   F  +LR 
Sbjct: 81  KGLQDCNGHFGHVRLPLPAFHIGYLKLIIMILQNICK--TCARVLLTDAERRQFLRELRK 138

Query: 199 PALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYK--NRTKKKDAI 256
           P +  L R  + KKI E  +K S CPHC   NG ++K  +++++H+KY   N++     +
Sbjct: 139 PGIDNLKRTQICKKINEQCRKASQCPHCDATNGQIRKVSVVRLAHDKYTKYNKSTAAKKV 198

Query: 257 VEDLLAEYN----EAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL 312
               +AEY     EA K N E+E H K  + + L+PL VL LF+ I   D  LL +N   
Sbjct: 199 APPGMAEYQKSFEEAKKNNTELEKHVK-KVYEDLHPLRVLNLFKLITPSDCELLGINPAE 257

Query: 313 SKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
            +P   +   +  PP CIRPSV  D  S+ D
Sbjct: 258 GRPEMFLWQFVPAPPICIRPSVAQDGGSNED 288



 Score =  149 bits (376), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 115/351 (32%), Positives = 163/351 (46%), Gaps = 84/351 (23%)

Query: 1104 EACREKYVRAQIEPATAVGAL--------------------------------------- 1124
            E C EKY RA++EP  AVGA+                                       
Sbjct: 1070 ELCLEKYSRAKVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMNLTAGVPRIKEIIN 1129

Query: 1125 AAQSIGEPGTQMTL-----------------KTFHFAGEVCEYIEEVFVPDDSFILIKLD 1167
            A+++I  P  +  L                 KT+    EV  + E+++    + I + +D
Sbjct: 1130 ASKTIATPFVKCPLLNDKDLDVARLVKARMEKTYLH--EVLHFAEDMWSARSAVICLAVD 1187

Query: 1168 MDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFLILKPKDSSKSFNSK----- 1219
             + +    +EV +++I   I + + +   S  L V G    I    D S    ++     
Sbjct: 1188 TEYLVNRQIEVTVENIATTILKNKKLKVKSEDLNVKGKCIFIRVTHDGSAPTTARGTAAK 1247

Query: 1220 ---------------MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLR 1264
                           ++ +K+ +P + I G     RA+I+  + E   +Y ++VEG  LR
Sbjct: 1248 GKPTLDEGGSDLLLRVHHLKRAIPELAISGYPEATRAIINTSEHEK-PEYTVVVEGYGLR 1306

Query: 1265 DVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADL 1324
              + T GV G K  SN+  E+   LGIEAAR TI  EI  VM +  M ID RH  L+AD+
Sbjct: 1307 ACIGTEGVDGTKVKSNSVMEMRDVLGIEAARYTIANEIATVMAD--MDIDPRHMQLLADV 1364

Query: 1325 MTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVS 1375
            MT KGEVLGITR GL+KM++SVL LASFE T DHLFDAA   +TD I GVS
Sbjct: 1365 MTYKGEVLGITRFGLSKMRDSVLQLASFEKTPDHLFDAAAGMKTDRIEGVS 1415



 Score =  147 bits (372), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 100/281 (35%), Positives = 146/281 (51%), Gaps = 27/281 (9%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ I+TP +   L  D DLD AR+VK R+E+T L EV  + E+++    
Sbjct: 1120 GVPRIKEIINASKTIATPFVKCPLLNDKDLDVARLVKARMEKTYLHEVLHFAEDMWSARS 1179

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFLILKPKDSSKSF 880
            + I + +D + +    +EV +++I   I + + +   S  L V G    I    D S   
Sbjct: 1180 AVICLAVDTEYLVNRQIEVTVENIATTILKNKKLKVKSEDLNVKGKCIFIRVTHDGSAPT 1239

Query: 881  NS--------------------KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKL 920
             +                    +++ +K+ +P + I G     RA+I+  + E   +Y +
Sbjct: 1240 TARGTAAKGKPTLDEGGSDLLLRVHHLKRAIPELAISGYPEATRAIINTSEHEK-PEYTV 1298

Query: 921  LVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFR 980
            +VEG  LR  + T GV G K  SN+  E+   LGIEAAR TI  EI  VM +  M ID R
Sbjct: 1299 VVEGYGLRACIGTEGVDGTKVKSNSVMEMRDVLGIEAARYTIANEIATVMAD--MDIDPR 1356

Query: 981  HPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDP 1021
            H  L+AD+MT KGEVLG  T   L ++ D ++   S    P
Sbjct: 1357 HMQLLADVMTYKGEVLGI-TRFGLSKMRDSVLQLASFEKTP 1396



 Score =  104 bits (260), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 47/59 (79%), Positives = 50/59 (84%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV NSFF+GLTP EF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 842 PAKGFVANSFFTGLTPYEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSTQYD 900



 Score = 56.2 bits (134), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/40 (62%), Positives = 31/40 (77%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           LM  K+NL TP+NGE +I+ATQDFIT  YLL+ K  FF+R
Sbjct: 532 LMGVKNNLSTPKNGEPIISATQDFITAAYLLSSKENFFDR 571


>gi|212538083|ref|XP_002149197.1| DNA-directed RNA polymerase III largest subunit, putative
           [Talaromyces marneffei ATCC 18224]
 gi|210068939|gb|EEA23030.1| DNA-directed RNA polymerase III largest subunit, putative
           [Talaromyces marneffei ATCC 18224]
          Length = 1439

 Score =  270 bits (690), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 133/281 (47%), Positives = 181/281 (64%), Gaps = 29/281 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+ L+NRQPSLHKLSI++H  KV P+RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 469 DGDIALYNRQPSLHKLSILSHFVKVRPYRTFRMNECVCNPYNADFDGDEMNLHIPQTEEA 528

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R+EA+               LM  K+NLVTP+NGE +I A QDFI+  Y+L+ K+ FF+R
Sbjct: 529 RSEAME--------------LMGVKNNLVTPKNGEPIIGAIQDFISAAYVLSSKDNFFDR 574

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
               +I   ++       G   RF      P   ++  ++WTGKQ+F+++++PN+D PV 
Sbjct: 575 RSFTQICLYML-------GPETRF---DLPPPAILKPQMMWTGKQVFNILMRPNKDDPVK 624

Query: 521 ANLKTKGRAYTA-----NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            N+    R + A      ++    D ++++RNSE++ G MDKST+GSG K NVFYI+LRD
Sbjct: 625 VNIDAACREFKAPKDGQPKDLDPNDGWLVIRNSEIMCGVMDKSTIGSGKKDNVFYIMLRD 684

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           FG   A   M RLS++ + +  N GFSIGI DV P +  VQ
Sbjct: 685 FGPPAAAEGMNRLSKLCARWFTNVGFSIGITDVYPSERLVQ 725



 Score =  222 bits (566), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 170/494 (34%), Positives = 242/494 (48%), Gaps = 105/494 (21%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETL--DSKEFLQ----------- 1043
            G   PV   R  +  +A   + ++  L   EI A++ E L  + K +++           
Sbjct: 928  GKAKPVHFDRTYNHAMAVTHNNNERGLQPSEIRAITEELLSEERKRYVRKGLFGEDLPYK 987

Query: 1044 ---DTSENFVRDIKKFLEEFSK--KESVTSHQDKVSQPLREQ----ILSHQDKIGHGRES 1094
               D   + +   + FL+   +  ++   + +  +   L +Q     L H  K+  G   
Sbjct: 988  DDSDYGTDQLESARAFLDSIQEHIEKKAVAMEKAMDSALSDQEARMALDHVGKLSEGSLR 1047

Query: 1095 NPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGE-------- 1146
                S      C  KY +A+IEP  AVGA+ AQSIGEPGTQMTLKTFHFAG         
Sbjct: 1048 YFIKS------CLFKYEKAKIEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVGNLALTQG 1101

Query: 1147 -------------------VCEY---------------IEEVFVPD------------DS 1160
                                C                 IE+ F+ D            + 
Sbjct: 1102 VPRIKEIINASKEISTPVITCHLAIPHELHAARIAKGRIEKTFLRDIIHYIRESWTDKEG 1161

Query: 1161 FILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGH-LTVS---GHSFLILKPKDSSKSF 1216
            +I +KL+ D I  L LE+ +  I+  I   R   G  LTV     H  + +    SSK+ 
Sbjct: 1162 YITVKLNWDTIENLQLELSLRQIKDAITSHRRFKGSDLTVDVLRSHIKIRVDMDPSSKAG 1221

Query: 1217 NSK-------------MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 1263
             SK             +  +K++LP + + G     RA+IH E   G+   KLLVEG  L
Sbjct: 1222 LSKTDIAATSADPYLRLKHLKRMLPDIQVLGHPQARRAIIHSE--RGLN--KLLVEGYGL 1277

Query: 1264 RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 1323
            R  M T GV+GV+  +NN  E+   LGIEAAR TI+ E+  VM++  M ID RH  L+AD
Sbjct: 1278 RACMNTDGVEGVRTKTNNVMEMRAVLGIEAARETIINEMGEVMKD--MDIDPRHMHLLAD 1335

Query: 1324 LMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLP 1383
            +MT+ GEVLGITR G+AKM++SVL LASFE T+DHLFDA   G+TD + GVSECIIMG  
Sbjct: 1336 IMTTNGEVLGITRFGMAKMRDSVLQLASFEKTADHLFDAGGTGRTDRVEGVSECIIMGKT 1395

Query: 1384 MNVGTGLIKLLQAV 1397
            +++GTG +++++ +
Sbjct: 1396 VSLGTGAMEVVRKL 1409



 Score =  170 bits (430), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 102/270 (37%), Positives = 144/270 (53%), Gaps = 18/270 (6%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G ++  D V  Q+ ++I  +  Y  +  R    +G LDRR+G + K   C TCG    DC
Sbjct: 28  GALSDND-VISQAVVEISDRRFYDLERDRVVQENGPLDRRLGISGKMETCLTCGLGHKDC 86

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFG++ L LP FHIGYF+ VI ILQ ICK   C+ +LL E +   F  ++R P L  L
Sbjct: 87  NGHFGHVKLVLPAFHIGYFKRVIGILQVICKE--CSTILLPEAERRAFLKEMRRPRLDNL 144

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKYKNRTKKKDA------- 255
            R  + K+++E  KK   CP CG +NGVVKK G   LKI HEK+++  +   A       
Sbjct: 145 RRLQIAKRVVERCKKTRDCPRCGAVNGVVKKAGTAALKIVHEKFRHFNQSTSAKKVPPIS 204

Query: 256 --IVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELS 313
             + ++ LA   EA   NP+++   K      L+ L V+ LF+ I   D  LL ++    
Sbjct: 205 KIVFDNSLA---EARASNPDVDRFYKKAQ-DDLHALRVMNLFKKITNADCELLGLDPTEV 260

Query: 314 KPSDLILTRLLVPPNCIRPSVISDLKSDND 343
           +P   +   +  PPNCIRPSV  D  S+ D
Sbjct: 261 RPETFLWQYIPAPPNCIRPSVSQDGASNED 290



 Score =  164 bits (414), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 111/266 (41%), Positives = 151/266 (56%), Gaps = 24/266 (9%)

Query: 749  TLELWNPGDYKLSQDGVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTL 808
            T      G+  L+Q GVPRIKEIINAS+ ISTP+IT +L    +L  ARI KGR+E+T L
Sbjct: 1087 TFHFAGVGNLALTQ-GVPRIKEIINASKEISTPVITCHLAIPHELHAARIAKGRIEKTFL 1145

Query: 809  GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGH-LTVS--- 864
             ++  YI E +   + +I +KL+ D I  L LE+ +  I+  I   R   G  LTV    
Sbjct: 1146 RDIIHYIRESWTDKEGYITVKLNWDTIENLQLELSLRQIKDAITSHRRFKGSDLTVDVLR 1205

Query: 865  GHSFLILKPKDSSKSFNSK-------------MYQMKQLLPSVVIKGVQGINRAVIHEED 911
             H  + +    SSK+  SK             +  +K++LP + + G     RA+IH E 
Sbjct: 1206 SHIKIRVDMDPSSKAGLSKTDIAATSADPYLRLKHLKRMLPDIQVLGHPQARRAIIHSE- 1264

Query: 912  VEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVME 971
              G+   KLLVEG  LR  M T GV+GV+  +NN  E+   LGIEAAR TI+ E+  VM+
Sbjct: 1265 -RGLN--KLLVEGYGLRACMNTDGVEGVRTKTNNVMEMRAVLGIEAARETIINEMGEVMK 1321

Query: 972  NHGMSIDFRHPMLVADLMTSKGEVLG 997
            +  M ID RH  L+AD+MT+ GEVLG
Sbjct: 1322 D--MDIDPRHMHLLADIMTTNGEVLG 1345



 Score =  105 bits (262), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 46/59 (77%), Positives = 52/59 (88%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSFFS L+PTEFFFH M GREGL+DTAVKTAETGYM RRL+KSLEDL  +YD
Sbjct: 843 PSKGFVRNSFFSSLSPTEFFFHAMSGREGLIDTAVKTAETGYMSRRLMKSLEDLSAKYD 901



 Score = 54.7 bits (130), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 24/46 (52%), Positives = 33/46 (71%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRI 67
           LM  K+NLVTP+NGE +I A QDFI+  Y+L+ K+ FF+R    +I
Sbjct: 535 LMGVKNNLVTPKNGEPIIGAIQDFISAAYVLSSKDNFFDRRSFTQI 580



 Score = 43.9 bits (102), Expect = 0.68,   Method: Compositional matrix adjust.
 Identities = 19/41 (46%), Positives = 30/41 (73%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 708
            D  FDA   G+TD + GVSECIIMG  +++GTG +++++ +
Sbjct: 1369 DHLFDAGGTGRTDRVEGVSECIIMGKTVSLGTGAMEVVRKL 1409


>gi|407917443|gb|EKG10751.1| RNA polymerase alpha subunit [Macrophomina phaseolina MS6]
          Length = 1466

 Score =  270 bits (690), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 131/277 (47%), Positives = 183/277 (66%), Gaps = 15/277 (5%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++H+AKV P RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 469 DGDIVLFNRQPSLHKLSILSHKAKVRPWRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 528

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EA+               LM  K+NL TP+NG  +IAA QDFIT  +L T+K+ F +R
Sbjct: 529 RTEAIE--------------LMGVKNNLATPKNGTPIIAAIQDFITCAFLTTRKDLFLDR 574

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                + S +    S       ++      P V ++   +WTGKQ+++++++P +   V 
Sbjct: 575 KTFALMCSYMFNGDSVRDPETGKYHKIDLPPPVILKPQALWTGKQVWNVLMRPYKASKVL 634

Query: 521 ANLKTKGRAYTAN-EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            NL    + Y  N ++    D+++++RNSE++ G MDKST+G G K +VFY+++RDFG D
Sbjct: 635 VNLDAACKQYKGNKKDLNEDDAWLVVRNSEVMCGVMDKSTVGDGKKDSVFYVMMRDFGPD 694

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
            AV AM RL+++++ +L NRGFSIG+ DVTPG   V+
Sbjct: 695 YAVQAMNRLAKLSARWLTNRGFSIGVSDVTPGSKLVE 731



 Score =  215 bits (547), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 137/377 (36%), Positives = 197/377 (52%), Gaps = 94/377 (24%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEV------------------ 1147
            C  K+ ++ ++P  AVGA+ AQSIGEPGTQMTLKTFHFAG                    
Sbjct: 1073 CLTKHAQSHVQPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIINAS 1132

Query: 1148 ---------CE---------------------------YIEEVFVPDDSFILIKLDMDRI 1171
                     CE                           YIE+V+  D +++ +++D + +
Sbjct: 1133 KTISTPIITCELENKKDIRAARLVKARVEKTYLKDITHYIEDVWYDDGNYLNMRIDWETV 1192

Query: 1172 RLLHLEVDIDSIRYCI------------ERTRGISGHL--------------------TV 1199
              L LE+  + +   I             R      HL                    T 
Sbjct: 1193 EALGLELTKNDLELAILKAPKLKIGADGGRIEFFKNHLRIYVPDVNDPSNEKQRKAAATR 1252

Query: 1200 SGHSFLILKPKDSSK-SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLV 1258
            SG S    K K+S++ ++ +++  +K+ +P + IKG     RA+I +ED        L+V
Sbjct: 1253 SGAS----KAKNSTEDAYFARIQLLKRAIPEIAIKGYPEATRAIIKKED-NADEDISLIV 1307

Query: 1259 EGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHP 1318
            EG  L+ +MAT G++G +C SN+  E +  LGIEAAR+TI+ EI  VM +  M ID RH 
Sbjct: 1308 EGYGLKLIMATPGIRGTQCYSNSVLECFAVLGIEAARTTIIKEIASVMGS--MDIDPRHM 1365

Query: 1319 MLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECI 1378
             L+AD+MT KG++LGITR GLAKM++SVL LASFE T DHLF+A + G++D + GVSECI
Sbjct: 1366 QLLADVMTYKGDILGITRFGLAKMRDSVLQLASFEKTPDHLFEAGYRGKSDGVQGVSECI 1425

Query: 1379 IMGLPMNVGTGLIKLLQ 1395
            I+G  M +GTG  K+++
Sbjct: 1426 ILGQSMGIGTGSFKVVR 1442



 Score =  165 bits (418), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 107/300 (35%), Positives = 158/300 (52%), Gaps = 20/300 (6%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLY---CQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNL 141
           G ++ +D V Q + I++  +++Y      P RT   HG +D RMG + K A C TCG++L
Sbjct: 25  GILSNQDIVNQ-AVIEVSDRHVYDAVGNGPNRTVTKHGPMDGRMGISSKSAACETCGEDL 83

Query: 142 SDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPAL 201
             C GHFG++ L LP FHIGY + +I +L  ICK   C+ +LL E     +   LR P L
Sbjct: 84  KSCNGHFGHVKLALPAFHIGYLKMIIEVLHCICKE--CSNILLDEASRQRYTKSLRRPDL 141

Query: 202 SYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKYK--NRTKKKDAIV 257
             L R ++ KKI    +KV  CPHCG  NG V+K     LKI H K+   N++  K   +
Sbjct: 142 DSLQRTAICKKISGECRKVKKCPHCGATNGPVRKVAGHPLKIVHLKFDAYNKSNAKRKEM 201

Query: 258 EDLLAEYNEAVKF----NPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELS 313
                E++++ +     N E++ H +   +  +NPL VL LF+ I   D PLL M+    
Sbjct: 202 PRGKPEFDKSFEIAKQGNAELDKHIRKA-VDDMNPLRVLNLFKRIKTTDCPLLGMSK--G 258

Query: 314 KPSDLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLS--IMAHRAKVLPHRTF 371
           +P   I   +  PP  IRPSV  +  +  D +  N+   + ++S  I A  AK LP +T 
Sbjct: 259 RPEMFIWQYVPAPPVTIRPSVAQEAATTEDDIT-NKLGDIVQISSLIRAGLAKGLPVQTI 317



 Score =  156 bits (395), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 105/291 (36%), Positives = 159/291 (54%), Gaps = 41/291 (14%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIIT  L+   D+  AR+VK R+E+T L ++  YIE+V+  D 
Sbjct: 1121 GVPRIKEIINASKTISTPIITCELENKKDIRAARLVKARVEKTYLKDITHYIEDVWYDDG 1180

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCI------------ERTRGISGHL---------- 861
            +++ +++D + +  L LE+  + +   I             R      HL          
Sbjct: 1181 NYLNMRIDWETVEALGLELTKNDLELAILKAPKLKIGADGGRIEFFKNHLRIYVPDVNDP 1240

Query: 862  ----------TVSGHSFLILKPKDSSK-SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEE 910
                      T SG S    K K+S++ ++ +++  +K+ +P + IKG     RA+I +E
Sbjct: 1241 SNEKQRKAAATRSGAS----KAKNSTEDAYFARIQLLKRAIPEIAIKGYPEATRAIIKKE 1296

Query: 911  DVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVM 970
            D        L+VEG  L+ +MAT G++G +C SN+  E +  LGIEAAR+TI+ EI  VM
Sbjct: 1297 D-NADEDISLIVEGYGLKLIMATPGIRGTQCYSNSVLECFAVLGIEAARTTIIKEIASVM 1355

Query: 971  ENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDP 1021
             +  M ID RH  L+AD+MT KG++LG  T   L ++ D ++   S    P
Sbjct: 1356 GS--MDIDPRHMQLLADVMTYKGDILGI-TRFGLAKMRDSVLQLASFEKTP 1403



 Score =  102 bits (254), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 47/63 (74%), Positives = 51/63 (80%)

Query: 606 GDVTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           G +   +GFV NSF+SGLTP EF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL  
Sbjct: 845 GRLPDAKGFVANSFYSGLTPYEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSA 904

Query: 666 QYD 668
           QYD
Sbjct: 905 QYD 907



 Score = 50.1 bits (118), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 25/56 (44%), Positives = 34/56 (60%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKV 77
           LM  K+NL TP+NG  +IAA QDFIT  +L T+K+ F +R     + S +  G  V
Sbjct: 535 LMGVKNNLATPKNGTPIIAAIQDFITCAFLTTRKDLFLDRKTFALMCSYMFNGDSV 590



 Score = 45.4 bits (106), Expect = 0.22,   Method: Compositional matrix adjust.
 Identities = 18/39 (46%), Positives = 28/39 (71%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  F+A + G++D + GVSECII+G  M +GTG  K+++
Sbjct: 1404 DHLFEAGYRGKSDGVQGVSECIILGQSMGIGTGSFKVVR 1442


>gi|295668637|ref|XP_002794867.1| DNA-directed RNA polymerase III subunit RPC1 [Paracoccidioides sp.
           'lutzii' Pb01]
 gi|226285560|gb|EEH41126.1| DNA-directed RNA polymerase III subunit RPC1 [Paracoccidioides sp.
           'lutzii' Pb01]
          Length = 1425

 Score =  270 bits (689), Expect = 5e-69,   Method: Compositional matrix adjust.
 Identities = 132/280 (47%), Positives = 183/280 (65%), Gaps = 28/280 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++H  KV PHRTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 438 DGDIVLFNRQPSLHKLSILSHFVKVRPHRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 497

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NLVTP+NGE +I+A QDFIT  Y+L+ KN F++R
Sbjct: 498 RAEAME--------------LMGVKNNLVTPKNGEPIISAIQDFITAAYMLSSKNVFYDR 543

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
               ++   ++   +       RF      P   ++  ++WTGKQ+F+++++PN+D PV 
Sbjct: 544 KTFTQVCLYMLLPGT-------RF---DLPPPSILKPQMLWTGKQVFNILMRPNKDSPVL 593

Query: 521 ANLKTKGRAYTANE----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL    R + A +    +    D ++ +RNSE++ G MDK T+GSG K +VFY++LRD+
Sbjct: 594 VNLDAACREFKAPKGTPRDLDANDRWLCIRNSEVMCGVMDKYTIGSGKKDSVFYVMLRDY 653

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           G  +A   M RLSR+ + ++ + GFSIGI DV PG   ++
Sbjct: 654 GPAIAAEGMNRLSRLCARWITDLGFSIGITDVYPGDRLLE 693



 Score =  228 bits (582), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 178/509 (34%), Positives = 250/509 (49%), Gaps = 105/509 (20%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQ------------- 1043
            GN  PV   R            SD  L   EI+ L  ++L +KE  +             
Sbjct: 896  GNARPVNFDRTFTHSEVTTFDNSDKGLLPDEIMTLC-QSLLAKERARLNRYDLMGNRLDY 954

Query: 1044 -DTSENFV------RDIKKFLEEF--SKKESVTSHQDKVSQPLREQILSHQDKIGHGRES 1094
             D S+N +      RD  + +E++  SK E + S     +   R + ++H  KI   R  
Sbjct: 955  MDRSDNGIDQLESARDYLQSIEDYISSKAEKLRSIDGGNNGQGRGRGINHTAKIS-ARTL 1013

Query: 1095 NPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------- 1145
              F ++C       KY +AQ+EP  AVGA+ AQSIGEPGTQMTLKTFHFAG         
Sbjct: 1014 AAFITSCLV-----KYKKAQVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQG 1068

Query: 1146 -----EVCEYIEEVFVP----------------------------------------DDS 1160
                 E+    +E+  P                                        +D+
Sbjct: 1069 VPRIKEIINASKEISTPVITCQLVNKGDLRAAQIVKGRVEKTFMRDVIYYIEEDWTGNDA 1128

Query: 1161 FILIKLDMDRIRLLHLEVDIDSIRYCIE------------RTRGISGHLTVSGHSFLILK 1208
            +I IK+D   I+ L LE+ +  I   I+            R+ G   H+ V   +     
Sbjct: 1129 YINIKIDFSTIQNLQLELGLQDILAAIKKHKRFKSADLKFRSFGSHIHIFVDQQATRTAL 1188

Query: 1209 PKDSSKSFNSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLR 1264
             K    +  +  Y     +K+L+P++ + G    +RA+I  +  E  T   LLVEG  LR
Sbjct: 1189 SKSEEAATGADPYIRLKHLKRLIPTIQVLGHPQCSRAIIRTD--ETCTTNTLLVEGYGLR 1246

Query: 1265 DVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADL 1324
            D M T G+ G    +NN  E    LGIEAAR+TI+ EI  VM++  M+ID RH  L+AD+
Sbjct: 1247 DCMTTDGIDGRNTRTNNIMETRLVLGIEAARTTIVEEIGEVMKD--MAIDPRHMQLLADV 1304

Query: 1325 MTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPM 1384
            MT KGEVLGITR GLAKM++SVL LASFE T+DHLFDA   G+TD I GVSECII+G  +
Sbjct: 1305 MTYKGEVLGITRFGLAKMRDSVLQLASFEKTADHLFDAGGAGRTDLIEGVSECIIVGKGI 1364

Query: 1385 NVGTGLIKLLQAVPRSEPV--PRTLLFDN 1411
            ++GTG +++++A+  SE    PR  +F++
Sbjct: 1365 SLGTGSMEVIRALNFSEGQIGPRKTVFED 1393



 Score =  171 bits (434), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 101/261 (38%), Positives = 137/261 (52%), Gaps = 32/261 (12%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G ++ +D V Q + +++  + L+  +  R  +PHG LD RMG + K   C TCG  L  C
Sbjct: 30  GVLSTQDIVSQ-AVVEVSDRKLFDLEKDRAIVPHGPLDGRMGISSKSGTCDTCGGGLQIC 88

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFG++ L LP FH+GYF+ VI+ILQ ICK+  C+ +LL E +   F  +LR P +  L
Sbjct: 89  SGHFGHVRLVLPAFHVGYFKLVISILQEICKD--CSHILLPEPERRSFLKELRRPGIDNL 146

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKYKNRTKKKDAIVEDLLA 262
            R  + KKI E  +K   C +C  INGVVKK G   LKISHEK++               
Sbjct: 147 RRMQIVKKINERCRKTRTCYNCNAINGVVKKAGTSALKISHEKFR--------------- 191

Query: 263 EYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTR 322
                      IE H K      L+PL VL+LF  I  ED  LL +N   ++P   +   
Sbjct: 192 -----------IEKHFKKAH-DDLHPLRVLKLFRRISNEDCELLGLNPAEARPEVFLWQY 239

Query: 323 LLVPPNCIRPSVISDLKSDND 343
           +  PP CIRPSV  +  S  D
Sbjct: 240 IPAPPVCIRPSVGQEAASTED 260



 Score =  160 bits (404), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 104/250 (41%), Positives = 143/250 (57%), Gaps = 20/250 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+IT  L    DL  A+IVKGR+E+T + +V  YIEE +  +D
Sbjct: 1068 GVPRIKEIINASKEISTPVITCQLVNKGDLRAAQIVKGRVEKTFMRDVIYYIEEDWTGND 1127

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIE------------RTRGISGHLTVSGHSFLIL 871
            ++I IK+D   I+ L LE+ +  I   I+            R+ G   H+ V   +    
Sbjct: 1128 AYINIKIDFSTIQNLQLELGLQDILAAIKKHKRFKSADLKFRSFGSHIHIFVDQQATRTA 1187

Query: 872  KPKDSSKSFNSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927
              K    +  +  Y     +K+L+P++ + G    +RA+I  +  E  T   LLVEG  L
Sbjct: 1188 LSKSEEAATGADPYIRLKHLKRLIPTIQVLGHPQCSRAIIRTD--ETCTTNTLLVEGYGL 1245

Query: 928  RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 987
            RD M T G+ G    +NN  E    LGIEAAR+TI+ EI  VM++  M+ID RH  L+AD
Sbjct: 1246 RDCMTTDGIDGRNTRTNNIMETRLVLGIEAARTTIVEEIGEVMKD--MAIDPRHMQLLAD 1303

Query: 988  LMTSKGEVLG 997
            +MT KGEVLG
Sbjct: 1304 VMTYKGEVLG 1313



 Score =  105 bits (263), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 47/59 (79%), Positives = 52/59 (88%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFVQNSFFSGL+PTEF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  +YD
Sbjct: 811 PAKGFVQNSFFSGLSPTEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSTRYD 869



 Score = 57.4 bits (137), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 24/40 (60%), Positives = 32/40 (80%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           LM  K+NLVTP+NGE +I+A QDFIT  Y+L+ KN F++R
Sbjct: 504 LMGVKNNLVTPKNGEPIISAIQDFITAAYMLSSKNVFYDR 543



 Score = 47.8 bits (112), Expect = 0.044,   Method: Compositional matrix adjust.
 Identities = 25/57 (43%), Positives = 39/57 (68%), Gaps = 2/57 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPV--PRTLLFDN 722
            D  FDA   G+TD I GVSECII+G  +++GTG +++++A+  SE    PR  +F++
Sbjct: 1337 DHLFDAGGAGRTDLIEGVSECIIVGKGISLGTGSMEVIRALNFSEGQIGPRKTVFED 1393


>gi|328858469|gb|EGG07581.1| hypothetical protein MELLADRAFT_47986 [Melampsora larici-populina
           98AG31]
          Length = 1421

 Score =  270 bits (689), Expect = 6e-69,   Method: Compositional matrix adjust.
 Identities = 137/277 (49%), Positives = 183/277 (66%), Gaps = 29/277 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIM+HRAK+ P RT RFNECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 473 DGDVVLFNRQPSLHKLSIMSHRAKIRPWRTLRFNECVCTPYNADFDGDEMNLHVPQTEEA 532

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EA                LM  K NLVTPRNGE +IAATQDFIT  YLL++K+ F++R
Sbjct: 533 RTEATE--------------LMNVKYNLVTPRNGEPIIAATQDFITASYLLSRKDNFYDR 578

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q  +    L   T  I             P V  +   +WTGKQ+F+++++PN+  PV 
Sbjct: 579 QQFTQALQYLSDATLHI----------DLPPPVIWKPIRLWTGKQVFNVLMRPNKASPVK 628

Query: 521 ANLKTK-GRAYTANEEF----CHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            N++ K    + A  EF       D +++++NSE++ G +DK+ +G G K ++F ++ RD
Sbjct: 629 VNIEAKCATHHKALPEFLPDMSPNDGWLVIQNSEIMCGVVDKAIVGGGKKDSIFAVINRD 688

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
           +G D AV AM RL+++++ +L N GFSIG+GDVTPG+
Sbjct: 689 YGPDEAVKAMNRLAKVSARWLANMGFSIGVGDVTPGE 725



 Score =  241 bits (616), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 170/493 (34%), Positives = 235/493 (47%), Gaps = 82/493 (16%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G+G PVE  R      A  S      L   EI+    + L    F +  +  F   +  F
Sbjct: 932  GDGEPVEFARTWRHSKATISHLDGRGLYPYEIVQTVAKRLAEPRFAKACTTRFTDSVLNF 991

Query: 1057 LEEFSKKESVTSHQDKVSQPLREQI--LSHQDKIGHGRESNPFPSACKAEA--------- 1105
            +     K + T        P  E       +  +  G   N    A K +          
Sbjct: 992  ITNSVAKPAATYRASYGMYPAMEMDGDWDEETDLSAGVTGNKKIVANKTQVTLKQIDTFL 1051

Query: 1106 --CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGE----------------- 1146
              C  KYV+A++EP TAVGA+ AQSIGEPGTQMTLKTFHFAG                  
Sbjct: 1052 DYCWVKYVKAKVEPGTAVGAVGAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIIN 1111

Query: 1147 -------------------------VCEYIEEVFVPDDSFIL------------IKLDMD 1169
                                     V   +E+ ++ D + ++            I +DMD
Sbjct: 1112 ASKVINGPIINAPLVANQSERAARIVKARLEKTYLGDITSVIEGMYSNESMYVGIHIDMD 1171

Query: 1170 RIRLLHLEVDIDSIRYCI----------ERTRGISGHLTVSGHSFLILKPKDSSKSFNSK 1219
             +R L LEV +D+I++ I          ++ + I     +  +   +L   ++   F  K
Sbjct: 1172 TVRRLQLEVTLDTIKWSIVNAPKLKIREDQIQVIPRKNRIRVYVDGVLADGENVLPFYQK 1231

Query: 1220 MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSS 1279
            +  ++++LP VVIKG+    R VI++       +Y+LLVEG  LR+VM T GV G     
Sbjct: 1232 LMFLRRVLPGVVIKGLSKAGRTVINKNT---SNEYELLVEGYGLREVMTTDGVVGTHTMP 1288

Query: 1280 NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGL 1339
            N+  E    LGIEA R+ I+ EI   M++HG+ +D RH ML+ D+M  KGEVLGITR G+
Sbjct: 1289 NHIMEAQSILGIEAGRNCIIKEISYTMDSHGLKVDPRHMMLLGDIMCYKGEVLGITRFGV 1348

Query: 1340 AKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMN-VGTGLIKLLQAVP 1398
            AKMK+S    +SFE T+DHLFDAA Y + D I GVSECIIMG P N +GT    L+  +P
Sbjct: 1349 AKMKDSASFFSSFEKTTDHLFDAALYSKRDAIEGVSECIIMGNPANDIGTSAACLVSDLP 1408

Query: 1399 RSEPVPRTLLFDN 1411
               P PR LLF+N
Sbjct: 1409 VLPP-PRKLLFEN 1420



 Score =  193 bits (490), Expect = 6e-46,   Method: Compositional matrix adjust.
 Identities = 100/233 (42%), Positives = 135/233 (57%), Gaps = 5/233 (2%)

Query: 113 RTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQS 172
           + P   G+LD R+GT+ K   C TC   ++DCVGH+ YI L LPVFHIGYFR VI +LQ 
Sbjct: 62  KKPAKGGVLDTRLGTSDKSGTCGTCNAKMADCVGHYSYIKLILPVFHIGYFRAVIQMLQD 121

Query: 173 ICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGV 232
           ICK  TCARV+L EE    +  + R P L  L R+   K++    +KV  CP+CG  NG+
Sbjct: 122 ICK--TCARVMLSEEDRRVYLQRFRRPNLENLQRQHYAKQVNTACRKVLTCPYCGATNGI 179

Query: 233 VKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVL 292
           VKK G L+I HEK+  R KKK   +E     +  A+K   E+  H      + +NPL VL
Sbjct: 180 VKKVGALRIVHEKF--RAKKKADELEAFRDTFINAIKETRELAPHLHKAQ-EDMNPLRVL 236

Query: 293 QLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDNDVV 345
            LF  +   D  LL ++ E+ +P + I   + VPP CIRPSV  +  ++ D V
Sbjct: 237 NLFRRVTPSDCELLGLDPEVGRPEEYIWQYIHVPPVCIRPSVTQEAATNEDDV 289



 Score =  166 bits (419), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 98/244 (40%), Positives = 143/244 (58%), Gaps = 13/244 (5%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ I+ PII A L  +     ARIVK RLE+T LG++   IE ++  + 
Sbjct: 1102 GVPRIKEIINASKVINGPIINAPLVANQSERAARIVKARLEKTYLGDITSVIEGMYSNES 1161

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCI----------ERTRGISGHLTVSGHSFLILKP 873
             ++ I +DMD +R L LEV +D+I++ I          ++ + I     +  +   +L  
Sbjct: 1162 MYVGIHIDMDTVRRLQLEVTLDTIKWSIVNAPKLKIREDQIQVIPRKNRIRVYVDGVLAD 1221

Query: 874  KDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMAT 933
             ++   F  K+  ++++LP VVIKG+    R VI++       +Y+LLVEG  LR+VM T
Sbjct: 1222 GENVLPFYQKLMFLRRVLPGVVIKGLSKAGRTVINKNTS---NEYELLVEGYGLREVMTT 1278

Query: 934  YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
             GV G     N+  E    LGIEA R+ I+ EI   M++HG+ +D RH ML+ D+M  KG
Sbjct: 1279 DGVVGTHTMPNHIMEAQSILGIEAGRNCIIKEISYTMDSHGLKVDPRHMMLLGDIMCYKG 1338

Query: 994  EVLG 997
            EVLG
Sbjct: 1339 EVLG 1342



 Score = 98.6 bits (244), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 45/61 (73%), Positives = 51/61 (83%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV+NSF SGL  TEF FH + GREGLVDTAVKTAETGYMQRRL+K+LEDL  +YD 
Sbjct: 847 PAKGFVRNSFHSGLRATEFLFHAISGREGLVDTAVKTAETGYMQRRLMKALEDLSTRYDD 906

Query: 670 S 670
           S
Sbjct: 907 S 907



 Score = 60.8 bits (146), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 28/42 (66%), Positives = 34/42 (80%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 63
           LM  K NLVTPRNGE +IAATQDFIT  YLL++K+ F++R Q
Sbjct: 539 LMNVKYNLVTPRNGEPIIAATQDFITASYLLSRKDNFYDRQQ 580



 Score = 55.1 bits (131), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 30/56 (53%), Positives = 35/56 (62%), Gaps = 2/56 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMN-VGTGLIKLLQAVPRSEPVPRTLLFDN 722
            D  FDAA Y + D I GVSECIIMG P N +GT    L+  +P   P PR LLF+N
Sbjct: 1366 DHLFDAALYSKRDAIEGVSECIIMGNPANDIGTSAACLVSDLPVLPP-PRKLLFEN 1420


>gi|225678717|gb|EEH17001.1| DNA-directed RNA polymerase III subunit RPC1 [Paracoccidioides
           brasiliensis Pb03]
          Length = 1449

 Score =  269 bits (688), Expect = 8e-69,   Method: Compositional matrix adjust.
 Identities = 132/280 (47%), Positives = 182/280 (65%), Gaps = 28/280 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++H  KV PHRTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 461 DGDIVLFNRQPSLHKLSILSHFVKVRPHRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 520

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NLVTP+NGE +I+A QDFIT  Y+L+ KN F++R
Sbjct: 521 RAEAME--------------LMGVKNNLVTPKNGEPIISAIQDFITAAYMLSSKNVFYDR 566

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                +   ++   +       RF      P   ++  ++WTGKQ+F+++++PN+D PV 
Sbjct: 567 KTFTHVCLYMLLPGT-------RF---DLPPPSILKPQMLWTGKQVFNILMRPNKDSPVL 616

Query: 521 ANLKTKGRAYTANE----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL    R + A +    +    D ++ +RNSE++ G MDK T+GSG K +VFY++LRD+
Sbjct: 617 VNLDAACREFKAPKGTPRDLDANDRWLCIRNSEVMCGVMDKYTIGSGKKDSVFYVMLRDY 676

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           G  +A   M RLSR+ + ++ + GFSIGI DV PG   ++
Sbjct: 677 GPAIAAEGMNRLSRLCARWITDLGFSIGITDVYPGDRLLE 716



 Score =  222 bits (565), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 175/509 (34%), Positives = 246/509 (48%), Gaps = 104/509 (20%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNE-------TLDSKEFL------Q 1043
            GN  PV   R            SD  L   EI+ L          +LD  + +       
Sbjct: 919  GNARPVNFDRTFTHSEVTTFDNSDKGLLPDEIMTLCQSLLAKERASLDRYDLMGNRLDYM 978

Query: 1044 DTSENFV------RDIKKFLEEF--SKKESVTS-HQDKVSQPLREQILSHQDKIGHGRES 1094
            D S+N +      RD  + +E++  SK E + S      +     + ++H  KI   R  
Sbjct: 979  DRSDNGIDQLESARDYLQSIEDYISSKAEKLRSIDGGNNNGQGGGRGINHTAKIS-ARTL 1037

Query: 1095 NPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------- 1145
              F ++C       KY +AQ+EP  AVGA+ AQSIGEPGTQMTLKTFHFAG         
Sbjct: 1038 AAFITSCLV-----KYKKAQVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQG 1092

Query: 1146 -----EVCEYIEEVFVP----------------------------------------DDS 1160
                 E+    +E+  P                                        +D+
Sbjct: 1093 VPRIKEIINASKEISTPVITCQLVNKGDLRAAQIVKGRVEKTFMRDIIYYIEEDWTGNDA 1152

Query: 1161 FILIKLDMDRIRLLHLEVDIDSIRYCIE------------RTRGISGHLTVSGHSFLILK 1208
            +I IK+D   I+ L LE+ +  I   I+            R+ G   H+ V   +     
Sbjct: 1153 YINIKIDFSTIQNLQLELGLQDILSAIKKHKRFKSADLKFRSFGSHIHIFVDQQATRTAL 1212

Query: 1209 PKDSSKSFNSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLR 1264
             K    +  +  Y     +K+L+P++ + G    +RA+I  +  E  T   LLVEG  LR
Sbjct: 1213 SKSEEAATGADPYIRLKHLKRLIPTIQVLGHPQCSRAIIRTD--ETCTTNTLLVEGYGLR 1270

Query: 1265 DVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADL 1324
            D M T G+ G    +NN  E    LGIEAAR+TI+ EI  VM++  M+ID RH  L+AD+
Sbjct: 1271 DCMTTDGIDGRNTRTNNIMETRLVLGIEAARTTIVEEIGEVMKD--MAIDPRHMQLLADV 1328

Query: 1325 MTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPM 1384
            MT KGEVLGITR GLAKM++SVL LASFE T+DHLFDA   G+TD I GVSECII+G  +
Sbjct: 1329 MTYKGEVLGITRFGLAKMRDSVLQLASFEKTADHLFDAGGAGRTDLIEGVSECIIVGKGI 1388

Query: 1385 NVGTGLIKLLQAVPRSEPV--PRTLLFDN 1411
            ++GTG +++++A+   E    PR  +F++
Sbjct: 1389 SLGTGSMEVIRALNFCEGQIGPRKTVFED 1417



 Score =  166 bits (420), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 98/233 (42%), Positives = 134/233 (57%), Gaps = 12/233 (5%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G ++ +D V Q + +++  + L+  +  R  +PHG LD RMG + K   C TCG  L  C
Sbjct: 30  GVLSTQDIVSQ-AVVEVSDRKLFDLEKDRAIVPHGPLDGRMGISSKSGTCDTCGGGLQLC 88

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFG++ L LP FH+GYF+ VI+ILQ ICK+  C+ +LL E +   F  +LR P +  L
Sbjct: 89  SGHFGHVRLVLPAFHVGYFKLVISILQEICKD--CSHILLPEPERRSFLKELRRPGIDNL 146

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKYK----NRTKKKDAIVE 258
            R  + KKI E  +K   C +C  INGVVKK G   LKISHEK++    + + KK     
Sbjct: 147 RRMQIVKKINERCRKTRTCYNCNAINGVVKKAGTSALKISHEKFRAFNTSTSVKKVPPPS 206

Query: 259 DLLAE--YNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMN 309
            +  +  + EA K NPEIE H K      L+PL VL+LF  I  ED  LL +N
Sbjct: 207 KIFFDRSFEEAKKSNPEIEKHFKKAH-DDLHPLRVLKLFRRISNEDCELLGLN 258



 Score =  159 bits (402), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 103/250 (41%), Positives = 143/250 (57%), Gaps = 20/250 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+IT  L    DL  A+IVKGR+E+T + ++  YIEE +  +D
Sbjct: 1092 GVPRIKEIINASKEISTPVITCQLVNKGDLRAAQIVKGRVEKTFMRDIIYYIEEDWTGND 1151

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIE------------RTRGISGHLTVSGHSFLIL 871
            ++I IK+D   I+ L LE+ +  I   I+            R+ G   H+ V   +    
Sbjct: 1152 AYINIKIDFSTIQNLQLELGLQDILSAIKKHKRFKSADLKFRSFGSHIHIFVDQQATRTA 1211

Query: 872  KPKDSSKSFNSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927
              K    +  +  Y     +K+L+P++ + G    +RA+I  +  E  T   LLVEG  L
Sbjct: 1212 LSKSEEAATGADPYIRLKHLKRLIPTIQVLGHPQCSRAIIRTD--ETCTTNTLLVEGYGL 1269

Query: 928  RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 987
            RD M T G+ G    +NN  E    LGIEAAR+TI+ EI  VM++  M+ID RH  L+AD
Sbjct: 1270 RDCMTTDGIDGRNTRTNNIMETRLVLGIEAARTTIVEEIGEVMKD--MAIDPRHMQLLAD 1327

Query: 988  LMTSKGEVLG 997
            +MT KGEVLG
Sbjct: 1328 VMTYKGEVLG 1337



 Score =  107 bits (266), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 48/59 (81%), Positives = 52/59 (88%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFVQNSFFSGLTPTEF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  +YD
Sbjct: 834 PAKGFVQNSFFSGLTPTEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSTRYD 892



 Score = 57.4 bits (137), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 24/40 (60%), Positives = 32/40 (80%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           LM  K+NLVTP+NGE +I+A QDFIT  Y+L+ KN F++R
Sbjct: 527 LMGVKNNLVTPKNGEPIISAIQDFITAAYMLSSKNVFYDR 566



 Score = 46.2 bits (108), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 24/57 (42%), Positives = 38/57 (66%), Gaps = 2/57 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPV--PRTLLFDN 722
            D  FDA   G+TD I GVSECII+G  +++GTG +++++A+   E    PR  +F++
Sbjct: 1361 DHLFDAGGAGRTDLIEGVSECIIVGKGISLGTGSMEVIRALNFCEGQIGPRKTVFED 1417


>gi|226294925|gb|EEH50345.1| DNA-directed RNA polymerase III subunit RPC1 [Paracoccidioides
           brasiliensis Pb18]
          Length = 1458

 Score =  269 bits (687), Expect = 9e-69,   Method: Compositional matrix adjust.
 Identities = 132/280 (47%), Positives = 182/280 (65%), Gaps = 28/280 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++H  KV PHRTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 470 DGDIVLFNRQPSLHKLSILSHFVKVRPHRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 529

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  K+NLVTP+NGE +I+A QDFIT  Y+L+ KN F++R
Sbjct: 530 RAEAME--------------LMGVKNNLVTPKNGEPIISAIQDFITAAYMLSSKNVFYDR 575

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                +   ++   +       RF      P   ++  ++WTGKQ+F+++++PN+D PV 
Sbjct: 576 KTFTHVCLYMLLPGT-------RF---DLPPPSILKPQMLWTGKQVFNILMRPNKDSPVL 625

Query: 521 ANLKTKGRAYTANE----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL    R + A +    +    D ++ +RNSE++ G MDK T+GSG K +VFY++LRD+
Sbjct: 626 VNLDAACREFKAPKGPPRDLDANDRWLCIRNSEVMCGVMDKYTIGSGKKDSVFYVMLRDY 685

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           G  +A   M RLSR+ + ++ + GFSIGI DV PG   ++
Sbjct: 686 GPAIAAEGMNRLSRLCARWITDLGFSIGITDVYPGDRLLE 725



 Score =  222 bits (565), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 147/379 (38%), Positives = 202/379 (53%), Gaps = 76/379 (20%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEY 1150
            +C  KY +AQ+EP  AVGA+ AQSIGEPGTQMTLKTFHFAG              E+   
Sbjct: 1052 SCLVKYKKAQVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIINA 1111

Query: 1151 IEEVFVP----------------------------------------DDSFILIKLDMDR 1170
             +E+  P                                        +D++I IK+D   
Sbjct: 1112 SKEISTPVITCQLVNKGDLRAAQIVKGRVEKTFMRDIIYYIEEDWTGNDAYINIKIDFST 1171

Query: 1171 IRLLHLEVDIDSIRYCIE------------RTRGISGHLTVSGHSFLILKPKDSSKSFNS 1218
            I+ L LE+ +  I   I+            R+ G   H+ V   +      K    +  +
Sbjct: 1172 IQNLQLELGLQDILSAIKKHKRFKSADLKFRSFGSHIHIFVDQQATRTALSKSEEAATGA 1231

Query: 1219 KMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 1274
              Y     +K+L+P++ + G    +RA+I  +  E  T   LLVEG  LRD M T G+ G
Sbjct: 1232 DPYIRLKHLKRLIPTIQVLGHPQCSRAIIRTD--ETCTTNTLLVEGYGLRDCMTTDGIDG 1289

Query: 1275 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGI 1334
                +NN  E    LGIEAAR+TI+ EI  VM++  M+ID RH  L+AD+MT KGEVLGI
Sbjct: 1290 RNTRTNNIMETRLVLGIEAARTTIVEEIGEVMKD--MAIDPRHMQLLADVMTYKGEVLGI 1347

Query: 1335 TRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            TR GLAKM++SVL LASFE T+DHLFDA   G+TD I GVSECII+G  +++GTG ++++
Sbjct: 1348 TRFGLAKMRDSVLQLASFEKTADHLFDAGGAGRTDLIEGVSECIIVGKGISLGTGSMEVI 1407

Query: 1395 QAVPRSEPV--PRTLLFDN 1411
            +A+   E    PR  +F++
Sbjct: 1408 RALNFCEGQIGPRKTVFED 1426



 Score =  186 bits (471), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 109/267 (40%), Positives = 150/267 (56%), Gaps = 12/267 (4%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G ++ +D V Q + +++  + L+  +  R  +PHG LD RMG + K   C TCG  L  C
Sbjct: 30  GVLSTQDIVSQ-AVVEVSDRKLFDLEKDRAIVPHGPLDGRMGISSKSGTCDTCGGGLQLC 88

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFG++ L LP FH+GYF+ VI+ILQ ICK+  C+ +LL E +   F  +LR P +  L
Sbjct: 89  SGHFGHVRLVLPAFHVGYFKLVISILQEICKD--CSHILLPEPERRSFLKELRRPGIDNL 146

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKYK----NRTKKKDAIVE 258
            R  + KKI E  +K   C +C  INGVVKK G   LKISHEK++    + + KK     
Sbjct: 147 RRMQIVKKINERCRKTRTCYNCNAINGVVKKAGTSALKISHEKFRAFNTSTSVKKVPPPS 206

Query: 259 DLLAE--YNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPS 316
            +  +  + EA K NPEIE H K      L+PL VL+LF  I  ED  LL +N   ++P 
Sbjct: 207 KIFFDRSFEEAKKSNPEIEKHFKKAH-DDLHPLRVLKLFRRISNEDCELLGLNPAEARPE 265

Query: 317 DLILTRLLVPPNCIRPSVISDLKSDND 343
             +   +  PP CIRPSV  +  S  D
Sbjct: 266 VFLWQYIPAPPVCIRPSVGQEAASTED 292



 Score =  159 bits (403), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 103/250 (41%), Positives = 143/250 (57%), Gaps = 20/250 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+IT  L    DL  A+IVKGR+E+T + ++  YIEE +  +D
Sbjct: 1101 GVPRIKEIINASKEISTPVITCQLVNKGDLRAAQIVKGRVEKTFMRDIIYYIEEDWTGND 1160

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIE------------RTRGISGHLTVSGHSFLIL 871
            ++I IK+D   I+ L LE+ +  I   I+            R+ G   H+ V   +    
Sbjct: 1161 AYINIKIDFSTIQNLQLELGLQDILSAIKKHKRFKSADLKFRSFGSHIHIFVDQQATRTA 1220

Query: 872  KPKDSSKSFNSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927
              K    +  +  Y     +K+L+P++ + G    +RA+I  +  E  T   LLVEG  L
Sbjct: 1221 LSKSEEAATGADPYIRLKHLKRLIPTIQVLGHPQCSRAIIRTD--ETCTTNTLLVEGYGL 1278

Query: 928  RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 987
            RD M T G+ G    +NN  E    LGIEAAR+TI+ EI  VM++  M+ID RH  L+AD
Sbjct: 1279 RDCMTTDGIDGRNTRTNNIMETRLVLGIEAARTTIVEEIGEVMKD--MAIDPRHMQLLAD 1336

Query: 988  LMTSKGEVLG 997
            +MT KGEVLG
Sbjct: 1337 VMTYKGEVLG 1346



 Score =  107 bits (266), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 48/59 (81%), Positives = 52/59 (88%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFVQNSFFSGLTPTEF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  +YD
Sbjct: 843 PAKGFVQNSFFSGLTPTEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSTRYD 901



 Score = 57.4 bits (137), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 24/40 (60%), Positives = 32/40 (80%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           LM  K+NLVTP+NGE +I+A QDFIT  Y+L+ KN F++R
Sbjct: 536 LMGVKNNLVTPKNGEPIISAIQDFITAAYMLSSKNVFYDR 575



 Score = 45.8 bits (107), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 24/57 (42%), Positives = 38/57 (66%), Gaps = 2/57 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPV--PRTLLFDN 722
            D  FDA   G+TD I GVSECII+G  +++GTG +++++A+   E    PR  +F++
Sbjct: 1370 DHLFDAGGAGRTDLIEGVSECIIVGKGISLGTGSMEVIRALNFCEGQIGPRKTVFED 1426


>gi|169597423|ref|XP_001792135.1| hypothetical protein SNOG_01497 [Phaeosphaeria nodorum SN15]
 gi|160707519|gb|EAT91146.2| hypothetical protein SNOG_01497 [Phaeosphaeria nodorum SN15]
          Length = 1473

 Score =  268 bits (686), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 135/296 (45%), Positives = 186/296 (62%), Gaps = 19/296 (6%)

Query: 322 RLLVPPNCIR-PSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTP 380
           RL  P   +R   V+     D D+VLFNRQPSLHKLSI++HRAK+ P RTFR NECVC P
Sbjct: 462 RLQGPAAALRFGDVVERHLEDGDIVLFNRQPSLHKLSILSHRAKIRPWRTFRLNECVCNP 521

Query: 381 YNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAA 440
           YNADFDGDEMN+H+PQTEEAR EA                LM  K NL TP+NG  +IAA
Sbjct: 522 YNADFDGDEMNLHVPQTEEARTEATE--------------LMGVKYNLATPKNGTPIIAA 567

Query: 441 TQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVI 500
            QDFIT  ++L+ K+ F++R    +I + +            ++      P V  +   +
Sbjct: 568 IQDFITAAFILSNKSNFYDRRTFCQIVNYMFTGEGAYDPDTGKYLPIEIPPPVIWKPQAL 627

Query: 501 WTGKQIFSLILKPNRDCPVNANLKTKGRAYTANE----EFCHRDSYVILRNSELLAGSMD 556
           WTGKQ+F+L+++PN+   V  NL+   + Y   +    +    D+Y+I+RNSE++ G MD
Sbjct: 628 WTGKQVFNLLMRPNKQSRVLVNLEAGCKQYKPVQGRAPDLDENDAYLIIRNSEVMCGVMD 687

Query: 557 KSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
           KST+G G K +VFY+++RDFG + AV  M RL+R+++ +L N GFS+GI DVTPG+
Sbjct: 688 KSTVGDGKKESVFYVMMRDFGPEHAVQGMNRLARLSARWLTNNGFSLGISDVTPGE 743



 Score =  185 bits (470), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 116/277 (41%), Positives = 162/277 (58%), Gaps = 23/277 (8%)

Query: 1146 EVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTR----GISGHLTVSG 1201
            ++  Y+E+V+ P  +++ +++D D +  L +++    I   I + +    G +G      
Sbjct: 1182 DIINYVEDVWHPTGAYVAMRIDWDTVNALFVDITPHEIVNAINKHKPLKWGKAGTKVRIS 1241

Query: 1202 HSFL---ILKPKDSSK------SFNSKMY-----QMKQLLPSVVIKGVQGINRAVIHEE- 1246
             S +   I  P  S K      S N K Y     Q+K L+P VVIKG  G  RA+I +E 
Sbjct: 1242 SSLIRVEIADPSASKKRPAAKASKNHKEYFERVQQVKNLIPHVVIKGYDGCTRAIIKKET 1301

Query: 1247 --DVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKL 1304
              +  G  + +LLVEG  L+D + T G++  K  SN+  EV   LGIEAAR+TIM EI  
Sbjct: 1302 TPNKNGDYECELLVEGYGLKDCLTTPGIEPYKTMSNHVMEVRTVLGIEAARATIMREISA 1361

Query: 1305 VMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAF 1364
            VM N  M ID RH  L+AD+MT KG+V GITR GL K ++SVL LASFE T DHLF+AA 
Sbjct: 1362 VMGN--MDIDPRHMALLADVMTFKGDVYGITRFGLQKTRDSVLQLASFEKTPDHLFEAAA 1419

Query: 1365 YGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSE 1401
             G+TD I GVSE IIMG  M +GTG +++++ +   E
Sbjct: 1420 RGKTDTIDGVSESIIMGQSMKLGTGALQVVRPLKLGE 1456



 Score =  161 bits (407), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 106/255 (41%), Positives = 144/255 (56%), Gaps = 23/255 (9%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS  ISTP+IT  L        ARIVK R+E+T L ++  Y+E+V+ P  
Sbjct: 1136 GVPRIKEIINASSTISTPVITCVLSNKISESAARIVKARVEKTYLRDIINYVEDVWHPTG 1195

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTR----GISGHLTVSGHSFL---ILKPKDS 876
            +++ +++D D +  L +++    I   I + +    G +G       S +   I  P  S
Sbjct: 1196 AYVAMRIDWDTVNALFVDITPHEIVNAINKHKPLKWGKAGTKVRISSSLIRVEIADPSAS 1255

Query: 877  SK------SFNSKMY-----QMKQLLPSVVIKGVQGINRAVIHEE---DVEGVTKYKLLV 922
             K      S N K Y     Q+K L+P VVIKG  G  RA+I +E   +  G  + +LLV
Sbjct: 1256 KKRPAAKASKNHKEYFERVQQVKNLIPHVVIKGYDGCTRAIIKKETTPNKNGDYECELLV 1315

Query: 923  EGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHP 982
            EG  L+D + T G++  K  SN+  EV   LGIEAAR+TIM EI  VM N  M ID RH 
Sbjct: 1316 EGYGLKDCLTTPGIEPYKTMSNHVMEVRTVLGIEAARATIMREISAVMGN--MDIDPRHM 1373

Query: 983  MLVADLMTSKGEVLG 997
             L+AD+MT KG+V G
Sbjct: 1374 ALLADVMTFKGDVYG 1388



 Score =  157 bits (396), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 98/273 (35%), Positives = 144/273 (52%), Gaps = 16/273 (5%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLY----CQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G  + +D V Q + I++  +N+Y      D  R    +G +D  MG + K   C TCG+ 
Sbjct: 26  GIYSNQDIVNQ-AVIEVSDRNVYDLTPAADNTRALTANGPMDPLMGISSKTGECGTCGEK 84

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
           L  C GHFG+I L LP FH+GY + +I +L  ICK+  C+RVLL E +   +   +R P 
Sbjct: 85  LDKCNGHFGHIKLALPAFHVGYLKHIIEVLNCICKD--CSRVLLDEVERRRYLRSMRRPD 142

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKYK--NR----TKK 252
           +  L R ++ KK+LE  +K   CP+C  + G V+K     LKI H +Y   NR    TKK
Sbjct: 143 MDTLRRTAISKKVLEDCRKKKTCPYCDALQGTVRKVPGHPLKIIHNRYDAFNRSTAKTKK 202

Query: 253 KDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL 312
             A   +    +  A   NP+++ H K   +  ++PL  L LF+ I  ED  LL M  E 
Sbjct: 203 PPAGKIEFDQSFETAKAANPDLDKHLKKA-VDDMHPLRTLNLFKKISPEDCELLAMIPED 261

Query: 313 SKPSDLILTRLLVPPNCIRPSVISDLKSDNDVV 345
           ++P  LI   + VPP  +RPSV+ +  +  D V
Sbjct: 262 ARPEMLIWEYMPVPPVALRPSVMQEGGATEDDV 294



 Score =  103 bits (256), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 46/58 (79%), Positives = 50/58 (86%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV NSF+SGLTP+EF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 866 AKGFVSNSFYSGLTPSEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSAQYD 923



 Score = 67.8 bits (164), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 29/40 (72%), Positives = 34/40 (85%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            C  KY R++++P  AVGA+ AQSIGEPGTQMTLKTFHFAG
Sbjct: 1088 CLTKYHRSRVQPGHAVGAIGAQSIGEPGTQMTLKTFHFAG 1127



 Score = 52.4 bits (124), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 23/57 (40%), Positives = 35/57 (61%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVF 78
           LM  K NL TP+NG  +IAA QDFIT  ++L+ K+ F++R    +I + +  G   +
Sbjct: 548 LMGVKYNLATPKNGTPIIAAIQDFITAAFILSNKSNFYDRRTFCQIVNYMFTGEGAY 604



 Score = 43.9 bits (102), Expect = 0.66,   Method: Compositional matrix adjust.
 Identities = 21/45 (46%), Positives = 30/45 (66%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSE 712
            D  F+AA  G+TD I GVSE IIMG  M +GTG +++++ +   E
Sbjct: 1412 DHLFEAAARGKTDTIDGVSESIIMGQSMKLGTGALQVVRPLKLGE 1456


>gi|343427900|emb|CBQ71425.1| probable RPO31-DNA-directed RNA polymerase III, 160 KD subunit
           [Sporisorium reilianum SRZ2]
          Length = 1400

 Score =  268 bits (686), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 134/282 (47%), Positives = 177/282 (62%), Gaps = 29/282 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIM+HRAK+ P RTFR NEC C PYNADFDGDEMN+H+PQTEEA
Sbjct: 455 DGDIVLFNRQPSLHKLSIMSHRAKIRPWRTFRLNECACNPYNADFDGDEMNMHVPQTEEA 514

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R E              A VLM  K NLVTPRNGE +IAA QDFIT  YL+++++ FF+R
Sbjct: 515 RTE--------------ATVLMGVKHNLVTPRNGEPIIAAIQDFITASYLISKRDRFFDR 560

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           AQ  +I S        I             P   ++   +WTGKQ+ S +++PNR  P  
Sbjct: 561 AQFSQICSYFADADLQI----------DLPPPAIMKPVRLWTGKQVMSCLIRPNRKSPHL 610

Query: 521 ANLKTKGRAYTA-----NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL+ + R +        ++    D ++++ NSE++ G  DKST+G G K +VF ++LRD
Sbjct: 611 VNLEAQCRTFEKPTGGHPKDMSPNDGWLVIVNSEVMCGVFDKSTVGDGKKNSVFGVMLRD 670

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           +G D A+TAM RL++  + +L N+GFS+GI DV PG     N
Sbjct: 671 YGPDAAITAMNRLAKTCARWLANQGFSLGINDVIPGPNLRDN 712



 Score =  215 bits (548), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 159/499 (31%), Positives = 235/499 (47%), Gaps = 90/499 (18%)

Query: 993  GEVLGNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRD 1052
             E+ GN  P+E  RL    +A         L   EI+ + +  L S+ F++  ++ ++  
Sbjct: 910  AELEGNAMPIEPFRLWRHCLAITHHIEGRGLYPYEIMEVVDRELGSERFVKTCTQKYLDS 969

Query: 1053 IKKFLEEFSKKESVT--SHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKA------- 1103
            +++FL E   K +V   S         RE+       +  G + + +             
Sbjct: 970  VREFLSENVYKRAVQMRSAFGMYGAEEREEHWDEHTDLSLGADRDQWAIVNNKTKIKQVA 1029

Query: 1104 -----EACREKYVRAQIEPATAVGAL---------------------------------- 1124
                 + C +KY++A+IEP +AVGA+                                  
Sbjct: 1030 ILEFLQQCYKKYMKAKIEPGSAVGAVGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRI 1089

Query: 1125 -----AAQSIGEPGTQMTLKTFH---------------FAGEVCEYIEEVFVPDDSFILI 1164
                 AA+SI  P  +  L +                 + G++   IEE +    +++ +
Sbjct: 1090 KEIINAAKSINTPIIEAKLVSEKSERTARIVKGRIEKTYLGDIASVIEEAWAAQYTYLGV 1149

Query: 1165 KLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPK------------DS 1212
             +DMD I+ L LE+ ++ I++ I      +  L +     +++  K            D 
Sbjct: 1150 HIDMDAIQKLQLEITLNDIKWAIVN----APKLKIKEERVMVVPKKNRIRIYVPPEGLDK 1205

Query: 1213 SKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGV 1272
                   +  +K+ LPS+++KG+    RAVI +E        KLLVEG  L  VM T GV
Sbjct: 1206 EGEVYYNLKALKRALPSIIVKGIPQATRAVISDEK----GTRKLLVEGYGLLKVMTTEGV 1261

Query: 1273 KGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL 1332
             G    +N+  E+   LGIEAAR+++  EI+  M  HGMSID RH ML+AD MT KGEVL
Sbjct: 1262 IGTLTHTNHVMEMQTVLGIEAARTSVYREIEHTMSAHGMSIDPRHIMLLADTMTYKGEVL 1321

Query: 1333 GITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLP-MNVGTGLI 1391
            GITR G+AKMK+SVL LASFE T+DHLFDAA +G+ D + GVSE IIMG P   VGTG+ 
Sbjct: 1322 GITRFGVAKMKDSVLMLASFEKTTDHLFDAALFGKKDEVLGVSESIIMGNPAQTVGTGMP 1381

Query: 1392 KLLQAVPRSEPVPRTLLFD 1410
             L+   P   P  R LLFD
Sbjct: 1382 ALVVPAPVLPPR-RALLFD 1399



 Score =  195 bits (496), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 111/263 (42%), Positives = 152/263 (57%), Gaps = 8/263 (3%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYC-QDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSD 143
           G ++K+D V   S I++ +++LY   + +R P+ +G LDRR+G + K + C TC   ++D
Sbjct: 19  GVLSKQDIVNM-SEIEVTTRDLYTIGEAERKPVANGTLDRRLGVSDKNSLCETCHLKMAD 77

Query: 144 CVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSY 203
           CVGH+GYI L LPVFH+G+F+  + ILQSICKN  CA VLL E     F  + R P L  
Sbjct: 78  CVGHYGYIKLVLPVFHVGFFKHTVAILQSICKN--CATVLLEEPDRRKFLKRFRKPNLEN 135

Query: 204 LVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAE 263
           L R    K +    +KV  CP CG  NG VKK G LKI HEK+  R KK  A  ++  A 
Sbjct: 136 LDRTRTFKAVNTIARKVLYCPKCGYTNGTVKKQGQLKIVHEKF--RAKKTAAEHDEFKAS 193

Query: 264 YNEAVKF-NPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTR 322
           ++  +K  N +I  H      + LNPL+ L LF+ I  ED  LL +  E  +P + I   
Sbjct: 194 FSTNIKMGNGDISPHLNKAQ-EDLNPLKALDLFKRISDEDCELLGLRPEFGRPEEYIWQY 252

Query: 323 LLVPPNCIRPSVISDLKSDNDVV 345
           + VPP CIRPSV  D  ++ D V
Sbjct: 253 ICVPPVCIRPSVAQDGATNEDDV 275



 Score =  169 bits (427), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 100/246 (40%), Positives = 142/246 (57%), Gaps = 20/246 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA+++I+TPII A L  +     ARIVKGR+E+T LG++   IEE +    
Sbjct: 1085 GVPRIKEIINAAKSINTPIIEAKLVSEKSERTARIVKGRIEKTYLGDIASVIEEAWAAQY 1144

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPK--------- 874
            +++ + +DMD I+ L LE+ ++ I++ I      +  L +     +++  K         
Sbjct: 1145 TYLGVHIDMDAIQKLQLEITLNDIKWAIVN----APKLKIKEERVMVVPKKNRIRIYVPP 1200

Query: 875  ---DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVM 931
               D        +  +K+ LPS+++KG+    RAVI +E        KLLVEG  L  VM
Sbjct: 1201 EGLDKEGEVYYNLKALKRALPSIIVKGIPQATRAVISDEK----GTRKLLVEGYGLLKVM 1256

Query: 932  ATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTS 991
             T GV G    +N+  E+   LGIEAAR+++  EI+  M  HGMSID RH ML+AD MT 
Sbjct: 1257 TTEGVIGTLTHTNHVMEMQTVLGIEAARTSVYREIEHTMSAHGMSIDPRHIMLLADTMTY 1316

Query: 992  KGEVLG 997
            KGEVLG
Sbjct: 1317 KGEVLG 1322



 Score =  108 bits (270), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 50/75 (66%), Positives = 58/75 (77%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV+NSFFSGL+PTEF FH + GREGLVDTAVKTAETGYMQRRL+K+LEDL   YD+
Sbjct: 829 PSKGFVRNSFFSGLSPTEFLFHAISGREGLVDTAVKTAETGYMQRRLMKALEDLSTHYDL 888

Query: 670 SFDAAFYGQTDCISG 684
           S   +  G    I G
Sbjct: 889 SVRNSVGGVVQFIYG 903



 Score = 65.1 bits (157), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 30/49 (61%), Positives = 38/49 (77%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIAS 69
           VLM  K NLVTPRNGE +IAA QDFIT  YL+++++ FF+RAQ  +I S
Sbjct: 520 VLMGVKHNLVTPRNGEPIIAAIQDFITASYLISKRDRFFDRAQFSQICS 568



 Score = 47.4 bits (111), Expect = 0.068,   Method: Compositional matrix adjust.
 Identities = 28/55 (50%), Positives = 33/55 (60%), Gaps = 2/55 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLP-MNVGTGLIKLLQAVPRSEPVPRTLLFD 721
            D  FDAA +G+ D + GVSE IIMG P   VGTG+  L+   P   P  R LLFD
Sbjct: 1346 DHLFDAALFGKKDEVLGVSESIIMGNPAQTVGTGMPALVVPAPVLPPR-RALLFD 1399


>gi|388857575|emb|CCF48724.1| probable RPO31-DNA-directed RNA polymerase III, 160 KD subunit
           [Ustilago hordei]
          Length = 1400

 Score =  268 bits (685), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 134/282 (47%), Positives = 180/282 (63%), Gaps = 29/282 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIM+HRAK+ P RTFR NEC C PYNADFDGDEMN+H+PQTEEA
Sbjct: 455 DGDIVLFNRQPSLHKLSIMSHRAKIRPWRTFRLNECACNPYNADFDGDEMNMHVPQTEEA 514

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R E              A +LM  K NLVTPRNGE +IAA QDFIT  YL+++++ FF+R
Sbjct: 515 RTE--------------ATILMGVKHNLVTPRNGEPIIAAIQDFITASYLISKRDRFFDR 560

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           AQ  ++ S   AD      I          P   ++   +WTGKQ+ S +++PNR  P  
Sbjct: 561 AQFAQVCS-YFADADLQIDI---------PPPAIMKPVRLWTGKQVMSCLIRPNRKSPHL 610

Query: 521 ANLKTKGRAYTA-----NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL+ + R +        ++    D ++++ NSE++ G  DKST+G G K +VF ++LRD
Sbjct: 611 INLEAQCRTFEKPKGGHPKDMSPNDGWLVIVNSEVMCGVFDKSTVGDGKKNSVFGVMLRD 670

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           +G D A+TAM RL++  + +L N+GFS+GI DV PG    +N
Sbjct: 671 YGPDAAITAMNRLAKTCARWLANQGFSLGINDVIPGPNLRKN 712



 Score =  213 bits (541), Expect = 9e-52,   Method: Compositional matrix adjust.
 Identities = 160/499 (32%), Positives = 237/499 (47%), Gaps = 90/499 (18%)

Query: 993  GEVLGNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRD 1052
             E+ GN  P+E  RL    +A         +   EI+ +    L S  F+   ++ +   
Sbjct: 910  AELEGNAMPIEPFRLWRHCMAITHHIPGRGMYPYEIMEIVERELKSPRFVNTCTQKYRDS 969

Query: 1053 IKKFLEEFSKKESVTSHQ--DKVSQPLREQILSHQDKIGHGRESNPFP-----SACKAEA 1105
            + +FL E   K +V   Q         R +       +  G + + +      +  K  A
Sbjct: 970  VYEFLSENVYKRAVEVRQAFGMYGAEERAEYWDEHTDLSFGADRDAWAIVNNKTKIKEVA 1029

Query: 1106 -------CREKYVRAQIEPATAVGAL---------------------------------- 1124
                   C  KY++A+IEP +AVGA+                                  
Sbjct: 1030 ILEFLNQCYIKYMKAKIEPGSAVGAVGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRI 1089

Query: 1125 -----AAQSIGEPGTQMTLKTFH---------------FAGEVCEYIEEVFVPDDSFILI 1164
                 AA+SI  P  +  L +                 + G++   IEE +    +++ +
Sbjct: 1090 KEIINAAKSINTPIIEAKLVSEKSEQSARIVKGRIEKTYLGDIASVIEEAWAAQYTYLGV 1149

Query: 1165 KLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF-------- 1216
             +DM+ I+ L LE+ ++ I++ I      +  L +     +++  K+  + +        
Sbjct: 1150 HIDMEAIQKLQLEITLNDIKWAIVN----APKLKIKEERVMVIPKKNRIRIYVPPEGIDK 1205

Query: 1217 NSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGV 1272
             S++Y     +K+ LPS+V+KG+    RAVI +E        KLLVEG  L  VM T GV
Sbjct: 1206 ESEVYYNLKALKRTLPSIVVKGIPQATRAVISDEK----GTRKLLVEGYGLLKVMTTEGV 1261

Query: 1273 KGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL 1332
             G +  +N+  E+   LGIEAAR+++  EI+  M  HGMSID RH ML+AD MT KGEVL
Sbjct: 1262 IGTQTHTNHVMEMQSVLGIEAARTSVYREIEHTMSAHGMSIDPRHVMLLADTMTYKGEVL 1321

Query: 1333 GITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLP-MNVGTGLI 1391
            GITR G+AKMK+SVL LASFE T+DHLFDAA +G+ D + GVSE IIMG P   VGTG+ 
Sbjct: 1322 GITRFGVAKMKDSVLMLASFEKTTDHLFDAALFGKKDEVLGVSESIIMGNPAQTVGTGMP 1381

Query: 1392 KLLQAVPRSEPVPRTLLFD 1410
             L+   P + P  R LLFD
Sbjct: 1382 ALVVPAP-TLPPRRALLFD 1399



 Score =  195 bits (496), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 112/263 (42%), Positives = 151/263 (57%), Gaps = 8/263 (3%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYC-QDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSD 143
           G ++K+D V   S I++ +++LY   + +R P+ +G LDRR+G + K + C TC   ++D
Sbjct: 19  GVLSKQDIVNM-SEIEVTTRDLYTIGEAERKPVANGTLDRRLGVSDKNSLCETCHLKMAD 77

Query: 144 CVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSY 203
           CVGH+GYI L LPVFH+G+F+  I ILQSICKN  CA VLL E     F  + R P L  
Sbjct: 78  CVGHYGYIKLVLPVFHVGFFKHTIAILQSICKN--CATVLLEEPDRRKFLKRFRKPNLEN 135

Query: 204 LVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAE 263
           L R    K +    +KV  CP CG  NG VKK G LKI HEK+  R KK  A  ++  A 
Sbjct: 136 LDRTRAFKAVNTIARKVLYCPKCGYTNGTVKKQGQLKIVHEKF--RAKKTAAEHDEFRAS 193

Query: 264 YNEAVKF-NPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTR 322
           +   +K  N +I  H      + LNPL+ L LF+ I  ED  LL +  E  +P + I   
Sbjct: 194 FATNIKMGNGDISPHLNRAQ-EDLNPLKALDLFKRISDEDCELLGLRPEFGRPEEYIWQY 252

Query: 323 LLVPPNCIRPSVISDLKSDNDVV 345
           + VPP CIRPSV  D  ++ D V
Sbjct: 253 ICVPPVCIRPSVAQDGATNEDDV 275



 Score =  172 bits (435), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 101/246 (41%), Positives = 148/246 (60%), Gaps = 20/246 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA+++I+TPII A L  +     ARIVKGR+E+T LG++   IEE +    
Sbjct: 1085 GVPRIKEIINAAKSINTPIIEAKLVSEKSEQSARIVKGRIEKTYLGDIASVIEEAWAAQY 1144

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF--- 880
            +++ + +DM+ I+ L LE+ ++ I++ I      +  L +     +++  K+  + +   
Sbjct: 1145 TYLGVHIDMEAIQKLQLEITLNDIKWAIVN----APKLKIKEERVMVIPKKNRIRIYVPP 1200

Query: 881  -----NSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVM 931
                  S++Y     +K+ LPS+V+KG+    RAVI +E        KLLVEG  L  VM
Sbjct: 1201 EGIDKESEVYYNLKALKRTLPSIVVKGIPQATRAVISDEK----GTRKLLVEGYGLLKVM 1256

Query: 932  ATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTS 991
             T GV G +  +N+  E+   LGIEAAR+++  EI+  M  HGMSID RH ML+AD MT 
Sbjct: 1257 TTEGVIGTQTHTNHVMEMQSVLGIEAARTSVYREIEHTMSAHGMSIDPRHVMLLADTMTY 1316

Query: 992  KGEVLG 997
            KGEVLG
Sbjct: 1317 KGEVLG 1322



 Score =  110 bits (274), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 51/75 (68%), Positives = 58/75 (77%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV+NSFFSGLTPTEF FH + GREGLVDTAVKTAETGYMQRRL+K+LEDL   YD+
Sbjct: 829 PSKGFVRNSFFSGLTPTEFLFHAISGREGLVDTAVKTAETGYMQRRLMKALEDLSTHYDL 888

Query: 670 SFDAAFYGQTDCISG 684
           S   +  G    I G
Sbjct: 889 SVRNSVGGVVQFIYG 903



 Score = 64.3 bits (155), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 28/49 (57%), Positives = 38/49 (77%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIAS 69
           +LM  K NLVTPRNGE +IAA QDFIT  YL+++++ FF+RAQ  ++ S
Sbjct: 520 ILMGVKHNLVTPRNGEPIIAAIQDFITASYLISKRDRFFDRAQFAQVCS 568



 Score = 48.1 bits (113), Expect = 0.032,   Method: Compositional matrix adjust.
 Identities = 28/55 (50%), Positives = 34/55 (61%), Gaps = 2/55 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLP-MNVGTGLIKLLQAVPRSEPVPRTLLFD 721
            D  FDAA +G+ D + GVSE IIMG P   VGTG+  L+   P + P  R LLFD
Sbjct: 1346 DHLFDAALFGKKDEVLGVSESIIMGNPAQTVGTGMPALVVPAP-TLPPRRALLFD 1399


>gi|358342624|dbj|GAA33483.2| DNA-directed RNA polymerase III subunit RPC1 [Clonorchis sinensis]
          Length = 1462

 Score =  268 bits (685), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 134/284 (47%), Positives = 180/284 (63%), Gaps = 33/284 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D++LFNRQPSLH++SI A +A V P RTFRFN C C P+NADFDGDEMNVHLPQTE A
Sbjct: 533 DGDIILFNRQPSLHRVSIQAFKAVVKPFRTFRFNPCCCNPFNADFDGDEMNVHLPQTEAA 592

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              AK LM +  N+V+P+NGE LI+  QD IT  +LLT K+ FF R
Sbjct: 593 RAE--------------AKHLMLSLRNIVSPKNGEPLISPIQDLITATHLLTLKDVFFTR 638

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAV-----IWTGKQIFSLILKPNR 515
            Q  ++AS +IA                + P+   + A+     +WTGKQ+FSLIL P+ 
Sbjct: 639 DQACQLASQIIAGN------------HLYQPIKLPKPAIMKPRRLWTGKQLFSLILSPHP 686

Query: 516 DCPVNANLKTKGRAYTAN--EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILL 573
              V  N++   ++  +N  EE C  D ++++ NS+LLAG  DK  LG G KA++FY LL
Sbjct: 687 STGVKINIRQATKSVYSNRGEEMCPNDGFILIHNSQLLAGCADKKLLGGGSKASIFYSLL 746

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           R++G +    AMWRL+R++ FYL +RGFSIG+G+V P Q  V++
Sbjct: 747 RNYGSETCADAMWRLARISLFYLAHRGFSIGLGEVMPSQELVKS 790



 Score =  136 bits (342), Expect = 9e-29,   Method: Compositional matrix adjust.
 Identities = 106/325 (32%), Positives = 159/325 (48%), Gaps = 70/325 (21%)

Query: 1107 REKYVRAQIEPATAVGAL---------------------------------------AAQ 1127
            +EKY +A IEP +AVGAL                                       AA 
Sbjct: 1097 KEKYEKALIEPGSAVGALCGQSVGEPATQMTLKTFHFAGVASMNITQGVPRMREIVNAAA 1156

Query: 1128 SIGEPGTQMTLKTFHFAGEVCEYIE----------------EVFVPDDSFILIKLDMDRI 1171
             I  P   +TL T  F+  +   ++                +   P+D ++ +KLD  R 
Sbjct: 1157 KIKTPLLTVTL-TDPFSASLARQVKLAIEPTRLADISISLRQCLTPEDVYVSVKLDEKR- 1214

Query: 1172 RLLHLEVDIDSIRYCIERT--RGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPS 1229
             +    +    +   I+ T  R +         +F+ + P D     N+ +  + ++L  
Sbjct: 1215 -MARRGITTARVASVIQSTKLRKVKLSRVTYSKNFVYVYPVD----LNT-LETVVKVLED 1268

Query: 1230 VVIKGVQGINRAVIHEE-DVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKT 1288
            VV+KG+ G+ R VI ++ D+E    +++ VEG  LR+VM   GV      SNN  EV + 
Sbjct: 1269 VVVKGIPGVARVVIQQDKDLE----HRIYVEGAKLREVMCVPGVVPECTRSNNILEVEQV 1324

Query: 1289 LGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLN 1348
            LG+EAAR  ++ E+  VME HG+ ++ RH ML+AD+MT++GEV G  R G+AK K SVL 
Sbjct: 1325 LGVEAARRVVIDELLAVMEGHGVEVNIRHVMLLADVMTNRGEVYGYQRTGMAKAKNSVLC 1384

Query: 1349 LASFENTSDHLFDAAFYGQTDCISG 1373
            LASFE T DHLF+AA++GQ D + G
Sbjct: 1385 LASFERTGDHLFEAAYHGQDDKVIG 1409



 Score =  123 bits (309), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 95/315 (30%), Positives = 158/315 (50%), Gaps = 20/315 (6%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPR++EI+NA+  I TP++T  L        AR VK  +E T L ++   + +   P+D
Sbjct: 1144 GVPRMREIVNAAAKIKTPLLTVTLTDPFSASLARQVKLAIEPTRLADISISLRQCLTPED 1203

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERT--RGISGHLTVSGHSFLILKPKDSSKSFN 881
             ++ +KLD  R  +    +    +   I+ T  R +         +F+ + P D     N
Sbjct: 1204 VYVSVKLDEKR--MARRGITTARVASVIQSTKLRKVKLSRVTYSKNFVYVYPVD----LN 1257

Query: 882  SKMYQMKQLLPSVVIKGVQGINRAVIHEE-DVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
            + +  + ++L  VV+KG+ G+ R VI ++ D+E    +++ VEG  LR+VM   GV    
Sbjct: 1258 T-LETVVKVLEDVVVKGIPGVARVVIQQDKDLE----HRIYVEGAKLREVMCVPGVVPEC 1312

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNGT 1000
              SNN  EV + LG+EAAR  ++ E+  VME HG+ ++ RH ML+AD+MT++GEV G   
Sbjct: 1313 TRSNNILEVEQVLGVEAARRVVIDELLAVMEGHGVEVNIRHVMLLADVMTNRGEVYGYQR 1372

Query: 1001 PVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVR------DIK 1054
                K     +   +  R+   L         ++ + S  F    SE ++         K
Sbjct: 1373 TGMAKAKNSVLCLASFERTGDHLFEAAYHGQDDKVIGSVRFYSSDSELWLSFECAKFKAK 1432

Query: 1055 KFLEEFSKKESVTSH 1069
               E F+++ S+T+H
Sbjct: 1433 DVREYFAREVSITAH 1447



 Score =  102 bits (254), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 47/64 (73%), Positives = 53/64 (82%), Gaps = 1/64 (1%)

Query: 606 GDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           G  TP  +GFV NSF+SGLTP+EFFFH M GREGL DTAVKTA+TGYMQRRL+K LEDL 
Sbjct: 902 GSRTPEAKGFVGNSFYSGLTPSEFFFHAMSGREGLTDTAVKTADTGYMQRRLIKFLEDLT 961

Query: 665 VQYD 668
           + YD
Sbjct: 962 IAYD 965



 Score = 66.6 bits (161), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 40/115 (34%), Positives = 63/115 (54%), Gaps = 8/115 (6%)

Query: 232 VVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEV 291
           V K   L    H+ Y+    K    ++D + EY+  +  NPE+      GL + + P   
Sbjct: 233 VTKGANLSYAVHDVYRYAKSK----IDDHVNEYSSVILENPELSTLLHKGL-EIIRPARA 287

Query: 292 LQLFEAIPLEDIPLLLM---NAELSKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
           LQLF  IP  D+PLL+M   ++  + P DLI+ R+ V P+ IRPSV+S+++S  +
Sbjct: 288 LQLFSKIPESDLPLLMMPGGDSWTTHPKDLIVQRVPVAPSSIRPSVVSEVRSGTN 342



 Score = 58.9 bits (141), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 29/65 (44%), Positives = 42/65 (64%)

Query: 14  ATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIA 73
           A R   + LM +  N+V+P+NGE LI+  QD IT  +LLT K+ FF R Q  ++AS +IA
Sbjct: 591 AARAEAKHLMLSLRNIVSPKNGEPLISPIQDLITATHLLTLKDVFFTRDQACQLASQIIA 650

Query: 74  GRKVF 78
           G  ++
Sbjct: 651 GNHLY 655


>gi|453086139|gb|EMF14181.1| DNA-directed RNA polymerase III subunit RPC1 [Mycosphaerella
           populorum SO2202]
          Length = 1484

 Score =  267 bits (683), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 133/287 (46%), Positives = 187/287 (65%), Gaps = 30/287 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++HRAK+ P RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 476 DGDIVLFNRQPSLHKLSILSHRAKIRPWRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 535

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EA                LM  K+NL TP+NG  +IAA QDFITG YL++QK+ FF+R
Sbjct: 536 RTEATE--------------LMGVKNNLSTPKNGSPIIAAIQDFITGAYLISQKDRFFSR 581

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAV-----IWTGKQIFSLILKPNR 515
               R  + ++    +       ++ + + P+V    A+     +WTGKQI++L++KP+ 
Sbjct: 582 ----RHFTHVVGFMYNAMQAKDPYTGKEY-PIVIPPPAIWKPQALWTGKQIWNLLIKPHP 636

Query: 516 DCPVNANLKTKGRAYTANE------EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVF 569
           D PVN NL+ + + Y          +    DSY+++RNSE++ G  DK+T+G G K ++F
Sbjct: 637 DYPVNVNLEARLKQYAPPTRPNDIPDMVDTDSYLVIRNSEVMCGGFDKATIGDGKKDSLF 696

Query: 570 YILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           Y+++RDFG D A  AM RL+++++ +L  +GFSIGI DV P +   +
Sbjct: 697 YVIMRDFGADYAAAAMTRLAKLSARWLGEQGFSIGISDVYPSEKLTK 743



 Score =  183 bits (465), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 113/280 (40%), Positives = 164/280 (58%), Gaps = 29/280 (10%)

Query: 1143 FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI--------- 1193
            + G++ +Y+E+V+  +  +I ++++  +I  L L + ++ +   IERT+G          
Sbjct: 1155 YLGDIVDYVEDVWHANGCYINMRVNWQQIGNLGLRIGMEHLLDAIERTKGFKTLGVSARN 1214

Query: 1194 SGHLTVSGHSFLILKPKDSSKSFNSK---------------MYQMKQLLPSVVIKGVQGI 1238
            SG+  +  +  L  K +   ++  SK               ++ +K+ LP VV+KG    
Sbjct: 1215 SGYNHIRVNISLPEKERSRRQTSASKGRITESDGSELMFMQVHTLKRKLPEVVVKGYPDA 1274

Query: 1239 NRAVIHEEDVE---GVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAAR 1295
            +RA+I ++D +   G     + VEG  L+  M T GV G +  SNN  E    LGIEAAR
Sbjct: 1275 HRAIIKKDDKKDRNGKEPISVFVEGYGLKQCMTTDGVDGYRTKSNNVMECRDVLGIEAAR 1334

Query: 1296 STIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENT 1355
             TI+ EI  VM +  M ID RH  L+AD+MT KGEVLGITR GLAKM++SVL LASFE T
Sbjct: 1335 KTIIDEIDAVMGS--MDIDPRHMQLLADVMTYKGEVLGITRFGLAKMRDSVLQLASFEKT 1392

Query: 1356 SDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 1395
             DHLF+AA   + D I GVSECIIMG  M+VGTG +K+++
Sbjct: 1393 PDHLFEAAAKMKKDDIEGVSECIIMGQSMSVGTGAMKVVR 1432



 Score =  175 bits (444), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 99/261 (37%), Positives = 139/261 (53%), Gaps = 16/261 (6%)

Query: 96  QSHIQIVSKNLY----CQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYI 151
           QS + +  +NLY     Q   RT   HG LD R+GT+ K   C TCGQ L +C GHFG++
Sbjct: 36  QSVVNVADRNLYDLALTQGGPRTITKHGPLDGRLGTSAKNGQCGTCGQGLKECNGHFGHV 95

Query: 152 DLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKK 211
            L LP FH GY + +I  +  +CK+  C+RVLL E++   +   LR P L  L +  + K
Sbjct: 96  KLALPCFHYGYLKRIIEAMNCVCKD--CSRVLLPEQEKRNYLKALRRPGLDGLRKDVITK 153

Query: 212 KILETTKKVSVCPHCGEINGVVKKCG--LLKISHEKY------KNRTKKKDAIVEDLLAE 263
           KI    +KV VCPHCG  NG V+K     +K+ H KY        ++K K   ++     
Sbjct: 154 KISAECRKVKVCPHCGAYNGPVRKVAGHPIKMFHNKYAIYTNSNAKSKVKPPEMQAFEKT 213

Query: 264 YNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL-SKPSDLILTR 322
           + EA+K + EIE H K  +   L PL VL + + +P  D+ LL M+     +P  +I T 
Sbjct: 214 FEEAIKVDKEIERHMKR-VADDLTPLRVLNILKKVPNTDVELLGMDPHSGGRPEYMIWTH 272

Query: 323 LLVPPNCIRPSVISDLKSDND 343
           +  PP  IRPSV  +  S  D
Sbjct: 273 IPAPPVAIRPSVAQETASTED 293



 Score =  152 bits (385), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 104/285 (36%), Positives = 155/285 (54%), Gaps = 30/285 (10%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+IT +LD   +   AR  K  +E+T LG++ +Y+E+V+  + 
Sbjct: 1112 GVPRIKEIINASKVISTPVITCHLDSPYEDMAARFAKALMEKTYLGDIVDYVEDVWHANG 1171

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---------SGHLTVSGHSFLILKPK 874
             +I ++++  +I  L L + ++ +   IERT+G          SG+  +  +  L  K +
Sbjct: 1172 CYINMRVNWQQIGNLGLRIGMEHLLDAIERTKGFKTLGVSARNSGYNHIRVNISLPEKER 1231

Query: 875  DSSKSFNSK---------------MYQMKQLLPSVVIKGVQGINRAVIHEEDVE---GVT 916
               ++  SK               ++ +K+ LP VV+KG    +RA+I ++D +   G  
Sbjct: 1232 SRRQTSASKGRITESDGSELMFMQVHTLKRKLPEVVVKGYPDAHRAIIKKDDKKDRNGKE 1291

Query: 917  KYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMS 976
               + VEG  L+  M T GV G +  SNN  E    LGIEAAR TI+ EI  VM +  M 
Sbjct: 1292 PISVFVEGYGLKQCMTTDGVDGYRTKSNNVMECRDVLGIEAARKTIIDEIDAVMGS--MD 1349

Query: 977  IDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDP 1021
            ID RH  L+AD+MT KGEVLG  T   L ++ D ++   S    P
Sbjct: 1350 IDPRHMQLLADVMTYKGEVLGI-TRFGLAKMRDSVLQLASFEKTP 1393



 Score =  103 bits (257), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 47/60 (78%), Positives = 52/60 (86%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV +SFFSGLTPTEF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD++
Sbjct: 862 AKGFVFDSFFSGLTPTEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSAQYDLT 921



 Score = 62.4 bits (150), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/40 (67%), Positives = 33/40 (82%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            C  K+ ++++E   AVGA+ AQSIGEPGTQMTLKTFHFAG
Sbjct: 1064 CMLKFEKSKVEAGHAVGAVGAQSIGEPGTQMTLKTFHFAG 1103



 Score = 57.4 bits (137), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 25/40 (62%), Positives = 32/40 (80%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           LM  K+NL TP+NG  +IAA QDFITG YL++QK+ FF+R
Sbjct: 542 LMGVKNNLSTPKNGSPIIAAIQDFITGAYLISQKDRFFSR 581



 Score = 43.5 bits (101), Expect = 0.86,   Method: Compositional matrix adjust.
 Identities = 21/39 (53%), Positives = 28/39 (71%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  F+AA   + D I GVSECIIMG  M+VGTG +K+++
Sbjct: 1394 DHLFEAAAKMKKDDIEGVSECIIMGQSMSVGTGAMKVVR 1432


>gi|320592285|gb|EFX04724.1| DNA-directed RNA polymerase 3 largest [Grosmannia clavigera kw1407]
          Length = 1390

 Score =  267 bits (683), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 133/274 (48%), Positives = 177/274 (64%), Gaps = 28/274 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIM+H  KV P RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 415 DGDIVLFNRQPSLHKLSIMSHLVKVRPWRTFRLNECVCGPYNADFDGDEMNLHVPQTEEA 474

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL               LM  K NL TP+NGE +IAATQDFIT  YL++ K+ FF R
Sbjct: 475 RAEAL--------------TLMGVKHNLATPKNGEPIIAATQDFITAAYLISSKDRFFTR 520

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                + + +   +  +             P   ++   +WTGKQ+F+++++PN+   V 
Sbjct: 521 HTFAYMCAHMTGSSEQL----------DIPPPAILKPQALWTGKQVFNIMMRPNKSSKVL 570

Query: 521 ANLKTKGRAYTAN----EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL  K +AY        +    D+++++RNSE++ G MDKST+GSG K +VFY++LRD+
Sbjct: 571 VNLDAKCKAYKRRPGEAPDMDPEDNFLVVRNSEVMCGRMDKSTVGSGKKDSVFYVILRDY 630

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           G D AVTAM RL+R+ + ++ N G SIG+ DV P
Sbjct: 631 GPDEAVTAMNRLARLCARFMGNFGLSIGVFDVFP 664



 Score =  155 bits (393), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 142/519 (27%), Positives = 227/519 (43%), Gaps = 113/519 (21%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALS------------------------ 1032
            G+  PV  +R      +   S ++PSL    I+A+                         
Sbjct: 873  GSAVPVNFERSWTHAESITWSNAEPSLDPDTIMAVCDSLLADERAKYIRRHLVTDALLDY 932

Query: 1033 NETLDSKEFLQDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGR 1092
            N+  D+   LQ+ +  F+ D+++F+++  + + +T+ ++++ +     + SH+  I    
Sbjct: 933  NDQSDASLDLQEGARKFLDDVRQFVQK--RADRLTNAKERLVETFDASLASHRSYIDKTA 990

Query: 1093 ESNPFPSACKAEACREKYVRAQIEPA---TAVGALAAQSIGEPGTQMTLKTFHFAG---- 1145
            + +          C +K+ +A +EP     AVGA +    G   T  T      AG    
Sbjct: 991  KVSEKTLRAFVVMCLDKFRKAHVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSIT 1050

Query: 1146 -----------------------------------------------EVCEYIEEVFVPD 1158
                                                           +V  Y+EE +  +
Sbjct: 1051 EGVPRIKEIINASKKINTPIITCPLQNPRQIEAAHIVKGRIEKTYISDVLSYVEEEWDGN 1110

Query: 1159 DSFILIKLDMDRIRLLHLEVDIDSI--RYCIERTRGISGHLTVSG--HSFLILKPKDSSK 1214
            +  I++K+D   +  L L V +  I    C ++   I  +L  +    S + +  ++   
Sbjct: 1111 EGRIIMKVDQQALNDLQLGVGLHDIALSVCKQKKLKIDENLVFADTFASTITIIVRNGGA 1170

Query: 1215 SFNSKMYQ-------------------MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYK 1255
             + S+                      +++ LP++ I G     RAVI  E  E    + 
Sbjct: 1171 DYGSRRSAATKAKASADNQDLLFRVNFLRRQLPAIGISGYPDAARAVIQTEKDE----HT 1226

Query: 1256 LLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDF 1315
            + VEG  LR+ + T GV G    +N+  E    LGIEAAR +I  EIK VM +  M+ID 
Sbjct: 1227 VYVEGYGLRECINTEGVIGTGVVTNSIMECLDILGIEAARKSIAVEIKNVMRD--MNIDP 1284

Query: 1316 RHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVS 1375
            RH  L+AD+MT KG+VLGITR GLAKM++SVL LASFE T DHLFDA    + D I GVS
Sbjct: 1285 RHMELLADVMTYKGQVLGITRFGLAKMRDSVLQLASFEKTPDHLFDAVAGLKEDPIQGVS 1344

Query: 1376 ECIIMGLPMNVGT---GLIKLLQAVPRSEPVPRTLLFDN 1411
            E +IMG  M+VGT   G+I+ L   P  +  P+  +F++
Sbjct: 1345 ESVIMGQSMSVGTGGFGMIRRLGLQP-DDFAPQQTVFED 1382



 Score =  132 bits (333), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 97/282 (34%), Positives = 146/282 (51%), Gaps = 30/282 (10%)

Query: 763  DGVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPD 822
            +GVPRIKEIINAS+ I+TPIIT  L     ++ A IVKGR+E+T + +V  Y+EE +  +
Sbjct: 1051 EGVPRIKEIINASKKINTPIITCPLQNPRQIEAAHIVKGRIEKTYISDVLSYVEEEWDGN 1110

Query: 823  DSFILIKLDMDRIRLLHLEVDIDSI--RYCIERTRGISGHLTVSG--HSFLILKPKDSSK 878
            +  I++K+D   +  L L V +  I    C ++   I  +L  +    S + +  ++   
Sbjct: 1111 EGRIIMKVDQQALNDLQLGVGLHDIALSVCKQKKLKIDENLVFADTFASTITIIVRNGGA 1170

Query: 879  SFNSKMYQ-------------------MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYK 919
             + S+                      +++ LP++ I G     RAVI  E  E    + 
Sbjct: 1171 DYGSRRSAATKAKASADNQDLLFRVNFLRRQLPAIGISGYPDAARAVIQTEKDE----HT 1226

Query: 920  LLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDF 979
            + VEG  LR+ + T GV G    +N+  E    LGIEAAR +I  EIK VM +  M+ID 
Sbjct: 1227 VYVEGYGLRECINTEGVIGTGVVTNSIMECLDILGIEAARKSIAVEIKNVMRD--MNIDP 1284

Query: 980  RHPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDP 1021
            RH  L+AD+MT KG+VLG  T   L ++ D ++   S    P
Sbjct: 1285 RHMELLADVMTYKGQVLGI-TRFGLAKMRDSVLQLASFEKTP 1325



 Score =  102 bits (254), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 46/57 (80%), Positives = 50/57 (87%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFVQNSF+SGL PTEF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 790 KGFVQNSFYSGLLPTEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSTQYD 846



 Score = 97.4 bits (241), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 62/171 (36%), Positives = 87/171 (50%), Gaps = 7/171 (4%)

Query: 179 CARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGL 238
           C RVLL E     F  +LR P +  L +  + KK+ E  KK   CP+C  +NG +KK G 
Sbjct: 67  CGRVLLMESDRRTFLKELRKPGIDNLRKTQICKKVNEICKKCKECPYCQSLNGSIKKIGP 126

Query: 239 LKISHEKY----KNRTKKK--DAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVL 292
           LK++H+++    K+   KK   A   +    ++EA K  P++E H    L + L+PL VL
Sbjct: 127 LKVAHDRFAAFNKSTAAKKIPPARKREFEHSFSEARKRIPDLEKHLHRAL-EDLDPLHVL 185

Query: 293 QLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
            LF+ I   D  LL ++    +P   I   L  PP CIRPSV     S  D
Sbjct: 186 NLFKKISPSDCELLGLDPLDGRPEMFIWQYLPAPPVCIRPSVQQQSSSTED 236



 Score = 56.6 bits (135), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 25/40 (62%), Positives = 30/40 (75%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           LM  K NL TP+NGE +IAATQDFIT  YL++ K+ FF R
Sbjct: 481 LMGVKHNLATPKNGEPIIAATQDFITAAYLISSKDRFFTR 520


>gi|430813213|emb|CCJ29412.1| unnamed protein product [Pneumocystis jirovecii]
          Length = 1390

 Score =  267 bits (683), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 176/497 (35%), Positives = 263/497 (52%), Gaps = 82/497 (16%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G+  PVE  R  +      S      L   EI+  + + L++ +F ++ +ENF   I  F
Sbjct: 891  GDNCPVEFSRTWNHCHNITSKIQSKGLLPYEIIETTRKYLENPKF-KNCTENFKNSILNF 949

Query: 1057 LEE--------FSKKESVTSHQDKVSQPLREQILSHQD-KIGHGRESNPFPSACK----- 1102
            +++          ++ ++ S  +  +    + I++ +  +I   +  +      K     
Sbjct: 950  IQKNIAEHLAAIRERRNLPSFLEHTNDSKYKNIINEESLEIDSKKTVDSIFKVTKHQLLT 1009

Query: 1103 -AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEV-------------- 1147
              + C EKY+++++EP TAVGA+ AQSIGEPGTQMTLKTFHFAG                
Sbjct: 1010 YLQLCLEKYIKSKVEPGTAVGAVGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEI 1069

Query: 1148 -------------CEYIEE---------------------------VFVPDDSFILIKLD 1167
                         C+ + E                           V+ P  S+I IK+D
Sbjct: 1070 INAAKIISTPIVTCKLVAEDDTRSARVVKGRVEKTYMKDITTFIEEVYGPTSSYIGIKID 1129

Query: 1168 MDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFL--ILKPKDSSKSFNSKMYQ 1222
             + +  L LE+ ID I   I +   +   +  +++S    +   +   D  K F+   Y+
Sbjct: 1130 WNTVNRLQLEITIDEIAASIWQAPKLKISNTKVSISSEDKIKVYVSNDDKDKEFDEVYYK 1189

Query: 1223 M---KQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSS 1279
            +   K+ LP V++KG+   +RAVI   +++   K  LLVEG  LRDV+ T GV G K S+
Sbjct: 1190 LQHYKRTLPHVIVKGIPSTSRAVI---NIDEKGKNTLLVEGYGLRDVINTDGVVGTKTST 1246

Query: 1280 NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGL 1339
            N+  E+ + LGIEAAR++I+ EI + M +HGM+ID RH ML+ D+MT +GE+LGITR G+
Sbjct: 1247 NHVMEMKQVLGIEAARASIIKEIDITMSSHGMNIDPRHVMLLGDVMTYRGEILGITRFGV 1306

Query: 1340 AKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPR 1399
            AKMK SVL LASFE T+DHLFDAA     D I GVSECII+G P  +GTGL +L++ +  
Sbjct: 1307 AKMKNSVLMLASFEKTTDHLFDAAARLTKDSIEGVSECIILGKPAPIGTGLFRLVRRINI 1366

Query: 1400 SE-PVPRTLLFDNPEFH 1415
             E P P++LLFDN  F+
Sbjct: 1367 EEYPKPKSLLFDNSNFY 1383



 Score =  222 bits (566), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 117/271 (43%), Positives = 163/271 (60%), Gaps = 43/271 (15%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+D+VLFNRQPSLHKLSI+ H  KV P +TFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 455 DDDIVLFNRQPSLHKLSILCH--KVRPWKTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 512

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM+ K+NLVTPRNG+ +IAA QDF+T  YL++QK+ F++R
Sbjct: 513 RAEAIE--------------LMSVKNNLVTPRNGDPIIAAIQDFVTASYLISQKDNFYDR 558

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                I S ++     I            +PV+     V +  +  + +     +  P  
Sbjct: 559 KTFTHICSFMVDANMHI---------DLPSPVII--KPVPYGQESKYLMSFSSPKGIP-- 605

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
                         + C  D Y+++R SE++ G MDKST+G G K ++FY++L+++G   
Sbjct: 606 --------------DLCINDGYLLIRGSEIMCGVMDKSTVGDGKKNSIFYVILKNYGPTE 651

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           A  AM RL+++ + ++ N GFSIGI DV PG
Sbjct: 652 AAEAMNRLAKLCARWIGNHGFSIGINDVQPG 682



 Score =  184 bits (466), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 104/242 (42%), Positives = 155/242 (64%), Gaps = 11/242 (4%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ ISTPI+T  L  + D   AR+VKGR+E+T + ++  +IEEV+ P  
Sbjct: 1062 GVPRIKEIINAAKIISTPIVTCKLVAEDDTRSARVVKGRVEKTYMKDITTFIEEVYGPTS 1121

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFL--ILKPKDSSK 878
            S+I IK+D + +  L LE+ ID I   I +   +   +  +++S    +   +   D  K
Sbjct: 1122 SYIGIKIDWNTVNRLQLEITIDEIAASIWQAPKLKISNTKVSISSEDKIKVYVSNDDKDK 1181

Query: 879  SFNSKMYQM---KQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYG 935
             F+   Y++   K+ LP V++KG+   +RAVI   +++   K  LLVEG  LRDV+ T G
Sbjct: 1182 EFDEVYYKLQHYKRTLPHVIVKGIPSTSRAVI---NIDEKGKNTLLVEGYGLRDVINTDG 1238

Query: 936  VKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            V G K S+N+  E+ + LGIEAAR++I+ EI + M +HGM+ID RH ML+ D+MT +GE+
Sbjct: 1239 VVGTKTSTNHVMEMKQVLGIEAARASIIKEIDITMSSHGMNIDPRHVMLLGDVMTYRGEI 1298

Query: 996  LG 997
            LG
Sbjct: 1299 LG 1300



 Score =  170 bits (430), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 102/276 (36%), Positives = 147/276 (53%), Gaps = 29/276 (10%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRM---------------GT 127
           IE  V     + +Q  +++ ++ LY     R+ + +G LD+R                GT
Sbjct: 16  IEFGVFGPKDIIKQGVLEVSTRELY-NIIDRSTVRNGALDKRQHKKIRGKPSISNYTQGT 74

Query: 128 NQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEE 187
           + K+A C TCG+ +  CVGHFGY+ L LPVFHIGYF+ +I ILQ+ICK+  C+++LL  +
Sbjct: 75  SDKQAICETCGEKIVTCVGHFGYVKLILPVFHIGYFKTIITILQNICKD--CSKILLKLK 132

Query: 188 KAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYK 247
               F  +LR      L +  + K+I +T KKV +CP+C    GVVKK G LKI HEK+K
Sbjct: 133 DTYSFLKELRKAETDNLKKSQIYKRINDTCKKVRICPNCQSTQGVVKKVGALKIIHEKFK 192

Query: 248 NRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLL 307
            + +K           +   +K  P+++ H        LNPL+VL LF+ IP  D  LL 
Sbjct: 193 YKFQK----------TFETILKSTPDMKTHLSKAH-DDLNPLKVLNLFKQIPPMDCELLG 241

Query: 308 MNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
           +N    +P   I   +  PP CIRPS+  D  S  D
Sbjct: 242 INPLKGRPEMFIWQCIPAPPVCIRPSISQDGASTED 277



 Score =  107 bits (267), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 50/75 (66%), Positives = 58/75 (77%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV+NSF+SGLTPTEF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL +QYD 
Sbjct: 806 PAKGFVKNSFYSGLTPTEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSLQYDG 865

Query: 670 SFDAAFYGQTDCISG 684
           +   +  G    I G
Sbjct: 866 TVRNSSSGIVQFIYG 880



 Score = 60.1 bits (144), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 26/51 (50%), Positives = 38/51 (74%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLI 72
           LM+ K+NLVTPRNG+ +IAA QDF+T  YL++QK+ F++R     I S ++
Sbjct: 519 LMSVKNNLVTPRNGDPIIAAIQDFVTASYLISQKDNFYDRKTFTHICSFMV 569



 Score = 60.1 bits (144), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 30/60 (50%), Positives = 39/60 (65%), Gaps = 1/60 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSE-PVPRTLLFDNPEFH 726
            D  FDAA     D I GVSECII+G P  +GTGL +L++ +   E P P++LLFDN  F+
Sbjct: 1324 DHLFDAAARLTKDSIEGVSECIILGKPAPIGTGLFRLVRRINIEEYPKPKSLLFDNSNFY 1383


>gi|322696737|gb|EFY88525.1| DNA-directed RNA polymerase III largest subunit [Metarhizium
           acridum CQMa 102]
          Length = 1017

 Score =  267 bits (683), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 136/297 (45%), Positives = 185/297 (62%), Gaps = 29/297 (9%)

Query: 318 LILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECV 377
            + T L+    CI   V+     D D+VLFNRQPSLHKLSIM+H  KV P RTFR NECV
Sbjct: 12  FVDTELVANELCI-GDVVERHIEDGDIVLFNRQPSLHKLSIMSHFVKVRPWRTFRLNECV 70

Query: 378 CTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELL 437
           C PYNADFDGDEMN+H+PQTEEAR EA+               LM  K NL+TP++GE +
Sbjct: 71  CNPYNADFDGDEMNLHVPQTEEARTEAMS--------------LMGVKHNLITPKSGEPI 116

Query: 438 IAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRT 497
           IAATQDFIT  YLL+ K+ FF+R     I   ++   + +             P   +  
Sbjct: 117 IAATQDFITAAYLLSYKDRFFDRKAFTTICMHMLDGRNQL----------DLPPPAIIVP 166

Query: 498 AVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTAN----EEFCHRDSYVILRNSELLAG 553
             +WTGKQIF+++++PN   PV  NL  + ++         +    D ++++RNS+++ G
Sbjct: 167 KTLWTGKQIFNVLMRPNNRSPVMVNLDARCKSCVTRPGQYPDMDPNDGWLVVRNSQVMCG 226

Query: 554 SMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
            MDKST+G G K ++FY++LRD+G D AV+AM RL+++ + YL NRGFSIG+GDV P
Sbjct: 227 QMDKSTVGPGKKDSIFYVILRDYGPDEAVSAMNRLAKLCARYLTNRGFSIGVGDVYP 283



 Score =  154 bits (388), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 96/196 (48%), Positives = 123/196 (62%), Gaps = 12/196 (6%)

Query: 1207 LKPKDSSKSFNSKMYQM-------KQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVE 1259
            L P+  +KS   +   M       ++ LPSV I G     RA+I  E  E  T Y++LVE
Sbjct: 789  LPPRSKTKSAAEESRDMMLRANFLRRTLPSVPISGYPEATRALI--ETTEENT-YRVLVE 845

Query: 1260 GDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPM 1319
            G  LR  MAT GV G +  +N+  E  + LGIEAAR+TI  EI  VM    M ID RH  
Sbjct: 846  GYGLRGCMATEGVVGTQVRTNSVMECVQILGIEAARTTIANEIAEVMGY--MGIDLRHMQ 903

Query: 1320 LVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECII 1379
            L+AD+MT KGEVLGITR GL+K + SVL+LASFE T+DHLFDA    +TD I GVSE II
Sbjct: 904  LLADVMTYKGEVLGITRFGLSKTRGSVLHLASFEKTADHLFDAVAGMKTDRIEGVSESII 963

Query: 1380 MGLPMNVGTGLIKLLQ 1395
            +G  ++VGTG  ++++
Sbjct: 964  LGQTISVGTGGFEVVR 979



 Score =  131 bits (330), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 94/251 (37%), Positives = 134/251 (53%), Gaps = 22/251 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
           GVPRI EIINAS+ ISTP+IT  L     ++ A++VK R+E+T + ++  +IE  +    
Sbjct: 672 GVPRINEIINASKAISTPVITCPLLNKWQIEAAKVVKARIEKTYISDILCFIEVEWDSKS 731

Query: 824 SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSFLI-------LKP 873
             I++++D D +  +   V +  +   I   R +      ++V      +       L P
Sbjct: 732 GHIVMQVDTDTLANMQAGVCVFDVAQAICDQRKLKVRPEDISVDKDMIFVRIRETDDLPP 791

Query: 874 KDSSKSFNSKMYQM-------KQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDN 926
           +  +KS   +   M       ++ LPSV I G     RA+I  E  E  T Y++LVEG  
Sbjct: 792 RSKTKSAAEESRDMMLRANFLRRTLPSVPISGYPEATRALI--ETTEENT-YRVLVEGYG 848

Query: 927 LRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVA 986
           LR  MAT GV G +  +N+  E  + LGIEAAR+TI  EI  VM    M ID RH  L+A
Sbjct: 849 LRGCMATEGVVGTQVRTNSVMECVQILGIEAARTTIANEIAEVMGY--MGIDLRHMQLLA 906

Query: 987 DLMTSKGEVLG 997
           D+MT KGEVLG
Sbjct: 907 DVMTYKGEVLG 917



 Score = 98.6 bits (244), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 44/57 (77%), Positives = 51/57 (89%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NSF+S L PTEF FH++ GREGLVDTAVKTAETGYM RRL+KSLEDL V+YD
Sbjct: 409 KGFVKNSFYSALLPTEFLFHSISGREGLVDTAVKTAETGYMSRRLMKSLEDLSVKYD 465



 Score = 76.3 bits (186), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 57/179 (31%), Positives = 81/179 (45%), Gaps = 37/179 (20%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILA------------------LSNETL-- 1036
            G GTPV+  R      +      +PSL   EI                    L NE L  
Sbjct: 492  GAGTPVQFHRTWTHAESLTRDDDEPSLMPHEIGVICDSVLEPYRGRYVRKGLLHNEELNY 551

Query: 1037 -DSKEFLQDTSEN---FVRDIKKFLEEFS----KKESVTSHQDKVSQPLREQILSHQDKI 1088
             D  ++  D  E+   F++ IK +++  +    K  ++  +Q     P+RE    H D  
Sbjct: 552  EDDSDYAIDEHESGRRFLKSIKSYIDGLASRLRKVRTIAGYQGNT--PIRETAQDHVD-- 607

Query: 1089 GHGRESNPFPSACK--AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
               R +    +  +     C +K+ +A +EP   VGA+ AQSIGEPGTQMTLKTFHFAG
Sbjct: 608  ---RTAKVAATTLRLFIRLCLDKFTKAHVEPGHPVGAVGAQSIGEPGTQMTLKTFHFAG 663



 Score = 59.7 bits (143), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 28/54 (51%), Positives = 37/54 (68%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           LM  K NL+TP++GE +IAATQDFIT  YLL+ K+ FF+R     I   ++ GR
Sbjct: 100 LMGVKHNLITPKSGEPIIAATQDFITAAYLLSYKDRFFDRKAFTTICMHMLDGR 153


>gi|452982836|gb|EME82594.1| hypothetical protein MYCFIDRAFT_187946 [Pseudocercospora fijiensis
           CIRAD86]
          Length = 1442

 Score =  267 bits (682), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 131/280 (46%), Positives = 181/280 (64%), Gaps = 28/280 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++HRAK+ P RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 478 DGDIVLFNRQPSLHKLSILSHRAKIRPWRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 537

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EA                LM  K NL TP+NG  +IAA QDFITG YL++QK+ FF+R
Sbjct: 538 RTEATE--------------LMGVKHNLATPKNGTPIIAAIQDFITGAYLVSQKDLFFSR 583

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSW----NPVVFVRTAVIWTGKQIFSLILKPNRD 516
            Q  ++   +     +   +   ++   +     P    +   +WTGKQ+++L++KP+  
Sbjct: 584 RQFTQVVGFMY----NAMQVKDPYTGEEYPIQIPPPAIWKPQCLWTGKQVWNLLIKPHPK 639

Query: 517 CPVNANLKTKGRAYTAN------EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFY 570
            PVN NL+ K + Y          +    DSY+++RNSE++ G+ DK+T+G G K +VFY
Sbjct: 640 YPVNVNLEAKLKQYAPPTRKGDIPDMVDTDSYLVIRNSEVMCGAFDKATIGDGKKDSVFY 699

Query: 571 ILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           ++LRDFG + A  AM RL+++++ +L  +GFSIGI DV P
Sbjct: 700 VILRDFGPEYAAAAMTRLAKLSARWLGEQGFSIGISDVYP 739



 Score =  215 bits (547), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 175/498 (35%), Positives = 233/498 (46%), Gaps = 106/498 (21%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETL------------DSKEFLQD 1044
            G+  PV  +R     I      ++ +L+  EI    N TL            D K    D
Sbjct: 948  GSAKPVNFERTWMHSITSTWDNAERALTQSEIETYVNTTLNKERAKLGRFTEDRKPLPYD 1007

Query: 1045 TSENFVRDIKKFLEEFSKKESVTSH-QDKVSQPLREQILSHQDKIGHGRESNPFPSA--- 1100
              +    D  ++  +F   + VT+   DKVS+     ++S Q+++ +         A   
Sbjct: 1008 DDKPMSTDQSEYSRQFL--DVVTNFIMDKVSK-----MVSTQNRLKNSDGVFKLSQAALD 1060

Query: 1101 CKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCE 1149
            C    C  K+ +++ E   AVGA+ AQSIGEPGTQMTLKTFHFAG            + E
Sbjct: 1061 CFLHLCLHKFEKSKTEAGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKE 1120

Query: 1150 YIEEVFVPDDSFILIKLDMD--------------------------------------RI 1171
             I    V     I   LD                                        RI
Sbjct: 1121 IINASKVISTPVITCALDSKYEEMAGRFAKALIEKTYLGDIVDYVEDVWHANGCYINMRI 1180

Query: 1172 RLLHLE-----VDIDSIRYCIERTRG---ISGHLTVSGHSFLIL-------KPK------ 1210
                +E     + +  I  CIERT+G   +      SGH  + +       +PK      
Sbjct: 1181 NWAQVENLGLRISMYEILNCIERTKGFKTLGVSARPSGHHHIRVNMSPPDDRPKPRRAIS 1240

Query: 1211 --------DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVE---GVTKYKLLVE 1259
                    DSS+     ++ +K+ LP+VV+KG     RA+I ++D +   G     +LVE
Sbjct: 1241 GKPRGPEPDSSELMFMHLHSLKRKLPAVVVKGYPDAQRAIIKKDDKKDSTGQEPISVLVE 1300

Query: 1260 GDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPM 1319
            G  L+  M T GV G    SNN  E+   LGIEAAR TI+ EI  VM   GM ID RH  
Sbjct: 1301 GYGLQLCMTTEGVDGYHTKSNNVMEMRDVLGIEAARKTIIDEISSVM--GGMDIDPRHMQ 1358

Query: 1320 LVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECII 1379
            L+AD+MT KGEVLGITR GLAKM++SVL LASFE T DHLFDAA   + D I GVSECII
Sbjct: 1359 LLADVMTYKGEVLGITRFGLAKMRDSVLQLASFEKTPDHLFDAAARMKKDDIEGVSECII 1418

Query: 1380 MGLPMNVGTGLIKLLQAV 1397
            MG  M+VGTG +K+++ V
Sbjct: 1419 MGQSMSVGTGAMKVVRPV 1436



 Score =  162 bits (410), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 94/257 (36%), Positives = 134/257 (52%), Gaps = 16/257 (6%)

Query: 100 QIVSKNLYCQDPQ----RTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPL 155
           QIV +NLY    Q    R     G LD R+GT+ K   C TCGQ L +C GHFG++ L L
Sbjct: 42  QIVDRNLYDLQLQPGAPRNITKQGPLDPRLGTSSKNGTCATCGQGLKECNGHFGHVKLAL 101

Query: 156 PVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILE 215
           P FH GY + +I  +  +CK  TC++VLL E++   +   LR P L  L +  + KKI  
Sbjct: 102 PCFHYGYLKRIIEAMNCVCK--TCSKVLLPEKEKRNYLKALRRPGLDGLRKDVITKKISA 159

Query: 216 TTKKVSVCPHCGEINGVVKKCG--LLKISHEK---YKNRTKKKDAIVEDLLA---EYNEA 267
             +KV  CPHC  +NG V+K     +K+ H +   Y N   K     +++ A    + EA
Sbjct: 160 ECRKVKYCPHCSSLNGPVRKVAGHPIKMFHNRWAVYTNSNAKSKVKPQEMQAFERTFEEA 219

Query: 268 VKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL-SKPSDLILTRLLVP 326
           +K + ++E H K      L PL VL + + +P  D+ LL M+     +P  +I T +  P
Sbjct: 220 IKADKDVERHMKRA-TDDLTPLRVLNILKKVPNADVELLGMDPHSGGRPEHMIWTHIPAP 278

Query: 327 PNCIRPSVISDLKSDND 343
           P  IRPSV  +  S  D
Sbjct: 279 PVAIRPSVAQETASTED 295



 Score =  159 bits (403), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 108/285 (37%), Positives = 155/285 (54%), Gaps = 30/285 (10%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+IT  LD   +    R  K  +E+T LG++ +Y+E+V+  + 
Sbjct: 1114 GVPRIKEIINASKVISTPVITCALDSKYEEMAGRFAKALIEKTYLGDIVDYVEDVWHANG 1173

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRG---ISGHLTVSGHSFLIL-------KP 873
             +I ++++  ++  L L + +  I  CIERT+G   +      SGH  + +       +P
Sbjct: 1174 CYINMRINWAQVENLGLRISMYEILNCIERTKGFKTLGVSARPSGHHHIRVNMSPPDDRP 1233

Query: 874  K--------------DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVE---GVT 916
            K              DSS+     ++ +K+ LP+VV+KG     RA+I ++D +   G  
Sbjct: 1234 KPRRAISGKPRGPEPDSSELMFMHLHSLKRKLPAVVVKGYPDAQRAIIKKDDKKDSTGQE 1293

Query: 917  KYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMS 976
               +LVEG  L+  M T GV G    SNN  E+   LGIEAAR TI+ EI  VM   GM 
Sbjct: 1294 PISVLVEGYGLQLCMTTEGVDGYHTKSNNVMEMRDVLGIEAARKTIIDEISSVM--GGMD 1351

Query: 977  IDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDP 1021
            ID RH  L+AD+MT KGEVLG  T   L ++ D ++   S    P
Sbjct: 1352 IDPRHMQLLADVMTYKGEVLGI-TRFGLAKMRDSVLQLASFEKTP 1395



 Score =  103 bits (257), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 47/60 (78%), Positives = 52/60 (86%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV +SFFSGLTPTEF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD++
Sbjct: 864 AKGFVFDSFFSGLTPTEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSAQYDLT 923



 Score = 58.9 bits (141), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 27/56 (48%), Positives = 37/56 (66%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKV 77
           LM  K NL TP+NG  +IAA QDFITG YL++QK+ FF+R Q  ++   +    +V
Sbjct: 544 LMGVKHNLATPKNGTPIIAAIQDFITGAYLVSQKDLFFSRRQFTQVVGFMYNAMQV 599



 Score = 46.6 bits (109), Expect = 0.10,   Method: Compositional matrix adjust.
 Identities = 23/41 (56%), Positives = 29/41 (70%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 708
            D  FDAA   + D I GVSECIIMG  M+VGTG +K+++ V
Sbjct: 1396 DHLFDAAARMKKDDIEGVSECIIMGQSMSVGTGAMKVVRPV 1436


>gi|390350087|ref|XP_001182534.2| PREDICTED: DNA-directed RNA polymerase III subunit RPC1-like
           [Strongylocentrotus purpuratus]
          Length = 485

 Score =  267 bits (682), Expect = 4e-68,   Method: Compositional matrix adjust.
 Identities = 140/276 (50%), Positives = 170/276 (61%), Gaps = 50/276 (18%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIMAH+A+V P RTFRFN CVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 214 DGDIVLFNRQPSLHKLSIMAHKARVKPFRTFRFNACVCTPYNADFDGDEMNLHLPQTEEA 273

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEAL               LM  KSNLVTPRNGE LIAA QDFITG YLLT K  FF+R
Sbjct: 274 KAEAL--------------TLMGVKSNLVTPRNGEPLIAAIQDFITGAYLLTSKEVFFDR 319

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           ++  ++ + +++       I       +  P    +   +WTGKQ+FSLIL+PN D  V 
Sbjct: 320 SRACQLVAAMLSSQETNMRI-------TLPPPAIQKPVRLWTGKQVFSLILRPNSDSDVK 372

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           ANL+ KG+ YT+ E+ C  DS+                          F  L R   E+ 
Sbjct: 373 ANLRAKGKNYTSGEDLCVNDSF--------------------------FLGLPR---EEY 403

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           A  AM R++++   YL NRGFSIGIGDVTPG G +Q
Sbjct: 404 AADAMSRMAKLCPAYLSNRGFSIGIGDVTPGAGLLQ 439



 Score = 70.5 bits (171), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 32/60 (53%), Positives = 43/60 (71%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFFR 80
            LM  KSNLVTPRNGE LIAA QDFITG YLLT K  FF+R++  ++ + +++ ++   R
Sbjct: 279 TLMGVKSNLVTPRNGEPLIAAIQDFITGAYLLTSKEVFFDRSRACQLVAAMLSSQETNMR 338


>gi|219121691|ref|XP_002181195.1| rna polymerase C 157 kDa [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217407181|gb|EEC47118.1| rna polymerase C 157 kDa [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 1281

 Score =  267 bits (682), Expect = 4e-68,   Method: Compositional matrix adjust.
 Identities = 138/290 (47%), Positives = 180/290 (62%), Gaps = 25/290 (8%)

Query: 322 RLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPY 381
           R LV  N     V+     D+DVVLFNRQPSLHK+SIMAHRAKV+  +TFRFN CVC PY
Sbjct: 396 RELVAKNLRYGDVVERHMEDDDVVLFNRQPSLHKVSIMAHRAKVMEWKTFRFNTCVCAPY 455

Query: 382 NADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAAT 441
           NADFDGDEMN+HLPQTEEAR E              A +LM  K NL TPRNGE L+AA+
Sbjct: 456 NADFDGDEMNMHLPQTEEARTE--------------ASLLMGVKHNLTTPRNGEPLVAAS 501

Query: 442 QDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIW 501
           QDF++  Y+LTQ++ FF R Q  ++ S     + DI                 +R   +W
Sbjct: 502 QDFLSASYMLTQRDRFFTREQFCQLVSYYSDASEDI----------DIPFPTILRPVELW 551

Query: 502 TGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLG 561
           TGKQ+F ++L+PNR   V  + + K + YT N+ FC  D +V  RNSEL++G++ K ++G
Sbjct: 552 TGKQVFGMMLRPNRKSSVLVSFENKEKNYTTNKYFCKNDGWVAFRNSELVSGNIAKKSIG 611

Query: 562 SGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYL-MNRGFSIGIGDVTP 610
            G K+ + YILLRD G   A + M R ++  S ++  +RG SIGI DVTP
Sbjct: 612 DGSKSGLLYILLRDCGVHEAASCMDRWAKFCSRFMGGHRGLSIGISDVTP 661



 Score =  228 bits (581), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 154/443 (34%), Positives = 225/443 (50%), Gaps = 84/443 (18%)

Query: 998  NGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEF--LQDTSENFVRDIKK 1055
            N  PV+ +RL   I       ++  LSA  +     + L    F  L  T   F+++I+ 
Sbjct: 870  NDRPVDFERLRLHISQTTPCPTEDCLSAAALSTTVEKKLAEPRFQALLPTGRVFMQEIRD 929

Query: 1056 FLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQI 1115
            F    ++ ++    + ++   L E +                          +K + A +
Sbjct: 930  FFNSLAENQNSRMTETQLELLLTEAL--------------------------DKCMLAYV 963

Query: 1116 EPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFVPDDSFILI 1164
            EP  AVGA+ AQSI EPGTQMTLKTFHF+G            + E I    +     I  
Sbjct: 964  EPGEAVGAIGAQSISEPGTQMTLKTFHFSGISSMNVTLGVPRLKEIINAAKLISTPIITA 1023

Query: 1165 KLDMDRIRL-------------------------------LHLEVDIDSIRYCIERTRGI 1193
            KL+ D  ++                               + +E+D+D+I          
Sbjct: 1024 KLECDNNKVAARIVKAVIEKTTLGEVSKYMKEVYAPGSCYISVELDMDAIEQL------- 1076

Query: 1194 SGHLTVSGHSF---LILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEG 1250
               L V  HS    ++   K  +K  N+ M  +K  LP+V+++G+  + RAVI+E +  G
Sbjct: 1077 --KLNVDVHSVRRSILYGTKGIAK--NAGMQMLKAALPNVIVQGIPTVARAVINESNQSG 1132

Query: 1251 VTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHG 1310
               Y LL+EG  L+DVM + G+ G+  ++N+  EV   LG+EAAR+ I  EI  +M  +G
Sbjct: 1133 TPTYNLLMEGYGLQDVMGSPGIDGLHTTTNHVLEVEDVLGVEAARTQISAEIDNIMSAYG 1192

Query: 1311 MSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDC 1370
            + ID RH +L++D+MT KGEVLGITR G++KM+ESVL LASFE T+DHLFDAA +G+TD 
Sbjct: 1193 IGIDQRHLLLLSDVMTFKGEVLGITRFGVSKMRESVLMLASFEKTTDHLFDAAVHGRTDT 1252

Query: 1371 ISGVSECIIMGLPMNVGTGLIKL 1393
            I GVSECIIMG+ + VGTGL  L
Sbjct: 1253 IVGVSECIIMGMEVPVGTGLPAL 1275



 Score =  190 bits (482), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 104/235 (44%), Positives = 149/235 (63%), Gaps = 22/235 (9%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPR+KEIINA++ ISTPIITA L+ D +   ARIVK  +E+TTLGEV +Y++EV+ P  
Sbjct: 1002 GVPRLKEIINAAKLISTPIITAKLECDNNKVAARIVKAVIEKTTLGEVSKYMKEVYAPGS 1061

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCI-ERTRGISGHLTVSGHSFLILKPKDSSKSFNS 882
             +I ++LDMD I  L L VD+ S+R  I   T+GI+                      N+
Sbjct: 1062 CYISVELDMDAIEQLKLNVDVHSVRRSILYGTKGIAK---------------------NA 1100

Query: 883  KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCS 942
             M  +K  LP+V+++G+  + RAVI+E +  G   Y LL+EG  L+DVM + G+ G+  +
Sbjct: 1101 GMQMLKAALPNVIVQGIPTVARAVINESNQSGTPTYNLLMEGYGLQDVMGSPGIDGLHTT 1160

Query: 943  SNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +N+  EV   LG+EAAR+ I  EI  +M  +G+ ID RH +L++D+MT KGEVLG
Sbjct: 1161 TNHVLEVEDVLGVEAARTQISAEIDNIMSAYGIGIDQRHLLLLSDVMTFKGEVLG 1215



 Score =  158 bits (399), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 94/233 (40%), Positives = 136/233 (58%), Gaps = 9/233 (3%)

Query: 111 PQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINIL 170
           P R P   G LD R+G + K + C TC + L DC GHFGYI L LPVFHIG+ R  +++L
Sbjct: 2   PSRKPAHGGCLDPRLGVSDKVSACATCKRKLVDCAGHFGYIRLALPVFHIGFLRHTLHLL 61

Query: 171 QSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEIN 230
           Q +CK  TC+RVL+ E       +++R+P    L + +L KK++E  KKV VCPHCG  N
Sbjct: 62  QCVCK--TCSRVLMPESDRQKHLSRMRSPKTDALSKAALFKKVVEKCKKVRVCPHCGGHN 119

Query: 231 GVVKK---CGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLI--QT 285
           G VKK      LKI HE+YK R  + +  +++L+A    ++K N ++        +  + 
Sbjct: 120 GTVKKITGVPTLKIVHERYKGRNAEDE--LDELIANLEVSLKMNKDVGTAISGSSLPYED 177

Query: 286 LNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDL 338
           L P   L++F  I  +D  +L ++  + +P  LIL  +LVPP  IRPSV  D+
Sbjct: 178 LLPTRALEIFTHISDDDCEVLWIDPLIGRPETLILQSILVPPVPIRPSVAMDV 230



 Score =  104 bits (260), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 47/63 (74%), Positives = 54/63 (85%)

Query: 608 VTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           +   +GFV NSF++GLT TEFFFH MGGREGLVDTAVKTAETGYM RRL+K+LEDL +QY
Sbjct: 782 IPSAKGFVANSFYTGLTATEFFFHAMGGREGLVDTAVKTAETGYMARRLMKALEDLSLQY 841

Query: 668 DMS 670
           D S
Sbjct: 842 DSS 844



 Score = 60.5 bits (145), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 26/49 (53%), Positives = 36/49 (73%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIAS 69
           +LM  K NL TPRNGE L+AA+QDF++  Y+LTQ++ FF R Q  ++ S
Sbjct: 480 LLMGVKHNLTTPRNGEPLVAASQDFLSASYMLTQRDRFFTREQFCQLVS 528



 Score = 50.4 bits (119), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 24/37 (64%), Positives = 28/37 (75%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 704
            D  FDAA +G+TD I GVSECIIMG+ + VGTGL  L
Sbjct: 1239 DHLFDAAVHGRTDTIVGVSECIIMGMEVPVGTGLPAL 1275


>gi|198457645|ref|XP_002136234.1| GA22253, partial [Drosophila pseudoobscura pseudoobscura]
 gi|198142520|gb|EDY71256.1| GA22253, partial [Drosophila pseudoobscura pseudoobscura]
          Length = 419

 Score =  266 bits (681), Expect = 5e-68,   Method: Compositional matrix adjust.
 Identities = 154/346 (44%), Positives = 209/346 (60%), Gaps = 58/346 (16%)

Query: 1108 EKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYIEE 1153
            ++Y RA  EP TAVGA+AAQSIGEPGTQMTLKTFHFAG              E+    + 
Sbjct: 50   DRYNRAVSEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIVEIINATKT 109

Query: 1154 VFVPD-----------------------------DSFILI---------KLDMDRIRL-- 1173
            +  P                               SFI +          + +D  R+  
Sbjct: 110  ISTPIITAELQENSSMEYARHVKSRIEKTTLGELSSFIEVVCGPYSCHLAMGIDMSRIKV 169

Query: 1174 LHLEVDIDSIRYCI--ERTRGISGHLTVSGHSFLILKPKDSSK--SFNSKMYQMKQLLPS 1229
            L L +++++I  CI   R R     + ++  +  I+   +SS+  + N+++ ++   L +
Sbjct: 170  LGLHINLETIVACILKSRMRLKPAQVEIAARTSRIIVRVESSRTSTINAELARLALSLQN 229

Query: 1230 VVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTL 1289
            VV+ G+  I RAVI  +D      YKL +EG  LR+V++TYGV G +  SNN  E+++TL
Sbjct: 230  VVVAGLPNIARAVIAVDDTRQPAIYKLCIEGYGLREVISTYGVVGERTRSNNICEIFQTL 289

Query: 1290 GIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNL 1349
            GIEAAR+ IM+EI  VME HGMS+D+RH ML+A  MT++GEVLGITRHGLAKM+ESV NL
Sbjct: 290  GIEAARTIIMSEITEVMEGHGMSVDWRHIMLLASQMTARGEVLGITRHGLAKMRESVFNL 349

Query: 1350 ASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 1395
            ASFE T+DHLFDAA+YGQTD I+GVSE II+G+P  +GTG+ KLL 
Sbjct: 350  ASFEKTADHLFDAAYYGQTDTINGVSERIILGMPAGIGTGIFKLLH 395



 Score =  206 bits (524), Expect = 8e-50,   Method: Compositional matrix adjust.
 Identities = 109/239 (45%), Positives = 162/239 (67%), Gaps = 4/239 (1%)

Query: 763 DGVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPD 822
            GVPRI EIINA++ ISTPIITA L +++ ++YAR VK R+E+TTLGE+  +IE V  P 
Sbjct: 95  QGVPRIVEIINATKTISTPIITAELQENSSMEYARHVKSRIEKTTLGELSSFIEVVCGPY 154

Query: 823 DSFILIKLDMDRIRLLHLEVDIDSIRYCI--ERTRGISGHLTVSGHSFLILKPKDSSKS- 879
              + + +DM RI++L L +++++I  CI   R R     + ++  +  I+   +SS++ 
Sbjct: 155 SCHLAMGIDMSRIKVLGLHINLETIVACILKSRMRLKPAQVEIAARTSRIIVRVESSRTS 214

Query: 880 -FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 938
             N+++ ++   L +VV+ G+  I RAVI  +D      YKL +EG  LR+V++TYGV G
Sbjct: 215 TINAELARLALSLQNVVVAGLPNIARAVIAVDDTRQPAIYKLCIEGYGLREVISTYGVVG 274

Query: 939 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +  SNN  E+++TLGIEAAR+ IM+EI  VME HGMS+D+RH ML+A  MT++GEVLG
Sbjct: 275 ERTRSNNICEIFQTLGIEAARTIIMSEITEVMEGHGMSVDWRHIMLLASQMTARGEVLG 333



 Score = 58.2 bits (139), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 25/39 (64%), Positives = 31/39 (79%)

Query: 668 DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
           D  FDAA+YGQTD I+GVSE II+G+P  +GTG+ KLL 
Sbjct: 357 DHLFDAAYYGQTDTINGVSERIILGMPAGIGTGIFKLLH 395


>gi|321260548|ref|XP_003194994.1| DNA-directed RNA polymerase III largest subunit [Cryptococcus
           gattii WM276]
 gi|317461466|gb|ADV23207.1| DNA-directed RNA polymerase III largest subunit, putative
           [Cryptococcus gattii WM276]
          Length = 1463

 Score =  266 bits (681), Expect = 5e-68,   Method: Compositional matrix adjust.
 Identities = 139/278 (50%), Positives = 181/278 (65%), Gaps = 31/278 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIM HR +V P RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 467 DGDIVLFNRQPSLHKLSIMCHRVRVRPWRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 526

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL               LM+ K NLVTPRNGE +IAA QDFIT  YLL++++ F++R
Sbjct: 527 RTEALE--------------LMSVKKNLVTPRNGEPIIAAIQDFITAAYLLSRRDRFYDR 572

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q  +IAS L     D    I+      W PV       +WTGKQIF+L+++PN++  V 
Sbjct: 573 QQFTQIASYL----GDANLKIEMPPPTIWKPV------RLWTGKQIFNLLMRPNKESKVL 622

Query: 521 ANLKTKGRAYT--ANE-----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILL 573
            NL+ K R     A E     +    D Y++++NSE++ G  DK+T+G G K +VF ++L
Sbjct: 623 VNLEAKCRTLVDPAKEDRFPPDMSPNDGYLVIQNSEIMCGVFDKNTVGDGKKNSVFGVIL 682

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           RD+G + A  AM RL+++ + +L N GFS+GI DV PG
Sbjct: 683 RDYGPEEAAQAMNRLAKIAARWLANIGFSLGINDVIPG 720



 Score =  244 bits (624), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 150/382 (39%), Positives = 213/382 (55%), Gaps = 70/382 (18%)

Query: 1076 PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQ 1135
            P  +++L + +K+    + N F      E CR +Y+RA+IEP + VGA+ AQSIGEPGTQ
Sbjct: 1058 PAVQRVLENANKVTEA-QVNSF-----LENCRIRYLRAKIEPGSTVGAVGAQSIGEPGTQ 1111

Query: 1136 MTLKTFHFAG-----------EVCEYIE------------EVFVPD-------------- 1158
            MTLKTFHFAG            + E I             E+ +P+              
Sbjct: 1112 MTLKTFHFAGVASMNVTLGVPRIKEIINAAKVISTPIIAAELAIPESETAARIVKGRIEK 1171

Query: 1159 -----------------DSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLT 1198
                             +++I + +DMD +R L LE+ ++SI++ + R   +    G + 
Sbjct: 1172 TVLGDIAAVIEESWTNANAYIEVHIDMDAVRRLQLEISLESIKWALVRANKLKIPEGSIH 1231

Query: 1199 VSGHS-----FLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTK 1253
            +S  +     ++    KD       ++  +K+ +PSV +KG+  I R V+  +D +    
Sbjct: 1232 ISQKTSRIRIWIDESDKDKGVGIYERLKFLKRAIPSVQVKGLPAIERGVV-TKDEKNEKI 1290

Query: 1254 YKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSI 1313
            ++LLV G  L +VM T GV G+K  +N+  E  + LGIEAARSTI  EI+  M++HGMSI
Sbjct: 1291 HRLLVTGYGLSEVMGTEGVDGLKTKTNHVMETQQVLGIEAARSTIYNEIQTTMKSHGMSI 1350

Query: 1314 DFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISG 1373
            D RH ML+ D+MT KGEVLGITR G+ KMK+SVL LASFE T+DHLFDA+ Y + D I G
Sbjct: 1351 DPRHVMLLGDVMTYKGEVLGITRFGVQKMKDSVLMLASFEKTTDHLFDASLYSKKDEIQG 1410

Query: 1374 VSECIIMGLPM-NVGTGLIKLL 1394
            VSECIIMG P    GT L  ++
Sbjct: 1411 VSECIIMGTPAPGCGTSLASIV 1432



 Score =  211 bits (538), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 113/250 (45%), Positives = 149/250 (59%), Gaps = 9/250 (3%)

Query: 97  SHIQIVSKNLY--CQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLP 154
           S +Q+    LY   +D  RT    G LD RMG N+K   C TCG++   CVGH+GYI L 
Sbjct: 40  SEVQVSIAELYQNNEDGSRTTALQGPLDARMGPNEKGKKCATCGEDTQKCVGHYGYIKLV 99

Query: 155 LPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKIL 214
           LPVFHIGYFR  IN+L  ICK  TCARVLL E + A F  + R P L  L R+S  K +L
Sbjct: 100 LPVFHIGYFRPTINMLSCICK--TCARVLLPETERASFLKRFRRPNLESLQRQSAAKAVL 157

Query: 215 ETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEI 274
              KK ++C +CG  NG+VKK G L+ISHE Y  R  K  ++ ++ +A +  AV  N  +
Sbjct: 158 AACKKQNICTYCGAPNGIVKKSGPLRISHEPY--RAAKMASMKDEWMATFKNAVAENQAV 215

Query: 275 EAHKKFG-LIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPS 333
             H   G  +  LNPL+VL LFE +  ED  LL ++ ++ +P D I   + VPP CIRPS
Sbjct: 216 ATH--LGKAVDDLNPLKVLNLFERVTAEDCELLSLHPDVGRPEDYIWQYISVPPPCIRPS 273

Query: 334 VISDLKSDND 343
           V S+  ++ D
Sbjct: 274 VASEAGNNED 283



 Score =  185 bits (469), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 104/242 (42%), Positives = 151/242 (62%), Gaps = 9/242 (3%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ ISTPII A L        ARIVKGR+E+T LG++   IEE +   +
Sbjct: 1130 GVPRIKEIINAAKVISTPIIAAELAIPESETAARIVKGRIEKTVLGDIAAVIEESWTNAN 1189

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHS-----FLILKPKD 875
            ++I + +DMD +R L LE+ ++SI++ + R   +    G + +S  +     ++    KD
Sbjct: 1190 AYIEVHIDMDAVRRLQLEISLESIKWALVRANKLKIPEGSIHISQKTSRIRIWIDESDKD 1249

Query: 876  SSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYG 935
                   ++  +K+ +PSV +KG+  I R V+  +D +    ++LLV G  L +VM T G
Sbjct: 1250 KGVGIYERLKFLKRAIPSVQVKGLPAIERGVV-TKDEKNEKIHRLLVTGYGLSEVMGTEG 1308

Query: 936  VKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            V G+K  +N+  E  + LGIEAARSTI  EI+  M++HGMSID RH ML+ D+MT KGEV
Sbjct: 1309 VDGLKTKTNHVMETQQVLGIEAARSTIYNEIQTTMKSHGMSIDPRHVMLLGDVMTYKGEV 1368

Query: 996  LG 997
            LG
Sbjct: 1369 LG 1370



 Score =  110 bits (275), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 49/68 (72%), Positives = 55/68 (80%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV+NSFFSGLTP EF FH M GREGLVDTAVKTAETGYM RRL+K+LEDLC  YD+
Sbjct: 843 PSKGFVRNSFFSGLTPPEFLFHAMSGREGLVDTAVKTAETGYMARRLMKALEDLCTHYDL 902

Query: 670 SFDAAFYG 677
           S   +  G
Sbjct: 903 SVRNSVGG 910



 Score = 65.1 bits (157), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 30/50 (60%), Positives = 39/50 (78%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM+ K NLVTPRNGE +IAA QDFIT  YLL++++ F++R Q  +IAS L
Sbjct: 533 LMSVKKNLVTPRNGEPIIAAIQDFITAAYLLSRRDRFYDRQQFTQIASYL 582



 Score = 40.8 bits (94), Expect = 5.4,   Method: Compositional matrix adjust.
 Identities = 20/39 (51%), Positives = 24/39 (61%), Gaps = 1/39 (2%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPM-NVGTGLIKLL 705
            D  FDA+ Y + D I GVSECIIMG P    GT L  ++
Sbjct: 1394 DHLFDASLYSKKDEIQGVSECIIMGTPAPGCGTSLASIV 1432


>gi|405121486|gb|AFR96255.1| DNA-directed RNA polymerase III largest subunit [Cryptococcus
           neoformans var. grubii H99]
          Length = 1437

 Score =  266 bits (680), Expect = 6e-68,   Method: Compositional matrix adjust.
 Identities = 139/278 (50%), Positives = 181/278 (65%), Gaps = 31/278 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIM HR +V P RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 467 DGDIVLFNRQPSLHKLSIMCHRVRVRPWRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 526

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL               LM+ K NLVTPRNGE +IAA QDFIT  YLL++++ F++R
Sbjct: 527 RTEALE--------------LMSVKKNLVTPRNGEPIIAAIQDFITAAYLLSRRDRFYDR 572

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q  +IAS L     D    I+      W PV       +WTGKQIF+L+++PN++  V 
Sbjct: 573 QQFTQIASYL----GDANLKIEMPPPTIWKPV------RLWTGKQIFNLLMRPNKESKVL 622

Query: 521 ANLKTKGRAYT--ANE-----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILL 573
            NL+ K R     A E     +    D Y++++NSE++ G  DK+T+G G K +VF ++L
Sbjct: 623 VNLEAKCRTLVDPAKEDRFPPDMSPNDGYLVIQNSEIMCGVFDKNTVGDGKKNSVFGVIL 682

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           RD+G + A  AM RL+++ + +L N GFS+GI DV PG
Sbjct: 683 RDYGPEEAAQAMNRLAKIAARWLANIGFSLGINDVIPG 720



 Score =  240 bits (613), Expect = 4e-60,   Method: Compositional matrix adjust.
 Identities = 141/325 (43%), Positives = 196/325 (60%), Gaps = 35/325 (10%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIE 1152
            E CR +Y+RA+IEP + VGA+ AQSIGEPGTQMTLKTFHFAG            + E I 
Sbjct: 1080 ENCRIRYLRAKIEPGSTVGAVGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIIN 1139

Query: 1153 ------------EVFVPDDSFI--LIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SG 1195
                        E+ +P+      ++K  +++  L  LE+ ++SI++ + R   +    G
Sbjct: 1140 AAKVISTPIIAAELAIPESETAARIVKGRIEKTVLGDLEISLESIKWALVRANKLKIPEG 1199

Query: 1196 HLTVSGHS-----FLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEG 1250
             + +S  +     ++    KD       ++  +K+ +PSV +KG+  I R V+  +D + 
Sbjct: 1200 SIHISQKTSRIRIWIDESDKDKGVGIYERLKFLKRAIPSVQVKGLPAIERGVV-TKDEKN 1258

Query: 1251 VTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHG 1310
               ++LLV G  L +VM T GV G+K  +N+  E  + LGIEAARSTI  EI+  M++HG
Sbjct: 1259 EKIHRLLVTGYGLSEVMGTEGVDGLKTKTNHVMETQQVLGIEAARSTIYNEIQTTMKSHG 1318

Query: 1311 MSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDC 1370
            MSID RH ML+ D+MT KGEVLGITR G+ KMK+SVL LASFE T+DHLFDA+ Y + D 
Sbjct: 1319 MSIDPRHVMLLGDVMTYKGEVLGITRFGVQKMKDSVLMLASFEKTTDHLFDASLYSKKDE 1378

Query: 1371 ISGVSECIIMGLPM-NVGTGLIKLL 1394
            I GVSECIIMG P    GT L  ++
Sbjct: 1379 IQGVSECIIMGTPAPGCGTSLASIV 1403



 Score =  212 bits (540), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 113/249 (45%), Positives = 148/249 (59%), Gaps = 7/249 (2%)

Query: 97  SHIQIVSKNLY--CQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLP 154
           S +Q+    LY   +D  RT    G LD RMG N+K   C TCG++   CVGH+GYI L 
Sbjct: 40  SEVQVSIAELYQNNEDGSRTTALQGPLDARMGPNEKGKKCATCGEDTQKCVGHYGYIKLV 99

Query: 155 LPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKIL 214
           LPVFHIGYFR  IN+L  ICK  TCARVLL E + A F  + R P L  L R+S  K +L
Sbjct: 100 LPVFHIGYFRPTINMLSCICK--TCARVLLPETERASFLKRFRRPNLESLQRQSAAKAVL 157

Query: 215 ETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEI 274
              KK ++C +CG  NG+VKK G L+ISHE Y  R  K  ++ ++ +A +  AV  N  +
Sbjct: 158 AACKKQNICTYCGAPNGIVKKSGPLRISHEPY--RAAKMASMKDEWMATFKNAVAENQAV 215

Query: 275 EAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSV 334
             H     +  LNPL+VL LFE I  ED  LL ++ ++ +P D I   + VPP CIRPSV
Sbjct: 216 ATHLSKA-VDDLNPLKVLNLFERITAEDCELLSLHPDVGRPEDYIWQYISVPPPCIRPSV 274

Query: 335 ISDLKSDND 343
            S+  ++ D
Sbjct: 275 ASEAGNNED 283



 Score =  150 bits (378), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 95/236 (40%), Positives = 134/236 (56%), Gaps = 26/236 (11%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ ISTPII A L        ARIVKGR+E+T LG++     E+ +   
Sbjct: 1130 GVPRIKEIINAAKVISTPIIAAELAIPESETAARIVKGRIEKTVLGDL-----EISLESI 1184

Query: 824  SFILIKLDMDRIR--LLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             + L++ +  +I    +H+      IR  I+ +                   KD      
Sbjct: 1185 KWALVRANKLKIPEGSIHISQKTSRIRIWIDES------------------DKDKGVGIY 1226

Query: 882  SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
             ++  +K+ +PSV +KG+  I R V+  +D +    ++LLV G  L +VM T GV G+K 
Sbjct: 1227 ERLKFLKRAIPSVQVKGLPAIERGVV-TKDEKNEKIHRLLVTGYGLSEVMGTEGVDGLKT 1285

Query: 942  SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +N+  E  + LGIEAARSTI  EI+  M++HGMSID RH ML+ D+MT KGEVLG
Sbjct: 1286 KTNHVMETQQVLGIEAARSTIYNEIQTTMKSHGMSIDPRHVMLLGDVMTYKGEVLG 1341



 Score =  110 bits (274), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 49/68 (72%), Positives = 55/68 (80%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV+NSFFSGLTP EF FH M GREGLVDTAVKTAETGYM RRL+K+LEDLC  YD+
Sbjct: 843 PSKGFVRNSFFSGLTPPEFLFHAMSGREGLVDTAVKTAETGYMARRLMKALEDLCTHYDL 902

Query: 670 SFDAAFYG 677
           S   +  G
Sbjct: 903 SVRNSVGG 910



 Score = 64.7 bits (156), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 30/50 (60%), Positives = 39/50 (78%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM+ K NLVTPRNGE +IAA QDFIT  YLL++++ F++R Q  +IAS L
Sbjct: 533 LMSVKKNLVTPRNGEPIIAAIQDFITAAYLLSRRDRFYDRQQFTQIASYL 582



 Score = 40.8 bits (94), Expect = 5.6,   Method: Compositional matrix adjust.
 Identities = 20/39 (51%), Positives = 24/39 (61%), Gaps = 1/39 (2%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPM-NVGTGLIKLL 705
            D  FDA+ Y + D I GVSECIIMG P    GT L  ++
Sbjct: 1365 DHLFDASLYSKKDEIQGVSECIIMGTPAPGCGTSLASIV 1403


>gi|71024147|ref|XP_762303.1| hypothetical protein UM06156.1 [Ustilago maydis 521]
 gi|46101808|gb|EAK87041.1| hypothetical protein UM06156.1 [Ustilago maydis 521]
          Length = 1400

 Score =  266 bits (679), Expect = 7e-68,   Method: Compositional matrix adjust.
 Identities = 134/282 (47%), Positives = 180/282 (63%), Gaps = 29/282 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIM+HRAK+ P RTFR NEC C PYNADFDGDEMN+H+PQTEEA
Sbjct: 455 DGDIVLFNRQPSLHKLSIMSHRAKIRPWRTFRLNECACNPYNADFDGDEMNMHVPQTEEA 514

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R E              A VLM  K NLVTPRNGE +IAA QDFIT  YL+++++ FF+R
Sbjct: 515 RTE--------------ATVLMGVKHNLVTPRNGEPIIAAIQDFITASYLISKRDRFFDR 560

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           AQ  +I S      +D+   I         P   ++   +WTGKQ+ S +++PNR  P  
Sbjct: 561 AQFSQICSYF--SDADLHIDIP--------PPAIMKPVRLWTGKQVMSCLIRPNRKSPHL 610

Query: 521 ANLKTKGRAYTA-----NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL+ + R +        ++    D ++++ NS+++ G  DKST+G G K +VF ++LRD
Sbjct: 611 VNLEAQCRTFEKPTGGHPKDMSPNDGWLVIVNSQVMCGVFDKSTVGDGKKNSVFGVMLRD 670

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           +G D A+TAM RL++  + +L N+GFS+GI DV PG     N
Sbjct: 671 YGPDAAITAMNRLAKTCARWLANQGFSLGINDVIPGPKLRMN 712



 Score =  210 bits (534), Expect = 6e-51,   Method: Compositional matrix adjust.
 Identities = 158/495 (31%), Positives = 231/495 (46%), Gaps = 82/495 (16%)

Query: 993  GEVLGNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRD 1052
             E+ GN  P+E  RL    +A     +   L   EI+ +    L S  F++  ++ +   
Sbjct: 910  AELEGNAMPIEPFRLWRHCLAITHHVAGRGLLPYEIMEVVKRELSSDRFVKTCTQKYRDS 969

Query: 1053 IKKFLEEFSKKESVTSHQ--DKVSQPLREQILSHQDKIGHGRESNPFPSACKA------- 1103
            + +FL E   + ++   +         RE+    Q  +  G +   +             
Sbjct: 970  VYEFLYENVYQRAIKMREAFGMYGADSREEHWDEQTDLSLGADRAQWAIVNNKTKIKEVA 1029

Query: 1104 -----EACREKYVRAQIEPATAVGAL---------------------------------- 1124
                 E C  KY++A+IEP +AVGA+                                  
Sbjct: 1030 VLAFLEQCYIKYMKAKIEPGSAVGAVGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRI 1089

Query: 1125 -----AAQSIGEPGTQMTLKTFH---------------FAGEVCEYIEEVFVPDDSFILI 1164
                 AA+ I  P  +  L +                 + G++   IEE +    +++ +
Sbjct: 1090 KEIINAAKVINTPIIEAKLVSEKSERAARIVKGRIEKTYLGDIASVIEEAWAAQYTYLGV 1149

Query: 1165 KLDMDRIRLLHLEVDIDSIRYCIERTRGISGH-----LTVSGHSFLILKPKDSSKSFNSK 1219
             +DM+ I+ L LE+ ++ I++ I     +        +    +   I  P ++       
Sbjct: 1150 HIDMEAIQKLQLEITLNDIKWAIVNAPKLKIKEERVMVVPKKNRIRIYVPPEAPDKEGDV 1209

Query: 1220 MYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 1276
             Y +K L   LPS+V+KG+    RAVI +E        KLLVEG  L  VM T GV G +
Sbjct: 1210 YYNLKALKRALPSIVVKGIPQATRAVISDEK----GTRKLLVEGYGLLKVMTTEGVIGTQ 1265

Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITR 1336
              +N+  E+   LGIEAAR+++  EI+  M  HGMSID RH ML+AD MT KGEVLGITR
Sbjct: 1266 THTNHVMEMQAVLGIEAARTSVYREIEHTMSAHGMSIDPRHIMLLADTMTYKGEVLGITR 1325

Query: 1337 HGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLP-MNVGTGLIKLLQ 1395
             G+AKMK+SVL LASFE T+DHLFDAA +G+ D + GVSE IIMG P   VGTG+  L+ 
Sbjct: 1326 FGVAKMKDSVLMLASFEKTTDHLFDAALFGKKDEVLGVSESIIMGNPAQTVGTGMPALVV 1385

Query: 1396 AVPRSEPVPRTLLFD 1410
              P + P  R LLFD
Sbjct: 1386 PAP-TLPPRRALLFD 1399



 Score =  188 bits (478), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 111/263 (42%), Positives = 151/263 (57%), Gaps = 8/263 (3%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYC-QDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSD 143
           G ++K+D V   S I++ +++LY   + +R P+ +G LDRR+G + K + C TC   ++D
Sbjct: 19  GVLSKQDIVNM-SEIEVTTRDLYTIGESERKPVANGTLDRRLGVSDKNSLCETCHLKMAD 77

Query: 144 CVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSY 203
           CVGH+GYI L LPVFH+G+F+  + ILQSICKN  CA VLL E     F  + R P L  
Sbjct: 78  CVGHYGYIKLVLPVFHVGFFKHTVAILQSICKN--CATVLLEEPDRRKFLKRFRRPNLEN 135

Query: 204 LVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAE 263
           L R    K +    +KV  CP CG  NG VKK G LKI HEK+  R KK  A  ++  A 
Sbjct: 136 LDRTRTFKAVNTIARKVLYCPKCGYTNGTVKKQGQLKIVHEKF--RAKKTAAEHDEFKAS 193

Query: 264 YNEAVKF-NPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTR 322
           +   +K  N +I  H      + LNPL+ L LF+ I  ED  LL +  E  +P + I   
Sbjct: 194 FATNIKMGNGDISPHLNKAQ-EDLNPLKALDLFKRISDEDCELLGLRPEFGRPEEYIWQY 252

Query: 323 LLVPPNCIRPSVISDLKSDNDVV 345
           + VPP CIRPSV  D  ++ D V
Sbjct: 253 ICVPPVCIRPSVAQDGATNEDDV 275



 Score =  168 bits (426), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 101/242 (41%), Positives = 141/242 (58%), Gaps = 12/242 (4%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ I+TPII A L  +     ARIVKGR+E+T LG++   IEE +    
Sbjct: 1085 GVPRIKEIINAAKVINTPIIEAKLVSEKSERAARIVKGRIEKTYLGDIASVIEEAWAAQY 1144

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGH-----LTVSGHSFLILKPKDSSK 878
            +++ + +DM+ I+ L LE+ ++ I++ I     +        +    +   I  P ++  
Sbjct: 1145 TYLGVHIDMEAIQKLQLEITLNDIKWAIVNAPKLKIKEERVMVVPKKNRIRIYVPPEAPD 1204

Query: 879  SFNSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYG 935
                  Y +K L   LPS+V+KG+    RAVI +E        KLLVEG  L  VM T G
Sbjct: 1205 KEGDVYYNLKALKRALPSIVVKGIPQATRAVISDEK----GTRKLLVEGYGLLKVMTTEG 1260

Query: 936  VKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            V G +  +N+  E+   LGIEAAR+++  EI+  M  HGMSID RH ML+AD MT KGEV
Sbjct: 1261 VIGTQTHTNHVMEMQAVLGIEAARTSVYREIEHTMSAHGMSIDPRHIMLLADTMTYKGEV 1320

Query: 996  LG 997
            LG
Sbjct: 1321 LG 1322



 Score =  109 bits (273), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 51/75 (68%), Positives = 58/75 (77%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV+NSFFSGLTPTEF FH + GREGLVDTAVKTAETGYMQRRL+K+LEDL   YD+
Sbjct: 829 PSKGFVRNSFFSGLTPTEFLFHAISGREGLVDTAVKTAETGYMQRRLMKALEDLSTHYDL 888

Query: 670 SFDAAFYGQTDCISG 684
           S   +  G    I G
Sbjct: 889 SVRNSVGGVVQFIYG 903



 Score = 65.1 bits (157), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 30/49 (61%), Positives = 38/49 (77%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIAS 69
           VLM  K NLVTPRNGE +IAA QDFIT  YL+++++ FF+RAQ  +I S
Sbjct: 520 VLMGVKHNLVTPRNGEPIIAAIQDFITASYLISKRDRFFDRAQFSQICS 568



 Score = 48.1 bits (113), Expect = 0.034,   Method: Compositional matrix adjust.
 Identities = 28/55 (50%), Positives = 34/55 (61%), Gaps = 2/55 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLP-MNVGTGLIKLLQAVPRSEPVPRTLLFD 721
            D  FDAA +G+ D + GVSE IIMG P   VGTG+  L+   P + P  R LLFD
Sbjct: 1346 DHLFDAALFGKKDEVLGVSESIIMGNPAQTVGTGMPALVVPAP-TLPPRRALLFD 1399


>gi|256083198|ref|XP_002577836.1| RNA polymerase Rpb1 [Schistosoma mansoni]
 gi|360044779|emb|CCD82327.1| putative rna polymerase Rpb1 [Schistosoma mansoni]
          Length = 1342

 Score =  266 bits (679), Expect = 8e-68,   Method: Compositional matrix adjust.
 Identities = 136/277 (49%), Positives = 176/277 (63%), Gaps = 23/277 (8%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+D+VLFNRQPSLH++SI A RA V P RTFRFN C CTP+NADFDGDEMN+HLPQTE A
Sbjct: 466 DDDIVLFNRQPSLHRVSIQAFRAVVKPFRTFRFNPCCCTPFNADFDGDEMNIHLPQTEAA 525

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              AK LM +  N+V+P+NGE LI+  QD IT  +LLT K+ F NR
Sbjct: 526 RAE--------------AKHLMLSLKNIVSPKNGEPLISPIQDLITATHLLTLKDVFLNR 571

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q   +A+ L+A   +  G +         P +    A +WTGKQIF LIL P+    + 
Sbjct: 572 DQACTLAAQLLA--GNHLGRLLSLP----KPAILWPVA-LWTGKQIFGLILSPHPSTGIK 624

Query: 521 ANLK--TKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            NL+  TK    +  +E C  D +V+++NSELLAG +DK  LG G K+++FY LLRD+G 
Sbjct: 625 VNLRVPTKSMYSSKGQEMCPNDGFVLIQNSELLAGCVDKKLLGGGSKSSIFYTLLRDYGR 684

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFV 615
           +    AMWRL R+  F+L +RGFSIG+G+V P    V
Sbjct: 685 EACADAMWRLGRIALFFLAHRGFSIGLGEVMPSSDLV 721



 Score =  186 bits (471), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 99/263 (37%), Positives = 162/263 (61%), Gaps = 12/263 (4%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQ-DPQRTPIPHGLLDRRMGTNQKEANCTTCGQNL 141
           I+  +  E  +++ SH+Q++   LY +    R  + +GLLD R+G N+++  C TCG + 
Sbjct: 17  IKFQLCSEGDLKRLSHVQVLKCLLYAEGQSNRRALDYGLLDPRLGANKRDELCATCGLDY 76

Query: 142 SDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPAL 201
             C+GH+GY DLP P++H+GY   ++ ILQ+ICK  TC+RVLL E++ A F     NP+L
Sbjct: 77  QTCIGHWGYFDLPTPIYHVGYTWHIVKILQTICK--TCSRVLLPEQQRARFSISCSNPSL 134

Query: 202 SYLVRKSLKKKILETTKKVSVCPHCGEINGVVKK-CGLLKISHEKYKNRTKKKDAIVEDL 260
            Y+ +K L+K I + + +V VCP C  +NGVV K   L  + H+ +++   K    V++ 
Sbjct: 135 DYVHKKQLRKAIHKLSSRVHVCPFCSALNGVVTKGTSLSYVVHDIFRHAKAK----VDEY 190

Query: 261 LAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLM---NAELSKPSD 317
           + E+ + +  N ++    + GL + + P + LQLF  IP ED+PLLLM   +   + P +
Sbjct: 191 VNEFAKVITENTDLAPVVRKGL-EIIRPGKALQLFSKIPEEDLPLLLMPFDSQWTTHPRN 249

Query: 318 LILTRLLVPPNCIRPSVISDLKS 340
           LI+ R+ V P+ IRPSV+S+++S
Sbjct: 250 LIVQRVPVCPSAIRPSVVSEVRS 272



 Score =  132 bits (332), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 101/346 (29%), Positives = 162/346 (46%), Gaps = 80/346 (23%)

Query: 1039 KEFLQDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFP 1098
            KEF+ ++    +R  +++  E +   ++ +  +++++      L+H              
Sbjct: 981  KEFIHNSVCPRIRKWQEWCTEHANGSNLINQNERLTRTQLRIFLTH-------------- 1026

Query: 1099 SACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG------------- 1145
                    +EKY +A IEP TAVGAL  QS+GEP TQMTLKTFHFAG             
Sbjct: 1027 -------VKEKYEKALIEPGTAVGALCGQSVGEPATQMTLKTFHFAGVASMNITQGVPRM 1079

Query: 1146 -EVCEYIEEVFVP------DDSFIL-----IKLDMDRIRL---------------LHLEV 1178
             E+      +  P       D F       +KL ++  RL               +++ +
Sbjct: 1080 REIVNAAARIKTPLICVTLTDPFSASLARQVKLSIEPTRLADISLSLSQCLTPEYVYVAI 1139

Query: 1179 DIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMY------------QMKQL 1226
             +D  R  ++R RGI+     +      LK    S+   SK Y             + +L
Sbjct: 1140 KLDKKR--MDR-RGITTPQVATAIQTTKLKKTKLSRVTYSKDYIFVYPVDLNALETVVKL 1196

Query: 1227 LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVY 1286
            +  V++KG+ G++R VI ++  E +    + VEG  LR+VM   GV   +  SNN  EV 
Sbjct: 1197 VEDVIVKGIPGVSRVVIQQDKGEHI----IFVEGARLREVMCIPGVVAERTRSNNILEVE 1252

Query: 1287 KTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL 1332
            + LG+EAAR  ++ E+  VME HG+ ++ RH ML+AD+MT+K   +
Sbjct: 1253 QVLGVEAARRVVIDELLAVMEGHGVEVNVRHVMLLADVMTNKWSTM 1298



 Score =  124 bits (310), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 76/235 (32%), Positives = 128/235 (54%), Gaps = 13/235 (5%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPR++EI+NA+  I TP+I   L        AR VK  +E T L ++   + +   P+ 
Sbjct: 1075 GVPRMREIVNAAARIKTPLICVTLTDPFSASLARQVKLSIEPTRLADISLSLSQCLTPEY 1134

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHS--FLILKPKDSSKSFN 881
             ++ IKLD  + R+    +    +   I+ T+     L+   +S  ++ + P D +    
Sbjct: 1135 VYVAIKLD--KKRMDRRGITTPQVATAIQTTKLKKTKLSRVTYSKDYIFVYPVDLNA--- 1189

Query: 882  SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
              +  + +L+  V++KG+ G++R VI ++  E +    + VEG  LR+VM   GV   + 
Sbjct: 1190 --LETVVKLVEDVIVKGIPGVSRVVIQQDKGEHI----IFVEGARLREVMCIPGVVAERT 1243

Query: 942  SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL 996
             SNN  EV + LG+EAAR  ++ E+  VME HG+ ++ RH ML+AD+MT+K   +
Sbjct: 1244 RSNNILEVEQVLGVEAARRVVIDELLAVMEGHGVEVNVRHVMLLADVMTNKWSTM 1298



 Score =  102 bits (254), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 48/64 (75%), Positives = 53/64 (82%), Gaps = 1/64 (1%)

Query: 606 GDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           G  TP  +GFV NSF+SGL+P+EFFFH M GREGL DTAVKTA+TGYMQRRLVK LEDL 
Sbjct: 835 GSRTPEAKGFVGNSFYSGLSPSEFFFHAMSGREGLTDTAVKTADTGYMQRRLVKFLEDLA 894

Query: 665 VQYD 668
           V YD
Sbjct: 895 VAYD 898



 Score = 55.8 bits (133), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 28/61 (45%), Positives = 39/61 (63%)

Query: 14  ATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIA 73
           A R   + LM +  N+V+P+NGE LI+  QD IT  +LLT K+ F NR Q   +A+ L+A
Sbjct: 524 AARAEAKHLMLSLKNIVSPKNGEPLISPIQDLITATHLLTLKDVFLNRDQACTLAAQLLA 583

Query: 74  G 74
           G
Sbjct: 584 G 584


>gi|398409068|ref|XP_003855999.1| DNA-directed RNA polymerase III subunit RPO31 [Zymoseptoria tritici
           IPO323]
 gi|339475884|gb|EGP90975.1| hypothetical protein MYCGRDRAFT_83445 [Zymoseptoria tritici IPO323]
          Length = 1435

 Score =  266 bits (679), Expect = 9e-68,   Method: Compositional matrix adjust.
 Identities = 133/286 (46%), Positives = 182/286 (63%), Gaps = 40/286 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSI++HRAK+ P RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 415 DGDIVLFNRQPSLHKLSILSHRAKIRPWRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 474

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EA                LM  K NL TP+NG  +IAA QDFITG +L+++K+ FFNR
Sbjct: 475 RTEATE--------------LMGVKHNLATPKNGTPIIAAIQDFITGAFLISRKDQFFNR 520

Query: 461 AQ----------TMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLI 510
            Q           +++   L  +T +    I+  +   W P        +WTGKQI+ ++
Sbjct: 521 RQFNQAVTFMYDGLQVKDPLTGETHN----IEIPAPAIWKP------QTLWTGKQIWDVL 570

Query: 511 LKPNRDCPVNANLKTKGRAYTAN------EEFCHRDSYVILRNSELLAGSMDKSTLGSGG 564
           +KP+R  PVN NL+ K +++         ++    DSY+++RNS  + G  DK+T+G G 
Sbjct: 571 MKPHRHYPVNVNLEAKLKSFAPPKRKGDIDDMVDSDSYLVIRNSVTMCGGFDKATVGDGK 630

Query: 565 KANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           K +VFY+++RDFG D A  AM RL+++++ +L  +GFSIGI DV P
Sbjct: 631 KTSVFYVIMRDFGVDYAAAAMTRLAKLSARWLGEQGFSIGISDVYP 676



 Score =  184 bits (466), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 112/279 (40%), Positives = 158/279 (56%), Gaps = 28/279 (10%)

Query: 1143 FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI--------- 1193
            + G++ +YIE+V+     +I ++++ +++  L L + +  I   I R++G          
Sbjct: 1094 YLGDIVDYIEDVWHAHGCYINMRVNWEQVENLGLRITMWHITEAINRSKGFKSMGVSASA 1153

Query: 1194 -SGHLTV-------------SGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGIN 1239
               H+ V             +    L     D S+    +++ +K+ LP+VV+KG     
Sbjct: 1154 SESHIRVRLTLPDSSKLRKAAATKHLRFSDNDDSEVLFMQIHTLKRKLPAVVVKGYPDAA 1213

Query: 1240 RAVIHEED---VEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARS 1296
            RA++ ++D     G     +LVEG  L+  M T GV G +  SNN  E    LGIEAAR 
Sbjct: 1214 RAIMKKDDKADASGREPISVLVEGYGLKACMTTDGVDGYRTKSNNVMECKDVLGIEAARK 1273

Query: 1297 TIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTS 1356
            TI+ EI  VM   GM ID RH  L+AD+MT KGEVLGITR GLAKM++SVL LASFE T 
Sbjct: 1274 TIIDEISAVM--GGMDIDPRHMQLLADVMTYKGEVLGITRFGLAKMRDSVLQLASFEKTP 1331

Query: 1357 DHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 1395
            DHLF+AA   + D I GVSECIIMG  M VGTG +K+++
Sbjct: 1332 DHLFEAAAKMKKDDIEGVSECIIMGQVMGVGTGAMKVVR 1370



 Score =  179 bits (454), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 104/261 (39%), Positives = 141/261 (54%), Gaps = 16/261 (6%)

Query: 96  QSHIQIVSKNLYCQDPQ----RTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYI 151
           QS + +  +NLY    Q    R+   HG LD+R+GT+ K   C TCGQ L +C GHFG++
Sbjct: 40  QSVVPVADRNLYDLATQPGAGRSITKHGPLDQRLGTSSKNGLCGTCGQGLKECNGHFGHV 99

Query: 152 DLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKK 211
            L LP FH GY + VI+ L  +CK   C+RVLL E+    +   LR P L  L ++ L K
Sbjct: 100 KLALPCFHYGYIKKVIDALNCVCKE--CSRVLLPEKDKRAYLKSLRRPGLDGLRKEVLTK 157

Query: 212 KILETTKKVSVCPHCGEINGVVKKC--GLLKISHEKY------KNRTKKKDAIVEDLLAE 263
           KI    +KV VCPHC   NG V+K     +K+ H KY        ++K K A ++   A 
Sbjct: 158 KISAECRKVKVCPHCSAFNGPVRKVPGHPVKMFHNKYAIYTNSNAKSKVKPAHMQAFEAT 217

Query: 264 YNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL-SKPSDLILTR 322
           + EA+K NPEIE H K      L PL VL + + +P  D+ LL M+     +P  +I T 
Sbjct: 218 FEEAIKANPEIERHMKRA-ADDLTPLRVLNILKKVPNADVELLGMDPHSGGRPEYMIWTS 276

Query: 323 LLVPPNCIRPSVISDLKSDND 343
           +  PP  IRPSV  +  S  D
Sbjct: 277 IPAPPVAIRPSVAQETASTED 297



 Score =  153 bits (386), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 102/284 (35%), Positives = 149/284 (52%), Gaps = 29/284 (10%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS++ISTP+IT  LD   +    R  K  +E+T LG++ +YIE+V+    
Sbjct: 1051 GVPRIKEIINASKSISTPVITCALDSPYEEMAGRFAKALIEKTYLGDIVDYIEDVWHAHG 1110

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI----------SGHLTV---------- 863
             +I ++++ +++  L L + +  I   I R++G             H+ V          
Sbjct: 1111 CYINMRVNWEQVENLGLRITMWHITEAINRSKGFKSMGVSASASESHIRVRLTLPDSSKL 1170

Query: 864  ---SGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEE---DVEGVTK 917
               +    L     D S+    +++ +K+ LP+VV+KG     RA++ ++   D  G   
Sbjct: 1171 RKAAATKHLRFSDNDDSEVLFMQIHTLKRKLPAVVVKGYPDAARAIMKKDDKADASGREP 1230

Query: 918  YKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSI 977
              +LVEG  L+  M T GV G +  SNN  E    LGIEAAR TI+ EI  VM   GM I
Sbjct: 1231 ISVLVEGYGLKACMTTDGVDGYRTKSNNVMECKDVLGIEAARKTIIDEISAVM--GGMDI 1288

Query: 978  DFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDP 1021
            D RH  L+AD+MT KGEVLG  T   L ++ D ++   S    P
Sbjct: 1289 DPRHMQLLADVMTYKGEVLGI-TRFGLAKMRDSVLQLASFEKTP 1331



 Score =  102 bits (255), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 46/60 (76%), Positives = 52/60 (86%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV +SFFSGL+PTEF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD++
Sbjct: 801 AKGFVVDSFFSGLSPTEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSAQYDLT 860



 Score = 67.0 bits (162), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 53/161 (32%), Positives = 78/161 (48%), Gaps = 15/161 (9%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSK--EFLQDTSENFVRDIK 1054
            GN  PV   R     I      S+  L+  EI  + +ETLD +  + ++ T +      K
Sbjct: 885  GNAKPVNFDRTWMHAITSTWDNSERGLTQNEIEEMVHETLDKERAKLVRITDDGLPLPYK 944

Query: 1055 KFLE------EFSKK--ESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSA--CKAE 1104
                      E+S+   + VT++   + + +R+ + S     G         SA  C   
Sbjct: 945  DATPKSTDQLEYSRTFLDDVTNY---IFKHVRKLVSSQHRHRGSDDVFKLSQSALECFLY 1001

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
             C  K+ ++++E   AVGA+ AQSIGEPGTQMTLKTFHFAG
Sbjct: 1002 LCLRKFEKSKVEAGHAVGAVGAQSIGEPGTQMTLKTFHFAG 1042



 Score = 58.5 bits (140), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 27/56 (48%), Positives = 38/56 (67%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKV 77
           LM  K NL TP+NG  +IAA QDFITG +L+++K+ FFNR Q  +  + +  G +V
Sbjct: 481 LMGVKHNLATPKNGTPIIAAIQDFITGAFLISRKDQFFNRRQFNQAVTFMYDGLQV 536



 Score = 42.4 bits (98), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 21/39 (53%), Positives = 27/39 (69%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  F+AA   + D I GVSECIIMG  M VGTG +K+++
Sbjct: 1332 DHLFEAAAKMKKDDIEGVSECIIMGQVMGVGTGAMKVVR 1370


>gi|409049560|gb|EKM59037.1| hypothetical protein PHACADRAFT_169499 [Phanerochaete carnosa
           HHB-10118-sp]
          Length = 1403

 Score =  265 bits (678), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 137/282 (48%), Positives = 183/282 (64%), Gaps = 35/282 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIM HR KV P R+FR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 449 DGDIVLFNRQPSLHKLSIMCHRVKVRPWRSFRLNECVCGPYNADFDGDEMNLHVPQTEEA 508

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL               LM+ K NLVTPRNGE +IAA QDFIT  +LL++++ FF+R
Sbjct: 509 RTEALE--------------LMSVKHNLVTPRNGEPVIAAIQDFITASFLLSRRDRFFDR 554

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q  +I S L AD      I          P   ++   +WTGKQIF+++++PNR   V 
Sbjct: 555 CQFTQICSYL-ADADLQIDI---------PPPTILKPQRLWTGKQIFNVLMRPNRHSRVR 604

Query: 521 ANLKTK--------GRAY---TANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVF 569
            N++++         +AY   T  ++    D ++++ NSE++ G MDK+T+GSG K ++F
Sbjct: 605 VNVESRCNKVEKPDPKAYPRMTPVDDMSPNDGWLVIVNSEIMCGVMDKATVGSGKKKSIF 664

Query: 570 YILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
            ++LRD+G   A TAM RL+++ + YL N GFS+GI DV PG
Sbjct: 665 GVILRDYGPHEAATAMGRLAKLCARYLANYGFSLGINDVIPG 706



 Score =  205 bits (522), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 163/493 (33%), Positives = 236/493 (47%), Gaps = 83/493 (16%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G+  PVE  R      A  +SRS   L   EIL   N+ L   +F  + S  ++  I++F
Sbjct: 914  GDAQPVEYLRAWSHASAI-ASRSSRGLFPFEILEFVNQELAKPKFTGECSAAYLSTIREF 972

Query: 1057 LEEF--SKKESVTSHQDKVSQPLREQILSHQDKIGHG-RESNPFPSACKAEA-------- 1105
            + E    +  ++   +       RE   S    +  G  E++      +++         
Sbjct: 973  VSEHIAQRLANIRKSRGMFEALEREPEWSEHTDLSMGASEADKVIVDNRSKVTEDQVRTF 1032

Query: 1106 ---CREKYVRAQIEPAT---AVGAL----------------------------------- 1124
               C  KYV+A+IEP +   AVGA                                    
Sbjct: 1033 LAICWTKYVKAKIEPGSTVGAVGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEII 1092

Query: 1125 -AAQSIGEPGTQMTLKTFHFAG---------------EVCEYIEEVFVPDDSFILIKLDM 1168
             AA+ I  P     L T                    +V   +EE + P+ ++I + +DM
Sbjct: 1093 NAAKVISTPIISCKLVTSDNEASARIVKGRLEKTHLRDVAGVLEEAWAPEYTYIGVIVDM 1152

Query: 1169 DRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF---NSKMYQMKQ 1225
              I+ L LE+ +D I++ I     ++  L +   S  ++  K+  + +     K Y++++
Sbjct: 1153 KTIQDLQLELTLDDIKWAIV----VAKKLKIKQESITVIPKKNRLRIYVDGPDKYYRLRE 1208

Query: 1226 L---LPSVVIKGVQGINRAVIHEEDVEGVTKYK----LLVEGDNLRDVMATYGVKGVKCS 1278
            L   LP VV+KGV  I RA+I+ +D +     K    LLVEG  L+ VM T G+ G   +
Sbjct: 1209 LKRALPEVVVKGVPTIRRAIINIKDKDDARGKKGDKELLVEGYGLQKVMTTQGIVGEHTT 1268

Query: 1279 SNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHG 1338
            SN+  E  + LGIEAAR  I+ EI+  M +HGMSID RH ML+ D+MT KGEVLGITR G
Sbjct: 1269 SNHVIETAQVLGIEAARRAIINEIQYTMASHGMSIDPRHVMLLGDVMTYKGEVLGITRFG 1328

Query: 1339 LAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 1398
            +AKMK+SVL LASFE T+DHLFDA+  G+TD I GVSE IIMG P  +    +  L   P
Sbjct: 1329 VAKMKDSVLMLASFEKTTDHLFDASALGKTDSILGVSESIIMGNPAAMTGTSMPALVTPP 1388

Query: 1399 RSEPVPRTLLFDN 1411
                 PR LLF++
Sbjct: 1389 PPLSKPRKLLFES 1401



 Score =  191 bits (486), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 100/247 (40%), Positives = 143/247 (57%), Gaps = 5/247 (2%)

Query: 97  SHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP 156
           +  ++  ++LY     R P+ +G+LDRR+GT +K A C TCG N  DCVGH+ YI L +P
Sbjct: 30  AEFEVTHRDLYTAT-DRLPVKNGVLDRRLGTTEKNAFCETCGLNSVDCVGHYAYIKLAVP 88

Query: 157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILET 216
           VFHIGYF+  I ILQ ICK  +CARVLL E     +  + R P+L  + R++L K +   
Sbjct: 89  VFHIGYFKHCITILQCICK--SCARVLLEEPDRRSYLKRFRRPSLENIQRQALIKAVNAL 146

Query: 217 TKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEA 276
            +K   CP+C   NG VKK   LKI H+K+  R KK    +E     ++ A++   ++  
Sbjct: 147 ARKTVYCPYCASTNGAVKKASALKIIHDKF--RAKKTVDEMEKWKKTFSSAIEAQKDLAM 204

Query: 277 HKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVIS 336
           +    + + LNPL+VL LF+ I  ED  LL +  E ++P + I   + VPP  IRPSV  
Sbjct: 205 YVNRAVHEELNPLKVLDLFKRISDEDCELLGLRPEFARPEEYIWQYISVPPVAIRPSVAQ 264

Query: 337 DLKSDND 343
           D  S+ D
Sbjct: 265 DGASNED 271



 Score =  178 bits (451), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 106/244 (43%), Positives = 151/244 (61%), Gaps = 14/244 (5%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ ISTPII+  L    +   ARIVKGRLE+T L +V   +EE + P+ 
Sbjct: 1084 GVPRIKEIINAAKVISTPIISCKLVTSDNEASARIVKGRLEKTHLRDVAGVLEEAWAPEY 1143

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF--- 880
            ++I + +DM  I+ L LE+ +D I++ I     ++  L +   S  ++  K+  + +   
Sbjct: 1144 TYIGVIVDMKTIQDLQLELTLDDIKWAIV----VAKKLKIKQESITVIPKKNRLRIYVDG 1199

Query: 881  NSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYK----LLVEGDNLRDVMAT 933
              K Y++++L   LP VV+KGV  I RA+I+ +D +     K    LLVEG  L+ VM T
Sbjct: 1200 PDKYYRLRELKRALPEVVVKGVPTIRRAIINIKDKDDARGKKGDKELLVEGYGLQKVMTT 1259

Query: 934  YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
             G+ G   +SN+  E  + LGIEAAR  I+ EI+  M +HGMSID RH ML+ D+MT KG
Sbjct: 1260 QGIVGEHTTSNHVIETAQVLGIEAARRAIINEIQYTMASHGMSIDPRHVMLLGDVMTYKG 1319

Query: 994  EVLG 997
            EVLG
Sbjct: 1320 EVLG 1323



 Score =  106 bits (265), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 48/68 (70%), Positives = 55/68 (80%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV+NSF++GLTPTEF FH + GREGLVDTAVKTAETGYMQRRL+K+LEDL   YD 
Sbjct: 829 PSKGFVRNSFYTGLTPTEFLFHAISGREGLVDTAVKTAETGYMQRRLMKALEDLVTHYDS 888

Query: 670 SFDAAFYG 677
           S   A  G
Sbjct: 889 SVRNAVGG 896



 Score = 62.4 bits (150), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 29/50 (58%), Positives = 38/50 (76%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM+ K NLVTPRNGE +IAA QDFIT  +LL++++ FF+R Q  +I S L
Sbjct: 515 LMSVKHNLVTPRNGEPVIAAIQDFITASFLLSRRDRFFDRCQFTQICSYL 564


>gi|403375855|gb|EJY87901.1| RNA polymerase III [Oxytricha trifallax]
          Length = 1365

 Score =  265 bits (678), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 132/271 (48%), Positives = 174/271 (64%), Gaps = 25/271 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + DVVLFNRQPSLH++SIMAHRA+V+P RT RFNECVCTPYNADFDGDEMN+HLPQ+EEA
Sbjct: 406 NGDVVLFNRQPSLHRVSIMAHRARVMPSRTLRFNECVCTPYNADFDGDEMNIHLPQSEEA 465

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A++LM  K NL+ PR+GE LIA TQDF+T  YL+TQK+ F NR
Sbjct: 466 RAE--------------ARILMDVKQNLLIPRSGEPLIAPTQDFLTSSYLITQKDKFLNR 511

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            + M+I +        I             P   ++   +WTGKQI +++L+PNR   V 
Sbjct: 512 NEFMQICAYFWDANEKI----------EIPPPTIIKPVELWTGKQIINVLLRPNRKSYVY 561

Query: 521 ANLKTKGRAYTA-NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            N   K R Y+   E  C  D +VI +NSEL+ G++ K+T+GSG K  +FY L RD   +
Sbjct: 562 VNTVVKERNYSGVGEHMCPNDGWVIFQNSELICGNLCKTTMGSGSKTGLFYSLQRDNSVE 621

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           VA   M R+++ ++ ++ + G SIGI DVTP
Sbjct: 622 VAAQCMLRVAKFSARWIGSHGMSIGISDVTP 652



 Score =  248 bits (634), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 169/470 (35%), Positives = 255/470 (54%), Gaps = 75/470 (15%)

Query: 998  NGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEF----LQDTSENFVRDI 1053
            N  PV LKRL+  +I +N+ ++   ++   +L    +    K +    +++ S  F+   
Sbjct: 862  NSLPVSLKRLMI-MIKENTKQTAKVINEDILLPFQIDQFKDKIYEICPVKNISMKFIEQF 920

Query: 1054 KKFLE----EFSKKESVTSHQDKVSQPLREQILSHQ--DKIGHGRESN-PFPSACKAEAC 1106
            K+FL+    + +K+ +    +D + Q   EQ +  +  DK+      N  F +  + E  
Sbjct: 921  KEFLDTIINQVAKQRTDLGLKDGLKQIPTEQEIKKERFDKVVQKLLRNFTFLTLSQLEDF 980

Query: 1107 RE----KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVC 1148
                  KY RAQI+P  AVGA+AAQSIGEPGTQMTLKTFHFAG              E+ 
Sbjct: 981  TNLVWLKYRRAQIQPGEAVGAVAAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEII 1040

Query: 1149 EYIEEV----------------------------------------FVPDDSFILIKLDM 1168
               +E+                                        + P   ++ +KLD+
Sbjct: 1041 NATKEISTPIISARLVNDVDLISARIVKGRIEKTKLGDIAKYIKEVYTPRGCYLEVKLDI 1100

Query: 1169 DRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFLILKPKDSSK-SFNSKMYQMK 1224
            D I  L LE+ I  ++  I +T  I      + V  H  + ++P D+++ +    M Q+K
Sbjct: 1101 DAITALKLELTIHDVKNAIIKTPKIKVKENKIEVIDHRVVHIQPHDTTRDNMYFSMQQLK 1160

Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYE 1284
             +LP+V +KG+  + RAVI +++ +  +K+ LLVEG  L+ VM+T G+      SN+  E
Sbjct: 1161 NMLPNVSVKGIPTVVRAVISKQE-QDQSKHHLLVEGYGLKQVMSTPGIDFRSTKSNHVIE 1219

Query: 1285 VYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKE 1344
              + LGIEAAR TI+ EI+  M++HGM+ID RH  L+AD+MT KG+VLGITR G++KMK 
Sbjct: 1220 TEQVLGIEAARQTIINEIQYTMQSHGMNIDPRHIQLLADIMTFKGQVLGITRFGVSKMKN 1279

Query: 1345 SVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            S L LASFE T+DHL+D+A + + D ISGVSECIIMG  + +GTGL K++
Sbjct: 1280 STLMLASFEMTTDHLYDSAVHCKKDEISGVSECIIMGNMIPIGTGLFKVV 1329



 Score =  200 bits (508), Expect = 6e-48,   Method: Compositional matrix adjust.
 Identities = 109/238 (45%), Positives = 160/238 (67%), Gaps = 5/238 (2%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ ISTPII+A L  D DL  ARIVKGR+E+T LG++ +YI+EV+ P  
Sbjct: 1032 GVPRIKEIINATKEISTPIISARLVNDVDLISARIVKGRIEKTKLGDIAKYIKEVYTPRG 1091

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFLILKPKDSSK-S 879
             ++ +KLD+D I  L LE+ I  ++  I +T  I      + V  H  + ++P D+++ +
Sbjct: 1092 CYLEVKLDIDAITALKLELTIHDVKNAIIKTPKIKVKENKIEVIDHRVVHIQPHDTTRDN 1151

Query: 880  FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
                M Q+K +LP+V +KG+  + RAVI +++ +  +K+ LLVEG  L+ VM+T G+   
Sbjct: 1152 MYFSMQQLKNMLPNVSVKGIPTVVRAVISKQE-QDQSKHHLLVEGYGLKQVMSTPGIDFR 1210

Query: 940  KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
               SN+  E  + LGIEAAR TI+ EI+  M++HGM+ID RH  L+AD+MT KG+VLG
Sbjct: 1211 STKSNHVIETEQVLGIEAARQTIINEIQYTMQSHGMNIDPRHIQLLADIMTFKGQVLG 1268



 Score =  144 bits (363), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 84/210 (40%), Positives = 121/210 (57%), Gaps = 9/210 (4%)

Query: 114 TPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSI 173
           TP   G LD RMG +++   C TC + L+DC GHFGY+ L LPVFH+GYF+  +NILQ  
Sbjct: 3   TPQKGGPLDTRMGISERGKFCETCKKALADCPGHFGYVKLELPVFHVGYFKHSVNILQCT 62

Query: 174 CKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVV 233
           CK   C+ +LL + +   +  ++R    S   R +L K I+   KKV +CPHCG  NG V
Sbjct: 63  CKE--CSNLLLDDVEKVKYIRQMRARNDSQ-ARIALFKTIVAQCKKVKICPHCGFYNGTV 119

Query: 234 KKCGLL--KISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEV 291
           KK      +I H+KYK     K A  +DL+ E++  +  N  IEA  K    + L+P +V
Sbjct: 120 KKMPNFPTRIIHDKYKG---GKGADQDDLINEFSHVMSLNGNIEASLKSSY-EELDPQKV 175

Query: 292 LQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
             +F  I  E++ L  M+ +L KP D+++T
Sbjct: 176 YNIFSRIKDENVILFDMDHKLCKPIDMLIT 205



 Score =  106 bits (265), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 48/57 (84%), Positives = 54/57 (94%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV NSF+SGLT TEFFFHT+GGREGLVDTAVKTAETGYMQRRL+K+LEDL V+YD
Sbjct: 778 KGFVGNSFYSGLTATEFFFHTIGGREGLVDTAVKTAETGYMQRRLMKALEDLSVKYD 834



 Score = 60.1 bits (144), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 27/50 (54%), Positives = 37/50 (74%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIAS 69
           ++LM  K NL+ PR+GE LIA TQDF+T  YL+TQK+ F NR + M+I +
Sbjct: 470 RILMDVKQNLLIPRSGEPLIAPTQDFLTSSYLITQKDKFLNRNEFMQICA 519



 Score = 43.1 bits (100), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 20/38 (52%), Positives = 28/38 (73%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 705
            D  +D+A + + D ISGVSECIIMG  + +GTGL K++
Sbjct: 1292 DHLYDSAVHCKKDEISGVSECIIMGNMIPIGTGLFKVV 1329


>gi|154300910|ref|XP_001550869.1| conserved hypothetical protein [Botryotinia fuckeliana B05.10]
          Length = 1468

 Score =  265 bits (678), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 132/277 (47%), Positives = 179/277 (64%), Gaps = 31/277 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIM+H AK+ P RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 463 DGDIVLFNRQPSLHKLSIMSHYAKIRPWRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 522

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EA+               LM  K+NL TP+NGE +I+ATQDFIT  YLL+ K  FF+R
Sbjct: 523 RTEAIN--------------LMGVKNNLSTPKNGEPIISATQDFITAAYLLSNKENFFDR 568

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                I   ++               +  +P + ++   +WTGKQ+FS++++PN+   + 
Sbjct: 569 KTFTNICMYMVD---------ANLHLQLPDPAI-LKPQALWTGKQVFSVLMRPNKQDNIL 618

Query: 521 ANLKTKGRAYTAN-------EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILL 573
            N+  K R +  +        +    D ++++RNSE++ G MDKST+GSG K ++FY++L
Sbjct: 619 VNVDAKCRDFVPSMVPKGFANDMEANDGWLVIRNSEVMCGLMDKSTVGSGKKDSIFYVIL 678

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           RD+G D AV AM RLS++++ YL N GFSIGI DV P
Sbjct: 679 RDYGPDAAVVAMNRLSKLSARYLTNMGFSIGISDVYP 715



 Score =  203 bits (517), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 113/271 (41%), Positives = 156/271 (57%), Gaps = 10/271 (3%)

Query: 79  FRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCG 138
           F+ L  G  + +D V Q   I++ +K LY  D  RT IPHG +D R+GT+ K   C TC 
Sbjct: 19  FKELKFGIQSNQDIVNQ-GVIEVSNKMLYNVDAGRTAIPHGPVDPRLGTSSKSGRCDTCD 77

Query: 139 QNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN 198
           + L DC GHFG++ LPLP FHIGY + +I ILQ++CK  TCARVLL + +   F  +LR 
Sbjct: 78  KGLQDCNGHFGHVRLPLPAFHIGYLKLIIMILQNVCK--TCARVLLTDAERRQFLKELRK 135

Query: 199 PALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYK--NRTKKKDAI 256
           P +  L R  + KKI E  +K S CPHC   NG ++K   ++++H+KY   N++     +
Sbjct: 136 PGIDNLKRTQICKKINEQCRKASQCPHCNATNGQIRKISPVRLAHDKYTKYNKSTAAKKV 195

Query: 257 VEDLLAEYN----EAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL 312
           V   +AEY     EA K N E+E H K  + + L+PL VL LF+ I   D  LL +N   
Sbjct: 196 VPPGMAEYQKSFEEAKKHNTELEKHVK-KVYEDLHPLRVLNLFKLITPSDCELLGINPAE 254

Query: 313 SKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
            +P   +   +  PP CIRPSV  D  S+ D
Sbjct: 255 GRPEMFLWQFVPAPPICIRPSVQQDGGSNED 285



 Score =  182 bits (462), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 134/387 (34%), Positives = 188/387 (48%), Gaps = 83/387 (21%)

Query: 1104 EACREKYVRAQIEPATAVGAL--------------------------------------- 1124
            E C EKY RA++EP  AVGA+                                       
Sbjct: 1067 ELCLEKYSRAKVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMNLTAGVPRIKEIIN 1126

Query: 1125 AAQSIGEPGTQMTL---KTFHFA------------GEVCEYIEEVFVPDDSFILIKLDMD 1169
            A+++I  P  +  L   K    A             EV  + E+++    + I + +D +
Sbjct: 1127 ASKTIATPFVKCPLLNSKELEVARLVKARMEKTYLHEVLHFAEDMWSAKSAIICLAVDTE 1186

Query: 1170 RIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFLILKPKDSSKSFNSK------- 1219
             +    +EV +++I + I + + +   S  L V G+   I    D S    ++       
Sbjct: 1187 YLVNRQIEVTVENIAHTILKNKKLKVRSEDLHVKGNCIFINVTHDGSVPTTARGAAAKGK 1246

Query: 1220 -------------MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDV 1266
                         ++ +K+ +P + I G     RA+I+  + + V +Y ++VEG  LR  
Sbjct: 1247 PSLDEGGSDLLLRVHHLKRAVPELAISGYPEATRAIINTSE-DAVPEYTVVVEGYGLRAC 1305

Query: 1267 MATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMT 1326
            + T GV G K  SN+  E+   LGIEAARSTI  EI  VM +  M ID RH  L+AD+MT
Sbjct: 1306 IGTEGVDGTKVKSNSVMEMRDVLGIEAARSTIANEIATVMAD--MDIDPRHMQLLADVMT 1363

Query: 1327 SKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNV 1386
             KGEVLGITR GL+KM++SVL LASFE T DHLFDAA   +TD I GVSECIIMG  M V
Sbjct: 1364 YKGEVLGITRFGLSKMRDSVLQLASFEKTPDHLFDAAAGMKTDRIEGVSECIIMGQTMGV 1423

Query: 1387 GTGLIKLLQAV---PRSEPVPRTLLFD 1410
            GTG  K+++A+   P    V  TL  D
Sbjct: 1424 GTGAFKVVRALDLTPEDLKVKPTLFED 1450



 Score =  147 bits (370), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 98/281 (34%), Positives = 149/281 (53%), Gaps = 27/281 (9%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ I+TP +   L    +L+ AR+VK R+E+T L EV  + E+++    
Sbjct: 1117 GVPRIKEIINASKTIATPFVKCPLLNSKELEVARLVKARMEKTYLHEVLHFAEDMWSAKS 1176

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFLILKPKDSSKSF 880
            + I + +D + +    +EV +++I + I + + +   S  L V G+   I    D S   
Sbjct: 1177 AIICLAVDTEYLVNRQIEVTVENIAHTILKNKKLKVRSEDLHVKGNCIFINVTHDGSVPT 1236

Query: 881  NS--------------------KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKL 920
             +                    +++ +K+ +P + I G     RA+I+  + + V +Y +
Sbjct: 1237 TARGAAAKGKPSLDEGGSDLLLRVHHLKRAVPELAISGYPEATRAIINTSE-DAVPEYTV 1295

Query: 921  LVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFR 980
            +VEG  LR  + T GV G K  SN+  E+   LGIEAARSTI  EI  VM +  M ID R
Sbjct: 1296 VVEGYGLRACIGTEGVDGTKVKSNSVMEMRDVLGIEAARSTIANEIATVMAD--MDIDPR 1353

Query: 981  HPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDP 1021
            H  L+AD+MT KGEVLG  T   L ++ D ++   S    P
Sbjct: 1354 HMQLLADVMTYKGEVLGI-TRFGLSKMRDSVLQLASFEKTP 1393



 Score =  104 bits (260), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 47/59 (79%), Positives = 50/59 (84%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV NSFF+GLTP EF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 839 PAKGFVANSFFTGLTPYEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSTQYD 897



 Score = 56.2 bits (134), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/40 (62%), Positives = 31/40 (77%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           LM  K+NL TP+NGE +I+ATQDFIT  YLL+ K  FF+R
Sbjct: 529 LMGVKNNLSTPKNGEPIISATQDFITAAYLLSNKENFFDR 568



 Score = 48.9 bits (115), Expect = 0.023,   Method: Compositional matrix adjust.
 Identities = 29/57 (50%), Positives = 34/57 (59%), Gaps = 3/57 (5%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV---PRSEPVPRTLLFD 721
            D  FDAA   +TD I GVSECIIMG  M VGTG  K+++A+   P    V  TL  D
Sbjct: 1394 DHLFDAAAGMKTDRIEGVSECIIMGQTMGVGTGAFKVVRALDLTPEDLKVKPTLFED 1450


>gi|50549343|ref|XP_502142.1| YALI0C22550p [Yarrowia lipolytica]
 gi|49648009|emb|CAG82462.1| YALI0C22550p [Yarrowia lipolytica CLIB122]
          Length = 1483

 Score =  265 bits (678), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 136/276 (49%), Positives = 182/276 (65%), Gaps = 29/276 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH+LSI+AH A++ P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 459 DGDVVLFNRQPSLHRLSILAHFAQIRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 518

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EA+               LM  K NLVTPR+GE +IAATQDFITG +L+++K+   +R
Sbjct: 519 RTEAM--------------CLMGVKHNLVTPRSGEPIIAATQDFITGSFLISKKDYMIDR 564

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
               R    L+A  SD  G ++        P    +   +WTGKQ+FSL+++PN+   V 
Sbjct: 565 ----RTFCQLLAMMSD--GDMQ----FDIPPPAIQKPVQLWTGKQVFSLLIRPNKSSKVI 614

Query: 521 ANLKTKGRAYTANEEFCHR-----DSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL  K + +    +   R     D ++++RNS+++ G+MDK+TLG G K +VFY +LRD
Sbjct: 615 INLDAKNKTFQPPPQGYPRDMSPNDGFLVIRNSQVMCGAMDKATLGDGKKDSVFYSILRD 674

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           +G D A  AM R++++ + +L  RGFSIGI DVTPG
Sbjct: 675 YGPDEAAGAMNRMAKLCARWLGGRGFSIGISDVTPG 710



 Score =  208 bits (529), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 121/295 (41%), Positives = 180/295 (61%), Gaps = 31/295 (10%)

Query: 1145 GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSG 1201
            G++  YI++ +    + + +++D + I  L LE+D+D IR  I +   +    G +++  
Sbjct: 1178 GDIAHYIQDEYSYAKASVRVRIDFNTIDHLLLEIDMDQIREAIIKAPKLKLKPGQVSIEE 1237

Query: 1202 HSFLILK-PKDSSKSFNS-----------------------KMYQMKQLLPSVVIKGVQG 1237
              ++ +    D+ K   S                       +   +K++LP+VV+KG   
Sbjct: 1238 EKYIRVDIESDAVKKNGSTTIIDTDGEIFEEGVESDTAMFLRTQHLKRVLPNVVVKGFTD 1297

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            I+RAVI+  + +    ++LLVEG  LR VM T GV G + S+N+  EV + LGIEAAR++
Sbjct: 1298 ISRAVINIREKDNT--HELLVEGYGLRHVMTTSGVIGTQTSTNHVLEVKEVLGIEAARAS 1355

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI   M  HGMS+D RH  L+ D+MT KG+VLGITR GLAKM++SVL LASFE T+D
Sbjct: 1356 IIHEIDYTMSKHGMSVDPRHITLLGDVMTYKGDVLGITRFGLAKMRDSVLQLASFEKTTD 1415

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ--AVPRSEPVPRTLLFD 1410
            HLFDAAFY +TD + GVSECII+G  M++GTG  K+LQ  A+ + +  P+ LLF+
Sbjct: 1416 HLFDAAFYMKTDDVEGVSECIILGQGMSIGTGAFKVLQPLALDKVKIGPKPLLFE 1470



 Score =  192 bits (488), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 103/263 (39%), Positives = 147/263 (55%), Gaps = 3/263 (1%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G IE        + + S +++ +++LY     R P+ +G LD RMG +   + C TC + 
Sbjct: 22  GGIEFGALSPQEILKLSEVEVATRDLYDLQKGRAPMEYGALDPRMGVSSNMSKCKTCAEP 81

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
           L+ C GHFG++ L LP FHIGYF+  I+ILQ++CK+  CAR+LL +E    F  +LR P 
Sbjct: 82  LATCPGHFGHVKLALPCFHIGYFKATISILQNVCKD--CARILLSDEDRRKFLTELRRPG 139

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDL 260
           +  L R  + KK+ E  KK   C HC  INGVVKK G LKI H+K+++  KK      + 
Sbjct: 140 IDNLRRMQILKKVNEQCKKQRRCVHCNSINGVVKKAGPLKIIHDKFRHVGKKIPEEKTEF 199

Query: 261 LAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
              +N A +  P++E  +K  +   LNPL+V  LF  I   D  LL M+    +P   I 
Sbjct: 200 DNSFNTAKESIPDVERLQKKAM-DDLNPLKVFNLFREILPMDCELLGMDPGKGRPETYIW 258

Query: 321 TRLLVPPNCIRPSVISDLKSDND 343
             +  PP CIRPSV+ D  S+ D
Sbjct: 259 RYMPAPPVCIRPSVMQDSASNED 281



 Score =  177 bits (449), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 105/261 (40%), Positives = 156/261 (59%), Gaps = 29/261 (11%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIIT  L+ +T+L  ARIVKGR+E+T LG++  YI++ +    
Sbjct: 1133 GVPRIKEIINASKAISTPIITTVLNNETELQAARIVKGRIEKTLLGDIAHYIQDEYSYAK 1192

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSFLILK-PKDSSKS 879
            + + +++D + I  L LE+D+D IR  I +   +    G +++    ++ +    D+ K 
Sbjct: 1193 ASVRVRIDFNTIDHLLLEIDMDQIREAIIKAPKLKLKPGQVSIEEEKYIRVDIESDAVKK 1252

Query: 880  FNS-----------------------KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVT 916
              S                       +   +K++LP+VV+KG   I+RAVI+  + +   
Sbjct: 1253 NGSTTIIDTDGEIFEEGVESDTAMFLRTQHLKRVLPNVVVKGFTDISRAVINIREKDNT- 1311

Query: 917  KYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMS 976
             ++LLVEG  LR VM T GV G + S+N+  EV + LGIEAAR++I+ EI   M  HGMS
Sbjct: 1312 -HELLVEGYGLRHVMTTSGVIGTQTSTNHVLEVKEVLGIEAARASIIHEIDYTMSKHGMS 1370

Query: 977  IDFRHPMLVADLMTSKGEVLG 997
            +D RH  L+ D+MT KG+VLG
Sbjct: 1371 VDPRHITLLGDVMTYKGDVLG 1391



 Score =  100 bits (249), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 48/79 (60%), Positives = 57/79 (72%), Gaps = 4/79 (5%)

Query: 599 RGFSIGIGDVTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVK 658
           R FS+      P +GFV+NSF+SGL P EF FH + GREGLVDTAVKTAETGYM RRL+K
Sbjct: 826 RKFSV----TPPSKGFVRNSFYSGLDPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMK 881

Query: 659 SLEDLCVQYDMSFDAAFYG 677
           SLEDL  +YD +   +  G
Sbjct: 882 SLEDLSARYDSTVRTSSNG 900



 Score = 76.6 bits (187), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 33/42 (78%), Positives = 37/42 (88%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            +AC  KY +AQ+EP TAVGA+ AQSIGEPGTQMTLKTFHFAG
Sbjct: 1083 QACLRKYQKAQVEPGTAVGAIGAQSIGEPGTQMTLKTFHFAG 1124



 Score = 57.4 bits (137), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 29/56 (51%), Positives = 40/56 (71%), Gaps = 2/56 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ--AVPRSEPVPRTLLFD 721
            D  FDAAFY +TD + GVSECII+G  M++GTG  K+LQ  A+ + +  P+ LLF+
Sbjct: 1415 DHLFDAAFYMKTDDVEGVSECIILGQGMSIGTGAFKVLQPLALDKVKIGPKPLLFE 1470



 Score = 54.7 bits (130), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 24/40 (60%), Positives = 32/40 (80%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           LM  K NLVTPR+GE +IAATQDFITG +L+++K+   +R
Sbjct: 525 LMGVKHNLVTPRSGEPIIAATQDFITGSFLISKKDYMIDR 564


>gi|168009054|ref|XP_001757221.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162691719|gb|EDQ78080.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 1397

 Score =  265 bits (678), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 178/470 (37%), Positives = 241/470 (51%), Gaps = 75/470 (15%)

Query: 998  NGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFL 1057
            +G P  L R+L    A   S     L   EI  L NE L   +   +T   F   +KKF+
Sbjct: 922  DGAPFNLDRMLMKTKATCPSYGQLGLPPTEIEKLFNERLTKPDMTSETVGAFKTSLKKFM 981

Query: 1058 EEFSKKESVTSHQDKVSQPLR------EQILSHQDKIGHGRESNPFPSACKAE----ACR 1107
            +   K     S + K+  PL       + +L        G  S      C  +     C 
Sbjct: 982  DSCIKDN--ISTRTKLGLPLDCNGGPDQTLLESTATYISGLTSRQL-EICLLQVFLDTCI 1038

Query: 1108 EKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYIEE 1153
            ++Y   ++EP  AVGA+ AQSIGEPGTQMTLKTFHFAG              E+    + 
Sbjct: 1039 KRYHMKRVEPGAAVGAVGAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKN 1098

Query: 1154 VFVPDDSFILI----------------------------------------KLDMDRIRL 1173
            +  P  + +L+                                        KLDM RI  
Sbjct: 1099 ISTPIITAVLVSGNDEKAARIVKGRIEKTTLGEVAKSIKTVLRASQAIISVKLDMKRIDA 1158

Query: 1174 LHLEVDIDSIRYCIERTRGIS-GHLT---VSGHSFLILKPKDSSKSFNSKMYQMKQLLPS 1229
            L L+++ D++   I +T  I   H+    V     +++ P          ++ +  +LP 
Sbjct: 1159 LQLDINSDTVALAIVQTPKIKLKHVNIRIVDRDKLIVIPPDQDKGKLYFYLHSLCNMLPK 1218

Query: 1230 VVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTL 1289
            V++KG+  + RAVI++E  +GV  Y LLVEG NL+ VM   GV G    SN+  E  +TL
Sbjct: 1219 VIVKGIPSVERAVINKE--KGV--YNLLVEGTNLKAVMGISGVNGKLTKSNHVIEAEQTL 1274

Query: 1290 GIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNL 1349
            GIEAAR+ I+ EI+  M +HGM+ID RH ML+AD+MT KGEVLGITR G+AKMK+SVL L
Sbjct: 1275 GIEAARNVIIDEIQYTMGSHGMTIDARHMMLLADVMTYKGEVLGITRFGIAKMKDSVLML 1334

Query: 1350 ASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPR 1399
            ASFE T+DHLFDAA +G+ D I GVSECIIMG+PM +GTGL K+ Q V +
Sbjct: 1335 ASFEKTTDHLFDAAIHGRVDKIEGVSECIIMGIPMPIGTGLFKIRQKVEK 1384



 Score =  256 bits (654), Expect = 6e-65,   Method: Compositional matrix adjust.
 Identities = 128/273 (46%), Positives = 179/273 (65%), Gaps = 27/273 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIM+HRA+++P RT RFNE VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 463 DGDIVLFNRQPSLHRMSIMSHRARIMPWRTLRFNESVCNPYNADFDGDEMNLHVPQTEEA 522

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL              +LM   +NL TP+NGE+L+A+TQDF+T  YL T+K+ F++R
Sbjct: 523 RTEAL--------------MLMGVANNLCTPKNGEILVASTQDFLTSSYLFTRKDTFYDR 568

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A T   A   + D ++   +          P + ++   +WTGKQ+FS++++PN    V 
Sbjct: 569 A-TFTQACVYMGDAAENIDL--------PTPSI-IKPMELWTGKQLFSVLVRPNAKTRVF 618

Query: 521 ANLKTKGRAY--TANE-EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFG 577
            NL +  + Y   AN+   C  D YV  RNSEL+ G + K+TLG+G K  +F +LLRD+G
Sbjct: 619 VNLVSYEKNYDKKANKGSMCPTDGYVYFRNSELICGQLGKATLGNGNKDGLFTVLLRDYG 678

Query: 578 EDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
            + A   M RL+++++ ++ N GFSIGI DV P
Sbjct: 679 NEAAAVCMNRLAKLSARWIGNHGFSIGIDDVAP 711



 Score =  199 bits (505), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 114/238 (47%), Positives = 152/238 (63%), Gaps = 8/238 (3%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+NISTPIITA L    D   ARIVKGR+E+TTLGEV + I+ V     
Sbjct: 1085 GVPRIKEIINASKNISTPIITAVLVSGNDEKAARIVKGRIEKTTLGEVAKSIKTVLRASQ 1144

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS-GHLT---VSGHSFLILKPKDSSKS 879
            + I +KLDM RI  L L+++ D++   I +T  I   H+    V     +++ P      
Sbjct: 1145 AIISVKLDMKRIDALQLDINSDTVALAIVQTPKIKLKHVNIRIVDRDKLIVIPPDQDKGK 1204

Query: 880  FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
                ++ +  +LP V++KG+  + RAVI++E  +GV  Y LLVEG NL+ VM   GV G 
Sbjct: 1205 LYFYLHSLCNMLPKVIVKGIPSVERAVINKE--KGV--YNLLVEGTNLKAVMGISGVNGK 1260

Query: 940  KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
               SN+  E  +TLGIEAAR+ I+ EI+  M +HGM+ID RH ML+AD+MT KGEVLG
Sbjct: 1261 LTKSNHVIEAEQTLGIEAARNVIIDEIQYTMGSHGMTIDARHMMLLADVMTYKGEVLG 1318



 Score =  183 bits (464), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 102/252 (40%), Positives = 156/252 (61%), Gaps = 14/252 (5%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           GT++K+D V+  S + +    LY   P+R P P+ ++D R+GT  K+  C+TC   L+DC
Sbjct: 34  GTMSKQDIVKA-SELHVYESMLYTM-PERNPAPYSVVDTRLGTTNKKGECSTCFGKLADC 91

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFG+  L +PVFHIGY + ++ ILQ ICK  +CAR+L+ EE+      K+RNP +  L
Sbjct: 92  PGHFGHTKLEMPVFHIGYLKNILQILQCICK--SCARILMPEEECKLILRKMRNPRIEVL 149

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKCGL--LKISHEKYKNRTKKKDAIVEDLLA 262
            R+++ KK+++  K+V VC  CG+ NGVVKK     +K+ H+KY      K    E+++ 
Sbjct: 150 QRRAVLKKVIDRCKRVRVCTRCGDYNGVVKKMAQPPVKLIHDKYGKALDLK----EEMIV 205

Query: 263 EYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTR 322
              +A+K  PE++      +   L+P+ VLQLFE++  +D  +L + AE  +P  LI+T 
Sbjct: 206 SLEDAMKCKPELKNCINR-VYDNLDPMRVLQLFESMIEQDCEVLDL-AE--RPEKLIVTH 261

Query: 323 LLVPPNCIRPSV 334
           L+VPP  IRPSV
Sbjct: 262 LIVPPVAIRPSV 273



 Score =  108 bits (271), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 51/63 (80%), Positives = 56/63 (88%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D TP G+GFV NSF+SGL+ TEFFFHTMGGREGLVDTAVKTAETGYM RRL+K+LEDL  
Sbjct: 831 DRTPQGKGFVANSFYSGLSATEFFFHTMGGREGLVDTAVKTAETGYMSRRLMKALEDLSA 890

Query: 666 QYD 668
           QYD
Sbjct: 891 QYD 893



 Score = 58.2 bits (139), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 26/43 (60%), Positives = 32/43 (74%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPR 710
            D  FDAA +G+ D I GVSECIIMG+PM +GTGL K+ Q V +
Sbjct: 1342 DHLFDAAIHGRVDKIEGVSECIIMGIPMPIGTGLFKIRQKVEK 1384



 Score = 57.4 bits (137), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 23/42 (54%), Positives = 34/42 (80%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRA 62
           +LM   +NL TP+NGE+L+A+TQDF+T  YL T+K+ F++RA
Sbjct: 528 MLMGVANNLCTPKNGEILVASTQDFLTSSYLFTRKDTFYDRA 569


>gi|347831184|emb|CCD46881.1| similar to DNA-directed RNA polymerase iii largest subunit
           [Botryotinia fuckeliana]
          Length = 1442

 Score =  265 bits (677), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 132/277 (47%), Positives = 179/277 (64%), Gaps = 31/277 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIM+H AK+ P RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 466 DGDIVLFNRQPSLHKLSIMSHYAKIRPWRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 525

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EA+               LM  K+NL TP+NGE +I+ATQDFIT  YLL+ K  FF+R
Sbjct: 526 RTEAIN--------------LMGVKNNLSTPKNGEPIISATQDFITAAYLLSNKENFFDR 571

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                I   ++               +  +P + ++   +WTGKQ+FS++++PN+   + 
Sbjct: 572 KTFTNICMYMVD---------ANLHLQLPDPAI-LKPQALWTGKQVFSVLMRPNKQDNIL 621

Query: 521 ANLKTKGRAYTAN-------EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILL 573
            N+  K R +  +        +    D ++++RNSE++ G MDKST+GSG K ++FY++L
Sbjct: 622 VNVDAKCRDFVPSMVPKGFANDMEANDGWLVIRNSEVMCGLMDKSTVGSGKKDSIFYVIL 681

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           RD+G D AV AM RLS++++ YL N GFSIGI DV P
Sbjct: 682 RDYGPDAAVVAMNRLSKLSARYLTNMGFSIGISDVYP 718



 Score =  225 bits (573), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 149/358 (41%), Positives = 198/358 (55%), Gaps = 54/358 (15%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCE 1149
            E C EKY RA++EP  AVGA+ AQSIGEPGTQMTLKTFHFAG              E+  
Sbjct: 1070 ELCLEKYSRAKVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMNLTAGVPRIKEIIN 1129

Query: 1150 YIEEVFVPDDSFILI---KLDMDRIRLLH--------LEVDIDSIRYCIERTRGI---SG 1195
              + +  P     L+   +L++ R+   H        +EV +++I + I + + +   S 
Sbjct: 1130 ASKTIATPFVKCPLLNSKELEVARLVKAHTEYLVNRQIEVTVENIAHTILKNKKLKVRSE 1189

Query: 1196 HLTVSGHSFLILKPKDSSKSFNSK--------------------MYQMKQLLPSVVIKGV 1235
             L V G+   I    D S    ++                    ++ +K+ +P + I G 
Sbjct: 1190 DLHVKGNCIFINVTHDGSVPTTARGAAAKGKPSLDEGGSDLLLRVHHLKRAVPELAISGY 1249

Query: 1236 QGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAAR 1295
                RA+I+  + + V +Y ++VEG  LR  + T GV G K  SN+  E+   LGIEAAR
Sbjct: 1250 PEATRAIINTSE-DAVPEYTVVVEGYGLRACIGTEGVDGTKVKSNSVMEMRDVLGIEAAR 1308

Query: 1296 STIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENT 1355
            STI  EI  VM +  M ID RH  L+AD+MT KGEVLGITR GL+KM++SVL LASFE T
Sbjct: 1309 STIANEIATVMAD--MDIDPRHMQLLADVMTYKGEVLGITRFGLSKMRDSVLQLASFEKT 1366

Query: 1356 SDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV---PRSEPVPRTLLFD 1410
             DHLFDAA   +TD I GVSECIIMG  M VGTG  K+++A+   P    V  TL  D
Sbjct: 1367 PDHLFDAAAGMKTDRIEGVSECIIMGQTMGVGTGAFKVVRALDLTPEDLKVKPTLFED 1424



 Score =  203 bits (516), Expect = 6e-49,   Method: Compositional matrix adjust.
 Identities = 113/271 (41%), Positives = 156/271 (57%), Gaps = 10/271 (3%)

Query: 79  FRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCG 138
           F+ L  G  + +D V Q   I++ +K LY  D  RT IPHG +D R+GT+ K   C TC 
Sbjct: 22  FKELKFGIQSNQDIVNQ-GVIEVSNKMLYNVDAGRTAIPHGPVDPRLGTSSKSGRCDTCD 80

Query: 139 QNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN 198
           + L DC GHFG++ LPLP FHIGY + +I ILQ++CK  TCARVLL + +   F  +LR 
Sbjct: 81  KGLQDCNGHFGHVRLPLPAFHIGYLKLIIMILQNVCK--TCARVLLTDAERRQFLKELRK 138

Query: 199 PALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYK--NRTKKKDAI 256
           P +  L R  + KKI E  +K S CPHC   NG ++K   ++++H+KY   N++     +
Sbjct: 139 PGIDNLKRTQICKKINEQCRKASQCPHCNATNGQIRKISPVRLAHDKYTKYNKSTAAKKV 198

Query: 257 VEDLLAEYN----EAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL 312
           V   +AEY     EA K N E+E H K  + + L+PL VL LF+ I   D  LL +N   
Sbjct: 199 VPPGMAEYQKSFEEAKKHNTELEKHVK-KVYEDLHPLRVLNLFKLITPSDCELLGINPAE 257

Query: 313 SKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
            +P   +   +  PP CIRPSV  D  S+ D
Sbjct: 258 GRPEMFLWQFVPAPPICIRPSVQQDGGSNED 288



 Score =  121 bits (304), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 96/262 (36%), Positives = 136/262 (51%), Gaps = 18/262 (6%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ I+TP +   L    +L+ AR+VK   E     ++     EV V + 
Sbjct: 1120 GVPRIKEIINASKTIATPFVKCPLLNSKELEVARLVKAHTEYLVNRQI-----EVTVENI 1174

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNS- 882
            +  ++K    ++R   L V  + I   I  T   S   T  G +    K K S     S 
Sbjct: 1175 AHTILKNKKLKVRSEDLHVKGNCI--FINVTHDGSVPTTARGAA---AKGKPSLDEGGSD 1229

Query: 883  ---KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
               +++ +K+ +P + I G     RA+I+  + + V +Y ++VEG  LR  + T GV G 
Sbjct: 1230 LLLRVHHLKRAVPELAISGYPEATRAIINTSE-DAVPEYTVVVEGYGLRACIGTEGVDGT 1288

Query: 940  KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG 999
            K  SN+  E+   LGIEAARSTI  EI  VM +  M ID RH  L+AD+MT KGEVLG  
Sbjct: 1289 KVKSNSVMEMRDVLGIEAARSTIANEIATVMAD--MDIDPRHMQLLADVMTYKGEVLGI- 1345

Query: 1000 TPVELKRLLDDIIAKNSSRSDP 1021
            T   L ++ D ++   S    P
Sbjct: 1346 TRFGLSKMRDSVLQLASFEKTP 1367



 Score =  104 bits (260), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 47/59 (79%), Positives = 50/59 (84%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV NSFF+GLTP EF FH M GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 842 PAKGFVANSFFTGLTPYEFIFHAMSGREGLVDTAVKTAETGYMSRRLMKSLEDLSTQYD 900



 Score = 56.2 bits (134), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/40 (62%), Positives = 31/40 (77%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           LM  K+NL TP+NGE +I+ATQDFIT  YLL+ K  FF+R
Sbjct: 532 LMGVKNNLSTPKNGEPIISATQDFITAAYLLSNKENFFDR 571



 Score = 48.5 bits (114), Expect = 0.026,   Method: Compositional matrix adjust.
 Identities = 29/57 (50%), Positives = 34/57 (59%), Gaps = 3/57 (5%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV---PRSEPVPRTLLFD 721
            D  FDAA   +TD I GVSECIIMG  M VGTG  K+++A+   P    V  TL  D
Sbjct: 1368 DHLFDAAAGMKTDRIEGVSECIIMGQTMGVGTGAFKVVRALDLTPEDLKVKPTLFED 1424


>gi|392572905|gb|EIW66048.1| hypothetical protein TREMEDRAFT_72470 [Tremella mesenterica DSM
           1558]
          Length = 1457

 Score =  265 bits (677), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 134/278 (48%), Positives = 174/278 (62%), Gaps = 31/278 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+ LFNRQPSLHKLSIM HR +V P RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 467 DGDIALFNRQPSLHKLSIMCHRVRVRPWRTFRLNECVCNPYNADFDGDEMNLHIPQTEEA 526

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL               LM+ K NLVTPRNGE +IAA QDFITG +LL++++ FF+R
Sbjct: 527 RTEALE--------------LMSVKKNLVTPRNGEPIIAAIQDFITGSFLLSRRDRFFSR 572

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q  +I S       DI             P    +   +WTGKQIF++++KPNR   + 
Sbjct: 573 QQFTQICSFFCDADLDI----------DIPPPTIWKPQRLWTGKQIFNVLMKPNRRSRIK 622

Query: 521 ANLKTKGRAYTANEEFCH-------RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILL 573
            NL+ K R     +   H        D Y+++ NSE++ G  DK+T+G G K +VF ++L
Sbjct: 623 VNLEAKCRTMKDPDPKDHFPPDMSPNDGYLVIVNSEIMCGVFDKNTVGDGKKKSVFGVIL 682

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           RD+G D A   M RL+++ + +L N+GFS+GI DV PG
Sbjct: 683 RDYGPDEAAAGMNRLAKLAARWLANQGFSLGINDVIPG 720



 Score =  196 bits (498), Expect = 9e-47,   Method: Compositional matrix adjust.
 Identities = 134/373 (35%), Positives = 196/373 (52%), Gaps = 70/373 (18%)

Query: 1104 EACREKYVRAQIEPATAVGAL--------------------------------------- 1124
            E CR +Y+R++IEP + VGA+                                       
Sbjct: 1073 EICRIRYLRSKIEPGSTVGAVGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIIN 1132

Query: 1125 AAQSIGEPGTQMTL---KTFHFA------------GEVCEYIEEVFVPDDSFILIKLDMD 1169
            A+++I  P     L    + H A            G++   IEE +     +I++ +D++
Sbjct: 1133 ASKTISTPIITAELVNATSEHAARIVKGRVEKTVLGDIASVIEESWSNAMGYIMVHIDLE 1192

Query: 1170 RIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSF-----LILKPK-----DSSKSFNSK 1219
             ++ L LE+ +DSI+   E   G    LT S  SF     + + P+     D ++    +
Sbjct: 1193 AVQRLQLEITLDSIK---ESLIGSKLKLTQSSFSFHKGSRIQIYPEVSGKGDKTEGLYER 1249

Query: 1220 MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSS 1279
            +  +K+ LP V IKG+   +R VI  +D +     +LLV G  L +VM T GV G +  +
Sbjct: 1250 LKALKRALPDVQIKGLPQADRGVI-TKDEKNQNINRLLVTGYGLAEVMGTDGVDGRRTKT 1308

Query: 1280 NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGL 1339
            N+  E  + LGIEAAR+TI  EI+  M++HGMSID RH ML+ D+MT KGEVLGITR G+
Sbjct: 1309 NHVMETAEVLGIEAARTTIYNEIQHTMQSHGMSIDPRHVMLLGDVMTYKGEVLGITRFGV 1368

Query: 1340 AKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPM-NVGTGLIKLLQAVP 1398
             KMK+SVL LASFE T+DHLFDA+ + + D I GVSECIIMG P  + GT +  ++   P
Sbjct: 1369 QKMKDSVLMLASFEKTTDHLFDASLFSKKDEIQGVSECIIMGTPAPSCGTSMASIVTPAP 1428

Query: 1399 RSEPVPRTLLFDN 1411
               P  + LLF++
Sbjct: 1429 LL-PGRKRLLFED 1440



 Score =  189 bits (481), Expect = 9e-45,   Method: Compositional matrix adjust.
 Identities = 108/273 (39%), Positives = 155/273 (56%), Gaps = 16/273 (5%)

Query: 97  SHIQIVSKNLYC--QDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLP 154
           S +++   +LY   +D  RT    G LD RMG N+K   C TCG+  + CVGH+G+I L 
Sbjct: 40  SEVEVSVADLYVNNEDGSRTTAKDGPLDGRMGPNEKGRRCLTCGEEPAKCVGHYGFIKLA 99

Query: 155 LPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKIL 214
           LPVFHIGYFR  IN+L  ICK  TC+R+LL  ++   F  + R+  +    R S  K +L
Sbjct: 100 LPVFHIGYFRPTINMLSCICK--TCSRILLPRQERETFLRRFRHANIDSRQRTSANKSVL 157

Query: 215 ETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEI 274
              KK ++C HCG  NG VKK G +KI HE +  R KK  A+  D  +++  A+    +I
Sbjct: 158 TLCKKQNICAHCGAANGPVKKVGAMKIVHEPF--RAKKMGAMKADFESKFTTAIA--DDI 213

Query: 275 EAHKKFG-LIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPS 333
                 G +++ LNP++VL LF+ I  ED  LL ++ E+ +P D I   + VPP  IRPS
Sbjct: 214 TLKGNLGSVVEDLNPVKVLALFQRITAEDCELLSLHPEVGRPEDYIWRYVSVPPPAIRPS 273

Query: 334 VISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVL 366
           V S+  ++ D +         KL+ +AH  K+L
Sbjct: 274 VASESGNNEDDLTV-------KLAEIAHYNKLL 299



 Score =  178 bits (452), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 108/244 (44%), Positives = 150/244 (61%), Gaps = 14/244 (5%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA L   T    ARIVKGR+E+T LG++   IEE +    
Sbjct: 1123 GVPRIKEIINASKTISTPIITAELVNATSEHAARIVKGRVEKTVLGDIASVIEESWSNAM 1182

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSF-----LILKPK---- 874
             +I++ +D++ ++ L LE+ +DSI+   E   G    LT S  SF     + + P+    
Sbjct: 1183 GYIMVHIDLEAVQRLQLEITLDSIK---ESLIGSKLKLTQSSFSFHKGSRIQIYPEVSGK 1239

Query: 875  -DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMAT 933
             D ++    ++  +K+ LP V IKG+   +R VI  +D +     +LLV G  L +VM T
Sbjct: 1240 GDKTEGLYERLKALKRALPDVQIKGLPQADRGVI-TKDEKNQNINRLLVTGYGLAEVMGT 1298

Query: 934  YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
             GV G +  +N+  E  + LGIEAAR+TI  EI+  M++HGMSID RH ML+ D+MT KG
Sbjct: 1299 DGVDGRRTKTNHVMETAEVLGIEAARTTIYNEIQHTMQSHGMSIDPRHVMLLGDVMTYKG 1358

Query: 994  EVLG 997
            EVLG
Sbjct: 1359 EVLG 1362



 Score =  101 bits (252), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 43/61 (70%), Positives = 53/61 (86%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV+NSF++GL+PTEF FH + GREGLVDTAVKTAETGYM RRL+K++EDL   YD+
Sbjct: 843 PSKGFVRNSFYTGLSPTEFLFHAISGREGLVDTAVKTAETGYMARRLMKAMEDLSTHYDL 902

Query: 670 S 670
           S
Sbjct: 903 S 903



 Score = 63.5 bits (153), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 29/48 (60%), Positives = 38/48 (79%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIAS 69
           LM+ K NLVTPRNGE +IAA QDFITG +LL++++ FF+R Q  +I S
Sbjct: 533 LMSVKKNLVTPRNGEPIIAAIQDFITGSFLLSRRDRFFSRQQFTQICS 580



 Score = 42.0 bits (97), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 23/56 (41%), Positives = 33/56 (58%), Gaps = 2/56 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPM-NVGTGLIKLLQAVPRSEPVPRTLLFDN 722
            D  FDA+ + + D I GVSECIIMG P  + GT +  ++   P   P  + LLF++
Sbjct: 1386 DHLFDASLFSKKDEIQGVSECIIMGTPAPSCGTSMASIVTPAPLL-PGRKRLLFED 1440


>gi|313241408|emb|CBY33677.1| unnamed protein product [Oikopleura dioica]
          Length = 1360

 Score =  265 bits (677), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 135/268 (50%), Positives = 180/268 (67%), Gaps = 26/268 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH+ S+M+H+ KV+P +TFRFNECVC PYNADFDGDEMNVHLPQT EA
Sbjct: 391 DGDIVLFNRQPSLHRQSMMSHQVKVMPWKTFRFNECVCAPYNADFDGDEMNVHLPQTNEA 450

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R+EA+              VLM  KSN +T R+GE L+A+ QDFIT  YLLTQK+ FF  
Sbjct: 451 RSEAM--------------VLMGVKSNTLTCRSGEPLVASIQDFITAMYLLTQKDVFFTH 496

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            + +R+ +T+ A          +   R  +P + +R   +W+GKQ+FS  ++  +   + 
Sbjct: 497 QEFLRLITTVTARN--------KGRLRIPHPCI-LRPTPLWSGKQVFSSEIEKGK--WIW 545

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
                 G +  + E  C+ DS+V++RNSEL+AG+MDK++LGSG K  VFY+L RD+GE+ 
Sbjct: 546 RGTACVGYSKNSPEMICN-DSWVLIRNSELVAGTMDKNSLGSGSKKQVFYMLTRDYGEEA 604

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           A  AMWR+ R+   YL NRGFSIGIGDV
Sbjct: 605 AAQAMWRMCRIGPRYLSNRGFSIGIGDV 632



 Score =  246 bits (627), Expect = 9e-62,   Method: Compositional matrix adjust.
 Identities = 172/500 (34%), Positives = 259/500 (51%), Gaps = 105/500 (21%)

Query: 994  EVLGNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLD----SKEFLQDTSENF 1049
            E+ G+  PV+  R+  D I +  S+ D +L   EI  L  E+++     K F +   E F
Sbjct: 840  EMEGDSRPVDFDRVWTDSICRFGSQKDRALCCDEIKDLVRESVEKVKKDKRF-KYNDEGF 898

Query: 1050 VRDIKKFLE----EFSKKES--VTSHQDKVS-------QPLREQIL---SHQDKIG---- 1089
                + FL+    EF+ K++  V SH +          +  R Q L   + QD++     
Sbjct: 899  GVGFRNFLDNTTIEFADKQADIVKSHWESYGVYAKSDEERARYQALRTTAKQDELSSDLT 958

Query: 1090 HGRESNPFPSACK------------AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMT 1137
                 + F   C              E C  KY +A++EP T VGA+ A SIGEP TQMT
Sbjct: 959  QTVADSVFLHLCAYLSDQTILFKLFVERCALKYFKARMEPGTCVGAICATSIGEPATQMT 1018

Query: 1138 LKTFH------------------------------------------FA----------- 1144
            LKTFH                                          FA           
Sbjct: 1019 LKTFHFAGVASMNITQGVPRIEQIINNTQKIKTPIIMAKLTTEDSKEFAQEVASKLEKTT 1078

Query: 1145 -GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSG 1201
             GE+CE+I+EV   D+SF+L+KLD  R+RLL + V ++SI++   I   +   G +   G
Sbjct: 1079 LGEICEFIQEVHNADESFLLLKLDTKRVRLLKMRVTVESIKHSIAISSLKLKLGQIIAHG 1138

Query: 1202 HSFLILKPKDSSKSFNSKMYQM-----KQLLPSVVIKGVQGINRAVI-HEEDVEGVTKYK 1255
             S L +     S S+N   +QM     K  + +V+++G++ INRAVI H++  EG   Y+
Sbjct: 1139 ESILTIH----SSSYNDSEWQMSLPNLKDSICAVLVQGLKEINRAVISHQDKKEGF--YE 1192

Query: 1256 LLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDF 1315
            ++++G++L  V+AT G+   + SSN+  +V++ LG+EAARSTI+ E+   M +HG+ +D 
Sbjct: 1193 MIIDGNDLGGVLATRGIDWSRTSSNHIPKVFEILGVEAARSTIINEMTNTMGHHGIHVDR 1252

Query: 1316 RHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVS 1375
            RH M++AD MT  G V G TR GLA +  S L+L+SFE TSD L++AA+YGQ D ++G S
Sbjct: 1253 RHLMMLADYMTYTGPVFGCTRIGLANVSNSPLHLSSFEKTSDILYNAAYYGQRDSLAGPS 1312

Query: 1376 ECIIMGLPMNVGTGLIKLLQ 1395
              +I+G+P+ +GTGL KL Q
Sbjct: 1313 AALILGVPIELGTGLFKLYQ 1332



 Score =  183 bits (464), Expect = 8e-43,   Method: Compositional matrix adjust.
 Identities = 100/242 (41%), Positives = 158/242 (65%), Gaps = 14/242 (5%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRI++IIN ++ I TPII A L  +   ++A+ V  +LE+TTLGE+CE+I+EV   D+
Sbjct: 1035 GVPRIEQIINNTQKIKTPIIMAKLTTEDSKEFAQEVASKLEKTTLGEICEFIQEVHNADE 1094

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
            SF+L+KLD  R+RLL + V ++SI++   I   +   G +   G S L +     S S+N
Sbjct: 1095 SFLLLKLDTKRVRLLKMRVTVESIKHSIAISSLKLKLGQIIAHGESILTIH----SSSYN 1150

Query: 882  SKMYQM-----KQLLPSVVIKGVQGINRAVI-HEEDVEGVTKYKLLVEGDNLRDVMATYG 935
               +QM     K  + +V+++G++ INRAVI H++  EG   Y+++++G++L  V+AT G
Sbjct: 1151 DSEWQMSLPNLKDSICAVLVQGLKEINRAVISHQDKKEGF--YEMIIDGNDLGGVLATRG 1208

Query: 936  VKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            +   + SSN+  +V++ LG+EAARSTI+ E+   M +HG+ +D RH M++AD MT  G V
Sbjct: 1209 IDWSRTSSNHIPKVFEILGVEAARSTIINEMTNTMGHHGIHVDRRHLMMLADYMTYTGPV 1268

Query: 996  LG 997
             G
Sbjct: 1269 FG 1270



 Score =  120 bits (300), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 77/229 (33%), Positives = 107/229 (46%), Gaps = 62/229 (27%)

Query: 112 QRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQ 171
           ++ P  HG+ D ++G  +K   C TCG +   CVGHFG+I L LP+FH GY     N+LQ
Sbjct: 51  KKEPTTHGVFDPKLGPYEKGNLCPTCGNDRISCVGHFGHIKLALPIFHTGYLPHTYNLLQ 110

Query: 172 SICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEING 231
            ICK   C+RVLL ++                     + +K               E NG
Sbjct: 111 MICKG--CSRVLLEDD---------------------VDEK---------------EYNG 132

Query: 232 VVKKCGLLKISHEKYK-NRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLE 290
            +KK G  K  HE+YK   T  K + ++D  ++     K                     
Sbjct: 133 PIKKVGFHKFLHERYKFKNTATKTSRIQDHPSQMQFKAK--------------------- 171

Query: 291 VLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLK 339
             +LF+ IP ED PLL M  +   PSDLILT++ V P+ IRPSV SD++
Sbjct: 172 --ELFDNIPKEDYPLLCMAVDSVHPSDLILTQIPVSPSVIRPSVTSDIR 218



 Score =  117 bits (292), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 53/57 (92%), Positives = 55/57 (96%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTA TGYMQRRLVK+LE LCVQYD
Sbjct: 760 RGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTASTGYMQRRLVKALEGLCVQYD 816



 Score = 59.3 bits (142), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 30/60 (50%), Positives = 40/60 (66%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFFR 80
           VLM  KSN +T R+GE L+A+ QDFIT  YLLTQK+ FF   + +R+ +T+ A  K   R
Sbjct: 456 VLMGVKSNTLTCRSGEPLVASIQDFITAMYLLTQKDVFFTHQEFLRLITTVTARNKGRLR 515



 Score = 48.5 bits (114), Expect = 0.026,   Method: Compositional matrix adjust.
 Identities = 19/39 (48%), Positives = 30/39 (76%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D+ ++AA+YGQ D ++G S  +I+G+P+ +GTGL KL Q
Sbjct: 1294 DILYNAAYYGQRDSLAGPSAALILGVPIELGTGLFKLYQ 1332


>gi|393235145|gb|EJD42702.1| beta and beta-prime subunits of DNA dependent RNA-polymerase
           [Auricularia delicata TFB-10046 SS5]
          Length = 1404

 Score =  265 bits (676), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 138/284 (48%), Positives = 179/284 (63%), Gaps = 38/284 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D++LFNRQPSLHKLSIM HRAKV P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 449 DGDIILFNRQPSLHKLSIMCHRAKVRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEA 508

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A  LM   +NLVTPRNGE +IAA QDFIT  YLL +K+ F+ R
Sbjct: 509 RAE--------------ASQLMWVVNNLVTPRNGEPVIAAIQDFITASYLLCRKDRFYTR 554

Query: 461 AQTMRIASTLIADTSDICGII-KRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           AQ            + ICG            P V ++ A +WTGKQIFS +L+PN+   V
Sbjct: 555 AQ-----------FTQICGYFGDALVHIELPPPVILKPARLWTGKQIFSCLLRPNKSTNV 603

Query: 520 NANLKTKGRAY------------TANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKAN 567
             N++TK   +            T   +    D ++++ NSE+++G++DK+T+GSG K +
Sbjct: 604 LVNVETKCNQFEKPDPKHYPSWMTPENDLSLNDGWLVIVNSEIMSGTLDKATIGSGKKKS 663

Query: 568 VFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           VF  +++D+G   A  AM RL+++ + +L N GFSIGI DVTPG
Sbjct: 664 VFGAIMKDYGPQEAALAMGRLAKLCARFLANFGFSIGINDVTPG 707



 Score =  240 bits (612), Expect = 5e-60,   Method: Compositional matrix adjust.
 Identities = 171/498 (34%), Positives = 247/498 (49%), Gaps = 101/498 (20%)

Query: 1001 PVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEF 1060
            PVE  R      A  ++R  P L   EI  L+  T+ S   L D  E+++  ++ F+   
Sbjct: 919  PVEFVRAWKHAFA-TAAREGPGLLPYEIEELAKTTISSFGALADAEEDYLNTVEDFVR-- 975

Query: 1061 SKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAE---------------- 1104
                 +   +   +   R  +L  +DK G  R  N   +A   E                
Sbjct: 976  -----INLVEKLAAIRRRYGLLDGRDKPG-ARSKNRDWNAGAGEDVINAVNNTLKVAKPQ 1029

Query: 1105 ------ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG------------- 1145
                   C  +YV+++IEP + VGA+ AQSIGEPGTQMTLK+FHFAG             
Sbjct: 1030 LLLFLQNCWSRYVQSKIEPGSNVGAIGAQSIGEPGTQMTLKSFHFAGLASMNVTLGVPRI 1089

Query: 1146 -EVCEYIEEVFVP----------------------------------------DDSFILI 1164
             E+    + +  P                                        D ++I I
Sbjct: 1090 KEIINAAKTIATPIISCMLVDRQSEQSARSVKGRLEKTRLGDIASVIEEAWAPDYTYIGI 1149

Query: 1165 KLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNS------ 1218
             +D+  I  L LE+ +D I++ I R +     L +   +  +L  K+  + +        
Sbjct: 1150 IVDVLAIHRLQLELSLDDIKWAIVRAK----KLKIKEGTVSVLPSKNRIRIYVEGETSYF 1205

Query: 1219 KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYK----LLVEGDNLRDVMATYGVKG 1274
            ++ ++++ LP V++KGV  + RAVI ++D E     K    L+VEG  L++VM T G+ G
Sbjct: 1206 RLRELRRALPDVIVKGVPSVQRAVIVKKDKEDRRGKKGEKELIVEGYGLQEVMITDGIIG 1265

Query: 1275 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGI 1334
               +SN+  EV K LGIEAAR+TI+ +I   M  HG+++D RH ML+ D MT+KGEVLGI
Sbjct: 1266 THTTSNHIIEVAKVLGIEAARATIVDQIGYTMREHGLTVDARHIMLLGDCMTTKGEVLGI 1325

Query: 1335 TRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLP-MNVGTGLIKL 1393
            TR G+AKMK+SVL LASFE T+DHLFDAA  G+ D ++GVSE IIMG P    GT L  L
Sbjct: 1326 TRFGVAKMKDSVLMLASFEKTTDHLFDAAAVGKNDSLTGVSEAIIMGNPSAKFGTSLPAL 1385

Query: 1394 LQAVPRSEPVPRTLLFDN 1411
            +   P +   PR LLF++
Sbjct: 1386 VTPAP-TLSTPRPLLFES 1402



 Score =  209 bits (532), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 112/261 (42%), Positives = 151/261 (57%), Gaps = 5/261 (1%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           I+ ++    ++ Q S  ++  ++LY  +    P  +G LDRR+GT +K   C TCG    
Sbjct: 16  IQFSLLNPQQIVQLSEFEVTHRDLYIPE-DHVPAKNGPLDRRLGTVEKNTTCETCGHPTQ 74

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALS 202
           DCVGH+ YI L LPVFH+GYFR  INILQ ICK  TCARV+L E +   + A+ R P L 
Sbjct: 75  DCVGHYAYIKLMLPVFHVGYFRHTINILQQICK--TCARVMLSESERRTYLARFRRPGLE 132

Query: 203 YLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLA 262
            L R +L K +    +KV VCP+C  ING VKK G LKI H+KY  R KK    +E   +
Sbjct: 133 NLQRLTLCKAVNTLCRKVIVCPYCASINGTVKKGGTLKIVHDKY--RAKKTADEMEKFKS 190

Query: 263 EYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTR 322
            +  AV+F  ++  +    +I+ LNPL+VL LF+ I  ED  LL M     +P   +   
Sbjct: 191 TFKSAVEFQKDLGTYLSKAVIEELNPLKVLDLFKRISDEDCELLGMKPVHGRPEHYLWQY 250

Query: 323 LLVPPNCIRPSVISDLKSDND 343
           + VPP CIRPSV  D  S+ D
Sbjct: 251 ISVPPVCIRPSVAQDGGSNED 271



 Score =  179 bits (455), Expect = 9e-42,   Method: Compositional matrix adjust.
 Identities = 102/244 (41%), Positives = 150/244 (61%), Gaps = 14/244 (5%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ I+TPII+  L        AR VKGRLE+T LG++   IEE + PD 
Sbjct: 1085 GVPRIKEIINAAKTIATPIISCMLVDRQSEQSARSVKGRLEKTRLGDIASVIEEAWAPDY 1144

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNS- 882
            ++I I +D+  I  L LE+ +D I++ I R +     L +   +  +L  K+  + +   
Sbjct: 1145 TYIGIIVDVLAIHRLQLELSLDDIKWAIVRAK----KLKIKEGTVSVLPSKNRIRIYVEG 1200

Query: 883  -----KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYK----LLVEGDNLRDVMAT 933
                 ++ ++++ LP V++KGV  + RAVI ++D E     K    L+VEG  L++VM T
Sbjct: 1201 ETSYFRLRELRRALPDVIVKGVPSVQRAVIVKKDKEDRRGKKGEKELIVEGYGLQEVMIT 1260

Query: 934  YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
             G+ G   +SN+  EV K LGIEAAR+TI+ +I   M  HG+++D RH ML+ D MT+KG
Sbjct: 1261 DGIIGTHTTSNHIIEVAKVLGIEAARATIVDQIGYTMREHGLTVDARHIMLLGDCMTTKG 1320

Query: 994  EVLG 997
            EVLG
Sbjct: 1321 EVLG 1324



 Score = 99.4 bits (246), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 45/66 (68%), Positives = 53/66 (80%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSF 671
           +GFV NSF++GLT TEF  H + GREGLVDTAVKTAETGYMQRRL+K+LEDL  QYD+S 
Sbjct: 832 KGFVSNSFYTGLTATEFLLHAISGREGLVDTAVKTAETGYMQRRLMKALEDLTTQYDLSV 891

Query: 672 DAAFYG 677
             +  G
Sbjct: 892 RNSVGG 897



 Score = 58.2 bits (139), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 28/46 (60%), Positives = 34/46 (73%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRI 67
           LM   +NLVTPRNGE +IAA QDFIT  YLL +K+ F+ RAQ  +I
Sbjct: 515 LMWVVNNLVTPRNGEPVIAAIQDFITASYLLCRKDRFYTRAQFTQI 560



 Score = 44.3 bits (103), Expect = 0.53,   Method: Compositional matrix adjust.
 Identities = 26/56 (46%), Positives = 33/56 (58%), Gaps = 2/56 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLP-MNVGTGLIKLLQAVPRSEPVPRTLLFDN 722
            D  FDAA  G+ D ++GVSE IIMG P    GT L  L+   P +   PR LLF++
Sbjct: 1348 DHLFDAAAVGKNDSLTGVSEAIIMGNPSAKFGTSLPALVTPAP-TLSTPRPLLFES 1402


>gi|443899688|dbj|GAC77017.1| RNA polymerase III, large subunit [Pseudozyma antarctica T-34]
          Length = 1400

 Score =  265 bits (676), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 133/282 (47%), Positives = 179/282 (63%), Gaps = 29/282 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIM+HR KV P RTFR NEC C PYNADFDGDEMN+H+PQTEEA
Sbjct: 455 DGDIVLFNRQPSLHKLSIMSHRVKVRPWRTFRLNECACNPYNADFDGDEMNMHVPQTEEA 514

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R E              A +LM  K NLVTPRNGE ++AA QDFIT  YL+++++ FF+R
Sbjct: 515 RTE--------------ATILMGVKHNLVTPRNGEPIVAAIQDFITASYLISKRDRFFDR 560

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           AQ  +I S   AD +    I          P   ++   +WTGKQ+ S +++PN   P  
Sbjct: 561 AQFSQICS-YFADANLHIDI---------PPPAIMKPVRLWTGKQVMSCLIRPNSKSPHI 610

Query: 521 ANLKTKGRAYTA-----NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL+ + R +        ++    D ++++ NSE++ G  DKST+G G K +VF ++LRD
Sbjct: 611 VNLEAQCRTFEKPTGGHPKDMSPNDGWLVIVNSEVMCGVFDKSTVGDGKKNSVFGVMLRD 670

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           +G D A+TAM RL++  + +L N+GFS+GI DV PG    +N
Sbjct: 671 YGPDAAITAMNRLAKTCARWLANQGFSLGINDVIPGPNLRKN 712



 Score =  220 bits (561), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 184/602 (30%), Positives = 274/602 (45%), Gaps = 102/602 (16%)

Query: 891  LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVY 950
            LP    K    +++  +      G+T  + L  G + R+ +    VK  +         Y
Sbjct: 818  LPHFPKKSKDPLSKGFVRNSFFSGLTPTEFLFHGISGREGLVDTAVKTAETG-------Y 870

Query: 951  KTLGIEAARSTIMTEIKLVMENH-GMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRLLD 1009
                +  A   + T   L + N  G  + F    +  D      E+ GN  P+E  RL  
Sbjct: 871  MQRRLMKALEDLSTHYDLSVRNSVGGVVQF----IYGDDGLDPAELEGNAMPIEPFRLWR 926

Query: 1010 DIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEFSKKESVTSH 1069
              IA         L   EI+ +    L S +F+   ++ +   + +FL E   K +V + 
Sbjct: 927  HCIAITRHLPGRGLFPYEIMEIVKRELTSPKFVNTCTQKYRDSVHEFLHENVFKRAVATR 986

Query: 1070 QD---KVSQPLREQILSHQD-KIGHGRESNPF--------PSACKA--EACREKYVRAQI 1115
            +      ++   E    H D  IG  R+             +A  A  + C  KY+RA+I
Sbjct: 987  EAFGMYGAEEREEHWDEHTDLSIGANRDQWAIVDNKTKVKEAAVLAFLQQCYIKYMRAKI 1046

Query: 1116 EPATAVGAL---------------------------------------AAQSIGEPGTQM 1136
            EP +AVGA+                                       AA+ I  P  + 
Sbjct: 1047 EPGSAVGAVGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIINAAKVINTPIIEA 1106

Query: 1137 TLKTFH---------------FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDID 1181
             L +                 + G++   IEE +    +++ + +DMD I+ L LE+ ++
Sbjct: 1107 KLVSEKSERAARIVKGRIEKTYLGDIASVIEEAWAAQYTYLGVHIDMDAIQKLQLEITLN 1166

Query: 1182 SIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF--------NSKMY----QMKQLLPS 1229
             I++ I      +  L +     +++  K+  + +         S++Y     +K+ LPS
Sbjct: 1167 DIKWAIVN----APKLKIKEERVMVVPKKNRIRIYVPPEGVDKESEVYYNLKALKRALPS 1222

Query: 1230 VVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTL 1289
            +V+KG+    RAVI +E        KLLVEG  L  VM T GV G +  +N+  E+   L
Sbjct: 1223 IVVKGIPQATRAVISDEK----GTRKLLVEGYGLLKVMTTEGVIGTQTHTNHVMEMQSVL 1278

Query: 1290 GIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNL 1349
            GIEAAR+++  EI+  M  HGMSID RH ML+AD MT KGEVLGITR G+AKMK+SVL L
Sbjct: 1279 GIEAARTSVYREIETTMSAHGMSIDPRHIMLLADTMTYKGEVLGITRFGVAKMKDSVLML 1338

Query: 1350 ASFENTSDHLFDAAFYGQTDCISGVSECIIMGLP-MNVGTGLIKLLQAVPRSEPVPRTLL 1408
            ASFE T+DHLFDAA +G+ D + GVSE IIMG P   VGTG+  L+   P+  P  R LL
Sbjct: 1339 ASFEKTTDHLFDAALFGKKDEVLGVSESIIMGNPAQTVGTGMPALVVPAPKLPPR-RALL 1397

Query: 1409 FD 1410
            FD
Sbjct: 1398 FD 1399



 Score =  189 bits (481), Expect = 7e-45,   Method: Compositional matrix adjust.
 Identities = 113/263 (42%), Positives = 151/263 (57%), Gaps = 8/263 (3%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYC-QDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSD 143
           G ++K+D V   S I++ +++LY   + +R P+ +G LDRR+G + K + C TC   ++D
Sbjct: 19  GVLSKQDIVNM-SEIEVTTRDLYTIGEAERRPVANGTLDRRLGVSDKNSLCETCHLKMAD 77

Query: 144 CVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSY 203
           CVGH+GYI L LPVFHIG+F+  + ILQSICKN  CA VLL E     F  + R P L  
Sbjct: 78  CVGHYGYIKLVLPVFHIGFFKHTVAILQSICKN--CATVLLEEPDRRKFLKRFRRPNLEN 135

Query: 204 LVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAE 263
           L R    K +    +KV  CP CG  NG VKK G LKI HEK+  R KK  A  E+  A 
Sbjct: 136 LDRTRTFKAVNTIARKVLYCPKCGYTNGTVKKQGQLKIVHEKF--RAKKTAAEHEEFRAS 193

Query: 264 YNEAVKF-NPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTR 322
           +   +K  N +I  H      + LNPL+ L LF+ I  ED  LL +  E  +P + I   
Sbjct: 194 FATNIKMGNGDITPHLNKAQ-EDLNPLKALDLFKRISDEDCELLGLRPEFGRPEEYIWQY 252

Query: 323 LLVPPNCIRPSVISDLKSDNDVV 345
           + VPP CIRPSV  D  ++ D V
Sbjct: 253 ICVPPVCIRPSVAQDGATNEDDV 275



 Score =  172 bits (435), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 102/246 (41%), Positives = 147/246 (59%), Gaps = 20/246 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ I+TPII A L  +     ARIVKGR+E+T LG++   IEE +    
Sbjct: 1085 GVPRIKEIINAAKVINTPIIEAKLVSEKSERAARIVKGRIEKTYLGDIASVIEEAWAAQY 1144

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF--- 880
            +++ + +DMD I+ L LE+ ++ I++ I      +  L +     +++  K+  + +   
Sbjct: 1145 TYLGVHIDMDAIQKLQLEITLNDIKWAIVN----APKLKIKEERVMVVPKKNRIRIYVPP 1200

Query: 881  -----NSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVM 931
                  S++Y     +K+ LPS+V+KG+    RAVI +E        KLLVEG  L  VM
Sbjct: 1201 EGVDKESEVYYNLKALKRALPSIVVKGIPQATRAVISDEK----GTRKLLVEGYGLLKVM 1256

Query: 932  ATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTS 991
             T GV G +  +N+  E+   LGIEAAR+++  EI+  M  HGMSID RH ML+AD MT 
Sbjct: 1257 TTEGVIGTQTHTNHVMEMQSVLGIEAARTSVYREIETTMSAHGMSIDPRHIMLLADTMTY 1316

Query: 992  KGEVLG 997
            KGEVLG
Sbjct: 1317 KGEVLG 1322



 Score =  106 bits (265), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 50/73 (68%), Positives = 57/73 (78%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSF 671
           +GFV+NSFFSGLTPTEF FH + GREGLVDTAVKTAETGYMQRRL+K+LEDL   YD+S 
Sbjct: 831 KGFVRNSFFSGLTPTEFLFHGISGREGLVDTAVKTAETGYMQRRLMKALEDLSTHYDLSV 890

Query: 672 DAAFYGQTDCISG 684
             +  G    I G
Sbjct: 891 RNSVGGVVQFIYG 903



 Score = 63.9 bits (154), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 28/49 (57%), Positives = 38/49 (77%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIAS 69
           +LM  K NLVTPRNGE ++AA QDFIT  YL+++++ FF+RAQ  +I S
Sbjct: 520 ILMGVKHNLVTPRNGEPIVAAIQDFITASYLISKRDRFFDRAQFSQICS 568



 Score = 49.3 bits (116), Expect = 0.018,   Method: Compositional matrix adjust.
 Identities = 28/55 (50%), Positives = 34/55 (61%), Gaps = 2/55 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLP-MNVGTGLIKLLQAVPRSEPVPRTLLFD 721
            D  FDAA +G+ D + GVSE IIMG P   VGTG+  L+   P+  P  R LLFD
Sbjct: 1346 DHLFDAALFGKKDEVLGVSESIIMGNPAQTVGTGMPALVVPAPKLPPR-RALLFD 1399


>gi|58268624|ref|XP_571468.1| DNA-directed RNA polymerase iii largest subunit [Cryptococcus
           neoformans var. neoformans JEC21]
 gi|57227703|gb|AAW44161.1| DNA-directed RNA polymerase iii largest subunit, putative
           [Cryptococcus neoformans var. neoformans JEC21]
          Length = 1466

 Score =  264 bits (675), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 138/278 (49%), Positives = 183/278 (65%), Gaps = 31/278 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIM HR +V P RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 467 DGDIVLFNRQPSLHKLSIMCHRVRVRPWRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 526

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL               LM+ K NLVTPRNGE +IAA QDFIT  YLL++++ F++R
Sbjct: 527 RTEALE--------------LMSVKKNLVTPRNGEPIIAAIQDFITAAYLLSRRDRFYDR 572

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q  +I S L  D +++   I+      W PV       +WTGKQIF+L+++PN++  V 
Sbjct: 573 QQFTQIVSYL--DDANL--KIEMPPPTIWKPV------RLWTGKQIFNLLMRPNKESKVL 622

Query: 521 ANLKTKGRAYT--ANE-----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILL 573
            NL+ K R     A E     +    D Y++++NSE++ G  DK+T+G G K +VF ++L
Sbjct: 623 VNLEAKCRTLVDPAKEDRFPPDMSPNDGYLVIQNSEIMCGVFDKNTVGDGKKNSVFGVIL 682

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           RD+G + A  AM RL+++ + +L N GFS+GI DV PG
Sbjct: 683 RDYGPEEAAQAMNRLAKIAARWLANIGFSLGINDVIPG 720



 Score =  249 bits (636), Expect = 8e-63,   Method: Compositional matrix adjust.
 Identities = 155/400 (38%), Positives = 222/400 (55%), Gaps = 75/400 (18%)

Query: 1076 PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQ 1135
            P  +++L + +K+   + S+        E CR +Y+RA+IEP + VGA+ AQSIGEPGTQ
Sbjct: 1058 PAVQRVLENANKVTEAQLSSFL------ENCRIRYLRAKIEPGSTVGAVGAQSIGEPGTQ 1111

Query: 1136 MTLKTFHFAG-----------EVCEYIE------------EVFVPD-------------- 1158
            MTLKTFHFAG            + E I             E+ +P+              
Sbjct: 1112 MTLKTFHFAGVASMNVTLGVPRIKEIINAAKVISTPIIAAELAIPESETAARIVKGRIEK 1171

Query: 1159 -----------------DSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLT 1198
                             +++I + +DMD +R L LE+ ++SI++ + R   +    G + 
Sbjct: 1172 TVLGDIAAVIEESWTNANAYIEVHIDMDAVRRLQLEISLESIKWALVRANKLKIPEGSIH 1231

Query: 1199 VSGHS-----FLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTK 1253
            +S  +     ++    KD       ++  +K+ +PSV +KG+  I R V+  +D +    
Sbjct: 1232 ISQKTSRIRIWIDESDKDKGVGIYERLKFLKRAIPSVQVKGLPAIERGVV-TKDEKNEKI 1290

Query: 1254 YKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSI 1313
            ++LLV G  L +VM T GV G+K  +N+  E  + LGIEAARSTI  EI+  M++HGMSI
Sbjct: 1291 HRLLVTGYGLSEVMGTEGVDGLKTKTNHVMETQQVLGIEAARSTIYNEIQTTMKSHGMSI 1350

Query: 1314 DFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISG 1373
            D RH ML+ D+MT KGEVLGITR G+ KMK+SVL LASFE T+DHLFDA+ Y + D I G
Sbjct: 1351 DPRHVMLLGDVMTYKGEVLGITRFGVQKMKDSVLMLASFEKTTDHLFDASLYSKKDEIQG 1410

Query: 1374 VSECIIMGLPM-NVGTGLIKLLQAVPRSEPVP--RTLLFD 1410
            VSECIIMG P    GT L  ++   P   P+P  + LLF+
Sbjct: 1411 VSECIIMGTPAPGCGTSLASIVTPAP---PLPSKKPLLFE 1447



 Score =  213 bits (542), Expect = 7e-52,   Method: Compositional matrix adjust.
 Identities = 114/249 (45%), Positives = 148/249 (59%), Gaps = 7/249 (2%)

Query: 97  SHIQIVSKNLY--CQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLP 154
           S +Q+    LY   +D  RT    G LD RMG N+K   C TCG++   CVGH+GYI L 
Sbjct: 40  SEVQVSIAELYQNNEDGTRTTALQGPLDARMGPNEKGKKCATCGEDTQKCVGHYGYIKLV 99

Query: 155 LPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKIL 214
           LPVFHIGYFR  IN+L  ICK  TCARVLL E + A F  + R P L  L R+S  K +L
Sbjct: 100 LPVFHIGYFRPTINMLSCICK--TCARVLLPETERASFLKRFRRPNLESLQRQSAAKAVL 157

Query: 215 ETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEI 274
              KK ++C +CG  NG+VKK G L+ISHE Y  R  K  ++ ++ +A +  AV  N  +
Sbjct: 158 AACKKQNICTYCGAPNGIVKKSGPLRISHEPY--RAAKMASMKDEWMATFKNAVAENQAV 215

Query: 275 EAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSV 334
             H     +  LNPL+VL LFE I  ED  LL ++ E+ +P D I   + VPP CIRPSV
Sbjct: 216 ATHLAKA-VDDLNPLKVLNLFERITAEDCELLSLHPEVGRPEDYIWQYISVPPPCIRPSV 274

Query: 335 ISDLKSDND 343
            S+  ++ D
Sbjct: 275 ASEAGNNED 283



 Score =  185 bits (469), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 104/242 (42%), Positives = 151/242 (62%), Gaps = 9/242 (3%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ ISTPII A L        ARIVKGR+E+T LG++   IEE +   +
Sbjct: 1130 GVPRIKEIINAAKVISTPIIAAELAIPESETAARIVKGRIEKTVLGDIAAVIEESWTNAN 1189

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHS-----FLILKPKD 875
            ++I + +DMD +R L LE+ ++SI++ + R   +    G + +S  +     ++    KD
Sbjct: 1190 AYIEVHIDMDAVRRLQLEISLESIKWALVRANKLKIPEGSIHISQKTSRIRIWIDESDKD 1249

Query: 876  SSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYG 935
                   ++  +K+ +PSV +KG+  I R V+  +D +    ++LLV G  L +VM T G
Sbjct: 1250 KGVGIYERLKFLKRAIPSVQVKGLPAIERGVV-TKDEKNEKIHRLLVTGYGLSEVMGTEG 1308

Query: 936  VKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            V G+K  +N+  E  + LGIEAARSTI  EI+  M++HGMSID RH ML+ D+MT KGEV
Sbjct: 1309 VDGLKTKTNHVMETQQVLGIEAARSTIYNEIQTTMKSHGMSIDPRHVMLLGDVMTYKGEV 1368

Query: 996  LG 997
            LG
Sbjct: 1369 LG 1370



 Score =  110 bits (275), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 49/68 (72%), Positives = 55/68 (80%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV+NSFFSGLTP EF FH M GREGLVDTAVKTAETGYM RRL+K+LEDLC  YD+
Sbjct: 843 PSKGFVRNSFFSGLTPPEFLFHAMSGREGLVDTAVKTAETGYMARRLMKALEDLCTHYDL 902

Query: 670 SFDAAFYG 677
           S   +  G
Sbjct: 903 SVRNSVGG 910



 Score = 63.2 bits (152), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 29/50 (58%), Positives = 38/50 (76%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM+ K NLVTPRNGE +IAA QDFIT  YLL++++ F++R Q  +I S L
Sbjct: 533 LMSVKKNLVTPRNGEPIIAAIQDFITAAYLLSRRDRFYDRQQFTQIVSYL 582



 Score = 45.8 bits (107), Expect = 0.18,   Method: Compositional matrix adjust.
 Identities = 26/57 (45%), Positives = 33/57 (57%), Gaps = 6/57 (10%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPM-NVGTGLIKLLQAVPRSEPVP--RTLLFD 721
            D  FDA+ Y + D I GVSECIIMG P    GT L  ++   P   P+P  + LLF+
Sbjct: 1394 DHLFDASLYSKKDEIQGVSECIIMGTPAPGCGTSLASIVTPAP---PLPSKKPLLFE 1447


>gi|134113452|ref|XP_774751.1| hypothetical protein CNBF4300 [Cryptococcus neoformans var.
           neoformans B-3501A]
 gi|50257395|gb|EAL20104.1| hypothetical protein CNBF4300 [Cryptococcus neoformans var.
           neoformans B-3501A]
          Length = 1466

 Score =  264 bits (675), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 138/278 (49%), Positives = 183/278 (65%), Gaps = 31/278 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIM HR +V P RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 467 DGDIVLFNRQPSLHKLSIMCHRVRVRPWRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 526

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL               LM+ K NLVTPRNGE +IAA QDFIT  YLL++++ F++R
Sbjct: 527 RTEALE--------------LMSVKKNLVTPRNGEPIIAAIQDFITAAYLLSRRDRFYDR 572

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q  +I S L  D +++   I+      W PV       +WTGKQIF+L+++PN++  V 
Sbjct: 573 QQFTQIVSYL--DDANL--KIEMPPPTIWKPV------RLWTGKQIFNLLMRPNKESKVL 622

Query: 521 ANLKTKGRAYT--ANE-----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILL 573
            NL+ K R     A E     +    D Y++++NSE++ G  DK+T+G G K +VF ++L
Sbjct: 623 VNLEAKCRTLVDPAKEDRFPPDMSPNDGYLVIQNSEIMCGVFDKNTVGDGKKNSVFGVIL 682

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           RD+G + A  AM RL+++ + +L N GFS+GI DV PG
Sbjct: 683 RDYGPEEAAQAMNRLAKIAARWLANIGFSLGINDVIPG 720



 Score =  249 bits (636), Expect = 8e-63,   Method: Compositional matrix adjust.
 Identities = 155/400 (38%), Positives = 222/400 (55%), Gaps = 75/400 (18%)

Query: 1076 PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQ 1135
            P  +++L + +K+   + S+        E CR +Y+RA+IEP + VGA+ AQSIGEPGTQ
Sbjct: 1058 PAVQRVLENANKVTEAQLSSFL------ENCRIRYLRAKIEPGSTVGAVGAQSIGEPGTQ 1111

Query: 1136 MTLKTFHFAG-----------EVCEYIE------------EVFVPD-------------- 1158
            MTLKTFHFAG            + E I             E+ +P+              
Sbjct: 1112 MTLKTFHFAGVASMNVTLGVPRIKEIINAAKVISTPIIAAELAIPESETAARIVKGRIEK 1171

Query: 1159 -----------------DSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLT 1198
                             +++I + +DMD +R L LE+ ++SI++ + R   +    G + 
Sbjct: 1172 TVLGDIAAVIEESWTNANAYIEVHIDMDAVRRLQLEISLESIKWALVRANKLKIPEGSIH 1231

Query: 1199 VSGHS-----FLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTK 1253
            +S  +     ++    KD       ++  +K+ +PSV +KG+  I R V+  +D +    
Sbjct: 1232 ISQKTSRIRIWIDESDKDKGVGIYERLKFLKRAIPSVQVKGLPAIERGVV-TKDEKNEKI 1290

Query: 1254 YKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSI 1313
            ++LLV G  L +VM T GV G+K  +N+  E  + LGIEAARSTI  EI+  M++HGMSI
Sbjct: 1291 HRLLVTGYGLSEVMGTEGVDGLKTKTNHVMETQQVLGIEAARSTIYNEIQTTMKSHGMSI 1350

Query: 1314 DFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISG 1373
            D RH ML+ D+MT KGEVLGITR G+ KMK+SVL LASFE T+DHLFDA+ Y + D I G
Sbjct: 1351 DPRHVMLLGDVMTYKGEVLGITRFGVQKMKDSVLMLASFEKTTDHLFDASLYSKKDEIQG 1410

Query: 1374 VSECIIMGLPM-NVGTGLIKLLQAVPRSEPVP--RTLLFD 1410
            VSECIIMG P    GT L  ++   P   P+P  + LLF+
Sbjct: 1411 VSECIIMGTPAPGCGTSLASIVTPAP---PLPSKKPLLFE 1447



 Score =  213 bits (542), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 114/249 (45%), Positives = 148/249 (59%), Gaps = 7/249 (2%)

Query: 97  SHIQIVSKNLY--CQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLP 154
           S +Q+    LY   +D  RT    G LD RMG N+K   C TCG++   CVGH+GYI L 
Sbjct: 40  SEVQVSIAELYQNNEDGTRTTALQGPLDARMGPNEKGKKCATCGEDTQKCVGHYGYIKLV 99

Query: 155 LPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKIL 214
           LPVFHIGYFR  IN+L  ICK  TCARVLL E + A F  + R P L  L R+S  K +L
Sbjct: 100 LPVFHIGYFRPTINMLSCICK--TCARVLLPETERASFLKRFRRPNLESLQRQSAAKAVL 157

Query: 215 ETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEI 274
              KK ++C +CG  NG+VKK G L+ISHE Y  R  K  ++ ++ +A +  AV  N  +
Sbjct: 158 AACKKQNICTYCGAPNGIVKKSGPLRISHEPY--RAAKMASMKDEWMATFKNAVAENQAV 215

Query: 275 EAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSV 334
             H     +  LNPL+VL LFE I  ED  LL ++ E+ +P D I   + VPP CIRPSV
Sbjct: 216 ATHLAKA-VDDLNPLKVLNLFERITAEDCELLSLHPEVGRPEDYIWQYISVPPPCIRPSV 274

Query: 335 ISDLKSDND 343
            S+  ++ D
Sbjct: 275 ASEAGNNED 283



 Score =  185 bits (469), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 104/242 (42%), Positives = 151/242 (62%), Gaps = 9/242 (3%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ ISTPII A L        ARIVKGR+E+T LG++   IEE +   +
Sbjct: 1130 GVPRIKEIINAAKVISTPIIAAELAIPESETAARIVKGRIEKTVLGDIAAVIEESWTNAN 1189

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHS-----FLILKPKD 875
            ++I + +DMD +R L LE+ ++SI++ + R   +    G + +S  +     ++    KD
Sbjct: 1190 AYIEVHIDMDAVRRLQLEISLESIKWALVRANKLKIPEGSIHISQKTSRIRIWIDESDKD 1249

Query: 876  SSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYG 935
                   ++  +K+ +PSV +KG+  I R V+  +D +    ++LLV G  L +VM T G
Sbjct: 1250 KGVGIYERLKFLKRAIPSVQVKGLPAIERGVV-TKDEKNEKIHRLLVTGYGLSEVMGTEG 1308

Query: 936  VKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            V G+K  +N+  E  + LGIEAARSTI  EI+  M++HGMSID RH ML+ D+MT KGEV
Sbjct: 1309 VDGLKTKTNHVMETQQVLGIEAARSTIYNEIQTTMKSHGMSIDPRHVMLLGDVMTYKGEV 1368

Query: 996  LG 997
            LG
Sbjct: 1369 LG 1370



 Score =  110 bits (275), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 49/68 (72%), Positives = 55/68 (80%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV+NSFFSGLTP EF FH M GREGLVDTAVKTAETGYM RRL+K+LEDLC  YD+
Sbjct: 843 PSKGFVRNSFFSGLTPPEFLFHAMSGREGLVDTAVKTAETGYMARRLMKALEDLCTHYDL 902

Query: 670 SFDAAFYG 677
           S   +  G
Sbjct: 903 SVRNSVGG 910



 Score = 63.2 bits (152), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 29/50 (58%), Positives = 38/50 (76%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM+ K NLVTPRNGE +IAA QDFIT  YLL++++ F++R Q  +I S L
Sbjct: 533 LMSVKKNLVTPRNGEPIIAAIQDFITAAYLLSRRDRFYDRQQFTQIVSYL 582



 Score = 45.8 bits (107), Expect = 0.18,   Method: Compositional matrix adjust.
 Identities = 26/57 (45%), Positives = 33/57 (57%), Gaps = 6/57 (10%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPM-NVGTGLIKLLQAVPRSEPVP--RTLLFD 721
            D  FDA+ Y + D I GVSECIIMG P    GT L  ++   P   P+P  + LLF+
Sbjct: 1394 DHLFDASLYSKKDEIQGVSECIIMGTPAPGCGTSLASIVTPAP---PLPSKKPLLFE 1447


>gi|255076723|ref|XP_002502032.1| predicted protein [Micromonas sp. RCC299]
 gi|226517297|gb|ACO63290.1| predicted protein [Micromonas sp. RCC299]
          Length = 1479

 Score =  264 bits (674), Expect = 3e-67,   Method: Compositional matrix adjust.
 Identities = 131/274 (47%), Positives = 179/274 (65%), Gaps = 26/274 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DV+LFNRQPSLHK+SIMAHRA+V+P RT RFNECVCTPYNADFDGDEMN+H PQTEEA
Sbjct: 471 DGDVLLFNRQPSLHKMSIMAHRARVMPWRTLRFNECVCTPYNADFDGDEMNIHCPQTEEA 530

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM+  +NL TP+NGE+L+AATQDF+T  Y+LT ++ F +R
Sbjct: 531 RAEAIN--------------LMSVHNNLCTPKNGEILVAATQDFLTASYILTARDHFLDR 576

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           AQ       LIA   D    +   +     PV       +WTGKQ+FS++++P     V 
Sbjct: 577 AQV----GALIAYMGDALMAVDLPTPAIIKPV------ELWTGKQLFSVLIRPRAVDRVF 626

Query: 521 ANLKTKGRAYTANE--EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            NL+   + Y+  +    C RD YV ++NSE++ G + K+TLGSG K  +FY+L  ++G 
Sbjct: 627 VNLEVAEKNYSKKDTRHMCPRDGYVCIQNSEIMCGQLGKATLGSGNKNGLFYVLNSEYGS 686

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
           +   + M R++++++ +L  RGFS+GI DVTPG 
Sbjct: 687 EQTASCMNRVAKLSARWLGTRGFSVGIDDVTPGH 720



 Score =  253 bits (645), Expect = 7e-64,   Method: Compositional matrix adjust.
 Identities = 156/369 (42%), Positives = 212/369 (57%), Gaps = 74/369 (20%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCE 1149
            E C  KY   +IEP +AVGA+ AQSIGEPGTQMTLKTFHFAG              E+  
Sbjct: 1025 ERCVRKYSAKRIEPGSAVGAVGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIIN 1084

Query: 1150 YIEEVFVP--------DDS--------------------------------FILIKLDMD 1169
              + +  P        DD+                                ++ + LD  
Sbjct: 1085 AAKNISTPIITATLECDDNVKAARVVKGRVEKTTLGEVCKFIDVVYNPSACYVEVCLDPA 1144

Query: 1170 RIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSGHSFL-ILKPKDSSKS---------- 1215
             I  L L+V ++S+R+ +    + +  +  +  +G + + +L P + SKS          
Sbjct: 1145 VISALQLDVTVESVRHSLITAPKLKLKANTVLHAGENLIHVLPPDEESKSKAAAAQGAAA 1204

Query: 1216 FNSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGV 1272
            +   ++ ++ L   +P+V+++G+  ++RAVI+  DV G  KY L+VEG NL+ VM   GV
Sbjct: 1205 YRRALFHLQTLRTAVPNVIVQGIPSVSRAVIN--DV-GQGKYNLVVEGTNLQAVMGVEGV 1261

Query: 1273 KGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL 1332
            KG   ++N+  E  +TLGIEAARS I+ EI   M+ HGMSID RH ML+AD+MT KGEVL
Sbjct: 1262 KGTHTTTNHVMEAERTLGIEAARSCIIKEINDTMKAHGMSIDARHSMLLADVMTYKGEVL 1321

Query: 1333 GITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIK 1392
            GITR G+AKMK+SVL LASFE T+DHLFDAA +G+TD I GVSECIIMG+PM VGTG+ K
Sbjct: 1322 GITRFGMAKMKDSVLMLASFEKTTDHLFDAALHGRTDTIDGVSECIIMGIPMPVGTGMFK 1381

Query: 1393 LLQAVPRSE 1401
            L     R E
Sbjct: 1382 LQHRAMRLE 1390



 Score =  199 bits (505), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 113/251 (45%), Positives = 167/251 (66%), Gaps = 20/251 (7%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++NISTPIITA L+ D ++  AR+VKGR+E+TTLGEVC++I+ V+ P  
Sbjct: 1075 GVPRIKEIINAAKNISTPIITATLECDDNVKAARVVKGRVEKTTLGEVCKFIDVVYNPSA 1134

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSGHSFL-ILKPKDSSKS 879
             ++ + LD   I  L L+V ++S+R+ +    + +  +  +  +G + + +L P + SKS
Sbjct: 1135 CYVEVCLDPAVISALQLDVTVESVRHSLITAPKLKLKANTVLHAGENLIHVLPPDEESKS 1194

Query: 880  ----------FNSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDN 926
                      +   ++ ++ L   +P+V+++G+  ++RAVI+  DV G  KY L+VEG N
Sbjct: 1195 KAAAAQGAAAYRRALFHLQTLRTAVPNVIVQGIPSVSRAVIN--DV-GQGKYNLVVEGTN 1251

Query: 927  LRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVA 986
            L+ VM   GVKG   ++N+  E  +TLGIEAARS I+ EI   M+ HGMSID RH ML+A
Sbjct: 1252 LQAVMGVEGVKGTHTTTNHVMEAERTLGIEAARSCIIKEINDTMKAHGMSIDARHSMLLA 1311

Query: 987  DLMTSKGEVLG 997
            D+MT KGEVLG
Sbjct: 1312 DVMTYKGEVLG 1322



 Score =  192 bits (488), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 106/238 (44%), Positives = 143/238 (60%), Gaps = 15/238 (6%)

Query: 100 QIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEAN-CTTCGQNLSDCVGHFGYIDLPLPVF 158
            +  +NLY Q PQR P+ +G+LD RMGT  K+   C TC   L DC GHFGY+ L LPVF
Sbjct: 56  HVFERNLY-QMPQRVPLKNGILDPRMGTTDKKGTECATCKGKLIDCAGHFGYVKLELPVF 114

Query: 159 HIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTK 218
           HIGYF+ +I ILQ +CK   C+RV+L EE+   +  + RNP L  + +++L KK+ +  K
Sbjct: 115 HIGYFKNIIAILQQVCKE--CSRVMLPEEERQQYLKRFRNPRLEIVPKRALSKKLADKCK 172

Query: 219 KVSVCPHCGEINGVVKKCGL-LKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAH 277
           +  +CP CG  NG VK+ G  LKI HEKY     K   ++E  + E+ EAVK N +++A+
Sbjct: 173 RCRICPSCGAANGAVKRTGASLKIVHEKY----SKNPELMEAYVKEFEEAVKHNDQLKAN 228

Query: 278 KKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSV 334
                +Q  LNP+ V  +   I   D  LL +     +P  LILT L VPP CIRPSV
Sbjct: 229 --LARVQDDLNPIRVESILSKISPMDCELLDV---ADRPEHLILTHLPVPPVCIRPSV 281



 Score =  106 bits (265), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 49/64 (76%), Positives = 56/64 (87%), Gaps = 1/64 (1%)

Query: 606 GDVTPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           G+ TP  +GFV NSFFSG+ PTEFFFHTM GREGLVDTAVKTAETGYM RRL+K+LEDL 
Sbjct: 837 GEKTPAAKGFVANSFFSGMRPTEFFFHTMAGREGLVDTAVKTAETGYMSRRLMKALEDLS 896

Query: 665 VQYD 668
           ++YD
Sbjct: 897 LRYD 900



 Score = 59.7 bits (143), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 28/45 (62%), Positives = 32/45 (71%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSE 712
            D  FDAA +G+TD I GVSECIIMG+PM VGTG+ KL     R E
Sbjct: 1346 DHLFDAALHGRTDTIDGVSECIIMGIPMPVGTGMFKLQHRAMRLE 1390



 Score = 58.2 bits (139), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 24/42 (57%), Positives = 34/42 (80%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 63
           LM+  +NL TP+NGE+L+AATQDF+T  Y+LT ++ F +RAQ
Sbjct: 537 LMSVHNNLCTPKNGEILVAATQDFLTASYILTARDHFLDRAQ 578


>gi|385303556|gb|EIF47620.1| dna-directed rna polymerase iii largest subunit [Dekkera
           bruxellensis AWRI1499]
          Length = 1472

 Score =  263 bits (671), Expect = 8e-67,   Method: Compositional matrix adjust.
 Identities = 131/281 (46%), Positives = 182/281 (64%), Gaps = 29/281 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + D+VLFNRQPSLH+LSI+AH   V   RTFRFNECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 468 EGDIVLFNRQPSLHRLSILAHYVTVKKWRTFRFNECVCAPYNADFDGDEMNLHVPQTEEA 527

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A  LM  KSNL+TP++GE +IAATQDFITG +L+T K++F++R
Sbjct: 528 RAE--------------AATLMGVKSNLLTPKSGEPIIAATQDFITGSFLITXKDSFYDR 573

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A    +   +++D +    +          P   ++ A +WTGKQI+SL+++PN +  V 
Sbjct: 574 AVFTEMC-VMMSDGATKFDV---------PPPTILKPAYMWTGKQIYSLLIRPNHESKVL 623

Query: 521 ANLKTKGRAYTANE-----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            N  +K + +   +     E    D YV++RNS+LL+G MDK+ LG G K ++FY +LRD
Sbjct: 624 LNFDSKSKTFIPPKDGLPNEMSPNDGYVLVRNSQLLSGVMDKALLGGGKKTSLFYTILRD 683

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           +G D A  AM R++++ + Y+  +GFSIGI DV P +   Q
Sbjct: 684 YGADEAAKAMNRMAKLAARYMGEKGFSIGINDVIPSEPVKQ 724



 Score =  206 bits (523), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 125/301 (41%), Positives = 174/301 (57%), Gaps = 39/301 (12%)

Query: 1146 EVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTR-------------- 1191
            +V  YIE+V+    +++ +K+D+D I  L LE+ ID I   I +T+              
Sbjct: 1161 DVTYYIEDVYKESQAYLQVKIDLDTIEKLQLELTIDQIMDAIVKTKLKIPRSCXSIVGKN 1220

Query: 1192 -------------GISGHLTVSGHSFLILKPKDSSK-------SFNSKMYQMKQLLPSVV 1231
                         G     + S      L  KD  +       S   KM Q+K+ L  VV
Sbjct: 1221 KIQILVSEMGLENGKPSSRSTSSREIAALAKKDPDERDRLERSSLFYKMQQLKRQLTKVV 1280

Query: 1232 IKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGI 1291
            +KG+  + +AVI+  D +G  K +LLVEG  L+DVMAT GV   K  +N+  E++  LGI
Sbjct: 1281 VKGLPEVAKAVINVRD-DG--KKELLVEGYGLKDVMATDGVIATKTKTNHVIEIFHVLGI 1337

Query: 1292 EAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLAS 1351
            EAARS+I++EI   M +HGM +D RH  L+AD+MT KGE+LGITR GLAKM++SV+ LAS
Sbjct: 1338 EAARSSIVSEIDYTMRSHGMVVDPRHLQLLADVMTYKGEILGITRFGLAKMRDSVMQLAS 1397

Query: 1352 FENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL--LQAVPRSEPVPRTLLF 1409
            FE T+DHLFDAAFY + D + GVSE II+G  M++GTG  KL     +P  +  P+  LF
Sbjct: 1398 FEKTTDHLFDAAFYTKDDKVEGVSERIILGQTMSIGTGSFKLSVQNNIPPEKLEPKKTLF 1457

Query: 1410 D 1410
            +
Sbjct: 1458 E 1458



 Score =  182 bits (462), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 114/268 (42%), Positives = 154/268 (57%), Gaps = 37/268 (13%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPII A L  D D   AR+VKGR+E+TTL +V  YIE+V+    
Sbjct: 1115 GVPRIKEIINASKLISTPIIKAVLVNDKDERAARVVKGRVEKTTLEDVTYYIEDVYKESQ 1174

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTR---------------------------G 856
            +++ +K+D+D I  L LE+ ID I   I +T+                           G
Sbjct: 1175 AYLQVKIDLDTIEKLQLELTIDQIMDAIVKTKLKIPRSCXSIVGKNKIQILVSEMGLENG 1234

Query: 857  ISGHLTVSGHSFLILKPKDSSK-------SFNSKMYQMKQLLPSVVIKGVQGINRAVIHE 909
                 + S      L  KD  +       S   KM Q+K+ L  VV+KG+  + +AVI+ 
Sbjct: 1235 KPSSRSTSSREIAALAKKDPDERDRLERSSLFYKMQQLKRQLTKVVVKGLPEVAKAVINV 1294

Query: 910  EDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLV 969
             D +G  K +LLVEG  L+DVMAT GV   K  +N+  E++  LGIEAARS+I++EI   
Sbjct: 1295 RD-DG--KKELLVEGYGLKDVMATDGVIATKTKTNHVIEIFHVLGIEAARSSIVSEIDYT 1351

Query: 970  MENHGMSIDFRHPMLVADLMTSKGEVLG 997
            M +HGM +D RH  L+AD+MT KGE+LG
Sbjct: 1352 MRSHGMVVDPRHLQLLADVMTYKGEILG 1379



 Score =  174 bits (441), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 105/277 (37%), Positives = 156/277 (56%), Gaps = 15/277 (5%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           GL  G ++ E+ V Q S +++ ++NL+  D  R P+ +G LD RMG +   A C TC  N
Sbjct: 15  GLQFGALSNEEIVSQ-SEVEVSTRNLFDLDKGRVPVSNGALDPRMGISSSMAECATCHGN 73

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
           L+ C GHFG+I L LPVFH+GYF+  I +LQ+ICKN  C+ VLL E+    + A+LR P 
Sbjct: 74  LATCHGHFGHIKLALPVFHVGYFKATIQVLQTICKN--CSAVLLDEBSKRKYLAELRRPD 131

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKK-------CGLLKISHEKYKNRTKKK 253
           +  L +  + KK+L+  KK   C  CG +NGVVK+          LKI H+ ++   KK 
Sbjct: 132 IDNLRKMKIVKKVLDQAKKQRRCLVCGALNGVVKRAAAGGGGAAALKIVHDSFRWVGKKG 191

Query: 254 DAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMN-AEL 312
                    ++ +  + NP++E   K    + LNPL VL LF+ I   D  LL ++ A+ 
Sbjct: 192 AEEKTRWNDDFQKYFRQNPDLERFYK-RCYEDLNPLRVLNLFKQITPTDCELLGIDPAKG 250

Query: 313 SKPSDLILTRLLVPPNCIRPSVI---SDLKSDNDVVL 346
            +P   I   L  PP CIRPSV+   S+  +++D+ +
Sbjct: 251 GRPEMYIWRYLPAPPVCIRPSVMMGQSNTSNEDDLTV 287



 Score = 96.3 bits (238), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 42/57 (73%), Positives = 48/57 (84%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV +SF+SGL P EFFFH + GREGLVDTAVKTAETGY  RRL+KS+EDL  QYD
Sbjct: 844 KGFVSDSFYSGLNPPEFFFHAISGREGLVDTAVKTAETGYTSRRLMKSMEDLSTQYD 900



 Score = 72.8 bits (177), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 71/251 (28%), Positives = 108/251 (43%), Gaps = 45/251 (17%)

Query: 932  ATYGVKGVKCSSNNTYEV-YKTLGIEAARSTIMTEIKLVMENHGMSI-DFRHPMLVADLM 989
            A  G +G+  ++  T E  Y +  +  +   + T+    + N G  I  FR+     D M
Sbjct: 864  AISGREGLVDTAVKTAETGYTSRRLMKSMEDLSTQYDGTVRNSGDGIVQFRYGADGLDPM 923

Query: 990  TSKGEVLGNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLD------------ 1037
                E+ G+  PV  +R  +       + SD +L   E+  + N TL+            
Sbjct: 924  ----EMEGDAVPVNFERTWEHCFFVTLNHSDKALYPYEVTDIVNNTLNPLRDSLIRRDNL 979

Query: 1038 ----------SKEFL--QDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSHQ 1085
                        E++   D   NF   IKKF+    KK  V +   +    L   ++  +
Sbjct: 980  GKIVAKNXENKIEYVDKNDAKRNFYESIKKFVR---KKVGVIAKM-REGHSLDPMLIKPK 1035

Query: 1086 DKIGHGRESNPF----------PSACKAEA-CREKYVRAQIEPATAVGALAAQSIGEPGT 1134
            +K+   +    +          P   K    C  KY++A++EP TAVGA+ A SIGEPGT
Sbjct: 1036 NKVVTNKAVEXYLINKLQKISVPMIKKFLGLCLTKYIKARVEPGTAVGAVGAHSIGEPGT 1095

Query: 1135 QMTLKTFHFAG 1145
            QMTLKTFHFAG
Sbjct: 1096 QMTLKTFHFAG 1106



 Score = 60.8 bits (146), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 26/41 (63%), Positives = 36/41 (87%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRA 62
           LM  KSNL+TP++GE +IAATQDFITG +L+T K++F++RA
Sbjct: 534 LMGVKSNLLTPKSGEPIIAATQDFITGSFLITXKDSFYDRA 574



 Score = 47.0 bits (110), Expect = 0.081,   Method: Compositional matrix adjust.
 Identities = 25/56 (44%), Positives = 34/56 (60%), Gaps = 2/56 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL--LQAVPRSEPVPRTLLFD 721
            D  FDAAFY + D + GVSE II+G  M++GTG  KL     +P  +  P+  LF+
Sbjct: 1403 DHLFDAAFYTKDDKVEGVSERIILGQTMSIGTGSFKLSVQNNIPPEKLEPKKTLFE 1458


>gi|346324489|gb|EGX94086.1| DNA-directed RNA polymerase III [Cordyceps militaris CM01]
          Length = 1486

 Score =  262 bits (670), Expect = 8e-67,   Method: Compositional matrix adjust.
 Identities = 125/274 (45%), Positives = 177/274 (64%), Gaps = 28/274 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIM+H AK+ P RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 511 DGDIVLFNRQPSLHKLSIMSHLAKIRPWRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 570

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EA+               LM  + NL TP++G  +I ATQDFIT  +LL+ K+ FF+R
Sbjct: 571 RTEAI--------------TLMGVRHNLTTPKDGAPIIGATQDFITAAFLLSSKDRFFDR 616

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                +   ++   + +             P   +    +WTGKQ+F+++++PN++  + 
Sbjct: 617 KTFTYMCMHMLDSQTRL----------DLPPPTIIAPVALWTGKQLFNVMMRPNKESNIR 666

Query: 521 ANLKTKGRAYTANE----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            N ++K + ++       +    D ++++RNSE++ G MDK+T+G+G K +VFY++LRDF
Sbjct: 667 INFESKCKTFSGKSKNIPDMDPNDGWLVVRNSEVMCGVMDKATVGTGKKDSVFYVMLRDF 726

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           G D A TAM RL+R+ +  L NRGFSIG+GDV P
Sbjct: 727 GADHAATAMNRLARLCARTLTNRGFSIGVGDVCP 760



 Score =  208 bits (530), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 175/524 (33%), Positives = 254/524 (48%), Gaps = 99/524 (18%)

Query: 970  MENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSR-SDPSLSAQEI 1028
            ME  G  + F      A+  T   E +   TP E + L  +++A   +R     L   E 
Sbjct: 967  MEGSGAPVQFVRTWRHAENTTWDNEEVAL-TPNEARELCGNMLASERNRFPRKGLLHGED 1025

Query: 1029 LALSNETLDSKEFLQDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKI 1088
            LA +    D  ++  D  E      +KF+ E   K+ V +  DK+ +      L+ +DK 
Sbjct: 1026 LAYT----DVSDYAVDEHEG----ARKFITEV--KDFVGALADKLERVRALAGLAGKDKT 1075

Query: 1089 GHGRESNPFPSACKAEA---------CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLK 1139
            G   + +   +A K  A         C  KY +AQ+EP  AVGA+ AQSIGEPGTQMTLK
Sbjct: 1076 GSAAQDHADRTA-KITATTLRLFIKLCLHKYKKAQVEPGHAVGAVGAQSIGEPGTQMTLK 1134

Query: 1140 TFHFAG------------------------------------------EVCEYIEEVFV- 1156
            TFHFAG                                           V   IE++F+ 
Sbjct: 1135 TFHFAGVAGMSITQGVPRIKEIINASKAISTPVITCPLMNNQQIEAAKVVKARIEKIFLQ 1194

Query: 1157 -----------PDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRG----------ISG 1195
                       PD+  +++++D   +  +HL +DI  I   I + R           I  
Sbjct: 1195 DVLQYVEDEWRPDEGNVVVQVDRQVLADMHLGIDIQDIAQAICKDRKMKIQATDVAIIGD 1254

Query: 1196 HLTVSGHSFLILKPKDSSKSFNS------KMYQMKQLLPSVVIKGVQGINRAVIHEEDVE 1249
             +++  H  +  K    SK+         +   ++++LP++ I G    +RA+I  E  E
Sbjct: 1255 RISIRVHDNIGAKRTTRSKTGEDTSDMLLRANALRRMLPALPISGYPNASRALI--ETCE 1312

Query: 1250 GVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENH 1309
              T +++LVEG   +  M T GV G K  +N+  E  + LGIEAAR+TI  EI+ VM+  
Sbjct: 1313 DST-HRVLVEGYGYQACMTTEGVIGTKVRTNSVTECNEVLGIEAARTTIAFEIEQVMKF- 1370

Query: 1310 GMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTD 1369
             M ID RH  L+AD MT KGE+LGITR GL+KM++SVL+LASFE T DHLF+AA   +TD
Sbjct: 1371 -MEIDHRHMQLLADAMTFKGEILGITRFGLSKMRDSVLHLASFEKTPDHLFEAAAGMKTD 1429

Query: 1370 CISGVSECIIMGLPMNVGTGLIKLLQ--AVPRSEPVPRTLLFDN 1411
             I GVSE IIMG  M VGTG  ++++   +  ++   R  LF++
Sbjct: 1430 KIEGVSEGIIMGQGMAVGTGAFQVVRRLGIAAADVGQRETLFED 1473



 Score =  202 bits (515), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 112/271 (41%), Positives = 158/271 (58%), Gaps = 10/271 (3%)

Query: 79  FRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCG 138
           FRG+  G  + +D +  Q+  +I ++ LY  +  R P  +G LD ++GT+ K   C TC 
Sbjct: 66  FRGIKFGIQSNQD-ISNQAVTEISNRLLYDIENNRAPYQNGPLDYQLGTSSKTGKCATCN 124

Query: 139 QNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN 198
           ++L +C GHFGY+ LPLPVFH+GY R +I+ILQ ICK+  C RVLL E     F A+LR 
Sbjct: 125 ESLQNCNGHFGYVRLPLPVFHVGYLRFIISILQEICKD--CGRVLLEEPHRRQFLAELRR 182

Query: 199 PALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTK----KKD 254
           P +  L R  + K+I E  +K   C +CG +NG ++K G+LK+ H+K+ +  K    KK 
Sbjct: 183 PFIDNLRRTQICKRINEQCRKTKNCAYCGSVNGQIRKFGVLKLVHDKFASFNKSTAIKKV 242

Query: 255 AIVEDLL--AEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL 312
                +L  A + EA + NPE+E H +  + + LNPL VL LF+ I   D  LL +NA  
Sbjct: 243 PPESKVLFEASFTEAKRENPELEKHLRKAM-EDLNPLRVLNLFKMITATDCELLGLNAAE 301

Query: 313 SKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
            +P   I   L  PP CIRPSV  D  S+ D
Sbjct: 302 GRPEMFIWQFLPAPPVCIRPSVAQDNASNED 332



 Score =  146 bits (368), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 98/274 (35%), Positives = 152/274 (55%), Gaps = 22/274 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+IT  L  +  ++ A++VK R+E+  L +V +Y+E+ + PD+
Sbjct: 1149 GVPRIKEIINASKAISTPVITCPLMNNQQIEAAKVVKARIEKIFLQDVLQYVEDEWRPDE 1208

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRG----------ISGHLTVSGHSFLILKP 873
              +++++D   +  +HL +DI  I   I + R           I   +++  H  +  K 
Sbjct: 1209 GNVVVQVDRQVLADMHLGIDIQDIAQAICKDRKMKIQATDVAIIGDRISIRVHDNIGAKR 1268

Query: 874  KDSSKSFNS------KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927
               SK+         +   ++++LP++ I G    +RA+I  E  E  T +++LVEG   
Sbjct: 1269 TTRSKTGEDTSDMLLRANALRRMLPALPISGYPNASRALI--ETCEDST-HRVLVEGYGY 1325

Query: 928  RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 987
            +  M T GV G K  +N+  E  + LGIEAAR+TI  EI+ VM+   M ID RH  L+AD
Sbjct: 1326 QACMTTEGVIGTKVRTNSVTECNEVLGIEAARTTIAFEIEQVMKF--MEIDHRHMQLLAD 1383

Query: 988  LMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDP 1021
             MT KGE+LG  T   L ++ D ++   S    P
Sbjct: 1384 AMTFKGEILGI-TRFGLSKMRDSVLHLASFEKTP 1416



 Score =  102 bits (253), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 45/59 (76%), Positives = 51/59 (86%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSF++GL PTEF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 884 PSKGFVKNSFYTGLYPTEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSTQYD 942



 Score = 50.1 bits (118), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 21/40 (52%), Positives = 29/40 (72%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           LM  + NL TP++G  +I ATQDFIT  +LL+ K+ FF+R
Sbjct: 577 LMGVRHNLTTPKDGAPIIGATQDFITAAFLLSSKDRFFDR 616


>gi|400602522|gb|EJP70124.1| DNA-directed RNA polymerase III subunit RPC1 [Beauveria bassiana
           ARSEF 2860]
          Length = 1443

 Score =  262 bits (669), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 127/274 (46%), Positives = 177/274 (64%), Gaps = 28/274 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIM+H  KV P RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 466 DGDIVLFNRQPSLHKLSIMSHLVKVRPWRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 525

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EA+               LM  + NL TP++G  +I ATQDFIT  +LL+ K+ FF+R
Sbjct: 526 RTEAI--------------TLMGVRHNLTTPKDGAPIIGATQDFITAAFLLSSKDRFFDR 571

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                +   ++   +       RF      P   +    +WTGKQ+F+++++PN++  + 
Sbjct: 572 KTFTYMCMHMLETNT-------RF---DLPPPTIIAPVALWTGKQLFNVMMRPNKESKIR 621

Query: 521 ANLKTKGRAYTANE----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            N ++K + ++       +    D ++++RNSE++ G MDK+T+G+G K +VFY++LRDF
Sbjct: 622 INFESKCKTFSGKSKNIPDMDPNDGWLVVRNSEVMCGVMDKATVGTGKKDSVFYVMLRDF 681

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           G D A TAM RL+R+ +  L NRGFSIG+GDV P
Sbjct: 682 GADHAATAMNRLARLCARTLTNRGFSIGVGDVFP 715



 Score =  207 bits (527), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 113/271 (41%), Positives = 158/271 (58%), Gaps = 10/271 (3%)

Query: 79  FRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCG 138
           FRG+  G  + +D +  Q+  +I ++ LY  +  R P  +G LD ++GT+ K   C TC 
Sbjct: 21  FRGIKFGIQSNQD-ISNQAVTEISNRLLYDIENNRAPYQNGPLDYQLGTSSKTGKCATCN 79

Query: 139 QNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN 198
           ++L +C GHFGY+ LPLPVFH+GY R +I+ILQ ICK+  C RVLL E +   F ++LR 
Sbjct: 80  ESLQNCNGHFGYVRLPLPVFHVGYLRFIISILQEICKD--CGRVLLDEPQRQQFLSELRR 137

Query: 199 PALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEK---YKNRTKKKDA 255
           P +  L R  + KKI E  +K   CP+CG +NG ++K G+LK+ H+K   Y   T  K  
Sbjct: 138 PLIDNLRRTQICKKINEQCRKTKNCPYCGSVNGQIRKFGVLKLVHDKFISYNKSTAIKKV 197

Query: 256 IVEDLL---AEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL 312
             E  +   A + EA + NPE+E H +  + + LNPL VL LF+ I   D  LL +NA  
Sbjct: 198 PPESKILFDASFTEAKRENPELEKHLRKAM-EDLNPLRVLNLFKLITATDCELLGLNATE 256

Query: 313 SKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
            +P   I   L  PP CIRPSV  D  S+ D
Sbjct: 257 GRPEMFIWQFLPAPPVCIRPSVAQDNASNED 287



 Score =  195 bits (495), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 137/380 (36%), Positives = 196/380 (51%), Gaps = 79/380 (20%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-------------------- 1145
            C  KY +AQ+EP  AVGA+ AQSIGEPGTQMTLKTFHFAG                    
Sbjct: 1056 CLHKYKKAQVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIINAS 1115

Query: 1146 ----------------------EVCEYIEEVFV------------PDDSFILIKLDMDRI 1171
                                   V   IE++F+            PD+  +++++D   +
Sbjct: 1116 KLISTPVITCPLMNNQQIEAAKVVKARIEKIFLEDVLHYIEDEWRPDEGNVVVQVDRQAL 1175

Query: 1172 RLLHLEVDIDSIRYCIERTRGISGHLT------------VSGHSFLILKPKDSSKSFNS- 1218
              +HL + I  I   I + R +    T            V  ++ ++ K     K+    
Sbjct: 1176 ADMHLGIGIHDIAQAICKDRKMKIQATDVAIIGDRISIRVRDNASVLAKRTTRGKAAEDT 1235

Query: 1219 -----KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVK 1273
                 +   ++++LP++ I G    +RA+I  E  E  T +++LVEG   +  + T GV 
Sbjct: 1236 SDMLLRANALRRMLPALPISGYPDASRALI--ETCEDGT-HRVLVEGYGFQACLTTEGVI 1292

Query: 1274 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 1333
            G +  +N+  E    LGIEAAR+TI  EI+ VM+   M ID RH  L+AD MT KGE+LG
Sbjct: 1293 GTQVRTNSVTECNDVLGIEAARTTIAFEIEQVMKF--MEIDHRHMQLLADAMTFKGEILG 1350

Query: 1334 ITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            ITR GL+KM++SVL+LASFE T DHLF+AA   +TD I GVSE IIMG  M VGTG  ++
Sbjct: 1351 ITRFGLSKMRDSVLHLASFEKTPDHLFEAAAGMKTDEIEGVSEGIIMGQGMAVGTGAFQV 1410

Query: 1394 LQ--AVPRSEPVPRTLLFDN 1411
            ++   +  ++   R  LF++
Sbjct: 1411 VRRLGIAAADVGQRETLFED 1430



 Score =  135 bits (340), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 95/276 (34%), Positives = 149/276 (53%), Gaps = 24/276 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTP+IT  L  +  ++ A++VK R+E+  L +V  YIE+ + PD+
Sbjct: 1104 GVPRIKEIINASKLISTPVITCPLMNNQQIEAAKVVKARIEKIFLEDVLHYIEDEWRPDE 1163

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLT------------VSGHSFLIL 871
              +++++D   +  +HL + I  I   I + R +    T            V  ++ ++ 
Sbjct: 1164 GNVVVQVDRQALADMHLGIGIHDIAQAICKDRKMKIQATDVAIIGDRISIRVRDNASVLA 1223

Query: 872  KPKDSSKSFNS------KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD 925
            K     K+         +   ++++LP++ I G    +RA+I  E  E  T +++LVEG 
Sbjct: 1224 KRTTRGKAAEDTSDMLLRANALRRMLPALPISGYPDASRALI--ETCEDGT-HRVLVEGY 1280

Query: 926  NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 985
              +  + T GV G +  +N+  E    LGIEAAR+TI  EI+ VM+   M ID RH  L+
Sbjct: 1281 GFQACLTTEGVIGTQVRTNSVTECNDVLGIEAARTTIAFEIEQVMKF--MEIDHRHMQLL 1338

Query: 986  ADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDP 1021
            AD MT KGE+LG  T   L ++ D ++   S    P
Sbjct: 1339 ADAMTFKGEILGI-TRFGLSKMRDSVLHLASFEKTP 1373



 Score =  102 bits (253), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 45/59 (76%), Positives = 51/59 (86%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSF++GL PTEF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 839 PSKGFVKNSFYTGLYPTEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSTQYD 897



 Score = 50.1 bits (118), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 21/40 (52%), Positives = 29/40 (72%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           LM  + NL TP++G  +I ATQDFIT  +LL+ K+ FF+R
Sbjct: 532 LMGVRHNLTTPKDGAPIIGATQDFITAAFLLSSKDRFFDR 571


>gi|145342014|ref|XP_001416093.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144576317|gb|ABO94385.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 1395

 Score =  261 bits (666), Expect = 3e-66,   Method: Compositional matrix adjust.
 Identities = 129/272 (47%), Positives = 182/272 (66%), Gaps = 25/272 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D++LFNRQPSLHK+SIMAH+A+++  RT RFNECVCTPYNADFDGDEMN+H PQTEEA
Sbjct: 469 DGDILLFNRQPSLHKMSIMAHKARIMECRTLRFNECVCTPYNADFDGDEMNIHCPQTEEA 528

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM  + NL TP+NGE+LIAATQDF+T  +LLT K+AFF+R
Sbjct: 529 RAEAMQ--------------LMGVQHNLCTPKNGEILIAATQDFLTAAFLLTIKDAFFDR 574

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           +Q      +L+A   D        S     P + ++   +WTGKQ+FS++++P     + 
Sbjct: 575 SQF----GSLVAYMGDAL-----LSVDLPTPAI-LKPIELWTGKQVFSVLIRPKASDHIY 624

Query: 521 ANLKTKGRAYTANEE-FCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            NL+   + Y   ++  C  D YV ++NSE+++G + K+TLGSG K+ +FY+L  ++G +
Sbjct: 625 VNLEVAEKLYNKKDKTMCPDDGYVCIQNSEIISGQLGKATLGSGNKSGLFYVLNIEYGAE 684

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
            A  AM RL+++++ +L  RGFSIGI DV+P 
Sbjct: 685 AAANAMNRLAKLSARWLGTRGFSIGIDDVSPA 716



 Score =  227 bits (578), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 118/255 (46%), Positives = 170/255 (66%), Gaps = 9/255 (3%)

Query: 1145 GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSG 1201
            GE+C  I  V  P D ++ + LDM+ I  L L+V I S+R  +    + +    H+ ++G
Sbjct: 1120 GEICSEINIVVRPHDLYLELMLDMEAINQLQLDVTIHSVRLAVLGAPKLKLKPQHVLIAG 1179

Query: 1202 HSFLILKPKDSSKSFNSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLV 1258
             + L + P + +      ++ ++ +   +P+V+++G+  + RAVI+++   G   Y L+V
Sbjct: 1180 ENILHVLPSEEALIEKRALFTLQHMRLAIPAVIVQGIPSVGRAVINDK---GDGTYNLIV 1236

Query: 1259 EGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHP 1318
            EG NL+ VM   G+KG +  +N+  E  +TLGIEAAR+ I+ EI   M  HGMSID RH 
Sbjct: 1237 EGVNLQSVMGIEGIKGTETRTNHVMECERTLGIEAARACIIEEIDSTMGAHGMSIDNRHS 1296

Query: 1319 MLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECI 1378
            ML+AD+MT KGEVLGITR G+AKMK+SVL LASFE T+DHLFDAA +G+TD I GVSECI
Sbjct: 1297 MLLADVMTYKGEVLGITRFGMAKMKDSVLMLASFEKTTDHLFDAALHGRTDYIDGVSECI 1356

Query: 1379 IMGLPMNVGTGLIKL 1393
            IMG+PM +GTG+ +L
Sbjct: 1357 IMGIPMPIGTGMFRL 1371



 Score =  208 bits (529), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 110/240 (45%), Positives = 147/240 (61%), Gaps = 13/240 (5%)

Query: 100 QIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEAN-CTTCGQNLSDCVGHFGYIDLPLPVF 158
            +  +NLY Q PQRTP+P+G+LD RMGT  K    C TC  N+ DC GHFGYI L LPVF
Sbjct: 54  HVFERNLY-QMPQRTPMPNGILDPRMGTTDKRGGECATCRGNMVDCAGHFGYIKLELPVF 112

Query: 159 HIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTK 218
           HIGYF+ +I++LQ +CKN  C+R+LL E+    F  + RNP L    R+ L KK+ E  K
Sbjct: 113 HIGYFKNIISVLQCVCKN--CSRILLNEDDQDMFLKRYRNPRLEITQRRLLYKKLTEKCK 170

Query: 219 KVSVCPHCGEINGVVKKCG-LLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAH 277
           +   CPHCG+ NGV K+ G  LKI HEKY     K  A++E+ + E+  A+K+N ++ A 
Sbjct: 171 RCRTCPHCGDYNGVTKRAGQTLKIVHEKY----SKNPALLEEFMKEFETALKYNEQLRAS 226

Query: 278 KKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD 337
               +   LNP+ VL + + +   D  LL +     +P  L+LT L VPP CIRPSV  D
Sbjct: 227 LP-KVQDDLNPIRVLGILQRVTSADCELLDI---ADRPEHLLLTHLPVPPCCIRPSVEMD 282



 Score =  202 bits (513), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 111/240 (46%), Positives = 156/240 (65%), Gaps = 9/240 (3%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+NISTPIITA L  D D+  AR+VKGR+E+TTLGE+C  I  V  P D
Sbjct: 1075 GVPRIKEIINASKNISTPIITASLMSDRDVKAARVVKGRVEKTTLGEICSEINIVVRPHD 1134

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSGHSFLILKPKDSS--- 877
             ++ + LDM+ I  L L+V I S+R  +    + +    H+ ++G + L + P + +   
Sbjct: 1135 LYLELMLDMEAINQLQLDVTIHSVRLAVLGAPKLKLKPQHVLIAGENILHVLPSEEALIE 1194

Query: 878  KSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVK 937
            K     +  M+  +P+V+++G+  + RAVI++   +G   Y L+VEG NL+ VM   G+K
Sbjct: 1195 KRALFTLQHMRLAIPAVIVQGIPSVGRAVIND---KGDGTYNLIVEGVNLQSVMGIEGIK 1251

Query: 938  GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            G +  +N+  E  +TLGIEAAR+ I+ EI   M  HGMSID RH ML+AD+MT KGEVLG
Sbjct: 1252 GTETRTNHVMECERTLGIEAARACIIEEIDSTMGAHGMSIDNRHSMLLADVMTYKGEVLG 1311



 Score =  108 bits (269), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 50/64 (78%), Positives = 56/64 (87%), Gaps = 1/64 (1%)

Query: 606 GDVTPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           G+ TP  +GFV NSFFSG+ PTEFFFHTM GREGLVDTAVKTAETGYM RRL+K+LEDL 
Sbjct: 834 GEKTPAAKGFVANSFFSGMRPTEFFFHTMAGREGLVDTAVKTAETGYMSRRLMKALEDLS 893

Query: 665 VQYD 668
           +QYD
Sbjct: 894 LQYD 897



 Score = 77.8 bits (190), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 55/152 (36%), Positives = 77/152 (50%), Gaps = 15/152 (9%)

Query: 998  NGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFL 1057
            +  P+E KR L ++   NS+R +P  +   + A     LD     Q    N + ++ +  
Sbjct: 926  DAQPIEFKRCLMNVRGLNSARGEPPATRSALDA----ALD-----QFKRNNRIINVDEEG 976

Query: 1058 EEFSKKESVTSHQDKVSQ----PLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRA 1113
            E    +E V S    +SQ     +R  I++  +    G   +        +AC  KY   
Sbjct: 977  ESAETRELVYSA--GISQLFYENMRTFIINEVESPSDGVYMSDRQMKAFLDACARKYTEK 1034

Query: 1114 QIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            +IEP TAVGA+ AQSIGEPGTQMTLKTFHFAG
Sbjct: 1035 RIEPGTAVGAIGAQSIGEPGTQMTLKTFHFAG 1066



 Score = 61.6 bits (148), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 27/42 (64%), Positives = 35/42 (83%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 63
           LM  + NL TP+NGE+LIAATQDF+T  +LLT K+AFF+R+Q
Sbjct: 535 LMGVQHNLCTPKNGEILIAATQDFLTAAFLLTIKDAFFDRSQ 576



 Score = 57.0 bits (136), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 24/37 (64%), Positives = 30/37 (81%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 704
            D  FDAA +G+TD I GVSECIIMG+PM +GTG+ +L
Sbjct: 1335 DHLFDAALHGRTDYIDGVSECIIMGIPMPIGTGMFRL 1371


>gi|426198021|gb|EKV47947.1| hypothetical protein AGABI2DRAFT_202225 [Agaricus bisporus var.
           bisporus H97]
          Length = 1402

 Score =  260 bits (665), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 136/284 (47%), Positives = 180/284 (63%), Gaps = 38/284 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIM HRAKV P RTFR NECVC PYNADFDGDEMN+H+PQT+EA
Sbjct: 447 DGDIVLFNRQPSLHKLSIMCHRAKVRPWRTFRLNECVCGPYNADFDGDEMNLHVPQTDEA 506

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL               LM+ K NLVTPRNG+ +IAA QDFIT  YLL++K+ FF+R
Sbjct: 507 RAEALE--------------LMSVKHNLVTPRNGDPVIAAIQDFITASYLLSRKDTFFDR 552

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q  +I      D +    I     W+          A +WTGKQ+F+++++PN++  V 
Sbjct: 553 RQFTQIC-CYFGDANMQIDIPPPTIWKP---------ARLWTGKQVFNVLMRPNKNSEVL 602

Query: 521 ANLKTK-------------GRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKAN 567
            N++ K              R   AN +    D ++++ NSE++ G MDK+T+GSG K +
Sbjct: 603 VNVECKCNKWEEAKPENYPSRMIPAN-DLSPNDGWLVVVNSEIMCGVMDKATVGSGKKKS 661

Query: 568 VFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           +F ++LRD+G   A  AM RL+++ + YL N GFS+GI DV PG
Sbjct: 662 IFGVILRDYGPHEAAAAMNRLAKLCARYLANYGFSLGINDVIPG 705



 Score =  217 bits (552), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 165/498 (33%), Positives = 248/498 (49%), Gaps = 95/498 (19%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G+  P++L+R    + A ++ R+  SL   E+L L+++TL +  F+ + ++ ++  ++ F
Sbjct: 913  GDAQPIDLERTWRHVSA-SAGRAGRSLLPFEVLELTDQTLATPRFVNEFTQTYLDILRDF 971

Query: 1057 LEEFSKKESVTSHQDK-----------------VSQPLREQILSHQDKIGHGRESN--PF 1097
            +     +      Q +                 +S    +  LS  D      E     F
Sbjct: 972  IHNNVARNIAEHRQSRGMFEALERDTEWDADTDLSMGATDSDLSIVDNKAKVTEEQLRRF 1031

Query: 1098 PSACKAEACREKYVRAQIEPATAVGAL--------------------------------- 1124
               C A     KY +A+IEP + VGA+                                 
Sbjct: 1032 LHVCWA-----KYAKARIEPGSTVGAVGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPR 1086

Query: 1125 ------AAQSIGEPGTQMTLKTFH---------------FAGEVCEYIEEVFVPDDSFIL 1163
                  AA++I  P     L T                   G+V   +EE + P+  +I 
Sbjct: 1087 IKEIINAAKAISTPIISCKLVTRSSEASARIVKGRLEKTLLGDVASVLEEAWAPEYVYIC 1146

Query: 1164 IKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF---NSKM 1220
            I +D + IR L LE+ +D I++ I   +     L V   S +++  K   + +     K 
Sbjct: 1147 ILIDTEAIRKLQLELTLDDIKWAIVNWK----KLKVKQESIIVIPNKQRLRIYVDGQDKY 1202

Query: 1221 YQMKQL---LPSVVIKGVQGINRAVIH---EEDVEGVTKYK-LLVEGDNLRDVMATYGVK 1273
            Y++++L   LP++V+KGV  I+RA+I+   ++D +G    K LLVEG  L+  M T GV 
Sbjct: 1203 YRLRELKRGLPNIVVKGVPTISRAIINIKDQDDAKGKKGDKELLVEGYGLQKCMITEGVV 1262

Query: 1274 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 1333
            G   +SN+  EV + LGIEAAR TI+ EI+  M++H M ID RH ML+ D+MT KGEVLG
Sbjct: 1263 GEATTSNHVIEVAQVLGIEAARRTIINEIQYTMKSHDMIIDPRHVMLLGDVMTYKGEVLG 1322

Query: 1334 ITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLP-MNVGTGLIK 1392
            ITR G+AKMK+SVL LASFE T+DHLFDA+ +G+TD ISGVSE IIMG P    GT +  
Sbjct: 1323 ITRFGVAKMKDSVLMLASFEKTTDHLFDASAFGKTDSISGVSESIIMGNPAATCGTSMPA 1382

Query: 1393 LLQAVPRSEPVPRTLLFD 1410
            L++  P  +  PR LLF+
Sbjct: 1383 LVRPSPVLKK-PRKLLFE 1399



 Score =  202 bits (515), Expect = 9e-49,   Method: Compositional matrix adjust.
 Identities = 107/247 (43%), Positives = 145/247 (58%), Gaps = 5/247 (2%)

Query: 97  SHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP 156
           S  +I  ++LY     R P+ +G+LDRR+GT  K A C TCGQ+   CVGH+ YI L +P
Sbjct: 30  SEFEITHRDLYTP-VDRLPVQNGVLDRRLGTTDKNAFCETCGQSYVHCVGHYAYIKLVVP 88

Query: 157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILET 216
           VFHIGYF+ +I++LQ+ICK  TCARVLL E     F  + R P L  + R++L K +  T
Sbjct: 89  VFHIGYFKHIISVLQAICK--TCARVLLEEPDRRTFIKRFRRPNLENIQRQALSKSVNAT 146

Query: 217 TKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEA 276
            +KV  CP+C  ING VKK G LKI H+K+  R KK    +E     + +AV+   E+  
Sbjct: 147 ARKVVHCPYCSAINGTVKKAGALKIIHDKF--RAKKTAEEMEKWKKTFTKAVEAQKELSM 204

Query: 277 HKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVIS 336
           +      + LNPL+VL LF  +  ED  LL +     +P + +   L VPP CIRPSV  
Sbjct: 205 YLNKAAHEELNPLKVLDLFRRVSDEDCELLGLQPAWGRPEEFVWQYLSVPPVCIRPSVAQ 264

Query: 337 DLKSDND 343
           D  S+ D
Sbjct: 265 DGASNED 271



 Score =  182 bits (461), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 109/244 (44%), Positives = 154/244 (63%), Gaps = 14/244 (5%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ ISTPII+  L   +    ARIVKGRLE+T LG+V   +EE + P+ 
Sbjct: 1083 GVPRIKEIINAAKAISTPIISCKLVTRSSEASARIVKGRLEKTLLGDVASVLEEAWAPEY 1142

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF--- 880
             +I I +D + IR L LE+ +D I++ I   +     L V   S +++  K   + +   
Sbjct: 1143 VYICILIDTEAIRKLQLELTLDDIKWAIVNWK----KLKVKQESIIVIPNKQRLRIYVDG 1198

Query: 881  NSKMYQMKQL---LPSVVIKGVQGINRAVIH---EEDVEGVTKYK-LLVEGDNLRDVMAT 933
              K Y++++L   LP++V+KGV  I+RA+I+   ++D +G    K LLVEG  L+  M T
Sbjct: 1199 QDKYYRLRELKRGLPNIVVKGVPTISRAIINIKDQDDAKGKKGDKELLVEGYGLQKCMIT 1258

Query: 934  YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
             GV G   +SN+  EV + LGIEAAR TI+ EI+  M++H M ID RH ML+ D+MT KG
Sbjct: 1259 EGVVGEATTSNHVIEVAQVLGIEAARRTIINEIQYTMKSHDMIIDPRHVMLLGDVMTYKG 1318

Query: 994  EVLG 997
            EVLG
Sbjct: 1319 EVLG 1322



 Score =  104 bits (260), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 46/61 (75%), Positives = 53/61 (86%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV+NSF+SGL  TEF FH + GREGLVDTAVKTAETGYMQRRL+K+LEDL  QYD+
Sbjct: 828 PSKGFVRNSFYSGLVATEFLFHAISGREGLVDTAVKTAETGYMQRRLMKALEDLTTQYDL 887

Query: 670 S 670
           S
Sbjct: 888 S 888



 Score = 61.2 bits (147), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 28/46 (60%), Positives = 36/46 (78%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRI 67
           LM+ K NLVTPRNG+ +IAA QDFIT  YLL++K+ FF+R Q  +I
Sbjct: 513 LMSVKHNLVTPRNGDPVIAAIQDFITASYLLSRKDTFFDRRQFTQI 558



 Score = 46.6 bits (109), Expect = 0.099,   Method: Compositional matrix adjust.
 Identities = 27/55 (49%), Positives = 35/55 (63%), Gaps = 2/55 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLP-MNVGTGLIKLLQAVPRSEPVPRTLLFD 721
            D  FDA+ +G+TD ISGVSE IIMG P    GT +  L++  P  +  PR LLF+
Sbjct: 1346 DHLFDASAFGKTDSISGVSESIIMGNPAATCGTSMPALVRPSPVLKK-PRKLLFE 1399


>gi|403416877|emb|CCM03577.1| predicted protein [Fibroporia radiculosa]
          Length = 1403

 Score =  260 bits (665), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 136/282 (48%), Positives = 177/282 (62%), Gaps = 35/282 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIM HR KV P R+FR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 449 DGDVVLFNRQPSLHKLSIMCHRVKVRPWRSFRLNECVCGPYNADFDGDEMNLHVPQTEEA 508

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL               LM+ K NLVTPRNGE +IAA QDFIT  +LL++++ FF+R
Sbjct: 509 RTEALE--------------LMSVKHNLVTPRNGEPVIAAIQDFITASFLLSRRDTFFDR 554

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q  +I S       D    I       W PV       +WTGKQIF+++++PN+   V 
Sbjct: 555 RQFTQICSYF----GDANMQIDIPPPTIWKPV------RLWTGKQIFNVLMRPNKSSNVM 604

Query: 521 ANLKTKGRAYTANEEFCH-----------RDSYVILRNSELLAGSMDKSTLGSGGKANVF 569
            N+++K       +  C+            D ++++ NSE++ G MDK+T+GSG K +VF
Sbjct: 605 VNVESKCNKQEKPDPKCYPRMNAAPDLSPNDGWLVIVNSEIMCGVMDKATVGSGKKKSVF 664

Query: 570 YILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
            I++RD+G   A  AM RL+++ + YL N GFS+GI DV PG
Sbjct: 665 GIIMRDYGPHEAAAAMNRLAKLCARYLANYGFSLGINDVIPG 706



 Score =  217 bits (552), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 147/373 (39%), Positives = 202/373 (54%), Gaps = 70/373 (18%)

Query: 1104 EACREKYVRAQIEPATAVGAL--------------------------------------- 1124
            E C  KYV+A+IEP + VGA+                                       
Sbjct: 1034 EICWTKYVKAKIEPGSTVGAVGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIIN 1093

Query: 1125 AAQSIGEPGTQMTLKTFH---------------FAGEVCEYIEEVFVPDDSFILIKLDMD 1169
            AA+SI  P     L T                   G+V   +EE + P+ ++I I +DM 
Sbjct: 1094 AAKSISTPIISCKLVTADNEASARIVKGRLEKTHLGDVASVLEEAWAPEYTYIGIIVDMK 1153

Query: 1170 RIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF---NSKMYQMKQL 1226
             I+ L LE+ +D I++ I   +     L +   +  I+  K+  + +     K Y++++L
Sbjct: 1154 TIQDLQLEMTLDDIKWGIVAAK----KLKIKQEAITIIPRKNRLRVYVDGQDKYYRLREL 1209

Query: 1227 ---LPSVVIKGVQGINRAVIH---EEDVEGVTKYK-LLVEGDNLRDVMATYGVKGVKCSS 1279
               LP VV+KGV  I RA+I+   ++D  G    K LLVEG  L+ VM T G+ G + +S
Sbjct: 1210 KRALPDVVVKGVPTIRRAIINIKEDDDHRGKKGDKELLVEGYGLQKVMVTQGIIGEQTTS 1269

Query: 1280 NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGL 1339
            N+  EV + LGIEAAR TI+ EI+  M +HGMSID RH ML+ D+M+ KGEVLGITR G+
Sbjct: 1270 NHIIEVAQVLGIEAARRTIINEIQYTMSSHGMSIDPRHVMLLGDVMSYKGEVLGITRFGV 1329

Query: 1340 AKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLP-MNVGTGLIKLLQAVP 1398
            AKMK+SVL LASFE T+DHLFDAA YG+TD I+GVSE IIMG P +  GT +  L+   P
Sbjct: 1330 AKMKDSVLMLASFEKTTDHLFDAAAYGKTDSIAGVSESIIMGNPAVMTGTSMPALVTPAP 1389

Query: 1399 RSEPVPRTLLFDN 1411
                 PR LLF++
Sbjct: 1390 HIGK-PRKLLFES 1401



 Score =  192 bits (488), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 103/247 (41%), Positives = 141/247 (57%), Gaps = 5/247 (2%)

Query: 97  SHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP 156
           S  ++  ++LY     R P+ +G+LDRR+GT +K A C TCG +  DCVGH+ YI L +P
Sbjct: 30  SEFEVTHRDLYTP-VDRHPVKNGVLDRRLGTTEKSAFCETCGLSSVDCVGHYAYIRLTVP 88

Query: 157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILET 216
           VFHIGYF+  I ILQ ICK  TCARVLL E     +  + R P L  + R++L K +   
Sbjct: 89  VFHIGYFKHTIAILQCICK--TCARVLLEEPDRRTYLKRFRRPNLENIQRQALSKAVNTL 146

Query: 217 TKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEA 276
            +K   CP+C   NG VKK G LKI H+K+  R KK    +E     +  AV+   E+  
Sbjct: 147 ARKAVYCPYCSSTNGTVKKAGALKIIHDKF--RAKKTADEMEKWKTTFTSAVEAQKELGM 204

Query: 277 HKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVIS 336
           +    + + LNPL+VL LF+ I  ED  LL +     +P + +   + VPP CIRPSV  
Sbjct: 205 YLNKAVHEDLNPLKVLNLFKRISDEDCELLGLRPAHGRPEEYVWQYISVPPVCIRPSVAQ 264

Query: 337 DLKSDND 343
           D  S+ D
Sbjct: 265 DGASNED 271



 Score =  183 bits (465), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 110/244 (45%), Positives = 156/244 (63%), Gaps = 14/244 (5%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA+++ISTPII+  L    +   ARIVKGRLE+T LG+V   +EE + P+ 
Sbjct: 1084 GVPRIKEIINAAKSISTPIISCKLVTADNEASARIVKGRLEKTHLGDVASVLEEAWAPEY 1143

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF--- 880
            ++I I +DM  I+ L LE+ +D I++ I   +     L +   +  I+  K+  + +   
Sbjct: 1144 TYIGIIVDMKTIQDLQLEMTLDDIKWGIVAAK----KLKIKQEAITIIPRKNRLRVYVDG 1199

Query: 881  NSKMYQMKQL---LPSVVIKGVQGINRAVIH---EEDVEGVTKYK-LLVEGDNLRDVMAT 933
              K Y++++L   LP VV+KGV  I RA+I+   ++D  G    K LLVEG  L+ VM T
Sbjct: 1200 QDKYYRLRELKRALPDVVVKGVPTIRRAIINIKEDDDHRGKKGDKELLVEGYGLQKVMVT 1259

Query: 934  YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
             G+ G + +SN+  EV + LGIEAAR TI+ EI+  M +HGMSID RH ML+ D+M+ KG
Sbjct: 1260 QGIIGEQTTSNHIIEVAQVLGIEAARRTIINEIQYTMSSHGMSIDPRHVMLLGDVMSYKG 1319

Query: 994  EVLG 997
            EVLG
Sbjct: 1320 EVLG 1323



 Score =  105 bits (261), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 47/68 (69%), Positives = 55/68 (80%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV+NSF++GL+PTEF FH + GREGLVDTAVKTAETGYMQRRL+K+LEDL   YD 
Sbjct: 829 PSKGFVRNSFYTGLSPTEFLFHAISGREGLVDTAVKTAETGYMQRRLMKALEDLVTHYDS 888

Query: 670 SFDAAFYG 677
           S   A  G
Sbjct: 889 SVRNAVGG 896



 Score = 61.2 bits (147), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 28/48 (58%), Positives = 37/48 (77%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIAS 69
           LM+ K NLVTPRNGE +IAA QDFIT  +LL++++ FF+R Q  +I S
Sbjct: 515 LMSVKHNLVTPRNGEPVIAAIQDFITASFLLSRRDTFFDRRQFTQICS 562



 Score = 48.5 bits (114), Expect = 0.030,   Method: Compositional matrix adjust.
 Identities = 28/56 (50%), Positives = 35/56 (62%), Gaps = 2/56 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLP-MNVGTGLIKLLQAVPRSEPVPRTLLFDN 722
            D  FDAA YG+TD I+GVSE IIMG P +  GT +  L+   P     PR LLF++
Sbjct: 1347 DHLFDAAAYGKTDSIAGVSESIIMGNPAVMTGTSMPALVTPAPHIGK-PRKLLFES 1401


>gi|167537656|ref|XP_001750496.1| hypothetical protein [Monosiga brevicollis MX1]
 gi|163771036|gb|EDQ84710.1| predicted protein [Monosiga brevicollis MX1]
          Length = 1414

 Score =  260 bits (665), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 155/368 (42%), Positives = 208/368 (56%), Gaps = 63/368 (17%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYIEEV 1154
            K+ R  +EP TAVGA+ AQSIGEPGTQMTLKTFHFAG              E+    + +
Sbjct: 1041 KFRRTVVEPGTAVGAIGAQSIGEPGTQMTLKTFHFAGVAAMNVTLGVPRIKEIINAAKNI 1100

Query: 1155 FVP----------------------------------------DDSFILIKLDMDRIRLL 1174
              P                                        D  ++ +KL++  I+  
Sbjct: 1101 STPVITAKLENDREESFARQVKARLETLTLGEVADHFDVVCNEDGGYVRVKLNLKVIQRK 1160

Query: 1175 HLEVDIDSIRYCIERTRGIS---GHLTVSGHSFLILKPKDSSKSFNSKMYQMKQL---LP 1228
            HLEV +++I   I  +R       HL+V         P   SK+  ++++ ++ L   LP
Sbjct: 1161 HLEVTMNTIIDSIAASRLTKIKHEHLSVMSSEVFQAVPVCDSKTVANRVHALRHLANVLP 1220

Query: 1229 SVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKT 1288
            + VI G+ GI RA+I ++  EG   + + ++G +L+ VMAT GV G     N+  E+ +T
Sbjct: 1221 NCVITGLPGIRRAIIAKDPNEGT--FSIAIDGTDLKGVMATPGVIGTTVDCNHVMELEQT 1278

Query: 1289 LGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLN 1348
            LGIEAARS IM +++ VM N+G+ I+ RH ML++DLMT KGEVLGITR G+AKMKESV  
Sbjct: 1279 LGIEAARSIIMDQVQYVMSNYGIHINPRHTMLMSDLMTFKGEVLGITRFGIAKMKESVFM 1338

Query: 1349 LASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSE-PVPRTL 1407
            LASFE T+DHLFDAA  G TD + GVSECII+G+PM +GTGL KLL      E P  R L
Sbjct: 1339 LASFEKTTDHLFDAALRGTTDSVDGVSECIILGVPMRIGTGLFKLLHETKVEEQPKRRPL 1398

Query: 1408 LFDNPEFH 1415
            LFD  +FH
Sbjct: 1399 LFDQEQFH 1406



 Score =  257 bits (657), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 130/289 (44%), Positives = 174/289 (60%), Gaps = 42/289 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D  LFNRQPSLH++SIM HR K  P RTFRFNECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 441 DGDYALFNRQPSLHRMSIMCHRVKARPWRTFRFNECVCKPYNADFDGDEMNLHVPQTEEA 500

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE              A +L+    NL TP NGE LIAA QDFITG +L++QK+ FF +
Sbjct: 501 KAE--------------AALLLRTTHNLCTPCNGEPLIAACQDFITGCFLISQKDTFFTK 546

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+ M++          +C         S      V+   +WTGKQ+FS++++P++D P  
Sbjct: 547 AKVMQM----------VCAFSDGSLKISLPVPAIVKPVAMWTGKQVFSMMMRPSKDDPHQ 596

Query: 521 ANLKTKGRAYTANEE-----------------FCHRDSYVILRNSELLAGSMDKSTLGSG 563
            +L  K +++  N E                  C  D +VI+R+S LL G +DK+ +G  
Sbjct: 597 VDLTEKNKSFDKNYEKSEVKKLGRDLTIGERSLCPEDGFVIIRSSRLLCGFLDKANVGE- 655

Query: 564 GKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
            K+ +FY LLRD+    AV  M R++++T+ YLM RGFSIG+ DVTP Q
Sbjct: 656 SKSTIFYRLLRDYSAQAAVDGMLRMTKLTTRYLMERGFSIGLEDVTPPQ 704



 Score =  184 bits (468), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 105/240 (43%), Positives = 154/240 (64%), Gaps = 8/240 (3%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++NISTP+ITA L+ D +  +AR VK RLE  TLGEV ++ + V   D 
Sbjct: 1086 GVPRIKEIINAAKNISTPVITAKLENDREESFARQVKARLETLTLGEVADHFDVVCNEDG 1145

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSFLILKPKDSSKSF 880
             ++ +KL++  I+  HLEV +++I   I  +R       HL+V         P   SK+ 
Sbjct: 1146 GYVRVKLNLKVIQRKHLEVTMNTIIDSIAASRLTKIKHEHLSVMSSEVFQAVPVCDSKTV 1205

Query: 881  NSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVK 937
             ++++ ++ L   LP+ VI G+ GI RA+I ++  EG   + + ++G +L+ VMAT GV 
Sbjct: 1206 ANRVHALRHLANVLPNCVITGLPGIRRAIIAKDPNEGT--FSIAIDGTDLKGVMATPGVI 1263

Query: 938  GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            G     N+  E+ +TLGIEAARS IM +++ VM N+G+ I+ RH ML++DLMT KGEVLG
Sbjct: 1264 GTTVDCNHVMELEQTLGIEAARSIIMDQVQYVMSNYGIHINPRHTMLMSDLMTFKGEVLG 1323



 Score =  184 bits (466), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 99/239 (41%), Positives = 143/239 (59%), Gaps = 9/239 (3%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           +Q+ S +++ SK  Y   P R P P G LDRR+G   K  +C TC QNL  C GHFG+I+
Sbjct: 28  MQRLSEVRVYSKEFYTGLPDRKPAPFGPLDRRLGAFDKSLDCATCSQNLRKCEGHFGHIE 87

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKK 212
           L LPVFH+G+F+  ++ LQ ICK  +C+RV+L  ++A  F  +L++P L    R ++ K+
Sbjct: 88  LELPVFHVGFFKATLSCLQRICK--SCSRVMLSHKQATVFLRRLQDPNLERGPRAAIIKE 145

Query: 213 ILETTKK-VSVCPHCGEINGVVK--KCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVK 269
           + +  +K  + CPHC   NGVVK  K  +L+I HE++   TKK + + E     + EA  
Sbjct: 146 VGDQCRKNAASCPHCSACNGVVKRPKNSVLRIVHERF---TKKNNRLREAHHQLFQEAAS 202

Query: 270 FNPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPP 327
              ++ A  K   +Q  LNPL  LQL  A+P +D PLL M+    +P  LILT L+VPP
Sbjct: 203 EVKDLSASLKADKVQDELNPLRALQLLRAVPDQDCPLLDMDPFCGRPEKLILTNLIVPP 261



 Score =  106 bits (264), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 47/60 (78%), Positives = 53/60 (88%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF++GLTP EFFFHTM GREGLVDTAVKTAETGYMQRRL+K+LEDL V YD +
Sbjct: 827 AKGFVANSFYTGLTPAEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKALEDLVVHYDTT 886



 Score = 69.3 bits (168), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 34/60 (56%), Positives = 39/60 (65%), Gaps = 1/60 (1%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSE-PVPRTLLFDNPEFH 726
            D  FDAA  G TD + GVSECII+G+PM +GTGL KLL      E P  R LLFD  +FH
Sbjct: 1347 DHLFDAALRGTTDSVDGVSECIILGVPMRIGTGLFKLLHETKVEEQPKRRPLLFDQEQFH 1406



 Score = 57.8 bits (138), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 26/54 (48%), Positives = 36/54 (66%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           +L+    NL TP NGE LIAA QDFITG +L++QK+ FF +A+ M++      G
Sbjct: 506 LLLRTTHNLCTPCNGEPLIAACQDFITGCFLISQKDTFFTKAKVMQMVCAFSDG 559


>gi|224060165|ref|XP_002300065.1| predicted protein [Populus trichocarpa]
 gi|222847323|gb|EEE84870.1| predicted protein [Populus trichocarpa]
          Length = 1394

 Score =  260 bits (664), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 154/408 (37%), Positives = 226/408 (55%), Gaps = 55/408 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH++SIM HRA+++P RT RFNE VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 456 DGDVVLFNRQPSLHRMSIMCHRARIMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EA               +LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+K+ F++R
Sbjct: 516 RTEAF--------------LLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A    +  + + D  D+  +          P V  +   +WTGKQ+FS++L+P+ +  V 
Sbjct: 562 A-AFSLMCSYMNDGMDLVDL--------PTPSVL-KPIELWTGKQLFSVLLRPHANVRVY 611

Query: 521 ANLKTKGRAYT--------ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYIL 572
            NL  K + Y+          E  C  D YV  RNSEL++G + K+TLG+G K  ++ IL
Sbjct: 612 VNLILKEKNYSRPNKEHKKERETMCPNDGYVYFRNSELISGQLGKATLGNGNKDGLYSIL 671

Query: 573 LRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSFFSGLTPTEFFFHT 632
           LRD+    A T M RL+++++ ++ N GFSIGI DV PG+  +      G T +  + H 
Sbjct: 672 LRDYNAYAAATCMNRLAKLSARWIGNHGFSIGIDDVQPGKKLIDE---KGKTISNGYRHC 728

Query: 633 -------MGGREGLVD--TAVKTAETGYMQR--RLVKSLEDLCVQYDMSFDAAFYGQTDC 681
                   GGR  L     A +T ET   +R  +L +   D+C++     ++        
Sbjct: 729 NKLIADYNGGRLALKSGCDATQTLETEITERLNKLREEAGDVCMKELHWRNSPLI----- 783

Query: 682 ISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQ 729
              +S+C   G P+N+   +  + Q        P   + D    HFP+
Sbjct: 784 ---MSQCGSKGSPINISQMIACVGQQSVGGSRAPDGFI-DRSLPHFPR 827



 Score =  211 bits (538), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 120/260 (46%), Positives = 164/260 (63%), Gaps = 9/260 (3%)

Query: 1145 GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHL---TVSG 1201
            G+V + I+ V     + + + LDM  IR   L +D + +R  I  T  I   L    V  
Sbjct: 1134 GQVAKSIKIVMTSRSASVKVTLDMKTIREAQLSLDANIVRELILETPKIKRKLQRINVLE 1193

Query: 1202 HSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHE------EDVEGVTKYK 1255
               L + P       + +++ +K +LP+VV+KG++ + R VI +      E+ +G  KY 
Sbjct: 1194 DGKLEVFPGGDRNKLHFELHSLKNMLPAVVVKGIKTVERVVIAQKKLDDAENDQGGPKYN 1253

Query: 1256 LLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDF 1315
            + VEG  L+ VM T GV G K  SN+  EV +TLGIEAAR  I+ EIK  ME+HGMSID 
Sbjct: 1254 MFVEGMGLQAVMGTEGVDGRKTKSNHIIEVQETLGIEAARKCIIDEIKGTMESHGMSIDI 1313

Query: 1316 RHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVS 1375
            RH ML+AD+MTS+G VLGITR G+ KM +SVL LASFE TSDHLF+A+  G+ D I GVS
Sbjct: 1314 RHMMLLADVMTSRGVVLGITRFGIQKMDKSVLMLASFEKTSDHLFNASVKGKDDKIEGVS 1373

Query: 1376 ECIIMGLPMNVGTGLIKLLQ 1395
            ECIIMG+P+ +GTG++K+ Q
Sbjct: 1374 ECIIMGIPVAIGTGVLKIQQ 1393



 Score =  188 bits (477), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 107/243 (44%), Positives = 152/243 (62%), Gaps = 9/243 (3%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIIN ++ ISTPIIT  L+ +++++ ARI+KGR+++T LG+V + I+ V     
Sbjct: 1089 GVPRIKEIINGAKRISTPIITVELEHNSNVNAARIIKGRIQKTVLGQVAKSIKIVMTSRS 1148

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHL---TVSGHSFLILKPKDSSKSF 880
            + + + LDM  IR   L +D + +R  I  T  I   L    V     L + P       
Sbjct: 1149 ASVKVTLDMKTIREAQLSLDANIVRELILETPKIKRKLQRINVLEDGKLEVFPGGDRNKL 1208

Query: 881  NSKMYQMKQLLPSVVIKGVQGINRAVIHE------EDVEGVTKYKLLVEGDNLRDVMATY 934
            + +++ +K +LP+VV+KG++ + R VI +      E+ +G  KY + VEG  L+ VM T 
Sbjct: 1209 HFELHSLKNMLPAVVVKGIKTVERVVIAQKKLDDAENDQGGPKYNMFVEGMGLQAVMGTE 1268

Query: 935  GVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGE 994
            GV G K  SN+  EV +TLGIEAAR  I+ EIK  ME+HGMSID RH ML+AD+MTS+G 
Sbjct: 1269 GVDGRKTKSNHIIEVQETLGIEAARKCIIDEIKGTMESHGMSIDIRHMMLLADVMTSRGV 1328

Query: 995  VLG 997
            VLG
Sbjct: 1329 VLG 1331



 Score =  149 bits (376), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 88/241 (36%), Positives = 132/241 (54%), Gaps = 22/241 (9%)

Query: 110 DPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINI 169
           D  +  I  GLLD RMG   K   C TCG + +DC GHFGY++L LPV+++GY   +++I
Sbjct: 52  DANKKAIVGGLLDTRMGAPNKHGTCQTCGGSFTDCPGHFGYLNLVLPVYNVGYLSTILDI 111

Query: 170 LQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILE-----TTKKVSVCP 224
           L+ ICK  +C+RVL+ E+    +  ++RNP    L +  L K+I++      + K   C 
Sbjct: 112 LKCICK--SCSRVLVDEKLRKSYLKRMRNPRTEPLKKNELMKEIVKKCSSMASSKAVKCL 169

Query: 225 HCGEINGVVKKCG-LLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLI 283
            CG +NG+VKK G ++ I H++ K        +++  L E   A+      EA    GL 
Sbjct: 170 RCGYMNGMVKKAGSVVGIIHDRSK--------LIDGYLEECKSAIGHTR--EARAPIGLA 219

Query: 284 Q-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDN 342
              LNP+ VL LF+ +  ED  LL +     +P  LI+T + VPP  IRPSV ++    N
Sbjct: 220 TYILNPVRVLSLFQRMVEEDCELLYLQG---RPEKLIITTIAVPPISIRPSVFTEGSQSN 276

Query: 343 D 343
           +
Sbjct: 277 E 277



 Score =  108 bits (271), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 52/70 (74%), Positives = 57/70 (81%), Gaps = 1/70 (1%)

Query: 609 TPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV NSF+SGL+ TEFFFHTMGGREGLVDTAVKTA+TGYM RRL K LEDLCVQY
Sbjct: 831 TPAAKGFVANSFYSGLSATEFFFHTMGGREGLVDTAVKTADTGYMARRLSKGLEDLCVQY 890

Query: 668 DMSFDAAFYG 677
           D +   A  G
Sbjct: 891 DNTVQDAGGG 900



 Score = 78.2 bits (191), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 56/165 (33%), Positives = 77/165 (46%), Gaps = 23/165 (13%)

Query: 999  GTPVELKRLLDDIIAKNSSRSDPSLS-------AQEILALSNETLDSKEFLQDTSENFVR 1051
            G P+   RL   + A   +  D  LS        Q +L   N TLD        SE+F +
Sbjct: 921  GVPLNFDRLFMKVKATCGAEEDEYLSPSDISNIVQSLLLKHNGTLDGI-----CSESFRK 975

Query: 1052 DIKKFLEEFSKK-ESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKA------- 1103
             +  FL + +K+ E +    D V     E I + +   G  + +                
Sbjct: 976  SLSSFLGDQAKRLECLMKLVDGVEVENFENIKNVEGLTGISKNTEKIAQKVSGITEKQLE 1035

Query: 1104 ---EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
               + C ++YV  +IEP TA+GA+ AQSIGEPGTQMTLKTFHFAG
Sbjct: 1036 VFLKTCLDRYVWKRIEPGTAIGAIGAQSIGEPGTQMTLKTFHFAG 1080



 Score = 57.4 bits (137), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 22/42 (52%), Positives = 36/42 (85%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRA 62
           +LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+K+ F++RA
Sbjct: 521 LLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDRA 562



 Score = 49.3 bits (116), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 21/39 (53%), Positives = 30/39 (76%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  F+A+  G+ D I GVSECIIMG+P+ +GTG++K+ Q
Sbjct: 1355 DHLFNASVKGKDDKIEGVSECIIMGIPVAIGTGVLKIQQ 1393


>gi|422295501|gb|EKU22800.1| DNA-directed RNA polymerase III subunit RPC1, partial
           [Nannochloropsis gaditana CCMP526]
          Length = 535

 Score =  259 bits (663), Expect = 5e-66,   Method: Compositional matrix adjust.
 Identities = 141/274 (51%), Positives = 173/274 (63%), Gaps = 29/274 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAHR KV+P RTFRFNECVC PYNADFDGDEMN+HLPQTEEA
Sbjct: 147 DEDVVLFNRQPSLHKLSIMAHRVKVMPWRTFRFNECVCAPYNADFDGDEMNMHLPQTEEA 206

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A  LM   SNLVTPRNGE ++AATQDFITG YLLTQK+ F  R
Sbjct: 207 RAE--------------AATLMGVTSNLVTPRNGEPMVAATQDFITGAYLLTQKDVFLTR 252

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
               R+A+ L      I             P   V    +WTGKQ+FSL++K +     +
Sbjct: 253 EAFCRLAAYLGDAAEHI----------DLPPPSIVWPHQLWTGKQVFSLLIKASHRVDCD 302

Query: 521 ANLKTKGRAYTANEE---FCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFG 577
            NL+ + R Y+  E     C +D +V +R SEL++G++ K TLG G K  ++Y+LLRD G
Sbjct: 303 VNLEMEERNYSKAEAMAYLCPQDGFVCIRRSELVSGNLCKKTLG-GQKGGLYYVLLRDKG 361

Query: 578 EDVAVTAMWRLSRMTSFYL-MNRGFSIGIGDVTP 610
            + A   M RL+++    +  +RGFSIGI DV P
Sbjct: 362 AEHAARCMNRLAKLCGRLIGGHRGFSIGIDDVMP 395



 Score = 67.4 bits (163), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 32/51 (62%), Positives = 37/51 (72%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
            LM   SNLVTPRNGE ++AATQDFITG YLLTQK+ F  R    R+A+ L
Sbjct: 212 TLMGVTSNLVTPRNGEPMVAATQDFITGAYLLTQKDVFLTREAFCRLAAYL 262


>gi|353234990|emb|CCA67009.1| probable RPO31-DNA-directed RNA polymerase III, 160 KD subunit
           [Piriformospora indica DSM 11827]
          Length = 1371

 Score =  259 bits (662), Expect = 9e-66,   Method: Compositional matrix adjust.
 Identities = 131/282 (46%), Positives = 178/282 (63%), Gaps = 35/282 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH+LSIM HRAK+ P RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 448 DGDIVLFNRQPSLHRLSIMCHRAKIRPWRTFRLNECVCGPYNADFDGDEMNLHVPQTEEA 507

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL               LM+ K NLVTP+NGE +IAATQDFIT  +LL+ K+ F++R
Sbjct: 508 RTEALQ--------------LMSVKLNLVTPKNGEPVIAATQDFITAAFLLSGKDRFYDR 553

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q  +I S +    S I             P    +   +WTGKQ+F ++++P+R     
Sbjct: 554 RQFTQICSYMADAQSHI----------DIPPPTIWKPKQLWTGKQVFGVLMRPSRKSRSF 603

Query: 521 ANLKTKGRAYTANE-----------EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVF 569
            NL+T+ + Y A +           +    D ++++ NS+++ G MDK+T+GSG K ++F
Sbjct: 604 VNLETRCQTYQAPKADRLHGFTPLPDLSPNDGWLVIVNSQVMCGVMDKATVGSGKKKSIF 663

Query: 570 YILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
            +LLRD+G D A  AM RL+++ + +L N G S+GI DV PG
Sbjct: 664 GVLLRDYGPDEAANAMNRLAKLCARWLTNVGMSLGINDVIPG 705



 Score =  201 bits (512), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 106/244 (43%), Positives = 146/244 (59%), Gaps = 5/244 (2%)

Query: 100 QIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFH 159
           ++  ++LY     R P  +G+LDRR+GT +K ANC TCG N  DCVGHF Y+ L LPVFH
Sbjct: 33  EVTHRDLYTP-ADRLPSQNGVLDRRLGTTEKSANCETCGLNTVDCVGHFAYMKLALPVFH 91

Query: 160 IGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKK 219
           IGYFR ++ ILQ ICK  TCARV+L E     F  + R P L  L R+SL K++L  ++K
Sbjct: 92  IGYFRHILTILQCICK--TCARVMLTESARRAFLRRFRRPTLENLARQSLCKQVLAISRK 149

Query: 220 VSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKK 279
           V+ C HCG ING VKK   LKI HE+++ +   ++A  E     ++ A+K   +++    
Sbjct: 150 VNTCQHCGAINGTVKKAAALKIVHERFRQKKLTEEA--EKWRQSFSNAIKVQNDLDRALS 207

Query: 280 FGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLK 339
               + LNPL+VL LF+ +  ED  L+ M    S+P   +   + VPP  IRPSV  D  
Sbjct: 208 IKGAEELNPLKVLDLFKRMTAEDCELVGMKPSHSRPEHYLWQYIAVPPVAIRPSVNQDGA 267

Query: 340 SDND 343
           S+ D
Sbjct: 268 SNED 271



 Score =  197 bits (502), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 160/512 (31%), Positives = 243/512 (47%), Gaps = 99/512 (19%)

Query: 969  VMENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDPSLSAQEI 1028
            V  +HG  + F    +  D       + G   P++L R      A  S R   SLS  EI
Sbjct: 888  VRNSHGGIVQF----MYGDDGLDPASLEGEAQPLDLNRSWMHAEAV-SGRHGRSLSPAEI 942

Query: 1029 LALSNETLDSKEFLQDTSENFVRDIKKFLEEF-SKKESVTSHQDKVSQPLREQILSHQDK 1087
            + L++E +   +F +  S  + R +  F+    S+ E++    +    P    +LS    
Sbjct: 943  INLTDEFVKGDDFAKQCSVVYARAVTNFIRGICSRMEAIGRRHNLPKTPQDHTVLSESVL 1002

Query: 1088 IGHGRESNPFPSACKA---------EACREKYVRAQIEPAT---AVGALAAQSIGEPGTQ 1135
            + HG +     + CK          + C+++Y RA++EP +   AVGA +    G   T 
Sbjct: 1003 VYHG-DYIAAENKCKVTKQHLETFLQICKDRYSRAKVEPGSTVGAVGAQSIGEPGTQMTL 1061

Query: 1136 MTL------------------------KTFH---------------------------FA 1144
             T                         KT +                           + 
Sbjct: 1062 KTFHFAGVASMNVTLGVPRIKEIINASKTINTPIITTKLVASDSERAARIVKGRLEKTYL 1121

Query: 1145 GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSF 1204
            G++   IEE +  +  ++ I LD + I+ L LE+ +D +++ I   R             
Sbjct: 1122 GDIAAVIEEAWSSEGVYLGIHLDYEAIQKLQLELTLDDVKWAIISARK------------ 1169

Query: 1205 LILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIH---EEDVEGVTKYK-LLVEG 1260
              LK KDS+  F+  +Y  + +       G+  + RA+I+   ++D  G    K L+VEG
Sbjct: 1170 --LKLKDSASGFS--IYFARLI-------GIPSVQRAIINIKEKDDSRGRKGEKELIVEG 1218

Query: 1261 DNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPML 1320
            + L+ VM T G+ G    SN+  EV K LGIEAAR TI+ EI+  M  HGM ID RH ML
Sbjct: 1219 NGLQQVMTTPGIIGEHTISNHIIEVEKVLGIEAARRTIINEIEYTMSQHGMYIDPRHIML 1278

Query: 1321 VADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIM 1380
            + D+MT KG+VLGITR G++KMK+SVL LASFE T+DHLFDA+ +G+ D + GVSE II+
Sbjct: 1279 LGDVMTYKGQVLGITRFGVSKMKDSVLMLASFEKTTDHLFDASAFGKNDSVLGVSESIIL 1338

Query: 1381 GLP-MNVGTGLIKLLQAVPRSEPVPRTLLFDN 1411
            G P  + GT +  L+    R+ PV R L+F++
Sbjct: 1339 GNPAASCGTSMPGLVNN-SRATPVRRRLVFES 1369



 Score =  162 bits (411), Expect = 9e-37,   Method: Compositional matrix adjust.
 Identities = 102/238 (42%), Positives = 139/238 (58%), Gaps = 27/238 (11%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ I+TPIIT  L        ARIVKGRLE+T LG++   IEE +  + 
Sbjct: 1077 GVPRIKEIINASKTINTPIITTKLVASDSERAARIVKGRLEKTYLGDIAAVIEEAWSSEG 1136

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSK 883
             ++ I LD + I+ L LE+ +D +++ I   R               LK KDS+  F+  
Sbjct: 1137 VYLGIHLDYEAIQKLQLELTLDDVKWAIISARK--------------LKLKDSASGFS-- 1180

Query: 884  MYQMKQLLPSVVIKGVQGINRAVIH---EEDVEGVTKYK-LLVEGDNLRDVMATYGVKGV 939
            +Y  + +       G+  + RA+I+   ++D  G    K L+VEG+ L+ VM T G+ G 
Sbjct: 1181 IYFARLI-------GIPSVQRAIINIKEKDDSRGRKGEKELIVEGNGLQQVMTTPGIIGE 1233

Query: 940  KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
               SN+  EV K LGIEAAR TI+ EI+  M  HGM ID RH ML+ D+MT KG+VLG
Sbjct: 1234 HTISNHIIEVEKVLGIEAARRTIINEIEYTMSQHGMYIDPRHIMLLGDVMTYKGQVLG 1291



 Score = 98.2 bits (243), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 45/61 (73%), Positives = 52/61 (85%), Gaps = 1/61 (1%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV+NSFFSGL+PTEF FH + GREGLVDTAVKTAETGYMQRRL+K+ +DL   YD 
Sbjct: 828 PSKGFVRNSFFSGLSPTEFVFHAISGREGLVDTAVKTAETGYMQRRLMKA-KDLTTHYDF 886

Query: 670 S 670
           S
Sbjct: 887 S 887



 Score = 59.7 bits (143), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 28/50 (56%), Positives = 38/50 (76%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM+ K NLVTP+NGE +IAATQDFIT  +LL+ K+ F++R Q  +I S +
Sbjct: 514 LMSVKLNLVTPKNGEPVIAATQDFITAAFLLSGKDRFYDRRQFTQICSYM 563


>gi|308800888|ref|XP_003075225.1| RNA polymerase I, large subunit (ISS) [Ostreococcus tauri]
 gi|116061779|emb|CAL52497.1| RNA polymerase I, large subunit (ISS) [Ostreococcus tauri]
          Length = 1406

 Score =  259 bits (661), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 130/272 (47%), Positives = 176/272 (64%), Gaps = 25/272 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D++LFNRQPSLHK+SIMAH+A+V+P RT R NECVCTPYNADFDGDEMN+H PQTEEA
Sbjct: 470 DGDILLFNRQPSLHKMSIMAHKARVMPCRTLRLNECVCTPYNADFDGDEMNIHCPQTEEA 529

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM    NL TP+NGE+L+AATQDF+T  +LLT K+ FF+R
Sbjct: 530 RAEAMQ--------------LMGVHHNLCTPKNGEILVAATQDFLTAAFLLTAKDVFFDR 575

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           +Q       L+A   D        S     P + V+   +WTGKQIF ++++P     + 
Sbjct: 576 SQV----GQLVAYMGDAL-----LSVDLPTPAI-VKPIEMWTGKQIFGMLIRPKASDQIF 625

Query: 521 ANLKTKGRAYTANEE-FCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            NL+   + Y   ++  C  D YV ++NSE++AG + K+TLGSG K  +FY+L  ++G  
Sbjct: 626 VNLEVAEKLYNKKDKTMCPDDGYVCIQNSEIMAGRLGKATLGSGNKNGLFYVLNIEYGPV 685

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
            A  AM RL+++++ +L  RGFSIGI DV+P 
Sbjct: 686 AAADAMNRLAKLSARWLGTRGFSIGIDDVSPA 717



 Score =  256 bits (654), Expect = 6e-65,   Method: Compositional matrix adjust.
 Identities = 169/470 (35%), Positives = 247/470 (52%), Gaps = 100/470 (21%)

Query: 998  NGTPVELKRLLDDIIAKNSSRSDPSLSAQEILAL------------SNETLDSKEFL--Q 1043
            N  P+E KR L ++   + +R +  ++   + A             + +  D +E +   
Sbjct: 927  NAQPIEFKRCLMNVKGLHPARGEAPVTKAVLHAALAKFKKENKLLNTGDEADGQELVYGG 986

Query: 1044 DTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKA 1103
              SE F R + +F+   S+ ES +     +S+                 + N F      
Sbjct: 987  GISELFFRQMSEFIT--SEIESPSDGGAVISE----------------SQLNTF-----L 1023

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCE 1149
            + C +KY   +IEP TAVGA+ AQSIGEPGTQMTLKTFHFAG              E+  
Sbjct: 1024 DVCMQKYNAKRIEPGTAVGAVGAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIIN 1083

Query: 1150 YIEEVFVP-------------------------------DDSFILIK---------LDMD 1169
              + +  P                                D+ I+++         LD++
Sbjct: 1084 ASKSISTPIISASLMSDRDVKAARVVKGRVEKTTLGEICSDAGIVVRSHEVYLELVLDLE 1143

Query: 1170 RIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQL 1226
             I  L L+V I + R  +    + +    H+ ++G + L + P + S      ++ ++ +
Sbjct: 1144 AINQLQLDVTIHTARTAVLAAPKLKLKPQHVLIAGPNVLHVLPTEESLVEGKALFALQHM 1203

Query: 1227 ---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTY 1283
               +P V+++G+  + RAVI++   +G   Y LLVEG NL+ VM   GVKG++ ++NN  
Sbjct: 1204 RLAIPGVIVQGIPSVGRAVIND---KGDGTYNLLVEGINLQAVMGIDGVKGIETTTNNVM 1260

Query: 1284 EVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMK 1343
            E  +TLGIEAAR+ I+ EI   M  HGMSID RH ML+AD+MT KGEVLGITR G+AKMK
Sbjct: 1261 ECERTLGIEAARACIIKEIDDTMRAHGMSIDNRHSMLLADVMTYKGEVLGITRFGMAKMK 1320

Query: 1344 ESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            +SVL LASFE T+DHLFDAA +G+TD I GVSECIIMG+PM +GTG+ +L
Sbjct: 1321 DSVLMLASFEKTTDHLFDAALHGRTDYIDGVSECIIMGIPMPIGTGMFRL 1370



 Score =  205 bits (522), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 110/240 (45%), Positives = 148/240 (61%), Gaps = 13/240 (5%)

Query: 100 QIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEAN-CTTCGQNLSDCVGHFGYIDLPLPVF 158
            +  +NLY Q PQRTP+ +G+LD RMGT  K    C TC  ++ DC GHFGYI L LPVF
Sbjct: 55  HVFERNLY-QMPQRTPMVNGILDPRMGTTDKRGGECATCRGSMVDCAGHFGYIKLELPVF 113

Query: 159 HIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTK 218
           HIGYF+ +I++LQ +CK   C+R+LL E+  A F  + RNP L    R+ L KK+ E  K
Sbjct: 114 HIGYFKNIISVLQCVCKG--CSRILLNEDDQATFLKRYRNPRLELTQRRLLYKKLTEKCK 171

Query: 219 KVSVCPHCGEINGVVKKCG-LLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAH 277
           +  +CPHCG+ NGV K+ G  LKI HEKY     K  A++E+ L E+  A+K+N ++ A 
Sbjct: 172 RCRICPHCGDYNGVTKRAGQTLKIVHEKY----SKNPALLEEFLKEFETALKYNEQLRAS 227

Query: 278 KKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD 337
               +   LNP+ VL + + I  +D  LL +     +P  L+LT L VPP CIRPSV  D
Sbjct: 228 LP-KVQDDLNPIRVLSILQRITDQDCELLDI---ADRPEHLLLTHLPVPPCCIRPSVEMD 283



 Score =  191 bits (485), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 106/240 (44%), Positives = 155/240 (64%), Gaps = 9/240 (3%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS++ISTPII+A L  D D+  AR+VKGR+E+TTLGE+C     V    +
Sbjct: 1074 GVPRIKEIINASKSISTPIISASLMSDRDVKAARVVKGRVEKTTLGEICSDAGIVVRSHE 1133

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSGHSFLILKPKDSSKSF 880
             ++ + LD++ I  L L+V I + R  +    + +    H+ ++G + L + P + S   
Sbjct: 1134 VYLELVLDLEAINQLQLDVTIHTARTAVLAAPKLKLKPQHVLIAGPNVLHVLPTEESLVE 1193

Query: 881  NSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVK 937
               ++ ++ +   +P V+++G+  + RAVI+++   G   Y LLVEG NL+ VM   GVK
Sbjct: 1194 GKALFALQHMRLAIPGVIVQGIPSVGRAVINDK---GDGTYNLLVEGINLQAVMGIDGVK 1250

Query: 938  GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            G++ ++NN  E  +TLGIEAAR+ I+ EI   M  HGMSID RH ML+AD+MT KGEVLG
Sbjct: 1251 GIETTTNNVMECERTLGIEAARACIIKEIDDTMRAHGMSIDNRHSMLLADVMTYKGEVLG 1310



 Score =  104 bits (260), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 48/64 (75%), Positives = 55/64 (85%), Gaps = 1/64 (1%)

Query: 606 GDVTPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           G+ TP  +GFV NSF+SG+ PTEFFFHTM GREGLVDTAVKTAETGYM RRL+K+LEDL 
Sbjct: 835 GEKTPAAKGFVANSFYSGMRPTEFFFHTMAGREGLVDTAVKTAETGYMSRRLMKALEDLS 894

Query: 665 VQYD 668
           + YD
Sbjct: 895 LSYD 898



 Score = 60.1 bits (144), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 25/50 (50%), Positives = 37/50 (74%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM    NL TP+NGE+L+AATQDF+T  +LLT K+ FF+R+Q  ++ + +
Sbjct: 536 LMGVHHNLCTPKNGEILVAATQDFLTAAFLLTAKDVFFDRSQVGQLVAYM 585



 Score = 57.0 bits (136), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 24/37 (64%), Positives = 30/37 (81%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 704
            D  FDAA +G+TD I GVSECIIMG+PM +GTG+ +L
Sbjct: 1334 DHLFDAALHGRTDYIDGVSECIIMGIPMPIGTGMFRL 1370


>gi|409075371|gb|EKM75752.1| hypothetical protein AGABI1DRAFT_79519 [Agaricus bisporus var.
           burnettii JB137-S8]
          Length = 1402

 Score =  259 bits (661), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 134/283 (47%), Positives = 178/283 (62%), Gaps = 36/283 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIM HRAKV P RTFR NECVC PYNADFDGDEMN+H+PQT+EA
Sbjct: 447 DGDIVLFNRQPSLHKLSIMCHRAKVRPWRTFRLNECVCGPYNADFDGDEMNLHVPQTDEA 506

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL               LM+ K NLVTPRNG+ +IAA QDFIT  YLL++K+ FF+R
Sbjct: 507 RAEALE--------------LMSVKHNLVTPRNGDPVIAAIQDFITASYLLSRKDTFFDR 552

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNR----- 515
            Q  +I      D +    I     W+          A +WTGKQ+F+++++PN+     
Sbjct: 553 RQFTQIC-CYFGDANMQIDIPPPTIWKP---------ARLWTGKQVFNVLMRPNKISEVL 602

Query: 516 ---DCPVNANLKTKGRAYTAN----EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANV 568
              +C  N   + K   Y +      +    D ++++ NSE++ G MDK+T+GSG K ++
Sbjct: 603 VNVECKCNKWEEAKPENYPSRMIPANDLSPNDGWLVVVNSEIMCGVMDKATVGSGKKKSI 662

Query: 569 FYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           F ++LRD+G   A  AM RL+++ + YL N GFS+GI DV PG
Sbjct: 663 FGVILRDYGPHEAAAAMNRLAKLCARYLANYGFSLGINDVIPG 705



 Score =  217 bits (552), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 164/498 (32%), Positives = 248/498 (49%), Gaps = 95/498 (19%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G+  P++L+R    + A ++ R+  SL   E+L L+++TL +  F+ + ++ ++  ++ F
Sbjct: 913  GDAQPIDLERTWRHVSA-SAGRAGRSLLPFEVLELTDQTLATPRFVNEFTQTYLDILRDF 971

Query: 1057 LEEFSKKESVTSHQDK-----------------VSQPLREQILSHQDKIGHGRESN--PF 1097
            +     +      Q +                 +S    +  LS  D      E     F
Sbjct: 972  IHNNVARNIAEHRQSRGMFEALERDTEWDADTDLSMGATDSDLSIVDNKAKVTEEQLRKF 1031

Query: 1098 PSACKAEACREKYVRAQIEPATAVGAL--------------------------------- 1124
               C A     KY +A+IEP + VGA+                                 
Sbjct: 1032 LHVCWA-----KYAKARIEPGSTVGAVGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPR 1086

Query: 1125 ------AAQSIGEPGTQMTLKTFH---------------FAGEVCEYIEEVFVPDDSFIL 1163
                  AA++I  P     L T                   G+V   +EE + P+  +I 
Sbjct: 1087 IKEIINAAKAISTPIISCKLVTRSSEASARIVKGRLEKTLLGDVASVLEEAWAPEYVYIC 1146

Query: 1164 IKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF---NSKM 1220
            I +D + IR L LE+ +D +++ I   +     L V   S +++  K   + +     K 
Sbjct: 1147 ILIDTEAIRKLQLELTLDDVKWAIVNWK----KLKVKQESIIVIPNKQRLRIYVDGQDKY 1202

Query: 1221 YQMKQL---LPSVVIKGVQGINRAVIH---EEDVEGVTKYK-LLVEGDNLRDVMATYGVK 1273
            Y++++L   LP++V+KGV  I+RA+I+   ++D +G    K LLVEG  L+  M T GV 
Sbjct: 1203 YRLRELKRGLPNIVVKGVPTISRAIINIKDQDDAKGKKGDKELLVEGYGLQKCMITEGVV 1262

Query: 1274 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 1333
            G   +SN+  EV + LGIEAAR TI+ EI+  M++H M ID RH ML+ D+MT KGEVLG
Sbjct: 1263 GEATTSNHVIEVAQVLGIEAARRTIINEIQYTMKSHDMIIDPRHVMLLGDVMTYKGEVLG 1322

Query: 1334 ITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLP-MNVGTGLIK 1392
            ITR G+AKMK+SVL LASFE T+DHLFDA+ +G+TD ISGVSE IIMG P    GT +  
Sbjct: 1323 ITRFGVAKMKDSVLMLASFEKTTDHLFDASAFGKTDSISGVSESIIMGNPAATCGTSMPA 1382

Query: 1393 LLQAVPRSEPVPRTLLFD 1410
            L++  P  +  PR LLF+
Sbjct: 1383 LVRPSPVLKK-PRKLLFE 1399



 Score =  202 bits (515), Expect = 9e-49,   Method: Compositional matrix adjust.
 Identities = 107/247 (43%), Positives = 145/247 (58%), Gaps = 5/247 (2%)

Query: 97  SHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP 156
           S  +I  ++LY     R P+ +G+LDRR+GT  K A C TCGQ+   CVGH+ YI L +P
Sbjct: 30  SEFEITHRDLYTP-VDRLPVQNGVLDRRLGTTDKNAFCETCGQSYVHCVGHYAYIKLVVP 88

Query: 157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILET 216
           VFHIGYF+ +I++LQ+ICK  TCARVLL E     F  + R P L  + R++L K +  T
Sbjct: 89  VFHIGYFKHIISVLQAICK--TCARVLLEEPDRRTFIKRFRRPNLENIQRQALSKSVNAT 146

Query: 217 TKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEA 276
            +KV  CP+C  ING VKK G LKI H+K+  R KK    +E     + +AV+   E+  
Sbjct: 147 ARKVVHCPYCSAINGTVKKAGALKIIHDKF--RAKKTAEEMEKWKKTFTKAVEAQKELSM 204

Query: 277 HKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVIS 336
           +      + LNPL+VL LF  +  ED  LL +     +P + +   L VPP CIRPSV  
Sbjct: 205 YLNKAAHEELNPLKVLDLFRRVSDEDCELLGLQPAWGRPEEFVWQYLSVPPVCIRPSVAQ 264

Query: 337 DLKSDND 343
           D  S+ D
Sbjct: 265 DGASNED 271



 Score =  181 bits (459), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 108/244 (44%), Positives = 154/244 (63%), Gaps = 14/244 (5%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ ISTPII+  L   +    ARIVKGRLE+T LG+V   +EE + P+ 
Sbjct: 1083 GVPRIKEIINAAKAISTPIISCKLVTRSSEASARIVKGRLEKTLLGDVASVLEEAWAPEY 1142

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF--- 880
             +I I +D + IR L LE+ +D +++ I   +     L V   S +++  K   + +   
Sbjct: 1143 VYICILIDTEAIRKLQLELTLDDVKWAIVNWK----KLKVKQESIIVIPNKQRLRIYVDG 1198

Query: 881  NSKMYQMKQL---LPSVVIKGVQGINRAVIH---EEDVEGVTKYK-LLVEGDNLRDVMAT 933
              K Y++++L   LP++V+KGV  I+RA+I+   ++D +G    K LLVEG  L+  M T
Sbjct: 1199 QDKYYRLRELKRGLPNIVVKGVPTISRAIINIKDQDDAKGKKGDKELLVEGYGLQKCMIT 1258

Query: 934  YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
             GV G   +SN+  EV + LGIEAAR TI+ EI+  M++H M ID RH ML+ D+MT KG
Sbjct: 1259 EGVVGEATTSNHVIEVAQVLGIEAARRTIINEIQYTMKSHDMIIDPRHVMLLGDVMTYKG 1318

Query: 994  EVLG 997
            EVLG
Sbjct: 1319 EVLG 1322



 Score =  104 bits (260), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 46/61 (75%), Positives = 53/61 (86%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV+NSF+SGL  TEF FH + GREGLVDTAVKTAETGYMQRRL+K+LEDL  QYD+
Sbjct: 828 PSKGFVRNSFYSGLVATEFLFHAISGREGLVDTAVKTAETGYMQRRLMKALEDLTTQYDL 887

Query: 670 S 670
           S
Sbjct: 888 S 888



 Score = 61.2 bits (147), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 28/46 (60%), Positives = 36/46 (78%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRI 67
           LM+ K NLVTPRNG+ +IAA QDFIT  YLL++K+ FF+R Q  +I
Sbjct: 513 LMSVKHNLVTPRNGDPVIAAIQDFITASYLLSRKDTFFDRRQFTQI 558



 Score = 46.6 bits (109), Expect = 0.10,   Method: Compositional matrix adjust.
 Identities = 27/55 (49%), Positives = 35/55 (63%), Gaps = 2/55 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLP-MNVGTGLIKLLQAVPRSEPVPRTLLFD 721
            D  FDA+ +G+TD ISGVSE IIMG P    GT +  L++  P  +  PR LLF+
Sbjct: 1346 DHLFDASAFGKTDSISGVSESIIMGNPAATCGTSMPALVRPSPVLKK-PRKLLFE 1399


>gi|449540821|gb|EMD31809.1| hypothetical protein CERSUDRAFT_144684 [Ceriporiopsis subvermispora
           B]
          Length = 1403

 Score =  259 bits (661), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 135/288 (46%), Positives = 178/288 (61%), Gaps = 35/288 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIM HR KV P RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 449 DGDIVLFNRQPSLHKLSIMCHRVKVRPWRTFRLNECVCGPYNADFDGDEMNLHVPQTEEA 508

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL               LM+ K NLVTPRNGE +IAA QDFIT  +LL+Q++ FF+R
Sbjct: 509 RTEALE--------------LMSVKHNLVTPRNGEPVIAAIQDFITASFLLSQRDRFFDR 554

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q  +I S L AD      I     W+            +WTGKQIF+++++PNR   V 
Sbjct: 555 RQFTQICSYL-ADADLKIDIPPPTIWKPQR---------LWTGKQIFNVLMRPNRSSKVL 604

Query: 521 ANLKTKGRAYTANEEFCH-----------RDSYVILRNSELLAGSMDKSTLGSGGKANVF 569
            N+++K          C+            D ++++ NSE++ G MDK+T+GSG K ++F
Sbjct: 605 VNVESKCAKEEKPNVACYPMKKPAPDLAPNDGWLVIVNSEIMCGVMDKATVGSGKKKSIF 664

Query: 570 YILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
            +++RD+G   A  AM R++++ + +L N GFS+GI DV PG    Q 
Sbjct: 665 GVIMRDYGPHEAAAAMNRVAKVCARWLANFGFSLGINDVIPGPQLSQQ 712



 Score =  217 bits (552), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 169/493 (34%), Positives = 245/493 (49%), Gaps = 85/493 (17%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G+  PVE  R      +  +SRS   L   EIL   +  L ++ F  +    ++  ++ F
Sbjct: 914  GDAQPVEFLRAWSHA-SSIASRSTRGLLPFEILEFVDRELANRRFTSECMPAYLAIVRSF 972

Query: 1057 L-EEFSKKESVTSHQDKVSQPL-REQILSHQDKIGHG-RESNPFPSACKAEA-------- 1105
            + +  + K +    Q  +   L RE     +  +  G  +++      KA+         
Sbjct: 973  ISDHIANKLAEVRRQHGMYDALEREAEWDEETDLSLGASDADKATVDNKAKVTEEQLRVF 1032

Query: 1106 ---CREKYVRAQIEPATAVGAL-------------------------------------- 1124
               C  KYV+A+IEP + VGA+                                      
Sbjct: 1033 LDICWTKYVKAKIEPGSTVGAVGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEII 1092

Query: 1125 -AAQSIGEPGTQMTLKTFH---------------FAGEVCEYIEEVFVPDDSFILIKLDM 1168
             AA+ I  P     L T +                 G+V   +EE + P+ ++I I +D+
Sbjct: 1093 NAAKVISTPIISCRLVTANSEASARIVKGRLEKTLLGDVAAVLEEAWAPEYTYIGIIVDV 1152

Query: 1169 DRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF---NSKMYQMKQ 1225
              I+ L LE+ +D I++ I   +     L +   S  ++  ++  + +     K Y++++
Sbjct: 1153 KTIQDLQLELTLDDIKWAIVNAK----KLKIKQESITVIPRRNRLRIYIDGQDKYYRLRE 1208

Query: 1226 L---LPSVVIKGVQGINRAVIH---EEDVEGVTKYK-LLVEGDNLRDVMATYGVKGVKCS 1278
            L   LP VV+KGV  I RA+I+   ++DV G    K LLVEG  L+ VM T G+ G   S
Sbjct: 1209 LKRTLPDVVVKGVPTIRRAIINIKEKDDVRGNKGDKELLVEGYGLQKVMTTLGIVGEHTS 1268

Query: 1279 SNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHG 1338
            SN+  EV + LGIEAAR TI+ EI+  M++HGMSID RH ML+ D+MT KGEVLGITR G
Sbjct: 1269 SNHIVEVCQVLGIEAARQTIINEIQYTMQSHGMSIDPRHVMLLGDVMTYKGEVLGITRFG 1328

Query: 1339 LAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNV-GTGLIKLLQAV 1397
            +AKMK+SVL LASFE T+DHLFDAA  G+TD I+GVSE IIMG P    GT +  L+   
Sbjct: 1329 VAKMKDSVLMLASFEKTTDHLFDAAALGKTDSIAGVSESIIMGNPAAATGTSMPALVTPA 1388

Query: 1398 PRSEPVPRTLLFD 1410
            P S   PR LLF+
Sbjct: 1389 P-SLGKPRKLLFE 1400



 Score =  200 bits (508), Expect = 6e-48,   Method: Compositional matrix adjust.
 Identities = 112/255 (43%), Positives = 146/255 (57%), Gaps = 17/255 (6%)

Query: 95  QQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLP 154
           Q S  ++  ++LY     R P+ +G+LDRR+GT +K A C TCG N  DCVGH+ YI L 
Sbjct: 28  QISEFEVTHRDLYTA-VDRLPVKNGVLDRRLGTTEKGAFCETCGLNSVDCVGHYAYIKLV 86

Query: 155 LPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKIL 214
           +PVFHIGYF+  I ILQ ICK  TCARVLL E     +  + R P L  L R+SL K + 
Sbjct: 87  VPVFHIGYFKHTIGILQCICK--TCARVLLEEPDRRTYLKRFRRPNLENLQRQSLIKAVN 144

Query: 215 ETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEI 274
              +K   CP+C   NG VKK G LKI H+K+  R KK      D + ++     F P I
Sbjct: 145 GLARKTVYCPYCSATNGAVKKAGTLKIIHDKF--RAKK----TADEMEKWKRT--FAPAI 196

Query: 275 EAHKKFGLI------QTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPN 328
           EA K+ G+       + LNPL+VL LF+ I  ED  LL +  E  +P + +   + VPP 
Sbjct: 197 EAQKELGMYINKAVHEDLNPLKVLDLFKRISDEDCELLGLRPEYGRPEEYVWQYISVPPV 256

Query: 329 CIRPSVISDLKSDND 343
           CIRPSV  D  S+ D
Sbjct: 257 CIRPSVAQDGASNED 271



 Score =  185 bits (469), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 111/244 (45%), Positives = 155/244 (63%), Gaps = 14/244 (5%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ ISTPII+  L        ARIVKGRLE+T LG+V   +EE + P+ 
Sbjct: 1084 GVPRIKEIINAAKVISTPIISCRLVTANSEASARIVKGRLEKTLLGDVAAVLEEAWAPEY 1143

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF--- 880
            ++I I +D+  I+ L LE+ +D I++ I   +     L +   S  ++  ++  + +   
Sbjct: 1144 TYIGIIVDVKTIQDLQLELTLDDIKWAIVNAK----KLKIKQESITVIPRRNRLRIYIDG 1199

Query: 881  NSKMYQMKQL---LPSVVIKGVQGINRAVIH---EEDVEGVTKYK-LLVEGDNLRDVMAT 933
              K Y++++L   LP VV+KGV  I RA+I+   ++DV G    K LLVEG  L+ VM T
Sbjct: 1200 QDKYYRLRELKRTLPDVVVKGVPTIRRAIINIKEKDDVRGNKGDKELLVEGYGLQKVMTT 1259

Query: 934  YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
             G+ G   SSN+  EV + LGIEAAR TI+ EI+  M++HGMSID RH ML+ D+MT KG
Sbjct: 1260 LGIVGEHTSSNHIVEVCQVLGIEAARQTIINEIQYTMQSHGMSIDPRHVMLLGDVMTYKG 1319

Query: 994  EVLG 997
            EVLG
Sbjct: 1320 EVLG 1323



 Score =  105 bits (261), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 47/68 (69%), Positives = 55/68 (80%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV+NSF++GL+PTEF FH + GREGLVDTAVKTAETGYMQRRL+K+LEDL   YD 
Sbjct: 829 PSKGFVRNSFYTGLSPTEFLFHAISGREGLVDTAVKTAETGYMQRRLMKALEDLVTHYDS 888

Query: 670 SFDAAFYG 677
           S   A  G
Sbjct: 889 SVRNAVGG 896



 Score = 63.5 bits (153), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 30/50 (60%), Positives = 38/50 (76%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM+ K NLVTPRNGE +IAA QDFIT  +LL+Q++ FF+R Q  +I S L
Sbjct: 515 LMSVKHNLVTPRNGEPVIAAIQDFITASFLLSQRDRFFDRRQFTQICSYL 564



 Score = 45.4 bits (106), Expect = 0.22,   Method: Compositional matrix adjust.
 Identities = 28/55 (50%), Positives = 33/55 (60%), Gaps = 2/55 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNV-GTGLIKLLQAVPRSEPVPRTLLFD 721
            D  FDAA  G+TD I+GVSE IIMG P    GT +  L+   P S   PR LLF+
Sbjct: 1347 DHLFDAAALGKTDSIAGVSESIIMGNPAAATGTSMPALVTPAP-SLGKPRKLLFE 1400


>gi|402589186|gb|EJW83118.1| hypothetical protein WUBG_05969 [Wuchereria bancrofti]
          Length = 409

 Score =  258 bits (660), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 141/280 (50%), Positives = 195/280 (69%), Gaps = 13/280 (4%)

Query: 1145 GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTR-----GISGHLTV 1199
            GE+C+YIEEV++PDD FIL+K++  R+RLL LE+ + SI   I  ++      IS  +T+
Sbjct: 131  GEICDYIEEVYLPDDCFILLKINAKRVRLLQLEITMSSIAQSICTSKLPVPVRIS-QITI 189

Query: 1200 SGHSFLILKPKDSSKSFNSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKL 1256
             G + + ++P + +K   SKM  ++ L   + +VV+KG+ GI R VIH ++ +G   YKL
Sbjct: 190  LGKTIMTIRPPELAKC--SKMMAIQYLKYNIGNVVVKGLPGIVRCVIHADEKKG-DSYKL 246

Query: 1257 LVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFR 1316
            LVEG + R+VMAT GV G +   NN   V   LGIEAARS+I++EI   M +HG+ +D R
Sbjct: 247  LVEGIDYREVMATVGVDGRRTYFNNALTVADVLGIEAARSSIISEILSTMASHGIGLDQR 306

Query: 1317 HPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSE 1376
            H ML+ADLMT +GEVLGITR+GL KMKESVL LASFE T+DHLF+AAF+ Q D I GVSE
Sbjct: 307  HVMLLADLMTYRGEVLGITRNGLVKMKESVLLLASFEKTADHLFEAAFFSQEDKICGVSE 366

Query: 1377 CIIMGLPMNVGTGLIKLLQAVPRSEPVPR-TLLFDNPEFH 1415
            CII+G P+ +GTGL KLL    +   + R + +F++PEF+
Sbjct: 367  CIILGTPITIGTGLFKLLYNHGKQLTISRMSTIFESPEFN 406



 Score =  214 bits (545), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 120/243 (49%), Positives = 165/243 (67%), Gaps = 12/243 (4%)

Query: 763 DGVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPD 822
            GVPRIKEIIN  + ISTP+ITA L  + D   AR VK R+E+TTLGE+C+YIEEV++PD
Sbjct: 85  QGVPRIKEIINGVKLISTPLITAALTNEKDEKLARRVKARIEKTTLGEICDYIEEVYLPD 144

Query: 823 DSFILIKLDMDRIRLLHLEVDIDSIRYCIERTR-----GISGHLTVSGHSFLILKPKDSS 877
           D FIL+K++  R+RLL LE+ + SI   I  ++      IS  +T+ G + + ++P + +
Sbjct: 145 DCFILLKINAKRVRLLQLEITMSSIAQSICTSKLPVPVRIS-QITILGKTIMTIRPPELA 203

Query: 878 KSFNSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATY 934
           K   SKM  ++ L   + +VV+KG+ GI R VIH ++ +G   YKLLVEG + R+VMAT 
Sbjct: 204 KC--SKMMAIQYLKYNIGNVVVKGLPGIVRCVIHADEKKG-DSYKLLVEGIDYREVMATV 260

Query: 935 GVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGE 994
           GV G +   NN   V   LGIEAARS+I++EI   M +HG+ +D RH ML+ADLMT +GE
Sbjct: 261 GVDGRRTYFNNALTVADVLGIEAARSSIISEILSTMASHGIGLDQRHVMLLADLMTYRGE 320

Query: 995 VLG 997
           VLG
Sbjct: 321 VLG 323



 Score = 62.4 bits (150), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 29/40 (72%), Positives = 31/40 (77%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            C  K+  A  EP TAVGA+AA SIGEP TQMTLKTFHFAG
Sbjct: 38   CLRKFRCAICEPGTAVGAIAATSIGEPSTQMTLKTFHFAG 77



 Score = 61.2 bits (147), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 29/61 (47%), Positives = 41/61 (67%), Gaps = 1/61 (1%)

Query: 668 DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPR-TLLFDNPEFH 726
           D  F+AAF+ Q D I GVSECII+G P+ +GTGL KLL    +   + R + +F++PEF+
Sbjct: 347 DHLFEAAFFSQEDKICGVSECIILGTPITIGTGLFKLLYNHGKQLTISRMSTIFESPEFN 406

Query: 727 F 727
            
Sbjct: 407 L 407


>gi|361128129|gb|EHL00082.1| putative DNA-directed RNA polymerase III subunit RPC1 [Glarea
           lozoyensis 74030]
          Length = 869

 Score =  258 bits (660), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 147/353 (41%), Positives = 195/353 (55%), Gaps = 65/353 (18%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIM+H  KV P RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 97  DGDIVLFNRQPSLHKLSIMSHYVKVRPWRTFRLNECVCNPYNADFDGDEMNLHVPQTEEA 156

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EA+               LM  K+NL TP+NGE +I+ATQDFIT  YLL+ K  FF+R
Sbjct: 157 RTEAIN--------------LMGVKNNLSTPKNGEPIISATQDFITAAYLLSSKENFFDR 202

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV- 519
                                     +++  +  ++   +WTGKQ+FS++++PN+  PV 
Sbjct: 203 --------------------------KTFTNISILKPEALWTGKQVFSVLMRPNKLSPVK 236

Query: 520 ----------NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKS---TLGSGGKA 566
                     N +++            C  D  +    S  L+G  +++    + +  K 
Sbjct: 237 RLVSIAYKETNEDIQKYNEGKLEKAAGCDLDESLENSISGKLSGVREQAGNYCIETLSKW 296

Query: 567 NVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVT-P----------GQGFV 615
           N   I+ +   +   +     ++ +    +  +  + G  D T P           +GFV
Sbjct: 297 NSPLIMAKSGSKGSNINVAQMVAVVGQQIIGGKRVAEGFQDRTLPHFLKNARHALAKGFV 356

Query: 616 QNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            NSFF+GLTPTEF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 357 VNSFFTGLTPTEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSTQYD 409



 Score =  211 bits (537), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 158/429 (36%), Positives = 218/429 (50%), Gaps = 60/429 (13%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G+  PV  KR             DP L   ++ A  +E L  +   +  + +FV  I   
Sbjct: 436  GSAVPVNFKRTFSHAENLTWKNDDPCLLPYQVTAYCDEYLAEQ---KKNARDFVETIANH 492

Query: 1057 LEEFSKKESVTSHQDKVSQPLREQI---------LSHQDKIGH----------GRESNPF 1097
            ++  + K  + + ++K   P  EQ           + +DK             G   N F
Sbjct: 493  VKLLATK--MANIREKSGLPRLEQDPNLSGQRYDATREDKQARLRVERVAKVSGPTLNKF 550

Query: 1098 PSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------E 1146
             S C +     KY +A +EP  AVGA+ AQSIGEPGTQMTLKTFHFAG            
Sbjct: 551  ISLCLS-----KYAKAHVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPR 605

Query: 1147 VCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLI 1206
            + E I    V  D +I       R   + ++V+        E T G  G    +      
Sbjct: 606  IKEIINASKVIKDVYI-------RPGCVFIKVN--------ETTGGNLGARGAAAAKTKA 650

Query: 1207 LKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDV 1266
                 ++     +M  +K++LP++ I G    +RAVI+       +K +++VEG  LR  
Sbjct: 651  KDEGINASELALRMNHLKRVLPAIAISGYPEASRAVINSSQE---SKNEVVVEGYGLRAC 707

Query: 1267 MATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMT 1326
            M T GV G + +SN+  E+   LGIEAAR+TI  EI +VM    M ID RH  L+AD+MT
Sbjct: 708  MNTIGVIGTQVTSNSVMEMKDVLGIEAARTTIAQEIGVVMGQ--MDIDPRHMQLLADVMT 765

Query: 1327 SKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNV 1386
             KGEVLGITR GL+KM++SVL LASFE T DHLFDAA   ++D I GVSECIIMG  M+V
Sbjct: 766  YKGEVLGITRFGLSKMRDSVLQLASFEKTPDHLFDAAAGMKSDKIEGVSECIIMGQTMSV 825

Query: 1387 GTGLIKLLQ 1395
            GTG  ++++
Sbjct: 826  GTGAFQVVR 834



 Score = 90.9 bits (224), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 58/139 (41%), Positives = 82/139 (58%), Gaps = 6/139 (4%)

Query: 883  KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCS 942
            +M  +K++LP++ I G    +RAVI+       +K +++VEG  LR  M T GV G + +
Sbjct: 663  RMNHLKRVLPAIAISGYPEASRAVINSSQE---SKNEVVVEGYGLRACMNTIGVIGTQVT 719

Query: 943  SNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNGTPV 1002
            SN+  E+   LGIEAAR+TI  EI +VM    M ID RH  L+AD+MT KGEVLG  T  
Sbjct: 720  SNSVMEMKDVLGIEAARTTIAQEIGVVMGQ--MDIDPRHMQLLADVMTYKGEVLGI-TRF 776

Query: 1003 ELKRLLDDIIAKNSSRSDP 1021
             L ++ D ++   S    P
Sbjct: 777  GLSKMRDSVLQLASFEKTP 795



 Score = 60.8 bits (146), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 69/286 (24%), Positives = 125/286 (43%), Gaps = 30/286 (10%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIA----STLIAGRKV 77
           LM  K+NL TP+NGE +I+ATQDFIT  YLL+ K  FF+R     I+      L  G++V
Sbjct: 163 LMGVKNNLSTPKNGEPIISATQDFITAAYLLSSKENFFDRKTFTNISILKPEALWTGKQV 222

Query: 78  FFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTC 137
           F        + + +++     +  ++     +D Q+     G L++  G +  E+   + 
Sbjct: 223 F------SVLMRPNKLSPVKRLVSIAYKETNEDIQK--YNEGKLEKAAGCDLDESLENSI 274

Query: 138 GQNLSD--------CVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKA 189
              LS         C+      + PL +   G     IN+ Q +       +++ G+  A
Sbjct: 275 SGKLSGVREQAGNYCIETLSKWNSPLIMAKSGSKGSNINVAQMVA--VVGQQIIGGKRVA 332

Query: 190 AGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGL----LKISHEK 245
            GF+ +   P      R +L K  +  +    + P     + +  + GL    +K +   
Sbjct: 333 EGFQDRTL-PHFLKNARHALAKGFVVNSFFTGLTPTEFLFHAISGREGLVDTAVKTAETG 391

Query: 246 YKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEV 291
           Y +R   K   +EDL  +Y++ V+ +       +FG    L+P+++
Sbjct: 392 YMSRRLMKS--LEDLSTQYDDTVRNSSGGVVQFQFG-ADKLDPVDM 434



 Score = 45.4 bits (106), Expect = 0.24,   Method: Compositional matrix adjust.
 Identities = 27/71 (38%), Positives = 44/71 (61%), Gaps = 5/71 (7%)

Query: 668 DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ--AVPRSEPVPRTLLFDNPEF 725
           D  FDAA   ++D I GVSECIIMG  M+VGTG  ++++   +  S+   +  +F++  +
Sbjct: 796 DHLFDAAAGMKSDKIEGVSECIIMGQTMSVGTGAFQVVRRLGLKESDTQSKRTVFEDA-W 854

Query: 726 HFPQVYYERRR 736
            + Q+  ERR+
Sbjct: 855 KWDQI--ERRK 863


>gi|449462093|ref|XP_004148776.1| PREDICTED: DNA-directed RNA polymerase III subunit rpc1-like [Cucumis
            sativus]
          Length = 1400

 Score =  258 bits (660), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 180/498 (36%), Positives = 254/498 (51%), Gaps = 97/498 (19%)

Query: 998  NGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSEN------FVR 1051
            +G P+  +RL     A   S  +  LS  E     +ET++ +    D S        FV 
Sbjct: 913  SGAPLNFERLFLKAKATCPSDGNKILSPSEF----SETVEDRLSKDDASPECGCSPAFVG 968

Query: 1052 DIKKFLEEFSKKE-----------------SVTSHQDKVSQPLREQILSHQDKIGHGRES 1094
             +K FL ++ + +                 S+ S  D  +  +R +++ +   + H R+ 
Sbjct: 969  SLKIFLNKYVEAQKKSWGTLLADNESAVDKSIISSSDNDNIVIRNKVVQNIAGVTH-RQL 1027

Query: 1095 NPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------- 1145
              F      + C  +Y   +IE  TA+GA+ AQSIGEPGTQMTLKTFHFAG         
Sbjct: 1028 QVF-----LDTCLSRYHTKKIEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNVTLG 1082

Query: 1146 -----EVCEYIEEVFVP--------DD--------------------------------S 1160
                 E+    + +  P        DD                                +
Sbjct: 1083 VPRIKEIINGAKRISTPIVTAALTHDDNVNIARMVKARIEKTNLGQIAKCIQIVMSSRSA 1142

Query: 1161 FILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSFLILKPKDSSKS-F 1216
             I IKLDM++IR   L VD + ++  I  T  +     H+ V     L + P+D+ ++  
Sbjct: 1143 LIEIKLDMEKIRDAELYVDANVVKQAILVTPKLKLKHEHINVLDDRKLRVLPQDADRNKL 1202

Query: 1217 NSKMYQMKQLLPSVVIKGVQGINRAVIHEE--DVEGVTKYKLLVEGDNLRDVMATYGVKG 1274
            +  ++ +K +LP VV+KG++ + RAVI EE        K+ LLVEG  L+ VM T GV G
Sbjct: 1203 HFNLHFLKNMLPGVVVKGIKTVGRAVIKEEKDKARNAKKFSLLVEGTGLQAVMGTEGVDG 1262

Query: 1275 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGI 1334
                SN+  EV + LGIEAAR  I+ EIK  ME+HGMSID RH ML+ DLMT +GEVLGI
Sbjct: 1263 CNTKSNHIIEVQQVLGIEAARKCIIEEIKYTMESHGMSIDIRHMMLLGDLMTFRGEVLGI 1322

Query: 1335 TRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            TR G+ KM +SVL LASFE T+DHLF+A+  G+ D I GVSEC+IMG+PM +GTG++K+ 
Sbjct: 1323 TRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDDKIEGVSECVIMGIPMPLGTGMLKVR 1382

Query: 1395 QAVPRSEPVPRTLLFDNP 1412
            Q V     VP+ L +  P
Sbjct: 1383 QRV----SVPQQLPYGPP 1396



 Score =  254 bits (648), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 125/284 (44%), Positives = 180/284 (63%), Gaps = 33/284 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH++SIM HR +V+P RT RFNE VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 450 DGDVVLFNRQPSLHRMSIMCHRVRVMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEA 509

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EA+              +LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+K+ F++R
Sbjct: 510 RTEAI--------------LLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDR 555

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPV-VFVRTAVIWTGKQIFSLILKPNRDCPV 519
           A    +  + + D  D+  +          P    V+   +WTGKQ+FS++++P+    V
Sbjct: 556 A-AFSLMCSYMGDGMDLVDL----------PTPALVKPIELWTGKQLFSVLVRPHASMKV 604

Query: 520 NANLKTKGRAYTA-------NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYIL 572
             NL  K ++Y+         E  C  D +V  RNSEL++G + K+TLG+G K  ++ +L
Sbjct: 605 YLNLTVKEKSYSKVKGNEKERETMCPNDGFVYFRNSELISGQVGKATLGNGNKDGLYSVL 664

Query: 573 LRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           LRD+    A   M RL+++++ ++ N GFSIGI DV PG   V+
Sbjct: 665 LRDYKAHAAAVCMNRLAKLSARWIGNHGFSIGIDDVQPGDQLVK 708



 Score =  197 bits (500), Expect = 5e-47,   Method: Compositional matrix adjust.
 Identities = 110/240 (45%), Positives = 153/240 (63%), Gaps = 6/240 (2%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIIN ++ ISTPI+TA L  D +++ AR+VK R+E+T LG++ + I+ V     
Sbjct: 1082 GVPRIKEIINGAKRISTPIVTAALTHDDNVNIARMVKARIEKTNLGQIAKCIQIVMSSRS 1141

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSFLILKPKDSSKS- 879
            + I IKLDM++IR   L VD + ++  I  T  +     H+ V     L + P+D+ ++ 
Sbjct: 1142 ALIEIKLDMEKIRDAELYVDANVVKQAILVTPKLKLKHEHINVLDDRKLRVLPQDADRNK 1201

Query: 880  FNSKMYQMKQLLPSVVIKGVQGINRAVIHEED--VEGVTKYKLLVEGDNLRDVMATYGVK 937
             +  ++ +K +LP VV+KG++ + RAVI EE        K+ LLVEG  L+ VM T GV 
Sbjct: 1202 LHFNLHFLKNMLPGVVVKGIKTVGRAVIKEEKDKARNAKKFSLLVEGTGLQAVMGTEGVD 1261

Query: 938  GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            G    SN+  EV + LGIEAAR  I+ EIK  ME+HGMSID RH ML+ DLMT +GEVLG
Sbjct: 1262 GCNTKSNHIIEVQQVLGIEAARKCIIEEIKYTMESHGMSIDIRHMMLLGDLMTFRGEVLG 1321



 Score =  170 bits (431), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 105/249 (42%), Positives = 135/249 (54%), Gaps = 30/249 (12%)

Query: 102 VSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIG 161
           V K LY  D  R PI  GLLD RMG   K   C TC  N  DC GH+GY++L LPVF++G
Sbjct: 46  VYKGLY-YDTTRKPIDGGLLDPRMGPANKGCKCATCHANFGDCPGHYGYVNLALPVFNVG 104

Query: 162 YFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKI------LE 215
           YF  ++ IL+ ICK  +C+R+LL E+    F  K+RNP L  L +  L KKI      L 
Sbjct: 105 YFTTILEILKCICK--SCSRILLEEKLFKDFLRKMRNPKLEALRKVDLVKKIIKKCSTLT 162

Query: 216 TTKKVSVCPHCGEINGVVKKC-GLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEI 274
           T  K + C  CG +NG VKK   +L I H  Y+ R+K    + EDL A YN +       
Sbjct: 163 TGNKSTRCSRCGYLNGSVKKAVSMLGILH--YRARSKDAGVVSEDLRAPYNVSNDI---- 216

Query: 275 EAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSV 334
                      LNP  VL LF+ +  ED  LL ++   ++P  LI+T +LVPP  IRPSV
Sbjct: 217 -----------LNPFRVLCLFQRMSDEDCELLFLS---NRPEKLIITNVLVPPIAIRPSV 262

Query: 335 ISDLKSDND 343
           I D    N+
Sbjct: 263 IMDGSQSNE 271



 Score =  106 bits (264), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 50/67 (74%), Positives = 56/67 (83%), Gaps = 1/67 (1%)

Query: 609 TPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV NSF+SGLT TEFFFHTMGGREGLVDTAVKTA+TGYM RRL+K+LEDL + Y
Sbjct: 824 TPAAKGFVANSFYSGLTATEFFFHTMGGREGLVDTAVKTADTGYMSRRLIKALEDLSIHY 883

Query: 668 DMSFDAA 674
           D S   A
Sbjct: 884 DSSVRNA 890



 Score = 57.0 bits (136), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 22/42 (52%), Positives = 36/42 (85%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRA 62
           +LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+K+ F++RA
Sbjct: 515 LLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDRA 556



 Score = 52.8 bits (125), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 26/56 (46%), Positives = 37/56 (66%), Gaps = 4/56 (7%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNP 723
            D  F+A+  G+ D I GVSEC+IMG+PM +GTG++K+ Q V     VP+ L +  P
Sbjct: 1345 DHLFNASVNGRDDKIEGVSECVIMGIPMPLGTGMLKVRQRV----SVPQQLPYGPP 1396


>gi|302673160|ref|XP_003026267.1| hypothetical protein SCHCODRAFT_71335 [Schizophyllum commune H4-8]
 gi|300099948|gb|EFI91364.1| hypothetical protein SCHCODRAFT_71335 [Schizophyllum commune H4-8]
          Length = 1402

 Score =  258 bits (659), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 135/283 (47%), Positives = 178/283 (62%), Gaps = 36/283 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIM HR KV P R+FR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 447 DGDIVLFNRQPSLHKLSIMCHRVKVRPWRSFRLNECVCGPYNADFDGDEMNLHVPQTEEA 506

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL               LM+ K NLVTPRNG+ +IAA QDFIT  YLL++K+ FF+R
Sbjct: 507 RTEALE--------------LMSVKHNLVTPRNGDPVIAAIQDFITASYLLSRKDTFFDR 552

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNR----- 515
               +I   L AD +    I          P   ++   +WTGKQIF+++++PNR     
Sbjct: 553 RAFTQICCYL-ADANMQIDI---------PPPTILKPQRLWTGKQIFNVLMRPNRKSKVF 602

Query: 516 ---DCPVNANLKTKGRAYTANE----EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANV 568
              +C  N   + K   Y A E    +    D ++++ NSE++ G MDK+T+GSG K ++
Sbjct: 603 VNVECKCNKVEEVKKEHYPAIEKPRNDLMANDGWLVIVNSEIMCGLMDKATIGSGKKKSI 662

Query: 569 FYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           F ++LRD+G   A  AM R++++ + YL N GFS+GI DV PG
Sbjct: 663 FGVILRDYGPHEAAAAMNRVAKLCARYLANYGFSLGINDVIPG 705



 Score =  238 bits (608), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 177/493 (35%), Positives = 251/493 (50%), Gaps = 85/493 (17%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G+  P++ +R      A  +SR    L   E++ L N  +   +++ + +  ++  I+ F
Sbjct: 913  GDAQPIDFERAWVHSAAI-ASRKGRGLLPFEVMDLMNSEMAKSKWVSECTTTYMDSIRDF 971

Query: 1057 LEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSAC---KAEACRE----- 1108
            +EE   K      + +      E+I    +++     ++    A    KA+         
Sbjct: 972  IEEKVAKRLAILRERRGMYDAMERIDDWDEEMDLSMGASDADKAVVDNKAKVTEAQLRTF 1031

Query: 1109 ------KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVC 1148
                  KYV+A+IEP + VGA+ AQSIGEPGTQMTLKTFHFAG              E+ 
Sbjct: 1032 LQIAWTKYVKARIEPGSTVGAVGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEII 1091

Query: 1149 EYIEEVFVPDDSFILIKLD----------------------------------------M 1168
               + +  P  S  L+  D                                        M
Sbjct: 1092 NASKNISTPIISCKLVTRDSEASARIVKGRLEKTMLGDIASVLEEAWAPDYTYIGIIVDM 1151

Query: 1169 DRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF---NSKMYQMKQ 1225
              I+ L LE+ +D I++ I  TR     L V   S ++L  K+  + +   + K Y+++ 
Sbjct: 1152 RAIQKLQLEMTLDDIKWAIVSTR----KLKVKQESIVVLSRKNRLRIYIEGDEKFYRIRD 1207

Query: 1226 L---LPSVVIKGVQGINRAVIH---EEDVEGVTKYK-LLVEGDNLRDVMATYGVKGVKCS 1278
            L   L  VV+KGV  I+RAVI+   ++D  G    K LLVEG  L+  M T GV G   +
Sbjct: 1208 LKRNLADVVVKGVPSIHRAVINIKEKDDYRGKKGDKELLVEGYGLQKCMITEGVVGEMTT 1267

Query: 1279 SNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHG 1338
            SN+  EV + LGIEAAR TI+ EI+  M++H M+ID RH ML+ D+M+ KGEVLGITR G
Sbjct: 1268 SNHVIEVAQVLGIEAARRTIINEIQYTMKSHDMNIDPRHVMLLGDVMSYKGEVLGITRFG 1327

Query: 1339 LAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLP-MNVGTGLIKLLQAV 1397
            +AKMK+SVL LASFE T+DHLFDAA YG++D I+GVSE IIMG P    GT +  L+   
Sbjct: 1328 VAKMKDSVLMLASFEKTTDHLFDAAAYGKSDAIAGVSESIIMGNPAAQCGTSMPALVTPA 1387

Query: 1398 PRSEPVPRTLLFD 1410
            P S   PR LLF+
Sbjct: 1388 P-SISKPRPLLFE 1399



 Score =  191 bits (484), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 103/247 (41%), Positives = 140/247 (56%), Gaps = 5/247 (2%)

Query: 97  SHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP 156
           S  +I  ++LY     R P+  G+LDRR+GT  K A C TCGQ+  +CVGH+ YI L +P
Sbjct: 30  SEFEITHRDLYTAT-DRLPVKDGVLDRRLGTTDKSAFCETCGQSSVNCVGHYAYIKLCVP 88

Query: 157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILET 216
           VFHIGYF+  I ILQ ICK  TCARVLL E +   F  + R   L  + R++L K +   
Sbjct: 89  VFHIGYFKHTIGILQCICK--TCARVLLEEPERRTFLKRFRRSNLENMQRQALTKAVNTA 146

Query: 217 TKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEA 276
            +KV  CP+C   NG VKK G LKI H+K+  R+KK    +E     +  A++   E+  
Sbjct: 147 ARKVVYCPYCAATNGTVKKAGALKIIHDKF--RSKKTADEMERWKRTFASAIEAQKELAQ 204

Query: 277 HKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVIS 336
                + + LNPL+VL LF  I  ED  LL +  +  +P + +   + VPP  IRPSV  
Sbjct: 205 FLNKAVNEDLNPLKVLDLFRRISDEDCELLGLRPKFGRPEEFLWQYISVPPVAIRPSVAQ 264

Query: 337 DLKSDND 343
           D  S+ D
Sbjct: 265 DGASNED 271



 Score =  186 bits (473), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 114/244 (46%), Positives = 155/244 (63%), Gaps = 14/244 (5%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+NISTPII+  L        ARIVKGRLE+T LG++   +EE + PD 
Sbjct: 1083 GVPRIKEIINASKNISTPIISCKLVTRDSEASARIVKGRLEKTMLGDIASVLEEAWAPDY 1142

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF--- 880
            ++I I +DM  I+ L LE+ +D I++ I  TR     L V   S ++L  K+  + +   
Sbjct: 1143 TYIGIIVDMRAIQKLQLEMTLDDIKWAIVSTR----KLKVKQESIVVLSRKNRLRIYIEG 1198

Query: 881  NSKMYQMKQL---LPSVVIKGVQGINRAVIH---EEDVEGVTKYK-LLVEGDNLRDVMAT 933
            + K Y+++ L   L  VV+KGV  I+RAVI+   ++D  G    K LLVEG  L+  M T
Sbjct: 1199 DEKFYRIRDLKRNLADVVVKGVPSIHRAVINIKEKDDYRGKKGDKELLVEGYGLQKCMIT 1258

Query: 934  YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
             GV G   +SN+  EV + LGIEAAR TI+ EI+  M++H M+ID RH ML+ D+M+ KG
Sbjct: 1259 EGVVGEMTTSNHVIEVAQVLGIEAARRTIINEIQYTMKSHDMNIDPRHVMLLGDVMSYKG 1318

Query: 994  EVLG 997
            EVLG
Sbjct: 1319 EVLG 1322



 Score =  102 bits (254), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 44/61 (72%), Positives = 53/61 (86%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV+NSF++GL  TEF FH + GREGLVDTAVKTAETGYMQRRL+K+LEDL  QYD+
Sbjct: 828 PSKGFVRNSFYTGLVATEFLFHAISGREGLVDTAVKTAETGYMQRRLMKALEDLTTQYDL 887

Query: 670 S 670
           +
Sbjct: 888 T 888



 Score = 59.3 bits (142), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 28/50 (56%), Positives = 36/50 (72%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM+ K NLVTPRNG+ +IAA QDFIT  YLL++K+ FF+R    +I   L
Sbjct: 513 LMSVKHNLVTPRNGDPVIAAIQDFITASYLLSRKDTFFDRRAFTQICCYL 562



 Score = 48.5 bits (114), Expect = 0.026,   Method: Compositional matrix adjust.
 Identities = 28/55 (50%), Positives = 34/55 (61%), Gaps = 2/55 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLP-MNVGTGLIKLLQAVPRSEPVPRTLLFD 721
            D  FDAA YG++D I+GVSE IIMG P    GT +  L+   P S   PR LLF+
Sbjct: 1346 DHLFDAAAYGKSDAIAGVSESIIMGNPAAQCGTSMPALVTPAP-SISKPRPLLFE 1399


>gi|169869303|ref|XP_001841218.1| DNA-directed RNA polymerase III largest subunit [Coprinopsis
           cinerea okayama7#130]
 gi|116497686|gb|EAU80581.1| DNA-directed RNA polymerase III largest subunit [Coprinopsis
           cinerea okayama7#130]
          Length = 1403

 Score =  258 bits (658), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 132/283 (46%), Positives = 179/283 (63%), Gaps = 36/283 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIM HRAK+ P RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 447 DGDIVLFNRQPSLHKLSIMCHRAKIRPWRTFRLNECVCGPYNADFDGDEMNLHVPQTEEA 506

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL               LM+ K NLVTPRNGE +I+A QDFIT  +L+++K+ FF+R
Sbjct: 507 RTEALE--------------LMSVKHNLVTPRNGEPVISAIQDFITASFLISRKDRFFDR 552

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +  +I   L     D    I       W PV       +WTGKQIF+++++PN+   + 
Sbjct: 553 REFTQICCYL----GDADLHIDIPPPTIWKPV------QLWTGKQIFNVLMRPNKQSKIF 602

Query: 521 ANLKTKGRAY------------TANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANV 568
            N+++K + +            T   +    D ++++ NSE++ G MDK+T+GSG K ++
Sbjct: 603 INVESKCQKWEEAKPQNFPPRITLQPDLSPNDGWLVVVNSEIMCGVMDKATVGSGKKKSI 662

Query: 569 FYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           F ++LRD+G   A  AM RL+++ + YL N GFS+GI DV PG
Sbjct: 663 FGVILRDYGPHEAAIAMGRLAKLCARYLANYGFSLGINDVIPG 705



 Score =  209 bits (533), Expect = 7e-51,   Method: Compositional matrix adjust.
 Identities = 164/499 (32%), Positives = 243/499 (48%), Gaps = 95/499 (19%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G+  P+++ R      A+ S+R    L   EI+ +   TL S  F Q     +   ++ F
Sbjct: 913  GDAQPLDMDRSWRHAQAR-SNRKTRGLLPFEIIQIVETTLASPRFTQSCLPAYCDAVRDF 971

Query: 1057 LEE--FSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKA----------- 1103
            + +   S+  SV +  D      + +    +  +  G        ACK            
Sbjct: 972  IVKKVASRVASVRAKHDMFDALEKPEEWDEEMDLTLGASE-----ACKRVVDNKAKVTES 1026

Query: 1104 ------EACREKYVRAQIEPATAVGAL--------------------------------- 1124
                  + C E+YV+A+IEP + VGA+                                 
Sbjct: 1027 HLRIFLDICWERYVKARIEPGSTVGAVGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPR 1086

Query: 1125 ------AAQSIGEPGTQMTLKTFH---------------FAGEVCEYIEEVFVPDDSFIL 1163
                  AA++I  P     L T                   G+V   +EE + PD ++I 
Sbjct: 1087 IKEIINAAKAISTPIISCKLVTPDSEPSARIVKGRLEKTLLGDVVSVLEEAWAPDYTYIG 1146

Query: 1164 IKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF---NSKM 1220
            I +D+D I+ L LE+ +D I++ I   +     L +   S  I+  K+  + +     K 
Sbjct: 1147 IIVDVDAIQKLQLELTLDDIKWAIVAAK----KLKIKQESITIIPRKNRLRIYVDGEDKF 1202

Query: 1221 YQMKQL---LPSVVIKGVQGINRAVIH----EEDVEGVTKYKLLVEGDNLRDVMATYGVK 1273
            Y++++L   L  VV+KG+  I RA+I+    ++D       +LLVEG  L+  M T GV 
Sbjct: 1203 YRIRELRRGLADVVVKGLPTIQRAIINIKDKDDDRGKKGDKELLVEGYGLQKCMITEGVV 1262

Query: 1274 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 1333
            G   +SN+  EV + LGIEAAR TI+ EI+  M++H M+ID RH ML+ D+MT KGEVLG
Sbjct: 1263 GEFTTSNHVIEVAQVLGIEAARRTIINEIQYTMKSHDMNIDPRHVMLLGDVMTYKGEVLG 1322

Query: 1334 ITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNV-GTGLIK 1392
            ITR G+AKMK+SVL LASFE T+DHLFDA+ YG+TD I+GVSE IIMG P  + GT +  
Sbjct: 1323 ITRFGVAKMKDSVLMLASFEKTTDHLFDASAYGKTDSIAGVSESIIMGNPAAMCGTSMPA 1382

Query: 1393 LLQAVPRSEPVPRTLLFDN 1411
            LL   P  +  PR L+F++
Sbjct: 1383 LLSTTPVVKK-PRKLVFES 1400



 Score =  202 bits (513), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 107/247 (43%), Positives = 144/247 (58%), Gaps = 5/247 (2%)

Query: 97  SHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP 156
           S  ++  ++LY    +R P+ HG+LDRR+GT +K A C TCGQ+  +CVGH+ YI L +P
Sbjct: 30  SEFEVTHRDLYTPT-ERLPVKHGVLDRRLGTTEKSAFCETCGQSSVNCVGHYAYIKLCVP 88

Query: 157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILET 216
           VFHIGYF+  I ILQSICK  +CARVLL E     +  + R P L  + R++L K +   
Sbjct: 89  VFHIGYFKHTIGILQSICK--SCARVLLEEPDRRTYLKRFRRPNLENIHRQALFKAVNSM 146

Query: 217 TKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEA 276
            +KV  CP+C   NG VK  G LKI H+K+  R KK    +E     +  AV+   E+  
Sbjct: 147 ARKVVYCPYCSATNGAVKTAGALKIIHDKF--RAKKTADELEKWKKTFVAAVEAQKELGM 204

Query: 277 HKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVIS 336
           +    +++ LNPL+VL LF  I  ED  LL +  E  +P   I   L VPP CIRPSV  
Sbjct: 205 YLNKAVVEDLNPLKVLDLFRRISDEDCELLGLRPEWGRPEQFIWQYLSVPPVCIRPSVAQ 264

Query: 337 DLKSDND 343
           D  S+ D
Sbjct: 265 DGASNED 271



 Score =  174 bits (440), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 107/244 (43%), Positives = 151/244 (61%), Gaps = 14/244 (5%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ ISTPII+  L        ARIVKGRLE+T LG+V   +EE + PD 
Sbjct: 1083 GVPRIKEIINAAKAISTPIISCKLVTPDSEPSARIVKGRLEKTLLGDVVSVLEEAWAPDY 1142

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF--- 880
            ++I I +D+D I+ L LE+ +D I++ I   +     L +   S  I+  K+  + +   
Sbjct: 1143 TYIGIIVDVDAIQKLQLELTLDDIKWAIVAAK----KLKIKQESITIIPRKNRLRIYVDG 1198

Query: 881  NSKMYQMKQL---LPSVVIKGVQGINRAVIH----EEDVEGVTKYKLLVEGDNLRDVMAT 933
              K Y++++L   L  VV+KG+  I RA+I+    ++D       +LLVEG  L+  M T
Sbjct: 1199 EDKFYRIRELRRGLADVVVKGLPTIQRAIINIKDKDDDRGKKGDKELLVEGYGLQKCMIT 1258

Query: 934  YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
             GV G   +SN+  EV + LGIEAAR TI+ EI+  M++H M+ID RH ML+ D+MT KG
Sbjct: 1259 EGVVGEFTTSNHVIEVAQVLGIEAARRTIINEIQYTMKSHDMNIDPRHVMLLGDVMTYKG 1318

Query: 994  EVLG 997
            EVLG
Sbjct: 1319 EVLG 1322



 Score =  104 bits (259), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 46/61 (75%), Positives = 53/61 (86%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV+NSF+SGL  TEF FH + GREGLVDTAVKTAETGYMQRRL+K+LEDL  QYD+
Sbjct: 828 PSKGFVRNSFYSGLVATEFLFHAISGREGLVDTAVKTAETGYMQRRLMKALEDLTTQYDL 887

Query: 670 S 670
           S
Sbjct: 888 S 888



 Score = 57.8 bits (138), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 26/50 (52%), Positives = 37/50 (74%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM+ K NLVTPRNGE +I+A QDFIT  +L+++K+ FF+R +  +I   L
Sbjct: 513 LMSVKHNLVTPRNGEPVISAIQDFITASFLISRKDRFFDRREFTQICCYL 562



 Score = 47.8 bits (112), Expect = 0.043,   Method: Compositional matrix adjust.
 Identities = 27/56 (48%), Positives = 36/56 (64%), Gaps = 2/56 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNV-GTGLIKLLQAVPRSEPVPRTLLFDN 722
            D  FDA+ YG+TD I+GVSE IIMG P  + GT +  LL   P  +  PR L+F++
Sbjct: 1346 DHLFDASAYGKTDSIAGVSESIIMGNPAAMCGTSMPALLSTTPVVKK-PRKLVFES 1400


>gi|384246317|gb|EIE19808.1| beta and beta-prime subunits of DNA dependent RNA-polymerase
           [Coccomyxa subellipsoidea C-169]
          Length = 1328

 Score =  257 bits (657), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 127/277 (45%), Positives = 176/277 (63%), Gaps = 25/277 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIMAHRA+++P RTFRFNECVC PYNADFDGDEMNVH+PQTEEA
Sbjct: 407 DGDIVLFNRQPSLHRMSIMAHRARIMPWRTFRFNECVCNPYNADFDGDEMNVHVPQTEEA 466

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A  LM    NL TP++GE+LIAATQDF+T  +LLT K+ F++R
Sbjct: 467 RAE--------------ASELMGVMRNLCTPKSGEILIAATQDFLTSAFLLTSKDRFYSR 512

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q  ++A   + D  D   + +            ++   +WTGKQ+FS++++PN    + 
Sbjct: 513 TQVAQLA-CFMGDGMDAVDLPQ---------PALLKPLELWTGKQLFSMLIRPNSLTRLL 562

Query: 521 ANLKTKGRAY-TANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            NL+T  + Y   +   C RD +V+ +NS L+ G + K TLG G K+ +F +L  DF  +
Sbjct: 563 VNLETAEKTYLKGSGVMCPRDGFVVFQNSTLMCGRLGKVTLGGGNKSGLFQVLANDFSSE 622

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
            A   M RLS++++ ++   GFSIG+ DVTP    +Q
Sbjct: 623 AAGAVMRRLSKLSARFIGEHGFSIGVDDVTPALRLLQ 659



 Score =  204 bits (520), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 118/256 (46%), Positives = 158/256 (61%), Gaps = 27/256 (10%)

Query: 1145 GEVCEYIEEVFVPD-----DSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTV 1199
            G+V + I  V  P       +F+ I+LD   I+ L L+++  ++R  I     ++  L V
Sbjct: 1077 GQVAKRIRAVLKPSLTHQVGAFVEIRLDKVVIQALQLDINAHTVRDAI-----VASKLKV 1131

Query: 1200 SGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVE 1259
             G  F               ++ +   LP V++ G+  + RAV+  +  E   KY L VE
Sbjct: 1132 -GMGF--------------ALHNLMTALPHVIVAGIASVERAVVTFD--EKTCKYSLGVE 1174

Query: 1260 GDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPM 1319
            G +L  VM T GV G + ++N+  E  + LGIEAAR+ IMTEI+  M +HGM+ID RH M
Sbjct: 1175 GMDLTAVMGTLGVDGCRTATNHVMETERVLGIEAARTKIMTEIQTTMSSHGMTIDARHTM 1234

Query: 1320 LVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECII 1379
            L+AD MT KGEVLGITR G+AKMK+SVL LASFE T+DHLFDAA +G+TD I+GVSE II
Sbjct: 1235 LLADCMTYKGEVLGITRFGIAKMKDSVLMLASFEKTTDHLFDAALHGRTDDITGVSESII 1294

Query: 1380 MGLPMNVGTGLIKLLQ 1395
            MG+PM  GTGL KL Q
Sbjct: 1295 MGIPMPTGTGLFKLHQ 1310



 Score =  201 bits (511), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 110/248 (44%), Positives = 148/248 (59%), Gaps = 12/248 (4%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D + + S +Q+  ++LY + P+R P P+G LD R+G + + + C+TCGQNL+DC GHFGY
Sbjct: 4   DEIIKASELQVYERSLY-KMPERKPAPNGTLDPRLGVSNRSSKCSTCGQNLADCTGHFGY 62

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           I L LPVFHIGY +  +  LQ ICK  TC+ +LL EE    F    RNP L  + R  L 
Sbjct: 63  IKLWLPVFHIGYLKSTLTTLQCICK--TCSSILLPEEDYRRFLRLFRNPRLERVARAGLF 120

Query: 211 KKILETTKKVSVCPHCGEINGVVKKC-GLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVK 269
           K++ E  K+V  C HCG  NGVV+   G LK+ H+KY    K+     E+  AE++EAV 
Sbjct: 121 KRVAEKCKRVRQCTHCGSTNGVVRHVPGGLKLFHDKYARNIKEH----EEYAAEFDEAVL 176

Query: 270 FNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
            N +++ H    +   LNP+ VL LF AI  E   LL +     +P  LI+T L VPP C
Sbjct: 177 HNEQMK-HCLHKVGDDLNPIRVLALFSAITDEACELLDLAG---RPEHLIMTHLPVPPVC 232

Query: 330 IRPSVISD 337
           IRPSV  D
Sbjct: 233 IRPSVEMD 240



 Score =  169 bits (427), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 101/239 (42%), Positives = 139/239 (58%), Gaps = 27/239 (11%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPD- 822
            GVPRIKEIINAS+NISTP++   L+       AR+VK RLERT LG+V + I  V  P  
Sbjct: 1032 GVPRIKEIINASKNISTPVMNVTLEVANSEAAARMVKARLERTALGQVAKRIRAVLKPSL 1091

Query: 823  ----DSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSK 878
                 +F+ I+LD   I+ L L+++  ++R  I     ++  L V G  F          
Sbjct: 1092 THQVGAFVEIRLDKVVIQALQLDINAHTVRDAI-----VASKLKV-GMGF---------- 1135

Query: 879  SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 938
                 ++ +   LP V++ G+  + RAV+  +  E   KY L VEG +L  VM T GV G
Sbjct: 1136 ----ALHNLMTALPHVIVAGIASVERAVVTFD--EKTCKYSLGVEGMDLTAVMGTLGVDG 1189

Query: 939  VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             + ++N+  E  + LGIEAAR+ IMTEI+  M +HGM+ID RH ML+AD MT KGEVLG
Sbjct: 1190 CRTATNHVMETERVLGIEAARTKIMTEIQTTMSSHGMTIDARHTMLLADCMTYKGEVLG 1248



 Score =  108 bits (271), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 61/124 (49%), Positives = 76/124 (61%), Gaps = 7/124 (5%)

Query: 606 GDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           GD TP G+GFV  SF+SGL+PTEFFFHTM GREGLVDTAVKTAETGYM RRL+KSLEDL 
Sbjct: 772 GDRTPEGKGFVAASFYSGLSPTEFFFHTMAGREGLVDTAVKTAETGYMSRRLMKSLEDLY 831

Query: 665 VQYDMSFDAAFYG------QTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTL 718
             YD +   +  G        D +  V+     G P+++   L  +    PR   +P   
Sbjct: 832 THYDSTVRNSAGGIVQLTYGDDGLDPVAMEAQEGKPVDLTRSLSVVHATTPRRPQLPENA 891

Query: 719 LFDN 722
           + D+
Sbjct: 892 MEDD 895



 Score = 57.4 bits (137), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 25/47 (53%), Positives = 35/47 (74%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIA 68
           LM    NL TP++GE+LIAATQDF+T  +LLT K+ F++R Q  ++A
Sbjct: 473 LMGVMRNLCTPKSGEILIAATQDFLTSAFLLTSKDRFYSRTQVAQLA 519



 Score = 55.1 bits (131), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 26/39 (66%), Positives = 30/39 (76%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  FDAA +G+TD I+GVSE IIMG+PM  GTGL KL Q
Sbjct: 1272 DHLFDAALHGRTDDITGVSESIIMGIPMPTGTGLFKLHQ 1310


>gi|449683564|ref|XP_002165029.2| PREDICTED: DNA-directed RNA polymerase III subunit RPC1-like,
           partial [Hydra magnipapillata]
          Length = 537

 Score =  257 bits (657), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 130/264 (49%), Positives = 175/264 (66%), Gaps = 5/264 (1%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G I   +   D++QQ S +Q V+K LY QD  RTP+P+G+LD+++G + K+  C TCG+ 
Sbjct: 19  GSISFGLFSADQIQQLSTVQCVTKTLYSQDAARTPVPYGVLDKKLGISGKDKVCDTCGKT 78

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
           L DCVGH+GYIDL LPVFHIGYFR  I ILQ ICKN  C+R+LL +E    +   LR P 
Sbjct: 79  LVDCVGHYGYIDLELPVFHIGYFRSTIVILQQICKN--CSRILLNDEDRTTYIKALRRPG 136

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDL 260
           L+ L RK+L KKI+   KKV+ C +C + NG VKK G++KI HEKYK   K  D I+ D 
Sbjct: 137 LTSLQRKTLHKKIIMKCKKVTTCFYCNDRNGNVKKLGMMKILHEKYKTTRKVDDGIITDF 196

Query: 261 LAEYNEAVKFNPEIEA-HKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLI 319
              +NEA+ +N E++    K  L+  LNPL+V  +F+ I  ED  LL M     +P DLI
Sbjct: 197 KNSFNEAIVYNKELDGITSKMNLV--LNPLKVFHIFQNITDEDCYLLGMVPASGRPEDLI 254

Query: 320 LTRLLVPPNCIRPSVISDLKSDND 343
           +TR+ VPP CIRPSVIS+L++ ++
Sbjct: 255 ITRVPVPPACIRPSVISELQAGSN 278



 Score =  146 bits (368), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 69/93 (74%), Positives = 73/93 (78%), Gaps = 14/93 (15%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DNDVVLFNRQPSLH+LSIMAH A V PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 459 DNDVVLFNRQPSLHRLSIMAHYATVRPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 518

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRN 433
           +AEAL               LM  KSNL+TPRN
Sbjct: 519 KAEAL--------------TLMGTKSNLITPRN 537


>gi|397622848|gb|EJK66806.1| hypothetical protein THAOC_12234 [Thalassiosira oceanica]
          Length = 1020

 Score =  257 bits (656), Expect = 4e-65,   Method: Compositional matrix adjust.
 Identities = 134/294 (45%), Positives = 179/294 (60%), Gaps = 30/294 (10%)

Query: 322 RLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPY 381
           R L   N     ++     D D+VLFNRQPSLHKLSIM+H+ KVL  RTFRFN CVC PY
Sbjct: 62  RELAAANLRVGDIVERHMEDGDIVLFNRQPSLHKLSIMSHQVKVLQWRTFRFNICVCAPY 121

Query: 382 NADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAAT 441
           NADFDGDEMN+HLPQTEEAR E              A +LM    NL TPRNGE L+A +
Sbjct: 122 NADFDGDEMNMHLPQTEEARGE--------------ASMLMGVHHNLATPRNGEPLVACS 167

Query: 442 QDFITGGYLLTQKNAFFNRAQTMRIASTL-IADTSDICGIIKRFSWRSWNPVVFVRTAVI 500
           QDF++  YL+TQ++ FF++     + +   +AD      I          P + ++   +
Sbjct: 168 QDFLSAAYLITQRDQFFDKGMFCTLCAYFGLADEQIDVPI----------PAI-IKPVAL 216

Query: 501 WTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEE---FCHRDSYVILRNSELLAGSMDK 557
           WTGKQ+F+ I++PNR C    N + K R Y ++++   FC  D +V  RNSEL++G++ K
Sbjct: 217 WTGKQVFTAIVRPNRQCDQFVNFEMKERNYNSSKKMKHFCPNDGWVAFRNSELVSGNIAK 276

Query: 558 STLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYL-MNRGFSIGIGDVTP 610
            T+G G K  + Y+LLRD G + A   M R S++ S Y  M+RGFSIGI DV+P
Sbjct: 277 KTIGDGSKTGLLYVLLRDCGPEEAARFMDRFSKLCSRYFGMHRGFSIGISDVSP 330



 Score =  251 bits (641), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 177/482 (36%), Positives = 251/482 (52%), Gaps = 85/482 (17%)

Query: 998  NGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEF--LQDTSENFVRDIKK 1055
            N  PV+  RL   I   N    + +L   E+       L+   F  L    ++F+ +I  
Sbjct: 537  NDRPVQFDRLHLHITQTNPCPDESNLLEDELTDKVKRCLEEDRFQKLLPNGKSFLAEITS 596

Query: 1056 FLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACRE---KYVR 1112
            F ++ +KK++ T      +  + ++I +          S  F      E  R+   KY +
Sbjct: 597  FFDDIAKKQTETIGTCDDAVHIEQRIWN----------SCRFTETQVNEFLRQSLTKYTK 646

Query: 1113 AQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYIEEVFVP- 1157
            A +EP  AVGA  AQSI EPGTQMTLKTFHFAG              E+    + +  P 
Sbjct: 647  ALVEPGEAVGATGAQSISEPGTQMTLKTFHFAGVSSMNVTLGVPRLKEIINGSKNISTPI 706

Query: 1158 -------DDSFI---LIKLDMDRIRL---------------LHLEVDID----------- 1181
                   D++ +   ++K  +++  L                +L + +D           
Sbjct: 707  ITAKLVQDNNKVGARIVKAGIEKTTLGEISICIKEVYSSSDCYLSIQLDMKAIEQLRLNI 766

Query: 1182 ---SIRYCIER-TRG----------ISGHLTV---SGHSFLILKPKDSSKSFNS-KMYQM 1223
               S+R CI + TRG          +  H+ V   S     +  P D S S     M  +
Sbjct: 767  DAVSVRRCILKGTRGQTRPAVLRGLLEKHVLVKKGSKSKLRVYVPTDKSDSPTYFTMQAL 826

Query: 1224 KQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTY 1283
            K  LP V+++G+  +NRAVI+EE   G   Y LLVEG  L +VM + GV G   ++N+  
Sbjct: 827  KVALPGVIVQGISSVNRAVINEESKGGKPSYHLLVEGCGLAEVMGSPGVDGKFTTTNHIM 886

Query: 1284 EVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMK 1343
            EV +TLG+EAAR++I +EI  +M  +G+ ID RH ML++D+MT KGEVLGITR G+AKM+
Sbjct: 887  EVEQTLGVEAARTSISSEISYIMTAYGIGIDSRHLMLLSDVMTFKGEVLGITRFGVAKMR 946

Query: 1344 ESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPR-SEP 1402
            ESVL LASFE T+DHLFDAA +G+ D I+GVSECIIMG+P+ +GTGL KLL+   R SEP
Sbjct: 947  ESVLMLASFEKTTDHLFDAAVHGRADAINGVSECIIMGIPVPIGTGLFKLLKRATRPSEP 1006

Query: 1403 VP 1404
             P
Sbjct: 1007 DP 1008



 Score =  193 bits (491), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 114/249 (45%), Positives = 155/249 (62%), Gaps = 15/249 (6%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
           GVPR+KEIIN S+NISTPIITA L +D +   ARIVK  +E+TTLGE+   I+EV+   D
Sbjct: 688 GVPRLKEIINGSKNISTPIITAKLVQDNNKVGARIVKAGIEKTTLGEISICIKEVYSSSD 747

Query: 824 SFILIKLDMDRIRLLHLEVDIDSIRYCIER-TRG----------ISGHLTV---SGHSFL 869
            ++ I+LDM  I  L L +D  S+R CI + TRG          +  H+ V   S     
Sbjct: 748 CYLSIQLDMKAIEQLRLNIDAVSVRRCILKGTRGQTRPAVLRGLLEKHVLVKKGSKSKLR 807

Query: 870 ILKPKDSSKSFNS-KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLR 928
           +  P D S S     M  +K  LP V+++G+  +NRAVI+EE   G   Y LLVEG  L 
Sbjct: 808 VYVPTDKSDSPTYFTMQALKVALPGVIVQGISSVNRAVINEESKGGKPSYHLLVEGCGLA 867

Query: 929 DVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADL 988
           +VM + GV G   ++N+  EV +TLG+EAAR++I +EI  +M  +G+ ID RH ML++D+
Sbjct: 868 EVMGSPGVDGKFTTTNHIMEVEQTLGVEAARTSISSEISYIMTAYGIGIDSRHLMLLSDV 927

Query: 989 MTSKGEVLG 997
           MT KGEVLG
Sbjct: 928 MTFKGEVLG 936



 Score = 62.8 bits (151), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 30/49 (61%), Positives = 37/49 (75%), Gaps = 1/49 (2%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPR-SEPVP 715
            D  FDAA +G+ D I+GVSECIIMG+P+ +GTGL KLL+   R SEP P
Sbjct: 960  DHLFDAAVHGRADAINGVSECIIMGIPVPIGTGLFKLLKRATRPSEPDP 1008



 Score = 53.5 bits (127), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 21/42 (50%), Positives = 31/42 (73%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRA 62
           +LM    NL TPRNGE L+A +QDF++  YL+TQ++ FF++ 
Sbjct: 146 MLMGVHHNLATPRNGEPLVACSQDFLSAAYLITQRDQFFDKG 187


>gi|297746170|emb|CBI16226.3| unnamed protein product [Vitis vinifera]
          Length = 1819

 Score =  257 bits (656), Expect = 4e-65,   Method: Compositional matrix adjust.
 Identities = 124/274 (45%), Positives = 178/274 (64%), Gaps = 27/274 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH++SIM HRA+++P RT RFNE VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 454 DGDVVLFNRQPSLHRMSIMCHRARIMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEA 513

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL              +LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+K+ F++R
Sbjct: 514 RTEAL--------------MLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDR 559

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A    +  + + D  D+  +          P + ++   +WTGKQ+F+++L+P+ +  V 
Sbjct: 560 A-AFSLMCSYMGDGMDLVDLP--------TPAI-IKAMELWTGKQLFNVLLRPHANVRVY 609

Query: 521 ANLKTKGRAYT---ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFG 577
            NL    + Y      E  C  D +V  RNSEL++G + K+TLG+G K  +F +LLRD+ 
Sbjct: 610 LNLTVMEKTYNKRRGKETMCPSDGFVYFRNSELISGQLGKATLGNGNKDGLFSVLLRDYN 669

Query: 578 EDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
              A   M RL+++++ ++ N GFSIGI DV PG
Sbjct: 670 AHAAAACMNRLAKLSARWIGNHGFSIGIDDVQPG 703



 Score =  243 bits (621), Expect = 5e-61,   Method: Compositional matrix adjust.
 Identities = 149/355 (41%), Positives = 205/355 (57%), Gaps = 63/355 (17%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCE 1149
            + C  +Y   +IE  TA+GA+ A SIGEPGTQMTLKTFHFAG              E+  
Sbjct: 1457 DTCISRYQLKRIEAGTAIGAIGAHSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIIN 1516

Query: 1150 YIEEVFVPDDSFIL---------------------------IKLDM-DRIRLLHLEVDID 1181
              + +  P  +  L                           IK+ +  R+ L+ + +D++
Sbjct: 1517 GAKRISTPIITAALECNNNVKTARMVKGRIERTTLGQVAKSIKIVLTSRLALIAVALDME 1576

Query: 1182 SI------------RYCIERTRGI---SGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQL 1226
             I            R  I R R I     H+ V     L + P+    + + +++ +K L
Sbjct: 1577 GIQASQLSIDSNIVRESILRNRRIKLKQQHIKVLDAGKLEVHPQGDRSTIHFELHALKNL 1636

Query: 1227 LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVY 1286
            LP+VV+KG++ + RAVI++++     KY LLVEG  L+ VM T GV G + +SN+  EV 
Sbjct: 1637 LPTVVVKGIETVERAVINKDN---KVKYNLLVEGTGLQTVMGTEGVIGRETTSNHIIEVQ 1693

Query: 1287 KTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESV 1346
            +TLGIEAAR  I+ EI+  M +HGMSID RH ML+ADLMT +GEVLGITR G+ KM +SV
Sbjct: 1694 QTLGIEAARKCIINEIQYTMASHGMSIDIRHMMLLADLMTFRGEVLGITRFGIQKMDKSV 1753

Query: 1347 LNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL---LQAVP 1398
            L LASFE T+DHLF+A+  G+ D I GVSECIIMG+PM +GTG++K+   LQ VP
Sbjct: 1754 LMLASFEKTADHLFNASVSGRDDKIEGVSECIIMGIPMQLGTGILKVRQRLQQVP 1808



 Score =  204 bits (519), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 112/237 (47%), Positives = 158/237 (66%), Gaps = 6/237 (2%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIIN ++ ISTPIITA L+ + ++  AR+VKGR+ERTTLG+V + I+ V     
Sbjct: 1507 GVPRIKEIINGAKRISTPIITAALECNNNVKTARMVKGRIERTTLGQVAKSIKIVLTSRL 1566

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFLILKPKDSSKSF 880
            + I + LDM+ I+   L +D + +R  I R R I     H+ V     L + P+    + 
Sbjct: 1567 ALIAVALDMEGIQASQLSIDSNIVRESILRNRRIKLKQQHIKVLDAGKLEVHPQGDRSTI 1626

Query: 881  NSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
            + +++ +K LLP+VV+KG++ + RAVI++++     KY LLVEG  L+ VM T GV G +
Sbjct: 1627 HFELHALKNLLPTVVVKGIETVERAVINKDNK---VKYNLLVEGTGLQTVMGTEGVIGRE 1683

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SN+  EV +TLGIEAAR  I+ EI+  M +HGMSID RH ML+ADLMT +GEVLG
Sbjct: 1684 TTSNHIIEVQQTLGIEAARKCIINEIQYTMASHGMSIDIRHMMLLADLMTFRGEVLG 1740



 Score =  160 bits (405), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 102/281 (36%), Positives = 152/281 (54%), Gaps = 32/281 (11%)

Query: 90  EDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFG 149
           E  + + + +Q+     Y  D  R PI +GLLD RMG   K   C TC  N  DC GH G
Sbjct: 31  ESEISKAAEVQVWRGVYY--DANRKPIENGLLDPRMGPANKNGTCATCLGNFRDCPGHCG 88

Query: 150 YIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSL 209
           Y+ L LPV+++GY   +++IL+ ICK  +C+RVLL E+ +  +  K+R+  +  L +  L
Sbjct: 89  YLTLALPVYNVGYLSTIVDILKCICK--SCSRVLLDEKASKDYLKKMRSQKMEALKKAEL 146

Query: 210 KKKILE------TTKKVSVCPHCGEINGVVKKC-GLLKISHEKYKNRTKKKDAIVEDLLA 262
            KKI++      ++KK   C  CG +NG+VKK   +L I H++ K        I +  L 
Sbjct: 147 MKKIVQKCTAMASSKKAVKCSRCGYMNGIVKKAVSVLGIIHDRSK--------IADGSLE 198

Query: 263 EYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTR 322
           E + A+    E +A   F ++  LNP++VL LF+ +  ED  LL + AE  +P  L+LT 
Sbjct: 199 ECSSAISHTKESKA--SFSVVDILNPVKVLSLFKRMMDEDCDLLNL-AE--RPEKLVLTN 253

Query: 323 LLVPPNCIRPSVISD---LKSDNDVV-----LFNRQPSLHK 355
           + VPP  IRPSV  D     ++NDV      +     SLH+
Sbjct: 254 IGVPPIAIRPSVFMDGGTQSNENDVTERLKRIIQANASLHQ 294



 Score =  103 bits (256), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 47/61 (77%), Positives = 55/61 (90%), Gaps = 1/61 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV +SF++GLT TEFFFHTMGGREGLVDTAVKTA+TGYM RRL+K+LEDL +QY
Sbjct: 824 TPDAKGFVASSFYTGLTATEFFFHTMGGREGLVDTAVKTADTGYMSRRLMKALEDLSIQY 883

Query: 668 D 668
           D
Sbjct: 884 D 884



 Score = 57.0 bits (136), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 22/42 (52%), Positives = 36/42 (85%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRA 62
           +LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+K+ F++RA
Sbjct: 519 MLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDRA 560



 Score = 52.8 bits (125), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 25/45 (55%), Positives = 33/45 (73%), Gaps = 3/45 (6%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL---LQAVP 709
            D  F+A+  G+ D I GVSECIIMG+PM +GTG++K+   LQ VP
Sbjct: 1764 DHLFNASVSGRDDKIEGVSECIIMGIPMQLGTGILKVRQRLQQVP 1808


>gi|225435153|ref|XP_002284657.1| PREDICTED: DNA-directed RNA polymerase III subunit rpc1-like [Vitis
           vinifera]
          Length = 1383

 Score =  256 bits (655), Expect = 5e-65,   Method: Compositional matrix adjust.
 Identities = 124/274 (45%), Positives = 178/274 (64%), Gaps = 27/274 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH++SIM HRA+++P RT RFNE VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 454 DGDVVLFNRQPSLHRMSIMCHRARIMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEA 513

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL              +LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+K+ F++R
Sbjct: 514 RTEAL--------------MLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDR 559

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A    +  + + D  D+  +          P + ++   +WTGKQ+F+++L+P+ +  V 
Sbjct: 560 A-AFSLMCSYMGDGMDLVDL--------PTPAI-IKPVELWTGKQLFNVLLRPHANVRVY 609

Query: 521 ANLKTKGRAYT---ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFG 577
            NL    + Y      E  C  D +V  RNSEL++G + K+TLG+G K  +F +LLRD+ 
Sbjct: 610 LNLTVMEKTYNKRRGKETMCPSDGFVYFRNSELISGQLGKATLGNGNKDGLFSVLLRDYN 669

Query: 578 EDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
              A   M RL+++++ ++ N GFSIGI DV PG
Sbjct: 670 AHAAAACMNRLAKLSARWIGNHGFSIGIDDVQPG 703



 Score =  253 bits (645), Expect = 8e-64,   Method: Compositional matrix adjust.
 Identities = 175/469 (37%), Positives = 248/469 (52%), Gaps = 77/469 (16%)

Query: 998  NGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFL 1057
            +G P+   RL   + A   +  + SLSA +I        +     +  S+ F  ++  FL
Sbjct: 913  DGFPLNFNRLFLKVKATCPAGENASLSALQIEETVKRLKEHNTSAEGCSDAFKTNLSGFL 972

Query: 1058 EEFSKK-----ESVTSHQDKVSQPLREQILSHQDKIGH---GRESNPFPSACKAEACREK 1109
            EE  +K     E++  H + V     E+ L  Q+K      G  S         + C  +
Sbjct: 973  EECKEKFKNTREALGLHGEHVG----EENLDIQEKFAKNISGITSKQL--QVFLDTCISR 1026

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYIEEVF 1155
            Y   +IE  TA+GA+ A SIGEPGTQMTLKTFHFAG              E+    + + 
Sbjct: 1027 YQLKRIEAGTAIGAIGAHSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIINGAKRIS 1086

Query: 1156 VPDDSFIL---------------------------IKLDM-DRIRLLHLEVDIDSI---- 1183
             P  +  L                           IK+ +  R+ L+ + +D++ I    
Sbjct: 1087 TPIITAALECNNNVKTARMVKGRIERTTLGQVAKSIKIVLTSRLALIAVALDMEGIQASQ 1146

Query: 1184 --------RYCIERTRGI---SGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVI 1232
                    R  I R R I     H+ V     L + P+    + + +++ +K LLP+VV+
Sbjct: 1147 LSIDSNIVRESILRNRRIKLKQQHIKVLDAGKLEVHPQGDRSTIHFELHALKNLLPTVVV 1206

Query: 1233 KGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIE 1292
            KG++ + RAVI++++     KY LLVEG  L+ VM T GV G + +SN+  EV +TLGIE
Sbjct: 1207 KGIETVERAVINKDN---KVKYNLLVEGTGLQTVMGTEGVIGRETTSNHIIEVQQTLGIE 1263

Query: 1293 AARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASF 1352
            AAR  I+ EI+  M +HGMSID RH ML+ADLMT +GEVLGITR G+ KM +SVL LASF
Sbjct: 1264 AARKCIINEIQYTMASHGMSIDIRHMMLLADLMTFRGEVLGITRFGIQKMDKSVLMLASF 1323

Query: 1353 ENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL---LQAVP 1398
            E T+DHLF+A+  G+ D I GVSECIIMG+PM +GTG++K+   LQ VP
Sbjct: 1324 EKTADHLFNASVSGRDDKIEGVSECIIMGIPMQLGTGILKVRQRLQQVP 1372



 Score =  204 bits (519), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 112/237 (47%), Positives = 158/237 (66%), Gaps = 6/237 (2%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIIN ++ ISTPIITA L+ + ++  AR+VKGR+ERTTLG+V + I+ V     
Sbjct: 1071 GVPRIKEIINGAKRISTPIITAALECNNNVKTARMVKGRIERTTLGQVAKSIKIVLTSRL 1130

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFLILKPKDSSKSF 880
            + I + LDM+ I+   L +D + +R  I R R I     H+ V     L + P+    + 
Sbjct: 1131 ALIAVALDMEGIQASQLSIDSNIVRESILRNRRIKLKQQHIKVLDAGKLEVHPQGDRSTI 1190

Query: 881  NSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
            + +++ +K LLP+VV+KG++ + RAVI++++     KY LLVEG  L+ VM T GV G +
Sbjct: 1191 HFELHALKNLLPTVVVKGIETVERAVINKDNK---VKYNLLVEGTGLQTVMGTEGVIGRE 1247

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SN+  EV +TLGIEAAR  I+ EI+  M +HGMSID RH ML+ADLMT +GEVLG
Sbjct: 1248 TTSNHIIEVQQTLGIEAARKCIINEIQYTMASHGMSIDIRHMMLLADLMTFRGEVLG 1304



 Score =  160 bits (404), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 102/281 (36%), Positives = 152/281 (54%), Gaps = 32/281 (11%)

Query: 90  EDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFG 149
           E  + + + +Q+     Y  D  R PI +GLLD RMG   K   C TC  N  DC GH G
Sbjct: 31  ESEISKAAEVQVWRGVYY--DANRKPIENGLLDPRMGPANKNGTCATCLGNFRDCPGHCG 88

Query: 150 YIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSL 209
           Y+ L LPV+++GY   +++IL+ ICK  +C+RVLL E+ +  +  K+R+  +  L +  L
Sbjct: 89  YLTLALPVYNVGYLSTIVDILKCICK--SCSRVLLDEKASKDYLKKMRSQKMEALKKAEL 146

Query: 210 KKKILE------TTKKVSVCPHCGEINGVVKKC-GLLKISHEKYKNRTKKKDAIVEDLLA 262
            KKI++      ++KK   C  CG +NG+VKK   +L I H++ K        I +  L 
Sbjct: 147 MKKIVQKCTAMASSKKAVKCSRCGYMNGIVKKAVSVLGIIHDRSK--------IADGSLE 198

Query: 263 EYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTR 322
           E + A+    E +A   F ++  LNP++VL LF+ +  ED  LL + AE  +P  L+LT 
Sbjct: 199 ECSSAISHTKESKA--SFSVVDILNPVKVLSLFKRMMDEDCDLLNL-AE--RPEKLVLTN 253

Query: 323 LLVPPNCIRPSVISD---LKSDNDVV-----LFNRQPSLHK 355
           + VPP  IRPSV  D     ++NDV      +     SLH+
Sbjct: 254 IGVPPIAIRPSVFMDGGTQSNENDVTERLKRIIQANASLHQ 294



 Score =  103 bits (257), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 47/61 (77%), Positives = 55/61 (90%), Gaps = 1/61 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV +SF++GLT TEFFFHTMGGREGLVDTAVKTA+TGYM RRL+K+LEDL +QY
Sbjct: 824 TPDAKGFVASSFYTGLTATEFFFHTMGGREGLVDTAVKTADTGYMSRRLMKALEDLSIQY 883

Query: 668 D 668
           D
Sbjct: 884 D 884



 Score = 57.0 bits (136), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 22/42 (52%), Positives = 36/42 (85%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRA 62
           +LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+K+ F++RA
Sbjct: 519 MLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDRA 560



 Score = 52.8 bits (125), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 25/45 (55%), Positives = 33/45 (73%), Gaps = 3/45 (6%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL---LQAVP 709
            D  F+A+  G+ D I GVSECIIMG+PM +GTG++K+   LQ VP
Sbjct: 1328 DHLFNASVSGRDDKIEGVSECIIMGIPMQLGTGILKVRQRLQQVP 1372


>gi|392569146|gb|EIW62320.1| beta and beta-prime subunits of DNA dependent RNA-polymerase
           [Trametes versicolor FP-101664 SS1]
          Length = 1403

 Score =  256 bits (655), Expect = 5e-65,   Method: Compositional matrix adjust.
 Identities = 133/282 (47%), Positives = 178/282 (63%), Gaps = 35/282 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+ LFNRQPSLHKLSIM HR KV P R+FR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 449 DGDIALFNRQPSLHKLSIMCHRIKVRPWRSFRLNECVCGPYNADFDGDEMNLHVPQTEEA 508

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL               LM+ K NLVTPRNGE +IAA QDFIT  +LL++++ FF+R
Sbjct: 509 RTEALE--------------LMSVKHNLVTPRNGEPVIAAIQDFITASFLLSRRDTFFDR 554

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q  +I S   AD      I     W+   PV       +WTGKQ+F+++++PNR   V 
Sbjct: 555 RQFTQICS-YFADADLQIDIPPPAIWK---PV------RLWTGKQVFNVLMRPNRQSKVF 604

Query: 521 ANLKTKGRAYTANEEFCH-----------RDSYVILRNSELLAGSMDKSTLGSGGKANVF 569
            N+++K       +  C+            D ++++ NSE++ G MDK+T+GSG K +VF
Sbjct: 605 VNVESKCNKEDKPQAACYPRMRPAPDLSPNDGWLVIVNSEIMCGVMDKATVGSGKKKSVF 664

Query: 570 YILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
            +++RD+G   A  AM R++++ + YL N GFS+GI DV PG
Sbjct: 665 GVIMRDYGPHEAAAAMNRVAKLCARYLANIGFSLGINDVIPG 706



 Score =  215 bits (548), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 142/372 (38%), Positives = 201/372 (54%), Gaps = 70/372 (18%)

Query: 1104 EACREKYVRAQIEPATAVGAL--------------------------------------- 1124
            + C  KYV+A+IEP + VGA+                                       
Sbjct: 1034 DVCWTKYVKAKIEPGSTVGAVGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIIN 1093

Query: 1125 AAQSIGEPGTQMTLKTFH---------------FAGEVCEYIEEVFVPDDSFILIKLDMD 1169
            AA++I  P     L  +                  G++   +EE + P+ ++I + +DM 
Sbjct: 1094 AAKAISTPIISCKLVAYDSEASARIVKGRLERTHVGDIASVLEEAWAPEYTYIGVIVDMK 1153

Query: 1170 RIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF---NSKMYQMKQL 1226
             I+ L LE+ +D I++ I   R     L +   S  ++  K+  + +     K Y++++L
Sbjct: 1154 TIQDLQLELTLDDIKWAIVGAR----KLKIKQESITVIPRKNRLRIYVDGADKYYRLREL 1209

Query: 1227 ---LPSVVIKGVQGINRAVIH---EEDVEGVTKYK-LLVEGDNLRDVMATYGVKGVKCSS 1279
               LP VV+KGV  I RA+I+     D  G    K LLVEG  L+ VM T G+ G + +S
Sbjct: 1210 KRALPDVVVKGVPTIRRAIINIKENNDHRGKKGDKELLVEGYGLQKVMTTQGIVGEQTTS 1269

Query: 1280 NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGL 1339
            N+  E+ + LGIEAAR TI+ EI+  M++HGMSID RH ML+ D+M+ KGEVLGITR G+
Sbjct: 1270 NHVIEIAQVLGIEAARRTIINEIQYTMQSHGMSIDPRHVMLLGDVMSYKGEVLGITRFGV 1329

Query: 1340 AKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNV-GTGLIKLLQAVP 1398
            AKMK+SVL LASFE T+DHLFDA+ YG+TD I+GVSE IIMG P  + GT +  L+   P
Sbjct: 1330 AKMKDSVLMLASFEKTTDHLFDASAYGKTDSIAGVSESIIMGNPAAMTGTSMPALITPAP 1389

Query: 1399 RSEPVPRTLLFD 1410
             S   PR LLF+
Sbjct: 1390 -SISKPRKLLFE 1400



 Score =  194 bits (492), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 112/255 (43%), Positives = 142/255 (55%), Gaps = 21/255 (8%)

Query: 97  SHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP 156
           +  ++  ++LY     R P+ +G+LDRR+GT +K A C TCG N  DCVGH+ YI L +P
Sbjct: 30  AEFEVTHRDLYTP-IDRLPVKNGVLDRRLGTTEKSAFCETCGLNSVDCVGHYAYIKLVVP 88

Query: 157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILET 216
           VFHIGYF+  I ILQ ICK  TCARVLL E     +  + R P L  L R +L K +   
Sbjct: 89  VFHIGYFKHTIGILQCICK--TCARVLLEEPDRRSYLKRFRRPNLENLQRMTLVKSVNAL 146

Query: 217 TKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVK--FNPEI 274
            +K   CP+C   NG VKK G LKI H+K+  R KK         AE  E  K  F P I
Sbjct: 147 ARKTVYCPYCAATNGTVKKAGALKIIHDKF--RAKKT--------AEEMEKWKRTFAPAI 196

Query: 275 EAHKKFGLI------QTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPN 328
           EA K+ G+       + LNPL+VL LF+ I  ED  LL +  E  +P   I   + VPP 
Sbjct: 197 EAQKELGMYVNKAIHEDLNPLKVLDLFKRISDEDCELLGLRPEYGRPEQYIWQYISVPPV 256

Query: 329 CIRPSVISDLKSDND 343
            IRPSV  D  S+ D
Sbjct: 257 AIRPSVAQDGASNED 271



 Score =  181 bits (459), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 108/244 (44%), Positives = 153/244 (62%), Gaps = 14/244 (5%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ ISTPII+  L        ARIVKGRLERT +G++   +EE + P+ 
Sbjct: 1084 GVPRIKEIINAAKAISTPIISCKLVAYDSEASARIVKGRLERTHVGDIASVLEEAWAPEY 1143

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF--- 880
            ++I + +DM  I+ L LE+ +D I++ I   R     L +   S  ++  K+  + +   
Sbjct: 1144 TYIGVIVDMKTIQDLQLELTLDDIKWAIVGAR----KLKIKQESITVIPRKNRLRIYVDG 1199

Query: 881  NSKMYQMKQL---LPSVVIKGVQGINRAVIH---EEDVEGVTKYK-LLVEGDNLRDVMAT 933
              K Y++++L   LP VV+KGV  I RA+I+     D  G    K LLVEG  L+ VM T
Sbjct: 1200 ADKYYRLRELKRALPDVVVKGVPTIRRAIINIKENNDHRGKKGDKELLVEGYGLQKVMTT 1259

Query: 934  YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
             G+ G + +SN+  E+ + LGIEAAR TI+ EI+  M++HGMSID RH ML+ D+M+ KG
Sbjct: 1260 QGIVGEQTTSNHVIEIAQVLGIEAARRTIINEIQYTMQSHGMSIDPRHVMLLGDVMSYKG 1319

Query: 994  EVLG 997
            EVLG
Sbjct: 1320 EVLG 1323



 Score =  106 bits (264), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 48/68 (70%), Positives = 55/68 (80%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV+NSF++GLTPTEF FH + GREGLVDTAVKTAETGYMQRRL+K+LEDL   YD 
Sbjct: 829 PSKGFVRNSFYTGLTPTEFLFHAISGREGLVDTAVKTAETGYMQRRLMKALEDLVTHYDS 888

Query: 670 SFDAAFYG 677
           S   A  G
Sbjct: 889 SVRNAVGG 896



 Score = 61.2 bits (147), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 28/48 (58%), Positives = 37/48 (77%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIAS 69
           LM+ K NLVTPRNGE +IAA QDFIT  +LL++++ FF+R Q  +I S
Sbjct: 515 LMSVKHNLVTPRNGEPVIAAIQDFITASFLLSRRDTFFDRRQFTQICS 562



 Score = 48.5 bits (114), Expect = 0.029,   Method: Compositional matrix adjust.
 Identities = 28/55 (50%), Positives = 35/55 (63%), Gaps = 2/55 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNV-GTGLIKLLQAVPRSEPVPRTLLFD 721
            D  FDA+ YG+TD I+GVSE IIMG P  + GT +  L+   P S   PR LLF+
Sbjct: 1347 DHLFDASAYGKTDSIAGVSESIIMGNPAAMTGTSMPALITPAP-SISKPRKLLFE 1400


>gi|336373147|gb|EGO01485.1| hypothetical protein SERLA73DRAFT_103293 [Serpula lacrymans var.
           lacrymans S7.3]
          Length = 1400

 Score =  256 bits (653), Expect = 8e-65,   Method: Compositional matrix adjust.
 Identities = 133/282 (47%), Positives = 180/282 (63%), Gaps = 35/282 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + D+VLFNRQPSLHKLSIM HRA++ P R+FR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 446 NGDIVLFNRQPSLHKLSIMCHRARIRPWRSFRLNECVCGPYNADFDGDEMNLHVPQTEEA 505

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL               LM+ K NLVTPRNGE +IAA QDFIT  YL+++K+ FF+R
Sbjct: 506 RTEALE--------------LMSVKHNLVTPRNGEPVIAAIQDFITASYLISRKDTFFDR 551

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
               +I     AD      I     W+   PV       +WTGKQIF+++++PN+D  V 
Sbjct: 552 RSFTQIC-CYFADADMQIDIPPPAIWK---PV------RLWTGKQIFNVLMRPNKDSKVF 601

Query: 521 ANLKTK-GRAYTANEEFCHR----------DSYVILRNSELLAGSMDKSTLGSGGKANVF 569
            N+++K  +      EF  R          D ++++ NSE++ G MDK+T+GSG K ++F
Sbjct: 602 VNVESKCNKPQEPKAEFYPRMKPAPDLSPNDGWLVIVNSEIMCGVMDKATVGSGKKKSIF 661

Query: 570 YILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
            +++RD+G   A  AM RL+++ + +L N GFS+GI DV PG
Sbjct: 662 GVIMRDYGPHEAAAAMNRLAKLCARWLANFGFSLGINDVIPG 703



 Score =  224 bits (572), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 167/493 (33%), Positives = 245/493 (49%), Gaps = 85/493 (17%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G+  P+E +R     ++  + R   SL   E+L + ++ L +K F  + +  ++  I+ +
Sbjct: 911  GDAQPIEFERAWSHALSIGNRRGR-SLLPYEVLEIVDQELSTKRFTTECTAAYLATIRGY 969

Query: 1057 LEEFSKKESVTSHQDKVSQPLREQIL------------SHQDK--IGHGRESNPFPSACK 1102
            + +       T  Q +      E+              S  DK  + +  +       C 
Sbjct: 970  ITDNVAHTLATMRQSRGMFDALERAAEWDADTDLSLGASDADKAIVDNKSKVTEDQLRCF 1029

Query: 1103 AEACREKYVRAQIEPATAVGAL-------------------------------------- 1124
             E C  KYV+A+IEP + VGA+                                      
Sbjct: 1030 LELCWVKYVKARIEPGSTVGAVGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEII 1089

Query: 1125 -AAQSIGEPGTQMTLKTFH---------------FAGEVCEYIEEVFVPDDSFILIKLDM 1168
             AA++I  P     L T                   G+V   +EE + P+ ++I + +D+
Sbjct: 1090 NAAKAISTPIISCKLVTSDSEASARIVKGRLEKTHLGDVASVLEEAWAPEYTYIGVIVDV 1149

Query: 1169 DRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF---NSKMY---Q 1222
            D I+ L LE+ +D I++ I   +     L +   S  +L  K+  + +     K Y   +
Sbjct: 1150 DAIQKLQLELTLDDIKWGIVAAK----KLKIKQESITVLPRKNRLRIYIDGQDKYYRLRE 1205

Query: 1223 MKQLLPSVVIKGVQGINRAVIH---EEDVEGVTKYK-LLVEGDNLRDVMATYGVKGVKCS 1278
            +K+LLP VV+KGV  I RA+I+   ++D +G    K LLVEG  L+ VM T G+ G   S
Sbjct: 1206 LKRLLPDVVVKGVPTIQRAIINIKEKDDAKGKKGDKELLVEGYGLQKVMVTEGIVGEHTS 1265

Query: 1279 SNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHG 1338
            SN+  EV + LGIEAAR TI+ EI+  M++HGMSID RH ML+ D+M+ KGEVLGITR G
Sbjct: 1266 SNHVIEVAQVLGIEAARRTIINEIQYTMQSHGMSIDPRHVMLLGDVMSYKGEVLGITRFG 1325

Query: 1339 LAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLP-MNVGTGLIKLLQAV 1397
            +AKMK+SVL LASFE T+DHLFDAA +G+ D I+GVSE IIMG P  N GT +  L    
Sbjct: 1326 VAKMKDSVLMLASFEKTTDHLFDAAAFGKNDSIAGVSESIIMGNPAANCGTSMPALFSPA 1385

Query: 1398 PRSEPVPRTLLFD 1410
            P     PR LLF+
Sbjct: 1386 PIITK-PRKLLFE 1397



 Score =  188 bits (478), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 112/244 (45%), Positives = 156/244 (63%), Gaps = 14/244 (5%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ ISTPII+  L        ARIVKGRLE+T LG+V   +EE + P+ 
Sbjct: 1081 GVPRIKEIINAAKAISTPIISCKLVTSDSEASARIVKGRLEKTHLGDVASVLEEAWAPEY 1140

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF--- 880
            ++I + +D+D I+ L LE+ +D I++ I   +     L +   S  +L  K+  + +   
Sbjct: 1141 TYIGVIVDVDAIQKLQLELTLDDIKWGIVAAK----KLKIKQESITVLPRKNRLRIYIDG 1196

Query: 881  NSKMY---QMKQLLPSVVIKGVQGINRAVIH---EEDVEGVTKYK-LLVEGDNLRDVMAT 933
              K Y   ++K+LLP VV+KGV  I RA+I+   ++D +G    K LLVEG  L+ VM T
Sbjct: 1197 QDKYYRLRELKRLLPDVVVKGVPTIQRAIINIKEKDDAKGKKGDKELLVEGYGLQKVMVT 1256

Query: 934  YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
             G+ G   SSN+  EV + LGIEAAR TI+ EI+  M++HGMSID RH ML+ D+M+ KG
Sbjct: 1257 EGIVGEHTSSNHVIEVAQVLGIEAARRTIINEIQYTMQSHGMSIDPRHVMLLGDVMSYKG 1316

Query: 994  EVLG 997
            EVLG
Sbjct: 1317 EVLG 1320



 Score =  186 bits (472), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 108/255 (42%), Positives = 140/255 (54%), Gaps = 24/255 (9%)

Query: 97  SHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP 156
           S  Q+  ++LY     R P+  G+LDRR+GT +K   C TCG +  DCVGH+ YI L +P
Sbjct: 30  SEFQVTHRDLYTPT-DRLPVKDGVLDRRLGTTEKNTFCETCGLSSVDCVGHYAYIKLVVP 88

Query: 157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILET 216
           VFHIGYF+  I ILQ      TCARVLL E     +  + R P L  + R+SL K +   
Sbjct: 89  VFHIGYFKHTIGILQC-----TCARVLLEEPDRRVYLKRFRRPNLENIQRQSLSKAVNTM 143

Query: 217 TKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVK--FNPEI 274
           ++K   CP+C   NG VKK G LKI H+K+  R KK         AE  E  K  F P +
Sbjct: 144 SRKCVYCPYCSATNGAVKKAGALKIIHDKF--RAKKT--------AEEMEKWKRTFAPAV 193

Query: 275 EAHKKFGLI------QTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPN 328
           EA K+ G+       + LNPL+VL LF+ I  ED  LL +     +P + I   + VPP 
Sbjct: 194 EAQKELGMYLNKAVHEDLNPLKVLDLFKRISDEDCELLGLRPAHGRPEEYIWQYISVPPV 253

Query: 329 CIRPSVISDLKSDND 343
           CIRPSV  D  S+ D
Sbjct: 254 CIRPSVAQDGASNED 268



 Score =  103 bits (258), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 46/61 (75%), Positives = 53/61 (86%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV+NSF+SGL  TEF FH + GREGLVDTAVKTAETGYMQRRL+K+LEDL  QYD+
Sbjct: 826 PSKGFVRNSFYSGLRATEFLFHAISGREGLVDTAVKTAETGYMQRRLMKALEDLTTQYDL 885

Query: 670 S 670
           S
Sbjct: 886 S 886



 Score = 59.3 bits (142), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 27/46 (58%), Positives = 35/46 (76%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRI 67
           LM+ K NLVTPRNGE +IAA QDFIT  YL+++K+ FF+R    +I
Sbjct: 512 LMSVKHNLVTPRNGEPVIAAIQDFITASYLISRKDTFFDRRSFTQI 557



 Score = 46.6 bits (109), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 27/55 (49%), Positives = 32/55 (58%), Gaps = 2/55 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLP-MNVGTGLIKLLQAVPRSEPVPRTLLFD 721
            D  FDAA +G+ D I+GVSE IIMG P  N GT +  L    P     PR LLF+
Sbjct: 1344 DHLFDAAAFGKNDSIAGVSESIIMGNPAANCGTSMPALFSPAPIITK-PRKLLFE 1397


>gi|395330745|gb|EJF63128.1| beta and beta-prime subunits of DNA dependent RNA-polymerase
           [Dichomitus squalens LYAD-421 SS1]
          Length = 1404

 Score =  256 bits (653), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 134/283 (47%), Positives = 177/283 (62%), Gaps = 36/283 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+ LFNRQPSLHKLSIM HR KV P R+FR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 449 DGDIALFNRQPSLHKLSIMCHRIKVRPWRSFRLNECVCGPYNADFDGDEMNLHVPQTEEA 508

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL               LM+ K NLVTPRNGE +IAA QDFIT  +LL++++ FF+R
Sbjct: 509 RTEALE--------------LMSVKHNLVTPRNGEPVIAAIQDFITASFLLSRRDTFFDR 554

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q  +I S    D      I     WR   PV       +WTGKQIF+++++PNR   V 
Sbjct: 555 RQFTQICS-YFGDADLQIDIPPPTIWR---PV------RLWTGKQIFNVLMRPNRKSRVF 604

Query: 521 ANLKTKGRAYTANEEFCH------------RDSYVILRNSELLAGSMDKSTLGSGGKANV 568
            N+++K       +  C+             D ++++ NSE++ G MDK+T+GSG K +V
Sbjct: 605 VNVESKCNKEEKADTKCYPWIGKPAPDLSPNDGWLVIVNSEIMCGVMDKATVGSGKKKSV 664

Query: 569 FYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           F +++RD+G   A  AM R++++ + YL N GFS+GI DV PG
Sbjct: 665 FGVIMRDYGPHEAAAAMNRVAKLCARYLANFGFSLGINDVIPG 707



 Score =  218 bits (555), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 168/493 (34%), Positives = 246/493 (49%), Gaps = 85/493 (17%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G+  PVE +R      +  + RS   L   EI+   +  L ++ F  + +  ++  I+KF
Sbjct: 915  GDAQPVEYERAWIHACSV-APRSTRGLLPFEIMDHVDRALATRRFTSECTAAYIATIRKF 973

Query: 1057 LEE-FSKK-----------ESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKA- 1103
            + E  ++K           E++   ++  +        S+ DKI    +        K  
Sbjct: 974  ISENIAQKLGEVRKAHGMFEALEREEEWDADTDLSMGASYADKIAVDNKVKVTEEQLKLF 1033

Query: 1104 -EACREKYVRAQIEPATAVGAL-------------------------------------- 1124
             + C  KYV+A+IEP + VGA+                                      
Sbjct: 1034 LDICWTKYVKAKIEPGSTVGAVGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEII 1093

Query: 1125 -AAQSIGEPGTQMTLKTFH---------------FAGEVCEYIEEVFVPDDSFILIKLDM 1168
             AA++I  P     L T                   G++   +EE + P+ ++I I +D 
Sbjct: 1094 NAAKAISTPIISCKLVTADSEASARIVKGRLERTHIGDIASILEEAWAPEYTYIGIIVDA 1153

Query: 1169 DRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF---NSKMYQMKQ 1225
              I+ L LE+ +D I++ I   R     L +   S  I+  K+  + +     K Y++++
Sbjct: 1154 KTIQDLQLELTLDDIKWAIVAAR----KLKIKQESITIIPRKNRLRIYIDGPDKYYRLRE 1209

Query: 1226 L---LPSVVIKGVQGINRAVIH---EEDVEGVTKYK-LLVEGDNLRDVMATYGVKGVKCS 1278
            L   LP VV+KGV  I RA+I+    +D  G    K LLVEG  L+ VM T G+ G + +
Sbjct: 1210 LKRALPDVVVKGVPTIRRAIINIKEGDDHRGKKGDKELLVEGYGLQKVMTTQGIVGEQTT 1269

Query: 1279 SNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHG 1338
            SN+  EV + LGIEAAR TI+ EI   M++HGMSID RH ML+ D+M+ KGEVLGITR G
Sbjct: 1270 SNHVIEVAQVLGIEAARKTIINEINYTMKSHGMSIDPRHVMLLGDVMSYKGEVLGITRFG 1329

Query: 1339 LAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNV-GTGLIKLLQAV 1397
            +AKMK+SVL LASFE T+DHLFDA+ YG+TD I+GVSE IIMG P  + GT +  L+   
Sbjct: 1330 VAKMKDSVLMLASFEKTTDHLFDASAYGKTDAIAGVSESIIMGNPAAMTGTSMPALVTPA 1389

Query: 1398 PRSEPVPRTLLFD 1410
            P S   PR LLF+
Sbjct: 1390 P-SISKPRKLLFE 1401



 Score =  199 bits (505), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 113/255 (44%), Positives = 145/255 (56%), Gaps = 21/255 (8%)

Query: 97  SHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP 156
           +  ++  ++LY     R P+ +G+LDRR+GT +K A C TCG N  DCVGH+ YI L +P
Sbjct: 30  AEFEVTHRDLYTP-IDRLPVKNGVLDRRLGTTEKSAYCETCGLNSVDCVGHYAYIKLVVP 88

Query: 157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILET 216
           VFHIGYF+  I+ILQ ICK  TCARVLL E     +  + R P L  L R +L K +L  
Sbjct: 89  VFHIGYFKHTISILQCICK--TCARVLLEEPDRRAYLKRFRRPNLENLQRLNLCKAVLAL 146

Query: 217 TKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVK--FNPEI 274
            +K   CP+C   NGVVKK G LKI H+K+  R KK         AE  E  K  F P +
Sbjct: 147 ARKTVYCPYCSATNGVVKKAGALKIIHDKF--RAKKT--------AEEMEKWKRTFGPAV 196

Query: 275 EAHKKFGLI------QTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPN 328
           EA K+ G+       + LNPL+VL LF+ I  ED  LL +  E  +P   I   + VPP 
Sbjct: 197 EAQKELGMYINKAVHEDLNPLKVLDLFKRISNEDCELLGLRPEFGRPEQFIWQYISVPPV 256

Query: 329 CIRPSVISDLKSDND 343
            IRPSV  D  S+ D
Sbjct: 257 AIRPSVAQDGASNED 271



 Score =  180 bits (457), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 110/244 (45%), Positives = 152/244 (62%), Gaps = 14/244 (5%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ ISTPII+  L        ARIVKGRLERT +G++   +EE + P+ 
Sbjct: 1085 GVPRIKEIINAAKAISTPIISCKLVTADSEASARIVKGRLERTHIGDIASILEEAWAPEY 1144

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF--- 880
            ++I I +D   I+ L LE+ +D I++ I   R     L +   S  I+  K+  + +   
Sbjct: 1145 TYIGIIVDAKTIQDLQLELTLDDIKWAIVAAR----KLKIKQESITIIPRKNRLRIYIDG 1200

Query: 881  NSKMYQMKQL---LPSVVIKGVQGINRAVIH---EEDVEGVTKYK-LLVEGDNLRDVMAT 933
              K Y++++L   LP VV+KGV  I RA+I+    +D  G    K LLVEG  L+ VM T
Sbjct: 1201 PDKYYRLRELKRALPDVVVKGVPTIRRAIINIKEGDDHRGKKGDKELLVEGYGLQKVMTT 1260

Query: 934  YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
             G+ G + +SN+  EV + LGIEAAR TI+ EI   M++HGMSID RH ML+ D+M+ KG
Sbjct: 1261 QGIVGEQTTSNHVIEVAQVLGIEAARKTIINEINYTMKSHGMSIDPRHVMLLGDVMSYKG 1320

Query: 994  EVLG 997
            EVLG
Sbjct: 1321 EVLG 1324



 Score =  106 bits (264), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 48/68 (70%), Positives = 55/68 (80%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV+NSF++GLTPTEF FH + GREGLVDTAVKTAETGYMQRRL+K+LEDL   YD 
Sbjct: 830 PSKGFVRNSFYTGLTPTEFLFHAISGREGLVDTAVKTAETGYMQRRLMKALEDLVTHYDS 889

Query: 670 SFDAAFYG 677
           S   A  G
Sbjct: 890 SVRNAVGG 897



 Score = 61.2 bits (147), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 28/48 (58%), Positives = 37/48 (77%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIAS 69
           LM+ K NLVTPRNGE +IAA QDFIT  +LL++++ FF+R Q  +I S
Sbjct: 515 LMSVKHNLVTPRNGEPVIAAIQDFITASFLLSRRDTFFDRRQFTQICS 562



 Score = 48.5 bits (114), Expect = 0.029,   Method: Compositional matrix adjust.
 Identities = 28/55 (50%), Positives = 35/55 (63%), Gaps = 2/55 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNV-GTGLIKLLQAVPRSEPVPRTLLFD 721
            D  FDA+ YG+TD I+GVSE IIMG P  + GT +  L+   P S   PR LLF+
Sbjct: 1348 DHLFDASAYGKTDAIAGVSESIIMGNPAAMTGTSMPALVTPAP-SISKPRKLLFE 1401


>gi|393215308|gb|EJD00799.1| beta and beta-prime subunits of DNA dependent RNA-polymerase
           [Fomitiporia mediterranea MF3/22]
          Length = 1403

 Score =  256 bits (653), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 133/288 (46%), Positives = 178/288 (61%), Gaps = 35/288 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIM HR KV P R+FR NECVC PY ADFDGDEMN+H+PQTEEA
Sbjct: 449 DGDVVLFNRQPSLHKLSIMCHRVKVRPWRSFRLNECVCGPYGADFDGDEMNIHVPQTEEA 508

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL               LM+ K NLVTPRNGE +I+A QDFIT  +LL+Q++ FF+R
Sbjct: 509 RTEAL--------------TLMSIKLNLVTPRNGEPVISAIQDFITASFLLSQRDRFFDR 554

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q  +I S        I             P   ++   +WTGKQIF+++++PN+   V 
Sbjct: 555 QQFAQICSYFCDADLQI----------DIPPPTILKPQRLWTGKQIFNVLMRPNKRSNVL 604

Query: 521 ANLKTK----GRAYTAN-------EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVF 569
            N+++K     +   AN        +    D Y+++ NSE++ G MDK+T+GSG K ++F
Sbjct: 605 VNVESKCNKEQKPDPANYPRMNPAPDLSPNDGYLVIVNSEIMCGVMDKATVGSGKKRSIF 664

Query: 570 YILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
            ++LRD+G D A  AM R++++ + +L N GFS+GI DV PG     N
Sbjct: 665 GVILRDYGPDEAAAAMNRIAKLCARWLSNIGFSLGINDVIPGPTLSAN 712



 Score =  224 bits (571), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 172/514 (33%), Positives = 253/514 (49%), Gaps = 117/514 (22%)

Query: 993  GEVLGNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRD 1052
            G + G+  PVEL R      A  SSR    L   EI+ L +E L SK+F    S+ ++  
Sbjct: 910  GCLEGDAQPVELNRSWSHARAI-SSRRGRGLLPYEIIDLVDEELSSKKFTGVCSDTYIAV 968

Query: 1053 IKKFLEEFSKKESVTSHQDKVSQPLREQILSH------QDKIGHGRESNPFPSACKAE-- 1104
            +++F+             D   +PL EQ   H      Q +     +++    A  AE  
Sbjct: 969  LRQFI------------YDNAVKPLAEQRKEHGMYDALQKEDEWDADTDLSMGATDAEFK 1016

Query: 1105 ------------------ACREKYVRAQIEPATAVGAL---------------------- 1124
                               C +KY++A+IEP + VGA+                      
Sbjct: 1017 IISNQIKVTHTHLLTFLTLCLKKYLKAKIEPGSTVGAVGAQSIGEPGTQMTLKTFHFAGV 1076

Query: 1125 -----------------AAQSIGEPGTQMTL-----------------KTFHFAGEVCEY 1150
                             AA++I  P     L                 KT    G+V   
Sbjct: 1077 ASMNVTLGVPRIKEIINAAKTISTPIISCRLVNNMSEASARIVKGRLEKTL--LGDVASV 1134

Query: 1151 IEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPK 1210
            +EE + P+ ++I I +DMD ++ L LE+ +D I++ I   +     L V   S +++  K
Sbjct: 1135 LEEAWAPEYTYIGIIVDMDAVQKLQLELTLDDIKWAIVAAK----KLKVKQESIIVIPKK 1190

Query: 1211 DSSKSF---NSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYK----LLVEG 1260
            +  + +     K Y++++L   LPSVV+KG+Q + RA+I+ +D +     K    +LVEG
Sbjct: 1191 NRLRIYINGEDKFYRLRELRRALPSVVVKGIQTVQRAIINIKDKDDHRGKKGDKEMLVEG 1250

Query: 1261 DNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPML 1320
              L+ VM T G+ G   ++N+  E    LGIEAAR+ I+ EI+ +M+ HGMSID RH ML
Sbjct: 1251 YGLQKVMITDGIVGEYATTNHIIETAAVLGIEAARANIINEIQFIMKEHGMSIDPRHVML 1310

Query: 1321 VADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIM 1380
            + D+MT KGE+LGITR G+AKMK+SVL LASFE T+DHLFDA+ YG+TD I GVSE IIM
Sbjct: 1311 LGDVMTYKGEILGITRFGVAKMKDSVLMLASFEKTTDHLFDASAYGKTDSILGVSESIIM 1370

Query: 1381 GLP-MNVGTGLIKLLQAVPRSEPV--PRTLLFDN 1411
            G P    GT +  L+   P   P+  PR L+F++
Sbjct: 1371 GNPAAKCGTSMPSLVTPPP---PISKPRKLIFED 1401



 Score =  197 bits (502), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 105/247 (42%), Positives = 143/247 (57%), Gaps = 5/247 (2%)

Query: 97  SHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP 156
           S  Q+  ++LY     R P+  G+LDRR+GT +K A C TCG + +DCVGH+ YI L LP
Sbjct: 30  SEFQVTHQDLYTP-VDRVPVRDGVLDRRLGTTEKSAFCETCGLSSADCVGHYAYIKLALP 88

Query: 157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILET 216
           VFH+GY + ++ ILQ ICK  +CARVLL E     +  + R P L  + R SL K I  +
Sbjct: 89  VFHVGYLKHIVTILQCICK--SCARVLLSEPDRRTYLKRFRRPHLENIHRTSLVKSINSS 146

Query: 217 TKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEA 276
            +KV  CP+C   NG VKK G +KI H+K+  R KK    +E     + +A++   EI  
Sbjct: 147 ARKVVYCPYCSSTNGTVKKAGAIKIVHDKF--RAKKTADELERFKRSFAKAIEGQKEIGM 204

Query: 277 HKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVIS 336
           +    + + LNPL+VL LF  I  ED  LL +N    +P + I   + VPP CIRPSV  
Sbjct: 205 YINKAVQEDLNPLKVLDLFRRISDEDCELLGLNPSHGRPEEYIWQYISVPPVCIRPSVAQ 264

Query: 337 DLKSDND 343
           D  S+ D
Sbjct: 265 DGASNED 271



 Score =  188 bits (478), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 106/244 (43%), Positives = 156/244 (63%), Gaps = 14/244 (5%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ ISTPII+  L  +     ARIVKGRLE+T LG+V   +EE + P+ 
Sbjct: 1084 GVPRIKEIINAAKTISTPIISCRLVNNMSEASARIVKGRLEKTLLGDVASVLEEAWAPEY 1143

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF--- 880
            ++I I +DMD ++ L LE+ +D I++ I   +     L V   S +++  K+  + +   
Sbjct: 1144 TYIGIIVDMDAVQKLQLELTLDDIKWAIVAAK----KLKVKQESIIVIPKKNRLRIYING 1199

Query: 881  NSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYK----LLVEGDNLRDVMAT 933
              K Y++++L   LPSVV+KG+Q + RA+I+ +D +     K    +LVEG  L+ VM T
Sbjct: 1200 EDKFYRLRELRRALPSVVVKGIQTVQRAIINIKDKDDHRGKKGDKEMLVEGYGLQKVMIT 1259

Query: 934  YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
             G+ G   ++N+  E    LGIEAAR+ I+ EI+ +M+ HGMSID RH ML+ D+MT KG
Sbjct: 1260 DGIVGEYATTNHIIETAAVLGIEAARANIINEIQFIMKEHGMSIDPRHVMLLGDVMTYKG 1319

Query: 994  EVLG 997
            E+LG
Sbjct: 1320 EILG 1323



 Score =  105 bits (261), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 46/61 (75%), Positives = 53/61 (86%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV+NSF++GL PTEF FH + GREGLVDTAVKTAETGYMQRRL+K+LEDL   YDM
Sbjct: 829 PSKGFVRNSFYTGLLPTEFLFHAISGREGLVDTAVKTAETGYMQRRLMKALEDLTTMYDM 888

Query: 670 S 670
           S
Sbjct: 889 S 889



 Score = 60.8 bits (146), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 28/48 (58%), Positives = 37/48 (77%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIAS 69
           LM+ K NLVTPRNGE +I+A QDFIT  +LL+Q++ FF+R Q  +I S
Sbjct: 515 LMSIKLNLVTPRNGEPVISAIQDFITASFLLSQRDRFFDRQQFAQICS 562



 Score = 44.7 bits (104), Expect = 0.38,   Method: Compositional matrix adjust.
 Identities = 27/58 (46%), Positives = 35/58 (60%), Gaps = 6/58 (10%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLP-MNVGTGLIKLLQAVPRSEPV--PRTLLFDN 722
            D  FDA+ YG+TD I GVSE IIMG P    GT +  L+   P   P+  PR L+F++
Sbjct: 1347 DHLFDASAYGKTDSILGVSESIIMGNPAAKCGTSMPSLVTPPP---PISKPRKLIFED 1401


>gi|390600773|gb|EIN10167.1| beta and beta-prime subunits of DNA dependent RNA-polymerase
           [Punctularia strigosozonata HHB-11173 SS5]
          Length = 1405

 Score =  255 bits (652), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 132/283 (46%), Positives = 180/283 (63%), Gaps = 36/283 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIM HR KV P RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 449 DGDIVLFNRQPSLHKLSIMCHRVKVRPWRTFRLNECVCGPYNADFDGDEMNLHVPQTEEA 508

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL               LM  K NLV+PRNGE +IAA QDFIT  +LL+Q++ FF+R
Sbjct: 509 RTEALE--------------LMNIKHNLVSPRNGEPVIAAIQDFITASFLLSQRDRFFDR 554

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           +Q  ++ S   AD +    I     W+            +WTGKQ+F+++++PN+   + 
Sbjct: 555 SQFTQVCS-YFADANLHIDIPPPTIWKPQR---------LWTGKQVFNVLMRPNKKSNIL 604

Query: 521 ANLKTKGRAYTA--NEEFCHR----------DSYVILRNSELLAGSMDKSTLGSGGKANV 568
            N+++K     A   E +  R          D ++++ NSE++ G MDK+TLGSG K ++
Sbjct: 605 VNVESKCNKVEAPKAENYPKRMKPINDLAPNDGWLVVVNSEIMCGVMDKATLGSGKKKSI 664

Query: 569 FYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           F ++LRD+G   A  AM R++++++ +L N GFS+GI DV PG
Sbjct: 665 FGVILRDYGPHEAAAAMNRVAKLSARWLANYGFSLGINDVIPG 707



 Score =  220 bits (561), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 166/495 (33%), Positives = 246/495 (49%), Gaps = 88/495 (17%)

Query: 997  GNGTPVELKRLLDDIIAKN-SSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKK 1055
            G+  P++++R      A++ SSR+  SL   E+L +++  L   +F+ + +  +   ++ 
Sbjct: 915  GDAQPLDMERAWTH--ARSISSRAGRSLLPYEVLEITDAELSQSKFVSECTAAYRATVRG 972

Query: 1056 FLEEF--SKKESVTSHQDKVSQPLREQILSHQDKIGHGR---ESNPFPSACKA------- 1103
            F+ E    +   V   +       RE        +  G    E     +  K        
Sbjct: 973  FVTEHIAHRLAEVRRSRGMFDALEREDEWDSDTDLSMGADVTEKAYVENKSKVTEDQLRM 1032

Query: 1104 --EACREKYVRAQIEPATAVGALAAQSIG------------------------------- 1130
              + C  KYV+A+IEP + VGA+ AQSIG                               
Sbjct: 1033 FLQLCWVKYVKAKIEPGSTVGAVGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEI 1092

Query: 1131 ---------------------EPGTQMT---LKTFHFAGEVCEYIEEVFVPDDSFILIKL 1166
                                 EP  ++    L+  H    V   +EE + P+ ++I + +
Sbjct: 1093 INAAKVISTPIISCKLVTPNSEPSARIVKGRLEKTHLGDVVAAVLEEAWAPEYTYIGVIV 1152

Query: 1167 DMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNS---KMYQM 1223
            D D I+ L LE+ +D I++ I   +     L +   S  ++  ++  + +     K Y++
Sbjct: 1153 DTDAIQKLQLELTLDDIKWAIVNAK----KLKIKQESITVIPRRNRLRIYIDGIDKYYRL 1208

Query: 1224 KQL---LPSVVIKGVQGINRAVIH---EEDVEGVT-KYKLLVEGDNLRDVMATYGVKGVK 1276
            ++L   LP VV+KGV  I RAVI+   ++D +G     +LLVEG  L+ VM T G+ G  
Sbjct: 1209 RELKRQLPDVVVKGVPSIRRAVINIKEKDDPKGKKGDNELLVEGYGLQKVMTTEGIVGEH 1268

Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITR 1336
             SSN+  EV + LGIEA+R TI+ EI+  M +HGMSID RH  L+ D+MT KGEVLGITR
Sbjct: 1269 TSSNHIIEVAQVLGIEASRRTIINEIQYTMVSHGMSIDPRHITLLGDVMTYKGEVLGITR 1328

Query: 1337 HGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLP-MNVGTGLIKLLQ 1395
             G+AKMK+SVL LASFE T+DHLFDA+ YG+ D I+GVSE IIMG P  N GT L  L+ 
Sbjct: 1329 FGVAKMKDSVLMLASFEKTTDHLFDASAYGKNDSIAGVSESIIMGNPAANCGTSLPALVT 1388

Query: 1396 AVPRSEPVPRTLLFD 1410
              P     PR LLF+
Sbjct: 1389 PAPNISK-PRKLLFE 1402



 Score =  197 bits (500), Expect = 5e-47,   Method: Compositional matrix adjust.
 Identities = 107/247 (43%), Positives = 142/247 (57%), Gaps = 5/247 (2%)

Query: 97  SHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP 156
           S  ++  ++LY     RTP+ +G+LDRR+GT++K A C TCG +  DCVGH+ YI L +P
Sbjct: 30  SEFEVTHRDLYTA-LDRTPVKNGVLDRRLGTSEKNAFCETCGLSYVDCVGHYAYIKLVVP 88

Query: 157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILET 216
           VFHIGYF+  I  LQ ICK  TCARVLL E     +  + R P L  L R++L K +   
Sbjct: 89  VFHIGYFKHTIAALQCICK--TCARVLLEEPDRRTYLKRFRRPNLENLQRQALCKAVNSA 146

Query: 217 TKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEA 276
            +KV  CP+C   NG VKK G LKI H+K+  R KK    +E     ++ AV    E+  
Sbjct: 147 ARKVVYCPYCAATNGTVKKAGALKIIHDKF--RAKKTAEEMERWKKTFSNAVDAQKELAT 204

Query: 277 HKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVIS 336
           +    + + LNPL+VL LF  I  ED  LL M  E  +P + I   + VPP  IRPSV  
Sbjct: 205 YIGRAVHEDLNPLKVLDLFRRISDEDCELLGMKPEQGRPEEFIWQYISVPPVAIRPSVAQ 264

Query: 337 DLKSDND 343
           D  S+ D
Sbjct: 265 DGASNED 271



 Score =  173 bits (439), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 108/245 (44%), Positives = 153/245 (62%), Gaps = 15/245 (6%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYI-EEVFVPD 822
            GVPRIKEIINA++ ISTPII+  L        ARIVKGRLE+T LG+V   + EE + P+
Sbjct: 1085 GVPRIKEIINAAKVISTPIISCKLVTPNSEPSARIVKGRLEKTHLGDVVAAVLEEAWAPE 1144

Query: 823  DSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNS 882
             ++I + +D D I+ L LE+ +D I++ I   +     L +   S  ++  ++  + +  
Sbjct: 1145 YTYIGVIVDTDAIQKLQLELTLDDIKWAIVNAK----KLKIKQESITVIPRRNRLRIYID 1200

Query: 883  ---KMYQMKQL---LPSVVIKGVQGINRAVIH---EEDVEGVT-KYKLLVEGDNLRDVMA 932
               K Y++++L   LP VV+KGV  I RAVI+   ++D +G     +LLVEG  L+ VM 
Sbjct: 1201 GIDKYYRLRELKRQLPDVVVKGVPSIRRAVINIKEKDDPKGKKGDNELLVEGYGLQKVMT 1260

Query: 933  TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK 992
            T G+ G   SSN+  EV + LGIEA+R TI+ EI+  M +HGMSID RH  L+ D+MT K
Sbjct: 1261 TEGIVGEHTSSNHIIEVAQVLGIEASRRTIINEIQYTMVSHGMSIDPRHITLLGDVMTYK 1320

Query: 993  GEVLG 997
            GEVLG
Sbjct: 1321 GEVLG 1325



 Score =  105 bits (263), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 47/68 (69%), Positives = 55/68 (80%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV+NSF+SGL PTEF FH + GREGLVDTAVKTAETGYMQRRL+K+LEDL   YD+
Sbjct: 830 PSKGFVRNSFYSGLLPTEFLFHAISGREGLVDTAVKTAETGYMQRRLMKALEDLTTHYDL 889

Query: 670 SFDAAFYG 677
           +   A  G
Sbjct: 890 TVRNAIGG 897



 Score = 60.5 bits (145), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 27/48 (56%), Positives = 37/48 (77%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIAS 69
           LM  K NLV+PRNGE +IAA QDFIT  +LL+Q++ FF+R+Q  ++ S
Sbjct: 515 LMNIKHNLVSPRNGEPVIAAIQDFITASFLLSQRDRFFDRSQFTQVCS 562



 Score = 48.9 bits (115), Expect = 0.021,   Method: Compositional matrix adjust.
 Identities = 28/55 (50%), Positives = 33/55 (60%), Gaps = 2/55 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLP-MNVGTGLIKLLQAVPRSEPVPRTLLFD 721
            D  FDA+ YG+ D I+GVSE IIMG P  N GT L  L+   P     PR LLF+
Sbjct: 1349 DHLFDASAYGKNDSIAGVSESIIMGNPAANCGTSLPALVTPAPNISK-PRKLLFE 1402


>gi|224003141|ref|XP_002291242.1| DNA directed RNA polymerase III, largest subunit [Thalassiosira
           pseudonana CCMP1335]
 gi|220973018|gb|EED91349.1| DNA directed RNA polymerase III, largest subunit [Thalassiosira
           pseudonana CCMP1335]
          Length = 1422

 Score =  255 bits (652), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 141/335 (42%), Positives = 195/335 (58%), Gaps = 51/335 (15%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIM+H+ KV+P RTFRFN CVC PYNADFDGDEMN+HLPQTEEA
Sbjct: 479 DGDVVLFNRQPSLHKLSIMSHQVKVMPWRTFRFNICVCAPYNADFDGDEMNMHLPQTEEA 538

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R E              A +LM    NL TPRNGE L+A +QDF++  YL+TQ++ FF+R
Sbjct: 539 RIE--------------ANMLMGVHHNLATPRNGEPLVACSQDFLSAAYLITQRDQFFSR 584

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWN---PV-VFVRTAVIWTGKQIFSLILKPNRD 516
                            C ++  F         P+   ++   +WTGKQ+F+ I+KPN+ 
Sbjct: 585 EM--------------FCSLVSYFGLAEEQIDVPLPAILKPVPLWTGKQVFTCIVKPNKQ 630

Query: 517 CPVNANLKTKGRAYTANEE---FCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILL 573
                N + K + Y  N++   FC  D +V  RNSEL++G++ K T+G G K  + Y+LL
Sbjct: 631 TTALVNFEMKEKNYDTNKKLKHFCPNDGWVAFRNSELISGNIAKKTIGDGSKTGLLYVLL 690

Query: 574 RDFGEDVAVTAMWRLSRMTSFYL-MNRGFSIGIGDVTPGQGFVQNSFFSGLTPTEFFFHT 632
           RD G   A   M R S++ S Y  M+RGFSIGI DV+P          + L   ++   +
Sbjct: 691 RDCGSAEAARFMDRFSKLCSRYFGMHRGFSIGISDVSPS---------AKLKKMKYDILS 741

Query: 633 MGGREGLVDTAVKTAETGYMQRR----LVKSLEDL 663
            G ++   + A+K  + G ++ R    L++SLE++
Sbjct: 742 TGYKKA--EEAIKKYDEGTLELRPGCDLLQSLEEI 774



 Score =  242 bits (618), Expect = 9e-61,   Method: Compositional matrix adjust.
 Identities = 157/369 (42%), Positives = 208/369 (56%), Gaps = 75/369 (20%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYIEEV 1154
            KY +A +EP  AVGA+ AQSI EPGTQMTLKTFHFAG              E+    + +
Sbjct: 1044 KYTKAMVEPGEAVGAIGAQSISEPGTQMTLKTFHFAGVSSMNVTLGVPRLKEIINASKNI 1103

Query: 1155 FVP--------DDS--------------------------------FILIKLDMDRIRLL 1174
              P        DD+                                ++ I LDMD IR L
Sbjct: 1104 STPIITAKLVQDDNKVGARIVKAGIEKTTLGEISIYVKEVYSSGDCYLSILLDMDAIRQL 1163

Query: 1175 HLEVDIDSIRYCIERTRGISG-------------HLTV---SGHSFLILKPKDSSKSFNS 1218
             L +D  S+R CI   +G+ G             H+ V   S     +  P         
Sbjct: 1164 RLNIDAVSVRRCI--LKGVRGQTRPPILRSLTDKHVLVKKGSKSKLRVFVPDKGETPTYF 1221

Query: 1219 KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCS 1278
             M  +K  LP V+++G+  +NRAVI+EE+  G T+Y LLVEG  L +VM + GV G   +
Sbjct: 1222 LMQALKVALPRVIVQGISTVNRAVINEENKGGKTQYHLLVEGYGLAEVMGSPGVDGRHTT 1281

Query: 1279 SNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHG 1338
            +N+  EV +TLG+EAAR++I +EI  +M  +G+ ID RH +L++D+MT KGEVLGITR G
Sbjct: 1282 TNHIIEVEQTLGVEAARTSISSEISYIMNAYGIGIDSRHLLLLSDVMTFKGEVLGITRFG 1341

Query: 1339 LAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 1398
            +AKM+ESVL LASFE T+DHL DAA +G+TD I GVSECIIMG+P+ +GTGL KLL+   
Sbjct: 1342 VAKMRESVLMLASFEKTTDHLLDAAVHGRTDAIDGVSECIIMGIPIPIGTGLFKLLKRAT 1401

Query: 1399 RS---EPVP 1404
            R+   EPVP
Sbjct: 1402 RASKPEPVP 1410



 Score =  199 bits (506), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 113/250 (45%), Positives = 157/250 (62%), Gaps = 18/250 (7%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPR+KEIINAS+NISTPIITA L +D +   ARIVK  +E+TTLGE+  Y++EV+   D
Sbjct: 1089 GVPRLKEIINASKNISTPIITAKLVQDDNKVGARIVKAGIEKTTLGEISIYVKEVYSSGD 1148

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISG-------------HLTV---SGHS 867
             ++ I LDMD IR L L +D  S+R CI   +G+ G             H+ V   S   
Sbjct: 1149 CYLSILLDMDAIRQLRLNIDAVSVRRCI--LKGVRGQTRPPILRSLTDKHVLVKKGSKSK 1206

Query: 868  FLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927
              +  P          M  +K  LP V+++G+  +NRAVI+EE+  G T+Y LLVEG  L
Sbjct: 1207 LRVFVPDKGETPTYFLMQALKVALPRVIVQGISTVNRAVINEENKGGKTQYHLLVEGYGL 1266

Query: 928  RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 987
             +VM + GV G   ++N+  EV +TLG+EAAR++I +EI  +M  +G+ ID RH +L++D
Sbjct: 1267 AEVMGSPGVDGRHTTTNHIIEVEQTLGVEAARTSISSEISYIMNAYGIGIDSRHLLLLSD 1326

Query: 988  LMTSKGEVLG 997
            +MT KGEVLG
Sbjct: 1327 VMTFKGEVLG 1336



 Score =  187 bits (474), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 105/249 (42%), Positives = 149/249 (59%), Gaps = 9/249 (3%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           +Q+ +  Q+ S++L+   PQR P  +G+LD R+G + K + C TC   L+DC GHFGYI 
Sbjct: 51  MQRLAEFQVTSRDLFTM-PQRLPARNGVLDPRLGVSDKVSTCATCKLKLADCAGHFGYIR 109

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKK 212
           L LPVFHIGY +  +N+LQ ICK  +C+RVLL + +      K+RNP    L + S+ KK
Sbjct: 110 LALPVFHIGYLKHTLNLLQCICK--SCSRVLLTDAERKMLLKKMRNPRTDVLGKASVFKK 167

Query: 213 ILETTKKVSVCPHCGEINGVVKK---CGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVK 269
           +L+  KK   CP+C + NG VKK      LKI HE+YK R  + +  VEDLL     A+ 
Sbjct: 168 VLDKCKKAHQCPYCHKPNGTVKKVHGAPTLKIIHERYKGRHMEDE--VEDLLQSLQGAMI 225

Query: 270 FNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
            N EI  H     ++ L P  VL+LF+ +  +D  +L +   + +P +LIL  +LVPP  
Sbjct: 226 TNLEIN-HALRVAVEDLLPTRVLELFKGMTDDDCEVLWVAPWIGRPENLILEHILVPPVP 284

Query: 330 IRPSVISDL 338
           IRPSV  D+
Sbjct: 285 IRPSVAMDV 293



 Score =  105 bits (262), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 48/61 (78%), Positives = 54/61 (88%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV NSF+SGLT TEF FHTMGGREGLVDTAVKTAETGYM RRL+K+LEDL ++YD 
Sbjct: 852 PAKGFVANSFYSGLTATEFIFHTMGGREGLVDTAVKTAETGYMARRLMKALEDLSLRYDN 911

Query: 670 S 670
           S
Sbjct: 912 S 912



 Score = 54.3 bits (129), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 22/41 (53%), Positives = 31/41 (75%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           +LM    NL TPRNGE L+A +QDF++  YL+TQ++ FF+R
Sbjct: 544 MLMGVHHNLATPRNGEPLVACSQDFLSAAYLITQRDQFFSR 584



 Score = 43.5 bits (101), Expect = 0.81,   Method: Compositional matrix adjust.
 Identities = 30/51 (58%), Positives = 37/51 (72%), Gaps = 3/51 (5%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS---EPVP 715
            D   DAA +G+TD I GVSECIIMG+P+ +GTGL KLL+   R+   EPVP
Sbjct: 1360 DHLLDAAVHGRTDAIDGVSECIIMGIPIPIGTGLFKLLKRATRASKPEPVP 1410


>gi|336386001|gb|EGO27147.1| hypothetical protein SERLADRAFT_446372 [Serpula lacrymans var.
           lacrymans S7.9]
          Length = 1403

 Score =  255 bits (652), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 133/282 (47%), Positives = 179/282 (63%), Gaps = 35/282 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + D+VLFNRQPSLHKLSIM HR K+ P R+FR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 449 NGDIVLFNRQPSLHKLSIMCHRVKIRPWRSFRLNECVCGPYNADFDGDEMNLHVPQTEEA 508

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL               LM+ K NLVTPRNGE +IAA QDFIT  YL+++K+ FF+R
Sbjct: 509 RTEALE--------------LMSVKHNLVTPRNGEPVIAAIQDFITASYLISRKDTFFDR 554

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
               +I     AD      I     W+   PV       +WTGKQIF+++++PN+D  V 
Sbjct: 555 RSFTQIC-CYFADADMQIDIPPPAIWK---PV------RLWTGKQIFNVLMRPNKDSKVF 604

Query: 521 ANLKTK-GRAYTANEEFCHR----------DSYVILRNSELLAGSMDKSTLGSGGKANVF 569
            N+++K  +      EF  R          D ++++ NSE++ G MDK+T+GSG K ++F
Sbjct: 605 VNVESKCNKPQEPKAEFYPRMKPAPDLSPNDGWLVIVNSEIMCGVMDKATVGSGKKKSIF 664

Query: 570 YILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
            +++RD+G   A  AM RL+++ + +L N GFS+GI DV PG
Sbjct: 665 GVIMRDYGPHEAAAAMNRLAKLCARWLANFGFSLGINDVIPG 706



 Score =  224 bits (572), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 167/493 (33%), Positives = 245/493 (49%), Gaps = 85/493 (17%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G+  P+E +R     ++  + R   SL   E+L + ++ L +K F  + +  ++  I+ +
Sbjct: 914  GDAQPIEFERAWSHALSIGNRRGR-SLLPYEVLEIVDQELSTKRFTTECTAAYLATIRGY 972

Query: 1057 LEEFSKKESVTSHQDKVSQPLREQIL------------SHQDK--IGHGRESNPFPSACK 1102
            + +       T  Q +      E+              S  DK  + +  +       C 
Sbjct: 973  ITDNVAHTLATMRQSRGMFDALERAAEWDADTDLSLGASDADKAIVDNKSKVTEDQLRCF 1032

Query: 1103 AEACREKYVRAQIEPATAVGAL-------------------------------------- 1124
             E C  KYV+A+IEP + VGA+                                      
Sbjct: 1033 LELCWVKYVKARIEPGSTVGAVGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEII 1092

Query: 1125 -AAQSIGEPGTQMTLKTFH---------------FAGEVCEYIEEVFVPDDSFILIKLDM 1168
             AA++I  P     L T                   G+V   +EE + P+ ++I + +D+
Sbjct: 1093 NAAKAISTPIISCKLVTSDSEASARIVKGRLEKTHLGDVASVLEEAWAPEYTYIGVIVDV 1152

Query: 1169 DRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF---NSKMY---Q 1222
            D I+ L LE+ +D I++ I   +     L +   S  +L  K+  + +     K Y   +
Sbjct: 1153 DAIQKLQLELTLDDIKWGIVAAK----KLKIKQESITVLPRKNRLRIYIDGQDKYYRLRE 1208

Query: 1223 MKQLLPSVVIKGVQGINRAVIH---EEDVEGVTKYK-LLVEGDNLRDVMATYGVKGVKCS 1278
            +K+LLP VV+KGV  I RA+I+   ++D +G    K LLVEG  L+ VM T G+ G   S
Sbjct: 1209 LKRLLPDVVVKGVPTIQRAIINIKEKDDAKGKKGDKELLVEGYGLQKVMVTEGIVGEHTS 1268

Query: 1279 SNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHG 1338
            SN+  EV + LGIEAAR TI+ EI+  M++HGMSID RH ML+ D+M+ KGEVLGITR G
Sbjct: 1269 SNHVIEVAQVLGIEAARRTIINEIQYTMQSHGMSIDPRHVMLLGDVMSYKGEVLGITRFG 1328

Query: 1339 LAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLP-MNVGTGLIKLLQAV 1397
            +AKMK+SVL LASFE T+DHLFDAA +G+ D I+GVSE IIMG P  N GT +  L    
Sbjct: 1329 VAKMKDSVLMLASFEKTTDHLFDAAAFGKNDSIAGVSESIIMGNPAANCGTSMPALFSPA 1388

Query: 1398 PRSEPVPRTLLFD 1410
            P     PR LLF+
Sbjct: 1389 PIITK-PRKLLFE 1400



 Score =  194 bits (492), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 117/290 (40%), Positives = 154/290 (53%), Gaps = 28/290 (9%)

Query: 97  SHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP 156
           S  Q+  ++LY     R P+  G+LDRR+GT +K   C TCG +  DCVGH+ YI L +P
Sbjct: 30  SEFQVTHRDLYTPT-DRLPVKDGVLDRRLGTTEKNTFCETCGLSSVDCVGHYAYIKLVVP 88

Query: 157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILET 216
           VFHIGYF+  I ILQ +CK  TCARVLL E     +  + R P L  + R+SL K +   
Sbjct: 89  VFHIGYFKHTIGILQCVCK--TCARVLLEEPDRRVYLKRFRRPNLENIQRQSLSKAVNTM 146

Query: 217 TKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVK--FNPEI 274
           ++K   CP+C   NG VKK G LKI H+K+  R KK         AE  E  K  F P +
Sbjct: 147 SRKCVYCPYCSATNGAVKKAGALKIIHDKF--RAKKT--------AEEMEKWKRTFAPAV 196

Query: 275 EAHKKFGLI------QTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPN 328
           EA K+ G+       + LNPL+VL LF+ I  ED  LL +     +P + I   + VPP 
Sbjct: 197 EAQKELGMYLNKAVHEDLNPLKVLDLFKRISDEDCELLGLRPAHGRPEEYIWQYISVPPV 256

Query: 329 CIRPSVISDLKSDND-------VVLFNRQPSLHKLSIMAHRAKVLPHRTF 371
           CIRPSV  D  S+ D        ++F        LS  A  A+ + H  F
Sbjct: 257 CIRPSVAQDGASNEDDLTVKLTEIVFTNALIKQGLSKGAPTAQFMEHWEF 306



 Score =  188 bits (478), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 112/244 (45%), Positives = 156/244 (63%), Gaps = 14/244 (5%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ ISTPII+  L        ARIVKGRLE+T LG+V   +EE + P+ 
Sbjct: 1084 GVPRIKEIINAAKAISTPIISCKLVTSDSEASARIVKGRLEKTHLGDVASVLEEAWAPEY 1143

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF--- 880
            ++I + +D+D I+ L LE+ +D I++ I   +     L +   S  +L  K+  + +   
Sbjct: 1144 TYIGVIVDVDAIQKLQLELTLDDIKWGIVAAK----KLKIKQESITVLPRKNRLRIYIDG 1199

Query: 881  NSKMY---QMKQLLPSVVIKGVQGINRAVIH---EEDVEGVTKYK-LLVEGDNLRDVMAT 933
              K Y   ++K+LLP VV+KGV  I RA+I+   ++D +G    K LLVEG  L+ VM T
Sbjct: 1200 QDKYYRLRELKRLLPDVVVKGVPTIQRAIINIKEKDDAKGKKGDKELLVEGYGLQKVMVT 1259

Query: 934  YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
             G+ G   SSN+  EV + LGIEAAR TI+ EI+  M++HGMSID RH ML+ D+M+ KG
Sbjct: 1260 EGIVGEHTSSNHVIEVAQVLGIEAARRTIINEIQYTMQSHGMSIDPRHVMLLGDVMSYKG 1319

Query: 994  EVLG 997
            EVLG
Sbjct: 1320 EVLG 1323



 Score =  103 bits (258), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 46/61 (75%), Positives = 53/61 (86%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV+NSF+SGL  TEF FH + GREGLVDTAVKTAETGYMQRRL+K+LEDL  QYD+
Sbjct: 829 PSKGFVRNSFYSGLRATEFLFHAISGREGLVDTAVKTAETGYMQRRLMKALEDLTTQYDL 888

Query: 670 S 670
           S
Sbjct: 889 S 889



 Score = 59.3 bits (142), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 27/46 (58%), Positives = 35/46 (76%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRI 67
           LM+ K NLVTPRNGE +IAA QDFIT  YL+++K+ FF+R    +I
Sbjct: 515 LMSVKHNLVTPRNGEPVIAAIQDFITASYLISRKDTFFDRRSFTQI 560



 Score = 46.6 bits (109), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 27/55 (49%), Positives = 32/55 (58%), Gaps = 2/55 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLP-MNVGTGLIKLLQAVPRSEPVPRTLLFD 721
            D  FDAA +G+ D I+GVSE IIMG P  N GT +  L    P     PR LLF+
Sbjct: 1347 DHLFDAAAFGKNDSIAGVSESIIMGNPAANCGTSMPALFSPAPIITK-PRKLLFE 1400


>gi|195566968|ref|XP_002107047.1| GD17238 [Drosophila simulans]
 gi|194204444|gb|EDX18020.1| GD17238 [Drosophila simulans]
          Length = 370

 Score =  255 bits (651), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 124/226 (54%), Positives = 155/226 (68%), Gaps = 23/226 (10%)

Query: 372 RFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTP 431
           RFNEC CTPYNADFDGDEMN+HLPQTEEARAEAL              +LM N+SNLVTP
Sbjct: 162 RFNECACTPYNADFDGDEMNLHLPQTEEARAEAL--------------ILMGNQSNLVTP 207

Query: 432 RNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNP 491
           +NGE+LIAATQDFITGGYLLTQK  F  + + M++A+  +A+      I          P
Sbjct: 208 KNGEILIAATQDFITGGYLLTQKEVFLTKEEAMQLAACFLANEDSTMHI-------KLPP 260

Query: 492 VVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELL 551
              ++   +WTGKQ+FSL+++PN D  V  N+  KGR YT N++ C  DS++ +RNSEL+
Sbjct: 261 PALLKPRRLWTGKQMFSLLMRPNDDSQVRLNMVNKGRNYTGNKDLCSNDSWIHIRNSELM 320

Query: 552 AGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLS--RMTSFY 595
            G MDK+T+GSG K  +FY+LLRDFGE  A  AMWRL+  RMT FY
Sbjct: 321 CGVMDKATMGSGTKQCIFYLLLRDFGELHATKAMWRLARVRMTRFY 366



 Score = 78.6 bits (192), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 34/53 (64%), Positives = 44/53 (83%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIA 73
           +LM N+SNLVTP+NGE+LIAATQDFITGGYLLTQK  F  + + M++A+  +A
Sbjct: 196 ILMGNQSNLVTPKNGEILIAATQDFITGGYLLTQKEVFLTKEEAMQLAACFLA 248


>gi|452825408|gb|EME32405.1| DNA-directed RNA polymerase subunit [Galdieria sulphuraria]
          Length = 1423

 Score =  255 bits (651), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 176/476 (36%), Positives = 249/476 (52%), Gaps = 79/476 (16%)

Query: 997  GNGTPVELKRLLDDIIAKNS--SRSDPSLSAQEILALSNE-TLDSKEFLQDTSENF--VR 1051
            G   P+ L++LL+D  A+ +  S+ +P L+  E++  ++  T  S    +D+  +   +R
Sbjct: 940  GANCPLNLEQLLEDSKAEGTIKSKGEPRLNPDEVIHYADSLTFHSFGAFEDSESHLKILR 999

Query: 1052 DIKKFLEEFSKK-----ESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEAC 1106
            D+K FL   ++K     E ++S     S  LR+ I         G   +   +  +    
Sbjct: 1000 DVKNFLSSIARKHEMELERISSSCSNGSM-LRDTI-----DAAFGLRKSQLDALVRRIV- 1052

Query: 1107 REKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIE--- 1152
              K  R +IEP TAVGA+ AQSIGEPGTQMTLKTFHFAG            + E I    
Sbjct: 1053 -HKLQRFKIEPGTAVGAIGAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASP 1111

Query: 1153 ---------EVFVPDD-------------------------------SFILIKLDMDRIR 1172
                     E+  P+D                                +I ++LD + I 
Sbjct: 1112 IINTPVITAELVSPNDITIARIVKGRIERTTLGEICNFIKEVYRRNQVYISLQLDKELIS 1171

Query: 1173 LLHLEVDIDSIRYCIERTRGI----SGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLP 1228
             L L+VD++ +R  I     +    +    VS     I  P  +S     +M  +K+ LP
Sbjct: 1172 RLQLDVDVNVVRNAIVNNSKLRLKENDIAVVSDDRLHIFVPSKASGDLYFQMNSLKRQLP 1231

Query: 1229 SVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKT 1288
             VV++G+  I RAVIH++D +    Y+LLVEG +L  VM T GV+G   +SN+   V K 
Sbjct: 1232 HVVVQGISSIKRAVIHQKDDK---SYQLLVEGSDLLSVMTTAGVEGTCTTSNHVIIVEKV 1288

Query: 1289 LGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLN 1348
            LGIEAAR T+ +EI+  M +HGMSID RH  L+AD+M+ +GE+LGITR G+ KMK S + 
Sbjct: 1289 LGIEAARKTVASEIQYTMASHGMSIDTRHVALLADVMSFRGEILGITRFGIGKMKTSAIM 1348

Query: 1349 LASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP 1404
            LASFE T DHLFDAA Y   D + GVSEC+IMG+P+ +GTGL  LL+    S  VP
Sbjct: 1349 LASFEKTVDHLFDAALYKTQDDVVGVSECVIMGMPVPLGTGLFGLLRNDRNSVVVP 1404



 Score =  243 bits (619), Expect = 7e-61,   Method: Compositional matrix adjust.
 Identities = 131/281 (46%), Positives = 171/281 (60%), Gaps = 36/281 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND+VLFNRQPSLH++SIM HR KV P RTFR NECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 470 DNDIVLFNRQPSLHRVSIMCHRVKVFPCRTFRLNECVCTPYNADFDGDEMNMHVPQTEEA 529

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A  LM  + NLVTPRNGE LIAATQDF++  Y  T K+ + +R
Sbjct: 530 RAE--------------AATLMCVQENLVTPRNGEPLIAATQDFLSACYKFTCKDVYLDR 575

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCP-- 518
           A+  RI    ++    +      +  +  NP + ++   +WTGKQ  S IL   R CP  
Sbjct: 576 AEFTRI--IFLSGLQSVA-----YDLKLPNPAI-IKPFEMWTGKQAISFIL---RLCPGF 624

Query: 519 --VNANLKTKGRAYTANEE-------FCHRDSYVILRNSELLAGSMDKSTLGSGGKANVF 569
             + A +  K  ++ +  E        C  D YV +RN ELL G + K++LGSG K ++F
Sbjct: 625 QTMTAYVYEKQWSHPSGYESNFLAPHLCKNDGYVYIRNGELLCGQLGKASLGSGSKRSLF 684

Query: 570 YILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           Y+L R+ G   A +AM  +S+  S +  + GFS+GI DVTP
Sbjct: 685 YLLSREGGNSAAASAMSMISKFASRWFSDFGFSLGIDDVTP 725



 Score =  201 bits (511), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 111/238 (46%), Positives = 154/238 (64%), Gaps = 7/238 (2%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS  I+TP+ITA L    D+  ARIVKGR+ERTTLGE+C +I+EV+  + 
Sbjct: 1099 GVPRIKEIINASPIINTPVITAELVSPNDITIARIVKGRIERTTLGEICNFIKEVYRRNQ 1158

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI----SGHLTVSGHSFLILKPKDSSKS 879
             +I ++LD + I  L L+VD++ +R  I     +    +    VS     I  P  +S  
Sbjct: 1159 VYISLQLDKELISRLQLDVDVNVVRNAIVNNSKLRLKENDIAVVSDDRLHIFVPSKASGD 1218

Query: 880  FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
               +M  +K+ LP VV++G+  I RAVIH++D +    Y+LLVEG +L  VM T GV+G 
Sbjct: 1219 LYFQMNSLKRQLPHVVVQGISSIKRAVIHQKDDK---SYQLLVEGSDLLSVMTTAGVEGT 1275

Query: 940  KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
              +SN+   V K LGIEAAR T+ +EI+  M +HGMSID RH  L+AD+M+ +GE+LG
Sbjct: 1276 CTTSNHVIIVEKVLGIEAARKTVASEIQYTMASHGMSIDTRHVALLADVMSFRGEILG 1333



 Score =  184 bits (466), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 102/257 (39%), Positives = 150/257 (58%), Gaps = 7/257 (2%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           I+  V + + V + S  +I S++LY Q P R P   G+LD  +G + K   C TCG++L+
Sbjct: 28  IQFCVPRAEDVARTSVTRITSRDLYTQ-PLRKPAAGGVLDLHLGPSDKTGQCQTCGESLA 86

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA-- 200
            CVGHFG I L  PVFH+GYF+    ILQ +CK   C+RVLL +E  + F  KLR+P   
Sbjct: 87  TCVGHFGDISLAFPVFHMGYFKATYFILQCVCK--ACSRVLLPKELVSEFLHKLRSPITR 144

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDL 260
            +   RK++ K IL+  K    CP CG  NG VKK G++K+ H+ + +  K  +   E+ 
Sbjct: 145 ANPSKRKAVLKNILKLCKSRKHCPFCGSPNGAVKKVGVMKLIHDPFSS-AKDTEEEKENF 203

Query: 261 LAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
           L +++       ++  H +   +  LNPL VL++   IP ED+ LL M+   ++P +L+L
Sbjct: 204 LRKFHFVADNLSDVSPHIQKA-VDDLNPLRVLEILSRIPPEDVILLGMDPTYNRPENLLL 262

Query: 321 TRLLVPPNCIRPSVISD 337
           T   VPP C+RPSV SD
Sbjct: 263 TNFPVPPACLRPSVCSD 279



 Score =  110 bits (274), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 52/69 (75%), Positives = 59/69 (85%), Gaps = 1/69 (1%)

Query: 601 FSIGIGDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKS 659
           F+ G+   TP  +GFV+NSFFSG+T TEFFFHTM GREGLVDTAVKTAETGYMQRRL+K+
Sbjct: 842 FASGMSARTPWAKGFVKNSFFSGMTATEFFFHTMAGREGLVDTAVKTAETGYMQRRLMKA 901

Query: 660 LEDLCVQYD 668
           LEDL V YD
Sbjct: 902 LEDLSVNYD 910



 Score = 55.8 bits (133), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/46 (56%), Positives = 33/46 (71%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRI 67
           LM  + NLVTPRNGE LIAATQDF++  Y  T K+ + +RA+  RI
Sbjct: 536 LMCVQENLVTPRNGEPLIAATQDFLSACYKFTCKDVYLDRAEFTRI 581



 Score = 50.4 bits (119), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 25/48 (52%), Positives = 31/48 (64%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP 715
            D  FDAA Y   D + GVSEC+IMG+P+ +GTGL  LL+    S  VP
Sbjct: 1357 DHLFDAALYKTQDDVVGVSECVIMGMPVPLGTGLFGLLRNDRNSVVVP 1404


>gi|170106087|ref|XP_001884255.1| predicted protein [Laccaria bicolor S238N-H82]
 gi|164640601|gb|EDR04865.1| predicted protein [Laccaria bicolor S238N-H82]
          Length = 1397

 Score =  254 bits (649), Expect = 3e-64,   Method: Compositional matrix adjust.
 Identities = 130/278 (46%), Positives = 177/278 (63%), Gaps = 31/278 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D++LFNRQPSLHKLSIM HRAK+ P RTFR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 447 DGDIILFNRQPSLHKLSIMCHRAKIRPWRTFRLNECVCGPYNADFDGDEMNLHVPQTEEA 506

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL               LM  K NLVTPRNGE +IAA QDFIT  +LL++K+ F +R
Sbjct: 507 RTEALE--------------LMNVKHNLVTPRNGEPVIAAIQDFITASFLLSRKDQFLDR 552

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q  +I     AD      I     W+   PV       +WTGKQIF+++++PN+   + 
Sbjct: 553 RQFTQIC-CYFADADMQIDIPPPTIWK---PV------RLWTGKQIFNVLIRPNKKSNIL 602

Query: 521 ANLKTKGRAYT-------ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILL 573
            N+++K   +         + +    D ++++ NSE++ G MDK+T+GSG K ++F +++
Sbjct: 603 VNVESKCHKWEEAKPENYPSPDLSPNDGWLVIVNSEIMCGVMDKATVGSGKKKSIFGVIM 662

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           RD+G   A  AM RL+++ + +L N GFS+GI DV PG
Sbjct: 663 RDYGPHEAAAAMNRLAKLCARWLANYGFSLGINDVIPG 700



 Score =  201 bits (512), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 157/493 (31%), Positives = 239/493 (48%), Gaps = 85/493 (17%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G+  P++L R  +  +A    RS       EI  L +  L +  F+ + +  ++  IK F
Sbjct: 908  GDAQPIDLDRSWNHSLAI-GGRSGRGFLPFEISELVDRELGTHRFISECTAAYLDLIKGF 966

Query: 1057 L-EEFSKKESVTSHQDKVSQPLREQI-----------LSHQDKIGHGRESNPFPSACKA- 1103
            + +  ++K +       + + L  +             S  DK     +S    S  +  
Sbjct: 967  VADHIAQKVANVRKSRGMFEALEREAEWDAETDLSLGASDADKAIVDNKSKVTESQLRKF 1026

Query: 1104 -EACREKYVRAQIEPATAVGAL-------------------------------------- 1124
             + C  KYV+A+IEP + VGA+                                      
Sbjct: 1027 LDLCWVKYVKARIEPGSTVGAVGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEII 1086

Query: 1125 -AAQSIGEPGTQMTLKTFH---------------FAGEVCEYIEEVFVPDDSFILIKLDM 1168
             AA++I  P     L T                   G++   +EE + P+ ++I I +D+
Sbjct: 1087 NAAKAISTPIISCKLVTSDSEASARIVKARLEKTLLGDIASVLEEAWAPEYTYIGIIVDV 1146

Query: 1169 DRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF---NSKMYQMKQ 1225
            + I+ L LE+ +D I++ I   +     L +   S  ++  K+  + +     K Y++++
Sbjct: 1147 NAIQKLQLELTLDDIKWAIVNAK----KLKIKQESITVMPRKNRLRIYIDGQDKYYRLRE 1202

Query: 1226 L---LPSVVIKGVQGINRAVIHEEDVEGVTKYK----LLVEGDNLRDVMATYGVKGVKCS 1278
            L   L  VV+KGV  I RA+I+ +D       K    LLVEG  L+  M T G+ G + S
Sbjct: 1203 LKRGLADVVVKGVGTIQRAIINIKDKNDARGKKGDKELLVEGYGLQKCMITEGIVGEQTS 1262

Query: 1279 SNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHG 1338
            SN+  EV + LGIEAAR TI+ EI+  M++H M ID RH ML+ D+M+ KGEVLGITR G
Sbjct: 1263 SNHVIEVAQVLGIEAARQTIINEIQYTMKSHDMIIDPRHVMLLGDVMSYKGEVLGITRFG 1322

Query: 1339 LAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNV-GTGLIKLLQAV 1397
            + KMK+SVL LASFE T+DHLFDA+ +G+ D I+GVSE IIMG P  + GT +  L    
Sbjct: 1323 VGKMKDSVLMLASFEKTTDHLFDASAFGKNDSIAGVSESIIMGNPAAMCGTSMPALFSTT 1382

Query: 1398 PRSEPVPRTLLFD 1410
            P  +  PR LLF+
Sbjct: 1383 PTLKK-PRRLLFE 1394



 Score =  190 bits (483), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 109/253 (43%), Positives = 144/253 (56%), Gaps = 17/253 (6%)

Query: 97  SHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP 156
           S  ++  ++LY     R P+ +G+LDRR+GT  K A C TCGQ+  +CVGH+ YI L +P
Sbjct: 30  SEFEVTHRDLYTPT-DRQPVKNGVLDRRLGTTDKGAFCETCGQSSVNCVGHYAYIKLVVP 88

Query: 157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILET 216
           VFHIGYF+  I +LQ+ICK  TCARVLL E     F  + R P L  + R+SL K +   
Sbjct: 89  VFHIGYFKHTIAVLQAICK--TCARVLLEETDRRIFIKRFRRPNLENMQRQSLSKAVNTM 146

Query: 217 TKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEA 276
            +KV  CP+C   NG VKK G LKI H+K+  R KK      D L  + +   F P +EA
Sbjct: 147 ARKVVYCPYCSATNGAVKKAGALKIIHDKF--RAKK----TADELERWKKT--FAPALEA 198

Query: 277 HKKFGLI------QTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCI 330
            K+  +       + LN L+VL LF  I  ED  LL ++ +  +P   I   L VPP CI
Sbjct: 199 QKELAMYINKAVHEDLNALKVLDLFRRISDEDCELLGLHPDWGRPEQFIWQYLSVPPVCI 258

Query: 331 RPSVISDLKSDND 343
           RPSV  D  S+ D
Sbjct: 259 RPSVAQDGASNED 271



 Score =  172 bits (437), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 103/244 (42%), Positives = 149/244 (61%), Gaps = 14/244 (5%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ ISTPII+  L        ARIVK RLE+T LG++   +EE + P+ 
Sbjct: 1078 GVPRIKEIINAAKAISTPIISCKLVTSDSEASARIVKARLEKTLLGDIASVLEEAWAPEY 1137

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF--- 880
            ++I I +D++ I+ L LE+ +D I++ I   +     L +   S  ++  K+  + +   
Sbjct: 1138 TYIGIIVDVNAIQKLQLELTLDDIKWAIVNAK----KLKIKQESITVMPRKNRLRIYIDG 1193

Query: 881  NSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYK----LLVEGDNLRDVMAT 933
              K Y++++L   L  VV+KGV  I RA+I+ +D       K    LLVEG  L+  M T
Sbjct: 1194 QDKYYRLRELKRGLADVVVKGVGTIQRAIINIKDKNDARGKKGDKELLVEGYGLQKCMIT 1253

Query: 934  YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
             G+ G + SSN+  EV + LGIEAAR TI+ EI+  M++H M ID RH ML+ D+M+ KG
Sbjct: 1254 EGIVGEQTSSNHVIEVAQVLGIEAARQTIINEIQYTMKSHDMIIDPRHVMLLGDVMSYKG 1313

Query: 994  EVLG 997
            EVLG
Sbjct: 1314 EVLG 1317



 Score =  103 bits (258), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 46/61 (75%), Positives = 53/61 (86%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV+NSF+SGL  TEF FH + GREGLVDTAVKTAETGYMQRRL+K+LEDL  QYD+
Sbjct: 823 PSKGFVRNSFYSGLRATEFLFHAISGREGLVDTAVKTAETGYMQRRLMKALEDLTTQYDL 882

Query: 670 S 670
           S
Sbjct: 883 S 883



 Score = 57.0 bits (136), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 27/46 (58%), Positives = 34/46 (73%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRI 67
           LM  K NLVTPRNGE +IAA QDFIT  +LL++K+ F +R Q  +I
Sbjct: 513 LMNVKHNLVTPRNGEPVIAAIQDFITASFLLSRKDQFLDRRQFTQI 558



 Score = 44.3 bits (103), Expect = 0.54,   Method: Compositional matrix adjust.
 Identities = 25/55 (45%), Positives = 33/55 (60%), Gaps = 2/55 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNV-GTGLIKLLQAVPRSEPVPRTLLFD 721
            D  FDA+ +G+ D I+GVSE IIMG P  + GT +  L    P  +  PR LLF+
Sbjct: 1341 DHLFDASAFGKNDSIAGVSESIIMGNPAAMCGTSMPALFSTTPTLKK-PRRLLFE 1394


>gi|290999395|ref|XP_002682265.1| predicted protein [Naegleria gruberi]
 gi|284095892|gb|EFC49521.1| predicted protein [Naegleria gruberi]
          Length = 1426

 Score =  254 bits (648), Expect = 3e-64,   Method: Compositional matrix adjust.
 Identities = 128/270 (47%), Positives = 170/270 (62%), Gaps = 24/270 (8%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + D  LFNRQPSLH+LSIM HR KVLP+RTFRFN C C PYNADFDGDEMNVH+PQTEEA
Sbjct: 470 NGDYALFNRQPSLHRLSIMCHRVKVLPYRTFRFNVCDCAPYNADFDGDEMNVHIPQTEEA 529

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEA               +LM    NL+TP+NG+ +I+  QDF+T  + +T+KN FF+R
Sbjct: 530 KAEA--------------GMLMDILKNLITPKNGDPVISCNQDFLTAAWKMTRKNTFFDR 575

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+   + S +  +   I             P   ++   +WTGKQ+FSL++KPN +  V 
Sbjct: 576 AEFCMLCSYMGIEDKKI----------DLPPPTILKPIELWTGKQLFSLLVKPNNNTNVF 625

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            N +TK + Y  +E  C  D YV  RNS L+ G++DK  LG G K+++FY+L+R  G   
Sbjct: 626 VNFETKAKNYLKDETMCPNDGYVCFRNSYLICGNLDKKILGDGSKSSLFYVLIRTVGPAY 685

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           A   M R++R+ S +LMN GFSIGI DV P
Sbjct: 686 AAACMARVARVASRWLMNYGFSIGIDDVMP 715



 Score =  202 bits (514), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 110/262 (41%), Positives = 160/262 (61%), Gaps = 14/262 (5%)

Query: 88  TKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGH 147
           T ED +++ S +QI +++ Y   P +   PHG LD R+GT  K+  C TCG  ++DC+GH
Sbjct: 38  TPED-IRRMSTVQIYNQHYYT--PDKRGFPHGPLDPRLGTGTKKDICETCGLGVADCIGH 94

Query: 148 FGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRK 207
           +GY+ L LPVFHIG+   V+ +LQ ICK+  C+RVLL + +   FR K + P +    +K
Sbjct: 95  YGYVKLELPVFHIGFISNVVEVLQRICKD--CSRVLLSDSEIQSFRNKFKRP-MDNQQKK 151

Query: 208 SLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKK-----DAIVEDLLA 262
           +L KK+ E  KK S CPHCG +NG V K   +KI HEKYK  + +K     D    +  +
Sbjct: 152 ALYKKVGELCKKCSQCPHCGSLNGKVTKLNAIKIVHEKYKVASTRKGKDDIDQQSREFQS 211

Query: 263 EYNEAVKFNPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
           E+  AV+ NPEIE     G  Q  +NP+  L+LF+ I   D+ +L MN ++ +P + ILT
Sbjct: 212 EFGLAVQLNPEIEPF--LGEAQDDINPIRCLRLFKNISDTDVEVLNMNPKVVRPENFILT 269

Query: 322 RLLVPPNCIRPSVISDLKSDND 343
            +LVPP  IRP+V +D  ++ D
Sbjct: 270 HILVPPLVIRPTVNTDGGTNED 291



 Score =  189 bits (480), Expect = 9e-45,   Method: Compositional matrix adjust.
 Identities = 119/297 (40%), Positives = 173/297 (58%), Gaps = 30/297 (10%)

Query: 1145 GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCI--------ERTRGISGH 1196
            G+V  YI EV+     +I I LD+ +I  L L++  ++++  I        E+ +  S  
Sbjct: 1136 GQVVNYIREVYNLGICYIEIDLDVKQISALQLDITPETVKNSILYSPLMKFEKGKEKSKD 1195

Query: 1197 LT-VSGHSFLILKPKDSSKSF-----NSKMY----QMKQLLPSVVIKGVQGINRAVIHEE 1246
             T +S    L+   K   + +       +MY    ++K+ LP V++ G+   NRAVI+EE
Sbjct: 1196 KTKLSDEPNLVQIQKGKVRVYPPSVDRDRMYFNIQKLKRYLPEVIVAGIPTTNRAVINEE 1255

Query: 1247 DVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVM 1306
                     LLVEG +L  VM T GV      +NN  E+ +TLGIE+AR  IM EIK   
Sbjct: 1256 K----GNVYLLVEGTDLLAVMGTPGVLAKTTKTNNIIEISQTLGIESARQLIMDEIKYTT 1311

Query: 1307 ENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYG 1366
             ++GM+ID RH  L+AD+MT KG++ GI RHG+ K+++SVL +ASFE T+DHLF+AA + 
Sbjct: 1312 GSYGMNIDTRHIKLLADIMTFKGDIFGIQRHGIIKIRDSVLKMASFEQTTDHLFEAASHT 1371

Query: 1367 QTDCISGVSECIIMGLPMNVGTGLIKLLQAV----PRSEPVPRTLLFDNPEFHTNTL 1419
            + D ++GVSECIIMG+P+ +GTGL +LLQ       RS P+ R      P F T +L
Sbjct: 1372 RVDDVNGVSECIIMGVPIPIGTGLFRLLQDAHVDKKRSLPINRK----KPIFSTKSL 1424



 Score =  163 bits (413), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 107/258 (41%), Positives = 150/258 (58%), Gaps = 28/258 (10%)

Query: 764  GVPRIKEIINASRNISTPIITAYLD------KDTDLDYARIVKGRLERTTLGEVCEYIEE 817
            GVPRIKEII+A++NISTPIITAYLD      K      AR+VKGR+E+TTLG+V  YI E
Sbjct: 1085 GVPRIKEIIDATKNISTPIITAYLDTPLTATKKQKEMAARVVKGRIEKTTLGQVVNYIRE 1144

Query: 818  VFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCI--------ERTRGISGHLT-VSGHSF 868
            V+     +I I LD+ +I  L L++  ++++  I        E+ +  S   T +S    
Sbjct: 1145 VYNLGICYIEIDLDVKQISALQLDITPETVKNSILYSPLMKFEKGKEKSKDKTKLSDEPN 1204

Query: 869  LILKPKDSSKSF-----NSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYK 919
            L+   K   + +       +MY    ++K+ LP V++ G+   NRAVI+EE         
Sbjct: 1205 LVQIQKGKVRVYPPSVDRDRMYFNIQKLKRYLPEVIVAGIPTTNRAVINEEK----GNVY 1260

Query: 920  LLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDF 979
            LLVEG +L  VM T GV      +NN  E+ +TLGIE+AR  IM EIK    ++GM+ID 
Sbjct: 1261 LLVEGTDLLAVMGTPGVLAKTTKTNNIIEISQTLGIESARQLIMDEIKYTTGSYGMNIDT 1320

Query: 980  RHPMLVADLMTSKGEVLG 997
            RH  L+AD+MT KG++ G
Sbjct: 1321 RHIKLLADIMTFKGDIFG 1338



 Score =  112 bits (279), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 51/64 (79%), Positives = 57/64 (89%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSFF+GLTPTEFFFHTMGGREG+VDTAVKTAETGYMQRRL+K+LEDL V YD S
Sbjct: 840 AKGFVSNSFFTGLTPTEFFFHTMGGREGIVDTAVKTAETGYMQRRLMKALEDLFVAYDGS 899

Query: 671 FDAA 674
             +A
Sbjct: 900 VRSA 903



 Score = 70.5 bits (171), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 52/144 (36%), Positives = 75/144 (52%), Gaps = 29/144 (20%)

Query: 1017 SRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEEFS--------KKESV-- 1066
            ++ + +L+  EI     + LDS  FL++   N   D  KF++E S        K E++  
Sbjct: 947  TKDEKALTPDEI----RQKLDS--FLKEKESNIFSD--KFIDELSTFTNNYIFKLENLLK 998

Query: 1067 -----TSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAV 1121
                  S +D+      E+++ + +KI   + ++ F       ACR KY RA  EP   V
Sbjct: 999  GVAAANSIRDENENNAWEKVVHYIEKITDRQLTSFF------RACRSKYFRALAEPGEPV 1052

Query: 1122 GALAAQSIGEPGTQMTLKTFHFAG 1145
            G +A QSIGEP TQMTLKTFHFAG
Sbjct: 1053 GGIAGQSIGEPTTQMTLKTFHFAG 1076



 Score = 52.0 bits (123), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 26/53 (49%), Positives = 36/53 (67%), Gaps = 4/53 (7%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV----PRSEPVPR 716
            D  F+AA + + D ++GVSECIIMG+P+ +GTGL +LLQ       RS P+ R
Sbjct: 1362 DHLFEAASHTRVDDVNGVSECIIMGVPIPIGTGLFRLLQDAHVDKKRSLPINR 1414



 Score = 50.4 bits (119), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 21/51 (41%), Positives = 35/51 (68%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           +LM    NL+TP+NG+ +I+  QDF+T  + +T+KN FF+RA+   + S +
Sbjct: 535 MLMDILKNLITPKNGDPVISCNQDFLTAAWKMTRKNTFFDRAEFCMLCSYM 585


>gi|300122349|emb|CBK22921.2| unnamed protein product [Blastocystis hominis]
          Length = 1576

 Score =  253 bits (647), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 130/281 (46%), Positives = 180/281 (64%), Gaps = 40/281 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DV LFNRQPSLH++SIM+HR KVLP +TFRFNEC C+PYNADFDGDEMN+H+PQTEEA
Sbjct: 428 DGDVSLFNRQPSLHRMSIMSHRVKVLPWKTFRFNECDCSPYNADFDGDEMNIHIPQTEEA 487

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R E              A+ LM  K N+V PR+GE LI ATQDFITG ++LTQ++ F +R
Sbjct: 488 RIE--------------ARELMGIKHNIVNPRSGEPLITATQDFITGAFVLTQRDVFLSR 533

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                          D C ++   S     P      A++WTGKQ+FS++LKPN    V 
Sbjct: 534 L--------------DFCRLVAFLSDAQETP------AMLWTGKQVFSMLLKPNPQEGVV 573

Query: 521 ANLKTKGRAYT-----ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            +L+ K + +      +N   C +D YV+++NSELL G++DK+ +G G K  +  +L+RD
Sbjct: 574 LSLEMKAKNFQMSKVDSNLWMCPQDGYVVIQNSELLCGNIDKNCVG-GNKKGLVCVLIRD 632

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           F  +  V A+ RL+++TS +LM+ GF+IG+ DV+P +  +Q
Sbjct: 633 FTPEDTVKALGRLTKLTSRFLMDYGFTIGLDDVSPDERLLQ 673



 Score =  223 bits (569), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 136/366 (37%), Positives = 203/366 (55%), Gaps = 82/366 (22%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG----------------------- 1145
            KY R+ +EP  AVGA++ QS GEP TQMTLKTFHFAG                       
Sbjct: 1055 KYRRSIVEPGEAVGAISGQSFGEPATQMTLKTFHFAGVASMDITQGVPRIKEIINAVPSI 1114

Query: 1146 ------------------EVCE-------------YIEEVFVPDDSFILIKLDMDRIRLL 1174
                               VC+             +I+EV+ P+  F+ ++LDM+ I  L
Sbjct: 1115 STPIITVELLNNQDEISARVCKGRLERTLLGEVAAFIKEVYTPEMCFLDVQLDMEAIHKL 1174

Query: 1175 HLEVDIDSIRYCIERT----RGISGHLTVSGHSFLILKPK----DSSKSFNSK------- 1219
            +L +  DS+R  I ++    +    H+T+SG S L + P      ++K F+         
Sbjct: 1175 YLPITPDSVRRAIIQSKLKLKLKDEHVTISGKSGLRIIPPPPVITAAKRFDPASLSLAAN 1234

Query: 1220 ----------MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKY-KLLVEGDNLRDVMA 1268
                      + ++K++LP+V++ G+  ++RAV+++  VE  T +  LL++G  L  VM 
Sbjct: 1235 RNRGDDQYFTLQRLKEMLPAVIVNGIPTVHRAVLNK--VEKPTAHMNLLIDGTGLLQVMG 1292

Query: 1269 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK 1328
            T GV   K  +N+  E+   LGIEAAR+ ++ E+     ++G+SID RH ML+AD MT K
Sbjct: 1293 TVGVDHTKTVTNHVLEINSVLGIEAARTVLIQEVSNTYGSYGLSIDIRHQMLLADCMTFK 1352

Query: 1329 GEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGT 1388
            G+VLG+TR G+ KMKESV+ LASFE T+DHLFDAA +G+ D I GVS+ +IMG+P+ VGT
Sbjct: 1353 GQVLGMTRFGIEKMKESVMTLASFEKTADHLFDAALHGRRDNIIGVSDRVIMGIPILVGT 1412

Query: 1389 GLIKLL 1394
            G+  ++
Sbjct: 1413 GVFSII 1418



 Score =  174 bits (440), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 105/260 (40%), Positives = 157/260 (60%), Gaps = 28/260 (10%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA  +ISTPIIT  L  + D   AR+ KGRLERT LGEV  +I+EV+ P+ 
Sbjct: 1100 GVPRIKEIINAVPSISTPIITVELLNNQDEISARVCKGRLERTLLGEVAAFIKEVYTPEM 1159

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERT----RGISGHLTVSGHSFLILKPK----D 875
             F+ ++LDM+ I  L+L +  DS+R  I ++    +    H+T+SG S L + P      
Sbjct: 1160 CFLDVQLDMEAIHKLYLPITPDSVRRAIIQSKLKLKLKDEHVTISGKSGLRIIPPPPVIT 1219

Query: 876  SSKSFNSK-----------------MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKY 918
            ++K F+                   + ++K++LP+V++ G+  ++RAV+++  VE  T +
Sbjct: 1220 AAKRFDPASLSLAANRNRGDDQYFTLQRLKEMLPAVIVNGIPTVHRAVLNK--VEKPTAH 1277

Query: 919  -KLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSI 977
              LL++G  L  VM T GV   K  +N+  E+   LGIEAAR+ ++ E+     ++G+SI
Sbjct: 1278 MNLLIDGTGLLQVMGTVGVDHTKTVTNHVLEINSVLGIEAARTVLIQEVSNTYGSYGLSI 1337

Query: 978  DFRHPMLVADLMTSKGEVLG 997
            D RH ML+AD MT KG+VLG
Sbjct: 1338 DIRHQMLLADCMTFKGQVLG 1357



 Score =  173 bits (439), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 93/247 (37%), Positives = 146/247 (59%), Gaps = 11/247 (4%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           + ++S +++ + +++CQ   R P+P+G+LDRR+G + K   C TCG+N++ C GHFG I 
Sbjct: 1   MNRESVVEVCATDIFCQQ-SRDPMPNGVLDRRLGVSSKSEICQTCGKNIATCPGHFGTIH 59

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKK 212
           L +PVFHIGY   +I IL+SICK   C R LL  E    +  K  NP    L ++   K+
Sbjct: 60  LVMPVFHIGYINMIIGILRSICKK--CGRCLLSYEDREHYLRKFLNPYTDVLHKRQYNKQ 117

Query: 213 ILETTKKVSVCPHCGEINGVVKK---CGLLKISHEKYKNR-TKKKDAIVEDLLAEYNEAV 268
           +++  +KV  CP+C  +NG VKK      ++I H    N+ T+++   + D  A    A 
Sbjct: 118 VIDLCRKVYECPYCHAVNGEVKKIPGTASIRIEHILPPNKLTEEEQRAIHDSFA---SAC 174

Query: 269 KFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPN 328
           K+N ++ ++      + L    VL LF+ IP ED+PLL +N    +P +L+LT ++VPP 
Sbjct: 175 KYNADLHSYIDRAH-EDLTAQVVLDLFKLIPSEDLPLLWINELSGRPENLLLTDIIVPPV 233

Query: 329 CIRPSVI 335
            IRPSV+
Sbjct: 234 TIRPSVV 240



 Score =  110 bits (275), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 48/64 (75%), Positives = 56/64 (87%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV NSF+SGLTP EFFFHTMGGREGLVD+AVKTA+TGYMQRRL+K+LEDLC+ YD +
Sbjct: 792 AKGFVANSFYSGLTPMEFFFHTMGGREGLVDSAVKTADTGYMQRRLMKALEDLCISYDNT 851

Query: 671 FDAA 674
              A
Sbjct: 852 VRTA 855



 Score = 57.4 bits (137), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 26/50 (52%), Positives = 35/50 (70%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM  K N+V PR+GE LI ATQDFITG ++LTQ++ F +R    R+ + L
Sbjct: 494 LMGIKHNIVNPRSGEPLITATQDFITGAFVLTQRDVFLSRLDFCRLVAFL 543



 Score = 43.1 bits (100), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 19/38 (50%), Positives = 28/38 (73%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 705
            D  FDAA +G+ D I GVS+ +IMG+P+ VGTG+  ++
Sbjct: 1381 DHLFDAALHGRRDNIIGVSDRVIMGIPILVGTGVFSII 1418


>gi|357138371|ref|XP_003570766.1| PREDICTED: DNA-directed RNA polymerase III subunit rpc1-like
           [Brachypodium distachyon]
          Length = 1400

 Score =  253 bits (647), Expect = 5e-64,   Method: Compositional matrix adjust.
 Identities = 129/307 (42%), Positives = 181/307 (58%), Gaps = 45/307 (14%)

Query: 329 CIRPSVISDLK---------SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCT 379
           C R     DLK          D D+VLFNRQPSLH++SIM+HRA+++P RT RFNE VC 
Sbjct: 428 CDRSRAARDLKYGCIVERHLEDGDIVLFNRQPSLHRMSIMSHRARIMPWRTLRFNESVCN 487

Query: 380 PYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIA 439
           PYNADFDGDEMN+H+PQTEEAR EA               +LM  +SNL TP+NGE+L+A
Sbjct: 488 PYNADFDGDEMNLHVPQTEEARTEAF--------------LLMGVQSNLCTPKNGEILVA 533

Query: 440 ATQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAV 499
           +TQDF+T  +L+T+K+ F++R+    + S L     +I                 ++   
Sbjct: 534 STQDFLTSSFLVTRKDTFYDRSYFTLLCSYLGDAMENI----------DLPTPAIIKPVE 583

Query: 500 IWTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEE------------FCHRDSYVILRN 547
           +WTGKQ+FS++++PN    V  NL  + + Y  ++E             C  D +V  RN
Sbjct: 584 LWTGKQLFSVLVRPNACTKVFLNLTVEEKVYIKHKERDKKAITVLEETMCPNDGFVYFRN 643

Query: 548 SELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           SELL+G + K TLG+G K  +F +LLRD+    A + M RL++ ++ ++ N GFSIG+ D
Sbjct: 644 SELLSGQLGKKTLGNGNKEGMFSVLLRDYNSHAAASCMNRLAKFSARFIGNHGFSIGVDD 703

Query: 608 VTPGQGF 614
           V PGQ  
Sbjct: 704 VQPGQSL 710



 Score =  244 bits (624), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 179/500 (35%), Positives = 245/500 (49%), Gaps = 109/500 (21%)

Query: 999  GTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRD-IKKFL 1057
            G+P+ L +L   + A    R   +LS   IL + N+TL    F Q+TS     D +K+ L
Sbjct: 918  GSPLNLDQLFMKVKATCPQRGHDTLSPDVILQMFNDTL----FKQETSSGRCSDKLKEML 973

Query: 1058 EEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAE------------- 1104
             +F         +D+V      +   H D+   GR  +       A+             
Sbjct: 974  TKFL--------EDRVKMLRSTRRALHIDEDHVGRRDSSVEECIAADISGISAKQLQVFL 1025

Query: 1105 -ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFH--------------------- 1142
              C  +Y    IE   +VG + A SIGEPGTQMTLKTFH                     
Sbjct: 1026 DTCFSRYHSKIIEAGASVGPIGAHSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIIN 1085

Query: 1143 ---------------------FA------------GEVCEYIEEVFVPDDSFILIKLDMD 1169
                                 FA            GEV   I  VF   DS +++KLDM+
Sbjct: 1086 AAKKTSTPIITTELLSGQDKSFAVKVKSSIEKVVLGEVAAAINIVFKETDSNLVVKLDME 1145

Query: 1170 RIRLL-HLEVDIDSIRYCIERTRGI-------SGHLTVSGHSFLILKPKDSSKS-FNSKM 1220
            RI    ++ +  DS+R  I   R I       S H+ V   + L +      KS    ++
Sbjct: 1146 RIEAQGYMGISSDSVRLSILNHRRIRLELKLTSEHVCVVDQAKLRIHAAGKGKSGLLLEL 1205

Query: 1221 YQMKQLLPSVVIKGVQGINRAVI-----HEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 1275
            + +K +LP V++KG+  + RAV+     H++  +   +Y LLVEG NL  V+ T GV   
Sbjct: 1206 HNLKSMLPKVIVKGIPTVERAVVNPVFRHDKTFD---RYNLLVEGTNLLAVLGTPGVDAK 1262

Query: 1276 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGIT 1335
            K  SN+  EV +TLGIEAAR +I+ EI+   EN+ M ID RH ML+AD+MTSKGEVL +T
Sbjct: 1263 KTKSNHIMEVSQTLGIEAARRSIIDEIRYTFENNNMMIDLRHMMLLADVMTSKGEVLPMT 1322

Query: 1336 RHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 1395
             HG+AKMK SVL LASFE T DHLF+A++ G+ D I GVSEC+IMG+PM  GTG++K+ Q
Sbjct: 1323 AHGIAKMKTSVLMLASFERTMDHLFNASYAGRVDEIEGVSECVIMGMPMKPGTGILKVKQ 1382

Query: 1396 AVPRSEPVPRTLLFDNPEFH 1415
             +P           D PEF 
Sbjct: 1383 RLP-----------DLPEFQ 1391



 Score =  171 bits (433), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 107/247 (43%), Positives = 146/247 (59%), Gaps = 17/247 (6%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++  STPIIT  L    D  +A  VK  +E+  LGEV   I  VF   D
Sbjct: 1076 GVPRIKEIINAAKKTSTPIITTELLSGQDKSFAVKVKSSIEKVVLGEVAAAINIVFKETD 1135

Query: 824  SFILIKLDMDRIRLL-HLEVDIDSIRYCIERTRGI-------SGHLTVSGHSFLILKPKD 875
            S +++KLDM+RI    ++ +  DS+R  I   R I       S H+ V   + L +    
Sbjct: 1136 SNLVVKLDMERIEAQGYMGISSDSVRLSILNHRRIRLELKLTSEHVCVVDQAKLRIHAAG 1195

Query: 876  SSKS-FNSKMYQMKQLLPSVVIKGVQGINRAVI-----HEEDVEGVTKYKLLVEGDNLRD 929
              KS    +++ +K +LP V++KG+  + RAV+     H++  +   +Y LLVEG NL  
Sbjct: 1196 KGKSGLLLELHNLKSMLPKVIVKGIPTVERAVVNPVFRHDKTFD---RYNLLVEGTNLLA 1252

Query: 930  VMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLM 989
            V+ T GV   K  SN+  EV +TLGIEAAR +I+ EI+   EN+ M ID RH ML+AD+M
Sbjct: 1253 VLGTPGVDAKKTKSNHIMEVSQTLGIEAARRSIIDEIRYTFENNNMMIDLRHMMLLADVM 1312

Query: 990  TSKGEVL 996
            TSKGEVL
Sbjct: 1313 TSKGEVL 1319



 Score =  147 bits (371), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 92/245 (37%), Positives = 132/245 (53%), Gaps = 24/245 (9%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           ++Q +  Q+ +  +Y  D    P+P+GLLD RMG + K   C TC  + ++C GHFGYI 
Sbjct: 40  IRQSAAAQVWNTRIY--DSSLKPVPNGLLDPRMGASDKCGECATCHGSYTECPGHFGYIK 97

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKK 212
           L LPVF++GYF  ++ +L+ ICK   C+RVLL E     F  K+RNP      R S+  K
Sbjct: 98  LALPVFNVGYFNKILAVLKCICKG--CSRVLLTENIHQEFLKKMRNPRAD---RSSIMIK 152

Query: 213 ILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNP 272
           + +  +  S C  CG ING+VKK G         +   K+   IV D     + + +   
Sbjct: 153 VRDKCRP-SRCSWCGYINGIVKKEG---------RRALKQTVVIVHDCSKNLDASTEEVR 202

Query: 273 EIEAHKKFGL----IQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPN 328
            + +HKK  L    + TL+P+ VL LF  I  ED  LL +     +P +LI+T + VPP 
Sbjct: 203 SVLSHKKEKLSITSVHTLDPVTVLSLFRRITDEDCELLAIG---ERPENLIITDIAVPPV 259

Query: 329 CIRPS 333
            IRPS
Sbjct: 260 PIRPS 264



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 50/81 (61%), Positives = 59/81 (72%), Gaps = 1/81 (1%)

Query: 605 IGDVTPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDL 663
           I   TP  +GFV NSF++GLT +EFFFHTMGGREGLVDTAVKTA+TGY+ RRL+K LEDL
Sbjct: 824 INSKTPAAKGFVANSFYTGLTASEFFFHTMGGREGLVDTAVKTADTGYLSRRLMKGLEDL 883

Query: 664 CVQYDMSFDAAFYGQTDCISG 684
            V YD +   A  G    + G
Sbjct: 884 SVFYDQTVRNASGGIVQFVYG 904



 Score = 57.4 bits (137), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 24/51 (47%), Positives = 39/51 (76%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           +LM  +SNL TP+NGE+L+A+TQDF+T  +L+T+K+ F++R+    + S L
Sbjct: 514 LLMGVQSNLCTPKNGEILVASTQDFLTSSFLVTRKDTFYDRSYFTLLCSYL 564



 Score = 55.5 bits (132), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/60 (43%), Positives = 37/60 (61%), Gaps = 11/60 (18%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHF 727
            D  F+A++ G+ D I GVSEC+IMG+PM  GTG++K+ Q +P           D PEF +
Sbjct: 1344 DHLFNASYAGRVDEIEGVSECVIMGMPMKPGTGILKVKQRLP-----------DLPEFQY 1392


>gi|326437302|gb|EGD82872.1| hypothetical protein PTSG_12033 [Salpingoeca sp. ATCC 50818]
          Length = 1034

 Score =  253 bits (646), Expect = 5e-64,   Method: Compositional matrix adjust.
 Identities = 156/376 (41%), Positives = 219/376 (58%), Gaps = 66/376 (17%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCE 1149
            +A   K++   +EP TAVGA+AAQSIGEPGTQMTL+TFHFAG              E+  
Sbjct: 657  DAALHKFLGCVMEPGTAVGAIAAQSIGEPGTQMTLRTFHFAGVAAMNVTLGVPRIKEIIN 716

Query: 1150 YIEEVFVP----------------------------------------DDSFILIKLDMD 1169
              +++  P                                        ++S++ +KLD+ 
Sbjct: 717  AAKKISTPVIEAPLEEADNAAYARRVKGRIETITLEEVAEYVRIFCSDNESYVAVKLDLQ 776

Query: 1170 RIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSFLILKPKDSSKSFNSKMY---QM 1223
            RI  L LE+D+  + + I   R +      + +   S   + P+  ++  ++ ++    +
Sbjct: 777  RIANLFLEIDVQGVVFRIVSDRKLKVKPNDVDIKSASLFHVYPRPDTRKPSNPVHLLQAL 836

Query: 1224 KQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTY 1283
            +Q L +VV++G++ +NRA++++E   GV  +KL ++G N+R VM+T GV G K   N+  
Sbjct: 837  QQKLGTVVVQGLENVNRAIVNDEG--GV--HKLFIDGTNMRGVMSTLGVLGEKVKCNHVM 892

Query: 1284 EVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMK 1343
            EV KTLGIEAAR  IM +++ VM N+G+SID RH ML+ DLMT KGEVLGITR G+AKMK
Sbjct: 893  EVEKTLGIEAARQVIMDQVQYVMSNYGISIDPRHTMLMGDLMTFKGEVLGITRFGIAKMK 952

Query: 1344 ESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPV 1403
            +SV  LASFE T DHLFDAA  G TD I GVSECII+G PM VGTG   LLQ+ P ++  
Sbjct: 953  DSVFMLASFEKTIDHLFDAAMRGTTDPIEGVSECIIVGKPMKVGTGAFSLLQSPPPNQQP 1012

Query: 1404 P--RTLLFDNPEFHTN 1417
            P  R LLFD  E+H +
Sbjct: 1013 PKRRKLLFDVDEYHPH 1028



 Score =  218 bits (555), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 167/458 (36%), Positives = 225/458 (49%), Gaps = 98/458 (21%)

Query: 195 KLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKY-KNRTKKK 253
           +L  P L    R+++ K+  +  KK   CPHCG  N  VKK   +KI HE Y K    ++
Sbjct: 12  RLLAPHLESNQRQAIIKEAGDLCKKTLRCPHCGAQNATVKKVPPMKIVHELYVKKHEAER 71

Query: 254 D----------AIVEDLLAE-----YNEAVKFNPEIEAHKKFGLIQ-----TLNPLEVLQ 293
           D          A     L E     ++E      E++  +   L Q      LNPL VL+
Sbjct: 72  DRPTHVESAGVAACSYFLHELPTRLHDELAAAAEEVDGLRSL-LRQDRAQDVLNPLRVLE 130

Query: 294 LFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKS------------- 340
           LF  IP  D  +L + A   +P  L+LT ++ PP CIRPSV+ D  +             
Sbjct: 131 LFRNIPDSDCLILDLGA---RPESLLLTSIICPPGCIRPSVMRDASATSSSEDPISLARN 187

Query: 341 ------------DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGD 388
                       + D VLFNRQPSLH++SIM H+AK  P RTFRFNECVC PYNADFDGD
Sbjct: 188 LSIGDKVLRHLLEGDYVLFNRQPSLHRMSIMCHKAKPRPWRTFRFNECVCKPYNADFDGD 247

Query: 389 EMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGG 448
           EMN+H+PQTEEARAE              A  LM   +NL TP NG+ LIAATQDFITG 
Sbjct: 248 EMNLHVPQTEEARAE--------------AAELMLTTNNLCTPCNGKPLIAATQDFITGA 293

Query: 449 YLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTA--VIWTGKQI 506
           +             +M I +T  A  + +C  + R+S     P + +  +       KQ+
Sbjct: 294 H------------TSMHIDATTHA-RAHMCTCM-RWSGFFLPPPLGLDCSHHQPRICKQV 339

Query: 507 FSLILKPNRDCPVNANLKTKGRAYT---ANEE--------------FCHRDSYVILRNSE 549
            SL+LKPN+  P    L+   R+Y    A +E               C  D +V++R S+
Sbjct: 340 ISLLLKPNKFDPTEIYLQANNRSYDKDYAKQEVGCFGGKPTLGEKTLCPEDGFVLIRKSQ 399

Query: 550 LLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWR 587
           LL+G +DK  +G   K+++FY LL  +G   A     R
Sbjct: 400 LLSGFLDKGIIGE-SKSSIFYALLCHYGAPKAAEVRMR 436



 Score =  188 bits (478), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 104/240 (43%), Positives = 157/240 (65%), Gaps = 10/240 (4%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
           GVPRIKEIINA++ ISTP+I A L++  +  YAR VKGR+E  TL EV EY+      ++
Sbjct: 707 GVPRIKEIINAAKKISTPVIEAPLEEADNAAYARRVKGRIETITLEEVAEYVRIFCSDNE 766

Query: 824 SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSFLILKPKDSSKSF 880
           S++ +KLD+ RI  L LE+D+  + + I   R +      + +   S   + P+  ++  
Sbjct: 767 SYVAVKLDLQRIANLFLEIDVQGVVFRIVSDRKLKVKPNDVDIKSASLFHVYPRPDTRKP 826

Query: 881 NSKMY---QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVK 937
           ++ ++    ++Q L +VV++G++ +NRA++++E   GV  +KL ++G N+R VM+T GV 
Sbjct: 827 SNPVHLLQALQQKLGTVVVQGLENVNRAIVNDEG--GV--HKLFIDGTNMRGVMSTLGVL 882

Query: 938 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
           G K   N+  EV KTLGIEAAR  IM +++ VM N+G+SID RH ML+ DLMT KGEVLG
Sbjct: 883 GEKVKCNHVMEVEKTLGIEAARQVIMDQVQYVMSNYGISIDPRHTMLMGDLMTFKGEVLG 942



 Score = 56.2 bits (134), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 37/65 (56%), Positives = 42/65 (64%), Gaps = 3/65 (4%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP--RTLLFDNPEF 725
            D  FDAA  G TD I GVSECII+G PM VGTG   LLQ+ P ++  P  R LLFD  E+
Sbjct: 966  DHLFDAAMRGTTDPIEGVSECIIVGKPMKVGTGAFSLLQSPPPNQQPPKRRKLLFDVDEY 1025

Query: 726  HFPQV 730
            H P V
Sbjct: 1026 H-PHV 1029


>gi|294917153|ref|XP_002778409.1| DNA-directed RNA polymerase III largest subunit, putative
           [Perkinsus marinus ATCC 50983]
 gi|239886802|gb|EER10204.1| DNA-directed RNA polymerase III largest subunit, putative
           [Perkinsus marinus ATCC 50983]
          Length = 1719

 Score =  253 bits (646), Expect = 6e-64,   Method: Compositional matrix adjust.
 Identities = 135/292 (46%), Positives = 181/292 (61%), Gaps = 39/292 (13%)

Query: 330 IRPSVISDLK---------SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTP 380
           IR  + +DL+          D DVVLFNRQPSLHK+SIMAHRAKV+P RTFRFNECVC+P
Sbjct: 408 IREELAADLQYGDVVERHLQDGDVVLFNRQPSLHKMSIMAHRAKVMPWRTFRFNECVCSP 467

Query: 381 YNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAA 440
           YNADFDGDEMNVHLPQT+EARAEAL               LM  ++NL+T +NGE ++AA
Sbjct: 468 YNADFDGDEMNVHLPQTQEARAEAL--------------ALMGVQNNLITSKNGEPIVAA 513

Query: 441 TQDFITGGYLLTQKNAFFNRAQTMRIASTL--IADTSDICGIIKRFSWRSWNPVVFVRTA 498
           TQDF+T  +LLTQ++ F  + +   IA      A+T ++             P   ++  
Sbjct: 514 TQDFLTSAWLLTQRDTFLTKDKIANIAMYFGKAAETLEL------------PPPTIMKPI 561

Query: 499 VIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEE-FCHRDSYVILRNSELLAGSMDK 557
            +WTGKQ+ SL+L+P+    V  NL+   + Y+  +  FC  D YVI  NSEL+AG++ K
Sbjct: 562 QLWTGKQLISLMLRPSHKSTVLVNLEMAEKNYSHGDPYFCRNDGYVIFYNSELIAGNLGK 621

Query: 558 STLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVT 609
             LG G K  + ++L+RD    VA   + RLS++++ +L  RG S GI DVT
Sbjct: 622 KILG-GSKPGLTFVLIRDNSPAVAAACLGRLSKLSARWLGTRGMSFGIDDVT 672



 Score =  157 bits (398), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 89/254 (35%), Positives = 148/254 (58%), Gaps = 21/254 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA+++ISTPII+  L++D     A +VK +++RT LG++CEYI++V+ P  
Sbjct: 1050 GVPRIKEIINAAKHISTPIISCKLEQDRVEAAAFMVKSKIQRTLLGDICEYIKQVYEPSG 1109

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTV-------SGHSFLILKPKDS 876
             ++++KL  + +R + L++ +D ++  +     + G L +        G   L ++P  +
Sbjct: 1110 VYLIVKLCGETLRRMQLDLTMDELKEALCAKGALPGGLKIRPECIESRGKLKLAIRPAGA 1169

Query: 877  SKSFNS-----------KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTK---YKLLV 922
              S              ++  ++  LP   +KG++  +R V+++E+ +  +K   Y LLV
Sbjct: 1170 VDSRGRTLPPNPETLWFEVQALRNALPQAPVKGLKQCSRVVVNKEEAKDGSKDTIYSLLV 1229

Query: 923  EGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHP 982
            EG  L+DVM   GV   K  SN+  EV   LGIEAAR +IM+EI ++M++ GMS+D+RH 
Sbjct: 1230 EGYGLQDVMGIEGVVAEKSVSNHVLEVQSVLGIEAARKSIMSEIDVIMKHFGMSVDYRHI 1289

Query: 983  MLVADLMTSKGEVL 996
             ++ D     G  L
Sbjct: 1290 QMLGDCTGEYGSEL 1303



 Score =  134 bits (338), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 87/228 (38%), Positives = 124/228 (54%), Gaps = 14/228 (6%)

Query: 119 GLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPT 178
           G  D R+G   + ++C TCG+N  +C GHFG I L LPVFH+GYFR V  +L +ICK   
Sbjct: 31  GCHDPRLGAMNRMSDCQTCGKNFRECPGHFGSIKLVLPVFHVGYFRHVQLLLSAICKR-- 88

Query: 179 CARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKC-- 236
           C RVLL  EK + +  + R        +K + +K+++T KKV  CP+C   NG VKK   
Sbjct: 89  CGRVLLAPEKRSVWLNRTRKATKDVQQQKGVFRKLVDTCKKVRQCPYCDAYNGAVKKGTR 148

Query: 237 GLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFE 296
           G + + HE  K++ K       +   +Y++AV  NPEI  H      + L PL +L L  
Sbjct: 149 GYMTLVHELPKDQAKV------EYQQQYSDAVNNNPEIGNHLSKVAYEDLTPLHLLPLLA 202

Query: 297 AIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSV-ISDLKSDND 343
            +P  D  +L +  +   P  L++T + V P CIRPSV I D  +  D
Sbjct: 203 KMPPSDQEMLKLPPQ---PERLVVTHVPVSPVCIRPSVQIGDAGTQED 247



 Score =  127 bits (320), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 92/305 (30%), Positives = 137/305 (44%), Gaps = 81/305 (26%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYI 1151
            C  KY RA +EP  AVGA +AQSIGEP TQMTLKTFHFAG              E+    
Sbjct: 1002 CARKYRRALMEPGEAVGATSAQSIGEPATQMTLKTFHFAGVASMNVTLGVPRIKEIINAA 1061

Query: 1152 EEVFVPDDSFILIKLDMDRI---------------------------------------- 1171
            + +  P    I  KL+ DR+                                        
Sbjct: 1062 KHISTP---IISCKLEQDRVEAAAFMVKSKIQRTLLGDICEYIKQVYEPSGVYLIVKLCG 1118

Query: 1172 ---RLLHLEVDIDSIRYCIERTRGISGHLTV-------SGHSFLILKPKDSSKSFNS--- 1218
               R + L++ +D ++  +     + G L +        G   L ++P  +  S      
Sbjct: 1119 ETLRRMQLDLTMDELKEALCAKGALPGGLKIRPECIESRGKLKLAIRPAGAVDSRGRTLP 1178

Query: 1219 --------KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTK---YKLLVEGDNLRDVM 1267
                    ++  ++  LP   +KG++  +R V+++E+ +  +K   Y LLVEG  L+DVM
Sbjct: 1179 PNPETLWFEVQALRNALPQAPVKGLKQCSRVVVNKEEAKDGSKDTIYSLLVEGYGLQDVM 1238

Query: 1268 ATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTS 1327
               GV   K  SN+  EV   LGIEAAR +IM+EI ++M++ GMS+D+RH  ++ D    
Sbjct: 1239 GIEGVVAEKSVSNHVLEVQSVLGIEAARKSIMSEIDVIMKHFGMSVDYRHIQMLGDCTGE 1298

Query: 1328 KGEVL 1332
             G  L
Sbjct: 1299 YGSEL 1303



 Score =  107 bits (266), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 46/59 (77%), Positives = 56/59 (94%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
           +GFV++SFFSGL P E+FFHTMGGREGLVDTAVKTAETGYMQR+L+K+LEDL ++YDM+
Sbjct: 799 RGFVEDSFFSGLNPFEYFFHTMGGREGLVDTAVKTAETGYMQRKLIKALEDLGLKYDMT 857



 Score = 52.8 bits (125), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 34/48 (70%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIA 68
            LM  ++NL+T +NGE ++AATQDF+T  +LLTQ++ F  + +   IA
Sbjct: 493 ALMGVQNNLITSKNGEPIVAATQDFLTSAWLLTQRDTFLTKDKIANIA 540


>gi|389744278|gb|EIM85461.1| beta and beta-prime subunits of DNA dependent RNA-polymerase
           [Stereum hirsutum FP-91666 SS1]
          Length = 1404

 Score =  253 bits (646), Expect = 6e-64,   Method: Compositional matrix adjust.
 Identities = 135/283 (47%), Positives = 176/283 (62%), Gaps = 36/283 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIM HR KV P R+FR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 449 DGDIVLFNRQPSLHKLSIMCHRVKVRPWRSFRLNECVCNPYNADFDGDEMNLHVPQTEEA 508

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL               LM  K N+VTPRNGE +IAA QDFIT  YLL++++ FF+R
Sbjct: 509 RTEALE--------------LMNVKHNMVTPRNGEPVIAAIQDFITASYLLSRRDQFFDR 554

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q  +I S   AD      I     W+   PV       +WTGKQ+F++++ PN+   V 
Sbjct: 555 RQFTQICS-YFADADLQIDIPPPTIWK---PV------RLWTGKQVFNVLMHPNKKSNVL 604

Query: 521 ANLKTK--------GRAYT----ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANV 568
            N++TK         +AY        +    D ++++ NSE++ G MDK+T+G G K  V
Sbjct: 605 VNVETKCNNQQKPDSKAYPRIKDPAPDLSPNDGWLVIVNSEIMCGVMDKATVGGGKKKMV 664

Query: 569 FYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           F I++RD+G   A  AM RL+++ + +L N GFS+GI DV PG
Sbjct: 665 FGIIMRDYGPHEAAAAMNRLAKLCARWLANFGFSLGINDVIPG 707



 Score =  234 bits (596), Expect = 4e-58,   Method: Compositional matrix adjust.
 Identities = 171/495 (34%), Positives = 244/495 (49%), Gaps = 87/495 (17%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G+  P+E  R      A  + RS   L   E+L +++  L  + F  + S  ++  I+ F
Sbjct: 915  GDAQPIEFVRAWSHA-ASIAGRSLRGLLPYEVLEITDRELAKQRFTVECSAAYIATIRSF 973

Query: 1057 LEEFSKKESVTSHQDK--VSQPLREQILSHQDKIGHGR---ESNPFPSACKA-------- 1103
            + E        + Q +       RE     +  +  G    E     +  K         
Sbjct: 974  VLENVATRLADARQSRGMFDALYREAEWDEETDLSMGATAAEKAIVDNKAKVTEDQLLSF 1033

Query: 1104 -EACREKYVRAQIEPATAVGALAAQSIG-------------------------------- 1130
               C  KYVRA+IEP + VGA+ AQSIG                                
Sbjct: 1034 LNICWTKYVRAKIEPGSTVGAVGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEII 1093

Query: 1131 --------------------EPGTQMT---LKTFHFAGEVCEYIEEVFVPDDSFILIKLD 1167
                                EP  ++    L+  H  G++   +EE + P+ ++I I +D
Sbjct: 1094 NAAKVISTPIISCKLVTADSEPSARIVKGRLEKTHL-GDIAAVLEEAWAPEYTYIGIMVD 1152

Query: 1168 MDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF---NSKMY--- 1221
            M+ ++ L LE+ +D I++ I + +     L V      I+  K+  + +     K Y   
Sbjct: 1153 MESVQKLQLELTLDDIKWGIVKAK----KLKVKQEQITIIPKKNRLRLYIDGQDKYYRLR 1208

Query: 1222 QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYK----LLVEGDNLRDVMATYGVKGVKC 1277
            ++K+LLP VV+KGV  I RAVI+ +D +     K    LLVEG  L+ VM T G+ G + 
Sbjct: 1209 ELKRLLPDVVVKGVPTIARAVINVKDKDDGRGKKGDRELLVEGYGLQKVMTTEGIVGEQT 1268

Query: 1278 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRH 1337
            SSN+  E  + LGIEAAR TI+ EI+  M +HGMSID RH ML+ D+MT KGEVLGITR 
Sbjct: 1269 SSNHVIETAQVLGIEAARLTIINEIQYTMGSHGMSIDPRHVMLLGDVMTYKGEVLGITRF 1328

Query: 1338 GLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLP-MNVGTGLIKLLQA 1396
            G+AKMK+SVL LASFE T+DHLFDA+ +G+TD ++GVSE IIMG P  N GT +  L   
Sbjct: 1329 GVAKMKDSVLMLASFEKTTDHLFDASAWGKTDSVAGVSESIIMGNPAANCGTSMPALYSP 1388

Query: 1397 VPRSEPVPRTLLFDN 1411
             PR    PR LLF++
Sbjct: 1389 APRISK-PRKLLFED 1402



 Score =  199 bits (506), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 115/266 (43%), Positives = 152/266 (57%), Gaps = 22/266 (8%)

Query: 86  TVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCV 145
           T+  +D V + S  Q+  ++LY     R P+  G+LDRR+GT++K A C TCG N  DCV
Sbjct: 20  TLNSQD-VVKISEFQVTHRDLYTAT-DRVPVKDGVLDRRLGTSEKNAFCETCGLNSVDCV 77

Query: 146 GHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLV 205
           GH+ YI L +PVFHIGYF+  I ILQ ICK  TCARVLL E     F  + R P L  + 
Sbjct: 78  GHYAYIKLVVPVFHIGYFKHTIGILQCICK--TCARVLLEEPDRRVFIKRFRRPNLENVQ 135

Query: 206 RKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYN 265
           R+++ K +    +K   CP+C   NG VKK G LKI H+K+  R KK         AE  
Sbjct: 136 RQAIFKAVNGAARKTVYCPYCSATNGAVKKAGALKIVHDKF--RAKKT--------AEEM 185

Query: 266 EAVK--FNPEIEAHKKFG------LIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSD 317
           E  K  F P +EA K+ G      +++ LN L+VL LF+ I  ED  LL +  E ++P +
Sbjct: 186 EKFKRSFAPAVEAQKELGQYINKAVMEDLNALKVLDLFKRISAEDCELLGLRPEYNRPEE 245

Query: 318 LILTRLLVPPNCIRPSVISDLKSDND 343
            I   + VPP CIRPSV  D  S+ D
Sbjct: 246 FIWQYISVPPVCIRPSVQQDGASNED 271



 Score =  185 bits (469), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 111/244 (45%), Positives = 153/244 (62%), Gaps = 14/244 (5%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ ISTPII+  L        ARIVKGRLE+T LG++   +EE + P+ 
Sbjct: 1085 GVPRIKEIINAAKVISTPIISCKLVTADSEPSARIVKGRLEKTHLGDIAAVLEEAWAPEY 1144

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF--- 880
            ++I I +DM+ ++ L LE+ +D I++ I + +     L V      I+  K+  + +   
Sbjct: 1145 TYIGIMVDMESVQKLQLELTLDDIKWGIVKAK----KLKVKQEQITIIPKKNRLRLYIDG 1200

Query: 881  NSKMY---QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYK----LLVEGDNLRDVMAT 933
              K Y   ++K+LLP VV+KGV  I RAVI+ +D +     K    LLVEG  L+ VM T
Sbjct: 1201 QDKYYRLRELKRLLPDVVVKGVPTIARAVINVKDKDDGRGKKGDRELLVEGYGLQKVMTT 1260

Query: 934  YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
             G+ G + SSN+  E  + LGIEAAR TI+ EI+  M +HGMSID RH ML+ D+MT KG
Sbjct: 1261 EGIVGEQTSSNHVIETAQVLGIEAARLTIINEIQYTMGSHGMSIDPRHVMLLGDVMTYKG 1320

Query: 994  EVLG 997
            EVLG
Sbjct: 1321 EVLG 1324



 Score =  108 bits (271), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 49/68 (72%), Positives = 57/68 (83%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV+NSF+SGL+PTEF FH + GREGLVDTAVKTAETGYMQRRL+K+LEDL  QYD+
Sbjct: 830 PSKGFVRNSFYSGLSPTEFLFHAISGREGLVDTAVKTAETGYMQRRLMKALEDLTTQYDL 889

Query: 670 SFDAAFYG 677
           S   A  G
Sbjct: 890 SVRNATGG 897



 Score = 60.8 bits (146), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 28/48 (58%), Positives = 36/48 (75%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIAS 69
           LM  K N+VTPRNGE +IAA QDFIT  YLL++++ FF+R Q  +I S
Sbjct: 515 LMNVKHNMVTPRNGEPVIAAIQDFITASYLLSRRDQFFDRRQFTQICS 562



 Score = 50.4 bits (119), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 27/56 (48%), Positives = 35/56 (62%), Gaps = 2/56 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLP-MNVGTGLIKLLQAVPRSEPVPRTLLFDN 722
            D  FDA+ +G+TD ++GVSE IIMG P  N GT +  L    PR    PR LLF++
Sbjct: 1348 DHLFDASAWGKTDSVAGVSESIIMGNPAANCGTSMPALYSPAPRISK-PRKLLFED 1402


>gi|356541271|ref|XP_003539102.1| PREDICTED: DNA-directed RNA polymerase III subunit rpc1-like
           [Glycine max]
          Length = 1391

 Score =  252 bits (644), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 126/282 (44%), Positives = 181/282 (64%), Gaps = 34/282 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIM HRA+++P RT RFNE VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 453 DGDIVLFNRQPSLHRMSIMCHRARIMPWRTLRFNESVCNPYNADFDGDEMNLHVPQTEEA 512

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EA+              +LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+K+ F++R
Sbjct: 513 RTEAI--------------LLMGVENNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDR 558

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           + T  +  + I D  D   +          P + V+   +W+GKQ+FS+IL+P+ +  V 
Sbjct: 559 S-TFSLICSYIGDGMDPIDLP--------TPAI-VKPVELWSGKQLFSIILRPHANMRVY 608

Query: 521 ANLKTKGRAYTAN----------EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFY 570
            NL  K R YT +          +  C  D +V  RNSEL++G + K TLG+G K  +F 
Sbjct: 609 VNLTVKERNYTEDKKIKDKKIEWKTLCPNDGFVYFRNSELISGQVGKVTLGNGNKDGLFS 668

Query: 571 ILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
           +LLRD+    A + M RL+++++ ++ N GFSIGI DV P +
Sbjct: 669 VLLRDYRAHAAASCMNRLAKLSARWIGNHGFSIGIDDVQPKE 710



 Score =  224 bits (571), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 166/483 (34%), Positives = 250/483 (51%), Gaps = 89/483 (18%)

Query: 987  DLMTSKGEVLGNGTPVELKRLL--DDIIAKNSSRSDPSLSAQEILALSNETLDSKE---- 1040
            D M   G    NG P+  +RL      I  N    D  LS+ ++  + +E L   +    
Sbjct: 908  DGMDPAGMEGKNGKPLNFERLFLKSKAICPNDE-DDEILSSSDVSKVVHEKLSEFDMSRL 966

Query: 1041 -----FLQDTSENFVRDIKKFLEEFSK--KESVTSHQDKVSQPLRE--QILSHQDKIGHG 1091
                 F    S +FV  ++ F+++ +K  +E  T   D+ SQ L++  Q +S   +    
Sbjct: 967  AEKGVFEVGFSADFVESLQSFIKDNAKLTEEGFT---DEHSQNLKKFGQRISGITR---- 1019

Query: 1092 RESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG------ 1145
            ++ + F + C +     +Y   ++E    VGA  A SIGEPGTQMTLKTFHFAG      
Sbjct: 1020 KQLDVFLNICLS-----RYHSKKMEAGAPVGATGAHSIGEPGTQMTLKTFHFAGVASMNV 1074

Query: 1146 --------EVCEYIEEVFVPDDSFILIKLD------------------------------ 1167
                    E+    +++  P  + IL + D                              
Sbjct: 1075 TLGVPRVKEIMNGNKKISTPIITAILERDDNANTARIVKGRIEKTNLGQVAKSIKVVMTS 1134

Query: 1168 ----------MDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSFLILKPKDSSK 1214
                      M RI+  HL +D + ++  I RT+       H+ +     L + P+D  +
Sbjct: 1135 RSASVVITLDMKRIQDAHLNIDANIVKESILRTKKTKLKPEHIKILDIKKLEVVPQDVDR 1194

Query: 1215 S-FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVK 1273
            S  + +++ +K LLP+VV+KG++ ++R VI ++      K++LLVEG   R+VM   G+ 
Sbjct: 1195 SKIHFQLHYLKNLLPTVVVKGIKTVDRVVISKD--TKAEKFRLLVEGTGFREVMGVEGID 1252

Query: 1274 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVM-ENHGMSIDFRHPMLVADLMTSKGEVL 1332
            G K  SN+ +EV  TLGIEAAR +I+ EIK  M + HGM+ID RH ML+AD+MT+ G +L
Sbjct: 1253 GRKTVSNHIHEVRDTLGIEAARESIVKEIKYTMVDTHGMNIDIRHMMLLADMMTATGHIL 1312

Query: 1333 GITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIK 1392
            GI R G++KM +SVL LASFE T+D LF A+  G+ D I GVSE IIMG+P+ +GTG+IK
Sbjct: 1313 GINRFGISKMGKSVLMLASFERTADILFQASVRGRDDSIGGVSESIIMGIPIQIGTGMIK 1372

Query: 1393 LLQ 1395
            + Q
Sbjct: 1373 VKQ 1375



 Score =  194 bits (494), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 105/239 (43%), Positives = 159/239 (66%), Gaps = 7/239 (2%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPR+KEI+N ++ ISTPIITA L++D + + ARIVKGR+E+T LG+V + I+ V     
Sbjct: 1077 GVPRVKEIMNGNKKISTPIITAILERDDNANTARIVKGRIEKTNLGQVAKSIKVVMTSRS 1136

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSFLILKPKDSSKS- 879
            + ++I LDM RI+  HL +D + ++  I RT+       H+ +     L + P+D  +S 
Sbjct: 1137 ASVVITLDMKRIQDAHLNIDANIVKESILRTKKTKLKPEHIKILDIKKLEVVPQDVDRSK 1196

Query: 880  FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
             + +++ +K LLP+VV+KG++ ++R VI ++      K++LLVEG   R+VM   G+ G 
Sbjct: 1197 IHFQLHYLKNLLPTVVVKGIKTVDRVVISKD--TKAEKFRLLVEGTGFREVMGVEGIDGR 1254

Query: 940  KCSSNNTYEVYKTLGIEAARSTIMTEIKLVM-ENHGMSIDFRHPMLVADLMTSKGEVLG 997
            K  SN+ +EV  TLGIEAAR +I+ EIK  M + HGM+ID RH ML+AD+MT+ G +LG
Sbjct: 1255 KTVSNHIHEVRDTLGIEAARESIVKEIKYTMVDTHGMNIDIRHMMLLADMMTATGHILG 1313



 Score =  148 bits (373), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 97/259 (37%), Positives = 140/259 (54%), Gaps = 20/259 (7%)

Query: 90  EDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFG 149
           E  + + + +Q+   + Y  D  + PI  GLLD RMG   K   C TC  N  DC GH+G
Sbjct: 35  ESEISKIAEVQVWKGSYY--DSFKKPIHGGLLDPRMGPANKSLVCATCDGNFHDCPGHYG 92

Query: 150 YIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKS- 208
           Y++L LPVF++GY   ++ IL+ ICK   CAR+LL E+       K+R+   S L +   
Sbjct: 93  YLNLALPVFNVGYLSTIVEILKCICKG--CARILLDEDTRKKHLKKMRSSKKSELDKIDF 150

Query: 209 LKKKILETTKKVSVCPHCGEINGVVKKC-GLLKISHEKYKNRTKKKDAIVEDLLAEYNEA 267
           +K ++++   KV  CP CG ING VKK    L I H+  K R    + IVE+L +  +  
Sbjct: 151 VKVRVIKDCSKVVNCPRCGYINGSVKKLPASLTIIHDCSKCR----NYIVEELDSALSRM 206

Query: 268 VKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPP 327
                      +      LNP +VL LF+ +  ED  LL + AE  +P  LI+T ++VPP
Sbjct: 207 KDSRATTNVSNRI-----LNPFQVLSLFKRMLDEDCELLYV-AE--RPEKLIMTNVVVPP 258

Query: 328 NCIRPSVISD--LKSDNDV 344
             IRPSV+ D  L ++ND+
Sbjct: 259 IAIRPSVVMDESLSNENDI 277



 Score =  101 bits (252), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 48/67 (71%), Positives = 56/67 (83%), Gaps = 1/67 (1%)

Query: 609 TPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV NSF+SGL+ TEFFFHTMGGREGLVDTAVKTA+TGYM R+L+KSLEDL + Y
Sbjct: 830 TPAAKGFVANSFYSGLSATEFFFHTMGGREGLVDTAVKTADTGYMSRQLMKSLEDLFLHY 889

Query: 668 DMSFDAA 674
           D +   A
Sbjct: 890 DYTVRNA 896



 Score = 56.6 bits (135), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/54 (44%), Positives = 40/54 (74%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           +LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+K+ F++R+    I S +  G
Sbjct: 518 LLMGVENNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDRSTFSLICSYIGDG 571



 Score = 48.9 bits (115), Expect = 0.021,   Method: Compositional matrix adjust.
 Identities = 21/39 (53%), Positives = 29/39 (74%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D+ F A+  G+ D I GVSE IIMG+P+ +GTG+IK+ Q
Sbjct: 1337 DILFQASVRGRDDSIGGVSESIIMGIPIQIGTGMIKVKQ 1375


>gi|242073562|ref|XP_002446717.1| hypothetical protein SORBIDRAFT_06g021120 [Sorghum bicolor]
 gi|241937900|gb|EES11045.1| hypothetical protein SORBIDRAFT_06g021120 [Sorghum bicolor]
          Length = 1391

 Score =  252 bits (644), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 124/286 (43%), Positives = 177/286 (61%), Gaps = 38/286 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH++SIM+HRA+++P RT RFNE VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 444 DGDVVLFNRQPSLHRMSIMSHRARIMPWRTLRFNESVCNPYNADFDGDEMNLHVPQTEEA 503

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL              +LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+K+ F++R
Sbjct: 504 RTEAL--------------MLMGVQNNLCTPKNGEILVASTQDFLTSSFLVTRKDTFYDR 549

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           +    + S L     +I                 ++   +WTGKQ+FS++++PN    V 
Sbjct: 550 SSFTLLCSYLGDAMENI----------DLPTPALIKPIELWTGKQLFSVLVRPNAHTRVF 599

Query: 521 ANLKTKGRAYT--------------ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKA 566
            NL  + + Y+                E  C  D YV  RNSELL+G + K+TLG+G K 
Sbjct: 600 LNLAVQEKIYSKKKGKKEAGEETMCGRETMCPNDGYVYFRNSELLSGQVGKATLGNGNKD 659

Query: 567 NVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
            ++ +LLRD+    A + M RL++ ++ ++ N GFSIG+ DV PG+
Sbjct: 660 GLYSVLLRDYNSHAAASCMNRLAKFSARFIGNHGFSIGVDDVQPGE 705



 Score =  223 bits (569), Expect = 5e-55,   Method: Compositional matrix adjust.
 Identities = 122/256 (47%), Positives = 170/256 (66%), Gaps = 5/256 (1%)

Query: 1145 GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSG 1201
            GEV   I+ V       +++KLDM  I  LH+ +  DS++  I    + +  S H+ V  
Sbjct: 1119 GEVAVAIQIVLKSSQPNLIVKLDMQLIESLHMGISADSVQLSILNHPKIKLKSEHVRVID 1178

Query: 1202 HSFLILKPKDSSK-SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVT-KYKLLVE 1259
             + L + P  + K     +++ +K +LP V++KG+  + R VI E  V+  T +Y+LLVE
Sbjct: 1179 RAKLRIYPAGTDKRKLQLELHNLKSILPKVIVKGIPTVERVVIDEVKVKNETERYQLLVE 1238

Query: 1260 GDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPM 1319
            G NL  VM T GV   K  SN+  E  +TLGIEAAR +I+ EI+  M++HGM+ID RH M
Sbjct: 1239 GTNLLAVMGTPGVDATKTKSNHIMETNQTLGIEAARRSIIDEIQYTMKSHGMNIDRRHMM 1298

Query: 1320 LVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECII 1379
            L+ADLMT KGE+LGITR+G+AKMK SVL LASFE TS+HLF+A++ G+ D I GVSECII
Sbjct: 1299 LLADLMTYKGEILGITRYGIAKMKSSVLMLASFEKTSEHLFNASYSGREDQIEGVSECII 1358

Query: 1380 MGLPMNVGTGLIKLLQ 1395
            MG+PM +GTG++K+ Q
Sbjct: 1359 MGIPMQLGTGILKVRQ 1374



 Score =  192 bits (487), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 111/239 (46%), Positives = 151/239 (63%), Gaps = 5/239 (2%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA+R ISTPIITA L    D+  ARIVKG +E+  LGEV   I+ V     
Sbjct: 1074 GVPRIKEIINAARKISTPIITAQLLSKKDVLSARIVKGSMEKAVLGEVAVAIQIVLKSSQ 1133

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSGHSFLILKPKDSSK-S 879
              +++KLDM  I  LH+ +  DS++  I    + +  S H+ V   + L + P  + K  
Sbjct: 1134 PNLIVKLDMQLIESLHMGISADSVQLSILNHPKIKLKSEHVRVIDRAKLRIYPAGTDKRK 1193

Query: 880  FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVT-KYKLLVEGDNLRDVMATYGVKG 938
               +++ +K +LP V++KG+  + R VI E  V+  T +Y+LLVEG NL  VM T GV  
Sbjct: 1194 LQLELHNLKSILPKVIVKGIPTVERVVIDEVKVKNETERYQLLVEGTNLLAVMGTPGVDA 1253

Query: 939  VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             K  SN+  E  +TLGIEAAR +I+ EI+  M++HGM+ID RH ML+ADLMT KGE+LG
Sbjct: 1254 TKTKSNHIMETNQTLGIEAARRSIIDEIQYTMKSHGMNIDRRHMMLLADLMTYKGEILG 1312



 Score =  153 bits (387), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 94/258 (36%), Positives = 140/258 (54%), Gaps = 28/258 (10%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           I  +V     +++ + +Q+ +  +Y  D +  P+P+GLLD RMG   K   C+TC    S
Sbjct: 27  IRFSVLSGSEIRKSAEVQVWNNRIYGHDMK--PVPNGLLDPRMGVPNKREKCSTCHGEFS 84

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALS 202
           DC GHFGY+ L LPVF++G+F C++++L+ ICK  +C+RVLL E+    F  K+RNP   
Sbjct: 85  DCPGHFGYLKLALPVFNVGFFNCILDVLKCICK--SCSRVLLFEKDRREFLKKMRNPRAD 142

Query: 203 YLVRKSLKKKILETTKKVSVCPHCGEINGVVKK--CGLLKISHEKYKNRTKKKDAIVEDL 260
            L + +  KK+ +   K+S CP C   NGVVKK   GL+ +      + +K  D   E+L
Sbjct: 143 ALQKSATMKKVRDKC-KLSCCPRCDYRNGVVKKGRAGLIVV-----HDCSKVLDGHTEEL 196

Query: 261 ---LAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSD 317
              L    E V  N           ++ L+P  VL LF  +  ED  LL +     +P  
Sbjct: 197 KNALQNKKEKVSANS----------VRVLDPATVLSLFRRMTDEDCELLNLG---DRPEK 243

Query: 318 LILTRLLVPPNCIRPSVI 335
           LI++ + VPP  IRPSV+
Sbjct: 244 LIVSEIAVPPVPIRPSVV 261



 Score =  106 bits (264), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 59/114 (51%), Positives = 72/114 (63%), Gaps = 9/114 (7%)

Query: 605 IGDVTPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDL 663
           I   TP  +GFV NSF++GLT TEFFFHTMGGREGLVDTAVKTAETGYM RRL+K LEDL
Sbjct: 821 INSKTPAAKGFVANSFYTGLTATEFFFHTMGGREGLVDTAVKTAETGYMSRRLMKGLEDL 880

Query: 664 CVQYDMSFDAA-------FYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPR 710
            V YD +   A        YG  D +         G+P+N+    +K++   P+
Sbjct: 881 SVFYDQTVRNASGGIVQFLYGD-DGMDPAKMEGKDGMPLNLDQLFMKVMATCPQ 933



 Score = 70.9 bits (172), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 52/162 (32%), Positives = 82/162 (50%), Gaps = 24/162 (14%)

Query: 998  NGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTS------ENFVR 1051
            +G P+ L +L   ++A    R   +LS + I     + L+ K    DTS      E F +
Sbjct: 914  DGMPLNLDQLFMKVMATCPQRGSDTLSPEAI----KQMLEDKLLQHDTSSDGGCSEEFKK 969

Query: 1052 DIKKFLE---EFSK--KESVTSHQDKVSQP---LREQILSHQDKIGHGRESNPFPSACKA 1103
            ++ +FL+   E  K  + ++  H+D V +    + E + +    I   ++   F      
Sbjct: 970  NLTEFLDKRIELMKCTRRALHLHEDHVEKKDSCVEESVAAIISGIS-AKQLQVF-----L 1023

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            + C  +Y   +IE   ++GA+ AQSIGEPGTQMTLKTFHFAG
Sbjct: 1024 DTCLSRYQSKKIEAGASIGAIGAQSIGEPGTQMTLKTFHFAG 1065



 Score = 56.6 bits (135), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/51 (45%), Positives = 39/51 (76%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           +LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+K+ F++R+    + S L
Sbjct: 509 MLMGVQNNLCTPKNGEILVASTQDFLTSSFLVTRKDTFYDRSSFTLLCSYL 559



 Score = 52.4 bits (124), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 21/36 (58%), Positives = 30/36 (83%)

Query: 671  FDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            F+A++ G+ D I GVSECIIMG+PM +GTG++K+ Q
Sbjct: 1339 FNASYSGREDQIEGVSECIIMGIPMQLGTGILKVRQ 1374


>gi|67476290|ref|XP_653748.1| DNA-directed RNA polymerase III largest subunit [Entamoeba
           histolytica HM-1:IMSS]
 gi|56470729|gb|EAL48362.1| DNA-directed RNA polymerase III largest subunit, putative
           [Entamoeba histolytica HM-1:IMSS]
 gi|449705808|gb|EMD45780.1| DNA-directed RNA polymerase III largest subunit, putative
           [Entamoeba histolytica KU27]
          Length = 1379

 Score =  252 bits (644), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 125/277 (45%), Positives = 172/277 (62%), Gaps = 25/277 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND+VLFNRQPSLH++SIM HRAK+LP RT RFNECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 472 DNDIVLFNRQPSLHRISIMCHRAKILPWRTLRFNECVCTPYNADFDGDEMNLHVPQTEEA 531

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE L              +LM +  NL TPR G+++IA TQDF+T  YLLT K+     
Sbjct: 532 RAECL--------------MLMHSAKNLQTPRTGQMIIAETQDFLTTSYLLTSKDFVIEE 577

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              M+ A       ++I                +++   +WTGKQ++ L LKPN+   VN
Sbjct: 578 EDMMQWACWFHNAGTEI----------DLPTPAYLKPKKLWTGKQLYGLALKPNKHEGVN 627

Query: 521 ANLKTKGRAYTANEEF-CHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            +L    + Y+   ++ C +D ++  +NS+LL+G ++KS +GSG K  +F+++LRD+G  
Sbjct: 628 ISLDVPSKLYSKEGKWMCVKDGWICFKNSQLLSGQIEKSIIGSGNKTGLFHLILRDYGTL 687

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
            +   M  +SR  + +L + GFSIGI DVTP     Q
Sbjct: 688 ESAKIMAHISRFCARFLGDYGFSIGISDVTPSADLTQ 724



 Score =  190 bits (483), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 108/257 (42%), Positives = 163/257 (63%), Gaps = 7/257 (2%)

Query: 1146 EVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGH 1202
            E+ + ++ VF P +++I +KLD + I+ L LE  I+ ++  +   RG+      + +   
Sbjct: 1115 EIAKSVKIVFKPAEAYISVKLDFETIKQLELECTIEKVQDVLLNYRGLKLKDNQVIIRNK 1174

Query: 1203 SFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDN 1262
              L +    SS S    +  ++  L  V++ G++   RAVI++        ++LLVEG  
Sbjct: 1175 QKLRVYVDKSSTSLLFALNSLRNQLLEVIVCGIENTGRAVINKNK----GSFELLVEGSE 1230

Query: 1263 LRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVA 1322
            L  VM T GV G + +SN+   V K LGIEAARSTI++EIK VM+ +G+SID RH +L++
Sbjct: 1231 LLKVMGTPGVIGEETTSNHIAVVEKVLGIEAARSTIISEIKNVMDAYGLSIDVRHLLLLS 1290

Query: 1323 DLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGL 1382
            DLMT KG +LGITR+G++KMK+SV   ASFE T+DHLFDAA + + D I GVSE II+G 
Sbjct: 1291 DLMTFKGVILGITRYGISKMKDSVFTFASFERTNDHLFDAAVHSRKDEIKGVSESIIVGN 1350

Query: 1383 PMNVGTGLIKLLQAVPR 1399
             + +GTGL+++L   P+
Sbjct: 1351 QVGLGTGLMQILYDPPK 1367



 Score =  173 bits (438), Expect = 8e-40,   Method: Compositional matrix adjust.
 Identities = 102/237 (43%), Positives = 147/237 (62%), Gaps = 7/237 (2%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ I TPI+TA L    D+  ARIVKGR+E T L E+ + ++ VF P +
Sbjct: 1069 GVPRIKEIINASKKIQTPIVTAKLVNSQDVTSARIVKGRIEATRLKEIAKSVKIVFKPAE 1128

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFLILKPKDSSKSF 880
            ++I +KLD + I+ L LE  I+ ++  +   RG+      + +     L +    SS S 
Sbjct: 1129 AYISVKLDFETIKQLELECTIEKVQDVLLNYRGLKLKDNQVIIRNKQKLRVYVDKSSTSL 1188

Query: 881  NSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
               +  ++  L  V++ G++   RAVI++        ++LLVEG  L  VM T GV G +
Sbjct: 1189 LFALNSLRNQLLEVIVCGIENTGRAVINKNK----GSFELLVEGSELLKVMGTPGVIGEE 1244

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SN+   V K LGIEAARSTI++EIK VM+ +G+SID RH +L++DLMT KG +LG
Sbjct: 1245 TTSNHIAVVEKVLGIEAARSTIISEIKNVMDAYGLSIDVRHLLLLSDLMTFKGVILG 1301



 Score =  165 bits (417), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 90/259 (34%), Positives = 149/259 (57%), Gaps = 13/259 (5%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           I+ T+  ++ + ++S  ++    L+ Q   R P P+G+LDRR+G     + C TCG+ + 
Sbjct: 37  IQFTMFSQEEMNRESEFEVTEHFLF-QPNTRKPNPNGVLDRRLGVCDSLSVCETCGKRIE 95

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALS 202
           +C GHF  I+L LPVFHIG+FR +I +LQ +CKN  C R+LL  E+   +  ++RN    
Sbjct: 96  ECSGHFAVINLELPVFHIGFFRPIIQVLQCVCKN--CNRILLTNEERDFYLRRMRNKKTD 153

Query: 203 YLVRKSLKKKILETTKK-VSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLL 261
            + R  L + ++   +K  + CPHC  ING +KK G L++ H+KY      +D  + ++ 
Sbjct: 154 TVARTYLVRALIAQCRKHYNSCPHCNAINGSIKKYGNLRLVHDKY-----HRDPTITEMN 208

Query: 262 AEYN---EAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDL 318
             Y+   E++K + +I A       + L+P +VL +F ++  EDI  +  + + + P ++
Sbjct: 209 EFYDGFEESIKLDKDINAFIN-NAQEDLDPRKVLSIFRSLIREDIETMDFDPDNAPPENM 267

Query: 319 ILTRLLVPPNCIRPSVISD 337
           ILT + VPP  IRPSV  D
Sbjct: 268 ILTSVPVPPIAIRPSVAMD 286



 Score =  106 bits (264), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 50/67 (74%), Positives = 58/67 (86%), Gaps = 1/67 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV+NSFF+GL  TEFFFHTMGGREGLVD+AVKTAETGYMQRRL+K+LEDL V Y
Sbjct: 840 TPQAKGFVKNSFFTGLNATEFFFHTMGGREGLVDSAVKTAETGYMQRRLMKALEDLHVHY 899

Query: 668 DMSFDAA 674
           D +  +A
Sbjct: 900 DGTVRSA 906



 Score = 47.8 bits (112), Expect = 0.053,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 30/48 (62%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIA 68
           +LM +  NL TPR G+++IA TQDF+T  YLLT K+        M+ A
Sbjct: 537 MLMHSAKNLQTPRTGQMIIAETQDFLTTSYLLTSKDFVIEEEDMMQWA 584



 Score = 41.6 bits (96), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 20/43 (46%), Positives = 29/43 (67%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPR 710
            D  FDAA + + D I GVSE II+G  + +GTGL+++L   P+
Sbjct: 1325 DHLFDAAVHSRKDEIKGVSESIIVGNQVGLGTGLMQILYDPPK 1367


>gi|449525688|ref|XP_004169848.1| PREDICTED: LOW QUALITY PROTEIN: DNA-directed RNA polymerase III
           subunit rpc1-like, partial [Cucumis sativus]
          Length = 693

 Score =  252 bits (643), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 125/284 (44%), Positives = 180/284 (63%), Gaps = 33/284 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH++SIM HR +V+P RT RFNE VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 148 DGDVVLFNRQPSLHRMSIMCHRVRVMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEA 207

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EA+              +LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+K+ F++R
Sbjct: 208 RTEAI--------------LLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDR 253

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPV-VFVRTAVIWTGKQIFSLILKPNRDCPV 519
           A    +  + + D  D+  +          P    V+   +WTGKQ+FS++++P+    V
Sbjct: 254 A-AFSLMCSYMGDGMDLVDL----------PTPALVKPIELWTGKQLFSVLVRPHASMKV 302

Query: 520 NANLKTKGRAYTA-------NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYIL 572
             NL  K ++Y+         E  C  D +V  RNSEL++G + K+TLG+G K  ++ +L
Sbjct: 303 YLNLTVKEKSYSKVKGNEKERETMCPNDGFVYFRNSELISGQVGKATLGNGNKDGLYSVL 362

Query: 573 LRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           LRD+    A   M RL+++++ ++ N GFSIGI DV PG   V+
Sbjct: 363 LRDYKAHAAAVCMNRLAKLSARWIGNHGFSIGIDDVQPGDQLVK 406



 Score =  105 bits (262), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 50/67 (74%), Positives = 56/67 (83%), Gaps = 1/67 (1%)

Query: 609 TPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV NSF+SGLT TEFFFHTMGGREGLVDTAVKTA+TGYM RRL+K+LEDL + Y
Sbjct: 522 TPAAKGFVANSFYSGLTATEFFFHTMGGREGLVDTAVKTADTGYMSRRLIKALEDLSIHY 581

Query: 668 DMSFDAA 674
           D S   A
Sbjct: 582 DSSVRNA 588



 Score = 57.0 bits (136), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 22/42 (52%), Positives = 36/42 (85%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRA 62
           +LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+K+ F++RA
Sbjct: 213 LLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDRA 254


>gi|316997021|dbj|BAJ52638.1| RNA polymerase III largest subunit [Monosiga ovata]
          Length = 931

 Score =  252 bits (643), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 151/370 (40%), Positives = 209/370 (56%), Gaps = 60/370 (16%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIG--------------------------------- 1130
            +AC +KY RA IE  TAVGA+  QS+G                                 
Sbjct: 555  QACCDKYQRACIEAGTAVGAVCGQSLGEPTTQMTLKTFHFSGIASMNITLGVPRIKEIIN 614

Query: 1131 --------------EPG-TQMTLKTFH------FAGEVCEYIEEVFVPDDSFILIKLDMD 1169
                          EPG T M+ +           GE+ +YIEEV  P   ++L+KLDM 
Sbjct: 615  AVKNTSTPIITAVLEPGSTAMSAQIVKSRIEKTLLGEIMDYIEEVLTPSGCYVLVKLDMA 674

Query: 1170 RIRLLHLEVDIDSIRYCI-ERTRGI----SGHLTVSGHSFLILKPKDSSKSFNSKMYQMK 1224
            R+  L LEVD+ ++   I ER   +         + G+   +  P  S  +    + Q+K
Sbjct: 675  RVHKLQLEVDVHTVETAILERCGKLKLKRQNVWVMRGNKIAVSPPSQSKSNAYFVLQQLK 734

Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYE 1284
              LP VVI+GV  I+RAV+ + D +G   +K+L EGDNL  VM T GV G + +SN+  +
Sbjct: 735  AELPHVVIRGVDRISRAVVQKVDEKGRAVFKVLAEGDNLLHVMGTRGVLGTRVTSNHILD 794

Query: 1285 VYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKE 1344
            V +TLGIEAAR+TI++E+   +  +G+SID+RH  ++ADLMTS+GEVLGITR G+AKM E
Sbjct: 795  VERTLGIEAARATIISEVGQTVAPYGVSIDWRHLSILADLMTSRGEVLGITRFGIAKMNE 854

Query: 1345 SVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSE-PV 1403
             VL LASFE T+D LFDAA +G  D I GVSECII+G+P+++GTGL  L++     + P 
Sbjct: 855  RVLMLASFEKTNDILFDAAVHGLKDDIDGVSECIILGVPISLGTGLFSLMRRADNIQPPT 914

Query: 1404 PRTLLFDNPE 1413
             R++LFD PE
Sbjct: 915  RRSVLFDRPE 924



 Score =  209 bits (531), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 112/239 (46%), Positives = 157/239 (65%), Gaps = 5/239 (2%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
           GVPRIKEIINA +N STPIITA L+  +    A+IVK R+E+T LGE+ +YIEEV  P  
Sbjct: 605 GVPRIKEIINAVKNTSTPIITAVLEPGSTAMSAQIVKSRIEKTLLGEIMDYIEEVLTPSG 664

Query: 824 SFILIKLDMDRIRLLHLEVDIDSIRYCI-ERTRGI----SGHLTVSGHSFLILKPKDSSK 878
            ++L+KLDM R+  L LEVD+ ++   I ER   +         + G+   +  P  S  
Sbjct: 665 CYVLVKLDMARVHKLQLEVDVHTVETAILERCGKLKLKRQNVWVMRGNKIAVSPPSQSKS 724

Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 938
           +    + Q+K  LP VVI+GV  I+RAV+ + D +G   +K+L EGDNL  VM T GV G
Sbjct: 725 NAYFVLQQLKAELPHVVIRGVDRISRAVVQKVDEKGRAVFKVLAEGDNLLHVMGTRGVLG 784

Query: 939 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            + +SN+  +V +TLGIEAAR+TI++E+   +  +G+SID+RH  ++ADLMTS+GEVLG
Sbjct: 785 TRVTSNHILDVERTLGIEAARATIISEVGQTVAPYGVSIDWRHLSILADLMTSRGEVLG 843



 Score =  182 bits (461), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 101/245 (41%), Positives = 140/245 (57%), Gaps = 49/245 (20%)

Query: 391 NVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYL 450
           N+H+PQTE ARAEAL              VLM  KSN+ TPRNG+ LIAATQDF+TG +L
Sbjct: 1   NIHVPQTETARAEAL--------------VLMGTKSNICTPRNGDPLIAATQDFLTGAFL 46

Query: 451 LTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLI 510
           L+ ++  F R +  ++A+ L    + +             P   V+   +W+GKQ+ SL+
Sbjct: 47  LSLRDTLFTRQRFCQLATYLTEGRTFV----------KLPPPCIVKPVQMWSGKQLLSLL 96

Query: 511 LKP----NRDCPVN--ANLKTKGRAYTANE-------------------EFCHRDSYVIL 545
           L+P     +  P N   NL+T+ ++Y+ ++                     C  D Y+++
Sbjct: 97  LRPVVAPGQPLPRNNCINLETQTKSYSDSKISLSPDAPDAVAQYSKPVLSMCPEDGYLVI 156

Query: 546 RNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGI 605
           RNSELL G +DKS LGSG K  +FY+LLRD GE  A  AM RL+++ SF+LMNRGFSIGI
Sbjct: 157 RNSELLCGVLDKSVLGSGSKTTIFYVLLRDCGEQAAADAMSRLAKVASFFLMNRGFSIGI 216

Query: 606 GDVTP 610
            DV P
Sbjct: 217 TDVRP 221



 Score =  112 bits (279), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 49/60 (81%), Positives = 56/60 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV+NSF++GLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRL+K+LEDL   YD+S
Sbjct: 346 AKGFVRNSFYTGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLMKALEDLSTHYDLS 405



 Score = 64.7 bits (156), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 29/55 (52%), Positives = 40/55 (72%)

Query: 21 VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
          VLM  KSN+ TPRNG+ LIAATQDF+TG +LL+ ++  F R +  ++A+ L  GR
Sbjct: 16 VLMGTKSNICTPRNGDPLIAATQDFLTGAFLLSLRDTLFTRQRFCQLATYLTEGR 70



 Score = 61.2 bits (147), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 29/58 (50%), Positives = 41/58 (70%), Gaps = 1/58 (1%)

Query: 668 DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSE-PVPRTLLFDNPE 724
           D+ FDAA +G  D I GVSECII+G+P+++GTGL  L++     + P  R++LFD PE
Sbjct: 867 DILFDAAVHGLKDDIDGVSECIILGVPISLGTGLFSLMRRADNIQPPTRRSVLFDRPE 924


>gi|407043155|gb|EKE41776.1| DNA-directed RNA polymerase III largest subunit, putative
           [Entamoeba nuttalli P19]
          Length = 1379

 Score =  251 bits (642), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 125/277 (45%), Positives = 171/277 (61%), Gaps = 25/277 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND+VLFNRQPSLH++SIM HRAK+LP RT RFNECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 472 DNDIVLFNRQPSLHRISIMCHRAKILPWRTLRFNECVCTPYNADFDGDEMNLHVPQTEEA 531

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE L              +LM +  NL TPR G+++IA TQDF+T  YLLT K+     
Sbjct: 532 RAECL--------------MLMHSAKNLQTPRTGQMIIAETQDFLTTSYLLTSKDFVIEE 577

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              M+ A       ++I                +++   +WTGKQ++ L LKPN+   VN
Sbjct: 578 EDMMQWACWFHNAGTEI----------DLPTPAYLKPKKLWTGKQLYGLALKPNKHEGVN 627

Query: 521 ANLKTKGRAYTANEEF-CHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            +L    + Y+   ++ C +D ++  +NS+LL G ++KS +GSG K  +F+++LRD+G  
Sbjct: 628 ISLDVPSKLYSKEGKWMCVKDGWICFKNSQLLCGQIEKSIIGSGNKTGLFHLILRDYGTL 687

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
            +   M  +SR  + +L + GFSIGI DVTP     Q
Sbjct: 688 ESAKIMAHISRFCARFLGDYGFSIGISDVTPSADLTQ 724



 Score =  190 bits (483), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 108/257 (42%), Positives = 163/257 (63%), Gaps = 7/257 (2%)

Query: 1146 EVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGH 1202
            E+ + ++ VF P +++I +KLD + I+ L LE  I+ ++  +   RG+      + +   
Sbjct: 1115 EIAKSVKIVFKPAEAYISVKLDFETIKQLELECTIEKVQDVLLNYRGLKLKDNQVIIRNK 1174

Query: 1203 SFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDN 1262
              L +    SS S    +  ++  L  V++ G++   RAVI++        ++LLVEG  
Sbjct: 1175 QKLRVYVDKSSTSLLFALNSLRNQLLEVIVCGIENTGRAVINKNK----GSFELLVEGSE 1230

Query: 1263 LRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVA 1322
            L  VM T GV G + +SN+   V K LGIEAARSTI++EIK VM+ +G+SID RH +L++
Sbjct: 1231 LLKVMGTPGVIGEETTSNHIAVVEKVLGIEAARSTIISEIKNVMDAYGLSIDVRHLLLLS 1290

Query: 1323 DLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGL 1382
            DLMT KG +LGITR+G++KMK+SV   ASFE T+DHLFDAA + + D I GVSE II+G 
Sbjct: 1291 DLMTFKGVILGITRYGISKMKDSVFTFASFERTNDHLFDAAVHSRKDEIKGVSESIIVGN 1350

Query: 1383 PMNVGTGLIKLLQAVPR 1399
             + +GTGL+++L   P+
Sbjct: 1351 QVGLGTGLMQILYDPPK 1367



 Score =  173 bits (438), Expect = 8e-40,   Method: Compositional matrix adjust.
 Identities = 102/237 (43%), Positives = 147/237 (62%), Gaps = 7/237 (2%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ I TPI+TA L    D+  ARIVKGR+E T L E+ + ++ VF P +
Sbjct: 1069 GVPRIKEIINASKKIQTPIVTAKLVNSQDVTSARIVKGRIEATRLKEIAKSVKIVFKPAE 1128

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFLILKPKDSSKSF 880
            ++I +KLD + I+ L LE  I+ ++  +   RG+      + +     L +    SS S 
Sbjct: 1129 AYISVKLDFETIKQLELECTIEKVQDVLLNYRGLKLKDNQVIIRNKQKLRVYVDKSSTSL 1188

Query: 881  NSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
               +  ++  L  V++ G++   RAVI++        ++LLVEG  L  VM T GV G +
Sbjct: 1189 LFALNSLRNQLLEVIVCGIENTGRAVINKNK----GSFELLVEGSELLKVMGTPGVIGEE 1244

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SN+   V K LGIEAARSTI++EIK VM+ +G+SID RH +L++DLMT KG +LG
Sbjct: 1245 TTSNHIAVVEKVLGIEAARSTIISEIKNVMDAYGLSIDVRHLLLLSDLMTFKGVILG 1301



 Score =  165 bits (417), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 90/259 (34%), Positives = 149/259 (57%), Gaps = 13/259 (5%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           I+ T+  ++ + ++S  ++    L+ Q   R P P+G+LDRR+G     + C TCG+ + 
Sbjct: 37  IQFTMFSQEEMNRESEFEVTEHFLF-QPNTRKPNPNGVLDRRLGVCDSLSVCETCGKRIE 95

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALS 202
           +C GHF  I+L LPVFHIG+FR +I +LQ +CKN  C R+LL  E+   +  ++RN    
Sbjct: 96  ECSGHFAVINLELPVFHIGFFRPIIQVLQCVCKN--CNRILLTNEERDFYLRRMRNKKTD 153

Query: 203 YLVRKSLKKKILETTKK-VSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLL 261
            + R  L + ++   +K  + CPHC  ING +KK G L++ H+KY      +D  + ++ 
Sbjct: 154 TVARTYLVRALIAQCRKHYNSCPHCNAINGSIKKYGNLRLVHDKY-----HRDPTITEMN 208

Query: 262 AEYN---EAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDL 318
             Y+   E++K + +I A       + L+P +VL +F ++  EDI  +  + + + P ++
Sbjct: 209 EFYDGFEESIKLDKDINAFVN-NAQEDLDPRKVLSIFRSLIREDIETMDFDPDNAPPENM 267

Query: 319 ILTRLLVPPNCIRPSVISD 337
           ILT + VPP  IRPSV  D
Sbjct: 268 ILTSVPVPPIAIRPSVAMD 286



 Score =  106 bits (264), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 50/67 (74%), Positives = 58/67 (86%), Gaps = 1/67 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV+NSFF+GL  TEFFFHTMGGREGLVD+AVKTAETGYMQRRL+K+LEDL V Y
Sbjct: 840 TPQAKGFVKNSFFTGLNATEFFFHTMGGREGLVDSAVKTAETGYMQRRLMKALEDLHVHY 899

Query: 668 DMSFDAA 674
           D +  +A
Sbjct: 900 DGTVRSA 906



 Score = 47.8 bits (112), Expect = 0.053,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 30/48 (62%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIA 68
           +LM +  NL TPR G+++IA TQDF+T  YLLT K+        M+ A
Sbjct: 537 MLMHSAKNLQTPRTGQMIIAETQDFLTTSYLLTSKDFVIEEEDMMQWA 584



 Score = 41.6 bits (96), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 20/43 (46%), Positives = 29/43 (67%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPR 710
            D  FDAA + + D I GVSE II+G  + +GTGL+++L   P+
Sbjct: 1325 DHLFDAAVHSRKDEIKGVSESIIVGNQVGLGTGLMQILYDPPK 1367


>gi|302808041|ref|XP_002985715.1| hypothetical protein SELMODRAFT_446351 [Selaginella moellendorffii]
 gi|300146624|gb|EFJ13293.1| hypothetical protein SELMODRAFT_446351 [Selaginella moellendorffii]
          Length = 1393

 Score =  251 bits (642), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 121/272 (44%), Positives = 171/272 (62%), Gaps = 25/272 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIM HRA+V+P RT RFNE VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 468 DGDIVLFNRQPSLHRMSIMCHRARVMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEA 527

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL               LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+++ F++R
Sbjct: 528 RTEAL--------------TLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRRDTFYDR 573

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q   + S +      I                 ++   +WTGKQ+F ++++P+    V 
Sbjct: 574 GQFALMCSYMGDAVEHI----------DLPTPAILKPVELWTGKQLFGVLIRPSARIKVF 623

Query: 521 ANLKTKGRAY-TANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            N     + +    E  C +D YV  +NSEL+ G + K TLG+G K  +F +LLRD+GE 
Sbjct: 624 LNFVVCEKNHKKGTETMCPKDGYVFFKNSELICGQLGKGTLGNGSKDGLFTVLLRDYGEQ 683

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
            A + M RL+++++ ++ N GFSIGI DV PG
Sbjct: 684 AAASCMNRLAKLSARWIGNHGFSIGIDDVQPG 715



 Score =  232 bits (591), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 127/277 (45%), Positives = 180/277 (64%), Gaps = 14/277 (5%)

Query: 1145 GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISG------HLT 1198
            G+V + I+ V  P  +F+ IKLDMDRI  L L++  +++   + +   I        H+ 
Sbjct: 1123 GDVAKSIKIVLRPGQAFVSIKLDMDRIYSLQLDIRAETVAEAVLKFPKIKSMKLKEQHVK 1182

Query: 1199 VSG-HSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLL 1257
            V+   S  +  P+   K     ++ ++ +LP V++KG+  + RAVI++E      KY LL
Sbjct: 1183 VNDDRSISLTTPESDRKKMLFALHSLQNMLPKVIVKGIPTVERAVINQEK----GKYNLL 1238

Query: 1258 VEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRH 1317
            VEG NL+ VM T GV G + +SN+ +E  + LGIEAAR+ I+ EI+  M +HGMSID RH
Sbjct: 1239 VEGTNLKAVMGTEGVDGRETTSNHIFETVEVLGIEAARNGIIKEIQYTMGSHGMSIDQRH 1298

Query: 1318 PMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSEC 1377
             ML+AD+MT +GE+LGITR G+AKMK+SVL LASFE T+DHLF A+ +G+TD I GVSEC
Sbjct: 1299 MMLLADVMTYRGEILGITRFGMAKMKDSVLMLASFEKTTDHLFAASVHGRTDQIEGVSEC 1358

Query: 1378 IIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEF 1414
            IIMG+PM +GTGL K+ Q V R   +P+ +    P F
Sbjct: 1359 IIMGIPMPLGTGLFKVRQKVGR---IPKLIYGPPPLF 1392



 Score =  202 bits (514), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 111/241 (46%), Positives = 157/241 (65%), Gaps = 11/241 (4%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA L  + D+  ARIVKGR+E+T LG+V + I+ V  P  
Sbjct: 1078 GVPRIKEIINASKKISTPIITAKLVSENDVKAARIVKGRIEKTALGDVAKSIKIVLRPGQ 1137

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISG------HLTVS-GHSFLILKPKDS 876
            +F+ IKLDMDRI  L L++  +++   + +   I        H+ V+   S  +  P+  
Sbjct: 1138 AFVSIKLDMDRIYSLQLDIRAETVAEAVLKFPKIKSMKLKEQHVKVNDDRSISLTTPESD 1197

Query: 877  SKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGV 936
             K     ++ ++ +LP V++KG+  + RAVI++E      KY LLVEG NL+ VM T GV
Sbjct: 1198 RKKMLFALHSLQNMLPKVIVKGIPTVERAVINQEK----GKYNLLVEGTNLKAVMGTEGV 1253

Query: 937  KGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL 996
             G + +SN+ +E  + LGIEAAR+ I+ EI+  M +HGMSID RH ML+AD+MT +GE+L
Sbjct: 1254 DGRETTSNHIFETVEVLGIEAARNGIIKEIQYTMGSHGMSIDQRHMMLLADVMTYRGEIL 1313

Query: 997  G 997
            G
Sbjct: 1314 G 1314



 Score =  194 bits (494), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 109/249 (43%), Positives = 155/249 (62%), Gaps = 11/249 (4%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + V + + +QI   +LY Q P+R P+P+G+LD R+GT+ K+  CTTC   L+DC GHFGY
Sbjct: 43  EEVTKTAEVQIFEHSLY-QLPERKPLPYGVLDTRLGTSNKKGQCTTCDGKLADCPGHFGY 101

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNP-TCARVLLGEEKAAGFRAKLRNPALSYLVRKSL 209
           I L LPVFHIGYF+ +I ILQ ICK   +   V+  +E+   ++ +++NP    L +K  
Sbjct: 102 IKLELPVFHIGYFKDIIVILQCICKASFSLLEVVASQEERQKWQRRMQNPRSEILRKKEY 161

Query: 210 KKKILETTKKVSVCPHCGEINGVVKKCG-LLKISHEKYKNRTKKKDAIVEDLLAEYNEAV 268
            KKI +  KKV  CP CG+INGVVKK G  LKI H+KY     K     E++  ++++AV
Sbjct: 162 LKKINDLCKKVRACPRCGDINGVVKKLGSTLKIIHDKY----AKNYEAFEEMAHKFDDAV 217

Query: 269 KFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPN 328
           K N E++ + K  + + L PL+VL LFE I  ED  +L +   + +P  LI+  + VPP 
Sbjct: 218 KVNKEMKGYMK-NIQEDLTPLKVLGLFEKIIGEDCVVLDL---VDRPEQLIVQHMPVPPV 273

Query: 329 CIRPSVISD 337
            IRPSV  D
Sbjct: 274 AIRPSVEMD 282



 Score =  109 bits (273), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 67/133 (50%), Positives = 81/133 (60%), Gaps = 11/133 (8%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D TP  +GFV NSF+SGLT TEF FHTMGGREGLVDTAVKTAETGYM RRL+K+LEDL  
Sbjct: 834 DKTPQAKGFVANSFYSGLTATEFIFHTMGGREGLVDTAVKTAETGYMSRRLMKALEDLSC 893

Query: 666 QYDMSFDAA-------FYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPR--SEPVPR 716
           QYD +   +        YG  D +  VS     G P+N+   L+K     PR  +  +P 
Sbjct: 894 QYDGTVRNSSGVIVQLIYGD-DSMDPVSMEGQNGTPLNLDRVLMKAKATCPRGTTPALPP 952

Query: 717 TLLFDNPEFHFPQ 729
           + L+   E  F Q
Sbjct: 953 SELWKIVESKFSQ 965



 Score = 83.2 bits (204), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 60/161 (37%), Positives = 88/161 (54%), Gaps = 29/161 (18%)

Query: 998  NGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSE---NFVRDIK 1054
            NGTP+ L R+L    A     + P+L   E+  +    ++SK F QD SE    F+  ++
Sbjct: 925  NGTPLNLDRVLMKAKATCPRGTTPALPPSELWKI----VESK-FSQDGSECSTAFLDSLR 979

Query: 1055 KFL-EEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEA-------- 1105
            KFL +EF   ++++S + ++S PL        D  G+  + N   +     +        
Sbjct: 980  KFLRKEF---DTISSTRKRLSLPL--------DDFGNVDDENVAANVSGLTSRQLEVFLN 1028

Query: 1106 -CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
             C  +Y R +++P TAVGA+ AQSIGEPGTQMTLKTFHFAG
Sbjct: 1029 TCIGRYHRKKLDPGTAVGAIGAQSIGEPGTQMTLKTFHFAG 1069



 Score = 57.0 bits (136), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 29/58 (50%), Positives = 38/58 (65%), Gaps = 3/58 (5%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEF 725
            D  F A+ +G+TD I GVSECIIMG+PM +GTGL K+ Q V R   +P+ +    P F
Sbjct: 1338 DHLFAASVHGRTDQIEGVSECIIMGIPMPLGTGLFKVRQKVGR---IPKLIYGPPPLF 1392



 Score = 56.6 bits (135), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/42 (50%), Positives = 35/42 (83%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 63
           LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+++ F++R Q
Sbjct: 534 LMGVQNNLCTPKNGEILVASTQDFLTSSFLITRRDTFYDRGQ 575


>gi|237842187|ref|XP_002370391.1| DNA-directed RNA polymerase III largest subunit, putative
           [Toxoplasma gondii ME49]
 gi|211968055|gb|EEB03251.1| DNA-directed RNA polymerase III largest subunit, putative
           [Toxoplasma gondii ME49]
 gi|221502846|gb|EEE28560.1| DNA-directed RNA polymerase III largest subunit, putative
           [Toxoplasma gondii VEG]
          Length = 1746

 Score =  251 bits (641), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 131/277 (47%), Positives = 171/277 (61%), Gaps = 32/277 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + DVVLFNRQPSLH++SIMAHRA+V+P RTFRFNECVC+PYNADFDGDEMN+HLPQT EA
Sbjct: 529 NGDVVLFNRQPSLHRMSIMAHRARVMPWRTFRFNECVCSPYNADFDGDEMNLHLPQTHEA 588

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL               LM   +NLVTP+NGE LIAATQDF++  Y+LT K+ F  R
Sbjct: 589 RAEAL--------------YLMGVVNNLVTPKNGEPLIAATQDFLSSSYMLTHKDVFLTR 634

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q   I S      S +             P   ++   +WTGKQ+ S++L+PNR+  V 
Sbjct: 635 DQFCLICSYFTDGLSRV----------DLPPPTILKPVELWTGKQVISVLLRPNRNSFVM 684

Query: 521 ANLKTKGRAYTANE-------EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILL 573
            N + K R ++A           C  D+YVI R+SEL+AG + K  LG   K  +F+ L+
Sbjct: 685 VNFQLKEREFSAARIPPGEAPFMCPSDAYVIFRHSELVAGCIGKKVLGD-AKFGLFFHLI 743

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           RD     A   M R++++++ +  NRG +IGI DVTP
Sbjct: 744 RDNSPAQAAACMGRIAKLSARWFANRGMTIGIDDVTP 780



 Score =  214 bits (546), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 134/351 (38%), Positives = 194/351 (55%), Gaps = 66/351 (18%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKT---------------------------- 1140
            KYV+A  E   AVGA+ AQSIGEPGTQMTLKT                            
Sbjct: 1370 KYVKAISEAGEAVGAMGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIINAAQKI 1429

Query: 1141 --------------FHFA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLL 1174
                          +++A             E C YI+EV+ PD +++++KLD   IR L
Sbjct: 1430 QTPIIVVPLVNDEDYNYAVMVKNRIEKTLLSECCSYIKEVYAPDGAWLVVKLDQHTIRKL 1489

Query: 1175 HLEVDIDSIRYCIERTRGISGHLTVSGHSFLIL---KPKDSSKSFNSKMYQMKQL---LP 1228
             L+++ ++++  I R   ++  + ++ +S  I+   K +      N   +Q++ L   L 
Sbjct: 1490 FLDINANTVKDAILRQTAVN-KVRITKNSVEIINEWKVRVMPPGGNQIFFQLQALKLGLL 1548

Query: 1229 SVVIKGVQGINRAVIHEEDVEGVTK-----YKLLVEGDNLRDVMATYGVKGVKCSSNNTY 1283
            ++V+ G + + R VI  E VE   K     Y L VEG  LRDVM T GVK ++ +SN+  
Sbjct: 1549 NIVLCGHKDVKRGVIKCEQVEQPDKTKKTVYGLAVEGYGLRDVMGTQGVKALQATSNHVM 1608

Query: 1284 EVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMK 1343
            EV + LGIEAAR+ I++EI+  M+ + M ID RH  L+ D+MT +GEVLGI R G+ KM+
Sbjct: 1609 EVAQILGIEAARAVIISEIRKCMDAYSMDIDCRHMTLLGDVMTFRGEVLGINRFGIQKMR 1668

Query: 1344 ESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
             S L LASFE T++HLF+AA + + D + GVSECIIMG  +++GTG   LL
Sbjct: 1669 ASTLMLASFEETNEHLFEAAVHHRADPVKGVSECIIMGKQVSLGTGSFDLL 1719



 Score =  179 bits (455), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 103/245 (42%), Positives = 153/245 (62%), Gaps = 12/245 (4%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ I TPII   L  D D +YA +VK R+E+T L E C YI+EV+ PD 
Sbjct: 1415 GVPRIKEIINAAQKIQTPIIVVPLVNDEDYNYAVMVKNRIEKTLLSECCSYIKEVYAPDG 1474

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLIL---KPKDSSKSF 880
            +++++KLD   IR L L+++ ++++  I R   ++  + ++ +S  I+   K +      
Sbjct: 1475 AWLVVKLDQHTIRKLFLDINANTVKDAILRQTAVN-KVRITKNSVEIINEWKVRVMPPGG 1533

Query: 881  NSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTK-----YKLLVEGDNLRDVMA 932
            N   +Q++ L   L ++V+ G + + R VI  E VE   K     Y L VEG  LRDVM 
Sbjct: 1534 NQIFFQLQALKLGLLNIVLCGHKDVKRGVIKCEQVEQPDKTKKTVYGLAVEGYGLRDVMG 1593

Query: 933  TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK 992
            T GVK ++ +SN+  EV + LGIEAAR+ I++EI+  M+ + M ID RH  L+ D+MT +
Sbjct: 1594 TQGVKALQATSNHVMEVAQILGIEAARAVIISEIRKCMDAYSMDIDCRHMTLLGDVMTFR 1653

Query: 993  GEVLG 997
            GEVLG
Sbjct: 1654 GEVLG 1658



 Score =  139 bits (349), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 87/258 (33%), Positives = 137/258 (53%), Gaps = 40/258 (15%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           ++  V   + + + S ++I ++ +Y  +   TP P+G+LD R+G N+ ++ C TCG  L 
Sbjct: 115 VQFDVLSGEEISRYSEVEIHNREIYV-NMTNTPHPYGVLDLRLGPNKSDSRCQTCGHTLL 173

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALS 202
            C GH+GY+DL  PV+H+GYF+ V+ IL  ICK  TCA +L   E+      ++R     
Sbjct: 174 QCTGHWGYMDLQAPVYHVGYFKYVLQILYCICK--TCAALLQPPEQKEKLLLRIRRHQSD 231

Query: 203 YLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKY---KNRTKKKDA---I 256
            +V++ L K+ +E  KKVS C  CG   GV+K+  ++K S +++   ++  K K+     
Sbjct: 232 PIVKRLLFKRTVEACKKVSKCFECGAPQGVLKR--VVKPSLDQFMKIRHVVKSKEGRAMT 289

Query: 257 VEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPS 316
           VED                          L+PL V  L E I   +  +L    ++  P 
Sbjct: 290 VED-------------------------DLDPLYVKNLLERIRPSECEIL----DIVSPE 320

Query: 317 DLILTRLLVPPNCIRPSV 334
            L+L+RLLVPP+CIRPSV
Sbjct: 321 KLLLSRLLVPPSCIRPSV 338



 Score =  102 bits (255), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 46/59 (77%), Positives = 53/59 (89%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
           +GFV +SF+SGL P EFFFHTM GREGLVDTAVKTAETGYMQRRL+K+LEDL ++YD S
Sbjct: 906 RGFVASSFYSGLQPDEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKALEDLSIRYDNS 964



 Score = 57.4 bits (137), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 28/53 (52%), Positives = 34/53 (64%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           LM   +NLVTP+NGE LIAATQDF++  Y+LT K+ F  R Q   I S    G
Sbjct: 595 LMGVVNNLVTPKNGEPLIAATQDFLSSSYMLTHKDVFLTRDQFCLICSYFTDG 647


>gi|221482258|gb|EEE20613.1| DNA-directed RNA polymerase III largest subunit, putative
           [Toxoplasma gondii GT1]
          Length = 1747

 Score =  251 bits (641), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 131/277 (47%), Positives = 171/277 (61%), Gaps = 32/277 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + DVVLFNRQPSLH++SIMAHRA+V+P RTFRFNECVC+PYNADFDGDEMN+HLPQT EA
Sbjct: 530 NGDVVLFNRQPSLHRMSIMAHRARVMPWRTFRFNECVCSPYNADFDGDEMNLHLPQTHEA 589

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL               LM   +NLVTP+NGE LIAATQDF++  Y+LT K+ F  R
Sbjct: 590 RAEAL--------------YLMGVVNNLVTPKNGEPLIAATQDFLSSSYMLTHKDVFLTR 635

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q   I S      S +             P   ++   +WTGKQ+ S++L+PNR+  V 
Sbjct: 636 DQFCLICSYFTDGLSRV----------DLPPPTILKPVELWTGKQVISVLLRPNRNSFVM 685

Query: 521 ANLKTKGRAYTANE-------EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILL 573
            N + K R ++A           C  D+YVI R+SEL+AG + K  LG   K  +F+ L+
Sbjct: 686 VNFQLKEREFSAARIPPGEAPFMCPSDAYVIFRHSELVAGCIGKKVLGD-AKFGLFFHLI 744

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           RD     A   M R++++++ +  NRG +IGI DVTP
Sbjct: 745 RDNSPAQAAACMGRIAKLSARWFANRGMTIGIDDVTP 781



 Score =  214 bits (545), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 134/351 (38%), Positives = 194/351 (55%), Gaps = 66/351 (18%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKT---------------------------- 1140
            KYV+A  E   AVGA+ AQSIGEPGTQMTLKT                            
Sbjct: 1371 KYVKAISEAGEAVGAMGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIINAAQKI 1430

Query: 1141 --------------FHFA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLL 1174
                          +++A             E C YI+EV+ PD +++++KLD   IR L
Sbjct: 1431 QTPIIVVPLVNDEDYNYAVMVKNRIEKTLLSECCSYIKEVYAPDGAWLVVKLDQHTIRKL 1490

Query: 1175 HLEVDIDSIRYCIERTRGISGHLTVSGHSFLIL---KPKDSSKSFNSKMYQMKQL---LP 1228
             L+++ ++++  I R   ++  + ++ +S  I+   K +      N   +Q++ L   L 
Sbjct: 1491 FLDINANTVKDAILRQTAVN-KVRITKNSVEIINEWKVRVMPPGGNQIFFQLQALKLGLL 1549

Query: 1229 SVVIKGVQGINRAVIHEEDVEGVTK-----YKLLVEGDNLRDVMATYGVKGVKCSSNNTY 1283
            ++V+ G + + R VI  E VE   K     Y L VEG  LRDVM T GVK ++ +SN+  
Sbjct: 1550 NIVLCGHKDVKRGVIKCEQVEQPDKTKKTVYGLAVEGYGLRDVMGTQGVKALQATSNHVM 1609

Query: 1284 EVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMK 1343
            EV + LGIEAAR+ I++EI+  M+ + M ID RH  L+ D+MT +GEVLGI R G+ KM+
Sbjct: 1610 EVAQILGIEAARAVIISEIRKCMDAYSMDIDCRHMTLLGDVMTFRGEVLGINRFGIQKMR 1669

Query: 1344 ESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
             S L LASFE T++HLF+AA + + D + GVSECIIMG  +++GTG   LL
Sbjct: 1670 ASTLMLASFEETNEHLFEAAVHHRADPVKGVSECIIMGKQVSLGTGSFDLL 1720



 Score =  179 bits (455), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 103/245 (42%), Positives = 153/245 (62%), Gaps = 12/245 (4%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ I TPII   L  D D +YA +VK R+E+T L E C YI+EV+ PD 
Sbjct: 1416 GVPRIKEIINAAQKIQTPIIVVPLVNDEDYNYAVMVKNRIEKTLLSECCSYIKEVYAPDG 1475

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLIL---KPKDSSKSF 880
            +++++KLD   IR L L+++ ++++  I R   ++  + ++ +S  I+   K +      
Sbjct: 1476 AWLVVKLDQHTIRKLFLDINANTVKDAILRQTAVN-KVRITKNSVEIINEWKVRVMPPGG 1534

Query: 881  NSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTK-----YKLLVEGDNLRDVMA 932
            N   +Q++ L   L ++V+ G + + R VI  E VE   K     Y L VEG  LRDVM 
Sbjct: 1535 NQIFFQLQALKLGLLNIVLCGHKDVKRGVIKCEQVEQPDKTKKTVYGLAVEGYGLRDVMG 1594

Query: 933  TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK 992
            T GVK ++ +SN+  EV + LGIEAAR+ I++EI+  M+ + M ID RH  L+ D+MT +
Sbjct: 1595 TQGVKALQATSNHVMEVAQILGIEAARAVIISEIRKCMDAYSMDIDCRHMTLLGDVMTFR 1654

Query: 993  GEVLG 997
            GEVLG
Sbjct: 1655 GEVLG 1659



 Score =  139 bits (350), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 93/293 (31%), Positives = 148/293 (50%), Gaps = 55/293 (18%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           ++  V   + + + S ++I ++ +Y  +   TP P+G+LD R+G N+ ++ C TCG  L 
Sbjct: 116 VQFDVLSGEEISRYSEVEIHNREIYV-NMTNTPHPYGVLDLRLGPNKSDSRCQTCGHTLL 174

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALS 202
            C GH+GY+DL  PV+H+GYF+ V+ IL  ICK  TCA +L   E+      ++R     
Sbjct: 175 QCTGHWGYMDLQAPVYHVGYFKYVLQILYCICK--TCAALLQPPEQKEKLLLRIRRHQSD 232

Query: 203 YLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKY---KNRTKKKDA---I 256
            +V++ L K+ +E  KKVS C  CG   GV+K+  ++K S +++   ++  K K+     
Sbjct: 233 PIVKRLLFKRTVEACKKVSKCFECGAPQGVLKR--VVKPSLDQFMKIRHVVKSKEGRAMT 290

Query: 257 VEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPS 316
           VED                          L+PL V  L E I   +  +L    ++  P 
Sbjct: 291 VED-------------------------DLDPLYVKNLLERIRPSECEIL----DIVSPE 321

Query: 317 DLILTRLLVPPNCIRPS---------------VISDLKSDNDVVLFNRQPSLH 354
            L+L+RLLVPP+CIRPS               V+SD+   N+V+  + Q   H
Sbjct: 322 KLLLSRLLVPPSCIRPSVTIGEQGTTEDDLTCVLSDIAELNNVLQSHVQAGFH 374



 Score =  102 bits (255), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 46/59 (77%), Positives = 53/59 (89%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
           +GFV +SF+SGL P EFFFHTM GREGLVDTAVKTAETGYMQRRL+K+LEDL ++YD S
Sbjct: 907 RGFVASSFYSGLQPDEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKALEDLSIRYDNS 965



 Score = 57.4 bits (137), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 28/53 (52%), Positives = 34/53 (64%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           LM   +NLVTP+NGE LIAATQDF++  Y+LT K+ F  R Q   I S    G
Sbjct: 596 LMGVVNNLVTPKNGEPLIAATQDFLSSSYMLTHKDVFLTRDQFCLICSYFTDG 648


>gi|392592712|gb|EIW82038.1| beta and beta-prime subunits of DNA dependent RNA-polymerase
           [Coniophora puteana RWD-64-598 SS2]
          Length = 1407

 Score =  250 bits (639), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 133/283 (46%), Positives = 180/283 (63%), Gaps = 35/283 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + DVVLFNRQPSLHKLSIM HR KV P R+FR NECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 449 NGDVVLFNRQPSLHKLSIMCHRVKVRPWRSFRLNECVCGPYNADFDGDEMNLHVPQTEEA 508

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL               LM+ K NLVTPRNGE +IAA QDFIT  YL+++++ FF+R
Sbjct: 509 RTEALE--------------LMSVKHNLVTPRNGEPVIAAIQDFITASYLISRRDTFFDR 554

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
               +I   L AD      I     W+   PV       +WTGKQIF+++++PN+   + 
Sbjct: 555 RSFTQICCYL-ADGDLQIDIPPPTIWK---PV------RLWTGKQIFNVLMRPNKQSKIF 604

Query: 521 ANLKTKGR----AYTAN-------EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVF 569
            N+++K      A  A+        +    D ++++ NSE++ G MDK+T+GSG K ++F
Sbjct: 605 VNVESKCNKPQDAKAADYPRMKPLPDLSPNDGWLVVVNSEIMCGVMDKATVGSGKKKSIF 664

Query: 570 YILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
            ++LRD+G   A  AM R++++ + YL N GFS+GI DV PG+
Sbjct: 665 GVILRDYGPHEAAAAMNRVAKLCARYLANCGFSLGINDVIPGR 707



 Score =  216 bits (550), Expect = 8e-53,   Method: Compositional matrix adjust.
 Identities = 149/379 (39%), Positives = 204/379 (53%), Gaps = 78/379 (20%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIG--------------------------------- 1130
            E    KYVRA+IEP + VGA+ AQSIG                                 
Sbjct: 1034 ELSWSKYVRAKIEPGSTVGAVGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIIN 1093

Query: 1131 -------------------EPGTQMT---LKTFHFAGEVCEYIEEVFVPDDSFILIKLDM 1168
                               EP  ++    L+  H  G+V   +EE + P+ ++I + +DM
Sbjct: 1094 AAKAISTPIISCKLVTSDSEPSARIVKGRLEKTHL-GDVASLLEEAWAPEYTYIGVIVDM 1152

Query: 1169 DRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNS------KMYQ 1222
            D IR L LE+ +D I++ I   R     L +   S  ++  +   + +        ++ +
Sbjct: 1153 DAIRKLQLELTLDDIKWAIVAAR----KLKIKQESITVIPRRSRLRIYIDGPDKYYRLRE 1208

Query: 1223 MKQLLPSVVIKGVQGINRAVIH---EEDVEGVTKYK-LLVEGDNLRDVMATYGVKGVKCS 1278
            +K+LL  VV+KGV  I+RAVI+   ++D +G    K LLVEG  L+ VM T G+ G   +
Sbjct: 1209 LKRLLSDVVVKGVSTISRAVINIKEKDDAKGKKGDKELLVEGYGLQKVMITEGIVGEHTT 1268

Query: 1279 SNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK----GEVLGI 1334
            SN+  E  + LGIEAAR TI+ EI+  M  HGM+ID RH ML+ D+M+ K    GEVLGI
Sbjct: 1269 SNHVIETSQVLGIEAARRTIINEIQTTMSAHGMTIDPRHVMLLGDIMSYKACCSGEVLGI 1328

Query: 1335 TRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLP-MNVGTGLIKL 1393
            TR G+AKMK+SVL LASFE T+DHLFDAA +G+ D I+GVSE IIMG P  N GT +  L
Sbjct: 1329 TRFGVAKMKDSVLMLASFEKTTDHLFDAAAFGKNDSIAGVSESIIMGNPAANCGTSMPAL 1388

Query: 1394 -LQAVPRSEPVPRTLLFDN 1411
             L A P S+  PR LLF+ 
Sbjct: 1389 FLPAPPISK--PRKLLFEG 1405



 Score =  191 bits (485), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 106/253 (41%), Positives = 145/253 (57%), Gaps = 17/253 (6%)

Query: 97  SHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP 156
           S  Q+  ++LY     R P+  G+LDRR+GT +K A C TCG +  DCVGH+ YI L +P
Sbjct: 30  SEFQVTHRDLYTPT-DRLPVKDGVLDRRLGTTEKSAFCETCGLSSVDCVGHYAYIKLAVP 88

Query: 157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILET 216
           V+HIGYF+  I ILQ+ICK  TCARVLL E     +  + R P L  + R++L K +   
Sbjct: 89  VYHIGYFKHSIAILQAICK--TCARVLLEEPDRRTYLKRFRRPNLENIQRQALCKAVNTM 146

Query: 217 TKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEA 276
            +KV  CP+C   NG VKK G LKI H+K+  R KK    VE+ + ++  +  F P +EA
Sbjct: 147 ARKVVYCPYCSATNGAVKKAGALKIIHDKF--RAKK---TVEE-MEKWKRS--FAPAVEA 198

Query: 277 HKKFGLI------QTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCI 330
            K+ G+       + +NPL  L LF+ +  ED  LL +     +P   I   + VPP CI
Sbjct: 199 QKELGIYLNKAVHEDINPLRALDLFKRMSNEDCELLGLKPSFGRPEQYIWQYISVPPVCI 258

Query: 331 RPSVISDLKSDND 343
           RPSV  D  S+ D
Sbjct: 259 RPSVAQDGASNED 271



 Score =  177 bits (450), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 108/248 (43%), Positives = 152/248 (61%), Gaps = 18/248 (7%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ ISTPII+  L        ARIVKGRLE+T LG+V   +EE + P+ 
Sbjct: 1084 GVPRIKEIINAAKAISTPIISCKLVTSDSEPSARIVKGRLEKTHLGDVASLLEEAWAPEY 1143

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNS- 882
            ++I + +DMD IR L LE+ +D I++ I   R     L +   S  ++  +   + +   
Sbjct: 1144 TYIGVIVDMDAIRKLQLELTLDDIKWAIVAAR----KLKIKQESITVIPRRSRLRIYIDG 1199

Query: 883  -----KMYQMKQLLPSVVIKGVQGINRAVIH---EEDVEGVTKYK-LLVEGDNLRDVMAT 933
                 ++ ++K+LL  VV+KGV  I+RAVI+   ++D +G    K LLVEG  L+ VM T
Sbjct: 1200 PDKYYRLRELKRLLSDVVVKGVSTISRAVINIKEKDDAKGKKGDKELLVEGYGLQKVMIT 1259

Query: 934  YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK- 992
             G+ G   +SN+  E  + LGIEAAR TI+ EI+  M  HGM+ID RH ML+ D+M+ K 
Sbjct: 1260 EGIVGEHTTSNHVIETSQVLGIEAARRTIINEIQTTMSAHGMTIDPRHVMLLGDIMSYKA 1319

Query: 993  ---GEVLG 997
               GEVLG
Sbjct: 1320 CCSGEVLG 1327



 Score =  108 bits (270), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 49/68 (72%), Positives = 56/68 (82%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV+NSF+SGL PTEF FH + GREGLVDTAVKTAETGYMQRRL+K+LEDL  QYD+
Sbjct: 829 PSKGFVRNSFYSGLLPTEFLFHAISGREGLVDTAVKTAETGYMQRRLMKALEDLTTQYDL 888

Query: 670 SFDAAFYG 677
           S   A  G
Sbjct: 889 SVRTATGG 896



 Score = 60.1 bits (144), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 28/53 (52%), Positives = 37/53 (69%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           LM+ K NLVTPRNGE +IAA QDFIT  YL+++++ FF+R    +I   L  G
Sbjct: 515 LMSVKHNLVTPRNGEPVIAAIQDFITASYLISRRDTFFDRRSFTQICCYLADG 567



 Score = 47.4 bits (111), Expect = 0.064,   Method: Compositional matrix adjust.
 Identities = 30/57 (52%), Positives = 36/57 (63%), Gaps = 4/57 (7%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLP-MNVGTGLIKL-LQAVPRSEPVPRTLLFDN 722
            D  FDAA +G+ D I+GVSE IIMG P  N GT +  L L A P S+  PR LLF+ 
Sbjct: 1351 DHLFDAAAFGKNDSIAGVSESIIMGNPAANCGTSMPALFLPAPPISK--PRKLLFEG 1405


>gi|167385199|ref|XP_001737245.1| DNA-directed RNA polymerase III subunit RPC1 [Entamoeba dispar
           SAW760]
 gi|165900031|gb|EDR26493.1| DNA-directed RNA polymerase III subunit RPC1, putative [Entamoeba
           dispar SAW760]
          Length = 1379

 Score =  250 bits (639), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 124/277 (44%), Positives = 171/277 (61%), Gaps = 25/277 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND+VLFNRQPSLH++SIM H+AK+LP RT RFNECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 472 DNDIVLFNRQPSLHRISIMCHKAKILPWRTLRFNECVCTPYNADFDGDEMNLHVPQTEEA 531

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE L              +LM +  NL TPR G+++IA TQDF+T  YLLT K+     
Sbjct: 532 RAECL--------------MLMHSAKNLQTPRTGQMIIAETQDFLTTSYLLTSKDFVIEE 577

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              M+ A       ++I                +++   +WTGKQ++ L LKPN+   VN
Sbjct: 578 EDMMQWACWFHNAGTEI----------DLPTPAYLKPKKLWTGKQLYGLALKPNKHEGVN 627

Query: 521 ANLKTKGRAYTANEEF-CHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            +L    + Y+   ++ C +D ++  +NS+LL G ++KS +GSG K  +F+++LRD+G  
Sbjct: 628 ISLDVPSKLYSKEGKWMCVKDGWICFKNSQLLCGQIEKSIIGSGNKTGLFHLILRDYGTL 687

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
            +   M  +SR  + +L + GFSIGI DVTP     Q
Sbjct: 688 ESAKIMAHISRFCARFLGDYGFSIGISDVTPSADLTQ 724



 Score =  190 bits (482), Expect = 7e-45,   Method: Compositional matrix adjust.
 Identities = 109/257 (42%), Positives = 166/257 (64%), Gaps = 7/257 (2%)

Query: 1146 EVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGH 1202
            E+ + I+ VF P +++I +KLD + I+ L LE  I+ ++  +   RG+      + +   
Sbjct: 1115 EIAKSIKIVFKPAEAYISVKLDFETIKQLELECTIEKVQDVLLNYRGLKLKDNQVIIRNK 1174

Query: 1203 SFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDN 1262
              L +    +S S    +  ++  L  V++ G++   RAVI++   +G+  ++LLVEG  
Sbjct: 1175 QKLRVYVDKASTSLLFALNSLRNQLLEVIVCGIENTGRAVINKN--KGL--FELLVEGSE 1230

Query: 1263 LRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVA 1322
            L  VM T GV G + +SN+   V K LGIEAARSTI++EIK VM+ +G+SID RH +L++
Sbjct: 1231 LLKVMGTPGVIGEETTSNHIAVVEKVLGIEAARSTIISEIKNVMDAYGLSIDVRHLLLLS 1290

Query: 1323 DLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGL 1382
            DLMT KG +LGITR+G++KMK+SV   ASFE T+DHLFDAA + + D I GVSE II+G 
Sbjct: 1291 DLMTFKGVILGITRYGISKMKDSVFTFASFERTNDHLFDAAVHSRKDEIKGVSESIIVGN 1350

Query: 1383 PMNVGTGLIKLLQAVPR 1399
             + +GTGL+++L   P+
Sbjct: 1351 QVGLGTGLMQILYDPPK 1367



 Score =  173 bits (439), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 104/237 (43%), Positives = 150/237 (63%), Gaps = 7/237 (2%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ I TPI+TA L    DL  ARIVKGR+E T L E+ + I+ VF P +
Sbjct: 1069 GVPRIKEIINASKKIQTPIVTAKLVNSQDLTSARIVKGRIEATRLKEIAKSIKIVFKPAE 1128

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFLILKPKDSSKSF 880
            ++I +KLD + I+ L LE  I+ ++  +   RG+      + +     L +    +S S 
Sbjct: 1129 AYISVKLDFETIKQLELECTIEKVQDVLLNYRGLKLKDNQVIIRNKQKLRVYVDKASTSL 1188

Query: 881  NSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
               +  ++  L  V++ G++   RAVI++   +G+  ++LLVEG  L  VM T GV G +
Sbjct: 1189 LFALNSLRNQLLEVIVCGIENTGRAVINKN--KGL--FELLVEGSELLKVMGTPGVIGEE 1244

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SN+   V K LGIEAARSTI++EIK VM+ +G+SID RH +L++DLMT KG +LG
Sbjct: 1245 TTSNHIAVVEKVLGIEAARSTIISEIKNVMDAYGLSIDVRHLLLLSDLMTFKGVILG 1301



 Score =  166 bits (421), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 91/259 (35%), Positives = 150/259 (57%), Gaps = 13/259 (5%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           I+ T+  ++ + ++S  ++    L+ Q   R P P+G+LDRR+G     + C TCG+ + 
Sbjct: 37  IQFTMFSQEEMNRESEFEVTEHFLF-QPNTRKPNPNGVLDRRLGVCDSLSVCETCGKRIE 95

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALS 202
           +C GHF  I+L LPVFHIG+FR +I +LQ +CKN  C R+LL  E+   +  ++RN    
Sbjct: 96  ECSGHFAVINLELPVFHIGFFRPIIQVLQCVCKN--CNRILLTNEERDFYLRRMRNKKTD 153

Query: 203 YLVRKSLKKKILETTKK-VSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLL 261
            + R  L + ++   +K  + CPHC  ING +KK G L++ H+KY      +DA + ++ 
Sbjct: 154 TVARTYLVRALITQCRKHYNSCPHCNAINGSIKKYGNLRLVHDKY-----HRDATITEMN 208

Query: 262 AEYN---EAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDL 318
             Y+   E++K + +I A       + L+P +VL +F ++  EDI  +  + + + P ++
Sbjct: 209 EFYDGFEESIKLDKDINAFVD-NAQEDLDPRKVLSIFRSLIREDIETMDFDPDNAPPENM 267

Query: 319 ILTRLLVPPNCIRPSVISD 337
           ILT + VPP  IRPSV  D
Sbjct: 268 ILTSVPVPPIAIRPSVAMD 286



 Score =  106 bits (264), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 50/67 (74%), Positives = 58/67 (86%), Gaps = 1/67 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV+NSFF+GL  TEFFFHTMGGREGLVD+AVKTAETGYMQRRL+K+LEDL V Y
Sbjct: 840 TPQAKGFVKNSFFTGLNATEFFFHTMGGREGLVDSAVKTAETGYMQRRLMKALEDLHVHY 899

Query: 668 DMSFDAA 674
           D +  +A
Sbjct: 900 DGTVRSA 906



 Score = 59.3 bits (142), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/40 (65%), Positives = 31/40 (77%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            C++K +R+  E  T VGALA QS+GEP TQM LKTFHFAG
Sbjct: 1021 CQKKGLRSVCEAGTPVGALAGQSMGEPSTQMVLKTFHFAG 1060



 Score = 47.8 bits (112), Expect = 0.052,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 30/48 (62%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIA 68
           +LM +  NL TPR G+++IA TQDF+T  YLLT K+        M+ A
Sbjct: 537 MLMHSAKNLQTPRTGQMIIAETQDFLTTSYLLTSKDFVIEEEDMMQWA 584



 Score = 41.6 bits (96), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 20/43 (46%), Positives = 29/43 (67%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPR 710
            D  FDAA + + D I GVSE II+G  + +GTGL+++L   P+
Sbjct: 1325 DHLFDAAVHSRKDEIKGVSESIIVGNQVGLGTGLMQILYDPPK 1367


>gi|195399319|ref|XP_002058268.1| GJ15583 [Drosophila virilis]
 gi|194150692|gb|EDW66376.1| GJ15583 [Drosophila virilis]
          Length = 295

 Score =  250 bits (639), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 135/267 (50%), Positives = 183/267 (68%), Gaps = 9/267 (3%)

Query: 1145 GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCI--ERTRGISGHL-TVSG 1201
            GE+  Y+E V  P    ++I +D  RI++L L +D+DSI   I   R R   G L  V  
Sbjct: 17   GELSSYVELVCGPQSCHLVIGIDAARIKVLGLHIDLDSIMCSILKSRLRIKPGQLHAVPK 76

Query: 1202 HSFLILKPKDS-SKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEG 1260
             S ++++ + + + + N+++ ++   + +VV+ G+  I RAVI  +D      YKL +EG
Sbjct: 77   KSRIMVRVEATRNATINAELARLATTIQNVVVAGLPNIARAVIAVDDAHQPPTYKLCIEG 136

Query: 1261 DNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPML 1320
              LR+V+ATYGV G +  SNN  E+Y+TLGIEAAR+ IM+EI  VME HGMS+D+RH ML
Sbjct: 137  YGLREVIATYGVVGERTRSNNICEIYQTLGIEAARTIIMSEITDVMEGHGMSVDWRHIML 196

Query: 1321 VADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIM 1380
            +A  MT++GEVLGITRHGLAKM+ESV NLASFE T+DHLFDAA+YGQTD I+GVSE II+
Sbjct: 197  LASQMTARGEVLGITRHGLAKMRESVFNLASFEKTADHLFDAAYYGQTDAINGVSERIIL 256

Query: 1381 GLPMNVGTGLIKLLQ-----AVPRSEP 1402
            G+P  +GTG+ KLLQ      VP  EP
Sbjct: 257  GMPAGIGTGIFKLLQLHEDKQVPPIEP 283



 Score =  168 bits (426), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 93/209 (44%), Positives = 138/209 (66%), Gaps = 4/209 (1%)

Query: 793 LDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCI- 851
           +++AR VK R+E+TTLGE+  Y+E V  P    ++I +D  RI++L L +D+DSI   I 
Sbjct: 1   MEFARQVKARIEKTTLGELSSYVELVCGPQSCHLVIGIDAARIKVLGLHIDLDSIMCSIL 60

Query: 852 -ERTRGISGHL-TVSGHSFLILKPKDS-SKSFNSKMYQMKQLLPSVVIKGVQGINRAVIH 908
             R R   G L  V   S ++++ + + + + N+++ ++   + +VV+ G+  I RAVI 
Sbjct: 61  KSRLRIKPGQLHAVPKKSRIMVRVEATRNATINAELARLATTIQNVVVAGLPNIARAVIA 120

Query: 909 EEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKL 968
            +D      YKL +EG  LR+V+ATYGV G +  SNN  E+Y+TLGIEAAR+ IM+EI  
Sbjct: 121 VDDAHQPPTYKLCIEGYGLREVIATYGVVGERTRSNNICEIYQTLGIEAARTIIMSEITD 180

Query: 969 VMENHGMSIDFRHPMLVADLMTSKGEVLG 997
           VME HGMS+D+RH ML+A  MT++GEVLG
Sbjct: 181 VMEGHGMSVDWRHIMLLASQMTARGEVLG 209



 Score = 61.2 bits (147), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 30/51 (58%), Positives = 36/51 (70%), Gaps = 5/51 (9%)

Query: 668 DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ-----AVPRSEP 713
           D  FDAA+YGQTD I+GVSE II+G+P  +GTG+ KLLQ      VP  EP
Sbjct: 233 DHLFDAAYYGQTDAINGVSERIILGMPAGIGTGIFKLLQLHEDKQVPPIEP 283


>gi|357148941|ref|XP_003574945.1| PREDICTED: DNA-directed RNA polymerase III subunit rpc1-like
           [Brachypodium distachyon]
          Length = 1392

 Score =  250 bits (639), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 124/288 (43%), Positives = 176/288 (61%), Gaps = 36/288 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIM+HRA+++P RT RFNE VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 444 DGDIVLFNRQPSLHRMSIMSHRARIMPWRTLRFNESVCNPYNADFDGDEMNLHVPQTEEA 503

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL              +LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+K+ F++R
Sbjct: 504 RTEAL--------------MLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDNFYDR 549

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           +    + S L     +I                 ++   +WTGKQ+FS++++PN    V 
Sbjct: 550 SYFTLLCSYLGDAMENI----------DLPTPAIIKPLELWTGKQLFSVLVRPNACTKVY 599

Query: 521 ANLKTKGRAYTANEE------------FCHRDSYVILRNSELLAGSMDKSTLGSGGKANV 568
            NL  + + Y    E             C  D YV  RNSELL+G + K TLG+G K  +
Sbjct: 600 LNLTVEEKIYMKRRERDKNAVSVLEETMCPNDGYVYFRNSELLSGQVGKKTLGNGNKDGM 659

Query: 569 FYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           F +L+RD+    A + M RL++ ++ ++ N GFSIG+ DV PG+   Q
Sbjct: 660 FSVLVRDYNSHAAASCMNRLAKFSARFIGNHGFSIGVDDVQPGESLNQ 707



 Score =  239 bits (609), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 165/467 (35%), Positives = 247/467 (52%), Gaps = 76/467 (16%)

Query: 999  GTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQD-TSENFVRDIKKFL 1057
            G+P+ L +L   + A    R    LS + I+ + N+ L  ++      S+ F   + KF 
Sbjct: 915  GSPLNLDQLFMKVKATCPQRGHDMLSPEAIMQMLNDKLSEQDMSSGGCSDKFKELLTKFF 974

Query: 1058 EEF-----SKKESVTSHQDKVS---QPLREQILSHQDKIGHGRESNPFPSACKAEACREK 1109
            E+      S + ++   +D V      + E+I ++   I   ++   F      + C  +
Sbjct: 975  EDRIKMLRSTRRTLHLDEDHVGMKDSSIEERIAANISGIS-AKQLQVF-----LDTCLSR 1028

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG------------------------ 1145
            Y    IE   ++GA+ AQSIGEPGTQMTLKTFHFAG                        
Sbjct: 1029 YHSKIIEAGASIGAIGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIINAAKNIS 1088

Query: 1146 ------------------EVCEYIEEVFVPDDSFIL------------IKLDMDRIRLL- 1174
                              +V  Y+E+V + + + ++            +KLDM RI    
Sbjct: 1089 TPIITAELLSGQDMSFAVKVKRYVEKVVLGEVAAVIKIVLKSSQPNLVVKLDMQRIEAQG 1148

Query: 1175 HLEVDIDSIRYCIERTRGI---SGHLTVSGHSFLILKPKDSSKS-FNSKMYQMKQLLPSV 1230
            ++ +  DS++  I R   I   S H+ V   + L + P  + KS    +++ +K +LP V
Sbjct: 1149 YMGISSDSVQQSIIRHPKIKLKSEHVRVIDGAKLRIYPTGTDKSKLQLELHTLKSMLPKV 1208

Query: 1231 VIKGVQGINRAVIH--EEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKT 1288
            ++KG+  + RAV++  +   + + +Y LLVEG NL  V+ T GV   K  SN+  EV +T
Sbjct: 1209 IVKGIPTVERAVVNPVKRPDKTLDRYNLLVEGTNLLKVLGTPGVDAKKTKSNHIMEVNQT 1268

Query: 1289 LGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLN 1348
            LGIEAAR +I+ EI+   E++ M ID RH ML+ADLMT KGEVLGITR G+ KMK SVL 
Sbjct: 1269 LGIEAARRSIIDEIRYTFESNNMIIDQRHMMLLADLMTYKGEVLGITRFGIVKMKSSVLM 1328

Query: 1349 LASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 1395
            LASFE T +HLF+A++ G+ D I GVSECIIMG+PM +G+G++K+ Q
Sbjct: 1329 LASFEKTLEHLFNASYSGREDEIEGVSECIIMGIPMTLGSGILKVRQ 1375



 Score =  171 bits (433), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 106/241 (43%), Positives = 149/241 (61%), Gaps = 7/241 (2%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++NISTPIITA L    D+ +A  VK  +E+  LGEV   I+ V     
Sbjct: 1073 GVPRIKEIINAAKNISTPIITAELLSGQDMSFAVKVKRYVEKVVLGEVAAVIKIVLKSSQ 1132

Query: 824  SFILIKLDMDRIRLL-HLEVDIDSIRYCIERTRGI---SGHLTVSGHSFLILKPKDSSKS 879
              +++KLDM RI    ++ +  DS++  I R   I   S H+ V   + L + P  + KS
Sbjct: 1133 PNLVVKLDMQRIEAQGYMGISSDSVQQSIIRHPKIKLKSEHVRVIDGAKLRIYPTGTDKS 1192

Query: 880  -FNSKMYQMKQLLPSVVIKGVQGINRAVIH--EEDVEGVTKYKLLVEGDNLRDVMATYGV 936
                +++ +K +LP V++KG+  + RAV++  +   + + +Y LLVEG NL  V+ T GV
Sbjct: 1193 KLQLELHTLKSMLPKVIVKGIPTVERAVVNPVKRPDKTLDRYNLLVEGTNLLKVLGTPGV 1252

Query: 937  KGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL 996
               K  SN+  EV +TLGIEAAR +I+ EI+   E++ M ID RH ML+ADLMT KGEVL
Sbjct: 1253 DAKKTKSNHIMEVNQTLGIEAARRSIIDEIRYTFESNNMIIDQRHMMLLADLMTYKGEVL 1312

Query: 997  G 997
            G
Sbjct: 1313 G 1313



 Score =  155 bits (391), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 98/248 (39%), Positives = 140/248 (56%), Gaps = 30/248 (12%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           ++Q +  Q+ +  +Y  D +  P+P+GLLD RMG   K   C TC  +  +C GHFGY+ 
Sbjct: 37  IRQSAETQVWNNRIYGNDMK--PVPNGLLDPRMGAANKFGECATCHGSYHECPGHFGYLK 94

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKK 212
           L LPVF++G+F  ++++L+SICK   C+R+LL E+    F  K+RNP L  L + +L KK
Sbjct: 95  LVLPVFNVGFFNNILDVLKSICKG--CSRILLHEKDQREFLKKMRNPRLEPLHKAALMKK 152

Query: 213 ILETTKKVSVCPHCGEINGVVKKC--GLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           + +   K+S CP CG INGV KK   GLL I H+     +K  D   E+L +        
Sbjct: 153 VRDKC-KLSRCPSCGYINGVAKKGRPGLL-IVHDC----SKTLDGSTEELRSAL------ 200

Query: 271 NPEIEAHKKFGL----IQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVP 326
                +HKK  L    + TL+P  VL LF+ +  ED  LL +     +P  LI+T + VP
Sbjct: 201 -----SHKKEKLSISSVHTLDPATVLSLFKRMTDEDCELLNLG---DRPEKLIITEIAVP 252

Query: 327 PNCIRPSV 334
           P  IRPSV
Sbjct: 253 PVPIRPSV 260



 Score =  104 bits (260), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 52/77 (67%), Positives = 58/77 (75%), Gaps = 1/77 (1%)

Query: 609 TPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV NSF++GLT TEFFFHTMGGREGLVDTAVKTAETGYM RRL+K LEDL V Y
Sbjct: 825 TPAAKGFVANSFYTGLTATEFFFHTMGGREGLVDTAVKTAETGYMSRRLMKGLEDLSVFY 884

Query: 668 DMSFDAAFYGQTDCISG 684
           D +   A  G    + G
Sbjct: 885 DQTVRNASSGIVQFVYG 901



 Score = 55.5 bits (132), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/51 (45%), Positives = 39/51 (76%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           +LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+K+ F++R+    + S L
Sbjct: 509 MLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDNFYDRSYFTLLCSYL 559



 Score = 51.2 bits (121), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 27/63 (42%), Positives = 39/63 (61%), Gaps = 7/63 (11%)

Query: 644  VKTAETGYMQRRLVKSLEDLCVQYDMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIK 703
            VK   +  M     K+LE L       F+A++ G+ D I GVSECIIMG+PM +G+G++K
Sbjct: 1320 VKMKSSVLMLASFEKTLEHL-------FNASYSGREDEIEGVSECIIMGIPMTLGSGILK 1372

Query: 704  LLQ 706
            + Q
Sbjct: 1373 VRQ 1375


>gi|255582063|ref|XP_002531828.1| DNA-directed RNA polymerase III largest subunit, putative [Ricinus
           communis]
 gi|223528524|gb|EEF30548.1| DNA-directed RNA polymerase III largest subunit, putative [Ricinus
           communis]
          Length = 1383

 Score =  250 bits (639), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 127/286 (44%), Positives = 182/286 (63%), Gaps = 35/286 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH++SIM HRA+++P RT RFNE VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 427 DGDVVLFNRQPSLHRMSIMCHRARIMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEA 486

Query: 401 RAEALPSLHKLSIMAHRAKVLMA-NKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           R EAL              +LM  +++NL TP+NGE+L+A+TQDF+T  +L+T+++ F++
Sbjct: 487 RTEAL--------------LLMGVSQNNLCTPKNGEILVASTQDFLTSSFLITRRDTFYD 532

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           RA    +  + + D  D+  +          P +  +   +WTGKQ+FS++L+PN +  V
Sbjct: 533 RA-AFSLMCSYMNDGMDLIDL--------PTPAIL-KPIELWTGKQLFSVLLRPNANVRV 582

Query: 520 NANLKTKGRAYTA--------NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYI 571
             NL  + + Y+          E  C  D +V +RNSEL++G + K+TLG+G K  ++ I
Sbjct: 583 YVNLIVREKIYSKPKKGDKREKETMCPNDGFVYIRNSELISGQLGKATLGNGNKDGLYSI 642

Query: 572 LLRDFGEDVAVTAMWRLS--RMTSFYLMNRGFSIGIGDVTPGQGFV 615
           LLRD+    A T M RL+  R  + ++ N GFSIGI DV PG+  +
Sbjct: 643 LLRDYNPHAAATCMNRLAKLRQVARWIGNHGFSIGIDDVQPGKKLI 688



 Score =  216 bits (550), Expect = 7e-53,   Method: Compositional matrix adjust.
 Identities = 122/269 (45%), Positives = 170/269 (63%), Gaps = 12/269 (4%)

Query: 1145 GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSG 1201
            G+V + I+ V     + ++I LDM  I+   L +D + ++  I RT  I     H+ V  
Sbjct: 1107 GQVAKSIKIVMTSRSASVVITLDMKTIQNAQLSLDANIVKEAILRTPRIKLKPQHIKVLD 1166

Query: 1202 HSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEG------VTKYK 1255
               L + P    +  + +++ +K LLPS++++G++ + RAVI ++  +G      +  Y 
Sbjct: 1167 TRKLEVIPLGDRERVHFELHNLKNLLPSIIVQGIKTVERAVIAQKKHDGKANDQELPTYN 1226

Query: 1256 LLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDF 1315
            +LVEG  L  VM T GV G K +SN+  EV K LGIEAAR  I+ EI   ME+HGMSID 
Sbjct: 1227 MLVEGMGLDLVMGTEGVDGCKTTSNHVMEVQKFLGIEAARKCIIDEINQTMEHHGMSIDI 1286

Query: 1316 RHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVS 1375
            RH ML+ DLMT KGEVLGITR G+ KM +SVL LASFE T+DHL+ AA +G+ D I GVS
Sbjct: 1287 RHMMLLGDLMTFKGEVLGITRFGIQKMDKSVLMLASFEKTADHLYHAAVFGRDDKIEGVS 1346

Query: 1376 ECIIMGLPMNVGTGLIKLLQAVPRSEPVP 1404
            ECIIMG+PM +GTG++K+ Q   R +P P
Sbjct: 1347 ECIIMGIPMQIGTGILKVQQ---RVDPPP 1372



 Score =  190 bits (483), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 108/243 (44%), Positives = 154/243 (63%), Gaps = 9/243 (3%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIIN ++ ISTPIITA L+++T++  ARI KGR+++T LG+V + I+ V     
Sbjct: 1062 GVPRIKEIINGAKKISTPIITAELEQNTNVTAARIAKGRIQKTVLGQVAKSIKIVMTSRS 1121

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSFLILKPKDSSKSF 880
            + ++I LDM  I+   L +D + ++  I RT  I     H+ V     L + P    +  
Sbjct: 1122 ASVVITLDMKTIQNAQLSLDANIVKEAILRTPRIKLKPQHIKVLDTRKLEVIPLGDRERV 1181

Query: 881  NSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEG------VTKYKLLVEGDNLRDVMATY 934
            + +++ +K LLPS++++G++ + RAVI ++  +G      +  Y +LVEG  L  VM T 
Sbjct: 1182 HFELHNLKNLLPSIIVQGIKTVERAVIAQKKHDGKANDQELPTYNMLVEGMGLDLVMGTE 1241

Query: 935  GVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGE 994
            GV G K +SN+  EV K LGIEAAR  I+ EI   ME+HGMSID RH ML+ DLMT KGE
Sbjct: 1242 GVDGCKTTSNHVMEVQKFLGIEAARKCIIDEINQTMEHHGMSIDIRHMMLLGDLMTFKGE 1301

Query: 995  VLG 997
            VLG
Sbjct: 1302 VLG 1304



 Score =  155 bits (391), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 95/244 (38%), Positives = 141/244 (57%), Gaps = 23/244 (9%)

Query: 110 DPQRTPIPHGLLDRRMGTNQKEAN-CTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVIN 168
           D  R PI  GLLD R+G   K+++ C TCG +  +C GHFGY++L LPVF++GY   +++
Sbjct: 22  DSTRKPIQAGLLDPRLGPATKQSSACETCGADFHECPGHFGYLNLVLPVFNVGYMSNILD 81

Query: 169 ILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILE-----TTKKVSVC 223
           IL+ ICK  +C+R+L  E+       K+RNP + +L +  L KKI++     T+ K   C
Sbjct: 82  ILKCICK--SCSRILYDEKLCKADLKKMRNPRIEHLRKSELVKKIVKKCSSMTSNKAVKC 139

Query: 224 PHCGEINGVVKKCG-LLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGL 282
             CG++NG+VKK G +L I H++ K        +V+  L E   A+    E  A      
Sbjct: 140 TRCGDMNGMVKKAGSVLSIIHDRAK--------LVDGYLEECRSAIAHTKESRAPISLA- 190

Query: 283 IQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD-LKS- 340
              L P++VL LF+ IP ED  +L +     +P  LI+T + VPP  IRPSV +D L+S 
Sbjct: 191 TYILTPVKVLSLFKRIPEEDCEVLGL---YDRPEKLIITNIAVPPISIRPSVFTDGLQSN 247

Query: 341 DNDV 344
           +ND+
Sbjct: 248 ENDI 251



 Score =  102 bits (254), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 47/61 (77%), Positives = 52/61 (85%), Gaps = 1/61 (1%)

Query: 609 TPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV NSF+SGL  TEFFFHTM GREGLVDTAVKTA+TGYM RRL+K LEDL +QY
Sbjct: 805 TPAAKGFVANSFYSGLMATEFFFHTMAGREGLVDTAVKTADTGYMSRRLIKGLEDLSIQY 864

Query: 668 D 668
           D
Sbjct: 865 D 865



 Score = 77.4 bits (189), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 56/164 (34%), Positives = 77/164 (46%), Gaps = 22/164 (13%)

Query: 999  GTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQD--TSENFVRDIKKF 1056
            G P+ L RL   + A    R +  LS  +I  +    L   +       SE F + +  F
Sbjct: 895  GVPLNLDRLFSKVKATCPVREEDYLSPLDISDVVENLLLKHDMALGGICSEAFKKSLTSF 954

Query: 1057 LEEFSKK-ESVTSHQDKVSQPLREQI--------------LSHQDKIGHGRESNPFPSAC 1101
            L   +K+ ES+    D V  P  E I              L+H+      R+   F    
Sbjct: 955  LGSHAKRLESMMKLADGVEDPTSENIQTGGIRGNSKIIERLAHKIFGVSERQIEVF---- 1010

Query: 1102 KAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
              + C  +Y+  ++EP TA+GA+ AQSIGEPGTQMTLKTFHFAG
Sbjct: 1011 -VKTCINRYLWKRVEPGTAIGAIGAQSIGEPGTQMTLKTFHFAG 1053



 Score = 54.7 bits (130), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 25/48 (52%), Positives = 34/48 (70%), Gaps = 3/48 (6%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP 715
            D  + AA +G+ D I GVSECIIMG+PM +GTG++K+ Q   R +P P
Sbjct: 1328 DHLYHAAVFGRDDKIEGVSECIIMGIPMQIGTGILKVQQ---RVDPPP 1372



 Score = 53.5 bits (127), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 36/42 (85%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRA 62
           ++  +++NL TP+NGE+L+A+TQDF+T  +L+T+++ F++RA
Sbjct: 493 LMGVSQNNLCTPKNGEILVASTQDFLTSSFLITRRDTFYDRA 534


>gi|115459150|ref|NP_001053175.1| Os04g0492300 [Oryza sativa Japonica Group]
 gi|38346223|emb|CAE02045.2| OJ990528_30.3 [Oryza sativa Japonica Group]
 gi|38347455|emb|CAD41360.2| OSJNBa0076N16.24 [Oryza sativa Japonica Group]
 gi|113564746|dbj|BAF15089.1| Os04g0492300 [Oryza sativa Japonica Group]
 gi|116310339|emb|CAH67354.1| OSIGBa0130B08.14 [Oryza sativa Indica Group]
 gi|116310740|emb|CAH67535.1| H0425E08.3 [Oryza sativa Indica Group]
 gi|215768005|dbj|BAH00234.1| unnamed protein product [Oryza sativa Japonica Group]
 gi|218195112|gb|EEC77539.1| hypothetical protein OsI_16437 [Oryza sativa Indica Group]
          Length = 1383

 Score =  250 bits (638), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 124/283 (43%), Positives = 176/283 (62%), Gaps = 31/283 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIM+HRA+++P RT RFNE VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 444 DGDIVLFNRQPSLHRMSIMSHRARIMPWRTLRFNESVCNPYNADFDGDEMNLHVPQTEEA 503

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL              +LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+K+ F++R
Sbjct: 504 RTEAL--------------MLMGVQNNLCTPKNGEILVASTQDFLTSSFLVTRKDNFYDR 549

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           +    + S L     +I                 ++   +WTGKQ+FS++++PN    V 
Sbjct: 550 SSFSLLCSYLGDAMENI----------DLPTPALIKPIELWTGKQLFSVLVRPNACTKVF 599

Query: 521 ANLKTKGRAYTA-------NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILL 573
            NL  K + Y          E  C  D +V  RNSELL+G + K+TLG+G K  +F  L+
Sbjct: 600 LNLTVKEKIYKTPKGSTLEPEAMCPNDGFVYFRNSELLSGQVGKATLGNGNKDGMFSTLV 659

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           RD+    A + M RL++ ++ ++ N GFSIG+ DV PG+   Q
Sbjct: 660 RDYNSHAAASCMNRLAKFSARFIGNHGFSIGVDDVQPGEHLNQ 702



 Score =  236 bits (602), Expect = 8e-59,   Method: Compositional matrix adjust.
 Identities = 127/255 (49%), Positives = 173/255 (67%), Gaps = 4/255 (1%)

Query: 1145 GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSG 1201
            GEV E I+ V       +++KLDM RI  LH+ +  DS++  I    + +  S H+ V  
Sbjct: 1112 GEVAEAIKIVLKSSQPNLVVKLDMQRIEALHMGISADSVQLSILNHPKIKLKSEHVRVID 1171

Query: 1202 HSFLILKPKDSSKS-FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEG 1260
             S L + P    KS    +++ +K +LP V++KG+  + RAVI E   E   +YKLLVEG
Sbjct: 1172 KSKLRIYPAGIDKSKLLYELHHLKSMLPKVIVKGIPTVERAVISETGEENDKRYKLLVEG 1231

Query: 1261 DNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPML 1320
             NL  VM T GV  +K  SN+  EV +TLGIEAAR +I+ EI+  M++HGM+ID RH ML
Sbjct: 1232 TNLLAVMGTPGVDAMKTKSNHIMEVNRTLGIEAARRSIIDEIQYTMKSHGMNIDSRHMML 1291

Query: 1321 VADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIM 1380
            +ADLMT KGE+LGITR+G+AKMK SVL LASFE T++HLF+A++ G+ D I GVSECIIM
Sbjct: 1292 LADLMTYKGEILGITRYGIAKMKSSVLMLASFEKTAEHLFNASYSGREDQIEGVSECIIM 1351

Query: 1381 GLPMNVGTGLIKLLQ 1395
            G+PM +GTG++K+ Q
Sbjct: 1352 GIPMQLGTGILKVRQ 1366



 Score =  205 bits (522), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 116/238 (48%), Positives = 155/238 (65%), Gaps = 4/238 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ ISTPIITA L  + D+  ARIVKG +E+  LGEV E I+ V     
Sbjct: 1067 GVPRIKEIINAAKKISTPIITAELLSEKDVLSARIVKGSMEKAVLGEVAEAIKIVLKSSQ 1126

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSGHSFLILKPKDSSKS- 879
              +++KLDM RI  LH+ +  DS++  I    + +  S H+ V   S L + P    KS 
Sbjct: 1127 PNLVVKLDMQRIEALHMGISADSVQLSILNHPKIKLKSEHVRVIDKSKLRIYPAGIDKSK 1186

Query: 880  FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
               +++ +K +LP V++KG+  + RAVI E   E   +YKLLVEG NL  VM T GV  +
Sbjct: 1187 LLYELHHLKSMLPKVIVKGIPTVERAVISETGEENDKRYKLLVEGTNLLAVMGTPGVDAM 1246

Query: 940  KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            K  SN+  EV +TLGIEAAR +I+ EI+  M++HGM+ID RH ML+ADLMT KGE+LG
Sbjct: 1247 KTKSNHIMEVNRTLGIEAARRSIIDEIQYTMKSHGMNIDSRHMMLLADLMTYKGEILG 1304



 Score =  155 bits (391), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 96/250 (38%), Positives = 146/250 (58%), Gaps = 30/250 (12%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + V+Q + +Q+ +  +Y  + +  P+P+GLLD RMG   K   C+TC  + ++C GHFGY
Sbjct: 35  NEVRQSAEVQVWNSRIY--NHEMKPVPNGLLDTRMGAANKLGECSTCHGSFAECPGHFGY 92

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           + L LPVF++G+F C++++L+ ICK  +C+RVLL E+    F  K+RNP    L + ++ 
Sbjct: 93  LKLALPVFNVGFFNCILDVLKCICK--SCSRVLLMEKDRLEFLKKMRNPKADPLQKSAIM 150

Query: 211 KKILETTKKVSVCPHCGEINGVVKK--CGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAV 268
           KK+ +   K+S CP CG INGV KK   GL+ I H+     +K  D   E+L     +A+
Sbjct: 151 KKVRDKC-KLSRCPWCGFINGVAKKGRAGLI-ILHDC----SKTLDGSTEEL----RDAL 200

Query: 269 KFNPEIEAHKKFGL----IQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLL 324
                  +HKK  L    ++ L+P  VL LF+ +  ED  LL +     +P  LI+T + 
Sbjct: 201 -------SHKKEKLSISAVRMLDPAIVLSLFKRMTDEDCELLNLG---DRPEKLIVTEIA 250

Query: 325 VPPNCIRPSV 334
           VPP  IRPSV
Sbjct: 251 VPPVPIRPSV 260



 Score =  104 bits (260), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 52/74 (70%), Positives = 57/74 (77%), Gaps = 1/74 (1%)

Query: 605 IGDVTPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDL 663
           I   TP  +GFV NSF++GLT TEFFFHTMGGREGLVDTAVKTAETGYM RRL+K LEDL
Sbjct: 814 INSKTPAAKGFVANSFYTGLTATEFFFHTMGGREGLVDTAVKTAETGYMSRRLMKGLEDL 873

Query: 664 CVQYDMSFDAAFYG 677
            V YD +   A  G
Sbjct: 874 SVFYDQTVRNASGG 887



 Score = 77.4 bits (189), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 54/164 (32%), Positives = 79/164 (48%), Gaps = 28/164 (17%)

Query: 998  NGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQD--TSENFVRDIKK 1055
            +G P+ L +L   ++A    R   +LS  EIL + N+ L   +   D   SE F + +  
Sbjct: 907  DGKPLNLDQLFMKVMATCPQRGQNTLSPGEILQILNDKLSEHDASSDDGCSEKFKQLLTY 966

Query: 1056 FLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKA------------ 1103
            FLE+          + K+ +  R  +L  +D +G    S  F  +  A            
Sbjct: 967  FLED----------RIKLLKSTRRALLLDEDHVGERHSS--FEESIAANISGISVKQLQV 1014

Query: 1104 --EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
              + C  +Y   +IE   ++GA+ AQSIGEPGTQMTLKTFHFAG
Sbjct: 1015 FLDTCLSRYHLKKIEAGASIGAIGAQSIGEPGTQMTLKTFHFAG 1058



 Score = 55.5 bits (132), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/51 (45%), Positives = 39/51 (76%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           +LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+K+ F++R+    + S L
Sbjct: 509 MLMGVQNNLCTPKNGEILVASTQDFLTSSFLVTRKDNFYDRSSFSLLCSYL 559



 Score = 52.4 bits (124), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 21/36 (58%), Positives = 30/36 (83%)

Query: 671  FDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            F+A++ G+ D I GVSECIIMG+PM +GTG++K+ Q
Sbjct: 1331 FNASYSGREDQIEGVSECIIMGIPMQLGTGILKVRQ 1366


>gi|414586610|tpg|DAA37181.1| TPA: putative DNA-directed RNA polymerase family protein [Zea mays]
          Length = 1030

 Score =  250 bits (638), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 124/289 (42%), Positives = 176/289 (60%), Gaps = 41/289 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH++SIM HRA+++P RT RFNE VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 444 DGDVVLFNRQPSLHRMSIMCHRARIMPWRTLRFNESVCNPYNADFDGDEMNLHVPQTEEA 503

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL              +LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+K+ F++R
Sbjct: 504 RTEAL--------------MLMGVQNNLCTPKNGEILVASTQDFLTSSFLVTRKDTFYDR 549

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           +    + S L     +I                 ++   +WTGKQ+FS++++PN    V 
Sbjct: 550 SSFTLLCSYLGDGMENI----------DLPTPALIKPVELWTGKQLFSVLVRPNAHTKVF 599

Query: 521 ANLKTKGRAYT-----------------ANEEFCHRDSYVILRNSELLAGSMDKSTLGSG 563
            NL  + + Y+                   E  C  D YV  RNSELL+G + K+TLG+G
Sbjct: 600 LNLAVQEKIYSKKKGKKEGGEEVKETMCGRETMCPNDGYVYFRNSELLSGQVGKATLGNG 659

Query: 564 GKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
            K  ++ +LLRD+    A + M RL++ ++ ++ N GFSIG+ DV PG+
Sbjct: 660 NKDGLYSVLLRDYNSHAAASCMNRLAKFSARFIGNHGFSIGVDDVQPGE 708



 Score =  151 bits (381), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 93/255 (36%), Positives = 139/255 (54%), Gaps = 22/255 (8%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           I  +V     +++ + +Q+ +  +Y  D   TP+P+GLLD RMG   K   C TC    S
Sbjct: 27  IRFSVLSGSEIRKSAEVQVWNNRIY--DRDMTPVPNGLLDPRMGIPTKRGKCNTCHGEFS 84

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALS 202
           DC GHFGY+ L LPVF++G+F C++++L+ ICK  +C+RVLL E+    F  K+RNP   
Sbjct: 85  DCPGHFGYLKLALPVFNVGFFNCILDVLKCICK--SCSRVLLIEKDRREFLKKMRNPRAD 142

Query: 203 YLVRKSLKKKILETTKKVSVCPHCGEINGVVKK--CGLLKISHEKYKNRTKKKDAIVEDL 260
            L + +  KK+ +   K+S CP C   NGVVKK   GL+ + H+  K        +++  
Sbjct: 143 ALQKSATMKKVRDKC-KLSCCPRCDYRNGVVKKGRAGLI-VVHDCSK--------VLDGH 192

Query: 261 LAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
             E   A++   E  +      +  L+P  VL LF  +  ED  LL +     +P  LI+
Sbjct: 193 TEELKNALQNKKEKVSASS---VLVLDPATVLSLFRRMIDEDCELLNLG---DRPEKLIV 246

Query: 321 TRLLVPPNCIRPSVI 335
           T + VPP  IRPSV+
Sbjct: 247 TEIAVPPVPIRPSVV 261



 Score =  105 bits (262), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 59/114 (51%), Positives = 72/114 (63%), Gaps = 9/114 (7%)

Query: 605 IGDVTPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDL 663
           I   TP  +GFV NSF++GLT TEFFFHTMGGREGLVDTAVKTAETGYM RRL+K LEDL
Sbjct: 824 INSKTPAAKGFVANSFYTGLTATEFFFHTMGGREGLVDTAVKTAETGYMSRRLMKGLEDL 883

Query: 664 CVQYDMSFDAA-------FYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPR 710
            V YD +   A        YG  D +         G+P+N+    +K++   P+
Sbjct: 884 SVFYDQTVRNASGGIVQFLYGD-DGMDPAKMEGKDGMPLNLDQLFMKVMATCPQ 936



 Score = 57.0 bits (136), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 24/54 (44%), Positives = 40/54 (74%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           +LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+K+ F++R+    + S L  G
Sbjct: 509 MLMGVQNNLCTPKNGEILVASTQDFLTSSFLVTRKDTFYDRSSFTLLCSYLGDG 562


>gi|388580014|gb|EIM20332.1| beta and beta-prime subunits of DNA dependent RNA-polymerase
           [Wallemia sebi CBS 633.66]
          Length = 1409

 Score =  250 bits (638), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 126/275 (45%), Positives = 169/275 (61%), Gaps = 29/275 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D++LFNRQPSLH+LSIM H  KV P RT R NEC C PYNADFDGDEMN+H+PQTEEA
Sbjct: 451 DRDLILFNRQPSLHRLSIMCHYVKVRPWRTLRLNECACNPYNADFDGDEMNMHVPQTEEA 510

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R E              A+ LM  K N+VTPRNGE +IAA QDFIT  YLL++K+   +R
Sbjct: 511 RTE--------------AQELMGVKHNMVTPRNGEPIIAAIQDFITAAYLLSKKDYLLDR 556

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +  ++ S L      I             P   ++   +WTGKQI S++++PN+  PV 
Sbjct: 557 QEFSQVVSYLDHANMHI----------DLPPPAILKPKRMWTGKQILSILMRPNKSSPVL 606

Query: 521 ANLKTKGRAYTAN-----EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            NL+ K R           +    D Y+++RNS+++ G  DK+T+G G K +VF ++LRD
Sbjct: 607 VNLEAKNRTNHPPPKGMLPDMSSNDGYLVIRNSQIMCGHFDKATVGDGKKNSVFGVILRD 666

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           +G D AV AM RL+R+ + +L + GFS+GI DV P
Sbjct: 667 YGPDEAVNAMNRLARVCARWLASVGFSLGISDVMP 701



 Score =  224 bits (571), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 148/376 (39%), Positives = 202/376 (53%), Gaps = 61/376 (16%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYI 1151
            C +KYV++++EP T VG + AQSIGEPGTQMTLKTFHFAG              E+    
Sbjct: 1034 CWQKYVKSKVEPGTTVGPIGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIINAA 1093

Query: 1152 EEVFVP----------------------------------------DDSFILIKLDMDRI 1171
            + +  P                                        D + + + +DMD +
Sbjct: 1094 KAISTPIISSKLYDDQSESAARIVKGRLEKTYLGDIASHIEESYRGDCNAVSVFVDMDAV 1153

Query: 1172 RLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQL---LP 1228
            + L LE+ +  I   I + + +         ++   + + S K      +  + L   L 
Sbjct: 1154 QKLQLELKLSDIATAIAKDKKLKVKKEDIKENYTKNRIRISVKLGPDAFHITRHLRRNLE 1213

Query: 1229 SVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKT 1288
             VV+ G+ GI RA+I+  + E   K +LLVEG  L DVM T G+ G + SSN+  EV   
Sbjct: 1214 HVVVAGIPGITRAIININEKENKRK-ELLVEGYGLLDVMTTEGIIGTRTSSNHVMEVQNV 1272

Query: 1289 LGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLN 1348
            LGIEAARS+I+ EI  VM +HGM ID RH  L++D MT KGEVLGITR G+AKMK+SVL 
Sbjct: 1273 LGIEAARSSIINEIDNVMSSHGMGIDNRHIQLLSDSMTFKGEVLGITRFGVAKMKDSVLM 1332

Query: 1349 LASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPM-NVGTGLIKLLQAVPRSEPVPRTL 1407
            LASFE T+DHLF+AAF+ + D I GVSE IIMG P  N GT +  L+   P   P  R L
Sbjct: 1333 LASFEKTTDHLFNAAFHAKRDAIEGVSESIIMGNPAENCGTSMPSLILPKPNLPPT-RKL 1391

Query: 1408 LFDNPEFHTNTLAAVP 1423
            +F++  F +++  A P
Sbjct: 1392 IFES-AFKSSSKHARP 1406



 Score =  214 bits (544), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 111/247 (44%), Positives = 146/247 (59%), Gaps = 5/247 (2%)

Query: 97  SHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP 156
           S  ++    LY   P R P  +G+LDRR GT+ K  +C TCG+++++CVGH+GYI L LP
Sbjct: 30  SETEVTHNGLYNPTPDRAPQRNGVLDRRFGTSDKSGSCDTCGESMAECVGHYGYIKLALP 89

Query: 157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILET 216
           VFHIGYFR +I ILQ ICKN  CARVLL EE+   +  + R P L  L R++  K +   
Sbjct: 90  VFHIGYFRDIIAILQDICKN--CARVLLTEEQRRSYLKRFRRPNLENLQRQTACKAVNTA 147

Query: 217 TKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEA 276
            +K   CP+C   NGVVKK GLLKI HEK+  R KK     ++ +  +N A+  + EI  
Sbjct: 148 CRKNLYCPYCQSTNGVVKKTGLLKIVHEKF--RAKKTQGEQQEFVNTFNTAINMSKEIAP 205

Query: 277 HKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVIS 336
           H        LNPL VL LF  I  ED  LL MN + ++P   +   + VPP CIRPSV  
Sbjct: 206 HLNKAQ-DDLNPLRVLDLFTRISNEDCELLGMNPKEARPEQYVWQYMHVPPVCIRPSVAQ 264

Query: 337 DLKSDND 343
           D  ++ D
Sbjct: 265 DGATNED 271



 Score =  168 bits (426), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 104/237 (43%), Positives = 144/237 (60%), Gaps = 4/237 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ ISTPII++ L  D     ARIVKGRLE+T LG++  +IEE +  D 
Sbjct: 1082 GVPRIKEIINAAKAISTPIISSKLYDDQSESAARIVKGRLEKTYLGDIASHIEESYRGDC 1141

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSK 883
            + + + +DMD ++ L LE+ +  I   I + + +         ++   + + S K     
Sbjct: 1142 NAVSVFVDMDAVQKLQLELKLSDIATAIAKDKKLKVKKEDIKENYTKNRIRISVKLGPDA 1201

Query: 884  MYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
             +  + L   L  VV+ G+ GI RA+I+  + E   K +LLVEG  L DVM T G+ G +
Sbjct: 1202 FHITRHLRRNLEHVVVAGIPGITRAIININEKENKRK-ELLVEGYGLLDVMTTEGIIGTR 1260

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             SSN+  EV   LGIEAARS+I+ EI  VM +HGM ID RH  L++D MT KGEVLG
Sbjct: 1261 TSSNHVMEVQNVLGIEAARSSIINEIDNVMSSHGMGIDNRHIQLLSDSMTFKGEVLG 1317



 Score =  104 bits (259), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 46/61 (75%), Positives = 52/61 (85%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV+NSFFSGL+P EF FH + GREGLVDTAVKTAETGYMQRRL+K+LEDL   YD 
Sbjct: 825 PSKGFVRNSFFSGLSPPEFLFHAISGREGLVDTAVKTAETGYMQRRLMKALEDLSAHYDR 884

Query: 670 S 670
           S
Sbjct: 885 S 885



 Score = 58.2 bits (139), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 27/52 (51%), Positives = 36/52 (69%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           Q LM  K N+VTPRNGE +IAA QDFIT  YLL++K+   +R +  ++ S L
Sbjct: 515 QELMGVKHNMVTPRNGEPIIAAIQDFITAAYLLSKKDYLLDRQEFSQVVSYL 566



 Score = 44.3 bits (103), Expect = 0.50,   Method: Compositional matrix adjust.
 Identities = 25/56 (44%), Positives = 33/56 (58%), Gaps = 2/56 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPM-NVGTGLIKLLQAVPRSEPVPRTLLFDN 722
            D  F+AAF+ + D I GVSE IIMG P  N GT +  L+   P   P  R L+F++
Sbjct: 1341 DHLFNAAFHAKRDAIEGVSESIIMGNPAENCGTSMPSLILPKPNLPPT-RKLIFES 1395


>gi|402226085|gb|EJU06145.1| subunit of DNA dependent RNA-polymerase [Dacryopinax sp. DJM-731
           SS1]
          Length = 1455

 Score =  249 bits (636), Expect = 7e-63,   Method: Compositional matrix adjust.
 Identities = 138/324 (42%), Positives = 175/324 (54%), Gaps = 77/324 (23%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DV+LFNRQPSLHKLSIM HR KV P RTFR NECVC PY ADFDGDEMN+H+PQTEEA
Sbjct: 456 DGDVILFNRQPSLHKLSIMCHRVKVRPWRTFRLNECVCGPYGADFDGDEMNIHVPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL               LM+ K NLVTPRNGE +IAATQDF+T  YLL+ ++ F++R
Sbjct: 516 RTEALE--------------LMSVKKNLVTPRNGEPVIAATQDFVTAAYLLSNRDTFYDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNR----- 515
               +I + +     DI             P    R   +WTGKQIF+++++PN      
Sbjct: 562 RAFTQICTYMADALEDI----------DLPPPTIWRPECLWTGKQIFNVLMRPNSKSRVL 611

Query: 516 ---DCPVNANLKTKGRAY------------------------TANE-------------E 535
              + P N   K   R Y                         A E             +
Sbjct: 612 VNVESPCNRGEKPTARYYPLSLRTLKPGRSGDPQFSFAELERQAEEAEKTGKMKDDPYAD 671

Query: 536 FCH--------RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWR 587
           FC          D ++++ NSE++ G MDK+T+GSG K +VF  +LRDFG D A   M R
Sbjct: 672 FCQPLPMDLSPNDGWLVIVNSEIMCGVMDKATVGSGKKKSVFGAMLRDFGPDAAAAGMNR 731

Query: 588 LSRMTSFYLMNRGFSIGIGDVTPG 611
           L+++   +L N GFS+GI DVTPG
Sbjct: 732 LAKLCGRWLSNFGFSLGISDVTPG 755



 Score =  234 bits (596), Expect = 4e-58,   Method: Compositional matrix adjust.
 Identities = 174/494 (35%), Positives = 253/494 (51%), Gaps = 78/494 (15%)

Query: 993  GEVLGNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRD 1052
            G + G   PV+  R      A  ++R   +L   EI+ L+NE L  ++F  + S  ++  
Sbjct: 959  GCLEGQAQPVDFDRAWMHAGAI-TARDGRALLPFEIMDLTNEILQRRKFKTECSTQYLDS 1017

Query: 1053 IKKFLEEFSKKESVTSHQDKVSQPLREQI---------LSHQDKIGHGRESNPFPSACKA 1103
            ++ +++  ++       + K+   +             L   +K     E+    ++   
Sbjct: 1018 LRAYIQAIARHLGNVRQEYKMYDAVDRDDDWDADTDLSLGAGEKEQQALENRIKITSAHV 1077

Query: 1104 EA----CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVC 1148
            E+    C  KYV+++IEP + VGA+ AQSIGEPGTQMTLKTFHFAG            + 
Sbjct: 1078 ESFLNTCWAKYVKSKIEPGSTVGAVGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIK 1137

Query: 1149 EYI-------------------------------EEVFVPDDSFILIKLDMDRIRLLHLE 1177
            E I                               E+ ++ D + ++ +        + + 
Sbjct: 1138 EIINAAKVISTPIISAKLVERKNETAARIVKGRLEKTYLGDVASVIEEAWAGEYTYIGVH 1197

Query: 1178 VDIDSIRYC--------IERTRGISGHLTVSGHSFLILKPKDSSKSF----NSKMYQM-- 1223
            +D+D+IR          ++R    S  + V   +  +   K+  K F      K Y++  
Sbjct: 1198 LDMDAIRKLQLELTIEDVKRAIVNSSKVKVKDGNITVDSRKNRLKIFFDSGEFKYYELRA 1257

Query: 1224 -KQLLPSVVIKGVQGINRAVIHEEDVEGVTKYK-----LLVEGDNLRDVMATYGVKGVKC 1277
             K++L  +V+KG   I RAVI++ + +   + K     LLVEG  L +VM T GV G + 
Sbjct: 1258 TKRVLADIVVKGSSQIQRAVINKIEKDKSPRGKPGENELLVEGYGLLEVMTTEGVVGEET 1317

Query: 1278 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRH 1337
            + N+  EV K LGIEAARSTI+ EI+  MENHGM+ID RH ML+ D+MT KGEVLGITR 
Sbjct: 1318 TGNHVIEVGKVLGIEAARSTIIHEIQYTMENHGMNIDPRHVMLLGDVMTYKGEVLGITRF 1377

Query: 1338 GLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPM-NVGTGLIKLLQA 1396
            G+AKMK+SVL LASFE T+DHLFDAA YG++D I GVSE IIMG P  N GT +  L+  
Sbjct: 1378 GVAKMKDSVLMLASFEKTTDHLFDAAAYGKSDAILGVSESIIMGNPANNCGTSMPALVTP 1437

Query: 1397 VPRSEPVPRTLLFD 1410
             P   P  R LLF+
Sbjct: 1438 AP-VLPKRRALLFE 1450



 Score =  186 bits (471), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 112/242 (46%), Positives = 154/242 (63%), Gaps = 8/242 (3%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ ISTPII+A L +  +   ARIVKGRLE+T LG+V   IEE +  + 
Sbjct: 1132 GVPRIKEIINAAKVISTPIISAKLVERKNETAARIVKGRLEKTYLGDVASVIEEAWAGEY 1191

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFLILKPKDSSKSF 880
            ++I + LDMD IR L LE+ I+ ++  I  +  +    G++TV      +    DS +  
Sbjct: 1192 TYIGVHLDMDAIRKLQLELTIEDVKRAIVNSSKVKVKDGNITVDSRKNRLKIFFDSGEFK 1251

Query: 881  NSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYK-----LLVEGDNLRDVMATYG 935
              ++   K++L  +V+KG   I RAVI++ + +   + K     LLVEG  L +VM T G
Sbjct: 1252 YYELRATKRVLADIVVKGSSQIQRAVINKIEKDKSPRGKPGENELLVEGYGLLEVMTTEG 1311

Query: 936  VKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            V G + + N+  EV K LGIEAARSTI+ EI+  MENHGM+ID RH ML+ D+MT KGEV
Sbjct: 1312 VVGEETTGNHVIEVGKVLGIEAARSTIIHEIQYTMENHGMNIDPRHVMLLGDVMTYKGEV 1371

Query: 996  LG 997
            LG
Sbjct: 1372 LG 1373



 Score =  180 bits (456), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 106/262 (40%), Positives = 150/262 (57%), Gaps = 7/262 (2%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           I+ ++ K   V + S  +I   +LY +   R P P+G+LDRR+G   K + C TCGQ   
Sbjct: 16  IQFSLLKPQDVVKISEFEIPHHDLYTRG-TRDPAPNGVLDRRLGVIDKTSVCETCGQTAQ 74

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALS 202
            CVGH+ YI L LPVFH+GYF+ VI+ILQ ICK  TC+RV+L E     F  + R P L 
Sbjct: 75  TCVGHYAYIKLTLPVFHVGYFKHVISILQCICK--TCSRVMLEEADRRKFLRRFRRPGLE 132

Query: 203 YLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGL-LKISHEKYKNRTKKKDAIVEDLL 261
            L R++  K +    +KV+ CP+C   NG+VKK    +KI HEK+  R+KK +       
Sbjct: 133 NLQRQATFKAVNTQCRKVTYCPYCMSTNGIVKKAKKDIKIVHEKF--RSKKTEDERLKWR 190

Query: 262 AEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
             +N+A+++  ++  H     ++ ++PL VL LFE I  ED  LL M+ E  +P   I  
Sbjct: 191 EGFNKAIEYQKDLAPHIAKA-VEDMHPLRVLTLFENITDEDCELLGMHPEHGRPEQFIWH 249

Query: 322 RLLVPPNCIRPSVISDLKSDND 343
            + VPP  IRPSV  D  S+ D
Sbjct: 250 YISVPPVAIRPSVQQDGASNED 271



 Score =  102 bits (253), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 45/61 (73%), Positives = 51/61 (83%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV NSF++GL PTEF FH + GREGLVDTAVKTAETGYMQRRL+K+LEDL   YD 
Sbjct: 878 PSKGFVSNSFYTGLRPTEFLFHAISGREGLVDTAVKTAETGYMQRRLMKALEDLVTHYDT 937

Query: 670 S 670
           S
Sbjct: 938 S 938



 Score = 59.7 bits (143), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 26/50 (52%), Positives = 37/50 (74%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           LM+ K NLVTPRNGE +IAATQDF+T  YLL+ ++ F++R    +I + +
Sbjct: 522 LMSVKKNLVTPRNGEPVIAATQDFVTAAYLLSNRDTFYDRRAFTQICTYM 571



 Score = 47.0 bits (110), Expect = 0.084,   Method: Compositional matrix adjust.
 Identities = 28/55 (50%), Positives = 33/55 (60%), Gaps = 2/55 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPM-NVGTGLIKLLQAVPRSEPVPRTLLFD 721
            D  FDAA YG++D I GVSE IIMG P  N GT +  L+   P   P  R LLF+
Sbjct: 1397 DHLFDAAAYGKSDAILGVSESIIMGNPANNCGTSMPALVTPAP-VLPKRRALLFE 1450


>gi|357472537|ref|XP_003606553.1| DNA-directed RNA polymerase [Medicago truncatula]
 gi|355507608|gb|AES88750.1| DNA-directed RNA polymerase [Medicago truncatula]
          Length = 807

 Score =  249 bits (636), Expect = 8e-63,   Method: Compositional matrix adjust.
 Identities = 125/284 (44%), Positives = 183/284 (64%), Gaps = 32/284 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++S+M+HRA+V+P RT RFNE VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 213 DGDIVIFNRQPSLHRMSMMSHRARVMPWRTLRFNESVCNPYNADFDGDEMNLHVPQTEEA 272

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL              +LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+K+ F++R
Sbjct: 273 RTEAL--------------LLMTVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDR 318

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           +    I S +  D  D   +          P + ++   +W+GKQ+FS++L+P+ +  V 
Sbjct: 319 SSFSLICSYM-GDGMDPIDLP--------TPAI-IKPVELWSGKQLFSILLRPHANVRVY 368

Query: 521 ANLKTKGRAYTAN-----EEF---CHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYIL 572
            NL  K + Y +       EF   C  D +V  RNSEL++G + K TLG+G K  +F +L
Sbjct: 369 VNLTVKEKNYGSKLDDREREFKTMCPDDGFVYFRNSELISGQLGKVTLGNGNKDGLFSVL 428

Query: 573 LRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           LRD+  D A + M RL+++++ ++ N GFSIGI DV P    ++
Sbjct: 429 LRDYKSDAAASCMNRLAKLSARWIGNHGFSIGIDDVQPKDKLIK 472



 Score = 67.0 bits (162), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 28/47 (59%), Positives = 38/47 (80%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLV 657
            +GFV++SFF+GL+ TEFFFHTMGGREGLVDTAV+ +    ++R  +
Sbjct: 719 AKGFVKDSFFTGLSATEFFFHTMGGREGLVDTAVRVSAMVILRRDFI 765



 Score = 56.6 bits (135), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 24/54 (44%), Positives = 40/54 (74%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           +LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+K+ F++R+    I S +  G
Sbjct: 278 LLMTVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDRSSFSLICSYMGDG 331


>gi|401403150|ref|XP_003881423.1| putative DNA-directed RNA polymerase III largest subunit [Neospora
           caninum Liverpool]
 gi|325115835|emb|CBZ51390.1| putative DNA-directed RNA polymerase III largest subunit [Neospora
           caninum Liverpool]
          Length = 1769

 Score =  248 bits (633), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 130/277 (46%), Positives = 169/277 (61%), Gaps = 32/277 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + DVVLFNRQPSLH++SIMAHRA+V+P RTFRFNECVC+PYNADFDGDEMN+HLPQT EA
Sbjct: 556 NGDVVLFNRQPSLHRMSIMAHRARVMPWRTFRFNECVCSPYNADFDGDEMNLHLPQTHEA 615

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL               LM   +NLVTP+NGE LIAATQDF++  Y+LT K+ F  R
Sbjct: 616 RAEAL--------------YLMGVVNNLVTPKNGEPLIAATQDFLSSSYMLTHKDVFLTR 661

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q   I S      S +             P   ++   +WTGKQ+  ++L+PN +  V 
Sbjct: 662 DQFCLICSYFTDGLSQV----------DLPPPTVLKPVELWTGKQVIGVLLRPNGNSFVM 711

Query: 521 ANLKTKGRAYTA-------NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILL 573
            N + K R + A       +   C  D+YVI R+SELLAG + K  LG   K  +F+ L+
Sbjct: 712 VNFQLKEREFAAARIPPGESPFMCPSDAYVIFRHSELLAGCIGKKVLGD-AKFGLFFHLI 770

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           RD     A   M R++++++ +  NRG +IGI DVTP
Sbjct: 771 RDNSPAQAAACMTRIAKLSARWFANRGMTIGIDDVTP 807



 Score =  214 bits (544), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 134/351 (38%), Positives = 193/351 (54%), Gaps = 66/351 (18%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKT---------------------------- 1140
            KYV+A  E   AVGA+ AQSIGEPGTQMTLKT                            
Sbjct: 1393 KYVKAISEAGEAVGAMGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIINAAQKI 1452

Query: 1141 --------------FHFA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLL 1174
                          +++A             E C YI+EV+ PD +++++KLD   IR L
Sbjct: 1453 QTPIIVVPLVNDEDYNYAVMVKNRIEKTLLSECCSYIKEVYAPDGAWLVVKLDQHTIRKL 1512

Query: 1175 HLEVDIDSIRYCIERTRGISGHLTVSGHSFLIL---KPKDSSKSFNSKMYQMKQL---LP 1228
             L+++ ++++  I R   ++  + ++  S  I+   K +      N   +Q++ L   L 
Sbjct: 1513 FLDINANTVKEAILRQTAVN-KVRITKSSVEIINEWKVRVMPPGGNQIFFQLQALKIGLL 1571

Query: 1229 SVVIKGVQGINRAVIHEEDVEGVTK-----YKLLVEGDNLRDVMATYGVKGVKCSSNNTY 1283
            ++V+ G + + R VI  E VE   K     Y L VEG  LRDVM T GVK ++ +SN+  
Sbjct: 1572 NIVLCGHKDVKRGVIKCEHVEQPDKTKKTVYGLAVEGYGLRDVMGTQGVKALQATSNHVM 1631

Query: 1284 EVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMK 1343
            EV + LGIEAAR+ I++EI+  M+ + M ID RH  L+ D+MT +GEVLGI R G+ KM+
Sbjct: 1632 EVAQILGIEAARAVIISEIRKCMDAYSMDIDCRHMTLLGDVMTFRGEVLGINRFGIQKMR 1691

Query: 1344 ESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
             S L LASFE T++HLF+AA + + D + GVSECIIMG  +++GTG   LL
Sbjct: 1692 ASTLMLASFEETNEHLFEAAVHHRADPVKGVSECIIMGKQVSLGTGSFDLL 1742



 Score =  179 bits (454), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 103/245 (42%), Positives = 152/245 (62%), Gaps = 12/245 (4%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ I TPII   L  D D +YA +VK R+E+T L E C YI+EV+ PD 
Sbjct: 1438 GVPRIKEIINAAQKIQTPIIVVPLVNDEDYNYAVMVKNRIEKTLLSECCSYIKEVYAPDG 1497

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLIL---KPKDSSKSF 880
            +++++KLD   IR L L+++ ++++  I R   ++  + ++  S  I+   K +      
Sbjct: 1498 AWLVVKLDQHTIRKLFLDINANTVKEAILRQTAVN-KVRITKSSVEIINEWKVRVMPPGG 1556

Query: 881  NSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTK-----YKLLVEGDNLRDVMA 932
            N   +Q++ L   L ++V+ G + + R VI  E VE   K     Y L VEG  LRDVM 
Sbjct: 1557 NQIFFQLQALKIGLLNIVLCGHKDVKRGVIKCEHVEQPDKTKKTVYGLAVEGYGLRDVMG 1616

Query: 933  TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK 992
            T GVK ++ +SN+  EV + LGIEAAR+ I++EI+  M+ + M ID RH  L+ D+MT +
Sbjct: 1617 TQGVKALQATSNHVMEVAQILGIEAARAVIISEIRKCMDAYSMDIDCRHMTLLGDVMTFR 1676

Query: 993  GEVLG 997
            GEVLG
Sbjct: 1677 GEVLG 1681



 Score =  145 bits (366), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 92/287 (32%), Positives = 149/287 (51%), Gaps = 43/287 (14%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           ++  V   + + + S ++I ++ +Y  +   TP P+G+LD R+G N+ ++ C TCG  L 
Sbjct: 142 VQFDVLSGEEISRYSEVEIQNREIYV-NMTSTPHPYGVLDLRLGPNKSDSRCQTCGHTLL 200

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALS 202
            C GH+GY+DL  PV+H+GYF+ V+ IL  ICK  TCA +L   E+     +++R     
Sbjct: 201 QCTGHWGYMDLQAPVYHVGYFKYVLQILYCICK--TCAALLQPPEQKEKLLSRIRRHQSD 258

Query: 203 YLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLA 262
            +V++ L K+ +E  KKVS C  CG   GV+K+  ++K S +++                
Sbjct: 259 PIVKRLLFKRTVEACKKVSKCFECGAPQGVLKR--VVKPSLDQF---------------M 301

Query: 263 EYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTR 322
           +    VKF    +  +   +   L+PL V  L E I   +  +L    ++  P  L+L+R
Sbjct: 302 KIRHVVKF----KEGRALTVEDDLDPLYVKNLLERIRPSECEIL----DIVSPEKLLLSR 353

Query: 323 LLVPPNCIRPS---------------VISDLKSDNDVVLFNRQPSLH 354
           LLVPP+CIRPS               V+SD+   N+V+L + Q   H
Sbjct: 354 LLVPPSCIRPSVTIGEQGTTEDDLTCVLSDIAELNNVLLSHVQAGFH 400



 Score =  104 bits (260), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 47/59 (79%), Positives = 53/59 (89%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
           +GFV NSF+SGL P EFFFHTM GREGLVDTAVKTAETGYMQRRL+K+LEDL ++YD S
Sbjct: 933 RGFVANSFYSGLQPDEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKALEDLSIRYDNS 991



 Score = 57.4 bits (137), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 28/53 (52%), Positives = 34/53 (64%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           LM   +NLVTP+NGE LIAATQDF++  Y+LT K+ F  R Q   I S    G
Sbjct: 622 LMGVVNNLVTPKNGEPLIAATQDFLSSSYMLTHKDVFLTRDQFCLICSYFTDG 674


>gi|8777343|dbj|BAA96933.1| DNA-directed RNA polymerase II largest chain [Arabidopsis thaliana]
          Length = 1383

 Score =  248 bits (632), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 126/277 (45%), Positives = 176/277 (63%), Gaps = 29/277 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + DVVLFNRQPSLH++SIM HRA+++P RT RFNE VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 456 EGDVVLFNRQPSLHRMSIMCHRARIMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EA+               LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+K+ F++R
Sbjct: 516 RTEAI--------------TLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A    I S +  D  D        S     P + ++   +WTGKQIFS++L+PN    V 
Sbjct: 562 AAFSLICSYM-GDGMD--------SIDLPTPTI-LKPIELWTGKQIFSVLLRPNASIRVY 611

Query: 521 ANLKTKGRAYTA-----NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
             L  K + +       +E  C  D +V  RNSEL++G + K+TLG+G K  ++ ILLRD
Sbjct: 612 VTLNVKEKNFKKGEHGFDETMCINDGWVYFRNSELISGQLGKATLGNGNKDGLYSILLRD 671

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
           +    A   M RL+++++ ++   GFSIGI DV PG+
Sbjct: 672 YNSHAAAVCMNRLAKLSARWIGIHGFSIGIDDVQPGE 708



 Score =  208 bits (529), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 121/270 (44%), Positives = 169/270 (62%), Gaps = 14/270 (5%)

Query: 1145 GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSG 1201
            G+V E IE +     + + I LD   I    L +   S++  I +T  I      + V  
Sbjct: 1109 GQVAESIEVLMTSTSASVRIILDNKIIEEACLSITPWSVKNSILKTPRIKLNDNDIRVLD 1168

Query: 1202 HSFLILKPKDSSKS-FNSKMYQMKQLLPSVVIKGVQGINRAVIHEE-----DVEGVTKYK 1255
                I    D S++ FN  ++ +K +LP++++ G++ + R V+ E+      ++G TK+K
Sbjct: 1169 TGLDITPVVDKSRAHFN--LHNLKNVLPNIIVNGIKTVERVVVAEDMDKSKQIDGKTKWK 1226

Query: 1256 LLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDF 1315
            L VEG NL  VM T G+ G   +SNN  EV KTLGIEAAR+TI+ EI  VM NHGMSID 
Sbjct: 1227 LFVEGTNLLAVMGTPGINGRTTTSNNVVEVSKTLGIEAARTTIIDEIGTVMGNHGMSIDI 1286

Query: 1316 RHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVS 1375
            RH ML+AD+MT +GEVLGI R G+ KM +SVL  ASFE T DHLF AA  G+ D I GV+
Sbjct: 1287 RHMMLLADVMTYRGEVLGIQRTGIQKMDKSVLMQASFERTGDHLFSAAASGKVDNIEGVT 1346

Query: 1376 ECIIMGLPMNVGTGLIKLLQAVPRSEPVPR 1405
            EC+IMG+PM +GTG++K+LQ   R++ +P+
Sbjct: 1347 ECVIMGIPMKLGTGILKVLQ---RTDDLPK 1373



 Score =  189 bits (480), Expect = 9e-45,   Method: Compositional matrix adjust.
 Identities = 112/243 (46%), Positives = 153/243 (62%), Gaps = 11/243 (4%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRI EIINAS+NISTP+I+A L+   +L  AR VKGR+E+TTLG+V E IE +     
Sbjct: 1064 GVPRINEIINASKNISTPVISAELENPLELTSARWVKGRIEKTTLGQVAESIEVLMTSTS 1123

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFLILKPKDSSKS- 879
            + + I LD   I    L +   S++  I +T  I      + V      I    D S++ 
Sbjct: 1124 ASVRIILDNKIIEEACLSITPWSVKNSILKTPRIKLNDNDIRVLDTGLDITPVVDKSRAH 1183

Query: 880  FNSKMYQMKQLLPSVVIKGVQGINRAVIHEE-----DVEGVTKYKLLVEGDNLRDVMATY 934
            FN  ++ +K +LP++++ G++ + R V+ E+      ++G TK+KL VEG NL  VM T 
Sbjct: 1184 FN--LHNLKNVLPNIIVNGIKTVERVVVAEDMDKSKQIDGKTKWKLFVEGTNLLAVMGTP 1241

Query: 935  GVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGE 994
            G+ G   +SNN  EV KTLGIEAAR+TI+ EI  VM NHGMSID RH ML+AD+MT +GE
Sbjct: 1242 GINGRTTTSNNVVEVSKTLGIEAARTTIIDEIGTVMGNHGMSIDIRHMMLLADVMTYRGE 1301

Query: 995  VLG 997
            VLG
Sbjct: 1302 VLG 1304



 Score =  139 bits (349), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 96/289 (33%), Positives = 151/289 (52%), Gaps = 31/289 (10%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           I  +V  +  V + + +Q+ +  LY  D    P  +GLLD RMG   K++ CTTC  N  
Sbjct: 26  INFSVLSDLEVMKAAEVQVWNIGLY--DHSFKPYENGLLDPRMGPPNKKSICTTCEGNFQ 83

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALS 202
           +C GH+GY+ L LPV+++GYF  +++IL+ ICK   C+ +LL E+       K+RNP + 
Sbjct: 84  NCPGHYGYLKLDLPVYNVGYFNFILDILKCICKR--CSNMLLDEKLYEDHLRKMRNPRME 141

Query: 203 YLVRKSLKKKILE-----TTKKVSVCPHCGEINGVVKKCGL---LKISHEKYKNRTKKKD 254
            L +  L K +++      ++++  C  CG +NG+VKK      + ISH++ K    + D
Sbjct: 142 PLKKTELAKAVVKKCSTMASQRIITCKKCGYLNGMVKKIAAQFGIGISHDRSKIHGGEID 201

Query: 255 AIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSK 314
                +          NP         L   L+P  VL LF+ +  +D  LL +     +
Sbjct: 202 ECKSAISHTKQSTAAINP---------LTYVLDPNLVLGLFKRMSDKDCELLYI---AYR 249

Query: 315 PSDLILTRLLVPPNCIRPSV-ISDLKS-DNDVVLFNRQ-----PSLHKL 356
           P +LI+T +LVPP  IRPSV I  ++S +ND+    +Q      SLHK+
Sbjct: 250 PENLIITCMLVPPLSIRPSVMIGGIQSNENDLTARLKQIILGNASLHKI 298



 Score =  103 bits (258), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 47/58 (81%), Positives = 51/58 (87%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV NSF+SGLT TEFFFHTMGGREGLVDTAVKTA TGYM RRL+K+LEDL V YD
Sbjct: 831 AKGFVANSFYSGLTATEFFFHTMGGREGLVDTAVKTASTGYMSRRLMKALEDLLVHYD 888



 Score = 64.7 bits (156), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 50/152 (32%), Positives = 73/152 (48%), Gaps = 17/152 (11%)

Query: 998  NGTPVELKRLLDDIIAKNSSRSDPS-LSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            +G P+   RL   + A    RS  + LS++E+     E L   +  +  ++ FV+ +++F
Sbjct: 917  DGAPLNFNRLFLKVQATCPPRSHHTYLSSEELSQKFEEELVRHDKSRVCTDAFVKSLREF 976

Query: 1057 LEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPF---PSACKAEACREKYVRA 1113
            +     K +        S P   Q+L      G   E  P          + C  +Y   
Sbjct: 977  VSLLGVKSA--------SPP---QVLYKAS--GQKYEILPLIYINMQVFVKICVFRYREK 1023

Query: 1114 QIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            +IE  TA+G + AQSIGEPGTQMTLKTFHFAG
Sbjct: 1024 KIEAGTAIGTIGAQSIGEPGTQMTLKTFHFAG 1055



 Score = 57.4 bits (137), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 25/53 (47%), Positives = 39/53 (73%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+K+ F++RA    I S +  G
Sbjct: 522 LMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDRAAFSLICSYMGDG 574



 Score = 53.9 bits (128), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 24/49 (48%), Positives = 36/49 (73%), Gaps = 3/49 (6%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPR 716
            D  F AA  G+ D I GV+EC+IMG+PM +GTG++K+LQ   R++ +P+
Sbjct: 1328 DHLFSAAASGKVDNIEGVTECVIMGIPMKLGTGILKVLQ---RTDDLPK 1373


>gi|145359470|ref|NP_200812.2| nuclear RNA polymerase C1 [Arabidopsis thaliana]
 gi|332009886|gb|AED97269.1| nuclear RNA polymerase C1 [Arabidopsis thaliana]
          Length = 1376

 Score =  248 bits (632), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 126/277 (45%), Positives = 176/277 (63%), Gaps = 29/277 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + DVVLFNRQPSLH++SIM HRA+++P RT RFNE VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 456 EGDVVLFNRQPSLHRMSIMCHRARIMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EA+               LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+K+ F++R
Sbjct: 516 RTEAI--------------TLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A    I S +  D  D        S     P + ++   +WTGKQIFS++L+PN    V 
Sbjct: 562 AAFSLICSYM-GDGMD--------SIDLPTPTI-LKPIELWTGKQIFSVLLRPNASIRVY 611

Query: 521 ANLKTKGRAYTA-----NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
             L  K + +       +E  C  D +V  RNSEL++G + K+TLG+G K  ++ ILLRD
Sbjct: 612 VTLNVKEKNFKKGEHGFDETMCINDGWVYFRNSELISGQLGKATLGNGNKDGLYSILLRD 671

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
           +    A   M RL+++++ ++   GFSIGI DV PG+
Sbjct: 672 YNSHAAAVCMNRLAKLSARWIGIHGFSIGIDDVQPGE 708



 Score =  208 bits (529), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 121/270 (44%), Positives = 169/270 (62%), Gaps = 14/270 (5%)

Query: 1145 GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSG 1201
            G+V E IE +     + + I LD   I    L +   S++  I +T  I      + V  
Sbjct: 1102 GQVAESIEVLMTSTSASVRIILDNKIIEEACLSITPWSVKNSILKTPRIKLNDNDIRVLD 1161

Query: 1202 HSFLILKPKDSSKS-FNSKMYQMKQLLPSVVIKGVQGINRAVIHEE-----DVEGVTKYK 1255
                I    D S++ FN  ++ +K +LP++++ G++ + R V+ E+      ++G TK+K
Sbjct: 1162 TGLDITPVVDKSRAHFN--LHNLKNVLPNIIVNGIKTVERVVVAEDMDKSKQIDGKTKWK 1219

Query: 1256 LLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDF 1315
            L VEG NL  VM T G+ G   +SNN  EV KTLGIEAAR+TI+ EI  VM NHGMSID 
Sbjct: 1220 LFVEGTNLLAVMGTPGINGRTTTSNNVVEVSKTLGIEAARTTIIDEIGTVMGNHGMSIDI 1279

Query: 1316 RHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVS 1375
            RH ML+AD+MT +GEVLGI R G+ KM +SVL  ASFE T DHLF AA  G+ D I GV+
Sbjct: 1280 RHMMLLADVMTYRGEVLGIQRTGIQKMDKSVLMQASFERTGDHLFSAAASGKVDNIEGVT 1339

Query: 1376 ECIIMGLPMNVGTGLIKLLQAVPRSEPVPR 1405
            EC+IMG+PM +GTG++K+LQ   R++ +P+
Sbjct: 1340 ECVIMGIPMKLGTGILKVLQ---RTDDLPK 1366



 Score =  189 bits (480), Expect = 9e-45,   Method: Compositional matrix adjust.
 Identities = 112/243 (46%), Positives = 153/243 (62%), Gaps = 11/243 (4%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRI EIINAS+NISTP+I+A L+   +L  AR VKGR+E+TTLG+V E IE +     
Sbjct: 1057 GVPRINEIINASKNISTPVISAELENPLELTSARWVKGRIEKTTLGQVAESIEVLMTSTS 1116

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFLILKPKDSSKS- 879
            + + I LD   I    L +   S++  I +T  I      + V      I    D S++ 
Sbjct: 1117 ASVRIILDNKIIEEACLSITPWSVKNSILKTPRIKLNDNDIRVLDTGLDITPVVDKSRAH 1176

Query: 880  FNSKMYQMKQLLPSVVIKGVQGINRAVIHEE-----DVEGVTKYKLLVEGDNLRDVMATY 934
            FN  ++ +K +LP++++ G++ + R V+ E+      ++G TK+KL VEG NL  VM T 
Sbjct: 1177 FN--LHNLKNVLPNIIVNGIKTVERVVVAEDMDKSKQIDGKTKWKLFVEGTNLLAVMGTP 1234

Query: 935  GVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGE 994
            G+ G   +SNN  EV KTLGIEAAR+TI+ EI  VM NHGMSID RH ML+AD+MT +GE
Sbjct: 1235 GINGRTTTSNNVVEVSKTLGIEAARTTIIDEIGTVMGNHGMSIDIRHMMLLADVMTYRGE 1294

Query: 995  VLG 997
            VLG
Sbjct: 1295 VLG 1297



 Score =  138 bits (348), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 96/289 (33%), Positives = 151/289 (52%), Gaps = 31/289 (10%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           I  +V  +  V + + +Q+ +  LY  D    P  +GLLD RMG   K++ CTTC  N  
Sbjct: 26  INFSVLSDLEVMKAAEVQVWNIGLY--DHSFKPYENGLLDPRMGPPNKKSICTTCEGNFQ 83

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALS 202
           +C GH+GY+ L LPV+++GYF  +++IL+ ICK   C+ +LL E+       K+RNP + 
Sbjct: 84  NCPGHYGYLKLDLPVYNVGYFNFILDILKCICKR--CSNMLLDEKLYEDHLRKMRNPRME 141

Query: 203 YLVRKSLKKKILE-----TTKKVSVCPHCGEINGVVKKCGL---LKISHEKYKNRTKKKD 254
            L +  L K +++      ++++  C  CG +NG+VKK      + ISH++ K    + D
Sbjct: 142 PLKKTELAKAVVKKCSTMASQRIITCKKCGYLNGMVKKIAAQFGIGISHDRSKIHGGEID 201

Query: 255 AIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSK 314
                +          NP         L   L+P  VL LF+ +  +D  LL +     +
Sbjct: 202 ECKSAISHTKQSTAAINP---------LTYVLDPNLVLGLFKRMSDKDCELLYI---AYR 249

Query: 315 PSDLILTRLLVPPNCIRPSV-ISDLKS-DNDVVLFNRQ-----PSLHKL 356
           P +LI+T +LVPP  IRPSV I  ++S +ND+    +Q      SLHK+
Sbjct: 250 PENLIITCMLVPPLSIRPSVMIGGIQSNENDLTARLKQIILGNASLHKI 298



 Score =  103 bits (258), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 47/58 (81%), Positives = 51/58 (87%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV NSF+SGLT TEFFFHTMGGREGLVDTAVKTA TGYM RRL+K+LEDL V YD
Sbjct: 831 AKGFVANSFYSGLTATEFFFHTMGGREGLVDTAVKTASTGYMSRRLMKALEDLLVHYD 888



 Score = 64.7 bits (156), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 48/149 (32%), Positives = 74/149 (49%), Gaps = 18/149 (12%)

Query: 998  NGTPVELKRLLDDIIAKNSSRSDPS-LSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            +G P+   RL   + A    RS  + LS++E+     E L   +  +  ++ FV+ +++F
Sbjct: 917  DGAPLNFNRLFLKVQATCPPRSHHTYLSSEELSQKFEEELVRHDKSRVCTDAFVKSLREF 976

Query: 1057 LEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIE 1116
            +     K +        S P   Q+L     +   ++   F      + C  +Y   +IE
Sbjct: 977  VSLLGVKSA--------SPP---QVLYKASGVTD-KQLEVF-----VKICVFRYREKKIE 1019

Query: 1117 PATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
              TA+G + AQSIGEPGTQMTLKTFHFAG
Sbjct: 1020 AGTAIGTIGAQSIGEPGTQMTLKTFHFAG 1048



 Score = 57.4 bits (137), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 25/53 (47%), Positives = 39/53 (73%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+K+ F++RA    I S +  G
Sbjct: 522 LMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDRAAFSLICSYMGDG 574



 Score = 53.9 bits (128), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 24/49 (48%), Positives = 36/49 (73%), Gaps = 3/49 (6%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPR 716
            D  F AA  G+ D I GV+EC+IMG+PM +GTG++K+LQ   R++ +P+
Sbjct: 1321 DHLFSAAASGKVDNIEGVTECVIMGIPMKLGTGILKVLQ---RTDDLPK 1366


>gi|428186682|gb|EKX55532.1| hypothetical protein GUITHDRAFT_156792 [Guillardia theta CCMP2712]
          Length = 1281

 Score =  247 bits (630), Expect = 4e-62,   Method: Compositional matrix adjust.
 Identities = 129/285 (45%), Positives = 169/285 (59%), Gaps = 39/285 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+DVVLFNRQPSLH++SIMAHRAKVL  RT RFNECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 429 DDDVVLFNRQPSLHRISIMAHRAKVLKWRTLRFNECVCNPYNADFDGDEMNLHVPQTEEA 488

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+               LM   +NL TP++G ++IAATQDF+TG YL+++KN FF+ 
Sbjct: 489 RAEAIE--------------LMGVVNNLCTPKDGSIMIAATQDFLTGSYLISRKNTFFHE 534

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNR----- 515
           AQ     S       D              P   ++   +WTGKQ+ S++LKP +     
Sbjct: 535 AQMWYYCSFTCDAKEDF----------ELEPPAIIKPMRLWTGKQLLSMLLKPRKNTRSL 584

Query: 516 --DCPVNANLKTKGRAYTANEE--------FCHRDSYVILRNSELLAGSMDKSTLGSGGK 565
             D  V  N +     Y    +         C  D+YV  RNSEL+ G++ KSTLG+G K
Sbjct: 585 ETDVEVLVNTELGESQYEKKSDNDIDKGRYMCPHDNYVCFRNSELMCGNLGKSTLGAGNK 644

Query: 566 ANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
            ++FY LLRD   + A   M +L+++ S ++   GF+ GI DV P
Sbjct: 645 NSLFYTLLRDCDAETAADRMTKLAKLCSRWMGLHGFTFGIEDVMP 689



 Score =  211 bits (536), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 154/451 (34%), Positives = 229/451 (50%), Gaps = 62/451 (13%)

Query: 611  GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
             +GFV+NSFF+GL PTEFF HTM GREGLVDTAVKTAE GYM RRL+KSLEDL + YD +
Sbjct: 814  AKGFVENSFFTGLNPTEFFMHTMTGREGLVDTAVKTAECGYMARRLMKSLEDLSIHYDST 873

Query: 671  FDAAF-------YGQTDCISGVSECIIM---GLPMNV------GTGLIKLLQAVPRSEPV 714
               +        YG      G+   ++    G P+N+         L+       RS P 
Sbjct: 874  VRNSHGCIVQFRYGD----DGLDPMLMEDDDGKPINMKRMIQRSCALLGCYGDEERS-PA 928

Query: 715  PRTLLFDNPEFHFPQVYYERRRDYSVKVTASVKV--TLELWNPGDYKLSQD--------- 763
              TL+ +    HF      R R    +  ++V       +  PG     +          
Sbjct: 929  NFTLMTEEQLKHFLDEIICRYRRAVAEPGSAVGALGAQSIGEPGTQMTLKTFHFAGIASM 988

Query: 764  ----GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVF 819
                GVPRIKEIINAS+ ISTP++   L  D D   ARI+KGR+ERTTLG+V +YI++VF
Sbjct: 989  NVTLGVPRIKEIINASKIISTPVVEVPLQLDRDEINARIIKGRIERTTLGQVAKYIKQVF 1048

Query: 820  VPDDSFILIKLDMDRIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSGHSFLILKPKDS 876
             P   ++++KLDM  ++ L L +   +++  I    + +    H++  G   L++ P   
Sbjct: 1049 APSRCYVVVKLDMQCVQDLQLNLSASTVKKAILSDPKLKVKEQHISSKGTDKLLIHPPHD 1108

Query: 877  SKSFNSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMA 932
             +S  S  + +  L   L +V++ G+  I RAVI   +V+ G   Y+LLVEG  L++VMA
Sbjct: 1109 GRSKESLHFMLINLASQLRNVIVCGIPTIRRAVIQSTEVKGGGNSYQLLVEGTGLQEVMA 1168

Query: 933  TYGVKGVKCSSNNTYEV----------------YKTLGIEAARSTIMTEIKLVMENHGMS 976
            T GVKG    +N+  E+                 + LGI       M E  +++ +   +
Sbjct: 1169 TSGVKGASAKTNHVMEMQTVRERRREKGRRERRGEVLGITRFGLAKMKESVMMLASFEKT 1228

Query: 977  IDFRHPMLV---ADLMTSKGEVLGNGTPVEL 1004
            +D  +   +   +D ++   E +  GTPV++
Sbjct: 1229 VDHLYDAAIHGRSDQISGVSECIIMGTPVQI 1259



 Score =  158 bits (400), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 94/232 (40%), Positives = 124/232 (53%), Gaps = 15/232 (6%)

Query: 109 QDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVIN 168
           Q   R    +G LDRRMGT  K   CTTC + L  C GHFGY+ L LPVFH GYF+ +I 
Sbjct: 11  QPATREAALNGPLDRRMGTTDKSLTCTTCHEPLQTCAGHFGYLKLTLPVFHQGYFKAIIT 70

Query: 169 ILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGE 228
           IL  ICK  +C+RVLL  +  +   + +R     +L R +  + I E  KK+SVCP CG 
Sbjct: 71  ILSCICK--SCSRVLLDPDNYSSALSFMRRVQDDHLRRAAKLRAITEECKKISVCPRCGA 128

Query: 229 INGVVKK-----CGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFG-L 282
            NG +KK        L + H+K+    ++K      L AE           +  +  G  
Sbjct: 129 CNGPIKKIPAGGSRYLMLIHDKFAKHEEQKLEFHSMLAAEDKSFSLTKRSQDMKQAIGKA 188

Query: 283 IQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSV 334
            Q L+PL VL +F+ IP ED+       E S+P +LI+T L VPP CIRPSV
Sbjct: 189 AQDLDPLTVLDMFQRIPDEDV-------EHSRPEELIITHLPVPPCCIRPSV 233



 Score =  155 bits (391), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 98/269 (36%), Positives = 144/269 (53%), Gaps = 35/269 (13%)

Query: 1145 GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSG 1201
            G+V +YI++VF P   ++++KLDM  ++ L L +   +++  I    + +    H++  G
Sbjct: 1038 GQVAKYIKQVFAPSRCYVVVKLDMQCVQDLQLNLSASTVKKAILSDPKLKVKEQHISSKG 1097

Query: 1202 HSFLILKPKDSSKSFNSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGV-TKYKLL 1257
               L++ P    +S  S  + +  L   L +V++ G+  I RAVI   +V+G    Y+LL
Sbjct: 1098 TDKLLIHPPHDGRSKESLHFMLINLASQLRNVIVCGIPTIRRAVIQSTEVKGGGNSYQLL 1157

Query: 1258 VEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRH 1317
            VEG  L++VMAT GVKG    +N+  E+         +       +              
Sbjct: 1158 VEGTGLQEVMATSGVKGASAKTNHVMEMQTVRERRREKGRRERRGE-------------- 1203

Query: 1318 PMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSEC 1377
                         VLGITR GLAKMKESV+ LASFE T DHL+DAA +G++D ISGVSEC
Sbjct: 1204 -------------VLGITRFGLAKMKESVMMLASFEKTVDHLYDAAIHGRSDQISGVSEC 1250

Query: 1378 IIMGLPMNVGTGLIKLL-QAVPRSEPVPR 1405
            IIMG P+ +GTG  K+L Q  P+    PR
Sbjct: 1251 IIMGTPVQIGTGSFKVLHQTDPQDAVRPR 1279



 Score = 58.2 bits (139), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 24/42 (57%), Positives = 34/42 (80%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 63
           LM   +NL TP++G ++IAATQDF+TG YL+++KN FF+ AQ
Sbjct: 495 LMGVVNNLCTPKDGSIMIAATQDFLTGSYLISRKNTFFHEAQ 536



 Score = 55.1 bits (131), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 27/50 (54%), Positives = 35/50 (70%), Gaps = 1/50 (2%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL-QAVPRSEPVPR 716
            D  +DAA +G++D ISGVSECIIMG P+ +GTG  K+L Q  P+    PR
Sbjct: 1230 DHLYDAAIHGRSDQISGVSECIIMGTPVQIGTGSFKVLHQTDPQDAVRPR 1279


>gi|303276410|ref|XP_003057499.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226461851|gb|EEH59144.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 1591

 Score =  246 bits (629), Expect = 5e-62,   Method: Compositional matrix adjust.
 Identities = 127/273 (46%), Positives = 172/273 (63%), Gaps = 38/273 (13%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D DV+LFNRQPSLHK+SIMAHRAK++P RT RFNECVC PYNADFDGDEMN+H PQTEE
Sbjct: 470 NDGDVLLFNRQPSLHKMSIMAHRAKIMPWRTLRFNECVCAPYNADFDGDEMNIHCPQTEE 529

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           ARAEA+               LM    NL TP+NGE+LIAATQDF+T  YLLT +++F +
Sbjct: 530 ARAEAIE--------------LMGVHKNLCTPKNGEILIAATQDFLTASYLLTSRDSFLD 575

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           RAQ       L+A   D   ++       W+P  + R  V     Q+F            
Sbjct: 576 RAQV----GLLVAMMGD--ALMSGAYSLHWSP--YDRVGV--ASDQVF------------ 613

Query: 520 NANLKTKGRAY-TANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
             NL+   ++Y    +  C RD YV ++NSE++ G + K+TLG G K  +FY+L  ++G 
Sbjct: 614 -VNLEVAEKSYGKVGKHMCPRDGYVCVQNSEIMCGQLGKATLGGGNKTGLFYVLNSEYGP 672

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           +V  +AM R++++++ +L +RGFS+GI DVTPG
Sbjct: 673 EVTASAMNRVAKLSARWLGSRGFSVGIDDVTPG 705



 Score =  243 bits (621), Expect = 4e-61,   Method: Compositional matrix adjust.
 Identities = 151/374 (40%), Positives = 205/374 (54%), Gaps = 83/374 (22%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYI 1151
            C +KY   +IEP +AVGA+ AQSIGEPGTQMTLKTFHFAG              E+    
Sbjct: 1176 CVQKYDAKRIEPGSAVGAVGAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINAS 1235

Query: 1152 EEVFVP--------DDS--------------------------------FILIKLDMDRI 1171
            + +  P        DD                                 ++ + LD D I
Sbjct: 1236 KNISTPIITATLACDDDVKAARVVKGRVEKTTLGEVCKHIHVVFDPTACYLEVALDPDVI 1295

Query: 1172 RLLHLEVDIDSIRYCIERTRGISGH----LTVSGHSFLILKPKDSS-------------- 1213
            R L L+V + +++  +  T  +       L  +G+   +L P  S               
Sbjct: 1296 RALQLDVTVATVKRALLSTTKLKLKPNRVLERAGNVLHVLPPDASDAAAARTAAARDAVG 1355

Query: 1214 ------KSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVM 1267
                   +FN  +  ++  +P+V+++G+  ++RAVI++   +G  K  L+VEG +LR VM
Sbjct: 1356 PAAIHRDAFN--LQNLRTAVPNVIVQGIPSVSRAVIND---KGGGKLNLVVEGTDLRAVM 1410

Query: 1268 ATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTS 1327
            AT G++G + ++N+  E  +TLGIEAAR  I+ EI   M+ HGMSID RH ML+AD+MT 
Sbjct: 1411 ATEGIEGTRTTTNHVMEAERTLGIEAARFCIIKEINDTMKAHGMSIDARHSMLLADVMTY 1470

Query: 1328 KGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVG 1387
            KGEVLGITR G+AKMK+SVL LASFE T+DHLFDAA  G+ D I GVSECIIMG+PM VG
Sbjct: 1471 KGEVLGITRFGMAKMKDSVLMLASFEKTTDHLFDAALRGRVDTIDGVSECIIMGIPMPVG 1530

Query: 1388 TGLIKLLQAVPRSE 1401
            TG+ KL     R E
Sbjct: 1531 TGMFKLRHRAMRLE 1544



 Score =  204 bits (520), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 113/241 (46%), Positives = 151/241 (62%), Gaps = 15/241 (6%)

Query: 100 QIVSKNLYCQDPQRTPIPHGLLDRRMGT-NQKEANCTTCGQNLSDCVGHFGYIDLPLPVF 158
            +  +NLY Q PQR P+P G+LD RMGT ++K A C TC   L DC GHFGY+ L LPVF
Sbjct: 56  HVYERNLY-QMPQRVPLPGGILDPRMGTTDKKGAECATCKGKLIDCAGHFGYVKLELPVF 114

Query: 159 HIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTK 218
           HIGYF+ VI+ILQ +CK  TC+RV+L EE+   +  + RNP L  + R++L KK+ +  K
Sbjct: 115 HIGYFKNVISILQQVCK--TCSRVMLPEEEHEQYLRRFRNPRLENVPRRALSKKMADRCK 172

Query: 219 KVSVCPHCGEINGVVKKCGL-LKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAH 277
           +   C +CG  NGVVK+ G  LKI HEKY     K   ++E+ L ++ EAVKFN +++  
Sbjct: 173 RCRTCYYCGAANGVVKRAGQSLKIVHEKY----SKNPELMEEYLKQFEEAVKFNDQLK-- 226

Query: 278 KKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVIS 336
           +    +Q  LNP+ V+ +F  I   D  LL +     +P  LILT L VPP CIRPSV  
Sbjct: 227 QNLSRVQDDLNPIRVISIFRRISPMDCELLDI---ADRPEHLILTHLPVPPVCIRPSVEM 283

Query: 337 D 337
           D
Sbjct: 284 D 284



 Score =  196 bits (497), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 113/258 (43%), Positives = 161/258 (62%), Gaps = 29/258 (11%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+NISTPIITA L  D D+  AR+VKGR+E+TTLGEVC++I  VF P  
Sbjct: 1224 GVPRIKEIINASKNISTPIITATLACDDDVKAARVVKGRVEKTTLGEVCKHIHVVFDPTA 1283

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGH----LTVSGHSFLILKPKDSS-- 877
             ++ + LD D IR L L+V + +++  +  T  +       L  +G+   +L P  S   
Sbjct: 1284 CYLEVALDPDVIRALQLDVTVATVKRALLSTTKLKLKPNRVLERAGNVLHVLPPDASDAA 1343

Query: 878  ------------------KSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYK 919
                               +FN  +  ++  +P+V+++G+  ++RAVI++   +G  K  
Sbjct: 1344 AARTAAARDAVGPAAIHRDAFN--LQNLRTAVPNVIVQGIPSVSRAVIND---KGGGKLN 1398

Query: 920  LLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDF 979
            L+VEG +LR VMAT G++G + ++N+  E  +TLGIEAAR  I+ EI   M+ HGMSID 
Sbjct: 1399 LVVEGTDLRAVMATEGIEGTRTTTNHVMEAERTLGIEAARFCIIKEINDTMKAHGMSIDA 1458

Query: 980  RHPMLVADLMTSKGEVLG 997
            RH ML+AD+MT KGEVLG
Sbjct: 1459 RHSMLLADVMTYKGEVLG 1476



 Score =  106 bits (264), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 49/64 (76%), Positives = 56/64 (87%), Gaps = 1/64 (1%)

Query: 606 GDVTPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           G+ TP  +GFV NSFFSG+ PTEFFFHTM GREGLVDTAVKTAETGYM RRL+K+LEDL 
Sbjct: 823 GEKTPAAKGFVANSFFSGMRPTEFFFHTMAGREGLVDTAVKTAETGYMSRRLMKALEDLS 882

Query: 665 VQYD 668
           ++YD
Sbjct: 883 LRYD 886



 Score = 60.5 bits (145), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 26/42 (61%), Positives = 33/42 (78%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 63
           LM    NL TP+NGE+LIAATQDF+T  YLLT +++F +RAQ
Sbjct: 537 LMGVHKNLCTPKNGEILIAATQDFLTASYLLTSRDSFLDRAQ 578



 Score = 56.6 bits (135), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 27/45 (60%), Positives = 30/45 (66%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSE 712
            D  FDAA  G+ D I GVSECIIMG+PM VGTG+ KL     R E
Sbjct: 1500 DHLFDAALRGRVDTIDGVSECIIMGIPMPVGTGMFKLRHRAMRLE 1544


>gi|6624245|dbj|BAA88487.1| RNA polymerase III largest subunit [Lethenteron reissneri]
          Length = 538

 Score =  246 bits (628), Expect = 7e-62,   Method: Compositional matrix adjust.
 Identities = 126/227 (55%), Positives = 163/227 (71%), Gaps = 22/227 (9%)

Query: 391 NVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYL 450
           N+HLPQTEEA+AEAL              +LM  K+NLVTPRNGE LIAA QDFITGGYL
Sbjct: 1   NLHLPQTEEAKAEAL--------------ILMGTKANLVTPRNGEPLIAAIQDFITGGYL 46

Query: 451 LTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLI 510
           LT K+ FF+RA+  +IA++++A     C    R +     P V V+   +WTGKQ+FSLI
Sbjct: 47  LTHKDTFFDRARASQIAASMLAG----CDSAVRITLP--RPAV-VKPVSLWTGKQVFSLI 99

Query: 511 LKPNRDCPVNANLKTKGRAYTAN-EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVF 569
           L+PN   PV  NL+T+G+ YT + E+ C  DS+V++ NSELLAGS+DKSTLGSG KA+VF
Sbjct: 100 LRPNPRDPVRLNLRTRGKQYTGHGEDLCTSDSFVVIENSELLAGSLDKSTLGSGSKASVF 159

Query: 570 YILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           Y+LLRD+G++ A   M RL+RMT  +L NRGFS+GIGDVTPG+G ++
Sbjct: 160 YLLLRDWGQEAAACGMSRLARMTPAFLSNRGFSVGIGDVTPGRGLLR 206



 Score =  118 bits (295), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 52/63 (82%), Positives = 58/63 (92%)

Query: 608 VTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           +   +GFV NSF+SGL+PTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC QY
Sbjct: 322 IPAAKGFVANSFYSGLSPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCAQY 381

Query: 668 DMS 670
           D++
Sbjct: 382 DLT 384



 Score = 81.3 bits (199), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 36/54 (66%), Positives = 46/54 (85%)

Query: 21 VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
          +LM  K+NLVTPRNGE LIAA QDFITGGYLLT K+ FF+RA+  +IA++++AG
Sbjct: 16 ILMGTKANLVTPRNGEPLIAAIQDFITGGYLLTHKDTFFDRARASQIAASMLAG 69



 Score = 53.9 bits (128), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 37/133 (27%), Positives = 72/133 (54%), Gaps = 8/133 (6%)

Query: 1000 TPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKFLEE 1059
            +P++ +R+L  +       ++ +LS+ ++L      L+S E ++    +F++D++ FLE 
Sbjct: 412  SPLDFQRVLSHVKCNYPCPTESALSSSQLLLSGRAALESSELMECHGGDFLQDLRLFLEL 471

Query: 1060 FSKKESVTSHQDKV--SQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEP 1117
            +S +   T  +  +  S     +IL   D++       P       + CR+KY+R+++EP
Sbjct: 472  YSARIHKTRQKYGINDSGTTTPRILYQLDRV------TPTQLERFLQTCRDKYLRSRMEP 525

Query: 1118 ATAVGALAAQSIG 1130
             +AVGA+ AQSIG
Sbjct: 526  GSAVGAVCAQSIG 538


>gi|323457244|gb|EGB13110.1| hypothetical protein AURANDRAFT_35850 [Aureococcus anophagefferens]
          Length = 1398

 Score =  246 bits (627), Expect = 8e-62,   Method: Compositional matrix adjust.
 Identities = 133/280 (47%), Positives = 172/280 (61%), Gaps = 34/280 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIM+H  KV+P RTFRFNECVC PYNADFDGDEMN+HLPQTEEA
Sbjct: 446 DGDVVLFNRQPSLHKLSIMSHEVKVMPWRTFRFNECVCAPYNADFDGDEMNMHLPQTEEA 505

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A  LM   +N+ TPRNGE L+AATQDF+T  +L+TQ++ FF+R
Sbjct: 506 RAE--------------ASALMNVATNICTPRNGEPLVAATQDFVTASFLVTQRDVFFDR 551

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDC-PV 519
                +A+  + D  +   +          P   ++   +WTGKQ+FSLI++P     P 
Sbjct: 552 DAFCALAA-YVGDALERVDV---------PPPAILKPVRLWTGKQLFSLIVRPTVAAKPE 601

Query: 520 NA------NLKTKGRAYTAN--EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYI 571
           N       + +   R YT +  E  C  D YV+ R S LL G++ K T+G G K  + Y 
Sbjct: 602 NGGAWPCVSFECAERNYTGSGIETMCPMDGYVLFRRSSLLCGNIAKKTVGDGSKKGLVYE 661

Query: 572 LLRDFGEDVAVTAMWRLSRMTSFYL-MNRGFSIGIGDVTP 610
           L R+ G   A T M RL+++++ YL  ++GFSIGI DVTP
Sbjct: 662 LYREHGPAAAATFMNRLAKLSARYLGYHKGFSIGIDDVTP 701



 Score =  219 bits (558), Expect = 9e-54,   Method: Compositional matrix adjust.
 Identities = 119/261 (45%), Positives = 166/261 (63%), Gaps = 10/261 (3%)

Query: 1145 GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGH----LTVS 1200
            GE+C+ ++EV+ P   ++ ++LD   I  LHL+VD  + R  + +    SG     +   
Sbjct: 1116 GEICKSMKEVYGPRSCYVSVELDATLIADLHLDVDAAAARKRVLQAVMASGRAPPVIRAL 1175

Query: 1201 GHSFLILKPKDSSKSFNS------KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKY 1254
             +  ++L P   ++   S       M  +K  LPS+V+ GV  INRAV++E++      Y
Sbjct: 1176 KNEHVLLNPNHRNRDMLSDDRTYFAMQALKSALPSIVVGGVSSINRAVVNEDEGSSPATY 1235

Query: 1255 KLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSID 1314
             LLVEG  L DVM T GV G + ++N+  E+   LGIEAARSTI  EI  +M  +G+ ID
Sbjct: 1236 HLLVEGYGLADVMGTPGVDGRRTTTNHVAEIEAVLGIEAARSTIANEITYIMSAYGIGID 1295

Query: 1315 FRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGV 1374
             RH ML++D+MT KG VLGITR G++KM+ESVL LASFE T+DHLFDAA +G+ D I GV
Sbjct: 1296 ARHLMLLSDVMTFKGVVLGITRFGVSKMRESVLMLASFERTTDHLFDAAAHGRRDNIVGV 1355

Query: 1375 SECIIMGLPMNVGTGLIKLLQ 1395
            SECIIMG+P+ +G G  KLL+
Sbjct: 1356 SECIIMGIPIPLGCGSFKLLR 1376



 Score =  198 bits (503), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 109/244 (44%), Positives = 152/244 (62%), Gaps = 10/244 (4%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPR+ EIINAS+NISTPIITA+LD  +    AR+VK RLE+TTLGE+C+ ++EV+ P  
Sbjct: 1071 GVPRLTEIINASKNISTPIITAHLDNPSSTTAARVVKARLEKTTLGEICKSMKEVYGPRS 1130

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGH----LTVSGHSFLILKPKDSSKS 879
             ++ ++LD   I  LHL+VD  + R  + +    SG     +    +  ++L P   ++ 
Sbjct: 1131 CYVSVELDATLIADLHLDVDAAAARKRVLQAVMASGRAPPVIRALKNEHVLLNPNHRNRD 1190

Query: 880  FNS------KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMAT 933
              S       M  +K  LPS+V+ GV  INRAV++E++      Y LLVEG  L DVM T
Sbjct: 1191 MLSDDRTYFAMQALKSALPSIVVGGVSSINRAVVNEDEGSSPATYHLLVEGYGLADVMGT 1250

Query: 934  YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
             GV G + ++N+  E+   LGIEAARSTI  EI  +M  +G+ ID RH ML++D+MT KG
Sbjct: 1251 PGVDGRRTTTNHVAEIEAVLGIEAARSTIANEITYIMSAYGIGIDARHLMLLSDVMTFKG 1310

Query: 994  EVLG 997
             VLG
Sbjct: 1311 VVLG 1314



 Score =  169 bits (427), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 87/241 (36%), Positives = 136/241 (56%), Gaps = 25/241 (10%)

Query: 111 PQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINIL 170
           P R P P+G LD R+G   K+  C TC + +  C GHFG + L LPVFH+GYF+ V+ IL
Sbjct: 18  PSRKPAPNGCLDLRLGAANKQTACATCHKRVDQCAGHFGVVRLELPVFHVGYFKHVLTIL 77

Query: 171 QSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEIN 230
           Q +CK   C+R L+  ++      ++R+P    L +++L K++++  K  S CP+CG  N
Sbjct: 78  QCVCKE--CSRALVHPQERTTLLRRMRDPRADALRKQALYKRVVDRCKAASKCPYCGARN 135

Query: 231 GVVKK---CGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQT-- 285
           G V+K    G LK+SHEK++   K++D + +D  + Y E+++           G + T  
Sbjct: 136 GPVRKVAGAGALKLSHEKWRG-VKREDLLDDDEFSAYAESLE--------SALGAVPTSA 186

Query: 286 ---------LNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVIS 336
                    L+P++V  + E I  +D  LL ++  + +P +L+L  LLVPP  IRPSV  
Sbjct: 187 TATKAPPTVLSPVDVRAILEKISDDDCDLLWIDPRVGRPENLVLKTLLVPPTPIRPSVAV 246

Query: 337 D 337
           D
Sbjct: 247 D 247



 Score =  109 bits (272), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 50/65 (76%), Positives = 59/65 (90%), Gaps = 1/65 (1%)

Query: 605 IGDVTPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDL 663
           +G+++PG +GFV NSF+SGLT TEFFFHTMGGREGLVDTAVKTA+TGYM RRL+K+LEDL
Sbjct: 820 VGELSPGARGFVANSFYSGLTATEFFFHTMGGREGLVDTAVKTAQTGYMARRLMKALEDL 879

Query: 664 CVQYD 668
            V YD
Sbjct: 880 SVGYD 884



 Score = 63.2 bits (152), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 50/164 (30%), Positives = 72/164 (43%), Gaps = 28/164 (17%)

Query: 997  GNGTPVELKRLL-----DDIIAKNSSRSDPSLSAQEILALSNETLDSKEF--LQDTSENF 1049
            G+  PV+  RLL     DD    + +  D   +A   +A +    D+  F  L   +  F
Sbjct: 912  GDSMPVDFGRLLHRVRHDDAALSSRAPRDLDAAAVAAVAEACGAGDAGPFGRLGPLAAKF 971

Query: 1050 VRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEA---- 1105
              D   FL + S++             + ++ L  +D  G    +  F     ++     
Sbjct: 972  RGDAAGFLRDLSER-------------MADRELQMKDHCGDAALARLFDDVALSQGDLDR 1018

Query: 1106 ----CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
                  +KY R  +EP  AVGA+ AQ I EPGTQMTLKTFHFAG
Sbjct: 1019 FQAGALDKYTRGVVEPGEAVGAIGAQCISEPGTQMTLKTFHFAG 1062



 Score = 56.2 bits (134), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/41 (56%), Positives = 32/41 (78%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
            LM   +N+ TPRNGE L+AATQDF+T  +L+TQ++ FF+R
Sbjct: 511 ALMNVATNICTPRNGEPLVAATQDFVTASFLVTQRDVFFDR 551



 Score = 49.7 bits (117), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 23/39 (58%), Positives = 29/39 (74%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  FDAA +G+ D I GVSECIIMG+P+ +G G  KLL+
Sbjct: 1338 DHLFDAAAHGRRDNIVGVSECIIMGIPIPLGCGSFKLLR 1376


>gi|422295500|gb|EKU22799.1| DNA-directed RNA polymerase subunit A' [Nannochloropsis gaditana
            CCMP526]
          Length = 620

 Score =  245 bits (626), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 151/379 (39%), Positives = 203/379 (53%), Gaps = 78/379 (20%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYIEEV 1154
            +Y RA +EP  AVGA+ AQSI EP TQMTLKTFHFAG              E+    +E+
Sbjct: 241  RYNRACVEPGEAVGAVGAQSISEPATQMTLKTFHFAGVASMNVTLGVPRLKEIINASKEI 300

Query: 1155 ----------------------------------------FVPDDSFILIKLDMDRIRLL 1174
                                                    + P   ++ I LD + I  L
Sbjct: 301  STPIITAALVQDRSETAARVAKAAIERTTIGQVARHIKEVYAPHMVYVEILLDQEAITKL 360

Query: 1175 HLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKD---------------------SS 1213
            HL VD  S+R  I R    +  L       ++  P+                      S 
Sbjct: 361  HLRVDAASVRMAILRGPHRASVLKALKERDVLYDPRHPDRLRVLPPELKEGRAGNAVPSE 420

Query: 1214 KSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVT-KYKLLVEGDNLRDVMATYGV 1272
            +     +  +K  LP+V+++G+  +NRA++++  VEG   +Y LL+EG  L DVM T GV
Sbjct: 421  RRIYFVIQALKVALPAVMVRGISTVNRAIVNK--VEGEEDRYNLLIEGYGLADVMGTPGV 478

Query: 1273 KGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL 1332
             G +  SN+  EV + LGIEAAR+ + TEI+ +M+ +G+ ID RH ML++D+MT KGEVL
Sbjct: 479  DGRQAKSNHIIEVERVLGIEAARAVVGTEIENIMQAYGIRIDTRHRMLLSDVMTFKGEVL 538

Query: 1333 GITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIK 1392
            GITR G+AKM+ESVL LASFE T+DHLFDAA +G+TD I GVSECIIMG+P+ +GTGL K
Sbjct: 539  GITRFGVAKMRESVLMLASFEKTTDHLFDAAVHGRTDAIVGVSECIIMGIPIPLGTGLFK 598

Query: 1393 LLQAVPRSEPVPRTLLFDN 1411
            LL  VP+     R  L D 
Sbjct: 599  LLHDVPKPGIATRKGLLDE 617



 Score =  179 bits (455), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 105/256 (41%), Positives = 151/256 (58%), Gaps = 24/256 (9%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
           GVPR+KEIINAS+ ISTPIITA L +D     AR+ K  +ERTT+G+V  +I+EV+ P  
Sbjct: 286 GVPRLKEIINASKEISTPIITAALVQDRSETAARVAKAAIERTTIGQVARHIKEVYAPHM 345

Query: 824 SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKD-------- 875
            ++ I LD + I  LHL VD  S+R  I R    +  L       ++  P+         
Sbjct: 346 VYVEILLDQEAITKLHLRVDAASVRMAILRGPHRASVLKALKERDVLYDPRHPDRLRVLP 405

Query: 876 -------------SSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVT-KYKLL 921
                        S +     +  +K  LP+V+++G+  +NRA++++  VEG   +Y LL
Sbjct: 406 PELKEGRAGNAVPSERRIYFVIQALKVALPAVMVRGISTVNRAIVNK--VEGEEDRYNLL 463

Query: 922 VEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRH 981
           +EG  L DVM T GV G +  SN+  EV + LGIEAAR+ + TEI+ +M+ +G+ ID RH
Sbjct: 464 IEGYGLADVMGTPGVDGRQAKSNHIIEVERVLGIEAARAVVGTEIENIMQAYGIRIDTRH 523

Query: 982 PMLVADLMTSKGEVLG 997
            ML++D+MT KGEVLG
Sbjct: 524 RMLLSDVMTFKGEVLG 539



 Score = 65.5 bits (158), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 31/55 (56%), Positives = 37/55 (67%)

Query: 668 DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDN 722
           D  FDAA +G+TD I GVSECIIMG+P+ +GTGL KLL  VP+     R  L D 
Sbjct: 563 DHLFDAAVHGRTDAIVGVSECIIMGIPIPLGTGLFKLLHDVPKPGIATRKGLLDE 617


>gi|297793561|ref|XP_002864665.1| hypothetical protein ARALYDRAFT_496142 [Arabidopsis lyrata subsp.
           lyrata]
 gi|297310500|gb|EFH40924.1| hypothetical protein ARALYDRAFT_496142 [Arabidopsis lyrata subsp.
           lyrata]
          Length = 1376

 Score =  245 bits (626), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 123/277 (44%), Positives = 174/277 (62%), Gaps = 29/277 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + D VLFNRQPSLH++SIM HRA+++P RT RFNE VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 456 EGDAVLFNRQPSLHRMSIMCHRARIMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EA+               LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+K+ F++R
Sbjct: 516 RTEAI--------------TLMGVQNNLCTPKNGEILVASTQDFLTTSFLITRKDTFYDR 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A    I S +  D  D   +          P +  +   +WTGKQ+FS++L+PN    V 
Sbjct: 562 AAFSLICSYM-GDGMDAIDLP--------TPTIL-KPIELWTGKQLFSVLLRPNASVRVY 611

Query: 521 ANLKTKGRAYTA-----NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
             L  K + +       +E  C  D +V  RNSEL++G + K+TLG+G K  ++ ILLRD
Sbjct: 612 VTLNVKEKNFKKGEHGFDETMCVNDGWVYFRNSELISGQLGKATLGNGNKDGLYSILLRD 671

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
           +    A   M RL+++++ ++   GFSIGI DV PG+
Sbjct: 672 YNSHAAAVCMNRLAKLSARWIGIHGFSIGIDDVQPGE 708



 Score =  209 bits (531), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 120/270 (44%), Positives = 169/270 (62%), Gaps = 14/270 (5%)

Query: 1145 GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSG 1201
            G+V E IE +     + + I LD   I    L +   S++  I +T  I      + V  
Sbjct: 1102 GQVAESIEVLMTSTSASVRIILDNKIIEEACLSISPWSVKNSILKTPRIKLNDNDIRVLD 1161

Query: 1202 HSFLILKPKDSSKS-FNSKMYQMKQLLPSVVIKGVQGINRAVIHEE-----DVEGVTKYK 1255
                I    D S++ FN  ++ +K +LP++++ G++ + R V+ E+      ++G T++K
Sbjct: 1162 TGLDITPVVDKSRTHFN--LHNLKNVLPNIIVNGIKTVERVVVAEDMDKNKQIDGKTRWK 1219

Query: 1256 LLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDF 1315
            L VEG NL  VM T G+ G   +SNN  EV KTLGIEAAR+TI+ EI  VM NHGMSID 
Sbjct: 1220 LFVEGTNLLAVMGTPGINGRTTTSNNVVEVSKTLGIEAARTTIIDEIGTVMGNHGMSIDI 1279

Query: 1316 RHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVS 1375
            RH ML+AD+MT +GEVLGI R G+ KM +SVL  ASFE T DHLF AA  G+ D I GV+
Sbjct: 1280 RHMMLLADVMTYRGEVLGIQRTGIQKMDKSVLMQASFERTGDHLFSAAISGKVDNIEGVT 1339

Query: 1376 ECIIMGLPMNVGTGLIKLLQAVPRSEPVPR 1405
            EC+IMG+PM +GTG++K+LQ   R++ +P+
Sbjct: 1340 ECVIMGIPMKLGTGILKVLQ---RTDDLPK 1366



 Score =  189 bits (479), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 111/243 (45%), Positives = 153/243 (62%), Gaps = 11/243 (4%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRI EIINAS+NISTP+I+A L+   +L  AR VKGR+E+TTLG+V E IE +     
Sbjct: 1057 GVPRINEIINASKNISTPVISAELENPLELTSARWVKGRIEKTTLGQVAESIEVLMTSTS 1116

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFLILKPKDSSKS- 879
            + + I LD   I    L +   S++  I +T  I      + V      I    D S++ 
Sbjct: 1117 ASVRIILDNKIIEEACLSISPWSVKNSILKTPRIKLNDNDIRVLDTGLDITPVVDKSRTH 1176

Query: 880  FNSKMYQMKQLLPSVVIKGVQGINRAVIHEE-----DVEGVTKYKLLVEGDNLRDVMATY 934
            FN  ++ +K +LP++++ G++ + R V+ E+      ++G T++KL VEG NL  VM T 
Sbjct: 1177 FN--LHNLKNVLPNIIVNGIKTVERVVVAEDMDKNKQIDGKTRWKLFVEGTNLLAVMGTP 1234

Query: 935  GVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGE 994
            G+ G   +SNN  EV KTLGIEAAR+TI+ EI  VM NHGMSID RH ML+AD+MT +GE
Sbjct: 1235 GINGRTTTSNNVVEVSKTLGIEAARTTIIDEIGTVMGNHGMSIDIRHMMLLADVMTYRGE 1294

Query: 995  VLG 997
            VLG
Sbjct: 1295 VLG 1297



 Score =  135 bits (341), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 89/289 (30%), Positives = 146/289 (50%), Gaps = 31/289 (10%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           I  +V  +  V + + +Q+   N Y  +    P  +GLLD RMG   K++ CTTC  N  
Sbjct: 26  INFSVLSDLEVMKAAEVQVWKNNYY--ETNLKPYENGLLDARMGPPNKKSICTTCDGNFQ 83

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALS 202
           +C GH+GY+ L LPV+++G+F  +++IL+ ICK   C+ +LL E+       K+RNP + 
Sbjct: 84  NCPGHYGYLKLDLPVYNVGFFNFILDILKCICKR--CSNMLLDEKLYEDHLRKMRNPKME 141

Query: 203 YLVRKSLKKKILE-----TTKKVSVCPHCGEINGVVKKCGL---LKISHEKYKNRTKKKD 254
            L +  L K +++      ++++  C  CG +NG+VKK      + ISH++ K    + D
Sbjct: 142 PLKKTELAKAVVKKCSTMASQRIITCKKCGYLNGMVKKIAAQMGIGISHDRSKIHGGEVD 201

Query: 255 AIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSK 314
                +          NP         L   L+P  VL LF+ +  +D  LL +     +
Sbjct: 202 ECKSAISHTKESTRAINP---------LTYVLDPNLVLGLFKGMSDKDCELLYI---AHR 249

Query: 315 PSDLILTRLLVPPNCIRPSVI--SDLKSDNDV-----VLFNRQPSLHKL 356
           P +LI T +LVPP  IRPSV+      ++ND+     ++      LH++
Sbjct: 250 PENLITTCMLVPPLSIRPSVMIGGTRSNENDITERLKLIIQNNACLHRI 298



 Score =  103 bits (258), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 47/58 (81%), Positives = 51/58 (87%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV NSF+SGLT TEFFFHTMGGREGLVDTAVKTA TGYM RRL+K+LEDL V YD
Sbjct: 831 AKGFVANSFYSGLTATEFFFHTMGGREGLVDTAVKTASTGYMSRRLMKALEDLLVHYD 888



 Score = 67.8 bits (164), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 48/149 (32%), Positives = 72/149 (48%), Gaps = 18/149 (12%)

Query: 998  NGTPVELKRLLDDIIAKNSSRSDPS-LSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            +G P+   RL   I A    RS  + LS++E+     E L   +  +  ++ FV+ +++F
Sbjct: 917  DGAPLNFDRLFLKIQATCPPRSHHNYLSSEELSQKFEEELVRHDKSRVCTDAFVKSLREF 976

Query: 1057 LEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIE 1116
            +     K + T      +  + ++ L    KI                 C  +Y   +IE
Sbjct: 977  VSLLGVKSASTPQVLYKASGVTDKQLEVFVKI-----------------CVSRYREKKIE 1019

Query: 1117 PATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
              TA+G + AQSIGEPGTQMTLKTFHFAG
Sbjct: 1020 AGTAIGTIGAQSIGEPGTQMTLKTFHFAG 1048



 Score = 57.0 bits (136), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 25/53 (47%), Positives = 39/53 (73%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+K+ F++RA    I S +  G
Sbjct: 522 LMGVQNNLCTPKNGEILVASTQDFLTTSFLITRKDTFYDRAAFSLICSYMGDG 574



 Score = 54.7 bits (130), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 24/49 (48%), Positives = 36/49 (73%), Gaps = 3/49 (6%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPR 716
            D  F AA  G+ D I GV+EC+IMG+PM +GTG++K+LQ   R++ +P+
Sbjct: 1321 DHLFSAAISGKVDNIEGVTECVIMGIPMKLGTGILKVLQ---RTDDLPK 1366


>gi|302785289|ref|XP_002974416.1| hypothetical protein SELMODRAFT_442419 [Selaginella moellendorffii]
 gi|300158014|gb|EFJ24638.1| hypothetical protein SELMODRAFT_442419 [Selaginella moellendorffii]
          Length = 1348

 Score =  245 bits (626), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 122/276 (44%), Positives = 168/276 (60%), Gaps = 29/276 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIM HRA+V+P RT RFNE VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 468 DGDIVLFNRQPSLHRMSIMCHRARVMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEA 527

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL               LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+++ F++R
Sbjct: 528 RTEAL--------------TLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRRDTFYDR 573

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q   + S +      I                 ++   +WTGKQ+F ++++P+    V 
Sbjct: 574 GQFALMCSYMGDAVEHI----------DLPTPAILKPVELWTGKQLFGVLIRPSARIKVF 623

Query: 521 ANLKTKGRAY-TANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            N     + +    E  C +D YV  +NSEL+ G + K TLG+G K  +F +LLRD+GE 
Sbjct: 624 LNFVVCEKNHKKGTETMCPKDGYVFFKNSELICGQLGKGTLGNGSKDGLFTVLLRDYGEQ 683

Query: 580 VAVTAMWRLSRMTSFYLM----NRGFSIGIGDVTPG 611
            A + M RL+++   Y      N GFSIGI DV PG
Sbjct: 684 AAASCMNRLAKLRHSYFARWIGNHGFSIGIDDVQPG 719



 Score =  202 bits (514), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 113/256 (44%), Positives = 162/256 (63%), Gaps = 11/256 (4%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ ISTPIITA L  + D+  ARIVKGR+E+T LG+V + I+ V  P  
Sbjct: 1082 GVPRIKEIINASKKISTPIITAKLVSENDVKAARIVKGRIEKTALGDVAKSIKIVLRPGQ 1141

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISG------HLTVS-GHSFLILKPKDS 876
            +F+ IKLDMDRI  L L++  +++   + +   I        H+ V+   S  +  P+  
Sbjct: 1142 AFVSIKLDMDRIYSLQLDIRAETVAEAVLKFPKIKSMKLKEQHVKVNDDRSISLTTPESD 1201

Query: 877  SKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGV 936
             K     ++ ++ +LP V++KG+  + RAVI++E      KY LLVEG NL+ VM T GV
Sbjct: 1202 RKKMLFALHSLQNMLPKVIVKGIPTVERAVINQEK----GKYNLLVEGTNLKAVMGTEGV 1257

Query: 937  KGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL 996
             G + +SN+ +E  + LGIEAAR+ I+ EI+  M +HGMSID RH ML+AD+MT +GE  
Sbjct: 1258 DGRETTSNHIFETVEVLGIEAARNGIIKEIQYTMGSHGMSIDQRHMMLLADVMTYRGEFW 1317

Query: 997  GNGTPVELKRLLDDII 1012
            G+    E + L  D++
Sbjct: 1318 GSRELEEFQSLFMDLL 1333



 Score =  195 bits (495), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 109/249 (43%), Positives = 155/249 (62%), Gaps = 11/249 (4%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + V + + +QI   +LY Q P+R P+P+G+LD R+GT+ K+  CTTC   L+DC GHFGY
Sbjct: 43  EEVTKTAEVQIFEHSLY-QLPERKPLPYGVLDTRLGTSNKKGQCTTCDGKLADCPGHFGY 101

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNP-TCARVLLGEEKAAGFRAKLRNPALSYLVRKSL 209
           I L LPVFHIGYF+ +I ILQ ICK   +   V+  +E+   ++ +++NP    L +K  
Sbjct: 102 IKLELPVFHIGYFKDIIVILQCICKASFSFLEVVASQEERQKWQRRMQNPRSEILRKKEY 161

Query: 210 KKKILETTKKVSVCPHCGEINGVVKKCG-LLKISHEKYKNRTKKKDAIVEDLLAEYNEAV 268
            KKI +  KKV  CP CG+INGVVKK G  LKI H+KY     K     E++  ++++AV
Sbjct: 162 LKKINDLCKKVRACPRCGDINGVVKKLGSTLKIIHDKY----AKNYEAFEEMAHKFDDAV 217

Query: 269 KFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPN 328
           K N E++ + K  + + L PL+VL LFE I  ED  +L +   + +P  LI+  + VPP 
Sbjct: 218 KVNKEMKGYMK-NIQEDLTPLKVLGLFEKIIGEDCVVLDL---VDRPEQLIVQHMPVPPV 273

Query: 329 CIRPSVISD 337
            IRPSV  D
Sbjct: 274 AIRPSVEMD 282



 Score =  138 bits (347), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 78/196 (39%), Positives = 118/196 (60%), Gaps = 11/196 (5%)

Query: 1145 GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISG------HLT 1198
            G+V + I+ V  P  +F+ IKLDMDRI  L L++  +++   + +   I        H+ 
Sbjct: 1127 GDVAKSIKIVLRPGQAFVSIKLDMDRIYSLQLDIRAETVAEAVLKFPKIKSMKLKEQHVK 1186

Query: 1199 VSG-HSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLL 1257
            V+   S  +  P+   K     ++ ++ +LP V++KG+  + RAVI++E      KY LL
Sbjct: 1187 VNDDRSISLTTPESDRKKMLFALHSLQNMLPKVIVKGIPTVERAVINQEK----GKYNLL 1242

Query: 1258 VEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRH 1317
            VEG NL+ VM T GV G + +SN+ +E  + LGIEAAR+ I+ EI+  M +HGMSID RH
Sbjct: 1243 VEGTNLKAVMGTEGVDGRETTSNHIFETVEVLGIEAARNGIIKEIQYTMGSHGMSIDQRH 1302

Query: 1318 PMLVADLMTSKGEVLG 1333
             ML+AD+MT +GE  G
Sbjct: 1303 MMLLADVMTYRGEFWG 1318



 Score =  110 bits (274), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 67/133 (50%), Positives = 81/133 (60%), Gaps = 11/133 (8%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D TP  +GFV NSF+SGLT TEF FHTMGGREGLVDTAVKTAETGYM RRL+K+LEDL  
Sbjct: 838 DKTPQAKGFVANSFYSGLTATEFIFHTMGGREGLVDTAVKTAETGYMSRRLMKALEDLSC 897

Query: 666 QYDMSFDAA-------FYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPR--SEPVPR 716
           QYD +   +        YG  D +  VS     G P+N+   L+K     PR  +  +P 
Sbjct: 898 QYDGTVRNSSGVIVQLIYGD-DSMDPVSMEGQNGTPLNLDRVLMKAKATCPRGATPALPP 956

Query: 717 TLLFDNPEFHFPQ 729
           + L+   E  F Q
Sbjct: 957 SELWKIVESKFSQ 969



 Score = 82.8 bits (203), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 60/159 (37%), Positives = 90/159 (56%), Gaps = 25/159 (15%)

Query: 998  NGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSE---NFVRDIK 1054
            NGTP+ L R+L    A     + P+L   E+  +    ++SK F QD SE    F+  ++
Sbjct: 929  NGTPLNLDRVLMKAKATCPRGATPALPPSELWKI----VESK-FSQDGSECSMAFLDSLR 983

Query: 1055 KFL-EEFSKKESVTSHQDKVSQPLR-------EQILSHQDKIGHGRESNPFPSACKAEAC 1106
            KFL +EF   ++++S + ++S PL        E + ++   +   R+   F + C     
Sbjct: 984  KFLRKEF---DTISSTRKRLSLPLEDFGNLDDENVAANVSGL-TSRQLEVFLNTCIG--- 1036

Query: 1107 REKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
              +Y R +++P TAVGA+ AQSIGEPGTQMTLKTFHFAG
Sbjct: 1037 --RYHRKKLDPGTAVGAIGAQSIGEPGTQMTLKTFHFAG 1073



 Score = 56.6 bits (135), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/42 (50%), Positives = 35/42 (83%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 63
           LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+++ F++R Q
Sbjct: 534 LMGVQNNLCTPKNGEILVASTQDFLTSSFLITRRDTFYDRGQ 575


>gi|316997003|dbj|BAJ52629.1| RNA polymerase III largest subunit [Stephanoeca diplocostata]
          Length = 933

 Score =  245 bits (626), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 153/371 (41%), Positives = 204/371 (54%), Gaps = 72/371 (19%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-------------------- 1145
            C  KY RA IEP +AVGA+ AQSIGEPGTQMTLKTFHFAG                    
Sbjct: 566  CAFKYARASIEPGSAVGAVGAQSIGEPGTQMTLKTFHFAGIAAMNITQGVPRIKEIINAS 625

Query: 1146 ------------------------EVCEY-IEEVFVPDDSF----------ILIKLDMD- 1169
                                     VC+  +E   + D +           + I + +D 
Sbjct: 626  KNISTPVITAPIAHVPESNMTEVAHVCKARVERCLLKDITISFTEVFTPNRVYITVHLDL 685

Query: 1170 -RIRLLHLEVDIDSIRYCIERTRGISGHLTVS---GHSFLILKPKDSSKSFNSKMYQMKQ 1225
             RI  L LE+D+ ++   +  +     H  +     H  + + P  S+KS  +  Y ++ 
Sbjct: 686  ERIHRLRLELDMQTVIDALLASSLKLKHTNIEHDPAHGKIRVFPPASAKS--TPFYALQA 743

Query: 1226 L---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNT 1282
            L   LP+V+++G + INR +I     +G T+ KLLVEG ++R VM T G+ G    +N+ 
Sbjct: 744  LRDALPNVIVRGDKNINRVIIQ----QGKTETKLLVEGTDMRAVMGTRGIVGTAVVTNHL 799

Query: 1283 YEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKM 1342
             +    LGIEAAR+TI+ EI+  M  HGM+ID RH ML+ADLMT KGE+LGITR G+AKM
Sbjct: 800  MDAEACLGIEAARATIIREIQTTMSAHGMTIDSRHVMLLADLMTFKGEILGITRFGIAKM 859

Query: 1343 KESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA---VPR 1399
            K S   LASFE T+DHLFDAA +G +D ISGVSECII+G PM +GTGL  L+        
Sbjct: 860  KSSTFMLASFEKTTDHLFDAALHGNSDPISGVSECIILGKPMKIGTGLFDLVHGDTVKAH 919

Query: 1400 SEPVPRTLLFD 1410
             +PV R LLF+
Sbjct: 920  VKPVRRNLLFE 930



 Score =  188 bits (478), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 105/230 (45%), Positives = 140/230 (60%), Gaps = 32/230 (13%)

Query: 391 NVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYL 450
           N+H+PQTEEARAEAL               LM  KSN+ TPRNGE LIAA QDFITG YL
Sbjct: 1   NLHVPQTEEARAEALE--------------LMGTKSNICTPRNGEPLIAAIQDFITGAYL 46

Query: 451 LTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLI 510
           LTQK+ F +R+Q    AS LIA  S   G I      +      V+   +WTGKQI S++
Sbjct: 47  LTQKDQFLSRSQ----ASQLIAYMSG--GDIPV----TMPAPAIVKPVALWTGKQIASVM 96

Query: 511 LKPNR---DCPVNANLKTKG-----RAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGS 562
           LK N+   D  V    KT+        +   +  C  D Y+++ NSEL+ G++DK++ G 
Sbjct: 97  LKTNKYATDIRVTVEKKTRASYKPTEVHDQTKSMCPNDGYLVIYNSELICGTLDKASTGD 156

Query: 563 GGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
           G K+ +FY++LRD+G+D A  AM RL+++ S++L  RGFSIGIGDV+P Q
Sbjct: 157 GSKSTIFYVILRDYGKDAAAEAMLRLAKLASYFLHTRGFSIGIGDVSPSQ 206



 Score =  174 bits (440), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 101/243 (41%), Positives = 149/243 (61%), Gaps = 15/243 (6%)

Query: 764 GVPRIKEIINASRNISTPIITA---YLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFV 820
           GVPRIKEIINAS+NISTP+ITA   ++ +    + A + K R+ER  L ++     EVF 
Sbjct: 614 GVPRIKEIINASKNISTPVITAPIAHVPESNMTEVAHVCKARVERCLLKDITISFTEVFT 673

Query: 821 PDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVS---GHSFLILKPKDSS 877
           P+  +I + LD++RI  L LE+D+ ++   +  +     H  +     H  + + P  S+
Sbjct: 674 PNRVYITVHLDLERIHRLRLELDMQTVIDALLASSLKLKHTNIEHDPAHGKIRVFPPASA 733

Query: 878 KSFNSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATY 934
           KS  +  Y ++ L   LP+V+++G + INR +I +    G T+ KLLVEG ++R VM T 
Sbjct: 734 KS--TPFYALQALRDALPNVIVRGDKNINRVIIQQ----GKTETKLLVEGTDMRAVMGTR 787

Query: 935 GVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGE 994
           G+ G    +N+  +    LGIEAAR+TI+ EI+  M  HGM+ID RH ML+ADLMT KGE
Sbjct: 788 GIVGTAVVTNHLMDAEACLGIEAARATIIREIQTTMSAHGMTIDSRHVMLLADLMTFKGE 847

Query: 995 VLG 997
           +LG
Sbjct: 848 ILG 850



 Score =  105 bits (262), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 61/120 (50%), Positives = 72/120 (60%), Gaps = 11/120 (9%)

Query: 606 GDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           G   P  +GFV NSFFSGLTP+EFFFHTM GREGLVDTAVKTAETGYM RRL+K+LEDL 
Sbjct: 323 GSADPNAKGFVSNSFFSGLTPSEFFFHTMCGREGLVDTAVKTAETGYMSRRLMKALEDLS 382

Query: 665 VQYDMSFDAA-------FYGQT--DCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP 715
             YD+    +        YG    D      +    G+P+N+   L  L     RS+P P
Sbjct: 383 TDYDLRVQNSSGTMVQFCYGDDGLDPAGMEGDGATEGMPVNL-EHLWALEVTAHRSDPAP 441



 Score = 68.2 bits (165), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 35/52 (67%), Positives = 39/52 (75%), Gaps = 4/52 (7%)

Query: 22 LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIA 73
          LM  KSN+ TPRNGE LIAA QDFITG YLLTQK+ F +R+Q    AS LIA
Sbjct: 17 LMGTKSNICTPRNGEPLIAAIQDFITGAYLLTQKDQFLSRSQ----ASQLIA 64



 Score = 59.7 bits (143), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 30/57 (52%), Positives = 37/57 (64%), Gaps = 3/57 (5%)

Query: 668 DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA---VPRSEPVPRTLLFD 721
           D  FDAA +G +D ISGVSECII+G PM +GTGL  L+         +PV R LLF+
Sbjct: 874 DHLFDAALHGNSDPISGVSECIILGKPMKIGTGLFDLVHGDTVKAHVKPVRRNLLFE 930


>gi|221058803|ref|XP_002260047.1| DNA-directed RNA polymerase 3 largest subunit [Plasmodium knowlesi
           strain H]
 gi|193810120|emb|CAQ41314.1| DNA-directed RNA polymerase 3 largest subunit,putative [Plasmodium
           knowlesi strain H]
          Length = 1970

 Score =  244 bits (624), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 128/281 (45%), Positives = 170/281 (60%), Gaps = 31/281 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIM H+A+V+ ++TFRFNECVC+PYNADFDGDEMN+H+PQTEEA
Sbjct: 510 DGDIVLFNRQPSLHRMSIMCHKARVMKYKTFRFNECVCSPYNADFDGDEMNLHVPQTEEA 569

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL               LM  K NL+TP+NGE++IA TQDF++  Y++T K+ F +R
Sbjct: 570 RAEAL--------------YLMNVKHNLITPKNGEVMIALTQDFLSASYVITNKDTFLDR 615

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPV-VFVRTAVIWTGKQIFSLILKPNRDCPV 519
                + S       DI             PV   ++   +WTGKQ+ S+++KPNR    
Sbjct: 616 DSFCLLCSYFSDAKVDI-----------ELPVPAILKPKELWTGKQLISVLIKPNRKENT 664

Query: 520 NANLKTKGRAYTAN----EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
             N + K R Y+      +  C  DSYV    SEL+ GS+ K  LGS  K  +FY L+  
Sbjct: 665 IINFEMKEREYSTKNGDLKYMCLNDSYVCFYKSELICGSLGKKVLGS-SKYGLFYYLIHH 723

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
               VAV  M R S++TS Y  N+G +IGI DVTP +  +Q
Sbjct: 724 NSSHVAVKVMNRFSKLTSRYFSNKGMTIGIDDVTPSETLIQ 764



 Score =  126 bits (316), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 65/141 (46%), Positives = 93/141 (65%)

Query: 1254 YKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSI 1313
            Y +LVEG++L  V+   GV      SN+   V++ LGIEAAR TI+ EIK  +E + + I
Sbjct: 1788 YSILVEGNSLNYVLGLEGVDFKHIISNHVINVFQVLGIEAARVTIINEIKKCVEAYSIDI 1847

Query: 1314 DFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISG 1373
            D RH ML+AD+M   G++LGI R G+ K + S L LASFE T++HLF ++F+   D I+ 
Sbjct: 1848 DIRHIMLLADIMAFTGDILGINRFGIQKARHSTLMLASFEETNEHLFVSSFFKNKDEINN 1907

Query: 1374 VSECIIMGLPMNVGTGLIKLL 1394
            +SE II+G  + +GTG  +LL
Sbjct: 1908 ISESIIVGKNIPIGTGSFQLL 1928



 Score =  111 bits (277), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 49/62 (79%), Positives = 55/62 (88%)

Query: 609 TPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +  +GFVQNSF+SGL PTEFFFHTM GREGLVDTAVKTAETGYMQRRL+K+LEDL + YD
Sbjct: 881 SESRGFVQNSFYSGLNPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKALEDLSIHYD 940

Query: 669 MS 670
            S
Sbjct: 941 YS 942



 Score =  107 bits (266), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 88/253 (34%), Positives = 139/253 (54%), Gaps = 28/253 (11%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G + KE+ + + S ++I+++ +Y ++    P P+G+LD ++G ++  + C TC +N  +C
Sbjct: 43  GIMNKEE-IIKCSEVKILNREMY-KNNTGIPYPYGVLDLKLGAHKSNSLCETCNKNFMNC 100

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFGYI+L  P+FH+GY++ +I IL  ICK   C+ +LL  EK   +    R  +    
Sbjct: 101 SGHFGYIELNYPLFHVGYYKYIIYILYCICK--VCSHILLTNEKLEFYTNLKRRASEDKF 158

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEY 264
            +K + KKIL + KKV+ C  CG   GV+KK  ++K S +++    K K  I        
Sbjct: 159 FKKHIFKKILNSCKKVTKCYRCGYPQGVIKK--IIKPSLDQF---MKLKHVI-------- 205

Query: 265 NEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLL 324
              +K N ++   +       LN L VL LF+ +    + LL     +  P  L++T LL
Sbjct: 206 --KIKENGKMVIKE-----DDLNSLYVLNLFKNMNPYHVKLL----NVENPEKLLITALL 254

Query: 325 VPPNCIRPSVISD 337
           VPPN IRPSVI D
Sbjct: 255 VPPNTIRPSVIID 267



 Score = 75.9 bits (185), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 50/166 (30%), Positives = 84/166 (50%), Gaps = 27/166 (16%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS NI TPI+   L    + ++A ++K +LE+TT+ ++C YI+E +    
Sbjct: 1484 GVPRIKEIINASSNIQTPILNIPLQVKDNYNFALMMKSKLEKTTIRDICLYIKEDYTSRG 1543

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISG----------------HLTVSGHS 867
             F+ +K +   I  L L ++  +I+  I R   I+                 H+++    
Sbjct: 1544 IFLSVKFNEQLIHNLFLNINAYTIKDIIMRQSHINKIKINKIVVEVVNAYKLHMSLKNDE 1603

Query: 868  FLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVE 913
            FL             ++  +K+ L  ++I G + I R +I +E+VE
Sbjct: 1604 FLFF-----------QIESLKKGLLDLLIHGDKDIKRCIIKKEEVE 1638



 Score = 72.4 bits (176), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 37/80 (46%), Positives = 52/80 (65%)

Query: 918  YKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSI 977
            Y +LVEG++L  V+   GV      SN+   V++ LGIEAAR TI+ EIK  +E + + I
Sbjct: 1788 YSILVEGNSLNYVLGLEGVDFKHIISNHVINVFQVLGIEAARVTIINEIKKCVEAYSIDI 1847

Query: 978  DFRHPMLVADLMTSKGEVLG 997
            D RH ML+AD+M   G++LG
Sbjct: 1848 DIRHIMLLADIMAFTGDILG 1867



 Score = 60.1 bits (144), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 26/37 (70%), Positives = 30/37 (81%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            KY +    P  AVG+++AQSIGEPGTQMTLKTFHFAG
Sbjct: 1439 KYFKYISSPGDAVGSISAQSIGEPGTQMTLKTFHFAG 1475



 Score = 52.8 bits (125), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 21/40 (52%), Positives = 31/40 (77%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           LM  K NL+TP+NGE++IA TQDF++  Y++T K+ F +R
Sbjct: 576 LMNVKHNLITPKNGEVMIALTQDFLSASYVITNKDTFLDR 615


>gi|198461889|ref|XP_001352259.2| GA14391 [Drosophila pseudoobscura pseudoobscura]
 gi|198142492|gb|EAL29345.2| GA14391 [Drosophila pseudoobscura pseudoobscura]
          Length = 644

 Score =  244 bits (622), Expect = 4e-61,   Method: Compositional matrix adjust.
 Identities = 126/260 (48%), Positives = 170/260 (65%), Gaps = 8/260 (3%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           ++  ++  D +QQ++ ++I SKNLY    QR P+P G+LDRRMG + K+A C TCG  L+
Sbjct: 18  VQFGISGADEIQQEALVRITSKNLY--QGQRQPVPSGVLDRRMGISTKDAVCETCGHGLN 75

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALS 202
           +C+GHFGY+DL LPVFHIG+FR  INILQ ICK  +CA+V+L  E    F  KL NP  S
Sbjct: 76  ECIGHFGYLDLALPVFHIGHFRATINILQMICK--SCAQVMLNFEDRLSFEKKLHNPNFS 133

Query: 203 YLVRKSLKKKILETTKKVSVCPHCGEINGVVKKC-GLLKISHEKYKNRTKKKDAIVEDLL 261
           YL +K+L  ++L   KKV+ CPHCG  NG VKK  GLLKI H+ YK R  K DA+    +
Sbjct: 134 YLGKKALHAQMLAKAKKVTKCPHCGTANGGVKKGPGLLKILHDPYKGR--KVDAVFTSNM 191

Query: 262 AEYNEAVKFNPEIE-AHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
            E   + +FN ++      +   + L PL VL LFE IP  D+ LL M +  + P  LI+
Sbjct: 192 DEMLRSTEFNRDLNLTLSNYSTAEELTPLMVLDLFEQIPQSDVALLGMCSRGAHPKHLIV 251

Query: 321 TRLLVPPNCIRPSVISDLKS 340
           TR+ VPP CIRPSV+S++K+
Sbjct: 252 TRVFVPPACIRPSVLSEVKA 271



 Score =  238 bits (606), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 116/207 (56%), Positives = 140/207 (67%), Gaps = 21/207 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND+VLFNRQPSLHK+SIM HRAKV P RTFRFNEC CTPYNADFDGDEMN+HLPQTEEA
Sbjct: 455 DNDIVLFNRQPSLHKMSIMCHRAKVQPQRTFRFNECACTPYNADFDGDEMNLHLPQTEEA 514

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL              +LM N+SNLVTP+NGE+LIAATQDFITGGYLLTQK  F  +
Sbjct: 515 RAEAL--------------ILMGNQSNLVTPKNGEILIAATQDFITGGYLLTQKEVFLTK 560

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            + M++A+  + +      I              ++   +WTGKQIFSL+++PN D  + 
Sbjct: 561 EEAMQLAACFLDNEDSTMNI-------QIPAPALLKPRRLWTGKQIFSLLMRPNSDSHIR 613

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRN 547
            N+  KGR YT N + C  DS + L N
Sbjct: 614 LNMVNKGRNYTKNMDLCINDSCMWLFN 640



 Score = 77.0 bits (188), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 33/52 (63%), Positives = 43/52 (82%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLI 72
           +LM N+SNLVTP+NGE+LIAATQDFITGGYLLTQK  F  + + M++A+  +
Sbjct: 520 ILMGNQSNLVTPKNGEILIAATQDFITGGYLLTQKEVFLTKEEAMQLAACFL 571


>gi|156088925|ref|XP_001611869.1| RNA polymerase Rpb1, domain containing protein [Babesia bovis]
 gi|154799123|gb|EDO08301.1| RNA polymerase Rpb1, domain containing protein [Babesia bovis]
          Length = 1541

 Score =  243 bits (621), Expect = 5e-61,   Method: Compositional matrix adjust.
 Identities = 128/276 (46%), Positives = 165/276 (59%), Gaps = 30/276 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + DVVLFNRQPSLH++SIMAHR +V+P  TFRFNECVC PYNADFDGDEMN+HLPQT EA
Sbjct: 510 NGDVVLFNRQPSLHRMSIMAHRVRVMPGSTFRFNECVCQPYNADFDGDEMNLHLPQTYEA 569

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEA   LH +S++            NL TPRNGE LIAA QDF+   YLLT K+ F  R
Sbjct: 570 KAEA---LHLMSVL-----------HNLTTPRNGEPLIAAVQDFLCASYLLTSKDRFLTR 615

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +            C      S     P   +   ++WTGKQ+F+ +L+PNR C V 
Sbjct: 616 AEFCQAC----------CHFTDAASQVDLPPPAIIYPVMLWTGKQVFNALLRPNRRCKVV 665

Query: 521 ANLKTKGRAYT-----ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            N + K R +       N   C +D YVI  NSEL++G++ K  LG+  K  +FY LL  
Sbjct: 666 VNFECKEREFQDPPVGKNACMCPKDGYVIFHNSELVSGALGKKALGA-SKDGLFYQLLTR 724

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
               +A   M R+S++TS +L   G +IG+ DV PG
Sbjct: 725 NNRYIAAECMLRVSKLTSRWLAGFGMTIGLDDVRPG 760



 Score =  187 bits (476), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 125/352 (35%), Positives = 180/352 (51%), Gaps = 63/352 (17%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKT------------------------- 1140
            C + Y RA   P  A+GAL AQSIGEPGTQMTLKT                         
Sbjct: 1186 CWKDYQRAICVPGEAIGALGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIINAS 1245

Query: 1141 -----------------FHFA------------GEVCEYIEEVFVPDDSFILIKLDMDRI 1171
                             F +A            G+VC  I+E+F P  + + + L+ + I
Sbjct: 1246 STIQTPIIEVPLINNKDFEYALMVKARIEKTTLGQVCSDIKEIFGPTGAQLRVTLNENLI 1305

Query: 1172 RLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQ------ 1225
            + L L++D   +R  I     +     +  H+  ++     +    +  +Q  Q      
Sbjct: 1306 KKLLLQIDAFKVREII-LDNSVMTKFKLGKHAISVVNKYQLNIDLATSQHQFFQQHALIV 1364

Query: 1226 LLPSVVIKGVQGINRAVIHEE-DVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYE 1284
             L  +++ G + I RAVI +E D +G  +Y+L VEG  L++V+   GVK     SN+  E
Sbjct: 1365 TLLQIMVAGGKSIKRAVIKKETDADGF-RYQLAVEGYGLQEVIGAAGVKSTGVKSNHVLE 1423

Query: 1285 VYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKE 1344
            V K LGIEAARS I++EI+  M+ + + ID R+  L+ D+MT +GEV+GI R G+ KM+ 
Sbjct: 1424 VAKVLGIEAARSVIISEIQKCMDAYSIDIDQRYMKLLGDVMTFRGEVIGINRFGIQKMRA 1483

Query: 1345 SVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA 1396
            S L LASFE T++HLF+AA +   D I GVSECIIMG  + +GTG   +L A
Sbjct: 1484 STLMLASFEETNEHLFEAAVHRLRDPIKGVSECIIMGKQVPLGTGAFDVLLA 1535



 Score =  155 bits (391), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 93/241 (38%), Positives = 141/241 (58%), Gaps = 9/241 (3%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS  I TPII   L  + D +YA +VK R+E+TTLG+VC  I+E+F P  
Sbjct: 1234 GVPRIKEIINASSTIQTPIIEVPLINNKDFEYALMVKARIEKTTLGQVCSDIKEIFGPTG 1293

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSK 883
            + + + L+ + I+ L L++D   +R  I     +     +  H+  ++     +    + 
Sbjct: 1294 AQLRVTLNENLIKKLLLQIDAFKVREII-LDNSVMTKFKLGKHAISVVNKYQLNIDLATS 1352

Query: 884  MYQMKQ------LLPSVVIKGVQGINRAVIHEE-DVEGVTKYKLLVEGDNLRDVMATYGV 936
             +Q  Q       L  +++ G + I RAVI +E D +G  +Y+L VEG  L++V+   GV
Sbjct: 1353 QHQFFQQHALIVTLLQIMVAGGKSIKRAVIKKETDADGF-RYQLAVEGYGLQEVIGAAGV 1411

Query: 937  KGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL 996
            K     SN+  EV K LGIEAARS I++EI+  M+ + + ID R+  L+ D+MT +GEV+
Sbjct: 1412 KSTGVKSNHVLEVAKVLGIEAARSVIISEIQKCMDAYSIDIDQRYMKLLGDVMTFRGEVI 1471

Query: 997  G 997
            G
Sbjct: 1472 G 1472



 Score =  138 bits (348), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 89/258 (34%), Positives = 134/258 (51%), Gaps = 30/258 (11%)

Query: 80  RGLIEGT---VTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTT 136
           R  IEG    V   + + + S +QI+ + LY  +    P+P G+LD ++G+N+  + C T
Sbjct: 89  RCTIEGVQFDVMGSEVISRISELQIMKRELY-DNSNNEPLPLGVLDLKLGSNRGGSLCHT 147

Query: 137 CGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKL 196
           CG++L  CVGH+G+I L +PVFHIG+F+  I IL  ICK   CA +LL E     F    
Sbjct: 148 CGKDLKQCVGHWGHIQLQMPVFHIGFFKYTIQILYCICKR--CAFLLLPENTVKRFLEAH 205

Query: 197 RNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAI 256
           R      L+R  L K+I++  +K++ CP C    GV+++  ++K                
Sbjct: 206 RRRMDDPLLRPLLFKQIMQECRKITKCPRCEARQGVIRR--IVK---------------P 248

Query: 257 VEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPS 316
           V D   +    +K+    E  K   + + LNPL V QLFE+I      +L     +  P 
Sbjct: 249 VMDQFMKLRHVIKYK---EGGKLHSIEEDLNPLVVKQLFESIDPTHAKIL----NVVSPE 301

Query: 317 DLILTRLLVPPNCIRPSV 334
            L++  L VPP+CIRPSV
Sbjct: 302 KLLINNLAVPPSCIRPSV 319



 Score =  101 bits (251), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 49/68 (72%), Positives = 54/68 (79%), Gaps = 1/68 (1%)

Query: 601 FSIGIGDVTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSL 660
           F IG  D    +GFV NSFFSGL P EFFFHTM GREGL+DTAVKT+ETGYMQRRL+K+L
Sbjct: 873 FDIGCMDAK-SRGFVANSFFSGLGPEEFFFHTMSGREGLIDTAVKTSETGYMQRRLMKAL 931

Query: 661 EDLCVQYD 668
           E L V YD
Sbjct: 932 EVLAVCYD 939



 Score = 53.1 bits (126), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 25/42 (59%), Positives = 29/42 (69%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 63
           LM+   NL TPRNGE LIAA QDF+   YLLT K+ F  RA+
Sbjct: 576 LMSVLHNLTTPRNGEPLIAAVQDFLCASYLLTSKDRFLTRAE 617


>gi|78190665|gb|ABB29654.1| RNA polymerase III large subunit [Suberites fuscus]
          Length = 269

 Score =  243 bits (620), Expect = 7e-61,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 169/238 (71%), Gaps = 4/238 (1%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
           GVPRIKEIINAS+ ISTPIITA+L  D+D ++AR+VKGR+E+T LGEV  YIEEV+ PD 
Sbjct: 9   GVPRIKEIINASKAISTPIITAHLKVDSDPEHARVVKGRIEKTLLGEVARYIEEVYEPDG 68

Query: 824 SFILIKLDMDRIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSGHSFLILKPKDSSK-S 879
            +I I LD +RI+LL LE+D  ++++ I    + +    H+++   S + + P D+ K S
Sbjct: 69  CYIKICLDSNRIKLLKLEIDTWTVQFAICSAPKLKIKPKHVSIRTTSVMYVYPPDNQKTS 128

Query: 880 FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
               +  +K  LPSVV+KG+  + RA+IH ++ +G  KYKLLVEG NL  VMAT GV+G 
Sbjct: 129 LYYTIQSLKVQLPSVVVKGISSVTRAIIHMDEGKGGAKYKLLVEGMNLCAVMATMGVEGT 188

Query: 940 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
           K +SN+T E  K LGIEAAR TI+ EI   M NHGMSID RH ML+ADLMT KGEVLG
Sbjct: 189 KTTSNHTAESEKALGIEAARQTIINEIVYTMVNHGMSIDARHVMLLADLMTFKGEVLG 246



 Score =  212 bits (540), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 117/216 (54%), Positives = 149/216 (68%), Gaps = 4/216 (1%)

Query: 1145 GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSG 1201
            GEV  YIEEV+ PD  +I I LD +RI+LL LE+D  ++++ I    + +    H+++  
Sbjct: 54   GEVARYIEEVYEPDGCYIKICLDSNRIKLLKLEIDTWTVQFAICSAPKLKIKPKHVSIRT 113

Query: 1202 HSFLILKPKDSSK-SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEG 1260
             S + + P D+ K S    +  +K  LPSVV+KG+  + RA+IH ++ +G  KYKLLVEG
Sbjct: 114  TSVMYVYPPDNQKTSLYYTIQSLKVQLPSVVVKGISSVTRAIIHMDEGKGGAKYKLLVEG 173

Query: 1261 DNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPML 1320
             NL  VMAT GV+G K +SN+T E  K LGIEAAR TI+ EI   M NHGMSID RH ML
Sbjct: 174  MNLCAVMATMGVEGTKTTSNHTAESEKALGIEAARQTIINEIVYTMVNHGMSIDARHVML 233

Query: 1321 VADLMTSKGEVLGITRHGLAKMKESVLNLASFENTS 1356
            +ADLMT KGEVLGITR GLAKMKESVL LASFE T+
Sbjct: 234  LADLMTFKGEVLGITRFGLAKMKESVLMLASFEKTA 269


>gi|357472549|ref|XP_003606559.1| DNA-directed RNA polymerase subunit beta [Medicago truncatula]
 gi|355507614|gb|AES88756.1| DNA-directed RNA polymerase subunit beta [Medicago truncatula]
          Length = 1036

 Score =  242 bits (618), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 122/284 (42%), Positives = 180/284 (63%), Gaps = 32/284 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH++S+M HRA+V+P RT RFNE VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 300 DGDVVLFNRQPSLHRMSMMCHRARVMPWRTLRFNESVCNPYNADFDGDEMNIHVPQTEEA 359

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL              +LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+K+ F++R
Sbjct: 360 RTEAL--------------LLMTVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDR 405

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           + T  +  + + D  D   +          P + ++   +W+GKQ+F+++L+P+ +  V 
Sbjct: 406 S-TFSLICSYMGDGMDPVDLP--------TPAI-IKPVELWSGKQLFNILLRPHANVRVY 455

Query: 521 ANLKTKGRAYTAN-----EEF---CHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYIL 572
             L    + Y +       EF   C  D +V  RNSEL++G + K TLG+G K  +F +L
Sbjct: 456 VTLTVMEKNYGSKLDDREREFKTMCPDDGFVYFRNSELISGQLGKVTLGNGNKDGLFSVL 515

Query: 573 LRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           LRD+    A + M RL+++++ ++ N GFSIGI DV P    ++
Sbjct: 516 LRDYKSYAAASCMNRLAKLSARWIGNHGFSIGIDDVQPKDKLIK 559



 Score = 89.4 bits (220), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 47/86 (54%), Positives = 57/86 (66%), Gaps = 20/86 (23%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTA-------------------VKTAE 648
           TP  +GFV++SFF+GL+ TEFFFHTMGGREGLVDTA                   VKTA+
Sbjct: 675 TPDAKGFVKDSFFTGLSATEFFFHTMGGREGLVDTAVRVSAMVTLKERLYHELRWVKTAD 734

Query: 649 TGYMQRRLVKSLEDLCVQYDMSFDAA 674
           TGYM RRL+K+LEDL + YD +   A
Sbjct: 735 TGYMSRRLMKALEDLFLHYDYTVRDA 760



 Score = 69.3 bits (168), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 31/55 (56%), Positives = 44/55 (80%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEV 818
            GVPRI+EII+ +RNI TPIITA L+++ + + AR VKGR+E+T LG+VC   ++V
Sbjct: 969  GVPRIQEIIDGARNIKTPIITAILEREDNAETARAVKGRIEKTNLGQVCNCSKKV 1023



 Score = 62.8 bits (151), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 57/176 (32%), Positives = 83/176 (47%), Gaps = 24/176 (13%)

Query: 987  DLMTSKGEVLGNGTPVELKRLLDDIIAKNSSRSDPS-LSAQEILALSNETLD----SKEF 1041
            D M   G    NG P+   RL     A   +  D + LS+ ++  + +E L     SK  
Sbjct: 772  DGMDPAGMEGKNGKPLNFDRLFLRSKAICPADGDDTILSSSDVHKVLHEKLSEVGMSKLV 831

Query: 1042 LQDTSEN-----------FVRDIKKFLEEFSK-KESVTSHQDKVSQPLREQILSHQDKIG 1089
             ++ S N           F++ ++ F+ E +K  ES+T       + L+   +S    I 
Sbjct: 832  EKNASNNDITPAVGFSTDFLKSLQSFVGENTKLTESITEDDSNNLKNLK-NFISRISGIS 890

Query: 1090 HGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
              R+   F      + C  +Y   +IE  T +GA+ AQSIGEPGTQMTLKTFHFAG
Sbjct: 891  R-RQLEVF-----LDICLSRYRIKKIEAGTPIGAIGAQSIGEPGTQMTLKTFHFAG 940



 Score = 56.6 bits (135), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/54 (44%), Positives = 40/54 (74%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           +LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+K+ F++R+    I S +  G
Sbjct: 365 LLMTVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDRSTFSLICSYMGDG 418


>gi|349604034|gb|AEP99696.1| DNA-directed RNA polymerase III subunit RPC1-like protein, partial
            [Equus caballus]
          Length = 176

 Score =  241 bits (616), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 120/171 (70%), Positives = 137/171 (80%), Gaps = 1/171 (0%)

Query: 1246 EDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLV 1305
            ++  G  KYKLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+TI+ EI+  
Sbjct: 1    DEQSGKEKYKLLVEGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAARTTIINEIQYT 60

Query: 1306 MENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFY 1365
            M NHGMSID RH ML++DLMT KGEVLGITR GLAKMKESVL LASFE T+DHLFDAA++
Sbjct: 61   MVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLASFEKTADHLFDAAYF 120

Query: 1366 GQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRT-LLFDNPEFH 1415
            GQ D + GVSECIIMG+PMN+GTGL KLL    R    PR  L+FD  EFH
Sbjct: 121  GQKDSVCGVSECIIMGIPMNIGTGLFKLLHKANRDPSPPRRPLIFDTNEFH 171



 Score =  127 bits (319), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 63/88 (71%), Positives = 73/88 (82%)

Query: 910 EDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLV 969
           ++  G  KYKLLVEGDNLR VMAT+GVKG + +SNNTYEV KTLGIEAAR+TI+ EI+  
Sbjct: 1   DEQSGKEKYKLLVEGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGIEAARTTIINEIQYT 60

Query: 970 MENHGMSIDFRHPMLVADLMTSKGEVLG 997
           M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 61  MVNHGMSIDRRHVMLLSDLMTYKGEVLG 88



 Score = 82.4 bits (202), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 668 DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRT-LLFDNPEFH 726
           D  FDAA++GQ D + GVSECIIMG+PMN+GTGL KLL    R    PR  L+FD  EFH
Sbjct: 112 DHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKANRDPSPPRRPLIFDTNEFH 171

Query: 727 FPQV 730
            P V
Sbjct: 172 IPLV 175


>gi|334188504|ref|NP_001190573.1| nuclear RNA polymerase C1 [Arabidopsis thaliana]
 gi|332009887|gb|AED97270.1| nuclear RNA polymerase C1 [Arabidopsis thaliana]
          Length = 1391

 Score =  241 bits (614), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 126/284 (44%), Positives = 176/284 (61%), Gaps = 36/284 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + DVVLFNRQPSLH++SIM HRA+++P RT RFNE VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 466 EGDVVLFNRQPSLHRMSIMCHRARIMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEA 525

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EA+               LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+K+ F++R
Sbjct: 526 RTEAI--------------TLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDR 571

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A    I S +  D  D        S     P + ++   +WTGKQIFS++L+PN    V 
Sbjct: 572 AAFSLICSYM-GDGMD--------SIDLPTPTI-LKPIELWTGKQIFSVLLRPNASIRVY 621

Query: 521 ANLKTKGRAYTA-----NEEFCHRDSYVILRNSELLAGSMDKST-------LGSGGKANV 568
             L  K + +       +E  C  D +V  RNSEL++G + K+T       LG+G K  +
Sbjct: 622 VTLNVKEKNFKKGEHGFDETMCINDGWVYFRNSELISGQLGKATLALDIFPLGNGNKDGL 681

Query: 569 FYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
           + ILLRD+    A   M RL+++++ ++   GFSIGI DV PG+
Sbjct: 682 YSILLRDYNSHAAAVCMNRLAKLSARWIGIHGFSIGIDDVQPGE 725



 Score =  187 bits (474), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 116/270 (42%), Positives = 165/270 (61%), Gaps = 16/270 (5%)

Query: 1145 GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSG 1201
            G+V E IE +     + + I LD   I    L +   S++  I +T  I      + V  
Sbjct: 1119 GQVAESIEVLMTSTSASVRIILDNKIIEEACLSITPWSVKNSILKTPRIKLNDNDIRVLD 1178

Query: 1202 HSFLILKPKDSSKS-FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLV-- 1258
                I    D S++ FN  ++ +K +LP++++ G++ + R V+  ED++ +   KL++  
Sbjct: 1179 TGLDITPVVDKSRAHFN--LHNLKNVLPNIIVNGIKTVERVVV-AEDMDKMLA-KLIIPC 1234

Query: 1259 ---EGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDF 1315
                  NL  VM T G+ G   +SNN  EV KTLGIEAAR+TI+ EI  VM NHGMSID 
Sbjct: 1235 PRWACTNLLAVMGTPGINGRTTTSNNVVEVSKTLGIEAARTTIIDEIGTVMGNHGMSIDI 1294

Query: 1316 RHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVS 1375
            RH ML+AD+MT +GEVLGI R G+ KM +SVL  ASFE T DHLF AA  G+ D I GV+
Sbjct: 1295 RHMMLLADVMTYRGEVLGIQRTGIQKMDKSVLMQASFERTGDHLFSAAASGKVDNIEGVT 1354

Query: 1376 ECIIMGLPMNVGTGLIKLLQAVPRSEPVPR 1405
            EC+IMG+PM +GTG++K+LQ   R++ +P+
Sbjct: 1355 ECVIMGIPMKLGTGILKVLQ---RTDDLPK 1381



 Score =  168 bits (425), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 107/243 (44%), Positives = 149/243 (61%), Gaps = 13/243 (5%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRI EIINAS+NISTP+I+A L+   +L  AR VKGR+E+TTLG+V E IE +     
Sbjct: 1074 GVPRINEIINASKNISTPVISAELENPLELTSARWVKGRIEKTTLGQVAESIEVLMTSTS 1133

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFLILKPKDSSKS- 879
            + + I LD   I    L +   S++  I +T  I      + V      I    D S++ 
Sbjct: 1134 ASVRIILDNKIIEEACLSITPWSVKNSILKTPRIKLNDNDIRVLDTGLDITPVVDKSRAH 1193

Query: 880  FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLV-----EGDNLRDVMATY 934
            FN  ++ +K +LP++++ G++ + R V+  ED++ +   KL++        NL  VM T 
Sbjct: 1194 FN--LHNLKNVLPNIIVNGIKTVERVVV-AEDMDKMLA-KLIIPCPRWACTNLLAVMGTP 1249

Query: 935  GVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGE 994
            G+ G   +SNN  EV KTLGIEAAR+TI+ EI  VM NHGMSID RH ML+AD+MT +GE
Sbjct: 1250 GINGRTTTSNNVVEVSKTLGIEAARTTIIDEIGTVMGNHGMSIDIRHMMLLADVMTYRGE 1309

Query: 995  VLG 997
            VLG
Sbjct: 1310 VLG 1312



 Score =  134 bits (338), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 96/297 (32%), Positives = 152/297 (51%), Gaps = 37/297 (12%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           I  +V  +  V + + +Q+ +  LY  D    P  +GLLD RMG   K++ CTTC  N  
Sbjct: 26  INFSVLSDLEVMKAAEVQVWNIGLY--DHSFKPYENGLLDPRMGPPNKKSICTTCEGNFQ 83

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICK--------NPTCARVLLGEEKAAGFRA 194
           +C GH+GY+ L LPV+++GYF  +++IL+ ICK        +  C+ +LL E+       
Sbjct: 84  NCPGHYGYLKLDLPVYNVGYFNFILDILKCICKVTELADYVSLRCSNMLLDEKLYEDHLR 143

Query: 195 KLRNPALSYLVRKSLKKKILE-----TTKKVSVCPHCGEINGVVKKCGL---LKISHEKY 246
           K+RNP +  L +  L K +++      ++++  C  CG +NG+VKK      + ISH++ 
Sbjct: 144 KMRNPRMEPLKKTELAKAVVKKCSTMASQRIITCKKCGYLNGMVKKIAAQFGIGISHDRS 203

Query: 247 KNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLL 306
           K    + D     +          NP         L   L+P  VL LF+ +  +D  LL
Sbjct: 204 KIHGGEIDECKSAISHTKQSTAAINP---------LTYVLDPNLVLGLFKRMSDKDCELL 254

Query: 307 LMNAELSKPSDLILTRLLVPPNCIRPSV-ISDLKS-DNDVVLFNRQ-----PSLHKL 356
            +     +P +LI+T +LVPP  IRPSV I  ++S +ND+    +Q      SLHK+
Sbjct: 255 YI---AYRPENLIITCMLVPPLSIRPSVMIGGIQSNENDLTARLKQIILGNASLHKI 308



 Score =  103 bits (258), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 47/58 (81%), Positives = 51/58 (87%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV NSF+SGLT TEFFFHTMGGREGLVDTAVKTA TGYM RRL+K+LEDL V YD
Sbjct: 848 AKGFVANSFYSGLTATEFFFHTMGGREGLVDTAVKTASTGYMSRRLMKALEDLLVHYD 905



 Score = 65.1 bits (157), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 48/149 (32%), Positives = 74/149 (49%), Gaps = 18/149 (12%)

Query: 998  NGTPVELKRLLDDIIAKNSSRSDPS-LSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            +G P+   RL   + A    RS  + LS++E+     E L   +  +  ++ FV+ +++F
Sbjct: 934  DGAPLNFNRLFLKVQATCPPRSHHTYLSSEELSQKFEEELVRHDKSRVCTDAFVKSLREF 993

Query: 1057 LEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIE 1116
            +     K +        S P   Q+L     +   ++   F      + C  +Y   +IE
Sbjct: 994  VSLLGVKSA--------SPP---QVLYKASGVTD-KQLEVF-----VKICVFRYREKKIE 1036

Query: 1117 PATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
              TA+G + AQSIGEPGTQMTLKTFHFAG
Sbjct: 1037 AGTAIGTIGAQSIGEPGTQMTLKTFHFAG 1065



 Score = 57.8 bits (138), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 25/53 (47%), Positives = 39/53 (73%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+K+ F++RA    I S +  G
Sbjct: 532 LMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDRAAFSLICSYMGDG 584



 Score = 53.5 bits (127), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 24/49 (48%), Positives = 36/49 (73%), Gaps = 3/49 (6%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPR 716
            D  F AA  G+ D I GV+EC+IMG+PM +GTG++K+LQ   R++ +P+
Sbjct: 1336 DHLFSAAASGKVDNIEGVTECVIMGIPMKLGTGILKVLQ---RTDDLPK 1381


>gi|260820184|ref|XP_002605415.1| hypothetical protein BRAFLDRAFT_74232 [Branchiostoma floridae]
 gi|229290748|gb|EEN61425.1| hypothetical protein BRAFLDRAFT_74232 [Branchiostoma floridae]
          Length = 384

 Score =  240 bits (612), Expect = 5e-60,   Method: Compositional matrix adjust.
 Identities = 115/214 (53%), Positives = 152/214 (71%), Gaps = 11/214 (5%)

Query: 90  EDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFG 149
           ++ ++QQSHI +VSKNLY QD ++ P+P+G+LD  MGT+ K+ +C TCG+NL+DCVGH+G
Sbjct: 25  DEEMRQQSHIHVVSKNLYNQDSRQVPVPYGVLDNHMGTSTKDKSCETCGKNLADCVGHYG 84

Query: 150 YIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSL 209
           Y+DL LPVFH+GYF+ +I++LQ ICK  +C+RVLLG++    F   LR P LSYL RK L
Sbjct: 85  YVDLELPVFHVGYFKSIIHVLQCICK--SCSRVLLGKDDRKTFSDTLRRPNLSYLQRKGL 142

Query: 210 KKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVK 269
           KKKI E  +KVS C HCG +NG VKKCGLLKI HE+YK+  K  D +V D  + +  AV+
Sbjct: 143 KKKINEKCRKVSYCSHCGALNGPVKKCGLLKIVHERYKSTKKVVDPVVTDFQSSFQSAVE 202

Query: 270 FNPEIEAHKKFGLI----QTLNPLEVLQLFEAIP 299
            N EIE     GLI    + LNP+  L +F  IP
Sbjct: 203 HNKEIE-----GLIPRAQENLNPMVALHMFSRIP 231


>gi|389585038|dbj|GAB67769.1| DNA-directed RNA polymerase III largest subunit [Plasmodium
           cynomolgi strain B]
          Length = 1969

 Score =  240 bits (612), Expect = 5e-60,   Method: Compositional matrix adjust.
 Identities = 125/280 (44%), Positives = 170/280 (60%), Gaps = 29/280 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + D+VLFNRQPSLH++SIM H+A+V+ ++TFRFNECVC+PYNADFDGDEMN+H+PQTEEA
Sbjct: 544 NGDIVLFNRQPSLHRMSIMCHKARVMKYKTFRFNECVCSPYNADFDGDEMNLHVPQTEEA 603

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL               LM  K NL+TP+NGE++IA TQDF++  Y++T K+ F +R
Sbjct: 604 RAEAL--------------YLMNVKHNLITPKNGEVMIALTQDFLSASYVITNKDTFLDR 649

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                + S       DI   +         P + ++   +WTGKQ+ S+++KPNR     
Sbjct: 650 DSFCLLCSYFSDAKVDIELPV---------PAI-LKPKELWTGKQLISVLIKPNRKENTI 699

Query: 521 ANLKTKGRAYTAN----EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            N + K R Y+      +  C  DSYV    SEL+ GS+ K  LGS  K  +FY L+   
Sbjct: 700 INFELKEREYSTKNGDLKHMCLNDSYVCFYKSELICGSLGKKVLGS-SKYGLFYYLIHHN 758

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
              VA+  M R S++TS Y  N+G +IGI DVTP    +Q
Sbjct: 759 SSYVALKIMNRFSKLTSRYFTNKGMTIGIDDVTPSDTLIQ 798



 Score =  119 bits (298), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 62/138 (44%), Positives = 89/138 (64%)

Query: 1257 LVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFR 1316
            L +G+ L  V+   GV      SN+   V++ LGIEAAR TI+ EIK  +E + + ID R
Sbjct: 1809 LEKGNALNYVLGLEGVDFKHIISNHVINVFQVLGIEAARVTIINEIKKCIEAYSIDIDIR 1868

Query: 1317 HPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSE 1376
            H ML+AD+M   G++LGI R G+ K + S L LASFE T++HLF ++F+   D I+ +SE
Sbjct: 1869 HIMLLADIMAFTGDILGINRFGIQKARHSTLMLASFEETNEHLFVSSFFKNRDEINNISE 1928

Query: 1377 CIIMGLPMNVGTGLIKLL 1394
             II+G  + +GTG  +LL
Sbjct: 1929 SIIVGKNIPIGTGAFQLL 1946



 Score =  111 bits (277), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 51/70 (72%), Positives = 59/70 (84%), Gaps = 1/70 (1%)

Query: 601 FSIGIGDVTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSL 660
           F+I   D +  +GFVQNSF++GL PTEFFFHTM GREGLVDTAVKTAETGYMQRRL+K+L
Sbjct: 908 FNIHCKD-SESRGFVQNSFYTGLNPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKAL 966

Query: 661 EDLCVQYDMS 670
           EDL + YD S
Sbjct: 967 EDLSIHYDYS 976



 Score =  108 bits (270), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 89/259 (34%), Positives = 132/259 (50%), Gaps = 40/259 (15%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G + KE+ + + S ++I+++ +Y ++    P P+G+LD ++G ++  + C TC +N  +C
Sbjct: 103 GIMNKEE-IIKCSEVKILNREMY-KNNTGIPYPYGVLDLKLGAHKSNSLCETCNRNFMNC 160

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFGYI+L  P+FH+GY++ +I IL  ICK   C+ +LL  EK   +    R       
Sbjct: 161 SGHFGYIELNYPLFHVGYYKYIIYILYCICK--VCSHILLSNEKLEFYTNLKRRTVEDKF 218

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKC------GLLKISHEKYKNRTKKKDAIVE 258
            +K + KKIL + KKV+ C  CG   GV+KK         +K+ H   K +   K  I E
Sbjct: 219 FKKHIFKKILNSCKKVTKCYRCGYPQGVIKKIIKPSLDQFMKLKH-VIKTKENGKMVIKE 277

Query: 259 DLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDL 318
           D                          LN L VL LF+ +    I LL     +  P  L
Sbjct: 278 D-------------------------DLNSLYVLNLFKNMNPYHIKLL----NVENPEKL 308

Query: 319 ILTRLLVPPNCIRPSVISD 337
           ++T LLVPPN IRPSVI D
Sbjct: 309 LITALLVPPNTIRPSVIID 327



 Score = 77.4 bits (189), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 51/166 (30%), Positives = 84/166 (50%), Gaps = 27/166 (16%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS  I TPI+   L    + ++A ++K +LE+TT+ ++C YI+E +    
Sbjct: 1523 GVPRIKEIINASSTIQTPILNIPLQVKDNYNFALMMKSKLEKTTIRDICLYIKEDYTSRG 1582

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISG----------------HLTVSGHS 867
             F+ +K + + I  L L ++  SI+  I R   I+                 H+++    
Sbjct: 1583 IFLSVKFNEELIHNLFLNINAYSIKEIIMRQSHINKIKINKVVVEVVNEYKLHMSLKNGE 1642

Query: 868  FLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVE 913
            FL             +M  +K+ L  ++I G + I R +I +E+VE
Sbjct: 1643 FLFF-----------QMESLKKGLLDLLIHGDKDIKRCIIKKEEVE 1677



 Score = 64.7 bits (156), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 34/77 (44%), Positives = 48/77 (62%)

Query: 921  LVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFR 980
            L +G+ L  V+   GV      SN+   V++ LGIEAAR TI+ EIK  +E + + ID R
Sbjct: 1809 LEKGNALNYVLGLEGVDFKHIISNHVINVFQVLGIEAARVTIINEIKKCIEAYSIDIDIR 1868

Query: 981  HPMLVADLMTSKGEVLG 997
            H ML+AD+M   G++LG
Sbjct: 1869 HIMLLADIMAFTGDILG 1885



 Score = 60.1 bits (144), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 26/37 (70%), Positives = 30/37 (81%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            KY +    P  AVG+++AQSIGEPGTQMTLKTFHFAG
Sbjct: 1478 KYFKYISAPGDAVGSISAQSIGEPGTQMTLKTFHFAG 1514



 Score = 52.8 bits (125), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 21/40 (52%), Positives = 31/40 (77%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           LM  K NL+TP+NGE++IA TQDF++  Y++T K+ F +R
Sbjct: 610 LMNVKHNLITPKNGEVMIALTQDFLSASYVITNKDTFLDR 649


>gi|156096092|ref|XP_001614080.1| DNA-directed RNA polymerase III largest subunit [Plasmodium vivax
           Sal-1]
 gi|148802954|gb|EDL44353.1| DNA-directed RNA polymerase III largest subunit, putative
           [Plasmodium vivax]
          Length = 1946

 Score =  239 bits (611), Expect = 6e-60,   Method: Compositional matrix adjust.
 Identities = 134/316 (42%), Positives = 181/316 (57%), Gaps = 37/316 (11%)

Query: 309 NAELSKPSDLILTRLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPH 368
           N  ++K S     + LV  N     V+     D D+VLFNRQPSLH++SIM H+A+V+ +
Sbjct: 487 NPAINKISLKYANKRLVVENLQVGDVVERHLVDGDIVLFNRQPSLHRMSIMCHKARVMKY 546

Query: 369 RTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNL 428
           +TFRFNECVC+PYNADFDGDEMN+H+PQTEEARAEAL               LM  K+NL
Sbjct: 547 KTFRFNECVCSPYNADFDGDEMNLHVPQTEEARAEAL--------------YLMNVKNNL 592

Query: 429 VTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRS 488
           +TP+NGE++IA TQDF++  Y++T K+ F +R                 C +   FS   
Sbjct: 593 ITPKNGEVIIALTQDFLSASYVITNKDTFLDR--------------DSFCLLCSYFSDAK 638

Query: 489 WN---PV-VFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTAN----EEFCHRD 540
            N   PV   ++   +WTGKQ+ S+++KPN       N + K R Y+      +  C  D
Sbjct: 639 VNIDLPVPAILKPKELWTGKQLISVLIKPNTKENTIINFEIKEREYSTKNGDLKHMCLND 698

Query: 541 SYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRG 600
           SYV    SEL+ GS+ K  LGS  K  +FY L+      VA+  M R S++TS Y  N+G
Sbjct: 699 SYVCFYKSELICGSLGKKVLGS-SKYGLFYYLIHHNSSYVALKIMNRFSKLTSRYFSNKG 757

Query: 601 FSIGIGDVTPGQGFVQ 616
            +IGI DVTP    +Q
Sbjct: 758 MTIGIDDVTPSDTLLQ 773



 Score =  126 bits (317), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 65/141 (46%), Positives = 93/141 (65%)

Query: 1254 YKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSI 1313
            Y +LVEG++L  V+   GV      SN+   V++ LGIEAAR TI+ EIK  +E + + I
Sbjct: 1783 YSILVEGNSLNYVLGLEGVDFKHIISNHVINVFQVLGIEAARVTIINEIKKCVEAYSIDI 1842

Query: 1314 DFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISG 1373
            D RH ML+AD+M   G++LGI R G+ K + S L LASFE T++HLF ++F+   D I+ 
Sbjct: 1843 DIRHIMLLADIMAFTGDILGINRFGIQKARHSTLMLASFEETNEHLFVSSFFKNRDEINN 1902

Query: 1374 VSECIIMGLPMNVGTGLIKLL 1394
            +SE II+G  + +GTG  +LL
Sbjct: 1903 ISESIIVGKNIPIGTGAFQLL 1923



 Score =  115 bits (287), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 86/259 (33%), Positives = 132/259 (50%), Gaps = 40/259 (15%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G + KE+ + + S ++I+++ +Y ++    P P+G+LD ++G ++  + C TC +N  +C
Sbjct: 63  GIMDKEE-IIKCSEVKILNREMY-KNNTGIPYPYGVLDLKLGAHKSNSLCETCHRNFMNC 120

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFGYI+L  P+FH+GY++ +I IL  ICK   C+ +LL  EK   +    R       
Sbjct: 121 SGHFGYIELNYPLFHVGYYKYIIYILYCICK--VCSHILLTNEKLEFYTNLKRRTVEDKF 178

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKC------GLLKISHEKYKNRTKKKDAIVE 258
            ++ + KKIL + KKV+ C  CG   GV+KK         +K+ H   K +   K  I E
Sbjct: 179 FKRHIFKKILNSCKKVTKCYRCGYPQGVIKKIIKPSLDQFMKLKH-VIKTKENGKMVIKE 237

Query: 259 DLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDL 318
           D                          LN L VL LF+ +    + LL     +  P  L
Sbjct: 238 D-------------------------DLNSLYVLNLFKNMNPYHVKLL----NVESPEKL 268

Query: 319 ILTRLLVPPNCIRPSVISD 337
           ++T LLVPPN IRPSV+ D
Sbjct: 269 LITALLVPPNTIRPSVVID 287



 Score =  110 bits (274), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 48/62 (77%), Positives = 55/62 (88%)

Query: 609 TPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +  +GFVQNSF++GL PTEFFFHTM GREGLVDTAVKTAETGYMQRRL+K+LEDL + YD
Sbjct: 890 SESRGFVQNSFYTGLNPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKALEDLSIHYD 949

Query: 669 MS 670
            S
Sbjct: 950 FS 951



 Score = 77.0 bits (188), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 52/166 (31%), Positives = 82/166 (49%), Gaps = 27/166 (16%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS  I TPI+   L      ++A ++K +LE+TT+ ++C YI+E +    
Sbjct: 1487 GVPRIKEIINASSTIQTPILNIPLQVKDSYNFALMMKSKLEKTTVRDICLYIKEDYTARG 1546

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISG----------------HLTVSGHS 867
             F+ +K +   I  L L ++  +IR  I R   IS                 H+++    
Sbjct: 1547 IFLSVKFNEQLIHNLFLNINAYTIRDIIMRQSHISKIKINKILVEVVDAYKLHMSLKNDE 1606

Query: 868  FLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVE 913
            FL             +M  +K+ L  ++I G + I R +I +E+VE
Sbjct: 1607 FLFF-----------QMEALKKGLLDLLIHGDKDIKRCIIKKEEVE 1641



 Score = 72.8 bits (177), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 37/80 (46%), Positives = 52/80 (65%)

Query: 918  YKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSI 977
            Y +LVEG++L  V+   GV      SN+   V++ LGIEAAR TI+ EIK  +E + + I
Sbjct: 1783 YSILVEGNSLNYVLGLEGVDFKHIISNHVINVFQVLGIEAARVTIINEIKKCVEAYSIDI 1842

Query: 978  DFRHPMLVADLMTSKGEVLG 997
            D RH ML+AD+M   G++LG
Sbjct: 1843 DIRHIMLLADIMAFTGDILG 1862



 Score = 59.3 bits (142), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/37 (70%), Positives = 30/37 (81%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            KY +    P  AVG+++AQSIGEPGTQMTLKTFHFAG
Sbjct: 1442 KYFKYISAPGDAVGSISAQSIGEPGTQMTLKTFHFAG 1478



 Score = 52.8 bits (125), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 21/40 (52%), Positives = 32/40 (80%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           LM  K+NL+TP+NGE++IA TQDF++  Y++T K+ F +R
Sbjct: 585 LMNVKNNLITPKNGEVIIALTQDFLSASYVITNKDTFLDR 624


>gi|124513306|ref|XP_001350009.1| DNA-directed RNA polymerase 3 largest subunit [Plasmodium
           falciparum 3D7]
 gi|23615426|emb|CAD52417.1| DNA-directed RNA polymerase 3 largest subunit [Plasmodium
           falciparum 3D7]
          Length = 2356

 Score =  239 bits (610), Expect = 8e-60,   Method: Compositional matrix adjust.
 Identities = 123/281 (43%), Positives = 171/281 (60%), Gaps = 31/281 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIM H+AK++  +TFRFNECVC+PYNADFDGDEMN+H+PQTEEA
Sbjct: 568 DGDIVLFNRQPSLHRMSIMCHKAKIMDFKTFRFNECVCSPYNADFDGDEMNLHVPQTEEA 627

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL               LM  K NL+TP+NGE++IA TQDF++  Y++T K+ F +R
Sbjct: 628 RAEAL--------------YLMNVKHNLITPKNGEVIIALTQDFLSASYIITNKDTFLDR 673

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPV-VFVRTAVIWTGKQIFSLILKPNRDCPV 519
             T  +  +  +D S    +          P+   ++   +WTGKQ+ S+++KPN+    
Sbjct: 674 -DTFCLLCSYFSDASLYIEL----------PIPAILKPKELWTGKQLISVLIKPNKKENT 722

Query: 520 NANLKTKGRAYTAN----EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
             N + + R Y+      +  C  DSYV    SEL+ GS+ K  LGS  K  +FY L+  
Sbjct: 723 IINFEIQEREYSNKFGDLKHLCLNDSYVCFYKSELICGSLGKKVLGS-SKYGLFYYLIHH 781

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
               +A+  M RLS++TS Y  N+G +IGI DV P Q   +
Sbjct: 782 NSSHIALKIMNRLSKLTSRYFSNKGMTIGIDDVRPSQTLTE 822



 Score =  140 bits (354), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 92/253 (36%), Positives = 142/253 (56%), Gaps = 28/253 (11%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G ++KED ++  S ++I+++ +Y ++    P P+G+LD ++G ++  + C TC + L +C
Sbjct: 41  GIMSKEDIIKY-SEVKIMNREMY-KNNSGIPYPYGVLDLKLGAHKSNSVCETCNKKLINC 98

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFGYI+L  PVFHIGY++ +I+IL  ICK   C+ +LL +EK   +    +       
Sbjct: 99  SGHFGYIELNYPVFHIGYYKYIIHILYCICK--YCSSLLLSKEKIDFYCNLKKKSTDDSF 156

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEY 264
            +K L K+IL   KKV+ C  CG   GV+KK  ++K S +++    K K  +        
Sbjct: 157 YKKHLFKRILNNCKKVNKCYICGNPQGVIKK--IIKPSLDQF---MKLKHIL-------- 203

Query: 265 NEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLL 324
              VK N ++   +     + LN L VL+LF+ I    + LL     +  P  LI+T LL
Sbjct: 204 --KVKENGKMIIKE-----EDLNSLYVLKLFKNINPYHVKLL----NIENPEKLIITALL 252

Query: 325 VPPNCIRPSVISD 337
           VPPN IRPSVI D
Sbjct: 253 VPPNTIRPSVIID 265



 Score =  129 bits (323), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 69/165 (41%), Positives = 100/165 (60%)

Query: 1252 TKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM 1311
            T Y +LVEG++L  V+   GV      SN+   V++ LGIEAAR TI+ EIK  +E + +
Sbjct: 2188 TVYSILVEGNSLNYVLGLEGVDFKHIISNHVINVFQVLGIEAARITIINEIKKCVEAYSI 2247

Query: 1312 SIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCI 1371
             ID RH ML+AD+M   G++LGI R G+ K ++S L LASFE T++HLF ++F+   D I
Sbjct: 2248 DIDIRHIMLLADIMAFTGDILGINRFGIQKARQSTLMLASFEETNEHLFVSSFFKNVDEI 2307

Query: 1372 SGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHT 1416
            + +SE II+G  + +GTG  +LL      +      L +  E  T
Sbjct: 2308 NNISESIIVGKNIPIGTGAFQLLYDYKFEKETKNLTLLEKAERET 2352



 Score =  112 bits (280), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 48/62 (77%), Positives = 56/62 (90%)

Query: 609  TPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +  +GFVQNSF++GL+PTEFFFHTM GREGLVDTAVKTAETGYMQRRL+K+LEDL + YD
Sbjct: 939  SESRGFVQNSFYTGLSPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKALEDLSIHYD 998

Query: 669  MS 670
             S
Sbjct: 999  YS 1000



 Score = 80.9 bits (198), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 51/156 (32%), Positives = 90/156 (57%), Gaps = 7/156 (4%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS +I TPI+   L+ + + ++A ++K +LE+TT+ ++C YI+E +    
Sbjct: 1827 GVPRIKEIINASNSIQTPILNIPLEVNDNYNFALMMKSKLEKTTIRDICMYIKEDYTSRG 1886

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISG------HLTVSGHSFLILKPKDSS 877
             F+ +K + + I+ L L ++  +I+  I +   I+       H+ V     L +  K+  
Sbjct: 1887 VFLSVKFNEELIQKLFLNINAYNIKDIILKQSHINKIKINKIHINVINKYKLHISLKNDE 1946

Query: 878  KSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVE 913
              F  +M  +K+ L  ++I G + I R +I +ED+E
Sbjct: 1947 FIF-FQMESLKKGLLDLLIYGDKDIKRCIIKKEDIE 1981



 Score = 73.2 bits (178), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 38/82 (46%), Positives = 53/82 (64%)

Query: 916  TKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM 975
            T Y +LVEG++L  V+   GV      SN+   V++ LGIEAAR TI+ EIK  +E + +
Sbjct: 2188 TVYSILVEGNSLNYVLGLEGVDFKHIISNHVINVFQVLGIEAARITIINEIKKCVEAYSI 2247

Query: 976  SIDFRHPMLVADLMTSKGEVLG 997
             ID RH ML+AD+M   G++LG
Sbjct: 2248 DIDIRHIMLLADIMAFTGDILG 2269



 Score = 61.2 bits (147), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 26/37 (70%), Positives = 30/37 (81%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            KY +    P  AVG+++AQSIGEPGTQMTLKTFHFAG
Sbjct: 1782 KYFKYISTPGDAVGSISAQSIGEPGTQMTLKTFHFAG 1818



 Score = 52.8 bits (125), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 21/40 (52%), Positives = 31/40 (77%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           LM  K NL+TP+NGE++IA TQDF++  Y++T K+ F +R
Sbjct: 634 LMNVKHNLITPKNGEVIIALTQDFLSASYIITNKDTFLDR 673


>gi|195566966|ref|XP_002107046.1| GD17237 [Drosophila simulans]
 gi|194204443|gb|EDX18019.1| GD17237 [Drosophila simulans]
          Length = 289

 Score =  239 bits (609), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 124/260 (47%), Positives = 170/260 (65%), Gaps = 8/260 (3%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           ++  ++  D +QQ++ ++I+SKNLY    QR P+P+G+LDRRMG + K+A C TCGQ L+
Sbjct: 18  VQFGISGADEIQQEALVRIISKNLY--QAQRQPVPYGVLDRRMGISTKDAMCDTCGQGLN 75

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALS 202
           +C+GHFGY+DL LPVFHIG+FR  INILQ ICK   CA V+L  E    +  KL NP  S
Sbjct: 76  ECIGHFGYLDLALPVFHIGHFRSTINILQMICK--VCAHVMLKPEDRQLYEKKLHNPNFS 133

Query: 203 YLVRKSLKKKILETTKKVSVCPHCGEINGVVKKC-GLLKISHEKYKNRTKKKDAIVEDLL 261
           YL +K+L  ++L   KKV+ CPHCG  NG VKK  GLLKI H+ YK R  K D +    +
Sbjct: 134 YLGKKALHVQMLAKAKKVTKCPHCGSPNGGVKKGPGLLKILHDPYKGR--KMDLLFTSNM 191

Query: 262 AEYNEAVKFNPEIEAH-KKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
            E   + + N ++ +    +   + L PL VL LFE IP  D+ LL M +  + P  LI+
Sbjct: 192 NEMLHSTQANRDLNSTLGNYSTAEELTPLMVLDLFEQIPQRDVALLGMCSHDAHPKHLIV 251

Query: 321 TRLLVPPNCIRPSVISDLKS 340
           TR+ VPP CIRPSV+S++K+
Sbjct: 252 TRVFVPPACIRPSVLSEVKA 271


>gi|195173803|ref|XP_002027675.1| GL20670 [Drosophila persimilis]
 gi|194114614|gb|EDW36657.1| GL20670 [Drosophila persimilis]
          Length = 424

 Score =  237 bits (605), Expect = 4e-59,   Method: Compositional matrix adjust.
 Identities = 116/207 (56%), Positives = 140/207 (67%), Gaps = 21/207 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND+VLFNRQPSLHK+SIM HRAKV P RTFRFNEC CTPYNADFDGDEMN+HLPQTEEA
Sbjct: 235 DNDIVLFNRQPSLHKMSIMCHRAKVQPQRTFRFNECACTPYNADFDGDEMNLHLPQTEEA 294

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL              +LM N+SNLVTP+NGE+LIAATQDFITGGYLLTQK  F  +
Sbjct: 295 RAEAL--------------ILMGNQSNLVTPKNGEILIAATQDFITGGYLLTQKEVFLTK 340

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            + M++A+  + +      I              ++   +WTGKQIFSL+++PN D  + 
Sbjct: 341 EEAMQLAACFLDNEDSTMNI-------QIPAPALLKPRRLWTGKQIFSLLMRPNSDSHIR 393

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRN 547
            N+  KGR YT N + C  DS + L N
Sbjct: 394 LNMVNKGRNYTKNMDLCINDSCMWLFN 420



 Score = 77.0 bits (188), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 33/52 (63%), Positives = 43/52 (82%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLI 72
           +LM N+SNLVTP+NGE+LIAATQDFITGGYLLTQK  F  + + M++A+  +
Sbjct: 300 ILMGNQSNLVTPKNGEILIAATQDFITGGYLLTQKEVFLTKEEAMQLAACFL 351



 Score = 58.2 bits (139), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 27/50 (54%), Positives = 36/50 (72%)

Query: 291 VLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKS 340
           VL LFE IP  D+ LL M +  + P  LI+TR+ VPP CIRPSV+S++K+
Sbjct: 2   VLDLFEQIPQSDVALLGMCSRGAHPKHLIVTRVFVPPACIRPSVLSEVKA 51


>gi|401882581|gb|EJT46834.1| DNA-directed RNA polymerase iii largest subunit [Trichosporon asahii
            var. asahii CBS 2479]
          Length = 1433

 Score =  237 bits (604), Expect = 4e-59,   Method: Compositional matrix adjust.
 Identities = 147/360 (40%), Positives = 197/360 (54%), Gaps = 67/360 (18%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIE 1152
            E CR +Y+ A+IEP + VGA+ AQSIGEPGTQMTLKTFHFAG            + E I 
Sbjct: 1047 ENCRTRYLLAKIEPGSTVGAVGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIIN 1106

Query: 1153 EVFVPDDSFILIKL-------------------------------------------DMD 1169
               V     I ++L                                           DMD
Sbjct: 1107 AAKVISTPIITVELQKPESEPVARIVKGRIERTTLGEIASIIEEAWTGAGAFIEIHIDMD 1166

Query: 1170 RIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSGH----SFLILKP--KDSSKSFNSKM 1220
             I+ L LE+ +D+I+  +    + +     +T++         +  P  KD       ++
Sbjct: 1167 AIQKLQLEITLDTIKTALVLAPKLKIKDSDVTINSRKARLKIYVADPLDKDKCDGVYERL 1226

Query: 1221 YQMKQLLPSVVIKGVQGINRAVI-HEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSS 1279
              +K+ +PSV +KG+  ++R+VI H+E  +G  +YKLLV G  L++VM T GV G +  +
Sbjct: 1227 KSLKRAIPSVQVKGLPEVDRSVITHDEKKKG--EYKLLVTGYGLQEVMGTDGVNGYQTRT 1284

Query: 1280 NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGL 1339
            N+  E  K LGIEAAR TI  EI+  M +HGMSID RH ML+ D+MT KGEVLGITR G+
Sbjct: 1285 NHVMETAKVLGIEAARQTIYDEIQHTMRSHGMSIDPRHVMLLGDVMTYKGEVLGITRFGV 1344

Query: 1340 AKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPM-NVGTGLIKLLQAVP 1398
             KMK+SVL LASFE T+DHLFDA+ Y + D I GVSECIIMG P  + GT L  ++   P
Sbjct: 1345 QKMKDSVLMLASFEKTTDHLFDASLYSKVDDIQGVSECIIMGTPAPSCGTSLASIVTPPP 1404



 Score =  200 bits (509), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 105/284 (36%), Positives = 150/284 (52%), Gaps = 55/284 (19%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHK+SIM HR +V P RTFR NECVC PYNADFDGDEMN+H       
Sbjct: 475 DGDIVLFNRQPSLHKISIMCHRVRVRPWRTFRLNECVCNPYNADFDGDEMNLH------- 527

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
                                          R      +   DFIT  YLL++++   +R
Sbjct: 528 -------------------------------RGSSYRGSGAHDFITASYLLSRRDRLLDR 556

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q  +I S L     +I             P    +   +WTGKQ+++L+++PN+   V 
Sbjct: 557 QQFTQICSYLGDGDLEI----------DLPPPTIWKPVRLWTGKQVYNLLMRPNKKSKVL 606

Query: 521 ANLKTKGRAYTANE-------EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILL 573
            NL+ K R             +    D Y++++NSE++ G  DK+T+G G K +VF ++L
Sbjct: 607 INLEAKCRTLIEPRKEDKFFMDMAPNDGYLVIQNSEIMCGVFDKNTVGDGKKNSVFGVML 666

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           RD+G + A  AM RL+++++ +L N+GFS+GI DV PG+    N
Sbjct: 667 RDYGPNEAAIAMTRLAKLSARWLANQGFSLGINDVIPGEMLQSN 710



 Score =  192 bits (487), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 112/244 (45%), Positives = 153/244 (62%), Gaps = 12/244 (4%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ ISTPIIT  L K      ARIVKGR+ERTTLGE+   IEE +    
Sbjct: 1097 GVPRIKEIINAAKVISTPIITVELQKPESEPVARIVKGRIERTTLGEIASIIEEAWTGAG 1156

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSGH----SFLILKP--K 874
            +FI I +DMD I+ L LE+ +D+I+  +    + +     +T++         +  P  K
Sbjct: 1157 AFIEIHIDMDAIQKLQLEITLDTIKTALVLAPKLKIKDSDVTINSRKARLKIYVADPLDK 1216

Query: 875  DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVI-HEEDVEGVTKYKLLVEGDNLRDVMAT 933
            D       ++  +K+ +PSV +KG+  ++R+VI H+E  +G  +YKLLV G  L++VM T
Sbjct: 1217 DKCDGVYERLKSLKRAIPSVQVKGLPEVDRSVITHDEKKKG--EYKLLVTGYGLQEVMGT 1274

Query: 934  YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
             GV G +  +N+  E  K LGIEAAR TI  EI+  M +HGMSID RH ML+ D+MT KG
Sbjct: 1275 DGVNGYQTRTNHVMETAKVLGIEAARQTIYDEIQHTMRSHGMSIDPRHVMLLGDVMTYKG 1334

Query: 994  EVLG 997
            EVLG
Sbjct: 1335 EVLG 1338



 Score =  124 bits (312), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 68/172 (39%), Positives = 100/172 (58%), Gaps = 3/172 (1%)

Query: 172 SICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEING 231
           + C   TCARVLL  E+ A +  + R P +  L R++  K +L + KKV+ CP+C   NG
Sbjct: 125 TCCSASTCARVLLPPEERASYLKRFRRPRIEMLQRQAASKGVLASCKKVTTCPYCFAPNG 184

Query: 232 VVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEV 291
           +VKK G LKISHE +++  K  DA  E  L  +   V     I +H     ++ LNPL+V
Sbjct: 185 IVKKSGTLKISHEPFRS-NKNADAKAE-WLNGFKAVVSEQSAIGSHLGKS-VEDLNPLKV 241

Query: 292 LQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
           L+LF  +  ED  LL ++ ++ +P D + T + VPP CIRPSV S+  ++ D
Sbjct: 242 LELFRRVTAEDCELLSLHPDVGRPEDYLWTYISVPPPCIRPSVASEAGNNED 293



 Score =  108 bits (270), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 49/68 (72%), Positives = 56/68 (82%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV+NSFFSGLTPTEF FH + GREGLVDTAVKTAETGYM RRL+K+LEDL  QYD+
Sbjct: 815 PSKGFVRNSFFSGLTPTEFLFHAISGREGLVDTAVKTAETGYMARRLMKALEDLSTQYDL 874

Query: 670 SFDAAFYG 677
           S   +  G
Sbjct: 875 SVRNSVGG 882



 Score = 43.1 bits (100), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 21/43 (48%), Positives = 26/43 (60%), Gaps = 1/43 (2%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPM-NVGTGLIKLLQAVP 709
            D  FDA+ Y + D I GVSECIIMG P  + GT L  ++   P
Sbjct: 1362 DHLFDASLYSKVDDIQGVSECIIMGTPAPSCGTSLASIVTPPP 1404


>gi|406700618|gb|EKD03783.1| DNA-directed RNA polymerase iii largest subunit [Trichosporon asahii
            var. asahii CBS 8904]
          Length = 1433

 Score =  237 bits (604), Expect = 4e-59,   Method: Compositional matrix adjust.
 Identities = 147/360 (40%), Positives = 197/360 (54%), Gaps = 67/360 (18%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIE 1152
            E CR +Y+ A+IEP + VGA+ AQSIGEPGTQMTLKTFHFAG            + E I 
Sbjct: 1047 ENCRTRYLLAKIEPGSTVGAVGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIIN 1106

Query: 1153 EVFVPDDSFILIKL-------------------------------------------DMD 1169
               V     I ++L                                           DMD
Sbjct: 1107 AAKVISTPIITVELQKPESEPVARIVKGRIERTTLGEIASIIEEAWTGAGAFIEIHIDMD 1166

Query: 1170 RIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSGH----SFLILKP--KDSSKSFNSKM 1220
             I+ L LE+ +D+I+  +    + +     +T++         +  P  KD       ++
Sbjct: 1167 AIQKLQLEITLDTIKTALVLAPKLKIKDSDVTINSRKARLKIYVADPLDKDKCDGVYERL 1226

Query: 1221 YQMKQLLPSVVIKGVQGINRAVI-HEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSS 1279
              +K+ +PSV +KG+  ++R+VI H+E  +G  +YKLLV G  L++VM T GV G +  +
Sbjct: 1227 KSLKRAIPSVQVKGLPEVDRSVITHDEKKKG--EYKLLVTGYGLQEVMGTDGVNGYQTRT 1284

Query: 1280 NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGL 1339
            N+  E  K LGIEAAR TI  EI+  M +HGMSID RH ML+ D+MT KGEVLGITR G+
Sbjct: 1285 NHVMETAKVLGIEAARQTIYDEIQHTMRSHGMSIDPRHVMLLGDVMTYKGEVLGITRFGV 1344

Query: 1340 AKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPM-NVGTGLIKLLQAVP 1398
             KMK+SVL LASFE T+DHLFDA+ Y + D I GVSECIIMG P  + GT L  ++   P
Sbjct: 1345 QKMKDSVLMLASFEKTTDHLFDASLYSKVDDIQGVSECIIMGTPAPSCGTSLASIVTPPP 1404



 Score =  200 bits (509), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 105/284 (36%), Positives = 150/284 (52%), Gaps = 55/284 (19%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHK+SIM HR +V P RTFR NECVC PYNADFDGDEMN+H       
Sbjct: 475 DGDIVLFNRQPSLHKISIMCHRVRVRPWRTFRLNECVCNPYNADFDGDEMNLH------- 527

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
                                          R      +   DFIT  YLL++++   +R
Sbjct: 528 -------------------------------RGSSYRGSGAHDFITASYLLSRRDRLLDR 556

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q  +I S L     +I             P    +   +WTGKQ+++L+++PN+   V 
Sbjct: 557 QQFTQICSYLGDGDLEI----------DLPPPTIWKPVRLWTGKQVYNLLMRPNKKSKVL 606

Query: 521 ANLKTKGRAYTANE-------EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILL 573
            NL+ K R             +    D Y++++NSE++ G  DK+T+G G K +VF ++L
Sbjct: 607 INLEAKCRTLIEPRKEDKFFMDMAPNDGYLVIQNSEIMCGVFDKNTVGDGKKNSVFGVML 666

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           RD+G + A  AM RL+++++ +L N+GFS+GI DV PG+    N
Sbjct: 667 RDYGPNEAAIAMTRLAKLSARWLANQGFSLGINDVIPGEMLQSN 710



 Score =  192 bits (487), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 112/244 (45%), Positives = 153/244 (62%), Gaps = 12/244 (4%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ ISTPIIT  L K      ARIVKGR+ERTTLGE+   IEE +    
Sbjct: 1097 GVPRIKEIINAAKVISTPIITVELQKPESEPVARIVKGRIERTTLGEIASIIEEAWTGAG 1156

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSGH----SFLILKP--K 874
            +FI I +DMD I+ L LE+ +D+I+  +    + +     +T++         +  P  K
Sbjct: 1157 AFIEIHIDMDAIQKLQLEITLDTIKTALVLAPKLKIKDSDVTINSRKARLKIYVADPLDK 1216

Query: 875  DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVI-HEEDVEGVTKYKLLVEGDNLRDVMAT 933
            D       ++  +K+ +PSV +KG+  ++R+VI H+E  +G  +YKLLV G  L++VM T
Sbjct: 1217 DKCDGVYERLKSLKRAIPSVQVKGLPEVDRSVITHDEKKKG--EYKLLVTGYGLQEVMGT 1274

Query: 934  YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
             GV G +  +N+  E  K LGIEAAR TI  EI+  M +HGMSID RH ML+ D+MT KG
Sbjct: 1275 DGVNGYQTRTNHVMETAKVLGIEAARQTIYDEIQHTMRSHGMSIDPRHVMLLGDVMTYKG 1334

Query: 994  EVLG 997
            EVLG
Sbjct: 1335 EVLG 1338



 Score =  124 bits (312), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 68/172 (39%), Positives = 100/172 (58%), Gaps = 3/172 (1%)

Query: 172 SICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEING 231
           + C   TCARVLL  E+ A +  + R P +  L R++  K +L + KKV+ CP+C   NG
Sbjct: 125 TCCSASTCARVLLPPEERASYLKRFRRPRIEMLQRQAASKGVLASCKKVTTCPYCFAPNG 184

Query: 232 VVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEV 291
           +VKK G LKISHE +++  K  DA  E  L  +   V     I +H     ++ LNPL+V
Sbjct: 185 IVKKSGTLKISHEPFRS-NKNADAKAE-WLNGFKAVVSEQSAIGSHLGKS-VEDLNPLKV 241

Query: 292 LQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
           L+LF  +  ED  LL ++ ++ +P D + T + VPP CIRPSV S+  ++ D
Sbjct: 242 LELFRRVTAEDCELLSLHPDVGRPEDYLWTYISVPPPCIRPSVASEAGNNED 293



 Score =  108 bits (270), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 49/68 (72%), Positives = 56/68 (82%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV+NSFFSGLTPTEF FH + GREGLVDTAVKTAETGYM RRL+K+LEDL  QYD+
Sbjct: 815 PSKGFVRNSFFSGLTPTEFLFHAISGREGLVDTAVKTAETGYMARRLMKALEDLSTQYDL 874

Query: 670 SFDAAFYG 677
           S   +  G
Sbjct: 875 SVRNSVGG 882



 Score = 43.1 bits (100), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 21/43 (48%), Positives = 26/43 (60%), Gaps = 1/43 (2%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPM-NVGTGLIKLLQAVP 709
            D  FDA+ Y + D I GVSECIIMG P  + GT L  ++   P
Sbjct: 1362 DHLFDASLYSKVDDIQGVSECIIMGTPAPSCGTSLASIVTPPP 1404


>gi|195175837|ref|XP_002028612.1| GL10266 [Drosophila persimilis]
 gi|194105884|gb|EDW27927.1| GL10266 [Drosophila persimilis]
          Length = 260

 Score =  236 bits (603), Expect = 5e-59,   Method: Compositional matrix adjust.
 Identities = 120/234 (51%), Positives = 168/234 (71%), Gaps = 4/234 (1%)

Query: 1166 LDMDRIRLLHLEVDIDSIRYCI--ERTRGISGHLTVSGHSFLILKPKDSSKS--FNSKMY 1221
            +DM RI++L L +++++I  CI   R R     + ++  +  I+   +SS++   N+++ 
Sbjct: 3    IDMSRIKVLGLHINLETIVACILKSRMRLKPAQVEIAARTSRIIVRVESSRTSTINAELA 62

Query: 1222 QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNN 1281
            ++   L +VV+ G+  I RAVI  +D      YKL +EG  LR+V++TYGV G +  SNN
Sbjct: 63   RLALSLQNVVVAGLPNIARAVIAVDDTRQPAIYKLCIEGYGLREVISTYGVVGERTRSNN 122

Query: 1282 TYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAK 1341
              E+++TLGIEAAR+ IM+EI  VME HGMS+D+RH ML+A  MT++GEVLGITRHGLAK
Sbjct: 123  ICEIFQTLGIEAARTIIMSEITEVMEGHGMSVDWRHIMLLASQMTARGEVLGITRHGLAK 182

Query: 1342 MKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 1395
            M+ESV NLASFE T+DHLFDAA+YGQTD I+GVSE II+G+P  +GTG+ KLL 
Sbjct: 183  MRESVFNLASFEKTADHLFDAAYYGQTDTINGVSERIILGMPAGIGTGIFKLLH 236



 Score =  138 bits (347), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 74/172 (43%), Positives = 114/172 (66%), Gaps = 4/172 (2%)

Query: 830 LDMDRIRLLHLEVDIDSIRYCI--ERTRGISGHLTVSGHSFLILKPKDSSKS--FNSKMY 885
           +DM RI++L L +++++I  CI   R R     + ++  +  I+   +SS++   N+++ 
Sbjct: 3   IDMSRIKVLGLHINLETIVACILKSRMRLKPAQVEIAARTSRIIVRVESSRTSTINAELA 62

Query: 886 QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNN 945
           ++   L +VV+ G+  I RAVI  +D      YKL +EG  LR+V++TYGV G +  SNN
Sbjct: 63  RLALSLQNVVVAGLPNIARAVIAVDDTRQPAIYKLCIEGYGLREVISTYGVVGERTRSNN 122

Query: 946 TYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             E+++TLGIEAAR+ IM+EI  VME HGMS+D+RH ML+A  MT++GEVLG
Sbjct: 123 ICEIFQTLGIEAARTIIMSEITEVMEGHGMSVDWRHIMLLASQMTARGEVLG 174



 Score = 57.8 bits (138), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 25/39 (64%), Positives = 31/39 (79%)

Query: 668 DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
           D  FDAA+YGQTD I+GVSE II+G+P  +GTG+ KLL 
Sbjct: 198 DHLFDAAYYGQTDTINGVSERIILGMPAGIGTGIFKLLH 236


>gi|222629113|gb|EEE61245.1| hypothetical protein OsJ_15297 [Oryza sativa Japonica Group]
          Length = 1321

 Score =  236 bits (602), Expect = 7e-59,   Method: Compositional matrix adjust.
 Identities = 127/255 (49%), Positives = 173/255 (67%), Gaps = 4/255 (1%)

Query: 1145 GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSG 1201
            GEV E I+ V       +++KLDM RI  LH+ +  DS++  I    + +  S H+ V  
Sbjct: 1050 GEVAEAIKIVLKSSQPNLVVKLDMQRIEALHMGISADSVQLSILNHPKIKLKSEHVRVID 1109

Query: 1202 HSFLILKPKDSSKS-FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEG 1260
             S L + P    KS    +++ +K +LP V++KG+  + RAVI E   E   +YKLLVEG
Sbjct: 1110 KSKLRIYPAGIDKSKLLYELHHLKSMLPKVIVKGIPTVERAVISETGEENDKRYKLLVEG 1169

Query: 1261 DNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPML 1320
             NL  VM T GV  +K  SN+  EV +TLGIEAAR +I+ EI+  M++HGM+ID RH ML
Sbjct: 1170 TNLLAVMGTPGVDAMKTKSNHIMEVNRTLGIEAARRSIIDEIQYTMKSHGMNIDSRHMML 1229

Query: 1321 VADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIM 1380
            +ADLMT KGE+LGITR+G+AKMK SVL LASFE T++HLF+A++ G+ D I GVSECIIM
Sbjct: 1230 LADLMTYKGEILGITRYGIAKMKSSVLMLASFEKTAEHLFNASYSGREDQIEGVSECIIM 1289

Query: 1381 GLPMNVGTGLIKLLQ 1395
            G+PM +GTG++K+ Q
Sbjct: 1290 GIPMQLGTGILKVRQ 1304



 Score =  205 bits (522), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 116/238 (48%), Positives = 155/238 (65%), Gaps = 4/238 (1%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA++ ISTPIITA L  + D+  ARIVKG +E+  LGEV E I+ V     
Sbjct: 1005 GVPRIKEIINAAKKISTPIITAELLSEKDVLSARIVKGSMEKAVLGEVAEAIKIVLKSSQ 1064

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSGHSFLILKPKDSSKS- 879
              +++KLDM RI  LH+ +  DS++  I    + +  S H+ V   S L + P    KS 
Sbjct: 1065 PNLVVKLDMQRIEALHMGISADSVQLSILNHPKIKLKSEHVRVIDKSKLRIYPAGIDKSK 1124

Query: 880  FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
               +++ +K +LP V++KG+  + RAVI E   E   +YKLLVEG NL  VM T GV  +
Sbjct: 1125 LLYELHHLKSMLPKVIVKGIPTVERAVISETGEENDKRYKLLVEGTNLLAVMGTPGVDAM 1184

Query: 940  KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            K  SN+  EV +TLGIEAAR +I+ EI+  M++HGM+ID RH ML+ADLMT KGE+LG
Sbjct: 1185 KTKSNHIMEVNRTLGIEAARRSIIDEIQYTMKSHGMNIDSRHMMLLADLMTYKGEILG 1242



 Score =  153 bits (386), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 95/250 (38%), Positives = 144/250 (57%), Gaps = 29/250 (11%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + V+Q + +Q+ +  +Y  + +  P+P+GLLD RMG   K   C+TC  + ++C GHFGY
Sbjct: 35  NEVRQSAEVQVWNSRIY--NHEMKPVPNGLLDTRMGAANKLGECSTCHGSFAECPGHFGY 92

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           + L LPVF++G+F C++++L+ ICK  +C+RVLL E+    F  K+RNP    L + ++ 
Sbjct: 93  LKLALPVFNVGFFNCILDVLKCICK--SCSRVLLMEKDRLEFLKKMRNPKADPLQKSAIM 150

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGL--LKISHEKYKNRTKKKDAIVEDLLAEYNEAV 268
           KK+ +   K+S CP CG ING V K G   L I H+     +K  D   E+L     +A+
Sbjct: 151 KKVRDKC-KLSRCPWCGFINGSVAKKGRAGLIILHDC----SKTLDGSTEEL----RDAL 201

Query: 269 KFNPEIEAHKKFGL----IQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLL 324
                  +HKK  L    ++ L+P  VL LF+ +  ED  LL +     +P  LI+T + 
Sbjct: 202 -------SHKKEKLSISAVRMLDPAIVLSLFKRMTDEDCELLNLG---DRPEKLIVTEIA 251

Query: 325 VPPNCIRPSV 334
           VPP  IRPSV
Sbjct: 252 VPPVPIRPSV 261



 Score =  122 bits (306), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 50/65 (76%), Positives = 59/65 (90%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIM+HRA+++P RT RFNE VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 445 DGDIVLFNRQPSLHRMSIMSHRARIMPWRTLRFNESVCNPYNADFDGDEMNLHVPQTEEA 504

Query: 401 RAEAL 405
           R EAL
Sbjct: 505 RTEAL 509



 Score =  107 bits (266), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 66/222 (29%), Positives = 105/222 (47%), Gaps = 47/222 (21%)

Query: 406 PSLHKLSIMAHRAKVL----MANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRA 461
           PSLH++SIM+HRA+++    +    ++  P N +                     F    
Sbjct: 455 PSLHRMSIMSHRARIMPWRTLRFNESVCNPYNAD---------------------FDGDE 493

Query: 462 QTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNA 521
             + +  T  A T  +               + +    +WTGKQ+FS++++PN    V  
Sbjct: 494 MNLHVPQTEEARTEAL---------------MLMGPIELWTGKQLFSVLVRPNACTKVFL 538

Query: 522 NLKTKGRAYTAN-------EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLR 574
           NL  K + Y          E  C  D +V  RNSELL+G + K+TLG+G K  +F  L+R
Sbjct: 539 NLTVKEKIYKTPKGSTLEPEAMCPNDGFVYFRNSELLSGQVGKATLGNGNKDGMFSTLVR 598

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           D+    A + M RL++ ++ ++ N GFSIG+ DV PG+   Q
Sbjct: 599 DYNSHAAASCMNRLAKFSARFIGNHGFSIGVDDVQPGEHLNQ 640



 Score =  105 bits (261), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 52/74 (70%), Positives = 57/74 (77%), Gaps = 1/74 (1%)

Query: 605 IGDVTPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDL 663
           I   TP  +GFV NSF++GLT TEFFFHTMGGREGLVDTAVKTAETGYM RRL+K LEDL
Sbjct: 752 INSKTPAAKGFVANSFYTGLTATEFFFHTMGGREGLVDTAVKTAETGYMSRRLMKGLEDL 811

Query: 664 CVQYDMSFDAAFYG 677
            V YD +   A  G
Sbjct: 812 SVFYDQTVRNASGG 825



 Score = 77.4 bits (189), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 54/164 (32%), Positives = 79/164 (48%), Gaps = 28/164 (17%)

Query: 998  NGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQD--TSENFVRDIKK 1055
            +G P+ L +L   ++A    R   +LS  EIL + N+ L   +   D   SE F + +  
Sbjct: 845  DGKPLNLDQLFMKVMATCPQRGQNTLSPGEILQILNDKLSEHDASSDDGCSEKFKQLLTY 904

Query: 1056 FLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKA------------ 1103
            FLE+          + K+ +  R  +L  +D +G    S  F  +  A            
Sbjct: 905  FLED----------RIKLLKSTRRALLLDEDHVGERHSS--FEESIAANISGISVKQLQV 952

Query: 1104 --EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
              + C  +Y   +IE   ++GA+ AQSIGEPGTQMTLKTFHFAG
Sbjct: 953  FLDTCLSRYHLKKIEAGASIGAIGAQSIGEPGTQMTLKTFHFAG 996



 Score = 52.4 bits (124), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 21/36 (58%), Positives = 30/36 (83%)

Query: 671  FDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            F+A++ G+ D I GVSECIIMG+PM +GTG++K+ Q
Sbjct: 1269 FNASYSGREDQIEGVSECIIMGIPMQLGTGILKVRQ 1304


>gi|133354|sp|P27625.1|RPC1_PLAFA RecName: Full=DNA-directed RNA polymerase III subunit RPC1;
           Short=RNA polymerase III subunit C1; AltName:
           Full=DNA-directed RNA polymerase III largest subunit;
           AltName: Full=RNA polymerase III subunit C160
 gi|160596|gb|AAA29729.1| RNA polymerase III largest subunit [Plasmodium falciparum]
          Length = 2339

 Score =  236 bits (601), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 122/281 (43%), Positives = 170/281 (60%), Gaps = 31/281 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIM H+AK++  +TFRFNECVC+PYNADFDGDEMN+ +PQTEEA
Sbjct: 568 DGDIVLFNRQPSLHRMSIMCHKAKIMDFKTFRFNECVCSPYNADFDGDEMNLDVPQTEEA 627

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL               LM  K NL+TP+NGE++IA TQDF++  Y++T K+ F +R
Sbjct: 628 RAEAL--------------YLMNVKHNLITPKNGEVIIALTQDFLSASYIITNKDTFLDR 673

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPV-VFVRTAVIWTGKQIFSLILKPNRDCPV 519
             T  +  +  +D S    +          P+   ++   +WTGKQ+ S+++KPN+    
Sbjct: 674 -DTFCLLCSYFSDASLYIEL----------PIPAILKPKELWTGKQLISVLIKPNKKENT 722

Query: 520 NANLKTKGRAYTAN----EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
             N + + R Y+      +  C  DSYV    SEL+ GS+ K  LGS  K  +FY L+  
Sbjct: 723 IINFEIQEREYSNKFGDLKHLCLNDSYVCFYKSELICGSLGKKVLGS-SKYGLFYYLIHH 781

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
               +A+  M RLS++TS Y  N+G +IGI DV P Q   +
Sbjct: 782 NSSHIALKIMNRLSKLTSRYFSNKGMTIGIDDVRPSQTLTE 822



 Score =  140 bits (354), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 92/253 (36%), Positives = 142/253 (56%), Gaps = 28/253 (11%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G ++KED ++  S ++I+++ +Y ++    P P+G+LD ++G ++  + C TC + L +C
Sbjct: 41  GIMSKEDIIKY-SEVKIMNREMY-KNNSGIPYPYGVLDLKLGAHKSNSVCETCNKKLINC 98

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFGYI+L  PVFHIGY++ +I+IL  ICK   C+ +LL +EK   +    +       
Sbjct: 99  SGHFGYIELNYPVFHIGYYKYIIHILYCICK--YCSSLLLSKEKIDFYCNLKKKSTDDSF 156

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEY 264
            +K L K+IL   KKV+ C  CG   GV+KK  ++K S +++    K K  +        
Sbjct: 157 YKKHLFKRILNNCKKVNKCYICGNPQGVIKK--IIKPSLDQF---MKLKHIL-------- 203

Query: 265 NEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLL 324
              VK N ++   +     + LN L VL+LF+ I    + LL     +  P  LI+T LL
Sbjct: 204 --KVKENGKMIIKE-----EDLNSLYVLKLFKNINPYHVKLL----NIENPEKLIITALL 252

Query: 325 VPPNCIRPSVISD 337
           VPPN IRPSVI D
Sbjct: 253 VPPNTIRPSVIID 265



 Score =  129 bits (323), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 69/165 (41%), Positives = 100/165 (60%)

Query: 1252 TKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM 1311
            T Y +LVEG++L  V+   GV      SN+   V++ LGIEAAR TI+ EIK  +E + +
Sbjct: 2171 TVYSILVEGNSLNYVLGLEGVDFKHIISNHVINVFQVLGIEAARITIINEIKKCVEAYSI 2230

Query: 1312 SIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCI 1371
             ID RH ML+AD+M   G++LGI R G+ K ++S L LASFE T++HLF ++F+   D I
Sbjct: 2231 DIDIRHIMLLADIMAFTGDILGINRFGIQKARQSTLMLASFEETNEHLFVSSFFKNVDEI 2290

Query: 1372 SGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHT 1416
            + +SE II+G  + +GTG  +LL      +      L +  E  T
Sbjct: 2291 NNISESIIVGKNIPIGTGAFQLLYDYKLEKETKNLTLLEKAERET 2335



 Score =  112 bits (280), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 48/62 (77%), Positives = 56/62 (90%)

Query: 609  TPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +  +GFVQNSF++GL+PTEFFFHTM GREGLVDTAVKTAETGYMQRRL+K+LEDL + YD
Sbjct: 939  SESRGFVQNSFYTGLSPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKALEDLSIHYD 998

Query: 669  MS 670
             S
Sbjct: 999  YS 1000



 Score = 80.9 bits (198), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 51/156 (32%), Positives = 90/156 (57%), Gaps = 7/156 (4%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS +I TPI+   L+ + + ++A ++K +LE+TT+ ++C YI+E +    
Sbjct: 1816 GVPRIKEIINASNSIQTPILNIPLEVNDNYNFALMMKSKLEKTTIRDICMYIKEDYTSRG 1875

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISG------HLTVSGHSFLILKPKDSS 877
             F+ +K + + I+ L L ++  +I+  I +   I+       H+ V     L +  K+  
Sbjct: 1876 VFLSVKFNEELIQKLFLNINAYNIKDIILKQSHINKIKINKIHINVINKYKLHISLKNDE 1935

Query: 878  KSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVE 913
              F  +M  +K+ L  ++I G + I R +I +ED+E
Sbjct: 1936 FIF-FQMESLKKGLLDLLIYGDKDIKRCIIKKEDIE 1970



 Score = 73.2 bits (178), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 38/82 (46%), Positives = 53/82 (64%)

Query: 916  TKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM 975
            T Y +LVEG++L  V+   GV      SN+   V++ LGIEAAR TI+ EIK  +E + +
Sbjct: 2171 TVYSILVEGNSLNYVLGLEGVDFKHIISNHVINVFQVLGIEAARITIINEIKKCVEAYSI 2230

Query: 976  SIDFRHPMLVADLMTSKGEVLG 997
             ID RH ML+AD+M   G++LG
Sbjct: 2231 DIDIRHIMLLADIMAFTGDILG 2252



 Score = 61.2 bits (147), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 26/37 (70%), Positives = 30/37 (81%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            KY +    P  AVG+++AQSIGEPGTQMTLKTFHFAG
Sbjct: 1771 KYFKYISTPGDAVGSISAQSIGEPGTQMTLKTFHFAG 1807



 Score = 53.1 bits (126), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 21/40 (52%), Positives = 31/40 (77%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           LM  K NL+TP+NGE++IA TQDF++  Y++T K+ F +R
Sbjct: 634 LMNVKHNLITPKNGEVIIALTQDFLSASYIITNKDTFLDR 673


>gi|440296621|gb|ELP89407.1| DNA-directed RNA polymerase III subunit RPC1, putative [Entamoeba
           invadens IP1]
          Length = 1381

 Score =  234 bits (598), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 120/271 (44%), Positives = 172/271 (63%), Gaps = 25/271 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIM H AKVLP RT RFNECVCTPYNADFDGDEMN+H+PQTEEA
Sbjct: 474 DGDIVLFNRQPSLHRISIMCHIAKVLPWRTMRFNECVCTPYNADFDGDEMNLHVPQTEEA 533

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE L              +LM +  NL TPR G+++IA TQDF+T  +LLT K+ F   
Sbjct: 534 RAECL--------------MLMHSAKNLQTPRTGQMIIAETQDFLTVSFLLTAKD-FVVT 578

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            + M + S    +     G+  R    +     +++   +WTGKQ++ L L+PN +  V+
Sbjct: 579 EEEMMLWSCWFHNA----GVEIRLPTPA-----YLKPKKLWTGKQLYGLALRPNPNFGVD 629

Query: 521 ANLKTKGRAYTANEEF-CHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
             L    + Y+   ++ C +D ++  ++S+L+ G +DK+ +GSG K+ +F+++LRD+G  
Sbjct: 630 ICLDAPSKNYSKEGKWMCMKDGWICFKHSQLVCGQIDKAIIGSGNKSGLFHLILRDYGLL 689

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
            +   M  +SR  + +L + GFSIGI DVTP
Sbjct: 690 DSAKMMAHISRFCARFLGDYGFSIGISDVTP 720



 Score =  182 bits (463), Expect = 8e-43,   Method: Compositional matrix adjust.
 Identities = 103/257 (40%), Positives = 160/257 (62%), Gaps = 7/257 (2%)

Query: 1146 EVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGH 1202
            E+ + ++ VF P ++++ IKLD + I+ L LE   + +   +  TRG+      + V   
Sbjct: 1117 EIAKSVKIVFKPAEAYVSIKLDFETIKQLQLECSAEKVHDILLNTRGLKLKEKQVLVRNV 1176

Query: 1203 SFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDN 1262
              L +     + S    +  ++  L  +++ G++G  RAVI++  +     ++LLVEG  
Sbjct: 1177 DKLRVYVDKVNTSLLFSLNALRNQLLEIIVCGIEGTGRAVINKSKI----GFELLVEGSE 1232

Query: 1263 LRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVA 1322
            L  VM   GV G   + N+   V K LGIEAARSTI++EIK VM+ +G+SID RH +L++
Sbjct: 1233 LLKVMGVAGVIGESTTCNHIMVVEKVLGIEAARSTIISEIKNVMDAYGLSIDIRHLLLLS 1292

Query: 1323 DLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGL 1382
            DLMT KG +LGITR+G++KMK+SV   ASFE T+DHLFDAA + + + I+GVSE II+G 
Sbjct: 1293 DLMTFKGVILGITRYGISKMKDSVFTFASFERTNDHLFDAAVHSRQNDIAGVSESIIVGN 1352

Query: 1383 PMNVGTGLIKLLQAVPR 1399
             + +GTGL+ ++   P+
Sbjct: 1353 QVGLGTGLMSIMYDPPK 1369



 Score =  168 bits (426), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 99/237 (41%), Positives = 144/237 (60%), Gaps = 7/237 (2%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS+ I TPI+TA L    D+  ARIVKGR+E T L E+ + ++ VF P +
Sbjct: 1071 GVPRIKEIINASKKIQTPIVTAKLVNSKDVTSARIVKGRIEATKLKEIAKSVKIVFKPAE 1130

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---SGHLTVSGHSFLILKPKDSSKSF 880
            +++ IKLD + I+ L LE   + +   +  TRG+      + V     L +     + S 
Sbjct: 1131 AYVSIKLDFETIKQLQLECSAEKVHDILLNTRGLKLKEKQVLVRNVDKLRVYVDKVNTSL 1190

Query: 881  NSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
               +  ++  L  +++ G++G  RAVI++  +     ++LLVEG  L  VM   GV G  
Sbjct: 1191 LFSLNALRNQLLEIIVCGIEGTGRAVINKSKI----GFELLVEGSELLKVMGVAGVIGES 1246

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             + N+   V K LGIEAARSTI++EIK VM+ +G+SID RH +L++DLMT KG +LG
Sbjct: 1247 TTCNHIMVVEKVLGIEAARSTIISEIKNVMDAYGLSIDIRHLLLLSDLMTFKGVILG 1303



 Score =  163 bits (413), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 91/227 (40%), Positives = 134/227 (59%), Gaps = 9/227 (3%)

Query: 113 RTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQS 172
           R P P G+LDRR+G       C TCG+N+ +C GHFG I+L LPVFHIG+FR +I +LQ 
Sbjct: 70  RQPNPDGVLDRRLGVCDSVNTCKTCGKNVDECCGHFGEINLALPVFHIGFFRPIIQVLQC 129

Query: 173 ICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKK-ILETTKKVSVCPHCGEING 231
           +CKN  C R+LL +E+   +  ++RN     + R  L +  I++  K  + CPHC  ING
Sbjct: 130 VCKN--CNRLLLTDEEREYYLKRMRNKTTDTIQRTMLVRALIVQCRKHYNGCPHCNAING 187

Query: 232 VVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQT-LNPLE 290
            V+K G +K+ H+KY       +  + +    ++E++K + EI A    G  Q  L+PL 
Sbjct: 188 SVRKYGNIKLVHDKYHKDPNLNE--MNEFYDGFDESIKMDKEIGAF--LGNAQEDLDPLR 243

Query: 291 VLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD 337
           VL +F+++  EDI  +  + + + P  LILT + VPP  IRPSV  D
Sbjct: 244 VLNIFKSLVREDIEAMDFSPD-APPEKLILTSVPVPPLTIRPSVSMD 289



 Score =  105 bits (262), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 50/67 (74%), Positives = 58/67 (86%), Gaps = 1/67 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV+NSFF+GL  TEFFFHTMGGREGLVD+AVKTAETGYMQRRL+K+LEDL V Y
Sbjct: 842 TPQAKGFVKNSFFTGLNATEFFFHTMGGREGLVDSAVKTAETGYMQRRLMKALEDLHVHY 901

Query: 668 DMSFDAA 674
           D +  +A
Sbjct: 902 DGTVRSA 908



 Score = 61.2 bits (147), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 27/42 (64%), Positives = 31/42 (73%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            + C +K +R   EP T VGALA QS+GEP TQM LKTFHFAG
Sbjct: 1021 KVCEQKGLRNICEPGTPVGALAGQSMGEPSTQMVLKTFHFAG 1062



 Score = 44.3 bits (103), Expect = 0.55,   Method: Compositional matrix adjust.
 Identities = 20/45 (44%), Positives = 29/45 (64%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 65
           +LM +  NL TPR G+++IA TQDF+T  +LLT K+      + M
Sbjct: 539 MLMHSAKNLQTPRTGQMIIAETQDFLTVSFLLTAKDFVVTEEEMM 583


>gi|157875469|ref|XP_001686126.1| putative DNA-directed RNA polymerase III largest subunit
           [Leishmania major strain Friedlin]
 gi|68129200|emb|CAJ07737.1| putative DNA-directed RNA polymerase III largest subunit
           [Leishmania major strain Friedlin]
          Length = 1582

 Score =  233 bits (595), Expect = 5e-58,   Method: Compositional matrix adjust.
 Identities = 121/271 (44%), Positives = 166/271 (61%), Gaps = 25/271 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + D +LFNRQPSLH++S+MAHRA+VLP RTFRFNEC C PYNADFDGDEMN+H+ QTEEA
Sbjct: 455 NGDYILFNRQPSLHRISLMAHRARVLPFRTFRFNECCCAPYNADFDGDEMNIHVVQTEEA 514

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              AK LM    N++T +NGE +IA TQDF+T  YL+T ++A F+R
Sbjct: 515 RAE--------------AKELMLTSHNIITAKNGEPIIACTQDFLTAAYLVTSRDALFDR 560

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A   ++ S  + + +     I         P + ++ A +WTGKQ+F LIL+P  +  + 
Sbjct: 561 ASFTQMVSHWLGNETQYALPI---------PAI-LKPAELWTGKQLFELILRPTPETQLL 610

Query: 521 ANLKTKGRAYT-ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            NL+ K R Y+ A       + YV   +S  L+G +DK  LG G K  +F  L    G +
Sbjct: 611 LNLEAKARFYSGAGRHDDPAEGYVAFLDSVFLSGRLDKKLLGGGAKDGLFARLYALGGGE 670

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
              T M R+++ T+ YL N GFS+G+GDV+P
Sbjct: 671 QTATCMSRIAQFTARYLQNYGFSLGLGDVSP 701



 Score =  162 bits (409), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 92/237 (38%), Positives = 136/237 (57%), Gaps = 11/237 (4%)

Query: 119 GLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPT 178
           G+ D R+G + + + C TCGQ   +C GH G+IDL +PVFH+GYF  VI + ++ICK   
Sbjct: 54  GVNDGRLGPSDRLSVCNTCGQRSIECTGHAGHIDLEVPVFHLGYFSAVIRVCRTICKR-- 111

Query: 179 CARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGL 238
           C+ VLL  E+   +  +LR+       R ++ K I E   K  VC  CG +NG V++   
Sbjct: 112 CSNVLLTREEMEYYLHRLRSTTHEPQQRAAIIKGIQEDAYKTRVCLMCGGLNGTVRRVRP 171

Query: 239 LKISHEKYKNRTKKKDAIVEDLLAEYNE----AVKFNPEIEAHKKFGLIQTLNPLEVLQL 294
           ++I HEKY    ++ +   ED  A + E    AV  N E+ AHK+F + + L+P  V +L
Sbjct: 172 MRIVHEKYLVDLRRGEQANEDPTAFFQEELRSAVMHNSEVGAHKEF-VHEFLHPQRVKKL 230

Query: 295 FEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRP---SVISDLKSDNDVVLFN 348
           FEAIP E +PLL +    S P  L+++ LLVPP C+RP   S  S ++ D+    +N
Sbjct: 231 FEAIPQEQVPLLGLQPGTS-PCSLLISTLLVPPVCVRPRGMSTTSHIREDDLTTQYN 286



 Score =  149 bits (375), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 96/259 (37%), Positives = 144/259 (55%), Gaps = 16/259 (6%)

Query: 1146 EVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSI--RYCIERTRGISG--HLT--- 1198
            E+   + EV  P   +I I L+M+ I  L L +D   +  R      R +S   HL+   
Sbjct: 1234 EITREMVEVVTPRAYYIHIFLNMELIERLLLPIDAAVVCQRLYAAAARPMSPLRHLSEAC 1293

Query: 1199 ---VSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYK 1255
               VS  S +I   +      +  +  +  LLP +V+ GV G+NR +I +         K
Sbjct: 1294 ADVVSRDSLVIKSYEKDPARVHFNVQHLLTLLPDLVVGGVPGVNRVMIADRS------EK 1347

Query: 1256 LLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDF 1315
            LL EG  L  VM+   V GV+ + N+   + + LGIEAAR TI+ EI  +++ + ++ID 
Sbjct: 1348 LLAEGAELLSVMSLPYVDGVRTTCNHVAVIERALGIEAARETIVKEITSILQAYSLNIDI 1407

Query: 1316 RHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVS 1375
            RH  L+AD+MTS+G VLGITR+G+ KM  +VL +ASFE T++HL++AA   + D    VS
Sbjct: 1408 RHIYLLADVMTSRGVVLGITRYGIQKMNNNVLTMASFERTTEHLYNAAMTEREDVNLSVS 1467

Query: 1376 ECIIMGLPMNVGTGLIKLL 1394
            E II+G P+ +GT    +L
Sbjct: 1468 ESIIIGKPIPLGTSSFNIL 1486



 Score =  133 bits (334), Expect = 9e-28,   Method: Compositional matrix adjust.
 Identities = 94/257 (36%), Positives = 139/257 (54%), Gaps = 29/257 (11%)

Query: 764  GVPRIKEIINASRNISTPIITAYL---DKDTDLDYA----------RIVKGRLERTTLGE 810
            GVPR+ EIINA+++I+TP+ITA +   D+ T +D A          R VKG +ER  L E
Sbjct: 1175 GVPRLVEIINANKSIATPVITAPIVLEDEFTSIDLASASRTQYQAARAVKGLMERVLLKE 1234

Query: 811  VCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSI--RYCIERTRGISG--HLT---- 862
            +   + EV  P   +I I L+M+ I  L L +D   +  R      R +S   HL+    
Sbjct: 1235 ITREMVEVVTPRAYYIHIFLNMELIERLLLPIDAAVVCQRLYAAAARPMSPLRHLSEACA 1294

Query: 863  --VSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKL 920
              VS  S +I   +      +  +  +  LLP +V+ GV G+NR +I +         KL
Sbjct: 1295 DVVSRDSLVIKSYEKDPARVHFNVQHLLTLLPDLVVGGVPGVNRVMIADRS------EKL 1348

Query: 921  LVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFR 980
            L EG  L  VM+   V GV+ + N+   + + LGIEAAR TI+ EI  +++ + ++ID R
Sbjct: 1349 LAEGAELLSVMSLPYVDGVRTTCNHVAVIERALGIEAARETIVKEITSILQAYSLNIDIR 1408

Query: 981  HPMLVADLMTSKGEVLG 997
            H  L+AD+MTS+G VLG
Sbjct: 1409 HIYLLADVMTSRGVVLG 1425



 Score = 95.5 bits (236), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 42/59 (71%), Positives = 51/59 (86%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
           +GFV +SF+SGL+PTEFFFH M GREG+VDTAVKTAETGY+ RRL K++E+L V YD S
Sbjct: 828 RGFVASSFYSGLSPTEFFFHGMAGREGIVDTAVKTAETGYIYRRLSKAMENLSVGYDAS 886



 Score = 58.5 bits (140), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 27/42 (64%), Positives = 30/42 (71%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            EA   K  R   EP T  GA+AAQS+GEP TQMTL+TFHFAG
Sbjct: 1125 EASARKVHRKLCEPGTPCGAIAAQSVGEPSTQMTLRTFHFAG 1166



 Score = 52.0 bits (123), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 33/48 (68%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIAS 69
           LM    N++T +NGE +IA TQDF+T  YL+T ++A F+RA   ++ S
Sbjct: 521 LMLTSHNIITAKNGEPIIACTQDFLTAAYLVTSRDALFDRASFTQMVS 568


>gi|66475716|ref|XP_627674.1| DNA-directed RNA polymerase III C1 subunit [Cryptosporidium parvum
           Iowa II]
 gi|46229106|gb|EAK89955.1| DNA-directed RNA polymerase III C1 subunit [Cryptosporidium parvum
           Iowa II]
          Length = 1871

 Score =  233 bits (594), Expect = 5e-58,   Method: Compositional matrix adjust.
 Identities = 122/273 (44%), Positives = 165/273 (60%), Gaps = 29/273 (10%)

Query: 343 DVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARA 402
           D+VLFNRQPSLH+LSIM+H+  V+P RTFRFNEC C PYNADFDGDEMN+HLPQ E AR+
Sbjct: 453 DIVLFNRQPSLHRLSIMSHKVVVMPWRTFRFNECACAPYNADFDGDEMNLHLPQNELARS 512

Query: 403 EALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 462
           E              +K LM   +NLVTPRNGE LIAATQDF+ G Y+LT ++ F  R Q
Sbjct: 513 E--------------SKHLMGLMNNLVTPRNGEPLIAATQDFLLGMYVLTGRDIFLTRDQ 558

Query: 463 TMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCP--VN 520
             +            C            P   ++   +WTGKQ+F++IL+PN +    ++
Sbjct: 559 FSQYC----------CHFSNGQIPMELPPPTILKPVELWTGKQVFNMILRPNSNEKERID 608

Query: 521 ANLKTKGRAYTAN---EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFG 577
            + + K R Y +    ++ C  + YV++R+SELLAG++ K  LG G K  +F+ +L +  
Sbjct: 609 VSFELKERDYDSKSDLKDLCPNEGYVVVRHSELLAGAIGKKVLGGGSKEGLFFYILLENN 668

Query: 578 EDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
              +   M R+SR  S YL N+G +IGI DVTP
Sbjct: 669 AKKSSECMGRISRFVSRYLANKGMTIGIDDVTP 701



 Score =  192 bits (488), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 135/400 (33%), Positives = 198/400 (49%), Gaps = 94/400 (23%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKT----------------------- 1140
            +A   KY++A  EP  AVGA+AAQSIGEPGTQMTLKT                       
Sbjct: 1447 KASWSKYMKAITEPGEAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIIN 1506

Query: 1141 -------------------FHFA------------GEVCEYIEEVFVPDDSFILIKLDMD 1169
                               F++A             EV   IEE++ P+  FI I L+ +
Sbjct: 1507 AATKILTPIIEAKLENDSDFNYAQIVKGSIVKTLLNEVVSDIEELYSPNGVFININLNEE 1566

Query: 1170 RIRLLHLEVDIDSIRYCIERTRGIS----------------------GHLTVSGHSFLIL 1207
             I+  +L+++  ++R  I     IS                      G ++  G S   +
Sbjct: 1567 TIKGHYLDINAYTVRDSIVSHGPISKIKLKLEDIQVLDLWKLSILIGGGISQIGSSSNNI 1626

Query: 1208 KPKDSSKSFNSKM-------YQ---MKQLLPSVVIKGVQGINRAVIHEEDVEGVTK---- 1253
                +  + N+ +       +Q   +K+ L +VV+ G+ GI R+VI ++D E        
Sbjct: 1627 NGTGNVNTLNTGIGNTMNVYFQTQLLKKGLQNVVVSGIPGIKRSVIRQDDKEDPITGEKR 1686

Query: 1254 --YKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM 1311
              Y L VEG  L  +M   G+ G    SN+  EV + LGIEAAR  I+ E++  M+ + M
Sbjct: 1687 KCYSLAVEGYGLLKLMGINGIIGTTTVSNHVMEVREVLGIEAARKVIIQEVQKCMDAYSM 1746

Query: 1312 SIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCI 1371
             ID RH  L+AD+MT +G+VLGI+R G+ KM+ S L LASFE T++HLF+AAF  + D +
Sbjct: 1747 DIDLRHIQLLADIMTFRGDVLGISRFGIQKMRTSTLMLASFEETNEHLFEAAFQNRVDPV 1806

Query: 1372 SGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDN 1411
             GVSEC+IMG P+ +GTG   +L   P +  + ++ LF N
Sbjct: 1807 FGVSECVIMGKPIKIGTGSFDILYNSPSN--IQKSKLFLN 1844



 Score =  147 bits (370), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 98/272 (36%), Positives = 146/272 (53%), Gaps = 38/272 (13%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA+  I TPII A L+ D+D +YA+IVKG + +T L EV   IEE++ P+ 
Sbjct: 1497 GVPRIKEIINAATKILTPIIEAKLENDSDFNYAQIVKGSIVKTLLNEVVSDIEELYSPNG 1556

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS----------------------GHL 861
             FI I L+ + I+  +L+++  ++R  I     IS                      G +
Sbjct: 1557 VFININLNEETIKGHYLDINAYTVRDSIVSHGPISKIKLKLEDIQVLDLWKLSILIGGGI 1616

Query: 862  TVSGHSFLILKPKDSSKSFNSKM-------YQ---MKQLLPSVVIKGVQGINRAVIHEED 911
            +  G S   +    +  + N+ +       +Q   +K+ L +VV+ G+ GI R+VI ++D
Sbjct: 1617 SQIGSSSNNINGTGNVNTLNTGIGNTMNVYFQTQLLKKGLQNVVVSGIPGIKRSVIRQDD 1676

Query: 912  VEGVTK------YKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTE 965
             E          Y L VEG  L  +M   G+ G    SN+  EV + LGIEAAR  I+ E
Sbjct: 1677 KEDPITGEKRKCYSLAVEGYGLLKLMGINGIIGTTTVSNHVMEVREVLGIEAARKVIIQE 1736

Query: 966  IKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            ++  M+ + M ID RH  L+AD+MT +G+VLG
Sbjct: 1737 VQKCMDAYSMDIDLRHIQLLADIMTFRGDVLG 1768



 Score =  136 bits (343), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 86/262 (32%), Positives = 135/262 (51%), Gaps = 51/262 (19%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           +E +   +D + + +H++++ + +Y +     P+  G+LD R+G ++ +A C++CG  L 
Sbjct: 40  VEFSAMGKDEIARSAHMEVLHREIY-RPMTNIPLQGGVLDSRLGAHRADAQCSSCGGTLK 98

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLL-GEEKAAGFRAKLRNPAL 201
            C GH+GYIDL  PVFH+GYF+ +  +L  ICK  +C   LL GEEK    R  L     
Sbjct: 99  TCGGHWGYIDLQQPVFHVGYFKHLYGVLCCICK--SCGAFLLKGEEK----RQHLARLKQ 152

Query: 202 SYLVRKSLK---KKILETTKKVSVCPHCGEINGVVKKC------GLLKISHEKYKNRTKK 252
           SY +  S +   +K++E  KKV  CP C    G +++         +K++H      T K
Sbjct: 153 SYSIAHSYRLQFRKLVERCKKVKTCPRCMSQQGQLRRTIRPTLDQFMKLTH------TIK 206

Query: 253 KDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL 312
            D        EY                  ++ L P+ V  L E +P +D+ +L    E 
Sbjct: 207 VDG------KEY------------------VEDLTPIFVQTLLERVPYQDLDIL----ET 238

Query: 313 SKPSDLILTRLLVPPNCIRPSV 334
            KP +L+++RL VPPNCIRPSV
Sbjct: 239 FKPGNLLISRLPVPPNCIRPSV 260



 Score =  110 bits (276), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 49/59 (83%), Positives = 54/59 (91%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
           +GFV NSFFSGL P EFFFHTM GREGLVDTAVKTAETGYMQRRLVK+LEDLC++YD +
Sbjct: 827 RGFVGNSFFSGLQPDEFFFHTMSGREGLVDTAVKTAETGYMQRRLVKALEDLCIKYDQT 885



 Score = 54.7 bits (130), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 26/42 (61%), Positives = 31/42 (73%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 63
           LM   +NLVTPRNGE LIAATQDF+ G Y+LT ++ F  R Q
Sbjct: 517 LMGLMNNLVTPRNGEPLIAATQDFLLGMYVLTGRDIFLTRDQ 558



 Score = 46.6 bits (109), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 22/52 (42%), Positives = 33/52 (63%), Gaps = 2/52 (3%)

Query: 671  FDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDN 722
            F+AAF  + D + GVSEC+IMG P+ +GTG   +L   P +  + ++ LF N
Sbjct: 1795 FEAAFQNRVDPVFGVSECVIMGKPIKIGTGSFDILYNSPSN--IQKSKLFLN 1844


>gi|32398906|emb|CAD98371.1| DNA-directed RNA polymerase II/III subunit, probable
           [Cryptosporidium parvum]
          Length = 1907

 Score =  233 bits (594), Expect = 6e-58,   Method: Compositional matrix adjust.
 Identities = 122/273 (44%), Positives = 165/273 (60%), Gaps = 29/273 (10%)

Query: 343 DVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARA 402
           D+VLFNRQPSLH+LSIM+H+  V+P RTFRFNEC C PYNADFDGDEMN+HLPQ E AR+
Sbjct: 489 DIVLFNRQPSLHRLSIMSHKVVVMPWRTFRFNECACAPYNADFDGDEMNLHLPQNELARS 548

Query: 403 EALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 462
           E              +K LM   +NLVTPRNGE LIAATQDF+ G Y+LT ++ F  R Q
Sbjct: 549 E--------------SKHLMGLMNNLVTPRNGEPLIAATQDFLLGMYVLTGRDIFLTRDQ 594

Query: 463 TMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCP--VN 520
             +            C            P   ++   +WTGKQ+F++IL+PN +    ++
Sbjct: 595 FSQYC----------CHFSNGQIPMELPPPTILKPVELWTGKQVFNMILRPNSNEKERID 644

Query: 521 ANLKTKGRAYTAN---EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFG 577
            + + K R Y +    ++ C  + YV++R+SELLAG++ K  LG G K  +F+ +L +  
Sbjct: 645 VSFELKERDYDSKSDLKDLCPNEGYVVVRHSELLAGAIGKKVLGGGSKEGLFFYILLENN 704

Query: 578 EDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
              +   M R+SR  S YL N+G +IGI DVTP
Sbjct: 705 AKKSSECMGRISRFVSRYLANKGMTIGIDDVTP 737



 Score =  192 bits (488), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 135/400 (33%), Positives = 198/400 (49%), Gaps = 94/400 (23%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKT----------------------- 1140
            +A   KY++A  EP  AVGA+AAQSIGEPGTQMTLKT                       
Sbjct: 1483 KASWSKYMKAITEPGEAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIIN 1542

Query: 1141 -------------------FHFA------------GEVCEYIEEVFVPDDSFILIKLDMD 1169
                               F++A             EV   IEE++ P+  FI I L+ +
Sbjct: 1543 AATKILTPIIEAKLENDSDFNYAQIVKGSIVKTLLNEVVSDIEELYSPNGVFININLNEE 1602

Query: 1170 RIRLLHLEVDIDSIRYCIERTRGIS----------------------GHLTVSGHSFLIL 1207
             I+  +L+++  ++R  I     IS                      G ++  G S   +
Sbjct: 1603 TIKGHYLDINAYTVRDSIVSHGPISKIKLKLEDIQVLDLWKLSILIGGGISQIGSSSNNI 1662

Query: 1208 KPKDSSKSFNSKM-------YQ---MKQLLPSVVIKGVQGINRAVIHEEDVEGVTK---- 1253
                +  + N+ +       +Q   +K+ L +VV+ G+ GI R+VI ++D E        
Sbjct: 1663 NGTGNVNTLNTGIGNTMNVYFQTQLLKKGLQNVVVSGIPGIKRSVIRQDDKEDPITGEKR 1722

Query: 1254 --YKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM 1311
              Y L VEG  L  +M   G+ G    SN+  EV + LGIEAAR  I+ E++  M+ + M
Sbjct: 1723 KCYSLAVEGYGLLKLMGINGIIGTTTVSNHVMEVREVLGIEAARKVIIQEVQKCMDAYSM 1782

Query: 1312 SIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCI 1371
             ID RH  L+AD+MT +G+VLGI+R G+ KM+ S L LASFE T++HLF+AAF  + D +
Sbjct: 1783 DIDLRHIQLLADIMTFRGDVLGISRFGIQKMRTSTLMLASFEETNEHLFEAAFQNRVDPV 1842

Query: 1372 SGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDN 1411
             GVSEC+IMG P+ +GTG   +L   P +  + ++ LF N
Sbjct: 1843 FGVSECVIMGKPIKIGTGSFDILYNSPSN--IQKSKLFLN 1880



 Score =  146 bits (369), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 98/272 (36%), Positives = 146/272 (53%), Gaps = 38/272 (13%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA+  I TPII A L+ D+D +YA+IVKG + +T L EV   IEE++ P+ 
Sbjct: 1533 GVPRIKEIINAATKILTPIIEAKLENDSDFNYAQIVKGSIVKTLLNEVVSDIEELYSPNG 1592

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS----------------------GHL 861
             FI I L+ + I+  +L+++  ++R  I     IS                      G +
Sbjct: 1593 VFININLNEETIKGHYLDINAYTVRDSIVSHGPISKIKLKLEDIQVLDLWKLSILIGGGI 1652

Query: 862  TVSGHSFLILKPKDSSKSFNSKM-------YQ---MKQLLPSVVIKGVQGINRAVIHEED 911
            +  G S   +    +  + N+ +       +Q   +K+ L +VV+ G+ GI R+VI ++D
Sbjct: 1653 SQIGSSSNNINGTGNVNTLNTGIGNTMNVYFQTQLLKKGLQNVVVSGIPGIKRSVIRQDD 1712

Query: 912  VEGVTK------YKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTE 965
             E          Y L VEG  L  +M   G+ G    SN+  EV + LGIEAAR  I+ E
Sbjct: 1713 KEDPITGEKRKCYSLAVEGYGLLKLMGINGIIGTTTVSNHVMEVREVLGIEAARKVIIQE 1772

Query: 966  IKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            ++  M+ + M ID RH  L+AD+MT +G+VLG
Sbjct: 1773 VQKCMDAYSMDIDLRHIQLLADIMTFRGDVLG 1804



 Score =  137 bits (344), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 86/262 (32%), Positives = 135/262 (51%), Gaps = 51/262 (19%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           +E +   +D + + +H++++ + +Y +     P+  G+LD R+G ++ +A C++CG  L 
Sbjct: 76  VEFSAMGKDEIARSAHMEVLHREIY-RPMTNIPLQGGVLDSRLGAHRADAQCSSCGGTLK 134

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLL-GEEKAAGFRAKLRNPAL 201
            C GH+GYIDL  PVFH+GYF+ +  +L  ICK  +C   LL GEEK    R  L     
Sbjct: 135 TCGGHWGYIDLQQPVFHVGYFKHLYGVLCCICK--SCGAFLLKGEEK----RQHLARLKQ 188

Query: 202 SYLVRKSLK---KKILETTKKVSVCPHCGEINGVVKKC------GLLKISHEKYKNRTKK 252
           SY +  S +   +K++E  KKV  CP C    G +++         +K++H      T K
Sbjct: 189 SYSIAHSYRLQFRKLVERCKKVKTCPRCMSQQGQLRRTIRPTLDQFMKLTH------TIK 242

Query: 253 KDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL 312
            D        EY                  ++ L P+ V  L E +P +D+ +L    E 
Sbjct: 243 VDG------KEY------------------VEDLTPIFVQTLLERVPYQDLDIL----ET 274

Query: 313 SKPSDLILTRLLVPPNCIRPSV 334
            KP +L+++RL VPPNCIRPSV
Sbjct: 275 FKPGNLLISRLPVPPNCIRPSV 296



 Score =  110 bits (276), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 49/59 (83%), Positives = 54/59 (91%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
           +GFV NSFFSGL P EFFFHTM GREGLVDTAVKTAETGYMQRRLVK+LEDLC++YD +
Sbjct: 863 RGFVGNSFFSGLQPDEFFFHTMSGREGLVDTAVKTAETGYMQRRLVKALEDLCIKYDQT 921



 Score = 54.3 bits (129), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 26/42 (61%), Positives = 31/42 (73%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 63
           LM   +NLVTPRNGE LIAATQDF+ G Y+LT ++ F  R Q
Sbjct: 553 LMGLMNNLVTPRNGEPLIAATQDFLLGMYVLTGRDIFLTRDQ 594



 Score = 46.6 bits (109), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 22/52 (42%), Positives = 33/52 (63%), Gaps = 2/52 (3%)

Query: 671  FDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDN 722
            F+AAF  + D + GVSEC+IMG P+ +GTG   +L   P +  + ++ LF N
Sbjct: 1831 FEAAFQNRVDPVFGVSECVIMGKPIKIGTGSFDILYNSPSN--IQKSKLFLN 1880


>gi|302840215|ref|XP_002951663.1| hypothetical protein VOLCADRAFT_81566 [Volvox carteri f.
           nagariensis]
 gi|300262911|gb|EFJ47114.1| hypothetical protein VOLCADRAFT_81566 [Volvox carteri f.
           nagariensis]
          Length = 1365

 Score =  233 bits (594), Expect = 6e-58,   Method: Compositional matrix adjust.
 Identities = 123/271 (45%), Positives = 167/271 (61%), Gaps = 26/271 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH++SIMA RAKV   RT RFNEC C+P+NADFDGDEMN+HLPQTEEA
Sbjct: 396 DGDVVLFNRQPSLHRISIMAFRAKVRTWRTLRFNECACSPFNADFDGDEMNLHLPQTEEA 455

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA                LM + +NL TP+NG+++IAATQDF+T  +LLT K+ F+ R
Sbjct: 456 RAEAFN--------------LMGSVNNLATPKNGDIMIAATQDFLTCAFLLTSKDRFYTR 501

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           ++   + +T+      I                 ++   +WTGKQ+FS +++P     V 
Sbjct: 502 SEFCGLLATMADGLEHI----------DLPTPALLKPLELWTGKQLFSCLVRPAAAVRVF 551

Query: 521 ANLKTKGRAYT-ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            NL+   + Y+   E  C  D +V  RNSEL++G + K  LG+  K+ +F  L  D+   
Sbjct: 552 VNLEMAEKIYSKKGEHMCPNDGWVCFRNSELISGRLGKVVLGA-SKSGLFGTLNCDYSPY 610

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
            A +AM RL++M + ++ NRGFSIGI DVTP
Sbjct: 611 AAASAMSRLAKMAARHMGNRGFSIGIDDVTP 641



 Score =  207 bits (527), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 114/245 (46%), Positives = 163/245 (66%), Gaps = 11/245 (4%)

Query: 1159 DSFILIKLDMDRIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSGHSFLILKPKDSSKS 1215
            ++ I I+LDM  I  L L++D  +++Y I    + +    H+       +++ P+D+S+ 
Sbjct: 1090 EAVISIRLDMASIDALQLDIDGHTVKYSILAHPKLKLKEQHVRAVAQDKVLVYPQDASR- 1148

Query: 1216 FNSKMYQMKQLL---PSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGV 1272
                ++ ++ LL   P V++ G+  + RAVI ++  +   KY LLVEG N++ VM T GV
Sbjct: 1149 -QGLLFCLEGLLGKLPGVIVMGIPTVERAVITKDKGD---KYSLLVEGTNVQAVMGTLGV 1204

Query: 1273 KGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL 1332
             G + ++N+  E+ K +GIEAARS IM+EIK  M +HGMSID RH ML+AD M+ KGEVL
Sbjct: 1205 LGTQTTTNHVAEIEKFMGIEAARSAIMSEIKYTMGSHGMSIDDRHIMLLADCMSYKGEVL 1264

Query: 1333 GITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIK 1392
            GITR G+AKMK+SVL+ ASFE T+DHLFDAA +G+ D + GVSE IIMG+PM  GTGL K
Sbjct: 1265 GITRFGIAKMKDSVLHTASFEKTADHLFDAAIHGRMDDVVGVSESIIMGIPMPTGTGLFK 1324

Query: 1393 LLQAV 1397
            +   V
Sbjct: 1325 IRHNV 1329



 Score =  196 bits (499), Expect = 7e-47,   Method: Compositional matrix adjust.
 Identities = 110/234 (47%), Positives = 142/234 (60%), Gaps = 19/234 (8%)

Query: 111 PQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINIL 170
           P+R P P+G+LDRR+G + K   C TCGQ L+DC GHFGYI L LPVFHIGYF+  I IL
Sbjct: 2   PERVPHPNGVLDRRLGISNKNYVCETCGQRLADCAGHFGYIRLELPVFHIGYFKNTIQIL 61

Query: 171 QSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEIN 230
           Q ICK  TC+RVLL EE+   +  + RNP +  + R  + +K+ +  K+   CPHCGE N
Sbjct: 62  QCICK--TCSRVLLPEEERKIWLKRFRNPRVERVQRVFMFRKLNDRCKRQKNCPHCGEYN 119

Query: 231 GVVKKC-GLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPL 289
             VKK  G+LKI HE+Y       DAI      +YN+ +K  P +  H+   +   L+PL
Sbjct: 120 ATVKKATGVLKIIHERYAKNESLADAI------KYNDQLK--PHL--HR---MADDLHPL 166

Query: 290 EVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
            V  LFE IP ED+ LL +     +P DL+ T L VPP  IRPSV  D  S+ D
Sbjct: 167 RVRALFENIPDEDLDLLDIQG---RPEDLVTTHLAVPPVAIRPSVEMDGSSNED 217



 Score =  182 bits (462), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 109/264 (41%), Positives = 158/264 (59%), Gaps = 35/264 (13%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPD- 822
            GVPRIKEIINA++NISTPI+   L  D D+  AR+VKGRLE+TTLG+V  +I+ V  P  
Sbjct: 1007 GVPRIKEIINAAKNISTPIMKVALAVDGDVKAARLVKGRLEKTTLGQVARHIKIVLKPGR 1066

Query: 823  -----------------------DSFILIKLDMDRIRLLHLEVDIDSIRYCI---ERTRG 856
                                   ++ I I+LDM  I  L L++D  +++Y I    + + 
Sbjct: 1067 GGGDAMTMPGSGGAYGGGPRLHGEAVISIRLDMASIDALQLDIDGHTVKYSILAHPKLKL 1126

Query: 857  ISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLL---PSVVIKGVQGINRAVIHEEDVE 913
               H+       +++ P+D+S+     ++ ++ LL   P V++ G+  + RAVI ++  +
Sbjct: 1127 KEQHVRAVAQDKVLVYPQDASR--QGLLFCLEGLLGKLPGVIVMGIPTVERAVITKDKGD 1184

Query: 914  GVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENH 973
               KY LLVEG N++ VM T GV G + ++N+  E+ K +GIEAARS IM+EIK  M +H
Sbjct: 1185 ---KYSLLVEGTNVQAVMGTLGVLGTQTTTNHVAEIEKFMGIEAARSAIMSEIKYTMGSH 1241

Query: 974  GMSIDFRHPMLVADLMTSKGEVLG 997
            GMSID RH ML+AD M+ KGEVLG
Sbjct: 1242 GMSIDDRHIMLLADCMSYKGEVLG 1265



 Score =  107 bits (267), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 53/80 (66%), Positives = 61/80 (76%), Gaps = 1/80 (1%)

Query: 606 GDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           GD TP G+GFV NSF+SGL+ TEF+FHTMGGREGLVDTAVKTAETGYM RRL+K+LEDL 
Sbjct: 760 GDKTPAGKGFVANSFYSGLSATEFWFHTMGGREGLVDTAVKTAETGYMSRRLMKALEDLY 819

Query: 665 VQYDMSFDAAFYGQTDCISG 684
             YD +   A  G    + G
Sbjct: 820 AHYDSTVRNASGGIVQLLYG 839



 Score = 65.1 bits (157), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 28/40 (70%), Positives = 32/40 (80%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            C  KY   +I+P + VGA+ AQSIGEPGTQMTLKTFHFAG
Sbjct: 959  CLTKYATKRIDPGSTVGAVGAQSIGEPGTQMTLKTFHFAG 998



 Score = 56.6 bits (135), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 24/53 (45%), Positives = 39/53 (73%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           LM + +NL TP+NG+++IAATQDF+T  +LLT K+ F+ R++   + +T+  G
Sbjct: 462 LMGSVNNLATPKNGDIMIAATQDFLTCAFLLTSKDRFYTRSEFCGLLATMADG 514



 Score = 48.9 bits (115), Expect = 0.022,   Method: Compositional matrix adjust.
 Identities = 23/41 (56%), Positives = 28/41 (68%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 708
            D  FDAA +G+ D + GVSE IIMG+PM  GTGL K+   V
Sbjct: 1289 DHLFDAAIHGRMDDVVGVSESIIMGIPMPTGTGLFKIRHNV 1329


>gi|146098608|ref|XP_001468425.1| putative DNA-directed RNA polymerase III largest subunit
           [Leishmania infantum JPCM5]
 gi|134072793|emb|CAM71509.1| putative DNA-directed RNA polymerase III largest subunit
           [Leishmania infantum JPCM5]
          Length = 1590

 Score =  233 bits (593), Expect = 7e-58,   Method: Compositional matrix adjust.
 Identities = 121/271 (44%), Positives = 166/271 (61%), Gaps = 25/271 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + D +LFNRQPSLH++S+MAHRA+VLP RTFRFNEC C PYNADFDGDEMN+H+ QTEEA
Sbjct: 455 NGDYILFNRQPSLHRISLMAHRARVLPFRTFRFNECCCAPYNADFDGDEMNIHVVQTEEA 514

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              AK LM    N++T +NGE +IA TQDF+T  YL+T ++A F+R
Sbjct: 515 RAE--------------AKELMLTSHNIITAKNGEPIIACTQDFLTAAYLVTARDALFDR 560

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A   ++ S  + + +     I         P + ++ A +WTGKQ+F LIL+P  +  + 
Sbjct: 561 ASFTQMVSHWLGNETQYTLPI---------PAI-LKPAELWTGKQLFELILRPTPETQLL 610

Query: 521 ANLKTKGRAYT-ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            NL+ K R Y+ A       + YV   +S  L+G +DK  LG G K  +F  L    G +
Sbjct: 611 LNLEAKARFYSGAGRHDDPAEGYVAFLDSVFLSGRLDKKLLGGGAKDGLFARLYALGGGE 670

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
              T M R+++ T+ YL N GFS+G+GDV+P
Sbjct: 671 QTATCMSRIAQFTARYLQNYGFSLGLGDVSP 701



 Score =  159 bits (402), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 90/237 (37%), Positives = 135/237 (56%), Gaps = 11/237 (4%)

Query: 119 GLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPT 178
           G+ D R+G + + + C TCGQ   +C GH G+IDL +PVFH+GYF  VI + ++ICK   
Sbjct: 54  GVNDGRLGPSDRLSVCNTCGQRSIECTGHAGHIDLEVPVFHLGYFSAVIRVCRTICKR-- 111

Query: 179 CARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGL 238
           C+ VLL  E+   +  +LR+       R ++ K I E   K  VC  CG +NG V++   
Sbjct: 112 CSNVLLTREEMEYYLHRLRSTTHEPQQRAAIIKGIQEDAYKTRVCLMCGGLNGTVRRVRP 171

Query: 239 LKISHEKYKNRTKKKDAIVEDLLAEYNE----AVKFNPEIEAHKKFGLIQTLNPLEVLQL 294
           ++I HEKY    ++ +   ED  A + E    A   N E+ AHK+F + + L+P  V +L
Sbjct: 172 MRIVHEKYLVDLRRGEQANEDPTAFFQEELRSAAMHNSEVGAHKEF-VHEFLHPQRVKEL 230

Query: 295 FEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRP---SVISDLKSDNDVVLFN 348
           FEAIP E +PLL +    S P  L+++ LLVPP C+RP   S  + ++ D+    +N
Sbjct: 231 FEAIPREQVPLLGLQPGTS-PCSLLISTLLVPPVCVRPRGMSTTNHIREDDLTTQYN 286



 Score =  149 bits (376), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 101/297 (34%), Positives = 160/297 (53%), Gaps = 22/297 (7%)

Query: 1108 EKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEVCEYIEEVFVPDDSFILIKLD 1167
            +++    + PA+     AA+++     ++ LK      E+   + EV  P   +I I L+
Sbjct: 1207 DEFTSIDLAPASRTQYQAARAVKGLMERVLLK------EIAREMVEVVTPRAYYIHIFLN 1260

Query: 1168 MDRIRLLHLEVDIDSI--RYCIERTRGISG--HLT------VSGHSFLILKPKDSSKSFN 1217
            M+ I  L L +D   +  R      R +S   HL+      VS  S ++   +      +
Sbjct: 1261 MELIERLLLPIDAAVVCQRLYAAAARPMSPLRHLSEACVDVVSRDSLVVKSYEKDPARVH 1320

Query: 1218 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 1277
              +  +  LLP +V+ GV G+NR +I +         KLL EG  L  VM+   V GV+ 
Sbjct: 1321 FNVQHLLTLLPDLVVGGVPGVNRVMIADRS------EKLLAEGAELLSVMSLPYVDGVRT 1374

Query: 1278 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRH 1337
            + N+   + + LGIEAAR TI+ EI  +++ + ++ID RH  L+AD+MTS+G VLGITR+
Sbjct: 1375 TCNHVAVIERALGIEAARETIVKEITSILQAYSLNIDIRHIYLLADVMTSRGVVLGITRY 1434

Query: 1338 GLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            G+ KM  +VL +ASFE T++HL++AA   + D    VSE II+G P+ +GT    +L
Sbjct: 1435 GIQKMNNNVLTMASFERTTEHLYNAAMTEREDVNLSVSESIIIGKPIPLGTSSFNIL 1491



 Score =  132 bits (332), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 93/257 (36%), Positives = 139/257 (54%), Gaps = 29/257 (11%)

Query: 764  GVPRIKEIINASRNISTPIITAYL---DKDTDLDYA----------RIVKGRLERTTLGE 810
            GVPR+ EIINA+++I+TP+ITA +   D+ T +D A          R VKG +ER  L E
Sbjct: 1180 GVPRLVEIINANKSIATPVITAPIVLEDEFTSIDLAPASRTQYQAARAVKGLMERVLLKE 1239

Query: 811  VCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSI--RYCIERTRGISG--HLT---- 862
            +   + EV  P   +I I L+M+ I  L L +D   +  R      R +S   HL+    
Sbjct: 1240 IAREMVEVVTPRAYYIHIFLNMELIERLLLPIDAAVVCQRLYAAAARPMSPLRHLSEACV 1299

Query: 863  --VSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKL 920
              VS  S ++   +      +  +  +  LLP +V+ GV G+NR +I +         KL
Sbjct: 1300 DVVSRDSLVVKSYEKDPARVHFNVQHLLTLLPDLVVGGVPGVNRVMIADRS------EKL 1353

Query: 921  LVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFR 980
            L EG  L  VM+   V GV+ + N+   + + LGIEAAR TI+ EI  +++ + ++ID R
Sbjct: 1354 LAEGAELLSVMSLPYVDGVRTTCNHVAVIERALGIEAARETIVKEITSILQAYSLNIDIR 1413

Query: 981  HPMLVADLMTSKGEVLG 997
            H  L+AD+MTS+G VLG
Sbjct: 1414 HIYLLADVMTSRGVVLG 1430



 Score = 95.1 bits (235), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 42/59 (71%), Positives = 51/59 (86%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
           +GFV +SF+SGL+PTEFFFH M GREG+VDTAVKTAETGY+ RRL K++E+L V YD S
Sbjct: 828 RGFVASSFYSGLSPTEFFFHGMAGREGIVDTAVKTAETGYIYRRLSKAMENLSVGYDAS 886



 Score = 58.5 bits (140), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 27/42 (64%), Positives = 30/42 (71%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            EA   K  R   EP T  GA+AAQS+GEP TQMTL+TFHFAG
Sbjct: 1130 EASARKVHRKLCEPGTPCGAIAAQSVGEPSTQMTLRTFHFAG 1171



 Score = 52.0 bits (123), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 33/48 (68%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIAS 69
           LM    N++T +NGE +IA TQDF+T  YL+T ++A F+RA   ++ S
Sbjct: 521 LMLTSHNIITAKNGEPIIACTQDFLTAAYLVTARDALFDRASFTQMVS 568


>gi|67612875|ref|XP_667260.1| DNA-directed RNA polymerase II/III subunit [Cryptosporidium hominis
           TU502]
 gi|54658380|gb|EAL37032.1| DNA-directed RNA polymerase II/III subunit [Cryptosporidium
           hominis]
          Length = 1869

 Score =  233 bits (593), Expect = 7e-58,   Method: Compositional matrix adjust.
 Identities = 122/273 (44%), Positives = 165/273 (60%), Gaps = 29/273 (10%)

Query: 343 DVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARA 402
           D+VLFNRQPSLH+LSIM+H+  V+P RTFRFNEC C PYNADFDGDEMN+HLPQ E AR+
Sbjct: 453 DIVLFNRQPSLHRLSIMSHKVVVMPWRTFRFNECACAPYNADFDGDEMNLHLPQNELARS 512

Query: 403 EALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 462
           E              +K LM   +NLVTPRNGE LIAATQDF+ G Y+LT ++ F  R Q
Sbjct: 513 E--------------SKHLMGLMNNLVTPRNGEPLIAATQDFLLGMYVLTGRDIFLTRDQ 558

Query: 463 TMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKP--NRDCPVN 520
             +            C            P   ++   +WTGKQ+F++IL+P  N +  ++
Sbjct: 559 FSQYC----------CHFSNGQIPMELPPPTILKPVELWTGKQVFNMILRPNSNENERID 608

Query: 521 ANLKTKGRAYTAN---EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFG 577
            + + K R Y +    ++ C  + YV++R+SELLAG++ K  LG G K  +F+ +L +  
Sbjct: 609 VSFELKERDYDSKSDLKDLCPNEGYVVVRHSELLAGAIGKKVLGGGSKEGLFFYILLENN 668

Query: 578 EDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
              +   M R+SR  S YL N+G +IGI DVTP
Sbjct: 669 AKKSSECMGRISRFVSRYLANKGMTIGIDDVTP 701



 Score =  193 bits (490), Expect = 6e-46,   Method: Compositional matrix adjust.
 Identities = 136/400 (34%), Positives = 198/400 (49%), Gaps = 94/400 (23%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKT----------------------- 1140
            +A   KY++A  EP  AVGA+AAQSIGEPGTQMTLKT                       
Sbjct: 1445 KASWSKYMKAITEPGEAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIIN 1504

Query: 1141 -------------------FHFA------------GEVCEYIEEVFVPDDSFILIKLDMD 1169
                               F++A             EV   IEE++ P+  FI I L+ +
Sbjct: 1505 AATKILTPIIEAKLENDSDFNYAQIVKGSIVKTLLNEVVSDIEELYSPNGVFININLNEE 1564

Query: 1170 RIRLLHLEVDIDSIRYCIERTRGIS----------------------GHLTVSGHSFLIL 1207
             I+  +L+++  ++R  I     IS                      G ++  G S   +
Sbjct: 1565 TIKGHYLDINAYTVRDSIVSHGPISKIKLKLEDIQVLDLWKLSILIGGGISQIGSSSNNI 1624

Query: 1208 KPKDSSKSFNSKM-------YQ---MKQLLPSVVIKGVQGINRAVIHEEDVEGVTK---- 1253
                +  + N+ M       +Q   +K+ L +VV+ G+ GI R+VI ++D E        
Sbjct: 1625 NGTGTVNASNTGMGNTMNVYFQTQLLKKGLQNVVVSGIPGIKRSVIRQDDKEDPITGEKR 1684

Query: 1254 --YKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM 1311
              Y L VEG  L  +M   G+ G    SN+  EV + LGIEAAR  I+ E++  M+ + M
Sbjct: 1685 KCYSLAVEGYGLLKLMGINGIIGTTTVSNHVMEVREVLGIEAARKVIIQEVQKCMDAYSM 1744

Query: 1312 SIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCI 1371
             ID RH  L+AD+MT +G+VLGI+R G+ KM+ S L LASFE T++HLF+AAF  + D +
Sbjct: 1745 DIDLRHIQLLADIMTFRGDVLGISRFGIQKMRTSTLMLASFEETNEHLFEAAFQNRVDPV 1804

Query: 1372 SGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDN 1411
             GVSEC+IMG P+ +GTG   +L   P +  + ++ LF N
Sbjct: 1805 FGVSECVIMGKPIKIGTGSFDILYNSPSN--IQKSKLFLN 1842



 Score =  147 bits (372), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 99/272 (36%), Positives = 146/272 (53%), Gaps = 38/272 (13%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA+  I TPII A L+ D+D +YA+IVKG + +T L EV   IEE++ P+ 
Sbjct: 1495 GVPRIKEIINAATKILTPIIEAKLENDSDFNYAQIVKGSIVKTLLNEVVSDIEELYSPNG 1554

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS----------------------GHL 861
             FI I L+ + I+  +L+++  ++R  I     IS                      G +
Sbjct: 1555 VFININLNEETIKGHYLDINAYTVRDSIVSHGPISKIKLKLEDIQVLDLWKLSILIGGGI 1614

Query: 862  TVSGHSFLILKPKDSSKSFNSKM-------YQ---MKQLLPSVVIKGVQGINRAVIHEED 911
            +  G S   +    +  + N+ M       +Q   +K+ L +VV+ G+ GI R+VI ++D
Sbjct: 1615 SQIGSSSNNINGTGTVNASNTGMGNTMNVYFQTQLLKKGLQNVVVSGIPGIKRSVIRQDD 1674

Query: 912  VEGVTK------YKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTE 965
             E          Y L VEG  L  +M   G+ G    SN+  EV + LGIEAAR  I+ E
Sbjct: 1675 KEDPITGEKRKCYSLAVEGYGLLKLMGINGIIGTTTVSNHVMEVREVLGIEAARKVIIQE 1734

Query: 966  IKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            ++  M+ + M ID RH  L+AD+MT +G+VLG
Sbjct: 1735 VQKCMDAYSMDIDLRHIQLLADIMTFRGDVLG 1766



 Score =  137 bits (345), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 84/261 (32%), Positives = 135/261 (51%), Gaps = 49/261 (18%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           +E +   +D + + +H++++ + +Y +     P+  G+LD R+G ++ +A C++CG  L 
Sbjct: 40  VEFSAMGKDEIARSAHMEVLHREIY-RPMTNIPLQGGVLDSRLGAHRADAQCSSCGGTLK 98

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALS 202
            C GH+GYIDL  PVFH+GYF+ +  +L  ICK  +C   LL  E+     AKL+    S
Sbjct: 99  TCGGHWGYIDLQQPVFHVGYFKHLYGVLCCICK--SCGAFLLKGEEKRQHLAKLKQ---S 153

Query: 203 YLVRKSLK---KKILETTKKVSVCPHCGEINGVVKKC------GLLKISHEKYKNRTKKK 253
           Y +  S +   +K++E  KKV  CP C    G +++         +K++H      T K 
Sbjct: 154 YSIAHSYRLQFRKLVERCKKVKTCPRCMSQQGQLRRTIRPTLDQFMKLTH------TIKV 207

Query: 254 DAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELS 313
           D        EY                  ++ L P+ V  L E +P +D+ +L    E  
Sbjct: 208 DG------KEY------------------VEDLTPIFVQTLLERVPYQDLDIL----ETF 239

Query: 314 KPSDLILTRLLVPPNCIRPSV 334
           KP +L+++RL VPPNCIRPSV
Sbjct: 240 KPGNLLISRLPVPPNCIRPSV 260



 Score =  110 bits (276), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 49/59 (83%), Positives = 54/59 (91%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
           +GFV NSFFSGL P EFFFHTM GREGLVDTAVKTAETGYMQRRLVK+LEDLC++YD +
Sbjct: 827 RGFVGNSFFSGLQPDEFFFHTMSGREGLVDTAVKTAETGYMQRRLVKALEDLCIKYDQT 885



 Score = 54.3 bits (129), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 26/42 (61%), Positives = 31/42 (73%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 63
           LM   +NLVTPRNGE LIAATQDF+ G Y+LT ++ F  R Q
Sbjct: 517 LMGLMNNLVTPRNGEPLIAATQDFLLGMYVLTGRDIFLTRDQ 558



 Score = 46.6 bits (109), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 22/52 (42%), Positives = 33/52 (63%), Gaps = 2/52 (3%)

Query: 671  FDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDN 722
            F+AAF  + D + GVSEC+IMG P+ +GTG   +L   P +  + ++ LF N
Sbjct: 1793 FEAAFQNRVDPVFGVSECVIMGKPIKIGTGSFDILYNSPSN--IQKSKLFLN 1842


>gi|398022082|ref|XP_003864203.1| DNA-directed RNA polymerase III largest subunit , putative
           [Leishmania donovani]
 gi|322502438|emb|CBZ37521.1| DNA-directed RNA polymerase III largest subunit , putative
           [Leishmania donovani]
          Length = 1590

 Score =  233 bits (593), Expect = 8e-58,   Method: Compositional matrix adjust.
 Identities = 121/271 (44%), Positives = 166/271 (61%), Gaps = 25/271 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + D +LFNRQPSLH++S+MAHRA+VLP RTFRFNEC C PYNADFDGDEMN+H+ QTEEA
Sbjct: 455 NGDYILFNRQPSLHRISLMAHRARVLPFRTFRFNECCCAPYNADFDGDEMNIHVVQTEEA 514

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              AK LM    N++T +NGE +IA TQDF+T  YL+T ++A F+R
Sbjct: 515 RAE--------------AKELMLTSHNIITAKNGEPIIACTQDFLTAAYLVTARDALFDR 560

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A   ++ S  + + +     I         P + ++ A +WTGKQ+F LIL+P  +  + 
Sbjct: 561 ASFTQMVSHWLGNETQYTLPI---------PAI-LKPAELWTGKQLFELILRPTPETQLL 610

Query: 521 ANLKTKGRAYT-ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            NL+ K R Y+ A       + YV   +S  L+G +DK  LG G K  +F  L    G +
Sbjct: 611 LNLEAKARFYSGAGRHDDPAEGYVAFLDSVFLSGRLDKKLLGGGAKDGLFARLYALGGGE 670

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
              T M R+++ T+ YL N GFS+G+GDV+P
Sbjct: 671 QTATCMSRIAQFTARYLQNYGFSLGLGDVSP 701



 Score =  159 bits (401), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 90/237 (37%), Positives = 135/237 (56%), Gaps = 11/237 (4%)

Query: 119 GLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPT 178
           G+ D R+G + + + C TCGQ   +C GH G+IDL +PVFH+GYF  VI + ++ICK   
Sbjct: 54  GVNDGRLGPSDRLSVCNTCGQRSIECTGHAGHIDLEVPVFHLGYFSAVIRVCRTICKR-- 111

Query: 179 CARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGL 238
           C+ VLL  E+   +  +LR+       R ++ K I E   K  VC  CG +NG V++   
Sbjct: 112 CSNVLLTREEMEYYLHRLRSTTHEPQQRAAIIKGIQEDAYKTRVCLMCGGLNGTVRRVRP 171

Query: 239 LKISHEKYKNRTKKKDAIVEDLLAEYNE----AVKFNPEIEAHKKFGLIQTLNPLEVLQL 294
           ++I HEKY    ++ +   ED  A + E    A   N E+ AHK+F + + L+P  V +L
Sbjct: 172 MRIVHEKYLVDLRRGEQANEDPTAFFQEELRSAAMHNSEVGAHKEF-VHEFLHPQRVKEL 230

Query: 295 FEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRP---SVISDLKSDNDVVLFN 348
           FEAIP E +PLL +    S P  L+++ LLVPP C+RP   S  + ++ D+    +N
Sbjct: 231 FEAIPREQVPLLGLQPGTS-PCSLLISTLLVPPVCVRPRGMSTTNHIREDDLTTQYN 286



 Score =  149 bits (376), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 101/297 (34%), Positives = 160/297 (53%), Gaps = 22/297 (7%)

Query: 1108 EKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEVCEYIEEVFVPDDSFILIKLD 1167
            +++    + PA+     AA+++     ++ LK      E+   + EV  P   +I I L+
Sbjct: 1207 DEFTSIDLAPASRTQYQAARAVKGLMERVLLK------EIAREMVEVVTPRAYYIHIFLN 1260

Query: 1168 MDRIRLLHLEVDIDSI--RYCIERTRGISG--HLT------VSGHSFLILKPKDSSKSFN 1217
            M+ I  L L +D   +  R      R +S   HL+      VS  S ++   +      +
Sbjct: 1261 MELIERLLLPIDAAVVCQRLYAAAARPMSPLRHLSEACVDVVSRDSLVVKSYEKDPARVH 1320

Query: 1218 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 1277
              +  +  LLP +V+ GV G+NR +I +         KLL EG  L  VM+   V GV+ 
Sbjct: 1321 FNVQHLLTLLPDLVVGGVPGVNRVMIADRS------EKLLAEGAELLSVMSLPYVDGVRT 1374

Query: 1278 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRH 1337
            + N+   + + LGIEAAR TI+ EI  +++ + ++ID RH  L+AD+MTS+G VLGITR+
Sbjct: 1375 TCNHVAVIERALGIEAARETIVREITSILQAYSLNIDIRHIYLLADVMTSRGVVLGITRY 1434

Query: 1338 GLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            G+ KM  +VL +ASFE T++HL++AA   + D    VSE II+G P+ +GT    +L
Sbjct: 1435 GIQKMNNNVLTMASFERTTEHLYNAAMTEREDVNLSVSESIIIGKPIPLGTSSFNIL 1491



 Score =  132 bits (332), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 93/257 (36%), Positives = 139/257 (54%), Gaps = 29/257 (11%)

Query: 764  GVPRIKEIINASRNISTPIITAYL---DKDTDLDYA----------RIVKGRLERTTLGE 810
            GVPR+ EIINA+++I+TP+ITA +   D+ T +D A          R VKG +ER  L E
Sbjct: 1180 GVPRLVEIINANKSIATPVITAPIVLEDEFTSIDLAPASRTQYQAARAVKGLMERVLLKE 1239

Query: 811  VCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSI--RYCIERTRGISG--HLT---- 862
            +   + EV  P   +I I L+M+ I  L L +D   +  R      R +S   HL+    
Sbjct: 1240 IAREMVEVVTPRAYYIHIFLNMELIERLLLPIDAAVVCQRLYAAAARPMSPLRHLSEACV 1299

Query: 863  --VSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKL 920
              VS  S ++   +      +  +  +  LLP +V+ GV G+NR +I +         KL
Sbjct: 1300 DVVSRDSLVVKSYEKDPARVHFNVQHLLTLLPDLVVGGVPGVNRVMIADRS------EKL 1353

Query: 921  LVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFR 980
            L EG  L  VM+   V GV+ + N+   + + LGIEAAR TI+ EI  +++ + ++ID R
Sbjct: 1354 LAEGAELLSVMSLPYVDGVRTTCNHVAVIERALGIEAARETIVREITSILQAYSLNIDIR 1413

Query: 981  HPMLVADLMTSKGEVLG 997
            H  L+AD+MTS+G VLG
Sbjct: 1414 HIYLLADVMTSRGVVLG 1430



 Score = 95.1 bits (235), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 42/59 (71%), Positives = 51/59 (86%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
           +GFV +SF+SGL+PTEFFFH M GREG+VDTAVKTAETGY+ RRL K++E+L V YD S
Sbjct: 828 RGFVASSFYSGLSPTEFFFHGMAGREGIVDTAVKTAETGYIYRRLSKAMENLSVGYDAS 886



 Score = 58.5 bits (140), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 27/42 (64%), Positives = 30/42 (71%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            EA   K  R   EP T  GA+AAQS+GEP TQMTL+TFHFAG
Sbjct: 1130 EASARKVHRKLCEPGTPCGAIAAQSVGEPSTQMTLRTFHFAG 1171



 Score = 52.0 bits (123), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 33/48 (68%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIAS 69
           LM    N++T +NGE +IA TQDF+T  YL+T ++A F+RA   ++ S
Sbjct: 521 LMLTSHNIITAKNGEPIIACTQDFLTAAYLVTARDALFDRASFTQMVS 568


>gi|401428277|ref|XP_003878621.1| DNA-directed RNA polymerase III largest subunit ,putative
           [Leishmania mexicana MHOM/GT/2001/U1103]
 gi|322494870|emb|CBZ30173.1| DNA-directed RNA polymerase III largest subunit ,putative
           [Leishmania mexicana MHOM/GT/2001/U1103]
          Length = 1589

 Score =  232 bits (592), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 120/271 (44%), Positives = 165/271 (60%), Gaps = 25/271 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + D +LFNRQPSLH++S+MAHRA+VLP RTFRFNEC C PYNADFDGDEMN+H+ QTEEA
Sbjct: 455 NGDYILFNRQPSLHRISLMAHRARVLPFRTFRFNECCCAPYNADFDGDEMNIHVVQTEEA 514

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              AK LM    N++T +NGE +IA TQDF+T  YL+T ++A F+R
Sbjct: 515 RAE--------------AKELMLTSHNIITAKNGEPIIACTQDFLTAAYLVTARDALFDR 560

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A   ++ S  +   +     I         P + ++ A +W+GKQ+F LIL+P  +  + 
Sbjct: 561 ASFTQMVSHWLGSETQYALPI---------PAI-LKPAELWSGKQLFELILRPTSETQLL 610

Query: 521 ANLKTKGRAYT-ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            NL+ K R Y+ A       + YV   +S  L+G +DK  LG G K  +F  L    G +
Sbjct: 611 LNLEAKARFYSGAGRHDDPAEGYVAFLDSVFLSGRLDKKLLGGGAKDGLFARLYALGGGE 670

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
              T M R+++ T+ YL N GFS+G+GDV+P
Sbjct: 671 QTATCMSRIAQFTARYLQNYGFSLGLGDVSP 701



 Score =  162 bits (409), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 92/237 (38%), Positives = 135/237 (56%), Gaps = 11/237 (4%)

Query: 119 GLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPT 178
           G+ D R+G + + + C TCGQ   +C GH G+IDL  PVFH+GYF  VI + ++ICK   
Sbjct: 54  GVNDGRLGPSDRLSVCNTCGQRSIECTGHAGHIDLEAPVFHLGYFSAVIRVCRTICKR-- 111

Query: 179 CARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGL 238
           C+ VLL  E+   +  +LR+       R ++ K I E   K  VC  CG +NG V++   
Sbjct: 112 CSNVLLTREEMEYYLHRLRSTTHEPQQRAAIIKGIQEDAYKTRVCLMCGGLNGTVRRVRP 171

Query: 239 LKISHEKYKNRTKKKDAIVEDLLAEYNE----AVKFNPEIEAHKKFGLIQTLNPLEVLQL 294
           ++I HEKY    ++ +   ED  A + E    A   N E+ AHK+F + + L+P  V +L
Sbjct: 172 MRIVHEKYLVDLRRGEQANEDPTAFFQEELRSAAMQNSEVGAHKEF-VHEFLHPQRVKEL 230

Query: 295 FEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRP---SVISDLKSDNDVVLFN 348
           FEAIPLE +PLL +    S P  L+++ LLVPP C+RP   S  S ++ D+    +N
Sbjct: 231 FEAIPLEQVPLLGLQPGTS-PCSLLISTLLVPPVCVRPRGMSTTSHIREDDLTTQYN 286



 Score =  146 bits (369), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 94/259 (36%), Positives = 143/259 (55%), Gaps = 16/259 (6%)

Query: 1146 EVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSI--RYCIERTRGISG--HLT--- 1198
            E+   + EV  P   +I I L+M+ I  L L +D   +  R      R +S   HL+   
Sbjct: 1239 EITREMVEVVTPRTYYIHIFLNMELIERLLLPIDATVVCQRLYAAAARPMSPLRHLSEAC 1298

Query: 1199 ---VSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYK 1255
               VS  S ++   +      +  +  +  LLP +V+ GV G+NR +I +         K
Sbjct: 1299 VDVVSRDSLVVKSYEKDPARVHFNVQHLLTLLPDLVVGGVPGVNRVMIADRS------EK 1352

Query: 1256 LLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDF 1315
            LL EG  L  VM+   V GV+ + N+   + + LGIEAAR TI+ E   +++ + ++ID 
Sbjct: 1353 LLAEGAELLSVMSLPYVDGVRTTCNHVAVIERALGIEAARETIVKETTSILQAYSLNIDI 1412

Query: 1316 RHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVS 1375
            RH  L+AD+MTS+G VLGITR+G+ KM  +VL +ASFE T++HL++AA   + D    VS
Sbjct: 1413 RHIYLLADVMTSRGVVLGITRYGIQKMNNNVLTMASFERTTEHLYNAAMTEREDVNLSVS 1472

Query: 1376 ECIIMGLPMNVGTGLIKLL 1394
            E II+G P+ +GT    +L
Sbjct: 1473 ESIIIGKPIPLGTSSFSIL 1491



 Score =  130 bits (328), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 92/257 (35%), Positives = 138/257 (53%), Gaps = 29/257 (11%)

Query: 764  GVPRIKEIINASRNISTPIITAYL---DKDTDLDYA----------RIVKGRLERTTLGE 810
            GVPR+ EIINA+++I+TP+ITA +   D+ T +D A          R VKG +ER  L E
Sbjct: 1180 GVPRLVEIINANKSIATPVITAPIVLEDEFTSIDLASATRTQHQAARAVKGLMERVLLKE 1239

Query: 811  VCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSI--RYCIERTRGISG--HLT---- 862
            +   + EV  P   +I I L+M+ I  L L +D   +  R      R +S   HL+    
Sbjct: 1240 ITREMVEVVTPRTYYIHIFLNMELIERLLLPIDATVVCQRLYAAAARPMSPLRHLSEACV 1299

Query: 863  --VSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKL 920
              VS  S ++   +      +  +  +  LLP +V+ GV G+NR +I +         KL
Sbjct: 1300 DVVSRDSLVVKSYEKDPARVHFNVQHLLTLLPDLVVGGVPGVNRVMIADRS------EKL 1353

Query: 921  LVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFR 980
            L EG  L  VM+   V GV+ + N+   + + LGIEAAR TI+ E   +++ + ++ID R
Sbjct: 1354 LAEGAELLSVMSLPYVDGVRTTCNHVAVIERALGIEAARETIVKETTSILQAYSLNIDIR 1413

Query: 981  HPMLVADLMTSKGEVLG 997
            H  L+AD+MTS+G VLG
Sbjct: 1414 HIYLLADVMTSRGVVLG 1430



 Score = 94.7 bits (234), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 41/59 (69%), Positives = 51/59 (86%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
           +GFV +SF+SGL+PTEFFFH M GREG+VDTAVKTAETGY+ RRL K++E+L + YD S
Sbjct: 828 RGFVASSFYSGLSPTEFFFHGMAGREGIVDTAVKTAETGYIYRRLSKAMENLSIGYDAS 886



 Score = 58.5 bits (140), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 27/42 (64%), Positives = 30/42 (71%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            EA   K  R   EP T  GA+AAQS+GEP TQMTL+TFHFAG
Sbjct: 1130 EASARKVHRKLCEPGTPCGAIAAQSVGEPSTQMTLRTFHFAG 1171



 Score = 52.0 bits (123), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 33/48 (68%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIAS 69
           LM    N++T +NGE +IA TQDF+T  YL+T ++A F+RA   ++ S
Sbjct: 521 LMLTSHNIITAKNGEPIIACTQDFLTAAYLVTARDALFDRASFTQMVS 568


>gi|68070079|ref|XP_676951.1| DNA-directed RNA polymerase 3 largest subunit [Plasmodium berghei
           strain ANKA]
 gi|56496875|emb|CAI00330.1| DNA-directed RNA polymerase 3 largest subunit, putative [Plasmodium
           berghei]
          Length = 1490

 Score =  232 bits (591), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 121/277 (43%), Positives = 170/277 (61%), Gaps = 31/277 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIM H+A+V+ ++TFRFNECVC+PYNADFDGDEMN+H+PQTEE+
Sbjct: 497 DGDIVLFNRQPSLHRMSIMCHKARVMDYKTFRFNECVCSPYNADFDGDEMNLHVPQTEES 556

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL               LM  K NL+TP+NGE++IA TQDF++  Y++T K+ F +R
Sbjct: 557 RAEAL--------------YLMNVKHNLITPKNGEVIIALTQDFLSASYVITNKDTFLDR 602

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPV-VFVRTAVIWTGKQIFSLILKPNRDCPV 519
                + S       DI             PV   ++   +WTGKQ+ S+++KPN+    
Sbjct: 603 DLFCLLCSYFSDAKIDI-----------ELPVPAILKPKELWTGKQLISVLIKPNKSENT 651

Query: 520 NANLKTKGRAYTANE---EFCHR-DSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
             N + K R Y+      ++  R DSYV    SEL+ GS+ K  LG+  K  +FY L+ +
Sbjct: 652 IINFEMKEREYSTKNGDLKYLSRDDSYVCFYKSELICGSLGKKVLGA-SKYGLFYYLIHN 710

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
               +A+  M R S+++S Y  N+G +IGI DVTP +
Sbjct: 711 NSTQIALQIMNRFSKLSSRYFSNKGMTIGIDDVTPSR 747



 Score =  144 bits (363), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 90/254 (35%), Positives = 135/254 (53%), Gaps = 28/254 (11%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G + KED ++  S ++I+++ +Y  +    P P+G+LD R+G ++  + C TC + L +C
Sbjct: 39  GIMGKEDIIRY-SEVKILNREMYKNNSNGVPYPYGVLDLRLGAHKSNSICETCKKKLINC 97

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGF-RAKLRNPALSY 203
            GHFGYI+L  PVFHIGY++ +I+IL  ICK  TC+ +LL  EK   F   K +      
Sbjct: 98  SGHFGYIELNYPVFHIGYYKYIIHILYCICK--TCSHLLLPLEKIEFFSNLKKKKNIDDS 155

Query: 204 LVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAE 263
           L ++   K+IL   KKV+ C +CG   GV+KK                    I++  L +
Sbjct: 156 LFKRQFFKRILSICKKVNKCYNCGSPQGVIKK--------------------IIKPSLDQ 195

Query: 264 YNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRL 323
           + +        E  K+    + LN L VL+LF+ I     P  +    +  P  LI+T L
Sbjct: 196 FMKLKHIVKVKENGKQVIKEEDLNSLYVLKLFKNIN----PFYIKLLNIENPEKLIITTL 251

Query: 324 LVPPNCIRPSVISD 337
           +VPPN IRPSVI D
Sbjct: 252 IVPPNTIRPSVIID 265



 Score =  111 bits (277), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 48/62 (77%), Positives = 55/62 (88%)

Query: 609 TPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +  +GFVQNSF++GL PTEFFFHTM GREGLVDTAVKTAETGYMQRRL+K+LEDL + YD
Sbjct: 868 SESRGFVQNSFYTGLNPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKALEDLSIHYD 927

Query: 669 MS 670
            S
Sbjct: 928 YS 929



 Score = 57.0 bits (136), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 28/35 (80%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHF 1143
            KY +    P  AVG+++AQSIGEPGTQMTLKTFHF
Sbjct: 1456 KYFKYISSPGDAVGSISAQSIGEPGTQMTLKTFHF 1490



 Score = 52.4 bits (124), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 21/40 (52%), Positives = 31/40 (77%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           LM  K NL+TP+NGE++IA TQDF++  Y++T K+ F +R
Sbjct: 563 LMNVKHNLITPKNGEVIIALTQDFLSASYVITNKDTFLDR 602


>gi|82794246|ref|XP_728359.1| RNA polymerase A/beta'/A'' subunit [Plasmodium yoelii yoelii 17XNL]
 gi|23484677|gb|EAA19924.1| RNA polymerase A/beta'/A'' subunit, putative [Plasmodium yoelii
           yoelii]
          Length = 2020

 Score =  232 bits (591), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 121/277 (43%), Positives = 170/277 (61%), Gaps = 31/277 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIM H+A+V+ ++TFRFNECVC+PYNADFDGDEMN+H+PQTEE+
Sbjct: 504 DGDIVLFNRQPSLHRMSIMCHKARVMDYKTFRFNECVCSPYNADFDGDEMNLHVPQTEES 563

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL               LM  K NL+TP+NGE++IA TQDF++  Y++T K+ F +R
Sbjct: 564 RAEAL--------------YLMNVKHNLITPKNGEVIIALTQDFLSASYVITNKDTFLDR 609

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPV-VFVRTAVIWTGKQIFSLILKPNRDCPV 519
                  S       DI             PV   ++   +WTGKQ+ S+++KPN++   
Sbjct: 610 DLFCLXCSYFSDAKIDI-----------ELPVPAILKPKELWTGKQLISVLIKPNKNENT 658

Query: 520 NANLKTKGRAYTANE---EFCHR-DSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
             N + K R Y+      ++  R DSYV    SEL+ GS+ K  LG+  K  +FY L+ +
Sbjct: 659 IINFEMKEREYSTKNGDLKYLSRDDSYVCFYKSELICGSLGKKVLGA-SKYGLFYYLIHN 717

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
               +A+  M R S+++S Y  N+G +IGI DVTP +
Sbjct: 718 NSTQIALQIMNRFSKLSSRYFSNKGMTIGIDDVTPSR 754



 Score =  145 bits (366), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 95/254 (37%), Positives = 141/254 (55%), Gaps = 28/254 (11%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G + KED ++  S ++I+++ +Y  +    P P+G+LD R+G ++  + C TC + L +C
Sbjct: 39  GIMGKEDIIRY-SEVKILNREMYKNNSNGVPYPYGVLDLRLGAHKSNSICETCKKKLINC 97

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGF-RAKLRNPALSY 203
            GHFGYI+L  PVFHIGY++ +I+IL  ICK  TC+ +LL  EK   F   K +      
Sbjct: 98  SGHFGYIELNYPVFHIGYYKYIIHILYCICK--TCSHILLPLEKIEFFSNLKKKKNIDDS 155

Query: 204 LVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAE 263
           L ++   K+IL   KKV+ C +CG   GV+KK  ++K S +++     K   IV+     
Sbjct: 156 LFKRQFFKRILSICKKVNKCYNCGSPQGVIKK--IIKPSLDQF----MKLKHIVK----- 204

Query: 264 YNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRL 323
               VK     E  K+    + LN L VL+LF+ I     P  +    +  P  LI+T L
Sbjct: 205 ----VK-----ENGKQVIKEEDLNSLYVLKLFKNIN----PFYIKLLNIENPEKLIITTL 251

Query: 324 LVPPNCIRPSVISD 337
           +VPPN IRPSVI D
Sbjct: 252 IVPPNTIRPSVIID 265



 Score =  114 bits (286), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 66/173 (38%), Positives = 95/173 (54%), Gaps = 30/173 (17%)

Query: 1252 TKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKT----------------------- 1288
            T+Y +LVEG+ L  ++   GV      SN+   V++                        
Sbjct: 1823 TQYSILVEGNALNYILGLEGVDFKHIISNHVINVFQVCSRKNTKNILIIQFYLHCYTYLF 1882

Query: 1289 -------LGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAK 1341
                   LGIEAAR TI+ EIK  +E + + ID RH ML+AD+M   GE+LGI R G+ K
Sbjct: 1883 FHIFAQVLGIEAARVTIINEIKKCIEAYSIDIDIRHIMLLADIMAFTGEILGINRFGIQK 1942

Query: 1342 MKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
             ++S L LASFE T++HLF ++F+   D I+ +SE II+G  + +GTG  +LL
Sbjct: 1943 ARQSTLMLASFEETNEHLFVSSFFKNNDEINNISESIIVGKNIPIGTGSFELL 1995



 Score =  111 bits (277), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 48/62 (77%), Positives = 55/62 (88%)

Query: 609 TPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +  +GFVQNSF++GL PTEFFFHTM GREGLVDTAVKTAETGYMQRRL+K+LEDL + YD
Sbjct: 875 SESRGFVQNSFYTGLNPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKALEDLSIHYD 934

Query: 669 MS 670
            S
Sbjct: 935 YS 936



 Score = 76.3 bits (186), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 49/166 (29%), Positives = 86/166 (51%), Gaps = 27/166 (16%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINAS  I TPI+   L    + ++A ++K +LE+T++ ++CEYI+E +    
Sbjct: 1512 GVPRIKEIINASSIIQTPILNIPLRIKDNYNFALMMKSKLEKTSIRDICEYIKENYCSKG 1571

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISG----------------HLTVSGHS 867
             +I IK + D I+ L L ++  +IR  I +   IS                 H+++    
Sbjct: 1572 IYISIKFNEDLIQKLFLNINAYTIRDIILKQTHISKIKINKIYIDVINDYKLHISIKNDE 1631

Query: 868  FLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVE 913
            F+             ++  +K+ L  +++ G + I R +I +E++E
Sbjct: 1632 FIFF-----------QIESLKKGLLDLLVYGDKDIKRCIIKKEEIE 1666



 Score = 61.2 bits (147), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 26/37 (70%), Positives = 30/37 (81%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            KY +    P  AVG+++AQSIGEPGTQMTLKTFHFAG
Sbjct: 1467 KYFKYISSPGDAVGSISAQSIGEPGTQMTLKTFHFAG 1503



 Score = 60.1 bits (144), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 38/112 (33%), Positives = 53/112 (47%), Gaps = 30/112 (26%)

Query: 916  TKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKT----------------------- 952
            T+Y +LVEG+ L  ++   GV      SN+   V++                        
Sbjct: 1823 TQYSILVEGNALNYILGLEGVDFKHIISNHVINVFQVCSRKNTKNILIIQFYLHCYTYLF 1882

Query: 953  -------LGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
                   LGIEAAR TI+ EIK  +E + + ID RH ML+AD+M   GE+LG
Sbjct: 1883 FHIFAQVLGIEAARVTIINEIKKCIEAYSIDIDIRHIMLLADIMAFTGEILG 1934



 Score = 52.4 bits (124), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 21/40 (52%), Positives = 31/40 (77%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           LM  K NL+TP+NGE++IA TQDF++  Y++T K+ F +R
Sbjct: 570 LMNVKHNLITPKNGEVIIALTQDFLSASYVITNKDTFLDR 609


>gi|429329501|gb|AFZ81260.1| DNA-directed RNA polymerase III C1 subunit, putative [Babesia equi]
          Length = 1548

 Score =  231 bits (590), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 121/284 (42%), Positives = 167/284 (58%), Gaps = 38/284 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAHR +V+P  TFRFNECVC PYNADFDGDEMN+HLPQT EA
Sbjct: 509 DGDIVIFNRQPSLHRMSIMAHRVRVMPGSTFRFNECVCQPYNADFDGDEMNMHLPQTYEA 568

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE   SL+ LS++            NL TPRNG+ LIAA QDF++  YLLT K+ F  R
Sbjct: 569 RAE---SLYLLSVL-----------QNLTTPRNGDPLIAAVQDFLSASYLLTSKDRFLTR 614

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q  +I       +  +             P   +   ++WTGKQIF+++L+P+R   V 
Sbjct: 615 KQFCQICCYFTNASIQV----------DIPPPAIIYPTMLWTGKQIFNVLLRPSRKSNVI 664

Query: 521 ANLKTKGRAYTANEEF-------------CHRDSYVILRNSELLAGSMDKSTLGSGGKAN 567
            N + + R +   +++             C +D YVI  NSEL+ G++   +LG+  K  
Sbjct: 665 VNFECREREFHNIKDYEHNYGMTNLHQCMCPKDGYVIFYNSELMCGALGVKSLGA-SKGG 723

Query: 568 VFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           +FY LL+     +A   M R+S++ S +L   G +IG+ DV PG
Sbjct: 724 LFYQLLKKNSSKIAAECMLRVSKLASRWLAEFGMTIGLDDVRPG 767



 Score =  176 bits (447), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 118/351 (33%), Positives = 176/351 (50%), Gaps = 65/351 (18%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSI------------------------GEPGTQMTLKT- 1140
            C + Y +   EP  A+GAL AQSI                        G P  Q  +   
Sbjct: 1197 CWKDYQKGVCEPGEAIGALGAQSIGEPATQMTLKTFHFAGVASMNVTLGVPRIQEIINAS 1256

Query: 1141 -----------------FHFA------------GEVCEYIEEVFVPDDSFILIKLDMDRI 1171
                             + +A            G++C  I E+F P+   ++IKL+ + I
Sbjct: 1257 ASIITPIIEVPLVNKHDYDYALSVKARIEKTTLGQICSDIRELFTPNGIRLIIKLNANVI 1316

Query: 1172 RLLHLEVDIDSIRYCIERTRGISG--------HLTVSGHSFLILKPKDSSKSFNSKMYQM 1223
            + L L+VD   +R  I     I          H       +L L P   ++ F  + + +
Sbjct: 1317 QDLFLQVDAYRVRDKILEQGSIKKIKINKQDVHTLDKWQLYLDL-PATETQLF--QQHAL 1373

Query: 1224 KQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTY 1283
               L  +V+ G + I RA+I  E+     +Y++ VEG  L++VM  YGV+     +N+ Y
Sbjct: 1374 INGLLDLVVAGGKRIKRAIIKRENTASGCQYQIAVEGYGLQEVMGAYGVQSNAVKTNHIY 1433

Query: 1284 EVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMK 1343
            EV + LGIEAARSTI++EI+  M+ + + ID R+  L+ D+MTS+GEV+GI RHG+ K +
Sbjct: 1434 EVAQVLGIEAARSTIISEIQKCMDAYSIDIDGRYMKLLGDIMTSRGEVIGINRHGIKKRR 1493

Query: 1344 ESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
             S L LASFE T++HLF+AA + + D + GVSECII+G  M +GTG   LL
Sbjct: 1494 TSALMLASFEETNEHLFEAAVHSRKDPVKGVSECIIVGKQMPLGTGSFDLL 1544



 Score =  160 bits (406), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 97/242 (40%), Positives = 143/242 (59%), Gaps = 11/242 (4%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRI+EIINAS +I TPII   L    D DYA  VK R+E+TTLG++C  I E+F P+ 
Sbjct: 1245 GVPRIQEIINASASIITPIIEVPLVNKHDYDYALSVKARIEKTTLGQICSDIRELFTPNG 1304

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISG--------HLTVSGHSFLILKPKD 875
              ++IKL+ + I+ L L+VD   +R  I     I          H       +L L P  
Sbjct: 1305 IRLIIKLNANVIQDLFLQVDAYRVRDKILEQGSIKKIKINKQDVHTLDKWQLYLDL-PAT 1363

Query: 876  SSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYG 935
             ++ F  + + +   L  +V+ G + I RA+I  E+     +Y++ VEG  L++VM  YG
Sbjct: 1364 ETQLF--QQHALINGLLDLVVAGGKRIKRAIIKRENTASGCQYQIAVEGYGLQEVMGAYG 1421

Query: 936  VKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            V+     +N+ YEV + LGIEAARSTI++EI+  M+ + + ID R+  L+ D+MTS+GEV
Sbjct: 1422 VQSNAVKTNHIYEVAQVLGIEAARSTIISEIQKCMDAYSIDIDGRYMKLLGDIMTSRGEV 1481

Query: 996  LG 997
            +G
Sbjct: 1482 IG 1483



 Score =  130 bits (327), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 79/225 (35%), Positives = 119/225 (52%), Gaps = 36/225 (16%)

Query: 115 PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSIC 174
           P P G LD+R+G ++ E  C+TCG++ + CVGH+GY+ L LPVFH+G+F+ +  IL  IC
Sbjct: 125 PQPLGALDKRLGCSRNEMTCSTCGKDNNHCVGHWGYVKLELPVFHVGFFKYLNQILYCIC 184

Query: 175 KNPTCARVLLGEEKAAGFRAKLRNPAL-SYLVRKSLKKKILETTKKVSVCPHCGEINGVV 233
           K   C+ +LL E+    ++ ++RN  +   L + SL +KIL+  K    C  CG   G V
Sbjct: 185 KR--CSNLLLPEDSIKKYQ-EIRNKGIDDPLFKVSLFRKILQECKNKKTCDRCGAPQGTV 241

Query: 234 KKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQT----LNPL 289
           K+                    IV+  L ++         +  HK+ G +Q     LNP+
Sbjct: 242 KR--------------------IVKPTLDQFMRM----KHVVRHKESGKVQARDEELNPI 277

Query: 290 EVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSV 334
            V  LFEA+    + LL     ++ P  +I+T L + PNCIRPSV
Sbjct: 278 VVKHLFEAMDPAHVKLL----NIASPEKMIITNLAISPNCIRPSV 318



 Score =  103 bits (257), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 48/74 (64%), Positives = 58/74 (78%), Gaps = 1/74 (1%)

Query: 601 FSIGIGDVTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSL 660
           F+IG  D    +GFV NSFFSGL P EFFFHTM GREGL+DTAVKT+ETGYMQR+L+K +
Sbjct: 880 FNIGCRDAK-SRGFVANSFFSGLEPEEFFFHTMSGREGLIDTAVKTSETGYMQRKLMKVM 938

Query: 661 EDLCVQYDMSFDAA 674
           EDL + YD +  A+
Sbjct: 939 EDLAICYDHTVRAS 952



 Score = 51.6 bits (122), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 24/46 (52%), Positives = 31/46 (67%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRI 67
           L++   NL TPRNG+ LIAA QDF++  YLLT K+ F  R Q  +I
Sbjct: 575 LLSVLQNLTTPRNGDPLIAAVQDFLSASYLLTSKDRFLTRKQFCQI 620


>gi|340503712|gb|EGR30247.1| hypothetical protein IMG5_137010 [Ichthyophthirius multifiliis]
          Length = 1464

 Score =  231 bits (589), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 115/274 (41%), Positives = 161/274 (58%), Gaps = 27/274 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + ++VLFNRQPSLH++SIMA +A +    T RFNEC C P+NADFDGDEMN+H+PQT EA
Sbjct: 446 NGEIVLFNRQPSLHRISIMAFKANIQKWNTLRFNECCCAPFNADFDGDEMNIHVPQTIEA 505

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+ L+  K NL++P+NGE +IA  QDF+T  YL+T K+ FF+R
Sbjct: 506 RAE--------------AQYLLDVKQNLISPKNGETIIALVQDFLTASYLITHKDMFFDR 551

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A   ++ +        I             P   +    +WTGKQ    +L PNR   + 
Sbjct: 552 AAFSQLCTYFSDGNEQI----------QLPPPAVILPVEMWTGKQAIDAMLIPNRKNKII 601

Query: 521 ANLKTKGRAYTANEE---FCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFG 577
            NL  K + Y   ++    C +D YV+ +NSELL G++ K+TLGSG K  +FY L RD  
Sbjct: 602 VNLTLKEKCYNTKKDREIMCPKDGYVVFQNSELLCGNLGKTTLGSGNKNGLFYRLSRDNS 661

Query: 578 EDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           + +A   M R +++++ +L N G +IGI DVTP 
Sbjct: 662 QQIAAAVMTRFAKLSARWLSNYGMTIGISDVTPS 695



 Score =  169 bits (429), Expect = 8e-39,   Method: Compositional matrix adjust.
 Identities = 117/357 (32%), Positives = 182/357 (50%), Gaps = 70/357 (19%)

Query: 1108 EKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG---------------------- 1145
            E+Y +  +EP  AVGA+ A SI EP TQMTLK+FHFAG                      
Sbjct: 1079 ERYPQMLVEPGEAVGAIGATSISEPATQMTLKSFHFAGIASMNITQGVPRMKEIIDAAKN 1138

Query: 1146 --------------EVCEY--------IEEVFV------------PDDSFILIKLD---M 1168
                          +  EY        IE+ ++            P D  + I+L+   +
Sbjct: 1139 ISTPVIDVKLLPEYQTDEYNFRSIRLQIEKTYLGEICEFYKEAYSPKDCHLHIQLNQQQL 1198

Query: 1169 DRIRLLHLEVDIDS-IRYCIERTRGISGHLTV----SGHSF----LILKPKDSSKSFNSK 1219
            ++ R L L++  ++ I+  +E  + I     V     G  F     I    D  K+   K
Sbjct: 1199 EKYRTLGLQIPTENIIKGILETAKDIKMEQIVEVKEQGSHFSTALKIYPTNDLKKNVFFK 1258

Query: 1220 MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYK--LLVEGDNLRDVMATYGVKGVKC 1277
            +   K++LP+ V+ G++ + R  I ++  +    YK  L VEG+ L+ ++    V     
Sbjct: 1259 IQNWKKILPTAVVSGMKNVKRVNISKDKKKNEQHYKFDLFVEGNALKQILMLEKVDFSST 1318

Query: 1278 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRH 1337
            S+ + YEV++ LGIEAAR TI+ EI   +++H +++D RH +LVAD++TSKG + G TR 
Sbjct: 1319 STVDIYEVFEVLGIEAARKTIINEITKTIKSHSLNVDTRHLVLVADVLTSKGRLYGSTRQ 1378

Query: 1338 GLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            G+  MK+S L LASFE T++ L++AA  G+ D + GVSE II+G  + +GTG   +L
Sbjct: 1379 GINFMKDSTLMLASFEKTTEILYNAALQGRKDLLEGVSERIIIGQNIPMGTGTFNVL 1435



 Score =  141 bits (356), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 87/250 (34%), Positives = 146/250 (58%), Gaps = 16/250 (6%)

Query: 764  GVPRIKEIINASRNISTPIITAYL--DKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEII+A++NISTP+I   L  +  TD    R ++ ++E+T LGE+CE+ +E + P
Sbjct: 1125 GVPRMKEIIDAAKNISTPVIDVKLLPEYQTDEYNFRSIRLQIEKTYLGEICEFYKEAYSP 1184

Query: 822  DDSFILIKLD---MDRIRLLHLEVDIDSI-RYCIERTRGISGHLTV----SGHSF----L 869
             D  + I+L+   +++ R L L++  ++I +  +E  + I     V     G  F     
Sbjct: 1185 KDCHLHIQLNQQQLEKYRTLGLQIPTENIIKGILETAKDIKMEQIVEVKEQGSHFSTALK 1244

Query: 870  ILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYK--LLVEGDNL 927
            I    D  K+   K+   K++LP+ V+ G++ + R  I ++  +    YK  L VEG+ L
Sbjct: 1245 IYPTNDLKKNVFFKIQNWKKILPTAVVSGMKNVKRVNISKDKKKNEQHYKFDLFVEGNAL 1304

Query: 928  RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 987
            + ++    V     S+ + YEV++ LGIEAAR TI+ EI   +++H +++D RH +LVAD
Sbjct: 1305 KQILMLEKVDFSSTSTVDIYEVFEVLGIEAARKTIINEITKTIKSHSLNVDTRHLVLVAD 1364

Query: 988  LMTSKGEVLG 997
            ++TSKG + G
Sbjct: 1365 VLTSKGRLYG 1374



 Score =  134 bits (336), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 85/260 (32%), Positives = 135/260 (51%), Gaps = 12/260 (4%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEAN--CTTCG 138
           G I+ ++     +   S I +     Y     + P+  G LD RMG + +E N  C TC 
Sbjct: 1   GSIQYSILTSQEIIDMSEICLTEPQFY-NPATKVPLSRGPLDLRMGLSMRENNQKCQTCQ 59

Query: 139 QNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN 198
            ++ DC GHFGYI L LP+FH+G+F  +INILQ ICKN  C  +LL  ++    + +++ 
Sbjct: 60  MDMIDCPGHFGYIKLVLPIFHVGFFTEIINILQCICKN--CGEILLNIDEKLACKKRMQR 117

Query: 199 P--ALSYLVRKSLKKKILETTKK--VSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKD 254
                +Y +R  +  K+ +  KK   S C  C   NG +KK   +  +   ++N TK + 
Sbjct: 118 AINEKNYQLRMLIYTKMRKECKKGANSRCRICDYKNGNLKKMPKMPTTIS-FQNHTKMES 176

Query: 255 AIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSK 314
              E   +E  +       ++  +   +IQ  NPL+   LF+ I   D+  +L N + + 
Sbjct: 177 DFREIKKSENLQQENLRKILDQKQLKDMIQLYNPLQTFNLFKKIAQSDV--ILFNIDQNH 234

Query: 315 PSDLILTRLLVPPNCIRPSV 334
           P DLILT ++VPP+CIRP++
Sbjct: 235 PIDLILTHIIVPPSCIRPTI 254



 Score = 98.2 bits (243), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 43/58 (74%), Positives = 50/58 (86%)

Query: 613 GFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
           GFV+NSFF+GL+  EFFFHTM GRE LVDTAVKTA+TGYM RRLVK LEDL + YD++
Sbjct: 833 GFVRNSFFTGLSAPEFFFHTMAGRESLVDTAVKTADTGYMSRRLVKMLEDLSINYDLT 890



 Score = 55.5 bits (132), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/55 (43%), Positives = 36/55 (65%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           Q L+  K NL++P+NGE +IA  QDF+T  YL+T K+ FF+RA   ++ +    G
Sbjct: 510 QYLLDVKQNLISPKNGETIIALVQDFLTASYLITHKDMFFDRAAFSQLCTYFSDG 564


>gi|209881813|ref|XP_002142344.1| DNA-directed RNA polymerase III largest subunit [Cryptosporidium
           muris RN66]
 gi|209557950|gb|EEA07995.1| DNA-directed RNA polymerase III largest subunit, putative
           [Cryptosporidium muris RN66]
          Length = 1803

 Score =  231 bits (589), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 124/278 (44%), Positives = 168/278 (60%), Gaps = 30/278 (10%)

Query: 343 DVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARA 402
           D VLFNRQPSLH+LSIM+HR  V+P RTFRFNEC C PYNADFDGDEMN+H+PQ E ARA
Sbjct: 454 DSVLFNRQPSLHRLSIMSHRVVVMPWRTFRFNECACAPYNADFDGDEMNLHMPQNELARA 513

Query: 403 EALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 462
           E              AK LM    NLVTPRNGE L+AATQDF+ G YLLT ++ F  R Q
Sbjct: 514 E--------------AKYLMGLVHNLVTPRNGEPLVAATQDFLLGIYLLTSRDVFLTRDQ 559

Query: 463 TMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPN--RDCPVN 520
             +         +D C  ++        P   ++   +WTGKQ+F+++++PN      + 
Sbjct: 560 FSQYCCYF----TDGCIPVE------LPPPSILKPIELWTGKQVFNVLIRPNPSERQHII 609

Query: 521 ANLKTKGRAYTAN---EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFG 577
            N + K R Y      ++ C  + +VI+R+SELLAG++ K  LG G K  +F+ +LR+  
Sbjct: 610 VNFELKERDYDTKLDLKDLCPNEGFVIVRHSELLAGAVGKKVLG-GSKEGLFFHILRENS 668

Query: 578 EDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFV 615
            + +   M R++R  S YL  +G +IGI DVTP +G +
Sbjct: 669 NEKSAEVMGRVARFVSRYLAQKGMTIGIDDVTPNEGLL 706



 Score =  178 bits (451), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 127/384 (33%), Positives = 185/384 (48%), Gaps = 91/384 (23%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGE---------------------------------- 1131
            C  KY++A ++P  AVGA+AAQSIGE                                  
Sbjct: 1398 CWLKYMKAIVQPGDAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIINAA 1457

Query: 1132 -----PGTQMTLKT---------------FHFAGEVCEYIEEVFVPDDSFILIKLDMDRI 1171
                 P  Q  LK                 +   EVC +IEEV+ P    + I L    I
Sbjct: 1458 TKILTPIIQAPLKNPWDYKCAQMVKGKIVKYLLREVCTHIEEVYSPQGVCLNIYLCEKTI 1517

Query: 1172 RLLHLEVDIDSIRYCIE------RTRGISGHLTVSGHSFLILKPKDS--------SKSFN 1217
            + L+L+++  ++R  I       + R   G + +     L + P D+        S S N
Sbjct: 1518 QNLYLDINAYTVRDSIYSHGQICKLRLKEGDIQIINQWTLAVYPPDTIEKGSRSGSTSSN 1577

Query: 1218 SKM--------------YQMKQL---LPSVVIKGVQGINRAVIHEEDV------EGVTKY 1254
            + +              +Q+K L   L +V++ G+ GI R+VI +++V      +   KY
Sbjct: 1578 NNLSLTSGSGPSSLNVLFQLKILKRGLQNVIVSGISGIRRSVIRQDEVVDPNTGKKRHKY 1637

Query: 1255 KLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSID 1314
             L VEG  L  +M   G+ G+   SN+  E  + LGIEAARS I  E+   M+ + M ID
Sbjct: 1638 SLAVEGYGLSALMGISGLIGISTVSNHIIETKEVLGIEAARSVIAQEVLKCMDAYSMDID 1697

Query: 1315 FRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGV 1374
             RH  L+AD+MT +G+VLGI+R G+ KM+ S L LASFE T++HLF+AAF  + D + GV
Sbjct: 1698 LRHIQLLADVMTFRGDVLGISRFGIQKMRTSTLMLASFEETNEHLFEAAFQNRIDPVDGV 1757

Query: 1375 SECIIMGLPMNVGTGLIKLLQAVP 1398
            SEC+IMG P+ +GTG   +L   P
Sbjct: 1758 SECVIMGKPIKIGTGAFDILFQSP 1781



 Score =  138 bits (348), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 97/271 (35%), Positives = 143/271 (52%), Gaps = 37/271 (13%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA+  I TPII A L    D   A++VKG++ +  L EVC +IEEV+ P  
Sbjct: 1446 GVPRIKEIINAATKILTPIIQAPLKNPWDYKCAQMVKGKIVKYLLREVCTHIEEVYSPQG 1505

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIE------RTRGISGHLTVSGHSFLILKPKDS- 876
              + I L    I+ L+L+++  ++R  I       + R   G + +     L + P D+ 
Sbjct: 1506 VCLNIYLCEKTIQNLYLDINAYTVRDSIYSHGQICKLRLKEGDIQIINQWTLAVYPPDTI 1565

Query: 877  -------SKSFNSKM--------------YQMKQL---LPSVVIKGVQGINRAVIHEEDV 912
                   S S N+ +              +Q+K L   L +V++ G+ GI R+VI +++V
Sbjct: 1566 EKGSRSGSTSSNNNLSLTSGSGPSSLNVLFQLKILKRGLQNVIVSGISGIRRSVIRQDEV 1625

Query: 913  ------EGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEI 966
                  +   KY L VEG  L  +M   G+ G+   SN+  E  + LGIEAARS I  E+
Sbjct: 1626 VDPNTGKKRHKYSLAVEGYGLSALMGISGLIGISTVSNHIIETKEVLGIEAARSVIAQEV 1685

Query: 967  KLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
               M+ + M ID RH  L+AD+MT +G+VLG
Sbjct: 1686 LKCMDAYSMDIDLRHIQLLADVMTFRGDVLG 1716



 Score =  132 bits (333), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 80/253 (31%), Positives = 140/253 (55%), Gaps = 33/253 (13%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           +E +V   D++   +H++++ + +Y +    TP+  G+LD ++G ++ +A C++CG NL 
Sbjct: 41  VEFSVMSSDQIACSAHMEVIHREIY-KPLTTTPMSGGVLDLKLGAHRADAQCSSCGGNLR 99

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLL-GEEKAAGFRAKLRNPAL 201
            C GH+GYI L  PVFH+GYF+ +  +L  +CK  +C   LL G EK        ++ +L
Sbjct: 100 TCGGHWGYIQLQQPVFHVGYFKHLYGVLCCLCK--SCGAFLLRGNEKKFYLNRLKQSYSL 157

Query: 202 SYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLL 261
           ++  +    +K+++  KKV +C +C    G +++  L++ + +++   T     +V+   
Sbjct: 158 AHAYKLQF-RKLIDRCKKVKICSNCNAQQGQLRR--LIRPTLDQFMKLTH----VVKS-- 208

Query: 262 AEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
                        E+H     I+ L PL V  L + +P ED+ +L    E+ KP  L+L+
Sbjct: 209 -------------ESHD---YIEDLTPLFVQTLLQKVPYEDLDIL----EMFKPDRLLLS 248

Query: 322 RLLVPPNCIRPSV 334
           RL VPPNCIRPSV
Sbjct: 249 RLPVPPNCIRPSV 261



 Score =  111 bits (277), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 49/63 (77%), Positives = 56/63 (88%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSF 671
           +GFV NSFFSGL P EFFFHTM GREGLVDTAVKTAETGYMQRRL+K+LEDLCV+YD + 
Sbjct: 827 RGFVANSFFSGLQPDEFFFHTMSGREGLVDTAVKTAETGYMQRRLIKALEDLCVKYDQTV 886

Query: 672 DAA 674
            ++
Sbjct: 887 RSS 889



 Score = 55.1 bits (131), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 26/44 (59%), Positives = 31/44 (70%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 63
           + LM    NLVTPRNGE L+AATQDF+ G YLLT ++ F  R Q
Sbjct: 516 KYLMGLVHNLVTPRNGEPLVAATQDFLLGIYLLTSRDVFLTRDQ 559



 Score = 46.2 bits (108), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 19/39 (48%), Positives = 26/39 (66%)

Query: 671  FDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 709
            F+AAF  + D + GVSEC+IMG P+ +GTG   +L   P
Sbjct: 1743 FEAAFQNRIDPVDGVSECVIMGKPIKIGTGAFDILFQSP 1781


>gi|70935749|ref|XP_738918.1| DNA-directed RNA polymerase 3 largest subunit [Plasmodium chabaudi
           chabaudi]
 gi|56515510|emb|CAH78774.1| DNA-directed RNA polymerase 3 largest subunit, putative [Plasmodium
           chabaudi chabaudi]
          Length = 417

 Score =  231 bits (588), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 122/277 (44%), Positives = 171/277 (61%), Gaps = 31/277 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIM H+A+V+ ++TFRFNECVC+PYNADFDGDEMN+H+PQTEE+
Sbjct: 119 DGDIVLFNRQPSLHRMSIMCHKARVMDYKTFRFNECVCSPYNADFDGDEMNLHVPQTEES 178

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL               LM  K NL+TP+NGE++IA TQDF++  Y++T K+ F +R
Sbjct: 179 RAEAL--------------YLMNVKHNLITPKNGEVIIALTQDFLSASYVITNKDTFLDR 224

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPV-VFVRTAVIWTGKQIFSLILKPNRDCPV 519
                + S       DI             PV   ++   +WTGKQ+ S+++KPN++   
Sbjct: 225 DLFCLLCSYFSDAKIDI-----------ELPVPAILKPKELWTGKQLISVLIKPNKNENT 273

Query: 520 NANLKTKGRAYTANE---EFCHR-DSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
             N + K R Y+      ++  R DSYV    SEL+ GS+ K  LG+  K  +FY L+ +
Sbjct: 274 IINFEMKEREYSTKNGDLKYLSRDDSYVCFYKSELICGSLGKKVLGA-SKYGLFYYLIHN 332

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
               VA+  M R S+++S Y  N+G +IGI DVTP +
Sbjct: 333 NSTQVALQIMNRFSKLSSRYFSNKGMTIGIDDVTPSR 369



 Score = 52.0 bits (123), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 21/40 (52%), Positives = 31/40 (77%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           LM  K NL+TP+NGE++IA TQDF++  Y++T K+ F +R
Sbjct: 185 LMNVKHNLITPKNGEVIIALTQDFLSASYVITNKDTFLDR 224


>gi|407410320|gb|EKF32797.1| DNA-directed RNA polymerase III largest subunit, putative
           [Trypanosoma cruzi marinkellei]
          Length = 1629

 Score =  231 bits (588), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 123/271 (45%), Positives = 162/271 (59%), Gaps = 25/271 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + DVVLFNRQPSLH++S+MAHRA+VLP RTFRFNEC C PYNADFDGDEMNVHL QTEEA
Sbjct: 535 NGDVVLFNRQPSLHRISMMAHRARVLPFRTFRFNECCCAPYNADFDGDEMNVHLVQTEEA 594

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA                LM+   N++  +NGE +IA TQDF+   YL+T ++ FF+R
Sbjct: 595 RAEAFE--------------LMSTAKNIINAKNGEPIIACTQDFLVAAYLVTSRDVFFDR 640

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           +Q   + S  +       G + +F  R   P +   T  +WTGKQ+F LIL+P+ +  V 
Sbjct: 641 SQMSWMVSHWL-------GPVTQF--RLPIPTILKPTE-LWTGKQVFELILRPSPEVNVL 690

Query: 521 ANLKTKGRAYTANEEF-CHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            NL+   + YT      C  + YV   +S  ++G +DK  LG G K  +F  L    G  
Sbjct: 691 LNLEAATKFYTKKGRHDCAAEGYVAFLDSHFISGRLDKKLLGGGAKDGLFARLHTLAGGG 750

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
                M R+++ TS YL N GFS+G+GDV P
Sbjct: 751 YTARIMSRIAQFTSRYLTNYGFSLGLGDVAP 781



 Score =  139 bits (350), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 82/238 (34%), Positives = 134/238 (56%), Gaps = 11/238 (4%)

Query: 118 HGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNP 177
           +G+ D R+G   + + C TCG    DCVGH G+IDL  PVFH+G+F  ++ I ++ICK  
Sbjct: 133 YGVNDPRLGVCDRVSVCATCGLRSIDCVGHPGHIDLETPVFHLGFFSTILRICRTICKR- 191

Query: 178 TCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCG 237
            C+ +LL + +   ++ +L +  L  L R +L K I +   K  VC  CG +NG V++  
Sbjct: 192 -CSHLLLDDAEIEYYKRRLSSTKLDPLQRAALVKTIQKEAYKTRVCLKCGGLNGDVRRVR 250

Query: 238 LLKISHEKYKNRTKKKDAIVEDLLA----EYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQ 293
            L++ HEKY+   ++ +  VE +      E   A  +N  +E  K+  + + L+P  V Q
Sbjct: 251 PLRLVHEKYRVEPRRGEESVEGIETFFDYELRTACAYNKVVEESKE-NVHEFLDPARVRQ 309

Query: 294 LFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRP---SVISDLKSDNDVVLFN 348
           LF A+P +++ LL +    S P DL++T LLVPP  +RP   S  ++++ D+    +N
Sbjct: 310 LFLAVPPDEVLLLGLQPGTS-PVDLLVTTLLVPPVSVRPRGSSGTANIRDDDLTGQYN 366



 Score =  138 bits (347), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 78/169 (46%), Positives = 106/169 (62%), Gaps = 6/169 (3%)

Query: 1226 LLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEV 1285
            LLP VV+ G+ GINRA+I     E      +L EG  LR VM    V+  +   N+   V
Sbjct: 1419 LLPDVVVGGIAGINRAMISSNGGE------VLAEGAELRAVMNLPEVESTRVVCNHVAVV 1472

Query: 1286 YKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKES 1345
             + LGIEAAR  I+ EI+ +++ + +SID RH  L+ADLMT +G VLGITR+G+ KM  +
Sbjct: 1473 ERVLGIEAARQVIVNEIQGILKAYSLSIDIRHIYLLADLMTQRGVVLGITRYGIQKMNFN 1532

Query: 1346 VLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            VL +ASFE T+DHL++AA   + D    VSE II+G P+ +GT    LL
Sbjct: 1533 VLTMASFERTTDHLYNAAATQRVDENLSVSESIIIGKPVPLGTTSFSLL 1581



 Score =  113 bits (283), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 90/269 (33%), Positives = 136/269 (50%), Gaps = 43/269 (15%)

Query: 764  GVPRIKEIINASRNISTPIITAYL--------------------DKDTDLDY---ARIVK 800
            GVPR+ EIINA+RNI+TP++TA +                    ++D+   +    R VK
Sbjct: 1260 GVPRLVEIINANRNIATPVVTAPVRRQRQNNSLSIKQEVVGEGCEEDSQEVFEKRVRRVK 1319

Query: 801  GRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCI--ERTRGIS 858
             ++ER  L EV   I EV    + ++ + L+M  I  L L ++  ++R  I     R +S
Sbjct: 1320 SQVERVMLKEVASEIVEVCTSTEFYLRVHLNMSLITKLCLPINAITVRQRILAAAARPMS 1379

Query: 859  G-------HLTVSGHSFLILKP---KDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIH 908
                     + V     L ++P   + +   FN  +  +  LLP VV+ G+ GINRA+I 
Sbjct: 1380 PLRLLREECVEVVSLDTLAVRPYFLEANRVHFN--LRHVLALLPDVVVGGIAGINRAMIS 1437

Query: 909  EEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKL 968
                E      +L EG  LR VM    V+  +   N+   V + LGIEAAR  I+ EI+ 
Sbjct: 1438 SNGGE------VLAEGAELRAVMNLPEVESTRVVCNHVAVVERVLGIEAARQVIVNEIQG 1491

Query: 969  VMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +++ + +SID RH  L+ADLMT +G VLG
Sbjct: 1492 ILKAYSLSIDIRHIYLLADLMTQRGVVLG 1520



 Score =  102 bits (255), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 45/58 (77%), Positives = 53/58 (91%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGY+ RRL+K++E+L V+YD
Sbjct: 907 ARGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYIYRRLMKAMENLSVRYD 964



 Score = 62.0 bits (149), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/40 (65%), Positives = 30/40 (75%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            C  KY+    EP T  GA+AAQS+GEP TQMTL+TFHFAG
Sbjct: 1212 CASKYILKACEPGTPCGAIAAQSVGEPSTQMTLRTFHFAG 1251



 Score = 50.4 bits (119), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 30/42 (71%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 63
           LM+   N++  +NGE +IA TQDF+   YL+T ++ FF+R+Q
Sbjct: 601 LMSTAKNIINAKNGEPIIACTQDFLVAAYLVTSRDVFFDRSQ 642


>gi|407849768|gb|EKG04383.1| DNA-directed RNA polymerase III largest subunit, putative
           [Trypanosoma cruzi]
          Length = 1553

 Score =  231 bits (588), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 123/271 (45%), Positives = 162/271 (59%), Gaps = 25/271 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + DVVLFNRQPSLH++S+MAHRA+VLP RTFRFNEC C PYNADFDGDEMNVHL QTEEA
Sbjct: 460 NGDVVLFNRQPSLHRISMMAHRARVLPFRTFRFNECCCAPYNADFDGDEMNVHLVQTEEA 519

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA                LM+   N++  +NGE +IA TQDF+   YL+T ++ FF+R
Sbjct: 520 RAEAFE--------------LMSTAKNIINAKNGEPIIACTQDFLVAAYLVTSRDVFFDR 565

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           +Q   + S  +       G + +F  R   P +   T  +WTGKQ+F LIL+P+ +  V 
Sbjct: 566 SQMSWMVSHWL-------GPVTQF--RLPIPTILKPTE-LWTGKQVFELILRPSPEVNVL 615

Query: 521 ANLKTKGRAYTANEEF-CHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            NL+   + YT      C  + YV   +S  ++G +DK  LG G K  +F  L    G  
Sbjct: 616 LNLEAATKFYTKKGRHDCAAEGYVAFLDSRFISGRLDKKLLGGGAKDGLFARLHTLSGGG 675

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
                M R+++ TS YL N GFS+G+GDV P
Sbjct: 676 YTARIMSRIAQFTSRYLTNYGFSLGLGDVAP 706



 Score =  142 bits (359), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 98/261 (37%), Positives = 143/261 (54%), Gaps = 20/261 (7%)

Query: 1146 EVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCI--ERTRGISG-------H 1196
            EV   I EV   ++ ++ + L+M  I  L L ++  ++R  I     R +S         
Sbjct: 1253 EVASEIVEVCTSNEFYLRVHLNMSLIAKLWLPINAITVRQRILAAAARPMSPLRLLREEC 1312

Query: 1197 LTVSGHSFLILKP---KDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTK 1253
            + V     L ++P   +     FN  +  +  LLP VV+ G+ GINRA+I     E    
Sbjct: 1313 VEVVSLDTLAVRPYFLEAHRVHFN--LRHVLALLPDVVVGGIAGINRAMISSNGAE---- 1366

Query: 1254 YKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSI 1313
              +L EG  LR VM   GV+  +   N+   V + LGIEAAR  I+ EI+ +++ + +SI
Sbjct: 1367 --VLAEGAELRAVMNLPGVESTRVVCNHVAVVERVLGIEAARQVIVNEIQGILKAYSLSI 1424

Query: 1314 DFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISG 1373
            D RH  L+ADLMT +G VLGITR+G+ KM  +VL +ASFE T+DHL++AA   + D    
Sbjct: 1425 DIRHIYLLADLMTQRGVVLGITRYGIQKMNFNVLTMASFERTTDHLYNAAATQRVDENLS 1484

Query: 1374 VSECIIMGLPMNVGTGLIKLL 1394
            VSE II+G P+ +GT    LL
Sbjct: 1485 VSESIIIGKPVPLGTTSFSLL 1505



 Score =  136 bits (343), Expect = 8e-29,   Method: Compositional matrix adjust.
 Identities = 80/238 (33%), Positives = 133/238 (55%), Gaps = 11/238 (4%)

Query: 118 HGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNP 177
           +G+ D R+G   + + C TCG    DC+GH G+IDL  PVFH+G+F  ++ I ++ICK  
Sbjct: 58  YGVNDPRLGVCDRVSFCATCGLRSIDCIGHPGHIDLETPVFHLGFFTTILRICRTICKR- 116

Query: 178 TCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCG 237
            C+ +LL + +   ++ +L +  L  L R +L K I     K  VC  CG +NG V++  
Sbjct: 117 -CSHLLLDDAEIEYYKRRLSSTKLEPLQRAALVKTIQREAYKTRVCLKCGGLNGDVRRVR 175

Query: 238 LLKISHEKYKNRTKKKDAIVEDLLA----EYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQ 293
            L++ HEKY+   ++ +  VE +      E   A  +N  +E  K+  + + L+P  V Q
Sbjct: 176 PLRLVHEKYRVEPRRGEESVEGVETFFDYELRAACAYNKVVEESKE-NVHEFLDPARVRQ 234

Query: 294 LFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRP---SVISDLKSDNDVVLFN 348
           +F A+P +++ LLL     + P DL++T LLVPP  +RP   S  ++++ D+    +N
Sbjct: 235 MFLAVPPDEV-LLLGLLPGTSPVDLLVTTLLVPPVSVRPRGSSGTANIRDDDLTGQYN 291



 Score =  120 bits (302), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 91/269 (33%), Positives = 138/269 (51%), Gaps = 43/269 (15%)

Query: 764  GVPRIKEIINASRNISTPIITAYL--------------------DKDTDLDY---ARIVK 800
            GVPR+ EIINA+RNI+TP++TA +                    ++D+  ++    R VK
Sbjct: 1184 GVPRLVEIINANRNIATPVVTAPVRRHRRGKSLSIKQEVVGESCEEDSQEEFEKRVRRVK 1243

Query: 801  GRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCI--ERTRGIS 858
             ++ER  L EV   I EV   ++ ++ + L+M  I  L L ++  ++R  I     R +S
Sbjct: 1244 SQVERVLLKEVASEIVEVCTSNEFYLRVHLNMSLIAKLWLPINAITVRQRILAAAARPMS 1303

Query: 859  G-------HLTVSGHSFLILKP---KDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIH 908
                     + V     L ++P   +     FN  +  +  LLP VV+ G+ GINRA+I 
Sbjct: 1304 PLRLLREECVEVVSLDTLAVRPYFLEAHRVHFN--LRHVLALLPDVVVGGIAGINRAMIS 1361

Query: 909  EEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKL 968
                E      +L EG  LR VM   GV+  +   N+   V + LGIEAAR  I+ EI+ 
Sbjct: 1362 SNGAE------VLAEGAELRAVMNLPGVESTRVVCNHVAVVERVLGIEAARQVIVNEIQG 1415

Query: 969  VMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +++ + +SID RH  L+ADLMT +G VLG
Sbjct: 1416 ILKAYSLSIDIRHIYLLADLMTQRGVVLG 1444



 Score =  102 bits (254), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 45/58 (77%), Positives = 53/58 (91%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGY+ RRL+K++E+L V+YD
Sbjct: 832 ARGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYIYRRLMKAMENLSVRYD 889



 Score = 62.0 bits (149), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/40 (65%), Positives = 30/40 (75%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            C  KY+    EP T  GA+AAQS+GEP TQMTL+TFHFAG
Sbjct: 1136 CASKYILKACEPGTPCGAIAAQSVGEPSTQMTLRTFHFAG 1175



 Score = 50.1 bits (118), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 30/42 (71%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 63
           LM+   N++  +NGE +IA TQDF+   YL+T ++ FF+R+Q
Sbjct: 526 LMSTAKNIINAKNGEPIIACTQDFLVAAYLVTSRDVFFDRSQ 567


>gi|71665443|ref|XP_819691.1| DNA-directed RNA polymerase III largest subunit [Trypanosoma cruzi
           strain CL Brener]
 gi|70885004|gb|EAN97840.1| DNA-directed RNA polymerase III largest subunit, putative
           [Trypanosoma cruzi]
          Length = 1553

 Score =  230 bits (586), Expect = 6e-57,   Method: Compositional matrix adjust.
 Identities = 123/271 (45%), Positives = 161/271 (59%), Gaps = 25/271 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + DVVLFNRQPSLH++S+MAHRA+VLP RTFRFNEC C PYNADFDGDEMNVHL QTEEA
Sbjct: 460 NGDVVLFNRQPSLHRISMMAHRARVLPFRTFRFNECCCAPYNADFDGDEMNVHLVQTEEA 519

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA                LM    N++  +NGE +IA TQDF+   YL+T ++ FF+R
Sbjct: 520 RAEAFE--------------LMLTAKNIINAKNGEPIIACTQDFLVAAYLVTSRDVFFDR 565

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           +Q   + S  +       G + +F  R   P +   T  +WTGKQ+F LIL+P+ +  V 
Sbjct: 566 SQMSWMVSHWL-------GPVTQF--RLPIPTILKPTE-LWTGKQVFELILRPSPEVNVL 615

Query: 521 ANLKTKGRAYTANEEF-CHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            NL+   + YT      C  + YV   +S  ++G +DK  LG G K  +F  L    G  
Sbjct: 616 LNLEAATKFYTKKGRHDCAAEGYVAFLDSRFISGRLDKKLLGGGAKDGLFARLHTLSGGG 675

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
                M R+++ TS YL N GFS+G+GDV P
Sbjct: 676 YTARIMSRIAQFTSRYLTNYGFSLGLGDVAP 706



 Score =  139 bits (350), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 78/169 (46%), Positives = 106/169 (62%), Gaps = 6/169 (3%)

Query: 1226 LLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEV 1285
            LLP VV+ G+ GINRA+I     E      +L EG  LR VM    V+  +   N+   V
Sbjct: 1343 LLPDVVVGGIAGINRAMISSNGAE------VLAEGAELRAVMNLPEVESTRVVCNHVAVV 1396

Query: 1286 YKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKES 1345
             + LGIEAAR  I+ EI+ +++ + +SID RH  L+ADLMT +G VLGITR+G+ KM  +
Sbjct: 1397 ERVLGIEAARQVIVNEIQGILKAYSLSIDIRHIYLLADLMTQRGVVLGITRYGIQKMNFN 1456

Query: 1346 VLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            VL +ASFE T+DHL++AA   + D    VSE II+G P+ +GT    LL
Sbjct: 1457 VLTMASFERTTDHLYNAAATQRVDENLSVSESIIIGKPVPLGTTSFSLL 1505



 Score =  137 bits (344), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 81/238 (34%), Positives = 133/238 (55%), Gaps = 11/238 (4%)

Query: 118 HGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNP 177
           +G+ D R+G   + + C TCG    DCVGH G+IDL  PVFH+G+F  ++ I ++ICK  
Sbjct: 58  YGVNDPRLGVCDRVSFCATCGLRSIDCVGHPGHIDLETPVFHLGFFTTILRICRTICKR- 116

Query: 178 TCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCG 237
            C+ +LL + +   ++ +L +  L  L R +L K I     K  VC  CG +NG V++  
Sbjct: 117 -CSHLLLDDAEIEYYKRRLSSTKLEPLQRAALVKTIQREAYKTRVCLKCGGLNGDVRRVR 175

Query: 238 LLKISHEKYKNRTKKKDAIVEDLLA----EYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQ 293
            L++ HEKY+   ++ +  VE +      E   A  +N  +E  K+  + + L+P  V Q
Sbjct: 176 PLRLVHEKYRVEPRRGEESVEGVETFFDYELRAACAYNKVVEESKE-NVHEFLDPARVRQ 234

Query: 294 LFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRP---SVISDLKSDNDVVLFN 348
           +F A+P +++ LLL     + P DL++T LLVPP  +RP   S  ++++ D+    +N
Sbjct: 235 MFLAVPPDEV-LLLGLLPGTSPVDLLVTTLLVPPVSVRPRGSSGTANIRDDDLTGQYN 291



 Score =  116 bits (290), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 90/269 (33%), Positives = 136/269 (50%), Gaps = 43/269 (15%)

Query: 764  GVPRIKEIINASRNISTPIITAYL--------------------DKDTDLDY---ARIVK 800
            GVPR+ EIINA+RNI+TP++TA +                    ++D+  ++    R VK
Sbjct: 1184 GVPRLVEIINANRNIATPVVTAPVRRHRRGKSLSIKQEVVGESCEEDSQEEFEKRVRRVK 1243

Query: 801  GRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCI--ERTRGIS 858
             ++ER  L EV   I EV    + ++ + L+M  I  L L ++  ++R  I     R +S
Sbjct: 1244 SQVERVLLKEVASEIVEVCTSTEFYLRVHLNMSLIAKLWLPINAITVRQRILAAAARPMS 1303

Query: 859  G-------HLTVSGHSFLILKP---KDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIH 908
                     + V     L ++P   +     FN  +  +  LLP VV+ G+ GINRA+I 
Sbjct: 1304 PLRLLREECVEVVSLDTLAVRPYFLEAHRVHFN--LRHVLALLPDVVVGGIAGINRAMIS 1361

Query: 909  EEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKL 968
                E      +L EG  LR VM    V+  +   N+   V + LGIEAAR  I+ EI+ 
Sbjct: 1362 SNGAE------VLAEGAELRAVMNLPEVESTRVVCNHVAVVERVLGIEAARQVIVNEIQG 1415

Query: 969  VMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +++ + +SID RH  L+ADLMT +G VLG
Sbjct: 1416 ILKAYSLSIDIRHIYLLADLMTQRGVVLG 1444



 Score =  102 bits (255), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 45/58 (77%), Positives = 53/58 (91%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV NSF+SGLTPTEFFFHTM GREGLVDTAVKTAETGY+ RRL+K++E+L V+YD
Sbjct: 832 ARGFVANSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYIYRRLMKAMENLSVRYD 889



 Score = 62.0 bits (149), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/40 (65%), Positives = 30/40 (75%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            C  KY+    EP T  GA+AAQS+GEP TQMTL+TFHFAG
Sbjct: 1136 CASKYILKACEPGTPCGAIAAQSVGEPSTQMTLRTFHFAG 1175



 Score = 49.3 bits (116), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 29/42 (69%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 63
           LM    N++  +NGE +IA TQDF+   YL+T ++ FF+R+Q
Sbjct: 526 LMLTAKNIINAKNGEPIIACTQDFLVAAYLVTSRDVFFDRSQ 567


>gi|154417868|ref|XP_001581953.1| RNA polymerase Rpb1, domain 2 family protein [Trichomonas vaginalis
           G3]
 gi|121916185|gb|EAY20967.1| RNA polymerase Rpb1, domain 2 family protein [Trichomonas vaginalis
           G3]
          Length = 1657

 Score =  229 bits (585), Expect = 6e-57,   Method: Compositional matrix adjust.
 Identities = 115/277 (41%), Positives = 166/277 (59%), Gaps = 25/277 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND VLFNRQPSLH++SIM  RAKV+   T RFNE VC P+NADFDGDEMNVHLPQT EA
Sbjct: 431 DNDTVLFNRQPSLHRISIMGFRAKVMEWCTMRFNESVCAPFNADFDGDEMNVHLPQTLEA 490

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
            A+              A+ LM    NL +PR GE+++A TQDF++G ++LT+KN F + 
Sbjct: 491 AAD--------------ARYLMNVLYNLFSPRAGEMIVAPTQDFLSGAFILTRKNVFLDY 536

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           +    + S +  +  ++             P   V+   +WTGKQ+ SL++ PN+   ++
Sbjct: 537 SHFTFLISQIFDNLEEV----------DIPPPAIVKPYQLWTGKQVVSLMIAPNKKTDLH 586

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
              +   + YT N+E C +D YV   ++ +++G ++KS +G GG  +++ I+ RD     
Sbjct: 587 FTHQVGNKEYTGNKEMCKKDGYVSFLDNYMVSGVLEKSLIG-GGPKSLWAIMARDHSPKF 645

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           A   M R+++M+  YLMNRGFSIGI DV P +    N
Sbjct: 646 AAVCMQRIAKMSCRYLMNRGFSIGIMDVRPDENLTNN 682



 Score =  192 bits (487), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 130/379 (34%), Positives = 193/379 (50%), Gaps = 68/379 (17%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYI 1151
            C  +  ++  EP   VGA+A QSIGEP TQMTL++FHFAG              EV   +
Sbjct: 991  CMHRCEKSMAEPGMTVGAVAGQSIGEPATQMTLRSFHFAGVASMNVTLGVPRIEEVMNAV 1050

Query: 1152 EEVFVP----------------------------------------DDSFILIKLDMDRI 1171
             E+  P                                           +I I+LD + I
Sbjct: 1051 SEIKTPIITANLLSQRDEIAARIVKGIIDRVTLGQVCKHIEYNQNEKSCYIDIELDAEII 1110

Query: 1172 RLLHLEVDIDSIRYCIERTR--GISGHLTVSG--HSFLILKPKDSSKSFNSKMYQMKQLL 1227
            R   L +  +++R  I  T   G+    T +   ++  +     + K+F+  M Q+   L
Sbjct: 1111 REAKLNITSETVRRSIVNTPKIGVKDENTANNGDYNVRVFMQGANPKAFSFIMQQLMLKL 1170

Query: 1228 PSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYK 1287
            P VV+ GV G+ R  + +E+      +KL VEG+    V+ T G+   +  SN+  +V K
Sbjct: 1171 PDVVVSGVPGVERVHVGKEN----GCFKLFVEGNPFLKVLNTPGIDPKRTVSNHVLDVEK 1226

Query: 1288 TLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVL 1347
             LG+EAARS I++EI  VM+N+ ++ID RH ML++DLMT +G+VLG+TRHGLAK   S L
Sbjct: 1227 VLGVEAARSVIISEITNVMKNYSLNIDRRHLMLLSDLMTIRGKVLGVTRHGLAKTSVSSL 1286

Query: 1348 NLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL---QAVPRSEPVP 1404
             LASFE T +HLF+AAF+   +  +GVS  +I+G    +G+G+I +L   + + R+   P
Sbjct: 1287 KLASFETTQEHLFNAAFHNVDEVANGVSASVILGNFAPIGSGMIDVLVSDELLKRTSLTP 1346

Query: 1405 RTLLFD---NPEFHTNTLA 1420
            R  L +   NP F T   A
Sbjct: 1347 RCHLIEDYINPMFLTAPYA 1365



 Score =  159 bits (401), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 86/222 (38%), Positives = 134/222 (60%), Gaps = 13/222 (5%)

Query: 119 GLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPT 178
           G LD R+G   K   C TCGQ   +C GHFG ++L LPV++IG++  +++ L+ ICK  T
Sbjct: 31  GTLDLRLGAASKNQICQTCGQPQENCPGHFGSLELVLPVYNIGFYPAILHCLKCICK--T 88

Query: 179 CARVLL-GEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCG 237
           C+ +LL  EE  +  +     P  +   +    K +++  +KV++CPHCG ING VKK  
Sbjct: 89  CSNILLPNEEINSRLKKFYSKPPQTVSAKIDRVKALMKECEKVTICPHCGAINGPVKKTK 148

Query: 238 L-LKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKF--GLIQTLNPLEVLQL 294
             L I+H    N  +K D + E  L++++   K + + + +KK+   +   + PL  LQL
Sbjct: 149 TTLIITH----NVGQKNDKLREPFLSKFS---KLDIKGDDYKKYLDNICDDITPLRALQL 201

Query: 295 FEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVIS 336
           F+AIP   IPLLL    +S P+D+I+T +++PPNCIRP+VI+
Sbjct: 202 FKAIPTRQIPLLLSGFSVSSPADMIITSIVIPPNCIRPAVIA 243



 Score =  152 bits (385), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 101/266 (37%), Positives = 150/266 (56%), Gaps = 21/266 (7%)

Query: 736  RDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINASRNISTPIITAYLDKDTDLDY 795
            R +     AS+ VTL             GVPRI+E++NA   I TPIITA L    D   
Sbjct: 1024 RSFHFAGVASMNVTL-------------GVPRIEEVMNAVSEIKTPIITANLLSQRDEIA 1070

Query: 796  ARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTR 855
            ARIVKG ++R TLG+VC++IE        +I I+LD + IR   L +  +++R  I  T 
Sbjct: 1071 ARIVKGIIDRVTLGQVCKHIEYNQNEKSCYIDIELDAEIIREAKLNITSETVRRSIVNTP 1130

Query: 856  --GISGHLTVSG--HSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEED 911
              G+    T +   ++  +     + K+F+  M Q+   LP VV+ GV G+ R  + +E+
Sbjct: 1131 KIGVKDENTANNGDYNVRVFMQGANPKAFSFIMQQLMLKLPDVVVSGVPGVERVHVGKEN 1190

Query: 912  VEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVME 971
                  +KL VEG+    V+ T G+   +  SN+  +V K LG+EAARS I++EI  VM+
Sbjct: 1191 ----GCFKLFVEGNPFLKVLNTPGIDPKRTVSNHVLDVEKVLGVEAARSVIISEITNVMK 1246

Query: 972  NHGMSIDFRHPMLVADLMTSKGEVLG 997
            N+ ++ID RH ML++DLMT +G+VLG
Sbjct: 1247 NYSLNIDRRHLMLLSDLMTIRGKVLG 1272



 Score =  102 bits (254), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 43/59 (72%), Positives = 54/59 (91%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
           +GF+ +SF++GLTP++FFFHTMGGREGLVD AVKTA+TGYMQRRL+KSLEDL + YD +
Sbjct: 801 KGFIASSFYTGLTPSDFFFHTMGGREGLVDAAVKTAQTGYMQRRLMKSLEDLVIAYDQT 859



 Score = 47.4 bits (111), Expect = 0.065,   Method: Compositional matrix adjust.
 Identities = 19/39 (48%), Positives = 29/39 (74%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 60
           LM    NL +PR GE+++A TQDF++G ++LT+KN F +
Sbjct: 497 LMNVLYNLFSPRAGEMIVAPTQDFLSGAFILTRKNVFLD 535


>gi|6624243|dbj|BAA88486.1| RNA polymerase III largest subunit [Eptatretus burgeri]
          Length = 537

 Score =  229 bits (585), Expect = 7e-57,   Method: Compositional matrix adjust.
 Identities = 111/225 (49%), Positives = 152/225 (67%), Gaps = 21/225 (9%)

Query: 391 NVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYL 450
           N+HLPQTEEA+AEAL              VLM  K+N+VTPRNGE LIAA QDF+T  YL
Sbjct: 1   NLHLPQTEEAKAEAL--------------VLMGTKANMVTPRNGEPLIAAIQDFLTAAYL 46

Query: 451 LTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLI 510
           LT K+ F +R++  ++ + ++A       +  R       P   +    +WTGKQIFSL+
Sbjct: 47  LTHKDTFLDRSRACQLIAAILAGQD----VAMRLEL---PPPAILCPVCLWTGKQIFSLL 99

Query: 511 LKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFY 570
           L+P++ CP+  NL+TKG+ Y+  E+ C  DS+V+L N ELLAGS+DK+TLGSG K ++FY
Sbjct: 100 LRPSQSCPIMPNLRTKGKQYSGGEDLCPNDSFVVLHNGELLAGSLDKATLGSGSKNSIFY 159

Query: 571 ILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFV 615
           +LL+D+G+  A  AM RL+R++  YL +RGFSIGIGDVTPG G +
Sbjct: 160 VLLQDWGQTAATDAMSRLARISPAYLSHRGFSIGIGDVTPGPGLL 204



 Score =  118 bits (295), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 53/63 (84%), Positives = 59/63 (93%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSF 671
           +GFV NSF+SGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC+ YD++ 
Sbjct: 325 KGFVANSFYSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCLAYDLTV 384

Query: 672 DAA 674
            +A
Sbjct: 385 RSA 387



 Score = 71.6 bits (174), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 31/60 (51%), Positives = 44/60 (73%)

Query: 21 VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFFR 80
          VLM  K+N+VTPRNGE LIAA QDF+T  YLLT K+ F +R++  ++ + ++AG+ V  R
Sbjct: 16 VLMGTKANMVTPRNGEPLIAAIQDFLTAAYLLTHKDTFLDRSRACQLIAAILAGQDVAMR 75



 Score = 53.9 bits (128), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 39/139 (28%), Positives = 69/139 (49%), Gaps = 14/139 (10%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G   P+E  R+L  + A +    + +LSA ++ A +   L  +       + FV ++ +F
Sbjct: 408  GRDRPLEPVRVLASVFANHPCGDEIALSAIQLEAEAERLLRGEGPCAVCGKAFVEELAEF 467

Query: 1057 LEEFSKKESVTSH-----QDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYV 1111
            L + + +     H      +  ++P+   IL H ++I   +    F + C      +KY+
Sbjct: 468  LRQLAMRVKRVRHIYGVNDNGSTEPM---ILYHLERITPSQLEIFFSTCC------DKYL 518

Query: 1112 RAQIEPATAVGALAAQSIG 1130
            RA+IEP +AVGA+ AQSIG
Sbjct: 519  RARIEPGSAVGAVCAQSIG 537


>gi|389603516|ref|XP_001564320.2| putative DNA-directed RNA polymerase III largest subunit
           [Leishmania braziliensis MHOM/BR/75/M2904]
 gi|322504664|emb|CAM38379.2| putative DNA-directed RNA polymerase III largest subunit
           [Leishmania braziliensis MHOM/BR/75/M2904]
          Length = 1581

 Score =  229 bits (583), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 123/272 (45%), Positives = 168/272 (61%), Gaps = 27/272 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + D VLFNRQPSLH++S+MAHRA+VLP RTFRFNEC C PYNADFDGDEMN+H+ QTEEA
Sbjct: 455 NGDYVLFNRQPSLHRISLMAHRARVLPFRTFRFNECCCAPYNADFDGDEMNIHVVQTEEA 514

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              AK L+ +  +++T +NGE +IA TQDF+T  YL+T ++A F+R
Sbjct: 515 RAE--------------AKELLLSSHHIITAKNGEPIIACTQDFLTAAYLVTARDALFDR 560

Query: 461 AQ-TMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           A  T  ++  L A+T     I          P + ++ A +WTGKQ+F LIL+P  +  +
Sbjct: 561 ATFTQMVSHWLDAETQFALPI----------PAI-LKPAELWTGKQLFELILRPTPETQL 609

Query: 520 NANLKTKGRAYT-ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
             NL+ K R Y+ A       + YV   +S  L+G +DK  LG G K  +F  L    G 
Sbjct: 610 LLNLEAKTRFYSGAGRHDDPAEGYVAFLDSIFLSGRLDKKLLGGGAKDGLFARLYALGGG 669

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           +   T M R+++ T+ YL N GFS+G+GDV+P
Sbjct: 670 EQTATCMSRIAQFTARYLQNYGFSLGLGDVSP 701



 Score =  163 bits (413), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 91/237 (38%), Positives = 139/237 (58%), Gaps = 11/237 (4%)

Query: 119 GLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPT 178
           G+ D R+G + + + C TCGQ   +C GH G+I+L +PVFH+GYF  VI + ++ICK   
Sbjct: 54  GVNDPRLGPSDRLSVCNTCGQCSIECTGHAGHINLEVPVFHLGYFSAVIRVCRTICKR-- 111

Query: 179 CARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGL 238
           C+ VLL  E+   +  +LR+ +     R +L K I E   K  VC  CG +NG V++   
Sbjct: 112 CSNVLLTREEMEYYLHRLRSTSHEPQQRAALIKAIQEDAYKTRVCLMCGGLNGTVRRVRP 171

Query: 239 LKISHEKYKNRTKKKDAIVEDLLAEYNEAVK----FNPEIEAHKKFGLIQTLNPLEVLQL 294
           +++ HEKY    ++ +   ED  A + EA++     N E+ +HK+F + + L+P  V  L
Sbjct: 172 MRVIHEKYLVELRRGEQANEDPTAFFQEALRSAALHNSEVGSHKEF-VHEFLHPQRVKAL 230

Query: 295 FEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRP---SVISDLKSDNDVVLFN 348
           FEAIPLE +PLL +    S PS L+++ LLVPP C+RP   S  S ++ D+    +N
Sbjct: 231 FEAIPLEQVPLLGLQPGTS-PSSLLISTLLVPPVCVRPRGMSTTSHIREDDLTTQYN 286



 Score =  156 bits (394), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 102/261 (39%), Positives = 149/261 (57%), Gaps = 20/261 (7%)

Query: 1146 EVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSI--RYCIERTRGISG--HLT--- 1198
            E+   + EV  P   +I I LD+  I  L L +D   +  R      R +S   HL+   
Sbjct: 1233 EITREMVEVVTPRQYYIQIFLDIGLIERLLLPIDAAVVCQRLYAAAARPMSPLRHLSEAC 1292

Query: 1199 --VSGHSFLILKP--KDSSK-SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTK 1253
              +     LI+KP  KD ++  FN  +  +  LLP +V+ G+ G+NR +I +        
Sbjct: 1293 VDMVSRDSLIVKPYEKDPARVHFN--IQHLLTLLPELVVGGIPGVNRVMIADRS------ 1344

Query: 1254 YKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSI 1313
             KLL EG  L  VM+   V GV+ + N+   V + LGIEAAR TI+ EI  +++ + +SI
Sbjct: 1345 EKLLAEGAELLSVMSLPYVDGVRTTCNHVAVVERVLGIEAARETIVKEITSILQAYSLSI 1404

Query: 1314 DFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISG 1373
            D RH  L+AD+MTS+G VLGITR+G+ KM  +VL +ASFE T++HL++AA   + D    
Sbjct: 1405 DIRHIYLLADVMTSRGVVLGITRYGIQKMNNNVLTMASFERTTEHLYNAAMTEREDVNLS 1464

Query: 1374 VSECIIMGLPMNVGTGLIKLL 1394
            VSECII+G P+ +GT    +L
Sbjct: 1465 VSECIIIGKPIPLGTSSFNIL 1485



 Score =  138 bits (348), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 100/259 (38%), Positives = 143/259 (55%), Gaps = 33/259 (12%)

Query: 764  GVPRIKEIINASRNISTPIITAYL---DKDTDLDYA----------RIVKGRLERTTLGE 810
            GVPR+ EIINA++NI+TP+ITA +   D+ T +D A          R VKG +ER  L E
Sbjct: 1174 GVPRLVEIINANKNIATPVITAPILLEDEFTSIDLASARRTQYQAARAVKGLMERVLLKE 1233

Query: 811  VCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSI--RYCIERTRGISG--HLT---- 862
            +   + EV  P   +I I LD+  I  L L +D   +  R      R +S   HL+    
Sbjct: 1234 ITREMVEVVTPRQYYIQIFLDIGLIERLLLPIDAAVVCQRLYAAAARPMSPLRHLSEACV 1293

Query: 863  -VSGHSFLILKP--KDSSK-SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKY 918
             +     LI+KP  KD ++  FN  +  +  LLP +V+ G+ G+NR +I +         
Sbjct: 1294 DMVSRDSLIVKPYEKDPARVHFN--IQHLLTLLPELVVGGIPGVNRVMIADRS------E 1345

Query: 919  KLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSID 978
            KLL EG  L  VM+   V GV+ + N+   V + LGIEAAR TI+ EI  +++ + +SID
Sbjct: 1346 KLLAEGAELLSVMSLPYVDGVRTTCNHVAVVERVLGIEAARETIVKEITSILQAYSLSID 1405

Query: 979  FRHPMLVADLMTSKGEVLG 997
             RH  L+AD+MTS+G VLG
Sbjct: 1406 IRHIYLLADVMTSRGVVLG 1424



 Score = 95.1 bits (235), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 42/59 (71%), Positives = 51/59 (86%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
           +GFV +SF+SGL+PTEFFFH M GREG+VDTAVKTAETGY+ RRL K++E+L V YD S
Sbjct: 828 RGFVASSFYSGLSPTEFFFHGMAGREGIVDTAVKTAETGYIYRRLSKAMENLSVGYDTS 886



 Score = 55.8 bits (133), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/42 (61%), Positives = 29/42 (69%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            E    K  R   EP T  GA+AAQS+GEP TQMTL+TFHFAG
Sbjct: 1124 EDSARKVHRKLCEPGTPCGAIAAQSVGEPSTQMTLRTFHFAG 1165



 Score = 48.5 bits (114), Expect = 0.025,   Method: Compositional matrix adjust.
 Identities = 21/57 (36%), Positives = 36/57 (63%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVF 78
           L+ +  +++T +NGE +IA TQDF+T  YL+T ++A F+RA   ++ S  +     F
Sbjct: 521 LLLSSHHIITAKNGEPIIACTQDFLTAAYLVTARDALFDRATFTQMVSHWLDAETQF 577


>gi|321452423|gb|EFX63811.1| hypothetical protein DAPPUDRAFT_66722 [Daphnia pulex]
          Length = 187

 Score =  228 bits (580), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 109/183 (59%), Positives = 139/183 (75%), Gaps = 1/183 (0%)

Query: 1234 GVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEA 1293
            G   ++R +I  +D     +Y LLVEG+N+R+VMATYG++G   +SNN  EV+ TLGIEA
Sbjct: 1    GFDDVSRVIIKMDDSRNTPRYSLLVEGNNMREVMATYGIQGSSTTSNNILEVFSTLGIEA 60

Query: 1294 ARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFE 1353
            A++TI  EI+  ME+HGMS+D RH  L++DLM+ +GE+LGITRHGLAKMK SVL LASFE
Sbjct: 61   AKATIAKEIQSTMESHGMSVDRRHVALLSDLMSCRGEILGITRHGLAKMKSSVLMLASFE 120

Query: 1354 NTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNP 1412
             TSDHLFDAA+YGQ D +SGVSE IIMG+PM +GTG  KLL    +S +P  R L+FD P
Sbjct: 121  RTSDHLFDAAYYGQEDEVSGVSERIIMGVPMGIGTGSFKLLYKTGKSVQPKTRPLIFDVP 180

Query: 1413 EFH 1415
            E+H
Sbjct: 181  EYH 183



 Score =  115 bits (288), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 52/100 (52%), Positives = 74/100 (74%)

Query: 898 GVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEA 957
           G   ++R +I  +D     +Y LLVEG+N+R+VMATYG++G   +SNN  EV+ TLGIEA
Sbjct: 1   GFDDVSRVIIKMDDSRNTPRYSLLVEGNNMREVMATYGIQGSSTTSNNILEVFSTLGIEA 60

Query: 958 ARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
           A++TI  EI+  ME+HGMS+D RH  L++DLM+ +GE+LG
Sbjct: 61  AKATIAKEIQSTMESHGMSVDRRHVALLSDLMSCRGEILG 100



 Score = 77.8 bits (190), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 37/64 (57%), Positives = 45/64 (70%), Gaps = 1/64 (1%)

Query: 668 DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS-EPVPRTLLFDNPEFH 726
           D  FDAA+YGQ D +SGVSE IIMG+PM +GTG  KLL    +S +P  R L+FD PE+H
Sbjct: 124 DHLFDAAYYGQEDEVSGVSERIIMGVPMGIGTGSFKLLYKTGKSVQPKTRPLIFDVPEYH 183

Query: 727 FPQV 730
            P V
Sbjct: 184 VPMV 187


>gi|449512000|ref|XP_002199667.2| PREDICTED: DNA-directed RNA polymerase III subunit RPC1-like,
           partial [Taeniopygia guttata]
          Length = 345

 Score =  227 bits (578), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 114/191 (59%), Positives = 148/191 (77%), Gaps = 3/191 (1%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
           GVPRIKEIINAS+ ISTPIITA LDKD D D+AR+VKGR+E+T LGE+ EYIEEVF+PDD
Sbjct: 137 GVPRIKEIINASKAISTPIITAQLDKDDDPDFARLVKGRIEKTLLGEISEYIEEVFLPDD 196

Query: 824 SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
            FIL+KL ++RIRLL LEV+ +++RY  C+ + R   G + V G + + + P+++SKS  
Sbjct: 197 CFILVKLSLERIRLLRLEVNAETVRYSICVSKLRVKPGDVAVHGEAVVCVTPRENSKSSM 256

Query: 882 SKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
             + Q +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG K
Sbjct: 257 YYVLQSLKEELPKVVVQGIPEVSRAVIHVDEQSGKEKYKLLVEGDNLRAVMATHGVKGTK 316

Query: 941 CSSNNTYEVYK 951
            SSNNTYEV K
Sbjct: 317 TSSNNTYEVEK 327



 Score =  220 bits (561), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 138/334 (41%), Positives = 190/334 (56%), Gaps = 76/334 (22%)

Query: 1018 RSDPSLSAQEILALSNETLDSKEFL--QDTSENFVRDIKKFLEEFSKKESVTSHQ----- 1070
            RS+P+LS  E++  S   +   EFL  QD+   F+++IKKF++  S+K   T  +     
Sbjct: 6    RSEPALSKNELVLTSESIMKKNEFLCCQDS---FLQEIKKFIKGVSEKIKKTRDKYGIND 62

Query: 1071 DKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIG 1130
            +  ++P   ++L   D+I       P       E CR+KY+RAQ+EP +AVGAL AQSIG
Sbjct: 63   NGTTEP---RVLYQLDRI------TPTQLEKFLETCRDKYMRAQMEPGSAVGALCAQSIG 113

Query: 1131 EPGTQMTLKTFH------------------------------------------FA---- 1144
            EPGTQMTLKTFH                                          FA    
Sbjct: 114  EPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAISTPIITAQLDKDDDPDFARLVK 173

Query: 1145 --------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGIS 1194
                    GE+ EYIEEVF+PDD FIL+KL ++RIRLL LEV+ +++RY  C+ + R   
Sbjct: 174  GRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLLRLEVNAETVRYSICVSKLRVKP 233

Query: 1195 GHLTVSGHSFLILKPKDSSKSFNSKMYQ-MKQLLPSVVIKGVQGINRAVIHEEDVEGVTK 1253
            G + V G + + + P+++SKS    + Q +K+ LP VV++G+  ++RAVIH ++  G  K
Sbjct: 234  GDVAVHGEAVVCVTPRENSKSSMYYVLQSLKEELPKVVVQGIPEVSRAVIHVDEQSGKEK 293

Query: 1254 YKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYK 1287
            YKLLVEGDNLR VMAT+GVKG K SSNNTYEV K
Sbjct: 294  YKLLVEGDNLRAVMATHGVKGTKTSSNNTYEVEK 327


>gi|443919746|gb|ELU39822.1| DNA-directed RNA polymerase III largest subunit [Rhizoctonia solani
           AG-1 IA]
          Length = 385

 Score =  226 bits (576), Expect = 7e-56,   Method: Compositional matrix adjust.
 Identities = 116/268 (43%), Positives = 163/268 (60%), Gaps = 36/268 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIM HRAK+ P RTFR NEC C PY ADFDGDEMN+H+PQTEEA
Sbjct: 140 DGDIVLFNRQPSLHKLSIMCHRAKIRPWRTFRLNECACGPYGADFDGDEMNMHVPQTEEA 199

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EA               +LM  + N+VTPRNGE +I+A QDFIT  +LL+ K  FF+R
Sbjct: 200 RTEAF--------------ILMNVRQNIVTPRNGEPIISAIQDFITASFLLSSKERFFDR 245

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q  +I S L  D      I          P   ++ A +WTGKQIF++++KPN+   V 
Sbjct: 246 RQFTQICSYL-GDAELQIDI---------PPPTIIKPARLWTGKQIFNVLMKPNKASNVR 295

Query: 521 ANLKTK-GRAYTAN-----------EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANV 568
            N++ +    +  N            +    D ++++ NSE++ G MDK+T+G+G K ++
Sbjct: 296 VNVEARCSTMHKPNPKNFPSYMKPAPDLSPNDGWLVIVNSEIMCGVMDKATVGAGKKKSI 355

Query: 569 FYILLRDFGEDVAVTAMWRLSRMTSFYL 596
           F +++RD+G + A   M RL+++ + +L
Sbjct: 356 FGVIIRDYGANEAAITMGRLAKLCARWL 383



 Score = 58.9 bits (141), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 27/51 (52%), Positives = 36/51 (70%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           +LM  + N+VTPRNGE +I+A QDFIT  +LL+ K  FF+R Q  +I S L
Sbjct: 205 ILMNVRQNIVTPRNGEPIISAIQDFITASFLLSSKERFFDRRQFTQICSYL 255


>gi|414586606|tpg|DAA37177.1| TPA: putative DNA-directed RNA polymerase family protein [Zea mays]
          Length = 336

 Score =  226 bits (576), Expect = 8e-56,   Method: Compositional matrix adjust.
 Identities = 124/265 (46%), Positives = 173/265 (65%), Gaps = 8/265 (3%)

Query: 1145 GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSG 1201
            GEV   I+ V       +++KLDM  I  LH+ +  DS++  I    + +  S H+ V  
Sbjct: 64   GEVAATIQTVLKSSLPNLVVKLDMQLIETLHMGISADSVKLSILNHPKLKLKSEHVRVID 123

Query: 1202 HSFLILKPKDSSK-SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVT-KYKLLVE 1259
             + L + P  + K     +++ +K +LP V++KG+  + R VI E  V   T +Y+LLVE
Sbjct: 124  RAKLRIYPAGTDKLKLQLELHNLKSILPKVIVKGIPTVERVVIDEVKVNNATERYQLLVE 183

Query: 1260 GDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPM 1319
            G NL  VM T GV   K  SN+  E  +TLGIEAAR +I+ EI+  M++HGM+ID RH M
Sbjct: 184  GTNLLAVMGTPGVDARKTKSNHIMETNQTLGIEAARRSIIDEIQYTMKSHGMNIDRRHMM 243

Query: 1320 LVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECII 1379
            L+ADLMT KGE+LGITR+G+AKMK SVL LASFE T++HLF+A++ G+ D I GVSECII
Sbjct: 244  LLADLMTYKGEILGITRYGIAKMKSSVLMLASFEKTAEHLFNASYSGRQDQIEGVSECII 303

Query: 1380 MGLPMNVGTGLIKLLQAVPRSEPVP 1404
            MG+PM +GTG++K+ Q   R + VP
Sbjct: 304  MGIPMQLGTGILKVRQ---RLDHVP 325



 Score =  192 bits (489), Expect = 9e-46,   Method: Compositional matrix adjust.
 Identities = 110/239 (46%), Positives = 150/239 (62%), Gaps = 5/239 (2%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
           GVPRIKEIINA++ ISTPIITA L    D+  ARIVKG +E+  LGEV   I+ V     
Sbjct: 19  GVPRIKEIINAAKKISTPIITAQLLSRKDVLSARIVKGSMEKAVLGEVAATIQTVLKSSL 78

Query: 824 SFILIKLDMDRIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSGHSFLILKPKDSSK-S 879
             +++KLDM  I  LH+ +  DS++  I    + +  S H+ V   + L + P  + K  
Sbjct: 79  PNLVVKLDMQLIETLHMGISADSVKLSILNHPKLKLKSEHVRVIDRAKLRIYPAGTDKLK 138

Query: 880 FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVT-KYKLLVEGDNLRDVMATYGVKG 938
              +++ +K +LP V++KG+  + R VI E  V   T +Y+LLVEG NL  VM T GV  
Sbjct: 139 LQLELHNLKSILPKVIVKGIPTVERVVIDEVKVNNATERYQLLVEGTNLLAVMGTPGVDA 198

Query: 939 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            K  SN+  E  +TLGIEAAR +I+ EI+  M++HGM+ID RH ML+ADLMT KGE+LG
Sbjct: 199 RKTKSNHIMETNQTLGIEAARRSIIDEIQYTMKSHGMNIDRRHMMLLADLMTYKGEILG 257



 Score = 53.9 bits (128), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 24/45 (53%), Positives = 34/45 (75%), Gaps = 3/45 (6%)

Query: 671 FDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP 715
           F+A++ G+ D I GVSECIIMG+PM +GTG++K+ Q   R + VP
Sbjct: 284 FNASYSGRQDQIEGVSECIIMGIPMQLGTGILKVRQ---RLDHVP 325


>gi|196004558|ref|XP_002112146.1| hypothetical protein TRIADDRAFT_55878 [Trichoplax adhaerens]
 gi|190586045|gb|EDV26113.1| hypothetical protein TRIADDRAFT_55878 [Trichoplax adhaerens]
          Length = 941

 Score =  225 bits (573), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 121/251 (48%), Positives = 165/251 (65%), Gaps = 14/251 (5%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           VQ+Q+HI++VSKNLY +D QR+P+ +G+LDRRMGT+ K  +C TC + L+DCVGH+GY+D
Sbjct: 28  VQRQAHIRVVSKNLYGEDTQRSPVSYGVLDRRMGTSSKNKSCETCRKGLADCVGHYGYLD 87

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLR---NPALSYLVRKSL 209
           L LPVFH G+++  I ILQ ICK   C+RVLL     A +   L+      L    RK+L
Sbjct: 88  LALPVFHCGFYKATITILQCICKK--CSRVLLS---PADYDQNLQIATRTRLGLQSRKAL 142

Query: 210 KKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYK-NRTKKKDAI--VEDLLAEYNE 266
           +KK+ E  +K++VCP CG ING+VKK G  KI HEK++ N+     AI   +DLL    +
Sbjct: 143 QKKVHEKCRKMAVCPSCGAINGIVKKAGSFKIIHEKHRLNKKLSSIAISQTQDLL---QD 199

Query: 267 AVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVP 326
           AV+ N ++E        + LNPL VL+LF  +  ED  L+ M     +P DLI+ RLLVP
Sbjct: 200 AVESNKDLENFVASKSQEILNPLLVLKLFSGMSDEDCLLVGMKPNNGRPEDLIIERLLVP 259

Query: 327 PNCIRPSVISD 337
           P CIRPSV++D
Sbjct: 260 PLCIRPSVMTD 270



 Score =  178 bits (452), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 107/250 (42%), Positives = 134/250 (53%), Gaps = 71/250 (28%)

Query: 362 RAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVL 421
           +AK++P+RTFRFNECVCTP+NADFDGDEMN+HLPQTEEARAEAL              VL
Sbjct: 446 KAKIMPNRTFRFNECVCTPFNADFDGDEMNIHLPQTEEARAEAL--------------VL 491

Query: 422 MANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGII 481
           M +KSN+VTPR+GE LIAA QDFITG YLLTQK+ F +RA+  +  S+++          
Sbjct: 492 MQSKSNMVTPRSGEPLIAAIQDFITGAYLLTQKDVFLDRAKVSQFCSSMLDS-------- 543

Query: 482 KRFSWRSWNPV-VFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRD 540
           +  S     PV   ++   +WTGKQ+ S +L P                      FC   
Sbjct: 544 RTASTEIDLPVPSIIKPVQLWTGKQVISALLSP----------------LDVVFAFCVLL 587

Query: 541 SYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRG 600
             V+  N E + G +DKSTLGSG ++                               NRG
Sbjct: 588 D-VVFHNGEHICGVLDKSTLGSGSRS-------------------------------NRG 615

Query: 601 FSIGIGDVTP 610
           FSIGI DVTP
Sbjct: 616 FSIGISDVTP 625



 Score =  109 bits (272), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 48/63 (76%), Positives = 56/63 (88%)

Query: 608 VTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           V   +GFV+NSF+SGL PTEFFFHTM GREGLVDTAVKTAETGY+QRRL+KSLEDL ++Y
Sbjct: 747 VPAAKGFVENSFYSGLEPTEFFFHTMAGREGLVDTAVKTAETGYLQRRLIKSLEDLAIRY 806

Query: 668 DMS 670
           D +
Sbjct: 807 DTT 809



 Score = 79.7 bits (195), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 35/42 (83%), Positives = 39/42 (92%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            ++C  KYVRA+IEP TAVGA+AAQSIGEPGTQMTLKTFHFAG
Sbjct: 893  QSCGNKYVRAKIEPGTAVGAIAAQSIGEPGTQMTLKTFHFAG 934



 Score = 72.0 bits (175), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 43/55 (78%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM +KSN+VTPR+GE LIAA QDFITG YLLTQK+ F +RA+  +  S+++  R
Sbjct: 490 VLMQSKSNMVTPRSGEPLIAAIQDFITGAYLLTQKDVFLDRAKVSQFCSSMLDSR 544


>gi|71029280|ref|XP_764283.1| DNA-directed RNA polymerase III largest subunit [Theileria parva
           strain Muguga]
 gi|68351237|gb|EAN32000.1| DNA-directed RNA polymerase III largest subunit, putative
           [Theileria parva]
          Length = 1617

 Score =  225 bits (573), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 124/312 (39%), Positives = 168/312 (53%), Gaps = 62/312 (19%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + D+V+FNRQPSLH+LSIM HRA+V+   TFRFNECVC PYNADFDGDEMN+HLPQT EA
Sbjct: 505 NGDIVIFNRQPSLHRLSIMCHRARVMNGSTFRFNECVCLPYNADFDGDEMNLHLPQTYEA 564

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA   LH LS++            NL TPRNGE LIA  QDF+   YLLT K+ F NR
Sbjct: 565 RAEA---LHLLSVL-----------KNLTTPRNGEPLIAPVQDFLCASYLLTNKDMFLNR 610

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+  +I S     T  I             P   +    +WTGKQ+FS+++KPN    V 
Sbjct: 611 AEFSQIISYFTDGTIHI----------DLPPPSIIHPVTLWTGKQVFSVLIKPNNKSKVM 660

Query: 521 ANLKTKGRAYTANEEF-------------------------------------CHRDSYV 543
            N++ + R YT  +++                                     C  D YV
Sbjct: 661 VNIRVREREYTDPKQYYENLNKKGSEDSKVNKKSGNPSNDTNPRSFIKLDDCMCPSDGYV 720

Query: 544 ILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSI 603
           ++  SEL+ GS+   +LG+  K  +FY L+      ++   M R+S+++S +L   G +I
Sbjct: 721 VIYKSELMCGSLGVRSLGA-SKGGLFYELMLKNSPKISSECMLRVSKLSSRWLSEFGMTI 779

Query: 604 GIGDVTPGQGFV 615
           G+ DVTP +  +
Sbjct: 780 GLDDVTPSRELI 791



 Score =  198 bits (504), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 126/350 (36%), Positives = 180/350 (51%), Gaps = 67/350 (19%)

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFH--------------------------- 1142
            Y ++  EP  A+GAL +QSIGEP TQMTLKTFH                           
Sbjct: 1271 YQKSLCEPGEAIGALGSQSIGEPATQMTLKTFHFAGVASMNVTLGVPRIQEIINATSLIA 1330

Query: 1143 ---------------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLH 1175
                           FA            G++C  I++++ P  S +L  L+ D I  LH
Sbjct: 1331 TPIIEVPLEDNTDYDFALKVKSKIEKTTLGQICLNIKQLYTPQMSKLLFTLNRDLIEQLH 1390

Query: 1176 LEVDIDSIR------YCIERTR-GISGHLTVSGHSFLILKPKDSSKSF--NSKMYQMKQL 1226
            ++V+ D +R       C+ + +   S   ++      I  P +    F  NS +  + QL
Sbjct: 1391 IQVNADKVRDIIIDSGCLGKVKIHKSCVYSIGKWQICIELPSNQQHFFQQNSLISGLTQL 1450

Query: 1227 LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVY 1286
                V+ G + + RAVI  E       Y++ VEG  L++VM  YGV      SN+  EV 
Sbjct: 1451 ----VVAGSKSVKRAVIKRESTPQGPNYQIAVEGYGLQEVMGCYGVMSSAVKSNHVAEVA 1506

Query: 1287 KTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESV 1346
            K LGIEAARS I++EI+  M+ + + ID R+  L+ D+MT +GEV+GI R G+ KM+ S 
Sbjct: 1507 KVLGIEAARSVIISEIQRCMDAYSIDIDCRYMKLLGDVMTFRGEVVGINRFGIQKMRSSA 1566

Query: 1347 LNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA 1396
            L LASFE T+DHL +AA + + D I GVSECIIMG P+++GTG   +L +
Sbjct: 1567 LMLASFEETNDHLLEAALHHRRDPIKGVSECIIMGKPISLGTGSFDILMS 1616



 Score =  157 bits (397), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 94/243 (38%), Positives = 142/243 (58%), Gaps = 13/243 (5%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRI+EIINA+  I+TPII   L+ +TD D+A  VK ++E+TTLG++C  I++++ P  
Sbjct: 1315 GVPRIQEIINATSLIATPIIEVPLEDNTDYDFALKVKSKIEKTTLGQICLNIKQLYTPQM 1374

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIR------YCIERTR-GISGHLTVSGHSFLILKPKDS 876
            S +L  L+ D I  LH++V+ D +R       C+ + +   S   ++      I  P + 
Sbjct: 1375 SKLLFTLNRDLIEQLHIQVNADKVRDIIIDSGCLGKVKIHKSCVYSIGKWQICIELPSNQ 1434

Query: 877  SKSF--NSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATY 934
               F  NS +  + QL    V+ G + + RAVI  E       Y++ VEG  L++VM  Y
Sbjct: 1435 QHFFQQNSLISGLTQL----VVAGSKSVKRAVIKRESTPQGPNYQIAVEGYGLQEVMGCY 1490

Query: 935  GVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGE 994
            GV      SN+  EV K LGIEAARS I++EI+  M+ + + ID R+  L+ D+MT +GE
Sbjct: 1491 GVMSSAVKSNHVAEVAKVLGIEAARSVIISEIQRCMDAYSIDIDCRYMKLLGDVMTFRGE 1550

Query: 995  VLG 997
            V+G
Sbjct: 1551 VVG 1553



 Score =  142 bits (357), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 88/246 (35%), Positives = 128/246 (52%), Gaps = 35/246 (14%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           + + S I+I  K LY  +  R P  +G LD R+G N K+A C TCG+  ++CVGH+G+I 
Sbjct: 100 ISRASEIEIEHKQLYVMN-SRKPCVYGPLDSRLGCNNKDAICETCGKGYNECVGHWGHIK 158

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKK 212
           L LPVFHIG+F+  I IL  ICK   C+ +LL EE    F    +      +++  + K 
Sbjct: 159 LALPVFHIGFFKYTIQILYCICKK--CSSLLLSEESIKKFYELHKKAQDDPVLKPLIFKN 216

Query: 213 ILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNP 272
           I++  KK+S CP C    GV+KK                    IV+ ++ ++ +      
Sbjct: 217 IVQDCKKISKCPRCEAPQGVIKK--------------------IVKPIIDQFMKL----K 252

Query: 273 EIEAHKKFGLIQT----LNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPN 328
            I  +K++G ++T    LNPL V  LFE I     P+      +  P  LI++ L  PPN
Sbjct: 253 HIYKYKEYGKMKTVEEELNPLVVKHLFENID----PVHSKVLNIVHPEKLIISNLAAPPN 308

Query: 329 CIRPSV 334
           CIRPSV
Sbjct: 309 CIRPSV 314



 Score =  103 bits (257), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 48/70 (68%), Positives = 56/70 (80%), Gaps = 1/70 (1%)

Query: 601 FSIGIGDVTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSL 660
           F++G  D    +GFV NSFF+GL P EFFFHTM GREGL+DTAVKT+ETGYMQRRL+K +
Sbjct: 900 FTMGCKDAK-SRGFVANSFFTGLEPEEFFFHTMSGREGLIDTAVKTSETGYMQRRLMKVM 958

Query: 661 EDLCVQYDMS 670
           EDL V YD S
Sbjct: 959 EDLSVCYDYS 968



 Score = 56.2 bits (134), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 27/53 (50%), Positives = 33/53 (62%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           L++   NL TPRNGE LIA  QDF+   YLLT K+ F NRA+  +I S    G
Sbjct: 571 LLSVLKNLTTPRNGEPLIAPVQDFLCASYLLTNKDMFLNRAEFSQIISYFTDG 623



 Score = 42.4 bits (98), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 19/40 (47%), Positives = 27/40 (67%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA 707
            D   +AA + + D I GVSECIIMG P+++GTG   +L +
Sbjct: 1577 DHLLEAALHHRRDPIKGVSECIIMGKPISLGTGSFDILMS 1616


>gi|443919745|gb|ELU39821.1| DNA-directed RNA polymerase III largest subunit [Rhizoctonia solani
            AG-1 IA]
          Length = 679

 Score =  224 bits (570), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 164/469 (34%), Positives = 235/469 (50%), Gaps = 100/469 (21%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G+  PV+  R     +A   SR   SL   E+  L    L S  F  + +  +++ I+ F
Sbjct: 217  GDAQPVDYTRAWSHSLA-TGSREGRSLYPYEVTELIKAELSSPRFQNECTPAYIQSIEIF 275

Query: 1057 LEE---------------FSKKESVTSHQDKVSQPL-----REQILSHQDKIGHGRESNP 1096
            L                 F   E      D     L      + I+ +  K+   +    
Sbjct: 276  LRTSVVDKMAACRDQHGMFDAIERSEEWDDDTDLSLGAAEYEKTIVDNMTKVTESQLRRF 335

Query: 1097 FPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEV--------- 1147
                   + C  KY +A+IEPA     + AQSIGEPGTQMTLKTFHFAG           
Sbjct: 336  L------DICWTKYAKARIEPA-----VGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVP 384

Query: 1148 ------------------CEYI---------------EEVFVPDDSFIL----------- 1163
                              C  +               E+ ++ D + +L           
Sbjct: 385  RIKEIINASKAISTPIITCRLVASDSETSARIVKGRLEKTYLGDIASVLEEAWGASYTYV 444

Query: 1164 -IKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF---NSK 1219
             I +DM+ I+ L L++ +D +++ I   +     L V  H+  I   K+  + +    +K
Sbjct: 445  GIHIDMEAIQKLQLDITLDDVKWAILNNK----KLKVKEHNVTIPPRKNRLRIYVDGENK 500

Query: 1220 MY---QMKQLLPSVVIKGVQGINRAVIH--EEDVEGVTK--YKLLVEGDNLRDVMATYGV 1272
             Y   Q+K++LPSVV+KG+  I RA+I+  ++D +   +   +LLVEG  L++VM T G+
Sbjct: 501  YYRLRQLKRILPSVVVKGIPTIQRAIINVLDKDSDDCKRGDKELLVEGYGLKEVMNTDGI 560

Query: 1273 KGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL 1332
             G K +SN+  EV + LGIEAAR TI+ EI+  M++HGM++D RH ML+ D+MT KG+VL
Sbjct: 561  IGEKTTSNHIMEVEQVLGIEAARKTIIGEIQYTMQSHGMNVDPRHIMLLGDVMTYKGQVL 620

Query: 1333 GITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMG 1381
            GITR G+AKMK+SVL LASFE T+DHLFDAA Y + D ISGVSE IIMG
Sbjct: 621  GITRFGVAKMKDSVLMLASFEKTTDHLFDAAGYAKNDNISGVSESIIMG 669



 Score =  183 bits (464), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 107/244 (43%), Positives = 158/244 (64%), Gaps = 14/244 (5%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
           GVPRIKEIINAS+ ISTPIIT  L        ARIVKGRLE+T LG++   +EE +    
Sbjct: 382 GVPRIKEIINASKAISTPIITCRLVASDSETSARIVKGRLEKTYLGDIASVLEEAWGASY 441

Query: 824 SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF--- 880
           +++ I +DM+ I+ L L++ +D +++ I   +     L V  H+  I   K+  + +   
Sbjct: 442 TYVGIHIDMEAIQKLQLDITLDDVKWAILNNK----KLKVKEHNVTIPPRKNRLRIYVDG 497

Query: 881 NSKMY---QMKQLLPSVVIKGVQGINRAVIH--EEDVEGVTK--YKLLVEGDNLRDVMAT 933
            +K Y   Q+K++LPSVV+KG+  I RA+I+  ++D +   +   +LLVEG  L++VM T
Sbjct: 498 ENKYYRLRQLKRILPSVVVKGIPTIQRAIINVLDKDSDDCKRGDKELLVEGYGLKEVMNT 557

Query: 934 YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
            G+ G K +SN+  EV + LGIEAAR TI+ EI+  M++HGM++D RH ML+ D+MT KG
Sbjct: 558 DGIIGEKTTSNHIMEVEQVLGIEAARKTIIGEIQYTMQSHGMNVDPRHIMLLGDVMTYKG 617

Query: 994 EVLG 997
           +VLG
Sbjct: 618 QVLG 621



 Score = 93.6 bits (231), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 45/78 (57%), Positives = 53/78 (67%), Gaps = 17/78 (21%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVK----------- 658
           P +GFV+NSF++GL PTEF FH + GREGLVDTAVKTAETGYM RRL+K           
Sbjct: 115 PAKGFVRNSFYTGLLPTEFLFHAISGREGLVDTAVKTAETGYMARRLMKVYNHAKTKHLR 174

Query: 659 ------SLEDLCVQYDMS 670
                 +LEDL  QYD+S
Sbjct: 175 TYNAQQALEDLTTQYDLS 192


>gi|399218552|emb|CCF75439.1| unnamed protein product [Babesia microti strain RI]
          Length = 1459

 Score =  223 bits (569), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 121/285 (42%), Positives = 161/285 (56%), Gaps = 35/285 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIMAHRA V+   T RFNECVC+PYNADFDGDEMN+H PQTEEA
Sbjct: 431 DGDIVLFNRQPSLHRMSIMAHRAIVMQGSTLRFNECVCSPYNADFDGDEMNLHFPQTEEA 490

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA                LM   +NL +P+NGE L+AA QDF++  YLLT K+ F ++
Sbjct: 491 RAEAFH--------------LMGVLNNLTSPKNGEPLVAAVQDFLSASYLLTSKDYFLDK 536

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +   +  +       I             P   +    +WTGKQ+FSL+L PNR     
Sbjct: 537 KKIFNLCCSFCDGIEHI----------DVPPPAIIYPIQLWTGKQVFSLLLSPNRKDRTY 586

Query: 521 ANLKTKGR----------AYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFY 570
            NL+ K R           Y  ++     D YV++ NSEL+ GS+ K+TLG  GK+ + +
Sbjct: 587 INLELKEREFKPYKSNTSVYGNSDVMSPSDGYVVVSNSELMCGSVGKNTLGP-GKSGLIF 645

Query: 571 ILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFV 615
            LLR+ G       + R+S++T  +L   G SIGI DV P    +
Sbjct: 646 HLLRNQGSKSTSKFLSRISKLTCRWLCEYGLSIGIDDVIPSHELI 690



 Score =  199 bits (507), Expect = 8e-48,   Method: Compositional matrix adjust.
 Identities = 131/353 (37%), Positives = 176/353 (49%), Gaps = 70/353 (19%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG------------------- 1145
            +C   Y  A  EP  AVGAL AQSIGEPGTQMTLKTFHFAG                   
Sbjct: 1112 SCWRDYKNAIAEPGDAVGALGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIINA 1171

Query: 1146 ----------------------------------EVCEYIEEVFVPDDSFILIKLDMDRI 1171
                                               +C+  E+++ P  SFI++ +D    
Sbjct: 1172 TANIQTPIIEVPLVSSKFEAALINKYRIEKTTIGNICKKFEDIYSPHGSFIILTIDQGIC 1231

Query: 1172 RLLHLEVDIDSIRYCIERTRGIS-------GHLTVSGHSFLILKPKDSSKSFNSKMYQMK 1224
              L L +  + ++  I     I+           +      IL P  +   +   M+Q +
Sbjct: 1232 ADLGLCISANHVKEVIVGYSSINKIRLDKNSIYVLDNDRLAILVPHTNCGLY---MFQKQ 1288

Query: 1225 QL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNN 1281
             L   L S+V+ G + + R VI +E  E    Y L VEG  L ++M   GV G K  SN+
Sbjct: 1289 SLIDGLMSLVLSGEKFVKRGVIKKEGGE----YHLAVEGYGLLNIMGIPGVVGTKVKSNH 1344

Query: 1282 TYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAK 1341
              EV K LGIEAARS I++EI   M+ + + ID+RH  L+ D+MT +GEVLGI R G+ K
Sbjct: 1345 VIEVAKVLGIEAARSVIISEICKCMDAYSIEIDYRHMCLLGDVMTFRGEVLGINRFGIQK 1404

Query: 1342 MKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            M+ S L LASFE T++HLF+AA + + D I GVSECII G P+ +GTG   LL
Sbjct: 1405 MRTSTLMLASFEETNEHLFEAAVHNRRDPICGVSECIITGKPIKLGTGSFDLL 1457



 Score =  140 bits (352), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 93/244 (38%), Positives = 134/244 (54%), Gaps = 18/244 (7%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA+ NI TPII   L   +  + A I K R+E+TT+G +C+  E+++ P  
Sbjct: 1161 GVPRIKEIINATANIQTPIIEVPL-VSSKFEAALINKYRIEKTTIGNICKKFEDIYSPHG 1219

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS-------GHLTVSGHSFLILKPKDS 876
            SFI++ +D      L L +  + ++  I     I+           +      IL P  +
Sbjct: 1220 SFIILTIDQGICADLGLCISANHVKEVIVGYSSINKIRLDKNSIYVLDNDRLAILVPHTN 1279

Query: 877  SKSFNSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMAT 933
               +   M+Q + L   L S+V+ G + + R VI +E  E    Y L VEG  L ++M  
Sbjct: 1280 CGLY---MFQKQSLIDGLMSLVLSGEKFVKRGVIKKEGGE----YHLAVEGYGLLNIMGI 1332

Query: 934  YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
             GV G K  SN+  EV K LGIEAARS I++EI   M+ + + ID+RH  L+ D+MT +G
Sbjct: 1333 PGVVGTKVKSNHVIEVAKVLGIEAARSVIISEICKCMDAYSIEIDYRHMCLLGDVMTFRG 1392

Query: 994  EVLG 997
            EVLG
Sbjct: 1393 EVLG 1396



 Score =  136 bits (343), Expect = 8e-29,   Method: Compositional matrix adjust.
 Identities = 85/254 (33%), Positives = 130/254 (51%), Gaps = 46/254 (18%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           + +QS I I ++ +Y     + P P+G+LD R+GTN+ +  C TC   L++C+GH+GYID
Sbjct: 27  IAKQSEIPINNREIYYYLSNK-PFPYGVLDLRLGTNRNDQKCKTCNLGLTECLGHWGYID 85

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAK---LRNPALSYLVRKSL 209
           L LPVFHIG+F+  I IL  ICK   C+ +L+ E+    F+ +     +P    L +K L
Sbjct: 86  LHLPVFHIGFFKYTIQILSCICKK--CSYLLISEDNMKRFKDQALITTDP----LAKKIL 139

Query: 210 KKKILETTKKVSVCPHCGEINGVVKKC------GLLKISHEKYKNRTKKKDAIVEDLLAE 263
            K+++   +KV  CP C    G +K+         +KI H   + +  K   + ED    
Sbjct: 140 FKRLVAECRKVIKCPRCNSTQGSLKRIVKPTLDQFMKIRHTVKQKQGGKMQTVEED---- 195

Query: 264 YNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRL 323
                                 L+PL V  LF++I     P  L+   + KP +LI++ +
Sbjct: 196 ----------------------LDPLYVKSLFKSIN----PAHLLVLNIDKPENLIISSI 229

Query: 324 LVPPNCIRPSVISD 337
            VPP+CIRPSV  D
Sbjct: 230 PVPPSCIRPSVTLD 243



 Score =  103 bits (256), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 57/108 (52%), Positives = 69/108 (63%), Gaps = 14/108 (12%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSF 671
           +GFV NSFF+GL P EFFFHTM GREGL+DTAVKTAETGYMQRRL+K+LEDL V YD + 
Sbjct: 811 RGFVANSFFTGLDPQEFFFHTMSGREGLIDTAVKTAETGYMQRRLMKALEDLSVCYDHTV 870

Query: 672 DAA-------FYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSE 712
             +        YG      G+S C +    M      +K+LQA   S+
Sbjct: 871 RTSDGQVVQFLYGD----DGISPCSLGVFHME---DTLKMLQARSNSK 911



 Score = 50.4 bits (119), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 21/53 (39%), Positives = 33/53 (62%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           LM   +NL +P+NGE L+AA QDF++  YLLT K+ F ++ +   +  +   G
Sbjct: 497 LMGVLNNLTSPKNGEPLVAAVQDFLSASYLLTSKDYFLDKKKIFNLCCSFCDG 549



 Score = 41.2 bits (95), Expect = 4.4,   Method: Compositional matrix adjust.
 Identities = 19/35 (54%), Positives = 24/35 (68%)

Query: 671  FDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 705
            F+AA + + D I GVSECII G P+ +GTG   LL
Sbjct: 1423 FEAAVHNRRDPICGVSECIITGKPIKLGTGSFDLL 1457


>gi|326435508|gb|EGD81078.1| RNA polymerase III large subunit [Salpingoeca sp. ATCC 50818]
          Length = 1377

 Score =  223 bits (569), Expect = 5e-55,   Method: Compositional matrix adjust.
 Identities = 129/278 (46%), Positives = 182/278 (65%), Gaps = 12/278 (4%)

Query: 1146 EVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSGH 1202
            EV EY+      ++S++ +KLD+ RI  L LE+D+  + + I   R +      + +   
Sbjct: 1096 EVAEYVRIFCSDNESYVAVKLDLQRIANLFLEIDVQGVVFRIVSDRKLKVKPNDVDIKSA 1155

Query: 1203 SFLILKPKDSSKSFNSKMY---QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVE 1259
            S   + P+  ++  ++ ++    ++Q L +VV++G++ +NRA++++E   GV  +KL ++
Sbjct: 1156 SLFHVYPRPDTRKPSNPVHLLQALQQKLGTVVVQGLENVNRAIVNDEG--GV--HKLFID 1211

Query: 1260 GDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPM 1319
            G N+R VM+T GV G K   N+  EV KTLGIEAAR  IM +++ VM N+G+SID RH M
Sbjct: 1212 GTNMRGVMSTLGVLGEKVKCNHVMEVEKTLGIEAARQVIMDQVQYVMSNYGISIDPRHTM 1271

Query: 1320 LVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECII 1379
            L+ DLMT KGEVLGITR G+AKMK+SV  LASFE T DHLFDAA  G TD I GVSECII
Sbjct: 1272 LMGDLMTFKGEVLGITRFGIAKMKDSVFMLASFEKTIDHLFDAAMRGTTDPIEGVSECII 1331

Query: 1380 MGLPMNVGTGLIKLLQAVPRSEPVP--RTLLFDNPEFH 1415
            +G PM VGTG   LLQ+ P ++  P  R LLFD  E+H
Sbjct: 1332 VGKPMKVGTGAFSLLQSPPPNQQPPKRRKLLFDVDEYH 1369



 Score =  208 bits (530), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 128/292 (43%), Positives = 167/292 (57%), Gaps = 55/292 (18%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + D VLFNRQPSLH++SIM H+AK  P RTFRFNECVC PYNADFDGDEMN+H+PQTEEA
Sbjct: 451 EGDYVLFNRQPSLHRMSIMCHKAKPRPWRTFRFNECVCKPYNADFDGDEMNLHVPQTEEA 510

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A  LM   +NL TP NG+ LIAATQDFITG YLLT K+ F +R
Sbjct: 511 RAE--------------AAELMLTTNNLCTPCNGKPLIAATQDFITGAYLLTTKDVFLSR 556

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
               ++A   + D   +  +          P   ++   +WTGKQ+ SL+LKPN+  P  
Sbjct: 557 QDIAQLA-CYMGDGELLVHL---------PPPTIIKPMKLWTGKQVISLLLKPNKFDPTE 606

Query: 521 ANLKTKGRAYT---ANEEF-----------CHRDSYVILRNSELLAGSMDKSTLGSGGKA 566
             L+   R+Y    A +EF           C  D +V++R S+LL+G +DK  +G   K+
Sbjct: 607 IYLQANNRSYDKDYAKQEFGGKPTLGEKTLCPEDGFVLIRKSQLLSGFLDKGIIGE-SKS 665

Query: 567 NVFYIL--------LRDFGEDVAV--------TAMWRLSRMTSFYLMNRGFS 602
           ++FY L        L  F   V +          M RLS++T+ +LMNRGFS
Sbjct: 666 SIFYALLSSRLHPPLSSFISRVGILRCCVCGLQCMKRLSKLTTRFLMNRGFS 717



 Score =  177 bits (448), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 98/235 (41%), Positives = 152/235 (64%), Gaps = 10/235 (4%)

Query: 769  KEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILI 828
            +EIINA++ ISTP+I A L++  +  YAR VKGR+E  TL EV EY+      ++S++ +
Sbjct: 1055 QEIINAAKKISTPVIEAPLEEADNAAYARRVKGRIETITLEEVAEYVRIFCSDNESYVAV 1114

Query: 829  KLDMDRIRLLHLEVDIDSIRYCIERTRGIS---GHLTVSGHSFLILKPKDSSKSFNSKMY 885
            KLD+ RI  L LE+D+  + + I   R +      + +   S   + P+  ++  ++ ++
Sbjct: 1115 KLDLQRIANLFLEIDVQGVVFRIVSDRKLKVKPNDVDIKSASLFHVYPRPDTRKPSNPVH 1174

Query: 886  ---QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCS 942
                ++Q L +VV++G++ +NRA++++E   GV  +KL ++G N+R VM+T GV G K  
Sbjct: 1175 LLQALQQKLGTVVVQGLENVNRAIVNDEG--GV--HKLFIDGTNMRGVMSTLGVLGEKVK 1230

Query: 943  SNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             N+  EV KTLGIEAAR  IM +++ VM N+G+SID RH ML+ DLMT KGEVLG
Sbjct: 1231 CNHVMEVEKTLGIEAARQVIMDQVQYVMSNYGISIDPRHTMLMGDLMTFKGEVLG 1285



 Score =  171 bits (433), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 97/253 (38%), Positives = 143/253 (56%), Gaps = 9/253 (3%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           GT++ + ++Q+ S + + +  +Y     R  +  G LDRRMG   K   C+TC  ++ +C
Sbjct: 19  GTMSSQ-QMQRLSEVNVYAPEMYAAS-NRKAVDFGPLDRRMGAFDKATPCSTCALDMREC 76

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
           VGHFG+I+L LPVFHIGYF+  +N+LQ ICK  TC+RVL+ ++    +  +L  P L   
Sbjct: 77  VGHFGHIELELPVFHIGYFKATVNVLQRICK--TCSRVLMTDDLLFTYTDRLLAPHLESN 134

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEY 264
            R+++ K+  +  KK   CPHCG  N  VKK   +KI HE Y  + + +   + D LA  
Sbjct: 135 QRQAIIKEAGDLCKKTLRCPHCGAQNATVKKVPPMKIVHELYVKKHEAERTRLHDELAAA 194

Query: 265 NEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLL 324
            E V     +    +      LNPL VL+LF  IP  D  +L + A   +P  L+LT ++
Sbjct: 195 AEEVDGLRSLLRQDRAQ--DVLNPLRVLELFRNIPDSDCLILDLGA---RPESLLLTSII 249

Query: 325 VPPNCIRPSVISD 337
            PP CIRPSV+ D
Sbjct: 250 CPPGCIRPSVMRD 262



 Score =  108 bits (270), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 48/60 (80%), Positives = 55/60 (91%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV+NSF++GLTPTEFFFHTM GREGLVDTAVKTAETGYMQRRLVK+LEDL  +YD +
Sbjct: 845 ARGFVENSFYTGLTPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLVKALEDLSARYDTT 904



 Score = 57.0 bits (136), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 28/53 (52%), Positives = 35/53 (66%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           LM   +NL TP NG+ LIAATQDFITG YLLT K+ F +R    ++A  +  G
Sbjct: 517 LMLTTNNLCTPCNGKPLIAATQDFITGAYLLTTKDVFLSRQDIAQLACYMGDG 569



 Score = 56.6 bits (135), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 35/61 (57%), Positives = 40/61 (65%), Gaps = 2/61 (3%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVP--RTLLFDNPEF 725
            D  FDAA  G TD I GVSECII+G PM VGTG   LLQ+ P ++  P  R LLFD  E+
Sbjct: 1309 DHLFDAAMRGTTDPIEGVSECIIVGKPMKVGTGAFSLLQSPPPNQQPPKRRKLLFDVDEY 1368

Query: 726  H 726
            H
Sbjct: 1369 H 1369


>gi|84997133|ref|XP_953288.1| DNA-directed RNA polymerase III largest subunit (RPC homologue)
           [Theileria annulata strain Ankara]
 gi|65304284|emb|CAI76663.1| DNA-directed RNA polymerase III largest subunit (RPC homologue),
           putative [Theileria annulata]
          Length = 1648

 Score =  223 bits (568), Expect = 7e-55,   Method: Compositional matrix adjust.
 Identities = 121/313 (38%), Positives = 167/313 (53%), Gaps = 63/313 (20%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + D+V+FNRQPSLH+LSIM HRA+V+   TFRFNECVC PYNADFDGDEMN+HLPQT EA
Sbjct: 513 NGDIVIFNRQPSLHRLSIMCHRARVMSGSTFRFNECVCLPYNADFDGDEMNLHLPQTYEA 572

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA   LH LS++            NL TPRNGE LIA  QDF+   YLLT K+ F NR
Sbjct: 573 RAEA---LHLLSVL-----------KNLTTPRNGEPLIAPVQDFLCASYLLTSKDMFLNR 618

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           ++  ++ S     T  +             P   +    +WTGKQ+FS+++KPN    V 
Sbjct: 619 SEFSQVISYFTDGTIQV----------DLPPPSIIHPVTLWTGKQVFSVLIKPNNKSKVM 668

Query: 521 ANLKTKGRAYTANEEF--------------------------------------CHRDSY 542
            N++ + R YT   ++                                      C  D Y
Sbjct: 669 VNIRVREREYTDPNQYYKNLNKDNLEGGKVENTKSQTSSNDVKPVSFMKLDDCMCPSDGY 728

Query: 543 VILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFS 602
           V++  SEL+ GS+   +LG+  K  +FY L+      ++   M R+S+++S +L   G +
Sbjct: 729 VVIYKSELMCGSLGVRSLGA-SKGGLFYELMLKNSPKISSECMLRVSKLSSRWLSEFGMT 787

Query: 603 IGIGDVTPGQGFV 615
           IG+ DVTP +  +
Sbjct: 788 IGLDDVTPSKELI 800



 Score =  194 bits (494), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 130/362 (35%), Positives = 184/362 (50%), Gaps = 77/362 (21%)

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFH--------------------------- 1142
            Y ++  EP  A+GAL +QSIGEP TQMTLKTFH                           
Sbjct: 1288 YQKSLCEPGEAIGALGSQSIGEPATQMTLKTFHFAGVASMNVTLGVPRIQEIINATSLIA 1347

Query: 1143 ---------------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLH 1175
                           FA            G++C  I++++ P +S +L  L+ + I  LH
Sbjct: 1348 TPIIEVPLEDKTSYEFALKVKSKIEKTTLGQICLNIKQLYTPQNSKLLFTLNRNLIEQLH 1407

Query: 1176 LEVDIDSIRYCI---ERTRGISGHLTV---SGHSFLILKPKDSSKSF------------N 1217
            LE  I+S ++ I     T  I  +L +   +G    +  PK+S  S              
Sbjct: 1408 LE--INSNKFLIIPDFYTHHIYTYLDIIIETGSFGKVKIPKNSVYSIGDWQICIELPSNQ 1465

Query: 1218 SKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 1274
               +Q   L   L  +V+ G + I RAVI  E       Y++ VEG  L++VM +YGV  
Sbjct: 1466 QHFFQQNALISGLTQLVVAGYKSIKRAVIKRESTPQGPNYQIAVEGYGLQEVMGSYGVMS 1525

Query: 1275 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGI 1334
                SN+  EV K LGIEAARS I++EI+  M+ + + ID R+  L+ D+MT +GEV+GI
Sbjct: 1526 SAVKSNHVSEVAKVLGIEAARSVIISEIQKCMDAYSIDIDCRYMKLLGDVMTFRGEVVGI 1585

Query: 1335 TRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
             R G+ KM+ S L LASFE T+DHL +AA + + D I GVSECIIMG P+++GTG   +L
Sbjct: 1586 NRFGIQKMRSSALMLASFEETNDHLLEAALHHRRDPIKGVSECIIMGKPISLGTGSFDIL 1645

Query: 1395 QA 1396
             +
Sbjct: 1646 MS 1647



 Score =  149 bits (375), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 96/255 (37%), Positives = 144/255 (56%), Gaps = 23/255 (9%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRI+EIINA+  I+TPII   L+  T  ++A  VK ++E+TTLG++C  I++++ P +
Sbjct: 1332 GVPRIQEIINATSLIATPIIEVPLEDKTSYEFALKVKSKIEKTTLGQICLNIKQLYTPQN 1391

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCI---ERTRGISGHLTV---SGHSFLILKPKDSS 877
            S +L  L+ + I  LHLE  I+S ++ I     T  I  +L +   +G    +  PK+S 
Sbjct: 1392 SKLLFTLNRNLIEQLHLE--INSNKFLIIPDFYTHHIYTYLDIIIETGSFGKVKIPKNSV 1449

Query: 878  KSF------------NSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLV 922
             S                 +Q   L   L  +V+ G + I RAVI  E       Y++ V
Sbjct: 1450 YSIGDWQICIELPSNQQHFFQQNALISGLTQLVVAGYKSIKRAVIKRESTPQGPNYQIAV 1509

Query: 923  EGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHP 982
            EG  L++VM +YGV      SN+  EV K LGIEAARS I++EI+  M+ + + ID R+ 
Sbjct: 1510 EGYGLQEVMGSYGVMSSAVKSNHVSEVAKVLGIEAARSVIISEIQKCMDAYSIDIDCRYM 1569

Query: 983  MLVADLMTSKGEVLG 997
             L+ D+MT +GEV+G
Sbjct: 1570 KLLGDVMTFRGEVVG 1584



 Score =  135 bits (339), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 99/310 (31%), Positives = 147/310 (47%), Gaps = 43/310 (13%)

Query: 40  AATQDFI----TGGYLLTQKNAFFNRAQT---MRIASTLIAGRKVFFRGLIEGTVTKEDR 92
           A ++DF+    T    + + ++F   AQT   +R    L +  K     L    +   D 
Sbjct: 41  ANSKDFVKSEPTKKAEIVKSSSFMMEAQTEGFLRKEYVLPSTNKTIIDSLQFDVMASSD- 99

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGT--------NQKEANCTTCGQNLSDC 144
           + + S I+I  K LY  +  R P  +G LD R+G         N K+A C TCG+  ++C
Sbjct: 100 ISRASEIEIEHKQLYLIN-SRKPCLYGPLDSRLGCFLMVITGCNNKDAICETCGKGYNEC 158

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
           VGH+G+I L LPVFHIG+F+  I IL  ICK   C+ +LL EE    F    +      +
Sbjct: 159 VGHWGHIKLALPVFHIGFFKYTIQILYCICKK--CSSLLLSEESIKKFYELHKKAQDDPV 216

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEY 264
           ++  + K I++  KK+S CP C    GV+KK                    IV+ ++ ++
Sbjct: 217 LKPLIFKNIVQDCKKISKCPRCQSPQGVIKK--------------------IVKPIIDQF 256

Query: 265 NEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLL 324
            +        E+ K   + + LNPL V  LFE I     P+      +  P  LI++ L 
Sbjct: 257 MKLKHIVKYKESGKMKTVEEELNPLVVKHLFENID----PVHSKVLNIVHPEKLIISNLP 312

Query: 325 VPPNCIRPSV 334
            PPNCIRPSV
Sbjct: 313 APPNCIRPSV 322



 Score =  103 bits (258), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 59/127 (46%), Positives = 75/127 (59%), Gaps = 17/127 (13%)

Query: 601  FSIGIGDVTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSL 660
            F++G  D    +GFV NSFF+GL P EFFFHTM GREGL+DTAVKT+ETGYMQRRL+K +
Sbjct: 909  FTMGCKDAK-SRGFVANSFFTGLEPEEFFFHTMSGREGLIDTAVKTSETGYMQRRLMKVM 967

Query: 661  EDLCVQYDMSFDAA-------FYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEP 713
            EDL V YD S   +        YG  D +S +S+           T L   L  +    P
Sbjct: 968  EDLSVCYDYSVRTSDGQIVQFLYGD-DGLSSLSKSCF--------TNLKSSLDHIKHINP 1018

Query: 714  VPRTLLF 720
            + + L+F
Sbjct: 1019 INKQLIF 1025



 Score = 54.3 bits (129), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 25/53 (47%), Positives = 33/53 (62%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           L++   NL TPRNGE LIA  QDF+   YLLT K+ F NR++  ++ S    G
Sbjct: 579 LLSVLKNLTTPRNGEPLIAPVQDFLCASYLLTSKDMFLNRSEFSQVISYFTDG 631



 Score = 42.4 bits (98), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 19/40 (47%), Positives = 27/40 (67%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA 707
            D   +AA + + D I GVSECIIMG P+++GTG   +L +
Sbjct: 1608 DHLLEAALHHRRDPIKGVSECIIMGKPISLGTGSFDILMS 1647


>gi|196004556|ref|XP_002112145.1| hypothetical protein TRIADDRAFT_55877 [Trichoplax adhaerens]
 gi|190586044|gb|EDV26112.1| hypothetical protein TRIADDRAFT_55877 [Trichoplax adhaerens]
          Length = 258

 Score =  222 bits (566), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 122/234 (52%), Positives = 160/234 (68%), Gaps = 5/234 (2%)

Query: 1145 GEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCI---ERTRGISGHLTVSG 1201
            GEVCEYIEEV  P D ++ +K+DM+RI+LL LE+  ++IR  I    + +     + +  
Sbjct: 15   GEVCEYIEEVVSPTDCYLKLKIDMERIKLLKLEITKETIRASICNFPKLKLKPHDVVIED 74

Query: 1202 HSFLILKPKDSSK-SFNSKMYQMKQLLPSVVIKGVQGINRAVIH-EEDVEGVTKYKLLVE 1259
               +++ P +S K S    +  +K  +P+V++KG+  + R VIH +ED  G  K+KL VE
Sbjct: 75   PDIILVYPSESLKVSIFHGLQILKASIPNVIVKGIPTVTRTVIHVDEDASGNKKFKLYVE 134

Query: 1260 GDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPM 1319
            G++L  V+ T GVKG+  +SN+T  V K LGIEAAR+TI+ EI   M NHGM +D RH M
Sbjct: 135  GEDLLSVITTRGVKGIGTNSNHTTVVEKVLGIEAARATIINEILFTMVNHGMHLDNRHVM 194

Query: 1320 LVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISG 1373
            L+ADLMT KGEVLGITR GLAKMKESVL LASFENT+DHLFDAA  GQ D I G
Sbjct: 195  LLADLMTFKGEVLGITRFGLAKMKESVLMLASFENTTDHLFDAAICGQEDPIIG 248



 Score =  182 bits (463), Expect = 9e-43,   Method: Compositional matrix adjust.
 Identities = 100/207 (48%), Positives = 140/207 (67%), Gaps = 5/207 (2%)

Query: 796 ARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCI---E 852
           AR+VKGR+E+TTLGEVCEYIEEV  P D ++ +K+DM+RI+LL LE+  ++IR  I    
Sbjct: 2   ARMVKGRIEKTTLGEVCEYIEEVVSPTDCYLKLKIDMERIKLLKLEITKETIRASICNFP 61

Query: 853 RTRGISGHLTVSGHSFLILKPKDSSK-SFNSKMYQMKQLLPSVVIKGVQGINRAVIH-EE 910
           + +     + +     +++ P +S K S    +  +K  +P+V++KG+  + R VIH +E
Sbjct: 62  KLKLKPHDVVIEDPDIILVYPSESLKVSIFHGLQILKASIPNVIVKGIPTVTRTVIHVDE 121

Query: 911 DVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVM 970
           D  G  K+KL VEG++L  V+ T GVKG+  +SN+T  V K LGIEAAR+TI+ EI   M
Sbjct: 122 DASGNKKFKLYVEGEDLLSVITTRGVKGIGTNSNHTTVVEKVLGIEAARATIINEILFTM 181

Query: 971 ENHGMSIDFRHPMLVADLMTSKGEVLG 997
            NHGM +D RH ML+ADLMT KGEVLG
Sbjct: 182 VNHGMHLDNRHVMLLADLMTFKGEVLG 208


>gi|70928323|ref|XP_736389.1| hypothetical protein [Plasmodium chabaudi chabaudi]
 gi|56510883|emb|CAH84617.1| hypothetical protein PC301140.00.0 [Plasmodium chabaudi chabaudi]
          Length = 273

 Score =  222 bits (566), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 118/270 (43%), Positives = 166/270 (61%), Gaps = 31/270 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIM H+A+V+ ++TFRFNECVC+PYNADFDGDEMN+H+PQTEE+
Sbjct: 29  DGDIVLFNRQPSLHRMSIMCHKARVMDYKTFRFNECVCSPYNADFDGDEMNLHVPQTEES 88

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL               LM  K NL+TP+NGE++IA TQDF++  Y++T K+ F +R
Sbjct: 89  RAEAL--------------YLMNVKHNLITPKNGEVIIALTQDFLSASYVITNKDTFLDR 134

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPV-VFVRTAVIWTGKQIFSLILKPNRDCPV 519
                + S       DI             PV   ++   +WTGKQ+ S+++KPN++   
Sbjct: 135 DLFCLLCSYFSDAKIDI-----------ELPVPAILKPKELWTGKQLISVLIKPNKNENT 183

Query: 520 NANLKTKGRAYTANE---EFCHR-DSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
             N + K R Y+      ++  R DSYV    SEL+ GS+ K  LG+  K  +FY L+ +
Sbjct: 184 IINFEMKEREYSTKNGDLKYLSRDDSYVCFYKSELICGSLGKKVLGA-SKYGLFYYLIHN 242

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGI 605
               VA+  M R S+++S Y  N+G +IGI
Sbjct: 243 NSTQVALQIMNRFSKLSSRYFSNKGMTIGI 272



 Score = 52.4 bits (124), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 21/40 (52%), Positives = 31/40 (77%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           LM  K NL+TP+NGE++IA TQDF++  Y++T K+ F +R
Sbjct: 95  LMNVKHNLITPKNGEVIIALTQDFLSASYVITNKDTFLDR 134


>gi|336260159|ref|XP_003344876.1| hypothetical protein SMAC_06162 [Sordaria macrospora k-hell]
 gi|380089075|emb|CCC13019.1| unnamed protein product [Sordaria macrospora k-hell]
          Length = 1474

 Score =  222 bits (565), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 155/423 (36%), Positives = 214/423 (50%), Gaps = 97/423 (22%)

Query: 1056 FLEEFSKKESVTSHQD-KVSQPLREQIL-SHQDKIGHGRESN--PFPSACKAEACREKYV 1111
             L+EF+  E   +  D K+  P  E+I  +H D++    E+    F + C +     K+ 
Sbjct: 1007 LLKEFAAWEKKQNGGDIKMLDPEEEEIQQAHVDRVAKVSEATLRKFMNLCLS-----KFD 1061

Query: 1112 RAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEV------------------------ 1147
            +A++EP  AVGA+ AQSIGEPGTQMTLKTFHFAG                          
Sbjct: 1062 KAKVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIIGASKLISTP 1121

Query: 1148 ---CE---------------------------YIEEVFVPDDSFILIKLDMDRIRLLHLE 1177
               CE                           Y+E+V++PD + I++K+DM  +  + L 
Sbjct: 1122 VISCELENNVDIKAARIVKGKIEKTFISDVIQYVEDVWLPDVAKIVLKIDMQALSDMQLG 1181

Query: 1178 VDIDSIRYCI-------------------------ERTRGISGHLTVSGHSFLILKPKDS 1212
            + +  I   I                          R R  +    +     L+    ++
Sbjct: 1182 IGLREIMVAIVKAKKLKLKVEMDDLKIGPDNTIEAARVRAAA----IEKGQLLLTTSDET 1237

Query: 1213 SKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGV 1272
            +  F  ++  +K++LP+V I G     RA+I   +     ++K+LVEG  LR  M T GV
Sbjct: 1238 AADFQLRVNFLKRMLPAVPISGYPEAFRAIIQSSE---SNEHKVLVEGYGLRACMTTEGV 1294

Query: 1273 KGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL 1332
             G KC SN+  E    LGIEAAR+TI  EI  VM +  M ID RH  L+AD+MT KGE+L
Sbjct: 1295 IGTKCISNSIMECRDVLGIEAARTTIAKEIGSVMGD--MGIDPRHMDLLADVMTYKGEIL 1352

Query: 1333 GITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIK 1392
            GITRHGLAKM++SVL LASFE T DHLFDAA   +TD I GVSECIIMG  M +GTG  +
Sbjct: 1353 GITRHGLAKMRDSVLQLASFERTPDHLFDAAAGMKTDRILGVSECIIMGQTMKIGTGAFQ 1412

Query: 1393 LLQ 1395
            +++
Sbjct: 1413 VVR 1415



 Score =  207 bits (527), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 115/277 (41%), Positives = 154/277 (55%), Gaps = 59/277 (21%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHKLSIM+HRAKV P RTFR NECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 468 DGDIVLFNRQPSLHKLSIMSHRAKVRPWRTFRLNECVCTPYNADFDGDEMNLHLPQTEEA 527

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+                     NL+             DFIT  YLL+ K+ F +R
Sbjct: 528 RAEAI---------------------NLMG------------DFITAAYLLSSKDLFLDR 554

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                I + ++   + +             P   ++   +WTGKQIF+++++PN+  PV 
Sbjct: 555 KTFTYICTQMLLGETHL----------DLPPPTIIKPVEMWTGKQIFNVLMRPNKQSPVL 604

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            NL+ K + Y A             +  EL    +D   L    K +VFY++LRD+G + 
Sbjct: 605 VNLEAKNKVYKA-------------KPGELPDMDIDDCYL---VKNSVFYVILRDWGPEH 648

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           A  AM RL+++ +  L  RGFSIG+GDV P +   ++
Sbjct: 649 AAQAMNRLAKLCARTLTLRGFSIGVGDVYPSKDLTEH 685



 Score =  191 bits (485), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 105/271 (38%), Positives = 153/271 (56%), Gaps = 10/271 (3%)

Query: 79  FRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCG 138
           FR L  G  + +D V Q   +++    LY  +  R   PHG LD R+GT+ K   C TC 
Sbjct: 21  FRALQFGVQSHQDIVNQ-GVLEVSDNLLYDVENGRRTFPHGPLDPRLGTSSKTGTCETCN 79

Query: 139 QNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN 198
             L  C GHFG++ LPLPVFHIGY + +   LQ+ICK  TC++VLL EE  A F   LR 
Sbjct: 80  LPLQSCAGHFGHVRLPLPVFHIGYLKYIQATLQNICK--TCSKVLLEEEPKAKFLKALRA 137

Query: 199 PALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKY----KNRTKKKD 254
           P +  L R ++ KKI +  +K   CP+CG+  GV++K  ++K++H+K+    K+  +KK 
Sbjct: 138 PGIDNLKRSAILKKINDECRKQKTCPYCGDTQGVIRKLSVMKLTHDKFSHFNKSTAQKKV 197

Query: 255 AIVEDLL--AEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL 312
             V      + + +A  F P++E H K  +   ++PL+VL+LF+ I  ED  LL +N   
Sbjct: 198 PPVAKAAFDSSFIQAKTFTPDLEKHSKKAM-DDMDPLKVLKLFKKITAEDCELLGLNPSE 256

Query: 313 SKPSDLILTRLLVPPNCIRPSVISDLKSDND 343
            +P   +   L  PP CIRPSV  +  S+ D
Sbjct: 257 GRPEMFLWQYLPAPPICIRPSVQQEAASNED 287



 Score =  156 bits (394), Expect = 9e-35,   Method: Compositional matrix adjust.
 Identities = 97/259 (37%), Positives = 144/259 (55%), Gaps = 34/259 (13%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEII AS+ ISTP+I+  L+ + D+  ARIVKG++E+T + +V +Y+E+V++PD 
Sbjct: 1104 GVPRIKEIIGASKLISTPVISCELENNVDIKAARIVKGKIEKTFISDVIQYVEDVWLPDV 1163

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCI-------------------------ERTRGIS 858
            + I++K+DM  +  + L + +  I   I                          R R  +
Sbjct: 1164 AKIVLKIDMQALSDMQLGIGLREIMVAIVKAKKLKLKVEMDDLKIGPDNTIEAARVRAAA 1223

Query: 859  GHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKY 918
                +     L+    +++  F  ++  +K++LP+V I G     RA+I   +     ++
Sbjct: 1224 ----IEKGQLLLTTSDETAADFQLRVNFLKRMLPAVPISGYPEAFRAIIQSSE---SNEH 1276

Query: 919  KLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSID 978
            K+LVEG  LR  M T GV G KC SN+  E    LGIEAAR+TI  EI  VM +  M ID
Sbjct: 1277 KVLVEGYGLRACMTTEGVIGTKCISNSIMECRDVLGIEAARTTIAKEIGSVMGD--MGID 1334

Query: 979  FRHPMLVADLMTSKGEVLG 997
             RH  L+AD+MT KGE+LG
Sbjct: 1335 PRHMDLLADVMTYKGEILG 1353



 Score =  103 bits (256), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 45/59 (76%), Positives = 51/59 (86%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           P +GFV+NSF++GL PTEF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL  QYD
Sbjct: 802 PSKGFVRNSFYTGLVPTEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSTQYD 860



 Score = 43.5 bits (101), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 21/39 (53%), Positives = 27/39 (69%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
            D  FDAA   +TD I GVSECIIMG  M +GTG  ++++
Sbjct: 1377 DHLFDAAAGMKTDRILGVSECIIMGQTMKIGTGAFQVVR 1415


>gi|340056888|emb|CCC51227.1| DNA-directed RNA polymerase iii largest subunit [Trypanosoma vivax
           Y486]
          Length = 1533

 Score =  222 bits (565), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 116/271 (42%), Positives = 160/271 (59%), Gaps = 25/271 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + D+VLFNRQPSLH++S+MAHRA+VLP RTFRFNEC C PYNADFDGDEMNVH  QTEEA
Sbjct: 460 NGDIVLFNRQPSLHRVSMMAHRARVLPFRTFRFNECCCAPYNADFDGDEMNVHFVQTEEA 519

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL               LM+   N+++ +NGE +IA TQDF+   YL+T ++ F +R
Sbjct: 520 RAEALH--------------LMSTARNIISAKNGEPIIACTQDFLAAAYLVTARDVFLDR 565

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           +Q  +  S  +              +R   P + ++   +WTGKQ+F LI++P+ +  V 
Sbjct: 566 SQLSQFVSHWLGSGEQ---------FRLPVPAI-LKPVELWTGKQLFELIIRPSPEVGVL 615

Query: 521 ANLKTKGRAYT-ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            +L+   + Y+      C  + YV   +S  ++G MDK  LG G K  +F  L    G  
Sbjct: 616 LSLEAPTKFYSREGRHDCVAEGYVSFIDSRYISGRMDKRLLGGGSKDGLFARLHTLAGGQ 675

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
                M R+++ TS YL N GFS+G+GDV P
Sbjct: 676 YTARVMSRIAQFTSRYLTNYGFSLGLGDVAP 706



 Score =  144 bits (363), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 129/442 (29%), Positives = 212/442 (47%), Gaps = 67/442 (15%)

Query: 970  MENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVELKRLLDDIIAKNSSR-SDPS-----L 1023
            MEN G   D   P ++ +L       L   TP  +K  L+    K   +  +PS     +
Sbjct: 1097 MENRGDEEDKSDPCVLEELQVE----LIPLTPAMIKAFLEQCAQKYVRKFCEPSTPCGAI 1152

Query: 1024 SAQEILALSNE-TLDSKEFLQDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQIL 1082
            +AQ +   S + TL +  F   +S N  + + + +E  +   ++ +    ++ P+R+   
Sbjct: 1153 AAQSVGEPSTQMTLRTFHFAGVSSMNITQGVPRLVEVINANRNIAT--PVITAPVRQLP- 1209

Query: 1083 SHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFH 1142
                  G  + S  F         R ++V+AQ+E                  ++ L+   
Sbjct: 1210 ------GEEKSSESFVQ-------RVRHVKAQVE------------------RVLLR--- 1235

Query: 1143 FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCI--ERTRGISGH---- 1196
               EV   I EV    D  + + L+MD I  L L ++  ++R  I     R +S      
Sbjct: 1236 ---EVTLEIVEVCSARDFCLRVHLNMDVITRLQLPINAFTVRQRILAAAARPMSPLRILN 1292

Query: 1197 ----LTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVT 1252
                + +S  + ++     + ++ +  +  +  LLP VV+ G+ GINRA+I     E   
Sbjct: 1293 EDCVMAISPEALVVYPGYQTERNVHYLLRTILGLLPDVVVGGIGGINRAMISSNGTE--- 1349

Query: 1253 KYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMS 1312
               +L EG  LR VM+   V+G + + N+   + + LGIEAAR  I+ EI+ +++ + +S
Sbjct: 1350 ---VLAEGAELRAVMSLPSVEGSRVTCNHVAVIERVLGIEAARQVIVDEIQNILKAYSLS 1406

Query: 1313 IDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCIS 1372
            ID RH  L+ADLMT +G VLGITR+G+ KM  +VL LASFE T+DHL++AA   + D   
Sbjct: 1407 IDIRHVYLLADLMTQRGVVLGITRYGIQKMNFNVLTLASFERTTDHLYNAAATQRVDRNL 1466

Query: 1373 GVSECIIMGLPMNVGTGLIKLL 1394
             VS+ II+G  + +GT    LL
Sbjct: 1467 SVSDSIIVGKTVPLGTTSFGLL 1488



 Score =  138 bits (348), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 85/237 (35%), Positives = 130/237 (54%), Gaps = 11/237 (4%)

Query: 119 GLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPT 178
           G+ D R+G   + + C TCG    DCVGH G+IDL  PVFH+G+F  V+ I ++ICK   
Sbjct: 59  GVNDTRLGVCDRSSVCGTCGLGYVDCVGHPGHIDLGAPVFHLGFFSTVMRICRTICKR-- 116

Query: 179 CARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGL 238
           C+ VLL   +   ++ +L +  L  L R  L K I     K  VC  CG +NGVV++   
Sbjct: 117 CSHVLLDNVEIDYYKRRLSSTKLEPLQRAMLIKMIQTDAYKTRVCLKCGGLNGVVRRIRP 176

Query: 239 LKISHEKYKNRTKKKDAIVED----LLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQL 294
           +++ HEK +   ++ +  VED       E   A  +N  +E  + + +   L+P+ V QL
Sbjct: 177 MRLVHEKCRVVLRRGEESVEDPSKLFDVELRTARLYNKSLEECRDY-VHDFLDPVRVRQL 235

Query: 295 FEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRP---SVISDLKSDNDVVLFN 348
           F+AIP E+  LL +   +S P DL++T LLVPP  +RP   S  + ++ D+    +N
Sbjct: 236 FQAIPPEEFALLGLAPGVS-PLDLLMTTLLVPPVQVRPRGSSGTATIRDDDLTAQYN 291



 Score =  130 bits (327), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 87/252 (34%), Positives = 138/252 (54%), Gaps = 24/252 (9%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDK--------DTDLDYARIVKGRLERTTLGEVCEYI 815
            GVPR+ E+INA+RNI+TP+ITA + +        ++ +   R VK ++ER  L EV   I
Sbjct: 1182 GVPRLVEVINANRNIATPVITAPVRQLPGEEKSSESFVQRVRHVKAQVERVLLREVTLEI 1241

Query: 816  EEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCI--ERTRGISGH--------LTVSG 865
             EV    D  + + L+MD I  L L ++  ++R  I     R +S          + +S 
Sbjct: 1242 VEVCSARDFCLRVHLNMDVITRLQLPINAFTVRQRILAAAARPMSPLRILNEDCVMAISP 1301

Query: 866  HSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD 925
             + ++     + ++ +  +  +  LLP VV+ G+ GINRA+I     E      +L EG 
Sbjct: 1302 EALVVYPGYQTERNVHYLLRTILGLLPDVVVGGIGGINRAMISSNGTE------VLAEGA 1355

Query: 926  NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 985
             LR VM+   V+G + + N+   + + LGIEAAR  I+ EI+ +++ + +SID RH  L+
Sbjct: 1356 ELRAVMSLPSVEGSRVTCNHVAVIERVLGIEAARQVIVDEIQNILKAYSLSIDIRHVYLL 1415

Query: 986  ADLMTSKGEVLG 997
            ADLMT +G VLG
Sbjct: 1416 ADLMTQRGVVLG 1427



 Score =  100 bits (248), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 44/58 (75%), Positives = 53/58 (91%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV +SF+SGLTPTEFFFHTM GREGLVDTAVKTAETGY+ RRL+K++E+L V+YD
Sbjct: 832 ARGFVASSFYSGLTPTEFFFHTMAGREGLVDTAVKTAETGYIYRRLMKAMENLSVRYD 889



 Score = 49.3 bits (116), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 20/57 (35%), Positives = 35/57 (61%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVF 78
           LM+   N+++ +NGE +IA TQDF+   YL+T ++ F +R+Q  +  S  +   + F
Sbjct: 526 LMSTARNIISAKNGEPIIACTQDFLAAAYLVTARDVFLDRSQLSQFVSHWLGSGEQF 582


>gi|342183998|emb|CCC93479.1| DNA-directed RNA polymerase iii largest subunit [Trypanosoma
           congolense IL3000]
          Length = 1537

 Score =  222 bits (565), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 116/271 (42%), Positives = 162/271 (59%), Gaps = 25/271 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + D++LFNRQPSLH++S+MAHRA+VLP RTFRFNEC C PYNADFDGDEMNVH  QTEEA
Sbjct: 460 NGDLILFNRQPSLHRVSMMAHRARVLPFRTFRFNECCCAPYNADFDGDEMNVHFVQTEEA 519

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL               LM+   N+++ +NGE +IA TQDF+   YL T ++ FF+R
Sbjct: 520 RAEALQ--------------LMSTAKNIISTKNGEPIIACTQDFLAAAYLATGRDVFFDR 565

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +  ++ S  +       G + +F  R   P +   T  +WTGKQ+F LIL+P+ +  + 
Sbjct: 566 LEMSQMVSYWL-------GPVTQF--RLPIPAILKPTE-LWTGKQLFELILRPSPEVDIL 615

Query: 521 ANLKTKGRAYTANEEF-CHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
              +   + YT   +  C  + YV   +S  ++G +DK  LG G K  +F  L    G +
Sbjct: 616 LTFEAPTKFYTKKGKHDCASEGYVAFLDSCFISGRLDKKLLGGGAKDGLFARLHTLAGGE 675

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
                M R+++ T+ YL N GFS+G+GDV P
Sbjct: 676 YTARVMSRIAQFTTRYLTNYGFSLGLGDVAP 706



 Score =  176 bits (445), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 126/361 (34%), Positives = 179/361 (49%), Gaps = 78/361 (21%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYI 1151
            C +KY+R   EP T  GA+AAQS+GEP TQMTL+TFHFAG              EV    
Sbjct: 1138 CADKYIRKACEPGTPCGAIAAQSVGEPSTQMTLRTFHFAGVASMNITQGVPRLVEVINAN 1197

Query: 1152 EEVFVP------------DDS-------FILIKLDMDRIRL------------------- 1173
              +  P            D+S        + +K  ++R+ L                   
Sbjct: 1198 RSIATPVVTAPVLRMQGEDESSENFQKRVVFVKAQVERVLLREVASEIVEVCSSDVFYLR 1257

Query: 1174 LHLEVD-IDSIRYCI------ERTRGISGHL----------TVSGHSF--LILKPKDS-S 1213
            +HL +  I  +R  I      ER    +GHL           +  HS   L + P  S +
Sbjct: 1258 IHLNMSVIKKLRLPINAITVRERILAAAGHLMSPLRMISENCIEVHSLDTLAVYPYISDT 1317

Query: 1214 KSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVK 1273
            +  +  + ++  LLP VV+ G+ GINRA+I            +L EG  LR VM  +GV+
Sbjct: 1318 RWVHFTLRRILSLLPDVVVGGISGINRAMISS------AGNAILAEGAELRAVMNLWGVE 1371

Query: 1274 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 1333
              +   N+   V + LGIEAAR  I+ EI+ +++ + +SID RH  L+ADLMT +G VLG
Sbjct: 1372 STRVGCNHVAVVERVLGIEAARRVIVDEIQSILKAYSLSIDVRHIYLLADLMTQRGVVLG 1431

Query: 1334 ITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            ITR+G+ KM  +VL +ASFE T+DHL+ AA   + D    VS+ II+G  + +GT    L
Sbjct: 1432 ITRYGIQKMNFNVLTMASFERTTDHLYSAAATQRVDRNLSVSDSIIVGKSVPLGTTSFTL 1491

Query: 1394 L 1394
            L
Sbjct: 1492 L 1492



 Score =  138 bits (347), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 80/219 (36%), Positives = 123/219 (56%), Gaps = 8/219 (3%)

Query: 118 HGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNP 177
           +G+ D R+G   + + C TCG N  +CVGH G+IDL  PVFH+G+F  V+ I ++ICK  
Sbjct: 58  YGVNDTRLGVCDRISLCETCGLNNVECVGHPGHIDLEAPVFHLGFFSTVLRICRTICKR- 116

Query: 178 TCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCG 237
            C+ VLL + +   ++ +L +  L  L R +L K I     K  +C  CG +NGVV++  
Sbjct: 117 -CSHVLLDDTEIEYYKRRLSSSTLEPLQRMTLIKTIQTDAYKTHICLKCGGLNGVVRRVR 175

Query: 238 LLKISHEKYKNRTKKKDAIVED----LLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQ 293
            +++ HEKY    ++ +  VE        E   A  +N  I  +K+  +   L+P+ V Q
Sbjct: 176 PMRLVHEKYSVYLRRGEGSVEKPESFFDVELQTACAYNKTISENKE-NVHDFLDPVRVRQ 234

Query: 294 LFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRP 332
           LF A+P + + LL + A    P DL++T LLVPP  +RP
Sbjct: 235 LFLAVPPDQVVLLGL-APGVNPVDLLMTTLLVPPVQVRP 272



 Score =  133 bits (335), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 92/255 (36%), Positives = 141/255 (55%), Gaps = 30/255 (11%)

Query: 764  GVPRIKEIINASRNISTPIITAYL------DKDTDLDYARIV--KGRLERTTLGEVCEYI 815
            GVPR+ E+INA+R+I+TP++TA +      D+ ++    R+V  K ++ER  L EV   I
Sbjct: 1186 GVPRLVEVINANRSIATPVVTAPVLRMQGEDESSENFQKRVVFVKAQVERVLLREVASEI 1245

Query: 816  EEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHL----------TVSG 865
             EV   D  ++ I L+M  I+ L L ++  ++R   ER    +GHL           +  
Sbjct: 1246 VEVCSSDVFYLRIHLNMSVIKKLRLPINAITVR---ERILAAAGHLMSPLRMISENCIEV 1302

Query: 866  HSF--LILKPKDS-SKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLV 922
            HS   L + P  S ++  +  + ++  LLP VV+ G+ GINRA+I            +L 
Sbjct: 1303 HSLDTLAVYPYISDTRWVHFTLRRILSLLPDVVVGGISGINRAMISS------AGNAILA 1356

Query: 923  EGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHP 982
            EG  LR VM  +GV+  +   N+   V + LGIEAAR  I+ EI+ +++ + +SID RH 
Sbjct: 1357 EGAELRAVMNLWGVESTRVGCNHVAVVERVLGIEAARRVIVDEIQSILKAYSLSIDVRHI 1416

Query: 983  MLVADLMTSKGEVLG 997
             L+ADLMT +G VLG
Sbjct: 1417 YLLADLMTQRGVVLG 1431



 Score =  105 bits (262), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 45/58 (77%), Positives = 54/58 (93%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV NSF+SGL+PTEFFFHTM GREGLVDTAVKTAETGY+ RRL+K++E+LCV+YD
Sbjct: 832 ARGFVANSFYSGLSPTEFFFHTMAGREGLVDTAVKTAETGYIYRRLMKAMENLCVRYD 889



 Score = 47.8 bits (112), Expect = 0.041,   Method: Compositional matrix adjust.
 Identities = 19/48 (39%), Positives = 32/48 (66%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIAS 69
           LM+   N+++ +NGE +IA TQDF+   YL T ++ FF+R +  ++ S
Sbjct: 526 LMSTAKNIISTKNGEPIIACTQDFLAAAYLATGRDVFFDRLEMSQMVS 573


>gi|71746952|ref|XP_822531.1| DNA-directed RNA polymerase III largest subunit [Trypanosoma
           brucei]
 gi|70832199|gb|EAN77703.1| DNA-directed RNA polymerase III largest subunit [Trypanosoma brucei
           brucei strain 927/4 GUTat10.1]
          Length = 1530

 Score =  221 bits (563), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 116/271 (42%), Positives = 164/271 (60%), Gaps = 25/271 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + D+VLFNRQPSLH++S+MAHRA+VLP RTFRFNEC C PYNADFDGDEMNVH  QTE+A
Sbjct: 460 NGDLVLFNRQPSLHRVSMMAHRARVLPFRTFRFNECCCAPYNADFDGDEMNVHFVQTEKA 519

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL               LM+   N+++ +NGE +IA TQDF+   YL+T ++ FF+R
Sbjct: 520 RAEALQ--------------LMSTARNIISAKNGEPIIACTQDFLAAAYLVTSRDVFFDR 565

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +  ++ S  +       G + +F  R   P + ++   +WTGKQ+F LI++P+ +  V 
Sbjct: 566 GEFSQMVSHWL-------GPVTQF--RLPIPAI-LKPVELWTGKQLFELIVRPSPEVDVL 615

Query: 521 ANLKTKGRAYT-ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            + +   + YT   +  C  + YV   +S  ++G +DK  LG G K  +F  L    G  
Sbjct: 616 LSFEAPTKFYTRKGKHDCAEEGYVAFLDSCFISGRLDKKLLGGGAKDGLFARLHTIAGGG 675

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
                M R+++ TS YL N GFS+G+GDV P
Sbjct: 676 YTARVMSRIAQFTSRYLTNYGFSLGLGDVAP 706



 Score =  150 bits (379), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 103/291 (35%), Positives = 153/291 (52%), Gaps = 32/291 (10%)

Query: 1146 EVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGH--------- 1196
            EV   I EV    + ++ + L+M  I  LHL ++  ++R   +R    +GH         
Sbjct: 1232 EVVSEIVEVCSDTEFYLRVHLNMSVITKLHLPINAITVR---QRILAAAGHTMSPLRMLN 1288

Query: 1197 ---LTVSGHSFLILKPK-DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVT 1252
               + V     L + P    ++  +  + ++  LLP VV+ G+ GINRA+I     E   
Sbjct: 1289 EDCIEVFSLDTLAVYPHFQDARWVHFSLRRILGLLPDVVVGGIGGINRAMISSNGTE--- 1345

Query: 1253 KYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMS 1312
               +L EG  LR VM  +GV   +   N+   V + LGIEAAR  I+ EI+ +++ + +S
Sbjct: 1346 ---VLAEGAELRAVMNLWGVDSTRVVCNHVAVVERVLGIEAARRVIVDEIQNILKAYSLS 1402

Query: 1313 IDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCIS 1372
            ID RH  L+ADLMT +G VLGITR+G+ KM  +VL +ASFE T+DHL++AA   + D   
Sbjct: 1403 IDVRHVYLLADLMTQRGVVLGITRYGIQKMNFNVLTMASFERTTDHLYNAAATQRVDRDL 1462

Query: 1373 GVSECIIMGLPMNVGTGLIKLL-------QAVPRSEPVPRTLLFDNPEFHT 1416
             VS+ II+G P+ +GT    LL         +P    V R +    P FHT
Sbjct: 1463 SVSDSIIVGKPVPLGTTSFDLLLDGSISNDVLPPQRCVKRGM---GPNFHT 1510



 Score =  138 bits (347), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 80/219 (36%), Positives = 126/219 (57%), Gaps = 8/219 (3%)

Query: 118 HGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNP 177
           +G+ D R+G   + + C TCG N  +CVGH G+IDL  PVFH+G+F  V+ I ++ICK  
Sbjct: 58  YGVNDARLGVCDRLSICETCGLNSIECVGHPGHIDLEAPVFHLGFFTTVLRICRTICKR- 116

Query: 178 TCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCG 237
            C+ VLL + +   ++ +L + +L  L R  L K I     K  VC  CG +NGVV++  
Sbjct: 117 -CSHVLLDDTEIDYYKRRLSSSSLEPLQRTMLIKTIQTDAYKTRVCLKCGGLNGVVRRVR 175

Query: 238 LLKISHEKYKNRTKKKDAIVED----LLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQ 293
            +++ HEKY    ++ +   E+      AE   A  +N  +   ++F +   L+P+ V Q
Sbjct: 176 PMRLVHEKYHVEPRRGEGPRENPGGFFDAELRTACAYNKVVGECREF-VHDFLDPVRVRQ 234

Query: 294 LFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRP 332
           LF A+P  ++ LL +   +S P+DL++T LLVPP  +RP
Sbjct: 235 LFLAVPPGEVILLGLAPGVS-PTDLLMTTLLVPPVPVRP 272



 Score =  132 bits (332), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 90/255 (35%), Positives = 138/255 (54%), Gaps = 30/255 (11%)

Query: 764  GVPRIKEIINASRNISTPIITA-YLDKDTDLDY-------ARIVKGRLERTTLGEVCEYI 815
            GVPR+ E+INA+RNI+TP++TA  L  + + ++       AR VK ++ER  L EV   I
Sbjct: 1178 GVPRLVEVINANRNIATPVVTAPVLLMEGEENHCEIFRKRARFVKAQIERVLLREVVSEI 1237

Query: 816  EEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGH------------LTV 863
             EV    + ++ + L+M  I  LHL ++  ++R   +R    +GH            + V
Sbjct: 1238 VEVCSDTEFYLRVHLNMSVITKLHLPINAITVR---QRILAAAGHTMSPLRMLNEDCIEV 1294

Query: 864  SGHSFLILKPK-DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLV 922
                 L + P    ++  +  + ++  LLP VV+ G+ GINRA+I     E      +L 
Sbjct: 1295 FSLDTLAVYPHFQDARWVHFSLRRILGLLPDVVVGGIGGINRAMISSNGTE------VLA 1348

Query: 923  EGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHP 982
            EG  LR VM  +GV   +   N+   V + LGIEAAR  I+ EI+ +++ + +SID RH 
Sbjct: 1349 EGAELRAVMNLWGVDSTRVVCNHVAVVERVLGIEAARRVIVDEIQNILKAYSLSIDVRHV 1408

Query: 983  MLVADLMTSKGEVLG 997
             L+ADLMT +G VLG
Sbjct: 1409 YLLADLMTQRGVVLG 1423



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 44/58 (75%), Positives = 53/58 (91%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV NSF+SGL+PTEFFFHTM GREGLVDTAVKTAETGY+ RRL+K++E+L V+YD
Sbjct: 832 ARGFVANSFYSGLSPTEFFFHTMAGREGLVDTAVKTAETGYIYRRLMKAMENLSVRYD 889



 Score = 64.7 bits (156), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 27/40 (67%), Positives = 31/40 (77%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            C  KY+R   EP T  GA+AAQS+GEP TQMTL+TFHFAG
Sbjct: 1130 CASKYLRKACEPGTPCGAIAAQSVGEPSTQMTLRTFHFAG 1169



 Score = 49.7 bits (117), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 19/48 (39%), Positives = 33/48 (68%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIAS 69
           LM+   N+++ +NGE +IA TQDF+   YL+T ++ FF+R +  ++ S
Sbjct: 526 LMSTARNIISAKNGEPIIACTQDFLAAAYLVTSRDVFFDRGEFSQMVS 573


>gi|261332267|emb|CBH15261.1| DNA-directed RNA polymerase iii largest subunit [Trypanosoma brucei
           gambiense DAL972]
          Length = 1530

 Score =  221 bits (563), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 116/271 (42%), Positives = 164/271 (60%), Gaps = 25/271 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + D+VLFNRQPSLH++S+MAHRA+VLP RTFRFNEC C PYNADFDGDEMNVH  QTE+A
Sbjct: 460 NGDLVLFNRQPSLHRVSMMAHRARVLPFRTFRFNECCCAPYNADFDGDEMNVHFVQTEKA 519

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL               LM+   N+++ +NGE +IA TQDF+   YL+T ++ FF+R
Sbjct: 520 RAEALQ--------------LMSTARNIISAKNGEPIIACTQDFLAAAYLVTSRDVFFDR 565

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +  ++ S  +       G + +F  R   P + ++   +WTGKQ+F LI++P+ +  V 
Sbjct: 566 GEFSQMVSHWL-------GPVTQF--RLPIPAI-LKPVELWTGKQLFELIVRPSPEVDVL 615

Query: 521 ANLKTKGRAYT-ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            + +   + YT   +  C  + YV   +S  ++G +DK  LG G K  +F  L    G  
Sbjct: 616 LSFEAPTKFYTRKGKHDCAEEGYVAFLDSCFISGRLDKKLLGGGAKDGLFARLHTIAGGG 675

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
                M R+++ TS YL N GFS+G+GDV P
Sbjct: 676 YTARVMSRIAQFTSRYLTNYGFSLGLGDVAP 706



 Score =  149 bits (376), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 103/291 (35%), Positives = 153/291 (52%), Gaps = 32/291 (10%)

Query: 1146 EVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGH--------- 1196
            EV   I EV    + ++ + L+M  I  LHL ++  ++R   +R    +GH         
Sbjct: 1232 EVVSEIVEVCSDTEFYLRVHLNMSVITKLHLPINAITVR---QRILAAAGHTMSPLRMLN 1288

Query: 1197 ---LTVSGHSFLILKPK-DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVT 1252
               + V     L + P    ++  +  + ++  LLP VV+ G+ GINRA+I     E   
Sbjct: 1289 EDCIEVFSLDTLAVYPHFQDARWVHFSLRRILGLLPDVVVGGIGGINRAMISSNGTE--- 1345

Query: 1253 KYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMS 1312
               +L EG  LR VM  +GV   +   N+   V + LGIEAAR  I+ EI+ +++ + +S
Sbjct: 1346 ---VLAEGAELRAVMNLWGVDSTRVICNHVAVVERVLGIEAARRVIVDEIQNILKAYSLS 1402

Query: 1313 IDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCIS 1372
            ID RH  L+ADLMT +G VLGITR+G+ KM  +VL +ASFE T+DHL++AA   + D   
Sbjct: 1403 IDVRHVYLLADLMTQRGVVLGITRYGIQKMNFNVLTMASFERTTDHLYNAAATQRVDRDL 1462

Query: 1373 GVSECIIMGLPMNVGTGLIKLL-------QAVPRSEPVPRTLLFDNPEFHT 1416
             VS+ II+G P+ +GT    LL         +P    V R +    P FHT
Sbjct: 1463 SVSDSIIVGKPVPLGTTSFDLLLDGSISNDILPPQRCVKRGM---GPNFHT 1510



 Score =  138 bits (347), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 80/219 (36%), Positives = 126/219 (57%), Gaps = 8/219 (3%)

Query: 118 HGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNP 177
           +G+ D R+G   + + C TCG N  +CVGH G+IDL  PVFH+G+F  V+ I ++ICK  
Sbjct: 58  YGVNDARLGVCDRLSICETCGLNSIECVGHPGHIDLEAPVFHLGFFTTVLRICRTICKR- 116

Query: 178 TCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCG 237
            C+ VLL + +   ++ +L + +L  L R  L K I     K  VC  CG +NGVV++  
Sbjct: 117 -CSHVLLDDTEIDYYKRRLSSSSLEPLQRTMLIKTIQTDAYKTRVCLKCGGLNGVVRRVR 175

Query: 238 LLKISHEKYKNRTKKKDAIVED----LLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQ 293
            +++ HEKY    ++ +   E+      AE   A  +N  +   ++F +   L+P+ V Q
Sbjct: 176 PMRLVHEKYHVEPRRGEGPRENPGGFFDAELRTACAYNKVVGECREF-VHDFLDPVRVRQ 234

Query: 294 LFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRP 332
           LF A+P  ++ LL +   +S P+DL++T LLVPP  +RP
Sbjct: 235 LFLAVPPGEVILLGLAPGVS-PTDLLMTTLLVPPVPVRP 272



 Score =  132 bits (331), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 90/255 (35%), Positives = 138/255 (54%), Gaps = 30/255 (11%)

Query: 764  GVPRIKEIINASRNISTPIITA-YLDKDTDLDY-------ARIVKGRLERTTLGEVCEYI 815
            GVPR+ E+INA+RNI+TP++TA  L  + + ++       AR VK ++ER  L EV   I
Sbjct: 1178 GVPRLVEVINANRNIATPVVTAPVLLMEGEENHCEIFRKRARFVKAQIERVLLREVVSEI 1237

Query: 816  EEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGH------------LTV 863
             EV    + ++ + L+M  I  LHL ++  ++R   +R    +GH            + V
Sbjct: 1238 VEVCSDTEFYLRVHLNMSVITKLHLPINAITVR---QRILAAAGHTMSPLRMLNEDCIEV 1294

Query: 864  SGHSFLILKPK-DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLV 922
                 L + P    ++  +  + ++  LLP VV+ G+ GINRA+I     E      +L 
Sbjct: 1295 FSLDTLAVYPHFQDARWVHFSLRRILGLLPDVVVGGIGGINRAMISSNGTE------VLA 1348

Query: 923  EGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHP 982
            EG  LR VM  +GV   +   N+   V + LGIEAAR  I+ EI+ +++ + +SID RH 
Sbjct: 1349 EGAELRAVMNLWGVDSTRVICNHVAVVERVLGIEAARRVIVDEIQNILKAYSLSIDVRHV 1408

Query: 983  MLVADLMTSKGEVLG 997
             L+ADLMT +G VLG
Sbjct: 1409 YLLADLMTQRGVVLG 1423



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 44/58 (75%), Positives = 53/58 (91%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV NSF+SGL+PTEFFFHTM GREGLVDTAVKTAETGY+ RRL+K++E+L V+YD
Sbjct: 832 ARGFVANSFYSGLSPTEFFFHTMAGREGLVDTAVKTAETGYIYRRLMKAMENLSVRYD 889



 Score = 64.7 bits (156), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 27/40 (67%), Positives = 31/40 (77%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            C  KY+R   EP T  GA+AAQS+GEP TQMTL+TFHFAG
Sbjct: 1130 CASKYLRKACEPGTPCGAIAAQSVGEPSTQMTLRTFHFAG 1169



 Score = 49.7 bits (117), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 19/48 (39%), Positives = 33/48 (68%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIAS 69
           LM+   N+++ +NGE +IA TQDF+   YL+T ++ FF+R +  ++ S
Sbjct: 526 LMSTARNIISAKNGEPIIACTQDFLAAAYLVTSRDVFFDRGEFSQMVS 573


>gi|133355|sp|P08968.1|RPC1_TRYBB RecName: Full=DNA-directed RNA polymerase III subunit RPC1;
           Short=RNA polymerase III subunit C1; AltName:
           Full=DNA-directed RNA polymerase III largest subunit;
           AltName: Full=RNA polymerase III subunit C160
 gi|10524|emb|CAA31014.1| unnamed protein product [Trypanosoma brucei]
          Length = 1530

 Score =  221 bits (562), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 116/271 (42%), Positives = 164/271 (60%), Gaps = 25/271 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + D+VLFNRQPSLH++S+MAHRA+VLP RTFRFNEC C PYNADFDGDEMNVH  QTE+A
Sbjct: 460 NGDLVLFNRQPSLHRVSMMAHRARVLPFRTFRFNECCCAPYNADFDGDEMNVHFVQTEKA 519

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL               LM+   N+++ +NGE +IA TQDF+   YL+T ++ FF+R
Sbjct: 520 RAEALQ--------------LMSTARNIISAKNGEPIIACTQDFLAAAYLVTSRDVFFDR 565

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +  ++ S  +       G + +F  R   P + ++   +WTGKQ+F LI++P+ +  V 
Sbjct: 566 GEFSQMVSHWL-------GPVTQF--RLPIPAI-LKPVELWTGKQLFELIVRPSPEVDVL 615

Query: 521 ANLKTKGRAYT-ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            + +   + YT   +  C  + YV   +S  ++G +DK  LG G K  +F  L    G  
Sbjct: 616 LSFEAPTKFYTRKGKHDCAEEGYVAFLDSCFISGRLDKKLLGGGAKDGLFARLHTIAGGG 675

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
                M R+++ TS YL N GFS+G+GDV P
Sbjct: 676 YTARVMSRIAQFTSRYLTNYGFSLGLGDVAP 706



 Score =  149 bits (377), Expect = 9e-33,   Method: Compositional matrix adjust.
 Identities = 103/291 (35%), Positives = 153/291 (52%), Gaps = 32/291 (10%)

Query: 1146 EVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGH--------- 1196
            EV   I EV    + ++ + L+M  I  LHL ++  ++R   +R    +GH         
Sbjct: 1232 EVVSEIVEVCSDTEFYLRVHLNMSVITKLHLPINAITVR---QRILAAAGHTMSPLRMLN 1288

Query: 1197 ---LTVSGHSFLILKPK-DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVT 1252
               + V     L + P    ++  +  + ++  LLP VV+ G+ GINRA+I     E   
Sbjct: 1289 EDCIEVFSLDTLAVYPHFQDARWVHFSLRRILGLLPDVVVGGIGGINRAMISSNGTE--- 1345

Query: 1253 KYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMS 1312
               +L EG  LR VM  +GV   +   N+   V + LGIEAAR  I+ EI+ +++ + +S
Sbjct: 1346 ---VLAEGAELRAVMNLWGVDSTRVVCNHVAVVERVLGIEAARRVIVDEIQNILKAYSLS 1402

Query: 1313 IDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCIS 1372
            ID RH  L+ADLMT +G VLGITR+G+ KM  +VL +ASFE T+DHL++AA   + D   
Sbjct: 1403 IDVRHVYLLADLMTQRGVVLGITRYGIQKMNFNVLTMASFERTTDHLYNAAATQRVDRDL 1462

Query: 1373 GVSECIIMGLPMNVGTGLIKLL-------QAVPRSEPVPRTLLFDNPEFHT 1416
             VS+ II+G P+ +GT    LL         +P    V R +    P FHT
Sbjct: 1463 SVSDSIIVGKPVPLGTTSFDLLLDGSISNDILPPQRCVKRGM---GPNFHT 1510



 Score =  138 bits (347), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 80/219 (36%), Positives = 126/219 (57%), Gaps = 8/219 (3%)

Query: 118 HGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNP 177
           +G+ D R+G   + + C TCG N  +CVGH G+IDL  PVFH+G+F  V+ I ++ICK  
Sbjct: 58  YGVNDARLGVCDRLSICETCGLNSIECVGHPGHIDLEAPVFHLGFFTTVLRICRTICKR- 116

Query: 178 TCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCG 237
            C+ VLL + +   ++ +L + +L  L R  L K I     K  VC  CG +NGVV++  
Sbjct: 117 -CSHVLLDDTEIDYYKRRLSSSSLEPLQRTMLIKTIQTDAYKTRVCLKCGGLNGVVRRVR 175

Query: 238 LLKISHEKYKNRTKKKDAIVED----LLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQ 293
            +++ HEKY    ++ +   E+      AE   A  +N  +   ++F +   L+P+ V Q
Sbjct: 176 PMRLVHEKYHVEPRRGEGPRENPGGFFDAELRTACAYNKVVGECREF-VHDFLDPVRVRQ 234

Query: 294 LFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRP 332
           LF A+P  ++ LL +   +S P+DL++T LLVPP  +RP
Sbjct: 235 LFLAVPPGEVILLGLAPGVS-PTDLLMTTLLVPPVPVRP 272



 Score =  132 bits (332), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 90/255 (35%), Positives = 138/255 (54%), Gaps = 30/255 (11%)

Query: 764  GVPRIKEIINASRNISTPIITA-YLDKDTDLDY-------ARIVKGRLERTTLGEVCEYI 815
            GVPR+ E+INA+RNI+TP++TA  L  + + ++       AR VK ++ER  L EV   I
Sbjct: 1178 GVPRLVEVINANRNIATPVVTAPVLLMEGEENHCEIFRKRARFVKAQIERVLLREVVSEI 1237

Query: 816  EEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGH------------LTV 863
             EV    + ++ + L+M  I  LHL ++  ++R   +R    +GH            + V
Sbjct: 1238 VEVCSDTEFYLRVHLNMSVITKLHLPINAITVR---QRILAAAGHTMSPLRMLNEDCIEV 1294

Query: 864  SGHSFLILKPK-DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLV 922
                 L + P    ++  +  + ++  LLP VV+ G+ GINRA+I     E      +L 
Sbjct: 1295 FSLDTLAVYPHFQDARWVHFSLRRILGLLPDVVVGGIGGINRAMISSNGTE------VLA 1348

Query: 923  EGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHP 982
            EG  LR VM  +GV   +   N+   V + LGIEAAR  I+ EI+ +++ + +SID RH 
Sbjct: 1349 EGAELRAVMNLWGVDSTRVVCNHVAVVERVLGIEAARRVIVDEIQNILKAYSLSIDVRHV 1408

Query: 983  MLVADLMTSKGEVLG 997
             L+ADLMT +G VLG
Sbjct: 1409 YLLADLMTQRGVVLG 1423



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 44/58 (75%), Positives = 53/58 (91%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV NSF+SGL+PTEFFFHTM GREGLVDTAVKTAETGY+ RRL+K++E+L V+YD
Sbjct: 832 ARGFVANSFYSGLSPTEFFFHTMAGREGLVDTAVKTAETGYIYRRLMKAMENLSVRYD 889



 Score = 64.7 bits (156), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 27/40 (67%), Positives = 31/40 (77%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            C  KY+R   EP T  GA+AAQS+GEP TQMTL+TFHFAG
Sbjct: 1130 CASKYLRKACEPGTPCGAIAAQSVGEPSTQMTLRTFHFAG 1169



 Score = 49.7 bits (117), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 19/48 (39%), Positives = 33/48 (68%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIAS 69
           LM+   N+++ +NGE +IA TQDF+   YL+T ++ FF+R +  ++ S
Sbjct: 526 LMSTARNIISAKNGEPIIACTQDFLAAAYLVTSRDVFFDRGEFSQMVS 573


>gi|162223|gb|AAA30233.1| RNA polymerase III [Trypanosoma brucei]
          Length = 1530

 Score =  221 bits (562), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 116/271 (42%), Positives = 164/271 (60%), Gaps = 25/271 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + D+VLFNRQPSLH++S+MAHRA+VLP RTFRFNEC C PYNADFDGDEMNVH  QTE+A
Sbjct: 460 NGDLVLFNRQPSLHRVSMMAHRARVLPFRTFRFNECCCAPYNADFDGDEMNVHFVQTEKA 519

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL               LM+   N+++ +NGE +IA TQDF+   YL+T ++ FF+R
Sbjct: 520 RAEALQ--------------LMSTARNIISAKNGEPIIACTQDFLAAAYLVTSRDVFFDR 565

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +  ++ S  +       G + +F  R   P + ++   +WTGKQ+F LI++P+ +  V 
Sbjct: 566 GEFSQMVSHWL-------GPVTQF--RLPIPAI-LKPVELWTGKQLFELIVRPSPEVDVL 615

Query: 521 ANLKTKGRAYT-ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            + +   + YT   +  C  + YV   +S  ++G +DK  LG G K  +F  L    G  
Sbjct: 616 LSFEAPTKFYTRKGKHDCAEEGYVAFLDSCFISGRLDKKLLGGGAKDGLFARLHTIAGGG 675

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
                M R+++ TS YL N GFS+G+GDV P
Sbjct: 676 YTARVMSRIAQFTSRYLTNYGFSLGLGDVAP 706



 Score =  150 bits (378), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 103/291 (35%), Positives = 153/291 (52%), Gaps = 32/291 (10%)

Query: 1146 EVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGH--------- 1196
            EV   I EV    + ++ + L+M  I  LHL ++  ++R   +R    +GH         
Sbjct: 1232 EVVSEIVEVCSDTEFYLRVHLNMSVITKLHLPINAITVR---QRILAAAGHTMSPLRMLN 1288

Query: 1197 ---LTVSGHSFLILKPK-DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVT 1252
               + V     L + P    ++  +  + ++  LLP VV+ G+ GINRA+I     E   
Sbjct: 1289 EDCIEVFSLDTLAVYPHFQDARWVHFSLRRILGLLPEVVVGGIGGINRAMISSNGTE--- 1345

Query: 1253 KYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMS 1312
               +L EG  LR VM  +GV   +   N+   V + LGIEAAR  I+ EI+ +++ + +S
Sbjct: 1346 ---VLAEGAELRAVMNLWGVDSTRVVCNHVAVVERVLGIEAARRVIVDEIQNILKAYSLS 1402

Query: 1313 IDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCIS 1372
            ID RH  L+ADLMT +G VLGITR+G+ KM  +VL +ASFE T+DHL++AA   + D   
Sbjct: 1403 IDVRHVYLLADLMTQRGVVLGITRYGIQKMNFNVLTMASFERTTDHLYNAAATQRVDRDL 1462

Query: 1373 GVSECIIMGLPMNVGTGLIKLL-------QAVPRSEPVPRTLLFDNPEFHT 1416
             VS+ II+G P+ +GT    LL         +P    V R +    P FHT
Sbjct: 1463 SVSDSIIVGKPVPLGTTSFDLLLDGSISNDVLPPQRCVKRGM---GPNFHT 1510



 Score =  138 bits (347), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 80/219 (36%), Positives = 126/219 (57%), Gaps = 8/219 (3%)

Query: 118 HGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNP 177
           +G+ D R+G   + + C TCG N  +CVGH G+IDL  PVFH+G+F  V+ I ++ICK  
Sbjct: 58  YGVNDARLGVCDRLSICETCGLNSIECVGHPGHIDLEAPVFHLGFFTTVLRICRTICKR- 116

Query: 178 TCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCG 237
            C+ VLL + +   ++ +L + +L  L R  L K I     K  VC  CG +NGVV++  
Sbjct: 117 -CSHVLLDDTEIDYYKRRLSSSSLEPLQRTMLIKTIQTDAYKTRVCLKCGGLNGVVRRVR 175

Query: 238 LLKISHEKYKNRTKKKDAIVED----LLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQ 293
            +++ HEKY    ++ +   E+      AE   A  +N  +   ++F +   L+P+ V Q
Sbjct: 176 PMRLVHEKYHVEPRRGEGPRENPGGFFDAELRTACAYNKVVGECREF-VHDFLDPVRVRQ 234

Query: 294 LFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRP 332
           LF A+P  ++ LL +   +S P+DL++T LLVPP  +RP
Sbjct: 235 LFLAVPPGEVILLGLAPGVS-PTDLLMTTLLVPPVPVRP 272



 Score =  132 bits (332), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 90/255 (35%), Positives = 138/255 (54%), Gaps = 30/255 (11%)

Query: 764  GVPRIKEIINASRNISTPIITA-YLDKDTDLDY-------ARIVKGRLERTTLGEVCEYI 815
            GVPR+ E+INA+RNI+TP++TA  L  + + ++       AR VK ++ER  L EV   I
Sbjct: 1178 GVPRLVEVINANRNIATPVVTAPVLLMEGEENHCEIFRKRARFVKAQIERVLLREVVSEI 1237

Query: 816  EEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGH------------LTV 863
             EV    + ++ + L+M  I  LHL ++  ++R   +R    +GH            + V
Sbjct: 1238 VEVCSDTEFYLRVHLNMSVITKLHLPINAITVR---QRILAAAGHTMSPLRMLNEDCIEV 1294

Query: 864  SGHSFLILKPK-DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLV 922
                 L + P    ++  +  + ++  LLP VV+ G+ GINRA+I     E      +L 
Sbjct: 1295 FSLDTLAVYPHFQDARWVHFSLRRILGLLPEVVVGGIGGINRAMISSNGTE------VLA 1348

Query: 923  EGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHP 982
            EG  LR VM  +GV   +   N+   V + LGIEAAR  I+ EI+ +++ + +SID RH 
Sbjct: 1349 EGAELRAVMNLWGVDSTRVVCNHVAVVERVLGIEAARRVIVDEIQNILKAYSLSIDVRHV 1408

Query: 983  MLVADLMTSKGEVLG 997
             L+ADLMT +G VLG
Sbjct: 1409 YLLADLMTQRGVVLG 1423



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 44/58 (75%), Positives = 53/58 (91%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV NSF+SGL+PTEFFFHTM GREGLVDTAVKTAETGY+ RRL+K++E+L V+YD
Sbjct: 832 ARGFVANSFYSGLSPTEFFFHTMAGREGLVDTAVKTAETGYIYRRLMKAMENLSVRYD 889



 Score = 64.3 bits (155), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 27/40 (67%), Positives = 31/40 (77%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            C  KY+R   EP T  GA+AAQS+GEP TQMTL+TFHFAG
Sbjct: 1130 CASKYLRKACEPGTPCGAIAAQSVGEPSTQMTLRTFHFAG 1169



 Score = 49.7 bits (117), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 19/48 (39%), Positives = 33/48 (68%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIAS 69
           LM+   N+++ +NGE +IA TQDF+   YL+T ++ FF+R +  ++ S
Sbjct: 526 LMSTARNIISAKNGEPIIACTQDFLAAAYLVTSRDVFFDRGEFSQMVS 573


>gi|387593897|gb|EIJ88921.1| RNA polymerase 2 [Nematocida parisii ERTm3]
          Length = 1284

 Score =  219 bits (558), Expect = 9e-54,   Method: Compositional matrix adjust.
 Identities = 121/269 (44%), Positives = 165/269 (61%), Gaps = 32/269 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+DVVLFNRQPSLH+LSIMAH+ KVLP RT RFNECVC+PYNADFDGDEMN+HLPQT EA
Sbjct: 432 DSDVVLFNRQPSLHRLSIMAHKVKVLPGRTLRFNECVCSPYNADFDGDEMNIHLPQTVEA 491

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL               LM  K+NL  PRNG+ LIAATQDFITG YL+T+K+ FF +
Sbjct: 492 RVEALE--------------LMGVKNNLSVPRNGQPLIAATQDFITGSYLITKKSTFFTK 537

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q  +  +  + ++++          R       +R AVI+TGK +FS  L       ++
Sbjct: 538 KQFGQFITYALPNSTE----------RIRAKPTILRPAVIYTGKTLFSTALN------LS 581

Query: 521 ANLKTKGRAYTANE-EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            +++ + R YT +       +   ++R+ E+L G  DK  +G+  +  +F+  LR+ G  
Sbjct: 582 ISVEIRTRNYTPSTVPSAQNEGVFVMRDGEILFGRADKRIVGA-EEGTIFHYELREGGPL 640

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           V V A+  ++R+ S YL   GFSIG+ DV
Sbjct: 641 VVVKALDAIARLCSRYLGESGFSIGLDDV 669



 Score =  186 bits (472), Expect = 9e-44,   Method: Compositional matrix adjust.
 Identities = 124/318 (38%), Positives = 174/318 (54%), Gaps = 47/318 (14%)

Query: 1111 VRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYIEEVFV 1156
            +++QIE  TAVGALAAQSIGEPGTQMTLKTFH AG              E+      +  
Sbjct: 973  LKSQIEYGTAVGALAAQSIGEPGTQMTLKTFHLAGTSGASITLGVPRLKEIINASTAIST 1032

Query: 1157 P-------DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRG---ISGHLTVSGHSFLI 1206
            P       D  F  I    DR++ + +    +S+   I +T     IS  L +  +    
Sbjct: 1033 PLIKIIPLDGHFKYIP---DRVQPILISDLAESV--SINKTSAVFKISSSLIMKYNVDKE 1087

Query: 1207 LKPKDSSKSFNSKMYQ--MKQLLPSVV-------IKGVQGINRAVIHEEDVEGVTKYKLL 1257
            +K     K  ++  ++  +++ LPS V       +KG+  + R +         T  +++
Sbjct: 1088 IKSLGGVKKDDTYYWEAPLEKYLPSEVDKLLKTKVKGISSVTRVI--------TTDTEII 1139

Query: 1258 VEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRH 1317
             EG  L D++   GV   + S+NN YE YKTLGIEAAR +I+ EI+  +  HG+S+D RH
Sbjct: 1140 AEGTGLLDILGVEGVNSARTSTNNIYETYKTLGIEAARESIVKEIQYTIGQHGISVDTRH 1199

Query: 1318 PMLVADLMTSKGEVLGITRHGLAKM-KESVLNLASFENTSDHLFDAAFYGQTDCISGVSE 1376
              L+AD+M   GE+ G+TR GL KM   SVL LASFE T +HLF A++ G  D I+GVSE
Sbjct: 1200 IGLLADVMCFTGEICGMTRFGLQKMGGSSVLTLASFEQTGEHLFTASYSGYEDQINGVSE 1259

Query: 1377 CIIMGLPMNVGTGLIKLL 1394
            CII G  + +GTG  K+L
Sbjct: 1260 CIISGQRIPIGTGSFKIL 1277



 Score =  141 bits (356), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 89/261 (34%), Positives = 142/261 (54%), Gaps = 9/261 (3%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           I+  +  E  ++  S + + S++LY  +  + P   G LD R+G + K+A C+TCG+ ++
Sbjct: 13  IKFEILTEKEIRGMSVLSVTSRDLYSSE-NKAPATTGPLDLRLGPSTKDAVCSTCGEKMA 71

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALS 202
           +CVGHFG+I+L LPV+H G  +    +LQS+CK   C+ +LL  E  A    KLR    +
Sbjct: 72  ECVGHFGHIELALPVYHPGLLKNTHKVLQSVCKQ--CSSILLPAEVQAQLLIKLRARKGN 129

Query: 203 YLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLA 262
             + + + KK+ + +KK   C  C  ING+V+K G  K  H  +  R KK D   E    
Sbjct: 130 RTLEQRVIKKVFDESKKTVECFSCNSINGIVRKTG-FKFFHRVH--RLKKHDTQKEIERT 186

Query: 263 EYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTR 322
            Y+ +VK NPE+         + L+P+ V ++   I  +   LL ++ ++     L++T 
Sbjct: 187 LYSASVKDNPELTNWINNTPDEYLSPITVQEVLRNITEDAKSLLGVSCDV---VSLMITC 243

Query: 323 LLVPPNCIRPSVISDLKSDND 343
           L VPP  IRPSV+S   S N+
Sbjct: 244 LPVPPGTIRPSVMSLDSSSNE 264



 Score = 97.4 bits (241), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 73/242 (30%), Positives = 120/242 (49%), Gaps = 50/242 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLD-YARIVKGRLERTTLGEVCEYIEEVFVPD 822
            GVPR+KEIINAS  ISTP+I     K   LD + + +  R++   + ++ E +      +
Sbjct: 1016 GVPRLKEIINASTAISTPLI-----KIIPLDGHFKYIPDRVQPILISDLAESVS----IN 1066

Query: 823  DSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNS 882
             +  + K+    I   +++ +I S+        G+                KD +  + +
Sbjct: 1067 KTSAVFKISSSLIMKYNVDKEIKSLG-------GVK---------------KDDTYYWEA 1104

Query: 883  KMYQMKQLLPSVV-------IKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYG 935
             +   ++ LPS V       +KG+  + R +         T  +++ EG  L D++   G
Sbjct: 1105 PL---EKYLPSEVDKLLKTKVKGISSVTRVI--------TTDTEIIAEGTGLLDILGVEG 1153

Query: 936  VKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            V   + S+NN YE YKTLGIEAAR +I+ EI+  +  HG+S+D RH  L+AD+M   GE+
Sbjct: 1154 VNSARTSTNNIYETYKTLGIEAARESIVKEIQYTIGQHGISVDTRHIGLLADVMCFTGEI 1213

Query: 996  LG 997
             G
Sbjct: 1214 CG 1215



 Score = 96.3 bits (238), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 51/63 (80%)

Query: 606 GDVTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           GD    +GFV++SF +GL PTEFFFH + GREGLVDTAVKTAETGYMQRRL+K LE + V
Sbjct: 769 GDTNASRGFVRSSFCAGLLPTEFFFHAVSGREGLVDTAVKTAETGYMQRRLMKVLEGVYV 828

Query: 666 QYD 668
            YD
Sbjct: 829 AYD 831



 Score = 60.8 bits (146), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 27/42 (64%), Positives = 33/42 (78%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 63
           LM  K+NL  PRNG+ LIAATQDFITG YL+T+K+ FF + Q
Sbjct: 498 LMGVKNNLSVPRNGQPLIAATQDFITGSYLITKKSTFFTKKQ 539


>gi|387595902|gb|EIJ93525.1| RNA polymerase 2 [Nematocida parisii ERTm1]
          Length = 1284

 Score =  219 bits (558), Expect = 9e-54,   Method: Compositional matrix adjust.
 Identities = 121/269 (44%), Positives = 165/269 (61%), Gaps = 32/269 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+DVVLFNRQPSLH+LSIMAH+ KVLP RT RFNECVC+PYNADFDGDEMN+HLPQT EA
Sbjct: 432 DSDVVLFNRQPSLHRLSIMAHKVKVLPGRTLRFNECVCSPYNADFDGDEMNIHLPQTVEA 491

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R EAL               LM  K+NL  PRNG+ LIAATQDFITG YL+T+K+ FF +
Sbjct: 492 RVEALE--------------LMGVKNNLSVPRNGQPLIAATQDFITGSYLITKKSTFFTK 537

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q  +  +  + ++++          R       +R AVI+TGK +FS  L       ++
Sbjct: 538 KQFGQFITYALPNSTE----------RIRAKPTILRPAVIYTGKTLFSTALN------LS 581

Query: 521 ANLKTKGRAYTANE-EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            +++ + R YT +       +   ++R+ E+L G  DK  +G+  +  +F+  LR+ G  
Sbjct: 582 ISVEIRTRNYTPSTVPSAQNEGVFVMRDGEILFGRADKRIVGA-EEGTIFHYELREGGPL 640

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           V V A+  ++R+ S YL   GFSIG+ DV
Sbjct: 641 VVVKALDAIARLCSRYLGESGFSIGLDDV 669



 Score =  186 bits (472), Expect = 9e-44,   Method: Compositional matrix adjust.
 Identities = 124/318 (38%), Positives = 174/318 (54%), Gaps = 47/318 (14%)

Query: 1111 VRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYIEEVFV 1156
            +++QIE  TAVGALAAQSIGEPGTQMTLKTFH AG              E+      +  
Sbjct: 973  LKSQIEYGTAVGALAAQSIGEPGTQMTLKTFHLAGTSGASITLGVPRLKEIINASTAIST 1032

Query: 1157 P-------DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRG---ISGHLTVSGHSFLI 1206
            P       D  F  I    DR++ + +    +S+   I +T     IS  L +  +    
Sbjct: 1033 PLIKIIPLDGHFKYIP---DRVQPILISDLAESV--SINKTSAVFKISSSLIMKYNVDKE 1087

Query: 1207 LKPKDSSKSFNSKMYQ--MKQLLPSVV-------IKGVQGINRAVIHEEDVEGVTKYKLL 1257
            +K     K  ++  ++  +++ LPS V       +KG+  + R +         T  +++
Sbjct: 1088 IKSLGGVKKDDTYYWEAPLEKYLPSEVDKLLKTKVKGISSVTRVI--------TTDTEII 1139

Query: 1258 VEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRH 1317
             EG  L D++   GV   + S+NN YE YKTLGIEAAR +I+ EI+  +  HG+S+D RH
Sbjct: 1140 AEGTGLLDILGVEGVNSARTSTNNIYETYKTLGIEAARESIVKEIQYTIGQHGISVDTRH 1199

Query: 1318 PMLVADLMTSKGEVLGITRHGLAKM-KESVLNLASFENTSDHLFDAAFYGQTDCISGVSE 1376
              L+AD+M   GE+ G+TR GL KM   SVL LASFE T +HLF A++ G  D I+GVSE
Sbjct: 1200 IGLLADVMCFTGEICGMTRFGLQKMGGSSVLTLASFEQTGEHLFTASYSGYEDQINGVSE 1259

Query: 1377 CIIMGLPMNVGTGLIKLL 1394
            CII G  + +GTG  K+L
Sbjct: 1260 CIISGQRIPIGTGSFKIL 1277



 Score =  141 bits (356), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 89/261 (34%), Positives = 142/261 (54%), Gaps = 9/261 (3%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           I+  +  E  ++  S + + S++LY  +  + P   G LD R+G + K+A C+TCG+ ++
Sbjct: 13  IKFEILTEKEIRGMSVLSVTSRDLYSSE-NKAPATTGPLDLRLGPSTKDAVCSTCGEKMA 71

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALS 202
           +CVGHFG+I+L LPV+H G  +    +LQS+CK   C+ +LL  E  A    KLR    +
Sbjct: 72  ECVGHFGHIELALPVYHPGLLKNTHKVLQSVCKQ--CSSILLPAEVQAQLLIKLRARKGN 129

Query: 203 YLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLA 262
             + + + KK+ + +KK   C  C  ING+V+K G  K  H  +  R KK D   E    
Sbjct: 130 RTLEQRVIKKVFDESKKTVECFSCNSINGIVRKTG-FKFFHRVH--RLKKHDTQKEIERT 186

Query: 263 EYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTR 322
            Y+ +VK NPE+         + L+P+ V ++   I  +   LL ++ ++     L++T 
Sbjct: 187 LYSASVKDNPELTNWINNTPDEYLSPITVQEVLRNITEDAKSLLGVSCDV---VSLMITC 243

Query: 323 LLVPPNCIRPSVISDLKSDND 343
           L VPP  IRPSV+S   S N+
Sbjct: 244 LPVPPGTIRPSVMSLDSSSNE 264



 Score = 97.4 bits (241), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 73/242 (30%), Positives = 120/242 (49%), Gaps = 50/242 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLD-YARIVKGRLERTTLGEVCEYIEEVFVPD 822
            GVPR+KEIINAS  ISTP+I     K   LD + + +  R++   + ++ E +      +
Sbjct: 1016 GVPRLKEIINASTAISTPLI-----KIIPLDGHFKYIPDRVQPILISDLAESVS----IN 1066

Query: 823  DSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNS 882
             +  + K+    I   +++ +I S+        G+                KD +  + +
Sbjct: 1067 KTSAVFKISSSLIMKYNVDKEIKSLG-------GVK---------------KDDTYYWEA 1104

Query: 883  KMYQMKQLLPSVV-------IKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYG 935
             +   ++ LPS V       +KG+  + R +         T  +++ EG  L D++   G
Sbjct: 1105 PL---EKYLPSEVDKLLKTKVKGISSVTRVI--------TTDTEIIAEGTGLLDILGVEG 1153

Query: 936  VKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            V   + S+NN YE YKTLGIEAAR +I+ EI+  +  HG+S+D RH  L+AD+M   GE+
Sbjct: 1154 VNSARTSTNNIYETYKTLGIEAARESIVKEIQYTIGQHGISVDTRHIGLLADVMCFTGEI 1213

Query: 996  LG 997
             G
Sbjct: 1214 CG 1215



 Score = 96.3 bits (238), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 51/63 (80%)

Query: 606 GDVTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           GD    +GFV++SF +GL PTEFFFH + GREGLVDTAVKTAETGYMQRRL+K LE + V
Sbjct: 769 GDTNASRGFVRSSFCAGLLPTEFFFHAVSGREGLVDTAVKTAETGYMQRRLMKVLEGVYV 828

Query: 666 QYD 668
            YD
Sbjct: 829 AYD 831



 Score = 60.8 bits (146), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 27/42 (64%), Positives = 33/42 (78%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 63
           LM  K+NL  PRNG+ LIAATQDFITG YL+T+K+ FF + Q
Sbjct: 498 LMGVKNNLSVPRNGQPLIAATQDFITGSYLITKKSTFFTKKQ 539


>gi|403223773|dbj|BAM41903.1| DNA-directed RNA polymerase III largest subunit RPC1 [Theileria
           orientalis strain Shintoku]
          Length = 1643

 Score =  216 bits (551), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 128/328 (39%), Positives = 168/328 (51%), Gaps = 82/328 (25%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + D+V+FNRQPSLH+LSIM HRA+++   TFRFNECVCTPYNADFDGDEMN+HLPQT EA
Sbjct: 514 NGDLVIFNRQPSLHRLSIMCHRARIMRGSTFRFNECVCTPYNADFDGDEMNIHLPQTYEA 573

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE   SLH LS+           + NL TPRNGE LIA  QDF+   YLLT K+ F  R
Sbjct: 574 KAE---SLHLLSV-----------QKNLTTPRNGEPLIAPVQDFLCSSYLLTNKDMFLTR 619

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWN----PVVFVRTAVIWTGKQIFSLILKPNRD 516
           AQ               C II  F+  S +    P   V    +WTGKQ F+++++PNR 
Sbjct: 620 AQ--------------FCQIISYFTDASIHVDLPPPSIVHPVTLWTGKQAFNVLIRPNRA 665

Query: 517 CPVNANLKTK-------------------------------------------------G 527
             V  NL+ K                                                 G
Sbjct: 666 SKVMVNLRVKEREFMDPNVYYKSGGKGARGMGDNRTKRRGPEDMDLDEEEDEQNSRESWG 725

Query: 528 RAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWR 587
            A   +E  C  D YV++  SELL+GS+   +LG   K  +FY L+      V+   M R
Sbjct: 726 AAVKLDECMCPHDGYVVIYKSELLSGSLGVRSLGP-TKGGLFYELMLKNSAKVSSECMLR 784

Query: 588 LSRMTSFYLMNRGFSIGIGDVTPGQGFV 615
           +S+++S +L   G +IG+ DVTP +  +
Sbjct: 785 VSKLSSRWLSEYGMTIGLDDVTPSEELI 812



 Score =  199 bits (506), Expect = 9e-48,   Method: Compositional matrix adjust.
 Identities = 126/356 (35%), Positives = 183/356 (51%), Gaps = 75/356 (21%)

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFH--------------------------- 1142
            Y +   EP  A+GAL AQSIGEP TQMTLKTFH                           
Sbjct: 1293 YQKCICEPGEAIGALGAQSIGEPATQMTLKTFHFAGVASMNVTLGVPRIKEIIGASAKIA 1352

Query: 1143 ---------------FA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLH 1175
                           FA            G+VC  +++++ P  S +L+ L+   I  L+
Sbjct: 1353 TPIIEVPLEEKTNYDFALKVKSRIEKTTLGQVCTSVKQMYTPQSSKLLLTLNQKLINQLY 1412

Query: 1176 LEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF------------NSKMYQM 1223
            L ++ + +R    R   I   +   G    I+ PK S  +             + + +Q 
Sbjct: 1413 LPINANKVR---TRVVEIISQIKKIGK---IVIPKSSVYAVGEWQICMDLGPTHHQFFQQ 1466

Query: 1224 KQLLPSV---VIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSN 1280
              L+ S+   V+ G + + RAVI  E+      Y++ VEG  L++VM   GV      SN
Sbjct: 1467 NTLVTSILQLVVAGCKEVKRAVIKRENTAAGPNYQIAVEGYGLKEVMGADGVLWSSVKSN 1526

Query: 1281 NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLA 1340
            + +EV + LGIEAARS I++EI+  M+ + + ID R+  L+AD+MT KG+V+GI RHG+ 
Sbjct: 1527 HVFEVAEVLGIEAARSVIISEIQKCMDAYSIDIDGRYMKLLADVMTFKGQVIGINRHGIR 1586

Query: 1341 KMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA 1396
            KM+ S L L+SFE T+DHLFDAA + + D I GVSECIIMG P+++GTG   ++ A
Sbjct: 1587 KMRSSTLMLSSFEQTNDHLFDAAVHHRKDPIKGVSECIIMGKPISLGTGSFDIMMA 1642



 Score =  151 bits (382), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 92/249 (36%), Positives = 143/249 (57%), Gaps = 21/249 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEII AS  I+TPII   L++ T+ D+A  VK R+E+TTLG+VC  +++++ P  
Sbjct: 1337 GVPRIKEIIGASAKIATPIIEVPLEEKTNYDFALKVKSRIEKTTLGQVCTSVKQMYTPQS 1396

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF--- 880
            S +L+ L+   I  L+L ++ + +R    R   I   +   G    I+ PK S  +    
Sbjct: 1397 SKLLLTLNQKLINQLYLPINANKVR---TRVVEIISQIKKIGK---IVIPKSSVYAVGEW 1450

Query: 881  ---------NSKMYQMKQLLPSV---VIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLR 928
                     + + +Q   L+ S+   V+ G + + RAVI  E+      Y++ VEG  L+
Sbjct: 1451 QICMDLGPTHHQFFQQNTLVTSILQLVVAGCKEVKRAVIKRENTAAGPNYQIAVEGYGLK 1510

Query: 929  DVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADL 988
            +VM   GV      SN+ +EV + LGIEAARS I++EI+  M+ + + ID R+  L+AD+
Sbjct: 1511 EVMGADGVLWSSVKSNHVFEVAEVLGIEAARSVIISEIQKCMDAYSIDIDGRYMKLLADV 1570

Query: 989  MTSKGEVLG 997
            MT KG+V+G
Sbjct: 1571 MTFKGQVIG 1579



 Score =  127 bits (320), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 85/255 (33%), Positives = 135/255 (52%), Gaps = 46/255 (18%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMG--------TNQKEANCTTCGQNLSDC 144
           + + + I+I +++LY     + P P+G+LD R+G         N  +  C TCG+ L +C
Sbjct: 102 ISRAAEIEIKNRDLYYYLTNK-PYPYGVLDSRLGLKLIWNLGCNTNDMTCETCGKGLIEC 160

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEE-----KAAGFRAKLRNP 199
           +GH+GY+ L LPVFH+G+F+ VI +L  ICK  +C  +LL E+     K   F+  + +P
Sbjct: 161 IGHWGYVKLELPVFHVGFFKYVIQVLYCICKKCSC--LLLPEDSIRKLKEQFFKRPIEDP 218

Query: 200 ALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVED 259
            +  L+ +S    +L+  +KV  CP C    G +KK  ++K + +++    K K  I + 
Sbjct: 219 VVKSLIFRS----VLDMCRKVKFCPRCEAPQGSIKK--VVKPTTDQF---MKLKHCIKQ- 268

Query: 260 LLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLI 319
                    K +  +E       ++ L PL V QLFE I  + I   +MN E   P  LI
Sbjct: 269 ---------KGSSRVE-------VEELTPLVVKQLFENI--DPIHCKVMNIE--NPERLI 308

Query: 320 LTRLLVPPNCIRPSV 334
           +T L  PPNCIRP++
Sbjct: 309 ITSLAAPPNCIRPTI 323



 Score =  101 bits (252), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 47/70 (67%), Positives = 55/70 (78%), Gaps = 1/70 (1%)

Query: 601 FSIGIGDVTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSL 660
           F +G  D    +GFV NSFF+GL P EFFFHTM GREGL+DTAVKT+ETGYMQRRL+K +
Sbjct: 921 FPMGCKDAK-SRGFVANSFFTGLEPEEFFFHTMSGREGLIDTAVKTSETGYMQRRLMKFM 979

Query: 661 EDLCVQYDMS 670
           EDL + YD S
Sbjct: 980 EDLAICYDHS 989



 Score = 55.1 bits (131), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 26/48 (54%), Positives = 32/48 (66%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIAS 69
           L++ + NL TPRNGE LIA  QDF+   YLLT K+ F  RAQ  +I S
Sbjct: 580 LLSVQKNLTTPRNGEPLIAPVQDFLCSSYLLTNKDMFLTRAQFCQIIS 627



 Score = 46.6 bits (109), Expect = 0.094,   Method: Compositional matrix adjust.
 Identities = 21/40 (52%), Positives = 28/40 (70%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQA 707
            D  FDAA + + D I GVSECIIMG P+++GTG   ++ A
Sbjct: 1603 DHLFDAAVHHRKDPIKGVSECIIMGKPISLGTGSFDIMMA 1642


>gi|357616542|gb|EHJ70255.1| hypothetical protein KGM_16522 [Danaus plexippus]
          Length = 241

 Score =  216 bits (550), Expect = 8e-53,   Method: Compositional matrix adjust.
 Identities = 105/220 (47%), Positives = 150/220 (68%), Gaps = 8/220 (3%)

Query: 74  GRKVFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEAN 133
           GRK+     +   V     +QQ +HIQ+++KNLY QD QR P  +G+LDRRMGTNQK+AN
Sbjct: 12  GRKI---SHVTFNVDSATEIQQAAHIQVITKNLYAQDGQRVPASYGVLDRRMGTNQKDAN 68

Query: 134 CTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFR 193
           C TCG  L++CVGH+GY++L LPVFH+GYFR +I ILQ+ICKN  CA+V+L +     F 
Sbjct: 69  CETCGLGLAECVGHYGYVELALPVFHVGYFRSIITILQTICKN--CAKVMLPDTIKKSFS 126

Query: 194 AKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKK--CGLLKISHEKYKNRTK 251
            K  +P L+YL +K+L+  +L+  K  + CP+C  +NG+VKK   G+LKI H+KY+ + K
Sbjct: 127 RKFMHPDLTYLHKKNLRAAVLKKAKTCTKCPYCESLNGIVKKSPAGILKIIHDKYRTK-K 185

Query: 252 KKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEV 291
             D  V+ +L ++NEA + N E+ +    GLI  ++PLEV
Sbjct: 186 PTDPAVQKVLKDFNEAKESNKELASMINSGLIIEMSPLEV 225


>gi|449016275|dbj|BAM79677.1| RNA polymerase III largest subunit [Cyanidioschyzon merolae strain
           10D]
          Length = 1930

 Score =  211 bits (538), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 121/275 (44%), Positives = 160/275 (58%), Gaps = 25/275 (9%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH+LSIMAH  KV+  RTFRFNECVC PYNADFDGDEMN+H+PQT   
Sbjct: 733 DGDLVLFNRQPSLHRLSIMAHSVKVIAGRTFRFNECVCAPYNADFDGDEMNLHVPQT--- 789

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
                            A+ L+A   NL++PRNGE LIA TQDFIT  YLLT K+ F+ R
Sbjct: 790 -----------EEARAEARALLAVPQNLLSPRNGEPLIACTQDFITALYLLTHKDVFYGR 838

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              ++  S  +   +    I+ R       P +      +WTGKQ+FS +++ +      
Sbjct: 839 WAAVQCLSFGLEPEAS-AAILGRLP----EPAIL-HPLPLWTGKQLFSALVQADPALSDE 892

Query: 521 A-----NLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
           A           +AYT    +C  D+YV +R++EL++G + K TLGS  K ++ Y+L R+
Sbjct: 893 AVRVLICFDATEKAYTHEGIWCRADAYVCVRSAELISGQVAKRTLGSQSKQSLLYVLQRE 952

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
            G  +AV  M RL+R  S +L   GFS GI DV P
Sbjct: 953 AGPLLAVRCMNRLARFASRWLSEYGFSFGIDDVRP 987



 Score =  145 bits (367), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 78/198 (39%), Positives = 118/198 (59%), Gaps = 20/198 (10%)

Query: 1216 FNSKMYQMKQLLPSVVIKGVQGINRAVIHE-----EDVEGVT---------------KYK 1255
            +   + Q+++L+P +V+ G+  I R V  +      D  G +                 +
Sbjct: 1606 WEPALAQLQRLVPELVVSGLASIARVVWSQALSPASDSAGKSGEAAAAAAAASAATESIQ 1665

Query: 1256 LLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDF 1315
            LL E +++R VM T G+       N+   V + LGIEAARSTI+ E+   M  HG+++D 
Sbjct: 1666 LLAETEDMRSVMNTQGIDASSVYCNHVLVVEQVLGIEAARSTIVKEVLETMAAHGVTLDA 1725

Query: 1316 RHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVS 1375
            RH  L++D+MT  G+VLGITR G++KM++S L LASFE T DHLF+AA   ++D I GVS
Sbjct: 1726 RHVDLLSDMMTQSGQVLGITRFGISKMRQSTLMLASFEKTVDHLFEAAVRSRSDRIRGVS 1785

Query: 1376 ECIIMGLPMNVGTGLIKL 1393
            E +IMG P+ +GTG++ +
Sbjct: 1786 ERVIMGKPVPLGTGMVSV 1803



 Score =  119 bits (297), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 71/190 (37%), Positives = 102/190 (53%), Gaps = 20/190 (10%)

Query: 58  FFNRAQTMRIAS----TLIAGRKVFFRGL--IEGTVTKEDRVQQQSHIQIVSKNLYCQDP 111
              R Q  R  S    TL    +V  R L  I+  +   D +++ S I++  K LY   P
Sbjct: 144 LLEREQARRALSARPVTLRDDTQVLSRSLEAIQFRIPSVDDIRRASVIEMNRKQLYT--P 201

Query: 112 QRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQ 171
           +   +PHG LD+ +G + K   C TCG +L+DC GHFG+I+L LPVFH+GY   ++ +LQ
Sbjct: 202 EHDIVPHGALDKHLGVSDKNERCATCGLSLADCAGHFGHIELVLPVFHVGYLSFLLQVLQ 261

Query: 172 SICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVR------KSLKKKILETTKKVSVCPH 225
            ICK   C+ +L      A F   LR+    +  R      +SL K+ LE  K+ S+C H
Sbjct: 262 CICKR--CSGLLAD----AQFVEHLRHQQREHRARNTPGYLQSLLKRHLEWAKRSSICRH 315

Query: 226 CGEINGVVKK 235
           CG  NG+V+K
Sbjct: 316 CGAPNGLVRK 325



 Score = 99.4 bits (246), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 46/64 (71%), Positives = 52/64 (81%), Gaps = 1/64 (1%)

Query: 606  GDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
            GD +P   GFV NSF+SG+   EFFFH+M GREGLVDTAVKTAETGYMQRR +K+LEDL 
Sbjct: 1106 GDKSPEAGGFVANSFYSGMNAIEFFFHSMAGREGLVDTAVKTAETGYMQRRFMKALEDLR 1165

Query: 665  VQYD 668
            V YD
Sbjct: 1166 VAYD 1169



 Score = 78.2 bits (191), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 45/138 (32%), Positives = 72/138 (52%), Gaps = 20/138 (14%)

Query: 880  FNSKMYQMKQLLPSVVIKGVQGINRAVIHE-----EDVEGVT---------------KYK 919
            +   + Q+++L+P +V+ G+  I R V  +      D  G +                 +
Sbjct: 1606 WEPALAQLQRLVPELVVSGLASIARVVWSQALSPASDSAGKSGEAAAAAAAASAATESIQ 1665

Query: 920  LLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDF 979
            LL E +++R VM T G+       N+   V + LGIEAARSTI+ E+   M  HG+++D 
Sbjct: 1666 LLAETEDMRSVMNTQGIDASSVYCNHVLVVEQVLGIEAARSTIVKEVLETMAAHGVTLDA 1725

Query: 980  RHPMLVADLMTSKGEVLG 997
            RH  L++D+MT  G+VLG
Sbjct: 1726 RHVDLLSDMMTQSGQVLG 1743



 Score = 65.5 bits (158), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 31/37 (83%), Positives = 32/37 (86%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            K  RA IEP TAVGA+AAQSIGEP TQMTLKTFHFAG
Sbjct: 1356 KLRRALIEPGTAVGAIAAQSIGEPSTQMTLKTFHFAG 1392



 Score = 52.8 bits (125), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 23/34 (67%), Positives = 27/34 (79%)

Query: 28  NLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           NL++PRNGE LIA TQDFIT  YLLT K+ F+ R
Sbjct: 805 NLLSPRNGEPLIACTQDFITALYLLTHKDVFYGR 838



 Score = 49.7 bits (117), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 23/52 (44%), Positives = 33/52 (63%)

Query: 286 LNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD 337
           L PL VL+L   I   D+  L M+ + ++P D++L  + VPP CIRPSV +D
Sbjct: 497 LTPLHVLELLRNIAPADLEALGMDPDTTRPEDMLLRCVAVPPVCIRPSVCND 548



 Score = 45.4 bits (106), Expect = 0.24,   Method: Compositional matrix adjust.
 Identities = 25/58 (43%), Positives = 36/58 (62%), Gaps = 5/58 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLD-----KDTDLDYARIVKGRLERTTLGEVCEYIE 816
            GVPRIKE++NA+R I+TP++TAYL+     +      A  ++ RLE   L +V  Y E
Sbjct: 1401 GVPRIKELVNATRRIATPLVTAYLETTAPGQQEPRALAYNLQRRLECRRLKQVIRYGE 1458


>gi|31417307|gb|AAH14399.1| POLR3A protein [Homo sapiens]
          Length = 162

 Score =  211 bits (538), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 103/149 (69%), Positives = 124/149 (83%)

Query: 1223 MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNT 1282
            +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG + +SNNT
Sbjct: 8    LKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTRTTSNNT 67

Query: 1283 YEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKM 1342
            YEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLGITR GLAKM
Sbjct: 68   YEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKM 127

Query: 1343 KESVLNLASFENTSDHLFDAAFYGQTDCI 1371
            KESVL LASFE T+DHLFDAA++GQ D +
Sbjct: 128  KESVLMLASFEKTADHLFDAAYFGQKDSV 156



 Score =  151 bits (381), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 74/111 (66%), Positives = 91/111 (81%)

Query: 887 MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNT 946
           +K+ LP VV++G+  ++RAVIH ++  G  KYKLLVEGDNLR VMAT+GVKG + +SNNT
Sbjct: 8   LKEDLPKVVVQGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTRTTSNNT 67

Query: 947 YEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
           YEV KTLGIEAAR+TI+ EI+  M NHGMSID RH ML++DLMT KGEVLG
Sbjct: 68  YEVEKTLGIEAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLG 118


>gi|294878143|ref|XP_002768279.1| DNA-directed RNA polymerase III largest subunit, putative [Perkinsus
            marinus ATCC 50983]
 gi|239870527|gb|EER00997.1| DNA-directed RNA polymerase III largest subunit, putative [Perkinsus
            marinus ATCC 50983]
          Length = 1133

 Score =  211 bits (536), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 133/374 (35%), Positives = 191/374 (51%), Gaps = 81/374 (21%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYI 1151
            C  KY RA +EP  AVGA +AQSIGEP TQMTLKTFHFAG              E+    
Sbjct: 731  CARKYRRALMEPGEAVGATSAQSIGEPATQMTLKTFHFAGVASMNVTLGVPRIKEIINAA 790

Query: 1152 EEVFVPDDSFILIKLDMDRI---------------------------------------- 1171
            + +  P    I  KL+ DR+                                        
Sbjct: 791  KHISTP---IISCKLEQDRVEAAAFMVKSKIQRTLLGDICEYIKQVYEPSGVYLIVKLCG 847

Query: 1172 ---RLLHLEVDIDSIRYCIERTRGISGHLTV-------SGHSFLILKPKDSSKSFNS--- 1218
               R + L++ +D ++  +     + G L +        G   L ++P  +  S      
Sbjct: 848  ETLRRMQLDLTMDELKEALCAKGALPGGLKIRPECIESRGKLKLAIRPAGAVDSRGRTLP 907

Query: 1219 --------KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTK---YKLLVEGDNLRDVM 1267
                    ++  ++  LP   +KG++  +R V+++E+ +  +K   Y LLVEG  L+DVM
Sbjct: 908  PNPETLWFEVQALRNALPQAPVKGLKQCSRVVVNKEEAKDGSKDTIYSLLVEGYGLQDVM 967

Query: 1268 ATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTS 1327
               GV   K  SN+  EV   LGIEAAR +IM+EI ++M++ GMS+D+RH  ++ D MT 
Sbjct: 968  GIEGVVAEKSVSNHVLEVQSVLGIEAARKSIMSEIDVIMKHFGMSVDYRHIQMLGDCMTY 1027

Query: 1328 KGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVG 1387
            +GE LGI R G++KM  S + LASFE TSD LF+AA + + D + GVSE IIMG P+++G
Sbjct: 1028 RGETLGINRFGISKMSNSTMMLASFEKTSDFLFEAAVFNRPDPVVGVSESIIMGNPVHLG 1087

Query: 1388 TGLIKLLQAVPRSE 1401
            TGL KL+  VP+ E
Sbjct: 1088 TGLFKLMYDVPKEE 1101



 Score =  169 bits (427), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 93/255 (36%), Positives = 153/255 (60%), Gaps = 21/255 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPRIKEIINA+++ISTPII+  L++D     A +VK +++RT LG++CEYI++V+ P  
Sbjct: 779  GVPRIKEIINAAKHISTPIISCKLEQDRVEAAAFMVKSKIQRTLLGDICEYIKQVYEPSG 838

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVS-------GHSFLILKPKDS 876
             ++++KL  + +R + L++ +D ++  +     + G L +        G   L ++P  +
Sbjct: 839  VYLIVKLCGETLRRMQLDLTMDELKEALCAKGALPGGLKIRPECIESRGKLKLAIRPAGA 898

Query: 877  SKSFNS-----------KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTK---YKLLV 922
              S              ++  ++  LP   +KG++  +R V+++E+ +  +K   Y LLV
Sbjct: 899  VDSRGRTLPPNPETLWFEVQALRNALPQAPVKGLKQCSRVVVNKEEAKDGSKDTIYSLLV 958

Query: 923  EGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHP 982
            EG  L+DVM   GV   K  SN+  EV   LGIEAAR +IM+EI ++M++ GMS+D+RH 
Sbjct: 959  EGYGLQDVMGIEGVVAEKSVSNHVLEVQSVLGIEAARKSIMSEIDVIMKHFGMSVDYRHI 1018

Query: 983  MLVADLMTSKGEVLG 997
             ++ D MT +GE LG
Sbjct: 1019 QMLGDCMTYRGETLG 1033



 Score =  135 bits (339), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 95/281 (33%), Positives = 147/281 (52%), Gaps = 18/281 (6%)

Query: 67  IASTLIAGRKVFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQ-RTPIPHGLLDRRM 125
           I S    G     +G+  G ++ E+ + +   ++++++  +  DP     +  G  D R+
Sbjct: 35  IPSDENGGESYAIKGVDFGIMSGEE-ISKYGEVEVLNQGYF--DPMTHKQLALGCHDPRL 91

Query: 126 GTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLG 185
           G   + ++C TCG+N  +C GHFG I L LPVFH+GYFR V  +L +ICK   C RVLL 
Sbjct: 92  GAMNRMSDCQTCGKNFRECPGHFGSIKLVLPVFHVGYFRHVQLLLSAICKR--CGRVLLA 149

Query: 186 EEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKC--GLLKISH 243
            EK + +  + R        +K + +K+++T KKV  CP+C   NG VKK   G + + H
Sbjct: 150 PEKRSVWLNRTRKATKDVQQQKGVFRKLVDTCKKVRQCPYCDAYNGAVKKGTRGYMTLVH 209

Query: 244 EKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDI 303
           E  K++ K       +   +Y++AV  NPEI  H      + L PL +L L   +P  D 
Sbjct: 210 ELPKDQAKV------EYQQQYSDAVSNNPEIGNHLSKVAYEDLTPLHLLPLLAKMPPSDQ 263

Query: 304 PLLLMNAELSKPSDLILTRLLVPPNCIRPSV-ISDLKSDND 343
            +L +  +   P  L++T + V P CIRPSV I D  +  D
Sbjct: 264 EMLKLPPQ---PERLVVTHVPVSPVCIRPSVQIGDAGTQED 301



 Score =  106 bits (265), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 46/59 (77%), Positives = 56/59 (94%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
           +GFV++SFFSGL P E+FFHTMGGREGLVDTAVKTAETGYMQR+L+K+LEDL ++YDM+
Sbjct: 528 RGFVEDSFFSGLNPFEYFFHTMGGREGLVDTAVKTAETGYMQRKLIKALEDLGLKYDMT 586



 Score = 70.9 bits (172), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 38/92 (41%), Positives = 55/92 (59%), Gaps = 2/92 (2%)

Query: 519 VNANLKTKGRAYTANEE-FCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFG 577
           V  NL+   + Y+  +  FC  D YVI  NSEL+AG++ K  LG G K  + ++L+RD  
Sbjct: 311 VLVNLEMAEKNYSHGDPYFCRNDGYVIFYNSELIAGNLGKKILG-GSKPGLTFVLIRDNS 369

Query: 578 EDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVT 609
             VA   + RLS++++ +L  RG S GI DVT
Sbjct: 370 PAVAAACLGRLSKLSARWLGTRGMSFGIDDVT 401



 Score = 50.4 bits (119), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 23/45 (51%), Positives = 32/45 (71%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSE 712
            D  F+AA + + D + GVSE IIMG P+++GTGL KL+  VP+ E
Sbjct: 1057 DFLFEAAVFNRPDPVVGVSESIIMGNPVHLGTGLFKLMYDVPKEE 1101


>gi|429962254|gb|ELA41798.1| hypothetical protein VICG_01150 [Vittaforma corneae ATCC 50505]
          Length = 1442

 Score =  210 bits (535), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 122/301 (40%), Positives = 172/301 (57%), Gaps = 52/301 (17%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D++LFNRQPSLH++SIMAH+A++  HRT RFNECVC PYNADFDGDEMN+H PQT EA
Sbjct: 417 DGDILLFNRQPSLHRMSIMAHKARIHQHRTLRFNECVCAPYNADFDGDEMNIHFPQTFEA 476

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+ LM  K N+ T RNGE LI+ TQDF+TG YLLT KNAFF R
Sbjct: 477 RAE--------------AEELMGVKQNICTARNGEPLISCTQDFLTGVYLLTSKNAFFTR 522

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILK-------- 512
            +  ++ S             K+F   + +P + +    ++TGKQ+F  +++        
Sbjct: 523 KEFSQLCSYASG---------KKFQRIAIHPAIILPIE-LFTGKQVFEFLIEFSLSFAPK 572

Query: 513 ------PNR---------DCP-VNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMD 556
                 P++         D P  N NLK + R++   ++    D YV + N+  + G +D
Sbjct: 573 SFTSIYPSQPSVTQSNINDIPRKNINLKARNRSFKDEDD--PNDGYVEILNNRYICGRLD 630

Query: 557 KSTLGSGG-KANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFV 615
           KS +G    K ++ Y LL+   ++ AV AM  +S + S YL  +GFSIG+ DV P +  +
Sbjct: 631 KSIIGGENRKGSLIYQLLK-VSKECAVVAMNSISSLASRYLSEKGFSIGLDDVFPSEILI 689

Query: 616 Q 616
           +
Sbjct: 690 K 690



 Score =  196 bits (498), Expect = 8e-47,   Method: Compositional matrix adjust.
 Identities = 129/336 (38%), Positives = 185/336 (55%), Gaps = 64/336 (19%)

Query: 1115 IEPATAVGALAAQSIGEPGTQMTLKTFHFAG----------------------------- 1145
            ++P TAVGA+A QSIGEPGTQMTLKTFHF G                             
Sbjct: 1108 VDPGTAVGAIAGQSIGEPGTQMTLKTFHFTGVASMNVTLGVPRLKEIINASANISTPIIK 1167

Query: 1146 ------------EVCEYIEEVFVPDDSFILIKLDM----DRIRL-----------LHLEV 1178
                         V   IE++   D   I+ K+      DRI L           L LE+
Sbjct: 1168 AKLMTKGLESAKVVKGRIEKLLFKD---IVYKISYATTPDRISLSFSVDQNLVEKLRLEI 1224

Query: 1179 DIDSIRYCIERT-RGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQG 1237
             ID I   +    +G S  +     ++ I + K++S     ++ + ++ L +  I G++G
Sbjct: 1225 GIDQIGAILNAAIKGSSVEVQNDTITYSIKRVKENSY---FQIEKTRKQLLNTKISGIEG 1281

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            +NR +++  D + V +Y+LLVEG  L  V+   GV+ +  +SN+  EV KTLGIEAARS 
Sbjct: 1282 VNRVIVNCLD-KSVDEYELLVEGRCLGKVLNVPGVESLSTTSNDILEVEKTLGIEAARSL 1340

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            IM E++  M  +G+ +D RH ML+AD M  KGE+LGITR G+ KM+ S L LASFE T+D
Sbjct: 1341 IMKEVEYTMGKYGIKVDHRHTMLLADTMAFKGEILGITRFGIGKMRTSTLMLASFEQTAD 1400

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            +LF+AA  G  + + GVSE II+G+P+++GTG +KL
Sbjct: 1401 YLFNAAIRGLDEYVRGVSESIILGIPISLGTGAMKL 1436



 Score =  148 bits (373), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 92/235 (39%), Positives = 140/235 (59%), Gaps = 6/235 (2%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPR+KEIINAS NISTPII A L     L+ A++VKGR+E+    ++   I     PD 
Sbjct: 1147 GVPRLKEIINASANISTPIIKAKL-MTKGLESAKVVKGRIEKLLFKDIVYKISYATTPDR 1205

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERT-RGISGHLTVSGHSFLILKPKDSSKSFNS 882
              +   +D + +  L LE+ ID I   +    +G S  +     ++ I + K++S     
Sbjct: 1206 ISLSFSVDQNLVEKLRLEIGIDQIGAILNAAIKGSSVEVQNDTITYSIKRVKENSYF--- 1262

Query: 883  KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCS 942
            ++ + ++ L +  I G++G+NR +++  D + V +Y+LLVEG  L  V+   GV+ +  +
Sbjct: 1263 QIEKTRKQLLNTKISGIEGVNRVIVNCLD-KSVDEYELLVEGRCLGKVLNVPGVESLSTT 1321

Query: 943  SNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            SN+  EV KTLGIEAARS IM E++  M  +G+ +D RH ML+AD M  KGE+LG
Sbjct: 1322 SNDILEVEKTLGIEAARSLIMKEVEYTMGKYGIKVDHRHTMLLADTMAFKGEILG 1376



 Score =  116 bits (291), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 94/309 (30%), Positives = 141/309 (45%), Gaps = 54/309 (17%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           +++ Q S + + SK LY     R P   G LD R+G + K   C+TC +N+ +C GHFG 
Sbjct: 25  EQISQLSVVTLDSKTLY-DIESRKPYSGGPLDLRLGVSTKSGICSTCKENIQNCAGHFGQ 83

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           I L LP +HIG+ +  ++IL  ICK  TC  +L+      GF  KL   + S  +  S  
Sbjct: 84  IQLILPCYHIGFLKQTLSILNCICK--TCGALLI------GFSRKLSYSSSSQNIDDSRS 135

Query: 211 KKI-----LETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYN 265
             I         + + VC  C   NG +KK    +I HE  KN +K +  ++E       
Sbjct: 136 NSINFDAVKNECRNIKVCHKCKSSNGTIKKNTGFRIYHE-IKN-SKGESTLIE------- 186

Query: 266 EAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLV 325
                               +NP   L +F  I  ED P L +  +   P +LI+  +LV
Sbjct: 187 --------------------INPQTCLNIFGMIEEEDYPFLNLKDD---PCNLIIQNILV 223

Query: 326 PPNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADF 385
            P+CIRPSV  D++ +     FN      KLS + +  K+L     + N       N D+
Sbjct: 224 SPSCIRPSV--DMQDEG----FNEDDLTVKLSEIINTNKLLEDSIRKGNSLPII--NEDW 275

Query: 386 DGDEMNVHL 394
           D  ++ V+L
Sbjct: 276 DYLQLQVNL 284



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 46/62 (74%), Positives = 53/62 (85%)

Query: 609 TPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +  +GFV NSFFSGLT  EFFFH + GREGLVDTAVKTAETGYMQRRL+K+LEDL V+YD
Sbjct: 795 SESKGFVLNSFFSGLTSYEFFFHAVSGREGLVDTAVKTAETGYMQRRLMKALEDLSVKYD 854

Query: 669 MS 670
            +
Sbjct: 855 YT 856



 Score = 59.7 bits (143), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 31/64 (48%), Positives = 41/64 (64%), Gaps = 1/64 (1%)

Query: 13  YATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLI 72
           +  R   + LM  K N+ T RNGE LI+ TQDF+TG YLLT KNAFF R +  ++ S   
Sbjct: 474 FEARAEAEELMGVKQNICTARNGEPLISCTQDFLTGVYLLTSKNAFFTRKEFSQLCS-YA 532

Query: 73  AGRK 76
           +G+K
Sbjct: 533 SGKK 536



 Score = 40.8 bits (94), Expect = 5.0,   Method: Compositional matrix adjust.
 Identities = 18/37 (48%), Positives = 27/37 (72%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 704
            D  F+AA  G  + + GVSE II+G+P+++GTG +KL
Sbjct: 1400 DYLFNAAIRGLDEYVRGVSESIILGIPISLGTGAMKL 1436


>gi|118346269|ref|XP_977135.1| RNA polymerase Rpb1, domain 2 family protein [Tetrahymena
           thermophila]
 gi|89288380|gb|EAR86368.1| RNA polymerase Rpb1, domain 2 family protein [Tetrahymena
           thermophila SB210]
          Length = 1418

 Score =  209 bits (533), Expect = 7e-51,   Method: Compositional matrix adjust.
 Identities = 112/281 (39%), Positives = 164/281 (58%), Gaps = 32/281 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + +++LFNRQPSLH++SIMA +A +    T RFNEC C P+NADFDGDEMN+H+PQT EA
Sbjct: 407 NGEILLFNRQPSLHRISIMAFKANIQKWNTIRFNECCCAPFNADFDGDEMNIHVPQTIEA 466

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+ L+  K NL++P+NGE       DF+T  YL+T K+ FF+R
Sbjct: 467 RAE--------------AQYLLDVKQNLISPKNGE-------DFLTTAYLITHKDMFFDR 505

Query: 461 AQTMRIASTLIADTSDI----CGIIKRFSWRSWNPVVF----VRTAVIWTGKQIFSLILK 512
           A   +  +        I      II     + +   +F     +   +WTGKQI  +IL+
Sbjct: 506 AAFCQCCTYFSDGIERIDLPPPAIILPVGMKYYLLNIFQSQIYQQKEMWTGKQIIDVILR 565

Query: 513 PNRDCPVNANLKTKGRAYTANEE---FCHRDSYVILRNSELLAGSMDKSTLGSGGKANVF 569
           PNR   +  NL  K + Y   ++    C  D YV+ ++SEL+ G++ K+TLGSG K  +F
Sbjct: 566 PNRFSNIIVNLILKEKCYDTKQDRGVMCPTDGYVVFQSSELMCGNLGKTTLGSGNKNGLF 625

Query: 570 YILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           Y L RD  + +A + M R +++++ ++ N G +IGI DVTP
Sbjct: 626 YRLSRDNSQYMAASVMSRFAKLSARWITNYGMTIGISDVTP 666



 Score =  164 bits (415), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 115/357 (32%), Positives = 179/357 (50%), Gaps = 71/357 (19%)

Query: 1108 EKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYIEE 1153
            E+Y +  +EP  AVGA+ A SI EP TQMTLK+FHFAG              E+ +  ++
Sbjct: 1034 ERYPQMLVEPGEAVGAVGATSISEPATQMTLKSFHFAGVASMNITQGVPRMKEIIDAAKK 1093

Query: 1154 VFVP------------DDSFILIKLDMDR------------------------------- 1170
            +  P            + S+  I+L +++                               
Sbjct: 1094 ISTPIIDVKLLPQFQSEHSYRSIRLQIEKTYLGEISNFYQEVYSPKDCHLYIEYNKKKLE 1153

Query: 1171 -IRLLHLEVDIDSIRYCI-ERTRGISGHLTVSGHSFLILKP--------KDSSKSFNSKM 1220
              RL  LE+ + SI+  I E  + I     ++      LKP         D  K+   K+
Sbjct: 1154 QFRLYGLEIPLSSIKKGILEIAKDIKEDQIIAVKD-QDLKPVGIKINPGNDVKKNVFFKI 1212

Query: 1221 YQMKQLLPSVVIKGVQGINRAVIHEEDVEGVT---KYKLLVEGDNLRDVMATYGVKGVKC 1277
               K++LP  V+ G++ + R  I ++  +G     K+ L VEG++ + V+    V     
Sbjct: 1213 QNWKKILPGAVVSGMKDVKRVSISKDKKKGDKNEYKFDLFVEGNSFKQVLQLDEVDFANT 1272

Query: 1278 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRH 1337
             S + +EV + LG+EAAR TI+ EI   +++H +++D RH +LVAD++TSKG + G TR 
Sbjct: 1273 LSVDIFEVLQILGVEAARKTIINEITKTIKSHSLNVDRRHLILVADVLTSKGRLHGSTRQ 1332

Query: 1338 GLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            G+  MK+S L LASFE T++ L++AA  G+ D + GVSE II+G  + +GTG   LL
Sbjct: 1333 GINSMKDSTLMLASFEKTTEILYNAALQGRKDTLEGVSERIIIGQNIPMGTGTFNLL 1389



 Score =  127 bits (320), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 84/251 (33%), Positives = 142/251 (56%), Gaps = 17/251 (6%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYA-RIVKGRLERTTLGEVCEYIEEVFVPD 822
            GVPR+KEII+A++ ISTPII   L      +++ R ++ ++E+T LGE+  + +EV+ P 
Sbjct: 1080 GVPRMKEIIDAAKKISTPIIDVKLLPQFQSEHSYRSIRLQIEKTYLGEISNFYQEVYSPK 1139

Query: 823  DSFILI---KLDMDRIRLLHLEVDIDSIRYCI-ERTRGISGHLTVSGHSFLILKP----- 873
            D  + I   K  +++ RL  LE+ + SI+  I E  + I     ++      LKP     
Sbjct: 1140 DCHLYIEYNKKKLEQFRLYGLEIPLSSIKKGILEIAKDIKEDQIIAVKD-QDLKPVGIKI 1198

Query: 874  ---KDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVT---KYKLLVEGDNL 927
                D  K+   K+   K++LP  V+ G++ + R  I ++  +G     K+ L VEG++ 
Sbjct: 1199 NPGNDVKKNVFFKIQNWKKILPGAVVSGMKDVKRVSISKDKKKGDKNEYKFDLFVEGNSF 1258

Query: 928  RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 987
            + V+    V      S + +EV + LG+EAAR TI+ EI   +++H +++D RH +LVAD
Sbjct: 1259 KQVLQLDEVDFANTLSVDIFEVLQILGVEAARKTIINEITKTIKSHSLNVDRRHLILVAD 1318

Query: 988  LMTSKGEVLGN 998
            ++TSKG + G+
Sbjct: 1319 VLTSKGRLHGS 1329



 Score = 88.6 bits (218), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 72/233 (30%), Positives = 110/233 (47%), Gaps = 45/233 (19%)

Query: 113 RTPIPHGLLDRRMGTNQKEAN--CTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINIL 170
           R P+  G LD RMG + +E N  C TC                        +F  VINIL
Sbjct: 17  RAPLNRGPLDLRMGPSMRENNLKCQTC------------------------FFGDVINIL 52

Query: 171 QSICKNPTCARVLLGEEKAAGFRAKLRNPA--LSYLVRKSLKKKILETTKKVS--VCPHC 226
           Q ICK  +C +VLL E++      +++      +Y +R  L  K+ +  KK +   C  C
Sbjct: 53  QCICK--SCGKVLLDEDEKKNSMKRMQKAIDDKNYQLRADLYVKMRKECKKGANQKCRSC 110

Query: 227 GEINGVVKKCGLLKISHEKYKNRTKKKDAI-----VEDLLAEYNEAVKFNPEIEAHKKFG 281
           G  NG +KK   +  +   + ++TK +         ED+  E    +     +E+     
Sbjct: 111 GYKNGPLKKMPKMPTTIS-FSDQTKLEQDFRDIRESEDIFQENLRKI-----LESKNMKE 164

Query: 282 LIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSV 334
           +I+ LNPLE  ++F  I  ++I  LL N + + P DLILT ++ PP CIRP+V
Sbjct: 165 MIEILNPLETYKIFRKITCDEI--LLFNIQQNHPCDLILTHIIAPPACIRPTV 215



 Score = 85.5 bits (210), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 41/58 (70%), Positives = 47/58 (81%), Gaps = 4/58 (6%)

Query: 613 GFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
           GFV+NSFF+GL+  EFFFHTM GRE LVDTAVKTA+TG    RLVK LEDL V YD++
Sbjct: 797 GFVRNSFFTGLSAPEFFFHTMAGRESLVDTAVKTADTG----RLVKMLEDLSVNYDLT 850



 Score = 42.7 bits (99), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 20/43 (46%), Positives = 28/43 (65%), Gaps = 7/43 (16%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRA 62
           Q L+  K NL++P+NGE       DF+T  YL+T K+ FF+RA
Sbjct: 471 QYLLDVKQNLISPKNGE-------DFLTTAYLITHKDMFFDRA 506


>gi|296417679|ref|XP_002838480.1| hypothetical protein [Tuber melanosporum Mel28]
 gi|295634419|emb|CAZ82671.1| unnamed protein product [Tuber melanosporum]
          Length = 449

 Score =  209 bits (533), Expect = 7e-51,   Method: Compositional matrix adjust.
 Identities = 139/373 (37%), Positives = 197/373 (52%), Gaps = 71/373 (19%)

Query: 1106 CREKYVRAQIEPATAVGALAAQ-------------------------------------- 1127
            C  KY +A++EP +AVGA+ AQ                                      
Sbjct: 62   CLSKYEKAKVEPGSAVGAVGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIINAS 121

Query: 1128 -SIGEPGTQMTLKTFH---------------FAGEVCEYIEEVFVPDDSFILIKLDMDRI 1171
             +I  P    TL T                 +  ++  YIE+V   DD++I I+LD + I
Sbjct: 122  KAISTPIITCTLVTEDDERAARIVKGRIEKTYLEDIISYIEDVCSRDDNYISIRLDQETI 181

Query: 1172 RLLHLEVDIDSIRYCI--ERTRGISGHLTVSGHSFLIL----------KPKDSSKSFNSK 1219
              L LE+ ID I   +   + + I   + V G+   I           + KD S  F  +
Sbjct: 182  SKLQLELTIDDIVTALVKAKLKIIRQDIRVIGNRIRIYVHEMAEKDRKRTKDESDVF-LR 240

Query: 1220 MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSS 1279
            +  +K+ LP VV+KG     RAV+ ++D  G  K ++LVEG  L+  M T GV G K  S
Sbjct: 241  VQNLKRALPRVVVKGYPNAARAVVKKDDKTG--KNQILVEGYGLKLCMNTDGVVGTKTKS 298

Query: 1280 NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGL 1339
            N+  E+ + LGIEAAR +I+ EI   M  HGM ID RH  L+ D+MT KGEVLGITR GL
Sbjct: 299  NSIMEMREVLGIEAARGSIIDEISYTMREHGMDIDPRHMQLLGDVMTYKGEVLGITRFGL 358

Query: 1340 AKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ--AV 1397
            AKM++SVL LASFE T+DHLF+AAF+ ++D + GVSECII+G  M++GTG  K+++   +
Sbjct: 359  AKMRDSVLQLASFEKTTDHLFEAAFHMKSDAVEGVSECIILGQSMSIGTGSFKVVRRLMI 418

Query: 1398 PRSEPVPRTLLFD 1410
               + VP+ L+F+
Sbjct: 419  DPCDLVPKKLVFE 431



 Score =  175 bits (444), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 111/246 (45%), Positives = 147/246 (59%), Gaps = 15/246 (6%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
           GVPRIKEIINAS+ ISTPIIT  L  + D   ARIVKGR+E+T L ++  YIE+V   DD
Sbjct: 110 GVPRIKEIINASKAISTPIITCTLVTEDDERAARIVKGRIEKTYLEDIISYIEDVCSRDD 169

Query: 824 SFILIKLDMDRIRLLHLEVDIDSIRYCI--ERTRGISGHLTVSGHSFLIL---------- 871
           ++I I+LD + I  L LE+ ID I   +   + + I   + V G+   I           
Sbjct: 170 NYISIRLDQETISKLQLELTIDDIVTALVKAKLKIIRQDIRVIGNRIRIYVHEMAEKDRK 229

Query: 872 KPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVM 931
           + KD S  F  ++  +K+ LP VV+KG     RAV+ ++D  G  K ++LVEG  L+  M
Sbjct: 230 RTKDESDVF-LRVQNLKRALPRVVVKGYPNAARAVVKKDDKTG--KNQILVEGYGLKLCM 286

Query: 932 ATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTS 991
            T GV G K  SN+  E+ + LGIEAAR +I+ EI   M  HGM ID RH  L+ D+MT 
Sbjct: 287 NTDGVVGTKTKSNSIMEMREVLGIEAARGSIIDEISYTMREHGMDIDPRHMQLLGDVMTY 346

Query: 992 KGEVLG 997
           KGEVLG
Sbjct: 347 KGEVLG 352



 Score = 52.0 bits (123), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 25/66 (37%), Positives = 42/66 (63%), Gaps = 5/66 (7%)

Query: 668 DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ--AVPRSEPVPRTLLFDNPE- 724
           D  F+AAF+ ++D + GVSECII+G  M++GTG  K+++   +   + VP+ L+F+    
Sbjct: 376 DHLFEAAFHMKSDAVEGVSECIILGQSMSIGTGSFKVVRRLMIDPCDLVPKKLVFEEAYA 435

Query: 725 --FHFP 728
             +H P
Sbjct: 436 KMYHHP 441


>gi|300707342|ref|XP_002995883.1| hypothetical protein NCER_101107 [Nosema ceranae BRL01]
 gi|239605116|gb|EEQ82212.1| hypothetical protein NCER_101107 [Nosema ceranae BRL01]
          Length = 1335

 Score =  205 bits (521), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 125/344 (36%), Positives = 187/344 (54%), Gaps = 67/344 (19%)

Query: 1107 REKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------------- 1145
            ++K     IEP TAVGA+A QSIGEPGTQMTLKTFHFAG                     
Sbjct: 997  KQKIKNCLIEPGTAVGAIAGQSIGEPGTQMTLKTFHFAGVASMNITLGVPRLIEIINAVV 1056

Query: 1146 --------------------------------EVCEYIEEVFVPDDSFILIKLDMDRIRL 1173
                                            ++C ++ +    D  FI  K+D++ I  
Sbjct: 1057 NINTPIINVSLDKNDLLNAQIVKGRVLKVLFKDICNHVTDSVCKDGIFIDFKIDLNLINK 1116

Query: 1174 LHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVV-- 1231
            L L++D+ SI+    +   I+  +T+     L +  K+S    N  +Y +++L   ++  
Sbjct: 1117 LRLQIDMKSIK----QNLNITEQITIINEDTLRVNLKNS---INHAIYNLQKLKKKIMNT 1169

Query: 1232 -IKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLG 1290
             I G+  +N+ +IH +  +G+  +K ++EG  L+ ++   GV     +SN   E+ + LG
Sbjct: 1170 KINGLSSVNKVLIHND--KGM--FKCIIEGYGLQSILGLKGVDYTTTTSNAILEIQEVLG 1225

Query: 1291 IEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLA 1350
            IEAAR+ I++EI+ V+  HG+ ID RH ML+AD MT KGEVLGITR G++KM  S L LA
Sbjct: 1226 IEAARAHIISEIEYVVGKHGIKIDPRHVMLLADTMTYKGEVLGITRFGISKMSCSTLMLA 1285

Query: 1351 SFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            SFE TS+HLF+AA   ++D + GVSE II+G  + +GTG ++L 
Sbjct: 1286 SFEQTSEHLFEAAIRSRSDEVKGVSESIILGKNIGIGTGEVQLF 1329



 Score =  191 bits (484), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 112/276 (40%), Positives = 153/276 (55%), Gaps = 36/276 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + DVVLFNRQPSLH++SIM+H   +  ++T RFNECVC PYNADFDGDEMN+H+PQT EA
Sbjct: 451 NGDVVLFNRQPSLHRMSIMSHFVNIHKNKTLRFNECVCAPYNADFDGDEMNIHVPQTVEA 510

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
            +E +               LM  K N+VT R+GE LIAATQDFIT  YL+T ++ FFNR
Sbjct: 511 ISECIE--------------LMGVKENIVTARHGEPLIAATQDFITALYLITSRDTFFNR 556

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLI----LKPNRD 516
            +  ++ S        I             P + V+   ++TGKQ+   +    LK   D
Sbjct: 557 QKFGQLLSCFCETRIKI------------TPAI-VQPIELFTGKQLVEAMIHSSLKKKSD 603

Query: 517 CPVNANLKTKGRAYTANEEFCH-RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
                NLKTK R++T      H  D + +++N   + G +DK+ +G   K N     L  
Sbjct: 604 V-FKLNLKTKNRSFT---NLWHVNDGFFVIKNGNYMFGRIDKNIVGGESKCNSLLYELLK 659

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
             +  A   M+ ++R+ S YL   GFSIG+ DV PG
Sbjct: 660 IDKLSASAMMFNITRIASRYLGEVGFSIGLVDVLPG 695



 Score =  149 bits (375), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 90/237 (37%), Positives = 143/237 (60%), Gaps = 15/237 (6%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPR+ EIINA  NI+TPII   LDK+ DL  A+IVKGR+ +    ++C ++ +    D 
Sbjct: 1044 GVPRLIEIINAVVNINTPIINVSLDKN-DLLNAQIVKGRVLKVLFKDICNHVTDSVCKDG 1102

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSK 883
             FI  K+D++ I  L L++D+ SI+    +   I+  +T+     L +  K+S    N  
Sbjct: 1103 IFIDFKIDLNLINKLRLQIDMKSIK----QNLNITEQITIINEDTLRVNLKNS---INHA 1155

Query: 884  MYQMKQLLPSVV---IKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
            +Y +++L   ++   I G+  +N+ +IH +  +G+  +K ++EG  L+ ++   GV    
Sbjct: 1156 IYNLQKLKKKIMNTKINGLSSVNKVLIHND--KGM--FKCIIEGYGLQSILGLKGVDYTT 1211

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SN   E+ + LGIEAAR+ I++EI+ V+  HG+ ID RH ML+AD MT KGEVLG
Sbjct: 1212 TTSNAILEIQEVLGIEAARAHIISEIEYVVGKHGIKIDPRHVMLLADTMTYKGEVLG 1268



 Score =  128 bits (322), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 95/306 (31%), Positives = 153/306 (50%), Gaps = 30/306 (9%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           I  ++   + +++ S   + +K+LY     + P+P+G LDRR+G + K+  C TCG+N+ 
Sbjct: 15  ISFSLLSSEEIEKISVHTLTTKDLY-DATTKLPMPNGPLDRRLGISNKKDTCFTCGENII 73

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA-L 201
           +C+GHFG + L LPVF+IG  +  ++IL  +CK  TC R+LL ++K   ++  +R  A  
Sbjct: 74  NCLGHFGNVKLVLPVFNIGLIKQTLSILSCVCK--TCGRLLLSDKKKILYKDMIRETANR 131

Query: 202 SYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHE--------KYKNRTKKK 253
           + LV   +++KI+   KK++ C  C   NG +KK    KI HE           N+ + +
Sbjct: 132 NDLVL--IQRKIVLECKKMTKCVLCHAYNGTIKKGTGFKILHEIEVVELKNSDTNKLRTE 189

Query: 254 DAIVEDLLAEYNEAVKFNPEIEAHKK--FGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAE 311
           +    DL A        N +    KK  F     +NP   L +F  I  ED   L +   
Sbjct: 190 EITGFDLGATSENKNTTNSKARRDKKNTFKKCIDINPQMALNIFSLIKSEDYEFLGLE-- 247

Query: 312 LSKPSDLILTRLLVPPNCIRPSV---ISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPH 368
              P   I+  ++VPP CIRPSV     D  +++D+ +        K+S + H  +VL  
Sbjct: 248 -DSPVKFIIQNIIVPPACIRPSVGMAEKDSTNEDDLTI--------KISEIIHTNEVLKE 298

Query: 369 RTFRFN 374
              R N
Sbjct: 299 SIDRGN 304



 Score =  108 bits (270), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 49/69 (71%), Positives = 60/69 (86%), Gaps = 1/69 (1%)

Query: 608 VTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQ 666
           +TP  +GFV+NSFF+G+TPTEFFFH + GREGLVDTAVKTAETGY QRRL+K+LEDL V+
Sbjct: 806 ITPESKGFVENSFFTGMTPTEFFFHAVSGREGLVDTAVKTAETGYTQRRLMKALEDLNVK 865

Query: 667 YDMSFDAAF 675
           YD S  ++F
Sbjct: 866 YDYSVRSSF 874



 Score = 57.4 bits (137), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 30/62 (48%), Positives = 39/62 (62%), Gaps = 1/62 (1%)

Query: 14  ATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIA 73
           A   C + LM  K N+VT R+GE LIAATQDFIT  YL+T ++ FFNR +  ++ S    
Sbjct: 510 AISECIE-LMGVKENIVTARHGEPLIAATQDFITALYLITSRDTFFNRQKFGQLLSCFCE 568

Query: 74  GR 75
            R
Sbjct: 569 TR 570


>gi|399949784|gb|AFP65441.1| RNA polymerase III largest subunit [Chroomonas mesostigmatica
           CCMP1168]
          Length = 1328

 Score =  205 bits (521), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 110/293 (37%), Positives = 173/293 (59%), Gaps = 46/293 (15%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           +ND+VLFNRQPSLH++SIMAHR K++P +TF+FNEC+C PYNADFDGDEMN+H+PQT++A
Sbjct: 435 NNDIVLFNRQPSLHRISIMAHRIKLIPGKTFKFNECICKPYNADFDGDEMNIHVPQTQKA 494

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+  L+ +              +NL +P NGE  ++ATQDF++  +L+T K+ FF+ 
Sbjct: 495 RAEAISLLNII--------------TNLNSPANGESQVSATQDFLSASFLITSKDQFFSE 540

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLIL--------- 511
           ++   + S L          ++ F  +   P + ++   +WTGKQIFSL++         
Sbjct: 541 SEIGEVFSIL---------KLEEFKHKKTEPSI-LKPHKLWTGKQIFSLVISRKIERSLK 590

Query: 512 ---KPNRDCPVNANLKTK-GRAYTANEEFCHR-----DSYVILRNSELLAGSMDKSTLGS 562
              + N  C +N  +  K  + Y+ N++ C       D ++  +N ELLAG + K T+GS
Sbjct: 591 IRRRKNISCDINNLIYQKMEKLYSLNKKHCSSSLCPFDGWIFFKNGELLAGQVGKLTIGS 650

Query: 563 GGKANV--FYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQG 613
           G K ++  F+  L  F  +     + ++S++TS +L + GFS    ++ P  G
Sbjct: 651 GNKNSLLNFFSNLDSF--NFLTKCLLKISKLTSGWLSDFGFSFSFKEILPTFG 701



 Score =  120 bits (301), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 104/353 (29%), Positives = 168/353 (47%), Gaps = 77/353 (21%)

Query: 1113 AQIEPATAVGALAAQSIGEPGTQM----------------------------------TL 1138
             +IEP T VGA++AQS+GEP TQM                                  +L
Sbjct: 985  CKIEPGTCVGAISAQSLGEPATQMTLQTFHFTGIADMNITLGVPRLNEIMNASKKIAVSL 1044

Query: 1139 KTFHF--------------------AGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEV 1178
              F+F                     G++CE +     P + FI I L     R  +L +
Sbjct: 1045 IKFNFFSMGKKLNFYKFKIQIEKIYLGDICEKLNLKIEPKEIFIEIFLKGKNFRNFNLNI 1104

Query: 1179 DIDSIRYCI-------ERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMY--QMKQLLPS 1229
               +I   I       +++R            F + K KD+S S  +  +  + ++ LPS
Sbjct: 1105 RFKAIIKKIKEIGTFWKKSRFFYNPFCNFIQIFPLKKCKDNSVSDETSHFVNRCRKDLPS 1164

Query: 1230 VVIKGVQG-----INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYE 1284
            ++I G        I++  +H   +   +K+  ++E D++ D    Y      C+  +   
Sbjct: 1165 ILIFGFVNVENIEIDKNFLHSSILLKNSKFWKILELDSV-DKSTIY------CT--HILT 1215

Query: 1285 VYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKE 1344
            +++T GIEAAR +I+ EIK + + + +SI+ R+ +L+AD+MT  GE+LG TR+GLAKMK+
Sbjct: 1216 IFETFGIEAARESIILEIKTIFDLYKISINKRYLVLLADVMTFYGEILGATRYGLAKMKK 1275

Query: 1345 SVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 1397
            + L LASFE T ++LF A+     D I  VSE II+G   + GTG++ L  ++
Sbjct: 1276 NFLVLASFEKTIENLFSASIKISKDEILSVSESIILGKNPSNGTGIVSLNSSI 1328



 Score =  116 bits (291), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 85/251 (33%), Positives = 129/251 (51%), Gaps = 24/251 (9%)

Query: 97  SHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP 156
           S IQ+ +  LY +    T I  G+LD +MG   K   C TC +NL  C+GH GYI L LP
Sbjct: 29  SSIQLANSFLYSKFSTET-IQGGILDSKMGAINKTL-CKTCKKNLKKCLGHCGYIKLFLP 86

Query: 157 VFHIGYFRCVINILQSICKNPTCARVLL--GEEKAAGFR--AKLRNPALSYLVRKSLKKK 212
           VF+IGY + +  ILQ ICK   C+R+L+  G+++ A  +   K+R     Y  R      
Sbjct: 87  VFNIGYLKAIQIILQIICK--ACSRILVEPGKKRKAFVKRIRKIRKKGEHY--RIEYITD 142

Query: 213 ILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNP 272
           +L+  K   +CP+C   NG +KK G  +  H            I ED +  ++E  K   
Sbjct: 143 LLKKCKNSDLCPYCLSRNGRIKKSGNYEFIHT---------IEIEEDGIPLFHEK-KTEK 192

Query: 273 EIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRP 332
            + A ++      LNPL +  LF+ I  ED+ +L ++   ++P +L+   + VPP  +RP
Sbjct: 193 VLTAFEEI----ELNPLNIFLLFQKIKFEDLEILDIDEIETRPENLLTCFIPVPPLIVRP 248

Query: 333 SVISDLKSDND 343
           S+I   K  N+
Sbjct: 249 SIILKEKMSNE 259



 Score = 94.4 bits (233), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 38/59 (64%), Positives = 52/59 (88%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
           +GF++NSF+ GL   +FFFH+M GREGLVDTA+KTAE+GY+QRR++K+LED+ V YD+S
Sbjct: 818 KGFIENSFYEGLDGIDFFFHSMAGREGLVDTAIKTAESGYLQRRMIKTLEDIIVFYDLS 876



 Score = 80.9 bits (198), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 70/249 (28%), Positives = 128/249 (51%), Gaps = 25/249 (10%)

Query: 764  GVPRIKEIINASRNISTPIIT-AYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPD 822
            GVPR+ EI+NAS+ I+  +I   +      L++ +  K ++E+  LG++CE +     P 
Sbjct: 1026 GVPRLNEIMNASKKIAVSLIKFNFFSMGKKLNFYKF-KIQIEKIYLGDICEKLNLKIEPK 1084

Query: 823  DSFILIKLDMDRIRLLHLEVDIDSIRYCI-------ERTRGISGHLTVSGHSFLILKPKD 875
            + FI I L     R  +L +   +I   I       +++R            F + K KD
Sbjct: 1085 EIFIEIFLKGKNFRNFNLNIRFKAIIKKIKEIGTFWKKSRFFYNPFCNFIQIFPLKKCKD 1144

Query: 876  SSKSFNSKMY--QMKQLLPSVVIKGVQG-----INRAVIHEEDVEGVTKYKLLVEGDNLR 928
            +S S  +  +  + ++ LPS++I G        I++  +H   +   +K+  ++E D++ 
Sbjct: 1145 NSVSDETSHFVNRCRKDLPSILIFGFVNVENIEIDKNFLHSSILLKNSKFWKILELDSV- 1203

Query: 929  DVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADL 988
            D    Y      C+  +   +++T GIEAAR +I+ EIK + + + +SI+ R+ +L+AD+
Sbjct: 1204 DKSTIY------CT--HILTIFETFGIEAARESIILEIKTIFDLYKISINKRYLVLLADV 1255

Query: 989  MTSKGEVLG 997
            MT  GE+LG
Sbjct: 1256 MTFYGEILG 1264



 Score = 43.9 bits (102), Expect = 0.67,   Method: Compositional matrix adjust.
 Identities = 18/45 (40%), Positives = 31/45 (68%)

Query: 27  SNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           +NL +P NGE  ++ATQDF++  +L+T K+ FF+ ++   + S L
Sbjct: 506 TNLNSPANGESQVSATQDFLSASFLITSKDQFFSESEIGEVFSIL 550


>gi|145492039|ref|XP_001432018.1| hypothetical protein [Paramecium tetraurelia strain d4-2]
 gi|124399125|emb|CAK64620.1| unnamed protein product [Paramecium tetraurelia]
          Length = 1360

 Score =  202 bits (515), Expect = 8e-49,   Method: Compositional matrix adjust.
 Identities = 108/278 (38%), Positives = 166/278 (59%), Gaps = 29/278 (10%)

Query: 343 DVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARA 402
           D+V+FNRQPSLH++S+MA RA+V    T RFNECVCTP+NADFDGDEMN+HLPQT EAR+
Sbjct: 422 DIVIFNRQPSLHRISMMAFRARVDKWHTLRFNECVCTPFNADFDGDEMNIHLPQTYEARS 481

Query: 403 EALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 462
           EAL              +LM  K NL T ++GE L+   QDF+T  +L+T K+ F++R Q
Sbjct: 482 EAL--------------ILMDVKKNLKTIKSGESLVCLLQDFLTTAWLITNKDVFYSREQ 527

Query: 463 TMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNAN 522
            M+  +   +D+++   +          P + ++   +WTGKQ+ + +L PNR   +  N
Sbjct: 528 FMQFCAAF-SDSNEQIDLPA--------PTI-LKPKQLWTGKQVINALLVPNRKTRLVLN 577

Query: 523 LKTK-GRAYTANEEFCHR---DSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
           L+ K   A+    ++      D YV+    EL+ G++ K  LG+  K  +FY L+RD   
Sbjct: 578 LEAKESNAFKGKLDYLWMDPGDGYVVFDKCELVCGNIGKKVLGA-SKLGLFYALIRDNST 636

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
            +A + M R ++++S ++ + G +IGIGDV   +  ++
Sbjct: 637 QIAASVMQRFAKLSSRWISHYGMTIGIGDVMAPKSLIE 674



 Score =  120 bits (300), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 67/190 (35%), Positives = 111/190 (58%), Gaps = 4/190 (2%)

Query: 1222 QMKQLLPSVVIKGVQGINRAVIH---EEDVEGVT-KYKLLVEGDNLRDVMATYGVKGVKC 1277
            ++++ L  + I G   I + VI    ++D E V  + +L   G   ++++    +   + 
Sbjct: 1161 ELQRKLLRLHIYGCANIKQTVIQVTDKDDKENVKGEARLFASGIGFKEILRLDNIDWKRT 1220

Query: 1278 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRH 1337
             SN+  E+   LGIEAAR +I+ E+   M++H +SID RH +L+A+LMT KG +LG TR 
Sbjct: 1221 VSNHIMEIQSALGIEAARQSIVNEVYTTMQSHSISIDIRHILLLAELMTFKGRILGFTRQ 1280

Query: 1338 GLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 1397
            G+ ++K S L LASFE T D  F+AA  G+ D ++G S+ +I+G  +  GTG+  L+  V
Sbjct: 1281 GIDQLKNSALMLASFEKTMDVFFNAAIQGKQDSMNGASQRVIIGQNVPQGTGMFDLMFPV 1340

Query: 1398 PRSEPVPRTL 1407
              +  +  T+
Sbjct: 1341 KENTILESTI 1350



 Score = 93.6 bits (231), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 40/60 (66%), Positives = 49/60 (81%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV+NSF++G+   EF+FH M GREGL DTAVKTA TGYMQRRLVK LEDL + YD++
Sbjct: 789 AKGFVKNSFYTGMDAIEFYFHNMAGREGLTDTAVKTATTGYMQRRLVKMLEDLHIAYDLT 848



 Score = 92.0 bits (227), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 76/279 (27%), Positives = 136/279 (48%), Gaps = 55/279 (19%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARI------------------------- 798
            GVPR+ EIINAS+ I TP I   L     +D+A+                          
Sbjct: 1008 GVPRLNEIINASKEIKTPQINVKLINRQVMDHAKQFAKSGDPQYEYAHRAVIHSAQQAQD 1067

Query: 799  VKGRLERTTLGEVCEYIEEVFVPDDSFILIKLD---MDRIRL-------------LHLEV 842
            V  ++E+T L ++ + ++E++  D+ +I ++LD   + R++L               L++
Sbjct: 1068 VNIQIEQTKLMQILKKMDEIYTADNCYIELELDCHCLARLKLEFVTPKYVCALILKELKL 1127

Query: 843  DIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGI 902
              D ++Y ++  R     +TV   S      K  S++    + ++++ L  + I G   I
Sbjct: 1128 SPDDVKYDLKIIR-----ITVKKSS-----KKKQSENLLFLIKELQRKLLRLHIYGCANI 1177

Query: 903  NRAVIH---EEDVEGVT-KYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAA 958
             + VI    ++D E V  + +L   G   ++++    +   +  SN+  E+   LGIEAA
Sbjct: 1178 KQTVIQVTDKDDKENVKGEARLFASGIGFKEILRLDNIDWKRTVSNHIMEIQSALGIEAA 1237

Query: 959  RSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            R +I+ E+   M++H +SID RH +L+A+LMT KG +LG
Sbjct: 1238 RQSIVNEVYTTMQSHSISIDIRHILLLAELMTFKGRILG 1276



 Score = 80.5 bits (197), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 106/235 (45%), Gaps = 47/235 (20%)

Query: 116 IPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICK 175
           I HG LD RMG + ++  C++C   L++C GHFGYI L LP++H+G+F  V+  L+ +C 
Sbjct: 47  IEHGPLDLRMGQSLRDTQCSSCTL-LNECPGHFGYIPLQLPIYHLGFFTHVVKCLKCLCY 105

Query: 176 NPTCARVLLGEEKAAGFRAKLRN--PALSYLVRKSLKKKILETTKKVSVCPHC-GEINGV 232
              C +V L  ++      K+ +     SY  +  + KK+L+  +    CPHC  E  G 
Sbjct: 106 K--CGQVRLTPDEINQLTQKMVHCIQTRSYNAQLKVFKKVLKKCRSNKQCPHCYCEQIGE 163

Query: 233 VKKCGLLKISHEKYKNRTKKKDA--IVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLE 290
            KK                K DA  I+ D +                        +N L 
Sbjct: 164 AKKLA--------------KGDAGKIILDTM-----------------------DINALY 186

Query: 291 VLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVI--SDLKSDND 343
               F  IP +   L  +N  L+  SDL+ + +  PPN IRPS +  +  K+D D
Sbjct: 187 AWNQFSNIPKQHQFLFCINPFLNDLSDLLTSIIPAPPNNIRPSKMLSNTTKADED 241



 Score = 52.4 bits (124), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 22/38 (57%), Positives = 29/38 (76%)

Query: 1108 EKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            E+++   + P T+VG + +QSIGEP TQMTLKTFH AG
Sbjct: 962  ERFLTMVMAPGTSVGPITSQSIGEPATQMTLKTFHSAG 999



 Score = 47.4 bits (111), Expect = 0.063,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 35/59 (59%)

Query: 13  YATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           Y  R+   +LM  K NL T ++GE L+   QDF+T  +L+T K+ F++R Q M+  +  
Sbjct: 477 YEARSEALILMDVKKNLKTIKSGESLVCLLQDFLTTAWLITNKDVFYSREQFMQFCAAF 535


>gi|74830400|emb|CAI39062.1| DNA-directed RNA polymerase III largest subunit [Paramecium
           tetraurelia]
          Length = 1368

 Score =  202 bits (515), Expect = 8e-49,   Method: Compositional matrix adjust.
 Identities = 108/278 (38%), Positives = 166/278 (59%), Gaps = 29/278 (10%)

Query: 343 DVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARA 402
           D+V+FNRQPSLH++S+MA RA+V    T RFNECVCTP+NADFDGDEMN+HLPQT EAR+
Sbjct: 422 DIVIFNRQPSLHRISMMAFRARVDKWHTLRFNECVCTPFNADFDGDEMNIHLPQTYEARS 481

Query: 403 EALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 462
           EAL              +LM  K NL T ++GE L+   QDF+T  +L+T K+ F++R Q
Sbjct: 482 EAL--------------ILMDVKKNLKTIKSGESLVCLLQDFLTTAWLITNKDVFYSREQ 527

Query: 463 TMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNAN 522
            M+  +   +D+++   +          P + ++   +WTGKQ+ + +L PNR   +  N
Sbjct: 528 FMQFCAAF-SDSNEQIDLPA--------PTI-LKPKQLWTGKQVINALLVPNRKTRLVLN 577

Query: 523 LKTK-GRAYTANEEFCHR---DSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
           L+ K   A+    ++      D YV+    EL+ G++ K  LG+  K  +FY L+RD   
Sbjct: 578 LEAKESNAFKGKLDYLWMDPGDGYVVFDKCELVCGNIGKKVLGA-SKLGLFYALIRDNST 636

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
            +A + M R ++++S ++ + G +IGIGDV   +  ++
Sbjct: 637 QIAASVMQRFAKLSSRWISHYGMTIGIGDVMAPKSLIE 674



 Score =  120 bits (300), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 67/190 (35%), Positives = 111/190 (58%), Gaps = 4/190 (2%)

Query: 1222 QMKQLLPSVVIKGVQGINRAVIH---EEDVEGVT-KYKLLVEGDNLRDVMATYGVKGVKC 1277
            ++++ L  + I G   I + VI    ++D E V  + +L   G   ++++    +   + 
Sbjct: 1169 ELQRKLLRLHIYGCANIKQTVIQVTDKDDKENVKGEARLFASGIGFKEILRLDNIDWKRT 1228

Query: 1278 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRH 1337
             SN+  E+   LGIEAAR +I+ E+   M++H +SID RH +L+A+LMT KG +LG TR 
Sbjct: 1229 VSNHIMEIQSALGIEAARQSIVNEVYTTMQSHSISIDIRHILLLAELMTFKGRILGFTRQ 1288

Query: 1338 GLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 1397
            G+ ++K S L LASFE T D  F+AA  G+ D ++G S+ +I+G  +  GTG+  L+  V
Sbjct: 1289 GIDQLKNSALMLASFEKTMDVFFNAAIQGKQDSMNGASQRVIIGQNVPQGTGMFDLMFPV 1348

Query: 1398 PRSEPVPRTL 1407
              +  +  T+
Sbjct: 1349 KENTILESTI 1358



 Score = 93.6 bits (231), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 40/60 (66%), Positives = 49/60 (81%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV+NSF++G+   EF+FH M GREGL DTAVKTA TGYMQRRLVK LEDL + YD++
Sbjct: 797 AKGFVKNSFYTGMDAIEFYFHNMAGREGLTDTAVKTATTGYMQRRLVKMLEDLHIAYDLT 856



 Score = 92.0 bits (227), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 76/279 (27%), Positives = 136/279 (48%), Gaps = 55/279 (19%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARI------------------------- 798
            GVPR+ EIINAS+ I TP I   L     +D+A+                          
Sbjct: 1016 GVPRLNEIINASKEIKTPQINVKLINRQVMDHAKQFAKSGDPQYEYAHRAVIHSAQQAQD 1075

Query: 799  VKGRLERTTLGEVCEYIEEVFVPDDSFILIKLD---MDRIRL-------------LHLEV 842
            V  ++E+T L ++ + ++E++  D+ +I ++LD   + R++L               L++
Sbjct: 1076 VNIQIEQTKLMQILKKMDEIYTADNCYIELELDCHCLARLKLEFVTPKYVCALILKELKL 1135

Query: 843  DIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGI 902
              D ++Y ++  R     +TV   S      K  S++    + ++++ L  + I G   I
Sbjct: 1136 SPDDVKYDLKIIR-----ITVKKSS-----KKKQSENLLFLIKELQRKLLRLHIYGCANI 1185

Query: 903  NRAVIH---EEDVEGVT-KYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAA 958
             + VI    ++D E V  + +L   G   ++++    +   +  SN+  E+   LGIEAA
Sbjct: 1186 KQTVIQVTDKDDKENVKGEARLFASGIGFKEILRLDNIDWKRTVSNHIMEIQSALGIEAA 1245

Query: 959  RSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            R +I+ E+   M++H +SID RH +L+A+LMT KG +LG
Sbjct: 1246 RQSIVNEVYTTMQSHSISIDIRHILLLAELMTFKGRILG 1284



 Score = 80.1 bits (196), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 106/235 (45%), Gaps = 47/235 (20%)

Query: 116 IPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICK 175
           I HG LD RMG + ++  C++C   L++C GHFGYI L LP++H+G+F  V+  L+ +C 
Sbjct: 47  IEHGPLDLRMGQSLRDTQCSSCTL-LNECPGHFGYIPLQLPIYHLGFFTHVVKCLKCLCY 105

Query: 176 NPTCARVLLGEEKAAGFRAKLRN--PALSYLVRKSLKKKILETTKKVSVCPHC-GEINGV 232
              C +V L  ++      K+ +     SY  +  + KK+L+  +    CPHC  E  G 
Sbjct: 106 K--CGQVRLTPDEINQLTQKMVHCIQTRSYNAQLKVFKKVLKKCRSNKQCPHCYCEQIGE 163

Query: 233 VKKCGLLKISHEKYKNRTKKKDA--IVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLE 290
            KK                K DA  I+ D +                        +N L 
Sbjct: 164 AKKLA--------------KGDAGKIILDTM-----------------------DINALY 186

Query: 291 VLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVI--SDLKSDND 343
               F  IP +   L  +N  L+  SDL+ + +  PPN IRPS +  +  K+D D
Sbjct: 187 AWNQFSNIPKQHQFLFCINPFLNDLSDLLTSIIPAPPNNIRPSKMLSNTTKADED 241



 Score = 52.4 bits (124), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 22/38 (57%), Positives = 29/38 (76%)

Query: 1108 EKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            E+++   + P T+VG + +QSIGEP TQMTLKTFH AG
Sbjct: 970  ERFLTMVMAPGTSVGPITSQSIGEPATQMTLKTFHSAG 1007



 Score = 47.4 bits (111), Expect = 0.066,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 35/59 (59%)

Query: 13  YATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           Y  R+   +LM  K NL T ++GE L+   QDF+T  +L+T K+ F++R Q M+  +  
Sbjct: 477 YEARSEALILMDVKKNLKTIKSGESLVCLLQDFLTTAWLITNKDVFYSREQFMQFCAAF 535


>gi|357472533|ref|XP_003606551.1| DNA-directed RNA polymerase [Medicago truncatula]
 gi|355507606|gb|AES88748.1| DNA-directed RNA polymerase [Medicago truncatula]
          Length = 550

 Score =  201 bits (512), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 136/397 (34%), Positives = 199/397 (50%), Gaps = 105/397 (26%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCE 1149
            + C  +Y   +IE  T +GA+ A SIGEPGTQMTLKTFHFAG              E+  
Sbjct: 147  DICLSRYRLKKIEAGTPIGAIGAHSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIIEIIN 206

Query: 1150 YIEEVFVP--------DD--------------------------------SFILIKLDMD 1169
                +  P        DD                                + + I LDM 
Sbjct: 207  GASNIKTPIITAILERDDNAKTAKIVKGCIEKTNLGQVAKSIKVVYSNKLAAVFISLDMG 266

Query: 1170 RIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLIL-------KPKDSSKS-FNSKMY 1221
             I    L +D + ++  I +T    G L +   +  IL       +P+ SS+S    ++ 
Sbjct: 267  IIEKAGLNIDANIVKESILQT----GKLKLKPENVKILDIKKLQVEPQGSSRSELLFQLN 322

Query: 1222 QMKQLLPSVVIKGVQGINRAVIHEEDVE------------------------GVTKYKLL 1257
             +K LLPSVV+KGV+ + R V+  + ++                         V + +++
Sbjct: 323  NLKNLLPSVVVKGVKTVERTVLEIKKIKTNSGKESEKYTLLGMSVAPKECSRSVLRRRMI 382

Query: 1258 VEGD------------NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLV 1305
            + G+             L++VM   GV G K  +N+  E+   LGIEAAR  I+ +I+  
Sbjct: 383  LTGNIIVASSLVLLNKGLKEVMGIEGVDGHKTVTNHIIELMNILGIEAARYGIIDQIQYT 442

Query: 1306 MENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFY 1365
            M+ HGMSID RH ML+AD+MT +G+VLG+TRHG+ KM  S L LASFE+++D+LFDA+  
Sbjct: 443  MKQHGMSIDVRHIMLLADMMTVRGQVLGMTRHGIQKMGRSALMLASFESSTDYLFDASLR 502

Query: 1366 GQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEP 1402
            G+ D I GVS+CIIMG P+++GTG+I++ Q   R EP
Sbjct: 503  GKGDPIEGVSDCIIMGKPIHIGTGMIEVKQ---RLEP 536



 Score =  150 bits (378), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 99/278 (35%), Positives = 151/278 (54%), Gaps = 48/278 (17%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
           GVPRI EIIN + NI TPIITA L++D +   A+IVKG +E+T LG+V + I+ V+    
Sbjct: 197 GVPRIIEIINGASNIKTPIITAILERDDNAKTAKIVKGCIEKTNLGQVAKSIKVVYSNKL 256

Query: 824 SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLIL-------KPKDS 876
           + + I LDM  I    L +D + ++  I +T    G L +   +  IL       +P+ S
Sbjct: 257 AAVFISLDMGIIEKAGLNIDANIVKESILQT----GKLKLKPENVKILDIKKLQVEPQGS 312

Query: 877 SKS-FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVE---------------------- 913
           S+S    ++  +K LLPSVV+KGV+ + R V+  + ++                      
Sbjct: 313 SRSELLFQLNNLKNLLPSVVVKGVKTVERTVLEIKKIKTNSGKESEKYTLLGMSVAPKEC 372

Query: 914 --GVTKYKLLVEGD------------NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAAR 959
              V + ++++ G+             L++VM   GV G K  +N+  E+   LGIEAAR
Sbjct: 373 SRSVLRRRMILTGNIIVASSLVLLNKGLKEVMGIEGVDGHKTVTNHIIELMNILGIEAAR 432

Query: 960 STIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             I+ +I+  M+ HGMSID RH ML+AD+MT +G+VLG
Sbjct: 433 YGIIDQIQYTMKQHGMSIDVRHIMLLADMMTVRGQVLG 470



 Score = 50.4 bits (119), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 24/46 (52%), Positives = 33/46 (71%), Gaps = 3/46 (6%)

Query: 668 DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEP 713
           D  FDA+  G+ D I GVS+CIIMG P+++GTG+I++ Q   R EP
Sbjct: 494 DYLFDASLRGKGDPIEGVSDCIIMGKPIHIGTGMIEVKQ---RLEP 536



 Score = 42.7 bits (99), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 18/25 (72%), Positives = 22/25 (88%)

Query: 644 VKTAETGYMQRRLVKSLEDLCVQYD 668
           VKTA+TGYM RRL+K+LEDL + YD
Sbjct: 2   VKTADTGYMSRRLMKALEDLFLHYD 26


>gi|392512733|emb|CAD25541.2| DNA-DIRECTED RNA POLYMERASE III 160 kDa SUBUNIT (LARGEST SUBUNIT)
           [Encephalitozoon cuniculi GB-M1]
          Length = 1316

 Score =  198 bits (503), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 118/280 (42%), Positives = 159/280 (56%), Gaps = 38/280 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIM+H+ +V  ++T RFNECVCTPYNADFDGDEMNVH+PQTE+A
Sbjct: 427 DGDMVLFNRQPSLHRMSIMSHKVRVHRNKTLRFNECVCTPYNADFDGDEMNVHVPQTEKA 486

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A VLM+  +N+VTPR+GE ++AATQDFITG YL+T K+ FF+R
Sbjct: 487 RAE--------------ASVLMSVSNNIVTPRHGEPIVAATQDFITGLYLITGKDTFFDR 532

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAV-IWTGKQIFSLILKPNRDCPV 519
            +  ++ S               FS         +R  V ++TGKQ+  +++K +    +
Sbjct: 533 ERFGQLVSY--------------FSEARVGVKPAIRKPVELFTGKQLIEVLIKDSFTASI 578

Query: 520 NANLKTKGRAYT---ANEEFCHRD-----SYVILRNSELLAGSMDKSTLGSGGKANVFYI 571
             N  T   A +    N  F   D     S  IL NS    G +DKS +G   K +    
Sbjct: 579 ERNAVTGNMAVSLVGKNRSFKTHDDPNDGSVAILDNSYYF-GRLDKSIVGGENKRDSLIY 637

Query: 572 LLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
            +       AV AM  ++++ S YL   GFSIG+ DV PG
Sbjct: 638 AIMKVSSMAAVRAMNSITKLCSRYLGETGFSIGLDDVQPG 677



 Score =  192 bits (488), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 129/336 (38%), Positives = 182/336 (54%), Gaps = 54/336 (16%)

Query: 1108 EKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYIEE 1153
            +K +   +EP T VGA+A QSIGEPGTQMTLKTFHFAG              E+   +  
Sbjct: 979  QKMMNLIVEPGTTVGAIAGQSIGEPGTQMTLKTFHFAGVASMNITLGVPRLKEIINAVCN 1038

Query: 1154 VFVP------DDSFIL-----IKLDMDRIRL-----------------LHLEVDIDSIR- 1184
            +  P      DD   L     IK  +DRI L                 L + VD++S+  
Sbjct: 1039 ISTPIINAELDDPHDLFRTEVIKGRLDRISLKDVCSSLTEVISKDEIFLDIRVDLESLSR 1098

Query: 1185 -------YCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQG 1237
                   + IE+       + V   + L +  K  +      + ++K+ L +  I G   
Sbjct: 1099 LKLNLDIHKIEKLLNNHDQVRVVNENTLRVSIKKITDQSYFNLQRIKKKLLNTKICGAPQ 1158

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            +NR +I+     G+  Y L++EG  L +V+   GVK +  +SN+  EV + LGIEAAR+ 
Sbjct: 1159 VNRVIINSS--RGL--YSLVIEGRGLLNVINIDGVKAINTTSNSITEVEEVLGIEAARAQ 1214

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  + NHG+ ID RH ML+AD MT +GEV GITR G++KM  S L LASFE TSD
Sbjct: 1215 IIHEIEYTISNHGIKIDPRHIMLLADTMTYRGEVFGITRFGISKMSRSTLMLASFEQTSD 1274

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            +LF+AA   ++D I GVSE II+G+P+ +GTG + L
Sbjct: 1275 YLFEAAVQSKSDEICGVSESIILGIPICIGTGSMDL 1310



 Score =  151 bits (382), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 93/234 (39%), Positives = 138/234 (58%), Gaps = 8/234 (3%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPR+KEIINA  NISTPII A LD   DL    ++KGRL+R +L +VC  + EV   D+
Sbjct: 1025 GVPRLKEIINAVCNISTPIINAELDDPHDLFRTEVIKGRLDRISLKDVCSSLTEVISKDE 1084

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSK 883
             F+ I++D++ +  L L +DI    + IE+       + V   + L +  K  +      
Sbjct: 1085 IFLDIRVDLESLSRLKLNLDI----HKIEKLLNNHDQVRVVNENTLRVSIKKITDQSYFN 1140

Query: 884  MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSS 943
            + ++K+ L +  I G   +NR +I+     G+  Y L++EG  L +V+   GVK +  +S
Sbjct: 1141 LQRIKKKLLNTKICGAPQVNRVIINSS--RGL--YSLVIEGRGLLNVINIDGVKAINTTS 1196

Query: 944  NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            N+  EV + LGIEAAR+ I+ EI+  + NHG+ ID RH ML+AD MT +GEV G
Sbjct: 1197 NSITEVEEVLGIEAARAQIIHEIEYTISNHGIKIDPRHIMLLADTMTYRGEVFG 1250



 Score =  129 bits (324), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 93/269 (34%), Positives = 138/269 (51%), Gaps = 32/269 (11%)

Query: 100 QIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFH 159
           +I SK+LY     R P+P+G LD R+G   K+  C TCG+ L+ C+GHFG + L LPVF+
Sbjct: 34  EISSKDLY-DISTRAPLPNGPLDLRLGVGNKKDKCATCGEGLATCIGHFGEVRLVLPVFN 92

Query: 160 IGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKK 219
           +G  +  I+ L  +CK  +C  +LL E+K   F+ KLR  +     +  L++ + E  KK
Sbjct: 93  VGLIKNTISTLNCLCK--SCGSILLNEKKKIYFKKKLRESSGGNDTKLILRRIVAE-CKK 149

Query: 220 VSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKK 279
           V+VC  C   NG +KK    +I HE      +KKD              K +  + +   
Sbjct: 150 VNVCFVCSFRNGQIKKTFGFRIVHEVEDLEKRKKD-----------RGSKGSDGVHS--- 195

Query: 280 FGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLK 339
               + +NPL  L +F  +  +D  LL     L  PS LI+  ++VPP+CIRPSV  D +
Sbjct: 196 -SCCEEINPLVALNVFNMMKEDDYELL---GFLESPSRLIIQNVIVPPSCIRPSVSMDDE 251

Query: 340 SDN--DVVLFNRQPSLHKLSIMAHRAKVL 366
             N  D+ +        K+S + H  KVL
Sbjct: 252 GTNEDDITI--------KISEIVHTNKVL 272



 Score =  102 bits (253), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 49/66 (74%), Positives = 54/66 (81%), Gaps = 1/66 (1%)

Query: 606 GDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           G  TP  +GFV NSFF GLT  EFFFH + GREGLVDTAVKTAETGYMQRRL+K+LEDL 
Sbjct: 789 GSRTPESKGFVLNSFFDGLTSPEFFFHAVSGREGLVDTAVKTAETGYMQRRLMKALEDLS 848

Query: 665 VQYDMS 670
           +QYD S
Sbjct: 849 IQYDGS 854



 Score = 60.5 bits (145), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 28/55 (50%), Positives = 40/55 (72%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM+  +N+VTPR+GE ++AATQDFITG YL+T K+ FF+R +  ++ S     R
Sbjct: 492 VLMSVSNNIVTPRHGEPIVAATQDFITGLYLITGKDTFFDRERFGQLVSYFSEAR 546


>gi|19074431|ref|NP_585937.1| DNA-DIRECTED RNA POLYMERASE III 160 kDa SUBUNIT (LARGEST SUBUNIT)
           [Encephalitozoon cuniculi GB-M1]
          Length = 1349

 Score =  197 bits (502), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 117/279 (41%), Positives = 160/279 (57%), Gaps = 36/279 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIM+H+ +V  ++T RFNECVCTPYNADFDGDEMNVH+PQTE+A
Sbjct: 460 DGDMVLFNRQPSLHRMSIMSHKVRVHRNKTLRFNECVCTPYNADFDGDEMNVHVPQTEKA 519

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A VLM+  +N+VTPR+GE ++AATQDFITG YL+T K+ FF+R
Sbjct: 520 RAE--------------ASVLMSVSNNIVTPRHGEPIVAATQDFITGLYLITGKDTFFDR 565

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +  ++ S        +   I++       PV       ++TGKQ+  +++K +    + 
Sbjct: 566 ERFGQLVSYFSEARVGVKPAIRK-------PV------ELFTGKQLIEVLIKDSFTASIE 612

Query: 521 ANLKTKGRAYT---ANEEFCHRD-----SYVILRNSELLAGSMDKSTLGSGGKANVFYIL 572
            N  T   A +    N  F   D     S  IL NS    G +DKS +G   K +     
Sbjct: 613 RNAVTGNMAVSLVGKNRSFKTHDDPNDGSVAILDNSYYF-GRLDKSIVGGENKRDSLIYA 671

Query: 573 LRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           +       AV AM  ++++ S YL   GFSIG+ DV PG
Sbjct: 672 IMKVSSMAAVRAMNSITKLCSRYLGETGFSIGLDDVQPG 710



 Score =  192 bits (489), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 129/336 (38%), Positives = 182/336 (54%), Gaps = 54/336 (16%)

Query: 1108 EKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYIEE 1153
            +K +   +EP T VGA+A QSIGEPGTQMTLKTFHFAG              E+   +  
Sbjct: 1012 QKMMNLIVEPGTTVGAIAGQSIGEPGTQMTLKTFHFAGVASMNITLGVPRLKEIINAVCN 1071

Query: 1154 VFVP------DDSFIL-----IKLDMDRIRL-----------------LHLEVDIDSIR- 1184
            +  P      DD   L     IK  +DRI L                 L + VD++S+  
Sbjct: 1072 ISTPIINAELDDPHDLFRTEVIKGRLDRISLKDVCSSLTEVISKDEIFLDIRVDLESLSR 1131

Query: 1185 -------YCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQG 1237
                   + IE+       + V   + L +  K  +      + ++K+ L +  I G   
Sbjct: 1132 LKLNLDIHKIEKLLNNHDQVRVVNENTLRVSIKKITDQSYFNLQRIKKKLLNTKICGAPQ 1191

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            +NR +I+     G+  Y L++EG  L +V+   GVK +  +SN+  EV + LGIEAAR+ 
Sbjct: 1192 VNRVIINSS--RGL--YSLVIEGRGLLNVINIDGVKAINTTSNSITEVEEVLGIEAARAQ 1247

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  + NHG+ ID RH ML+AD MT +GEV GITR G++KM  S L LASFE TSD
Sbjct: 1248 IIHEIEYTISNHGIKIDPRHIMLLADTMTYRGEVFGITRFGISKMSRSTLMLASFEQTSD 1307

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            +LF+AA   ++D I GVSE II+G+P+ +GTG + L
Sbjct: 1308 YLFEAAVQSKSDEICGVSESIILGIPICIGTGSMDL 1343



 Score =  152 bits (383), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 93/234 (39%), Positives = 138/234 (58%), Gaps = 8/234 (3%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPR+KEIINA  NISTPII A LD   DL    ++KGRL+R +L +VC  + EV   D+
Sbjct: 1058 GVPRLKEIINAVCNISTPIINAELDDPHDLFRTEVIKGRLDRISLKDVCSSLTEVISKDE 1117

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSK 883
             F+ I++D++ +  L L +DI    + IE+       + V   + L +  K  +      
Sbjct: 1118 IFLDIRVDLESLSRLKLNLDI----HKIEKLLNNHDQVRVVNENTLRVSIKKITDQSYFN 1173

Query: 884  MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSS 943
            + ++K+ L +  I G   +NR +I+     G+  Y L++EG  L +V+   GVK +  +S
Sbjct: 1174 LQRIKKKLLNTKICGAPQVNRVIINSS--RGL--YSLVIEGRGLLNVINIDGVKAINTTS 1229

Query: 944  NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            N+  EV + LGIEAAR+ I+ EI+  + NHG+ ID RH ML+AD MT +GEV G
Sbjct: 1230 NSITEVEEVLGIEAARAQIIHEIEYTISNHGIKIDPRHIMLLADTMTYRGEVFG 1283



 Score =  129 bits (324), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 93/269 (34%), Positives = 138/269 (51%), Gaps = 32/269 (11%)

Query: 100 QIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFH 159
           +I SK+LY     R P+P+G LD R+G   K+  C TCG+ L+ C+GHFG + L LPVF+
Sbjct: 67  EISSKDLY-DISTRAPLPNGPLDLRLGVGNKKDKCATCGEGLATCIGHFGEVRLVLPVFN 125

Query: 160 IGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKK 219
           +G  +  I+ L  +CK  +C  +LL E+K   F+ KLR  +     +  L++ + E  KK
Sbjct: 126 VGLIKNTISTLNCLCK--SCGSILLNEKKKIYFKKKLRESSGGNDTKLILRRIVAE-CKK 182

Query: 220 VSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKK 279
           V+VC  C   NG +KK    +I HE      +KKD              K +  + +   
Sbjct: 183 VNVCFVCSFRNGQIKKTFGFRIVHEVEDLEKRKKD-----------RGSKGSDGVHS--- 228

Query: 280 FGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLK 339
               + +NPL  L +F  +  +D  LL     L  PS LI+  ++VPP+CIRPSV  D +
Sbjct: 229 -SCCEEINPLVALNVFNMMKEDDYELL---GFLESPSRLIIQNVIVPPSCIRPSVSMDDE 284

Query: 340 SDN--DVVLFNRQPSLHKLSIMAHRAKVL 366
             N  D+ +        K+S + H  KVL
Sbjct: 285 GTNEDDITI--------KISEIVHTNKVL 305



 Score =  102 bits (253), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 49/66 (74%), Positives = 54/66 (81%), Gaps = 1/66 (1%)

Query: 606 GDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           G  TP  +GFV NSFF GLT  EFFFH + GREGLVDTAVKTAETGYMQRRL+K+LEDL 
Sbjct: 822 GSRTPESKGFVLNSFFDGLTSPEFFFHAVSGREGLVDTAVKTAETGYMQRRLMKALEDLS 881

Query: 665 VQYDMS 670
           +QYD S
Sbjct: 882 IQYDGS 887



 Score = 60.5 bits (145), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 28/55 (50%), Positives = 40/55 (72%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM+  +N+VTPR+GE ++AATQDFITG YL+T K+ FF+R +  ++ S     R
Sbjct: 525 VLMSVSNNIVTPRHGEPIVAATQDFITGLYLITGKDTFFDRERFGQLVSYFSEAR 579


>gi|449330082|gb|AGE96346.1| DNA-directed RNA polymerase III 160 kDa subunit [Encephalitozoon
           cuniculi]
          Length = 1349

 Score =  197 bits (502), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 117/279 (41%), Positives = 160/279 (57%), Gaps = 36/279 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIM+H+ +V  ++T RFNECVCTPYNADFDGDEMNVH+PQTE+A
Sbjct: 460 DGDMVLFNRQPSLHRMSIMSHKVRVHRNKTLRFNECVCTPYNADFDGDEMNVHVPQTEKA 519

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A VLM+  +N+VTPR+GE ++AATQDFITG YL+T K+ FF+R
Sbjct: 520 RAE--------------ASVLMSVSNNIVTPRHGEPIVAATQDFITGLYLITGKDTFFDR 565

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +  ++ S        +   I++       PV       ++TGKQ+  +++K +    + 
Sbjct: 566 ERFGQLVSYFSEARVGVKPAIRK-------PV------ELFTGKQLIEVLIKDSFTASIE 612

Query: 521 ANLKTKGRAYT---ANEEFCHRD-----SYVILRNSELLAGSMDKSTLGSGGKANVFYIL 572
            N  T   A +    N  F   D     S  IL NS    G +DKS +G   K +     
Sbjct: 613 RNAVTGNMAVSLVGKNRSFKTHDDPNDGSVAILDNSYYF-GRLDKSIVGGENKRDSLIYA 671

Query: 573 LRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           +       AV AM  ++++ S YL   GFSIG+ DV PG
Sbjct: 672 IMKVSSMAAVRAMNSITKLCSRYLGETGFSIGLDDVQPG 710



 Score =  192 bits (488), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 129/336 (38%), Positives = 182/336 (54%), Gaps = 54/336 (16%)

Query: 1108 EKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYIEE 1153
            +K +   +EP T VGA+A QSIGEPGTQMTLKTFHFAG              E+   +  
Sbjct: 1012 QKMMNLIVEPGTTVGAIAGQSIGEPGTQMTLKTFHFAGVASMNITLGVPRLKEIINAVCN 1071

Query: 1154 VFVP------DDSFIL-----IKLDMDRIRL-----------------LHLEVDIDSIR- 1184
            +  P      DD   L     IK  +DRI L                 L + VD++S+  
Sbjct: 1072 ISTPIINAELDDPHDLFRTEVIKGRLDRISLKDVCSSLTEVISKDEIFLDIRVDLESLSR 1131

Query: 1185 -------YCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQG 1237
                   + IE+       + V   + L +  K  +      + ++K+ L +  I G   
Sbjct: 1132 LKLNLDIHKIEKLLNNHDQVRVVNENTLRVSIKKITDQSYFNLQRIKKKLLNTKICGAPQ 1191

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            +NR +I+     G+  Y L++EG  L +V+   GVK +  +SN+  EV + LGIEAAR+ 
Sbjct: 1192 VNRVIINSS--RGL--YSLVIEGRGLLNVINIDGVKAINTTSNSITEVEEVLGIEAARAQ 1247

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI+  + NHG+ ID RH ML+AD MT +GEV GITR G++KM  S L LASFE TSD
Sbjct: 1248 IIHEIEYTISNHGIKIDPRHIMLLADTMTYRGEVFGITRFGISKMSRSTLMLASFEQTSD 1307

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            +LF+AA   ++D I GVSE II+G+P+ +GTG + L
Sbjct: 1308 YLFEAAVQSKSDEICGVSESIILGIPICIGTGSMDL 1343



 Score =  151 bits (382), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 93/234 (39%), Positives = 138/234 (58%), Gaps = 8/234 (3%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPR+KEIINA  NISTPII A LD   DL    ++KGRL+R +L +VC  + EV   D+
Sbjct: 1058 GVPRLKEIINAVCNISTPIINAELDDPHDLFRTEVIKGRLDRISLKDVCSSLTEVISKDE 1117

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSK 883
             F+ I++D++ +  L L +DI    + IE+       + V   + L +  K  +      
Sbjct: 1118 IFLDIRVDLESLSRLKLNLDI----HKIEKLLNNHDQVRVVNENTLRVSIKKITDQSYFN 1173

Query: 884  MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSS 943
            + ++K+ L +  I G   +NR +I+     G+  Y L++EG  L +V+   GVK +  +S
Sbjct: 1174 LQRIKKKLLNTKICGAPQVNRVIINSS--RGL--YSLVIEGRGLLNVINIDGVKAINTTS 1229

Query: 944  NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            N+  EV + LGIEAAR+ I+ EI+  + NHG+ ID RH ML+AD MT +GEV G
Sbjct: 1230 NSITEVEEVLGIEAARAQIIHEIEYTISNHGIKIDPRHIMLLADTMTYRGEVFG 1283



 Score =  129 bits (324), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 93/269 (34%), Positives = 139/269 (51%), Gaps = 32/269 (11%)

Query: 100 QIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFH 159
           +I SK+LY     R P+P+G LD R+G   K+  C TCG+ L+ C+GHFG + L LPVF+
Sbjct: 67  EISSKDLY-DISTRAPLPNGPLDLRLGVGNKKDKCATCGEGLATCIGHFGEVRLVLPVFN 125

Query: 160 IGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKK 219
           +G  +  I+ L  +CK  +C  +LL E+K   F+ KLR  +     +  L++ + E  KK
Sbjct: 126 VGLIKNTISTLNCLCK--SCGSILLNEKKKIYFKKKLRESSGGNDTKLILRRIVAE-CKK 182

Query: 220 VSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKK 279
           V+VC  C   NG +KK    +I HE      +KKD           +  K +  + +   
Sbjct: 183 VNVCFVCSFRNGQIKKTFGFRIVHEVEDLEKRKKD-----------KGSKGSDGVHS--- 228

Query: 280 FGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLK 339
               + +NPL  L +F  +  +D  LL     L  PS LI+  ++VPP+CIRPSV  D +
Sbjct: 229 -SCCEEINPLVALNVFNMMKEDDYELL---GFLESPSRLIIQNVIVPPSCIRPSVSMDDE 284

Query: 340 SDN--DVVLFNRQPSLHKLSIMAHRAKVL 366
             N  D+ +        K+S + H  KVL
Sbjct: 285 GTNEDDITI--------KISEIVHTNKVL 305



 Score =  102 bits (253), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 49/66 (74%), Positives = 54/66 (81%), Gaps = 1/66 (1%)

Query: 606 GDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           G  TP  +GFV NSFF GLT  EFFFH + GREGLVDTAVKTAETGYMQRRL+K+LEDL 
Sbjct: 822 GSRTPESKGFVLNSFFDGLTSPEFFFHAVSGREGLVDTAVKTAETGYMQRRLMKALEDLS 881

Query: 665 VQYDMS 670
           +QYD S
Sbjct: 882 IQYDGS 887



 Score = 60.5 bits (145), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 28/55 (50%), Positives = 40/55 (72%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           VLM+  +N+VTPR+GE ++AATQDFITG YL+T K+ FF+R +  ++ S     R
Sbjct: 525 VLMSVSNNIVTPRHGEPIVAATQDFITGLYLITGKDTFFDRERFGQLVSYFSEAR 579


>gi|253747557|gb|EET02185.1| DNA-directed RNA polymerase subunit A' [Giardia intestinalis ATCC
            50581]
          Length = 1742

 Score =  197 bits (500), Expect = 5e-47,   Method: Compositional matrix adjust.
 Identities = 136/394 (34%), Positives = 199/394 (50%), Gaps = 94/394 (23%)

Query: 1107 REKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYIE 1152
            R KY+R  +EP +  GA+AAQS+GEP TQMTLK+FH AG              E+ + + 
Sbjct: 1280 RRKYIRLNLEPGSPCGAVAAQSVGEPSTQMTLKSFHHAGLASMNITQGVPRLKEIVDGVV 1339

Query: 1153 EVFVP-------------DDSFILIKLDMDRIRLL------------------------- 1174
            ++  P             +D  I+ +  +++ R++                         
Sbjct: 1340 KISTPITTVELHIDADEEEDPAIITEKYLEKARMMKNIIECTYLGQISASIIECYSQSSC 1399

Query: 1175 HLEVDIDSIRYCIERTRGISGHLTV-----------------------------SGHSFL 1205
            H+EV++D     I    G++G +TV                             SG  F 
Sbjct: 1400 HIEVNLD---MKIIADMGLAGVITVETVVASILHNDKAKKLVGQDHSSGSVSIHSGTRFS 1456

Query: 1206 ILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHE--EDVEG-------VTKYKL 1256
            +     S ++    +  +K LLP + + G+   +RAVI+E  E  +G       +TKY L
Sbjct: 1457 VRPITQSRENLLFDIQSLKLLLPMIPVSGIATCSRAVINEYKEITQGGTISSAPLTKYNL 1516

Query: 1257 LVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFR 1316
            LVEG  L+ ++   G+   +  SNN  EV  TLGIEAA +TI  EIK  M++HGM++D R
Sbjct: 1517 LVEGVGLQSILNVSGIDFTRTLSNNIIEVANTLGIEAAVATIANEIKACMDSHGMAVDMR 1576

Query: 1317 HPMLVADLMTSKGEVLGITRHGLAKMK-ESVLNLASFENTSDHLFDAAFYGQTDCISGVS 1375
            H  L+AD+M  KG+VLG TR GL KMK +SV+ LASFE T +HLF+AA   + D  +GV+
Sbjct: 1577 HIRLLADIMCFKGKVLGFTRFGLTKMKADSVIMLASFEKTGEHLFNAALGNKIDETNGVT 1636

Query: 1376 ECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLF 1409
            E II+G PM++GTG   LLQA    E   +T+ +
Sbjct: 1637 ESIILGKPMSMGTGSFSLLQAPYFDEKTGKTIEY 1670



 Score =  184 bits (466), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 111/313 (35%), Positives = 170/313 (54%), Gaps = 43/313 (13%)

Query: 328 NCIRPS-VISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFD 386
           N +RP+ ++      ND +LFNRQPSLH++SIM   A +  +RTF FN  VC+P+NADFD
Sbjct: 665 NSLRPNDIVYRHLLPNDTLLFNRQPSLHRMSIMQFNAVIHENRTFSFNPIVCSPFNADFD 724

Query: 387 GDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFIT 446
           GDEMN+   Q +EARAE              A +LM +  N+++PR+GE +I  TQDF+T
Sbjct: 725 GDEMNIFYMQGQEARAE--------------AGILMGSHENIISPRHGECMIGLTQDFLT 770

Query: 447 GGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSW-RSW------------NPVV 493
           G YLL+ K  F  R    +  S       D    +  +++ R +            + V 
Sbjct: 771 GIYLLSGKGIFMTRQDYCQHVSYGCDGFGDATYGVSLYNYGREFIKSIHSRRGTEEDTVG 830

Query: 494 FVRTAV-----------IWTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEE---FCHR 539
           FV+              +++GKQ+ S+++K N    V+ NL+   + Y  +++       
Sbjct: 831 FVKVPCLAQPCIVYPRQLYSGKQVLSVLMKGNDFDSVSINLEHGDKTYKKSDDKRALSVG 890

Query: 540 DSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNR 599
           D YV+++NSE LAG + K+ L S  K  +FY L++++G   A   M R +++ + +LMN 
Sbjct: 891 DDYVVIQNSEHLAGRLTKAFLAS-SKNCIFYFLVQNYGPVSAARIMLRFAKVAARFLMNY 949

Query: 600 GFSIGIGDVTPGQ 612
           GF+IGI DV P Q
Sbjct: 950 GFTIGIDDVMPSQ 962



 Score =  132 bits (331), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 95/267 (35%), Positives = 142/267 (53%), Gaps = 33/267 (12%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTD------------LDYARIVKGRLERTTLGEV 811
            GVPR+KEI++    ISTPI T  L  D D            L+ AR++K  +E T LG++
Sbjct: 1327 GVPRLKEIVDGVVKISTPITTVELHIDADEEEDPAIITEKYLEKARMMKNIIECTYLGQI 1386

Query: 812  CEYIEEVFVPDDSFILIKLDMDRIR------LLHLEVDIDSIRYCIERTRGI-----SGH 860
               I E +      I + LDM  I       ++ +E  + SI +  +  + +     SG 
Sbjct: 1387 SASIIECYSQSSCHIEVNLDMKIIADMGLAGVITVETVVASILHNDKAKKLVGQDHSSGS 1446

Query: 861  LTV-SGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHE--EDVEG--- 914
            +++ SG  F +     S ++    +  +K LLP + + G+   +RAVI+E  E  +G   
Sbjct: 1447 VSIHSGTRFSVRPITQSRENLLFDIQSLKLLLPMIPVSGIATCSRAVINEYKEITQGGTI 1506

Query: 915  ----VTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVM 970
                +TKY LLVEG  L+ ++   G+   +  SNN  EV  TLGIEAA +TI  EIK  M
Sbjct: 1507 SSAPLTKYNLLVEGVGLQSILNVSGIDFTRTLSNNIIEVANTLGIEAAVATIANEIKACM 1566

Query: 971  ENHGMSIDFRHPMLVADLMTSKGEVLG 997
            ++HGM++D RH  L+AD+M  KG+VLG
Sbjct: 1567 DSHGMAVDMRHIRLLADIMCFKGKVLG 1593



 Score = 91.3 bits (225), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 69/226 (30%), Positives = 107/226 (47%), Gaps = 26/226 (11%)

Query: 86  TVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCV 145
           +V   + + + S +QI +  LY   P  +P  +G+LD+R+G + K   C TCG++   C+
Sbjct: 33  SVLSSNALMKLSEVQITTPILYEHYP--SPARNGVLDKRLGLSDKVGRCATCGKDTKMCI 90

Query: 146 GHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLV 205
           GHFG I L LPVFH G       +L  IC  P C+RV + E     ++      +L++  
Sbjct: 91  GHFGTIALALPVFHPGLINDARTMLSIIC--PFCSRVKISEADRHKYK------SLNHKH 142

Query: 206 RKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYN 265
             S+ K+  E  KK   CP C   + V KK    ++  E +   +  K      +LA   
Sbjct: 143 SLSIVKEAQEQAKKQVNCPFCHAPSTVCKKSQGFRVLREMHYEESATK------ILA--- 193

Query: 266 EAVKFNPEIEAHKKFGLIQTL-----NPLEVLQLFEAIPLEDIPLL 306
             +K   EIE  K   L Q L     +P++ L + + +P  D P L
Sbjct: 194 GVIKHQKEIE--KIQDLDQRLRNHVVDPIQALHILKKVPECDYPYL 237



 Score = 84.0 bits (206), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 35/59 (59%), Positives = 46/59 (77%)

Query: 612  QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GF+ NSF++GL P EF  H   GR+G++D+A KTA+TGY+QRRLVK LEDL V YD +
Sbjct: 1086 KGFILNSFYTGLLPFEFLAHARAGRDGVIDSACKTADTGYLQRRLVKCLEDLSVSYDFT 1144



 Score = 49.3 bits (116), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 29/41 (70%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           +LM +  N+++PR+GE +I  TQDF+TG YLL+ K  F  R
Sbjct: 744 ILMGSHENIISPRHGECMIGLTQDFLTGIYLLSGKGIFMTR 784



 Score = 42.0 bits (97), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 38/77 (49%), Gaps = 1/77 (1%)

Query: 671  FDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFD-NPEFHFPQ 729
            F+AA   + D  +GV+E II+G PM++GTG   LLQA    E   +T+ +   P   F  
Sbjct: 1621 FNAALGNKIDETNGVTESIILGKPMSMGTGSFSLLQAPYFDEKTGKTIEYQPKPVTRFLG 1680

Query: 730  VYYERRRDYSVKVTASV 746
                R+ D  V    S 
Sbjct: 1681 EVLNRQYDEEVDAIVSA 1697


>gi|396081638|gb|AFN83253.1| DNA-directed RNA polymerase subunit alpha [Encephalitozoon romaleae
           SJ-2008]
          Length = 1315

 Score =  196 bits (499), Expect = 7e-47,   Method: Compositional matrix adjust.
 Identities = 114/283 (40%), Positives = 158/283 (55%), Gaps = 44/283 (15%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D++LFNRQPSLH++SIM+H+ K+  ++T RFNECVCTPYNADFDGDEMNVH+PQTE+A
Sbjct: 426 DGDMILFNRQPSLHRMSIMSHKVKIHNNKTLRFNECVCTPYNADFDGDEMNVHVPQTEKA 485

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A +LM+  +N+VTPR+GE +IA TQDFITG YL+T K+ FF+R
Sbjct: 486 RAE--------------ASILMSVSNNIVTPRHGEPIIAPTQDFITGLYLITGKDTFFDR 531

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +  ++ S       +I   I+R       PV       ++TGKQ+   ++K +      
Sbjct: 532 ERFGQLVSYFSGTRVNIKPAIRR-------PV------ELFTGKQLIEALIKDSF----- 573

Query: 521 ANLKTKGRAYT--------ANEEFCHR----DSYVILRNSELLAGSMDKSTLGSGGKANV 568
             +K +   Y          N  F  R    D  VI+ ++    G +DKS +G   K N 
Sbjct: 574 GGIKERSTEYQDKSISLIGKNRSFKSRNDPNDGNVIILDNSYYFGRLDKSIIGGENKKNS 633

Query: 569 FYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
               +       AV  M  ++++ S YL   GFSIG+ DV PG
Sbjct: 634 LIYAIMKVSNKAAVRVMNSITKLCSRYLGEVGFSIGLDDVQPG 676



 Score =  194 bits (494), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 130/344 (37%), Positives = 179/344 (52%), Gaps = 62/344 (18%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG------------------E 1146
            A  +K +   IEP T VGA+A QSIGEPGTQMTLKTFHFAG                   
Sbjct: 975  AISQKMIDLIIEPGTTVGAIAGQSIGEPGTQMTLKTFHFAGVASMNITLGVPRLKEIINA 1034

Query: 1147 VCE------------------------------------YIEEVFVPDDSFILIKLDMDR 1170
            VC                                      I EV   D+ F+ I +D++ 
Sbjct: 1035 VCNISTPIINAELSDPNDLFRAEVIKGRIDKISLKDICCLITEVIGKDEIFLDITIDLES 1094

Query: 1171 IRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSV 1230
            +  L L +DI    Y IE++  I     V G + L +  K  +      + ++K+ L   
Sbjct: 1095 LSRLKLNLDI----YKIEKSLSIHDQTEVIGENSLRIHVKKINDQSYFNLQKIKKKLLGT 1150

Query: 1231 VIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLG 1290
             I G   ++R +I+         Y L++EG  L +V+ T G+K    +SN+  EV + LG
Sbjct: 1151 KICGAPQVSRVIINSNR----GHYSLVIEGRGLLNVINTDGIKSSTTTSNSVTEVEEVLG 1206

Query: 1291 IEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLA 1350
            IEAAR+ I+ EI+  + NHG+ ID RH ML+AD MT +GEV GITR G++KM  S L LA
Sbjct: 1207 IEAARAQIIHEIEYTISNHGIKIDPRHIMLLADTMTYRGEVFGITRFGISKMSRSTLMLA 1266

Query: 1351 SFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            SFE TSD+LF+AA   ++D I GVSE II+G+P+ +GTG + L 
Sbjct: 1267 SFEQTSDYLFEAAVQSKSDEICGVSESIILGIPICIGTGSMDLF 1310



 Score =  145 bits (367), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 92/234 (39%), Positives = 136/234 (58%), Gaps = 8/234 (3%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPR+KEIINA  NISTPII A L    DL  A ++KGR+++ +L ++C  I EV   D+
Sbjct: 1024 GVPRLKEIINAVCNISTPIINAELSDPNDLFRAEVIKGRIDKISLKDICCLITEVIGKDE 1083

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSK 883
             F+ I +D++ +  L L +DI    Y IE++  I     V G + L +  K  +      
Sbjct: 1084 IFLDITIDLESLSRLKLNLDI----YKIEKSLSIHDQTEVIGENSLRIHVKKINDQSYFN 1139

Query: 884  MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSS 943
            + ++K+ L    I G   ++R +I+         Y L++EG  L +V+ T G+K    +S
Sbjct: 1140 LQKIKKKLLGTKICGAPQVSRVIINSNR----GHYSLVIEGRGLLNVINTDGIKSSTTTS 1195

Query: 944  NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            N+  EV + LGIEAAR+ I+ EI+  + NHG+ ID RH ML+AD MT +GEV G
Sbjct: 1196 NSVTEVEEVLGIEAARAQIIHEIEYTISNHGIKIDPRHIMLLADTMTYRGEVFG 1249



 Score =  139 bits (351), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 93/269 (34%), Positives = 138/269 (51%), Gaps = 33/269 (12%)

Query: 100 QIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFH 159
           +I SK+LY     R P+P+G LD R+G   K+  C TCG+ L+ C+GHFG + L LP+F+
Sbjct: 34  EISSKDLY-DISTRIPLPNGPLDLRLGVGNKKDKCATCGEGLATCIGHFGEVRLALPIFN 92

Query: 160 IGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKK 219
           +G  +  I+ L  +CK  +C  +LLGE+K   F+ KLR        R  L+K I E  KK
Sbjct: 93  VGLIKNTISTLNCLCK--SCGSILLGEKKKIYFKRKLRESTGGNDTRLILRKVIAE-CKK 149

Query: 220 VSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKK 279
            ++C  C   NG VKK    +I+HE   +  KK+D        +      + P  E    
Sbjct: 150 ANMCFVCSSRNGQVKKTFGFRIAHEIEDSERKKRD-------KDGKGPGGYFPHHEE--- 199

Query: 280 FGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLK 339
                 +NPL  L +F+ +  +D  LL  +     P  LI+  ++VPP+CIRPSV  D +
Sbjct: 200 ------MNPLMALNIFKMMKEDDYELLGFS---ESPDRLIIQNVIVPPSCIRPSVSMDDE 250

Query: 340 SDN--DVVLFNRQPSLHKLSIMAHRAKVL 366
             N  D+ +        K+S + H  K+L
Sbjct: 251 GTNEDDITI--------KISEIVHTNKIL 271



 Score =  100 bits (249), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 48/63 (76%), Positives = 53/63 (84%), Gaps = 1/63 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV NSFF GLT  EFFFH + GREGLVDTAVKTAETGYMQRRL+K+LEDL +QY
Sbjct: 791 TPESKGFVLNSFFDGLTSPEFFFHAVSGREGLVDTAVKTAETGYMQRRLMKALEDLSIQY 850

Query: 668 DMS 670
           D S
Sbjct: 851 DGS 853



 Score = 58.2 bits (139), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 27/55 (49%), Positives = 39/55 (70%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           +LM+  +N+VTPR+GE +IA TQDFITG YL+T K+ FF+R +  ++ S     R
Sbjct: 491 ILMSVSNNIVTPRHGEPIIAPTQDFITGLYLITGKDTFFDRERFGQLVSYFSGTR 545


>gi|162606212|ref|XP_001713621.1| RNA polymerase III largest subunit [Guillardia theta]
 gi|13794541|gb|AAK39916.1|AF165818_124 RNA polymerase III largest subunit [Guillardia theta]
          Length = 1289

 Score =  196 bits (499), Expect = 7e-47,   Method: Compositional matrix adjust.
 Identities = 100/283 (35%), Positives = 162/283 (57%), Gaps = 38/283 (13%)

Query: 342 NDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEAR 401
           ND++LFNRQPSLH+LSIMAHR ++   +TFR N CVC PYNADFDGDEMN+H+PQ+E +R
Sbjct: 412 NDIILFNRQPSLHRLSIMAHRIRIFKEKTFRLNHCVCKPYNADFDGDEMNLHVPQSETSR 471

Query: 402 AEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRA 461
            EA+               L+ + +N  TPRNGE+LIA +QDF++  ++LT +N FFN+ 
Sbjct: 472 TEAI--------------TLLNSYNNFYTPRNGEILIACSQDFLSYSFILTSRNIFFNKE 517

Query: 462 QTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNA 521
           +   + S  ++D            + +  P + ++  ++WTGKQIFS IL  +++     
Sbjct: 518 EVTGLISGEVSDL-----------FNNILPAI-LKPKILWTGKQIFSEILFFDKNYYHLN 565

Query: 522 NLKTKGRAYTANEEFCHR------------DSYVILRNSELLAGSMDKSTLGSGGKANVF 569
            +K +   Y   E+F  R            + + I++N+ +L+G + K++LG+G K ++F
Sbjct: 566 LIKKQKTNYQIREKFTSRQFNTCSPFVCPIEGWTIIKNNLILSGRLGKTSLGTGNKMSLF 625

Query: 570 YILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
                +      + ++ ++S +   +  N GFS  I +V P +
Sbjct: 626 SFSRNNNSASEILNSILKISILNQNWFSNYGFSFSINNVKPSK 668



 Score = 97.8 bits (242), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 57/132 (43%), Positives = 76/132 (57%), Gaps = 1/132 (0%)

Query: 1261 DNLRDVMATY-GVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPM 1319
            DN  D++    G+   K   NN   +Y  LGIEA+R  I+ EI    ++HG+  D RH  
Sbjct: 1158 DNRFDILLNIPGIIFRKLYCNNINSIYNFLGIEASRELIVLEITNTFKSHGIFSDNRHVY 1217

Query: 1320 LVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECII 1379
            L+AD MT  G ++GI R GL   KESV  LASFE T ++LF+A+         GVS+ II
Sbjct: 1218 LLADYMTFNGFIIGINREGLTCNKESVFLLASFEKTMENLFNASLNHTKSKYIGVSDAII 1277

Query: 1380 MGLPMNVGTGLI 1391
             G  + +GTGLI
Sbjct: 1278 FGNSIPIGTGLI 1289



 Score = 92.4 bits (228), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 40/64 (62%), Positives = 51/64 (79%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSF 671
           +G ++NSF+SGL   EFFFH+M GREGL+DTAVKTAE GY+QRRLVKSLED+ +  D + 
Sbjct: 792 KGLIENSFYSGLDSKEFFFHSMAGREGLIDTAVKTAEIGYLQRRLVKSLEDISIMNDSTV 851

Query: 672 DAAF 675
             +F
Sbjct: 852 RDSF 855



 Score = 81.6 bits (200), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 60/228 (26%), Positives = 103/228 (45%), Gaps = 35/228 (15%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           IE  +   + +   S IQ+ + N++ +D + T     LLD ++G N +   C+ C     
Sbjct: 9   IEFKIFSREEISGYSTIQLTNSNIFLKD-KNTSQEGSLLDEKLG-NIRNQICSFCKDKFK 66

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAA-GFRAKLRNPAL 201
            C GH+G++ L +PV ++G+ + +  ILQ +CK   C+ +LL   K    F   L   + 
Sbjct: 67  FCQGHYGHLRLSMPVLNLGFIKTIQCILQMVCK--RCSSLLLRSSKEKIHFSFLLGKNSN 124

Query: 202 SYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLL 261
           + + +K +   ILE  K    CP+C   NG ++K   L   H+            +++  
Sbjct: 125 NKVEKKKIYFNILEKCKSHRKCPNCEFSNGKIRKISNLAFLHD------------IDNSK 172

Query: 262 AEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMN 309
            E NE                   L PL++ Q+F  I  ED+ L+ +N
Sbjct: 173 NEINE------------------ILGPLKIFQIFSKINAEDLELIGVN 202



 Score = 58.9 bits (141), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 63/254 (24%), Positives = 111/254 (43%), Gaps = 34/254 (13%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGR------LERTTLGEVCEYIEE 817
            G+PRI EI++ S+N   P+I+       D+++    K +      L++  +G +   IE 
Sbjct: 992  GIPRINEILSNSKNTKFPLISY------DINFFEFNKKKSRLKFFLKKIKIGFLINSIE- 1044

Query: 818  VFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSS 877
            +F+    F+ +K+    I+ ++  +D   I Y I +    +  +      F+  K K+  
Sbjct: 1045 IFL-HRGFVSVKIHF--IKKIYEYLDQSKIYYFIIKKFHDNTKIIKKSTVFICKKKKNVV 1101

Query: 878  KSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYK-------LLVEG------ 924
              F+   +++        +  +   N   IH  D+     Y+        L         
Sbjct: 1102 LQFHKNDFKIDDF----NLNFINLYNFFRIHFGDIVLTGFYESSKINCNFLFNNLEIKIS 1157

Query: 925  DNLRDVMATY-GVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPM 983
            DN  D++    G+   K   NN   +Y  LGIEA+R  I+ EI    ++HG+  D RH  
Sbjct: 1158 DNRFDILLNIPGIIFRKLYCNNINSIYNFLGIEASRELIVLEITNTFKSHGIFSDNRHVY 1217

Query: 984  LVADLMTSKGEVLG 997
            L+AD MT  G ++G
Sbjct: 1218 LLADYMTFNGFIIG 1231



 Score = 55.1 bits (131), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 22/31 (70%), Positives = 27/31 (87%)

Query: 1115 IEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            I+P T VG ++AQS+GEPGTQMTL+TFH AG
Sbjct: 953  IDPGTGVGCISAQSLGEPGTQMTLQTFHSAG 983



 Score = 52.0 bits (123), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 23/53 (43%), Positives = 37/53 (69%), Gaps = 4/53 (7%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           L+ + +N  TPRNGE+LIA +QDF++  ++LT +N FFN+ +     + LI+G
Sbjct: 477 LLNSYNNFYTPRNGEILIACSQDFLSYSFILTSRNIFFNKEE----VTGLISG 525


>gi|303389791|ref|XP_003073127.1| DNA-directed RNA polymerase subunit alpha [Encephalitozoon
            intestinalis ATCC 50506]
 gi|303302272|gb|ADM11767.1| DNA-directed RNA polymerase subunit alpha [Encephalitozoon
            intestinalis ATCC 50506]
          Length = 1315

 Score =  194 bits (493), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 126/340 (37%), Positives = 179/340 (52%), Gaps = 62/340 (18%)

Query: 1108 EKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFH------------------------- 1142
            +K +   IEP T VGA+A QSIGEPGTQMTLKTFH                         
Sbjct: 978  QKMMDLIIEPGTTVGAIAGQSIGEPGTQMTLKTFHFAGVASMNITLGVPRLKEIINAVCN 1037

Query: 1143 ----------------FAGEV-------------CEYIEEVFVPDDSFILIKLDMDRIRL 1173
                            FA EV             C  + EV   ++ F+ I +D++ +  
Sbjct: 1038 ISTPIINAELNDSQNLFAAEVIKGRIGRISLKDICSSLTEVVDKEEIFLDIAIDLESLSR 1097

Query: 1174 LHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIK 1233
            L L +DI    + IER   +   + + G++ L +  K  +      + ++K+ L    I 
Sbjct: 1098 LKLNLDI----HKIERLLSLHDQIRIVGNNVLRVFIKKITDQSYFNLQKIKKKLLGTRIC 1153

Query: 1234 GVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEA 1293
            G   I+R +I+        +Y L++EG  L  V+ T G++    +SN+  EV + LGIEA
Sbjct: 1154 GAPQISRVIINSNK----GQYSLVIEGTGLLSVINTDGIRCSSVTSNSVTEVEEVLGIEA 1209

Query: 1294 ARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFE 1353
            AR+ I+ EI+  + NHG+ ID RH ML+AD MT +GEV GITR G++KM  S L LASFE
Sbjct: 1210 ARAQIIHEIEYTISNHGIKIDPRHIMLLADTMTYRGEVFGITRFGISKMSRSTLMLASFE 1269

Query: 1354 NTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
             TSD+LF+AA   ++D I GVSE II+G+P+ +GTG I L
Sbjct: 1270 QTSDYLFEAAAQNKSDEICGVSESIILGIPICIGTGSIDL 1309



 Score =  193 bits (491), Expect = 6e-46,   Method: Compositional matrix adjust.
 Identities = 112/283 (39%), Positives = 161/283 (56%), Gaps = 44/283 (15%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIM+H+ KV  ++T RFNECVCTPYNADFDGDEMNVH+PQTE+A
Sbjct: 426 DGDMVLFNRQPSLHRMSIMSHKVKVHGNKTLRFNECVCTPYNADFDGDEMNVHVPQTEKA 485

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              + +LM+  +N+VTPR+GE ++AATQDFITG YL+T K+ FF+R
Sbjct: 486 RAE--------------SSILMSVSNNIVTPRHGEPIVAATQDFITGLYLITGKDTFFDR 531

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILK-------- 512
            +  ++ S        +   IK+       PV       ++TGKQ+   ++K        
Sbjct: 532 ERFGQLVSYFSETRISMKPAIKK-------PV------ELFTGKQLVEALIKDSFAASRE 578

Query: 513 ----PNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANV 568
               P   C    +L  K R++  +++    D  VI+ ++    G +DKS +G   K + 
Sbjct: 579 DYRSPYGGC---ISLVGKNRSFKTHDD--PNDGSVIILDNLYYFGRLDKSIIGGENKKDS 633

Query: 569 FYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
               +       A+  M  ++++ S YL   GFSIG+ DV PG
Sbjct: 634 LIYAIMKVSNKAAIRVMNSITKLCSRYLGEVGFSIGLDDVQPG 676



 Score =  147 bits (370), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 88/234 (37%), Positives = 137/234 (58%), Gaps = 8/234 (3%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPR+KEIINA  NISTPII A L+   +L  A ++KGR+ R +L ++C  + EV   ++
Sbjct: 1024 GVPRLKEIINAVCNISTPIINAELNDSQNLFAAEVIKGRIGRISLKDICSSLTEVVDKEE 1083

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSK 883
             F+ I +D++ +  L L +DI    + IER   +   + + G++ L +  K  +      
Sbjct: 1084 IFLDIAIDLESLSRLKLNLDI----HKIERLLSLHDQIRIVGNNVLRVFIKKITDQSYFN 1139

Query: 884  MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSS 943
            + ++K+ L    I G   I+R +I+        +Y L++EG  L  V+ T G++    +S
Sbjct: 1140 LQKIKKKLLGTRICGAPQISRVIINSNK----GQYSLVIEGTGLLSVINTDGIRCSSVTS 1195

Query: 944  NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            N+  EV + LGIEAAR+ I+ EI+  + NHG+ ID RH ML+AD MT +GEV G
Sbjct: 1196 NSVTEVEEVLGIEAARAQIIHEIEYTISNHGIKIDPRHIMLLADTMTYRGEVFG 1249



 Score =  131 bits (329), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 102/305 (33%), Positives = 151/305 (49%), Gaps = 41/305 (13%)

Query: 100 QIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFH 159
           +I SK+LY  +  R P+P+G LD R+G   K+  C TCG+ L+ C+GHFG + L LPVF+
Sbjct: 34  EISSKDLYDIN-TRVPLPNGPLDLRLGVGNKKDKCATCGEGLATCIGHFGEVKLVLPVFN 92

Query: 160 IGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKK 219
           IG  +  I+ L  +CK  +C  +LLGE+K   F+ KLR  +     +  L+K I E  KK
Sbjct: 93  IGLVKNTISTLNCLCK--SCGSILLGEKKKIYFKKKLRESSGGNDTKLILRKIIAE-CKK 149

Query: 220 VSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKK 279
            +VC  C   NG VKK    ++ HE            +EDL     +  K +  + +   
Sbjct: 150 ANVCFVCSSRNGQVKKTFGFRMVHE------------IEDLEKRKKDKNKGSGGVNSSD- 196

Query: 280 FGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLK 339
               + +NPL  L +F  +  +D  LL  +     P  LI+  ++VPP+CIRPSV  D +
Sbjct: 197 ---YEEINPLMALNIFRMMKEDDYELLGFS---ESPERLIIQSIIVPPSCIRPSVSMDDE 250

Query: 340 SDN--DVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEM------N 391
             N  D+ +        K+S + H  KVL     + N       N D+D  ++      N
Sbjct: 251 GTNEDDITI--------KISEIVHTNKVLKEGIEKGNP--LNLINEDWDHLQLQCALLIN 300

Query: 392 VHLPQ 396
             LPQ
Sbjct: 301 SELPQ 305



 Score =  103 bits (258), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 50/66 (75%), Positives = 55/66 (83%), Gaps = 1/66 (1%)

Query: 606 GDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           G  TP  +GFV+NSFF GLT  EFFFH + GREGLVDTAVKTAETGYMQRRL+K+LEDL 
Sbjct: 788 GSRTPESKGFVRNSFFDGLTSPEFFFHAVSGREGLVDTAVKTAETGYMQRRLMKALEDLS 847

Query: 665 VQYDMS 670
           VQYD S
Sbjct: 848 VQYDGS 853



 Score = 59.3 bits (142), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 26/49 (53%), Positives = 39/49 (79%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIAS 69
           +LM+  +N+VTPR+GE ++AATQDFITG YL+T K+ FF+R +  ++ S
Sbjct: 491 ILMSVSNNIVTPRHGEPIVAATQDFITGLYLITGKDTFFDRERFGQLVS 539


>gi|401826841|ref|XP_003887513.1| DNA-directed RNA polymerase subunit beta [Encephalitozoon hellem
           ATCC 50504]
 gi|392998519|gb|AFM98532.1| DNA-directed RNA polymerase subunit beta' [Encephalitozoon hellem
           ATCC 50504]
          Length = 1314

 Score =  194 bits (492), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 111/278 (39%), Positives = 158/278 (56%), Gaps = 34/278 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIM+H+ KV   +T RFNECVCTPYNADFDGDEMNVH+PQTE+A
Sbjct: 425 DGDMVLFNRQPSLHRMSIMSHKVKVHNSKTLRFNECVCTPYNADFDGDEMNVHVPQTEKA 484

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A +LM+  +N+VTPR+GE +IAATQDFITG YL+T K+ FF+R
Sbjct: 485 RAE--------------ASILMSVSNNIVTPRHGEPIIAATQDFITGLYLITGKDTFFDR 530

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +  ++ S       ++   IK+       PV       ++TGKQ+   ++K +      
Sbjct: 531 ERFGQLVSYFSETRINVKPAIKK-------PV------ELFTGKQLVEALIKDSFYGSSE 577

Query: 521 ANLKTKGRAYT---ANEEFCH----RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILL 573
             +  + ++ +    N  F       D  V++ ++    G +DKS +G   K +     +
Sbjct: 578 GAMSLQDKSISLIGKNRSFKSFSDPNDGSVVILDNAYYFGRLDKSIIGGENKKDSLIYAI 637

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
                  AV  M  ++++ S YL   GFSIG+ DV PG
Sbjct: 638 MKVSNKAAVRVMNSITKLCSRYLGEVGFSIGLDDVQPG 675



 Score =  188 bits (478), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 128/342 (37%), Positives = 180/342 (52%), Gaps = 66/342 (19%)

Query: 1108 EKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG------------------EVCE 1149
            +K +   IEP T VGA+A QSIGEPGTQMTLKTFHFAG                   VC 
Sbjct: 977  QKMMDLIIEPGTTVGAIAGQSIGEPGTQMTLKTFHFAGVASMNITLGVPRLKEIINAVCN 1036

Query: 1150 ------------------------------------YIEEVFVPDDSFILIKLDMDRIRL 1173
                                                 I EV   D+ F+ + +D++ +  
Sbjct: 1037 ISTPIINAELDDPYNLFRAEVIKGRIDKISLKDVCCLITEVIGKDEIFLDVTIDLETLSR 1096

Query: 1174 LHLEVDIDSIRYCIERTRGISGHLTVSGHSFL--ILKPKDSSKSFNSKMYQMKQLLPSVV 1231
            L L +DI    + IE++  +     V+  + +   +K  D    FN  + ++K+ L    
Sbjct: 1097 LKLNLDI----HKIEKSLNLPDQTKVTSENSIRVYVKKIDDQSYFN--LQKVKKKLLGTR 1150

Query: 1232 IKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGI 1291
            I G   ++R +I+         Y L++EG  L +V+ T GVK    +SN+  EV + LGI
Sbjct: 1151 ICGAPQVSRVIINSNR----GHYSLVIEGHGLLNVINTDGVKSSTTTSNSVTEVEEVLGI 1206

Query: 1292 EAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLAS 1351
            EAAR+ I+ EI+  + NHG+ ID RH ML+AD MT +GEV GITR G++KM  S L LAS
Sbjct: 1207 EAARAQIIHEIEYTISNHGIKIDPRHIMLLADTMTYRGEVFGITRFGISKMSRSTLMLAS 1266

Query: 1352 FENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            FE TSD+LF+AA   ++D I GVSE II+G+P+ +GTG + L
Sbjct: 1267 FEQTSDYLFEAAVQSKSDEICGVSESIILGIPICIGTGSMDL 1308



 Score =  142 bits (357), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 92/236 (38%), Positives = 139/236 (58%), Gaps = 12/236 (5%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPR+KEIINA  NISTPII A LD   +L  A ++KGR+++ +L +VC  I EV   D+
Sbjct: 1023 GVPRLKEIINAVCNISTPIINAELDDPYNLFRAEVIKGRIDKISLKDVCCLITEVIGKDE 1082

Query: 824  SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFL--ILKPKDSSKSFN 881
             F+ + +D++ +  L L +DI    + IE++  +     V+  + +   +K  D    FN
Sbjct: 1083 IFLDVTIDLETLSRLKLNLDI----HKIEKSLNLPDQTKVTSENSIRVYVKKIDDQSYFN 1138

Query: 882  SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
              + ++K+ L    I G   ++R +I+         Y L++EG  L +V+ T GVK    
Sbjct: 1139 --LQKVKKKLLGTRICGAPQVSRVIINSNR----GHYSLVIEGHGLLNVINTDGVKSSTT 1192

Query: 942  SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +SN+  EV + LGIEAAR+ I+ EI+  + NHG+ ID RH ML+AD MT +GEV G
Sbjct: 1193 TSNSVTEVEEVLGIEAARAQIIHEIEYTISNHGIKIDPRHIMLLADTMTYRGEVFG 1248



 Score =  127 bits (318), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 100/305 (32%), Positives = 145/305 (47%), Gaps = 42/305 (13%)

Query: 100 QIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFH 159
           +I SK+LY     R P+ +G LD R+G   K+  C TCG+ L+ C+GHFG + L LPVF+
Sbjct: 34  EISSKDLY-DISTRVPLSNGPLDLRLGVGNKKDKCATCGEGLATCIGHFGEVKLVLPVFN 92

Query: 160 IGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKK 219
           IG  +  I+ L  +CK  +C  +LL E+K   F+ KLR        +  L+K I E  KK
Sbjct: 93  IGLIKSTISTLNCLCK--SCGCILLSEKKKIYFKKKLRESTGGNDTKLILRKVIAE-CKK 149

Query: 220 VSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKK 279
            ++C  C   NG VKK    +I HE      +KKD                    +    
Sbjct: 150 ANMCFVCSSRNGQVKKTFGFRIVHEIEDPEKRKKDR-----------------SAKGGTH 192

Query: 280 FGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLK 339
           F   + +NPL  L +F+ +  +D  LL  +     P  LI+  ++VPP+CIRPSV  D +
Sbjct: 193 FSHYEDINPLTALNVFKMMKEDDYELLGFS---ESPERLIIQNVIVPPSCIRPSVSMDDE 249

Query: 340 SDN--DVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEM------N 391
             N  D+ +        K+S + H  KVL     + N       N D+D  ++      N
Sbjct: 250 GTNEDDITI--------KISEIVHTNKVLKEGIEKGNP--LNLINEDWDHLQLQCALLIN 299

Query: 392 VHLPQ 396
             LPQ
Sbjct: 300 SELPQ 304



 Score =  102 bits (253), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 49/66 (74%), Positives = 54/66 (81%), Gaps = 1/66 (1%)

Query: 606 GDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           G  TP  +GFV NSFF GLT  EFFFH + GREGLVDTAVKTAETGYMQRRL+K+LEDL 
Sbjct: 787 GSKTPESKGFVLNSFFDGLTSPEFFFHAVSGREGLVDTAVKTAETGYMQRRLMKALEDLS 846

Query: 665 VQYDMS 670
           +QYD S
Sbjct: 847 IQYDGS 852



 Score = 60.1 bits (144), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 27/49 (55%), Positives = 39/49 (79%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIAS 69
           +LM+  +N+VTPR+GE +IAATQDFITG YL+T K+ FF+R +  ++ S
Sbjct: 490 ILMSVSNNIVTPRHGEPIIAATQDFITGLYLITGKDTFFDRERFGQLVS 538


>gi|116753354|ref|YP_842472.1| DNA-directed RNA polymerase subunit A' [Methanosaeta thermophila
           PT]
 gi|116664805|gb|ABK13832.1| DNA-directed RNA polymerase, subunit A' [Methanosaeta thermophila
           PT]
          Length = 876

 Score =  192 bits (489), Expect = 8e-46,   Method: Compositional matrix adjust.
 Identities = 108/268 (40%), Positives = 154/268 (57%), Gaps = 29/268 (10%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D D+VLFNRQPSLH++SIMAHR KV+P++TFR N  VC PYNADFDGDEMN+H+PQTEE
Sbjct: 407 ADGDIVLFNRQPSLHRMSIMAHRVKVMPYKTFRLNPAVCPPYNADFDGDEMNLHVPQTEE 466

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           ARAE              A++LM  + N+++PR G  +I    D++TG +LLT K    N
Sbjct: 467 ARAE--------------AEILMRVQENILSPRFGGPIIGGIHDYVTGSFLLTHKERRLN 512

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           + + M +   L  D SDI   +      + +P         WTGKQIFSLIL  + +   
Sbjct: 513 KDRLMEVLKKL--DISDIP--VPAGYDENGDPY--------WTGKQIFSLILPKDLNLTF 560

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            A+  +         E C  D+YV++RN  LL G++D   +G+  K  V   +++++   
Sbjct: 561 KADFCSN--CPVCKGEDCENDAYVVIRNGVLLKGTIDAEAVGA-FKGKVIDRIIKEYDPG 617

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           VA   + R++ +    +M  GFS GI D
Sbjct: 618 VASQFLDRMTLLALRGIMLAGFSFGISD 645



 Score =  104 bits (259), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 71/253 (28%), Positives = 119/253 (47%), Gaps = 44/253 (17%)

Query: 94  QQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDL 153
           ++ S +++++ + Y  D    PI  GL+D R+G       C TCG    +C GHFG+IDL
Sbjct: 21  RKMSVVKVITADTY--DDDGFPIEMGLMDPRLGVIDPGLRCRTCGGRPGECPGHFGHIDL 78

Query: 154 PLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKI 213
             PV H+G+ + +  IL++IC+   C++++L E +   F  ++R         + +  K+
Sbjct: 79  VAPVIHVGFAKLIRKILRAICRE--CSKLMLSELEKKEFLRQIRTLEDLGQPTEDVVNKV 136

Query: 214 LETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPE 273
               +K   CP+CG     +K                ++  + +ED              
Sbjct: 137 FAEARKHKTCPYCGAPQREIK---------------FERPLSYIED-------------- 167

Query: 274 IEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPS 333
              HK       L P ++   FE I  EDI ++ MN E ++P   ILT L VPP  +RPS
Sbjct: 168 --GHK-------LTPSDIRDRFERISDEDIMVMGMNPETARPEWTILTVLPVPPVTMRPS 218

Query: 334 VI--SDLKSDNDV 344
           +   S  +S++D+
Sbjct: 219 ITLESGQRSEDDL 231



 Score = 89.7 bits (221), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 37/57 (64%), Positives = 50/57 (87%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFV++S+  GL+PTEFFFH +GGREGLVDTA++T+++GY+QRRLV +L+DL V YD
Sbjct: 774 HGFVESSYKKGLSPTEFFFHAIGGREGLVDTAIRTSQSGYLQRRLVNALQDLEVNYD 830



 Score = 41.6 bits (96), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 17/52 (32%), Positives = 30/52 (57%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           ++LM  + N+++PR G  +I    D++TG +LLT K    N+ + M +   L
Sbjct: 472 EILMRVQENILSPRFGGPIIGGIHDYVTGSFLLTHKERRLNKDRLMEVLKKL 523


>gi|402469132|gb|EJW04186.1| hypothetical protein EDEG_01518 [Edhazardia aedis USNM 41457]
          Length = 586

 Score =  192 bits (488), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 108/251 (43%), Positives = 155/251 (61%), Gaps = 10/251 (3%)

Query: 1143 FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGH 1202
            +  ++C  + E++   +  + +++D  +I+ L LE+ I  I + I     I     +  H
Sbjct: 339  YIKDICPSLTEIYGLKELCLELEIDTQKIKDLRLELTIPDIIHAISLQTKIVKENIIQKH 398

Query: 1203 SFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDN 1262
            + + +  K    +F     QMK+ +  +VIKG++ + R V++E+      KY L+VEG  
Sbjct: 399  NKIQIFVKKDYYAFK----QMKRKIWDLVIKGLKNVTRCVVNEDK----NKYNLIVEGTG 450

Query: 1263 LRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVA 1322
            L D++AT G+K     SNN  E Y  LGIEAAR +I+ EI   MENHG++I+ RH  L+A
Sbjct: 451  LLDILATIGIK--TAISNNVMENYDVLGIEAARQSIINEILYTMENHGITINRRHVELLA 508

Query: 1323 DLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGL 1382
            D MT KG+ LGITRHG++KMK S L LASFE TSDHLF+A   G+ D I GVSECIIMG 
Sbjct: 509  DTMTYKGQTLGITRHGISKMKMSTLMLASFEQTSDHLFEATLKGKIDEIKGVSECIIMGK 568

Query: 1383 PMNVGTGLIKL 1393
             M VGTG+++L
Sbjct: 569  KMGVGTGVVEL 579



 Score =  126 bits (316), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 75/205 (36%), Positives = 119/205 (58%), Gaps = 10/205 (4%)

Query: 793 LDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIE 852
           L+ A I+K R+E+T + ++C  + E++   +  + +++D  +I+ L LE+ I  I + I 
Sbjct: 325 LENAHIIKSRIEKTYIKDICPSLTEIYGLKELCLELEIDTQKIKDLRLELTIPDIIHAIS 384

Query: 853 RTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDV 912
               I     +  H+ + +  K    +F     QMK+ +  +VIKG++ + R V++E+  
Sbjct: 385 LQTKIVKENIIQKHNKIQIFVKKDYYAFK----QMKRKIWDLVIKGLKNVTRCVVNEDK- 439

Query: 913 EGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMEN 972
               KY L+VEG  L D++AT G+K     SNN  E Y  LGIEAAR +I+ EI   MEN
Sbjct: 440 ---NKYNLIVEGTGLLDILATIGIK--TAISNNVMENYDVLGIEAARQSIINEILYTMEN 494

Query: 973 HGMSIDFRHPMLVADLMTSKGEVLG 997
           HG++I+ RH  L+AD MT KG+ LG
Sbjct: 495 HGITINRRHVELLADTMTYKGQTLG 519



 Score = 63.5 bits (153), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 27/30 (90%), Positives = 28/30 (93%)

Query: 1116 EPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            EP TAVGA+A QSIGEPGTQMTLKTFHFAG
Sbjct: 105  EPGTAVGAIAGQSIGEPGTQMTLKTFHFAG 134



 Score = 46.6 bits (109), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 21/37 (56%), Positives = 26/37 (70%)

Query: 668 DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 704
           D  F+A   G+ D I GVSECIIMG  M VGTG+++L
Sbjct: 543 DHLFEATLKGKIDEIKGVSECIIMGKKMGVGTGVVEL 579


>gi|327351526|gb|EGE80383.1| hypothetical protein BDDG_03324 [Ajellomyces dermatitidis ATCC 18188]
          Length = 572

 Score =  192 bits (488), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 132/363 (36%), Positives = 185/363 (50%), Gaps = 74/363 (20%)

Query: 1105 ACREKYVRAQIEPATAVGAL---------------------------------------A 1125
            AC  KY RAQ+EP  AVGA+                                       A
Sbjct: 165  ACLTKYKRAQVEPGHAVGAVGAQSIGEPGTQMTLKTFHFAGVAGMSITQGVPRIKEIINA 224

Query: 1126 AQSIGEPGTQMTLKTFH---------------FAGEVCEYIEEVFVPDDSFILIKLDMDR 1170
            ++ I  P     L   H               F  ++  YIEE +  ++++I IK+D   
Sbjct: 225  SKEISTPVITCELVNKHDLRAAQIVKGRVEKTFIRDIIYYIEEDWTGNEAYINIKIDFST 284

Query: 1171 IRLLHLEVDIDSIRYCIE------------RTRGISGHLTVSGHSFLILKPKDSSKSFNS 1218
            I+ L LE+++  I   I+            R+ G   H+ V  H+      K    +  +
Sbjct: 285  IQNLQLELNLQDILVAIKKHKRFKSADLKFRSFGSHIHIFVDQHATRTALSKTEEAATGA 344

Query: 1219 KMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 1274
              Y     +K+L+P++ + G     RA+I  ++    T   LLVEG  LRD M T G+ G
Sbjct: 345  DPYIRLKHLKRLIPNIQVIGHPQCARAIIRTDETN--TTNTLLVEGYGLRDCMTTDGING 402

Query: 1275 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGI 1334
                +NN  E    LGIEAAR+TI+ EI  VM++  MSID RH  L+AD+MT KGEVLGI
Sbjct: 403  HHTRTNNIMEARTVLGIEAARTTIVDEISEVMKD--MSIDPRHMQLLADVMTYKGEVLGI 460

Query: 1335 TRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            TR GLAKM++SVL LASFE T+DHLFDA   G+TD I GVSECII+G  +++GTG ++++
Sbjct: 461  TRFGLAKMRDSVLQLASFEKTADHLFDAGGAGRTDLIEGVSECIIVGKSVSLGTGAMEVV 520

Query: 1395 QAV 1397
            +A+
Sbjct: 521  RAL 523



 Score =  160 bits (404), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 103/250 (41%), Positives = 144/250 (57%), Gaps = 20/250 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
           GVPRIKEIINAS+ ISTP+IT  L    DL  A+IVKGR+E+T + ++  YIEE +  ++
Sbjct: 214 GVPRIKEIINASKEISTPVITCELVNKHDLRAAQIVKGRVEKTFIRDIIYYIEEDWTGNE 273

Query: 824 SFILIKLDMDRIRLLHLEVDIDSIRYCIE------------RTRGISGHLTVSGHSFLIL 871
           ++I IK+D   I+ L LE+++  I   I+            R+ G   H+ V  H+    
Sbjct: 274 AYINIKIDFSTIQNLQLELNLQDILVAIKKHKRFKSADLKFRSFGSHIHIFVDQHATRTA 333

Query: 872 KPKDSSKSFNSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927
             K    +  +  Y     +K+L+P++ + G     RA+I  ++    T   LLVEG  L
Sbjct: 334 LSKTEEAATGADPYIRLKHLKRLIPNIQVIGHPQCARAIIRTDETN--TTNTLLVEGYGL 391

Query: 928 RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 987
           RD M T G+ G    +NN  E    LGIEAAR+TI+ EI  VM++  MSID RH  L+AD
Sbjct: 392 RDCMTTDGINGHHTRTNNIMEARTVLGIEAARTTIVDEISEVMKD--MSIDPRHMQLLAD 449

Query: 988 LMTSKGEVLG 997
           +MT KGEVLG
Sbjct: 450 VMTYKGEVLG 459



 Score = 45.8 bits (107), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 31/41 (75%)

Query: 668 DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 708
           D  FDA   G+TD I GVSECII+G  +++GTG +++++A+
Sbjct: 483 DHLFDAGGAGRTDLIEGVSECIIVGKSVSLGTGAMEVVRAL 523


>gi|260820176|ref|XP_002605411.1| hypothetical protein BRAFLDRAFT_120654 [Branchiostoma floridae]
 gi|229290744|gb|EEN61421.1| hypothetical protein BRAFLDRAFT_120654 [Branchiostoma floridae]
          Length = 975

 Score =  192 bits (488), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 98/177 (55%), Positives = 131/177 (74%), Gaps = 3/177 (1%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
           GVPRIKEIINAS+NISTPIITA L+ D+  ++AR VKGR+E++ LGEV EY+EEV++PDD
Sbjct: 795 GVPRIKEIINASKNISTPIITAQLEDDSSAEFARRVKGRIEKSLLGEVTEYMEEVYLPDD 854

Query: 824 SFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKS-F 880
            F+LIKL MDRI+LL LEV  D+IRY  C  + R    ++ V G S L + P ++++S  
Sbjct: 855 CFLLIKLHMDRIKLLKLEVSADTIRYSICTSKLRIKPANIVVHGESILCVTPSETAQSTM 914

Query: 881 NSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVK 937
              M ++K+ LP VVIKG+  ++RAVIH ++  G  +YKLLVEGDNLR V+AT G +
Sbjct: 915 YYNMQKLKETLPKVVIKGIDSVSRAVIHLDEKGGQQQYKLLVEGDNLRAVIATPGTQ 971



 Score =  155 bits (392), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 112/341 (32%), Positives = 171/341 (50%), Gaps = 79/341 (23%)

Query: 997  GNGTPVELKRLLDDIIAKNSSRSDPSLSAQEILALSNETLDSKEFLQDTSENFVRDIKKF 1056
            G  TPV+ +R+LD I A +    +P L++ E++  + + +DS EF+   SE + ++IK F
Sbjct: 646  GKDTPVDFQRVLDHIRAVHRCEGEPVLTSPELVKTTAKMVDSPEFMS-VSEEYRKEIKDF 704

Query: 1057 LEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAE------------ 1104
            + E + +   T  + K++              G G  + P P   + E            
Sbjct: 705  VAEIAARVEATHEKYKIT-------------TGPGNSTQP-PVLLQLERITPTQLKQFLI 750

Query: 1105 ACREKYVRAQIEPAT-----------AVGAL-----------------------AAQSIG 1130
              R+KY+RA+IEP +            V +L                       A+++I 
Sbjct: 751  MVRDKYLRAKIEPESMPVLSKMKYHNKVTSLCVKLLNHVAHITLGVPRIKEIINASKNIS 810

Query: 1131 EPGTQMTLK---TFHFA------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLLH 1175
             P     L+   +  FA            GEV EY+EEV++PDD F+LIKL MDRI+LL 
Sbjct: 811  TPIITAQLEDDSSAEFARRVKGRIEKSLLGEVTEYMEEVYLPDDCFLLIKLHMDRIKLLK 870

Query: 1176 LEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKS-FNSKMYQMKQLLPSVVI 1232
            LEV  D+IRY  C  + R    ++ V G S L + P ++++S     M ++K+ LP VVI
Sbjct: 871  LEVSADTIRYSICTSKLRIKPANIVVHGESILCVTPSETAQSTMYYNMQKLKETLPKVVI 930

Query: 1233 KGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVK 1273
            KG+  ++RAVIH ++  G  +YKLLVEGDNLR V+AT G +
Sbjct: 931  KGIDSVSRAVIHLDEKGGQQQYKLLVEGDNLRAVIATPGTQ 971



 Score =  117 bits (294), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 72/160 (45%), Positives = 92/160 (57%), Gaps = 23/160 (14%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV+NSF+SGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC  YD+ 
Sbjct: 562 AKGFVENSFYSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCSHYDLM 621

Query: 671 FDAA-------FYGQTDCISGVSECIIMGLPMNVG-TGLIKLLQAVPRSEPVP------- 715
              +        YG      G+    + G    V    ++  ++AV R E  P       
Sbjct: 622 VRNSMGEIIQFMYGG----DGLDPAAMEGKDTPVDFQRVLDHIRAVHRCEGEPVLTSPEL 677

Query: 716 ---RTLLFDNPEF-HFPQVYYERRRDYSVKVTASVKVTLE 751
                 + D+PEF    + Y +  +D+  ++ A V+ T E
Sbjct: 678 VKTTAKMVDSPEFMSVSEEYRKEIKDFVAEIAARVEATHE 717


>gi|145509313|ref|XP_001440599.1| hypothetical protein [Paramecium tetraurelia strain d4-2]
 gi|124407819|emb|CAK73202.1| unnamed protein product [Paramecium tetraurelia]
          Length = 1353

 Score =  191 bits (486), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 106/279 (37%), Positives = 163/279 (58%), Gaps = 38/279 (13%)

Query: 343 DVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARA 402
           D+V+FNRQPSLH++S+MA RA+V    T RFNECVCTP+NADFDGDEMN+HLPQT EAR+
Sbjct: 422 DIVIFNRQPSLHRISMMAFRARVDKWHTLRFNECVCTPFNADFDGDEMNIHLPQTYEARS 481

Query: 403 EALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 462
           EAL              +LM  K NL T ++GE L+   QDF+T  +L+T K+ F++R Q
Sbjct: 482 EAL--------------ILMDVKKNLKTIKSGESLVCLLQDFLTTAWLITNKDVFYSREQ 527

Query: 463 TMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNAN 522
            M+  +   +D+++   +          P + ++   +WTGKQ+ + +L PNR       
Sbjct: 528 FMQFCAAF-SDSNEQIDLPA--------PTI-LKPKQLWTGKQVINALLVPNR------- 570

Query: 523 LKTKGRAYTANEEF--CHRD---SYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFG 577
            KT+ +     E +  C      + V+    EL+ G++ K  LG+  K  +FY L+RD  
Sbjct: 571 -KTRLKVTHLKESWTICGWTLVMASVVFDKCELVCGNIGKKVLGA-SKLGLFYALIRDNS 628

Query: 578 EDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
             +A + M R ++++S ++ + G +IGIGDV   +  ++
Sbjct: 629 TQIAASVMQRFAKLSSRWISHYGMTIGIGDVMAPKSLIE 667



 Score =  120 bits (301), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 67/192 (34%), Positives = 112/192 (58%), Gaps = 8/192 (4%)

Query: 1222 QMKQLLPSVVIKGVQGINRAVIH------EEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 1275
            ++++ L  + I G   I + VI       +E+V+G  + +L   G   ++++    +   
Sbjct: 1154 ELQRKLLRLHIYGCANIKQTVIQVTDKDDKENVKG--EARLFASGIGFKEILRLDNIDWK 1211

Query: 1276 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGIT 1335
            +  SN+  E+   LGIEAAR +I+ E+   M++H +SID RH +L+A+LMT KG +LG T
Sbjct: 1212 RTVSNHIMEIQSALGIEAARQSIVNEVYTTMQSHSISIDIRHILLLAELMTFKGRILGFT 1271

Query: 1336 RHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 1395
            R G+ ++K S L LASFE T D  F+AA  G+ D ++G S+ +I+G  +  GTG+  L+ 
Sbjct: 1272 RQGIDQLKNSALMLASFEKTMDVFFNAAIQGKQDSMNGASQRVIIGQNVPQGTGMFDLMF 1331

Query: 1396 AVPRSEPVPRTL 1407
             V  +  +  T+
Sbjct: 1332 PVKENTILESTI 1343



 Score = 93.6 bits (231), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 40/60 (66%), Positives = 49/60 (81%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV+NSF++G+   EF+FH M GREGL DTAVKTA TGYMQRRLVK LEDL + YD++
Sbjct: 782 AKGFVKNSFYTGMDAIEFYFHNMAGREGLTDTAVKTATTGYMQRRLVKMLEDLHIAYDLT 841



 Score = 92.4 bits (228), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 76/281 (27%), Positives = 137/281 (48%), Gaps = 59/281 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARI------------------------- 798
            GVPR+ EIINAS+ I TP I   L     +D+A+                          
Sbjct: 1001 GVPRLNEIINASKEIKTPQINVKLINRQVMDHAKQFAKSGDPQYEYAHRAVIHSAQQAQD 1060

Query: 799  VKGRLERTTLGEVCEYIEEVFVPDDSFILIKLD---MDRIRL-------------LHLEV 842
            V  ++E+T L ++ + ++E++  D+ +I ++LD   + R++L               L++
Sbjct: 1061 VNIQIEQTKLMQILKKMDEIYTADNCYIELELDCHCLARLKLEFVTPKYVCALILKELKL 1120

Query: 843  DIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGI 902
              D ++Y ++  R     +TV   S      K  S++    + ++++ L  + I G   I
Sbjct: 1121 SPDDVKYDLKIIR-----ITVKKSS-----KKKQSENLLFLIKELQRKLLRLHIYGCANI 1170

Query: 903  NRAVIH------EEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIE 956
             + VI       +E+V+G  + +L   G   ++++    +   +  SN+  E+   LGIE
Sbjct: 1171 KQTVIQVTDKDDKENVKG--EARLFASGIGFKEILRLDNIDWKRTVSNHIMEIQSALGIE 1228

Query: 957  AARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            AAR +I+ E+   M++H +SID RH +L+A+LMT KG +LG
Sbjct: 1229 AARQSIVNEVYTTMQSHSISIDIRHILLLAELMTFKGRILG 1269



 Score = 80.5 bits (197), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 106/235 (45%), Gaps = 47/235 (20%)

Query: 116 IPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICK 175
           I HG LD RMG + ++  C++C   L++C GHFGYI L LP++H+G+F  V+  L+ +C 
Sbjct: 47  IEHGPLDLRMGQSLRDTQCSSCTL-LNECPGHFGYIPLQLPIYHLGFFTHVVKCLKCLCY 105

Query: 176 NPTCARVLLGEEKAAGFRAKLRN--PALSYLVRKSLKKKILETTKKVSVCPHC-GEINGV 232
              C +V L  ++      K+ +     SY  +  + KK+L+  +    CPHC  E  G 
Sbjct: 106 K--CGQVRLTPDEINQLTQKMVHCIQTRSYNAQLKVFKKVLKKCRSNKQCPHCYCEQIGE 163

Query: 233 VKKCGLLKISHEKYKNRTKKKDA--IVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLE 290
            KK                K DA  I+ D +                        +N L 
Sbjct: 164 AKKLA--------------KGDAGKIILDTM-----------------------DINALY 186

Query: 291 VLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVI--SDLKSDND 343
               F  IP +   L  +N  L+  SDL+ + +  PPN IRPS +  +  K+D D
Sbjct: 187 AWNQFSNIPKQHQFLFCINPFLNDLSDLLTSIIPAPPNNIRPSKMLSNTTKADED 241



 Score = 52.4 bits (124), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 22/38 (57%), Positives = 29/38 (76%)

Query: 1108 EKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            E+++   + P T+VG + +QSIGEP TQMTLKTFH AG
Sbjct: 955  ERFLTMVMAPGTSVGPITSQSIGEPATQMTLKTFHSAG 992



 Score = 47.4 bits (111), Expect = 0.064,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 35/59 (59%)

Query: 13  YATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           Y  R+   +LM  K NL T ++GE L+   QDF+T  +L+T K+ F++R Q M+  +  
Sbjct: 477 YEARSEALILMDVKKNLKTIKSGESLVCLLQDFLTTAWLITNKDVFYSREQFMQFCAAF 535


>gi|160331067|ref|XP_001712241.1| rpc1 [Hemiselmis andersenii]
 gi|159765688|gb|ABW97916.1| rpc1 [Hemiselmis andersenii]
          Length = 1323

 Score =  190 bits (483), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 106/286 (37%), Positives = 159/286 (55%), Gaps = 44/286 (15%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           +ND++LFNRQPSLH++SIMAHR K++  +T + NEC+C PYNADFDGDEMN+H+PQT++A
Sbjct: 433 NNDIILFNRQPSLHRISIMAHRTKIISGKTLKINECICKPYNADFDGDEMNIHIPQTQKA 492

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE++  L+ +               N+ +P  GE +IAATQDF++  ++LT KN FF+ 
Sbjct: 493 RAESISLLNLV--------------KNINSPGTGESMIAATQDFLSASFVLTSKNQFFSH 538

Query: 461 AQTMRIASTL----IADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRD 516
            Q  +I   L    I   + I  ++K F               +WTGKQIFSLI+   + 
Sbjct: 539 DQIGKILHLLELGNIEKENFIPALLKPFQ--------------MWTGKQIFSLIVFSKKK 584

Query: 517 CPVNANLKTKGRAYTANEE------------FCHRDSYVILRNSELLAGSMDKSTLGSGG 564
              N     +G  +   E+             C  D +++ +N  LLAG + KS+LG G 
Sbjct: 585 KDKNKKKNFQGSIFHLMEKNYSLGKKQCSPFLCPFDGWILFKNRNLLAGQLGKSSLGFGN 644

Query: 565 KANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           K ++F         +  +  + ++S+MTS +  + GFS GI  +TP
Sbjct: 645 KFSIFSSFSIFNSNNFILNCLLKISKMTSSWFSDFGFSFGIESITP 690



 Score =  137 bits (344), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 105/351 (29%), Positives = 163/351 (46%), Gaps = 69/351 (19%)

Query: 1108 EKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFA----------------------- 1144
            E   + ++EP ++VGALAAQSIGEPGTQMTL+TFH A                       
Sbjct: 975  ENCSKLKMEPGSSVGALAAQSIGEPGTQMTLQTFHHAGISDLNITQGVPRINEIMNASKK 1034

Query: 1145 ------------------------------GEVCEYIEEVFVPDDSFILIKLDMDRIRLL 1174
                                          GE+C   + +   +  FI I    + ++ L
Sbjct: 1035 ILSPIVSFKFFNLGKKNFFQCKLQIEKIYFGEICSKFDIIIDSELIFIDIFFKKNFLKKL 1094

Query: 1175 HLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKG 1234
             L ++   I   +++  GI+     S   F   K +   + F SK  + K      ++K 
Sbjct: 1095 GLNLNFKKI---VQKIGGINSFWNKS--RFFYQKSRYFMRIFPSKPTEKKTFSYIELLKI 1149

Query: 1235 VQGINRAVIHEE-----DVEGVTKYK------LLVEGDNLRDVMATYGVKGVKCSSNNTY 1283
            +    +     E     D + ++ Y+      +      L D      V      SN+  
Sbjct: 1150 IYSCKKDFSQIEICGFSDSKNISFYQKFQISSVFCLNSKLLDAFDLLFVNLQSIYSNHIL 1209

Query: 1284 EVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMK 1343
             + +T GIEA+R  I+ EI+ + + H +SI+ +H  L+A++MT +G++LGITR+G++KMK
Sbjct: 1210 MILETFGIEASRKAIIIEIQKIFQLHNISINKKHFFLLAEIMTFQGKILGITRYGISKMK 1269

Query: 1344 ESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            E++L LASFE T + LF+AA     D I GVSE II+G     GTGL+ L+
Sbjct: 1270 ENILVLASFEKTIETLFNAALKTSKDKILGVSESIILGRKPPNGTGLVTLI 1320



 Score =  117 bits (293), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 87/258 (33%), Positives = 131/258 (50%), Gaps = 39/258 (15%)

Query: 97  SHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP 156
           S IQI +K LY  +    P   GLLD  +G N+K   C +C +N S C GHFGYI L LP
Sbjct: 29  SQIQITNKFLY-SNFSSQPCQGGLLDSTLGANKKNI-CKSCKKNQSYCSGHFGYIKLFLP 86

Query: 157 VFHIGYFRCVINILQSICKNPTCARVLL--GEEKAAGFRA------KLRNPALSYLVRKS 208
           V +IGY + +  IL  ICK  +C+RVL+  G+ +   F+       K     L YL    
Sbjct: 87  VLNIGYLKAIQLILSMICK--SCSRVLVHPGKRRNYFFKVIRKIKKKGEGQKLDYL---- 140

Query: 209 LKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYN--E 266
              +I +  +++  CP C   NG ++K G L   H+ +K +  KK+         +N   
Sbjct: 141 --SEISQECRQIDYCPFCWSKNGSIRKFGTLGFVHD-FKFQKNKKN------FQNFNCSA 191

Query: 267 AVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVP 326
           ++ F  +I           L+PL + ++F+ I  ED  LL  ++  + P+ LIL  L VP
Sbjct: 192 SLVFTEKI-----------LDPLGIFKIFQKISREDWELLDFDSIETHPTHLILYYLPVP 240

Query: 327 PNCIRPSV-ISDLKSDND 343
           P  +RP+V IS+  ++ D
Sbjct: 241 PLGVRPTVFISETMTNED 258



 Score = 90.5 bits (223), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 40/63 (63%), Positives = 50/63 (79%), Gaps = 1/63 (1%)

Query: 609 TPGQ-GFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
            P Q GF+Q SF  GL   +FFFH++ GREGLVDTA+KTAETGY+QRRL+K+LED+ + Y
Sbjct: 809 NPSQNGFIQRSFLQGLNSVDFFFHSIAGREGLVDTAIKTAETGYLQRRLMKTLEDVVIFY 868

Query: 668 DMS 670
           D S
Sbjct: 869 DYS 871



 Score = 75.9 bits (185), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 64/252 (25%), Positives = 119/252 (47%), Gaps = 18/252 (7%)

Query: 757  DYKLSQDGVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIE 816
            D  ++Q GVPRI EI+NAS+ I +PI++         ++ +  K ++E+   GE+C   +
Sbjct: 1015 DLNITQ-GVPRINEIMNASKKILSPIVSFKFFNLGKKNFFQ-CKLQIEKIYFGEICSKFD 1072

Query: 817  EVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDS 876
             +   +  FI I    + ++ L L ++   I   +++  GI+     S   F   K +  
Sbjct: 1073 IIIDSELIFIDIFFKKNFLKKLGLNLNFKKI---VQKIGGINSFWNKS--RFFYQKSRYF 1127

Query: 877  SKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEE-----DVEGVTKYK------LLVEGD 925
             + F SK  + K      ++K +    +     E     D + ++ Y+      +     
Sbjct: 1128 MRIFPSKPTEKKTFSYIELLKIIYSCKKDFSQIEICGFSDSKNISFYQKFQISSVFCLNS 1187

Query: 926  NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLV 985
             L D      V      SN+   + +T GIEA+R  I+ EI+ + + H +SI+ +H  L+
Sbjct: 1188 KLLDAFDLLFVNLQSIYSNHILMILETFGIEASRKAIIIEIQKIFQLHNISINKKHFFLL 1247

Query: 986  ADLMTSKGEVLG 997
            A++MT +G++LG
Sbjct: 1248 AEIMTFQGKILG 1259



 Score = 45.1 bits (105), Expect = 0.33,   Method: Compositional matrix adjust.
 Identities = 21/47 (44%), Positives = 30/47 (63%)

Query: 28  NLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
           N+ +P  GE +IAATQDF++  ++LT KN FF+  Q  +I   L  G
Sbjct: 505 NINSPGTGESMIAATQDFLSASFVLTSKNQFFSHDQIGKILHLLELG 551


>gi|347522775|ref|YP_004780345.1| DNA-directed RNA polymerase subunit A' [Pyrolobus fumarii 1A]
 gi|343459657|gb|AEM38093.1| DNA-directed RNA polymerase subunit A' [Pyrolobus fumarii 1A]
          Length = 882

 Score =  188 bits (478), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 104/270 (38%), Positives = 149/270 (55%), Gaps = 29/270 (10%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
            D D+VLFNRQPSLH++SIMAH  +VLP +TFR N  VC PYNADFDGDEMN+H+P+TEE
Sbjct: 414 KDGDIVLFNRQPSLHRMSIMAHIVRVLPGKTFRLNLLVCPPYNADFDGDEMNLHVPRTEE 473

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           A+AE              A+ LM  + +++TPR G ++I   QD+I+G YLLT K     
Sbjct: 474 AQAE--------------ARELMLVQFHILTPRYGGVIIGGLQDYISGAYLLTSKATILT 519

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
                      + D  D+    K +      PV+ +    +WTGKQ+ SL L   +D   
Sbjct: 520 -----------LDDVVDLLAAAK-YEGEIPEPVI-LSPKKLWTGKQLVSLFLP--KDFTF 564

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
               K    A+  ++E C  DSY++++N ELL G  DK  +G+    +V + L +++G D
Sbjct: 565 RGKAKISSGAFACSDELCWNDSYIVIKNGELLEGVFDKKAIGAEQTESVLHQLTKEYGFD 624

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVT 609
                M  L +M   Y+   GF++ + DV 
Sbjct: 625 YVRRLMDTLFKMFLRYIEKHGFTMTLEDVA 654



 Score =  119 bits (297), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 81/262 (30%), Positives = 127/262 (48%), Gaps = 51/262 (19%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D +++ S + I +  LY  DP   PIP GL+D R+G       C TCG +   C GHFG 
Sbjct: 18  DEIRKMSVVAITTDQLY--DPDGRPIPGGLMDPRLGAAIPGQRCETCGNDYRLCPGHFGR 75

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGF-----RAKLRNPALSYLV 205
           I+L LPV ++G+ R +  IL++ C+N  C R+ L E +   +     R K + P L+   
Sbjct: 76  IELALPVINVGFARHIYEILRATCRN--CGRIKLPERELKRYLKLLERLKNKWPLLA--- 130

Query: 206 RKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEK-YKNRTKKKDAIVEDLLAEY 264
            K+L  ++ +   K + CPHC E N         KI  EK YK    +    V       
Sbjct: 131 -KALINEVKQRAAKTTECPHCKEHN--------YKIVFEKPYKYYEDRPAGRV------- 174

Query: 265 NEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLL 324
                                LNP EV    E IP +D+ LL ++ + ++P  ++LT L 
Sbjct: 175 --------------------PLNPREVRSRLEKIPDDDVKLLGLDPKEARPEWMVLTVLP 214

Query: 325 VPPNCIRPSVI--SDLKSDNDV 344
           VPP  +RPS++  + +++++D+
Sbjct: 215 VPPIHVRPSIVLETGIRAEDDL 236



 Score = 94.4 bits (233), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 41/64 (64%), Positives = 53/64 (82%), Gaps = 1/64 (1%)

Query: 606 GDVTPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           GD+ P  +GFV + F+ GLTPTE FFH  GGREGLVDTAV+T+++GYMQRRL+ +L+DL 
Sbjct: 774 GDLGPAARGFVYHGFYDGLTPTEVFFHAAGGREGLVDTAVRTSQSGYMQRRLINALQDLR 833

Query: 665 VQYD 668
           V+YD
Sbjct: 834 VEYD 837


>gi|119719203|ref|YP_919698.1| DNA-directed RNA polymerase subunit A' [Thermofilum pendens Hrk 5]
 gi|119524323|gb|ABL77695.1| DNA-directed RNA polymerase, subunit A' [Thermofilum pendens Hrk 5]
          Length = 888

 Score =  188 bits (478), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 107/277 (38%), Positives = 153/277 (55%), Gaps = 47/277 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH++SIMAH  KVLP++TFR N  V  PYNADFDGDEMN+H+PQ+EEA
Sbjct: 417 DGDVVLFNRQPSLHRISIMAHIVKVLPYKTFRLNLLVTIPYNADFDGDEMNLHVPQSEEA 476

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+ LM  + +++TPR G  +I    D+I+G YLLT+K+A  ++
Sbjct: 477 RAE--------------ARELMLVQEHIMTPRYGAPIIGGLHDYISGSYLLTRKDALLDK 522

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVV---FVRTAVIWTGKQIFSLILKPNRDC 517
              +R+    I +  D              P+V    ++    WTGKQI S+ L      
Sbjct: 523 KSALRL--LYIGNNCD--------------PLVEPAIIKPGPYWTGKQIVSMFLP----- 561

Query: 518 PVNANLKTKGRAYTA------NEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYI 571
                L   GRA  A      +EE+C  D YV++++ +LL G  DK  +G+     V + 
Sbjct: 562 ---KGLNYVGRASVAPASGKCDEEYCENDGYVLIKDGKLLLGVFDKQAIGAEKHGTVLHE 618

Query: 572 LLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           ++R+FG + A   M  + ++   YL   GF++G+  V
Sbjct: 619 IVREFGVEKAKELMDGMFKVFIAYLDMHGFTMGVDSV 655



 Score =  106 bits (265), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 74/258 (28%), Positives = 127/258 (49%), Gaps = 47/258 (18%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           +++ + ++I +  LY  D +  PIP GL+DRRMG+ +  A C TCG   ++C GHFGYI+
Sbjct: 23  IRKIAVLRIETSELY--DEEGFPIPGGLMDRRMGSIEPGAVCQTCGNRFTNCPGHFGYIE 80

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKK 212
           L  PV H  +   +  +L++ C    C R+ L EEK    + ++   +  +    SLK K
Sbjct: 81  LARPVIHPSFAPYIAILLKATCNR--CGRLKLPEEKINKAKKRMEVYSAKW---PSLKTK 135

Query: 213 ----ILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAV 268
               +L+   K +VCPHCG                 +YK R  K     E+         
Sbjct: 136 YANTLLKEAAKATVCPHCGA---------------PQYKIRLDKPYTFYEE--------- 171

Query: 269 KFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPN 328
                    ++ GL++ L PLE+ +    IP  D+ ++ ++ + ++P  ++L  + V P 
Sbjct: 172 ---------REEGLVK-LTPLEIWERLSRIPEGDLRVVGIDPKEARPEWMVLRVIPVVPP 221

Query: 329 CIRPSVI--SDLKSDNDV 344
            +RPS+   S  +S++D+
Sbjct: 222 SVRPSITLESGDRSEDDL 239



 Score = 86.3 bits (212), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 50/64 (78%), Gaps = 1/64 (1%)

Query: 606 GDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           GD++P  +GFV +SF  GL+P EFFFH + GREGLVDTAV+TA++GYM RRL  +++D  
Sbjct: 776 GDLSPLAKGFVYSSFRRGLSPVEFFFHAISGREGLVDTAVRTAQSGYMYRRLQSAMQDFY 835

Query: 665 VQYD 668
           V YD
Sbjct: 836 VSYD 839



 Score = 43.5 bits (101), Expect = 0.79,   Method: Compositional matrix adjust.
 Identities = 17/46 (36%), Positives = 30/46 (65%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRI 67
           LM  + +++TPR G  +I    D+I+G YLLT+K+A  ++   +R+
Sbjct: 483 LMLVQEHIMTPRYGAPIIGGLHDYISGSYLLTRKDALLDKKSALRL 528


>gi|150399424|ref|YP_001323191.1| DNA-directed RNA polymerase subunit A' [Methanococcus vannielii SB]
 gi|1173129|sp|P41556.1|RPOA1_METVS RecName: Full=DNA-directed RNA polymerase subunit A'
 gi|505292|emb|CAA51728.1| DNA-directed RNA polymerase [Methanococcus vannielii]
 gi|150012127|gb|ABR54579.1| DNA-directed RNA polymerase subunit A' [Methanococcus vannielii SB]
          Length = 889

 Score =  186 bits (473), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 108/284 (38%), Positives = 152/284 (53%), Gaps = 39/284 (13%)

Query: 328 NCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDG 387
           N +   V+     D DVVL+NRQPSLH++SIMAH+ KVLP+RTFR N CVC PYNADFDG
Sbjct: 410 NIVDGMVVERHLGDGDVVLYNRQPSLHRMSIMAHKVKVLPYRTFRHNLCVCPPYNADFDG 469

Query: 388 DEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITG 447
           DEMNVH+PQ+EEARAE              A+ LM  + ++++PR G  +I A  DF++G
Sbjct: 470 DEMNVHVPQSEEARAE--------------AETLMLVEKHIISPRYGGPIIGAIHDFVSG 515

Query: 448 GYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIF 507
            Y+LT  N   + A T+  +S               F      P         ++GK +F
Sbjct: 516 AYVLTSSNFIKDEALTLLKSSG--------------FGSELGEPDFVENGIEYYSGKSLF 561

Query: 508 SLILKPNRDCPVNANLKTKGRA----YTANEEFCHRDSYVILRNSELLAGSMDKSTLGSG 563
           S  L      P   NL+ K +          E C  D++VI+RN  L+ G +DK+  G+ 
Sbjct: 562 SKTL------PKGLNLQYKAKVCKKCVQCKREECENDAFVIIRNGRLVQGVIDKNGFGA- 614

Query: 564 GKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
               V   +++DFG + A T +   ++M+   +M RGF+ GI D
Sbjct: 615 ETGVVLNTIVKDFGSEDARTFLDSATKMSVKSMMLRGFTTGIDD 658



 Score =  102 bits (255), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 73/257 (28%), Positives = 120/257 (46%), Gaps = 42/257 (16%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           ++++  S  +IV+ + Y  D    PI  GL+D R+G       C +C   +  C GHFG+
Sbjct: 21  EQIRTMSVAKIVTADTY--DDDGYPIDGGLMDTRLGVIDPGLVCKSCSGRVGTCPGHFGH 78

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           I+L   V HIG+ + +  +L+++C  P C +V + E K   +  K+           +L 
Sbjct: 79  IELSKSVIHIGFAKDIYKLLKAVC--PHCGKVTVTEIKRDEYLEKMLKLEEDGGDPWTLS 136

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
             +L+   K SVCP CGE+               KY                     +K+
Sbjct: 137 DDLLKEAAKSSVCPSCGEV---------------KYD--------------------IKY 161

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           +     H+  G  Q  L   EV ++ E IP ED  LL +N+ +++P  ++LT L VPP  
Sbjct: 162 DKPTTYHQLDGKSQKQLTSSEVREILEKIPNEDCKLLGINSRVARPEYMVLTVLPVPPVT 221

Query: 330 IRPSVI--SDLKSDNDV 344
           +RPS+   S  +S++D+
Sbjct: 222 VRPSITLESGERSEDDL 238



 Score = 87.4 bits (215), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 36/57 (63%), Positives = 47/57 (82%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFV++ +  GL PTE+FFH MGGREGLVD AV+TA++GYMQRRLV +L+D+  +YD
Sbjct: 787 HGFVRSCYKKGLAPTEYFFHAMGGREGLVDQAVRTAQSGYMQRRLVNALQDIKAEYD 843


>gi|302348974|ref|YP_003816612.1| DNA-directed RNA polymerase subunit A [Acidilobus saccharovorans
           345-15]
 gi|302329386|gb|ADL19581.1| DNA-directed RNA polymerase subunit A [Acidilobus saccharovorans
           345-15]
          Length = 889

 Score =  186 bits (472), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 107/268 (39%), Positives = 148/268 (55%), Gaps = 29/268 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIM H+ +V+P RTFR N  VC PYNADFDGDEMN+H+P+ EEA
Sbjct: 422 DGDIVLFNRQPSLHRMSIMGHKVRVMPGRTFRLNLLVCAPYNADFDGDEMNLHVPRLEEA 481

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL               L+  +++++TPR G  +I   QD+I+G YLLT K   F+R
Sbjct: 482 RAEAL--------------NLLLVENHILTPRYGGPIIGGRQDYISGAYLLTVKTTLFDR 527

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
               R    L+A  S        +S     P + ++   +WTGKQ+ SL L    D   +
Sbjct: 528 EAVGR----LLAAAS--------YSGELPEPAI-LKPRPLWTGKQLVSLFLP--SDFNFS 572

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
              K        + E C  DSYV++R   LL G  DK+T+G+    +V + +  ++G   
Sbjct: 573 GRAKINAGDLKCDGEDCFFDSYVVIRRGRLLEGVFDKNTIGAEQPESVLHYIALEYGNAA 632

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           A   +  + RM    L  RGFSI I D+
Sbjct: 633 ARQLLDTMYRMFIRMLELRGFSISISDI 660



 Score = 89.4 bits (220), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 71/261 (27%), Positives = 120/261 (45%), Gaps = 53/261 (20%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           +++ + + ++   +Y  D   +P+  GL D   G  +    C  CG    DC GHFG ID
Sbjct: 27  IREMAKVTVIRPEIYEVDG--SPVMGGLRDPHFGAIEPGERCPVCGNTRQDCPGHFGKID 84

Query: 153 LPLPVF--HIGYFRCVINILQSICKNPTCARVLLGEEKAA---GFRAKLRN--PALSYLV 205
           L  PV   H+G    +  +LQS C+  +C R+L+  +KAA   G   +LR   P L+ + 
Sbjct: 85  LARPVVLPHLG--DKIYQLLQSTCR--SCGRILIPPQKAAYMLGIYRRLREKWPLLADI- 139

Query: 206 RKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYN 265
                +++++     + CPHCG                ++YK +           +  YN
Sbjct: 140 ---FVEEVIKEASSATECPHCGA---------------KQYKIK----------FIKPYN 171

Query: 266 EAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLV 325
              +  PE E          L P +V +  E IP +D+ LL  + + ++P   +LT L V
Sbjct: 172 -FYEVRPEGEVR--------LTPSDVRERLEKIPDDDVELLGWDPKSARPEWAVLTVLPV 222

Query: 326 PPNCIRPSVI--SDLKSDNDV 344
           PP  +RPS+   S  ++++D+
Sbjct: 223 PPLSVRPSITMESGSRAEDDL 243



 Score = 88.2 bits (217), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 53/136 (38%), Positives = 77/136 (56%), Gaps = 11/136 (8%)

Query: 544 ILRNSELLAGSMDKSTLGSGGKANVFYILLRD--FGEDVAVTAMWRL--SRMTSFYLMNR 599
           I++  + L     K+ +G     N  +I+ R    G D+ +T M  +   +      + R
Sbjct: 709 IIQRLQKLRDDAGKTAIGYMNPFNNAFIMARTGARGSDINITQMAAMLGQQTVRGRRIVR 768

Query: 600 GFSIGI------GDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYM 652
           GF          GD++P  +GFV ++F  GL P E FFH  GGREGLVDTA+KT+++GYM
Sbjct: 769 GFRTRTLPHFRPGDLSPEARGFVVSNFRDGLKPHEVFFHAAGGREGLVDTALKTSQSGYM 828

Query: 653 QRRLVKSLEDLCVQYD 668
           QRRL+ +L+DL V YD
Sbjct: 829 QRRLINALQDLHVAYD 844


>gi|409095098|ref|ZP_11215122.1| DNA-directed RNA polymerase subunit A' [Thermococcus zilligii AN1]
          Length = 907

 Score =  186 bits (471), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 101/282 (35%), Positives = 157/282 (55%), Gaps = 40/282 (14%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
            D D+VLFNRQPSLH++SIMAHR +V+P+RTFR N  VC PYNADFDGDEMN+H+PQTEE
Sbjct: 417 EDGDIVLFNRQPSLHRMSIMAHRVRVMPYRTFRLNLSVCPPYNADFDGDEMNLHVPQTEE 476

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           A+AE              AK+LM  ++++++PR G  +IA  QD I+GGYLLT++ A+F 
Sbjct: 477 AQAE--------------AKILMEVQNHIISPRYGGPIIAGIQDHISGGYLLTREGAYFT 522

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           R +  ++ +    D   +             P  F     +W+GK +FSL+L  +     
Sbjct: 523 RLEVEQMIAFAGIDVDKLP-----------EPDKFENGQPLWSGKTVFSLLLPSDLTIWY 571

Query: 520 NANLKTKGRAYTANEEFCHR--------------DSYVILRNSELLAGSMDKSTLGSGGK 565
              L  +     A E+                  D +V ++N  LL+G++DK+  G    
Sbjct: 572 RNKLCDEPERCEALEKLIEEKLLPDPEEVRKLACDGFVYIQNGRLLSGAIDKTVYGR-ED 630

Query: 566 ANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
             +  +++R++G + A   + +++R+T + + +RGF+  I D
Sbjct: 631 GKLLDVIVREYGVERARQFLDQVTRLTIWVITHRGFTTAIDD 672



 Score =  115 bits (289), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 77/272 (28%), Positives = 129/272 (47%), Gaps = 37/272 (13%)

Query: 75  RKVFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANC 134
           RKV   G IE  +     +++ S  +I   + Y +D    PI  GL+D+R+G       C
Sbjct: 5   RKVI--GSIEFGILSPQEIRKMSAAEITVPDTYDEDG--YPIEGGLMDKRLGVIDPGLRC 60

Query: 135 TTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA 194
            TCG    +C GHFG+I+L  PV H+G+ + ++ +L+S C+   C R+ L +E+  G+  
Sbjct: 61  ETCGAKAGECPGHFGHIELARPVVHVGFAKTILRVLESTCRE--CGRIKLTDEEIEGYMK 118

Query: 195 KLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKD 254
           K          R  L ++I +  K+  VCPHCG     +           K++  T   +
Sbjct: 119 KFEVIGDRKKARDDLIREIHKKAKERMVCPHCGAPQFPL-----------KFERPTVYWE 167

Query: 255 AIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSK 314
              ++   +Y                     + P E+    E IP  D+PLL ++ E S+
Sbjct: 168 LRKDEEGNDYR------------------HRMMPNEIRDRLERIPDGDLPLLGLHPENSR 209

Query: 315 PSDLILTRLLVPPNCIRPSVI--SDLKSDNDV 344
           P  ++LT L VPP  +RPS+   S +++++D+
Sbjct: 210 PEWMVLTVLPVPPVTMRPSITLESGIRAEDDL 241



 Score = 95.5 bits (236), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 41/57 (71%), Positives = 50/57 (87%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV NS+ SGLTP E+FFH MGGREGLVDTAV+TA++GYMQRRL+ +L+DL V YD
Sbjct: 801 RGFVTNSYKSGLTPQEYFFHAMGGREGLVDTAVRTAQSGYMQRRLINALQDLKVDYD 857



 Score = 51.6 bits (122), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 31/133 (23%), Positives = 63/133 (47%), Gaps = 24/133 (18%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFF 79
           ++LM  ++++++PR G  +IA  QD I+GGYLLT++ A+F R +  ++         + F
Sbjct: 482 KILMEVQNHIISPRYGGPIIAGIQDHISGGYLLTREGAYFTRLEVEQM---------IAF 532

Query: 80  RGLIEGTVTKEDRVQQ---------------QSHIQIVSKNLYCQDPQRTPIPHGLLDRR 124
            G+    + + D+ +                 S + I  +N  C +P+R      L++ +
Sbjct: 533 AGIDVDKLPEPDKFENGQPLWSGKTVFSLLLPSDLTIWYRNKLCDEPERCEALEKLIEEK 592

Query: 125 MGTNQKEANCTTC 137
           +  + +E     C
Sbjct: 593 LLPDPEEVRKLAC 605


>gi|452210795|ref|YP_007490909.1| DNA-directed RNA polymerase subunit A'' [Methanosarcina mazei Tuc01]
 gi|452100697|gb|AGF97637.1| DNA-directed RNA polymerase subunit A'' [Methanosarcina mazei Tuc01]
          Length = 407

 Score =  186 bits (471), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 118/343 (34%), Positives = 176/343 (51%), Gaps = 56/343 (16%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIE 1152
            E   E+Y  + IEP  A G +AAQSIGEPGTQMT++TFH+AG            + E ++
Sbjct: 44   ERVMEEYTVSCIEPCDAAGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVD 103

Query: 1153 EVFVPDDSFILIKL----------DMDRIRLLHLEVDIDSIRYCIERTRGISG------- 1195
               +P    + I L          D ++ R L  E++   I +  + T  +S        
Sbjct: 104  ARKIPSTPMMTIALSKEHPEDYAYDREKTRALAWEIEATKIDHIADVTTDLSQMKLIIDL 163

Query: 1196 -HLTVSGHSFLILKPKDS-SKSFN----------------------SKMYQMKQLLPSVV 1231
                + G +  I + K+  ++  N                       ++ Q+ + + +V 
Sbjct: 164  HEKAMEGRNITIDRVKEKFNEELNVLVSISPDIDNQIVITPGEPSYRELLQLAKSIHNVT 223

Query: 1232 IKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGI 1291
            +KG++GI R V+ +E  E    Y L  EG  LR+V+   GV   + S+NN  E+Y+ LGI
Sbjct: 224  LKGIEGIKRVVVRKEGEE----YTLYTEGSALREVLQFEGVDRTRTSTNNINEIYEVLGI 279

Query: 1292 EAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLAS 1351
            EAAR+ I+ E    +   G+++D RH MLVADLMTS GEV  I RHG++  K SV   A+
Sbjct: 280  EAARNAIIKEATDTLREQGLTVDIRHIMLVADLMTSDGEVKQIGRHGISGEKASVFARAA 339

Query: 1352 FENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            FE T +HL DA   G  D + GV+E II+G P+ +GTG + L+
Sbjct: 340  FEVTVNHLLDAGMRGYVDQLQGVTENIIVGQPIRMGTGDVHLI 382



 Score =  112 bits (280), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 74/238 (31%), Positives = 126/238 (52%), Gaps = 18/238 (7%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYA------RIVKGRLERTTLGEVCEYIEE 817
           G+PR+ EI++A +  STP++T  L K+   DYA      R +   +E T +  + +    
Sbjct: 94  GLPRLIEIVDARKIPSTPMMTIALSKEHPEDYAYDREKTRALAWEIEATKIDHIAD---- 149

Query: 818 VFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSS 877
               D S + + +D+    +    + ID ++        +   ++    + +++ P + S
Sbjct: 150 -VTTDLSQMKLIIDLHEKAMEGRNITIDRVKEKFNEELNVLVSISPDIDNQIVITPGEPS 208

Query: 878 KSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVK 937
                ++ Q+ + + +V +KG++GI R V+ +E  E    Y L  EG  LR+V+   GV 
Sbjct: 209 YR---ELLQLAKSIHNVTLKGIEGIKRVVVRKEGEE----YTLYTEGSALREVLQFEGVD 261

Query: 938 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
             + S+NN  E+Y+ LGIEAAR+ I+ E    +   G+++D RH MLVADLMTS GEV
Sbjct: 262 RTRTSTNNINEIYEVLGIEAARNAIIKEATDTLREQGLTVDIRHIMLVADLMTSDGEV 319


>gi|448737565|ref|ZP_21719605.1| DNA-directed RNA polymerase subunit A'' [Halococcus thailandensis JCM
            13552]
 gi|445803709|gb|EMA53992.1| DNA-directed RNA polymerase subunit A'' [Halococcus thailandensis JCM
            13552]
          Length = 393

 Score =  186 bits (471), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 116/355 (32%), Positives = 186/355 (52%), Gaps = 58/355 (16%)

Query: 1091 GRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG----- 1145
            GR+     +A  AEA   +Y+  ++EP   VG ++AQSIGEPGTQMT+ TFH+AG     
Sbjct: 31   GRDVTDEQAASIAEAVESRYLDTRVEPLDPVGTVSAQSIGEPGTQMTMNTFHYAGVAEID 90

Query: 1146 ------EVCEYIEEVFVPDDSFILIKLD----------------MDRIRLLHLE------ 1177
                   + E ++    PD   + + LD                ++  R+L L       
Sbjct: 91   VTQGLPRLIELVDARKTPDTPMMTVYLDEQHAENREKAHEVVWNIESTRILALGDVSTNV 150

Query: 1178 ------------------VDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSK 1219
                              +  +++   IE + G+   +T +G +      + S +    +
Sbjct: 151  ADMLVQVNLNEQTLDERLISAETVAEVIEDSLGV--EVTQTGTTIEFGPEQPSYR----R 204

Query: 1220 MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSS 1279
            + Q+ + L  +V KG+  ++R VI +E+VEG  ++ L  EG    DV+   GV   + + 
Sbjct: 205  LLQLVEELREIVFKGIDEVSRVVIRKEEVEGNEEFILYTEGSAFGDVLDIEGVDASRTTC 264

Query: 1280 NNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEVLGITRHG 1338
            NN +EVY+ LG+EAAR TI+ E    +E  G+  ++ RH MLVAD+MT++G +  I RHG
Sbjct: 265  NNIHEVYRNLGVEAARETIIDETMNTLEEQGLGDVNIRHLMLVADIMTAEGTIESIGRHG 324

Query: 1339 LAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            ++  K+SVL  A+FE T +HL DAA +G+ D + GV+E +I+G P+ +GTG + L
Sbjct: 325  ISGNKDSVLARAAFEVTVNHLLDAAVHGEVDDLDGVTENVIVGKPIKLGTGDVNL 379



 Score =  110 bits (274), Expect = 7e-21,   Method: Composition-based stats.
 Identities = 71/238 (29%), Positives = 131/238 (55%), Gaps = 20/238 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T YLD+    + + A  V   +E T    LG+V   + + 
Sbjct: 94  GLPRLIELVDARKTPDTPMMTVYLDEQHAENREKAHEVVWNIESTRILALGDVSTNVAD- 152

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSK 878
                  +L++++++   L    +  +++   IE + G+   +T +G +      + S +
Sbjct: 153 -------MLVQVNLNEQTLDERLISAETVAEVIEDSLGV--EVTQTGTTIEFGPEQPSYR 203

Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 938
               ++ Q+ + L  +V KG+  ++R VI +E+VEG  ++ L  EG    DV+   GV  
Sbjct: 204 ----RLLQLVEELREIVFKGIDEVSRVVIRKEEVEGNEEFILYTEGSAFGDVLDIEGVDA 259

Query: 939 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEV 995
            + + NN +EVY+ LG+EAAR TI+ E    +E  G+  ++ RH MLVAD+MT++G +
Sbjct: 260 SRTTCNNIHEVYRNLGVEAARETIIDETMNTLEEQGLGDVNIRHLMLVADIMTAEGTI 317


>gi|21228372|ref|NP_634294.1| DNA-directed RNA polymerase subunit A'' [Methanosarcina mazei Go1]
 gi|23822083|sp|Q8PUR2.1|RPOA2_METMA RecName: Full=DNA-directed RNA polymerase subunit A''
 gi|20906842|gb|AAM31966.1| DNA-directed RNA polymerase subunit A'' [Methanosarcina mazei Go1]
          Length = 408

 Score =  186 bits (471), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 118/343 (34%), Positives = 176/343 (51%), Gaps = 56/343 (16%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIE 1152
            E   E+Y  + IEP  A G +AAQSIGEPGTQMT++TFH+AG            + E ++
Sbjct: 45   ERVMEEYTVSCIEPCDAAGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVD 104

Query: 1153 EVFVPDDSFILIKL----------DMDRIRLLHLEVDIDSIRYCIERTRGISG------- 1195
               +P    + I L          D ++ R L  E++   I +  + T  +S        
Sbjct: 105  ARKIPSTPMMTIALSKEHPEDYAYDREKTRALAWEIEATKIDHIADVTTDLSQMKLIIDL 164

Query: 1196 -HLTVSGHSFLILKPKDS-SKSFN----------------------SKMYQMKQLLPSVV 1231
                + G +  I + K+  ++  N                       ++ Q+ + + +V 
Sbjct: 165  HEKAMEGRNITIDRVKEKFNEELNVLVSISPDIDNQIVITPGEPSYRELLQLAKSIHNVT 224

Query: 1232 IKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGI 1291
            +KG++GI R V+ +E  E    Y L  EG  LR+V+   GV   + S+NN  E+Y+ LGI
Sbjct: 225  LKGIEGIKRVVVRKEGEE----YTLYTEGSALREVLQFEGVDRTRTSTNNINEIYEVLGI 280

Query: 1292 EAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLAS 1351
            EAAR+ I+ E    +   G+++D RH MLVADLMTS GEV  I RHG++  K SV   A+
Sbjct: 281  EAARNAIIKEATDTLREQGLTVDIRHIMLVADLMTSDGEVKQIGRHGISGEKASVFARAA 340

Query: 1352 FENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            FE T +HL DA   G  D + GV+E II+G P+ +GTG + L+
Sbjct: 341  FEVTVNHLLDAGMRGYVDQLQGVTENIIVGQPIRMGTGDVHLI 383



 Score =  112 bits (279), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 74/238 (31%), Positives = 126/238 (52%), Gaps = 18/238 (7%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYA------RIVKGRLERTTLGEVCEYIEE 817
           G+PR+ EI++A +  STP++T  L K+   DYA      R +   +E T +  + +    
Sbjct: 95  GLPRLIEIVDARKIPSTPMMTIALSKEHPEDYAYDREKTRALAWEIEATKIDHIAD---- 150

Query: 818 VFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSS 877
               D S + + +D+    +    + ID ++        +   ++    + +++ P + S
Sbjct: 151 -VTTDLSQMKLIIDLHEKAMEGRNITIDRVKEKFNEELNVLVSISPDIDNQIVITPGEPS 209

Query: 878 KSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVK 937
                ++ Q+ + + +V +KG++GI R V+ +E  E    Y L  EG  LR+V+   GV 
Sbjct: 210 YR---ELLQLAKSIHNVTLKGIEGIKRVVVRKEGEE----YTLYTEGSALREVLQFEGVD 262

Query: 938 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
             + S+NN  E+Y+ LGIEAAR+ I+ E    +   G+++D RH MLVADLMTS GEV
Sbjct: 263 RTRTSTNNINEIYEVLGIEAARNAIIKEATDTLREQGLTVDIRHIMLVADLMTSDGEV 320


>gi|448725403|ref|ZP_21707861.1| DNA-directed RNA polymerase subunit A'' [Halococcus morrhuae DSM
            1307]
 gi|133430|sp|P15353.1|RPOA2_HALMO RecName: Full=DNA-directed RNA polymerase subunit A''; Short=Subunit
            C
 gi|43622|emb|CAA40432.1| C subunit [Halococcus morrhuae]
 gi|445798520|gb|EMA48923.1| DNA-directed RNA polymerase subunit A'' [Halococcus morrhuae DSM
            1307]
          Length = 393

 Score =  186 bits (471), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 115/356 (32%), Positives = 185/356 (51%), Gaps = 58/356 (16%)

Query: 1090 HGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG---- 1145
             GR+     +   AEA   +Y+  ++EP   VG ++AQSIGEPGTQMT+ TFH+AG    
Sbjct: 30   EGRDVTDEQAVSIAEAVESRYLDTRVEPLDPVGTVSAQSIGEPGTQMTMNTFHYAGVAEI 89

Query: 1146 -------EVCEYIEEVFVPDDSFILIKLD----------------MDRIRLLHLE----- 1177
                    + E ++    PD   + + LD                ++  R+L L      
Sbjct: 90   DVTQGLPRLIELVDARKTPDTPMMTVYLDDQHAENREKAHEVVWNIESTRILALGDVSTN 149

Query: 1178 -------------------VDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNS 1218
                               +  +++   IE + G+   +T +G + +   P + S     
Sbjct: 150  VADMLVQVNLNEQTLDERMISAETVAEIIEDSLGV--EVTQTG-TTIEFGPAEPSYR--- 203

Query: 1219 KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCS 1278
            ++ Q+ + L  +V KG++ ++R VI +EDV+   ++ L  EG    DV+   GV   + +
Sbjct: 204  RLLQLVEELREIVFKGIEEVSRVVIRKEDVDDGEEFILYTEGSAFGDVLDIEGVDASRTT 263

Query: 1279 SNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRH 1337
             NN +EVY+ LG+EAAR TI+ E    +E  G+  ++ RH MLVAD+MT++G +  I RH
Sbjct: 264  CNNIHEVYRNLGVEAARETIIDETMNTLEEQGLGDVNIRHLMLVADIMTAEGTIESIGRH 323

Query: 1338 GLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            G++  K SVL  A+FE T +HL DAA +G+ D + GV+E +I+G P+ +GTG + L
Sbjct: 324  GISGNKNSVLARAAFEVTVNHLLDAAVHGEVDDLDGVTENVIVGKPIKLGTGDVNL 379



 Score =  105 bits (262), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 71/238 (29%), Positives = 131/238 (55%), Gaps = 20/238 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T YLD     + + A  V   +E T    LG+V   + + 
Sbjct: 94  GLPRLIELVDARKTPDTPMMTVYLDDQHAENREKAHEVVWNIESTRILALGDVSTNVAD- 152

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSK 878
                  +L++++++   L    +  +++   IE + G+   +T +G + +   P + S 
Sbjct: 153 -------MLVQVNLNEQTLDERMISAETVAEIIEDSLGV--EVTQTG-TTIEFGPAEPSY 202

Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 938
               ++ Q+ + L  +V KG++ ++R VI +EDV+   ++ L  EG    DV+   GV  
Sbjct: 203 R---RLLQLVEELREIVFKGIEEVSRVVIRKEDVDDGEEFILYTEGSAFGDVLDIEGVDA 259

Query: 939 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEV 995
            + + NN +EVY+ LG+EAAR TI+ E    +E  G+  ++ RH MLVAD+MT++G +
Sbjct: 260 SRTTCNNIHEVYRNLGVEAARETIIDETMNTLEEQGLGDVNIRHLMLVADIMTAEGTI 317


>gi|124028420|ref|YP_001013740.1| DNA-directed RNA polymerase subunit A' [Hyperthermus butylicus DSM
           5456]
 gi|123979114|gb|ABM81395.1| DNA-directed RNA polymerase subunit A' [Hyperthermus butylicus DSM
           5456]
          Length = 881

 Score =  185 bits (470), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 103/274 (37%), Positives = 153/274 (55%), Gaps = 39/274 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIMAH  KVLP +TFR N  VC PYNADFDGDEMN+H+P+TEEA
Sbjct: 414 DGDIVLFNRQPSLHRMSIMAHIVKVLPGKTFRLNLLVCPPYNADFDGDEMNLHVPRTEEA 473

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE              A+ LM  + ++++PR G  +I   QD+I+G YLLT K      
Sbjct: 474 QAE--------------ARELMLVQYHILSPRYGGPIIGGLQDYISGAYLLTSK------ 513

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNP-VVFVRTAVIWTGKQIFSLILKPNRDCPV 519
                  +TL+    D+  ++    +R   P    +     WTGKQ+ SL L      P 
Sbjct: 514 -------ATLLTQ-EDVIDLLSAAGYRGEIPEPAILSPKKRWTGKQLVSLFL------PK 559

Query: 520 NANLKTKGRA----YTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
           + N K K R     +   +E+C  DS+++++  ELL G +DK  +G+    N+ + L+++
Sbjct: 560 DFNFKGKARVSAGIFMCEDEWCWNDSFIVIKKGELLTGVLDKKAIGAEQPENMMHWLVKE 619

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVT 609
           +G D A      + +M   ++  RGF++ + DV 
Sbjct: 620 YGTDYARYVYDNMFKMFIRFIEKRGFTMTVDDVA 653



 Score =  120 bits (300), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 80/257 (31%), Positives = 127/257 (49%), Gaps = 41/257 (15%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D +++ S   IV+  LY +D +  PIP GL+D R+G       C TCG +   C GHFG 
Sbjct: 19  DEIRKMSVTAIVTSELYDEDGR--PIPGGLMDPRLGAIAPGQICPTCGNDAKGCPGHFGR 76

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSY-LVRKSL 209
           I+L  PV H+G+ + + ++L++ C+   C R+LL E +A  +   L      + L+ K L
Sbjct: 77  IELVRPVIHVGFAKYIYDVLRATCRQ--CGRLLLPENEAKRYLRLLERLEERWPLLAKML 134

Query: 210 KKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVK 269
              +     KV+ CPHCG                 +YK   +K     ED          
Sbjct: 135 VAVVKRKAAKVTECPHCGT---------------RQYKIVFEKPYTFYED---------- 169

Query: 270 FNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
             PE       G +Q LNPLE+    E +P +D  LL  + E ++P  ++LT L VPP  
Sbjct: 170 -RPE-------GRVQ-LNPLEIRSRLERVPNDDARLLGFDPESARPEWMVLTVLPVPPIH 220

Query: 330 IRPSVI--SDLKSDNDV 344
           +RPS++  + +++++D+
Sbjct: 221 VRPSIVLETGIRAEDDL 237



 Score = 92.8 bits (229), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 41/64 (64%), Positives = 53/64 (82%), Gaps = 1/64 (1%)

Query: 606 GDVTPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           GD+ P  +GFV +SF+ GLTP E FFH  GGREGLVDTAV+T+++GYMQRRL+ +L+DL 
Sbjct: 773 GDLGPAARGFVYHSFYLGLTPVEVFFHAAGGREGLVDTAVRTSQSGYMQRRLINALQDLR 832

Query: 665 VQYD 668
           V+YD
Sbjct: 833 VEYD 836


>gi|159118719|ref|XP_001709578.1| DNA-directed RNA polymerase subunit A' [Giardia lamblia ATCC 50803]
 gi|133352|sp|P25202.1|RPC1_GIALA RecName: Full=DNA-directed RNA polymerase III subunit RPC1;
           Short=RNA polymerase III subunit C1; AltName:
           Full=DNA-directed RNA polymerase III largest subunit;
           AltName: Full=RNA polymerase III subunit C160
 gi|9364|emb|CAA42895.1| subunit A of DNA dependent RNA polymerase III [Giardia
           intestinalis]
 gi|157437695|gb|EDO81904.1| DNA-directed RNA polymerase subunit A [Giardia lamblia ATCC 50803]
          Length = 1741

 Score =  185 bits (470), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 111/313 (35%), Positives = 169/313 (53%), Gaps = 43/313 (13%)

Query: 328 NCIRPS-VISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFD 386
           N +RP+ ++      ND +LFNRQPSLH++SIM   A +  +RTF FN  VC+P+NADFD
Sbjct: 665 NSLRPNDIVYRHLLPNDTLLFNRQPSLHRMSIMQFNAVIHENRTFSFNPVVCSPFNADFD 724

Query: 387 GDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFIT 446
           GDEMN+   Q +EARAE              A +LM +  N+++PR+GE +I  TQDF+T
Sbjct: 725 GDEMNIFYMQGQEARAE--------------AGILMGSHENIISPRHGECMIGLTQDFLT 770

Query: 447 GGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSW-RSW------------NPVV 493
           G YLL+ K  F  R +  +  S       D    +  +++ R +            + V 
Sbjct: 771 GIYLLSGKGIFMTRQEYCQHVSYGCDGFGDATYGVSLYNYGREFIKSIHDRRGTEEDTVG 830

Query: 494 FVRTAV-----------IWTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEE---FCHR 539
           FV+              +++GKQ+ S+++K N    VN NL+   + Y  + +       
Sbjct: 831 FVKVPCLSQPCIVYPRQLYSGKQVLSVLMKGNDFDSVNINLEHGDKTYKKDSDRRALSVN 890

Query: 540 DSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNR 599
           D Y+I++NSE L G + K+ L S  K  +FY L++++G   A   M R +++ + +LMN 
Sbjct: 891 DDYIIIQNSEHLVGRLTKTFLAS-SKNCIFYFLVQNYGPVSAARIMLRFAKVAARFLMNY 949

Query: 600 GFSIGIGDVTPGQ 612
           GF+IGI DV P Q
Sbjct: 950 GFTIGIDDVMPSQ 962



 Score =  164 bits (415), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 112/301 (37%), Positives = 169/301 (56%), Gaps = 22/301 (7%)

Query: 1143 FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLE--VDIDSIRYCI---ERTRGISGHL 1197
            + G++   I E +      I + LDM  I  + L   + ++++   I   ++ + + G  
Sbjct: 1382 YLGQISASIIECYSQSVCHIEVNLDMKIIADMGLAGIITVETVVASILHNDKAKKLVGQD 1441

Query: 1198 TVSG----HSFLILKPKDSSKSFNSKMY---QMKQLLPSVVIKGVQGINRAVIHE--EDV 1248
              SG    HS      +  ++S +  ++    +K LLP + + G+   +RAVI+E  E  
Sbjct: 1442 QSSGSVSIHSATRFSVRPLTQSRDDLLFDIQSLKLLLPMIPVSGISTCSRAVINEYKEFC 1501

Query: 1249 EG------VTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEI 1302
            +G      +TKY LLVEG  L++++   G+   +  SNN  EV  TLGIEAA +TI  EI
Sbjct: 1502 QGATSSAPLTKYNLLVEGIGLQNILNVSGIDFTRTLSNNIVEVANTLGIEAAVATISNEI 1561

Query: 1303 KLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMK-ESVLNLASFENTSDHLFD 1361
            K  M++HGM++D RH  L+AD+M  +G VLG TR GL KMK +SV+ LASFE T +HLF+
Sbjct: 1562 KACMDSHGMAVDMRHIRLLADIMCFRGRVLGFTRFGLTKMKADSVIMLASFEKTGEHLFN 1621

Query: 1362 AAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHTNTLAA 1421
            AA   + D  +GV+E II+G PM++GTG   LLQA    E   +T+ +  P+  T  L  
Sbjct: 1622 AALGNKVDEANGVTESIILGKPMSMGTGSFSLLQAPYFDEKTGKTIEY-QPKQTTRFLGE 1680

Query: 1422 V 1422
            V
Sbjct: 1681 V 1681



 Score =  129 bits (325), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 93/266 (34%), Positives = 142/266 (53%), Gaps = 32/266 (12%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTD------------LDYARIVKGRLERTTLGEV 811
            GVPR+KEI++    ISTPI T  L  D D            L+ AR++K  +E T LG++
Sbjct: 1327 GVPRLKEIVDGVVKISTPITTVELHVDVDKEELAATVTEKYLEKARMMKNIIECTYLGQI 1386

Query: 812  CEYIEEVFVPDDSFILIKLDMDRIRLLHLE--VDIDSIRYCI---ERTRGISGHLTVSG- 865
               I E +      I + LDM  I  + L   + ++++   I   ++ + + G    SG 
Sbjct: 1387 SASIIECYSQSVCHIEVNLDMKIIADMGLAGIITVETVVASILHNDKAKKLVGQDQSSGS 1446

Query: 866  ---HSFLILKPKDSSKSFNSKMY---QMKQLLPSVVIKGVQGINRAVIHE--EDVEG--- 914
               HS      +  ++S +  ++    +K LLP + + G+   +RAVI+E  E  +G   
Sbjct: 1447 VSIHSATRFSVRPLTQSRDDLLFDIQSLKLLLPMIPVSGISTCSRAVINEYKEFCQGATS 1506

Query: 915  ---VTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVME 971
               +TKY LLVEG  L++++   G+   +  SNN  EV  TLGIEAA +TI  EIK  M+
Sbjct: 1507 SAPLTKYNLLVEGIGLQNILNVSGIDFTRTLSNNIVEVANTLGIEAAVATISNEIKACMD 1566

Query: 972  NHGMSIDFRHPMLVADLMTSKGEVLG 997
            +HGM++D RH  L+AD+M  +G VLG
Sbjct: 1567 SHGMAVDMRHIRLLADIMCFRGRVLG 1592



 Score = 94.7 bits (234), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 63/222 (28%), Positives = 109/222 (49%), Gaps = 18/222 (8%)

Query: 86  TVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCV 145
           +V   + + + S +QI +  LY   P  +P  +G+LD+R+G + K   C TCG++   C+
Sbjct: 33  SVLSSNALMKLSEVQITTPILYEHYP--SPATNGVLDKRLGLSDKVGKCATCGKDTKMCI 90

Query: 146 GHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLV 205
           GHFG I L LPVFH G       +L  +C  P C+RV + E        +L+   L++  
Sbjct: 91  GHFGTISLALPVFHPGLINDARTMLSIVC--PFCSRVKISEAD------RLKYKVLNHKF 142

Query: 206 RKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHE-KYKNRTKKKDAIVEDLLAEY 264
             ++ K+  E  KK   CP C   + + KK    ++  E  Y+ R  K   I+ D++   
Sbjct: 143 SLAIVKEAQEQAKKQVNCPFCHAPSTICKKSQGFRVLREMHYEERATK---ILADVIKHQ 199

Query: 265 NEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLL 306
            +  K   E++   +  ++   +P++ L + + +P  D P L
Sbjct: 200 KDIEKIQ-ELDQRLRNHVV---DPIQALHILQKVPECDYPYL 237



 Score = 84.0 bits (206), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 35/60 (58%), Positives = 46/60 (76%)

Query: 611  GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
             +GF+ NSF++GL P EF  H   GR+G++D+A KTA+TGY+QRRLVK LEDL V YD +
Sbjct: 1085 AKGFILNSFYTGLLPFEFLAHARAGRDGVIDSACKTADTGYLQRRLVKCLEDLSVSYDFT 1144



 Score = 60.8 bits (146), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 25/39 (64%), Positives = 31/39 (79%)

Query: 1107 REKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            R KY+R  +EP +  GA+AAQS+GEP TQMTLK+FH AG
Sbjct: 1280 RRKYIRLNLEPGSPCGAVAAQSVGEPSTQMTLKSFHHAG 1318



 Score = 49.7 bits (117), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 20/43 (46%), Positives = 30/43 (69%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 63
           +LM +  N+++PR+GE +I  TQDF+TG YLL+ K  F  R +
Sbjct: 744 ILMGSHENIISPRHGECMIGLTQDFLTGIYLLSGKGIFMTRQE 786



 Score = 42.0 bits (97), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 21/50 (42%), Positives = 31/50 (62%)

Query: 671  FDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLF 720
            F+AA   + D  +GV+E II+G PM++GTG   LLQA    E   +T+ +
Sbjct: 1620 FNAALGNKVDEANGVTESIILGKPMSMGTGSFSLLQAPYFDEKTGKTIEY 1669


>gi|386001093|ref|YP_005919392.1| DNA-directed RNA polymerase subunit A' [Methanosaeta harundinacea
           6Ac]
 gi|312183603|gb|ADQ42371.1| DNA-directed RNA polymerase subunit A' [Methanosaeta harundinacea
           6Ac]
 gi|357209149|gb|AET63769.1| DNA-directed RNA polymerase subunit A' [Methanosaeta harundinacea
           6Ac]
          Length = 878

 Score =  185 bits (469), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 104/272 (38%), Positives = 152/272 (55%), Gaps = 39/272 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIM+HR  V+PH+TFR N  VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 410 DGDIVLFNRQPSLHRMSIMSHRVIVMPHKTFRLNPAVCPPYNADFDGDEMNLHVPQTEEA 469

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A++LM  + N+++PR G  +I    D++TG +LLT  +   +R
Sbjct: 470 RAE--------------AEILMRVQENILSPRFGGPIIGGIHDYVTGNFLLTHGDRRISR 515

Query: 461 AQTMRIASTLIA-DTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            + M +   L   +  +  G         WN          WTGKQIFSLIL      P 
Sbjct: 516 IEVMEVLKKLHHLEIPEPVG---------WNEA----GEPYWTGKQIFSLIL------PR 556

Query: 520 NANLKTKG----RAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
             NL+ K        +   E C  D+YV++R+ ++L G++D + +G+  K  +   ++++
Sbjct: 557 GLNLEFKASFCKNCDSCKREACDDDAYVVIRDGKILTGTIDAAAVGA-FKGKITDRVIKE 615

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           +G  V    +  +++M    +M  GFS GI D
Sbjct: 616 YGPTVGAGFIDGMTQMAIRGIMLAGFSFGIDD 647



 Score =  109 bits (272), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 72/253 (28%), Positives = 121/253 (47%), Gaps = 44/253 (17%)

Query: 94  QQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDL 153
           ++ S ++I++ + Y  D    PI  GL+D R+G       C +CG    +C GHFG+IDL
Sbjct: 23  RRMSVVKIITADTY--DDDGFPIEMGLMDPRLGVIDPGLRCRSCGGRPGECPGHFGHIDL 80

Query: 154 PLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKI 213
             PV H+G+ + +  IL++IC++  C+R++L E +   +  ++            +  K+
Sbjct: 81  IAPVIHVGFAKLIRKILRAICRD--CSRLMLLENEKRMYLEQIETLVRLGQTTDDVVNKV 138

Query: 214 LETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPE 273
               +K  VCP+CG     +K                ++  A VE               
Sbjct: 139 FSEARKHKVCPYCGAPQQEIK---------------FERPLAYVE--------------- 168

Query: 274 IEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPS 333
            E HK       L P ++   FE IP EDI ++ MN + ++P  ++LT L VPP  +RPS
Sbjct: 169 -EGHK-------LTPSDIRDRFEKIPDEDIKVMGMNPDTARPEWMLLTVLPVPPVTMRPS 220

Query: 334 VI--SDLKSDNDV 344
           +   S  +S++D+
Sbjct: 221 ITLESGQRSEDDL 233



 Score = 92.4 bits (228), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 38/57 (66%), Positives = 50/57 (87%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFVQ+S+  GL PTEFFFH +GGREGLVDTA++T+++GY+QRRL+ +L+DL VQYD
Sbjct: 776 HGFVQSSYKEGLNPTEFFFHAIGGREGLVDTAIRTSQSGYLQRRLINALQDLEVQYD 832


>gi|385805645|ref|YP_005842043.1| DNA-directed RNA polymerase subunit alpha [Fervidicoccus fontis
           Kam940]
 gi|383795508|gb|AFH42591.1| DNA-directed RNA polymerase subunit alpha [Fervidicoccus fontis
           Kam940]
          Length = 882

 Score =  184 bits (468), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 102/272 (37%), Positives = 149/272 (54%), Gaps = 37/272 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIMAH+ KVLP RTFR N  VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 415 DGDIVLFNRQPSLHRMSIMAHQVKVLPGRTFRLNLLVCPPYNADFDGDEMNLHVPQTEEA 474

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              AK LM  + ++++PR G  +I   QD+I+GGYLLT K     +
Sbjct: 475 RAE--------------AKELMLVQRHILSPRYGGPIIGGLQDYISGGYLLTSKATLLEK 520

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              + + S        + G  +        P ++      WTGKQ+ SL L      P +
Sbjct: 521 EDVIEVLS--------VTGYKEELP----EPAIY-SPKEFWTGKQLVSLFL------PKD 561

Query: 521 ANLKTKGRAYTAN----EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
             LKTK           +E C  DSY++++  ++  G +DK ++G+    + ++ + +++
Sbjct: 562 FTLKTKASINAGKLKCEDEDCLNDSYIVIKKGKMHTGVIDKKSIGAQQPESFYHWITKEY 621

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           G D A      + +M   Y+   GF++ + DV
Sbjct: 622 GSDYARYISDVMFKMFIRYIEKHGFTMSLDDV 653



 Score =  112 bits (279), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 75/266 (28%), Positives = 125/266 (46%), Gaps = 43/266 (16%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           I+ +V   D +++ S +QI++   Y  D    PI  G++D R+G  +    C  CG  + 
Sbjct: 11  IKLSVLSPDEIRRMSKVQIITAETY--DDDGLPIQGGVMDPRLGVIEPGQKCPVCGNTMQ 68

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLR--NPA 200
            C GHFG+I+L  PV HIGY + + ++L+  C    C R+LL EE+   +   +R     
Sbjct: 69  SCPGHFGHIELAKPVIHIGYVKEIYDLLRGTCWK--CGRILLPEEEIKQYLDLMRRVEKY 126

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDL 260
           + +L+ + L + I +   K +VCPHCG            KI  E+               
Sbjct: 127 MPFLLPR-LYEHIKQKASKTTVCPHCG--------AAQRKIKLER--------------- 162

Query: 261 LAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
                      P     ++ G  + L P E+       P +D+ L  +N E S+P   IL
Sbjct: 163 -----------PTTFLEEEKGSSRKLAPDEIRNRLSNTPDDDVRLFGINPEDSRPEWFIL 211

Query: 321 TRLLVPPNCIRPSVI--SDLKSDNDV 344
           T L VPP  +RPS++  + +++++D+
Sbjct: 212 TVLPVPPVQVRPSIMLETGIRAEDDL 237



 Score = 85.9 bits (211), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 38/65 (58%), Positives = 51/65 (78%), Gaps = 1/65 (1%)

Query: 607 DVTPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV NSF +GL P E F+H  GGREGLVDTAV+T+++GYMQRRL+ +L D+ +
Sbjct: 775 DKSPASRGFVYNSFRTGLNPVELFYHAAGGREGLVDTAVRTSQSGYMQRRLINALLDVRI 834

Query: 666 QYDMS 670
           +YD S
Sbjct: 835 EYDGS 839


>gi|357472543|ref|XP_003606556.1| DNA-directed RNA polymerase [Medicago truncatula]
 gi|355507611|gb|AES88753.1| DNA-directed RNA polymerase [Medicago truncatula]
          Length = 281

 Score =  184 bits (468), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 108/262 (41%), Positives = 158/262 (60%), Gaps = 17/262 (6%)

Query: 1147 VCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLI 1206
            V + I+ V+    + + I LDM  I    L +D + ++  I +T    G L +   +  I
Sbjct: 6    VAKSIKVVYSYTLAAVFISLDMGIIEKAGLNIDANIVKESILQT----GKLKLKPENIKI 61

Query: 1207 LKPKD---SSKSFNS-----KMYQMKQLLPSVVIKGVQGINRAVIH-----EEDVEGVTK 1253
            L  K        FN      ++  +K LLPSVV+KGV+ + R V+       ++ +    
Sbjct: 62   LDIKKLQVEPPGFNPNEILFQLNNLKNLLPSVVVKGVKTVERTVLKIKKNKTDNGKESET 121

Query: 1254 YKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSI 1313
            Y LL EG+ L++VM   GV G K  +N+  E+   LGIEAAR  I+ +I+  M+ HGMSI
Sbjct: 122  YTLLAEGEGLKEVMGIEGVDGHKTVTNHIIEMRNVLGIEAARYGIIDQIQYTMKQHGMSI 181

Query: 1314 DFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISG 1373
            D RH ML+AD+MT +G+VLG+TRHG+ KM  S L LASFE+++D+LFDA+  G+ D I G
Sbjct: 182  DVRHIMLLADMMTVRGQVLGMTRHGIQKMGRSALMLASFESSTDYLFDASLRGKGDPIEG 241

Query: 1374 VSECIIMGLPMNVGTGLIKLLQ 1395
            VS+CIIMG P+ +GTG+I++ Q
Sbjct: 242  VSDCIIMGKPIQIGTGMIEVKQ 263



 Score =  108 bits (271), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 73/200 (36%), Positives = 109/200 (54%), Gaps = 17/200 (8%)

Query: 811 VCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLI 870
           V + I+ V+    + + I LDM  I    L +D + ++  I +T    G L +   +  I
Sbjct: 6   VAKSIKVVYSYTLAAVFISLDMGIIEKAGLNIDANIVKESILQT----GKLKLKPENIKI 61

Query: 871 LKPKD---SSKSFNS-----KMYQMKQLLPSVVIKGVQGINRAVIH-----EEDVEGVTK 917
           L  K        FN      ++  +K LLPSVV+KGV+ + R V+       ++ +    
Sbjct: 62  LDIKKLQVEPPGFNPNEILFQLNNLKNLLPSVVVKGVKTVERTVLKIKKNKTDNGKESET 121

Query: 918 YKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSI 977
           Y LL EG+ L++VM   GV G K  +N+  E+   LGIEAAR  I+ +I+  M+ HGMSI
Sbjct: 122 YTLLAEGEGLKEVMGIEGVDGHKTVTNHIIEMRNVLGIEAARYGIIDQIQYTMKQHGMSI 181

Query: 978 DFRHPMLVADLMTSKGEVLG 997
           D RH ML+AD+MT +G+VLG
Sbjct: 182 DVRHIMLLADMMTVRGQVLG 201



 Score = 49.7 bits (117), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 21/39 (53%), Positives = 29/39 (74%)

Query: 668 DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 706
           D  FDA+  G+ D I GVS+CIIMG P+ +GTG+I++ Q
Sbjct: 225 DYLFDASLRGKGDPIEGVSDCIIMGKPIQIGTGMIEVKQ 263


>gi|337283879|ref|YP_004623353.1| DNA-directed RNA polymerase subunit A [Pyrococcus yayanosii CH1]
 gi|334899813|gb|AEH24081.1| DNA-directed RNA polymerase subunit A [Pyrococcus yayanosii CH1]
          Length = 396

 Score =  184 bits (467), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 123/351 (35%), Positives = 185/351 (52%), Gaps = 59/351 (16%)

Query: 1099 SACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EV 1147
             A   E  RE Y RA +EP  AVG +AAQSIGEP TQMTL TFH+AG            +
Sbjct: 45   EAIIEEVVRE-YERALVEPGEAVGTVAAQSIGEPSTQMTLNTFHYAGVAEINVTLGLPRI 103

Query: 1148 CEYIEEVFVPDDSFILIKLD----MDR-----------------------IRLLHLE--V 1178
             E ++    P    + + LD     DR                       I L+++E  V
Sbjct: 104  IEIVDARKNPSTPMMTVYLDEEHRHDRAKAEEVARRIEGTTVENLARSTTIDLINMEFIV 163

Query: 1179 DID---------SIRYCIERTRGI--SGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLL 1227
            +ID         S+   +++ +G   S    V G++ LI++PK + K   S + ++ + +
Sbjct: 164  EIDPERLEKSGLSMERILKKLQGSFKSAEFEVEGYT-LIVRPKKAEKI--SDLRRLAEKV 220

Query: 1228 PSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYK 1287
                +KG+ G+ + ++ +E  E    Y +  EG N + V+   GV   +  +NN +E+ +
Sbjct: 221  KKHRLKGLSGVGKTIVRKEGDE----YVIYTEGSNFKQVLKVPGVDPTRTRTNNIHEIAE 276

Query: 1288 TLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVL 1347
             LGIEAAR+ I+ EI   M   G+ +D RH MLVAD+MT  G V  I RHG+   KESVL
Sbjct: 277  VLGIEAARNAIIEEIVNTMREQGLEVDIRHIMLVADIMTLDGIVRPIGRHGVVGEKESVL 336

Query: 1348 NLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 1398
              A+FE T+ HLF+AA  G+ D ++GV E +++G P+ VGTG+++L   +P
Sbjct: 337  ARAAFEITTQHLFEAAERGEIDNLNGVIENVLIGQPVPVGTGIVRLAMKLP 387



 Score =  110 bits (275), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 76/234 (32%), Positives = 131/234 (55%), Gaps = 18/234 (7%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARI--VKGRLERTTLGEVCEYIEEVFVP 821
           G+PRI EI++A +N STP++T YLD++   D A+   V  R+E TT+  +      + + 
Sbjct: 99  GLPRIIEIVDARKNPSTPMMTVYLDEEHRHDRAKAEEVARRIEGTTVENLARSTT-IDLI 157

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI--SGHLTVSGHSFLILKPKDSSKS 879
           +  FI +++D +R+    L     S+   +++ +G   S    V G++ LI++PK + K 
Sbjct: 158 NMEFI-VEIDPERLEKSGL-----SMERILKKLQGSFKSAEFEVEGYT-LIVRPKKAEKI 210

Query: 880 FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
             S + ++ + +    +KG+ G+ + ++ +E  E    Y +  EG N + V+   GV   
Sbjct: 211 --SDLRRLAEKVKKHRLKGLSGVGKTIVRKEGDE----YVIYTEGSNFKQVLKVPGVDPT 264

Query: 940 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
           +  +NN +E+ + LGIEAAR+ I+ EI   M   G+ +D RH MLVAD+MT  G
Sbjct: 265 RTRTNNIHEIAEVLGIEAARNAIIEEIVNTMREQGLEVDIRHIMLVADIMTLDG 318



 Score = 41.2 bits (95), Expect = 4.5,   Method: Compositional matrix adjust.
 Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 11/75 (14%)

Query: 635 GREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAAFYGQTDCISGVSECIIMGLP 694
           GR G+V         G  +  L ++  ++  Q+   F+AA  G+ D ++GV E +++G P
Sbjct: 324 GRHGVV---------GEKESVLARAAFEITTQH--LFEAAERGEIDNLNGVIENVLIGQP 372

Query: 695 MNVGTGLIKLLQAVP 709
           + VGTG+++L   +P
Sbjct: 373 VPVGTGIVRLAMKLP 387


>gi|389860841|ref|YP_006363081.1| DNA-directed RNA polymerase subunit A' [Thermogladius
           cellulolyticus 1633]
 gi|388525745|gb|AFK50943.1| DNA-directed RNA polymerase subunit A' [Thermogladius
           cellulolyticus 1633]
          Length = 880

 Score =  184 bits (467), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 104/263 (39%), Positives = 153/263 (58%), Gaps = 28/263 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH++S+MAH  +VLP++TFR N  VC PYNADFDGDEMN+H+PQ+EEA
Sbjct: 411 DGDVVLFNRQPSLHRISVMAHIVRVLPYKTFRLNLLVCPPYNADFDGDEMNLHVPQSEEA 470

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A++LM  + +++TPR G  +I   QD+I+G +LLT K+    +
Sbjct: 471 RAE--------------ARILMLVEKHILTPRYGGPIIGGLQDYISGAFLLTNKSTILTK 516

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A+ + + S      S     I+R       PV +      WTGKQI S+ L  + +   N
Sbjct: 517 AEVIDLLSVAGYKGSLPEPAIQR-------PVEY------WTGKQIVSVFLPGDFNYKRN 563

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           A + +   A    +E C  DS VI++  +LL G +DK+++G     ++ + L+++ GEDV
Sbjct: 564 AKIAS-ASALRCIDEDCPHDSLVIIKKGQLLEGVIDKASIGREEPESLVHWLIKEHGEDV 622

Query: 581 AVTAMWRLSRMTSFYLMNRGFSI 603
           A   M  + RM   +    GF++
Sbjct: 623 ARKFMDNVYRMFIRFSEMYGFTM 645



 Score =  103 bits (256), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 72/259 (27%), Positives = 124/259 (47%), Gaps = 44/259 (16%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D +++ S   I++ ++Y  D    P+  G++D+R+G  + +  C  CG    +C GHFG+
Sbjct: 15  DEIRRMSVTNIITSDVY--DSDGAPVDGGVMDKRLGAIEPKEVCPICGNTRDECPGHFGH 72

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA---LSYLVRK 207
           I+L  PV H G+ + +   L++ C+   C RV L E +   +   L++     L YLV K
Sbjct: 73  IELAKPVIHAGFAKHIHMYLKTTCR--VCGRVKLPENERQLYLKLLKDLEDLNLKYLV-K 129

Query: 208 SLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEA 267
            L + I +       CPHCG                 +YK +  K     ED        
Sbjct: 130 RLHEFIRKRAAAQQTCPHCGA---------------PQYKIKLDKPHTFYED-------- 166

Query: 268 VKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPP 327
                     ++ G+++ L P EV    E IP +D+ LL  +   ++P  ++LT L VPP
Sbjct: 167 ----------REEGIVK-LTPAEVRSRLEKIPDDDVRLLGGDPTDARPEWMVLTVLPVPP 215

Query: 328 NCIRPSVI--SDLKSDNDV 344
             +RPS++  + ++S++D+
Sbjct: 216 RAVRPSILLETGIRSEDDL 234



 Score = 85.9 bits (211), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 41/85 (48%), Positives = 56/85 (65%), Gaps = 1/85 (1%)

Query: 587 RLSRMTSFYLMNRGFSIGIGDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVK 645
           R  R+T  Y+         GD+ P  +GFV   F +GL+P E FFH  GGREGL+DTAV+
Sbjct: 753 RGKRLTRGYMDRSLPHFKPGDLGPEARGFVARGFVNGLSPIEMFFHAAGGREGLIDTAVR 812

Query: 646 TAETGYMQRRLVKSLEDLCVQYDMS 670
           T+++GYMQRRL+ +L+D+ V  D S
Sbjct: 813 TSQSGYMQRRLINALQDVRVDIDGS 837



 Score = 43.1 bits (100), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 20/57 (35%), Positives = 36/57 (63%), Gaps = 2/57 (3%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRK 76
           ++LM  + +++TPR G  +I   QD+I+G +LLT K+    +A+ + + S  +AG K
Sbjct: 475 RILMLVEKHILTPRYGGPIIGGLQDYISGAFLLTNKSTILTKAEVIDLLS--VAGYK 529


>gi|218884685|ref|YP_002429067.1| DNA-directed RNA polymerase subunit A' [Desulfurococcus
           kamchatkensis 1221n]
 gi|218766301|gb|ACL11700.1| DNA-directed RNA polymerase subunit A' [Desulfurococcus
           kamchatkensis 1221n]
          Length = 886

 Score =  184 bits (467), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 97/252 (38%), Positives = 147/252 (58%), Gaps = 30/252 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++S+MAH  +VLP++TFR N  VC PYNADFDGDEMN+H+PQ+EEA
Sbjct: 417 DGDIVLFNRQPSLHRISVMAHVVRVLPYKTFRLNLLVCPPYNADFDGDEMNLHVPQSEEA 476

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A++LM  + +++TPR G  +I   QD+I+G Y+LT K      
Sbjct: 477 RAE--------------ARLLMLVERHILTPRYGGPIIGGLQDYISGAYILTSK------ 516

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNP-VVFVRTAVIWTGKQIFSLILKPNRDCPV 519
                   T + D  D+  ++    ++   P    ++   +WTGKQ+ SL L  + +   
Sbjct: 517 --------TTLLDKDDVVDLLSSTGYKGELPEPAILKPRALWTGKQLVSLFLPKDFNYKR 568

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           N+ + +   A    +E C  DS VI+RN  LL G +DK+++G     ++ + L++++GED
Sbjct: 569 NSKIGSAA-ALRCIDEDCPHDSLVIIRNGVLLEGVLDKASIGREEPESLVHWLIKEYGED 627

Query: 580 VAVTAMWRLSRM 591
                M R+ +M
Sbjct: 628 YGRMFMDRVYKM 639



 Score =  106 bits (265), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 73/259 (28%), Positives = 121/259 (46%), Gaps = 44/259 (16%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D +++ S  QI S  +Y  D   +PI  G++DRR+G  +    C  CG     C GHFG+
Sbjct: 21  DEIRKMSVTQIFSSEVYDND--GSPIDGGVMDRRLGAIEPGETCPICGNTRDSCPGHFGH 78

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGF---RAKLRNPALSYLVRK 207
           I+L  PV H G+ + ++  L++ C+N  C R+ + EE+   +    + L+     YL+ K
Sbjct: 79  IELAKPVIHAGFAKQILIYLKATCRN--CGRLKIPEEEKGEYLRLLSDLQELGAPYLI-K 135

Query: 208 SLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEA 267
              + I         CPHCG                ++YK + +K     E         
Sbjct: 136 RFHEYIRRRASTADTCPHCGA---------------KQYKVKLEKPHTFYE--------- 171

Query: 268 VKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPP 327
                      + GL++ L P EV    E I  +D+ LL  +   ++P  ++LT L VPP
Sbjct: 172 ---------QTERGLLK-LTPSEVRGRLEKISNDDVKLLGGDPNDTRPEWMVLTVLPVPP 221

Query: 328 NCIRPSVI--SDLKSDNDV 344
             +RPSV+  + ++S++D+
Sbjct: 222 RSVRPSVLLETGIRSEDDL 240



 Score = 85.5 bits (210), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 41/85 (48%), Positives = 55/85 (64%), Gaps = 1/85 (1%)

Query: 587 RLSRMTSFYLMNRGFSIGIGDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVK 645
           R  R+T  YL          D+ P  +GF+ + F  GL P E FFH   GREGL+DTAV+
Sbjct: 759 RGKRLTRGYLGRALSHFKPEDLGPEARGFIASGFVHGLNPVEMFFHAAAGREGLIDTAVR 818

Query: 646 TAETGYMQRRLVKSLEDLCVQYDMS 670
           T+++GYMQRRL+ +L+DL V+YD S
Sbjct: 819 TSQSGYMQRRLINALQDLRVEYDGS 843


>gi|57641017|ref|YP_183495.1| DNA-directed RNA polymerase subunit A' [Thermococcus kodakarensis
           KOD1]
 gi|57159341|dbj|BAD85271.1| DNA-directed RNA polymerase, subunit A' [Thermococcus kodakarensis
           KOD1]
          Length = 906

 Score =  184 bits (467), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 102/282 (36%), Positives = 158/282 (56%), Gaps = 40/282 (14%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
            D DVVLFNRQPSLH++SIMAHR +V+P+RTFR N  VC PYNADFDGDEMN+H+PQTEE
Sbjct: 417 EDGDVVLFNRQPSLHRMSIMAHRVRVMPYRTFRLNLPVCPPYNADFDGDEMNLHVPQTEE 476

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           A+AE              AK+LM  ++++++PR G  LIA  QD I+GGYLLT++ A+F 
Sbjct: 477 AQAE--------------AKILMEVQNHIISPRYGGPLIAGIQDHISGGYLLTREGAYFT 522

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           R +  ++      D +++             P  +     +W+GK IFSL+L  +     
Sbjct: 523 RYEVEQMLMFAGMDVNELP-----------EPDKYENGEPLWSGKTIFSLLLPDDLTIWY 571

Query: 520 NANLKTKGRAYTANEEFCHR--------------DSYVILRNSELLAGSMDKSTLGSGGK 565
              L  +     A E+                  D +V ++N +LL+G++DK   G    
Sbjct: 572 RNKLCDEPERCEALEKLIEEKLIPDPEEVRKLAYDGFVYIQNGKLLSGAVDKKAYGR-ED 630

Query: 566 ANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
             +  I++R++G + A   + +++++T + + ++GF+  I D
Sbjct: 631 GKLLDIIVREYGVERARQFLDQVTKLTIWVITHKGFTTAIDD 672



 Score =  112 bits (279), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 77/271 (28%), Positives = 127/271 (46%), Gaps = 45/271 (16%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G IE  +     +++ S  +I   + Y  D    PI  GL+D+R+G       C TCG  
Sbjct: 9   GSIEFGILSPQEIRKMSAAEITVPDTY--DDDGYPIEGGLMDKRLGVIDPGLRCETCGAR 66

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKL---- 196
             +C GHFG+I+L  PV H+G+ + +  +L+S C+   C R+ L +E+   +  K     
Sbjct: 67  AGECPGHFGHIELARPVIHVGFAKTIHRVLESTCRE--CGRIKLTDEEIEEYMQKFEVMG 124

Query: 197 -RNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDA 255
            R  A+  L+     K+I +  K+  VCPHCG     +K           ++  T   + 
Sbjct: 125 DRKGAVDKLI-----KEIHKKAKERMVCPHCGAPQFPIK-----------FERPTIYWEL 168

Query: 256 IVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKP 315
             ++   EY                     + P EV    E IP +D+PLL ++ E S+P
Sbjct: 169 RKDEEGNEYK------------------HRMMPSEVRDRLEKIPDKDLPLLGLHPEKSRP 210

Query: 316 SDLILTRLLVPPNCIRPSVI--SDLKSDNDV 344
             ++LT L VPP  +RPS+   S +++++D+
Sbjct: 211 EWMVLTVLPVPPVTMRPSITLESGIRAEDDL 241



 Score = 95.5 bits (236), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 41/57 (71%), Positives = 50/57 (87%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV NS+ SGLTP E+FFH MGGREGLVDTAV+TA++GYMQRRL+ +L+DL V YD
Sbjct: 801 RGFVTNSYKSGLTPQEYFFHAMGGREGLVDTAVRTAQSGYMQRRLINALQDLKVDYD 857



 Score = 49.3 bits (116), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 20/44 (45%), Positives = 33/44 (75%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 63
           ++LM  ++++++PR G  LIA  QD I+GGYLLT++ A+F R +
Sbjct: 482 KILMEVQNHIISPRYGGPLIAGIQDHISGGYLLTREGAYFTRYE 525


>gi|297619552|ref|YP_003707657.1| DNA-directed RNA polymerase subunit A' [Methanococcus voltae A3]
 gi|297378529|gb|ADI36684.1| DNA-directed RNA polymerase subunit A' [Methanococcus voltae A3]
          Length = 888

 Score =  184 bits (466), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 103/267 (38%), Positives = 148/267 (55%), Gaps = 31/267 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVL+NRQPSLH++SIMAH+ KVLP+RTFR N CVC PYNADFDGDEMNVH+PQ+EEA
Sbjct: 423 DGDVVLYNRQPSLHRMSIMAHKVKVLPYRTFRHNLCVCPPYNADFDGDEMNVHVPQSEEA 482

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+ LM  + ++V+PR G  +I A  DFI+G Y+LT  N  FN+
Sbjct: 483 RAE--------------AETLMLVEKHIVSPRFGGPIIGAIHDFISGAYVLTSSN--FNK 526

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q + +  +              F      P V      +++G+ +F   L       + 
Sbjct: 527 DQALSLLRS------------AGFKSELGEPDVLENGEELYSGRSLFGTALPEG--LSLE 572

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
              KT  +     +E C  + YV+++N +LL G +DK+  GS     V   ++++FG + 
Sbjct: 573 YKSKTCKKCDDCKKENCEHEGYVLIKNGKLLKGVIDKNGFGSEAGI-VLNTIVKEFGSEA 631

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           A   +   +RM+   +M +GF+ GI D
Sbjct: 632 ARKFLDSATRMSIKAMMIKGFTTGIDD 658



 Score =  105 bits (263), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 75/248 (30%), Positives = 115/248 (46%), Gaps = 42/248 (16%)

Query: 100 QIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFH 159
           +IV+ + Y  D    PI  GL+D R+G       C +CG  +  C GHFG+I+L  PV H
Sbjct: 30  KIVTADTY--DDDGYPIDGGLMDTRLGVIDPGLVCKSCGGRVGTCPGHFGHIELSKPVVH 87

Query: 160 IGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKK 219
           IG+ + +  IL++ C  P C +V L E + A +  K+            L  +IL+   K
Sbjct: 88  IGFAKDIYKILKATC--PHCGKVTLSESRKAEYLEKMEKLLEDGGDMWILCDEILKEAAK 145

Query: 220 VSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKK 279
            S+CP CGE+               KY                     +K++     H+ 
Sbjct: 146 GSICPECGEV---------------KYD--------------------IKYDKPSTYHQI 170

Query: 280 FGLI-QTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVI--S 336
            G   + L   EV ++ E IP  D  LL +N  +++P  +ILT L VPP  +RPS+   S
Sbjct: 171 DGKASRQLTSSEVREILEKIPANDCKLLGINHIVARPEYMILTVLPVPPVTVRPSITLES 230

Query: 337 DLKSDNDV 344
             +S++D+
Sbjct: 231 GERSEDDL 238



 Score = 86.7 bits (213), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 35/57 (61%), Positives = 48/57 (84%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFV++ +  GL+P+E+FFH MGGREGLVD AV+TA++GYMQRRLV +L+D+  +YD
Sbjct: 787 HGFVRSCYKKGLSPSEYFFHAMGGREGLVDQAVRTAQSGYMQRRLVNALQDIRAEYD 843


>gi|308161109|gb|EFO63568.1| DNA-directed RNA polymerase subunit A' [Giardia lamblia P15]
          Length = 1741

 Score =  184 bits (466), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 113/316 (35%), Positives = 166/316 (52%), Gaps = 49/316 (15%)

Query: 328 NCIRPS-VISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFD 386
           N +RP+ ++      ND +LFNRQPSLH++SIM   A +  +RTF FN  VC+P+NADFD
Sbjct: 665 NSLRPNDIVYRHLLPNDTLLFNRQPSLHRMSIMQFNAVIHENRTFSFNPVVCSPFNADFD 724

Query: 387 GDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFIT 446
           GDEMN+   Q +EARAE              A +LM +  N+++PR+GE +I  TQDF+T
Sbjct: 725 GDEMNIFYMQGQEARAE--------------AGILMGSHENIISPRHGECMIGLTQDFLT 770

Query: 447 GGYLLTQKNAFFNR---AQTMRIASTLIADTS------------------------DICG 479
           G YLL+ K  F  R    Q +        D +                        D  G
Sbjct: 771 GIYLLSGKGIFMTRQDYCQHVSYGCDGFGDATYGVSLYNYGREFIKSIHDRRGTEEDTVG 830

Query: 480 IIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEE---F 536
            +K     S   +V+ R   +++GKQ+ S+++K N    VN NL+   + Y  +      
Sbjct: 831 FVK-VPCLSQPCIVYPRQ--LYSGKQVLSVLMKGNDFDSVNINLEHGDKTYKKDSNRRAL 887

Query: 537 CHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYL 596
              D Y+I++NSE L G + K+ L S  K  +FY L++++G   A   M R +++ + +L
Sbjct: 888 SINDDYIIIQNSEHLVGRLTKTFLAS-SKNCIFYFLVQNYGPVSAARIMLRFAKVAARFL 946

Query: 597 MNRGFSIGIGDVTPGQ 612
           MN GF+IGI DV P Q
Sbjct: 947 MNYGFTIGIDDVMPSQ 962



 Score =  166 bits (421), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 110/288 (38%), Positives = 163/288 (56%), Gaps = 21/288 (7%)

Query: 1143 FAGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLE--VDIDSIRYCI---ERTRGISGHL 1197
            + G++   I E +      I + LDM  I  + L   + ++++   I   ++ + + G  
Sbjct: 1382 YLGQISASIIECYSQSVCHIEVNLDMKIIADMGLAGIITVETVVASILHNDKAKKLVGQD 1441

Query: 1198 TVSG----HSFLILKPKDSSKSFNSKMY---QMKQLLPSVVIKGVQGINRAVIHE--EDV 1248
              SG    HS      +  ++S +  ++    +K LLP + I G+   NRAVI+E  E  
Sbjct: 1442 QSSGSVSIHSATRFSVRPLTQSRDDLLFDIQSLKLLLPVIPISGIPTCNRAVINEYKEFC 1501

Query: 1249 EG------VTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEI 1302
            +G      +TKY LLVEG  L+ ++   G+   +  SNN  EV  TLGIEAA +TI  EI
Sbjct: 1502 QGTTNSAPLTKYNLLVEGTGLQSILNVSGIDFTRTLSNNIVEVANTLGIEAAVATIANEI 1561

Query: 1303 KLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMK-ESVLNLASFENTSDHLFD 1361
            K  M++HGM++D RH  L+AD+M  +G VLG TR GL KMK +SV+ LASFE T +HLF+
Sbjct: 1562 KACMDSHGMAVDMRHIRLLADIMCFRGRVLGFTRFGLTKMKADSVIMLASFEKTGEHLFN 1621

Query: 1362 AAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLF 1409
            AA   + D  +GV+E II+G PM++GTG   LLQA    E   +T+ +
Sbjct: 1622 AALGNKVDEANGVTESIILGKPMSMGTGSFSLLQAPYFDEKTGKTIEY 1669



 Score =  132 bits (331), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 95/266 (35%), Positives = 141/266 (53%), Gaps = 32/266 (12%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTD------------LDYARIVKGRLERTTLGEV 811
            GVPR+KEI++    ISTPI T  L  D D            L+ AR++K  +E T LG++
Sbjct: 1327 GVPRLKEIVDGVVKISTPITTVELHVDVDKEEMATMVTEKYLEKARMMKNIIECTYLGQI 1386

Query: 812  CEYIEEVFVPDDSFILIKLDMDRIRLLHLE--VDIDSIRYCI---ERTRGISGHLTVSG- 865
               I E +      I + LDM  I  + L   + ++++   I   ++ + + G    SG 
Sbjct: 1387 SASIIECYSQSVCHIEVNLDMKIIADMGLAGIITVETVVASILHNDKAKKLVGQDQSSGS 1446

Query: 866  ---HSFLILKPKDSSKSFNSKMY---QMKQLLPSVVIKGVQGINRAVIHE--EDVEG--- 914
               HS      +  ++S +  ++    +K LLP + I G+   NRAVI+E  E  +G   
Sbjct: 1447 VSIHSATRFSVRPLTQSRDDLLFDIQSLKLLLPVIPISGIPTCNRAVINEYKEFCQGTTN 1506

Query: 915  ---VTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVME 971
               +TKY LLVEG  L+ ++   G+   +  SNN  EV  TLGIEAA +TI  EIK  M+
Sbjct: 1507 SAPLTKYNLLVEGTGLQSILNVSGIDFTRTLSNNIVEVANTLGIEAAVATIANEIKACMD 1566

Query: 972  NHGMSIDFRHPMLVADLMTSKGEVLG 997
            +HGM++D RH  L+AD+M  +G VLG
Sbjct: 1567 SHGMAVDMRHIRLLADIMCFRGRVLG 1592



 Score = 96.3 bits (238), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 62/221 (28%), Positives = 108/221 (48%), Gaps = 16/221 (7%)

Query: 86  TVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCV 145
           +V   + + + S +QI +  LY   P  +P  +G+LD+R+G + K   C TCG++   C+
Sbjct: 33  SVLSSNALMKLSEVQITTPILYEHYP--SPAANGVLDKRLGLSDKVGRCATCGKDTKMCI 90

Query: 146 GHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLV 205
           GHFG I L LPVFH G       +L  +C  P C+RV + E        +L+   L++  
Sbjct: 91  GHFGTISLALPVFHPGLINDARTMLSVVC--PFCSRVKISEAD------RLKYKVLNHKF 142

Query: 206 RKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYN 265
             S+ K+  E  KK   CP C   + + KK    ++  E +   +  K  I+ D++    
Sbjct: 143 SLSIVKEAQEQAKKQVNCPFCHAPSTICKKSQGFRVLREMHYEESANK--ILADVIKHQK 200

Query: 266 EAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLL 306
           +  K   E++   +  ++   +P++ L + + +P  D P L
Sbjct: 201 DIEKIQ-ELDQRLRNHVV---DPIQALHILQKVPECDYPYL 237



 Score = 84.0 bits (206), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 35/60 (58%), Positives = 46/60 (76%)

Query: 611  GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
             +GF+ NSF++GL P EF  H   GR+G++D+A KTA+TGY+QRRLVK LEDL V YD +
Sbjct: 1085 AKGFILNSFYTGLLPFEFLAHARAGRDGVIDSACKTADTGYLQRRLVKCLEDLSVSYDFT 1144



 Score = 60.8 bits (146), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 25/39 (64%), Positives = 31/39 (79%)

Query: 1107 REKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            R KY+R  +EP +  GA+AAQS+GEP TQMTLK+FH AG
Sbjct: 1280 RRKYIRLNLEPGSPCGAVAAQSVGEPSTQMTLKSFHHAG 1318



 Score = 49.3 bits (116), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 29/41 (70%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           +LM +  N+++PR+GE +I  TQDF+TG YLL+ K  F  R
Sbjct: 744 ILMGSHENIISPRHGECMIGLTQDFLTGIYLLSGKGIFMTR 784



 Score = 42.0 bits (97), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 21/50 (42%), Positives = 31/50 (62%)

Query: 671  FDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLF 720
            F+AA   + D  +GV+E II+G PM++GTG   LLQA    E   +T+ +
Sbjct: 1620 FNAALGNKVDEANGVTESIILGKPMSMGTGSFSLLQAPYFDEKTGKTIEY 1669


>gi|159905693|ref|YP_001549355.1| DNA-directed RNA polymerase subunit A' [Methanococcus maripaludis
           C6]
 gi|159887186|gb|ABX02123.1| DNA-directed RNA polymerase subunit A' [Methanococcus maripaludis
           C6]
          Length = 889

 Score =  184 bits (466), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 108/274 (39%), Positives = 152/274 (55%), Gaps = 31/274 (11%)

Query: 334 VISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVH 393
           VI    SD DVVL+NRQPSLH++SIMAH+ KVLP+RTFR N CVC PYNADFDGDEMNVH
Sbjct: 416 VIERHLSDGDVVLYNRQPSLHRMSIMAHKVKVLPYRTFRHNLCVCPPYNADFDGDEMNVH 475

Query: 394 LPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 453
           +PQ+EEARAE              A+ LM  + ++V+PR G  +I A  DFI+G Y+LT 
Sbjct: 476 VPQSEEARAE--------------AETLMLVEKHIVSPRFGGPIIGAIHDFISGAYVLTS 521

Query: 454 KNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKP 513
                + A T+  +S L  +  +   +  +  +              ++GK +FS  L  
Sbjct: 522 SLFTKDEALTLLKSSGLSTELGEADVVENKVEY--------------YSGKSLFSKTLPE 567

Query: 514 NRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILL 573
                  A +  K    T  E  C  D+YV++RN +LL G +DK+  GS     +   L+
Sbjct: 568 GLSLQYRAKICKKCDNCTKEE--CEHDAYVVIRNGKLLQGVIDKNGFGSEA-GIILNTLV 624

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           +DFG + A   +   ++M+   L+ +GF+ GI D
Sbjct: 625 KDFGSEDARVFLDSATKMSIKALVLKGFTTGIDD 658



 Score =  107 bits (267), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 76/257 (29%), Positives = 122/257 (47%), Gaps = 42/257 (16%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           ++++  S  +IV+ + Y  D    PI  GL+D R+G       C +C   +  C GHFG+
Sbjct: 21  EQIRTMSVAKIVTADTY--DDDGYPIDGGLMDTRLGVIDPGLVCKSCSGRVGTCPGHFGH 78

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           I+L  PV HIG+ + +  IL+++C  P C +V + E K   +  K+           +L 
Sbjct: 79  IELSKPVIHIGFAKDIYKILKAVC--PHCGKVTITEIKRDEYLEKMAKLEEDGGDPWTLC 136

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
             +L+   K SVCP CGE+                      K D             VK+
Sbjct: 137 DDLLKEAAKGSVCPACGEV----------------------KAD-------------VKY 161

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           +     H+  G  Q  L   EV ++ E IP ED  LL +N+++++P  ++LT L VPP  
Sbjct: 162 DKPTAYHQLDGKAQKQLTSSEVREILEKIPGEDCKLLGINSKVARPEYMVLTVLPVPPVT 221

Query: 330 IRPSVI--SDLKSDNDV 344
           +RPS+   S  +S++D+
Sbjct: 222 VRPSITLESGERSEDDL 238



 Score = 87.4 bits (215), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 36/57 (63%), Positives = 47/57 (82%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFV++ +  GL PTE+FFH MGGREGLVD AV+TA++GYMQRRLV +L+D+  +YD
Sbjct: 787 HGFVRSCYKKGLAPTEYFFHAMGGREGLVDQAVRTAQSGYMQRRLVNALQDIRAEYD 843


>gi|330507365|ref|YP_004383793.1| DNA-directed RNA polymerase subunit A' [Methanosaeta concilii GP6]
 gi|328928173|gb|AEB67975.1| DNA-directed RNA polymerase subunit A' [Methanosaeta concilii GP6]
          Length = 875

 Score =  184 bits (466), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 102/272 (37%), Positives = 151/272 (55%), Gaps = 38/272 (13%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D D+VLFNRQPSLH++SIM+HR KV+P++TFR N  VC PYNADFDGDEMN+H+PQTEE
Sbjct: 407 ADGDIVLFNRQPSLHRMSIMSHRVKVMPYKTFRLNPAVCPPYNADFDGDEMNMHVPQTEE 466

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           ARAE              A++LM  + N+++PR G  +I    D++TG +LLT      +
Sbjct: 467 ARAE--------------AEILMRVQENILSPRFGGPIIGGIHDYVTGSFLLTHGRKPID 512

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSW-NPVVFVRTAVIWTGKQIFSLILKPNRDCP 518
           R   M               ++K+F       P   +     WTGKQIFSLIL    D  
Sbjct: 513 RRGAME--------------LLKKFDITELPAPEGELNGEPYWTGKQIFSLILPRGLDLN 558

Query: 519 VNANLKTKGRAYTAN---EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
             A+       Y  +    E C  D+YV++++ +L  G++D   +G+  K  +   ++++
Sbjct: 559 FKADF-----CYNCDVCKNEECENDAYVVIQDGQLKIGTIDAKAVGA-FKGKITDRIIKE 612

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           +   VA   + R++R+    +M+ GFS GI D
Sbjct: 613 YSPSVASEFLDRMTRLALRGIMHAGFSFGIDD 644



 Score =  100 bits (249), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 69/253 (27%), Positives = 119/253 (47%), Gaps = 44/253 (17%)

Query: 94  QQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDL 153
           ++ S ++I++ + Y  D    PI  GL+D R+G       C +CG    +C GHFG+IDL
Sbjct: 21  RKMSVVKIITADTY--DDDGFPIEMGLMDPRLGVIDPGLRCRSCGGRPGECPGHFGHIDL 78

Query: 154 PLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKI 213
             PV H+G+ + +  +L++IC++  C+R++L + +   +  +++       +      K+
Sbjct: 79  IAPVIHVGFAKLIRKVLRAICRD--CSRLMLKDNEKKMYLEQIQELERLGQMTDDTVNKV 136

Query: 214 LETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPE 273
               +K   CP+CG     +K                       E  L+ Y E       
Sbjct: 137 FAEARKNKTCPYCGAPQQEIK----------------------FERPLS-YIE------- 166

Query: 274 IEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPS 333
            E HK       L   ++   FE +P EDI ++ MN   ++P  +ILT L VPP  +RPS
Sbjct: 167 -EGHK-------LTASDIRDRFEKVPDEDIQVMGMNPATARPEWMILTVLPVPPVTMRPS 218

Query: 334 VI--SDLKSDNDV 344
           +   S  +S++D+
Sbjct: 219 ITLESGQRSEDDL 231



 Score = 89.7 bits (221), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 37/57 (64%), Positives = 50/57 (87%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFV++S+  GL PTEFFFH +GGREGLVDTA++T+++GY+QRRLV +L+DL V+YD
Sbjct: 773 HGFVESSYKDGLNPTEFFFHAIGGREGLVDTAIRTSQSGYLQRRLVNALQDLEVKYD 829


>gi|150402532|ref|YP_001329826.1| DNA-directed RNA polymerase subunit A' [Methanococcus maripaludis
           C7]
 gi|150033562|gb|ABR65675.1| DNA-directed RNA polymerase subunit A' [Methanococcus maripaludis
           C7]
          Length = 889

 Score =  184 bits (466), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 107/274 (39%), Positives = 153/274 (55%), Gaps = 31/274 (11%)

Query: 334 VISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVH 393
           VI    SD DVVL+NRQPSLH++SIMAH+ KVLP+RTFR N CVC PYNADFDGDEMNVH
Sbjct: 416 VIERHLSDGDVVLYNRQPSLHRMSIMAHKVKVLPYRTFRHNLCVCPPYNADFDGDEMNVH 475

Query: 394 LPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 453
           +PQ+EEARAE              A+ LM  + ++V+PR G  +I A  DFI+G Y+LT 
Sbjct: 476 VPQSEEARAE--------------AETLMLVEKHIVSPRFGGPIIGAIHDFISGAYVLTS 521

Query: 454 KNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKP 513
                + A T+  +S L  +  +   +  +  +              ++GK +FS  L  
Sbjct: 522 SLFTKDEALTLLKSSGLDNELGEADVVENKVEY--------------YSGKSLFSKTLPE 567

Query: 514 NRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILL 573
                  A +  K    T  +E C  D+YV++RN +LL G +DK+  GS     +   L+
Sbjct: 568 GLSLQYRAKICKK--CDTCTKEECEHDAYVVIRNGKLLQGVIDKNGFGSEA-GIILNTLV 624

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           +DFG + A   +   ++M+   ++ +GF+ GI D
Sbjct: 625 KDFGSEDARVFLDSATKMSIKAMVLKGFTTGIDD 658



 Score =  108 bits (271), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 77/257 (29%), Positives = 122/257 (47%), Gaps = 42/257 (16%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           ++++  S  +IV+ + Y  D    PI  GL+D R+G       C +C   +  C GHFG+
Sbjct: 21  EQIRTMSVAKIVTADTY--DDDGYPIDGGLMDTRLGVIDPGLVCKSCSGRVGTCPGHFGH 78

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           I+L  PV HIG+ + +  IL+++C  P C +V + E K   +  K+           +L 
Sbjct: 79  IELSKPVIHIGFAKDIYKILKAVC--PHCGKVTITEIKRDEYLEKMAKLEEDGGDPWTLC 136

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
             +L+   K SVCP CGE+                      K D             VK+
Sbjct: 137 DDLLKEAAKGSVCPSCGEV----------------------KAD-------------VKY 161

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           +     H+  G  Q  L   EV ++ E IP ED  LL +NA++++P  ++LT L VPP  
Sbjct: 162 DKPTAYHQLDGKAQKQLTSSEVREILEKIPGEDCKLLGINAKVARPEYMVLTVLPVPPVT 221

Query: 330 IRPSVI--SDLKSDNDV 344
           +RPS+   S  +S++D+
Sbjct: 222 VRPSITLESGERSEDDL 238



 Score = 87.4 bits (215), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 36/57 (63%), Positives = 47/57 (82%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFV++ +  GL PTE+FFH MGGREGLVD AV+TA++GYMQRRLV +L+D+  +YD
Sbjct: 787 HGFVRSCYKKGLAPTEYFFHAMGGREGLVDQAVRTAQSGYMQRRLVNALQDIRAEYD 843


>gi|20090126|ref|NP_616201.1| DNA-directed RNA polymerase subunit A'' [Methanosarcina acetivorans
            C2A]
 gi|22096090|sp|Q8TRB8.1|RPOA2_METAC RecName: Full=DNA-directed RNA polymerase subunit A''
 gi|19915106|gb|AAM04681.1| DNA-directed RNA polymerase, subunit A [Methanosarcina acetivorans
            C2A]
          Length = 397

 Score =  183 bits (465), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 116/337 (34%), Positives = 172/337 (51%), Gaps = 56/337 (16%)

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFVPD 1158
            Y  + IEP  A G +AAQSIGEPGTQMT++TFH+AG            + E ++   +P 
Sbjct: 48   YATSCIEPCDAAGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVDARKIPS 107

Query: 1159 DSFILIKL----------DMDRIRLLHLEVDIDSIRYCIERTRGISG--------HLTVS 1200
               + I L          D ++ R L  E++   I +  + T  +S            + 
Sbjct: 108  TPMMTIALSKEHPEDYAYDREKTRALAWEIEATKIDHIADVTTDLSQMKLIIDLHEKAME 167

Query: 1201 GHSFLILKPKDS-SKSFN----------------------SKMYQMKQLLPSVVIKGVQG 1237
            G +  I + K+  ++  N                       ++ Q+ + + +V +KG++G
Sbjct: 168  GRNITIDQVKEKFNEELNVLVSISPDIDNQIVITPGEPSYRELLQLAKSIHNVTLKGIEG 227

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            I R V+ +E  E    Y L  EG  LRDV+   GV   + S+NN  E+Y+ LGIEAAR+ 
Sbjct: 228  IKRVVVRKEGEE----YTLYTEGSALRDVLQFEGVDKTRTSTNNINEIYEVLGIEAARNA 283

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ E    +   G+++D RH MLVADLMT  GEV  I RHG++  K SV   A+FE T +
Sbjct: 284  IIKEATDTLREQGLTVDIRHIMLVADLMTCDGEVKQIGRHGISGEKASVFARAAFEVTVN 343

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            HL DA   G  D + GV+E II+G P+ +GTG + L+
Sbjct: 344  HLLDAGMRGDVDQLQGVTENIIVGQPIRMGTGDVHLI 380



 Score =  113 bits (282), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 74/238 (31%), Positives = 125/238 (52%), Gaps = 18/238 (7%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYA------RIVKGRLERTTLGEVCEYIEE 817
           G+PR+ EI++A +  STP++T  L K+   DYA      R +   +E T +  + +    
Sbjct: 92  GLPRLIEIVDARKIPSTPMMTIALSKEHPEDYAYDREKTRALAWEIEATKIDHIAD---- 147

Query: 818 VFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSS 877
               D S + + +D+    +    + ID ++        +   ++    + +++ P + S
Sbjct: 148 -VTTDLSQMKLIIDLHEKAMEGRNITIDQVKEKFNEELNVLVSISPDIDNQIVITPGEPS 206

Query: 878 KSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVK 937
                ++ Q+ + + +V +KG++GI R V+ +E  E    Y L  EG  LRDV+   GV 
Sbjct: 207 YR---ELLQLAKSIHNVTLKGIEGIKRVVVRKEGEE----YTLYTEGSALRDVLQFEGVD 259

Query: 938 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
             + S+NN  E+Y+ LGIEAAR+ I+ E    +   G+++D RH MLVADLMT  GEV
Sbjct: 260 KTRTSTNNINEIYEVLGIEAARNAIIKEATDTLREQGLTVDIRHIMLVADLMTCDGEV 317


>gi|296109331|ref|YP_003616280.1| DNA-directed RNA polymerase subunit A' [methanocaldococcus infernus
           ME]
 gi|295434145|gb|ADG13316.1| DNA-directed RNA polymerase subunit A' [Methanocaldococcus infernus
           ME]
          Length = 886

 Score =  183 bits (465), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 103/267 (38%), Positives = 148/267 (55%), Gaps = 31/267 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VL+NRQPSLH++SIM H+ +VLP+RTFR N CVC PYNADFDGDEMN+H PQTEEA
Sbjct: 420 DGDIVLYNRQPSLHRMSIMGHKVRVLPYRTFRHNLCVCPPYNADFDGDEMNLHAPQTEEA 479

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+ LM  + ++++PR G  +I A  DFI+G Y+LT  N F   
Sbjct: 480 RAE--------------AETLMLVEKHILSPRFGGPIIGAIHDFISGAYILTS-NYFTKD 524

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
             T+ + S  I D               W P        +++GK+IFS  L    +    
Sbjct: 525 EATLILRSGGIKD-------------ELWEPDKVENGIPLYSGKKIFSKALPKGLNLRYK 571

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           AN+  K    +  +E C  D+YVI+++ EL+ G +DK   G+     + + ++++FG + 
Sbjct: 572 ANICRK--CDSCKKENCEYDAYVIIKDGELVKGVIDKKGYGAES-GLILHTIVKEFGPEA 628

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGD 607
               +   ++M    LM RGF+ GI D
Sbjct: 629 GRKFLDSSTKMAIRTLMLRGFTTGIDD 655



 Score =  118 bits (295), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 71/244 (29%), Positives = 122/244 (50%), Gaps = 38/244 (15%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D +++ S  +IV+ + Y +D    PI  GL+D R+G       C TCG  + +C GHFG+
Sbjct: 18  DYIRKMSVAKIVTPDTYDEDG--YPIEGGLMDPRLGVIDPGLRCKTCGGRIGECPGHFGH 75

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           I+L  P+ H+G+ + +  IL+++C  P C R+L+ E K      K+         +    
Sbjct: 76  IELAKPIIHVGFAKTIYKILKAVC--PHCGRILIPENKRREILEKMEKLEREGGNKWEAC 133

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           K+  +   K+SVCP+CGE+               K++ + +K  +            ++ 
Sbjct: 134 KETYQEASKISVCPYCGEV---------------KWEIKFEKPSSFYR---------IEE 169

Query: 271 NPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCI 330
             EI+          L+P +V ++ E IP ED  LL +N ++++P  ++LT L VPP  +
Sbjct: 170 GAEIK----------LSPADVREILEKIPDEDCILLGLNPKVARPEWMVLTVLPVPPVTV 219

Query: 331 RPSV 334
           RPS+
Sbjct: 220 RPSI 223



 Score = 88.2 bits (217), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 36/59 (61%), Positives = 50/59 (84%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            GFV++S+  GL+PTEFFFH +GGREGLVD AV+TA++GYMQRRL+ +L+DL  ++D +
Sbjct: 784 HGFVRSSYKKGLSPTEFFFHAIGGREGLVDQAVRTAQSGYMQRRLINALQDLKSEFDFT 842


>gi|154151471|ref|YP_001405089.1| DNA-directed RNA polymerase subunit A'' [Methanoregula boonei 6A8]
 gi|154000023|gb|ABS56446.1| DNA-directed RNA polymerase, subunit A'' [Methanoregula boonei 6A8]
          Length = 390

 Score =  183 bits (465), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 121/354 (34%), Positives = 183/354 (51%), Gaps = 63/354 (17%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCE 1149
            E   ++Y   +IE   AVG +AAQSIGEPGTQMT++TFH+AG              E+ +
Sbjct: 42   ERVEKEYQSTRIEACEAVGVIAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIMD 101

Query: 1150 YIEEVFVPDDSFIL---IKLDMDRIRLLHLEV---------DIDS------------IRY 1185
              +E   P  +  L     +D DR R +  ++         DI +            ++ 
Sbjct: 102  ARKEPSTPTMTVYLETEYGIDRDRAREVSWQIEAAPLHEFGDITTDMENMQVVVHLNVKV 161

Query: 1186 CIERTRGISGHLTVS-------------------GHSFLILKPKDSSKSFNSKMYQMKQL 1226
            C +R    S  + V+                    ++ LI  PKD     N  ++Q+ + 
Sbjct: 162  CEKRKISPSEIMEVAPKKIRDRRHYRDFEHDVDEANATLIFTPKDRESYQN--LFQLAEH 219

Query: 1227 LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVY 1286
            + +V+++G+  I R V+ +E  E    Y L  EG NL+DV    GV   +  +NN  E+ 
Sbjct: 220  VRNVIVQGIDDILRVVVRKEAGE----YILYTEGSNLKDVFDVAGVDTTRTRTNNISEIA 275

Query: 1287 KTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESV 1346
            + LGIEAAR+ I+ E +  +   G+ +D RH MLV+D+M  +GEV  I RHG+A  KESV
Sbjct: 276  QVLGIEAARNAIIHEAQSTLNEQGILVDVRHIMLVSDMMCMEGEVKQIGRHGIAGEKESV 335

Query: 1347 LNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS 1400
            L+ A+FE T +HL DAA   +TD +SGV+E +I+G P+ +GTG +KL+    R 
Sbjct: 336  LSRAAFEVTVNHLLDAAVANETDELSGVTENVIVGQPIQLGTGDVKLVAVKQRE 389



 Score =  105 bits (261), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 78/254 (30%), Positives = 127/254 (50%), Gaps = 47/254 (18%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A +  STP +T YL+ +   D D AR V  ++E   L E           
Sbjct: 92  GLPRLIEIMDARKEPSTPTMTVYLETEYGIDRDRAREVSWQIEAAPLHE----------- 140

Query: 822 DDSFILIKLDMDRIRLL-HLEVDIDSIRYCIERTRGISGHLTVS---------------- 864
              F  I  DM+ ++++ HL     +++ C +R    S  + V+                
Sbjct: 141 ---FGDITTDMENMQVVVHL-----NVKVCEKRKISPSEIMEVAPKKIRDRRHYRDFEHD 192

Query: 865 ---GHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLL 921
               ++ LI  PKD     N  ++Q+ + + +V+++G+  I R V+ +E  E    Y L 
Sbjct: 193 VDEANATLIFTPKDRESYQN--LFQLAEHVRNVIVQGIDDILRVVVRKEAGE----YILY 246

Query: 922 VEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRH 981
            EG NL+DV    GV   +  +NN  E+ + LGIEAAR+ I+ E +  +   G+ +D RH
Sbjct: 247 TEGSNLKDVFDVAGVDTTRTRTNNISEIAQVLGIEAARNAIIHEAQSTLNEQGILVDVRH 306

Query: 982 PMLVADLMTSKGEV 995
            MLV+D+M  +GEV
Sbjct: 307 IMLVSDMMCMEGEV 320


>gi|45358926|ref|NP_988483.1| DNA-directed RNA polymerase subunit A' [Methanococcus maripaludis
           S2]
 gi|45047792|emb|CAF30919.1| RNA polymerase, alpha subunit [Methanococcus maripaludis S2]
          Length = 889

 Score =  183 bits (465), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 109/274 (39%), Positives = 152/274 (55%), Gaps = 31/274 (11%)

Query: 334 VISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVH 393
           VI    SD D+VL+NRQPSLH++SIMAH+ KVLP+RTFR N CVC PYNADFDGDEMNVH
Sbjct: 416 VIERHLSDGDIVLYNRQPSLHRMSIMAHKVKVLPYRTFRHNLCVCPPYNADFDGDEMNVH 475

Query: 394 LPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 453
           +PQ+EEARAE              A+ LM  + ++V+PR G  +I A  DFI+G Y+LT 
Sbjct: 476 VPQSEEARAE--------------AEKLMLVEKHIVSPRFGGPIIGAIHDFISGAYVLTS 521

Query: 454 KNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKP 513
                + A T+  +S L  +  +              P V       ++GK +FS  L  
Sbjct: 522 SLFTKDEALTLLKSSGLNVELGE--------------PDVIENNIEYYSGKSLFSKTLPE 567

Query: 514 NRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILL 573
                  A +  K    T  +E C  D+YV++RN +LL G +DK+  GS     V   L+
Sbjct: 568 GLSLQYRAKICKK--CDTCTKEECEHDAYVVIRNGKLLRGVIDKNGFGSEA-GIVLNTLV 624

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           +DFG + A   +   ++M+   ++ +GF+ GI D
Sbjct: 625 KDFGSEDARLFLDAATKMSIKAMVLKGFTTGIDD 658



 Score =  108 bits (270), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 77/257 (29%), Positives = 122/257 (47%), Gaps = 42/257 (16%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           ++++  S  +IV+ + Y  D    PI  GL+D R+G       C +C   +  C GHFG+
Sbjct: 21  EQIRTMSVAKIVTADTY--DDDGYPIDGGLMDTRLGVIDPGLVCKSCSGRVGTCPGHFGH 78

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           I+L  PV HIG+ + +  IL+++C  P C +V + E K   +  K+           +L 
Sbjct: 79  IELSKPVVHIGFAKDIYKILKAVC--PHCGKVTITEIKRDEYLEKMAKLEEDGGDPWTLC 136

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
             +L+   K SVCP CGE+                      K D             VK+
Sbjct: 137 DDLLKEAAKGSVCPSCGEV----------------------KAD-------------VKY 161

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           +     H+  G  Q  L   EV ++ E IP ED  LL +NA++++P  ++LT L VPP  
Sbjct: 162 DKPTAYHQLDGKAQKQLTSSEVREILEKIPAEDCKLLGINAKVARPEFMVLTVLPVPPVT 221

Query: 330 IRPSVI--SDLKSDNDV 344
           +RPS+   S  +S++D+
Sbjct: 222 VRPSITLESGERSEDDL 238



 Score = 87.4 bits (215), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 36/57 (63%), Positives = 47/57 (82%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFV++ +  GL PTE+FFH MGGREGLVD AV+TA++GYMQRRLV +L+D+  +YD
Sbjct: 787 HGFVRSCYKKGLAPTEYFFHAMGGREGLVDQAVRTAQSGYMQRRLVNALQDIRAEYD 843


>gi|297527624|ref|YP_003669648.1| DNA-directed RNA polymerase subunit A' [Staphylothermus hellenicus
           DSM 12710]
 gi|297256540|gb|ADI32749.1| DNA-directed RNA polymerase subunit A' [Staphylothermus hellenicus
           DSM 12710]
          Length = 886

 Score =  183 bits (465), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 102/270 (37%), Positives = 151/270 (55%), Gaps = 40/270 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIMAH  +VLP++TFR N  VC PYNADFDGDEMN+H+PQ+EEA
Sbjct: 417 DGDIVLFNRQPSLHRISIMAHVVRVLPYKTFRLNLLVCPPYNADFDGDEMNLHVPQSEEA 476

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A++LM  + +++TPR G  +I   QD+I+G +LLT K+    R
Sbjct: 477 RAE--------------ARMLMLVEKHILTPRYGGPIIGGLQDYISGAFLLTSKSTLLTR 522

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNP-VVFVRTAVIWTGKQIFSLILKPNRDCPV 519
                          D+  ++    +R   P    ++    WTGKQ+ SL L      P 
Sbjct: 523 --------------EDVIELLGVAGYRGKLPEPAILKPKQYWTGKQLISLFL------PD 562

Query: 520 NANLKTKGRAYTAN-----EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLR 574
           + N K   +   A      +E C  DS VI++N  LL G +DK+++G     ++ + L++
Sbjct: 563 DFNYKRPAKIAGATALRCIDEDCPHDSLVIVKNGVLLEGVLDKASIGREEPESLIHWLVK 622

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIG 604
           ++GED+A   M  + +M   +    GF++G
Sbjct: 623 EYGEDIARLFMDYVYKMFLRFAEKYGFTMG 652



 Score =  107 bits (266), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 76/265 (28%), Positives = 125/265 (47%), Gaps = 44/265 (16%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G ++ E+ +++ S   I++  +Y  D    PI  G++DRR+G  +    C  CG     C
Sbjct: 15  GILSPEE-IRKMSVTTIITSEVYDND--GAPIDGGVMDRRLGAIEPREVCPVCGNTRESC 71

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA---KLRNPAL 201
            GHFG+I+L  PV H+ + + +   L++ C+   C R+ + EE+   +      L+   L
Sbjct: 72  PGHFGHIELARPVIHVSFVKHIHMYLKTTCR--VCGRIKIKEEERKKYLELLNSLKELGL 129

Query: 202 SYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLL 261
            YLV K L + I         CPHCG                ++YK R +K     ED  
Sbjct: 130 DYLV-KRLHEYIRRKAAATQRCPHCGA---------------KQYKIRLEKPHTFYEDRG 173

Query: 262 AEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
            E                 G ++ LNP+EV    E I  ED+ LL  +   ++P  ++LT
Sbjct: 174 EE-----------------GYVK-LNPIEVRARLEKILDEDVRLLGGDPVDARPEWMVLT 215

Query: 322 RLLVPPNCIRPSVI--SDLKSDNDV 344
            L VPP  +RPS++  + ++S++D+
Sbjct: 216 VLPVPPRSVRPSILLETGIRSEDDL 240



 Score = 86.7 bits (213), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 41/83 (49%), Positives = 54/83 (65%), Gaps = 1/83 (1%)

Query: 587 RLSRMTSFYLMNRGFSIGIGDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVK 645
           R  R+T  Y+         GD+ P  +GFV + F  GL P E FFH   GREGL DTAV+
Sbjct: 759 RGRRITRGYMHRTLPHFKPGDLGPEARGFVAHGFVDGLNPIEVFFHAAAGREGLTDTAVR 818

Query: 646 TAETGYMQRRLVKSLEDLCVQYD 668
           T+++GYMQRRL+ +L+DL V+YD
Sbjct: 819 TSQSGYMQRRLINALQDLRVEYD 841


>gi|374633178|ref|ZP_09705545.1| DNA-directed RNA polymerase, subunit A'''' [Metallosphaera
            yellowstonensis MK1]
 gi|373524662|gb|EHP69539.1| DNA-directed RNA polymerase, subunit A'''' [Metallosphaera
            yellowstonensis MK1]
          Length = 397

 Score =  183 bits (464), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 132/390 (33%), Positives = 196/390 (50%), Gaps = 61/390 (15%)

Query: 1055 KFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQ 1114
            KFLEE  +  S T  ++ V++ LRE IL+ Q  I           A K       Y+ + 
Sbjct: 14   KFLEEELQLISNTLPKNVVAK-LREAILNSQIPIERDEIKKIIDEAVK------DYLGSL 66

Query: 1115 IEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFVPDDSFIL 1163
            + P  A+G +AAQSIGEPGTQMTL+TFHFAG            + E ++   VP    + 
Sbjct: 67   VHPGEAIGVVAAQSIGEPGTQMTLRTFHFAGVRELNVTLGLPRLIEIVDARKVPSTPMMT 126

Query: 1164 IKLDM----DRIRLLHL--EVDIDSIRYCIERTRGISGHLTVSGH--------------- 1202
            I L+     DR + L +  +++   I   +E        +++S H               
Sbjct: 127  IYLEKEYANDREKALEVARKIEYTRIENVVETVSLDVASMSISLHLDPTLLEDKGLTVED 186

Query: 1203 -----------SFLILKPKDSSK--SFNS-----KMYQMKQLLPSVVIKGVQGINRAVIH 1244
                        + I +P + +   SF S      ++++++ + S  IKGV+GI RA++ 
Sbjct: 187  VEKAIKKLKLGKYEIERPDERTIQISFESMDSITALFKVREKILSTKIKGVKGIKRAIVQ 246

Query: 1245 EEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKL 1304
            +   E    Y ++ +G NL  V+   G+   +  +NN +EV   LGIEA R  IM EIK 
Sbjct: 247  KRGEE----YVIITDGSNLEGVLGVKGIDIRRIETNNLHEVENVLGIEAVRELIMKEIKR 302

Query: 1305 VMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAF 1364
            V++  G+ +D RH  LV+D+MT  GEV  I RHG+   K SVL  A+FE T  HL DAA 
Sbjct: 303  VLDEQGLDVDIRHIELVSDIMTRTGEVRQIGRHGVTGEKTSVLARAAFEVTVKHLLDAAA 362

Query: 1365 YGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
             G  +   GV E II+G P+ +GTG+++LL
Sbjct: 363  RGDMEEFKGVVENIIIGQPIKLGTGMVELL 392



 Score =  105 bits (262), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 72/234 (30%), Positives = 125/234 (53%), Gaps = 12/234 (5%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A +  STP++T YL+K+   D + A  V  ++E T +  V E +      
Sbjct: 106 GLPRLIEIVDARKVPSTPMMTIYLEKEYANDREKALEVARKIEYTRIENVVETVS----L 161

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
           D + + I L +D   L    + ++ +   I++ +   G   +       ++    S    
Sbjct: 162 DVASMSISLHLDPTLLEDKGLTVEDVEKAIKKLK--LGKYEIERPDERTIQISFESMDSI 219

Query: 882 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
           + ++++++ + S  IKGV+GI RA++ +   E    Y ++ +G NL  V+   G+   + 
Sbjct: 220 TALFKVREKILSTKIKGVKGIKRAIVQKRGEE----YVIITDGSNLEGVLGVKGIDIRRI 275

Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            +NN +EV   LGIEA R  IM EIK V++  G+ +D RH  LV+D+MT  GEV
Sbjct: 276 ETNNLHEVENVLGIEAVRELIMKEIKRVLDEQGLDVDIRHIELVSDIMTRTGEV 329


>gi|126465703|ref|YP_001040812.1| DNA-directed RNA polymerase subunit A' [Staphylothermus marinus F1]
 gi|126014526|gb|ABN69904.1| DNA-directed RNA polymerase, subunit A' [Staphylothermus marinus
           F1]
          Length = 886

 Score =  183 bits (464), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 102/270 (37%), Positives = 151/270 (55%), Gaps = 40/270 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIMAH  +VLP++TFR N  VC PYNADFDGDEMN+H+PQ+EEA
Sbjct: 417 DGDIVLFNRQPSLHRISIMAHVVRVLPYKTFRLNLLVCPPYNADFDGDEMNLHVPQSEEA 476

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A++LM  + +++TPR G  +I   QD+I+G +LLT K+    R
Sbjct: 477 RAE--------------ARMLMLVEKHILTPRYGGPIIGGLQDYISGAFLLTSKSTLLTR 522

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNP-VVFVRTAVIWTGKQIFSLILKPNRDCPV 519
                          D+  ++    +R   P    ++    WTGKQ+ SL L      P 
Sbjct: 523 --------------EDVIELLGVAGYRGKLPEPAILKPKQYWTGKQLISLFL------PD 562

Query: 520 NANLKTKGRAYTAN-----EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLR 574
           + N K   +   A      +E C  DS VI++N  LL G +DK+++G     ++ + L++
Sbjct: 563 DFNYKRPAKMAGATALRCIDEDCPHDSIVIVKNGVLLEGVLDKASIGREEPESLIHWLVK 622

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIG 604
           ++GED+A   M  + +M   +    GF++G
Sbjct: 623 EYGEDIARLFMDYVYKMFLRFAEKYGFTMG 652



 Score =  104 bits (260), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 74/265 (27%), Positives = 126/265 (47%), Gaps = 44/265 (16%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G ++ E+ +++ S   I++  +Y  D    PI  G++DRR+G  +    C  CG     C
Sbjct: 15  GILSPEE-IRKMSVTTIITSEVYDND--GAPIDGGVMDRRLGAIEPREVCPVCGNTRESC 71

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA---KLRNPAL 201
            GHFG+I+L  PV H+ + + +   L++ C+   C R+ + E++   +      L+   L
Sbjct: 72  PGHFGHIELARPVIHVSFVKHIHMYLKTTCR--VCGRIKIKEDERKRYLELLNSLKELGL 129

Query: 202 SYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLL 261
            YLV K L + I         CPHCG                ++Y+ R +K  +  ED  
Sbjct: 130 EYLV-KRLHEYIRRKAAATQRCPHCGA---------------KQYRIRLEKPHSFYEDRG 173

Query: 262 AEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
            E                 G ++ LNP+EV    E I  ED+ LL  +   ++P  ++LT
Sbjct: 174 EE-----------------GYVK-LNPIEVRARLEKILDEDVRLLGGDPIDARPEWMVLT 215

Query: 322 RLLVPPNCIRPSVI--SDLKSDNDV 344
            L VPP  +RPS++  + ++S++D+
Sbjct: 216 VLPVPPRSVRPSILLETGIRSEDDL 240



 Score = 86.7 bits (213), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 41/83 (49%), Positives = 54/83 (65%), Gaps = 1/83 (1%)

Query: 587 RLSRMTSFYLMNRGFSIGIGDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVK 645
           R  R+T  Y+         GD+ P  +GFV + F  GL P E FFH   GREGL DTAV+
Sbjct: 759 RGRRITRGYMHRTLPHFKPGDLGPEARGFVAHGFVDGLNPIEVFFHAAAGREGLTDTAVR 818

Query: 646 TAETGYMQRRLVKSLEDLCVQYD 668
           T+++GYMQRRL+ +L+DL V+YD
Sbjct: 819 TSQSGYMQRRLINALQDLRVEYD 841


>gi|340624673|ref|YP_004743126.1| DNA-directed RNA polymerase subunit A' [Methanococcus maripaludis
           X1]
 gi|339904941|gb|AEK20383.1| DNA-directed RNA polymerase subunit A' [Methanococcus maripaludis
           X1]
          Length = 889

 Score =  183 bits (464), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 109/274 (39%), Positives = 152/274 (55%), Gaps = 31/274 (11%)

Query: 334 VISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVH 393
           VI    SD D+VL+NRQPSLH++SIMAH+ KVLP+RTFR N CVC PYNADFDGDEMNVH
Sbjct: 416 VIERHLSDGDIVLYNRQPSLHRMSIMAHKVKVLPYRTFRHNLCVCPPYNADFDGDEMNVH 475

Query: 394 LPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 453
           +PQ+EEARAE              A+ LM  + ++V+PR G  +I A  DFI+G Y+LT 
Sbjct: 476 VPQSEEARAE--------------AEKLMLVEKHIVSPRFGGPIIGAIHDFISGAYVLTS 521

Query: 454 KNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKP 513
                + A T+  +S L  +  +              P V       ++GK +FS  L  
Sbjct: 522 SLFTKDEALTLLKSSGLNVELGE--------------PDVVENNIEYYSGKSLFSKTLPE 567

Query: 514 NRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILL 573
                  A +  K    T  +E C  D+YV++RN +LL G +DK+  GS     V   L+
Sbjct: 568 GLSLQYRAKICKK--CDTCTKEECEHDAYVVIRNGKLLRGVIDKNGFGSEA-GIVLNTLV 624

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           +DFG + A   +   ++M+   ++ +GF+ GI D
Sbjct: 625 KDFGSEDARLFLDAATKMSIKAMVLKGFTTGIDD 658



 Score =  108 bits (270), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 77/257 (29%), Positives = 122/257 (47%), Gaps = 42/257 (16%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           ++++  S  +IV+ + Y  D    PI  GL+D R+G       C +C   +  C GHFG+
Sbjct: 21  EQIRTMSVAKIVTADTY--DDDGYPIDGGLMDTRLGVIDPGLVCKSCSGRVGTCPGHFGH 78

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           I+L  PV HIG+ + +  IL+++C  P C +V + E K   +  K+           +L 
Sbjct: 79  IELSKPVVHIGFAKDIYKILKAVC--PHCGKVTITEIKRDEYLEKMAKLKEDGGDPWTLC 136

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
             +L+   K SVCP CGE+                      K D             VK+
Sbjct: 137 DDLLKEAAKGSVCPSCGEV----------------------KAD-------------VKY 161

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           +     H+  G  Q  L   EV ++ E IP ED  LL +NA++++P  ++LT L VPP  
Sbjct: 162 DKPTAYHQLDGKAQKQLTSSEVREILEKIPAEDCKLLGINAKVARPEFMVLTVLPVPPVT 221

Query: 330 IRPSVI--SDLKSDNDV 344
           +RPS+   S  +S++D+
Sbjct: 222 VRPSITLESGERSEDDL 238



 Score = 87.4 bits (215), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 36/57 (63%), Positives = 47/57 (82%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFV++ +  GL PTE+FFH MGGREGLVD AV+TA++GYMQRRLV +L+D+  +YD
Sbjct: 787 HGFVRSCYKKGLAPTEYFFHAMGGREGLVDQAVRTAQSGYMQRRLVNALQDIRAEYD 843


>gi|294495211|ref|YP_003541704.1| DNA-directed RNA polymerase, subunit A' [Methanohalophilus mahii DSM
            5219]
 gi|292666210|gb|ADE36059.1| DNA-directed RNA polymerase, subunit A' [Methanohalophilus mahii DSM
            5219]
          Length = 385

 Score =  183 bits (464), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 114/346 (32%), Positives = 181/346 (52%), Gaps = 58/346 (16%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCE 1149
            E   E Y ++ +EP  AVG ++AQSIGEPGTQMT++TFH+AG              E+ +
Sbjct: 44   EKLLETYDKSCVEPCEAVGVISAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVD 103

Query: 1150 ------------YIEEVFVPDDSF-------------------------ILIKLDMDRIR 1172
                        ++++ ++ D  F                         + + +D++   
Sbjct: 104  ARKRPSTPMMTVHLDKEYLEDRDFANKIAWMIEATHVEHLADVTTDLPNMQLVIDLNEKA 163

Query: 1173 LLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVI 1232
            +   EV I+S+   +E   G+S        + L++K K+ S     ++ Q+ + + ++ +
Sbjct: 164  MNKREVGIESVMEKLEHGLGVSVVQAKEVSNQLLIKLKEPS---YRELLQLAKKINTITL 220

Query: 1233 KGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIE 1292
            KG+ GI R V+ +ED E    Y+L  EG  L+ V+   GV   + S+NN  E+Y+  GIE
Sbjct: 221  KGIDGIKRVVVRKEDGE----YRLYTEGSELKKVLEIDGVDPTRTSTNNIGEIYEVFGIE 276

Query: 1293 AARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASF 1352
            AAR+ I+ E    +   G+ +D RH MLVAD+M+  GEV  I RHG++  K SV   A+F
Sbjct: 277  AARNAIIKEATDTLREQGLEVDVRHIMLVADIMSCDGEVKQIGRHGISGEKASVFARAAF 336

Query: 1353 ENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 1398
            E T +HL DA   G+ D +SGV+E II+G P+ +GTG + L+   P
Sbjct: 337  EVTVNHLLDAGLRGEVDELSGVTENIIVGQPIKLGTGDVHLVSRNP 382



 Score =  119 bits (299), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 77/234 (32%), Positives = 132/234 (56%), Gaps = 14/234 (5%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A +  STP++T +LDK+   D D+A  +   +E T +    E++ +V   
Sbjct: 94  GLPRLIEIVDARKRPSTPMMTVHLDKEYLEDRDFANKIAWMIEATHV----EHLADVTTD 149

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             +  L+ +D++   +   EV I+S+   +E   G+S        + L++K K+ S    
Sbjct: 150 LPNMQLV-IDLNEKAMNKREVGIESVMEKLEHGLGVSVVQAKEVSNQLLIKLKEPS---Y 205

Query: 882 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
            ++ Q+ + + ++ +KG+ GI R V+ +ED E    Y+L  EG  L+ V+   GV   + 
Sbjct: 206 RELLQLAKKINTITLKGIDGIKRVVVRKEDGE----YRLYTEGSELKKVLEIDGVDPTRT 261

Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
           S+NN  E+Y+  GIEAAR+ I+ E    +   G+ +D RH MLVAD+M+  GEV
Sbjct: 262 STNNIGEIYEVFGIEAARNAIIKEATDTLREQGLEVDVRHIMLVADIMSCDGEV 315


>gi|240103982|ref|YP_002960291.1| DNA-directed RNA polymerase subunit A' [Thermococcus gammatolerans
           EJ3]
 gi|239911536|gb|ACS34427.1| DNA-directed RNA polymerase subunit A' (rpoA1) [Thermococcus
           gammatolerans EJ3]
          Length = 905

 Score =  183 bits (464), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 100/282 (35%), Positives = 159/282 (56%), Gaps = 40/282 (14%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
            D D+VLFNRQPSLH++SIMAHR +V+P++TFR N  VC PYNADFDGDEMN+H+PQTEE
Sbjct: 417 EDGDIVLFNRQPSLHRMSIMAHRVRVMPYKTFRLNLPVCPPYNADFDGDEMNLHVPQTEE 476

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           A+AE              AK+LM  ++++++PR G  LIA  QD I+GGYLLT++ A+F 
Sbjct: 477 AQAE--------------AKILMEVQNHIISPRYGGPLIAGIQDHISGGYLLTREGAYFT 522

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLIL-------- 511
           R++  ++ +    D  ++             P        +W+GK IFSL+L        
Sbjct: 523 RSEVEQMLTFAGVDVDELP-----------KPDKVENGVELWSGKTIFSLLLPDDLTLWY 571

Query: 512 ------KPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGK 565
                 +P R   +   ++ K             D +V ++N +LL+G++DK   G    
Sbjct: 572 RNKLCDEPERCEAIEKLIEEKLVPDPEEVRKIAYDGFVYIQNGKLLSGAIDKKAYGR-ED 630

Query: 566 ANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
             +  I++R++G + A   + +++++T + + ++GF+  I D
Sbjct: 631 GKLLDIIVREYGVERARQFLDQVTKLTIWVITHKGFTTAIDD 672



 Score =  112 bits (279), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 75/266 (28%), Positives = 124/266 (46%), Gaps = 35/266 (13%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G IE  +     +++ S  +I   + Y  D    PI  GL+D+R+G       C TCG  
Sbjct: 9   GSIEFGILSPQEIRKMSAAEITVPDTY--DDDGYPIEGGLMDKRLGVIDPGLRCETCGAR 66

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
             +C GHFG+I+L  PV H+G+ + +  +L+S C+   C R+ L +E+   +  K     
Sbjct: 67  AGECPGHFGHIELARPVVHVGFAKTIQRVLESTCRE--CGRIKLTDEEIEEYMKKFEVIG 124

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDL 260
                +  L K+I +  K+  VCPHCG     +           K++  T   +   ++ 
Sbjct: 125 DRKKDKDRLIKEIHKKAKERMVCPHCGAPQFPI-----------KFERPTIYYELRRDEE 173

Query: 261 LAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
             EY                     + P E+    E IP +D+PLL ++ E S+P  +IL
Sbjct: 174 GNEYK------------------HRMMPSEIRDRLERIPDKDLPLLGLHPEKSRPEWMIL 215

Query: 321 TRLLVPPNCIRPSVI--SDLKSDNDV 344
           T L VPP  +RPS+   S +++++D+
Sbjct: 216 TVLPVPPVTMRPSITLESGIRAEDDL 241



 Score = 95.1 bits (235), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 41/58 (70%), Positives = 50/58 (86%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV NS+ SGLTP E+FFH MGGREGLVDTAV+TA++GYMQRRL+ +L+DL V YD
Sbjct: 800 ARGFVVNSYKSGLTPQEYFFHAMGGREGLVDTAVRTAQSGYMQRRLINALQDLKVDYD 857



 Score = 51.2 bits (121), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 31/127 (24%), Positives = 63/127 (49%), Gaps = 24/127 (18%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFF 79
           ++LM  ++++++PR G  LIA  QD I+GGYLLT++ A+F R++  ++ +         F
Sbjct: 482 KILMEVQNHIISPRYGGPLIAGIQDHISGGYLLTREGAYFTRSEVEQMLT---------F 532

Query: 80  RGLIEGTVTKEDRVQQ---------------QSHIQIVSKNLYCQDPQRTPIPHGLLDRR 124
            G+    + K D+V+                   + +  +N  C +P+R      L++ +
Sbjct: 533 AGVDVDELPKPDKVENGVELWSGKTIFSLLLPDDLTLWYRNKLCDEPERCEAIEKLIEEK 592

Query: 125 MGTNQKE 131
           +  + +E
Sbjct: 593 LVPDPEE 599


>gi|390939171|ref|YP_006402909.1| DNA-directed RNA polymerase subunit A' [Desulfurococcus fermentans
           DSM 16532]
 gi|390192278|gb|AFL67334.1| DNA-directed RNA polymerase subunit A' [Desulfurococcus fermentans
           DSM 16532]
          Length = 886

 Score =  182 bits (463), Expect = 8e-43,   Method: Compositional matrix adjust.
 Identities = 96/252 (38%), Positives = 147/252 (58%), Gaps = 30/252 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++S+MAH  +VLP++TFR N  VC PYNADFDGDEMN+H+PQ+EEA
Sbjct: 417 DGDIVLFNRQPSLHRISVMAHVVRVLPYKTFRLNLLVCPPYNADFDGDEMNLHVPQSEEA 476

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A++LM  + +++TPR G  +I   QD+I+G Y+LT K      
Sbjct: 477 RAE--------------ARLLMLVERHILTPRYGGPIIGGLQDYISGAYILTSK------ 516

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNP-VVFVRTAVIWTGKQIFSLILKPNRDCPV 519
                   T + D  D+  ++    ++   P    ++   +WTGKQ+ SL L  + +   
Sbjct: 517 --------TTLLDKDDVVDLLSSTGYKGELPEPAILKPRALWTGKQLVSLFLPKDFNYKR 568

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           N+ + +   A    +E C  DS VI++N  LL G +DK+++G     ++ + L++++GED
Sbjct: 569 NSKIGSAA-ALRCIDEDCPHDSLVIIKNGVLLEGVLDKASIGREEPESLVHWLIKEYGED 627

Query: 580 VAVTAMWRLSRM 591
                M R+ +M
Sbjct: 628 YGRMFMDRVYKM 639



 Score =  108 bits (269), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 72/259 (27%), Positives = 123/259 (47%), Gaps = 44/259 (16%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D +++ S  QI S  +Y  D   +PI  G++DRR+G  +    C  CG     C GHFG+
Sbjct: 21  DEIRKMSVTQIFSSEVYDND--GSPIDGGVMDRRLGAIEPGETCPICGNTRDSCPGHFGH 78

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGF---RAKLRNPALSYLVRK 207
           I+L  PV H+G+ + ++  L++ C+N  C R+ + EE+   +    + L+     YL+++
Sbjct: 79  IELAKPVIHVGFAKQILIYLKATCRN--CGRLKIPEEEKGEYLRLLSDLQELGAPYLIKR 136

Query: 208 SLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEA 267
              + I         CPHCG                ++YK + +K     E         
Sbjct: 137 -FHEYIRRKASTADTCPHCGA---------------KQYKIKLEKPHTFYE--------- 171

Query: 268 VKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPP 327
                      + GL++ L P EV    E I  +D+ LL  +   ++P  ++LT L VPP
Sbjct: 172 ---------QTERGLLK-LTPSEVRGRLEKISNDDVKLLGGDPSDARPEWMVLTVLPVPP 221

Query: 328 NCIRPSVI--SDLKSDNDV 344
             +RPSV+  + ++S++D+
Sbjct: 222 RSVRPSVLLETGIRSEDDL 240



 Score = 85.5 bits (210), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 41/85 (48%), Positives = 55/85 (64%), Gaps = 1/85 (1%)

Query: 587 RLSRMTSFYLMNRGFSIGIGDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVK 645
           R  R+T  YL          D+ P  +GF+ + F  GL P E FFH   GREGL+DTAV+
Sbjct: 759 RGKRLTRGYLGRALPHFKPEDLGPEARGFIASGFVHGLNPVEMFFHAAAGREGLIDTAVR 818

Query: 646 TAETGYMQRRLVKSLEDLCVQYDMS 670
           T+++GYMQRRL+ +L+DL V+YD S
Sbjct: 819 TSQSGYMQRRLINALQDLRVEYDGS 843


>gi|14591328|ref|NP_143406.1| DNA-directed RNA polymerase subunit A' [Pyrococcus horikoshii OT3]
 gi|3257973|dbj|BAA30656.1| 907aa long hypothetical DNA-directed RNA polymerase subunit A'
           [Pyrococcus horikoshii OT3]
          Length = 907

 Score =  182 bits (463), Expect = 8e-43,   Method: Compositional matrix adjust.
 Identities = 100/281 (35%), Positives = 160/281 (56%), Gaps = 40/281 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIMAHR +V+P++TFR N  VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 418 DGDIVLFNRQPSLHRMSIMAHRVRVMPYKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEA 477

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE              AK+LM  ++++++PR G  +I   QD I+GGYLLT++ A+F R
Sbjct: 478 QAE--------------AKILMEVQNHIISPRYGGPIIGGIQDHISGGYLLTREGAYFTR 523

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +   +   L+    DI  + +   + +  P        +W+GK IFSL+L  +      
Sbjct: 524 EE---VEQMLMFAGVDIKELPEPDKYENGKP--------LWSGKTIFSLLLPDDLTVWYR 572

Query: 521 ANLKTKGRAYTANEEFCHR--------------DSYVILRNSELLAGSMDKSTLGSGGKA 566
             L  +     A E+                  D +V ++N +LL+G++DK   G     
Sbjct: 573 NKLCDEEEKCEALEKLIEEKLIPDPEEVRKLAYDGFVYIQNGKLLSGAIDKKAYGR-EDG 631

Query: 567 NVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            +  +++R++G + A   + +++++T + + ++GF+ GI D
Sbjct: 632 IILDLIVREYGVERARQFLDQVTKLTIWVITHKGFTTGIDD 672



 Score =  113 bits (283), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 76/269 (28%), Positives = 127/269 (47%), Gaps = 41/269 (15%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G IE  +     +++ S +++   + Y  D    PI  G++D+RMG       C TCG  
Sbjct: 9   GSIEFGILSPQEIRKMSAVEVTVPDTY--DDDGYPIEGGVMDKRMGVIDPGLRCETCGAK 66

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
             +C GHFG+I+L  PV H+G+ + +  IL+S C+   C R+ L +E+   +  KL    
Sbjct: 67  AGECPGHFGHIELARPVIHVGFAKTIHRILESTCRE--CGRIKLTDEEIEEYMKKLE--- 121

Query: 201 LSYLVRKSLKKKILETTKKVS---VCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIV 257
           L+   R  + K + E  KK     VCPHCG     +           K++  T   +   
Sbjct: 122 LAKNRRSEVNKILKEIHKKARERMVCPHCGAPQYPI-----------KFEKPTIYWELRK 170

Query: 258 EDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSD 317
           ++   EY                     + P E+    E IP +D+PLL ++ E S+P  
Sbjct: 171 DEQGNEYK------------------HRMMPTEIRDRLEKIPDKDLPLLGLHPEKSRPEW 212

Query: 318 LILTRLLVPPNCIRPSVI--SDLKSDNDV 344
           ++LT L VPP  +RPS+   + +++++D+
Sbjct: 213 MVLTVLPVPPVTVRPSITLETGIRAEDDL 241



 Score = 94.0 bits (232), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 40/57 (70%), Positives = 50/57 (87%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV NS+ SGL+P E+FFH MGGREGLVDTAV+TA++GYMQRRL+ +L+DL V YD
Sbjct: 801 KGFVVNSYKSGLSPQEYFFHAMGGREGLVDTAVRTAQSGYMQRRLINALQDLKVDYD 857



 Score = 47.4 bits (111), Expect = 0.061,   Method: Compositional matrix adjust.
 Identities = 18/44 (40%), Positives = 32/44 (72%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 63
           ++LM  ++++++PR G  +I   QD I+GGYLLT++ A+F R +
Sbjct: 482 KILMEVQNHIISPRYGGPIIGGIQDHISGGYLLTREGAYFTREE 525


>gi|14520831|ref|NP_126306.1| DNA-directed RNA polymerase subunit A' [Pyrococcus abyssi GE5]
 gi|5458047|emb|CAB49537.1| rpoA1 DNA-directed RNA polymerase, subunit A' [Pyrococcus abyssi
           GE5]
 gi|380741373|tpe|CCE70007.1| TPA: DNA-directed RNA polymerase subunit alpha [Pyrococcus abyssi
           GE5]
          Length = 907

 Score =  182 bits (463), Expect = 9e-43,   Method: Compositional matrix adjust.
 Identities = 100/281 (35%), Positives = 160/281 (56%), Gaps = 40/281 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIMAHR +V+P+RTFR N  VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 418 DGDIVLFNRQPSLHRMSIMAHRVRVMPYRTFRLNLAVCPPYNADFDGDEMNLHVPQTEEA 477

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE              A++LM  ++++++PR G  +I   QD I+GGYLLT++ A+F R
Sbjct: 478 QAE--------------ARILMEVQNHIISPRYGGPIIGGIQDHISGGYLLTREGAYFTR 523

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +   +   L+    DI  + +   + +  P        +W+GK IFSL+L  +      
Sbjct: 524 EE---VEQMLMFAGVDIKELPEPDKYENGKP--------LWSGKTIFSLLLPDDLTVWYR 572

Query: 521 ANLKTKGRAYTANEEFCHR--------------DSYVILRNSELLAGSMDKSTLGSGGKA 566
             L  +     A E+                  D +V ++N +LL+G++DK   G     
Sbjct: 573 NKLCDEPERCEALEKLIEEKLMPDPEEVRKLAYDGFVYIQNGKLLSGAIDKKAYGR-EDG 631

Query: 567 NVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            +  +++R++G + A   + +++++T + + ++GF+ GI D
Sbjct: 632 IILDLIVREYGVERARQFLDQVTKLTIWVITHKGFTTGIDD 672



 Score =  112 bits (279), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 76/269 (28%), Positives = 126/269 (46%), Gaps = 41/269 (15%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G IE  +     +++ S +++   + Y  D    PI  G++D+RMG       C TCG  
Sbjct: 9   GSIEFGILSPQEIRKMSAVEVTVPDTY--DDDGYPIEGGVMDKRMGVIDPGLRCETCGAK 66

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
             +C GHFG+I+L  PV H+G+ + +  IL+S C+   C R+ L +E+   +  KL    
Sbjct: 67  AGECPGHFGHIELARPVIHVGFAKTIHRILESTCRE--CGRIKLTDEEIEEYMKKLE--- 121

Query: 201 LSYLVRKSLKKKILETTKKVS---VCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIV 257
           L+   R  + K + E  KK     VCPHCG     +           K++  T   +   
Sbjct: 122 LAKNRRSEVNKILKEIHKKARERMVCPHCGAPQYPI-----------KFEKPTIYWELRK 170

Query: 258 EDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSD 317
           ++   EY                     + P E+    E IP +D+PLL ++ E S+P  
Sbjct: 171 DEQGNEYK------------------HRMMPTEIRDRLEKIPDKDLPLLGLHPEKSRPEW 212

Query: 318 LILTRLLVPPNCIRPSVI--SDLKSDNDV 344
           ++LT L VPP   RPS+   + +++++D+
Sbjct: 213 MVLTVLPVPPVTARPSITLETGIRAEDDL 241



 Score = 94.0 bits (232), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 40/57 (70%), Positives = 50/57 (87%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV NS+ SGL+P E+FFH MGGREGLVDTAV+TA++GYMQRRL+ +L+DL V YD
Sbjct: 801 KGFVVNSYKSGLSPQEYFFHAMGGREGLVDTAVRTAQSGYMQRRLINALQDLKVDYD 857



 Score = 47.0 bits (110), Expect = 0.071,   Method: Compositional matrix adjust.
 Identities = 18/44 (40%), Positives = 32/44 (72%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 63
           ++LM  ++++++PR G  +I   QD I+GGYLLT++ A+F R +
Sbjct: 482 RILMEVQNHIISPRYGGPIIGGIQDHISGGYLLTREGAYFTREE 525


>gi|116753355|ref|YP_842473.1| DNA-directed RNA polymerase subunit A'' [Methanosaeta thermophila PT]
 gi|116664806|gb|ABK13833.1| DNA-directed RNA polymerase, subunit A' [Methanosaeta thermophila PT]
          Length = 384

 Score =  182 bits (463), Expect = 9e-43,   Method: Compositional matrix adjust.
 Identities = 117/335 (34%), Positives = 177/335 (52%), Gaps = 55/335 (16%)

Query: 1108 EKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFV 1156
            E Y  A++EP  AVG +AAQSIGEPGTQMT++TFH+AG            + E ++   +
Sbjct: 48   EDYEHARVEPCEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVDARKI 107

Query: 1157 PDDSFILIKL--------DMDR--------IRLLHL--------------EVDIDSIRY- 1185
            P    + I+L        DM R          +LHL              E++ D++   
Sbjct: 108  PSTPTMTIRLLPEYASDRDMAREVAWAIEATSILHLGSIATDLAEMNVVIELNEDAMAQR 167

Query: 1186 ------CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGIN 1239
                    E+ R  +G       + +I+ P++ S     ++ Q+ + +  V +KGV GI 
Sbjct: 168  KITAEDVAEKLRDATGLTVDQKGNTIIMAPEEPS---YRELLQLVERIKKVTLKGVDGIK 224

Query: 1240 RAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIM 1299
            R VI +E  E    Y L  EG +L++V+   GV   +  +NN  E+ + LGIEAAR+ I+
Sbjct: 225  RVVIRKEGDE----YVLYTEGSSLKEVLEFEGVDPTRTKTNNINEICEVLGIEAARNAII 280

Query: 1300 TEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHL 1359
             E    +   G+ +D RH MLVAD+MT  G+V  I RHG++  K SVL  A+FE T +H+
Sbjct: 281  NEATETLREQGLQVDVRHIMLVADIMTCDGDVKQIGRHGVSGEKASVLARAAFEVTVNHI 340

Query: 1360 FDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
             DAA  G  D + GV+E +I+G P+ +GTG ++L+
Sbjct: 341  LDAAIRGDVDDLRGVTENVIVGQPIRLGTGDVQLV 375



 Score =  102 bits (254), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 76/237 (32%), Positives = 124/237 (52%), Gaps = 23/237 (9%)

Query: 764 GVPRIKEIINASRNISTPIITAYL--DKDTDLDYARIVKGRLERTT---LGEVCEYIEEV 818
           G+PR+ EI++A +  STP +T  L  +  +D D AR V   +E T+   LG +   + E+
Sbjct: 94  GLPRLIEIVDARKIPSTPTMTIRLLPEYASDRDMAREVAWAIEATSILHLGSIATDLAEM 153

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSK 878
            V      +I+L+ D +    +     +     E+ R  +G       + +I+ P++ S 
Sbjct: 154 NV------VIELNEDAMAQRKI-----TAEDVAEKLRDATGLTVDQKGNTIIMAPEEPS- 201

Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 938
               ++ Q+ + +  V +KGV GI R VI +E  E    Y L  EG +L++V+   GV  
Sbjct: 202 --YRELLQLVERIKKVTLKGVDGIKRVVIRKEGDE----YVLYTEGSSLKEVLEFEGVDP 255

Query: 939 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            +  +NN  E+ + LGIEAAR+ I+ E    +   G+ +D RH MLVAD+MT  G+V
Sbjct: 256 TRTKTNNINEICEVLGIEAARNAIINEATETLREQGLQVDVRHIMLVADIMTCDGDV 312


>gi|390960611|ref|YP_006424445.1| DNA-directed RNA polymerase subunit A'' [Thermococcus sp. CL1]
 gi|390518919|gb|AFL94651.1| DNA-directed RNA polymerase subunit A'' [Thermococcus sp. CL1]
          Length = 391

 Score =  182 bits (463), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 119/347 (34%), Positives = 179/347 (51%), Gaps = 60/347 (17%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG------------------ 1145
            E   ++Y RA IEP  A+G +AAQSIGEP TQMTL TFH+AG                  
Sbjct: 47   EETVKEYQRALIEPGEAIGTVAAQSIGEPSTQMTLNTFHYAGVAEINVTLGLPRIIEIVD 106

Query: 1146 --------------------------EVCEYIE----EVFVPDDSFILIK----LDMDRI 1171
                                      EV   IE    E    + S  ++     +D+D  
Sbjct: 107  ARKNPSTPIMTVYLDEKHRHDREKALEVARRIEGTTLENLARETSIDILNYEFIVDIDPE 166

Query: 1172 RLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVV 1231
            RL    +D++ I+  +E +   S    + G++ LI++PK   K   S + ++ + +    
Sbjct: 167  RLEKAGLDMERIQRKLESSFK-SAEFEIDGYT-LIMRPKKVGKL--SDLRRLAEKVKKHR 222

Query: 1232 IKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGI 1291
            +KG+ G+ + +I +E  E    Y +  EG N + V+   GV   +  +NN +E+ + LGI
Sbjct: 223  LKGLSGVGKTIIRKEGDE----YVIYTEGSNFKQVLKVPGVDPTRTRTNNIWEIAEVLGI 278

Query: 1292 EAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLAS 1351
            EAAR+ I+ EI   M   G+ +D RH MLVAD+MT  G +L I RHG+   K SVL  A+
Sbjct: 279  EAARNAIIEEIVNTMREQGLEVDVRHIMLVADMMTLDGVILPIGRHGIVGEKASVLARAA 338

Query: 1352 FENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 1398
            FE T+ HLF+AA  G+ D ++GV E +++G P+ VGTG++KL   +P
Sbjct: 339  FEITTQHLFEAAERGEVDPLNGVVENVLIGQPVPVGTGMVKLAMNLP 385



 Score =  118 bits (295), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 82/238 (34%), Positives = 132/238 (55%), Gaps = 14/238 (5%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PRI EI++A +N STPI+T YLD+    D + A  V  R+E TTL  +      + + 
Sbjct: 97  GLPRIIEIVDARKNPSTPIMTVYLDEKHRHDREKALEVARRIEGTTLENLARETS-IDIL 155

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
           +  FI+   D+D  RL    +D++ I+  +E +   S    + G++ LI++PK   K   
Sbjct: 156 NYEFIV---DIDPERLEKAGLDMERIQRKLESSFK-SAEFEIDGYT-LIMRPKKVGKL-- 208

Query: 882 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
           S + ++ + +    +KG+ G+ + +I +E  E    Y +  EG N + V+   GV   + 
Sbjct: 209 SDLRRLAEKVKKHRLKGLSGVGKTIIRKEGDE----YVIYTEGSNFKQVLKVPGVDPTRT 264

Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG 999
            +NN +E+ + LGIEAAR+ I+ EI   M   G+ +D RH MLVAD+MT  G +L  G
Sbjct: 265 RTNNIWEIAEVLGIEAARNAIIEEIVNTMREQGLEVDVRHIMLVADMMTLDGVILPIG 322


>gi|73671119|ref|YP_307134.1| DNA-directed RNA polymerase subunit A'' [Methanosarcina barkeri str.
            Fusaro]
 gi|72398281|gb|AAZ72554.1| DNA-directed RNA polymerase, subunit A' [Methanosarcina barkeri str.
            Fusaro]
          Length = 426

 Score =  182 bits (463), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 118/346 (34%), Positives = 173/346 (50%), Gaps = 62/346 (17%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIE 1152
            E   E+Y  + IEP  A G +AAQSIGEPGTQMT++TFH+AG            + E ++
Sbjct: 44   EQVMEEYRSSCIEPCDAAGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVD 103

Query: 1153 EVFVPDDSFILIKL----------DMDRIRLLHLEVDIDSIRYCIERTRGISG------- 1195
               +P    + I L          D ++ R L  E++   I +  + T  +S        
Sbjct: 104  ARKIPSTPMMTIALSKENPEDYAYDREKTRALAWEIEATKIDHIADVTTDLSQMKLIIDL 163

Query: 1196 -HLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLP-------------------------- 1228
                + G +  I + K+    FN ++  M  + P                          
Sbjct: 164  HEKAMEGRNITIDQVKE---KFNEELNVMVTISPDIDNQIIIAPGEPSYRELLQLAKSIH 220

Query: 1229 SVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKT 1288
            +V +KG++GI R V+ +E  E    Y L  EG  LR+V+   GV   + S+NN  E+Y+ 
Sbjct: 221  NVTLKGIEGIKRVVVRKEGEE----YTLYTEGSALREVLQFDGVDKTRTSTNNINEIYEV 276

Query: 1289 LGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLN 1348
            LGIEAAR+ I+ E    +   G+++D RH MLV+DLMT  GEV  I RHG++  K SV  
Sbjct: 277  LGIEAARNAIIKEATDTLREQGLTVDIRHIMLVSDLMTCDGEVKQIGRHGISGEKASVFA 336

Query: 1349 LASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
             A+FE T +HL DA   G  D + GV+E II+G P+ +GTG + L+
Sbjct: 337  RAAFEVTVNHLLDAGMRGDVDQLQGVTENIIVGQPIRMGTGDVHLI 382



 Score =  110 bits (275), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 73/238 (30%), Positives = 125/238 (52%), Gaps = 18/238 (7%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYA------RIVKGRLERTTLGEVCEYIEE 817
           G+PR+ EI++A +  STP++T  L K+   DYA      R +   +E T +  + +    
Sbjct: 94  GLPRLIEIVDARKIPSTPMMTIALSKENPEDYAYDREKTRALAWEIEATKIDHIAD---- 149

Query: 818 VFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSS 877
               D S + + +D+    +    + ID ++        +   ++    + +I+ P + S
Sbjct: 150 -VTTDLSQMKLIIDLHEKAMEGRNITIDQVKEKFNEELNVMVTISPDIDNQIIIAPGEPS 208

Query: 878 KSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVK 937
                ++ Q+ + + +V +KG++GI R V+ +E  E    Y L  EG  LR+V+   GV 
Sbjct: 209 YR---ELLQLAKSIHNVTLKGIEGIKRVVVRKEGEE----YTLYTEGSALREVLQFDGVD 261

Query: 938 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
             + S+NN  E+Y+ LGIEAAR+ I+ E    +   G+++D RH MLV+DLMT  GEV
Sbjct: 262 KTRTSTNNINEIYEVLGIEAARNAIIKEATDTLREQGLTVDIRHIMLVSDLMTCDGEV 319


>gi|88601372|ref|YP_501550.1| DNA-directed RNA polymerase, subunit A'' [Methanospirillum hungatei
            JF-1]
 gi|88186834|gb|ABD39831.1| DNA-directed RNA polymerase, subunit A' [Methanospirillum hungatei
            JF-1]
          Length = 653

 Score =  182 bits (463), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 112/341 (32%), Positives = 173/341 (50%), Gaps = 59/341 (17%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYIEEV 1154
            +Y   +IEP  AVG +AAQSIGEPGTQMT++TFH+AG              E+ +  +E 
Sbjct: 312  EYKHTRIEPCEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIMDARKEP 371

Query: 1155 FVPDDSFIL---IKLDMDRIRLLHLEV-------------DIDSIRYCIERTRGISGHLT 1198
              P  +  L      D D+ R +  ++             D+ +++  +   + +     
Sbjct: 372  STPTMTIYLREGYSTDRDKARQVSWQIEAAPLQEFGDITTDMANMQIVVHVNKAVCEKRK 431

Query: 1199 VSGHSFLILKPKD-------------------------SSKSFNSKMYQMKQLLPSVVIK 1233
            +S    L   PK                            +     ++Q+K+ + +V+++
Sbjct: 432  ISVREILETAPKKIKERRHYRDFEFETNESEGLLIFIPKDRGSYQNLFQLKEHVRNVIVQ 491

Query: 1234 GVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEA 1293
            G+  I R V+ +E  E    Y L  EG NL+DV A  GV   +  +NN  E+ + LG+EA
Sbjct: 492  GIDDIERVVVRKESGE----YILYTEGSNLKDVFAIRGVDTTRTRTNNINEISQVLGVEA 547

Query: 1294 ARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFE 1353
            AR+ I+ E    +   G+ +D RH MLVAD+M  +GEV  I RHG+A  KESVL+ A+FE
Sbjct: 548  ARNAIINEALATLSEQGIMVDVRHIMLVADMMCMEGEVKQIGRHGIAGEKESVLSRAAFE 607

Query: 1354 NTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
             T +HL DAA   + D + GV+E +I+G P+ +GTG +KL+
Sbjct: 608  VTVNHLLDAAVAHEADILCGVTENVIVGQPIQLGTGDVKLV 648



 Score =  108 bits (270), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 76/240 (31%), Positives = 121/240 (50%), Gaps = 19/240 (7%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDK--DTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A +  STP +T YL +   TD D AR V  ++E   L E  +        
Sbjct: 357 GLPRLIEIMDARKEPSTPTMTIYLREGYSTDRDKARQVSWQIEAAPLQEFGD-----ITT 411

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHL------TVSGHSFLILKPKD 875
           D + + I + +++      ++ +  I     +      H       T      LI  PKD
Sbjct: 412 DMANMQIVVHVNKAVCEKRKISVREILETAPKKIKERRHYRDFEFETNESEGLLIFIPKD 471

Query: 876 SSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYG 935
                N  ++Q+K+ + +V+++G+  I R V+ +E  E    Y L  EG NL+DV A  G
Sbjct: 472 RGSYQN--LFQLKEHVRNVIVQGIDDIERVVVRKESGE----YILYTEGSNLKDVFAIRG 525

Query: 936 VKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
           V   +  +NN  E+ + LG+EAAR+ I+ E    +   G+ +D RH MLVAD+M  +GEV
Sbjct: 526 VDTTRTRTNNINEISQVLGVEAARNAIINEALATLSEQGIMVDVRHIMLVADMMCMEGEV 585


>gi|386001094|ref|YP_005919393.1| DNA-directed RNA polymerase subunit A'' [Methanosaeta harundinacea
            6Ac]
 gi|312183605|gb|ADQ42372.1| DNA-directed RNA polymerase subunit A'' [Methanosaeta harundinacea
            6Ac]
 gi|357209150|gb|AET63770.1| DNA-directed RNA polymerase subunit A'' [Methanosaeta harundinacea
            6Ac]
          Length = 378

 Score =  182 bits (462), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 117/334 (35%), Positives = 174/334 (52%), Gaps = 57/334 (17%)

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFVPD 1158
            Y R+++EP  AVG +AAQSIGEPGTQMT++TFH+AG            + E ++   +P 
Sbjct: 50   YERSKVEPCEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVDARKIPS 109

Query: 1159 DSFILIKLD----MDR------------IRLLHL---EVDIDSIRYCI------------ 1187
               + I+LD    +DR              +LHL     D+  +   I            
Sbjct: 110  TPTMTIRLDKEYALDRDIAREVAWSIESTNILHLGSIATDLAEMNVVIDLNEEALLQRKI 169

Query: 1188 ------ER-TRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINR 1240
                  ER   G        G+  ++  P+ S +     + Q+ + + ++ +KG++GI R
Sbjct: 170  TASEVAERLAEGTKLSADQRGNQIIMTPPEPSYRD----LLQLVEKIKTISLKGIEGIKR 225

Query: 1241 AVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMT 1300
             VI +E  E    Y L  EG  L+DV+   GV   +  +NN  E+   LGIEAAR+ I+ 
Sbjct: 226  VVIRKEGDE----YVLYTEGSALKDVIQFKGVDPTRTKTNNITEIGDVLGIEAARNAIIN 281

Query: 1301 EIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLF 1360
            E    +   G+S+D RH MLVAD+MT  GEV  I RHG++  K SVL  A+FE T +H+ 
Sbjct: 282  EATDTLREQGLSVDVRHIMLVADIMTCDGEVKQIGRHGVSGEKASVLARAAFEVTVNHIL 341

Query: 1361 DAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            DAA  G  D + GV+E +I+G P+ +GTG ++L+
Sbjct: 342  DAAVRGDVDDLRGVTENVIVGQPIQLGTGDVQLV 375



 Score =  107 bits (267), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 77/237 (32%), Positives = 122/237 (51%), Gaps = 23/237 (9%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTT---LGEVCEYIEEV 818
           G+PR+ EI++A +  STP +T  LDK+   D D AR V   +E T    LG +   + E+
Sbjct: 94  GLPRLIEIVDARKIPSTPTMTIRLDKEYALDRDIAREVAWSIESTNILHLGSIATDLAEM 153

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSK 878
            V         +D++   LL  ++    +   +     +S      G+  ++  P+ S +
Sbjct: 154 NVV--------IDLNEEALLQRKITASEVAERLAEGTKLSADQ--RGNQIIMTPPEPSYR 203

Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 938
                + Q+ + + ++ +KG++GI R VI +E  E    Y L  EG  L+DV+   GV  
Sbjct: 204 D----LLQLVEKIKTISLKGIEGIKRVVIRKEGDE----YVLYTEGSALKDVIQFKGVDP 255

Query: 939 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            +  +NN  E+   LGIEAAR+ I+ E    +   G+S+D RH MLVAD+MT  GEV
Sbjct: 256 TRTKTNNITEIGDVLGIEAARNAIINEATDTLREQGLSVDVRHIMLVADIMTCDGEV 312


>gi|254169237|ref|ZP_04876071.1| DNA-directed RNA polymerase, subunit A'' [Aciduliprofundum boonei
            T469]
 gi|289596764|ref|YP_003483460.1| DNA-directed RNA polymerase, subunit A'' [Aciduliprofundum boonei
            T469]
 gi|197621833|gb|EDY34414.1| DNA-directed RNA polymerase, subunit A'' [Aciduliprofundum boonei
            T469]
 gi|289534551|gb|ADD08898.1| DNA-directed RNA polymerase, subunit A'' [Aciduliprofundum boonei
            T469]
          Length = 516

 Score =  182 bits (462), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 119/349 (34%), Positives = 183/349 (52%), Gaps = 58/349 (16%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIE 1152
            E   E Y + +++P  AVG +AAQSIGEPGTQMTL+TFH+AG            + E ++
Sbjct: 173  ERTVEVYKKREVDPYEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEMNVTLGLPRLIEIVD 232

Query: 1153 EVFVPDDSFILIKL------DMDRIRLLHLEV------DIDSIRYCIE------------ 1188
               +P    + I L      D D+++ +  ++      DI ++   I             
Sbjct: 233  ARSMPSTPVMQIHLKEGVREDEDKVKEVAKKIESTNIIDIGNVVTNIADMSVVIVPDKKK 292

Query: 1189 -RTRGISGHLTVSGHSFLILK---------------PKDSSKSFNSKMYQMKQLLPSVVI 1232
               RGI     V   S L L+               P+ S K    K+YQ+ + + S+ +
Sbjct: 293  MENRGIKKEDIVESLSKLKLQKLTVEIEDDRIKLKLPEPSYK----KLYQLTESVKSLTL 348

Query: 1233 KGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIE 1292
            +G++GI+RA++ +   +   ++ +  +G NL+DV+    V G +  +NN  E+   LGIE
Sbjct: 349  RGIKGISRAIVRKS--QDNREWVIYTQGSNLKDVLDIEEVDGARTRTNNIIEIADVLGIE 406

Query: 1293 AARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASF 1352
            AAR+ IM E    ++  G+++D RH MLVAD+MT  G V  I RHG+A  KESVL  A+F
Sbjct: 407  AARNAIMEEAINTLQQQGLNVDMRHIMLVADIMTYNGSVEAIGRHGIAGEKESVLARAAF 466

Query: 1353 ENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSE 1401
            E T+ HL  A   G+ D + GV+E II+G P+ +GTG + L+   P+ E
Sbjct: 467  EITAKHLLTAGVLGEEDKLRGVAENIIVGQPVTLGTGAVTLIYK-PKKE 514



 Score = 97.8 bits (242), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 75/252 (29%), Positives = 129/252 (51%), Gaps = 41/252 (16%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTL---GEVCEYIEE- 817
           G+PR+ EI++A    STP++  +L +    D D  + V  ++E T +   G V   I + 
Sbjct: 223 GLPRLIEIVDARSMPSTPVMQIHLKEGVREDEDKVKEVAKKIESTNIIDIGNVVTNIADM 282

Query: 818 --VFVPDDSFI----LIKLD----MDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHS 867
             V VPD   +    + K D    + +++L  L V+I+  R  ++               
Sbjct: 283 SVVIVPDKKKMENRGIKKEDIVESLSKLKLQKLTVEIEDDRIKLKL-------------- 328

Query: 868 FLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927
                P+ S K    K+YQ+ + + S+ ++G++GI+RA++ +   +   ++ +  +G NL
Sbjct: 329 -----PEPSYK----KLYQLTESVKSLTLRGIKGISRAIVRKS--QDNREWVIYTQGSNL 377

Query: 928 RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 987
           +DV+    V G +  +NN  E+   LGIEAAR+ IM E    ++  G+++D RH MLVAD
Sbjct: 378 KDVLDIEEVDGARTRTNNIIEIADVLGIEAARNAIMEEAINTLQQQGLNVDMRHIMLVAD 437

Query: 988 LMTSKGEVLGNG 999
           +MT  G V   G
Sbjct: 438 IMTYNGSVEAIG 449


>gi|330507366|ref|YP_004383794.1| DNA-directed RNA polymerase subunit A' [Methanosaeta concilii GP6]
 gi|328928174|gb|AEB67976.1| DNA-directed RNA polymerase, subunit A' [Methanosaeta concilii GP6]
          Length = 379

 Score =  182 bits (462), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 117/337 (34%), Positives = 175/337 (51%), Gaps = 55/337 (16%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEV 1154
             +  Y  +++EP  AVG +AAQSIGEPGTQMT++TFH+AG            + E ++  
Sbjct: 46   VKADYEHSRVEPCEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVDAR 105

Query: 1155 FVPDDSFILIKL------DMDRIR----------LLHL---EVDIDSIRYCIERTRGISG 1195
             +P    + IKL      D D  R          +LHL     D+  +   IE   G   
Sbjct: 106  KIPSTPTMTIKLTPEYAHDRDLAREVAWAIESSSILHLGSIATDLAEMNVIIELNPGALE 165

Query: 1196 HLTVSG------------------HSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQG 1237
               ++                    + L++ P++ S     ++ Q+ + +  + +KGV+G
Sbjct: 166  QRKITAEEVAAKLKEETGLDVDQKENLLVMAPEEPS---YRELLQLVEKIKKLSLKGVEG 222

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            I R VI +E  E    Y L  EG +L+ VM   GV   +  +NN  E+ + LGIEAAR+ 
Sbjct: 223  IKRVVIRKEGDE----YILYTEGSSLKKVMQFEGVDPTRIKTNNISEIGEVLGIEAARNA 278

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ E    +   G+S+D RH MLVAD+MT  GE+  I RHG++  K SVL  A+FE T +
Sbjct: 279  IINEATDTLREQGLSVDVRHIMLVADIMTVDGELKQIGRHGVSGEKASVLARAAFEVTVN 338

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            H+ DAA  G  D + GV+E +I+G P+ +GTG +KL+
Sbjct: 339  HILDAAVRGDVDDLKGVTENVIVGQPIQLGTGDVKLV 375



 Score = 95.9 bits (237), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 72/237 (30%), Positives = 123/237 (51%), Gaps = 23/237 (9%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTT---LGEVCEYIEEV 818
           G+PR+ EI++A +  STP +T  L  +   D D AR V   +E ++   LG +   + E+
Sbjct: 94  GLPRLIEIVDARKIPSTPTMTIKLTPEYAHDRDLAREVAWAIESSSILHLGSIATDLAEM 153

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSK 878
            V         ++++   L   ++  + +   ++   G+         + L++ P++ S 
Sbjct: 154 NVI--------IELNPGALEQRKITAEEVAAKLKEETGLD---VDQKENLLVMAPEEPS- 201

Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 938
               ++ Q+ + +  + +KGV+GI R VI +E  E    Y L  EG +L+ VM   GV  
Sbjct: 202 --YRELLQLVEKIKKLSLKGVEGIKRVVIRKEGDE----YILYTEGSSLKKVMQFEGVDP 255

Query: 939 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            +  +NN  E+ + LGIEAAR+ I+ E    +   G+S+D RH MLVAD+MT  GE+
Sbjct: 256 TRIKTNNISEIGEVLGIEAARNAIINEATDTLREQGLSVDVRHIMLVADIMTVDGEL 312


>gi|305663642|ref|YP_003859930.1| DNA-directed RNA polymerase, subunit A' [Ignisphaera aggregans DSM
           17230]
 gi|304378211|gb|ADM28050.1| DNA-directed RNA polymerase, subunit A' [Ignisphaera aggregans DSM
           17230]
          Length = 884

 Score =  182 bits (461), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 99/269 (36%), Positives = 152/269 (56%), Gaps = 29/269 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+ +FNRQPSLH++S+M H  KVLP +TFR +  VC PYNADFDGDEMN+H+PQTE+A
Sbjct: 417 DGDIAIFNRQPSLHRMSMMGHIIKVLPGKTFRLHLAVCPPYNADFDGDEMNLHIPQTEDA 476

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE               ++L+  +++++TPR G ++I A QD+I+G Y+LT K     +
Sbjct: 477 RAE--------------TRLLLKVQNHILTPRYGGIIIGAIQDYISGAYILTIKTTLLKK 522

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              + + S          G++K        P +      +WTGKQI S+ L  + +    
Sbjct: 523 EDVIDLLSA--------AGVVKELP----EPAIL-SPKRLWTGKQIISMFLPEDFNYHGK 569

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           AN+ + G     + E C  DSYV++R  +LL G +DK T+G+  + ++ Y L +++G + 
Sbjct: 570 ANI-SSGPLKCEDIE-CFWDSYVVVRKGKLLMGVLDKKTIGAEQQDSLLYWLAKEYGVEY 627

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVT 609
               M  + RM    L  RGF++ + DV 
Sbjct: 628 VALFMDHVFRMFIRVLEKRGFTLRLDDVA 656



 Score =  119 bits (299), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 79/261 (30%), Positives = 128/261 (49%), Gaps = 47/261 (18%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D +++ S +QIVS   Y +D   TPI   ++D R+G  +    C  CG  +  C GHFG+
Sbjct: 19  DEIRRMSVVQIVSPETYDED--GTPISGSVMDPRLGAIEPGQTCPICGNTMKACPGHFGH 76

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGF-----RAKLRNPALSYLV 205
           I+L LPV ++ Y + + ++L++ C N  C R+ +   +   +     + K R P L+   
Sbjct: 77  IELALPVINVLYVKHIYDLLRATCAN--CGRIKVSPSEIEKYMVYLRKLKARYPYLAKRF 134

Query: 206 RKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYN 265
            + +KKK +    KV+VCPHCG                ++ K + +K    VE       
Sbjct: 135 SEFIKKKAI----KVTVCPHCGA---------------KQPKIKLEKPTTFVEQ------ 169

Query: 266 EAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLV 325
                      H++   +  LNPL V    E IP EDI LL  +   S+P  ++ T L V
Sbjct: 170 -----------HEESKEVVRLNPLTVRSRLERIPNEDIELLGYDPRDSRPEWMVFTVLPV 218

Query: 326 PPNCIRPSVI--SDLKSDNDV 344
           PP  IRPS++  + ++S++D+
Sbjct: 219 PPTSIRPSILIETGIRSEDDL 239



 Score = 97.1 bits (240), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 46/83 (55%), Positives = 60/83 (72%), Gaps = 1/83 (1%)

Query: 587 RLSRMTSFYLMNRGFSIGIGDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVK 645
           R  R+   Y+     S G  D+ P  +GFV NSF+SGL+PTE F H  GGREGLVDTAV+
Sbjct: 757 RGERIWRGYMGRPISSYGQNDLGPLARGFVVNSFYSGLSPTEMFMHAAGGREGLVDTAVR 816

Query: 646 TAETGYMQRRLVKSLEDLCVQYD 668
           T+++GYMQRRL+ +L+DL V+YD
Sbjct: 817 TSQSGYMQRRLINALQDLYVEYD 839


>gi|223478217|ref|YP_002582841.1| DNA-directed RNA polymerase subunit A' [Thermococcus sp. AM4]
 gi|214033443|gb|EEB74270.1| DNA-directed RNA polymerase subunit A' [Thermococcus sp. AM4]
          Length = 905

 Score =  182 bits (461), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 99/282 (35%), Positives = 158/282 (56%), Gaps = 40/282 (14%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
            D D+VLFNRQPSLH++SIMAHR +V+P++TFR N  VC PYNADFDGDEMN+H+PQTEE
Sbjct: 417 EDGDIVLFNRQPSLHRMSIMAHRVRVMPYKTFRLNLPVCPPYNADFDGDEMNLHVPQTEE 476

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           A+AE              AK+LM  ++++++PR G  LIA  QD I+GGYLLT++ A+F 
Sbjct: 477 AQAE--------------AKILMEVQNHIISPRYGGPLIAGIQDHISGGYLLTREGAYFT 522

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           R++  ++ +    D  ++             P        +W+GK IFSL+L  +     
Sbjct: 523 RSEVEQMLTFAGVDVDELP-----------EPDKVENGVELWSGKTIFSLLLPDDLTIWY 571

Query: 520 NANLKTKGRAYTANEEFCHR--------------DSYVILRNSELLAGSMDKSTLGSGGK 565
              L  +     A E+                  D +V ++N +LL+G++DK   G    
Sbjct: 572 RNKLCDEPERCEALEKLIEEKLVPDPEEVRKLAYDGFVYIQNGKLLSGAIDKKAYGR-ED 630

Query: 566 ANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
             +  +++R++G + A   + +++++T + + ++GF+  I D
Sbjct: 631 GKLLDLIVREYGVERARQFLDQVTKLTIWVITHKGFTTAIDD 672



 Score =  112 bits (279), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 75/266 (28%), Positives = 124/266 (46%), Gaps = 35/266 (13%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G IE  +     +++ S  +I   + Y  D    PI  GL+D+R+G       C TCG  
Sbjct: 9   GSIEFGILSPQEIRKMSAAEITVPDTY--DDDGYPIEGGLMDKRLGVIDPGLRCETCGAR 66

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
             +C GHFG+I+L  PV H+G+ + +  +L+S C+   C R+ L +E+   +  K     
Sbjct: 67  AGECPGHFGHIELARPVVHVGFAKTIQRVLESTCRE--CGRIKLTDEEIEEYMKKFEVIG 124

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDL 260
                +  L K+I +  K+  VCPHCG     +           K++  T   +   ++ 
Sbjct: 125 DRKKDKDRLIKEIHKKAKERMVCPHCGAPQFPI-----------KFERPTIYYELRRDEE 173

Query: 261 LAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
             EY                     + P E+    E IP +D+PLL ++ E S+P  +IL
Sbjct: 174 GNEYK------------------HRMMPSEIRDRLERIPDKDLPLLGLHPEKSRPEWMIL 215

Query: 321 TRLLVPPNCIRPSVI--SDLKSDNDV 344
           T L VPP  +RPS+   S +++++D+
Sbjct: 216 TVLPVPPVTMRPSITLESGIRAEDDL 241



 Score = 95.1 bits (235), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 41/58 (70%), Positives = 50/58 (86%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV NS+ SGLTP E+FFH MGGREGLVDTAV+TA++GYMQRRL+ +L+DL V YD
Sbjct: 800 ARGFVVNSYKSGLTPQEYFFHAMGGREGLVDTAVRTAQSGYMQRRLINALQDLKVDYD 857



 Score = 50.8 bits (120), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 31/127 (24%), Positives = 63/127 (49%), Gaps = 24/127 (18%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFF 79
           ++LM  ++++++PR G  LIA  QD I+GGYLLT++ A+F R++  ++ +         F
Sbjct: 482 KILMEVQNHIISPRYGGPLIAGIQDHISGGYLLTREGAYFTRSEVEQMLT---------F 532

Query: 80  RGLIEGTVTKEDRVQQ---------------QSHIQIVSKNLYCQDPQRTPIPHGLLDRR 124
            G+    + + D+V+                   + I  +N  C +P+R      L++ +
Sbjct: 533 AGVDVDELPEPDKVENGVELWSGKTIFSLLLPDDLTIWYRNKLCDEPERCEALEKLIEEK 592

Query: 125 MGTNQKE 131
           +  + +E
Sbjct: 593 LVPDPEE 599


>gi|312136874|ref|YP_004004211.1| DNA-directed RNA polymerase, subunit a' [Methanothermus fervidus DSM
            2088]
 gi|311224593|gb|ADP77449.1| DNA-directed RNA polymerase, subunit A' [Methanothermus fervidus DSM
            2088]
          Length = 385

 Score =  182 bits (461), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 115/341 (33%), Positives = 188/341 (55%), Gaps = 59/341 (17%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCE 1149
            E  +E+Y  AQ+E   AVG +AAQSIGEPGTQMT++TFH+AG              E+ +
Sbjct: 45   EKTKERYKNAQVEEGEAVGTVAAQSIGEPGTQMTMRTFHYAGVAEVNVTLGLPRLIEIVD 104

Query: 1150 YIEEVFVP------------DDSFI---------------LIKLDMDRIRL-LHLEVDID 1181
              +++  P            D+ F+               L    +D I + ++ E+D +
Sbjct: 105  ARKKISTPIMTIYFEDDKKNDEEFVKNFSNNIIRTNLEDVLKNFSVDYIEMCVNAEIDEE 164

Query: 1182 SIR-------YCIERTRGISGHLTVSGHSFLILKPKDSS-KSFNSKMYQMKQLLPSVVIK 1233
             I+         +E+ +     + ++G+  L  KP+ ++ +S      ++++L  S    
Sbjct: 165  KIKDRGLDYKKIMEKIKKTFKDVEINGNK-LKFKPRQATIRSLRLLADKVRKLHVS---- 219

Query: 1234 GVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEA 1293
            G++ I +AVI +E+ E V    ++ EG NL  ++   GV   + ++N+ +E+ K LGIEA
Sbjct: 220  GIKDITKAVIRKEEDEFV----VVTEGSNLSKILKMDGVDKTRTTTNDIHEIEKVLGIEA 275

Query: 1294 ARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFE 1353
            AR+ I+ E K  +E  G+++D RH MLVADLMTS G +  I RHG++  K SVL  A+FE
Sbjct: 276  ARNAIIREAKNTLEEQGLTVDIRHIMLVADLMTSDGTIKPIGRHGVSGEKASVLARAAFE 335

Query: 1354 NTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
             TS HL  A+  G+ D ++G++E +I+G P+ +GTG IK++
Sbjct: 336  ETSKHLLQASMRGEKDRLAGITENVIVGQPIPLGTGSIKVV 376



 Score =  107 bits (266), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 75/235 (31%), Positives = 131/235 (55%), Gaps = 19/235 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYL--DKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A + ISTPI+T Y   DK  D ++ +     + RT L +V +     F  
Sbjct: 95  GLPRLIEIVDARKKISTPIMTIYFEDDKKNDEEFVKNFSNNIIRTNLEDVLKN----FSV 150

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSS-KSF 880
           D   + +  ++D  ++    +D   I   +E+ +     + ++G+  L  KP+ ++ +S 
Sbjct: 151 DYIEMCVNAEIDEEKIKDRGLDYKKI---MEKIKKTFKDVEINGNK-LKFKPRQATIRSL 206

Query: 881 NSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
                ++++L  S    G++ I +AVI +E+ E V    ++ EG NL  ++   GV   +
Sbjct: 207 RLLADKVRKLHVS----GIKDITKAVIRKEEDEFV----VVTEGSNLSKILKMDGVDKTR 258

Query: 941 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            ++N+ +E+ K LGIEAAR+ I+ E K  +E  G+++D RH MLVADLMTS G +
Sbjct: 259 TTTNDIHEIEKVLGIEAARNAIIREAKNTLEEQGLTVDIRHIMLVADLMTSDGTI 313


>gi|336476454|ref|YP_004615595.1| DNA-directed RNA polymerase subunit A'' [Methanosalsum zhilinae DSM
            4017]
 gi|335929835|gb|AEH60376.1| DNA-directed RNA polymerase, subunit A'' [Methanosalsum zhilinae DSM
            4017]
          Length = 385

 Score =  181 bits (460), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 116/342 (33%), Positives = 174/342 (50%), Gaps = 58/342 (16%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIE 1152
            E   E Y  A +EP  AVG ++AQSIGEPGTQMT++TFH+AG            + E ++
Sbjct: 44   ERLLENYDYACVEPCEAVGVVSAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVD 103

Query: 1153 EVFVPDDSFILIKL------DMDRIR---------------------------------- 1172
                P    + I L      D D+ R                                  
Sbjct: 104  ARKEPSTPMMTIALEQEYATDRDKARKLAWDIQSTHIEHLADVTTDMANMQLVIDLHEKT 163

Query: 1173 LLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVI 1232
            ++H E++I+ I   +    G++  +     + +I+KPK+ S     ++ Q+ + +  + +
Sbjct: 164  MIHREINIEDIADRLRDGLGVNVQIPEVPDNQIIVKPKEPSY---RELLQLAKKVHGITL 220

Query: 1233 KGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIE 1292
            KG++GI R VI +E  E    Y L  EG  L+DV+   GV   +  +NN  E+Y   G+E
Sbjct: 221  KGIEGIKRVVIRKEGDE----YTLYTEGSMLKDVIKIEGVDASRIYTNNIGEIYSVFGVE 276

Query: 1293 AARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASF 1352
            AAR+ I+ E    +   G+++D RH MLVAD+MT  GEV  I RHG++  K SV   A+F
Sbjct: 277  AARNAIIHEASETLREQGLTVDDRHIMLVADIMTCDGEVKQIGRHGISGEKASVFARAAF 336

Query: 1353 ENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            E T +HL DA   G  D +SGV+E II+G P+ +GTG + L+
Sbjct: 337  EVTVNHLLDAGMRGDIDKLSGVTENIIVGQPIKLGTGNVHLV 378



 Score =  117 bits (294), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 75/234 (32%), Positives = 133/234 (56%), Gaps = 14/234 (5%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A +  STP++T  L+++  TD D AR +   ++ T +    E++ +V   
Sbjct: 94  GLPRLIEIVDARKEPSTPMMTIALEQEYATDRDKARKLAWDIQSTHI----EHLADV-TT 148

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
           D + + + +D+    ++H E++I+ I   +    G++  +     + +I+KPK+ S    
Sbjct: 149 DMANMQLVIDLHEKTMIHREINIEDIADRLRDGLGVNVQIPEVPDNQIIVKPKEPSYR-- 206

Query: 882 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
            ++ Q+ + +  + +KG++GI R VI +E  E    Y L  EG  L+DV+   GV   + 
Sbjct: 207 -ELLQLAKKVHGITLKGIEGIKRVVIRKEGDE----YTLYTEGSMLKDVIKIEGVDASRI 261

Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            +NN  E+Y   G+EAAR+ I+ E    +   G+++D RH MLVAD+MT  GEV
Sbjct: 262 YTNNIGEIYSVFGVEAARNAIIHEASETLREQGLTVDDRHIMLVADIMTCDGEV 315


>gi|212223365|ref|YP_002306601.1| DNA-directed RNA polymerase subunit A'' [Thermococcus onnurineus NA1]
 gi|226699349|sp|B6YT17.1|RPOA2_THEON RecName: Full=DNA-directed RNA polymerase subunit A''
 gi|212008322|gb|ACJ15704.1| DNA-directed RNA polymerase, subunit A'' [Thermococcus onnurineus
            NA1]
          Length = 391

 Score =  181 bits (460), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 115/346 (33%), Positives = 180/346 (52%), Gaps = 58/346 (16%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIE 1152
            E   ++Y  + +EP  A+G +AAQSIGEP TQMTL TFH+AG            + E ++
Sbjct: 47   EETVKEYQNSLVEPGEAIGTVAAQSIGEPSTQMTLNTFHYAGVAEINVTLGLPRIIEIVD 106

Query: 1153 EVFVPDDSFILIKLD----MDRIRLLH----------------LEVDIDSIRYCIE---- 1188
                P    + + LD     DR + L                 + +DI +  + +E    
Sbjct: 107  ARKNPSTPIMTVYLDEKHRYDREKALEVARRIEGTTLENLAREMSIDILNFEFIVEIDPE 166

Query: 1189 --RTRGI--------------SGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVI 1232
                 G+              S    V G++ LI++PK  +K   S + ++ + +    +
Sbjct: 167  RLEKSGLDMEKIQKKLESSFKSAEFEVDGYT-LIMRPKKVTKL--SDLRRLSEKVKKHRL 223

Query: 1233 KGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIE 1292
            KG+ G+ + +I +E  E    Y +  EG N + ++   GV   +  +NN +E+ + LGIE
Sbjct: 224  KGLSGVGKTIIRKEGDE----YVIYTEGSNFKQILKVPGVDPTRTRTNNIHEIAEVLGIE 279

Query: 1293 AARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASF 1352
            AAR+ I+ EI   M + G+ +D RH MLVAD+MT  G +L I RHG+   K SVL  A+F
Sbjct: 280  AARNAIIEEIVNTMRDQGLEVDVRHIMLVADMMTLDGVILPIGRHGIVGEKASVLARAAF 339

Query: 1353 ENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 1398
            E T+ HLF+AA  G+TD ++GV E +++G P+ VGTG++KL   +P
Sbjct: 340  EITTQHLFEAAERGETDPLNGVVENVLIGQPVPVGTGIVKLAMNLP 385



 Score =  117 bits (293), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 81/238 (34%), Positives = 135/238 (56%), Gaps = 14/238 (5%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PRI EI++A +N STPI+T YLD+    D + A  V  R+E TTL  +   +  + + 
Sbjct: 97  GLPRIIEIVDARKNPSTPIMTVYLDEKHRYDREKALEVARRIEGTTLENLAREMS-IDIL 155

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
           +  FI+   ++D  RL    +D++ I+  +E +   S    V G++ LI++PK  +K   
Sbjct: 156 NFEFIV---EIDPERLEKSGLDMEKIQKKLESSFK-SAEFEVDGYT-LIMRPKKVTKL-- 208

Query: 882 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
           S + ++ + +    +KG+ G+ + +I +E  E    Y +  EG N + ++   GV   + 
Sbjct: 209 SDLRRLSEKVKKHRLKGLSGVGKTIIRKEGDE----YVIYTEGSNFKQILKVPGVDPTRT 264

Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG 999
            +NN +E+ + LGIEAAR+ I+ EI   M + G+ +D RH MLVAD+MT  G +L  G
Sbjct: 265 RTNNIHEIAEVLGIEAARNAIIEEIVNTMRDQGLEVDVRHIMLVADMMTLDGVILPIG 322



 Score = 43.9 bits (102), Expect = 0.68,   Method: Compositional matrix adjust.
 Identities = 18/39 (46%), Positives = 29/39 (74%)

Query: 671 FDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 709
           F+AA  G+TD ++GV E +++G P+ VGTG++KL   +P
Sbjct: 347 FEAAERGETDPLNGVVENVLIGQPVPVGTGIVKLAMNLP 385


>gi|327401231|ref|YP_004342070.1| DNA-directed RNA polymerase subunit A'' [Archaeoglobus veneficus
            SNP6]
 gi|327316739|gb|AEA47355.1| DNA-directed RNA polymerase subunit A'' [Archaeoglobus veneficus
            SNP6]
          Length = 376

 Score =  181 bits (460), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 118/368 (32%), Positives = 181/368 (49%), Gaps = 77/368 (20%)

Query: 1096 PFPSACKAE--------------------ACREKYVRAQIEPATAVGALAAQSIGEPGTQ 1135
            P PS+ KAE                     C + Y+   +EP  A G +AAQSIGEPGTQ
Sbjct: 13   PLPSSVKAELKAELEKLGVNKTTARKIVERCYQAYLANLMEPGEAAGIVAAQSIGEPGTQ 72

Query: 1136 MTLKTFHFAG--------------------------------------------EVCEYI 1151
            MT++TFH+AG                                            EV   I
Sbjct: 73   MTMRTFHYAGVAEIDVTLGLPRLIEILDVRKNPSTPMMTIRLTEEYAKDRNKAREVANRI 132

Query: 1152 EEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTR-----GISGHLTVSGHSFLI 1206
            E  ++ D + I   +   RI +   E  ++  +  +E  +     G+   +       +I
Sbjct: 133  EATYILDIADIATDIRHMRIIISPDEKALERKQLTLEEVKKRLEKGLKTEVIEEDGRLII 192

Query: 1207 LKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDV 1266
               + S K+      ++K+L    V+ G++ I R +I +ED E    Y L  EG NL+ V
Sbjct: 193  PITEPSYKALMDTFDKLKKL----VLAGIKEIRRVIIRKEDDE----YVLYTEGSNLKKV 244

Query: 1267 MATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMT 1326
            M   GV   +  +N+ YE+Y+ LGIEAAR+ ++ E    +E  G+ ++ RH MLVAD+MT
Sbjct: 245  MKIKGVDPTRTLTNDIYEIYEVLGIEAARNAVIREAISTLEEQGLEVNVRHIMLVADVMT 304

Query: 1327 SKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNV 1386
            + GE+  I RHG+A  K+S+L  A+FE T ++L DAA  G+ D +SG++E II+G P+ +
Sbjct: 305  ADGELKQIGRHGVAGEKQSILARAAFEMTVNNLLDAAVRGEIDRLSGITENIIVGQPIKL 364

Query: 1387 GTGLIKLL 1394
            GTG ++L+
Sbjct: 365  GTGDVELI 372



 Score =  107 bits (267), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 72/234 (30%), Positives = 126/234 (53%), Gaps = 17/234 (7%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++  +N STP++T  L ++   D + AR V  R+E T + ++ +        
Sbjct: 91  GLPRLIEILDVRKNPSTPMMTIRLTEEYAKDRNKAREVANRIEATYILDIAD-----IAT 145

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
           D   + I +  D   L   ++ ++ ++  +E+  G+   +       +I   + S K+  
Sbjct: 146 DIRHMRIIISPDEKALERKQLTLEEVKKRLEK--GLKTEVIEEDGRLIIPITEPSYKALM 203

Query: 882 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
               ++K+L    V+ G++ I R +I +ED E    Y L  EG NL+ VM   GV   + 
Sbjct: 204 DTFDKLKKL----VLAGIKEIRRVIIRKEDDE----YVLYTEGSNLKKVMKIKGVDPTRT 255

Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            +N+ YE+Y+ LGIEAAR+ ++ E    +E  G+ ++ RH MLVAD+MT+ GE+
Sbjct: 256 LTNDIYEIYEVLGIEAARNAVIREAISTLEEQGLEVNVRHIMLVADVMTADGEL 309


>gi|389852852|ref|YP_006355086.1| DNA-directed RNA polymerase subunit A' [Pyrococcus sp. ST04]
 gi|388250158|gb|AFK23011.1| DNA-directed RNA polymerase subunit A' [Pyrococcus sp. ST04]
          Length = 907

 Score =  181 bits (459), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 99/281 (35%), Positives = 160/281 (56%), Gaps = 40/281 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIMAHR +V+P++TFR N  VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 418 DGDIVLFNRQPSLHRMSIMAHRVRVMPYKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEA 477

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE              A++LM  ++++++PR G  +I   QD I+GGYLLT++ A+F R
Sbjct: 478 QAE--------------ARILMEVQNHIISPRYGGPIIGGIQDHISGGYLLTREGAYFTR 523

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +   +   L+    DI  + +   + +  P        +W+GK IFSL+L  +      
Sbjct: 524 EE---VEQMLMFAGVDIKELPEPDKYENGKP--------LWSGKTIFSLLLPDDLTVWYR 572

Query: 521 ANLKTKGRAYTANEEFCHR--------------DSYVILRNSELLAGSMDKSTLGSGGKA 566
             L  +     A E+                  D +V ++N +LL+G++DK   G     
Sbjct: 573 NKLCDEPERCEALEKLIEEKLIPDPEEVRKLAYDGFVYIQNGKLLSGAIDKKAYGR-EDG 631

Query: 567 NVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            +  +++R++G + A   + +++++T + + ++GF+ GI D
Sbjct: 632 IILDLIVREYGIERARQFLDQVTKLTIWVITHKGFTTGIDD 672



 Score =  115 bits (287), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 77/269 (28%), Positives = 127/269 (47%), Gaps = 41/269 (15%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G IE  +     +++ S +++   + Y  D    PI  G++D+RMG       C TCG  
Sbjct: 9   GSIEFGILSPQEIRKMSAVEVTVPDTY--DDDGYPIEGGVMDKRMGVIDPGLRCETCGAR 66

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
             +C GHFG+I+L  PV H+G+ + +  +L+S C+   C R+ L +E+   +  KL    
Sbjct: 67  AGECPGHFGHIELARPVIHVGFAKTIHRVLESTCRE--CGRIKLTDEEIEEYMKKLE--- 121

Query: 201 LSYLVRKSLKKKILETTKKVS---VCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIV 257
           L+   R  + K + E  KK     VCPHCG     +           K++  T   +   
Sbjct: 122 LAKNRRSEVNKILKEIHKKARERMVCPHCGAPQYPI-----------KFEKPTIYWELRK 170

Query: 258 EDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSD 317
           ++   EY                     + P EV    E IP ED+PLL ++ E S+P  
Sbjct: 171 DEQGNEYK------------------HRMMPTEVRDRLEKIPDEDLPLLGLHPEKSRPEW 212

Query: 318 LILTRLLVPPNCIRPSVI--SDLKSDNDV 344
           ++LT L VPP  +RPS+   + +++++D+
Sbjct: 213 MVLTVLPVPPVTVRPSITLETGIRAEDDL 241



 Score = 94.0 bits (232), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 40/57 (70%), Positives = 50/57 (87%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV NS+ SGL+P E+FFH MGGREGLVDTAV+TA++GYMQRRL+ +L+DL V YD
Sbjct: 801 RGFVVNSYKSGLSPQEYFFHAMGGREGLVDTAVRTAQSGYMQRRLINALQDLKVDYD 857



 Score = 47.4 bits (111), Expect = 0.068,   Method: Compositional matrix adjust.
 Identities = 18/44 (40%), Positives = 32/44 (72%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 63
           ++LM  ++++++PR G  +I   QD I+GGYLLT++ A+F R +
Sbjct: 482 RILMEVQNHIISPRYGGPIIGGIQDHISGGYLLTREGAYFTREE 525


>gi|375083052|ref|ZP_09730090.1| DNA-directed RNA polymerase subunit A' [Thermococcus litoralis DSM
           5473]
 gi|374742288|gb|EHR78688.1| DNA-directed RNA polymerase subunit A' [Thermococcus litoralis DSM
           5473]
          Length = 905

 Score =  181 bits (459), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 100/283 (35%), Positives = 159/283 (56%), Gaps = 44/283 (15%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIMAHR +V+P++TFR N  VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 418 DGDIVLFNRQPSLHRMSIMAHRVRVMPYKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEA 477

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE              AK+LM  ++++++PR G  +I   QD I+GGYLLT++ A+F +
Sbjct: 478 QAE--------------AKILMEVQNHILSPRYGGPIIGGIQDHISGGYLLTREGAYFTK 523

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLIL--------- 511
            +  ++      D  ++             P         W+GK IFSL+L         
Sbjct: 524 YEVEQMLMFAGVDVKELP-----------KPDKVENGVEYWSGKTIFSLLLPDDLTIWYR 572

Query: 512 -----KPNRDCPVNANLKTKGRAYTANEEF--CHRDSYVILRNSELLAGSMDKSTLGSGG 564
                 P++  P+   ++ K     + EE      D +V +RN +LL+G++DK   G   
Sbjct: 573 NKLCDDPSQCEPIEKLIEEK--LVPSEEEIREVATDGFVYIRNGKLLSGAIDKKAYGR-E 629

Query: 565 KANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
              +  I++R++G + A   + +++++  + + ++GF+ GI D
Sbjct: 630 DGKILDIIVREYGVERARQFLDQVTKLAIWVITHKGFTTGIDD 672



 Score =  119 bits (298), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 75/266 (28%), Positives = 128/266 (48%), Gaps = 35/266 (13%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G IE  +     +++ S  +I   + Y +D    PI  GL+DRR+G       C TCG N
Sbjct: 9   GSIEFGILSPQEIRKMSAAEITVPDTYSEDG--YPIDGGLMDRRLGVIDPNLRCETCGAN 66

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
             +C GHFG+I+L  PV H+G+ + +  IL+S C+   C R+ L +E+   +  K     
Sbjct: 67  YKECPGHFGHIELARPVIHVGFAKTIYRILESTCRE--CGRIRLTDEEIEEYMTKFSVNE 124

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDL 260
                  +L  +I +  ++  VCPHCG                 +Y+ + ++     E  
Sbjct: 125 ARKSEIDALVTEIYKKARERMVCPHCGA---------------PQYQIKFERPTIYWE-- 167

Query: 261 LAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
                  ++ + E   +K       + P E+    E IP +D+PLL ++ E S+P  ++L
Sbjct: 168 -------IRRDEEGNEYK-----HRMMPSEIRDRLEKIPDKDLPLLGLDPEKSRPEWMVL 215

Query: 321 TRLLVPPNCIRPSVI--SDLKSDNDV 344
           T L VPP  +RPS+   S +++++D+
Sbjct: 216 TVLPVPPVTVRPSITLESGIRAEDDL 241



 Score = 94.7 bits (234), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 40/58 (68%), Positives = 50/58 (86%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GF+ NS+ SGLTP E+FFH MGGREGLVDTAV+TA++GYMQRRL+ +L+DL V YD
Sbjct: 800 AKGFIVNSYKSGLTPQEYFFHAMGGREGLVDTAVRTAQSGYMQRRLINALQDLKVDYD 857



 Score = 47.0 bits (110), Expect = 0.085,   Method: Compositional matrix adjust.
 Identities = 29/127 (22%), Positives = 61/127 (48%), Gaps = 24/127 (18%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFF 79
           ++LM  ++++++PR G  +I   QD I+GGYLLT++ A+F + +  ++         + F
Sbjct: 482 KILMEVQNHILSPRYGGPIIGGIQDHISGGYLLTREGAYFTKYEVEQM---------LMF 532

Query: 80  RGLIEGTVTKEDRVQQ---------------QSHIQIVSKNLYCQDPQRTPIPHGLLDRR 124
            G+    + K D+V+                   + I  +N  C DP +      L++ +
Sbjct: 533 AGVDVKELPKPDKVENGVEYWSGKTIFSLLLPDDLTIWYRNKLCDDPSQCEPIEKLIEEK 592

Query: 125 MGTNQKE 131
           +  +++E
Sbjct: 593 LVPSEEE 599


>gi|11499473|ref|NP_070714.1| DNA-directed RNA polymerase subunit A'' [Archaeoglobus fulgidus DSM
            4304]
 gi|14548238|sp|O28390.1|RPOA2_ARCFU RecName: Full=DNA-directed RNA polymerase subunit A''
 gi|2648655|gb|AAB89364.1| DNA-directed RNA polymerase, subunit A'' (rpoA2) [Archaeoglobus
            fulgidus DSM 4304]
          Length = 380

 Score =  181 bits (459), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 121/372 (32%), Positives = 185/372 (49%), Gaps = 85/372 (22%)

Query: 1096 PFPSACK--------------------AEACREKYVRAQIEPATAVGALAAQSIGEPGTQ 1135
            PFP A K                     E C + Y+   +EP  A G +AAQSIGEPGTQ
Sbjct: 14   PFPPAVKEEIKAELEKHGLKKTEAKKVVEKCFQAYLANLMEPGEAAGIVAAQSIGEPGTQ 73

Query: 1136 MTLKTFHFAG--------------------------------------------EVCEYI 1151
            MT++TFH+AG                                            EV   I
Sbjct: 74   MTMRTFHYAGVAEINVTLGLPRLIEILDVRKNPSTPMMTIRLLPEYAKDREKAREVANRI 133

Query: 1152 EEVFVPDDSFILIKLDMDRIRLL------HLE---VDIDSIRYCIERTRGISGHLTVSGH 1202
            E  +V D + I  ++D+ R  ++       LE   + ++ ++  I +        T  G 
Sbjct: 134  EATYVKDVADI--EVDIRRFTIIVKPDEKALERKGLTVEDLKSKIGKALKTEVEETEQGL 191

Query: 1203 SFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDN 1262
            +  I +P     S+ + M    +L  +V++ G++ I R +I +E+ E    Y L  EG N
Sbjct: 192  AVQITEP-----SYKALMAAFDKLKDTVIM-GLKEIKRVIIRKEEDE----YVLYTEGSN 241

Query: 1263 LRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVA 1322
            L+ +M   GV   + ++NN YE+Y+ LGIEAAR+ I+ E    +E  G+ +D RH MLVA
Sbjct: 242  LKKIMKVKGVDFTRTTTNNIYEIYEVLGIEAARNAIIREALDTLEEQGLEVDVRHIMLVA 301

Query: 1323 DLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGL 1382
            D+MT+ GE+  I RHG+A  K+S+L  A+FE T ++L DAA  G+ D + G++E II+G 
Sbjct: 302  DVMTADGELRQIGRHGVAGEKQSILARAAFEMTVNNLLDAAVRGEEDHLRGITENIIVGQ 361

Query: 1383 PMNVGTGLIKLL 1394
            P+ +GTG ++L+
Sbjct: 362  PIKLGTGDVELV 373



 Score =  108 bits (269), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 76/234 (32%), Positives = 126/234 (53%), Gaps = 17/234 (7%)

Query: 764 GVPRIKEIINASRNISTPIITAYL--DKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++  +N STP++T  L  +   D + AR V  R+E T + +V +    + V 
Sbjct: 92  GLPRLIEILDVRKNPSTPMMTIRLLPEYAKDREKAREVANRIEATYVKDVAD----IEVD 147

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
              F +I +  D   L    + ++ ++  I +        T  G +  I +P     S+ 
Sbjct: 148 IRRFTII-VKPDEKALERKGLTVEDLKSKIGKALKTEVEETEQGLAVQITEP-----SYK 201

Query: 882 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
           + M    +L  +V++ G++ I R +I +E+ E    Y L  EG NL+ +M   GV   + 
Sbjct: 202 ALMAAFDKLKDTVIM-GLKEIKRVIIRKEEDE----YVLYTEGSNLKKIMKVKGVDFTRT 256

Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
           ++NN YE+Y+ LGIEAAR+ I+ E    +E  G+ +D RH MLVAD+MT+ GE+
Sbjct: 257 TTNNIYEIYEVLGIEAARNAIIREALDTLEEQGLEVDVRHIMLVADVMTADGEL 310


>gi|126178252|ref|YP_001046217.1| DNA-directed RNA polymerase, subunit A'' [Methanoculleus marisnigri
            JR1]
 gi|126178265|ref|YP_001046230.1| DNA-directed RNA polymerase, subunit A'' [Methanoculleus marisnigri
            JR1]
 gi|125861046|gb|ABN56235.1| SSU ribosomal protein S2P [Methanoculleus marisnigri JR1]
 gi|125861059|gb|ABN56248.1| DNA-directed RNA polymerase, subunit A' [Methanoculleus marisnigri
            JR1]
          Length = 390

 Score =  181 bits (459), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 116/341 (34%), Positives = 177/341 (51%), Gaps = 59/341 (17%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYIEEV 1154
            +Y +++IEP  AVG +AAQSIGEPGTQMT++TFH+AG              E+ +   E 
Sbjct: 46   EYQKSRIEPCEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIMDARREP 105

Query: 1155 FVPDDSFILIK---LDMDRIRL---------LH----LEVDIDSIRYCIERTRGISGHLT 1198
              P  +  L+     + DR R          LH    + +D+++++  +   + +     
Sbjct: 106  STPTMAVHLLDDWAFNRDRAREVSWQIEAAPLHEFGDITIDMENMQVLVMLNKAVCDRRK 165

Query: 1199 VSGHSFLIL------------------KPKDSSKSFNSK-------MYQMKQLLPSVVIK 1233
            +S    L                     PK +S +F  K       ++Q+ + +  V+++
Sbjct: 166  ISIDEILEAGPRKMREKRHFRDFDVEGDPKRASITFTPKNRESYQNLFQLAEHVRHVIVQ 225

Query: 1234 GVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEA 1293
            G+  I R V+ +E  E    Y L  EG NL+DV    GV   +  SNN  E+   LGIEA
Sbjct: 226  GIDDIERVVVRKEGGE----YILYTEGSNLKDVFEVEGVDTSRTRSNNISEIADVLGIEA 281

Query: 1294 ARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFE 1353
             R+ I+ E    +   G+ +D RH MLVAD+M  +GEV  I RHG+A  KESVL+ A+FE
Sbjct: 282  GRNAIIQEALSTLNEQGIGVDVRHIMLVADMMCMEGEVKQIGRHGIAGEKESVLSRAAFE 341

Query: 1354 NTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
             T +HL DAA   + D ++GV+E +I+G P+ +GTG +KL+
Sbjct: 342  VTVNHLLDAAIANEVDELNGVTENVIVGQPIQLGTGDVKLI 382



 Score = 99.0 bits (245), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 79/253 (31%), Positives = 119/253 (47%), Gaps = 45/253 (17%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A R  STP +  +L  D   + D AR V  ++E   L E           
Sbjct: 91  GLPRLIEIMDARREPSTPTMAVHLLDDWAFNRDRAREVSWQIEAAPLHE----------- 139

Query: 822 DDSFILIKLDMDRIRLLHL---------EVDIDSIRYCIERTRGISGHL---TVSGHSFL 869
              F  I +DM+ +++L +         ++ ID I     R      H     V G    
Sbjct: 140 ---FGDITIDMENMQVLVMLNKAVCDRRKISIDEILEAGPRKMREKRHFRDFDVEG---- 192

Query: 870 ILKPKDSSKSFNSK-------MYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLV 922
              PK +S +F  K       ++Q+ + +  V+++G+  I R V+ +E  E    Y L  
Sbjct: 193 --DPKRASITFTPKNRESYQNLFQLAEHVRHVIVQGIDDIERVVVRKEGGE----YILYT 246

Query: 923 EGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHP 982
           EG NL+DV    GV   +  SNN  E+   LGIEA R+ I+ E    +   G+ +D RH 
Sbjct: 247 EGSNLKDVFEVEGVDTSRTRSNNISEIADVLGIEAGRNAIIQEALSTLNEQGIGVDVRHI 306

Query: 983 MLVADLMTSKGEV 995
           MLVAD+M  +GEV
Sbjct: 307 MLVADMMCMEGEV 319


>gi|341581877|ref|YP_004762369.1| DNA-directed RNA polymerase subunit A' [Thermococcus sp. 4557]
 gi|340809535|gb|AEK72692.1| DNA-directed RNA polymerase subunit A' [Thermococcus sp. 4557]
          Length = 905

 Score =  181 bits (458), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 99/281 (35%), Positives = 156/281 (55%), Gaps = 40/281 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIMAHR +V+P+RTFR N  VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 418 DGDIVLFNRQPSLHRMSIMAHRVRVMPYRTFRLNLSVCPPYNADFDGDEMNLHVPQTEEA 477

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE              A++LM  ++++++PR G  LIA  QD I+GGYLLT++ A+F R
Sbjct: 478 QAE--------------ARILMEVQNHIISPRYGGPLIAGIQDHISGGYLLTREGAYFTR 523

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           ++  ++      D  ++             P        +W+GK IFSL+L  +      
Sbjct: 524 SEVEQMLMFAGIDIRELP-----------EPDKVEDGVELWSGKTIFSLVLPEDLTIWYR 572

Query: 521 ANLKTKGRAYTANEEFCHR--------------DSYVILRNSELLAGSMDKSTLGSGGKA 566
             L  +     A E+                  D +V ++N +LL+G++DK   G     
Sbjct: 573 NKLCDEPERCEALEKLIEEKLVPDPGEVRKLAYDGFVYIQNGKLLSGAIDKKAYGR-EDG 631

Query: 567 NVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            +  +++R++G D A   + +++++  + + ++GF+  I D
Sbjct: 632 KLLDLIVREYGVDRARQFLDQVTKLAIWTITHKGFTTAIDD 672



 Score =  114 bits (284), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 74/266 (27%), Positives = 124/266 (46%), Gaps = 35/266 (13%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G IE  +     +++ S  +I   + Y  D    PI  GL+D+R+G       C TCG  
Sbjct: 9   GSIEFGILSPQEIRKMSAAEITVPDTY--DDDGYPIEGGLMDKRLGVVDPGLRCETCGAR 66

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
             DC GHFG+++L  P+ H+G+ + +  +L+S C+   C R+ L +E+   +  K     
Sbjct: 67  AGDCPGHFGHVELARPIVHVGFAKTIHRVLESTCRE--CGRIKLTDEEIEEYMHKFEVMG 124

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDL 260
                +  L K+I +  K+  VCPHCG     +           K++  T   +   ++ 
Sbjct: 125 DRKKAKDRLIKEIHKKAKERMVCPHCGAPQFPI-----------KFERPTIYWELRKDEE 173

Query: 261 LAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
             EY                     + P EV    E IP +D+PLL ++ E ++P  +IL
Sbjct: 174 GNEYR------------------HRMMPSEVRDRLEKIPDKDLPLLGLHPEKARPEWMIL 215

Query: 321 TRLLVPPNCIRPSVI--SDLKSDNDV 344
           T L VPP  +RPS+   S +++++D+
Sbjct: 216 TVLPVPPVTMRPSITLESGIRAEDDL 241



 Score = 95.9 bits (237), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 41/57 (71%), Positives = 50/57 (87%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV NS+ SGLTP E+FFH MGGREGLVDTAV+TA++GYMQRRL+ +L+DL V YD
Sbjct: 801 KGFVTNSYKSGLTPQEYFFHAMGGREGLVDTAVRTAQSGYMQRRLINALQDLKVDYD 857



 Score = 51.6 bits (122), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 36/117 (30%), Positives = 62/117 (52%), Gaps = 16/117 (13%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFF 79
           ++LM  ++++++PR G  LIA  QD I+GGYLLT++ A+F R++  ++   + AG  +  
Sbjct: 482 RILMEVQNHIISPRYGGPLIAGIQDHISGGYLLTREGAYFTRSEVEQM--LMFAG--IDI 537

Query: 80  RGLIEGTVTKEDRVQQQSHIQIVS-----------KNLYCQDPQRTPIPHGLLDRRM 125
           R L E     ED V+  S   I S           +N  C +P+R      L++ ++
Sbjct: 538 RELPEPDKV-EDGVELWSGKTIFSLVLPEDLTIWYRNKLCDEPERCEALEKLIEEKL 593


>gi|18977935|ref|NP_579292.1| DNA-directed RNA polymerase subunit A' [Pyrococcus furiosus DSM
           3638]
 gi|18893705|gb|AAL81687.1| DNA-directed RNA polymerase subunit a' [Pyrococcus furiosus DSM
           3638]
          Length = 907

 Score =  181 bits (458), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 101/282 (35%), Positives = 161/282 (57%), Gaps = 41/282 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIMAHR +V+P+RTFR N  VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 415 DGDIVLFNRQPSLHRMSIMAHRVRVMPYRTFRLNLAVCPPYNADFDGDEMNLHVPQTEEA 474

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE              A++LM  ++++++PR G  +I   QD I+GGYLLT++ A+F R
Sbjct: 475 QAE--------------ARILMEVQNHIISPRYGGPIIGGIQDHISGGYLLTREGAYFTR 520

Query: 461 AQTMRIASTLIADTSDICGIIKRFSW-RSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            +   +   L+    DI  + +   +  + NP        +W+GK IFSL+L  +     
Sbjct: 521 DE---VEQMLMFAGVDITELPEPDKYDENGNP--------LWSGKTIFSLLLPEDLTVWY 569

Query: 520 NANLKTKGRAYTANEEFCHR--------------DSYVILRNSELLAGSMDKSTLGSGGK 565
              L  +     A E+                  D +V ++N +LL+G++DK   G    
Sbjct: 570 RNKLCDEPERCEALEKLIEEKLMPDPEEVRKLAYDGFVYIQNGKLLSGAIDKKAYGR-ED 628

Query: 566 ANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
             +  +++R++G + A   + +++++T + + ++GF+ GI D
Sbjct: 629 GIILDLIVREYGVERARQFLDQVTKLTIWVITHKGFTTGIDD 670



 Score =  114 bits (284), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 76/269 (28%), Positives = 127/269 (47%), Gaps = 41/269 (15%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G IE  +     +++ S +++   + Y  D    PI  G++D+RMG       C TCG  
Sbjct: 6   GSIEFGILSPQEIRKMSAVEVTVPDTY--DDDGYPIEGGVMDKRMGVIDPGLRCETCGGR 63

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKL---R 197
             +C GHFG+I+L  PV H+G+ + +  IL+S C+   C R+ L +E+   +  K+   R
Sbjct: 64  AGECPGHFGHIELARPVIHVGFAKTIYRILESTCRE--CGRIKLTDEEIEEYMKKIELAR 121

Query: 198 NPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIV 257
           N    +     + K+I +  K+  VCPHCG     +           K++  T   +   
Sbjct: 122 NRRSEF---NEIIKEIHKKAKERMVCPHCGAPQYPI-----------KFEKPTIYWEIRK 167

Query: 258 EDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSD 317
           ++   EY                     L P EV    E IP +D+PLL ++ E S+P  
Sbjct: 168 DEQGNEYR------------------HRLMPTEVRDWLEKIPDKDLPLLGLDPEKSRPEW 209

Query: 318 LILTRLLVPPNCIRPSVI--SDLKSDNDV 344
           ++LT L VPP   RPS+   + +++++D+
Sbjct: 210 MVLTVLPVPPVTARPSITLETGIRAEDDL 238



 Score = 96.3 bits (238), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 41/57 (71%), Positives = 51/57 (89%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV NS+ SGLTP E+FFH MGGREGLVDTAV+TA++GYMQRRL+ +L+DL V+YD
Sbjct: 799 KGFVVNSYKSGLTPQEYFFHAMGGREGLVDTAVRTAQSGYMQRRLINALQDLKVEYD 855



 Score = 47.0 bits (110), Expect = 0.090,   Method: Compositional matrix adjust.
 Identities = 18/44 (40%), Positives = 32/44 (72%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 63
           ++LM  ++++++PR G  +I   QD I+GGYLLT++ A+F R +
Sbjct: 479 RILMEVQNHIISPRYGGPIIGGIQDHISGGYLLTREGAYFTRDE 522


>gi|397652056|ref|YP_006492637.1| DNA-directed RNA polymerase subunit A' [Pyrococcus furiosus COM1]
 gi|393189647|gb|AFN04345.1| DNA-directed RNA polymerase subunit A' [Pyrococcus furiosus COM1]
          Length = 910

 Score =  181 bits (458), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 101/282 (35%), Positives = 161/282 (57%), Gaps = 41/282 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIMAHR +V+P+RTFR N  VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 418 DGDIVLFNRQPSLHRMSIMAHRVRVMPYRTFRLNLAVCPPYNADFDGDEMNLHVPQTEEA 477

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE              A++LM  ++++++PR G  +I   QD I+GGYLLT++ A+F R
Sbjct: 478 QAE--------------ARILMEVQNHIISPRYGGPIIGGIQDHISGGYLLTREGAYFTR 523

Query: 461 AQTMRIASTLIADTSDICGIIKRFSW-RSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            +   +   L+    DI  + +   +  + NP        +W+GK IFSL+L  +     
Sbjct: 524 DE---VEQMLMFAGVDITELPEPDKYDENGNP--------LWSGKTIFSLLLPEDLTVWY 572

Query: 520 NANLKTKGRAYTANEEFCHR--------------DSYVILRNSELLAGSMDKSTLGSGGK 565
              L  +     A E+                  D +V ++N +LL+G++DK   G    
Sbjct: 573 RNKLCDEPERCEALEKLIEEKLMPDPEEVRKLAYDGFVYIQNGKLLSGAIDKKAYGR-ED 631

Query: 566 ANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
             +  +++R++G + A   + +++++T + + ++GF+ GI D
Sbjct: 632 GIILDLIVREYGVERARQFLDQVTKLTIWVITHKGFTTGIDD 673



 Score =  114 bits (284), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 76/269 (28%), Positives = 127/269 (47%), Gaps = 41/269 (15%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G IE  +     +++ S +++   + Y  D    PI  G++D+RMG       C TCG  
Sbjct: 9   GSIEFGILSPQEIRKMSAVEVTVPDTY--DDDGYPIEGGVMDKRMGVIDPGLRCETCGGR 66

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKL---R 197
             +C GHFG+I+L  PV H+G+ + +  IL+S C+   C R+ L +E+   +  K+   R
Sbjct: 67  AGECPGHFGHIELARPVIHVGFAKTIYRILESTCRE--CGRIKLTDEEIEEYMKKIELAR 124

Query: 198 NPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIV 257
           N    +     + K+I +  K+  VCPHCG     +           K++  T   +   
Sbjct: 125 NRRSEF---NEIIKEIHKKAKERMVCPHCGAPQYPI-----------KFEKPTIYWEIRK 170

Query: 258 EDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSD 317
           ++   EY                     L P EV    E IP +D+PLL ++ E S+P  
Sbjct: 171 DEQGNEYR------------------HRLMPTEVRDWLEKIPDKDLPLLGLDPEKSRPEW 212

Query: 318 LILTRLLVPPNCIRPSVI--SDLKSDNDV 344
           ++LT L VPP   RPS+   + +++++D+
Sbjct: 213 MVLTVLPVPPVTARPSITLETGIRAEDDL 241



 Score = 96.3 bits (238), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 41/57 (71%), Positives = 51/57 (89%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV NS+ SGLTP E+FFH MGGREGLVDTAV+TA++GYMQRRL+ +L+DL V+YD
Sbjct: 802 KGFVVNSYKSGLTPQEYFFHAMGGREGLVDTAVRTAQSGYMQRRLINALQDLKVEYD 858



 Score = 46.6 bits (109), Expect = 0.092,   Method: Compositional matrix adjust.
 Identities = 18/44 (40%), Positives = 32/44 (72%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 63
           ++LM  ++++++PR G  +I   QD I+GGYLLT++ A+F R +
Sbjct: 482 RILMEVQNHIISPRYGGPIIGGIQDHISGGYLLTREGAYFTRDE 525


>gi|284162089|ref|YP_003400712.1| DNA-directed RNA polymerase subunit A' [Archaeoglobus profundus DSM
           5631]
 gi|284012086|gb|ADB58039.1| DNA-directed RNA polymerase subunit A' [Archaeoglobus profundus DSM
           5631]
          Length = 871

 Score =  180 bits (457), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 105/267 (39%), Positives = 151/267 (56%), Gaps = 31/267 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIMAH  +VLP +TFR N  VC PYNADFDGDEMN+H+PQ+ EA
Sbjct: 405 DGDIVLFNRQPSLHRMSIMAHYVRVLPGKTFRLNPAVCPPYNADFDGDEMNLHVPQSIEA 464

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE              AK+LMA + ++++PR G  +I    D I+G YLLT+    F++
Sbjct: 465 QAE--------------AKILMAVQQHILSPRFGGPIIGGIHDHISGLYLLTRGEKLFSK 510

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            + M +      D  ++             P V       WTGKQIFS IL P+      
Sbjct: 511 EEVMYLLGPF--DLKELP-----------EPKVVKDGKPYWTGKQIFSAIL-PDVTLEFK 556

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           A +  KG      +E C  D+YVI++N EL+ G++D+  +G+  K  +   ++R +G DV
Sbjct: 557 AEI-CKG-CNECKKESCEYDAYVIIKNGELIRGTIDEKAVGA-FKGIIIDEIVRKYGNDV 613

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           A   +  ++ +    +M  GF+IGI D
Sbjct: 614 AKKFIDDMTHLAIRAIMLTGFTIGIDD 640



 Score =  105 bits (262), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 78/266 (29%), Positives = 120/266 (45%), Gaps = 68/266 (25%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           +++ S  +IVS   Y  D    PI  GL+D R+G       C TCG    +C GHFG+I+
Sbjct: 19  IRRMSVAKIVSAETY--DDDGFPIEGGLMDPRLGVIDPGLRCRTCGGKAGECPGHFGHIE 76

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRK----- 207
           L  PV H+GY + +  +L + C+   C R+ L +        K+R+  L  + R+     
Sbjct: 77  LAAPVIHVGYAKLIAKLLNATCRE--CGRLRLPD--------KVRDKFLDEIERRKELGQ 126

Query: 208 ---SLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEY 264
               + K +    K V  CPHCG                                  AE 
Sbjct: 127 DYDEIIKDVYRRAKAVKKCPHCG----------------------------------AEA 152

Query: 265 NEAVKFNPE----IEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
            E VKF       I+ HK       L PL+V +  E IP +D+P+L ++ +  +P  L++
Sbjct: 153 VE-VKFEKPTFYYIDEHK-------LTPLDVREWLEKIPDDDLPVLGIDPKACRPEWLVI 204

Query: 321 TRLLVPPNCIRPSVI--SDLKSDNDV 344
           T L VPP  +RPS+I  +  +S++D+
Sbjct: 205 TVLPVPPVTVRPSIILETGQRSEDDL 230



 Score = 85.1 bits (209), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 39/81 (48%), Positives = 58/81 (71%), Gaps = 9/81 (11%)

Query: 597 MNRGFS--------IGIGDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTA 647
           +NRG++           GD++   +GFV++S+  GL P EFFFH MGGREGLVDTA +T+
Sbjct: 747 INRGYTYTNRTLPHFKPGDLSARARGFVESSYKRGLNPIEFFFHAMGGREGLVDTACRTS 806

Query: 648 ETGYMQRRLVKSLEDLCVQYD 668
            +GY+QRR++ +L+D+ V+YD
Sbjct: 807 ISGYLQRRMINALQDIKVEYD 827


>gi|156937038|ref|YP_001434834.1| DNA-directed RNA polymerase subunit A' [Ignicoccus hospitalis
           KIN4/I]
 gi|156566022|gb|ABU81427.1| DNA-directed RNA polymerase, subunit A' [Ignicoccus hospitalis
           KIN4/I]
          Length = 889

 Score =  180 bits (457), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 98/269 (36%), Positives = 150/269 (55%), Gaps = 29/269 (10%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
            D DVVLFNRQPSLH++SIMAH  +VLP +TFR    VC PYNADFDGDEMN+H+PQ+EE
Sbjct: 421 QDGDVVLFNRQPSLHRMSIMAHLVRVLPGKTFRLCPLVCPPYNADFDGDEMNLHVPQSEE 480

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           ARAEAL               LM  + ++++PR G  +I   QD+I+G YLLT      +
Sbjct: 481 ARAEALE--------------LMLVEKHILSPRYGGPIIGGLQDYISGAYLLTTVATLLD 526

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           R           +D  ++ G+   +      P + +    +WTGKQ+FS+ L  + +   
Sbjct: 527 R-----------SDVQELLGVTG-YEGELPEPAI-LSPKTVWTGKQLFSVFLPKDFNYSG 573

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            AN+ T       ++E+C  DS+V++R+ EL+ G +DK ++G     ++ + ++ ++G +
Sbjct: 574 KANISTG--ELKCDDEYCFYDSFVVVRDGELVEGVLDKKSIGHEQPKSLMHWIVYEYGPE 631

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
                  R  +M   ++  RGF+    DV
Sbjct: 632 KGREIYDRAFKMFLRFIEKRGFTTRYDDV 660



 Score =  110 bits (274), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 74/261 (28%), Positives = 122/261 (46%), Gaps = 49/261 (18%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D +++ + + +V+   Y  D    P+  G++D RMG       C TCG  L DC GHFGY
Sbjct: 26  DEIRKMAVVAVVTDQAY--DEAGMPVEGGIMDPRMGVTSPGQRCPTCGNTLHDCPGHFGY 83

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGF-----RAKLRNPALSYLV 205
           I+L  PV H  +   + + L++ C+   C RV L +E+   F     + + + P L+  V
Sbjct: 84  IELVKPVIHYEFVPHIYDALRATCR--VCGRVKLSDEEIDKFLRLYEKLEKKWPLLARRV 141

Query: 206 RKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYN 265
              ++KK      KV  CPHCG                ++YK + +K    +E+ +    
Sbjct: 142 TAFVRKK----AAKVMECPHCGA---------------KQYKIKLEKPYNFIEERMPR-- 180

Query: 266 EAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLV 325
                            +  LNP EV    E IP +D  +L  + + ++P   +LT L V
Sbjct: 181 -----------------LHYLNPEEVRSRLENIPDKDAKVLGFDPKEARPEWAVLTVLPV 223

Query: 326 PPNCIRPSVI--SDLKSDNDV 344
           PP  +RPS+I  + ++S++D+
Sbjct: 224 PPVTVRPSIILETGMRSEDDL 244



 Score = 99.0 bits (245), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 44/80 (55%), Positives = 60/80 (75%), Gaps = 1/80 (1%)

Query: 606 GDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           GD++P  +GFV++SF+ GLTPTE FFH  GGREGLVDTAV+T+++GYMQRRL+ +L+DL 
Sbjct: 781 GDISPDARGFVKHSFYEGLTPTEVFFHAAGGREGLVDTAVRTSQSGYMQRRLINALQDLK 840

Query: 665 VQYDMSFDAAFYGQTDCISG 684
           V YD +   A+      + G
Sbjct: 841 VDYDGTVKDAWGALYQSVYG 860


>gi|341581878|ref|YP_004762370.1| DNA-directed RNA polymerase subunit A'' [Thermococcus sp. 4557]
 gi|340809536|gb|AEK72693.1| DNA-directed RNA polymerase subunit A'' [Thermococcus sp. 4557]
          Length = 391

 Score =  180 bits (457), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 122/351 (34%), Positives = 178/351 (50%), Gaps = 59/351 (16%)

Query: 1099 SACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EV 1147
             A   E  RE Y  A +EP  A+G +AAQSIGEP TQMTL TFH+AG            +
Sbjct: 43   EAIIEETVRE-YQNALVEPGEAIGTVAAQSIGEPSTQMTLNTFHYAGVAEINVTLGLPRI 101

Query: 1148 CEYIEEVFVPDDSFILIKLD----MDRIRLLHL--------------EVDIDSIRY---- 1185
             E ++    P    + + LD     DR + L +              E+ ID + Y    
Sbjct: 102  IEIVDARKNPSTPIMTVYLDEKHRYDREKALEVARRIEGTTLENLAREMSIDILNYEFVV 161

Query: 1186 --CIER-----------TRGISG-----HLTVSGHSFLILKPKDSSKSFNSKMYQMKQLL 1227
               +ER            R + G        V G++ LI++PK   K   S + ++ + +
Sbjct: 162  DIDLERLEKAGLDMEKVQRKLEGSFKSAEFEVDGYT-LIMRPKKVGKL--SDLRRLAEKV 218

Query: 1228 PSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYK 1287
                +KG+ G+ + +I +E  E    Y +  EG N + V+   GV   +  +NN +E+  
Sbjct: 219  KKHRLKGLSGVGKTIIRKEGDE----YVIYTEGSNFKQVLKVPGVDPTRTRTNNIWEIAD 274

Query: 1288 TLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVL 1347
             LGIEAAR+ I+ EI   M   G+ +D RH MLVAD+MT  G +L I RHG+   K SVL
Sbjct: 275  VLGIEAARNAIIEEIVNTMREQGLEVDVRHIMLVADMMTLDGVILPIGRHGIVGEKASVL 334

Query: 1348 NLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 1398
              A+FE T+ HLF+AA  G  D ++GV E +++G P+ VGTG++KL   +P
Sbjct: 335  ARAAFEITTQHLFEAAERGDEDPLNGVVENVLIGQPVPVGTGMVKLAMNLP 385



 Score =  117 bits (293), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 81/238 (34%), Positives = 132/238 (55%), Gaps = 14/238 (5%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PRI EI++A +N STPI+T YLD+    D + A  V  R+E TTL  +   +  + + 
Sbjct: 97  GLPRIIEIVDARKNPSTPIMTVYLDEKHRYDREKALEVARRIEGTTLENLAREMS-IDIL 155

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
           +  F++   D+D  RL    +D++ ++  +E +   S    V G++ LI++PK   K   
Sbjct: 156 NYEFVV---DIDLERLEKAGLDMEKVQRKLEGSFK-SAEFEVDGYT-LIMRPKKVGKL-- 208

Query: 882 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
           S + ++ + +    +KG+ G+ + +I +E  E    Y +  EG N + V+   GV   + 
Sbjct: 209 SDLRRLAEKVKKHRLKGLSGVGKTIIRKEGDE----YVIYTEGSNFKQVLKVPGVDPTRT 264

Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG 999
            +NN +E+   LGIEAAR+ I+ EI   M   G+ +D RH MLVAD+MT  G +L  G
Sbjct: 265 RTNNIWEIADVLGIEAARNAIIEEIVNTMREQGLEVDVRHIMLVADMMTLDGVILPIG 322


>gi|284162090|ref|YP_003400713.1| DNA-directed RNA polymerase subunit A'' [Archaeoglobus profundus DSM
            5631]
 gi|284012087|gb|ADB58040.1| DNA-directed RNA polymerase, subunit A'' [Archaeoglobus profundus DSM
            5631]
          Length = 377

 Score =  180 bits (457), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 120/342 (35%), Positives = 173/342 (50%), Gaps = 62/342 (18%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-------------------- 1145
            C E Y R  +EP  AVG +AAQSIGEP TQMT++TFH+AG                    
Sbjct: 40   CVEVYYRNLVEPGEAVGIIAAQSIGEPATQMTMRTFHYAGVAEINVTLGLPRLIEILDVR 99

Query: 1146 ------------------------EVCEYIEEVFVPD------DSF---ILIKLDMDRIR 1172
                                    EV   IE   V D      D +   I+IK D   ++
Sbjct: 100  KKPSTPMMTIRLLPEYAKDKEKAKEVARRIEATHVTDVADISVDIYGLKIIIKPDEKALK 159

Query: 1173 LLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVI 1232
               L V+  S++  +ER   +   +     + +I    D  K + + M    +L   V I
Sbjct: 160  EKSLTVE--SLKKTLERK--LKTEIGEENGNLVIQVSPDVDKPYKTLMDIFDKLKKEV-I 214

Query: 1233 KGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIE 1292
             G++ I R +I +E  E    Y L  EG NL+ VM   GV   +  +N+ YE+Y+ LGIE
Sbjct: 215  AGIKEIKRVIIRKEGDE----YVLYTEGSNLKKVMKVKGVDFTRTLTNDIYEIYEVLGIE 270

Query: 1293 AARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASF 1352
            AAR+ I+ E K  +E  G+ +D RH MLVAD+MT+ G +  I RHG+A  K+S+L  A+F
Sbjct: 271  AARAAIIKEAKETLEEQGLDVDVRHIMLVADVMTADGYLKQIGRHGVAGAKQSILARAAF 330

Query: 1353 ENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            E T + L DAA  G+ D + G++E II+G P+ +GTG ++L+
Sbjct: 331  EVTVNVLLDAAVKGEVDYLKGITENIIVGQPIKLGTGDVELV 372



 Score =  104 bits (260), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 76/232 (32%), Positives = 124/232 (53%), Gaps = 14/232 (6%)

Query: 764 GVPRIKEIINASRNISTPIITAYL--DKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++  +  STP++T  L  +   D + A+ V  R+E T + +V +   +++  
Sbjct: 88  GLPRLIEILDVRKKPSTPMMTIRLLPEYAKDKEKAKEVARRIEATHVTDVADISVDIY-- 145

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
               I+IK D   ++   L V+  S++  +ER   +   +     + +I    D  K + 
Sbjct: 146 -GLKIIIKPDEKALKEKSLTVE--SLKKTLERK--LKTEIGEENGNLVIQVSPDVDKPYK 200

Query: 882 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
           + M    +L   V I G++ I R +I +E  E    Y L  EG NL+ VM   GV   + 
Sbjct: 201 TLMDIFDKLKKEV-IAGIKEIKRVIIRKEGDE----YVLYTEGSNLKKVMKVKGVDFTRT 255

Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
            +N+ YE+Y+ LGIEAAR+ I+ E K  +E  G+ +D RH MLVAD+MT+ G
Sbjct: 256 LTNDIYEIYEVLGIEAARAAIIKEAKETLEEQGLDVDVRHIMLVADVMTADG 307


>gi|219852751|ref|YP_002467183.1| DNA-directed RNA polymerase subunit A'' [Methanosphaerula palustris
            E1-9c]
 gi|219547010|gb|ACL17460.1| DNA-directed RNA polymerase, subunit A'' [Methanosphaerula palustris
            E1-9c]
          Length = 395

 Score =  180 bits (457), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 112/350 (32%), Positives = 181/350 (51%), Gaps = 64/350 (18%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFVP 1157
            ++   +IEP  AVG +AAQSIGEPGTQMT++TFH+AG            + E ++    P
Sbjct: 47   EFKSTRIEPLEAVGVIAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIMDARREP 106

Query: 1158 DDSFILIKL------DMDRIRLLHLEV-------------DIDSIRYCIERTRGISGHLT 1198
                + + L      D D+ R++  ++             D+++++  ++  + +     
Sbjct: 107  STPTMTVHLSDEYNNDRDKARMVSWQIEAAPLHEFGDIITDMENMQVLVKLNKAVCEKRK 166

Query: 1199 VS---------------------------GHSFLILKPKDSSKSFNSKMYQMKQLLPSVV 1231
            +S                             + +   PKD     N  ++Q+ + + +V+
Sbjct: 167  ISVDVVSETAPRKIRERRHYRDFEAEANIDEAIITFTPKDRESYQN--LFQLAEHVRNVI 224

Query: 1232 IKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGI 1291
            ++G+  I R V+ +E  E    Y L  EG NL+DV    GV   +  +NN  E+ + LGI
Sbjct: 225  VQGIDDIERVVVRKESGE----YILYTEGSNLKDVFEVAGVDTSRTRTNNISEISQVLGI 280

Query: 1292 EAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLAS 1351
            EAAR+ I+ E    +   G+ +D RH MLV+D+M   GEV  I RHG+A  KESVL+ A+
Sbjct: 281  EAARNAIIAEALSTLGEQGIRVDVRHIMLVSDMMCMDGEVKQIGRHGIAGEKESVLSRAA 340

Query: 1352 FENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSE 1401
            FE T +HL DAA   + D ++GV+E +I+G P+ +GTG +KL+ A PR++
Sbjct: 341  FEVTVNHLLDAAVANEVDELNGVTENVIVGQPIQLGTGDVKLI-ARPRNQ 389



 Score =  110 bits (274), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 77/239 (32%), Positives = 125/239 (52%), Gaps = 17/239 (7%)

Query: 764 GVPRIKEIINASRNISTPIITAYL--DKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A R  STP +T +L  + + D D AR+V  ++E   L E  + I ++   
Sbjct: 92  GLPRLIEIMDARREPSTPTMTVHLSDEYNNDRDKARMVSWQIEAAPLHEFGDIITDM--- 148

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDS---IRYCIERT--RGISGHLTVSGHSFLILKPKDS 876
           ++  +L+KL+        + VD+ S    R   ER   R       +   + +   PKD 
Sbjct: 149 ENMQVLVKLNKAVCEKRKISVDVVSETAPRKIRERRHYRDFEAEANID-EAIITFTPKDR 207

Query: 877 SKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGV 936
               N  ++Q+ + + +V+++G+  I R V+ +E  E    Y L  EG NL+DV    GV
Sbjct: 208 ESYQN--LFQLAEHVRNVIVQGIDDIERVVVRKESGE----YILYTEGSNLKDVFEVAGV 261

Query: 937 KGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
              +  +NN  E+ + LGIEAAR+ I+ E    +   G+ +D RH MLV+D+M   GEV
Sbjct: 262 DTSRTRTNNISEISQVLGIEAARNAIIAEALSTLGEQGIRVDVRHIMLVSDMMCMDGEV 320


>gi|57641016|ref|YP_183494.1| DNA-directed RNA polymerase subunit A'' [Thermococcus kodakarensis
            KOD1]
 gi|73917871|sp|Q5JE34.1|RPOA2_PYRKO RecName: Full=DNA-directed RNA polymerase subunit A''
 gi|57159340|dbj|BAD85270.1| DNA-directed RNA polymerase, subunit A'' [Thermococcus kodakarensis
            KOD1]
          Length = 391

 Score =  180 bits (457), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 118/346 (34%), Positives = 179/346 (51%), Gaps = 59/346 (17%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIE 1152
            E  RE Y +A IEP  AVG +AAQSIGEP TQMTL TFH+AG            + E ++
Sbjct: 48   ETVRE-YQKALIEPGEAVGTVAAQSIGEPSTQMTLNTFHYAGVAEINVTLGLPRIIEIVD 106

Query: 1153 EVFVPDDSFILIKLD----MDRIRLLHLE----------------VDIDSIRYCIE---- 1188
                P    + + LD     DR + L +                 +DI ++ Y +E    
Sbjct: 107  ARKNPSTPIMTVYLDEEHRYDRDKALEVARRIEGTTLENLAREETIDILNMEYVVEIDPE 166

Query: 1189 -----------RTRGISG-----HLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVI 1232
                         R ++G          G++ L+++PK  +K   S + ++ + +    +
Sbjct: 167  RLEKAGLDMEKVVRKLTGSFKSAEFEAEGYT-LVVRPKKVTKL--SDLRKIAEKVKKHRL 223

Query: 1233 KGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIE 1292
            KG+ G+ + +I +E  E    Y +  EG N + V+   GV   +  +NN +E+ + LGIE
Sbjct: 224  KGLSGVGKTIIRKEGDE----YVIYTEGSNFKQVLKVPGVDPTRTRTNNIWEIAEVLGIE 279

Query: 1293 AARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASF 1352
            AAR+ I+ EI   M   G+ +D RH MLVAD+MT  G +  I RHG+   K SVL  A+F
Sbjct: 280  AARNAIIDEIVSTMREQGLEVDVRHIMLVADMMTLDGVIRPIGRHGIVGEKASVLARAAF 339

Query: 1353 ENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 1398
            E T+ HLF AA  G+ D ++GV E +++G P+ VGTG++KL  ++P
Sbjct: 340  EITTQHLFAAAERGEVDPLNGVVENVLIGQPVPVGTGIVKLAMSLP 385



 Score =  112 bits (279), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 77/234 (32%), Positives = 128/234 (54%), Gaps = 18/234 (7%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PRI EI++A +N STPI+T YLD++   D D A  V  R+E TTL  +    EE    
Sbjct: 97  GLPRIIEIVDARKNPSTPIMTVYLDEEHRYDRDKALEVARRIEGTTLENLAR--EETIDI 154

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI--SGHLTVSGHSFLILKPKDSSKS 879
            +   ++++D +R+    L+++       + +  G   S      G++ L+++PK  +K 
Sbjct: 155 LNMEYVVEIDPERLEKAGLDME-----KVVRKLTGSFKSAEFEAEGYT-LVVRPKKVTKL 208

Query: 880 FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
             S + ++ + +    +KG+ G+ + +I +E  E    Y +  EG N + V+   GV   
Sbjct: 209 --SDLRKIAEKVKKHRLKGLSGVGKTIIRKEGDE----YVIYTEGSNFKQVLKVPGVDPT 262

Query: 940 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
           +  +NN +E+ + LGIEAAR+ I+ EI   M   G+ +D RH MLVAD+MT  G
Sbjct: 263 RTRTNNIWEIAEVLGIEAARNAIIDEIVSTMREQGLEVDVRHIMLVADMMTLDG 316


>gi|322369998|ref|ZP_08044560.1| DNA-directed RNA polymerase subunit A'' [Haladaptatus paucihalophilus
            DX253]
 gi|320550334|gb|EFW91986.1| DNA-directed RNA polymerase subunit A'' [Haladaptatus paucihalophilus
            DX253]
          Length = 393

 Score =  180 bits (456), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 116/354 (32%), Positives = 182/354 (51%), Gaps = 60/354 (16%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A+A   +Y+  +++P   VG ++AQSIGEPGTQMT+ TFH+AG            + E +
Sbjct: 44   AKAVEHRYLDTRVDPLDPVGTVSAQSIGEPGTQMTMNTFHYAGVAEMDVTQGLPRLIELV 103

Query: 1152 EEVFVPDDSFILIKLD--------------------------------MDRIRLLHLEVD 1179
            +    PD   + + L+                                 D I  ++L  D
Sbjct: 104  DARKTPDTPIMTVYLEDEYAENREKAHEVVWNIEATKILALGDISTNVADMIVSINLNED 163

Query: 1180 --------IDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVV 1231
                    ID +   IE + G+    T    S +   P   S     K+ Q+ + L  +V
Sbjct: 164  TLEERMITIDEVASIIEDSLGVQ---TTQQGSVIEFGPDQPSYR---KLLQLVEELREIV 217

Query: 1232 IKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGI 1291
             KG++ I+R VI  E ++   ++ L  EG    D +   GV   + + NN +E+Y+TLG+
Sbjct: 218  FKGIEEISRVVIRRESLDDGEEFVLYTEGSAFSDTLEIEGVDASRTTCNNIHEIYRTLGV 277

Query: 1292 EAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLA 1350
            EAAR +I+ E    +E  G+  ++ RH MLVAD+MT++G +  I RHG++  KESVL  A
Sbjct: 278  EAARESIIEETMDTLEEQGLGDVNVRHLMLVADIMTNRGTIESIGRHGISGSKESVLARA 337

Query: 1351 SFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL-LQAVPR-SEP 1402
            +FE T +HL DAA +G+ D ++GV E +I+G P+ +GTG + L + +V R +EP
Sbjct: 338  AFEVTVNHLLDAAIHGEVDDLNGVIENVIVGKPIKLGTGDVNLRMGSVSRGAEP 391



 Score =  103 bits (258), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 69/238 (28%), Positives = 125/238 (52%), Gaps = 20/238 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TPI+T YL+ +   + + A  V   +E T    LG++   + + 
Sbjct: 95  GLPRLIELVDARKTPDTPIMTVYLEDEYAENREKAHEVVWNIEATKILALGDISTNVAD- 153

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSK 878
                  +++ ++++   L    + ID +   IE + G+    T    S +   P   S 
Sbjct: 154 -------MIVSINLNEDTLEERMITIDEVASIIEDSLGVQ---TTQQGSVIEFGPDQPSY 203

Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 938
               K+ Q+ + L  +V KG++ I+R VI  E ++   ++ L  EG    D +   GV  
Sbjct: 204 R---KLLQLVEELREIVFKGIEEISRVVIRRESLDDGEEFVLYTEGSAFSDTLEIEGVDA 260

Query: 939 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEV 995
            + + NN +E+Y+TLG+EAAR +I+ E    +E  G+  ++ RH MLVAD+MT++G +
Sbjct: 261 SRTTCNNIHEIYRTLGVEAARESIIEETMDTLEEQGLGDVNVRHLMLVADIMTNRGTI 318


>gi|169806385|ref|XP_001827937.1| DNA-directed RNA polymerase, beta' subunit-160 kD subunit
           [Enterocytozoon bieneusi H348]
 gi|161779005|gb|EDQ31032.1| DNA-directed RNA polymerase, beta' subunit-160 kD subunit
           [Enterocytozoon bieneusi H348]
          Length = 1174

 Score =  180 bits (456), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 110/270 (40%), Positives = 157/270 (58%), Gaps = 40/270 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIMAHR K+  +RTF+FNE VC PYNADFDGDEMN+HLPQT+ A
Sbjct: 408 DGDIVLFNRQPSLHRMSIMAHRVKLHDNRTFQFNESVCNPYNADFDGDEMNIHLPQTKAA 467

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AEA+               LM+ K N+ T +N E LI+ TQDFITG YLLT KN    +
Sbjct: 468 QAEAIE--------------LMSIKKNICTIKNNEPLISPTQDFITGMYLLTNKNKILTK 513

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAV-IWTGKQIFSLILKPNRDCPV 519
            +  ++   +           KR        +    T + ++TGKQI   +L       V
Sbjct: 514 TEFYKLIGHIHHG--------KRIIIEPSIIIYKSTTVIKLFTGKQIVDYMLH-----SV 560

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGK-ANVFYILLRDFGE 578
             NLKTK R    N+E       VI++NS+L+ G++DKS +G+  K +++ Y L +    
Sbjct: 561 TINLKTKNR----NKE------DVIIKNSKLIQGTIDKSIIGAENKNSSLIYQLFKQSKV 610

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           +  +  +  +S+++  Y+M  GFSIG+ D+
Sbjct: 611 E-CIKFINNISKISIRYIMEYGFSIGLDDI 639



 Score =  173 bits (438), Expect = 7e-40,   Method: Compositional matrix adjust.
 Identities = 134/397 (33%), Positives = 201/397 (50%), Gaps = 54/397 (13%)

Query: 612  QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSF 671
            +GFV NSFF+GL   EFFFH + GREGLVDTAVKTA+TGYMQRRL+K+LE+L ++YD + 
Sbjct: 757  RGFVYNSFFTGLKAYEFFFHAISGREGLVDTAVKTADTGYMQRRLMKALENLSIKYDNTV 816

Query: 672  DAA-------FYGQTDCISGVSECIIMGLPMNVGTGL-IKLLQAVPRSEPVPRTLLFDNP 723
                       YG+        E I   +   +  G  +  + A    EP  +  L    
Sbjct: 817  RNNNNEIIQFLYGEDGKDPLYDETIDATIKKFIEPGTAVGAIAAQSIGEPGTQMTL---K 873

Query: 724  EFHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINASRNISTPII 783
             FHF  V             AS+ +TL             GVPRIKEIINA+  ISTPII
Sbjct: 874  TFHFAGV-------------ASMNITL-------------GVPRIKEIINATSTISTPII 907

Query: 784  TAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVD 843
            +    K+ +L  A I+K +LE+  L ++ + I+ ++  + +      +M    +  L+ +
Sbjct: 908  SV---KNVNLQDAYIIKQKLEKNVLKDIIKRIDIMYTHEKNI----FNMIFTCISPLDNN 960

Query: 844  IDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNS-KMYQMKQLLPSVVIKGVQGI 902
            I   + CI+     S + T+   +            +N   ++++K  L +  I G+   
Sbjct: 961  ILE-KLCIKPLS--SKYNTMDLFNDNNYNYYQYKFKYNGFNIFKIKNTLLNTQISGLTNT 1017

Query: 903  NRAVIHEEDVEGVTKYKLLVEGD--NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARS 960
            N+  I E + +    Y+LL+     +L  ++ T  +      +NN  E+  TLGIEAAR 
Sbjct: 1018 NKVFIKETNKD----YELLISSSFGDLPYILGTEFINPYTTITNNILEIESTLGIEAARE 1073

Query: 961  TIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +I+ EI+  +  HG+ I+ RH ML+AD MT KG VLG
Sbjct: 1074 SIINEIEYTIGTHGIQINCRHLMLLADTMTIKGHVLG 1110



 Score =  160 bits (405), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 113/326 (34%), Positives = 168/326 (51%), Gaps = 52/326 (15%)

Query: 1111 VRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFVPDD 1159
            ++  IEP TAVGA+AAQSIGEPGTQMTLKTFHFAG            + E I        
Sbjct: 845  IKKFIEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINATSTIST 904

Query: 1160 SFILIK-LDMDRIRLLHLEVDIDSIRYCIERTRGISGH-LTVSGHSFLILKPKDS----- 1212
              I +K +++    ++  +++ + ++  I+R   +  H   +    F  + P D+     
Sbjct: 905  PIISVKNVNLQDAYIIKQKLEKNVLKDIIKRIDIMYTHEKNIFNMIFTCISPLDNNILEK 964

Query: 1213 ------SKSFNS---------------------KMYQMKQLLPSVVIKGVQGINRAVIHE 1245
                  S  +N+                      ++++K  L +  I G+   N+  I E
Sbjct: 965  LCIKPLSSKYNTMDLFNDNNYNYYQYKFKYNGFNIFKIKNTLLNTQISGLTNTNKVFIKE 1024

Query: 1246 EDVEGVTKYKLLVEGD--NLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIK 1303
             + +    Y+LL+     +L  ++ T  +      +NN  E+  TLGIEAAR +I+ EI+
Sbjct: 1025 TNKD----YELLISSSFGDLPYILGTEFINPYTTITNNILEIESTLGIEAARESIINEIE 1080

Query: 1304 LVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAA 1363
              +  HG+ I+ RH ML+AD MT KG VLGITR G+ K   S L LASFE TSD LF AA
Sbjct: 1081 YTIGTHGIQINCRHLMLLADTMTIKGHVLGITRFGM-KYFNSTLMLASFEQTSDFLFQAA 1139

Query: 1364 FYGQTDCISGVSECIIMGLPMNVGTG 1389
               + D +SGVS+ II+G  +++GTG
Sbjct: 1140 IEEREDIVSGVSDSIILGKNISIGTG 1165



 Score =  125 bits (315), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 81/225 (36%), Positives = 109/225 (48%), Gaps = 44/225 (19%)

Query: 113 RTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQS 172
           R P   G LD ++G +  E  C TC Q L DC GH+G I L LPVFHI  F+ +INIL S
Sbjct: 39  RKPFSGGPLDLKLGVSTTETKCETCNQGLQDCPGHWGKISLILPVFHIALFKEIINILNS 98

Query: 173 ICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGV 232
           ICK   C+ +L+  +     ++K+                I++  KK+  C +C   NG+
Sbjct: 99  ICK--KCSSLLI--KNKHDIKSKVN---------------IVDQCKKIKQCYNCNSFNGI 139

Query: 233 VKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVL 292
           VKK    +I HE  K+ +K KD                   +E +K F     LNPL V 
Sbjct: 140 VKKSNGFRIFHEFRKSNSKSKD-------------------MEDNKLF--CDELNPLTVY 178

Query: 293 QLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD 337
            LF+ I   D+  L        P +L++  LLVPP CIRPSV  D
Sbjct: 179 NLFKNIKETDLLFL----SCKNPCNLLIKTLLVPPCCIRPSVDMD 219



 Score = 48.1 bits (113), Expect = 0.036,   Method: Compositional matrix adjust.
 Identities = 23/55 (41%), Positives = 34/55 (61%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRK 76
           LM+ K N+ T +N E LI+ TQDFITG YLLT KN    + +  ++   +  G++
Sbjct: 474 LMSIKKNICTIKNNEPLISPTQDFITGMYLLTNKNKILTKTEFYKLIGHIHHGKR 528


>gi|268323372|emb|CBH36960.1| probable DNA-directed RNA polymerase, subunit A' [uncultured
           archaeon]
          Length = 889

 Score =  179 bits (455), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 110/287 (38%), Positives = 153/287 (53%), Gaps = 40/287 (13%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
            D D+VLFNRQPSLH+LSIMAH  +V+P RTFR N  VC PYNAD+DGDEMN+H+ QTEE
Sbjct: 410 QDGDIVLFNRQPSLHRLSIMAHYVRVMPGRTFRLNPTVCPPYNADYDGDEMNMHVLQTEE 469

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           ARAE              AK+LMA K N+++PR G  +I    D+ITG ++LT     F 
Sbjct: 470 ARAE--------------AKILMAVKRNIMSPRFGRPIIGGIHDYITGLFILTWGEKRFE 515

Query: 460 RAQTMRIASTL-IADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCP 518
           + +   + + + I D  +  G    F   S   V +      WTGKQ+F  IL      P
Sbjct: 516 KEKAQDMLNRINIHDLGEPAGT---FESSSGIQVPY------WTGKQLFGRIL------P 560

Query: 519 VNANLKTKG--------RAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFY 570
              +L+ +G        R     +E C R++YV+++   LL G +D+  +GS  K  +  
Sbjct: 561 KQMDLQFRGVVCGKCIERGEKCKKENCPREAYVVIKEGNLLCGVIDEMAIGS-FKGKIIE 619

Query: 571 ILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV-TPGQGFVQ 616
            + R +GED A   +   +R+    +   GFS GI D   P +G  Q
Sbjct: 620 QIFRLYGEDEAKKFINDSARLAINCIKQSGFSFGISDEDIPKEGKAQ 666



 Score =  115 bits (287), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 74/257 (28%), Positives = 119/257 (46%), Gaps = 45/257 (17%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           +++ S  +I++ + Y +D    PI  GL+++R+G       C TCG  + +C GHFG+I+
Sbjct: 19  IRKMSASKIITPDTYGEDG--FPIELGLVNQRIGVIDPGLRCKTCGGRMGECPGHFGHIE 76

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKK 212
           L  P+ H+GY + +  IL + C+   C +VLLGEE  A F   +            + K 
Sbjct: 77  LAAPIIHVGYAKMIYRILAATCRR--CGKVLLGEEARAKFLDGIEQQKEKQADVGDVVKL 134

Query: 213 ILETTKKVSVCPHCGEINGVV---KKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVK 269
           + +   K  VCP C EI   +   K  G ++I  E  + R                    
Sbjct: 135 VFKEAAKNDVCPFCDEIQKRIKYDKPTGYIEIDKEDKERR-------------------- 174

Query: 270 FNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
                           L P +V +  E IP +DIPL  M+ + ++P  +I+T L VPP  
Sbjct: 175 ----------------LMPTDVRERLEKIPDDDIPLFGMDPKNARPEWMIITVLPVPPVT 218

Query: 330 IRPSVI--SDLKSDNDV 344
            RPS+   S  +S++D+
Sbjct: 219 ARPSITLESGQRSEDDL 235



 Score = 78.2 bits (191), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 34/57 (59%), Positives = 45/57 (78%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFV+ SF  GLT TE+F H +GGRE LVDTAV+T+++GY QRRL+ +L+DL V+ D
Sbjct: 786 HGFVRASFKDGLTATEYFLHAVGGREALVDTAVRTSQSGYFQRRLINALQDLEVKND 842


>gi|289193126|ref|YP_003459067.1| DNA-directed RNA polymerase, subunit A'' [Methanocaldococcus sp.
            FS406-22]
 gi|288939576|gb|ADC70331.1| DNA-directed RNA polymerase, subunit A'' [Methanocaldococcus sp.
            FS406-22]
          Length = 387

 Score =  179 bits (455), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 121/336 (36%), Positives = 176/336 (52%), Gaps = 63/336 (18%)

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVC------- 1148
            Y +A +EP  AVG +AAQSIGEPGTQMT++TFH+AG              E+        
Sbjct: 49   YRKALVEPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRMIEIVDARKEPS 108

Query: 1149 ---------------EYIEEVFVPDDSFIL---------------IKLDMDRIRLLHLEV 1178
                           E  EE+    +S  L               IK+++D  RL    +
Sbjct: 109  TPIMTIYLKEEYNSREKAEEIAKEIESLTLGSIAESISIDLWTQSIKVELDEERLADRGL 168

Query: 1179 DIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSS-KSFNSKMYQMKQLLPSVVIKGVQG 1237
             ID +   I++   +   + V G S L LK K  S K+   ++ ++K    ++ +KG+ G
Sbjct: 169  TIDDVVEAIKKKLKVK--IDVEG-SVLYLKIKTPSIKALRKRIPKIK----NIQLKGIPG 221

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            I R ++ +E  E    Y L  +G NLR+V    GV   +  +NN  E+ + LGIEAAR+ 
Sbjct: 222  IERVLVKKEKDE----YVLYTQGSNLREVFKIEGVDTTRTITNNIIEIQEVLGIEAARNA 277

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ E++  +E  G+ +D RH MLVAD+MT+ GEV  I RHG+A  K SVL  A+FE T  
Sbjct: 278  IINEMRNTLEQQGLEVDIRHLMLVADMMTADGEVKPIGRHGVAGEKGSVLARAAFEETVK 337

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            HL+ AA  G  D + GV E +I+G P+ +GTG ++L
Sbjct: 338  HLYAAAERGDVDKLKGVIENVIVGKPIYLGTGCVEL 373



 Score =  117 bits (294), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 82/234 (35%), Positives = 130/234 (55%), Gaps = 17/234 (7%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD-TDLDYARIVKGRLERTTLGEVCEYIEEVFVPD 822
           G+PR+ EI++A +  STPI+T YL ++    + A  +   +E  TLG + E I      D
Sbjct: 93  GLPRMIEIVDARKEPSTPIMTIYLKEEYNSREKAEEIAKEIESLTLGSIAESIS----ID 148

Query: 823 DSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSS-KSFN 881
                IK+++D  RL    + ID +   I++   +   + V G S L LK K  S K+  
Sbjct: 149 LWTQSIKVELDEERLADRGLTIDDVVEAIKKKLKVK--IDVEG-SVLYLKIKTPSIKALR 205

Query: 882 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
            ++ ++K    ++ +KG+ GI R ++ +E  E    Y L  +G NLR+V    GV   + 
Sbjct: 206 KRIPKIK----NIQLKGIPGIERVLVKKEKDE----YVLYTQGSNLREVFKIEGVDTTRT 257

Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            +NN  E+ + LGIEAAR+ I+ E++  +E  G+ +D RH MLVAD+MT+ GEV
Sbjct: 258 ITNNIIEIQEVLGIEAARNAIINEMRNTLEQQGLEVDIRHLMLVADMMTADGEV 311


>gi|15920465|ref|NP_376134.1| DNA-directed RNA polymerase subunit A' [Sulfolobus tokodaii str. 7]
          Length = 884

 Score =  179 bits (454), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 108/275 (39%), Positives = 153/275 (55%), Gaps = 30/275 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++S+M H+ KVLP RTFR N  VC PYNADFDGDEMN+H+PQ+EEA
Sbjct: 417 DGDIVLFNRQPSLHRISMMGHKVKVLPGRTFRLNLLVCPPYNADFDGDEMNLHVPQSEEA 476

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
            AEA     K  ++ HR         N++TPR G  ++   QD+I+G YLLT K     R
Sbjct: 477 IAEA-----KEIMLVHR---------NIITPRYGGPIMGGAQDYISGAYLLTVKTTLLTR 522

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +      T I   +D  G I         P +       +TGKQI SL L  + +    
Sbjct: 523 EEV-----TTILGVTDFMGEIG-------EPAILAPREY-YTGKQIVSLFLPKDFNFHGQ 569

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           AN+    RA     E C  DSY++++N  LL G +DK  +G+    ++ + L+R++G + 
Sbjct: 570 ANISKGFRA--CKNEVCPHDSYIVIKNGILLEGVLDKKAIGNQQPESILHWLVREYGTEY 627

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVT-PGQGF 614
               M  + ++   ++  RGF++ + DVT P Q F
Sbjct: 628 GRWVMDNVFKLFIRFIELRGFTMTLDDVTIPPQAF 662



 Score =  113 bits (282), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 80/261 (30%), Positives = 130/261 (49%), Gaps = 49/261 (18%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D +++ S   I++  +Y +D   TPI  G++D R+G  +    C TCG  L+ C GHFG+
Sbjct: 21  DEIRKMSVTAIITSEVYDED--GTPIEGGVMDPRLGVIEPGQKCPTCGNTLNGCPGHFGH 78

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFR-----AKLRNPALSYLV 205
           I+L  PV H+G+ + V +IL++ C++  C R+ + EE    +       K R P+ +  +
Sbjct: 79  IELVRPVIHVGFVKHVYDILRATCRH--CGRLKIKEEDLQRYSRIYHAIKDRWPSAARRL 136

Query: 206 RKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYN 265
            + +KK  ++  +    CPHCGE           KI  EK  N               Y 
Sbjct: 137 VEYIKKNAMKNME----CPHCGEKQ--------FKIKLEKPYNF--------------YE 170

Query: 266 EAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLV 325
           E           +K G+I+ L P ++ +  E IP  D  LL  + + S+P  +ILT L V
Sbjct: 171 E-----------RKEGVIR-LTPSDIRERLERIPDSDYELLGYDPKYSRPEWMILTVLPV 218

Query: 326 PPNCIRPSVI--SDLKSDNDV 344
           PP  IRPS+   S +++++D+
Sbjct: 219 PPITIRPSITIESGIRAEDDL 239



 Score = 96.7 bits (239), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 45/74 (60%), Positives = 57/74 (77%), Gaps = 2/74 (2%)

Query: 606 GDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           GD++P  +GFV NSF  GLTP E FFH  GGREGLVDTAVKT+++GYMQRRL+ +L DL 
Sbjct: 776 GDISPDARGFVHNSFTRGLTPIEMFFHAAGGREGLVDTAVKTSQSGYMQRRLINALSDLR 835

Query: 665 VQYDMSFDAAFYGQ 678
           V+YD +   + YG+
Sbjct: 836 VEYDGTV-RSLYGE 848


>gi|307595331|ref|YP_003901648.1| DNA-directed RNA polymerase subunit A' [Vulcanisaeta distributa DSM
           14429]
 gi|307550532|gb|ADN50597.1| DNA-directed RNA polymerase subunit A' [Vulcanisaeta distributa DSM
           14429]
          Length = 891

 Score =  179 bits (454), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 99/265 (37%), Positives = 153/265 (57%), Gaps = 31/265 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + D+VLFNRQPSLH++S+M H  +VLP RTFR +  VC PYNADFDGDEMN+H+PQ EEA
Sbjct: 428 NGDIVLFNRQPSLHRMSMMGHIVRVLPGRTFRLHLAVCPPYNADFDGDEMNLHVPQNEEA 487

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              AK LM  +++++TPR G  +I A QD+ITGGYLLT+K+ F N+
Sbjct: 488 RAE--------------AKTLMLVQNHIITPRYGGPIIGARQDYITGGYLLTRKDTFVNK 533

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              M + +    D     G I         P + +    +WTGKQ+ S++L  +    +N
Sbjct: 534 ELLMYLLAAANYD-----GEID-------EPAI-MHPKELWTGKQVVSMLLPKD----LN 576

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
               T  +    +   C+ D Y+++ N  +  G +DK ++G+    ++++++++ +G D 
Sbjct: 577 WVQPTAIKESCKDPYNCYTDEYIVVVNGYMATGVLDKKSIGAEQVDSLWHVVVKRYGNDY 636

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGI 605
           A   +  + R    +L  RGF++GI
Sbjct: 637 ARKWVDSVLRALLRFLDLRGFTMGI 661



 Score =  117 bits (293), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 74/257 (28%), Positives = 128/257 (49%), Gaps = 46/257 (17%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           I+ ++   D ++  S ++I +   Y  D    P+  GL+DRR+G  +  A C TCG    
Sbjct: 23  IKFSILSPDVIRSMSVMEITTSETY--DEAGRPMVGGLMDRRLGVVEPGARCETCGNPPD 80

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGF-----RAKLR 197
            C GHFG I+L  PV H+ Y + + ++L++ C+   C R+LL +E+   +     R ++R
Sbjct: 81  KCPGHFGRIELARPVIHVEYAKYIHDLLRTTCRE--CGRILLTDEEIEKYSKRLARLRVR 138

Query: 198 NPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIV 257
              L+  + + ++KK +E T    VCPHCG                ++YK R ++     
Sbjct: 139 WKLLADRLIERIRKKAMERT----VCPHCGA---------------KQYKIRFERPYTFY 179

Query: 258 EDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSD 317
           E+                  K+ G+++ L+P+++ +  E IP  D+ LL  + + ++P  
Sbjct: 180 EE------------------KENGVLEKLDPMKIRERLEKIPDSDLELLGWDPKFARPEW 221

Query: 318 LILTRLLVPPNCIRPSV 334
            ILT L VPP  +RPS+
Sbjct: 222 AILTVLPVPPPQVRPSI 238



 Score = 93.6 bits (231), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 41/64 (64%), Positives = 53/64 (82%), Gaps = 1/64 (1%)

Query: 606 GDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           GD+ P  +GFV+N+F  GLTP EFFFH  GGR+GLVDTAV+TA++GYMQRRL+ +L+D+ 
Sbjct: 785 GDLGPMAKGFVRNNFKVGLTPVEFFFHAAGGRDGLVDTAVRTAQSGYMQRRLINALQDIY 844

Query: 665 VQYD 668
           V YD
Sbjct: 845 VAYD 848



 Score = 50.8 bits (120), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 22/46 (47%), Positives = 33/46 (71%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 65
           + LM  +++++TPR G  +I A QD+ITGGYLLT+K+ F N+   M
Sbjct: 492 KTLMLVQNHIITPRYGGPIIGARQDYITGGYLLTRKDTFVNKELLM 537


>gi|342306129|dbj|BAK54218.1| DNA-directed RNA polymerase subunit A' [Sulfolobus tokodaii str. 7]
          Length = 880

 Score =  179 bits (454), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 108/275 (39%), Positives = 153/275 (55%), Gaps = 30/275 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++S+M H+ KVLP RTFR N  VC PYNADFDGDEMN+H+PQ+EEA
Sbjct: 413 DGDIVLFNRQPSLHRISMMGHKVKVLPGRTFRLNLLVCPPYNADFDGDEMNLHVPQSEEA 472

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
            AEA     K  ++ HR         N++TPR G  ++   QD+I+G YLLT K     R
Sbjct: 473 IAEA-----KEIMLVHR---------NIITPRYGGPIMGGAQDYISGAYLLTVKTTLLTR 518

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +      T I   +D  G I         P +       +TGKQI SL L  + +    
Sbjct: 519 EEV-----TTILGVTDFMGEIG-------EPAILAPREY-YTGKQIVSLFLPKDFNFHGQ 565

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           AN+    RA     E C  DSY++++N  LL G +DK  +G+    ++ + L+R++G + 
Sbjct: 566 ANISKGFRA--CKNEVCPHDSYIVIKNGILLEGVLDKKAIGNQQPESILHWLVREYGTEY 623

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVT-PGQGF 614
               M  + ++   ++  RGF++ + DVT P Q F
Sbjct: 624 GRWVMDNVFKLFIRFIELRGFTMTLDDVTIPPQAF 658



 Score =  112 bits (281), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 80/261 (30%), Positives = 130/261 (49%), Gaps = 49/261 (18%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D +++ S   I++  +Y +D   TPI  G++D R+G  +    C TCG  L+ C GHFG+
Sbjct: 17  DEIRKMSVTAIITSEVYDED--GTPIEGGVMDPRLGVIEPGQKCPTCGNTLNGCPGHFGH 74

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-----KLRNPALSYLV 205
           I+L  PV H+G+ + V +IL++ C++  C R+ + EE    +       K R P+ +  +
Sbjct: 75  IELVRPVIHVGFVKHVYDILRATCRH--CGRLKIKEEDLQRYSRIYHAIKDRWPSAARRL 132

Query: 206 RKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYN 265
            + +KK  ++  +    CPHCGE           KI  EK  N               Y 
Sbjct: 133 VEYIKKNAMKNME----CPHCGEKQ--------FKIKLEKPYNF--------------YE 166

Query: 266 EAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLV 325
           E           +K G+I+ L P ++ +  E IP  D  LL  + + S+P  +ILT L V
Sbjct: 167 E-----------RKEGVIR-LTPSDIRERLERIPDSDYELLGYDPKYSRPEWMILTVLPV 214

Query: 326 PPNCIRPSVI--SDLKSDNDV 344
           PP  IRPS+   S +++++D+
Sbjct: 215 PPITIRPSITIESGIRAEDDL 235



 Score = 96.7 bits (239), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 45/74 (60%), Positives = 57/74 (77%), Gaps = 2/74 (2%)

Query: 606 GDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           GD++P  +GFV NSF  GLTP E FFH  GGREGLVDTAVKT+++GYMQRRL+ +L DL 
Sbjct: 772 GDISPDARGFVHNSFTRGLTPIEMFFHAAGGREGLVDTAVKTSQSGYMQRRLINALSDLR 831

Query: 665 VQYDMSFDAAFYGQ 678
           V+YD +   + YG+
Sbjct: 832 VEYDGTV-RSLYGE 844


>gi|156937039|ref|YP_001434835.1| DNA-directed RNA polymerase subunit A [Ignicoccus hospitalis KIN4/I]
 gi|156566023|gb|ABU81428.1| DNA-directed RNA polymerase, subunit A [Ignicoccus hospitalis KIN4/I]
          Length = 422

 Score =  179 bits (454), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 118/337 (35%), Positives = 178/337 (52%), Gaps = 57/337 (16%)

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCE------ 1149
            ++RAQ+EP  AVG +AAQSIGEP TQMTL+TFH+AG              E+ +      
Sbjct: 68   FLRAQVEPGEAVGTVAAQSIGEPSTQMTLRTFHYAGVKELNVTLGLPRLIEIVDARRTPS 127

Query: 1150 ------YIEEVFVPDDSFIL---IKLDMDRIRLLHLEVDIDSIRYCI--------ERTRG 1192
                  Y++E    D    L    K++M ++  +   V+ID     I           +G
Sbjct: 128  TPTMTVYLDEEHRHDKEKALEVARKIEMTKVENVASSVEIDWFETTIIVRLDPEMMEDKG 187

Query: 1193 ISGHLTVSGHSFLILK------PKDS--------SKSFNS--KMYQMKQLLPSVVIKGVQ 1236
            I+    +   + L +K      P D          +++ S  ++ +++  + S  IKG++
Sbjct: 188  ITRDDVIKAINRLRIKGRAEPDPDDEYAVLVRLDPEAYTSIGELQKVRDKVLSAKIKGIK 247

Query: 1237 GINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARS 1296
            GINR ++ + + E    Y L+ +G NL  V+   GV   +  S++  E+ + LGIEAAR 
Sbjct: 248  GINRVIVQQREDE----YVLVTDGSNLAQVLEVEGVDPTRTVSDSIKEIEEVLGIEAARQ 303

Query: 1297 TIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTS 1356
             I+ EI  V+EN G+ +D RH ML+AD MT  GEV  + RHG+A  K SVL  A+FE T 
Sbjct: 304  AIINEILDVLENQGLDVDRRHIMLLADAMTWSGEVRQVGRHGIAGTKPSVLARAAFEVTV 363

Query: 1357 DHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
              L DAA  G+ D + GV+E II+G P+ +GTG++ L
Sbjct: 364  KQLVDAAVEGEVDELKGVTENIIIGQPIPLGTGMVLL 400



 Score =  107 bits (267), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 76/236 (32%), Positives = 128/236 (54%), Gaps = 13/236 (5%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A R  STP +T YLD++   D + A  V  ++E T +  V   +E  +  
Sbjct: 112 GLPRLIEIVDARRTPSTPTMTVYLDEEHRHDKEKALEVARKIEMTKVENVASSVEIDWF- 170

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
            ++ I+++LD + +      +  D +   I R R I G           +  +   +++ 
Sbjct: 171 -ETTIIVRLDPEMME--DKGITRDDVIKAINRLR-IKGRAEPDPDDEYAVLVRLDPEAYT 226

Query: 882 S--KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
           S  ++ +++  + S  IKG++GINR ++ + + E    Y L+ +G NL  V+   GV   
Sbjct: 227 SIGELQKVRDKVLSAKIKGIKGINRVIVQQREDE----YVLVTDGSNLAQVLEVEGVDPT 282

Query: 940 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
           +  S++  E+ + LGIEAAR  I+ EI  V+EN G+ +D RH ML+AD MT  GEV
Sbjct: 283 RTVSDSIKEIEEVLGIEAARQAIINEILDVLENQGLDVDRRHIMLLADAMTWSGEV 338


>gi|330833901|ref|YP_004408629.1| DNA-directed RNA polymerase subunit A' [Metallosphaera cuprina
           Ar-4]
 gi|329566040|gb|AEB94145.1| DNA-directed RNA polymerase subunit A' [Metallosphaera cuprina
           Ar-4]
          Length = 886

 Score =  179 bits (453), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 102/269 (37%), Positives = 147/269 (54%), Gaps = 29/269 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++S+M HR +VLP RTFR N  VC PYNADFDGDEMN+H+PQ+EEA
Sbjct: 419 DGDIVIFNRQPSLHRISMMGHRVRVLPGRTFRLNLLVCPPYNADFDGDEMNLHVPQSEEA 478

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
            AE               K LM    N++TPR G  +I + QD+I+G YLLT K    + 
Sbjct: 479 IAE--------------TKELMTVHRNILTPRYGGPIIGSAQDYISGAYLLTVKTTLLSE 524

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +   I    +AD +   G           P +      ++TGKQI S  L    +    
Sbjct: 525 DEVQTILG--VADINKDLG----------EPAILA-PKRLYTGKQIVSHFLPEEFNFHGP 571

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           AN+ +  R  +  +E C  DSYV+++  +LL G  DK  LG+    ++ + L+R++ ED 
Sbjct: 572 ANISSGVR--SCKDEDCPHDSYVVIKRGKLLEGVFDKKALGNQQAESILHWLVREYDEDY 629

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVT 609
            +  M  L ++   Y+   G ++ + DVT
Sbjct: 630 VLWLMDNLFKVFLRYIELHGLTMTLSDVT 658



 Score =  116 bits (290), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 80/261 (30%), Positives = 130/261 (49%), Gaps = 49/261 (18%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D +++ S   I++ ++Y +D   TPI   ++D R+G  +    C  CG  +  C GHFG+
Sbjct: 23  DEIRKMSVTAIITADVYDEDG--TPIEGSVMDSRLGIIEPGQKCPVCGNVIGSCPGHFGH 80

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-----KLRNPALSYLV 205
           I+L  PV H+G+ + V ++L+S CK   C R+ + EE    ++      K R P+ +   
Sbjct: 81  IELVRPVIHVGFVKHVYDLLRSTCKR--CGRIKINEEDIQKYKKIHDAIKKRWPSAA--- 135

Query: 206 RKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYN 265
            K L   + + + K + CPHC E          LKI  EK  N                 
Sbjct: 136 -KRLVDHVKKASMKATTCPHCSEKQ--------LKIKLEKPYN----------------- 169

Query: 266 EAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLV 325
               F  E    +K GL++ L PL++ +  E IP  D+ LL  +  +S+P  +ILT L V
Sbjct: 170 ----FFEE----RKEGLMR-LTPLDIRERLENIPDSDVELLGYDPTVSRPEWIILTVLPV 220

Query: 326 PPNCIRPSVI--SDLKSDNDV 344
           PP  IRPS++  S +++++D+
Sbjct: 221 PPITIRPSIMIESGIRAEDDL 241



 Score = 89.0 bits (219), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 40/73 (54%), Positives = 55/73 (75%), Gaps = 2/73 (2%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D++P  +GF+ +SF SGL P E FFH  GGREGLVDTAV+T+++GYMQRRL+ +L DL +
Sbjct: 779 DISPEARGFIYSSFRSGLNPIETFFHAAGGREGLVDTAVRTSQSGYMQRRLINALSDLRI 838

Query: 666 QYDMSFDAAFYGQ 678
           +YD +     YG+
Sbjct: 839 EYDGTV-RTLYGE 850


>gi|330040372|ref|XP_003239880.1| RNA polymerase III largest subunit [Cryptomonas paramecium]
 gi|327206805|gb|AEA38982.1| RNA polymerase III largest subunit [Cryptomonas paramecium]
          Length = 1298

 Score =  179 bits (453), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 102/291 (35%), Positives = 150/291 (51%), Gaps = 43/291 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND +LFNRQPSLH++SIM+HR K++P++TF+ N C C PYNADFDGDEMN+H+PQT++A
Sbjct: 417 DNDTILFNRQPSLHRVSIMSHRIKIVPNKTFKLNSCSCKPYNADFDGDEMNIHVPQTQKA 476

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R+E++              VLM    N +TPRNGEL I+ TQD ++  +L+T +N FF+ 
Sbjct: 477 RSESM--------------VLMNLALNTITPRNGELQISPTQDLLSLSFLMTSRNQFFSL 522

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDC--- 517
                   +       +  IIK        PV       +WTGKQ+F  IL  N D    
Sbjct: 523 ETFSNFYISKDKKNFPVPSIIK--------PV------QLWTGKQVFFSILCINHDLSDE 568

Query: 518 -------PVNANLKTKGRAYTANEE-----FCHRDSYVILRNSELLAGSMDKSTLGSGGK 565
                  P     +   + Y+ N++      C  D +V+ +  EL++G + K ++G    
Sbjct: 569 KKNRFYQPDINVFQNTEKTYSLNKQQCSPFVCPHDGWVVFKKKELISGRIGKQSIGPNNS 628

Query: 566 ANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
            +  Y L         + ++ + S +    +   GFSIGI DV P     Q
Sbjct: 629 FSFLYTLANLHSFCSIINSISKYSYIALKSISEYGFSIGIDDVIPNYKLSQ 679



 Score =  121 bits (303), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 65/151 (43%), Positives = 99/151 (65%), Gaps = 4/151 (2%)

Query: 1247 DVEGVTKYK----LLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEI 1302
            D   +++YK     +++G NL  +     V      SN+ ++  KTLGIEAARS I+ E+
Sbjct: 1144 DKRLISQYKKNPEFILKGSNLMSLANFSFVNQKTIYSNHIFDTVKTLGIEAARSVIVIEL 1203

Query: 1303 KLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDA 1362
            +++ E +G+ I+ +H  L++DLMT +GE+LGITR+GLAK+K + L LASFE T ++LF +
Sbjct: 1204 EIIFEAYGIKINKKHLSLLSDLMTFQGEILGITRYGLAKIKSNTLVLASFEKTVENLFTS 1263

Query: 1363 AFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            A     D + GVSE II+G  + +GTGL+ L
Sbjct: 1264 AIKISKDQVCGVSENIILGKEIPIGTGLVSL 1294



 Score =  119 bits (297), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 82/246 (33%), Positives = 120/246 (48%), Gaps = 38/246 (15%)

Query: 105 NLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFR 164
           N +CQ         GLLD ++G +QK   C  C +++ +C GHFGYI L LPVF+IGY +
Sbjct: 35  NKFCQG--------GLLDDKLGCHQKFL-CKICEKSIKECTGHFGYIKLYLPVFNIGYLK 85

Query: 165 CVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKK--KILETTKKVSV 222
            V  +LQ +CK  +C+RVL+  +K       +     S      +K   KI++  K  + 
Sbjct: 86  SVQTLLQIVCK--SCSRVLVKSKKTKTNILNISKEIGSGKEYNFIKHIIKIVQNIKTNTN 143

Query: 223 CPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGL 282
           C HC   NG+VKK G     H+                       V F    E  KK   
Sbjct: 144 CVHCNSKNGIVKKLGNFNFIHD-----------------------VTFWQSFENKKKKPN 180

Query: 283 IQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRP--SVISDLKS 340
           +  LNPL+  ++F+ I   D+ L+ M    S+P +LILT + VPP  IRP  SV   + +
Sbjct: 181 LIILNPLKAFRIFQKIGTNDLNLIGMEQINSRPENLILTYITVPPLTIRPSISVTETITN 240

Query: 341 DNDVVL 346
           ++D+ L
Sbjct: 241 EDDLTL 246



 Score = 85.1 bits (209), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 38/62 (61%), Positives = 45/62 (72%)

Query: 613 GFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFD 672
           GF+  SF  GLT   FF HTM GREGL+DTA+KTA+TGY+QRRL+K LED+   YD S  
Sbjct: 791 GFIVYSFQEGLTNKNFFLHTMAGREGLIDTAIKTAQTGYIQRRLIKFLEDIVCSYDFSTR 850

Query: 673 AA 674
            A
Sbjct: 851 TA 852



 Score = 75.9 bits (185), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 69/251 (27%), Positives = 119/251 (47%), Gaps = 32/251 (12%)

Query: 764  GVPRIKEIINASRNISTPIITAYLD---KDTDLDYARIVKGRLERTTLGEVCEYIEEVFV 820
            G  RI EI+NAS+ I+ P     L    K   L   +++KG     +L  +CE I+    
Sbjct: 999  GTCRINEILNASKTINFPTTKIQLTTSIKKHILGIKKLLKG----FSLKNICEVIKITLK 1054

Query: 821  PDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF 880
             +     IKL+++    +   ++++ I+  I+  +  S         F++ K K+  K F
Sbjct: 1055 ANKLKCDIKLNLNEFLFICKLIELNEIKKKIKNYQIKS--------KFVMKKTKNKLKIF 1106

Query: 881  NSKMYQMKQLLPSVVIKGVQGINRAVIHEEDV----------EGVTKYK----LLVEGDN 926
                Y           K ++ IN    H  D+            +++YK     +++G N
Sbjct: 1107 ---FYNSSFTCKFTHFKLMKLINFCKNHLVDLPLNKSLTPDKRLISQYKKNPEFILKGSN 1163

Query: 927  LRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVA 986
            L  +     V      SN+ ++  KTLGIEAARS I+ E++++ E +G+ I+ +H  L++
Sbjct: 1164 LMSLANFSFVNQKTIYSNHIFDTVKTLGIEAARSVIVIELEIIFEAYGIKINKKHLSLLS 1223

Query: 987  DLMTSKGEVLG 997
            DLMT +GE+LG
Sbjct: 1224 DLMTFQGEILG 1234



 Score = 48.1 bits (113), Expect = 0.040,   Method: Compositional matrix adjust.
 Identities = 20/36 (55%), Positives = 26/36 (72%)

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            ++    +P + VGA A QSIGEP TQ+TL+TFH AG
Sbjct: 955  FLSCLTDPGSPVGAEAGQSIGEPSTQLTLQTFHSAG 990



 Score = 44.7 bits (104), Expect = 0.40,   Method: Compositional matrix adjust.
 Identities = 20/39 (51%), Positives = 27/39 (69%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFF 59
           VLM    N +TPRNGEL I+ TQD ++  +L+T +N FF
Sbjct: 482 VLMNLALNTITPRNGELQISPTQDLLSLSFLMTSRNQFF 520


>gi|15897170|ref|NP_341775.1| DNA-directed RNA polymerase subunit A'' [Sulfolobus solfataricus P2]
 gi|239782144|pdb|3HKZ|C Chain C, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
 gi|239782157|pdb|3HKZ|M Chain M, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
 gi|13813359|gb|AAK40565.1| DNA-directed RNA polymerase, subunit A'' (rpoA2) [Sulfolobus
            solfataricus P2]
          Length = 395

 Score =  178 bits (452), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 127/392 (32%), Positives = 196/392 (50%), Gaps = 65/392 (16%)

Query: 1054 KKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRA 1113
            K +LEE  K+ S    Q K+   L+  IL+ +  +        F  A K      +Y   
Sbjct: 10   KPYLEEKVKQASNILPQ-KIVDDLKNLILNKEIIVTRDEIDKIFDLAIK------EYSEG 62

Query: 1114 QIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFVPDDSFI 1162
             I P  A+G +AAQS+GEPGTQMTL+TFHFAG            + E ++   VP    +
Sbjct: 63   LIAPGEAIGIVAAQSVGEPGTQMTLRTFHFAGIRELNVTLGLPRLIEIVDAKKVPSTPMM 122

Query: 1163 LIKL----DMDRIRLLHL----------------EVDIDSIRYCIE------RTRGIS-- 1194
             I L      DR + L +                 +DI S+   ++      + +G++  
Sbjct: 123  TIYLTDEYKRDRDKALEVARKLEYTKIENVVSSTSIDIASMSIILQLDNEMLKDKGVTVD 182

Query: 1195 ------GHLTVSGHSFLILKPKDSSKSFN-------SKMYQMKQLLPSVVIKGVQGINRA 1241
                  G L +    F+I + +DS+ + N       + +++++  + +  IKG++GI RA
Sbjct: 183  DVKKAIGRLKLG--DFMIEESEDSTLNINFANIDSIAALFKLRDKILNTKIKGIKGIKRA 240

Query: 1242 VIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTE 1301
            ++ ++  E    Y +L +G NL  V++  GV   K  +NN  E+ +  GIEAAR  I+ E
Sbjct: 241  IVQKKGDE----YIILTDGSNLSGVLSVKGVDVAKVETNNIREIEEVFGIEAAREIIIRE 296

Query: 1302 IKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFD 1361
            I  V+   G+ +D RH +L+AD+MT  G V  I RHG+   K SVL  A+FE T  HL D
Sbjct: 297  ISKVLAEQGLDVDIRHILLIADVMTRTGIVRQIGRHGVTGEKNSVLARAAFEVTVKHLLD 356

Query: 1362 AAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            AA  G  +   GV E II+G P+ +GTG+++L
Sbjct: 357  AAARGDVEEFKGVVENIIIGHPIKLGTGMVEL 388



 Score =  107 bits (266), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 76/243 (31%), Positives = 127/243 (52%), Gaps = 34/243 (13%)

Query: 764 GVPRIKEIINASRNISTPIITAYL------DKDTDLDYARIVKGRLERTTLGEVCEYIEE 817
           G+PR+ EI++A +  STP++T YL      D+D  L+ AR    +LE T +  V      
Sbjct: 103 GLPRLIEIVDAKKVPSTPMMTIYLTDEYKRDRDKALEVAR----KLEYTKIENVVSSTS- 157

Query: 818 VFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSS 877
               D + + I L +D   L    V +D ++  I       G L +    F+I + +DS+
Sbjct: 158 ---IDIASMSIILQLDNEMLKDKGVTVDDVKKAI-------GRLKLG--DFMIEESEDST 205

Query: 878 KSFN-------SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDV 930
            + N       + +++++  + +  IKG++GI RA++ ++  E    Y +L +G NL  V
Sbjct: 206 LNINFANIDSIAALFKLRDKILNTKIKGIKGIKRAIVQKKGDE----YIILTDGSNLSGV 261

Query: 931 MATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMT 990
           ++  GV   K  +NN  E+ +  GIEAAR  I+ EI  V+   G+ +D RH +L+AD+MT
Sbjct: 262 LSVKGVDVAKVETNNIREIEEVFGIEAAREIIIREISKVLAEQGLDVDIRHILLIADVMT 321

Query: 991 SKG 993
             G
Sbjct: 322 RTG 324


>gi|320101549|ref|YP_004177141.1| DNA-directed RNA polymerase subunit A' [Desulfurococcus mucosus DSM
           2162]
 gi|319753901|gb|ADV65659.1| DNA-directed RNA polymerase, subunit A' [Desulfurococcus mucosus
           DSM 2162]
          Length = 885

 Score =  178 bits (452), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 97/270 (35%), Positives = 151/270 (55%), Gaps = 30/270 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH++S+MAH  +VLP++TFR N  VC PYNADFDGDEMN+H+PQ+EEA
Sbjct: 416 DGDVVLFNRQPSLHRISVMAHIVRVLPYKTFRLNLLVCPPYNADFDGDEMNLHVPQSEEA 475

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R E              A++LM  + +++TPR G  +I   QD+I+G Y+LT K    ++
Sbjct: 476 RTE--------------ARLLMLVERHILTPRYGGPIIGGLQDYISGAYILTSKTTLLSK 521

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNP-VVFVRTAVIWTGKQIFSLILKPNRDCPV 519
                          D+  ++    ++   P    ++   +WTGKQ+ SL L  + +   
Sbjct: 522 --------------DDVVDLLAVTGYKGEIPEPAILKPRELWTGKQLVSLFLPKDFNYKR 567

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           N+ + +   A    +E C  DS VI++N  LL G +DK+++G     ++ + L++++GED
Sbjct: 568 NSKIGSAA-ALRCIDEDCPHDSMVIVKNGVLLEGVLDKASIGREEPESLVHWLIKEYGED 626

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVT 609
                M R+ +M        GF++    +T
Sbjct: 627 YGRMFMDRVYKMFIRMSEKHGFTMSYSHLT 656



 Score =  112 bits (279), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 77/259 (29%), Positives = 124/259 (47%), Gaps = 44/259 (16%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D +++ S  QI S  +Y  D   +PI  G++DRR+G  +    C  CG     C GHFG+
Sbjct: 20  DEIRKMSVTQIFSAEVYDND--GSPIDGGVMDRRLGAIEPGEACPICGNTRDSCPGHFGH 77

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFR---AKLRNPALSYLVRK 207
           I+L  PV H+G+ + ++  L++ C+N  C R+ + EE+   +    + L      YL+ K
Sbjct: 78  IELAKPVIHVGFVKHILMYLRATCRN--CGRLKIPEEERNEYLRLLSDLHELGAPYLI-K 134

Query: 208 SLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEA 267
              + I        VCPHCG     VK+          YK + +K     E         
Sbjct: 135 RFHEYIRRKASAAEVCPHCG-----VKQ----------YKVKLEKPHTFYE--------- 170

Query: 268 VKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPP 327
                      + GL++ L P EV    E IP +D+ LL  +   ++P  ++LT L VPP
Sbjct: 171 ---------QTEKGLVK-LTPSEVRGRLEKIPDDDVKLLGGDPRDARPEWMVLTVLPVPP 220

Query: 328 NCIRPSVI--SDLKSDNDV 344
             +RPSV+  + ++S++D+
Sbjct: 221 RSVRPSVLLETGIRSEDDL 239



 Score = 88.2 bits (217), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 42/85 (49%), Positives = 56/85 (65%), Gaps = 1/85 (1%)

Query: 587 RLSRMTSFYLMNRGFSIGIGDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVK 645
           R  R+T  YL          D+ P  +GF+ N F +GL P E FFH   GREGL+DTAV+
Sbjct: 758 RGKRLTRGYLGRALPHFKPEDLGPEARGFIANGFVNGLNPVEMFFHAAAGREGLIDTAVR 817

Query: 646 TAETGYMQRRLVKSLEDLCVQYDMS 670
           T+++GYMQRRL+ +L+DL V+YD S
Sbjct: 818 TSQSGYMQRRLINALQDLRVEYDGS 842


>gi|435852041|ref|YP_007313627.1| DNA-directed RNA polymerase, subunit A'' [Methanomethylovorans
            hollandica DSM 15978]
 gi|433662671|gb|AGB50097.1| DNA-directed RNA polymerase, subunit A'' [Methanomethylovorans
            hollandica DSM 15978]
          Length = 380

 Score =  178 bits (452), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 113/342 (33%), Positives = 176/342 (51%), Gaps = 58/342 (16%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCE 1149
            E  +E Y  A++EP  AVG ++AQSIGEPGTQMT++TFH+AG              E+ +
Sbjct: 44   EKVKESYEYAKVEPCEAVGVVSAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVD 103

Query: 1150 YIEEVFVPDDSFILIK---LDMDRIRLLHLEV-------------DIDSIRYCIERTRGI 1193
              +E   P  +  +++    D D++R L  E+             D+ +++  I+     
Sbjct: 104  ARKEPSTPTMTISVLEEYAQDRDKVRKLAWEIEATHIDQLADVTTDLLNMQLIIDLHEKT 163

Query: 1194 SGHLTVSGHSF---------------------LILKPKDSSKSFNSKMYQMKQLLPSVVI 1232
              H ++S                         LI+ PK+ S     ++ QM + + S+ +
Sbjct: 164  LNHRSISVDELIEKLSDKLDVQVRLSENIENQLIVNPKEPSY---RELLQMAKNINSITL 220

Query: 1233 KGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIE 1292
            KG++G+ R VI ++  E    Y L  EG  L+ V+   GV   +  +NN  E+Y   GIE
Sbjct: 221  KGIEGVKRVVIRKDSDE----YMLYTEGSQLKKVLEVEGVDISRTYTNNISEIYDVFGIE 276

Query: 1293 AARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASF 1352
            AAR+ I+ E    +   G+++D RH MLV+D+M   GEV  I RHG++  K SV   A+F
Sbjct: 277  AARNAIIKEATSTLGEQGLTVDIRHIMLVSDIMCCDGEVKQIGRHGISGEKASVFARAAF 336

Query: 1353 ENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            E T +HL DA   G  D ++GV+E II+G P+ +GTG + L+
Sbjct: 337  EVTVNHLLDAGMRGDIDELNGVTENIIVGQPIKLGTGDVHLV 378



 Score =  101 bits (252), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 69/234 (29%), Positives = 123/234 (52%), Gaps = 14/234 (5%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A +  STP +T  + ++   D D  R +   +E T + ++ +   ++   
Sbjct: 94  GLPRLIEIVDARKEPSTPTMTISVLEEYAQDRDKVRKLAWEIEATHIDQLADVTTDLL-- 151

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             +  LI +D+    L H  + +D +   +     +   L+ +  + LI+ PK+ S    
Sbjct: 152 --NMQLI-IDLHEKTLNHRSISVDELIEKLSDKLDVQVRLSENIENQLIVNPKEPSYR-- 206

Query: 882 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
            ++ QM + + S+ +KG++G+ R VI ++  E    Y L  EG  L+ V+   GV   + 
Sbjct: 207 -ELLQMAKNINSITLKGIEGVKRVVIRKDSDE----YMLYTEGSQLKKVLEVEGVDISRT 261

Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            +NN  E+Y   GIEAAR+ I+ E    +   G+++D RH MLV+D+M   GEV
Sbjct: 262 YTNNISEIYDVFGIEAARNAIIKEATSTLGEQGLTVDIRHIMLVSDIMCCDGEV 315


>gi|284174416|ref|ZP_06388385.1| DNA-directed RNA polymerase subunit A'' [Sulfolobus solfataricus
            98/2]
 gi|384433683|ref|YP_005643041.1| DNA-directed RNA polymerase subunit A'' [Sulfolobus solfataricus
            98/2]
 gi|14548240|sp|P58192.1|RPOA2_SULSO RecName: Full=DNA-directed RNA polymerase subunit A''
 gi|167744882|pdb|2PMZ|C Chain C, Archaeal Rna Polymerase From Sulfolobus Solfataricus
 gi|167744893|pdb|2PMZ|G Chain G, Archaeal Rna Polymerase From Sulfolobus Solfataricus
 gi|261601837|gb|ACX91440.1| DNA-directed RNA polymerase, subunit A'' [Sulfolobus solfataricus
            98/2]
          Length = 392

 Score =  178 bits (452), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 127/392 (32%), Positives = 196/392 (50%), Gaps = 65/392 (16%)

Query: 1054 KKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRA 1113
            K +LEE  K+ S    Q K+   L+  IL+ +  +        F  A K      +Y   
Sbjct: 7    KPYLEEKVKQASNILPQ-KIVDDLKNLILNKEIIVTRDEIDKIFDLAIK------EYSEG 59

Query: 1114 QIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFVPDDSFI 1162
             I P  A+G +AAQS+GEPGTQMTL+TFHFAG            + E ++   VP    +
Sbjct: 60   LIAPGEAIGIVAAQSVGEPGTQMTLRTFHFAGIRELNVTLGLPRLIEIVDAKKVPSTPMM 119

Query: 1163 LIKL----DMDRIRLLHL----------------EVDIDSIRYCIE------RTRGIS-- 1194
             I L      DR + L +                 +DI S+   ++      + +G++  
Sbjct: 120  TIYLTDEYKRDRDKALEVARKLEYTKIENVVSSTSIDIASMSIILQLDNEMLKDKGVTVD 179

Query: 1195 ------GHLTVSGHSFLILKPKDSSKSFN-------SKMYQMKQLLPSVVIKGVQGINRA 1241
                  G L +    F+I + +DS+ + N       + +++++  + +  IKG++GI RA
Sbjct: 180  DVKKAIGRLKLG--DFMIEESEDSTLNINFANIDSIAALFKLRDKILNTKIKGIKGIKRA 237

Query: 1242 VIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTE 1301
            ++ ++  E    Y +L +G NL  V++  GV   K  +NN  E+ +  GIEAAR  I+ E
Sbjct: 238  IVQKKGDE----YIILTDGSNLSGVLSVKGVDVAKVETNNIREIEEVFGIEAAREIIIRE 293

Query: 1302 IKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFD 1361
            I  V+   G+ +D RH +L+AD+MT  G V  I RHG+   K SVL  A+FE T  HL D
Sbjct: 294  ISKVLAEQGLDVDIRHILLIADVMTRTGIVRQIGRHGVTGEKNSVLARAAFEVTVKHLLD 353

Query: 1362 AAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            AA  G  +   GV E II+G P+ +GTG+++L
Sbjct: 354  AAARGDVEEFKGVVENIIIGHPIKLGTGMVEL 385



 Score =  106 bits (265), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 76/243 (31%), Positives = 127/243 (52%), Gaps = 34/243 (13%)

Query: 764 GVPRIKEIINASRNISTPIITAYL------DKDTDLDYARIVKGRLERTTLGEVCEYIEE 817
           G+PR+ EI++A +  STP++T YL      D+D  L+ AR    +LE T +  V      
Sbjct: 100 GLPRLIEIVDAKKVPSTPMMTIYLTDEYKRDRDKALEVAR----KLEYTKIENVVSSTS- 154

Query: 818 VFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSS 877
               D + + I L +D   L    V +D ++  I       G L +    F+I + +DS+
Sbjct: 155 ---IDIASMSIILQLDNEMLKDKGVTVDDVKKAI-------GRLKLG--DFMIEESEDST 202

Query: 878 KSFN-------SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDV 930
            + N       + +++++  + +  IKG++GI RA++ ++  E    Y +L +G NL  V
Sbjct: 203 LNINFANIDSIAALFKLRDKILNTKIKGIKGIKRAIVQKKGDE----YIILTDGSNLSGV 258

Query: 931 MATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMT 990
           ++  GV   K  +NN  E+ +  GIEAAR  I+ EI  V+   G+ +D RH +L+AD+MT
Sbjct: 259 LSVKGVDVAKVETNNIREIEEVFGIEAAREIIIREISKVLAEQGLDVDIRHILLIADVMT 318

Query: 991 SKG 993
             G
Sbjct: 319 RTG 321


>gi|268323373|emb|CBH36961.1| probable DNA-directed RNA polymerase subunit A'' [uncultured
            archaeon]
          Length = 445

 Score =  178 bits (452), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 117/341 (34%), Positives = 181/341 (53%), Gaps = 60/341 (17%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEY 1150
            A  +KY  AQ+EP  AVG +AAQSIGEPGTQMT++TFH+AG              E+ + 
Sbjct: 109  AVEQKYEEAQVEPREAVGIVAAQSIGEPGTQMTMRTFHYAGVGAIYITLGLPRIIEIVDA 168

Query: 1151 IEEVFVPDDSFILI-----------KLDMDRIRLLHLEVDIDSIRYCIE----------- 1188
             +++  P     L+           K+ M+ I   H+  DI  ++  IE           
Sbjct: 169  RKKLSTPTMKVKLVSEFASERNKAEKIAME-IEETHIR-DIAKVKAAIEDMSVWIVLNAK 226

Query: 1189 ----------------RTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVI 1232
                            +  G +  + V G   L +  KD  K+++  + +++  + + ++
Sbjct: 227  ELKRRYIMSDEVEQTIKDIGTALLVEVVGDGKLRIHVKD--KTYHD-LLRLEAKVSNTLV 283

Query: 1233 KGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIE 1292
            KG+ GI RA++   D  G  +Y L  EG  L+ V+   GV   + ++NN  E+   LGIE
Sbjct: 284  KGIDGIKRALVRR-DPSG--EYVLYTEGSALKKVLKVEGVDSRRTTTNNINEISDVLGIE 340

Query: 1293 AARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASF 1352
            AAR+ I+ E+   ++  G+ +D RH  L+AD MT  GEV  I RHG+A  K SVL+ A+F
Sbjct: 341  AARNAIIEEMASTLDEQGLDVDPRHITLIADTMTMDGEVKQIGRHGIAGEKASVLSRAAF 400

Query: 1353 ENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            E T D+L +AA +G+TD + GV+E +I+G P+ +GTG I+L
Sbjct: 401  EVTVDNLLEAAMHGETDALKGVTENVIVGQPIKLGTGAIEL 441



 Score = 85.9 bits (211), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 124/234 (52%), Gaps = 14/234 (5%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PRI EI++A + +STP +   L  +  ++ + A  +   +E T + ++ +    +   
Sbjct: 158 GLPRIIEIVDARKKLSTPTMKVKLVSEFASERNKAEKIAMEIEETHIRDIAKVKAAI--- 214

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
           +D  + I L+   ++  ++  D   +   I +  G +  + V G   L +  KD  K+++
Sbjct: 215 EDMSVWIVLNAKELKRRYIMSD--EVEQTI-KDIGTALLVEVVGDGKLRIHVKD--KTYH 269

Query: 882 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
             + +++  + + ++KG+ GI RA++   D  G  +Y L  EG  L+ V+   GV   + 
Sbjct: 270 D-LLRLEAKVSNTLVKGIDGIKRALVRR-DPSG--EYVLYTEGSALKKVLKVEGVDSRRT 325

Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
           ++NN  E+   LGIEAAR+ I+ E+   ++  G+ +D RH  L+AD MT  GEV
Sbjct: 326 TTNNINEISDVLGIEAARNAIIEEMASTLDEQGLDVDPRHITLIADTMTMDGEV 379



 Score = 44.7 bits (104), Expect = 0.45,   Method: Compositional matrix adjust.
 Identities = 18/40 (45%), Positives = 28/40 (70%)

Query: 665 VQYDMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 704
           V  D   +AA +G+TD + GV+E +I+G P+ +GTG I+L
Sbjct: 402 VTVDNLLEAAMHGETDALKGVTENVIVGQPIKLGTGAIEL 441


>gi|170291135|ref|YP_001737951.1| DNA-directed RNA polymerase subunit A [Candidatus Korarchaeum
           cryptofilum OPF8]
 gi|170175215|gb|ACB08268.1| DNA-directed RNA polymerase subunit A [Candidatus Korarchaeum
           cryptofilum OPF8]
          Length = 1324

 Score =  178 bits (451), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 99/264 (37%), Positives = 149/264 (56%), Gaps = 32/264 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D V+FNRQPSLHKLS++ HR KVLP  TFR +  VC PYNADFDGDEMN+H+PQ  + 
Sbjct: 436 DGDYVIFNRQPSLHKLSMLGHRVKVLPGATFRLHPAVCVPYNADFDGDEMNLHVPQILDG 495

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
             E               + LM  K N+++PR G  +I A QDFIT  Y++T+K+A F++
Sbjct: 496 SVE--------------VRELMGVKYNMLSPRTGGSIIGARQDFITALYMITKKDALFDK 541

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +  RI S          GI +        P +  R   +WTGKQ+ S++L   +D    
Sbjct: 542 NEATRILSR--------AGITQLPE-----PAI-KRPKRLWTGKQLISMLLP--KDLNFE 585

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGS--GGKANVFYILLRDFGE 578
              K+  +A    +  C  D YV++R  +LL+G +D + +G+   G+  +  +L+RD+GE
Sbjct: 586 GIAKSAVKASECKDPSCLGDGYVLIREGKLLSGVLDDNIVGTLVKGRLTLIDVLIRDYGE 645

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFS 602
           DVA+  + +L ++ S  ++  G +
Sbjct: 646 DVAIEFLNKLLKIASKEVLLYGIT 669



 Score =  119 bits (298), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 116/429 (27%), Positives = 193/429 (44%), Gaps = 85/429 (19%)

Query: 1037 DSKEFLQDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQ--ILSHQDKIGHGRES 1094
            D  +  ++   N  R I+K+++E  +K  V+  +DK+ + L+E    LS  D I HG  +
Sbjct: 896  DPTKLFRNEPVNLERIIRKYVKE-ERKRGVS--KDKIEELLKEANLPLSLADAI-HG--A 949

Query: 1095 NPFPSACKA--EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG------- 1145
             P  S  K      +E + RA++E  T +G ++AQSI EP TQM L+TFH  G       
Sbjct: 950  RPKESELKEIIAELKEGFERAKVEVLTPIGLISAQSIAEPTTQMVLRTFHAPGLLAMDVT 1009

Query: 1146 -EVCEYIEEVFVPDDSF--------------------ILIKLDMDRIRLLHLEVDIDSIR 1184
              V  + E VF    S                     IL  L   R+R L  E  ID+  
Sbjct: 1010 HGVERFKELVFYASTSTPTMKIYLKQKCQEDISNLRKILRNLKELRVRDLIEEYAIDNFN 1069

Query: 1185 Y----------------CIER--------TRGISGHLTVSGHSFLIL--------KPKDS 1212
            Y                 +ER         +G+ G + +     ++         KP  +
Sbjct: 1070 YRLTIKPDKRALENNMIPMERFLNIIRATAKGMKGEVELEDDRIIVDLYEAAERDKPLQT 1129

Query: 1213 SKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGV 1272
             +S++ ++           + GV+GI RA +   + +G  +Y +   G NL  V++   V
Sbjct: 1130 LRSWSYRILDKP-------VSGVRGIKRAWVETVETDGRKEYIIRTSGSNLAAVLSMSCV 1182

Query: 1273 KGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG--- 1329
               +  +N+  E+ + LGIEAAR+ I  E+  ++E  G+ +D R+  LVAD+MT  G   
Sbjct: 1183 DIARTITNDCKEIERVLGIEAARNCIFNELASILEEQGLEVDRRYISLVADIMTYSGTIE 1242

Query: 1330 ----EVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMN 1385
                +  G++    ++MK  +  +A FE T+  + + A  G+ + I G  + +IMG    
Sbjct: 1243 AIRLQAAGVSSGFFSEMKTPLSKMA-FEWTTHVILNTARRGEVNKILGPLDALIMGQTPP 1301

Query: 1386 VGTGLIKLL 1394
            +GTG + +L
Sbjct: 1302 IGTGKVSVL 1310



 Score = 90.5 bits (223), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 75/265 (28%), Positives = 117/265 (44%), Gaps = 57/265 (21%)

Query: 82  LIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNL 141
           +I G ++  D  ++   I+I     Y  D    P+  G+LD R+GT      C  CG   
Sbjct: 21  VIFGLISPAD-ARKIGFIEITEPTAY--DEGGLPVQGGVLDPRLGTINPRQRCPVCGNLP 77

Query: 142 SDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPAL 201
            +C GHFG I+L +PV HIGY + + ++L ++C    C +VLL +E+    R++L   A 
Sbjct: 78  KNCPGHFGRIELAMPVIHIGYVKRIKDVLNTVCHK--CGKVLLPQER----RSQLIERAH 131

Query: 202 SY------------LVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNR 249
            Y            LVR+ ++ ++    KK   CPHCG     V +  L     E YK  
Sbjct: 132 EYARDNPEKVVDDELVRE-VRDQVKVYAKKHKKCPHCG---APVHRVEL----EEVYKFI 183

Query: 250 TKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMN 309
            K+ +                             + L P E+  + E I  +D  L+  +
Sbjct: 184 VKEPEP----------------------------RRLWPNEIRDILEKISDDDSLLIGFD 215

Query: 310 AELSKPSDLILTRLLVPPNCIRPSV 334
            + ++P   +LT LLVPP   RPS+
Sbjct: 216 PKKARPEWAVLTVLLVPPLTARPSI 240



 Score = 75.1 bits (183), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 32/64 (50%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 606 GDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           GD++P  +GFV+NS+ SGL P EF FH M  RE L+D   +T ++GY  RR+  SL+D+ 
Sbjct: 812 GDLSPEARGFVKNSYVSGLNPAEFIFHAMSSRESLIDKGRRTEDSGYFYRRVANSLKDVY 871

Query: 665 VQYD 668
           V YD
Sbjct: 872 VSYD 875



 Score = 72.8 bits (177), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 64/243 (26%), Positives = 118/243 (48%), Gaps = 23/243 (9%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GV R KE++  + + STP +  YL +    D + + K  L       V + IEE  + + 
Sbjct: 1011 GVERFKELVFYA-STSTPTMKIYLKQKCQEDISNLRK-ILRNLKELRVRDLIEEYAIDNF 1068

Query: 824  SFIL-IKLDMDRIR--LLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLIL--------K 872
            ++ L IK D   +   ++ +E  ++ IR      +G+ G + +     ++         K
Sbjct: 1069 NYRLTIKPDKRALENNMIPMERFLNIIRAT---AKGMKGEVELEDDRIIVDLYEAAERDK 1125

Query: 873  PKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMA 932
            P  + +S++ ++           + GV+GI RA +   + +G  +Y +   G NL  V++
Sbjct: 1126 PLQTLRSWSYRILDKP-------VSGVRGIKRAWVETVETDGRKEYIIRTSGSNLAAVLS 1178

Query: 933  TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK 992
               V   +  +N+  E+ + LGIEAAR+ I  E+  ++E  G+ +D R+  LVAD+MT  
Sbjct: 1179 MSCVDIARTITNDCKEIERVLGIEAARNCIFNELASILEEQGLEVDRRYISLVADIMTYS 1238

Query: 993  GEV 995
            G +
Sbjct: 1239 GTI 1241



 Score = 50.8 bits (120), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 33/48 (68%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIAS 69
           LM  K N+++PR G  +I A QDFIT  Y++T+K+A F++ +  RI S
Sbjct: 502 LMGVKYNMLSPRTGGSIIGARQDFITALYMITKKDALFDKNEATRILS 549


>gi|133433|sp|P09847.2|RPOA2_METTW RecName: Full=DNA-directed RNA polymerase subunit A''; Short=Subunit
            C
 gi|809728|emb|CAA30839.1| unnamed protein product [Methanothermobacter thermautotrophicus]
          Length = 449

 Score =  178 bits (451), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 136/443 (30%), Positives = 209/443 (47%), Gaps = 86/443 (19%)

Query: 1012 IAKNSSRSDPSLSAQEILAL------SNETLDSKEFLQDTSENFVRDIKKFLEEFSKKES 1065
            IA+     DP L   +++ L       N  L+ +E L+   + ++R +K        +E 
Sbjct: 30   IAEEEKLKDPEL--HDLVRLFSRICERNRGLEGEELLKAVEDEYLRILKV-------REL 80

Query: 1066 VTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALA 1125
            V   + K    L E+I     +  HG   +      +    R  Y RA +E   AVG +A
Sbjct: 81   VKRKRAKFPPRLIEEIAEAIKR--HGLSDDELDELVRG--VRRAYERAMVEAGEAVGTVA 136

Query: 1126 AQSIGEPGTQMTLKTFHFAG--------------EVCEYIEEVFVP------------DD 1159
            AQS+GEPGTQMT++TFH+AG              E+ +  +++  P            D+
Sbjct: 137  AQSVGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDARKKISTPTMSIYFEGDRKYDE 196

Query: 1160 SFILIK----------------------------LDMDRIRLLHLEVDIDSIRYCIERTR 1191
             F+  K                            LD ++IR  HLE D   I   +E+T 
Sbjct: 197  EFVRKKANKICKSTLNDVLKNFSIQYADMSVEAELDEEKIREKHLEYD--DIIAKVEKT- 253

Query: 1192 GISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGV 1251
                 + +  +      PK + +       ++++L     I GV+ I + VI +ED E V
Sbjct: 254  --FKKVEIDNNILRFEPPKPTIRELRLLADKVRKLQ----ISGVKNIGKVVIRKEDDEWV 307

Query: 1252 TKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM 1311
                +  EG NL D     GV  V+ ++N+ +E+   LGIEAAR+ I+ E K  ME  G+
Sbjct: 308  ----IHTEGSNLGDRFKEEGVDKVRTTTNDIHEIETVLGIEAARNAIIHEAKRTMEEQGL 363

Query: 1312 SIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCI 1371
            ++D RH MLVAD+MT+ G V  I RHG++  K SVL  ASFE T  HL  A+  G+ D +
Sbjct: 364  TVDIRHIMLVADMMTADGSVKSIGRHGISGEKASVLARASFEETGKHLLRASIRGEVDHL 423

Query: 1372 SGVSECIIMGLPMNVGTGLIKLL 1394
            +G+ E II+G P+ +GTG + ++
Sbjct: 424  TGIIENIIIGQPIPLGTGSVSVI 446



 Score =  110 bits (275), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 78/238 (32%), Positives = 127/238 (53%), Gaps = 17/238 (7%)

Query: 764 GVPRIKEIINASRNISTPIITAYL--DKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A + ISTP ++ Y   D+  D ++ R    ++ ++TL +V +     +  
Sbjct: 165 GLPRLIEIVDARKKISTPTMSIYFEGDRKYDEEFVRKKANKICKSTLNDVLKNFSIQYA- 223

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
            D  +  +LD ++IR  HLE D   I   +E+T      + +  +      PK + +   
Sbjct: 224 -DMSVEAELDEEKIREKHLEYD--DIIAKVEKT---FKKVEIDNNILRFEPPKPTIRELR 277

Query: 882 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
               ++++L     I GV+ I + VI +ED E V    +  EG NL D     GV  V+ 
Sbjct: 278 LLADKVRKLQ----ISGVKNIGKVVIRKEDDEWV----IHTEGSNLGDRFKEEGVDKVRT 329

Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG 999
           ++N+ +E+   LGIEAAR+ I+ E K  ME  G+++D RH MLVAD+MT+ G V   G
Sbjct: 330 TTNDIHEIETVLGIEAARNAIIHEAKRTMEEQGLTVDIRHIMLVADMMTADGSVKSIG 387


>gi|401016|sp|P31813.1|RPOA1_THECE RecName: Full=DNA-directed RNA polymerase subunit A'
 gi|48141|emb|CAA47723.1| Subunit A' of DNA-dependent RNA polymerase [Thermococcus celer]
          Length = 905

 Score =  178 bits (451), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 101/281 (35%), Positives = 154/281 (54%), Gaps = 40/281 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH++SIMAHR +V+P+RTFR N  VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 418 DGDVVLFNRQPSLHRMSIMAHRVRVMPYRTFRLNLSVCPPYNADFDGDEMNLHVPQTEEA 477

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE              AK+LM  ++++++PR G  LIA  QD I+GGYLLT++ A+F R
Sbjct: 478 QAE--------------AKILMEVQNHIISPRYGGPLIAGIQDHISGGYLLTREGAYFER 523

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLIL--------- 511
            +  ++      D             R   P        +W+GK IFSL+L         
Sbjct: 524 TEVEQMLMFAGVDVD-----------RLPEPDKVENGVELWSGKTIFSLLLPKDLTIWYR 572

Query: 512 -----KPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKA 566
                +P R   +   ++ K             D +  + N +LL+G++DK+  G     
Sbjct: 573 NKLCDEPGRCEALEKLIEEKLIPDEEEVRALAYDGFTYILNGKLLSGAIDKTAYGR-EDG 631

Query: 567 NVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            +  I++R++G + A   + +++++  + + ++GF+  I D
Sbjct: 632 KLLDIIVREYGVERARQFLDQVTKLAIWVITHKGFTTAIDD 672



 Score =  112 bits (281), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 72/266 (27%), Positives = 125/266 (46%), Gaps = 35/266 (13%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G I+  +     +++ S  +I   + Y +D    PI  GL+D+R+G       C TCG  
Sbjct: 9   GSIDFGILSPQEIRKMSAAEITVPDTYDEDGY--PIEGGLMDKRLGVIDPGLRCETCGAR 66

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
             +C GHFG+++L  PV H+G+ + +  +L+S C+   C R+ L +E+   +  K     
Sbjct: 67  AGECPGHFGHVELARPVIHVGFAKTIHRVLESTCRE--CGRIKLTDEEIEEYFHKFEVTG 124

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDL 260
                +  L K+I +  K+  VCPHCG     +           K++  T   +   ++ 
Sbjct: 125 NRKKAKDRLIKEIHKKAKERMVCPHCGSPQFPI-----------KFERPTVYWELRKDEE 173

Query: 261 LAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
             EY                     + P EV    E IP  D+PL+ ++AE ++P  ++L
Sbjct: 174 GNEYK------------------HRMMPSEVRDRLEKIPDRDLPLIGLDAEKARPEWMVL 215

Query: 321 TRLLVPPNCIRPSVI--SDLKSDNDV 344
           T L VPP  +RPS+   S +++++D+
Sbjct: 216 TVLPVPPVTMRPSITLESGIRAEDDL 241



 Score = 95.9 bits (237), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 41/58 (70%), Positives = 51/58 (87%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV NS+ SGLTP E+FFH MGGREGLVDTAV+TA++GYMQRRL+ +L+DL V+YD
Sbjct: 800 ARGFVINSYKSGLTPQEYFFHAMGGREGLVDTAVRTAQSGYMQRRLINALQDLKVEYD 857



 Score = 50.8 bits (120), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 31/130 (23%), Positives = 62/130 (47%), Gaps = 24/130 (18%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFF 79
           ++LM  ++++++PR G  LIA  QD I+GGYLLT++ A+F R +  ++         + F
Sbjct: 482 KILMEVQNHIISPRYGGPLIAGIQDHISGGYLLTREGAYFERTEVEQM---------LMF 532

Query: 80  RGLIEGTVTKEDRVQQ---------------QSHIQIVSKNLYCQDPQRTPIPHGLLDRR 124
            G+    + + D+V+                   + I  +N  C +P R      L++ +
Sbjct: 533 AGVDVDRLPEPDKVENGVELWSGKTIFSLLLPKDLTIWYRNKLCDEPGRCEALEKLIEEK 592

Query: 125 MGTNQKEANC 134
           +  +++E   
Sbjct: 593 LIPDEEEVRA 602


>gi|159905692|ref|YP_001549354.1| DNA-directed RNA polymerase subunit A'' [Methanococcus maripaludis
            C6]
 gi|226699055|sp|A9A9U9.1|RPOA2_METM6 RecName: Full=DNA-directed RNA polymerase subunit A''
 gi|159887185|gb|ABX02122.1| DNA-directed RNA polymerase, subunit A'' [Methanococcus maripaludis
            C6]
          Length = 386

 Score =  178 bits (451), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 117/328 (35%), Positives = 173/328 (52%), Gaps = 50/328 (15%)

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYIEE-- 1153
            Y R  +EP  AVG +AAQSIGEPGTQMT++TFH+AG              E+ +  +E  
Sbjct: 49   YERTLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRMIEIVDARKEPS 108

Query: 1154 -----VFVPDD--------SFILIKLDMDRIRLLHLEVDIDSIRYCIE--------RTRG 1192
                 +++ DD        S +   ++   +  +  ++ +D I  CI          +RG
Sbjct: 109  TPTMTIYLNDDFKGDREKASMVAKNIESTNVESVSEDISVDLINECITIVLNTHQLESRG 168

Query: 1193 IS-GHLTVSGHSFLILKPKDSSKSFNSK-----MYQMKQLLPSVV---IKGVQGINRAVI 1243
            ++   +  S  S + LK +D     N K     +  +++ LP V    +KGVQ I R +I
Sbjct: 169  LTVADVIESIKSKMKLKIEDHENVLNLKIKTPSLKALRKRLPKVRAIHLKGVQNIKRVII 228

Query: 1244 HEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIK 1303
             +E    V +Y L  EG N+++V    GV   K ++NN  E+   LGIEAAR+ I+ E+ 
Sbjct: 229  RKE----VDEYILYSEGSNIKEVFDIEGVDTTKTTTNNIVEIQDVLGIEAARNAIIYEMD 284

Query: 1304 LVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAA 1363
              + N G+++D RH M+VADLM + G V  I RHG+   K SVL  A+FE T  HL+ A+
Sbjct: 285  ATLGNQGLTVDKRHLMMVADLMCTDGVVKPIGRHGIGGEKASVLARAAFEETVKHLYSAS 344

Query: 1364 FYGQTDCISGVSECIIMGLPMNVGTGLI 1391
              G  D + GV E II+G P+ +GTG I
Sbjct: 345  MRGYVDELGGVVENIIVGKPIAMGTGCI 372



 Score =  102 bits (255), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 78/236 (33%), Positives = 127/236 (53%), Gaps = 20/236 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A +  STP +T YL+ D   D + A +V   +E T +  V E I    + 
Sbjct: 93  GLPRMIEIVDARKEPSTPTMTIYLNDDFKGDREKASMVAKNIESTNVESVSEDISVDLIN 152

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGH-SFLILKPKDSS-KS 879
           +   I++       R L +   I+SI+  ++        L +  H + L LK K  S K+
Sbjct: 153 ECITIVLNTHQLESRGLTVADVIESIKSKMK--------LKIEDHENVLNLKIKTPSLKA 204

Query: 880 FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
              ++ +++    ++ +KGVQ I R +I +E    V +Y L  EG N+++V    GV   
Sbjct: 205 LRKRLPKVR----AIHLKGVQNIKRVIIRKE----VDEYILYSEGSNIKEVFDIEGVDTT 256

Query: 940 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
           K ++NN  E+   LGIEAAR+ I+ E+   + N G+++D RH M+VADLM + G V
Sbjct: 257 KTTTNNIVEIQDVLGIEAARNAIIYEMDATLGNQGLTVDKRHLMMVADLMCTDGVV 312


>gi|389852851|ref|YP_006355085.1| DNA-directed RNA polymerase subunit A'' [Pyrococcus sp. ST04]
 gi|388250157|gb|AFK23010.1| DNA-directed RNA polymerase subunit A'' [Pyrococcus sp. ST04]
          Length = 396

 Score =  178 bits (451), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 118/346 (34%), Positives = 180/346 (52%), Gaps = 58/346 (16%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIE 1152
            E   ++Y RA +EP  AVG +AAQSIGEP TQMTL TFH+AG            + E ++
Sbjct: 49   EEVVKEYERALVEPGEAVGTVAAQSIGEPSTQMTLNTFHYAGVAEINVTLGLPRIIEIVD 108

Query: 1153 EVFVPDDSFILIKLD----MDR-----------------------IRLLHLE--VDID-- 1181
                P    + + LD     DR                       I L+++E  V+ID  
Sbjct: 109  ARKNPSTPMMTVYLDEEHRYDRAKAEEVARRIEGTTLENLARTTTIDLINMEFIVEIDPE 168

Query: 1182 -------SIRYCIERTRGI--SGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVI 1232
                   ++   +++ +G   S      G++ LI++PK   K   S + +  + +    +
Sbjct: 169  RLEKSGLTMEKILKKLQGSFKSAEFEAEGYT-LIVRPKKVEKI--SDLRRFAEKVKKHRL 225

Query: 1233 KGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIE 1292
            KG+ G+ + ++ +E  E    Y +  EG N + V+   GV   +  +NN +E+ + LGIE
Sbjct: 226  KGLSGVGKTIVRKEGDE----YVIYTEGSNFKQVLKVPGVDPTRTKTNNIHEIAEVLGIE 281

Query: 1293 AARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASF 1352
            AAR+ I+ EI   M   G+ +D RH MLVAD+MT  G V  I RHG+   K SVL  A+F
Sbjct: 282  AARNAIIEEIVNTMREQGLEVDIRHIMLVADIMTLDGVVRPIGRHGVVGEKASVLARAAF 341

Query: 1353 ENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 1398
            E T+ HLF+AA  G+ D ++GV E +++G P+ VGTG++KL   +P
Sbjct: 342  EITTQHLFEAAERGEVDNLNGVIENVLIGQPVPVGTGIVKLTMRLP 387



 Score =  108 bits (269), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 77/236 (32%), Positives = 129/236 (54%), Gaps = 18/236 (7%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARI--VKGRLERTTLGEVCEYIEEVFVP 821
           G+PRI EI++A +N STP++T YLD++   D A+   V  R+E TTL E       + + 
Sbjct: 99  GLPRIIEIVDARKNPSTPMMTVYLDEEHRYDRAKAEEVARRIEGTTL-ENLARTTTIDLI 157

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI--SGHLTVSGHSFLILKPKDSSKS 879
           +  FI +++D +R+    L     ++   +++ +G   S      G++ LI++PK   K 
Sbjct: 158 NMEFI-VEIDPERLEKSGL-----TMEKILKKLQGSFKSAEFEAEGYT-LIVRPKKVEKI 210

Query: 880 FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
             S + +  + +    +KG+ G+ + ++ +E  E    Y +  EG N + V+   GV   
Sbjct: 211 --SDLRRFAEKVKKHRLKGLSGVGKTIVRKEGDE----YVIYTEGSNFKQVLKVPGVDPT 264

Query: 940 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
           +  +NN +E+ + LGIEAAR+ I+ EI   M   G+ +D RH MLVAD+MT  G V
Sbjct: 265 RTKTNNIHEIAEVLGIEAARNAIIEEIVNTMREQGLEVDIRHIMLVADIMTLDGVV 320



 Score = 42.0 bits (97), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 17/39 (43%), Positives = 28/39 (71%)

Query: 671 FDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 709
           F+AA  G+ D ++GV E +++G P+ VGTG++KL   +P
Sbjct: 349 FEAAERGEVDNLNGVIENVLIGQPVPVGTGIVKLTMRLP 387


>gi|212223364|ref|YP_002306600.1| DNA-directed RNA polymerase subunit A' [Thermococcus onnurineus
           NA1]
 gi|212008321|gb|ACJ15703.1| Subunit A' of DNA-dependent RNA polymerase [Thermococcus onnurineus
           NA1]
          Length = 905

 Score =  177 bits (450), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 103/281 (36%), Positives = 158/281 (56%), Gaps = 40/281 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIMAHR +V+P++TFR N  VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 418 DGDIVLFNRQPSLHRMSIMAHRVRVMPYKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEA 477

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE              AK+LM  ++++++PR G  LIA  QD I+GGYLLT++ A+F R
Sbjct: 478 QAE--------------AKILMEVQNHIISPRYGGPLIAGIQDHISGGYLLTREGAYFTR 523

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKP------- 513
           ++   +   L+    D+  + K        P        +W+GK IFSL+L         
Sbjct: 524 SE---VEQMLMFAGVDVDKLPK--------PDKVENGVELWSGKTIFSLLLPEDLTIWYR 572

Query: 514 NRDCP----VNANLKTKGRAYTANEEFCHR---DSYVILRNSELLAGSMDKSTLGSGGKA 566
           N+ C       A  K        +EE   +   D +  + N +LL+G +DK   G     
Sbjct: 573 NKLCDDPERCEALEKLIEEKLIPDEEEVRKLAYDGFTYILNGKLLSGVVDKKAYGR-EDG 631

Query: 567 NVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            +  I++R++G + A   + +++++  + + ++GF+  I D
Sbjct: 632 KILDIIVREYGVERARQFLDQVTKLAIWVITHKGFTTAIDD 672



 Score =  112 bits (281), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 73/266 (27%), Positives = 124/266 (46%), Gaps = 35/266 (13%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G IE  +     +++ S  +I   + Y  D    PI  GL+D+R+G       C TCG  
Sbjct: 9   GSIEFGILSPQEIRKMSAAEITVPDTY--DDDGYPIEGGLMDKRLGVIDPGLRCETCGAR 66

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
             DC GHFG+++L  P+ H+G+ + +  +L+S C+   C R+ L +E+   +  K     
Sbjct: 67  AGDCPGHFGHVELARPIIHVGFAKTIHRVLESTCRE--CGRIKLTDEEIDEYMKKFEVMG 124

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDL 260
                +  L K+I +  K+  VCPHCG     +           K++  T   +   ++ 
Sbjct: 125 DRKKAKDRLIKEIHKKAKERMVCPHCGAPQFPI-----------KFERPTIYWELRRDEE 173

Query: 261 LAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
             EY                     + P EV    E IP +D+PLL ++ E ++P  ++L
Sbjct: 174 GNEYR------------------HRMMPSEVRDRLEKIPDKDLPLLGLHPEKARPEWMVL 215

Query: 321 TRLLVPPNCIRPSVI--SDLKSDNDV 344
           T L VPP  +RPS+   S +++++D+
Sbjct: 216 TVLPVPPVTMRPSITLESGIRAEDDL 241



 Score = 95.1 bits (235), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 41/58 (70%), Positives = 50/58 (86%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV NS+ SGLTP E+FFH MGGREGLVDTAV+TA++GYMQRRL+ +L+DL V YD
Sbjct: 800 ARGFVVNSYKSGLTPQEYFFHAMGGREGLVDTAVRTAQSGYMQRRLINALQDLKVDYD 857



 Score = 56.2 bits (134), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 33/127 (25%), Positives = 64/127 (50%), Gaps = 24/127 (18%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFF 79
           ++LM  ++++++PR G  LIA  QD I+GGYLLT++ A+F R++  ++         + F
Sbjct: 482 KILMEVQNHIISPRYGGPLIAGIQDHISGGYLLTREGAYFTRSEVEQM---------LMF 532

Query: 80  RGLIEGTVTKEDRVQQ---------------QSHIQIVSKNLYCQDPQRTPIPHGLLDRR 124
            G+    + K D+V+                   + I  +N  C DP+R      L++ +
Sbjct: 533 AGVDVDKLPKPDKVENGVELWSGKTIFSLLLPEDLTIWYRNKLCDDPERCEALEKLIEEK 592

Query: 125 MGTNQKE 131
           +  +++E
Sbjct: 593 LIPDEEE 599


>gi|134045260|ref|YP_001096746.1| DNA-directed RNA polymerase subunit A' [Methanococcus maripaludis
           C5]
 gi|132662885|gb|ABO34531.1| DNA-directed RNA polymerase, subunit A' [Methanococcus maripaludis
           C5]
          Length = 889

 Score =  177 bits (450), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 105/268 (39%), Positives = 148/268 (55%), Gaps = 31/268 (11%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           S+ D+VL+NRQPSLH++SIMAH+ KVLP+RTFR N CVC PYNADFDGDEMNVH+PQ+EE
Sbjct: 422 SNGDIVLYNRQPSLHRMSIMAHKVKVLPYRTFRHNLCVCPPYNADFDGDEMNVHVPQSEE 481

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           ARAE              A+ LM  + ++V+PR G  +I    DFI+G Y+LT      +
Sbjct: 482 ARAE--------------AENLMLVEKHIVSPRFGGPIIGGIHDFISGAYILTSSLFTKD 527

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            A T+  +S L  D  +              P +       ++GK +FS  L        
Sbjct: 528 EALTLLNSSGLNLDLGE--------------PDLVENKVEYYSGKTLFSKTLPEGLSLQY 573

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            A +  K    T  E  C  D+YV++RN +LL G +DK+  GS     V   L++DFG +
Sbjct: 574 RAKICKKCDNCTKEE--CEHDAYVVIRNGKLLRGVIDKNGFGSEA-GIVLNTLVKDFGSE 630

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            A   +   ++M+   ++ +GF+ GI D
Sbjct: 631 DARLFLDAATKMSIKAMVLKGFTTGIDD 658



 Score =  108 bits (270), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 77/257 (29%), Positives = 122/257 (47%), Gaps = 42/257 (16%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           ++++  S  +IV+ + Y  D    PI  GL+D R+G       C +C   +  C GHFG+
Sbjct: 21  EQIRTMSVAKIVTADTY--DDDGYPIDGGLMDTRLGVIDPGLVCKSCSGRVGTCPGHFGH 78

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           I+L  PV HIG+ + +  IL+++C  P C +V + E K   +  K+           +L 
Sbjct: 79  IELSKPVIHIGFAKDIYKILKAVC--PHCGKVAITELKRDEYLEKMAKLEEDGGDPWTLC 136

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
             +L+   K SVCP CGE+                      K D             VK+
Sbjct: 137 DDLLKEAAKGSVCPSCGEV----------------------KAD-------------VKY 161

Query: 271 NPEIEAHKKFGLIQ-TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           +     H+  G  Q  L   EV ++ E IP ED  LL +NA++++P  ++LT L VPP  
Sbjct: 162 DKPTAYHQLDGKAQKQLTSSEVREILEKIPAEDCRLLGINAKVARPEFMVLTVLPVPPVT 221

Query: 330 IRPSVI--SDLKSDNDV 344
           +RPS+   S  +S++D+
Sbjct: 222 VRPSITLESGERSEDDL 238



 Score = 87.4 bits (215), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 36/57 (63%), Positives = 47/57 (82%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFV++ +  GL PTE+FFH MGGREGLVD AV+TA++GYMQRRLV +L+D+  +YD
Sbjct: 787 HGFVRSCYKKGLAPTEYFFHAMGGREGLVDQAVRTAQSGYMQRRLVNALQDIRAEYD 843


>gi|383320561|ref|YP_005381402.1| DNA-directed RNA polymerase, subunit A' [Methanocella conradii
           HZ254]
 gi|379321931|gb|AFD00884.1| DNA-directed RNA polymerase, subunit A' [Methanocella conradii
           HZ254]
          Length = 877

 Score =  177 bits (450), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 107/285 (37%), Positives = 151/285 (52%), Gaps = 43/285 (15%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIM H  KV+PH+TFR N  VC PYNADFDGDEMN+H+PQ  EA
Sbjct: 407 DGDIVLFNRQPSLHRMSIMGHFVKVMPHKTFRLNPAVCAPYNADFDGDEMNLHVPQNMEA 466

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
            AE              A++LM  + N+++PR G  +I    D I+G YLLT+ N  FN 
Sbjct: 467 MAE--------------ARILMLVQQNILSPRFGGPIIGGLHDHISGIYLLTKGNQMFNE 512

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAV-IWTGKQIFSLILKPNRDCPV 519
           A+ +               ++++   R       V   V  WTGKQIFS IL      P 
Sbjct: 513 AEAL--------------DLLRKTGVRELPEPAKVEGGVQYWTGKQIFSTIL------PR 552

Query: 520 NANLKTKGR----AYTANEEFCHRDSYVILRNSELLAGSMDKSTLGS-GGKANVFYILLR 574
             NL  K +         +E C +D+YV +R+  L  G +D+  +G+  GK  +   +++
Sbjct: 553 TLNLTYKAKICENCEVCKKEECDKDAYVTIRDGVLKTGVIDEKAIGAFSGK--IVDRIVK 610

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV-TPGQGFVQNS 618
            + ED A   +  ++R+    +M  GFS GI D   P +  VQ +
Sbjct: 611 TYDEDTAAKFIDDVTRLAIRAIMKFGFSYGISDTDIPREAKVQTT 655



 Score =  104 bits (260), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 74/256 (28%), Positives = 120/256 (46%), Gaps = 49/256 (19%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           +++ S  +I++ + Y  D    PI  GL+D R+G       C TCG    +C GHFG+I+
Sbjct: 20  IRKMSVTKIITADTY--DDDGYPIDMGLMDPRLGVIDPGLRCRTCGGRPGECPGHFGHIE 77

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKK 212
           L  PV H+G+ R +  IL + C+   C R++L E+  A +   LR    S  + + +   
Sbjct: 78  LAAPVIHVGFARLLRKILMTTCRR--CGRLMLDEKAKAEY---LRQIKTSMRLGQPIDDI 132

Query: 213 ILETTK--KVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           +    K  K + CP+CGE               E+ + + +K    +ED           
Sbjct: 133 VKNVFKDAKAATCPYCGE---------------EQKEIKFEKPTGYIED----------- 166

Query: 271 NPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCI 330
                 HK       L P +V    E IP EDI +  M+ + ++P  ++LT L VPP  +
Sbjct: 167 -----GHK-------LMPTDVRDRLEMIPDEDIEVFGMDPKNARPEWMVLTVLPVPPVTV 214

Query: 331 RPSVI--SDLKSDNDV 344
           RPS+   S  +S++D+
Sbjct: 215 RPSITLESGQRSEDDL 230



 Score = 92.4 bits (228), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 39/57 (68%), Positives = 51/57 (89%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV++S+  GL PTEFFFH MGGREGLVDTAV+T+++GY+QRRLV +L+DL V+YD
Sbjct: 774 RGFVESSYKKGLNPTEFFFHAMGGREGLVDTAVRTSQSGYLQRRLVNALQDLEVKYD 830


>gi|327401232|ref|YP_004342071.1| DNA-directed RNA polymerase subunit A' [Archaeoglobus veneficus
           SNP6]
 gi|327316740|gb|AEA47356.1| DNA-directed RNA polymerase subunit A' [Archaeoglobus veneficus
           SNP6]
          Length = 871

 Score =  177 bits (450), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 105/279 (37%), Positives = 160/279 (57%), Gaps = 34/279 (12%)

Query: 330 IRPSVISDLK-SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGD 388
           + P +I + +  D D+VLFNRQPSLH++SIMAH  +VLP++TFR N  VC PYNADFDGD
Sbjct: 393 LEPGMIVERQLKDGDIVLFNRQPSLHRMSIMAHYVRVLPYKTFRLNPAVCPPYNADFDGD 452

Query: 389 EMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGG 448
           EMN+H+PQ+ EA+AE              AKVLMA + ++++PR G  +I    D I+G 
Sbjct: 453 EMNLHVPQSLEAQAE--------------AKVLMAVQEHILSPRFGGPIIGGIHDHISGL 498

Query: 449 YLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFS 508
           YLLT+    F R + M I   L  + +++             P    +  ++WTGKQ+FS
Sbjct: 499 YLLTRGEKLFTREEAMSILKAL--NITEL-------------PEPKYKEKLLWTGKQLFS 543

Query: 509 LILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANV 568
           LIL P+      A +  +G      EE  + D+YVI++N EL+ G++D+  +G+  K  +
Sbjct: 544 LIL-PDISIEFKAEI-CQGCEECKKEECEY-DAYVIIKNGELICGTIDEKAVGA-FKGII 599

Query: 569 FYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
              ++R +G +     +  ++++    +M  GFS GI D
Sbjct: 600 IDEIMRKYGSEETKRFIDNMTQLAIRAIMYTGFSFGISD 638



 Score =  106 bits (265), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 73/257 (28%), Positives = 119/257 (46%), Gaps = 50/257 (19%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           +++ S  +I++   Y  D    PI  GL+D R+G       C TCG    +C GHFG+I+
Sbjct: 19  IRRMSVAKIITPETY--DDDGFPIEAGLMDPRLGVIDPGLRCRTCGGKAGECPGHFGHIE 76

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKL---RNPALSYLVRKSL 209
           L  PV H+GY + +  +L + C+   C R+LL ++K   F  ++   R+    Y   + +
Sbjct: 77  LAAPVIHVGYAKLIAKLLNATCRE--CGRILLKDDKRDKFIEEIERKRDLGQDY---EDV 131

Query: 210 KKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVK 269
            K++   TK V  CPHCG           ++I  EK                        
Sbjct: 132 VKEVFRITKAVKKCPHCG--------MDQIEIKFEK----------------------PT 161

Query: 270 FNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           F  E E          L P ++ +  E IP +D+P   M+ +  +P  ++LT L VPP  
Sbjct: 162 FFYEGE--------HRLTPKDIRERLEKIPDDDLPAFGMDPKAVRPEWMVLTVLPVPPVT 213

Query: 330 IRPSVI--SDLKSDNDV 344
           +RPS+I  +  +S++D+
Sbjct: 214 VRPSIILETGQRSEDDL 230



 Score = 90.1 bits (222), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 37/58 (63%), Positives = 50/58 (86%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV++S+  GL P EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L+DL V+YD
Sbjct: 768 ARGFVRSSYKEGLNPIEFFFHAMGGREGLVDTAVRTSQSGYLQRRLINALQDLKVEYD 825


>gi|282163889|ref|YP_003356274.1| DNA-directed RNA polymerase subunit A'' [Methanocella paludicola
            SANAE]
 gi|282156203|dbj|BAI61291.1| DNA-directed RNA polymerase subunit A'' [Methanocella paludicola
            SANAE]
          Length = 389

 Score =  177 bits (450), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 115/336 (34%), Positives = 183/336 (54%), Gaps = 49/336 (14%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIE 1152
            E  RE Y  A++E   AVG +AAQSIGEPGTQMT++TFH+AG            + E ++
Sbjct: 45   EKTREAYSHAKVENCEAVGMVAAQSIGEPGTQMTMRTFHYAGVAEIDVTLGLPRLIEIVD 104

Query: 1153 EVFVPDDSFILIKL------DMDRIRLLHLEV------DIDSI---------------RY 1185
                P    + I L      + D +R L  E+      DI SI               + 
Sbjct: 105  ARREPSTPMMTIHLSPEISGNRDPVRKLAWELEETTVSDIGSIATNLNDMTIIIDLNEKQ 164

Query: 1186 CIERTRGISGHLTVSGH-SFLILKPKDSSKSFNSK------MYQMKQLLPSVVIKGVQGI 1238
             ++R+  I   +   G  + L +   D+  + + +      + QM + + ++++KG++GI
Sbjct: 165  VLQRSMTIDEVMGKIGEVTGLKIDVNDNRLTVHPEGESYRDLLQMVETIRTILLKGIKGI 224

Query: 1239 NRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTI 1298
            +R VI +E+ E    Y +  +G  L+ V+   GV   +  +NN  E+ + LGIEAAR+ I
Sbjct: 225  SRVVIRKEENE----YVIYTQGSALKKVIHFDGVDASRTKTNNINEISEVLGIEAARNAI 280

Query: 1299 MTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDH 1358
            + E    +   G+++D RH MLVAD+M+  GEV  I RHG++  K SVL+ A+FE T +H
Sbjct: 281  INEALDTLSEQGLTVDIRHIMLVADMMSIDGEVKQIGRHGISGEKASVLSRAAFEVTVNH 340

Query: 1359 LFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            L DAA  G+ D ++GV+E +I+G P+ +GTG ++L+
Sbjct: 341  LLDAAVAGEVDELTGVTENVIVGQPIQLGTGDVELI 376



 Score =  102 bits (255), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 71/234 (30%), Positives = 128/234 (54%), Gaps = 17/234 (7%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A R  STP++T +L  +   + D  R +   LE TT+ ++      +   
Sbjct: 95  GLPRLIEIVDARREPSTPMMTIHLSPEISGNRDPVRKLAWELEETTVSDIGSIATNL--- 151

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
           +D  I+I  D++  ++L   + ID +   I    G+   + V+ +   +    +S +   
Sbjct: 152 NDMTIII--DLNEKQVLQRSMTIDEVMGKIGEVTGLK--IDVNDNRLTVHPEGESYRD-- 205

Query: 882 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
             + QM + + ++++KG++GI+R VI +E+ E    Y +  +G  L+ V+   GV   + 
Sbjct: 206 --LLQMVETIRTILLKGIKGISRVVIRKEENE----YVIYTQGSALKKVIHFDGVDASRT 259

Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            +NN  E+ + LGIEAAR+ I+ E    +   G+++D RH MLVAD+M+  GEV
Sbjct: 260 KTNNINEISEVLGIEAARNAIINEALDTLSEQGLTVDIRHIMLVADMMSIDGEV 313


>gi|336121472|ref|YP_004576247.1| DNA-directed RNA polymerase subunit A' [Methanothermococcus
           okinawensis IH1]
 gi|334855993|gb|AEH06469.1| DNA-directed RNA polymerase subunit A' [Methanothermococcus
           okinawensis IH1]
          Length = 888

 Score =  177 bits (450), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 102/271 (37%), Positives = 150/271 (55%), Gaps = 39/271 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + D+VL+NRQPSLH++SIMAH+ KVLP+RTFR N CVC PYNADFDGDEMN+H+PQ EEA
Sbjct: 423 NGDIVLYNRQPSLHRMSIMAHKVKVLPYRTFRHNLCVCPPYNADFDGDEMNLHVPQLEEA 482

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+ LM  + ++V+PR G  +I A  DFI+G Y+LT      + 
Sbjct: 483 RAE--------------AENLMLVEKHIVSPRYGGPIIGAIHDFISGAYILTSSYFTKDE 528

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A  +   S L  D  +              P +      +++GK +FS      R  P +
Sbjct: 529 ASIILRGSGLKDDLGE--------------PDIVKDGVELYSGKNLFS------RTLPHD 568

Query: 521 ANLKTKG----RAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL+ +     +     EE C  D+YV+++N +L+ G +DK+  GS     +   ++R+F
Sbjct: 569 LNLRYRAKICKKCDKCEEENCPYDAYVLIKNGKLIKGVIDKNGYGSEA-GIILNTIVREF 627

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           G + A   +   ++M+   LM +GF+ GI D
Sbjct: 628 GSEEARKFLDTSTKMSIRALMIKGFTTGIDD 658



 Score =  115 bits (288), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 75/256 (29%), Positives = 126/256 (49%), Gaps = 40/256 (15%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + +++ S  +IV+ + Y  D    PI  GL+D R+G       C TCG  +  C GHFG+
Sbjct: 21  EHIRKISVAKIVTADTY--DDDGYPIDGGLMDTRLGVIDPGLVCKTCGGRVGSCPGHFGH 78

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           I+L  PV HIG+ + +  IL+++C  P C RV + E K A +  K++        + +L 
Sbjct: 79  IELSKPVVHIGFAKDIYKILKAVC--PHCGRVAISESKRAEYLEKMKRLEEEGGDKWALA 136

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
            +IL+      VCP+CGE+   +K                             Y++   +
Sbjct: 137 DEILKEAAGKDVCPYCGEVKYDIK-----------------------------YSKPTTY 167

Query: 271 NPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCI 330
             +I+   +    + +   EV ++ E IP ED  LL +N E+++P  ++LT L VPP  +
Sbjct: 168 Y-QIDGKSQ----RQITSSEVREILEKIPDEDCTLLGINPEVARPEWMVLTVLPVPPVTV 222

Query: 331 RPSVI--SDLKSDNDV 344
           RPS+   S  +S++D+
Sbjct: 223 RPSITLESGERSEDDL 238



 Score = 89.4 bits (220), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 37/57 (64%), Positives = 48/57 (84%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFV++ +  GL+PTE+FFH MGGREGLVD AV+TA++GYMQRRLV +L+DL  +YD
Sbjct: 787 HGFVRSCYKKGLSPTEYFFHAMGGREGLVDQAVRTAQSGYMQRRLVNALQDLKAEYD 843


>gi|315425378|dbj|BAJ47044.1| DNA-directed RNA polymerase subunit A [Candidatus Caldiarchaeum
           subterraneum]
 gi|315426559|dbj|BAJ48189.1| DNA-directed RNA polymerase subunit A' [Candidatus Caldiarchaeum
           subterraneum]
 gi|343485295|dbj|BAJ50949.1| DNA-directed RNA polymerase subunit A' [Candidatus Caldiarchaeum
           subterraneum]
          Length = 1254

 Score =  177 bits (449), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 97/269 (36%), Positives = 153/269 (56%), Gaps = 44/269 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIMAH  +VLP++T R N  VCTPYNADFDGDEMN+H+PQ+EEA
Sbjct: 413 DGDIVLFNRQPSLHRMSIMAHYVRVLPYKTLRLNPAVCTPYNADFDGDEMNLHVPQSEEA 472

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           + E              A+ L+  ++N+++PR G  +I   +DF+T  YLLT+      +
Sbjct: 473 QTE--------------ARELLVVENNIISPRYGAPIIGVIRDFLTSLYLLTRDETKLTK 518

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTA-VIWTGKQIFSLILKPNRDCPV 519
                         S++  ++    +R   P   V+    +WTGKQ+FSL+L      P 
Sbjct: 519 --------------SELAMLLAAIKYRGPIPPPAVKDPEPMWTGKQVFSLLL------PK 558

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           + N  TK  ++T  E        V+++N +L++G +DK ++G     ++ + L RD+G D
Sbjct: 559 DFNHVTKS-SFTNTE--------VVVKNGQLISGVIDKGSVGVEKANSILHRLARDYGSD 609

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           VA   +  + R+ + ++  +GFS  + D+
Sbjct: 610 VARQFLDNVVRLANTFIELKGFSFAVDDL 638



 Score =  158 bits (400), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 114/358 (31%), Positives = 171/358 (47%), Gaps = 53/358 (14%)

Query: 1092 RESNPFPSACK--AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG---- 1145
            R++NP   A     E    KY  +  EP  AVG + AQSIGEPGTQ+TL+TFHFAG    
Sbjct: 902  RKTNPPAEAVDKIVEEVVSKYNASLAEPGDAVGVVTAQSIGEPGTQLTLRTFHFAGVGEQ 961

Query: 1146 -------EVCEYIEEVFVPDDSFILIKL------DMDRIR-------------------- 1172
                    + E ++    P    + I L      ++ + R                    
Sbjct: 962  SILKGLPRLIEIVDARRTPTTPIMYIPLTPEYASNLAKARKLAKQIQHTTLGDLISEVLV 1021

Query: 1173 -----LLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLL 1227
                  L +++D  S+       R I   L   G  +   K   S K     +  + ++ 
Sbjct: 1022 NYKRGTLEVQLDAKSLEEHGVTKRDIEKALKGVGAEYDEEKRVISVKLDEEGLMDIARVR 1081

Query: 1228 PSVVIKGVQGINR----AVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTY 1283
              +    V+GI R     V  E+D     +Y +  EG NLR+VM   GV   +  +N+ Y
Sbjct: 1082 ERISSIKVKGIRRIKKATVFKEKD-----EYVIRTEGSNLREVMEVPGVDWRRIKTNDIY 1136

Query: 1284 EVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMK 1343
            E+ +  GIEAAR+ I+ E K V+E+ G+ +D RH +L+AD+MT  G V  I RHG+ K+K
Sbjct: 1137 EIAEVFGIEAARNAIVEEAKAVLEDQGLDVDIRHLLLLADMMTVSGSVKQIGRHGVVKLK 1196

Query: 1344 ESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSE 1401
             SVL  A++E +   L +AA  G+ D + G  E I++G  + VGTG++ LL +  + E
Sbjct: 1197 SSVLARAAYEISVQTLLEAAARGEVDSLKGNVERILIGREIQVGTGMVTLLMSHEKGE 1254



 Score =  127 bits (319), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 82/256 (32%), Positives = 127/256 (49%), Gaps = 40/256 (15%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D +++ S  +I+S + Y +D    PIP  ++D R+GT +    C TCG     C GHFG 
Sbjct: 18  DLIRKMSVAEIISPDTYDEDG--LPIPTSVMDPRLGTLEPGQRCKTCGNTYLGCPGHFGR 75

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           I+LP+PV H+G+ + +  +L+S C+  +C R+LL E+    + A+L     + L  K+L 
Sbjct: 76  IELPVPVIHVGFAKTIYELLKSTCR--SCGRILLPEDDCKKYHAELERLRANNLPFKNLI 133

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
            KI +      VCPHCGE          LK+  EK  +             +E +E+   
Sbjct: 134 YKIKQKAMNTQVCPHCGEKQ--------LKLELEKPTS------------FSEMSESGS- 172

Query: 271 NPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCI 330
                          LNP  V    E IP  D+ LL +N + S+P  ++LT L VPP  +
Sbjct: 173 -------------TKLNPSTVRARLERIPDADLVLLDINPQTSRPEWMVLTVLPVPPVYV 219

Query: 331 RPSVI--SDLKSDNDV 344
           RPS+   S  +S++D+
Sbjct: 220 RPSITLESGYRSEDDL 235



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 79/255 (30%), Positives = 131/255 (51%), Gaps = 37/255 (14%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            G+PR+ EI++A R  +TPI+   L  +  ++L  AR +  +++ TTLG++   I EV V 
Sbjct: 966  GLPRLIEIVDARRTPTTPIMYIPLTPEYASNLAKARKLAKQIQHTTLGDL---ISEVLV- 1021

Query: 822  DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
                     +  R   L +++D  S+       R I   L   G  +      D  K   
Sbjct: 1022 ---------NYKR-GTLEVQLDAKSLEEHGVTKRDIEKALKGVGAEY------DEEKRVI 1065

Query: 882  S---------KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMA 932
            S          + ++++ + S+ +KG++ I +A + +E  E    Y +  EG NLR+VM 
Sbjct: 1066 SVKLDEEGLMDIARVRERISSIKVKGIRRIKKATVFKEKDE----YVIRTEGSNLREVME 1121

Query: 933  TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK 992
              GV   +  +N+ YE+ +  GIEAAR+ I+ E K V+E+ G+ +D RH +L+AD+MT  
Sbjct: 1122 VPGVDWRRIKTNDIYEIAEVFGIEAARNAIVEEAKAVLEDQGLDVDIRHLLLLADMMTVS 1181

Query: 993  GEV--LGNGTPVELK 1005
            G V  +G    V+LK
Sbjct: 1182 GSVKQIGRHGVVKLK 1196



 Score = 92.8 bits (229), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 42/73 (57%), Positives = 55/73 (75%), Gaps = 1/73 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D++P  +GFV NSF SGL P EFFFH +GGR+GLVDTAV+T ++GYMQRRL+ +LE L +
Sbjct: 760 DLSPRARGFVYNSFVSGLDPLEFFFHAVGGRDGLVDTAVRTQQSGYMQRRLINALEALYI 819

Query: 666 QYDMSFDAAFYGQ 678
            YD +   A  G+
Sbjct: 820 DYDGTVRTADEGR 832


>gi|223478062|ref|YP_002582842.1| DNA-directed RNA polymerase subunit A'' [Thermococcus sp. AM4]
 gi|214033288|gb|EEB74115.1| DNA-directed RNA polymerase subunit A'' [Thermococcus sp. AM4]
          Length = 391

 Score =  177 bits (449), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 115/346 (33%), Positives = 175/346 (50%), Gaps = 58/346 (16%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIE 1152
            E    +Y RA +EP   +G +AAQSIGEP TQMTL TFH+AG            + E ++
Sbjct: 47   EDAVNEYKRALVEPGEPIGTVAAQSIGEPSTQMTLNTFHYAGVAEINVTLGLPRIIEIVD 106

Query: 1153 EVFVPDDSFILIKLDMD-------------RIRLLHLE-------VDIDSIRYCIE---- 1188
                P    + + LD D             RI    +E       +DI +  + +E    
Sbjct: 107  ARKNPSTPVMTVFLDEDHRHDLEKAREVARRIEGTTIENLAREMSIDILNFEFIVELDPE 166

Query: 1189 --RTRGI--------------SGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVI 1232
                 G+              S      G+S LI++PK  +K   S + ++ + +    +
Sbjct: 167  RLEKSGLDMERILKKLSGSFKSAEFEADGYS-LIVRPKKVTKL--SDLRKLAEKVKKHRL 223

Query: 1233 KGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIE 1292
            KG+ G+ + +I +E  E    Y +  EG N + V+   GV   +  +NN +E+   LGIE
Sbjct: 224  KGLSGVGKTIIRKEGDE----YVIYTEGSNFKQVLKVPGVDPTRTRTNNIWEIADVLGIE 279

Query: 1293 AARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASF 1352
            AAR+ I+ EI   M   G+ +D RH MLVAD+MT  G +  I RHG+   K SVL  A+F
Sbjct: 280  AARNAIIEEIVNTMREQGLEVDIRHIMLVADMMTLDGVIRPIGRHGIVGEKSSVLARAAF 339

Query: 1353 ENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 1398
            E T+ HLF+AA  G+ D ++GV E +++G P+ VGTG+++L  ++P
Sbjct: 340  EITTQHLFEAAERGEVDPLNGVVENVLIGQPVPVGTGIVRLTMSLP 385



 Score =  117 bits (293), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 79/234 (33%), Positives = 132/234 (56%), Gaps = 18/234 (7%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PRI EI++A +N STP++T +LD+D   DL+ AR V  R+E TT+  +   +  + + 
Sbjct: 97  GLPRIIEIVDARKNPSTPVMTVFLDEDHRHDLEKAREVARRIEGTTIENLAREMS-IDIL 155

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI--SGHLTVSGHSFLILKPKDSSKS 879
           +  FI ++LD +R+    L+++       +++  G   S      G+S LI++PK  +K 
Sbjct: 156 NFEFI-VELDPERLEKSGLDME-----RILKKLSGSFKSAEFEADGYS-LIVRPKKVTKL 208

Query: 880 FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
             S + ++ + +    +KG+ G+ + +I +E  E    Y +  EG N + V+   GV   
Sbjct: 209 --SDLRKLAEKVKKHRLKGLSGVGKTIIRKEGDE----YVIYTEGSNFKQVLKVPGVDPT 262

Query: 940 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
           +  +NN +E+   LGIEAAR+ I+ EI   M   G+ +D RH MLVAD+MT  G
Sbjct: 263 RTRTNNIWEIADVLGIEAARNAIIEEIVNTMREQGLEVDIRHIMLVADMMTLDG 316


>gi|256070852|ref|XP_002571756.1| DNA-directed RNA polymerase III largest subunit [Schistosoma
           mansoni]
          Length = 629

 Score =  177 bits (449), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 97/262 (37%), Positives = 156/262 (59%), Gaps = 12/262 (4%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQ-DPQRTPIPHGLLDRRMGTNQKEANCTTCGQNL 141
           I+  +  E  +++ SHIQ++   LY +    R  + +GLLD R+G N+++  C TCG + 
Sbjct: 17  IKFQLCSEGDLKRLSHIQVLKCLLYAEGQSNRRALDYGLLDPRLGANKRDELCATCGLDY 76

Query: 142 SDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPAL 201
             C+GH+GY DLP P++H+GY   ++ ILQ+ICK  TC+RVLL E++ A F     NP L
Sbjct: 77  QKCIGHWGYFDLPTPIYHVGYTWHIVKILQTICK--TCSRVLLPEQQRARFLISCSNPNL 134

Query: 202 SYLVRKSLKKKILETTKKVSVCPHCGEINGVVKK-CGLLKISHEKYKNRTKKKDAIVEDL 260
            Y+ +K L+  I + + ++ VCP C   NGVV K   L  + H+ +++   K D  V+  
Sbjct: 135 DYVHKKQLRNAIHKLSSRIHVCPFCSAFNGVVTKGMSLPYVVHDIFRHAKAKVDEYVD-- 192

Query: 261 LAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAE---LSKPSD 317
             E+ + +  N E+    + GL + + P + +QLF  IP ED+PLLLM  +    + P +
Sbjct: 193 --EFAKVITKNTELAPVVRKGL-EIIRPGKAMQLFSRIPEEDLPLLLMPFDSRWTTHPRN 249

Query: 318 LILTRLLVPPNCIRPSVISDLK 339
           LI+ R+ V P+ I PSV+S+++
Sbjct: 250 LIVQRVPVCPSAIGPSVVSEVR 271


>gi|14520832|ref|NP_126307.1| DNA-directed RNA polymerase subunit A'' [Pyrococcus abyssi GE5]
 gi|14548247|sp|Q9V113.1|RPOA2_PYRAB RecName: Full=DNA-directed RNA polymerase subunit A''
 gi|5458048|emb|CAB49538.1| rpoA2 DNA-directed RNA polymerase, subunit A'' [Pyrococcus abyssi
            GE5]
 gi|380741374|tpe|CCE70008.1| TPA: DNA-directed RNA polymerase subunit A'' [Pyrococcus abyssi GE5]
          Length = 397

 Score =  177 bits (448), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 123/379 (32%), Positives = 190/379 (50%), Gaps = 62/379 (16%)

Query: 1071 DKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIG 1130
            + V Q L E+++ + +K    + +         E  +E Y RA +EP  AVG +AAQSIG
Sbjct: 20   ESVKQELYEKLIKYNEKY---KLTKAEVETIIDEVVKE-YERALVEPGEAVGTVAAQSIG 75

Query: 1131 EPGTQMTLKTFHFAG-----------EVCEYIEEVFVPDDSFILIKLDMD---------- 1169
            EP TQMTL TFH+AG            + E ++    P    + + LD +          
Sbjct: 76   EPSTQMTLNTFHYAGVAEINVTLGLPRIIEIVDARKNPSTPMMTVYLDEEHRYDREKAEE 135

Query: 1170 ---RIRLLHLE-------VDIDSIRYCIE------RTRGI--------------SGHLTV 1199
               RI    LE       +D+ ++ + +E         G+              S    +
Sbjct: 136  VARRIEGTTLENLARTTTLDLINMEFIVEIDPERLEKSGLTMEKVLKKLQSSFKSAEFEM 195

Query: 1200 SGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVE 1259
             G++ LI++PK   K   S + ++ + +    +KG+ G+ + ++ +E  E    Y +  E
Sbjct: 196  EGYT-LIVRPKKFEKI--SDLRRLAEKVKKHRLKGLSGVGKTIVRKEGDE----YVIYTE 248

Query: 1260 GDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPM 1319
            G N + V+   GV   +  +NN +E+ + LGIEAAR+ I+ EI   M   G+ +D RH M
Sbjct: 249  GSNFKQVLKVPGVDPTRTKTNNIHEIAEVLGIEAARNAIIEEIMNTMREQGLEVDIRHIM 308

Query: 1320 LVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECII 1379
            LVAD+MT  G V  I RHG+   K SVL  A+FE T  HLF+AA  G+ D +SGV E ++
Sbjct: 309  LVADIMTLDGVVRPIGRHGVVGEKASVLARAAFEITVQHLFEAAERGEVDNLSGVIENVL 368

Query: 1380 MGLPMNVGTGLIKLLQAVP 1398
            +G P+ VGTG++KL   +P
Sbjct: 369  IGQPVPVGTGMVKLTMKLP 387



 Score =  107 bits (266), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 76/236 (32%), Positives = 129/236 (54%), Gaps = 18/236 (7%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PRI EI++A +N STP++T YLD++   D + A  V  R+E TTL  +        + 
Sbjct: 99  GLPRIIEIVDARKNPSTPMMTVYLDEEHRYDREKAEEVARRIEGTTLENLARTTTLDLI- 157

Query: 822 DDSFILIKLDMDRIRL--LHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKS 879
           +  FI +++D +R+    L +E  +  ++   +     S    + G++ LI++PK   K 
Sbjct: 158 NMEFI-VEIDPERLEKSGLTMEKVLKKLQSSFK-----SAEFEMEGYT-LIVRPKKFEKI 210

Query: 880 FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
             S + ++ + +    +KG+ G+ + ++ +E  E    Y +  EG N + V+   GV   
Sbjct: 211 --SDLRRLAEKVKKHRLKGLSGVGKTIVRKEGDE----YVIYTEGSNFKQVLKVPGVDPT 264

Query: 940 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
           +  +NN +E+ + LGIEAAR+ I+ EI   M   G+ +D RH MLVAD+MT  G V
Sbjct: 265 RTKTNNIHEIAEVLGIEAARNAIIEEIMNTMREQGLEVDIRHIMLVADIMTLDGVV 320



 Score = 44.7 bits (104), Expect = 0.40,   Method: Compositional matrix adjust.
 Identities = 26/75 (34%), Positives = 42/75 (56%), Gaps = 11/75 (14%)

Query: 635 GREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAAFYGQTDCISGVSECIIMGLP 694
           GR G+V         G     L ++  ++ VQ+   F+AA  G+ D +SGV E +++G P
Sbjct: 324 GRHGVV---------GEKASVLARAAFEITVQH--LFEAAERGEVDNLSGVIENVLIGQP 372

Query: 695 MNVGTGLIKLLQAVP 709
           + VGTG++KL   +P
Sbjct: 373 VPVGTGMVKLTMKLP 387


>gi|332796431|ref|YP_004457931.1| DNA-directed RNA polymerase subunit A' [Acidianus hospitalis W1]
 gi|332694166|gb|AEE93633.1| DNA-directed RNA polymerase subunit A' [Acidianus hospitalis W1]
          Length = 880

 Score =  177 bits (448), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 105/272 (38%), Positives = 152/272 (55%), Gaps = 29/272 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++S+MAH+ KVLP RTFR N  VC PYNADFDGDEMN+H+PQ+EEA
Sbjct: 413 DGDIVIFNRQPSLHRISMMAHKVKVLPGRTFRLNLLVCPPYNADFDGDEMNLHVPQSEEA 472

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
            AE              AK LM    N++TPR G  ++ + QD+I+G YLLT K      
Sbjct: 473 IAE--------------AKELMTVHKNILTPRYGGPIMGSAQDYISGAYLLTVKTTLLTE 518

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +   I    +A+ S   G           P +      ++TGKQ+ SL L  + +    
Sbjct: 519 DEVQTILG--VANISKDIG----------EPAILA-PKRLYTGKQVVSLFLPEDFNYHGQ 565

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           AN+ +  R  T  +E C  DSY++++N +LL G  DK  LG+    ++ + L+R++ ED 
Sbjct: 566 ANIASGPRLCT--DEDCPHDSYIVIKNGKLLEGVFDKKALGNQQPESILHWLIREYPEDY 623

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
            +  M  + ++   Y+   G ++ I DVT  Q
Sbjct: 624 GLWLMDNIFKVFIRYIEIHGLTMSIDDVTISQ 655



 Score =  115 bits (288), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 75/262 (28%), Positives = 132/262 (50%), Gaps = 51/262 (19%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D +++ S   I++  +Y +D   TPI   ++D R+G  +    C TCG  + +C GHFG+
Sbjct: 17  DEIRKMSVTAIITSEVYDED--GTPIEGSVMDPRLGVIEPGQRCPTCGNMMGNCPGHFGH 74

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-----KLRNPALSYLV 205
           I+L  PV H+G+ + + ++L++ C+   C R+ L +++   +R        R P+ +   
Sbjct: 75  IELVKPVIHVGFVKHIYDLLRATCRR--CGRIKLEDQELERYRRIYHAINKRWPSAA--- 129

Query: 206 RKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEK-YKNRTKKKDAIVEDLLAEY 264
            K L + I +++ K  VCPHCGE          LKI  EK Y    ++K+ +V       
Sbjct: 130 -KRLVEHIKKSSMKAPVCPHCGEKQ--------LKIKLEKPYNFYEERKEGVVR------ 174

Query: 265 NEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLL 324
                                L P+++    E IP +D+ LL  + + S+P  +ILT L 
Sbjct: 175 ---------------------LTPVDIRDRLERIPDDDVELLGYDPKTSRPEWMILTVLP 213

Query: 325 VPPNCIRPSVI--SDLKSDNDV 344
           VPP  IRPS++  + +++++D+
Sbjct: 214 VPPITIRPSIMIENGIRAEDDL 235



 Score = 85.1 bits (209), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 37/69 (53%), Positives = 50/69 (72%), Gaps = 1/69 (1%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GF+ +SF SGL P E FFH   GREGLVDTAV+T+++GYMQRRL+ +L DL ++YD +
Sbjct: 778 ARGFIYSSFRSGLNPIELFFHAAAGREGLVDTAVRTSQSGYMQRRLINALSDLRIEYDGT 837

Query: 671 FDAAFYGQT 679
                YG+ 
Sbjct: 838 V-RTLYGEV 845


>gi|337283878|ref|YP_004623352.1| DNA-directed RNA polymerase subunit alpha [Pyrococcus yayanosii
           CH1]
 gi|334899812|gb|AEH24080.1| DNA-directed RNA polymerase subunit alpha [Pyrococcus yayanosii
           CH1]
          Length = 907

 Score =  177 bits (448), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 95/281 (33%), Positives = 155/281 (55%), Gaps = 40/281 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIMAHR +V+P++TFR N  VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 418 DGDIVLFNRQPSLHRMSIMAHRVRVMPYKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEA 477

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE              A++LM  ++++++PR G  +I   QD I+GGYLLT++ A+F R
Sbjct: 478 QAE--------------ARILMEVQNHIISPRYGGPIIGGIQDHISGGYLLTREGAYFTR 523

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +  ++      D  ++             P  +     +W+GK IFSL+L  +      
Sbjct: 524 EEVEQMLMFAGVDVKELP-----------EPDKYENGKPLWSGKTIFSLLLPDDLTVWYR 572

Query: 521 ANLKTKGRAYTANEEFCHR--------------DSYVILRNSELLAGSMDKSTLGSGGKA 566
             L  +     A E+                  D +V ++N +LL+G++DK   G     
Sbjct: 573 NKLCDEPERCEALEKLIEEKLMPDPEEVRKLAYDGFVYIQNGKLLSGAIDKKAYGR-EDG 631

Query: 567 NVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            +  +++R++G + A   + +++++  + + ++GF+  I D
Sbjct: 632 IILDLIVREYGVERARQFLDQVTKLAIWVITHKGFTTAIDD 672



 Score =  114 bits (284), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 77/269 (28%), Positives = 127/269 (47%), Gaps = 41/269 (15%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G IE  +     +++ S +++   + Y  D    PI  G++D+RMG       C TCG  
Sbjct: 9   GSIEFGILSPQEIRKMSAVEVTVPDTY--DDDGYPIEGGVMDKRMGVIDPGLRCETCGAR 66

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
             +C GHFG+I+L  PV H+G+ + +  IL+S C+   C R+ L +E+   +  KL    
Sbjct: 67  AGECPGHFGHIELARPVIHVGFAKTIHRILESTCRE--CGRIKLTDEEIEEYMKKL---E 121

Query: 201 LSYLVRKSLKKKILETTKKVS---VCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIV 257
           L+   R  + K + E  KK     VCPHCG     +           K++  T   +   
Sbjct: 122 LAGNRRSEVNKILKEIHKKARERMVCPHCGAPQFPI-----------KFEKPTIYWEIRK 170

Query: 258 EDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSD 317
           ++   EY                     + P EV    E IP +D+PLL ++ E S+P  
Sbjct: 171 DEQGNEYR------------------HRMMPTEVRDRLEKIPDKDLPLLGLHPEKSRPEW 212

Query: 318 LILTRLLVPPNCIRPSVI--SDLKSDNDV 344
           ++LT L VPP  +RPS+   + +++++D+
Sbjct: 213 MVLTVLPVPPVTVRPSITLETGIRAEDDL 241



 Score = 95.1 bits (235), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 41/57 (71%), Positives = 50/57 (87%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV NS+ SGLTP E+FFH MGGREGLVDTAV+TA++GYMQRRL+ +L+DL V YD
Sbjct: 801 RGFVVNSYKSGLTPQEYFFHAMGGREGLVDTAVRTAQSGYMQRRLINALQDLKVDYD 857



 Score = 47.4 bits (111), Expect = 0.069,   Method: Compositional matrix adjust.
 Identities = 18/44 (40%), Positives = 32/44 (72%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 63
           ++LM  ++++++PR G  +I   QD I+GGYLLT++ A+F R +
Sbjct: 482 RILMEVQNHIISPRYGGPIIGGIQDHISGGYLLTREGAYFTREE 525


>gi|390960610|ref|YP_006424444.1| DNA-directed RNA polymerase subunit A' [Thermococcus sp. CL1]
 gi|390518918|gb|AFL94650.1| DNA-directed RNA polymerase subunit A' [Thermococcus sp. CL1]
          Length = 905

 Score =  177 bits (448), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 98/281 (34%), Positives = 154/281 (54%), Gaps = 40/281 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIMAHR +V+P+RTFR N  VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 418 DGDIVLFNRQPSLHRMSIMAHRVRVMPYRTFRLNLSVCPPYNADFDGDEMNLHVPQTEEA 477

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE              AK+LM  ++++++PR G  LIA  QD I+GGYLLT++ A+F R
Sbjct: 478 QAE--------------AKILMEVQNHIISPRYGGPLIAGIQDHISGGYLLTREGAYFTR 523

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           ++  ++      +   +             P        +W+GK IFSL+L  +      
Sbjct: 524 SEVEQMLMFAGINVDKLP-----------EPDKVENGVELWSGKTIFSLLLPDDLTIWYR 572

Query: 521 ANLKTKGRAYTANEEFCHR--------------DSYVILRNSELLAGSMDKSTLGSGGKA 566
             L  +     A E+                  D +  ++N +LL+G++DK   G     
Sbjct: 573 NKLCDEPERCEALEKLIEEKLVPDPEEVRKLAYDGFTYIQNGKLLSGAIDKKAYGR-EDG 631

Query: 567 NVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            +  I++R++G + A   + +++++  + + ++GF+  I D
Sbjct: 632 KLLDIIVREYGVERARQFLDQVTKLAIWVITHKGFTTAIDD 672



 Score =  111 bits (278), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 72/266 (27%), Positives = 124/266 (46%), Gaps = 35/266 (13%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G IE  +     +++ S  +I   + Y  D    PI  GL+D+R+G       C TCG  
Sbjct: 9   GSIEFGILSPQEIRKMSAAEITVPDTY--DDDGYPIEGGLMDKRLGVVDPGLRCETCGAR 66

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
             +C GHFG+++L  P+ H+G+ + +  +L+S C+   C R+ L +E+   +  K     
Sbjct: 67  AGECPGHFGHVELARPIIHVGFAKTIHRVLESTCRE--CGRIKLTDEEIEEYMHKFEVMG 124

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDL 260
                +  L K+I +  K+  VCPHCG     +           K++  T   +   ++ 
Sbjct: 125 DRKKAKDRLIKEIHKKAKERMVCPHCGAPQFPI-----------KFERPTIYWELRKDEE 173

Query: 261 LAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
             EY                     + P EV    E IP +D+PLL ++ E ++P  ++L
Sbjct: 174 GNEYR------------------HRMMPSEVRDRLEKIPDKDLPLLGLHPEKARPEWMVL 215

Query: 321 TRLLVPPNCIRPSVI--SDLKSDNDV 344
           T L VPP  +RPS+   S +++++D+
Sbjct: 216 TVLPVPPVTMRPSITLESGIRAEDDL 241



 Score = 95.5 bits (236), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 41/57 (71%), Positives = 50/57 (87%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV NS+ SGLTP E+FFH MGGREGLVDTAV+TA++GYMQRRL+ +L+DL V YD
Sbjct: 801 RGFVTNSYKSGLTPQEYFFHAMGGREGLVDTAVRTAQSGYMQRRLINALQDLKVDYD 857



 Score = 52.0 bits (123), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 31/127 (24%), Positives = 63/127 (49%), Gaps = 24/127 (18%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFF 79
           ++LM  ++++++PR G  LIA  QD I+GGYLLT++ A+F R++  ++         + F
Sbjct: 482 KILMEVQNHIISPRYGGPLIAGIQDHISGGYLLTREGAYFTRSEVEQM---------LMF 532

Query: 80  RGLIEGTVTKEDRVQQ---------------QSHIQIVSKNLYCQDPQRTPIPHGLLDRR 124
            G+    + + D+V+                   + I  +N  C +P+R      L++ +
Sbjct: 533 AGINVDKLPEPDKVENGVELWSGKTIFSLLLPDDLTIWYRNKLCDEPERCEALEKLIEEK 592

Query: 125 MGTNQKE 131
           +  + +E
Sbjct: 593 LVPDPEE 599


>gi|300122988|emb|CBK23995.2| unnamed protein product [Blastocystis hominis]
          Length = 1828

 Score =  177 bits (448), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 101/279 (36%), Positives = 155/279 (55%), Gaps = 41/279 (14%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           ++ D+VLFNRQPSLHK+SIM HR +VL + TFR N    TPYNADFDGDEMN+H+PQT +
Sbjct: 422 NNGDIVLFNRQPSLHKMSIMGHRVRVLNYSTFRLNLSCTTPYNADFDGDEMNIHVPQTVQ 481

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           ARAE               +++M +K N+++P++   ++   QD + G   LTQ++ F  
Sbjct: 482 ARAEV-------------TELMMVHK-NIISPKSNGPVMGIVQDTLLGSQKLTQRDTFVA 527

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFV------RTAVIWTGKQIFSLILKP 513
           +   M     ++    D  G I         P+  V      +   +WTGKQ++SLIL  
Sbjct: 528 KDMMM----NMVMWVDDFDGNI---------PIPAVTAHKDGKLVPLWTGKQMYSLIL-- 572

Query: 514 NRDCPVNANLKTKGRAYTANEE--FCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYI 571
               P + N++     Y  N++      D  V++   ELL G +DK+++G+     + ++
Sbjct: 573 ----PKDLNIQRFSTPYDKNKKVPLNMMDCEVLIEEGELLMGIIDKNSIGNTKSGGITHV 628

Query: 572 LLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           L+ D G D A   +    RM +++LMNRGFS+G+GD+ P
Sbjct: 629 LMNDRGPDAAKAFLGLNQRMVNYWLMNRGFSVGLGDMVP 667



 Score = 95.1 bits (235), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 40/58 (68%), Positives = 49/58 (84%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
             GFV NS+  GLTP EF+FH MGGREG++DTAVKT++TGY+QRRL+KS+EDL V YD
Sbjct: 792 AHGFVVNSYLKGLTPQEFYFHAMGGREGIIDTAVKTSKTGYIQRRLIKSMEDLMVYYD 849



 Score = 70.5 bits (171), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 59/233 (25%), Positives = 90/233 (38%), Gaps = 39/233 (16%)

Query: 115 PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSIC 174
           P+  GL D RMGT      C TC ++  DC GHFG+I L   +FH G+   +  +L  IC
Sbjct: 54  PVKGGLNDPRMGTISSSGKCETCNRSYEDCPGHFGHIHLNAEIFHTGFLDIIYRVLTCIC 113

Query: 175 KNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVK 234
            N  C + L+             N            +K+     +V     C   +G   
Sbjct: 114 FN--CGKCLVPRGDIPENETDTDN-----------CRKLSRVFNRVKTIKDCSREHG--- 157

Query: 235 KCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQL 294
            CG        + +   +   I+     + N+ V                 ++P  V  L
Sbjct: 158 GCG------HAWPHLLSRSLKILITYKNDDNQEVS--------------DYISPSSVKDL 197

Query: 295 FEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVI---SDLKSDNDV 344
           F  I  ED   +  N    KP  +IL+ + VPP  +RP V+   S   S++D+
Sbjct: 198 FRKISPEDCRFMGFNYPEIKPEYMILSEIPVPPLAVRPPVMLPGSTTPSEDDI 250



 Score = 53.1 bits (126), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 22/37 (59%), Positives = 28/37 (75%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            ++++AQ+      G +AAQSIGEP TQMTL TFHFAG
Sbjct: 1060 RFMKAQVAAGEVCGIVAAQSIGEPATQMTLNTFHFAG 1096



 Score = 40.8 bits (94), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 26/70 (37%), Positives = 38/70 (54%), Gaps = 2/70 (2%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR++EIIN  + ISTP +T  L KD     + A+ ++  L   TL +V    E  + P
Sbjct: 1105 GVPRLEEIINCVKEISTPTMTLKLRKDLRGSREDAQRIQNTLGLATLDKVISSAEIYYDP 1164

Query: 822  DDSFILIKLD 831
            D    ++K D
Sbjct: 1165 DPVNTVVKQD 1174


>gi|340344217|ref|ZP_08667349.1| DNA-directed RNA polymerase subunit A [Candidatus Nitrosoarchaeum
           koreensis MY1]
 gi|339519358|gb|EGP93081.1| DNA-directed RNA polymerase subunit A [Candidatus Nitrosoarchaeum
           koreensis MY1]
          Length = 1263

 Score =  177 bits (448), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 94/269 (34%), Positives = 152/269 (56%), Gaps = 35/269 (13%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           ++ D+VLFNRQPSLH++SIMAH  +VLP +TFR +  VC PYNADFDGDEMN+H+PQ+EE
Sbjct: 415 ANGDIVLFNRQPSLHQMSIMAHYVRVLPGKTFRLHPSVCPPYNADFDGDEMNLHVPQSEE 474

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           ARAEA+              +LM  +  L++PR G  +I A +DF+TG YLLT+ +    
Sbjct: 475 ARAEAI--------------LLMRVQDQLISPRYGGPIIGALRDFVTGAYLLTKDDTVLT 520

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
             +    A            ++  ++ +   P    +  +++TGKQ+FSL L  + +  +
Sbjct: 521 PQEFYNYA------------MLGGYTDKLPKPATKTKDGLMYTGKQLFSLFLPKDFNYVI 568

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            +        ++   +   +D  V+++N ELL+G +DKS++G+    +V + + +D+G  
Sbjct: 569 TSK-------WSKGTKGAQKD--VVIKNGELLSGVIDKSSIGAEEPESVLHRIAKDYGNT 619

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
            A   +  +  M   Y+ + GFS G  D+
Sbjct: 620 KAKNFLNSILIMVKQYITHYGFSYGYADL 648



 Score =  142 bits (357), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 100/334 (29%), Positives = 162/334 (48%), Gaps = 42/334 (12%)

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFVPD 1158
            Y +A++EP  AVG + AQSIGEPGTQMTL+TFHFAG            + E ++    P 
Sbjct: 930  YNKAKVEPGQAVGIITAQSIGEPGTQMTLRTFHFAGIAERNVTLGLPRLIELVDARKKPV 989

Query: 1159 DSFILIKLDMDRIRLLHLEVDI---------------------DSIRYCIERTRGISGHL 1197
               + I LD +  +     +DI                       I+  +   R      
Sbjct: 990  TPTMDIYLDNESKKSREKAIDIARNVLQTKVSALISDSETDYTSQIKLILSANRLKERGC 1049

Query: 1198 TVSGHSFLILKPKDSSKSFNSKMYQMKQL----LPSVVIKGVQGINRAVIHEEDVEGVT- 1252
            TVS     +   K         +  +K +     P+V+    + +N  V    D+E VT 
Sbjct: 1050 TVSEVEAALQSNKKFKIETTGDLITLKLVDESDAPTVIAIRNKVLNTTVKGVPDIERVTL 1109

Query: 1253 -----KYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVME 1307
                 ++ +   G N+  V+   G+      +NN +E+  TLGIEA+R+ ++ E+K  +E
Sbjct: 1110 VQKDDEWVIQTTGSNIAKVLEVQGIDKKNVRTNNVFEIAGTLGIEASRNALINELKNTLE 1169

Query: 1308 NHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQ 1367
            + G+ +D R+ MLV+DLM S+G +  I RHG+A  K+SVL  A+FE T   +  AA  G+
Sbjct: 1170 DQGLEVDNRYIMLVSDLMCSRGYMQQIGRHGIAGTKDSVLARAAFEITVPTIAHAALAGE 1229

Query: 1368 TDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSE 1401
             + + G++E +I+G  + +G+G + L   V + +
Sbjct: 1230 VEQLKGITENVIVGSMIPIGSGTVDLYMQVSKKK 1263



 Score =  112 bits (279), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 75/255 (29%), Positives = 124/255 (48%), Gaps = 41/255 (16%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           +++ S  +I +   Y +D    P+  GL+D R+GT +    C TCG   + C GHFG+I+
Sbjct: 22  IRKYSVAEITAPETYDEDGM--PVQGGLMDGRLGTLEPGQKCLTCGNTAARCPGHFGHIE 79

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKSLKK 211
           L  PV HI +   +  +LQS C+  +CAR+ + +E    FR  K ++ A + +  K + +
Sbjct: 80  LAEPVLHIAFIDNIYKLLQSTCR--SCARLKVPQEDLEEFRKIKEKHAAYTVISEKRIPE 137

Query: 212 KILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFN 271
           +I+E  KK   CPHCG+                +Y+    K    VE             
Sbjct: 138 QIIEKAKKAKECPHCGKT---------------QYELIFTKPTIFVE------------K 170

Query: 272 PEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIR 331
            EI  H+       L P+ + + F  I  +D+ LL  +   ++P   IL  L VPP  +R
Sbjct: 171 TEIGEHR-------LLPITIRERFTQIIDDDLNLLSYDPVTARPEWFILQALPVPPVTVR 223

Query: 332 PSVI--SDLKSDNDV 344
           PS+I  + ++S++D+
Sbjct: 224 PSIILETGIRSEDDL 238



 Score = 83.2 bits (204), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 34/58 (58%), Positives = 47/58 (81%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
             GFV++++  GL+  EFFFH MGGREGLVDTAV+T ++GYMQRRL+ +LE + ++YD
Sbjct: 775 AHGFVKSNYREGLSALEFFFHAMGGREGLVDTAVRTQQSGYMQRRLINALEHIRLEYD 832



 Score = 79.0 bits (193), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 60/237 (25%), Positives = 113/237 (47%), Gaps = 26/237 (10%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTD------LDYAR-IVKGRLERTTLGEVCEYIE 816
            G+PR+ E+++A +   TP +  YLD ++       +D AR +++ ++         +Y  
Sbjct: 974  GLPRLIELVDARKKPVTPTMDIYLDNESKKSREKAIDIARNVLQTKVSALISDSETDYTS 1033

Query: 817  EVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDS 876
            +          IKL +   RL      +  +   ++  +      T      + LK  D 
Sbjct: 1034 Q----------IKLILSANRLKERGCTVSEVEAALQSNKKFKIETT---GDLITLKLVDE 1080

Query: 877  SKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGV 936
            S +    +  ++  + +  +KGV  I R  + ++D E V +      G N+  V+   G+
Sbjct: 1081 SDA--PTVIAIRNKVLNTTVKGVPDIERVTLVQKDDEWVIQ----TTGSNIAKVLEVQGI 1134

Query: 937  KGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
                  +NN +E+  TLGIEA+R+ ++ E+K  +E+ G+ +D R+ MLV+DLM S+G
Sbjct: 1135 DKKNVRTNNVFEIAGTLGIEASRNALINELKNTLEDQGLEVDNRYIMLVSDLMCSRG 1191


>gi|171186406|ref|YP_001795325.1| DNA-directed RNA polymerase subunit A' [Pyrobaculum neutrophilum
           V24Sta]
 gi|170935618|gb|ACB40879.1| DNA-directed RNA polymerase subunit A' [Pyrobaculum neutrophilum
           V24Sta]
          Length = 884

 Score =  177 bits (448), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 105/271 (38%), Positives = 151/271 (55%), Gaps = 37/271 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIM H  KVLP RTFR +  VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 423 DGDIVLFNRQPSLHRVSIMGHIVKVLPGRTFRLHLAVCPPYNADFDGDEMNLHVPQTEEA 482

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+ LM  + +++TPR G  +I A QD+I G YLL+QK+ F  +
Sbjct: 483 RAE--------------ARTLMLVEKHIITPRYGGAIIGARQDYIIGAYLLSQKSTFLTK 528

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNP--VVFVRTAVIWTGKQIFSLILKPNRDCP 518
            +   +A  L A  S            + +P    F+    +WTGKQ+ S  L  + +  
Sbjct: 529 KE---LAYLLGAGKS------------TEDPPEPAFLHPVELWTGKQVISHFLPKDLNWV 573

Query: 519 VNANLKTKGR-AYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFG 577
                K+K + AY      C  D ++I+ N  ++ G +DK ++G+    ++++ + RD+ 
Sbjct: 574 QPTAFKSKCQDAYR-----CAGDEWIIIINGVMVKGVLDKKSIGAEQVDSLWHRIARDYP 628

Query: 578 EDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
            +VA   +    R+   YL  RGF+ GI  V
Sbjct: 629 PEVARRWLDSSLRLFLRYLDLRGFTFGIDSV 659



 Score =  112 bits (281), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 70/255 (27%), Positives = 126/255 (49%), Gaps = 40/255 (15%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           +++ S +++ +  +Y  D    P+  G+ DRR+G  +  A C TCGQ    C GHFG+++
Sbjct: 28  IRKYSVMEVTTSEVY--DEGGLPVRGGIADRRLGVAEPGARCETCGQTHDVCPGHFGHVE 85

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSY-LVRKSLKK 211
           L  PV H+ Y R + ++L++ C  P C R++L +E+   +R +L      + L+  +L +
Sbjct: 86  LVKPVIHVEYARIIYDVLRTTC--PNCGRIMLKDEEIQRYRERLTKLKSKWRLLAMNLHE 143

Query: 212 KILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFN 271
           KI +   +   CPHCG               +++ K R ++     E+   E    VK +
Sbjct: 144 KIRKKASERMTCPHCG---------------YKRNKVRFERPYYFYEE--TEEGALVKLD 186

Query: 272 PEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIR 331
           PE+                +      +P ED+ LL +N  +++P   IL  L VPP  +R
Sbjct: 187 PEV----------------LRDRLAKVPNEDLELLGLNPSVARPEWAILKVLPVPPPHVR 230

Query: 332 PSVI--SDLKSDNDV 344
           PS+   + ++S++D+
Sbjct: 231 PSIQLETGIRSEDDL 245



 Score = 85.5 bits (210), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 37/64 (57%), Positives = 48/64 (75%), Gaps = 1/64 (1%)

Query: 606 GDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           GD+ P   GFV   F  GLTP E+FFH   GR+GL+DTAV+TA++GYMQRRL+ +L+D+ 
Sbjct: 780 GDIGPHAGGFVGRCFRCGLTPVEYFFHAAAGRDGLIDTAVRTAQSGYMQRRLINALQDVY 839

Query: 665 VQYD 668
           V YD
Sbjct: 840 VAYD 843



 Score = 45.8 bits (107), Expect = 0.18,   Method: Compositional matrix adjust.
 Identities = 22/56 (39%), Positives = 35/56 (62%), Gaps = 3/56 (5%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           + LM  + +++TPR G  +I A QD+I G YLL+QK+ F  + +   +A  L AG+
Sbjct: 487 RTLMLVEKHIITPRYGGAIIGARQDYIIGAYLLSQKSTFLTKKE---LAYLLGAGK 539


>gi|448497569|ref|ZP_21610522.1| DNA-directed RNA polymerase subunit A'' [Halorubrum coriense DSM
            10284]
 gi|445699800|gb|ELZ51820.1| DNA-directed RNA polymerase subunit A'' [Halorubrum coriense DSM
            10284]
          Length = 404

 Score =  177 bits (448), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 111/349 (31%), Positives = 176/349 (50%), Gaps = 65/349 (18%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIE 1152
            E  + +Y R +++P   VG ++AQSIGEPGTQMT+ TFH+AG            + E ++
Sbjct: 52   EGVQNRYERTRVDPLDPVGTVSAQSIGEPGTQMTMNTFHYAGVAEIDVTQGLPRLIELVD 111

Query: 1153 EVFVPDDSFILIKLD----------------MDRIRLLHL------------EVDIDS-- 1182
                PD   + + LD                ++  R+L L             +D++   
Sbjct: 112  ARKTPDTPMMTVHLDGEYATDREKAHEVVWSIEATRILALGDVSTNVADMLVRIDLNDDT 171

Query: 1183 -----------------IRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQ 1225
                             I   IE   G+         + +   P + S     ++ Q+ +
Sbjct: 172  LLERWPTHSDPTEIAQIIAETIEDALGVDAR---QAGTVIEFGPNEPSYR---ELLQLVE 225

Query: 1226 LLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEV 1285
             L  +V KG++ I R VI +E+++G  ++ L  EG    D +   GV   + + NN +E+
Sbjct: 226  RLREIVFKGIEEIERVVIRKEEIDGDEEFVLYTEGSAFGDTLDIEGVDASRTTCNNIHEI 285

Query: 1286 YKTLGIEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMKE 1344
            Y+ LG+EAAR TI+ E K  +E  G+  ++ RH MLVAD+MT+ GE+  I RHG++  K+
Sbjct: 286  YRNLGVEAARETIIDETKNTLEEQGLDDVNVRHLMLVADIMTNNGEIESIGRHGISGNKD 345

Query: 1345 SVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            SVL  A+FE T +HL DAA +G+ D + GV E +I G P+++GTG + L
Sbjct: 346  SVLARAAFEVTVNHLLDAAIHGEYDDLDGVIENVIAGKPISMGTGDVDL 394



 Score =  108 bits (271), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 76/244 (31%), Positives = 128/244 (52%), Gaps = 25/244 (10%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T +LD +  TD + A  V   +E T    LG+V   + + 
Sbjct: 102 GLPRLIELVDARKTPDTPMMTVHLDGEYATDREKAHEVVWSIEATRILALGDVSTNVAD- 160

Query: 819 FVPDDSFILIKLDMDRIRLLH---LEVDIDSIRYCIERTRGISGHLTVSGH---SFLILK 872
                  +L+++D++   LL       D   I   I  T  I   L V      + +   
Sbjct: 161 -------MLVRIDLNDDTLLERWPTHSDPTEIAQIIAET--IEDALGVDARQAGTVIEFG 211

Query: 873 PKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMA 932
           P + S     ++ Q+ + L  +V KG++ I R VI +E+++G  ++ L  EG    D + 
Sbjct: 212 PNEPSYR---ELLQLVERLREIVFKGIEEIERVVIRKEEIDGDEEFVLYTEGSAFGDTLD 268

Query: 933 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTS 991
             GV   + + NN +E+Y+ LG+EAAR TI+ E K  +E  G+  ++ RH MLVAD+MT+
Sbjct: 269 IEGVDASRTTCNNIHEIYRNLGVEAARETIIDETKNTLEEQGLDDVNVRHLMLVADIMTN 328

Query: 992 KGEV 995
            GE+
Sbjct: 329 NGEI 332


>gi|222478543|ref|YP_002564780.1| DNA-directed RNA polymerase subunit A'' [Halorubrum lacusprofundi
            ATCC 49239]
 gi|222451445|gb|ACM55710.1| DNA-directed RNA polymerase, subunit A'' [Halorubrum lacusprofundi
            ATCC 49239]
          Length = 404

 Score =  176 bits (447), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 111/350 (31%), Positives = 178/350 (50%), Gaps = 65/350 (18%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A     +Y+  +++P   VG ++AQSIGEPGTQMT+ TFH+AG            + E +
Sbjct: 51   ATGVENRYIETRVDPLDPVGTVSAQSIGEPGTQMTMNTFHYAGVAEIDVTQGLPRLIELV 110

Query: 1152 EEVFVPDDSFILIKLD----------------MDRIRLLHL------------EVDIDS- 1182
            +    PD   + + LD                ++  R+L L             +D++  
Sbjct: 111  DARKTPDTPMMTVHLDDEYGTDREKAHEVVWSIEATRILALGDVSTNVADMLVRIDLNDD 170

Query: 1183 ------------------IRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMK 1224
                              I   IE + G++   T    + +   P + S     ++ Q+ 
Sbjct: 171  TLLERWPTHSDPSKVAAIIAETIEDSLGVN---TRQSGTVVEFGPNEPSYR---ELLQLV 224

Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYE 1284
            + L  +V KG++ I R VI +E+++G  ++ L  EG    D +   GV   + + NN +E
Sbjct: 225  ERLREIVFKGIEEIERVVIRKEEIDGDEEFVLYTEGSAFGDALDIEGVDASRTTCNNIHE 284

Query: 1285 VYKTLGIEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMK 1343
            +Y+ LG+EAAR TI+ E K  +E  G+  ++ RH MLVAD+MT+ GE+  I RHG++  K
Sbjct: 285  IYRNLGVEAARETIIDETKNTLEEQGLDDVNVRHLMLVADMMTTNGEIDSIGRHGISGSK 344

Query: 1344 ESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            +SVL  A+FE T +HL DAA +G+ D + GV E +I G P+++GTG + L
Sbjct: 345  DSVLARAAFEVTVNHLLDAAIHGEYDELDGVIENVIAGKPISLGTGDVDL 394



 Score =  109 bits (272), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 75/242 (30%), Positives = 128/242 (52%), Gaps = 21/242 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T +LD +  TD + A  V   +E T    LG+V   + + 
Sbjct: 102 GLPRLIELVDARKTPDTPMMTVHLDDEYGTDREKAHEVVWSIEATRILALGDVSTNVAD- 160

Query: 819 FVPDDSFILIKLDMDRIRLLH---LEVDIDSIRYCIERTRGIS-GHLTVSGHSFLILKPK 874
                  +L+++D++   LL       D   +   I  T   S G  T    + +   P 
Sbjct: 161 -------MLVRIDLNDDTLLERWPTHSDPSKVAAIIAETIEDSLGVNTRQSGTVVEFGPN 213

Query: 875 DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATY 934
           + S     ++ Q+ + L  +V KG++ I R VI +E+++G  ++ L  EG    D +   
Sbjct: 214 EPSYR---ELLQLVERLREIVFKGIEEIERVVIRKEEIDGDEEFVLYTEGSAFGDALDIE 270

Query: 935 GVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKG 993
           GV   + + NN +E+Y+ LG+EAAR TI+ E K  +E  G+  ++ RH MLVAD+MT+ G
Sbjct: 271 GVDASRTTCNNIHEIYRNLGVEAARETIIDETKNTLEEQGLDDVNVRHLMLVADMMTTNG 330

Query: 994 EV 995
           E+
Sbjct: 331 EI 332


>gi|448434393|ref|ZP_21586203.1| DNA-directed RNA polymerase subunit A'' [Halorubrum tebenquichense
            DSM 14210]
 gi|445685309|gb|ELZ37664.1| DNA-directed RNA polymerase subunit A'' [Halorubrum tebenquichense
            DSM 14210]
          Length = 404

 Score =  176 bits (447), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 112/349 (32%), Positives = 179/349 (51%), Gaps = 65/349 (18%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIE 1152
            E  R +Y + +++P   VG ++AQSIGEPGTQMT+ TFH+AG            + E ++
Sbjct: 52   EGVRNRYEQTRVDPLDPVGTVSAQSIGEPGTQMTMNTFHYAGVAEIDVTQGLPRLIELVD 111

Query: 1153 EVFVPDDSFILIKLD----------------MDRIRLLHL------------EVDIDS-- 1182
                PD   + + L+                ++  R+L L             +D++   
Sbjct: 112  ARKTPDTPMMTVHLEDEYATDREKAHEVVWSIEATRILALGDVSTNVADMLVRIDLNDDT 171

Query: 1183 -----------------IRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQ 1225
                             I   IE   G++   + +   F    P + S     ++ Q+ +
Sbjct: 172  LLERWPTHSNPSEIAEIIAETIEDALGVNARQSGTVIEF---GPNEPSYR---ELLQLVE 225

Query: 1226 LLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEV 1285
             L  +V KG++ I R VI +E+++G  ++ L  EG    D +A  GV   + + NN +E+
Sbjct: 226  RLREIVFKGIEEIERVVIRKEEIDGDEEFVLYTEGSAFGDTLAIEGVDASRSTCNNIHEI 285

Query: 1286 YKTLGIEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMKE 1344
            Y+ LG+EAAR TI+ E K  +E  G+  ++ RH MLVAD+MT+ GE+  I RHG++  K+
Sbjct: 286  YRNLGVEAARETIIDETKNTLEEQGLDDVNVRHLMLVADIMTNNGEIESIGRHGISGNKD 345

Query: 1345 SVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            SVL  A+FE T +HL DAA +G+ D + GV E +I G P+++GTG + L
Sbjct: 346  SVLARAAFEVTVNHLLDAAIHGEYDELDGVIENVIAGKPISMGTGDVDL 394



 Score =  108 bits (269), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 75/242 (30%), Positives = 132/242 (54%), Gaps = 21/242 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T +L+ +  TD + A  V   +E T    LG+V   + + 
Sbjct: 102 GLPRLIELVDARKTPDTPMMTVHLEDEYATDREKAHEVVWSIEATRILALGDVSTNVAD- 160

Query: 819 FVPDDSFILIKLDMDRIRLLH---LEVDIDSIRYCIERTRGISGHLTVSG-HSFLILKPK 874
                  +L+++D++   LL       +   I   I  T  I   L V+   S  +++  
Sbjct: 161 -------MLVRIDLNDDTLLERWPTHSNPSEIAEIIAET--IEDALGVNARQSGTVIEFG 211

Query: 875 DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATY 934
            +  S+  ++ Q+ + L  +V KG++ I R VI +E+++G  ++ L  EG    D +A  
Sbjct: 212 PNEPSYR-ELLQLVERLREIVFKGIEEIERVVIRKEEIDGDEEFVLYTEGSAFGDTLAIE 270

Query: 935 GVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKG 993
           GV   + + NN +E+Y+ LG+EAAR TI+ E K  +E  G+  ++ RH MLVAD+MT+ G
Sbjct: 271 GVDASRSTCNNIHEIYRNLGVEAARETIIDETKNTLEEQGLDDVNVRHLMLVADIMTNNG 330

Query: 994 EV 995
           E+
Sbjct: 331 EI 332


>gi|325969566|ref|YP_004245758.1| DNA-directed RNA polymerase subunit A' [Vulcanisaeta moutnovskia
           768-28]
 gi|323708769|gb|ADY02256.1| DNA-directed RNA polymerase subunit A' [Vulcanisaeta moutnovskia
           768-28]
          Length = 891

 Score =  176 bits (447), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 99/265 (37%), Positives = 154/265 (58%), Gaps = 31/265 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + D+VLFNRQPSLH++S+M H  +VLP RTFR +  VC PYNADFDGDEMN+H+PQ EEA
Sbjct: 428 NGDIVLFNRQPSLHRMSMMGHIVRVLPGRTFRLHLAVCPPYNADFDGDEMNLHVPQNEEA 487

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+ LM  +++++TPR G  +I A QD+ITGGYLLT+K+   N+
Sbjct: 488 RAE--------------ARTLMIVQNHIITPRYGGPIIGARQDYITGGYLLTRKDNLINK 533

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                + + L+A  ++  G I         P + +    +WTGKQ+ S++L  +    +N
Sbjct: 534 E----LLTYLLA-AANYDGEID-------EPAI-MHPKELWTGKQVISMLLPKD----LN 576

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
               T  +        C+ D Y+I+ N  +  G +DK ++G+    ++++++++ +G D 
Sbjct: 577 WVQPTAIKESCKEPYNCYTDEYIIIVNGYMATGVLDKKSIGAEQVDSLWHVVVKRYGNDY 636

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGI 605
           A   +  + R    +L  RGFS+GI
Sbjct: 637 ARRWVDSILRALLRFLDLRGFSMGI 661



 Score =  117 bits (292), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 76/257 (29%), Positives = 127/257 (49%), Gaps = 46/257 (17%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           I+ ++   D ++  S ++I +   Y  D    P+  GL+DRR+G  +  A C TCG    
Sbjct: 23  IKFSILSPDIIRSLSVMEITTSETY--DEAGRPMVGGLMDRRLGVVEPGARCETCGNPPD 80

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGF-----RAKLR 197
            C GHFG I+L  PV H+ Y + V ++L++ C+   C R+LL +E+   +     R + R
Sbjct: 81  KCPGHFGRIELARPVIHVEYAKYVHDLLRTTCRE--CGRILLTDEEIEKYSKRLERLRAR 138

Query: 198 NPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIV 257
              LS  + + ++KK +E T    VCPHCG                ++YK R ++     
Sbjct: 139 WKLLSDRLIERIRKKAMERT----VCPHCGA---------------KQYKVRFERPYTFY 179

Query: 258 EDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSD 317
           E+                  K+ G+++ L+P+++ +  E IP  D+ LL  + + ++P  
Sbjct: 180 EE------------------KENGVLEKLDPMKIRERLEKIPDSDLVLLGWDPKFARPEW 221

Query: 318 LILTRLLVPPNCIRPSV 334
            ILT L VPP  +RPS+
Sbjct: 222 AILTVLPVPPPQVRPSI 238



 Score = 94.7 bits (234), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 41/64 (64%), Positives = 54/64 (84%), Gaps = 1/64 (1%)

Query: 606 GDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           GD+ P  +GFV+N+F +GLTP EFFFH  GGR+GLVDTAV+TA++GYMQRRL+ +L+D+ 
Sbjct: 785 GDLGPIAKGFVRNNFKTGLTPLEFFFHAAGGRDGLVDTAVRTAQSGYMQRRLINALQDIY 844

Query: 665 VQYD 668
           V YD
Sbjct: 845 VTYD 848



 Score = 47.8 bits (112), Expect = 0.045,   Method: Compositional matrix adjust.
 Identities = 20/42 (47%), Positives = 31/42 (73%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 61
           + LM  +++++TPR G  +I A QD+ITGGYLLT+K+   N+
Sbjct: 492 RTLMIVQNHIITPRYGGPIIGARQDYITGGYLLTRKDNLINK 533


>gi|315230006|ref|YP_004070442.1| DNA-directed RNA polymerase subunit A' [Thermococcus barophilus MP]
 gi|315183034|gb|ADT83219.1| DNA-directed RNA polymerase subunit A' [Thermococcus barophilus MP]
          Length = 906

 Score =  176 bits (447), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 98/281 (34%), Positives = 158/281 (56%), Gaps = 40/281 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIMAHR +V+P++TFR N  VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 418 DGDIVLFNRQPSLHRMSIMAHRVRVMPYKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEA 477

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE              A++LM  ++++++PR G  +I   QD I+GGYLLT++ A+F R
Sbjct: 478 QAE--------------ARILMEVQNHIISPRYGGPIIGGIQDHISGGYLLTREGAYFTR 523

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLIL--------- 511
           ++   +   L+    DI  + +        P         W+GK IFSL+L         
Sbjct: 524 SE---VEQMLMFAGVDIDKLPE--------PDKVEDGIEYWSGKTIFSLLLPDDLTIWYR 572

Query: 512 -----KPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKA 566
                 P++  P+   ++ K             D +V ++N +LL+G++DK   G     
Sbjct: 573 NKLCDDPSKCEPLEKLIEEKLLPDPEEVRKLAYDGFVYIQNGKLLSGAIDKKAYGR-EDG 631

Query: 567 NVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            +  I++R++G + A   + +++++  + + ++GF+  I D
Sbjct: 632 KILDIIVREYGVERARQFLDQVTKLAIWVITHKGFTTAIDD 672



 Score =  117 bits (293), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 77/266 (28%), Positives = 123/266 (46%), Gaps = 35/266 (13%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G IE  +     +++ S  +I   + Y  D    PI  GL+D+R+G       C TCG  
Sbjct: 9   GSIEFGILSPQEIRKMSAAEITVPDTY--DDDGYPIEGGLMDKRLGVIDPGLRCETCGAR 66

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
             DC GHFG+I+L  PV H+G+ + +  IL+S C+   C R+ L +E+   +  K     
Sbjct: 67  YGDCPGHFGHIELARPVIHVGFAKTIYRILESTCRE--CGRIKLTDEEIEEYMKKFELIG 124

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDL 260
                +  L K+I +  K+  VCPHCG     +           K++  T   +   ++ 
Sbjct: 125 DRKKTKDKLIKEIHKKAKERMVCPHCGAPQFPL-----------KFERPTIYWELRRDEQ 173

Query: 261 LAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
             EY                     + P EV    E IP  D+PLL ++ E S+P  ++L
Sbjct: 174 GNEYK------------------HRMMPTEVRDRLEKIPDRDLPLLGLHPEKSRPEWMVL 215

Query: 321 TRLLVPPNCIRPSVI--SDLKSDNDV 344
           T L VPP  +RPS+   S +++++D+
Sbjct: 216 TVLPVPPVTVRPSITLESGIRAEDDL 241



 Score = 95.1 bits (235), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 41/58 (70%), Positives = 50/58 (86%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV NS+ SGLTP E+FFH MGGREGLVDTAV+TA++GYMQRRL+ +L+DL V YD
Sbjct: 800 ARGFVINSYKSGLTPQEYFFHAMGGREGLVDTAVRTAQSGYMQRRLINALQDLKVDYD 857



 Score = 47.8 bits (112), Expect = 0.042,   Method: Compositional matrix adjust.
 Identities = 18/44 (40%), Positives = 33/44 (75%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 63
           ++LM  ++++++PR G  +I   QD I+GGYLLT++ A+F R++
Sbjct: 482 RILMEVQNHIISPRYGGPIIGGIQDHISGGYLLTREGAYFTRSE 525


>gi|379005505|ref|YP_005261177.1| DNA-directed RNA polymerase subunit A'' [Pyrobaculum oguniense TE7]
 gi|375160958|gb|AFA40570.1| DNA-directed RNA polymerase subunit A'' [Pyrobaculum oguniense TE7]
          Length = 884

 Score =  176 bits (446), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 105/269 (39%), Positives = 149/269 (55%), Gaps = 33/269 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++S+M H  KVLP RTFR +  VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 423 DGDIVLFNRQPSLHRVSMMGHLVKVLPGRTFRLHLAVCPPYNADFDGDEMNLHVPQTEEA 482

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A++LM  +++++TPR G  +I A QD+I G YLL+ K  F  +
Sbjct: 483 RAE--------------ARLLMLVENHIITPRYGGAIIGARQDYIIGAYLLSHKTTFLTK 528

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +   +A  L A  S+              P +      +WTGKQI S  L  + +    
Sbjct: 529 KE---VAFLLGAGKSEE---------DPPEPAILYPVE-LWTGKQIISHFLPKDFNWVQP 575

Query: 521 ANLKTKGR-AYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
              K+K + AYT     CH D ++I+ N  L  G +DK ++G+    ++++ + RD+  D
Sbjct: 576 TAFKSKCQDAYT-----CHGDEWIIVLNGYLAKGVLDKKSIGAEQVDSLWHRIARDYPPD 630

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           VA   +    R+   YL  RGF+  +  V
Sbjct: 631 VARRWLDSSLRLFLRYLDLRGFTFAMDSV 659



 Score =  115 bits (288), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 74/255 (29%), Positives = 129/255 (50%), Gaps = 40/255 (15%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           +++ S +++ +  +Y  D    P+  G+ DRR+G  +  A C TCGQ    C GHFG+I+
Sbjct: 28  IRKYSVMEVTTSEVY--DEGGLPVRGGISDRRLGVAEPGARCETCGQTHDVCPGHFGHIE 85

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSY-LVRKSLKK 211
           L  PV H+G+ R + +IL++ C  P C R++L +E+ A +R +L   +  + L+ ++L +
Sbjct: 86  LVKPVVHVGFARVIYDILRTTC--PNCGRIMLRDEEIARYRERLTRLSKRWRLLAQNLHE 143

Query: 212 KILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFN 271
           +I     +   CPHCG               +++ K R ++     E+   E    VK +
Sbjct: 144 RIRRKAAERMTCPHCG---------------YKRNKVRFERPYYFYEE--TENGALVKLD 186

Query: 272 PEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIR 331
           PE+    + G                IP ED+ LL +N  + +P   IL  L VPP  +R
Sbjct: 187 PEM-LRDRLG---------------KIPSEDLELLGINPSVFRPEWAILKVLPVPPPHVR 230

Query: 332 PSVI--SDLKSDNDV 344
           PS+   + ++S++D+
Sbjct: 231 PSIQLETGIRSEDDL 245



 Score = 84.0 bits (206), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 36/65 (55%), Positives = 50/65 (76%), Gaps = 1/65 (1%)

Query: 605 IGDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDL 663
           +GD+     GFV++ F  GLTP E+FFH   GR+GL+DTAV+TA++GYMQRRL+ +L+D+
Sbjct: 779 VGDIGAFSGGFVKHCFRCGLTPVEYFFHAAAGRDGLIDTAVRTAQSGYMQRRLINALQDV 838

Query: 664 CVQYD 668
            V YD
Sbjct: 839 YVAYD 843



 Score = 44.3 bits (103), Expect = 0.53,   Method: Compositional matrix adjust.
 Identities = 21/56 (37%), Positives = 35/56 (62%), Gaps = 3/56 (5%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           ++LM  +++++TPR G  +I A QD+I G YLL+ K  F  + +   +A  L AG+
Sbjct: 487 RLLMLVENHIITPRYGGAIIGARQDYIIGAYLLSHKTTFLTKKE---VAFLLGAGK 539


>gi|332157774|ref|YP_004423053.1| DNA-directed RNA polymerase subunit A' [Pyrococcus sp. NA2]
 gi|331033237|gb|AEC51049.1| DNA-directed RNA polymerase subunit A' [Pyrococcus sp. NA2]
          Length = 906

 Score =  176 bits (446), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 98/282 (34%), Positives = 156/282 (55%), Gaps = 41/282 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIMAHR +V+P++TFR N  VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 418 DGDIVLFNRQPSLHRMSIMAHRVRVMPYKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEA 477

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE              AK+LM  ++++++PR G  +I   QD I+GGYLLT++ A+F R
Sbjct: 478 QAE--------------AKILMEVQNHILSPRYGGPIIGGIQDHISGGYLLTREGAYFTR 523

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTA-VIWTGKQIFSLILKPNRDCPV 519
            +  ++      D  ++             P  +      +W+GK IFSL+L  +     
Sbjct: 524 EEVEQMLMFAGLDIKELP-----------EPDKYDENGRPLWSGKTIFSLLLPDDLTVWY 572

Query: 520 NANLKTKGRAYTANEEFCHR--------------DSYVILRNSELLAGSMDKSTLGSGGK 565
              L  +     A E                   D +V ++N +LL+G++DK   G    
Sbjct: 573 RNKLCDEPERCEALERLIEEKLMPDPEEVRKLAYDGFVYIQNGKLLSGAIDKKAYGR-ED 631

Query: 566 ANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
             +  +++R++G + A   + +++++T + + ++GF+ GI D
Sbjct: 632 GIILDLIVREYGVERARQFLDQVTKLTIWVITHKGFTTGIDD 673



 Score =  112 bits (280), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 76/269 (28%), Positives = 126/269 (46%), Gaps = 41/269 (15%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G IE  +     +++ S +++   + Y  D    PI  G++D+RMG       C TCG  
Sbjct: 9   GSIEFGILSPQEIRKMSAVEVTVPDTY--DDDGYPIEGGVMDKRMGVIDPGLRCETCGAK 66

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
             +C GHFG+I+L  PV H+G+ + +  IL+S C+   C R+ L +E+   +  KL    
Sbjct: 67  AGECPGHFGHIELARPVIHVGFAKTIHRILESTCRE--CGRIKLTDEEIEEYMKKLE--- 121

Query: 201 LSYLVRKSLKKKILETTKKVS---VCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIV 257
           L+   R  + K + E  KK     VCPHCG     +           K++  T   +   
Sbjct: 122 LAKNRRSEVNKILKEIHKKARERMVCPHCGAPQYPI-----------KFEKPTIYWELRK 170

Query: 258 EDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSD 317
           ++   EY                     + P E+    E IP +D+PLL ++ E S+P  
Sbjct: 171 DEQGNEYK------------------HRMMPTEIRDRLEKIPDKDLPLLGLHPEKSRPEW 212

Query: 318 LILTRLLVPPNCIRPSVI--SDLKSDNDV 344
           ++LT L VPP   RPS+   + +++++D+
Sbjct: 213 MVLTVLPVPPVTARPSITLETGIRAEDDL 241



 Score = 94.0 bits (232), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 40/58 (68%), Positives = 50/58 (86%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV NS+ SGL+P E+FFH MGGREGLVDTAV+TA++GYMQRRL+ +L+DL V YD
Sbjct: 801 ARGFVVNSYKSGLSPQEYFFHAMGGREGLVDTAVRTAQSGYMQRRLINALQDLKVDYD 858



 Score = 46.6 bits (109), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 18/44 (40%), Positives = 32/44 (72%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 63
           ++LM  ++++++PR G  +I   QD I+GGYLLT++ A+F R +
Sbjct: 482 KILMEVQNHILSPRYGGPIIGGIQDHISGGYLLTREGAYFTREE 525


>gi|448494510|ref|ZP_21609497.1| DNA-directed RNA polymerase subunit A'' [Halorubrum californiensis
            DSM 19288]
 gi|445689345|gb|ELZ41585.1| DNA-directed RNA polymerase subunit A'' [Halorubrum californiensis
            DSM 19288]
          Length = 404

 Score =  176 bits (446), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 111/350 (31%), Positives = 176/350 (50%), Gaps = 65/350 (18%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            AE    +Y + +++P   VG ++AQSIGEPGTQMT+ TFH+AG            + E +
Sbjct: 51   AEGVENRYEQTRVDPLDPVGTVSAQSIGEPGTQMTMNTFHYAGVAEIDVTQGLPRLIELV 110

Query: 1152 EEVFVPDDSFILIKLD----------------MDRIRLLHL------------EVDIDS- 1182
            +    PD   + + LD                ++  R+L L             +D++  
Sbjct: 111  DARKTPDTPMMTVHLDGEYATDREKAHEVVWSIEATRILALGDVSTNVADMLVRIDLNDD 170

Query: 1183 ------------------IRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMK 1224
                              I   IE   G+         + +   P + S     ++ Q+ 
Sbjct: 171  TLLERWPTHSDPTEIAGIIAETIEDALGVDAR---QAGTVIEFGPNEPSYR---ELLQLV 224

Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYE 1284
            + L  +V KG++ I R VI +E+++G  ++ L  EG    D +   GV   + + NN +E
Sbjct: 225  EQLREIVFKGIEEIERVVIRKEEIDGDEEFVLYTEGSAFGDALDIEGVDASRTTCNNIHE 284

Query: 1285 VYKTLGIEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMK 1343
            +Y+ LG+EAAR TI+ E K  +E  G+  ++ RH MLVAD+MT+ GE+  I RHG++  K
Sbjct: 285  IYRNLGVEAARETIIDETKNTLEEQGLDDVNVRHLMLVADIMTNNGEIESIGRHGISGNK 344

Query: 1344 ESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            +SVL  A+FE T +HL DAA +G+ D + GV E +I G P+++GTG + L
Sbjct: 345  DSVLARAAFEVTVNHLLDAAIHGEYDDLDGVIENVIAGKPISMGTGDVDL 394



 Score =  108 bits (269), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 76/244 (31%), Positives = 128/244 (52%), Gaps = 25/244 (10%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T +LD +  TD + A  V   +E T    LG+V   + + 
Sbjct: 102 GLPRLIELVDARKTPDTPMMTVHLDGEYATDREKAHEVVWSIEATRILALGDVSTNVAD- 160

Query: 819 FVPDDSFILIKLDMDRIRLLH---LEVDIDSIRYCIERTRGISGHLTVSGH---SFLILK 872
                  +L+++D++   LL       D   I   I  T  I   L V      + +   
Sbjct: 161 -------MLVRIDLNDDTLLERWPTHSDPTEIAGIIAET--IEDALGVDARQAGTVIEFG 211

Query: 873 PKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMA 932
           P + S     ++ Q+ + L  +V KG++ I R VI +E+++G  ++ L  EG    D + 
Sbjct: 212 PNEPSYR---ELLQLVEQLREIVFKGIEEIERVVIRKEEIDGDEEFVLYTEGSAFGDALD 268

Query: 933 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTS 991
             GV   + + NN +E+Y+ LG+EAAR TI+ E K  +E  G+  ++ RH MLVAD+MT+
Sbjct: 269 IEGVDASRTTCNNIHEIYRNLGVEAARETIIDETKNTLEEQGLDDVNVRHLMLVADIMTN 328

Query: 992 KGEV 995
            GE+
Sbjct: 329 NGEI 332


>gi|448734899|ref|ZP_21717119.1| DNA-directed RNA polymerase subunit A'' [Halococcus salifodinae DSM
            8989]
 gi|445799529|gb|EMA49908.1| DNA-directed RNA polymerase subunit A'' [Halococcus salifodinae DSM
            8989]
          Length = 398

 Score =  176 bits (446), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 109/343 (31%), Positives = 182/343 (53%), Gaps = 58/343 (16%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A A  E+Y+  +++P   VG ++AQSIGEPGTQMT+ TFH+AG            + E +
Sbjct: 43   ATAVEERYLDTRVDPLDPVGTVSAQSIGEPGTQMTMNTFHYAGVAEIDVTQGLPRLIELV 102

Query: 1152 EEVFVPDDSFILIKLD----------------MDRIRLLHL------------EVDI--- 1180
            +    PD   + + LD                ++  R+L L            ++D+   
Sbjct: 103  DARKTPDTPMMTVHLDGEYATDREKAHEVVWGIEATRILALGDVSTNVADMLVQIDLNDQ 162

Query: 1181 ---------DSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVV 1231
                     + +   IE + G+   +T SG +      + S +     + Q+ + L  +V
Sbjct: 163  TLEERMITPEEVAEIIEDSLGVD--VTQSGTTVEFGPEQPSYRD----LLQLVEELREIV 216

Query: 1232 IKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGI 1291
             KG+  ++R VI +E+++   ++ L  EG    DV+   GV   + + NN +E++  LG+
Sbjct: 217  FKGIDEVSRVVIRKEELDTGEEFVLYTEGSAFGDVLDIEGVDASRTTCNNIHEIHSNLGV 276

Query: 1292 EAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLA 1350
            EAAR TI+ E    +E  G+ +++ RH MLVAD+MT++G +  I RHG++  K+SVL  A
Sbjct: 277  EAARETIIEETMDTLEEQGLGNVNIRHLMLVADIMTAEGTIESIGRHGISGSKDSVLARA 336

Query: 1351 SFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            +FE T +HL DAA +G+ D ++GV+E +I+G P+ +GTG + L
Sbjct: 337  AFEVTVNHLLDAAVHGEVDDLNGVTENVIVGKPIKLGTGDVNL 379



 Score = 99.8 bits (247), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 69/238 (28%), Positives = 129/238 (54%), Gaps = 20/238 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T +LD +  TD + A  V   +E T    LG+V   + + 
Sbjct: 94  GLPRLIELVDARKTPDTPMMTVHLDGEYATDREKAHEVVWGIEATRILALGDVSTNVAD- 152

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSK 878
                  +L+++D++   L    +  + +   IE + G+   +T SG +      + S +
Sbjct: 153 -------MLVQIDLNDQTLEERMITPEEVAEIIEDSLGVD--VTQSGTTVEFGPEQPSYR 203

Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 938
                + Q+ + L  +V KG+  ++R VI +E+++   ++ L  EG    DV+   GV  
Sbjct: 204 D----LLQLVEELREIVFKGIDEVSRVVIRKEELDTGEEFVLYTEGSAFGDVLDIEGVDA 259

Query: 939 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEV 995
            + + NN +E++  LG+EAAR TI+ E    +E  G+ +++ RH MLVAD+MT++G +
Sbjct: 260 SRTTCNNIHEIHSNLGVEAARETIIEETMDTLEEQGLGNVNIRHLMLVADIMTAEGTI 317


>gi|70606495|ref|YP_255365.1| DNA-directed RNA polymerase subunit A' [Sulfolobus acidocaldarius
           DSM 639]
 gi|449066707|ref|YP_007433789.1| DNA-directed RNA polymerase subunit A' [Sulfolobus acidocaldarius
           N8]
 gi|449068981|ref|YP_007436062.1| DNA-directed RNA polymerase subunit A' [Sulfolobus acidocaldarius
           Ron12/I]
 gi|73920763|sp|P11512.2|RPOA1_SULAC RecName: Full=DNA-directed RNA polymerase subunit A'
 gi|68567143|gb|AAY80072.1| DNA-directed RNA polymerase subunit A' [Sulfolobus acidocaldarius
           DSM 639]
 gi|449035215|gb|AGE70641.1| DNA-directed RNA polymerase subunit A' [Sulfolobus acidocaldarius
           N8]
 gi|449037489|gb|AGE72914.1| DNA-directed RNA polymerase subunit A' [Sulfolobus acidocaldarius
           Ron12/I]
          Length = 880

 Score =  176 bits (446), Expect = 9e-41,   Method: Compositional matrix adjust.
 Identities = 100/269 (37%), Positives = 150/269 (55%), Gaps = 29/269 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH++S+MAH+ +VLP RTFR N   C PYNADFDGDEMN+H+PQ+EEA
Sbjct: 413 DGDVVLFNRQPSLHRISMMAHKVRVLPGRTFRLNLLDCPPYNADFDGDEMNLHVPQSEEA 472

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
            AE              A+ LM    N++TPR G  +I   QD+I+G YLL+ K      
Sbjct: 473 IAE--------------ARELMLVHKNIITPRYGGPIIGGGQDYISGAYLLSVKTTLL-- 516

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
             T+   +T++   +D  G +   +  +  P         +TGKQ+ SL L  + +    
Sbjct: 517 --TVEEVATILG-VTDFVGELGEPAILAPKPY--------YTGKQVISLFLPKDFNFHGP 565

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           AN+    RA    +E C  DS+++++N  LL G  DK  +G+    ++ +  +R++G + 
Sbjct: 566 ANISKGPRA--CKDEICPHDSFIVIKNGLLLEGVFDKKAIGNQQPESMLHWSIREYGTEY 623

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVT 609
               M  + +M   +L  RGF++ + D+T
Sbjct: 624 GKWLMDNVFKMFIRFLEMRGFTMTLEDIT 652



 Score =  118 bits (296), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 86/278 (30%), Positives = 134/278 (48%), Gaps = 58/278 (20%)

Query: 78  FFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTC 137
             RG+  G ++  + ++Q S   I++  +Y +D   TPI  G++D ++G  +    C  C
Sbjct: 5   IIRGVKFGVLSPNE-IRQMSVTAIITSEVYDED--GTPIEGGVMDPKLGVIEPGQKCPVC 61

Query: 138 GQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFR---- 193
           G  L+ C GHFG+I+L  PV HIGY + + + L+S C    C R+ + E+    ++    
Sbjct: 62  GNTLAGCPGHFGHIELIKPVIHIGYVKHIYDFLRSTCWR--CGRIKIKEQDLERYKRIYN 119

Query: 194 -AKLRNPALSYLVRKSLKKKILETTKKVSV----CPHCGEINGVVKKCGLLKISHEKYKN 248
             KLR P        S  ++++E  KK+S+    CPHCGE           KI  EK  N
Sbjct: 120 AIKLRWP--------SAARRLVEYIKKISIKNLECPHCGEKQ--------FKIKLEKPYN 163

Query: 249 RTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLM 308
                                FN E     + G I  L+P E+    E IP  D+ LL  
Sbjct: 164 ---------------------FNEE-----RNGSIVKLSPSEIRDRLERIPDSDVELLGY 197

Query: 309 NAELSKPSDLILTRLLVPPNCIRPSVI--SDLKSDNDV 344
           + + S+P  +ILT L VPP  IRPS+   S +++++D+
Sbjct: 198 DPKSSRPEWMILTVLPVPPITIRPSITIESGIRAEDDL 235



 Score = 94.7 bits (234), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 43/73 (58%), Positives = 56/73 (76%), Gaps = 2/73 (2%)

Query: 606 GDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           GD+ P  +GFV+NSF  GL+P E FFH  GGREGLVDTAVKT+++GYMQRRL+ +L DL 
Sbjct: 772 GDIAPEARGFVKNSFMRGLSPYEMFFHAAGGREGLVDTAVKTSQSGYMQRRLINALSDLR 831

Query: 665 VQYDMSFDAAFYG 677
           ++YD +   + YG
Sbjct: 832 IEYDGTV-RSLYG 843


>gi|46670|emb|CAA32925.1| RNA polymerase subunit A (AA 1-880) [Sulfolobus acidocaldarius]
          Length = 880

 Score =  176 bits (446), Expect = 9e-41,   Method: Compositional matrix adjust.
 Identities = 100/269 (37%), Positives = 150/269 (55%), Gaps = 29/269 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH++S+MAH+ +VLP RTFR N   C PYNADFDGDEMN+H+PQ+EEA
Sbjct: 413 DGDVVLFNRQPSLHRISMMAHKVRVLPGRTFRLNLLDCPPYNADFDGDEMNLHVPQSEEA 472

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
            AE              A+ LM    N++TPR G  +I   QD+I+G YLL+ K      
Sbjct: 473 IAE--------------ARELMLVHKNIITPRYGGPIIGGGQDYISGAYLLSVKTTLL-- 516

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
             T+   +T++   +D  G +   +  +  P         +TGKQ+ SL L  + +    
Sbjct: 517 --TVEEVATILG-VTDFVGELGEPAILAPKPY--------YTGKQVISLFLPKDFNFHGP 565

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           AN+    RA    +E C  DS+++++N  LL G  DK  +G+    ++ +  +R++G + 
Sbjct: 566 ANISKGPRA--CKDEICPHDSFIVIKNGLLLEGVFDKKAIGNQQPESMLHWSIREYGTEY 623

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVT 609
               M  + +M   +L  RGF++ + D+T
Sbjct: 624 GKWLMDNVFKMFIRFLEMRGFTMTLEDIT 652



 Score =  118 bits (296), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 86/278 (30%), Positives = 134/278 (48%), Gaps = 58/278 (20%)

Query: 78  FFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTC 137
             RG+  G ++  + ++Q S   I++  +Y +D   TPI  G++D ++G  +    C  C
Sbjct: 5   IIRGVKFGVLSPNE-IRQMSVTAIITSEVYDED--GTPIEGGVMDPKLGVIEPGEKCPVC 61

Query: 138 GQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFR---- 193
           G  L+ C GHFG+I+L  PV HIGY + + + L+S C    C R+ + E+    ++    
Sbjct: 62  GNTLAGCPGHFGHIELIKPVIHIGYVKHIYDFLRSTCWR--CGRIKIKEQDLERYKRIYN 119

Query: 194 -AKLRNPALSYLVRKSLKKKILETTKKVSV----CPHCGEINGVVKKCGLLKISHEKYKN 248
             KLR P        S  ++++E  KK+S+    CPHCGE           KI  EK  N
Sbjct: 120 AIKLRWP--------SAARRLVEYIKKISIKNLECPHCGEKQ--------FKIKLEKPYN 163

Query: 249 RTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLM 308
                                FN E     + G I  L+P E+    E IP  D+ LL  
Sbjct: 164 ---------------------FNEE-----RNGSIVKLSPSEIRDRLERIPDSDVELLGY 197

Query: 309 NAELSKPSDLILTRLLVPPNCIRPSVI--SDLKSDNDV 344
           + + S+P  +ILT L VPP  IRPS+   S +++++D+
Sbjct: 198 DPKSSRPEWMILTVLPVPPITIRPSITIESGIRAEDDL 235



 Score = 94.7 bits (234), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 43/73 (58%), Positives = 56/73 (76%), Gaps = 2/73 (2%)

Query: 606 GDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           GD+ P  +GFV+NSF  GL+P E FFH  GGREGLVDTAVKT+++GYMQRRL+ +L DL 
Sbjct: 772 GDIAPEARGFVKNSFMRGLSPYEMFFHAAGGREGLVDTAVKTSQSGYMQRRLINALSDLR 831

Query: 665 VQYDMSFDAAFYG 677
           ++YD +   + YG
Sbjct: 832 IEYDGTV-RSLYG 843


>gi|410670215|ref|YP_006922586.1| DNA-directed RNA polymerase subunit A'' [Methanolobus psychrophilus
            R15]
 gi|409169343|gb|AFV23218.1| DNA-directed RNA polymerase subunit A'' [Methanolobus psychrophilus
            R15]
          Length = 380

 Score =  176 bits (446), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 115/342 (33%), Positives = 173/342 (50%), Gaps = 58/342 (16%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIE 1152
            E   E Y  A +EP  AVG ++AQSIGEPGTQMT++TFH+AG            + E ++
Sbjct: 44   ERLLESYQYALVEPCEAVGVVSAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVD 103

Query: 1153 EVFVPDDSFILIKL------DMDRIRLLHLEVDIDSIRYCIERTRGISGH---------- 1196
               +P    + I L      D D  R L  E++   I    + T  ++            
Sbjct: 104  ARKLPSTPMMTIALESGYATDRDLARALAWEIEATHIENLADITTDLANMQLIIDLNEKN 163

Query: 1197 ----------------------LTVSGH--SFLILKPKDSSKSFNSKMYQMKQLLPSVVI 1232
                                  +TVSG+  + +IL P   S     ++ Q+ + + ++ +
Sbjct: 164  LVQRSLTPDQIADKIRDEMDVVVTVSGNISNQIILTPNAPSYR---ELLQLAKNIHTITL 220

Query: 1233 KGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIE 1292
            KG++GI R VI ++  E    Y L  EG  L++V+   GV   +  +NN  E+Y   GIE
Sbjct: 221  KGIEGIKRVVIRKDGEE----YTLYTEGSQLKEVLQIEGVDVTRTYTNNVEEIYDVFGIE 276

Query: 1293 AARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASF 1352
            AAR+ I+TE    +   G+++D RH MLV+D+M   GEV  I RHG++  K SV   A+F
Sbjct: 277  AARNAIITEANNTLGEQGLTVDIRHIMLVSDIMCCDGEVKQIGRHGISGEKASVFARAAF 336

Query: 1353 ENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            E T +HL DA   G  D ++GV+E II+G P+ +GTG + L+
Sbjct: 337  EVTVNHLLDAGMRGDLDELNGVTENIIVGQPIKLGTGDVHLI 378



 Score =  105 bits (262), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 74/236 (31%), Positives = 126/236 (53%), Gaps = 18/236 (7%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A +  STP++T  L+    TD D AR +   +E T +  + +        
Sbjct: 94  GLPRLIEIVDARKLPSTPMMTIALESGYATDRDLARALAWEIEATHIENLAD-----ITT 148

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGH--SFLILKPKDSSKS 879
           D + + + +D++   L+   +  D I   I     +   +TVSG+  + +IL P   S  
Sbjct: 149 DLANMQLIIDLNEKNLVQRSLTPDQIADKIRDEMDVV--VTVSGNISNQIILTPNAPSYR 206

Query: 880 FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
              ++ Q+ + + ++ +KG++GI R VI ++  E    Y L  EG  L++V+   GV   
Sbjct: 207 ---ELLQLAKNIHTITLKGIEGIKRVVIRKDGEE----YTLYTEGSQLKEVLQIEGVDVT 259

Query: 940 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
           +  +NN  E+Y   GIEAAR+ I+TE    +   G+++D RH MLV+D+M   GEV
Sbjct: 260 RTYTNNVEEIYDVFGIEAARNAIITEANNTLGEQGLTVDIRHIMLVSDIMCCDGEV 315


>gi|18977934|ref|NP_579291.1| DNA-directed RNA polymerase subunit A'' [Pyrococcus furiosus DSM
            3638]
 gi|397652055|ref|YP_006492636.1| DNA-directed RNA polymerase subunit A'' [Pyrococcus furiosus COM1]
 gi|22096091|sp|Q8U0M5.1|RPOA2_PYRFU RecName: Full=DNA-directed RNA polymerase subunit A''
 gi|18893704|gb|AAL81686.1| DNA-directed RNA polymerase subunit a [Pyrococcus furiosus DSM 3638]
 gi|393189646|gb|AFN04344.1| DNA-directed RNA polymerase subunit A'' [Pyrococcus furiosus COM1]
          Length = 397

 Score =  176 bits (446), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 119/344 (34%), Positives = 178/344 (51%), Gaps = 64/344 (18%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFVP 1157
            +Y RA +EP   VG +AAQSIGEP TQMTL TFH+AG            + E ++    P
Sbjct: 54   EYERALVEPGEPVGTVAAQSIGEPSTQMTLNTFHYAGVAEINVTLGLPRIIEIVDARKNP 113

Query: 1158 DDSFILIKLD----MDRIR-----------------------LLHLE--VDIDSIRYCIE 1188
                + + LD     DR +                       L++ E  V+ID  R  +E
Sbjct: 114  STPMMTVYLDEEHRYDRAKAEEVARRIEGTTLENLARSTTLDLINFEFIVEIDPER--LE 171

Query: 1189 RTRGI--------------SGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKG 1234
            R+ G+              S    V G++ LI++PK + K   S + +  + +    +KG
Sbjct: 172  RS-GLTMEKVVKKLESSFKSAEFEVDGYT-LIVRPKKADKI--SDLRRFAEKIKKHRLKG 227

Query: 1235 VQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAA 1294
            + G+ + ++ +E  E    Y +  EG N + V+   GV   +  +NN +E+ + LGIEAA
Sbjct: 228  LSGVGKTIVRKEGDE----YVIYTEGSNFKQVLKVPGVDPTRTRTNNIHEIAEVLGIEAA 283

Query: 1295 RSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFEN 1354
            R+ I+ EI   M+  G+ +D RH MLVAD+MT  G V  I RHG+   K SVL  A+FE 
Sbjct: 284  RNAIIDEIVSTMQEQGLEVDIRHIMLVADMMTLDGIVRPIGRHGVVGEKSSVLARAAFEI 343

Query: 1355 TSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 1398
            T  HLF+AA  G+ D ++GV E +++G P+ VGTG++KL   +P
Sbjct: 344  TVQHLFEAAEKGEVDNLNGVIENVLIGQPVPVGTGMVKLTMKLP 387



 Score =  110 bits (276), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 76/232 (32%), Positives = 128/232 (55%), Gaps = 14/232 (6%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARI--VKGRLERTTLGEVCEYIEEVFVP 821
           G+PRI EI++A +N STP++T YLD++   D A+   V  R+E TTL  +        + 
Sbjct: 99  GLPRIIEIVDARKNPSTPMMTVYLDEEHRYDRAKAEEVARRIEGTTLENLARSTTLDLI- 157

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             +F  I +++D  RL    + ++ +   +E +   S    V G++ LI++PK + K   
Sbjct: 158 --NFEFI-VEIDPERLERSGLTMEKVVKKLESSFK-SAEFEVDGYT-LIVRPKKADKI-- 210

Query: 882 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
           S + +  + +    +KG+ G+ + ++ +E  E    Y +  EG N + V+   GV   + 
Sbjct: 211 SDLRRFAEKIKKHRLKGLSGVGKTIVRKEGDE----YVIYTEGSNFKQVLKVPGVDPTRT 266

Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
            +NN +E+ + LGIEAAR+ I+ EI   M+  G+ +D RH MLVAD+MT  G
Sbjct: 267 RTNNIHEIAEVLGIEAARNAIIDEIVSTMQEQGLEVDIRHIMLVADMMTLDG 318



 Score = 43.5 bits (101), Expect = 0.99,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 42/75 (56%), Gaps = 11/75 (14%)

Query: 635 GREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAAFYGQTDCISGVSECIIMGLP 694
           GR G+V         G     L ++  ++ VQ+   F+AA  G+ D ++GV E +++G P
Sbjct: 324 GRHGVV---------GEKSSVLARAAFEITVQH--LFEAAEKGEVDNLNGVIENVLIGQP 372

Query: 695 MNVGTGLIKLLQAVP 709
           + VGTG++KL   +P
Sbjct: 373 VPVGTGMVKLTMKLP 387


>gi|407461850|ref|YP_006773167.1| bifunctional DNA-directed RNA polymerase subunit A'/A'' [Candidatus
           Nitrosopumilus koreensis AR1]
 gi|407045472|gb|AFS80225.1| bifunctional DNA-directed RNA polymerase subunit A'/A'' [Candidatus
           Nitrosopumilus koreensis AR1]
          Length = 1263

 Score =  176 bits (445), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 97/271 (35%), Positives = 154/271 (56%), Gaps = 39/271 (14%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D D+V+FNRQPSLH++SIMAH  +VLP +TFR +  VC PYNADFDGDEMN+H+PQ+EE
Sbjct: 415 ADGDIVMFNRQPSLHQMSIMAHYVRVLPGKTFRLHPSVCPPYNADFDGDEMNLHVPQSEE 474

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           ARAEA+              +LM  +  L++PR G  +I A +DF+TG YLLT+ +   +
Sbjct: 475 ARAEAI--------------LLMRVQDQLISPRYGGPIIGALRDFVTGAYLLTKDDTTLS 520

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
             +   +A            ++  ++     P    +    +TGKQ+FSL L  + +  +
Sbjct: 521 IQEFSNLA------------MLGGYTDPLPKPATKTKDGPAYTGKQLFSLFLPKDFNYVI 568

Query: 520 NANLK--TKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFG 577
            +     TKG+          +D  V+++N EL++G +DKS++G+    +V + + +D+G
Sbjct: 569 TSKWSKGTKGKP---------KD--VVIKNGELISGVIDKSSIGAEEPESVLHRIAKDYG 617

Query: 578 EDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
             V  T +  +  M   ++ + GFS G GD+
Sbjct: 618 NAVGKTFLNSILIMVKQFITHYGFSYGYGDL 648



 Score =  142 bits (357), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 102/335 (30%), Positives = 167/335 (49%), Gaps = 44/335 (13%)

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFVPD 1158
            Y +A++EP  AVG + AQSIGEPGTQMTL+TFHFAG            + E ++    P 
Sbjct: 930  YNKAKVEPGQAVGIITAQSIGEPGTQMTLRTFHFAGIKERNVTLGLPRLIELVDARKKPV 989

Query: 1159 DSFILIKLDMDRIRLLHLEVDI--------------DS-IRYCIE----------RTRGI 1193
               + I LD +  +     +D+              DS   Y  E          + RG 
Sbjct: 990  TPTMDIYLDEESKKSREKAIDVARNVLQTKVSALIADSETDYATEIKLVLSENRLKERGC 1049

Query: 1194 S-GHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVT 1252
            S   +  +  S    K + + +    K+ +      ++ I+  + +N  V    D+E VT
Sbjct: 1050 SIAEVEAALSSNKKFKLETTGELITLKLVEESDTATAIAIRN-KVLNTTVKGVPDIERVT 1108

Query: 1253 ------KYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVM 1306
                  ++ +   G N+  V+   G+      +NN +E+  TLGIEAAR++++ E+   +
Sbjct: 1109 LVQKDDEWVIQTTGSNVAKVLEVKGIDKKNVRTNNVFEIAGTLGIEAARNSLINELNSTL 1168

Query: 1307 ENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYG 1366
            E+ G+ +D R+ MLVADLM S+G +  I RHG+A  K+SVL  A+FE T   +  AA  G
Sbjct: 1169 EDQGLEVDNRYIMLVADLMCSRGYMQQIGRHGIAGTKDSVLARAAFEITVPTIAHAALGG 1228

Query: 1367 QTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSE 1401
            + + + G++E +I+G  + +G+G + L   V + +
Sbjct: 1229 EIEQLKGITENVIVGSNIPIGSGTVDLYMQVSKKK 1263



 Score =  108 bits (271), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 72/255 (28%), Positives = 124/255 (48%), Gaps = 41/255 (16%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           +++ S  +I +   Y +D    P+  GL+D R+GT +    C TCG   + C GHFG+++
Sbjct: 22  IRKYSVAEITAPETYDEDGM--PVQGGLMDGRLGTLEPGQKCLTCGNTAARCPGHFGHLE 79

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKSLKK 211
           L  PV HI +   +  +LQS C+  +CAR+ + +E    F+  K ++ A + + +K + +
Sbjct: 80  LAEPVLHIAFIDNIYKLLQSTCR--SCARLKVPQEDLDVFKTIKDKHAAYTVISQKRIPE 137

Query: 212 KILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFN 271
           +I+E  KK   CPHCG+                +Y+    K    VE             
Sbjct: 138 QIIEKAKKAKECPHCGKT---------------QYELIFTKPTIFVE------------K 170

Query: 272 PEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIR 331
            EI  H+       L P+ + + F  I  ED+ LL  +   ++P   +L    VPP  +R
Sbjct: 171 TEIGEHR-------LLPITIRERFSQILDEDLELLSYDPITARPEWFVLQAFPVPPVTVR 223

Query: 332 PSVI--SDLKSDNDV 344
           PS+I  + ++S++D+
Sbjct: 224 PSIILETGIRSEDDL 238



 Score = 82.8 bits (203), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 34/58 (58%), Positives = 47/58 (81%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
             GFV++++  GL+  EFFFH MGGREGLVDTAV+T ++GYMQRRL+ +LE + ++YD
Sbjct: 775 AHGFVKSNYREGLSALEFFFHAMGGREGLVDTAVRTQQSGYMQRRLINALEHIRLEYD 832



 Score = 82.4 bits (202), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 65/237 (27%), Positives = 115/237 (48%), Gaps = 26/237 (10%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTD------LDYAR-IVKGRLERTTLGEVCEYIE 816
            G+PR+ E+++A +   TP +  YLD+++       +D AR +++ ++         +Y  
Sbjct: 974  GLPRLIELVDARKKPVTPTMDIYLDEESKKSREKAIDVARNVLQTKVSALIADSETDYAT 1033

Query: 817  EVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDS 876
            E          IKL +   RL      I  +   +   +     L  +G   + LK  + 
Sbjct: 1034 E----------IKLVLSENRLKERGCSIAEVEAALSSNKKFK--LETTGE-LITLKLVEE 1080

Query: 877  SKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGV 936
            S +  +   + K L  +  +KGV  I R  + ++D E V +      G N+  V+   G+
Sbjct: 1081 SDTATAIAIRNKVL--NTTVKGVPDIERVTLVQKDDEWVIQ----TTGSNVAKVLEVKGI 1134

Query: 937  KGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
                  +NN +E+  TLGIEAAR++++ E+   +E+ G+ +D R+ MLVADLM S+G
Sbjct: 1135 DKKNVRTNNVFEIAGTLGIEAARNSLINELNSTLEDQGLEVDNRYIMLVADLMCSRG 1191


>gi|70606494|ref|YP_255364.1| DNA-directed RNA polymerase subunit A'' [Sulfolobus acidocaldarius
            DSM 639]
 gi|449066706|ref|YP_007433788.1| DNA-directed RNA polymerase subunit A'' [Sulfolobus acidocaldarius
            N8]
 gi|449068980|ref|YP_007436061.1| DNA-directed RNA polymerase subunit A'' [Sulfolobus acidocaldarius
            Ron12/I]
 gi|73920764|sp|P11514.2|RPOA2_SULAC RecName: Full=DNA-directed RNA polymerase subunit A''; Short=Subunit
            C
 gi|68567142|gb|AAY80071.1| DNA-directed RNA polymerase subunit A'' [Sulfolobus acidocaldarius
            DSM 639]
 gi|449035214|gb|AGE70640.1| DNA-directed RNA polymerase subunit A'' [Sulfolobus acidocaldarius
            N8]
 gi|449037488|gb|AGE72913.1| DNA-directed RNA polymerase subunit A'' [Sulfolobus acidocaldarius
            Ron12/I]
          Length = 393

 Score =  176 bits (445), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 120/339 (35%), Positives = 180/339 (53%), Gaps = 62/339 (18%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFVP 1157
            +Y ++ IEP  A+G + AQS+GEPGTQMTL+TFHFAG            + E ++   VP
Sbjct: 56   EYQQSLIEPGEAIGVVTAQSVGEPGTQMTLRTFHFAGIRELNVTLGLPRLIEIVDARKVP 115

Query: 1158 DDSFILI------KLDMD-------RIRLLHLE-------VDIDSIRYCIE------RTR 1191
                + I      K D D       RI    +E       VDI ++   ++      + +
Sbjct: 116  STPMMTIYLTDEYKTDKDKALDIARRIEYTRVENVVSSVSVDISNMSITLQFDQEMLKDK 175

Query: 1192 GIS-------------GHLTVSG---HSFLILKPK-DSSKSFNSKMYQMKQLLPSVVIKG 1234
            G+S             G + +     +SF I   K DS  +    +++M++ + +  IKG
Sbjct: 176  GVSIEEIKKIITKLKLGEIRIEDNDEYSFTIYFEKIDSIMA----LFKMREKILNTKIKG 231

Query: 1235 VQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAA 1294
            V+GI RA++ ++  E    Y ++ +G NL  +M   GV   K  +NN +EV + LGIEAA
Sbjct: 232  VKGIKRAIVQKKGDE----YVIITDGSNLEGIMNVTGVDINKIQTNNIHEVEEVLGIEAA 287

Query: 1295 RSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFEN 1354
            R  I  EIK V+E  G+ +D RH +LV+D+MT  G++  I RHG+   K SVL  A+FE 
Sbjct: 288  RELISREIKKVLEEQGLDVDMRHIVLVSDIMTRTGDIRQIGRHGVTGEKSSVLARAAFEV 347

Query: 1355 TSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            T  HL DAA  G+ +   GV E II+G P+ +GTG+++L
Sbjct: 348  TVKHLLDAAARGEREEFKGVIENIIIGQPIRLGTGIVEL 386



 Score =  111 bits (277), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 85/242 (35%), Positives = 131/242 (54%), Gaps = 28/242 (11%)

Query: 764 GVPRIKEIINASRNISTPIITAYL------DKDTDLDYARIVKGRLERTTLGEVCEYIEE 817
           G+PR+ EI++A +  STP++T YL      DKD  LD AR    R+E T      E +  
Sbjct: 101 GLPRLIEIVDARKVPSTPMMTIYLTDEYKTDKDKALDIAR----RIEYTR----VENVVS 152

Query: 818 VFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSG---HSFLILKPK 874
               D S + I L  D+  L    V I+ I+  I + +   G + +     +SF I   K
Sbjct: 153 SVSVDISNMSITLQFDQEMLKDKGVSIEEIKKIITKLK--LGEIRIEDNDEYSFTIYFEK 210

Query: 875 -DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMAT 933
            DS  +    +++M++ + +  IKGV+GI RA++ ++  E    Y ++ +G NL  +M  
Sbjct: 211 IDSIMA----LFKMREKILNTKIKGVKGIKRAIVQKKGDE----YVIITDGSNLEGIMNV 262

Query: 934 YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
            GV   K  +NN +EV + LGIEAAR  I  EIK V+E  G+ +D RH +LV+D+MT  G
Sbjct: 263 TGVDINKIQTNNIHEVEEVLGIEAARELISREIKKVLEEQGLDVDMRHIVLVSDIMTRTG 322

Query: 994 EV 995
           ++
Sbjct: 323 DI 324


>gi|45358927|ref|NP_988484.1| DNA-directed RNA polymerase subunit A'' [Methanococcus maripaludis
            S2]
 gi|74553842|sp|Q6LXI7.1|RPOA2_METMP RecName: Full=DNA-directed RNA polymerase subunit A''
 gi|45047793|emb|CAF30920.1| RNA polymerase, A/beta'/A' subunit [Methanococcus maripaludis S2]
          Length = 386

 Score =  176 bits (445), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 115/330 (34%), Positives = 172/330 (52%), Gaps = 50/330 (15%)

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYIEEVF 1155
            Y R  +EP  AVG +AAQSIGEPGTQMT++TFH+AG              E+ +  +E  
Sbjct: 49   YERTLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRMIEIVDARKEPS 108

Query: 1156 VP------DDSF---------ILIKLDMDRIRLLHLEVDIDSIRYCIE--------RTRG 1192
             P      +D F         +   ++   +  +  ++ +D +  CI          +RG
Sbjct: 109  TPTMTIYLNDEFKGNREKAATVAKNIESTNVESVSEDISVDLVNECITIILNNQQLESRG 168

Query: 1193 ISGHLTVSG-HSFLILKPKDSSKSFNSK-----MYQMKQLLPSVV---IKGVQGINRAVI 1243
            ++    +    S + LK +D     N K     +  +++ LP V    +KGVQ I R +I
Sbjct: 169  LTVPDVIDAIKSKMKLKIEDHENVLNLKIKTPSLKALRKRLPKVRAIHLKGVQNIKRVII 228

Query: 1244 HEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIK 1303
             +E    V +Y L  EG N+++V    GV   K ++NN  E+   LGIEAAR+ I+ E+ 
Sbjct: 229  RKE----VDEYILYSEGSNIKEVFDIEGVDTTKTTTNNIVEIQDVLGIEAARNAIIYEMD 284

Query: 1304 LVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAA 1363
              + N G+++D RH M+VADLM + G V  I RHG+   K SVL  A+FE T  HL+ A+
Sbjct: 285  ATLGNQGLTVDKRHLMMVADLMCTDGVVKPIGRHGIGGEKASVLARAAFEETVKHLYSAS 344

Query: 1364 FYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
              G  D + GV E II+G P+++GTG I +
Sbjct: 345  MRGYVDELGGVVENIIVGKPISMGTGCIDI 374



 Score = 99.8 bits (247), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 77/236 (32%), Positives = 126/236 (53%), Gaps = 20/236 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A +  STP +T YL+ +   + + A  V   +E T +  V E I    V 
Sbjct: 93  GLPRMIEIVDARKEPSTPTMTIYLNDEFKGNREKAATVAKNIESTNVESVSEDISVDLVN 152

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGH-SFLILKPKDSS-KS 879
           +   I++       R L +   ID+I+  ++        L +  H + L LK K  S K+
Sbjct: 153 ECITIILNNQQLESRGLTVPDVIDAIKSKMK--------LKIEDHENVLNLKIKTPSLKA 204

Query: 880 FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
              ++ +++    ++ +KGVQ I R +I +E    V +Y L  EG N+++V    GV   
Sbjct: 205 LRKRLPKVR----AIHLKGVQNIKRVIIRKE----VDEYILYSEGSNIKEVFDIEGVDTT 256

Query: 940 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
           K ++NN  E+   LGIEAAR+ I+ E+   + N G+++D RH M+VADLM + G V
Sbjct: 257 KTTTNNIVEIQDVLGIEAARNAIIYEMDATLGNQGLTVDKRHLMMVADLMCTDGVV 312


>gi|159490800|ref|XP_001703361.1| predicted protein [Chlamydomonas reinhardtii]
 gi|158280285|gb|EDP06043.1| predicted protein [Chlamydomonas reinhardtii]
          Length = 1167

 Score =  176 bits (445), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 124/295 (42%), Positives = 163/295 (55%), Gaps = 35/295 (11%)

Query: 1128 SIGEPGTQMTLKTFHFAGEVCEYIEEVFVPDDSFILIK---LDMDRIRLLHLEVDIDSIR 1184
            SIGEPGTQMTLKTFHFAG V      + VP    I+     +    I+++ L VD D   
Sbjct: 829  SIGEPGTQMTLKTFHFAG-VASMNVTLGVPRIKEIINAARTISTPIIKVVALAVDND--- 884

Query: 1185 YCIERTRGISGHL------TVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGI 1238
              ++  R + G L       V+ H  ++LKP    +     +     L P++   G  G 
Sbjct: 885  --VKAARLVKGRLEKTTLGQVARHIKIVLKP---GRVAGGSLAGSPDLSPALSPGGPDGG 939

Query: 1239 NRAV--------IHEE-------DVEGVTKYKLLVEGDNLRDVMATYGV-KGVKCSSNNT 1282
              A         IH E       D+  +   +L ++G  +  VM    V + V       
Sbjct: 940  TGAYGGGTSGPRIHGEAAISIRLDMSTIEALQLDIDGHTV-IVMGIPTVERAVITKEKGD 998

Query: 1283 YEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKM 1342
             E+ K +GIEAARS IM+EIK  M +HGMSID RH ML+AD M+ KGEVLGITR G+AKM
Sbjct: 999  KEIEKYMGIEAARSAIMSEIKYTMSSHGMSIDDRHIMLLADCMSYKGEVLGITRFGIAKM 1058

Query: 1343 KESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 1397
            K+SVL+ ASFE T+DHLFDAA +G+ D + GVSE IIMG+PM  GTGL ++   V
Sbjct: 1059 KDSVLHTASFEKTADHLFDAAIHGRVDDVVGVSESIIMGIPMPTGTGLFRIRHNV 1113



 Score =  132 bits (332), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 139/487 (28%), Positives = 187/487 (38%), Gaps = 204/487 (41%)

Query: 552  AGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
            A ++  S +  G K+ +F  L  D+    A +AM RL++M + ++ NRGFSIGI DV   
Sbjct: 726  ANNLMGSVVLGGSKSGLFGTLNCDYSPYAAASAMSRLAKMAARHMGNRGFSIGIDDV--- 782

Query: 612  QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSF 671
                        TP             L     +T + GY    L+              
Sbjct: 783  ------------TPAPV----------LEKAKAETVQKGYSP--LI-------------- 804

Query: 672  DAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPVPRTLLFDNPEFHFPQVY 731
                         +S+C   G P+N+   +  + Q     EP  +  L     FHF  V 
Sbjct: 805  -------------MSQCGSKGSPINIAQMVACVGQQSSIGEPGTQMTL---KTFHFAGV- 847

Query: 732  YERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINASRNISTPII-TAYLDKD 790
                        AS+ VTL             GVPRIKEIINA+R ISTPII    L  D
Sbjct: 848  ------------ASMNVTL-------------GVPRIKEIINAARTISTPIIKVVALAVD 882

Query: 791  TDLDYARIVKGRLERTTLGEVCEYIEEVFVP----------------------------- 821
             D+  AR+VKGRLE+TTLG+V  +I+ V  P                             
Sbjct: 883  NDVKAARLVKGRLEKTTLGQVARHIKIVLKPGRVAGGSLAGSPDLSPALSPGGPDGGTGA 942

Query: 822  -----------DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLI 870
                        ++ I I+LDM  I  L L++D               GH          
Sbjct: 943  YGGGTSGPRIHGEAAISIRLDMSTIEALQLDID---------------GH---------- 977

Query: 871  LKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDV 930
                                  +V++ G+  + RAVI +E            +GD     
Sbjct: 978  ----------------------TVIVMGIPTVERAVITKE------------KGDK---- 999

Query: 931  MATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMT 990
                             E+ K +GIEAARS IM+EIK  M +HGMSID RH ML+AD M+
Sbjct: 1000 -----------------EIEKYMGIEAARSAIMSEIKYTMSSHGMSIDDRHIMLLADCMS 1042

Query: 991  SKGEVLG 997
             KGEVLG
Sbjct: 1043 YKGEVLG 1049



 Score =  119 bits (298), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 52/64 (81%), Positives = 57/64 (89%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH++SIMA RAKV   RT RFNEC C+P+NADFDGDEMN+HLPQTEEA
Sbjct: 663 DGDVVLFNRQPSLHRISIMAFRAKVRTWRTLRFNECACSPFNADFDGDEMNLHLPQTEEA 722

Query: 401 RAEA 404
           RAEA
Sbjct: 723 RAEA 726



 Score =  107 bits (268), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 48/90 (53%), Positives = 63/90 (70%), Gaps = 3/90 (3%)

Query: 99  IQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVF 158
           +Q+  + LY + P+R P  +G+LDRR+G + K   C TCG  L+DC GHFGYI L LPVF
Sbjct: 368 LQVYERALY-KMPERVPAANGVLDRRLGVSNKNYVCETCGHKLADCAGHFGYIKLELPVF 426

Query: 159 HIGYFRCVINILQSICKNPTCARVLLGEEK 188
           HIGYF+  + ILQ ICK   C+RVLL +E+
Sbjct: 427 HIGYFKNTVQILQCICK--ACSRVLLPDEE 454



 Score = 59.7 bits (143), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 34/79 (43%), Positives = 49/79 (62%), Gaps = 4/79 (5%)

Query: 265 NEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLL 324
           ++A+K+N +++ H    L   L+PL V  LFEAIP ED+ LL +     +P DL++T + 
Sbjct: 460 SDAMKYNDQLKGHLHR-LADDLHPLRVRALFEAIPDEDLDLLDIQG---RPEDLVVTHVA 515

Query: 325 VPPNCIRPSVISDLKSDND 343
           VPP  IRPSV  D  S+ D
Sbjct: 516 VPPVAIRPSVEMDGASNED 534



 Score = 48.9 bits (115), Expect = 0.021,   Method: Compositional matrix adjust.
 Identities = 22/41 (53%), Positives = 28/41 (68%)

Query: 668  DMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 708
            D  FDAA +G+ D + GVSE IIMG+PM  GTGL ++   V
Sbjct: 1073 DHLFDAAIHGRVDDVVGVSESIIMGIPMPTGTGLFRIRHNV 1113


>gi|67517057|ref|XP_658413.1| hypothetical protein AN0809.2 [Aspergillus nidulans FGSC A4]
 gi|40746483|gb|EAA65639.1| hypothetical protein AN0809.2 [Aspergillus nidulans FGSC A4]
 gi|259488909|tpe|CBF88741.1| TPA: DNA-directed RNA polymerase Fragment (EC 2.7.7.6)
           [Source:UniProtKB/TrEMBL;Acc:Q873Q6] [Aspergillus
           nidulans FGSC A4]
          Length = 1745

 Score =  176 bits (445), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 98/279 (35%), Positives = 152/279 (54%), Gaps = 36/279 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DV+LFNRQPSLHK S+M HR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE+
Sbjct: 452 DGDVILFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEES 511

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L +L+++            N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 512 RAE----LQQLALVPQ----------NIVSPQRNGPLMGIVQDTLCGIYKICRRDVFLTK 557

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M I    +    D  G+I         P    +    WTGKQ+ S++       P  
Sbjct: 558 EQVMNI----MMWVPDWDGVIP--------PPAIFKPRPRWTGKQMISMVF------PSG 599

Query: 521 ANL---KTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFG 577
            NL    +KG A ++ +    +D  V++   +L+ G ++K  +G+ G   V +I+  ++G
Sbjct: 600 LNLMRTDSKGAAPSSEKYSPLQDGNVLIHEGQLMYGMLNKKIVGASG-GGVIHIIFNEYG 658

Query: 578 EDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
            D AV        + +++L++ GFSIGIGD  P    +Q
Sbjct: 659 ADAAVAFFNGAQAIVNYWLLHNGFSIGIGDTIPNDQTIQ 697



 Score =  102 bits (253), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 60/181 (33%), Positives = 96/181 (53%), Gaps = 15/181 (8%)

Query: 1224 KQLLPSVVIKGVQGINRAVIHEEDVEGVTK---------------YKLLVEGDNLRDVMA 1268
            + LL ++ ++GV G+ RA I+E+    V +               + L   G +L +V+A
Sbjct: 1285 QHLLDTLNLRGVPGVERAFINEKKKIRVQEDGALTDEQSDPLCREWILETSGSSLAEVLA 1344

Query: 1269 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK 1328
              GV   +  SN   EV++  GIEAAR+ ++ E  +V+   G  ++ RH  L+ D+MT +
Sbjct: 1345 IPGVDATRTYSNQFIEVFEVFGIEAARAAVLREFTVVLSFDGSYVNHRHLALLVDVMTMR 1404

Query: 1329 GEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGT 1388
            G +  +TRHG+ +     L   SFE T + L +AA +G+ D   GVSE +I+G     GT
Sbjct: 1405 GYLTPVTRHGINRADNGALMRCSFEETVEILLEAAAFGELDDCRGVSENLILGQMAPAGT 1464

Query: 1389 G 1389
            G
Sbjct: 1465 G 1465



 Score = 99.8 bits (247), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QR+LVK+LE++ V
Sbjct: 811 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMV 870

Query: 666 QYD 668
           +YD
Sbjct: 871 KYD 873



 Score = 89.4 bits (220), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 76/289 (26%), Positives = 135/289 (46%), Gaps = 59/289 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N + NI TP +T Y + +   D + A+ ++  +E T L  + E  E  + P
Sbjct: 1117 GVPRLKEILNVATNIKTPSMTVYQEPERAHDKEGAKQLRSAVEYTNLRSITEATEIYYDP 1176

Query: 822  DDSFILIKLDMDRIR---LLHLEVDIDS-------IRYCIERTRGISGHLTVSGHSFLIL 871
            D    +I+ D D +    ++  +V+ DS       +R  + R + +   LTV   +  I 
Sbjct: 1177 DIQTTVIENDRDMVESYFIIPEDVNDDSSRQSKWLLRIILSRAKLLDKGLTVQDVATKIK 1236

Query: 872  K--PKD-----SSKSFNSKMYQMKQ-------------------------LLPSVVIKGV 899
            +  P+D     S  + + ++ +++Q                         LL ++ ++GV
Sbjct: 1237 QAYPRDIAVIFSDNNADEQVIRIRQIQDYKEDEDDDDIEYDVTLKKLEQHLLDTLNLRGV 1296

Query: 900  QGINRAVIHEEDVEGVT---------------KYKLLVEGDNLRDVMATYGVKGVKCSSN 944
             G+ RA I+E+    V                ++ L   G +L +V+A  GV   +  SN
Sbjct: 1297 PGVERAFINEKKKIRVQEDGALTDEQSDPLCREWILETSGSSLAEVLAIPGVDATRTYSN 1356

Query: 945  NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
               EV++  GIEAAR+ ++ E  +V+   G  ++ RH  L+ D+MT +G
Sbjct: 1357 QFIEVFEVFGIEAARAAVLREFTVVLSFDGSYVNHRHLALLVDVMTMRG 1405



 Score = 80.9 bits (198), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 56/228 (24%), Positives = 102/228 (44%), Gaps = 40/228 (17%)

Query: 110 DPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINI 169
           D ++ P   GL D R+GT  ++ NC TC +   +C GHFG+I+L  PVFHIG+   +  +
Sbjct: 45  DQRQRPRTKGLNDPRLGTIDRQWNCETCEEGQKECPGHFGHIELATPVFHIGFLTKIKKL 104

Query: 170 LQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKSLKKKIL-------------- 214
           L+++C N  C ++           A ++R+P   +     L K IL              
Sbjct: 105 LETVCHN--CGKIKANTSDPKFLDALRIRDPKRRFDHIWRLSKDILICEADPPPEDDEYG 162

Query: 215 -ETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPE 273
            E++K V +   CG     V+K G+  +         K   ++++++  +  E     P+
Sbjct: 163 KESSKPVRLHGGCGNAQPTVRKEGITLV------GTWKPSKSMMDEMDMQQPEKKIITPQ 216

Query: 274 IEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
           +                 L +F  I  ED+ ++ ++ + ++P  +ILT
Sbjct: 217 M----------------ALNIFRNISHEDVRIMGLSNDYARPEWMILT 248



 Score = 56.6 bits (135), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/41 (60%), Positives = 28/41 (68%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            A   ++ +A   P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1068 AIESRFAKAAAAPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1108


>gi|353232989|emb|CCD80344.1| putative dna-directed RNA polymerase III largest subunit
           [Schistosoma mansoni]
          Length = 470

 Score =  176 bits (445), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 97/262 (37%), Positives = 156/262 (59%), Gaps = 12/262 (4%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQ-DPQRTPIPHGLLDRRMGTNQKEANCTTCGQNL 141
           I+  +  E  +++ SHIQ++   LY +    R  + +GLLD R+G N+++  C TCG + 
Sbjct: 17  IKFQLCSEGDLKRLSHIQVLKCLLYAEGQSNRRALDYGLLDPRLGANKRDELCATCGLDY 76

Query: 142 SDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPAL 201
             C+GH+GY DLP P++H+GY   ++ ILQ+ICK  TC+RVLL E++ A F     NP L
Sbjct: 77  QKCIGHWGYFDLPTPIYHVGYTWHIVKILQTICK--TCSRVLLPEQQRARFLISCSNPNL 134

Query: 202 SYLVRKSLKKKILETTKKVSVCPHCGEINGVVKK-CGLLKISHEKYKNRTKKKDAIVEDL 260
            Y+ +K L+  I + + ++ VCP C   NGVV K   L  + H+ +++   K D  V+  
Sbjct: 135 DYVHKKQLRNAIHKLSSRIHVCPFCSAFNGVVTKGMSLPYVVHDIFRHAKAKVDEYVD-- 192

Query: 261 LAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAE---LSKPSD 317
             E+ + +  N E+    + GL + + P + +QLF  IP ED+PLLLM  +    + P +
Sbjct: 193 --EFAKVITKNTELAPVVRKGL-EIIRPGKAMQLFSRIPEEDLPLLLMPFDSRWTTHPRN 249

Query: 318 LILTRLLVPPNCIRPSVISDLK 339
           LI+ R+ V P+ I PSV+S+++
Sbjct: 250 LIVQRVPVCPSAIGPSVVSEVR 271


>gi|150402533|ref|YP_001329827.1| DNA-directed RNA polymerase subunit A'' [Methanococcus maripaludis
            C7]
 gi|166229259|sp|A6VGV0.1|RPOA2_METM7 RecName: Full=DNA-directed RNA polymerase subunit A''
 gi|150033563|gb|ABR65676.1| DNA-directed RNA polymerase, subunit A'' [Methanococcus maripaludis
            C7]
          Length = 386

 Score =  176 bits (445), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 117/328 (35%), Positives = 171/328 (52%), Gaps = 50/328 (15%)

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCE------ 1149
            Y R  +EP  AVG +AAQSIGEPGTQMT++TFH+AG              E+ +      
Sbjct: 49   YERTLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRMIEIVDARKEPS 108

Query: 1150 ------YIEEVFVPD---DSFILIKLDMDRIRLLHLEVDIDSIRYCIE--------RTRG 1192
                  Y+ + F  D    S +   ++   +  +  ++ +D I  CI          +RG
Sbjct: 109  TPTMTIYLNDEFKGDREKASMVAKNIESTDVESVSEDISVDLINECITIVLNMHQLESRG 168

Query: 1193 IS-GHLTVSGHSFLILKPKDSSKSFNSK-----MYQMKQLLPSVV---IKGVQGINRAVI 1243
            ++   +  S  S + LK +D     N K     +  +++ LP V    +KGVQ I R +I
Sbjct: 169  LTVADVIESIKSKMKLKIEDHENVLNLKIKTPSLKALRKRLPKVRAIHLKGVQNIKRVII 228

Query: 1244 HEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIK 1303
             +E    V +Y L  EG N+++V    GV   K ++NN  E+   LGIEAAR+ I+ E+ 
Sbjct: 229  RKE----VDEYILYSEGSNIKEVFDIEGVDTTKTTTNNIVEIQDVLGIEAARNAIIYEMD 284

Query: 1304 LVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAA 1363
              + N G+++D RH M+VADLM + G V  I RHG+   K SVL  A+FE T  HL+ A+
Sbjct: 285  ATLGNQGLTVDKRHLMMVADLMCTDGVVKPIGRHGIGGEKASVLARAAFEETVKHLYSAS 344

Query: 1364 FYGQTDCISGVSECIIMGLPMNVGTGLI 1391
              G  D + GV E II+G P+ +GTG I
Sbjct: 345  MRGYVDELGGVVENIIVGKPIAMGTGCI 372



 Score =  102 bits (253), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 79/243 (32%), Positives = 125/243 (51%), Gaps = 34/243 (13%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A +  STP +T YL+ +   D + A +V   +E T +  V E I    + 
Sbjct: 93  GLPRMIEIVDARKEPSTPTMTIYLNDEFKGDREKASMVAKNIESTDVESVSEDISVDLI- 151

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS-GHLTVSGHSFLILKPKDSSKSF 880
            +  I I L+M ++                  +RG++   +  S  S + LK +D     
Sbjct: 152 -NECITIVLNMHQLE-----------------SRGLTVADVIESIKSKMKLKIEDHENVL 193

Query: 881 NSK-----MYQMKQLLPSVV---IKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMA 932
           N K     +  +++ LP V    +KGVQ I R +I +E    V +Y L  EG N+++V  
Sbjct: 194 NLKIKTPSLKALRKRLPKVRAIHLKGVQNIKRVIIRKE----VDEYILYSEGSNIKEVFD 249

Query: 933 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK 992
             GV   K ++NN  E+   LGIEAAR+ I+ E+   + N G+++D RH M+VADLM + 
Sbjct: 250 IEGVDTTKTTTNNIVEIQDVLGIEAARNAIIYEMDATLGNQGLTVDKRHLMMVADLMCTD 309

Query: 993 GEV 995
           G V
Sbjct: 310 GVV 312


>gi|167044137|gb|ABZ08820.1| putative RNA polymerase Rpb1, domain 2 [uncultured marine
           crenarchaeote HF4000_APKG5C13]
          Length = 1268

 Score =  176 bits (445), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 97/269 (36%), Positives = 152/269 (56%), Gaps = 35/269 (13%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           SD DVVLFNRQPSLH++SIMAH  +VLP +TFR +  VC PYNADFDGDEMN+H+PQ+EE
Sbjct: 415 SDGDVVLFNRQPSLHQMSIMAHHVRVLPGKTFRLHPSVCPPYNADFDGDEMNLHVPQSEE 474

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           ARAEA+              +LM  +  L++PR G  +I   +DFITG YLLT+ +    
Sbjct: 475 ARAEAM--------------LLMRVQEQLISPRFGGPIIGGLRDFITGAYLLTKDDTTLT 520

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           + +    A            ++  +  +   P +  +  +++TGKQ+FSL L      P 
Sbjct: 521 KQEFSNFA------------MLGGYDEKLPEPKINNKNGLLYTGKQLFSLFL------PS 562

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           + N     + ++       +D  V+++N EL++G +DKS++G+    +V + + +D+G +
Sbjct: 563 DFNFVMTSK-WSKGIHGKQKD--VVIKNGELVSGVIDKSSIGAEEPESVLHRIAKDYGNE 619

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
            A   +  +  +   ++ N GFS G  D+
Sbjct: 620 KAKKFLNSILIIIKQFITNYGFSYGYSDL 648



 Score =  114 bits (285), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 60/163 (36%), Positives = 99/163 (60%), Gaps = 4/163 (2%)

Query: 1232 IKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGI 1291
            ++GV  I R  + EE+ +    + +   G NL  V++  GV      +NN +E+   LGI
Sbjct: 1103 VRGVPDIERITLKEENGD----WLIQTTGSNLAKVISVKGVDRNNVRTNNVFEISTVLGI 1158

Query: 1292 EAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLAS 1351
            EAAR++++ E+K  +EN G+ +D R+ MLVADLM  KG +  I RHG+A  K+SVL  A+
Sbjct: 1159 EAARTSLINELKATLENQGLEVDVRYLMLVADLMCHKGYLQQIGRHGIAGSKDSVLARAA 1218

Query: 1352 FENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            FE T   + +AA  G+ + + G++E +I+G  + +G+G + + 
Sbjct: 1219 FEITVPTIANAAKLGEVEKLKGITENVIVGSLIPIGSGTVDIF 1261



 Score = 97.4 bits (241), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 69/261 (26%), Positives = 124/261 (47%), Gaps = 41/261 (15%)

Query: 87  VTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVG 146
           V   + +++ S  +I +   Y +D     +  GL+D R+GT +    C TCG   + C G
Sbjct: 16  VWSPNEIRKYSVSEITAPETYDEDGM--AVQGGLMDGRLGTLEPGQKCLTCGNTSARCPG 73

Query: 147 HFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGF-RAKLRNPALSYLV 205
           HFG+++L  PV HI +   +  +L + C+  +C+R+ + +E    F + K  + + + + 
Sbjct: 74  HFGHVELAEPVLHIAFIDNIHKLLNATCR--SCSRLKVPQEVLDEFLKFKKYSASFAVIS 131

Query: 206 RKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYN 265
           +K + ++I E  KK   CPHCG+I     +  L+      +  +TK         L E  
Sbjct: 132 QKRIPEQIFEKAKKSKECPHCGKI-----QYDLIFTKPTIFIEKTK---------LGE-- 175

Query: 266 EAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLV 325
                               L P+ + + F  I  +D+ LL  N + ++P   IL  L V
Sbjct: 176 ------------------NRLLPITIRERFSQIIDDDLRLLNYNVDTARPEWFILQVLPV 217

Query: 326 PPNCIRPSVI--SDLKSDNDV 344
           PP  +RPS+I  + ++S++D+
Sbjct: 218 PPVTVRPSIILETGIRSEDDL 238



 Score = 83.2 bits (204), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 66/236 (27%), Positives = 115/236 (48%), Gaps = 19/236 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLE------RTTLGEVCEYIEE 817
            G+PRI E+++A +  STP +  YLDKD+        +  ++      +TT+ ++  +  E
Sbjct: 974  GLPRIIELVDARKKPSTPSMDIYLDKDSKSSKEEKKEKAIQTAREILQTTVADLLVHPAE 1033

Query: 818  VFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSS 877
                 D    I L +D  RL      +D I    E  +  +  L  +  +  ++   D+ 
Sbjct: 1034 T----DYQTKITLSVDNNRLKIRGCTLDDITSAFEANKKFNLKLDNNTITLQLVTESDAP 1089

Query: 878  KSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVK 937
                  +  ++  +    ++GV  I R  + EE+ +    + +   G NL  V++  GV 
Sbjct: 1090 T-----VIALRNKVLKTTVRGVPDIERITLKEENGD----WLIQTTGSNLAKVISVKGVD 1140

Query: 938  GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
                 +NN +E+   LGIEAAR++++ E+K  +EN G+ +D R+ MLVADLM  KG
Sbjct: 1141 RNNVRTNNVFEISTVLGIEAARTSLINELKATLENQGLEVDVRYLMLVADLMCHKG 1196



 Score = 82.0 bits (201), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 34/57 (59%), Positives = 46/57 (80%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFV+++F  GL+  EFFFH MGGREGLVDTAV+T ++GYMQRRL+ + E + ++YD
Sbjct: 776 HGFVKSNFRDGLSVLEFFFHAMGGREGLVDTAVRTQQSGYMQRRLINAFEHIRLEYD 832



 Score = 58.5 bits (140), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 32/88 (36%), Positives = 49/88 (55%), Gaps = 6/88 (6%)

Query: 1061 SKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACR---EKYVRAQIEP 1117
            + K+ +TS   K ++    ++ S    +  G  ++          C+   E Y ++++EP
Sbjct: 881  ATKDEITSISKKYTKAFNPKLTSM---VNDGLHNSKLSKEGLENVCKKGLELYDKSKVEP 937

Query: 1118 ATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
              AVG + AQSIGEPGTQMTL+TFH AG
Sbjct: 938  GQAVGIVTAQSIGEPGTQMTLRTFHTAG 965


>gi|448476272|ref|ZP_21603436.1| DNA-directed RNA polymerase subunit A'' [Halorubrum aidingense JCM
            13560]
 gi|445815821|gb|EMA65740.1| DNA-directed RNA polymerase subunit A'' [Halorubrum aidingense JCM
            13560]
          Length = 403

 Score =  176 bits (445), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 111/350 (31%), Positives = 178/350 (50%), Gaps = 65/350 (18%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A     +Y+  +++P   VG ++AQSIGEPGTQMT+ TFH+AG            + E +
Sbjct: 50   ATGVENRYIETRVDPLDPVGTVSAQSIGEPGTQMTMNTFHYAGVAEIDVTQGLPRLIELV 109

Query: 1152 EEVFVPDDSFILIKLD----------------MDRIRLLHL------------EVDIDS- 1182
            +    PD   + + LD                ++  R+L L             +D++  
Sbjct: 110  DARKTPDTPMMTVHLDGEYATDREKAHEVVWSIEATRILALGDVSTNVADMLVRIDLNDD 169

Query: 1183 ------------------IRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMK 1224
                              I   IE + G++   T    + +   P + S     ++ Q+ 
Sbjct: 170  TLLERWPTHSDPSEVAAIIAETIEDSLGVN---TRQSGTVVEFGPSEPSYR---ELLQLV 223

Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYE 1284
            + L  +V KG++ I R VI +E+++G  ++ L  EG    D +   GV   + + NN +E
Sbjct: 224  ERLREIVFKGIEEIERVVIRKEEIDGDEEFVLYTEGSAFGDTLDIEGVDASRTTCNNIHE 283

Query: 1285 VYKTLGIEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMK 1343
            +Y+ LG+EAAR TI+ E K  +E  G+  ++ RH MLVAD+MT+ GE+  I RHG++  K
Sbjct: 284  IYRNLGVEAARETIIDETKNTLEEQGLDDVNVRHLMLVADIMTNNGEIDSIGRHGISGSK 343

Query: 1344 ESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            +SVL  A+FE T +HL DAA +G+ D + GV E +I G P+++GTG + L
Sbjct: 344  DSVLARAAFEVTVNHLLDAAIHGEYDELDGVIENVIAGKPISLGTGDVDL 393



 Score =  109 bits (272), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 76/242 (31%), Positives = 131/242 (54%), Gaps = 21/242 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T +LD +  TD + A  V   +E T    LG+V   + + 
Sbjct: 101 GLPRLIELVDARKTPDTPMMTVHLDGEYATDREKAHEVVWSIEATRILALGDVSTNVAD- 159

Query: 819 FVPDDSFILIKLDMDRIRLLH---LEVDIDSIRYCIERTRGISGHLTV-SGHSFLILKPK 874
                  +L+++D++   LL       D   +   I  T  I   L V +  S  +++  
Sbjct: 160 -------MLVRIDLNDDTLLERWPTHSDPSEVAAIIAET--IEDSLGVNTRQSGTVVEFG 210

Query: 875 DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATY 934
            S  S+  ++ Q+ + L  +V KG++ I R VI +E+++G  ++ L  EG    D +   
Sbjct: 211 PSEPSYR-ELLQLVERLREIVFKGIEEIERVVIRKEEIDGDEEFVLYTEGSAFGDTLDIE 269

Query: 935 GVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKG 993
           GV   + + NN +E+Y+ LG+EAAR TI+ E K  +E  G+  ++ RH MLVAD+MT+ G
Sbjct: 270 GVDASRTTCNNIHEIYRNLGVEAARETIIDETKNTLEEQGLDDVNVRHLMLVADIMTNNG 329

Query: 994 EV 995
           E+
Sbjct: 330 EI 331


>gi|161527856|ref|YP_001581682.1| bifunctional DNA-directed RNA polymerase subunit A'/A''
           [Nitrosopumilus maritimus SCM1]
 gi|160339157|gb|ABX12244.1| DNA-directed RNA polymerase subunit A' [Nitrosopumilus maritimus
           SCM1]
          Length = 1263

 Score =  176 bits (445), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 97/271 (35%), Positives = 154/271 (56%), Gaps = 39/271 (14%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D D+V+FNRQPSLH++SIMAH  +VLP +TFR +  VC PYNADFDGDEMN+H+PQ+EE
Sbjct: 415 ADGDIVMFNRQPSLHQMSIMAHYVRVLPGKTFRLHPSVCPPYNADFDGDEMNLHVPQSEE 474

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           ARAEA+              +LM  +  L++PR G  +I A +DF+TG YLLT+ +    
Sbjct: 475 ARAEAI--------------LLMRVQDQLISPRYGGPIIGALRDFVTGAYLLTKDDTVLT 520

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
             +   +A            ++  ++     P    +    +TGKQ+FSL L  + +  +
Sbjct: 521 VQEFSNLA------------MLGGYTDPLPKPGTKTKDGPAYTGKQLFSLFLPKDFNYVI 568

Query: 520 NANLK--TKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFG 577
            +     TKG+A         +D  V+++N EL++G +DKS++G+    +V + + +D+G
Sbjct: 569 TSKWSKGTKGQA---------KD--VVIKNGELISGVIDKSSIGAEEPESVLHRIAKDYG 617

Query: 578 EDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
             V  + +  +  M   ++ + GFS G GD+
Sbjct: 618 NAVGKSFLNSILIMVKQFITHYGFSYGYGDL 648



 Score =  140 bits (353), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 101/336 (30%), Positives = 171/336 (50%), Gaps = 46/336 (13%)

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIE------ 1152
            Y +A++EP  AVG + AQSIGEPGTQMTL+TFHFAG            + E ++      
Sbjct: 930  YNKAKVEPGQAVGIITAQSIGEPGTQMTLRTFHFAGIKERNVTLGLPRLIELVDARKKPV 989

Query: 1153 ----EVFVPDDS------FILIKLDMDRIRLLHLEVDIDSIRYCIE----------RTRG 1192
                ++++ D+S       I +  ++ + ++  L  D ++  Y  E          R RG
Sbjct: 990  TPTMDIYLDDESKKSREKAIEVARNVLQTKVSALIADSET-DYATEIKLILSENRLRERG 1048

Query: 1193 IS-GHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGV 1251
             S   +  +  S    K + + +    K+ +       + I+  + +N  V    D+E V
Sbjct: 1049 CSIAEVEAALSSNKKFKMETTGELITLKLVEESDTATVIAIRN-KVLNTTVKGVPDIERV 1107

Query: 1252 T------KYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLV 1305
            T      ++ +   G N+  V+   G+      +NN +E+  TLGIEAAR+ ++ E+   
Sbjct: 1108 TLVQKDDEWVIQTTGSNVAKVLEVKGIDKRNVRTNNVFEIAGTLGIEAARNALINELNST 1167

Query: 1306 MENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFY 1365
            +E+ G+ +D R+ MLVADLM S+G +  I RHG+A  K+SVL  A+FE T   +  AA  
Sbjct: 1168 LEDQGLEVDNRYIMLVADLMCSRGYMQQIGRHGIAGTKDSVLARAAFEITVPTIAHAALG 1227

Query: 1366 GQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSE 1401
            G+ + + G++E +I+G  + +G+G + L   V + +
Sbjct: 1228 GEIEQLKGITENVIVGSNIPIGSGTVDLYMQVSKKK 1263



 Score =  109 bits (273), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 72/255 (28%), Positives = 124/255 (48%), Gaps = 41/255 (16%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           +++ S  +I +   Y +D    P+  GL+D R+GT +    C TCG   + C GHFG+++
Sbjct: 22  IRKYSVAEITAPETYDEDGM--PVQGGLMDGRLGTLEPGQKCLTCGNTAARCPGHFGHLE 79

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKSLKK 211
           L  PV HI +   +  +LQS C+  +CAR+ + +E    F+  K ++ A + + +K + +
Sbjct: 80  LAEPVLHIAFIDNIYKLLQSTCR--SCARLKVPQEDLNVFKTIKEKHAAYTVISQKRIPE 137

Query: 212 KILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFN 271
           +I+E  KK   CPHCG+                +Y+    K    VE             
Sbjct: 138 QIIEKAKKAKECPHCGKT---------------QYELIFTKPTIFVE------------K 170

Query: 272 PEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIR 331
            EI  H+       L P+ + + F  I  ED+ LL  +   ++P   +L    VPP  +R
Sbjct: 171 TEIGEHR-------LLPITIRERFSQIIDEDLELLSYDPVTARPEWFVLQAFPVPPVTVR 223

Query: 332 PSVI--SDLKSDNDV 344
           PS+I  + ++S++D+
Sbjct: 224 PSIILETGIRSEDDL 238



 Score = 82.8 bits (203), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 34/58 (58%), Positives = 47/58 (81%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
             GFV++++  GL+  EFFFH MGGREGLVDTAV+T ++GYMQRRL+ +LE + ++YD
Sbjct: 775 AHGFVKSNYREGLSALEFFFHAMGGREGLVDTAVRTQQSGYMQRRLINALEHIRLEYD 832



 Score = 79.0 bits (193), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 60/231 (25%), Positives = 111/231 (48%), Gaps = 14/231 (6%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTL-GEVCEYIEEVFVPD 822
            G+PR+ E+++A +   TP +  YLD ++     + ++  + R  L  +V   I +     
Sbjct: 974  GLPRLIELVDARKKPVTPTMDIYLDDESKKSREKAIE--VARNVLQTKVSALIADSET-- 1029

Query: 823  DSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNS 882
            D    IKL +   RL      I  +   +   +      T    +  +++  D++     
Sbjct: 1030 DYATEIKLILSENRLRERGCSIAEVEAALSSNKKFKMETTGELITLKLVEESDTAT---- 1085

Query: 883  KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCS 942
             +  ++  + +  +KGV  I R  + ++D E V +      G N+  V+   G+      
Sbjct: 1086 -VIAIRNKVLNTTVKGVPDIERVTLVQKDDEWVIQ----TTGSNVAKVLEVKGIDKRNVR 1140

Query: 943  SNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
            +NN +E+  TLGIEAAR+ ++ E+   +E+ G+ +D R+ MLVADLM S+G
Sbjct: 1141 TNNVFEIAGTLGIEAARNALINELNSTLEDQGLEVDNRYIMLVADLMCSRG 1191


>gi|167044066|gb|ABZ08751.1| putative RNA polymerase Rpb1, domain 2, partial [uncultured marine
           crenarchaeote HF4000_APKG4H17]
          Length = 993

 Score =  175 bits (444), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 98/269 (36%), Positives = 152/269 (56%), Gaps = 35/269 (13%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           SD DVVLFNRQPSLH++SIMAH  +VLP +TFR +  VC PYNADFDGDEMN+H+PQ+EE
Sbjct: 144 SDGDVVLFNRQPSLHQMSIMAHHVRVLPGKTFRLHPSVCPPYNADFDGDEMNLHVPQSEE 203

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           ARAEA+              +LM  +  L++PR G  +I   +DFITG YLLT+ +    
Sbjct: 204 ARAEAI--------------MLMRVQEQLISPRFGGPIIGGLRDFITGAYLLTKDDTTLT 249

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           + +    A            ++  +      P +  +   ++TGKQ+FSL L      P 
Sbjct: 250 KQEFSNFA------------MLGGYDGELPEPKIKNKNGPLYTGKQLFSLFL------PS 291

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           + NL    + ++       +D  ++++N EL++G +DKS++G+    +V + + +D+G +
Sbjct: 292 DFNLILTSK-WSKGTNGKLKD--IVIKNGELVSGVIDKSSIGAEEPESVLHRIAKDYGNE 348

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
            A T +  +  +   ++ N GFS G  D+
Sbjct: 349 KAKTFLNSILIIIKQFITNYGFSYGYSDL 377



 Score =  147 bits (371), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 116/389 (29%), Positives = 188/389 (48%), Gaps = 67/389 (17%)

Query: 1061 SKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACR---EKYVRAQIEP 1117
            + K+ +T+   K ++    ++ S  +   H  +SN    A   + C+   E Y ++Q+EP
Sbjct: 610  ATKDEITNISKKYTKTFNPRLTSMVNDALH--KSN-LSKAGLEDVCKKGLELYDKSQVEP 666

Query: 1118 ATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFVPDDSFILIKL 1166
              AVG + AQSIGEPGTQMTL+TFH AG            + E ++    P    + I L
Sbjct: 667  GQAVGIVTAQSIGEPGTQMTLRTFHTAGIAEKNVTLGLPRIIELVDARKKPSTPSMDIYL 726

Query: 1167 DMDRIR-------------------LLHLEVDID---SIRYCIERTRGISGHLTVSGHSF 1204
            D D                      LL   V+ D    I   I+  R     L   G +F
Sbjct: 727  DKDSKSSKEKAIETAKNILQTTVSDLLTHPVETDYQTKITLTIDDAR-----LKTRGCAF 781

Query: 1205 L-ILKPKDSSKSF------NSKMYQ------------MKQLLPSVVIKGVQGINRAVIHE 1245
              ++   +++K F      N+   Q            ++  +    ++GV  I R  + E
Sbjct: 782  EDVMAALETNKKFKAICDNNTITLQFVDELDAAAVVVLRNKVLKTTVRGVPDIARLTLKE 841

Query: 1246 EDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLV 1305
            E+ E    + +   G NL +V++  GV      +NN +E+   LGIEAAR++++ E+K  
Sbjct: 842  ENGE----WLIQTTGSNLAEVLSVKGVDRNNVRTNNVFEISTVLGIEAARNSLINELKGT 897

Query: 1306 MENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFY 1365
            +EN G+ +D R+ MLVADLM  KG +  I RHG+A  K+SVL  A+FE T   + +AA  
Sbjct: 898  LENQGLEVDIRYLMLVADLMCHKGHLQQIGRHGIAGTKDSVLARAAFEITVPTIANAAKL 957

Query: 1366 GQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            G+ + + G++E +I+G  + +G+G + + 
Sbjct: 958  GEIEELKGITENVIVGSQIPIGSGTVDIF 986



 Score = 90.9 bits (224), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 119/234 (50%), Gaps = 15/234 (6%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVK--GRLERTTLGEVCEYIEEVFVP 821
           G+PRI E+++A +  STP +  YLDKD+     + ++    + +TT+ ++  +  E    
Sbjct: 703 GLPRIIELVDARKKPSTPSMDIYLDKDSKSSKEKAIETAKNILQTTVSDLLTHPVET--- 759

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
            D    I L +D  RL       + +   +E  +       +  ++ + L+  D   +  
Sbjct: 760 -DYQTKITLTIDDARLKTRGCAFEDVMAALETNKKFKA---ICDNNTITLQFVDELDA-- 813

Query: 882 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
           + +  ++  +    ++GV  I R  + EE+ E    + +   G NL +V++  GV     
Sbjct: 814 AAVVVLRNKVLKTTVRGVPDIARLTLKEENGE----WLIQTTGSNLAEVLSVKGVDRNNV 869

Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            +NN +E+   LGIEAAR++++ E+K  +EN G+ +D R+ MLVADLM  KG +
Sbjct: 870 RTNNVFEISTVLGIEAARNSLINELKGTLENQGLEVDIRYLMLVADLMCHKGHL 923



 Score = 83.6 bits (205), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 35/57 (61%), Positives = 47/57 (82%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFV+++F  GL+  EFFFH MGGREGLVDTAV+T ++GYMQRRL+ +LE + ++YD
Sbjct: 505 HGFVKSNFRDGLSVLEFFFHAMGGREGLVDTAVRTQQSGYMQRRLINALEHIRLEYD 561


>gi|294946553|ref|XP_002785113.1| DNA-directed RNA polymerase subunit A', putative [Perkinsus marinus
           ATCC 50983]
 gi|239898547|gb|EER16909.1| DNA-directed RNA polymerase subunit A', putative [Perkinsus marinus
           ATCC 50983]
          Length = 465

 Score =  175 bits (444), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 85/147 (57%), Positives = 104/147 (70%), Gaps = 23/147 (15%)

Query: 330 IRPSVISDLK---------SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTP 380
           IR  + +DL+          D DVVLFNRQPSLHK+SIMAHRAKV+P RTFRFNECVC+P
Sbjct: 317 IREELAADLQYGDVVERHLQDGDVVLFNRQPSLHKMSIMAHRAKVMPWRTFRFNECVCSP 376

Query: 381 YNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAA 440
           YNADFDGDEMNVHLPQT+EARAEAL               LM  ++NL+T +NGE ++AA
Sbjct: 377 YNADFDGDEMNVHLPQTQEARAEAL--------------ALMGVQNNLITSKNGEPIVAA 422

Query: 441 TQDFITGGYLLTQKNAFFNRAQTMRIA 467
           TQDF+T  +LLTQ++ F  + +   IA
Sbjct: 423 TQDFLTSAWLLTQRDTFLTKDKIANIA 449



 Score = 65.9 bits (159), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 55/165 (33%), Positives = 83/165 (50%), Gaps = 12/165 (7%)

Query: 182 VLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKC--GLL 239
           VLL  EK + +  + R        +K + +K+++T KKV  CP+C   NG VKK   G +
Sbjct: 1   VLLAPEKRSVWLNRTRKATKDVQQQKGVFRKLVDTCKKVRQCPYCDAYNGAVKKGTRGYM 60

Query: 240 KISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIP 299
            + HE  K++ K       +   +Y++AV  NPEI  H      + L PL +L L   +P
Sbjct: 61  TLVHELPKDQAKV------EYQQQYSDAVSNNPEIGNHLSKVAYEDLTPLHLLPLLAKMP 114

Query: 300 LEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSV-ISDLKSDND 343
             D  +L +  +   P  L++T + V P CIRPSV I D  +  D
Sbjct: 115 PSDQEMLKLPPQ---PERLVVTHVPVSPVCIRPSVQIGDAGTQED 156



 Score = 52.8 bits (125), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 34/48 (70%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIA 68
            LM  ++NL+T +NGE ++AATQDF+T  +LLTQ++ F  + +   IA
Sbjct: 402 ALMGVQNNLITSKNGEPIVAATQDFLTSAWLLTQRDTFLTKDKIANIA 449


>gi|14591327|ref|NP_143405.1| DNA-directed RNA polymerase subunit A'' [Pyrococcus horikoshii OT3]
 gi|14548239|sp|O93777.1|RPOA2_PYRHO RecName: Full=DNA-directed RNA polymerase subunit A''
 gi|3257972|dbj|BAA30655.1| 397aa long hypothetical DNA-directed RNA polymerase subunit A''
            [Pyrococcus horikoshii OT3]
          Length = 397

 Score =  175 bits (444), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 117/341 (34%), Positives = 174/341 (51%), Gaps = 58/341 (17%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFVP 1157
            +Y +A IEP  AVG +AAQSIGEP TQMTL TFH+AG            + E ++    P
Sbjct: 54   EYEKALIEPGEAVGTVAAQSIGEPSTQMTLNTFHYAGVAEINVTLGLPRIIEIVDARKNP 113

Query: 1158 DDSFILIKLDMD-------------RIRLLHLE-------VDIDSIRYCIE------RTR 1191
                + + LD +             RI    LE       +D+ ++ + +E         
Sbjct: 114  STPMMTVYLDEEHRYDREKAEEVARRIEGTTLENLARTTTLDLINMEFIVEVDPERLEKS 173

Query: 1192 GI--------------SGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQG 1237
            G+              S      G++ LI++PK   K   S + ++ + +    +KG+ G
Sbjct: 174  GLTMEKILKKLQSSFKSAEFEADGYT-LIVRPKKIEKI--SDLRRLSEKVKKHRLKGLSG 230

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            + + +I +E  E    Y +  EG N + V+   GV   +  +NN +E+ + LGIEAAR+ 
Sbjct: 231  VGKTIIRKEGDE----YVIYTEGSNFKQVLKVPGVDPTRTRTNNIHEIAEVLGIEAARNA 286

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            I+ EI   M   G+ +D RH MLVAD+MT  G V  I RHG+   K SVL  A+FE T  
Sbjct: 287  IIEEIINTMHEQGLEVDIRHIMLVADIMTLDGVVRPIGRHGVVGEKASVLARAAFEITVQ 346

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 1398
            HLF+AA  G+ D +SGV E +++G P+ VGTG++KL   +P
Sbjct: 347  HLFEAAERGEVDNLSGVIENVLIGQPVPVGTGMVKLTMKLP 387



 Score =  105 bits (263), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 77/236 (32%), Positives = 128/236 (54%), Gaps = 18/236 (7%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PRI EI++A +N STP++T YLD++   D + A  V  R+E TTL  +        + 
Sbjct: 99  GLPRIIEIVDARKNPSTPMMTVYLDEEHRYDREKAEEVARRIEGTTLENLARTTTLDLI- 157

Query: 822 DDSFILIKLDMDRIRL--LHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKS 879
           +  FI +++D +R+    L +E  +  ++   +     S      G++ LI++PK   K 
Sbjct: 158 NMEFI-VEVDPERLEKSGLTMEKILKKLQSSFK-----SAEFEADGYT-LIVRPKKIEKI 210

Query: 880 FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
             S + ++ + +    +KG+ G+ + +I +E  E    Y +  EG N + V+   GV   
Sbjct: 211 --SDLRRLSEKVKKHRLKGLSGVGKTIIRKEGDE----YVIYTEGSNFKQVLKVPGVDPT 264

Query: 940 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
           +  +NN +E+ + LGIEAAR+ I+ EI   M   G+ +D RH MLVAD+MT  G V
Sbjct: 265 RTRTNNIHEIAEVLGIEAARNAIIEEIINTMHEQGLEVDIRHIMLVADIMTLDGVV 320



 Score = 44.7 bits (104), Expect = 0.38,   Method: Compositional matrix adjust.
 Identities = 26/75 (34%), Positives = 42/75 (56%), Gaps = 11/75 (14%)

Query: 635 GREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAAFYGQTDCISGVSECIIMGLP 694
           GR G+V         G     L ++  ++ VQ+   F+AA  G+ D +SGV E +++G P
Sbjct: 324 GRHGVV---------GEKASVLARAAFEITVQH--LFEAAERGEVDNLSGVIENVLIGQP 372

Query: 695 MNVGTGLIKLLQAVP 709
           + VGTG++KL   +P
Sbjct: 373 VPVGTGMVKLTMKLP 387


>gi|355570730|ref|ZP_09042000.1| DNA-directed RNA polymerase, subunit A'' [Methanolinea tarda NOBI-1]
 gi|354826012|gb|EHF10228.1| DNA-directed RNA polymerase, subunit A'' [Methanolinea tarda NOBI-1]
          Length = 391

 Score =  175 bits (444), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 111/341 (32%), Positives = 176/341 (51%), Gaps = 59/341 (17%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYIEEV 1154
            +Y   +IE   AVG +AAQSIGEPGTQMT++TFH+AG              E+ +  +E 
Sbjct: 46   EYANTRIEACEAVGIIAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIMDARKEP 105

Query: 1155 FVPDDSFIL---IKLDMDRIRLLHLE-------------VDIDSIRYCIERTRGISGHLT 1198
              P  +  L      D DR R +  +             +D+++++  ++    +     
Sbjct: 106  STPTMTIYLEGEYATDRDRAREVSWQIEAAPLHEFGDIVIDMENMQIVVQLNTQVCEKRR 165

Query: 1199 VSGHSFLILKPK------------------DSSKSFNSK-------MYQMKQLLPSVVIK 1233
            ++    +   P+                  +++  F+ K       ++Q+ + + +V+++
Sbjct: 166  IAVSDIIDSAPRKIRDRRHYRDFECEVDVNNATMIFSPKDRESYQNLFQLAEHVRNVIVQ 225

Query: 1234 GVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEA 1293
            G+  I R V+ +E  E    Y L  EG NL+DV    GV   +  +NN  E+ + LGIEA
Sbjct: 226  GIDDIERVVVRKESGE----YILYTEGSNLKDVFEVEGVDTTRTRTNNISEIAQVLGIEA 281

Query: 1294 ARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFE 1353
            AR+ I+ E    +   G+ +D RH MLVAD+M   GEV  I RHG+A  KESVL+ A+FE
Sbjct: 282  ARNAIIHEALSTLSEQGILVDVRHIMLVADMMCMDGEVKQIGRHGIAGEKESVLSRAAFE 341

Query: 1354 NTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
             T +HL DAA   + D +SGV+E +I+G P+ +GTG +KL+
Sbjct: 342  VTVNHLLDAAIANEVDELSGVTENVIVGQPIQLGTGDVKLI 382



 Score =  107 bits (266), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 79/239 (33%), Positives = 129/239 (53%), Gaps = 17/239 (7%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A +  STP +T YL+ +  TD D AR V  ++E   L E  + + ++   
Sbjct: 91  GLPRLIEIMDARKEPSTPTMTIYLEGEYATDRDRAREVSWQIEAAPLHEFGDIVIDM--- 147

Query: 822 DDSFILIKLDMDRIRLLHLEVD--IDSI-RYCIERT--RGISGHLTVSGHSFLILKPKDS 876
           ++  I+++L+        + V   IDS  R   +R   R     + V+ ++ +I  PKD 
Sbjct: 148 ENMQIVVQLNTQVCEKRRIAVSDIIDSAPRKIRDRRHYRDFECEVDVN-NATMIFSPKDR 206

Query: 877 SKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGV 936
               N  ++Q+ + + +V+++G+  I R V+ +E  E    Y L  EG NL+DV    GV
Sbjct: 207 ESYQN--LFQLAEHVRNVIVQGIDDIERVVVRKESGE----YILYTEGSNLKDVFEVEGV 260

Query: 937 KGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
              +  +NN  E+ + LGIEAAR+ I+ E    +   G+ +D RH MLVAD+M   GEV
Sbjct: 261 DTTRTRTNNISEIAQVLGIEAARNAIIHEALSTLSEQGILVDVRHIMLVADMMCMDGEV 319


>gi|332157773|ref|YP_004423052.1| DNA-directed RNA polymerase subunit A' [Pyrococcus sp. NA2]
 gi|331033236|gb|AEC51048.1| DNA-directed RNA polymerase subunit A' [Pyrococcus sp. NA2]
          Length = 397

 Score =  175 bits (444), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 116/346 (33%), Positives = 176/346 (50%), Gaps = 58/346 (16%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIE 1152
            E   ++Y RA +EP  AVG +AAQSIGEP TQMTL TFH+AG            + E ++
Sbjct: 49   EEVVKEYERALVEPGEAVGTVAAQSIGEPSTQMTLNTFHYAGVAEINVTLGLPRIIEIVD 108

Query: 1153 EVFVPDDSFILIKLDMD-------------RIRLLHLE-------VDIDSIRYCIE---- 1188
                P    + + LD +             RI    LE       +D+ ++ + +E    
Sbjct: 109  ARKNPSTPMMTVYLDEEHRYDRAKAEEVARRIEGTTLENLARTTTLDLINMEFIVEIDPE 168

Query: 1189 --RTRGI--------------SGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVI 1232
                 G+              S      G++ LI++PK   K   S + ++ + +    +
Sbjct: 169  RLEKSGLTMEKILKKLQSSFKSAEFEADGYT-LIVRPKKVEKI--SDLRRLAEKVKKHRL 225

Query: 1233 KGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIE 1292
            KG+ G+ + ++ +E  E    Y +  EG N + V+   GV   +  +NN +E+ + LGIE
Sbjct: 226  KGLSGVGKTIVRKEGDE----YVIYTEGSNFKQVLKVPGVDPTRTRTNNIHEIAEVLGIE 281

Query: 1293 AARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASF 1352
            AAR+ I+ EI   M   G+ +D RH MLVAD+MT  G V  I RHG+   K SVL  A+F
Sbjct: 282  AARNAIIEEIVNTMREQGLEVDIRHIMLVADIMTLDGVVRPIGRHGVVGEKASVLARAAF 341

Query: 1353 ENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 1398
            E T  HLF+AA  G+ D ++GV E +++G P+ VGTG++KL   +P
Sbjct: 342  EITVQHLFEAAERGEVDNLNGVIENVLIGQPVPVGTGMVKLTMRLP 387



 Score =  107 bits (266), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 76/236 (32%), Positives = 128/236 (54%), Gaps = 18/236 (7%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARI--VKGRLERTTLGEVCEYIEEVFVP 821
           G+PRI EI++A +N STP++T YLD++   D A+   V  R+E TTL  +        + 
Sbjct: 99  GLPRIIEIVDARKNPSTPMMTVYLDEEHRYDRAKAEEVARRIEGTTLENLARTTTLDLI- 157

Query: 822 DDSFILIKLDMDRIRL--LHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKS 879
           +  FI +++D +R+    L +E  +  ++   +     S      G++ LI++PK   K 
Sbjct: 158 NMEFI-VEIDPERLEKSGLTMEKILKKLQSSFK-----SAEFEADGYT-LIVRPKKVEKI 210

Query: 880 FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
             S + ++ + +    +KG+ G+ + ++ +E  E    Y +  EG N + V+   GV   
Sbjct: 211 --SDLRRLAEKVKKHRLKGLSGVGKTIVRKEGDE----YVIYTEGSNFKQVLKVPGVDPT 264

Query: 940 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
           +  +NN +E+ + LGIEAAR+ I+ EI   M   G+ +D RH MLVAD+MT  G V
Sbjct: 265 RTRTNNIHEIAEVLGIEAARNAIIEEIVNTMREQGLEVDIRHIMLVADIMTLDGVV 320



 Score = 42.7 bits (99), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 20/54 (37%), Positives = 36/54 (66%), Gaps = 2/54 (3%)

Query: 656 LVKSLEDLCVQYDMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 709
           L ++  ++ VQ+   F+AA  G+ D ++GV E +++G P+ VGTG++KL   +P
Sbjct: 336 LARAAFEITVQH--LFEAAERGEVDNLNGVIENVLIGQPVPVGTGMVKLTMRLP 387


>gi|15678327|ref|NP_275442.1| DNA-directed RNA polymerase subunit alpha [Methanothermobacter
           thermautotrophicus str. Delta H]
 gi|2621352|gb|AAB84805.1| DNA-dependent RNA polymerase, subunit A' [Methanothermobacter
           thermautotrophicus str. Delta H]
          Length = 664

 Score =  175 bits (444), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 105/267 (39%), Positives = 148/267 (55%), Gaps = 36/267 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++S+MAHRA+VLP++TFR N CVC PYNADFDGDEMN+H+ QTEE+
Sbjct: 203 DGDIVLFNRQPSLHRMSLMAHRARVLPYKTFRLNLCVCPPYNADFDGDEMNIHVLQTEES 262

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              AK LM  + ++++PR G  +I +  D I+G YLLT+K A F  
Sbjct: 263 RAE--------------AKTLMLVQEHMISPRFGGPIIGSINDQISGLYLLTRKFAEFEE 308

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +  ++                    RS    +  R    W+GK+IFSLIL  +      
Sbjct: 309 EEVFQL-------------------LRSAGISLPSRRGTKWSGKEIFSLILPDDLSMTYR 349

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           A++    R     E+ C  D+YV++ N  L +G +DK T G+     + +I +R++G D 
Sbjct: 350 ADVCR--RCQECIEDGCEYDAYVVIENGRLESGVIDKKTCGAFSGRLLGHI-IREYGTDE 406

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           A   +   SR+    LM  GF+  I D
Sbjct: 407 AREFLESASRLAIAVLMRTGFTTSIMD 433



 Score = 87.0 bits (214), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 37/57 (64%), Positives = 47/57 (82%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFVQ+S+  GL P EFFFH MGGR+ LVDTAV+TA++GYMQRRL+ +L+DL V  D
Sbjct: 563 RGFVQSSYREGLDPIEFFFHAMGGRDALVDTAVRTAQSGYMQRRLINALQDLTVDED 619


>gi|327311709|ref|YP_004338606.1| DNA-directed RNA polymerase subunit alpha [Thermoproteus uzoniensis
           768-20]
 gi|326948188|gb|AEA13294.1| DNA-directed RNA polymerase subunit alpha [Thermoproteus uzoniensis
           768-20]
          Length = 884

 Score =  175 bits (444), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 99/267 (37%), Positives = 148/267 (55%), Gaps = 35/267 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+ LFNRQPSLH++S+M H  +VLP RTFR +  VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 423 DGDIALFNRQPSLHRVSMMGHIVRVLPGRTFRIHLAVCPPYNADFDGDEMNLHIPQTEEA 482

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+ LM  + ++VTPR G  +I A QD+I G YLL++K     +
Sbjct: 483 RAE--------------ARTLMLVQEHIVTPRYGGAIIGARQDYIIGAYLLSRKTTLLTK 528

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +   +A  +  +  D+             P + +    +WTGKQI S+ L  +    +N
Sbjct: 529 KEAAYLAGAMKLE-GDLP-----------EPAI-MHPVELWTGKQIISMALPKD----LN 571

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
               T  ++       C  D ++I+ N  ++ G++DK ++G+    ++++ + RD+  DV
Sbjct: 572 WVQPTAFKSACKEPYTCETDEWIIIINGNMVTGTLDKKSIGAEQVDSLWHRIARDYPSDV 631

Query: 581 AVTAMWRLSRMTSF--YLMNRGFSIGI 605
           A    W  S +  F  +L  RGFSIG+
Sbjct: 632 A--RKWLDSSLRVFLRFLDLRGFSIGL 656



 Score =  116 bits (290), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 75/257 (29%), Positives = 131/257 (50%), Gaps = 40/257 (15%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D +++ S ++I +  +Y  D    PI  GL+DRR+G  +  A C TCGQ    C GHFG+
Sbjct: 26  DLIRRYSVLEITTSEIY--DEGGLPIRGGLMDRRLGVAEPGARCETCGQPYDVCPGHFGH 83

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSY-LVRKSL 209
           I+L  PV H+ + R + ++L++ C  P C R++L +E+   +  +L+     + L+  +L
Sbjct: 84  IELAKPVIHVEFARFIYDVLRATC--PNCGRIMLKDEEIKRYSERLQRLKGRWKLLATNL 141

Query: 210 KKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVK 269
            +KIL    + + CPHCG               +++ K R ++           YN    
Sbjct: 142 HEKILRKAAERTTCPHCG---------------YKRNKVRFERP----------YN---- 172

Query: 270 FNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           F  E E     G +  L+P  +L+    +P  D+ LL ++  +++P   IL  L VPP  
Sbjct: 173 FYEETET----GALVKLDPETILERLVKVPNSDLELLGVDPTVARPEWGILRTLPVPPPH 228

Query: 330 IRPSVI--SDLKSDNDV 344
           +RPS+   + ++S++D+
Sbjct: 229 VRPSIQLETGIRSEDDL 245



 Score = 90.5 bits (223), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 38/65 (58%), Positives = 51/65 (78%), Gaps = 1/65 (1%)

Query: 605 IGDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDL 663
           +GD+ P   GFV +SF  GLTP E+FFH  GGR+GL+DTAV+TA++GYMQRR++ +L+D 
Sbjct: 779 VGDIGPFSGGFVSSSFVKGLTPVEYFFHAAGGRDGLIDTAVRTAQSGYMQRRIINALQDA 838

Query: 664 CVQYD 668
            V YD
Sbjct: 839 YVAYD 843



 Score = 43.1 bits (100), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 18/52 (34%), Positives = 30/52 (57%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           + LM  + ++VTPR G  +I A QD+I G YLL++K     + +   +A  +
Sbjct: 487 RTLMLVQEHIVTPRYGGAIIGARQDYIIGAYLLSRKTTLLTKKEAAYLAGAM 538


>gi|408402779|ref|YP_006860762.1| DNA-directed RNA polymerase subunit A [Candidatus Nitrososphaera
           gargensis Ga9.2]
 gi|300521498|gb|ADK25960.1| RNA polymerase A [Candidatus Nitrososphaera gargensis]
 gi|408363375|gb|AFU57105.1| DNA-directed RNA polymerase subunit A [Candidatus Nitrososphaera
           gargensis Ga9.2]
          Length = 1273

 Score =  175 bits (444), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 93/269 (34%), Positives = 148/269 (55%), Gaps = 35/269 (13%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D D+V+FNRQPSLH++SIMAH  KVLP+RTFR +  VC PYNADFDGDEMN+H+PQ+EE
Sbjct: 414 ADGDIVIFNRQPSLHRMSIMAHSVKVLPYRTFRLHPAVCPPYNADFDGDEMNLHVPQSEE 473

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           ARAE              A +LM  +  L++PR G  +I   +DFITG ++LT       
Sbjct: 474 ARAE--------------ATLLMRVQDQLISPRYGGPIIGGIRDFITGAFMLT------- 512

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
                R  +TL  D      +I  +      P +      +++G+Q+FSL L  + +  +
Sbjct: 513 -----RDGTTLTKDEFANLAMIGGYEGPLPEPAITKDGQRLYSGRQLFSLFLPKDFNFII 567

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            +      +    +         V+++N EL++G +DK+++G+    +V + + +D+G +
Sbjct: 568 TSKWNKAAKGEGKD---------VVIKNGELISGVIDKASIGAEEPDSVLHRIAKDYGTN 618

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
            A   +  +  M   Y+ +RGF+ G  D+
Sbjct: 619 AARKFLDSILTMLKTYITHRGFTYGYSDL 647



 Score =  164 bits (414), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 123/338 (36%), Positives = 172/338 (50%), Gaps = 53/338 (15%)

Query: 1112 RAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFVPDDS 1160
            RA  EP  AVG + AQSIGEPGTQMTL+TFHFAG            + E ++    P   
Sbjct: 931  RALAEPGEAVGVVTAQSIGEPGTQMTLRTFHFAGVKERNVTLGLPRLIELVDARKKPVTP 990

Query: 1161 FILIKLD----MDRIRLLHL--EVDIDSIRYCIERTR-GISGHLTV---------SGHSF 1204
             + I LD    + R + L +  E+    I   IER+    SG LT           G +F
Sbjct: 991  TMDIYLDEEHRVSREKALEVAREILFTRIGDLIERSETDYSGVLTFHLSEAKLAERGCTF 1050

Query: 1205 LILKP--KDSSKSF----NSKMYQMKQLLP----------------SVVIKGVQGINRAV 1242
              ++   + S K +    N     +K  +P                +  +KGV  I R  
Sbjct: 1051 ADVQEVLEGSKKKYTVKPNENKLSIKITVPDEPDAQTLLTLKSKLLNTRVKGVPDIERVT 1110

Query: 1243 IHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEI 1302
            I ++D E V +      G NL  V+A  GV   + ++NN YE+++TLGIEAAR+ ++ EI
Sbjct: 1111 IVKQDEEWVIQ----TAGSNLAKVVAVDGVDLTRVTTNNVYEIWQTLGIEAARTALIKEI 1166

Query: 1303 KLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDA 1362
               +E  G+ +D RH MLVADLMTSKG +  I RHG+A  K SVL  A+FE T   +  A
Sbjct: 1167 TNTLEEQGLEVDTRHIMLVADLMTSKGYLQQIGRHGIAGTKTSVLARAAFEITVPTIARA 1226

Query: 1363 AFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS 1400
            +  GQ + + GV+E +I+G  + VGTG++ L   V  S
Sbjct: 1227 SLEGQIETLKGVTENVIVGATVPVGTGMVDLYMKVKDS 1264



 Score =  108 bits (270), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 77/268 (28%), Positives = 128/268 (47%), Gaps = 43/268 (16%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G I+ +V     V++ S  +I +   Y +D    P+  GL+D R+GT +    C TCG  
Sbjct: 9   GGIKFSVWSPTEVRKFSVAEITAPETYDEDGM--PVQGGLMDNRLGTLEPGQKCATCGNT 66

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
            + C GHFG+I+L  PV HI +   +  +L   C+  +C R+ L  E+   +++ +R+  
Sbjct: 67  SAKCPGHFGHIELAEPVLHIAFVDDIHKLLLISCR--SCNRIKLEPEELTHYKS-IRDTK 123

Query: 201 LSYLV--RKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVE 258
            +Y V   +++K +I+E  KKV VCPHCG+               E+Y     K    VE
Sbjct: 124 AAYAVITLENIKDEIIERAKKVKVCPHCGK---------------EQYDLIFTKPTIFVE 168

Query: 259 DLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDL 318
              A  N                    L P+ + +    IP +D+ LL  +   ++P   
Sbjct: 169 KTDAGENR-------------------LLPITIRERLSHIPDDDLTLLGYDPRTARPEWF 209

Query: 319 ILTRLLVPPNCIRPSVI--SDLKSDNDV 344
           +L  L VPP  +RPS+I  + ++S++D+
Sbjct: 210 VLQVLPVPPVTVRPSIILETGIRSEDDL 237



 Score = 89.7 bits (221), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 68/232 (29%), Positives = 117/232 (50%), Gaps = 13/232 (5%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLE--RTTLGEVCEYIEEVFVP 821
            G+PR+ E+++A +   TP +  YLD++  +   + ++   E   T +G++ E  E     
Sbjct: 973  GLPRLIELVDARKKPVTPTMDIYLDEEHRVSREKALEVAREILFTRIGDLIERSET---- 1028

Query: 822  DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             D   ++   +   +L         ++  +E ++    +      + L +K     +   
Sbjct: 1029 -DYSGVLTFHLSEAKLAERGCTFADVQEVLEGSK--KKYTVKPNENKLSIKITVPDEPDA 1085

Query: 882  SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
              +  +K  L +  +KGV  I R  I ++D E V +      G NL  V+A  GV   + 
Sbjct: 1086 QTLLTLKSKLLNTRVKGVPDIERVTIVKQDEEWVIQ----TAGSNLAKVVAVDGVDLTRV 1141

Query: 942  SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
            ++NN YE+++TLGIEAAR+ ++ EI   +E  G+ +D RH MLVADLMTSKG
Sbjct: 1142 TTNNVYEIWQTLGIEAARTALIKEITNTLEEQGLEVDTRHIMLVADLMTSKG 1193



 Score = 89.7 bits (221), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 38/65 (58%), Positives = 52/65 (80%), Gaps = 1/65 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D  P  +GFV++++  GL+P EFFFH MGGREGLVDTAV+T ++GYMQRRL+ +LE L +
Sbjct: 769 DANPDAKGFVKSNYRDGLSPLEFFFHAMGGREGLVDTAVRTQQSGYMQRRLINALEHLKI 828

Query: 666 QYDMS 670
           +YD +
Sbjct: 829 EYDQT 833


>gi|146302820|ref|YP_001190136.1| DNA-directed RNA polymerase subunit A'' [Metallosphaera sedula DSM
            5348]
 gi|172046881|sp|A4YCR0.1|RPOA2_METS5 RecName: Full=DNA-directed RNA polymerase subunit A''
 gi|145701070|gb|ABP94212.1| DNA-directed RNA polymerase, subunit A' [Metallosphaera sedula DSM
            5348]
          Length = 392

 Score =  175 bits (444), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 117/346 (33%), Positives = 173/346 (50%), Gaps = 64/346 (18%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIE 1152
            E   + Y+ + + P  A+G +AAQSIGEPGTQMTL+TFHFAG            + E ++
Sbjct: 50   EIVMKDYLSSLVHPGEAIGVVAAQSIGEPGTQMTLRTFHFAGVRELNVTLGLPRLIEIVD 109

Query: 1153 EVFVPDDSFILIKLDMD--RIRLLHLEV----DIDSIRYCIERTRGISGHLTVSGHSFLI 1206
               VP    + I L+ +  + R + LEV    +   + + +E       +L V G   ++
Sbjct: 110  ARKVPSTPMMTIYLNEEYAKDRDMALEVARRIEYTRVEHVVETV-----NLDVGGMGIIL 164

Query: 1207 -----------LKPKDSSKSFN---------------------------SKMYQMKQLLP 1228
                       L  +D  K                              + +++ ++ + 
Sbjct: 165  KLDPVLLKDKGLSTEDVEKVIKKLKMGDYRVENSDEYTIAIYFENMETVTGLFKAREKIL 224

Query: 1229 SVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKT 1288
            S  IKGV+GI RA+I ++  E    Y ++ +G NL  V+   GV   +  +NN +EV   
Sbjct: 225  STKIKGVKGIKRAIIRKKGDE----YVIITDGSNLEGVLGVKGVDVSRIETNNLHEVESV 280

Query: 1289 LGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLN 1348
            LG+EAAR  I  EIK V+E  G+ +D RH  LV+D+MT  GEV  I RHG+   K SVL 
Sbjct: 281  LGVEAARELITREIKRVLEEQGLDVDIRHIELVSDIMTRTGEVRQIGRHGVTGEKTSVLA 340

Query: 1349 LASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
             A+FE T  HL DAA  G  +   GV E II+G P+ +GTG+++LL
Sbjct: 341  RAAFEVTVKHLLDAAARGDMEEFKGVVENIIIGQPIKLGTGMVELL 386



 Score =  105 bits (262), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 75/234 (32%), Positives = 123/234 (52%), Gaps = 12/234 (5%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A +  STP++T YL+++   D D A  V  R+E T      E++ E    
Sbjct: 100 GLPRLIEIVDARKVPSTPMMTIYLNEEYAKDRDMALEVARRIEYTR----VEHVVETVNL 155

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
           D   + I L +D + L    +  + +   I++ +   G   V       +     +    
Sbjct: 156 DVGGMGIILKLDPVLLKDKGLSTEDVEKVIKKLK--MGDYRVENSDEYTIAIYFENMETV 213

Query: 882 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
           + +++ ++ + S  IKGV+GI RA+I ++  E    Y ++ +G NL  V+   GV   + 
Sbjct: 214 TGLFKAREKILSTKIKGVKGIKRAIIRKKGDE----YVIITDGSNLEGVLGVKGVDVSRI 269

Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            +NN +EV   LG+EAAR  I  EIK V+E  G+ +D RH  LV+D+MT  GEV
Sbjct: 270 ETNNLHEVESVLGVEAARELITREIKRVLEEQGLDVDIRHIELVSDIMTRTGEV 323


>gi|288931146|ref|YP_003435206.1| DNA-directed RNA polymerase subunit A' [Ferroglobus placidus DSM
           10642]
 gi|288893394|gb|ADC64931.1| DNA-directed RNA polymerase subunit A' [Ferroglobus placidus DSM
           10642]
          Length = 870

 Score =  175 bits (443), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 98/267 (36%), Positives = 149/267 (55%), Gaps = 35/267 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIMAH  +VLP++TFR N  VC PYNADFDGDEMN+H+PQ+ EA
Sbjct: 405 DGDIVLFNRQPSLHRMSIMAHYVRVLPYKTFRLNPAVCPPYNADFDGDEMNLHVPQSIEA 464

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE              AK+LMA + ++++PR G  +I    D I+G YLLT+    F++
Sbjct: 465 QAE--------------AKILMAVQEHILSPRFGGPIIGGIHDHISGLYLLTRGEKLFSK 510

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            + M +   +  +       I    + S            WTGKQIFS+IL    D  + 
Sbjct: 511 EEVMELIRPINVEK------IPEPKYDSK-----------WTGKQIFSMILP---DITLE 550

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
              +          E C  D+YV++RN EL+ G++D+  +G+  K  +   ++R +G + 
Sbjct: 551 FKAEICQGCEKCEGENCPHDAYVVIRNGELIKGTIDEKAVGA-FKGIIIDEIVRKYGTEE 609

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           A   +  ++++    +M  GF++GI D
Sbjct: 610 AKKFIDNMTQLAIRAIMFFGFTVGIDD 636



 Score =  107 bits (268), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 77/267 (28%), Positives = 120/267 (44%), Gaps = 50/267 (18%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           I+  V     +++ S  +I +   Y  D    PI  GL+D R+G       C TCG    
Sbjct: 9   IKFEVLSPQEIRRMSVAKIFTPETYSDD--GYPIESGLMDPRLGVVDPGLRCRTCGGKAG 66

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA---KLRNP 199
           +C GHFG+I+L  PV H+GY + +  +L   C+   C R+LL +E+   + A   KL+  
Sbjct: 67  ECPGHFGHIELAAPVIHVGYAKLIARLLNGTCRE--CGRILLKDERRDKYIAQIEKLKEL 124

Query: 200 ALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVED 259
             +Y     + K++   TK V  CPHCG           +++  EK              
Sbjct: 125 GQNY---DEVVKEVFRVTKAVKKCPHCG--------ADQIEVKFEK-------------- 159

Query: 260 LLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLI 319
               Y E          HK       L P +V +  E IP ED+P   ++ +  +P   +
Sbjct: 160 -PTFYYEG--------DHK-------LTPKDVRERLEKIPDEDLPAFGIDPKACRPEWFV 203

Query: 320 LTRLLVPPNCIRPSVI--SDLKSDNDV 344
           LT L VPP  +RPS+I  +  +S++D+
Sbjct: 204 LTVLPVPPVTVRPSIILETGQRSEDDL 230



 Score = 90.5 bits (223), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 37/58 (63%), Positives = 52/58 (89%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV++S+ SGL+P EFFFH +GGREGLVDTAV+T+++GY+QRRL+ +L+DL V+YD
Sbjct: 766 ARGFVRSSYKSGLSPVEFFFHAVGGREGLVDTAVRTSQSGYLQRRLINALQDLKVEYD 823


>gi|55379094|ref|YP_136944.1| DNA-directed RNA polymerase subunit A'' [Haloarcula marismortui ATCC
            43049]
 gi|448655082|ref|ZP_21681934.1| DNA-directed RNA polymerase subunit A'' [Haloarcula californiae ATCC
            33799]
 gi|448680461|ref|ZP_21690778.1| DNA-directed RNA polymerase subunit A'' [Haloarcula argentinensis DSM
            12282]
 gi|74552623|sp|Q5UZR5.1|RPOA2_HALMA RecName: Full=DNA-directed RNA polymerase subunit A''
 gi|55231819|gb|AAV47238.1| RNA polymerase Rpb1 domain 5 [Haloarcula marismortui ATCC 43049]
 gi|445765531|gb|EMA16669.1| DNA-directed RNA polymerase subunit A'' [Haloarcula californiae ATCC
            33799]
 gi|445768905|gb|EMA19982.1| DNA-directed RNA polymerase subunit A'' [Haloarcula argentinensis DSM
            12282]
          Length = 395

 Score =  175 bits (443), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 110/350 (31%), Positives = 180/350 (51%), Gaps = 65/350 (18%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A+A   +Y+  +++P   VG ++AQSIGEPGTQMT+ TFH+AG            + E +
Sbjct: 45   AKAVETRYLDTRVDPLDPVGTVSAQSIGEPGTQMTMNTFHYAGVAEIDVTQGLPRLIELV 104

Query: 1152 EEVFVPDDSFILIKLD----------------MDRIRLLHL------------EVDI--- 1180
            +    PD   + + LD                ++  R+L L            E+D+   
Sbjct: 105  DARKTPDTPMMTVHLDEEYATDRERAHEVVWKIEATRILALGDISTNVADMLVEIDLNED 164

Query: 1181 ----------------DSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMK 1224
                            + I   IE   G+S   T    + +   P++ S      + Q+ 
Sbjct: 165  TLLERWPTVNDTDAIAEEIAETIESNLGVS---TRQAGTLIEFGPEEPSYR---DLLQLV 218

Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYE 1284
            + L  +V KG++ I R VI +E+ +   ++ L  EG +  +V+   GV   + + NN +E
Sbjct: 219  EELREIVFKGIEEITRVVIRKEETDNGEEFVLYTEGSDFGEVLDIEGVDASRTTCNNIHE 278

Query: 1285 VYKTLGIEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMK 1343
            +Y+ LG+EAAR T++ E    +E  G+  ++ RH MLVAD+MT++G +  I RHG++  K
Sbjct: 279  IYRELGVEAARETLINETMNTLEEQGLDDVNVRHLMLVADIMTNEGTIESIGRHGISGSK 338

Query: 1344 ESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            +SVL  A+FE T +HL DAA +G+ D + GV+E +I+G P+ +GTG + L
Sbjct: 339  DSVLARAAFEVTVNHLLDAAIHGEVDELDGVTENVIVGKPIKLGTGDVNL 388



 Score =  106 bits (264), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 70/245 (28%), Positives = 131/245 (53%), Gaps = 27/245 (11%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T +LD++  TD + A  V  ++E T    LG++   + + 
Sbjct: 96  GLPRLIELVDARKTPDTPMMTVHLDEEYATDRERAHEVVWKIEATRILALGDISTNVAD- 154

Query: 819 FVPDDSFILIKLDMDRIRLLH-------LEVDIDSIRYCIERTRGISGHLTVSGHSFLIL 871
                  +L+++D++   LL         +   + I   IE   G+S   T    + +  
Sbjct: 155 -------MLVEIDLNEDTLLERWPTVNDTDAIAEEIAETIESNLGVS---TRQAGTLIEF 204

Query: 872 KPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVM 931
            P++ S      + Q+ + L  +V KG++ I R VI +E+ +   ++ L  EG +  +V+
Sbjct: 205 GPEEPSYR---DLLQLVEELREIVFKGIEEITRVVIRKEETDNGEEFVLYTEGSDFGEVL 261

Query: 932 ATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMT 990
              GV   + + NN +E+Y+ LG+EAAR T++ E    +E  G+  ++ RH MLVAD+MT
Sbjct: 262 DIEGVDASRTTCNNIHEIYRELGVEAARETLINETMNTLEEQGLDDVNVRHLMLVADIMT 321

Query: 991 SKGEV 995
           ++G +
Sbjct: 322 NEGTI 326


>gi|15679065|ref|NP_276182.1| DNA-directed RNA polymerase subunit A'' [Methanothermobacter
            thermautotrophicus str. Delta H]
 gi|6685899|sp|O27126.1|RPOA2_METTH RecName: Full=DNA-directed RNA polymerase subunit A''
 gi|2622151|gb|AAB85543.1| DNA-dependent RNA polymerase, subunit A'' [Methanothermobacter
            thermautotrophicus str. Delta H]
          Length = 451

 Score =  175 bits (443), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 114/343 (33%), Positives = 175/343 (51%), Gaps = 67/343 (19%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYI 1151
             R  Y RA++E   AVG +AAQS+GEPGTQMT++TFH+AG              E+ +  
Sbjct: 117  VRRAYDRARVEAGEAVGTVAAQSVGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDAR 176

Query: 1152 EEVFVP------------DDSFI----------------------------LIKLDMDRI 1171
            +++  P            D+ F+                            + +LD ++I
Sbjct: 177  KKISTPTMSIYFEGDLRYDEEFVRRKANKIGKSTLNDVLKNFSIQYADMSVVAELDEEKI 236

Query: 1172 RLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVV 1231
            +  HLE D   I   +E+T      + +  +      PK + +       ++++L     
Sbjct: 237  QEKHLEYD--EILAKVEKT---FKKVEIDNNILRFEPPKPTIRELRLLADKVRKLQ---- 287

Query: 1232 IKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGI 1291
            I GV+ I + VI +ED E V    +  EG NL  V+   GV  V+ ++N+ +E+   LGI
Sbjct: 288  ISGVKNIGKVVIRKEDDEWV----IHTEGSNLGAVLKEEGVDKVRTTTNDIHEIETVLGI 343

Query: 1292 EAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLAS 1351
            EAAR+ I+ E K  ME  G+++D RH MLVAD+MT+ G V  I RHG++  K SVL  AS
Sbjct: 344  EAARNAIIHEAKRTMEEQGLTVDIRHIMLVADMMTADGSVKSIGRHGISGEKASVLARAS 403

Query: 1352 FENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            FE T  HL  A+  G+ D ++G+ E II+G P+ +GTG + ++
Sbjct: 404  FEETGKHLLRASIRGEVDHLTGIIENIIIGQPIPLGTGSVSVV 446



 Score =  110 bits (276), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 77/238 (32%), Positives = 129/238 (54%), Gaps = 17/238 (7%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A + ISTP ++ Y + D   D ++ R    ++ ++TL +V +     +  
Sbjct: 165 GLPRLIEIVDARKKISTPTMSIYFEGDLRYDEEFVRRKANKIGKSTLNDVLKNFSIQYA- 223

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
            D  ++ +LD ++I+  HLE D   I   +E+T      + +  +      PK + +   
Sbjct: 224 -DMSVVAELDEEKIQEKHLEYD--EILAKVEKT---FKKVEIDNNILRFEPPKPTIRELR 277

Query: 882 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
               ++++L     I GV+ I + VI +ED E V    +  EG NL  V+   GV  V+ 
Sbjct: 278 LLADKVRKLQ----ISGVKNIGKVVIRKEDDEWV----IHTEGSNLGAVLKEEGVDKVRT 329

Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG 999
           ++N+ +E+   LGIEAAR+ I+ E K  ME  G+++D RH MLVAD+MT+ G V   G
Sbjct: 330 TTNDIHEIETVLGIEAARNAIIHEAKRTMEEQGLTVDIRHIMLVADMMTADGSVKSIG 387


>gi|344213106|ref|YP_004797426.1| DNA-directed RNA polymerase subunit A'' [Haloarcula hispanica ATCC
            33960]
 gi|343784461|gb|AEM58438.1| DNA-directed RNA polymerase subunit A'' [Haloarcula hispanica ATCC
            33960]
          Length = 395

 Score =  175 bits (443), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 110/350 (31%), Positives = 180/350 (51%), Gaps = 65/350 (18%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A+A   +Y+  +++P   VG ++AQSIGEPGTQMT+ TFH+AG            + E +
Sbjct: 45   AKAVESRYLDTRVDPLDPVGTVSAQSIGEPGTQMTMNTFHYAGVAEIDVTQGLPRLIELV 104

Query: 1152 EEVFVPDDSFILIKLD----------------MDRIRLLHL------------EVDI--- 1180
            +    PD   + + LD                ++  R+L L            E+D+   
Sbjct: 105  DARKTPDTPMMTVHLDEEYADDRERAHEVVWKIEATRILALGDISTNVADMLVEIDLNED 164

Query: 1181 ----------------DSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMK 1224
                            + I   IE   G+S   T    + +   P++ S      + Q+ 
Sbjct: 165  TLLERWPTVNDTDAIAEEIAETIESNLGVS---TRQAGTVIEFGPEEPSYR---DLLQLV 218

Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYE 1284
            + L  +V KG++ I R VI +E+ +   ++ L  EG +  +V+   GV   + + NN +E
Sbjct: 219  EELREIVFKGIEEITRVVIRKEETDNGEEFVLYTEGSDFGEVLDIEGVDASRTTCNNIHE 278

Query: 1285 VYKTLGIEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMK 1343
            +Y+ LG+EAAR T++ E    +E  G+  ++ RH MLVAD+MT++G +  I RHG++  K
Sbjct: 279  IYRELGVEAARETLINETMNTLEEQGLDDVNVRHLMLVADIMTNEGTIESIGRHGISGSK 338

Query: 1344 ESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            +SVL  A+FE T +HL DAA +G+ D + GV+E +I+G P+ +GTG + L
Sbjct: 339  DSVLARAAFEVTVNHLLDAAIHGEVDELDGVTENVIVGKPIKLGTGDVNL 388



 Score =  103 bits (257), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 69/245 (28%), Positives = 130/245 (53%), Gaps = 27/245 (11%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T +LD++   D + A  V  ++E T    LG++   + + 
Sbjct: 96  GLPRLIELVDARKTPDTPMMTVHLDEEYADDRERAHEVVWKIEATRILALGDISTNVAD- 154

Query: 819 FVPDDSFILIKLDMDRIRLLH-------LEVDIDSIRYCIERTRGISGHLTVSGHSFLIL 871
                  +L+++D++   LL         +   + I   IE   G+S   T    + +  
Sbjct: 155 -------MLVEIDLNEDTLLERWPTVNDTDAIAEEIAETIESNLGVS---TRQAGTVIEF 204

Query: 872 KPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVM 931
            P++ S      + Q+ + L  +V KG++ I R VI +E+ +   ++ L  EG +  +V+
Sbjct: 205 GPEEPSYR---DLLQLVEELREIVFKGIEEITRVVIRKEETDNGEEFVLYTEGSDFGEVL 261

Query: 932 ATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMT 990
              GV   + + NN +E+Y+ LG+EAAR T++ E    +E  G+  ++ RH MLVAD+MT
Sbjct: 262 DIEGVDASRTTCNNIHEIYRELGVEAARETLINETMNTLEEQGLDDVNVRHLMLVADIMT 321

Query: 991 SKGEV 995
           ++G +
Sbjct: 322 NEGTI 326


>gi|118431618|ref|NP_148215.2| DNA-directed RNA polymerase subunit A' [Aeropyrum pernix K1]
 gi|116062942|dbj|BAA80857.2| DNA-directed RNA polymerase subunit A [Aeropyrum pernix K1]
          Length = 891

 Score =  175 bits (443), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 94/268 (35%), Positives = 144/268 (53%), Gaps = 29/268 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + D+VLFNRQPSLH++SIM H  +V+P +TFR N  VC PYNADFDGDEMN+H+P+ EEA
Sbjct: 421 NGDIVLFNRQPSLHRMSIMGHIVRVMPGKTFRLNLLVCPPYNADFDGDEMNLHVPRLEEA 480

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE              A+ +M  + +++TPR G  +I   QD+++G YLLT K   F +
Sbjct: 481 QAE--------------AREIMLVEKHILTPRYGGPIIGGRQDYVSGAYLLTVKTRLFTK 526

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +  R+ S            +  +      P + ++   +WTGKQ+ S+ L    D    
Sbjct: 527 EEVERLLS------------VAGYKGDLPEPAI-LKPEPLWTGKQLASIFLP--EDLSFK 571

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
              KT       ++E C  DSY+++ N +LL G +DK  +G+    N+ +I+  ++G   
Sbjct: 572 GKSKTNAGDLACSDELCLHDSYIVITNGKLLEGVLDKKAIGAEEPNNLLHIIALEYGNSK 631

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           A   +    RM    L  RG +I + D+
Sbjct: 632 ARQLLDSFYRMFIRMLELRGLTISLHDI 659



 Score = 89.4 bits (220), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 72/259 (27%), Positives = 112/259 (43%), Gaps = 50/259 (19%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           ++Q + + +V  +LY  D   TP+  GL D   G  +    C  CG +  +C GHFG I+
Sbjct: 27  IRQLAKVTVVRGDLYEADG--TPVSGGLRDPHFGAIEPGERCPVCGNSREECPGHFGKIE 84

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN-----PALSYLVRK 207
           L  PV    Y   V  ILQ+ C+   C R+ L EEK   +R   R      P L+    K
Sbjct: 85  LARPVLIPHYTDYVYKILQATCR--VCGRITLPEEKIKYYRLIFRRLRGKWPQLA----K 138

Query: 208 SLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEA 267
           +    +++   + + CPHCG+                +YK                    
Sbjct: 139 TFATMVVKEAAQATQCPHCGK---------------PQYK-------------------V 164

Query: 268 VKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPP 327
           V   P     KK      L P E+ +  E    E I +L ++ E S+P  ++ T L+VPP
Sbjct: 165 VYIRPFHFYEKKPEGDVKLTPSEIRERLEKTGSE-IEILGVHPERSRPEWMVATVLIVPP 223

Query: 328 NCIRPSVI--SDLKSDNDV 344
             +RPS+   + L+S++D+
Sbjct: 224 LAVRPSITLETGLRSEDDL 242



 Score = 87.8 bits (216), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 39/63 (61%), Positives = 49/63 (77%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D+ P   GFV++SF  GL PTE FFH   GREGLVDTAVKT+++GYMQRRL+ +L+D+ V
Sbjct: 781 DIEPEAWGFVRSSFRKGLRPTEVFFHAAAGREGLVDTAVKTSQSGYMQRRLINALQDIVV 840

Query: 666 QYD 668
            YD
Sbjct: 841 TYD 843



 Score = 42.4 bits (98), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 20/55 (36%), Positives = 33/55 (60%), Gaps = 2/55 (3%)

Query: 22  LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRK 76
           +M  + +++TPR G  +I   QD+++G YLLT K   F + +  R+ S  +AG K
Sbjct: 487 IMLVEKHILTPRYGGPIIGGRQDYVSGAYLLTVKTRLFTKEEVERLLS--VAGYK 539


>gi|448664668|ref|ZP_21684306.1| DNA-directed RNA polymerase subunit A'' [Haloarcula amylolytica JCM
            13557]
 gi|445774255|gb|EMA25276.1| DNA-directed RNA polymerase subunit A'' [Haloarcula amylolytica JCM
            13557]
          Length = 395

 Score =  175 bits (443), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 110/350 (31%), Positives = 180/350 (51%), Gaps = 65/350 (18%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A+A   +Y+  +++P   VG ++AQSIGEPGTQMT+ TFH+AG            + E +
Sbjct: 45   AKAVESRYLDTRVDPLDPVGTVSAQSIGEPGTQMTMNTFHYAGVAEIDVTQGLPRLIELV 104

Query: 1152 EEVFVPDDSFILIKLD----------------MDRIRLLHL------------EVDI--- 1180
            +    PD   + + LD                ++  R+L L            E+D+   
Sbjct: 105  DARKTPDTPMMTVHLDEEYADDRERAHEVVWKIEATRILALGDISTNVADMLVEIDLNED 164

Query: 1181 ----------------DSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMK 1224
                            + I   IE   G+S   T    + +   P++ S      + Q+ 
Sbjct: 165  TLLERWPTVNDTDAIAEEIAETIESNLGVS---TRQAGTVIEFGPEEPSYR---DLLQLV 218

Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYE 1284
            + L  +V KG++ I R VI +E+ +   ++ L  EG +  +V+   GV   + + NN +E
Sbjct: 219  EELREIVFKGIEEITRVVIRKEETDNGEEFVLYTEGSDFGEVLDIEGVDASRTTCNNIHE 278

Query: 1285 VYKTLGIEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMK 1343
            +Y+ LG+EAAR T++ E    +E  G+  ++ RH MLVAD+MT++G +  I RHG++  K
Sbjct: 279  IYRELGVEAARETLINETMNTLEEQGLDDVNVRHLMLVADIMTNEGTIESIGRHGISGSK 338

Query: 1344 ESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            +SVL  A+FE T +HL DAA +G+ D + GV+E +I+G P+ +GTG + L
Sbjct: 339  DSVLARAAFEVTVNHLLDAAIHGEVDELDGVTENVIVGKPIKLGTGDVNL 388



 Score =  103 bits (257), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 69/245 (28%), Positives = 130/245 (53%), Gaps = 27/245 (11%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T +LD++   D + A  V  ++E T    LG++   + + 
Sbjct: 96  GLPRLIELVDARKTPDTPMMTVHLDEEYADDRERAHEVVWKIEATRILALGDISTNVAD- 154

Query: 819 FVPDDSFILIKLDMDRIRLLH-------LEVDIDSIRYCIERTRGISGHLTVSGHSFLIL 871
                  +L+++D++   LL         +   + I   IE   G+S   T    + +  
Sbjct: 155 -------MLVEIDLNEDTLLERWPTVNDTDAIAEEIAETIESNLGVS---TRQAGTVIEF 204

Query: 872 KPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVM 931
            P++ S      + Q+ + L  +V KG++ I R VI +E+ +   ++ L  EG +  +V+
Sbjct: 205 GPEEPSYR---DLLQLVEELREIVFKGIEEITRVVIRKEETDNGEEFVLYTEGSDFGEVL 261

Query: 932 ATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMT 990
              GV   + + NN +E+Y+ LG+EAAR T++ E    +E  G+  ++ RH MLVAD+MT
Sbjct: 262 DIEGVDASRTTCNNIHEIYRELGVEAARETLINETMNTLEEQGLDDVNVRHLMLVADIMT 321

Query: 991 SKGEV 995
           ++G +
Sbjct: 322 NEGTI 326


>gi|297619551|ref|YP_003707656.1| DNA-directed RNA polymerase subunit A'' [Methanococcus voltae A3]
 gi|297378528|gb|ADI36683.1| DNA-directed RNA polymerase, subunit A'' [Methanococcus voltae A3]
          Length = 387

 Score =  175 bits (443), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 117/330 (35%), Positives = 172/330 (52%), Gaps = 48/330 (14%)

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYIEEVF 1155
            Y R  +EP  AVG +AAQSIGEPGTQMT++TFH+AG              E+ +  +E  
Sbjct: 49   YERTLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRMIEIVDARKEPS 108

Query: 1156 VPDDSFILIK-LDMDRIRLLHLEVDIDS--------------IRYCIE--------RTRG 1192
             P  +  L++    DR +   +  +I+S              +  CI           R 
Sbjct: 109  TPTMTINLLEDYKYDREKAQQVAKNIESTTVESVADNISVNLVEECISIILNAEKLEKRN 168

Query: 1193 ISGHLTVSG-HSFLILKPKDSSKSFNSK-----MYQMKQLLPSVV---IKGVQGINRAVI 1243
            +S    V+   S + LK      + N K     +  +++ LP V    +KGV  I R +I
Sbjct: 169  LSVEDVVNSIKSKMKLKIDQDGYALNLKIKTPTLKALRKRLPKVRAIHLKGVSNITRVII 228

Query: 1244 HEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIK 1303
             +ED  G  +Y L  EG NL++V    GV   K ++NN  E+   LG+EAAR+ I+ E+ 
Sbjct: 229  RKED--GSEEYILYSEGSNLKEVFEIEGVDPSKTTTNNIIEIQDVLGVEAARNAIIYEMA 286

Query: 1304 LVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAA 1363
              + N G+++D RH M+V+DLMT+ G V  I RHG+   K SVL  A+FE T  HL+ A+
Sbjct: 287  ATLSNQGLTVDPRHLMMVSDLMTTDGVVKPIGRHGIGGEKASVLARAAFEETVKHLYSAS 346

Query: 1364 FYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
              G +D + GV E II+G P+++GTG I +
Sbjct: 347  MRGYSDELDGVVENIIVGKPISIGTGCINV 376



 Score =  102 bits (254), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 78/237 (32%), Positives = 125/237 (52%), Gaps = 20/237 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYL--DKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A +  STP +T  L  D   D + A+ V   +E TT+  V + I    V 
Sbjct: 93  GLPRMIEIVDARKEPSTPTMTINLLEDYKYDREKAQQVAKNIESTTVESVADNISVNLVE 152

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
           +   I++  +    R L +E  ++SI+  ++      G+        L LK K  +    
Sbjct: 153 ECISIILNAEKLEKRNLSVEDVVNSIKSKMKLKIDQDGY-------ALNLKIKTPT---- 201

Query: 882 SKMYQMKQLLPSVV---IKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 938
             +  +++ LP V    +KGV  I R +I +ED  G  +Y L  EG NL++V    GV  
Sbjct: 202 --LKALRKRLPKVRAIHLKGVSNITRVIIRKED--GSEEYILYSEGSNLKEVFEIEGVDP 257

Query: 939 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            K ++NN  E+   LG+EAAR+ I+ E+   + N G+++D RH M+V+DLMT+ G V
Sbjct: 258 SKTTTNNIIEIQDVLGVEAARNAIIYEMAATLSNQGLTVDPRHLMMVSDLMTTDGVV 314


>gi|448411892|ref|ZP_21576248.1| DNA-directed RNA polymerase subunit A'' [Halosimplex carlsbadense
            2-9-1]
 gi|445669826|gb|ELZ22434.1| DNA-directed RNA polymerase subunit A'' [Halosimplex carlsbadense
            2-9-1]
          Length = 401

 Score =  175 bits (443), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 113/358 (31%), Positives = 182/358 (50%), Gaps = 64/358 (17%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A+A   KYV  +++P   VG ++AQSIGEPGTQMT+ TFH+AG            + E +
Sbjct: 43   AKAVESKYVDTRVDPLDPVGTVSAQSIGEPGTQMTMNTFHYAGVAEIDVTQGLPRLIELV 102

Query: 1152 EEVFVPDDSFILIKLD----------------MDRIRLLHL------------EVDIDS- 1182
            +    PD   + I L+                ++  ++L L            +VD++  
Sbjct: 103  DARKEPDTPMMTIHLEDEYAEERERAHEVVWEIESTKILQLGDVSTNVADMLVQVDLNED 162

Query: 1183 ------------------IRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMK 1224
                              I   IE   G+   +     + +   P + S      + Q+ 
Sbjct: 163  TLEERWPTADNLESVVTDIASTIESKLGV--EVQTPAPTVVQFGPDEPSYR---DLLQLV 217

Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYE 1284
            + L  +V KG++ ++R VI +E+ +   ++ L  EG  L DV+   GV   + + NN +E
Sbjct: 218  EELRDIVFKGIEEVSRVVIRKEETDDGEEFVLYTEGSALGDVLGLDGVDASRTTCNNIHE 277

Query: 1285 VYKTLGIEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMK 1343
            +++ LGIEAAR  I+ E    +E  G+  ++ RH MLVAD+MT++G +  I RHG++  K
Sbjct: 278  IHRQLGIEAAREAIINETMNTLEEQGLDDVNIRHLMLVADIMTNRGSIESIGRHGISGNK 337

Query: 1344 ESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSE 1401
            ESVL  A+FE T +HL DAA +G+ D ++GV+E +I+G P+ +GTG + L  A  R +
Sbjct: 338  ESVLARAAFEVTVNHLLDAAIHGEVDDLNGVTENVIVGKPIKLGTGDVDLRMAAGRGD 395



 Score = 96.7 bits (239), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 68/245 (27%), Positives = 127/245 (51%), Gaps = 26/245 (10%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTT---LGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T +L+ +   + + A  V   +E T    LG+V   + + 
Sbjct: 94  GLPRLIELVDARKEPDTPMMTIHLEDEYAEERERAHEVVWEIESTKILQLGDVSTNVAD- 152

Query: 819 FVPDDSFILIKLDMDRIRLL-------HLEVDIDSIRYCIERTRGISGHLTVSGHSFLIL 871
                  +L+++D++   L        +LE  +  I   IE   G+   +     + +  
Sbjct: 153 -------MLVQVDLNEDTLEERWPTADNLESVVTDIASTIESKLGV--EVQTPAPTVVQF 203

Query: 872 KPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVM 931
            P + S      + Q+ + L  +V KG++ ++R VI +E+ +   ++ L  EG  L DV+
Sbjct: 204 GPDEPSYR---DLLQLVEELRDIVFKGIEEVSRVVIRKEETDDGEEFVLYTEGSALGDVL 260

Query: 932 ATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMT 990
              GV   + + NN +E+++ LGIEAAR  I+ E    +E  G+  ++ RH MLVAD+MT
Sbjct: 261 GLDGVDASRTTCNNIHEIHRQLGIEAAREAIINETMNTLEEQGLDDVNIRHLMLVADIMT 320

Query: 991 SKGEV 995
           ++G +
Sbjct: 321 NRGSI 325


>gi|84490159|ref|YP_448391.1| DNA-directed RNA polymerase subunit A'' [Methanosphaera stadtmanae
            DSM 3091]
 gi|84373478|gb|ABC57748.1| RpoA2 [Methanosphaera stadtmanae DSM 3091]
          Length = 389

 Score =  174 bits (442), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 118/345 (34%), Positives = 185/345 (53%), Gaps = 63/345 (18%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYI 1151
             +E Y R ++EP  +VG +AAQS+GEPGTQMT++TFH+AG              EV +  
Sbjct: 47   VKEAYEREEVEPGESVGTIAAQSVGEPGTQMTMRTFHYAGVVELNVTLGLPRLIEVVDAR 106

Query: 1152 EEVFVP------------DDSFI------LIKLDMDRI----------RLLHLEVDIDSI 1183
            +++  P            D+ FI      + K+ ++ +           ++  E+D D +
Sbjct: 107  KKISTPTMDIFFADDYKNDEEFIRKMGNKIGKITLNDVIKNFNVNYMDNIITAEIDQDIL 166

Query: 1184 RYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNS-------KMYQ-MKQL------LPS 1229
                ER   +S    V   +F  +K  ++  SF +       KM Q +++L      +  
Sbjct: 167  D---ERRLELSEVTAVIEKTFKQVKINNNLLSFETTFSKDEEKMQQGIRELRLLADKIRD 223

Query: 1230 VVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTL 1289
            + I GV+GI + VI  E  E V    +  EG N+  ++   GV  VK ++N+ +E+ K L
Sbjct: 224  LQISGVKGIGKVVIRHEHNEWV----IHTEGSNIGAILKIDGVDIVKTTTNDIFEIEKVL 279

Query: 1290 GIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNL 1349
            GIEAAR+ I+ E+   ME  G+S+D RH MLVAD+MTS+G V  I RHG++  K SVL  
Sbjct: 280  GIEAARNAIIHELYTTMEEQGLSVDIRHIMLVADMMTSEGVVKSIGRHGISGEKSSVLAR 339

Query: 1350 ASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            A+FE T  HL +A+  G+TD ++G+ E +I+G P+  GTG + ++
Sbjct: 340  AAFEETGKHLLNASIRGETDKLTGIIENVIVGQPIPHGTGSVGVI 384



 Score =  103 bits (258), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 78/240 (32%), Positives = 129/240 (53%), Gaps = 21/240 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ E+++A + ISTP +  +   D   D ++ R +  ++ + TL +V +     ++ 
Sbjct: 95  GLPRLIEVVDARKKISTPTMDIFFADDYKNDEEFIRKMGNKIGKITLNDVIKNFNVNYM- 153

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERT---RGISGHLTVSGHSFLILKPKDSSK 878
            D+ I  ++D D +    LE  +  +   IE+T     I+ +L     SF     KD  K
Sbjct: 154 -DNIITAEIDQDILDERRLE--LSEVTAVIEKTFKQVKINNNLL----SFETTFSKDEEK 206

Query: 879 SFNSKMYQMKQL---LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYG 935
                + +++ L   +  + I GV+GI + VI  E  E V    +  EG N+  ++   G
Sbjct: 207 -MQQGIRELRLLADKIRDLQISGVKGIGKVVIRHEHNEWV----IHTEGSNIGAILKIDG 261

Query: 936 VKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
           V  VK ++N+ +E+ K LGIEAAR+ I+ E+   ME  G+S+D RH MLVAD+MTS+G V
Sbjct: 262 VDIVKTTTNDIFEIEKVLGIEAARNAIIHELYTTMEEQGLSVDIRHIMLVADMMTSEGVV 321


>gi|385805644|ref|YP_005842042.1| DNA-directed RNA polymerase subunit A'' [Fervidicoccus fontis Kam940]
 gi|383795507|gb|AFH42590.1| DNA-directed RNA polymerase subunit A'' [Fervidicoccus fontis Kam940]
          Length = 409

 Score =  174 bits (442), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 118/342 (34%), Positives = 180/342 (52%), Gaps = 55/342 (16%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIE 1152
            E   + Y+ + +EP   +G + AQSIGEPGTQMTL+TFH+AG            + E ++
Sbjct: 47   ELTVQTYLNSLVEPGEPIGTVTAQSIGEPGTQMTLRTFHYAGVRELNVTLGLPRLIEIVD 106

Query: 1153 EVFVPDDSFILIKLDMD-------------RIRLLHLE-----VDID----SIRYCIE-- 1188
               VP    + + LD +             RI    +E     V+ D    SIR  ++  
Sbjct: 107  ARKVPSTPMMEVYLDEEHKYDREKAKEVARRIEFTKIENVANVVEADLFSNSIRVELDPA 166

Query: 1189 --RTRGIS-------------GHLTVSGHSFLILKPKDSSK-SFNSKMYQMKQLLPSVVI 1232
                +G++             G   ++G + + +  K+SS  S+ SK    ++ + ++ I
Sbjct: 167  MLEDKGLTVEEVYEVIKKSNVGKAEITGENTIAIYLKESSDLSYISKK---REKVLNLKI 223

Query: 1233 KGVQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGI 1291
            KG+ GI RA+I     E G  +Y ++ +G NL  V+   GV   +  +N+ YE    LGI
Sbjct: 224  KGIAGIKRAIIQSRRGEDGREEYVIVTDGSNLEQVLKVKGVDPTRTRTNSVYETMMVLGI 283

Query: 1292 EAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLAS 1351
            EAAR  I+ EI  V+   G+ +D RH  LVAD+MT  G V  I RHG++  KES L  A+
Sbjct: 284  EAARKVIINEIMNVLREQGLDVDVRHVYLVADIMTQTGVVRQIGRHGVSGEKESFLARAA 343

Query: 1352 FENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            FE T+ HLF+A+  G+TD + GV+E +I+G  + VGTG+I+L
Sbjct: 344  FEMTTKHLFEASTQGKTDELKGVTENVIVGQVIPVGTGMIEL 385



 Score =  107 bits (266), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 75/236 (31%), Positives = 128/236 (54%), Gaps = 13/236 (5%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A +  STP++  YLD++   D + A+ V  R+E T +  V   +E     
Sbjct: 97  GLPRLIEIVDARKVPSTPMMEVYLDEEHKYDREKAKEVARRIEFTKIENVANVVEADLFS 156

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSK-SF 880
           +     I++++D   L    + ++ +   I+++    G   ++G + + +  K+SS  S+
Sbjct: 157 NS----IRVELDPAMLEDKGLTVEEVYEVIKKSN--VGKAEITGENTIAIYLKESSDLSY 210

Query: 881 NSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVKGV 939
            SK    ++ + ++ IKG+ GI RA+I     E G  +Y ++ +G NL  V+   GV   
Sbjct: 211 ISKK---REKVLNLKIKGIAGIKRAIIQSRRGEDGREEYVIVTDGSNLEQVLKVKGVDPT 267

Query: 940 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
           +  +N+ YE    LGIEAAR  I+ EI  V+   G+ +D RH  LVAD+MT  G V
Sbjct: 268 RTRTNSVYETMMVLGIEAARKVIINEIMNVLREQGLDVDVRHVYLVADIMTQTGVV 323


>gi|340624674|ref|YP_004743127.1| DNA-directed RNA polymerase subunit A'' [Methanococcus maripaludis
            X1]
 gi|339904942|gb|AEK20384.1| DNA-directed RNA polymerase subunit A'' [Methanococcus maripaludis
            X1]
          Length = 386

 Score =  174 bits (442), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 114/330 (34%), Positives = 172/330 (52%), Gaps = 50/330 (15%)

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYIEEVF 1155
            Y R  +EP  AVG +AAQSIGEPGTQMT++TFH+AG              E+ +  +E  
Sbjct: 49   YERTLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRMIEIVDARKEPS 108

Query: 1156 VP------DDSF---------ILIKLDMDRIRLLHLEVDIDSIRYCIE--------RTRG 1192
             P      +D F         +   ++   +  +  ++ +D +  CI          +RG
Sbjct: 109  TPTMTIYLNDEFKGDREKAATVAKNIESTNVESVSEDISVDLVNECITIILNNQQLESRG 168

Query: 1193 ISGHLTVSG-HSFLILKPKDSSKSFNSK-----MYQMKQLLPSVV---IKGVQGINRAVI 1243
            ++    +    S + LK +D     N K     +  +++ LP V    +KGVQ I R +I
Sbjct: 169  LTVPDVIDAIKSKMKLKIEDHENVLNLKIKTPSLKALRKRLPKVRAIHLKGVQNIKRVII 228

Query: 1244 HEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIK 1303
             +E    V +Y L  EG N+++V    GV   K ++NN  E+   LGIEAAR+ I+ E+ 
Sbjct: 229  RKE----VDEYILYSEGSNIKEVFDIEGVDTTKTTTNNIVEIQDVLGIEAARNAIIYEMD 284

Query: 1304 LVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAA 1363
              + N G+++D RH M+VAD+M + G V  I RHG+   K SVL  A+FE T  HL+ A+
Sbjct: 285  ATLGNQGLTVDKRHLMMVADIMCTDGVVKPIGRHGIGGEKASVLARAAFEETVKHLYSAS 344

Query: 1364 FYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
              G  D + GV E II+G P+++GTG I +
Sbjct: 345  MRGYVDELGGVVENIIVGKPISMGTGCIDI 374



 Score =  100 bits (249), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 77/236 (32%), Positives = 126/236 (53%), Gaps = 20/236 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A +  STP +T YL+ +   D + A  V   +E T +  V E I    V 
Sbjct: 93  GLPRMIEIVDARKEPSTPTMTIYLNDEFKGDREKAATVAKNIESTNVESVSEDISVDLVN 152

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGH-SFLILKPKDSS-KS 879
           +   I++       R L +   ID+I+  ++        L +  H + L LK K  S K+
Sbjct: 153 ECITIILNNQQLESRGLTVPDVIDAIKSKMK--------LKIEDHENVLNLKIKTPSLKA 204

Query: 880 FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
              ++ +++    ++ +KGVQ I R +I +E    V +Y L  EG N+++V    GV   
Sbjct: 205 LRKRLPKVR----AIHLKGVQNIKRVIIRKE----VDEYILYSEGSNIKEVFDIEGVDTT 256

Query: 940 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
           K ++NN  E+   LGIEAAR+ I+ E+   + N G+++D RH M+VAD+M + G V
Sbjct: 257 KTTTNNIVEIQDVLGIEAARNAIIYEMDATLGNQGLTVDKRHLMMVADIMCTDGVV 312


>gi|448638072|ref|ZP_21676123.1| DNA-directed RNA polymerase subunit A'' [Haloarcula sinaiiensis ATCC
            33800]
 gi|445763958|gb|EMA15132.1| DNA-directed RNA polymerase subunit A'' [Haloarcula sinaiiensis ATCC
            33800]
          Length = 395

 Score =  174 bits (442), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 110/350 (31%), Positives = 180/350 (51%), Gaps = 65/350 (18%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A+A   +Y+  +++P   VG ++AQSIGEPGTQMT+ TFH+AG            + E +
Sbjct: 45   AKAVETRYLDTRVDPLDPVGTVSAQSIGEPGTQMTMNTFHYAGVAEIDVTQGLPRLIELV 104

Query: 1152 EEVFVPDDSFILIKLD----------------MDRIRLLHL------------EVDI--- 1180
            +    PD   + + LD                ++  R+L L            E+D+   
Sbjct: 105  DARKTPDTPMMTVHLDEEYATDRERAHEVVWKIEATRILALGDISTNVADMLVEIDLNED 164

Query: 1181 ----------------DSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMK 1224
                            + I   IE   G+S   T    + +   P++ S      + Q+ 
Sbjct: 165  TLLERWPTVNDTDAIAEEIAETIESNLGVS---TRQAGTVIEFGPEEPSYR---DLLQLV 218

Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYE 1284
            + L  +V KG++ I R VI +E+ +   ++ L  EG +  +V+   GV   + + NN +E
Sbjct: 219  EELREIVFKGIEEITRVVIRKEETDNGEEFVLYTEGSDFGEVLDIEGVDASRTTCNNIHE 278

Query: 1285 VYKTLGIEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMK 1343
            +Y+ LG+EAAR T++ E    +E  G+  ++ RH MLVAD+MT++G +  I RHG++  K
Sbjct: 279  IYRELGVEAARETLINETMNTLEEQGLDDVNVRHLMLVADIMTNEGTIESIGRHGISGSK 338

Query: 1344 ESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            +SVL  A+FE T +HL DAA +G+ D + GV+E +I+G P+ +GTG + L
Sbjct: 339  DSVLARAAFEVTVNHLLDAAIHGEVDELDGVTENVIVGKPIKLGTGDVNL 388



 Score =  105 bits (263), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 70/245 (28%), Positives = 131/245 (53%), Gaps = 27/245 (11%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T +LD++  TD + A  V  ++E T    LG++   + + 
Sbjct: 96  GLPRLIELVDARKTPDTPMMTVHLDEEYATDRERAHEVVWKIEATRILALGDISTNVAD- 154

Query: 819 FVPDDSFILIKLDMDRIRLLH-------LEVDIDSIRYCIERTRGISGHLTVSGHSFLIL 871
                  +L+++D++   LL         +   + I   IE   G+S   T    + +  
Sbjct: 155 -------MLVEIDLNEDTLLERWPTVNDTDAIAEEIAETIESNLGVS---TRQAGTVIEF 204

Query: 872 KPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVM 931
            P++ S      + Q+ + L  +V KG++ I R VI +E+ +   ++ L  EG +  +V+
Sbjct: 205 GPEEPSYR---DLLQLVEELREIVFKGIEEITRVVIRKEETDNGEEFVLYTEGSDFGEVL 261

Query: 932 ATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMT 990
              GV   + + NN +E+Y+ LG+EAAR T++ E    +E  G+  ++ RH MLVAD+MT
Sbjct: 262 DIEGVDASRTTCNNIHEIYRELGVEAARETLINETMNTLEEQGLDDVNVRHLMLVADIMT 321

Query: 991 SKGEV 995
           ++G +
Sbjct: 322 NEGTI 326


>gi|150399425|ref|YP_001323192.1| DNA-directed RNA polymerase subunit A'' [Methanococcus vannielii SB]
 gi|1173130|sp|P14247.2|RPOA2_METVS RecName: Full=DNA-directed RNA polymerase subunit A''
 gi|505293|emb|CAA51729.1| DNA-directed RNA polymerase [Methanococcus vannielii]
 gi|150012128|gb|ABR54580.1| DNA-directed RNA polymerase, subunit A'' [Methanococcus vannielii SB]
          Length = 386

 Score =  174 bits (442), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 118/330 (35%), Positives = 173/330 (52%), Gaps = 50/330 (15%)

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYIEEVF 1155
            Y R  IEP  AVG +AAQSIGEPGTQMT++TFH+AG              E+ +  +E  
Sbjct: 49   YSRTVIEPGEAVGVIAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRMIEIVDARKEPS 108

Query: 1156 VPDDSFIL---IKLDMDR------------IRLLHLEVDIDSIRYCIERTRGI----SGH 1196
             P  S  L    K D +             +  +  ++ +D +  CI     +    S  
Sbjct: 109  TPTMSIYLRGDYKYDRESAAIVSKNIESTTVESVSEDISVDLVNECITIVLDVQQLESRQ 168

Query: 1197 LTVSG-----HSFLILKPKDSSKSFNSK-----MYQMKQLLPSVV---IKGVQGINRAVI 1243
            LTV+       S + LK +++    + K     +  +++ LP V    +KGV  I R +I
Sbjct: 169  LTVNNVVEAIKSKMKLKIEENENILSLKIKTPSLKALRKRLPKVREIHLKGVPNIKRVII 228

Query: 1244 HEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIK 1303
             +E    + +Y L  EG NL++V    GV   K ++NN  E+   LG+EAAR+ I+ E+ 
Sbjct: 229  RKE----IDEYVLYSEGSNLKEVFEIDGVDTTKTTTNNIVEIQDVLGVEAARNAIIREMD 284

Query: 1304 LVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAA 1363
              + N G+++D RH M+VADLMT+ G V  I RHG+   K SVL  A+FE T  HL+ A+
Sbjct: 285  ATLGNQGLTVDKRHLMMVADLMTTDGVVKPIGRHGIGGEKASVLARAAFEETVKHLYSAS 344

Query: 1364 FYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
              G  D +SGV E II+G P+++GTG I +
Sbjct: 345  MRGYVDDLSGVVENIIVGKPISMGTGCINV 374



 Score =  105 bits (261), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 78/235 (33%), Positives = 124/235 (52%), Gaps = 18/235 (7%)

Query: 764 GVPRIKEIINASRNISTPIITAYL--DKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A +  STP ++ YL  D   D + A IV   +E TT+  V E I    V 
Sbjct: 93  GLPRMIEIVDARKEPSTPTMSIYLRGDYKYDRESAAIVSKNIESTTVESVSEDISVDLV- 151

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSS-KSF 880
            +  I I LD+ ++    L V+       +E  +           + L LK K  S K+ 
Sbjct: 152 -NECITIVLDVQQLESRQLTVN-----NVVEAIKSKMKLKIEENENILSLKIKTPSLKAL 205

Query: 881 NSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
             ++ +++++     +KGV  I R +I +E    + +Y L  EG NL++V    GV   K
Sbjct: 206 RKRLPKVREIH----LKGVPNIKRVIIRKE----IDEYVLYSEGSNLKEVFEIDGVDTTK 257

Query: 941 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            ++NN  E+   LG+EAAR+ I+ E+   + N G+++D RH M+VADLMT+ G V
Sbjct: 258 TTTNNIVEIQDVLGVEAARNAIIREMDATLGNQGLTVDKRHLMMVADLMTTDGVV 312


>gi|448466833|ref|ZP_21599255.1| DNA-directed RNA polymerase subunit A'' [Halorubrum kocurii JCM
            14978]
 gi|445813259|gb|EMA63239.1| DNA-directed RNA polymerase subunit A'' [Halorubrum kocurii JCM
            14978]
          Length = 404

 Score =  174 bits (442), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 110/350 (31%), Positives = 178/350 (50%), Gaps = 65/350 (18%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A     +Y+  +++P   VG ++AQSIGEPGTQMT+ TFH+AG            + E +
Sbjct: 51   ATGVENRYIETRVDPLDPVGTVSAQSIGEPGTQMTMNTFHYAGVAEIDVTQGLPRLIELV 110

Query: 1152 EEVFVPDDSFILIKLD----------------MDRIRLLHL------------EVDIDS- 1182
            +    PD   + + L+                ++  R+L L             +D++  
Sbjct: 111  DARKTPDTPMMTVHLEGEYATDRQKAHEVVWSIEATRILALGDVSTNVADMLVRIDLNDD 170

Query: 1183 ------------------IRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMK 1224
                              I   IE + G++   T    + +   P + S     ++ Q+ 
Sbjct: 171  TLLERWPTHSDPSEVAAIISETIEDSLGVN---TRQSGTVVEFGPNEPSYR---ELLQLV 224

Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYE 1284
            + L  +V KG++ I R VI +E+++G  ++ L  EG    D +   GV   + + NN +E
Sbjct: 225  ERLREIVFKGIEEIERVVIRKEEIDGEEEFVLYTEGSAFGDTLDIEGVDASRTTCNNIHE 284

Query: 1285 VYKTLGIEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMK 1343
            +Y+ LG+EAAR TI+ E K  +E  G+  ++ RH MLVAD+MT+ GE+  I RHG++  K
Sbjct: 285  IYRNLGVEAARETIIDETKNTLEEQGLDDVNVRHLMLVADIMTNNGEIESIGRHGISGSK 344

Query: 1344 ESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            +SVL  A+FE T +HL DAA +G+ D + GV E +I G P+++GTG + L
Sbjct: 345  DSVLARAAFEVTVNHLLDAAVHGEYDELDGVIENVIAGKPISLGTGDVDL 394



 Score =  106 bits (264), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 74/242 (30%), Positives = 127/242 (52%), Gaps = 21/242 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T +L+ +  TD   A  V   +E T    LG+V   + + 
Sbjct: 102 GLPRLIELVDARKTPDTPMMTVHLEGEYATDRQKAHEVVWSIEATRILALGDVSTNVAD- 160

Query: 819 FVPDDSFILIKLDMDRIRLLH---LEVDIDSIRYCIERTRGIS-GHLTVSGHSFLILKPK 874
                  +L+++D++   LL       D   +   I  T   S G  T    + +   P 
Sbjct: 161 -------MLVRIDLNDDTLLERWPTHSDPSEVAAIISETIEDSLGVNTRQSGTVVEFGPN 213

Query: 875 DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATY 934
           + S     ++ Q+ + L  +V KG++ I R VI +E+++G  ++ L  EG    D +   
Sbjct: 214 EPSYR---ELLQLVERLREIVFKGIEEIERVVIRKEEIDGEEEFVLYTEGSAFGDTLDIE 270

Query: 935 GVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKG 993
           GV   + + NN +E+Y+ LG+EAAR TI+ E K  +E  G+  ++ RH MLVAD+MT+ G
Sbjct: 271 GVDASRTTCNNIHEIYRNLGVEAARETIIDETKNTLEEQGLDDVNVRHLMLVADIMTNNG 330

Query: 994 EV 995
           E+
Sbjct: 331 EI 332


>gi|257386580|ref|YP_003176353.1| DNA-directed RNA polymerase subunit A'' [Halomicrobium mukohataei DSM
            12286]
 gi|257168887|gb|ACV46646.1| DNA-directed RNA polymerase, subunit A'' [Halomicrobium mukohataei
            DSM 12286]
          Length = 395

 Score =  174 bits (441), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 109/347 (31%), Positives = 177/347 (51%), Gaps = 59/347 (17%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A+A + +Y   +++P   VG ++AQSIGEPGTQMT+ TFH+AG            + E +
Sbjct: 45   AKAVQSRYQETRVDPLDPVGTVSAQSIGEPGTQMTMNTFHYAGVAEIDVTQGLPRLIELV 104

Query: 1152 EEVFVPD---------DSF-------------------------------ILIKLDMDRI 1171
            +    PD         D +                               +L+++D++  
Sbjct: 105  DARKTPDTPMMTVHLEDEYATDREKAHEVVWKIEATRILALGDISTNVADMLVQIDLNEE 164

Query: 1172 RLLHLEVDIDSIRYCIER-TRGISGHLTVSGH---SFLILKPKDSSKSFNSKMYQMKQLL 1227
             L+     +D +    E     I   L V      + +   P++ S      + Q+ + L
Sbjct: 165  TLMERWPTVDQVEDVAEEIAETIESKLAVQTRQAGTMIEFGPEEPSYR---DLLQLVEEL 221

Query: 1228 PSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYK 1287
              VV KG++ I+R VI +E+ +   ++ L  EG    DV+   G+   + + NN +E+Y+
Sbjct: 222  REVVFKGIEDISRVVIRKEETDEGEEFVLYTEGSAFGDVLGIEGIDASRTTCNNIHEIYR 281

Query: 1288 TLGIEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMKESV 1346
             LGIEAAR T++ E    +E  G+  ++ RH MLVAD+MT++GE+  I RHG++  KESV
Sbjct: 282  NLGIEAARETLINETMHTLEEQGLDDVNIRHLMLVADIMTNRGEIESIGRHGISGNKESV 341

Query: 1347 LNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            L  A++E T +HL DAA +G+ D + GV E +I+G P+ +GTG + L
Sbjct: 342  LARAAYEVTVNHLLDAAIHGEVDVLEGVIENVIVGKPVQLGTGDVDL 388



 Score =  108 bits (270), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 70/242 (28%), Positives = 129/242 (53%), Gaps = 21/242 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T +L+ +  TD + A  V  ++E T    LG++   + + 
Sbjct: 96  GLPRLIELVDARKTPDTPMMTVHLEDEYATDREKAHEVVWKIEATRILALGDISTNVAD- 154

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIER-TRGISGHLTVSGH---SFLILKPK 874
                  +L+++D++   L+     +D +    E     I   L V      + +   P+
Sbjct: 155 -------MLVQIDLNEETLMERWPTVDQVEDVAEEIAETIESKLAVQTRQAGTMIEFGPE 207

Query: 875 DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATY 934
           + S      + Q+ + L  VV KG++ I+R VI +E+ +   ++ L  EG    DV+   
Sbjct: 208 EPSYR---DLLQLVEELREVVFKGIEDISRVVIRKEETDEGEEFVLYTEGSAFGDVLGIE 264

Query: 935 GVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKG 993
           G+   + + NN +E+Y+ LGIEAAR T++ E    +E  G+  ++ RH MLVAD+MT++G
Sbjct: 265 GIDASRTTCNNIHEIYRNLGIEAARETLINETMHTLEEQGLDDVNIRHLMLVADIMTNRG 324

Query: 994 EV 995
           E+
Sbjct: 325 EI 326


>gi|355712747|gb|AES04452.1| polymerase III polypeptide A, 155kDa [Mustela putorius furo]
          Length = 248

 Score =  174 bits (441), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 85/111 (76%), Positives = 89/111 (80%), Gaps = 14/111 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHKLSIMAH AKV PHRTFRFNECVCTPYNADFDGDEMN+HLPQTEEA
Sbjct: 152 DGDVVLFNRQPSLHKLSIMAHLAKVKPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEA 211

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLL 451
           +AEAL              VLM  K+NLVTPRNGE LIAA QDF+TG YLL
Sbjct: 212 KAEAL--------------VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLL 248



 Score = 54.7 bits (130), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 25/32 (78%), Positives = 27/32 (84%)

Query: 21  VLMANKSNLVTPRNGELLIAATQDFITGGYLL 52
           VLM  K+NLVTPRNGE LIAA QDF+TG YLL
Sbjct: 217 VLMGTKANLVTPRNGEPLIAAIQDFLTGAYLL 248


>gi|448444628|ref|ZP_21589918.1| DNA-directed RNA polymerase subunit A'' [Halorubrum saccharovorum DSM
            1137]
 gi|445686041|gb|ELZ38382.1| DNA-directed RNA polymerase subunit A'' [Halorubrum saccharovorum DSM
            1137]
          Length = 404

 Score =  174 bits (441), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 110/350 (31%), Positives = 177/350 (50%), Gaps = 65/350 (18%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A     +Y+  +++P   VG ++AQSIGEPGTQMT+ TFH+AG            + E +
Sbjct: 51   ATGVENRYIETRVDPLDPVGTVSAQSIGEPGTQMTMNTFHYAGVAEIDVTQGLPRLIELV 110

Query: 1152 EEVFVPDDSFILIKLD----------------MDRIRLLHL------------EVDIDS- 1182
            +    PD   + + L+                ++  R+L L             +D++  
Sbjct: 111  DARKTPDTPMMTVHLEGEHATDREKAHEVVWSIEATRILALGDVSTNVADMLVRIDLNDD 170

Query: 1183 ------------------IRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMK 1224
                              I   IE + G+    T    + +   P + S     ++ Q+ 
Sbjct: 171  TLLERWPTHSDPSEVAAIIAETIEDSLGVD---TRQSGTVVEFGPNEPSYR---ELLQLV 224

Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYE 1284
            + L  +V KG++ I R VI +E+++G  ++ L  EG    D +   GV   + + NN +E
Sbjct: 225  ERLREIVFKGIEEIERVVIRKEEIDGDEEFVLYTEGSAFGDALDIEGVDASRTTCNNIHE 284

Query: 1285 VYKTLGIEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMK 1343
            +Y+ LG+EAAR TI+ E K  +E  G+  ++ RH MLVAD+MT+ GE+  I RHG++  K
Sbjct: 285  IYRNLGVEAARETIIDETKNTLEEQGLDDVNVRHLMLVADIMTNNGEIESIGRHGISGSK 344

Query: 1344 ESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            +SVL  A+FE T +HL DAA +G+ D + GV E +I G P+++GTG + L
Sbjct: 345  DSVLARAAFEVTVNHLLDAAIHGEYDELDGVIENVIAGKPISLGTGDVDL 394



 Score =  106 bits (265), Expect = 8e-20,   Method: Composition-based stats.
 Identities = 74/242 (30%), Positives = 128/242 (52%), Gaps = 21/242 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T +L+ +  TD + A  V   +E T    LG+V   + + 
Sbjct: 102 GLPRLIELVDARKTPDTPMMTVHLEGEHATDREKAHEVVWSIEATRILALGDVSTNVAD- 160

Query: 819 FVPDDSFILIKLDMDRIRLLH---LEVDIDSIRYCIERTRGIS-GHLTVSGHSFLILKPK 874
                  +L+++D++   LL       D   +   I  T   S G  T    + +   P 
Sbjct: 161 -------MLVRIDLNDDTLLERWPTHSDPSEVAAIIAETIEDSLGVDTRQSGTVVEFGPN 213

Query: 875 DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATY 934
           + S     ++ Q+ + L  +V KG++ I R VI +E+++G  ++ L  EG    D +   
Sbjct: 214 EPSYR---ELLQLVERLREIVFKGIEEIERVVIRKEEIDGDEEFVLYTEGSAFGDALDIE 270

Query: 935 GVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKG 993
           GV   + + NN +E+Y+ LG+EAAR TI+ E K  +E  G+  ++ RH MLVAD+MT+ G
Sbjct: 271 GVDASRTTCNNIHEIYRNLGVEAARETIIDETKNTLEEQGLDDVNVRHLMLVADIMTNNG 330

Query: 994 EV 995
           E+
Sbjct: 331 EI 332


>gi|240103981|ref|YP_002960290.1| DNA-directed RNA polymerase subunit A'' [Thermococcus gammatolerans
            EJ3]
 gi|259494163|sp|C5A207.1|RPOA2_THEGJ RecName: Full=DNA-directed RNA polymerase subunit A''
 gi|239911535|gb|ACS34426.1| DNA-directed RNA polymerase subunit A' (rpoA2) [Thermococcus
            gammatolerans EJ3]
          Length = 391

 Score =  174 bits (441), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 111/346 (32%), Positives = 175/346 (50%), Gaps = 58/346 (16%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIE 1152
            E    +Y +A +EP   +G +AAQSIGEP TQMTL TFH+AG            + E ++
Sbjct: 47   EDAVNEYRKALVEPGEPIGTVAAQSIGEPSTQMTLNTFHYAGVAEINVTLGLPRIIEIVD 106

Query: 1153 EVFVPDDSFILI------KLDMDRIRLL--------------HLEVDIDSIRYCIE---- 1188
                P    + +      + D+++ R +               + +DI +  + +E    
Sbjct: 107  ARKNPSTPVMTVFLDEEHRYDLEKAREVARRIEGTTIENLAREMSIDILNFEFIVEIDPE 166

Query: 1189 --RTRGI--------------SGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVI 1232
                 G+              S      G+S LI++PK  +K   S + ++ + +    +
Sbjct: 167  RLEKSGLDMERILKKLSGSFKSAEFEAEGYS-LIVRPKKVTKL--SDLRKLAEKVKKHRL 223

Query: 1233 KGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIE 1292
            KG+ G+ + +I +E  E    Y +  EG N + V+   GV   +  +NN +E+   LGIE
Sbjct: 224  KGLSGVGKTIIRKEGDE----YVIYTEGSNFKQVLKVPGVDPTRTRTNNIWEIADVLGIE 279

Query: 1293 AARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASF 1352
            AAR+ I+ EI   M   G+ +D RH MLVAD+MT  G +  I RHG+   K SVL  A+F
Sbjct: 280  AARNAIIEEIVNTMREQGLEVDIRHIMLVADMMTLDGVIRPIGRHGIVGEKSSVLARAAF 339

Query: 1353 ENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 1398
            E T+ HLF+AA  G+ D ++GV E +++G P+ VGTG++KL   +P
Sbjct: 340  EITTQHLFEAAERGEVDPLNGVVENVLIGQPVPVGTGIVKLTMNLP 385



 Score =  115 bits (287), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 79/234 (33%), Positives = 132/234 (56%), Gaps = 18/234 (7%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PRI EI++A +N STP++T +LD++   DL+ AR V  R+E TT+  +   +  + + 
Sbjct: 97  GLPRIIEIVDARKNPSTPVMTVFLDEEHRYDLEKAREVARRIEGTTIENLAREMS-IDIL 155

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI--SGHLTVSGHSFLILKPKDSSKS 879
           +  FI+   ++D  RL    +D++ I   +++  G   S      G+S LI++PK  +K 
Sbjct: 156 NFEFIV---EIDPERLEKSGLDMERI---LKKLSGSFKSAEFEAEGYS-LIVRPKKVTKL 208

Query: 880 FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
             S + ++ + +    +KG+ G+ + +I +E  E    Y +  EG N + V+   GV   
Sbjct: 209 --SDLRKLAEKVKKHRLKGLSGVGKTIIRKEGDE----YVIYTEGSNFKQVLKVPGVDPT 262

Query: 940 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
           +  +NN +E+   LGIEAAR+ I+ EI   M   G+ +D RH MLVAD+MT  G
Sbjct: 263 RTRTNNIWEIADVLGIEAARNAIIEEIVNTMREQGLEVDIRHIMLVADMMTLDG 316


>gi|448457214|ref|ZP_21595709.1| DNA-directed RNA polymerase subunit A'' [Halorubrum lipolyticum DSM
            21995]
 gi|445810795|gb|EMA60810.1| DNA-directed RNA polymerase subunit A'' [Halorubrum lipolyticum DSM
            21995]
          Length = 404

 Score =  174 bits (441), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 110/350 (31%), Positives = 177/350 (50%), Gaps = 65/350 (18%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A     +Y+  +++P   VG ++AQSIGEPGTQMT+ TFH+AG            + E +
Sbjct: 51   ATGVENRYIETRVDPLDPVGTVSAQSIGEPGTQMTMNTFHYAGVAEIDVTQGLPRLIELV 110

Query: 1152 EEVFVPDDSFILIKLD----------------MDRIRLLHL------------EVDIDS- 1182
            +    PD   + + L+                ++  R+L L             +D++  
Sbjct: 111  DARKTPDTPMMTVHLEGEYATDRQKAHEVVWSIEATRILALGDVSTNVADMLVRIDLNDD 170

Query: 1183 ------------------IRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMK 1224
                              I   IE + G+    T    + +   P + S     ++ Q+ 
Sbjct: 171  TLLERWPTHSDPSEVAAIIAETIEDSLGVD---TRQSGTVVEFGPNEPSYR---ELLQLV 224

Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYE 1284
            + L  +V KG++ I R VI +E+++G  ++ L  EG    D +   GV   + + NN +E
Sbjct: 225  ERLREIVFKGIEEIERVVIRKEEIDGEEEFVLYTEGSAFGDTLDIEGVDASRTTCNNIHE 284

Query: 1285 VYKTLGIEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMK 1343
            +Y+ LG+EAAR TI+ E K  +E  G+  ++ RH MLVAD+MT+ GE+  I RHG++  K
Sbjct: 285  IYRNLGVEAARETIIDETKNTLEEQGLDDVNVRHLMLVADIMTNNGEIESIGRHGISGSK 344

Query: 1344 ESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            +SVL  A+FE T +HL DAA +G+ D + GV E +I G P+++GTG + L
Sbjct: 345  DSVLARAAFEVTVNHLLDAAIHGEYDELDGVIENVIAGKPISLGTGDVDL 394



 Score =  105 bits (263), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 74/242 (30%), Positives = 127/242 (52%), Gaps = 21/242 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T +L+ +  TD   A  V   +E T    LG+V   + + 
Sbjct: 102 GLPRLIELVDARKTPDTPMMTVHLEGEYATDRQKAHEVVWSIEATRILALGDVSTNVAD- 160

Query: 819 FVPDDSFILIKLDMDRIRLLH---LEVDIDSIRYCIERTRGIS-GHLTVSGHSFLILKPK 874
                  +L+++D++   LL       D   +   I  T   S G  T    + +   P 
Sbjct: 161 -------MLVRIDLNDDTLLERWPTHSDPSEVAAIIAETIEDSLGVDTRQSGTVVEFGPN 213

Query: 875 DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATY 934
           + S     ++ Q+ + L  +V KG++ I R VI +E+++G  ++ L  EG    D +   
Sbjct: 214 EPSYR---ELLQLVERLREIVFKGIEEIERVVIRKEEIDGEEEFVLYTEGSAFGDTLDIE 270

Query: 935 GVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKG 993
           GV   + + NN +E+Y+ LG+EAAR TI+ E K  +E  G+  ++ RH MLVAD+MT+ G
Sbjct: 271 GVDASRTTCNNIHEIYRNLGVEAARETIIDETKNTLEEQGLDDVNVRHLMLVADIMTNNG 330

Query: 994 EV 995
           E+
Sbjct: 331 EI 332


>gi|145592516|ref|YP_001154518.1| DNA-directed RNA polymerase subunit A' [Pyrobaculum arsenaticum DSM
           13514]
 gi|145284284|gb|ABP51866.1| DNA-directed RNA polymerase, subunit A' [Pyrobaculum arsenaticum
           DSM 13514]
          Length = 884

 Score =  174 bits (441), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 104/269 (38%), Positives = 149/269 (55%), Gaps = 33/269 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++S+M H  KVLP RTFR +  VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 423 DGDIVLFNRQPSLHRVSMMGHLVKVLPGRTFRLHLAVCPPYNADFDGDEMNLHVPQTEEA 482

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A++LM  +++++TPR G  +I A QD+I G YLL+ K  F  +
Sbjct: 483 RAE--------------ARLLMLVENHIITPRYGGAIIGARQDYIIGAYLLSHKTTFLTK 528

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +   +A  L A  S+              P +      +WTGKQI S  L  + +    
Sbjct: 529 KE---VAFLLGAGKSEE---------DPPEPAILYPVE-LWTGKQIISHFLPKDFNWVQP 575

Query: 521 ANLKTKGR-AYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
              K+K + AYT     C+ D ++I+ N  L  G +DK ++G+    ++++ + RD+  D
Sbjct: 576 TAFKSKCQDAYT-----CYGDEWIIVLNGYLAKGVLDKKSIGAEQVDSLWHRIARDYPPD 630

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           VA   +    R+   YL  RGF+  +  V
Sbjct: 631 VARRWLDSSLRLFLRYLDLRGFTFAMDSV 659



 Score =  115 bits (289), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 73/255 (28%), Positives = 128/255 (50%), Gaps = 40/255 (15%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           +++ S +++ +  +Y  D    P+  G+ DRR+G  +  A C TCGQ    C GHFG+I+
Sbjct: 28  IRKYSVMEVTTSEVY--DEGGLPVRGGISDRRLGVAEPGARCETCGQTHDVCPGHFGHIE 85

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSY-LVRKSLKK 211
           L  PV H+G+ R + +IL++ C  P C R++L +E+ A +R +L   +  + L+ ++L +
Sbjct: 86  LVKPVVHVGFARVIYDILRTTC--PNCGRIMLRDEEIARYRERLTRLSKRWRLLAQNLHE 143

Query: 212 KILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFN 271
           +I     +   CPHCG               +++ K R ++     E+   E    VK +
Sbjct: 144 RIRRKAAERMTCPHCG---------------YKRNKVRFERPYYFYEE--TENGALVKLD 186

Query: 272 PEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIR 331
           PE+   +                   IP ED+ LL +N  + +P   IL  L VPP  +R
Sbjct: 187 PEMLRDR----------------LSKIPSEDLELLGINPSVFRPEWAILKVLPVPPPHVR 230

Query: 332 PSVI--SDLKSDNDV 344
           PS+   + ++S++D+
Sbjct: 231 PSIQLETGIRSEDDL 245



 Score = 84.0 bits (206), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 36/65 (55%), Positives = 50/65 (76%), Gaps = 1/65 (1%)

Query: 605 IGDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDL 663
           +GD+     GFV++ F  GLTP E+FFH   GR+GL+DTAV+TA++GYMQRRL+ +L+D+
Sbjct: 779 VGDIGAFSGGFVKHCFRCGLTPVEYFFHAAAGRDGLIDTAVRTAQSGYMQRRLINALQDV 838

Query: 664 CVQYD 668
            V YD
Sbjct: 839 YVAYD 843



 Score = 44.3 bits (103), Expect = 0.51,   Method: Compositional matrix adjust.
 Identities = 21/56 (37%), Positives = 35/56 (62%), Gaps = 3/56 (5%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           ++LM  +++++TPR G  +I A QD+I G YLL+ K  F  + +   +A  L AG+
Sbjct: 487 RLLMLVENHIITPRYGGAIIGARQDYIIGAYLLSHKTTFLTKKE---VAFLLGAGK 539


>gi|134045259|ref|YP_001096745.1| DNA-directed RNA polymerase subunit A'' [Methanococcus maripaludis
            C5]
 gi|166229258|sp|A4FWF5.1|RPOA2_METM5 RecName: Full=DNA-directed RNA polymerase subunit A''
 gi|132662884|gb|ABO34530.1| DNA-directed RNA polymerase, subunit A' ' [Methanococcus maripaludis
            C5]
          Length = 386

 Score =  174 bits (441), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 115/330 (34%), Positives = 170/330 (51%), Gaps = 50/330 (15%)

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCE------ 1149
            Y R  +EP  AVG +AAQSIGEPGTQMT++TFH+AG              E+ +      
Sbjct: 49   YERTLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRMIEIVDARKEPS 108

Query: 1150 ------YIEEVFVPD---DSFILIKLDMDRIRLLHLEVDIDSIRYCIE--------RTRG 1192
                  Y+ + F  D    S +   ++   +  +  ++ +D +  CI          +RG
Sbjct: 109  TPTMTIYLNDEFKGDREKASMVAKNIESTNVESVSEDISVDLVNECITIILNSQQLESRG 168

Query: 1193 ISGHLTVSG-HSFLILKPKDSSKSFNSK-----MYQMKQLLPSVV---IKGVQGINRAVI 1243
            ++    +    S + LK  D     N K     +  +++ LP V    +KGVQ I R +I
Sbjct: 169  LTVPDVIEAIKSKMKLKIDDHENVLNLKIKTPSLKALRKRLPKVRAIHLKGVQNIKRVII 228

Query: 1244 HEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIK 1303
             +E    V +Y L  EG N+++V    GV   K ++NN  E+   LGIEAAR+ I+ E+ 
Sbjct: 229  RKE----VDEYILYSEGSNIKEVFDIEGVDTTKTTTNNIVEIQDVLGIEAARNAIIYEMD 284

Query: 1304 LVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAA 1363
              + N G+++D RH M+VADLM + G V  I RHG+   K SVL  A+FE T  HL+ A+
Sbjct: 285  ATLGNQGLTVDKRHLMMVADLMCTDGVVKPIGRHGIGGEKASVLARAAFEETVKHLYSAS 344

Query: 1364 FYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
              G  D + GV E II+G P+ +GTG I +
Sbjct: 345  MRGYVDELGGVVENIIVGKPIAMGTGCIDI 374



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 77/236 (32%), Positives = 127/236 (53%), Gaps = 20/236 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A +  STP +T YL+ +   D + A +V   +E T +  V E I    V 
Sbjct: 93  GLPRMIEIVDARKEPSTPTMTIYLNDEFKGDREKASMVAKNIESTNVESVSEDISVDLVN 152

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGH-SFLILKPKDSS-KS 879
           +   I++       R L +   I++I+  ++        L +  H + L LK K  S K+
Sbjct: 153 ECITIILNSQQLESRGLTVPDVIEAIKSKMK--------LKIDDHENVLNLKIKTPSLKA 204

Query: 880 FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
              ++ +++    ++ +KGVQ I R +I +E    V +Y L  EG N+++V    GV   
Sbjct: 205 LRKRLPKVR----AIHLKGVQNIKRVIIRKE----VDEYILYSEGSNIKEVFDIEGVDTT 256

Query: 940 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
           K ++NN  E+   LGIEAAR+ I+ E+   + N G+++D RH M+VADLM + G V
Sbjct: 257 KTTTNNIVEIQDVLGIEAARNAIIYEMDATLGNQGLTVDKRHLMMVADLMCTDGVV 312


>gi|448683948|ref|ZP_21692568.1| DNA-directed RNA polymerase subunit A'' [Haloarcula japonica DSM
            6131]
 gi|189332912|dbj|BAG41984.1| RNA polymerase subunit C [Haloarcula japonica]
 gi|445783521|gb|EMA34350.1| DNA-directed RNA polymerase subunit A'' [Haloarcula japonica DSM
            6131]
          Length = 395

 Score =  174 bits (440), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 110/347 (31%), Positives = 180/347 (51%), Gaps = 59/347 (17%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A+A   +Y+  +++P   VG ++AQSIGEPGTQMT+ TFH+AG            + E +
Sbjct: 45   AKAVETRYLDTRVDPLDPVGTVSAQSIGEPGTQMTMNTFHYAGVAEIDVTQGLPRLIELV 104

Query: 1152 EEVFVPDDSFILIKLD----------------MDRIRLLHL------------EVDI--- 1180
            +    PD   + + LD                ++  R+L L            E+D+   
Sbjct: 105  DARKTPDTPMMTVHLDEEYATDRERAHEVVWKIEATRILALGDISTNVADMLVEIDLNED 164

Query: 1181 ----------DSIRYCIERTRGISGHLTVSGH---SFLILKPKDSSKSFNSKMYQMKQLL 1227
                      D+     E    I  +L VS     + +   P++ S      + Q+ + L
Sbjct: 165  TLLERWPTVNDTDAIAEEIAETIESNLGVSARQAGTVIEFGPEEPSYR---DLLQLVEEL 221

Query: 1228 PSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYK 1287
              +V KG++ I R VI +E+ +   ++ L  EG +  +V+   GV   + + NN +E+Y+
Sbjct: 222  REIVFKGIEEITRVVIRKEETDNGEEFVLYTEGSDFGEVLDIEGVDASRTTCNNIHEIYR 281

Query: 1288 TLGIEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMKESV 1346
             LG+EAAR T++ E    +E  G+  ++ RH MLVAD+MT++G +  I RHG++  K+SV
Sbjct: 282  ELGVEAARETLINETMNTLEEQGLDDVNVRHLMLVADIMTNEGTIESIGRHGISGSKDSV 341

Query: 1347 LNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            L  A+FE T +HL DAA +G+ D + GV+E +I+G P+ +GTG + L
Sbjct: 342  LARAAFEVTVNHLLDAAIHGEVDELDGVTENVIVGKPIKLGTGDVNL 388



 Score =  106 bits (264), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 73/244 (29%), Positives = 133/244 (54%), Gaps = 25/244 (10%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T +LD++  TD + A  V  ++E T    LG++   + + 
Sbjct: 96  GLPRLIELVDARKTPDTPMMTVHLDEEYATDRERAHEVVWKIEATRILALGDISTNVAD- 154

Query: 819 FVPDDSFILIKLDMDRIRLLH---LEVDIDSIRYCIERTRGISGHLTVSGH---SFLILK 872
                  +L+++D++   LL       D D+I   I  T  I  +L VS     + +   
Sbjct: 155 -------MLVEIDLNEDTLLERWPTVNDTDAIAEEIAET--IESNLGVSARQAGTVIEFG 205

Query: 873 PKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMA 932
           P++ S      + Q+ + L  +V KG++ I R VI +E+ +   ++ L  EG +  +V+ 
Sbjct: 206 PEEPSYR---DLLQLVEELREIVFKGIEEITRVVIRKEETDNGEEFVLYTEGSDFGEVLD 262

Query: 933 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTS 991
             GV   + + NN +E+Y+ LG+EAAR T++ E    +E  G+  ++ RH MLVAD+MT+
Sbjct: 263 IEGVDASRTTCNNIHEIYRELGVEAARETLINETMNTLEEQGLDDVNVRHLMLVADIMTN 322

Query: 992 KGEV 995
           +G +
Sbjct: 323 EGTI 326


>gi|304315186|ref|YP_003850333.1| DNA-directed RNA polymerase, subunit A' [Methanothermobacter
           marburgensis str. Marburg]
 gi|302588645|gb|ADL59020.1| DNA-directed RNA polymerase, subunit A' [Methanothermobacter
           marburgensis str. Marburg]
          Length = 1152

 Score =  174 bits (440), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 98/272 (36%), Positives = 146/272 (53%), Gaps = 46/272 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++S+MAH  +VLP++TFR N CVC PYNADFDGDEMN+H+ QTEE+
Sbjct: 690 DGDIVLFNRQPSLHRMSMMAHEVRVLPYKTFRLNLCVCPPYNADFDGDEMNMHVFQTEES 749

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              AK LM  + ++++PR G  +I    D I+G YLLT+K A F+ 
Sbjct: 750 RAE--------------AKTLMRVQEHILSPRFGGPIIGGIHDHISGAYLLTRKRAVFSE 795

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +  +I         D                   R    WTGK+IFS++L      P +
Sbjct: 796 DKVFQILKKAGLPLPD-------------------RRGRDWTGKEIFSMVL------PDD 830

Query: 521 ANLKTKGRAYTANEEF----CHRDSYVILRNSELLAGSMDKSTLGS-GGKANVFYILLRD 575
            N+  +       EE     C  D+YV++ N EL++G +D+   G+  GK  +   ++++
Sbjct: 831 LNMVYRAEICRKCEECLEMDCENDAYVVIENGELISGVIDEKAYGAFAGK--ILDHIVKE 888

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           +G D A   +   +++    +M+ GF+    D
Sbjct: 889 YGTDAARKFLDSATKLAIAGIMHAGFTTSTND 920



 Score = 89.4 bits (220), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 38/57 (66%), Positives = 47/57 (82%)

Query: 612  QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV +S+  GL P EFFFH MGGREGLVDTA++TA++GYMQRRLV +L+DL V  D
Sbjct: 1050 RGFVHSSYKEGLDPIEFFFHAMGGREGLVDTAIRTAQSGYMQRRLVNALQDLTVNED 1106



 Score = 88.6 bits (218), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 59/182 (32%), Positives = 90/182 (49%), Gaps = 10/182 (5%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G ++ ED +++ S  Q+V+ + Y +D    PI +GL+D R+G       C TCG    +C
Sbjct: 14  GLMSPED-IRKMSVTQVVTPDTYDEDG--YPIENGLMDPRLGVIDPSLRCRTCGAKGGEC 70

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFG I+L  PV H+G+   +  IL+SIC    C RVLL E +   +R ++        
Sbjct: 71  PGHFGSINLARPVIHVGFADTIHKILRSICWK--CGRVLLTEVEIEEYRQRILEAMEKEE 128

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEY 264
               + K+I    ++   CPHC E  G +K    + I    Y    K K   ++ LL E 
Sbjct: 129 SLTPIIKEIYAEARR-EECPHCEEEQGDIKLDKPVSIVENDY----KLKSGDIKKLLEEI 183

Query: 265 NE 266
           N+
Sbjct: 184 NK 185


>gi|448513824|ref|ZP_21616755.1| DNA-directed RNA polymerase subunit A'' [Halorubrum distributum JCM
            9100]
 gi|448526666|ref|ZP_21619935.1| DNA-directed RNA polymerase subunit A'' [Halorubrum distributum JCM
            10118]
 gi|445692977|gb|ELZ45140.1| DNA-directed RNA polymerase subunit A'' [Halorubrum distributum JCM
            9100]
 gi|445698893|gb|ELZ50931.1| DNA-directed RNA polymerase subunit A'' [Halorubrum distributum JCM
            10118]
          Length = 404

 Score =  174 bits (440), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 110/349 (31%), Positives = 176/349 (50%), Gaps = 65/349 (18%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIE 1152
            E    +Y + +++P   VG ++AQSIGEPGTQMT+ TFH+AG            + E ++
Sbjct: 52   EGVVNRYEQTRVDPLDPVGTVSAQSIGEPGTQMTMNTFHYAGVAEIDVTQGLPRLIELVD 111

Query: 1153 EVFVPDDSFILIKLD----------------MDRIRLLHL------------EVDIDS-- 1182
                PD   + + LD                ++  R+L L             +D++   
Sbjct: 112  ARKTPDTPMMTVHLDGEYATDREKAHEVVWSIEATRILALGDVSTNVADMLVRIDLNDDT 171

Query: 1183 -----------------IRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQ 1225
                             I   IE + G+         + +   P + S     ++ Q+ +
Sbjct: 172  LLERWPTHSDPTEVAEIIAKTIEDSLGVDAR---QAGTVIEFGPNEPSYR---ELLQLVE 225

Query: 1226 LLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEV 1285
             L  +V KG++ I R VI +E+++G  ++ L  EG    D +   GV   + + NN +E+
Sbjct: 226  RLREIVFKGIEEIERVVIRKEEIDGDEEFVLYTEGSAFGDTLDIEGVDASRTTCNNIHEI 285

Query: 1286 YKTLGIEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMKE 1344
            Y+ LG+EAAR TI+ E K  +E  G+  ++ RH MLVAD+MT+ GE+  I RHG++  K+
Sbjct: 286  YRNLGVEAARETIIDETKNTLEEQGLDDVNVRHLMLVADIMTNNGEIESIGRHGISGNKD 345

Query: 1345 SVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            SVL  A+FE T +HL DAA +G+ D + GV E +I G P+++GTG + L
Sbjct: 346  SVLARAAFEVTVNHLLDAAIHGEYDDLDGVIENVIAGKPISMGTGDVDL 394



 Score =  108 bits (271), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 75/244 (30%), Positives = 129/244 (52%), Gaps = 25/244 (10%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T +LD +  TD + A  V   +E T    LG+V   + + 
Sbjct: 102 GLPRLIELVDARKTPDTPMMTVHLDGEYATDREKAHEVVWSIEATRILALGDVSTNVAD- 160

Query: 819 FVPDDSFILIKLDMDRIRLLH---LEVDIDSIRYCIERTRGISGHLTVSGH---SFLILK 872
                  +L+++D++   LL       D   +   I +T  I   L V      + +   
Sbjct: 161 -------MLVRIDLNDDTLLERWPTHSDPTEVAEIIAKT--IEDSLGVDARQAGTVIEFG 211

Query: 873 PKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMA 932
           P + S     ++ Q+ + L  +V KG++ I R VI +E+++G  ++ L  EG    D + 
Sbjct: 212 PNEPSYR---ELLQLVERLREIVFKGIEEIERVVIRKEEIDGDEEFVLYTEGSAFGDTLD 268

Query: 933 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTS 991
             GV   + + NN +E+Y+ LG+EAAR TI+ E K  +E  G+  ++ RH MLVAD+MT+
Sbjct: 269 IEGVDASRTTCNNIHEIYRNLGVEAARETIIDETKNTLEEQGLDDVNVRHLMLVADIMTN 328

Query: 992 KGEV 995
            GE+
Sbjct: 329 NGEI 332


>gi|432329278|ref|YP_007247422.1| DNA-directed RNA polymerase, subunit A'' [Aciduliprofundum sp.
            MAR08-339]
 gi|432135987|gb|AGB05256.1| DNA-directed RNA polymerase, subunit A'' [Aciduliprofundum sp.
            MAR08-339]
          Length = 516

 Score =  174 bits (440), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 116/361 (32%), Positives = 180/361 (49%), Gaps = 59/361 (16%)

Query: 1085 QDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFA 1144
            Q K  HG   N F    K     E Y +  ++P  AVG +AAQSIGEPGTQMTL+TFH+A
Sbjct: 158  QAKNEHGLSKNEFNEVIKRTV--EVYRKRSVDPYEAVGIVAAQSIGEPGTQMTLRTFHYA 215

Query: 1145 G-----------EVCEYIEEVFVPDDSFILIKL------DMDRIRLLHLEVD-------I 1180
            G            + E ++   +P    + I L      D DR++ +  +++        
Sbjct: 216  GVAEMNVTLGLPRLIEIVDARSMPSTPVMEIHLKEGIREDEDRVKEVAKKIESTEIIDVA 275

Query: 1181 DSIRYCIERT------------RGISGH---------------LTVSGHSFLILKPKDSS 1213
            D I   ++ +            RG+                  + + G    I  P+ S 
Sbjct: 276  DVITSLVDMSVVIVPDKKKMEGRGVKKEDIVESLGKLKIQKLTVEIEGERIKIKLPEPSY 335

Query: 1214 KSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVK 1273
            K    K+Y + + +  + ++G++GI+RA++ +   +  +++ +  +G NL DV+    V 
Sbjct: 336  K----KLYLLSENIKGLTLRGIKGISRAIVRKS--QDNSEWVIYTQGSNLGDVLDIEEVD 389

Query: 1274 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 1333
              +  +NN  E+   LG+EAAR+ I+ E    +   G+++D RH MLVAD MT  G V  
Sbjct: 390  AARTRTNNIIEIADVLGVEAARNAIIEEALNTLHQQGLNVDIRHIMLVADTMTYNGTVEA 449

Query: 1334 ITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            I RHG+A  KESVL  A+FE TS HL  A   G+ D + GV+E II+G P+ +GTG + L
Sbjct: 450  IGRHGIAGEKESVLARAAFEITSKHLLTAGILGEEDQLRGVAENIIVGQPVTLGTGAVTL 509

Query: 1394 L 1394
            +
Sbjct: 510  V 510



 Score = 89.4 bits (220), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 65/238 (27%), Positives = 123/238 (51%), Gaps = 13/238 (5%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A    STP++  +L +    D D  + V  ++E T + +V + I  +   
Sbjct: 225 GLPRLIEIVDARSMPSTPVMEIHLKEGIREDEDRVKEVAKKIESTEIIDVADVITSLV-- 282

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
           D S +++    D+ ++    V  + I   + + +     + + G    I  P+ S K   
Sbjct: 283 DMSVVIVP---DKKKMEGRGVKKEDIVESLGKLKIQKLTVEIEGERIKIKLPEPSYK--- 336

Query: 882 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
            K+Y + + +  + ++G++GI+RA++ +   +  +++ +  +G NL DV+    V   + 
Sbjct: 337 -KLYLLSENIKGLTLRGIKGISRAIVRKS--QDNSEWVIYTQGSNLGDVLDIEEVDAART 393

Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG 999
            +NN  E+   LG+EAAR+ I+ E    +   G+++D RH MLVAD MT  G V   G
Sbjct: 394 RTNNIIEIADVLGVEAARNAIIEEALNTLHQQGLNVDIRHIMLVADTMTYNGTVEAIG 451


>gi|448482810|ref|ZP_21605581.1| DNA-directed RNA polymerase subunit A'' [Halorubrum arcis JCM 13916]
 gi|445821096|gb|EMA70892.1| DNA-directed RNA polymerase subunit A'' [Halorubrum arcis JCM 13916]
          Length = 404

 Score =  173 bits (439), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 110/349 (31%), Positives = 176/349 (50%), Gaps = 65/349 (18%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIE 1152
            E    +Y + +++P   VG ++AQSIGEPGTQMT+ TFH+AG            + E ++
Sbjct: 52   EGVVNRYEQTRVDPLDPVGTVSAQSIGEPGTQMTMNTFHYAGVAEIDVTQGLPRLIELVD 111

Query: 1153 EVFVPDDSFILIKLD----------------MDRIRLLHL------------EVDIDS-- 1182
                PD   + + LD                ++  R+L L             +D++   
Sbjct: 112  ARKTPDTPMMTVHLDGEYATDREKAHEVVWSIEATRILALGDVSTNVADMLVRIDLNDDT 171

Query: 1183 -----------------IRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQ 1225
                             I   IE + G+         + +   P + S     ++ Q+ +
Sbjct: 172  LLERWPTHSDPTEVAEIIAETIEDSLGVDAR---QAGTVIEFGPNEPSYR---ELLQLVE 225

Query: 1226 LLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEV 1285
             L  +V KG++ I R VI +E+++G  ++ L  EG    D +   GV   + + NN +E+
Sbjct: 226  RLREIVFKGIEEIERVVIRKEEIDGDEEFVLYTEGSAFGDTLDIEGVDASRTTCNNIHEI 285

Query: 1286 YKTLGIEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMKE 1344
            Y+ LG+EAAR TI+ E K  +E  G+  ++ RH MLVAD+MT+ GE+  I RHG++  K+
Sbjct: 286  YRNLGVEAARETIIDETKNTLEEQGLDDVNVRHLMLVADIMTNNGEIESIGRHGISGNKD 345

Query: 1345 SVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            SVL  A+FE T +HL DAA +G+ D + GV E +I G P+++GTG + L
Sbjct: 346  SVLARAAFEVTVNHLLDAAIHGEYDDLDGVIENVIAGKPISMGTGDVDL 394



 Score =  108 bits (271), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 75/246 (30%), Positives = 130/246 (52%), Gaps = 29/246 (11%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T +LD +  TD + A  V   +E T    LG+V   + + 
Sbjct: 102 GLPRLIELVDARKTPDTPMMTVHLDGEYATDREKAHEVVWSIEATRILALGDVSTNVAD- 160

Query: 819 FVPDDSFILIKLDMDRIRLLH--------LEVDIDSIRYCIERTRGISGHLTVSGHSFLI 870
                  +L+++D++   LL          EV  + I   IE + G+         + + 
Sbjct: 161 -------MLVRIDLNDDTLLERWPTHSDPTEV-AEIIAETIEDSLGVDAR---QAGTVIE 209

Query: 871 LKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDV 930
             P + S     ++ Q+ + L  +V KG++ I R VI +E+++G  ++ L  EG    D 
Sbjct: 210 FGPNEPSYR---ELLQLVERLREIVFKGIEEIERVVIRKEEIDGDEEFVLYTEGSAFGDT 266

Query: 931 MATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLM 989
           +   GV   + + NN +E+Y+ LG+EAAR TI+ E K  +E  G+  ++ RH MLVAD+M
Sbjct: 267 LDIEGVDASRTTCNNIHEIYRNLGVEAARETIIDETKNTLEEQGLDDVNVRHLMLVADIM 326

Query: 990 TSKGEV 995
           T+ GE+
Sbjct: 327 TNNGEI 332


>gi|448427504|ref|ZP_21583819.1| DNA-directed RNA polymerase subunit A'' [Halorubrum terrestre JCM
            10247]
 gi|448451258|ref|ZP_21592741.1| DNA-directed RNA polymerase subunit A'' [Halorubrum litoreum JCM
            13561]
 gi|445678191|gb|ELZ30685.1| DNA-directed RNA polymerase subunit A'' [Halorubrum terrestre JCM
            10247]
 gi|445810692|gb|EMA60708.1| DNA-directed RNA polymerase subunit A'' [Halorubrum litoreum JCM
            13561]
          Length = 404

 Score =  173 bits (439), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 110/349 (31%), Positives = 176/349 (50%), Gaps = 65/349 (18%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIE 1152
            E    +Y + +++P   VG ++AQSIGEPGTQMT+ TFH+AG            + E ++
Sbjct: 52   EGVVNRYEQTRVDPLDPVGTVSAQSIGEPGTQMTMNTFHYAGVAEIDVTQGLPRLIELVD 111

Query: 1153 EVFVPDDSFILIKLD----------------MDRIRLLHL------------EVDIDS-- 1182
                PD   + + LD                ++  R+L L             +D++   
Sbjct: 112  ARKTPDTPMMTVHLDGEYATDREKAHEVVWSIEATRILALGDVSTNVADMLVRIDLNDDT 171

Query: 1183 -----------------IRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQ 1225
                             I   IE + G+         + +   P + S     ++ Q+ +
Sbjct: 172  LLERWPTHSDPTEVAEIIAETIEDSLGVDAR---QAGTVIEFGPNEPSYR---ELLQLVE 225

Query: 1226 LLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEV 1285
             L  +V KG++ I R VI +E+++G  ++ L  EG    D +   GV   + + NN +E+
Sbjct: 226  RLREIVFKGIEEIERVVIRKEEIDGDEEFVLYTEGSAFGDTLDIEGVDASRTTCNNIHEI 285

Query: 1286 YKTLGIEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMKE 1344
            Y+ LG+EAAR TI+ E K  +E  G+  ++ RH MLVAD+MT+ GE+  I RHG++  K+
Sbjct: 286  YRNLGVEAARETIIDETKNTLEEQGLDDVNVRHLMLVADIMTNNGEIESIGRHGISGNKD 345

Query: 1345 SVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            SVL  A+FE T +HL DAA +G+ D + GV E +I G P+++GTG + L
Sbjct: 346  SVLARAAFEVTVNHLLDAAIHGEYDDLDGVIENVIAGKPISMGTGDVDL 394



 Score =  108 bits (271), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 75/246 (30%), Positives = 130/246 (52%), Gaps = 29/246 (11%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T +LD +  TD + A  V   +E T    LG+V   + + 
Sbjct: 102 GLPRLIELVDARKTPDTPMMTVHLDGEYATDREKAHEVVWSIEATRILALGDVSTNVAD- 160

Query: 819 FVPDDSFILIKLDMDRIRLLH--------LEVDIDSIRYCIERTRGISGHLTVSGHSFLI 870
                  +L+++D++   LL          EV  + I   IE + G+         + + 
Sbjct: 161 -------MLVRIDLNDDTLLERWPTHSDPTEV-AEIIAETIEDSLGVDAR---QAGTVIE 209

Query: 871 LKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDV 930
             P + S     ++ Q+ + L  +V KG++ I R VI +E+++G  ++ L  EG    D 
Sbjct: 210 FGPNEPSYR---ELLQLVERLREIVFKGIEEIERVVIRKEEIDGDEEFVLYTEGSAFGDT 266

Query: 931 MATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLM 989
           +   GV   + + NN +E+Y+ LG+EAAR TI+ E K  +E  G+  ++ RH MLVAD+M
Sbjct: 267 LDIEGVDASRTTCNNIHEIYRNLGVEAARETIIDETKNTLEEQGLDDVNVRHLMLVADIM 326

Query: 990 TSKGEV 995
           T+ GE+
Sbjct: 327 TNNGEI 332


>gi|284163649|ref|YP_003401928.1| DNA-directed RNA polymerase subunit A'' [Haloterrigena turkmenica DSM
            5511]
 gi|284013304|gb|ADB59255.1| DNA-directed RNA polymerase, subunit A'' [Haloterrigena turkmenica
            DSM 5511]
          Length = 397

 Score =  173 bits (439), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 109/350 (31%), Positives = 182/350 (52%), Gaps = 58/350 (16%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A+A   +Y+  +++P   VG ++AQSIGEPGTQ+T+ TFH+AG            + E +
Sbjct: 48   AKAVEARYLDTRVDPLDPVGTVSAQSIGEPGTQLTMNTFHYAGVAEIDVTQGLPRLIELV 107

Query: 1152 EEVFVPDDSFILIKLD----------------MDRIRLLHL--------------EVDID 1181
            +    PD   + + L+                ++  ++L L               ++ D
Sbjct: 108  DARKTPDTPMMTVYLEDEYAAEREKAHEVVWNIEATKILALGDVSTNVADMRVQISLNED 167

Query: 1182 SIRY----------CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVV 1231
            ++R            IE   G+S   TV   + +   P++ S      + Q+ + L  + 
Sbjct: 168  TLRERMITPEEVAEIIEDNLGVS---TVQQGTEIQFGPEEPSYR---DLLQLVEELRDIT 221

Query: 1232 IKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGI 1291
             KG++ ++R VI  E++E   ++ L  EG    DV+   GV   + + NN +E+++ LGI
Sbjct: 222  FKGIEEVSRVVIRREELEEGEQFVLYTEGSAFGDVLEIEGVDASRTTCNNIHEIHRNLGI 281

Query: 1292 EAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLA 1350
            EAAR  I+ E    +   G+  ++ RH MLVAD+MT++GE+  I RHG++  KESVL  A
Sbjct: 282  EAAREAIIEETNNTLAEQGLDDVNVRHLMLVADMMTNRGEIESIGRHGISGSKESVLARA 341

Query: 1351 SFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS 1400
            +FE T +HL +AA +G+TD + GV+E +I+G P+ +GTG + L     +S
Sbjct: 342  AFEVTVNHLLNAAIHGETDELDGVTENVIVGKPIKLGTGDVDLRMGSTKS 391



 Score = 99.4 bits (246), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 71/238 (29%), Positives = 125/238 (52%), Gaps = 20/238 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T YL+ +   + + A  V   +E T    LG+V   + ++
Sbjct: 99  GLPRLIELVDARKTPDTPMMTVYLEDEYAAEREKAHEVVWNIEATKILALGDVSTNVADM 158

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSK 878
            V     I +  D  R R++  E     +   IE   G+S   TV   + +   P++ S 
Sbjct: 159 RVQ----ISLNEDTLRERMITPE----EVAEIIEDNLGVS---TVQQGTEIQFGPEEPSY 207

Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 938
                + Q+ + L  +  KG++ ++R VI  E++E   ++ L  EG    DV+   GV  
Sbjct: 208 R---DLLQLVEELRDITFKGIEEVSRVVIRREELEEGEQFVLYTEGSAFGDVLEIEGVDA 264

Query: 939 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEV 995
            + + NN +E+++ LGIEAAR  I+ E    +   G+  ++ RH MLVAD+MT++GE+
Sbjct: 265 SRTTCNNIHEIHRNLGIEAAREAIIEETNNTLAEQGLDDVNVRHLMLVADMMTNRGEI 322


>gi|407464207|ref|YP_006775089.1| bifunctional DNA-directed RNA polymerase subunit A'/A'' [Candidatus
           Nitrosopumilus sp. AR2]
 gi|407047395|gb|AFS82147.1| bifunctional DNA-directed RNA polymerase subunit A'/A'' [Candidatus
           Nitrosopumilus sp. AR2]
          Length = 1263

 Score =  173 bits (439), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 100/277 (36%), Positives = 154/277 (55%), Gaps = 35/277 (12%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D D+V+FNRQPSLH++SIMAH  +VLP +TFR +  VC PYNADFDGDEMN+H+PQ+EE
Sbjct: 415 ADGDIVMFNRQPSLHQMSIMAHYVRVLPGKTFRLHPSVCPPYNADFDGDEMNLHVPQSEE 474

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           ARAEA+              +LM  +  L++PR G  +I A +DF+TG YLLT+ +    
Sbjct: 475 ARAEAI--------------LLMRVQDQLISPRYGGPIIGALRDFVTGAYLLTKDD---- 516

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
                   +TL         ++  ++     P    +    +TGKQ+FSL L  +     
Sbjct: 517 --------TTLSVQEFSNYAMLGGYTEPLPKPATKTKDGPAYTGKQLFSLFLPKD----F 564

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           N  L +K    T   E   +D  V+++N EL++G +DK+++G+    +V + + +D+G  
Sbjct: 565 NYVLTSKWSKGTKGPE---KD--VVIKNGELISGVIDKTSIGAEEPESVLHRITKDYGNA 619

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           V    +  +  M   ++ + GFS G GD+   +  VQ
Sbjct: 620 VGKNFLNSILIMVKQFITHYGFSYGYGDLEVPEKNVQ 656



 Score =  114 bits (285), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 75/255 (29%), Positives = 125/255 (49%), Gaps = 41/255 (16%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           +++ S  +I +   Y +D    P+  GL+D R+GT +    C TCG   + C GHFG+I+
Sbjct: 22  IRKYSVAEITAPETYDEDGM--PVQGGLMDGRLGTLEPGQKCLTCGNTAARCPGHFGHIE 79

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGF-RAKLRNPALSYLVRKSLKK 211
           L  P+ HI +   +  +LQS C+  +CAR+ + +E    F R K ++ A + + +K + +
Sbjct: 80  LAEPILHIAFIDNIYKLLQSTCR--SCARLKVPQEDLEAFKRIKDKHAAYTVVSQKRIPE 137

Query: 212 KILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFN 271
           +I+E  KK   CPHCG+                +Y+    K    VE             
Sbjct: 138 QIIEKAKKAKECPHCGKT---------------QYELVFTKPTIFVE------------K 170

Query: 272 PEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIR 331
            EI  H+       L P+ + + F  I  ED+ LL  +   ++P   IL  L VPP  +R
Sbjct: 171 TEIGEHR-------LLPITIRERFSQILDEDLELLSYDPITARPEWFILQALPVPPVTVR 223

Query: 332 PSVI--SDLKSDNDV 344
           PS+I  + ++S++D+
Sbjct: 224 PSIILETGIRSEDDL 238



 Score =  109 bits (273), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 59/173 (34%), Positives = 101/173 (58%), Gaps = 4/173 (2%)

Query: 1229 SVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKT 1288
            +  +KGV  I R  + ++D E V +      G N+  V+   G+      +NN +E+  T
Sbjct: 1095 NTTVKGVPDIERVTLVQKDDEWVIQ----TTGSNIAKVLEVKGIDKKNVRTNNVFEIAGT 1150

Query: 1289 LGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLN 1348
            LGIEAAR++++ E+   + + G+ +D R+ MLV+DLM S+G +  I RHG+A  K+SVL 
Sbjct: 1151 LGIEAARNSLIDELNHTLGDQGLEVDNRYIMLVSDLMCSRGYMQQIGRHGIAGTKDSVLA 1210

Query: 1349 LASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSE 1401
             A+FE T   +  AA  G+ + + G++E +I+G  + +G+G + L   V + +
Sbjct: 1211 RAAFEITVPTIAHAALGGEVEQLKGITENVIVGSNIPIGSGTVDLYMQVSKKK 1263



 Score = 84.7 bits (208), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 35/58 (60%), Positives = 48/58 (82%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
             GFV++++ +GLT  EFFFH MGGREGLVDTAV+T ++GYMQRRL+ +LE + ++YD
Sbjct: 775 AHGFVKSNYRTGLTALEFFFHAMGGREGLVDTAVRTQQSGYMQRRLINALEHIRLEYD 832



 Score = 73.2 bits (178), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 61/231 (26%), Positives = 111/231 (48%), Gaps = 14/231 (6%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTL-GEVCEYIEEVFVPD 822
            G+PR+ E+++A +   TP +  YLD+++     + ++  + R  L  +V   I       
Sbjct: 974  GLPRLIELVDARKKPVTPTMDIYLDEESKKSREKAIE--VARNVLQTKVSALIANTET-- 1029

Query: 823  DSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNS 882
            D    I+L +   RL      I  +   +   +     L  +G   + L   D + +  +
Sbjct: 1030 DYSTNIQLILSPNRLKERGCSIAEVEAALSSNKKFK--LETTGE-LITLNLVDEADTATA 1086

Query: 883  KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCS 942
               + K L  +  +KGV  I R  + ++D E V +      G N+  V+   G+      
Sbjct: 1087 IAIRNKVL--NTTVKGVPDIERVTLVQKDDEWVIQ----TTGSNIAKVLEVKGIDKKNVR 1140

Query: 943  SNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
            +NN +E+  TLGIEAAR++++ E+   + + G+ +D R+ MLV+DLM S+G
Sbjct: 1141 TNNVFEIAGTLGIEAARNSLIDELNHTLGDQGLEVDNRYIMLVSDLMCSRG 1191



 Score = 62.8 bits (151), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 27/36 (75%), Positives = 30/36 (83%)

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            Y  AQ+EP  AVG + AQSIGEPGTQMTL+TFHFAG
Sbjct: 930  YNNAQVEPGQAVGIITAQSIGEPGTQMTLRTFHFAG 965


>gi|448627102|ref|ZP_21671777.1| DNA-directed RNA polymerase subunit A'' [Haloarcula vallismortis ATCC
            29715]
 gi|445759730|gb|EMA11006.1| DNA-directed RNA polymerase subunit A'' [Haloarcula vallismortis ATCC
            29715]
          Length = 395

 Score =  173 bits (439), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 110/350 (31%), Positives = 180/350 (51%), Gaps = 65/350 (18%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A+A   +Y+  +++P   VG ++AQSIGEPGTQMT+ TFH+AG            + E +
Sbjct: 45   AKAVESRYLDTRVDPLDPVGTVSAQSIGEPGTQMTMNTFHYAGVAEIDVTQGLPRLIELV 104

Query: 1152 EEVFVPDDSFILIKLD----------------MDRIRLLHL------------EVDI--- 1180
            +    PD   + + LD                ++  R+L L            E+D+   
Sbjct: 105  DARKTPDTPMMTVHLDEEYADDRERAHEVVWKIEATRILALGDISTNVADMLVEIDLNED 164

Query: 1181 ----------------DSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMK 1224
                            + I   IE   G+S   T    + +   P++ S      + Q+ 
Sbjct: 165  TLLERWPTVNDTDAIAEEIAETIESNLGVS---TRQVGTVIEFGPEEPSYR---DLLQLV 218

Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYE 1284
            + L  +V KG++ I R VI +E+ +   ++ L  EG +  +V+   GV   + + NN +E
Sbjct: 219  EELREIVFKGIEEITRVVIRKEETDNGEEFVLYTEGSDFGEVLDIEGVDASRTTCNNIHE 278

Query: 1285 VYKTLGIEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMK 1343
            +Y+ LG+EAAR T++ E    +E  G+  ++ RH MLVAD+MT++G +  I RHG++  K
Sbjct: 279  IYRELGVEAARETLINETMNTLEEQGLDDVNVRHLMLVADIMTNEGTIESIGRHGISGSK 338

Query: 1344 ESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            +SVL  A+FE T +HL DAA +G+ D + GV+E +I+G P+ +GTG + L
Sbjct: 339  DSVLARAAFEVTVNHLLDAAIHGEVDELDGVTENVIVGKPIKLGTGDVNL 388



 Score =  103 bits (256), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 72/244 (29%), Positives = 132/244 (54%), Gaps = 25/244 (10%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T +LD++   D + A  V  ++E T    LG++   + + 
Sbjct: 96  GLPRLIELVDARKTPDTPMMTVHLDEEYADDRERAHEVVWKIEATRILALGDISTNVAD- 154

Query: 819 FVPDDSFILIKLDMDRIRLLH---LEVDIDSIRYCIERTRGISGHLTVSGH---SFLILK 872
                  +L+++D++   LL       D D+I   I  T  I  +L VS     + +   
Sbjct: 155 -------MLVEIDLNEDTLLERWPTVNDTDAIAEEIAET--IESNLGVSTRQVGTVIEFG 205

Query: 873 PKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMA 932
           P++ S      + Q+ + L  +V KG++ I R VI +E+ +   ++ L  EG +  +V+ 
Sbjct: 206 PEEPSYR---DLLQLVEELREIVFKGIEEITRVVIRKEETDNGEEFVLYTEGSDFGEVLD 262

Query: 933 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTS 991
             GV   + + NN +E+Y+ LG+EAAR T++ E    +E  G+  ++ RH MLVAD+MT+
Sbjct: 263 IEGVDASRTTCNNIHEIYRELGVEAARETLINETMNTLEEQGLDDVNVRHLMLVADIMTN 322

Query: 992 KGEV 995
           +G +
Sbjct: 323 EGTI 326


>gi|126460695|ref|YP_001056973.1| DNA-directed RNA polymerase subunit A' [Pyrobaculum calidifontis
           JCM 11548]
 gi|126250416|gb|ABO09507.1| DNA-directed RNA polymerase, subunit A' [Pyrobaculum calidifontis
           JCM 11548]
          Length = 884

 Score =  173 bits (439), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 105/273 (38%), Positives = 151/273 (55%), Gaps = 41/273 (15%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++S+M H  KVLP RTFR +  VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 423 DGDIVLFNRQPSLHRVSMMGHLVKVLPGRTFRLHLAVCPPYNADFDGDEMNLHVPQTEEA 482

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+ LM  + +++TPR G  +I A QD+I G YLL+ K+ F  +
Sbjct: 483 RAE--------------ARTLMLVEKHIITPRYGGAIIGARQDYIIGAYLLSHKSTFLTK 528

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNP--VVFVRTAVIWTGKQIFSLILKPNRDCP 518
            +   +A  L A  S            + +P     +    +WTGKQI S  L  + +  
Sbjct: 529 KE---VAYLLGAGKS------------AEDPPEPAILHPVELWTGKQIISHFLPKDLNWV 573

Query: 519 VNANLKTKGR-AYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFG 577
                K+K + AYT     C  D ++I+ N  L+ G +DK ++G+    ++++ + RD+ 
Sbjct: 574 QPTAFKSKCQDAYT-----CDGDEWIIVINGNLVKGVLDKKSIGAEQVDSLWHRIARDYP 628

Query: 578 EDVAVTAMWRLSRMTSF--YLMNRGFSIGIGDV 608
            +VA    W  S +  F  +L  RGF+ G+  V
Sbjct: 629 PEVA--GRWLDSSLRLFLRWLDLRGFTFGMDSV 659



 Score =  117 bits (293), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 74/257 (28%), Positives = 130/257 (50%), Gaps = 40/257 (15%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D +++ S +++ +  +Y  D    P+  G+ DRR+G ++  A C TCGQ    C GHFG+
Sbjct: 26  DMIRKYSVMEVTTSEVY--DEGGLPVRGGIADRRLGVSEPGARCETCGQTHDVCPGHFGH 83

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKL-RNPALSYLVRKSL 209
           I+L  PV H+GY R + ++L++ C  P C R++L +E+   ++ +L R      L+ ++L
Sbjct: 84  IELVKPVIHVGYARIIYDVLRATC--PNCGRIMLKDEEIKRYKERLDRLKGRWRLLAQNL 141

Query: 210 KKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVK 269
           ++KI +   + + CPHCG                  YK R K            +     
Sbjct: 142 QEKIKKKAAERATCPHCG------------------YK-RNK----------VRFERPYY 172

Query: 270 FNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           F  E E     G +  L+P  + +    +P +D+ LL +N  +++P   IL  L VPP  
Sbjct: 173 FYEETEN----GALVKLDPETLRERLAKVPNDDLELLGINPVVARPEWAILKVLPVPPPH 228

Query: 330 IRPSVI--SDLKSDNDV 344
           +RPS+   + ++S++D+
Sbjct: 229 VRPSIQLETGIRSEDDL 245



 Score = 82.8 bits (203), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 36/67 (53%), Positives = 50/67 (74%), Gaps = 2/67 (2%)

Query: 613 GFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFD 672
           GFV++ F  GL+P E+FFH   GR+GL+DTAV+TA++GYMQRRL+ +L+D+ V YD +  
Sbjct: 788 GFVKSCFRCGLSPVEYFFHAAAGRDGLIDTAVRTAQSGYMQRRLINALQDVYVAYDGT-- 845

Query: 673 AAFYGQT 679
             F G T
Sbjct: 846 VRFSGST 852



 Score = 44.3 bits (103), Expect = 0.53,   Method: Compositional matrix adjust.
 Identities = 21/56 (37%), Positives = 34/56 (60%), Gaps = 3/56 (5%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           + LM  + +++TPR G  +I A QD+I G YLL+ K+ F  + +   +A  L AG+
Sbjct: 487 RTLMLVEKHIITPRYGGAIIGARQDYIIGAYLLSHKSTFLTKKE---VAYLLGAGK 539


>gi|315230007|ref|YP_004070443.1| DNA-directed RNA polymerase subunit A'' [Thermococcus barophilus MP]
 gi|315183035|gb|ADT83220.1| DNA-directed RNA polymerase subunit A'' [Thermococcus barophilus MP]
          Length = 394

 Score =  173 bits (439), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 120/379 (31%), Positives = 192/379 (50%), Gaps = 62/379 (16%)

Query: 1071 DKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIG 1130
            +K  + L E+++ + +K    ++      A   E  +E Y  A +EP  A+G +AAQSIG
Sbjct: 20   EKTKEELYEKLVKYNEKYKLKKKEV---EAIIEEVVKE-YENAVVEPGEAIGTVAAQSIG 75

Query: 1131 EPGTQMTLKTFHFAG-----------EVCEYIEEVFVPDDSFILIKLD----MDRIRLLH 1175
            EP TQMTL TFH+AG            + E ++    P    + + LD     DR + L 
Sbjct: 76   EPSTQMTLNTFHYAGVAEINVTLGLPRIIEIVDARKNPSTPIMTVYLDEEHRYDREKALE 135

Query: 1176 ----------------LEVDIDSIRYCIE------RTRGIS--------------GHLTV 1199
                            + +DI ++ + +E         G++                  V
Sbjct: 136  VARKIEGTTLINLAQSMTMDILNMEFVVEIDPERLERSGLTMEKIKKKLESSFKTAEFEV 195

Query: 1200 SGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVE 1259
             G++ LI++PK + K   S + ++ + + S  +KG+ G+ + +I +E  E    Y +  E
Sbjct: 196  DGYT-LIVRPKKAEKL--SDLRRIAEKVKSHRLKGLSGVGKTIIRKEGDE----YVIYTE 248

Query: 1260 GDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPM 1319
            G N + V+   GV   +  +NN +E+ + LGIEAAR+ I+ EI   M+  G+ +D RH M
Sbjct: 249  GSNFKQVLKVPGVDPTRTRTNNIHEIAEVLGIEAARNAIIEEIVNTMQEQGLEVDVRHIM 308

Query: 1320 LVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECII 1379
            LVAD+MT  G V  I RHG+     SVL  A+FE T  HLF+AA  G+ D ++GV E ++
Sbjct: 309  LVADIMTLDGIVRPIGRHGVVGDPASVLARAAFEITVQHLFEAAERGEVDPLNGVVENVL 368

Query: 1380 MGLPMNVGTGLIKLLQAVP 1398
            +G P+ VGTG+++L   +P
Sbjct: 369  IGQPVPVGTGIVRLAMRLP 387



 Score =  112 bits (281), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 77/232 (33%), Positives = 134/232 (57%), Gaps = 14/232 (6%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PRI EI++A +N STPI+T YLD++   D + A  V  ++E TTL  + + +  + + 
Sbjct: 99  GLPRIIEIVDARKNPSTPIMTVYLDEEHRYDREKALEVARKIEGTTLINLAQSMT-MDIL 157

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
           +  F++   ++D  RL    + ++ I+  +E +   +    V G++ LI++PK + K   
Sbjct: 158 NMEFVV---EIDPERLERSGLTMEKIKKKLESSFK-TAEFEVDGYT-LIVRPKKAEKL-- 210

Query: 882 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
           S + ++ + + S  +KG+ G+ + +I +E  E    Y +  EG N + V+   GV   + 
Sbjct: 211 SDLRRIAEKVKSHRLKGLSGVGKTIIRKEGDE----YVIYTEGSNFKQVLKVPGVDPTRT 266

Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
            +NN +E+ + LGIEAAR+ I+ EI   M+  G+ +D RH MLVAD+MT  G
Sbjct: 267 RTNNIHEIAEVLGIEAARNAIIEEIVNTMQEQGLEVDVRHIMLVADIMTLDG 318



 Score = 42.0 bits (97), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 19/54 (35%), Positives = 36/54 (66%), Gaps = 2/54 (3%)

Query: 656 LVKSLEDLCVQYDMSFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 709
           L ++  ++ VQ+   F+AA  G+ D ++GV E +++G P+ VGTG+++L   +P
Sbjct: 336 LARAAFEITVQH--LFEAAERGEVDPLNGVVENVLIGQPVPVGTGIVRLAMRLP 387


>gi|167043884|gb|ABZ08573.1| putative RNA polymerase Rpb1, domain 2 [uncultured marine
           crenarchaeote HF4000_APKG3E18]
          Length = 1273

 Score =  173 bits (438), Expect = 8e-40,   Method: Compositional matrix adjust.
 Identities = 106/344 (30%), Positives = 179/344 (52%), Gaps = 57/344 (16%)

Query: 283 IQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIR--------PSV 334
           +Q    L + ++     +E +  L++N     P+       +V P+ ++        PS+
Sbjct: 349 VQIATKLTIPEIVTEWNIEKLKKLVVNG----PNTFPGVNYIVRPDGVKIRLDFVEDPSI 404

Query: 335 ISDLK----------SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNAD 384
           I+D            SD D+VLFNRQPSLH++SIMAH  +VLP +TFR +  VC PYNAD
Sbjct: 405 IADSLEIGYLVERHLSDGDIVLFNRQPSLHQMSIMAHHVRVLPGKTFRLHPSVCPPYNAD 464

Query: 385 FDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDF 444
           FDGDEMN+H+PQ+EEARAEA+              +LM  +  L++PR G  +I   +DF
Sbjct: 465 FDGDEMNLHVPQSEEARAEAM--------------LLMRVQEQLISPRFGGPIIGGLRDF 510

Query: 445 ITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGK 504
           ITG YLLT+ +    + +    A            ++ R+  +   P +  +  +++TGK
Sbjct: 511 ITGVYLLTKDDTTLTKQEFSNYA------------MLGRYDGKLPEPKINSKNGLLYTGK 558

Query: 505 QIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGG 564
           Q+FSL L      P + N     + ++       +D  V+++N EL++G +DK+ +G+  
Sbjct: 559 QLFSLFL------PSDFNFVMTSK-WSRGTNGKQKD--VVIKNGELVSGVIDKTGIGAEE 609

Query: 565 KANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
             ++ + + +D+G + A   +  +  +   ++ + GFS G  D+
Sbjct: 610 PESILHRIAKDYGNEKANKFLNSVLIIIKQFITDYGFSYGYSDL 653



 Score =  114 bits (285), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 61/163 (37%), Positives = 99/163 (60%), Gaps = 4/163 (2%)

Query: 1232 IKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGI 1291
            +KGV  I R  + EE+ +    + +   G NL  V++  GV      +NN +E+   LGI
Sbjct: 1108 VKGVPDIERLTLKEENGD----WLIQTTGSNLAKVISVKGVDKNNVRTNNVFEISTVLGI 1163

Query: 1292 EAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLAS 1351
            EAAR++++ E+K  +EN G+ +D R+ MLVADLM  KG +  I RHG+A  K+SVL  A+
Sbjct: 1164 EAARTSLINELKSTLENQGLEVDVRYLMLVADLMCHKGYLQQIGRHGIAGSKDSVLARAA 1223

Query: 1352 FENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            FE T   + +AA  G+ + + G++E +I+G  + +G+G + + 
Sbjct: 1224 FEITVPTIANAAKLGEIEELKGITENVIVGSLIPIGSGTVDIF 1266



 Score =  105 bits (261), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 73/262 (27%), Positives = 123/262 (46%), Gaps = 43/262 (16%)

Query: 87  VTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVG 146
           V   + +++ S  +I +   Y +D     +  GL+D R+GT +    C TCG   + C G
Sbjct: 21  VWSPNEIRKYSVAEITAPETYDEDGM--AVQGGLMDGRLGTLEPGQKCLTCGNTSARCPG 78

Query: 147 HFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGF-RAKLRNPALSYLV 205
           HFG+++L  PV HI +   +  +L + C+   C+R+ + +E    F + K  + + + L 
Sbjct: 79  HFGHVELAEPVLHIAFIDNIHKLLNATCR--ACSRLKVPQEVLDEFSKFKKYSASFTVLS 136

Query: 206 RKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYN 265
           RK + ++I E  KK   CPHCG+I                                   N
Sbjct: 137 RKRIPEQIFEKAKKSKECPHCGKIQ----------------------------------N 162

Query: 266 EAVKFNPEIEAHK-KFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLL 324
           + +   P I   K K G  + L P+ + + F  I  +D+ LL  N + ++P   IL  L 
Sbjct: 163 DLIFTKPTIFIEKTKLGENRLL-PITIRERFSQITDDDLRLLNYNVDTARPEWFILQALP 221

Query: 325 VPPNCIRPSVI--SDLKSDNDV 344
           VPP  +RPS+I  S ++S++D+
Sbjct: 222 VPPVTVRPSIILESGIRSEDDL 243



 Score = 82.0 bits (201), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 34/57 (59%), Positives = 46/57 (80%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFV+++F  GL+  EFFFH MGGREGLVDTAV+T ++GYMQRRL+ + E + ++YD
Sbjct: 781 HGFVKSNFRDGLSVLEFFFHAMGGREGLVDTAVRTQQSGYMQRRLINAFEHIRLEYD 837



 Score = 79.7 bits (195), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 66/236 (27%), Positives = 113/236 (47%), Gaps = 19/236 (8%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLE------RTTLGEVCEYIEE 817
            G+PRI E+++A +  STP +  YLDKD+        +  ++      +TT+ ++     E
Sbjct: 979  GLPRIIELVDARKKPSTPSMDIYLDKDSKSSKEEKKEKAIQIAREILQTTVADLLTRSAE 1038

Query: 818  VFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSS 877
                 D    I L +D  RL      +D I   +E  +        +  +  ++   D+ 
Sbjct: 1039 T----DYQTKITLTIDNNRLKIRGCLLDDIMSALETNKKFELERDNNTITLQLVTESDAP 1094

Query: 878  KSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVK 937
                  +  ++  +    +KGV  I R  + EE+ +    + +   G NL  V++  GV 
Sbjct: 1095 T-----VAALRNKVLKTTVKGVPDIERLTLKEENGD----WLIQTTGSNLAKVISVKGVD 1145

Query: 938  GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
                 +NN +E+   LGIEAAR++++ E+K  +EN G+ +D R+ MLVADLM  KG
Sbjct: 1146 KNNVRTNNVFEISTVLGIEAARTSLINELKSTLENQGLEVDVRYLMLVADLMCHKG 1201



 Score = 58.2 bits (139), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 25/38 (65%), Positives = 31/38 (81%)

Query: 1108 EKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            E Y ++++EP  AVG + AQSIGEPGTQMTL+TFH AG
Sbjct: 933  ELYDKSKVEPGQAVGIVTAQSIGEPGTQMTLRTFHTAG 970


>gi|124485980|ref|YP_001030596.1| hypothetical protein Mlab_1160 [Methanocorpusculum labreanum Z]
 gi|124363521|gb|ABN07329.1| DNA-directed RNA polymerase, subunit A'' [Methanocorpusculum
            labreanum Z]
          Length = 504

 Score =  173 bits (438), Expect = 8e-40,   Method: Compositional matrix adjust.
 Identities = 118/341 (34%), Positives = 174/341 (51%), Gaps = 59/341 (17%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFVP 1157
            +Y R +++P  AVG  AA SIGEPGTQMT++TFH+AG            + E ++    P
Sbjct: 161  EYERTRVQPCEAVGINAAHSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIMDARKEP 220

Query: 1158 DDSFILIKLDMD-------------RIRL--LH----LEVDIDSIRYCIERTRGISGHLT 1198
                + I LD D             +I    LH    +E DI  +   ++  + +     
Sbjct: 221  STPTMTIFLDKDYRESRDKAREVSWKIEAAPLHEFGDIETDIAEMCVLVQVNKEVCKKRK 280

Query: 1199 VSGHSFLI-----LKPKDSSKSF----------------NSKMYQ----MKQLLPSVVIK 1233
            ++    L      +K K   + F                N   YQ    + + +  V+++
Sbjct: 281  IAVSEVLARAPQKIKDKRHYRDFEVEVDEANGVLKFLPKNEDSYQNLFQLAEHVRQVIVQ 340

Query: 1234 GVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEA 1293
            G+  I R V+ +E+ E    Y L  EG NL+DV    GV   +  +NN  E+  TLG+EA
Sbjct: 341  GIDDIKRVVVRKENDE----YILHTEGSNLKDVFEIDGVDCTRTRTNNISEIASTLGVEA 396

Query: 1294 ARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFE 1353
            ARS I+ E    ++  G+S+D RH MLV+D+M   GEV  I RHG+A  KESVL+ ASFE
Sbjct: 397  ARSAIIYEAFTTLKEQGISVDLRHIMLVSDIMCMDGEVKQIGRHGIAGEKESVLSRASFE 456

Query: 1354 NTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
             T +HL DAA   + D +SGV+E +I+G P+ +GTG +KL+
Sbjct: 457  VTVNHLLDAAVAHEYDELSGVTENVIVGQPILLGTGDVKLM 497



 Score =  103 bits (256), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 76/239 (31%), Positives = 124/239 (51%), Gaps = 17/239 (7%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTL---GEVCEYIEEV 818
           G+PR+ EI++A +  STP +T +LDKD     D AR V  ++E   L   G++   I E+
Sbjct: 206 GLPRLIEIMDARKEPSTPTMTIFLDKDYRESRDKAREVSWKIEAAPLHEFGDIETDIAEM 265

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILK--PKDS 876
            V     + +  ++ + R + +   +      I+  R           +  +LK  PK+ 
Sbjct: 266 CV----LVQVNKEVCKKRKIAVSEVLARAPQKIKDKRHYRDFEVEVDEANGVLKFLPKNE 321

Query: 877 SKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGV 936
               N  ++Q+ + +  V+++G+  I R V+ +E+ E    Y L  EG NL+DV    GV
Sbjct: 322 DSYQN--LFQLAEHVRQVIVQGIDDIKRVVVRKENDE----YILHTEGSNLKDVFEIDGV 375

Query: 937 KGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
              +  +NN  E+  TLG+EAARS I+ E    ++  G+S+D RH MLV+D+M   GEV
Sbjct: 376 DCTRTRTNNISEIASTLGVEAARSAIIYEAFTTLKEQGISVDLRHIMLVSDIMCMDGEV 434


>gi|352682852|ref|YP_004893376.1| DNA-directed RNA polymerase subunit A' [Thermoproteus tenax Kra 1]
 gi|350275651|emb|CCC82298.1| DNA-directed RNA polymerase subunit A' [Thermoproteus tenax Kra 1]
          Length = 883

 Score =  172 bits (437), Expect = 9e-40,   Method: Compositional matrix adjust.
 Identities = 101/267 (37%), Positives = 150/267 (56%), Gaps = 35/267 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+ LFNRQPSLH++S+M H  +VLP RTFR +  VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 422 DGDIALFNRQPSLHRVSMMGHIVRVLPGRTFRLHLAVCPPYNADFDGDEMNLHIPQTEEA 481

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+ LM  + ++VTPR G  +I A QD+I G YLL++K     +
Sbjct: 482 RAE--------------ARTLMLVQEHIVTPRYGGAIIGARQDYIIGAYLLSRKTTLLTK 527

Query: 461 AQTMRIASTL-IADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            +   +   + + D      I+        +PV       +WTGKQI S+ L  + +   
Sbjct: 528 KEAAFLVGAMKLEDELPEPAIL--------HPV------ELWTGKQIISMTLPRDFNWVQ 573

Query: 520 NANLKTKGRAYTANEEF-CHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
               K+     T  E + C +D ++I+ N  LLAG++DK ++G+    ++++ + RD+  
Sbjct: 574 PTAFKS-----TCKEPYTCEKDEWIIIINGNLLAGTLDKKSIGAEQVDSLWHRIARDYSS 628

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGI 605
           DVA   +    R+   +L  RGFS+G+
Sbjct: 629 DVARRWLDSSLRLFLRFLDLRGFSMGL 655



 Score =  116 bits (290), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 75/257 (29%), Positives = 131/257 (50%), Gaps = 40/257 (15%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D +++ S ++I +  +Y  D    P+  GL+DRR+G  +  A C TCGQ+   C GHFG+
Sbjct: 25  DLIRRYSTLEITTSEIY--DEGGLPVRSGLMDRRLGVAEPGAKCETCGQSYDVCPGHFGH 82

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSY-LVRKSL 209
           I+L  PV H+ + R + ++L++ C  P C R++L +E+   +  +L+     + L+  +L
Sbjct: 83  IELAKPVIHVEFARFIYDVLRATC--PHCGRIMLKDEEIRRYSERLQRLKGRWKLLASNL 140

Query: 210 KKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVK 269
            +KIL    + + CPHCG               +++ K R ++           YN    
Sbjct: 141 HEKILRKAAERTTCPHCG---------------YKRNKIRFERP----------YN---- 171

Query: 270 FNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
           F  E E     G +  L+P  VL+    +P  D+ LL ++   ++P   IL  L VPP  
Sbjct: 172 FYEETET----GALIKLDPETVLERLVKVPNSDLELLGIDPTSARPEWAILRVLPVPPPH 227

Query: 330 IRPSVI--SDLKSDNDV 344
           +RPS+   + ++S++D+
Sbjct: 228 VRPSIQLETGIRSEDDL 244



 Score = 89.7 bits (221), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 38/65 (58%), Positives = 52/65 (80%), Gaps = 1/65 (1%)

Query: 605 IGDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDL 663
           +GD+ P   GFV++SF  GLTP E+FFH  GGR+GL+DTAV+TA++GYMQRR++ +L+D 
Sbjct: 778 VGDIGPFSGGFVRSSFKRGLTPIEYFFHAAGGRDGLIDTAVRTAQSGYMQRRIINALQDA 837

Query: 664 CVQYD 668
            V YD
Sbjct: 838 YVAYD 842


>gi|330833902|ref|YP_004408630.1| DNA-directed RNA polymerase subunit A'' [Metallosphaera cuprina Ar-4]
 gi|329566041|gb|AEB94146.1| DNA-directed RNA polymerase subunit A'' [Metallosphaera cuprina Ar-4]
          Length = 392

 Score =  172 bits (437), Expect = 9e-40,   Method: Compositional matrix adjust.
 Identities = 112/340 (32%), Positives = 169/340 (49%), Gaps = 64/340 (18%)

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFVPD 1158
            Y+ +   P  A+G +AAQSIGEPGTQMTL+TFHFAG            + E ++   +P 
Sbjct: 56   YLSSLAHPGEAIGVVAAQSIGEPGTQMTLRTFHFAGVRELNVTLGLPRLIEIVDSRKIPS 115

Query: 1159 DSFILIKL------DMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFL------- 1205
               + I L      D D+   +   ++   + + +E       +L V+G   +       
Sbjct: 116  TPMMTIYLTSEYAKDKDKALEVARRIEYTRVEHVVEAV-----NLDVAGMGIILKFDREL 170

Query: 1206 ------------------------ILKPKDSSKSFN-------SKMYQMKQLLPSVVIKG 1234
                                    I +P D + S         + ++++++ + S  IKG
Sbjct: 171  LEDKGLTTDDIEKVIKKLKLGEYSIDRPDDYTISIYFENMDTITGLFKIREKILSTKIKG 230

Query: 1235 VQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAA 1294
            ++GI RA++ +   E    Y ++ +G NL  V+   GV   +  +NN +EV   LGIEA 
Sbjct: 231  IKGIKRAIVQKRGEE----YVIVTDGSNLEGVLGVKGVDVSRIETNNLHEVENVLGIEAV 286

Query: 1295 RSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFEN 1354
            R  I  EIK V+E+ G+ +D RH  LV+D+MT  GEV  I RHG+   K SVL  A+FE 
Sbjct: 287  RELITKEIKKVLEDQGLDVDIRHIELVSDIMTRTGEVKQIGRHGVTGEKTSVLARAAFEV 346

Query: 1355 TSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            T  HL DAA  G  +   GV E II+G P+ +GTG+++LL
Sbjct: 347  TVKHLLDAAARGDMEEFKGVVENIIIGQPVKLGTGMVELL 386



 Score =  106 bits (265), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 81/245 (33%), Positives = 128/245 (52%), Gaps = 34/245 (13%)

Query: 764 GVPRIKEIINASRNISTPIITAYL------DKDTDLDYARIVKGRLERTTLGEVCEYIEE 817
           G+PR+ EI+++ +  STP++T YL      DKD  L+ AR    R+E T      E++ E
Sbjct: 100 GLPRLIEIVDSRKIPSTPMMTIYLTSEYAKDKDKALEVAR----RIEYTR----VEHVVE 151

Query: 818 VFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSS 877
               D + + I L  DR  L    +  D I   I++       L +  +S  I +P D +
Sbjct: 152 AVNLDVAGMGIILKFDRELLEDKGLTTDDIEKVIKK-------LKLGEYS--IDRPDDYT 202

Query: 878 KSFN-------SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDV 930
            S         + ++++++ + S  IKG++GI RA++ +   E    Y ++ +G NL  V
Sbjct: 203 ISIYFENMDTITGLFKIREKILSTKIKGIKGIKRAIVQKRGEE----YVIVTDGSNLEGV 258

Query: 931 MATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMT 990
           +   GV   +  +NN +EV   LGIEA R  I  EIK V+E+ G+ +D RH  LV+D+MT
Sbjct: 259 LGVKGVDVSRIETNNLHEVENVLGIEAVRELITKEIKKVLEDQGLDVDIRHIELVSDIMT 318

Query: 991 SKGEV 995
             GEV
Sbjct: 319 RTGEV 323


>gi|298674727|ref|YP_003726477.1| DNA-directed RNA polymerase subunit A' [Methanohalobium evestigatum
           Z-7303]
 gi|298287715|gb|ADI73681.1| DNA-directed RNA polymerase subunit A' [Methanohalobium evestigatum
           Z-7303]
          Length = 881

 Score =  172 bits (437), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 98/269 (36%), Positives = 149/269 (55%), Gaps = 33/269 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLHK+SIMAH  KVLP++TFR N  VC PYNADFDGDEMN+H+ QTEEA
Sbjct: 412 DGDIVIFNRQPSLHKMSIMAHHVKVLPYKTFRLNPAVCPPYNADFDGDEMNLHVLQTEEA 471

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A++LM  + N+++PR G  +I    D I+G +LLT+ +   ++
Sbjct: 472 RAE--------------AEILMKIQENILSPRFGGPIIGGIHDHISGMFLLTRTDNDISK 517

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRT--AVIWTGKQIFSLILKPNRDCP 518
                         +D   ++++   R        R      WTGKQIFS +L  + +  
Sbjct: 518 --------------NDALDLLRKSHIRQLPEPAGYRDDGEPYWTGKQIFSQLLPDDLNLE 563

Query: 519 VNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
             A + +K      N E C  D+YVI+ N EL+ G++D+  +G+  K ++   +++++G 
Sbjct: 564 YVAEVCSK--CDECNRENCENDAYVIIENGELITGTIDEKGIGA-FKGHIVDKIVKEYGS 620

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
             +   +  ++R+    +M  G S GI D
Sbjct: 621 TKSAEFIDDMTRLAIRAIMRSGLSFGISD 649



 Score =  106 bits (265), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 70/254 (27%), Positives = 119/254 (46%), Gaps = 44/254 (17%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           V++ S   I++ + Y  D    PI  GL+D R+G       C TCG    DC GHFG+I+
Sbjct: 24  VRKMSVTPIITADTY--DDDGYPIDMGLMDMRLGVIDPGLICKTCGSRAGDCPGHFGHIE 81

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKK 212
           L  PV H+G+ + ++  L+SIC+N  C+  LL  ++   +  +L+   +       L   
Sbjct: 82  LVAPVIHVGFNKLILKSLRSICRN--CSNFLLEPQRKNEYLEQLQQLKIMGHSTDDLVND 139

Query: 213 ILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNP 272
           + +  +K  VCPHC E               E+ + + +K    +E+             
Sbjct: 140 LFKEARKTKVCPHCNE---------------EQVEIKFEKPSDYIENG------------ 172

Query: 273 EIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRP 332
                      + L P E+ + FE +  +D+ L+ M+   ++P  +ILT L VPP  +RP
Sbjct: 173 -----------EKLTPTEIRERFENMSDDDVRLMGMDPSNARPEWMILTVLPVPPVTVRP 221

Query: 333 SVI--SDLKSDNDV 344
           S+   S  +S++D+
Sbjct: 222 SITLESGQRSEDDL 235



 Score = 93.2 bits (230), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 40/60 (66%), Positives = 52/60 (86%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
             GFV++S+ SGL PTE+FFH +GGREGLVDTAV+T+++GY+QRRLV +L+DL VQYD S
Sbjct: 777 AHGFVKSSYKSGLNPTEYFFHAVGGREGLVDTAVRTSQSGYLQRRLVNALQDLEVQYDGS 836


>gi|393794932|ref|ZP_10378296.1| bifunctional DNA-directed RNA polymerase subunit A'/A'' [Candidatus
           Nitrosoarchaeum limnia BG20]
          Length = 1263

 Score =  172 bits (436), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 93/269 (34%), Positives = 151/269 (56%), Gaps = 35/269 (13%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           ++ D+VLFNRQPSLH++SIMAH  +VLP +TFR +  VC PYNADFDGDEMN+H+PQ+EE
Sbjct: 415 ANGDIVLFNRQPSLHQMSIMAHYVRVLPGKTFRLHPSVCPPYNADFDGDEMNLHVPQSEE 474

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           ARAEA+              +LM  +  L++PR G  +I A +DF+TG YLLT+ +    
Sbjct: 475 ARAEAI--------------LLMRVQDQLISPRYGGPIIGALRDFVTGAYLLTKDDTLLT 520

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
             +    A            ++  ++ +   P    +   ++TGKQ+FSL L  + +  +
Sbjct: 521 PQEFYNYA------------MLGGYNEKFPKPGSKNKDGPMYTGKQLFSLFLPKDFNYVI 568

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            +        ++   +   +D  V+++N EL++G +DKS++G+    +V + + +D+G  
Sbjct: 569 TSK-------WSKGTKGAQKD--VVIKNGELISGVIDKSSIGAEEPESVLHRIAKDYGNT 619

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
            A   +  +  M   Y+ + GFS G  D+
Sbjct: 620 KAKNFLNSILIMVKQYITHYGFSYGYADL 648



 Score =  145 bits (366), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 108/344 (31%), Positives = 171/344 (49%), Gaps = 62/344 (18%)

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFVPD 1158
            Y +A++EP  AVG + AQSIGEPGTQMTL+TFHFAG            + E ++    P 
Sbjct: 930  YNKAKVEPGQAVGIITAQSIGEPGTQMTLRTFHFAGIAERNVTLGLPRLIELVDARKKPV 989

Query: 1159 DSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSF-----LILKPK--- 1210
               + I LD +  +    E  ID  R  ++    +S  ++ S   +     LIL P    
Sbjct: 990  TPTMDIYLDNESKK--SREKAIDVARNILQTK--VSALISDSETDYTTQIKLILSPNRLK 1045

Query: 1211 -------------DSSKSFNSKMYQMKQLL----------PSVV----------IKGVQG 1237
                          S+K F  KM    +L+          P+V+          +KGV  
Sbjct: 1046 ERGCTVGEVEAALQSNKKF--KMETTGELITLKLVEESDAPTVIAIRNKVLNTTVKGVPD 1103

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            I R  + ++D E V +      G N+  V+   G+      +NN +E+  TLGIEA+R+ 
Sbjct: 1104 IERVTLVQKDDEWVIQ----TTGSNIAKVLEVSGIDKKNVRTNNVFEIAGTLGIEASRNA 1159

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            ++ E+   +E+ G+ +D R+ MLV+DLM S+G +  I RHG+A  K+SVL  A+FE T  
Sbjct: 1160 LINELNNTLEDQGLEVDDRYIMLVSDLMCSRGYMQQIGRHGIAGTKDSVLARAAFEITVP 1219

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSE 1401
             +  AA  G+ + + G++E +I+G  + +G+G + L   V + +
Sbjct: 1220 TIAHAALAGEVEQLKGITENVIVGSIIPIGSGTVDLYMQVSKKK 1263



 Score =  112 bits (279), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 74/255 (29%), Positives = 124/255 (48%), Gaps = 41/255 (16%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           +++ S  +I +   Y +D    P+  GL+D R+GT +    C TCG   + C GHFG+I+
Sbjct: 22  IRKYSVAEITAPETYDEDGM--PVQGGLMDGRLGTLEPGQKCLTCGNTAARCPGHFGHIE 79

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKSLKK 211
           L  P+ HI +   +  +LQS C+  +CAR+ + +E    FR  K ++ A + +  K + +
Sbjct: 80  LAEPILHIAFIDNIYKLLQSTCR--SCARLKVPQEDLDEFRKIKEKHAAYTVISEKRIPE 137

Query: 212 KILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFN 271
           +I+E  KK   CPHCG+                +Y+    K    VE             
Sbjct: 138 QIIEKAKKAKECPHCGKT---------------QYELIFTKPTIFVE------------K 170

Query: 272 PEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIR 331
            EI  H+       L P+ + + F  I  +D+ LL  +   ++P   IL  L VPP  +R
Sbjct: 171 TEIGEHR-------LLPITIRERFSQIIDDDLHLLAYDPVTARPEWFILQALPVPPVTVR 223

Query: 332 PSVI--SDLKSDNDV 344
           PS+I  + ++S++D+
Sbjct: 224 PSIILETGIRSEDDL 238



 Score = 83.2 bits (204), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 34/58 (58%), Positives = 47/58 (81%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
             GFV++++  GL+  EFFFH MGGREGLVDTAV+T ++GYMQRRL+ +LE + ++YD
Sbjct: 775 AHGFVKSNYREGLSALEFFFHAMGGREGLVDTAVRTQQSGYMQRRLINALEHIRLEYD 832



 Score = 75.5 bits (184), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 57/237 (24%), Positives = 112/237 (47%), Gaps = 26/237 (10%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTD------LDYAR-IVKGRLERTTLGEVCEYIE 816
            G+PR+ E+++A +   TP +  YLD ++       +D AR I++ ++         +Y  
Sbjct: 974  GLPRLIELVDARKKPVTPTMDIYLDNESKKSREKAIDVARNILQTKVSALISDSETDYTT 1033

Query: 817  EVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDS 876
            +          IKL +   RL      +  +   ++  +      T    +  +++  D+
Sbjct: 1034 Q----------IKLILSPNRLKERGCTVGEVEAALQSNKKFKMETTGELITLKLVEESDA 1083

Query: 877  SKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGV 936
                   +  ++  + +  +KGV  I R  + ++D E V +      G N+  V+   G+
Sbjct: 1084 PT-----VIAIRNKVLNTTVKGVPDIERVTLVQKDDEWVIQ----TTGSNIAKVLEVSGI 1134

Query: 937  KGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
                  +NN +E+  TLGIEA+R+ ++ E+   +E+ G+ +D R+ MLV+DLM S+G
Sbjct: 1135 DKKNVRTNNVFEIAGTLGIEASRNALINELNNTLEDQGLEVDDRYIMLVSDLMCSRG 1191


>gi|242778248|ref|XP_002479200.1| DNA-dependent RNA polymerase II largest subunit, putative
           [Talaromyces stipitatus ATCC 10500]
 gi|218722819|gb|EED22237.1| DNA-dependent RNA polymerase II largest subunit, putative
           [Talaromyces stipitatus ATCC 10500]
          Length = 1755

 Score =  172 bits (436), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 101/278 (36%), Positives = 155/278 (55%), Gaps = 35/278 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DV+LFNRQPSLHK S+MAHR +V+P+ TFR N  V TPYNADFDGDEMN+H+PQ+EEA
Sbjct: 454 DGDVILFNRQPSLHKESMMAHRVRVMPYSTFRLNLSVTTPYNADFDGDEMNMHVPQSEEA 513

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L +L+++            N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 514 RAE----LQELALVPL----------NIVSPQRNGPLMGIVQDSLCGIYKICRRDVFLTK 559

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M     L+    D  G+I +       P + ++    WTGKQI S++L      P  
Sbjct: 560 DQVM----NLMLWVPDWDGVIPQ-------PAI-LKPRPRWTGKQIISMVL------PSG 601

Query: 521 ANLK--TKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            NL    K +A  + +     D  +++   +L+ G   K T+G+ G   + + +  ++G 
Sbjct: 602 LNLLRIDKDKAPLSEKFSPLADGGLLVHGGQLMYGMFSKKTVGASG-GGIVHTIFNEYGP 660

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           D AVT      R+ +++L++ GFSIGIGD  P +  ++
Sbjct: 661 DAAVTFFDGAQRVVNYWLLHNGFSIGIGDTIPDKKTIE 698



 Score =  103 bits (258), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 61/181 (33%), Positives = 95/181 (52%), Gaps = 15/181 (8%)

Query: 1224 KQLLPSVVIKGVQGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMA 1268
            + LL ++ ++GV G+ RA I+E+D   V                ++ L   G  L DV+ 
Sbjct: 1286 QHLLDTLTLRGVAGVERAFINEKDNVRVMEDGSLFQSKTDPLCKEWVLETSGSALADVLT 1345

Query: 1269 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK 1328
              GV   +  SN   EV++  GIEAAR+ ++ E+  V+   G  ++ RH  L+ D+MT +
Sbjct: 1346 IPGVDTSRTYSNQFIEVFEVFGIEAARTAVLRELTQVLAFDGSYVNHRHLALLVDVMTVR 1405

Query: 1329 GEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGT 1388
            G +  +TRHG+ +     L   SFE T + L +AA +G+ D   GVSE +I+G     GT
Sbjct: 1406 GYLTPVTRHGINRADNGALMRCSFEETVEILLEAAAFGELDDCRGVSENLILGQLAPAGT 1465

Query: 1389 G 1389
            G
Sbjct: 1466 G 1466



 Score =  102 bits (253), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 56/63 (88%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEF+FH MGGREGL+DTAVKTAETGY+QR+LVK+LE+L V
Sbjct: 812 DYSPESRGFVENSYLRGLTPTEFYFHAMGGREGLIDTAVKTAETGYIQRKLVKALEELMV 871

Query: 666 QYD 668
           +YD
Sbjct: 872 KYD 874



 Score = 90.9 bits (224), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 78/289 (26%), Positives = 134/289 (46%), Gaps = 59/289 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLD--KDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N + NI TP +T Y +  +  D + A+ ++  +E T+L  V E  E  + P
Sbjct: 1118 GVPRLKEILNVATNIKTPSMTVYQEPHRKHDKESAKQLRSVVEHTSLRSVTEATEIYYDP 1177

Query: 822  DDSFILIKLDMDRIR---LLHLEVDIDS-------IRYCIERTRGISGHLTVSGHSFLIL 871
            D    +I+ D D +    ++  +V  DS       +R  + R + +   LTV   +  I 
Sbjct: 1178 DIQSTVIENDRDMVESYFIIPEDVADDSSRQSKWLLRIVLSRPKLLDKGLTVQDVATRIK 1237

Query: 872  K--PKD-----SSKSFNSKMYQMKQ-------------------------LLPSVVIKGV 899
            +  P+D     S  + + ++ +++Q                         LL ++ ++GV
Sbjct: 1238 EQYPRDIAVIFSDNNADEQVIRIRQLHDAKEDEDEEDMEYDVTLKKLEQHLLDTLTLRGV 1297

Query: 900  QGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMATYGVKGVKCSSN 944
             G+ RA I+E+D   V                ++ L   G  L DV+   GV   +  SN
Sbjct: 1298 AGVERAFINEKDNVRVMEDGSLFQSKTDPLCKEWVLETSGSALADVLTIPGVDTSRTYSN 1357

Query: 945  NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
               EV++  GIEAAR+ ++ E+  V+   G  ++ RH  L+ D+MT +G
Sbjct: 1358 QFIEVFEVFGIEAARTAVLRELTQVLAFDGSYVNHRHLALLVDVMTVRG 1406



 Score = 75.1 bits (183), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 60/243 (24%), Positives = 102/243 (41%), Gaps = 60/243 (24%)

Query: 110 DPQRT-PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVIN 168
           D QR  P   G  D R+GT  ++  C TC +   +C GHFG+I+L  PVFHIG+      
Sbjct: 44  DEQRMRPRTKGPNDPRLGTLDRQYYCETCEEGQKECPGHFGHIELATPVFHIGFLTKTKK 103

Query: 169 ILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKK----ILETTKKVSVC- 223
           +L+++C N  C ++          +A + +P     +R    K+    I   +K V++C 
Sbjct: 104 LLETVCHN--CGKI----------KADMSDPKFQDALRIRDPKRRFDIIWRLSKDVAICE 151

Query: 224 -----------------PH-----CGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLL 261
                            PH     CG     ++K GL  +   K       +D I     
Sbjct: 152 ADPLPEDEDPFSKEGSKPHKGHGGCGNAQPTIRKEGLSLVGTWKPNKANMMEDDI----- 206

Query: 262 AEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
                      +I   +K    +T+ P     +F +I  ED+ ++ ++ + ++P  +ILT
Sbjct: 207 -----------DIPQPEK----RTITPAMAYNIFRSISHEDVRIMGLSNDYARPEWMILT 251

Query: 322 RLL 324
            L+
Sbjct: 252 VLI 254



 Score = 60.1 bits (144), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 27/41 (65%), Positives = 29/41 (70%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            A   ++ RAQ  P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1069 AIEMRFARAQANPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1109


>gi|329765754|ref|ZP_08257323.1| DNA-directed RNA polymerase subunit A' [Candidatus Nitrosoarchaeum
           limnia SFB1]
 gi|329137820|gb|EGG42087.1| DNA-directed RNA polymerase subunit A' [Candidatus Nitrosoarchaeum
           limnia SFB1]
          Length = 1263

 Score =  172 bits (436), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 93/269 (34%), Positives = 151/269 (56%), Gaps = 35/269 (13%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           ++ D+VLFNRQPSLH++SIMAH  +VLP +TFR +  VC PYNADFDGDEMN+H+PQ+EE
Sbjct: 415 ANGDIVLFNRQPSLHQMSIMAHYVRVLPGKTFRLHPSVCPPYNADFDGDEMNLHVPQSEE 474

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           ARAEA+              +LM  +  L++PR G  +I A +DF+TG YLLT+ +    
Sbjct: 475 ARAEAI--------------LLMRVQDQLISPRYGGPIIGALRDFVTGAYLLTKDDTLLT 520

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
             +    A            ++  ++ +   P    +   ++TGKQ+FSL L  + +  +
Sbjct: 521 PQEFYNYA------------MLGGYNEKFPKPGSKNKDGPMYTGKQLFSLFLPKDFNYVI 568

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            +        ++   +   +D  V+++N EL++G +DKS++G+    +V + + +D+G  
Sbjct: 569 TSK-------WSKGTKGAQKD--VVIKNGELISGVIDKSSIGAEEPESVLHRIAKDYGNT 619

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
            A   +  +  M   Y+ + GFS G  D+
Sbjct: 620 KAKNFLNSILIMVKQYITHYGFSYGYADL 648



 Score =  145 bits (366), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 108/344 (31%), Positives = 171/344 (49%), Gaps = 62/344 (18%)

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFVPD 1158
            Y +A++EP  AVG + AQSIGEPGTQMTL+TFHFAG            + E ++    P 
Sbjct: 930  YNKAKVEPGQAVGIITAQSIGEPGTQMTLRTFHFAGIAERNVTLGLPRLIELVDARKKPV 989

Query: 1159 DSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSF-----LILKPK--- 1210
               + I LD +  +    E  ID  R  ++    +S  ++ S   +     LIL P    
Sbjct: 990  TPTMDIYLDNESKK--SREKAIDVARNILQTK--VSALISDSETDYTTQIKLILSPNRLK 1045

Query: 1211 -------------DSSKSFNSKMYQMKQLL----------PSVV----------IKGVQG 1237
                          S+K F  KM    +L+          P+V+          +KGV  
Sbjct: 1046 ERGCTVGEVEAALQSNKKF--KMETTGELITLKLVEESDAPTVIAIRNKVLNTTVKGVPD 1103

Query: 1238 INRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 1297
            I R  + ++D E V +      G N+  V+   G+      +NN +E+  TLGIEA+R+ 
Sbjct: 1104 IERVTLVQKDDEWVIQ----TTGSNIAKVLEVSGIDKKNVRTNNVFEIAGTLGIEASRNA 1159

Query: 1298 IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSD 1357
            ++ E+   +E+ G+ +D R+ MLV+DLM S+G +  I RHG+A  K+SVL  A+FE T  
Sbjct: 1160 LINELNNTLEDQGLEVDDRYIMLVSDLMCSRGYMQQIGRHGIAGTKDSVLARAAFEITVP 1219

Query: 1358 HLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSE 1401
             +  AA  G+ + + G++E +I+G  + +G+G + L   V + +
Sbjct: 1220 TIAHAALAGEVEQLKGITENVIVGSIIPIGSGTVDLYMQVSKKK 1263



 Score =  112 bits (279), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 74/255 (29%), Positives = 124/255 (48%), Gaps = 41/255 (16%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           +++ S  +I +   Y +D    P+  GL+D R+GT +    C TCG   + C GHFG+I+
Sbjct: 22  IRKYSVAEITAPETYDEDGM--PVQGGLMDGRLGTLEPGQKCLTCGNTAARCPGHFGHIE 79

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKSLKK 211
           L  P+ HI +   +  +LQS C+  +CAR+ + +E    FR  K ++ A + +  K + +
Sbjct: 80  LAEPILHIAFIDNIYKLLQSTCR--SCARLKVPQEDLDEFRKIKEKHAAYTVISEKRIPE 137

Query: 212 KILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFN 271
           +I+E  KK   CPHCG+                +Y+    K    VE             
Sbjct: 138 QIIEKAKKAKECPHCGKT---------------QYELIFTKPTIFVE------------K 170

Query: 272 PEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIR 331
            EI  H+       L P+ + + F  I  +D+ LL  +   ++P   IL  L VPP  +R
Sbjct: 171 TEIGEHR-------LLPITIRERFSQIIDDDLHLLAYDPVTARPEWFILQALPVPPVTVR 223

Query: 332 PSVI--SDLKSDNDV 344
           PS+I  + ++S++D+
Sbjct: 224 PSIILETGIRSEDDL 238



 Score = 83.2 bits (204), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 34/58 (58%), Positives = 47/58 (81%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
             GFV++++  GL+  EFFFH MGGREGLVDTAV+T ++GYMQRRL+ +LE + ++YD
Sbjct: 775 AHGFVKSNYREGLSALEFFFHAMGGREGLVDTAVRTQQSGYMQRRLINALEHIRLEYD 832



 Score = 75.1 bits (183), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 57/237 (24%), Positives = 112/237 (47%), Gaps = 26/237 (10%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTD------LDYAR-IVKGRLERTTLGEVCEYIE 816
            G+PR+ E+++A +   TP +  YLD ++       +D AR I++ ++         +Y  
Sbjct: 974  GLPRLIELVDARKKPVTPTMDIYLDNESKKSREKAIDVARNILQTKVSALISDSETDYTT 1033

Query: 817  EVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDS 876
            +          IKL +   RL      +  +   ++  +      T    +  +++  D+
Sbjct: 1034 Q----------IKLILSPNRLKERGCTVGEVEAALQSNKKFKMETTGELITLKLVEESDA 1083

Query: 877  SKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGV 936
                   +  ++  + +  +KGV  I R  + ++D E V +      G N+  V+   G+
Sbjct: 1084 PT-----VIAIRNKVLNTTVKGVPDIERVTLVQKDDEWVIQ----TTGSNIAKVLEVSGI 1134

Query: 937  KGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
                  +NN +E+  TLGIEA+R+ ++ E+   +E+ G+ +D R+ MLV+DLM S+G
Sbjct: 1135 DKKNVRTNNVFEIAGTLGIEASRNALINELNNTLEDQGLEVDDRYIMLVSDLMCSRG 1191


>gi|452208507|ref|YP_007488629.1| DNA-directed RNA polymerase subunit A'' (subunit C) [Natronomonas
            moolapensis 8.8.11]
 gi|452084607|emb|CCQ37954.1| DNA-directed RNA polymerase subunit A'' (subunit C) [Natronomonas
            moolapensis 8.8.11]
          Length = 408

 Score =  172 bits (436), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 113/356 (31%), Positives = 185/356 (51%), Gaps = 60/356 (16%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEE 1153
                KY+  +++P   VG ++AQSIGEPGTQMT+ TFH+AG            + E ++ 
Sbjct: 46   GVESKYLENRVDPLDPVGTVSAQSIGEPGTQMTMNTFHYAGVAEIDVTQGLPRLIELVDA 105

Query: 1154 VFVPDDSFILIKLD----MDRIR--------------------------LLHLEVDIDSI 1183
               PD   + + LD     DR R                          L+ ++++ +++
Sbjct: 106  RKTPDTPMMTVHLDGVYAEDRERAHEVVWQIEATKILALGDVSTNVADMLVRIDLNEETL 165

Query: 1184 --RY-CIERTRGISGHLTVSGHSFLIL---KPKDSSKSFNSKMYQMKQLLP------SVV 1231
              R+  I+    I+G +  +  S L +   +P  +   F  +    +QLL        +V
Sbjct: 166  AERWPTIDDIDDIAGRIAGTIESELGVETDRPATTVIQFGPEEPSYRQLLQLVEDLREIV 225

Query: 1232 IKGVQGINRAVIHEEDVE------GVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEV 1285
             KG++ I+R VI +E+++      G  ++ L  EG NL+ V+   GV   + + NN +E+
Sbjct: 226  FKGIEEISRVVIRKEELDDTQSGSGREEFILYTEGSNLKKVLDIEGVDASRTTCNNIHEI 285

Query: 1286 YKTLGIEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMKE 1344
            +  LGIEAAR  I+ E    +E  G+  ++ RH MLVAD+MT+ G++  I RHG++  K+
Sbjct: 286  HNNLGIEAAREAIIEETMNTLEEQGLDDVNIRHLMLVADIMTNTGDIESIGRHGISGNKD 345

Query: 1345 SVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS 1400
            SVL  A+FE T +HL DAA +G+ D + GV+E +I+G P+ +GTG + L     +S
Sbjct: 346  SVLARAAFEVTVNHLLDAAIHGEVDDLDGVTENVIVGKPIKLGTGDVDLRMGARQS 401



 Score = 97.4 bits (241), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 74/249 (29%), Positives = 129/249 (51%), Gaps = 28/249 (11%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDK--DTDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T +LD     D + A  V  ++E T    LG+V   + + 
Sbjct: 95  GLPRLIELVDARKTPDTPMMTVHLDGVYAEDRERAHEVVWQIEATKILALGDVSTNVAD- 153

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRG-ISGHLTVS----GHSFLILKP 873
                  +L+++D++   L      ID I     R  G I   L V       + +   P
Sbjct: 154 -------MLVRIDLNEETLAERWPTIDDIDDIAGRIAGTIESELGVETDRPATTVIQFGP 206

Query: 874 KDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVE------GVTKYKLLVEGDNL 927
           ++ S     ++ Q+ + L  +V KG++ I+R VI +E+++      G  ++ L  EG NL
Sbjct: 207 EEPSYR---QLLQLVEDLREIVFKGIEEISRVVIRKEELDDTQSGSGREEFILYTEGSNL 263

Query: 928 RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVA 986
           + V+   GV   + + NN +E++  LGIEAAR  I+ E    +E  G+  ++ RH MLVA
Sbjct: 264 KKVLDIEGVDASRTTCNNIHEIHNNLGIEAAREAIIEETMNTLEEQGLDDVNIRHLMLVA 323

Query: 987 DLMTSKGEV 995
           D+MT+ G++
Sbjct: 324 DIMTNTGDI 332


>gi|432330444|ref|YP_007248587.1| DNA-directed RNA polymerase, subunit A'' [Methanoregula formicicum
            SMSP]
 gi|432137153|gb|AGB02080.1| DNA-directed RNA polymerase, subunit A'' [Methanoregula formicicum
            SMSP]
          Length = 391

 Score =  172 bits (436), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 109/346 (31%), Positives = 173/346 (50%), Gaps = 59/346 (17%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCE 1149
            E    +Y   +IE   AVG +AAQSIGEPGTQMT++TFH+AG              E+ +
Sbjct: 43   ERVNAEYQSTRIEACEAVGIIAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIMD 102

Query: 1150 YIEEVFVPDDSFIL---IKLDMDRIRLLHLEV-------------DIDSIRYCIERTRGI 1193
              +E   P  +  L      D D+ R +  ++             D+++++  +     +
Sbjct: 103  ARKEPSTPTMTVFLEPDYANDRDKAREVSWQIEAAPLHEFGDITTDMENMQVVVHLNTKV 162

Query: 1194 SGHLTVSGHSFLILKPKD-------------------------SSKSFNSKMYQMKQLLP 1228
                 ++    + + PK                            K     ++Q+ + + 
Sbjct: 163  CDKRKIAPSEIMEVAPKKIRDRRHYRDFEHEIDEATATIIFSPKDKESYQNLFQLAEHVR 222

Query: 1229 SVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKT 1288
            +V+++G+  I R V+ +E  E    Y L  EG NL+DV    GV   +  +NN  E+   
Sbjct: 223  NVIVQGIDDIIRVVVRKETGE----YILYTEGSNLKDVFDVTGVDTTRTRTNNISEIASV 278

Query: 1289 LGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLN 1348
            LGIEAAR+ ++ E    +   G+++D RH MLV+D+M  +GEV  I RHG+A  KESVL+
Sbjct: 279  LGIEAARNAVIHEAVSTLNEQGIAVDVRHLMLVSDMMCMEGEVKQIGRHGIAGEKESVLS 338

Query: 1349 LASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
             A+FE T +HL DAA   + D +SGV+E +I+G P+ +GTG +KL+
Sbjct: 339  RAAFEVTVNHLLDAAVANEVDELSGVTENVIVGQPIQLGTGDVKLI 384



 Score =  102 bits (253), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 76/254 (29%), Positives = 124/254 (48%), Gaps = 47/254 (18%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A +  STP +T +L+ D   D D AR V  ++E   L E           
Sbjct: 93  GLPRLIEIMDARKEPSTPTMTVFLEPDYANDRDKAREVSWQIEAAPLHE----------- 141

Query: 822 DDSFILIKLDMDRIRLL-HLEVDIDSIRYCIERTRGISGHLTVS---------------- 864
              F  I  DM+ ++++ HL     + + C +R    S  + V+                
Sbjct: 142 ---FGDITTDMENMQVVVHL-----NTKVCDKRKIAPSEIMEVAPKKIRDRRHYRDFEHE 193

Query: 865 ---GHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLL 921
                + +I  PKD     N  ++Q+ + + +V+++G+  I R V+ +E  E    Y L 
Sbjct: 194 IDEATATIIFSPKDKESYQN--LFQLAEHVRNVIVQGIDDIIRVVVRKETGE----YILY 247

Query: 922 VEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRH 981
            EG NL+DV    GV   +  +NN  E+   LGIEAAR+ ++ E    +   G+++D RH
Sbjct: 248 TEGSNLKDVFDVTGVDTTRTRTNNISEIASVLGIEAARNAVIHEAVSTLNEQGIAVDVRH 307

Query: 982 PMLVADLMTSKGEV 995
            MLV+D+M  +GEV
Sbjct: 308 LMLVSDMMCMEGEV 321


>gi|409095099|ref|ZP_11215123.1| DNA-directed RNA polymerase subunit A'' [Thermococcus zilligii AN1]
          Length = 391

 Score =  172 bits (435), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 115/346 (33%), Positives = 177/346 (51%), Gaps = 58/346 (16%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIE 1152
            E   ++Y +A +EP   VG +AAQSIGEP TQMTL TFH+AG            + E ++
Sbjct: 47   EEVVKEYEKALVEPGEPVGTVAAQSIGEPSTQMTLNTFHYAGVTEINVTLGLPRIIEIVD 106

Query: 1153 EVFVPDDSFILIKLDMD-------------RIRLLHLE-------VDIDSIRYCIE---- 1188
                P    + + LD +             RI    LE       +DI +  Y +E    
Sbjct: 107  ARKNPSTPIMTVYLDEEHRQDMAKALEVARRIEGTTLENLAREETIDILNFEYIVEVDPE 166

Query: 1189 ---RT--------RGISG-----HLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVI 1232
               +T        + +SG          G+  +I++P+   +   S + ++ + +    +
Sbjct: 167  RLEKTGLDMEKILKKLSGSFKNVEFEADGYR-IIVRPQKVGRL--SDLRRLAEKVKKHRL 223

Query: 1233 KGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIE 1292
            KG+ G+ + +I +E  E    Y +  EG NL+ V+   GV   +  +NN +E+ + LGIE
Sbjct: 224  KGLSGVGKTIIRKEGDE----YVIYTEGSNLKQVLKVPGVDPTRTRTNNIWEIAEVLGIE 279

Query: 1293 AARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASF 1352
            AAR+ I+ EI   M   G+ +D RH MLVAD+MT  G +  I RHG+   K SVL  ASF
Sbjct: 280  AARNAIIEEIVSTMREQGLEVDIRHIMLVADMMTLDGVIRPIGRHGVVGEKASVLARASF 339

Query: 1353 ENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 1398
            E T+ HLF+AA  G+ D ++GV E +++G P+ VGTG++ L   +P
Sbjct: 340  EITTTHLFEAAERGEVDPLNGVVENVLIGQPVPVGTGVVNLKMGLP 385



 Score =  110 bits (275), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 75/233 (32%), Positives = 130/233 (55%), Gaps = 16/233 (6%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARI--VKGRLERTTLGEVCEYIEEVFVP 821
           G+PRI EI++A +N STPI+T YLD++   D A+   V  R+E TTL  +    E + + 
Sbjct: 97  GLPRIIEIVDARKNPSTPIMTVYLDEEHRQDMAKALEVARRIEGTTLENLARE-ETIDIL 155

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSF-LILKPKDSSKSF 880
           +  +I+   ++D  RL    +D++ I   +++  G   ++      + +I++P+   +  
Sbjct: 156 NFEYIV---EVDPERLEKTGLDMEKI---LKKLSGSFKNVEFEADGYRIIVRPQKVGRL- 208

Query: 881 NSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
            S + ++ + +    +KG+ G+ + +I +E  E    Y +  EG NL+ V+   GV   +
Sbjct: 209 -SDLRRLAEKVKKHRLKGLSGVGKTIIRKEGDE----YVIYTEGSNLKQVLKVPGVDPTR 263

Query: 941 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
             +NN +E+ + LGIEAAR+ I+ EI   M   G+ +D RH MLVAD+MT  G
Sbjct: 264 TRTNNIWEIAEVLGIEAARNAIIEEIVSTMREQGLEVDIRHIMLVADMMTLDG 316


>gi|3172136|gb|AAC18417.1| RNA polymerase II largest subunit [Acanthamoeba castellanii]
          Length = 1569

 Score =  172 bits (435), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 96/272 (35%), Positives = 153/272 (56%), Gaps = 44/272 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DV++FNRQPSLHK+S+M H+ K++P+ TFR N  V TPYNADFDGDEMN+H+PQT  A
Sbjct: 367 DGDVIIFNRQPSLHKMSMMGHKVKIMPYSTFRLNLSVTTPYNADFDGDEMNMHVPQTPGA 426

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE +               LM     +VT ++ + +I   QD + GG LLTQ++ F  +
Sbjct: 427 RAEVIE--------------LMMVPKQIVTAQSNKPVIGIVQDTLLGGCLLTQRDTFIEK 472

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVV----FVRTAVIWTGKQIFSLILKPNRD 516
              M I   L                 SW+  V     ++   +WTGKQ+FSLI+  N +
Sbjct: 473 DVMMNILMWL----------------ESWDGTVPTPTILKPKQLWTGKQVFSLIIPRNTN 516

Query: 517 CPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
             VNA+ +    ++T        D+ V++   EL++G ++K TLG+  K+ + +++  + 
Sbjct: 517 F-VNADDEEPDMSFT--------DNKVLIEEGELVSGILNKKTLGTSHKS-LVHVIWNEH 566

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           G +V    + ++  + +++L++ GFS+G+GD 
Sbjct: 567 GSEVCKHFLNQVQHVVNYWLLHHGFSVGVGDT 598



 Score =  112 bits (279), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 66/179 (36%), Positives = 104/179 (58%), Gaps = 10/179 (5%)

Query: 1226 LLPSVVIKGVQGINRAVIHEE------DVEG-VTKYKLLV---EGDNLRDVMATYGVKGV 1275
            +L  + +KG++GI +  I E+      D  G  TK   LV   EG NL  VM+   V   
Sbjct: 1199 MLTEMDLKGIEGIKKVFIREDKNKVAIDARGEYTKANELVLDTEGTNLLAVMSHPDVDHT 1258

Query: 1276 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGIT 1335
            + +SNN  E  + LGIEA R+ ++ E++ V+   G  +++RH  ++AD+MT +G ++ IT
Sbjct: 1259 RTTSNNIIETIEVLGIEAVRNALLRELRNVISFDGAYVNYRHLAILADVMTYRGHLMAIT 1318

Query: 1336 RHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            RHG+ +++   L   SFE T+D L +AA + + D +SGVSE I++G    +GTG   L 
Sbjct: 1319 RHGINRVETGCLMRCSFEETADILLEAATFSELDPLSGVSENILLGQLPPLGTGCFDLF 1377



 Score =  102 bits (253), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 44/59 (74%), Positives = 53/59 (89%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
           +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKTAETGY+QRRLVK+LED+ V+YD +
Sbjct: 726 RGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDVMVKYDYT 784



 Score = 90.5 bits (223), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 85/290 (29%), Positives = 132/290 (45%), Gaps = 56/290 (19%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDY--ARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KE+IN ++ I TP +T YL+     D+  A+ V+  L+ TTL +V    E  + P
Sbjct: 1027 GVPRLKELINIAKTIKTPSLTVYLEPHCSRDHEAAKNVQCSLQHTTLRDVTAATEIFYDP 1086

Query: 822  DDSFILIKLDMDRIR------------------LLHLEVDID-------SIRYCIERTRG 856
            D    +I  D D +R                  LL +E++ +       S++   ER   
Sbjct: 1087 DPVNTVITEDQDFVRAYFLMPEEEINTSNLSPWLLRIELNREKMTDTKLSMQEIAERIHA 1146

Query: 857  -ISGHLTV----SGHSFLIL----------KPKDSSKSFNSKMYQMKQ----LLPSVVIK 897
               G L           LIL          K  D   S       +KQ    +L  + +K
Sbjct: 1147 DFGGDLNCIYNDDNADKLILRIRINNDEENKAPDQEGSVGDDDVFLKQIESNMLTEMDLK 1206

Query: 898  GVQGINRAVIHEE------DVEG-VTKYKLLV---EGDNLRDVMATYGVKGVKCSSNNTY 947
            G++GI +  I E+      D  G  TK   LV   EG NL  VM+   V   + +SNN  
Sbjct: 1207 GIEGIKKVFIREDKNKVAIDARGEYTKANELVLDTEGTNLLAVMSHPDVDHTRTTSNNII 1266

Query: 948  EVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            E  + LGIEA R+ ++ E++ V+   G  +++RH  ++AD+MT +G ++ 
Sbjct: 1267 ETIEVLGIEAVRNALLRELRNVISFDGAYVNYRHLAILADVMTYRGHLMA 1316



 Score = 56.2 bits (134), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/38 (60%), Positives = 30/38 (78%)

Query: 1108 EKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            +++ ++  +P   +GALAAQSIGEP TQMTL TFHFAG
Sbjct: 981  DRFYKSLCDPGEMIGALAAQSIGEPATQMTLNTFHFAG 1018



 Score = 48.1 bits (113), Expect = 0.032,   Method: Compositional matrix adjust.
 Identities = 19/46 (41%), Positives = 34/46 (73%), Gaps = 2/46 (4%)

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEK 188
           +C GHFG+++L  PVF+IG+   V+ IL+S+C +  C+++L+ E +
Sbjct: 1   ECPGHFGHLELAKPVFNIGFLTTVLKILRSVCFH--CSKLLVDEAQ 44


>gi|304315187|ref|YP_003850334.1| DNA-directed RNA polymerase, subunit A'' [Methanothermobacter
            marburgensis str. Marburg]
 gi|302588646|gb|ADL59021.1| DNA-directed RNA polymerase, subunit A'' [Methanothermobacter
            marburgensis str. Marburg]
          Length = 451

 Score =  172 bits (435), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 115/343 (33%), Positives = 176/343 (51%), Gaps = 67/343 (19%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYI 1151
             R  Y RA++E   AVG +AAQS+GEPGTQMT++TFH+AG              E+ +  
Sbjct: 117  VRRAYERAKVEAGEAVGTVAAQSVGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDAR 176

Query: 1152 EEVFVP------------DDSFI----------------------------LIKLDMDRI 1171
            +++  P            D+ F+                            + +LD ++I
Sbjct: 177  KKISTPTMSIYFEGDLRYDEEFVRKKANKIGKSTLNDVLKNFSIQYADMAVVAELDEEKI 236

Query: 1172 RLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVV 1231
               HLE D   I   +E+T      + +  +S L  +P+   K    ++  +   +  + 
Sbjct: 237  LEKHLEYD--DIIAKVEKT---FKKVEID-NSILRFEPQ---KPTIRELRLLADKVRKLQ 287

Query: 1232 IKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGI 1291
            I GV+ I + VI +ED E V    +  EG NL  V+   GV  V+ ++N+ +E+   LGI
Sbjct: 288  ISGVKNIGKVVIRKEDDEWV----IHTEGSNLGAVLKEEGVDKVRTTTNDIHEIETVLGI 343

Query: 1292 EAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLAS 1351
            EAAR+ I+ E K  ME  G+++D RH MLVAD+MT+ G V  I RHG++  K SVL  AS
Sbjct: 344  EAARNAIIHEAKRTMEEQGLTVDIRHIMLVADMMTADGSVKSIGRHGISGEKASVLARAS 403

Query: 1352 FENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            FE T  HL  A+  G+ D ++G+ E II+G P+ +GTG + ++
Sbjct: 404  FEETGKHLLRASIRGEVDHLTGIIENIIIGQPIPLGTGSVSVV 446



 Score =  107 bits (268), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 78/238 (32%), Positives = 130/238 (54%), Gaps = 17/238 (7%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A + ISTP ++ Y + D   D ++ R    ++ ++TL +V +     +  
Sbjct: 165 GLPRLIEIVDARKKISTPTMSIYFEGDLRYDEEFVRKKANKIGKSTLNDVLKNFSIQYA- 223

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
            D  ++ +LD ++I   HLE D   I   +E+T      + +  +S L  +P+   K   
Sbjct: 224 -DMAVVAELDEEKILEKHLEYD--DIIAKVEKT---FKKVEID-NSILRFEPQ---KPTI 273

Query: 882 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
            ++  +   +  + I GV+ I + VI +ED E V    +  EG NL  V+   GV  V+ 
Sbjct: 274 RELRLLADKVRKLQISGVKNIGKVVIRKEDDEWV----IHTEGSNLGAVLKEEGVDKVRT 329

Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG 999
           ++N+ +E+   LGIEAAR+ I+ E K  ME  G+++D RH MLVAD+MT+ G V   G
Sbjct: 330 TTNDIHEIETVLGIEAARNAIIHEAKRTMEEQGLTVDIRHIMLVADMMTADGSVKSIG 387


>gi|333986472|ref|YP_004519079.1| DNA-directed RNA polymerase subunit A' [Methanobacterium sp.
           SWAN-1]
 gi|333824616|gb|AEG17278.1| DNA-directed RNA polymerase subunit A' [Methanobacterium sp.
           SWAN-1]
          Length = 873

 Score =  172 bits (435), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 100/268 (37%), Positives = 145/268 (54%), Gaps = 38/268 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH++S+MAH  KVLP++TFR N CVC PYNADFDGDEMN+H+ QTEE+
Sbjct: 410 DGDVVLFNRQPSLHRMSMMAHEVKVLPYKTFRLNLCVCPPYNADFDGDEMNMHIFQTEES 469

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              AK LM  + ++++PR G  +I    D I+G YLLT+  + F+ 
Sbjct: 470 RAE--------------AKSLMRVQEHILSPRFGGPIIGGIHDHISGAYLLTRLGSNFS- 514

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                          D+  ++ R       P         WTGK+IFSL+L  + +   N
Sbjct: 515 -------------DEDVFQMVMRAGMPIPKP-----KGRDWTGKEIFSLLLPKDLNMVYN 556

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGS-GGKANVFYILLRDFGED 579
           A +  K       E  C  D+YV++ N EL  G++D+   G+  GK  +   +++++G D
Sbjct: 557 AEICRKCDECLKQE--CKNDAYVVIENGELKTGAIDEKAYGAFSGK--ILDSIVKEYGTD 612

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            A   +   +++    +M RGF+    D
Sbjct: 613 AAREFLDSSTKLAITGIMKRGFTTSTAD 640



 Score =  107 bits (268), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 73/244 (29%), Positives = 117/244 (47%), Gaps = 43/244 (17%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + +++ S  +IV+ + Y +D    PI  GL+D R+G       C +CG    DC GHFG+
Sbjct: 21  ENIRKMSVTKIVTPDTYDEDGY--PIEAGLMDPRLGVIDPGLRCRSCGSKGGDCQGHFGH 78

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           I+L  PV H+G+   +  +L+S CK   C RVLL E +   +R KL     +     S+ 
Sbjct: 79  INLARPVIHVGFADTIHKVLRSTCKE--CGRVLLTESEIVDYRDKLETHLKNNESITSII 136

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           K+I  T  +   CPHC                       T+++D  ++  ++        
Sbjct: 137 KEIY-TVARRDKCPHC----------------------ETEQEDVKIDKPVS-------- 165

Query: 271 NPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCI 330
              +E + K      L   EV +  EAIP ED   + +N+E+++P  ++LT L VPP  +
Sbjct: 166 --IVEGNYK------LTASEVRERLEAIPEEDYLFVGINSEVARPEWMVLTVLPVPPVTV 217

Query: 331 RPSV 334
           RPS+
Sbjct: 218 RPSI 221



 Score = 88.6 bits (218), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 38/56 (67%), Positives = 46/56 (82%)

Query: 613 GFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           GFV +S+  GL P EFFFH MGGREGLVDTA++TA++GYMQRRLV +L+DL V  D
Sbjct: 770 GFVHSSYKKGLDPLEFFFHAMGGREGLVDTAIRTAQSGYMQRRLVNALQDLSVHTD 825


>gi|448388146|ref|ZP_21565086.1| DNA-directed RNA polymerase subunit A'' [Haloterrigena salina JCM
            13891]
 gi|445670797|gb|ELZ23394.1| DNA-directed RNA polymerase subunit A'' [Haloterrigena salina JCM
            13891]
          Length = 397

 Score =  171 bits (434), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 108/350 (30%), Positives = 181/350 (51%), Gaps = 58/350 (16%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A A   +Y+  +++P   VG ++AQSIGEPGTQ+T+ TFH+AG            + E +
Sbjct: 48   ARAVESRYLDTRVDPLDPVGTVSAQSIGEPGTQLTMNTFHYAGVAEIDVTQGLPRLIELV 107

Query: 1152 EEVFVPDDSFILIKLD----------------MDRIRLLHL--------------EVDID 1181
            +    PD   + + L+                ++  ++L L               ++ D
Sbjct: 108  DARKTPDTPMMTVYLEDEYAAEREKAHEVVWNIEATKILALGDVSTNVADMRVQISLNED 167

Query: 1182 SIRY----------CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVV 1231
            ++R            IE   G+S   TV   + +   P++ S      + Q+ + L  + 
Sbjct: 168  TLRERMITPEEVAEIIEDNLGVS---TVQQGTEIQFGPEEPSYR---DLLQLVEELRDIT 221

Query: 1232 IKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGI 1291
             KG++ ++R VI  E+++   ++ L  EG    DV+   GV   + + NN +E+++ LGI
Sbjct: 222  FKGIEEVSRVVIRREELDVGEQFVLYTEGSAFGDVLEIEGVDASRTTCNNIHEIHRNLGI 281

Query: 1292 EAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLA 1350
            EAAR  I+ E    +   G+  ++ RH MLVAD+MT++GE+  I RHG++  KESVL  A
Sbjct: 282  EAAREAIIEETNNTLAEQGLDDVNVRHLMLVADMMTNRGEIESIGRHGISGSKESVLARA 341

Query: 1351 SFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS 1400
            +FE T +HL +AA +G+TD + GV+E +I+G P+ +GTG + L     +S
Sbjct: 342  AFEVTVNHLLNAAIHGETDELDGVTENVIVGKPIKLGTGDVDLRMGSTKS 391



 Score = 97.1 bits (240), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 70/238 (29%), Positives = 125/238 (52%), Gaps = 20/238 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T YL+ +   + + A  V   +E T    LG+V   + ++
Sbjct: 99  GLPRLIELVDARKTPDTPMMTVYLEDEYAAEREKAHEVVWNIEATKILALGDVSTNVADM 158

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSK 878
            V     I +  D  R R++  E     +   IE   G+S   TV   + +   P++ S 
Sbjct: 159 RVQ----ISLNEDTLRERMITPE----EVAEIIEDNLGVS---TVQQGTEIQFGPEEPSY 207

Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 938
                + Q+ + L  +  KG++ ++R VI  E+++   ++ L  EG    DV+   GV  
Sbjct: 208 R---DLLQLVEELRDITFKGIEEVSRVVIRREELDVGEQFVLYTEGSAFGDVLEIEGVDA 264

Query: 939 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEV 995
            + + NN +E+++ LGIEAAR  I+ E    +   G+  ++ RH MLVAD+MT++GE+
Sbjct: 265 SRTTCNNIHEIHRNLGIEAAREAIIEETNNTLAEQGLDDVNVRHLMLVADMMTNRGEI 322


>gi|336041419|gb|AEH95287.1| RNA polymerase II largest subunit [Malawimonas jakobiformis]
          Length = 1042

 Score =  171 bits (434), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 101/279 (36%), Positives = 154/279 (55%), Gaps = 35/279 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVV+FNRQP+LHK+S+M HR +VLP+ TFR N  V TPYNADFDGDEMN+H+PQ+ E 
Sbjct: 374 DGDVVVFNRQPTLHKMSMMGHRVRVLPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSHET 433

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE               + LM    N+V+P+  + ++   QD + G  L T+++ F  R
Sbjct: 434 RAE--------------LEELMMVPRNIVSPQANKPVMGIVQDSLLGTKLFTKRDTFLER 479

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNP-VVFVRTAVIWTGKQIFSLILKPNRDCPV 519
                    L+ +T     ++   SW    P    ++   +WTGKQ+FSLI+      PV
Sbjct: 480 --------DLVNNT-----LMWLPSWDGHVPKPAILKPKQLWTGKQVFSLIVP-----PV 521

Query: 520 NANLKTKGRA-YTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
           N   K+ G      N++F   D+ V +   E+L+G + K+T+G+    ++ +I+  + G 
Sbjct: 522 NVLRKSIGAPDKEDNDDFTASDTKVRIEQGEVLSGIVCKNTVGN-ASGSLVHIIWNELGH 580

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           +     +  +  + +++LMNRGFSIGIGD       +QN
Sbjct: 581 EATRNFLDSVQTVINYWLMNRGFSIGIGDTIADPATMQN 619



 Score = 99.8 bits (247), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 43/63 (68%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D+TP  +GFV+NS+  GL P EFFFH MGGREGL+DTAVKT+ETGY+QRRL+K++ED+ V
Sbjct: 732 DMTPESRGFVENSYLRGLNPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLMKAMEDVMV 791

Query: 666 QYD 668
           +YD
Sbjct: 792 KYD 794



 Score = 41.6 bits (96), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 45/186 (24%), Positives = 76/186 (40%), Gaps = 27/186 (14%)

Query: 149 GYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKS 208
           G+++L  PVFH G+F+ V+ +L+ +C    C+R+L         R      AL+   RK 
Sbjct: 1   GHVELAKPVFHYGFFKTVVKVLRCVCF--YCSRLLADTSDPRFLR------ALTLKNRKH 52

Query: 209 LKKKILETTKKVSVCPHCGEINGVVKKCGLLK--ISHEKYKNRTKKKDA----------- 255
             +++ +      VC   GE        G+L    S ++      KK A           
Sbjct: 53  RFREVHDCCVGRKVC-EAGEDGRRADPLGVLNDPSSQQQVPGAPGKKAAHGGCGNVQPHI 111

Query: 256 IVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKP 315
            VE +L    E  K + E +  K       L P +V  +   I  +D   L  N  L++P
Sbjct: 112 KVESMLRLVAEFPKRDDEAQPRK-----MVLTPEKVHNILSHISDDDCRALGFNPALARP 166

Query: 316 SDLILT 321
             ++++
Sbjct: 167 DWMVIS 172


>gi|119872216|ref|YP_930223.1| DNA-directed RNA polymerase subunit A' [Pyrobaculum islandicum DSM
           4184]
 gi|119673624|gb|ABL87880.1| DNA-directed RNA polymerase, subunit A' [Pyrobaculum islandicum DSM
           4184]
          Length = 884

 Score =  171 bits (434), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 100/273 (36%), Positives = 150/273 (54%), Gaps = 41/273 (15%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++S+M H  KVLP RTFR +  VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 423 DGDIVLFNRQPSLHRVSMMGHLVKVLPGRTFRLHLAVCPPYNADFDGDEMNLHVPQTEEA 482

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+ LM  + +++TPR G  +I A QD+I G Y+L+ K+ F  +
Sbjct: 483 RAE--------------ARTLMLVEKHIITPRYGGAIIGARQDYIIGAYILSHKSTFLTK 528

Query: 461 AQTMRI--ASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCP 518
            +   +  A   + D  +              P + +    +WTGKQI S  L  + +  
Sbjct: 529 KEVAYLLGAGKSVEDPPE--------------PAI-LHPVELWTGKQIISHFLPKDLNWV 573

Query: 519 VNANLKTKGR-AYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFG 577
                K+K + AY      C+ D ++I+ N  L+ G +DK ++G+    ++++ + RD+ 
Sbjct: 574 QPTAFKSKCQDAYK-----CNGDEWIIVINGNLVKGVLDKKSIGAEQVDSLWHRIARDYP 628

Query: 578 EDVAVTAMWRLSRMTSF--YLMNRGFSIGIGDV 608
            ++A    W  S +  F  +L  RGF+ G+  V
Sbjct: 629 PEIA--RQWLDSSLRVFLRFLDLRGFTFGMDSV 659



 Score =  114 bits (284), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 76/255 (29%), Positives = 125/255 (49%), Gaps = 40/255 (15%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           +++ S +++ +  +Y  D    P+  G+ DRR+G  +  A C TCGQ    C GHFG+I+
Sbjct: 28  IRKYSVMEVTTSEVY--DEGGLPVRGGVADRRLGVAEPGARCETCGQTHDVCPGHFGHIE 85

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSY-LVRKSLKK 211
           L  PV H+G+ R + +IL++ C  P C R++L +E+   +R +L      + L+  +L +
Sbjct: 86  LVKPVIHVGFARIIYDILRTTC--PNCGRIMLKDEEIQRYRERLTKLKGKWRLLALNLHE 143

Query: 212 KILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFN 271
           KI +   +   CPHCG                  YK R K +          +     F 
Sbjct: 144 KIRKKASERMTCPHCG------------------YK-RNKIR----------FERPYYFY 174

Query: 272 PEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIR 331
            E E     G +  L+P  +      IP ED+ LL +N  +++P   IL  L VPP  +R
Sbjct: 175 EETEE----GALVRLDPETLRDRLAKIPNEDLELLGINPSVARPEWAILKVLPVPPPHVR 230

Query: 332 PSVI--SDLKSDNDV 344
           PS+   S ++S++D+
Sbjct: 231 PSIQLESGVRSEDDL 245



 Score = 83.2 bits (204), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 36/64 (56%), Positives = 48/64 (75%), Gaps = 1/64 (1%)

Query: 606 GDVTPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           GD+ P   GFV+  F  GLTP E+FFH   GR+GL+DTAV+TA++GYMQRRL+ +L+D+ 
Sbjct: 780 GDIGPFVGGFVKRCFRCGLTPVEYFFHAAAGRDGLIDTAVRTAQSGYMQRRLINALQDVY 839

Query: 665 VQYD 668
             YD
Sbjct: 840 TAYD 843



 Score = 44.7 bits (104), Expect = 0.39,   Method: Compositional matrix adjust.
 Identities = 21/58 (36%), Positives = 35/58 (60%), Gaps = 3/58 (5%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKV 77
           + LM  + +++TPR G  +I A QD+I G Y+L+ K+ F  + +   +A  L AG+ V
Sbjct: 487 RTLMLVEKHIITPRYGGAIIGARQDYIIGAYILSHKSTFLTKKE---VAYLLGAGKSV 541


>gi|256811205|ref|YP_003128574.1| DNA-directed RNA polymerase subunit A'' [Methanocaldococcus fervens
            AG86]
 gi|256794405|gb|ACV25074.1| DNA-directed RNA polymerase, subunit A'' [Methanocaldococcus fervens
            AG86]
          Length = 387

 Score =  171 bits (434), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 121/334 (36%), Positives = 174/334 (52%), Gaps = 58/334 (17%)

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFVPD 1158
            Y  A +EP  AVG +AAQSIGEPGTQMT++TFH+AG            + E ++    P 
Sbjct: 49   YRNAMVEPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRMIEIVDARKEPS 108

Query: 1159 DSFILIKL------DMDR-------IRLLHLE-----VDID----SIRYCIERTRGISGH 1196
               + I L      D ++       I  L LE     + ID    SI+  ++  R     
Sbjct: 109  TPIMTIYLKEGYKNDKEKAEKIAKEIESLTLENIAESISIDLWTQSIKVELDENRLADRG 168

Query: 1197 LTVSGH----------------SFLILKPKDSS-KSFNSKMYQMKQLLPSVVIKGVQGIN 1239
            LT+                   S L LK K  S K+   ++ ++K    ++ +KG+ GI 
Sbjct: 169  LTIDDVVEAIKKKVKVKIDVEGSTLYLKIKTPSIKALRKRIPKIK----NIQLKGIPGIE 224

Query: 1240 RAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIM 1299
            R ++ +E  E    Y L  +G NLR+V    GV   +  +NN  E+ + LGIEAAR+ I+
Sbjct: 225  RVLVKKEGDE----YVLYSQGSNLREVFKIEGVDTTRTITNNIIEIQEVLGIEAARNAII 280

Query: 1300 TEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHL 1359
             E++  +E  G+ +D RH MLVAD+MT+ GEV  I RHG+A  K SVL  A+FE T  HL
Sbjct: 281  NEMRNTLEQQGLEVDIRHLMLVADMMTADGEVKPIGRHGVAGEKGSVLARAAFEETVKHL 340

Query: 1360 FDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            + AA  G  D + GV E +I+G P+ +GTG ++L
Sbjct: 341  YAAAERGDVDKLKGVIENVIVGKPIYLGTGCVEL 374



 Score =  105 bits (263), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 80/235 (34%), Positives = 125/235 (53%), Gaps = 18/235 (7%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDK--DTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A +  STPI+T YL +    D + A  +   +E  TL  + E I      
Sbjct: 93  GLPRMIEIVDARKEPSTPIMTIYLKEGYKNDKEKAEKIAKEIESLTLENIAESIS----I 148

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSS-KSF 880
           D     IK+++D  RL    + ID +   I++             S L LK K  S K+ 
Sbjct: 149 DLWTQSIKVELDENRLADRGLTIDDVVEAIKKK---VKVKIDVEGSTLYLKIKTPSIKAL 205

Query: 881 NSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
             ++ ++K    ++ +KG+ GI R ++ +E  E    Y L  +G NLR+V    GV   +
Sbjct: 206 RKRIPKIK----NIQLKGIPGIERVLVKKEGDE----YVLYSQGSNLREVFKIEGVDTTR 257

Query: 941 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
             +NN  E+ + LGIEAAR+ I+ E++  +E  G+ +D RH MLVAD+MT+ GEV
Sbjct: 258 TITNNIIEIQEVLGIEAARNAIINEMRNTLEQQGLEVDIRHLMLVADMMTADGEV 312


>gi|167042230|gb|ABZ06962.1| putative RNA polymerase Rpb1, domain 2 [uncultured marine
           crenarchaeote HF4000_ANIW93I24]
          Length = 1264

 Score =  171 bits (434), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 95/269 (35%), Positives = 151/269 (56%), Gaps = 35/269 (13%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           SD DVVLFNRQPSLH++SIMAH  +VLP +TFR +  VC PYNADFDGDEMN+H+PQ+EE
Sbjct: 415 SDGDVVLFNRQPSLHQMSIMAHHVRVLPGKTFRLHPSVCPPYNADFDGDEMNLHVPQSEE 474

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           ARAEA+              +LM  +  L++PR G  +I A +DFITG YLLT+ +    
Sbjct: 475 ARAEAM--------------LLMRVQEQLISPRFGGPIIGALRDFITGAYLLTKDDTTLT 520

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           + +    A            ++  +  +   P +  +   ++TGKQ+FSL L      P 
Sbjct: 521 KQEFSNYA------------MLGGYDEKLPEPKIKNKNGSLYTGKQLFSLFL------PS 562

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           + N     + ++       +D  V+++N EL++G +DK+ +G+    ++ + + +D+G +
Sbjct: 563 DFNFVMTSK-WSRGTNGKQKD--VVIKNGELVSGVIDKTGIGAEEPESILHRIAKDYGNE 619

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
            A   +  +  +   ++ + GFS G  D+
Sbjct: 620 KANKFLNSVLIIIKQFITDYGFSYGYSDL 648



 Score =  146 bits (368), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 100/339 (29%), Positives = 161/339 (47%), Gaps = 61/339 (17%)

Query: 1108 EKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG---------------------- 1145
            E Y ++++EP  AVG + AQSIGEPGTQMTL+TFH AG                      
Sbjct: 928  ELYDKSKVEPGQAVGIVTAQSIGEPGTQMTLRTFHTAGIAEKNVTLGLPRIIELVDARKK 987

Query: 1146 ----------------------EVCEYIEEVFVPD--------DSFILIKLDMDRIRLLH 1175
                                  ++   I +  V D        D    I L +D +RL +
Sbjct: 988  PSTPSMDIYLDKDSKSSKEKAIQIAREILQTTVADLLIRQAETDYQTKITLSVDNVRLKN 1047

Query: 1176 LEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGV 1235
                +D I   +E  +     L  +  +  ++   D +      +  ++  +    +KGV
Sbjct: 1048 RGCSLDDIMTALETNKKFELKLDNNIITLQLVAESDVAT-----VVALRNKVLKTTVKGV 1102

Query: 1236 QGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAAR 1295
              I R  + EE+ +    + +   G NL  V+   GV      +NN +E+   LGIEAAR
Sbjct: 1103 PDIERITLKEENGD----WLIQTTGSNLAKVIVVKGVDKNNVRTNNVFEISTVLGIEAAR 1158

Query: 1296 STIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENT 1355
            ++++ E+K  +EN G+ +D R+ MLVADLM  KG +  I RHG+A  K+SVL  A+FE T
Sbjct: 1159 TSLINELKATLENQGLEVDVRYLMLVADLMCHKGYLQQIGRHGIAGSKDSVLARAAFEIT 1218

Query: 1356 SDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
               + +AA  G+ + + G++E +I+G  + +G+G + + 
Sbjct: 1219 VPTIANAAKLGEIEELKGITENVIVGSLIPIGSGTVDIF 1257



 Score =  103 bits (257), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 71/258 (27%), Positives = 122/258 (47%), Gaps = 43/258 (16%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + +++ S +++ +   Y +D     +  GL+D R+GT +    C TCG   + C GHFG+
Sbjct: 20  NEIRKYSVVEVTAPETYDEDGM--AVQGGLMDGRLGTLEPGQKCLTCGNTSARCPGHFGH 77

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLV--RKS 208
           ++L  PV HI +   +  +LQ+ C+  +C+R+ + +E    F +KL+    S+ V  +K 
Sbjct: 78  VELSEPVLHIAFIDNIHKLLQATCR--SCSRLKVPQEVLDEF-SKLKKYRASFNVISQKR 134

Query: 209 LKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAV 268
           + ++I E  KK   CPHCG+I                                   NE +
Sbjct: 135 IPEQIFEKAKKSKECPHCGKIQ----------------------------------NELI 160

Query: 269 KFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPN 328
              P I   K       L P+ + + F  I  +D+ L+  N   ++P   IL  L VPP 
Sbjct: 161 FTKPTIFIEKTELGENRLLPITIRERFLQITDDDLELVNYNTATARPEWFILQALPVPPV 220

Query: 329 CIRPSVI--SDLKSDNDV 344
            +RPS+I  S ++S++D+
Sbjct: 221 TVRPSIILESGIRSEDDL 238



 Score = 97.4 bits (241), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 68/232 (29%), Positives = 116/232 (50%), Gaps = 15/232 (6%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLE--RTTLGEVCEYIEEVFVP 821
            G+PRI E+++A +  STP +  YLDKD+     + ++   E  +TT+ ++     E    
Sbjct: 974  GLPRIIELVDARKKPSTPSMDIYLDKDSKSSKEKAIQIAREILQTTVADLLIRQAET--- 1030

Query: 822  DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             D    I L +D +RL +    +D I   +E  +     L  +  +  ++   D +    
Sbjct: 1031 -DYQTKITLSVDNVRLKNRGCSLDDIMTALETNKKFELKLDNNIITLQLVAESDVAT--- 1086

Query: 882  SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
              +  ++  +    +KGV  I R  + EE+ +    + +   G NL  V+   GV     
Sbjct: 1087 --VVALRNKVLKTTVKGVPDIERITLKEENGD----WLIQTTGSNLAKVIVVKGVDKNNV 1140

Query: 942  SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
             +NN +E+   LGIEAAR++++ E+K  +EN G+ +D R+ MLVADLM  KG
Sbjct: 1141 RTNNVFEISTVLGIEAARTSLINELKATLENQGLEVDVRYLMLVADLMCHKG 1192



 Score = 82.0 bits (201), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 34/57 (59%), Positives = 46/57 (80%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFV+++F  GL+  EFFFH MGGREGLVDTAV+T ++GYMQRRL+ + E + ++YD
Sbjct: 776 HGFVKSNFRDGLSVLEFFFHAMGGREGLVDTAVRTQQSGYMQRRLINAFEHIRLEYD 832


>gi|374327623|ref|YP_005085823.1| DNA-directed RNA polymerase subunit alpha [Pyrobaculum sp. 1860]
 gi|356642892|gb|AET33571.1| DNA-directed RNA polymerase subunit alpha [Pyrobaculum sp. 1860]
          Length = 884

 Score =  171 bits (433), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 102/269 (37%), Positives = 148/269 (55%), Gaps = 33/269 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIM H  KVLP RTFR +  VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 423 DGDIVLFNRQPSLHRVSIMGHLVKVLPGRTFRLHLAVCPPYNADFDGDEMNLHVPQTEEA 482

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+ LM  + +++TPR G  +I A QD+I G YLL+ K  F  +
Sbjct: 483 RAE--------------ARTLMLVERHIITPRYGGAIIGARQDYIIGAYLLSLKTTFLTK 528

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +   +A  L A  S               P + +    +WTGKQI S  L  + +    
Sbjct: 529 KE---VAFLLGAGKS---------GEDPPEPAI-LHPVELWTGKQIISHFLPRDLNWVQP 575

Query: 521 ANLKTKGR-AYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
              K++ + AYT     C  D ++I+ N  ++ G +DK ++G+    ++++ + RD+  +
Sbjct: 576 TAFKSRCQDAYT-----CPTDEWIIIINGNMVKGVLDKKSIGAEQVDSLWHRIARDYPPE 630

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           VA   +    R+   YL  RGF+ G+  +
Sbjct: 631 VARRWLDSSLRLFLRYLDLRGFTFGMDSI 659



 Score =  117 bits (294), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 73/255 (28%), Positives = 130/255 (50%), Gaps = 40/255 (15%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           +++ S +++ +  +Y  D    P+  G+ DRR+G  +  A C TCGQ    C GHFG+I+
Sbjct: 28  IRKYSVMEVTTSEVY--DEGGLPVRGGIADRRLGVAEPGARCETCGQTHDVCPGHFGHIE 85

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSY-LVRKSLKK 211
           L  PV H+G+ R + +IL++ C  P C R++L +E+   +R +L      + L+ ++L +
Sbjct: 86  LVKPVVHVGFARVIYDILRTTC--PNCGRIMLKDEEIERYRERLTKLKKRWRLLAQNLHE 143

Query: 212 KILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFN 271
           KI +   +   CPHCG               ++K K R ++     E+   E    VK +
Sbjct: 144 KIRKKAAERVTCPHCG---------------YKKNKIRFERPYYFYEE--TEDGALVKLD 186

Query: 272 PEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIR 331
           PEI                + +    +P ED+ LL +N+ +++P   +L  L VPP  +R
Sbjct: 187 PEI----------------LRERLAKVPGEDLELLGINSSVARPEWAVLKVLPVPPPHVR 230

Query: 332 PSVI--SDLKSDNDV 344
           PS+   + ++S++D+
Sbjct: 231 PSIQLETGIRSEDDL 245



 Score = 84.0 bits (206), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 36/65 (55%), Positives = 50/65 (76%), Gaps = 1/65 (1%)

Query: 605 IGDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDL 663
           +GD+     GFV++ F  GLTP E+FFH   GR+GL+DTAV+TA++GYMQRRL+ +L+D+
Sbjct: 779 VGDIGAFSGGFVRSCFRCGLTPVEYFFHAAAGRDGLIDTAVRTAQSGYMQRRLINALQDV 838

Query: 664 CVQYD 668
            V YD
Sbjct: 839 YVAYD 843



 Score = 42.4 bits (98), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 21/56 (37%), Positives = 33/56 (58%), Gaps = 3/56 (5%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           + LM  + +++TPR G  +I A QD+I G YLL+ K  F  + +   +A  L AG+
Sbjct: 487 RTLMLVERHIITPRYGGAIIGARQDYIIGAYLLSLKTTFLTKKE---VAFLLGAGK 539


>gi|296243131|ref|YP_003650618.1| DNA-directed RNA polymerase subunit A' [Thermosphaera aggregans DSM
           11486]
 gi|296095715|gb|ADG91666.1| DNA-directed RNA polymerase, subunit A' [Thermosphaera aggregans
           DSM 11486]
          Length = 881

 Score =  171 bits (432), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 94/266 (35%), Positives = 149/266 (56%), Gaps = 32/266 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++S+MAH  +VLP++T R N  VC PYNADFDGDEMN+H+PQ+EEA
Sbjct: 412 DGDIVLFNRQPSLHRISVMAHVVRVLPYKTLRLNVLVCPPYNADFDGDEMNLHVPQSEEA 471

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A++LM  + +++TPR G  +I   QD+I+G ++LT K+    +
Sbjct: 472 RAE--------------ARLLMLVEKHILTPRYGGPIIGGLQDYISGAFVLTSKSTILRK 517

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +        +A+   + G  +        P +  +    WTGKQ+ S+ L  + +   N
Sbjct: 518 EE--------VAELLGVAGYHEAIP----EPAIL-KPKEYWTGKQLVSVFLPKDLNYRRN 564

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           + L     A    +E C  DS VI++   LL G +DK+++G     ++ + L++++GED+
Sbjct: 565 SKL-AGASALRCVDEDCPHDSIVIIKKGVLLEGVLDKASIGREEPESLIHWLIKEYGEDI 623

Query: 581 AVTAMWRLSRM----TSFYLMNRGFS 602
                 R+ +M    +  Y +  G+S
Sbjct: 624 GRLFKDRVYKMFLRASEKYGLTMGYS 649



 Score =  105 bits (262), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 72/260 (27%), Positives = 126/260 (48%), Gaps = 46/260 (17%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + +++ S  QI++ ++Y  D    PI  G++D+R+G  +    C  CG     C GHFG+
Sbjct: 16  EEIRKLSVTQIITSDVYDND--GAPIDGGVMDKRLGAIEPGETCPVCGNTRDSCPGHFGH 73

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           I+L  PV H G+ + ++  L++ C+   C R+ + E++   + A ++   L  L    L 
Sbjct: 74  IELTKPVIHAGFAKHILMYLKATCRE--CGRIKIPEKERQEYLALMKE--LEELNLIYLL 129

Query: 211 KKILETTKKVSV----CPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNE 266
           K+  E  K+ +     CPHCG                ++Y+ +  K  +  E        
Sbjct: 130 KRFYEYVKRKASAEMKCPHCGA---------------KQYRYKLDKPHSFYE-------- 166

Query: 267 AVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVP 326
                      K+ GL + L P ++    E IP ED+ LL  N E ++P  ++LT L VP
Sbjct: 167 ----------QKETGL-EKLWPTDIRVRLEKIPDEDVRLLGGNPEEARPEWMVLTVLPVP 215

Query: 327 PNCIRPSVI--SDLKSDNDV 344
           P  +RPSV+  + ++S++D+
Sbjct: 216 PRTVRPSVLLETGIRSEDDL 235



 Score = 83.6 bits (205), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 39/83 (46%), Positives = 54/83 (65%), Gaps = 1/83 (1%)

Query: 587 RLSRMTSFYLMNRGFSIGIGDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVK 645
           R  R++  YL          D+ P  +GF+ N F +GL   E FFH   GREGL+DTAV+
Sbjct: 754 RGKRLSRGYLYRPLPHFKQKDIGPEARGFIANGFVNGLEALEMFFHAAAGREGLIDTAVR 813

Query: 646 TAETGYMQRRLVKSLEDLCVQYD 668
           T+++GYMQRRL+ +L+DL V+YD
Sbjct: 814 TSQSGYMQRRLINALQDLRVEYD 836


>gi|452844541|gb|EME46475.1| hypothetical protein DOTSEDRAFT_70470 [Dothistroma septosporum
           NZE10]
          Length = 1773

 Score =  171 bits (432), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 100/276 (36%), Positives = 143/276 (51%), Gaps = 47/276 (17%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND ++FNRQPSLHK S+M HR KV+P+ TFR N  V +PYNADFDGDEMN+H+PQ+ E 
Sbjct: 451 DNDYIIFNRQPSLHKESMMGHRVKVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSHET 510

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    +  L  + H          N+V+P+    L+   QD + G Y++T+++ F + 
Sbjct: 511 RAE----VANLCAVPH----------NIVSPQKNGPLMGIVQDTMAGIYMMTRRDVFLDY 556

Query: 461 AQTMRIASTLIADTSDICGIIKRFSW-RSWN----PVVFVRTAVIWTGKQIFSLILKPNR 515
            Q M I                   W   W+    P   ++    WTGKQI SL L    
Sbjct: 557 EQVMNI-----------------LLWVPGWDGVVPPPAIIKPLPRWTGKQIASLAL---- 595

Query: 516 DCPVNAN-LKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLR 574
             P   N L+ K       EE   +D  ++++N E++ G M K  +G+ G   V + +  
Sbjct: 596 --PAGLNILRPKKDHMPLREE---KDDGLVIQNGEIIWGRMVKGIVGASG-GGVVHCIFN 649

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           D G D AV       R+  ++L++ GFS+GIGD  P
Sbjct: 650 DRGPDAAVEFFNAAQRIVCYWLLHNGFSVGIGDTIP 685



 Score =  115 bits (289), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 65/185 (35%), Positives = 103/185 (55%), Gaps = 15/185 (8%)

Query: 1225 QLLPSVVIKGVQGINRAVIHE-----EDVEGVTKYK----------LLVEGDNLRDVMAT 1269
             +L +VV++GV G+ RA + +     E  +G  K+           L  +G NL+D++A 
Sbjct: 1282 HMLDTVVLRGVSGVRRAFVSKDARLYEAPDGALKFSTQEEKCQEWLLDTDGVNLKDILAV 1341

Query: 1270 YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 1329
             GV   + + N+   + K  GIEA R+++M E+K V+ N G  ++ RH  ++ D+M ++G
Sbjct: 1342 EGVDPTRTTCNHFQSIMKVFGIEAVRASLMREMKDVLTNDGSYVNHRHMAILCDVMCARG 1401

Query: 1330 EVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
            E++ +TRHG+ +     L   SFE T + LFDAA  G+ D   GVSE II+G     GTG
Sbjct: 1402 ELMAVTRHGINRSDTGALMRCSFEETVEILFDAASSGELDDCRGVSENIILGQLAPSGTG 1461

Query: 1390 LIKLL 1394
               +L
Sbjct: 1462 EFDML 1466



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKTAETGY+QRRLVK+LE++ +
Sbjct: 805 DYSPASRGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEEVMI 864

Query: 666 QYD 668
           +YD
Sbjct: 865 KYD 867



 Score =  100 bits (249), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 77/262 (29%), Positives = 118/262 (45%), Gaps = 53/262 (20%)

Query: 110 DPQRT-PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVIN 168
           D QR  P   GL D ++GT  + + C TCG+   +C GHFG+I+L +PVFH+G+   +  
Sbjct: 42  DEQRNRPREKGLNDPKLGTIDRNSRCGTCGEEQLECPGHFGHIELAIPVFHVGFITKIKK 101

Query: 169 ILQSICKNPTCARVLLGEEKAAGFRA--KLRNPALSYLVRKSLKK--------------- 211
           IL+S+C N  C + LL +E++  F    KLR+P   +     L K               
Sbjct: 102 ILESVCHN--CGK-LLEDERSTAFAMALKLRDPKRRFEQITRLCKGKTDCAADEPEKDDG 158

Query: 212 KILETTKKVSVCPH--CGEINGVVKKCGLLKISHEKY-KNRTKKKDAIVEDLLAEYNEAV 268
              E  KK     H  CG +   ++K  L  I   K  KN     DA +E          
Sbjct: 159 NFGEDPKKPKQAGHGGCGNVQPTIRKEQLKLIGTWKMAKNEETGDDAGIEK--------- 209

Query: 269 KFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPN 328
                          + + P   L +F  I  ED+  L +N + ++P  ++LT L VPP 
Sbjct: 210 ---------------RPITPQMALNIFRNISEEDLARLGLNVDYARPEWMVLTVLPVPPP 254

Query: 329 CIRPSVISD-----LKSDNDVV 345
            +RPS+  D     ++S++D+ 
Sbjct: 255 AVRPSISVDGTSQGMRSEDDLT 276



 Score = 89.4 bits (220), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 75/296 (25%), Positives = 134/296 (45%), Gaps = 58/296 (19%)

Query: 759  KLSQDGVPRIKEIINASRNISTPIITAYLDKDTDL--DYARIVKGRLERTTLGEVCEYIE 816
            K +  GVPR+KEI+N + NI TP +  Y   +T    + A+ ++  +E T+L  V +  E
Sbjct: 1109 KTTTKGVPRLKEILNVAENIKTPNMKVYQLPETAQFQESAKQLRSMVEFTSLRGVTDETE 1168

Query: 817  EVFVPDDSFILIKLDMDRIRLLHLEVDIDS---------IRYCIERTRGISGHLTVS--- 864
              + PD    +I +D D +    +  D D          +R  + R + +   LTV+   
Sbjct: 1169 IYYDPDVQSTVIDVDKDMVEAHFIIPDDDENPDAQGKWLLRITLGRAKLLDKGLTVTNVA 1228

Query: 865  -------GHSFLILKPKDSSKS--FNSKMYQMKQ--------------------LLPSVV 895
                   G    ++   D++       +M    Q                    +L +VV
Sbjct: 1229 NRIKEMFGKDVAVIFADDNADECVIRVRMNTGGQNKDEEDAEEEEDTLKRLEAHMLDTVV 1288

Query: 896  IKGVQGINRAVIHE-----EDVEGVTKYK----------LLVEGDNLRDVMATYGVKGVK 940
            ++GV G+ RA + +     E  +G  K+           L  +G NL+D++A  GV   +
Sbjct: 1289 LRGVSGVRRAFVSKDARLYEAPDGALKFSTQEEKCQEWLLDTDGVNLKDILAVEGVDPTR 1348

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL 996
             + N+   + K  GIEA R+++M E+K V+ N G  ++ RH  ++ D+M ++GE++
Sbjct: 1349 TTCNHFQSIMKVFGIEAVRASLMREMKDVLTNDGSYVNHRHMAILCDVMCARGELM 1404



 Score = 55.5 bits (132), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/37 (64%), Positives = 28/37 (75%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            +++RA + P   VG LAAQSIGEP TQMTL TFH AG
Sbjct: 1069 RFLRALVSPGEMVGVLAAQSIGEPATQMTLNTFHLAG 1105


>gi|410722153|ref|ZP_11361465.1| DNA-directed RNA polymerase subunit A'', partial [Methanobacterium
           sp. Maddingley MBC34]
 gi|410597472|gb|EKQ52085.1| DNA-directed RNA polymerase subunit A'', partial [Methanobacterium
           sp. Maddingley MBC34]
          Length = 721

 Score =  171 bits (432), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 100/272 (36%), Positives = 148/272 (54%), Gaps = 46/272 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++S+MAH  KVLPH+TFR N CVC PYNADFDGDEMN+H+ QTEE+
Sbjct: 408 DGDIVLFNRQPSLHRMSMMAHEVKVLPHKTFRLNLCVCPPYNADFDGDEMNMHVFQTEES 467

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              AK LM  + ++++PR G  +I    D I+G YLLT++ + F  
Sbjct: 468 RAE--------------AKSLMRVQEHILSPRFGGPIIGGIHDHISGAYLLTREGSAFQE 513

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                              ++ +   +S  P+   R    WTGK+IFSL+L      P +
Sbjct: 514 ------------------DVVFQMLKKSQLPLPKPRNQE-WTGKEIFSLLL------PKD 548

Query: 521 ANLKTKGRAYTANEEF----CHRDSYVILRNSELLAGSMDKSTLGS-GGKANVFYILLRD 575
            N+  K       +E     C  D+YV++ N EL +G++D+   G+  GK  +   ++++
Sbjct: 549 LNMVYKAEICRKCDECLKQDCKNDAYVVIENGELKSGAIDEKAYGAFSGK--ILDSIVKE 606

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           +G D A   +   +++    +M RGF+    D
Sbjct: 607 YGTDRAREFLDAATKLAISGIMKRGFTTSTAD 638



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 74/249 (29%), Positives = 113/249 (45%), Gaps = 53/249 (21%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + +++ S  +IV+ + Y +D    PI  GL+D R+G       C +CG    DC GHFG+
Sbjct: 19  ENIRRMSVTKIVTPDTYDED--GYPIEAGLMDPRLGVIDPGLRCRSCGSKGGDCQGHFGH 76

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGF----RAKLRN-PALSYLV 205
           I+L  PV H+G+   +  IL+S C    C RVLL E +   +     ++L+N  +++ LV
Sbjct: 77  INLARPVVHVGFADTIHKILRSTCSE--CGRVLLTETERIDYGDRIGSRLKNEESITGLV 134

Query: 206 RKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYN 265
                 K + TT +   CPHC      VK    + I    YK                  
Sbjct: 135 ------KAVYTTARRDKCPHCDTEQEDVKIDKPVSIVEGNYK------------------ 170

Query: 266 EAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLV 325
                               L P EV +  E IP ED   L +N+++++P  ++LT L V
Sbjct: 171 --------------------LTPSEVRERLEKIPEEDYVYLGINSKVARPEWMVLTVLPV 210

Query: 326 PPNCIRPSV 334
           PP  +RPS+
Sbjct: 211 PPVTVRPSI 219


>gi|448731184|ref|ZP_21713487.1| DNA-directed RNA polymerase subunit A'' [Halococcus saccharolyticus
            DSM 5350]
 gi|445792778|gb|EMA43379.1| DNA-directed RNA polymerase subunit A'' [Halococcus saccharolyticus
            DSM 5350]
          Length = 397

 Score =  171 bits (432), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 104/338 (30%), Positives = 178/338 (52%), Gaps = 60/338 (17%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFVP 1157
            +Y+  +++P   VG ++AQSIGEPGTQMT+ TFH+AG            + E ++    P
Sbjct: 49   RYLDTRVDPLDPVGTVSAQSIGEPGTQMTMNTFHYAGVAEIDVTQGLPRLIELVDARKTP 108

Query: 1158 DDSFILIKLD----MDRIRLLHLEVDIDSIRYCIERTRGIS-GHLTVSGHSFLI------ 1206
            D   + + LD     DR +          + + IE TR ++ G ++ +    L+      
Sbjct: 109  DTPMMTVHLDGEYATDREKA-------HEVVWAIEATRILALGDVSTNVADMLVQIDLNE 161

Query: 1207 -------LKPKDSSKSFNSKM-----------------------YQMKQLLPSVVIKGVQ 1236
                   + P++ ++     +                        Q+ + L  +V KG+ 
Sbjct: 162  QTLEERMITPEEVAEIIEDSLGVDVVQSGTTVEFGPDQPSYRDLLQLVEELREIVFKGID 221

Query: 1237 GINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARS 1296
             ++R VI +E+++   ++ L  EG    DV+   GV   + + NN +E+++ LG+EAAR 
Sbjct: 222  EVSRVVIRKEELDEGEEFVLYTEGSAFGDVLDIEGVDASRTTCNNIHEIHRNLGVEAARE 281

Query: 1297 TIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENT 1355
            TI+ E    +E  G+ +++ RH MLVAD+MT++G +  I RHG++  K+SVL  A+FE T
Sbjct: 282  TIIEETMDTLEEQGLGNVNIRHLMLVADIMTTEGTIESIGRHGISGSKDSVLARAAFEVT 341

Query: 1356 SDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
             +HL DAA +G+ D ++GV+E +I+G P+ +GTG + L
Sbjct: 342  VNHLLDAAVHGEIDDLNGVTENVIVGKPIKLGTGDVNL 379



 Score =  100 bits (248), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 68/238 (28%), Positives = 127/238 (53%), Gaps = 20/238 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T +LD +  TD + A  V   +E T    LG+V   + + 
Sbjct: 94  GLPRLIELVDARKTPDTPMMTVHLDGEYATDREKAHEVVWAIEATRILALGDVSTNVAD- 152

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSK 878
                  +L+++D++   L    +  + +   IE + G+     V   + +   P   S 
Sbjct: 153 -------MLVQIDLNEQTLEERMITPEEVAEIIEDSLGVD---VVQSGTTVEFGPDQPSY 202

Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 938
                + Q+ + L  +V KG+  ++R VI +E+++   ++ L  EG    DV+   GV  
Sbjct: 203 R---DLLQLVEELREIVFKGIDEVSRVVIRKEELDEGEEFVLYTEGSAFGDVLDIEGVDA 259

Query: 939 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEV 995
            + + NN +E+++ LG+EAAR TI+ E    +E  G+ +++ RH MLVAD+MT++G +
Sbjct: 260 SRTTCNNIHEIHRNLGVEAARETIIEETMDTLEEQGLGNVNIRHLMLVADIMTTEGTI 317


>gi|73671120|ref|YP_307135.1| DNA-directed RNA polymerase subunit A' [Methanosarcina barkeri str.
           Fusaro]
 gi|72398282|gb|AAZ72555.1| DNA-directed RNA polymerase, subunit A' [Methanosarcina barkeri
           str. Fusaro]
          Length = 880

 Score =  171 bits (432), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 102/269 (37%), Positives = 150/269 (55%), Gaps = 33/269 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHK+SIMAH  KVLP++TFR N  VC PYNADFDGDEMN+H  QTEE+
Sbjct: 412 DGDIVLFNRQPSLHKMSIMAHSVKVLPNKTFRLNPAVCPPYNADFDGDEMNMHALQTEES 471

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              AK+LM  + N+++PR G  +I    D I+G +LLT        
Sbjct: 472 RAE--------------AKILMQVQENILSPRFGGPIIGGIHDHISGLFLLT-------- 509

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSW-NPVVFVRTA-VIWTGKQIFSLILKPNRDCP 518
               R  + + AD  D   ++++ + R   +P  +       WTGKQIFS IL  N +  
Sbjct: 510 ----RFENHIYAD--DAYDMLRKSNIRELPSPAGYDPDGKPYWTGKQIFSQILPKNLNTQ 563

Query: 519 VNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
             A + +        +E C  D+YV++R+ EL+ G++D++ +G+  K  V   ++++ G 
Sbjct: 564 FAAQVCS--HCDICKKEECPNDAYVVIRDGELIKGTIDEAAIGA-FKGKVQDRIIKEIGP 620

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           +V    +  ++ +    +M  G S GI D
Sbjct: 621 EVGARFIDNMTMLAVRAIMRTGLSFGIAD 649



 Score = 95.9 bits (237), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 71/254 (27%), Positives = 115/254 (45%), Gaps = 44/254 (17%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           +++ S   I++ + Y  D    PI  GL+D R+G       C TC     +C GHFG+I+
Sbjct: 24  IRKMSSTPIITADTY--DDDGFPIDMGLMDTRLGVIDPGLRCKTCSGRAGECPGHFGHIE 81

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKK 212
           L  PV H+G+ + +  +L++ C+   C+R+LL   +   F  +L        +   L  +
Sbjct: 82  LVAPVVHVGFNKVIRKLLRATCRK--CSRLLLDPAQKQHFLDQLIGIEEIGHMPDDLINE 139

Query: 213 ILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNP 272
             +   KV  CP+C E          L+I  EK                 EY E      
Sbjct: 140 AYKEASKVKTCPYCNEEQ--------LEIKFEKP---------------TEYLENG---- 172

Query: 273 EIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRP 332
                      + L P E+   FE IP +DI ++ M+ + ++P  +ILT L VPP  +RP
Sbjct: 173 -----------EKLTPTEIRDRFENIPDDDIRVIGMDPKNARPEWMILTVLPVPPVTVRP 221

Query: 333 SVI--SDLKSDNDV 344
           S+   S  +S++D+
Sbjct: 222 SITLESGQRSEDDL 235



 Score = 93.2 bits (230), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 41/66 (62%), Positives = 56/66 (84%), Gaps = 1/66 (1%)

Query: 606 GDV-TPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           GD+ +   GFV+ S+ SGL PTE+FFH +GGREGLVDTAV+T+++GY+QRRLV +L+DL 
Sbjct: 771 GDLGSDAHGFVKASYKSGLNPTEYFFHAIGGREGLVDTAVRTSQSGYLQRRLVNALQDLE 830

Query: 665 VQYDMS 670
           VQYD++
Sbjct: 831 VQYDLT 836


>gi|302348975|ref|YP_003816613.1| DNA-directed RNA polymerase subunit A'' [Acidilobus saccharovorans
            345-15]
 gi|302329387|gb|ADL19582.1| DNA-directed RNA polymerase subunit A'' [Acidilobus saccharovorans
            345-15]
          Length = 446

 Score =  171 bits (432), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 114/342 (33%), Positives = 180/342 (52%), Gaps = 58/342 (16%)

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFVPD 1158
            Y+ + ++P  AVG + AQSIGEPGTQMTL+TFH+AG            + E ++    P 
Sbjct: 79   YISSMVQPGEAVGVVTAQSIGEPGTQMTLRTFHYAGLMEFDVTLGLPRLIEIVDARHEPS 138

Query: 1159 DSFILIKLD------MDRIRLLHLEVD-------IDSIRYCI-ERT------------RG 1192
               + I L+      ++  R +  E++       +D I Y + +RT            RG
Sbjct: 139  TPMMKIYLEEKYADNLEMARKIAREIEYTTIGNIVDEISYTLGDRTFIVKLDPDMVTDRG 198

Query: 1193 ISGHLTVSGHSFLIL----KPKDS-------SKSF--NSKMYQMKQLLPSV------VIK 1233
            ++    +     L L    K +D        S+S   +  +Y ++     V       ++
Sbjct: 199  LTEDEIMEAFERLKLGDVGKGEDEYTVVLNVSESVLPDDALYDLRSYSEIVSKIKKGYVR 258

Query: 1234 GVQGINRAVI--HEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGI 1291
            G++GI R +I  H ++  G  +Y ++ EG NL +VM   GV   +  +NN YE+   LGI
Sbjct: 259  GIKGIKRTIIQEHTDEKTGKHEYVIIAEGSNLAEVMRVDGVDATRVETNNIYEIADVLGI 318

Query: 1292 EAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLAS 1351
            EAAR++I+ EI  V+++ G+ +D RH MLVAD+MT  G++  I R G+   K SV+  A+
Sbjct: 319  EAARNSIIKEIMDVLQSSGLDVDIRHVMLVADIMTWTGKIRQIGRLGVVGEKPSVIARAA 378

Query: 1352 FENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            FE T + L++AA  G+ +  SGV+E I+ GLP  VGTG++ L
Sbjct: 379  FEVTVNQLYNAAVKGEEEKFSGVTESIVAGLPPRVGTGIVML 420



 Score =  115 bits (287), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 80/245 (32%), Positives = 135/245 (55%), Gaps = 22/245 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A    STP++  YL++    +L+ AR +   +E TT+G + + I   +  
Sbjct: 123 GLPRLIEIVDARHEPSTPMMKIYLEEKYADNLEMARKIAREIEYTTIGNIVDEIS--YTL 180

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIER------TRGISGHLTVSGHSFLILKPKD 875
            D   ++KLD D +    L  D   I    ER       +G   +  V   S  +L P D
Sbjct: 181 GDRTFIVKLDPDMVTDRGLTED--EIMEAFERLKLGDVGKGEDEYTVVLNVSESVL-PDD 237

Query: 876 SS---KSFNSKMYQMKQLLPSVVIKGVQGINRAVI--HEEDVEGVTKYKLLVEGDNLRDV 930
           +    +S++  + ++K+      ++G++GI R +I  H ++  G  +Y ++ EG NL +V
Sbjct: 238 ALYDLRSYSEIVSKIKKGY----VRGIKGIKRTIIQEHTDEKTGKHEYVIIAEGSNLAEV 293

Query: 931 MATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMT 990
           M   GV   +  +NN YE+   LGIEAAR++I+ EI  V+++ G+ +D RH MLVAD+MT
Sbjct: 294 MRVDGVDATRVETNNIYEIADVLGIEAARNSIIKEIMDVLQSSGLDVDIRHVMLVADIMT 353

Query: 991 SKGEV 995
             G++
Sbjct: 354 WTGKI 358


>gi|422727796|gb|AFX61755.2| RNA polymerase I largest subunit, partial [Ascosphaera torchioi]
          Length = 1651

 Score =  171 bits (432), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 100/278 (35%), Positives = 151/278 (54%), Gaps = 35/278 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DV+LFNRQPSLHK S+MAHR +V+P+ TFR N  V TPYNADFDGDEMN+H+PQ+EEA
Sbjct: 366 DGDVILFNRQPSLHKESMMAHRVRVMPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSEEA 425

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L +L ++            N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 426 RAE----LKELCLVPL----------NIVSPQRNGPLMGIVQDTLCGIYKICRRDTFLTK 471

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M I   +     D  G+I +       P +F +    WTGKQI S++L      P  
Sbjct: 472 EQVMNIMMWV----PDWDGVIPQ-------PAIF-KPRPRWTGKQIISMVL------PAG 513

Query: 521 ANL--KTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            NL    K +A   +      D  + +   EL+ G   K ++G+ G   + + +  ++G 
Sbjct: 514 LNLLRLDKDKAPLGDRFSPPADGGLFVHGGELMFGMFSKKSVGAAG-GGIIHTIFNEYGH 572

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           +VA+        + +++L++ GFSIGIGD  P  G ++
Sbjct: 573 EVALNFFNGAQTVVNYWLLHNGFSIGIGDTIPDAGTIE 610



 Score =  104 bits (260), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 62/180 (34%), Positives = 94/180 (52%), Gaps = 15/180 (8%)

Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMAT 1269
             LL ++ ++GV G+ RA I+E+ +  V                ++ L   G  L +V+A 
Sbjct: 1200 HLLDTLTLRGVSGVERAFINEKTIVRVLEDGSLRKSSADPFCKEWVLETSGSALAEVLAI 1259

Query: 1270 YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 1329
             GV   +  SN   EV +  GIEAAR+ ++ E+  V+   G  ++ RH  L+ D+MTS G
Sbjct: 1260 PGVDATRTYSNQFSEVLEVFGIEAARAALLRELTQVLAFDGSYVNHRHLALLIDVMTSGG 1319

Query: 1330 EVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
             V+ +TRHG+ +     L   SFE T + L DAA + + D   GVSE +I+G     GTG
Sbjct: 1320 AVMAVTRHGINRTDTGALMRCSFEETVEILLDAAAFAELDDCRGVSENLILGQMAPAGTG 1379



 Score = 99.4 bits (246), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QR+LVK+LE++ V
Sbjct: 724 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMV 783

Query: 666 QYD 668
           +YD
Sbjct: 784 KYD 786



 Score = 91.3 bits (225), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 77/294 (26%), Positives = 136/294 (46%), Gaps = 60/294 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N ++NI TP +T Y D     + +  + ++  +E T+L  V E  E  + P
Sbjct: 1030 GVPRLKEILNVAKNIKTPSMTVYQDPSIAGEKETVKQLRSAVEHTSLRSVTEATEIYYDP 1089

Query: 822  DDSFILIKLDMDRIR---LLHLEVDIDS-------IRYCIERTRGISGHLTVSGHSFLIL 871
            D    +I+ D D +    ++  +V+ D        +R  + R + +  +LTV   +  I 
Sbjct: 1090 DIQSTVIEADRDMVESYFIIPEDVNDDMSRQSKWLLRIILSRAKLLDKNLTVQDVASKIK 1149

Query: 872  K--PKD-----SSKSFNSKMYQMKQ--------------------------LLPSVVIKG 898
            +  P+D     S  + + ++ +++Q                          LL ++ ++G
Sbjct: 1150 EEYPRDVAVIFSDNNADEQVIRIRQIHETKADEDEDDDTEYDVTLKRLEAHLLDTLTLRG 1209

Query: 899  VQGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMATYGVKGVKCSS 943
            V G+ RA I+E+ +  V                ++ L   G  L +V+A  GV   +  S
Sbjct: 1210 VSGVERAFINEKTIVRVLEDGSLRKSSADPFCKEWVLETSGSALAEVLAIPGVDATRTYS 1269

Query: 944  NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            N   EV +  GIEAAR+ ++ E+  V+   G  ++ RH  L+ D+MTS G V+ 
Sbjct: 1270 NQFSEVLEVFGIEAARAALLRELTQVLAFDGSYVNHRHLALLIDVMTSGGAVMA 1323



 Score = 58.5 bits (140), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 27/41 (65%), Positives = 28/41 (68%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            A   K+ RA   P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 981  AIENKFARAVANPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1021


>gi|212533501|ref|XP_002146907.1| DNA-dependent RNA polymerase II largest subunit, putative
           [Talaromyces marneffei ATCC 18224]
 gi|210072271|gb|EEA26360.1| DNA-dependent RNA polymerase II largest subunit, putative
           [Talaromyces marneffei ATCC 18224]
          Length = 1744

 Score =  170 bits (431), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 99/278 (35%), Positives = 155/278 (55%), Gaps = 35/278 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DV+LFNRQPSLHK S+M HR +V+P+ TFR N  V TPYNADFDGDEMN+H+PQ+EEA
Sbjct: 454 DGDVILFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTTPYNADFDGDEMNMHVPQSEEA 513

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE L    +L+++ +          N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 514 RAELL----QLALVPN----------NIVSPQRNGPLMGIVQDSLCGIYKICRRDVFLTK 559

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M     L+    D  G+I +       P + ++    WTGKQI S++L      P  
Sbjct: 560 DQVM----NLMLWVPDWDGVIPQ-------PAI-IKPRPRWTGKQIISMVL------PSG 601

Query: 521 AN-LKTKGRAYTANEEFCH-RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            N L+        +E+F    D  +++   +L+ G   K T+G+ G   V + +  ++G 
Sbjct: 602 LNLLRVDKDKAPLSEKFSPLTDGGILVHGGQLMYGMFSKKTVGASG-GGVVHTIFNEYGP 660

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           + AV+      R+ +++L++ GFSIGIGD  P +  ++
Sbjct: 661 EAAVSFFNGAQRVVNYWLLHNGFSIGIGDTIPDKKTIE 698



 Score =  104 bits (260), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 61/181 (33%), Positives = 95/181 (52%), Gaps = 15/181 (8%)

Query: 1224 KQLLPSVVIKGVQGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMA 1268
            + LL ++ ++GV G+ RA I+E+D   +                ++ L   G  L DV+ 
Sbjct: 1286 QHLLDTLTLRGVSGVERAFINEKDNARLMDDGSLFLSKADPLCKEWVLETSGTALADVLT 1345

Query: 1269 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK 1328
              GV   +  SN   EV++  GIEAARS ++ E+  V+   G  ++ RH  L+ D+MT +
Sbjct: 1346 IPGVDTTRTYSNQFIEVFEVFGIEAARSALLRELTQVLAFDGSYVNHRHLALLVDIMTVR 1405

Query: 1329 GEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGT 1388
            G +  +TRHG+ +     L   SFE T + L +AA +G+ D   GVSE +I+G     GT
Sbjct: 1406 GYLTPVTRHGINRADNGALMRCSFEETVEILLEAAAFGELDDCRGVSENLILGQLAPAGT 1465

Query: 1389 G 1389
            G
Sbjct: 1466 G 1466



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QR+LVK+LE+L V
Sbjct: 812 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEELMV 871

Query: 666 QYD 668
           +YD
Sbjct: 872 KYD 874



 Score = 90.9 bits (224), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 77/289 (26%), Positives = 133/289 (46%), Gaps = 59/289 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLD--KDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KE++N + NI TP +T Y +  +  D + A+ ++  +E T+L  V E  E  + P
Sbjct: 1118 GVPRLKELLNVATNIKTPSMTVYQESHRKHDKEAAKQLRSVVEHTSLRSVTEATEIYYDP 1177

Query: 822  DDSFILIKLDMDRIR---LLHLEVDIDS-------IRYCIERTRGISGHLTVSGHSFLIL 871
            D    +I  D D +    ++  +V  DS       +R  + R + +   LTV   +  I 
Sbjct: 1178 DIQSTVIDNDRDMVESYFIIPEDVTDDSSRQSKWLLRIVLNRAKLLDKGLTVQDVATRIK 1237

Query: 872  K--PKD-----SSKSFNSKMYQMKQ-------------------------LLPSVVIKGV 899
            +  P+D     S  + + ++ +++Q                         LL ++ ++GV
Sbjct: 1238 QQYPRDIAVIFSDNNADEQVIRIRQLHDAKEDEDEEDMEYDVTLKKLEQHLLDTLTLRGV 1297

Query: 900  QGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMATYGVKGVKCSSN 944
             G+ RA I+E+D   +                ++ L   G  L DV+   GV   +  SN
Sbjct: 1298 SGVERAFINEKDNARLMDDGSLFLSKADPLCKEWVLETSGTALADVLTIPGVDTTRTYSN 1357

Query: 945  NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
               EV++  GIEAARS ++ E+  V+   G  ++ RH  L+ D+MT +G
Sbjct: 1358 QFIEVFEVFGIEAARSALLRELTQVLAFDGSYVNHRHLALLVDIMTVRG 1406



 Score = 71.6 bits (174), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 59/243 (24%), Positives = 103/243 (42%), Gaps = 60/243 (24%)

Query: 110 DPQRT-PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVIN 168
           D QR  P   G  D R+GT  ++  C TC +   +C GH+G+I+L  PV+HIG+      
Sbjct: 44  DEQRMRPRTKGPNDPRLGTLDRQYYCETCEEGQKECPGHYGHIELATPVYHIGFLTKTKK 103

Query: 169 ILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKK----ILETTKKVSVC- 223
           +L+++C N  C ++          +A + +P     +R    K+    I   +K V++C 
Sbjct: 104 LLETVCHN--CGKI----------KADMSDPKFQDALRIRDPKRRFDIIWRLSKDVNICE 151

Query: 224 -----------------PH-----CGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLL 261
                            PH     CG     ++K GL  +   K  N+    D  V+   
Sbjct: 152 ADPIPEDEDPFSKEASKPHKGHGGCGNAQPTIRKEGLSLVGTWK-PNKANMMDDDVD--- 207

Query: 262 AEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
                     P+ E        +T+ P     +F +I  ED+ ++ ++ + ++P  +ILT
Sbjct: 208 ---------MPQPEK-------RTITPSMAYNIFRSISHEDVRIMGLSNDYARPEWMILT 251

Query: 322 RLL 324
            L+
Sbjct: 252 VLI 254



 Score = 58.2 bits (139), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 26/41 (63%), Positives = 29/41 (70%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            A   ++ +AQ  P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1069 AIEMRFAQAQANPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1109


>gi|21228373|ref|NP_634295.1| DNA-directed RNA polymerase subunit A' [Methanosarcina mazei Go1]
 gi|452210796|ref|YP_007490910.1| DNA-directed RNA polymerase subunit A' [Methanosarcina mazei Tuc01]
 gi|20906843|gb|AAM31967.1| DNA-directed RNA polymerase subunit A' [Methanosarcina mazei Go1]
 gi|452100698|gb|AGF97638.1| DNA-directed RNA polymerase subunit A' [Methanosarcina mazei Tuc01]
          Length = 880

 Score =  170 bits (431), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 101/269 (37%), Positives = 149/269 (55%), Gaps = 33/269 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D VLFNRQPSLHK+SIMAH  KVLP++TFR N  VC PYNADFDGDEMN+H  QTEE+
Sbjct: 412 DGDTVLFNRQPSLHKMSIMAHSVKVLPNKTFRLNPAVCPPYNADFDGDEMNMHALQTEES 471

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              AK+LM  + N+++PR G  +I    D I+G +LLT+   F NR
Sbjct: 472 RAE--------------AKILMQVQENILSPRFGGPIIGGIHDHISGLFLLTR---FENR 514

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSW-NPVVFVRTA-VIWTGKQIFSLILKPNRDCP 518
             +            D   ++++ S RS   P          WTGKQIFS IL    +  
Sbjct: 515 ISSF-----------DAYDLLRKSSARSLPEPAGHDEYGKPYWTGKQIFSQILPEGLNAE 563

Query: 519 VNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            +A + +     T  +E C  D+YV++R+ +L+ G++D++ +G+  K  +   ++++ G 
Sbjct: 564 FSAQVCS--HCDTCKKEECPNDAYVVIRDGKLITGTVDEAAIGA-FKGKIQDRIIKEIGP 620

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           +     +  ++++    +M  G S GI D
Sbjct: 621 EAGARFVDDMTKLAIRAIMRTGLSFGIAD 649



 Score = 96.3 bits (238), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 70/254 (27%), Positives = 117/254 (46%), Gaps = 44/254 (17%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           +++ S   I++ + Y  D    PI  GL+D ++G       C TC     +C GHFG+I+
Sbjct: 24  IRKMSATPIITADTY--DDDGFPIDMGLMDTKLGVIDPGLRCKTCSGRAGECPGHFGHIE 81

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKK 212
           L  PV H+G+ + +  +L++ C+   C+++LL   +   F  +L        +   L  +
Sbjct: 82  LVAPVVHVGFNKVIRKLLRATCRK--CSKILLEPAQKQQFLDQLTAVEEIGHMPDDLINE 139

Query: 213 ILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNP 272
           + +   KV  CP+C E          L+I  EK                +EY E      
Sbjct: 140 VYKEASKVKNCPYCNEEQ--------LEIKFEKP---------------SEYLENG---- 172

Query: 273 EIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRP 332
                      + L P E+   FE IP EDI ++ M+ + ++P  +ILT L VPP  +RP
Sbjct: 173 -----------EKLTPTEIRDRFENIPDEDIRVVGMDPKNARPEWMILTVLPVPPVTVRP 221

Query: 333 SVI--SDLKSDNDV 344
           S+   S  +S++D+
Sbjct: 222 SITLESGQRSEDDL 235



 Score = 93.2 bits (230), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 41/66 (62%), Positives = 56/66 (84%), Gaps = 1/66 (1%)

Query: 606 GDV-TPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           GD+ +   GFV+ S+ SGL PTE+FFH +GGREGLVDTAV+T+++GY+QRRLV +L+DL 
Sbjct: 771 GDLGSDAHGFVKASYKSGLNPTEYFFHAIGGREGLVDTAVRTSQSGYLQRRLVNALQDLE 830

Query: 665 VQYDMS 670
           VQYD++
Sbjct: 831 VQYDLT 836


>gi|386875147|ref|ZP_10117336.1| DNA-directed RNA polymerase subunit A' [Candidatus Nitrosopumilus
           salaria BD31]
 gi|386807026|gb|EIJ66456.1| DNA-directed RNA polymerase subunit A' [Candidatus Nitrosopumilus
           salaria BD31]
          Length = 1263

 Score =  170 bits (431), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 95/269 (35%), Positives = 152/269 (56%), Gaps = 35/269 (13%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D D+V+FNRQPSLH++SIMAH  +VLP +TFR +  VC PYNADFDGDEMN+H+PQ+EE
Sbjct: 415 ADGDIVMFNRQPSLHQMSIMAHYVRVLPGKTFRLHPSVCPPYNADFDGDEMNLHVPQSEE 474

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           ARAEA+              +LM  +  L++PR G  +I A +DF+TG YLLT+     +
Sbjct: 475 ARAEAI--------------LLMRVQDQLISPRYGGPIIGALRDFVTGAYLLTKDGTTLS 520

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
                      I + S++  ++  +      P    +    +TGKQ+FSL L  +     
Sbjct: 521 -----------IQEFSNLA-MLGGYKDALPKPATKTKDGPAYTGKQLFSLFLPKD----F 564

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           N  L +K   ++       +D  V+++N EL++G +DK+++G+    +V + + +D+G  
Sbjct: 565 NYVLTSK---WSKGTNGPPKD--VVIKNGELISGVIDKTSIGAEEPESVLHRITKDYGNA 619

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           +    +  +  M   ++ + GFS G GD+
Sbjct: 620 IGKNFLNSILIMVKQFITSYGFSYGFGDL 648



 Score =  137 bits (346), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 107/340 (31%), Positives = 169/340 (49%), Gaps = 54/340 (15%)

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEVCEYIEEVFVPDDSFILIKLDMD 1169
            Y +A++EP  AVG + AQSIGEPGTQMTL+TFHFAG     I+E  V      LI+L   
Sbjct: 930  YNKAKVEPGQAVGIITAQSIGEPGTQMTLRTFHFAG-----IKERNVTLGLPRLIELVDA 984

Query: 1170 RIRLLHLEVDI-------DSIRYCIERTRGI----------SGHLTVSGHSFLILKPK-- 1210
            R + +   +DI        S    IE  R +          +     S    LIL P   
Sbjct: 985  RKKPVTPTMDIYLDEESKKSREKAIEVARNVLQTKVSALISNSETDYSTQITLILSPNRL 1044

Query: 1211 ----------DSSKSFNSKMYQMKQLLPSVVIKGVQG-------------INRAVIHEED 1247
                      ++S + N K ++M+     + +K V+              +N  V    D
Sbjct: 1045 KERGCSIAEVEASLASNKK-FKMETTGELITLKLVEESDTATVIAIRNKVLNTTVKGVPD 1103

Query: 1248 VEGVT------KYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTE 1301
            +E VT      ++ +   G N+  V+   G+      +NN +E+  TLGIEAAR++++ E
Sbjct: 1104 IERVTLVQKDDEWVIQTTGSNIAKVLEVKGIDKRNVRTNNVFEIAGTLGIEAARNSLIDE 1163

Query: 1302 IKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFD 1361
            +   + + G+ +D R+ MLV+DLM S+G +  I RHG+A  K+SVL  A+FE T   +  
Sbjct: 1164 LNNTLGDQGLEVDNRYIMLVSDLMCSRGYMQQIGRHGIAGTKDSVLARAAFEITVPTIAH 1223

Query: 1362 AAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSE 1401
            AA  G+ + + G++E +I+G  + +G+G + L   V + +
Sbjct: 1224 AALGGEIEHLKGITENVIVGSNIPIGSGTVDLYMQVSKKK 1263



 Score =  114 bits (284), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 75/265 (28%), Positives = 129/265 (48%), Gaps = 41/265 (15%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           I+ +V     +++ S  +I +   Y +D    P+  GL+D R+GT +    C TCG   +
Sbjct: 12  IQFSVWSPTEIRKYSVAEITAPETYDEDGM--PVQGGLMDGRLGTLEPGQKCLTCGNTAA 69

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNPAL 201
            C GHFG+I+L  P+ HI +   +  +LQS C+  +CAR+ + +E    F+  K ++ A 
Sbjct: 70  RCPGHFGHIELAEPILHIAFIDNIYKLLQSTCR--SCARLKVPQEDLDAFKKIKDKHAAY 127

Query: 202 SYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLL 261
           + + +K + ++I+E  KK   CPHCG+                +Y+    K    VE   
Sbjct: 128 TVISQKRIPEQIIEKAKKAKECPHCGKT---------------QYELVFTKPTIFVE--- 169

Query: 262 AEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
                      EI  H+       L P+ + + F  I  ED+ +L  +   ++P   IL 
Sbjct: 170 ---------KTEIGEHR-------LLPITIRERFSQILDEDLEILSYDPRTARPEWFILQ 213

Query: 322 RLLVPPNCIRPSVI--SDLKSDNDV 344
            L VPP  +RPS+I  + ++S++D+
Sbjct: 214 ALPVPPVTVRPSIILETGIRSEDDL 238



 Score = 82.8 bits (203), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 34/58 (58%), Positives = 47/58 (81%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
             GFV++++  GL+  EFFFH MGGREGLVDTAV+T ++GYMQRRL+ +LE + ++YD
Sbjct: 775 AHGFVKSNYREGLSALEFFFHAMGGREGLVDTAVRTQQSGYMQRRLINALEHIRLEYD 832



 Score = 72.8 bits (177), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 59/236 (25%), Positives = 115/236 (48%), Gaps = 24/236 (10%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTL-GEVCEYIEEVFVPD 822
            G+PR+ E+++A +   TP +  YLD+++     + ++  + R  L  +V   I       
Sbjct: 974  GLPRLIELVDARKKPVTPTMDIYLDEESKKSREKAIE--VARNVLQTKVSALISNSETDY 1031

Query: 823  DSFILIKLDMDRIR-----LLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSS 877
             + I + L  +R++     +  +E  + S +     T G            + LK  + S
Sbjct: 1032 STQITLILSPNRLKERGCSIAEVEASLASNKKFKMETTG----------ELITLKLVEES 1081

Query: 878  KSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVK 937
             +  + +  ++  + +  +KGV  I R  + ++D E V +      G N+  V+   G+ 
Sbjct: 1082 DT--ATVIAIRNKVLNTTVKGVPDIERVTLVQKDDEWVIQ----TTGSNIAKVLEVKGID 1135

Query: 938  GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
                 +NN +E+  TLGIEAAR++++ E+   + + G+ +D R+ MLV+DLM S+G
Sbjct: 1136 KRNVRTNNVFEIAGTLGIEAARNSLIDELNNTLGDQGLEVDNRYIMLVSDLMCSRG 1191


>gi|118576747|ref|YP_876490.1| DNA-directed RNA polymerase, beta' subunit/160 kD subunit
           [Cenarchaeum symbiosum A]
 gi|118195268|gb|ABK78186.1| DNA-directed RNA polymerase, beta' subunit/160 kD subunit
           [Cenarchaeum symbiosum A]
          Length = 1260

 Score =  170 bits (431), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 96/268 (35%), Positives = 150/268 (55%), Gaps = 38/268 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAH  +VLP +TFR +  VC PYNADFDGDEMN+H+PQ+EEA
Sbjct: 416 DGDIVMFNRQPSLHQMSIMAHHVRVLPGKTFRLHPSVCPPYNADFDGDEMNLHVPQSEEA 475

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA+              +LM  +  L++PR G  +I   +DFITG YLLT+ +    R
Sbjct: 476 RAEAM--------------LLMRVQDQLISPRYGGPIIGGLRDFITGSYLLTKDDTTLTR 521

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +      T +A   D  G + +   +            ++TGKQ+FSL L  + +  + 
Sbjct: 522 EEF-----TNLAMLGDYGGALPKPGAKGQ----------LFTGKQLFSLFLPKDFNYIIT 566

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           +   +KG   T  +        V+++N EL++G +DKS++G+    +V + + +D+G   
Sbjct: 567 SKW-SKGTKGTPKD--------VVIKNGELISGVIDKSSIGAEEPESVLHRIAKDYGNAP 617

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           A   +  +  +   ++ + GFS G  D+
Sbjct: 618 AKKFLNSVLIIAKQFITHYGFSYGYADL 645



 Score =  139 bits (351), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 102/343 (29%), Positives = 171/343 (49%), Gaps = 60/343 (17%)

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTF---------------------------- 1141
            Y +A++EP  AVG + AQSIGEPGTQMTL+TF                            
Sbjct: 927  YNKAKVEPGQAVGIVTAQSIGEPGTQMTLRTFHFAGIKERNVTLGLPRLIELVDARKKPV 986

Query: 1142 ------HFAGE-------VCEYIEEVFVPDDSFILIKLDMD---RIRLLHLEVDIDSIRY 1185
                  H  GE         E  + V     S ++  +D D   +IRL   E  +D  R 
Sbjct: 987  TPTMDIHLDGESKGSRDRAIEIAKNVLQTKISALIADMDTDYSTQIRLGLDEGKMDD-RG 1045

Query: 1186 CI--ERTRGISGH----LTVSGHSFLILKPKDSSKSFNS-KMYQMKQLLPSVVIKGVQGI 1238
            C   +    ++ +    ++V G    +    D ++ +++  +  ++  + +  +KGV  +
Sbjct: 1046 CTPDDVAAALASNKKFKVSVEGRRLTL----DMAEEYDAPAVIAVRNKVLNTTVKGVPDV 1101

Query: 1239 NRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTI 1298
             R  + ++D E V +      G NL  V+A  G+   +  +NN +E+  TLGIEAAR+ +
Sbjct: 1102 ERLTLVQKDDEWVIQ----TTGSNLPKVLAVEGIDKRQVRTNNVFEIAGTLGIEAARNAL 1157

Query: 1299 MTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDH 1358
            + E++  +E+ G+ +D R+ MLV+DLM S+G +  I RHG+A  K+SVL  A+FE T   
Sbjct: 1158 INELRSTLEDQGLEVDIRYIMLVSDLMCSRGYMQQIGRHGIAGTKDSVLARAAFEITVPT 1217

Query: 1359 LFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRSE 1401
            +  AA  G+ + + GV+E +I+G  + +G+G + L   V + +
Sbjct: 1218 IAHAALSGEVEHLRGVTENVIVGSNIPIGSGTVDLYMQVAKKK 1260



 Score =  102 bits (253), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 69/262 (26%), Positives = 122/262 (46%), Gaps = 41/262 (15%)

Query: 86  TVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCV 145
           +V     +++ S  +I +   Y  D +  P+  GL+D R+GT +    C TCG   + C 
Sbjct: 15  SVWSPHEIRKYSVAEITAPETY--DEEGMPVQGGLMDGRLGTLEPGQKCLTCGNTAARCP 72

Query: 146 GHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGF-RAKLRNPALSYL 204
           GHFG+I+L  P+ HI +   +  +L  +C+  +C+R+ + +E+     + + R  A + +
Sbjct: 73  GHFGHIELAEPILHIAFIDNIHKLLLGMCR--SCSRLKVPQEELDSLSKIRRRESAYTVI 130

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEY 264
            +K + ++IL+  KK   CPHCG+                                  +Y
Sbjct: 131 SQKRIPEQILDRAKKSKECPHCGK---------------------------------TQY 157

Query: 265 NEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLL 324
            E +   P I   K       L P+ + + F  I  ED+ LL  +   ++P   IL  L 
Sbjct: 158 -ELIFTKPTIFIEKTEIGENRLLPITIREKFSQITNEDLVLLGYDPATARPEWFILQALP 216

Query: 325 VPPNCIRPSVI--SDLKSDNDV 344
           VPP  +RPS+I  + ++S++D+
Sbjct: 217 VPPVTVRPSIILETGIRSEDDL 238



 Score = 80.9 bits (198), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 34/62 (54%), Positives = 47/62 (75%)

Query: 607 DVTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQ 666
           D     GFV++++  GL+  EFFFH M GREGLVDTAV+T ++GYMQRRL+ +LE + ++
Sbjct: 768 DSPDAHGFVKSNYRDGLSALEFFFHAMAGREGLVDTAVRTQQSGYMQRRLINALEHIRLE 827

Query: 667 YD 668
           YD
Sbjct: 828 YD 829



 Score = 80.5 bits (197), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 64/240 (26%), Positives = 122/240 (50%), Gaps = 32/240 (13%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            G+PR+ E+++A +   TP +  +LD ++        KG  +R       E  + V     
Sbjct: 971  GLPRLIELVDARKKPVTPTMDIHLDGES--------KGSRDR-----AIEIAKNVLQTKI 1017

Query: 824  SFILIKLDMD---RIRLLHLEVDIDSIRYCI--ERTRGISGH----LTVSGHSFLILKPK 874
            S ++  +D D   +IRL   E  +D  R C   +    ++ +    ++V G    +    
Sbjct: 1018 SALIADMDTDYSTQIRLGLDEGKMDD-RGCTPDDVAAALASNKKFKVSVEGRRLTL---- 1072

Query: 875  DSSKSFNS-KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMAT 933
            D ++ +++  +  ++  + +  +KGV  + R  + ++D E V +      G NL  V+A 
Sbjct: 1073 DMAEEYDAPAVIAVRNKVLNTTVKGVPDVERLTLVQKDDEWVIQ----TTGSNLPKVLAV 1128

Query: 934  YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
             G+   +  +NN +E+  TLGIEAAR+ ++ E++  +E+ G+ +D R+ MLV+DLM S+G
Sbjct: 1129 EGIDKRQVRTNNVFEIAGTLGIEAARNALINELRSTLEDQGLEVDIRYIMLVSDLMCSRG 1188


>gi|126178251|ref|YP_001046216.1| DNA-directed RNA polymerase subunit A' [Methanoculleus marisnigri
           JR1]
 gi|126178264|ref|YP_001046229.1| DNA-directed RNA polymerase subunit A' [Methanoculleus marisnigri
           JR1]
 gi|125861045|gb|ABN56234.1| DNA-directed RNA polymerase, subunit A' [Methanoculleus marisnigri
           JR1]
 gi|125861058|gb|ABN56247.1| DNA-directed RNA polymerase, subunit A' [Methanoculleus marisnigri
           JR1]
          Length = 882

 Score =  170 bits (431), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 100/273 (36%), Positives = 147/273 (53%), Gaps = 41/273 (15%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND+VLFNRQPSLH++SIMAHR  V+  +TFR N  VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 414 DNDIVLFNRQPSLHRMSIMAHRVVVMDGKTFRLNPAVCPPYNADFDGDEMNLHIPQTEEA 473

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A++L++  SN+++PR G  +I    D I+G +LLT     F++
Sbjct: 474 RAE--------------AEILVSVSSNILSPRTGGPIIGGIHDHISGIFLLTHTVRHFSK 519

Query: 461 AQTMRIASTLIA------DTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPN 514
            + + +   L        D  D  G          NP        +WT KQ+FSL+L  N
Sbjct: 520 EEVLYLTQHLPVEHLPEPDRMDENG----------NP--------LWTNKQVFSLVLPDN 561

Query: 515 RDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLR 574
            +    A+  +     T   E C  D++V + N  L+ G++DK  +G+     + + ++R
Sbjct: 562 LNMVFQAS--SCQNCETCKREMCENDAFVRVVNGNLITGTIDKKGIGA-FDGQILHRIIR 618

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
             G   A   +  +++++   +M  GFS GI D
Sbjct: 619 QHGMKRAARFIDDVTKLSIRGIMLEGFSFGIDD 651



 Score =  112 bits (280), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 85/266 (31%), Positives = 132/266 (49%), Gaps = 43/266 (16%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G IE  +     +++ S  +I+  + Y  D    P P GL+D  +G       C TC Q 
Sbjct: 8   GRIEFGLFSPKEIRKMSVRKIIWADTY--DDDGFPYPQGLMDLNLGVIDPGLRCKTCDQK 65

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
            +DC GHFG+I+L  PV H+GY R +  +L+  C+  +C+R+L+  E+      K+  P 
Sbjct: 66  AADCPGHFGHIELAKPVIHVGYTRLIRKLLRVTCR--SCSRLLMTSEEV----EKIIGPE 119

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDL 260
            S L  + + +K +   KK  VCPHCGE          LKI+ EK    T   +  VED 
Sbjct: 120 DSELAGEIVSEKDI---KKERVCPHCGEQQ--------LKINFEKP---TTFSEVFVED- 164

Query: 261 LAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
                       ++E HK       L P ++    E IP +D+  L +N ++++P   IL
Sbjct: 165 ----------GRKVE-HK-------LTPADIRARLERIPDDDLRALGVNPDVARPEWTIL 206

Query: 321 TRLLVPPNCIRPSVI--SDLKSDNDV 344
           T L VPP  +RPS+I  +  +S++D+
Sbjct: 207 TVLPVPPVTMRPSIILENGQRSEDDL 232



 Score = 91.3 bits (225), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 37/57 (64%), Positives = 50/57 (87%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GF+ NS+ SGL+PTEFFFH +GGREGLVDTAV+T+++GY+QRR++ +L+DL V YD
Sbjct: 780 HGFITNSYKSGLSPTEFFFHAIGGREGLVDTAVRTSQSGYLQRRMINALQDLKVAYD 836


>gi|401020|sp|P29158.2|RPOA2_THECE RecName: Full=DNA-directed RNA polymerase subunit A''
 gi|48142|emb|CAA47724.1| Subunit A'' of DNA-dependent RNA polymerase [Thermococcus celer]
          Length = 393

 Score =  170 bits (431), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 114/342 (33%), Positives = 174/342 (50%), Gaps = 56/342 (16%)

Query: 1108 EKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFV 1156
            ++Y +A IEP  A+G +AAQSIGEP TQMTL TFH+AG            + E ++    
Sbjct: 51   KEYQKALIEPGEAIGTVAAQSIGEPSTQMTLNTFHYAGVAEINVTLGLPRIIEIVDARKN 110

Query: 1157 PDDSFILIKLDMD-------------RIRLLHLE-------VDIDSIRYCIE------RT 1190
            P    + + LD +             RI    LE       +DI +  + +E        
Sbjct: 111  PSTPIMTVYLDEEHRYDREKALEVARRIEGTSLENLARETTIDILNFEFIVEIDPERLEK 170

Query: 1191 RGI--------------SGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQ 1236
             G+              S    V G++ +I++PK   K   S + ++ + +    +KG+ 
Sbjct: 171  AGLDMERIQRKLESSFKSAEFEVDGYT-VIMRPKKVGKI--SSLRRLAEKVKKHRLKGLS 227

Query: 1237 GINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARS 1296
             + + VI ++   G  +Y +  EG N + V+   GV   +  +N+  E+ + LGIEAAR+
Sbjct: 228  RVGKTVITKDSKTG--EYIIRTEGSNFKQVLKVPGVDPTRTRTNDIREIAEVLGIEAARN 285

Query: 1297 TIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTS 1356
             I+ EI   ME  G+ +D RH MLVAD+MT  G +  I RHG+   K SVL  A+FE T+
Sbjct: 286  AIIDEILKTMEEQGLEVDVRHIMLVADMMTLDGVIRPIGRHGIVGEKASVLARAAFEITT 345

Query: 1357 DHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 1398
             HLF+AA  G  D ++GV E +++G P+ VGTG +KL   +P
Sbjct: 346  QHLFEAAERGAVDPLNGVVENVLIGQPVPVGTGTVKLAMNLP 387



 Score =  108 bits (271), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 78/232 (33%), Positives = 130/232 (56%), Gaps = 12/232 (5%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PRI EI++A +N STPI+T YLD++   D + A  V  R+E T+L  +     E  + 
Sbjct: 97  GLPRIIEIVDARKNPSTPIMTVYLDEEHRYDREKALEVARRIEGTSLENLAR---ETTID 153

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             +F  I +++D  RL    +D++ I+  +E +   S    V G++ +I++PK   K   
Sbjct: 154 ILNFEFI-VEIDPERLEKAGLDMERIQRKLESSFK-SAEFEVDGYT-VIMRPKKVGKI-- 208

Query: 882 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
           S + ++ + +    +KG+  + + VI ++   G  +Y +  EG N + V+   GV   + 
Sbjct: 209 SSLRRLAEKVKKHRLKGLSRVGKTVITKDSKTG--EYIIRTEGSNFKQVLKVPGVDPTRT 266

Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
            +N+  E+ + LGIEAAR+ I+ EI   ME  G+ +D RH MLVAD+MT  G
Sbjct: 267 RTNDIREIAEVLGIEAARNAIIDEILKTMEEQGLEVDVRHIMLVADMMTLDG 318


>gi|48477329|ref|YP_023035.1| DNA-directed RNA polymerase subunit A'' [Picrophilus torridus DSM
            9790]
 gi|48429977|gb|AAT42842.1| DNA-directed RNA polymerase subunit A'''' [Picrophilus torridus DSM
            9790]
          Length = 508

 Score =  170 bits (430), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 113/334 (33%), Positives = 170/334 (50%), Gaps = 58/334 (17%)

Query: 1112 RAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEV-----------CEYIEEVFVP--- 1157
            + +I+P  AVG +AAQSIGEPGTQMT++TFHFAG V            E ++   VP   
Sbjct: 172  KKEIDPYEAVGIIAAQSIGEPGTQMTMRTFHFAGVVEMNVTLGLPRLIEIVDARRVPSTP 231

Query: 1158 -------------------------------------DDSFILIKLDMDRIRLLHLEVDI 1180
                                                 D S + I + +D  +     V+I
Sbjct: 232  SMTIYLKKEYSNNEEKVRELIKTLENTALIDVADIITDVSEMSITVKLDERKSNERLVNI 291

Query: 1181 DSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINR 1240
            + I   I++ +GI    T    + L+   ++S K    K+YQ ++ L S+ IKGV  I R
Sbjct: 292  NDIMNAIQKLKGIMAAQT-DDKTILVKLQQESFK----KLYQTQEDLKSLTIKGVPKIKR 346

Query: 1241 AVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMT 1300
            A+   ++ E    +K+  +G NL+ V+    V   +  +N+  E+ + LGIEAAR+ I  
Sbjct: 347  AIARYDNSERC--WKIYTQGSNLKGVLDIDEVDPTRTYTNDIIEIEQVLGIEAARNAIYL 404

Query: 1301 EIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLF 1360
            E +  +   G+++D RH MLVAD+MT  G V  + R G++  K SVL  A+FE TS HL 
Sbjct: 405  EAERTLSEQGLNVDKRHLMLVADMMTFSGNVRAVGRQGISGRKSSVLARAAFEITSKHLL 464

Query: 1361 DAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
             A   G+ D ++GV+E II+G P+ +GTG I L+
Sbjct: 465  KAGLLGEVDQLAGVAENIIVGQPITLGTGAINLV 498



 Score =  106 bits (264), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 79/238 (33%), Positives = 128/238 (53%), Gaps = 14/238 (5%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A R  STP +T YL K+   + +  R +   LE T L +V + I +V   
Sbjct: 214 GLPRLIEIVDARRVPSTPSMTIYLKKEYSNNEEKVRELIKTLENTALIDVADIITDV--- 270

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             S + I + +D  +     V+I+ I   I++ +GI    T    + L+   ++S K   
Sbjct: 271 --SEMSITVKLDERKSNERLVNINDIMNAIQKLKGIMAAQT-DDKTILVKLQQESFK--- 324

Query: 882 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
            K+YQ ++ L S+ IKGV  I RA+   ++ E    +K+  +G NL+ V+    V   + 
Sbjct: 325 -KLYQTQEDLKSLTIKGVPKIKRAIARYDNSERC--WKIYTQGSNLKGVLDIDEVDPTRT 381

Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG 999
            +N+  E+ + LGIEAAR+ I  E +  +   G+++D RH MLVAD+MT  G V   G
Sbjct: 382 YTNDIIEIEQVLGIEAARNAIYLEAERTLSEQGLNVDKRHLMLVADMMTFSGNVRAVG 439


>gi|332796430|ref|YP_004457930.1| DNA-directed RNA polymerase subunit A'' [Acidianus hospitalis W1]
 gi|332694165|gb|AEE93632.1| DNA-directed RNA polymerase, subunit A'' [Acidianus hospitalis W1]
          Length = 392

 Score =  170 bits (430), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 128/392 (32%), Positives = 187/392 (47%), Gaps = 63/392 (16%)

Query: 1054 KKFLEEFSKKESVTSH-QDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVR 1112
            KK+LEE  K  S++      V Q LR+ I+S+   I             K       Y  
Sbjct: 7    KKYLEE--KLSSLSGKIPGSVIQKLRDAIISYPANITKEEIDKIINLTLK------DYDV 58

Query: 1113 AQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFVPDDSF 1161
            + I P  A G +AAQSIGEPGTQMTL+TFHFAG            + E ++   VP    
Sbjct: 59   SLINPGEAAGVVAAQSIGEPGTQMTLRTFHFAGVRELNVTLGLPRLIEIVDARKVPSTPM 118

Query: 1162 ILIKL----DMDRIRLLHL----------------EVDIDSIRYCIE------RTRGIS- 1194
            + I L      DR + + +                 +D+ S+   I       + +GI  
Sbjct: 119  MTIYLTDEYKTDREKAISIARKIEYTKIENVVDSTSIDMASMALIIHLDEKMLKDKGIEP 178

Query: 1195 ------------GHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAV 1242
                        G  T+     L +     +    + +++ ++ + +  IKG++GI RA+
Sbjct: 179  DEVEKVIRKLKLGDFTIDRPDELTITVTFQNMDSITGLFKAREKILNTKIKGIKGIKRAI 238

Query: 1243 IHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEI 1302
            + +   E    Y ++ +G NL  V+   GV   +  +NN +EV   LGIEAAR  I  EI
Sbjct: 239  VQKRGDE----YVIITDGSNLEGVLGIKGVDVSRIETNNLHEVENVLGIEAARELITREI 294

Query: 1303 KLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDA 1362
            K V+++ G+ +D RH  LVAD+MT  GEV  I RHG+   K SV   A+FE T  HL DA
Sbjct: 295  KKVLDDQGLDVDIRHVELVADIMTRTGEVRQIGRHGVTGEKTSVFAKAAFEVTVKHLLDA 354

Query: 1363 AFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            A  G  +   GV E II+G P+ +GTG+++LL
Sbjct: 355  AARGDVEEFRGVVENIIIGQPIKLGTGMVELL 386



 Score =  101 bits (252), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 72/234 (30%), Positives = 124/234 (52%), Gaps = 12/234 (5%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A +  STP++T YL  +  TD + A  +  ++E T +  V   ++   + 
Sbjct: 100 GLPRLIEIVDARKVPSTPMMTIYLTDEYKTDREKAISIARKIEYTKIENV---VDSTSID 156

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             S  LI + +D   L    ++ D +   I + +   G  T+     L +     +    
Sbjct: 157 MASMALI-IHLDEKMLKDKGIEPDEVEKVIRKLK--LGDFTIDRPDELTITVTFQNMDSI 213

Query: 882 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
           + +++ ++ + +  IKG++GI RA++ +   E    Y ++ +G NL  V+   GV   + 
Sbjct: 214 TGLFKAREKILNTKIKGIKGIKRAIVQKRGDE----YVIITDGSNLEGVLGIKGVDVSRI 269

Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            +NN +EV   LGIEAAR  I  EIK V+++ G+ +D RH  LVAD+MT  GEV
Sbjct: 270 ETNNLHEVENVLGIEAARELITREIKKVLDDQGLDVDIRHVELVADIMTRTGEV 323


>gi|448711916|ref|ZP_21701459.1| DNA-directed RNA polymerase subunit A'' [Halobiforma nitratireducens
            JCM 10879]
 gi|445791001|gb|EMA41650.1| DNA-directed RNA polymerase subunit A'' [Halobiforma nitratireducens
            JCM 10879]
          Length = 399

 Score =  170 bits (430), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 106/344 (30%), Positives = 174/344 (50%), Gaps = 59/344 (17%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A+A   +YV  +++P   VG ++AQSIGEPGTQ+T+ TFH+AG            + E +
Sbjct: 48   AKAVETRYVDTRVDPLDPVGTVSAQSIGEPGTQLTMNTFHYAGVAEIDVTQGLPRLIELV 107

Query: 1152 EEVFVPDDSFILIKLD----------------------------------------MDRI 1171
            +    PD   + + L+                                        ++R 
Sbjct: 108  DARKTPDTPMMTVHLEDEYATERERAHEVVWNIEATKILALGDVSTNVADMRVQISLNRD 167

Query: 1172 RLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVV 1231
             L    +  + +   IE   G+S   TV   + +   P++ S      + Q+ + L  + 
Sbjct: 168  TLEERMITPEEVAEIIEDELGVS---TVQQGTEIQFGPEEPSYR---DLLQLVEELRDIT 221

Query: 1232 IKGVQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLG 1290
             KG++ I+R VI  E+++ G  ++ L  EG    DV+   GV   + + NN +E+++ LG
Sbjct: 222  FKGIEDISRVVIRREEMDDGSEEFVLYTEGSAFGDVLEIEGVDASRTTCNNIHEIHRNLG 281

Query: 1291 IEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNL 1349
            IEAAR  I+ E    +   G+  ++ RH MLVAD+MT+ GE+  I RHG++  K+SVL  
Sbjct: 282  IEAAREAIIEETNNTLAEQGLDDVNVRHLMLVADIMTNNGEIESIGRHGISGSKDSVLAR 341

Query: 1350 ASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            A+FE T +HL +AA +G+ D + GV+E +I+G P+ +GTG + L
Sbjct: 342  AAFEVTVNHLLNAAIHGEVDTLQGVTENVIVGKPIKLGTGDVDL 385



 Score = 95.9 bits (237), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/239 (28%), Positives = 126/239 (52%), Gaps = 21/239 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T +L+ +  T+ + A  V   +E T    LG+V   + ++
Sbjct: 99  GLPRLIELVDARKTPDTPMMTVHLEDEYATERERAHEVVWNIEATKILALGDVSTNVADM 158

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSK 878
            V        ++ ++R  L    +  + +   IE   G+S   TV   + +   P++ S 
Sbjct: 159 RV--------QISLNRDTLEERMITPEEVAEIIEDELGVS---TVQQGTEIQFGPEEPSY 207

Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVK 937
                + Q+ + L  +  KG++ I+R VI  E+++ G  ++ L  EG    DV+   GV 
Sbjct: 208 R---DLLQLVEELRDITFKGIEDISRVVIRREEMDDGSEEFVLYTEGSAFGDVLEIEGVD 264

Query: 938 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEV 995
             + + NN +E+++ LGIEAAR  I+ E    +   G+  ++ RH MLVAD+MT+ GE+
Sbjct: 265 ASRTTCNNIHEIHRNLGIEAAREAIIEETNNTLAEQGLDDVNVRHLMLVADIMTNNGEI 323


>gi|214028076|gb|ACJ63307.1| RNA polymerase III large subunit [Asparagus officinalis]
          Length = 544

 Score =  170 bits (430), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 88/226 (38%), Positives = 133/226 (58%), Gaps = 25/226 (11%)

Query: 392 VHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLL 451
           +H+PQTEEAR EA                LM  ++NL TP+NGE+L+A+TQDF+T  +L+
Sbjct: 1   LHVPQTEEARTEAF--------------TLMGVQNNLCTPKNGEILVASTQDFLTSSFLI 46

Query: 452 TQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLIL 511
           T+K+ F++RA    +  + I D  ++  +          P   ++   +WTGKQ+FS+I+
Sbjct: 47  TRKDTFYDRA-AFSLMCSYIGDGMEVIDL---------PPPALIKPIELWTGKQLFSVIV 96

Query: 512 KPNRDCPVNANLKTKGRAYTANEE-FCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFY 570
           +PN    V  N   K R +  + E  C  D YV  RNS+L+ G + K TLG+G K  +F 
Sbjct: 97  RPNAQTRVFVNFVVKERIHVKDTETMCPHDGYVYFRNSDLICGQLGKVTLGNGNKNGLFS 156

Query: 571 ILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           +LLRD+  DVA + M RL+++++ ++ N GFSIGI DV PG+   Q
Sbjct: 157 VLLRDYNSDVAASCMNRLAKLSARWIGNHGFSIGIDDVQPGERLNQ 202



 Score =  105 bits (261), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 52/77 (67%), Positives = 60/77 (77%), Gaps = 1/77 (1%)

Query: 609 TPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV NSF++GLT TEFFFHTMGGREGLVDTAVKTAETGYM RRL+KSLEDL + Y
Sbjct: 318 TPAAKGFVANSFYTGLTATEFFFHTMGGREGLVDTAVKTAETGYMSRRLMKSLEDLSLYY 377

Query: 668 DMSFDAAFYGQTDCISG 684
           D +  ++  G    I G
Sbjct: 378 DQTVRSSNGGVVQFIYG 394



 Score = 57.4 bits (137), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 25/57 (43%), Positives = 41/57 (71%)

Query: 21 VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKV 77
           LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+K+ F++RA    + S +  G +V
Sbjct: 15 TLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDRAAFSLMCSYIGDGMEV 71


>gi|448303810|ref|ZP_21493756.1| DNA-directed RNA polymerase subunit A'' [Natronorubrum sulfidifaciens
            JCM 14089]
 gi|445592437|gb|ELY46624.1| DNA-directed RNA polymerase subunit A'' [Natronorubrum sulfidifaciens
            JCM 14089]
          Length = 399

 Score =  170 bits (430), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 106/343 (30%), Positives = 176/343 (51%), Gaps = 58/343 (16%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A+A   +Y+  +++P   VG ++AQSIGEPGTQ+T+ TFH+AG            + E +
Sbjct: 48   AKAVEARYLDTRVDPLDPVGTVSAQSIGEPGTQLTMNTFHYAGVAEIDVTQGLPRLIELV 107

Query: 1152 EEVFVPDDSFILIKLD----------------MDRIRLLHL----------EVDI----- 1180
            +    PD   + + L+                ++  ++L L           V I     
Sbjct: 108  DARKTPDTPMMTVYLEDEYATERERAHEVVWNLEATKILALGDVSTNVADMRVQISLNED 167

Query: 1181 ---------DSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVV 1231
                     + +   IE   G+S   T+   + +   P++ S      + Q+ + L  + 
Sbjct: 168  TLKERMITPEEVASIIEDNLGVS---TIQQGTEIQFGPEEPSYR---DLLQLVEELRDIT 221

Query: 1232 IKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGI 1291
             KG++ I+R VI  E++E   ++ L  EG    D +   GV   + + NN +E+++ LGI
Sbjct: 222  FKGIEDISRVVIRREELEDGEEFVLYTEGSAFGDALEIEGVDASRTTCNNIHEIHRNLGI 281

Query: 1292 EAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLA 1350
            EAAR  I+ E    +   G+  ++ RH MLVAD+MT++GE+  I RHG++  KESVL  A
Sbjct: 282  EAAREAIIEETNNTLAEQGLDDVNVRHLMLVADMMTNRGEIESIGRHGISGSKESVLARA 341

Query: 1351 SFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            +FE T +HL +AA +G+ D + GV+E +I+G P+ +GTG + L
Sbjct: 342  AFEVTVNHLLNAAIHGEVDDLDGVTENVIVGKPIKLGTGDVDL 384



 Score = 99.4 bits (246), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 71/238 (29%), Positives = 125/238 (52%), Gaps = 20/238 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T YL+ +  T+ + A  V   LE T    LG+V   + ++
Sbjct: 99  GLPRLIELVDARKTPDTPMMTVYLEDEYATERERAHEVVWNLEATKILALGDVSTNVADM 158

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSK 878
            V     I +  D  + R++  E     +   IE   G+S   T+   + +   P++ S 
Sbjct: 159 RVQ----ISLNEDTLKERMITPE----EVASIIEDNLGVS---TIQQGTEIQFGPEEPSY 207

Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 938
                + Q+ + L  +  KG++ I+R VI  E++E   ++ L  EG    D +   GV  
Sbjct: 208 R---DLLQLVEELRDITFKGIEDISRVVIRREELEDGEEFVLYTEGSAFGDALEIEGVDA 264

Query: 939 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEV 995
            + + NN +E+++ LGIEAAR  I+ E    +   G+  ++ RH MLVAD+MT++GE+
Sbjct: 265 SRTTCNNIHEIHRNLGIEAAREAIIEETNNTLAEQGLDDVNVRHLMLVADMMTNRGEI 322


>gi|282163888|ref|YP_003356273.1| DNA-directed RNA polymerase subunit A' [Methanocella paludicola
           SANAE]
 gi|282156202|dbj|BAI61290.1| DNA-directed RNA polymerase subunit A' [Methanocella paludicola
           SANAE]
          Length = 877

 Score =  170 bits (430), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 101/284 (35%), Positives = 151/284 (53%), Gaps = 41/284 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIM H  KV+P++TFR N  VC PYNADFDGDEMN+H+PQ  EA
Sbjct: 407 DGDIVLFNRQPSLHRMSIMGHFVKVMPNKTFRLNPAVCAPYNADFDGDEMNLHVPQNMEA 466

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
            AE              A++LM  + N+++PR G  +I    D I+G YLLT+    F+ 
Sbjct: 467 MAE--------------ARILMLVQENILSPRFGGPIIGGLHDHISGIYLLTKGYQMFSE 512

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            + + +   +          IK        P      A  W+GKQIFS+IL      P  
Sbjct: 513 TEALDVVRKV---------GIKELP----EPAKVENGAQYWSGKQIFSVIL------PKT 553

Query: 521 ANLKTKGR----AYTANEEFCHRDSYVILRNSELLAGSMDKSTLGS-GGKANVFYILLRD 575
            ++  K +         +E C +D+YV++R+  L  G++D+  +G+  GK  +   +++ 
Sbjct: 554 LSMTYKAKICENCEVCKKEECEKDAYVVIRDGVLKCGTVDEKAIGAFSGK--IVDRIVKT 611

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV-TPGQGFVQNS 618
           + ED A   +  ++R+    +M  GFS GI D   P +  VQ +
Sbjct: 612 YSEDTAAKFIDDVTRLAIRAIMRFGFSYGISDTDIPREAKVQTT 655



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 68/254 (26%), Positives = 119/254 (46%), Gaps = 45/254 (17%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           +++ S  ++++ + Y  D    PI  GL+D R+G       C TCG    +C GHFG+I+
Sbjct: 20  IRKMSVTKVITADTY--DDDGYPIDMGLMDPRLGVIDPGLRCKTCGGRPGECPGHFGHIE 77

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKK 212
           L  PV H+G+ R +  IL + C+   C +++L ++  A +  +++           + K 
Sbjct: 78  LASPVIHVGFARLLRKILMTTCRR--CGKLMLDDKAKADYIRQIKTNIRLGQPTDEIVKN 135

Query: 213 ILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNP 272
           + +  K  + CP+CGE               E+ + + +K    +ED             
Sbjct: 136 VFKDAKS-TTCPYCGE---------------EQKEIKFEKPTGYIED------------- 166

Query: 273 EIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRP 332
               HK       L P +V    E IP EDI +  M+ + ++P  ++LT L VPP  +RP
Sbjct: 167 ---GHK-------LMPTDVRDRLEMIPDEDIEVFGMDPKNARPEWMVLTVLPVPPVTVRP 216

Query: 333 SVI--SDLKSDNDV 344
           S+   S  +S++D+
Sbjct: 217 SITLESGQRSEDDL 230



 Score = 92.4 bits (228), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 39/57 (68%), Positives = 51/57 (89%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV++S+  GL PTEFFFH MGGREGLVDTAV+T+++GY+QRRLV +L+DL V+YD
Sbjct: 774 RGFVESSYKKGLNPTEFFFHAMGGREGLVDTAVRTSQSGYLQRRLVNALQDLEVKYD 830


>gi|15791387|ref|NP_281211.1| DNA-directed RNA polymerase subunit A'' [Halobacterium sp. NRC-1]
 gi|169237148|ref|YP_001690348.1| DNA-directed RNA polymerase subunit A'' [Halobacterium salinarum R1]
 gi|226734917|sp|B0R8D3.1|RPOA2_HALS3 RecName: Full=DNA-directed RNA polymerase subunit A''
 gi|338819302|sp|P0CX07.1|RPOA2_HALSA RecName: Full=DNA-directed RNA polymerase subunit A''; Short=Subunit
            C
 gi|43543|emb|CAA40427.1| RNA polymerase subunit C [Halobacterium salinarum]
 gi|10582042|gb|AAG20691.1| DNA-directed RNA polymerase subunit C [Halobacterium sp. NRC-1]
 gi|167728214|emb|CAP15002.1| DNA-directed RNA polymerase subunit A'' (subunit C) [Halobacterium
            salinarum R1]
          Length = 397

 Score =  169 bits (429), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 116/372 (31%), Positives = 195/372 (52%), Gaps = 61/372 (16%)

Query: 1077 LREQILSHQDKIGHGR-ESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQ 1135
            L++++L+  ++ G  + ++N   +A +A     +Y+  +++P   VG ++AQSIGEPGTQ
Sbjct: 23   LKDEVLATAEERGVTKSQANEIATAVEA-----QYLDTRVDPLDPVGTVSAQSIGEPGTQ 77

Query: 1136 MTLKTFHFAG-----------EVCEYIE----------EVFVPDD--------------- 1159
            MT+ TFH+AG            + E ++          EV++ D+               
Sbjct: 78   MTMNTFHYAGVAEMDVTQGLPRLIELVDARKTPDTPVMEVYLEDEYAEERERAHEVVWKI 137

Query: 1160 ---------------SFILIKLDMDRIRLLHLEVDIDSI-RYCIERTRGISGHLTVS-GH 1202
                           + +++++D++   L      +DS  +   E    I G+L V+   
Sbjct: 138  EATKILALGDISTNVADMVVRIDLNEDTLQERWPRVDSTTQIAGEVAETIEGNLGVTVTQ 197

Query: 1203 SFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDN 1262
               IL+   S  S+  ++ Q+ + L  +V KG++ ++R VI  E+ E   ++ L  EG  
Sbjct: 198  DGTILEFGPSEPSYR-ELLQLVEQLRDIVFKGIEEVSRVVIRREETERGEEFVLYTEGSA 256

Query: 1263 LRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMS-IDFRHPMLV 1321
             +  +   GV   + S NN +EV+KTLGIEAAR  I+ E    +E  G+  ++ RH MLV
Sbjct: 257  FKKALKIEGVDATRTSCNNIHEVHKTLGIEAAREAIINETMTTLEEQGLDDVNIRHLMLV 316

Query: 1322 ADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMG 1381
            AD+MT+ G +  I RHG++  K SVL  A+FE T +HL DAA +G++D + GV E +I+G
Sbjct: 317  ADIMTNDGTIESIGRHGISGNKNSVLARAAFEVTVNHLLDAAIHGESDDLDGVIENVIVG 376

Query: 1382 LPMNVGTGLIKL 1393
             P+ +GTG + L
Sbjct: 377  KPVRLGTGDVDL 388



 Score = 96.3 bits (238), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 73/239 (30%), Positives = 125/239 (52%), Gaps = 15/239 (6%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++  YL+ +   + + A  V  ++E T    LG++   +   
Sbjct: 96  GLPRLIELVDARKTPDTPVMEVYLEDEYAEERERAHEVVWKIEATKILALGDISTNVA-- 153

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVS-GHSFLILKPKDSS 877
               D  + I L+ D ++     VD  + +   E    I G+L V+      IL+   S 
Sbjct: 154 ----DMVVRIDLNEDTLQERWPRVD-STTQIAGEVAETIEGNLGVTVTQDGTILEFGPSE 208

Query: 878 KSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVK 937
            S+  ++ Q+ + L  +V KG++ ++R VI  E+ E   ++ L  EG   +  +   GV 
Sbjct: 209 PSYR-ELLQLVEQLRDIVFKGIEEVSRVVIRREETERGEEFVLYTEGSAFKKALKIEGVD 267

Query: 938 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEV 995
             + S NN +EV+KTLGIEAAR  I+ E    +E  G+  ++ RH MLVAD+MT+ G +
Sbjct: 268 ATRTSCNNIHEVHKTLGIEAAREAIINETMTTLEEQGLDDVNIRHLMLVADIMTNDGTI 326


>gi|11499472|ref|NP_070713.1| DNA-directed RNA polymerase subunit A' [Archaeoglobus fulgidus DSM
           4304]
 gi|2648656|gb|AAB89365.1| DNA-directed RNA polymerase, subunit A' (rpoA1) [Archaeoglobus
           fulgidus DSM 4304]
          Length = 867

 Score =  169 bits (429), Expect = 8e-39,   Method: Compositional matrix adjust.
 Identities = 102/271 (37%), Positives = 151/271 (55%), Gaps = 46/271 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIMAH  +VLP++TFR N  VC PYNADFDGDEMN+H+PQ+ EA
Sbjct: 405 DGDIVLFNRQPSLHRMSIMAHYVRVLPYKTFRLNPAVCPPYNADFDGDEMNLHVPQSLEA 464

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE              AK+LMA + ++++PR G  +I    D I+G YLLT+    F R
Sbjct: 465 QAE--------------AKILMAVQEHILSPRFGGPIIGGIHDHISGLYLLTRGEKKFTR 510

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            + M +  +L  D S+I             PV        +TGK+IFS IL        +
Sbjct: 511 EEAMELLRSL--DISEI-------------PV-----KDEYTGKEIFSFILP-------D 543

Query: 521 ANLKTKGRAYTANEEF----CHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
             L+ K       EE     C  D+YVI+ N +LL G++D+  +G+  K  +   + R +
Sbjct: 544 ITLEFKAEICQGCEECKGAECEYDAYVIIENGKLLKGTIDEKAVGA-FKGIIIDEIARKY 602

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           G+++A   +  ++++    +   GF++GI D
Sbjct: 603 GKEMAKKFIDDMTQLAIRIISKLGFTVGIDD 633



 Score =  111 bits (278), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 69/254 (27%), Positives = 117/254 (46%), Gaps = 44/254 (17%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           +++ S ++I++   Y  D    PI  GL+D R+G       C TCG    +C GHFG+++
Sbjct: 19  IRRMSVVKIITPETY--DDDGFPIDGGLMDTRLGVIDPGLRCKTCGGKAGECPGHFGHVE 76

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKK 212
           L  PV H+GY + +  +L   C    C R+LL +E+   F A++          + + K+
Sbjct: 77  LAAPVIHVGYAKMIARLLNGTCSE--CGRILLKDERRDKFIAEIERRKELNQSYEEVVKE 134

Query: 213 ILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNP 272
           +   TK    CPHCG                              E L  ++++   F  
Sbjct: 135 VFRLTKAAKKCPHCG-----------------------------AEQLEVKFDKPTFFY- 164

Query: 273 EIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRP 332
            +  H+       L P +V +  E IP +D+P   +N + ++P   +LT L VPP  +RP
Sbjct: 165 -LGEHR-------LTPKDVREWLEKIPDDDLPAFGINPKATRPEWFVLTVLPVPPVTVRP 216

Query: 333 SVI--SDLKSDNDV 344
           S+I  +  +S++D+
Sbjct: 217 SIILETGQRSEDDL 230



 Score = 88.2 bits (217), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 43/84 (51%), Positives = 61/84 (72%), Gaps = 4/84 (4%)

Query: 587 RLSRMTSFYLMNRGFS-IGIGDV-TPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAV 644
           R+SR   +   NR  S    GD+    +GFV++S+  GL+P EFFFH  GGREGLVDTAV
Sbjct: 739 RISR--GYTYTNRTLSHFKPGDLGAEARGFVRSSYKKGLSPVEFFFHAAGGREGLVDTAV 796

Query: 645 KTAETGYMQRRLVKSLEDLCVQYD 668
           +T+++GY+QRR++ +L+DL V+YD
Sbjct: 797 RTSQSGYLQRRMINALQDLKVEYD 820


>gi|294495210|ref|YP_003541703.1| DNA-directed RNA polymerase, subunit A' [Methanohalophilus mahii
           DSM 5219]
 gi|292666209|gb|ADE36058.1| DNA-directed RNA polymerase, subunit A' [Methanohalophilus mahii
           DSM 5219]
          Length = 886

 Score =  169 bits (429), Expect = 8e-39,   Method: Compositional matrix adjust.
 Identities = 97/269 (36%), Positives = 146/269 (54%), Gaps = 33/269 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHK+SIMAH+ KVLP++TF+ N  VC PYNADFDGDEMN+H+ QTEE+
Sbjct: 418 DGDIVLFNRQPSLHKMSIMAHKVKVLPNKTFKLNPAVCPPYNADFDGDEMNMHVLQTEES 477

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA               +LM  + N+++PR G  +I    D I+G +LLT+     ++
Sbjct: 478 RAEA--------------NILMQVQENILSPRFGGPIIGGIHDHISGMFLLTRNENMISK 523

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSW-NPVVFVRTA-VIWTGKQIFSLILKPNRDCP 518
                         +D   ++++   R    P  +       WTGKQIFS IL  + +  
Sbjct: 524 --------------NDALELLRKSEVRELPEPAGYTDVGDPFWTGKQIFSQILPKDLNLE 569

Query: 519 VNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
             AN+  K       +  C  D+YV++ N EL+ G++D+  +G+  K  +   +++ +G 
Sbjct: 570 FKANVCFKCDVCKGRD--CEYDAYVVVENGELVTGTIDEKAIGA-FKGKILDSIVKRYGT 626

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
             A   +  ++R+    +M  G S GI D
Sbjct: 627 TEAAQFVDDMTRLAIRGVMRTGLSFGISD 655



 Score =  107 bits (268), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 70/254 (27%), Positives = 118/254 (46%), Gaps = 44/254 (17%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           +++ S   I++ + Y  D    PI  GL+D R+G       C TCG    +C GHFG+I+
Sbjct: 30  IRKMSVTSIITADTY--DDDGYPIDMGLMDLRLGVIDPGLKCKTCGGRAGECPGHFGHIE 87

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKK 212
           L  PV H+G+ + +  IL+S C+N  C+ +LL +++   +  +     +   +   L   
Sbjct: 88  LVAPVLHVGFNKIIRKILRSTCRN--CSHLLLEDKQKKAYINQFAKLDVMSHLPDDLINN 145

Query: 213 ILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNP 272
           + +  +K  +CP+CGE          L+I  EK        D I  D             
Sbjct: 146 VFKEARKTKICPYCGEEQ--------LEIKFEK------PSDYIENDY------------ 179

Query: 273 EIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRP 332
                        L P E+    E IP +D+ ++ M+ E ++P  ++LT L VPP  +RP
Sbjct: 180 ------------KLTPTEIRDRLERIPDDDLKVMGMDPESARPEWMVLTVLAVPPVTVRP 227

Query: 333 SVI--SDLKSDNDV 344
           S+   S  +S++D+
Sbjct: 228 SITLESGQRSEDDL 241



 Score = 94.0 bits (232), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 40/60 (66%), Positives = 53/60 (88%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
             GFV++S+ SGL PTE+FFH++GGREGLVDTAV+T+++GY+QRRLV +L+DL VQYD S
Sbjct: 783 AHGFVKSSYKSGLNPTEYFFHSVGGREGLVDTAVRTSQSGYLQRRLVNALQDLEVQYDRS 842


>gi|237823478|pdb|2WAQ|C Chain C, The Complete Structure Of The Archaeal 13-Subunit Dna-
            Directed Rna Polymerase
 gi|237823492|pdb|2WB1|C Chain C, The Complete Structure Of The Archaeal 13-Subunit Dna-
            Directed Rna Polymerase
 gi|237823514|pdb|2WB1|Y Chain Y, The Complete Structure Of The Archaeal 13-Subunit Dna-
            Directed Rna Polymerase
          Length = 395

 Score =  169 bits (429), Expect = 8e-39,   Method: Compositional matrix adjust.
 Identities = 123/392 (31%), Positives = 187/392 (47%), Gaps = 65/392 (16%)

Query: 1054 KKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRA 1113
            K +LEE  K+ S    Q K+ + L+  I + +  +        F  A K      +Y   
Sbjct: 10   KSYLEEKVKQASNILPQ-KIVEDLKNLISNKEVLVTRDEIDKIFDLAIK------EYSEG 62

Query: 1114 QIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFVPDDSFI 1162
             I P  A+G +AAQS+GEPGTQMTL+TFHFAG            + E ++   VP    +
Sbjct: 63   LIAPGEAIGIVAAQSVGEPGTQMTLRTFHFAGIRELNVTLGLPRLIEIVDAKKVPSTPMM 122

Query: 1163 LI------------------KLDMDRIR---------------LLHLE--------VDID 1181
             I                  KL+  +I                +L L+        V +D
Sbjct: 123  TIYLTDEYKHDKEKALEVARKLEYTKIENVVSSTSIDIASMSIILQLDNEMLKDKGVTVD 182

Query: 1182 SIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRA 1241
             ++  I R +   G   +       L    ++    + +++++  + +  IKG++GI RA
Sbjct: 183  DVKKAINRLK--LGEFVIDESEGTTLNISFANIDSIAALFKLRDKILNTKIKGIKGIKRA 240

Query: 1242 VIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTE 1301
            ++ ++  E    Y +L +G NL  V++  GV   K  +NN  E+ +  GIEAAR  I+ E
Sbjct: 241  IVQKKGDE----YIILTDGSNLSGVLSVKGVDIAKVETNNIREIEEVFGIEAAREIIIRE 296

Query: 1302 IKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFD 1361
            I  V+   G+ +D RH +LVAD+MT  G V  I RHG+   K SVL  A+FE T  HL D
Sbjct: 297  ISKVLAEQGLDVDMRHILLVADVMTRTGVVRQIGRHGVTGEKNSVLARAAFEVTVKHLLD 356

Query: 1362 AAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            AA  G  +   GV E II+G P+ +GTG+++L
Sbjct: 357  AAARGDVEEFKGVVENIIIGHPIKLGTGMVEL 388



 Score =  103 bits (257), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 74/238 (31%), Positives = 122/238 (51%), Gaps = 20/238 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYL------DKDTDLDYARIVKGRLERTTLGEVCEYIEE 817
           G+PR+ EI++A +  STP++T YL      DK+  L+ AR    +LE T +  V      
Sbjct: 103 GLPRLIEIVDAKKVPSTPMMTIYLTDEYKHDKEKALEVAR----KLEYTKIENVVSSTS- 157

Query: 818 VFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSS 877
               D + + I L +D   L    V +D ++  I R +   G   +       L    ++
Sbjct: 158 ---IDIASMSIILQLDNEMLKDKGVTVDDVKKAINRLK--LGEFVIDESEGTTLNISFAN 212

Query: 878 KSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVK 937
               + +++++  + +  IKG++GI RA++ ++  E    Y +L +G NL  V++  GV 
Sbjct: 213 IDSIAALFKLRDKILNTKIKGIKGIKRAIVQKKGDE----YIILTDGSNLSGVLSVKGVD 268

Query: 938 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
             K  +NN  E+ +  GIEAAR  I+ EI  V+   G+ +D RH +LVAD+MT  G V
Sbjct: 269 IAKVETNNIREIEEVFGIEAAREIIIREISKVLAEQGLDVDMRHILLVADVMTRTGVV 326


>gi|325960115|ref|YP_004291581.1| DNA-directed RNA polymerase subunit A' [Methanobacterium sp. AL-21]
 gi|325331547|gb|ADZ10609.1| DNA-directed RNA polymerase subunit A' [Methanobacterium sp. AL-21]
          Length = 871

 Score =  169 bits (429), Expect = 8e-39,   Method: Compositional matrix adjust.
 Identities = 100/268 (37%), Positives = 149/268 (55%), Gaps = 38/268 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH++S+MAH  KVLP++TFR N CVC PYNADFDGDEMN+H+ QTEE+
Sbjct: 408 DGDVVLFNRQPSLHRMSMMAHEVKVLPYKTFRLNLCVCPPYNADFDGDEMNMHVFQTEES 467

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              AK LM  + ++++PR G  +I    D I+G YLLT++ + F+ 
Sbjct: 468 RAE--------------AKSLMRVQEHILSPRFGGPIIGGIHDHISGAYLLTREGSNFSE 513

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                          D+  ++KR   R   P     T   WTGKQ+FSL+L  + +    
Sbjct: 514 --------------EDVFQMVKR--ARMELPKA---TGKDWTGKQVFSLLLPNDLNMVYR 554

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGS-GGKANVFYILLRDFGED 579
           A +  K       E  C  D+YV++ + ++ +G+MD+   G+  GK  +   +++++G D
Sbjct: 555 AEICRKCDECLKLE--CKNDAYVVIEDGQIKSGAMDEKAYGAFSGK--ILDSIVKEYGTD 610

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            A   +   +++    +M RGF+    D
Sbjct: 611 KAREFLDTSTKLAIAGIMKRGFTTSTAD 638



 Score =  104 bits (259), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 71/244 (29%), Positives = 110/244 (45%), Gaps = 43/244 (17%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + +++ S  +IV+ + Y +D    PI  GL+D R+G       C +CG    DC GHFG+
Sbjct: 19  ENIRKMSVTKIVTPDTYDEDG--YPIEAGLMDPRLGVIDPGLRCRSCGSKGGDCQGHFGH 76

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           I+L  PV H+G+   +  IL+S CK+  C +VLL E +   ++ K+     +      + 
Sbjct: 77  INLARPVIHVGFADTIHKILRSTCKD--CGQVLLTESEKVDYKEKIETLIKNEESITGII 134

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           K+I    ++   CP CGE    VK    + I    YK                       
Sbjct: 135 KEIYAVARR-DKCPSCGEEQEDVKIDKPVSIVEGNYK----------------------- 170

Query: 271 NPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCI 330
                          L   EV +  EAIP +D   + +N E++KP  ++LT L VPP  +
Sbjct: 171 ---------------LTASEVRERLEAIPQDDYIYIGINHEVAKPEWMVLTVLPVPPVTV 215

Query: 331 RPSV 334
           RPS+
Sbjct: 216 RPSI 219



 Score = 90.1 bits (222), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 39/56 (69%), Positives = 47/56 (83%)

Query: 613 GFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           GFV +S+  GL P EFFFH MGGREGLVDTA++TA++GYMQRRLV +L+DL VQ D
Sbjct: 768 GFVHSSYKKGLDPLEFFFHAMGGREGLVDTAIRTAQSGYMQRRLVNALQDLNVQLD 823


>gi|91773157|ref|YP_565849.1| DNA-directed RNA polymerase subunit A'' [Methanococcoides burtonii
            DSM 6242]
 gi|91712172|gb|ABE52099.1| DNA-directed RNA polymerase subunit A'' [Methanococcoides burtonii
            DSM 6242]
          Length = 386

 Score =  169 bits (429), Expect = 8e-39,   Method: Compositional matrix adjust.
 Identities = 107/346 (30%), Positives = 170/346 (49%), Gaps = 58/346 (16%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIE 1152
            E     Y  A +EP  AVG ++AQSIGEPGTQMT++TFH+AG            + E ++
Sbjct: 44   ERVMADYNYACVEPCEAVGVVSAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVD 103

Query: 1153 EVFVPDDSFILIKL----------------------------------------DMDRIR 1172
                P    + + L                                        D++   
Sbjct: 104  ARKTPSTPMMTVALAKEHAADRDFARKVAWEIEATHIEHLADVTTDLANMNLILDLNEKM 163

Query: 1173 LLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVI 1232
            LL  ++D+D+I   +     ++  +     + +I+ PK+        + Q+ + +  + +
Sbjct: 164  LLQRDIDVDAIAEKLAEGLKVNVKIPSEVANQIIVIPKE---PLYRDLLQLAKNIHGITL 220

Query: 1233 KGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIE 1292
            KG++GI R VI ++  E    Y L  EG  L++++   G+   + S+NN  E+Y+  GIE
Sbjct: 221  KGIEGIKRVVIRKDGDE----YTLYTEGSMLKEILEVEGIDLSRTSTNNIGEIYEVFGIE 276

Query: 1293 AARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASF 1352
            AAR  I+ E    +   G+++D RH MLV+D+MT  GEV  I RHG++  K SV   A+F
Sbjct: 277  AARFAIIKEASDTLREQGLTVDIRHLMLVSDIMTCDGEVKQIGRHGISGEKASVFARAAF 336

Query: 1353 ENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 1398
            E T +HL DA   G  D ++GV+E II+G P+ +GTG + L+   P
Sbjct: 337  EVTVNHLLDAGMRGDIDELNGVTENIIVGQPIKLGTGDVHLVARNP 382



 Score =  114 bits (285), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 74/234 (31%), Positives = 129/234 (55%), Gaps = 14/234 (5%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A +  STP++T  L K+   D D+AR V   +E T +    E++ +V   
Sbjct: 94  GLPRLIEIVDARKTPSTPMMTVALAKEHAADRDFARKVAWEIEATHI----EHLADVTTD 149

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
             +  LI LD++   LL  ++D+D+I   +     ++  +     + +I+ PK+      
Sbjct: 150 LANMNLI-LDLNEKMLLQRDIDVDAIAEKLAEGLKVNVKIPSEVANQIIVIPKEP---LY 205

Query: 882 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
             + Q+ + +  + +KG++GI R VI ++  E    Y L  EG  L++++   G+   + 
Sbjct: 206 RDLLQLAKNIHGITLKGIEGIKRVVIRKDGDE----YTLYTEGSMLKEILEVEGIDLSRT 261

Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
           S+NN  E+Y+  GIEAAR  I+ E    +   G+++D RH MLV+D+MT  GEV
Sbjct: 262 STNNIGEIYEVFGIEAARFAIIKEASDTLREQGLTVDIRHLMLVSDIMTCDGEV 315


>gi|385773845|ref|YP_005646412.1| DNA-directed RNA polymerase subunit A'' [Sulfolobus islandicus
            HVE10/4]
 gi|385776480|ref|YP_005649048.1| DNA-directed RNA polymerase subunit A'' [Sulfolobus islandicus
            REY15A]
 gi|323475228|gb|ADX85834.1| DNA-directed RNA polymerase, subunit A'' [Sulfolobus islandicus
            REY15A]
 gi|323477960|gb|ADX83198.1| DNA-directed RNA polymerase, subunit A'' [Sulfolobus islandicus
            HVE10/4]
          Length = 392

 Score =  169 bits (429), Expect = 8e-39,   Method: Compositional matrix adjust.
 Identities = 124/392 (31%), Positives = 187/392 (47%), Gaps = 65/392 (16%)

Query: 1054 KKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRA 1113
            K +LEE  K+ S    Q K+ + L+  I + +  I        F  A K      +Y   
Sbjct: 7    KSYLEEKVKQASNILPQ-KIVEDLKNLISNKEVLITRDEIDKIFDLAIK------EYSEG 59

Query: 1114 QIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFVPDDSFI 1162
             I P  A+G +AAQS+GEPGTQMTL+TFHFAG            + E ++   VP    +
Sbjct: 60   LIAPGEAIGIVAAQSVGEPGTQMTLRTFHFAGIRELNVTLGLPRLIEIVDAKKVPSTPMM 119

Query: 1163 LI------------------KLDMDRIR---------------LLHLE--------VDID 1181
             I                  KL+  +I                +L L+        V +D
Sbjct: 120  TIYLTDEYKHDKEKALEVARKLEYTKIENVVSSTSIDIASMSIILQLDNEMLKDKGVTVD 179

Query: 1182 SIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRA 1241
             ++  I R +   G   +       L    ++    + +++++  + +  IKG++GI RA
Sbjct: 180  DVKKAINRLK--LGEFVIDESEGNTLNISFANIDSIAALFKLRDKILNTKIKGIKGIKRA 237

Query: 1242 VIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTE 1301
            ++ ++  E    Y +L +G NL  V++  GV   K  +NN  E+ +  GIEAAR  I+ E
Sbjct: 238  IVQKKGDE----YIILTDGSNLSGVLSVKGVDIAKVETNNIREIEEVFGIEAAREIIIRE 293

Query: 1302 IKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFD 1361
            I  V+   G+ +D RH +LVAD+MT  G V  I RHG+   K SVL  A+FE T  HL D
Sbjct: 294  ISKVLAEQGLDVDMRHILLVADVMTRTGVVRQIGRHGVTGEKNSVLARAAFEVTVKHLLD 353

Query: 1362 AAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            AA  G  +   GV E II+G P+ +GTG+++L
Sbjct: 354  AAARGDVEEFKGVVENIIIGHPIKLGTGMVEL 385



 Score =  102 bits (255), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 74/238 (31%), Positives = 122/238 (51%), Gaps = 20/238 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYL------DKDTDLDYARIVKGRLERTTLGEVCEYIEE 817
           G+PR+ EI++A +  STP++T YL      DK+  L+ AR    +LE T +  V      
Sbjct: 100 GLPRLIEIVDAKKVPSTPMMTIYLTDEYKHDKEKALEVAR----KLEYTKIENVVSSTS- 154

Query: 818 VFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSS 877
               D + + I L +D   L    V +D ++  I R +   G   +       L    ++
Sbjct: 155 ---IDIASMSIILQLDNEMLKDKGVTVDDVKKAINRLK--LGEFVIDESEGNTLNISFAN 209

Query: 878 KSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVK 937
               + +++++  + +  IKG++GI RA++ ++  E    Y +L +G NL  V++  GV 
Sbjct: 210 IDSIAALFKLRDKILNTKIKGIKGIKRAIVQKKGDE----YIILTDGSNLSGVLSVKGVD 265

Query: 938 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
             K  +NN  E+ +  GIEAAR  I+ EI  V+   G+ +D RH +LVAD+MT  G V
Sbjct: 266 IAKVETNNIREIEEVFGIEAAREIIIREISKVLAEQGLDVDMRHILLVADVMTRTGVV 323


>gi|242398380|ref|YP_002993804.1| DNA-directed RNA polymerase subunit alpha [Thermococcus sibiricus
           MM 739]
 gi|242264773|gb|ACS89455.1| DNA-directed RNA polymerase subunit alpha [Thermococcus sibiricus
           MM 739]
          Length = 905

 Score =  169 bits (429), Expect = 9e-39,   Method: Compositional matrix adjust.
 Identities = 97/288 (33%), Positives = 160/288 (55%), Gaps = 41/288 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + DVVLFNRQPSLH++SIMAHR +V+P++TFR N  VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 418 NGDVVLFNRQPSLHRMSIMAHRVRVMPYKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEA 477

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE              A++LM  ++++++PR G  +I   QD I+GGYLLT++ A+F +
Sbjct: 478 QAE--------------ARILMEVQNHILSPRYGGPIIGGIQDHISGGYLLTREGAYFTK 523

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLIL--------- 511
            +   +   L+    ++  + K        P         W+GK +FSL+L         
Sbjct: 524 YE---VEHMLMFAGVEVKELPK--------PDKVENGIEYWSGKTVFSLLLPENLTIWYR 572

Query: 512 -----KPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKA 566
                 P++  P+   ++ K        +    D +V +   +LL+G++DK   G     
Sbjct: 573 NKLCDDPSQCEPIEKLIEEKLIPSEKEVKKVATDGFVYILKGKLLSGAIDKKAYGR-EDG 631

Query: 567 NVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVT-PGQG 613
            +  I++R++G + A   + +++++  + + ++GF+ GI D   PG+ 
Sbjct: 632 ELLNIIVREYGVERARQFLDQVTKLAIWVITHKGFTTGIDDEDLPGEA 679



 Score =  120 bits (300), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 80/267 (29%), Positives = 128/267 (47%), Gaps = 37/267 (13%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G IE  V     +++ S  +I   + Y +D    PI  GL+DRR+G       C TCG N
Sbjct: 9   GSIEFGVLSPQEIRKMSAAEITVPDTYSEDGY--PIDGGLMDRRLGVIDPNLRCETCGAN 66

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLR-NP 199
             +C GHFG+I+L  PV H+G+ + +   L+S C+   C R+ L +E+   +  KL  N 
Sbjct: 67  YKECPGHFGHIELARPVIHVGFAKTIYRTLESTCRE--CGRIKLTDEEIEDYFGKLNINE 124

Query: 200 ALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVED 259
           A    +  +L  +I +  K+  VCPHCG     +           K++  T   +   ++
Sbjct: 125 ARKSEI-DALISEIHKKAKERMVCPHCGAPQFSI-----------KFERPTIYWELRTDE 172

Query: 260 LLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLI 319
              EY                     + P E+    E IP +D+PLL +N E S+P  ++
Sbjct: 173 EGNEYR------------------HRMMPSEIRDRLEKIPDKDLPLLGLNPENSRPEWMV 214

Query: 320 LTRLLVPPNCIRPSVI--SDLKSDNDV 344
           LT L VPP  +RPS+   S +++++D+
Sbjct: 215 LTVLPVPPVSVRPSITLESGIRAEDDL 241



 Score = 94.7 bits (234), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 40/58 (68%), Positives = 50/58 (86%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GF+ NS+ SGLTP E+FFH MGGREGLVDTAV+TA++GYMQRRL+ +L+DL V YD
Sbjct: 800 AKGFIVNSYKSGLTPQEYFFHAMGGREGLVDTAVRTAQSGYMQRRLINALQDLKVDYD 857



 Score = 48.1 bits (113), Expect = 0.036,   Method: Compositional matrix adjust.
 Identities = 30/127 (23%), Positives = 61/127 (48%), Gaps = 24/127 (18%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGRKVFF 79
           ++LM  ++++++PR G  +I   QD I+GGYLLT++ A+F + +   +         + F
Sbjct: 482 RILMEVQNHILSPRYGGPIIGGIQDHISGGYLLTREGAYFTKYEVEHM---------LMF 532

Query: 80  RGLIEGTVTKEDRVQQ---------------QSHIQIVSKNLYCQDPQRTPIPHGLLDRR 124
            G+    + K D+V+                  ++ I  +N  C DP +      L++ +
Sbjct: 533 AGVEVKELPKPDKVENGIEYWSGKTVFSLLLPENLTIWYRNKLCDDPSQCEPIEKLIEEK 592

Query: 125 MGTNQKE 131
           +  ++KE
Sbjct: 593 LIPSEKE 599


>gi|289193125|ref|YP_003459066.1| DNA-directed RNA polymerase subunit A' [Methanocaldococcus sp.
           FS406-22]
 gi|288939575|gb|ADC70330.1| DNA-directed RNA polymerase subunit A' [Methanocaldococcus sp.
           FS406-22]
          Length = 891

 Score =  169 bits (429), Expect = 9e-39,   Method: Compositional matrix adjust.
 Identities = 100/272 (36%), Positives = 147/272 (54%), Gaps = 41/272 (15%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VL+NRQPSLH++SIMAHR +VLP+RTFR N CVC PYNADFDGDEMN+H+PQ+   
Sbjct: 425 DGDIVLYNRQPSLHRMSIMAHRVRVLPYRTFRHNLCVCPPYNADFDGDEMNLHVPQS--- 481

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
                            A+ LM  + ++++PR G  +I A  DFI+G YLLT  N F   
Sbjct: 482 -----------EEARAEAEALMLVEKHILSPRFGGPIIGAIHDFISGAYLLTS-NYFTKD 529

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
             T+ + S  I D               W P        +++GK+IFS  L      P  
Sbjct: 530 EATLILRSGGIKD-------------ELWEPDKVENGVPLYSGKKIFSKAL------PKG 570

Query: 521 ANLKTKG----RAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKAN-VFYILLRD 575
            NL+ K     +     +E C  D+YV++++ EL+ G +DK+  G G +A  + + ++++
Sbjct: 571 LNLRYKAKICRKCDECKKEDCPYDAYVVIKDGELIKGVIDKN--GYGAEAGLILHTIVKE 628

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           FG +     +   ++M    +M RGF+ GI D
Sbjct: 629 FGPEAGRKFLDSATKMAIRAVMLRGFTTGIDD 660



 Score =  120 bits (302), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 76/244 (31%), Positives = 120/244 (49%), Gaps = 38/244 (15%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D +++ S  +IV+ + Y +D    PI  GL+D R+G       C TCG  + +C GHFG+
Sbjct: 23  DYIRKMSVAKIVTPDTYDEDGY--PIDGGLMDTRLGVIDPGLVCKTCGGRIGECPGHFGH 80

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           I+L  PV HIG+ + +  IL+++C  P C RV + E K      K++        +  + 
Sbjct: 81  IELAKPVIHIGFAKTIYKILKAVC--PHCGRVAISEAKRREILEKMKKLERDGGNKWEVC 138

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           +++ +   KV++CP+CGEI                      K D   E     Y   +  
Sbjct: 139 EEVYKEASKVTICPYCGEI----------------------KYDIKFEKPTTYYR--IDG 174

Query: 271 NPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCI 330
           N E          +TL P +V ++ E IP ED  LL +N E+++P  ++LT L VPP  +
Sbjct: 175 NEE----------KTLTPSDVREILEKIPDEDCILLGLNPEVARPEWMVLTVLPVPPVTV 224

Query: 331 RPSV 334
           RPS+
Sbjct: 225 RPSI 228



 Score = 89.7 bits (221), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 37/57 (64%), Positives = 49/57 (85%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFV++S+  GL+PTEFFFH MGGREGLVD AV+TA++GYMQRRL+ +L+DL  ++D
Sbjct: 789 HGFVRSSYKKGLSPTEFFFHAMGGREGLVDQAVRTAQSGYMQRRLINALQDLKTEFD 845


>gi|159040772|ref|YP_001540024.1| DNA-directed RNA polymerase subunit A' [Caldivirga maquilingensis
           IC-167]
 gi|157919607|gb|ABW01034.1| DNA-directed RNA polymerase subunit A' [Caldivirga maquilingensis
           IC-167]
          Length = 889

 Score =  169 bits (428), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 95/265 (35%), Positives = 146/265 (55%), Gaps = 31/265 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D VLFNRQPSLHK+S+M H  KVLP RTFR +  VC PYNADFDGDEMN+H+PQT EA
Sbjct: 426 DGDYVLFNRQPSLHKMSMMCHIVKVLPGRTFRLHLAVCPPYNADFDGDEMNLHVPQTPEA 485

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+ +M  ++ +VTPR G  +I A QD+I+GGYLL++K     R
Sbjct: 486 RAE--------------ARTIMLVQNFIVTPRYGGPIIGARQDYISGGYLLSRKGNVLTR 531

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            + + I   +            R + +   P + +    +WTGKQI S +L  +     N
Sbjct: 532 EKALFILGAV------------RENVQLEEPAI-MHPVELWTGKQIISTLLPKD----FN 574

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
               T  ++  ++   C  D Y+++ N  L  G +DK ++G+    ++ ++L++ +G + 
Sbjct: 575 FTQATSFKSTCSDPYRCDTDEYIVVVNGYLATGVLDKKSIGAEQVDSLLHVLVKRYGNEF 634

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGI 605
               +  + R+   Y+  RGF++ +
Sbjct: 635 GRRWIDSMFRLIIRYIDIRGFTMAL 659



 Score =  112 bits (281), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 72/255 (28%), Positives = 117/255 (45%), Gaps = 42/255 (16%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           I   V   D +++ S +++ +   Y  D    P+  GL+DRR+G ++ EA C TCG +  
Sbjct: 21  ISFNVLSPDLIRKMSVMEVTTSETY--DEAGNPVKGGLMDRRLGVDEPEARCETCGNDWR 78

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALS 202
            C GHFG I+L  PV H  + + + +IL++ C  P C R+ L +E+   +  +++   L 
Sbjct: 79  RCPGHFGRIELVRPVVHPEFVKPIYDILRATC--PNCGRLKLTDEEYKRYSERIKR--LK 134

Query: 203 YLVRKSLKKKILETTKKV---SVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVED 259
              R    + IL   KK    S CPHCG     ++                         
Sbjct: 135 KHWRALSDRLILRVKKKAAARSTCPHCGAPQPKIR------------------------- 169

Query: 260 LLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLI 319
                ++  KF  E E     G +  L+P+ + +  E +P +D+ LL  N   ++P   +
Sbjct: 170 ----LDKPFKFYTESED----GRLTRLDPVSIREWLEKVPDDDLELLGWNPSTARPEWAV 221

Query: 320 LTRLLVPPNCIRPSV 334
           LT L VPP  +RPS+
Sbjct: 222 LTVLPVPPPQVRPSI 236



 Score = 81.6 bits (200), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 34/64 (53%), Positives = 51/64 (79%), Gaps = 1/64 (1%)

Query: 606 GDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           GD  P  +GFV+++F  GL+P E+FFH  GGR+GLV+TAV+T+++GY QRRL+ +++D+ 
Sbjct: 783 GDKGPEARGFVKSNFRDGLSPIEYFFHAGGGRDGLVETAVRTSQSGYAQRRLINAMQDIY 842

Query: 665 VQYD 668
           V YD
Sbjct: 843 VAYD 846



 Score = 42.7 bits (99), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 19/48 (39%), Positives = 31/48 (64%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRI 67
           + +M  ++ +VTPR G  +I A QD+I+GGYLL++K     R + + I
Sbjct: 490 RTIMLVQNFIVTPRYGGPIIGARQDYISGGYLLSRKGNVLTREKALFI 537


>gi|350638666|gb|EHA27022.1| DNA-directed RNA polymerase II, largest subunit [Aspergillus niger
           ATCC 1015]
          Length = 1743

 Score =  169 bits (428), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 99/278 (35%), Positives = 150/278 (53%), Gaps = 35/278 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DV+LFNRQPSLHK S+M HR +V+P+ TFR N  V TPYNADFDGDEMN+H+PQ+EE+
Sbjct: 452 DGDVILFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSEES 511

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L +L+++            N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 512 RAE----LSQLALVPM----------NIVSPQRNGPLMGIVQDTLCGIYKICRRDVFLTK 557

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M I    +    D  G+I         P   ++    WTGKQ+ S+ L      P  
Sbjct: 558 DQVMNI----MMWVPDWDGVIP--------PPAILKPRPRWTGKQMISMAL------PSG 599

Query: 521 AN-LKTKGRAYTANEEFCH-RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            N L+        +E+F    D  +++ N +L+ G   K T+G+ G   V + +  ++G 
Sbjct: 600 LNLLRVDKDNSPLSEKFSPLADGGLLIHNGQLMYGMFSKKTVGASG-GGVIHTIFNEYGH 658

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
             AV       R+ +++L++ GFSIGIGD  P +  +Q
Sbjct: 659 GTAVAFFNGAQRIVNYWLLHNGFSIGIGDTIPDELTIQ 696



 Score =  103 bits (256), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 60/181 (33%), Positives = 96/181 (53%), Gaps = 15/181 (8%)

Query: 1224 KQLLPSVVIKGVQGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMA 1268
            + LL ++ ++GV G+ RA I+E+    V                ++ L   G +L +V+A
Sbjct: 1284 QHLLDTLTLRGVPGVERAFINEKSKVRVLEDGSLFASKTDPLCKEWVLETSGSSLGEVLA 1343

Query: 1269 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK 1328
              GV   +  SN   EV++  GIEAAR+ ++ E+  V+   G  ++ RH  L+ D+MT +
Sbjct: 1344 IPGVDATRTYSNQFIEVFEVFGIEAARTAVLRELTQVLAFDGSYVNHRHLALLVDVMTVR 1403

Query: 1329 GEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGT 1388
            G +  +TRHG+ +     L   SFE T + L +AA +G+ D   GVSE +I+G     GT
Sbjct: 1404 GYLTPVTRHGINRADNGALMRCSFEETVEILLEAAAFGELDDCRGVSENLILGQMAPAGT 1463

Query: 1389 G 1389
            G
Sbjct: 1464 G 1464



 Score = 99.4 bits (246), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QR+LVK+LE++ V
Sbjct: 810 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMV 869

Query: 666 QYD 668
           +YD
Sbjct: 870 KYD 872



 Score = 89.7 bits (221), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 77/289 (26%), Positives = 134/289 (46%), Gaps = 59/289 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLD--KDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N + NI TP +T Y +  +  D + A+ ++  +E T+L  V E  E  + P
Sbjct: 1116 GVPRLKEILNVATNIKTPSMTVYQEAARSFDKEGAKQLRSAVEHTSLRSVTEATEIYYDP 1175

Query: 822  DDSFILIKLDMDRIR---LLHLEVDIDS-------IRYCIERTRGISGHLTVSGHSFLIL 871
            D    +I+ D D +    ++  +V  D+       +R  + R + +   LTV   +  I 
Sbjct: 1176 DIQTTVIENDRDMVESYFIIPEDVTDDASRQSKWLLRIILSRPKLLDKGLTVQDVASRIK 1235

Query: 872  K--PKD-----SSKSFNSKMYQMKQ-------------------------LLPSVVIKGV 899
               PKD     S  + + ++ +++Q                         LL ++ ++GV
Sbjct: 1236 AAYPKDIAVIFSDNNADEQVIRIRQIQDYKEDEEDDDIEYDVTLKKLEQHLLDTLTLRGV 1295

Query: 900  QGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMATYGVKGVKCSSN 944
             G+ RA I+E+    V                ++ L   G +L +V+A  GV   +  SN
Sbjct: 1296 PGVERAFINEKSKVRVLEDGSLFASKTDPLCKEWVLETSGSSLGEVLAIPGVDATRTYSN 1355

Query: 945  NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
               EV++  GIEAAR+ ++ E+  V+   G  ++ RH  L+ D+MT +G
Sbjct: 1356 QFIEVFEVFGIEAARTAVLRELTQVLAFDGSYVNHRHLALLVDVMTVRG 1404



 Score = 79.3 bits (194), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 53/229 (23%), Positives = 101/229 (44%), Gaps = 42/229 (18%)

Query: 110 DPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINI 169
           D ++ P   GL D R+GT  ++ NC TC +   +C GHFG+I+L  PV+HIG+   +  +
Sbjct: 45  DQRQRPRTKGLNDPRLGTIDRQWNCETCEEGQKECPGHFGHIELATPVYHIGFLTKIKKL 104

Query: 170 LQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKSLKKKIL-------------- 214
           L+++C N  C ++           A ++R+P   +     L K +L              
Sbjct: 105 LETVCHN--CGKIKANTSDPKFLEALRMRDPKRRFDHIWRLSKDVLICEADPPPDDDEPF 162

Query: 215 --ETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNP 272
             E  K V +   CG     ++K G+  +        T K + +++++  +  E     P
Sbjct: 163 SKENAKPVRMHGGCGNAQPQIRKEGITLVG-------TWKPNKMMDEMDMQQPEKKVITP 215

Query: 273 EIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
           ++                 L +F  I  ED+ ++ ++ + ++P  +I+T
Sbjct: 216 QV----------------ALNVFRNISYEDVRIMGLSNDYARPEWMIIT 248



 Score = 56.6 bits (135), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/41 (60%), Positives = 28/41 (68%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            A   ++ +A   P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1067 AIESRFAKAGANPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1107


>gi|327242107|gb|AEA40832.1| RNA polymerase II largest subunit [Hypotrichomonas acosta]
          Length = 1042

 Score =  169 bits (428), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 102/278 (36%), Positives = 156/278 (56%), Gaps = 32/278 (11%)

Query: 333 SVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNV 392
           S++     D+D+V+FNRQPSLHK+S+M HRA+++P +TFR N CV TPYNADFDGDEMN+
Sbjct: 382 SIVERHLRDDDIVIFNRQPSLHKMSMMGHRARIMPGQTFRLNLCVTTPYNADFDGDEMNM 441

Query: 393 HLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLT 452
           H+PQ++ ARAE              AK +M   + +++P++   +I   QD + G  LL+
Sbjct: 442 HVPQSQMARAE--------------AKHIMLVPNQIISPQSACPIIGLVQDSLLGCRLLS 487

Query: 453 QKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLIL- 511
            ++ F  R +   +   +I D++DI             P   ++   +W+GKQ+FSL L 
Sbjct: 488 LRDTFLTRNEITNLMMWII-DSNDIV----------LPPPCILKPKELWSGKQVFSLFLP 536

Query: 512 KPNRDC-PVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLG-SGGKANVF 569
           K N D   V A+ K   +     E     D  VI+RN  LLAG +DK T+  S G  N  
Sbjct: 537 KINYDGFSVGADAKENTKEVNTWESPA--DLRVIIRNGNLLAGILDKKTVAKSAGSLN-- 592

Query: 570 YILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           ++++  +  + A   + +   + + +L NRGFSIG+ D
Sbjct: 593 HVVINSYSIETARQFLNQTQLIVNNWLENRGFSIGLSD 630



 Score = 89.4 bits (220), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 37/57 (64%), Positives = 46/57 (80%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GF ++SF  GLTP EFFFH MGGR G++DTA KT++TGY+QRRL KS+E  CV YD
Sbjct: 759 RGFCEHSFIQGLTPQEFFFHAMGGRVGIIDTACKTSDTGYIQRRLCKSMESHCVMYD 815


>gi|408381652|ref|ZP_11179200.1| DNA-directed RNA polymerase subunit A' [Methanobacterium formicicum
           DSM 3637]
 gi|407815583|gb|EKF86153.1| DNA-directed RNA polymerase subunit A' [Methanobacterium formicicum
           DSM 3637]
          Length = 871

 Score =  169 bits (428), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 99/268 (36%), Positives = 149/268 (55%), Gaps = 38/268 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++S+MAH  KVLP++TFR N CVC PYNADFDGDEMN+H+ QTEE+
Sbjct: 408 DGDIVLFNRQPSLHRMSMMAHEVKVLPYKTFRLNLCVCPPYNADFDGDEMNMHVFQTEES 467

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              AK LM  + ++++PR G  +I    D I+G YLLT++ + F  
Sbjct: 468 RAE--------------AKSLMRVQEHILSPRFGGPIIGGIHDHISGAYLLTREGSNFRE 513

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                          D+  ++K    +S  P+   R    WTGK+IFSL+L  + +    
Sbjct: 514 --------------DDVFQMLK----KSQLPIPKPRNQE-WTGKEIFSLLLPKDLNMVYK 554

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGS-GGKANVFYILLRDFGED 579
           A +  K       E  C  D+YV++ N +L +G++D+   G+  GK  +   +++++G D
Sbjct: 555 AEICRKCDECLRQE--CKNDAYVVIENGQLKSGAIDEKAYGAFSGK--ILDSVVKEYGTD 610

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            A   +   +++    +M RGF+    D
Sbjct: 611 RAREFLDAATKLAISGIMKRGFTTSTAD 638



 Score =  103 bits (257), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 71/244 (29%), Positives = 109/244 (44%), Gaps = 43/244 (17%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + +++ S  +IV+ + Y +D    PI  GL+D R+G       C +CG    DC GHFG+
Sbjct: 19  ENIRRMSVTKIVTPDTYDEDG--YPIEAGLMDPRLGVIDPGLRCRSCGSKGGDCQGHFGH 76

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           I+L  PV H+G+   +  IL+S C    C RVLL E +   +R ++ +   +      L 
Sbjct: 77  INLARPVVHVGFADTIHKILRSTCSE--CGRVLLTETERIDYRDRIESRLKNEESITGLV 134

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           K +  TT +   CPHC      VK    + I    YK                       
Sbjct: 135 KDVY-TTARRDKCPHCDTEQEDVKIDKPVSIVEGNYK----------------------- 170

Query: 271 NPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCI 330
                          L P EV +  E IP +D   L +N+++++P  ++LT L VPP  +
Sbjct: 171 ---------------LTPSEVRERLEKIPEDDYVYLGINSKVARPEWMVLTVLPVPPVTV 215

Query: 331 RPSV 334
           RPS+
Sbjct: 216 RPSI 219



 Score = 89.0 bits (219), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 38/56 (67%), Positives = 47/56 (83%)

Query: 613 GFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           GFV +S+ +GL P EFFFH MGGREGLVDTA++TA++GYMQRRLV +L+DL V  D
Sbjct: 768 GFVHSSYKTGLDPLEFFFHAMGGREGLVDTAIRTAQSGYMQRRLVNALQDLSVNAD 823


>gi|150401217|ref|YP_001324983.1| DNA-directed RNA polymerase subunit A'' [Methanococcus aeolicus
            Nankai-3]
 gi|166229257|sp|A6UV49.1|RPOA2_META3 RecName: Full=DNA-directed RNA polymerase subunit A''
 gi|150013920|gb|ABR56371.1| DNA-directed RNA polymerase, subunit A'' [Methanococcus aeolicus
            Nankai-3]
          Length = 397

 Score =  169 bits (428), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 111/332 (33%), Positives = 174/332 (52%), Gaps = 56/332 (16%)

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYIEEVF 1155
            Y R  +EP  +VG +AAQS+GEPGTQMT++TFH+AG              E+ +  +E  
Sbjct: 49   YERTLVEPNESVGVVAAQSLGEPGTQMTMRTFHYAGVAELNVTLGLPRMIEIVDARKEPS 108

Query: 1156 VPDDSFIL-------------IKLDMDRIRLLHL--EVDIDSIRYCIE--------RTRG 1192
             P  +  L             +  +++ I + ++  ++ ID ++  I         + R 
Sbjct: 109  TPTMTVYLTEDYAFDKSKAEEVAKNIESITVQNIAQDIHIDMVKLAINVVLNPESMKQRN 168

Query: 1193 ISG-------------HLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGIN 1239
            I+               +   G+   ++    S K+   ++ ++K    S+ +KGV  I 
Sbjct: 169  ITADDVMEAIKKKMKLKIEQEGNILRLIIKTPSLKALRKRIPKVK----SIHLKGVPNIP 224

Query: 1240 RAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIM 1299
            R ++ ++D  G  +Y L  EG NL  V    GV  V+ +SNN  E+   LGIEAAR+ I+
Sbjct: 225  RVIVKKDDTMG--EYILHSEGSNLSAVFEIDGVDMVRTTSNNIVEIQDVLGIEAARNAII 282

Query: 1300 TEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHL 1359
             EI  V+   G+++D RH M++AD+MT+ G V  I RHGL+  K SVL  A+FE T  HL
Sbjct: 283  NEISGVLNQQGLNVDIRHLMVIADIMTADGSVKSIGRHGLSGEKASVLARAAFEETVKHL 342

Query: 1360 FDAAFYGQTDCISGVSECIIMGLPMNVGTGLI 1391
            + AA  G +D +SGV E II+G P+++GTG +
Sbjct: 343  YSAAEKGHSDKLSGVVENIIVGKPISMGTGCV 374



 Score = 99.4 bits (246), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 73/240 (30%), Positives = 125/240 (52%), Gaps = 26/240 (10%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP-- 821
           G+PR+ EI++A +  STP +T YL +D    YA       +++   EV + IE + V   
Sbjct: 93  GLPRMIEIVDARKEPSTPTMTVYLTED----YA------FDKSKAEEVAKNIESITVQNI 142

Query: 822 --DDSFILIKLDMDRI----RLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKD 875
             D    ++KL ++ +     +    +  D +   I++   +   +   G+   ++    
Sbjct: 143 AQDIHIDMVKLAINVVLNPESMKQRNITADDVMEAIKKKMKLK--IEQEGNILRLIIKTP 200

Query: 876 SSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYG 935
           S K+   ++ ++K    S+ +KGV  I R ++ ++D  G  +Y L  EG NL  V    G
Sbjct: 201 SLKALRKRIPKVK----SIHLKGVPNIPRVIVKKDDTMG--EYILHSEGSNLSAVFEIDG 254

Query: 936 VKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
           V  V+ +SNN  E+   LGIEAAR+ I+ EI  V+   G+++D RH M++AD+MT+ G V
Sbjct: 255 VDMVRTTSNNIVEIQDVLGIEAARNAIINEISGVLNQQGLNVDIRHLMVIADIMTADGSV 314


>gi|410670214|ref|YP_006922585.1| DNA-directed RNA polymerase subunit alpha [Methanolobus
           psychrophilus R15]
 gi|409169342|gb|AFV23217.1| DNA-directed RNA polymerase subunit alpha [Methanolobus
           psychrophilus R15]
          Length = 880

 Score =  169 bits (428), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 98/269 (36%), Positives = 146/269 (54%), Gaps = 33/269 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHK+SIMAHR KVLP++TFR N  VC PYNADFDGDEMN+H+ QTEE+
Sbjct: 412 DGDIVLFNRQPSLHKMSIMAHRVKVLPYKTFRLNPAVCPPYNADFDGDEMNMHVLQTEES 471

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A +LM  + N+++PR G  +I    D I+G +LLT+     N 
Sbjct: 472 RAE--------------ASILMQVQENILSPRFGGPIIGGIHDHISGLFLLTR-----NE 512

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPN--RDCP 518
               + A+  +   SDI  + +  S+ +           +W GKQIFS IL      + P
Sbjct: 513 NSITKTAALELLRKSDIRVLPEPSSYTA-------DGEPLWNGKQIFSQILPKGLYLEFP 565

Query: 519 VNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
                K      T  +  C  ++YV++ N E++ G++D+  +G+  K  +   +++++G 
Sbjct: 566 AQVCFKCD----TCKKRDCEYEAYVVIENGEMIQGTIDEQAIGA-FKGKILDKVVKEYGT 620

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           +     +   +R+    +M  G S GI D
Sbjct: 621 EAGAKFVDDFTRLAIRGVMKTGLSFGISD 649



 Score =  114 bits (286), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 76/254 (29%), Positives = 121/254 (47%), Gaps = 44/254 (17%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           V++ S   IV+ + Y  D    PI  GL+D R+G       C TCG    +C GHFG+I+
Sbjct: 24  VRKMSVTSIVTADTY--DDDGYPIDMGLMDLRLGVIDPGLKCKTCGSRAGECPGHFGHIE 81

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKK 212
           L  PV H+G+ + +   L+SIC N  C+R+LL  ++   F A+L +      +   +  +
Sbjct: 82  LVAPVIHVGFNKTIRKALRSICHN--CSRLLLTADQKRNFLAQLESSKDMGHLPDDIVNE 139

Query: 213 ILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNP 272
           + +  +K  +CP+C               S E+ + + +K    +ED             
Sbjct: 140 VFKEARKTKICPYC---------------SSEQKEVKFEKPTDYIED------------- 171

Query: 273 EIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRP 332
               HK       L P E+   FE IP ED+ +L M+   ++P   ILT L VPP  +RP
Sbjct: 172 ---GHK-------LTPTEIRDRFENIPDEDVKVLGMDPSSARPEWTILTVLPVPPVTVRP 221

Query: 333 SVI--SDLKSDNDV 344
           S+   S  +S++D+
Sbjct: 222 SITLESGQRSEDDL 235



 Score = 92.4 bits (228), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 40/60 (66%), Positives = 52/60 (86%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            +GFV+ S+ SGL PTE+FFH +GGREGLVDTAV+T+++GY+QRRLV +L+DL VQYD S
Sbjct: 777 ARGFVKASYKSGLNPTEYFFHAIGGREGLVDTAVRTSQSGYLQRRLVNALQDLEVQYDGS 836


>gi|432329279|ref|YP_007247423.1| DNA-directed RNA polymerase subunit A' [Aciduliprofundum sp.
           MAR08-339]
 gi|432135988|gb|AGB05257.1| DNA-directed RNA polymerase subunit A' [Aciduliprofundum sp.
           MAR08-339]
          Length = 895

 Score =  169 bits (427), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 107/274 (39%), Positives = 151/274 (55%), Gaps = 42/274 (15%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++S+M H  KVLP RTFRFN  VC PYNADFDGDEMN+H+ Q+EEA
Sbjct: 421 DGDIVLFNRQPSLHRMSMMGHLVKVLPQRTFRFNLAVCPPYNADFDGDEMNLHVLQSEEA 480

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              AK+LM  + ++++PR G  +I    D IT  +LLT KN  F +
Sbjct: 481 RAE--------------AKILMLVQEHILSPRFGGPIIGGLHDHITAMFLLTHKNPKFTK 526

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            + + I S L  D+            R  N   F      + GK +FSLIL      P +
Sbjct: 527 DEAIHILSYLDYDSLP-------EPHRDENGNEF------YYGKDLFSLIL------PKD 567

Query: 521 ANLKTKGR----AYTANE---EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILL 573
            N++ K +    +   N+   E C  D+YV++RN +L+AG++D++ +GS     +  I  
Sbjct: 568 LNMEFKSKICDPSVCKNKCVYEKCPIDAYVVIRNGKLVAGTIDENAIGSMKGKLLDRIAK 627

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           R  G D A   +  ++R+    +  RGF+ GI D
Sbjct: 628 R--GSDTARKFIDDMTRLAVGVISYRGFTSGIDD 659



 Score =  117 bits (293), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 72/255 (28%), Positives = 123/255 (48%), Gaps = 45/255 (17%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           I+ ++   + +++ S +++++ + Y  D    PI  GL+D  MG  +    C TCG  + 
Sbjct: 15  IKFSLLSPEEIRRMSAVKVITADTY--DDDGFPIDKGLMDLHMGVIEPGLRCKTCGGKVD 72

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKL---RNP 199
           +C GHFG+I+L +PV H+G+ + + N L + C+   C R+ L +++   ++ K+   +N 
Sbjct: 73  ECPGHFGHIELAMPVIHVGFVKNIKNYLDATCRE--CGRIKLKDDEIEIYKQKIEEAKNM 130

Query: 200 ALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVED 259
             S L    + KKI++      +CPHCG                        ++  I  D
Sbjct: 131 GASPLELLFITKKIIDDASSRPICPHCG-----------------------AEQKKITLD 167

Query: 260 LLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLI 319
               + E        E  K       L P E+ +  E IP ED+PLL MN E ++P  ++
Sbjct: 168 KPTTFRE--------EGRK-------LTPKEIRERLERIPDEDLPLLGMNPETARPEWMV 212

Query: 320 LTRLLVPPNCIRPSV 334
           LT L VPP  +RP++
Sbjct: 213 LTVLPVPPVNVRPTI 227



 Score = 89.0 bits (219), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 38/58 (65%), Positives = 49/58 (84%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV++S+  GL PTE+FFH+MGGREGLVDTAV+T+ +GYMQRRL+ +LEDL V  D
Sbjct: 787 ARGFVESSYKKGLNPTEYFFHSMGGREGLVDTAVRTSRSGYMQRRLINALEDLKVTED 844


>gi|126465704|ref|YP_001040813.1| DNA-directed RNA polymerase subunit A'' [Staphylothermus marinus F1]
 gi|126014527|gb|ABN69905.1| DNA-directed RNA polymerase, subunit A' [Staphylothermus marinus F1]
          Length = 421

 Score =  169 bits (427), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 128/395 (32%), Positives = 195/395 (49%), Gaps = 59/395 (14%)

Query: 1050 VRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREK 1109
            +R IK+ LE   + E      +KV + LRE++     +  HG       +  K    R  
Sbjct: 5    IRSIKQ-LESLLENELKGKVSNKVYEELREKLKEAYKE--HGLYIEEVKAIIKETIDR-- 59

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFVPD 1158
            Y+R+Q EP   VG +AAQSIGEP TQMTL+TFH+AG            + E ++    P 
Sbjct: 60   YMRSQAEPGEPVGTVAAQSIGEPSTQMTLRTFHYAGVREFNVTLGLPRLIEIVDARKKPG 119

Query: 1159 DSFILIKLDMDR------------------IRLLHLEVDIDSIRYC-------IERTRGI 1193
               + I LD +                   I  +  E+++D            +   +GI
Sbjct: 120  TPIMEIPLDEEHKYDEEKAKKVARMIESTTIENISKEINVDPYEGATIVLDSEMLSDKGI 179

Query: 1194 SGHLTVSGHSFLIL-----KPKD---------SSKSFNSKMYQMKQLLPSVVIKGVQGIN 1239
            S    V     L L      P+D         S K   +K+ +++  + +  IKG++GI 
Sbjct: 180  SVDEVVKVLEKLKLGKVYVDPEDPYVIHIALRSEKIDYTKVEKIRTKIANTKIKGIKGIT 239

Query: 1240 RAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIM 1299
            + +I +   E    Y L+ EG NL +VM   GV   K  +NN  E+ + LGIEAAR+ I+
Sbjct: 240  KVIIQKRGDE----YILVAEGSNLAEVMKVPGVDYRKVYTNNIAEIEEILGIEAARAAII 295

Query: 1300 TEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHL 1359
             E K V+E+ G+ +D RH +L+AD+MT  G++  + R G+A  K SVL  A+FE T   L
Sbjct: 296  RETKNVLEDQGLDVDIRHLILLADMMTWTGKIRQVGRMGIAGEKPSVLARATFEMTVQKL 355

Query: 1360 FDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
             +AA  G+ D + GV E +I+G P+ VGTG++++ 
Sbjct: 356  VEAAVEGEVDMLKGVPENVIIGQPVPVGTGIVEIF 390



 Score = 97.8 bits (242), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 73/235 (31%), Positives = 128/235 (54%), Gaps = 14/235 (5%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A +   TPI+   LD++   D + A+ V   +E TT+  + +   E+ V 
Sbjct: 104 GLPRLIEIVDARKKPGTPIMEIPLDEEHKYDEEKAKKVARMIESTTIENISK---EINV- 159

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHS-FLILKPKDSSKSF 880
            D +    + +D   L    + +D +   +E+ +   G + V     ++I     S K  
Sbjct: 160 -DPYEGATIVLDSEMLSDKGISVDEVVKVLEKLK--LGKVYVDPEDPYVIHIALRSEKID 216

Query: 881 NSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
            +K+ +++  + +  IKG++GI + +I +   E    Y L+ EG NL +VM   GV   K
Sbjct: 217 YTKVEKIRTKIANTKIKGIKGITKVIIQKRGDE----YILVAEGSNLAEVMKVPGVDYRK 272

Query: 941 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
             +NN  E+ + LGIEAAR+ I+ E K V+E+ G+ +D RH +L+AD+MT  G++
Sbjct: 273 VYTNNIAEIEEILGIEAARAAIIRETKNVLEDQGLDVDIRHLILLADMMTWTGKI 327


>gi|145230824|ref|XP_001389676.1| DNA-directed RNA polymerase II subunit RPB1 [Aspergillus niger CBS
           513.88]
 gi|134055799|emb|CAK37321.1| unnamed protein product [Aspergillus niger]
          Length = 1747

 Score =  169 bits (427), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 99/278 (35%), Positives = 150/278 (53%), Gaps = 35/278 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DV+LFNRQPSLHK S+M HR +V+P+ TFR N  V TPYNADFDGDEMN+H+PQ+EE+
Sbjct: 452 DGDVILFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSEES 511

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L +L+++            N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 512 RAE----LSQLALVPM----------NIVSPQRNGPLMGIVQDTLCGIYKICRRDVFLTK 557

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M I    +    D  G+I         P   ++    WTGKQ+ S+ L      P  
Sbjct: 558 DQVMNI----MMWVPDWDGVIP--------PPAILKPRPRWTGKQMISMAL------PSG 599

Query: 521 AN-LKTKGRAYTANEEFCH-RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            N L+        +E+F    D  +++ N +L+ G   K T+G+ G   V + +  ++G 
Sbjct: 600 LNLLRVDKDNSPLSEKFSPLADGGLLIHNGQLMYGMFSKKTVGASG-GGVIHTIFNEYGH 658

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
             AV       R+ +++L++ GFSIGIGD  P +  +Q
Sbjct: 659 GTAVAFFNGAQRIVNYWLLHNGFSIGIGDTIPDELTIQ 696



 Score =  103 bits (256), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 60/181 (33%), Positives = 96/181 (53%), Gaps = 15/181 (8%)

Query: 1224 KQLLPSVVIKGVQGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMA 1268
            + LL ++ ++GV G+ RA I+E+    V                ++ L   G +L +V+A
Sbjct: 1284 QHLLDTLTLRGVPGVERAFINEKSKVRVLEDGSLFASKTDPLCKEWVLETSGSSLGEVLA 1343

Query: 1269 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK 1328
              GV   +  SN   EV++  GIEAAR+ ++ E+  V+   G  ++ RH  L+ D+MT +
Sbjct: 1344 IPGVDATRTYSNQFIEVFEVFGIEAARTAVLRELTQVLAFDGSYVNHRHLALLVDVMTVR 1403

Query: 1329 GEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGT 1388
            G +  +TRHG+ +     L   SFE T + L +AA +G+ D   GVSE +I+G     GT
Sbjct: 1404 GYLTPVTRHGINRADNGALMRCSFEETVEILLEAAAFGELDDCRGVSENLILGQMAPAGT 1463

Query: 1389 G 1389
            G
Sbjct: 1464 G 1464



 Score = 99.4 bits (246), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QR+LVK+LE++ V
Sbjct: 810 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMV 869

Query: 666 QYD 668
           +YD
Sbjct: 870 KYD 872



 Score = 89.7 bits (221), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 77/289 (26%), Positives = 134/289 (46%), Gaps = 59/289 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLD--KDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N + NI TP +T Y +  +  D + A+ ++  +E T+L  V E  E  + P
Sbjct: 1116 GVPRLKEILNVATNIKTPSMTVYQEAARSFDKEGAKQLRSAVEHTSLRSVTEATEIYYDP 1175

Query: 822  DDSFILIKLDMDRIR---LLHLEVDIDS-------IRYCIERTRGISGHLTVSGHSFLIL 871
            D    +I+ D D +    ++  +V  D+       +R  + R + +   LTV   +  I 
Sbjct: 1176 DIQTTVIENDRDMVESYFIIPEDVTDDASRQSKWLLRIILSRPKLLDKGLTVQDVASRIK 1235

Query: 872  K--PKD-----SSKSFNSKMYQMKQ-------------------------LLPSVVIKGV 899
               PKD     S  + + ++ +++Q                         LL ++ ++GV
Sbjct: 1236 AAYPKDIAVIFSDNNADEQVIRIRQIQDYKEDEEDDDIEYDVTLKKLEQHLLDTLTLRGV 1295

Query: 900  QGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMATYGVKGVKCSSN 944
             G+ RA I+E+    V                ++ L   G +L +V+A  GV   +  SN
Sbjct: 1296 PGVERAFINEKSKVRVLEDGSLFASKTDPLCKEWVLETSGSSLGEVLAIPGVDATRTYSN 1355

Query: 945  NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
               EV++  GIEAAR+ ++ E+  V+   G  ++ RH  L+ D+MT +G
Sbjct: 1356 QFIEVFEVFGIEAARTAVLRELTQVLAFDGSYVNHRHLALLVDVMTVRG 1404



 Score = 79.3 bits (194), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 53/229 (23%), Positives = 101/229 (44%), Gaps = 42/229 (18%)

Query: 110 DPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINI 169
           D ++ P   GL D R+GT  ++ NC TC +   +C GHFG+I+L  PV+HIG+   +  +
Sbjct: 45  DQRQRPRTKGLNDPRLGTIDRQWNCETCEEGQKECPGHFGHIELATPVYHIGFLTKIKKL 104

Query: 170 LQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKSLKKKIL-------------- 214
           L+++C N  C ++           A ++R+P   +     L K +L              
Sbjct: 105 LETVCHN--CGKIKANTSDPKFLEALRMRDPKRRFDHIWRLSKDVLICEADPPPDDDEPF 162

Query: 215 --ETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNP 272
             E  K V +   CG     ++K G+  +        T K + +++++  +  E     P
Sbjct: 163 SKENAKPVRMHGGCGNAQPQIRKEGITLVG-------TWKPNKMMDEMDMQQPEKKVITP 215

Query: 273 EIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
           ++                 L +F  I  ED+ ++ ++ + ++P  +I+T
Sbjct: 216 QV----------------ALNVFRNISYEDVRIMGLSNDYARPEWMIIT 248



 Score = 56.2 bits (134), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/41 (60%), Positives = 28/41 (68%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            A   ++ +A   P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1067 AIESRFAKAGANPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1107


>gi|358370099|dbj|GAA86711.1| DNA-dependent RNA polymerase II largest subunit [Aspergillus
           kawachii IFO 4308]
          Length = 1747

 Score =  169 bits (427), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 99/278 (35%), Positives = 150/278 (53%), Gaps = 35/278 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DV+LFNRQPSLHK S+M HR +V+P+ TFR N  V TPYNADFDGDEMN+H+PQ+EE+
Sbjct: 452 DGDVILFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSEES 511

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L +L+++            N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 512 RAE----LSQLALVPM----------NIVSPQRNGPLMGIVQDTLCGIYKICRRDVFLTK 557

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M I    +    D  G+I         P   ++    WTGKQ+ S+ L      P  
Sbjct: 558 DQVMNI----MMWVPDWDGVIP--------PPAILKPRPRWTGKQMISMAL------PSG 599

Query: 521 AN-LKTKGRAYTANEEFCH-RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            N L+        +E+F    D  +++ N +L+ G   K T+G+ G   V + +  ++G 
Sbjct: 600 LNLLRVDKDNSPLSEKFSPLADGGLLIHNGQLMYGMFSKKTVGASG-GGVIHTIFNEYGH 658

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
             AV       R+ +++L++ GFSIGIGD  P +  +Q
Sbjct: 659 GTAVAFFNGAQRIVNYWLLHNGFSIGIGDTIPDELTIQ 696



 Score =  103 bits (256), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 60/181 (33%), Positives = 96/181 (53%), Gaps = 15/181 (8%)

Query: 1224 KQLLPSVVIKGVQGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMA 1268
            + LL ++ ++GV G+ RA I+E+    V                ++ L   G +L +V+A
Sbjct: 1284 QHLLDTLTLRGVPGVERAFINEKSKVRVLEDGSLFASKTDPLCKEWVLETSGSSLGEVLA 1343

Query: 1269 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK 1328
              GV   +  SN   EV++  GIEAAR+ ++ E+  V+   G  ++ RH  L+ D+MT +
Sbjct: 1344 IPGVDATRTYSNQFIEVFEVFGIEAARTAVLRELTQVLAFDGSYVNHRHLALLVDVMTVR 1403

Query: 1329 GEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGT 1388
            G +  +TRHG+ +     L   SFE T + L +AA +G+ D   GVSE +I+G     GT
Sbjct: 1404 GYLTPVTRHGINRADNGALMRCSFEETVEILLEAAAFGELDDCRGVSENLILGQMAPAGT 1463

Query: 1389 G 1389
            G
Sbjct: 1464 G 1464



 Score = 99.4 bits (246), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QR+LVK+LE++ V
Sbjct: 810 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMV 869

Query: 666 QYD 668
           +YD
Sbjct: 870 KYD 872



 Score = 89.7 bits (221), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 77/289 (26%), Positives = 134/289 (46%), Gaps = 59/289 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLD--KDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N + NI TP +T Y +  +  D + A+ ++  +E T+L  V E  E  + P
Sbjct: 1116 GVPRLKEILNVATNIKTPSMTVYQEAARSFDKEGAKQLRSAVEHTSLRSVTEATEIYYDP 1175

Query: 822  DDSFILIKLDMDRIR---LLHLEVDIDS-------IRYCIERTRGISGHLTVSGHSFLIL 871
            D    +I+ D D +    ++  +V  D+       +R  + R + +   LTV   +  I 
Sbjct: 1176 DIQTTVIENDRDMVESYFIIPEDVTDDASRQSKWLLRIILSRPKLLDKGLTVQDVASRIK 1235

Query: 872  K--PKD-----SSKSFNSKMYQMKQ-------------------------LLPSVVIKGV 899
               PKD     S  + + ++ +++Q                         LL ++ ++GV
Sbjct: 1236 AAYPKDIAVIFSDNNADEQVIRIRQIQDYKEDEEDDDIEYDVTLKKLEQHLLDTLTLRGV 1295

Query: 900  QGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMATYGVKGVKCSSN 944
             G+ RA I+E+    V                ++ L   G +L +V+A  GV   +  SN
Sbjct: 1296 PGVERAFINEKSKVRVLEDGSLFASKTDPLCKEWVLETSGSSLGEVLAIPGVDATRTYSN 1355

Query: 945  NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
               EV++  GIEAAR+ ++ E+  V+   G  ++ RH  L+ D+MT +G
Sbjct: 1356 QFIEVFEVFGIEAARTAVLRELTQVLAFDGSYVNHRHLALLVDVMTVRG 1404



 Score = 80.1 bits (196), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 53/229 (23%), Positives = 102/229 (44%), Gaps = 42/229 (18%)

Query: 110 DPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINI 169
           D ++ P   GL D R+GT  ++ NC TC +   +C GHFG+I+L  PV+HIG+   +  +
Sbjct: 45  DQRQRPRTKGLNDPRLGTIDRQWNCETCEEGQKECPGHFGHIELATPVYHIGFLTKIKKL 104

Query: 170 LQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKSLKKKIL-------------- 214
           L+++C N  C ++           A ++R+P   +     L K +L              
Sbjct: 105 LETVCHN--CGKIKANTSDPKFLEALRMRDPKRRFDHIWRLSKDVLICEADPPPDDDEPF 162

Query: 215 --ETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNP 272
             E +K V +   CG     ++K G+  +        T K + +++++  +  E     P
Sbjct: 163 SKENSKPVRMHGGCGNAQPQIRKEGITLVG-------TWKPNKMMDEMDMQQPEKKVITP 215

Query: 273 EIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
           ++                 L +F  I  ED+ ++ ++ + ++P  +I+T
Sbjct: 216 QV----------------ALNVFRNISYEDVRIMGLSNDYARPEWMIIT 248



 Score = 56.6 bits (135), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/41 (60%), Positives = 28/41 (68%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            A   ++ +A   P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1067 AIESRFAKAGANPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1107


>gi|448383942|ref|ZP_21562940.1| DNA-directed RNA polymerase subunit A'' [Haloterrigena thermotolerans
            DSM 11522]
 gi|445658931|gb|ELZ11743.1| DNA-directed RNA polymerase subunit A'' [Haloterrigena thermotolerans
            DSM 11522]
          Length = 398

 Score =  169 bits (427), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 108/344 (31%), Positives = 178/344 (51%), Gaps = 59/344 (17%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A+A   +Y+  +++P   VG ++AQSIGEPGTQ+T+ TFH+AG            + E +
Sbjct: 48   AKAVETRYLDTRVDPLDPVGTVSAQSIGEPGTQLTMNTFHYAGVAEIDVTQGLPRLIELV 107

Query: 1152 EEVFVPDDSFILIKLD----------------MDRIRLLHL----------EVDI----- 1180
            +    PD   + + L+                ++  ++L L           V I     
Sbjct: 108  DARKTPDTPMMTVYLEGEYATEREKAHEVVWKIEATKILALGDVSTNVADMRVQISLNED 167

Query: 1181 ---------DSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVV 1231
                     D +   IE + G+    TV   + +   P++ S      + Q+ + L  + 
Sbjct: 168  TLKERMITPDEVAGIIEDSLGVQ---TVQQGTEIQFGPEEPSYR---DLLQLVEELRDIT 221

Query: 1232 IKGVQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLG 1290
             KG++ I+R VI  E+++ G  ++ L  EG    DV+   GV   + + NN +E+++ LG
Sbjct: 222  FKGIEDISRVVIRREELDNGNEEFVLYTEGSAFGDVLEIEGVDASRTTCNNIHEIHRNLG 281

Query: 1291 IEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNL 1349
            IEAAR  I+ E    +   G+  ++ RH MLVAD+MT++GE+  I RHG++  KESVL  
Sbjct: 282  IEAAREAIIEETNNTLAEQGLDDVNVRHLMLVADMMTNRGEIESIGRHGISGSKESVLAR 341

Query: 1350 ASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            A+FE T +HL +AA +G+ D + GV+E +I+G P+ +GTG + L
Sbjct: 342  AAFEVTVNHLLNAAIHGEVDDLDGVTENVIVGKPIKLGTGDVDL 385



 Score = 98.2 bits (243), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 71/239 (29%), Positives = 128/239 (53%), Gaps = 21/239 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T YL+ +  T+ + A  V  ++E T    LG+V   + ++
Sbjct: 99  GLPRLIELVDARKTPDTPMMTVYLEGEYATEREKAHEVVWKIEATKILALGDVSTNVADM 158

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSK 878
            V       I L+ D ++     +  D +   IE + G+    TV   + +   P++ S 
Sbjct: 159 RVQ------ISLNEDTLK--ERMITPDEVAGIIEDSLGVQ---TVQQGTEIQFGPEEPSY 207

Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVK 937
                + Q+ + L  +  KG++ I+R VI  E+++ G  ++ L  EG    DV+   GV 
Sbjct: 208 R---DLLQLVEELRDITFKGIEDISRVVIRREELDNGNEEFVLYTEGSAFGDVLEIEGVD 264

Query: 938 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEV 995
             + + NN +E+++ LGIEAAR  I+ E    +   G+  ++ RH MLVAD+MT++GE+
Sbjct: 265 ASRTTCNNIHEIHRNLGIEAAREAIIEETNNTLAEQGLDDVNVRHLMLVADMMTNRGEI 323


>gi|312136875|ref|YP_004004212.1| DNA-directed RNA polymerase, subunit a' [Methanothermus fervidus
           DSM 2088]
 gi|311224594|gb|ADP77450.1| DNA-directed RNA polymerase, subunit A' [Methanothermus fervidus
           DSM 2088]
          Length = 870

 Score =  169 bits (427), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 98/278 (35%), Positives = 152/278 (54%), Gaps = 58/278 (20%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++S+MAH  KVLP++TFR N CVC PYNADFDGDEMN+H+ QTEEA
Sbjct: 408 DGDIVLFNRQPSLHRMSMMAHEVKVLPYKTFRLNLCVCPPYNADFDGDEMNLHVLQTEEA 467

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE              AK LM  + ++++PR G  +I A  D I+G YLLT+K   F+ 
Sbjct: 468 QAE--------------AKTLMKVQEHILSPRFGGPIIGAIHDHISGAYLLTKKGTKFSE 513

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPN------ 514
            +  ++                    R+  P+   +    WTGK+IFS++L  +      
Sbjct: 514 DEVFQML------------------MRAGVPLP-KKKGRDWTGKEIFSVLLPDDLNLVYR 554

Query: 515 ----RDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGS-GGKANVF 569
               ++CP   + K K          C  D+YV++ N EL +G +D+  +G+  GK  + 
Sbjct: 555 AEICKNCP---DCKMKN---------CENDAYVLIENGELKSGVIDEKGIGAFSGK--IL 600

Query: 570 YILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
             +++++G D A   +  ++++    +M +GF+  + D
Sbjct: 601 DRIVKEYGPDKACEFLNAVTKLAIAVIMKKGFTTSLRD 638



 Score =  105 bits (261), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 72/252 (28%), Positives = 112/252 (44%), Gaps = 43/252 (17%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           IE T+   + ++  S ++I + + Y +D    PI  GL+D R+G       C TCG    
Sbjct: 11  IEFTLMSPEEIRNLSVVKIDTPDTYDEDG--YPIEGGLMDPRLGVIDPSLRCKTCGLRGG 68

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALS 202
            C GHFG I+L  PV H+G+   +  IL+S C+   C R+LL + +   +   L+     
Sbjct: 69  QCPGHFGRIELARPVIHVGFADVIHKILRSTCRK--CGRILLTKSEIEHYHDLLKQAEKK 126

Query: 203 YLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLA 262
            +    + K+I ET ++   CPHC E    +K    + I+ + YK               
Sbjct: 127 DMNIDPILKEIYETARR-EECPHCNEKQKEIKLDKPVTITEDGYK--------------- 170

Query: 263 EYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTR 322
                                  L P EV +  E IP ED  LL +N   ++P  ++LT 
Sbjct: 171 -----------------------LTPTEVRERLEKIPDEDCYLLGINPSAARPEYMVLTV 207

Query: 323 LLVPPNCIRPSV 334
           + VPP  +RPS+
Sbjct: 208 IPVPPVTMRPSI 219



 Score = 88.2 bits (217), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 37/56 (66%), Positives = 47/56 (83%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQ 666
            +GFV NS+  GL P EFFFH MGGREGLVDTA++TA++GYMQRRL+ +L+DL V+
Sbjct: 767 ARGFVYNSYRKGLDPLEFFFHAMGGREGLVDTAIRTAQSGYMQRRLINALQDLHVE 822


>gi|256811204|ref|YP_003128573.1| DNA-directed RNA polymerase subunit A' [Methanocaldococcus fervens
           AG86]
 gi|256794404|gb|ACV25073.1| DNA-directed RNA polymerase subunit A' [Methanocaldococcus fervens
           AG86]
          Length = 891

 Score =  169 bits (427), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 99/272 (36%), Positives = 152/272 (55%), Gaps = 41/272 (15%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VL+NRQPSLH++SIMAHR +VLP+RTFR N CVC PYNADFDGDEMN+H+PQ+   
Sbjct: 425 DGDIVLYNRQPSLHRMSIMAHRVRVLPYRTFRHNLCVCPPYNADFDGDEMNLHVPQS--- 481

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
                            A+ LM  + ++++PR G  +I A  DFI+G YLLT  +++F +
Sbjct: 482 -----------EEARAEAEALMLVEKHILSPRFGGPIIGAIHDFISGAYLLT--SSYFTK 528

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +     +TLI  +  I   +       W P        +++GK+IFS  L      P  
Sbjct: 529 DE-----ATLILRSGGIKDEL-------WEPDKVENGVPLYSGKKIFSKAL------PKG 570

Query: 521 ANLKTKG----RAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKAN-VFYILLRD 575
            NL+ K     +     +E C  D+YV++++ EL+ G +DK+  G G +A  + + ++++
Sbjct: 571 LNLRYKAKICRKCDECKKEECPYDAYVVIKDGELIKGVIDKN--GYGAEAGLILHTIVKE 628

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           FG +     +   ++M    +M RGF+ GI D
Sbjct: 629 FGPEAGRKFLDSATKMAIRAVMLRGFTTGIDD 660



 Score =  124 bits (311), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 78/244 (31%), Positives = 119/244 (48%), Gaps = 38/244 (15%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D ++Q S  +IV+ + Y +D    PI  GL+D R+G       C TCG  + +C GHFG+
Sbjct: 23  DYIRQMSVAKIVTPDTYDEDGY--PIDGGLMDTRLGVIDPGLVCKTCGGRIGECPGHFGH 80

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           I+L  PV HIG+ + +  IL+++C  P C RV + E K      K+         +  + 
Sbjct: 81  IELAKPVIHIGFAKTIYKILKAVC--PHCGRVAISETKRKEILEKMEKLERDGGNKWEVC 138

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           +++ +   KV++CPHCGEI                      K D   E     Y   +  
Sbjct: 139 EEVYKEASKVTICPHCGEI----------------------KYDIKFEKPTTYYR--IDG 174

Query: 271 NPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCI 330
           N E          +TL P +V ++ E IP ED  LL +N E+++P  ++LT L VPP  +
Sbjct: 175 NEE----------KTLTPSDVREILEKIPDEDCILLGLNPEVARPEWMVLTVLPVPPVTV 224

Query: 331 RPSV 334
           RPS+
Sbjct: 225 RPSI 228



 Score = 89.7 bits (221), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 37/57 (64%), Positives = 49/57 (85%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFV++S+  GL+PTEFFFH MGGREGLVD AV+TA++GYMQRRL+ +L+DL  ++D
Sbjct: 789 HGFVRSSYKKGLSPTEFFFHAMGGREGLVDQAVRTAQSGYMQRRLINALQDLKTEFD 845


>gi|408381653|ref|ZP_11179201.1| DNA-directed RNA polymerase subunit A'' [Methanobacterium formicicum
            DSM 3637]
 gi|407815584|gb|EKF86154.1| DNA-directed RNA polymerase subunit A'' [Methanobacterium formicicum
            DSM 3637]
          Length = 383

 Score =  169 bits (427), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 108/342 (31%), Positives = 175/342 (51%), Gaps = 61/342 (17%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCE-- 1149
             +  Y+R+++E   AVG +AAQS+GEPGTQMT++TFH+AG              E+ +  
Sbjct: 46   IKRAYIRSEVESGEAVGTVAAQSVGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDAR 105

Query: 1150 ----------YIEEVFVPDDSFIL--------------------------IKLDMDRIRL 1173
                      Y +E    D+ F+                           + +++D  ++
Sbjct: 106  KKISTPTMAIYFDEDHASDEEFVRTIANRIGKITLNDILKDFNVNYASMNMSIEIDEEQV 165

Query: 1174 LHLEVDIDSIRYCIERT-RGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVI 1232
                +D D +   IE+T + +  +  +      I  PK + +       +++ L     I
Sbjct: 166  KEKRLDYDEVMGKIEKTFKSVEINNNLLSFEPKITDPKHAIRELRLLADKVRDLQ----I 221

Query: 1233 KGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIE 1292
             G++ I + VI +E  E V    +  EG NL  V+   GV  V+ ++N+ +EV K LG+E
Sbjct: 222  SGIKNIGKVVIRKEGQEWV----IHTEGSNLGAVLKMDGVDRVRTTTNDIHEVEKVLGVE 277

Query: 1293 AARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASF 1352
            AAR++I+ E +  ME  G+++D RH MLVAD+MT+ G V  I RHG++  K SVL  ASF
Sbjct: 278  AARNSIIHEAQTTMEEQGLTVDVRHIMLVADMMTADGIVKSIGRHGISGEKASVLARASF 337

Query: 1353 ENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            E T  HL  A+  G+ D ++G+ E II+G P+ +GTG + ++
Sbjct: 338  EETGKHLLRASIRGEVDHLTGIIENIIIGQPIPLGTGSVGVI 379



 Score =  108 bits (269), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 71/233 (30%), Positives = 129/233 (55%), Gaps = 15/233 (6%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A + ISTP +  Y D+D  +D ++ R +  R+ + TL ++ +     F  
Sbjct: 94  GLPRLIEIVDARKKISTPTMAIYFDEDHASDEEFVRTIANRIGKITLNDILKD----FNV 149

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERT-RGISGHLTVSGHSFLILKPKDSSKSF 880
           + + + + +++D  ++    +D D +   IE+T + +  +  +      I  PK + +  
Sbjct: 150 NYASMNMSIEIDEEQVKEKRLDYDEVMGKIEKTFKSVEINNNLLSFEPKITDPKHAIREL 209

Query: 881 NSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
                +++ L     I G++ I + VI +E  E V    +  EG NL  V+   GV  V+
Sbjct: 210 RLLADKVRDLQ----ISGIKNIGKVVIRKEGQEWV----IHTEGSNLGAVLKMDGVDRVR 261

Query: 941 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
            ++N+ +EV K LG+EAAR++I+ E +  ME  G+++D RH MLVAD+MT+ G
Sbjct: 262 TTTNDIHEVEKVLGVEAARNSIIHEAQTTMEEQGLTVDVRHIMLVADMMTADG 314


>gi|397779348|ref|YP_006543821.1| DNA-directed RNA polymerase subunit A' [Methanoculleus bourgensis
           MS2]
 gi|396937850|emb|CCJ35105.1| DNA-directed RNA polymerase subunit A' [Methanoculleus bourgensis
           MS2]
          Length = 882

 Score =  169 bits (427), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 97/271 (35%), Positives = 151/271 (55%), Gaps = 37/271 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIMAHR  V+  +TFR N  VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 414 DGDIVLFNRQPSLHRMSIMAHRIVVMDGKTFRLNPAVCPPYNADFDGDEMNLHIPQTEEA 473

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A++L++ ++N+++PR G  +I    D I+G +LLT +   F +
Sbjct: 474 RAE--------------AEILVSVQANILSPRTGGPIIGGIHDHISGIFLLTHRMRHFRK 519

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              + +   L     D+  + +  S  S          ++WT KQ+FSLIL      P  
Sbjct: 520 EDVLYLTQHL-----DLDHLPEPDSVDS-------NGNLLWTNKQVFSLIL------PGE 561

Query: 521 ANLKTKGRA----YTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            N+  +  +     T   E C  D+YV + + +L+ G++DK  +G+     + + ++R +
Sbjct: 562 LNMIFRASSCQNCETCRREMCENDAYVRIIDGQLVTGTIDKKAIGA-FDGQILHRIIRQY 620

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           G   A   +  +++++   +M +GFS GI D
Sbjct: 621 GMKRAARFIDDVTKLSIRGIMLQGFSFGIDD 651



 Score =  112 bits (281), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 84/266 (31%), Positives = 131/266 (49%), Gaps = 43/266 (16%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G IE  +     +++ S  +I+  + Y  D    P P GL+D  +G       C TC Q 
Sbjct: 8   GRIEFGLFSPKEIRKMSVRKIIWADTY--DDDGFPYPQGLMDLHLGVIDPGLRCKTCDQK 65

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
            +DC GHFG+I+L  PV H+GY R +  +L+  C+  +C+R+L+  E+      K+  P 
Sbjct: 66  AADCPGHFGHIELAKPVIHVGYTRLIRKLLRVTCR--SCSRLLMTTEEV----EKIVGPE 119

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDL 260
            S L    + +K     KK  +CPHCGE          LKI+ EK    T   +  VED 
Sbjct: 120 ESDLTVDVVSEK---DVKKERICPHCGEQQ--------LKINFEKP---TTFSEVFVED- 164

Query: 261 LAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
                       ++E HK       L P ++    E IP +D+ L+ +N ++++P   IL
Sbjct: 165 ----------GRKVE-HK-------LTPADIRARLEKIPDDDLRLMGVNPDVARPEWTIL 206

Query: 321 TRLLVPPNCIRPSVI--SDLKSDNDV 344
           T L VPP  +RPS+I  +  +S++D+
Sbjct: 207 TVLPVPPVTMRPSIILENGQRSEDDL 232



 Score = 91.3 bits (225), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 37/57 (64%), Positives = 50/57 (87%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GF+ NS+ SGL+PTEFFFH +GGREGLVDTAV+T+++GY+QRR++ +L+DL V YD
Sbjct: 780 HGFIANSYKSGLSPTEFFFHAIGGREGLVDTAVRTSQSGYLQRRMINALQDLKVAYD 836


>gi|374633177|ref|ZP_09705544.1| DNA-directed RNA polymerase subunit A'' [Metallosphaera
           yellowstonensis MK1]
 gi|373524661|gb|EHP69538.1| DNA-directed RNA polymerase subunit A'' [Metallosphaera
           yellowstonensis MK1]
          Length = 886

 Score =  169 bits (427), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 100/269 (37%), Positives = 149/269 (55%), Gaps = 29/269 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + DVV+FNRQPSLH++S+M HR +VLP RTFR N  VC PYNADFDGDEMN+H+PQ+EEA
Sbjct: 419 NGDVVIFNRQPSLHRISMMGHRVRVLPGRTFRLNLLVCPPYNADFDGDEMNLHVPQSEEA 478

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
            AE               + LM    N++TPR G  +I + QD+I+G YLLT K      
Sbjct: 479 IAE--------------TRELMTVHRNILTPRYGGPIIGSAQDYISGAYLLTVKTTLLTE 524

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           ++   I    +AD S   G           P +      ++TGKQI S  L  + +    
Sbjct: 525 SEVQTILG--VADISKALG----------EPAILA-PKRLYTGKQILSYFLPEDFNFHGP 571

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           AN+ +  R  +  +E C  DS+++++  +LL G +DK  LG+    +V + L+R++ ED 
Sbjct: 572 ANISSGVR--SCKDEDCAHDSFLVIKQGKLLMGVLDKKALGNQQPESVLHWLVREYSEDY 629

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVT 609
            +  M  L ++   ++   G ++ + DVT
Sbjct: 630 VLWLMDNLFKVFLRFVELHGLTMTLSDVT 658



 Score =  117 bits (292), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 80/261 (30%), Positives = 132/261 (50%), Gaps = 49/261 (18%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D +++ S   I++  +Y +D   TPI   ++D R+G  +    C  CG  + +C GHFG+
Sbjct: 23  DEIRKMSVTAIITAEVYDED--GTPIEGSVMDPRLGVIEPGQKCPVCGNVIGNCPGHFGH 80

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-----KLRNPALSYLV 205
           I+L  PV H+G+ + V ++L+S C+   C RV L E++   ++      K R P+ +   
Sbjct: 81  IELIRPVIHVGFVKHVYDLLRSTCRR--CGRVKLHEDEIQKYKKIHEAIKRRWPSAA--- 135

Query: 206 RKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYN 265
            K L   + +++ K   CPHCGE          LKI  EK  N               Y 
Sbjct: 136 -KRLIDYVKKSSMKAPTCPHCGEKQ--------LKIKLEKPYNF--------------YE 172

Query: 266 EAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLV 325
           E           +K G+++ L PL++ +  E IP  D+ LL  + + S+P  +ILT L V
Sbjct: 173 E-----------RKEGMVR-LTPLDIRERLEKIPDSDVELLGYDPKSSRPEWIILTVLPV 220

Query: 326 PPNCIRPSVI--SDLKSDNDV 344
           PP  IRPS++  S +++++D+
Sbjct: 221 PPITIRPSIMIESGIRAEDDL 241



 Score = 91.3 bits (225), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 41/75 (54%), Positives = 56/75 (74%), Gaps = 2/75 (2%)

Query: 606 GDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           GD++P  +GF+ +SF SGL P E FFH  GGREGLVDTAV+T+++GYMQRRL+ +L DL 
Sbjct: 778 GDISPEARGFIYSSFRSGLNPVEMFFHAAGGREGLVDTAVRTSQSGYMQRRLINALSDLR 837

Query: 665 VQYDMSFDAAFYGQT 679
           ++YD +     YG+ 
Sbjct: 838 MEYDGTV-RTLYGEV 851


>gi|327242139|gb|AEA40848.1| RNA polymerase II largest subunit [Trichomonas gallinae]
          Length = 1019

 Score =  169 bits (427), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 106/317 (33%), Positives = 167/317 (52%), Gaps = 45/317 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND+V+FNRQPSLHK+S+M HRA ++P RTFR N C  TPYNADFDGDEMN+H+PQ++ A
Sbjct: 371 DNDIVIFNRQPSLHKMSMMGHRALLMPARTFRLNLCDTTPYNADFDGDEMNLHVPQSQAA 430

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE               + +MA    +++P+    +I   QD + G  LL++++ F  R
Sbjct: 431 RAE--------------VRHIMAVPKQIISPQANRPVIGLVQDALLGCRLLSKRDTFLTR 476

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLIL-KPNRDCPV 519
            Q M +   L  +   I             P   ++   +W+GKQ+FSL L K N D   
Sbjct: 477 NQVMNLMMWLPTNKDTILP-----------PPCILKPVQLWSGKQVFSLFLPKINYDHFS 525

Query: 520 NANLKTKGRAYT-ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
           N       +++  AN      D+ VI+R+  LLAG +DK++     + ++ ++++  +  
Sbjct: 526 NGARDDDKKSWMPAN------DTRVIIRDGHLLAGLLDKTSCAR-SEGSLTHVVINSYNT 578

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSFFSGLTPTEFFFHTMGGREG 638
           D+A   + +   + + +L +RGFSIG+ D    Q        S L   E     +   E 
Sbjct: 579 DIAKDFLNQTQLIVNNWLEHRGFSIGLIDCVVPQ--------SVLDQVE---EKINEVED 627

Query: 639 LVDTAVKTAETGYMQRR 655
            V   ++TA++G ++RR
Sbjct: 628 NVKGVIRTAQSGKLERR 644



 Score = 82.8 bits (203), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 35/57 (61%), Positives = 45/57 (78%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GF ++S+  GLTP EF FH MGGR G++DTA KT++TGY+QRRLVKS+E   V YD
Sbjct: 736 RGFCRHSYIEGLTPPEFLFHAMGGRTGIIDTACKTSDTGYIQRRLVKSMESHHVAYD 792



 Score = 55.1 bits (131), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 55/207 (26%), Positives = 82/207 (39%), Gaps = 43/207 (20%)

Query: 150 YIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSL 209
           YI L  P FH+G+ + V  ILQ +C    C R+               +P + Y+     
Sbjct: 1   YIKLAEPFFHVGFLKHVYKILQMVCHK--CGRL----------NCSYGDPEIQYIATHYK 48

Query: 210 KKK--------ILETTKKVSVCPHCG--EINGVVKKCGLLKI-------SHEKYKNRTKK 252
            K+        I  +T+  S  P     E   VV      +I        H + K   K 
Sbjct: 49  GKQRFDAIFNYIASSTRDCSDSPAAKDKESPDVVADERFWEIVNGDAISEHRRMKVPCKS 108

Query: 253 KDAIVE---DLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMN 309
           K   +E   D L +Y +  K   +            L+   VL++FE I  +D+ L+  N
Sbjct: 109 KPVAIEQGQDFLIKYKDTSKTEEDY-----------LSAEYVLRIFENISDQDVRLMGFN 157

Query: 310 AELSKPSDLILTRLLVPPNCIRPSVIS 336
            + S P  +IL  L VPP  +RP V+S
Sbjct: 158 VKRSHPKWMILKVLPVPPLAVRPQVVS 184


>gi|323462790|pdb|2Y0S|C Chain C, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
            P21 Space Group
 gi|323462812|pdb|2Y0S|Y Chain Y, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
            P21 Space Group
 gi|400260744|pdb|4AYB|C Chain C, Rnap At 3.2ang
 gi|400260761|pdb|4B1O|C Chain C, Archaeal Rnap-Dna Binary Complex At 4.32ang
 gi|400260787|pdb|4B1P|Y Chain Y, Archaeal Rnap-Dna Binary Complex At 4.32ang
 gi|219814431|gb|ACL36489.1| RNA polymerase subunit 1C [Sulfolobus shibatae B12]
          Length = 395

 Score =  169 bits (427), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 123/392 (31%), Positives = 187/392 (47%), Gaps = 65/392 (16%)

Query: 1054 KKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRA 1113
            K +LEE  K+ S    Q K+ + L+  I + +  +        F  A K      +Y   
Sbjct: 10   KSYLEEKVKQASNILPQ-KIVEDLKNLISNKEVLVTRDEIDKIFDLAIK------EYSEG 62

Query: 1114 QIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFVPDDSFI 1162
             I P  A+G +AAQS+GEPGTQMTL+TFHFAG            + E ++   VP    +
Sbjct: 63   LIAPGEAIGIVAAQSVGEPGTQMTLRTFHFAGIRELNVTLGLPRLIEIVDAKKVPSTPMM 122

Query: 1163 LI------------------KLDMDRIR---------------LLHLE--------VDID 1181
             I                  KL+  +I                +L L+        V +D
Sbjct: 123  TIYLTDEYKHDKEKALEVARKLEYTKIENVVSSTSIDIASMSIILQLDNEMLKDKGVTVD 182

Query: 1182 SIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRA 1241
             ++  I R +   G   +       L    ++    + +++++  + +  IKG++GI RA
Sbjct: 183  DVKKAINRLK--LGEFVIDESEGNTLNISFANIDSIAALFKLRDKILNTKIKGIKGIKRA 240

Query: 1242 VIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTE 1301
            ++ ++  E    Y +L +G NL  V++  GV   K  +NN  E+ +  GIEAAR  I+ E
Sbjct: 241  IVQKKGDE----YIILTDGSNLSGVLSVKGVDIAKVETNNIREIEEVFGIEAAREIIIRE 296

Query: 1302 IKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFD 1361
            I  V+   G+ +D RH +LVAD+MT  G V  I RHG+   K SVL  A+FE T  HL D
Sbjct: 297  ISKVLAEQGLDVDMRHILLVADVMTRTGVVRQIGRHGVTGEKNSVLARAAFEVTVKHLLD 356

Query: 1362 AAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            AA  G  +   GV E II+G P+ +GTG+++L
Sbjct: 357  AAARGDVEEFKGVVENIIIGHPIKLGTGMVEL 388



 Score =  102 bits (254), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 74/238 (31%), Positives = 122/238 (51%), Gaps = 20/238 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYL------DKDTDLDYARIVKGRLERTTLGEVCEYIEE 817
           G+PR+ EI++A +  STP++T YL      DK+  L+ AR    +LE T +  V      
Sbjct: 103 GLPRLIEIVDAKKVPSTPMMTIYLTDEYKHDKEKALEVAR----KLEYTKIENVVSSTS- 157

Query: 818 VFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSS 877
               D + + I L +D   L    V +D ++  I R +   G   +       L    ++
Sbjct: 158 ---IDIASMSIILQLDNEMLKDKGVTVDDVKKAINRLK--LGEFVIDESEGNTLNISFAN 212

Query: 878 KSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVK 937
               + +++++  + +  IKG++GI RA++ ++  E    Y +L +G NL  V++  GV 
Sbjct: 213 IDSIAALFKLRDKILNTKIKGIKGIKRAIVQKKGDE----YIILTDGSNLSGVLSVKGVD 268

Query: 938 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
             K  +NN  E+ +  GIEAAR  I+ EI  V+   G+ +D RH +LVAD+MT  G V
Sbjct: 269 IAKVETNNIREIEEVFGIEAAREIIIREISKVLAEQGLDVDMRHILLVADVMTRTGVV 326


>gi|448307076|ref|ZP_21496977.1| DNA-directed RNA polymerase subunit A'' [Natronorubrum bangense JCM
            10635]
 gi|445596623|gb|ELY50708.1| DNA-directed RNA polymerase subunit A'' [Natronorubrum bangense JCM
            10635]
          Length = 398

 Score =  169 bits (427), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 106/343 (30%), Positives = 176/343 (51%), Gaps = 58/343 (16%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A A   +Y+  +++P   VG ++AQSIGEPGTQ+T+ TFH+AG            + E +
Sbjct: 48   ARAVEARYLDTRVDPLDPVGTVSAQSIGEPGTQLTMNTFHYAGVAEIDVTQGLPRLIELV 107

Query: 1152 EEVFVPDDSFILIKLD----------------MDRIRLLHL----------EVDI----- 1180
            +    PD   + + L+                ++  ++L L           V I     
Sbjct: 108  DARKTPDTPMMTVYLEDEYATEREKAHEVVWNIEATKILALGDVSTNVADMRVQISLNED 167

Query: 1181 ---------DSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVV 1231
                     + +   IE   G+S   T+   + +   P++ S      + Q+ + L  + 
Sbjct: 168  TLKERMITPEEVASIIEDNLGVS---TIQQGTQIQFGPEEPSYR---DLLQLVEELREIT 221

Query: 1232 IKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGI 1291
             KG++ I+R VI  E++E   ++ L  EG    D +   GV   + + NN +E+++ LGI
Sbjct: 222  FKGIEEISRVVIRREELEDGEEFVLYTEGSAFGDALEIEGVDASRTTCNNIHEIHRNLGI 281

Query: 1292 EAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLA 1350
            EAAR TI+ E    +   G+  ++ RH MLVAD+MT++GE+  I RHG++  K+SVL  A
Sbjct: 282  EAARETIIEETNNTLAEQGLDDVNVRHLMLVADMMTNRGEIESIGRHGISGSKDSVLARA 341

Query: 1351 SFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            +FE T +HL +AA +G+ D + GV+E +I+G P+ +GTG + L
Sbjct: 342  AFEVTVNHLLNAAIHGEVDELDGVTENVIVGKPIKLGTGDVDL 384



 Score = 99.8 bits (247), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 71/238 (29%), Positives = 126/238 (52%), Gaps = 20/238 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T YL+ +  T+ + A  V   +E T    LG+V   + ++
Sbjct: 99  GLPRLIELVDARKTPDTPMMTVYLEDEYATEREKAHEVVWNIEATKILALGDVSTNVADM 158

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSK 878
            V     I +  D  + R++  E     +   IE   G+S   T+   + +   P++ S 
Sbjct: 159 RVQ----ISLNEDTLKERMITPE----EVASIIEDNLGVS---TIQQGTQIQFGPEEPSY 207

Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 938
                + Q+ + L  +  KG++ I+R VI  E++E   ++ L  EG    D +   GV  
Sbjct: 208 R---DLLQLVEELREITFKGIEEISRVVIRREELEDGEEFVLYTEGSAFGDALEIEGVDA 264

Query: 939 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEV 995
            + + NN +E+++ LGIEAAR TI+ E    +   G+  ++ RH MLVAD+MT++GE+
Sbjct: 265 SRTTCNNIHEIHRNLGIEAARETIIEETNNTLAEQGLDDVNVRHLMLVADMMTNRGEI 322


>gi|327242119|gb|AEA40838.1| RNA polymerase II largest subunit [Trichomonas gallinae]
          Length = 1019

 Score =  169 bits (427), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 106/317 (33%), Positives = 167/317 (52%), Gaps = 45/317 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND+V+FNRQPSLHK+S+M HRA ++P RTFR N C  TPYNADFDGDEMN+H+PQ++ A
Sbjct: 371 DNDIVIFNRQPSLHKMSMMGHRALLMPARTFRLNLCDTTPYNADFDGDEMNLHVPQSQAA 430

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE               + +MA    +++P+    +I   QD + G  LL++++ F  R
Sbjct: 431 RAE--------------VRHIMAVPKQIISPQANRPVIGLVQDALLGCRLLSKRDTFLTR 476

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLIL-KPNRDCPV 519
            Q M +   L  +   I             P   ++   +W+GKQ+FSL L K N D   
Sbjct: 477 NQVMNLMMWLPTNKDTILP-----------PPCILKPVQLWSGKQVFSLFLPKINYDHFS 525

Query: 520 NANLKTKGRAYT-ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
           N       +++  AN      D+ VI+R+  LLAG +DK++     + ++ ++++  +  
Sbjct: 526 NGASDDDKKSWMPAN------DTRVIIRDGHLLAGLLDKTSCAR-SEGSLTHVVINSYNT 578

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSFFSGLTPTEFFFHTMGGREG 638
           D+A   + +   + + +L +RGFSIG+ D    Q        S L   E     +   E 
Sbjct: 579 DIAKDFLNQTQLIVNNWLEHRGFSIGLIDCVVPQ--------SVLDQVE---EKINEVED 627

Query: 639 LVDTAVKTAETGYMQRR 655
            V   ++TA++G ++RR
Sbjct: 628 NVKGVIRTAQSGKLERR 644



 Score = 82.8 bits (203), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 35/57 (61%), Positives = 45/57 (78%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GF ++S+  GLTP EF FH MGGR G++DTA KT++TGY+QRRLVKS+E   V YD
Sbjct: 736 RGFCRHSYIEGLTPPEFLFHAMGGRTGIIDTACKTSDTGYIQRRLVKSMESHHVAYD 792



 Score = 55.8 bits (133), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 55/197 (27%), Positives = 82/197 (41%), Gaps = 23/197 (11%)

Query: 150 YIDLPLPVFHIGYFRCVINILQSICKNPTCARV--LLGEEK----AAGFRAKLRNPALSY 203
           YI L  P FH+G+ + V  ILQ +C    C R+    G+ +    A  F+ K R  A+  
Sbjct: 1   YIKLAEPFFHVGFLKHVYKILQMVCHK--CGRLNCSYGDPEIQYIATHFKGKQRFDAIFN 58

Query: 204 LVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKIS-HEKYKNRTKKKDAIVE---D 259
            +  S +        K    P         +      IS H + K   K K   +E   D
Sbjct: 59  YIASSTRDCSDSPAAKDKESPDVVADERFWEIVNGDAISEHRRMKVPCKSKPVAIEQGQD 118

Query: 260 LLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLI 319
            L +Y +  K   +            L+   VL++FE I  +D+ L+  N + S P  +I
Sbjct: 119 FLIKYKDTSKTEEDY-----------LSAEYVLRIFENISDQDVRLMGFNVKRSHPKWMI 167

Query: 320 LTRLLVPPNCIRPSVIS 336
           L  L VPP  +RP V+S
Sbjct: 168 LKVLPVPPLAVRPQVVS 184


>gi|333986473|ref|YP_004519080.1| DNA-directed RNA polymerase subunit A'' [Methanobacterium sp. SWAN-1]
 gi|333824617|gb|AEG17279.1| DNA-directed RNA polymerase subunit A'' [Methanobacterium sp. SWAN-1]
          Length = 390

 Score =  169 bits (427), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 113/346 (32%), Positives = 172/346 (49%), Gaps = 69/346 (19%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCE-- 1149
             ++ Y RA++E   AVG +AAQS+GEPGTQMT++TFH+AG              E+ +  
Sbjct: 52   IKKAYQRAKVENGEAVGTVAAQSVGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDAR 111

Query: 1150 ----------YIEEVFVPDDSFI----------------------------LIKLDMDRI 1171
                      Y EE +  D+ F+                             I++D D++
Sbjct: 112  KKISTPTMAIYFEEEYGADEEFVRKIANRIGKIILNDVLEDFNVNYANMSLTIEIDEDKV 171

Query: 1172 RLLHLEVD--IDSIRYCIERTRGISGHLTVSGHSFLILKPKDS-SKSFNSKMYQMKQLLP 1228
                LE D  I  I    ++             + L  +P  S SK    ++  +   + 
Sbjct: 172  NEKRLEYDEIIAKIEKAFKKVE--------IDKNVLSFEPTISESKHAIRELRLLADKVR 223

Query: 1229 SVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKT 1288
             + I GV+ I + VI +E     T++ +  EG NL  V+   GV   + ++N+ +EV K 
Sbjct: 224  DLQISGVKNIGKVVIRKEG----TEWAIHTEGSNLGAVLKMEGVDKTRTTTNDIHEVEKV 279

Query: 1289 LGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLN 1348
            LGIEA R+ I+ E +  ME  G+++D RH MLVAD+MTS G V  I RHG++  K SVL 
Sbjct: 280  LGIEAGRNAIIHEAQSTMEEQGLTVDVRHIMLVADMMTSDGIVKSIGRHGISGEKASVLA 339

Query: 1349 LASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
             ASFE T  HL  A+  G+ D ++G+ E II+G P+ +GTG + ++
Sbjct: 340  RASFEETGKHLLRASIRGEVDHLTGIIENIIIGQPIPLGTGSVGVV 385



 Score =  102 bits (254), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 122/235 (51%), Gaps = 19/235 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A + ISTP +  Y +++   D ++ R +  R+ +  L +V E     +  
Sbjct: 100 GLPRLIEIVDARKKISTPTMAIYFEEEYGADEEFVRKIANRIGKIILNDVLEDFNVNYA- 158

Query: 822 DDSFILIKLDMDRIRLLHLEVD--IDSIRYCIERTRGISGHLTVSGHSFLILKPKDS-SK 878
            +  + I++D D++    LE D  I  I    ++             + L  +P  S SK
Sbjct: 159 -NMSLTIEIDEDKVNEKRLEYDEIIAKIEKAFKKVE--------IDKNVLSFEPTISESK 209

Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 938
               ++  +   +  + I GV+ I + VI +E     T++ +  EG NL  V+   GV  
Sbjct: 210 HAIRELRLLADKVRDLQISGVKNIGKVVIRKEG----TEWAIHTEGSNLGAVLKMEGVDK 265

Query: 939 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
            + ++N+ +EV K LGIEA R+ I+ E +  ME  G+++D RH MLVAD+MTS G
Sbjct: 266 TRTTTNDIHEVEKVLGIEAGRNAIIHEAQSTMEEQGLTVDVRHIMLVADMMTSDG 320


>gi|227828175|ref|YP_002829955.1| DNA-directed RNA polymerase subunit A'' [Sulfolobus islandicus
            M.14.25]
 gi|227830882|ref|YP_002832662.1| DNA-directed RNA polymerase subunit A'' [Sulfolobus islandicus
            L.S.2.15]
 gi|229579768|ref|YP_002838167.1| DNA-directed RNA polymerase subunit A'' [Sulfolobus islandicus
            Y.G.57.14]
 gi|229581563|ref|YP_002839962.1| DNA-directed RNA polymerase subunit A'' [Sulfolobus islandicus
            Y.N.15.51]
 gi|229585404|ref|YP_002843906.1| DNA-directed RNA polymerase subunit A'' [Sulfolobus islandicus
            M.16.27]
 gi|238620365|ref|YP_002915191.1| DNA-directed RNA polymerase subunit A'' [Sulfolobus islandicus
            M.16.4]
 gi|284998389|ref|YP_003420157.1| DNA-directed RNA polymerase subunit A'' [Sulfolobus islandicus
            L.D.8.5]
 gi|259494157|sp|C3MZM9.1|RPOA2_SULIA RecName: Full=DNA-directed RNA polymerase subunit A''
 gi|259494158|sp|C4KIV9.1|RPOA2_SULIK RecName: Full=DNA-directed RNA polymerase subunit A''
 gi|259494159|sp|C3MRK4.1|RPOA2_SULIL RecName: Full=DNA-directed RNA polymerase subunit A''
 gi|259494160|sp|C3MYA0.1|RPOA2_SULIM RecName: Full=DNA-directed RNA polymerase subunit A''
 gi|259494161|sp|C3NFS2.1|RPOA2_SULIN RecName: Full=DNA-directed RNA polymerase subunit A''
 gi|259494162|sp|C3N7Q1.1|RPOA2_SULIY RecName: Full=DNA-directed RNA polymerase subunit A''
 gi|227457330|gb|ACP36017.1| DNA-directed RNA polymerase, subunit A'' [Sulfolobus islandicus
            L.S.2.15]
 gi|227459971|gb|ACP38657.1| DNA-directed RNA polymerase, subunit A'' [Sulfolobus islandicus
            M.14.25]
 gi|228010483|gb|ACP46245.1| DNA-directed RNA polymerase, subunit A'' [Sulfolobus islandicus
            Y.G.57.14]
 gi|228012279|gb|ACP48040.1| DNA-directed RNA polymerase, subunit A'' [Sulfolobus islandicus
            Y.N.15.51]
 gi|228020454|gb|ACP55861.1| DNA-directed RNA polymerase, subunit A'' [Sulfolobus islandicus
            M.16.27]
 gi|238381435|gb|ACR42523.1| DNA-directed RNA polymerase, subunit A'' [Sulfolobus islandicus
            M.16.4]
 gi|284446285|gb|ADB87787.1| DNA-directed RNA polymerase, subunit A'' [Sulfolobus islandicus
            L.D.8.5]
          Length = 392

 Score =  169 bits (427), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 123/392 (31%), Positives = 187/392 (47%), Gaps = 65/392 (16%)

Query: 1054 KKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRA 1113
            K +LEE  K+ S    Q K+ + L+  I + +  +        F  A K      +Y   
Sbjct: 7    KSYLEEKVKQASNILPQ-KIVEDLKNLISNKEVLVTRDEIDKIFDLAIK------EYSEG 59

Query: 1114 QIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFVPDDSFI 1162
             I P  A+G +AAQS+GEPGTQMTL+TFHFAG            + E ++   VP    +
Sbjct: 60   LIAPGEAIGIVAAQSVGEPGTQMTLRTFHFAGIRELNVTLGLPRLIEIVDAKKVPSTPMM 119

Query: 1163 LI------------------KLDMDRIR---------------LLHLE--------VDID 1181
             I                  KL+  +I                +L L+        V +D
Sbjct: 120  TIYLTDEYKHDKEKALEVARKLEYTKIENVVSSTSIDIASMSIILQLDNEMLKDKGVTVD 179

Query: 1182 SIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRA 1241
             ++  I R +   G   +       L    ++    + +++++  + +  IKG++GI RA
Sbjct: 180  DVKKAINRLK--LGEFVIDESEGNTLNISFANIDSIAALFKLRDKILNTKIKGIKGIKRA 237

Query: 1242 VIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTE 1301
            ++ ++  E    Y +L +G NL  V++  GV   K  +NN  E+ +  GIEAAR  I+ E
Sbjct: 238  IVQKKGDE----YIILTDGSNLSGVLSVKGVDIAKVETNNIREIEEVFGIEAAREIIIRE 293

Query: 1302 IKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFD 1361
            I  V+   G+ +D RH +LVAD+MT  G V  I RHG+   K SVL  A+FE T  HL D
Sbjct: 294  ISKVLAEQGLDVDMRHILLVADVMTRTGVVRQIGRHGVTGEKNSVLARAAFEVTVKHLLD 353

Query: 1362 AAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            AA  G  +   GV E II+G P+ +GTG+++L
Sbjct: 354  AAARGDVEEFKGVVENIIIGHPIKLGTGMVEL 385



 Score =  102 bits (254), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 74/238 (31%), Positives = 122/238 (51%), Gaps = 20/238 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYL------DKDTDLDYARIVKGRLERTTLGEVCEYIEE 817
           G+PR+ EI++A +  STP++T YL      DK+  L+ AR    +LE T +  V      
Sbjct: 100 GLPRLIEIVDAKKVPSTPMMTIYLTDEYKHDKEKALEVAR----KLEYTKIENVVSSTS- 154

Query: 818 VFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSS 877
               D + + I L +D   L    V +D ++  I R +   G   +       L    ++
Sbjct: 155 ---IDIASMSIILQLDNEMLKDKGVTVDDVKKAINRLK--LGEFVIDESEGNTLNISFAN 209

Query: 878 KSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVK 937
               + +++++  + +  IKG++GI RA++ ++  E    Y +L +G NL  V++  GV 
Sbjct: 210 IDSIAALFKLRDKILNTKIKGIKGIKRAIVQKKGDE----YIILTDGSNLSGVLSVKGVD 265

Query: 938 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
             K  +NN  E+ +  GIEAAR  I+ EI  V+   G+ +D RH +LVAD+MT  G V
Sbjct: 266 IAKVETNNIREIEEVFGIEAAREIIIREISKVLAEQGLDVDMRHILLVADVMTRTGVV 323


>gi|418204404|gb|AFX61756.1| RNA polymerase I largest subunit, partial [Ascosphaera variegata]
          Length = 1683

 Score =  168 bits (426), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 101/272 (37%), Positives = 148/272 (54%), Gaps = 35/272 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DV+LFNRQPSLHK S+MAHR +V+P+ TFR N  V TPYNADFDGDEMN+H+PQ+EE+
Sbjct: 433 DGDVILFNRQPSLHKESMMAHRVRVMPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSEES 492

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L +L+++            N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 493 RAE----LKELALVPL----------NIVSPQRNGPLMGIVQDTLCGIYKICRRDTFLTK 538

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              M I   +     D  G+I +       P + ++    WTGKQI S++L      P  
Sbjct: 539 EHVMNIMMWV----PDWDGVIPQ-------PAI-IKPRPRWTGKQIISMVL------PSG 580

Query: 521 ANL--KTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            NL    K  A  A       DS   +   EL+ G   K T+G+ G   V + +  ++G 
Sbjct: 581 LNLLRLDKDGAPLAERFSPINDSGCFIHGGELMFGQFSKKTVGATG-GGVIHTIFNEYGP 639

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           DV ++      R+ +++L++ GFSIGIGD  P
Sbjct: 640 DVCMSFFNGTQRVVNYWLLHNGFSIGIGDTIP 671



 Score = 99.8 bits (247), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 59/186 (31%), Positives = 96/186 (51%), Gaps = 16/186 (8%)

Query: 1219 KMYQMKQLLPSVVIKGVQGINRAVIHEE---------------DVEGVTKYKLLVEGDNL 1263
            K++Q   +L    ++GV G+ RA I+E+               + +   ++ L   G  L
Sbjct: 1262 KIFQ-AHMLDHCTLRGVSGVERAFINEKTHARIMPDGSLSKSAEDDNCKEWILETSGSAL 1320

Query: 1264 RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 1323
             DV+A  GV   +  SN   E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D
Sbjct: 1321 ADVLAIDGVDATRTYSNQFIEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLVD 1380

Query: 1324 LMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLP 1383
            +MTS+G ++ +TRHG+ +     L   SFE T + L +AA + + D   GVSE +I+G  
Sbjct: 1381 IMTSRGFLMAVTRHGINRSDTGALMRCSFEETVEILLEAAAFAELDDCRGVSENLILGQM 1440

Query: 1384 MNVGTG 1389
               GTG
Sbjct: 1441 APAGTG 1446



 Score = 99.0 bits (245), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QR+LVK+LE++ V
Sbjct: 791 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMV 850

Query: 666 QYD 668
           +YD
Sbjct: 851 KYD 853



 Score = 89.7 bits (221), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 75/290 (25%), Positives = 127/290 (43%), Gaps = 60/290 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N ++NI TP +T Y   +   + D  ++++ ++E TTL  V E IE  + P
Sbjct: 1097 GVPRLKEILNVAKNIKTPSMTVYQVPELAGNQDAVKVLRSKVEHTTLRSVAEMIEIYYDP 1156

Query: 822  DDSFILIKLDMD------------------------RIRLLHLEV--------DI-DSIR 848
            D    +I+ D D                        R+ L H+++        D+ D I+
Sbjct: 1157 DIRNTVIEADKDMVETYFIIPEDVQEKPEEQSQWLVRLVLSHIKLIDKGLTVQDVADRIK 1216

Query: 849  YCIERTRGISGHLTVSGHSFLILKP------KDSSKSFNSKMYQMK----QLLPSVVIKG 898
               E    +      S    + ++P       D     N   + +K     +L    ++G
Sbjct: 1217 ALFENDVNVMFSDDNSDQPVIRIRPLKGALDDDEEGDGNEMDHTLKIFQAHMLDHCTLRG 1276

Query: 899  VQGINRAVIHEE---------------DVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSS 943
            V G+ RA I+E+               + +   ++ L   G  L DV+A  GV   +  S
Sbjct: 1277 VSGVERAFINEKTHARIMPDGSLSKSAEDDNCKEWILETSGSALADVLAIDGVDATRTYS 1336

Query: 944  NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
            N   E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1337 NQFIEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLVDIMTSRG 1386



 Score = 77.0 bits (188), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 61/247 (24%), Positives = 107/247 (43%), Gaps = 42/247 (17%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D +++ S ++IV         QR P   GL D ++GT  +   C TC Q + DC GHFG+
Sbjct: 9   DEIKKMSVVKIVYPETMDDQRQR-PREEGLNDPKLGTIDRAFKCATCEQGIMDCPGHFGH 67

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARV---LLGEEKAAGFRAKLRNPALSYLVRK 207
           I+L  PVFHIG+   +  +L+++C N  C ++   +   + A   R +        + R 
Sbjct: 68  IELASPVFHIGFLTKIKKLLETVCIN--CGKIKADMTDPKYAEALRYRDPKRRFDAIWRL 125

Query: 208 SLKKKILETTKKVS-----------VCPH--CGEINGVVKKCGLLKISHEKYKNRTKKKD 254
              K + ETT  +            V  H  CG     +++ GL  +   K +    + D
Sbjct: 126 CKDKLLCETTPIIQEDAFGNAPPQIVYGHGGCGNPQPQIRREGLTLVGTWKPEKSVDQSD 185

Query: 255 AIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSK 314
           +                P ++        + + P E  ++F+ I   D+ LL ++ E ++
Sbjct: 186 SA---------------PPVK--------RVITPKEAREVFKNISSGDVRLLGLSNEYAR 222

Query: 315 PSDLILT 321
           P  +I+T
Sbjct: 223 PEWMIIT 229



 Score = 57.4 bits (137), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 26/41 (63%), Positives = 28/41 (68%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            A   ++ RA   P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1048 AIENRFARAIASPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1088


>gi|84490160|ref|YP_448392.1| DNA-directed RNA polymerase subunit A' [Methanosphaera stadtmanae
           DSM 3091]
 gi|84373479|gb|ABC57749.1| RpoA1 [Methanosphaera stadtmanae DSM 3091]
          Length = 873

 Score =  168 bits (426), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 103/272 (37%), Positives = 141/272 (51%), Gaps = 45/272 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++S+MAH  +VLP++TFR N CVC PYNADFDGDEMN+H+ QT EA
Sbjct: 408 DGDIVLFNRQPSLHRMSMMAHEVRVLPYKTFRLNLCVCPPYNADFDGDEMNMHVFQTPEA 467

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A  +M  + ++++PR G  +I A  D ITG YLLT  +  +  
Sbjct: 468 RAE--------------ANDIMKVQEHILSPRYGGPIIGAIHDHITGAYLLTHASTVYPE 513

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +  +              IIKR       P    R    WTGK+IFSL+L      P  
Sbjct: 514 DKAFQ--------------IIKRSKMEL--PESKGRD---WTGKEIFSLLL------PDK 548

Query: 521 ANLKTKG----RAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            NL  K     +      E C  D+YV++ N +LL G +D    GS G   +   +++ F
Sbjct: 549 LNLIYKAEICRKCEECKHENCEHDAYVVISNGQLLQGVVDDKGYGS-GSGKILDSIVKQF 607

Query: 577 GEDVAVTAMWRLSRMTSF-YLMNRGFSIGIGD 607
           G   A   +   +++  F  +M RGF+ G  D
Sbjct: 608 GPSEARYFLDHATKLAVFGGVMQRGFTTGTAD 639



 Score = 98.6 bits (244), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 70/242 (28%), Positives = 109/242 (45%), Gaps = 43/242 (17%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           +++ S  +IV+ + Y +D    PI  GL+D R+G       C TCG    DC GHFG+I+
Sbjct: 21  IRKMSVTKIVTPDTYDEDGY--PIESGLMDPRLGVIDPGLKCRTCGSKGGDCQGHFGHIN 78

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKK 212
              PV H+G+   +  IL+S C+   C RVLL + +   ++ KL     +      + K+
Sbjct: 79  FARPVIHVGFADTIHKILRSTCRK--CGRVLLTDTEKLEYKDKLEERIENGEDISKILKQ 136

Query: 213 ILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNP 272
           I    KK   CPHC E               E+ + +  K  ++VE              
Sbjct: 137 IHLAAKK-EKCPHCEE---------------EQIEIKIDKPISLVEGTY----------- 169

Query: 273 EIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRP 332
                        L   EV +  E IP ED   + +N ++++P  ++LT L VPP  +RP
Sbjct: 170 ------------KLTASEVRERLEMIPEEDYIFIGINPKVARPEWMVLTVLPVPPVTVRP 217

Query: 333 SV 334
           S+
Sbjct: 218 SI 219



 Score = 89.4 bits (220), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 41/64 (64%), Positives = 49/64 (76%), Gaps = 1/64 (1%)

Query: 606 GDV-TPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           GDV +   GFV +S+  GL P EFFFH MGGREGLVDTA++TA++GYMQRRLV +L DL 
Sbjct: 761 GDVGSKASGFVHSSYKKGLDPLEFFFHAMGGREGLVDTAIRTAQSGYMQRRLVNALHDLS 820

Query: 665 VQYD 668
           V  D
Sbjct: 821 VHED 824


>gi|433592801|ref|YP_007282297.1| DNA-directed RNA polymerase, subunit A'' [Natrinema pellirubrum DSM
            15624]
 gi|448335246|ref|ZP_21524396.1| DNA-directed RNA polymerase subunit A'' [Natrinema pellirubrum DSM
            15624]
 gi|433307581|gb|AGB33393.1| DNA-directed RNA polymerase, subunit A'' [Natrinema pellirubrum DSM
            15624]
 gi|445617627|gb|ELY71221.1| DNA-directed RNA polymerase subunit A'' [Natrinema pellirubrum DSM
            15624]
          Length = 398

 Score =  168 bits (426), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 108/344 (31%), Positives = 178/344 (51%), Gaps = 59/344 (17%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A+A   +Y+  +++P   VG ++AQSIGEPGTQ+T+ TFH+AG            + E +
Sbjct: 48   AKAVEARYLDTRVDPLDPVGTVSAQSIGEPGTQLTMNTFHYAGVAEIDVTQGLPRLIELV 107

Query: 1152 EEVFVPDDSFILIKLD----------------MDRIRLLHL----------EVDI----- 1180
            +    PD   + + L+                ++  ++L L           V I     
Sbjct: 108  DARKTPDTPMMTVYLEGEYATEREKAHEVVWKIEATKILALGDVSTNVADMRVQISLNED 167

Query: 1181 ---------DSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVV 1231
                     D +   IE + G+    TV   + +   P++ S      + Q+ + L  + 
Sbjct: 168  TLKERMITPDEVAGIIEDSLGVK---TVQQGTEIQFGPEEPSYR---DLLQLVEELRDIT 221

Query: 1232 IKGVQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLG 1290
             KG++ I+R VI  E+++ G  ++ L  EG    DV+   GV   + + NN +E+++ LG
Sbjct: 222  FKGIEDISRVVIRREELDNGNEEFVLYTEGSAFGDVLEIEGVDASRTTCNNIHEIHRNLG 281

Query: 1291 IEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNL 1349
            IEAAR  I+ E    +   G+  ++ RH MLVAD+MT++GE+  I RHG++  KESVL  
Sbjct: 282  IEAAREAIIEETNNTLAEQGLDDVNVRHLMLVADMMTNRGEIESIGRHGISGSKESVLAR 341

Query: 1350 ASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            A+FE T +HL +AA +G+ D + GV+E +I+G P+ +GTG + L
Sbjct: 342  AAFEVTVNHLLNAAIHGEVDDLDGVTENVIVGKPIKLGTGDVDL 385



 Score = 97.8 bits (242), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 71/239 (29%), Positives = 128/239 (53%), Gaps = 21/239 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T YL+ +  T+ + A  V  ++E T    LG+V   + ++
Sbjct: 99  GLPRLIELVDARKTPDTPMMTVYLEGEYATEREKAHEVVWKIEATKILALGDVSTNVADM 158

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSK 878
            V       I L+ D ++     +  D +   IE + G+    TV   + +   P++ S 
Sbjct: 159 RVQ------ISLNEDTLK--ERMITPDEVAGIIEDSLGVK---TVQQGTEIQFGPEEPSY 207

Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVK 937
                + Q+ + L  +  KG++ I+R VI  E+++ G  ++ L  EG    DV+   GV 
Sbjct: 208 R---DLLQLVEELRDITFKGIEDISRVVIRREELDNGNEEFVLYTEGSAFGDVLEIEGVD 264

Query: 938 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEV 995
             + + NN +E+++ LGIEAAR  I+ E    +   G+  ++ RH MLVAD+MT++GE+
Sbjct: 265 ASRTTCNNIHEIHRNLGIEAAREAIIEETNNTLAEQGLDDVNVRHLMLVADMMTNRGEI 323


>gi|298674726|ref|YP_003726476.1| DNA-directed RNA polymerase subunit A'' [Methanohalobium evestigatum
            Z-7303]
 gi|298287714|gb|ADI73680.1| DNA-directed RNA polymerase, subunit A'' [Methanohalobium evestigatum
            Z-7303]
          Length = 388

 Score =  168 bits (426), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 107/342 (31%), Positives = 166/342 (48%), Gaps = 58/342 (16%)

Query: 1108 EKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFV 1156
            + Y  A +EP  AVG ++AQSIGEPGTQMT++TFH+AG            + E ++    
Sbjct: 48   DNYGYACVEPCEAVGVVSAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVDARKT 107

Query: 1157 PDDSFILIKL----------------------------------------DMDRIRLLHL 1176
            P    + + L                                        D+    L   
Sbjct: 108  PSTPMMTVALEEGYSDSRDEARKLAWQIEATHIGHLGDVTTDLAQMQLVVDLHEKTLTQR 167

Query: 1177 EVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQ 1236
            E+ +D I   +     +   ++      +I++P   S     ++ Q+ + + +V +KG++
Sbjct: 168  EISVDEIAGILRDKLNVLVKISEGVDYQIIIQPNQPSYR---ELLQLAKNIHNVTLKGIE 224

Query: 1237 GINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARS 1296
            GI R VI ++  E    Y L  EG  L +V+   GV   +  +NN  E+Y+  GIEAAR+
Sbjct: 225  GIKRVVIRKDSDE----YTLYTEGSELNEVLKIEGVDVTRTYTNNIAEIYEVFGIEAARN 280

Query: 1297 TIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTS 1356
             ++ E    +   G+++D RH MLVAD+MT  GEV  I RHG++  K SV   A+FE T 
Sbjct: 281  ALVKEAMDTLSEQGLNVDIRHIMLVADIMTCDGEVKQIGRHGISGEKASVFARAAFEVTV 340

Query: 1357 DHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 1398
            +HL DA   G  D ++GV+E II+G P+ +GTG + L+   P
Sbjct: 341  NHLLDAGIRGDVDELNGVTENIIIGQPIKLGTGDVHLVATKP 382



 Score =  105 bits (261), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 69/234 (29%), Positives = 123/234 (52%), Gaps = 14/234 (5%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDK--DTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A +  STP++T  L++      D AR +  ++E T +G + +        
Sbjct: 94  GLPRLIEIVDARKTPSTPMMTVALEEGYSDSRDEARKLAWQIEATHIGHLGD-----VTT 148

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
           D + + + +D+    L   E+ +D I   +     +   ++      +I++P   S    
Sbjct: 149 DLAQMQLVVDLHEKTLTQREISVDEIAGILRDKLNVLVKISEGVDYQIIIQPNQPSYR-- 206

Query: 882 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
            ++ Q+ + + +V +KG++GI R VI ++  E    Y L  EG  L +V+   GV   + 
Sbjct: 207 -ELLQLAKNIHNVTLKGIEGIKRVVIRKDSDE----YTLYTEGSELNEVLKIEGVDVTRT 261

Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            +NN  E+Y+  GIEAAR+ ++ E    +   G+++D RH MLVAD+MT  GEV
Sbjct: 262 YTNNIAEIYEVFGIEAARNALVKEAMDTLSEQGLNVDIRHIMLVADIMTCDGEV 315


>gi|375083051|ref|ZP_09730089.1| DNA-directed RNA polymerase subunit A'' [Thermococcus litoralis DSM
            5473]
 gi|374742287|gb|EHR78687.1| DNA-directed RNA polymerase subunit A'' [Thermococcus litoralis DSM
            5473]
          Length = 394

 Score =  168 bits (426), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 114/342 (33%), Positives = 172/342 (50%), Gaps = 60/342 (17%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFVP 1157
            +Y +A IEP  AVG + AQSIGEP TQMTL TFH+AG            + E ++    P
Sbjct: 54   EYEKALIEPGEAVGTVTAQSIGEPSTQMTLNTFHYAGVAEINVTLGLPRIIEIVDARKNP 113

Query: 1158 DDSFILIKLDMD-------------RIR--------------LLHLE--VDID------- 1181
                + + LD +             RI               +L++E  VD+D       
Sbjct: 114  STPIMTVYLDEEHRYDSEKAREVARRIEGTTLESLARSMTLDILNMEFVVDVDPERLEKS 173

Query: 1182 -----SIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQ 1236
                  I+  +ER+   S  + V G++ +I   K    S    + ++   +    +KG+ 
Sbjct: 174  GLTMEKIQAKLERSFK-SAEIEVDGNTLIIRMKKVKGVS---TLRRLADKVKKHRLKGLS 229

Query: 1237 GINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARS 1296
            G+ + +I +E  E    Y +  EG N + V+   GV   +  +NN +E+ + LGIEAAR+
Sbjct: 230  GVGKTIIRKEGDE----YVIYTEGSNFKQVLKVPGVDPTRTRTNNIHEIAEVLGIEAARN 285

Query: 1297 TIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTS 1356
             I+ EI   M+  G+ +D RH MLVAD+MT  G V  I RHG+   K SVL  A+FE T 
Sbjct: 286  AIIEEITRTMQEQGLEVDVRHIMLVADMMTLDGIVRPIGRHGVVGTKASVLARAAFEITV 345

Query: 1357 DHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 1398
             HL  AA  G+ D ++GV E +++G P+ VGTG+++L   +P
Sbjct: 346  QHLLQAAERGEVDPLNGVVENVLIGQPVPVGTGIVRLAMKLP 387



 Score =  114 bits (286), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 78/232 (33%), Positives = 129/232 (55%), Gaps = 14/232 (6%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PRI EI++A +N STPI+T YLD++   D + AR V  R+E TTL  +   +  + + 
Sbjct: 99  GLPRIIEIVDARKNPSTPIMTVYLDEEHRYDSEKAREVARRIEGTTLESLARSMT-LDIL 157

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
           +  F++   D+D  RL    + ++ I+  +ER+   S  + V G++ +I   K    S  
Sbjct: 158 NMEFVV---DVDPERLEKSGLTMEKIQAKLERSFK-SAEIEVDGNTLIIRMKKVKGVS-- 211

Query: 882 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
             + ++   +    +KG+ G+ + +I +E  E    Y +  EG N + V+   GV   + 
Sbjct: 212 -TLRRLADKVKKHRLKGLSGVGKTIIRKEGDE----YVIYTEGSNFKQVLKVPGVDPTRT 266

Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
            +NN +E+ + LGIEAAR+ I+ EI   M+  G+ +D RH MLVAD+MT  G
Sbjct: 267 RTNNIHEIAEVLGIEAARNAIIEEITRTMQEQGLEVDVRHIMLVADMMTLDG 318


>gi|354609474|ref|ZP_09027430.1| DNA-directed RNA polymerase subunit A'' [Halobacterium sp. DL1]
 gi|353194294|gb|EHB59796.1| DNA-directed RNA polymerase subunit A'' [Halobacterium sp. DL1]
          Length = 394

 Score =  168 bits (426), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 115/349 (32%), Positives = 173/349 (49%), Gaps = 63/349 (18%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A A    Y+  +I+P   VG ++AQSIGEPGTQMT+ TFH+AG            + E +
Sbjct: 44   ATAVESSYLETRIDPLDPVGTVSAQSIGEPGTQMTMNTFHYAGVAEMDVTQGLPRLIELV 103

Query: 1152 EEVFVPD---------DSF-------------------------------ILIKLDMDRI 1171
            +    PD         D +                               +++++D++  
Sbjct: 104  DARKTPDTPVMNVFLEDEYAEERERAHEVVWKIEATKILALGDISTNVADMVVRIDLNED 163

Query: 1172 RLLH---LEVDIDSIRYCIERTRGISGHLTV---SGHSFLILKPKDSSKSFNSKMYQMKQ 1225
             LL    LE D   I   I  T  I G L V      + L   P + S     ++ Q+ +
Sbjct: 164  TLLERWPLENDTTEIAAEIAET--IEGSLGVDVTQQGTVLEFGPGEPSYR---ELLQLVE 218

Query: 1226 LLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEV 1285
             L  +V KG+  ++R VI  E+ +   ++ L  EG   +  +   GV   + + NN +EV
Sbjct: 219  QLRDIVFKGIDDVSRVVIRREETDRGEEFVLYTEGSAYKKALNIEGVDASRTTCNNIHEV 278

Query: 1286 YKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEVLGITRHGLAKMKE 1344
            +KTLGIEAAR  I+ E    +E  G+  ++ RH MLVAD+MT+ G +  I RHG++  K+
Sbjct: 279  HKTLGIEAAREAIIDETMSTLEEQGLGDVNIRHLMLVADIMTNDGTIQSIGRHGISGNKD 338

Query: 1345 SVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            SVL  A+FE T +HL DAA YG+ D + GV E +I+G P+ +GTG + L
Sbjct: 339  SVLARAAFEVTVNHLLDAAIYGEADDLDGVIENVIVGKPVRLGTGDVNL 387



 Score = 96.7 bits (239), Expect = 8e-17,   Method: Composition-based stats.
 Identities = 71/244 (29%), Positives = 125/244 (51%), Gaps = 25/244 (10%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++  +L+ +   + + A  V  ++E T    LG++   + + 
Sbjct: 95  GLPRLIELVDARKTPDTPVMNVFLEDEYAEERERAHEVVWKIEATKILALGDISTNVAD- 153

Query: 819 FVPDDSFILIKLDMDRIRLLH---LEVDIDSIRYCIERTRGISGHLTV---SGHSFLILK 872
                  +++++D++   LL    LE D   I   I  T  I G L V      + L   
Sbjct: 154 -------MVVRIDLNEDTLLERWPLENDTTEIAAEIAET--IEGSLGVDVTQQGTVLEFG 204

Query: 873 PKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMA 932
           P + S     ++ Q+ + L  +V KG+  ++R VI  E+ +   ++ L  EG   +  + 
Sbjct: 205 PGEPSYR---ELLQLVEQLRDIVFKGIDDVSRVVIRREETDRGEEFVLYTEGSAYKKALN 261

Query: 933 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTS 991
             GV   + + NN +EV+KTLGIEAAR  I+ E    +E  G+  ++ RH MLVAD+MT+
Sbjct: 262 IEGVDASRTTCNNIHEVHKTLGIEAAREAIIDETMSTLEEQGLGDVNIRHLMLVADIMTN 321

Query: 992 KGEV 995
            G +
Sbjct: 322 DGTI 325


>gi|333911408|ref|YP_004485141.1| DNA-directed RNA polymerase subunit A' [Methanotorris igneus Kol 5]
 gi|333751997|gb|AEF97076.1| DNA-directed RNA polymerase subunit A' [Methanotorris igneus Kol 5]
          Length = 890

 Score =  168 bits (426), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 101/272 (37%), Positives = 150/272 (55%), Gaps = 41/272 (15%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VL+NRQPSLH++SIMAHR KVLP+RTFR N CVC PYNADFDGDEMN+H+PQ+   
Sbjct: 424 DGDIVLYNRQPSLHRMSIMAHRVKVLPYRTFRHNLCVCPPYNADFDGDEMNLHVPQS--- 480

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
                            A+ LM  + ++++PR G  +I A  D+ITG YLLT  +++F +
Sbjct: 481 -----------EEARAEAEALMLVEKHILSPRFGGPIIGAIHDYITGAYLLT--SSYFTK 527

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +   I  +         G IK      W P        +++GK+IFS  L      P  
Sbjct: 528 DEASIILRS---------GGIKD---ELWEPDKIENGIPLYSGKKIFSKAL------PKG 569

Query: 521 ANLKTKG----RAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFY-ILLRD 575
            NLK +     +     +E C  D+YV+++N EL+ G +DK+  G G +A +    ++++
Sbjct: 570 LNLKYRAKICKKCDECKKEDCPHDAYVVIKNGELIKGVVDKN--GFGAEAGIILDTIVKE 627

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           FG + A   +   ++M    +M +GF+ GI D
Sbjct: 628 FGSEEARKFLDSSTKMAIRAIMIKGFTTGIDD 659



 Score =  117 bits (294), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 78/256 (30%), Positives = 124/256 (48%), Gaps = 40/256 (15%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + +++ S  +IV+ + Y  D    PI  GL+D R+G       C TCG  +  C GHFG+
Sbjct: 22  EHIRKMSVAKIVTADTY--DDDGYPIDGGLMDTRLGVIDPGLVCKTCGGRVGTCPGHFGH 79

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           I+L  PV HIG+ + +  IL+++C  P C R+ + E K   +  K++        +  + 
Sbjct: 80  IELAKPVIHIGFAKDIYKILKAVC--PHCGRIAINEVKIKEYLEKMKKLEEDGGDKWEVC 137

Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           +++L+   K +VCPHCGEI           I +EK      + D   E LL         
Sbjct: 138 EEVLKEAAKANVCPHCGEIK--------YDIKYEK-PTTYYQIDGKTEKLLT-------- 180

Query: 271 NPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCI 330
                            P +V ++ E IP ED  LL +N E+ +P  ++LT L VPP  +
Sbjct: 181 -----------------PSDVREILEKIPDEDCILLGLNPEVMRPEWMVLTVLPVPPVTV 223

Query: 331 RPSVI--SDLKSDNDV 344
           RPS+   S  +S++D+
Sbjct: 224 RPSITLESGERSEDDL 239



 Score = 88.6 bits (218), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 36/57 (63%), Positives = 48/57 (84%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFV++S+  GL+P E+FFH MGGREGLVD AV+TA++GYMQRRL+ +L+DL  +YD
Sbjct: 788 HGFVRSSYKKGLSPIEYFFHAMGGREGLVDQAVRTAQSGYMQRRLINALQDLRAEYD 844


>gi|418204398|gb|AFX61753.1| RNA polymerase I largest subunit, partial [Ascosphaera cf. larvis
           64254]
          Length = 1616

 Score =  168 bits (426), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 101/272 (37%), Positives = 148/272 (54%), Gaps = 35/272 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DV+LFNRQPSLHK S+MAHR +V+P+ TFR N  V TPYNADFDGDEMN+H+PQ+EE+
Sbjct: 433 DGDVILFNRQPSLHKESMMAHRVRVMPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSEES 492

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L +L+++            N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 493 RAE----LKELALVP----------LNIVSPQRNGPLMGIVQDTLCGIYKICRRDTFLTK 538

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              M I   +     D  G+I +       P + ++    WTGKQI S++L      P  
Sbjct: 539 EHVMNIMMWV----PDWDGVIPQ-------PAI-IKPRPRWTGKQIISMVL------PSG 580

Query: 521 ANL--KTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            NL    K  A  A       DS   +   EL+ G   K T+G+ G   V + +  ++G 
Sbjct: 581 LNLLRLDKDGAPLAERFSPINDSGCFIHGGELMFGQFSKKTVGATG-GGVIHTIFNEYGP 639

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           DV ++      R+ +++L++ GFSIGIGD  P
Sbjct: 640 DVCMSFFNGTQRVVNYWLLHNGFSIGIGDTIP 671



 Score = 99.0 bits (245), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QR+LVK+LE++ V
Sbjct: 791 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMV 850

Query: 666 QYD 668
           +YD
Sbjct: 851 KYD 853



 Score = 97.1 bits (240), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 58/186 (31%), Positives = 95/186 (51%), Gaps = 16/186 (8%)

Query: 1219 KMYQMKQLLPSVVIKGVQGINRAVIHEE---------------DVEGVTKYKLLVEGDNL 1263
            K++Q   +L    ++GV G+ RA I+E+               + +   ++ L   G  L
Sbjct: 1262 KIFQ-AHMLDHCTLRGVSGVERAFINEKTHARIMPDGSLSKSAEDDQCKEWILETSGSAL 1320

Query: 1264 RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 1323
             DV+   GV   +  SN   E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D
Sbjct: 1321 ADVLTIDGVDATRTYSNQFIEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLID 1380

Query: 1324 LMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLP 1383
            +MTS+G ++ +TRHG+ +     L   SFE T + L +AA + + D   GVSE +I+G  
Sbjct: 1381 IMTSRGFLMAVTRHGINRSDTGALMRCSFEETVEILLEAAAFAELDDCRGVSENLILGQM 1440

Query: 1384 MNVGTG 1389
               GTG
Sbjct: 1441 APAGTG 1446



 Score = 86.7 bits (213), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 74/290 (25%), Positives = 126/290 (43%), Gaps = 60/290 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N ++NI TP +T Y   +   + D  ++++ ++E TTL  V E IE  + P
Sbjct: 1097 GVPRLKEILNVAKNIKTPSMTVYQVPELAGNQDAVKVLRSKVEHTTLRSVAEMIEIYYDP 1156

Query: 822  DDSFILIKLDMD------------------------RIRLLHLEV--------DI-DSIR 848
            D    +I+ D D                        R+ L H+++        D+ D I+
Sbjct: 1157 DIRNTVIEADKDMVETYFIIPEDVQEKPEEQSQWLVRLVLSHIKLIDKGLTVQDVADRIK 1216

Query: 849  YCIERTRGISGHLTVSGHSFLILKP------KDSSKSFNSKMYQMK----QLLPSVVIKG 898
               E    +      S    + ++P       D     N   + +K     +L    ++G
Sbjct: 1217 ALFENDVNVMFSDDNSDQPVIRIRPLKGALDDDEEGDGNEMDHTLKIFQAHMLDHCTLRG 1276

Query: 899  VQGINRAVIHEE---------------DVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSS 943
            V G+ RA I+E+               + +   ++ L   G  L DV+   GV   +  S
Sbjct: 1277 VSGVERAFINEKTHARIMPDGSLSKSAEDDQCKEWILETSGSALADVLTIDGVDATRTYS 1336

Query: 944  NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
            N   E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1337 NQFIEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLIDIMTSRG 1386



 Score = 76.6 bits (187), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 59/247 (23%), Positives = 106/247 (42%), Gaps = 42/247 (17%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D +++ S ++IV         QR P   GL D ++GT  +   C TC Q + DC GHFG+
Sbjct: 9   DEIKKMSVVKIVYPETMDDQRQR-PREEGLNDPKLGTIDRAFKCATCEQGIMDCPGHFGH 67

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARV---LLGEEKAAGFRAKLRNPALSYLVRK 207
           I+L  PVFHIG+   +  +L+++C N  C ++   +   + A   R +        + R 
Sbjct: 68  IELASPVFHIGFLTKIKKLLETVCIN--CGKIKADMTDSKYAEALRYRDPKRRFDAIWRL 125

Query: 208 SLKKKILETTKKVSVCPH-------------CGEINGVVKKCGLLKISHEKYKNRTKKKD 254
              K + ETT  +   P              CG     +++ GL  +   K +    + +
Sbjct: 126 CKDKLLCETTPIIQDDPFSNAPPQILYGHGGCGNPQPQIRREGLTLVGTWKPEKSVDQSE 185

Query: 255 AIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSK 314
           +                P ++        + + P E  ++F+ I   D+ LL ++ E ++
Sbjct: 186 SA---------------PPVK--------RVITPKEAREVFKNISSGDVRLLGLSNEYAR 222

Query: 315 PSDLILT 321
           P  +I+T
Sbjct: 223 PEWMIIT 229



 Score = 57.4 bits (137), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 26/41 (63%), Positives = 28/41 (68%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            A   ++ RA   P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1048 AIENRFARAIASPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1088


>gi|429191197|ref|YP_007176875.1| DNA-directed RNA polymerase, subunit A'''' [Natronobacterium gregoryi
            SP2]
 gi|448326612|ref|ZP_21515961.1| DNA-directed RNA polymerase subunit A'' [Natronobacterium gregoryi
            SP2]
 gi|429135415|gb|AFZ72426.1| DNA-directed RNA polymerase, subunit A'''' [Natronobacterium gregoryi
            SP2]
 gi|445610904|gb|ELY64669.1| DNA-directed RNA polymerase subunit A'' [Natronobacterium gregoryi
            SP2]
          Length = 401

 Score =  168 bits (426), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 107/344 (31%), Positives = 178/344 (51%), Gaps = 59/344 (17%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A+A   +YV  ++EP   VG ++AQSIGEPGTQ+T+ TFH+AG            + E +
Sbjct: 48   AKAVETRYVDTRVEPLDPVGTVSAQSIGEPGTQLTMNTFHYAGVAEIDVTQGLPRLIELV 107

Query: 1152 EEVFVPDDSFILIKLD----------------MDRIRLLHL------------------- 1176
            +    PD   + + L+                ++  ++L L                   
Sbjct: 108  DARKTPDTPMMTVHLEDEYATERERAHEVVWNIEATKILALGDVSTNVADMRVQISLNED 167

Query: 1177 -----EVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVV 1231
                  ++ + +   IE + G+    TV   + +   P++ S      + Q+ + L  + 
Sbjct: 168  TLEERMIEPEEVAEIIEDSLGVD---TVQQGTQIQFGPEEPSYR---DLLQLVEELRDIT 221

Query: 1232 IKGVQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLG 1290
             KG++ I+R VI  E+++ G  ++ L  EG    DV+   GV   + + NN +E+++ LG
Sbjct: 222  FKGIEDISRVVIRREEMDDGSEEFVLYTEGSAFGDVLEIEGVDASRTTCNNIHEIHRNLG 281

Query: 1291 IEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNL 1349
            IEAAR  I+ E    +   G+  ++ RH MLVAD+MT++GE+  I RHG++  KESVL  
Sbjct: 282  IEAAREAIIEETNNTLAEQGLDDVNVRHLMLVADIMTNRGEIESIGRHGISGSKESVLAR 341

Query: 1350 ASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            A+FE T +HL +AA +G+ D + GV+E +I+G P+ +GTG + L
Sbjct: 342  AAFEVTVNHLLNAAIHGEIDDLDGVTENVIVGKPIKLGTGDVDL 385



 Score = 97.1 bits (240), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 67/239 (28%), Positives = 127/239 (53%), Gaps = 21/239 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T +L+ +  T+ + A  V   +E T    LG+V   + ++
Sbjct: 99  GLPRLIELVDARKTPDTPMMTVHLEDEYATERERAHEVVWNIEATKILALGDVSTNVADM 158

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSK 878
            V        ++ ++   L    ++ + +   IE + G+    TV   + +   P++ S 
Sbjct: 159 RV--------QISLNEDTLEERMIEPEEVAEIIEDSLGVD---TVQQGTQIQFGPEEPSY 207

Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVK 937
                + Q+ + L  +  KG++ I+R VI  E+++ G  ++ L  EG    DV+   GV 
Sbjct: 208 R---DLLQLVEELRDITFKGIEDISRVVIRREEMDDGSEEFVLYTEGSAFGDVLEIEGVD 264

Query: 938 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEV 995
             + + NN +E+++ LGIEAAR  I+ E    +   G+  ++ RH MLVAD+MT++GE+
Sbjct: 265 ASRTTCNNIHEIHRNLGIEAAREAIIEETNNTLAEQGLDDVNVRHLMLVADIMTNRGEI 323


>gi|387596460|gb|EIJ94081.1| DNA-directed RNA polymerase II subunit RPB1 [Nematocida parisii
           ERTm1]
          Length = 1612

 Score =  168 bits (426), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 104/269 (38%), Positives = 153/269 (56%), Gaps = 34/269 (12%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           S+ D VLFNRQPSLHK+S+MAHRA+V+ + TFR N  V  PYNADFDGDEMN+HLPQ+  
Sbjct: 424 SNGDTVLFNRQPSLHKMSMMAHRARVMKYSTFRLNLSVTAPYNADFDGDEMNLHLPQSIP 483

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           A+AE    L +L+++          + N+V+P++ + ++   QD + G Y LT+++ F  
Sbjct: 484 AQAE----LKELALV----------EKNIVSPQSNKPVMGIVQDTLMGVYKLTRRDLFLT 529

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           R+Q M +   +   +  I             P + +R AV++TGKQIFS  L P+     
Sbjct: 530 RSQVMHLHYAIDNGSKPI------------KPTI-LRPAVLYTGKQIFSATL-PDVTYKG 575

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
             +    G+ Y AN      DS V+++N ELLAG + K T+G+     + +++  DF   
Sbjct: 576 LHSEHVHGKNYRANP----MDSEVVIKNGELLAGIICKKTVGT-ASGGLIHVIANDFPRS 630

Query: 580 VAVTAMWRLSRMTSFYLMN-RGFSIGIGD 607
           V V  +  L R  S +LM    FS+GIGD
Sbjct: 631 VCVDFIDALQRAISTWLMAYETFSVGIGD 659



 Score =  114 bits (284), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 59/165 (35%), Positives = 98/165 (59%)

Query: 1230 VVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTL 1289
            +++KG+  I R  I E   E   ++ L  EG  L DV++   +   +  SN+  E+ +  
Sbjct: 1273 IMVKGMPKIKRVFISEIGTEDKKEFVLQTEGTGLLDVLSHPLIDPTRTVSNDPLEMCRVF 1332

Query: 1290 GIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNL 1349
            G+EAAR++I+ EI+LV+E+ G  ++FRH  ++AD+MT +G + GITRHG  + +   L  
Sbjct: 1333 GVEAARTSILNEIRLVIESDGSYVNFRHLAILADIMTQRGIICGITRHGTNRGESGALMR 1392

Query: 1350 ASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
             SFE T + L +AA   + D   GV E +++G   ++GTG+  +L
Sbjct: 1393 CSFEETVEILLEAAATAEIDRCKGVVESVMLGKIASIGTGITDVL 1437



 Score = 96.7 bits (239), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 68/260 (26%), Positives = 132/260 (50%), Gaps = 28/260 (10%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEIINA++ I TP +T YL ++    L+ A+  +  +ER  L ++    E ++ P
Sbjct: 1119 GVPRLKEIINAAQTIKTPSLTIYLKEEIRHTLEGAKRAQQEIERCYLKDILLKSEIIYDP 1178

Query: 822  -------DDSFI-----------------LIKLDMDRIRLLHLEVDIDSIRYCIERTRGI 857
                   D+ FI                 +++L++ R  ++   + I+ +   +  +   
Sbjct: 1179 TMRAVKADEDFIFAYGILDPTVYTPDSPWMLRLELSRSAMVDRGIRIEQVAKTLSHSTTY 1238

Query: 858  SGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTK 917
                +    S  I++ +  +      + +++  +  +++KG+  I R  I E   E   +
Sbjct: 1239 RCMHSDHNSSEQIIRCELPNN--EEALRKIETGVSCIMVKGMPKIKRVFISEIGTEDKKE 1296

Query: 918  YKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSI 977
            + L  EG  L DV++   +   +  SN+  E+ +  G+EAAR++I+ EI+LV+E+ G  +
Sbjct: 1297 FVLQTEGTGLLDVLSHPLIDPTRTVSNDPLEMCRVFGVEAARTSILNEIRLVIESDGSYV 1356

Query: 978  DFRHPMLVADLMTSKGEVLG 997
            +FRH  ++AD+MT +G + G
Sbjct: 1357 NFRHLAILADIMTQRGIICG 1376



 Score = 95.5 bits (236), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 40/59 (67%), Positives = 52/59 (88%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
           +GF+ +S+ +GL+P EFFFH MGGREGL+DTAVKTAETGY+QRRL+K+LED  V++D S
Sbjct: 788 RGFISSSYVAGLSPVEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKALEDAQVRHDKS 846



 Score = 86.7 bits (213), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 71/234 (30%), Positives = 113/234 (48%), Gaps = 28/234 (11%)

Query: 115 PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSIC 174
           P   GL+D R+GT+++   C+TCG     CVGHFGYI+L  PVFHIGY   +  +L+S+C
Sbjct: 42  PKEGGLVDLRLGTSERGFLCSTCGHRSDSCVGHFGYIELAKPVFHIGYIGKIKKVLESVC 101

Query: 175 KNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVK 234
              +  RV    EK+     K R    +   RK     I    K  +VC   GE+  V  
Sbjct: 102 FFCSKLRV----EKSILHSPKPR----TQKERKRRLNYIWNLAKNRAVC--MGEL--VES 149

Query: 235 KCGLLKISHEKYKNR--TKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVL 292
           +    +      +NR  T +K+ +      +  E+ +    + A K            VL
Sbjct: 150 EDNPEEKQRTGCENRQPTIRKEGLHLLAFQKGEESSEGKTMLSAEK------------VL 197

Query: 293 QLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDNDV 344
           ++   IP +DI  L  + E ++P  +I+  L VPP  +RPS++ +  L+ ++D+
Sbjct: 198 EILRRIPEDDIEALGFDLEKARPEWMIIRVLPVPPPQVRPSIVMEGSLRCEDDL 251



 Score = 51.6 bits (122), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 23/39 (58%), Positives = 27/39 (69%)

Query: 1107 REKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            R  +++A +     VG LAAQSIGEP TQMTL TFH AG
Sbjct: 1073 RTSFLKAIVSAGEMVGTLAAQSIGEPATQMTLNTFHLAG 1111


>gi|387594692|gb|EIJ89716.1| DNA-directed RNA polymerase II subunit RPB1 [Nematocida parisii
           ERTm3]
          Length = 1612

 Score =  168 bits (426), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 104/269 (38%), Positives = 153/269 (56%), Gaps = 34/269 (12%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           S+ D VLFNRQPSLHK+S+MAHRA+V+ + TFR N  V  PYNADFDGDEMN+HLPQ+  
Sbjct: 424 SNGDTVLFNRQPSLHKMSMMAHRARVMKYSTFRLNLSVTAPYNADFDGDEMNLHLPQSIP 483

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           A+AE    L +L+++          + N+V+P++ + ++   QD + G Y LT+++ F  
Sbjct: 484 AQAE----LKELALV----------EKNIVSPQSNKPVMGIVQDTLMGVYKLTRRDLFLT 529

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           R+Q M +   +   +  I             P + +R AV++TGKQIFS  L P+     
Sbjct: 530 RSQVMHLHYAIDNGSKPI------------KPTI-LRPAVLYTGKQIFSATL-PDVTYKG 575

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
             +    G+ Y AN      DS V+++N ELLAG + K T+G+     + +++  DF   
Sbjct: 576 LHSEHVHGKNYRANP----MDSEVVIKNGELLAGIICKKTVGT-ASGGLIHVIANDFPRS 630

Query: 580 VAVTAMWRLSRMTSFYLMN-RGFSIGIGD 607
           V V  +  L R  S +LM    FS+GIGD
Sbjct: 631 VCVDFIDALQRAISTWLMAYETFSVGIGD 659



 Score =  114 bits (284), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 59/165 (35%), Positives = 98/165 (59%)

Query: 1230 VVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTL 1289
            +++KG+  I R  I E   E   ++ L  EG  L DV++   +   +  SN+  E+ +  
Sbjct: 1273 IMVKGMPKIKRVFISEIGTEDKKEFVLQTEGTGLLDVLSHPLIDPTRTVSNDPLEMCRVF 1332

Query: 1290 GIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNL 1349
            G+EAAR++I+ EI+LV+E+ G  ++FRH  ++AD+MT +G + GITRHG  + +   L  
Sbjct: 1333 GVEAARTSILNEIRLVIESDGSYVNFRHLAILADIMTQRGIICGITRHGTNRGESGALMR 1392

Query: 1350 ASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
             SFE T + L +AA   + D   GV E +++G   ++GTG+  +L
Sbjct: 1393 CSFEETVEILLEAAATAEIDRCKGVVESVMLGKIASIGTGITDVL 1437



 Score = 96.7 bits (239), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 68/260 (26%), Positives = 132/260 (50%), Gaps = 28/260 (10%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEIINA++ I TP +T YL ++    L+ A+  +  +ER  L ++    E ++ P
Sbjct: 1119 GVPRLKEIINAAQTIKTPSLTIYLKEEIRHTLEGAKRAQQEIERCYLKDILLKSEIIYDP 1178

Query: 822  -------DDSFI-----------------LIKLDMDRIRLLHLEVDIDSIRYCIERTRGI 857
                   D+ FI                 +++L++ R  ++   + I+ +   +  +   
Sbjct: 1179 TMRAVKADEDFIFAYGILDPTVYTPDSPWMLRLELSRSAMVDRGIRIEQVAKTLSHSTTY 1238

Query: 858  SGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTK 917
                +    S  I++ +  +      + +++  +  +++KG+  I R  I E   E   +
Sbjct: 1239 RCMHSDHNSSEQIIRCELPNN--EEALRKIETGVSCIMVKGMPKIKRVFISEIGTEDKKE 1296

Query: 918  YKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSI 977
            + L  EG  L DV++   +   +  SN+  E+ +  G+EAAR++I+ EI+LV+E+ G  +
Sbjct: 1297 FVLQTEGTGLLDVLSHPLIDPTRTVSNDPLEMCRVFGVEAARTSILNEIRLVIESDGSYV 1356

Query: 978  DFRHPMLVADLMTSKGEVLG 997
            +FRH  ++AD+MT +G + G
Sbjct: 1357 NFRHLAILADIMTQRGIICG 1376



 Score = 95.5 bits (236), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 40/59 (67%), Positives = 52/59 (88%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
           +GF+ +S+ +GL+P EFFFH MGGREGL+DTAVKTAETGY+QRRL+K+LED  V++D S
Sbjct: 788 RGFISSSYVAGLSPVEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKALEDAQVRHDKS 846



 Score = 86.7 bits (213), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 71/234 (30%), Positives = 113/234 (48%), Gaps = 28/234 (11%)

Query: 115 PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSIC 174
           P   GL+D R+GT+++   C+TCG     CVGHFGYI+L  PVFHIGY   +  +L+S+C
Sbjct: 42  PKEGGLVDLRLGTSERGFLCSTCGHRSDSCVGHFGYIELAKPVFHIGYIGKIKKVLESVC 101

Query: 175 KNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVK 234
              +  RV    EK+     K R    +   RK     I    K  +VC   GE+  V  
Sbjct: 102 FFCSKLRV----EKSILHSPKPR----TQKERKRRLNYIWNLAKNRAVC--MGEL--VES 149

Query: 235 KCGLLKISHEKYKNR--TKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVL 292
           +    +      +NR  T +K+ +      +  E+ +    + A K            VL
Sbjct: 150 EDNPEEKQRTGCENRQPTIRKEGLHLLAFQKGEESSEGKTMLSAEK------------VL 197

Query: 293 QLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDNDV 344
           ++   IP +DI  L  + E ++P  +I+  L VPP  +RPS++ +  L+ ++D+
Sbjct: 198 EILRRIPEDDIEALGFDLEKARPEWMIIRVLPVPPPQVRPSIVMEGSLRCEDDL 251



 Score = 51.6 bits (122), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 23/39 (58%), Positives = 27/39 (69%)

Query: 1107 REKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            R  +++A +     VG LAAQSIGEP TQMTL TFH AG
Sbjct: 1073 RTSFLKAIVSAGEMVGTLAAQSIGEPATQMTLNTFHLAG 1111


>gi|418204396|gb|AFX61752.1| RNA polymerase I largest subunit, partial [Ascosphaera aggregata]
          Length = 1697

 Score =  168 bits (425), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 100/272 (36%), Positives = 150/272 (55%), Gaps = 35/272 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DV+LFNRQPSLHK S+MAH+ +V+P+ TFR N  V TPYNADFDGDEMN+H+PQ+EE+
Sbjct: 438 DGDVILFNRQPSLHKESMMAHKVRVMPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSEES 497

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE    L +L+++            N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 498 KAE----LRELALVPL----------NIVSPQRNGPLMGIVQDTLCGIYKICRRDTFLTK 543

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              M I   +     D  G+I +       P + ++    WTGKQI S++L      P  
Sbjct: 544 DHVMNIMMWV----PDWDGVIPQ-------PAI-LKPRPRWTGKQIISMVL------PSG 585

Query: 521 ANL--KTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            NL    K  A  A      +D  V +   EL+ G   K T+G+ G   V + +  ++G 
Sbjct: 586 LNLLRLDKDGAPLAERFSPLKDGGVFIHGGELMFGQFSKKTVGATG-GGVIHTIFNEYGS 644

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           DVA++      R+ +++L++ GFSIGIGD  P
Sbjct: 645 DVAMSFFNGAQRVVNYWLLHNGFSIGIGDTIP 676



 Score = 99.0 bits (245), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QR+LVK+LE++ V
Sbjct: 796 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMV 855

Query: 666 QYD 668
           +YD
Sbjct: 856 KYD 858



 Score = 95.9 bits (237), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 58/186 (31%), Positives = 96/186 (51%), Gaps = 16/186 (8%)

Query: 1219 KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGV---------------TKYKLLVEGDNL 1263
            K++Q + +L    ++GV G+ RA I+E+    +                ++ L   G +L
Sbjct: 1268 KIFQ-QHMLDGCTLRGVPGVERAFINEKTHARIMSDGSLRKSAEDPLCKEWILETSGSSL 1326

Query: 1264 RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 1323
              V+A  GV   +  SN   E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D
Sbjct: 1327 AAVLAIDGVDASRTYSNQFIEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLID 1386

Query: 1324 LMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLP 1383
            +MTS+G ++ +TRHG+ +     L   SFE T + L +AA + + D   GVSE +I+G  
Sbjct: 1387 IMTSRGFLMAVTRHGINRADTGALMRCSFEETVEILLEAAAFAELDDCRGVSENLILGQM 1446

Query: 1384 MNVGTG 1389
               GTG
Sbjct: 1447 APAGTG 1452



 Score = 80.1 bits (196), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 73/292 (25%), Positives = 127/292 (43%), Gaps = 63/292 (21%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N ++NI TP +T Y   +   + +  + ++ ++E TTL  V E +E  + P
Sbjct: 1102 GVPRLKEILNVAKNIKTPSMTVYQVPELAGNQEAVKYLRSKVEHTTLRSVAETVEIYYDP 1161

Query: 822  DDSFILIKLDMDRIR-LLHLEVDIDS---------IRYCIERTRGISGHLTV-------- 863
            D    +I+ D D +     +  D+           IR  +   + I   LTV        
Sbjct: 1162 DIRNTVIEADRDMVESYFIIPEDVQDKPEDQSQWLIRLVLSHVKLIDKGLTVQDVADRIK 1221

Query: 864  ---------------SGHSFLILKP--------KDSSKS----FNSKMYQMKQLLPSVVI 896
                           S    + ++P        +D S      +  K++Q + +L    +
Sbjct: 1222 SVYKNDITVMFSDDNSDQPVIRIRPYKEALSDEEDESDGGEMDYFLKIFQ-QHMLDGCTL 1280

Query: 897  KGVQGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMATYGVKGVKC 941
            +GV G+ RA I+E+    +                ++ L   G +L  V+A  GV   + 
Sbjct: 1281 RGVPGVERAFINEKTHARIMSDGSLRKSAEDPLCKEWILETSGSSLAAVLAIDGVDASRT 1340

Query: 942  SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
             SN   E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1341 YSNQFIEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLIDIMTSRG 1392



 Score = 79.0 bits (193), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 62/247 (25%), Positives = 112/247 (45%), Gaps = 38/247 (15%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D +++ S  +I       +  QR P   GL D R+GT  +   C TC + +++C GHFG+
Sbjct: 9   DEIKKMSVAKIEYPETMDEQRQR-PREAGLNDPRLGTIDRTWKCATCEEGINECPGHFGH 67

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKSL 209
           I+L  PVFHIG+   +  +L+++C N  C ++ + +       A + R+P   +     L
Sbjct: 68  IELASPVFHIGFLTKIKKLLETVCLN--CGKIKVNQNDPKYLDALRYRDPKRRFDAIWRL 125

Query: 210 KKKI---------------LETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKD 254
            K I                E  ++V     CG     +++ GL  +    +K R  +  
Sbjct: 126 SKDITTCEADPVVDEDDPFAERVERVPGHGGCGNAQPTIRREGLSLVG--TWKPRRSR-- 181

Query: 255 AIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSK 314
               D+L + ++  +  PE          +T+ P E   +F+ I   D+ LL ++ E ++
Sbjct: 182 ----DMLGDDDDMQQ--PE---------KRTITPREARAVFKNISSGDVRLLGLSNEYAR 226

Query: 315 PSDLILT 321
           P  +I+T
Sbjct: 227 PEWMIIT 233



 Score = 57.4 bits (137), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 26/41 (63%), Positives = 28/41 (68%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            A   ++ RA   P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1053 AIENRFARAVANPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1093


>gi|383320562|ref|YP_005381403.1| DNA-directed RNA polymerase subunit A'' [Methanocella conradii HZ254]
 gi|379321932|gb|AFD00885.1| DNA-directed RNA polymerase, subunit A'' [Methanocella conradii
            HZ254]
          Length = 388

 Score =  168 bits (425), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 113/342 (33%), Positives = 179/342 (52%), Gaps = 61/342 (17%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKT----------------------- 1140
            E  RE Y RA++E   AVG +AAQSIGEPGTQMT++T                       
Sbjct: 45   EKTREAYKRARVENCEAVGMVAAQSIGEPGTQMTMRTFHYAGVAEIDVTLGLPRLIEIVD 104

Query: 1141 -----------FHFAGEVCEY----------IEEVFVPDDSFI-------LIKLDMDRIR 1172
                        H   E+             +EE  V D + I        I +D++  +
Sbjct: 105  ARREPSTPMMTIHLLPEIAGNRDAVKKLGWDLEETNVSDIASISTNLADMTIIIDVNEKQ 164

Query: 1173 LLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVI 1232
            LL   + ++ +   I    G+   L V+  + + + P++ S      + QM + + ++++
Sbjct: 165  LLQRGMTMEEVADKIGEVTGLK--LDVN-ENRITVHPEEPSYR---DLLQMVETIRTILL 218

Query: 1233 KGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIE 1292
            KG++GI+R VI +E+ E    Y +  +G  L+ V+   GV   +  +NN  E+ + LGIE
Sbjct: 219  KGIKGISRVVIRKEENE----YVIYTQGSALKKVIHFEGVDAARTKTNNINEIAEVLGIE 274

Query: 1293 AARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASF 1352
            AAR+ I+ E    +   G+++D RH MLVAD+MT  GEV  I RHG++  K SVL+ A+F
Sbjct: 275  AARNAIINEALDTLSEQGLTVDIRHIMLVADMMTIDGEVKQIGRHGISGEKASVLSRAAF 334

Query: 1353 ENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            E T +HL DAA  G+ D ++GV+E +I+G P+ +GTG ++L+
Sbjct: 335  EVTVNHLLDAAVAGEVDELTGVTENVIVGQPIQLGTGDVELV 376



 Score = 97.8 bits (242), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 70/234 (29%), Positives = 128/234 (54%), Gaps = 17/234 (7%)

Query: 764 GVPRIKEIINASRNISTPIITAYL--DKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A R  STP++T +L  +   + D  + +   LE T + ++        + 
Sbjct: 95  GLPRLIEIVDARREPSTPMMTIHLLPEIAGNRDAVKKLGWDLEETNVSDIASI--STNLA 152

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
           D + I+   D++  +LL   + ++ +   I    G+   L V+  + + + P++ S    
Sbjct: 153 DMTIII---DVNEKQLLQRGMTMEEVADKIGEVTGLK--LDVN-ENRITVHPEEPSYR-- 204

Query: 882 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
             + QM + + ++++KG++GI+R VI +E+ E    Y +  +G  L+ V+   GV   + 
Sbjct: 205 -DLLQMVETIRTILLKGIKGISRVVIRKEENE----YVIYTQGSALKKVIHFEGVDAART 259

Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            +NN  E+ + LGIEAAR+ I+ E    +   G+++D RH MLVAD+MT  GEV
Sbjct: 260 KTNNINEIAEVLGIEAARNAIINEALDTLSEQGLTVDIRHIMLVADMMTIDGEV 313


>gi|254169021|ref|ZP_04875859.1| DNA-directed RNA polymerase subunit A' [Aciduliprofundum boonei
           T469]
 gi|197621991|gb|EDY34568.1| DNA-directed RNA polymerase subunit A' [Aciduliprofundum boonei
           T469]
          Length = 895

 Score =  168 bits (425), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 106/284 (37%), Positives = 156/284 (54%), Gaps = 43/284 (15%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH++S+M H  KV+P+RTFRFN  VC PYNADFDGDEMN+H+ Q+EEA
Sbjct: 421 DGDVVLFNRQPSLHRMSMMGHLVKVMPNRTFRFNLAVCPPYNADFDGDEMNLHVLQSEEA 480

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              AK+LM  + ++++PR G  +I    D IT  +LLT KN  F +
Sbjct: 481 RAE--------------AKILMLVQEHILSPRFGGPIIGGIHDHITAMFLLTHKNPKFTK 526

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            QT+ + S L  D  ++    K  +   +           + GK++FSLIL      P +
Sbjct: 527 EQTIHMLSYL--DYDELPEPHKDENGNEF-----------YYGKELFSLIL------PKD 567

Query: 521 ANLKTKGRAYTAN-------EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILL 573
            N++ K +    +        E C  D+YV++RN +L+AG++D++ +GS     +  I  
Sbjct: 568 LNMEFKSKICDPSVCNNKCVHEACPIDAYVVIRNGKLVAGTIDENAIGSMKGKLLDRIAK 627

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV-TPGQGFVQ 616
           R  G   A   +  ++R+    +  RGF+ GI D   P +  +Q
Sbjct: 628 R--GSKEARKFIDNMTRLAVGVISYRGFTSGIDDEDIPEEAIIQ 669



 Score =  114 bits (286), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 70/247 (28%), Positives = 118/247 (47%), Gaps = 45/247 (18%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + +++ S +++++ + Y  D    PI  GL+D  MG  +    C TCG  + +C GHFG+
Sbjct: 23  EEIRRMSAVKVITADTY--DDDGFPIDKGLMDLHMGVIEPGLRCKTCGGKVDECPGHFGH 80

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKL---RNPALSYLVRK 207
           I+L +PV H+G+ + + N L + C+   C R+ L +++   ++ K+   +    S L   
Sbjct: 81  IELAMPVIHVGFVKNIKNYLDATCRE--CGRIKLKDDEIEIYKQKIEEAKKMGASPLELL 138

Query: 208 SLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEA 267
            + KKI++      +CPHCG                        ++  I  D    + E 
Sbjct: 139 FITKKIIDDASSRPICPHCG-----------------------AEQKKITLDKPTTFRE- 174

Query: 268 VKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPP 327
                  E  K       L P E+ +  E IP ED+PLL MN E ++P  ++LT L VPP
Sbjct: 175 -------EGRK-------LTPKEIRERLERIPDEDLPLLGMNPETARPEWMVLTVLPVPP 220

Query: 328 NCIRPSV 334
             +RP++
Sbjct: 221 VNVRPTI 227



 Score = 89.0 bits (219), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 38/58 (65%), Positives = 50/58 (86%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV++S+  GL+PTE+FFH+MGGREGLVDTAV+T+ +GYMQRRL+ +LEDL V  D
Sbjct: 787 ARGFVESSYKKGLSPTEYFFHSMGGREGLVDTAVRTSRSGYMQRRLINALEDLKVIED 844


>gi|296243130|ref|YP_003650617.1| DNA-directed RNA polymerase subunit A' [Thermosphaera aggregans DSM
            11486]
 gi|296095714|gb|ADG91665.1| DNA-directed RNA polymerase, subunit A' [Thermosphaera aggregans DSM
            11486]
          Length = 408

 Score =  168 bits (425), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 110/348 (31%), Positives = 183/348 (52%), Gaps = 63/348 (18%)

Query: 1099 SACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEVCEY-------- 1150
             A   E  R +Y  + IEP  AVG +AAQS+GEP TQMTL+ FH+AG + EY        
Sbjct: 51   EAIVTEVIR-RYRSSMIEPGEAVGTVAAQSLGEPSTQMTLRVFHYAG-LREYNVTLGLPR 108

Query: 1151 --------------IEEVFVPDDSFILIKLDMDR---------------------IRLLH 1175
                          I E+++ D+     K D ++                     I L  
Sbjct: 109  LIEIVDARKKPETPITEIYLDDEH----KYDEEKAKELARTIETTLLENIAKGISIELTD 164

Query: 1176 LEVDID---------SIRYCIERTRGIS-GHLTVSGHSFLILKPKDSSKSFNSKMYQMKQ 1225
            + +++D         ++   IE  + ++ G +  S  + L+++ +   +    K  +++Q
Sbjct: 165  VTIELDQEMLSDKGITVETVIEALKSLNIGEVEWSEDNPLVIRIRFEEEVDYVKTEKIRQ 224

Query: 1226 LLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEV 1285
             + S  +KGV+GI + +I +   E    Y L+ EG NL ++M   G+   +  +NN +E+
Sbjct: 225  KILSTKLKGVRGIKKVIIQKRGNE----YVLIAEGSNLEELMRIPGIDHKRLYTNNVFEI 280

Query: 1286 YKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKES 1345
             + LGIEAAR+ I+ EIK V+++ G+ +D RH +L+AD+MT  G +  + R G+A  K+S
Sbjct: 281  ERVLGIEAARAAIIKEIKNVLDDQGLDVDIRHIILLADIMTWTGHIRQVGRMGVAGEKQS 340

Query: 1346 VLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            VL  A+FE T   L +AA  G++D + G++E IIMG  + VGTG++++
Sbjct: 341  VLARATFEMTVQKLLEAAAMGESDRLYGITENIIMGQVIPVGTGMVQI 388



 Score =  103 bits (258), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 70/233 (30%), Positives = 126/233 (54%), Gaps = 12/233 (5%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
           G+PR+ EI++A +   TPI   YLD +   D  +     L RT    + E I +    + 
Sbjct: 105 GLPRLIEIVDARKKPETPITEIYLDDEHKYDEEK--AKELARTIETTLLENIAKGISIEL 162

Query: 824 SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGIS-GHLTVSGHSFLILKPKDSSKSFNS 882
           + + I+LD + +    + V+       IE  + ++ G +  S  + L+++ +   +    
Sbjct: 163 TDVTIELDQEMLSDKGITVET-----VIEALKSLNIGEVEWSEDNPLVIRIRFEEEVDYV 217

Query: 883 KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCS 942
           K  +++Q + S  +KGV+GI + +I +   E    Y L+ EG NL ++M   G+   +  
Sbjct: 218 KTEKIRQKILSTKLKGVRGIKKVIIQKRGNE----YVLIAEGSNLEELMRIPGIDHKRLY 273

Query: 943 SNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
           +NN +E+ + LGIEAAR+ I+ EIK V+++ G+ +D RH +L+AD+MT  G +
Sbjct: 274 TNNVFEIERVLGIEAARAAIIKEIKNVLDDQGLDVDIRHIILLADIMTWTGHI 326


>gi|418204400|gb|AFX61754.1| RNA polymerase I largest subunit, partial [Ascosphaera larvis]
          Length = 1627

 Score =  168 bits (425), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 101/272 (37%), Positives = 148/272 (54%), Gaps = 35/272 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DV+LFNRQPSLHK S+MAHR +V+P+ TFR N  V TPYNADFDGDEMN+H+PQ+EE+
Sbjct: 433 DGDVILFNRQPSLHKESMMAHRVRVMPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSEES 492

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L +L+++            N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 493 RAE----LKELALVP----------LNIVSPQRNGPLMGIVQDTLCGIYKICRRDTFLTK 538

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              M I   +     D  G+I +       P + ++    WTGKQI S++L      P  
Sbjct: 539 EHVMNIMMWV----PDWDGVIPQ-------PAI-IKPRPRWTGKQIISMVL------PSG 580

Query: 521 ANL--KTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            NL    K  A  A       DS   +   EL+ G   K T+G+ G   V + +  ++G 
Sbjct: 581 LNLLRLDKDGAPLAERFSPINDSGCFIHGGELMFGQFSKKTVGATG-GGVIHTIFNEYGP 639

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           DV ++      R+ +++L++ GFSIGIGD  P
Sbjct: 640 DVCMSFFNGTQRVVNYWLLHNGFSIGIGDTIP 671



 Score = 98.6 bits (244), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QR+LVK+LE++ V
Sbjct: 791 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMV 850

Query: 666 QYD 668
           +YD
Sbjct: 851 KYD 853



 Score = 97.1 bits (240), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 58/186 (31%), Positives = 95/186 (51%), Gaps = 16/186 (8%)

Query: 1219 KMYQMKQLLPSVVIKGVQGINRAVIHEE---------------DVEGVTKYKLLVEGDNL 1263
            K++Q   +L    ++GV G+ RA I+E+               + +   ++ L   G  L
Sbjct: 1262 KIFQ-AHMLDHCTLRGVSGVERAFINEKTHARIMPDGSLSKSAEDDQCKEWILETSGSAL 1320

Query: 1264 RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 1323
             DV+   GV   +  SN   E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D
Sbjct: 1321 ADVLTIDGVDATRTYSNQFIEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLID 1380

Query: 1324 LMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLP 1383
            +MTS+G ++ +TRHG+ +     L   SFE T + L +AA + + D   GVSE +I+G  
Sbjct: 1381 IMTSRGFLMAVTRHGINRSDTGALMRCSFEETVEILLEAAAFAELDDCRGVSENLILGQM 1440

Query: 1384 MNVGTG 1389
               GTG
Sbjct: 1441 APAGTG 1446



 Score = 86.7 bits (213), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 74/290 (25%), Positives = 126/290 (43%), Gaps = 60/290 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N ++NI TP +T Y   +   + D  ++++ ++E TTL  V E IE  + P
Sbjct: 1097 GVPRLKEILNVAKNIKTPSMTVYQVPELAGNQDAVKVLRSKVEHTTLRSVAEMIEIYYDP 1156

Query: 822  DDSFILIKLDMD------------------------RIRLLHLEV--------DI-DSIR 848
            D    +I+ D D                        R+ L H+++        D+ D I+
Sbjct: 1157 DIRNTVIEADKDMVETYFIIPEDVQEKPEEQSQWLVRLVLSHIKLIDKGLTVQDVADRIK 1216

Query: 849  YCIERTRGISGHLTVSGHSFLILKP------KDSSKSFNSKMYQMK----QLLPSVVIKG 898
               E    +      S    + ++P       D     N   + +K     +L    ++G
Sbjct: 1217 ALFENDVNVMFSDDNSDQPVIRIRPLKGALDDDEEGDGNEMDHTLKIFQAHMLDHCTLRG 1276

Query: 899  VQGINRAVIHEE---------------DVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSS 943
            V G+ RA I+E+               + +   ++ L   G  L DV+   GV   +  S
Sbjct: 1277 VSGVERAFINEKTHARIMPDGSLSKSAEDDQCKEWILETSGSALADVLTIDGVDATRTYS 1336

Query: 944  NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
            N   E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1337 NQFIEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLIDIMTSRG 1386



 Score = 76.3 bits (186), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 59/247 (23%), Positives = 106/247 (42%), Gaps = 42/247 (17%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D +++ S ++IV         QR P   GL D ++GT  +   C TC Q + DC GHFG+
Sbjct: 9   DEIKKMSVVKIVYPETMDDQRQR-PREEGLNDPKLGTIDRAFKCATCEQGIMDCPGHFGH 67

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARV---LLGEEKAAGFRAKLRNPALSYLVRK 207
           I+L  PVFHIG+   +  +L+++C N  C ++   +   + A   R +        + R 
Sbjct: 68  IELASPVFHIGFLTKIKKLLETVCIN--CGKIKADMTDSKYAEALRYRDPKRRFDAIWRL 125

Query: 208 SLKKKILETTKKVSVCPH-------------CGEINGVVKKCGLLKISHEKYKNRTKKKD 254
              K + ETT  +   P              CG     +++ GL  +   K +    + +
Sbjct: 126 CKDKLLCETTPIIQDDPFSNAPPQILYGHGGCGNPQPQIRREGLTLVGTWKPEKSVDQSE 185

Query: 255 AIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSK 314
           +                P ++        + + P E  ++F+ I   D+ LL ++ E ++
Sbjct: 186 SA---------------PPVK--------RVITPKEAREVFKNISSGDVRLLGLSNEYAR 222

Query: 315 PSDLILT 321
           P  +I+T
Sbjct: 223 PEWMIIT 229



 Score = 57.4 bits (137), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 26/41 (63%), Positives = 28/41 (68%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            A   ++ RA   P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1048 AIENRFARAIASPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1088


>gi|374635618|ref|ZP_09707213.1| DNA-directed RNA polymerase subunit A' [Methanotorris formicicus
           Mc-S-70]
 gi|373561684|gb|EHP87913.1| DNA-directed RNA polymerase subunit A' [Methanotorris formicicus
           Mc-S-70]
          Length = 889

 Score =  168 bits (425), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 102/272 (37%), Positives = 152/272 (55%), Gaps = 41/272 (15%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VL+NRQPSLH++SIMAH+ KVLP+RTFR N CVC PYNADFDGDEMN+H+PQ+   
Sbjct: 424 DGDIVLYNRQPSLHRMSIMAHKVKVLPYRTFRHNLCVCPPYNADFDGDEMNLHVPQS--- 480

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
                            A+ LM  + ++++PR G  +I A  DFITG YLLT  +++F +
Sbjct: 481 -----------EEARAEAEALMLVEKHILSPRFGGPIIGAIHDFITGAYLLT--SSYFTK 527

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +    AS ++       G IK      W P        +++GK+IFS  L      P  
Sbjct: 528 DE----ASIILRG-----GGIKE---ELWEPDKIENGVPLYSGKKIFSKAL------PKG 569

Query: 521 ANLKTKG----RAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFY-ILLRD 575
            NLK +     +     +E C  D+YV+++N EL+ G +DK+  G G +A +    ++++
Sbjct: 570 LNLKYRAKICKKCDECKKEDCPHDAYVVIKNGELIKGVVDKN--GFGAEAGIILDTIVKE 627

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           FG + A   +   ++M    +M +GF+ GI D
Sbjct: 628 FGSEEARKFLDSSTKMAIRAIMIKGFTTGIDD 659



 Score =  117 bits (293), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 78/254 (30%), Positives = 122/254 (48%), Gaps = 40/254 (15%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           +++ S  +IV+ + Y  D    PI  GL+D R+G       C TCG  +  C GHFG+I+
Sbjct: 24  IRKMSVAKIVTADTY--DDDGYPIDGGLMDTRLGVIDPGLVCKTCGGRVGTCPGHFGHIE 81

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKK 212
           L  PV HIG+ + +  IL+++C  P C RV + E +   +  K++        +  + ++
Sbjct: 82  LAKPVIHIGFAKDIYRILKAVC--PHCGRVAINEVRVKEYLEKMKKLEEDGGDKWEICEE 139

Query: 213 ILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNP 272
           IL    K +VCPHCGEI           I +EK      + D   E LL           
Sbjct: 140 ILRDAAKANVCPHCGEIK--------YDIKYEK-PTTYYQIDGKTEKLLT---------- 180

Query: 273 EIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRP 332
                          P +V ++ E IP ED  LL +N E+ +P  ++LT L +PP  +RP
Sbjct: 181 ---------------PSDVREILEKIPDEDCVLLGLNPEVMRPEWMVLTVLPIPPVTVRP 225

Query: 333 SVI--SDLKSDNDV 344
           S+   S  +S++D+
Sbjct: 226 SITLESGERSEDDL 239



 Score = 89.0 bits (219), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 37/57 (64%), Positives = 48/57 (84%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFV++S+  GL+P E+FFH MGGREGLVD AV+TA++GYMQRRLV +L+DL  +YD
Sbjct: 788 HGFVRSSYKKGLSPIEYFFHAMGGREGLVDQAVRTAQSGYMQRRLVNALQDLKAEYD 844


>gi|320586791|gb|EFW99454.1| DNA-directed RNA polymerase 2 largest subunit [Grosmannia clavigera
           kw1407]
          Length = 1745

 Score =  168 bits (425), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 97/282 (34%), Positives = 147/282 (52%), Gaps = 51/282 (18%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D ++FNRQPSLHK S+M HR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQTEE 
Sbjct: 452 DGDFIIFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQTEET 511

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE               K L     N+V+P+    L+   QD + G Y L +++ F ++
Sbjct: 512 RAE--------------VKELCMVPLNIVSPQRNGPLMGIVQDTLAGAYKLCRRDVFLSK 557

Query: 461 AQTMRIASTLIADTSDICGIIKRFSW-RSWNPVVFVRTAVI-----WTGKQIFSLILKPN 514
            Q M I                   W   WN V+  R A++     WTGKQI SL++   
Sbjct: 558 EQVMNI-----------------MLWVPEWNGVI-PRPAILKPRPRWTGKQIMSLVI--- 596

Query: 515 RDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLR 574
              P   NL+        N++   +D  ++++  EL+ G   K ++G+ G   + +I   
Sbjct: 597 ---PKTINLR------MGNDDTALKDDGLLIQTGELMYGLPTKKSVGASG-GGIIHICFN 646

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           + G D A+  +    R+ +++L++ G SIGIGD  P +  ++
Sbjct: 647 ELGSDGAMAFLNGCQRVVNYWLLHNGHSIGIGDTIPDKATIE 688



 Score =  107 bits (266), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 61/185 (32%), Positives = 99/185 (53%), Gaps = 15/185 (8%)

Query: 1225 QLLPSVVIKGVQGINRAVIHEE---------------DVEGVTKYKLLVEGDNLRDVMAT 1269
             LL ++ ++GV GI RA ++++               D    T + L  EG  LR V+A 
Sbjct: 1288 HLLDTLTLRGVPGIERAFLNKDTVLIKTKDDALLAAKDDPACTAWYLDTEGSALRAVLAV 1347

Query: 1270 YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 1329
             GV   +  +N+ ++V    GIEAARST++ E+  V+   G  ++ RH  L+ D+MT +G
Sbjct: 1348 DGVDPKRTYTNDLHQVVDVFGIEAARSTLLRELTAVLSFDGSYVNHRHLALLVDVMTYRG 1407

Query: 1330 EVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
             +  +TRHG+ +     L   SFE T + L +AA  G+ D   G+SE +++G    +GTG
Sbjct: 1408 SIAAVTRHGINRADTGALMRCSFEETVEILLEAAAVGELDDCRGISENVMLGQLAPMGTG 1467

Query: 1390 LIKLL 1394
              ++L
Sbjct: 1468 HFEVL 1472



 Score =  102 bits (253), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+  
Sbjct: 802 DYSPEARGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDVSA 861

Query: 666 QYD 668
           +YD
Sbjct: 862 KYD 864



 Score = 85.9 bits (211), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 80/300 (26%), Positives = 133/300 (44%), Gaps = 75/300 (25%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTD-----LDYARIVKGRLERTTLGEVCEYIEEV 818
            GVPR+KEI+N + NI TP +  YLD D D      D A+ ++  +E T L  V    E  
Sbjct: 1117 GVPRLKEILNVASNIKTPSMAVYLD-DADERPPTQDRAKELRSIVEHTNLRSVTAVTEIY 1175

Query: 819  FVPD-------------DSFILIKLDMDRIRLLHLEVDIDS---IRYCIERTRGISGHLT 862
            + PD             +S+ LI  D      +   +D  S   +R  ++R + +   LT
Sbjct: 1176 YDPDLRWTNIVEDENILESYFLIPED------VATNLDQQSRWMLRITLDRQKLLDKGLT 1229

Query: 863  VSGHSFLILK--PKD-----SSKSFNSKMYQMK-------------------------QL 890
            +   +  I +  P D     S  + +S++ +++                          L
Sbjct: 1230 IEDVANRIKEEYPTDLGVIFSDNNADSQVIRVRTVRQDDEKDEDGALEDDVMLKRLETHL 1289

Query: 891  LPSVVIKGVQGINRAVIHEE---------------DVEGVTKYKLLVEGDNLRDVMATYG 935
            L ++ ++GV GI RA ++++               D    T + L  EG  LR V+A  G
Sbjct: 1290 LDTLTLRGVPGIERAFLNKDTVLIKTKDDALLAAKDDPACTAWYLDTEGSALRAVLAVDG 1349

Query: 936  VKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            V   +  +N+ ++V    GIEAARST++ E+  V+   G  ++ RH  L+ D+MT +G +
Sbjct: 1350 VDPKRTYTNDLHQVVDVFGIEAARSTLLRELTAVLSFDGSYVNHRHLALLVDVMTYRGSI 1409



 Score = 65.1 bits (157), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 43/156 (27%), Positives = 68/156 (43%), Gaps = 36/156 (23%)

Query: 115 PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSIC 174
           P   G+ D  +G+  ++  C TC +N+S+C GHFG+I+L  PV+H G+ +    +L+ +C
Sbjct: 50  PRDGGVNDPLLGSVDRQFKCKTCTENMSECPGHFGHIELAKPVYHPGFIKKTKKVLEIVC 109

Query: 175 KNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKSLKKKILETTKKVSVC---------- 223
            N  C+ VL          A   R+P       K+  +++ E  KK   C          
Sbjct: 110 HN--CSMVLADRSDPEFVAAVNTRDP-------KARFQRVWECCKKKRRCENEAKAEEEE 160

Query: 224 ------------PH----CGEINGVVKKCGLLKISH 243
                       PH    CG +   V++ GL   SH
Sbjct: 161 FDPNPSKIAKQQPHNHGGCGNMQPAVRQTGLQLWSH 196



 Score = 58.9 bits (141), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/37 (67%), Positives = 28/37 (75%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            ++ RA + P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1072 RWARAMVNPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1108


>gi|121701053|ref|XP_001268791.1| DNA-dependent RNA polymerase II largest subunit, putative
           [Aspergillus clavatus NRRL 1]
 gi|119396934|gb|EAW07365.1| DNA-dependent RNA polymerase II largest subunit, putative
           [Aspergillus clavatus NRRL 1]
          Length = 1765

 Score =  168 bits (425), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 98/272 (36%), Positives = 149/272 (54%), Gaps = 35/272 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DV+LFNRQPSLHK S+MAHR +V+P+ TFR N  V TPYNADFDGDEMN+H+PQ+EE+
Sbjct: 455 DGDVILFNRQPSLHKESMMAHRVRVMPYSTFRMNLSVTTPYNADFDGDEMNLHVPQSEES 514

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L +L+++            N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 515 RAE----LSQLALVPM----------NIVSPQRNGPLMGIVQDTLCGIYKICRRDIFLTK 560

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M I    +    D  G+I         P   ++    WTGKQ+ S+ L      P  
Sbjct: 561 EQVMNI----MLWVPDWDGVIP--------PPAILKPRPRWTGKQMISMAL------PSG 602

Query: 521 AN-LKTKGRAYTANEEFCH-RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            N L+ +    +  E+F    D  V++   +L+ G + K T+G+ G   V + +  ++G 
Sbjct: 603 LNLLRVEKDNSSLAEKFSPLTDGGVLIHGGQLMYGMLSKKTVGASG-GGVIHTIFNEYGP 661

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           + AV        + +++L++ GFSIGIGD  P
Sbjct: 662 ETAVAFFNGAQTIVNYWLLHNGFSIGIGDTIP 693



 Score =  105 bits (263), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 62/185 (33%), Positives = 98/185 (52%), Gaps = 15/185 (8%)

Query: 1224 KQLLPSVVIKGVQGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMA 1268
            + LL ++ ++GVQG+ RA I+E+    V                ++ L   G +L +V+A
Sbjct: 1288 QHLLDTLTLRGVQGVERAFINEKSKVRVLEDGSLFASKTDPLCKEWVLETSGSSLGEVLA 1347

Query: 1269 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK 1328
              GV   +  SN   EV++  GIEAAR+ ++ E+  V+   G  ++ RH  L+ D+MT +
Sbjct: 1348 VPGVDASRTYSNQFIEVFEVFGIEAARTAVLRELTQVLAFDGSYVNHRHLALLVDVMTVR 1407

Query: 1329 GEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGT 1388
            G +  +TRHG+ +     L   SFE T + L +AA +G+ D   GVSE +I+G     GT
Sbjct: 1408 GYLTPVTRHGINRADNGALMRCSFEETVEILLEAAAFGELDDCRGVSENLILGQMAPAGT 1467

Query: 1389 GLIKL 1393
            G   L
Sbjct: 1468 GEFDL 1472



 Score = 99.4 bits (246), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QR+LVK+LE++ V
Sbjct: 813 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMV 872

Query: 666 QYD 668
           +YD
Sbjct: 873 KYD 875



 Score = 90.5 bits (223), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 79/290 (27%), Positives = 132/290 (45%), Gaps = 60/290 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYL--DKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N + NI TP +T Y    K  D + A+ ++  +E T+L  V E  E  + P
Sbjct: 1119 GVPRLKEILNVATNIKTPSMTVYQMPSKCHDKESAKQLRSAVEHTSLRSVTEATEIYYDP 1178

Query: 822  DDSFILIKLDMDRIRLLHL----EVDIDS------IRYCIERTRGISGHLTVSGHSFLIL 871
            D    +I+ D D +    +      D  S      +R  + R + +   LTV   +  I 
Sbjct: 1179 DIQTTVIENDRDMVESYFIIPEDVTDASSRQSKWLLRIILSRPKLLDKGLTVQDVAARIK 1238

Query: 872  K--PKD-----SSKSFNSKMYQMKQ--------------------------LLPSVVIKG 898
            +  PKD     S  + + ++ +++Q                          LL ++ ++G
Sbjct: 1239 QAYPKDIAVIFSDNNADEQVIRIRQIQDYKEDEEHDDDIEYDVTLKKLEQHLLDTLTLRG 1298

Query: 899  VQGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMATYGVKGVKCSS 943
            VQG+ RA I+E+    V                ++ L   G +L +V+A  GV   +  S
Sbjct: 1299 VQGVERAFINEKSKVRVLEDGSLFASKTDPLCKEWVLETSGSSLGEVLAVPGVDASRTYS 1358

Query: 944  NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
            N   EV++  GIEAAR+ ++ E+  V+   G  ++ RH  L+ D+MT +G
Sbjct: 1359 NQFIEVFEVFGIEAARTAVLRELTQVLAFDGSYVNHRHLALLVDVMTVRG 1408



 Score = 80.5 bits (197), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 59/230 (25%), Positives = 101/230 (43%), Gaps = 40/230 (17%)

Query: 110 DPQRT-PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVIN 168
           D QR  P   GL D R+GT  ++ NC TC +   +C GHFG+I+L  PVFHIG+   V  
Sbjct: 44  DEQRMRPRTKGLNDPRLGTIDRQWNCETCEEGQKECPGHFGHIELATPVFHIGFLTKVKK 103

Query: 169 ILQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKSLKKKIL------------- 214
           +L+++C N    +    +  +    A ++R+P   +     L K +L             
Sbjct: 104 LLETVCHNCGKIKADTNQSDSKFLEALRMRDPKRRFDHIWRLSKDVLICEADPPADEDEP 163

Query: 215 ---ETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFN 271
              E++K V     CG     ++K G+  +   K       K  + ED + +  + V   
Sbjct: 164 FSKESSKPVRRHGGCGNAQPTIRKEGITLVGTWK-----PNKSMMDEDDMQQPEKKV--- 215

Query: 272 PEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
                         + PL  L +F  I  ED+ ++ ++ + ++P  +I+T
Sbjct: 216 --------------ITPLMALNVFRTISQEDVRIMGLSNDYARPEWMIIT 251



 Score = 56.6 bits (135), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/41 (60%), Positives = 28/41 (68%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            A   ++ +A   P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1070 AIESRFAKAAASPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1110


>gi|359417552|ref|ZP_09209681.1| DNA-directed RNA polymerase subunit A', partial [Candidatus
           Haloredivivus sp. G17]
 gi|358032104|gb|EHK00879.1| DNA-directed RNA polymerase subunit A' [Candidatus Haloredivivus
           sp. G17]
          Length = 515

 Score =  168 bits (425), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 94/269 (34%), Positives = 141/269 (52%), Gaps = 49/269 (18%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D D VLFNRQPSLH++SIMAH  KVLP+RTFR N  VC PYNADFDGDEMN+H+PQTEE
Sbjct: 76  TDGDTVLFNRQPSLHRMSIMAHEVKVLPYRTFRLNLNVCAPYNADFDGDEMNLHVPQTEE 135

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           ARAE              A  LM  + ++ +P+ G  ++   QD+++G YLLTQ++   +
Sbjct: 136 ARAE--------------ADELMKVQEHIKSPKMGGPIVGMLQDYVSGLYLLTQEDKELD 181

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           R Q   + +     T D+    K                   +G+++ S+ +  +    +
Sbjct: 182 REQAFNLLAEAGEHTKDLPDGEK------------------VSGRELVSIFIPDDISLTI 223

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           N                   D  V++ + EL+ G +D+  LG  G   +   L  ++G D
Sbjct: 224 NEG----------------EDDEVVIEDGELVKGVLDEDALGDYG-GEIIQQLDIEYGSD 266

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           +    + R+SR+ + +L  RGFSIG+ D+
Sbjct: 267 MVAEFLNRVSRVGAIFLTKRGFSIGLEDL 295



 Score = 62.8 bits (151), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/66 (42%), Positives = 42/66 (63%), Gaps = 1/66 (1%)

Query: 606 GDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           G+++P  +GFV +S   GL   E FFH M  R+ L D ++ T  +GYM RR+  +L+DL 
Sbjct: 416 GEMSPKSKGFVSSSILEGLDAQEMFFHQMAQRKALADKSLNTKTSGYMYRRISNTLQDLR 475

Query: 665 VQYDMS 670
           V+YD +
Sbjct: 476 VEYDQT 481


>gi|448347129|ref|ZP_21536008.1| DNA-directed RNA polymerase subunit A'' [Natrinema altunense JCM
            12890]
 gi|445631466|gb|ELY84698.1| DNA-directed RNA polymerase subunit A'' [Natrinema altunense JCM
            12890]
          Length = 398

 Score =  167 bits (424), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 109/341 (31%), Positives = 178/341 (52%), Gaps = 53/341 (15%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A+A   +Y+  ++EP   VG ++AQSIGEPGTQ+T+ TFH+AG            + E +
Sbjct: 48   AKAVETRYLDTRVEPLDPVGTVSAQSIGEPGTQLTMNTFHYAGVAEIDVTQGLPRLIELV 107

Query: 1152 EEVFVPDDSFILIKLD----------------MDRIRLLHL---EVDIDSIRYCI----- 1187
            +    PD   + + L+                ++  ++L L     ++  +R  I     
Sbjct: 108  DARKTPDTPMMTVYLEDEYATEREKAHEVVWNIEATQILALGDVSTNVADMRVQISLNED 167

Query: 1188 ---------ERTRGIS----GHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKG 1234
                     E   GI     G  TV   + +   P++ S      + Q+ + L  +  KG
Sbjct: 168  TLQERLITAEEVAGIIEDSLGVKTVQQGTQIEFGPEEPSYR---DLLQLVEELRDITFKG 224

Query: 1235 VQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEA 1293
            ++ ++R VI  E++E G  ++ L  EG    DV+   GV   + + NN +E+++ LGIEA
Sbjct: 225  IEEVSRVVIRREELETGTEEFVLYTEGSAFGDVLEIEGVDASRTTCNNIHEIHRNLGIEA 284

Query: 1294 ARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASF 1352
            AR  I+ E    +   G+  ++ RH MLVAD+MT++GE+  I RHG++  KESVL  A+F
Sbjct: 285  AREAIIEETNNTLAEQGLDDVNVRHLMLVADMMTNRGEIESIGRHGISGSKESVLARAAF 344

Query: 1353 ENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            E T +HL +AA +G+ D + GV+E +I+G P+ +GTG + L
Sbjct: 345  EVTVNHLLNAAIHGEVDELDGVTENVIVGKPIKLGTGDVDL 385



 Score = 99.4 bits (246), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 72/239 (30%), Positives = 127/239 (53%), Gaps = 21/239 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T YL+ +  T+ + A  V   +E T    LG+V   + ++
Sbjct: 99  GLPRLIELVDARKTPDTPMMTVYLEDEYATEREKAHEVVWNIEATQILALGDVSTNVADM 158

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSK 878
            V     I +  D  + RL+  E     +   IE + G+    TV   + +   P++ S 
Sbjct: 159 RVQ----ISLNEDTLQERLITAE----EVAGIIEDSLGVK---TVQQGTQIEFGPEEPSY 207

Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVK 937
                + Q+ + L  +  KG++ ++R VI  E++E G  ++ L  EG    DV+   GV 
Sbjct: 208 R---DLLQLVEELRDITFKGIEEVSRVVIRREELETGTEEFVLYTEGSAFGDVLEIEGVD 264

Query: 938 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEV 995
             + + NN +E+++ LGIEAAR  I+ E    +   G+  ++ RH MLVAD+MT++GE+
Sbjct: 265 ASRTTCNNIHEIHRNLGIEAAREAIIEETNNTLAEQGLDDVNVRHLMLVADMMTNRGEI 323


>gi|242398381|ref|YP_002993805.1| DNA-directed RNA polymerase subunit A'' [Thermococcus sibiricus MM
            739]
 gi|242264774|gb|ACS89456.1| DNA-directed RNA polymerase subunit A'' [Thermococcus sibiricus MM
            739]
          Length = 397

 Score =  167 bits (424), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 115/343 (33%), Positives = 172/343 (50%), Gaps = 60/343 (17%)

Query: 1108 EKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFV 1156
            ++Y +A +EP  AVG + AQSIGEP TQMTL TFH+AG            + E ++    
Sbjct: 55   QEYEQALVEPGEAVGTVTAQSIGEPSTQMTLNTFHYAGVAEINVTLGLPRIIEIVDARKN 114

Query: 1157 PDDSFILIKLDMD-------------RIR--------------LLHLE--VDID------ 1181
            P    + + LD +             RI               +L++E  VDID      
Sbjct: 115  PSTPIMTVHLDEEHRYNSEKALEVAKRIEGTTLESLARSMTLDILNMEFVVDIDPERLEK 174

Query: 1182 ------SIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGV 1235
                   I+  IER+   S  +   G + +I   K  + S    + ++   +    +KG+
Sbjct: 175  SGLTMEKIQAKIERSFK-SAEIETEGTTIIIRLKKAKNVS---TLRRLADKVKKHRLKGL 230

Query: 1236 QGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAAR 1295
             G+ + VI +E  E    Y +  EG N + V+   GV   +  +NN +E+ + LGIEAAR
Sbjct: 231  SGVGKTVIRKEGDE----YVIYTEGSNFKQVLKVPGVDPTRTKTNNIHEIAQVLGIEAAR 286

Query: 1296 STIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENT 1355
            + I+ EI   M+  G+ +D RH MLVAD+MT  G V  I RHG+   K SVL  A+FE T
Sbjct: 287  NAIIEEIVNTMQEQGLEVDVRHIMLVADMMTIDGVVRPIGRHGIVGTKASVLARAAFEIT 346

Query: 1356 SDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 1398
              HL  AA  G+ D ++GV E +++G P+ VGTG+++L   +P
Sbjct: 347  VQHLLQAAERGELDPLNGVVENVLIGQPVPVGTGIVRLAMKLP 389



 Score =  107 bits (266), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 77/234 (32%), Positives = 128/234 (54%), Gaps = 14/234 (5%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PRI EI++A +N STPI+T +LD++   + + A  V  R+E TTL  +   +  + + 
Sbjct: 101 GLPRIIEIVDARKNPSTPIMTVHLDEEHRYNSEKALEVAKRIEGTTLESLARSMT-LDIL 159

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
           +  F++   D+D  RL    + ++ I+  IER+   S  +   G + +I   K  + S  
Sbjct: 160 NMEFVV---DIDPERLEKSGLTMEKIQAKIERSFK-SAEIETEGTTIIIRLKKAKNVS-- 213

Query: 882 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
             + ++   +    +KG+ G+ + VI +E  E    Y +  EG N + V+   GV   + 
Sbjct: 214 -TLRRLADKVKKHRLKGLSGVGKTVIRKEGDE----YVIYTEGSNFKQVLKVPGVDPTRT 268

Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            +NN +E+ + LGIEAAR+ I+ EI   M+  G+ +D RH MLVAD+MT  G V
Sbjct: 269 KTNNIHEIAQVLGIEAARNAIIEEIVNTMQEQGLEVDVRHIMLVADMMTIDGVV 322


>gi|257076604|ref|ZP_05570965.1| DNA-directed RNA polymerase subunit A'' [Ferroplasma acidarmanus
            fer1]
          Length = 504

 Score =  167 bits (424), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 115/334 (34%), Positives = 171/334 (51%), Gaps = 58/334 (17%)

Query: 1112 RAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEV-----------CEYIEEVFVPDDS 1160
            + +I+P  AVG +AAQSIGEPGTQMT++TFHFAG V            E ++   +P   
Sbjct: 172  KREIDPFEAVGIIAAQSIGEPGTQMTMRTFHFAGVVEMNVTLGLPRLIEIVDARRIPSTP 231

Query: 1161 FILIKL------DMDRIRLL--HLE--------------------------------VDI 1180
             + I L      D +++R L  +LE                                V I
Sbjct: 232  SMTIYLTEKYRKDENKVRELIKNLENTTIIDVAEIVTDVGNMELTIRMDSNKSRDRLVSI 291

Query: 1181 DSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINR 1240
              I   +E+ +GI     V   +  I   ++S KS    +YQ+++ L S  IKGV  I+R
Sbjct: 292  GDILSALEKRKGII-FAQVDDSNISIKLQQESFKS----LYQVQEQLKSTPIKGVNKISR 346

Query: 1241 AVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMT 1300
            A+   +  E    + +  +G NLR+V+   GV   + ++N+  E+    GIEAAR+ I  
Sbjct: 347  AIARIDPKEDA--WVIYTQGSNLREVLNIEGVDSNRTTTNDIIEIENVFGIEAARNAIYR 404

Query: 1301 EIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLF 1360
            E +  +   G+++D RH MLVAD+MT  G V  + R G++  K SVL  A+FE TS HL 
Sbjct: 405  EAENTLSEQGLNVDKRHLMLVADMMTFSGAVRAVGRQGISGRKSSVLARAAFEITSKHLL 464

Query: 1361 DAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
             A   G+ D ++GV+E II+G P+ +GTG I L+
Sbjct: 465  KAGLLGEIDPLAGVAENIIVGQPITLGTGAIDLV 498



 Score =  103 bits (257), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 79/238 (33%), Positives = 127/238 (53%), Gaps = 14/238 (5%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A R  STP +T YL +    D +  R +   LE TT+ +V E + +V   
Sbjct: 214 GLPRLIEIVDARRIPSTPSMTIYLTEKYRKDENKVRELIKNLENTTIIDVAEIVTDV--- 270

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
            +  + I++D ++ R     V I  I   +E+ +GI     V   +  I   ++S KS  
Sbjct: 271 GNMELTIRMDSNKSR--DRLVSIGDILSALEKRKGII-FAQVDDSNISIKLQQESFKS-- 325

Query: 882 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
             +YQ+++ L S  IKGV  I+RA+   +  E    + +  +G NLR+V+   GV   + 
Sbjct: 326 --LYQVQEQLKSTPIKGVNKISRAIARIDPKEDA--WVIYTQGSNLREVLNIEGVDSNRT 381

Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG 999
           ++N+  E+    GIEAAR+ I  E +  +   G+++D RH MLVAD+MT  G V   G
Sbjct: 382 TTNDIIEIENVFGIEAARNAIYREAENTLSEQGLNVDKRHLMLVADMMTFSGAVRAVG 439


>gi|289581818|ref|YP_003480284.1| DNA-directed RNA polymerase subunit A'' [Natrialba magadii ATCC
            43099]
 gi|289531371|gb|ADD05722.1| DNA-directed RNA polymerase, subunit A'' [Natrialba magadii ATCC
            43099]
          Length = 399

 Score =  167 bits (423), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 107/344 (31%), Positives = 175/344 (50%), Gaps = 59/344 (17%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A+A   +YV  ++EP   VG ++AQSIGEPGTQ+T+ TFH+AG            + E +
Sbjct: 48   AKAVEARYVDTRVEPLDPVGTVSAQSIGEPGTQLTMNTFHYAGVAEIDVTQGLPRLIELV 107

Query: 1152 EEVFVPDDSFILIKLD----------------------------------------MDRI 1171
            +    PD   + + L+                                        ++R 
Sbjct: 108  DARKTPDTPMMTVYLEDEYATERERAHEVVWNIEATKILALGDVSTNVADMRVQISLNRD 167

Query: 1172 RLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVV 1231
             L    +  + +   IE   G+S   TV   + +   P++ S      + Q+ + L  + 
Sbjct: 168  TLEERMITPEEVAEIIEDNLGVS---TVQQGTDIQFGPEEPSYR---DLLQLVEELREIT 221

Query: 1232 IKGVQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLG 1290
             KG++ I+R VI  E+++ G  ++ L  EG    DV+   GV   + + NN +E+++ LG
Sbjct: 222  FKGIEEISRVVIRREEMDDGDEQFVLYTEGSAFGDVLEIEGVDASRTTCNNIHEIHRNLG 281

Query: 1291 IEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNL 1349
            IEAAR  I+ E    +   G+  ++ RH MLVAD+MT++GE+  I RHG++  K+SVL  
Sbjct: 282  IEAAREAIIEETNNTLAEQGLDDVNVRHLMLVADMMTNRGEIESIGRHGISGSKDSVLAR 341

Query: 1350 ASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            A+FE T +HL +AA +G+ D + GV+E +I+G P+ +GTG + L
Sbjct: 342  AAFEVTVNHLLNAAIHGEIDELDGVTENVIVGKPIKLGTGDVDL 385



 Score =  100 bits (250), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 70/239 (29%), Positives = 127/239 (53%), Gaps = 21/239 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T YL+ +  T+ + A  V   +E T    LG+V   + ++
Sbjct: 99  GLPRLIELVDARKTPDTPMMTVYLEDEYATERERAHEVVWNIEATKILALGDVSTNVADM 158

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSK 878
            V        ++ ++R  L    +  + +   IE   G+S   TV   + +   P++ S 
Sbjct: 159 RV--------QISLNRDTLEERMITPEEVAEIIEDNLGVS---TVQQGTDIQFGPEEPSY 207

Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVK 937
                + Q+ + L  +  KG++ I+R VI  E+++ G  ++ L  EG    DV+   GV 
Sbjct: 208 R---DLLQLVEELREITFKGIEEISRVVIRREEMDDGDEQFVLYTEGSAFGDVLEIEGVD 264

Query: 938 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEV 995
             + + NN +E+++ LGIEAAR  I+ E    +   G+  ++ RH MLVAD+MT++GE+
Sbjct: 265 ASRTTCNNIHEIHRNLGIEAAREAIIEETNNTLAEQGLDDVNVRHLMLVADMMTNRGEI 323


>gi|18312086|ref|NP_558753.1| DNA-directed RNA polymerase subunit A' [Pyrobaculum aerophilum str.
           IM2]
 gi|18159516|gb|AAL62935.1| DNA-directed RNA polymerase subunit A' (rpoA1) [Pyrobaculum
           aerophilum str. IM2]
          Length = 884

 Score =  167 bits (423), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 101/269 (37%), Positives = 147/269 (54%), Gaps = 33/269 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++S+M H  KVLP RTFR +  VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 423 DGDIVLFNRQPSLHRVSMMGHLVKVLPGRTFRLHLAVCPPYNADFDGDEMNLHVPQTEEA 482

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+ LM  + +++TPR G  +I A QD+I G YLL+ K+ F  +
Sbjct: 483 RAE--------------ARALMLVEKHIITPRYGGAIIGARQDYIIGAYLLSHKSTFLTK 528

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +   +A  L A  S                   +    +WTGKQI S  L  + +    
Sbjct: 529 KE---VAFLLGAGKSQ----------EDPPEPAILHPVELWTGKQIISHFLPKDLNWVQP 575

Query: 521 ANLKTKGR-AYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
              K+K + AYT     C  D ++I+ N  L+ G +DK ++G+    ++++ + RD+  +
Sbjct: 576 TAFKSKCQNAYT-----CPTDEWIIVINGNLVKGVLDKKSIGAEQVDSLWHRIARDYSPE 630

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           VA   +    R+   +L  RGF+ G+  +
Sbjct: 631 VARRWLDSSLRLFLRFLDLRGFTFGMDSI 659



 Score =  113 bits (283), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 72/265 (27%), Positives = 131/265 (49%), Gaps = 40/265 (15%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           I+  V   + +++ S +++ +  +Y  D    P+  G+ DRR+G  +  + C TCGQ   
Sbjct: 18  IKFGVLSPEMIRKYSVMEVTTSEVY--DEGGLPVRGGIADRRLGVAEPGSRCETCGQTHD 75

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN-PAL 201
            C GHFG+I+L  PV H+G+ R + ++L++ C  P C R++L +E+   +R +L    A 
Sbjct: 76  VCPGHFGHIELVKPVIHVGFARIIYDVLRATC--PNCGRIMLRDEEIERYRERLNKLKAR 133

Query: 202 SYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLL 261
             L+  +L +KI +   +   CPHCG               +++ K R ++     E+  
Sbjct: 134 WRLLALNLHEKIRKKATERMTCPHCG---------------YKRNKVRFERPYYFYEE-- 176

Query: 262 AEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
                            K G +  L+P  + +    +P ED+ LL +N  +++P   IL 
Sbjct: 177 ----------------TKSGALVKLDPEVLRERLSKVPSEDLELLGINPSVARPEWAILK 220

Query: 322 RLLVPPNCIRPSVI--SDLKSDNDV 344
            L VPP  +RPS+   + ++S++D+
Sbjct: 221 VLPVPPPHVRPSIQLETGIRSEDDL 245



 Score = 86.3 bits (212), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 37/65 (56%), Positives = 50/65 (76%), Gaps = 1/65 (1%)

Query: 605 IGDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDL 663
           +GD+     GFV+N F  GLTP E+FFH   GR+GL+DTAV+TA++GYMQRRL+ +L+D+
Sbjct: 779 VGDIGAFSGGFVRNCFRCGLTPVEYFFHAAAGRDGLIDTAVRTAQSGYMQRRLINALQDV 838

Query: 664 CVQYD 668
            V YD
Sbjct: 839 YVAYD 843



 Score = 43.9 bits (102), Expect = 0.60,   Method: Compositional matrix adjust.
 Identities = 21/56 (37%), Positives = 34/56 (60%), Gaps = 3/56 (5%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAGR 75
           + LM  + +++TPR G  +I A QD+I G YLL+ K+ F  + +   +A  L AG+
Sbjct: 487 RALMLVEKHIITPRYGGAIIGARQDYIIGAYLLSHKSTFLTKKE---VAFLLGAGK 539


>gi|48477330|ref|YP_023036.1| DNA-directed RNA polymerase subunit A' [Picrophilus torridus DSM
           9790]
 gi|48429978|gb|AAT42843.1| DNA-directed RNA polymerase subunit A' [Picrophilus torridus DSM
           9790]
          Length = 886

 Score =  167 bits (423), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 100/273 (36%), Positives = 147/273 (53%), Gaps = 40/273 (14%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           ++ D+VLFNRQPSLH++S+MAH  ++LP  TFRFN  VCTPYNADFDGDEMN+H+ Q+EE
Sbjct: 419 NEGDIVLFNRQPSLHRMSMMAHTVRILPGLTFRFNLAVCTPYNADFDGDEMNLHVVQSEE 478

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           ARAE              A+++M  +  +++PR G  +I A  D IT  +LLT  N  F 
Sbjct: 479 ARAE--------------ARIIMKVQEQIMSPRFGGPIIGAIHDHITALFLLTHNNPLFT 524

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
             +T+ + S +     DI         R   PV+ +     + G+ IFSL L P      
Sbjct: 525 EEETLHMTSYM-----DIS--------RMPEPVI-IDGKRYYHGRDIFSLTLPP------ 564

Query: 520 NANLKTKGRAYTANEEFCH-----RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLR 574
             N+K K    +  ++ C       D YV++R+ +L+ G++D   +G      V  I  R
Sbjct: 565 GLNVKFKSHLCSGAKDKCEYENDPNDIYVVIRDGKLIHGTIDDEAVGPFSGVIVDKI-FR 623

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            +G D A   +  ++R+   ++  RGFS GI D
Sbjct: 624 KYGPDAAARFLDNVTRLAIGFISYRGFSTGIRD 656



 Score =  102 bits (255), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 63/250 (25%), Positives = 116/250 (46%), Gaps = 51/250 (20%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D +++ S +++++ + Y  D    PI  GL+D  MG  +    C TCG  + +C GHFG+
Sbjct: 21  DEIRKMSQVKVITPDTY--DDDGYPIDKGLMDLHMGVIEPGLRCATCGGKVDECPGHFGH 78

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           I+L +PV H+G+ + +  +L S CK   C R+ L +E+   ++  + +  L++ VR   +
Sbjct: 79  IELAMPVVHVGFVKEIKTMLDSSCK--VCGRIKLTDEEIENYKKSIED--LNF-VRDDPE 133

Query: 211 ------KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEY 264
                 +KI +      +CPHCG                      ++    I++      
Sbjct: 134 IIDIKLRKITDLASSREICPHCG----------------------SESPKTIIDKPTTFR 171

Query: 265 NEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLL 324
             ++K  P+                E+ +  E IP +D+    +N + ++P  ++LT L 
Sbjct: 172 EGSIKITPK----------------EIRERLERIPDDDLIFYGLNKDSARPEWMVLTVLP 215

Query: 325 VPPNCIRPSV 334
           VPP  +RPS+
Sbjct: 216 VPPINVRPSI 225



 Score = 85.5 bits (210), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 41/82 (50%), Positives = 56/82 (68%), Gaps = 13/82 (15%)

Query: 597 MNRGFSIGIGDVTP----------GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKT 646
           +NRG+S   G   P           +GFV++S+ SGL+PTE+FFH++GGREGLVD AV+T
Sbjct: 763 LNRGYS---GRTLPHFKENDLGAYARGFVKSSYRSGLSPTEYFFHSIGGREGLVDIAVRT 819

Query: 647 AETGYMQRRLVKSLEDLCVQYD 668
           + +GYMQRRL+ + EDL    D
Sbjct: 820 SRSGYMQRRLINAFEDLKADED 841


>gi|13542011|ref|NP_111699.1| DNA-directed RNA polymerase subunit A'' [Thermoplasma volcanium GSS1]
          Length = 513

 Score =  167 bits (423), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 109/331 (32%), Positives = 174/331 (52%), Gaps = 59/331 (17%)

Query: 1115 IEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFVPDDSFIL 1163
            I+P  AVG +AAQSIGEPGTQMT++TFHFAG            + E ++   +P    + 
Sbjct: 182  IDPYEAVGIIAAQSIGEPGTQMTMRTFHFAGVREMNVTLGLPRLIEIVDARRIPSTPSMT 241

Query: 1164 IKLD----------MDRIRLLH---------LEVDI---------------------DSI 1183
            I L           MD ++ L          +  DI                     D +
Sbjct: 242  IYLKPEFETNDEVVMDVVKRLENTSVSDVADIITDIGELTITVRPDPNKMNDRLINQDDL 301

Query: 1184 RYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVI 1243
               I + +G++  +  SG   +I+KP+   +SF  K+Y +++ + ++ IKG+ GI RA+ 
Sbjct: 302  VNAIYKVKGVT-VMEESGQ--IIVKPQ--QESFK-KLYLLQEQIKALPIKGISGIKRAIA 355

Query: 1244 HEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIK 1303
              E  E   ++ +  +G NL+DV+    V   +  +N+  E+   LGIEAAR+ I+ E +
Sbjct: 356  RVEGKE--HRWVIYTQGSNLKDVLEVDEVDPTRTYTNDIVEIATVLGIEAARNAILNEAQ 413

Query: 1304 LVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAA 1363
              ++  G+++D RH MLVAD+MT  G V  + R G++  K SVL  A+FE T+ HL  A 
Sbjct: 414  RTLQEQGLNVDVRHLMLVADMMTFSGSVRAVGRTGISGRKSSVLARAAFEITTKHLLRAG 473

Query: 1364 FYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
              G+ D ++GV+E II+G P+ +GTG + ++
Sbjct: 474  IMGEVDKLAGVAENIIVGQPITLGTGAVDII 504



 Score =  107 bits (267), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 77/240 (32%), Positives = 138/240 (57%), Gaps = 19/240 (7%)

Query: 764 GVPRIKEIINASRNISTPIITAYL--DKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A R  STP +T YL  + +T+ +    V  RLE T++ +V + I ++   
Sbjct: 221 GLPRLIEIVDARRIPSTPSMTIYLKPEFETNDEVVMDVVKRLENTSVSDVADIITDI--- 277

Query: 822 DDSFILIKLDMDRI--RLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKS 879
            +  I ++ D +++  RL++     D +   I + +G++  +  SG   +I+KP+   +S
Sbjct: 278 GELTITVRPDPNKMNDRLINQ----DDLVNAIYKVKGVT-VMEESGQ--IIVKPQ--QES 328

Query: 880 FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
           F  K+Y +++ + ++ IKG+ GI RA+   E  E   ++ +  +G NL+DV+    V   
Sbjct: 329 FK-KLYLLQEQIKALPIKGISGIKRAIARVEGKE--HRWVIYTQGSNLKDVLEVDEVDPT 385

Query: 940 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG 999
           +  +N+  E+   LGIEAAR+ I+ E +  ++  G+++D RH MLVAD+MT  G V   G
Sbjct: 386 RTYTNDIVEIATVLGIEAARNAILNEAQRTLQEQGLNVDVRHLMLVADMMTFSGSVRAVG 445


>gi|548826|sp|Q03586.1|RPOA2_THEAC RecName: Full=DNA-directed RNA polymerase subunit A''
 gi|48093|emb|CAA48282.1| DNA-directed RNA polymerase [Thermoplasma acidophilum]
          Length = 508

 Score =  167 bits (423), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 108/331 (32%), Positives = 172/331 (51%), Gaps = 59/331 (17%)

Query: 1115 IEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFVPDDSFIL 1163
            I+P  AVG +AAQSIGEPGTQMT++TFHFAG            + E ++   +P    + 
Sbjct: 177  IDPYEAVGIIAAQSIGEPGTQMTMRTFHFAGVREMNVTLGLPRLIEIVDARRIPSTPSMT 236

Query: 1164 IKLD----------MDRIRLLHLE------------------------------VDIDSI 1183
            I L           MD ++ L                                 ++++ I
Sbjct: 237  IYLRPEYETNDEVVMDVVKRLENTSISDVADIITDIGELTVTVRPDPRKTKDRLIEMEDI 296

Query: 1184 RYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVI 1243
               I + +GI+  +  SG   +I+KP+   +SF  K+Y +++ +  + IKG+ GI RA+ 
Sbjct: 297  MNAISKIKGIT-VMEDSGQ--IIIKPQ--QESFK-KLYLLQEQIKGLTIKGISGIKRAIA 350

Query: 1244 HEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIK 1303
              E  E   ++ +  +G NL+DV+    V   +  +N+  E+   LGIEAAR+ I+ E  
Sbjct: 351  RVEGKE--HRWVIYTQGSNLKDVLEVDEVDPTRTYTNDIVEIANVLGIEAARNAILNEAL 408

Query: 1304 LVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAA 1363
              ++  G+++D RH MLVAD+MT  G V  + R G++  K SVL  A+FE T+ HL  A 
Sbjct: 409  RTLQEQGLNVDVRHLMLVADMMTFSGSVRAVGRTGISGRKSSVLARAAFEITTKHLLRAG 468

Query: 1364 FYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
              G+ D ++GV+E II+G P+ +GTG + ++
Sbjct: 469  IMGEVDKLAGVAENIIVGQPITLGTGAVDII 499



 Score =  108 bits (269), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 78/240 (32%), Positives = 134/240 (55%), Gaps = 19/240 (7%)

Query: 764 GVPRIKEIINASRNISTPIITAYL--DKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A R  STP +T YL  + +T+ +    V  RLE T++ +V + I ++   
Sbjct: 216 GLPRLIEIVDARRIPSTPSMTIYLRPEYETNDEVVMDVVKRLENTSISDVADIITDI--- 272

Query: 822 DDSFILIKLDMDRI--RLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKS 879
            +  + ++ D  +   RL+ +E     I   I + +GI+  +  SG   +I+KP+   +S
Sbjct: 273 GELTVTVRPDPRKTKDRLIEME----DIMNAISKIKGIT-VMEDSGQ--IIIKPQ--QES 323

Query: 880 FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
           F  K+Y +++ +  + IKG+ GI RA+   E  E   ++ +  +G NL+DV+    V   
Sbjct: 324 FK-KLYLLQEQIKGLTIKGISGIKRAIARVEGKE--HRWVIYTQGSNLKDVLEVDEVDPT 380

Query: 940 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG 999
           +  +N+  E+   LGIEAAR+ I+ E    ++  G+++D RH MLVAD+MT  G V   G
Sbjct: 381 RTYTNDIVEIANVLGIEAARNAILNEALRTLQEQGLNVDVRHLMLVADMMTFSGSVRAVG 440


>gi|16081521|ref|NP_393872.1| DNA-directed RNA polymerase subunit A'' [Thermoplasma acidophilum DSM
            1728]
 gi|10639564|emb|CAC11536.1| probable DNA-directed RNA polymerase, chain A [Thermoplasma
            acidophilum]
          Length = 511

 Score =  167 bits (423), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 108/331 (32%), Positives = 172/331 (51%), Gaps = 59/331 (17%)

Query: 1115 IEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFVPDDSFIL 1163
            I+P  AVG +AAQSIGEPGTQMT++TFHFAG            + E ++   +P    + 
Sbjct: 180  IDPYEAVGIIAAQSIGEPGTQMTMRTFHFAGVREMNVTLGLPRLIEIVDARRIPSTPSMT 239

Query: 1164 IKLD----------MDRIRLLHLE------------------------------VDIDSI 1183
            I L           MD ++ L                                 ++++ I
Sbjct: 240  IYLRPEYETNDEVVMDVVKRLENTSISDVADIITDIGELTVTVRPDPRKTKDRLIEMEDI 299

Query: 1184 RYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVI 1243
               I + +GI+  +  SG   +I+KP+   +SF  K+Y +++ +  + IKG+ GI RA+ 
Sbjct: 300  MNAISKIKGIT-VMEDSGQ--IIIKPQ--QESFK-KLYLLQEQIKGLTIKGISGIKRAIA 353

Query: 1244 HEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIK 1303
              E  E   ++ +  +G NL+DV+    V   +  +N+  E+   LGIEAAR+ I+ E  
Sbjct: 354  RVEGKE--HRWVIYTQGSNLKDVLEVDEVDPTRTYTNDIVEIANVLGIEAARNAILNEAL 411

Query: 1304 LVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAA 1363
              ++  G+++D RH MLVAD+MT  G V  + R G++  K SVL  A+FE T+ HL  A 
Sbjct: 412  RTLQEQGLNVDVRHLMLVADMMTFSGSVRAVGRTGISGRKSSVLARAAFEITTKHLLRAG 471

Query: 1364 FYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
              G+ D ++GV+E II+G P+ +GTG + ++
Sbjct: 472  IMGEVDKLAGVAENIIVGQPITLGTGAVDII 502



 Score =  108 bits (269), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 78/240 (32%), Positives = 134/240 (55%), Gaps = 19/240 (7%)

Query: 764 GVPRIKEIINASRNISTPIITAYL--DKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A R  STP +T YL  + +T+ +    V  RLE T++ +V + I ++   
Sbjct: 219 GLPRLIEIVDARRIPSTPSMTIYLRPEYETNDEVVMDVVKRLENTSISDVADIITDI--- 275

Query: 822 DDSFILIKLDMDRI--RLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKS 879
            +  + ++ D  +   RL+ +E     I   I + +GI+  +  SG   +I+KP+   +S
Sbjct: 276 GELTVTVRPDPRKTKDRLIEME----DIMNAISKIKGIT-VMEDSGQ--IIIKPQ--QES 326

Query: 880 FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
           F  K+Y +++ +  + IKG+ GI RA+   E  E   ++ +  +G NL+DV+    V   
Sbjct: 327 FK-KLYLLQEQIKGLTIKGISGIKRAIARVEGKE--HRWVIYTQGSNLKDVLEVDEVDPT 383

Query: 940 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG 999
           +  +N+  E+   LGIEAAR+ I+ E    ++  G+++D RH MLVAD+MT  G V   G
Sbjct: 384 RTYTNDIVEIANVLGIEAARNAILNEALRTLQEQGLNVDVRHLMLVADMMTFSGSVRAVG 443


>gi|402469133|gb|EJW04187.1| hypothetical protein EDEG_01519 [Edhazardia aedis USNM 41457]
          Length = 1093

 Score =  167 bits (423), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 88/173 (50%), Positives = 113/173 (65%), Gaps = 28/173 (16%)

Query: 342 NDVVLFNRQPSLHKLSIMAHRAKVLPH--RTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           ND+VLFNRQPSLH++SIMAH  KV+PH  RT RFNEC CTPYNADFDGDEMN+H+PQT E
Sbjct: 633 NDIVLFNRQPSLHRISIMAH--KVMPHINRTLRFNECCCTPYNADFDGDEMNIHVPQTLE 690

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           + +E              A+ L+   SNL TPRNGE LIA TQDFITG Y+LT K  FF 
Sbjct: 691 SMSE--------------ARTLLNISSNLCTPRNGEPLIACTQDFITGMYVLTSKQRFFG 736

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILK 512
           R +   +  + + D S    ++         P V +R  V++TGKQ+F++++K
Sbjct: 737 REEVGMLVGSFLHDFSLCENVL---------PAV-LRPVVLFTGKQVFNILVK 779



 Score = 82.4 bits (202), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 74/278 (26%), Positives = 129/278 (46%), Gaps = 40/278 (14%)

Query: 86  TVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCV 145
           TV  E+++++QS ++++   +Y ++  + P+ +G LD  +G+++    C  C +  S+C 
Sbjct: 17  TVLDEEKIRKQSSVEVLYNQMYGEN--KEPLLNGPLDPHLGSSRGTDECVICKE-TSNCP 73

Query: 146 GHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKL-----RNPA 200
           GHFG+++L LPVFH G+F+ V N+LQ +CK   C  +L+   K     A        N  
Sbjct: 74  GHFGHVNLVLPVFHCGFFKHVYNVLQCVCK--CCGELLIKSRKIEKNSASKDCDGDDNDI 131

Query: 201 LS-YLVRKSLKKKILETTKKVSVCPHCGEINGV-----------------VKK------C 236
           +S Y  R   K K+      V+   +    NG                  VKK       
Sbjct: 132 ISVYNKRGGAKSKLQGANTYVNTTYNAKSDNGQGLKSKNKNSKSNIDNNNVKKDTNTSII 191

Query: 237 GLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFE 296
           G  K++  +  + ++K  + +       N ++K  P  + +     I+ +NPL    LF+
Sbjct: 192 GGRKLTMRELIDESRKVKSCL--FCLSPNISIKRGPGYKLYYDTSKIE-INPLFAYNLFK 248

Query: 297 AIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSV 334
            I   D   L +      P +L++  + VPP+ IRPSV
Sbjct: 249 LIKESDYNDLHITFN---PVNLLIKSIPVPPSIIRPSV 283



 Score = 56.6 bits (135), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 30/53 (56%), Positives = 35/53 (66%), Gaps = 1/53 (1%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQT-MRIASTL 71
           + L+   SNL TPRNGE LIA TQDFITG Y+LT K  FF R +  M + S L
Sbjct: 696 RTLLNISSNLCTPRNGEPLIACTQDFITGMYVLTSKQRFFGREEVGMLVGSFL 748


>gi|399575813|ref|ZP_10769570.1| DNA-directed RNA polymerase, subunit a' [Halogranum salarium B-1]
 gi|399238524|gb|EJN59451.1| DNA-directed RNA polymerase, subunit a' [Halogranum salarium B-1]
          Length = 422

 Score =  167 bits (422), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 108/353 (30%), Positives = 176/353 (49%), Gaps = 62/353 (17%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            AEA   +Y+  +++P   VG ++AQSIGEPGTQMT+ TFH+AG            + E +
Sbjct: 59   AEAVENRYIDTRVDPLDPVGTVSAQSIGEPGTQMTMNTFHYAGVAEIDVTQGLPRLIELV 118

Query: 1152 EEVFVPDDSFILIKL------------------------DMDRIRLLHL----------- 1176
            +    PD   + + L                        D++  ++L L           
Sbjct: 119  DARKTPDTPMMTVHLESEEQNEAGIPFATDREYAHEVVWDIEATKILALGDVSTNVADML 178

Query: 1177 -EVDIDSIRYCIERTRG-----ISGHLTVSGHSFLILKPKDSSK--SFNSKMYQMKQLLP 1228
             ++D++         R      ++  +  +    L +K + S     F       +QLL 
Sbjct: 179  VQIDLNDDTLAERWPRANNVTEVAQEIAETIEDALGVKTRQSGTVIEFGPDQPSYRQLLQ 238

Query: 1229 ------SVVIKGVQGINRAVIHEEDV-EGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNN 1281
                   +  KG++ I+R VI +E + +G  ++ L  EG    DV++  GV   + + NN
Sbjct: 239  LVEELREITFKGIEEISRVVIRKEKMDDGEEEFVLYTEGSAFGDVLSIEGVDASRTTCNN 298

Query: 1282 TYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEVLGITRHGLA 1340
             +EVY+ LG+EAAR  I+ E    +   G+  ++ RH MLVAD+MT++G +  I RHG++
Sbjct: 299  IHEVYRELGVEAAREAIIEETMDTLREQGLDDVNIRHLMLVADIMTNRGTIESIGRHGIS 358

Query: 1341 KMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
              K+SVL  A+FE T +HL DAA +G++D + GV E +I+G P+ +GTG + L
Sbjct: 359  GSKDSVLARAAFEVTVNHLLDAAIHGESDDLDGVIENVIVGKPVAIGTGDVDL 411



 Score = 92.0 bits (227), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 72/252 (28%), Positives = 124/252 (49%), Gaps = 32/252 (12%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD----------TDLDYARIVKGRLERT---TLGE 810
           G+PR+ E+++A +   TP++T +L+ +          TD +YA  V   +E T    LG+
Sbjct: 110 GLPRLIELVDARKTPDTPMMTVHLESEEQNEAGIPFATDREYAHEVVWDIEATKILALGD 169

Query: 811 VCEYIEEVFVPDDSFILIKLDMDRI-----RLLHLEVDIDSIRYCIERTRGISGHLTVSG 865
           V   +       D  + I L+ D +     R  ++      I   IE   G+    T   
Sbjct: 170 VSTNVA------DMLVQIDLNDDTLAERWPRANNVTEVAQEIAETIEDALGVK---TRQS 220

Query: 866 HSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVE-GVTKYKLLVEG 924
            + +   P   S     ++ Q+ + L  +  KG++ I+R VI +E ++ G  ++ L  EG
Sbjct: 221 GTVIEFGPDQPSYR---QLLQLVEELREITFKGIEEISRVVIRKEKMDDGEEEFVLYTEG 277

Query: 925 DNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPM 983
               DV++  GV   + + NN +EVY+ LG+EAAR  I+ E    +   G+  ++ RH M
Sbjct: 278 SAFGDVLSIEGVDASRTTCNNIHEVYRELGVEAAREAIIEETMDTLREQGLDDVNIRHLM 337

Query: 984 LVADLMTSKGEV 995
           LVAD+MT++G +
Sbjct: 338 LVADIMTNRGTI 349


>gi|20978714|sp|Q979F5.1|RPOA2_THEVO RecName: Full=DNA-directed RNA polymerase subunit A''
 gi|14325444|dbj|BAB60348.1| DNA-directed RNA polymerase A'' [Thermoplasma volcanium GSS1]
          Length = 508

 Score =  167 bits (422), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 109/331 (32%), Positives = 174/331 (52%), Gaps = 59/331 (17%)

Query: 1115 IEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFVPDDSFIL 1163
            I+P  AVG +AAQSIGEPGTQMT++TFHFAG            + E ++   +P    + 
Sbjct: 177  IDPYEAVGIIAAQSIGEPGTQMTMRTFHFAGVREMNVTLGLPRLIEIVDARRIPSTPSMT 236

Query: 1164 IKLD----------MDRIRLLH---------LEVDI---------------------DSI 1183
            I L           MD ++ L          +  DI                     D +
Sbjct: 237  IYLKPEFETNDEVVMDVVKRLENTSVSDVADIITDIGELTITVRPDPNKMNDRLINQDDL 296

Query: 1184 RYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVI 1243
               I + +G++  +  SG   +I+KP+   +SF  K+Y +++ + ++ IKG+ GI RA+ 
Sbjct: 297  VNAIYKVKGVT-VMEESGQ--IIVKPQ--QESFK-KLYLLQEQIKALPIKGISGIKRAIA 350

Query: 1244 HEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIK 1303
              E  E   ++ +  +G NL+DV+    V   +  +N+  E+   LGIEAAR+ I+ E +
Sbjct: 351  RVEGKE--HRWVIYTQGSNLKDVLEVDEVDPTRTYTNDIVEIATVLGIEAARNAILNEAQ 408

Query: 1304 LVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAA 1363
              ++  G+++D RH MLVAD+MT  G V  + R G++  K SVL  A+FE T+ HL  A 
Sbjct: 409  RTLQEQGLNVDVRHLMLVADMMTFSGSVRAVGRTGISGRKSSVLARAAFEITTKHLLRAG 468

Query: 1364 FYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
              G+ D ++GV+E II+G P+ +GTG + ++
Sbjct: 469  IMGEVDKLAGVAENIIVGQPITLGTGAVDII 499



 Score =  107 bits (267), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 77/240 (32%), Positives = 138/240 (57%), Gaps = 19/240 (7%)

Query: 764 GVPRIKEIINASRNISTPIITAYL--DKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A R  STP +T YL  + +T+ +    V  RLE T++ +V + I ++   
Sbjct: 216 GLPRLIEIVDARRIPSTPSMTIYLKPEFETNDEVVMDVVKRLENTSVSDVADIITDI--- 272

Query: 822 DDSFILIKLDMDRI--RLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKS 879
            +  I ++ D +++  RL++     D +   I + +G++  +  SG   +I+KP+   +S
Sbjct: 273 GELTITVRPDPNKMNDRLINQ----DDLVNAIYKVKGVT-VMEESGQ--IIVKPQ--QES 323

Query: 880 FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
           F  K+Y +++ + ++ IKG+ GI RA+   E  E   ++ +  +G NL+DV+    V   
Sbjct: 324 FK-KLYLLQEQIKALPIKGISGIKRAIARVEGKE--HRWVIYTQGSNLKDVLEVDEVDPT 380

Query: 940 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG 999
           +  +N+  E+   LGIEAAR+ I+ E +  ++  G+++D RH MLVAD+MT  G V   G
Sbjct: 381 RTYTNDIVEIATVLGIEAARNAILNEAQRTLQEQGLNVDVRHLMLVADMMTFSGSVRAVG 440


>gi|410721845|ref|ZP_11361170.1| DNA-directed RNA polymerase, subunit A'''' [Methanobacterium sp.
            Maddingley MBC34]
 gi|410598194|gb|EKQ52780.1| DNA-directed RNA polymerase, subunit A'''' [Methanobacterium sp.
            Maddingley MBC34]
          Length = 383

 Score =  167 bits (422), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 112/339 (33%), Positives = 179/339 (52%), Gaps = 55/339 (16%)

Query: 1106 CREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCE-- 1149
             +  Y+R+++E   AVG +AAQS+GEPGTQMT++TFH+AG              E+ +  
Sbjct: 46   IKRAYIRSEVESGEAVGTVAAQSVGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDAR 105

Query: 1150 ----------YIEEVFVPDDSFI------LIKLDMDRI--------RLLHLEVDIDSIRY 1185
                      Y ++    D+ FI      + K+  + I          +++ V+ID    
Sbjct: 106  KKISTPTMAIYFDDDHASDEEFIRTIANRIGKITFNDILKDFNVNYASMNMSVEIDE-EL 164

Query: 1186 CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMK------QLLPSVV----IKGV 1235
              E+    +  +     +F  ++  ++  SF  K+ + K      +LL   V    I G+
Sbjct: 165  VKEKRLDYTEVMAKIEKAFKSVEINNNLLSFEPKITESKHAIRELRLLADKVRDLQISGI 224

Query: 1236 QGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAAR 1295
            + I + VI +E  E V    +  EG NL  V+   GV  V+ ++N+ +EV K LG+EAAR
Sbjct: 225  KNIGKVVIRKEGQEWV----IHTEGSNLGAVLKMEGVDPVRTTTNDIHEVEKVLGVEAAR 280

Query: 1296 STIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENT 1355
            ++I+ E +  ME  G+++D RH MLVAD+MT+ G V  I RHG++  K SVL  ASFE T
Sbjct: 281  NSIIHEAQTTMEEQGLTVDVRHIMLVADMMTADGIVKSIGRHGISGEKASVLARASFEET 340

Query: 1356 SDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
              HL  A+  G+ D ++G+ E II+G P+ +GTG + ++
Sbjct: 341  GKHLLRASIRGEVDHLTGIIENIIIGQPIPLGTGSVGVI 379



 Score =  100 bits (250), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 69/234 (29%), Positives = 126/234 (53%), Gaps = 17/234 (7%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A + ISTP +  Y D D  +D ++ R +  R+ + T  ++ +     F  
Sbjct: 94  GLPRLIEIVDARKKISTPTMAIYFDDDHASDEEFIRTIANRIGKITFNDILKD----FNV 149

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERT-RGISGHLTVSGHSFLILKPK-DSSKS 879
           + + + + +++D   +    +D   +   IE+  + +        ++ L  +PK   SK 
Sbjct: 150 NYASMNMSVEIDEELVKEKRLDYTEVMAKIEKAFKSVE-----INNNLLSFEPKITESKH 204

Query: 880 FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
              ++  +   +  + I G++ I + VI +E  E V    +  EG NL  V+   GV  V
Sbjct: 205 AIRELRLLADKVRDLQISGIKNIGKVVIRKEGQEWV----IHTEGSNLGAVLKMEGVDPV 260

Query: 940 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
           + ++N+ +EV K LG+EAAR++I+ E +  ME  G+++D RH MLVAD+MT+ G
Sbjct: 261 RTTTNDIHEVEKVLGVEAARNSIIHEAQTTMEEQGLTVDVRHIMLVADMMTADG 314


>gi|397771992|ref|YP_006539538.1| DNA-directed RNA polymerase, subunit A'' [Natrinema sp. J7-2]
 gi|448342575|ref|ZP_21531523.1| DNA-directed RNA polymerase subunit A'' [Natrinema gari JCM 14663]
 gi|397681085|gb|AFO55462.1| DNA-directed RNA polymerase, subunit A'' [Natrinema sp. J7-2]
 gi|445625330|gb|ELY78692.1| DNA-directed RNA polymerase subunit A'' [Natrinema gari JCM 14663]
          Length = 398

 Score =  167 bits (422), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 109/341 (31%), Positives = 178/341 (52%), Gaps = 53/341 (15%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A+A   +Y+  ++EP   VG ++AQSIGEPGTQ+T+ TFH+AG            + E +
Sbjct: 48   AKAVETRYLDTRVEPLDPVGTVSAQSIGEPGTQLTMNTFHYAGVAEIDVTQGLPRLIELV 107

Query: 1152 EEVFVPDDSFILIKLD----------------MDRIRLLHL---EVDIDSIRYCI----- 1187
            +    PD   + + L+                ++  ++L L     ++  +R  I     
Sbjct: 108  DARKTPDTPMMTVYLEDEYATEREKAHEVVWNIEATQILALGDVSTNVADMRVQISLNED 167

Query: 1188 ---------ERTRGIS----GHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKG 1234
                     E   GI     G  TV   + +   P++ S      + Q+ + L  +  KG
Sbjct: 168  TLQERLITAEEVAGIIEDSLGVKTVQQGTQIEFGPEEPSYR---DLLQLVEELRDITFKG 224

Query: 1235 VQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEA 1293
            ++ ++R VI  E++E G  ++ L  EG    DV+   GV   + + NN +E+++ LGIEA
Sbjct: 225  IEEVSRVVIRREELENGNEEFVLYTEGSAFGDVLEIEGVDASRTTCNNIHEIHRNLGIEA 284

Query: 1294 ARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASF 1352
            AR  I+ E    +   G+  ++ RH MLVAD+MT++GE+  I RHG++  KESVL  A+F
Sbjct: 285  AREAIIEETNNTLAEQGLDDVNVRHLMLVADMMTNRGEIESIGRHGISGSKESVLARAAF 344

Query: 1353 ENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            E T +HL +AA +G+ D + GV+E +I+G P+ +GTG + L
Sbjct: 345  EVTVNHLLNAAIHGEVDDLDGVTENVIVGKPIKLGTGDVDL 385



 Score = 98.6 bits (244), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 72/239 (30%), Positives = 127/239 (53%), Gaps = 21/239 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T YL+ +  T+ + A  V   +E T    LG+V   + ++
Sbjct: 99  GLPRLIELVDARKTPDTPMMTVYLEDEYATEREKAHEVVWNIEATQILALGDVSTNVADM 158

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSK 878
            V     I +  D  + RL+  E     +   IE + G+    TV   + +   P++ S 
Sbjct: 159 RVQ----ISLNEDTLQERLITAE----EVAGIIEDSLGVK---TVQQGTQIEFGPEEPSY 207

Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVK 937
                + Q+ + L  +  KG++ ++R VI  E++E G  ++ L  EG    DV+   GV 
Sbjct: 208 R---DLLQLVEELRDITFKGIEEVSRVVIRREELENGNEEFVLYTEGSAFGDVLEIEGVD 264

Query: 938 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEV 995
             + + NN +E+++ LGIEAAR  I+ E    +   G+  ++ RH MLVAD+MT++GE+
Sbjct: 265 ASRTTCNNIHEIHRNLGIEAAREAIIEETNNTLAEQGLDDVNVRHLMLVADMMTNRGEI 323


>gi|91773158|ref|YP_565850.1| DNA-directed RNA polymerase subunit A' [Methanococcoides burtonii
           DSM 6242]
 gi|91712173|gb|ABE52100.1| DNA-directed RNA polymerase subunit A' [Methanococcoides burtonii
           DSM 6242]
          Length = 883

 Score =  167 bits (422), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 98/269 (36%), Positives = 144/269 (53%), Gaps = 33/269 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLHK+SIMAHR KVLP++TF+ N  VC PYNADFDGDEMN+H+ QTEE+
Sbjct: 415 DGDIVLFNRQPSLHKMSIMAHRVKVLPNKTFKLNPAVCPPYNADFDGDEMNMHVLQTEES 474

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A +LM  + N+++PR G  +I    D I+G +LLT+   F ++
Sbjct: 475 RAE--------------ASILMQVQENILSPRFGGPIIGGIHDHISGLFLLTRNEKFISK 520

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSW-NPVVFVRTA-VIWTGKQIFSLILKPNRDCP 518
                         +D   ++++   R    P   +      W GKQIFS IL       
Sbjct: 521 --------------NDALELLRKSELRVLPEPAGHLEDGEPYWNGKQIFSQILPKGLYVE 566

Query: 519 VNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
             A +  K    T  +  C  D+YV++ + EL+ G++D+  +G+  K  V   ++++FG 
Sbjct: 567 FPAQVCFK--CDTCKKGDCEYDAYVVIEDGELIKGTIDEQAIGA-FKGRVLDKVVKEFGT 623

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
                 +   +R+    +M+ G S GI D
Sbjct: 624 TAGAKFVDDFTRLAIRGVMHTGLSFGISD 652



 Score =  103 bits (256), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 77/266 (28%), Positives = 120/266 (45%), Gaps = 44/266 (16%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G I+  +     V++ S   I++ + Y  D    PI  GL+D R+G       C +CG  
Sbjct: 15  GAIKFGLISPREVRKMSVTSIITADTY--DDDGYPIDMGLMDLRLGVIDPGLKCKSCGSR 72

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
             +C GHFG+I+L  PV H+G+ + +  IL+S+C    C+ +LL E K   F  +L    
Sbjct: 73  AGECPGHFGHIELVAPVIHVGFNKILRKILRSVCCK--CSSLLLEESKKRDFLEQLAKQK 130

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDL 260
               +   +   + +  +K   CP+C E          L I  EK               
Sbjct: 131 DMGHLPDDVINNVFKEARKSKTCPYCNEEQ--------LDIKFEKP-------------- 168

Query: 261 LAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
            +EY E          HK       L P E+   FE I  +DI ++ MN + ++P  +IL
Sbjct: 169 -SEYIE--------NGHK-------LTPTEIRDRFENISDDDIRVMGMNPDTARPEWMIL 212

Query: 321 TRLLVPPNCIRPSVI--SDLKSDNDV 344
           T L VPP  +RPS+   S  +S++D+
Sbjct: 213 TVLPVPPVTVRPSITLESGQRSEDDL 238



 Score = 92.4 bits (228), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 40/59 (67%), Positives = 51/59 (86%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            GFV+ S+ SGL PTE+FFH +GGREGLVDTAV+T+++GY+QRRLV +L+DL VQYD S
Sbjct: 781 HGFVKASYKSGLNPTEYFFHAIGGREGLVDTAVRTSQSGYLQRRLVNALQDLEVQYDGS 839


>gi|327242113|gb|AEA40835.1| RNA polymerase II largest subunit [Pentatrichomonas hominis]
          Length = 1721

 Score =  167 bits (422), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 99/269 (36%), Positives = 150/269 (55%), Gaps = 32/269 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND+V+FNRQPSLHK+S+M HRA ++  +TFR N CV TPYNADFDGDEMN+H+PQ++ A
Sbjct: 449 DNDIVIFNRQPSLHKMSMMGHRAFLMSGKTFRLNLCVTTPYNADFDGDEMNLHVPQSQTA 508

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE               + +MA    +++P+  + +I   QD + G  LL+ K+ F  R
Sbjct: 509 RAE--------------VRHIMAVPYQIISPQANKPIIGLVQDALLGSRLLSMKDTFLTR 554

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLIL-KPNRDCPV 519
            Q M +   L  +  +I             P   ++   +W+GKQIFSL + + N D   
Sbjct: 555 NQVMNLMMWLPNEKDNILP-----------PPCILKPVQLWSGKQIFSLFMPRINLDA-Y 602

Query: 520 NANLKTK-GRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
           +AN+  K G   T        D  VI+RN ELLAG +DK T+   G+ ++ ++++  +  
Sbjct: 603 SANVDEKRGDKKTM---IPDNDCKVIIRNGELLAGIIDKKTVAR-GEQSLIHVVINSYDI 658

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
             A   + +   + + +L +RGFSIG+ D
Sbjct: 659 KTAKDFLSQTQLIVNNWLEHRGFSIGLID 687



 Score =  111 bits (278), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 78/260 (30%), Positives = 132/260 (50%), Gaps = 30/260 (11%)

Query: 1163 LIKLDMDRIRLLHLEVDIDSIRYCIERTRG-------ISGHLTVSGHSF---LILKPKDS 1212
            +++ ++D   LL   V +  I+  IE +           G++  +  SF   + ++P  S
Sbjct: 1236 VLRFELDVKSLLASNVSLPEIQRAIENSYSSELFVSIFEGNMANAASSFPPVIRIRPTKS 1295

Query: 1213 SKSFNSK-------MYQMKQLL---PSVVIKGVQGINRAVIH--------EEDVEGVTKY 1254
                N K       + +++Q L    ++ IKG+ GI R  I         EED   V K 
Sbjct: 1296 LVQKNGKTDESEFFLREIEQQLYDERAISIKGIPGIRRVKIDQKAKRKVLEEDHHWVEKS 1355

Query: 1255 --KLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMS 1312
              +L+ EG  L+ ++    +      +N+  E+Y  LGIEAAR+++  E+ ++M+N G S
Sbjct: 1356 DPQLITEGTALKAILGLDHIDKKLTYTNDINEIYDVLGIEAARNSLCNEMMMIMDNAGAS 1415

Query: 1313 IDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCIS 1372
            ++ RH  L+AD MT  G +  ++RHG+ +     L  AS+E T D  FDA  + +TD + 
Sbjct: 1416 LNRRHLDLLADTMTQYGRLYPVSRHGINRTGTGTLARASYEQTIDVFFDACSFAETDPME 1475

Query: 1373 GVSECIIMGLPMNVGTGLIK 1392
             VS  II+G P + GTG+++
Sbjct: 1476 DVSSNIIVGKPSHAGTGIVE 1495



 Score =  102 bits (253), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 79/233 (33%), Positives = 110/233 (47%), Gaps = 32/233 (13%)

Query: 119 GLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPT 178
           GL D RMGT   E  C TCGQ+L +C GHFGYI+L  P FHIG+   V  ILQ +C    
Sbjct: 47  GLSDLRMGTQSPEYRCRTCGQDLQNCPGHFGYINLAEPFFHIGFSDKVYKILQMVCHK-- 104

Query: 179 CARVLLGEEKAAGFRAKLRNPALSYLVR----KSLKKKILET-TKKVSVCPHCGEINGVV 233
           C R+L+             +P + Y+V     K    +I E  + K   C H  E N   
Sbjct: 105 CGRLLV----------SYSDPEVQYIVTHFKGKDRFTRIFEKISGKTHKCAHPTEKNKDP 154

Query: 234 KKCGLLKISHEKYKNRTKKK-DAIVEDLLAEYNEAVKFNPEIEAHKKFGLI--------Q 284
            +    ++  E++ NR     +     +    NEAV   PE+   K F +I        +
Sbjct: 155 SQAD--EVVDEEFWNRVNGGLNGEHHRVKEPCNEAV---PEVAMGKDFLVIYKDGSKTDE 209

Query: 285 TLNPLE-VLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVIS 336
              P E VL +FE I  +D+ ++  + + S P  +ILT L VPP  +RP V S
Sbjct: 210 DYIPAERVLNIFENISDQDLRIMGFDPKRSHPKWMILTVLPVPPLSVRPQVSS 262



 Score = 75.9 bits (185), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 32/57 (56%), Positives = 42/57 (73%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GF ++S+  GL P EF FH M GR G++DTA KT++TGY+QRRL KS+E   V YD
Sbjct: 816 RGFCKHSYVEGLEPPEFIFHAMAGRTGIIDTACKTSDTGYIQRRLCKSMESHHVAYD 872



 Score = 73.2 bits (178), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 78/317 (24%), Positives = 134/317 (42%), Gaps = 85/317 (26%)

Query: 764  GVPRIKEIINASRNISTPIITAYLD---------------------------KDTDLDYA 796
            GVPR+ EI+N ++ I TP +T  LD                           ++ D   A
Sbjct: 1118 GVPRLNEIMNLAKQIKTPCVTVILDYNSNNQDDDGSDMDDEEDRSVRQRQNKQELDAALA 1177

Query: 797  RIVKGRLE---------------------RTTLGEVCEYIE-------EVFVPDDSFILI 828
            + V+  +E                      TT+ E  E+I        +  + + S  ++
Sbjct: 1178 KDVRANVECAAFKKFVTKSEIFYDPEPADNTTIDEDREWIGIYINNQLDFNIDNYSPWVL 1237

Query: 829  KLDMDRIRLLHLEVDIDSIRYCIERTRG-------ISGHLTVSGHSF---LILKPKDSSK 878
            + ++D   LL   V +  I+  IE +           G++  +  SF   + ++P  S  
Sbjct: 1238 RFELDVKSLLASNVSLPEIQRAIENSYSSELFVSIFEGNMANAASSFPPVIRIRPTKSLV 1297

Query: 879  SFNSK-------MYQMKQLL---PSVVIKGVQGINRAVIH--------EEDVEGVTKY-- 918
              N K       + +++Q L    ++ IKG+ GI R  I         EED   V K   
Sbjct: 1298 QKNGKTDESEFFLREIEQQLYDERAISIKGIPGIRRVKIDQKAKRKVLEEDHHWVEKSDP 1357

Query: 919  KLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSID 978
            +L+ EG  L+ ++    +      +N+  E+Y  LGIEAAR+++  E+ ++M+N G S++
Sbjct: 1358 QLITEGTALKAILGLDHIDKKLTYTNDINEIYDVLGIEAARNSLCNEMMMIMDNAGASLN 1417

Query: 979  FRHPMLVADLMTSKGEV 995
             RH  L+AD MT  G +
Sbjct: 1418 RRHLDLLADTMTQYGRL 1434



 Score = 54.3 bits (129), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 22/38 (57%), Positives = 28/38 (73%)

Query: 1108 EKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            E++ R+ + P   VG +A QSIGEP TQMTL TFH+AG
Sbjct: 1072 ERFYRSIVSPGEMVGTIAGQSIGEPSTQMTLNTFHYAG 1109


>gi|254169215|ref|ZP_04876049.1| RNA polymerase Rpb1, domain 2 family [Aciduliprofundum boonei T469]
 gi|197621811|gb|EDY34392.1| RNA polymerase Rpb1, domain 2 family [Aciduliprofundum boonei T469]
          Length = 661

 Score =  167 bits (422), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 105/284 (36%), Positives = 151/284 (53%), Gaps = 43/284 (15%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH++S+M H  KV+P+RTFRFN  VC PYNADFDGDEMN+H+ Q+EEA
Sbjct: 364 DGDVVLFNRQPSLHRMSMMGHLVKVMPNRTFRFNLAVCPPYNADFDGDEMNLHVLQSEEA 423

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              AK+LM  + ++++PR G  +I    D IT  +LLT KN  F +
Sbjct: 424 RAE--------------AKILMLVQEHILSPRFGGPIIGGIHDHITAMFLLTHKNPKFTK 469

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q + + S L  D                 P         + GK++FSLIL      P +
Sbjct: 470 EQAIHMLSYLDYDELP-------------EPHKDENGNEFYYGKELFSLIL------PKD 510

Query: 521 ANLKTKGRAYTAN-------EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILL 573
            N++ K +    +        E C  D+YV++RN +L+AG++D++ +GS     +  I  
Sbjct: 511 LNMEFKSKICDPSVCNNKCVHEACPIDAYVVIRNGKLVAGTIDENAIGSMKGKLLDRIAK 570

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV-TPGQGFVQ 616
           R  G   A   +  ++R+    +  RGF+ GI D   P +  +Q
Sbjct: 571 R--GSKEAREFIDNMTRLAVGVISYRGFTSGIDDEDIPEEAIIQ 612



 Score = 97.8 bits (242), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 60/204 (29%), Positives = 96/204 (47%), Gaps = 43/204 (21%)

Query: 134 CTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFR 193
           C TCG  + +C GHFG+I+L +PV H+G+ + + N L + C+   C R+ L +++   ++
Sbjct: 7   CKTCGGKVDECPGHFGHIELAMPVIHVGFVKNIKNYLDATCRE--CGRIKLKDDEIEIYK 64

Query: 194 AKL---RNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRT 250
            K+   +    S L    + KKI++      +CPHCG      KK  L K +  + + R 
Sbjct: 65  QKIEEAKKMGASPLELLFITKKIIDDASSRPICPHCG---AEQKKITLDKPTTFREEGR- 120

Query: 251 KKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNA 310
                                              L P E+ +  E IP ED+PLL MN 
Sbjct: 121 ----------------------------------KLTPKEIRERLERIPDEDLPLLGMNP 146

Query: 311 ELSKPSDLILTRLLVPPNCIRPSV 334
           E ++P  ++LT L VPP  +RP++
Sbjct: 147 ETARPEWMVLTVLPVPPVNVRPTI 170


>gi|110669643|gb|ABG81916.1| RNA polymerase II largest subunit, partial [Agonimia sp. AFTOL 684]
          Length = 1023

 Score =  166 bits (421), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 99/278 (35%), Positives = 154/278 (55%), Gaps = 34/278 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DV+LFNRQPSLHK S+M HR +V+P+ TFR N  V TPYNADFDGDEMN+H+PQ+EE 
Sbjct: 372 DGDVILFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSEET 431

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L +L ++            N+V+P+    L+   QD + G Y + +++ F +R
Sbjct: 432 RAE----LSQLCMVP----------LNIVSPQRNGPLMGIVQDTLCGIYKICRRDIFLSR 477

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            + M I    +    D  G+I +       P +F +    WTGKQ+ S++L P  +    
Sbjct: 478 EEVMNI----MLWVPDWDGVIPQ-------PAIF-KPRPRWTGKQMISMVLPPALNL--- 522

Query: 521 ANLKTKGRA-YTANEEFCHR-DSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
             ++  G+    A E F    DS + + + +LL G  +K ++G+G    + + +  +FG 
Sbjct: 523 --VRIDGKPNLPAGERFAPAGDSGLFVADGQLLFGLFNKKSVGTGSNG-IIHTIYNEFGH 579

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           + A+        + +++L++ GFSIGIGD  P  G V+
Sbjct: 580 ETAMGFFNGAQTVVNYWLLHNGFSIGIGDTVPDVGTVE 617



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 43/57 (75%), Positives = 52/57 (91%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QRRLVK+LE++ V+YD
Sbjct: 737 KGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEEVTVKYD 793



 Score = 54.3 bits (129), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 46/194 (23%), Positives = 79/194 (40%), Gaps = 37/194 (19%)

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALS 202
           +C GHFG I L +PV+H G+   V  IL+++C N    + +  EE       + R     
Sbjct: 1   ECPGHFGTIKLAVPVYHYGFLGKVKKILETVCHNCGKIKAVDSEELRYALSIRDRKKRFE 60

Query: 203 YLVRKSLKKKILETTK-----------KVSVCPH--CGEINGVVKKCGLLKISHEKYKNR 249
            + R S K+ I +              K     H  CG     ++K GL   +  +YK R
Sbjct: 61  LIWRLSQKQNICQADSADEEDDPFGKDKGGKIKHGGCGNAQPAIRKTGLELWA--QYKPR 118

Query: 250 TKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMN 309
               D   E+ + E ++                   + P + LQ+F+ +  + +  L +N
Sbjct: 119 KGDDD---EETVPEKSQ-------------------IWPAQALQVFQHLTDDTLETLGLN 156

Query: 310 AELSKPSDLILTRL 323
            + ++P  +IL  L
Sbjct: 157 LDFARPEWMILQSL 170



 Score = 42.0 bits (97), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 18/33 (54%), Positives = 22/33 (66%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMT 1137
            A   ++++A   P   VG LAAQSIGEP TQMT
Sbjct: 991  AVETRFIKATASPGEMVGVLAAQSIGEPATQMT 1023


>gi|432330443|ref|YP_007248586.1| DNA-directed RNA polymerase subunit A' [Methanoregula formicicum
           SMSP]
 gi|432137152|gb|AGB02079.1| DNA-directed RNA polymerase subunit A' [Methanoregula formicicum
           SMSP]
          Length = 879

 Score =  166 bits (421), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 99/267 (37%), Positives = 145/267 (54%), Gaps = 30/267 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH++SIMAHR KV+  RTFR N  VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 413 DGDVVLFNRQPSLHRMSIMAHRVKVMEGRTFRLNPAVCPPYNADFDGDEMNMHVPQTEEA 472

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA               +L++ + N+++PR G  +I    D ++G ++LT    +F +
Sbjct: 473 RAEA--------------SILISVQENILSPRFGGPIIGGIHDHVSGIFMLTHDLRWFTK 518

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q + +            GI      R   P         W+ KQ+FS+IL  N +   +
Sbjct: 519 EQALYLLR--------YTGI-----ERMPEPGKVEDGVEYWSNKQVFSVILPENLNMVFH 565

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           A+  +     T  +E C RD+YV + + +L +G++DK  +G+     V   ++R  G   
Sbjct: 566 AS--SCQNCDTCKKEVCERDAYVRIIDGKLESGTIDKKAIGA-FDGQVVNRIIRQQGMKR 622

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           A   +   ++++   +M  GFS GI D
Sbjct: 623 ATKFIDDFTKLSIRGIMLDGFSFGIDD 649



 Score =  114 bits (285), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 86/266 (32%), Positives = 126/266 (47%), Gaps = 44/266 (16%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G IE  +     +++ S  +I+  + Y  D    P P GL+D  +G       C TC Q 
Sbjct: 8   GQIEFGLLSPKEIREMSVRKIIWADTY--DDDGFPYPQGLMDLNLGVIDPGLRCKTCDQK 65

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
            SDC GHFG+I+L  PV H+GY R +  +L+  C+   C RVLL  E+         +  
Sbjct: 66  ASDCPGHFGHIELAKPVIHVGYTRLIRKLLRVTCR--ACGRVLLSPEEVEKVVGTEDDQT 123

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDL 260
              L  K +KK+         VCPHCGE          LKI+ EK    T   + +VED 
Sbjct: 124 GDLLSEKDVKKE--------RVCPHCGEQQ--------LKINFEKP---TTFSEVMVED- 163

Query: 261 LAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
                       ++E HK       L P ++    E IP ED+  L +N ++++P   IL
Sbjct: 164 ----------GKKVE-HK-------LTPADIRARLEKIPNEDLIPLGINPDVARPEWTIL 205

Query: 321 TRLLVPPNCIRPSVI--SDLKSDNDV 344
           T L VPP  +RPS+I  +  +S++D+
Sbjct: 206 TVLPVPPVTMRPSIILENGQRSEDDL 231



 Score = 89.4 bits (220), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 36/57 (63%), Positives = 49/57 (85%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GF+Q+S+  GL PTEFFFH +GGREGLVDTAV+T+++GY+QRR++ +L+DL V YD
Sbjct: 778 HGFIQHSYKGGLNPTEFFFHAIGGREGLVDTAVRTSQSGYLQRRMINALQDLKVAYD 834


>gi|154151472|ref|YP_001405090.1| DNA-directed RNA polymerase subunit A' [Methanoregula boonei 6A8]
 gi|154000024|gb|ABS56447.1| DNA-directed RNA polymerase subunit A' [Methanoregula boonei 6A8]
          Length = 879

 Score =  166 bits (421), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 95/267 (35%), Positives = 147/267 (55%), Gaps = 30/267 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIMAHR KV+  RTFR N  VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 413 DGDIVLFNRQPSLHRMSIMAHRIKVMEGRTFRLNPAVCPPYNADFDGDEMNLHVPQTEEA 472

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A +L + + N+++PR G  +I    D I+G ++LT    +F +
Sbjct: 473 RAE--------------ASILCSVQENILSPRFGGPIIGGIHDHISGIFMLTHDMRWFTK 518

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            + + +   +  D     G       ++ N + +      W+ KQ+FS IL    +   +
Sbjct: 519 EEALYLLKPVRVDHMPPPG-------KTENGIEY------WSNKQVFSQILPTALNMVFH 565

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           A+  +     T  +E C RD+YV +    L +G++DK  +G+     +   ++R +G   
Sbjct: 566 AS--SCQNCDTCKKELCERDAYVRIMGGRLESGTIDKKAIGA-FDGQIVNRIIRQYGMKR 622

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           A   + ++++++   +M  GFS GI D
Sbjct: 623 ATEFIDQVTKLSIRGIMIDGFSFGIDD 649



 Score =  110 bits (276), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 86/269 (31%), Positives = 126/269 (46%), Gaps = 50/269 (18%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G IE  +     +++ S  +I+  + Y  D    P P GL+D  +G       C TC Q 
Sbjct: 8   GKIEFGLLSPKEIREMSVRKIIWADTY--DDDGFPYPQGLMDLNLGVIDPGLRCKTCDQK 65

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGE---EKAAGFRAKLR 197
            SDC GHFG+I+L  PV H+GY R +  +L+  C+  +C R+LL     EK  G    L 
Sbjct: 66  ASDCPGHFGHIELAKPVIHVGYTRLIRKLLRVTCR--SCGRLLLSPDEVEKVVGTDEDLT 123

Query: 198 NPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIV 257
              +S            +  KK  VCPHCGE          LKI+ EK    T   + ++
Sbjct: 124 GDQISE-----------KDVKKERVCPHCGEQQ--------LKINFEKP---TTFSEVMI 161

Query: 258 EDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSD 317
           ED             ++E HK       L P ++    E IP ED+  L +N  +++P  
Sbjct: 162 ED-----------GKKVE-HK-------LTPADIRARLEKIPDEDLIPLGINPRVARPEW 202

Query: 318 LILTRLLVPPNCIRPSVI--SDLKSDNDV 344
            ILT L VPP  +RPS+I  +  +S++D+
Sbjct: 203 TILTVLPVPPVTMRPSIILENGQRSEDDL 231



 Score = 87.0 bits (214), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 35/57 (61%), Positives = 48/57 (84%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GF+ +S+  GL PTEFFFH +GGREGLVDTAV+T+++GY+QRR++ +L+DL V YD
Sbjct: 778 HGFIAHSYKGGLNPTEFFFHAIGGREGLVDTAVRTSQSGYLQRRMINALQDLKVAYD 834


>gi|295664232|ref|XP_002792668.1| DNA-directed RNA polymerase II subunit RPB1 [Paracoccidioides sp.
           'lutzii' Pb01]
 gi|226278782|gb|EEH34348.1| DNA-directed RNA polymerase II subunit RPB1 [Paracoccidioides sp.
           'lutzii' Pb01]
          Length = 1748

 Score =  166 bits (421), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 96/270 (35%), Positives = 150/270 (55%), Gaps = 31/270 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DV+LFNRQPSLHK S+MAHR +V+P+ TFR N  V TPYNADFDGDEMN+H+PQ+EEA
Sbjct: 462 DGDVILFNRQPSLHKESMMAHRVRVMPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSEEA 521

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L +L ++  +          +V+P+    L+   QD + G Y + +++ F ++
Sbjct: 522 RAE----LSQLCMVPLQ----------IVSPQRNGPLMGIVQDTLCGIYKICRRDVFLSK 567

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M I    +    D  G+I +       P + ++    WTGKQ+ S++L P     +N
Sbjct: 568 EQVMNI----LLWVPDWDGVIPQ-------PAI-LKPRPRWTGKQLISMVLPPG----LN 611

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
                + RA  + +     D  V++   EL+ G   K T+G+ G   + + +  ++G + 
Sbjct: 612 LLRVDRDRAPRSEKFSPPADGGVLVHGGELMYGMFSKKTVGATG-GGIIHTIFNEYGPET 670

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           A+        + +++L++ GFSIGIGD  P
Sbjct: 671 AMNFFNGAQTVVNYWLLHHGFSIGIGDTIP 700



 Score = 99.4 bits (246), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QR+LVK+LE++ V
Sbjct: 820 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMV 879

Query: 666 QYD 668
           +YD
Sbjct: 880 KYD 882



 Score = 98.6 bits (244), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 59/180 (32%), Positives = 92/180 (51%), Gaps = 15/180 (8%)

Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMAT 1269
             LL ++ ++GV GI RA I+E+    V                ++ L   G  L +V+  
Sbjct: 1294 HLLDTLTLRGVAGIERAFINEKSRVRVLEDGSLHQSSEDPLCKEWVLETSGSALGEVLTI 1353

Query: 1270 YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 1329
             GV   +  SN   E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1354 PGVDTTRTYSNQFVEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLVDVMTSRG 1413

Query: 1330 EVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
             ++ +TRHG+ +     L   SFE T + L DAA + + D   GVSE +I+G     GTG
Sbjct: 1414 FLMAVTRHGINRADTGALMRCSFEETVEILLDAAAFAELDDCRGVSENLILGQMAPAGTG 1473



 Score = 86.7 bits (213), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 76/288 (26%), Positives = 132/288 (45%), Gaps = 58/288 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLD--KDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N + +I TP +T Y D  +  D + A+ ++  +E T+L  V E  E  + P
Sbjct: 1126 GVPRLKEILNVATHIKTPSMTVYQDSSRAMDKESAKQLRSVVEHTSLRSVTEATEIYYDP 1185

Query: 822  DDSFILIKLDMDRIR---LLHLEVDIDS-------IRYCIERTRGISGHLTVSGHSFLI- 870
            D    +I+ D D +    ++  +V  DS       +R  + R + +  +LTV   +  I 
Sbjct: 1186 DIQSTVIEADRDMVESYFIIPEDVADDSSRQSKWLLRIILSRPKLLDKNLTVQDVAMRIK 1245

Query: 871  -LKPKD-----SSKSFNSKMYQMKQ------------------------LLPSVVIKGVQ 900
               P+D     S  + + ++ +++Q                        LL ++ ++GV 
Sbjct: 1246 DAYPQDIAVIFSDNNADEQVIRIRQIQDTKQDDDDDTEYDVTLKKLEGHLLDTLTLRGVA 1305

Query: 901  GINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMATYGVKGVKCSSNN 945
            GI RA I+E+    V                ++ L   G  L +V+   GV   +  SN 
Sbjct: 1306 GIERAFINEKSRVRVLEDGSLHQSSEDPLCKEWVLETSGSALGEVLTIPGVDTTRTYSNQ 1365

Query: 946  TYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
              E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1366 FVEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLVDVMTSRG 1413



 Score = 80.5 bits (197), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 59/233 (25%), Positives = 102/233 (43%), Gaps = 42/233 (18%)

Query: 108 CQDPQRT-PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCV 166
             D QR  P   GL D R+GT  +   C TC + ++ C GHFG+I+L  PVFHIG+   +
Sbjct: 48  ANDEQRQRPREKGLNDPRLGTIDRNWRCATCEEGINGCPGHFGHIELSTPVFHIGFLTKI 107

Query: 167 INILQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKSLKKKIL----------- 214
             +L+++C N  C ++           A + R+P   +     L K +L           
Sbjct: 108 KKLLETVCHN--CGKIKANTNDQKYLEALRFRDPKRRFDAIWRLSKDVLICEADPTPDDD 165

Query: 215 -----ETTKKVSVCPHCGEINGVVKKCGLLKISHEK-YKNRTKKKDAIVEDLLAEYNEAV 268
                E +K V     CG +   ++K G+  +   K  KNR      +++D+  +  E  
Sbjct: 166 DPFSKEASKPVRSHGGCGNMQPQIRKEGISLVGTWKPNKNRD-----MMDDMDIQQPEKR 220

Query: 269 KFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
           +  P++                 L +F  I  ED+ L+ ++ + ++P  +I+T
Sbjct: 221 QITPQM----------------ALNIFRNISEEDVRLMGLSNDYARPEWMIIT 257



 Score = 57.4 bits (137), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 26/41 (63%), Positives = 28/41 (68%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            A   ++ RA   P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1077 AIENRFSRAMANPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1117


>gi|226295248|gb|EEH50668.1| DNA-directed RNA polymerase II subunit RPB1 [Paracoccidioides
           brasiliensis Pb18]
          Length = 1746

 Score =  166 bits (421), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 96/270 (35%), Positives = 150/270 (55%), Gaps = 31/270 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DV+LFNRQPSLHK S+MAHR +V+P+ TFR N  V TPYNADFDGDEMN+H+PQ+EEA
Sbjct: 456 DGDVILFNRQPSLHKESMMAHRVRVMPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L +L ++  +          +V+P+    L+   QD + G Y + +++ F ++
Sbjct: 516 RAE----LSQLCMVPLQ----------IVSPQRNGPLMGIVQDTLCGIYKICRRDVFLSK 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M I    +    D  G+I +       P + ++    WTGKQ+ S++L P     +N
Sbjct: 562 EQVMNI----LLWVPDWDGVIPQ-------PAI-LKPRPRWTGKQLISMVLPPG----LN 605

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
                + RA  + +     D  V++   EL+ G   K T+G+ G   + + +  ++G + 
Sbjct: 606 LLRVDRDRAPRSEKFSPPADGGVLVHGGELMYGMFSKKTVGATG-GGIIHTIFNEYGPET 664

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           A+        + +++L++ GFSIGIGD  P
Sbjct: 665 AMNFFNGAQTVVNYWLLHHGFSIGIGDTIP 694



 Score = 99.4 bits (246), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QR+LVK+LE++ V
Sbjct: 814 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMV 873

Query: 666 QYD 668
           +YD
Sbjct: 874 KYD 876



 Score = 98.6 bits (244), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 59/180 (32%), Positives = 92/180 (51%), Gaps = 15/180 (8%)

Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMAT 1269
             LL ++ ++GV GI RA I+E+    V                ++ L   G  L +V+  
Sbjct: 1289 HLLDTLTLRGVAGIERAFINEKSRVRVLEDGSLHQSSEDPLCKEWVLETSGSALGEVLTI 1348

Query: 1270 YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 1329
             GV   +  SN   E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1349 PGVDTTRTYSNQFVEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLVDVMTSRG 1408

Query: 1330 EVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
             ++ +TRHG+ +     L   SFE T + L DAA + + D   GVSE +I+G     GTG
Sbjct: 1409 FLMAVTRHGINRADTGALMRCSFEETVEILLDAAAFAELDDCRGVSENLILGQMAPAGTG 1468



 Score = 86.3 bits (212), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 76/289 (26%), Positives = 132/289 (45%), Gaps = 59/289 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLD--KDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N + +I TP +T Y D  +  D + A+ ++  +E T+L  V E  E  + P
Sbjct: 1120 GVPRLKEILNVATHIKTPSMTVYQDSSRAMDKESAKQLRSVVEHTSLRSVTEATEIYYDP 1179

Query: 822  DDSFILIKLDMDRIR---LLHLEVDIDS-------IRYCIERTRGISGHLTVSGHSFLIL 871
            D    +I+ D D +    ++  +V  DS       +R  + R + +  +LTV   +  I 
Sbjct: 1180 DIQSTVIEADRDMVESYFIIPEDVADDSSRQSKWLLRIILSRPKLLDKNLTVQDVAMRIK 1239

Query: 872  K--PKD-----SSKSFNSKMYQMKQ-------------------------LLPSVVIKGV 899
               P+D     S  + + ++ +++Q                         LL ++ ++GV
Sbjct: 1240 DAYPQDIAVIFSDNNADEQVIRIRQIQDTKQDDDDDDTEYDVTLKKLEGHLLDTLTLRGV 1299

Query: 900  QGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMATYGVKGVKCSSN 944
             GI RA I+E+    V                ++ L   G  L +V+   GV   +  SN
Sbjct: 1300 AGIERAFINEKSRVRVLEDGSLHQSSEDPLCKEWVLETSGSALGEVLTIPGVDTTRTYSN 1359

Query: 945  NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
               E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1360 QFVEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLVDVMTSRG 1408



 Score = 83.6 bits (205), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 60/231 (25%), Positives = 103/231 (44%), Gaps = 42/231 (18%)

Query: 110 DPQRT-PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVIN 168
           D QR  P   GL D R+GT  +   C TC + ++DC GHFG+I+L  PVFHIG+   +  
Sbjct: 44  DEQRQRPREKGLNDPRLGTIDRNWRCATCEEGINDCPGHFGHIELSTPVFHIGFLTKIKK 103

Query: 169 ILQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKSLKKKIL------------- 214
           +L+++C N  C ++           A + R+P   +     L K +L             
Sbjct: 104 LLETVCHN--CGKIKANTNDQKYLEALRFRDPKRRFDAIWRLSKDVLICEADPTPDDDDP 161

Query: 215 ---ETTKKVSVCPHCGEINGVVKKCGLLKISHEK-YKNRTKKKDAIVEDLLAEYNEAVKF 270
              E +K V     CG +   ++K G+  +   K  KNR      +++D+  +  E  + 
Sbjct: 162 FSKEASKPVRSHGGCGNMQPQIRKEGISLVGTWKPNKNRD-----MMDDMDIQQPEKRQI 216

Query: 271 NPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
            P++                 L +F  I  ED+ L+ ++ + ++P  +I+T
Sbjct: 217 TPQM----------------ALNIFRNISEEDVRLMGLSNDYARPEWMIIT 251



 Score = 57.4 bits (137), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 26/41 (63%), Positives = 28/41 (68%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            A   ++ RA   P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1071 AIENRFSRAMANPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1111


>gi|296822712|ref|XP_002850330.1| DNA-directed RNA polymerase II subunit RPB1 [Arthroderma otae CBS
           113480]
 gi|238837884|gb|EEQ27546.1| DNA-directed RNA polymerase II subunit RPB1 [Arthroderma otae CBS
           113480]
          Length = 1748

 Score =  166 bits (421), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 96/277 (34%), Positives = 153/277 (55%), Gaps = 33/277 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D +LFNRQPSLHK S+M+HR +V+P+ TFR N  V TPYNADFDGDEMN+H+PQ+EEA
Sbjct: 455 DGDFILFNRQPSLHKESMMSHRVRVMPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSEEA 514

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L++L ++            N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 515 RAE----LNQLCLVPL----------NIVSPQRNGPLMGIVQDTLCGIYKICRRDVFLTK 560

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M I    +    D  G++ +       P + ++    W+GKQ+ S++L P  +    
Sbjct: 561 EQVMNI----LLWVPDWDGVLPQ-------PAI-LKPRPRWSGKQMISMVLPPGLNL--- 605

Query: 521 ANLKTKGRAYTANEEFCH-RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
             L+        +E+F    D  V++   EL+ G   K T+G+ G   V + +  ++G +
Sbjct: 606 --LRIDKDKSPISEKFSPLADGGVLVHGGELMYGMFSKKTVGASG-GGVVHTIFNEYGPE 662

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           VA++       + +++L++ GFSIGIGD  P    +Q
Sbjct: 663 VAMSFFNGAQTVVNYWLLHNGFSIGIGDTIPDLATIQ 699



 Score =  102 bits (254), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 60/180 (33%), Positives = 93/180 (51%), Gaps = 15/180 (8%)

Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMAT 1269
             LL ++ ++GV GI RA I+E+    V                ++ L   G  L DV+A 
Sbjct: 1288 HLLDTLTLRGVPGIERAFINEKSRTRVLEDGSLHQSASDPECKEWVLETSGSALADVLAI 1347

Query: 1270 YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 1329
             G+   +  SN   E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1348 PGIDASRTYSNQFVEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLVDVMTSRG 1407

Query: 1330 EVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
             ++ +TRHG+ +     L   SFE T + L DAA + + D   GVSE +I+G     GTG
Sbjct: 1408 FLMAVTRHGINRADTGALMRCSFEETVEILLDAAAFAELDDCRGVSENLILGQMAPAGTG 1467



 Score = 99.4 bits (246), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QR+LVK+LE++ V
Sbjct: 813 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMV 872

Query: 666 QYD 668
           +YD
Sbjct: 873 KYD 875



 Score = 88.6 bits (218), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 77/289 (26%), Positives = 133/289 (46%), Gaps = 59/289 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLD--YARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N + NI TP +T Y   +  +D   A+ ++  +E T+L  V E  E  + P
Sbjct: 1119 GVPRLKEILNVATNIKTPSMTVYQAPECRMDKESAKQLRSIVEHTSLRSVTESTEIYYDP 1178

Query: 822  DDSFILIKLDMDRIR---LLHLEVDIDS-------IRYCIERTRGISGHLTVSGHSFLIL 871
            D    +I+ D+D +    ++  +V  DS       +R  + R + +   LTV   +  I 
Sbjct: 1179 DIQSTVIENDIDMVESYFIIPEDVADDSSRQSKWLLRIILSRPKLLDKGLTVQDVATKIK 1238

Query: 872  K--PKD-----SSKSFNSKMYQMKQ-------------------------LLPSVVIKGV 899
            +  P+D     S  + + ++ +++Q                         LL ++ ++GV
Sbjct: 1239 EAYPQDIAVIFSDNNADEQVVRIRQIQDPKQDEDDDDTEYDVTLKKLESHLLDTLTLRGV 1298

Query: 900  QGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMATYGVKGVKCSSN 944
             GI RA I+E+    V                ++ L   G  L DV+A  G+   +  SN
Sbjct: 1299 PGIERAFINEKSRTRVLEDGSLHQSASDPECKEWVLETSGSALADVLAIPGIDASRTYSN 1358

Query: 945  NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
               E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1359 QFVEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLVDVMTSRG 1407



 Score = 84.7 bits (208), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 60/228 (26%), Positives = 105/228 (46%), Gaps = 38/228 (16%)

Query: 110 DPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINI 169
           D ++ P   GL D R+GT  +   C TC + ++DC GHFG+I+L  PVFHIG+   +  +
Sbjct: 45  DQRQRPREKGLNDPRLGTIDRNWRCATCEEGINDCPGHFGHIELSTPVFHIGFLTKIKKL 104

Query: 170 LQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKSLKKKIL-------------- 214
           L+++C N  C ++           A + R+P   +     L K IL              
Sbjct: 105 LETVCHN--CGKIKANASDQKYLDALRFRDPKKRFDAIWRLSKDILICEADPPEEDDPFA 162

Query: 215 -ETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPE 273
            E++K V     CG +   V+K G+  +   K    +K +D + ++             E
Sbjct: 163 KESSKPVQGHGGCGNVQPQVRKEGITLMGTWK---PSKMRDMMDDN-------------E 206

Query: 274 IEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
           I+  +K    + + P   L +F  I  ED+ L+ ++ + ++P  +I+T
Sbjct: 207 IQQPEK----KQITPQMALTIFRNISEEDVRLMGLSNDYARPEWMIIT 250



 Score = 55.8 bits (133), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/41 (60%), Positives = 28/41 (68%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            A   ++ +A   P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1070 AIESRFGKAAANPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1110


>gi|343172362|gb|AEL98885.1| DNA-directed RNA polymerase II subunit, partial [Silene latifolia]
 gi|343172364|gb|AEL98886.1| DNA-directed RNA polymerase II subunit, partial [Silene latifolia]
          Length = 408

 Score =  166 bits (421), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 99/271 (36%), Positives = 151/271 (55%), Gaps = 37/271 (13%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D D VLFNRQPSLHK+SIM HR K++P+ TFR N  V +PYNADFDGDEMN+H+PQ+ E
Sbjct: 168 NDGDFVLFNRQPSLHKMSIMGHRIKIMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSFE 227

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE L             +++M  K  +V+P+  + ++   QD + G   +T+++ F  
Sbjct: 228 TRAEVL-------------ELMMVPKC-IVSPQANKPVMGIVQDTLLGCRKITKRDTFIE 273

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           +   M I    +    D  G + + S         ++   IWTGKQ+F+LI+      P 
Sbjct: 274 KDVFMNI----LMWWEDFDGKVPQPS--------ILKPRPIWTGKQVFNLII------PK 315

Query: 520 NANLKTKGRAYTANEEFCH---RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
             NL  +  A+    E  H    D+ V++   ELLAG++ K TLG+GG  ++ +++  + 
Sbjct: 316 QINL-VRFAAWHQETETGHLTPGDTRVLIERGELLAGTLCKKTLGTGG-GSLIHVIWEEV 373

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           G D A   +     + +++L+  GFSIGIGD
Sbjct: 374 GPDAARKFLGHTQWLVNYWLLQNGFSIGIGD 404


>gi|289596765|ref|YP_003483461.1| DNA-directed RNA polymerase subunit A' [Aciduliprofundum boonei
           T469]
 gi|289534552|gb|ADD08899.1| DNA-directed RNA polymerase subunit A' [Aciduliprofundum boonei
           T469]
          Length = 895

 Score =  166 bits (421), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 105/284 (36%), Positives = 155/284 (54%), Gaps = 43/284 (15%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLH++S+M H  KV+P+RTFRFN  VC PYNADFDGDEMN+H+ Q+EEA
Sbjct: 421 DGDVVLFNRQPSLHRMSMMGHLVKVMPNRTFRFNLAVCPPYNADFDGDEMNLHVLQSEEA 480

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              AK+LM  + ++++PR G  +I    D IT  +LLT KN  F +
Sbjct: 481 RAE--------------AKILMLVQEHILSPRFGGPIIGGIHDHITAMFLLTHKNPKFTK 526

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q + + S L  D  ++    K  +   +           + GK++FSLIL      P +
Sbjct: 527 EQAIHMLSYL--DYDELPEPHKDENGNEF-----------YYGKELFSLIL------PKD 567

Query: 521 ANLKTKGRAYTAN-------EEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILL 573
            N++ K +    +        E C  D+YV++RN +L+AG++D++ +GS     +  I  
Sbjct: 568 LNMEFKSKICDPSVCNNKCVHEACPIDAYVVIRNGKLVAGTIDENAIGSMKGKLLDRIAK 627

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV-TPGQGFVQ 616
           R  G   A   +  ++R+    +  RGF+ GI D   P +  +Q
Sbjct: 628 R--GSKEAREFIDNMTRLAVGVISYRGFTSGIDDEDIPEEAIIQ 669



 Score =  114 bits (286), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 70/247 (28%), Positives = 118/247 (47%), Gaps = 45/247 (18%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           + +++ S +++++ + Y  D    PI  GL+D  MG  +    C TCG  + +C GHFG+
Sbjct: 23  EEIRRMSAVKVITADTY--DDDGFPIDKGLMDLHMGVIEPGLRCKTCGGKVDECPGHFGH 80

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKL---RNPALSYLVRK 207
           I+L +PV H+G+ + + N L + C+   C R+ L +++   ++ K+   +    S L   
Sbjct: 81  IELAMPVIHVGFVKNIKNYLDATCRE--CGRIKLKDDEIEIYKQKIEEAKKMGASPLELL 138

Query: 208 SLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEA 267
            + KKI++      +CPHCG      KK  L K +  + + R                  
Sbjct: 139 FITKKIIDDASSRPICPHCG---AEQKKITLDKPTTFREEGR------------------ 177

Query: 268 VKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPP 327
                             L P E+ +  E IP ED+PLL MN E ++P  ++LT L VPP
Sbjct: 178 -----------------KLTPKEIRERLERIPDEDLPLLGMNPETARPEWMVLTVLPVPP 220

Query: 328 NCIRPSV 334
             +RP++
Sbjct: 221 VNVRPTI 227



 Score = 89.0 bits (219), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 38/58 (65%), Positives = 50/58 (86%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV++S+  GL+PTE+FFH+MGGREGLVDTAV+T+ +GYMQRRL+ +LEDL V  D
Sbjct: 787 ARGFVESSYKKGLSPTEYFFHSMGGREGLVDTAVRTSRSGYMQRRLINALEDLKVIED 844


>gi|238487198|ref|XP_002374837.1| DNA-dependent RNA polymerase II largest subunit, putative
           [Aspergillus flavus NRRL3357]
 gi|317143741|ref|XP_001819667.2| DNA-directed RNA polymerase II subunit RPB1 [Aspergillus oryzae
           RIB40]
 gi|220699716|gb|EED56055.1| DNA-dependent RNA polymerase II largest subunit, putative
           [Aspergillus flavus NRRL3357]
          Length = 1744

 Score =  166 bits (421), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 100/272 (36%), Positives = 145/272 (53%), Gaps = 35/272 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DV+LFNRQPSLHK S+M HR +V+P+ TFR N  V TPYNADFDGDEMN+H+PQ+EE+
Sbjct: 453 DGDVILFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSEES 512

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE L            A V M    N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 513 RAELL----------QLALVPM----NIVSPQRNGPLMGIVQDTLCGIYKICRRDTFLTK 558

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M     L+    D  G+I         P   ++    WTGKQI S+ L      P  
Sbjct: 559 EQVM----NLMMWVPDWDGVIP--------PPAILKPRPRWTGKQIISMAL------PSG 600

Query: 521 ANLKTKGRAYTA-NEEFCH-RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            NL    +  +A +E+F    D  +++   +L+ G   K T+G+ G   V + +  ++G 
Sbjct: 601 LNLLRVDKDNSALSEKFAPLNDGGLLIHGGQLMYGMFSKKTVGASG-GGVIHTIFNEYGP 659

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
             AV        + +++L++ GFSIGIGD  P
Sbjct: 660 GTAVAFFNGAQAIVNYWLLHNGFSIGIGDTIP 691



 Score =  103 bits (257), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 62/181 (34%), Positives = 96/181 (53%), Gaps = 15/181 (8%)

Query: 1224 KQLLPSVVIKGVQGINRAVIHE-------EDVEGVT--------KYKLLVEGDNLRDVMA 1268
            + LL ++ ++GV G+ RA I+E       ED    T        ++ L   G  L +V+A
Sbjct: 1285 QHLLDTLTLRGVNGVERAFINEKSKVRVLEDGSLFTSKVDPLCKEWVLETSGSALGEVLA 1344

Query: 1269 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK 1328
              GV   +  SN   EV++  GIEAAR+ ++ E+  V+   G  ++ RH  L+ D+MT +
Sbjct: 1345 VPGVDATRTYSNQFIEVFEVFGIEAARTAVLRELTQVLAFDGSYVNHRHLALLVDVMTVR 1404

Query: 1329 GEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGT 1388
            G +  +TRHG+ +     L   SFE T + L +AA +G+ D   GVSE +I+G     GT
Sbjct: 1405 GYLTPVTRHGINRADNGALMRCSFEETVEILLEAAAFGELDDCRGVSENLILGQMAPAGT 1464

Query: 1389 G 1389
            G
Sbjct: 1465 G 1465



 Score = 99.4 bits (246), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QR+LVK+LE++ V
Sbjct: 811 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMV 870

Query: 666 QYD 668
           +YD
Sbjct: 871 KYD 873



 Score = 91.3 bits (225), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 80/289 (27%), Positives = 135/289 (46%), Gaps = 59/289 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLD--KDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N + NI TP +T Y +  +  D + A+ ++  +E T+L  V E  E  + P
Sbjct: 1117 GVPRLKEILNVATNIKTPSMTVYQEPGRTHDKEGAKQLRSVVEHTSLRSVTEATEIYYDP 1176

Query: 822  DDSFILIKLDMDRIR---LLHLEVDIDS-------IRYCIERTRGISGHLTVSGHSFLIL 871
            D    +I+ D D +    ++  +V  DS       +R  + R + +   LTV   +  I 
Sbjct: 1177 DIQSTVIENDRDMVESYFIIPEDVTDDSSRQSKWLLRIILSRPKLLDKGLTVQDVATRIK 1236

Query: 872  K--PKD-----SSKSFNSKMYQMKQ-------------------------LLPSVVIKGV 899
            +  PKD     S  + + ++ +++Q                         LL ++ ++GV
Sbjct: 1237 QAYPKDIAVIFSDNNADEQVIRIRQIQDHKEDEDDDDIEYDVTLKKLEQHLLDTLTLRGV 1296

Query: 900  QGINRAVIHE-------EDVEGVT--------KYKLLVEGDNLRDVMATYGVKGVKCSSN 944
             G+ RA I+E       ED    T        ++ L   G  L +V+A  GV   +  SN
Sbjct: 1297 NGVERAFINEKSKVRVLEDGSLFTSKVDPLCKEWVLETSGSALGEVLAVPGVDATRTYSN 1356

Query: 945  NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
               EV++  GIEAAR+ ++ E+  V+   G  ++ RH  L+ D+MT +G
Sbjct: 1357 QFIEVFEVFGIEAARTAVLRELTQVLAFDGSYVNHRHLALLVDVMTVRG 1405



 Score = 77.4 bits (189), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 55/213 (25%), Positives = 99/213 (46%), Gaps = 20/213 (9%)

Query: 110 DPQRT-PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVIN 168
           D QR  P   GL D R+GT  ++ NC TC +   +C GHFG+I+L  PVFHIG+   +  
Sbjct: 44  DEQRQRPRTKGLNDPRLGTIDRQWNCETCEEGQKECPGHFGHIELATPVFHIGFLTKIKK 103

Query: 169 ILQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKSLKKKILETTKKVSVC---P 224
           +L+++C N  C ++      +    A ++R+P   +         I   +K +++C   P
Sbjct: 104 LLETVCHN--CGKIKANTSDSKFLEALRMRDPKRRF-------DHIWRLSKDITICEADP 154

Query: 225 HCGEINGVVKKCGLLKISHEKYKNR--TKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGL 282
              E     K+       H    N   T +K+ I   L+  +  +     E++  +    
Sbjct: 155 PPDEDEPYAKESSKPTRMHGGCGNAQPTIRKEGIT--LVGTWKPSKSMMDEMDMQQPEK- 211

Query: 283 IQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKP 315
            +T+ P   L +F  I  ED+ ++ ++ + ++P
Sbjct: 212 -KTITPQMALNIFRNISHEDVRIMGLSNDYARP 243



 Score = 53.1 bits (126), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 24/41 (58%), Positives = 27/41 (65%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            A   ++ +A       VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1068 AIESRFAKANAPAGEMVGVLAAQSIGEPATQMTLNTFHFAG 1108


>gi|448336438|ref|ZP_21525537.1| DNA-directed RNA polymerase subunit A'' [Natrinema pallidum DSM 3751]
 gi|445629178|gb|ELY82472.1| DNA-directed RNA polymerase subunit A'' [Natrinema pallidum DSM 3751]
          Length = 398

 Score =  166 bits (421), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 108/341 (31%), Positives = 178/341 (52%), Gaps = 53/341 (15%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A+A   +Y+  ++EP   VG ++AQSIGEPGTQ+T+ TFH+AG            + E +
Sbjct: 48   AKAVETRYLDTRVEPLDPVGTVSAQSIGEPGTQLTMNTFHYAGVAEIDVTQGLPRLIELV 107

Query: 1152 EEVFVPDDSFILIKLD----------------MDRIRLLHL---EVDIDSIRYCI----- 1187
            +    PD   + + L+                ++  ++L L     ++  +R  I     
Sbjct: 108  DARKTPDTPMMTVYLEDEYATEREKAHEVVWNIEATQILALGDVSTNVADMRVQISLNKD 167

Query: 1188 ---------ERTRGIS----GHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKG 1234
                     E   GI     G  TV   + +   P++ S      + Q+ + L  +  KG
Sbjct: 168  TLQERLITAEEVAGIIEDSLGVKTVQQGTQIEFGPEEPSYR---DLLQLVEELRDITFKG 224

Query: 1235 VQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEA 1293
            ++ ++R VI  E+++ G  ++ L  EG    DV+   GV   + + NN +E+++ LGIEA
Sbjct: 225  IEEVSRVVIRREELDTGTEEFVLYTEGSAFGDVLEIEGVDASRTTCNNIHEIHRNLGIEA 284

Query: 1294 ARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASF 1352
            AR  I+ E    +   G+  ++ RH MLVAD+MT++GE+  I RHG++  KESVL  A+F
Sbjct: 285  AREAIIEETNNTLAEQGLDDVNVRHLMLVADMMTNRGEIESIGRHGISGSKESVLARAAF 344

Query: 1353 ENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            E T +HL +AA +G+ D + GV+E +I+G P+ +GTG + L
Sbjct: 345  EVTVNHLLNAAIHGEVDELDGVTENVIVGKPIKLGTGDVDL 385



 Score = 98.6 bits (244), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 67/239 (28%), Positives = 127/239 (53%), Gaps = 21/239 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T YL+ +  T+ + A  V   +E T    LG+V   + ++
Sbjct: 99  GLPRLIELVDARKTPDTPMMTVYLEDEYATEREKAHEVVWNIEATQILALGDVSTNVADM 158

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSK 878
            V        ++ +++  L    +  + +   IE + G+    TV   + +   P++ S 
Sbjct: 159 RV--------QISLNKDTLQERLITAEEVAGIIEDSLGVK---TVQQGTQIEFGPEEPSY 207

Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVK 937
                + Q+ + L  +  KG++ ++R VI  E+++ G  ++ L  EG    DV+   GV 
Sbjct: 208 R---DLLQLVEELRDITFKGIEEVSRVVIRREELDTGTEEFVLYTEGSAFGDVLEIEGVD 264

Query: 938 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEV 995
             + + NN +E+++ LGIEAAR  I+ E    +   G+  ++ RH MLVAD+MT++GE+
Sbjct: 265 ASRTTCNNIHEIHRNLGIEAAREAIIEETNNTLAEQGLDDVNVRHLMLVADMMTNRGEI 323


>gi|315056155|ref|XP_003177452.1| DNA-directed RNA polymerase II subunit RPB1 [Arthroderma gypseum
           CBS 118893]
 gi|311339298|gb|EFQ98500.1| DNA-directed RNA polymerase II subunit RPB1 [Arthroderma gypseum
           CBS 118893]
          Length = 1748

 Score =  166 bits (421), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 98/278 (35%), Positives = 153/278 (55%), Gaps = 35/278 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D +LFNRQPSLHK S+M+HR +V+P+ TFR N  V TPYNADFDGDEMN+H+PQ+EEA
Sbjct: 455 DGDFILFNRQPSLHKESMMSHRVRVMPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSEEA 514

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L++L ++            N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 515 RAE----LNQLCLVPL----------NIVSPQRNGPLMGIVQDTLCGIYKICRRDVFLTK 560

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M     L+    D  G++ +       P + ++    W+GKQ+ S++L      P  
Sbjct: 561 EQVM----NLLLWVPDWDGVLPQ-------PAI-LKPRPRWSGKQMISMVL------PSG 602

Query: 521 AN-LKTKGRAYTANEEFCH-RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            N L+        +E+F    D  V++   EL+ G   K T+G+ G   V + +  ++G 
Sbjct: 603 LNLLRIDKDKSPISEKFSPLADGGVLVHGGELMYGMFSKKTVGATG-GGVVHTIFNEYGP 661

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           D A++      R+ +++L++ GFSIGIGD  P    +Q
Sbjct: 662 DTAMSFFNGAQRVVNYWLLHNGFSIGIGDTIPDLATIQ 699



 Score =  103 bits (257), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 60/180 (33%), Positives = 94/180 (52%), Gaps = 15/180 (8%)

Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMAT 1269
             LL ++ ++GV GI+RA I+E+    V                ++ L   G  L DV+A 
Sbjct: 1288 HLLDTLTLRGVPGIDRAFINEKSRTRVLEDGSLHQSASDPECKEWVLETSGSALADVLAI 1347

Query: 1270 YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 1329
             G+   +  SN   E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1348 PGIDASRTYSNQFVEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLVDVMTSRG 1407

Query: 1330 EVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
             ++ +TRHG+ +     L   SFE T + L DAA + + D   GVSE +I+G     GTG
Sbjct: 1408 FLMAVTRHGINRADTGALMRCSFEETVEILLDAAAFAELDDCRGVSENLILGQMAPAGTG 1467



 Score = 99.4 bits (246), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QR+LVK+LE++ V
Sbjct: 813 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMV 872

Query: 666 QYD 668
           +YD
Sbjct: 873 KYD 875



 Score = 86.3 bits (212), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 75/289 (25%), Positives = 135/289 (46%), Gaps = 59/289 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYL--DKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N + NI TP +T Y   ++  + + A+ ++  +E T+L  V E  E  + P
Sbjct: 1119 GVPRLKEILNVATNIKTPSMTVYQAPERRMNKESAKQLRSIVEHTSLRSVTESTEIYYDP 1178

Query: 822  DDSFILIKLDMDRIR---LLHLEVDIDS-------IRYCIERTRGISGHLTVSGHSFLIL 871
            +    +I+ D+D +    ++  +V  DS       +R  + R + +   LTV   +  I 
Sbjct: 1179 NIQSTVIENDIDMVESYFIIPEDVADDSSRQSKWLLRIILSRPKLLDKGLTVQDVATKIK 1238

Query: 872  K--PKD-----SSKSFNSKMYQMKQ-------------------------LLPSVVIKGV 899
            +  P+D     S  + + ++ +++Q                         LL ++ ++GV
Sbjct: 1239 EAYPQDIAVIFSDNNADEQVVRIRQIQDPKQDEDDDDTEYDVTLKKLESHLLDTLTLRGV 1298

Query: 900  QGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMATYGVKGVKCSSN 944
             GI+RA I+E+    V                ++ L   G  L DV+A  G+   +  SN
Sbjct: 1299 PGIDRAFINEKSRTRVLEDGSLHQSASDPECKEWVLETSGSALADVLAIPGIDASRTYSN 1358

Query: 945  NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
               E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1359 QFVEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLVDVMTSRG 1407



 Score = 81.3 bits (199), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 58/222 (26%), Positives = 101/222 (45%), Gaps = 38/222 (17%)

Query: 110 DPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINI 169
           D ++ P   GL D R+GT  +   C TC + ++DC GHFG+I+L  PVFHIG+   +  +
Sbjct: 45  DQRQRPREKGLNDPRLGTIDRNWRCATCEEGINDCPGHFGHIELSTPVFHIGFLTKIKKL 104

Query: 170 LQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKSLKKKIL-------------- 214
           L+++C N  C ++           A + R+P   +     L K IL              
Sbjct: 105 LETVCHN--CGKIKANASDQKYLDALRFRDPKKRFDAIWRLSKDILVCEADPPEDDDPFA 162

Query: 215 -ETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPE 273
            E++K V     CG +   V+K G+  +   K    +K +D + ++             E
Sbjct: 163 KESSKPVQGHGGCGNVQPQVRKEGITLMGTWK---PSKMRDMMDDN-------------E 206

Query: 274 IEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKP 315
           I+  +K    + + P   L +F  I  ED+ L+ ++ + ++P
Sbjct: 207 IQQPEK----KQITPQMALTIFRNISEEDVRLMGLSNDYARP 244



 Score = 55.8 bits (133), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/41 (60%), Positives = 28/41 (68%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            A   ++ +A   P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1070 AIESRFGKAAANPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1110


>gi|20090127|ref|NP_616202.1| DNA-directed RNA polymerase subunit A' [Methanosarcina acetivorans
           C2A]
 gi|19915107|gb|AAM04682.1| DNA-directed RNA polymerase, subunit A [Methanosarcina acetivorans
           C2A]
          Length = 880

 Score =  166 bits (420), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 103/269 (38%), Positives = 148/269 (55%), Gaps = 33/269 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D VLFNRQPSLHK+SIMAH  KVLP++TFR N  VC PYNADFDGDEMN+H  QTEE+
Sbjct: 412 DGDTVLFNRQPSLHKMSIMAHSVKVLPNKTFRLNPAVCPPYNADFDGDEMNMHALQTEES 471

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              AK+LM  + N+++PR G  +I    D I+G +LLT+   F N 
Sbjct: 472 RAE--------------AKILMQVQENILSPRFGGPIIGGIHDHISGLFLLTR---FEN- 513

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSW-NPVVFVRTA-VIWTGKQIFSLILKPNRDCP 518
                I+S    D      I+++   R+   P          WTGKQIFS IL    +  
Sbjct: 514 ----HISSHEAYD------ILRKSRARNLPEPAGHDEDGKPFWTGKQIFSQILPETLNME 563

Query: 519 VNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
             A + +     T  +E C  D+YV++RN EL+ G++D++ +G+  K  +   ++++ G 
Sbjct: 564 FAAQVCS--HCDTCKKEECPNDAYVVIRNGELILGTIDEAAIGA-FKGKIQDRIIKEVGP 620

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           +     +  ++++    +M  G S GI D
Sbjct: 621 EAGARFVDDMTKLAIRSIMRTGLSFGIAD 649



 Score = 97.1 bits (240), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 70/254 (27%), Positives = 117/254 (46%), Gaps = 44/254 (17%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           +++ S   I++ + Y  D    PI  GL+D ++G       C TC     +C GHFG+I+
Sbjct: 24  IRKMSATPIITADTY--DDDGFPIDMGLMDTKLGVIDPGLRCKTCSGRAGECPGHFGHIE 81

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKK 212
           L  PV H+G+ + +  +L++ C+   C+R+LL   +   F  +L        +   L  +
Sbjct: 82  LVAPVVHVGFNKVIRKLLRATCRK--CSRLLLEPAQKQQFLDQLLAVEEIGHMPDDLINE 139

Query: 213 ILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNP 272
           + +   KV  CP+C E          L+I  EK                +EY E      
Sbjct: 140 VYKEASKVKTCPYCNEEQ--------LEIKFEKP---------------SEYLENG---- 172

Query: 273 EIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRP 332
                      + L P E+   FE +P EDI ++ M+ + ++P  +ILT L VPP  +RP
Sbjct: 173 -----------EKLTPTEIRDRFENVPDEDIRVIGMDPKNARPEWMILTVLPVPPVTVRP 221

Query: 333 SVI--SDLKSDNDV 344
           S+   S  +S++D+
Sbjct: 222 SITLESGQRSEDDL 235



 Score = 93.2 bits (230), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 41/66 (62%), Positives = 56/66 (84%), Gaps = 1/66 (1%)

Query: 606 GDV-TPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           GD+ +   GFV+ S+ SGL PTE+FFH +GGREGLVDTAV+T+++GY+QRRLV +L+DL 
Sbjct: 771 GDLGSDAHGFVKASYKSGLNPTEYFFHAIGGREGLVDTAVRTSQSGYLQRRLVNALQDLE 830

Query: 665 VQYDMS 670
           VQYD++
Sbjct: 831 VQYDLT 836


>gi|225677609|gb|EEH15893.1| DNA-directed RNA polymerase II subunit RPB1 [Paracoccidioides
           brasiliensis Pb03]
          Length = 2106

 Score =  166 bits (420), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 96/270 (35%), Positives = 150/270 (55%), Gaps = 31/270 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DV+LFNRQPSLHK S+MAHR +V+P+ TFR N  V TPYNADFDGDEMN+H+PQ+EEA
Sbjct: 456 DGDVILFNRQPSLHKESMMAHRVRVMPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L +L ++  +          +V+P+    L+   QD + G Y + +++ F ++
Sbjct: 516 RAE----LSQLCMVPLQ----------IVSPQRNGPLMGIVQDTLCGIYKICRRDVFLSK 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M I    +    D  G+I +       P + ++    WTGKQ+ S++L P     +N
Sbjct: 562 EQVMNI----LLWVPDWDGVIPQ-------PAI-LKPRPRWTGKQLISMVLPPG----LN 605

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
                + RA  + +     D  V++   EL+ G   K T+G+ G   + + +  ++G + 
Sbjct: 606 LLRVDRDRAPRSEKFSPPADGGVLVHGGELMYGMFSKKTVGATG-GGIIHTIFNEYGPET 664

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           A+        + +++L++ GFSIGIGD  P
Sbjct: 665 AMNFFNGAQTVVNYWLLHHGFSIGIGDTIP 694



 Score = 99.0 bits (245), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QR+LVK+LE++ V
Sbjct: 814 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMV 873

Query: 666 QYD 668
           +YD
Sbjct: 874 KYD 876



 Score = 98.2 bits (243), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 59/180 (32%), Positives = 92/180 (51%), Gaps = 15/180 (8%)

Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMAT 1269
             LL ++ ++GV GI RA I+E+    V                ++ L   G  L +V+  
Sbjct: 1289 HLLDTLTLRGVAGIERAFINEKSRVRVLEDGSLHQSSEDPLCKEWVLETSGSALGEVLTI 1348

Query: 1270 YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 1329
             GV   +  SN   E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1349 PGVDTTRTYSNQFVEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLVDVMTSRG 1408

Query: 1330 EVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
             ++ +TRHG+ +     L   SFE T + L DAA + + D   GVSE +I+G     GTG
Sbjct: 1409 FLMAVTRHGINRADTGALMRCSFEETVEILLDAAAFAELDDCRGVSENLILGQMAPAGTG 1468



 Score = 85.9 bits (211), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 76/289 (26%), Positives = 132/289 (45%), Gaps = 59/289 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLD--KDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N + +I TP +T Y D  +  D + A+ ++  +E T+L  V E  E  + P
Sbjct: 1120 GVPRLKEILNVATHIKTPSMTVYQDSSRAMDKESAKQLRSVVEHTSLRSVTEATEIYYDP 1179

Query: 822  DDSFILIKLDMDRIR---LLHLEVDIDS-------IRYCIERTRGISGHLTVSGHSFLIL 871
            D    +I+ D D +    ++  +V  DS       +R  + R + +  +LTV   +  I 
Sbjct: 1180 DIQSTVIEADRDMVESYFIIPEDVADDSSRQSKWLLRIILSRPKLLDKNLTVQDVAMRIK 1239

Query: 872  K--PKD-----SSKSFNSKMYQMKQ-------------------------LLPSVVIKGV 899
               P+D     S  + + ++ +++Q                         LL ++ ++GV
Sbjct: 1240 DAYPQDIAVIFSDNNADEQVIRIRQIQDTKQDDDDDDTEYDVTLKKLEGHLLDTLTLRGV 1299

Query: 900  QGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMATYGVKGVKCSSN 944
             GI RA I+E+    V                ++ L   G  L +V+   GV   +  SN
Sbjct: 1300 AGIERAFINEKSRVRVLEDGSLHQSSEDPLCKEWVLETSGSALGEVLTIPGVDTTRTYSN 1359

Query: 945  NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
               E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1360 QFVEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLVDVMTSRG 1408



 Score = 84.0 bits (206), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 60/231 (25%), Positives = 103/231 (44%), Gaps = 42/231 (18%)

Query: 110 DPQRT-PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVIN 168
           D QR  P   GL D R+GT  +   C TC + ++DC GHFG+I+L  PVFHIG+   +  
Sbjct: 44  DEQRQRPREKGLNDPRLGTIDRNWRCATCEEGINDCPGHFGHIELSTPVFHIGFLTKIKK 103

Query: 169 ILQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKSLKKKIL------------- 214
           +L+++C N  C ++           A + R+P   +     L K +L             
Sbjct: 104 LLETVCHN--CGKIKANTNDQKYLEALRFRDPKRRFDAIWRLSKDVLICEADPTPDDDDP 161

Query: 215 ---ETTKKVSVCPHCGEINGVVKKCGLLKISHEK-YKNRTKKKDAIVEDLLAEYNEAVKF 270
              E +K V     CG +   ++K G+  +   K  KNR      +++D+  +  E  + 
Sbjct: 162 FSKEASKPVRSHGGCGNMQPQIRKEGISLVGTWKPNKNRD-----MMDDMDIQQPEKRQI 216

Query: 271 NPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
            P++                 L +F  I  ED+ L+ ++ + ++P  +I+T
Sbjct: 217 TPQM----------------ALNIFRNISEEDVRLMGLSNDYARPEWMIIT 251



 Score = 57.4 bits (137), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 26/41 (63%), Positives = 28/41 (68%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            A   ++ RA   P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1071 AIENRFSRAMANPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1111


>gi|9955855|dbj|BAB12227.1| RNA polymerase II largest subunit [Aspergillus oryzae]
 gi|83767526|dbj|BAE57665.1| unnamed protein product [Aspergillus oryzae RIB40]
 gi|391867452|gb|EIT76698.1| RNA polymerase II, large subunit [Aspergillus oryzae 3.042]
          Length = 1748

 Score =  166 bits (420), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 100/272 (36%), Positives = 145/272 (53%), Gaps = 35/272 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DV+LFNRQPSLHK S+M HR +V+P+ TFR N  V TPYNADFDGDEMN+H+PQ+EE+
Sbjct: 453 DGDVILFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSEES 512

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE L            A V M    N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 513 RAELL----------QLALVPM----NIVSPQRNGPLMGIVQDTLCGIYKICRRDTFLTK 558

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M     L+    D  G+I         P   ++    WTGKQI S+ L      P  
Sbjct: 559 EQVM----NLMMWVPDWDGVIP--------PPAILKPRPRWTGKQIISMAL------PSG 600

Query: 521 ANLKTKGRAYTA-NEEFCH-RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            NL    +  +A +E+F    D  +++   +L+ G   K T+G+ G   V + +  ++G 
Sbjct: 601 LNLLRVDKDNSALSEKFAPLNDGGLLIHGGQLMYGMFSKKTVGASG-GGVIHTIFNEYGP 659

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
             AV        + +++L++ GFSIGIGD  P
Sbjct: 660 GTAVAFFNGAQAIVNYWLLHNGFSIGIGDTIP 691



 Score =  103 bits (257), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 62/181 (34%), Positives = 96/181 (53%), Gaps = 15/181 (8%)

Query: 1224 KQLLPSVVIKGVQGINRAVIHE-------EDVEGVT--------KYKLLVEGDNLRDVMA 1268
            + LL ++ ++GV G+ RA I+E       ED    T        ++ L   G  L +V+A
Sbjct: 1285 QHLLDTLTLRGVNGVERAFINEKSKVRVLEDGSLFTSKVDPLCKEWVLETSGSALGEVLA 1344

Query: 1269 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK 1328
              GV   +  SN   EV++  GIEAAR+ ++ E+  V+   G  ++ RH  L+ D+MT +
Sbjct: 1345 VPGVDATRTYSNQFIEVFEVFGIEAARTAVLRELTQVLAFDGSYVNHRHLALLVDVMTVR 1404

Query: 1329 GEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGT 1388
            G +  +TRHG+ +     L   SFE T + L +AA +G+ D   GVSE +I+G     GT
Sbjct: 1405 GYLTPVTRHGINRADNGALMRCSFEETVEILLEAAAFGELDDCRGVSENLILGQMAPAGT 1464

Query: 1389 G 1389
            G
Sbjct: 1465 G 1465



 Score = 99.4 bits (246), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QR+LVK+LE++ V
Sbjct: 811 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMV 870

Query: 666 QYD 668
           +YD
Sbjct: 871 KYD 873



 Score = 91.3 bits (225), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 80/289 (27%), Positives = 135/289 (46%), Gaps = 59/289 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLD--KDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N + NI TP +T Y +  +  D + A+ ++  +E T+L  V E  E  + P
Sbjct: 1117 GVPRLKEILNVATNIKTPSMTVYQEPGRTHDKEGAKQLRSVVEHTSLRSVTEATEIYYDP 1176

Query: 822  DDSFILIKLDMDRIR---LLHLEVDIDS-------IRYCIERTRGISGHLTVSGHSFLIL 871
            D    +I+ D D +    ++  +V  DS       +R  + R + +   LTV   +  I 
Sbjct: 1177 DIQSTVIENDRDMVESYFIIPEDVTDDSSRQSKWLLRIILSRPKLLDKGLTVQDVATRIK 1236

Query: 872  K--PKD-----SSKSFNSKMYQMKQ-------------------------LLPSVVIKGV 899
            +  PKD     S  + + ++ +++Q                         LL ++ ++GV
Sbjct: 1237 QAYPKDIAVIFSDNNADEQVIRIRQIQDHKEDEDDDDIEYDVTLKKLEQHLLDTLTLRGV 1296

Query: 900  QGINRAVIHE-------EDVEGVT--------KYKLLVEGDNLRDVMATYGVKGVKCSSN 944
             G+ RA I+E       ED    T        ++ L   G  L +V+A  GV   +  SN
Sbjct: 1297 NGVERAFINEKSKVRVLEDGSLFTSKVDPLCKEWVLETSGSALGEVLAVPGVDATRTYSN 1356

Query: 945  NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
               EV++  GIEAAR+ ++ E+  V+   G  ++ RH  L+ D+MT +G
Sbjct: 1357 QFIEVFEVFGIEAARTAVLRELTQVLAFDGSYVNHRHLALLVDVMTVRG 1405



 Score = 77.4 bits (189), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 55/213 (25%), Positives = 99/213 (46%), Gaps = 20/213 (9%)

Query: 110 DPQRT-PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVIN 168
           D QR  P   GL D R+GT  ++ NC TC +   +C GHFG+I+L  PVFHIG+   +  
Sbjct: 44  DEQRQRPRTKGLNDPRLGTIDRQWNCETCEEGQKECPGHFGHIELATPVFHIGFLTKIKK 103

Query: 169 ILQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKSLKKKILETTKKVSVC---P 224
           +L+++C N  C ++      +    A ++R+P   +         I   +K +++C   P
Sbjct: 104 LLETVCHN--CGKIKANTSDSKFLEALRMRDPKRRF-------DHIWRLSKDITICEADP 154

Query: 225 HCGEINGVVKKCGLLKISHEKYKNR--TKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGL 282
              E     K+       H    N   T +K+ I   L+  +  +     E++  +    
Sbjct: 155 PPDEDEPYAKESSKPTRMHGGCGNAQPTIRKEGIT--LVGTWKPSKSMMDEMDMQQPEK- 211

Query: 283 IQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKP 315
            +T+ P   L +F  I  ED+ ++ ++ + ++P
Sbjct: 212 -KTITPQMALNIFRNISHEDVRIMGLSNDYARP 243



 Score = 53.1 bits (126), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 24/41 (58%), Positives = 27/41 (65%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            A   ++ +A       VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1068 AIESRFAKANAPAGEMVGVLAAQSIGEPATQMTLNTFHFAG 1108


>gi|395646424|ref|ZP_10434284.1| DNA-directed RNA polymerase subunit A' [Methanofollis liminatans
           DSM 4140]
 gi|395443164|gb|EJG07921.1| DNA-directed RNA polymerase subunit A' [Methanofollis liminatans
           DSM 4140]
          Length = 880

 Score =  166 bits (420), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 95/269 (35%), Positives = 147/269 (54%), Gaps = 34/269 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIMAH  K++  +TFR N  VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 414 DGDIVLFNRQPSLHRMSIMAHHIKIMGGKTFRLNPAVCPPYNADFDGDEMNLHVPQTEEA 473

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
            AE              A++L+  + N+ +PR G  +I    D I+G +LLT +  +F +
Sbjct: 474 MAE--------------AEILVNVEENIRSPRFGGPIIGGIHDHISGIFLLTHEVRWFTK 519

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            + + +      +     G ++       N V +      W+ KQ+FS IL P     +N
Sbjct: 520 EEALYLLRHAEVEHLPEPGKVE-------NGVAY------WSNKQVFSAILPPG----IN 562

Query: 521 ANLKTKGRAY--TANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
              K     +  T  +E C +D+YV +R+ EL+ G++DK  +G+     +   ++R + +
Sbjct: 563 MIFKASSCKHCDTCKKELCDQDTYVKMRDGELITGTIDKKAIGA-FDGEIVNRIIRQYSQ 621

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
             A   +  ++R++   +M  GFS GI D
Sbjct: 622 KRAAQFINDVTRLSIRAIMFDGFSFGIDD 650



 Score =  110 bits (275), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 80/266 (30%), Positives = 127/266 (47%), Gaps = 43/266 (16%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G IE  +     ++Q S  +I+  + Y  D    P   GL+D  +G       C TC Q 
Sbjct: 8   GKIEFGLLSPKEIRQMSVRKIIWADTY--DDDGYPYSQGLMDLHLGVIDPGMRCKTCAQK 65

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
            SDC GHFG+I+L  PV H+GY R +  +L+  C+  +C R+LL  ++         + +
Sbjct: 66  ASDCPGHFGHIELAKPVIHVGYTRLIRKLLRVSCR--SCGRLLLSPDEITKIVGTEEDES 123

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDL 260
              +  K +KK+         VCP+CGE          LK++ EK    T   + +VE+ 
Sbjct: 124 GDLVTEKDIKKE--------RVCPYCGEQQ--------LKVNFEKP---TTFSEVVVEE- 163

Query: 261 LAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
                     N +   HK       L P ++    E IP +D+ LL +N ++++P   IL
Sbjct: 164 ----------NGKKGEHK-------LTPADIRARLERIPDDDLRLLGINPDVARPEWTIL 206

Query: 321 TRLLVPPNCIRPSVI--SDLKSDNDV 344
           T L VPP  +RPS+I  +  +S++D+
Sbjct: 207 TVLPVPPVTMRPSIILENGQRSEDDL 232



 Score = 92.0 bits (227), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 38/62 (61%), Positives = 53/62 (85%)

Query: 609 TPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +   GFV++S+ SGL PTEFFFH +GGREGLVDTAV+T+++GY+QRR++ +L+DL V+YD
Sbjct: 776 SAAHGFVRSSYKSGLNPTEFFFHAIGGREGLVDTAVRTSQSGYLQRRMINALQDLKVEYD 835

Query: 669 MS 670
            S
Sbjct: 836 RS 837


>gi|399949936|gb|AFP65592.1| DNA-directed RNA polymerase II largest chain [Chroomonas
           mesostigmatica CCMP1168]
          Length = 1473

 Score =  166 bits (420), Expect = 9e-38,   Method: Compositional matrix adjust.
 Identities = 92/271 (33%), Positives = 149/271 (54%), Gaps = 40/271 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHK+S+M H  K++ + TFR N    +PYNADFDGDEMN+HLPQT EA
Sbjct: 424 DGDVVLFNRQPSLHKMSMMGHVVKIMHYSTFRMNLSATSPYNADFDGDEMNLHLPQTIEA 483

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE L               L+   + +++ +  + ++   QD + GG+LL+ +++F NR
Sbjct: 484 KAELLN--------------LLMLPNCIISQQGNKPVMGIVQDSLVGGFLLSHRDSFLNR 529

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVV----FVRTAVIWTGKQIFSLILKPNRD 516
           +Q M +   L                + WN  +     ++  ++WTGKQIFS+ L     
Sbjct: 530 SQFMLLLMQL----------------QEWNGSIPFPTILKPRILWTGKQIFSVFLP---- 569

Query: 517 CPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
             +N   K+ G +         RD+ V++    L++G +DK ++G+ G  ++ +I  ++F
Sbjct: 570 -KINFLRKSLGHSEHEKSNISPRDTRVLILGGHLISGIIDKRSVGASG-GSLIHICWKEF 627

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           G   A   + +   + + +L ++GFS+GIGD
Sbjct: 628 GPKKASLFVSQFQLIVNTWLQSKGFSVGIGD 658



 Score =  100 bits (249), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 43/74 (58%), Positives = 59/74 (79%), Gaps = 7/74 (9%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSF 671
           +GFVQNS+ SGL+P EFFFH MGGREGL+DTA+KT+ETGY+QRRL K++E++ V+YD++ 
Sbjct: 787 RGFVQNSYISGLSPEEFFFHAMGGREGLIDTAIKTSETGYIQRRLSKAMENISVEYDLTV 846

Query: 672 DAA-------FYGQ 678
             +       FYG+
Sbjct: 847 RNSEGGIIEFFYGE 860



 Score = 98.2 bits (243), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 59/188 (31%), Positives = 108/188 (57%), Gaps = 14/188 (7%)

Query: 1220 MYQMKQLLPSVVIK--GVQGINRAVIHEEDV----------EGVTKYKLLVEGDNLRDVM 1267
            + ++K L+ ++ +K  G   I +A+I + D               +Y L  EG +LR ++
Sbjct: 1273 LIRLKYLIVNINLKIHGTSKIKKALIRKIDFPKFDPLKGSFRSQKEYVLDTEGVDLRYIL 1332

Query: 1268 ATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTS 1327
               G+  ++ SSN+  E+++ LG+EA+R  ++ E++ ++   G  ++ RH  L+ D+MT 
Sbjct: 1333 NFPGMDHIRSSSNDIVEIFRILGVEASRRILIQELRNLISFDGSYVNSRHLYLLVDIMTH 1392

Query: 1328 KGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMG-LPMNV 1386
            +G++L ITRHG+ K +   +   SFE T D L+ AA +G +D +  +S  +++G LP+ +
Sbjct: 1393 RGKLLSITRHGINKTEIGPIAKCSFEETIDILYQAAAFGISDNLKSISASVLLGQLPL-L 1451

Query: 1387 GTGLIKLL 1394
            GTG I L 
Sbjct: 1452 GTGKIDLF 1459



 Score = 75.1 bits (183), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 73/299 (24%), Positives = 136/299 (45%), Gaps = 66/299 (22%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARI--VKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEIIN SR   TP +T Y  K+      +I   +  LE  TL  + +    ++ P
Sbjct: 1099 GVPRLKEIINVSRTAKTPSLTIYFKKNFAFAIGKIKHFQQTLEYLTLKSLMDKSLFIYDP 1158

Query: 822  DDSFILIK--------------LDMDRIRL----LHLEVDID-------SIRYCIERTRG 856
            D    + K              +++D   L    L L++  +       SI   +E+ + 
Sbjct: 1159 DPYLTVFKKNRFMVENFYEIPEINLDNTSLGTWVLLLKIQPEEFVHRRLSIEQLVEKIKR 1218

Query: 857  ISGHLTV------SGHSFLILKPK-------------DSSKSFNS--------KMYQMKQ 889
             S  L++        H  L+++ K             + SK+F +         + ++K 
Sbjct: 1219 KSKPLSLLIINSNENHDCLLMRIKVFWPKFNWSKNLSNESKNFKTVFQIFERQYLIRLKY 1278

Query: 890  LLPSVVIK--GVQGINRAVIHEEDV----------EGVTKYKLLVEGDNLRDVMATYGVK 937
            L+ ++ +K  G   I +A+I + D               +Y L  EG +LR ++   G+ 
Sbjct: 1279 LIVNINLKIHGTSKIKKALIRKIDFPKFDPLKGSFRSQKEYVLDTEGVDLRYILNFPGMD 1338

Query: 938  GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL 996
             ++ SSN+  E+++ LG+EA+R  ++ E++ ++   G  ++ RH  L+ D+MT +G++L
Sbjct: 1339 HIRSSSNDIVEIFRILGVEASRRILIQELRNLISFDGSYVNSRHLYLLVDIMTHRGKLL 1397



 Score = 67.4 bits (163), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 61/225 (27%), Positives = 103/225 (45%), Gaps = 32/225 (14%)

Query: 119 GLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPT 178
           GL+D R+G   +   CTT      +C G+FG+++L  PVFH  +   V+ IL+  C +  
Sbjct: 47  GLMDPRLGAVDQNICCTTDMNEFIECPGYFGHLELAKPVFHESFMDFVLMILR--CVDHV 104

Query: 179 CARVLLG-EEKAAGFRAKLRNP--ALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKK 235
            +R++   +        K+RNP   LS L +       L++ K  S      E       
Sbjct: 105 TSRLIFNCDSPKVKNILKIRNPRQRLSMLSKLGSTSTGLKSEKNTSSDDFFEE------- 157

Query: 236 CGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLF 295
                I+++   +R    D     ++A++N+++   P           + L    + ++F
Sbjct: 158 ----NITYQPKYSR----DGWC--IIAKFNQSITSEPT----------RILGAERIHEIF 197

Query: 296 EAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKS 340
           E I   D   + +N  +SKP  +ILT L +PP  IRPSV+ D+ S
Sbjct: 198 EKISDLDSKKIGLNPSVSKPDWMILTVLPIPPPTIRPSVMFDMTS 242



 Score = 52.8 bits (125), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 21/37 (56%), Positives = 28/37 (75%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            +Y ++ I P   VG ++AQSIG+P TQMTL TFH+AG
Sbjct: 1054 QYRKSIINPGEMVGTISAQSIGQPATQMTLNTFHYAG 1090


>gi|45935349|gb|AAS79696.1| RNA polymerase III large subunit [Zamia muricata]
          Length = 548

 Score =  166 bits (420), Expect = 9e-38,   Method: Compositional matrix adjust.
 Identities = 87/223 (39%), Positives = 139/223 (62%), Gaps = 25/223 (11%)

Query: 390 MNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGY 449
           MN+H+PQTEEAR EAL               LM  ++NL TP+NGE+LIA+TQDF+T  +
Sbjct: 1   MNLHVPQTEEARTEAL--------------TLMGVQNNLCTPKNGEILIASTQDFLTSSF 46

Query: 450 LLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSL 509
           L+T+K+ F++RA +  +  + + D ++   +          P + ++   +WTGKQ+FS+
Sbjct: 47  LITRKDTFYDRA-SFCLMCSYMGDAAEPIDLP--------TPTI-LKPMELWTGKQLFSV 96

Query: 510 ILKPNRDCPVNANLKTKGRAYT-ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANV 568
           +++PN +  V  NL    + Y+ + E  C  D +V  RNSEL++G + K+TLG+G K  +
Sbjct: 97  LVRPNANVRVFVNLMLTEKNYSKSGETMCPNDGFVYFRNSELISGQIGKATLGNGNKDGL 156

Query: 569 FYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           F +LLRD+    A ++M RL+++++ ++ N GFSIGI DV PG
Sbjct: 157 FTVLLRDYNTHAAASSMNRLAKLSARWIGNHGFSIGIDDVQPG 199



 Score =  106 bits (264), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 60/111 (54%), Positives = 71/111 (63%), Gaps = 9/111 (8%)

Query: 607 DVTPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D TP  +GFV NSF++GLT TEFFFHTMGGREGLVDTAVKTAETGYM RRL+K+LEDL  
Sbjct: 318 DKTPAAKGFVANSFYTGLTATEFFFHTMGGREGLVDTAVKTAETGYMSRRLMKALEDLST 377

Query: 666 QYDMSFDAA-------FYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 709
            YD +   A        YG  D +  V+     G P+N+   L+K     P
Sbjct: 378 HYDGTVRNASGGIVQLLYGD-DAMDPVNMEGKNGTPLNLDRILMKAKATCP 427



 Score = 56.6 bits (135), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 23/42 (54%), Positives = 35/42 (83%)

Query: 21 VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRA 62
           LM  ++NL TP+NGE+LIA+TQDF+T  +L+T+K+ F++RA
Sbjct: 17 TLMGVQNNLCTPKNGEILIASTQDFLTSSFLITRKDTFYDRA 58


>gi|148642969|ref|YP_001273482.1| DNA-directed RNA polymerase subunit A' [Methanobrevibacter smithii
           ATCC 35061]
 gi|148551986|gb|ABQ87114.1| DNA-dependent RNA polymerase, subunit A', RpoA [Methanobrevibacter
           smithii ATCC 35061]
          Length = 894

 Score =  166 bits (420), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 98/274 (35%), Positives = 148/274 (54%), Gaps = 42/274 (15%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++S+MAH  +VLP++TFR N CVC PYNADFDGDEMN+H+ QT+E+
Sbjct: 412 DGDMVLFNRQPSLHRMSMMAHEVRVLPYKTFRLNLCVCPPYNADFDGDEMNMHVFQTDES 471

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              AK LM  + ++++PR G  +I A  D I+G YLLT+  + F+ 
Sbjct: 472 RAE--------------AKSLMRVQEHILSPRFGGPIIGAIHDHISGAYLLTKPGSEFSE 517

Query: 461 AQTMRIASTLIADTSDICGIIKR---FSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDC 517
            Q ++              II++   F+  + +P    R    WTGK++FSL+L      
Sbjct: 518 EQALQ--------------IIRKSHLFNNENVDPKHLKRKHKNWTGKELFSLLL------ 557

Query: 518 PVNANLKTKG----RAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILL 573
           P + NL  K     +     EE C  D+YV++ + EL  G +D+   GS     +   ++
Sbjct: 558 PDDLNLVYKAEICQKCDVCKEEACDIDAYVVIEDGELKHGVIDEKAYGSFS-GRILDKIV 616

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           +++G   A   + R + +    +M  G +    D
Sbjct: 617 KEYGPARAREFLDRSTDLAICGIMKTGITTSTND 650



 Score = 98.6 bits (244), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 73/262 (27%), Positives = 125/262 (47%), Gaps = 42/262 (16%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G ++ ED +++ S ++I + + Y +D    PI +GL+D  +G       C +CG    +C
Sbjct: 14  GLMSPED-IREMSVVKIETPDTYDEDG--YPIENGLMDPHLGVIDPSLKCRSCGYRGGEC 70

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFG I+L  PV H+G+   +  IL+S C    C RVLL +++   +  K+++    + 
Sbjct: 71  QGHFGSIELARPVIHVGFGDIIHKILRSTCNE--CGRVLLTDDEIFKYTEKIKDAQNHHE 128

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEY 264
               + K+I    ++  VCPHC                           +A  +D+  + 
Sbjct: 129 NLTKILKEIYNEARR-DVCPHC---------------------------EAAQDDITIDK 160

Query: 265 NEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLL 324
             ++    E E +K       L   EV +  E I  ED  +L +N E+++P  L+LT L 
Sbjct: 161 PVSIVQKMEGEDYK-------LTASEVRERLERISDEDAFVLGVNPEVARPEWLVLTVLP 213

Query: 325 VPPNCIRPSVISDL--KSDNDV 344
           VPP  +RPS+  D   +S++D+
Sbjct: 214 VPPVTVRPSITLDTGERSEDDL 235



 Score = 87.4 bits (215), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 37/56 (66%), Positives = 47/56 (83%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQ 666
            +GFV +S+  GL P EFFFH MGGREGLVDTA++TA++GYMQRRLV +L+DL V+
Sbjct: 779 AKGFVHSSYKKGLDPIEFFFHAMGGREGLVDTAIRTAQSGYMQRRLVNALQDLQVK 834


>gi|448354758|ref|ZP_21543513.1| DNA-directed RNA polymerase subunit A'' [Natrialba hulunbeirensis JCM
            10989]
 gi|445637089|gb|ELY90245.1| DNA-directed RNA polymerase subunit A'' [Natrialba hulunbeirensis JCM
            10989]
          Length = 399

 Score =  166 bits (420), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 106/344 (30%), Positives = 177/344 (51%), Gaps = 59/344 (17%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A+A   +YV  ++EP   VG ++AQSIGEPGTQ+T+ TFH+AG            + E +
Sbjct: 48   AKAVEARYVDTRVEPLDPVGTVSAQSIGEPGTQLTMNTFHYAGVAEIDVTQGLPRLIELV 107

Query: 1152 EEVFVPD---------DSF-------------------------------ILIKLDMDRI 1171
            +    PD         D F                               + +++ ++R 
Sbjct: 108  DARKTPDTPMMTVYLEDEFATERERAHEVVWNIEATKILALGDVSTNVADMRVQISLNRD 167

Query: 1172 RLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVV 1231
             L    +  + +   IE   G+S   TV   + +   P++ S      + Q+ + L  + 
Sbjct: 168  TLEERMITPEEVAEIIEDNLGVS---TVQQGTDIQFGPEEPSYR---DLLQLVEELREIT 221

Query: 1232 IKGVQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLG 1290
             KG++ ++R VI  E+++ G  ++ L  EG    DV+   GV   + + NN +E+++ LG
Sbjct: 222  FKGIEEVSRVVIRREELDDGDEQFVLYTEGSAFGDVLEIEGVDASRTTCNNIHEIHRNLG 281

Query: 1291 IEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNL 1349
            IEAAR  I+ E    +   G+  ++ RH MLV+D+MT++GE+  I RHG++  K+SVL  
Sbjct: 282  IEAAREAIIEETNNTLAEQGLDDVNVRHLMLVSDMMTNRGEIESIGRHGISGSKDSVLAR 341

Query: 1350 ASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            A+FE T +HL +AA +G+ D + GV+E +I+G P+ +GTG + L
Sbjct: 342  AAFEVTVNHLLNAAIHGEIDELDGVTENVIVGKPIKLGTGDVDL 385



 Score = 99.0 bits (245), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 68/239 (28%), Positives = 127/239 (53%), Gaps = 21/239 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T YL+ +  T+ + A  V   +E T    LG+V   + ++
Sbjct: 99  GLPRLIELVDARKTPDTPMMTVYLEDEFATERERAHEVVWNIEATKILALGDVSTNVADM 158

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSK 878
            V        ++ ++R  L    +  + +   IE   G+S   TV   + +   P++ S 
Sbjct: 159 RV--------QISLNRDTLEERMITPEEVAEIIEDNLGVS---TVQQGTDIQFGPEEPSY 207

Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVK 937
                + Q+ + L  +  KG++ ++R VI  E+++ G  ++ L  EG    DV+   GV 
Sbjct: 208 R---DLLQLVEELREITFKGIEEVSRVVIRREELDDGDEQFVLYTEGSAFGDVLEIEGVD 264

Query: 938 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEV 995
             + + NN +E+++ LGIEAAR  I+ E    +   G+  ++ RH MLV+D+MT++GE+
Sbjct: 265 ASRTTCNNIHEIHRNLGIEAAREAIIEETNNTLAEQGLDDVNVRHLMLVSDMMTNRGEI 323


>gi|222445206|ref|ZP_03607721.1| hypothetical protein METSMIALI_00829 [Methanobrevibacter smithii
           DSM 2375]
 gi|261350232|ref|ZP_05975649.1| DNA-directed RNA polymerase subunit A [Methanobrevibacter smithii
           DSM 2374]
 gi|222434771|gb|EEE41936.1| DNA-directed RNA polymerase subunit A' [Methanobrevibacter smithii
           DSM 2375]
 gi|288861018|gb|EFC93316.1| DNA-directed RNA polymerase subunit A [Methanobrevibacter smithii
           DSM 2374]
          Length = 894

 Score =  166 bits (420), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 98/274 (35%), Positives = 148/274 (54%), Gaps = 42/274 (15%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++S+MAH  +VLP++TFR N CVC PYNADFDGDEMN+H+ QT+E+
Sbjct: 412 DGDMVLFNRQPSLHRMSMMAHEVRVLPYKTFRLNLCVCPPYNADFDGDEMNMHVFQTDES 471

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              AK LM  + ++++PR G  +I A  D I+G YLLT+  + F+ 
Sbjct: 472 RAE--------------AKSLMRVQEHILSPRFGGPIIGAIHDHISGAYLLTKPGSEFSE 517

Query: 461 AQTMRIASTLIADTSDICGIIKR---FSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDC 517
            Q ++              II++   F+  + +P    R    WTGK++FSL+L      
Sbjct: 518 EQALQ--------------IIRKSHLFNNENVDPKHLKRKHENWTGKELFSLLL------ 557

Query: 518 PVNANLKTKG----RAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILL 573
           P + NL  K     +     EE C  D+YV++ + EL  G +D+   GS     +   ++
Sbjct: 558 PDDLNLVYKAEICQKCDVCKEEACDIDAYVVIEDGELKHGVIDEKAYGSFS-GRILDKIV 616

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           +++G   A   + R + +    +M  G +    D
Sbjct: 617 KEYGPARAREFLDRSTDLAICGIMKTGITTSTND 650



 Score = 98.6 bits (244), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 73/262 (27%), Positives = 125/262 (47%), Gaps = 42/262 (16%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G ++ ED +++ S ++I + + Y +D    PI +GL+D  +G       C +CG    +C
Sbjct: 14  GLMSPED-IREMSVVKIETPDTYDEDG--YPIENGLMDPHLGVIDPSLKCRSCGYRGGEC 70

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFG I+L  PV H+G+   +  IL+S C    C RVLL +++   +  K+++    + 
Sbjct: 71  QGHFGSIELARPVIHVGFGDIIHKILRSTCNE--CGRVLLTDDEIFKYTEKIKDAQNHHE 128

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEY 264
               + K+I    ++  VCPHC                           +A  +D+  + 
Sbjct: 129 NLTKILKEIYNEARR-DVCPHC---------------------------EAAQDDITIDK 160

Query: 265 NEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLL 324
             ++    E E +K       L   EV +  E I  ED  +L +N E+++P  L+LT L 
Sbjct: 161 PVSIVQKMEGEDYK-------LTASEVRERLERISDEDAFVLGVNPEVARPEWLVLTVLP 213

Query: 325 VPPNCIRPSVISDL--KSDNDV 344
           VPP  +RPS+  D   +S++D+
Sbjct: 214 VPPVTVRPSITLDTGERSEDDL 235



 Score = 87.4 bits (215), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 37/56 (66%), Positives = 47/56 (83%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQ 666
            +GFV +S+  GL P EFFFH MGGREGLVDTA++TA++GYMQRRLV +L+DL V+
Sbjct: 779 AKGFVHSSYKKGLDPIEFFFHAMGGREGLVDTAIRTAQSGYMQRRLVNALQDLQVK 834


>gi|119494984|ref|XP_001264289.1| DNA-dependent RNA polymerase II largest subunit, putative
           [Neosartorya fischeri NRRL 181]
 gi|119412451|gb|EAW22392.1| DNA-dependent RNA polymerase II largest subunit, putative
           [Neosartorya fischeri NRRL 181]
          Length = 1750

 Score =  166 bits (419), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 96/272 (35%), Positives = 148/272 (54%), Gaps = 35/272 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D++LFNRQPSLHK S+M HR +V+P+ TFR N  V TPYNADFDGDEMN+H+PQ+EE+
Sbjct: 453 DGDIILFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSEES 512

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L +L+++            N+V+P+    L+   QD + G Y + +++ F ++
Sbjct: 513 RAE----LKQLALVPL----------NIVSPQRNGPLMGIVQDTLCGIYKICRRDVFLSK 558

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M I    +    D  G+I         P   ++    WTGKQ+ S+ L      P  
Sbjct: 559 EQVMNI----MLWVPDWDGVIP--------PPAILKPRPRWTGKQMISMAL------PSG 600

Query: 521 AN-LKTKGRAYTANEEFCH-RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            N L+ +    +  E+F    D  +++   +L+ G   K T+G+ G   V + +  ++G 
Sbjct: 601 LNLLRVEKDNSSLAEKFSPLTDGGLLIHGGQLMYGMFSKKTVGASG-GGVIHTIFNEYGP 659

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           D AV        + +++L++ GFSIGIGD  P
Sbjct: 660 DTAVAFFNGAQTIVNYWLLHNGFSIGIGDTIP 691



 Score =  106 bits (264), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 62/185 (33%), Positives = 98/185 (52%), Gaps = 15/185 (8%)

Query: 1224 KQLLPSVVIKGVQGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMA 1268
            + LL ++ ++GVQG+ RA I+E+    V                ++ L   G +L +V+A
Sbjct: 1285 QHLLDTLTLRGVQGVERAFINEKSKVRVLEDGSLFASKTDPLCKEWVLETSGSSLGEVLA 1344

Query: 1269 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK 1328
              GV   +  SN   EV++  GIEAAR+ ++ E+  V+   G  ++ RH  L+ D+MT +
Sbjct: 1345 VPGVDATRTYSNQFIEVFEVFGIEAARTAVLRELTQVLAFDGSYVNHRHLALLVDVMTVR 1404

Query: 1329 GEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGT 1388
            G +  +TRHG+ +     L   SFE T + L +AA +G+ D   GVSE +I+G     GT
Sbjct: 1405 GYLTPVTRHGINRADNGALMRCSFEETVEILLEAAAFGELDDCRGVSENLILGQMAPAGT 1464

Query: 1389 GLIKL 1393
            G   L
Sbjct: 1465 GEFDL 1469



 Score = 99.4 bits (246), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QR+LVK+LE++ V
Sbjct: 811 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMV 870

Query: 666 QYD 668
           +YD
Sbjct: 871 KYD 873



 Score = 90.1 bits (222), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 79/289 (27%), Positives = 132/289 (45%), Gaps = 59/289 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYL--DKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N + NI TP +T Y    K  D + A+ ++  +E T+L  V E  E  + P
Sbjct: 1117 GVPRLKEILNVATNIKTPSMTVYQLPHKCHDKESAKQLRSVVEHTSLRSVTEATEIYYDP 1176

Query: 822  DDSFILIKLDMDRIRLLHL----EVDIDS------IRYCIERTRGISGHLTVSGHSFLIL 871
            D    +I+ D D +    +      D  S      +R  + R + +   LTV   +  I 
Sbjct: 1177 DIQTTVIENDRDMVESYFIIPEDVTDASSRQSKWLLRIILSRPKLLDKGLTVQDVAAKIK 1236

Query: 872  K--PKD-----SSKSFNSKMYQMKQ-------------------------LLPSVVIKGV 899
            +  PKD     S  + + ++ +++Q                         LL ++ ++GV
Sbjct: 1237 QAYPKDIAVIFSDNNADEQVIRIRQIQDYKEDEDDEDIEYDVTLKKLEQHLLDTLTLRGV 1296

Query: 900  QGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMATYGVKGVKCSSN 944
            QG+ RA I+E+    V                ++ L   G +L +V+A  GV   +  SN
Sbjct: 1297 QGVERAFINEKSKVRVLEDGSLFASKTDPLCKEWVLETSGSSLGEVLAVPGVDATRTYSN 1356

Query: 945  NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
               EV++  GIEAAR+ ++ E+  V+   G  ++ RH  L+ D+MT +G
Sbjct: 1357 QFIEVFEVFGIEAARTAVLRELTQVLAFDGSYVNHRHLALLVDVMTVRG 1405



 Score = 79.3 bits (194), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 58/230 (25%), Positives = 101/230 (43%), Gaps = 42/230 (18%)

Query: 110 DPQRT-PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVIN 168
           D QR  P   GL D R+GT  ++ NC TC +   +C GHFG+I+L  PVFHIG+   V  
Sbjct: 44  DEQRMRPRTKGLNDPRLGTIDRQWNCETCEEGQKECPGHFGHIELATPVFHIGFLTKVKK 103

Query: 169 ILQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKSLKKKIL------------- 214
           +L+++C N  C ++      +    A ++R+P   +     L K +L             
Sbjct: 104 LLETVCHN--CGKIKADTSDSKFLEALRMRDPKRRFDHIWRLSKDVLICEADPPPDEDEP 161

Query: 215 ---ETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFN 271
              E++K +     CG     ++K G+  +   K       K  + ED + +  + V   
Sbjct: 162 FSKESSKPLRRHGGCGNAQPTIRKEGITLVGTWK-----PNKSMMDEDEMQQPEKKV--- 213

Query: 272 PEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
                         + P   L +F  I  ED+ ++ ++ + ++P  +I+T
Sbjct: 214 --------------ITPQMALNVFRNISHEDVRIMGLSNDYARPEWMIIT 249



 Score = 56.2 bits (134), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/41 (60%), Positives = 28/41 (68%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            A   ++ +A   P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1068 AIESRFAKAGANPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1108


>gi|83320468|gb|ABC02861.1| RNA polymerase II largest subunit, partial [Orphella haysii]
          Length = 750

 Score =  166 bits (419), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 96/270 (35%), Positives = 149/270 (55%), Gaps = 37/270 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DNDVV+FNRQPSLHK+S+M HR +V+P  TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 381 DNDVVIFNRQPSLHKMSMMGHRVRVMPFSTFRLNLSVTSPYNADFDGDEMNMHVPQSEET 440

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE               K +      +V+P++ + ++   QD +      T+++ F   
Sbjct: 441 RAE--------------IKEICMVPRQIVSPQSNKPVMGIVQDTLAAIRKFTKRDCFLEA 486

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              M +  TL     +  GI+         P   ++  ++WTGKQI+SL++    +C   
Sbjct: 487 DLVMNLLMTL----PEWDGIVP--------PPCIMKPKMLWTGKQIYSLVIPKGTNC--- 531

Query: 521 ANLKTKGRAYTANEE--FCHR-DSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFG 577
                +  +   +EE  +C   D+ VI+ N ++LAG + K T+GS  +  + +I++ +FG
Sbjct: 532 ----YRFHSTHPDEENTWCSPGDTRVIIENGQVLAGIICKRTVGS-SEGGLIHIIMNEFG 586

Query: 578 EDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            +VA        R+ +++  N GFSIGIGD
Sbjct: 587 FEVATAFFNGTQRVINYWFQNYGFSIGIGD 616



 Score = 51.6 bits (122), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 52/218 (23%), Positives = 102/218 (46%), Gaps = 36/218 (16%)

Query: 150 YIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAK-LRNPALSYLVRKS 208
           +I+L  PV+HIG+   V  IL+ +C    C+++   E   A   AK +++P         
Sbjct: 1   HIELARPVYHIGFIIKVKKILECVCW--YCSKLKADETDPAFILAKSIQDP-------NK 51

Query: 209 LKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAE----- 263
             K++ +  K  ++C   G+ +G  ++   L  S  +  N +++    V+ +L +     
Sbjct: 52  RMKRVWDICKARTICESTGD-DGSGEQ---LASSINELPNESERMRNAVDGMLGDKRRKG 107

Query: 264 -----------YNEAVKFNPEIEAHKKFGLI----QTLNPLEVLQLFEAIPLEDIPLLLM 308
                        E +K N   +A      +    Q L+ ++VLQ+ + I  +D   + +
Sbjct: 108 HGGCGHRQPIFRKEGLKLNATFKAGSGEEGVAEGKQQLSVIQVLQVLKRITDDDSFAMGI 167

Query: 309 NAELSKPSDLILTRLLVPPNCIRPSVISDL--KSDNDV 344
           N + S+P  +IL+ + VPP  +RPS+  D   +S++D+
Sbjct: 168 NPDYSRPEWMILSVMPVPPMSVRPSIQMDATRQSEDDL 205


>gi|45935347|gb|AAS79695.1| RNA polymerase III large subunit [Cycas revoluta]
          Length = 548

 Score =  166 bits (419), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 88/223 (39%), Positives = 139/223 (62%), Gaps = 25/223 (11%)

Query: 390 MNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGY 449
           MN+H+PQTEEAR EAL              +LM  ++NL TP+NGE+LIA+TQDF+T  +
Sbjct: 1   MNLHVPQTEEARTEAL--------------MLMGVQNNLCTPKNGEILIASTQDFLTSSF 46

Query: 450 LLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSL 509
           L+T+K+ F++RA T  +  + + D  +   +          P + ++   +WTGKQ+FS+
Sbjct: 47  LITRKDTFYDRA-TFCLMCSYMGDAVEPIDLP--------TPTI-LKPIELWTGKQLFSV 96

Query: 510 ILKPNRDCPVNANLKTKGRAYTANEE-FCHRDSYVILRNSELLAGSMDKSTLGSGGKANV 568
           +++PN +  V  NL    + Y+ + E  C  D +V  RNSEL++G + K+TLG+G K  +
Sbjct: 97  LVRPNANVRVFVNLMLAEKNYSKSRETMCPNDGFVYFRNSELISGQIGKATLGNGNKDGL 156

Query: 569 FYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           F +LLRD+    A ++M RL+++++ ++ N GFSIGI DV PG
Sbjct: 157 FTVLLRDYNTHAAASSMNRLAKLSARWIGNHGFSIGIDDVQPG 199



 Score =  104 bits (260), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 52/79 (65%), Positives = 59/79 (74%), Gaps = 1/79 (1%)

Query: 607 DVTPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D TP  +GFV NSF++GLT TEFFFHTMGGREGLVDTAVKTAETGYM RRL+K+LEDL  
Sbjct: 318 DKTPAAKGFVANSFYTGLTATEFFFHTMGGREGLVDTAVKTAETGYMSRRLMKALEDLST 377

Query: 666 QYDMSFDAAFYGQTDCISG 684
            YD +   A  G    + G
Sbjct: 378 HYDGTVRNASGGIVQLLYG 396



 Score = 57.0 bits (136), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 23/42 (54%), Positives = 36/42 (85%)

Query: 21 VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRA 62
          +LM  ++NL TP+NGE+LIA+TQDF+T  +L+T+K+ F++RA
Sbjct: 17 MLMGVQNNLCTPKNGEILIASTQDFLTSSFLITRKDTFYDRA 58


>gi|70996164|ref|XP_752837.1| DNA-dependent RNA polymerase II largest subunit [Aspergillus
           fumigatus Af293]
 gi|66850472|gb|EAL90799.1| DNA-dependent RNA polymerase II largest subunit, putative
           [Aspergillus fumigatus Af293]
 gi|159131590|gb|EDP56703.1| DNA-dependent RNA polymerase II largest subunit, putative
           [Aspergillus fumigatus A1163]
          Length = 1750

 Score =  166 bits (419), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 96/272 (35%), Positives = 147/272 (54%), Gaps = 35/272 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D++LFNRQPSLHK S+M HR +V+P+ TFR N  V TPYNADFDGDEMN+H+PQ+EE+
Sbjct: 453 DGDIILFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSEES 512

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L +L+++            N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 513 RAE----LKQLALVPL----------NIVSPQRNGPLMGIVQDTLCGIYKICRRDVFLTK 558

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M I    +    D  G+I         P   ++    WTGKQ+ S+ L      P  
Sbjct: 559 EQVMNI----MLWVPDWDGVIP--------PPAILKPRPRWTGKQMISMAL------PSG 600

Query: 521 AN-LKTKGRAYTANEEFCH-RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            N L+ +    +  E+F    D  +++   +L+ G   K T+G+ G   V + +  ++G 
Sbjct: 601 LNLLRVEKDNSSLAEKFSPLTDGGLLIHGGQLMYGMFSKKTVGASG-GGVIHTIFNEYGP 659

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           D AV        + +++L++ GFSIGIGD  P
Sbjct: 660 DTAVAFFNGAQTIVNYWLLHNGFSIGIGDTIP 691



 Score =  106 bits (265), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 62/185 (33%), Positives = 98/185 (52%), Gaps = 15/185 (8%)

Query: 1224 KQLLPSVVIKGVQGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMA 1268
            + LL ++ ++GVQG+ RA I+E+    V                ++ L   G +L +V+A
Sbjct: 1285 QHLLDTLTLRGVQGVERAFINEKSKVRVLEDGSLFASKTDPLCKEWVLETSGSSLGEVLA 1344

Query: 1269 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK 1328
              GV   +  SN   EV++  GIEAAR+ ++ E+  V+   G  ++ RH  L+ D+MT +
Sbjct: 1345 VPGVDATRTYSNQFIEVFEVFGIEAARTAVLRELTQVLAFDGSYVNHRHLALLVDVMTVR 1404

Query: 1329 GEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGT 1388
            G +  +TRHG+ +     L   SFE T + L +AA +G+ D   GVSE +I+G     GT
Sbjct: 1405 GYLTPVTRHGINRADNGALMRCSFEETVEILLEAAAFGELDDCRGVSENLILGQMAPAGT 1464

Query: 1389 GLIKL 1393
            G   L
Sbjct: 1465 GEFDL 1469



 Score = 99.4 bits (246), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QR+LVK+LE++ V
Sbjct: 811 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMV 870

Query: 666 QYD 668
           +YD
Sbjct: 871 KYD 873



 Score = 89.0 bits (219), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 78/289 (26%), Positives = 133/289 (46%), Gaps = 59/289 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYL--DKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N + NI TP +T Y    +  D + A+ ++  +E T+L  V E  E  + P
Sbjct: 1117 GVPRLKEILNVATNIKTPSMTVYQLPHRCHDKESAKQLRSVVEHTSLRSVTEATEIYYDP 1176

Query: 822  DDSFILIKLDMDRIRLLHL--EVDIDS--------IRYCIERTRGISGHLTVSGHSFLIL 871
            D    +I+ D D +    +  E   D+        +R  + R + +   LTV   +  I 
Sbjct: 1177 DIQTTVIENDRDMVESYFIIPEDVTDATSRQSKWLLRIILSRPKLLDKGLTVQDVAAKIK 1236

Query: 872  K--PKD-----SSKSFNSKMYQMKQ-------------------------LLPSVVIKGV 899
            +  PKD     S  + + ++ +++Q                         LL ++ ++GV
Sbjct: 1237 QAYPKDIAVIFSDNNADEQVIRIRQIQDYKEDEDDEDIEYDVTLKKLEQHLLDTLTLRGV 1296

Query: 900  QGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMATYGVKGVKCSSN 944
            QG+ RA I+E+    V                ++ L   G +L +V+A  GV   +  SN
Sbjct: 1297 QGVERAFINEKSKVRVLEDGSLFASKTDPLCKEWVLETSGSSLGEVLAVPGVDATRTYSN 1356

Query: 945  NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
               EV++  GIEAAR+ ++ E+  V+   G  ++ RH  L+ D+MT +G
Sbjct: 1357 QFIEVFEVFGIEAARTAVLRELTQVLAFDGSYVNHRHLALLVDVMTVRG 1405



 Score = 79.3 bits (194), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 58/230 (25%), Positives = 101/230 (43%), Gaps = 42/230 (18%)

Query: 110 DPQRT-PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVIN 168
           D QR  P   GL D R+GT  ++ NC TC +   +C GHFG+I+L  PVFHIG+   V  
Sbjct: 44  DEQRMRPRTKGLNDPRLGTIDRQWNCETCEEGQKECPGHFGHIELATPVFHIGFLTKVKK 103

Query: 169 ILQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKSLKKKIL------------- 214
           +L+++C N  C ++      +    A ++R+P   +     L K +L             
Sbjct: 104 LLETVCHN--CGKIKADTSDSKFLEALRMRDPKRRFDHIWRLSKDVLICEADPPPDEDEP 161

Query: 215 ---ETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFN 271
              E++K +     CG     ++K G+  +   K       K  + ED + +  + V   
Sbjct: 162 FSKESSKPLRRHGGCGNAQPTIRKEGITLVGTWK-----PNKSMMDEDEMQQPEKKV--- 213

Query: 272 PEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
                         + P   L +F  I  ED+ ++ ++ + ++P  +I+T
Sbjct: 214 --------------ITPQMALNVFRNISHEDVRIMGLSNDYARPEWMIIT 249



 Score = 56.6 bits (135), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/41 (60%), Positives = 28/41 (68%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            A   ++ +A   P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1068 AIESRFAKAAANPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1108


>gi|146302819|ref|YP_001190135.1| DNA-directed RNA polymerase subunit A' [Metallosphaera sedula DSM
           5348]
 gi|145701069|gb|ABP94211.1| DNA-directed RNA polymerase, subunit A' [Metallosphaera sedula DSM
           5348]
          Length = 886

 Score =  166 bits (419), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 100/269 (37%), Positives = 145/269 (53%), Gaps = 29/269 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++S+M H+ +VLP RTFR N  VC PYNADFDGDEMN+H+PQ+EEA
Sbjct: 419 DGDIVIFNRQPSLHRISMMGHKVRVLPGRTFRLNLLVCPPYNADFDGDEMNLHVPQSEEA 478

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
            AE               K LM    N++TPR G  +I + QD+I+G YLLT K      
Sbjct: 479 IAE--------------TKELMTVHRNILTPRYGGPIIGSAQDYISGAYLLTVKTTLLTE 524

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +   I          +  I K        P +      ++TGKQI S  L  + +    
Sbjct: 525 DEVQTILG--------VANINKNLE----EPAILA-PKRLYTGKQIVSHFLPEDFNFHGP 571

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           AN+ +  R  +  +E C  DSYV+++  +LL G  DK  LG+    ++ + L+R++ ED 
Sbjct: 572 ANISSGVR--SCKDEDCPHDSYVVIKKGKLLEGVFDKKALGNQQAESILHWLVREYDEDY 629

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVT 609
            +  M  L ++   Y+   G ++ + DVT
Sbjct: 630 VLWLMDNLFKVFLRYIELHGLTMTLSDVT 658



 Score =  114 bits (286), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 80/261 (30%), Positives = 130/261 (49%), Gaps = 49/261 (18%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D +++ S   I++ ++Y +D   TPI   ++D R+G  +    C  CG  + +C GHFG+
Sbjct: 23  DEIRKMSVTAIITADVYDED--GTPIEGSVMDSRLGIIEPGQKCPICGNVIGNCPGHFGH 80

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-----KLRNPALSYLV 205
           I+L  PV H+G+ + V ++L+S C+   C RV + E     +R      K R P+ +   
Sbjct: 81  IELVRPVIHVGFVKHVYDLLRSTCRR--CGRVKISENDIEKYRKIYDAIKKRWPSAA--- 135

Query: 206 RKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYN 265
            K L   + +T+ K +VCPHC E          LKI  EK  N               Y 
Sbjct: 136 -KRLIDHVKKTSMKAAVCPHCSEKQ--------LKIKLEKPYNF--------------YE 172

Query: 266 EAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLV 325
           E           +K G+++ L P ++ +  E IP  D+ LL  +   S+P  +ILT L V
Sbjct: 173 E-----------RKEGVMR-LTPSDIRERLERIPDSDVELLGYDPTTSRPEWIILTVLPV 220

Query: 326 PPNCIRPSVI--SDLKSDNDV 344
           PP  IRPS++  S +++++D+
Sbjct: 221 PPITIRPSIMIESGIRAEDDL 241



 Score = 92.8 bits (229), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 43/74 (58%), Positives = 56/74 (75%), Gaps = 2/74 (2%)

Query: 606 GDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           GD+TP  +GF+ +SF SGL P E FFH  GGREGLVDTAV+T+++GYMQRRL+ +L DL 
Sbjct: 778 GDITPEARGFIYSSFRSGLNPIETFFHAAGGREGLVDTAVRTSQSGYMQRRLINALSDLR 837

Query: 665 VQYDMSFDAAFYGQ 678
           V+YD +     YG+
Sbjct: 838 VEYDGTV-RTLYGE 850


>gi|3063677|gb|AAC14137.1| RNA polymerase II largest subunit [Dictyostelium discoideum]
          Length = 757

 Score =  166 bits (419), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 96/272 (35%), Positives = 149/272 (54%), Gaps = 40/272 (14%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D DVV+FNRQPSLHK+S+M HR KV+P+ TFR N  V +PYNADFDGDEMN+H+PQT E
Sbjct: 368 NDGDVVIFNRQPSLHKMSMMGHRIKVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQTLE 427

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE +             +++M  +  +V+P++   ++   QD + G  L T+++ F  
Sbjct: 428 TRAEVI-------------EIMMVPRQ-IVSPQSNRPVMGIVQDTLLGSRLFTKRDCFME 473

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWN----PVVFVRTAVIWTGKQIFSLILKPNR 515
           +   M I   L                 SW+    P   ++   +WTGKQ+FSLI+ P+ 
Sbjct: 474 KDLVMNILMWL----------------PSWDGKVPPPAILKPKQLWTGKQLFSLII-PD- 515

Query: 516 DCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
              +N    T         E    D+ VI+  SELLAG + K +LG+    ++ ++++ +
Sbjct: 516 ---INLIRFTSTHNDKKPNECSAGDTRVIIERSELLAGILCKRSLGAAN-GSIIHVVMNE 571

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            G D     + +   + + +L+NRGF++GIGD
Sbjct: 572 HGHDTCRLFIDQTQTVVNHWLINRGFTMGIGD 603



 Score = 50.8 bits (120), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 31/88 (35%), Positives = 47/88 (53%), Gaps = 12/88 (13%)

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA--KLRNPA 200
           +C GHFG+I+L  PVFHIG+   V+ IL+ +C +  C++ LL +     FR   K+RN  
Sbjct: 1   ECPGHFGHIELAKPVFHIGFIDTVLKILRCVCYH--CSK-LLTDTNEHSFRQALKIRN-- 55

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGE 228
                +K     +++  K   VC   GE
Sbjct: 56  -----QKHRLNAVVDCCKNKKVCAIGGE 78



 Score = 50.1 bits (118), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 19/26 (73%), Positives = 22/26 (84%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGRE 637
           +GFV+NS+  GLTP EFFFH MGGRE
Sbjct: 732 RGFVENSYLRGLTPQEFFFHAMGGRE 757


>gi|325960114|ref|YP_004291580.1| DNA-directed RNA polymerase subunit A'' [Methanobacterium sp. AL-21]
 gi|325331546|gb|ADZ10608.1| DNA-directed RNA polymerase subunit A'' [Methanobacterium sp. AL-21]
          Length = 384

 Score =  165 bits (418), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 108/336 (32%), Positives = 169/336 (50%), Gaps = 61/336 (18%)

Query: 1112 RAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCE-------- 1149
            RA +E   AVG +AAQS+GEPGTQMT++TFH+AG              E+ +        
Sbjct: 52   RAGVENGEAVGTVAAQSVGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDARKKISTP 111

Query: 1150 ----YIEEVFVPDDSFIL--------------------------IKLDMDRIRLLHLEVD 1179
                Y +E +  D+ F+                           + +++D  ++    +D
Sbjct: 112  TMGIYFDEEYSADEEFVRRIANRIGKIILNDILKDFNVNYANMNLSIEIDEEKVADKRLD 171

Query: 1180 IDSIRYCIERT-RGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGI 1238
             D I   IE+  + +     +      I  PK + +       +++ L     I GV+ I
Sbjct: 172  YDEIIAKIEKAFKKVDIDKNLLSFEPTISDPKHAIRELRLLADKVRDLQ----ISGVKNI 227

Query: 1239 NRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTI 1298
             + VI +E  E    + +  EG NL  V+   GV   + S+N+ +EV K LG+EAAR+ I
Sbjct: 228  GKVVIRKEGPE----WAIHTEGSNLGAVLKMEGVNKTRTSTNDIHEVEKVLGVEAARNAI 283

Query: 1299 MTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDH 1358
            + E +  ME  G+++D RH MLVAD+MT+ G+V  I RHG++  K SVL  ASFE T  H
Sbjct: 284  IHEAQSTMEEQGLTVDVRHIMLVADMMTADGKVKSIGRHGISGEKASVLARASFEETGKH 343

Query: 1359 LFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            L  A+  G+ D ++G+ E II+G P+ +GTG + ++
Sbjct: 344  LLRASIRGEVDHLTGIIENIIIGQPIPLGTGSVGVV 379



 Score =  102 bits (254), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 125/235 (53%), Gaps = 15/235 (6%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A + ISTP +  Y D++   D ++ R +  R+ +  L ++ +     F  
Sbjct: 94  GLPRLIEIVDARKKISTPTMGIYFDEEYSADEEFVRRIANRIGKIILNDILKD----FNV 149

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERT-RGISGHLTVSGHSFLILKPKDSSKSF 880
           + + + + +++D  ++    +D D I   IE+  + +     +      I  PK + +  
Sbjct: 150 NYANMNLSIEIDEEKVADKRLDYDEIIAKIEKAFKKVDIDKNLLSFEPTISDPKHAIREL 209

Query: 881 NSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
                +++ L     I GV+ I + VI +E  E    + +  EG NL  V+   GV   +
Sbjct: 210 RLLADKVRDLQ----ISGVKNIGKVVIRKEGPE----WAIHTEGSNLGAVLKMEGVNKTR 261

Query: 941 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            S+N+ +EV K LG+EAAR+ I+ E +  ME  G+++D RH MLVAD+MT+ G+V
Sbjct: 262 TSTNDIHEVEKVLGVEAARNAIIHEAQSTMEEQGLTVDVRHIMLVADMMTADGKV 316


>gi|448417597|ref|ZP_21579453.1| DNA-directed RNA polymerase subunit A'' [Halosarcina pallida JCM
            14848]
 gi|445677551|gb|ELZ30051.1| DNA-directed RNA polymerase subunit A'' [Halosarcina pallida JCM
            14848]
          Length = 413

 Score =  165 bits (418), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 113/349 (32%), Positives = 179/349 (51%), Gaps = 61/349 (17%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A+A   +Y   +++P   VG ++AQSIGEPGTQMT+ TFH+AG            + E +
Sbjct: 47   AQAVEARYHDTRVDPLDPVGTVSAQSIGEPGTQMTMNTFHYAGVAEIDVTQGLPRLIELV 106

Query: 1152 EEVFVPDDSFILIKLD----------------MDRIRLLHL------------------- 1176
            +    PD   + + L+                M+  ++L L                   
Sbjct: 107  DARKTPDTPMMTVFLEGEYATERERAHEVVWSMEATKILALGDVSTNVADMVVRIDLNEE 166

Query: 1177 -------EVD-IDSIRYCIERTRGISGHLTVSGH-SFLILKPKDSSKSFNSKMYQMKQLL 1227
                    VD +D+I   I  T  I   L V+   S  +++    S S+  ++ Q+ + L
Sbjct: 167  TLLERWPTVDNVDTIAQEIAET--IEDALGVATQRSGTVVEFGPESPSYR-RLLQLVEEL 223

Query: 1228 PSVVIKGVQGINRAVIHEEDVEGV--TKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEV 1285
              +V KG++ + R VI +ED E     ++ L  EG    D +A  GV   + +SNN +E+
Sbjct: 224  RDIVFKGIEEVTRVVIRKEDNEETDGEEFVLYTEGSAFGDALAIEGVDASRTTSNNIHEI 283

Query: 1286 YKTLGIEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMKE 1344
            Y+ LG+EAAR +I+ E    +   G+  ++ RH MLVAD+MT++GE+  I RHG++  K+
Sbjct: 284  YRNLGVEAARESIIDETMNTLREQGLDDVNVRHLMLVADIMTNRGEIESIGRHGISGSKD 343

Query: 1345 SVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            SVL  A+FE T +HL DAA +G+ D + G+ E +I+G P+  GTG + L
Sbjct: 344  SVLARAAFEVTVNHLLDAAVHGEEDDLDGIIENVIVGKPIATGTGDVDL 392



 Score =  101 bits (252), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 71/242 (29%), Positives = 131/242 (54%), Gaps = 19/242 (7%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T +L+ +  T+ + A  V   +E T    LG+V   + + 
Sbjct: 98  GLPRLIELVDARKTPDTPMMTVFLEGEYATERERAHEVVWSMEATKILALGDVSTNVAD- 156

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSI-RYCIERTRGISGHLTVSGH-SFLILKPKDS 876
                  +++++D++   LL     +D++     E    I   L V+   S  +++    
Sbjct: 157 -------MVVRIDLNEETLLERWPTVDNVDTIAQEIAETIEDALGVATQRSGTVVEFGPE 209

Query: 877 SKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGV--TKYKLLVEGDNLRDVMATY 934
           S S+  ++ Q+ + L  +V KG++ + R VI +ED E     ++ L  EG    D +A  
Sbjct: 210 SPSYR-RLLQLVEELRDIVFKGIEEVTRVVIRKEDNEETDGEEFVLYTEGSAFGDALAIE 268

Query: 935 GVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKG 993
           GV   + +SNN +E+Y+ LG+EAAR +I+ E    +   G+  ++ RH MLVAD+MT++G
Sbjct: 269 GVDASRTTSNNIHEIYRNLGVEAARESIIDETMNTLREQGLDDVNVRHLMLVADIMTNRG 328

Query: 994 EV 995
           E+
Sbjct: 329 EI 330


>gi|15679064|ref|NP_276181.1| DNA-directed RNA polymerase subunit A' [Methanothermobacter
           thermautotrophicus str. Delta H]
 gi|6685898|sp|O27125.1|RPOA1_METTH RecName: Full=DNA-directed RNA polymerase subunit A'
 gi|2622150|gb|AAB85542.1| DNA-dependent RNA polymerase, subunit A' [Methanothermobacter
           thermautotrophicus str. Delta H]
          Length = 870

 Score =  165 bits (418), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 96/268 (35%), Positives = 147/268 (54%), Gaps = 38/268 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++S+MAH+ +VLP++TFR N CVC PYNADFDGDEMN+H+ QTEE+
Sbjct: 408 DGDIVLFNRQPSLHRMSMMAHQVRVLPYKTFRLNLCVCPPYNADFDGDEMNMHVFQTEES 467

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              AK LM  + ++++PR G  +I    D I+G YLLT+K+A F+ 
Sbjct: 468 RAE--------------AKTLMRVQEHILSPRFGGPIIGGIHDHISGAYLLTRKSAVFSE 513

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +  +I         D  G                     WTGK+IFS++L  + +    
Sbjct: 514 EKVFQILKKAGLPLPDSRG-------------------RDWTGKEIFSMVLPDDLNMVYR 554

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGS-GGKANVFYILLRDFGED 579
           A +  K       E  C  D+YV++ N +L++G +D+   G+  GK  +   +++++G D
Sbjct: 555 AEVCRK--CEECLEMECENDAYVVIENGQLISGVIDEKAYGAFAGK--ILDHIVKEYGTD 610

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            A   +   +++    +M+ GF+    D
Sbjct: 611 AAREFLDSATKLAIAGIMHAGFTTSTND 638



 Score =  105 bits (261), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 75/250 (30%), Positives = 118/250 (47%), Gaps = 44/250 (17%)

Query: 85  GTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDC 144
           G ++ ED +++ S  QIV+ + Y +D    PI +GL+D R+G       C TCG    +C
Sbjct: 14  GLMSPED-IRKMSVTQIVTPDTYDEDG--YPIENGLMDPRLGVIDPSLRCRTCGAKGGEC 70

Query: 145 VGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYL 204
            GHFG I+L  PV H+G+   +  IL+S C+   C RVLL E +   +R ++ +      
Sbjct: 71  PGHFGSINLARPVIHVGFADTIHKILRSTCRK--CGRVLLTETEIEEYRQRILDAMEKEE 128

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEY 264
               + K+I    ++   CPHC E               E+ + +  K  +IVE    +Y
Sbjct: 129 SLTPIIKEIYAEARR-DKCPHCEE---------------EQEEIKLDKPVSIVE---GDY 169

Query: 265 NEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLL 324
                                L P EV +  E I  +D  +L +N E+++P  ++LT L 
Sbjct: 170 K--------------------LTPSEVRERLERISDDDALILGVNPEVARPEWMVLTVLP 209

Query: 325 VPPNCIRPSV 334
           VPP  +RPS+
Sbjct: 210 VPPVTVRPSI 219



 Score = 87.4 bits (215), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 37/54 (68%), Positives = 46/54 (85%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           +GFV +S+  GL P EFFFH MGGREGLVDTA++TA++GYMQRRLV +L+DL V
Sbjct: 768 RGFVHSSYKEGLDPIEFFFHAMGGREGLVDTAIRTAQSGYMQRRLVNALQDLTV 821


>gi|435852040|ref|YP_007313626.1| DNA-directed RNA polymerase subunit A' [Methanomethylovorans
           hollandica DSM 15978]
 gi|433662670|gb|AGB50096.1| DNA-directed RNA polymerase subunit A' [Methanomethylovorans
           hollandica DSM 15978]
          Length = 880

 Score =  165 bits (418), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 96/271 (35%), Positives = 142/271 (52%), Gaps = 37/271 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D VLFNRQPSLHK+SIMAH+ KVLP++TFR N  VC PYNADFDGDEMN+H+ QTEE+
Sbjct: 412 DGDTVLFNRQPSLHKMSIMAHQVKVLPNKTFRLNPAVCPPYNADFDGDEMNMHVLQTEES 471

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A +LM  + N+++PR G  +I    D I+G +LLT+      +
Sbjct: 472 RAE--------------ASILMQVQENILSPRFGGPIIGGIHDHISGMFLLTRNENRITK 517

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSW-NPVVFVRTA-VIWTGKQIFSLILKP--NRD 516
            + +               ++++   R    P  +  T    W GKQIFS IL    N +
Sbjct: 518 NEALE--------------LLRKAEIRELPEPAGYKETGEPYWNGKQIFSQILPKGLNAE 563

Query: 517 CPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            P     K         +E C  ++YV++RN E++ G++D+  +G+  K  +   +++ +
Sbjct: 564 FPAEVCFKCD----VCKKEACEYNAYVVIRNGEMIQGTIDERAIGA-FKGIILDKVVKTY 618

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           G       +   +R+    +M  G S GI D
Sbjct: 619 GTTAGAKFIDDFTRLAIRGVMKTGLSFGISD 649



 Score =  102 bits (255), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 70/254 (27%), Positives = 116/254 (45%), Gaps = 44/254 (17%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           V++ S   I++ + Y  D    PI  GL+D R+G       C TC     +C GHFG+I+
Sbjct: 24  VRKMSVTNIITADTY--DDDGYPIDMGLMDLRLGVIDPGLKCKTCSSRAGECPGHFGHIE 81

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKK 212
           L  PV H+G+ + +   L+SIC+N  C+ +LL   +   F  ++        +   +   
Sbjct: 82  LVAPVVHVGFNKTIRKALRSICRN--CSALLLEPSQKKNFLTQIDKLHEMGHLPDPVIND 139

Query: 213 ILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNP 272
           + +  +K  VCPHCG                E+ + + +K    +ED             
Sbjct: 140 VFKEARKTKVCPHCGT---------------EQLEIKFEKPTEYIED------------- 171

Query: 273 EIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRP 332
               HK       L P E+   FE I  +D+ ++ M+   ++P  +ILT L VPP  +RP
Sbjct: 172 ---GHK-------LTPTEIRDRFENISDDDVKVIGMDPSCARPEWMILTVLPVPPVTVRP 221

Query: 333 SVI--SDLKSDNDV 344
           S+   S  +S++D+
Sbjct: 222 SITLESGQRSEDDL 235



 Score = 93.2 bits (230), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 39/60 (65%), Positives = 53/60 (88%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
             GFV+ S+ SGL+PTE+FFH++GGREGLVDTAV+T+++GY+QRRLV +L+DL VQYD +
Sbjct: 777 AHGFVKASYKSGLSPTEYFFHSIGGREGLVDTAVRTSQSGYLQRRLVNALQDLEVQYDAT 836


>gi|345004224|ref|YP_004807077.1| DNA-directed RNA polymerase subunit A' [halophilic archaeon DL31]
 gi|344319850|gb|AEN04704.1| DNA-directed RNA polymerase subunit A' [halophilic archaeon DL31]
          Length = 977

 Score =  165 bits (418), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 96/268 (35%), Positives = 142/268 (52%), Gaps = 44/268 (16%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D D+V+FNRQPSLH++SIMAH   V+P++TFR N  VCTPYNADFDGDEMN+H  Q EE
Sbjct: 484 TDGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTTVCTPYNADFDGDEMNMHALQNEE 543

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           ARAE              A+VLM  +  +++PR GE +I A QD I+G YLLT  N  F+
Sbjct: 544 ARAE--------------ARVLMRVQEQILSPRFGENIIGAIQDHISGTYLLTNSNPSFS 589

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
             Q + +      D                 P         WTG+ +FS +L      P 
Sbjct: 590 ENQALDLLRATSVD-------------ELPEPDGEENGQAYWTGRTVFSELL------PG 630

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           + +L+ +  A          D  V++ N +LL G++D+  +G+ G  ++   + +D+ + 
Sbjct: 631 DLDLEFRSEA----------DDEVVIENGQLLQGTIDEGAIGAFG-GDIVDTITKDYSKT 679

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            A   +  ++ +    +M+ GFSIGI D
Sbjct: 680 RARVFINEVATLAMRSIMHFGFSIGIDD 707



 Score =  107 bits (267), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 78/295 (26%), Positives = 127/295 (43%), Gaps = 58/295 (19%)

Query: 97  SHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP 156
           S  ++++ + Y  D    PI  GL+D R+G       C TCGQ+   C GHFG+I+L  P
Sbjct: 27  SATKVITADTY--DDDGYPIDMGLMDPRLGVIDPGLECRTCGQHSGSCNGHFGHIELAAP 84

Query: 157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILET 216
           V H+G+ + +  +L+  C++  C R+ L E++   F A+L+           + K  +  
Sbjct: 85  VIHVGFAKLIRRLLRGTCRD--CGRLSLTEDEQEEFAARLKRAKELGDDPDDVLKAAIRQ 142

Query: 217 TKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDA--------IVEDLLAEYNEA- 267
            +K S CP+CGE            I HEK     + +D         I E +  + +EA 
Sbjct: 143 ARKASRCPYCGETQ--------YDIKHEKPTTYYEVQDVLSGEYSELIAEAMQPDEDEAD 194

Query: 268 -------------------------VKFNPEIEAHKKFGLI----------QTLNPLEVL 292
                                     +F P  E  K                 L P ++ 
Sbjct: 195 DAGISPQELAEGTGIALDRINEIMSGEFRPREEDRKALEKALDVDLTVEDENKLMPSDIR 254

Query: 293 QLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDNDVV 345
             FE IP +D+  + +++E S+P  +I+T L VPP   RPS+  D   +S++D+ 
Sbjct: 255 DWFEDIPDDDLEHIGIDSEHSRPEWMIMTVLPVPPVTTRPSITLDNGQRSEDDLT 309



 Score = 91.3 bits (225), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 38/57 (66%), Positives = 49/57 (85%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFV+NS+ SGL+P EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 836 HGFVENSYRSGLSPREFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELEAQYD 892



 Score = 43.1 bits (100), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 20/46 (43%), Positives = 29/46 (63%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 65
           +VLM  +  +++PR GE +I A QD I+G YLLT  N  F+  Q +
Sbjct: 549 RVLMRVQEQILSPRFGENIIGAIQDHISGTYLLTNSNPSFSENQAL 594


>gi|46671|emb|CAA32926.1| RNA polymerase subunit C (AA 1-392) [Sulfolobus acidocaldarius]
          Length = 392

 Score =  165 bits (418), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 119/338 (35%), Positives = 173/338 (51%), Gaps = 61/338 (18%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFVP 1157
            +Y ++ IEP  A+G + AQS+GEPGTQMTL+TFHFAG            + E ++   VP
Sbjct: 56   EYQQSLIEPGEAIGVVTAQSVGEPGTQMTLRTFHFAGIRELNVTLGLPRLIEIVDARKVP 115

Query: 1158 DDSFILI------KLDMD-------RIRLLHLE-------VDIDSIRYCIE------RTR 1191
                + I      K D D       RI    +E       VDI ++   ++      + +
Sbjct: 116  STPMMTIYLTDEYKTDKDKALDIARRIEYTRVENVVSSVSVDISNMSITLQFDQEMLKDK 175

Query: 1192 GIS-------------GHLTVSG---HSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGV 1235
            G+S             G + +     +SF I   K  S     KM + K L+     KG 
Sbjct: 176  GVSIEEIKKIITKLKLGEIRIEDNDEYSFTIYFEKIDSIMALFKMRE-KILIQD---KGS 231

Query: 1236 QGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAAR 1295
            QG  RA++ ++  E    Y ++ +G NL  +M   GV   K  +NN +EV + LG+EAAR
Sbjct: 232  QGYKRAIVQKKGDE----YVIITDGSNLEGIMNVTGVDINKIQTNNIHEVEEVLGMEAAR 287

Query: 1296 STIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENT 1355
              I  EIK V+E  G+ +D RH +LV+D+MT  G++  I RHG+   K SVL  A+FE T
Sbjct: 288  ELISREIKKVLEEQGLDVDMRHIVLVSDIMTRTGDIRQIGRHGVTGEKSSVLARAAFEVT 347

Query: 1356 SDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
              HL DAA  G+ +   GV E II+G P+ +GTG+++L
Sbjct: 348  VKHLLDAAARGEREEFKGVIENIIIGQPIRLGTGIVEL 385



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 84/241 (34%), Positives = 124/241 (51%), Gaps = 27/241 (11%)

Query: 764 GVPRIKEIINASRNISTPIITAYL------DKDTDLDYARIVKGRLERTTLGEVCEYIEE 817
           G+PR+ EI++A +  STP++T YL      DKD  LD AR    R+E T      E +  
Sbjct: 101 GLPRLIEIVDARKVPSTPMMTIYLTDEYKTDKDKALDIAR----RIEYTR----VENVVS 152

Query: 818 VFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSG---HSFLILKPK 874
               D S + I L  D+  L    V I+ I+  I + +   G + +     +SF I   K
Sbjct: 153 SVSVDISNMSITLQFDQEMLKDKGVSIEEIKKIITKLK--LGEIRIEDNDEYSFTIYFEK 210

Query: 875 DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATY 934
             S     KM + K L+     KG QG  RA++ ++  E    Y ++ +G NL  +M   
Sbjct: 211 IDSIMALFKMRE-KILIQD---KGSQGYKRAIVQKKGDE----YVIITDGSNLEGIMNVT 262

Query: 935 GVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGE 994
           GV   K  +NN +EV + LG+EAAR  I  EIK V+E  G+ +D RH +LV+D+MT  G+
Sbjct: 263 GVDINKIQTNNIHEVEEVLGMEAARELISREIKKVLEEQGLDVDMRHIVLVSDIMTRTGD 322

Query: 995 V 995
           +
Sbjct: 323 I 323


>gi|258563154|ref|XP_002582322.1| DNA-directed RNA polymerase II largest subunit [Uncinocarpus reesii
           1704]
 gi|237907829|gb|EEP82230.1| DNA-directed RNA polymerase II largest subunit [Uncinocarpus reesii
           1704]
          Length = 1747

 Score =  165 bits (417), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 100/278 (35%), Positives = 152/278 (54%), Gaps = 35/278 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DV+LFNRQPSLHK S+MAHR +V+P+ TFR N  V TPYNADFDGDEMN+H+PQ+EEA
Sbjct: 408 DGDVILFNRQPSLHKESMMAHRVRVMPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSEEA 467

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L +L ++            N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 468 RAE----LSQLCLVPL----------NIVSPQRNGPLMGIVQDTLCGIYKICRRDVFLTK 513

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M I    +    +  G++ +       P + ++    WTGKQI S++L      P  
Sbjct: 514 EQVMNI----MLWVPEWDGVLPQ-------PAI-LKPRPRWTGKQIISMVL------PSG 555

Query: 521 ANLKTKGRAYTA-NEEFCH-RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            NL    R     +E+F    DS +++   EL+ G   K T+G+ G   + + +  ++G 
Sbjct: 556 LNLLRVDRDRVPLSEKFSPLTDSGLLVHGGELMYGMFSKKTVGATG-GGIVHTIYNEYGP 614

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           DV +        + +++L++ GFSIGIGD  P    +Q
Sbjct: 615 DVCMNFFNGAQTVVNYWLLHNGFSIGIGDTIPDLATIQ 652



 Score =  104 bits (259), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 63/180 (35%), Positives = 95/180 (52%), Gaps = 15/180 (8%)

Query: 1225 QLLPSVVIKGVQGINRAVIHEED----VEGVTKYK-----------LLVEGDNLRDVMAT 1269
             LL ++ ++GV G+ RA I+E+     VE  + YK           L   G  L DV+A 
Sbjct: 1241 HLLDTLTLRGVAGVERAFINEKSRVRQVEDGSLYKSAEDPQCKEWVLETSGSALGDVLAL 1300

Query: 1270 YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 1329
             GV   +  SN   E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1301 PGVDSTRTYSNQFIEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLCDVMTSRG 1360

Query: 1330 EVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
             ++ +TRHG+ +     L   SFE T + L DAA + + D   GVSE +I+G     GTG
Sbjct: 1361 FLMAVTRHGINRADTGALMRCSFEETVEILLDAAAFAELDDCRGVSENLILGQMAPAGTG 1420



 Score = 99.0 bits (245), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QR+LVK+LE++ V
Sbjct: 766 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMV 825

Query: 666 QYD 668
           +YD
Sbjct: 826 KYD 828



 Score = 92.8 bits (229), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 81/289 (28%), Positives = 135/289 (46%), Gaps = 59/289 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLD--KDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N + NI TP +T Y D  +  D + A+ ++  +E T+L  V E  E  + P
Sbjct: 1072 GVPRLKEILNVATNIKTPSMTVYQDPSRAMDKESAKQLRSIVEHTSLRSVTEATEIYYDP 1131

Query: 822  DDSFILIKLDMDRIR---LLHLEVDIDS-------IRYCIERTRGISGHLTVSGHSFLIL 871
            D    +I+ D+D +    ++  +V  DS       +R  + R + +   LTV   +  I 
Sbjct: 1132 DIQSTVIENDLDMVESYFIIPEDVMDDSSRQSKWLLRIILSRPKLLDKGLTVQDVAMKIK 1191

Query: 872  K--PKD-----SSKSFNSKMYQMKQ-------------------------LLPSVVIKGV 899
            +  P D     S  + + ++ +++Q                         LL ++ ++GV
Sbjct: 1192 ESYPSDIAVIFSDNNADEQVIRIRQIQDPKQDEDDDDTEYDVTLKKLESHLLDTLTLRGV 1251

Query: 900  QGINRAVIHEED----VEGVTKYK-----------LLVEGDNLRDVMATYGVKGVKCSSN 944
             G+ RA I+E+     VE  + YK           L   G  L DV+A  GV   +  SN
Sbjct: 1252 AGVERAFINEKSRVRQVEDGSLYKSAEDPQCKEWVLETSGSALGDVLALPGVDSTRTYSN 1311

Query: 945  NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
               E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1312 QFIEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLCDVMTSRG 1360



 Score = 77.0 bits (188), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 58/230 (25%), Positives = 102/230 (44%), Gaps = 42/230 (18%)

Query: 110 DPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINI 169
           D ++ P   GL D R+GT  +   C TC + ++DC GHFG+I+L  PVFHIG+   +  +
Sbjct: 45  DARQRPREKGLNDPRLGTIDRNWRCATCEEGINDCPGHFGHIELSTPVFHIGFLTKIKKL 104

Query: 170 LQSICKNPTCARVLLG---EEKAAGFRAKLRNPALSYLVRKSLKKKIL------------ 214
           L+++C N  C ++      ++   G R   R+P   +     L K +L            
Sbjct: 105 LETVCHN--CGKIKANTNDQKYLDGLR--FRDPKRRFDAIWRLSKDVLICEADPPEEDEP 160

Query: 215 ---ETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFN 271
              E+ K       CG     ++K G+  +   K     K +D I++D   +  E  +  
Sbjct: 161 FGKESAKMPKGHGGCGNAQPQIRKEGISLVGTWK---PNKMRD-IMDDTDIQQPEKKQIT 216

Query: 272 PEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
           P++                 L +F  I  ED+ +L ++ + ++P  +I+T
Sbjct: 217 PQM----------------ALNIFRNISEEDVRILGLSNDYARPEWMIIT 250



 Score = 57.0 bits (136), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 25/41 (60%), Positives = 28/41 (68%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            A   ++ +A   P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1023 AIESRFAKAAANPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1063


>gi|330795314|ref|XP_003285719.1| hypothetical protein DICPUDRAFT_149604 [Dictyostelium purpureum]
 gi|325084350|gb|EGC37780.1| hypothetical protein DICPUDRAFT_149604 [Dictyostelium purpureum]
          Length = 1755

 Score =  165 bits (417), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 96/272 (35%), Positives = 148/272 (54%), Gaps = 40/272 (14%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D DVV+FNRQPSLHK+S+M HR KV+P+ TFR N  V +PYNADFDGDEMN+H+PQT E
Sbjct: 443 NDGDVVIFNRQPSLHKMSMMGHRIKVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQTLE 502

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE +             +++M  +  +V+P++   ++   QD + G  L T+++ F  
Sbjct: 503 TRAEVI-------------EIMMVPR-QIVSPQSNRPVMGIVQDTLLGSRLFTKRDTFIE 548

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWN----PVVFVRTAVIWTGKQIFSLILKPNR 515
           R   M I   L                 SW+    P   ++   +WTGKQ+FSLI+ P+ 
Sbjct: 549 RDLVMNILMWL----------------PSWDGKVPPPAILKPKQLWTGKQLFSLII-PD- 590

Query: 516 DCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
              +N    T         E    D+ VI+   ELLAG + K +LG+    ++ ++++ +
Sbjct: 591 ---INLIRFTSTHNDKEPNECSAGDTRVIIERGELLAGILCKRSLGA-ANGSIIHVVMNE 646

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            G D     + +   + + +L+NRGF++GIGD
Sbjct: 647 HGHDTCRLFIDQTQTVVNHWLINRGFTMGIGD 678



 Score =  109 bits (273), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 83/307 (27%), Positives = 156/307 (50%), Gaps = 26/307 (8%)

Query: 1109 KYVRAQIEPATAVGALAAQSI---GEPGTQMTLKTFHFAGEVCEY--IEEVFVPDDSFIL 1163
            K V++ +E  T     +A  I    +P   +  +   F     E+   E+V V   S  L
Sbjct: 1152 KTVKSHLEYTTLANVTSATEIYYDPDPENTIISEDAEFVNSYFEFGMNEDVGVERMSPWL 1211

Query: 1164 IKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSF--LILKPK----DSSKSFN 1217
            +++++DR  +   ++ +  I  C+ R  G++ +   S  +   LIL+ +    +  K+ N
Sbjct: 1212 LRIELDRGMVTAKKLTMAEITQCVVRDFGLNLNCIFSDDNADKLILRIRMVESEDMKTEN 1271

Query: 1218 SKMYQM-----KQLLPSVVIKGVQGINRAVIHEED----------VEGVTKYKLLVEGDN 1262
                Q        +L  +V++G++GI +  +  +D               ++ L  +G +
Sbjct: 1272 DDDDQFLRRIESNMLSGMVLRGIKGIKKVFMRTDDKIPKILDDGSYGNREEWILDTDGVS 1331

Query: 1263 LRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVA 1322
            L +VM+   V   + +SN+  E+ + LGIEA R+ ++ E++ V+   G  +++RH  ++A
Sbjct: 1332 LLEVMSHPDVDHSRTTSNDIVEIIQVLGIEAVRNALLKELRAVISFDGSYVNYRHLAVLA 1391

Query: 1323 DLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGL 1382
            D+MT +G ++ ITRHG+ +++   L   SFE T + L DAA + +TD + GV+E II+G 
Sbjct: 1392 DVMTYRGHLMAITRHGINRVETGPLMRCSFEETVEILMDAAMFSETDDVKGVTENIILGQ 1451

Query: 1383 PMNVGTG 1389
               +GTG
Sbjct: 1452 LPPLGTG 1458



 Score =  100 bits (249), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 41/59 (69%), Positives = 53/59 (89%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
           +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKT+ETGY+QRRLVK++ED+ ++YD +
Sbjct: 807 RGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDVSIKYDAT 865



 Score = 92.8 bits (229), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 76/286 (26%), Positives = 134/286 (46%), Gaps = 52/286 (18%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEIIN ++ + TP +T YL      D+D A+ VK  LE TTL  V    E  + P
Sbjct: 1117 GVPRLKEIINIAKQVKTPSLTIYLKPHIARDMDCAKTVKSHLEYTTLANVTSATEIYYDP 1176

Query: 822  DDSFILIKLDMDRIR-------------------LLHLEVD----------IDSIRYCIE 852
            D    +I  D + +                    LL +E+D          +  I  C+ 
Sbjct: 1177 DPENTIISEDAEFVNSYFEFGMNEDVGVERMSPWLLRIELDRGMVTAKKLTMAEITQCVV 1236

Query: 853  RTRGISGHLTVSGHSF--LILKPK----DSSKSFNSKMYQM-----KQLLPSVVIKGVQG 901
            R  G++ +   S  +   LIL+ +    +  K+ N    Q        +L  +V++G++G
Sbjct: 1237 RDFGLNLNCIFSDDNADKLILRIRMVESEDMKTENDDDDQFLRRIESNMLSGMVLRGIKG 1296

Query: 902  INRAVIHEED----------VEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYK 951
            I +  +  +D               ++ L  +G +L +VM+   V   + +SN+  E+ +
Sbjct: 1297 IKKVFMRTDDKIPKILDDGSYGNREEWILDTDGVSLLEVMSHPDVDHSRTTSNDIVEIIQ 1356

Query: 952  TLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             LGIEA R+ ++ E++ V+   G  +++RH  ++AD+MT +G ++ 
Sbjct: 1357 VLGIEAVRNALLKELRAVISFDGSYVNYRHLAVLADVMTYRGHLMA 1402



 Score = 72.0 bits (175), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 54/160 (33%), Positives = 75/160 (46%), Gaps = 26/160 (16%)

Query: 119 GLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPT 178
           GLLD  MGT  K   C TC   +++C GHFG+I+L  PVFHIG+   V+ IL+ +C +  
Sbjct: 51  GLLDPAMGTIDKTQRCQTCSGTMAECPGHFGHIELAKPVFHIGFIDTVLKILRCVCFH-- 108

Query: 179 CARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCG----------- 227
           C++ LL +     FR      AL    +K     ++E  K   VC   G           
Sbjct: 109 CSK-LLTDTSEYSFRQ-----ALKIKNQKHRLNAVVEICKNKKVCAIGGNEEEEEHDLSK 162

Query: 228 ---EINGVVKK--CG--LLKISHEKYKNRTKKKDAIVEDL 260
              E++  VK   CG  L KI+ E  K   + KD   E +
Sbjct: 163 TDEELDKAVKHGGCGNVLPKITKEDLKIIVEFKDVTDESI 202



 Score = 57.0 bits (136), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 25/37 (67%), Positives = 29/37 (78%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            K+++A   P   VGALAAQSIGEP TQMTL TFH+AG
Sbjct: 1072 KFLQALAHPGEMVGALAAQSIGEPATQMTLNTFHYAG 1108


>gi|448396748|ref|ZP_21569196.1| DNA-directed RNA polymerase subunit A'' [Haloterrigena limicola JCM
            13563]
 gi|445673277|gb|ELZ25838.1| DNA-directed RNA polymerase subunit A'' [Haloterrigena limicola JCM
            13563]
          Length = 398

 Score =  165 bits (417), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 105/344 (30%), Positives = 178/344 (51%), Gaps = 59/344 (17%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A+A   +Y+  +++P   VG ++AQSIGEPGTQ+T+ TFH+AG            + E +
Sbjct: 48   AKAVETRYLDTRVDPLDPVGTVSAQSIGEPGTQLTMNTFHYAGVAEIDVTQGLPRLIELV 107

Query: 1152 EEVFVPDDSFILIKLDMD----RIRL--------------------------LHLEVDID 1181
            +    PD   + + L+ D    R R                           + + ++ D
Sbjct: 108  DARKTPDTPMMTVHLEGDYATERERAHEVVWKIEATKILALGDVSTNVADMRVQISLNED 167

Query: 1182 SIRY----------CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVV 1231
            +++            IE + G+    T+   + +   P++ S      + Q+ + L  + 
Sbjct: 168  TLKERLITPEEVAEIIEDSLGVK---TIQQGTQIEFGPEEPSYR---DLLQLVEELRDIT 221

Query: 1232 IKGVQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLG 1290
             KG++ I+R VI  E+++ G  ++ L  EG    DV+   GV   + + NN +E+ + LG
Sbjct: 222  FKGIEDISRVVIRREEMDDGSEEFVLYTEGSAFGDVLEIEGVDASRTTCNNIHEIRRNLG 281

Query: 1291 IEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNL 1349
            IEAAR  I+ E    +   G+  ++ RH MLVAD+MT++GE+  I RHG++  K+SVL  
Sbjct: 282  IEAAREAIIEETNNTLAEQGLDDVNVRHLMLVADIMTNRGEIESIGRHGISGSKDSVLAR 341

Query: 1350 ASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            A+FE T +HL +AA +G+ D + GV+E +I+G P+ +GTG + L
Sbjct: 342  AAFEVTVNHLLNAAIHGEIDELDGVTENVIVGKPIKLGTGDVDL 385



 Score = 95.5 bits (236), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 71/239 (29%), Positives = 127/239 (53%), Gaps = 21/239 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T +L+ D  T+ + A  V  ++E T    LG+V   + ++
Sbjct: 99  GLPRLIELVDARKTPDTPMMTVHLEGDYATERERAHEVVWKIEATKILALGDVSTNVADM 158

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSK 878
            V     I +  D  + RL+  E     +   IE + G+    T+   + +   P++ S 
Sbjct: 159 RVQ----ISLNEDTLKERLITPE----EVAEIIEDSLGVK---TIQQGTQIEFGPEEPSY 207

Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVK 937
                + Q+ + L  +  KG++ I+R VI  E+++ G  ++ L  EG    DV+   GV 
Sbjct: 208 R---DLLQLVEELRDITFKGIEDISRVVIRREEMDDGSEEFVLYTEGSAFGDVLEIEGVD 264

Query: 938 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEV 995
             + + NN +E+ + LGIEAAR  I+ E    +   G+  ++ RH MLVAD+MT++GE+
Sbjct: 265 ASRTTCNNIHEIRRNLGIEAAREAIIEETNNTLAEQGLDDVNVRHLMLVADIMTNRGEI 323


>gi|3172134|gb|AAC18416.1| RNA polymerase II largest subunit [Bonnemaisonia hamifera]
          Length = 1732

 Score =  165 bits (417), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 98/277 (35%), Positives = 147/277 (53%), Gaps = 32/277 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D VLFNRQPSLHK+SIM HR +VLP+ TFR N  V +PYNADFDGDEMN+H+PQT + 
Sbjct: 346 DGDYVLFNRQPSLHKMSIMGHRIRVLPYSTFRLNLSVTSPYNADFDGDEMNLHVPQTHQT 405

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    + +L ++ H           +V+P+  + ++   QD + G  L TQ++ F  R
Sbjct: 406 RAE----VQELMLVPH----------CIVSPQGNKPVMGIVQDTLLGCMLFTQRDTFLER 451

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              M     L+    D  G+I +       P ++ +   +WTGKQ+FSLIL      PVN
Sbjct: 452 DLMM----NLLMHVGDWDGVIPK-------PAIY-KPRPLWTGKQVFSLILP-----PVN 494

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
                         +    D+ V +   +L+ G +DK T+GS     + +I  ++FG  +
Sbjct: 495 IIRFNITHPDDEKTDISPGDTKVYISRGQLICGIVDKRTVGSSANG-LIHITWKEFGPKI 553

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
             T + ++  + + Y++ R  SIGIGD       ++N
Sbjct: 554 TDTLISQIQVLVNHYILQRRQSIGIGDTIADDATMRN 590



 Score =  105 bits (262), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 52/142 (36%), Positives = 87/142 (61%)

Query: 1253 KYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMS 1312
            ++ L  +G NL  VM+   V   + +SN+  E+++ LGIEA R  ++ EI+ V+   G  
Sbjct: 1259 EWVLDTDGVNLLAVMSHEAVDHTRTTSNDIVEIFEVLGIEAVREVLLNEIRGVISFDGAY 1318

Query: 1313 IDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCIS 1372
            +++RH  ++ D MT +G ++ ITRHG+ ++    L   SFE T+D L +AA +G+ D + 
Sbjct: 1319 VNYRHLAILVDTMTYRGHLMAITRHGVNRVDTGPLMKCSFEGTTDILLEAAMWGERDGLR 1378

Query: 1373 GVSECIIMGLPMNVGTGLIKLL 1394
            GV+E I++G    +GTG  +LL
Sbjct: 1379 GVTENIMLGQLAPIGTGSFRLL 1400



 Score =  102 bits (254), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 44/65 (67%), Positives = 57/65 (87%), Gaps = 1/65 (1%)

Query: 605 IGDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDL 663
           + D+ P  +GFV+NS+  GLTP+EFFFH MGGREGL+DTAVKTAETGY+QRRL+K++ED+
Sbjct: 701 LDDLGPESRGFVENSYLRGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAMEDI 760

Query: 664 CVQYD 668
            V+YD
Sbjct: 761 MVRYD 765



 Score = 80.9 bits (198), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 71/294 (24%), Positives = 128/294 (43%), Gaps = 61/294 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEIIN S+N  TP +T YL      D + A+ ++  L+ TTL +V +  E  + P
Sbjct: 1045 GVPRLKEIINVSKNTKTPSLTVYLKSQYAGDKEKAKEIQASLQHTTLHDVTQCTEIYYDP 1104

Query: 822  D-------------DSFI------------LIKLDMDRIRLLHLEVDIDSIRYCIERTRG 856
            D              SF             L+++ MD+  L   ++ +D I   I +  G
Sbjct: 1105 DPMDTVVDADREMVSSFFDLEEAPVGVSPWLLRIIMDKDMLQDRKISMDRIENMITQNFG 1164

Query: 857  ISGHLTVS--GHSFLILKPKDSSKSFNSKMYQM----------------------KQLLP 892
               H+  S      ++++ + + +S   K  +                        +LL 
Sbjct: 1165 NDVHVIRSQDNDEKMVMRLRVADESAQEKCGEEGGADIEEDDDEDSDDTFLRRLESELLS 1224

Query: 893  SVVIKGVQGINRAVIHEEDVEGV----------TKYKLLVEGDNLRDVMATYGVKGVKCS 942
             + + G+  I +  + +     V           ++ L  +G NL  VM+   V   + +
Sbjct: 1225 QMNLGGIPAIRKVFMRQSRFTFVDPGTGTHKSREEWVLDTDGVNLLAVMSHEAVDHTRTT 1284

Query: 943  SNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL 996
            SN+  E+++ LGIEA R  ++ EI+ V+   G  +++RH  ++ D MT +G ++
Sbjct: 1285 SNDIVEIFEVLGIEAVREVLLNEIRGVISFDGAYVNYRHLAILVDTMTYRGHLM 1338



 Score = 58.9 bits (141), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 52/204 (25%), Positives = 91/204 (44%), Gaps = 35/204 (17%)

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALS 202
           +C GHFG+++L  P+F+IG+    + IL+ +C    C+++L      A    K+  P   
Sbjct: 1   ECPGHFGHVELAKPMFNIGFINISLKILRCVCH--YCSKLLCSSASVAILH-KITKPT-- 55

Query: 203 YLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLA 262
                 ++  +  T+    +C   G        CG ++    KY     +  AI ED   
Sbjct: 56  ----DRMRTAMRFTSGAKKLCTAEG-------GCGHMQ---PKYSRDGFRIRAIFEDTAE 101

Query: 263 EYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTR 322
           E            A +K    QT+   +   +F+ I   +   + ++   S+P  LILT 
Sbjct: 102 E-----------SAERK----QTITAEKSYAIFKRISNSECEAMGLSWRWSRPEWLILTL 146

Query: 323 LLVPPNCIRPSVI-SDLKSDNDVV 345
           L VPP  +RPSV+   L++++D+ 
Sbjct: 147 LPVPPPQVRPSVMRGGLRNEDDLT 170



 Score = 53.1 bits (126), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 21/37 (56%), Positives = 29/37 (78%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            +++  ++ P   +GA+AAQSIGEP TQMTL TFH+AG
Sbjct: 1000 RFMMCRVAPGENIGAIAAQSIGEPATQMTLNTFHYAG 1036


>gi|448312199|ref|ZP_21501949.1| DNA-directed RNA polymerase subunit A'' [Natronolimnobius
            innermongolicus JCM 12255]
 gi|445602706|gb|ELY56678.1| DNA-directed RNA polymerase subunit A'' [Natronolimnobius
            innermongolicus JCM 12255]
          Length = 400

 Score =  165 bits (417), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 104/344 (30%), Positives = 175/344 (50%), Gaps = 59/344 (17%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A+A   +Y+  +++P   VG ++AQSIGEPGTQ+T+ TFH+AG            + E +
Sbjct: 48   AKAVEARYLDTRVDPLDPVGTVSAQSIGEPGTQLTMNTFHYAGVAEIDVTQGLPRLIELV 107

Query: 1152 EEVFVPDDSFILIKLD----------------------------------------MDRI 1171
            +    PD   + + L+                                        ++R 
Sbjct: 108  DARKTPDTPMMTVYLEDEYATERERAHEVVWKIEATKILALGDVSTNVADMRVQISLNRD 167

Query: 1172 RLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVV 1231
             L    +  + +   IE   G+S   TV   + +   P++ S      + Q+ + L  + 
Sbjct: 168  TLEERMITPEEVAEIIEDNLGVS---TVQQGTEIQFGPEEPSYR---DLLQLVEELRDIT 221

Query: 1232 IKGVQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLG 1290
             KG++ ++R VI  E+++ G  ++ L  EG    DV+   GV   + + NN +E+++ LG
Sbjct: 222  FKGIEEVSRVVIRREEMDDGDEQFVLYTEGSAFGDVLEIEGVDASRTTCNNIHEIHRNLG 281

Query: 1291 IEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNL 1349
            IEAAR  I+ E    +   G+  ++ RH MLVAD+MT++GE+  I RHG++  K+SVL  
Sbjct: 282  IEAAREAIIEETNNTLAEQGLDDVNVRHLMLVADMMTNRGEIESIGRHGISGSKDSVLAR 341

Query: 1350 ASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            A+FE T +HL +AA +G+ D + GV+E +I+G P+ +GTG + L
Sbjct: 342  AAFEVTVNHLLNAAIHGEIDSLQGVTENVIVGKPIKLGTGDVDL 385



 Score =  101 bits (251), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 69/239 (28%), Positives = 128/239 (53%), Gaps = 21/239 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T YL+ +  T+ + A  V  ++E T    LG+V   + ++
Sbjct: 99  GLPRLIELVDARKTPDTPMMTVYLEDEYATERERAHEVVWKIEATKILALGDVSTNVADM 158

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSK 878
            V        ++ ++R  L    +  + +   IE   G+S   TV   + +   P++ S 
Sbjct: 159 RV--------QISLNRDTLEERMITPEEVAEIIEDNLGVS---TVQQGTEIQFGPEEPSY 207

Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVK 937
                + Q+ + L  +  KG++ ++R VI  E+++ G  ++ L  EG    DV+   GV 
Sbjct: 208 R---DLLQLVEELRDITFKGIEEVSRVVIRREEMDDGDEQFVLYTEGSAFGDVLEIEGVD 264

Query: 938 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEV 995
             + + NN +E+++ LGIEAAR  I+ E    +   G+  ++ RH MLVAD+MT++GE+
Sbjct: 265 ASRTTCNNIHEIHRNLGIEAAREAIIEETNNTLAEQGLDDVNVRHLMLVADMMTNRGEI 323


>gi|383620452|ref|ZP_09946858.1| DNA-directed RNA polymerase subunit A'' [Halobiforma lacisalsi AJ5]
 gi|448697813|ref|ZP_21698691.1| DNA-directed RNA polymerase subunit A'' [Halobiforma lacisalsi AJ5]
 gi|445781179|gb|EMA32040.1| DNA-directed RNA polymerase subunit A'' [Halobiforma lacisalsi AJ5]
          Length = 404

 Score =  165 bits (417), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 107/341 (31%), Positives = 175/341 (51%), Gaps = 53/341 (15%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A+A   +YV  +++P   VG ++AQSIGEPGTQ+T+ TFH+AG            + E +
Sbjct: 48   AKAVETRYVDTRVDPLDPVGTVSAQSIGEPGTQLTMNTFHYAGVAEIDVTQGLPRLIELV 107

Query: 1152 EEVFVPDDSFILIKLD----------------MDRIRLLHL---EVDIDSIRYCIERTRG 1192
            +    PD   + + L+                ++  ++L L     ++  +R  I   R 
Sbjct: 108  DARKTPDTPMMTVHLEDEYATERERAHEVVWNIEATKILALGDVSTNVADMRVQISLNRD 167

Query: 1193 IS------------------GHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKG 1234
                                G  TV   + +   P++ S      + Q+ + L  +  KG
Sbjct: 168  TLEERMITPEEVAEIIEDNLGVQTVQQGTEIQFGPEEPSYR---DLLQLVEELRDITFKG 224

Query: 1235 VQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEA 1293
            ++ I+R VI  E+++ G  ++ L  EG    DV+   GV   + + NN +E+ + LGIEA
Sbjct: 225  IEDISRVVIRREEMDDGSEEFVLYTEGSAFGDVLEIEGVDASRTTCNNIHEIRRNLGIEA 284

Query: 1294 ARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASF 1352
            AR  I+ E    +   G+  ++ RH MLVAD+MT++GE+  I RHG++  KESVL  A+F
Sbjct: 285  AREAIIEETNNTLAEQGLDDVNVRHLMLVADIMTNRGEIESIGRHGISGSKESVLARAAF 344

Query: 1353 ENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            E T +HL +AA +G+ D + GV+E +I+G P+ +GTG + L
Sbjct: 345  EVTVNHLLNAAIHGEIDDLDGVTENVIVGKPIKLGTGDVDL 385



 Score = 96.3 bits (238), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 68/239 (28%), Positives = 125/239 (52%), Gaps = 21/239 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T +L+ +  T+ + A  V   +E T    LG+V   + ++
Sbjct: 99  GLPRLIELVDARKTPDTPMMTVHLEDEYATERERAHEVVWNIEATKILALGDVSTNVADM 158

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSK 878
            V        ++ ++R  L    +  + +   IE   G+    TV   + +   P++ S 
Sbjct: 159 RV--------QISLNRDTLEERMITPEEVAEIIEDNLGVQ---TVQQGTEIQFGPEEPSY 207

Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVK 937
                + Q+ + L  +  KG++ I+R VI  E+++ G  ++ L  EG    DV+   GV 
Sbjct: 208 R---DLLQLVEELRDITFKGIEDISRVVIRREEMDDGSEEFVLYTEGSAFGDVLEIEGVD 264

Query: 938 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEV 995
             + + NN +E+ + LGIEAAR  I+ E    +   G+  ++ RH MLVAD+MT++GE+
Sbjct: 265 ASRTTCNNIHEIRRNLGIEAAREAIIEETNNTLAEQGLDDVNVRHLMLVADIMTNRGEI 323


>gi|409722467|ref|ZP_11269917.1| DNA-directed RNA polymerase subunit A'' [Halococcus hamelinensis
            100A6]
 gi|448722479|ref|ZP_21705013.1| DNA-directed RNA polymerase subunit A'' [Halococcus hamelinensis
            100A6]
 gi|445789204|gb|EMA39893.1| DNA-directed RNA polymerase subunit A'' [Halococcus hamelinensis
            100A6]
          Length = 394

 Score =  164 bits (416), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 110/354 (31%), Positives = 179/354 (50%), Gaps = 58/354 (16%)

Query: 1092 RESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG------ 1145
            RE     +    +A   +Y+  ++EP   VG ++AQSIGEPGTQMT+ TFH+AG      
Sbjct: 32   REVTEDEATSIVDAVENRYLDTRVEPLDPVGTVSAQSIGEPGTQMTMNTFHYAGVAEIDV 91

Query: 1146 -----EVCEYIEEVFVPDDSFILIKLD----MDRIRLLHLEVDIDSIRY----------- 1185
                  + E ++    PD   + + LD     DR +   +  +I+S R            
Sbjct: 92   TQGLPRLIELVDARKTPDTPMMTVYLDGEYATDREKAHEVVWNIESTRILALGDVSTNVA 151

Query: 1186 -------------------------CIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKM 1220
                                      IE + G+   +  +G +      + S +     +
Sbjct: 152  DMLVQVSLNQQTLDERMISAEEVAEIIEDSLGVD--VARNGTTIEFGPAQPSYRG----L 205

Query: 1221 YQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSN 1280
             Q+ + L  +V KG++ ++R VI +E++E   ++ L  EG    D +   GV   + + N
Sbjct: 206  LQLVEELREIVFKGIEDVSRVVIRKEELEEGEEFVLYTEGSAFGDALDIEGVDASRTTCN 265

Query: 1281 NTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEVLGITRHGL 1339
            N +EVY+ LG+EAAR  I+ E    +E  G+  ++ RH MLVAD+MT++G +  I RHG+
Sbjct: 266  NIHEVYRNLGVEAAREIIIEETMNTLEEQGLGDVNIRHLMLVADIMTAEGTIESIGRHGI 325

Query: 1340 AKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            +  K+SVL  A+FE T +HL DAA +G+ D ++GV+E +I+G P+ +GTG + L
Sbjct: 326  SGNKDSVLARAAFEVTVNHLLDAAVHGEVDDLNGVAENVIVGKPIKLGTGDVTL 379



 Score = 98.2 bits (243), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 68/238 (28%), Positives = 127/238 (53%), Gaps = 20/238 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T YLD +  TD + A  V   +E T    LG+V   + + 
Sbjct: 94  GLPRLIELVDARKTPDTPMMTVYLDGEYATDREKAHEVVWNIESTRILALGDVSTNVAD- 152

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSK 878
                  +L+++ +++  L    +  + +   IE + G+   +  +G +      + S +
Sbjct: 153 -------MLVQVSLNQQTLDERMISAEEVAEIIEDSLGVD--VARNGTTIEFGPAQPSYR 203

Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 938
                + Q+ + L  +V KG++ ++R VI +E++E   ++ L  EG    D +   GV  
Sbjct: 204 G----LLQLVEELREIVFKGIEDVSRVVIRKEELEEGEEFVLYTEGSAFGDALDIEGVDA 259

Query: 939 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEV 995
            + + NN +EVY+ LG+EAAR  I+ E    +E  G+  ++ RH MLVAD+MT++G +
Sbjct: 260 SRTTCNNIHEVYRNLGVEAAREIIIEETMNTLEEQGLGDVNIRHLMLVADIMTAEGTI 317


>gi|12642610|gb|AAK00309.1|AF315819_1 DNA-dependent RNA polymerase II largest subunit RPB1 [Botryocladia
           uvarioides]
          Length = 1712

 Score =  164 bits (416), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 100/275 (36%), Positives = 146/275 (53%), Gaps = 33/275 (12%)

Query: 334 VISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVH 393
           VI  +K D D VLFNRQPSLHK+SIM HR +VLP+ TFR N  V +PYNADFDGDEMN+H
Sbjct: 341 VIRHIK-DGDYVLFNRQPSLHKMSIMGHRIRVLPYSTFRLNLSVTSPYNADFDGDEMNLH 399

Query: 394 LPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 453
           +PQ+   RAE    + +L ++ H           +V+P+  + ++   QD + G  L TQ
Sbjct: 400 VPQSHGTRAE----VQELMLVPH----------CIVSPQGNKPVMGIVQDTLLGCMLFTQ 445

Query: 454 KNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKP 513
           ++ F  R   M     L+    D  G++         P ++ +   +WTGKQIFSLIL  
Sbjct: 446 RDTFIERDVMM----NLLMHVGDWDGVVPE-------PAIY-KPRPLWTGKQIFSLILP- 492

Query: 514 NRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILL 573
               PVN             EE    D+ V +   +L+ G +DK T+GS     + ++  
Sbjct: 493 ----PVNLIRYNITHPDEEQEEISPGDTKVYISQGQLICGIVDKKTVGSSANG-LIHVTW 547

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           ++ G  V    + ++  + + Y++ RG SIGIGD 
Sbjct: 548 KECGPKVTAMMISQIQVLVNHYVLQRGQSIGIGDT 582



 Score =  107 bits (268), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 61/180 (33%), Positives = 103/180 (57%), Gaps = 10/180 (5%)

Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGVTK----YK------LLVEGDNLRDVMATYGVKG 1274
            +LL  + + G++ I++  + +   + + K    YK      L  +G NL+ VM    V  
Sbjct: 1226 ELLNKMPLGGIKDIHKVFMRQAKRQYIDKEYGKYKTDEEWVLDTDGVNLKAVMCHEAVDH 1285

Query: 1275 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGI 1334
             +  SN+  E+++TLGIEA R  ++ EI+ V+   G  +++RH  ++ D+MT +G ++ I
Sbjct: 1286 TRTMSNDIVEIFETLGIEAVREALLQEIRGVISFDGAYVNYRHLSILVDVMTYRGHLMAI 1345

Query: 1335 TRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            TRHG+ ++    L   SFE T+D L +AA +G  D + GVSE I++G    VGTG  K++
Sbjct: 1346 TRHGINRVDTGPLMKCSFEETTDILLEAATFGMRDNLQGVSENIVLGQLAPVGTGSFKMM 1405



 Score =  101 bits (252), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 56/63 (88%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D+ P  +GFV+NS+  GLTP+EFFFH MGGREGL+DTAVKTAETGY+QRRL+K++ED+ V
Sbjct: 704 DLGPESRGFVENSYLRGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAMEDVMV 763

Query: 666 QYD 668
           +YD
Sbjct: 764 RYD 766



 Score = 72.0 bits (175), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 71/302 (23%), Positives = 131/302 (43%), Gaps = 69/302 (22%)

Query: 764  GVPRIKEIINASRNISTPIITAYL-DK-DTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR++EIIN S++  TP +T YL DK   D   A+ ++  L+ T L +V       + P
Sbjct: 1042 GVPRLREIINVSKHTKTPSLTVYLRDKYSKDKGKAKEIQASLQATNLYDVTTSTAIYYDP 1101

Query: 822  D-------------DSFI------------LIKLDMDRIRLLHLEVDIDSIRYCIERTRG 856
            D              SF             L+++ +D+  L+   + +D I   +++  G
Sbjct: 1102 DPETTVIEEDREMVHSFYEVEDVPSDVAPWLLRITLDKEILIDRGIGMDHIENMMQQNFG 1161

Query: 857  ISGHLTVS--GHSFLILKPKDSSKSFNSKMYQ---------------------------- 886
               H+  S      L+++ +   +  N K  +                            
Sbjct: 1162 DDIHIVRSTDNDERLVIRLRVHDEGANIKYAEDGRREEGIDTGMDIDDEDDDDTDDAFLR 1221

Query: 887  --MKQLLPSVVIKGVQGINRAVIHEEDVEGVTK----YK------LLVEGDNLRDVMATY 934
                +LL  + + G++ I++  + +   + + K    YK      L  +G NL+ VM   
Sbjct: 1222 TLESELLNKMPLGGIKDIHKVFMRQAKRQYIDKEYGKYKTDEEWVLDTDGVNLKAVMCHE 1281

Query: 935  GVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGE 994
             V   +  SN+  E+++TLGIEA R  ++ EI+ V+   G  +++RH  ++ D+MT +G 
Sbjct: 1282 AVDHTRTMSNDIVEIFETLGIEAVREALLQEIRGVISFDGAYVNYRHLSILVDVMTYRGH 1341

Query: 995  VL 996
            ++
Sbjct: 1342 LM 1343



 Score = 63.9 bits (154), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 55/203 (27%), Positives = 96/203 (47%), Gaps = 33/203 (16%)

Query: 144 CVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSY 203
           C GHFG+I+L  P+++IG+ +  +++L+ +C    C+++L  +        K+  P    
Sbjct: 1   CPGHFGHIELAKPMYNIGFIKTTLSVLRCVCH--FCSKILCPDATVQSL-LKISKPT--- 54

Query: 204 LVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAE 263
            VR     K    TKK+     C   N     CG L+  + +   R +++    +D   E
Sbjct: 55  -VRLRNAMKYCSGTKKI-----CTGDN----SCGNLQPKYTREGFRIRQQ---FDDNHEE 101

Query: 264 YNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRL 323
           Y++  K  P + A K            V  +F+ I   D   L ++    +P +LILT L
Sbjct: 102 YSKENK-KPSLSAEK------------VYDIFKRISDRDSLALGLDPRWVRPENLILTVL 148

Query: 324 LVPPNCIRPSVI-SDLKSDNDVV 345
            VPP  +RPSV+   L++++D+ 
Sbjct: 149 PVPPLQVRPSVMHGGLRNEDDLT 171



 Score = 52.0 bits (123), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 22/37 (59%), Positives = 28/37 (75%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            +++ A   P   +GA+AAQSIGEP TQMTL TFH+AG
Sbjct: 997  RFLGAIAAPGENIGAIAAQSIGEPATQMTLNTFHYAG 1033


>gi|110669612|gb|ABG81901.1| RNA polymerase II largest subunit [Cladonia caroliniana]
          Length = 1016

 Score =  164 bits (416), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 97/271 (35%), Positives = 148/271 (54%), Gaps = 39/271 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D ++FNRQPSLHK S+M HR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 373 DGDFIIFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 432

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              +++ M    N+V P+    L+   QD + G Y + +++ F  +
Sbjct: 433 RAEV-------------SQLCMV-PLNIVPPQRNGPLMGIVQDTLCGIYKMCRRDVFLTK 478

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M I    +    D  G+I +       P + V+   +WTGKQI SL++      PV 
Sbjct: 479 EQVMNI----LLWVPDWDGVIPQ-------PAI-VKPRPLWTGKQILSLVM------PVG 520

Query: 521 ANLKTKGRAYTANEEFCH-RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            NL        +NE F   RD  +++   E++ G ++K T+G+ G   V +I+  + G +
Sbjct: 521 LNL-----LRVSNEGFSPLRDDGLLISGGEIMYGLLNKKTVGASG-GGVVHIIFNEKGPE 574

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
            A+        + +++L++ GFSIGIGD  P
Sbjct: 575 AAMKFFNGAQTVVNYWLLHNGFSIGIGDTIP 605



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+  
Sbjct: 725 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDVMA 784

Query: 666 QYD 668
           +YD
Sbjct: 785 KYD 787



 Score = 55.1 bits (131), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 48/195 (24%), Positives = 82/195 (42%), Gaps = 41/195 (21%)

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNPAL 201
           +C GHFG+I+L +PVFH+G+   +  +L+++C N  C ++ L E       A + R+P  
Sbjct: 1   ECPGHFGHIELAVPVFHVGFMTKIKKLLETVCHN--CGKIKLDESNPKFADALRFRDPKK 58

Query: 202 SY--LVRKSLKKKILETT---------KKVSVCPH----CGEINGVVKKCGLLKISHEKY 246
            +  + R    K + ETT         +K     H    CG +   +++ GL      K 
Sbjct: 59  RFDAIWRHCKVKMVCETTVALDEDAPPEKQKEPKHEHGGCGNVQPEIRREGLRLTGTWK- 117

Query: 247 KNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLL 306
               +K D   E    E                    + + P   L +F  I  EDI  L
Sbjct: 118 ---PQKGDEETEGQQPEK-------------------KPITPQMALNIFRHISEEDIATL 155

Query: 307 LMNAELSKPSDLILT 321
            ++ + ++P  +I+T
Sbjct: 156 GLSKDYARPEWMIIT 170



 Score = 42.4 bits (98), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 18/29 (62%), Positives = 21/29 (72%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMT 1137
            ++ RA + P   VG LAAQSIGEP TQMT
Sbjct: 988  RFSRAAVNPGEMVGVLAAQSIGEPATQMT 1016


>gi|45935339|gb|AAS79691.1| RNA polymerase III large subunit [Thuja occidentalis]
          Length = 546

 Score =  164 bits (416), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 90/223 (40%), Positives = 135/223 (60%), Gaps = 25/223 (11%)

Query: 390 MNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGY 449
           MN+H+PQTEEAR EAL               LM  ++NL TP+NGE+LIA+TQDF+T  +
Sbjct: 1   MNLHVPQTEEARTEAL--------------TLMGVQNNLCTPKNGEILIASTQDFLTSSF 46

Query: 450 LLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSL 509
           L+T+K+ F++RA  + +  T + D S+   +          P + ++   +WTGKQ+F++
Sbjct: 47  LITRKDTFYDRAAFL-LMCTYMGDASEHIDLP--------TPAI-LKPIELWTGKQLFTV 96

Query: 510 ILKPNRDCPVNANLKTKGRAYT-ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANV 568
           +++PN    V  NL    + Y+ + E  C  D  V  RNSELL+G + K+TLG+G K  +
Sbjct: 97  LVRPNAKMRVFVNLIVMEKNYSKSGETMCPNDGCVYFRNSELLSGQIGKATLGNGNKDGL 156

Query: 569 FYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           F ILLRD+    A   M RL+++++ ++ N GFSIGI DV PG
Sbjct: 157 FTILLRDYNSHAAACCMNRLAKLSARWIGNHGFSIGIDDVQPG 199



 Score =  105 bits (262), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 50/63 (79%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D TP  +GFV NSF+SGLT TEFFFHTMGGREGLVDTAVKTAETGYM RRL+K+LEDL  
Sbjct: 318 DKTPAAKGFVANSFYSGLTATEFFFHTMGGREGLVDTAVKTAETGYMSRRLMKALEDLST 377

Query: 666 QYD 668
            YD
Sbjct: 378 HYD 380



 Score = 57.0 bits (136), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 23/42 (54%), Positives = 35/42 (83%)

Query: 21 VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRA 62
           LM  ++NL TP+NGE+LIA+TQDF+T  +L+T+K+ F++RA
Sbjct: 17 TLMGVQNNLCTPKNGEILIASTQDFLTSSFLITRKDTFYDRA 58


>gi|120561233|gb|ABM27002.1| RNA polymerase II largest subunit, partial [Entophlyctis
           confervae-glomeratae]
          Length = 1013

 Score =  164 bits (416), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 98/270 (36%), Positives = 147/270 (54%), Gaps = 36/270 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+D+V+FNRQPSLHK+S+M HR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQ+ E 
Sbjct: 365 DDDIVIFNRQPSLHKMSMMGHRVRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSYET 424

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE +             ++ M  K  +V+P+    ++   QD + G    T+++ F  +
Sbjct: 425 KAELM-------------ELCMVPKQ-IVSPQKNAPIMGIVQDTLCGIRKFTKRDTFLRQ 470

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              M     L+    D  G I +       P + ++   +WTGKQI SLIL      P  
Sbjct: 471 DLVM----NLLMWVPDWDGTIPQ-------PAI-IKPVPLWTGKQIVSLIL------PAK 512

Query: 521 ANLKTKGRAYT---ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFG 577
            N+     AY    +N E    D  V++ N ELL+G +DKS +GS     V ++ + ++G
Sbjct: 513 INVTGMHTAYVQTPSNPEPDIPDCKVLIENGELLSGILDKSMVGS-SSGGVIHVAMNEYG 571

Query: 578 EDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            DVA         + +++L+  GFSIGIGD
Sbjct: 572 PDVAKAFFNGCQTVVNYWLLQHGFSIGIGD 601



 Score =  104 bits (260), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 48/63 (76%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D TP  +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKTAETGY+QRRLVK+LEDL  
Sbjct: 724 DHTPEARGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDLMA 783

Query: 666 QYD 668
           QYD
Sbjct: 784 QYD 786


>gi|448350442|ref|ZP_21539255.1| DNA-directed RNA polymerase subunit A'' [Natrialba taiwanensis DSM
            12281]
 gi|445636712|gb|ELY89872.1| DNA-directed RNA polymerase subunit A'' [Natrialba taiwanensis DSM
            12281]
          Length = 399

 Score =  164 bits (416), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 106/344 (30%), Positives = 176/344 (51%), Gaps = 59/344 (17%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A+A   +Y+  ++EP   VG ++AQSIGEPGTQ+T+ TFH+AG            + E +
Sbjct: 48   AKAVEARYIDTRVEPLEPVGTVSAQSIGEPGTQLTMNTFHYAGVAEIDVTQGLPRLIELV 107

Query: 1152 EEVFVPDDSFILIKLD----------------MDRIRLLHL----------EVDI----- 1180
            +    PD   + + L+                ++  ++L L           V I     
Sbjct: 108  DARKTPDTPMMTVYLEDEYATEREKAHEVVWNIEATKILALGDVSTNVADMRVQISLNEE 167

Query: 1181 ---------DSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVV 1231
                     D +   IE   G+     +   + +   P++ S      + Q+ + L  + 
Sbjct: 168  TLDERLITPDEVAEIIEDNLGVKA---IQNGTEIEFGPEEPSYR---DLLQLVEELRDIT 221

Query: 1232 IKGVQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLG 1290
             KG++ ++R VI  E++E G  ++ L  EG    DV+   GV   + + NN +E+++ LG
Sbjct: 222  FKGIEEVSRVVIRREELEEGDEQFVLYTEGSAFGDVLEIEGVDASRTTCNNIHEIHRNLG 281

Query: 1291 IEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNL 1349
            IEAAR  I+ E    +   G+  ++ RH MLVAD+MT++GE+  I RHG++  K+SVL  
Sbjct: 282  IEAAREAIIEETNNTLAEQGLDDVNVRHLMLVADIMTNRGEIESIGRHGISGSKDSVLAR 341

Query: 1350 ASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            A+FE T +HL +AA +G+ D + GV+E +I+G P+ +GTG + L
Sbjct: 342  AAFEVTVNHLLNAAIHGEIDELDGVAENVIVGKPIKLGTGDVDL 385



 Score = 97.1 bits (240), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 67/239 (28%), Positives = 124/239 (51%), Gaps = 21/239 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T YL+ +  T+ + A  V   +E T    LG+V   + ++
Sbjct: 99  GLPRLIELVDARKTPDTPMMTVYLEDEYATEREKAHEVVWNIEATKILALGDVSTNVADM 158

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSK 878
            V        ++ ++   L    +  D +   IE   G+     +   + +   P++ S 
Sbjct: 159 RV--------QISLNEETLDERLITPDEVAEIIEDNLGVKA---IQNGTEIEFGPEEPSY 207

Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVK 937
                + Q+ + L  +  KG++ ++R VI  E++E G  ++ L  EG    DV+   GV 
Sbjct: 208 R---DLLQLVEELRDITFKGIEEVSRVVIRREELEEGDEQFVLYTEGSAFGDVLEIEGVD 264

Query: 938 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEV 995
             + + NN +E+++ LGIEAAR  I+ E    +   G+  ++ RH MLVAD+MT++GE+
Sbjct: 265 ASRTTCNNIHEIHRNLGIEAAREAIIEETNNTLAEQGLDDVNVRHLMLVADIMTNRGEI 323


>gi|355570729|ref|ZP_09041999.1| DNA-directed RNA polymerase subunit A' [Methanolinea tarda NOBI-1]
 gi|354826011|gb|EHF10227.1| DNA-directed RNA polymerase subunit A' [Methanolinea tarda NOBI-1]
          Length = 879

 Score =  164 bits (416), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 95/272 (34%), Positives = 144/272 (52%), Gaps = 40/272 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIMAHR KV+  RTFR N  VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 413 DGDIVLFNRQPSLHRMSIMAHRVKVMDGRTFRLNPAVCPPYNADFDGDEMNLHIPQTEEA 472

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A +L+A + N+++PR G  +I    D ++G ++LT +  +  +
Sbjct: 473 RAE--------------AAILVAVEENILSPRFGGPIIGGIHDHVSGIFMLTNQLKWHTK 518

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAV-IWTGKQIFSLILKPNRDCPV 519
            + +               ++K        P   V+  V  W+ KQIFS++L      P 
Sbjct: 519 QEALY--------------LLKNIEIEHLPPPGMVKDGVPYWSNKQIFSIVL------PK 558

Query: 520 NANLKTKGRA----YTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
             N+  +  +     T   + C RD+YV + +  L +G++DK  +G+     +   ++R 
Sbjct: 559 ELNMVFRASSCQNCETCKRQECDRDAYVRIIDGNLESGTIDKKAIGA-FDGQIVNRIIRQ 617

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           +G   A   +  ++ +    +M  GFS GI D
Sbjct: 618 YGMKRAADFIDDITHLAIRAIMMNGFSFGIDD 649



 Score =  110 bits (275), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 89/269 (33%), Positives = 129/269 (47%), Gaps = 50/269 (18%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G IE  +     ++  S  +I+  + Y  D    P P GL+D  +G       C TC Q 
Sbjct: 8   GKIEFGLLSPKEIRTMSVRKIIWADTY--DDDGFPYPQGLMDLNLGVIDPGLRCKTCDQK 65

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGE---EKAAGFRAKLR 197
            SDC GHFG+I+L  PV H+GY R +  +L+  C+  +C+R+LL     EK  G    L 
Sbjct: 66  ASDCPGHFGHIELAKPVIHVGYTRLIRKLLRVTCR--SCSRLLLSPEEIEKVVGTEDDLT 123

Query: 198 NPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIV 257
              LS       +K I    KK  VCP+CGE          LKI+ EK    T   + I+
Sbjct: 124 GDVLS-------EKDI----KKERVCPYCGEQQ--------LKINFEKP---TTFSEIII 161

Query: 258 EDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSD 317
           ED             +IE HK       L P ++    E IP ED+  L +N ++++P  
Sbjct: 162 ED-----------GKKIE-HK-------LTPADIRARLEKIPDEDLRHLGINPDVARPEW 202

Query: 318 LILTRLLVPPNCIRPSVI--SDLKSDNDV 344
            +LT L VPP  +RPS+I  +  +S++D+
Sbjct: 203 TVLTVLPVPPVTMRPSIILENGQRSEDDL 231



 Score = 89.0 bits (219), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 36/57 (63%), Positives = 49/57 (85%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GF+ +S+ SGL PTEFFFH +GGREGLVDTAV+T+++GY+QRR++ +L+DL V YD
Sbjct: 778 HGFISHSYKSGLNPTEFFFHAIGGREGLVDTAVRTSQSGYLQRRMINALQDLKVAYD 834


>gi|448282777|ref|ZP_21474059.1| DNA-directed RNA polymerase subunit A'' [Natrialba magadii ATCC
            43099]
 gi|445575392|gb|ELY29867.1| DNA-directed RNA polymerase subunit A'' [Natrialba magadii ATCC
            43099]
          Length = 399

 Score =  164 bits (416), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 106/344 (30%), Positives = 174/344 (50%), Gaps = 59/344 (17%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A+A   +YV  ++EP   VG ++AQSIG PGTQ+T+ TFH+AG            + E +
Sbjct: 48   AKAVEARYVDTRVEPLDPVGTVSAQSIGGPGTQLTMNTFHYAGVAEIDVTQGLPRLIELV 107

Query: 1152 EEVFVPDDSFILIKLD----------------------------------------MDRI 1171
            +    PD   + + L+                                        ++R 
Sbjct: 108  DARKTPDTPMMTVYLEDEYATERERAHEVVWNIEATKILALGDVSTNVADMRVQISLNRD 167

Query: 1172 RLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVV 1231
             L    +  + +   IE   G+S   TV   + +   P++ S      + Q+ + L  + 
Sbjct: 168  TLEERMITPEEVAEIIEDNLGVS---TVQQGTDIQFGPEEPSYR---DLLQLVEELREIT 221

Query: 1232 IKGVQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLG 1290
             KG++ I+R VI  E+++ G  ++ L  EG    DV+   GV   + + NN +E+++ LG
Sbjct: 222  FKGIEEISRVVIRREEMDDGDEQFVLYTEGSAFGDVLEIEGVDASRTTCNNIHEIHRNLG 281

Query: 1291 IEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNL 1349
            IEAAR  I+ E    +   G+  ++ RH MLVAD+MT++GE+  I RHG++  K+SVL  
Sbjct: 282  IEAAREAIIEETNNTLAEQGLDDVNVRHLMLVADMMTNRGEIESIGRHGISGSKDSVLAR 341

Query: 1350 ASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            A+FE T +HL +AA +G+ D + GV+E +I+G P+ +GTG + L
Sbjct: 342  AAFEVTVNHLLNAAIHGEIDELDGVTENVIVGKPIKLGTGDVDL 385



 Score =  100 bits (250), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 70/239 (29%), Positives = 127/239 (53%), Gaps = 21/239 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T YL+ +  T+ + A  V   +E T    LG+V   + ++
Sbjct: 99  GLPRLIELVDARKTPDTPMMTVYLEDEYATERERAHEVVWNIEATKILALGDVSTNVADM 158

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSK 878
            V        ++ ++R  L    +  + +   IE   G+S   TV   + +   P++ S 
Sbjct: 159 RV--------QISLNRDTLEERMITPEEVAEIIEDNLGVS---TVQQGTDIQFGPEEPSY 207

Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVK 937
                + Q+ + L  +  KG++ I+R VI  E+++ G  ++ L  EG    DV+   GV 
Sbjct: 208 R---DLLQLVEELREITFKGIEEISRVVIRREEMDDGDEQFVLYTEGSAFGDVLEIEGVD 264

Query: 938 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEV 995
             + + NN +E+++ LGIEAAR  I+ E    +   G+  ++ RH MLVAD+MT++GE+
Sbjct: 265 ASRTTCNNIHEIHRNLGIEAAREAIIEETNNTLAEQGLDDVNVRHLMLVADMMTNRGEI 323


>gi|448356449|ref|ZP_21545182.1| DNA-directed RNA polymerase subunit A'' [Natrialba chahannaoensis JCM
            10990]
 gi|445653482|gb|ELZ06353.1| DNA-directed RNA polymerase subunit A'' [Natrialba chahannaoensis JCM
            10990]
          Length = 399

 Score =  164 bits (416), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 107/344 (31%), Positives = 178/344 (51%), Gaps = 59/344 (17%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A+A   +YV  ++EP   VG ++AQSIGEPGTQ+T+ TFH+AG            + E +
Sbjct: 48   AKAVEARYVDTRVEPLDPVGTVSAQSIGEPGTQLTMNTFHYAGVAEIDVTQGLPRLIELV 107

Query: 1152 EEVFVPDDSFILIKLD----------------MDRIRLLHL----------EVDI----- 1180
            +    PD   + + L+                ++  ++L L           V I     
Sbjct: 108  DARKTPDTPMMTVYLEDEFATERERAHEVVWNIEATKILALGDVSTNVADMRVQISLNQD 167

Query: 1181 ---------DSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVV 1231
                     + +   IE   G+S   TV   + +   P++ S      + Q+ + L  + 
Sbjct: 168  TLEERMITPEEVAEIIEDNLGVS---TVQDGTNIQFGPEEPSYR---DLLQLVEELREIT 221

Query: 1232 IKGVQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLG 1290
             KG++ ++R VI  E+++ G  ++ L  EG    DV+   GV   + + NN +E+++ LG
Sbjct: 222  FKGIEEVSRVVIRREEMDDGDEQFVLYTEGSAFGDVLEIEGVDASRTTCNNIHEIHRNLG 281

Query: 1291 IEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNL 1349
            IEAAR  I+ E    +   G+  ++ RH MLV+D+MT++GE+  I RHG++  K+SVL  
Sbjct: 282  IEAAREAIIEETNNTLAEQGLDDVNVRHLMLVSDMMTNRGEIESIGRHGISGSKDSVLAR 341

Query: 1350 ASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            A+FE T +HL +AA +G+ D + GV+E +I+G P+ +GTG + L
Sbjct: 342  AAFEVTVNHLLNAAIHGEIDELDGVTENVIVGKPIKLGTGDVDL 385



 Score = 97.8 bits (242), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 67/239 (28%), Positives = 127/239 (53%), Gaps = 21/239 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T YL+ +  T+ + A  V   +E T    LG+V   + ++
Sbjct: 99  GLPRLIELVDARKTPDTPMMTVYLEDEFATERERAHEVVWNIEATKILALGDVSTNVADM 158

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSK 878
            V        ++ +++  L    +  + +   IE   G+S   TV   + +   P++ S 
Sbjct: 159 RV--------QISLNQDTLEERMITPEEVAEIIEDNLGVS---TVQDGTNIQFGPEEPSY 207

Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVK 937
                + Q+ + L  +  KG++ ++R VI  E+++ G  ++ L  EG    DV+   GV 
Sbjct: 208 R---DLLQLVEELREITFKGIEEVSRVVIRREEMDDGDEQFVLYTEGSAFGDVLEIEGVD 264

Query: 938 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEV 995
             + + NN +E+++ LGIEAAR  I+ E    +   G+  ++ RH MLV+D+MT++GE+
Sbjct: 265 ASRTTCNNIHEIHRNLGIEAAREAIIEETNNTLAEQGLDDVNVRHLMLVSDMMTNRGEI 323


>gi|448297910|ref|ZP_21487944.1| DNA-directed RNA polymerase subunit A'' [Natronorubrum tibetense
            GA33]
 gi|445592636|gb|ELY46822.1| DNA-directed RNA polymerase subunit A'' [Natronorubrum tibetense
            GA33]
          Length = 397

 Score =  164 bits (416), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 101/343 (29%), Positives = 176/343 (51%), Gaps = 58/343 (16%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            ++A   +Y+  +++P   VG ++AQSIGEPGTQ+T+ TFH+AG            + E +
Sbjct: 48   SKAVEARYMDTRVDPLDPVGTVSAQSIGEPGTQLTMNTFHYAGVAEIDVTQGLPRLIELV 107

Query: 1152 EEVFVPDDSFILIKLD----------------MDRIRLLHLE------------------ 1177
            +    PD   + + L+                ++  ++L L                   
Sbjct: 108  DARKTPDTPMMTVYLEDEYATEREKAHEVVWNLEATKILALGDVSTNVADMRVQISLNKD 167

Query: 1178 ------VDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVV 1231
                  +  + +   IE   G+S   TV   + +   P++ S      + Q+ + L  + 
Sbjct: 168  TLEERMITAEEVAEIIEDNLGVS---TVQQGTEIQFGPEEPSYR---DLLQLVEELRDIT 221

Query: 1232 IKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGI 1291
             KG++ ++R VI  E+++   ++ L  EG    D +   GV   + + NN +E+++ LGI
Sbjct: 222  FKGIEEVSRVVIRREELDEGEQFVLYTEGSAFGDALEIDGVDASRTTCNNLHEIHRNLGI 281

Query: 1292 EAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLA 1350
            EAAR TI+ E    +   G+  ++ RH MLV+D+MT++GE+  I RHG++  K+SVL  A
Sbjct: 282  EAARETIIEETHNTLAEQGLDDVNVRHLMLVSDMMTNRGEIESIGRHGISGSKQSVLARA 341

Query: 1351 SFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            +FE T +HL +AA +G+ D + GV+E +I+G P+ +GTG + L
Sbjct: 342  AFEVTVNHLLNAAIHGEIDDLDGVTENVIVGKPIKLGTGDVDL 384



 Score = 97.8 bits (242), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 71/240 (29%), Positives = 127/240 (52%), Gaps = 24/240 (10%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T YL+ +  T+ + A  V   LE T    LG+V   + ++
Sbjct: 99  GLPRLIELVDARKTPDTPMMTVYLEDEYATEREKAHEVVWNLEATKILALGDVSTNVADM 158

Query: 819 FVPDDSFILIKLDMDRI--RLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDS 876
            V       I L+ D +  R++  E     +   IE   G+S   TV   + +   P++ 
Sbjct: 159 RVQ------ISLNKDTLEERMITAE----EVAEIIEDNLGVS---TVQQGTEIQFGPEEP 205

Query: 877 SKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGV 936
           S      + Q+ + L  +  KG++ ++R VI  E+++   ++ L  EG    D +   GV
Sbjct: 206 SYR---DLLQLVEELRDITFKGIEEVSRVVIRREELDEGEQFVLYTEGSAFGDALEIDGV 262

Query: 937 KGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEV 995
              + + NN +E+++ LGIEAAR TI+ E    +   G+  ++ RH MLV+D+MT++GE+
Sbjct: 263 DASRTTCNNLHEIHRNLGIEAARETIIEETHNTLAEQGLDDVNVRHLMLVSDMMTNRGEI 322


>gi|159040773|ref|YP_001540025.1| DNA-directed RNA polymerase subunit A'' [Caldivirga maquilingensis
            IC-167]
 gi|157919608|gb|ABW01035.1| DNA-directed RNA polymerase, subunit A'' [Caldivirga maquilingensis
            IC-167]
          Length = 388

 Score =  164 bits (416), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 108/352 (30%), Positives = 179/352 (50%), Gaps = 69/352 (19%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG------------------ 1145
            +A   +Y ++ ++P  A+G + AQS+GEP TQM L+TFH+AG                  
Sbjct: 49   KAVVAEYYKSIVDPGEAIGIVTAQSVGEPSTQMILRTFHYAGLREFSMALGLPRLIEIID 108

Query: 1146 --------------------------EVCEYIEEVFVPD----------DSFILIKLDMD 1169
                                      +V + I+ + + +          +S I+I LD D
Sbjct: 109  ARRKPQVPRMTIYLKPEYAHDEEKAHDVAKRIQAITIENLAKSVDVDYFNSTIIITLDED 168

Query: 1170 RIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLIL---KPKDSSKSFNSKMYQMKQL 1226
             +R   L V+   ++  ++R +G +G +TV G+S  +    +   + K    K+ Q K  
Sbjct: 169  ALRYRGLSVN--DVKKALDRIKGKAGEITVEGNSISVTVNAQEVSALKKMRDKILQTK-- 224

Query: 1227 LPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVY 1286
                 + G++GI +A++ + D     +Y +  EG NL  V+    V   +  S++ +EV 
Sbjct: 225  -----VAGIRGIKKALVMKTDN---NEYVIYTEGTNLEAVLLLDEVDSTRTISHDIHEVA 276

Query: 1287 KTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESV 1346
            + LGIEAAR+ IM E+K V+++ G+ +D RH M+VAD+MT  G+V  I RHG+A  K S 
Sbjct: 277  EVLGIEAARTMIMRELKAVLDDQGLDVDTRHLMMVADVMTWDGKVRQIGRHGVAGQKVSP 336

Query: 1347 LNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVP 1398
            L  A+FE T  +L +AA+ G+++   GV E II G  + +GTG ++L+   P
Sbjct: 337  LARAAFEVTVKNLIEAAYMGESEKFKGVVENIISGRYVPIGTGYVELMLEHP 388



 Score =  112 bits (280), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 76/237 (32%), Positives = 131/237 (55%), Gaps = 19/237 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EII+A R    P +T YL  +   D + A  V  R++  T+  + + ++  +  
Sbjct: 99  GLPRLIEIIDARRKPQVPRMTIYLKPEYAHDEEKAHDVAKRIQAITIENLAKSVDVDYF- 157

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLIL---KPKDSSK 878
            +S I+I LD D +R   L V+   ++  ++R +G +G +TV G+S  +    +   + K
Sbjct: 158 -NSTIIITLDEDALRYRGLSVN--DVKKALDRIKGKAGEITVEGNSISVTVNAQEVSALK 214

Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 938
               K+ Q K       + G++GI +A++ + D     +Y +  EG NL  V+    V  
Sbjct: 215 KMRDKILQTK-------VAGIRGIKKALVMKTDN---NEYVIYTEGTNLEAVLLLDEVDS 264

Query: 939 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            +  S++ +EV + LGIEAAR+ IM E+K V+++ G+ +D RH M+VAD+MT  G+V
Sbjct: 265 TRTISHDIHEVAEVLGIEAARTMIMRELKAVLDDQGLDVDTRHLMMVADVMTWDGKV 321


>gi|45935341|gb|AAS79692.1| RNA polymerase III large subunit [Taxus canadensis]
          Length = 546

 Score =  164 bits (415), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 88/223 (39%), Positives = 135/223 (60%), Gaps = 25/223 (11%)

Query: 390 MNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGY 449
           MN+H+PQTEEAR EAL              +LM  ++NL TP+NGE+LIA+TQDF+T  +
Sbjct: 1   MNLHVPQTEEARTEAL--------------MLMGVQNNLCTPKNGEILIASTQDFLTSSF 46

Query: 450 LLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSL 509
           L+T+K+ F++RA    +  + + D S+   +          P + ++   +WTGKQ+F++
Sbjct: 47  LITRKDTFYDRA-AFSLMCSYMGDASEHIDLP--------TPAI-LKPIELWTGKQLFTV 96

Query: 510 ILKPNRDCPVNANLKTKGRAYT-ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANV 568
           +++PN    V  NL    + Y+ + E  C  D  V  RNSELL+G + K+TLG+G K  +
Sbjct: 97  LVRPNAKMRVFVNLIVMEKNYSKSGETMCPNDGRVFFRNSELLSGQLGKATLGNGNKNGL 156

Query: 569 FYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           F +LLRD+    A   M RL+++++ ++ N GFSIGI DV PG
Sbjct: 157 FTVLLRDYNSHAAACCMNRLAKLSARWIGNHGFSIGIDDVQPG 199



 Score =  105 bits (263), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 50/63 (79%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D TP  +GFV NSF+SGLT TEFFFHTMGGREGLVDTAVKTAETGYM RRL+K+LEDL  
Sbjct: 318 DKTPAAKGFVANSFYSGLTATEFFFHTMGGREGLVDTAVKTAETGYMSRRLMKALEDLST 377

Query: 666 QYD 668
            YD
Sbjct: 378 HYD 380



 Score = 57.4 bits (137), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 23/42 (54%), Positives = 36/42 (85%)

Query: 21 VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRA 62
          +LM  ++NL TP+NGE+LIA+TQDF+T  +L+T+K+ F++RA
Sbjct: 17 MLMGVQNNLCTPKNGEILIASTQDFLTSSFLITRKDTFYDRA 58


>gi|238620364|ref|YP_002915190.1| DNA-directed RNA polymerase subunit A' [Sulfolobus islandicus
           M.16.4]
 gi|238381434|gb|ACR42522.1| DNA-directed RNA polymerase subunit A' [Sulfolobus islandicus
           M.16.4]
          Length = 880

 Score =  164 bits (415), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 103/280 (36%), Positives = 151/280 (53%), Gaps = 29/280 (10%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D DVVLFNRQPSLH++S+MAHR +VL   TFR N  VC PYNADFDGDEMN+H+PQ+EE
Sbjct: 412 TDGDVVLFNRQPSLHRISMMAHRVRVLKGLTFRLNLLVCPPYNADFDGDEMNLHVPQSEE 471

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           A AE              AK +M    N++TPR G  +I A QD+I+G YLLT K     
Sbjct: 472 AIAE--------------AKEIMLVHKNIITPRYGGPIIGAAQDYISGAYLLTVKTTLLT 517

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           + +  +I    +AD     G     + R +           +TGKQI S  L  + +   
Sbjct: 518 KEEAQQILG--VADVKIDLGEPAILAPREY-----------YTGKQIVSAFLPKDFNFHG 564

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            AN+ +  R      E C  DSYV+++N  LL G  DK  +G+    ++ + L++++ ++
Sbjct: 565 QANVSSGPR--LCKNEDCPHDSYVVIKNGILLEGVFDKKAIGNQQPESILHWLIKEYSDE 622

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQNSF 619
                M  L R+   ++  +GF++ + DV+ G    Q  +
Sbjct: 623 YGKWLMDNLFRVFIRFVELQGFTMRLEDVSLGDDVKQEIY 662



 Score =  114 bits (285), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 77/261 (29%), Positives = 124/261 (47%), Gaps = 49/261 (18%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D +++ S   I++ ++Y +D   TPI   ++D R+G  +    C TCG  L +C GHFG+
Sbjct: 17  DEIRKMSVTAIITPDVYDED--GTPIEGSVMDPRLGVIEPGQKCPTCGNTLGNCPGHFGH 74

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-----KLRNPALSYLV 205
           I+L  PV H+G+ + V   L++ C+   C RV + E++   +       K R P+ +  +
Sbjct: 75  IELVRPVIHVGFVKHVYEFLKATCRR--CGRVKISEDEIEKYSRIYNAIKKRWPSAARRL 132

Query: 206 RKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYN 265
            + +KK    T  K  VCPHCGE           KI  EK  N              E  
Sbjct: 133 TEYVKK----TAMKAQVCPHCGEKQ--------FKIKLEKPYN-----------FYEERK 169

Query: 266 EAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLV 325
           E V                 L P ++ +  E +P  D+ +L  +   S+P  +ILT L V
Sbjct: 170 EGV---------------AKLTPSDIRERLEKVPESDVEILGYDPTTSRPEWMILTVLPV 214

Query: 326 PPNCIRPSVI--SDLKSDNDV 344
           PP  IRPS++  S +++++D+
Sbjct: 215 PPITIRPSIMIESGIRAEDDL 235



 Score = 89.4 bits (220), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 40/73 (54%), Positives = 56/73 (76%), Gaps = 2/73 (2%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D++P  +GF+ +SF +GL PTE FFH  GGREGLVDTAV+T+++GYMQRRL+ +L DL  
Sbjct: 773 DISPEARGFIYSSFRTGLKPTELFFHAAGGREGLVDTAVRTSQSGYMQRRLINALSDLRA 832

Query: 666 QYDMSFDAAFYGQ 678
           +YD +   + YG+
Sbjct: 833 EYDGTV-RSLYGE 844


>gi|115492277|ref|XP_001210766.1| DNA-directed RNA polymerase II largest subunit [Aspergillus terreus
           NIH2624]
 gi|114197626|gb|EAU39326.1| DNA-directed RNA polymerase II largest subunit [Aspergillus terreus
           NIH2624]
          Length = 1742

 Score =  164 bits (415), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 96/272 (35%), Positives = 147/272 (54%), Gaps = 35/272 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DV+LFNRQPSLHK S+M HR +V+P+ TFR N  V TPYNADFDGDEMN+H+PQ+EE+
Sbjct: 454 DGDVILFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSEES 513

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L +L+++            N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 514 RAE----LSQLALVPM----------NIVSPQRNGPLMGIVQDTLCGIYKICRRDIFLTK 559

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M     ++    D  G+I         P   ++    WTGKQ+ S+ L      P  
Sbjct: 560 DQVM----NMMMWVPDWDGVIP--------PPAILKPRPRWTGKQMISMAL------PSG 601

Query: 521 ANLKTKGRAYTA-NEEFCH-RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            NL    +  +A +E+F    D  +++   +L+ G   K T+G+ G   V + +  ++G 
Sbjct: 602 LNLLRVDKDNSALSEKFSPLNDGGLLIHGGQLMYGMFSKKTVGASG-GGVIHTIFNEYGP 660

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
             AV        + +++L++ GFSIGIGD  P
Sbjct: 661 GTAVAFFNGAQSIVNYWLLHNGFSIGIGDTIP 692



 Score =  103 bits (256), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 60/181 (33%), Positives = 96/181 (53%), Gaps = 15/181 (8%)

Query: 1224 KQLLPSVVIKGVQGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMA 1268
            + LL ++ ++GV G+ RA I+E+    V                ++ L   G +L +V+A
Sbjct: 1286 QHLLDTLTLRGVPGVERAFINEKSKVRVLEDGSLFVSKTDPLCKEWVLETSGSSLGEVLA 1345

Query: 1269 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK 1328
              GV   +  SN   EV++  GIEAAR+ ++ E+  V+   G  ++ RH  L+ D+MT +
Sbjct: 1346 IPGVDATRTYSNQFIEVFEVFGIEAARTAVLRELTQVLAFDGSYVNHRHLALLVDVMTVR 1405

Query: 1329 GEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGT 1388
            G +  +TRHG+ +     L   SFE T + L +AA +G+ D   GVSE +I+G     GT
Sbjct: 1406 GYLTPVTRHGINRADNGALMRCSFEETVEILLEAAAFGELDDCRGVSENLILGQMAPAGT 1465

Query: 1389 G 1389
            G
Sbjct: 1466 G 1466



 Score = 99.4 bits (246), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QR+LVK+LE++ V
Sbjct: 812 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMV 871

Query: 666 QYD 668
           +YD
Sbjct: 872 KYD 874



 Score = 92.4 bits (228), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 79/289 (27%), Positives = 135/289 (46%), Gaps = 59/289 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N + NI TP +T Y +  T  D + A+ ++  +E T+L  V E  E  + P
Sbjct: 1118 GVPRLKEILNVATNIKTPSMTVYQEPYTCHDKESAKQLRSAVEHTSLRSVTEATEIYYDP 1177

Query: 822  DDSFILIKLDMDRIR---LLHLEVDIDS-------IRYCIERTRGISGHLTVSGHSFLIL 871
            D    +I+ D D +    ++  +V  DS       +R  + R + +   LTV   +  I 
Sbjct: 1178 DIQTTVIENDRDMVESYFIIPEDVTDDSTRQSKWLLRIILSRPKLLDKGLTVQDVATRIK 1237

Query: 872  K--PKD-----SSKSFNSKMYQMKQ-------------------------LLPSVVIKGV 899
            +  PKD     S  + + ++ +++Q                         LL ++ ++GV
Sbjct: 1238 QAYPKDIAVIFSDNNADEQVIRIRQIQDYKDDEDDDDIEYDVTLKKLEQHLLDTLTLRGV 1297

Query: 900  QGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMATYGVKGVKCSSN 944
             G+ RA I+E+    V                ++ L   G +L +V+A  GV   +  SN
Sbjct: 1298 PGVERAFINEKSKVRVLEDGSLFVSKTDPLCKEWVLETSGSSLGEVLAIPGVDATRTYSN 1357

Query: 945  NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
               EV++  GIEAAR+ ++ E+  V+   G  ++ RH  L+ D+MT +G
Sbjct: 1358 QFIEVFEVFGIEAARTAVLRELTQVLAFDGSYVNHRHLALLVDVMTVRG 1406



 Score = 72.0 bits (175), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 60/231 (25%), Positives = 102/231 (44%), Gaps = 55/231 (23%)

Query: 110 DPQRT-PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVIN 168
           D QR  P   GL D R+GT  ++ NC TC +   +C GHFG+I+L  PVFHIG+   +  
Sbjct: 44  DEQRQRPRTKGLNDPRLGTIDRQWNCETCEEGQKECPGHFGHIELATPVFHIGFLTKIKK 103

Query: 169 ILQSICKNPTCARVLLGEEKAAGFRA--------KLRNPALSYLVRKSLKKKIL------ 214
           +L+++C N  C ++     KA   ++        ++R+P   +     + K IL      
Sbjct: 104 LLETVCHN--CGKI-----KADSIQSDPKFLEALRMRDPKRRFDHIWRISKDILICQADP 156

Query: 215 ----------ETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEY 264
                     E++K V     CG     ++K G+  +   K  N+   +D + +      
Sbjct: 157 PPDDDDPFSKESSKPVRHHGGCGNSQPTIRKEGITLVGTWK-PNKMLDEDDMQQ------ 209

Query: 265 NEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKP 315
                  PE    KK     T+ P   L +F  I  ED+ ++ ++ + ++P
Sbjct: 210 -------PE----KK-----TITPQMALNVFRNISHEDVRIMGLSNDYARP 244



 Score = 56.6 bits (135), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/41 (60%), Positives = 28/41 (68%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            A   ++ +A   P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1069 AIETRFAKAAASPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1109


>gi|88601371|ref|YP_501549.1| DNA-directed RNA polymerase subunit A' [Methanospirillum hungatei
           JF-1]
 gi|88186833|gb|ABD39830.1| DNA-directed RNA polymerase, subunit A' [Methanospirillum hungatei
           JF-1]
          Length = 886

 Score =  164 bits (415), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 95/271 (35%), Positives = 145/271 (53%), Gaps = 38/271 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIMAH  +++  +TFR N  VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 420 DGDIVLFNRQPSLHRMSIMAHWVRLMDGKTFRLNPAVCPPYNADFDGDEMNLHIPQTEEA 479

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R E              A +L A + N+++PR G  +I    D I+G +LLT    +F +
Sbjct: 480 RVE--------------AAMLAAVQENILSPRFGGPIIGGIHDHISGIFLLTHTLRWFTK 525

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +T+ +      D             R   P         W+ KQIFS IL      P +
Sbjct: 526 EETIDLLKNNKID-------------RLGEPGKVEDGVKYWSNKQIFSKIL------PAD 566

Query: 521 ANLKTKGRAYTANEEF----CHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            N+  +  +    +E     C RD+YV + + EL++G +DK  +G+   A + + ++R +
Sbjct: 567 LNMVFRASSCKGCDECQRVDCERDAYVQIIDGELISGVIDKKAVGAFDGA-ILHRIIRQY 625

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           G + A   +  ++R++   +M+ GF+  I D
Sbjct: 626 GYERAARFIDDMTRLSIRAIMHDGFTFAIDD 656



 Score =  101 bits (252), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 78/266 (29%), Positives = 121/266 (45%), Gaps = 43/266 (16%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G IE  +     ++Q S  +I+  + Y  D    P P GL+D  +G       C TC Q 
Sbjct: 8   GKIEFGLLSPKEIRQMSVRKIIWADTY--DDDGFPYPQGLMDLHLGVIDPGLRCKTCSQK 65

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
             +C GHFG+I+L  PV H+GY R +  +L+  C+   C R+LL +E+      K+  P 
Sbjct: 66  AGECPGHFGHIELAKPVIHVGYTRLIRKLLRVTCRE--CGRLLLSDEEIE----KIIGPE 119

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDL 260
              +   S+ +K     KK  +CPHCGE          LKI+ EK            E  
Sbjct: 120 -EEMGSDSVSEK---DVKKERICPHCGEQQ--------LKINFEK-------PTTFAEIT 160

Query: 261 LAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
             E  + V+                L P ++    E IP +D+  L +   +++P   I+
Sbjct: 161 TDERGKKVE--------------NKLTPADIRARLEKIPDDDLQKLGIIGSVARPEWTIM 206

Query: 321 TRLLVPPNCIRPSVI--SDLKSDNDV 344
           T L VPP  +RPS+I  +  +S++D+
Sbjct: 207 TVLPVPPVTMRPSIILENGQRSEDDL 232



 Score = 94.0 bits (232), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 39/59 (66%), Positives = 51/59 (86%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            GFV NS+ SGL PTEFFFH +GGREGLVDTAV+T+++GY+QRR++ +L+DL V YDM+
Sbjct: 785 HGFVMNSYKSGLNPTEFFFHAIGGREGLVDTAVRTSQSGYLQRRMINALQDLKVAYDMT 843


>gi|294876122|ref|XP_002767562.1| DNA-directed RNA polymerase II largest subunit, putative [Perkinsus
           marinus ATCC 50983]
 gi|239869222|gb|EER00280.1| DNA-directed RNA polymerase II largest subunit, putative [Perkinsus
           marinus ATCC 50983]
          Length = 1667

 Score =  164 bits (415), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 95/280 (33%), Positives = 152/280 (54%), Gaps = 35/280 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND+V+FNRQPSLHK+S+M HRAK+LP  TFR N  V +PYNADFDGDEMN+HL Q+ E 
Sbjct: 463 DNDLVIFNRQPSLHKMSMMGHRAKILPFSTFRLNLSVTSPYNADFDGDEMNMHLAQSHET 522

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE               + +M     +V+P+    ++   QD +    LLT+++ F  +
Sbjct: 523 RAE--------------IRNIMMVPRQVVSPQGNRPVMGIVQDSLLASTLLTKRDTFIEK 568

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWN-PV-VFVRTAVIWTGKQIFSLILKPNRDCP 518
              M++   L+             SW   N P+   ++   +W+GKQ+FS++L P     
Sbjct: 569 DMCMQLLMWLLP-----------ASWDGGNMPMPCILKPRPLWSGKQLFSMLL-PKISLQ 616

Query: 519 VNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLG--SGGKANVFYILLRDF 576
            +A + +K R    +  F   D  VI++  E+++G + K T+G  SGG   + +I   D+
Sbjct: 617 KDAGIASKNRG--DDPWFSRSDCRVIIQEGEIMSGVICKKTVGASSGG---LIHITWLDY 671

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           G +     +  + R+ +F+L++ GF++G  D+    G +Q
Sbjct: 672 GPERTKQFIGGIQRLVNFWLLHHGFTVGCADIVANDGTMQ 711



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 57/179 (31%), Positives = 96/179 (53%), Gaps = 10/179 (5%)

Query: 1226 LLPSVVIKGVQGINRAVIHEE-------DVEGVTK---YKLLVEGDNLRDVMATYGVKGV 1275
            LL  + +KG+ G+ +  + ++       DV    +   + L  +G NL  V+    V   
Sbjct: 1323 LLSDLTLKGIPGVTKCYMRQDNRVQYSSDVGTFARSREWVLDTDGCNLEQVLTMEAVDST 1382

Query: 1276 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGIT 1335
            +  SN+  E+   LGIEA R  ++ E++ V+   G  +++RH  ++ D M  KG ++ IT
Sbjct: 1383 RTFSNDIVEILNVLGIEACRKALLNELRQVISFDGSYVNYRHMSVLCDTMCQKGHLMSIT 1442

Query: 1336 RHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            RHG+ +++   L  +SFE   + L DAA Y +TD + GVSE I++G    +GT   +LL
Sbjct: 1443 RHGINRVERGPLMRSSFEEMVEMLMDAACYAETDHMRGVSENIMLGQLAPIGTAECELL 1501



 Score = 97.4 bits (241), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 41/59 (69%), Positives = 52/59 (88%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
           +GFV+NS+ +GLTP EFFFH MGGREG++DTA KTAETGY+QRRL+KS+E + V+YD S
Sbjct: 831 RGFVENSYLAGLTPQEFFFHAMGGREGIIDTACKTAETGYIQRRLIKSMESIKVRYDGS 889



 Score = 63.2 bits (152), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 42/72 (58%), Gaps = 2/72 (2%)

Query: 112 QRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQ 171
           Q  P+  GL D R+G+      C TCG  + DC GHFG+++L  P++H G+ +  +  L+
Sbjct: 35  QSEPVRGGLSDPRLGSVDPRTPCETCGMKMRDCPGHFGHLELAKPMYHGGFLKTTLKALR 94

Query: 172 SICKNPTCARVL 183
            +C    C+++L
Sbjct: 95  CVCY--YCSKLL 104



 Score = 57.0 bits (136), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 28/61 (45%), Positives = 41/61 (67%), Gaps = 2/61 (3%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEIIN ++N+ TP +T YL  D  +D   A+ V+  LE T+LG++  Y + +F P
Sbjct: 1136 GVPRLKEIINVAKNLKTPSMTVYLHPDYASDDAKAKQVQSELEHTSLGKITSYTQILFDP 1195

Query: 822  D 822
            D
Sbjct: 1196 D 1196



 Score = 56.6 bits (135), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 41/147 (27%), Positives = 72/147 (48%), Gaps = 14/147 (9%)

Query: 1001 PVELKRLLDDIIAKNSSRSDPSL--SAQEILALSNETLDSKEFLQDTSENFVRDIKKFLE 1058
            P+ ++RL+D       +  DP +    QE++    ETLD    ++  +++ V      L 
Sbjct: 993  PINVRRLIDQCHYLFPAEEDPDVFYPPQEVVQKVEETLDRLRVIRGLTDDQV------LG 1046

Query: 1059 EFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPA 1118
              ++  +    Q  +   L  + L  +D++G  R  +      +     +++ ++ +   
Sbjct: 1047 WEAQHNATVVLQAHLRYHLASRKLLERDRLGQ-RAVDWLLGEVE-----QRFEKSLVAAG 1100

Query: 1119 TAVGALAAQSIGEPGTQMTLKTFHFAG 1145
             +VG +AAQSIGEP TQMTL TFHFAG
Sbjct: 1101 ESVGTIAAQSIGEPATQMTLNTFHFAG 1127



 Score = 55.1 bits (131), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 31/117 (26%), Positives = 58/117 (49%), Gaps = 10/117 (8%)

Query: 890  LLPSVVIKGVQGINRAVIHEE-------DVEGVTK---YKLLVEGDNLRDVMATYGVKGV 939
            LL  + +KG+ G+ +  + ++       DV    +   + L  +G NL  V+    V   
Sbjct: 1323 LLSDLTLKGIPGVTKCYMRQDNRVQYSSDVGTFARSREWVLDTDGCNLEQVLTMEAVDST 1382

Query: 940  KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL 996
            +  SN+  E+   LGIEA R  ++ E++ V+   G  +++RH  ++ D M  KG ++
Sbjct: 1383 RTFSNDIVEILNVLGIEACRKALLNELRQVISFDGSYVNYRHMSVLCDTMCQKGHLM 1439


>gi|327242127|gb|AEA40842.1| RNA polymerase II largest subunit [Trichomonas tenax]
          Length = 1016

 Score =  164 bits (415), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 102/316 (32%), Positives = 164/316 (51%), Gaps = 44/316 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND+V+FNRQPSLHK+S+M HRA ++P RTFR N C  TPYNADFDGDEMN+H+PQ++ A
Sbjct: 371 DNDIVIFNRQPSLHKMSMMGHRALLMPARTFRLNLCDTTPYNADFDGDEMNLHVPQSQTA 430

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE               + +MA    +++P+    +I   QD + G  LL++++ F  R
Sbjct: 431 RAE--------------VRHIMAVPKQIISPQANRPVIGLVQDALLGCRLLSKRDTFLTR 476

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M +   L  +   I             P   ++   +W+GKQ+FSL L       ++
Sbjct: 477 NQVMNLMMWLPTNKDTILP-----------PPCILKPVQLWSGKQVFSLFLP-----KIS 520

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            +  + G            DS VI+R+  LLAG +DK +     + ++ ++++  +  ++
Sbjct: 521 YDSYSNGATDKDKNWIPKNDSRVIIRDGNLLAGILDKRSCAR-SEGSLTHVVINSYNTNI 579

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGD-VTPGQGFVQNSFFSGLTPTEFFFHTMGGREGL 639
           A   + +   + + +L  RGFSI + D V P   FV +    G+   E         E +
Sbjct: 580 AKDFLNQTQLIVNNWLEYRGFSISLIDCVVP--HFVLDKVEEGIMQVE---------ENV 628

Query: 640 VDTAVKTAETGYMQRR 655
            +T ++TA++G + RR
Sbjct: 629 RET-IRTAQSGKLDRR 643



 Score = 82.8 bits (203), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 35/57 (61%), Positives = 45/57 (78%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GF ++S+  GLTP EF FH MGGR G++DTA KT++TGY+QRRLVKS+E   V YD
Sbjct: 735 RGFCKHSYIEGLTPPEFLFHAMGGRTGIIDTACKTSDTGYIQRRLVKSMESHHVAYD 791



 Score = 53.5 bits (127), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 61/221 (27%), Positives = 90/221 (40%), Gaps = 34/221 (15%)

Query: 150 YIDLPLPVFHIGYFRCVINILQSICKNPTCARV--LLGEEK----AAGFRAKLRNPALSY 203
           YI L  P FH+G+ + V  ILQ +C    C R+    G+ +    A  ++ K R   L  
Sbjct: 1   YIKLAEPFFHVGFLKHVYKILQMVCHK--CGRLNCSYGDPEIQYIATHYKGKQRFEKLFD 58

Query: 204 LVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKIS-HEKYKNRTKKKDAIVE---D 259
            V    K        K    P         +     +IS H + K   K K   +E   D
Sbjct: 59  YVADKNKDCCDSPNAKDQTNPDFVSDERFWEIVNGDEISEHRRIKVPCKSKSVAIEQGKD 118

Query: 260 LLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLI 319
            L +Y +  K   +            L+   VL++FE I  +D+ L+  N + S P  +I
Sbjct: 119 FLIKYKDTSKTEEDY-----------LSAEYVLRIFENISDQDVRLMGFNVKRSHPKWMI 167

Query: 320 LTRLLVPPNCIRPSVIS---DLKSDNDVVLFNRQPSLHKLS 357
           L  L VPP  +RP V+S    + S +D+         HKLS
Sbjct: 168 LKVLPVPPLAVRPQVVSPGQSVPSQDDIT--------HKLS 200


>gi|451994492|gb|EMD86962.1| hypothetical protein COCHEDRAFT_1217961 [Cochliobolus
           heterostrophus C5]
          Length = 1737

 Score =  164 bits (415), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 92/273 (33%), Positives = 149/273 (54%), Gaps = 33/273 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+DV++FNRQPSLHK S+M HR KV+P+ TFR N  V +PYNADFDGDEMN+H+PQ++E 
Sbjct: 447 DDDVIIFNRQPSLHKESMMGHRVKVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSDET 506

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    +  L ++  +          +V+P+  + L+   QD + G Y +T+++ F   
Sbjct: 507 RAE----IQNLCMVPKQ----------IVSPQKNQPLMGIVQDTLLGVYKMTRRDNFIPI 552

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M I    +    D  GI+         P + ++   +WTGKQI S+        P  
Sbjct: 553 EQVMPI----MMWVPDWDGILPE-------PAI-LKPRPLWTGKQIVSMAF------PRE 594

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            N++ K    T +++   +D  ++++  +L+ G + K  +G+     V +I+  + G D 
Sbjct: 595 VNIEKKEDDSTPSKDNDIKDKSLMIKGGQLIYGQVTKKIVGASA-GGVIHIVFNELGSDA 653

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQG 613
           AV       R+ +++L++ GFS G+GD  P  G
Sbjct: 654 AVKFFNSCQRICNWWLLHYGFSFGVGDTIPDPG 686



 Score =  105 bits (263), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 63/181 (34%), Positives = 97/181 (53%), Gaps = 15/181 (8%)

Query: 1224 KQLLPSVVIKGVQGINRAVIHEEDV---------------EGVTKYKLLVEGDNLRDVMA 1268
            K LL  V ++GV+G+ RA I E  V               +   ++ L   G +L +V+A
Sbjct: 1280 KHLLDDVTLRGVRGVERAFIREHTVTVEKEDRSLMHSKNNDLCKEWVLDTTGTSLAEVLA 1339

Query: 1269 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK 1328
              GV   K  SN+  E+   LGIEAAR+ ++ E+ +V+   G  ++ RH  L+ D+M  +
Sbjct: 1340 IEGVDATKTYSNSFIEILGVLGIEAARAGLLKELGMVLSFDGSYVNHRHMALLVDIMCQR 1399

Query: 1329 GEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGT 1388
            G ++ ITRHG+ +     L   SFE T + L +AA +G+ D   GVSE I++G    +GT
Sbjct: 1400 GLLMAITRHGINRNDTGALMRCSFEETVEILLEAAGFGELDDCRGVSENIMLGQLAPMGT 1459

Query: 1389 G 1389
            G
Sbjct: 1460 G 1460



 Score =  101 bits (251), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTP+EFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+ V
Sbjct: 803 DYSPESRGFVENSYLRGLTPSEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDVMV 862

Query: 666 QYD 668
           +YD
Sbjct: 863 KYD 865



 Score = 83.6 bits (205), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 72/289 (24%), Positives = 128/289 (44%), Gaps = 59/289 (20%)

Query: 764  GVPRIKEIINASRNISTP-IITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPD 822
            GVPR+KEI+N + NI TP ++    D       A++++  +E TTL  + + +E  + PD
Sbjct: 1112 GVPRLKEILNIAANIKTPSMLVRQADSKASQQQAKLLRSTIELTTLRSLTQAVELYYDPD 1171

Query: 823  DSFILIKLDMDRIRLLHLEVDIDSI---------RYCIERTRGISGHLT---VSGHSFLI 870
                L++ D D +    +  + D +         R  ++R + +   +T   V+G     
Sbjct: 1172 IQSTLVEDDQDMVESYFILPEEDEVIESQSKWLLRIILDRKKLLDKSITIGEVAGKIKEE 1231

Query: 871  LKPK----DSSKSFNSKMYQM---------------------------KQLLPSVVIKGV 899
             KP      S ++ + ++ ++                           K LL  V ++GV
Sbjct: 1232 FKPNLAVIFSDENADEQVMRVRFIWDQNLQKDDEDEDERDERWMRKLEKHLLDDVTLRGV 1291

Query: 900  QGINRAVIHEEDV---------------EGVTKYKLLVEGDNLRDVMATYGVKGVKCSSN 944
            +G+ RA I E  V               +   ++ L   G +L +V+A  GV   K  SN
Sbjct: 1292 RGVERAFIREHTVTVEKEDRSLMHSKNNDLCKEWVLDTTGTSLAEVLAIEGVDATKTYSN 1351

Query: 945  NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
            +  E+   LGIEAAR+ ++ E+ +V+   G  ++ RH  L+ D+M  +G
Sbjct: 1352 SFIEILGVLGIEAARAGLLKELGMVLSFDGSYVNHRHMALLVDIMCQRG 1400



 Score = 71.6 bits (174), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 56/216 (25%), Positives = 106/216 (49%), Gaps = 27/216 (12%)

Query: 112 QRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQ 171
           ++ P   GL D ++GT  +  +C TC +++  C GHFG+I+L  PVFH+G+   +  +L+
Sbjct: 47  KQKPREQGLNDPKLGTIDRMYSCATCKEDIQVCPGHFGHIELHTPVFHVGFVVKIKKLLE 106

Query: 172 SICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVR-KSLKK---KILETTKKVSVCPHCG 227
           ++C   TC  +          +A   +P      R K  KK   KI   ++  +VC    
Sbjct: 107 TVCH--TCGMI----------KADFNHPDWQAAARTKDAKKRFDKIWRMSRTKNVCVQDV 154

Query: 228 EINGVVKKCGLLKISHEKYKNR---TKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQ 284
           E +G  K+  + KI H    +R   T +K+ +   L   + ++ K + + +  +K    +
Sbjct: 155 EESG--KENKIPKIPHGGCGSRQPDTIRKEGL--KLTGTWKQSKKDDDDGQGDRK----E 206

Query: 285 TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
            + P +   +F+ +    + LL +NA+ ++P  +IL
Sbjct: 207 VITPKQAQTIFKLLSDNTLALLGLNADYARPEWMIL 242



 Score = 57.8 bits (138), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 24/38 (63%), Positives = 30/38 (78%)

Query: 1108 EKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            +++++A + P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1066 DRFLKAAVAPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1103


>gi|313127539|ref|YP_004037809.1| DNA-directed RNA polymerase subunit a' [Halogeometricum borinquense
            DSM 11551]
 gi|448285310|ref|ZP_21476554.1| DNA-directed RNA polymerase subunit A'' [Halogeometricum borinquense
            DSM 11551]
 gi|312293904|gb|ADQ68364.1| DNA-directed RNA polymerase, subunit A' [Halogeometricum borinquense
            DSM 11551]
 gi|445576880|gb|ELY31327.1| DNA-directed RNA polymerase subunit A'' [Halogeometricum borinquense
            DSM 11551]
          Length = 417

 Score =  164 bits (414), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 116/360 (32%), Positives = 185/360 (51%), Gaps = 61/360 (16%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A+A   +Y+  +++P   VG ++AQSIGEPGTQMT+ TFH+AG            + E +
Sbjct: 47   AQAVEARYLDTRVDPLDPVGTVSAQSIGEPGTQMTMNTFHYAGVAEIDVTQGLPRLIELV 106

Query: 1152 EEVFVPDDSFILIKLD----------------MDRIRLLHL------------EVDIDSI 1183
            +    PD   + + L+                M+  ++L L             +D++  
Sbjct: 107  DARKTPDTPMMTVFLEGEYATERERAHEVVWSMEATKILALGDVSTNVADMVVRIDLNE- 165

Query: 1184 RYCIERTRGISGHLTVSG------HSFLILKPKDSSK--SFNSKMYQMKQLLPSV----- 1230
               +ER   ++   TV+          L +K + S     F  +    ++LL  V     
Sbjct: 166  DTLMERWPTVNNVDTVAQEIAETIEDALGVKTRRSGTVVEFGPESPSYRRLLQLVEELRD 225

Query: 1231 -VIKGVQGINRAVIHEE--DVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYK 1287
             V KG++ I R VI +E  D  G  ++ L  EG    DV++  GV   + +SNN +E+++
Sbjct: 226  IVFKGIEDITRVVIRKEENDDTGEEEFVLYTEGSAFGDVLSIEGVDASRTTSNNIHEIHR 285

Query: 1288 TLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESV 1346
             LGIEAAR  I+ E    +   G+  ++ RH MLVAD+MT++GE+  I RHG++  K+SV
Sbjct: 286  NLGIEAAREAIIDETMNTLREQGLDDVNVRHLMLVADIMTNRGEIESIGRHGISGSKDSV 345

Query: 1347 LNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL----LQAVPRSEP 1402
            L  A+FE T +HL DAA +G+ D + GV E +I+G P+ +GTG + L    ++A   +EP
Sbjct: 346  LARAAFEVTVNHLLDAAIHGEEDDLDGVIENVIVGKPIAIGTGDVDLRMGSIEASTETEP 405



 Score = 97.8 bits (242), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 70/247 (28%), Positives = 131/247 (53%), Gaps = 29/247 (11%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T +L+ +  T+ + A  V   +E T    LG+V   + + 
Sbjct: 98  GLPRLIELVDARKTPDTPMMTVFLEGEYATERERAHEVVWSMEATKILALGDVSTNVAD- 156

Query: 819 FVPDDSFILIKLDMDRIRLL-------HLEVDIDSIRYCIERTRGISGHLTVSGHSFLIL 871
                  +++++D++   L+       +++     I   IE   G+      +  S  ++
Sbjct: 157 -------MVVRIDLNEDTLMERWPTVNNVDTVAQEIAETIEDALGVK-----TRRSGTVV 204

Query: 872 KPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEE--DVEGVTKYKLLVEGDNLRD 929
           +    S S+  ++ Q+ + L  +V KG++ I R VI +E  D  G  ++ L  EG    D
Sbjct: 205 EFGPESPSYR-RLLQLVEELRDIVFKGIEDITRVVIRKEENDDTGEEEFVLYTEGSAFGD 263

Query: 930 VMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADL 988
           V++  GV   + +SNN +E+++ LGIEAAR  I+ E    +   G+  ++ RH MLVAD+
Sbjct: 264 VLSIEGVDASRTTSNNIHEIHRNLGIEAAREAIIDETMNTLREQGLDDVNVRHLMLVADI 323

Query: 989 MTSKGEV 995
           MT++GE+
Sbjct: 324 MTNRGEI 330


>gi|451846374|gb|EMD59684.1| hypothetical protein COCSADRAFT_164565 [Cochliobolus sativus
           ND90Pr]
          Length = 1737

 Score =  164 bits (414), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 92/273 (33%), Positives = 149/273 (54%), Gaps = 33/273 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+DV++FNRQPSLHK S+M HR KV+P+ TFR N  V +PYNADFDGDEMN+H+PQ++E 
Sbjct: 447 DDDVIIFNRQPSLHKESMMGHRVKVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSDET 506

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    +  L ++  +          +V+P+  + L+   QD + G Y +T+++ F   
Sbjct: 507 RAE----IQNLCMVPKQ----------IVSPQKNQPLMGIVQDTLLGVYKMTRRDNFIPI 552

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M I   +     D  GI+         P + ++   +WTGKQI S+        P  
Sbjct: 553 EQVMPIMMWV----PDWDGILPE-------PAI-LKPRPLWTGKQIVSMAF------PRE 594

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            N++ K    T +++   +D  ++++  +L+ G + K  +G+     V +I+  + G D 
Sbjct: 595 VNIEKKEDDSTPSKDNDIKDKSLMIKGGQLIYGQVTKKIVGASA-GGVIHIVFNELGSDA 653

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQG 613
           AV       R+ +++L++ GFS G+GD  P  G
Sbjct: 654 AVKFFNSCQRICNWWLLHYGFSFGVGDTIPDPG 686



 Score =  105 bits (262), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 63/181 (34%), Positives = 97/181 (53%), Gaps = 15/181 (8%)

Query: 1224 KQLLPSVVIKGVQGINRAVIHEEDV---------------EGVTKYKLLVEGDNLRDVMA 1268
            K LL  V ++GV+G+ RA I E  V               +   ++ L   G +L +V+A
Sbjct: 1280 KHLLDDVTLRGVRGVERAFIREHTVTVEKEDRSLMHSKNNDLCKEWVLDTTGTSLAEVLA 1339

Query: 1269 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK 1328
              GV   K  SN+  E+   LGIEAAR+ ++ E+ +V+   G  ++ RH  L+ D+M  +
Sbjct: 1340 IEGVDATKTYSNSFIEILGVLGIEAARAGLLKELGMVLSFDGSYVNHRHMALLVDIMCQR 1399

Query: 1329 GEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGT 1388
            G ++ ITRHG+ +     L   SFE T + L +AA +G+ D   GVSE I++G    +GT
Sbjct: 1400 GLLMAITRHGINRNDTGALMRCSFEETVEILLEAAGFGELDDCRGVSENIMLGQLAPMGT 1459

Query: 1389 G 1389
            G
Sbjct: 1460 G 1460



 Score =  101 bits (251), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTP+EFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+ V
Sbjct: 803 DYSPESRGFVENSYLRGLTPSEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDVMV 862

Query: 666 QYD 668
           +YD
Sbjct: 863 KYD 865



 Score = 81.6 bits (200), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 71/289 (24%), Positives = 128/289 (44%), Gaps = 59/289 (20%)

Query: 764  GVPRIKEIINASRNISTP-IITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPD 822
            GVPR+KEI+N + NI TP ++    D       A++++  +E TTL  + + +E  + P+
Sbjct: 1112 GVPRLKEILNIAANIKTPSMLVRQADSKASQQQAKLLRSTIELTTLRSLTQAVELYYDPE 1171

Query: 823  DSFILIKLDMDRIRLLHLEVDIDSI---------RYCIERTRGISGHLT---VSGHSFLI 870
                L++ D D +    +  + D +         R  ++R + +   +T   V+G     
Sbjct: 1172 IQSTLVEDDQDMVESYFILPEEDEVIESQSKWLLRIILDRKKLLDKSITIGEVAGKIKEE 1231

Query: 871  LKPK----DSSKSFNSKMYQM---------------------------KQLLPSVVIKGV 899
             KP      S ++ + ++ ++                           K LL  V ++GV
Sbjct: 1232 FKPNLAVIFSDENADEQVMRVRFIWDQNLQKDDEDEDERDERWMRKLEKHLLDDVTLRGV 1291

Query: 900  QGINRAVIHEEDV---------------EGVTKYKLLVEGDNLRDVMATYGVKGVKCSSN 944
            +G+ RA I E  V               +   ++ L   G +L +V+A  GV   K  SN
Sbjct: 1292 RGVERAFIREHTVTVEKEDRSLMHSKNNDLCKEWVLDTTGTSLAEVLAIEGVDATKTYSN 1351

Query: 945  NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
            +  E+   LGIEAAR+ ++ E+ +V+   G  ++ RH  L+ D+M  +G
Sbjct: 1352 SFIEILGVLGIEAARAGLLKELGMVLSFDGSYVNHRHMALLVDIMCQRG 1400



 Score = 71.2 bits (173), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 56/216 (25%), Positives = 106/216 (49%), Gaps = 27/216 (12%)

Query: 112 QRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQ 171
           ++ P   GL D ++GT  +  +C TC +++  C GHFG+I+L  PVFH+G+   +  +L+
Sbjct: 47  KQKPREQGLNDPKLGTIDRMYSCATCKEDIQVCPGHFGHIELHTPVFHVGFVVKIKKLLE 106

Query: 172 SICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVR-KSLKK---KILETTKKVSVCPHCG 227
           ++C   TC  +          +A   +P      R K  KK   KI   ++  +VC    
Sbjct: 107 TVCH--TCGMI----------KADFNHPDWQAAARTKDAKKRFDKIWRMSRTKNVCVQDV 154

Query: 228 EINGVVKKCGLLKISHEKYKNR---TKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQ 284
           E +G  K+  + KI H    +R   T +K+ +   L   + ++ K + + +  +K    +
Sbjct: 155 EESG--KENKIPKIPHGGCGSRQPDTIRKEGL--KLTGTWKQSKKDDDDGQGDRK----E 206

Query: 285 TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
            + P +   +F+ +    + LL +NA+ ++P  +IL
Sbjct: 207 VITPKQAQTIFKLLSDNTLALLGLNADYARPEWMIL 242



 Score = 57.8 bits (138), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 24/38 (63%), Positives = 30/38 (78%)

Query: 1108 EKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            +++++A + P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1066 DRFLKAAVAPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1103


>gi|433637475|ref|YP_007283235.1| DNA-directed RNA polymerase, subunit A'' [Halovivax ruber XH-70]
 gi|433289279|gb|AGB15102.1| DNA-directed RNA polymerase, subunit A'' [Halovivax ruber XH-70]
          Length = 402

 Score =  164 bits (414), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 108/345 (31%), Positives = 176/345 (51%), Gaps = 57/345 (16%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A+A   +Y   +++P   VG ++AQSIGEPGTQ+T+ TFH+AG            + E +
Sbjct: 49   AQAVESQYRDTRVDPLDPVGTVSAQSIGEPGTQLTMNTFHYAGVAEIDVTQGLPRLIELV 108

Query: 1152 EEVFVPDDSFILIKLD----------------MDRIRLLHL---EVDIDSIRYCIE---- 1188
            +    PD   + + LD                ++  ++L L     ++  +R  I     
Sbjct: 109  DARKTPDTPTMTVHLDEEYATEREKAHEVVWKIEATKILALGDVSTNVADMRVVISLNED 168

Query: 1189 --RTRGIS------------GHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKG 1234
                R I+            G  TV   + +   P++ S      + Q+ + L  +  KG
Sbjct: 169  TLNERMITAEEVAEIIEDQLGVKTVQNGTTVEFGPEEPSYR---DLLQLVEELREITFKG 225

Query: 1235 VQGINRAVIHEEDVE-----GVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTL 1289
            ++ I+R VI  E+++        ++ L  EG    D +A  GV   + + NN +E+Y+ L
Sbjct: 226  IEDISRVVIRREEMDDSPFDADEEFVLYTEGSAFGDALAIEGVDASRTTCNNIHEIYRNL 285

Query: 1290 GIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLN 1348
            G+EAAR  I+ E K  +   G+ +I+ RH MLVAD+MT++G +  I RHG+A  KESVL 
Sbjct: 286  GVEAAREIIIEETKNTLVEQGLDNINVRHLMLVADIMTNEGTIESIGRHGIAGNKESVLA 345

Query: 1349 LASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
             A++E T +HL +A+ +G+ D I GV E +I+G P+ +GTG + L
Sbjct: 346  RAAYEVTVNHLLNASIHGEIDSIDGVIENVIVGRPVKLGTGDVDL 390



 Score = 94.7 bits (234), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 72/245 (29%), Positives = 128/245 (52%), Gaps = 29/245 (11%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP +T +LD++  T+ + A  V  ++E T    LG+V   +   
Sbjct: 100 GLPRLIELVDARKTPDTPTMTVHLDEEYATEREKAHEVVWKIEATKILALGDVSTNVA-- 157

Query: 819 FVPDDSFILIKLDMDRI--RLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDS 876
               D  ++I L+ D +  R++  E     +   IE   G+    TV   + +   P++ 
Sbjct: 158 ----DMRVVISLNEDTLNERMITAE----EVAEIIEDQLGVK---TVQNGTTVEFGPEEP 206

Query: 877 SKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVE-----GVTKYKLLVEGDNLRDVM 931
           S      + Q+ + L  +  KG++ I+R VI  E+++        ++ L  EG    D +
Sbjct: 207 SYR---DLLQLVEELREITFKGIEDISRVVIRREEMDDSPFDADEEFVLYTEGSAFGDAL 263

Query: 932 ATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMT 990
           A  GV   + + NN +E+Y+ LG+EAAR  I+ E K  +   G+ +I+ RH MLVAD+MT
Sbjct: 264 AIEGVDASRTTCNNIHEIYRNLGVEAAREIIIEETKNTLVEQGLDNINVRHLMLVADIMT 323

Query: 991 SKGEV 995
           ++G +
Sbjct: 324 NEGTI 328


>gi|384253754|gb|EIE27228.1| beta and beta-prime subunits of DNA dependent RNA-polymerase
           [Coccomyxa subellipsoidea C-169]
          Length = 1566

 Score =  164 bits (414), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 94/270 (34%), Positives = 147/270 (54%), Gaps = 36/270 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + D VLFNRQPSLHK+S+M H+ ++LP+ TFR N  V +PYNADFDGDEMN+H+PQT E 
Sbjct: 372 NGDYVLFNRQPSLHKMSMMGHKVRILPYSTFRLNLSVTSPYNADFDGDEMNMHVPQTPET 431

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R E               + +M    N+V+P+  + +I   QD + G  L+T+++ F  +
Sbjct: 432 RTE--------------TREIMMVPRNIVSPQANKPVIGIVQDTLLGCRLMTKRDTFIEK 477

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              M I   L     D  G I         P + ++   +WTGKQ+++L +         
Sbjct: 478 DLFMNILMWL----EDWDGKIPM-------PAI-LKPKPLWTGKQVYNLFMP-------R 518

Query: 521 ANLKTKGRAYTANE--EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            N++ +   Y  NE  +F   DS V+++N ELL G++ K TLG+    ++ +++  + G 
Sbjct: 519 VNIRRQSAWYKDNEPLDFSPSDSQVLIQNGELLTGTLCKKTLGASA-GSLIHVIWMEEGP 577

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           + A   + +    T+ +L+  GFSIGIGD 
Sbjct: 578 EAARAFLSQSQYTTNHWLLQHGFSIGIGDT 607



 Score =  103 bits (257), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 62/180 (34%), Positives = 101/180 (56%), Gaps = 11/180 (6%)

Query: 1226 LLPSVVIKGVQGINRAVIHE--------EDVEGVT---KYKLLVEGDNLRDVMATYGVKG 1274
            +L  V ++G+  I++  + E        +  +G T   ++ L  EG NL +VM    V  
Sbjct: 1208 MLSQVALQGIPDIHKVSLRESKRIVPSSDAPDGYTNDSEWVLDTEGVNLSEVMCHPDVDY 1267

Query: 1275 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGI 1334
             +  SN+  E+ + LGIEAAR+ ++ E++ V+E  G  +++RH   + D MTS+G  + I
Sbjct: 1268 RRTISNHLVEIIEVLGIEAARNALLKEMRGVIEFDGSYVNYRHLAALVDSMTSRGHFMAI 1327

Query: 1335 TRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            TRHG+ + +   L   SFE T D LF AA + + D ++GVSE I++G    +GTG   L+
Sbjct: 1328 TRHGINRQENGPLAQCSFEETVDILFRAAAFSEKDHMTGVSENIMLGQLAPLGTGSFGLM 1387



 Score = 97.1 bits (240), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 43/69 (62%), Positives = 55/69 (79%), Gaps = 1/69 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D+ P  +GFV+NS+  GLTP E FFH MGGREGL+DTAVKT+ TGY+QRRLVK++EDL +
Sbjct: 729 DLGPESRGFVENSYLRGLTPQELFFHAMGGREGLIDTAVKTSSTGYIQRRLVKAMEDLMI 788

Query: 666 QYDMSFDAA 674
           +YD +   A
Sbjct: 789 KYDGTVRTA 797



 Score = 77.4 bits (189), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 79/289 (27%), Positives = 134/289 (46%), Gaps = 55/289 (19%)

Query: 764  GVPRIKEIINASRNISTPIITAYL--DKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+ EIIN ++NI TP +T +L  +   D + A+ V+  LE TTL +V    E  + P
Sbjct: 1038 GVPRLTEIINIAKNIKTPSLTVFLLGEASRDREAAKQVQCSLEYTTLRKVTGATEIYYDP 1097

Query: 822  DDSFILIK----------------LDMDRIR--LLHLEVDID-------SIRYCIERTRG 856
            D +  +I                 +D++R+   LL +E++ D       S+    ER   
Sbjct: 1098 DPTTTVIDEDREFVENYFEMPDEDMDVNRMSPWLLRIELNRDMMVDKKLSMSDIAERINS 1157

Query: 857  -ISGHLTV----SGHSFLILK---------PKDSSKSFNSKMYQMK---QLLPSVVIKGV 899
                 LT          LIL+          +  ++S    ++  K    +L  V ++G+
Sbjct: 1158 EFEDELTCIFNDDNAPKLILRIRVLNDEGGKEAEAQSETDDVFLRKIEATMLSQVALQGI 1217

Query: 900  QGINRAVIHE--------EDVEGVT---KYKLLVEGDNLRDVMATYGVKGVKCSSNNTYE 948
              I++  + E        +  +G T   ++ L  EG NL +VM    V   +  SN+  E
Sbjct: 1218 PDIHKVSLRESKRIVPSSDAPDGYTNDSEWVLDTEGVNLSEVMCHPDVDYRRTISNHLVE 1277

Query: 949  VYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            + + LGIEAAR+ ++ E++ V+E  G  +++RH   + D MTS+G  + 
Sbjct: 1278 IIEVLGIEAARNALLKEMRGVIEFDGSYVNYRHLAALVDSMTSRGHFMA 1326



 Score = 49.7 bits (117), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 21/29 (72%), Positives = 23/29 (79%)

Query: 1117 PATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            P   +G +AAQSIGEP TQMTL TFHFAG
Sbjct: 1001 PGEMIGTVAAQSIGEPTTQMTLNTFHFAG 1029



 Score = 47.8 bits (112), Expect = 0.049,   Method: Compositional matrix adjust.
 Identities = 43/167 (25%), Positives = 78/167 (46%), Gaps = 27/167 (16%)

Query: 134 CTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFR 193
           CTT G N  D  G+FG+I+L  PVFHIG+ + ++ +L+  C +   +++L+ ++      
Sbjct: 7   CTTDGANQQDSPGYFGHIELAKPVFHIGWTKELMRVLR--CVSYHSSKLLVDKD------ 58

Query: 194 AKLRNPALSYLVRKSLKKKILETTKKVSVC------PHCGEINGVVKKCGLLKISHEKYK 247
               +P    ++R  +K     +   V+VC         G      K  GLL+I  E+  
Sbjct: 59  ----DPKFKQVMR--IKNGEARSRALVAVCGSKRFDEETGAPQPAYKFEGLLRIMAERIF 112

Query: 248 NRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQL 294
           +    +D    D+ AE    V+   EI A K   +++ ++  + + L
Sbjct: 113 SSADDEDI---DMGAE----VERRQEITAEKAHEILKRISDEDCIAL 152


>gi|284998388|ref|YP_003420156.1| DNA-directed RNA polymerase subunit A' [Sulfolobus islandicus
           L.D.8.5]
 gi|284446284|gb|ADB87786.1| DNA-directed RNA polymerase subunit A' [Sulfolobus islandicus
           L.D.8.5]
          Length = 880

 Score =  164 bits (414), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 102/272 (37%), Positives = 149/272 (54%), Gaps = 29/272 (10%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D DVVLFNRQPSLH++S+MAHR +VL   TFR N  VC PYNADFDGDEMN+H+PQ+EE
Sbjct: 412 TDGDVVLFNRQPSLHRISMMAHRVRVLKGLTFRLNLLVCPPYNADFDGDEMNLHVPQSEE 471

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           A AE              AK +M    N++TPR G  +I A QD+I+G YLLT K     
Sbjct: 472 AIAE--------------AKEIMLVHKNIITPRYGGPIIGAAQDYISGAYLLTVKTTLLT 517

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           + +  +I    +AD     G     + R +           +TGKQI S  L  + +   
Sbjct: 518 KEEAQQILG--VADVKIDLGEPAILAPREY-----------YTGKQIVSAFLPKDFNFHG 564

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            AN+ +  R      E C  DSYV+++N  LL G  DK  +G+    ++ + L++++ ++
Sbjct: 565 QANVSSGPR--LCKNEDCPHDSYVVIKNGILLEGVFDKKAIGNQQPESILHWLIKEYSDE 622

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
                M  L R+   ++  +GF++ + DV+ G
Sbjct: 623 YGKWLMDNLFRVFIRFVELQGFTMRLEDVSLG 654



 Score =  115 bits (287), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 77/261 (29%), Positives = 124/261 (47%), Gaps = 49/261 (18%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D +++ S   I++ ++Y +D   TPI   ++D R+G  +    C TCG  L +C GHFG+
Sbjct: 17  DEIRKMSVTAIITPDVYDED--GTPIEGSVMDPRLGVIEPGQKCPTCGNTLGNCPGHFGH 74

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-----KLRNPALSYLV 205
           I+L  PV H+G+ + V   L++ C+   C RV + E++   +       K R P+ +   
Sbjct: 75  IELVRPVIHVGFVKHVYEFLKATCRR--CGRVKISEDEIEKYSRIYNAIKKRWPSAA--- 129

Query: 206 RKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYN 265
            K L + + +T  K  VCPHCGE           KI  EK  N              E  
Sbjct: 130 -KRLTEYVKKTAMKAQVCPHCGEKQ--------FKIKLEKPYN-----------FYEERK 169

Query: 266 EAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLV 325
           E V                 L P ++ +  E +P  D+ +L  +   S+P  +ILT L V
Sbjct: 170 EGV---------------AKLTPSDIRERLEKVPESDVEILGYDPTTSRPEWMILTVLPV 214

Query: 326 PPNCIRPSVI--SDLKSDNDV 344
           PP  IRPS++  S +++++D+
Sbjct: 215 PPITIRPSIMIESGIRAEDDL 235



 Score = 88.6 bits (218), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 38/63 (60%), Positives = 51/63 (80%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D++P  +GF+ +SF +GL PTE FFH  GGREGLVDTAV+T+++GYMQRRL+ +L DL  
Sbjct: 773 DISPEARGFIYSSFRTGLKPTELFFHAAGGREGLVDTAVRTSQSGYMQRRLINALSDLRA 832

Query: 666 QYD 668
           +YD
Sbjct: 833 EYD 835


>gi|45935345|gb|AAS79694.1| RNA polymerase III large subunit [Pinus nigra]
          Length = 548

 Score =  164 bits (414), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 85/223 (38%), Positives = 138/223 (61%), Gaps = 25/223 (11%)

Query: 390 MNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGY 449
           MN+H+PQTEEAR EAL              +LM  ++NL TP+NG++L+A+TQDF+T  +
Sbjct: 1   MNLHVPQTEEARTEAL--------------MLMGVQNNLCTPKNGDILVASTQDFLTSSF 46

Query: 450 LLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSL 509
           L+T+K+ F++RA +  +  + + D ++   +          P + ++   +WTGKQ+FS+
Sbjct: 47  LITRKDTFYDRA-SFALMCSYMGDATEAIDLP--------TPAI-LKPVELWTGKQLFSV 96

Query: 510 ILKPNRDCPVNANLKTKGRAYT-ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANV 568
           +++PN +  V  NL    + Y+ + E  C  D  V  RNSEL++G + K+TLG+G K  +
Sbjct: 97  LVRPNANMRVFVNLIVMEKNYSKSGETMCRNDGCVCFRNSELISGQIGKATLGNGNKNGL 156

Query: 569 FYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           F +LLRD+    A + M RL+++++ ++ N GFSIGI DV PG
Sbjct: 157 FTVLLRDYNTHAAASCMNRLAKLSARWIGNHGFSIGIDDVQPG 199



 Score =  106 bits (265), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 59/111 (53%), Positives = 70/111 (63%), Gaps = 7/111 (6%)

Query: 607 DVTPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D+TP  +GFV NSF++GLT TEFFFHTMGGREGLVDTAVKTAETGYM RRL+K+LEDL  
Sbjct: 318 DMTPAAKGFVANSFYTGLTATEFFFHTMGGREGLVDTAVKTAETGYMSRRLMKALEDLST 377

Query: 666 QYDMSFDAAFYGQTDCISGVSECIIM------GLPMNVGTGLIKLLQAVPR 710
            YD +   A  G    + G             G P+N+   L+K     PR
Sbjct: 378 HYDGTVRNASGGIVQLLYGDDGMDPAHMEGNDGAPLNMDRLLMKTKATCPR 428



 Score = 55.5 bits (132), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 21/42 (50%), Positives = 36/42 (85%)

Query: 21 VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRA 62
          +LM  ++NL TP+NG++L+A+TQDF+T  +L+T+K+ F++RA
Sbjct: 17 MLMGVQNNLCTPKNGDILVASTQDFLTSSFLITRKDTFYDRA 58


>gi|227828174|ref|YP_002829954.1| DNA-directed RNA polymerase subunit A' [Sulfolobus islandicus
           M.14.25]
 gi|229585403|ref|YP_002843905.1| DNA-directed RNA polymerase subunit A' [Sulfolobus islandicus
           M.16.27]
 gi|385773844|ref|YP_005646411.1| DNA-directed RNA polymerase subunit A' [Sulfolobus islandicus
           HVE10/4]
 gi|385776479|ref|YP_005649047.1| DNA-directed RNA polymerase subunit A' [Sulfolobus islandicus
           REY15A]
 gi|227459970|gb|ACP38656.1| DNA-directed RNA polymerase subunit A' [Sulfolobus islandicus
           M.14.25]
 gi|228020453|gb|ACP55860.1| DNA-directed RNA polymerase subunit A' [Sulfolobus islandicus
           M.16.27]
 gi|323475227|gb|ADX85833.1| DNA-directed RNA polymerase subunit A' [Sulfolobus islandicus
           REY15A]
 gi|323477959|gb|ADX83197.1| DNA-directed RNA polymerase subunit A' [Sulfolobus islandicus
           HVE10/4]
          Length = 880

 Score =  163 bits (413), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 102/272 (37%), Positives = 149/272 (54%), Gaps = 29/272 (10%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D DVVLFNRQPSLH++S+MAHR +VL   TFR N  VC PYNADFDGDEMN+H+PQ+EE
Sbjct: 412 TDGDVVLFNRQPSLHRISMMAHRVRVLKGLTFRLNLLVCPPYNADFDGDEMNLHVPQSEE 471

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           A AE              AK +M    N++TPR G  +I A QD+I+G YLLT K     
Sbjct: 472 AIAE--------------AKEIMLVHKNIITPRYGGPIIGAAQDYISGAYLLTVKTTLLT 517

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           + +  +I    +AD     G     + R +           +TGKQI S  L  + +   
Sbjct: 518 KEEAQQILG--VADVKIDLGEPAILAPREY-----------YTGKQIVSAFLPKDFNFHG 564

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            AN+ +  R      E C  DSYV+++N  LL G  DK  +G+    ++ + L++++ ++
Sbjct: 565 QANVSSGPR--LCKNEDCPHDSYVVIKNGILLEGVFDKKAIGNQQPESILHWLIKEYSDE 622

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
                M  L R+   ++  +GF++ + DV+ G
Sbjct: 623 YGKWLMDNLFRVFIRFVELQGFTMRLEDVSLG 654



 Score =  114 bits (285), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 77/261 (29%), Positives = 124/261 (47%), Gaps = 49/261 (18%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D +++ S   I++ ++Y +D   TPI   ++D R+G  +    C TCG  L +C GHFG+
Sbjct: 17  DEIRKMSVTAIITPDVYDED--GTPIEGSVMDPRLGVIEPGQKCPTCGNTLGNCPGHFGH 74

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-----KLRNPALSYLV 205
           I+L  PV H+G+ + V   L++ C+   C RV + E++   +       K R P+ +  +
Sbjct: 75  IELVRPVIHVGFVKHVYEFLKATCRR--CGRVKISEDEIEKYSRIYNAIKKRWPSAARRL 132

Query: 206 RKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYN 265
            + +KK    T  K  VCPHCGE           KI  EK  N              E  
Sbjct: 133 TEYVKK----TAMKAQVCPHCGEKQ--------FKIKLEKPYN-----------FYEERK 169

Query: 266 EAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLV 325
           E V                 L P ++ +  E +P  D+ +L  +   S+P  +ILT L V
Sbjct: 170 EGV---------------AKLTPSDIRERLEKVPESDVEILGYDPTTSRPEWMILTVLPV 214

Query: 326 PPNCIRPSVI--SDLKSDNDV 344
           PP  IRPS++  S +++++D+
Sbjct: 215 PPITIRPSIMIESGIRAEDDL 235



 Score = 89.4 bits (220), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 40/73 (54%), Positives = 56/73 (76%), Gaps = 2/73 (2%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D++P  +GF+ +SF +GL PTE FFH  GGREGLVDTAV+T+++GYMQRRL+ +L DL  
Sbjct: 773 DISPEARGFIYSSFRTGLKPTELFFHAAGGREGLVDTAVRTSQSGYMQRRLINALSDLRA 832

Query: 666 QYDMSFDAAFYGQ 678
           +YD +   + YG+
Sbjct: 833 EYDGTV-RSLYGE 844


>gi|219852750|ref|YP_002467182.1| DNA-directed RNA polymerase subunit A' [Methanosphaerula palustris
           E1-9c]
 gi|219547009|gb|ACL17459.1| DNA-directed RNA polymerase subunit A' [Methanosphaerula palustris
           E1-9c]
          Length = 880

 Score =  163 bits (413), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 98/269 (36%), Positives = 149/269 (55%), Gaps = 34/269 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIMAHR KV+  RTFR N  VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 414 DGDIVLFNRQPSLHRMSIMAHRIKVMEGRTFRLNPAVCPPYNADFDGDEMNLHVPQTEEA 473

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A +L+A + N+++PR G  +I    D I+G ++LT    +F +
Sbjct: 474 RAE--------------ASILVAVQQNILSPRFGGPIIGGIHDHISGIFMLTHDLRWFAK 519

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              + +      D     G I+       N + +      W+ KQ+FS+IL PN    +N
Sbjct: 520 DDFLYLLKYYDFDHMPEPGKIE-------NGIPY------WSNKQVFSMIL-PNE---LN 562

Query: 521 ANLKTKGRAY--TANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
              K    A      ++ C RD++V +   +L+ G++DK ++G+     +   ++R +G 
Sbjct: 563 MVFKASSCANCDVCVKDQCERDAFVRILEGQLITGTIDKKSIGA-FDGEILNRIIRQYGM 621

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           + A   +  +++++   +M  GFS GI D
Sbjct: 622 ERAAKFIDDMTKLSIKGIMIDGFSFGIDD 650



 Score =  102 bits (253), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 81/266 (30%), Positives = 123/266 (46%), Gaps = 43/266 (16%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G IE  +     ++  S  +I+  + Y  D    P P GL+D  +G       C TC Q 
Sbjct: 8   GKIEFGLLSPKEIRTMSVRKIIWADTY--DDDGFPYPQGLMDLSLGVIDPGLRCKTCDQK 65

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
            +DC GHFG+I+L  PV H+GY R +  +L+  C+   C R+LL   +      K+   +
Sbjct: 66  AADCPGHFGHIELAKPVIHVGYTRLIRKLLRVTCRE--CGRLLLSSSEI----EKVTITS 119

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDL 260
              L    L +K +   KK   CPHC E          LKI+ E        K     ++
Sbjct: 120 EEDLTGDVLSEKDI---KKERTCPHCDEQQ--------LKINFE--------KPTTFSEV 160

Query: 261 LAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
           L E  + V+       HK       L P ++    E IP  D+ LL +N ++++P   IL
Sbjct: 161 LLEDGKKVE-------HK-------LTPADIRARLEKIPDSDLRLLGINPDVARPEWTIL 206

Query: 321 TRLLVPPNCIRPSVI--SDLKSDNDV 344
           T L VPP  +RPS+I  +  +S++D+
Sbjct: 207 TVLPVPPVTMRPSIILENGQRSEDDL 232



 Score = 91.3 bits (225), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 38/57 (66%), Positives = 51/57 (89%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFV++S+ SGL PTEFFFH +GGREGLVDTAV+T+++GY+QRRL+ +L+DL V+YD
Sbjct: 779 HGFVKHSYKSGLNPTEFFFHAIGGREGLVDTAVRTSQSGYLQRRLINALQDLKVEYD 835


>gi|227830881|ref|YP_002832661.1| DNA-directed RNA polymerase subunit A' [Sulfolobus islandicus
           L.S.2.15]
 gi|229579767|ref|YP_002838166.1| DNA-directed RNA polymerase subunit A' [Sulfolobus islandicus
           Y.G.57.14]
 gi|229581564|ref|YP_002839963.1| DNA-directed RNA polymerase subunit A' [Sulfolobus islandicus
           Y.N.15.51]
 gi|227457329|gb|ACP36016.1| DNA-directed RNA polymerase subunit A' [Sulfolobus islandicus
           L.S.2.15]
 gi|228010482|gb|ACP46244.1| DNA-directed RNA polymerase subunit A' [Sulfolobus islandicus
           Y.G.57.14]
 gi|228012280|gb|ACP48041.1| DNA-directed RNA polymerase subunit A' [Sulfolobus islandicus
           Y.N.15.51]
          Length = 880

 Score =  163 bits (413), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 102/272 (37%), Positives = 149/272 (54%), Gaps = 29/272 (10%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D DVVLFNRQPSLH++S+MAHR +VL   TFR N  VC PYNADFDGDEMN+H+PQ+EE
Sbjct: 412 TDGDVVLFNRQPSLHRISMMAHRVRVLKGLTFRLNLLVCPPYNADFDGDEMNLHVPQSEE 471

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           A AE              AK +M    N++TPR G  +I A QD+I+G YLLT K     
Sbjct: 472 AIAE--------------AKEIMLVHKNIITPRYGGPIIGAAQDYISGAYLLTVKTTLLT 517

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           + +  +I    +AD     G     + R +           +TGKQI S  L  + +   
Sbjct: 518 KEEAQQILG--VADVKIDLGEPAILAPREY-----------YTGKQIVSAFLPKDFNFHG 564

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            AN+ +  R      E C  DSYV+++N  LL G  DK  +G+    ++ + L++++ ++
Sbjct: 565 QANVSSGPR--LCKNEDCPHDSYVVIKNGILLEGVFDKKAIGNQQPESILHWLIKEYSDE 622

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
                M  L R+   ++  +GF++ + DV+ G
Sbjct: 623 YGKWLMDNLFRVFIRFVELQGFTMRLEDVSLG 654



 Score =  114 bits (285), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 77/261 (29%), Positives = 124/261 (47%), Gaps = 49/261 (18%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D +++ S   I++ ++Y +D   TPI   ++D R+G  +    C TCG  L +C GHFG+
Sbjct: 17  DEIRKMSVTAIITPDVYDED--GTPIEGSVMDPRLGVIEPGQKCPTCGNTLGNCPGHFGH 74

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-----KLRNPALSYLV 205
           I+L  PV H+G+ + V   L++ C+   C RV + E++   +       K R P+ +  +
Sbjct: 75  IELVRPVIHVGFVKHVYEFLKATCRR--CGRVKISEDEIEKYSRIYNAIKKRWPSAARRL 132

Query: 206 RKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYN 265
            + +KK    T  K  VCPHCGE           KI  EK  N              E  
Sbjct: 133 TEYVKK----TAMKAQVCPHCGEKQ--------FKIKLEKPYN-----------FYEERK 169

Query: 266 EAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLV 325
           E V                 L P ++ +  E +P  D+ +L  +   S+P  +ILT L V
Sbjct: 170 EGV---------------AKLTPSDIRERLEKVPESDVEILGYDPTTSRPEWMILTVLPV 214

Query: 326 PPNCIRPSVI--SDLKSDNDV 344
           PP  IRPS++  S +++++D+
Sbjct: 215 PPITIRPSIMIESGIRAEDDL 235



 Score = 89.4 bits (220), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 40/73 (54%), Positives = 56/73 (76%), Gaps = 2/73 (2%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D++P  +GF+ +SF +GL PTE FFH  GGREGLVDTAV+T+++GYMQRRL+ +L DL  
Sbjct: 773 DISPEARGFIYSSFRTGLKPTELFFHAAGGREGLVDTAVRTSQSGYMQRRLINALSDLRA 832

Query: 666 QYDMSFDAAFYGQ 678
           +YD +   + YG+
Sbjct: 833 EYDGTV-RSLYGE 844


>gi|66815437|ref|XP_641735.1| RNA polymerase II largest subunit [Dictyostelium discoideum AX4]
 gi|166202448|sp|P35084.2|RPB1_DICDI RecName: Full=DNA-directed RNA polymerase II subunit rpb1;
           Short=RNA polymerase II subunit B1; AltName:
           Full=DNA-directed RNA polymerase III subunit A
 gi|60469758|gb|EAL67745.1| RNA polymerase II largest subunit [Dictyostelium discoideum AX4]
          Length = 1727

 Score =  163 bits (413), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 95/272 (34%), Positives = 148/272 (54%), Gaps = 40/272 (14%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D DVV+FNRQPSLHK+S+M HR KV+P+ TFR N  V +PYNADFDGDEMN+H+PQT E
Sbjct: 442 NDGDVVIFNRQPSLHKMSMMGHRIKVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQTLE 501

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE +             +++M  +  +V+P++   ++   QD + G  L T+++ F  
Sbjct: 502 TRAEVI-------------EIMMVPRQ-IVSPQSNRPVMGIVQDTLLGSRLFTKRDCFME 547

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWN----PVVFVRTAVIWTGKQIFSLILKPNR 515
           +   M I   L                 SW+    P   ++   +WTGKQ+FSLI+ P+ 
Sbjct: 548 KDLVMNILMWL----------------PSWDGKVPPPAILKPKQLWTGKQLFSLII-PD- 589

Query: 516 DCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
              +N    T         E    D+ VI+   ELLAG + K +LG+    ++ ++++ +
Sbjct: 590 ---INLIRFTSTHNDKEPNECSAGDTRVIIERGELLAGILCKRSLGAAN-GSIIHVVMNE 645

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            G D     + +   + + +L+NRGF++GIGD
Sbjct: 646 HGHDTCRLFIDQTQTVVNHWLINRGFTMGIGD 677



 Score =  118 bits (296), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 89/319 (27%), Positives = 166/319 (52%), Gaps = 36/319 (11%)

Query: 1107 REKYVRAQIEPATAVGALAAQSIG-EPGTQMTLKTFHFAGEVCEYIEEVF-VPDD----- 1159
            R K V++Q+E  T     +A  I  +P  Q T+       E  E++   F +PD+     
Sbjct: 1149 RAKIVKSQLEYTTLANVTSATEIYYDPDPQNTI-----ISEDAEFVNSYFELPDEEIDVH 1203

Query: 1160 --SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSF--LILK-----PK 1210
              S  L+++++DR  +   ++ +  I  C+ R  G+S +   S  +   LIL+      +
Sbjct: 1204 SMSPWLLRIELDRGMVTDKKLTMADITQCVVRDFGLSLNCIFSDDNAEKLILRIRMVESQ 1263

Query: 1211 DSSKSFNSKMYQM-----KQLLPSVVIKGVQGINRAVIHEED-VEGVTK---------YK 1255
            ++  + N    Q        +L  +V++G++GI +  +  +D +  VT+         + 
Sbjct: 1264 ETKGTDNDDDDQFLRRIESNMLSEMVLRGIKGIKKVFMRTDDKIPKVTENGGFGVREEWI 1323

Query: 1256 LLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDF 1315
            L  +G +L +VM+   V   + +SN+  E+ + LGIEA R+ ++ E++ V+   G  +++
Sbjct: 1324 LDTDGVSLLEVMSHPDVDHTRTTSNDIVEIIQVLGIEAVRNALLKELRAVISFDGSYVNY 1383

Query: 1316 RHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVS 1375
            RH  ++AD+MT +G ++ ITRHG+ +++   L   SFE T + L DAA + +TD + GV+
Sbjct: 1384 RHLAILADVMTYRGHLMAITRHGINRVETGPLMRCSFEETVEILMDAAMFSETDDVKGVT 1443

Query: 1376 ECIIMGLPMNVGTGLIKLL 1394
            E II+G    +GTG  ++ 
Sbjct: 1444 ENIILGQLPPLGTGSFEVF 1462



 Score =  100 bits (249), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 41/59 (69%), Positives = 53/59 (89%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
           +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKT+ETGY+QRRLVK++ED+ ++YD +
Sbjct: 806 RGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDVSIKYDAT 864



 Score = 99.4 bits (246), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 79/286 (27%), Positives = 139/286 (48%), Gaps = 52/286 (18%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEIIN ++ + TP +T YL      D+D A+IVK +LE TTL  V    E  + P
Sbjct: 1116 GVPRLKEIINIAKQVKTPSLTIYLKPHMARDMDRAKIVKSQLEYTTLANVTSATEIYYDP 1175

Query: 822  DDSFILIKLDMDRIR------------------LLHLEVD----------IDSIRYCIER 853
            D    +I  D + +                   LL +E+D          +  I  C+ R
Sbjct: 1176 DPQNTIISEDAEFVNSYFELPDEEIDVHSMSPWLLRIELDRGMVTDKKLTMADITQCVVR 1235

Query: 854  TRGISGHLTVSGHSF--LILK-----PKDSSKSFNSKMYQM-----KQLLPSVVIKGVQG 901
              G+S +   S  +   LIL+      +++  + N    Q        +L  +V++G++G
Sbjct: 1236 DFGLSLNCIFSDDNAEKLILRIRMVESQETKGTDNDDDDQFLRRIESNMLSEMVLRGIKG 1295

Query: 902  INRAVIHEED-VEGVTK---------YKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYK 951
            I +  +  +D +  VT+         + L  +G +L +VM+   V   + +SN+  E+ +
Sbjct: 1296 IKKVFMRTDDKIPKVTENGGFGVREEWILDTDGVSLLEVMSHPDVDHTRTTSNDIVEIIQ 1355

Query: 952  TLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             LGIEA R+ ++ E++ V+   G  +++RH  ++AD+MT +G ++ 
Sbjct: 1356 VLGIEAVRNALLKELRAVISFDGSYVNYRHLAILADVMTYRGHLMA 1401



 Score = 73.9 bits (180), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 43/116 (37%), Positives = 61/116 (52%), Gaps = 12/116 (10%)

Query: 115 PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSIC 174
           P   GLLD  MGT  K   C TC   +++C GHFG+I+L  PVFHIG+   V+ IL+ +C
Sbjct: 47  PKAGGLLDPAMGTIDKTQRCQTCSGTMAECPGHFGHIELAKPVFHIGFIDTVLKILRCVC 106

Query: 175 KNPTCARVLLGEEKAAGFRA--KLRNPALSYLVRKSLKKKILETTKKVSVCPHCGE 228
            +  C++ LL +     FR   K+RN       +K     +++  K   VC   GE
Sbjct: 107 YH--CSK-LLTDTNEHSFRQALKIRN-------QKHRLNAVVDCCKNKKVCAIGGE 152



 Score = 57.8 bits (138), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 33/88 (37%), Positives = 48/88 (54%), Gaps = 17/88 (19%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYIEEV 1154
            K+++A   P   VGALAAQSIGEP TQMTL TFH+AG              E+    ++V
Sbjct: 1071 KFLQALAHPGEMVGALAAQSIGEPATQMTLNTFHYAGVSSKNVTLGVPRLKEIINIAKQV 1130

Query: 1155 FVPDDSFIL---IKLDMDRIRLLHLEVD 1179
              P  +  L   +  DMDR +++  +++
Sbjct: 1131 KTPSLTIYLKPHMARDMDRAKIVKSQLE 1158


>gi|397135918|gb|AFO11454.1| RNA polymerase I, partial [Citeromyces matritensis]
          Length = 860

 Score =  163 bits (413), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 93/272 (34%), Positives = 149/272 (54%), Gaps = 47/272 (17%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+D VLFNRQPSLHK+S+MAHR KV+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 249 DDDPVLFNRQPSLHKMSMMAHRVKVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 308

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE                 L +  S +V+P++ + ++   QD + G   +T +++F + 
Sbjct: 309 RAE--------------LSQLCSVPSQIVSPQSNKPVMGIVQDTLCGVRKMTLRDSFIDY 354

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVV----FVRTAVIWTGKQIFSLILKPNRD 516
            Q M +                 F    W+ V+     ++   +W+GKQ+FS+ +     
Sbjct: 355 DQVMSML----------------FWIPQWDGVIPQPAILKPKPLWSGKQLFSMAI----- 393

Query: 517 CPVNAN-LKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            P   + L+  G  Y         D+ +++RN E++ G +DK T+GS G   + + ++R+
Sbjct: 394 -PRGIHLLRLDGATY-----LSPNDTGMMIRNGEVMFGVVDKKTVGSAG-GGLVHTVMRE 446

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            G  +       + ++ +F+L++ GFSIGIGD
Sbjct: 447 KGSAICSDLFGNIQKVVNFWLLHNGFSIGIGD 478



 Score = 97.1 bits (240), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 51/63 (80%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTP EFFFH M GREGL DTAVKTA TGY+QRRLVK+LED+ V
Sbjct: 601 DYSPESKGFVENSYLRGLTPQEFFFHAMAGREGLXDTAVKTASTGYIQRRLVKALEDIMV 660

Query: 666 QYD 668
            YD
Sbjct: 661 HYD 663


>gi|45935353|gb|AAS79698.1| RNA polymerase III large subunit [Psilotum nudum]
          Length = 549

 Score =  163 bits (413), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 87/224 (38%), Positives = 134/224 (59%), Gaps = 26/224 (11%)

Query: 390 MNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGY 449
           MN+H+PQTEEAR EAL              +LM  +SNL TP+NGE+L+A+TQDF+T  +
Sbjct: 1   MNLHVPQTEEARTEAL--------------MLMGVQSNLCTPKNGEILVASTQDFLTSSF 46

Query: 450 LLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSL 509
           L+T+K+ F++R     +  + + D ++   +          P + ++   +WTGKQ+FS+
Sbjct: 47  LITRKDTFYDRG-AFGLMCSYMGDGAEHIDLP--------TPAI-LKPVELWTGKQLFSV 96

Query: 510 ILKPNRDCPVNANLKTKGRAYT--ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKAN 567
           +++PN    V  NL    + Y+    +  C  D YV  RNSEL++G + K TLG+G K  
Sbjct: 97  LVRPNASTRVFVNLVVMEKNYSKSGGDTMCPNDGYVYFRNSELISGQLGKGTLGNGNKNG 156

Query: 568 VFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           +F ILLRD+    A + M RL+++++ ++ N GFSIGI DV PG
Sbjct: 157 LFTILLRDYNTYAAASCMNRLAKLSARWIGNHGFSIGIDDVQPG 200



 Score =  104 bits (259), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 50/63 (79%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV NSF+SGLT TEFFFHTMGGREGLVDTAVKTAETGYM RRL+KSLEDL  
Sbjct: 319 DKSPQAKGFVANSFYSGLTATEFFFHTMGGREGLVDTAVKTAETGYMSRRLMKSLEDLYT 378

Query: 666 QYD 668
            YD
Sbjct: 379 HYD 381



 Score = 56.2 bits (134), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 22/42 (52%), Positives = 35/42 (83%)

Query: 21 VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRA 62
          +LM  +SNL TP+NGE+L+A+TQDF+T  +L+T+K+ F++R 
Sbjct: 17 MLMGVQSNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDRG 58


>gi|329132887|gb|AEB78334.1| RNA polymerase II largest subunit [Percolomonas cosmopolitus]
          Length = 1028

 Score =  163 bits (412), Expect = 7e-37,   Method: Compositional matrix adjust.
 Identities = 96/277 (34%), Positives = 154/277 (55%), Gaps = 40/277 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+D++LFNRQP+LHK+S+M HR KVLP+ TFR N  V +PYNADFDGDEMN+HLPQ+  A
Sbjct: 355 DDDLILFNRQPTLHKMSMMGHRVKVLPYSTFRLNVSVTSPYNADFDGDEMNLHLPQSLGA 414

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE               +++M +K N+V+ +    +IA  QD + G  L+T+++ F  +
Sbjct: 415 KAEL-------------QEMMMVSK-NIVSTQGNAPVIAIVQDALLGSVLMTKRDVFLEK 460

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              M     L  +          F+     P + ++   +W+GKQ+FSL+LK    C VN
Sbjct: 461 DIMMNCCMRLKEN----------FNGELPQPCI-LKPKQLWSGKQLFSLVLK---GCEVN 506

Query: 521 ----ANL-----KTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYI 571
               AN      K  G+ +  +E+ C  D+ V++   EL++G  DK TLG GG  ++ + 
Sbjct: 507 LFREANQYDDVKKIMGKEF--DEDICPMDTKVVISRGELISGVADKRTLGKGG-GSLIHT 563

Query: 572 LLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           +  ++    A   +  L  + +++++  G+SIG+ D 
Sbjct: 564 IFNEYSFIEASNFLNTLQWVVNYWMLQHGYSIGVEDT 600



 Score =  101 bits (251), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 50/81 (61%), Positives = 62/81 (76%), Gaps = 8/81 (9%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSF 671
           +GFVQNS+  GL P EFFFHTMGGREGL+DTAVKTA+TGY+QRRL+KS+ED  V+YD + 
Sbjct: 728 RGFVQNSYLRGLLPQEFFFHTMGGREGLIDTAVKTAKTGYIQRRLIKSMEDFQVKYDGTV 787

Query: 672 -DAA------FYGQTDCISGV 685
            D+A       YG+ D + GV
Sbjct: 788 RDSAGNILQFLYGE-DGMDGV 807



 Score = 59.7 bits (143), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 26/36 (72%), Positives = 29/36 (80%)

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            + RA ++P   VGALAAQSIGEP TQMTL TFHFAG
Sbjct: 988  FKRAFVQPGEMVGALAAQSIGEPATQMTLNTFHFAG 1023



 Score = 56.6 bits (135), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 55/202 (27%), Positives = 85/202 (42%), Gaps = 43/202 (21%)

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGF---------R 193
           +C GHFG+I+L   VFHI Y   V  IL+ IC    C+++L+  +   G          R
Sbjct: 1   ECPGHFGHINLAQDVFHISYVTTVAKILRCICYK--CSKLLVDIDSGDGLNQAGDENRKR 58

Query: 194 AKLRNPALSYLVRKSLK-KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKK 252
              R  +L  +V KS + +K+++ +++V  C          K  G  +   + YK    K
Sbjct: 59  IYERYQSLKNIVPKSKRFEKMVQLSREVHRC----------KNDGCTEEQPKSYKTDGLK 108

Query: 253 KDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL 312
            +AI+ +     N      PE    K                 E I  E    L    E 
Sbjct: 109 IEAILRN-----NNRENITPEAAKLK----------------LERISDEHARDLGFEPEH 147

Query: 313 SKPSDLILTRLLVPPNCIRPSV 334
            +P  +IL++L V P C+RPS+
Sbjct: 148 IRPHWMILSKLPVVPPCVRPSI 169


>gi|237823477|pdb|2WAQ|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna-
           Directed Rna Polymerase
 gi|237823490|pdb|2WB1|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna-
           Directed Rna Polymerase
 gi|237823512|pdb|2WB1|W Chain W, The Complete Structure Of The Archaeal 13-Subunit Dna-
           Directed Rna Polymerase
 gi|323462788|pdb|2Y0S|A Chain A, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
           P21 Space Group
 gi|323462810|pdb|2Y0S|W Chain W, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
           P21 Space Group
 gi|400260742|pdb|4AYB|A Chain A, Rnap At 3.2ang
 gi|400260759|pdb|4B1O|A Chain A, Archaeal Rnap-Dna Binary Complex At 4.32ang
 gi|400260785|pdb|4B1P|W Chain W, Archaeal Rnap-Dna Binary Complex At 4.32ang
 gi|219814429|gb|ACL36488.1| RNA polymerase subunit 1N [Sulfolobus shibatae B12]
          Length = 880

 Score =  163 bits (412), Expect = 8e-37,   Method: Compositional matrix adjust.
 Identities = 101/272 (37%), Positives = 149/272 (54%), Gaps = 29/272 (10%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D DVVLFNRQPSLH++S+MAHR +VL   TFR N  VC PYNADFDGDEMN+H+PQ+EE
Sbjct: 412 TDGDVVLFNRQPSLHRISMMAHRVRVLKGLTFRLNLLVCPPYNADFDGDEMNLHVPQSEE 471

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           A AE              AK +M    N++TPR G  +I A QD+I+G YLLT K     
Sbjct: 472 AIAE--------------AKEIMLVHKNIITPRYGGPIIGAAQDYISGAYLLTVKTTLLT 517

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           + +  +I    +AD     G     + R +           +TGKQ+ S  L  + +   
Sbjct: 518 KEEAQQILG--VADVKIDLGEPAILAPREY-----------YTGKQVVSAFLPKDFNFHG 564

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            AN+ +  R      E C  DSYV+++N  LL G  DK  +G+    ++ + L++++ ++
Sbjct: 565 QANVSSGPR--LCKNEDCPHDSYVVIKNGILLEGVFDKKAIGNQQPESILHWLIKEYSDE 622

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
                M  L R+   ++  +GF++ + DV+ G
Sbjct: 623 YGKWLMDNLFRVFIRFVELQGFTMRLEDVSLG 654



 Score =  114 bits (285), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 77/261 (29%), Positives = 124/261 (47%), Gaps = 49/261 (18%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D +++ S   I++ ++Y +D   TPI   ++D R+G  +    C TCG  L +C GHFG+
Sbjct: 17  DEIRKMSVTAIITPDVYDED--GTPIEGSVMDPRLGVIEPGQKCPTCGNTLGNCPGHFGH 74

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-----KLRNPALSYLV 205
           I+L  PV H+G+ + V   L++ C+   C RV + E++   +       K R P+ +  +
Sbjct: 75  IELVRPVIHVGFVKHVYEFLKATCRR--CGRVKISEDEIEKYSRIYNAIKKRWPSAARRL 132

Query: 206 RKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYN 265
            + +KK    T  K  VCPHCGE           KI  EK  N              E  
Sbjct: 133 TEYVKK----TAMKAQVCPHCGEKQ--------FKIKLEKPYN-----------FYEERK 169

Query: 266 EAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLV 325
           E V                 L P ++ +  E +P  D+ +L  +   S+P  +ILT L V
Sbjct: 170 EGV---------------AKLTPSDIRERLEKVPESDVEILGYDPTTSRPEWMILTVLPV 214

Query: 326 PPNCIRPSVI--SDLKSDNDV 344
           PP  IRPS++  S +++++D+
Sbjct: 215 PPITIRPSIMIESGIRAEDDL 235



 Score = 89.4 bits (220), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 40/73 (54%), Positives = 56/73 (76%), Gaps = 2/73 (2%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D++P  +GF+ +SF +GL PTE FFH  GGREGLVDTAV+T+++GYMQRRL+ +L DL  
Sbjct: 773 DISPEARGFIYSSFRTGLKPTELFFHAAGGREGLVDTAVRTSQSGYMQRRLINALSDLRA 832

Query: 666 QYDMSFDAAFYGQ 678
           +YD +   + YG+
Sbjct: 833 EYDGTV-RSLYGE 844


>gi|110669627|gb|ABG81908.1| RNA polymerase II largest subunit [Astrothelium cinnamomeum]
          Length = 1021

 Score =  163 bits (412), Expect = 8e-37,   Method: Compositional matrix adjust.
 Identities = 96/270 (35%), Positives = 141/270 (52%), Gaps = 38/270 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D ++FNRQPSLHK S+M HR KV+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 376 DGDFIIFNRQPSLHKESMMGHRVKVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 435

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE +               L     N+V+P+  + L+   QD + G Y + +K+ F  +
Sbjct: 436 RAEVMN--------------LCMVPLNIVSPQGNKPLMGIIQDTLCGIYKICRKDVFITK 481

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M   +TL+    D  G++         P   VR   +WTG+QI S+ L      P  
Sbjct: 482 EQVM---NTLLW-VPDWDGVVP--------PPTIVRPRPMWTGEQIISMAL------PAG 523

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            NL  K   +         D  + ++  EL+ G  +K  +G+G +  V + +  + G + 
Sbjct: 524 LNLFRKASTHNPPS-----DQGLFVKGGELMYGLFNKKIVGAGPQG-VIHSIYNEKGWEA 577

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           AV       R+  F+L++ GFS+GIGD  P
Sbjct: 578 AVAFFNAAQRIVCFWLLHNGFSVGIGDTIP 607



 Score = 99.0 bits (245), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 53/63 (84%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS   GLTPTEFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+  
Sbjct: 727 DYSPEARGFVENSCLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDVMA 786

Query: 666 QYD 668
           +YD
Sbjct: 787 KYD 789



 Score = 52.4 bits (124), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 51/204 (25%), Positives = 87/204 (42%), Gaps = 57/204 (27%)

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNPAL 201
           +C GHFG+I+L +PVFH+G+   +  +L+  C +  C ++L+ E   A   A K R+   
Sbjct: 1   ECPGHFGHIELAVPVFHVGFIGKIKKLLEICCHH--CGKILMDETNPAFIEAMKTRD--- 55

Query: 202 SYLVRKSLKKKIL---ETTKKVSVCPH---------------------CGEINGVVKKCG 237
               RK    KI    +T KK    P                      CG +   ++K G
Sbjct: 56  ----RKRRFDKIWTLCKTKKKCERDPQDDPNADENPDQPLKPSSTRGGCGNVAPGIRKDG 111

Query: 238 LLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEA 297
           L  +   K                  Y+++ + + E    KK+     + P +VL+ F  
Sbjct: 112 LKLLGTWK------------------YDKSEEEDEERRIEKKY-----ITPHQVLEAFNH 148

Query: 298 IPLEDIPLLLMNAELSKPSDLILT 321
           I  ED+  + + ++ +KP+ +ILT
Sbjct: 149 ISNEDLEKVGLGSDYAKPTWMILT 172


>gi|327242109|gb|AEA40833.1| RNA polymerase II largest subunit [Monocercomonas colubrorum]
          Length = 1019

 Score =  163 bits (412), Expect = 8e-37,   Method: Compositional matrix adjust.
 Identities = 91/267 (34%), Positives = 147/267 (55%), Gaps = 34/267 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           ++D+V+FNRQPSLHK+S+M HRA ++P  TFR N CV TPYNADFDGDEMN+H+PQ++ A
Sbjct: 374 EDDIVIFNRQPSLHKMSMMGHRAHLMPGSTFRLNLCVTTPYNADFDGDEMNLHVPQSQSA 433

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE               K +M   + ++TP++ + +I   QD +    L+T ++ F  R
Sbjct: 434 RAE--------------VKHIMLVPNQIITPQSNKPIIGLVQDALLACRLMTLRDTFLTR 479

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M +   +     D+             P   ++   +W+GKQ+FSL L        +
Sbjct: 480 NQVMNL--MMWIKKRDVI----------LPPPCILKPQQLWSGKQVFSLFLPEINHDGYS 527

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           +++K K           + D  VI+RN +LLAG +D  T+    K+ + ++++  + +D+
Sbjct: 528 SDVKDKSW-------LSYDDKRVIIRNGKLLAGILDSRTVARSEKS-LVHVIINSWDKDI 579

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           A   + +   + + +L +RGFSIGI D
Sbjct: 580 ARDFLNQTQLVVNNWLESRGFSIGIID 606



 Score = 89.7 bits (221), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 36/58 (62%), Positives = 47/58 (81%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GF ++S+  GLTP EFFFH+MGGR G++DTA KT++TGY+QRRL K +E  CVQYD
Sbjct: 734 AKGFCEHSYIQGLTPPEFFFHSMGGRTGIIDTACKTSDTGYIQRRLCKFMESHCVQYD 791



 Score = 61.6 bits (148), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 57/204 (27%), Positives = 91/204 (44%), Gaps = 31/204 (15%)

Query: 150 YIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSL 209
           +I+L  PVFHIGY   V  +LQ +C N  C R+L+   +      +L+   L+Y  ++ L
Sbjct: 1   HIELAEPVFHIGYVDVVYKLLQCVCHN--CGRLLVSYSE-----PELQKIVLNYHGKQRL 53

Query: 210 KKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVK 269
             +ILE TK    C H    NG         +  +  KN    K+  V D    Y++  +
Sbjct: 54  -VRILELTKSRHQCSHSKTPNGE-------DVHPDIVKNPAFWKELGVVDEDGNYDQDFR 105

Query: 270 -------FNPEIEAHKKFGL---------IQTLNPLEVLQLFEAIPLEDIPLLLMNAELS 313
                    PEI     F +            L+  +VL++ + +   D  +L  + E +
Sbjct: 106 KMDPCGQMIPEITKDGDFTIKMKDPSRNAQDALSAKKVLEILKHLSPLDTKILGFDEEKA 165

Query: 314 KPSDLILTRLLVPPNCIRPSVISD 337
           KP  +I T L VPP  +RP+++ D
Sbjct: 166 KPEWMICTILPVPPPHVRPAILMD 189


>gi|448363835|ref|ZP_21552430.1| DNA-directed RNA polymerase subunit A'' [Natrialba asiatica DSM
            12278]
 gi|445645419|gb|ELY98423.1| DNA-directed RNA polymerase subunit A'' [Natrialba asiatica DSM
            12278]
          Length = 399

 Score =  163 bits (412), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 105/344 (30%), Positives = 176/344 (51%), Gaps = 59/344 (17%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A+A   +Y+  ++EP   VG ++AQSIGEPGTQ+T+ TFH+AG            + E +
Sbjct: 48   AKAVEARYIDTRVEPLEPVGTVSAQSIGEPGTQLTMNTFHYAGVAEIDVTQGLPRLIELV 107

Query: 1152 EEVFVPDDSFILIKLD----------------MDRIRLLHL----------EVDI----- 1180
            +    PD   + + L+                ++  ++L L           V I     
Sbjct: 108  DARKTPDTPMMTVYLENEYATEREKAHEVVWNIEATKILALGDVSTNVADMRVQISLNEE 167

Query: 1181 ---------DSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVV 1231
                     D +   IE   G+     +   + +   P++ S      + Q+ + L  + 
Sbjct: 168  TLEERLITPDEVAEIIEDNLGVKA---IQNGTEIEFGPEEPSYR---DLLQLVEELRDIT 221

Query: 1232 IKGVQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLG 1290
             KG++ ++R VI  E+++ G  ++ L  EG    DV+   GV   + + NN +E+++ LG
Sbjct: 222  FKGIEEVSRVVIRREELDDGGEQFVLYTEGSAFGDVLEIDGVDASRTTCNNIHEIHRNLG 281

Query: 1291 IEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNL 1349
            IEAAR  I+ E    +   G+  ++ RH MLVAD+MT++GE+  I RHG++  K+SVL  
Sbjct: 282  IEAAREAIIEETNNTLAEQGLDDVNVRHLMLVADIMTNRGEIESIGRHGISGSKDSVLAR 341

Query: 1350 ASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            A+FE T +HL +AA +G+ D + GV+E +I+G P+ +GTG + L
Sbjct: 342  AAFEVTVNHLLNAAIHGEIDELDGVAENVIVGKPIKLGTGDVDL 385



 Score = 95.5 bits (236), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 66/239 (27%), Positives = 124/239 (51%), Gaps = 21/239 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T YL+ +  T+ + A  V   +E T    LG+V   + ++
Sbjct: 99  GLPRLIELVDARKTPDTPMMTVYLENEYATEREKAHEVVWNIEATKILALGDVSTNVADM 158

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSK 878
            V        ++ ++   L    +  D +   IE   G+     +   + +   P++ S 
Sbjct: 159 RV--------QISLNEETLEERLITPDEVAEIIEDNLGVKA---IQNGTEIEFGPEEPSY 207

Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVK 937
                + Q+ + L  +  KG++ ++R VI  E+++ G  ++ L  EG    DV+   GV 
Sbjct: 208 R---DLLQLVEELRDITFKGIEEVSRVVIRREELDDGGEQFVLYTEGSAFGDVLEIDGVD 264

Query: 938 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEV 995
             + + NN +E+++ LGIEAAR  I+ E    +   G+  ++ RH MLVAD+MT++GE+
Sbjct: 265 ASRTTCNNIHEIHRNLGIEAAREAIIEETNNTLAEQGLDDVNVRHLMLVADIMTNRGEI 323


>gi|45935335|gb|AAS79689.1| RNA polymerase III large subunit [Welwitschia mirabilis]
          Length = 548

 Score =  163 bits (412), Expect = 9e-37,   Method: Compositional matrix adjust.
 Identities = 87/223 (39%), Positives = 132/223 (59%), Gaps = 25/223 (11%)

Query: 390 MNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGY 449
           MN+H+PQTEEAR EAL              +LM  ++NL TP+NG++L+AATQDF+T  +
Sbjct: 1   MNLHVPQTEEARTEAL--------------MLMGVQNNLCTPKNGDILVAATQDFLTSSF 46

Query: 450 LLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSL 509
           L+T+K+ F++RA    + S +   T  I                 ++   +WTGKQ+FS+
Sbjct: 47  LITRKDTFYDRAAFSLMCSYMGDATESI----------DLPTPAILKPIELWTGKQLFSV 96

Query: 510 ILKPNRDCPVNANLKTKGRAYT-ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANV 568
           +++PN    V  NL    + Y+ + E  C  D  V  RNSEL++G + K+TLG+G K  +
Sbjct: 97  LVRPNAKMRVFVNLMVMEKNYSKSGETMCPNDGCVYFRNSELISGQLGKATLGNGNKNGL 156

Query: 569 FYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           F +LLRD+    A + M RL+++++ ++ N GFSIGI DV PG
Sbjct: 157 FTVLLRDYNAYAAASCMNRLAKLSARWIGNHGFSIGIDDVQPG 199



 Score =  105 bits (261), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 48/63 (76%), Positives = 54/63 (85%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSF 671
           +GFV NSF+SGLT TEFFFHTMGGREGLVDTAVKTAETGYM RRL+K+LEDL   YD + 
Sbjct: 324 KGFVANSFYSGLTATEFFFHTMGGREGLVDTAVKTAETGYMSRRLMKALEDLSAHYDGTV 383

Query: 672 DAA 674
            +A
Sbjct: 384 RSA 386



 Score = 56.6 bits (135), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 22/42 (52%), Positives = 36/42 (85%)

Query: 21 VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRA 62
          +LM  ++NL TP+NG++L+AATQDF+T  +L+T+K+ F++RA
Sbjct: 17 MLMGVQNNLCTPKNGDILVAATQDFLTSSFLITRKDTFYDRA 58


>gi|110669618|gb|ABG81904.1| RNA polymerase II largest subunit [Simonyella variegata]
          Length = 1013

 Score =  162 bits (411), Expect = 9e-37,   Method: Compositional matrix adjust.
 Identities = 112/345 (32%), Positives = 170/345 (49%), Gaps = 47/345 (13%)

Query: 278 KKFGLIQTLNPLEVL---QLFEAIP-LEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPS 333
           K    ++T+NP  +    +L E  P L      ++N + +K  DL   R+  PP      
Sbjct: 308 KTLTYVETVNPRNIAYLSRLVETGPNLHPGANYVINMDRTKTWDL--RRVKNPPRLEYGW 365

Query: 334 VISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVH 393
            +     D D ++FNRQPSLHK S+M HR KV+P  TFR N  V  PYNADFDGDEMN+H
Sbjct: 366 QVERHIDDGDYIIFNRQPSLHKESMMGHRVKVMPWSTFRLNLSVTGPYNADFDGDEMNLH 425

Query: 394 LPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 453
           +PQTE  RAE    + +L ++ H          N+V+P+    L+   QD + G Y + +
Sbjct: 426 VPQTEATRAE----VKELCMVPH----------NIVSPQRNGPLMGIVQDTLCGIYKICR 471

Query: 454 KNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKP 513
           ++ F  + Q M +    +    +  GI+ + +         ++   +WTGKQI SL L  
Sbjct: 472 RDVFLTQEQAMNV----LMWVPEWDGIMPQPA--------LLKPKPMWTGKQIISLAL-- 517

Query: 514 NRDCPVNANLKTKGRAYTANEEFCH--RDSYVILRNSELLAGSMDKSTLGSGGKANVFYI 571
               P   NL         +EE      D  + + N EL+ G   K ++G+ G   + ++
Sbjct: 518 ----PAGLNL------LRGSEEGMSPVNDDGLFVNNGELMFGLFSKKSVGASG-GGIIHV 566

Query: 572 LLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           +  + G D AV       ++ +++L+  GFSIGIGD TP    VQ
Sbjct: 567 IFNEKGPDAAVRFFNGAQQIVNYWLLQNGFSIGIGDTTPDPTTVQ 611



 Score = 90.9 bits (224), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 42/65 (64%), Positives = 51/65 (78%), Gaps = 1/65 (1%)

Query: 607 DVTPGQGFVQNSFFS-GLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P   ++   F S GLTPTEFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+  
Sbjct: 725 DYSPEAPWLCGKFLSXGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDVMA 784

Query: 666 QYDMS 670
           +YD +
Sbjct: 785 KYDTT 789



 Score = 72.4 bits (176), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 57/197 (28%), Positives = 92/197 (46%), Gaps = 17/197 (8%)

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNPAL 201
           +C GHFG+I+L  PVFHIG+      +L+++C N  C++VLL E   A   A ++R+P  
Sbjct: 1   ECPGHFGHIELAAPVFHIGFINKTKKLLETVCHN--CSKVLLDESNQAFAAALRIRDPKR 58

Query: 202 SYLVRKSLKKKILETTKKVSVC---PHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVE 258
            +         + +  K   +C   P   E     K+   +K +H    NR  +     E
Sbjct: 59  RF-------DTVHKLCKSRPICVPDPSPEEKEADPKEA--MKPTHGGCGNRHPQIRK--E 107

Query: 259 DLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDL 318
            L  +    V    + E        + + P   L +F  I  EDI  L ++ + ++P  +
Sbjct: 108 GLKIQGTWKVPKGEDEEERGATEEKRMITPQMALDIFRNISQEDIRKLGLSNDYARPEWM 167

Query: 319 ILTRLLVPPNCIRPSVI 335
           I+T L VPP  +RPSV+
Sbjct: 168 IITVLPVPPPQVRPSVV 184


>gi|325090959|gb|EGC44269.1| RNA polymerase II largest subunit [Ajellomyces capsulatus H88]
          Length = 1747

 Score =  162 bits (411), Expect = 9e-37,   Method: Compositional matrix adjust.
 Identities = 95/271 (35%), Positives = 149/271 (54%), Gaps = 33/271 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DV+LFNRQPSLHK S+M HR +V+P+ TFR N  V TPYNADFDGDEMN+H+PQ+EEA
Sbjct: 456 DGDVILFNRQPSLHKESMMGHRIRVMPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L +L ++  +          +V+P+    L+   QD + G Y + +++ F  +
Sbjct: 516 RAE----LSQLCMVPLQ----------IVSPQRNGPLMGIVQDTLCGIYKICRRDVFLTK 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M I    +    D  G+I +       P + ++    WTGKQ+ S++L P  +    
Sbjct: 562 EQVMNI----LLWVPDWDGVIPQ-------PAI-LKPRPRWTGKQMISMVLPPGLNL--- 606

Query: 521 ANLKTKGRAYTANEEFCH-RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
             L+        +E+F    D  +++ + EL+ G   K T+G+ G   V + +  ++G +
Sbjct: 607 --LRVDRDKAPLSEKFSPLADGGLLVHSGELMYGMFSKKTVGATG-GGVIHTIFNEYGPE 663

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
            A+        + +++L++ GFSIGIGD  P
Sbjct: 664 TAMNFFNGAQTVVNYWLLHHGFSIGIGDTIP 694



 Score = 99.4 bits (246), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QR+LVK+LE++ V
Sbjct: 814 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMV 873

Query: 666 QYD 668
           +YD
Sbjct: 874 KYD 876



 Score = 99.0 bits (245), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 59/180 (32%), Positives = 92/180 (51%), Gaps = 15/180 (8%)

Query: 1225 QLLPSVVIKGVQGINRAVIHEE---------------DVEGVTKYKLLVEGDNLRDVMAT 1269
             LL ++ ++GV GI RA I+E+               D     ++ L   G  L +V+  
Sbjct: 1289 HLLDTLTLRGVAGIERAFINEKSRVRVLEDGSLHQSADDPLCKEWVLETSGSALGEVLTI 1348

Query: 1270 YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 1329
             GV   +  SN   E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1349 PGVDTTRTYSNQFIEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLVDVMTSRG 1408

Query: 1330 EVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
             ++ +TRHG+ +     L   SFE T + L DAA + + D   GVSE +I+G     GTG
Sbjct: 1409 FLMAVTRHGINRADTGALMRCSFEETVEILLDAAAFAELDDCRGVSENLILGQMAPAGTG 1468



 Score = 87.0 bits (214), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 77/289 (26%), Positives = 129/289 (44%), Gaps = 59/289 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGR--LERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N + NI TP +T Y D    +D   + + R  +E T+L  V E  E  + P
Sbjct: 1120 GVPRLKEILNVATNIKTPSMTVYQDPSRAMDKESVKQLRSVVEHTSLRSVTETTEIYYDP 1179

Query: 822  DDSFILIKLDMDRIR---LLHLEVDIDS-------IRYCIERTRGISGHLTVSGHSFLIL 871
            D    +I+ D D +    ++  +V  DS       +R  + R + +   LTV   +  I 
Sbjct: 1180 DIQSTVIEADRDMVESYFIIPEDVADDSSRQSKWLLRIILSRPKLLDKSLTVQDVAMKIK 1239

Query: 872  K--PKD-----SSKSFNSKMYQMKQ-------------------------LLPSVVIKGV 899
               P+D     S  + + ++ +++Q                         LL ++ ++GV
Sbjct: 1240 DAYPQDIAVIFSDNNADEQVIRIRQVQDSKQDDDDDDTEYDVTLKKLESHLLDTLTLRGV 1299

Query: 900  QGINRAVIHEE---------------DVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSN 944
             GI RA I+E+               D     ++ L   G  L +V+   GV   +  SN
Sbjct: 1300 AGIERAFINEKSRVRVLEDGSLHQSADDPLCKEWVLETSGSALGEVLTIPGVDTTRTYSN 1359

Query: 945  NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
               E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1360 QFIEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLVDVMTSRG 1408



 Score = 85.5 bits (210), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 60/230 (26%), Positives = 105/230 (45%), Gaps = 40/230 (17%)

Query: 110 DPQRT-PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVIN 168
           D QR  P   GL D R+GT  +   C TC + ++DC GHFG+I+L  PVFHIG+   +  
Sbjct: 44  DEQRQRPREKGLNDPRLGTIDRNWRCATCEEGINDCPGHFGHIELSTPVFHIGFLTKIKK 103

Query: 169 ILQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKSLKKKIL------------- 214
           +L+++C N  C ++           A + R+P   +     L K +L             
Sbjct: 104 LLETVCHN--CGKIKANTTDQKYLEALRFRDPKRRFDAIWRLSKDVLICEADPSPDDDEP 161

Query: 215 ---ETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFN 271
              E +K V     CG I   ++K G+  +   K    +K +D +++D+  +  E  +  
Sbjct: 162 FAKEPSKPVRSHGGCGNIQPQIRKEGISLVGTWK---PSKNRD-MMDDMDVQQPEKRQIT 217

Query: 272 PEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
           P++                 L +F+ I  ED+ L+ ++ + ++P  +I+T
Sbjct: 218 PQM----------------ALNIFKTISEEDVRLMGLSNDYARPEWMIIT 251



 Score = 56.2 bits (134), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/41 (60%), Positives = 28/41 (68%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            A   ++ +A   P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1071 AIESRFSKAMANPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1111


>gi|150401218|ref|YP_001324984.1| DNA-directed RNA polymerase subunit A' [Methanococcus aeolicus
           Nankai-3]
 gi|150013921|gb|ABR56372.1| DNA-directed RNA polymerase subunit A' [Methanococcus aeolicus
           Nankai-3]
          Length = 888

 Score =  162 bits (411), Expect = 9e-37,   Method: Compositional matrix adjust.
 Identities = 96/267 (35%), Positives = 147/267 (55%), Gaps = 31/267 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VL+NRQPSLH++SIMAHR KVLP+RTFR N CVC PYNADFDGDEMN+H+PQ+   
Sbjct: 423 DGDIVLYNRQPSLHRMSIMAHRVKVLPYRTFRHNLCVCPPYNADFDGDEMNIHVPQS--- 479

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
                            A+ +M  ++++V+PR G  +I A  DFI+G Y+LT  +++F +
Sbjct: 480 -----------EEARAEAEAIMLVENHIVSPRYGGPIIGAIHDFISGAYVLT--SSYFTK 526

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +    AS L+   +               P        +++G+ +FS  L   ++  + 
Sbjct: 527 DE----ASILLRSAN--------LEMDLGAPDKIEDGVELYSGRTLFSKTLP--KELTLK 572

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
              KT  +     +E C  DSYV++ N ELL G +DK+  GS     +   L+++FG + 
Sbjct: 573 YRAKTCKKCEICEKEDCPHDSYVVIINGELLKGVIDKNGYGSEA-GIILNTLVKEFGSEQ 631

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           A   +   ++M+   +M +GF+ GI D
Sbjct: 632 ARIFLDTSTKMSIKSMMIKGFTTGIDD 658



 Score =  111 bits (277), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 78/266 (29%), Positives = 127/266 (47%), Gaps = 41/266 (15%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G++ G ++ E  +++ S  +IV+ + Y  D    PI  GL+D R+G       C TCG  
Sbjct: 12  GIVFGLLSPE-YIRKISVAKIVTADTY--DDDGYPIDGGLMDTRLGVIDPGLVCKTCGGR 68

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
           +  C GHFG+I+L  P  HIGY + +  IL+++C  P C +V L E +   +  K+    
Sbjct: 69  VGTCPGHFGHIELSKPAVHIGYAKDIYKILKAVC--PHCGKVALSETRRMEYLKKMETLE 126

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDL 260
                +  L   +L+      +CP+CGE                KY  +  K  A +   
Sbjct: 127 EEGGDKWQLADDVLKEGAGKDICPYCGET---------------KYDIKYSKPTAYL--- 168

Query: 261 LAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
                       +IE   +  L+ +    EV ++ E IP ED  L+ +N E+++P  +IL
Sbjct: 169 ------------QIEGKTQKQLMSS----EVREILEKIPDEDCMLIGVNPEVARPEWMIL 212

Query: 321 TRLLVPPNCIRPSVI--SDLKSDNDV 344
           T L VPP  +RPS+   S  +S++D+
Sbjct: 213 TSLPVPPVTVRPSITLESGERSEDDL 238



 Score = 92.8 bits (229), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 39/59 (66%), Positives = 51/59 (86%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            GFV++ + +G+TPTE+FFH MGGREGLVD AV+TA++GYMQRRLV +L+DL V+YD S
Sbjct: 787 HGFVRSCYKTGMTPTEYFFHAMGGREGLVDQAVRTAQSGYMQRRLVNALQDLKVEYDTS 845


>gi|378756428|gb|EHY66452.1| DNA-directed RNA polymerase II subunit RPB1 [Nematocida sp. 1
           ERTm2]
          Length = 1609

 Score =  162 bits (411), Expect = 9e-37,   Method: Compositional matrix adjust.
 Identities = 104/271 (38%), Positives = 155/271 (57%), Gaps = 38/271 (14%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           S+ D VLFNRQPSLHK+S+MAH+A+V+ + TFR N  V  PYNADFDGDEMN+HLPQ+  
Sbjct: 424 SNGDTVLFNRQPSLHKMSMMAHKARVMKYSTFRLNLSVTAPYNADFDGDEMNLHLPQSIP 483

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           A+ E    L +L+++          + N+V+P++ + ++   QD + G Y LT+++ F  
Sbjct: 484 AQTE----LKELALV----------EKNIVSPQSNKPVMGIVQDTLMGVYKLTRRDLFLT 529

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           ++Q M +   +     D  G       +   P +  R AV++TGKQIFS  L P+     
Sbjct: 530 KSQVMHLHYAI-----DNGG-------KYLKPTIL-RPAVLYTGKQIFSATL-PDVTYTG 575

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLG--SGGKANVFYILLRDFG 577
             +    G+ Y AN      D+ V+++N ELLAG + K T+G  SGG   + +++  DF 
Sbjct: 576 LHSEHVHGKNYKANP----MDTEVVIKNGELLAGIICKKTVGTASGG---LIHVIANDFP 628

Query: 578 EDVAVTAMWRLSRMTSFYLMN-RGFSIGIGD 607
             V V  +  L R  S +LM+   FS+GIGD
Sbjct: 629 RSVCVDFIDALQRAISSWLMSYETFSVGIGD 659



 Score =  117 bits (292), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 61/165 (36%), Positives = 96/165 (58%)

Query: 1230 VVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTL 1289
            +++KG+  I R  I E   E   +Y L  EG  L DV+    +   +  SN+  E+ +  
Sbjct: 1273 IMVKGMPKIKRVFISEIGAEDKKEYVLQTEGTGLMDVLGHPLIDPTRTVSNDPLEMSQVF 1332

Query: 1290 GIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNL 1349
            GIEAAR++I+ EI++V+E+ G  ++FRH  ++AD+MT +G + GITRHG  + +   L  
Sbjct: 1333 GIEAARTSILNEIRMVIESDGSYVNFRHLAILADIMTQRGHICGITRHGTNRGESGALMR 1392

Query: 1350 ASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
             SFE T + L +AA   + D   GV E +++G    +GTG+  LL
Sbjct: 1393 CSFEETVEILLEAAANAEIDRCKGVVESVMLGNVAAIGTGITDLL 1437



 Score = 99.0 bits (245), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 70/260 (26%), Positives = 131/260 (50%), Gaps = 28/260 (10%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEIINA++ I TP +T YL ++    L+ A+  +  +ER  L ++    E ++ P
Sbjct: 1119 GVPRLKEIINAAQTIKTPSLTIYLKEEIRNTLEGAKKAQQEIERCYLKDILLRSEIIYDP 1178

Query: 822  -------DDSFI-----------------LIKLDMDRIRLLHLEVDIDSIRYCIERTRGI 857
                   D+ FI                 +++L ++R  ++   + I+ +   I ++   
Sbjct: 1179 TMKAVKSDEDFIFAYGILDSTIYSPDSPWMLRLVLNRSAMVDRGIRIEQVTKTIAQS--T 1236

Query: 858  SGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTK 917
            +     S H+      +    +    + +++  +  +++KG+  I R  I E   E   +
Sbjct: 1237 TYRCMHSDHNSAEQIIRCELPNSEDLLRKIETSISCIMVKGMPKIKRVFISEIGAEDKKE 1296

Query: 918  YKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSI 977
            Y L  EG  L DV+    +   +  SN+  E+ +  GIEAAR++I+ EI++V+E+ G  +
Sbjct: 1297 YVLQTEGTGLMDVLGHPLIDPTRTVSNDPLEMSQVFGIEAARTSILNEIRMVIESDGSYV 1356

Query: 978  DFRHPMLVADLMTSKGEVLG 997
            +FRH  ++AD+MT +G + G
Sbjct: 1357 NFRHLAILADIMTQRGHICG 1376



 Score = 95.9 bits (237), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 40/59 (67%), Positives = 52/59 (88%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
           +GF+ +S+ +GL+P EFFFH MGGREGL+DTAVKTAETGY+QRRL+K+LED  V++D S
Sbjct: 788 RGFISSSYVAGLSPVEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKALEDAQVRHDKS 846



 Score = 88.6 bits (218), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 65/240 (27%), Positives = 111/240 (46%), Gaps = 40/240 (16%)

Query: 115 PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSIC 174
           P   GL+D R+GT+++   C+TCG     CVGHFGYI+L  PVFHIGY   +  +L+S+C
Sbjct: 42  PKEGGLVDLRLGTSERGFLCSTCGHRSDSCVGHFGYIELAKPVFHIGYIGKIKKVLESVC 101

Query: 175 KNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKSLKKKIL-------ETTKKVSVCPHC 226
              +  RV      +   R  K R   L+Y+   +  + I        E   + ++   C
Sbjct: 102 FFCSKLRVEKSSLPSPKPRTQKERKRRLNYIWNLAKNRAICMGEVVSNEDNPEETLRTGC 161

Query: 227 GEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTL 286
                 ++K GL  ++ +K +  ++ K                                L
Sbjct: 162 ENRQPTIRKEGLHLLAFQKGEESSEGK------------------------------TML 191

Query: 287 NPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDNDV 344
           +  +VL++   IP EDI  L  + E ++P  +++  L VPP  +RPS++ +  L+ ++D+
Sbjct: 192 SAEKVLEILRRIPEEDIEALGFDLEKARPEWMVIRILPVPPPQVRPSIVMEGSLRCEDDL 251



 Score = 53.5 bits (127), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 24/42 (57%), Positives = 28/42 (66%)

Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            E  R  +++A +     VG LAAQSIGEP TQMTL TFH AG
Sbjct: 1070 EQIRTSFLKAVVSAGEMVGTLAAQSIGEPATQMTLNTFHLAG 1111


>gi|302503240|ref|XP_003013580.1| hypothetical protein ARB_00027 [Arthroderma benhamiae CBS 112371]
 gi|291177145|gb|EFE32940.1| hypothetical protein ARB_00027 [Arthroderma benhamiae CBS 112371]
          Length = 1635

 Score =  162 bits (411), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 95/272 (34%), Positives = 150/272 (55%), Gaps = 35/272 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D +LFNRQPSLHK S+M+HR +V+P+ TFR N  V TPYNADFDGDEMN+H+PQ+EEA
Sbjct: 346 DGDFILFNRQPSLHKESMMSHRVRVMPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSEEA 405

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L++L ++            N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 406 RAE----LNQLCLVPL----------NIVSPQRNGPLMGIVQDTLCGIYKICRRDVFLTK 451

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M +    +    D  G++ +       P + ++    W+GKQ+ S++L      P  
Sbjct: 452 EQVMNV----LLWVPDWDGVLPQ-------PAI-LKPRPRWSGKQMISMVL------PSG 493

Query: 521 AN-LKTKGRAYTANEEFCH-RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            N L+        +E+F    D  V++   EL+ G   K T+G+ G   V + +  ++G 
Sbjct: 494 LNLLRIDKDKSPISEKFSPLADGGVLVHGGELMYGMFSKKTVGASG-GGVVHTIFNEYGP 552

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           D A++       + +++L++ GFSIGIGD  P
Sbjct: 553 DAAMSFFNGAQAVVNYWLLHNGFSIGIGDTIP 584



 Score =  103 bits (256), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 60/180 (33%), Positives = 94/180 (52%), Gaps = 15/180 (8%)

Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMAT 1269
             LL ++ ++GV GI+RA I+E+    V                ++ L   G  L DV+A 
Sbjct: 1179 HLLDTLTLRGVPGIDRAFINEKSRTRVLEDGSLHQSASDPECKEWVLETSGSALADVLAI 1238

Query: 1270 YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 1329
             G+   +  SN   E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1239 PGIDASRTYSNQFVEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLVDVMTSRG 1298

Query: 1330 EVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
             ++ +TRHG+ +     L   SFE T + L DAA + + D   GVSE +I+G     GTG
Sbjct: 1299 FLMAVTRHGINRADTGALMRCSFEETVEILLDAAAFAELDDCRGVSENLILGQMAPAGTG 1358



 Score = 99.4 bits (246), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QR+LVK+LE++ V
Sbjct: 704 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMV 763

Query: 666 QYD 668
           +YD
Sbjct: 764 KYD 766



 Score = 85.5 bits (210), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 75/289 (25%), Positives = 134/289 (46%), Gaps = 59/289 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDL--DYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N + NI TP +T Y   +  +  + A+ ++  +E T+L  V E  E  + P
Sbjct: 1010 GVPRLKEILNVATNIKTPSMTVYQAPECRMNKESAKQLRSIVEHTSLRSVTESTEIYYDP 1069

Query: 822  DDSFILIKLDMDRIR---LLHLEVDIDS-------IRYCIERTRGISGHLTVSGHSFLIL 871
            +    +I+ D+D +    ++  +V  DS       +R  + R + +   LTV   +  I 
Sbjct: 1070 NIQSTVIENDIDMVESYFIIPEDVADDSSRQSKWLLRIILSRPKLLDKGLTVQDVATKIK 1129

Query: 872  K--PKD-----SSKSFNSKMYQMKQ-------------------------LLPSVVIKGV 899
            +  P+D     S  + + ++ +++Q                         LL ++ ++GV
Sbjct: 1130 EAYPQDIAVIFSDNNADEQVVRIRQIQDPKQDEDDDDTEYDVTLKKLESHLLDTLTLRGV 1189

Query: 900  QGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMATYGVKGVKCSSN 944
             GI+RA I+E+    V                ++ L   G  L DV+A  G+   +  SN
Sbjct: 1190 PGIDRAFINEKSRTRVLEDGSLHQSASDPECKEWVLETSGSALADVLAIPGIDASRTYSN 1249

Query: 945  NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
               E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1250 QFVEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLVDVMTSRG 1298



 Score = 55.8 bits (133), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/41 (60%), Positives = 28/41 (68%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            A   ++ +A   P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 961  AIESRFGKAAANPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1001


>gi|154282795|ref|XP_001542193.1| DNA-directed RNA polymerase II largest subunit [Ajellomyces
           capsulatus NAm1]
 gi|150410373|gb|EDN05761.1| DNA-directed RNA polymerase II largest subunit [Ajellomyces
           capsulatus NAm1]
          Length = 1747

 Score =  162 bits (411), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 95/271 (35%), Positives = 148/271 (54%), Gaps = 33/271 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DV+LFNRQPSLHK S+M HR +V+P+ TFR N  V TPYNADFDGDEMN+H+PQ+EEA
Sbjct: 456 DGDVILFNRQPSLHKESMMGHRIRVMPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L +L ++  +          +V+P+    L+   QD + G Y + +++ F  +
Sbjct: 516 RAE----LSQLCMVPLQ----------IVSPQRNGPLMGIVQDTLCGIYKICRRDVFLTK 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M I    +    D  G+I +       P + ++    WTGKQ+ S++L P  +    
Sbjct: 562 EQVMNI----LLWVPDWDGVIPQ-------PAI-LKPRPRWTGKQMISMVLPPGLNL--- 606

Query: 521 ANLKTKGRAYTANEEFCH-RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
             L+        +E+F    D  +++   EL+ G   K T+G+ G   V + +  ++G +
Sbjct: 607 --LRVDRDKAPLSEKFSPLADGGLLVHGGELMYGMFSKKTVGATG-GGVIHTIFNEYGPE 663

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
            A+        + +++L++ GFSIGIGD  P
Sbjct: 664 TAMNFFNGAQTVVNYWLLHHGFSIGIGDTIP 694



 Score = 99.4 bits (246), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QR+LVK+LE++ V
Sbjct: 814 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMV 873

Query: 666 QYD 668
           +YD
Sbjct: 874 KYD 876



 Score = 99.0 bits (245), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 59/180 (32%), Positives = 92/180 (51%), Gaps = 15/180 (8%)

Query: 1225 QLLPSVVIKGVQGINRAVIHEE---------------DVEGVTKYKLLVEGDNLRDVMAT 1269
             LL ++ ++GV GI RA I+E+               D     ++ L   G  L +V+  
Sbjct: 1289 HLLDTLTLRGVAGIERAFINEKSRVRVLEDGSLHQSADDPLCKEWVLETSGSALGEVLTI 1348

Query: 1270 YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 1329
             GV   +  SN   E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1349 PGVDTTRTYSNQFIEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLVDVMTSRG 1408

Query: 1330 EVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
             ++ +TRHG+ +     L   SFE T + L DAA + + D   GVSE +I+G     GTG
Sbjct: 1409 FLMAVTRHGINRADTGALMRCSFEETVEILLDAAAFAELDDCRGVSENLILGQMAPAGTG 1468



 Score = 87.0 bits (214), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 77/289 (26%), Positives = 129/289 (44%), Gaps = 59/289 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGR--LERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N + NI TP +T Y D    +D   + + R  +E T+L  V E  E  + P
Sbjct: 1120 GVPRLKEILNVATNIKTPSMTVYQDPSRAMDKESVKQLRSVVEHTSLRSVTETTEIYYDP 1179

Query: 822  DDSFILIKLDMDRIR---LLHLEVDIDS-------IRYCIERTRGISGHLTVSGHSFLIL 871
            D    +I+ D D +    ++  +V  DS       +R  + R + +   LTV   +  I 
Sbjct: 1180 DIQSTVIEADRDMVESYFIIPEDVADDSSRQSKWLLRIILSRPKLLDKSLTVQDVAMKIK 1239

Query: 872  K--PKD-----SSKSFNSKMYQMKQ-------------------------LLPSVVIKGV 899
               P+D     S  + + ++ +++Q                         LL ++ ++GV
Sbjct: 1240 DAYPQDIAVIFSDNNADEQVIRIRQIQDSKQDDDDDDTEYDVTLKKLESHLLDTLTLRGV 1299

Query: 900  QGINRAVIHEE---------------DVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSN 944
             GI RA I+E+               D     ++ L   G  L +V+   GV   +  SN
Sbjct: 1300 AGIERAFINEKSRVRVLEDGSLHQSADDPLCKEWVLETSGSALGEVLTIPGVDTTRTYSN 1359

Query: 945  NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
               E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1360 QFIEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLVDVMTSRG 1408



 Score = 85.5 bits (210), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 60/230 (26%), Positives = 105/230 (45%), Gaps = 40/230 (17%)

Query: 110 DPQRT-PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVIN 168
           D QR  P   GL D R+GT  +   C TC + ++DC GHFG+I+L  PVFHIG+   +  
Sbjct: 44  DEQRQRPREKGLNDPRLGTIDRNWRCATCEEGINDCPGHFGHIELSTPVFHIGFLTKIKK 103

Query: 169 ILQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKSLKKKIL------------- 214
           +L+++C N  C ++           A + R+P   +     L K +L             
Sbjct: 104 LLETVCHN--CGKIKANTTDQKYLEALRFRDPKRRFDAIWRLSKDVLICEADPSPDDDEP 161

Query: 215 ---ETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFN 271
              E +K V     CG I   ++K G+  +   K    +K +D +++D+  +  E  +  
Sbjct: 162 FAKEPSKPVRSHGGCGNIQPQIRKEGISLVGTWK---PSKNRD-MMDDMDVQQPEKRQIT 217

Query: 272 PEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
           P++                 L +F+ I  ED+ L+ ++ + ++P  +I+T
Sbjct: 218 PQM----------------ALNIFKTISEEDVRLMGLSNDYARPEWMIIT 251



 Score = 56.2 bits (134), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/41 (60%), Positives = 28/41 (68%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            A   ++ +A   P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1071 AIESRFSKAMANPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1111


>gi|302662921|ref|XP_003023110.1| hypothetical protein TRV_02753 [Trichophyton verrucosum HKI 0517]
 gi|291187089|gb|EFE42492.1| hypothetical protein TRV_02753 [Trichophyton verrucosum HKI 0517]
          Length = 1744

 Score =  162 bits (411), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 95/272 (34%), Positives = 150/272 (55%), Gaps = 35/272 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D +LFNRQPSLHK S+M+HR +V+P+ TFR N  V TPYNADFDGDEMN+H+PQ+EEA
Sbjct: 455 DGDFILFNRQPSLHKESMMSHRVRVMPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSEEA 514

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L++L ++            N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 515 RAE----LNQLCLVPL----------NIVSPQRNGPLMGIVQDTLCGIYKICRRDVFLTK 560

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M +    +    D  G++ +       P + ++    W+GKQ+ S++L      P  
Sbjct: 561 EQVMNV----LLWVPDWDGVLPQ-------PAI-LKPRPRWSGKQMISMVL------PSG 602

Query: 521 AN-LKTKGRAYTANEEFCH-RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            N L+        +E+F    D  V++   EL+ G   K T+G+ G   V + +  ++G 
Sbjct: 603 LNLLRIDKDKSPISEKFSPLADGGVLVHGGELMYGMFSKKTVGASG-GGVVHTIFNEYGP 661

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           D A++       + +++L++ GFSIGIGD  P
Sbjct: 662 DAAMSFFNGAQAVVNYWLLHNGFSIGIGDTIP 693



 Score =  103 bits (256), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 60/180 (33%), Positives = 94/180 (52%), Gaps = 15/180 (8%)

Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMAT 1269
             LL ++ ++GV GI+RA I+E+    V                ++ L   G  L DV+A 
Sbjct: 1288 HLLDTLTLRGVPGIDRAFINEKSRTRVLEDGSLHQSASDPECKEWVLETSGSALADVLAI 1347

Query: 1270 YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 1329
             G+   +  SN   E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1348 PGIDASRTYSNQFVEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLVDVMTSRG 1407

Query: 1330 EVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
             ++ +TRHG+ +     L   SFE T + L DAA + + D   GVSE +I+G     GTG
Sbjct: 1408 FLMAVTRHGINRADTGALMRCSFEETVEILLDAAAFAELDDCRGVSENLILGQMAPAGTG 1467



 Score = 99.4 bits (246), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QR+LVK+LE++ V
Sbjct: 813 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMV 872

Query: 666 QYD 668
           +YD
Sbjct: 873 KYD 875



 Score = 85.5 bits (210), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 75/289 (25%), Positives = 134/289 (46%), Gaps = 59/289 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDL--DYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N + NI TP +T Y   +  +  + A+ ++  +E T+L  V E  E  + P
Sbjct: 1119 GVPRLKEILNVATNIKTPSMTVYQAPECRMNKESAKQLRSIVEHTSLRSVTESTEIYYDP 1178

Query: 822  DDSFILIKLDMDRIR---LLHLEVDIDS-------IRYCIERTRGISGHLTVSGHSFLIL 871
            +    +I+ D+D +    ++  +V  DS       +R  + R + +   LTV   +  I 
Sbjct: 1179 NIQSTVIENDIDMVESYFIIPEDVADDSSRQSKWLLRIILSRPKLLDKGLTVQDVATKIK 1238

Query: 872  K--PKD-----SSKSFNSKMYQMKQ-------------------------LLPSVVIKGV 899
            +  P+D     S  + + ++ +++Q                         LL ++ ++GV
Sbjct: 1239 EAYPQDIAVIFSDNNADEQVVRIRQIQDPKQDEDDDDTEYDVTLKKLESHLLDTLTLRGV 1298

Query: 900  QGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMATYGVKGVKCSSN 944
             GI+RA I+E+    V                ++ L   G  L DV+A  G+   +  SN
Sbjct: 1299 PGIDRAFINEKSRTRVLEDGSLHQSASDPECKEWVLETSGSALADVLAIPGIDASRTYSN 1358

Query: 945  NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
               E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1359 QFVEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLVDVMTSRG 1407



 Score = 84.7 bits (208), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 60/228 (26%), Positives = 105/228 (46%), Gaps = 38/228 (16%)

Query: 110 DPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINI 169
           D ++ P   GL D R+GT  +   C TC + ++DC GHFG+I+L  PVFHIG+   +  +
Sbjct: 45  DQRQRPREKGLNDPRLGTIDRNWRCATCEEGINDCPGHFGHIELSTPVFHIGFLTKIKKL 104

Query: 170 LQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKSLKKKIL-------------- 214
           L+++C N  C ++           A + R+P   +     L K IL              
Sbjct: 105 LETVCHN--CGKIKANASDQKYLDALRFRDPKKRFDAIWRLSKDILICEADPPEEDDPFA 162

Query: 215 -ETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPE 273
            E++K V     CG +   V+K G+  +   K    +K +D + ++             E
Sbjct: 163 KESSKPVQGHGGCGNVQPQVRKEGITLMGTWK---PSKMRDMMDDN-------------E 206

Query: 274 IEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
           I+  +K    + + P   L +F  I  ED+ L+ ++ + ++P  +I+T
Sbjct: 207 IQQPEK----KQITPQMALTIFRNISEEDVRLMGLSNDYARPEWMIIT 250



 Score = 55.8 bits (133), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/41 (60%), Positives = 28/41 (68%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            A   ++ +A   P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1070 AIESRFGKAAANPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1110


>gi|83320448|gb|ABC02851.1| RNA polymerase II largest subunit, partial [Rhopalomyces elegans]
          Length = 792

 Score =  162 bits (411), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 91/268 (33%), Positives = 146/268 (54%), Gaps = 32/268 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLHK+S+M HR +V+PH TFR N  V TPYNADFDGDEMN+H+PQ+ E+
Sbjct: 369 DGDLVIFNRQPSLHKMSMMGHRVRVMPHHTFRLNLSVTTPYNADFDGDEMNMHVPQSLES 428

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE               ++ M  +  +V+P+    ++   QD + G  + T+++ F +R
Sbjct: 429 KAEI-------------QEICMVPRQ-IVSPQKNAPVMGIVQDTLCGVNIFTRRDTFLSR 474

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            QTM           +I   +  +  R   P + ++   +WTGKQ+ +LI+       V+
Sbjct: 475 QQTM-----------NILMWVPNWDGRIPAPAI-LKPKPLWTGKQMLTLIIPKG----VS 518

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
                 G     +      D+ V++ N ELL G + K T+G G  + +  +++R+ G +V
Sbjct: 519 YTGAHSGNPDGEHPHLTPNDTKVLIENGELLTGIVCKKTVGVG--SALIQVIMREHGPEV 576

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
                  +  +T+++L+  GFSIGIGD 
Sbjct: 577 TKYFFNGIQHITNYWLLQHGFSIGIGDA 604



 Score =  102 bits (253), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 47/63 (74%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D TP  +GFV NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+ V
Sbjct: 726 DHTPASRGFVDNSYLRGLTPTEFFFHAMSGREGLIDTAVKTAETGYIQRRLVKALEDVMV 785

Query: 666 QYD 668
           +YD
Sbjct: 786 KYD 788



 Score = 46.2 bits (108), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 50/216 (23%), Positives = 96/216 (44%), Gaps = 26/216 (12%)

Query: 150 YIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAA-GFRAKLRNPALSYLVRKS 208
           +++L  PV+H+G+   V  IL+ +C    C+++ + E     G   ++ +P       K+
Sbjct: 1   HVELAKPVYHVGFLTKVKKILECVCF--YCSKLKVDESNPRFGLAMRIHDP-------KA 51

Query: 209 LKKKILETTKKVSVCPHCGEINGVVKKCG-------LLKISHEKYKNRTKKKDAIVEDLL 261
             K + E  K  ++C    E                L K    ++    +++  + ++ L
Sbjct: 52  RLKAVWELCKVKTMCDQDDEDADKRDDEDGEDEDTLLGKPKKHRHGGCGRRQPTLRKEGL 111

Query: 262 AEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
             Y  A + +   E +   G  Q + P + LQ+ + I  +D+  + ++ E ++P +LI+ 
Sbjct: 112 KLY--ATQRSSSKEQNPLEGK-QLVKPDQALQILKRISDDDLESMGLSVEFARPENLIIM 168

Query: 322 RLLVPPNCIRPSVISDLKSDNDVVLFNRQPSLHKLS 357
            L VPP  +RPS+  D  S  +  L       HKLS
Sbjct: 169 VLPVPPPQVRPSIQMDGTSKGEDDL------THKLS 198


>gi|15897171|ref|NP_341776.1| DNA-directed RNA polymerase subunit A' [Sulfolobus solfataricus P2]
 gi|284174417|ref|ZP_06388386.1| DNA-directed RNA polymerase subunit A' [Sulfolobus solfataricus
           98/2]
 gi|384433684|ref|YP_005643042.1| DNA-directed RNA polymerase subunit A' [Sulfolobus solfataricus
           98/2]
 gi|17368575|sp|Q980R2.1|RPOA1_SULSO RecName: Full=DNA-directed RNA polymerase subunit A'
 gi|167744881|pdb|2PMZ|A Chain A, Archaeal Rna Polymerase From Sulfolobus Solfataricus
 gi|167744892|pdb|2PMZ|Q Chain Q, Archaeal Rna Polymerase From Sulfolobus Solfataricus
 gi|239782143|pdb|3HKZ|A Chain A, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
 gi|239782156|pdb|3HKZ|I Chain I, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
 gi|13813360|gb|AAK40566.1| DNA-directed RNA polymerase, subunit A' (rpoA1) [Sulfolobus
           solfataricus P2]
 gi|261601838|gb|ACX91441.1| DNA-directed RNA polymerase subunit A' [Sulfolobus solfataricus
           98/2]
          Length = 880

 Score =  162 bits (411), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 100/271 (36%), Positives = 148/271 (54%), Gaps = 29/271 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++S+MAHR +VL   TFR N  VC PYNADFDGDEMN+H+PQ+EEA
Sbjct: 413 DGDIVLFNRQPSLHRISMMAHRVRVLKGLTFRLNLLVCPPYNADFDGDEMNLHVPQSEEA 472

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
            AE              AK +M    N++TPR G  +I A QD+I+G YLLT K     +
Sbjct: 473 IAE--------------AKEIMLVHKNIITPRYGGPIIGAAQDYISGAYLLTVKTTLLTK 518

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            +  +I    +AD     G     + R +           +TGKQ+ S  L  + +    
Sbjct: 519 EEAQQILG--VADVKIDLGEPAILAPREY-----------YTGKQVISAFLPKDFNFHGQ 565

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           AN+ +  R      E C  DSYV+++N  LL G  DK  +G+    ++ + L++++ ++ 
Sbjct: 566 ANVSSGPR--LCKNEDCPHDSYVVIKNGILLEGVFDKKAIGNQQPESILHWLIKEYSDEY 623

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
               M  L R+   ++  +GF++ + DV+ G
Sbjct: 624 GKWLMDNLFRVFIRFVELQGFTMRLEDVSLG 654



 Score =  110 bits (274), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 74/261 (28%), Positives = 127/261 (48%), Gaps = 49/261 (18%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D +++ S   I++ ++Y +D   TPI   ++D R+G  +    C TCG  L +C GHFG+
Sbjct: 17  DEIRKMSVTAIITPDVYDED--GTPIEGSVMDPRLGVIEPGQKCPTCGNTLGNCPGHFGH 74

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-----KLRNPALSYLV 205
           I+L  PV H+G  + +   L++ C+   C RV + E++   +       K R P+ +  +
Sbjct: 75  IELVRPVIHVGLVKHIYEFLKATCRR--CGRVKISEDEIEKYSRIYNAIKKRWPSAARRL 132

Query: 206 RKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYN 265
            + +KK    T  K  VCPHC E               ++YK + +K     E+      
Sbjct: 133 TEYVKK----TAMKAQVCPHCNE---------------KQYKIKLEKPYNFYEE------ 167

Query: 266 EAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLV 325
                       +K G +  L P ++ +  E IP  D+ +L  +   S+P  +ILT L V
Sbjct: 168 ------------RKEG-VAKLTPSDIRERLEKIPDSDVEILGYDPTTSRPEWMILTVLPV 214

Query: 326 PPNCIRPSVI--SDLKSDNDV 344
           PP  IRPS++  S +++++D+
Sbjct: 215 PPITIRPSIMIESGIRAEDDL 235



 Score = 89.7 bits (221), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 40/73 (54%), Positives = 56/73 (76%), Gaps = 2/73 (2%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D++P  +GF+ +SF +GL PTE FFH  GGREGLVDTAV+T+++GYMQRRL+ +L DL  
Sbjct: 773 DISPEARGFIYSSFRTGLKPTELFFHAAGGREGLVDTAVRTSQSGYMQRRLINALSDLRA 832

Query: 666 QYDMSFDAAFYGQ 678
           +YD +   + YG+
Sbjct: 833 EYDGTV-RSLYGE 844


>gi|390939170|ref|YP_006402908.1| DNA-directed RNA polymerase subunit A'' [Desulfurococcus fermentans
            DSM 16532]
 gi|390192277|gb|AFL67333.1| DNA-directed RNA polymerase, subunit A'' [Desulfurococcus fermentans
            DSM 16532]
          Length = 406

 Score =  162 bits (410), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 125/397 (31%), Positives = 204/397 (51%), Gaps = 68/397 (17%)

Query: 1050 VRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGHGRES-NPFPSACKAEACRE 1108
            + +I++ LEE   KE+V+    +V + +R ++L+   KI   RE+   F      E   E
Sbjct: 6    IEEIQQLLEE-RLKENVSP---QVYEEVRNKLLNIAGKIVITRETVERF-----IEHVIE 56

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEVCEY------------------ 1150
            +Y  + IEP  AVG +AAQS+GEP TQMTL+ FH+AG V EY                  
Sbjct: 57   RYHSSLIEPGEAVGTIAAQSLGEPSTQMTLRVFHYAG-VREYNVTLGLPRLIEIVDARKK 115

Query: 1151 ----IEEVFVPDD--------SFILIKLDMDRIRLLHLEVDID----------------- 1181
                I E+++ D+          I  K++   +  +  E+DID                 
Sbjct: 116  PETPIMEIYLVDEYRRSEEKAREIARKIESTYLENITRELDIDLIEGVATVRLDPEMLED 175

Query: 1182 ---SIRYCIERTRGISGHLTVSGHS--FLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQ 1236
               S+   IE+ + +       G     +I+  ++    + SK+ +++  L S+ +KG++
Sbjct: 176  KGLSVEVIIEKLKELDVDEVSRGDDPYEVIISLREEYLDY-SKLEKLRSKLLSLHLKGIK 234

Query: 1237 GINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARS 1296
             I + +I +   E    Y ++ EG NL ++M   GV   +  +NN +E+ + LGIEAAR 
Sbjct: 235  EIRKVIIQKRGDE----YVIISEGSNLEEIMRIEGVDWRRVYTNNIHEIERVLGIEAARQ 290

Query: 1297 TIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTS 1356
             I+ EIK ++++ G+ +D RH ML+AD+MT  G V  I R G+A  K SVL  A+FE T 
Sbjct: 291  AIIKEIKEILDDQGLDVDIRHIMLLADMMTWTGHVRQIGRMGVAGEKPSVLARATFEMTV 350

Query: 1357 DHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
              L ++A   + D + GV+E II+G  + VGTG++++
Sbjct: 351  QKLLESAATSEEDRLYGVTENIIIGQTIPVGTGMVQI 387



 Score = 95.9 bits (237), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 68/236 (28%), Positives = 128/236 (54%), Gaps = 16/236 (6%)

Query: 764 GVPRIKEIINASRNISTPIITAYL--DKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR+ EI++A +   TPI+  YL  +     + AR +  ++E T L  +   ++   + 
Sbjct: 102 GLPRLIEIVDARKKPETPIMEIYLVDEYRRSEEKAREIARKIESTYLENITRELDIDLIE 161

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRY--CIERTRGISGHLTVSGHSFLILKPKDSSKS 879
             + + +  +M   + L +EV I+ ++     E +RG   +        +I+  ++    
Sbjct: 162 GVATVRLDPEMLEDKGLSVEVIIEKLKELDVDEVSRGDDPY-------EVIISLREEYLD 214

Query: 880 FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
           + SK+ +++  L S+ +KG++ I + +I +   E    Y ++ EG NL ++M   GV   
Sbjct: 215 Y-SKLEKLRSKLLSLHLKGIKEIRKVIIQKRGDE----YVIISEGSNLEEIMRIEGVDWR 269

Query: 940 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
           +  +NN +E+ + LGIEAAR  I+ EIK ++++ G+ +D RH ML+AD+MT  G V
Sbjct: 270 RVYTNNIHEIERVLGIEAARQAIIKEIKEILDDQGLDVDIRHIMLLADMMTWTGHV 325


>gi|326480447|gb|EGE04457.1| DNA-directed RNA polymerase II largest subunit [Trichophyton
           equinum CBS 127.97]
          Length = 1712

 Score =  162 bits (410), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 95/272 (34%), Positives = 150/272 (55%), Gaps = 35/272 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D +LFNRQPSLHK S+M+HR +V+P+ TFR N  V TPYNADFDGDEMN+H+PQ+EEA
Sbjct: 455 DGDFILFNRQPSLHKESMMSHRVRVMPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSEEA 514

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L++L ++            N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 515 RAE----LNQLCLVPL----------NIVSPQRNGPLMGIVQDTLCGIYKICRRDVFLTK 560

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M +    +    D  G++ +       P + ++    W+GKQ+ S++L      P  
Sbjct: 561 EQVMNV----LLWVPDWDGVLPQ-------PAI-LKPRPRWSGKQMISMVL------PSG 602

Query: 521 AN-LKTKGRAYTANEEFCH-RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            N L+        +E+F    D  V++   EL+ G   K T+G+ G   V + +  ++G 
Sbjct: 603 LNLLRIDKDKSPISEKFSPLADGGVLVHGGELMYGMFSKKTVGASG-GGVVHTIFNEYGP 661

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           D A++       + +++L++ GFSIGIGD  P
Sbjct: 662 DAAMSFFNGAQAVVNYWLLHNGFSIGIGDTIP 693



 Score =  103 bits (256), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 60/180 (33%), Positives = 94/180 (52%), Gaps = 15/180 (8%)

Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMAT 1269
             LL ++ ++GV GI+RA I+E+    V                ++ L   G  L DV+A 
Sbjct: 1256 HLLDTLTLRGVPGIDRAFINEKSRTRVLEDGSLHQSASDPECKEWVLETSGSALADVLAI 1315

Query: 1270 YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 1329
             G+   +  SN   E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1316 PGIDASRTYSNQFVEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLVDVMTSRG 1375

Query: 1330 EVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
             ++ +TRHG+ +     L   SFE T + L DAA + + D   GVSE +I+G     GTG
Sbjct: 1376 FLMAVTRHGINRADTGALMRCSFEETVEILLDAAAFAELDDCRGVSENLILGQMAPAGTG 1435



 Score = 99.4 bits (246), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QR+LVK+LE++ V
Sbjct: 813 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMV 872

Query: 666 QYD 668
           +YD
Sbjct: 873 KYD 875



 Score = 86.3 bits (212), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 78/299 (26%), Positives = 138/299 (46%), Gaps = 63/299 (21%)

Query: 754  NPGDYKLSQDGVPRIKEIINASRNISTPIITAYLDKDTDL--DYARIVKGRLERTTLGEV 811
            NPG+      GVPR+KEI+N + NI TP +T Y   +  +  + A+ ++  +E T+L  V
Sbjct: 1081 NPGEMV----GVPRLKEILNVATNIKTPSMTVYQAPECRMNKESAKQLRSIVEHTSLRSV 1136

Query: 812  CEYIEEVFVPDDSFILIKLDMDRIR---LLHLEVDIDS-------IRYCIERTRGISGHL 861
             E  E  + P+    +I+ D+D +    ++  +V  DS       +R  + R + +   L
Sbjct: 1137 TESTEIYYDPNIQSTVIENDVDMVESYFIIPEDVADDSSRQSKWLLRIILSRPKLLDKGL 1196

Query: 862  TVSGHSFLILK--PKD-----SSKSFNSKMYQMKQ------------------------- 889
            TV   +  I +  P+D     S  + + ++ +++Q                         
Sbjct: 1197 TVQDVATKIKEAYPQDIAVIFSDNNADEQVVRIRQIQDPKQDEDDDDTEYDVTLKKLESH 1256

Query: 890  LLPSVVIKGVQGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMATY 934
            LL ++ ++GV GI+RA I+E+    V                ++ L   G  L DV+A  
Sbjct: 1257 LLDTLTLRGVPGIDRAFINEKSRTRVLEDGSLHQSASDPECKEWVLETSGSALADVLAIP 1316

Query: 935  GVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
            G+   +  SN   E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1317 GIDASRTYSNQFVEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLVDVMTSRG 1375



 Score = 84.3 bits (207), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 60/228 (26%), Positives = 105/228 (46%), Gaps = 38/228 (16%)

Query: 110 DPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINI 169
           D ++ P   GL D R+GT  +   C TC + ++DC GHFG+I+L  PVFHIG+   +  +
Sbjct: 45  DQRQRPREKGLNDPRLGTIDRNWRCATCEEGINDCPGHFGHIELSTPVFHIGFLTKIKKL 104

Query: 170 LQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKSLKKKIL-------------- 214
           L+++C N  C ++           A + R+P   +     L K IL              
Sbjct: 105 LETVCHN--CGKIKANASDQKYLDALRFRDPKKRFDAIWRLSKDILICEADPPEEDDPFA 162

Query: 215 -ETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPE 273
            E++K V     CG +   V+K G+  +   K    +K +D + ++             E
Sbjct: 163 KESSKPVQGHGGCGNVQPQVRKEGITLMGTWK---PSKMRDMMDDN-------------E 206

Query: 274 IEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
           I+  +K    + + P   L +F  I  ED+ L+ ++ + ++P  +I+T
Sbjct: 207 IQQPEK----KQITPQMALTIFRNISEEDVRLMGLSNDYARPEWMIIT 250


>gi|254571371|ref|XP_002492795.1| RNA polymerase II largest subunit B220 [Komagataella pastoris
           GS115]
 gi|238032593|emb|CAY70616.1| RNA polymerase II largest subunit B220 [Komagataella pastoris
           GS115]
 gi|328353197|emb|CCA39595.1| DNA-directed RNA polymerase II subunit A [Komagataella pastoris CBS
           7435]
          Length = 1743

 Score =  162 bits (410), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 92/272 (33%), Positives = 147/272 (54%), Gaps = 44/272 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+D VLFNRQPSLHK+S+MAHR KV+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 439 DDDPVLFNRQPSLHKMSMMAHRVKVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 498

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE                 L A    +V+P++ + ++   QD + G   +T ++ F   
Sbjct: 499 RAE--------------LSQLCAVPLQIVSPQSNKPVMGIVQDTLCGVRKMTLRDTFIEY 544

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVV----FVRTAVIWTGKQIFSLILKPNRD 516
            Q M +                 F   SW+ VV     ++   +WTGKQ+ S+ +     
Sbjct: 545 EQVMNML----------------FWVPSWDGVVPQPAILKPKPLWTGKQLLSIAI----- 583

Query: 517 CPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            P   +L+   R    N     +D+ +++ + +++ G +DK T+GSGG   + + ++R+ 
Sbjct: 584 -PSGIHLQ---RTDGGNSLLSPKDNGMLIVDGKVMFGVVDKKTVGSGG-GGLIHTVMREK 638

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           G  +       + ++ +++L++ GFSIGIGD 
Sbjct: 639 GPKICAELFGNIQKVVNYWLLHNGFSIGIGDA 670



 Score =  105 bits (262), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 89/291 (30%), Positives = 144/291 (49%), Gaps = 34/291 (11%)

Query: 1149 EYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTV----SGHSF 1204
            E +EE  +   S  L++L++DR R+L  ++ ++ +   I      S  L V         
Sbjct: 1181 EKVEET-IDKQSPWLLRLELDRARMLDKQLTMNQVADKISEV--FSDDLFVMWSEDNADK 1237

Query: 1205 LILK------PKDSSKSFNSKMYQM-----KQLLPSVVIKGVQGINRA--VIHE---EDV 1248
            LI++      PK   +   ++  QM       +L  + ++G+ GI++   V H+    D 
Sbjct: 1238 LIIRCRVIRDPKAMDEELEAEEDQMLKRIEAHMLDLIALRGIPGISKVYMVKHKVSVPDE 1297

Query: 1249 EGVTK----YKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKL 1304
             G  K    + L  +G NL +VMA  GV   +  SN+  E+   LGIEA RS++  EI  
Sbjct: 1298 SGEYKNEELWALETDGINLAEVMAVPGVDSSRTYSNSFVEILSVLGIEATRSSLYKEILN 1357

Query: 1305 VMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAF 1364
            V+   G  +++RH  L+ D+MTS+G ++ ITRHG+ +     L   SFE T + LF+A  
Sbjct: 1358 VIAFDGSYVNYRHMALLVDVMTSRGYLMAITRHGINRADTGALMRCSFEETVEILFEAGA 1417

Query: 1365 YGQTDCISGVSECIIMGLPMNVGTGLI------KLLQAVPRSEPVPRTLLF 1409
              + D   GVSE +++G    +GTG        KLL ++P ++  P   LF
Sbjct: 1418 AAELDDCRGVSENVMLGQLAPMGTGAFDVMIDEKLLTSLP-ADYAPTMPLF 1467



 Score =  104 bits (260), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 84/288 (29%), Positives = 138/288 (47%), Gaps = 54/288 (18%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N ++NI TP +T YLD++   D++ A++++  +E TTL  V    E  + P
Sbjct: 1099 GVPRLKEILNVAKNIKTPALTVYLDREIALDIEKAKVIQSSIEYTTLKNVTSATEIYYDP 1158

Query: 822  DDSFILIKLDMDRIRLL------HLEVDIDS-----IRYCIERTRGISGHLTV------- 863
            D +  +I+ D D +          +E  ID      +R  ++R R +   LT+       
Sbjct: 1159 DPTSTVIEEDFDTVEAYFSIPDEKVEETIDKQSPWLLRLELDRARMLDKQLTMNQVADKI 1218

Query: 864  ----SGHSFL----------------ILKPKDSSKSFNSKMYQM-----KQLLPSVVIKG 898
                S   F+                I  PK   +   ++  QM       +L  + ++G
Sbjct: 1219 SEVFSDDLFVMWSEDNADKLIIRCRVIRDPKAMDEELEAEEDQMLKRIEAHMLDLIALRG 1278

Query: 899  VQGINRA--VIHE---EDVEGVTK----YKLLVEGDNLRDVMATYGVKGVKCSSNNTYEV 949
            + GI++   V H+    D  G  K    + L  +G NL +VMA  GV   +  SN+  E+
Sbjct: 1279 IPGISKVYMVKHKVSVPDESGEYKNEELWALETDGINLAEVMAVPGVDSSRTYSNSFVEI 1338

Query: 950  YKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
               LGIEA RS++  EI  V+   G  +++RH  L+ D+MTS+G ++ 
Sbjct: 1339 LSVLGIEATRSSLYKEILNVIAFDGSYVNYRHMALLVDVMTSRGYLMA 1386



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 53/63 (84%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTP EFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+ V
Sbjct: 792 DFSPESKGFVENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDIMV 851

Query: 666 QYD 668
            YD
Sbjct: 852 HYD 854



 Score = 95.5 bits (236), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/237 (29%), Positives = 113/237 (47%), Gaps = 38/237 (16%)

Query: 112 QRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQ 171
           ++ P   GL D ++G+  +   C TCG+ +++C GHFG+++L  PVFHIG+   +  + +
Sbjct: 45  RQRPREGGLNDPKLGSIDRNFKCQTCGEGMAECPGHFGHMELAKPVFHIGFIPKIKKVCE 104

Query: 172 SICKNPTCARVLLGEEKAAGFRA-KLRNPALSY-LVRKSLKKKIL---------ETTKKV 220
            IC N  C ++LL E      +A ++R+P   +  V +  K K++          + +KV
Sbjct: 105 CICMN--CGKLLLDETNPTMAQAIRIRDPKKRFNAVWQLCKTKMVCEADAPVDEYSEQKV 162

Query: 221 SVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKF 280
                CG    VV+K G +K+     K+    +DA  E  L                   
Sbjct: 163 VSRGGCGNTQPVVRKDG-MKLWGTWKKSGFSDRDAQPERKL------------------- 202

Query: 281 GLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD 337
                L P E+L +F+ I  ED   L  N + ++P  +I+T L VPP  +RPS+  D
Sbjct: 203 -----LTPGEILNVFKHISPEDCFRLGFNEDYARPEWMIITVLPVPPPQVRPSIAMD 254



 Score = 53.5 bits (127), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 22/37 (59%), Positives = 28/37 (75%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            ++ R+ + P   VG +AAQSIGEP TQMTL TFH+AG
Sbjct: 1054 QFQRSLVHPGEMVGVIAAQSIGEPATQMTLNTFHYAG 1090


>gi|448330662|ref|ZP_21519941.1| DNA-directed RNA polymerase subunit A'' [Natrinema versiforme JCM
            10478]
 gi|445611166|gb|ELY64926.1| DNA-directed RNA polymerase subunit A'' [Natrinema versiforme JCM
            10478]
          Length = 398

 Score =  162 bits (410), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 103/344 (29%), Positives = 176/344 (51%), Gaps = 59/344 (17%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A A   +Y+  +++P   VG ++AQSIGEPGTQ+T+ TFH+AG            + E +
Sbjct: 48   AAAVETRYLNTRVDPLDPVGTVSAQSIGEPGTQLTMNTFHYAGVAEIDVTQGLPRLIELV 107

Query: 1152 EEVFVPDDSFILIKLD----------------MDRIRLLHL------------------- 1176
            +    PD   + + L+                ++  ++L L                   
Sbjct: 108  DARKTPDTPMMTVYLEGEYATEREKAHEVVWNIEATQILALGDVSTNVADMRVQIALNED 167

Query: 1177 -----EVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVV 1231
                  +  + +   IE + G+    T+   S +   P++ S      + Q+ + L  + 
Sbjct: 168  TLEERMISAEEVAEIIEDSLGVK---TIQQGSQIEFGPEEPSYR---DLLQLVEELRDIT 221

Query: 1232 IKGVQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLG 1290
             KG++ ++R VI  E+++ G  ++ L  EG    DV+   GV   + + NN +E+++ LG
Sbjct: 222  FKGIEEVSRVVIRREELDNGNEEFVLYTEGSAFGDVLDIEGVDASRTTCNNIHEIHRNLG 281

Query: 1291 IEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNL 1349
            IEAAR  I+ E    +   G+  ++ RH MLVAD+M+++GE+  I RHG++  KESVL  
Sbjct: 282  IEAAREAIIEETNNTLAEQGLDDVNVRHLMLVADMMSNRGEIESIGRHGISGSKESVLAR 341

Query: 1350 ASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            A+FE T +HL +AA +G+ D + GV+E +I+G P+ +GTG + L
Sbjct: 342  AAFEVTVNHLLNAAIHGEVDDLDGVTENVIVGKPIKLGTGDVDL 385



 Score = 95.5 bits (236), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 69/239 (28%), Positives = 126/239 (52%), Gaps = 21/239 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T YL+ +  T+ + A  V   +E T    LG+V   + ++
Sbjct: 99  GLPRLIELVDARKTPDTPMMTVYLEGEYATEREKAHEVVWNIEATQILALGDVSTNVADM 158

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSK 878
            V     I +  D    R++  E     +   IE + G+    T+   S +   P++ S 
Sbjct: 159 RVQ----IALNEDTLEERMISAE----EVAEIIEDSLGVK---TIQQGSQIEFGPEEPSY 207

Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVK 937
                + Q+ + L  +  KG++ ++R VI  E+++ G  ++ L  EG    DV+   GV 
Sbjct: 208 R---DLLQLVEELRDITFKGIEEVSRVVIRREELDNGNEEFVLYTEGSAFGDVLDIEGVD 264

Query: 938 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEV 995
             + + NN +E+++ LGIEAAR  I+ E    +   G+  ++ RH MLVAD+M+++GE+
Sbjct: 265 ASRTTCNNIHEIHRNLGIEAAREAIIEETNNTLAEQGLDDVNVRHLMLVADMMSNRGEI 323


>gi|302835796|ref|XP_002949459.1| hypothetical protein VOLCADRAFT_80692 [Volvox carteri f.
           nagariensis]
 gi|300265286|gb|EFJ49478.1| hypothetical protein VOLCADRAFT_80692 [Volvox carteri f.
           nagariensis]
          Length = 1879

 Score =  162 bits (410), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 98/272 (36%), Positives = 145/272 (53%), Gaps = 38/272 (13%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           ++ D+VLFNRQPSLHK+S+M HR ++LP+ TFR N  V TPYNADFDGDEMN+H+ QT E
Sbjct: 456 TNGDLVLFNRQPSLHKMSMMGHRVRILPYSTFRLNLSVTTPYNADFDGDEMNMHVAQTHE 515

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE               + LM    N+V+P+  + ++   QD + G  L+T+++ F  
Sbjct: 516 TRAE--------------MRELMMVPRNIVSPQANKPVMGIVQDSLLGTRLMTKRDIFIE 561

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPV-VFVRTAVIWTGKQIFSLILKPNRDCP 518
           +   M            I GI     W    P+   ++   +WTGKQIFS+ +       
Sbjct: 562 KDVFMNT----------IMGIE---DWDGTVPMPTILKPKPLWTGKQIFSMFVP------ 602

Query: 519 VNANLKTKGRAY--TANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            + NLK K   Y  T  ++    DS V++R+ ELL G++ K T+G+G    V    L + 
Sbjct: 603 -DVNLKNKSAWYKDTDVQDMSVDDSQVLIRSGELLTGALCKKTVGNGAGGLVHLTWL-EH 660

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           G   A   +  + R  +++++  G SIGIGD 
Sbjct: 661 GPHAARGFINNVQRTVNYWVLQHGMSIGIGDT 692



 Score =  106 bits (264), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 66/194 (34%), Positives = 103/194 (53%), Gaps = 10/194 (5%)

Query: 1211 DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVE-------GVTKYK---LLVEG 1260
            +S+      M ++   +  V + GV  I +  I  E+            KY+   L  EG
Sbjct: 1281 ESADPTEDTMLKLSAAIMDVRLHGVPNIRKVFIRAENQHIYDRERGSFRKYEEWILDTEG 1340

Query: 1261 DNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPML 1320
             NL  V+A  GV   +  SN+  EV + LGIEAAR+ ++ E++ V+   G  +++RH   
Sbjct: 1341 INLEQVLAFEGVDPRRTMSNSIIEVLEVLGIEAARAALLKEVRNVISFDGSYVNYRHLAC 1400

Query: 1321 VADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIM 1380
            + D+MT KG ++ ITRHG+ +     +   SFE T D L+ AA +G+ D ++GVS+ I+M
Sbjct: 1401 LVDIMTCKGCLMAITRHGINRNGNGPMTQCSFEETVDILYRAAMFGERDRLTGVSDNIMM 1460

Query: 1381 GLPMNVGTGLIKLL 1394
            G    +GTG   LL
Sbjct: 1461 GNMCPLGTGAFDLL 1474



 Score = 97.1 bits (240), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 43/62 (69%), Positives = 52/62 (83%), Gaps = 1/62 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D+ P  +GFV NS+  GLTP EFFFH MGGREGL+DTAVKTA TGY+QRRLVK++ED+ V
Sbjct: 814 DLGPEARGFVGNSYLRGLTPQEFFFHAMGGREGLIDTAVKTASTGYIQRRLVKAMEDMVV 873

Query: 666 QY 667
           +Y
Sbjct: 874 RY 875



 Score = 74.7 bits (182), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 70/288 (24%), Positives = 131/288 (45%), Gaps = 58/288 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYL------DKD--------------------TDLDYAR 797
            GVPR+ E+IN ++NI TP +T +L      +KD                    T++ Y  
Sbjct: 1122 GVPRLTELINLAKNIKTPTLTVHLLPGLRENKDRAKEVQAKLEYTCFKNVVKTTEIWYDP 1181

Query: 798  IVKGRLERTTLGEVCEYIEEVF----------VPDDSFILIKLDMDRIRLLHLEVDIDSI 847
            +  G   +T +GE  E +   +          +P  S  L++ +++R  +L   + + ++
Sbjct: 1182 VDPGNPNQTIIGEDEEMLSSYYDLAGEEDLAVLPRLSHWLLRFELNRGTMLDKGLTLGAV 1241

Query: 848  RYCIERTRGISGHLTVSGHS-------FLILKPKDSSKSFNSK-----MYQMKQLLPSVV 895
            +  ++       ++ V+  +         ++K +++SK  ++      M ++   +  V 
Sbjct: 1242 QKALQDEWEDFINVLVNDDNAEKLIMRIRVMKTEEASKDESADPTEDTMLKLSAAIMDVR 1301

Query: 896  IKGVQGINRAVIHEEDVE-------GVTKYK---LLVEGDNLRDVMATYGVKGVKCSSNN 945
            + GV  I +  I  E+            KY+   L  EG NL  V+A  GV   +  SN+
Sbjct: 1302 LHGVPNIRKVFIRAENQHIYDRERGSFRKYEEWILDTEGINLEQVLAFEGVDPRRTMSNS 1361

Query: 946  TYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
              EV + LGIEAAR+ ++ E++ V+   G  +++RH   + D+MT KG
Sbjct: 1362 IIEVLEVLGIEAARAALLKEVRNVISFDGSYVNYRHLACLVDIMTCKG 1409



 Score = 68.9 bits (167), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 40/99 (40%), Positives = 56/99 (56%), Gaps = 3/99 (3%)

Query: 119 GLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPT 178
           GL D RMGT  +   CTT G N +D  G+FG+I L  PV+HIG+ + VI +L+  C +  
Sbjct: 53  GLSDPRMGTMDRGGICTTDGANANDSPGYFGHIALARPVYHIGFIKTVIRVLR--CVSYH 110

Query: 179 CARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETT 217
            +R+L+ ++ A G R       L Y V     KK+ ETT
Sbjct: 111 TSRLLV-DKYAYGLRISDSEKRLRYFVHLCQGKKVDETT 148



 Score = 49.3 bits (116), Expect = 0.018,   Method: Compositional matrix adjust.
 Identities = 22/37 (59%), Positives = 26/37 (70%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            ++  A   P   VG +AAQS+GEP TQMTL TFHFAG
Sbjct: 1077 RFFLALSHPGDCVGTVAAQSLGEPTTQMTLNTFHFAG 1113


>gi|336476453|ref|YP_004615594.1| DNA-directed RNA polymerase subunit A' [Methanosalsum zhilinae DSM
           4017]
 gi|335929834|gb|AEH60375.1| DNA-directed RNA polymerase subunit A' [Methanosalsum zhilinae DSM
           4017]
          Length = 880

 Score =  162 bits (410), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 97/268 (36%), Positives = 140/268 (52%), Gaps = 31/268 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLHK+SIMAH  KVLP++TFR N  VC PYNADFDGDEMN+H+ Q  EA
Sbjct: 412 DGDIVIFNRQPSLHKMSIMAHTVKVLPYKTFRLNPSVCPPYNADFDGDEMNLHVLQNYEA 471

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
            AEA              K+LM  + N+++PR G   I    D I+G +LLT+     N+
Sbjct: 472 IAEA--------------KILMQVQENILSPRFGGPFIGGIHDHISGMFLLTRNEKQINK 517

Query: 461 AQTMRI-ASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
              + +   + +    +  G     S     P         W GKQIFS IL    D   
Sbjct: 518 HDALELLRKSEVRSLPEPAG-----SGEGGEPY--------WNGKQIFSQILPEGLDLEF 564

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            A +  K      +E  C  D+YV+++N ELL G++D+  +G+  K  V   +++++G  
Sbjct: 565 PAEVCMKCDVCKKSE--CEHDAYVVIKNGELLIGTIDERAIGA-FKGIVVDKIVKEYGTT 621

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
                +  ++++    +M  G S GI D
Sbjct: 622 RGAQFIDDVTKLAIRGIMRTGLSFGISD 649



 Score =  108 bits (270), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 80/266 (30%), Positives = 125/266 (46%), Gaps = 44/266 (16%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G I+  +     V++ S   I++ + Y  D    PI  GL+D R+G       C +CG  
Sbjct: 12  GAIKFGLISPREVRKMSITPIITADTY--DDDGYPIDMGLMDLRLGVIDPGLKCKSCGGR 69

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
             +C GHFG+I+L  PV HIG+ + +  IL+S C+   C+R+LL   K   + A L    
Sbjct: 70  AGECPGHFGHIELVAPVIHIGFNKTIRKILRSTCRK--CSRLLLEFSKKEEYLAHLETLK 127

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDL 260
               + +S   +I +  +K   CP+CGE          L+I  EK               
Sbjct: 128 EIGHLPESYINEIFKEARKSKTCPYCGEEQ--------LEIKFEK--------------- 164

Query: 261 LAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
            ++Y         IE  +K      L P E+    E IP +D+ ++ MN E ++P  +IL
Sbjct: 165 PSDY---------IENGEK------LTPTEIRDRLENIPDDDVKVMGMNPETARPEWMIL 209

Query: 321 TRLLVPPNCIRPSVI--SDLKSDNDV 344
           T L VPP  +RPS+   S  +S++D+
Sbjct: 210 TVLPVPPVTVRPSITLESGQRSEDDL 235



 Score = 92.4 bits (228), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 39/59 (66%), Positives = 52/59 (88%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
            GFV++S+ SGL PTE+FFH +GGREGLVDTAV+T+++GY+QRRLV +L+DL VQYD +
Sbjct: 778 HGFVKSSYKSGLNPTEYFFHAIGGREGLVDTAVRTSQSGYLQRRLVNALQDLEVQYDRT 836


>gi|29539342|dbj|BAC67672.1| DNA-directed RNA polymerase II largest subunit [Cyanidioschyzon
           merolae]
 gi|449019055|dbj|BAM82457.1| RNA polymerase II largest subunit [Cyanidioschyzon merolae strain
           10D]
          Length = 1819

 Score =  162 bits (410), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 94/269 (34%), Positives = 142/269 (52%), Gaps = 35/269 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + D+VLFNRQPSLH++SIM HR ++LP+ TFR N    +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 447 NGDLVLFNRQPSLHRMSIMGHRVRILPYSTFRMNLSATSPYNADFDGDEMNLHVPQSEEV 506

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE               K LMA   N+V+P+    ++   QD + G  L T ++ F   
Sbjct: 507 RAE--------------IKELMAVPKNIVSPQANRPVMGIVQDSLLGCMLFTLRDTFLEE 552

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                +   L             F  R   P + ++   +WTGKQIFSL+L      P  
Sbjct: 553 DTVFNLLLHL-----------PHFDGRIPAPAI-LKPRPLWTGKQIFSLLL------PDG 594

Query: 521 ANLKTKGRAYTANEE--FCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            NL+     +  +E       D+ V+++N EL+ G +DK T+GS    ++ ++  ++ G 
Sbjct: 595 VNLERLSNGHPDHERTIMTPSDTRVLIQNGELITGIVDKRTVGSSA-GSLIHVTWKESGP 653

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           +     +  +  + +++LM  G SIGIGD
Sbjct: 654 ERTSQLISDIQLLINYWLMQNGMSIGIGD 682



 Score = 99.0 bits (245), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 42/65 (64%), Positives = 56/65 (86%), Gaps = 1/65 (1%)

Query: 605 IGDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDL 663
           + D++P  +GFV+NS+  GLTP E FFH MGGREGL+DTAVKTAETGY+QRRL+K++ED+
Sbjct: 803 VDDLSPEARGFVENSYLRGLTPEEVFFHAMGGREGLIDTAVKTAETGYIQRRLMKAMEDI 862

Query: 664 CVQYD 668
            ++YD
Sbjct: 863 RIEYD 867



 Score = 90.1 bits (222), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 56/178 (31%), Positives = 91/178 (51%), Gaps = 10/178 (5%)

Query: 1226 LLPSVVIKGVQGINRAVIHEE-----DVEG-----VTKYKLLVEGDNLRDVMATYGVKGV 1275
            LL  + +KG+ GI +  + +      D E        ++ L  EG  L  V++   V   
Sbjct: 1316 LLEDMQLKGIPGIRKVFLRQTQRVLFDPEAGSFRSAPEWVLDTEGTALLAVLSHPDVDAR 1375

Query: 1276 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGIT 1335
            +  SN   EV + LGIEAAR  +  E+  V+   G S+ +RH  L+ ++MT +G ++ ++
Sbjct: 1376 RTISNEITEVLQVLGIEAARQALYNEMYAVLSFDGSSVGYRHLALLVEVMTCRGMLIPVS 1435

Query: 1336 RHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            R G+ +++   L   +FE T + L  AA +G  D   GVS+ +I+G    VGTG   L
Sbjct: 1436 RFGINRLETGPLMRCTFEETVEILATAATFGVRDACEGVSQAVILGQRAKVGTGAFSL 1493



 Score = 77.8 bits (190), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 65/237 (27%), Positives = 108/237 (45%), Gaps = 30/237 (12%)

Query: 115 PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSIC 174
           P   G+LD R+G   +   C TC  +  DC GHFG+I+L  PVF++     V+  L+ +C
Sbjct: 48  PKAGGVLDPRLGAIDRNFPCATCEGSSIDCPGHFGHIELVKPVFNVLMLSTVLKTLRCVC 107

Query: 175 KNPTCARVLLGEEKAAGFR-AKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVV 233
               C+R+L+    +   R A++++P   +       + + +      VC   G  +   
Sbjct: 108 Y--YCSRLLVDGSDSRMLRAARIKDPVKRF-------QAVFQLCNGTRVC--GGGADSSE 156

Query: 234 KKCGLLKISHEKYKNRTKKKDA-------IVED---LLAEYNEAVKFNPEIEAHKKFGLI 283
           ++  L     E  +   K ++        +  D   +LAE+ +A  F     A +K    
Sbjct: 157 EQLMLPAAVLEARERIGKPREGCGNLQPHVTRDGLRILAEFPDAEAF----AAERK---- 208

Query: 284 QTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKS 340
           Q L    V Q+F  I  ED+ LL  +   S+P  ++L+ L VPP  +RPS+  D  S
Sbjct: 209 QELAAERVQQIFRHIRDEDLELLGFHPRFSRPEWMVLSVLPVPPPHVRPSIQMDAVS 265



 Score = 77.0 bits (188), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 77/319 (24%), Positives = 123/319 (38%), Gaps = 89/319 (27%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPR+KE+IN +R   TP +T YL    D + A IV+  LE+  L +V E     F PD 
Sbjct: 1111 GVPRLKELINVARQAKTPSVTVYLKSGKDKELANIVQSELEQCRLRDVVESSAIYFDPDP 1170

Query: 824  SFILIKLD-------------MDRIR---------LLHLEVDID---------------- 845
            +  +++ D             MDR           +L  E+ ID                
Sbjct: 1171 ANTVVEADREWVRDYFDLPDEMDRPERLSPWLLRIVLSTEMMIDKRLRLSDVARRLRAEF 1230

Query: 846  ----SIRYCIERTRGISGHLTVSGHSFL--------------------ILKPKDSSKSFN 881
                S+ Y  +    +  H+ ++G  +                     +L P D +   N
Sbjct: 1231 GGDLSVVYSDDNAEQLVMHIRMAGDEYEKGALGVPILGESERLDDTLNLLGPGDMTAGGN 1290

Query: 882  SKMYQMKQ-----------------LLPSVVIKGVQGINRAVIHEE-----DVEG----- 914
              +  +                   LL  + +KG+ GI +  + +      D E      
Sbjct: 1291 QSLEALDSGTVEEQDDVFLKRIELALLEDMQLKGIPGIRKVFLRQTQRVLFDPEAGSFRS 1350

Query: 915  VTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHG 974
              ++ L  EG  L  V++   V   +  SN   EV + LGIEAAR  +  E+  V+   G
Sbjct: 1351 APEWVLDTEGTALLAVLSHPDVDARRTISNEITEVLQVLGIEAARQALYNEMYAVLSFDG 1410

Query: 975  MSIDFRHPMLVADLMTSKG 993
             S+ +RH  L+ ++MT +G
Sbjct: 1411 SSVGYRHLALLVEVMTCRG 1429



 Score = 58.5 bits (140), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 25/37 (67%), Positives = 30/37 (81%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            ++VRA+  P   VGA+AAQS+GEP TQMTL TFHFAG
Sbjct: 1066 RFVRARATPGEMVGAVAAQSLGEPATQMTLNTFHFAG 1102


>gi|189197231|ref|XP_001934953.1| DNA-directed RNA polymerase II subunit RPB1 [Pyrenophora
           tritici-repentis Pt-1C-BFP]
 gi|187980901|gb|EDU47527.1| DNA-directed RNA polymerase II subunit RPB1 [Pyrenophora
           tritici-repentis Pt-1C-BFP]
          Length = 1742

 Score =  162 bits (410), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 89/271 (32%), Positives = 149/271 (54%), Gaps = 33/271 (12%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D+DV++FNRQPSLHK S+M HR KV+P+ TFR N  V +PYNADFDGDEMN+H+PQ++E
Sbjct: 445 NDDDVIIFNRQPSLHKESMMGHRVKVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSDE 504

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE    +  L ++  +          +V+P+  + L+   QD + G Y +++++ F  
Sbjct: 505 TRAE----VQNLCMVPKQ----------IVSPQKNQPLMGIVQDTLLGVYKMSRRDNFIG 550

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
             Q M I    +    D  GI+         P + ++   +WTGKQ+ S+        P 
Sbjct: 551 IEQVMPI----LMWVPDWDGIVPE-------PAI-LKPRPLWTGKQLVSMAF------PK 592

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
             N++ K    + + +   RD  +++++ +L+ G + K  +G+     V +I+  + G D
Sbjct: 593 EVNIEKKEDDSSPSPQNDIRDKSLMIKSGQLIYGQVTKKIVGASA-GGVIHIIFNELGPD 651

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
            AV       R+ +++L++ GFS G+GD  P
Sbjct: 652 AAVKFFNACQRICNWWLLHHGFSFGVGDTIP 682



 Score =  101 bits (251), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTP+EFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+ V
Sbjct: 802 DYSPESRGFVENSYLRGLTPSEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDVMV 861

Query: 666 QYD 668
           +YD
Sbjct: 862 KYD 864



 Score = 99.0 bits (245), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 59/181 (32%), Positives = 93/181 (51%), Gaps = 15/181 (8%)

Query: 1224 KQLLPSVVIKGVQGINRAVI---------------HEEDVEGVTKYKLLVEGDNLRDVMA 1268
            + LL  V ++GV G+ RA I               H +      ++ L   G  L +V++
Sbjct: 1279 QHLLDDVTLRGVPGVERAFIREHCVTKKRDDGSLLHSKSSPECKEWVLDTTGTALAEVLS 1338

Query: 1269 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK 1328
              GV      SN+  E+   LGIEAAR+ ++ E+ +V+   G  ++ RH  L+ D+M  +
Sbjct: 1339 IPGVDATTTYSNSFIEILAVLGIEAARAGLLKELGMVLSFDGSYVNHRHMALLVDIMCQR 1398

Query: 1329 GEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGT 1388
            G ++ ITRHG+ +     L   SFE T + L +AA +G+ D   GVSE I++G    +GT
Sbjct: 1399 GVLMAITRHGINRNDTGALMRCSFEETVEILLEAAGFGELDDCRGVSENIMLGQLAPMGT 1458

Query: 1389 G 1389
            G
Sbjct: 1459 G 1459



 Score = 76.3 bits (186), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 68/293 (23%), Positives = 127/293 (43%), Gaps = 59/293 (20%)

Query: 764  GVPRIKEIINASRNISTP-IITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPD 822
            GVPR+KEI+N + NI TP ++   ++K  D   A+ ++  +E TTL  + + +E  + PD
Sbjct: 1111 GVPRLKEILNVAANIKTPSMLVRQINKKADQGDAKKLRSTIELTTLRSLTQAVELYYDPD 1170

Query: 823  DSFILIKLDMDRIRLLHLEVDIDSI---------RYCIERTRGISGHLT---VSGHSFLI 870
                 ++ D D +    +  + D +         R  ++R + +   +T   V+G     
Sbjct: 1171 IQSTRVEDDQDMVESYFILPEEDEVIESQSKWLLRIILDRKKLLDKSITIGEVAGKIKEE 1230

Query: 871  LKPK----DSSKSFNSKMYQMK---------------------------QLLPSVVIKGV 899
             KP      S ++ + ++ +++                            LL  V ++GV
Sbjct: 1231 FKPNLAVIFSDENADEQVMRVRFIWDQNLTKDDEDEDERDERWMRKLEQHLLDDVTLRGV 1290

Query: 900  QGINRAVI---------------HEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSN 944
             G+ RA I               H +      ++ L   G  L +V++  GV      SN
Sbjct: 1291 PGVERAFIREHCVTKKRDDGSLLHSKSSPECKEWVLDTTGTALAEVLSIPGVDATTTYSN 1350

Query: 945  NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +  E+   LGIEAAR+ ++ E+ +V+   G  ++ RH  L+ D+M  +G ++ 
Sbjct: 1351 SFIEILAVLGIEAARAGLLKELGMVLSFDGSYVNHRHMALLVDIMCQRGVLMA 1403



 Score = 72.8 bits (177), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 56/216 (25%), Positives = 104/216 (48%), Gaps = 28/216 (12%)

Query: 112 QRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQ 171
           ++ P   GL D ++GT  +  +C+TC +++  C GHFG+I+L  PVFH+G+   +  +L+
Sbjct: 47  KQKPREQGLNDPKLGTIDRMYHCSTCKEDIQVCPGHFGHIELHTPVFHVGFVVKIKKLLE 106

Query: 172 SICKNPTCARVLLGEEKAAGFRAKLRNP-ALSYLVRKSLKK---KILETTKKVSVCPHCG 227
           ++C   TC  +          +A   +P  ++    K  KK   KI   ++  S C   G
Sbjct: 107 TVCH--TCGLI----------KADFNHPDWIAATKTKDAKKRFDKIWRMSRTKSTCDADG 154

Query: 228 EINGVVKKCGLLKISH---EKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQ 284
             +G   K  + KI H      +  T +KD +   L A + +  K + +    +K    +
Sbjct: 155 PDSG---KDKIPKIPHGGCGSAQPDTIRKDGL--KLTATWKQKKKEDDDGSGDRK----E 205

Query: 285 TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
            + P +   +F+ +    + LL +NA+ ++P  +IL
Sbjct: 206 VITPKQAQTIFKLMTENTLALLGLNADYARPEWMIL 241



 Score = 57.8 bits (138), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 24/38 (63%), Positives = 30/38 (78%)

Query: 1108 EKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            +++++A + P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1065 DRFLKAAVAPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1102


>gi|13542012|ref|NP_111700.1| DNA-directed RNA polymerase subunit A' [Thermoplasma volcanium
           GSS1]
 gi|14325445|dbj|BAB60349.1| DNA-directed RNA polymerase A' [Thermoplasma volcanium GSS1]
          Length = 886

 Score =  162 bits (409), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 94/276 (34%), Positives = 147/276 (53%), Gaps = 48/276 (17%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + D+VLFNRQPSLH++S+M H  +VLP +TFRFN  VCTPYNADFDGDEMN+H+ Q EEA
Sbjct: 421 EGDIVLFNRQPSLHRMSMMGHTVRVLPGQTFRFNLAVCTPYNADFDGDEMNLHVIQKEEA 480

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+++M  +  +++PR G  +I    D +T  +LLT  N  F +
Sbjct: 481 RAE--------------ARIIMKVQEQIMSPRFGRPIIGGIHDHVTAMFLLTHNNPLFTQ 526

Query: 461 AQTMRIA----STLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRD 516
            + + I       LI D + + G  K++                ++G+ IFS IL     
Sbjct: 527 EEMIHIMCYVDPDLIPDATIVNG--KKY----------------YSGRNIFSTIL----- 563

Query: 517 CPVNANLKTKGRAYTANEEFCH-----RDSYVILRNSELLAGSMDKSTLGSGGKANVFYI 571
            P   NL+ + +  + + E C       D+YV + + +L+ G++D++ +     A +   
Sbjct: 564 -PKGLNLRFRSKLCSGSSETCEYEKEKEDTYVTIVDGKLIHGTIDEAAISPFSGA-IIDK 621

Query: 572 LLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           + R FG + A   + R++R+   ++   GFS GI D
Sbjct: 622 IFRKFGPNEAAKFIDRMTRLAVGFITYYGFSTGISD 657



 Score =  103 bits (258), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 62/247 (25%), Positives = 114/247 (46%), Gaps = 43/247 (17%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D +++ S +++++ + Y  D    PI HGL+D  MG  +    C TCG  + +C GHFG+
Sbjct: 19  DEIRKLSQVKVITADTY--DDDGYPIEHGLMDLHMGVIEPGLRCATCGGKVDECPGHFGH 76

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           I+L +PV H+G+ + +   L + CK  +C R+ L +++   +  +++         + ++
Sbjct: 77  IELAMPVVHVGFVKEIKMFLDATCK--SCGRIKLTDDEIKTYLPEVQKVDFETGDPEDIE 134

Query: 211 ---KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEA 267
              K+ ++   +  VCPHCG                        ++  I+ D    + E 
Sbjct: 135 LMTKRFVDLASQRMVCPHCG-----------------------AQQSKIILDKPTTFREE 171

Query: 268 VKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPP 327
                        G    + P E+ +  E IP +D+     N + ++P  +ILT L VPP
Sbjct: 172 -------------GTNVKITPKEIRERLERIPDDDLVFFGFNPKTARPEWMILTVLPVPP 218

Query: 328 NCIRPSV 334
             +RPS+
Sbjct: 219 INVRPSI 225



 Score = 88.2 bits (217), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 41/76 (53%), Positives = 57/76 (75%), Gaps = 7/76 (9%)

Query: 597 MNRGF------SIGIGDV-TPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAET 649
           +NRG+          GD+    +GFV++S+ +GLTPTE+FFH++GGREGLVDTAV+T+ +
Sbjct: 764 LNRGYYNRTLPHFKRGDIGADARGFVKSSYMTGLTPTEYFFHSIGGREGLVDTAVRTSRS 823

Query: 650 GYMQRRLVKSLEDLCV 665
           GYMQRRL+ + EDL V
Sbjct: 824 GYMQRRLINAFEDLKV 839


>gi|124028421|ref|YP_001013741.1| DNA-directed RNA polymerase subunit A'' [Hyperthermus butylicus DSM
            5456]
 gi|123979115|gb|ABM81396.1| DNA-directed RNA polymerase subunit A'' [Hyperthermus butylicus DSM
            5456]
          Length = 424

 Score =  162 bits (409), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 111/338 (32%), Positives = 181/338 (53%), Gaps = 53/338 (15%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFVP 1157
            +Y  +++EP   VG +AAQSIGEPGTQMTL+TFH+AG              E ++    P
Sbjct: 65   EYEYSKVEPGEPVGTVAAQSIGEPGTQMTLRTFHYAGIREFNVTLGLPRFIELVDARREP 124

Query: 1158 DDSFILIKLDMD-------------RIRLLHL-----EVDID--SIRYCIE------RTR 1191
                + I LD +             RI    +     EVDID  ++R  I+        +
Sbjct: 125  STPIMHIYLDEEHRYDENKAKEVARRIEFTRVINVASEVDIDLVNMRMVIKLDPVMLEDK 184

Query: 1192 GIS-------------GHLTVSGHSFLILK-PKDSSKSFNS-KMYQMKQLLPSVVIKGVQ 1236
            G++             G +     + L+L  P + S+ F+   + + ++ + +  IKG++
Sbjct: 185  GVTVEQVKKALERLKLGKVEQDPSNPLVLYIPIEISEGFSIIDLQKKREKILNAKIKGIR 244

Query: 1237 GINRAVIHE-EDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAAR 1295
             I R +I      +G T+Y L+ EG NL++V+   GV   +  +N+ +E+ + LGIEAAR
Sbjct: 245  KIRRVIIQSITGPDGRTEYFLVTEGSNLKEVLEVPGVDPRRIYTNSIHEIEEVLGIEAAR 304

Query: 1296 STIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENT 1355
            + ++ E+K V++  G+ +D RH MLVAD+MT  G V  I RHG++  K S    A+FE T
Sbjct: 305  TMLIREMKDVLDEQGLDVDIRHLMLVADIMTMTGRVRQIGRHGVSGEKPSPFARAAFEMT 364

Query: 1356 SDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            + +L+ AA  G+ D + GV+E +I+G  + VGTG++++
Sbjct: 365  TQNLYAAAVEGEVDRLLGVAETVIVGGVIRVGTGMVEV 402



 Score =  105 bits (263), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 77/237 (32%), Positives = 136/237 (57%), Gaps = 11/237 (4%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR  E+++A R  STPI+  YLD++   D + A+ V  R+E T +  V   ++   V 
Sbjct: 110 GLPRFIELVDARREPSTPIMHIYLDEEHRYDENKAKEVARRIEFTRVINVASEVDIDLV- 168

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILK-PKDSSKSF 880
            +  ++IKLD   + L    V ++ ++  +ER +   G +     + L+L  P + S+ F
Sbjct: 169 -NMRMVIKLDP--VMLEDKGVTVEQVKKALERLK--LGKVEQDPSNPLVLYIPIEISEGF 223

Query: 881 NS-KMYQMKQLLPSVVIKGVQGINRAVIHE-EDVEGVTKYKLLVEGDNLRDVMATYGVKG 938
           +   + + ++ + +  IKG++ I R +I      +G T+Y L+ EG NL++V+   GV  
Sbjct: 224 SIIDLQKKREKILNAKIKGIRKIRRVIIQSITGPDGRTEYFLVTEGSNLKEVLEVPGVDP 283

Query: 939 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            +  +N+ +E+ + LGIEAAR+ ++ E+K V++  G+ +D RH MLVAD+MT  G V
Sbjct: 284 RRIYTNSIHEIEEVLGIEAARTMLIREMKDVLDEQGLDVDIRHLMLVADIMTMTGRV 340


>gi|448366552|ref|ZP_21554675.1| DNA-directed RNA polymerase subunit A'' [Natrialba aegyptia DSM
            13077]
 gi|445654007|gb|ELZ06863.1| DNA-directed RNA polymerase subunit A'' [Natrialba aegyptia DSM
            13077]
          Length = 399

 Score =  162 bits (409), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 104/344 (30%), Positives = 175/344 (50%), Gaps = 59/344 (17%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A+A   +Y+  ++EP   VG ++AQSIGEPGTQ+T+ TFH+AG            + E +
Sbjct: 48   AKAVEARYIDTRVEPLEPVGTVSAQSIGEPGTQLTMNTFHYAGVAEIDVTQGLPRLIELV 107

Query: 1152 EEVFVPDDSFILIKLD----------------MDRIRLLHL----------EVDI----- 1180
            +    PD   + + L+                ++  ++L L           V I     
Sbjct: 108  DARKTPDTPMMTVYLEDEYATEREKAHEVVWNIEATKILALGDVSTNVADMRVQISLNEE 167

Query: 1181 ---------DSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVV 1231
                     D +   IE   G+     +   + +   P++ S      + Q+ + L  + 
Sbjct: 168  TLEERLITPDEVAEIIEDNLGVKA---IQNDTEIEFGPEEPSYR---DLLQLVEELRDIT 221

Query: 1232 IKGVQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLG 1290
             KG++ ++R VI  E+++ G  ++ L  EG    D +   GV   + + NN +E+++ LG
Sbjct: 222  FKGIEEVSRVVIRREELDDGDEQFVLYTEGSAFGDALEIEGVDASRTTCNNIHEIHRNLG 281

Query: 1291 IEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNL 1349
            IEAAR  I+ E    +   G+  ++ RH MLVAD+MT++GE+  I RHG++  K+SVL  
Sbjct: 282  IEAAREAIIEETNNTLAEQGLDDVNVRHLMLVADIMTNRGEIESIGRHGISGSKDSVLAR 341

Query: 1350 ASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            A+FE T +HL +AA +G+ D + GV+E +I+G P+ +GTG + L
Sbjct: 342  AAFEVTVNHLLNAAIHGEIDELDGVAENVIVGKPIKLGTGDVDL 385



 Score = 94.7 bits (234), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 65/239 (27%), Positives = 123/239 (51%), Gaps = 21/239 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T YL+ +  T+ + A  V   +E T    LG+V   + ++
Sbjct: 99  GLPRLIELVDARKTPDTPMMTVYLEDEYATEREKAHEVVWNIEATKILALGDVSTNVADM 158

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSK 878
            V        ++ ++   L    +  D +   IE   G+     +   + +   P++ S 
Sbjct: 159 RV--------QISLNEETLEERLITPDEVAEIIEDNLGVKA---IQNDTEIEFGPEEPSY 207

Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVE-GVTKYKLLVEGDNLRDVMATYGVK 937
                + Q+ + L  +  KG++ ++R VI  E+++ G  ++ L  EG    D +   GV 
Sbjct: 208 R---DLLQLVEELRDITFKGIEEVSRVVIRREELDDGDEQFVLYTEGSAFGDALEIEGVD 264

Query: 938 GVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEV 995
             + + NN +E+++ LGIEAAR  I+ E    +   G+  ++ RH MLVAD+MT++GE+
Sbjct: 265 ASRTTCNNIHEIHRNLGIEAAREAIIEETNNTLAEQGLDDVNVRHLMLVADIMTNRGEI 323


>gi|290983563|ref|XP_002674498.1| RNA polymerase II [Naegleria gruberi]
 gi|284088088|gb|EFC41754.1| RNA polymerase II [Naegleria gruberi]
          Length = 1757

 Score =  162 bits (409), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 96/270 (35%), Positives = 149/270 (55%), Gaps = 30/270 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DV+LFNRQPSLHK+S+M HR KV+P+ TFR N  V TPYNADFDGDEMN+H+PQ+ + 
Sbjct: 415 DGDVILFNRQPSLHKMSMMGHRIKVMPYSTFRMNLSVTTPYNADFDGDEMNLHVPQSLQT 474

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE L               LM    N++TP++   +IA  QD +     LT+++ F  +
Sbjct: 475 KAELLE--------------LMMVPRNIITPQSNRPVIALVQDTLLAASKLTRRDVFIAK 520

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPV-VFVRTAVIWTGKQIFSLIL-KPNRDCP 518
              M     LI    D  G +         PV   ++   +WTGKQ+F+ +L K N +  
Sbjct: 521 DLMMNCLMHLI----DFDGKL---------PVPAILKPKPLWTGKQLFTFLLPKVNLENT 567

Query: 519 VNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            + +     +    + +    D+ V++   EL++G +DK +LGS    ++ +I++ + G 
Sbjct: 568 SSTHEDLTDKKDHLDHDIPEFDTKVLIDRGELVSGVLDKKSLGS-SHGSLIHIIVNEKGV 626

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           +     + +  R+ + +L+NRGFSIGIGD 
Sbjct: 627 NEGKKFLGQCQRVINHWLINRGFSIGIGDT 656



 Score =  100 bits (250), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 42/57 (73%), Positives = 52/57 (91%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV NS+  GLTP EFFFHTMGGREGL+DTAVKT+ETGY+QRRL+K++ED+ V+YD
Sbjct: 784 RGFVANSYLRGLTPQEFFFHTMGGREGLIDTAVKTSETGYIQRRLIKAMEDIMVKYD 840



 Score = 97.8 bits (242), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 57/177 (32%), Positives = 96/177 (54%), Gaps = 9/177 (5%)

Query: 1226 LLPSVVIKGVQGINRAVIHEED---------VEGVTKYKLLVEGDNLRDVMATYGVKGVK 1276
            +L  + +KG + + +  + EE+         V  V ++ L  EG NL  V++   V    
Sbjct: 1295 MLNELALKGYKDLKKVFLREENDKKVFSSSGVATVKQWVLDTEGCNLLAVLSHPYVDHTI 1354

Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITR 1336
             +SN+  E+   LGIEA R+ +M E++ V+E  G  +++RH  ++ D+MT +G ++ ITR
Sbjct: 1355 TTSNDVNEILDVLGIEACRNALMREMRKVIEFDGSYVNYRHLAILCDVMTHRGGLMAITR 1414

Query: 1337 HGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            HG+ +     L   SFE T + L +AA +  TD + GVS  +++G    +GTG   L
Sbjct: 1415 HGINRSDTGPLMRCSFEETVEILIEAATFADTDTLKGVSANVMVGQLAPIGTGCFGL 1471



 Score = 94.4 bits (233), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 78/235 (33%), Positives = 115/235 (48%), Gaps = 41/235 (17%)

Query: 115 PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSIC 174
           P   GL+D RMGT     +C TCG N ++C GHFG++ +  PVF++ +   V+ +LQS+C
Sbjct: 17  PKESGLMDLRMGTIDHHLSCLTCGGNATECPGHFGHVRI-HPVFNVLFINTVVKVLQSVC 75

Query: 175 KNPTCARVL-----LGEEKAAGF-RAKLRNPALSYLVRKSLKKKILETTKK-------VS 221
            +  C ++L     L  +KA+ F   + R   +  L RK   K I+ET  K        +
Sbjct: 76  IH--CGKLLADKSSLQFKKASKFVNRRKRFKEMIDLCRKD--KCIIETGNKENEQNQEAN 131

Query: 222 VCPHCGEINGVVKKCGLL--KISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKK 279
           + P     NG    CG L  KIS +  K            + AEY +      + E  K 
Sbjct: 132 IDPTFQPRNG----CGGLQPKISRDGLK------------IFAEYKKDTSAEAKQELTK- 174

Query: 280 FGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSV 334
               Q L     LQ+F+ IP ED+ LL  + + ++P  +ILT L +PP  +RPSV
Sbjct: 175 ----QELTAERALQIFKRIPAEDLELLGFDKDNARPEWMILTCLPIPPPQVRPSV 225



 Score = 58.2 bits (139), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 34/117 (29%), Positives = 63/117 (53%), Gaps = 9/117 (7%)

Query: 890  LLPSVVIKGVQGINRAVIHEED---------VEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
            +L  + +KG + + +  + EE+         V  V ++ L  EG NL  V++   V    
Sbjct: 1295 MLNELALKGYKDLKKVFLREENDKKVFSSSGVATVKQWVLDTEGCNLLAVLSHPYVDHTI 1354

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SN+  E+   LGIEA R+ +M E++ V+E  G  +++RH  ++ D+MT +G ++ 
Sbjct: 1355 TTSNDVNEILDVLGIEACRNALMREMRKVIEFDGSYVNYRHLAILCDVMTHRGGLMA 1411



 Score = 55.5 bits (132), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 30/74 (40%), Positives = 47/74 (63%), Gaps = 2/74 (2%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KE++N ++NI TP +T YL+ +   D + A++VK  LE TTLG V      V+ P
Sbjct: 1106 GVPRLKELLNVAKNIKTPGLTIYLNNEYIGDFEKAKMVKEDLEYTTLGHVTAATSIVYDP 1165

Query: 822  DDSFILIKLDMDRI 835
            + +  +I+ D + I
Sbjct: 1166 EPANSVIEEDREFI 1179



 Score = 52.4 bits (124), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 23/39 (58%), Positives = 28/39 (71%)

Query: 1107 REKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            R ++     +P   VG++AAQSIGEP TQMTL TFHFAG
Sbjct: 1059 RMRFHNCLAQPGEMVGSVAAQSIGEPATQMTLNTFHFAG 1097


>gi|330931381|ref|XP_003303389.1| hypothetical protein PTT_15561 [Pyrenophora teres f. teres 0-1]
 gi|311320680|gb|EFQ88526.1| hypothetical protein PTT_15561 [Pyrenophora teres f. teres 0-1]
          Length = 1738

 Score =  162 bits (409), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 90/271 (33%), Positives = 147/271 (54%), Gaps = 33/271 (12%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D+DV++FNRQPSLHK S+M HR KV+P+ TFR N  V +PYNADFDGDEMN+H+PQ++E
Sbjct: 445 NDDDVIIFNRQPSLHKESMMGHRVKVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSDE 504

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE                + M  K  +V+P+  + L+   QD + G Y +++++ F  
Sbjct: 505 TRAEV-------------QNLCMVPK-QIVSPQKNQPLMGIVQDTLLGVYKMSRRDNFIG 550

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
             Q M I    +    D  GI+         P + ++   +WTGKQ+ S+        P 
Sbjct: 551 IEQVMPI----LMWVPDWDGIVPE-------PAI-LKPRPLWTGKQLVSMAF------PK 592

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
             N++ K    + + +   RD  +++++ +L+ G + K  +G+     V +I+  + G D
Sbjct: 593 EVNIEKKEDDSSPSPQNDIRDKSLMIKSGQLIYGQVTKKIVGASA-GGVIHIIFNELGPD 651

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
            AV       R+ +++L++ GFS G+GD  P
Sbjct: 652 AAVKFFNACQRICNWWLLHHGFSFGVGDTIP 682



 Score =  101 bits (251), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTP+EFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+ V
Sbjct: 802 DYSPESRGFVENSYLRGLTPSEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDVMV 861

Query: 666 QYD 668
           +YD
Sbjct: 862 KYD 864



 Score = 98.2 bits (243), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 59/180 (32%), Positives = 92/180 (51%), Gaps = 15/180 (8%)

Query: 1225 QLLPSVVIKGVQGINRAVI---------------HEEDVEGVTKYKLLVEGDNLRDVMAT 1269
             LL  V ++GV G+ RA I               H +      ++ L   G  L +V++ 
Sbjct: 1280 HLLDDVTLRGVPGVERAFIREHCVTKKRDDGSLLHSKSSPECKEWVLDTTGTALAEVLSI 1339

Query: 1270 YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 1329
             GV      SN+  E+   LGIEAAR+ ++ E+ +V+   G  ++ RH  L+ D+M  +G
Sbjct: 1340 PGVDASTTYSNSFIEILAVLGIEAARAGLLKELGMVLSFDGSYVNHRHMALLVDIMCQRG 1399

Query: 1330 EVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
             ++ ITRHG+ +     L   SFE T + L +AA +G+ D   GVSE I++G    +GTG
Sbjct: 1400 VLMAITRHGINRNDTGALMRCSFEETVEILLEAAGFGELDDCRGVSENIMLGQLAPMGTG 1459



 Score = 77.4 bits (189), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 69/293 (23%), Positives = 127/293 (43%), Gaps = 59/293 (20%)

Query: 764  GVPRIKEIINASRNISTP-IITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPD 822
            GVPR+KEI+N + NI TP ++   +DK  D   A+ ++  +E TTL  + + +E  + PD
Sbjct: 1111 GVPRLKEILNVAANIKTPSMLVRQIDKKADQGDAKKLRSTIELTTLRSLTQAVELYYDPD 1170

Query: 823  DSFILIKLDMDRIRLLHLEVDIDSI---------RYCIERTRGISGHLT---VSGHSFLI 870
                 ++ D D +    +  + D +         R  ++R + +   +T   V+G     
Sbjct: 1171 IQSTRVEDDQDMVESYFILPEEDEVIESQSKWLLRIILDRKKLLDKSITIGEVAGKIKEE 1230

Query: 871  LKPK----DSSKSFNSKMYQMK---------------------------QLLPSVVIKGV 899
             KP      S ++ + ++ +++                            LL  V ++GV
Sbjct: 1231 FKPNLAVIFSDENADEQVMRVRFIWDQNLTKDDEDEDERDERWMRKLEHHLLDDVTLRGV 1290

Query: 900  QGINRAVI---------------HEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSN 944
             G+ RA I               H +      ++ L   G  L +V++  GV      SN
Sbjct: 1291 PGVERAFIREHCVTKKRDDGSLLHSKSSPECKEWVLDTTGTALAEVLSIPGVDASTTYSN 1350

Query: 945  NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +  E+   LGIEAAR+ ++ E+ +V+   G  ++ RH  L+ D+M  +G ++ 
Sbjct: 1351 SFIEILAVLGIEAARAGLLKELGMVLSFDGSYVNHRHMALLVDIMCQRGVLMA 1403



 Score = 72.0 bits (175), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 56/216 (25%), Positives = 103/216 (47%), Gaps = 28/216 (12%)

Query: 112 QRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQ 171
           ++ P   GL D ++GT  +  +C+TC +++  C GHFG+I+L  PVFH+G+   +  +L+
Sbjct: 47  KQKPREQGLNDPKLGTIDRMYHCSTCKEDIQVCPGHFGHIELHTPVFHVGFVVKIKKLLE 106

Query: 172 SICKNPTCARVLLGEEKAAGFRAKLRNP-ALSYLVRKSLKK---KILETTKKVSVCPHCG 227
           ++C   TC  +          +A   +P  ++    K  KK   KI   ++  S C   G
Sbjct: 107 TVCH--TCGLI----------KADFNHPDWIAATKTKDAKKRFDKIWRMSRTKSTCDADG 154

Query: 228 EINGVVKKCGLLKISH---EKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQ 284
              G   K  + KI H      +  T +KD +   L A + +  K + +    +K    +
Sbjct: 155 PDAG---KDKIPKIPHGGCGSAQPDTIRKDGL--KLTATWKQKKKEDDDGSGDRK----E 205

Query: 285 TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
            + P +   +F+ +    + LL +NA+ ++P  +IL
Sbjct: 206 VITPKQAQTIFKLMTENTLALLGLNADYARPEWMIL 241



 Score = 57.8 bits (138), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 24/38 (63%), Positives = 30/38 (78%)

Query: 1108 EKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            +++++A + P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1065 DRFLKAAVAPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1102


>gi|12642612|gb|AAK00310.1|AF315820_1 DNA-dependent RNA polymerase II largest subunit RPB1 [Glaucosphaera
           vacuolata]
          Length = 1746

 Score =  162 bits (409), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 90/271 (33%), Positives = 143/271 (52%), Gaps = 42/271 (15%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D V+FNRQPSLHK+SIM HR KV+ + +FR N    +PYNADFDGDEMN+H+PQ+ +A
Sbjct: 424 DGDYVIFNRQPSLHKMSIMGHRVKVMRYSSFRLNLSCTSPYNADFDGDEMNLHVPQSPQA 483

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE +               LM     +V+P+  + ++   QD + G  L TQ++ F  +
Sbjct: 484 RAEVM--------------QLMMVPRCIVSPQGNKPVMGIVQDTLVGTMLFTQRDTFMEK 529

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWN----PVVFVRTAVIWTGKQIFSLILKPNRD 516
              M +                   +R W+    P   ++   +WTGKQ+FS+IL     
Sbjct: 530 DLVMNLL----------------LHFRGWDGVIPPPAILKPRQLWTGKQLFSMILP---- 569

Query: 517 CPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
              + NL      +  ++     D+ V++   ELL+G++DK T+GS   + + ++  ++ 
Sbjct: 570 ---DVNLVRFSNTHDDDDIENAGDTKVLISRGELLSGTVDKRTVGSAANS-LVHVTWKEH 625

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           G + A   +  +  + + +L+ RGFSIGIGD
Sbjct: 626 GPEGACDLISNIQTLVNHWLLQRGFSIGIGD 656



 Score =  110 bits (275), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 63/179 (35%), Positives = 102/179 (56%), Gaps = 10/179 (5%)

Query: 1226 LLPSVVIKGVQGINRAVIHEED-------VEGVT---KYKLLVEGDNLRDVMATYGVKGV 1275
            LL  + + GV  I +  + E D         G++   ++ L  +G NL  VM+   V   
Sbjct: 1292 LLSEMNLGGVPDIKKVYMREADRIVPDPRTGGLSVEKEWVLDTDGTNLLAVMSHKDVDYT 1351

Query: 1276 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGIT 1335
            +  SN+  E++ TLGIE  R+ ++ EI+ V+   G  +++RH  ++AD+MT +G ++ IT
Sbjct: 1352 RTVSNDVVEMFVTLGIEGVRAALLNEIRGVISFDGAYVNYRHLAILADIMTCRGHIMSIT 1411

Query: 1336 RHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            RHG+ +++   L   SFE T+D L +AA YG+ D + GV+E I++G    VGTG   LL
Sbjct: 1412 RHGINRVETGALMRCSFEETADILLEAAMYGEVDDMKGVAENIMLGQMAPVGTGEFGLL 1470



 Score = 99.8 bits (247), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/65 (67%), Positives = 56/65 (86%), Gaps = 1/65 (1%)

Query: 605 IGDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDL 663
           + D+ P  +GFV+NS+  GLT TEFFFH MGGREGL+DTAVKT+ETGY+QRRL+K+LED+
Sbjct: 777 LDDLGPESRGFVENSYLRGLTATEFFFHAMGGREGLIDTAVKTSETGYIQRRLIKALEDV 836

Query: 664 CVQYD 668
            V+YD
Sbjct: 837 MVKYD 841



 Score = 91.7 bits (226), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 65/240 (27%), Positives = 112/240 (46%), Gaps = 50/240 (20%)

Query: 115 PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSIC 174
           P   GL+D R+G   ++  C TC  +  +C GHFG+I+L  P+F+IG+F   + +L+ +C
Sbjct: 49  PKTEGLMDPRLGAIGRDLPCKTCHCDEKNCPGHFGHIELVKPMFNIGFFGMTLRVLRCVC 108

Query: 175 KNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK--------KKILETTKKVSVCPHC 226
               C+++L+            R+P   + V+K L+        KK+     KV +C HC
Sbjct: 109 F--FCSKLLIDP----------RDPKADFEVKKVLRIKNRINRLKKVQNLCSKVKICKHC 156

Query: 227 GEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTL 286
                   K GL                        ++    K + +    KK    Q +
Sbjct: 157 SNEQPKFAKEGL------------------------QFRAEFKGSADDTMEKK----QIV 188

Query: 287 NPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDNDV 344
           +  +VL +F+ I  +DI ++ ++ + S+P   ILT   VPP  IRPSV+ D  ++ ++D+
Sbjct: 189 SAEKVLSIFKHISDDDIEIMGLSPQHSRPEWFILTLFPVPPPHIRPSVMMDASMRGEDDL 248



 Score = 80.5 bits (197), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 71/294 (24%), Positives = 135/294 (45%), Gaps = 61/294 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVF-- 819
            GVPR+KEIIN +++  TP +T YL  +   D + A+ V+  L+ TTL  V +  E  +  
Sbjct: 1115 GVPRLKEIINVAKHCKTPSLTVYLRGEAARDAERAKQVQAELQHTTLNHVTQSTEIYYDP 1174

Query: 820  -------------------VPDD-------SFILIKLDMDRIRLLHLEVDIDSIRYCIER 853
                               +PDD       S  L++L++ +  +   ++ ++ ++  I  
Sbjct: 1175 NPQDTVIEADQELVRSYYELPDDENSSANLSPWLLRLNLSKEMMTDRKLSMNHVKNKIHH 1234

Query: 854  TRGISGHLTVS--GHSFLILKPKDSSKSFNSKMYQMK-------------------QLLP 892
              G   ++  S    + L+L+ + +++    KM + +                    LL 
Sbjct: 1235 DLGGDVNVMASEDNDANLVLRIRIAAQKEPEKMAEGEEHAQEEEEDECLFLRKVEGSLLS 1294

Query: 893  SVVIKGVQGINRAVIHEED-------VEGVT---KYKLLVEGDNLRDVMATYGVKGVKCS 942
             + + GV  I +  + E D         G++   ++ L  +G NL  VM+   V   +  
Sbjct: 1295 EMNLGGVPDIKKVYMREADRIVPDPRTGGLSVEKEWVLDTDGTNLLAVMSHKDVDYTRTV 1354

Query: 943  SNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL 996
            SN+  E++ TLGIE  R+ ++ EI+ V+   G  +++RH  ++AD+MT +G ++
Sbjct: 1355 SNDVVEMFVTLGIEGVRAALLNEIRGVISFDGAYVNYRHLAILADIMTCRGHIM 1408



 Score = 53.9 bits (128), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 22/37 (59%), Positives = 28/37 (75%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            +++ A+  P   +GA+A QSIGEP TQMTL TFHFAG
Sbjct: 1070 RFLHAKCPPGEMIGAVAPQSIGEPATQMTLNTFHFAG 1106


>gi|290984021|ref|XP_002674726.1| RNA polymerase II largest subunit [Naegleria gruberi]
 gi|284088318|gb|EFC41982.1| RNA polymerase II largest subunit [Naegleria gruberi]
          Length = 1650

 Score =  162 bits (409), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 94/269 (34%), Positives = 145/269 (53%), Gaps = 28/269 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHK+S+M HR KV+P+ TFR N  V TPYNADFDGDEMN+HLPQ+ + 
Sbjct: 419 DGDVVLFNRQPSLHKMSMMGHRVKVMPYSTFRLNLSVVTPYNADFDGDEMNLHLPQSLQT 478

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           + E L               LM    N++TP++   LIA  QD +  G   T+++ +  +
Sbjct: 479 KTELLE--------------LMMVPKNIITPQSHRPLIALVQDTLLAGSKCTRRDVYIEK 524

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              M     L           + F+ +   P + ++   +WTGKQ+FSL+L       ++
Sbjct: 525 DVMMNCLMYL-----------QDFNGQLPVPAI-LKPKPLWTGKQLFSLLLPSIDYYGIS 572

Query: 521 ANLKTK-GRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           +    + G     ++     D+ +I+ N ELL G +DK +LGS    ++ +I++ D G  
Sbjct: 573 STHDDEVGDLKHLDDHLPEFDTGIIISNGELLTGILDKKSLGS-SHGSLIHIIVNDKGTQ 631

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
                + +   + +++L+  GFS+GIGD 
Sbjct: 632 EGKKFLGQCQHVLNYWLLQHGFSVGIGDT 660



 Score =  101 bits (251), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 44/57 (77%), Positives = 51/57 (89%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV NS+  GLTP EFFFHTMGGREGL+DTAVKTAETGY+QRRLVK++ED+ V YD
Sbjct: 788 RGFVANSYLRGLTPQEFFFHTMGGREGLIDTAVKTAETGYIQRRLVKAMEDVKVNYD 844



 Score = 98.6 bits (244), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 84/283 (29%), Positives = 137/283 (48%), Gaps = 54/283 (19%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
            GVPR+KE+++ SRNI TP +T YL  D D + A++VK  LE + LG +    + ++ PD 
Sbjct: 1090 GVPRLKELLDVSRNIKTPGLTIYLKNDNDCEIAKMVKEELEYSNLGSITRSTQIIYDPDI 1149

Query: 824  SFILIKLDMDRIRLLHLEVDID-------SIRYCIERTRGISGHLTVSGHS--------- 867
               +I+ D   IR +  E  ID       S+R+ ++R   +S HL +S  +         
Sbjct: 1150 FNSVIESDQFFIREMLEEKTIDPNTFSPWSLRFVLDREM-MSEHLNMSQIANIIKQEFQN 1208

Query: 868  --------------FLILKPKDSSKSF--------NSKMYQ--MKQL----LPSVVIKGV 899
                           LI++ ++S KS         +S M    +K+L    L  + +KG 
Sbjct: 1209 DISCFYSDDNSEELILIIRIRNSEKSKSETEDDEEDSSMIVEFLKRLESNMLSQLSLKGH 1268

Query: 900  QGINRAVIHEED---------VEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVY 950
              + +    +++         VE  T++ L  EG +L  VM+   V      SN+  EV 
Sbjct: 1269 NNLKKVFYRKDENIKFFSNKGVEKKTRWSLETEGCDLLSVMSHPQVDFRNTLSNDVIEVE 1328

Query: 951  KTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
            K LGIEA R+ +M E++ V+E  G  +++RH  ++ D+MT  G
Sbjct: 1329 KVLGIEACRNLLMKELRKVIEFDGSYVNYRHLAILCDVMTQGG 1371



 Score = 97.1 bits (240), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 55/147 (37%), Positives = 83/147 (56%)

Query: 1248 VEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVME 1307
            VE  T++ L  EG +L  VM+   V      SN+  EV K LGIEA R+ +M E++ V+E
Sbjct: 1290 VEKKTRWSLETEGCDLLSVMSHPQVDFRNTLSNDVIEVEKVLGIEACRNLLMKELRKVIE 1349

Query: 1308 NHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQ 1367
              G  +++RH  ++ D+MT  G +  +TRHGLA+     L   SFE T + L +AA +  
Sbjct: 1350 FDGSYVNYRHLAILCDVMTQGGVITAVTRHGLARSDNGPLMRCSFEQTVEVLVEAAQFSD 1409

Query: 1368 TDCISGVSECIIMGLPMNVGTGLIKLL 1394
             D + GVS  +++G    +GTG   L+
Sbjct: 1410 VDTLKGVSANVMVGKLAPIGTGTFDLV 1436



 Score = 78.2 bits (191), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 108/235 (45%), Gaps = 43/235 (18%)

Query: 115 PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSIC 174
           P   GL+D RMGT     +C TCG  +S+C GHFG++++  P F+I + + ++ IL+  C
Sbjct: 47  PKEGGLMDLRMGTVNSALSCMTCGCGVSECPGHFGHVNI-HPTFNILFLKTIVKILKCTC 105

Query: 175 KNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHC--GEINGV 232
            +  C+R+L               P    + + + K+K      K+     C   +  G 
Sbjct: 106 VH--CSRLLFNR----------NTPEFKRIQQIANKRKRFNELMKLKPMDKCMIDDYTG- 152

Query: 233 VKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVL 292
              CG +       + +  K    +  +    NE  +   EI+A              VL
Sbjct: 153 ---CGGI-------QPKISKNQLSITQIFPNSNEIKQ---EIKAES------------VL 187

Query: 293 QLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDL--KSDNDVV 345
           Q+F+ I  +D+ LL  ++  S P  +ILT L VPP  +RPSV+  L  K+++D+ 
Sbjct: 188 QIFKRISTQDLELLGFDSINSNPEWMILTCLPVPPPHVRPSVMHGLNDKAEDDLT 242



 Score = 50.8 bits (120), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 21/36 (58%), Positives = 26/36 (72%)

Query: 1110 YVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            ++   ++P   VG +AAQSIGEP TQMTL TFH AG
Sbjct: 1046 FLNGLVQPGEMVGCIAAQSIGEPATQMTLNTFHNAG 1081


>gi|430812931|emb|CCJ29676.1| unnamed protein product [Pneumocystis jirovecii]
          Length = 1762

 Score =  162 bits (409), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 92/278 (33%), Positives = 149/278 (53%), Gaps = 54/278 (19%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D DVV+FNRQPSLHK+S+M HR KV+P+ TFR N  V  PYNADFDGDEMN+H+PQ+EE
Sbjct: 441 TDGDVVIFNRQPSLHKMSMMGHRVKVMPYSTFRINLSVTPPYNADFDGDEMNLHVPQSEE 500

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE +             ++ M  K  +V+P++ + ++   QD + G   LT+++ F +
Sbjct: 501 TRAEII-------------EICMVPK-QIVSPQSNKPVMGIVQDTLAGVKKLTRRDNFLS 546

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSW-RSWN----PVVFVRTAVIWTGKQIFSLILKPN 514
           + Q M I                   W   W+    P   ++   +WTGKQI S+++   
Sbjct: 547 KDQVMNI-----------------LLWVPEWDGNMPPPAIIKPKAMWTGKQILSMVIP-- 587

Query: 515 RDCPVNANLKTKGRAYTANEE----FCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFY 570
                      KG  +  ++E        D+ ++L N E++ G +DK T+G+  +  + +
Sbjct: 588 -----------KGINFIRDDEKQTPMTPDDTGMMLENGEIIYGIVDKKTVGA-SQGGLVH 635

Query: 571 ILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
            ++R+ G +V       +  + +++L++ GFSIGIGD 
Sbjct: 636 TIMREKGPEVCRVFFNGIQMVVNYWLLHNGFSIGIGDT 673



 Score =  108 bits (269), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 64/174 (36%), Positives = 102/174 (58%), Gaps = 9/174 (5%)

Query: 1225 QLLPSVVIKGVQGINRAVIHE-------EDVEGVTKYKLLVEGD--NLRDVMATYGVKGV 1275
             +L S+ ++GV  I+R  + E       E+ E V   + ++E D  NL +VMA   V   
Sbjct: 1275 HMLESISLRGVPNISRVFMMEHKTVYQSENGEFVRGEEWVLETDGINLAEVMAVENVDPR 1334

Query: 1276 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGIT 1335
            +  SN+  E+ + LGIEA R+ ++ E++ V+E  G  +++RH  L+AD MTS+G ++ IT
Sbjct: 1335 RTYSNSFVEILQVLGIEATRAALLKELRNVIEFDGSYVNYRHLSLLADTMTSRGHLMAIT 1394

Query: 1336 RHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
            RHG+ + +  VL   SFE T + L +AA  G+ D   G+SE I++G    +GTG
Sbjct: 1395 RHGINRAETGVLMRCSFEETVEILMEAAAAGEMDDCRGISENIMLGQLAPLGTG 1448



 Score =  100 bits (249), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 48/81 (59%), Positives = 60/81 (74%), Gaps = 8/81 (9%)

Query: 613 GFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFD 672
           GF++NS+  GLTP EFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+ V+YD +  
Sbjct: 802 GFIENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDVMVKYDGTVR 861

Query: 673 AAF-------YGQTDCISGVS 686
            +        YG+ D + GVS
Sbjct: 862 NSLGDIIQLVYGE-DGLDGVS 881



 Score = 88.6 bits (218), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 77/291 (26%), Positives = 132/291 (45%), Gaps = 57/291 (19%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N ++ I TP +T YL  +   D++ A+ V+  +E TTL  V    E  + P
Sbjct: 1102 GVPRLKEILNVAKTIKTPSLTIYLTPEVSKDMESAKQVQTAIEHTTLKTVTSVTEIFYDP 1161

Query: 822  DDSFILIKLDMDRIR--------------------LLHLEVDIDSIRYCIERTRGISGHL 861
            D    +I+ D   +                     LL LE+D   +         ++  +
Sbjct: 1162 DPQQTVIEEDRTFVEAFFAIPDEDVEANLHRQSSWLLRLELDRAKMLDKKLSMSDVAAKI 1221

Query: 862  TVSGH-SFLILKPKDSSKSFNSKMYQMK-------------------------QLLPSVV 895
            T S H    ++  +D++     +   +K                          +L S+ 
Sbjct: 1222 TESFHKDLFVIWSEDNADKLVIRCRVIKDEEKSFDDDDDDPIEEDVLLKRIESHMLESIS 1281

Query: 896  IKGVQGINRAVIHE-------EDVEGVTKYKLLVEGD--NLRDVMATYGVKGVKCSSNNT 946
            ++GV  I+R  + E       E+ E V   + ++E D  NL +VMA   V   +  SN+ 
Sbjct: 1282 LRGVPNISRVFMMEHKTVYQSENGEFVRGEEWVLETDGINLAEVMAVENVDPRRTYSNSF 1341

Query: 947  YEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             E+ + LGIEA R+ ++ E++ V+E  G  +++RH  L+AD MTS+G ++ 
Sbjct: 1342 VEILQVLGIEATRAALLKELRNVIEFDGSYVNYRHLSLLADTMTSRGHLMA 1392



 Score = 87.0 bits (214), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 64/218 (29%), Positives = 105/218 (48%), Gaps = 42/218 (19%)

Query: 119 GLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPT 178
           GLLD R+GT  +   C TCG+++++C GHFG+I+L  PVFHIG+   +  IL+ +C N  
Sbjct: 55  GLLDPRLGTIDRNFKCQTCGESMAECPGHFGHIELAKPVFHIGFLMKIKKILECVCLN-- 112

Query: 179 CARVLLGEEKAAGF--RAKLRNPALSYLVRKSL--KKKILETTKKV-------SVCPH-- 225
           C + L  +E +  F    + R+P    +   ++   K I E  + V       S+  H  
Sbjct: 113 CGK-LKADENSPKFLESQRYRDPKSRLIAVWNICKTKMICEIDQPVNDHYEAKSMIGHGG 171

Query: 226 CGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQT 285
           CG +  +++K GL   +  K   R K  ++ + D                        + 
Sbjct: 172 CGNLQPIIRKDGLKLWATYK---RPKDSESDLPDR-----------------------RL 205

Query: 286 LNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRL 323
           L PLEV  +F+ I  ED+  + +N E ++P  +I+T L
Sbjct: 206 LTPLEVYTVFKHISSEDMAKMGLNEEYARPDWMIITVL 243



 Score = 52.8 bits (125), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 22/37 (59%), Positives = 27/37 (72%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            +++ +   P   VG LAAQSIGEP TQMTL TFH+AG
Sbjct: 1057 RFIHSVANPGEMVGTLAAQSIGEPATQMTLNTFHYAG 1093


>gi|327294163|ref|XP_003231777.1| DNA-directed RNA polymerase II largest subunit [Trichophyton rubrum
           CBS 118892]
 gi|326465722|gb|EGD91175.1| DNA-directed RNA polymerase II largest subunit [Trichophyton rubrum
           CBS 118892]
          Length = 1744

 Score =  162 bits (409), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 94/272 (34%), Positives = 150/272 (55%), Gaps = 35/272 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D +LFNRQPSLHK S+M+HR +V+P+ TFR N  V TPYNADFDGDEMN+H+PQ+EEA
Sbjct: 455 DGDFILFNRQPSLHKESMMSHRVRVMPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSEEA 514

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L++L ++            N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 515 RAE----LNQLCLVPL----------NIVSPQRNGPLMGIVQDTLCGIYKICRRDVFLTK 560

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M +    +    D  G++ +       P + ++    W+GKQ+ S++L      P  
Sbjct: 561 EQVMNV----LLWVPDWDGVLPQ-------PAI-LKPRPRWSGKQMISMVL------PSG 602

Query: 521 AN-LKTKGRAYTANEEFCH-RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            N L+        +E+F    D  V++   EL+ G   K T+G+ G   + + +  ++G 
Sbjct: 603 LNLLRIDKDKSPISEKFSPLADGGVLVHGGELMYGMFSKKTVGASG-GGIVHTIFNEYGP 661

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           D A++       + +++L++ GFSIGIGD  P
Sbjct: 662 DAAMSFFNGAQAVVNYWLLHNGFSIGIGDTIP 693



 Score =  103 bits (256), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 60/180 (33%), Positives = 94/180 (52%), Gaps = 15/180 (8%)

Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMAT 1269
             LL ++ ++GV GI+RA I+E+    V                ++ L   G  L DV+A 
Sbjct: 1288 HLLDTLTLRGVPGIDRAFINEKSRTRVLEDGSLHQSASDPECKEWVLETSGSALADVLAI 1347

Query: 1270 YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 1329
             G+   +  SN   E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1348 PGIDASRTYSNQFVEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLVDVMTSRG 1407

Query: 1330 EVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
             ++ +TRHG+ +     L   SFE T + L DAA + + D   GVSE +I+G     GTG
Sbjct: 1408 FLMAVTRHGINRADTGALMRCSFEETVEILLDAAAFAELDDCRGVSENLILGQMAPAGTG 1467



 Score = 99.4 bits (246), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QR+LVK+LE++ V
Sbjct: 813 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMV 872

Query: 666 QYD 668
           +YD
Sbjct: 873 KYD 875



 Score = 85.5 bits (210), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 75/289 (25%), Positives = 134/289 (46%), Gaps = 59/289 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDL--DYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N + NI TP +T Y   +  +  + A+ ++  +E T+L  V E  E  + P
Sbjct: 1119 GVPRLKEILNVATNIKTPSMTVYQAPECRMNKESAKQLRSIVEHTSLRSVTESTEIYYDP 1178

Query: 822  DDSFILIKLDMDRIR---LLHLEVDIDS-------IRYCIERTRGISGHLTVSGHSFLIL 871
            +    +I+ D+D +    ++  +V  DS       +R  + R + +   LTV   +  I 
Sbjct: 1179 NIQSTVIENDIDMVESYFIIPEDVADDSSRQSKWLLRIILSRPKLLDKGLTVQDVATKIK 1238

Query: 872  K--PKD-----SSKSFNSKMYQMKQ-------------------------LLPSVVIKGV 899
            +  P+D     S  + + ++ +++Q                         LL ++ ++GV
Sbjct: 1239 EAYPQDIAVIFSDNNADEQVVRIRQIQDPKQDEDDDDTEYDVTLKKLESHLLDTLTLRGV 1298

Query: 900  QGINRAVIHEEDVEGV---------------TKYKLLVEGDNLRDVMATYGVKGVKCSSN 944
             GI+RA I+E+    V                ++ L   G  L DV+A  G+   +  SN
Sbjct: 1299 PGIDRAFINEKSRTRVLEDGSLHQSASDPECKEWVLETSGSALADVLAIPGIDASRTYSN 1358

Query: 945  NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
               E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1359 QFVEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLVDVMTSRG 1407



 Score = 84.7 bits (208), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 60/228 (26%), Positives = 105/228 (46%), Gaps = 38/228 (16%)

Query: 110 DPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINI 169
           D ++ P   GL D R+GT  +   C TC + ++DC GHFG+I+L  PVFHIG+   +  +
Sbjct: 45  DQRQRPREKGLNDPRLGTIDRNWRCATCEEGINDCPGHFGHIELSTPVFHIGFLTKIKKL 104

Query: 170 LQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKSLKKKIL-------------- 214
           L+++C N  C ++           A + R+P   +     L K IL              
Sbjct: 105 LETVCHN--CGKIKANASDQKYLDALRFRDPKKRFDAIWRLSKDILICEADPPEEDDPFA 162

Query: 215 -ETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPE 273
            E++K V     CG +   V+K G+  +   K    +K +D + ++             E
Sbjct: 163 KESSKPVQGHGGCGNVQPQVRKEGITLMGTWK---PSKMRDMMDDN-------------E 206

Query: 274 IEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
           I+  +K    + + P   L +F  I  ED+ L+ ++ + ++P  +I+T
Sbjct: 207 IQQPEK----KQITPQMALTIFRNISEEDVRLMGLSNDYARPEWMIIT 250



 Score = 55.8 bits (133), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/41 (60%), Positives = 28/41 (68%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            A   ++ +A   P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1070 AIESRFGKAAANPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1110


>gi|300712255|ref|YP_003738069.1| DNA-directed RNA polymerase subunit A'' [Halalkalicoccus jeotgali B3]
 gi|448295948|ref|ZP_21486009.1| DNA-directed RNA polymerase subunit A'' [Halalkalicoccus jeotgali B3]
 gi|299125938|gb|ADJ16277.1| DNA-directed RNA polymerase subunit A'' [Halalkalicoccus jeotgali B3]
 gi|445582671|gb|ELY37011.1| DNA-directed RNA polymerase subunit A'' [Halalkalicoccus jeotgali B3]
          Length = 395

 Score =  162 bits (409), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 105/345 (30%), Positives = 177/345 (51%), Gaps = 60/345 (17%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A     +Y+  +++P   VG ++AQSIGEPGTQMT+ TFH+AG            + E +
Sbjct: 45   ARGVESRYLDTRVDPLDPVGTVSAQSIGEPGTQMTMNTFHYAGVAEIDVTQGLPRLIELV 104

Query: 1152 EEVFVPDDSFILIKLD----------------MDRIRLLHL------------EVDI--- 1180
            +    PD   + + L+                ++  R+L L            ++D+   
Sbjct: 105  DARKTPDTPMMTVYLEDEYATDREKAHEVVWNIEATRILALGDVSTNVADMNVQIDLNED 164

Query: 1181 ---------DSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVV 1231
                     + +   IE + G+S   TV   + +   P+  S      + Q+ + L  +V
Sbjct: 165  TLAERLLTPEEVAEIIEDSLGVS---TVQQGTAIQFGPEQPSYR---DLLQLVEELREIV 218

Query: 1232 IKGVQGINRAVIHEEDVEGVTK--YKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTL 1289
             KG++ ++R V+ +ED +      + L  EG    D +A  GV   + + NN +E+Y +L
Sbjct: 219  FKGIEEVSRVVVRKEDTDEREDEEFVLYTEGSEFGDALAIEGVDASRTTCNNIHEIYSSL 278

Query: 1290 GIEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLN 1348
            G+EAAR TI+ E    +   G+  ++ RH MLV+D+MT++G +  I RHG++  K+SVL 
Sbjct: 279  GVEAARETIINETMDTLREQGLDDVNVRHLMLVSDIMTTRGTIESIGRHGISGNKDSVLA 338

Query: 1349 LASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
             A++E T +HL DAA +G+ D ++GV E +I+G P+ +GTG + L
Sbjct: 339  RAAYEVTVNHLLDAAIHGEVDDLNGVIENVIVGKPIKLGTGDVDL 383



 Score = 92.8 bits (229), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 74/242 (30%), Positives = 126/242 (52%), Gaps = 26/242 (10%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP++T YL+ +  TD + A  V   +E T    LG+V   +   
Sbjct: 96  GLPRLIELVDARKTPDTPMMTVYLEDEYATDREKAHEVVWNIEATRILALGDVSTNVA-- 153

Query: 819 FVPDDSFILIKLDMDRI--RLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDS 876
               D  + I L+ D +  RLL  E     +   IE + G+S   TV   + +   P+  
Sbjct: 154 ----DMNVQIDLNEDTLAERLLTPE----EVAEIIEDSLGVS---TVQQGTAIQFGPEQP 202

Query: 877 SKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTK--YKLLVEGDNLRDVMATY 934
           S      + Q+ + L  +V KG++ ++R V+ +ED +      + L  EG    D +A  
Sbjct: 203 SYR---DLLQLVEELREIVFKGIEEVSRVVVRKEDTDEREDEEFVLYTEGSEFGDALAIE 259

Query: 935 GVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKG 993
           GV   + + NN +E+Y +LG+EAAR TI+ E    +   G+  ++ RH MLV+D+MT++G
Sbjct: 260 GVDASRTTCNNIHEIYSSLGVEAARETIINETMDTLREQGLDDVNVRHLMLVSDIMTTRG 319

Query: 994 EV 995
            +
Sbjct: 320 TI 321


>gi|261189983|ref|XP_002621402.1| DNA-directed RNA polymerase II largest subunit [Ajellomyces
           dermatitidis SLH14081]
 gi|239591638|gb|EEQ74219.1| DNA-directed RNA polymerase II largest subunit [Ajellomyces
           dermatitidis SLH14081]
 gi|239612830|gb|EEQ89817.1| DNA-directed RNA polymerase II largest subunit [Ajellomyces
           dermatitidis ER-3]
 gi|327351995|gb|EGE80852.1| DNA-directed RNA polymerase [Ajellomyces dermatitidis ATCC 18188]
          Length = 1746

 Score =  161 bits (408), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 97/278 (34%), Positives = 151/278 (54%), Gaps = 35/278 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DV+LFNRQPSLHK S+M HR +V+P+ TFR N  V TPYNADFDGDEMN+H+PQ+EEA
Sbjct: 456 DGDVILFNRQPSLHKESMMGHRIRVMPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L +L ++  +          +V+P+    L+   QD + G Y +  ++ F  +
Sbjct: 516 RAE----LSQLCMVPLQ----------IVSPQRNGPLMGIVQDTLCGIYKICSRDVFLTK 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M I    +    D  G+I +       P + ++    WTGKQ+ S++L      P  
Sbjct: 562 EQIMNI----LLWVPDWDGVIPQ-------PAI-LKPRPRWTGKQVISMVL------PAG 603

Query: 521 ANLKTKGRAYTA-NEEFCH-RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            NL    R     +E+F    D  +++ + EL+ G   K T+G+ G   + + +  ++G 
Sbjct: 604 LNLLRVDRDKAPLSEKFSPLTDGGLLVHSGELMYGMFSKKTVGATG-GGIIHTIFNEYGP 662

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           ++A+        + +++L++ GFSIGIGD  P    +Q
Sbjct: 663 ELAMNFFNGAQTVVNYWLLHHGFSIGIGDTIPDLATIQ 700



 Score = 99.4 bits (246), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QR+LVK+LE++ V
Sbjct: 814 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMV 873

Query: 666 QYD 668
           +YD
Sbjct: 874 KYD 876



 Score = 98.6 bits (244), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 60/180 (33%), Positives = 94/180 (52%), Gaps = 15/180 (8%)

Query: 1225 QLLPSVVIKGVQGINRAVIHEED----VEGVTKYK-----------LLVEGDNLRDVMAT 1269
             LL ++ ++GV GI RA I+E+     +E  + Y+           L   G  L +V+  
Sbjct: 1289 HLLDTLTLRGVAGIERAFINEKSRVRVLEDGSLYQSAEDPLCKEWVLETSGSALGEVLTI 1348

Query: 1270 YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 1329
             GV   +  SN   E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1349 PGVDTTRTYSNQFIEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLVDVMTSRG 1408

Query: 1330 EVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
             ++ +TRHG+ +     L   SFE T + L DAA + + D   GVSE +I+G     GTG
Sbjct: 1409 FLMAVTRHGINRADTGALMRCSFEETVEILLDAAAFAELDDCRGVSENLILGQMAPAGTG 1468



 Score = 85.5 bits (210), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 60/230 (26%), Positives = 105/230 (45%), Gaps = 40/230 (17%)

Query: 110 DPQRT-PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVIN 168
           D QR  P   GL D R+GT  +   C TC + ++DC GHFG+I+L  PVFHIG+   +  
Sbjct: 44  DEQRQRPREKGLNDPRLGTIDRNWRCATCEEGINDCPGHFGHIELSTPVFHIGFLTKIKK 103

Query: 169 ILQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKSLKKKIL------------- 214
           +L+++C N  C ++           A + R+P   +     L K +L             
Sbjct: 104 LLETVCHN--CGKIKANTTDQKYLEALRFRDPKRRFDAIWRLSKDVLICEADPSPDDDDP 161

Query: 215 ---ETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFN 271
              E +K V     CG I   ++K G+  +   K    +K +D +++D+  +  E  +  
Sbjct: 162 FGKEPSKPVHSHGGCGNIQPQIRKEGISLVGTWK---PSKNRD-MMDDMDVQQPEKRQIT 217

Query: 272 PEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
           P++                 L +F+ I  ED+ L+ ++ + ++P  +I+T
Sbjct: 218 PQM----------------ALNIFKTISEEDVRLMGLSNDYARPEWMIIT 251



 Score = 84.7 bits (208), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 77/289 (26%), Positives = 131/289 (45%), Gaps = 59/289 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGR--LERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N + +I TP +T Y D    +D   + + R  +E T+L  V E  E  + P
Sbjct: 1120 GVPRLKEILNVATHIKTPSMTVYQDPSRAMDKESVKQLRSVVEHTSLRSVTEATEIYYDP 1179

Query: 822  DDSFILIKLDMDRIR---LLHLEVDIDS-------IRYCIERTRGISGHLTVSGHSFLI- 870
            D    +I+ D D +    ++  +V  DS       +R  + R + +   LTV   +  I 
Sbjct: 1180 DIQSTVIEADRDMVESYFIIPEDVADDSSHQSKWLLRIILSRPKLLDKSLTVQDVAMKIK 1239

Query: 871  -LKPKD-----SSKSFNSKMYQMKQ-------------------------LLPSVVIKGV 899
               P+D     S  + + ++ +++Q                         LL ++ ++GV
Sbjct: 1240 DAYPQDIAVIFSDNNADEQVIRIRQIQDSKQDDDDDDTEYDVTLKKLESHLLDTLTLRGV 1299

Query: 900  QGINRAVIHEED----VEGVTKYK-----------LLVEGDNLRDVMATYGVKGVKCSSN 944
             GI RA I+E+     +E  + Y+           L   G  L +V+   GV   +  SN
Sbjct: 1300 AGIERAFINEKSRVRVLEDGSLYQSAEDPLCKEWVLETSGSALGEVLTIPGVDTTRTYSN 1359

Query: 945  NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
               E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1360 QFIEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLVDVMTSRG 1408



 Score = 56.2 bits (134), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/41 (60%), Positives = 28/41 (68%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            A   ++ +A   P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1071 AIESRFSKAMANPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1111


>gi|45935343|gb|AAS79693.1| RNA polymerase III large subunit [Podocarpus macrophyllus]
          Length = 546

 Score =  161 bits (408), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 90/225 (40%), Positives = 135/225 (60%), Gaps = 29/225 (12%)

Query: 390 MNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGY 449
           MN+H+PQTEEAR EAL              +LM  ++NL TP+NGE+LIA+TQDF+T  +
Sbjct: 1   MNLHVPQTEEARTEAL--------------MLMGVQNNLCTPKNGEILIASTQDFLTSSF 46

Query: 450 LLTQKNAFFNRAQTMRIASTL--IADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIF 507
           L+T+K+ F++RA    + S +   A+  D+             P + ++   +WTGKQ+F
Sbjct: 47  LITRKDTFYDRAAFSLMCSYMGNAAEHIDL-----------PTPAI-LKPIELWTGKQLF 94

Query: 508 SLILKPNRDCPVNANLKTKGRAYT-ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKA 566
           S++++PN    V  NL    + Y+   E  C  D  V  RNSEL++G + K+TLG+G K 
Sbjct: 95  SVLVRPNTKMRVFVNLIVMEKNYSKCGETMCPNDGCVYFRNSELISGQVGKATLGNGNKN 154

Query: 567 NVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
            +F ILLRD+    A + M RL+++++ ++ N GFSIGI DV PG
Sbjct: 155 GLFSILLRDYNSHAAASCMNRLAKLSARWIGNHGFSIGIDDVQPG 199



 Score =  103 bits (258), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 51/72 (70%), Positives = 57/72 (79%), Gaps = 1/72 (1%)

Query: 607 DVTPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D TP  +GFV NSF++GLT TEFFFHTMGGREGLVDTAVKTAETGYM RRL+K+LEDL  
Sbjct: 318 DKTPAAKGFVANSFYTGLTATEFFFHTMGGREGLVDTAVKTAETGYMSRRLMKALEDLSS 377

Query: 666 QYDMSFDAAFYG 677
            YD +   A  G
Sbjct: 378 HYDGTVRNASGG 389



 Score = 57.4 bits (137), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 23/42 (54%), Positives = 36/42 (85%)

Query: 21 VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRA 62
          +LM  ++NL TP+NGE+LIA+TQDF+T  +L+T+K+ F++RA
Sbjct: 17 MLMGVQNNLCTPKNGEILIASTQDFLTSSFLITRKDTFYDRA 58


>gi|308808522|ref|XP_003081571.1| DNA-directed RNA polymerase (ISS) [Ostreococcus tauri]
 gi|116060036|emb|CAL56095.1| DNA-directed RNA polymerase (ISS) [Ostreococcus tauri]
          Length = 1673

 Score =  161 bits (408), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 96/268 (35%), Positives = 148/268 (55%), Gaps = 34/268 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + DVVLFNRQPSLHK+SIM HR +++P+ TFR N  V  PYNADFDGDEMN+HLPQ+ E 
Sbjct: 448 NGDVVLFNRQPSLHKMSIMGHRVRIMPYSTFRLNLSVTPPYNADFDGDEMNMHLPQSYET 507

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE               K LM     +V+P+  + ++A  QD + G  L+T+++ F  +
Sbjct: 508 KAE--------------VKELMMVPKMIVSPQANKPVMAIVQDTLLGCRLITKRDTFIPK 553

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              M I   L     D  G I +       P + ++   +WTGKQ+FS++L      P  
Sbjct: 554 DVFMNIIMWL----EDWDGKIPK-------PAI-LKPQPLWTGKQVFSMML------PKV 595

Query: 521 ANLKTKGRAYTANE-EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
             L+T   A  A++  F   D+ V +   ELL G++ K T+GSGG   + ++   ++G  
Sbjct: 596 NLLRTSAWARDADDVTFSVDDTGVRIEQGELLTGTLCKKTMGSGG-GGLIHVTWEEWGPI 654

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            A   + +   + +++L++ GF++GI D
Sbjct: 655 AARGLISQTQTLVNYWLLHHGFTVGIAD 682



 Score =  108 bits (270), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 62/179 (34%), Positives = 103/179 (57%), Gaps = 10/179 (5%)

Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGV----------TKYKLLVEGDNLRDVMATYGVKG 1274
            Q+L ++ ++G+  I +  I E     V          T++ L  EG NL +VMA   V  
Sbjct: 1281 QMLSNLALRGIPDIKKVFIREAKSNAVNPRTQLFEKHTEWMLDTEGVNLLEVMAHPDVDF 1340

Query: 1275 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGI 1334
             + +SN+  EV + LGIEA R+T++ E++ V+E  G  +++RH  ++ ++MT +G ++ I
Sbjct: 1341 TRTTSNHLIEVIQILGIEAVRNTLLRELRGVIEFDGSYVNYRHLAILVEVMTYRGHLVSI 1400

Query: 1335 TRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            TRHG+ + +   L   SFE T D L +AA + + D ++G SE I++G    +GTG  KL
Sbjct: 1401 TRHGINRAETGALMRCSFEETVDILMEAAAFSERDNMTGPSENIMLGQFCPIGTGEFKL 1459



 Score =  100 bits (249), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 42/57 (73%), Positives = 52/57 (91%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKT+ETGY+QRRLVK++ED+ V+YD
Sbjct: 811 RGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDVVVKYD 867



 Score = 87.4 bits (215), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 76/286 (26%), Positives = 133/286 (46%), Gaps = 53/286 (18%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEIIN ++ I TP +T  L  +  +D   A+ V+  LE TTL  V    E  + P
Sbjct: 1113 GVPRLKEIINIAKQIKTPSLTVALKPEFASDRTKAKDVQASLEYTTLHSVAAVTEVHYDP 1172

Query: 822  DDSFILIKLDMDRIRLLH--LEVDIDS-------IRYCIERTRGISGHLTVS-------- 864
            D +  +I+ D + +R  +   + D+D        +R  + R   +   L ++        
Sbjct: 1173 DPTDTVIEEDREFVRAYYEMPDEDVDPSRMSPWLLRIELNREMMVDKKLLMADVAERINE 1232

Query: 865  --GHSFLILKPKDSSKSFNSKMYQMK----------------------QLLPSVVIKGVQ 900
              G     +   D+S+    ++  MK                      Q+L ++ ++G+ 
Sbjct: 1233 DFGGDLSCIFNDDNSEKLVLRIRIMKAEGEKYDDSSIEDEVFLKRIETQMLSNLALRGIP 1292

Query: 901  GINRAVIHEEDVEGV----------TKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVY 950
             I +  I E     V          T++ L  EG NL +VMA   V   + +SN+  EV 
Sbjct: 1293 DIKKVFIREAKSNAVNPRTQLFEKHTEWMLDTEGVNLLEVMAHPDVDFTRTTSNHLIEVI 1352

Query: 951  KTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL 996
            + LGIEA R+T++ E++ V+E  G  +++RH  ++ ++MT +G ++
Sbjct: 1353 QILGIEAVRNTLLRELRGVIEFDGSYVNYRHLAILVEVMTYRGHLV 1398



 Score = 65.5 bits (158), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 58/208 (27%), Positives = 100/208 (48%), Gaps = 35/208 (16%)

Query: 115 PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSIC 174
           P   GL D RMGT  + A C T G +     G+FG+++L  PV+H G+   V+ +L+  C
Sbjct: 69  PKRGGLSDPRMGTMDRGAVCETDGCDSVQTPGYFGHLELAKPVYHHGFINVVLRVLR--C 126

Query: 175 KNPTCARVLLGEEKAAGFRA--KLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGV 232
              + +++LL +++   F    +++NP       K+  KK+ +  K  SVCP+ G     
Sbjct: 127 VGYSSSQLLLHKDEDPKFAQLMRIKNP-------KNRLKKLTDACKTKSVCPYTGTAQPQ 179

Query: 233 VKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVL 292
            +  G +KI+ E +K+R        ++LL E  E           +K      +     L
Sbjct: 180 YRLEG-MKITAE-FKHRD-------DELLPEGGE-----------RKV----VVTAERAL 215

Query: 293 QLFEAIPLEDIPLLLMNAELSKPSDLIL 320
           Q+ + I  ED  +L ++ E ++P  +IL
Sbjct: 216 QILKGISDEDCRVLGLDPEHARPDWMIL 243



 Score = 51.6 bits (122), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 22/37 (59%), Positives = 26/37 (70%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            ++  A   P   +G +AAQSIGEP TQMTL TFHFAG
Sbjct: 1068 RFKMALAPPGDGIGVVAAQSIGEPATQMTLNTFHFAG 1104


>gi|147921534|ref|YP_684650.1| DNA-directed RNA polymerase subunit A' [Methanocella arvoryzae
           MRE50]
 gi|110620046|emb|CAJ35324.1| DNA-directed RNA polymerase, subunit A1 [Methanocella arvoryzae
           MRE50]
          Length = 877

 Score =  161 bits (408), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 93/269 (34%), Positives = 145/269 (53%), Gaps = 34/269 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIM+H  +V+PH+TFR N  VC PYNADFDGDEMN+H+PQT EA
Sbjct: 407 DGDIVLFNRQPSLHRMSIMSHFVRVMPHKTFRLNPAVCAPYNADFDGDEMNLHVPQTMEA 466

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
            AE              A++LM  + N+++PR G  +I    D ++G YLLT+    +  
Sbjct: 467 LAE--------------ARILMLVQENILSPRFGGPIIGGLHDHVSGIYLLTKGYRLYTE 512

Query: 461 AQTMRIASTL-IADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
              + I S + + +  +         ++  N + +      ++GKQIFS IL    D   
Sbjct: 513 TDALEILSKVNVHELPE--------PYKVENGIRY------YSGKQIFSQILPKGLDMTY 558

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGS-GGKANVFYILLRDFGE 578
            A +           E C +D++V + + EL  G++D+  +G+  GK  +   +++ + E
Sbjct: 559 KAKICEN--CEECKGELCEKDAFVRISDGELKTGTIDEKAIGAFSGK--ILDRIIKTYDE 614

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
             A   +  ++R+    +  RGFS GI D
Sbjct: 615 HTASNFLDNVTRLAIRAITARGFSYGISD 643



 Score =  103 bits (257), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 73/260 (28%), Positives = 121/260 (46%), Gaps = 57/260 (21%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           +++ S  +I++ + Y  D    PI  GL+D R+G       C TCG    +C GHFG+I+
Sbjct: 20  IRKMSVTKIITADTY--DDDGYPIDMGLMDPRLGVIDPGLRCRTCGGRPGECPGHFGHIE 77

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKK 212
           L  PV H+G+ R +  +L++ C+   C R+L+ E+  A +  +++         + L + 
Sbjct: 78  LAAPVIHVGFARLLRKVLRTTCRK--CGRLLMDEKTKAEYLRQIQTA-------QRLGQP 128

Query: 213 ILETTKKV------SVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNE 266
           I E  K V      + CP+CGE               E+ + + +K    +ED       
Sbjct: 129 IDEIVKNVFKDAKGTTCPYCGE---------------EQKEIKFEKPTGYIED------- 166

Query: 267 AVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVP 326
                     HK       L P +V    E IP EDI +  M+   ++P  ++LT L VP
Sbjct: 167 ---------GHK-------LMPTDVRDRLEMIPDEDIEVFGMDPRNARPEWMVLTVLPVP 210

Query: 327 PNCIRPSVI--SDLKSDNDV 344
           P  +RPS+   S  +S++D+
Sbjct: 211 PVTVRPSITLESGQRSEDDL 230



 Score = 90.1 bits (222), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 38/57 (66%), Positives = 51/57 (89%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV++S+  GL PTEFFFH MGGREGLVDTAV+T+++GY+QRRLV +L+DL V++D
Sbjct: 774 RGFVESSYKKGLNPTEFFFHAMGGREGLVDTAVRTSQSGYLQRRLVNALQDLEVKHD 830


>gi|169806355|ref|XP_001827922.1| DNA-directed RNA polymerase II largest subunit [Enterocytozoon
           bieneusi H348]
 gi|161778990|gb|EDQ31017.1| DNA-directed RNA polymerase II largest subunit [Enterocytozoon
           bieneusi H348]
          Length = 1541

 Score =  161 bits (408), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 94/271 (34%), Positives = 149/271 (54%), Gaps = 49/271 (18%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND+VLFNRQPSLHK+S+M HRAK++ ++TFR N  V +PYNADFDGDEMN+H+PQ+   
Sbjct: 407 DNDIVLFNRQPSLHKMSMMGHRAKIMNNKTFRLNLSVTSPYNADFDGDEMNLHMPQSYNT 466

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           ++E +               L +   N+++P++ + +I   QD + G  L T KN FFN+
Sbjct: 467 KSELIN--------------LASVSRNIISPQSNKPVIGIVQDTLVGVRLFTLKNTFFNK 512

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAV-IWTGKQIFSLILKPNRDCPV 519
            +TM +  TL      +  II        NP++ +   + +W+G QIFS +  PN+    
Sbjct: 513 RETMNLLFTLDTLEEKVMEIIN-------NPILIIHNKISLWSGLQIFSAVF-PNK---- 560

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGS--GGKANVFYILLRDFG 577
             N   KG               V+++NS L+ G++ K T G+  GG   + +++  D+G
Sbjct: 561 -FNFNYKG---------------VVIKNSNLITGTLSKITCGATHGG---LIHVICNDYG 601

Query: 578 EDVAVTAMWRLSRMTSFYLMN-RGFSIGIGD 607
              A   +  + R+ + ++ +   F+IGIGD
Sbjct: 602 CLEATKFINNVQRLINHFMFHINSFTIGIGD 632



 Score =  121 bits (304), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 93/275 (33%), Positives = 154/275 (56%), Gaps = 25/275 (9%)

Query: 1149 EYIEEVF-VPDD------SFILIKLDMDRI----RLLHLEVDIDSIRYCIERTRGISGHL 1197
            E +E  F +PD+      S   I+ ++++     R L LE  I+ I+  I+    I  H+
Sbjct: 1091 ELVENYFEMPDEIDLDKCSSFCIRFELNKYHVIGRGLDLEYIIEKIKLNIKSMLDIGIHI 1150

Query: 1198 TVS--GHSFLILKPK----DSSKSFNSKMY-QMKQLLPSVVIKGVQGINRA-VIHEEDVE 1249
              S      LIL+ +    D  K  N K Y ++   L ++ I+G++GI +A +IH +D  
Sbjct: 1151 IYSLPTDEKLILRIRLILNDKIKE-NLKFYNELVDKLLNIHIQGLEGIKKAYLIHNKD-- 1207

Query: 1250 GVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENH 1309
                + L  +G N + +++   V G   +SN+ +E+Y+TLG+EA R TIMTE+ +V+EN+
Sbjct: 1208 --DTWTLQTDGINYQTILSFPNVDGSHTTSNDLFEIYETLGVEALRETIMTELTMVIENN 1265

Query: 1310 GMSIDFRHPMLVADLMTSKGEVLGITRHGLAK-MKESVLNLASFENTSDHLFDAAFYGQT 1368
            G  ++ RH  L++D+MT  G   GITRHG+ + +K S L  ASFE T D L +AA   + 
Sbjct: 1266 GSYVNSRHLSLLSDVMTVCGYPSGITRHGVNREIKASALKRASFEETVDILLEAAATAEE 1325

Query: 1369 DCISGVSECIIMGLPMNVGTGLIKLLQAVPRSEPV 1403
            +   G++E I+MG    +GTG I+L+  + + + +
Sbjct: 1326 NPAHGITENIMMGQLAPLGTGNIQLILDIKKLDQI 1360



 Score =  103 bits (256), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 83/269 (30%), Positives = 143/269 (53%), Gaps = 45/269 (16%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCE---------- 813
            GVPR+ EIIN ++NI TP++   L K+ DL   + ++ ++E ++L ++ E          
Sbjct: 1023 GVPRLNEIINTTKNIKTPLMIVQLQKN-DLQSCKNLRNKIEYSSLKDLYESFLLLYDPII 1081

Query: 814  ----------YIEEVF-VPDD------SFILIKLDMDRI----RLLHLEVDIDSIRYCIE 852
                       +E  F +PD+      S   I+ ++++     R L LE  I+ I+  I+
Sbjct: 1082 TDTILDEDKELVENYFEMPDEIDLDKCSSFCIRFELNKYHVIGRGLDLEYIIEKIKLNIK 1141

Query: 853  RTRGISGHLTVS--GHSFLILKPK----DSSKSFNSKMY-QMKQLLPSVVIKGVQGINRA 905
                I  H+  S      LIL+ +    D  K  N K Y ++   L ++ I+G++GI +A
Sbjct: 1142 SMLDIGIHIIYSLPTDEKLILRIRLILNDKIKE-NLKFYNELVDKLLNIHIQGLEGIKKA 1200

Query: 906  -VIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMT 964
             +IH +D      + L  +G N + +++   V G   +SN+ +E+Y+TLG+EA R TIMT
Sbjct: 1201 YLIHNKD----DTWTLQTDGINYQTILSFPNVDGSHTTSNDLFEIYETLGVEALRETIMT 1256

Query: 965  EIKLVMENHGMSIDFRHPMLVADLMTSKG 993
            E+ +V+EN+G  ++ RH  L++D+MT  G
Sbjct: 1257 ELTMVIENNGSYVNSRHLSLLSDVMTVCG 1285



 Score = 99.4 bits (246), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 46/90 (51%), Positives = 61/90 (67%), Gaps = 7/90 (7%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSF 671
           +GF+ NS+ +G+TP EF+FH MGGREGL+DTA+KTAETGY+QRRLVK++ED  V+ D S 
Sbjct: 756 RGFISNSYLTGMTPQEFYFHAMGGREGLIDTAIKTAETGYIQRRLVKAMEDAVVRSDSSV 815

Query: 672 DAAF-------YGQTDCISGVSECIIMGLP 694
              F       YG+      + E II+  P
Sbjct: 816 RNGFGKIYQFAYGEDGFNGKILEKIILNKP 845



 Score = 89.7 bits (221), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 67/234 (28%), Positives = 112/234 (47%), Gaps = 45/234 (19%)

Query: 115 PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSIC 174
           P  +GL+D RMGT +K   C TC +N+ DCVGHFG+I+L  P+FHIGY   +  +L+ IC
Sbjct: 41  PKENGLIDLRMGTTEKNFLCQTCNENMFDCVGHFGHIELCKPMFHIGYITKIKKLLECIC 100

Query: 175 KNPTCARV---LLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEING 231
               C+++    L +EK   +  +    A + L  K+      E  +K+  C        
Sbjct: 101 F--YCSKIKDFKLLKEKTKNYTLE---EAWNILKTKTFCDSENEKGEKIGCCNK----QP 151

Query: 232 VVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEV 291
           ++KK G+  I+  K  +   K                                 LN  +V
Sbjct: 152 IIKKEGMNLIAFMKGNDDEGK-------------------------------VILNGEKV 180

Query: 292 LQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD-LKSDNDV 344
             +F+ I   ++  +  N   S+P ++++T LLV P  +RPS+++D L+S++D+
Sbjct: 181 CNIFKKIDASELKFIGFNVN-SRPENMLITVLLVTPPSVRPSILTDGLRSEDDL 233



 Score = 57.4 bits (137), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 25/37 (67%), Positives = 27/37 (72%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            K   AQ+EP   VG LAAQS+GEP TQMTL TFH AG
Sbjct: 979  KLKEAQVEPNEMVGTLAAQSVGEPATQMTLNTFHLAG 1015



 Score = 40.0 bits (92), Expect = 8.8,   Method: Compositional matrix adjust.
 Identities = 20/59 (33%), Positives = 34/59 (57%)

Query: 13  YATRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTL 71
           Y T++    L +   N+++P++ + +I   QD + G  L T KN FFN+ +TM +  TL
Sbjct: 464 YNTKSELINLASVSRNIISPQSNKPVIGIVQDTLVGVRLFTLKNTFFNKRETMNLLFTL 522


>gi|110669633|gb|ABG81911.1| RNA polymerase II largest subunit [Mycoblastus sanguinarius]
          Length = 1016

 Score =  161 bits (408), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 97/277 (35%), Positives = 147/277 (53%), Gaps = 39/277 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D ++FNRQPSLHK S+M HR +V+P+ TFR N  V  PYNADFDGDEMN+H+PQ+EE 
Sbjct: 373 DGDYIIFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTGPYNADFDGDEMNLHVPQSEET 432

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE                 L     N+V+P+    L+   QD + G Y + +++ F ++
Sbjct: 433 RAE--------------VSGLCMVPLNIVSPQRNGPLMGIVQDTLCGIYKMCRRDVFLSK 478

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M I    +    D  G+I +       P +F +   +WTGKQI SL++      P  
Sbjct: 479 EQVMNI----LLWVPDWDGVIPQ-------PAIF-KPRPMWTGKQILSLVI------PAG 520

Query: 521 ANLKTKGRAYTANEEFCH-RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            NL        +NE F    D  +++   EL+ G  +K ++G+ G   V +I+  + G +
Sbjct: 521 LNL-----LRGSNEGFTSLTDDGLLVSGGELMYGLFNKKSVGATG-GGVIHIIYNEKGPE 574

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           VA+        + +++L++ GFSIGIGD  P +  +Q
Sbjct: 575 VAMNFFNGAQTVVNYWLLHNGFSIGIGDTIPDRNTIQ 611



 Score =  100 bits (249), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+  
Sbjct: 725 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDVMA 784

Query: 666 QYD 668
           +YD
Sbjct: 785 KYD 787



 Score = 55.8 bits (133), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 52/195 (26%), Positives = 88/195 (45%), Gaps = 41/195 (21%)

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNPAL 201
           +C GHFG+I+L +PVFH+G+   +  +L+++C N  C ++L+ E   A   A + R+P  
Sbjct: 1   ECPGHFGHIELAVPVFHVGFMTKIKKLLETVCHN--CGKILVDESNPAFADALRYRDPKR 58

Query: 202 SY--LVRKSLKKKILETT---------KKVSVCPH----CGEINGVVKKCGLLKISHEKY 246
            +  + R    K I ETT          K+    H    CG I   V++ GL      K 
Sbjct: 59  RFDAVWRLCKPKMICETTMTLDEDAPSDKMKEPKHDHGGCGNIQPEVRREGLRLNGTWK- 117

Query: 247 KNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLL 306
               +K D        E NE  +  PE          + + P   L +F  I  ++I  +
Sbjct: 118 ---AQKGD--------EENEGQQ--PE---------KKPITPQMALNIFRHISTDEIRRM 155

Query: 307 LMNAELSKPSDLILT 321
            ++ + ++P  +I+T
Sbjct: 156 GLSNDYARPEWMIIT 170



 Score = 42.7 bits (99), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 18/29 (62%), Positives = 21/29 (72%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMT 1137
            ++ RA + P   VG LAAQSIGEP TQMT
Sbjct: 988  RFCRAAVNPGEMVGVLAAQSIGEPATQMT 1016


>gi|113957534|gb|ABI49121.1| RNA polymerase II largest subunit [Pyxine subcinerea]
          Length = 1015

 Score =  161 bits (408), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 96/271 (35%), Positives = 151/271 (55%), Gaps = 39/271 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D ++FNRQPSLHK S+M HR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 372 DGDYIIFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 431

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    +++L ++            N+V+P+    L+   QD + G Y + +++ F N+
Sbjct: 432 RAE----VNQLCMVP----------LNIVSPQRNGPLMGIVQDTLCGIYKICRRDVFLNQ 477

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M I    +    D  GII +       P + ++ + +WTGKQI SL++ P       
Sbjct: 478 DQVMNI----LLWVPDWDGIIPQ-------PAI-LKPSPMWTGKQIISLVIPP------G 519

Query: 521 ANLKTKGRAYTANEEFCH-RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            NL   G     ++ F    DS +++ N EL+ G + K  +G+   A + +I+  + G +
Sbjct: 520 LNLGRSG-----DDGFSPIDDSGLLISNGELMYGLLSKKIVGA-SSAGIIHIVYNEKGPE 573

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
            A+        + +++L++ GFSIGIGD  P
Sbjct: 574 AAMAFFNGAQTVVNYWLLHNGFSIGIGDTIP 604



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+  
Sbjct: 724 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDVMA 783

Query: 666 QYD 668
           +YD
Sbjct: 784 KYD 786



 Score = 55.8 bits (133), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 49/194 (25%), Positives = 86/194 (44%), Gaps = 40/194 (20%)

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNPAL 201
           +C GHFG+I+L +PVFH G+   +  +L+ +C N  C ++L+ +   A   A ++R+P  
Sbjct: 1   ECPGHFGHIELAVPVFHTGFISKIKKLLEMVCHN--CGKILVDDSNPAFKDALRIRDPKK 58

Query: 202 SY--LVRKSLKKKILETT---------KKVSVCP---HCGEINGVVKKCGLLKISHEKYK 247
            +  + R    K I ETT          +  + P    CG +   V+K GL  I   K  
Sbjct: 59  RFDAIWRLCKTKMICETTIPQDDDSKDLQKDLGPGHGGCGNVQPEVRKDGLKLIGTWK-- 116

Query: 248 NRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLL 307
                              A K + E EA +     + + P   L +F  +  ED+  + 
Sbjct: 117 -------------------AQKGDDETEAQQPEK--KPITPQMALNIFRHMSAEDVKNIG 155

Query: 308 MNAELSKPSDLILT 321
           ++ + ++P  +I+T
Sbjct: 156 LSNDYARPEWMIIT 169



 Score = 42.4 bits (98), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 18/29 (62%), Positives = 21/29 (72%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMT 1137
            ++ RA + P   VG LAAQSIGEP TQMT
Sbjct: 987  RFCRATVSPGEMVGVLAAQSIGEPATQMT 1015


>gi|407852687|gb|EKG06051.1| RNA polymerase IIA largest subunit, putative, partial [Trypanosoma
           cruzi]
          Length = 1588

 Score =  161 bits (408), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 95/267 (35%), Positives = 144/267 (53%), Gaps = 39/267 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + DVVLFNRQP+LH++S+M HR +VL + TFR N    TPYNADFDGDEMN+H+PQ+   
Sbjct: 282 NGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNLSCTTPYNADFDGDEMNLHVPQSLLT 341

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE +             +++M  K N V+P      +   QD + G Y LT K+ F ++
Sbjct: 342 KAELI-------------EMMMVPK-NFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFLDK 387

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                +A  L     D+        W+   P V +R   +WTGKQ+FSLIL P  + P  
Sbjct: 388 YFVQSVALWL-----DL--------WQLPVPAV-LRPRPLWTGKQVFSLIL-PEVNHPAT 432

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
              +           F H DS +++R  +LL G + KS +G+    ++ +++  + G D 
Sbjct: 433 PQERPP---------FPHNDSSIMIRRGQLLCGPITKSIVGA-APGSLIHVIFNERGSDE 482

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGD 607
               +  + R+T+FYL+N GFS+G+ D
Sbjct: 483 VARFINGVQRITTFYLINFGFSVGVQD 509



 Score = 88.6 bits (218), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 73/281 (25%), Positives = 133/281 (47%), Gaps = 35/281 (12%)

Query: 1150 YIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKP 1209
            +I  + +  D F+   L+M  ++   L VD     Y IE     +G    +    + ++P
Sbjct: 1053 WIARLELDADMFVDKALNMKDVKQAILRVDDG---YVIE-----TGMANDTKERTIRMRP 1104

Query: 1210 K--DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEE----------DVEGVTKYKLL 1257
            K  D   S     + + +LL  V ++G+ G+ +A++ +            ++G   + + 
Sbjct: 1105 KKNDGVDSIPRLKHAIPELLARVHLRGIPGVRKALLKDRTTFTVDPATGKMKGEKTWLID 1164

Query: 1258 VEGDNLR-------DVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHG 1310
             +G  LR       D      +   + SSN   EV   LGIEAAR  ++ E++     +G
Sbjct: 1165 TDGTALRRAFIGIVDEKGNNIINATRTSSNKVPEVCSLLGIEAARYKMLHELREAYLAYG 1224

Query: 1311 MSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKES-VLNLASFENTSDHLFDAAFYGQTD 1369
            ++I++RH  ++ D +  +G ++ ++R G+ + + S  L   SFE T   L  AA +G+ D
Sbjct: 1225 LNINYRHYTVLVDTICQRGYLMAVSRVGINRSEMSGPLMRCSFEETVKVLMAAAAFGERD 1284

Query: 1370 CISGVSECIIMGLPMNVGTGLIKLL-------QAVPRSEPV 1403
             + GVS  +++G    +GTGL  L+       QAVP+ + V
Sbjct: 1285 PVRGVSANLVLGNQARIGTGLFDLVLNMAALQQAVPQEDAV 1325



 Score = 83.6 bits (205), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 34/57 (59%), Positives = 44/57 (77%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +G     +  GL P EFFFHTM GREGL+DTAVKT++TGY+QR+L+K+LED+   YD
Sbjct: 638 RGMANRGYVEGLKPHEFFFHTMAGREGLIDTAVKTSDTGYLQRKLIKALEDVHAAYD 694



 Score = 54.3 bits (129), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 51/216 (23%), Positives = 96/216 (44%), Gaps = 30/216 (13%)

Query: 804  ERTTLGEV---CEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGH 860
            ER  L EV     +I  + +  D F+   L+M  ++   L VD     Y IE     +G 
Sbjct: 1040 ERARLQEVENGSPWIARLELDADMFVDKALNMKDVKQAILRVDDG---YVIE-----TGM 1091

Query: 861  LTVSGHSFLILKPK--DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEE-------- 910
               +    + ++PK  D   S     + + +LL  V ++G+ G+ +A++ +         
Sbjct: 1092 ANDTKERTIRMRPKKNDGVDSIPRLKHAIPELLARVHLRGIPGVRKALLKDRTTFTVDPA 1151

Query: 911  --DVEGVTKYKLLVEGDNLR-------DVMATYGVKGVKCSSNNTYEVYKTLGIEAARST 961
               ++G   + +  +G  LR       D      +   + SSN   EV   LGIEAAR  
Sbjct: 1152 TGKMKGEKTWLIDTDGTALRRAFIGIVDEKGNNIINATRTSSNKVPEVCSLLGIEAARYK 1211

Query: 962  IMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            ++ E++     +G++I++RH  ++ D +  +G ++ 
Sbjct: 1212 MLHELREAYLAYGLNINYRHYTVLVDTICQRGYLMA 1247



 Score = 53.9 bits (128), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 23/39 (58%), Positives = 29/39 (74%)

Query: 1107 REKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            R KY+++ + P   +GA+AAQS GEP TQMTL TFH AG
Sbjct: 909  RTKYLQSLVSPGENIGAIAAQSCGEPATQMTLNTFHNAG 947


>gi|448330661|ref|ZP_21519940.1| DNA-directed RNA polymerase subunit A' [Natrinema versiforme JCM
           10478]
 gi|445611165|gb|ELY64925.1| DNA-directed RNA polymerase subunit A' [Natrinema versiforme JCM
           10478]
          Length = 975

 Score =  161 bits (408), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 102/275 (37%), Positives = 145/275 (52%), Gaps = 46/275 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 483 DGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQNEEA 542

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR GE +I A QD I+G YLLT  N  FN 
Sbjct: 543 RAE--------------ARVLMRVQEQMLSPRFGENIIGAIQDHISGMYLLTHDNPRFNE 588

Query: 461 AQTMR-IASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q +  + +T I +  D  G+                    WTG  +FS +L      P 
Sbjct: 589 TQALDLLRATRIDELPDPSGVDD-------------EGEPFWTGYDVFSELL------PD 629

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           + NL+  G   T  +E       V++ + +LL G++ +  +G  G   +   + + +G  
Sbjct: 630 DLNLEFTG---TVGDE-------VVVEDGQLLKGTIAEDEVGEFG-GEIVDTITKVYGNT 678

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVT-PGQG 613
            A   +  +S +    +M+ GFSIGI D T PG+ 
Sbjct: 679 RARIFVNEVSTLAMRAIMHFGFSIGIDDETIPGEA 713



 Score =  112 bits (279), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 84/290 (28%), Positives = 131/290 (45%), Gaps = 43/290 (14%)

Query: 94  QQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDL 153
           ++ S  +I++ + Y  D    PI  GL+D R+G       C TCG++   C GHFG+I+L
Sbjct: 23  REMSATKIITADTY--DDDGFPIDMGLMDPRLGVIDPGLECKTCGKHSGSCNGHFGHIEL 80

Query: 154 PLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKI 213
             PV H+G+ + +  +L+  C+   C+++LL E++   FR +L            + K  
Sbjct: 81  AAPVIHVGFTKLIRRLLRGTCRE--CSKLLLTEDERDEFRDQLTESRKLSRDLNDVTKAA 138

Query: 214 LETTKKVSVCPHCGEINGVV---------------------KKCGLLKISHEKYKNRTKK 252
           +   +K   CP CGEI   +                     +  G ++   E+   RT  
Sbjct: 139 IRQARKKDRCPFCGEIQYDIDHEKPTTYYEVQQVLTSEYSQRIAGAMQGDEEEGVERT-T 197

Query: 253 KDAIVEDL---LAEYNEAV--KFNPE------IEAHKKFGLIQT----LNPLEVLQLFEA 297
            D + E     L   NE +   F P       IE      L +     L P ++   FE 
Sbjct: 198 PDELAEQTEIELTRVNEILSGSFRPRESQRKAIEKALDIDLTEEDTNKLMPSDIRDWFEN 257

Query: 298 IPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDNDVV 345
           IP EDI +L +N E S+P  +ILT L VPP   RPS+  D   +S++D+ 
Sbjct: 258 IPDEDIEVLGINPERSRPEWMILTVLPVPPVTARPSITLDNGQRSEDDLT 307



 Score = 92.8 bits (229), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 39/58 (67%), Positives = 49/58 (84%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
             GFV+NS+ SGLTP EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 834 AHGFVENSYTSGLTPREFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALHELETQYD 891



 Score = 45.4 bits (106), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 29/46 (63%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 65
           +VLM  +  +++PR GE +I A QD I+G YLLT  N  FN  Q +
Sbjct: 547 RVLMRVQEQMLSPRFGENIIGAIQDHISGMYLLTHDNPRFNETQAL 592


>gi|397135932|gb|AFO11461.1| RNA polymerase I, partial [Candida blankii]
          Length = 872

 Score =  161 bits (407), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 97/271 (35%), Positives = 148/271 (54%), Gaps = 44/271 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+D VLFNRQPSLHK+S+MAHR KV+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 251 DDDPVLFNRQPSLHKMSMMAHRVKVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 310

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE       LS +A       A    +V+P++ + ++   QD + G   LT+++ F   
Sbjct: 311 RAE-------LSQIA-------AVPLQIVSPQSNKPVMGIVQDTLCGIRKLTRRDTFLEY 356

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVV----FVRTAVIWTGKQIFSLILKPNRD 516
            Q M I                 F    WN +V     ++   +WTGKQ+ SL +     
Sbjct: 357 DQVMNIL----------------FWVPQWNGIVPQPAILKPKPLWTGKQMVSLTI----- 395

Query: 517 CPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            P    L+   R          +D+ +++   E++ G++DK+T+GS G   + + ++R+ 
Sbjct: 396 -PSGIFLQ---RFDEGTTWLSPKDNGMLIAKGEIVYGAVDKATVGSTG-GGLIHTIMREK 450

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           G  V       + ++ +F+L++ GFSIGIGD
Sbjct: 451 GPQVCCNFFGAVQKVVNFWLLHNGFSIGIGD 481



 Score =  101 bits (252), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 43/57 (75%), Positives = 51/57 (89%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GF++NS+  GLTP EFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+ VQYD
Sbjct: 610 RGFIENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDIMVQYD 666


>gi|322369999|ref|ZP_08044561.1| DNA-directed RNA polymerase subunit A' [Haladaptatus
           paucihalophilus DX253]
 gi|320550335|gb|EFW91987.1| DNA-directed RNA polymerase subunit A' [Haladaptatus
           paucihalophilus DX253]
          Length = 976

 Score =  161 bits (407), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 98/270 (36%), Positives = 147/270 (54%), Gaps = 45/270 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 489 DGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQNEEA 548

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR GE +I A QD I+G YLLT  N  FN 
Sbjct: 549 RAE--------------ARVLMRVQEQIISPRFGENIIGAIQDHISGTYLLTHHNPHFNE 594

Query: 461 AQTMR-IASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q +  + +T I +  +  G     +     P         WTG+ +FS +L PN     
Sbjct: 595 TQALDLLRATRIDELPEEDG-----TEEDGTPY--------WTGQTLFSELL-PN----- 635

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
              ++ +  + T +         V++ N +L+ G++D+  +G+ G   +   + +++GE 
Sbjct: 636 --GIELEFTSSTGD--------TVVIENGQLIEGTIDEDAVGAFG-GEIVDTICKEYGET 684

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVT 609
            A   +  ++ +    +M+ GFSIGI D T
Sbjct: 685 RARHFINEVATLAMRAIMHFGFSIGIDDET 714



 Score =  110 bits (276), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 87/307 (28%), Positives = 134/307 (43%), Gaps = 72/307 (23%)

Query: 94  QQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDL 153
           ++ S  +I++ + Y  D    PI  GL+D R+G       C TCGQ+   C GHFG+I+L
Sbjct: 24  REMSATKIITADTY--DDDGFPIDMGLMDPRLGVIDPGLECKTCGQHSGSCNGHFGHIEL 81

Query: 154 PLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKL-RNPALSYLVRKSLKKK 212
             PV H+G+ + +  +L+  C++  C+R+LL EE+   +R  L R   L   +    K  
Sbjct: 82  AAPVIHVGFTKLIRRLLRGTCRD--CSRLLLTEEEKEKYRGMLTRTKELGNDITDVTKAA 139

Query: 213 ILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAV---- 268
           I E  KK   CPHCGE+           I+HEK     +    + + L +EY+E +    
Sbjct: 140 IREARKK-DRCPHCGEVQ--------YDINHEKPTTYYE----VQQVLTSEYSERIASRM 186

Query: 269 --------------------------------------KFNPE------IEAHKKFGL-- 282
                                                 +F P       IE      L  
Sbjct: 187 QGRNEEGDEDEDLEPVSPQELADKTDIDLSRINQIISGEFRPREADRKAIEKALSIDLTT 246

Query: 283 --IQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--L 338
             +  L P ++   FE IP +DI  L +++  S+P  +ILT L VPP   RPS+  D   
Sbjct: 247 EDMNKLMPSDIRDWFEDIPDQDIEALGIDSSRSRPEWMILTVLPVPPVTARPSITLDNGQ 306

Query: 339 KSDNDVV 345
           +S++D+ 
Sbjct: 307 RSEDDLT 313



 Score = 88.6 bits (218), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 37/58 (63%), Positives = 48/58 (82%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
             GFV++S+  GLTP EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 840 AHGFVEHSYTGGLTPLEFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELETQYD 897



 Score = 47.4 bits (111), Expect = 0.061,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 29/46 (63%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 65
           +VLM  +  +++PR GE +I A QD I+G YLLT  N  FN  Q +
Sbjct: 553 RVLMRVQEQIISPRFGENIIGAIQDHISGTYLLTHHNPHFNETQAL 598


>gi|452983085|gb|EME82843.1| hypothetical protein MYCFIDRAFT_58269 [Pseudocercospora fijiensis
           CIRAD86]
          Length = 1753

 Score =  161 bits (407), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 96/280 (34%), Positives = 141/280 (50%), Gaps = 45/280 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D ++FNRQPSLHK S+M HR KV+P+ TFR N  V +PYNADFDGDEMN+H+PQ  E 
Sbjct: 451 DGDYIIFNRQPSLHKESMMGHRVKVMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQGHET 510

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    +  L  + H          N+V+P+    L+   QD + G +++T+++   + 
Sbjct: 511 RAE----VANLCAVPH----------NIVSPQKNGPLMGIVQDTMAGIWMMTRRDTMMDY 556

Query: 461 AQTMRIASTLIADTSDICGIIKRFSW-RSWNPVV----FVRTAVIWTGKQIFSLILKPNR 515
            Q M I                   W   W+ V+     ++ +  WTGKQI SL L    
Sbjct: 557 EQVMNI-----------------LMWVPGWDGVIPTPAILKPSPRWTGKQIISLGL---- 595

Query: 516 DCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
             P+  N+  K  +   +     ++  V+++N EL+ G   K  +G+ G   V YI   D
Sbjct: 596 --PLGLNIFRK--SEEGDIPLLEKEEPVLIQNGELVWGRFTKKLVGASGGGVVHYI-FND 650

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFV 615
            G D  V       R+  ++L++ GFS+GIGD  P    V
Sbjct: 651 KGPDATVEFFNAAQRICCYWLLHHGFSVGIGDTVPDADLV 690



 Score =  110 bits (276), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 67/202 (33%), Positives = 107/202 (52%), Gaps = 17/202 (8%)

Query: 1210 KDSSKSFNSKMYQMKQL----LPSVVIKGVQGINRAVIHEEDV-------------EGVT 1252
            KD     +S+   +KQL    L +V+++GV G+ R  + + +              E   
Sbjct: 1264 KDEEGDESSEDDTLKQLAEHMLDNVILRGVNGVRRVFVSKANQIIEKPNGAMTQGGEESV 1323

Query: 1253 KYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMS 1312
            ++ L  +G NL+ V+A  GV   + + N+     K  GIEA R+++M E+K V+ N G  
Sbjct: 1324 EWYLDTDGVNLQKVLAVDGVDSARTTCNHFQSTMKVFGIEAVRASLMAEMKDVLTNDGSY 1383

Query: 1313 IDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCIS 1372
            ++ RH  ++ D+M ++GE++ +TRHG+ +     L   SFE T + LFDAA  G+ D   
Sbjct: 1384 VNHRHMAILCDVMCARGELMAVTRHGINRSDTGALMRCSFEETVEILFDAASSGELDDCR 1443

Query: 1373 GVSECIIMGLPMNVGTGLIKLL 1394
            GVSE II+G     GTG   +L
Sbjct: 1444 GVSENIILGQLAPSGTGEFDML 1465



 Score =  100 bits (250), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKTAETGY+QRRLVK+LE++ +
Sbjct: 805 DYSPASRGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEEIMI 864

Query: 666 QYD 668
           +YD
Sbjct: 865 KYD 867



 Score = 97.1 bits (240), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 74/261 (28%), Positives = 120/261 (45%), Gaps = 51/261 (19%)

Query: 110 DPQR-TPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVIN 168
           D QR  P   GL D ++GT  +   C TCG++  +C GHFG+I+L +PVFH+G+   +  
Sbjct: 42  DEQRHRPREKGLNDPKLGTIDRSQMCATCGESQQECPGHFGHIELAVPVFHVGFITKIKK 101

Query: 169 ILQSICKNPTCARVLLGE-----EKAAGFR-AKLRNPALSYLVRKSL-----------KK 211
           IL+S+C N  C ++L  E     ++A G R  K R  A++ L +  +           ++
Sbjct: 102 ILESVCHN--CGKLLEDESNPLFKRAVGLRDPKRRFEAVTRLCKPKMTCDLDAKNDDEQE 159

Query: 212 KILETTKKVSVCPH--CGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVK 269
                 KK     H  CG I   ++K  L      K       +D  VE           
Sbjct: 160 DFGSNPKKEKRPGHGGCGNIQPTIRKEQLKLNGTWKLGKNEDGEDNGVEK---------- 209

Query: 270 FNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
                         + + P EVL++F  I  +D+  L +N + ++P  ++LT L VPP  
Sbjct: 210 --------------KIITPQEVLRVFGLISEDDLLRLGLNVDYARPEWMVLTVLPVPPPA 255

Query: 330 IRPSVISD-----LKSDNDVV 345
           +RPS+  D     ++S++D+ 
Sbjct: 256 VRPSISVDGTSQGMRSEDDLT 276



 Score = 87.4 bits (215), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 75/295 (25%), Positives = 133/295 (45%), Gaps = 57/295 (19%)

Query: 759  KLSQDGVPRIKEIINASRNISTPIITAYL--DKDTDLDYARIVKGRLERTTLGEVCEYIE 816
            K +  GVPR+KEI+N + NI TP +  Y   +     D A++++ ++E T+L  V +  E
Sbjct: 1109 KTTTKGVPRLKEILNVADNIKTPNMKVYQLPEARAAQDSAKLLRSKVEFTSLRGVTDAAE 1168

Query: 817  EVFVPDDSFILIKLDMDRIRLLHL--EVDIDS--------IRYCIERTRGISGHLTVSGH 866
              + PD    +I  D D +    +  E   DS        +R+ + R + +   LTV+  
Sbjct: 1169 IYYDPDIESTVIDEDRDMVESYFIIPEEGADSPDAQSRWLLRFVLGRRQLLDKGLTVTQV 1228

Query: 867  S----------------------------FLILKPKDSSKSFNSKMYQMKQL----LPSV 894
            +                             L    KD     +S+   +KQL    L +V
Sbjct: 1229 AQKIKEVYTSDIAVIFSDDNAEQTVVRVRMLNRGDKDEEGDESSEDDTLKQLAEHMLDNV 1288

Query: 895  VIKGVQGINRAVIHEEDV-------------EGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
            +++GV G+ R  + + +              E   ++ L  +G NL+ V+A  GV   + 
Sbjct: 1289 ILRGVNGVRRVFVSKANQIIEKPNGAMTQGGEESVEWYLDTDGVNLQKVLAVDGVDSART 1348

Query: 942  SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL 996
            + N+     K  GIEA R+++M E+K V+ N G  ++ RH  ++ D+M ++GE++
Sbjct: 1349 TCNHFQSTMKVFGIEAVRASLMAEMKDVLTNDGSYVNHRHMAILCDVMCARGELM 1403



 Score = 55.8 bits (133), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/37 (64%), Positives = 28/37 (75%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            +++RA + P   VG LAAQSIGEP TQMTL TFH AG
Sbjct: 1069 RFLRALVSPGEMVGVLAAQSIGEPATQMTLNTFHLAG 1105


>gi|359294825|gb|AEV21783.1| RPB1, partial [Mortierella wolfii]
          Length = 464

 Score =  161 bits (407), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 93/271 (34%), Positives = 147/271 (54%), Gaps = 37/271 (13%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D DVV+FNRQPSLHK+S+M HR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQ+ E
Sbjct: 89  NDGDVVIFNRQPSLHKMSMMGHRIRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSVE 148

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE               ++ M  K  +V+P++ + ++   QD + G    T+++ F +
Sbjct: 149 TRAEL-------------TEICMVPKQ-IVSPQSNKPVMGIVQDTLCGIRKFTKRDCFLS 194

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPV-VFVRTAVIWTGKQIFSLILKPNRDCP 518
           +   M +             ++    W  + P    ++   +WTGKQI S+++      P
Sbjct: 195 KDLVMNL-------------VMWVPGWEGFLPTPAILKPKPLWTGKQILSMVI------P 235

Query: 519 VNANLKTKGRAYTANE--EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
              N  T    +  NE  +    D+ VI+ N ELLAG + K T+G+ G   + ++++   
Sbjct: 236 KGINCITYHSTHPDNEDTDISPGDTKVIVENGELLAGIVCKKTVGTSG-GGLIHVIMNQH 294

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           G +VA T       + +++L+  GFSIGIGD
Sbjct: 295 GPEVAKTFFNGCQTVVNYWLLQNGFSIGIGD 325


>gi|406865480|gb|EKD18522.1| DNA-directed RNA polymerase 2 largest subunit [Marssonina brunnea
           f. sp. 'multigermtubi' MB_m1]
          Length = 1738

 Score =  161 bits (407), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 96/282 (34%), Positives = 144/282 (51%), Gaps = 50/282 (17%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D ++FNRQPSLHK S+M HR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQTEE 
Sbjct: 451 DGDFIVFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQTEET 510

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE +               L     N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 511 RAEIM--------------NLCMVPLNIVSPQRNGPLMGIVQDTLAGVYKMCRRDCFVTK 556

Query: 461 AQTMRIASTLIADTSDICGIIKRFSW-RSWNPVV----FVRTAVIWTGKQIFSLILKPNR 515
              M I                   W   W+ V+     ++    WTGKQ+ S+I+    
Sbjct: 557 EHLMNI-----------------LLWVPEWDGVIPQPAILKPRPRWTGKQVVSMIIPKI- 598

Query: 516 DCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLG--SGGKANVFYILL 573
              VN N+   GR     E+   +D  +++   EL+ G M K  +G  SGG   + +I+ 
Sbjct: 599 ---VNLNMPNDGR-----EDAPLKDDGLLVHEGELMYGLMAKKNIGATSGG---IIHIIF 647

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFV 615
            + G D A+       R+ +++L++ GFSIGIGD  P +  +
Sbjct: 648 NEMGSDAAMAFFNGCQRVVNYWLLHNGFSIGIGDTVPDKSTI 689



 Score =  104 bits (260), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 59/185 (31%), Positives = 100/185 (54%), Gaps = 15/185 (8%)

Query: 1225 QLLPSVVIKGVQGINRAVIHEE---------------DVEGVTKYKLLVEGDNLRDVMAT 1269
             +L ++ ++GV+G++RA +++E               D     ++ L   G  L DV+  
Sbjct: 1279 HILDTLTLRGVKGVDRAFLNKETKLIETPAGGLLASKDDPRCEEWYLDTSGTELGDVLTI 1338

Query: 1270 YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 1329
             GV   +  SN+  +V++  GIEA RS +M E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1339 PGVDTTRTYSNHFIQVFQVFGIEATRSALMRELTQVLAFDGSYVNHRHLALLVDVMTSRG 1398

Query: 1330 EVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
             ++ ITRHG+ +     L   SFE T + L +AA  G+ D   G+SE +++G    +GTG
Sbjct: 1399 HLMAITRHGINRADTGALMRCSFEETVEILLEAAAVGELDDCRGISENVMLGQLAPMGTG 1458

Query: 1390 LIKLL 1394
             + +L
Sbjct: 1459 ELDVL 1463



 Score =  101 bits (251), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+  
Sbjct: 804 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDVMA 863

Query: 666 QYD 668
           +YD
Sbjct: 864 KYD 866



 Score = 87.8 bits (216), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 73/291 (25%), Positives = 137/291 (47%), Gaps = 57/291 (19%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVC----------- 812
            GVPR+KEI+N + NI TP +  YL+ + + + A++++  +E T L  V            
Sbjct: 1112 GVPRLKEILNVATNIKTPSMVVYLEGNGNQESAKLLRSAVEHTNLRSVTAATEIYHDPDI 1171

Query: 813  ---------EYIEEVFV-PDDSF--------ILIKLDMDRIRLLHLEVDIDSIRYCIERT 854
                     + +E  F+ PDDS          L++L +DR ++L   + ++ +   I+  
Sbjct: 1172 QSTTIEDDLDMVESYFIIPDDSHDAPDNQSRWLLRLVLDRQKMLDKGLRVEDVATKIKEA 1231

Query: 855  RGISGHLTVSGHSF------LILKPKDSSKSFNSKMYQ---MKQL----LPSVVIKGVQG 901
                  +  S ++       + +  +  SK  +  + Q   +K+L    L ++ ++GV+G
Sbjct: 1232 YQKDLAVIFSDNNAEEQVIRIRMINQSDSKFEDDDIEQDIMLKRLEAHILDTLTLRGVKG 1291

Query: 902  INRAVIHEE---------------DVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNT 946
            ++RA +++E               D     ++ L   G  L DV+   GV   +  SN+ 
Sbjct: 1292 VDRAFLNKETKLIETPAGGLLASKDDPRCEEWYLDTSGTELGDVLTIPGVDTTRTYSNHF 1351

Query: 947  YEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +V++  GIEA RS +M E+  V+   G  ++ RH  L+ D+MTS+G ++ 
Sbjct: 1352 IQVFQVFGIEATRSALMRELTQVLAFDGSYVNHRHLALLVDVMTSRGHLMA 1402



 Score = 78.2 bits (191), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 59/218 (27%), Positives = 99/218 (45%), Gaps = 20/218 (9%)

Query: 110 DPQRT-PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVIN 168
           D  RT P   GL D R+G+  ++  C TC QN+S+C GHFG+I+L  PV+H G+ +    
Sbjct: 44  DETRTKPRDQGLNDPRLGSIDRQFKCATCDQNMSECPGHFGHIELAKPVYHPGFLKKTKK 103

Query: 169 ILQSICKNPTCARVLLGEEKAAGFRA--KLRNPALSYLVRKSLKKKILETTKKVSVCPHC 226
           +L+ +C N  C RVLL     A ++A   +R+P   +         I    K   +C   
Sbjct: 104 LLEMVCHN--CGRVLLDRSNPA-YKAAVNIRDPKRRF-------DTIWRLCKPKMICDSD 153

Query: 227 GE---INGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLI 283
                 +G V    L K +H    N   +   +  +L   +      + E    +K    
Sbjct: 154 ASQEGADGSVDPKDLAKRAHGGCGNTQPEVRQVALELFGTWKVPKDEDNEGAQPEK---- 209

Query: 284 QTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
           + + P   L +F +I   +I  L ++ + ++P  +I+T
Sbjct: 210 RAITPEMALNVFRSISTSEIFDLGLSNDYARPEWMIIT 247



 Score = 58.2 bits (139), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 25/37 (67%), Positives = 29/37 (78%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            +++RA + P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1067 RFMRALVNPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1103


>gi|359294827|gb|AEV21784.1| RPB1, partial [Mortierella wolfii]
 gi|359294829|gb|AEV21785.1| RPB1, partial [Mortierella wolfii]
          Length = 467

 Score =  161 bits (407), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 93/271 (34%), Positives = 147/271 (54%), Gaps = 37/271 (13%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D DVV+FNRQPSLHK+S+M HR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQ+ E
Sbjct: 92  NDGDVVIFNRQPSLHKMSMMGHRIRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSVE 151

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE               ++ M  K  +V+P++ + ++   QD + G    T+++ F +
Sbjct: 152 TRAEL-------------TEICMVPKQ-IVSPQSNKPVMGIVQDTLCGIRKFTKRDCFLS 197

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPV-VFVRTAVIWTGKQIFSLILKPNRDCP 518
           +   M +             ++    W  + P    ++   +WTGKQI S+++      P
Sbjct: 198 KDLVMNL-------------VMWVPGWEGFLPTPAILKPKPLWTGKQILSMVI------P 238

Query: 519 VNANLKTKGRAYTANE--EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
              N  T    +  NE  +    D+ VI+ N ELLAG + K T+G+ G   + ++++   
Sbjct: 239 KGINCITYHSTHPDNEDTDISPGDTKVIVENGELLAGIVCKKTVGTSG-GGLIHVIMNQH 297

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           G +VA T       + +++L+  GFSIGIGD
Sbjct: 298 GPEVAKTFFNGCQTVVNYWLLQNGFSIGIGD 328


>gi|307353875|ref|YP_003894926.1| DNA-directed RNA polymerase subunit A' [Methanoplanus petrolearius
           DSM 11571]
 gi|307157108|gb|ADN36488.1| DNA-directed RNA polymerase subunit A' [Methanoplanus petrolearius
           DSM 11571]
          Length = 880

 Score =  161 bits (407), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 94/271 (34%), Positives = 148/271 (54%), Gaps = 38/271 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           ++D+VLFNRQPSLH++SIMAHR  ++  +TFR N  VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 414 NDDIVLFNRQPSLHRMSIMAHRVVLMDGKTFRLNPAVCPPYNADFDGDEMNLHVPQTEEA 473

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEA               +L +   N+++PR G  +I    D I+G ++LT +  +F++
Sbjct: 474 RAEAF--------------MLASVAENILSPRFGGPIIGGIHDHISGIFILTHQVKWFDK 519

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              + +      +     G ++       N + +      W+ KQ+FS+IL      P N
Sbjct: 520 KGVLYLLRASTPEHLPKPGKVE-------NGIEY------WSNKQVFSMIL------PDN 560

Query: 521 ANLKTKGRAY----TANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            N+  K  +     T  +E C RD+YV + + EL+ G +DK ++G+  K  +   ++R  
Sbjct: 561 LNMVYKASSCINCDTCKKEDCERDAYVKIIDGELICGVIDKESIGA-FKGKILQRIIRQV 619

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
             D     +  +++++   +M  GFS GI D
Sbjct: 620 SLDRGRQFVDDVTKLSIRGIMYDGFSFGIDD 650



 Score =  107 bits (266), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 78/266 (29%), Positives = 119/266 (44%), Gaps = 43/266 (16%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G IE  +     +++ S  +I+  + Y  D    P P GL+D  +G       C TCG  
Sbjct: 8   GKIEFGLLSPKDIRKMSVRKIIWADTY--DDDGFPYPQGLMDLHLGVIDPGLRCKTCGNR 65

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
            SDC GHFG+I+L  PV H+GY R +  +L+  C+   C R+LL E++            
Sbjct: 66  ASDCPGHFGHIELAKPVIHVGYTRLIRKLLRVSCRE--CGRLLLSEDEIHKVLGPEDERN 123

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDL 260
              +  K +KK+         VCP+CGE          LKI+ EK               
Sbjct: 124 EDVISEKDIKKE--------RVCPYCGEQQ--------LKINFEK--------------- 152

Query: 261 LAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
                    F+  +       +   L P ++    E IP ED+ LL +N E+++P    L
Sbjct: 153 ------PTTFSEVMTDENGRKIDHKLTPADIRARLEKIPDEDLRLLGINPEVARPEWTCL 206

Query: 321 TRLLVPPNCIRPSVI--SDLKSDNDV 344
           T L VPP  +RPS+I  +  +S++D+
Sbjct: 207 TVLPVPPVTMRPSIILENGQRSEDDL 232



 Score = 96.3 bits (238), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 40/60 (66%), Positives = 52/60 (86%)

Query: 609 TPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            P  GFV+NS+ SGLTPTEFFFH +GGREGLVDTAV+T+++GY+QRR++ +L+DL V YD
Sbjct: 776 APAHGFVRNSYKSGLTPTEFFFHAIGGREGLVDTAVRTSQSGYLQRRMINALQDLKVGYD 835


>gi|397135971|gb|AFO11480.1| RNA polymerase I, partial [Botryozyma nematodophila]
          Length = 872

 Score =  161 bits (407), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 95/273 (34%), Positives = 148/273 (54%), Gaps = 46/273 (16%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
            D D VLFNRQPSLHK+S+MAHR KV+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE
Sbjct: 250 QDGDPVLFNRQPSLHKMSMMAHRVKVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEE 309

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE L  L  +S+              +V+P++ + ++   QD + G   LT+++ F  
Sbjct: 310 TRAE-LSQLCMVSL-------------QIVSPQSNKPVMGIVQDSLCGIRKLTKRDTFIT 355

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSW-RSWNPVV----FVRTAVIWTGKQIFSLILKPN 514
             + M I                   W   WN +V     +R   +WTGKQ+ S+ +   
Sbjct: 356 FEEMMDI-----------------LMWVPDWNGIVVQPAIIRPKPLWTGKQVISMCI--- 395

Query: 515 RDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLR 574
              P   N++   R      +    D+ +++ N E++ G +DK T+G G + ++ + ++R
Sbjct: 396 ---PKGINIQ---RYEEGTGKLSPTDNGMLVDNGEIIYGVVDKKTVG-GKEGDLIHTIMR 448

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           + G  V       + ++ +F+L++ GFSIGIGD
Sbjct: 449 EKGNVVCCNFFTGIQQVVNFWLLHNGFSIGIGD 481



 Score =  102 bits (254), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 45/65 (69%), Positives = 55/65 (84%), Gaps = 1/65 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GF++NS+  GLTP EFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+ V
Sbjct: 604 DYSPESRGFIENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDVMV 663

Query: 666 QYDMS 670
           QYD +
Sbjct: 664 QYDTT 668


>gi|397135967|gb|AFO11478.1| RNA polymerase I, partial [Dipodascopsis anomala]
          Length = 872

 Score =  160 bits (406), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 95/273 (34%), Positives = 151/273 (55%), Gaps = 48/273 (17%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+D VLFNRQPSLHK+S+MAHR KV+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 251 DDDPVLFNRQPSLHKMSMMAHRVKVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 310

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE               ++L A    +V+P++ + ++   QD + G   +T++++F + 
Sbjct: 311 RAE--------------LRMLCAVPLQIVSPQSNKPVMGIVQDSLCGVRKMTKRDSFLSY 356

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVV----FVRTAVIWTGKQIFSLILKPNRD 516
            Q M I                 F   +W+ V+     ++    WTGKQ+ S+++     
Sbjct: 357 DQVMNIL----------------FWVPNWDGVIPQPAILKPKAYWTGKQMMSMVI----- 395

Query: 517 CPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLG--SGGKANVFYILLR 574
            P   N++   R    N     RD+ +++ N E++ G +DK T+G  SGG   + + ++R
Sbjct: 396 -PKGINMQ---RFDDKNTLLSVRDNGMMIENGEIMYGVVDKKTVGATSGG---LIHTIMR 448

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           D G       +  +  + +++L++ GFSIGIGD
Sbjct: 449 DKGPVPTRDFIGGVQTVVNYWLLHNGFSIGIGD 481



 Score = 99.8 bits (247), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 43/65 (66%), Positives = 55/65 (84%), Gaps = 1/65 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GF++NS+  GLTP EFFFH M GREG++DTAVKTAETGY+QRRLVK+LED+ V
Sbjct: 604 DYSPESRGFIENSYLRGLTPQEFFFHAMAGREGIIDTAVKTAETGYIQRRLVKALEDVMV 663

Query: 666 QYDMS 670
           +YD +
Sbjct: 664 KYDAT 668


>gi|120561199|gb|ABM26985.1| RNA polymerase II largest subunit, partial [Trichophyton rubrum]
          Length = 1015

 Score =  160 bits (406), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 94/272 (34%), Positives = 150/272 (55%), Gaps = 35/272 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D +LFNRQPSLHK S+M+HR +V+P+ TFR N  V TPYNADFDGDEMN+H+PQ+EEA
Sbjct: 371 DGDFILFNRQPSLHKESMMSHRVRVMPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSEEA 430

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L++L ++            N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 431 RAE----LNQLCLVP----------LNIVSPQRNGPLMGIVQDTLCGIYKICRRDVFLTK 476

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M +    +    D  G++ +       P + ++    W+GKQ+ S++L      P  
Sbjct: 477 EQVMNV----LLWVPDWDGVLPQ-------PAI-LKPRPRWSGKQMISMVL------PSG 518

Query: 521 AN-LKTKGRAYTANEEFCH-RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            N L+        +E+F    D  V++   EL+ G   K T+G+ G   + + +  ++G 
Sbjct: 519 LNLLRIDKDKSPISEKFSPLADGGVLVHGGELMYGMFSKKTVGASG-GGIVHTIFNEYGP 577

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           D A++       + +++L++ GFSIGIGD  P
Sbjct: 578 DAAMSFFNGAQAVVNYWLLHNGFSIGIGDTIP 609



 Score = 99.4 bits (246), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QR+LVK+LE++ V
Sbjct: 729 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMV 788

Query: 666 QYD 668
           +YD
Sbjct: 789 KYD 791



 Score = 46.6 bits (109), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 43/188 (22%), Positives = 81/188 (43%), Gaps = 38/188 (20%)

Query: 150 YIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKS 208
           +I+L  PVFHIG+   +  +L+++C N  C ++           A + R+P   +     
Sbjct: 1   HIELSTPVFHIGFLTKIKKLLETVCHN--CGKIKANASDQKYLDALRFRDPKKRFDAIWR 58

Query: 209 LKKKIL---------------ETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKK 253
           L K IL               E++K V     CG +   V+K G+  +   K    +K +
Sbjct: 59  LSKDILICEADPPEEDDPFAKESSKPVQGHGGCGNVQPQVRKEGITLMGTWK---PSKMR 115

Query: 254 DAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELS 313
           D + ++             EI+  +K    + + P   L +F  I  ED+ L+ ++ + +
Sbjct: 116 DMMDDN-------------EIQQPEK----KQITPQMALTIFRNISEEDVRLMGLSNDYA 158

Query: 314 KPSDLILT 321
           +P  +I+T
Sbjct: 159 RPEWMIIT 166


>gi|214028082|gb|ACJ63310.1| RNA polymerase III large subunit [Liriodendron tulipifera]
          Length = 546

 Score =  160 bits (406), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 87/230 (37%), Positives = 136/230 (59%), Gaps = 29/230 (12%)

Query: 392 VHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLL 451
           +++PQTEEAR EAL              +LM  ++NL TP+NGE+L+A+TQDF+T  +L+
Sbjct: 1   LYVPQTEEARTEAL--------------MLMGVQNNLCTPKNGEILVASTQDFLTSSFLI 46

Query: 452 TQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPV-VFVRTAVIWTGKQIFSLI 510
           T+K+ F++RA    +  + + D  D   +          P    ++   +WTGKQ+FS++
Sbjct: 47  TRKDTFYDRA-AFSLMCSYMGDGMDPIDL----------PTPALLKPIELWTGKQLFSVL 95

Query: 511 LKPNRDCPVNANLKTKGRAYTANEE---FCHRDSYVILRNSELLAGSMDKSTLGSGGKAN 567
           ++P+    V  NL    R Y  +++    C  D YV  RNSELL G + K+TLG+G K  
Sbjct: 96  IRPHARMRVYLNLTLTERIYDKSKDKKTMCPNDGYVYFRNSELLCGQLGKATLGNGNKDG 155

Query: 568 VFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           +F +LLRD+G   A + M RL+++++ ++ N GFSIGI DV PG+   +N
Sbjct: 156 LFSVLLRDYGAHAAASCMNRLAKLSARWIGNHGFSIGIDDVQPGEHLNRN 205



 Score =  103 bits (258), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 50/65 (76%), Positives = 54/65 (83%), Gaps = 1/65 (1%)

Query: 605 IGDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDL 663
           I   TP  +GFV NSF++GLT TEFFFHTMGGREGLVDTAVKTAETGYM RRL+KSLEDL
Sbjct: 316 INSKTPSAKGFVANSFYTGLTATEFFFHTMGGREGLVDTAVKTAETGYMSRRLMKSLEDL 375

Query: 664 CVQYD 668
              YD
Sbjct: 376 STYYD 380



 Score = 56.6 bits (135), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 22/42 (52%), Positives = 36/42 (85%)

Query: 21 VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRA 62
          +LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+K+ F++RA
Sbjct: 15 MLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDRA 56


>gi|120561213|gb|ABM26992.1| RNA polymerase II largest subunit, partial [Capniomyces stellatus]
          Length = 1024

 Score =  160 bits (406), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 93/270 (34%), Positives = 148/270 (54%), Gaps = 37/270 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+DVV+FNRQPSLHK+S+M HR KV+P+ TFR N  V +PYNADFDGDEMN+HLPQ+EE 
Sbjct: 377 DDDVVIFNRQPSLHKMSMMGHRVKVMPYSTFRLNLSVTSPYNADFDGDEMNLHLPQSEET 436

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    + +L ++  +          +V+P+  + ++   QD +    + T+++     
Sbjct: 437 RAE----IRELCMVPKQ----------IVSPQANKPVMGIVQDTLCALLMFTKRDTLMRL 482

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPV-VFVRTAVIWTGKQIFSLILKPNRDCPV 519
              M +             ++K   W    P    ++   +W+GKQIFSLI+      P 
Sbjct: 483 DMVMSL-------------LLKVPGWDGLIPTPCILKPQPLWSGKQIFSLII------PK 523

Query: 520 NANLKTKGRAYTANE-EFCH-RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFG 577
             N  T  + +  NE  +C   DS V++ N ELL+G + K T+G+  +  + +++  + G
Sbjct: 524 GINCYTFFKDHPDNETAWCSPGDSRVVIENGELLSGIICKQTVGA-VRGGIVHVIFNELG 582

Query: 578 EDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            + A        R+ + ++++ GFSIGIGD
Sbjct: 583 SEAAKIFFGGTQRVVNLWMLSNGFSIGIGD 612



 Score =  101 bits (252), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTP EF+FH MGGREGL+DTAVKTAETGY+QRRLVK+LED+ V
Sbjct: 735 DYSPQSRGFVENSYLRGLTPQEFYFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMV 794

Query: 666 QYD 668
            YD
Sbjct: 795 HYD 797


>gi|453086034|gb|EMF14076.1| DNA-dependent RNA polymerase II largest subunit [Mycosphaerella
           populorum SO2202]
          Length = 1780

 Score =  160 bits (406), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 94/280 (33%), Positives = 141/280 (50%), Gaps = 44/280 (15%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D ++FNRQPSLHK S+M HR KV+P+ TFR N  V +PYNADFDGDEMN+H+PQ+ E 
Sbjct: 451 DGDYIIFNRQPSLHKESMMGHRVKVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSHET 510

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R+E    +  L  + H          N+V+P+    L+   QD + G Y++T+++   + 
Sbjct: 511 RSE----VANLCAVPH----------NIVSPQKNGPLMGIVQDTMAGIYMMTKRDTMMDY 556

Query: 461 AQTMRIASTLIADTSDICGIIKRFSW-RSWNPVV----FVRTAVIWTGKQIFSLILKPNR 515
            Q M I                   W   W+ +V     ++    WTGKQI S+ L    
Sbjct: 557 EQVMNI-----------------MLWVPGWDGIVPQPAILKPVPRWTGKQIMSMGL---- 595

Query: 516 DCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
             P   N+   G     +      DS V+++N EL+ G + K  +G+ G   + +++  D
Sbjct: 596 --PSGLNIMKLGDD-EDHISLAEADSSVLVQNGELVWGRLTKKLVGASG-GGIVHLIFND 651

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFV 615
            G D  V       R+  ++L++ GFS+GIGD  P    V
Sbjct: 652 RGTDATVEFFNAAQRIVCYWLLHNGFSVGIGDTIPDADMV 691



 Score =  112 bits (280), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 63/186 (33%), Positives = 104/186 (55%), Gaps = 15/186 (8%)

Query: 1224 KQLLPSVVIKGVQGINRAVIHE-----EDVEG----------VTKYKLLVEGDNLRDVMA 1268
            + +L +VV++GVQG+ R  + +     E+ +G            ++ L  +G NL+DV+A
Sbjct: 1282 EHMLDNVVLRGVQGVRRVFVSKDLSMIEEADGKLVKSKNDKACEEWYLDTDGINLKDVLA 1341

Query: 1269 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK 1328
              GV   + + N+     +  GIEA R+++M E+K V+ N G  ++ RH  ++ D+M ++
Sbjct: 1342 VEGVDSTRTTCNHFQSTMRVFGIEAVRASLMRELKDVLTNDGSYVNHRHMAILCDVMCAR 1401

Query: 1329 GEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGT 1388
            GE++ +TRHG+ +     L   SFE T + LF+AA  G+ D   GVSE II+G     GT
Sbjct: 1402 GELMAVTRHGINRADTGALMRCSFEETVEILFEAASSGELDDCRGVSENIILGQLAPSGT 1461

Query: 1389 GLIKLL 1394
            G   +L
Sbjct: 1462 GEFDVL 1467



 Score =  104 bits (260), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 76/261 (29%), Positives = 122/261 (46%), Gaps = 51/261 (19%)

Query: 110 DPQRT-PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVIN 168
           D QR  P   GL D ++GT  +   C TCG++  +C GHFG+I+L +PV+H+GY   +  
Sbjct: 42  DEQRNRPRERGLNDPKLGTIDRSQMCATCGESQQECPGHFGHIELAVPVYHVGYITKIKK 101

Query: 169 ILQSICKNPTCARVLLGEEKAA-GFRAKLRNP-----ALSYLVRKSLKKKILETT----- 217
           IL+S+C N  C ++L  E         KLR+P     A++ L +  +  +  E +     
Sbjct: 102 ILESVCNN--CGKLLEDERNPTFALAIKLRDPKRRFEAVTRLCKPKMDCQTDEPSDEDGQ 159

Query: 218 -----KKVSVCPH--CGEINGVVKKCGLLKISHEKY-KNRTKKKDAIVEDLLAEYNEAVK 269
                KK  +  H  CG +   ++K GL  I   K  KN    +D   E           
Sbjct: 160 FGDDPKKPKLAGHGGCGNMQPTIRKDGLKLIGTWKMPKNEDTGEDNSPEK---------- 209

Query: 270 FNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
                         + + P + L++F  I  ED+  L +N + ++P  +ILT L VPP  
Sbjct: 210 --------------KPITPTDALRVFRNISDEDLYRLGLNVDYARPEWMILTVLPVPPPA 255

Query: 330 IRPSVISD-----LKSDNDVV 345
           +RPS+  D     ++S++D+ 
Sbjct: 256 VRPSISVDGTSQGMRSEDDLT 276



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKTAETGY+QRRLVK+LE++ +
Sbjct: 806 DYSPASRGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEEIMI 865

Query: 666 QYD 668
           +YD
Sbjct: 866 KYD 868



 Score = 92.4 bits (228), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 78/296 (26%), Positives = 142/296 (47%), Gaps = 58/296 (19%)

Query: 759  KLSQDGVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIE 816
            K +  GVPR+KEI+N + NI TP +  + +    T  + A++++ ++E T+L  V +  E
Sbjct: 1110 KTTTKGVPRLKEILNVADNIKTPNMRVFQEPHATTKQESAKLLRSKVEFTSLRGVTDAAE 1169

Query: 817  EVFVPDDSFILIKLDMDRIRLLHL------EVDIDS---IRYCIERTRGISGHLTVSGHS 867
              + PD    +I+ D D +    +        D  S   +R+ + R + +   LTV+  +
Sbjct: 1170 IYYDPDVQSTVIEEDRDMVESYFIIPEEGENPDAQSKWMLRFVLGRRQLLDKGLTVTNVA 1229

Query: 868  FLILK--PKDSSKSFN--------------------------SKMYQMKQL----LPSVV 895
              I +  PKD +  F+                          S+   +KQL    L +VV
Sbjct: 1230 EKIRETYPKDVAVIFSDDNSDEMVVRVRMTNQADKEEELGESSEDDTLKQLSEHMLDNVV 1289

Query: 896  IKGVQGINRAVIHE-----EDVEG----------VTKYKLLVEGDNLRDVMATYGVKGVK 940
            ++GVQG+ R  + +     E+ +G            ++ L  +G NL+DV+A  GV   +
Sbjct: 1290 LRGVQGVRRVFVSKDLSMIEEADGKLVKSKNDKACEEWYLDTDGINLKDVLAVEGVDSTR 1349

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL 996
             + N+     +  GIEA R+++M E+K V+ N G  ++ RH  ++ D+M ++GE++
Sbjct: 1350 TTCNHFQSTMRVFGIEAVRASLMRELKDVLTNDGSYVNHRHMAILCDVMCARGELM 1405



 Score = 55.5 bits (132), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/37 (64%), Positives = 28/37 (75%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            +++RA + P   VG LAAQSIGEP TQMTL TFH AG
Sbjct: 1070 RFLRALVSPGEMVGVLAAQSIGEPATQMTLNTFHLAG 1106


>gi|145351142|ref|XP_001419944.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144580177|gb|ABO98237.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 1646

 Score =  160 bits (406), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 94/269 (34%), Positives = 148/269 (55%), Gaps = 34/269 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + DVVLFNRQPSLHK+SIM HR +++P+ TFR N  V  PYNADFDGDEMN+HLPQ+ E 
Sbjct: 428 NGDVVLFNRQPSLHKMSIMGHRVRIMPYSTFRLNLSVTPPYNADFDGDEMNMHLPQSYET 487

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE               K LM     +V+P+  + ++A  QD + G  L+T+++ F  +
Sbjct: 488 RAE--------------VKELMMVPKMIVSPQANKPVMAIVQDTLLGCRLITKRDTFITK 533

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              M I   L     D  G + +       P + ++   +WTGKQ+FS++L      P  
Sbjct: 534 DVFMNIIMWL----EDWDGKVPK-------PAI-LKPQPLWTGKQVFSMML------PKV 575

Query: 521 ANLKTKGRAYTANE-EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
             L+T   A  +++  F   D+ V +   ELL G++ K T+GSGG   + ++   ++G  
Sbjct: 576 NLLRTSAWAKDSDDMAFSVDDTGVRIEQGELLTGTLCKKTMGSGG-GGLIHVTWEEWGPI 634

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
            A   + +   + ++++++ GF++GI D 
Sbjct: 635 AARGLISQTQTLVNYWVLHHGFTVGIADT 663



 Score =  109 bits (273), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 62/179 (34%), Positives = 105/179 (58%), Gaps = 10/179 (5%)

Query: 1225 QLLPSVVIKGVQGINRAVIHE----------EDVEGVTKYKLLVEGDNLRDVMATYGVKG 1274
            Q+L ++ ++G+  I +  I E          E  E  T++ L  EG NL +VMA   V  
Sbjct: 1261 QMLSNLALRGIPDIKKVFIREAKQNAINSKTELFEKTTEWMLDTEGVNLLEVMAHPDVDF 1320

Query: 1275 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGI 1334
             + +SN+  EV + LGIEA R+T++ E++ V+E  G  +++RH  ++ ++MT +G ++ I
Sbjct: 1321 TRTTSNHLIEVIQVLGIEAVRNTLLRELRGVIEFDGSYVNYRHLAILVEVMTYRGHLMSI 1380

Query: 1335 TRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
            TRHG+ +++   L   SFE T D L +A+ + + D ++G SE I++G    +GTG  KL
Sbjct: 1381 TRHGINRVETGPLMRCSFEETVDILMEASAFSERDNMTGPSENIMLGQFCPIGTGEFKL 1439



 Score =  100 bits (249), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 42/57 (73%), Positives = 52/57 (91%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKT+ETGY+QRRLVK++ED+ V+YD
Sbjct: 791 RGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDVVVKYD 847



 Score = 85.9 bits (211), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 79/286 (27%), Positives = 136/286 (47%), Gaps = 53/286 (18%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEIIN +++I TP +T  L  +   D   A+  +  LE TTL  V    E  + P
Sbjct: 1093 GVPRLKEIINIAKSIKTPSLTIALKPELAGDRTRAKDCQASLEYTTLHSVAAVTEVHYDP 1152

Query: 822  DDSFILIKLDMDRIRLLH--LEVDIDSIRYC-----IERTRGI----------------- 857
            D +  +I+ D + +R  +   + D+D  R       IE  R +                 
Sbjct: 1153 DPTDTVIEEDREFVRAYYEMPDEDVDPSRMSPWLLRIELNREMMVDKKLLMADVAERINE 1212

Query: 858  --SGHLTV----SGHSFLIL----------KPKDSSKSFNSKMYQMK-QLLPSVVIKGVQ 900
              +G L+          L+L          K +D+S      + +++ Q+L ++ ++G+ 
Sbjct: 1213 DFAGDLSCIFNDDNSEKLVLRIRIMNPEGVKYEDASTEDEVFLKRLETQMLSNLALRGIP 1272

Query: 901  GINRAVIHE----------EDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVY 950
             I +  I E          E  E  T++ L  EG NL +VMA   V   + +SN+  EV 
Sbjct: 1273 DIKKVFIREAKQNAINSKTELFEKTTEWMLDTEGVNLLEVMAHPDVDFTRTTSNHLIEVI 1332

Query: 951  KTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL 996
            + LGIEA R+T++ E++ V+E  G  +++RH  ++ ++MT +G ++
Sbjct: 1333 QVLGIEAVRNTLLRELRGVIEFDGSYVNYRHLAILVEVMTYRGHLM 1378



 Score = 68.2 bits (165), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 68/237 (28%), Positives = 111/237 (46%), Gaps = 40/237 (16%)

Query: 87  VTKEDRVQQQSHIQIVSKNLYCQD-PQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCV 145
           V   D +++ S   I +   Y +  P+R     GL D RMGT  + A C T G +     
Sbjct: 24  VLSPDEIRKMSVCAIETSETYEKGRPKRG----GLSDPRMGTMDRGAVCETDGCDSVQTP 79

Query: 146 GHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA--KLRNPALSY 203
           G+FG+++L  PV+H G+   V+ IL+  C   + +++LL +++   F    +++NP    
Sbjct: 80  GYFGHLELAKPVYHHGFINVVLRILR--CVGYSSSQLLLHKDEDPKFAQLMRIKNP---- 133

Query: 204 LVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAE 263
              K+  KK+ +  K  SVCP+ G      +  G +KI+ E +K+R        E+LL E
Sbjct: 134 ---KNRLKKLTDACKTKSVCPYTGTAQPQYRLEG-MKITAE-FKHRD-------EELLPE 181

Query: 264 YNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
             E               +I T      LQ+ +AI  ED   L ++ E ++P   IL
Sbjct: 182 GGER-------------KVIVTAE--RALQILKAISDEDCRALGLDPEHARPDWFIL 223



 Score = 51.2 bits (121), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 22/37 (59%), Positives = 26/37 (70%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            ++  A   P   +G +AAQSIGEP TQMTL TFHFAG
Sbjct: 1048 RFKMALAPPGDGIGTVAAQSIGEPATQMTLNTFHFAG 1084


>gi|159467413|ref|XP_001691886.1| DNA-directed RNA polymerase II, largest subunit [Chlamydomonas
           reinhardtii]
 gi|158278613|gb|EDP04376.1| DNA-directed RNA polymerase II, largest subunit [Chlamydomonas
           reinhardtii]
          Length = 1789

 Score =  160 bits (406), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 98/271 (36%), Positives = 145/271 (53%), Gaps = 38/271 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + D+VLFNRQPSLHK+S+M HR ++LP+ TFR N  V TPYNADFDGDEMN+H+ QT E 
Sbjct: 448 NGDLVLFNRQPSLHKMSMMGHRVRILPYSTFRLNLSVTTPYNADFDGDEMNMHVAQTHET 507

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE          MA+    LM    N+V+P+  + ++   QD + G  ++T+++ F  +
Sbjct: 508 RAE----------MAN----LMMVPRNIVSPQANKPVMGIVQDALLGTRMMTKRDIFIEK 553

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFV-RTAVIWTGKQIFSLILKPNRDCPV 519
              M            + GI     W    P+  V +   +WTGKQIFS+ +        
Sbjct: 554 DNFMNC----------VMGI---EDWDGTVPMPAVLKPRPLWTGKQIFSMFVP------- 593

Query: 520 NANLKTKGRAYTANE--EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFG 577
           + NLK K   Y   +  +    D+ V++R  ELL G++ K T+G+G    V    L + G
Sbjct: 594 DVNLKNKSAWYKDADVPDMSVDDAQVLIRQGELLTGALCKKTVGNGAGGLVHLTWL-EHG 652

Query: 578 EDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
              A   +  + R  +++++N G SIGIGD 
Sbjct: 653 PHAARGFINNVQRTVNYWVLNHGMSIGIGDT 683



 Score =  105 bits (263), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 66/194 (34%), Positives = 101/194 (52%), Gaps = 10/194 (5%)

Query: 1211 DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYK----------LLVEG 1260
            +S+      M ++   +  V + GV  I +  I  E+     K K          L  EG
Sbjct: 1272 ESADPTEDTMLKLSGAIMDVRLHGVPNIRKVFIRAENQHVYDKEKGAFRKYEEWILDTEG 1331

Query: 1261 DNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPML 1320
             NL  V+A  GV   +  SN+  EV + LGIEAAR+ +  E++ V++  G  +++RH   
Sbjct: 1332 INLEQVLAFEGVDSRRTMSNSIIEVLEVLGIEAARAALFKEVRNVIQFDGSYVNYRHLAC 1391

Query: 1321 VADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIM 1380
            + D+MT KG ++ ITRHG+ +     +   SFE T D L+ AA +G+ D + GVS+ I+M
Sbjct: 1392 LVDIMTCKGCLMAITRHGINRNGNGPMTQCSFEETVDILYRAAMFGERDKLMGVSDNIMM 1451

Query: 1381 GLPMNVGTGLIKLL 1394
            G    +GTG   LL
Sbjct: 1452 GNMCPLGTGSFDLL 1465



 Score = 97.1 bits (240), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 43/62 (69%), Positives = 52/62 (83%), Gaps = 1/62 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D+ P  +GFV NS+  GLTP EFFFH MGGREGL+DTAVKTA TGY+QRRLVK++ED+ V
Sbjct: 805 DLGPEARGFVGNSYLRGLTPQEFFFHAMGGREGLIDTAVKTASTGYIQRRLVKAMEDMVV 864

Query: 666 QY 667
           +Y
Sbjct: 865 RY 866



 Score = 74.3 bits (181), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 69/288 (23%), Positives = 129/288 (44%), Gaps = 58/288 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYL------DKD--------------------TDLDYAR 797
            GVPR+ E+IN ++NI TP +T +L      +KD                    T++ Y  
Sbjct: 1113 GVPRLTELINLAKNIKTPTLTVHLLPGLRENKDAAKEIQSKLEYTCFKNVVKTTEIWYDP 1172

Query: 798  IVKGRLERTTLGEVCEYIEEVF----------VPDDSFILIKLDMDRIRLLHLEVDIDSI 847
            +      +T +GE  E +   +          +P  S  L++ +++R  +L   + + ++
Sbjct: 1173 VDPANANQTVIGEDEEMLSSYYDLAGDEDLAVLPRLSHWLLRFELNRGAMLDKGLTLGAV 1232

Query: 848  RYCIERTRGISGHLTVSGHS-------FLILKPKDSSKSFNSK-----MYQMKQLLPSVV 895
            +  ++       ++ V+  +         ++K +++SK  ++      M ++   +  V 
Sbjct: 1233 QKALQDEWEDFINVLVNDDNAEKLIMRIRVVKTEEASKDESADPTEDTMLKLSGAIMDVR 1292

Query: 896  IKGVQGINRAVIHEEDVEGVTKYK----------LLVEGDNLRDVMATYGVKGVKCSSNN 945
            + GV  I +  I  E+     K K          L  EG NL  V+A  GV   +  SN+
Sbjct: 1293 LHGVPNIRKVFIRAENQHVYDKEKGAFRKYEEWILDTEGINLEQVLAFEGVDSRRTMSNS 1352

Query: 946  TYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
              EV + LGIEAAR+ +  E++ V++  G  +++RH   + D+MT KG
Sbjct: 1353 IIEVLEVLGIEAARAALFKEVRNVIQFDGSYVNYRHLACLVDIMTCKG 1400



 Score = 65.5 bits (158), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 45/138 (32%), Positives = 69/138 (50%), Gaps = 8/138 (5%)

Query: 83  IEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLS 142
           I+ +V     ++  S  +IV+   Y +     P   GL D RMGT  +   CTT G N +
Sbjct: 20  IQFSVWDPAEIKAYSVAEIVTSETYEKG---KPKLGGLSDPRMGTMDRGGICTTDGANAN 76

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEK---AAGFRAKLRNP 199
           D  G+FG+I L  PV+HIG+ + V+ +L+  C +   +R+L+ ++    A G R      
Sbjct: 77  DSPGYFGHIALARPVYHIGFIKTVVRVLR--CVSYHTSRLLVDKDDPKYAYGLRISDSEK 134

Query: 200 ALSYLVRKSLKKKILETT 217
            L Y V     KK+ E T
Sbjct: 135 RLRYFVHLCQGKKMDEAT 152



 Score = 49.3 bits (116), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 22/37 (59%), Positives = 26/37 (70%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            ++  AQ      VG +AAQS+GEP TQMTL TFHFAG
Sbjct: 1068 RFFLAQAHAGECVGTVAAQSLGEPTTQMTLNTFHFAG 1104


>gi|296417677|ref|XP_002838479.1| hypothetical protein [Tuber melanosporum Mel28]
 gi|295634418|emb|CAZ82670.1| unnamed protein product [Tuber melanosporum]
          Length = 442

 Score =  160 bits (406), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 91/222 (40%), Positives = 126/222 (56%), Gaps = 43/222 (19%)

Query: 390 MNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGY 449
           MN+H+PQTEEAR EA+               LM  K+NL TPRNGE +IAA QDFIT  Y
Sbjct: 1   MNLHVPQTEEARTEAIE--------------LMGVKNNLCTPRNGEPIIAAIQDFITASY 46

Query: 450 LLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSL 509
           LL+ K+ F+NR     I   ++     I   +         P + ++   +WTGKQIF+ 
Sbjct: 47  LLSSKDRFYNRKAFANICMYMVDGNMQIDLPL---------PAI-LKPQRLWTGKQIFNA 96

Query: 510 ILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVF 569
           +       P  A             + C  D ++++R SE++ G MDKST+GSG K +VF
Sbjct: 97  V-------PAKA------------PDMCPNDGWLVIRGSEIMCGLMDKSTVGSGKKDSVF 137

Query: 570 YILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           Y++LRD+G D AV AM RL+++ + +L N+GFSIGI DV PG
Sbjct: 138 YVILRDYGPDEAVQAMNRLAKLCARWLANQGFSIGINDVLPG 179



 Score =  102 bits (254), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 46/68 (67%), Positives = 54/68 (79%)

Query: 610 PGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDM 669
           P +GFV+NSF+SGL+PTEF FH + GREGLVDTAVKTAETGYM RRL+KSLEDL   YD 
Sbjct: 302 PSKGFVRNSFYSGLSPTEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSASYDY 361

Query: 670 SFDAAFYG 677
           +   +  G
Sbjct: 362 TVRTSSSG 369



 Score = 59.7 bits (143), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 28/53 (52%), Positives = 35/53 (66%)

Query: 22 LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIAG 74
          LM  K+NL TPRNGE +IAA QDFIT  YLL+ K+ F+NR     I   ++ G
Sbjct: 18 LMGVKNNLCTPRNGEPIIAAIQDFITASYLLSSKDRFYNRKAFANICMYMVDG 70


>gi|83320420|gb|ABC02837.1| RNA polymerase II largest subunit, partial [Rozella allomycis]
          Length = 809

 Score =  160 bits (406), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 97/281 (34%), Positives = 152/281 (54%), Gaps = 37/281 (13%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D DVVLFNRQPSLHK+S+M HR KV+P+ TFR N  V TPYNADFDGDEMN+H+PQ+ E
Sbjct: 168 NDGDVVLFNRQPSLHKMSMMGHRIKVMPYSTFRLNLSVTTPYNADFDGDEMNLHIPQSVE 227

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           A+AE    L +L+++           + +V+P++ +  +   QD + G    T++ +F N
Sbjct: 228 AKAE----LVELALVP----------TQIVSPQSNKPCMGIVQDTLCGVRKFTRRESFLN 273

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNP-VVFVRTAVIWTGKQIFSLILKPNRDCP 518
           +A  M I   L              SW    P    ++   +W+GKQIFS+I+      P
Sbjct: 274 KAMVMNIVMWLP-------------SWEGKLPRPCILKPVPLWSGKQIFSMII------P 314

Query: 519 VNANLKTKGRAYTANE--EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
              N  T    +  NE  +    D+ V++ + EL++G + K T+G      + +++  + 
Sbjct: 315 KGVNCVTFHSTHPDNEYSDISPGDTKVLIEDGELISGIVCKKTVGPAA-GGLIHVIYNEH 373

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           G +VA      +  + + +L+  GFSIGIGD    +  ++N
Sbjct: 374 GSEVAKQFFNGVQTVVNNWLLINGFSIGIGDTIADRQTMKN 414



 Score =  102 bits (255), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 45/64 (70%), Positives = 55/64 (85%), Gaps = 1/64 (1%)

Query: 606 GDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           GD  P  +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKTAETGY+QR+LVK+LED+ 
Sbjct: 526 GDYGPESRGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRKLVKALEDVM 585

Query: 665 VQYD 668
           ++YD
Sbjct: 586 IKYD 589


>gi|397135977|gb|AFO11483.1| RNA polymerase I, partial [Schizosaccharomyces pombe]
          Length = 868

 Score =  160 bits (406), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 94/268 (35%), Positives = 149/268 (55%), Gaps = 38/268 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVV+FNRQPSLHK+S+M HR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 251 DGDVVIFNRQPSLHKMSMMGHRIRVMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSEET 310

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE               ++ M  K  +V+P++ + ++   QD + G    + ++ F  R
Sbjct: 311 RAEI-------------QEITMVPKQ-IVSPQSNKPVMGIVQDTLAGVRKFSLRDNFLTR 356

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              M I   +     D  GI+         P V ++  V+WTGKQI SLI+      P  
Sbjct: 357 NAVMNIMLWV----PDWDGILP--------PPVILKPKVLWTGKQILSLII------PKG 398

Query: 521 ANL-KTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            NL +   +   +N      DS +++ N E++ G +DK T+G+  +  + + + ++ G +
Sbjct: 399 INLIRDDDKQSLSNPT----DSGMLIENGEIIYGVVDKKTVGA-SQGGLVHTIWKEKGPE 453

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           +       + R+ +++L++ GFSIGIGD
Sbjct: 454 ICKGFFNGIQRVVNYWLLHNGFSIGIGD 481



 Score = 99.8 bits (247), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 42/62 (67%), Positives = 52/62 (83%)

Query: 607 DVTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQ 666
           D    +GF++NS+  GLTP EFFFH M GREGL+DTAVKTAETGY+QRRLVK++ED+ V+
Sbjct: 605 DSPESRGFIENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKAMEDVMVR 664

Query: 667 YD 668
           YD
Sbjct: 665 YD 666


>gi|397135973|gb|AFO11481.1| RNA polymerase I, partial [Candida caseinolytica]
          Length = 872

 Score =  160 bits (406), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 94/268 (35%), Positives = 149/268 (55%), Gaps = 38/268 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+D VLFNRQPSLHK+S+MAHR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 251 DDDPVLFNRQPSLHKMSMMAHRVRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 310

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L +L+++  +          +V+P++ + ++   QD + G   LT ++ F N 
Sbjct: 311 RAE----LTQLAMVPLQ----------IVSPQSNKPVMGIVQDSLCGIRKLTLRDTFLNY 356

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPV-VFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q M +             ++    W    P+   ++   +WTGKQI SL +      P 
Sbjct: 357 EQVMNV-------------LLWVPDWDGQVPIPAIMKPKPLWTGKQIVSLCI------PK 397

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
             NL    R    N     +D+ +++ N E++ G +DK T+G+ G   + + ++R+ G  
Sbjct: 398 GINLI---RIDDNNPLSSPKDNGMLIENGEIIFGVVDKKTVGATG-GGLVHTIMREKGPQ 453

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           V       +  + +++L++ GFSIGIGD
Sbjct: 454 VCCNFFTGIQMVVNYWLLHNGFSIGIGD 481



 Score =  100 bits (249), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 53/63 (84%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GF++NS+  GLTP EFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+ V
Sbjct: 604 DYSPESKGFIENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDIMV 663

Query: 666 QYD 668
            YD
Sbjct: 664 HYD 666


>gi|448303811|ref|ZP_21493757.1| DNA-directed RNA polymerase subunit A' [Natronorubrum
           sulfidifaciens JCM 14089]
 gi|445592438|gb|ELY46625.1| DNA-directed RNA polymerase subunit A' [Natronorubrum
           sulfidifaciens JCM 14089]
          Length = 973

 Score =  160 bits (406), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 102/275 (37%), Positives = 145/275 (52%), Gaps = 46/275 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+++FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 481 DGDIIIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQNEEA 540

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR GE +I A QD I+G YLLT  N  FN 
Sbjct: 541 RAE--------------ARVLMRVQEQMLSPRFGENIIGAIQDHISGTYLLTHDNPRFNE 586

Query: 461 AQTMR-IASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q +  + +T I +  +  GI                    WTG  +FS +L      P 
Sbjct: 587 TQALDLLRATRIDELPEPSGIDD-------------EGKPFWTGYDVFSELL------PN 627

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           + NL+  G   T  E+       VI+ + +LL G++ +  +G  G   +   + + +G  
Sbjct: 628 DLNLEFTG---TIGED-------VIIEDGQLLEGTIAEDEVGEFG-GEIVDTITKVYGNT 676

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVT-PGQG 613
            A   +  +S +    +M+ GFSIGI D T PG+ 
Sbjct: 677 RARIFVNEISTLAMRAIMHFGFSIGIDDETIPGEA 711



 Score =  122 bits (307), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 91/308 (29%), Positives = 137/308 (44%), Gaps = 55/308 (17%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G I   + + +  ++ S  +I++ + Y  D    PI  GL+D R+G       C TCGQ+
Sbjct: 10  GAINFGLMEPEEYREMSATKIITADTY--DDDGFPIDMGLMDPRLGVIDPGLECKTCGQH 67

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
              C GHFG+I+L  PV H+G+ + +  +L+  C+   C+++LL E++   FRA +    
Sbjct: 68  SGSCNGHFGHIELAAPVIHVGFTKLIRRLLRGTCRE--CSKLLLTEDERDEFRADIEESR 125

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEK--------------Y 246
                   + K  +   +K   CPHCGEI           I HEK              Y
Sbjct: 126 KLSRDLNDVTKAAIRQARKKDRCPHCGEIQ--------YDIDHEKPTTYYEVQQVLTSEY 177

Query: 247 KNRT-------KKKDAIVEDLLAEYNE----------AVKFNPE------IEAHKKFGLI 283
             R        +  + +  D LAE  E          +  F P       IE      L 
Sbjct: 178 SQRIAAAMQGGEDGERMAPDELAEETEIDLTRINEILSGSFRPRESQRKSIEKALDIDLT 237

Query: 284 QT----LNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD-- 337
           +     L P ++   FEAIP EDI +L +N E S+P  +ILT L VPP   RPS+  D  
Sbjct: 238 EEDTNKLMPSDIRDWFEAIPDEDIEVLGINPERSRPEWMILTVLPVPPVTARPSITLDNG 297

Query: 338 LKSDNDVV 345
            +S++D+ 
Sbjct: 298 QRSEDDLT 305



 Score = 92.8 bits (229), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 39/58 (67%), Positives = 49/58 (84%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
             GFV+NS+ SGLTP EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 832 AHGFVENSYTSGLTPREFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELETQYD 889



 Score = 46.2 bits (108), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 29/46 (63%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 65
           +VLM  +  +++PR GE +I A QD I+G YLLT  N  FN  Q +
Sbjct: 545 RVLMRVQEQMLSPRFGENIIGAIQDHISGTYLLTHDNPRFNETQAL 590


>gi|19112465|ref|NP_595673.1| RNA polymerase II large subunit Rpb1 [Schizosaccharomyces pombe
           972h-]
 gi|548817|sp|P36594.1|RPB1_SCHPO RecName: Full=DNA-directed RNA polymerase II subunit rpb1;
           Short=RNA polymerase II subunit 1; Short=RNA polymerase
           II subunit B1; AltName: Full=DNA-directed RNA polymerase
           III largest subunit
 gi|256599715|pdb|3H0G|A Chain A, Rna Polymerase Ii From Schizosaccharomyces Pombe
 gi|256599727|pdb|3H0G|M Chain M, Rna Polymerase Ii From Schizosaccharomyces Pombe
 gi|5055|emb|CAA39916.1| RNA polymerase II large subunit [Schizosaccharomyces pombe]
 gi|6018696|emb|CAB57941.1| RNA polymerase II large subunit Rpb1 [Schizosaccharomyces pombe]
          Length = 1752

 Score =  160 bits (405), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 94/268 (35%), Positives = 149/268 (55%), Gaps = 38/268 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVV+FNRQPSLHK+S+M HR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 444 DGDVVIFNRQPSLHKMSMMGHRIRVMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSEET 503

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE               ++ M  K  +V+P++ + ++   QD + G    + ++ F  R
Sbjct: 504 RAEI-------------QEITMVPK-QIVSPQSNKPVMGIVQDTLAGVRKFSLRDNFLTR 549

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              M I    +    D  GI+         P V ++  V+WTGKQI SLI+      P  
Sbjct: 550 NAVMNI----MLWVPDWDGILP--------PPVILKPKVLWTGKQILSLII------PKG 591

Query: 521 ANL-KTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            NL +   +   +N      DS +++ N E++ G +DK T+G+  +  + + + ++ G +
Sbjct: 592 INLIRDDDKQSLSNPT----DSGMLIENGEIIYGVVDKKTVGA-SQGGLVHTIWKEKGPE 646

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           +       + R+ +++L++ GFSIGIGD
Sbjct: 647 ICKGFFNGIQRVVNYWLLHNGFSIGIGD 674



 Score =  110 bits (276), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 61/174 (35%), Positives = 97/174 (55%), Gaps = 9/174 (5%)

Query: 1225 QLLPSVVIKGVQGINRAVIHEEDV---------EGVTKYKLLVEGDNLRDVMATYGVKGV 1275
             +L S+ ++GV  I R  + E  +         E   ++ L  +G NL + M   GV   
Sbjct: 1272 HMLESISLRGVPNITRVYMMEHKIVRQIEDGTFERADEWVLETDGINLTEAMTVEGVDAT 1331

Query: 1276 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGIT 1335
            +  SN+  E+ + LGIEA RS ++ E++ V+E  G  +++RH  L+ D+MTS+G ++ IT
Sbjct: 1332 RTYSNSFVEILQILGIEATRSALLKELRNVIEFDGSYVNYRHLALLCDVMTSRGHLMAIT 1391

Query: 1336 RHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
            RHG+ + +   L   SFE T + L DAA  G+ D   G+SE I++G    +GTG
Sbjct: 1392 RHGINRAETGALMRCSFEETVEILMDAAASGEKDDCKGISENIMLGQLAPMGTG 1445



 Score = 99.0 bits (245), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 42/62 (67%), Positives = 52/62 (83%)

Query: 607 DVTPGQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQ 666
           D    +GF++NS+  GLTP EFFFH M GREGL+DTAVKTAETGY+QRRLVK++ED+ V+
Sbjct: 798 DSPESRGFIENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKAMEDVMVR 857

Query: 667 YD 668
           YD
Sbjct: 858 YD 859



 Score = 91.7 bits (226), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 76/290 (26%), Positives = 137/290 (47%), Gaps = 56/290 (19%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDK--DTDLDYARIVKGRLERTTLGEVC--------- 812
            GVPR+KEI+N ++NI TP +T YL      ++D A+ V+ ++E TTL  V          
Sbjct: 1100 GVPRLKEILNVAKNIKTPSLTIYLMPWIAANMDLAKNVQTQIEHTTLSTVTSATEIHYDP 1159

Query: 813  -----------EYIEEVF-VPDD---------SFILIKLDMDRIRLLHLEVDIDSIRYCI 851
                       +++E  F +PD+         S  L++L++DR ++L  ++ +  +   I
Sbjct: 1160 DPQDTVIEEDKDFVEAFFAIPDEEVEENLYKQSPWLLRLELDRAKMLDKKLSMSDVAGKI 1219

Query: 852  ERT--RGISGHLTVSGHSFLILKPK-----DSSKSFNSKMYQMK--------QLLPSVVI 896
              +  R +    +      LI++ +     D     +  M +           +L S+ +
Sbjct: 1220 AESFERDLFTIWSEDNADKLIIRCRIIRDDDRKAEDDDNMIEEDVFLKTIEGHMLESISL 1279

Query: 897  KGVQGINRAVIHEEDV---------EGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTY 947
            +GV  I R  + E  +         E   ++ L  +G NL + M   GV   +  SN+  
Sbjct: 1280 RGVPNITRVYMMEHKIVRQIEDGTFERADEWVLETDGINLTEAMTVEGVDATRTYSNSFV 1339

Query: 948  EVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            E+ + LGIEA RS ++ E++ V+E  G  +++RH  L+ D+MTS+G ++ 
Sbjct: 1340 EILQILGIEATRSALLKELRNVIEFDGSYVNYRHLALLCDVMTSRGHLMA 1389



 Score = 79.7 bits (195), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 58/209 (27%), Positives = 95/209 (45%), Gaps = 21/209 (10%)

Query: 119 GLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPT 178
           GLLD R+GT  ++  C TCG+ ++DC GHFG+I+L  PVFHIG+   +  IL+ +C N  
Sbjct: 54  GLLDPRLGTIDRQFKCQTCGETMADCPGHFGHIELAKPVFHIGFLSKIKKILECVCWN-- 111

Query: 179 CARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGL 238
           C ++ +             N    Y   K+    +    K   VC       G+      
Sbjct: 112 CGKLKIDSSNPK------FNDTQRYRDPKNRLNAVWNVCKTKMVCD-----TGLSAGSDN 160

Query: 239 LKISHEK----YKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQL 294
             +S+      +      +  I +D L  +    +   E +  +K    + L+PLEV  +
Sbjct: 161 FDLSNPSANMGHGGCGAAQPTIRKDGLRLWGSWKRGKDESDLPEK----RLLSPLEVHTI 216

Query: 295 FEAIPLEDIPLLLMNAELSKPSDLILTRL 323
           F  I  ED+  L +N + ++P  +I+T L
Sbjct: 217 FTHISSEDLAHLGLNEQYARPDWMIITVL 245



 Score = 54.3 bits (129), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 23/37 (62%), Positives = 28/37 (75%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            ++ +A + P   VG LAAQSIGEP TQMTL TFH+AG
Sbjct: 1055 RFQQAVVSPGEMVGTLAAQSIGEPATQMTLNTFHYAG 1091


>gi|21280517|gb|AAM45151.1|AF395110_1 RNA polymerase II largest subunit [Naegleria gruberi]
          Length = 1590

 Score =  160 bits (405), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 95/270 (35%), Positives = 152/270 (56%), Gaps = 30/270 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DV+LFNRQPSLHK+S+M HR KV+P+ TFR N  V TPYNADFDGDEMN+H+PQ+ + 
Sbjct: 371 DGDVILFNRQPSLHKMSMMGHRIKVMPYSTFRMNLSVTTPYNADFDGDEMNLHVPQSLQT 430

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE L    +L+++            N++TP++   +IA  QD +     LT+++ F  +
Sbjct: 431 KAELL----ELTMVPR----------NIITPQSNRPVIALVQDTLLAASKLTRRDVFIAK 476

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPV-VFVRTAVIWTGKQIFSLIL-KPNRDCP 518
              M     LI    D  G +         PV   ++   +WTGKQ+F+ +L K N +  
Sbjct: 477 DLMMNCLMHLI----DFDGKL---------PVPAILKPKPLWTGKQLFTFLLPKVNLENT 523

Query: 519 VNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            + +     +    + +    D+ V++   EL++G +DK +LGS    ++ +I++ + G 
Sbjct: 524 SSTHEDLTDKKDHLDHDIPEFDTKVLIDRGELVSGVLDKKSLGS-SHGSLIHIIVNEKGV 582

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           +     + +  R+ + +L+NRGFSIGIGD 
Sbjct: 583 NEGKKFLGQCQRVINHWLINRGFSIGIGDT 612



 Score =  101 bits (251), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 42/57 (73%), Positives = 52/57 (91%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV NS+  GLTP EFFFHTMGGREGL+DTAVKT+ETGY+QRRL+K++ED+ V+YD
Sbjct: 740 RGFVANSYLRGLTPQEFFFHTMGGREGLIDTAVKTSETGYIQRRLIKAMEDIMVKYD 796



 Score = 94.7 bits (234), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 56/177 (31%), Positives = 95/177 (53%), Gaps = 9/177 (5%)

Query: 1226 LLPSVVIKGVQGINRAVIHEED---------VEGVTKYKLLVEGDNLRDVMATYGVKGVK 1276
            +L  + +KG + + +  + EE+         V  V ++ L  EG NL  V++   V    
Sbjct: 1252 MLNELALKGYKDLKKVFLREENDKKVFSSSGVATVKQWVLDTEGCNLLAVLSHPYVDHTI 1311

Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITR 1336
             +SN+  E+   LGIEA R+ +M E++ V+E  G  +++RH  ++ D+MT +G ++ ITR
Sbjct: 1312 TTSNDVNEILDVLGIEACRNALMREMRKVIEFDGSYVNYRHLAILCDVMTHRGGLMAITR 1371

Query: 1337 HGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
             G+ +     L   SFE T + L +AA +  TD + GVS  +++G    +GTG   L
Sbjct: 1372 RGINRSDTGPLMRCSFEETVEILIEAATFADTDTLKGVSANVMVGQLAPIGTGCFGL 1428



 Score = 68.9 bits (167), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 65/207 (31%), Positives = 99/207 (47%), Gaps = 41/207 (19%)

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVL-----LGEEKAAGF-RAKL 196
           +C GHFG++ +  PVF++ +   V+ +LQS+C +  C ++L     L  +KA+ F   + 
Sbjct: 1   ECPGHFGHVRI-HPVFNVLFINTVVKVLQSVCIH--CGKLLADKSSLQFKKASKFVNRRK 57

Query: 197 RNPALSYLVRKSLKKKILETTKK-------VSVCPHCGEINGVVKKCGLL--KISHEKYK 247
           R   +  L RK   K I+ET  K        ++ P     NG    CG L  KIS +  K
Sbjct: 58  RFKEMIDLCRKD--KCIIETGNKENEQNQEANIDPTFQPRNG----CGGLQPKISRDGLK 111

Query: 248 NRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLL 307
                       + AEY +      + E  K     Q L     LQ+F+ IP ED+ LL 
Sbjct: 112 ------------IFAEYKKDTSAEAKQELTK-----QELTAERALQIFKRIPAEDLELLG 154

Query: 308 MNAELSKPSDLILTRLLVPPNCIRPSV 334
            + + ++P  +ILT L +PP  +RPSV
Sbjct: 155 FDKDNARPEWMILTCLPIPPPQVRPSV 181



 Score = 58.5 bits (140), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 34/117 (29%), Positives = 63/117 (53%), Gaps = 9/117 (7%)

Query: 890  LLPSVVIKGVQGINRAVIHEED---------VEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
            +L  + +KG + + +  + EE+         V  V ++ L  EG NL  V++   V    
Sbjct: 1252 MLNELALKGYKDLKKVFLREENDKKVFSSSGVATVKQWVLDTEGCNLLAVLSHPYVDHTI 1311

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SN+  E+   LGIEA R+ +M E++ V+E  G  +++RH  ++ D+MT +G ++ 
Sbjct: 1312 TTSNDVNEILDVLGIEACRNALMREMRKVIEFDGSYVNYRHLAILCDVMTHRGGLMA 1368



 Score = 55.1 bits (131), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 30/74 (40%), Positives = 47/74 (63%), Gaps = 2/74 (2%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KE++N ++NI TP +T YL+ +   D + A++VK  LE TTLG V      V+ P
Sbjct: 1063 GVPRLKELLNVAKNIKTPGLTIYLNNEYIGDFEKAKMVKEDLEYTTLGHVTAAASIVYDP 1122

Query: 822  DDSFILIKLDMDRI 835
            + +  +I+ D + I
Sbjct: 1123 EPANSVIEEDREFI 1136



 Score = 52.4 bits (124), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 22/30 (73%), Positives = 25/30 (83%)

Query: 1116 EPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            +P   VG++AAQSIGEP TQMTL TFHFAG
Sbjct: 1025 QPGEMVGSVAAQSIGEPATQMTLNTFHFAG 1054


>gi|397135956|gb|AFO11473.1| RNA polymerase I, partial [Komagataella pastoris]
          Length = 872

 Score =  160 bits (405), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 92/272 (33%), Positives = 146/272 (53%), Gaps = 44/272 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+D VLFNRQPSLHK+S+MAHR KV+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 251 DDDPVLFNRQPSLHKMSMMAHRVKVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 310

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE                 L A    +V+P++ + ++   QD + G   +T ++ F   
Sbjct: 311 RAE--------------LSQLCAVPLQIVSPQSNKPVMGIVQDTLCGVRKMTLRDTFIEY 356

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVV----FVRTAVIWTGKQIFSLILKPNRD 516
            Q M +                 F   SW+ VV     ++   +WTGKQ+ S+ +     
Sbjct: 357 EQVMNML----------------FWVPSWDGVVPQPAIMKPKPLWTGKQLLSIAI----- 395

Query: 517 CPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            P   +L+   R    N     +D+ +++ +  ++ G +DK T+GSGG   + + ++R+ 
Sbjct: 396 -PSGIHLQ---RTDGGNSLLSPKDNGMLIVDGNVMFGVVDKKTVGSGG-GGLIHTVMREK 450

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           G  +       + ++ +++L++ GFSIGIGD 
Sbjct: 451 GPKICAELFGNIQKVVNYWLLHNGFSIGIGDA 482



 Score =  100 bits (250), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 53/63 (84%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTP EFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+ V
Sbjct: 604 DFSPESKGFVENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDIMV 663

Query: 666 QYD 668
            YD
Sbjct: 664 HYD 666



 Score = 41.6 bits (96), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 21/52 (40%), Positives = 30/52 (57%)

Query: 286 LNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD 337
           L P E+L +F  I  ED   L  N + ++P  +I+T L VPP  +RPS+  D
Sbjct: 15  LTPGEILNVFRHISPEDCFRLGFNEDYARPEWMIITVLPVPPPQVRPSIAMD 66


>gi|397135922|gb|AFO11456.1| RNA polymerase I, partial [Pachysolen tannophilus]
          Length = 870

 Score =  160 bits (405), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 90/272 (33%), Positives = 146/272 (53%), Gaps = 46/272 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND VLFNRQPSLHK+S+M HR KV+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 249 DNDPVLFNRQPSLHKMSMMTHRVKVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 308

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE                 L A    +V+P++ + ++   QD + G   +T ++ F   
Sbjct: 309 RAE--------------LSQLCAVPLQIVSPQSNKPVMGIVQDTLCGIRKMTLRDVFIEY 354

Query: 461 AQTMRIASTLIADTSDICGIIKRFSW-RSWNPVV----FVRTAVIWTGKQIFSLILKPNR 515
            Q M I                   W  +W+ V+     ++   +WTGKQ+ S+++    
Sbjct: 355 DQVMNI-----------------LYWIPTWDGVIPEPTIIKPKPLWTGKQMLSMVI---- 393

Query: 516 DCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
             P   N++ K   +T        D+ +++ + E++ G ++K T+G+ G   + + ++R+
Sbjct: 394 --PKGINIERKDEKFTY---LSKDDTGMLIIDGEIMLGVVNKKTVGATG-GGLIHAVMRE 447

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            G  V       + ++ +++L++ GFSIGIGD
Sbjct: 448 KGPQVCADLFGNIQKVVNYWLLHNGFSIGIGD 479



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 53/63 (84%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTP EFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+ V
Sbjct: 602 DYSPESRGFVENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDIMV 661

Query: 666 QYD 668
            YD
Sbjct: 662 HYD 664



 Score = 44.3 bits (103), Expect = 0.54,   Method: Compositional matrix adjust.
 Identities = 24/63 (38%), Positives = 36/63 (57%), Gaps = 1/63 (1%)

Query: 286 LNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSV-ISDLKSDNDV 344
           L P E+L +F+ I  ED   L  N + ++P  +I+T L VPP  +RPSV ++D     D 
Sbjct: 13  LTPAEILNVFKHISPEDCKKLGFNEDYARPEWMIITVLPVPPPAVRPSVQVNDTARGEDD 72

Query: 345 VLF 347
           + F
Sbjct: 73  LTF 75


>gi|361124608|gb|EHK96688.1| putative DNA-directed RNA polymerase II subunit rpb1 [Glarea
           lozoyensis 74030]
          Length = 1727

 Score =  160 bits (405), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 97/283 (34%), Positives = 145/283 (51%), Gaps = 50/283 (17%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D ++FNRQPSLHK S+M HR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQTEE 
Sbjct: 449 DGDFIIFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQTEET 508

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE +               L     N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 509 RAEVM--------------NLCMVPLNIVSPQRNGPLMGIVQDTLAGVYKMCRRDVFITK 554

Query: 461 AQTMRIASTLIADTSDICGIIKRFSW-RSWNPVV----FVRTAVIWTGKQIFSLILKPNR 515
              M I                   W   W+ V+     ++    WTGKQI S+I+    
Sbjct: 555 EHLMNI-----------------LLWVPEWDGVIPQPAILKPRPRWTGKQIVSMII---- 593

Query: 516 DCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLG--SGGKANVFYILL 573
             P   NL T   A  A E+   +D  +++   EL+ G + K  +G  SGG   + +I+ 
Sbjct: 594 --PKIVNLHT---ANDAREDAPLKDDGLLVHEGELMFGLLTKKNVGASSGG---IIHIIF 645

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
            + G D A+       R+ +++L++ GFSIGIGD  P +  ++
Sbjct: 646 NEQGPDAAMAFFNGCQRVVNYWLLHNGFSIGIGDTIPDKSTIE 688



 Score =  101 bits (251), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+  
Sbjct: 802 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDVMA 861

Query: 666 QYD 668
           +YD
Sbjct: 862 KYD 864



 Score =  100 bits (249), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 58/185 (31%), Positives = 101/185 (54%), Gaps = 15/185 (8%)

Query: 1225 QLLPSVVIKGVQGINRAVIHEE---------------DVEGVTKYKLLVEGDNLRDVMAT 1269
             +L ++ ++GV G++RA +++E                 +  T++ L   G +L  V+  
Sbjct: 1279 HILDTLTLRGVPGVDRAFLNKETKLITTPDGGLLASKSDDRCTEWYLDTSGTSLAQVLTV 1338

Query: 1270 YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 1329
             GV   +  +N+  +V +  GIEAARS +M E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1339 PGVDTTRTYTNHFIQVLEVFGIEAARSALMRELTQVLAFDGSYVNHRHLALLVDVMTSRG 1398

Query: 1330 EVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
             ++ ITRHG+ +     L   SFE T + L +AA  G+ D   G+SE +++G    +GTG
Sbjct: 1399 LLMAITRHGINRADTGALMRCSFEETVEILLEAAAIGELDDCRGISENVMLGQLAPMGTG 1458

Query: 1390 LIKLL 1394
             +++L
Sbjct: 1459 ELEVL 1463



 Score = 82.4 bits (202), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 72/288 (25%), Positives = 127/288 (44%), Gaps = 58/288 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLD-KDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPD 822
            GVPR+KEI+N + NI TP +  Y + +D   D A++++  +E T L  V +  E    P+
Sbjct: 1111 GVPRLKEILNIASNIKTPSMVVYQEGEDASQDSAKLLRSAVEHTNLRSVMQATEIYHDPE 1170

Query: 823  DSFILIKLDMDRIRLL-------HLEVDIDS---IRYCIERTRGISGHLTVSGHSFLILK 872
                 I  D+D +          H  +D  S   +R  ++R + +   L V   +  I +
Sbjct: 1171 IQSTEIADDLDMVESFFIIPEEHHDSLDNQSRWLLRLILDRQKMLDKGLRVEDVAIKIKE 1230

Query: 873  --PKDSSKSFNSKMYQMK------------------------------QLLPSVVIKGVQ 900
              PKD +  F+    + +                               +L ++ ++GV 
Sbjct: 1231 NYPKDLAVIFSDNNAEKQVIRIRMIKAGDGKYDDDDIEEDIMLKRLEAHILDTLTLRGVP 1290

Query: 901  GINRAVIHEE---------------DVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNN 945
            G++RA +++E                 +  T++ L   G +L  V+   GV   +  +N+
Sbjct: 1291 GVDRAFLNKETKLITTPDGGLLASKSDDRCTEWYLDTSGTSLAQVLTVPGVDTTRTYTNH 1350

Query: 946  TYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
              +V +  GIEAARS +M E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1351 FIQVLEVFGIEAARSALMRELTQVLAFDGSYVNHRHLALLVDVMTSRG 1398



 Score = 73.6 bits (179), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 34/87 (39%), Positives = 53/87 (60%), Gaps = 5/87 (5%)

Query: 115 PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSIC 174
           P   GL D R+G+  ++  C TC Q +S+C GHFG+I+L  PVFH G+ + +  IL+ +C
Sbjct: 50  PRDQGLNDPRLGSIDRQFKCGTCDQQMSECPGHFGHIELAKPVFHPGFIKKIKKILEMVC 109

Query: 175 KNPTCARVLLGEEKAAGFRA--KLRNP 199
            N  C ++LL     A ++A   +R+P
Sbjct: 110 HN--CGKILLDRSNPA-YKAAVSIRDP 133



 Score = 56.6 bits (135), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/37 (62%), Positives = 29/37 (78%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            +++++ + P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1066 RFIKSLVNPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1102


>gi|397135924|gb|AFO11457.1| RNA polymerase I, partial [Peterozyma toletana]
          Length = 870

 Score =  160 bits (405), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 90/272 (33%), Positives = 147/272 (54%), Gaps = 46/272 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND VLFNRQPSLHK+S+MAHR KV+P+ +FR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 249 DNDPVLFNRQPSLHKMSMMAHRVKVMPYSSFRLNLSVTSPYNADFDGDEMNLHVPQSEET 308

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE                 + A    +++P++ + ++   QD + G   +T ++ F   
Sbjct: 309 RAE--------------LSQICAVPLQIISPQSNKPVMGIVQDTLCGVRKMTLRDVFIEY 354

Query: 461 AQTMRIASTLIADTSDICGIIKRFSW-RSWNPVV----FVRTAVIWTGKQIFSLILKPNR 515
            + M I                   W  SW+ V+     V+   +WTGKQ+ S+++    
Sbjct: 355 DEVMNI-----------------LYWIPSWDGVIPEPTIVKPKPLWTGKQMLSMVI---- 393

Query: 516 DCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
             P   NL+ K   +T      + D+ +++ + E++ G ++K T+G+ G   + + + R+
Sbjct: 394 --PKGINLERKDEKFTY---LSNDDTGMLIVDGEIMLGVVNKKTVGATG-GGLIHAVFRE 447

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            G  V       + ++ +++L++ GFSIGIGD
Sbjct: 448 KGPQVCADLFGNMQKVVNYWLLHYGFSIGIGD 479



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 53/63 (84%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTP EFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+ V
Sbjct: 602 DYSPESRGFVENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDIMV 661

Query: 666 QYD 668
            YD
Sbjct: 662 HYD 664


>gi|310789907|gb|EFQ25440.1| RNA polymerase Rpb1 [Glomerella graminicola M1.001]
          Length = 1753

 Score =  160 bits (405), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 95/270 (35%), Positives = 146/270 (54%), Gaps = 40/270 (14%)

Query: 343 DVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARA 402
           D ++FNRQPSLHK S+M HR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE RA
Sbjct: 453 DYIIFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRA 512

Query: 403 EALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQ 462
           E               K L     N+V+P+    L+   QD + G Y L +++ F ++ Q
Sbjct: 513 E--------------VKELCLVPINIVSPQRNGPLMGIVQDTLAGAYKLCRRDVFLSKEQ 558

Query: 463 TMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNAN 522
            M I   L     D  GII         P   VR    WTGKQI SL +          N
Sbjct: 559 VMNI--MLWVPNWD--GIIP--------PPAIVRPRPRWTGKQIMSLAV---------PN 597

Query: 523 LKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLG--SGGKANVFYILLRDFGEDV 580
           + +   A  + E+   +D  +++++ +++ G + K  +G  SGG   + +I+  + G + 
Sbjct: 598 IVSLHSAPDSKEDNPLKDEGLLIQSGQIMYGLLSKKNIGAASGG---IVHIVYNEHGPEA 654

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           A+  +  + ++ +++L++ GFSIGIGD  P
Sbjct: 655 AMKFLNGVQQVVNYWLLHNGFSIGIGDTIP 684



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 72/268 (26%), Positives = 131/268 (48%), Gaps = 31/268 (11%)

Query: 1158 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHS----FLILKP---- 1209
            D S  L++L +DR +LL  E+ ++ +   I+        +  S ++     + ++P    
Sbjct: 1201 DQSRWLLRLTLDRQKLLDKELTVEDVARRIKEEYPNDLAVIFSDNNAEEQIIRIRPMHAG 1260

Query: 1210 -----KDSSKSFNSKMYQMK---QLLPSVVIKGVQGINRAVIHEEDV------------- 1248
                 +D  K     +   +    LL ++ ++GV+GI RA +++E               
Sbjct: 1261 NDNKDEDGEKKIEDDVMLKRLETHLLDTLSLRGVKGIERAFLNKETKLIETEDGALLAAK 1320

Query: 1249 --EGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVM 1306
              E  +++ L   G  LR V+A  GV   +  +N+ ++V +  GIEAAR+ ++ E+  V+
Sbjct: 1321 ADERCSEWYLDTSGTALRQVLAVDGVDSNRTYTNHLWQVVEVFGIEAARAALVRELTQVL 1380

Query: 1307 ENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYG 1366
               G  ++ RH  L+ D+MT +G +  +TRHG+ +     L   SFE T + L +AA  G
Sbjct: 1381 AFDGSYVNHRHLALLCDVMTYRGTISAVTRHGINRADTGALMRCSFEETVEILLEAAAVG 1440

Query: 1367 QTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            + D   G+SE +++G    +GTG   +L
Sbjct: 1441 ELDDCRGISENVMLGQMAPMGTGHFDVL 1468



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTP+EFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+  
Sbjct: 804 DYSPEARGFVENSYLRGLTPSEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDVSA 863

Query: 666 QYD 668
           +YD
Sbjct: 864 KYD 866



 Score = 85.1 bits (209), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 73/294 (24%), Positives = 134/294 (45%), Gaps = 62/294 (21%)

Query: 764  GVPRIKEIINASRNISTPIITAYL--DKDTDLDYARIVKGRLERTTLGEVCEYIEEVF-- 819
            GVPR+KEI+N ++NI TP +  YL  + +   + A+ ++  +E TTL  V    E  +  
Sbjct: 1112 GVPRLKEILNLAQNIKTPSMVVYLSGEDNASQEAAKALRSTVEHTTLRSVTAVTEIYYDP 1171

Query: 820  ------VPDD---------------------SFILIKLDMDRIRLLHLEVDIDSIRYCIE 852
                  +PDD                     S  L++L +DR +LL  E+ ++ +   I+
Sbjct: 1172 EITSTNIPDDLDMVESYYLIPDESHDKTEDQSRWLLRLTLDRQKLLDKELTVEDVARRIK 1231

Query: 853  RTRGISGHLTVSGHS----FLILKP---------KDSSKSFNSKMYQMK---QLLPSVVI 896
                    +  S ++     + ++P         +D  K     +   +    LL ++ +
Sbjct: 1232 EEYPNDLAVIFSDNNAEEQIIRIRPMHAGNDNKDEDGEKKIEDDVMLKRLETHLLDTLSL 1291

Query: 897  KGVQGINRAVIHEEDV---------------EGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
            +GV+GI RA +++E                 E  +++ L   G  LR V+A  GV   + 
Sbjct: 1292 RGVKGIERAFLNKETKLIETEDGALLAAKADERCSEWYLDTSGTALRQVLAVDGVDSNRT 1351

Query: 942  SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
             +N+ ++V +  GIEAAR+ ++ E+  V+   G  ++ RH  L+ D+MT +G +
Sbjct: 1352 YTNHLWQVVEVFGIEAARAALVRELTQVLAFDGSYVNHRHLALLCDVMTYRGTI 1405



 Score = 64.7 bits (156), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 30/75 (40%), Positives = 46/75 (61%), Gaps = 3/75 (4%)

Query: 110 DPQRT-PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVIN 168
           D  RT P   GL D  +G+  ++  C TC Q + +C GHFG+I+L  PV+H G+ + V  
Sbjct: 44  DETRTKPRDGGLNDPLLGSIDRQFKCKTCSQAMGECPGHFGHIELAKPVYHPGFIKKVKK 103

Query: 169 ILQSICKNPTCARVL 183
           +L+ +C N  C++VL
Sbjct: 104 VLEIVCHN--CSKVL 116



 Score = 55.5 bits (132), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/37 (64%), Positives = 28/37 (75%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            ++ RA + P   VG +AAQSIGEP TQMTL TFHFAG
Sbjct: 1067 RWDRAFVSPGEMVGVIAAQSIGEPATQMTLNTFHFAG 1103


>gi|300712256|ref|YP_003738070.1| DNA-directed RNA polymerase subunit A' [Halalkalicoccus jeotgali
           B3]
 gi|448295949|ref|ZP_21486010.1| DNA-directed RNA polymerase subunit A' [Halalkalicoccus jeotgali
           B3]
 gi|299125939|gb|ADJ16278.1| DNA-directed RNA polymerase subunit A' [Halalkalicoccus jeotgali
           B3]
 gi|445582672|gb|ELY37012.1| DNA-directed RNA polymerase subunit A' [Halalkalicoccus jeotgali
           B3]
          Length = 986

 Score =  160 bits (404), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 101/267 (37%), Positives = 144/267 (53%), Gaps = 44/267 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q+EEA
Sbjct: 493 DGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNLHALQSEEA 552

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR GE +I A QD I+G YLLT +N  FN 
Sbjct: 553 RAE--------------ARVLMRVQEQILSPRFGENIIGAIQDHISGLYLLTHENPQFNE 598

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q +     L+  TS + G+ +        P     +   WTG+ IFS +L      P  
Sbjct: 599 TQAL----DLLRGTS-VDGLPE--------PDGEDESGEYWTGRTIFSQLL------PDG 639

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            +L+    A  A          V + +  LL G++D+  +G+ G   +   L++D  E  
Sbjct: 640 FDLEFTSSAGDA----------VTIEDGTLLEGTVDEDGVGAFG-GEIVDQLVKDHSETR 688

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           A   +  ++ +    +M+ GFSIGI D
Sbjct: 689 ARVFINEVASLAMRAIMHFGFSIGIDD 715



 Score =  115 bits (287), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 86/301 (28%), Positives = 132/301 (43%), Gaps = 65/301 (21%)

Query: 94  QQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDL 153
           ++ S  +I++ + Y  D    PI  GL+D R+G       C TCG++   C GHFG I+L
Sbjct: 24  REMSATKIITADTY--DDDGFPIDMGLMDPRLGVIDPGLECKTCGKHSGACNGHFGNIEL 81

Query: 154 PLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKI 213
             PV H+G+ + +  +L+  C+   C+R+LL E++   FR  L            + K  
Sbjct: 82  AAPVIHVGFTKLIRRLLRGTCRE--CSRLLLTEDEKEEFRESLVRTRELGDDANDVTKAA 139

Query: 214 LETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAV----- 268
           +   +K   CPHCGE+           I HEK     +    + + L +EY+E +     
Sbjct: 140 IRQARKADSCPHCGEVQ--------FDIQHEKPTTYYE----VQQVLTSEYSEQIAGAMQ 187

Query: 269 --------------------------------KFNP---EIEA-HKKFGL------IQTL 286
                                           +F P   + EA  K  G+      +  L
Sbjct: 188 PGEDEDDEATTPPELADETDIDVSRINQILSGEFRPRRADREAIEKALGIDLTEEDLNKL 247

Query: 287 NPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDNDV 344
            P ++   FE IP EDI +L MN E S+P  +ILT L VPP   RPS+  D   +S++D+
Sbjct: 248 MPSDIRDWFEDIPDEDIEVLGMNPEKSRPEWMILTVLPVPPVTARPSITLDNGQRSEDDL 307

Query: 345 V 345
            
Sbjct: 308 T 308



 Score = 91.7 bits (226), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 40/64 (62%), Positives = 53/64 (82%), Gaps = 1/64 (1%)

Query: 606 GDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           GD++    GFV+NS+ +GLTP EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L 
Sbjct: 837 GDLSAEAHGFVENSYRAGLTPREFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELE 896

Query: 665 VQYD 668
            QYD
Sbjct: 897 TQYD 900



 Score = 45.4 bits (106), Expect = 0.22,   Method: Compositional matrix adjust.
 Identities = 21/48 (43%), Positives = 31/48 (64%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRI 67
           +VLM  +  +++PR GE +I A QD I+G YLLT +N  FN  Q + +
Sbjct: 557 RVLMRVQEQILSPRFGENIIGAIQDHISGLYLLTHENPQFNETQALDL 604


>gi|320038943|gb|EFW20878.1| DNA-directed RNA polymerase II largest subunit [Coccidioides
           posadasii str. Silveira]
          Length = 1750

 Score =  160 bits (404), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 96/278 (34%), Positives = 152/278 (54%), Gaps = 35/278 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DV+LFNRQPSLHK S+MAHR +V+P+ TFR N  V TPYNADFDGDEMN+H+PQ+EEA
Sbjct: 456 DGDVILFNRQPSLHKESMMAHRVRVMPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L++L ++            N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 516 RAE----LNQLCLVPL----------NIVSPQRNGPLMGIVQDTLCGIYKICRRDVFLTK 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M     ++    +  G++ +       P + ++    WTGKQ+ S++L      P  
Sbjct: 562 EQVM----NMMLWVPEWDGVLPQ-------PAI-LKPRPRWTGKQMISMVL------PSG 603

Query: 521 ANLKTKGRAYTA-NEEFCH-RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            NL    R      E+F    D+ +++   EL+ G   K T+G+ G   + + +  ++G 
Sbjct: 604 LNLLRVDRDKVPLAEKFSPLTDTGLLVHGGELMYGMFSKKTVGATG-GGIIHTIYNEYGP 662

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           +V +        + +++L++ GFSIGIGD  P    +Q
Sbjct: 663 EVCMNFFNGAQTVVNYWLLHNGFSIGIGDTIPDLATIQ 700



 Score =  103 bits (257), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 62/180 (34%), Positives = 95/180 (52%), Gaps = 15/180 (8%)

Query: 1225 QLLPSVVIKGVQGINRAVIHEED----VEGVTKYK-----------LLVEGDNLRDVMAT 1269
             LL ++ ++GV G+ RA I+E+     +E  + YK           L   G  L DV+A 
Sbjct: 1290 HLLDTLTLRGVAGVERAFINEKSRVRTLEDGSLYKNSEDPQCKEWVLETSGSALGDVLAI 1349

Query: 1270 YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 1329
             GV   +  SN   E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1350 PGVDATRTYSNQFVEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLCDVMTSRG 1409

Query: 1330 EVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
             ++ +TRHG+ +     L   SFE T + L DAA + + D   GVSE +I+G     GTG
Sbjct: 1410 FLMAVTRHGINRADTGALMRCSFEETVEILLDAAAFAELDDCRGVSENLILGQMAPAGTG 1469



 Score = 99.0 bits (245), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QR+LVK+LE++ V
Sbjct: 814 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMV 873

Query: 666 QYD 668
           +YD
Sbjct: 874 KYD 876



 Score = 87.4 bits (215), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 78/290 (26%), Positives = 132/290 (45%), Gaps = 60/290 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLD--KDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N + +I TP +T Y D  +  D + A+ ++  +E T L  V E  E  + P
Sbjct: 1120 GVPRLKEILNVATHIKTPSMTVYQDPARAMDKESAKQLRSVVEHTNLRSVTEATEIYYDP 1179

Query: 822  DDSFILIKLDMDRIRLLHL--EVDIDSI--------RYCIERTRGISGHLTVSGHSFLIL 871
            D    +I+ D D +    +  E  +D +        R  + R + +   LTV   +  I 
Sbjct: 1180 DIQSTVIEADRDMVESYFIIPEDVMDDLSRQSKWLLRIILSRPKLLDKGLTVQDVAMKIK 1239

Query: 872  K--PKD-----SSKSFNSKMYQMKQ--------------------------LLPSVVIKG 898
            +  P+D     S  + + ++ +++Q                          LL ++ ++G
Sbjct: 1240 ESYPQDIAVIFSDNNADEQVIRIRQIQDPKQDEEDDDDTEYDVTLKKLEAHLLDTLTLRG 1299

Query: 899  VQGINRAVIHEED----VEGVTKYK-----------LLVEGDNLRDVMATYGVKGVKCSS 943
            V G+ RA I+E+     +E  + YK           L   G  L DV+A  GV   +  S
Sbjct: 1300 VAGVERAFINEKSRVRTLEDGSLYKNSEDPQCKEWVLETSGSALGDVLAIPGVDATRTYS 1359

Query: 944  NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
            N   E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1360 NQFVEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLCDVMTSRG 1409



 Score = 73.9 bits (180), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 52/221 (23%), Positives = 95/221 (42%), Gaps = 39/221 (17%)

Query: 112 QRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQ 171
           ++ P   GL D R+GT  +   C TC + ++DC GHFG+I+L  PVFHIG+   +  +L+
Sbjct: 47  RQRPREKGLNDPRLGTIDRNWRCATCEEGINDCPGHFGHIELSTPVFHIGFLTKIKKLLE 106

Query: 172 SICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKSLKKKIL---------------- 214
           ++C N  C ++           A + R+P   +     L K +L                
Sbjct: 107 TVCHN--CGKIKANTSDQKYLDALRFRDPKRRFDAIWRLSKDVLICEADPPPDDDDPFGK 164

Query: 215 ETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEI 274
           E++K V     CG     ++K G+  +   K      K   +++D   +  E  +  P++
Sbjct: 165 ESSKIVKGHGGCGNAQPQIRKEGISLVGTWK----PNKMRDMMDDTDIQQPEKKQITPQM 220

Query: 275 EAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKP 315
                            L +F  +  ED+ +L ++ + ++P
Sbjct: 221 ----------------ALNIFRNVSEEDVRILGLSNDYARP 245



 Score = 56.6 bits (135), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 25/41 (60%), Positives = 28/41 (68%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            A   ++ +A   P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1071 AIESRFAKAAANPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1111


>gi|119186393|ref|XP_001243803.1| hypothetical protein CIMG_03244 [Coccidioides immitis RS]
 gi|392870516|gb|EAS32326.2| DNA-directed RNA polymerase II largest subunit [Coccidioides
           immitis RS]
          Length = 1750

 Score =  160 bits (404), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 96/278 (34%), Positives = 152/278 (54%), Gaps = 35/278 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DV+LFNRQPSLHK S+MAHR +V+P+ TFR N  V TPYNADFDGDEMN+H+PQ+EEA
Sbjct: 456 DGDVILFNRQPSLHKESMMAHRVRVMPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L++L ++            N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 516 RAE----LNQLCLVPL----------NIVSPQRNGPLMGIVQDTLCGIYKICRRDVFLTK 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M     ++    +  G++ +       P + ++    WTGKQ+ S++L      P  
Sbjct: 562 EQVM----NMMLWVPEWDGVLPQ-------PAI-LKPRPRWTGKQMISMVL------PSG 603

Query: 521 ANLKTKGRAYTA-NEEFCH-RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            NL    R      E+F    D+ +++   EL+ G   K T+G+ G   + + +  ++G 
Sbjct: 604 LNLLRVDRDKVPLAEKFSPLTDTGLLVHGGELMYGMFSKKTVGATG-GGIIHTIYNEYGP 662

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           +V +        + +++L++ GFSIGIGD  P    +Q
Sbjct: 663 EVCMNFFNGAQTVVNYWLLHNGFSIGIGDTIPDLATIQ 700



 Score =  103 bits (257), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 62/180 (34%), Positives = 95/180 (52%), Gaps = 15/180 (8%)

Query: 1225 QLLPSVVIKGVQGINRAVIHEED----VEGVTKYK-----------LLVEGDNLRDVMAT 1269
             LL ++ ++GV G+ RA I+E+     +E  + YK           L   G  L DV+A 
Sbjct: 1290 HLLDTLTLRGVAGVERAFINEKSRVRTLEDGSLYKNSEDPQCKEWVLETSGSALGDVLAI 1349

Query: 1270 YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 1329
             GV   +  SN   E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1350 PGVDATRTYSNQFVEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLCDVMTSRG 1409

Query: 1330 EVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
             ++ +TRHG+ +     L   SFE T + L DAA + + D   GVSE +I+G     GTG
Sbjct: 1410 FLMAVTRHGINRADTGALMRCSFEETVEILLDAAAFAELDDCRGVSENLILGQMAPAGTG 1469



 Score = 99.0 bits (245), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QR+LVK+LE++ V
Sbjct: 814 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMV 873

Query: 666 QYD 668
           +YD
Sbjct: 874 KYD 876



 Score = 87.4 bits (215), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 78/290 (26%), Positives = 132/290 (45%), Gaps = 60/290 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLD--KDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N + +I TP +T Y D  +  D + A+ ++  +E T L  V E  E  + P
Sbjct: 1120 GVPRLKEILNVATHIKTPSMTVYQDPARAMDKESAKQLRSVVEHTNLRSVTEATEIYYDP 1179

Query: 822  DDSFILIKLDMDRIRLLHL--EVDIDSI--------RYCIERTRGISGHLTVSGHSFLIL 871
            D    +I+ D D +    +  E  +D +        R  + R + +   LTV   +  I 
Sbjct: 1180 DIQSTVIEADRDMVESYFIIPEDVMDDLSRQSKWLLRIILSRPKLLDKGLTVQDVAMKIK 1239

Query: 872  K--PKD-----SSKSFNSKMYQMKQ--------------------------LLPSVVIKG 898
            +  P+D     S  + + ++ +++Q                          LL ++ ++G
Sbjct: 1240 ESYPQDIAVIFSDNNADEQVIRIRQIQDPKQDEEDDDDTEYDVTLKKLEAHLLDTLTLRG 1299

Query: 899  VQGINRAVIHEED----VEGVTKYK-----------LLVEGDNLRDVMATYGVKGVKCSS 943
            V G+ RA I+E+     +E  + YK           L   G  L DV+A  GV   +  S
Sbjct: 1300 VAGVERAFINEKSRVRTLEDGSLYKNSEDPQCKEWVLETSGSALGDVLAIPGVDATRTYS 1359

Query: 944  NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
            N   E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1360 NQFVEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLCDVMTSRG 1409



 Score = 73.9 bits (180), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 52/221 (23%), Positives = 95/221 (42%), Gaps = 39/221 (17%)

Query: 112 QRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQ 171
           ++ P   GL D R+GT  +   C TC + ++DC GHFG+I+L  PVFHIG+   +  +L+
Sbjct: 47  RQRPREKGLNDPRLGTIDRNWRCATCEEGINDCPGHFGHIELSTPVFHIGFLTKIKKLLE 106

Query: 172 SICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKSLKKKIL---------------- 214
           ++C N  C ++           A + R+P   +     L K +L                
Sbjct: 107 TVCHN--CGKIKANTSDQKYLDALRFRDPKRRFDAIWRLSKDVLICEADPPPDDDDPFGK 164

Query: 215 ETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEI 274
           E++K V     CG     ++K G+  +   K      K   +++D   +  E  +  P++
Sbjct: 165 ESSKIVKGHGGCGNAQPQIRKEGISLVGTWK----PNKMRDMMDDTDIQQPEKKQITPQM 220

Query: 275 EAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKP 315
                            L +F  +  ED+ +L ++ + ++P
Sbjct: 221 ----------------ALNIFRNVSEEDVRILGLSNDYARP 245



 Score = 56.6 bits (135), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 25/41 (60%), Positives = 28/41 (68%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            A   ++ +A   P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1071 AIESRFAKAAANPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1111


>gi|448375015|ref|ZP_21558732.1| DNA-directed RNA polymerase subunit A' [Halovivax asiaticus JCM
           14624]
 gi|445659476|gb|ELZ12282.1| DNA-directed RNA polymerase subunit A' [Halovivax asiaticus JCM
           14624]
          Length = 986

 Score =  160 bits (404), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 100/270 (37%), Positives = 144/270 (53%), Gaps = 45/270 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+++FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 494 DGDIIIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQNEEA 553

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR GE +I A QD I+G YLLT +N  FN 
Sbjct: 554 RAE--------------ARVLMRVQEQILSPRFGENIIGAIQDHISGTYLLTHENPHFNE 599

Query: 461 AQTMR-IASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q +  + +T I +  +  G     +     P         WTG+ IFS +L      P 
Sbjct: 600 TQALDLLRATRIDELPEQSG-----TEEDGTPY--------WTGRAIFSELL------PD 640

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           + NL   G   T  E+       V++ + +L+ G++ +  +G  G   +   + + +G  
Sbjct: 641 DLNLTFTG---TVGED-------VVIEDGQLVEGTIAEDEVGGFG-GEIVDTITKVYGNT 689

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVT 609
            A   +  LS +    +M+ GFSIGI D T
Sbjct: 690 RARIFINELSTLAMRTIMHFGFSIGIDDET 719



 Score =  117 bits (292), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 86/302 (28%), Positives = 139/302 (46%), Gaps = 41/302 (13%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G I   + + +  ++ S  +I++ + Y  D    PI  GL+D R+G       C TCG++
Sbjct: 10  GSISFGLMEPEEYREMSATKIITADTY--DDDGFPIDMGLMDPRLGVIDPGLECKTCGKH 67

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
              C GHFG+I+L  PV H+G+ + +  +L+  C+   C+R+LL E++   FR ++    
Sbjct: 68  SGSCNGHFGHIELAAPVIHVGFTKLIRRLLRGTCRE--CSRLLLTEDERGEFRDQIDESR 125

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVV---------------------KKCGLL 239
                   + K  +   +K   CP CGEI   +                     +  G +
Sbjct: 126 KLGRDLNDVTKAAIRQARKKDRCPFCGEIQYDIDHEKPTTYYEVQEVLASEYSQRIAGAM 185

Query: 240 KISHEKYKNRTKKKD--AIVEDLLAEYNEAV--KFNPEIEA----HKKFGLIQT------ 285
           +   E+   RT   +  A  E  L   NE +   F P  E      K  G+  T      
Sbjct: 186 QGDEEEGIERTTPDELAAKTEIDLTRVNEILSGSFRPREEQREAIEKALGIDLTEEDTNK 245

Query: 286 LNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDND 343
           L P ++   FEAIP EDI +L ++++ S+P  +ILT L VPP   RPS+  D   +S++D
Sbjct: 246 LMPSDIRDWFEAIPDEDIEVLGIDSDRSRPEWMILTVLPVPPVTARPSITLDNGQRSEDD 305

Query: 344 VV 345
           + 
Sbjct: 306 LT 307



 Score = 91.7 bits (226), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 38/57 (66%), Positives = 49/57 (85%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFV+NS+ +GLTP EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 846 HGFVENSYTAGLTPREFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELEAQYD 902



 Score = 47.4 bits (111), Expect = 0.066,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 30/46 (65%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 65
           +VLM  +  +++PR GE +I A QD I+G YLLT +N  FN  Q +
Sbjct: 558 RVLMRVQEQILSPRFGENIIGAIQDHISGTYLLTHENPHFNETQAL 603


>gi|113707384|gb|ABI36591.1| RNA polymerase II largest subunit [Gyalideopsis vulgaris]
          Length = 1015

 Score =  160 bits (404), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 91/276 (32%), Positives = 151/276 (54%), Gaps = 37/276 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D ++FNRQPSLHK S+M HR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 372 DGDFIIFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 431

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    +++L ++            N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 432 RAE----VNQLCMVP----------LNIVSPQRNGPLMGIVQDTLCGIYKMCRRDVFLTK 477

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            + M I    +    D  G+I +       P +F +   +WTGKQI  L++ P  +    
Sbjct: 478 ERVMNI----LLWVPDWDGVIPQ-------PAIF-KPKPLWTGKQILGLVIPPGLNL--- 522

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
             L+     +     F   D  +++   EL+ G ++K ++G+ G   V +I+  + G +V
Sbjct: 523 --LRGSEEGF-----FPLNDDGLLIAGGELMYGLLNKKSVGASG-GGVIHIIFNEKGPEV 574

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           A+        + +++L++ GFSIGIGD  P +  ++
Sbjct: 575 AMNFFNGAQTVVNYWLLHNGFSIGIGDTIPDRNTIR 610



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+  
Sbjct: 724 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDVMA 783

Query: 666 QYD 668
           +YD
Sbjct: 784 KYD 786



 Score = 56.6 bits (135), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 46/194 (23%), Positives = 86/194 (44%), Gaps = 40/194 (20%)

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNPAL 201
           +C GHFG+I+L  PVFH+G+   +  +L+++C N  C ++L+ E   A   A + R+P  
Sbjct: 1   ECPGHFGHIELAAPVFHVGFLTKIKKLLETVCHN--CGKILVDESNPAFLEALRSRDPKR 58

Query: 202 SY-LVRKSLKKKIL---------ETTKKVSVCPH----CGEINGVVKKCGLLKISHEKYK 247
            + ++ +  K K++         + ++K     H    CG I   V++  L      K +
Sbjct: 59  RFDMIWRLCKPKLICETSMPLDDDHSEKTKEPRHDHGGCGNIQPEVRREALKLTGTWKAQ 118

Query: 248 NRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLL 307
               + +A                   +A KK      + P   L +F  I  EDI  + 
Sbjct: 119 KGDDEHEA------------------QQAEKK-----PITPQMALNVFRNISTEDIKTMG 155

Query: 308 MNAELSKPSDLILT 321
           ++ + ++P  +I+T
Sbjct: 156 LSNDYARPEWMIIT 169



 Score = 42.0 bits (97), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 17/29 (58%), Positives = 22/29 (75%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMT 1137
            ++++A + P   VG LAAQSIGEP TQMT
Sbjct: 987  RFLKAAVNPGEMVGVLAAQSIGEPATQMT 1015


>gi|303317798|ref|XP_003068901.1| DNA-directed RNA polymerase II largest subunit, putative
           [Coccidioides posadasii C735 delta SOWgp]
 gi|240108582|gb|EER26756.1| DNA-directed RNA polymerase II largest subunit, putative
           [Coccidioides posadasii C735 delta SOWgp]
          Length = 1746

 Score =  160 bits (404), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 96/278 (34%), Positives = 152/278 (54%), Gaps = 35/278 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DV+LFNRQPSLHK S+MAHR +V+P+ TFR N  V TPYNADFDGDEMN+H+PQ+EEA
Sbjct: 456 DGDVILFNRQPSLHKESMMAHRVRVMPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSEEA 515

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L++L ++            N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 516 RAE----LNQLCLVPL----------NIVSPQRNGPLMGIVQDTLCGIYKICRRDVFLTK 561

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M     ++    +  G++ +       P + ++    WTGKQ+ S++L      P  
Sbjct: 562 EQVM----NMMLWVPEWDGVLPQ-------PAI-LKPRPRWTGKQMISMVL------PSG 603

Query: 521 ANLKTKGRAYTA-NEEFCH-RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            NL    R      E+F    D+ +++   EL+ G   K T+G+ G   + + +  ++G 
Sbjct: 604 LNLLRVDRDKVPLAEKFSPLTDTGLLVHGGELMYGMFSKKTVGATG-GGIIHTIYNEYGP 662

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           +V +        + +++L++ GFSIGIGD  P    +Q
Sbjct: 663 EVCMNFFNGAQTVVNYWLLHNGFSIGIGDTIPDLATIQ 700



 Score =  103 bits (257), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 62/180 (34%), Positives = 95/180 (52%), Gaps = 15/180 (8%)

Query: 1225 QLLPSVVIKGVQGINRAVIHEED----VEGVTKYK-----------LLVEGDNLRDVMAT 1269
             LL ++ ++GV G+ RA I+E+     +E  + YK           L   G  L DV+A 
Sbjct: 1290 HLLDTLTLRGVAGVERAFINEKSRVRTLEDGSLYKNSEDPQCKEWVLETSGSALGDVLAI 1349

Query: 1270 YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 1329
             GV   +  SN   E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1350 PGVDATRTYSNQFVEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLCDVMTSRG 1409

Query: 1330 EVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
             ++ +TRHG+ +     L   SFE T + L DAA + + D   GVSE +I+G     GTG
Sbjct: 1410 FLMAVTRHGINRADTGALMRCSFEETVEILLDAAAFAELDDCRGVSENLILGQMAPAGTG 1469



 Score = 99.0 bits (245), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QR+LVK+LE++ V
Sbjct: 814 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMV 873

Query: 666 QYD 668
           +YD
Sbjct: 874 KYD 876



 Score = 87.4 bits (215), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 78/290 (26%), Positives = 132/290 (45%), Gaps = 60/290 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLD--KDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N + +I TP +T Y D  +  D + A+ ++  +E T L  V E  E  + P
Sbjct: 1120 GVPRLKEILNVATHIKTPSMTVYQDPARAMDKESAKQLRSVVEHTNLRSVTEATEIYYDP 1179

Query: 822  DDSFILIKLDMDRIRLLHL--EVDIDSI--------RYCIERTRGISGHLTVSGHSFLIL 871
            D    +I+ D D +    +  E  +D +        R  + R + +   LTV   +  I 
Sbjct: 1180 DIQSTVIEADRDMVESYFIIPEDVMDDLSRQSKWLLRIILSRPKLLDKGLTVQDVAMKIK 1239

Query: 872  K--PKD-----SSKSFNSKMYQMKQ--------------------------LLPSVVIKG 898
            +  P+D     S  + + ++ +++Q                          LL ++ ++G
Sbjct: 1240 ESYPQDIAVIFSDNNADEQVIRIRQIQDPKQDEEDDDDTEYDVTLKKLEAHLLDTLTLRG 1299

Query: 899  VQGINRAVIHEED----VEGVTKYK-----------LLVEGDNLRDVMATYGVKGVKCSS 943
            V G+ RA I+E+     +E  + YK           L   G  L DV+A  GV   +  S
Sbjct: 1300 VAGVERAFINEKSRVRTLEDGSLYKNSEDPQCKEWVLETSGSALGDVLAIPGVDATRTYS 1359

Query: 944  NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
            N   E+ +  GIEA R+ ++ E+  V+   G  ++ RH  L+ D+MTS+G
Sbjct: 1360 NQFVEILEVFGIEATRTALLRELTQVLAFDGSYVNHRHLALLCDVMTSRG 1409



 Score = 73.9 bits (180), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 52/221 (23%), Positives = 95/221 (42%), Gaps = 39/221 (17%)

Query: 112 QRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQ 171
           ++ P   GL D R+GT  +   C TC + ++DC GHFG+I+L  PVFHIG+   +  +L+
Sbjct: 47  RQRPREKGLNDPRLGTIDRNWRCATCEEGINDCPGHFGHIELSTPVFHIGFLTKIKKLLE 106

Query: 172 SICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKSLKKKIL---------------- 214
           ++C N  C ++           A + R+P   +     L K +L                
Sbjct: 107 TVCHN--CGKIKANTSDQKYLDALRFRDPKRRFDAIWRLSKDVLICEADPPPDDDDPFGK 164

Query: 215 ETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEI 274
           E++K V     CG     ++K G+  +   K      K   +++D   +  E  +  P++
Sbjct: 165 ESSKIVKGHGGCGNAQPQIRKEGISLVGTWK----PNKMRDMMDDTDIQQPEKKQITPQM 220

Query: 275 EAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKP 315
                            L +F  +  ED+ +L ++ + ++P
Sbjct: 221 ----------------ALNIFRNVSEEDVRILGLSNDYARP 245



 Score = 56.6 bits (135), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 25/41 (60%), Positives = 28/41 (68%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            A   ++ +A   P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1071 AIESRFAKAAANPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1111


>gi|429962270|gb|ELA41814.1| hypothetical protein VICG_01166 [Vittaforma corneae ATCC 50505]
          Length = 1569

 Score =  160 bits (404), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 93/273 (34%), Positives = 147/273 (53%), Gaps = 33/273 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND VLFNRQPSLHK+S+M HR KV+  ++FR N    +PYNADFDGDEMN+H+PQ+   
Sbjct: 407 DNDEVLFNRQPSLHKMSMMGHRVKVMSGKSFRLNLSATSPYNADFDGDEMNLHMPQSYAT 466

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE                +L A    +V+P++ + +I   QD + G  LLT ++AFFN+
Sbjct: 467 KAE--------------LGLLTAVDKQIVSPQSNKPVIGIVQDTLVGSRLLTVRDAFFNK 512

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAV-----IWTGKQIFSLILKPNR 515
            + M +  +              F  ++ + + ++R  +     +WTGKQ+FS IL P  
Sbjct: 513 REAMNLLYSF-----------NSFGKKNEDFLDYLRPTILQPVELWTGKQLFSAIL-PRI 560

Query: 516 DCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
               ++N                 DS  I+RN  LLAG +DK ++G+  +  + +I+  D
Sbjct: 561 FYMRDSNADISEMDNKGWNSINLTDSTAIIRNGVLLAGPIDKKSVGA-QQGGLIHIIFND 619

Query: 576 FGEDVAVTAMWRLSRMTSFYLMN-RGFSIGIGD 607
           +G + A   +  + R+ + +L++   FS+GIGD
Sbjct: 620 YGSEAAKNFIDNIQRIVTHFLLHISSFSVGIGD 652



 Score =  120 bits (302), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 84/275 (30%), Positives = 152/275 (55%), Gaps = 14/275 (5%)

Query: 1145 GEVCEYIEEVF-VPDD-------SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGH 1196
            G+  E++E  F +PD+       S  +I+L + R  ++   + ++ I   I +  G   H
Sbjct: 1112 GDDREFVETYFEMPDEDIDFDLLSKFVIRLVISRSSMVTRGLTLEFISSKIRKLYGSGIH 1171

Query: 1197 LTVSGHS--FLILKPK--DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVT 1252
            +  S  +   L+++ +   SS+   S + + +  +  + ++G   I +A +   +    +
Sbjct: 1172 IITSDENDERLVIRARFFASSEETLSSLKEAQAEILKIHLQGHTQIKKAYLTNLNKLDKS 1231

Query: 1253 KYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMS 1312
            ++ L  +G +   V++   + G +  +N+ Y +Y  LG+EAAR +I+ E+ LV+E++G S
Sbjct: 1232 EWCLQTDGIDFLSVLSAPNIDGTRVMANDIYVIYSVLGVEAARQSILNELSLVIEDNGSS 1291

Query: 1313 -IDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCI 1371
             ++ RH  L+AD+MT KG + GITRHG+++   SVL  ASFE T D L DAA   + D +
Sbjct: 1292 YVNHRHMSLLADVMTVKGYLTGITRHGVSRQSASVLKRASFEETVDVLLDAAANSELDAV 1351

Query: 1372 SGVSECIIMGLPMNVGTGLIKLLQAVPRSEP-VPR 1405
             GVSE I++G    VGTG + ++  + + E  +PR
Sbjct: 1352 KGVSENIMLGQLPPVGTGNVDIVLDIKKIEHIIPR 1386



 Score = 99.8 bits (247), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 42/59 (71%), Positives = 51/59 (86%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
           +GFVQNS+ SG+ P EFFFH MGGREG++DTA+KTAETGY+QRRLVK+LED  V +D S
Sbjct: 781 RGFVQNSYLSGMDPDEFFFHAMGGREGIIDTAIKTAETGYIQRRLVKALEDAIVHHDFS 839



 Score = 94.7 bits (234), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 73/269 (27%), Positives = 140/269 (52%), Gaps = 35/269 (13%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDK--DTDLDYARIVKGRLERTTLGEVCE-------- 813
            GVPR+ EIIN +++I TP +  +L+K   TD++ AR V+ ++E  +L  VCE        
Sbjct: 1045 GVPRLNEIINLAKSIKTPSMQIFLNKPLGTDIENARRVQNQIEFLSLKMVCEMSQILYDP 1104

Query: 814  ------------YIEEVF-VPDD-------SFILIKLDMDRIRLLHLEVDIDSIRYCIER 853
                        ++E  F +PD+       S  +I+L + R  ++   + ++ I   I +
Sbjct: 1105 KIRTTSIGDDREFVETYFEMPDEDIDFDLLSKFVIRLVISRSSMVTRGLTLEFISSKIRK 1164

Query: 854  TRGISGHLTVSGHS--FLILKPK--DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHE 909
              G   H+  S  +   L+++ +   SS+   S + + +  +  + ++G   I +A +  
Sbjct: 1165 LYGSGIHIITSDENDERLVIRARFFASSEETLSSLKEAQAEILKIHLQGHTQIKKAYLTN 1224

Query: 910  EDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLV 969
             +    +++ L  +G +   V++   + G +  +N+ Y +Y  LG+EAAR +I+ E+ LV
Sbjct: 1225 LNKLDKSEWCLQTDGIDFLSVLSAPNIDGTRVMANDIYVIYSVLGVEAARQSILNELSLV 1284

Query: 970  MENHGMS-IDFRHPMLVADLMTSKGEVLG 997
            +E++G S ++ RH  L+AD+MT KG + G
Sbjct: 1285 IEDNGSSYVNHRHMSLLADVMTVKGYLTG 1313



 Score = 84.7 bits (208), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 106/234 (45%), Gaps = 46/234 (19%)

Query: 115 PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSIC 174
           P  +GL+D RMGT ++   C TC     +CVGH+G+I+L  P+FHIGY   +   L+ +C
Sbjct: 42  PKENGLIDLRMGTTERSFLCQTCNSTSFECVGHYGHIELSKPMFHIGYLAKIKKTLECVC 101

Query: 175 KNPTCARVLLGEEKAAGFRAKLRNPALS--YLVRKSLKKKILETTKKVSVCPHCGEINGV 232
               C+++        G +  LR P L   + V KS  K I E          CG     
Sbjct: 102 F--YCSKI-------KGSKKNLR-PGLEDCWTVLKS--KSICEGEDIPEGKSGCGNRQPS 149

Query: 233 VKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVL 292
           ++K GL                    +L+A   E V    ++           LN   V 
Sbjct: 150 IRKDGL--------------------NLIAFMKEDVDGEGKV----------VLNGERVY 179

Query: 293 QLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVI--SDLKSDNDV 344
            + + IP ED   L  + +  +P  ++LT ++VPP  +RPS++    L++++D+
Sbjct: 180 NILKKIPTEDSMFLGFDPDNCRPEWMMLTTIIVPPPAMRPSIVLNGHLRAEDDL 233



 Score = 52.8 bits (125), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 23/39 (58%), Positives = 28/39 (71%)

Query: 1107 REKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            + K +RA++     VG LAAQS+GEP TQMTL TFH AG
Sbjct: 999  KTKILRAKVNANEMVGTLAAQSVGEPATQMTLNTFHLAG 1037


>gi|448497568|ref|ZP_21610521.1| DNA-directed RNA polymerase subunit A' [Halorubrum coriense DSM
           10284]
 gi|445699799|gb|ELZ51819.1| DNA-directed RNA polymerase subunit A' [Halorubrum coriense DSM
           10284]
          Length = 970

 Score =  160 bits (404), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 96/273 (35%), Positives = 138/273 (50%), Gaps = 55/273 (20%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 476 DGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQNEEA 535

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR G  +I A QD I+G YLLT  N  F+ 
Sbjct: 536 RAE--------------ARVLMRVQEQILSPRFGGNIIGAIQDHISGTYLLTHSNPEFSE 581

Query: 461 AQTM------RIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPN 514
            Q +      R+     AD  D  G                     WTG+ +FS +L  +
Sbjct: 582 TQALDLLRATRVDELPEADGVDDGG------------------QEFWTGRTLFSELLPDD 623

Query: 515 RDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLR 574
            D    ++                    V++ + +L+ G++D+  +G+ G   V   L +
Sbjct: 624 LDLSFTSSAGDD----------------VVIEDGQLIEGTIDEDAVGAFG-GEVVDTLTK 666

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           ++GE  A   +  ++ +    +MN GFSIGI D
Sbjct: 667 EYGETRARVFINEIASLAMRAIMNFGFSIGIDD 699



 Score =  107 bits (267), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 79/294 (26%), Positives = 125/294 (42%), Gaps = 57/294 (19%)

Query: 97  SHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP 156
           S  ++++ + Y  D    PI  GL+D R+G       C TCG +   C GHFG+I+L  P
Sbjct: 19  SATKVITADTY--DDDGYPIDMGLMDPRLGVIDPGLECRTCGSHSGSCNGHFGHIELAAP 76

Query: 157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILET 216
           V H+G+ + +  +L+S C+   C R+ L + +   FR +             + K  +  
Sbjct: 77  VIHVGFTKLIRRLLRSTCRE--CGRLALDDAQRDEFRDRYERAKELGDDEHDVLKAAVRQ 134

Query: 217 TKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDL---------------- 260
            +K S CP CGE    +K        HEK     + +D +  D                 
Sbjct: 135 ARKASTCPFCGEPQADIK--------HEKPTTYYEVQDVLSGDYSERIAAAMQPDEEEDD 186

Query: 261 -------LAEYNE----------AVKFNPEIEAHKKFGL----------IQTLNPLEVLQ 293
                  LAE  +          A +F P  E  +              +  L P ++  
Sbjct: 187 PGTSPQELAEKTDIAVDRINEIMAGEFRPRKEDRRAIEKALDVDLTEEDMNKLMPSDIRD 246

Query: 294 LFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDNDVV 345
            FE IP ED+ +L +++E S+P  +ILT L VPP   RPS+  D   +S++D+ 
Sbjct: 247 WFEDIPDEDLEVLGIDSEHSRPEWMILTVLPVPPVTTRPSITLDNGQRSEDDLT 300



 Score = 91.3 bits (225), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 38/57 (66%), Positives = 48/57 (84%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFV+NS+  GLTP EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 828 HGFVENSYRGGLTPQEFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELEAQYD 884


>gi|433637474|ref|YP_007283234.1| DNA-directed RNA polymerase subunit A'' [Halovivax ruber XH-70]
 gi|433289278|gb|AGB15101.1| DNA-directed RNA polymerase subunit A'' [Halovivax ruber XH-70]
          Length = 986

 Score =  160 bits (404), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 100/270 (37%), Positives = 144/270 (53%), Gaps = 45/270 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+++FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 494 DGDIIIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQNEEA 553

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR GE +I A QD I+G YLLT +N  FN 
Sbjct: 554 RAE--------------ARVLMRVQEQILSPRFGENIIGAIQDHISGTYLLTHENPHFNE 599

Query: 461 AQTMR-IASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q +  + +T I +  +  G     +     P         WTG+ IFS +L      P 
Sbjct: 600 TQALDLLRATRIDELPEQSG-----TEEDGTPY--------WTGRAIFSELL------PD 640

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           + NL   G   T  E+       V++ + +L+ G++ +  +G  G   +   + + +G  
Sbjct: 641 DLNLTFTG---TVGED-------VVIEDGQLVEGTIAEDEVGGFG-GEIVDTITKVYGNT 689

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVT 609
            A   +  LS +    +M+ GFSIGI D T
Sbjct: 690 RARIFINELSTLAMRTIMHFGFSIGIDDET 719



 Score =  114 bits (285), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 80/289 (27%), Positives = 133/289 (46%), Gaps = 41/289 (14%)

Query: 94  QQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDL 153
           ++ S  +I++ + Y  D    PI  GL+D R+G       C TCG++   C GHFG+I+L
Sbjct: 23  REMSATKIITADTY--DDDGFPIDMGLMDPRLGVIDPGLECKTCGKHSGSCNGHFGHIEL 80

Query: 154 PLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKI 213
             PV H+G+ + +  +L+  C+   C+R+LL E++   FR ++            + K  
Sbjct: 81  AAPVIHVGFTKLIRRLLRGTCRE--CSRLLLTEDERGEFRDQIDESRKLGRDLNDVTKAA 138

Query: 214 LETTKKVSVCPHCGEINGVV---------------------KKCGLLKISHEKYKNRTKK 252
           +   +K   CP CGEI   +                     +  G ++   E+   RT  
Sbjct: 139 IRQARKKDRCPFCGEIQYDIDHEKPTTYYEVQEVLASEYSQRIAGAMQGDEEEGIERTTP 198

Query: 253 KD--AIVEDLLAEYNEAV--KFNPEIEAHKKFGLIQTLN----------PLEVLQLFEAI 298
            +  A  E  L   NE +   F P  E  +      +++          P ++   FEAI
Sbjct: 199 DELAAKTEIDLTRVNEILSGSFRPREEQREAIEKALSIDLTEEDTNKLMPSDIRDWFEAI 258

Query: 299 PLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDNDVV 345
           P EDI +L ++++ S+P  +ILT L VPP   RPS+  D   +S++D+ 
Sbjct: 259 PDEDIEVLGIDSDRSRPEWMILTVLPVPPVTARPSITLDNGQRSEDDLT 307



 Score = 91.3 bits (225), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 38/57 (66%), Positives = 49/57 (85%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFV+NS+ +GLTP EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 846 HGFVENSYTAGLTPREFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELEAQYD 902



 Score = 47.4 bits (111), Expect = 0.067,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 30/46 (65%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 65
           +VLM  +  +++PR GE +I A QD I+G YLLT +N  FN  Q +
Sbjct: 558 RVLMRVQEQILSPRFGENIIGAIQDHISGTYLLTHENPHFNETQAL 603


>gi|448513825|ref|ZP_21616756.1| DNA-directed RNA polymerase subunit A' [Halorubrum distributum JCM
           9100]
 gi|448526665|ref|ZP_21619934.1| DNA-directed RNA polymerase subunit A' [Halorubrum distributum JCM
           10118]
 gi|445692978|gb|ELZ45141.1| DNA-directed RNA polymerase subunit A' [Halorubrum distributum JCM
           9100]
 gi|445698892|gb|ELZ50930.1| DNA-directed RNA polymerase subunit A' [Halorubrum distributum JCM
           10118]
          Length = 970

 Score =  160 bits (404), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 97/273 (35%), Positives = 140/273 (51%), Gaps = 55/273 (20%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 476 DGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQNEEA 535

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR G  +I A QD I+G YLLT  N  F+ 
Sbjct: 536 RAE--------------ARVLMRVQEQILSPRFGGNIIGAIQDHISGTYLLTHSNPEFSE 581

Query: 461 AQTM------RIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPN 514
            Q +      R+     AD  D  G  + F                WTG+ +FS +L  +
Sbjct: 582 TQALDLLRATRVDELPEADGVDDDG--REF----------------WTGRTLFSELLPDD 623

Query: 515 RDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLR 574
            D    ++                    V++ + +L+ G++D+  +G+ G   V   L +
Sbjct: 624 LDLSFTSSAGDS----------------VVIEDGQLIEGTIDEDAVGAFG-GEVVDTLTK 666

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           ++GE  A   +  ++ +    +MN GFSIGI D
Sbjct: 667 EYGETRARVFINEIASLAMRAIMNFGFSIGIDD 699



 Score =  107 bits (267), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 77/286 (26%), Positives = 125/286 (43%), Gaps = 41/286 (14%)

Query: 97  SHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP 156
           S  ++++ + Y  D    PI  GL+D R+G       C TCG +   C GHFG+I+L  P
Sbjct: 19  SATKVITADTY--DDDGYPIDMGLMDPRLGVIDPGLECRTCGSHSGSCNGHFGHIELAAP 76

Query: 157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILET 216
           V H+G+ + +  +L+S C+   C ++ L E +   FR +             + K  +  
Sbjct: 77  VIHVGFTKLIRRLLRSTCRE--CGKLALDEAQRDEFRDRYERAKELGDDEHDVLKAAVRQ 134

Query: 217 TKKVSVCPHCGEINGVVKK---------------------CGLLKISHEKYKNRTKKKDA 255
            +K S CP CGE    +K                         ++   E+    T  ++ 
Sbjct: 135 ARKASTCPFCGEPQADIKHEKPTTYYEVQDVLSGDYSERIAAAMQPDEEEDDPGTSPQEL 194

Query: 256 IVEDLLA--EYNE--AVKFNPEIEAHKKFGL----------IQTLNPLEVLQLFEAIPLE 301
             E  +A    NE  A +F P  E  +              +  L P ++   FE IP E
Sbjct: 195 ADETDIAVDRINEIMAGEFRPRKEDRRAIEKALDVDLTEEDMNKLMPSDIRDWFEDIPDE 254

Query: 302 DIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDNDVV 345
           D+ +L +++E S+P  +ILT L VPP   RPS+  D   +S++D+ 
Sbjct: 255 DLEVLGIDSEHSRPEWMILTVLPVPPVTTRPSITLDNGQRSEDDLT 300



 Score = 91.3 bits (225), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 38/57 (66%), Positives = 48/57 (84%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFV+NS+  GLTP EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 828 HGFVENSYRGGLTPQEFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELEAQYD 884


>gi|448427503|ref|ZP_21583818.1| DNA-directed RNA polymerase subunit A' [Halorubrum terrestre JCM
           10247]
 gi|445678190|gb|ELZ30684.1| DNA-directed RNA polymerase subunit A' [Halorubrum terrestre JCM
           10247]
          Length = 970

 Score =  160 bits (404), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 97/273 (35%), Positives = 140/273 (51%), Gaps = 55/273 (20%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 476 DGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQNEEA 535

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR G  +I A QD I+G YLLT  N  F+ 
Sbjct: 536 RAE--------------ARVLMRVQEQILSPRFGGNIIGAIQDHISGTYLLTHSNPEFSE 581

Query: 461 AQTM------RIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPN 514
            Q +      R+     AD  D  G  + F                WTG+ +FS +L  +
Sbjct: 582 TQALDLLRATRVDELPEADGVDDDG--REF----------------WTGRTLFSELLPDD 623

Query: 515 RDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLR 574
            D    ++                    V++ + +L+ G++D+  +G+ G   V   L +
Sbjct: 624 LDLSFTSSAGDS----------------VVIEDGQLIEGTIDEDAVGAFG-GEVVDTLTK 666

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           ++GE  A   +  ++ +    +MN GFSIGI D
Sbjct: 667 EYGETRARVFINEIASLAMRAIMNFGFSIGIDD 699



 Score =  107 bits (267), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 77/286 (26%), Positives = 125/286 (43%), Gaps = 41/286 (14%)

Query: 97  SHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP 156
           S  ++++ + Y  D    PI  GL+D R+G       C TCG +   C GHFG+I+L  P
Sbjct: 19  SATKVITADTY--DDDGYPIDMGLMDPRLGVIDPGLECRTCGSHSGSCNGHFGHIELAAP 76

Query: 157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILET 216
           V H+G+ + +  +L+S C+   C ++ L E +   FR +             + K  +  
Sbjct: 77  VIHVGFTKLIRRLLRSTCRE--CGKLALDEAQRDEFRDRYERAKELGDDEHDVLKAAVRQ 134

Query: 217 TKKVSVCPHCGEINGVVKK---------------------CGLLKISHEKYKNRTKKKDA 255
            +K S CP CGE    +K                         ++   E+    T  ++ 
Sbjct: 135 ARKASTCPFCGEPQADIKHEKPTTYYEVQDVLSGDYSERIAAAMQPDEEEDDPGTSPQEL 194

Query: 256 IVEDLLA--EYNE--AVKFNPEIEAHKKFGL----------IQTLNPLEVLQLFEAIPLE 301
             E  +A    NE  A +F P  E  +              +  L P ++   FE IP E
Sbjct: 195 ADETDIAVDRINEIMAGEFRPRKEDRRAIEKALDVDLTEEDMNKLMPSDIRDWFEDIPDE 254

Query: 302 DIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDNDVV 345
           D+ +L +++E S+P  +ILT L VPP   RPS+  D   +S++D+ 
Sbjct: 255 DLEVLGIDSEHSRPEWMILTVLPVPPVTTRPSITLDNGQRSEDDLT 300



 Score = 91.3 bits (225), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 38/57 (66%), Positives = 48/57 (84%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFV+NS+  GLTP EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 828 HGFVENSYRGGLTPQEFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELEAQYD 884


>gi|448482811|ref|ZP_21605582.1| DNA-directed RNA polymerase subunit A' [Halorubrum arcis JCM 13916]
 gi|445821097|gb|EMA70893.1| DNA-directed RNA polymerase subunit A' [Halorubrum arcis JCM 13916]
          Length = 970

 Score =  160 bits (404), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 97/273 (35%), Positives = 140/273 (51%), Gaps = 55/273 (20%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 476 DGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQNEEA 535

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR G  +I A QD I+G YLLT  N  F+ 
Sbjct: 536 RAE--------------ARVLMRVQEQILSPRFGGNIIGAIQDHISGTYLLTHSNPEFSE 581

Query: 461 AQTM------RIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPN 514
            Q +      R+     AD  D  G  + F                WTG+ +FS +L  +
Sbjct: 582 TQALDLLRATRVDELPEADGVDDDG--REF----------------WTGRTLFSELLPDD 623

Query: 515 RDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLR 574
            D    ++                    V++ + +L+ G++D+  +G+ G   V   L +
Sbjct: 624 LDLSFTSSAGDS----------------VVIEDGQLIEGTIDEDAVGAFG-GEVVDTLTK 666

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           ++GE  A   +  ++ +    +MN GFSIGI D
Sbjct: 667 EYGETRARVFINEIASLAMRAIMNFGFSIGIDD 699



 Score =  107 bits (267), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 77/286 (26%), Positives = 125/286 (43%), Gaps = 41/286 (14%)

Query: 97  SHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP 156
           S  ++++ + Y  D    PI  GL+D R+G       C TCG +   C GHFG+I+L  P
Sbjct: 19  SATKVITADTY--DDDGYPIDMGLMDPRLGVIDPGLECRTCGSHSGSCNGHFGHIELAAP 76

Query: 157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILET 216
           V H+G+ + +  +L+S C+   C ++ L E +   FR +             + K  +  
Sbjct: 77  VIHVGFTKLIRRLLRSTCRE--CGKLALDEAQRDEFRDRYERAKELGDDEHDVLKAAVRQ 134

Query: 217 TKKVSVCPHCGEINGVVKK---------------------CGLLKISHEKYKNRTKKKDA 255
            +K S CP CGE    +K                         ++   E+    T  ++ 
Sbjct: 135 ARKASTCPFCGEPQADIKHEKPTTYYEVQDVLSGDYSERIAAAMQPDEEEDDPGTSPQEL 194

Query: 256 IVEDLLA--EYNE--AVKFNPEIEAHKKFGL----------IQTLNPLEVLQLFEAIPLE 301
             E  +A    NE  A +F P  E  +              +  L P ++   FE IP E
Sbjct: 195 ADETDIAVDRINEIMAGEFRPRKEDRRAIEKALDIDLTEEDMNKLMPSDIRDWFEDIPDE 254

Query: 302 DIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDNDVV 345
           D+ +L +++E S+P  +ILT L VPP   RPS+  D   +S++D+ 
Sbjct: 255 DLEVLGIDSEHSRPEWMILTVLPVPPVTTRPSITLDNGQRSEDDLT 300



 Score = 91.3 bits (225), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 38/57 (66%), Positives = 48/57 (84%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFV+NS+  GLTP EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 828 HGFVENSYRGGLTPQEFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELEAQYD 884


>gi|448494509|ref|ZP_21609496.1| DNA-directed RNA polymerase subunit A' [Halorubrum californiensis
           DSM 19288]
 gi|445689344|gb|ELZ41584.1| DNA-directed RNA polymerase subunit A' [Halorubrum californiensis
           DSM 19288]
          Length = 970

 Score =  160 bits (404), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 96/273 (35%), Positives = 139/273 (50%), Gaps = 55/273 (20%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 476 DGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQNEEA 535

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR G  +I A QD I+G YLLT  N  F+ 
Sbjct: 536 RAE--------------ARVLMRVQEQILSPRFGGNIIGAIQDHISGTYLLTHSNPEFSE 581

Query: 461 AQTM------RIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPN 514
            Q +      R+     AD  D  G                    +WTG+ +FS +L  +
Sbjct: 582 TQALDLLRATRVDELPEADGVDDDG------------------RELWTGRTLFSELLPDD 623

Query: 515 RDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLR 574
            D    ++                    V++ + +L+ G++D+  +G+ G   V   L +
Sbjct: 624 LDLSFTSSAGDS----------------VVIEDGQLIEGTIDEDAVGAFG-GEVVDTLTK 666

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           ++GE  A   +  ++ +    +MN GFSIGI D
Sbjct: 667 EYGETRARVFINEIASLAMRAIMNFGFSIGIDD 699



 Score =  107 bits (267), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 79/294 (26%), Positives = 125/294 (42%), Gaps = 57/294 (19%)

Query: 97  SHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP 156
           S  ++++ + Y  D    PI  GL+D R+G       C TCG +   C GHFG+I+L  P
Sbjct: 19  SATKVITADTY--DDDGYPIDMGLMDPRLGVIDPGLECRTCGSHSGSCNGHFGHIELAAP 76

Query: 157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILET 216
           V H+G+ + +  +L+S C+   C R+ L + +   FR +             + K  +  
Sbjct: 77  VIHVGFTKLIRRLLRSTCRE--CGRLALDDAQRDEFRDRYERAKELGDDEHDVLKAAVRQ 134

Query: 217 TKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDL---------------- 260
            +K S CP CGE    +K        HEK     + +D +  D                 
Sbjct: 135 ARKASTCPFCGEPQADIK--------HEKPTTYYEVQDVLSGDYSERIAAAMQPDEEEDD 186

Query: 261 -------LAEYNE----------AVKFNPEIEAHKKFGL----------IQTLNPLEVLQ 293
                  LAE  +          A +F P  E  +              +  L P ++  
Sbjct: 187 PGTSPQELAEKTDIAVDRINEIMAGEFRPRKEDRRAIEKALDVDLTEEDMNKLMPSDIRD 246

Query: 294 LFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDNDVV 345
            FE IP ED+ +L +++E S+P  +ILT L VPP   RPS+  D   +S++D+ 
Sbjct: 247 WFEDIPDEDLEVLGIDSEHSRPEWMILTVLPVPPVTTRPSITLDNGQRSEDDLT 300



 Score = 91.3 bits (225), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 38/57 (66%), Positives = 48/57 (84%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFV+NS+  GLTP EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 828 HGFVENSYRGGLTPQEFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELEAQYD 884


>gi|448451259|ref|ZP_21592742.1| DNA-directed RNA polymerase subunit A' [Halorubrum litoreum JCM
           13561]
 gi|445810693|gb|EMA60709.1| DNA-directed RNA polymerase subunit A' [Halorubrum litoreum JCM
           13561]
          Length = 970

 Score =  159 bits (403), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 97/273 (35%), Positives = 140/273 (51%), Gaps = 55/273 (20%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 476 DGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQNEEA 535

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR G  +I A QD I+G YLLT  N  F+ 
Sbjct: 536 RAE--------------ARVLMRVQEQILSPRFGGNIIGAIQDHISGTYLLTHSNPEFSE 581

Query: 461 AQTM------RIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPN 514
            Q +      R+     AD  D  G  + F                WTG+ +FS +L  +
Sbjct: 582 TQALDLLRATRVDELPEADGVDDDG--REF----------------WTGRTLFSELLPDD 623

Query: 515 RDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLR 574
            D    ++                    V++ + +L+ G++D+  +G+ G   V   L +
Sbjct: 624 LDLSFTSSAGDS----------------VVIEDGQLIEGTIDEDAVGAFG-GEVVDTLTK 666

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           ++GE  A   +  ++ +    +MN GFSIGI D
Sbjct: 667 EYGETRARVFINEIASLAMRAIMNFGFSIGIDD 699



 Score =  107 bits (267), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 77/286 (26%), Positives = 125/286 (43%), Gaps = 41/286 (14%)

Query: 97  SHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP 156
           S  ++++ + Y  D    PI  GL+D R+G       C TCG +   C GHFG+I+L  P
Sbjct: 19  SATKVITADTY--DDDGYPIDMGLMDPRLGVIDPGLECRTCGSHSGSCNGHFGHIELAAP 76

Query: 157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILET 216
           V H+G+ + +  +L+S C+   C ++ L E +   FR +             + K  +  
Sbjct: 77  VIHVGFTKLIRRLLRSTCRE--CGKLALDEAQRDEFRDRYERAKELGDDEHDVLKAAVRQ 134

Query: 217 TKKVSVCPHCGEINGVVKK---------------------CGLLKISHEKYKNRTKKKDA 255
            +K S CP CGE    +K                         ++   E+    T  ++ 
Sbjct: 135 ARKASTCPFCGEPQADIKHEKPTTYYEVQDVLSGDYSERIAAAMQPDEEEDDPGTSPQEL 194

Query: 256 IVEDLLA--EYNE--AVKFNPEIEAHKKFGL----------IQTLNPLEVLQLFEAIPLE 301
             E  +A    NE  A +F P  E  +              +  L P ++   FE IP E
Sbjct: 195 ADETDIAVDRINEIMAGEFRPRKEDRRAIEKALDVDLTEEDMNKLMPSDIRDWFEDIPDE 254

Query: 302 DIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDNDVV 345
           D+ +L +++E S+P  +ILT L VPP   RPS+  D   +S++D+ 
Sbjct: 255 DLEVLGIDSEHSRPEWMILTVLPVPPVTTRPSITLDNGQRSEDDLT 300



 Score = 90.9 bits (224), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 38/57 (66%), Positives = 48/57 (84%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFV+NS+  GLTP EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 828 HGFVENSYRGGLTPQEFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELEAQYD 884


>gi|45935355|gb|AAS79699.1| RNA polymerase III large subunit [Nymphaea lotus]
          Length = 545

 Score =  159 bits (403), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 84/223 (37%), Positives = 134/223 (60%), Gaps = 27/223 (12%)

Query: 390 MNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGY 449
           MN+H+PQTEEARAEAL              +LM  ++NL TP+NGE+L+A+TQDF+T  +
Sbjct: 1   MNLHIPQTEEARAEAL--------------MLMGVQNNLCTPKNGEILVASTQDFLTSSF 46

Query: 450 LLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPV-VFVRTAVIWTGKQIFS 508
           L+T+K+ F++RA    +  + + D  D   +          P    ++   +WTGKQ+FS
Sbjct: 47  LITRKDTFYDRA-AFSLMCSYMGDGMDPIDL----------PTPALLKPIELWTGKQLFS 95

Query: 509 LILKPNRDCPVNANLKTKGRAYTANE-EFCHRDSYVILRNSELLAGSMDKSTLGSGGKAN 567
           ++++P+    +  NL  K +    N    C  D +V +RNSELL G + K+TLG+G K+ 
Sbjct: 96  VLIRPHASMRIYVNLFLKEKKCVKNRGTMCPNDGFVYIRNSELLCGQVGKATLGNGNKSG 155

Query: 568 VFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           +F +L+RD+    A + M RL+++++ ++ N GF+IGI DV P
Sbjct: 156 LFSVLIRDYNAHAAASCMNRLAKLSARWIGNHGFTIGIDDVQP 198



 Score =  104 bits (260), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 49/69 (71%), Positives = 57/69 (82%), Gaps = 1/69 (1%)

Query: 607 DVTPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV NSF++GLT TEFFFHTMGGREGLVDTAVKTA+TGYM RRL+KSLEDL +
Sbjct: 318 DKSPAAKGFVTNSFYTGLTATEFFFHTMGGREGLVDTAVKTADTGYMSRRLMKSLEDLSI 377

Query: 666 QYDMSFDAA 674
            YD +   A
Sbjct: 378 HYDQTVRNA 386



 Score = 56.6 bits (135), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 22/42 (52%), Positives = 36/42 (85%)

Query: 21 VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRA 62
          +LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+K+ F++RA
Sbjct: 17 MLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDRA 58


>gi|168066799|ref|XP_001785319.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162663074|gb|EDQ49860.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 1742

 Score =  159 bits (403), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 93/275 (33%), Positives = 148/275 (53%), Gaps = 43/275 (15%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D D VLFNRQPSLHK+SIM HR +++P+ TFR N  V +PYNADFDGDEMN+H+PQ+ E
Sbjct: 453 NDGDFVLFNRQPSLHKMSIMGHRIRIMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSFE 512

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE L             +++M  K  +V+P++   +I   QD + G   +T+++ F  
Sbjct: 513 TRAEVL-------------ELMMVPKC-IVSPQSNRPVIGIVQDTLLGCRKVTKRDTFIE 558

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAV----IWTGKQIFSLILKPNR 515
           +     I                   W  ++  + + T +    +WTGKQIFSLI+    
Sbjct: 559 KDVFYNIL----------------MWWEEFDGKIPIPTILKPRPLWTGKQIFSLII---- 598

Query: 516 DCPVNANLKTKGRAYTANE--EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILL 573
             P   NL  +   +   E  +    D+ V +   E++AG++ K TLG+ G+ ++ +++ 
Sbjct: 599 --PKQINLMRQAFWHPDGEYGDLSPGDTQVRIEKGEVVAGTLCKKTLGT-GQGSLIHVIW 655

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
            + G D A   +     + +++L+ +GFSIGIGD 
Sbjct: 656 EEVGPDAARKFLGHTQWLVNYWLLQQGFSIGIGDT 690



 Score =  100 bits (249), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 57/173 (32%), Positives = 97/173 (56%), Gaps = 9/173 (5%)

Query: 1226 LLPSVVIKGVQGINRAVIHE-------EDVEGVTK--YKLLVEGDNLRDVMATYGVKGVK 1276
            +L  + ++G+  I +  I E       E++  V +  + L  EG N+  VM    V   +
Sbjct: 1289 MLTEMALRGIPDIRKVFIKEDKKNRFDENLAFVVEQEWVLDTEGVNMLAVMCHEDVDASR 1348

Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITR 1336
             +SN+  EV + LGIEA R++++ E++ V+   G  +++RH  ++ D+MT +G ++ ITR
Sbjct: 1349 TTSNHLIEVIEVLGIEAVRNSLLKELRDVISFDGSYVNYRHLAILCDVMTYRGHLMAITR 1408

Query: 1337 HGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
            HG+ +     +   SFE T D L DAA Y + D + GV+E I++G    +GTG
Sbjct: 1409 HGINRNDTGPMMRCSFEETVDILLDAAVYAEADHLKGVTENIMLGQLAPIGTG 1461



 Score =  100 bits (248), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 42/57 (73%), Positives = 52/57 (91%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKT+ETGY+QRRLVK++ED+ V+YD
Sbjct: 818 RGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDVMVKYD 874



 Score = 94.4 bits (233), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 83/263 (31%), Positives = 135/263 (51%), Gaps = 20/263 (7%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D ++Q +  +I S   Y +     P   GL D R+GT  +   C TC  ++++C GHFGY
Sbjct: 26  DEIRQMAVCKIESSETYDRG---KPKIGGLSDPRLGTIDRHTKCETCAGSMTECPGHFGY 82

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKSL 209
           ++L  P+FHIG+ + V++IL+ +C N  C+R L  EE     +A K+RNP       K  
Sbjct: 83  LELAKPMFHIGFLKTVLSILRCVCYN--CSRCLADEEDHRFKQAKKVRNP-------KHR 133

Query: 210 KKKILETTKKVSVCPHCGEI--NGVVK-KCGLLKISHEKYKNRTKKKDAIVEDLLAEYNE 266
            KK+L+  K  + C    +I  N V+  +    K SH     +  K       ++AE+  
Sbjct: 134 LKKVLDCCKSKTKCDTGDDIDENDVMNGEENEKKKSHGGCGAQQPKISIDGMKIVAEFKP 193

Query: 267 AVKFNPEIEAH--KKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLL 324
           + K   E E H  +     Q L+  +VL + + I  E+  LL +N + ++P  +IL  L 
Sbjct: 194 SRKKGEEPEQHMPEPVERKQQLSAEKVLSILKRISDEECTLLGLNPKYARPDWMILQVLP 253

Query: 325 VPPNCIRPSVISD--LKSDNDVV 345
           +PP  +RPSV+ D   +S++D+ 
Sbjct: 254 IPPPPVRPSVMMDSSARSEDDLT 276



 Score = 75.9 bits (185), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 75/299 (25%), Positives = 128/299 (42%), Gaps = 77/299 (25%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDK--DTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR++EIIN ++ I TP +T YL    + + + A+ V+  LE TTL  V +  E  + P
Sbjct: 1119 GVPRLREIINVAKKIKTPSLTVYLKPGVNKEKERAKNVQCALEYTTLRSVTQATEIWYDP 1178

Query: 822  DDSFILIKLDMD-----------------------RIRL------------------LHL 840
            +    LI+ DM+                       RI L                  ++L
Sbjct: 1179 EPMSTLIEEDMEFVKSYYEMPDEDVAPEKISPWLLRIELNREMMVDKKLSMADIAEKINL 1238

Query: 841  EVDID-------------SIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQM 887
            E D D              +R  I       G +T      + LK  +S+          
Sbjct: 1239 EFDDDLTCIFNDDNAEKLILRIRIMNDEAPKGEMTEQSEDDVFLKKIESN---------- 1288

Query: 888  KQLLPSVVIKGVQGINRAVIHE-------EDVEGVTK--YKLLVEGDNLRDVMATYGVKG 938
              +L  + ++G+  I +  I E       E++  V +  + L  EG N+  VM    V  
Sbjct: 1289 --MLTEMALRGIPDIRKVFIKEDKKNRFDENLAFVVEQEWVLDTEGVNMLAVMCHEDVDA 1346

Query: 939  VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             + +SN+  EV + LGIEA R++++ E++ V+   G  +++RH  ++ D+MT +G ++ 
Sbjct: 1347 SRTTSNHLIEVIEVLGIEAVRNSLLKELRDVISFDGSYVNYRHLAILCDVMTYRGHLMA 1405



 Score = 52.4 bits (124), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 21/37 (56%), Positives = 28/37 (75%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            +++ + + P   +G +AAQSIGEP TQMTL TFHFAG
Sbjct: 1074 RFLMSLVAPGEMIGCVAAQSIGEPATQMTLNTFHFAG 1110


>gi|329132889|gb|AEB78335.1| Rpb1, partial [Jakoba libera]
          Length = 1040

 Score =  159 bits (403), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 91/272 (33%), Positives = 144/272 (52%), Gaps = 32/272 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DNDVVLFNRQP+LH++ +M HR K +  +TFR N  V +PYNADFDGDEMN+H PQ+   
Sbjct: 355 DNDVVLFNRQPTLHRMGMMGHRVKTMKFKTFRLNLSVTSPYNADFDGDEMNLHAPQSLLT 414

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE L               LM    N+++P++   ++   QD +     +T ++ F  R
Sbjct: 415 KAELLE--------------LMMIPKNMISPKSNSPVMGLVQDSLLACRRITLRDVFLER 460

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              M           +    +  F  +   P + ++   +WTGKQ+FS IL       VN
Sbjct: 461 DHFM-----------NCLMWVDDFDGQLPMPAI-LKPKPLWTGKQLFSQILP-----KVN 503

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
             L++K    + N      D+ VI+   ELLAG   K+T+G+  + ++ +++  + G +V
Sbjct: 504 LRLRSKDHPRSENTLVSPGDTQVIIEQGELLAGKCCKNTMGT-SQGSLVHVVYTEQGPEV 562

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
               M ++ R+ +++L+  GFSIGIGD  P +
Sbjct: 563 CARMMGQVQRLVNYWLLTVGFSIGIGDCVPDE 594



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 42/57 (73%), Positives = 53/57 (92%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV NS+ SGLTP EFFFH+MGGREG++DTAVKT+ETGY+QRRLVK++ED+ V+YD
Sbjct: 718 KGFVSNSYLSGLTPQEFFFHSMGGREGIIDTAVKTSETGYIQRRLVKAMEDIMVRYD 774



 Score = 57.0 bits (136), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 24/39 (61%), Positives = 29/39 (74%)

Query: 1107 REKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            R ++ +A I P   VG +AAQS+GEP TQMTL TFHFAG
Sbjct: 990  RTRFFQALITPGECVGVIAAQSVGEPATQMTLNTFHFAG 1028



 Score = 53.5 bits (127), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 49/195 (25%), Positives = 84/195 (43%), Gaps = 23/195 (11%)

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGE-EKAAGFRAKLRNPAL 201
           +C GHFG+I+L  P++H+GY   V  +L  +C    C+  L     K  G  AK  N  +
Sbjct: 1   ECPGHFGHIELAKPMYHVGYMNVVRKVLDCVCMK--CSSPLFNPVSKRLGELAKYCNSKV 58

Query: 202 SYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLL--KISHEKYKNRTKKKDAIVED 259
                +SL         + +     G ++ +   CG    KI+ ++Y    ++K      
Sbjct: 59  RMCGDRSLAAAGAAGGAEGAEGQGQGAMD-IDHGCGFTKPKITRKEYFLMKEEK------ 111

Query: 260 LLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLI 319
                      +P  E+  +    + L   E  Q+ +A+  E   +L  N   ++P  L+
Sbjct: 112 -----------SPGQESGSQKVSQRILTAEEAHQVLKALTNEACEMLGFNPNFARPDWLL 160

Query: 320 LTRLLVPPNCIRPSV 334
           +T L VPP  +RPS+
Sbjct: 161 VTVLPVPPPAVRPSI 175


>gi|214028084|gb|ACJ63311.1| RNA polymerase III large subunit [Papaver orientale]
          Length = 554

 Score =  159 bits (403), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 82/223 (36%), Positives = 134/223 (60%), Gaps = 27/223 (12%)

Query: 392 VHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLL 451
           +H+PQTEEAR EAL              +LM  ++NL TP+NGE+L+A+TQDF+T  +L+
Sbjct: 1   MHVPQTEEARTEAL--------------MLMGVQNNLCTPKNGEILVASTQDFLTSSFLI 46

Query: 452 TQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPV-VFVRTAVIWTGKQIFSLI 510
           T+++ F++RA +  +  + + D  D   +          P    ++   +WTGKQ+F+++
Sbjct: 47  TRRDTFYDRA-SFSLMCSYMGDAMDAIDL----------PTPALIKPVELWTGKQLFNVL 95

Query: 511 LKPNRDCPVNANLKTKGRAY-TANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVF 569
           ++P+    V  NL    ++Y    E  C  D +V  RNSEL+ G + K+TLG+G K  +F
Sbjct: 96  IRPHAQMRVFVNLTVFEKSYIKGRETLCPNDGFVYFRNSELICGQLGKATLGNGNKDGLF 155

Query: 570 YILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
            +LLRD+    A + M RL+++++ ++ N+GFSIGI DV PG+
Sbjct: 156 SVLLRDYDAHAAASCMNRLAKLSARWIGNQGFSIGISDVQPGK 198



 Score =  107 bits (267), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 50/71 (70%), Positives = 60/71 (84%), Gaps = 1/71 (1%)

Query: 608 VTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQ 666
           VTP  +GFV+NSF++GLT TEFFFHTMGGREGLVDTAVKTA+TGYM RRL+K+LEDL + 
Sbjct: 317 VTPDAKGFVENSFYTGLTATEFFFHTMGGREGLVDTAVKTADTGYMSRRLIKALEDLSIH 376

Query: 667 YDMSFDAAFYG 677
           YD +  +A  G
Sbjct: 377 YDSTVRSASGG 387



 Score = 55.8 bits (133), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/42 (50%), Positives = 36/42 (85%)

Query: 21 VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRA 62
          +LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+++ F++RA
Sbjct: 15 MLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRRDTFYDRA 56


>gi|448307075|ref|ZP_21496976.1| DNA-directed RNA polymerase subunit A' [Natronorubrum bangense JCM
           10635]
 gi|445596622|gb|ELY50707.1| DNA-directed RNA polymerase subunit A' [Natronorubrum bangense JCM
           10635]
          Length = 973

 Score =  159 bits (403), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 101/270 (37%), Positives = 141/270 (52%), Gaps = 45/270 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+++FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 481 DGDIIIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQNEEA 540

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR GE +I A QD I+G YLLT  N  FN 
Sbjct: 541 RAE--------------ARVLMRVQEQMLSPRFGENIIGAIQDHISGTYLLTHDNPRFNE 586

Query: 461 AQTMR-IASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q +  + +T I +  +  GI                    WTG  +FS +L      P 
Sbjct: 587 TQALDLLRATRIDELPEPSGIDD-------------EGKPFWTGYAVFSELL------PD 627

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           + NL   G   T  E+       VI+ + +LL G++ +  +G  G   +   + + +G  
Sbjct: 628 DLNLNFTG---TIGED-------VIIEDGQLLEGTIAEDEVGEFG-GEIVDTITKVYGNT 676

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVT 609
            A   +  LS +    +M+ GFSIGI D T
Sbjct: 677 RARIFVNELSTLAMRAIMHFGFSIGIDDET 706



 Score =  119 bits (299), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 91/290 (31%), Positives = 133/290 (45%), Gaps = 57/290 (19%)

Query: 100 QIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFH 159
           ++++ + Y  D    PI  GL+D R+G       C TCGQ+   C GHFG+I+L  PV H
Sbjct: 29  KVITADTY--DDDGFPIDMGLMDTRLGVIDPGLECPTCGQHSGSCPGHFGHIELAAPVIH 86

Query: 160 IGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA-LSYLVRKSLKKKILETTK 218
           +G+ + +  +L+  C+   C+R+LL E++   FR +L     LS   +  LK  I +  K
Sbjct: 87  VGFTKLIRRLLRGTCRE--CSRLLLTEDEKEEFRERLAEAKRLSRDPQDVLKAAIRQARK 144

Query: 219 KVSVCPHCGEINGVVKKCGLLKISHEK--------------YKNRTK------------K 252
           K   CPHCGE+           I HEK              Y  R               
Sbjct: 145 K-DRCPHCGEVQ--------YDIDHEKPTTYYEVQQVLTSEYSQRIAAAMQGGEDGKRMS 195

Query: 253 KDAIVEDL---LAEYNEAV--KFNPE------IEAHKKFGLIQ----TLNPLEVLQLFEA 297
            D + ++    L   NE +   F P       IE      L +     L P ++   FEA
Sbjct: 196 PDELADETDIDLTRINEILSGSFRPRESQRKSIEKALDIDLTEEDTNKLMPSDIRDWFEA 255

Query: 298 IPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDNDVV 345
           IP EDI +L +N+E S+P  +ILT L VPP   RPS+  D   +S++D+ 
Sbjct: 256 IPDEDIEVLGINSERSRPEWMILTVLPVPPVTTRPSITLDNGQRSEDDLT 305



 Score = 92.8 bits (229), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 39/58 (67%), Positives = 49/58 (84%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
             GFV+NS+ SGLTP EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 832 AHGFVENSYTSGLTPREFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELETQYD 889



 Score = 46.2 bits (108), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 29/46 (63%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 65
           +VLM  +  +++PR GE +I A QD I+G YLLT  N  FN  Q +
Sbjct: 545 RVLMRVQEQMLSPRFGENIIGAIQDHISGTYLLTHDNPRFNETQAL 590


>gi|124485981|ref|YP_001030597.1| DNA-directed RNA polymerase subunit A' [Methanocorpusculum
           labreanum Z]
 gi|124363522|gb|ABN07330.1| DNA-directed RNA polymerase, subunit A' [Methanocorpusculum
           labreanum Z]
          Length = 889

 Score =  159 bits (403), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 96/272 (35%), Positives = 151/272 (55%), Gaps = 29/272 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++SIM+H  KV+  RTFR N  VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 422 DGDIVLFNRQPSLHRMSIMSHHIKVMNGRTFRLNPAVCPPYNADFDGDEMNLHVPQTEEA 481

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A++L+A + N+++PR G  +I    D I+G +LLT +  ++ +
Sbjct: 482 RAE--------------AELLVAVQENILSPRFGGPIIGGLHDHISGIFLLTNQLKWYTK 527

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           ++ + +      +     G ++       N + +      W+ KQ FS+IL  + +    
Sbjct: 528 SEFLYLLKYTAMEHLPEPGKVE-------NGIPY------WSNKQAFSMILPKDVNMFYK 574

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           A         T N  FC  D++V + + EL++G++DK ++G+   A +   ++R  G   
Sbjct: 575 ATCCRNCDPCTKN-TFCPNDAFVRIVDGELISGTIDKKSVGAMDGA-ILNRIIRLHGTQR 632

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
           A   +  L++++   +M  GFS GI D   G+
Sbjct: 633 AKEYIDDLTKLSIRAIMLYGFSYGINDTDLGK 664



 Score =  114 bits (285), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 81/266 (30%), Positives = 131/266 (49%), Gaps = 38/266 (14%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G IE  +     ++  S  +++  + Y  D    P P GL+D  +G       C TCGQ 
Sbjct: 8   GKIEFGILSPKAIRDMSVCKVIWPDTY--DDDGFPYPKGLMDPSLGVIDPGLRCKTCGQK 65

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
             DC GHFG+IDL  PV H+GY R +  +L+  C++  C R+LL +E+   F A   +P 
Sbjct: 66  QGDCPGHFGHIDLAKPVIHVGYTRLIRKLLRVTCRD--CGRLLLDKEEIERFSALEDDP- 122

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDL 260
             Y      +K I    KK  +CP+CG+               +++K   +K  + VE +
Sbjct: 123 --YSAETIGEKDI----KKERICPYCGD---------------QQFKINFEKPTSFVE-I 160

Query: 261 LAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
           + E  E  K       HK     + L   ++ +  E IP +D+ LL ++ E+++P   +L
Sbjct: 161 VTEMGEDGK------VHKSE---RKLTSADIRERLEKIPDDDLRLLGIDPEVARPEWTVL 211

Query: 321 TRLLVPPNCIRPSVI--SDLKSDNDV 344
           T L VPP  +RPS+I  +  +S++D+
Sbjct: 212 TVLPVPPVTVRPSIILENGQRSEDDL 237



 Score = 91.7 bits (226), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 47/95 (49%), Positives = 64/95 (67%), Gaps = 14/95 (14%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSF 671
            GFV+NS+ SGL PTEFFFH +GGREGLVDTAV+T+++GY+QRR++ +L+DL V YD + 
Sbjct: 788 HGFVRNSYKSGLNPTEFFFHAIGGREGLVDTAVRTSQSGYLQRRMINALQDLKVAYDGTV 847

Query: 672 DAA-------FYGQ--TDCISGVSECIIMGLPMNV 697
            +         YG+  TD     S     GLP++V
Sbjct: 848 RSTGGKIIQFVYGEDGTDPAKSAS-----GLPVDV 877


>gi|281203888|gb|EFA78084.1| RNA polymerase II largest subunit [Polysphondylium pallidum PN500]
          Length = 2159

 Score =  159 bits (402), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 93/274 (33%), Positives = 146/274 (53%), Gaps = 45/274 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVV+FNRQPSLHK+S+M HR KV+P+ TFR N  V +PYNADFDGDEMN+H+PQ+ E 
Sbjct: 444 DGDVVIFNRQPSLHKMSMMGHRIKVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSLET 503

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE +             +++M  +  +V+P++   ++   QD + G    T+++ F  R
Sbjct: 504 RAEII-------------EIMMVPR-QIVSPQSNRPVMGIVQDTLLGSMKFTKRDTFVER 549

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWN----PVVFVRTAVIWTGKQIFSLILKPNRD 516
              M I   L                 SW+    P    +   +WTGKQ+FSLI+     
Sbjct: 550 DLMMNILMWL----------------PSWDGKIPPPAIWKPKKLWTGKQLFSLIIP---- 589

Query: 517 CPVNANLKTKGRAYTANEEFCHR---DSYVILRNSELLAGSMDKSTLGSGGKANVFYILL 573
              N NL+  G  ++  E+       D+ VI+   ELL G + K +LG+    ++ ++++
Sbjct: 590 ---NINLQRFGSTHSDKEKEKSEMAADTVVIIDQGELLTGILCKRSLGAAN-GSIIHVVM 645

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            + G D     + +   + + +L+N GF++GIGD
Sbjct: 646 NEHGHDSCRLFIDQTQTVVNHWLINHGFTVGIGD 679



 Score =  108 bits (271), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 95/360 (26%), Positives = 175/360 (48%), Gaps = 49/360 (13%)

Query: 1098 PSACKAEACREKYVRAQIEPATAVGALAAQSIG-EPGTQMTLKTFHFAGEVCEYIEE-VF 1155
            P A K ++ + K V+ Q+E  T     AA  I  +P  Q TL       E  E++   + 
Sbjct: 1143 PDAAK-DSEKAKSVQCQLEYTTMATVTAATEIYYDPDPQQTL-----VKEDEEFVSRYLL 1196

Query: 1156 VPDD--------SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRG-ISGHLTVSGHSFLI 1206
            +PDD        S  ++++++DR  +   ++ +  I  CI+R  G ++   +      LI
Sbjct: 1197 LPDDDTKADDVLSPWVLRIELDREMVTDKKLSLSDITQCIKRDFGRLNCIFSDDNADKLI 1256

Query: 1207 LKPK------------DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTK- 1253
            ++ +            D   +F  ++    ++L  +V+ G++GI +  +  +D   V + 
Sbjct: 1257 IRIRTIEDNDSKTDGNDDDDTFLRRIE--AKMLSEMVLCGIRGIKKVFMRHDDQVRVNEN 1314

Query: 1254 --------YKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLV 1305
                    + L  +G NL +VM+   V   +  SN+  E+ + LGIEA R+ ++ E++ V
Sbjct: 1315 GAYFSKKEWVLDTDGVNLLEVMSHPDVDHSRTVSNDIIEIIQVLGIEAVRNALLKELRAV 1374

Query: 1306 MENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFY 1365
            +   G  +++RH  ++AD+MT +G ++ I+RHG+ +++   L   SFE T + L DAA +
Sbjct: 1375 ISFDGSYVNYRHLAILADVMTYRGHLMAISRHGINRVESGPLMRCSFEETVEILMDAAMF 1434

Query: 1366 GQTDCISGVSECIIMGLPMNVGTG---------LIKLLQAVPRSEPVPRTLLFDNPEFHT 1416
             +TD + GV+E II+G    +GTG         +IK   ++   EP      ++ P   T
Sbjct: 1435 SETDDVKGVTENIILGQLPPLGTGSFEVYLNQDMIKNAHSIAMPEPSTMMSHYNEPGSQT 1494



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 42/59 (71%), Positives = 53/59 (89%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
           +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKT+ETGY+QRRLVK++ED+ V+YD +
Sbjct: 808 RGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDVSVKYDAT 866



 Score = 85.1 bits (209), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 71/287 (24%), Positives = 139/287 (48%), Gaps = 55/287 (19%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLE----------------- 804
            GVPR+KEIIN ++ + TP +T YL  D   D + A+ V+ +LE                 
Sbjct: 1118 GVPRLKEIINIAKTVKTPSLTIYLQPDAAKDSEKAKSVQCQLEYTTMATVTAATEIYYDP 1177

Query: 805  ---RTTLGEVCEYIEE-VFVPDD--------SFILIKLDMDRIRLLHLEVDIDSIRYCIE 852
               +T + E  E++   + +PDD        S  ++++++DR  +   ++ +  I  CI+
Sbjct: 1178 DPQQTLVKEDEEFVSRYLLLPDDDTKADDVLSPWVLRIELDREMVTDKKLSLSDITQCIK 1237

Query: 853  RTRG-ISGHLTVSGHSFLILKPK------------DSSKSFNSKMYQMKQLLPSVVIKGV 899
            R  G ++   +      LI++ +            D   +F  ++    ++L  +V+ G+
Sbjct: 1238 RDFGRLNCIFSDDNADKLIIRIRTIEDNDSKTDGNDDDDTFLRRIE--AKMLSEMVLCGI 1295

Query: 900  QGINRAVIHEEDVEGVTK---------YKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVY 950
            +GI +  +  +D   V +         + L  +G NL +VM+   V   +  SN+  E+ 
Sbjct: 1296 RGIKKVFMRHDDQVRVNENGAYFSKKEWVLDTDGVNLLEVMSHPDVDHSRTVSNDIIEII 1355

Query: 951  KTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            + LGIEA R+ ++ E++ V+   G  +++RH  ++AD+MT +G ++ 
Sbjct: 1356 QVLGIEAVRNALLKELRAVISFDGSYVNYRHLAILADVMTYRGHLMA 1402



 Score = 73.2 bits (178), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 33/82 (40%), Positives = 52/82 (63%), Gaps = 3/82 (3%)

Query: 119 GLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPT 178
           GL+D  MGT  K   C TC   +++C GHFG+I+L  PVFHIG+   V+ IL+ +C +  
Sbjct: 50  GLVDPHMGTIDKTQKCATCSGTMAECPGHFGHIELAKPVFHIGFINTVLKILKCVCYH-- 107

Query: 179 CARVLLGEEKAAGFRA-KLRNP 199
           C+++L+  +     +A K++NP
Sbjct: 108 CSKLLVDTDDIHFRQALKIKNP 129



 Score = 56.2 bits (134), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/37 (64%), Positives = 29/37 (78%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            K++ + + P   VGALAAQSIGEP TQMTL TFH+AG
Sbjct: 1073 KFLLSIVNPGEMVGALAAQSIGEPATQMTLNTFHYAG 1109


>gi|397135936|gb|AFO11463.1| RNA polymerase I, partial [Candida santjacobensis]
          Length = 873

 Score =  159 bits (402), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 95/271 (35%), Positives = 149/271 (54%), Gaps = 44/271 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+D VLFNRQPSLHK+S+MAHR KV+P+ TFR N  V TPYNADFDGDEMN+H+PQ+EE 
Sbjct: 251 DDDPVLFNRQPSLHKMSMMAHRVKVMPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSEET 310

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L +L ++  +          +V+P++ + ++   QD + G   +T+++ F   
Sbjct: 311 RAE----LSQLCMVPLQ----------IVSPQSNKPVMGIVQDTLCGIRKMTKRDTFIEF 356

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVV----FVRTAVIWTGKQIFSLILKPNRD 516
            Q M I                 F    W+ VV     ++   +WTGKQ+ SL +     
Sbjct: 357 DQVMNIL----------------FWVPHWDGVVPQPAILKPKPLWTGKQMASLCI----- 395

Query: 517 CPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            P    L+   R    N     +D+ +++   E++ G +DK T+G+ G   + + ++R+ 
Sbjct: 396 -PKGIFLQ---RFDEGNPLISPKDNGMLISKGEIMYGVVDKKTVGATG-GGLIHTIMREK 450

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           G  V  +    + ++ +F+L++ GFSIGIGD
Sbjct: 451 GPQVCSSFFGNIQKVVNFWLLHNGFSIGIGD 481



 Score = 98.2 bits (243), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 52/63 (82%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTP EFFFH M GREGL+DTAVKTAETGY+ RRLVK+LED+ V
Sbjct: 604 DYSPESKGFVENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIXRRLVKALEDIMV 663

Query: 666 QYD 668
            YD
Sbjct: 664 HYD 666


>gi|448375014|ref|ZP_21558731.1| DNA-directed RNA polymerase subunit A'' [Halovivax asiaticus JCM
            14624]
 gi|445659475|gb|ELZ12281.1| DNA-directed RNA polymerase subunit A'' [Halovivax asiaticus JCM
            14624]
          Length = 402

 Score =  159 bits (402), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 107/345 (31%), Positives = 176/345 (51%), Gaps = 57/345 (16%)

Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYI 1151
            A+A   +Y   +++P   VG ++AQSIGEPGTQ+T+ TFH+AG            + E +
Sbjct: 49   AQAVESQYRDTRVDPLDPVGTVSAQSIGEPGTQLTMNTFHYAGVAEIDVTQGLPRLIELV 108

Query: 1152 EEVFVPDDSFILIKLD----------------MDRIRLLHL---EVDIDSIRYCIERT-- 1190
            +    PD   + + L+                ++  ++L L     ++  +R  I     
Sbjct: 109  DARKTPDTPTMTVHLEEEYATEREKAHEVVWKIEATKILALGDVSTNVADMRVVISLNED 168

Query: 1191 ----RGIS------------GHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKG 1234
                R I+            G  TV   + +   P++ S      + Q+ + L  +  KG
Sbjct: 169  TLDERMITAEEVAEIIEDQLGVTTVQNGTTVEFGPEEPSYR---DLLQLVEELREITFKG 225

Query: 1235 VQGINRAVIHEEDVEGV-----TKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTL 1289
            ++ I+R VI  E+++        ++ L  EG    D +A  GV   + + NN +E+Y+ L
Sbjct: 226  IEDISRVVIRREEMDDSPFDADEEFVLYTEGSAFGDALAIEGVDASRTTCNNIHEIYRNL 285

Query: 1290 GIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLN 1348
            G+EAAR  I+ E K  +   G+ +I+ RH MLVAD+MT++G +  I RHG+A  KESVL 
Sbjct: 286  GVEAAREIIIEETKNTLVEQGLDNINVRHLMLVADIMTNEGTIESIGRHGIAGNKESVLA 345

Query: 1349 LASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
             A++E T +HL +A+ +G+ D I GV E +I+G P+ +GTG + L
Sbjct: 346  RAAYEVTVNHLLNASIHGEIDSIDGVIENVIVGRPVKLGTGDVDL 390



 Score = 94.7 bits (234), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 71/245 (28%), Positives = 129/245 (52%), Gaps = 29/245 (11%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP +T +L+++  T+ + A  V  ++E T    LG+V   +   
Sbjct: 100 GLPRLIELVDARKTPDTPTMTVHLEEEYATEREKAHEVVWKIEATKILALGDVSTNVA-- 157

Query: 819 FVPDDSFILIKLDMDRI--RLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDS 876
               D  ++I L+ D +  R++  E     +   IE   G++   TV   + +   P++ 
Sbjct: 158 ----DMRVVISLNEDTLDERMITAE----EVAEIIEDQLGVT---TVQNGTTVEFGPEEP 206

Query: 877 SKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGV-----TKYKLLVEGDNLRDVM 931
           S      + Q+ + L  +  KG++ I+R VI  E+++        ++ L  EG    D +
Sbjct: 207 SYR---DLLQLVEELREITFKGIEDISRVVIRREEMDDSPFDADEEFVLYTEGSAFGDAL 263

Query: 932 ATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLMT 990
           A  GV   + + NN +E+Y+ LG+EAAR  I+ E K  +   G+ +I+ RH MLVAD+MT
Sbjct: 264 AIEGVDASRTTCNNIHEIYRNLGVEAAREIIIEETKNTLVEQGLDNINVRHLMLVADIMT 323

Query: 991 SKGEV 995
           ++G +
Sbjct: 324 NEGTI 328


>gi|110669614|gb|ABG81902.1| RNA polymerase II largest subunit [Canoparmelia caroliniana]
          Length = 1016

 Score =  159 bits (402), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 95/277 (34%), Positives = 150/277 (54%), Gaps = 39/277 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D ++FNRQPSLHK S+M HR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 373 DGDYIIFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 432

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    +++L ++            N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 433 RAE----INQLCMVP----------LNIVSPQRNGPLMGIVQDTLCGIYKMCRRDVFLTK 478

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M I    +    D  G+I +       P + V+   +WTGKQI SL++      P  
Sbjct: 479 EQVMNI----LLWVPDWDGVIPQ-------PAI-VKPLAMWTGKQILSLVI------PTG 520

Query: 521 ANLKTKGRAYTANEEFCH-RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            NL        + E F    D  +++   EL+ G + K T+G+ G   + +I+  + G +
Sbjct: 521 LNL-----LRGSEEGFSPLNDDGLLISGGELMYGLLAKKTVGASG-GGLIHIVFNEKGPE 574

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
            A+        + +++L++ GFSIGIGD  P +  +Q
Sbjct: 575 AAMNFFNGAQTVVNYWLLHNGFSIGIGDTIPDRHTIQ 611



 Score =  100 bits (250), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+  
Sbjct: 725 DYSPESKGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDVMA 784

Query: 666 QYD 668
           +YD
Sbjct: 785 KYD 787



 Score = 58.2 bits (139), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 53/195 (27%), Positives = 87/195 (44%), Gaps = 41/195 (21%)

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNPAL 201
           +C GHFG+I+L +PV+H+G+   +  +L+++C N  C ++L+ E   A   A + R+P  
Sbjct: 1   ECPGHFGHIELAVPVYHVGFMTKIKKLLETVCHN--CGKILVDESNPAFADAIRRRDPKK 58

Query: 202 SY--LVRKSLKKKILETT---------KKVSVCPH----CGEINGVVKKCGLLKISHEKY 246
            +  + R    K I ETT          K     H    CG I   V++ GL      K 
Sbjct: 59  RFDMVWRLCKPKMICETTMALDNDVPSDKTKEPKHDHGGCGNIQPEVRREGLRLTGTWK- 117

Query: 247 KNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLL 306
               +K D        E NE  +  PE          + + P   L +F  I  EDI  +
Sbjct: 118 ---AQKGD--------EENEGQQ--PE---------KKPITPQMALNIFRHISTEDIKRI 155

Query: 307 LMNAELSKPSDLILT 321
            ++ + ++P  +I+T
Sbjct: 156 GLSNDYARPEWMIIT 170



 Score = 42.4 bits (98), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 18/29 (62%), Positives = 21/29 (72%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMT 1137
            ++ RA + P   VG LAAQSIGEP TQMT
Sbjct: 988  RFCRAAVNPGEMVGVLAAQSIGEPATQMT 1016


>gi|397135963|gb|AFO11476.1| RNA polymerase I, partial [Dipodascopsis uninucleata]
          Length = 871

 Score =  159 bits (402), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 96/270 (35%), Positives = 147/270 (54%), Gaps = 42/270 (15%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+D VLFNRQPSLHK+S+MAHR KV+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 251 DDDPVLFNRQPSLHKMSMMAHRVKVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 310

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE                 L A    +V+P++ + ++   QD + G   +T+++ F N 
Sbjct: 311 RAE--------------LSQLCAVPLQIVSPQSNKPVMGIVQDTLCGIRKMTKRDTFLNF 356

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNP-VVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q M I   +              +W    P    ++   +WTGKQ+ S+++      P 
Sbjct: 357 DQVMNILYWVP-------------NWDGSIPHPAILKPKPLWTGKQLLSMVI------PK 397

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLG--SGGKANVFYILLRDFG 577
             NL+   R    N     RD+ +++ N E++ G +DK T+G  SGG   + + ++R+ G
Sbjct: 398 GINLQ---RFDDKNTLLSPRDNGMMIENGEIMYGVVDKKTVGATSGG---LIHTIMREKG 451

Query: 578 EDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
             V       +  + +++L++ GFSIGIGD
Sbjct: 452 PTVTRDFFSGVQTVVNYWLLHNGFSIGIGD 481



 Score = 99.8 bits (247), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GF++NS+  GLTP EFFFH M GREG++DTAVKTAETGY+QRRLVK+LED+ V
Sbjct: 604 DYSPESRGFIENSYLRGLTPQEFFFHAMVGREGIIDTAVKTAETGYIQRRLVKALEDVSV 663

Query: 666 QYD 668
           QYD
Sbjct: 664 QYD 666


>gi|119643505|gb|ABL85574.1| RNA polymerase II largest subunit [Cetraria islandica]
          Length = 1003

 Score =  159 bits (402), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 94/271 (34%), Positives = 148/271 (54%), Gaps = 39/271 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D ++FNRQPSLHK S+M HR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 374 DGDYIIFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 433

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    +++L ++            N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 434 RAE----INQLCMVP----------LNIVSPQRNGPLMGIVQDTLCGIYKMCRRDVFLTK 479

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M I    +    D  G+I +       P + V+   +WTGKQI SL++      P  
Sbjct: 480 EQVMNI----LLWVPDWDGVIPQ-------PAI-VKPLAMWTGKQILSLVI------PTG 521

Query: 521 ANLKTKGRAYTANEEFCH-RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            NL        + E F    D  +++   EL+ G ++K  +G+ G   V +I+  + G +
Sbjct: 522 LNL-----LRGSEEGFSPLNDDGLLISGGELMYGLLNKKVVGASG-GGVIHIVFNEKGPE 575

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
            A++       + +++L++ GFSIGIGD  P
Sbjct: 576 AAMSFFNGAQTVVNYWLLHNGFSIGIGDTIP 606



 Score =  101 bits (251), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+  
Sbjct: 726 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDVMA 785

Query: 666 QYD 668
           +YD
Sbjct: 786 KYD 788


>gi|397135896|gb|AFO11443.1| RNA polymerase I, partial [Schwanniomyces etchellsii]
          Length = 872

 Score =  159 bits (402), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 93/267 (34%), Positives = 145/267 (54%), Gaps = 36/267 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND VLFNRQPSLHK+S+MAHR KV+P+ TFR N  V +PYNADFDGDEMN+H+PQ+ E 
Sbjct: 251 DNDPVLFNRQPSLHKMSMMAHRVKVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSHET 310

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE                 + A    +V+P++ + ++   QD + G   +T +++F   
Sbjct: 311 RAE--------------LSEICAVPLQIVSPQSNKPVMGIVQDTLCGVRKMTLRDSFIEY 356

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M     ++    +  GII         P   VR   +WTGKQI S+ +      P  
Sbjct: 357 DQVM----NMLYWIPNWNGIIP--------PPAVVRPKPLWTGKQILSMAI------PKG 398

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            +L+   R          +D+ +++ + E++ G +DK T+G+ G   + + ++R+ G  V
Sbjct: 399 IHLQ---RFDDGTNLLSPKDNGMLIVDGEIMFGVVDKKTVGATG-GGLIHTVMREKGPQV 454

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGD 607
                  + ++ +F+L++ GFSIGIGD
Sbjct: 455 CAQLFSSIQKVVNFWLLHNGFSIGIGD 481



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 53/63 (84%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTP EFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+ V
Sbjct: 604 DYSPESKGFVENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDIMV 663

Query: 666 QYD 668
            YD
Sbjct: 664 HYD 666


>gi|323454233|gb|EGB10103.1| hypothetical protein AURANDRAFT_36761 [Aureococcus anophagefferens]
          Length = 1738

 Score =  159 bits (402), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 97/274 (35%), Positives = 146/274 (53%), Gaps = 35/274 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+D+++FNRQPSLHK+SIMAHR KVL H TFR N  V +PYNADFDGDEMN+H+PQ   A
Sbjct: 378 DDDLIVFNRQPSLHKMSIMAHRVKVLDHSTFRLNLSVTSPYNADFDGDEMNLHVPQNVAA 437

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE               + LM    N+V+P++ + ++   QD +     +T K  F ++
Sbjct: 438 KAE--------------LQQLMMVPRNVVSPQSNKPVMGIVQDSLLASARMTSKETFIDQ 483

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                I    + D  D  G++ +       P + ++   +WTGKQIFSLIL         
Sbjct: 484 DLLFNIV-MWVGDDWD--GVVPQ-------PAI-LKPKPLWTGKQIFSLILP-------K 525

Query: 521 ANLKTKGRAYT--ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            N   KG  +           D  V++++  L+ G MDK +LG+ G  ++ +++  + G 
Sbjct: 526 LNFAGKGARFPKKGGNTLNWSDGEVLIQSGRLVTGVMDKKSLGTSG-GSLIHVIWLEMGH 584

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
             A+  + R+   T+ +L+N  FSIGIGD    Q
Sbjct: 585 VAAMHFLNRVQTTTNQWLVNVSFSIGIGDAVADQ 618



 Score = 95.1 bits (235), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 39/57 (68%), Positives = 50/57 (87%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NS+  GL+P EF+FH MGGREGL+DTA KTA+TGY+QRRLVKS+E + V+YD
Sbjct: 742 RGFVENSYLRGLSPQEFYFHAMGGREGLIDTACKTAQTGYLQRRLVKSMESIMVKYD 798



 Score = 88.2 bits (217), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 45/150 (30%), Positives = 82/150 (54%)

Query: 1250 GVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENH 1309
            G  ++ L  +G NL  ++    V   +  SN+  E+   +GIE  R  ++  ++ V+   
Sbjct: 1264 GDEEWVLETDGTNLAAILGDRDVDHTRTCSNDIVEICDVMGIEGTRQALLQMLREVISFD 1323

Query: 1310 GMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTD 1369
            G  +++RH  ++ D M  +G ++ I+RHG+ +     L  ASFE T + LF +A Y ++D
Sbjct: 1324 GAYVNYRHLAVLCDTMCFRGSLMAISRHGINRGDSGPLLSASFEETVEILFKSAVYARSD 1383

Query: 1370 CISGVSECIIMGLPMNVGTGLIKLLQAVPR 1399
             + GV+  I++G   +VG+G+  LL   P+
Sbjct: 1384 DVDGVTPNIMLGQLAHVGSGVCDLLLDTPQ 1413



 Score = 68.6 bits (166), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 69/257 (26%), Positives = 121/257 (47%), Gaps = 30/257 (11%)

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGE-----EKAAGFRAKLR 197
           D  GHFG+I+L  P +H+GY + V+  L+ +C +  C+R++        + A  ++A+ R
Sbjct: 8   DDPGHFGHIELARPCYHLGYIKEVLMCLRCVCFH--CSRLMADPSDYKVQGAQKYKAQKR 65

Query: 198 NPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIV 257
             A+  L R S K+    T  ++      GE  G V  CG L+ +   ++ RT +    +
Sbjct: 66  LEAMHGLCR-SKKRCEFATGAELQQAIMDGEQEGAVYGCGALQPT---FRRRTAQS---I 118

Query: 258 EDLLAEYNEAVKFNPEIEAHKKFG-LIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPS 316
           E         V+F P+ E     G   Q L+     ++   I  +D  +L ++ + ++P 
Sbjct: 119 E---------VEFQPDEETIPGTGDRKQILSAHRAYEVLRNISDKDAKMLGLDPKFARPE 169

Query: 317 DLILTRLLVPPNCIRPSVI---SDLKSDNDVV--LFNRQPSLHKLSIMAHRAKVLPHRTF 371
            L++T L V P  +RPS+    S+ +S++D+   L N   +   L  +  RA    H   
Sbjct: 170 WLLITVLPVAPPHVRPSIQLSDSNARSEDDLTHQLVNIVKANKTLESLC-RAGEANHVVS 228

Query: 372 RFNECVCTPYNADFDGD 388
           +F E +    NA FD +
Sbjct: 229 QFEELLQYKVNALFDNE 245



 Score = 63.9 bits (154), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 64/298 (21%), Positives = 124/298 (41%), Gaps = 67/298 (22%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVF-- 819
            GVPR+ EI+N ++ + TP +T YL  +   D + AR V+ +LE TTLG+V    + V+  
Sbjct: 1051 GVPRLNEILNVAKTVRTPSLTIYLAPEIKDDEEKAREVQAKLEHTTLGDVTTLTQIVYDP 1110

Query: 820  -------------------VPDDSF-------ILIKLDMDR-------IRL--------- 837
                               VPD+ F        +++++++R       +R+         
Sbjct: 1111 DATSTVVEDDREFVAAYCDVPDEDFDPKAMSPWVLRMELNREVVADKKLRMADVAATIAD 1170

Query: 838  -----LHLEVDIDSIRYCIERTRGISGHLTVSGH----SFLILKPKDSSKSFNSKMYQMK 888
                 LH     D+    + R R  SG     G     +    +  D   +F  ++    
Sbjct: 1171 EYGADLHCIYADDNADKLVLRVRIRSGGARAGGDDAAPALGDAEVDDDEWTFLRRI--EG 1228

Query: 889  QLLPSVVIKGVQGINRAVIHEEDVE----------GVTKYKLLVEGDNLRDVMATYGVKG 938
             +L  + ++GV  + +  I +  +           G  ++ L  +G NL  ++    V  
Sbjct: 1229 NMLSDLRLRGVPRVTKVYIKKTKMTRWDPDTGALGGDEEWVLETDGTNLAAILGDRDVDH 1288

Query: 939  VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL 996
             +  SN+  E+   +GIE  R  ++  ++ V+   G  +++RH  ++ D M  +G ++
Sbjct: 1289 TRTCSNDIVEICDVMGIEGTRQALLQMLREVISFDGAYVNYRHLAVLCDTMCFRGSLM 1346



 Score = 50.4 bits (119), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 22/37 (59%), Positives = 27/37 (72%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            ++V+A+       G LAAQS+GEP TQMTL TFHFAG
Sbjct: 1006 RFVQARAHAGEMCGVLAAQSMGEPATQMTLNTFHFAG 1042


>gi|168053159|ref|XP_001779005.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162669567|gb|EDQ56151.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 1646

 Score =  159 bits (402), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 92/272 (33%), Positives = 151/272 (55%), Gaps = 37/272 (13%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D D VLFNRQPSLHK+SIM HR +++P+ TFR N  V +PYNADFDGDEMN+H+PQ+ E
Sbjct: 453 NDGDFVLFNRQPSLHKMSIMGHRIRIMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSFE 512

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE L             +++M  K  +V+P++   +I   QD + G   +T+++ F  
Sbjct: 513 TRAEVL-------------ELMMVPKC-VVSPQSNRPVIGIVQDTLLGCRKVTKRDTFIE 558

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPV-VFVRTAVIWTGKQIFSLILKPNRDCP 518
           +     +   ++    +  G I         P+   ++   +WTGKQIF+LI+      P
Sbjct: 559 KD----VFYNILMWWEEFAGKI---------PIPTILKPRPLWTGKQIFTLII------P 599

Query: 519 VNANLKTKGRAYTANE--EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
              NL  +   +  +E  +    D+ V +   E++AG++ K TLG+ G+ ++ +++  + 
Sbjct: 600 KQINLMRQAFWHPDSEVGDLSPGDTQVRIEKGEVVAGTLCKKTLGT-GQGSLIHVIWEEV 658

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           G D A   +     + +++L+ +GFSIGIGD 
Sbjct: 659 GPDAARKFLGHTQWLVNYWLLQQGFSIGIGDT 690



 Score =  100 bits (248), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 42/57 (73%), Positives = 52/57 (91%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKT+ETGY+QRRLVK++ED+ V+YD
Sbjct: 818 RGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDVMVKYD 874



 Score = 99.8 bits (247), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 56/173 (32%), Positives = 93/173 (53%), Gaps = 9/173 (5%)

Query: 1226 LLPSVVIKGVQGINRAVIHEED---------VEGVTKYKLLVEGDNLRDVMATYGVKGVK 1276
            +L  + ++G+  I +  I E+           E   ++ L  EG N+  VM    V   +
Sbjct: 1274 MLTEMALRGIPDIRKVFIKEDKKNRFDENVAFEPEKEWILDTEGVNMLAVMCHEDVDASR 1333

Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITR 1336
              SN+  EV + LGIEA R+ ++ E++ V+   G  +++RH  ++ D+MT +G ++ ITR
Sbjct: 1334 TLSNHLIEVIEVLGIEAVRNALLKELRDVISFDGSYVNYRHLAILCDVMTYRGHLMAITR 1393

Query: 1337 HGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
            HG+ +     +   SFE T D L DAA Y + D + GV+E I++G    +GTG
Sbjct: 1394 HGINRNDTGPMMRCSFEETVDILLDAAVYAEADHLKGVTENIMLGQLAPIGTG 1446



 Score = 96.3 bits (238), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 82/267 (30%), Positives = 133/267 (49%), Gaps = 20/267 (7%)

Query: 87  VTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVG 146
           +   D ++Q S   I S   Y +     P   GL D R+GT  +   C TC  ++++C G
Sbjct: 22  IISPDEIRQMSVCLIESSETYDRG---KPKMGGLSDPRLGTIDRHTKCETCAGSMAECPG 78

Query: 147 HFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLV 205
           HFG+++L  P+FHIG+ + V++IL+ +C N  C+R L  EE     +A K+RNP      
Sbjct: 79  HFGHLELAKPMFHIGFLKTVLSILRCVCHN--CSRCLADEEDHRFKQARKVRNP------ 130

Query: 206 RKSLKKKILETTKKVSVCPHCGEINGVVKKCG---LLKISHEKYKNRTKKKDAIVEDLLA 262
            K   KK+L+  K  + C    E++    + G     K SH     +  K       L+A
Sbjct: 131 -KHRLKKVLDCCKSKTKCDAGDELDENDTRYGEETEKKKSHGGCGAQQPKTTIDGMKLVA 189

Query: 263 EYNEAVKFNPEIEAH--KKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
           E+  + K   E + H  +     Q L   +VL + + I  ED  +L +N + ++P  +IL
Sbjct: 190 EFKASRKKGDEQDQHMPEPVERKQQLTAEKVLSILKRISDEDCAILGLNPKFARPDWMIL 249

Query: 321 TRLLVPPNCIRPSVISD--LKSDNDVV 345
             L +PP  +RPSV+ D   +S++D+ 
Sbjct: 250 QALPIPPPPVRPSVMMDSSARSEDDLT 276



 Score = 72.4 bits (176), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 69/287 (24%), Positives = 127/287 (44%), Gaps = 53/287 (18%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDK--DTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR++EIIN ++   TP +T +L    + + + A+ V+  LE TTL  V +  E  + P
Sbjct: 1104 GVPRLREIINVAKKTKTPSLTVFLKPGINKEKEKAKNVQCALEYTTLRSVTQATEIWYDP 1163

Query: 822  DDSFILIKLDMDRIRLLHLEVDIDS---------IRYCIERTRGISGHLTVS-------- 864
            +    LI+ D++ +R  +   D D          +R  + R   +   L+++        
Sbjct: 1164 EPMSTLIEEDVEFVRSYYEMPDEDVAPEKISPWLLRIELNREMMVDKKLSMADIAEKINL 1223

Query: 865  -------------GHSFLILK--------PKDSSKSFNSKMYQMKQ----LLPSVVIKGV 899
                             LIL+        PK  +   +     +K+    +L  + ++G+
Sbjct: 1224 EFDDDLTCIFNDDNAEKLILRIRIMNDEAPKGEATEQSEDDVFLKKIESNMLTEMALRGI 1283

Query: 900  QGINRAVIHEED---------VEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVY 950
              I +  I E+           E   ++ L  EG N+  VM    V   +  SN+  EV 
Sbjct: 1284 PDIRKVFIKEDKKNRFDENVAFEPEKEWILDTEGVNMLAVMCHEDVDASRTLSNHLIEVI 1343

Query: 951  KTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            + LGIEA R+ ++ E++ V+   G  +++RH  ++ D+MT +G ++ 
Sbjct: 1344 EVLGIEAVRNALLKELRDVISFDGSYVNYRHLAILCDVMTYRGHLMA 1390



 Score = 52.4 bits (124), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 21/37 (56%), Positives = 28/37 (75%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            +++ + + P   +G +AAQSIGEP TQMTL TFHFAG
Sbjct: 1059 RFLMSLVAPGEMIGCVAAQSIGEPATQMTLNTFHFAG 1095


>gi|327242123|gb|AEA40840.1| RNA polymerase II largest subunit [Trichomitus batrachorum]
          Length = 1057

 Score =  159 bits (402), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 93/273 (34%), Positives = 146/273 (53%), Gaps = 28/273 (10%)

Query: 333 SVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNV 392
           SV+     DND+V+FNRQPSLHK+S+M H AK++  ++FR N CV TPYNADFDGDEMN+
Sbjct: 377 SVVERHLRDNDIVIFNRQPSLHKMSMMGHYAKLIRGQSFRLNLCVTTPYNADFDGDEMNL 436

Query: 393 HLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLT 452
           H+ QT++ARAE               K +MA    ++TP++ + +I   QD + G  LL+
Sbjct: 437 HVVQTQQARAE--------------VKHIMAVPYQIITPQSNKPIIGLVQDCLVGCRLLS 482

Query: 453 QKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILK 512
            ++ F  R + M +   ++    D+             P   V    +W+GKQ+FSL L 
Sbjct: 483 IRDTFLTRNELMNLMMWIMDTKPDLV----------LPPPCIVAPQELWSGKQVFSLFLP 532

Query: 513 PNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYIL 572
                  ++    KG   + N      D  VI+R+  LLAG +D  T+    + ++ +++
Sbjct: 533 QINLDKFSSPADDKGADKSWNSS---DDVRVIIRDGHLLAGIIDSKTVAK-SEGSLTHVV 588

Query: 573 LRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGI 605
           +  +  D A   + +   + + +L NRGFS+GI
Sbjct: 589 INSYSLDTAKAFLNQTQLVVNNWLENRGFSMGI 621



 Score = 94.0 bits (232), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 38/57 (66%), Positives = 49/57 (85%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV++S+  GLTP EFFFH+MGGR G++DTA KTA+TGY+QRRL K++E  CVQYD
Sbjct: 752 RGFVEHSYIQGLTPQEFFFHSMGGRTGIIDTACKTADTGYIQRRLCKTMESHCVQYD 808



 Score = 54.3 bits (129), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 58/207 (28%), Positives = 96/207 (46%), Gaps = 31/207 (14%)

Query: 150 YIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLG------EEKAAGFRAKLRNPALSY 203
           +I L   ++HIGY   V  ILQ +C  P+C+R+L+G      +E    ++ K R  A+  
Sbjct: 1   HIKLATVLYHIGYIDIVYKILQCVC--PSCSRLLVGYADPHVQEAVLRYKGKKRLLAIHA 58

Query: 204 LVRKS-------LKKKILETTKKVSVCPHCGEIN----GVVKKCGLLKI-----SHEKYK 247
           +  KS       L+KK  ++TK VS      + N      VK     KI       EK+K
Sbjct: 59  IATKSSTRYCKHLEKK--KSTKGVSGPNQAQQSNPEEADYVKNDRFWKIVTGSDDQEKWK 116

Query: 248 NRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLL 307
             ++     V +L  E +  +K   +  A  +  LI++   LE+L     I  +DI +L 
Sbjct: 117 RESQPCGNAVPELTKENDGHIK--KKDPARGEPDLIESSKVLEILH---NISEQDIRILG 171

Query: 308 MNAELSKPSDLILTRLLVPPNCIRPSV 334
            + +  +P  +++  L VPP  +RP +
Sbjct: 172 FDPQKCRPEWMMVKILPVPPPHVRPFI 198


>gi|255941856|ref|XP_002561697.1| Pc16g13990 [Penicillium chrysogenum Wisconsin 54-1255]
 gi|211586320|emb|CAP94069.1| Pc16g13990 [Penicillium chrysogenum Wisconsin 54-1255]
          Length = 1733

 Score =  159 bits (402), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 94/274 (34%), Positives = 141/274 (51%), Gaps = 35/274 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D +LFNRQPSLHK S+M HR +V+P  TFR N  V +PYNADFDGDEMN+H+PQ EE+
Sbjct: 449 DGDYILFNRQPSLHKESMMGHRVRVMPFSTFRMNLSVTSPYNADFDGDEMNLHVPQGEES 508

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L +L+++            N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 509 RAE----LAELTLVP----------KNIVSPQRNGPLMGIVQDTLCGIYKICRRDTFLTK 554

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M     L+    D  G I         P   ++    WTGKQ+ S+        P  
Sbjct: 555 DQVM----NLMLWVPDWDGAIP--------PPAIIKPRPRWTGKQMISMAF------PSG 596

Query: 521 AN-LKTKGRAYTANEEFCH-RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            N L+        +E+F    D  +++   +L+ G + K T+G+ G   V + +  ++G 
Sbjct: 597 LNLLRVDKDGSPLSEKFSPLNDGGLLIHGGQLMYGMLSKKTVGASG-GGVIHTIFNEYGP 655

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
           D  V        +  ++L++ GFSIGIGD  P Q
Sbjct: 656 DTCVKFFTGAQTIVGYWLLHNGFSIGIGDTIPDQ 689



 Score =  105 bits (262), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 62/181 (34%), Positives = 99/181 (54%), Gaps = 15/181 (8%)

Query: 1224 KQLLPSVVIKGVQGINRAVIHEED----VEGVT-----------KYKLLVEGDNLRDVMA 1268
            + LL ++ ++GV G++RA I+E+     VE  T           ++ L   G +L  V+A
Sbjct: 1280 QHLLDTLTLRGVPGVDRAFINEKSKVRVVEDGTLHTSKSDPLCKEWVLETSGSSLAAVLA 1339

Query: 1269 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK 1328
              GV   +  SN   E+++  GIEAAR+ ++ E+ LV+   G  ++ RH  L+ D+MT +
Sbjct: 1340 IPGVDASRTYSNQFIEIFEVFGIEAARTAVLRELTLVLAFDGSYVNHRHLALLVDVMTVR 1399

Query: 1329 GEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGT 1388
            G +  +TRHG+ +     L   SFE T + L +AA +G+ D   GVSE +I+G     GT
Sbjct: 1400 GYLTPVTRHGINRADNGALMRCSFEETVEILLEAAAFGELDDCRGVSENLILGQMAPAGT 1459

Query: 1389 G 1389
            G
Sbjct: 1460 G 1460



 Score = 99.4 bits (246), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QR+LVK+LE++ V
Sbjct: 807 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMV 866

Query: 666 QYD 668
           +YD
Sbjct: 867 KYD 869



 Score = 98.6 bits (244), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 64/241 (26%), Positives = 112/241 (46%), Gaps = 40/241 (16%)

Query: 110 DPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINI 169
           D ++ P   G+ D R+GT  ++ NC TC +   +C GHFG+I+L  PVFHIG+   +  +
Sbjct: 45  DQRQRPRTKGINDPRLGTIDRQYNCETCEEGPKECPGHFGHIELASPVFHIGFLTKIKKL 104

Query: 170 LQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKSLKKKIL-------------- 214
           L+++C N  C ++      +    A + R+P   +     L K +L              
Sbjct: 105 LETVCHN--CGKIKANTADSKFTEALRFRDPKRRFDAIWRLSKDVLVCEADAPADDEEFS 162

Query: 215 ETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEI 274
           + ++K      CG     V+K G+  +         K   A++ED +A+  + V      
Sbjct: 163 KESQKGRSHGGCGNAQPTVRKEGICLV------GTWKPSKAMMEDEMAQPEKKV------ 210

Query: 275 EAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSV 334
                      + P   L +F  I +ED+ ++ ++ + ++P  +ILT L VPP  +RPSV
Sbjct: 211 -----------ITPTMALNIFRNISVEDVRIMGLSNDYARPEWMILTVLPVPPPTVRPSV 259

Query: 335 I 335
           +
Sbjct: 260 V 260



 Score = 92.0 bits (227), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 79/288 (27%), Positives = 136/288 (47%), Gaps = 58/288 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLD--KDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N + NI TP +T Y +  K  D + A++++  +E T+L  V E  E  + P
Sbjct: 1113 GVPRLKEILNVATNIKTPSMTVYQEGVKTHDKEGAKLLRSLVEHTSLRSVTESTEIYYDP 1172

Query: 822  DDSFILIKLDMDRIRLLHL--EVDIDS--------IRYCIERTRGISGHLTVSGHSFLIL 871
            D    +I+ D D +    +  E + D         +R  + R   +   LTV   +  I 
Sbjct: 1173 DIQSTVIENDRDMVESYFIIPEDNADDASQQSKWLLRIVLSRRSLLDKGLTVQDVATRIK 1232

Query: 872  K--PKD-----SSKSFNSKMYQMKQ------------------------LLPSVVIKGVQ 900
            +  P+D     S  + + ++ +++Q                        LL ++ ++GV 
Sbjct: 1233 QAYPRDIAVIFSDNNADEQVIRIRQVQDYKDDEDEDIEYDVTLKKLEQHLLDTLTLRGVP 1292

Query: 901  GINRAVIHEED----VEGVT-----------KYKLLVEGDNLRDVMATYGVKGVKCSSNN 945
            G++RA I+E+     VE  T           ++ L   G +L  V+A  GV   +  SN 
Sbjct: 1293 GVDRAFINEKSKVRVVEDGTLHTSKSDPLCKEWVLETSGSSLAAVLAIPGVDASRTYSNQ 1352

Query: 946  TYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
              E+++  GIEAAR+ ++ E+ LV+   G  ++ RH  L+ D+MT +G
Sbjct: 1353 FIEIFEVFGIEAARTAVLRELTLVLAFDGSYVNHRHLALLVDVMTVRG 1400



 Score = 58.2 bits (139), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 26/41 (63%), Positives = 28/41 (68%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            A   ++ RA   P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1064 AIESRFARAAANPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1104


>gi|448297909|ref|ZP_21487943.1| DNA-directed RNA polymerase subunit A' [Natronorubrum tibetense
           GA33]
 gi|445592635|gb|ELY46821.1| DNA-directed RNA polymerase subunit A' [Natronorubrum tibetense
           GA33]
          Length = 975

 Score =  159 bits (402), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 100/275 (36%), Positives = 145/275 (52%), Gaps = 46/275 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 483 DGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQNEEA 542

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR GE +I A QD I+G YLLT  N  FN 
Sbjct: 543 RAE--------------ARVLMRVQEQILSPRFGENIIGAIQDHISGTYLLTHDNPRFNE 588

Query: 461 AQTMR-IASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q +  + +T I +  +  GI                    WTG  +FS +L      P 
Sbjct: 589 TQALDLLRATRIDELPEPSGIDD-------------EDEPFWTGHDVFSELL------PD 629

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           + NL+  G   T  ++       V++ + +LL G++ +  +G  G   +   + + +G  
Sbjct: 630 DLNLEFTG---TVGDQ-------VVVEDGQLLEGTIAEDEVGEFG-GEIVDTITKVYGNT 678

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVT-PGQG 613
            +   +  +S +    +M+ GFSIGI D T PG+ 
Sbjct: 679 RSRIFINEVSTLAMRAIMHFGFSIGIDDETIPGEA 713



 Score =  112 bits (281), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 84/302 (27%), Positives = 136/302 (45%), Gaps = 41/302 (13%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G I   + + +  ++ S  +I++ + Y  D    PI  GL+D R+G       C TCG++
Sbjct: 10  GSINFGLMEPEEYREMSATKIITADTY--DDDGFPIDMGLMDPRLGVIDPGLECKTCGKH 67

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
              C GHFG+I+L  PV H+G+ + +  +L+  C+   C+R+LL E++   FRA +    
Sbjct: 68  SGSCNGHFGHIELAAPVIHVGFTKLIRRLLRGTCRE--CSRLLLTEDERDEFRADITESR 125

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVV---------------------KKCGLL 239
                   + K  +   +K   CPHCGEI   +                     +    +
Sbjct: 126 KLGRDLNDVTKAAIRQARKKDRCPHCGEIQYDIDHEKPTTYYEVQQVLTSEYSQRIAAAM 185

Query: 240 KISHEKYKNRTKKKD--AIVEDLLAEYNEAV--KFNPE------IEAHKKFGLIQT---- 285
           +   E+   RT   +     E  L   NE +   F P       IE      L +     
Sbjct: 186 QGDEEEGIERTSPDELAGETEIELTRVNEILSGSFRPRESQRKAIEKALDIDLTEEDTNK 245

Query: 286 LNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDND 343
           L P ++   FE IP EDI +L ++++ S+P  +ILT L VPP   RPS+  D   +S++D
Sbjct: 246 LMPSDIRDWFENIPDEDIEVLGIDSDRSRPEWMILTVLPVPPVTARPSITLDNGQRSEDD 305

Query: 344 VV 345
           + 
Sbjct: 306 LT 307



 Score = 92.0 bits (227), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 39/58 (67%), Positives = 49/58 (84%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
             GFV+NS+ SGLTP EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 834 AHGFVENSYTSGLTPREFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELESQYD 891



 Score = 46.2 bits (108), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 29/46 (63%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 65
           +VLM  +  +++PR GE +I A QD I+G YLLT  N  FN  Q +
Sbjct: 547 RVLMRVQEQILSPRFGENIIGAIQDHISGTYLLTHDNPRFNETQAL 592


>gi|452823901|gb|EME30907.1| DNA-directed RNA polymerase II subunit A, partial [Galdieria
           sulphuraria]
          Length = 741

 Score =  159 bits (402), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 92/269 (34%), Positives = 142/269 (52%), Gaps = 30/269 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVVLFNRQPSLHK+SIM HR ++LP+ TFR N    +PYNADFDGDEMN+H+PQ  E 
Sbjct: 420 DGDVVLFNRQPSLHKMSIMGHRVRILPYSTFRLNLSATSPYNADFDGDEMNLHVPQFLEG 479

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE L               LM    N+V+P+  + ++   QD + G  L T ++ F  R
Sbjct: 480 KAEILE--------------LMMVPKNIVSPQANKPVMGLVQDTLLGCSLFTMRDVFITR 525

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCP-- 518
              M +              I+ F  +   P + ++   +WTGKQ+FS+I  PN +    
Sbjct: 526 DMMMNLLMH-----------IEGFDGQIPTPAI-LKPKELWTGKQLFSMI-TPNVNIIRF 572

Query: 519 VNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
              +++          +    D+ V++   EL+ G +DKST+G+    ++ ++  ++ G 
Sbjct: 573 AETHVEESDSDPIFGPDMTIHDTRVVISGGELVCGVIDKSTVGTRA-GSLIHVCWKEHGP 631

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           D     +  +  + + +L+ RGFSIGIGD
Sbjct: 632 DATCDFISSVQLLINHWLLQRGFSIGIGD 660



 Score = 77.8 bits (190), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 58/229 (25%), Positives = 111/229 (48%), Gaps = 33/229 (14%)

Query: 112 QRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQ 171
           Q  P   GL+D+R+G   ++  C TC  +  DC GHFG+I+L  PV++ G+    + +L+
Sbjct: 43  QGRPKEGGLMDQRLGAIDRDFPCRTCHSSFLDCPGHFGHIELAQPVYNPGFLASTLKVLR 102

Query: 172 SICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEING 231
            IC    C+++L+  E ++   ++L+   +  + + + +  +  +  ++  C  CG    
Sbjct: 103 CICY--YCSKLLINTEDSS-IASRLKQ--IEQIKKGTKRLGLFLSLPRLKECRFCGN--- 154

Query: 232 VVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEV 291
              +  LL             +DA+   ++AE+ +     PE    K+    Q +   + 
Sbjct: 155 --AQPKLL-------------RDAL--SIVAEFPDP----PEGGGEKR----QQITAEKA 189

Query: 292 LQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKS 340
             + + +  ED  +L  + E S+P  +I+T L VPP  +RPS++ D  S
Sbjct: 190 YNILKHMSDEDADILGFSREQSRPDWMIITILSVPPPHVRPSIMMDATS 238


>gi|397135954|gb|AFO11472.1| RNA polymerase I, partial [Phaffomyces opuntiae]
          Length = 871

 Score =  159 bits (402), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 93/273 (34%), Positives = 149/273 (54%), Gaps = 36/273 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND VLFNRQPSLHK+S+MAHR KV+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 251 DNDPVLFNRQPSLHKMSMMAHRVKVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 310

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE +               + A    +V+P++ +  +   QD + G   +T +++F   
Sbjct: 311 RAELMN--------------IAAVPLQIVSPQSNKPCMGIVQDTLAGVRKMTLRDSFIEY 356

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M I   +    SD  G+I +       P + ++   +W+GKQ+ S+ +      P  
Sbjct: 357 DQMMNILYWI----SDWDGVIPQ-------PAI-LKPKPLWSGKQMLSMTI------PKG 398

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            +L+      T       +D+ +++ N E+L G +DK T+G+     + + ++R+ G   
Sbjct: 399 IHLQRFDEGTTL---LSPKDNGMLIVNGEILFGVVDKKTVGA-TNGGLIHTVMREKGAAQ 454

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQG 613
                 ++ ++ +F+L++ GFSIGIGD     G
Sbjct: 455 CADLFGKIQKVVNFWLLHNGFSIGIGDTIADAG 487



 Score =  102 bits (254), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTP EF+FH MGGREGL+DTAVKTAETGY+QRRLVK+LED+ V
Sbjct: 604 DYSPESKGFVENSYLRGLTPQEFYFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMV 663

Query: 666 QYD 668
            YD
Sbjct: 664 HYD 666


>gi|449687727|ref|XP_002164354.2| PREDICTED: DNA-directed RNA polymerase II subunit RPB1-like isoform
           1, partial [Hydra magnipapillata]
          Length = 1595

 Score =  159 bits (401), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 95/278 (34%), Positives = 149/278 (53%), Gaps = 49/278 (17%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DNDVV+FNRQP+LHK+S+M HR KVLP  TFR N  V TPYNADFDGDEMN+H+PQ+ E 
Sbjct: 7   DNDVVVFNRQPTLHKMSMMGHRVKVLPWSTFRLNLSVTTPYNADFDGDEMNMHVPQSMET 66

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE               ++LM  +  ++TP++ +  +   QD +   Y  T+++ F  +
Sbjct: 67  RAEI-------------TEILMVPR-QIITPQSNKPCMGIVQDSLCAVYKFTKRDVFLEK 112

Query: 461 AQTMRIASTLIADTSDICGIIKRFSW-RSWN---PV-VFVRTAVIWTGKQIFSLILKPNR 515
              M +                   W R W+   P+   ++   +WTGKQIFSL++ P  
Sbjct: 113 DVVMNL-----------------LLWIRKWDGKFPIPAILKPKPLWTGKQIFSLLIPP-- 153

Query: 516 DCPVNANLKTKGRAYT---ANEEFCH---RDSYVILRNSELLAGSMDKSTLGSGGKANVF 569
                 N   +  A+    +N  +CH    D+ V++ +  L++G + K T+G  G + + 
Sbjct: 154 ----GINHSGEHSAHPDDESNGPYCHISPGDTKVLIEDGTLISGIICKKTVGPSGNS-LV 208

Query: 570 YILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           +I++ + G ++A      L ++T+ + +  G SIGIGD
Sbjct: 209 HIIMAEEGPEIAKEFYGDLQKVTNNWFLVEGHSIGIGD 246



 Score =  108 bits (269), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 59/183 (32%), Positives = 102/183 (55%), Gaps = 14/183 (7%)

Query: 1226 LLPSVVIKGVQGINRAVIH--------------EEDVEGVTKYKLLVEGDNLRDVMATYG 1271
            +L  + ++G++ I +  +H              E + + + ++ L  +G+ L  V++   
Sbjct: 848  MLTDMTLQGIESIAKVYMHLPSEESKKRVIFNAEGEFKHLQEWILETDGNGLMKVLSQKD 907

Query: 1272 VKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 1331
            +  V+ +SN+  E++  LGIEA R +I  E+  V+   G  +++RH  L+ D+MTSKG +
Sbjct: 908  IDPVRTTSNDICEIFSILGIEAVRKSIEKEMDHVISFDGSYVNYRHLSLLCDIMTSKGHL 967

Query: 1332 LGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLI 1391
            + ITRHG+ + +   L   SFE T D L +AAF+ + D + GVSE II+G    +GTG  
Sbjct: 968  MAITRHGINRQEVGCLMRCSFEETVDVLVEAAFHAEADNLRGVSENIILGQLPPIGTGCF 1027

Query: 1392 KLL 1394
             L+
Sbjct: 1028 NLM 1030



 Score =  100 bits (248), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 41/57 (71%), Positives = 52/57 (91%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NS+ +GLTPTEFFFH MGGREGL+DTAVKT+ETGY+QRRL+K++E + V YD
Sbjct: 375 RGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTSETGYIQRRLIKAMESVMVAYD 431



 Score = 85.1 bits (209), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 74/295 (25%), Positives = 132/295 (44%), Gaps = 61/295 (20%)

Query: 764 GVPRIKEIINASRNISTPIITAYL--DKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           GVPR+KEIIN S+   TP +T +L      D ++A+ V  RLE TTL +V       + P
Sbjct: 675 GVPRLKEIINVSKKPKTPSLTVFLLGQAARDAEHAKDVLCRLEHTTLRKVTANTAIFYDP 734

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYC-------IERTRGISGHLTVS------GHSF 868
           D    +I  D D + + +   D D  R         ++R R     L++          F
Sbjct: 735 DPQNTVIAEDQDFVNVYYEMPDFDPARMSPWLLRIELDRKRMTDSKLSMEQIAEKINQGF 794

Query: 869 ---------------LILKPK-----DSSKSFNS--KMYQMK----------QLLPSVVI 896
                          L+L+ +     D SK+     ++ +M+           +L  + +
Sbjct: 795 GDDLNCIYNDDNAEKLVLRIRIMGSGDDSKNMEDEEQLDKMEDDVFLRCIEANMLTDMTL 854

Query: 897 KGVQGINRAVIH--------------EEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCS 942
           +G++ I +  +H              E + + + ++ L  +G+ L  V++   +  V+ +
Sbjct: 855 QGIESIAKVYMHLPSEESKKRVIFNAEGEFKHLQEWILETDGNGLMKVLSQKDIDPVRTT 914

Query: 943 SNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
           SN+  E++  LGIEA R +I  E+  V+   G  +++RH  L+ D+MTSKG ++ 
Sbjct: 915 SNDICEIFSILGIEAVRKSIEKEMDHVISFDGSYVNYRHLSLLCDIMTSKGHLMA 969



 Score = 55.8 bits (133), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/33 (72%), Positives = 27/33 (81%)

Query: 1113 AQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            AQ +P   VGALAAQS+GEP TQMTL TFH+AG
Sbjct: 634  AQAQPGEMVGALAAQSLGEPATQMTLNTFHYAG 666


>gi|113957457|gb|ABI49115.1| RNA polymerase II largest subunit [Lobariella pallida]
          Length = 996

 Score =  159 bits (401), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 97/279 (34%), Positives = 152/279 (54%), Gaps = 43/279 (15%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D ++FNRQPSLHK S+M HR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 353 DGDYIIFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 412

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    +++L ++            N+V+P+    L+   QD + G Y L +++ F N+
Sbjct: 413 RAE----INQLCMVP----------LNIVSPQRNGPLMGIVQDTLCGIYKLCRRDVFLNK 458

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M I    +    D  G++ +       P + ++    WTGKQI SL++ P       
Sbjct: 459 EQVMNI----LLWVPDWDGVLPQ-------PAI-LKPRPKWTGKQIISLVIPP------G 500

Query: 521 ANLKTKGRAYTANEEFCH-RDSYVILRNSELLAGSMDKSTLG--SGGKANVFYILLRDFG 577
            NL       +++E F    D  + +   EL+ G  DK ++G  SGG   + +I+  + G
Sbjct: 501 LNL-----TRSSSEGFSPLNDDGLFVSGGELMYGLFDKKSVGATSGG---IIHIIFNEKG 552

Query: 578 EDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
            + A+        + +++L++ GFSIGIGD  P +  +Q
Sbjct: 553 PEAAMNFFNGAQTVVNYWLLHNGFSIGIGDTIPDRNTIQ 591



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+  
Sbjct: 705 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDVMA 764

Query: 666 QYD 668
           +YD
Sbjct: 765 KYD 767



 Score = 42.4 bits (98), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 18/29 (62%), Positives = 21/29 (72%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMT 1137
            ++ RA + P   VG LAAQSIGEP TQMT
Sbjct: 968  RFCRAAVNPGEMVGVLAAQSIGEPATQMT 996


>gi|342180836|emb|CCC90312.1| putative RNA polymerase IIA largest subunit [Trypanosoma congolense
           IL3000]
          Length = 1756

 Score =  159 bits (401), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 95/267 (35%), Positives = 144/267 (53%), Gaps = 39/267 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + DVVLFNRQP+LH++S+M HR +VL + TFR N    TPYNADFDGDEMN+H+PQ+   
Sbjct: 444 NGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNLSCTTPYNADFDGDEMNLHVPQSLLT 503

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE +             +++M  K N V+P      +   QD + G Y LT K+ F ++
Sbjct: 504 KAELI-------------EMMMVPK-NFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFLDK 549

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                +A  L     D+        W+   P V ++   +WTGKQ+FSLIL P  + P  
Sbjct: 550 YFVQSVALWL-----DL--------WQLPIPAV-LKPRPLWTGKQVFSLIL-PEVNHPTT 594

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            + K           F H DS V++R  ELL G + K  +G+    ++ +++  + G D 
Sbjct: 595 PHDKPP---------FPHNDSSVMIRRGELLCGPITKGIVGA-APGSLIHVIFNEQGSDE 644

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGD 607
               +  + R+T+F+L+N GFS+G+ D
Sbjct: 645 VARFINGVQRVTTFFLLNFGFSVGVQD 671



 Score = 85.9 bits (211), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 65/208 (31%), Positives = 103/208 (49%), Gaps = 22/208 (10%)

Query: 1211 DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHE-------EDVEGVTKYKLLV---EG 1260
            D + S       +  LL  V ++G+ G+ RA++ +       E    +T  K  V   +G
Sbjct: 1270 DGADSIPKLKRDIPALLARVHLRGIPGVRRALLKDTTKFTVDESTGKLTGEKTWVIDTDG 1329

Query: 1261 DNLRDVMATYGVKG---------VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM 1311
              LR   A  GV G          K SSN   EV   LGIEAAR  ++TE++     +G+
Sbjct: 1330 TALR--RAFIGVVGEDGKNIINATKTSSNKVPEVCSLLGIEAARYRMLTELREAYLAYGL 1387

Query: 1312 SIDFRHPMLVADLMTSKGEVLGITRHGLAKMKES-VLNLASFENTSDHLFDAAFYGQTDC 1370
            +I++RH  ++ D +  +G ++ ++R G+ +   S  L   SFE T   L  AA +G+ D 
Sbjct: 1388 NINYRHYTILVDTICQRGYLMAVSRTGINRSDTSGPLMRCSFEETVKVLMAAASFGEHDP 1447

Query: 1371 ISGVSECIIMGLPMNVGTGLIKLLQAVP 1398
            + GVS  +++G    VGTGL  L+  +P
Sbjct: 1448 VRGVSANLVLGNQARVGTGLFDLIINMP 1475



 Score = 85.5 bits (210), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 74/248 (29%), Positives = 114/248 (45%), Gaps = 43/248 (17%)

Query: 115 PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSIC 174
           P+  G+ D RMGT   E  C TC +   +C GHFGYI+L  PVF+IG F  V+ +L+ +C
Sbjct: 49  PVRGGINDLRMGTTDFEFACETCHRKHPECPGHFGYIELAEPVFNIGVFDLVLQVLKCVC 108

Query: 175 KNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVS--VCPHCGE---- 228
           K  +C  +LL   +A     KL N  L+ L R     K+ ET  ++S  +    G+    
Sbjct: 109 K--SCGALLLN-TRADDVHKKLHN--LTGLSRLRQAAKMAETKCRMSTDLEDEVGDDGLN 163

Query: 229 ---------ING--VVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAH 277
                    + G    + CG         + R  +   I   L+    +AV  + + E H
Sbjct: 164 GGSFGGGGAVTGARATRGCG-------ASQPRVSRFYGIYPTLIV---KAVHGDQDAEWH 213

Query: 278 KKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSV-IS 336
                       +V Q+ + +  ED  L+  +     P DL+LT L VPP  +RP++   
Sbjct: 214 AD----------KVRQVLDRVSDEDARLMGFDPLRCHPRDLVLTVLPVPPPQVRPAISFG 263

Query: 337 DLKSDNDV 344
            LKSD+++
Sbjct: 264 GLKSDDEL 271



 Score = 83.2 bits (204), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 34/57 (59%), Positives = 44/57 (77%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +G     +  GL P EFFFHTM GREGL+DTAVKT++TGY+QR+L+K+LED+   YD
Sbjct: 800 RGMANRGYVEGLKPHEFFFHTMAGREGLIDTAVKTSDTGYLQRKLIKALEDVHAAYD 856



 Score = 61.6 bits (148), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 70/295 (23%), Positives = 125/295 (42%), Gaps = 64/295 (21%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLD-YARIVKGRLERTTLGEVCEYIEEVFVPD 822
            GVPR+ E++N SR+     +T  L    D    A+  +  +E  TL  + + I+ ++ PD
Sbjct: 1118 GVPRLLELLNVSRHQKHASMTVTLFPPWDKKRVAQKAQHLIEYCTLESITQRIQFIYDPD 1177

Query: 823  DSFILIKLDMD----------------RIR--------LLHLEVDID----------SIR 848
                ++++D D                R+R        ++ LE+D+D           ++
Sbjct: 1178 PRHTVVEVDRDILELEWDVMDESDAEQRVREVEEGSPWVVRLELDVDMVTDKALDMKDVK 1237

Query: 849  YCIERT-------RGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQG 901
              I+R         G++ ++             D + S       +  LL  V ++G+ G
Sbjct: 1238 QAIQRVDTNYIIETGMANNVRRRTIRLRSRT-NDGADSIPKLKRDIPALLARVHLRGIPG 1296

Query: 902  INRAVIHE-------EDVEGVTKYKLLV---EGDNLRDVMATYGVKG---------VKCS 942
            + RA++ +       E    +T  K  V   +G  LR   A  GV G          K S
Sbjct: 1297 VRRALLKDTTKFTVDESTGKLTGEKTWVIDTDGTALR--RAFIGVVGEDGKNIINATKTS 1354

Query: 943  SNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            SN   EV   LGIEAAR  ++TE++     +G++I++RH  ++ D +  +G ++ 
Sbjct: 1355 SNKVPEVCSLLGIEAARYRMLTELREAYLAYGLNINYRHYTILVDTICQRGYLMA 1409



 Score = 50.4 bits (119), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 23/39 (58%), Positives = 27/39 (69%)

Query: 1107 REKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            R KY ++   P   +GA+AAQS GEP TQMTL TFH AG
Sbjct: 1071 RTKYHQSLATPGENIGAIAAQSCGEPATQMTLNTFHNAG 1109


>gi|340368153|ref|XP_003382617.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB1-like
           [Amphimedon queenslandica]
          Length = 1933

 Score =  159 bits (401), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 93/275 (33%), Positives = 148/275 (53%), Gaps = 40/275 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+D+++FNRQP+LHK+S+M HR K+LP  TFR N  V TPYNADFDGDEMN+H+PQ+ E 
Sbjct: 445 DDDLIVFNRQPTLHKMSMMGHRVKILPWSTFRLNLSVTTPYNADFDGDEMNLHVPQSLET 504

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE    + +L +M HR         N++TP++   ++   QD +T     T+++ F  +
Sbjct: 505 KAE----IQEL-MMVHR---------NILTPQSNRPVMGIVQDSLTAATKFTKRDVFLEK 550

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPV-VFVRTAVIWTGKQIFSLILKPNRDCPV 519
              M +   L              SW    PV   ++   +WTGKQ+FSLI+        
Sbjct: 551 ESMMNLLMWLP-------------SWDGKMPVPAILKPKPLWTGKQLFSLIIP-----GT 592

Query: 520 NANLKTKGRAYTANEE------FCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILL 573
           N N+      +  +E+          D+ V++ + +LL+G + K TLG+ G  ++ +++ 
Sbjct: 593 NVNVIRTHSTHPDDEDNGPYKWISPGDTKVLVEHGQLLSGILSKDTLGNKG-GSLMHVVA 651

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
            + G D+A      +  + + +LM  G SIGIGD 
Sbjct: 652 MELGPDIARNFYGNIQTVVNNFLMLEGHSIGIGDT 686



 Score =  107 bits (266), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 57/183 (31%), Positives = 102/183 (55%), Gaps = 14/183 (7%)

Query: 1226 LLPSVVIKGVQGINRAVIH--------------EEDVEGVTKYKLLVEGDNLRDVMATYG 1271
            LL  + ++G++ I++  +H              + + + + ++ L  +G NL  V++   
Sbjct: 1288 LLSDMTLQGIEQISKVYMHYPTQDSKKRIVISEQGEFKAIQEWILETDGVNLLRVLSEPS 1347

Query: 1272 VKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 1331
            V  V+ +SN+  E+++ LGIEA R  +  EI  V+   G  +++RH  L+ D+MT +G +
Sbjct: 1348 VDPVRTTSNHIVEIFQVLGIEAVRKALEKEINHVISFDGSYVNYRHLALLCDIMTCRGHL 1407

Query: 1332 LGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLI 1391
            + +TRHG+ + +   L   SFE T D L +AA + + D + GVSECI++G     GTG  
Sbjct: 1408 MAVTRHGVNRQEVGALMRCSFEETVDILMEAAGHAEVDKMQGVSECIMLGQLPKGGTGAF 1467

Query: 1392 KLL 1394
            +L+
Sbjct: 1468 ELM 1470



 Score = 96.7 bits (239), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 40/57 (70%), Positives = 50/57 (87%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NS+ +GLTP EFFFH MGGREGL+DTAVKT+ETGY+QRRL+K++E L   YD
Sbjct: 814 KGFVENSYLAGLTPNEFFFHAMGGREGLIDTAVKTSETGYIQRRLMKAMEGLMAHYD 870



 Score = 80.9 bits (198), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 70/296 (23%), Positives = 127/296 (42%), Gaps = 62/296 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYL--DKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEIIN S+   TP +T +L      D +  + V  R+E TTL +V       + P
Sbjct: 1114 GVPRLKEIINVSKKPKTPSLTIFLLGQAARDAEKCKDVLCRIEHTTLSKVTANTSIFYDP 1173

Query: 822  DDSFILIKLDMDRIRLLHLEVDIDS-------IRYCIERTRGISGHLTVS---------- 864
            D    +I  D + + + +   D D        +R  ++R R     LT+           
Sbjct: 1174 DPQNTVIAEDQEFVNVYYEMPDFDPALISPWLLRLELDRKRMTDKKLTMEQIAEKISSTF 1233

Query: 865  GHSFLILKPKDSSKSF---------NSKMYQMK--------------------QLLPSVV 895
            G     L   D+++           + + YQ +                     LL  + 
Sbjct: 1234 GDDLRCLFNDDNAEKLVLRIRLMNSDDQKYQSEADEEQLDKMEDETFLRCLEANLLSDMT 1293

Query: 896  IKGVQGINRAVIH--------------EEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
            ++G++ I++  +H              + + + + ++ L  +G NL  V++   V  V+ 
Sbjct: 1294 LQGIEQISKVYMHYPTQDSKKRIVISEQGEFKAIQEWILETDGVNLLRVLSEPSVDPVRT 1353

Query: 942  SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            +SN+  E+++ LGIEA R  +  EI  V+   G  +++RH  L+ D+MT +G ++ 
Sbjct: 1354 TSNHIVEIFQVLGIEAVRKALEKEINHVISFDGSYVNYRHLALLCDIMTCRGHLMA 1409



 Score = 63.5 bits (153), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 25/66 (37%), Positives = 41/66 (62%), Gaps = 2/66 (3%)

Query: 119 GLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPT 178
           GL+D R G   + + C TC  N++ C GHFG+I L  PVFH+ +   ++ I++ +C    
Sbjct: 53  GLMDPRQGVIDRASRCQTCAGNMNTCPGHFGHISLTKPVFHVCFMTKIVKIMRCVCF--Y 110

Query: 179 CARVLL 184
           C+R+L+
Sbjct: 111 CSRLLI 116



 Score = 58.9 bits (141), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/37 (64%), Positives = 30/37 (81%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            ++ RA ++P   VGALAAQS+GEP TQMTL TFH+AG
Sbjct: 1069 RFQRAHVQPGEMVGALAAQSLGEPATQMTLNTFHYAG 1105


>gi|327242135|gb|AEA40846.1| RNA polymerase II largest subunit [Trichomonas vaginalis]
          Length = 1018

 Score =  159 bits (401), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 87/267 (32%), Positives = 143/267 (53%), Gaps = 31/267 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+D+V+FNRQPSLHK+S+M HRA ++  RTFR N C  TPYNADFDGDEMN+H+PQ++ A
Sbjct: 371 DDDIVIFNRQPSLHKMSMMGHRALIMSGRTFRLNLCDTTPYNADFDGDEMNLHVPQSQTA 430

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R E               + +MA    +++P+  + +I   QD + G  LL++++ F  R
Sbjct: 431 RTE--------------VRHIMAVPKQIISPQANKPVIGLVQDALLGCRLLSKRDTFLTR 476

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M +   L      I             P   ++   +W+GKQ+FSL L       ++
Sbjct: 477 NQVMNLMMWLPTTKDTILP-----------PPCILKPVQLWSGKQVFSLFLP-----KIS 520

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            N  ++             D +VI+R+  LLAG +DK T+    + ++ ++++  +  ++
Sbjct: 521 HNSYSQDANKMDQNSIPLADRHVIIRDGNLLAGILDKKTVAR-SEGSLIHVVINSYNTNI 579

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           A   + +   + + +L +RGFSIG+ D
Sbjct: 580 AKDFLNQTQLIVNNWLEHRGFSIGLID 606



 Score = 85.5 bits (210), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 36/57 (63%), Positives = 46/57 (80%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GF +NS+ +GLTP EF FH MGGR G++DTA KT++TGY+QRRLVKS+E   V YD
Sbjct: 735 RGFCKNSYIAGLTPPEFLFHAMGGRTGIIDTACKTSDTGYIQRRLVKSMESHHVAYD 791



 Score = 50.4 bits (119), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 57/211 (27%), Positives = 86/211 (40%), Gaps = 51/211 (24%)

Query: 150 YIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLV-RKS 208
           YI L  P FH+G+      +LQ +C    C RVL              +P + Y+V    
Sbjct: 1   YIRLAEPFFHVGFLPHCYKLLQMLCHK--CGRVL----------CSYSDPEIQYIVTHYK 48

Query: 209 LKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAE----- 263
            K + L+  +K++             K G  K  H        + D  +++   E     
Sbjct: 49  GKNRFLKLFEKIA------------SKSG--KCQHSPDLKNPNEPDVCLDERFWELVNGD 94

Query: 264 -YNEAVKFN-------PEIEAHKKFGLIQT----------LNPLEVLQLFEAIPLEDIPL 305
            ++E V+         P IE  K F LI+           L+   VL++FE I  +D+ L
Sbjct: 95  SHSEHVRVKKPCNATVPAIEQGKDF-LIKLKDVSKTEEDYLSAEVVLRIFENISDQDVRL 153

Query: 306 LLMNAELSKPSDLILTRLLVPPNCIRPSVIS 336
           L  N + S P  +IL  L VPP  +RP V+S
Sbjct: 154 LGFNPKRSHPKWMILKILPVPPLAVRPQVVS 184


>gi|327242129|gb|AEA40843.1| RNA polymerase II largest subunit [Trichomonas vaginalis]
 gi|327242133|gb|AEA40845.1| RNA polymerase II largest subunit [Trichomonas vaginalis]
 gi|327242137|gb|AEA40847.1| RNA polymerase II largest subunit [Trichomonas vaginalis]
          Length = 1018

 Score =  159 bits (401), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 87/267 (32%), Positives = 143/267 (53%), Gaps = 31/267 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+D+V+FNRQPSLHK+S+M HRA ++  RTFR N C  TPYNADFDGDEMN+H+PQ++ A
Sbjct: 371 DDDIVIFNRQPSLHKMSMMGHRALIMSGRTFRLNLCDTTPYNADFDGDEMNLHVPQSQTA 430

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R E               + +MA    +++P+  + +I   QD + G  LL++++ F  R
Sbjct: 431 RTE--------------VRHIMAVPKQIISPQANKPVIGLVQDALLGCRLLSKRDTFLTR 476

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M +   L      I             P   ++   +W+GKQ+FSL L       ++
Sbjct: 477 NQVMNLMMWLPTTKDTILP-----------PPCILKPVQLWSGKQVFSLFLP-----KIS 520

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            N  ++             D +VI+R+  LLAG +DK T+    + ++ ++++  +  ++
Sbjct: 521 HNSYSQDANKMDQNSIPLADRHVIIRDGNLLAGILDKKTVAR-SEGSLIHVVINSYNTNI 579

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           A   + +   + + +L +RGFSIG+ D
Sbjct: 580 AKDFLNQTQLIVNNWLEHRGFSIGLID 606



 Score = 85.5 bits (210), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 36/57 (63%), Positives = 46/57 (80%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GF +NS+ +GLTP EF FH MGGR G++DTA KT++TGY+QRRLVKS+E   V YD
Sbjct: 735 RGFCKNSYIAGLTPPEFLFHAMGGRTGIIDTACKTSDTGYIQRRLVKSMESHHVAYD 791



 Score = 50.8 bits (120), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 57/211 (27%), Positives = 86/211 (40%), Gaps = 51/211 (24%)

Query: 150 YIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLV-RKS 208
           YI L  P FH+G+      +LQ +C    C RVL              +P + Y+V    
Sbjct: 1   YIRLAEPFFHVGFLPHCYKLLQMVCHK--CGRVL----------CSYSDPEIQYIVTHYK 48

Query: 209 LKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAE----- 263
            K + L+  +K++             K G  K  H        + D  +++   E     
Sbjct: 49  GKNRFLKLFEKIA------------SKSG--KCQHSPDLKNPNEPDVCLDERFWELVNGD 94

Query: 264 -YNEAVKFN-------PEIEAHKKFGLIQT----------LNPLEVLQLFEAIPLEDIPL 305
            ++E V+         P IE  K F LI+           L+   VL++FE I  +D+ L
Sbjct: 95  SHSEHVRVKKPCNATVPAIEQGKDF-LIKLKDVSKTEEDYLSAEVVLRIFENISDQDVRL 153

Query: 306 LLMNAELSKPSDLILTRLLVPPNCIRPSVIS 336
           L  N + S P  +IL  L VPP  +RP V+S
Sbjct: 154 LGFNPKRSHPKWMILKILPVPPLAVRPQVVS 184


>gi|120561217|gb|ABM26994.1| RNA polymerase II largest subunit, partial [Mucor hiemalis]
          Length = 1009

 Score =  159 bits (401), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 89/269 (33%), Positives = 144/269 (53%), Gaps = 33/269 (12%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D+DVV+FNRQPSLHK+S+M HR KV+P+ TFR N  V +PYNADFDGDEMN+H+PQ+ E
Sbjct: 363 NDDDVVIFNRQPSLHKMSMMGHRVKVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSLE 422

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE               ++ M  K  +V+P++ + ++   QD + G    T ++ F  
Sbjct: 423 TRAEV-------------TEICMVPKQ-IVSPQSNKPVMGIVQDTLCGIRKFTLRDCFMT 468

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSW-NPVVFVRTAVIWTGKQIFSLILKPNRDCP 518
           +   M I             ++   SW  +  P   ++   +WTGKQI S+++    +C 
Sbjct: 469 KDLVMNI-------------VMWVPSWDGYIPPPAILKPKPMWTGKQIVSMVIPKGINCQ 515

Query: 519 VNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
              +    G +          D+ VI+ N EL+ G + K T+G+ G   + + ++ + G 
Sbjct: 516 TFHSTHPDGESTL----ISPGDTRVIIENGELICGIVCKKTVGTAG-GGLIHTIMNELGP 570

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           + A   +    ++ +++L+  GFSIGIGD
Sbjct: 571 EAAKNFLGGTQQVVNYWLLQNGFSIGIGD 599



 Score =  103 bits (258), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 45/57 (78%), Positives = 53/57 (92%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NS+  GLTPTEFFFH MGGREGL+DTAVKTAETGY+QRRLVK+LED+ V+YD
Sbjct: 728 RGFVENSYLRGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDVMVKYD 784



 Score = 53.9 bits (128), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 53/195 (27%), Positives = 89/195 (45%), Gaps = 23/195 (11%)

Query: 150 YIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSL 209
           +I+L  PV+HIG+   V  IL+ +C +  C+++ + E      RAK    A + L     
Sbjct: 1   HIELAKPVYHIGFLTKVKKILECVCFH--CSKLKVDETNPRFIRAKKITDAKTKL----- 53

Query: 210 KKKILETTKKVSVCPHCGEI-NGVVKK----CGLLKISHEK--YKNRTKKKDAIVEDLLA 262
            + + +  K    C    E  +G+ +K     G  K +H    YK    +KD +   L A
Sbjct: 54  -RAVWDLAKTKMTCEGSDEAEDGLEEKEEFDNGKRKSTHGGCGYKQPLIRKDGL--KLYA 110

Query: 263 EYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTR 322
           ++      +   E        Q L   +VLQ+ + I  +DI  + ++ E ++P  +I T 
Sbjct: 111 QFRANAGDDNGGEGR------QQLTAAKVLQILKNISDQDIRDMGLSEEFARPEWMITTV 164

Query: 323 LLVPPNCIRPSVISD 337
           L VPP  +RPS+  D
Sbjct: 165 LPVPPPQVRPSIQMD 179


>gi|520517|gb|AAA50229.1| RNA polymerase II, largest subunit, partial [Ilyanassa obsoleta]
          Length = 1343

 Score =  159 bits (401), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 95/273 (34%), Positives = 142/273 (52%), Gaps = 27/273 (9%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
            DNDVV+FNRQP+LHK+S+M HR KVLP  TFR N  V TPYNADFDGDEMN+HLPQ+ E
Sbjct: 365 QDNDVVIFNRQPTLHKMSMMCHRVKVLPWSTFRMNLSVTTPYNADFDGDEMNLHLPQSLE 424

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE +               L A    ++TP+    ++   QD +T    +T+++ F  
Sbjct: 425 TRAEIMN--------------LCAVPRMIITPQANRPVMGIVQDTLTAVRKMTKRDVFLT 470

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           RAQ M +   L             +  R   P + ++   +WTGKQIFSL++    +   
Sbjct: 471 RAQMMHLLMFLPT-----------WDGRMPQPAI-IKPEPLWTGKQIFSLVIPGRVNVIR 518

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
             +    G      +     D+ V++ + EL++G + K TLG+    ++ +I+  + G +
Sbjct: 519 THSTHPDGEDSGPYKWISPGDTKVLIEDGELISGILCKKTLGTSA-GSLVHIVFLEMGFE 577

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
           VA      +  + + +L+  G SIGIGD    Q
Sbjct: 578 VAGELYGNIQTVVNNWLLIEGHSIGIGDTIADQ 610



 Score = 99.0 bits (245), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 40/57 (70%), Positives = 53/57 (92%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NS+ +GLTP+EF+FH MGGREGL+DTAVKTAETGY+QRRL+K++E + V+YD
Sbjct: 734 RGFVENSYLAGLTPSEFYFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVKYD 790



 Score = 84.3 bits (207), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 76/294 (25%), Positives = 130/294 (44%), Gaps = 60/294 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEIIN S+   TP +T YL+     D +  + V  RLE TTL +V       + P
Sbjct: 1034 GVPRLKEIINISKKPKTPSLTVYLNGPAARDAEKCKDVLCRLEHTTLRKVTANTAIYYDP 1093

Query: 822  DDSFILIKLDMDRIRLLHLEVDIDS-------IRYCIERTRGISGHLTVS---------- 864
            D    +I  D + + + +   D D+       +R  ++R R     LT+           
Sbjct: 1094 DPMNTVIVEDQEWVSIYYEMPDFDASRISPWLLRIELDRKRMTDKKLTMEQISEKITAGF 1153

Query: 865  GHSFLILKPKDSSK----------SFNSKMYQMKQ-----------------LLPSVVIK 897
            G     +   D+++          S +SKM   ++                 LL  + ++
Sbjct: 1154 GDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEEVVDKMEDDVFLRCIESNLLSDMTLQ 1213

Query: 898  GVQGINRAVIH--------------EEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSS 943
            G++ I +  +H              E + + V ++ L  +G +L  V++   V  V+  +
Sbjct: 1214 GIEAIAKVYMHLPTTDDKKRIHITEEGEFKAVAEWILETDGSSLMKVLSERDVDPVRTYT 1273

Query: 944  NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            N+  EV+ TLGIEA R  I  E+  V+   G  +++RH  L+ D+MT+KG ++ 
Sbjct: 1274 NDIVEVFATLGIEAVRKAIEREMVHVISFDGSYVNYRHLALLCDVMTAKGHLMA 1327



 Score = 75.5 bits (184), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 41/136 (30%), Positives = 73/136 (53%), Gaps = 14/136 (10%)

Query: 1226 LLPSVVIKGVQGINRAVIH--------------EEDVEGVTKYKLLVEGDNLRDVMATYG 1271
            LL  + ++G++ I +  +H              E + + V ++ L  +G +L  V++   
Sbjct: 1206 LLSDMTLQGIEAIAKVYMHLPTTDDKKRIHITEEGEFKAVAEWILETDGSSLMKVLSERD 1265

Query: 1272 VKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 1331
            V  V+  +N+  EV+ TLGIEA R  I  E+  V+   G  +++RH  L+ D+MT+KG +
Sbjct: 1266 VDPVRTYTNDIVEVFATLGIEAVRKAIEREMVHVISFDGSYVNYRHLALLCDVMTAKGHL 1325

Query: 1332 LGITRHGLAKMKESVL 1347
            + ITRHG+ + +   L
Sbjct: 1326 MAITRHGINRQETGAL 1341



 Score = 57.0 bits (136), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 24/37 (64%), Positives = 29/37 (78%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            ++ +AQ  P   VGALAAQS+GEP TQMTL TFH+AG
Sbjct: 989  RFQQAQAHPGEMVGALAAQSLGEPATQMTLNTFHYAG 1025


>gi|327242131|gb|AEA40844.1| RNA polymerase II largest subunit [Trichomonas vaginalis]
          Length = 1006

 Score =  159 bits (401), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 87/267 (32%), Positives = 143/267 (53%), Gaps = 31/267 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+D+V+FNRQPSLHK+S+M HRA ++  RTFR N C  TPYNADFDGDEMN+H+PQ++ A
Sbjct: 360 DDDIVIFNRQPSLHKMSMMGHRALIMSGRTFRLNLCDTTPYNADFDGDEMNLHVPQSQTA 419

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R E               + +MA    +++P+  + +I   QD + G  LL++++ F  R
Sbjct: 420 RTE--------------VRHIMAVPKQIISPQANKPVIGLVQDALLGCRLLSKRDTFLTR 465

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M +   L      I             P   ++   +W+GKQ+FSL L       ++
Sbjct: 466 NQVMNLMMWLPTTKDTILP-----------PPCILKPVQLWSGKQVFSLFLP-----KIS 509

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            N  ++             D +VI+R+  LLAG +DK T+    + ++ ++++  +  ++
Sbjct: 510 HNSYSQDANKMDQNSIPLADRHVIIRDGNLLAGILDKKTVAR-SEGSLIHVVINSYNTNI 568

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           A   + +   + + +L +RGFSIG+ D
Sbjct: 569 AKDFLNQTQLIVNNWLEHRGFSIGLID 595



 Score = 85.5 bits (210), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 36/57 (63%), Positives = 46/57 (80%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GF +NS+ +GLTP EF FH MGGR G++DTA KT++TGY+QRRLVKS+E   V YD
Sbjct: 724 RGFCKNSYIAGLTPPEFLFHAMGGRTGIIDTACKTSDTGYIQRRLVKSMESHHVAYD 780


>gi|302141712|emb|CBI18915.3| unnamed protein product [Vitis vinifera]
          Length = 1565

 Score =  159 bits (401), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 95/271 (35%), Positives = 147/271 (54%), Gaps = 35/271 (12%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D D VLFNRQPSLHK+SIM HR K++P+ TFR N  V +PYNADFDGDEMN+H+PQ+ E
Sbjct: 498 NDGDFVLFNRQPSLHKMSIMGHRIKIMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSFE 557

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE L             +++M  K  +V+P++   ++   QD + G   +T+++ F  
Sbjct: 558 TRAEVL-------------ELMMVPKC-IVSPQSNRPVMGIVQDTLLGCRKITKRDTFIE 603

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           +   M I    +    D  G I         P + ++   +WTGKQ+F+LI+      P 
Sbjct: 604 KDVFMNI----LMWWEDFDGKIP-------APAI-LKPRPLWTGKQVFNLII------PK 645

Query: 520 NANLKTKGRAYTANEE--FCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFG 577
             NL      ++ +E       D+ V +   ELLAG++ K TLG+    ++ +++  + G
Sbjct: 646 QINLLRTSAWHSESETGFITPGDTQVRIEKGELLAGTLCKKTLGT-STGSLIHVIWEEVG 704

Query: 578 EDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
            D A   +     + +++L+  GFSIGIGD 
Sbjct: 705 PDAARKFLGHTQWLVNYWLLQNGFSIGIGDT 735



 Score =  129 bits (323), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 88/300 (29%), Positives = 148/300 (49%), Gaps = 48/300 (16%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------EVCEYIEEV 1154
            +++++ + P   +G +AAQSIGEP TQMTL TFH+AG              E+    +++
Sbjct: 1000 RFLQSLVAPGEMIGCVAAQSIGEPATQMTLNTFHYAGVSAKNVTLGVPRLREIINVAKKI 1059

Query: 1155 FVPDDSFILIKLDM----DRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPK 1210
              P  S + +K D+    +R + +   ++  ++R   + T  IS  L             
Sbjct: 1060 KTPSLS-VYLKPDVSKTKERAKNVQCALEYTTLRSVTQATEKISPWLL------------ 1106

Query: 1211 DSSKSFNSKMY-QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMAT 1269
                  N +M  Q +     V +K ++ +              ++ L  EG NL  VM  
Sbjct: 1107 --RIELNREMMLQDESAEDDVFLKKIEKV--------------EWMLDTEGVNLLAVMCH 1150

Query: 1270 YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 1329
              V   + +SN+  EV + LGIEA R +++ E+++V+   G  +++RH  ++ D MT +G
Sbjct: 1151 EDVDARRTTSNHLIEVIEVLGIEAVRRSLLDELRVVISFDGSYVNYRHLAILCDTMTYRG 1210

Query: 1330 EVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
             ++ ITRHG+ +     +   SFE T D L DAA Y +TD + GV+E I++G    +GTG
Sbjct: 1211 HLMAITRHGINRNDTGPMMRCSFEETVDILLDAAVYAETDFLRGVTENIMLGQLAPIGTG 1270



 Score =  100 bits (250), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 42/57 (73%), Positives = 52/57 (91%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKT+ETGY+QRRLVK++ED+ V+YD
Sbjct: 863 RGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDIMVKYD 919



 Score = 86.3 bits (212), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 89/311 (28%), Positives = 144/311 (46%), Gaps = 71/311 (22%)

Query: 82  LIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQR-TPIPHGLLDRRMGTNQKEANCTTCGQN 140
           +++  +   D ++Q S +QI     + +  +R  P P GL D R+GT  ++  C TC  N
Sbjct: 17  MVQFGILSPDEIRQMSVVQIE----HSETTERGKPKPGGLSDPRLGTIDRKMKCETCTAN 72

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGE----------EKAA 190
           +++C GHFG+++L  P+FHIG+ + V++I++ +C N  C+++L  E           K A
Sbjct: 73  MAECPGHFGHLELAKPMFHIGFMKTVLSIMRCVCFN--CSKILADELTENVKWISKSKFA 130

Query: 191 GFRA---------------------KLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEI 229
             ++                     K+RNP       K+  KKIL+  K  S C    EI
Sbjct: 131 NMKSLKLGHSLLHCKSEDHKFKQAQKIRNP-------KNRLKKILDACKNKSKCEGGDEI 183

Query: 230 -------NGVVKK----CGLL--KISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEA 276
                  +  VKK    CG    K++ E  K            ++AEY    K N + E 
Sbjct: 184 ETQALDSDEPVKKSRGGCGAQQPKLTIEGMK------------MIAEYKIQRKKNDDPEQ 231

Query: 277 -HKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVI 335
             +     Q L+   VL + + I  ED  LL +N + ++P  +IL  L +PP  +RPSV+
Sbjct: 232 LPEPVERKQQLSAERVLNVLKRISDEDCILLGLNPKYARPDWMILQVLPIPPPPVRPSVM 291

Query: 336 SDLKSDNDVVL 346
            D  S ++  L
Sbjct: 292 MDTSSRSEASL 302



 Score = 66.2 bits (160), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 58/237 (24%), Positives = 106/237 (44%), Gaps = 70/237 (29%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTD--LDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR++EIIN ++ I TP ++ YL  D     + A+ V+  LE TTL  V +  E++   
Sbjct: 1045 GVPRLREIINVAKKIKTPSLSVYLKPDVSKTKERAKNVQCALEYTTLRSVTQATEKI--- 1101

Query: 822  DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
              S  L++++++R  +L  E   D +                                F 
Sbjct: 1102 --SPWLLRIELNREMMLQDESAEDDV--------------------------------FL 1127

Query: 882  SKMYQMKQLLPSVVIKGVQGIN-RAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
             K+ +++ +L        +G+N  AV+  EDV+                          +
Sbjct: 1128 KKIEKVEWML------DTEGVNLLAVMCHEDVD------------------------ARR 1157

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +SN+  EV + LGIEA R +++ E+++V+   G  +++RH  ++ D MT +G ++ 
Sbjct: 1158 TTSNHLIEVIEVLGIEAVRRSLLDELRVVISFDGSYVNYRHLAILCDTMTYRGHLMA 1214


>gi|242071129|ref|XP_002450841.1| hypothetical protein SORBIDRAFT_05g019520 [Sorghum bicolor]
 gi|241936684|gb|EES09829.1| hypothetical protein SORBIDRAFT_05g019520 [Sorghum bicolor]
          Length = 1874

 Score =  159 bits (401), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 97/272 (35%), Positives = 152/272 (55%), Gaps = 37/272 (13%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D D VLFNRQPSLHK+SIM HR K++P+ TFR N  V +PYNADFDGDEMN+H+PQ+ E
Sbjct: 450 NDGDFVLFNRQPSLHKMSIMGHRIKIMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSFE 509

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE L             +++M  K  +V+P++ + ++   QD + G   +T+++    
Sbjct: 510 TRAEVL-------------ELMMVPKC-IVSPQSNKPVMGIVQDTLLGCRKITKRDTLIE 555

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           +   M I    +    D  G I         P + ++   IWTGKQ+F+LI+      P 
Sbjct: 556 KDVFMNI----LMWWEDFDGKIPA-------PAI-LKPRPIWTGKQVFNLII------PR 597

Query: 520 NANLKTKGRAYTANEE---FCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
             NL  +  ++ ++EE       D+ V +   ELL+G++ K TLG+G   ++ +I+  + 
Sbjct: 598 QINL-IRFCSWHSDEEKGFVTPSDTVVRIEKGELLSGTLCKKTLGTGS-GSLIHIIWEEV 655

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           G D A   +     + +++L+  GFSIGIGD+
Sbjct: 656 GPDAARKFLGYTQWLVNYWLLQNGFSIGIGDM 687



 Score =  102 bits (253), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 60/178 (33%), Positives = 97/178 (54%), Gaps = 9/178 (5%)

Query: 1226 LLPSVVIKGVQGINRAVIHEEDV------EGVTKYK---LLVEGDNLRDVMATYGVKGVK 1276
            +L  + ++G+  IN+  I E  V      +G  ++K   L  +G NL  VM    V   +
Sbjct: 1287 MLAEMSLRGIPDINKVFIKEVKVNKFDVSDGFKEHKEWMLDTDGVNLLAVMCHEDVDATR 1346

Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITR 1336
             +SN+  EV + LGIEA R  ++ E++ V+   G  +++RH  ++ D MT +G ++ ITR
Sbjct: 1347 TTSNHLTEVIEVLGIEAVRRALLDELRSVISFDGSYVNYRHLAVLCDTMTYRGHLMAITR 1406

Query: 1337 HGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            HG+ +     L   SFE T D L DAA + ++D + GV+E I++G    +GTG   L 
Sbjct: 1407 HGINRNDTGPLMRCSFEETVDILLDAAVHAESDYLRGVTENIMLGQLAPIGTGGCSLF 1464



 Score =  101 bits (251), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 42/57 (73%), Positives = 52/57 (91%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKT+ETGY+QRRLVK++ED+ V+YD
Sbjct: 815 RGFVENSYLQGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDIMVKYD 871



 Score = 85.1 bits (209), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 68/249 (27%), Positives = 123/249 (49%), Gaps = 23/249 (9%)

Query: 82  LIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQR-TPIPHGLLDRRMGTNQKEANCTTCGQN 140
           L++  +   D ++Q S  QI     Y +  ++  P   GL D RMGT  ++  C TC   
Sbjct: 17  LVQFGILSPDEIRQMSVAQIE----YAETMEKGKPKAGGLSDPRMGTVDRKIKCQTCMSG 72

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNP 199
           +++C GHFG+++L  P+FHIG+ + V++I++ +C N  C+++L+ E+     +A K+RNP
Sbjct: 73  MAECPGHFGHLELAKPMFHIGFMKTVLSIMRCVCFN--CSKILVDEDNTKFKQALKIRNP 130

Query: 200 ALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVE- 258
                  K+  K+I +  K   V   CGE + +  +       H   +     +  I+  
Sbjct: 131 -------KNRLKRIYDACKTKKV---CGEGDDLDVQQQQDTDEHVNRRGGCGAQQPIITV 180

Query: 259 ---DLLAEYNEAVKFNPEIEAHKKF-GLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSK 314
               +L E+    K N + E   +     Q L+   VL + + I  ++  LL ++ +L++
Sbjct: 181 DGVKMLVEFKAPKKKNDDQEQLSELVEPKQILSAERVLNVLKNISDKESLLLGLHPKLAR 240

Query: 315 PSDLILTRL 323
           P  +IL  L
Sbjct: 241 PDWMILQVL 249



 Score = 76.6 bits (187), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 74/288 (25%), Positives = 131/288 (45%), Gaps = 54/288 (18%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDL--DYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR++EIIN ++ I TP ++ YL  + +   + A+ V+  LE TTL  V    E  + P
Sbjct: 1116 GVPRLREIINVAKKIKTPSLSVYLKPEVNKTKELAKSVQCALEYTTLRSVTHATEVWYDP 1175

Query: 822  DDSFILIKLDMDRI----RLLHLEVDIDSIRYCIER----------------------TR 855
            D    +I+ D++ +     +   ++D D I   + R                       R
Sbjct: 1176 DPMGTIIEEDLEFVLSYYEMPDEDIDPDKISPWLLRIELNREMMVDKKLSMADIANEINR 1235

Query: 856  GISGHLTV----SGHSFLILKPK----DSSK------SFNSKMYQMK---QLLPSVVIKG 898
               G L+          LIL+ +    ++S+      S   +++  K    +L  + ++G
Sbjct: 1236 EFDGDLSCIFSDDNADKLILRLRIINDEASRGEILDDSAGDEVFLKKIESNMLAEMSLRG 1295

Query: 899  VQGINRAVIHEEDV------EGVTKYK---LLVEGDNLRDVMATYGVKGVKCSSNNTYEV 949
            +  IN+  I E  V      +G  ++K   L  +G NL  VM    V   + +SN+  EV
Sbjct: 1296 IPDINKVFIKEVKVNKFDVSDGFKEHKEWMLDTDGVNLLAVMCHEDVDATRTTSNHLTEV 1355

Query: 950  YKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             + LGIEA R  ++ E++ V+   G  +++RH  ++ D MT +G ++ 
Sbjct: 1356 IEVLGIEAVRRALLDELRSVISFDGSYVNYRHLAVLCDTMTYRGHLMA 1403



 Score = 52.8 bits (125), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 21/37 (56%), Positives = 29/37 (78%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            ++ ++ + P+  +G +AAQSIGEP TQMTL TFHFAG
Sbjct: 1071 RFSQSLVAPSEMIGCVAAQSIGEPATQMTLNTFHFAG 1107


>gi|327242125|gb|AEA40841.1| RNA polymerase II largest subunit [Tritrichomonas foetus]
          Length = 1293

 Score =  159 bits (401), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 96/277 (34%), Positives = 147/277 (53%), Gaps = 47/277 (16%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D D+V+FNRQPSLHK+S+M H A +LP  TFR N CV TPYNADFDGDEMN+H+PQT+ 
Sbjct: 374 TDGDIVIFNRQPSLHKMSMMGHHALILPGSTFRLNLCVTTPYNADFDGDEMNLHVPQTQS 433

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
           ARAE               K +M   + ++TP+  + +I   QD +    LL+ K++F N
Sbjct: 434 ARAE--------------VKHIMLVPNQIITPQGNKPIIGLVQDSLLACRLLSLKSSFLN 479

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSW-RSWNPVVFVRTAVI--------WTGKQIFSLI 510
           R + M +                   W RS   +V     +I        W+GKQ+FSL 
Sbjct: 480 RNEMMNL-----------------MMWVRSKQNLVLPPPCIIHPGNKVFLWSGKQVFSLF 522

Query: 511 LKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFY 570
           L       +N +   KG A          D+ +I+R+ +LLAG +DK T+    K+ + +
Sbjct: 523 LP-----SINHDFVQKG-AKEPGSWIPVDDTRIIIRDGQLLAGILDKDTVAKSEKS-LAH 575

Query: 571 ILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           +++  + +++A   +     + + +L +RGFSIG+ D
Sbjct: 576 VVINSWDKNLARDFLSETQMVVNSWLESRGFSIGLID 612



 Score = 86.3 bits (212), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 35/57 (61%), Positives = 44/57 (77%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GF ++ F  GL P EFFFH M GREG++DTA KT++TGY+QRRL KS+E  CV YD
Sbjct: 741 RGFCRHCFLEGLNPPEFFFHAMAGREGIIDTACKTSDTGYIQRRLCKSMESHCVMYD 797



 Score = 68.9 bits (167), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 64/249 (25%), Positives = 112/249 (44%), Gaps = 49/249 (19%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+ E++N +R + TP +T YL+ D+  D D A+ ++  LE ++L ++    E  + P
Sbjct: 1044 GVPRLNEVMNLARVMKTPQVTVYLEPDSRGDKDKAKDIQAELEXSSLKKLVARSEIYYDP 1103

Query: 822  DD----------------------SFILIKLDMDRIRLLHLEVD----IDSIRYCIERTR 855
             D                      S  +++L +++  L+   ++    ++ I        
Sbjct: 1104 SDMNSMIEEDEWARYQGREDSSNLSPWVLRLVLNQAALVDKNINPIEIVEKINILYANVY 1163

Query: 856  GISGHLTVSGHSFLILKPKDSSKSFNSK-----MYQMKQLLPSVVIKGVQGINRAVI--- 907
                +   SG   + ++   + KSF  K      +  + L  S+ +KG++GINRAV+   
Sbjct: 1164 YAITNEGSSGDPIIRIRGLMNDKSFEDKDGRALQFAEQHLYDSLSLKGIEGINRAVMEET 1223

Query: 908  --HEEDVEGVT-----------KYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLG 954
              +E D E              ++ L  EG  LR+V+    V   +  SNN  E  + LG
Sbjct: 1224 TRYEVDPESNAFNTERKECKHKEWVLYTEGSALREVLNHPRVDCRRSVSNNILETLEILG 1283

Query: 955  IEAARSTIM 963
            IEAAR +I+
Sbjct: 1284 IEAARQSIL 1292



 Score = 54.3 bits (129), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 22/39 (56%), Positives = 28/39 (71%)

Query: 1107 REKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            + ++V+  + P   VG +A QSIGEP TQMTL TFHFAG
Sbjct: 997  KTRFVQTIVSPGEMVGTIAGQSIGEPSTQMTLNTFHFAG 1035



 Score = 48.5 bits (114), Expect = 0.024,   Method: Compositional matrix adjust.
 Identities = 38/121 (31%), Positives = 58/121 (47%), Gaps = 21/121 (17%)

Query: 1200 SGHSFLILKPKDSSKSFNSK-----MYQMKQLLPSVVIKGVQGINRAVI-----HEEDVE 1249
            SG   + ++   + KSF  K      +  + L  S+ +KG++GINRAV+     +E D E
Sbjct: 1172 SGDPIIRIRGLMNDKSFEDKDGRALQFAEQHLYDSLSLKGIEGINRAVMEETTRYEVDPE 1231

Query: 1250 GVT-----------KYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTI 1298
                          ++ L  EG  LR+V+    V   +  SNN  E  + LGIEAAR +I
Sbjct: 1232 SNAFNTERKECKHKEWVLYTEGSALREVLNHPRVDCRRSVSNNILETLEILGIEAARQSI 1291

Query: 1299 M 1299
            +
Sbjct: 1292 L 1292


>gi|448336439|ref|ZP_21525538.1| DNA-directed RNA polymerase subunit A' [Natrinema pallidum DSM
           3751]
 gi|445629179|gb|ELY82473.1| DNA-directed RNA polymerase subunit A' [Natrinema pallidum DSM
           3751]
          Length = 975

 Score =  159 bits (401), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 101/275 (36%), Positives = 146/275 (53%), Gaps = 46/275 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 483 DGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQNEEA 542

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR GE +I A QD I+G YLLT  N  FN 
Sbjct: 543 RAE--------------ARVLMRVQEQMLSPRFGENIIGAIQDHISGMYLLTHDNPRFNE 588

Query: 461 AQTMR-IASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q +  + +T I +  +  GI    +               WTG  +FS +L      P 
Sbjct: 589 TQALDLLRATRIDELPEPSGIDDEGT-------------PFWTGYDVFSELL------PD 629

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           + +L+  G   T  +E       V++ + +LL G++ +  +G  G   +   + + +G  
Sbjct: 630 DLDLEFTG---TIGDE-------VVIEDGQLLQGTIAEDEVGEFG-GEIVDTITKVYGNT 678

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVT-PGQG 613
            A   +  +S +    +M+ GFSIGI D T PG+ 
Sbjct: 679 RARIFVNEVSTLAMRAIMHFGFSIGIDDETIPGEA 713



 Score =  110 bits (275), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 83/290 (28%), Positives = 130/290 (44%), Gaps = 43/290 (14%)

Query: 94  QQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDL 153
           ++ S  +I++ + Y  D    PI  GL+D R+G       C TCG++   C GHFG+I+L
Sbjct: 23  REMSATKIITADTY--DDDGFPIDMGLMDPRLGVIDPGLECKTCGKHSGSCNGHFGHIEL 80

Query: 154 PLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKI 213
             PV H+G+ + +  +L+  C+   C+++LL E++   FR +L            + K  
Sbjct: 81  AAPVIHVGFTKLIRRLLRGTCRE--CSKLLLTEDERDEFRDQLDESRKLSRDLNDVTKAA 138

Query: 214 LETTKKVSVCPHCGEINGVVKK---------------------CGLLKISHEKYKNRTKK 252
           +   +K   CP CGEI   +                        G ++   E+   RT  
Sbjct: 139 IRQARKKDRCPFCGEIQYDIDHEKPTTYYEVQQVLTSEYSQSIAGAMQGDEEEGVERT-T 197

Query: 253 KDAIVEDL---LAEYNEAV--KFNPE------IEAHKKFGLIQT----LNPLEVLQLFEA 297
            D + E     L   NE +   F P       IE      L +     L P ++   FE 
Sbjct: 198 PDELAEQTEIELTRVNEILSGSFRPRESQRKAIEKALDIDLTEEDTNKLMPSDIRDWFEN 257

Query: 298 IPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDNDVV 345
           IP EDI +L +N + S+P  +ILT L VPP   RPS+  D   +S++D+ 
Sbjct: 258 IPDEDIEVLGINPDRSRPEWMILTVLPVPPVTARPSITLDNGQRSEDDLT 307



 Score = 92.8 bits (229), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 39/58 (67%), Positives = 49/58 (84%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
             GFV+NS+ SGLTP EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 834 AHGFVENSYTSGLTPREFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELETQYD 891



 Score = 45.8 bits (107), Expect = 0.20,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 29/46 (63%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 65
           +VLM  +  +++PR GE +I A QD I+G YLLT  N  FN  Q +
Sbjct: 547 RVLMRVQEQMLSPRFGENIIGAIQDHISGMYLLTHDNPRFNETQAL 592


>gi|340055761|emb|CCC50082.1| RNA polymerase IIA largest subunit, fragment, partial [Trypanosoma
           vivax Y486]
          Length = 1068

 Score =  158 bits (400), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 92/273 (33%), Positives = 139/273 (50%), Gaps = 39/273 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + DVVLFNRQP+LH++S+M HR +VL + TFR N    TPYNADFDGDEMN+H+PQ+   
Sbjct: 440 NGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNLSCTTPYNADFDGDEMNLHVPQSLLT 499

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE +               +M    N V+P      +   QD + G Y LT K+ F ++
Sbjct: 500 KAELIE--------------MMMVPKNFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFLDK 545

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                +A  L      I  I+K +               +WTGKQ+FSLIL P  + P  
Sbjct: 546 YFVQSVALWLDLWQLPIPAILKPYP--------------LWTGKQVFSLIL-PEVNHPAV 590

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
             +K           F H DS V++R  +LL G + K  +G+    ++ +++  + G D 
Sbjct: 591 QQVKPP---------FPHNDSSVVIRRGQLLCGPITKGIVGA-APGSLIHVIFNEHGSDE 640

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQG 613
               +  + R+T+++L+N GFS+G+ D     G
Sbjct: 641 VARFINGVQRVTTYFLLNFGFSVGVQDTVADAG 673



 Score = 82.8 bits (203), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 34/57 (59%), Positives = 44/57 (77%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +G     +  GL P EFFFHTM GREGL+DTAVKT++TGY+QR+L+K+LED+   YD
Sbjct: 796 RGMANRGYVEGLKPHEFFFHTMAGREGLIDTAVKTSDTGYLQRKLIKALEDVHAAYD 852



 Score = 79.7 bits (195), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 70/248 (28%), Positives = 110/248 (44%), Gaps = 47/248 (18%)

Query: 115 PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSIC 174
           P+  G+ D RMGT   E  C TC +   +C GHFGYI+L  P+F+IG F  V+ +L+ +C
Sbjct: 49  PVRGGINDLRMGTTDFEFACETCHRRHPECPGHFGYIELAEPMFNIGVFDLVLQVLKCVC 108

Query: 175 KNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVK 234
           K  +C  +LL             N + + L+            KK+        +  VVK
Sbjct: 109 K--SCGALLL-------------NTSDTNLL------------KKLQHAAGVNRLRQVVK 141

Query: 235 KCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVK----FNPEIEAHKKFGLIQTL---N 287
            CGL            ++ +++V  L  +   A +      P I   + +G+  TL    
Sbjct: 142 MCGLKCRMSTDMDATEERGESVVGALGTDGIGAARGCGASQPRIS--RIYGIYPTLLVKA 199

Query: 288 PLE----------VLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSV-IS 336
            LE          V Q+ + +   D  L+  +     P DL+LT L VPP  +RP++   
Sbjct: 200 SLEEQDSVWHADTVRQILDRVSDNDARLMGFDPLRCHPRDLVLTVLPVPPPQVRPAISFG 259

Query: 337 DLKSDNDV 344
            LKSD+++
Sbjct: 260 SLKSDDEL 267


>gi|1204085|emb|CAA47897.1| DNA-directed RNA polymerase [Euplotes octocarinatus]
          Length = 511

 Score =  158 bits (400), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 97/257 (37%), Positives = 146/257 (56%), Gaps = 15/257 (5%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           + Q S ++++   LY +D    P  +GLLD R+G + K   C TC  N  DC GH+GYI 
Sbjct: 39  IAQISELEVIECKLYDED-SYVPTAYGLLDPRLGVSTKSDICQTCKSNYVDCPGHYGYIK 97

Query: 153 LPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKK 212
           L LPV+HIG+F+ +I ILQ ICK   C+R LL  EK        +      + R  +++K
Sbjct: 98  LELPVYHIGFFKHIITILQCICKG--CSRFLLS-EKERKIILDKKIKITDPMQRDEIRRK 154

Query: 213 ILETTKKVSVCPHCGEINGVVKK-CGL-LKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
           +++  KKV  C  CG  NG VKK  G+  KI+H+ Y N  K+KD  ++++   +   +K 
Sbjct: 155 MIDDCKKVINCEFCGYFNGTVKKEPGIACKITHDLY-NIKKRKDDEMDNITQSFENILKI 213

Query: 271 NPEIEAHKKFGL---IQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPP 327
           N ++E    +GL    Q +NPL    L + I  +DIPL  MN +   P D+I+  ++VPP
Sbjct: 214 NKDVE----WGLNKMQQDINPLIAYNLLKNIRKDDIPLFDMNGKNINPCDMIVYYIIVPP 269

Query: 328 NCIRPSV-ISDLKSDND 343
            C+RPSV +++ K + D
Sbjct: 270 VCLRPSVAVTETKRNED 286



 Score = 87.4 bits (215), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 36/47 (76%), Positives = 40/47 (85%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDG 387
           D D VLFNRQPSLH+LSIM H+AKV+P +T RFNEC C PYNADFDG
Sbjct: 464 DGDSVLFNRQPSLHRLSIMCHKAKVMPWKTLRFNECCCGPYNADFDG 510


>gi|357483939|ref|XP_003612256.1| DNA-directed RNA polymerase [Medicago truncatula]
 gi|355513591|gb|AES95214.1| DNA-directed RNA polymerase [Medicago truncatula]
          Length = 1864

 Score =  158 bits (400), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 93/271 (34%), Positives = 146/271 (53%), Gaps = 35/271 (12%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D D VLFNRQPSLHK+SIM HR K++P+ TFR N  V +PYNADFDGDEMN+H+PQ+ E
Sbjct: 468 NDGDFVLFNRQPSLHKMSIMGHRIKIMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSFE 527

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE L             +++M  K  +V+P+    ++   QD + G   +T+++ F +
Sbjct: 528 TRAEVL-------------ELMMVPKC-IVSPQANRPVMGIVQDSLLGCRKITKRDTFIS 573

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           +   M           +I    + F  +   P + ++   +WTGKQ+F+LI+      P 
Sbjct: 574 KDVFM-----------NILMWWEDFDGKVPAPTI-LKPEPLWTGKQVFNLII------PK 615

Query: 520 NANLKTKGRAYTANEE--FCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFG 577
             NL      +  NE       D+ V +   ELL G++ K TLG+ G  ++ +++  + G
Sbjct: 616 QINLIRYSSWHNENERGPITPGDTMVRIEKGELLTGTLCKKTLGT-GTGSLIHVIWEEVG 674

Query: 578 EDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
            D A   +     + +++L+ + FSIGIGD 
Sbjct: 675 PDAARKFLGHTQWLVNYWLLQQAFSIGIGDT 705



 Score =  107 bits (266), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 61/178 (34%), Positives = 99/178 (55%), Gaps = 9/178 (5%)

Query: 1226 LLPSVVIKGVQGINRAVIHEEDV------EGVT---KYKLLVEGDNLRDVMATYGVKGVK 1276
            +L  + ++G+  IN+  I    +      EG     ++ L  EG NL  VM    V   +
Sbjct: 1305 MLTEMTLRGIPDINKVFIKNTKIQKFDENEGFKPHEEWMLDTEGVNLLAVMCHEDVDAKR 1364

Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITR 1336
             +SN+  EV + LGIEA R +++ E+++V+   G  +++RH  ++ D MT +G ++ ITR
Sbjct: 1365 TTSNHLIEVIEVLGIEAVRRSLLDELRVVISFDGSYVNYRHLAILCDTMTYRGHLMAITR 1424

Query: 1337 HGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            HG+ + +   +   SFE T D L DAA Y +TD + GV+E I++G    +GTG   LL
Sbjct: 1425 HGINRNETGPMMRCSFEETVDILLDAAVYAETDHLRGVTENIMLGQLAPIGTGECALL 1482



 Score =  100 bits (249), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 42/57 (73%), Positives = 52/57 (91%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKT+ETGY+QRRLVK++ED+ V+YD
Sbjct: 833 RGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDIMVKYD 889



 Score = 82.4 bits (202), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 77/288 (26%), Positives = 135/288 (46%), Gaps = 54/288 (18%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR++EIIN ++ I TP ++ YL  +     + A+ V+  LE TTL  V +  E  + P
Sbjct: 1134 GVPRLREIINVAKRIKTPSLSVYLKPEVCKTKERAKNVQCALEYTTLRSVTQATEVWYDP 1193

Query: 822  DDSFILIKLDMDRIR----LLHLEVDIDSI-----RYCIERTRGISGHLTVS------GH 866
            D    +I+ D+D ++    +   EV +D I     R  + R   +   L+++       H
Sbjct: 1194 DPMGTIIEEDVDFVKSYYEMPDEEVALDKISPWLLRIELNREMMVDKKLSMADIAEKINH 1253

Query: 867  SF---------------LILK--------PK----DSSKSFNSKMYQMK-QLLPSVVIKG 898
             F               LIL+        PK    D S   +  + +++  +L  + ++G
Sbjct: 1254 EFDGDLTCIFNDDNAEKLILRIRIMNDEAPKGDIQDESAEDDVFLKKIESNMLTEMTLRG 1313

Query: 899  VQGINRAVIHEEDV------EGVT---KYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEV 949
            +  IN+  I    +      EG     ++ L  EG NL  VM    V   + +SN+  EV
Sbjct: 1314 IPDINKVFIKNTKIQKFDENEGFKPHEEWMLDTEGVNLLAVMCHEDVDAKRTTSNHLIEV 1373

Query: 950  YKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             + LGIEA R +++ E+++V+   G  +++RH  ++ D MT +G ++ 
Sbjct: 1374 IEVLGIEAVRRSLLDELRVVISFDGSYVNYRHLAILCDTMTYRGHLMA 1421



 Score = 82.0 bits (201), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 75/249 (30%), Positives = 122/249 (48%), Gaps = 48/249 (19%)

Query: 119 GLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPT 178
           GL D R+GT  ++  C TC  ++++C GHFGY++L  P+FHIG+ + V++I++ +C N  
Sbjct: 57  GLSDPRLGTIDRKMKCETCTASMAECPGHFGYLELAKPMFHIGFLKTVLSIMRCVCFN-- 114

Query: 179 CARVLLGEEKAAGFRA-------------KLRNPALSYLVRKSLKKKILETTKKVSVCPH 225
           C+++L  E  +  F+              +++NP       K   +KIL+  K  + C  
Sbjct: 115 CSKILADEVLSRPFKPVLLINDHKFKQAMRIKNP-------KHRLRKILDACKNKTKCEG 167

Query: 226 CGEIN-------GVVKK----CGLL--KISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNP 272
             +I+         +KK    CG    KI+ E  K            ++AEY    K + 
Sbjct: 168 GDDIDLPEHDTKEPLKKSRGGCGAQQPKITIEGMK------------MIAEYKAQRKKSD 215

Query: 273 EIEA-HKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIR 331
           + E   +     QTL+   VL + + I  ED  LL +N + ++P  LIL  L +PP  +R
Sbjct: 216 DQEQLPEPVERKQTLSAERVLGVLKRISDEDCQLLGLNPKYARPDWLILQVLPIPPPPVR 275

Query: 332 PSVISDLKS 340
           PSV+ D  S
Sbjct: 276 PSVMMDTSS 284



 Score = 48.5 bits (114), Expect = 0.025,   Method: Compositional matrix adjust.
 Identities = 19/37 (51%), Positives = 28/37 (75%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            +++++ +     +G +AAQSIGEP TQMTL TFH+AG
Sbjct: 1089 RFLQSLVASGEMIGCVAAQSIGEPATQMTLNTFHYAG 1125


>gi|383620453|ref|ZP_09946859.1| DNA-directed RNA polymerase subunit A' [Halobiforma lacisalsi AJ5]
 gi|448697814|ref|ZP_21698692.1| DNA-directed RNA polymerase subunit A' [Halobiforma lacisalsi AJ5]
 gi|445781180|gb|EMA32041.1| DNA-directed RNA polymerase subunit A' [Halobiforma lacisalsi AJ5]
          Length = 974

 Score =  158 bits (400), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 99/270 (36%), Positives = 143/270 (52%), Gaps = 45/270 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 481 DGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQNEEA 540

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR GE +I A QD I+G YLLT  N  FN 
Sbjct: 541 RAE--------------ARVLMRVQEQILSPRFGENIIGAIQDHISGTYLLTHNNPRFNE 586

Query: 461 AQTMR-IASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q +  + +T I +  +  GI                    WTG  +FS +L      P 
Sbjct: 587 TQALDLLRATRIDELPEPSGIDD-------------EGEPFWTGYDVFSELL------PD 627

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           + NL+  G   T  E+       V++ + +LL G++ +  +G  G   +   + + +G+ 
Sbjct: 628 DLNLEFTG---TVGEK-------VVIEDGQLLEGTIAEDEVGEFG-GEIVDTITKIYGKT 676

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVT 609
            A   +  ++ +    +M+ GFSIGI D T
Sbjct: 677 RARIFINEVASLAMRSIMHFGFSIGIDDET 706



 Score =  113 bits (283), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 87/308 (28%), Positives = 137/308 (44%), Gaps = 55/308 (17%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G I   + + +  ++ S  +I++ + Y  D    PI  GL+D R+G       C TCG++
Sbjct: 10  GSINFGLMEPEEYREMSATKIITADTY--DDDGFPIDMGLMDPRLGVIDPGLECKTCGKH 67

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
              C GHFG+I+L  PV H+G+ + +  +L+  C+   C+++LL E++   FR ++    
Sbjct: 68  SGSCNGHFGHIELAAPVIHVGFTKLIRRLLRGTCRE--CSKLLLTEDERDEFRGQIDESR 125

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEK--------------Y 246
                   + K  +   +K   CPHCGEI           I HEK              Y
Sbjct: 126 KLGRDLNDVTKAAIRQARKKDRCPHCGEIQ--------YDIDHEKPTTYYEVQQVLTSEY 177

Query: 247 KNRTK------------KKDAIVEDL---LAEYNEAV--KFNPE------IEAHKKFGLI 283
             R                D + E+    L+  NE +   F P       IE      L 
Sbjct: 178 SQRIAGAMQGGEDGERMSPDELAEETDIELSRINEILSGSFRPRESQRKAIEKALDVDLT 237

Query: 284 Q----TLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD-- 337
           +     L P ++   FEAIP EDI +L ++ + S+P  +ILT L VPP   RPS+  D  
Sbjct: 238 EEDTNKLMPSDIRDWFEAIPDEDIEVLGIDPDRSRPEWMILTVLPVPPVTARPSITLDNG 297

Query: 338 LKSDNDVV 345
            +S++D+ 
Sbjct: 298 QRSEDDLT 305



 Score = 92.8 bits (229), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 39/58 (67%), Positives = 49/58 (84%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
             GFV+NS+ SGLTP EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 832 AHGFVENSYTSGLTPREFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELETQYD 889



 Score = 46.2 bits (108), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 29/46 (63%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 65
           +VLM  +  +++PR GE +I A QD I+G YLLT  N  FN  Q +
Sbjct: 545 RVLMRVQEQILSPRFGENIIGAIQDHISGTYLLTHNNPRFNETQAL 590


>gi|433592802|ref|YP_007282298.1| DNA-directed RNA polymerase subunit A' [Natrinema pellirubrum DSM
           15624]
 gi|448335247|ref|ZP_21524397.1| DNA-directed RNA polymerase subunit A' [Natrinema pellirubrum DSM
           15624]
 gi|433307582|gb|AGB33394.1| DNA-directed RNA polymerase subunit A' [Natrinema pellirubrum DSM
           15624]
 gi|445617628|gb|ELY71222.1| DNA-directed RNA polymerase subunit A' [Natrinema pellirubrum DSM
           15624]
          Length = 975

 Score =  158 bits (400), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 100/275 (36%), Positives = 145/275 (52%), Gaps = 46/275 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 483 DGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQNEEA 542

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR GE +I A QD I+G YLLT  N  FN 
Sbjct: 543 RAE--------------ARVLMRVQEQMLSPRFGENIIGAIQDHISGMYLLTHDNPRFNE 588

Query: 461 AQTMR-IASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q +  + +T I +  +  G+                    WTG  +FS +L      P 
Sbjct: 589 TQALDLLRATRIDELPEPSGVDD-------------EGEPFWTGHDVFSELL------PD 629

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           + +L+  G   T  +E       V++ + +LL G++ +  +G  G   +   + + +G  
Sbjct: 630 DLDLEFTG---TVGDE-------VVVEDGQLLKGTIAEDEVGEFG-GEIVDTITKVYGNT 678

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVT-PGQG 613
            A   +  +S +    +M+ GFSIGI D T PG+ 
Sbjct: 679 RARIFVNEVSTLAMRAIMHFGFSIGIDDETIPGEA 713



 Score =  112 bits (279), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 86/303 (28%), Positives = 136/303 (44%), Gaps = 43/303 (14%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G I   + + +  ++ S  +I++ + Y  D    PI  GL+D R+G       C TCG++
Sbjct: 10  GAITFGLMEPEEYREMSATKIITADTY--DDDGFPIDMGLMDPRLGVIDPGLECKTCGKH 67

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
              C GHFG+I+L  PV H+G+ + +  +L+  C+   C+R+LL E++   F  +L    
Sbjct: 68  SGSCNGHFGHIELAAPVIHVGFTKLIRRLLRGTCRE--CSRLLLTEDERDEFHDQLDESR 125

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVV---------------------KKCGLL 239
                   + K  +   +K   CP CGEI   +                     +  G +
Sbjct: 126 KLSRDLNDVTKAAIRQARKKDRCPFCGEIQYDIDHEKPTTYYEVQQVLTSEYSQRIAGAM 185

Query: 240 KISHEKYKNRTKKKDAIVEDL---LAEYNEAV--KFNPE------IEAHKKFGLIQT--- 285
           +   E+   RT   D + E     L   NE +   F P       IE      L +    
Sbjct: 186 QGDEEEGIERT-TPDELAEQTEIELTRVNEILSGSFRPRESQRKAIEKALDIDLTEEDTN 244

Query: 286 -LNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDN 342
            L P ++   FEAIP ED+ +L +N E S+P  +ILT L VPP   RPS+  D   +S++
Sbjct: 245 KLMPSDIRDWFEAIPDEDMEVLGINPERSRPEWMILTVLPVPPVTARPSITLDNGQRSED 304

Query: 343 DVV 345
           D+ 
Sbjct: 305 DLT 307



 Score = 92.8 bits (229), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 39/58 (67%), Positives = 49/58 (84%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
             GFV+NS+ SGLTP EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 834 AHGFVENSYTSGLTPREFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELETQYD 891



 Score = 45.8 bits (107), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 29/46 (63%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 65
           +VLM  +  +++PR GE +I A QD I+G YLLT  N  FN  Q +
Sbjct: 547 RVLMRVQEQMLSPRFGENIIGAIQDHISGMYLLTHDNPRFNETQAL 592


>gi|448316023|ref|ZP_21505661.1| DNA-directed RNA polymerase subunit A' [Natronococcus jeotgali DSM
           18795]
 gi|445610369|gb|ELY64143.1| DNA-directed RNA polymerase subunit A' [Natronococcus jeotgali DSM
           18795]
          Length = 975

 Score =  158 bits (400), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 99/270 (36%), Positives = 142/270 (52%), Gaps = 45/270 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 483 DGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQNEEA 542

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR GE +I A QD I+G YLLT  N  FN 
Sbjct: 543 RAE--------------ARVLMRVQEQILSPRFGENIIGAIQDHISGMYLLTHDNPRFNE 588

Query: 461 AQTMR-IASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q +  + +T I +  +  G+                    WTG  +FS +L      P 
Sbjct: 589 TQALDLLRATRIDELPEPSGVDD-------------EGEPFWTGYDVFSELL------PD 629

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           + NL+  G   T  ++       V++ N +LL G++ +  +G  G   +   + + +G  
Sbjct: 630 DLNLEFTG---TVGDD-------VVIENGQLLEGTVAEDEVGEFG-GEIVDTITKVYGNT 678

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVT 609
            A   +  +S +    +M+ GFSIGI D T
Sbjct: 679 RARIFVNEVSTLAMRAIMHFGFSIGIDDET 708



 Score =  116 bits (290), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 90/310 (29%), Positives = 139/310 (44%), Gaps = 57/310 (18%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G I   + + +  ++ S  +I++ + Y  D    PI  GL+D R+G       C TCG++
Sbjct: 10  GSINFGLMEPEEYREMSATKIITADTY--DDDGFPIDMGLMDPRLGVIDPGLECKTCGKH 67

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
              C GHFG+I+L  PV H+G+ + +  +L+  C+   C+R+LL E++   F  ++ +  
Sbjct: 68  SGSCNGHFGHIELAAPVIHVGFTKLIRRLLRGTCRE--CSRLLLTEDERGEFYDQIDDSR 125

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEK--------------Y 246
                   + K  +   +K   CPHCGEI           I HEK              Y
Sbjct: 126 KLGRDLNDVTKAAIRQARKKDRCPHCGEIQ--------YDIDHEKPTTYYEVQQVLASEY 177

Query: 247 KNRTK-----KKDAIVE----DLLAEYNE----------AVKFNPE------IEAHKKFG 281
             R        ++A +E    D LAE  E          +  F P       IE      
Sbjct: 178 SQRIAGAMQGDEEAGIERTTPDELAEKTEIDIGRVNEILSGSFRPREGQRKAIEKALDID 237

Query: 282 LIQT----LNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD 337
           L +     L P ++   FEAIP ED+ +L +N E S+P  +ILT L VPP   RPS+  D
Sbjct: 238 LTEEDTNKLMPSDIRDWFEAIPDEDMEVLGINPERSRPEWMILTVLPVPPVTARPSITLD 297

Query: 338 --LKSDNDVV 345
              +S++D+ 
Sbjct: 298 NGQRSEDDLT 307



 Score = 92.8 bits (229), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 39/57 (68%), Positives = 49/57 (85%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFV+NS+ SGLTP EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 835 HGFVENSYTSGLTPREFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELETQYD 891



 Score = 45.4 bits (106), Expect = 0.22,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 29/46 (63%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 65
           +VLM  +  +++PR GE +I A QD I+G YLLT  N  FN  Q +
Sbjct: 547 RVLMRVQEQILSPRFGENIIGAIQDHISGMYLLTHDNPRFNETQAL 592


>gi|154414043|ref|XP_001580050.1| RNA polymerase II [Trichomonas vaginalis G3]
 gi|121914263|gb|EAY19064.1| RNA polymerase II [Trichomonas vaginalis G3]
          Length = 1661

 Score =  158 bits (400), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 87/267 (32%), Positives = 143/267 (53%), Gaps = 31/267 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+D+V+FNRQPSLHK+S+M HRA ++  RTFR N C  TPYNADFDGDEMN+H+PQ++ A
Sbjct: 451 DDDIVIFNRQPSLHKMSMMGHRALIMSGRTFRLNLCDTTPYNADFDGDEMNLHVPQSQTA 510

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R E               + +MA    +++P+  + +I   QD + G  LL++++ F  R
Sbjct: 511 RTE--------------VRHIMAVPKQIISPQANKPVIGLVQDALLGCRLLSKRDTFLTR 556

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M +   L      I             P   ++   +W+GKQ+FSL L       ++
Sbjct: 557 NQVMNLMMWLPTTKDTILP-----------PPCILKPVQLWSGKQVFSLFLP-----KIS 600

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            N  ++             D +VI+R+  LLAG +DK T+    + ++ ++++  +  ++
Sbjct: 601 HNSYSQDANKMDQNSIPLADRHVIIRDGNLLAGILDKKTVAR-SEGSLIHVVINSYNTNI 659

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           A   + +   + + +L +RGFSIG+ D
Sbjct: 660 AKDFLNQTQLIVNNWLEHRGFSIGLID 686



 Score =  118 bits (295), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 91/317 (28%), Positives = 156/317 (49%), Gaps = 38/317 (11%)

Query: 1109 KYVRAQIEPATAVGAL----------AAQSIGEPGTQMTLKTFHFAGEVCEYIEEVFVPD 1158
            K VRAQIE A+    +            ++I EP T+       + G     +E+  + D
Sbjct: 1152 KAVRAQIESASFKKFVIKAEIYYDPNPEETIIEPDTKWINTRIRYGG-----VEDRELQD 1206

Query: 1159 DSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGH--LTVSGHSFLILKP----KDS 1212
             +  +++ +++R  ++    +I+SI   +++ +G+ G     +      I++     KD 
Sbjct: 1207 LAPWVLRFEINREEMI--ASNIESISDIVQKIKGMYGDKFFVIGDDDARIIRMQARLKDE 1264

Query: 1213 SKSFNSKMYQMK----QLLPSVVIKGVQGINRAVIHEE--------DVEGVTKYK---LL 1257
               F   +  ++    Q+  S  +KG+ GI+R  I+          +  G  K K   L 
Sbjct: 1265 QAEFAMDVKFLRETEQQMYKSFTLKGIPGISRVKINSAAEKMFLNPETHGFDKEKVSCLY 1324

Query: 1258 VEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRH 1317
             EG   R++++   V  V   +N+ Y+V   LGIEAAR ++  E+ L+MEN G +++ RH
Sbjct: 1325 TEGTAFREILSLDHVDTVHTITNDIYQVCDVLGIEAARHSLSYEMMLIMENAGAALNRRH 1384

Query: 1318 PMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSEC 1377
              L+AD MT  G +  ++RHG+ K     L  AS+E T+D  FDAA + + D +  VS  
Sbjct: 1385 LDLLADTMTQYGVLYPVSRHGINKTPTGTLMRASYEMTNDVFFDAAVFSEIDYMRDVSSN 1444

Query: 1378 IIMGLPMNVGTGLIKLL 1394
            II G P   GTG++++L
Sbjct: 1445 IIAGKPSRAGTGIVEVL 1461



 Score = 93.6 bits (231), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 77/246 (31%), Positives = 109/246 (44%), Gaps = 51/246 (20%)

Query: 119 GLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPT 178
           GL D RMGT  +E  C TCG+N  DC GHFGYI L  P FH+G+      +LQ +C    
Sbjct: 50  GLSDLRMGTQTRERLCDTCGRNQEDCPGHFGYIRLAEPFFHVGFLPHCYKLLQMVCHK-- 107

Query: 179 CARVLLGEEKAAGFRAKLRNPALSYLV-RKSLKKKILETTKKVSVCPHCGEINGVVKKCG 237
           C RVL              +P + Y+V     K + L+  +K++             K G
Sbjct: 108 CGRVL----------CSYSDPEIQYIVTHYKGKNRFLKLFEKIA------------SKSG 145

Query: 238 LLKISHEKYKNRTKKKDAIVEDLLAE------YNEAVKFN-------PEIEAHKKFGLIQ 284
             K  H        + D  +++   E      ++E V+         P IE  K F LI+
Sbjct: 146 --KCQHSPDLKNPNEPDVCLDERFWELVNGDSHSEHVRVKKPCNAAVPAIEQGKDF-LIK 202

Query: 285 T----------LNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSV 334
                      L+   VL++FE I  +D+ LL  N + S P  +IL  L VPP  +RP V
Sbjct: 203 LKDVSKTEEDYLSAEVVLRIFENISDQDVRLLGFNPKRSHPKWMILKILPVPPLAVRPQV 262

Query: 335 ISDLKS 340
           +S  +S
Sbjct: 263 VSPGQS 268



 Score = 85.5 bits (210), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 36/57 (63%), Positives = 46/57 (80%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GF +NS+ +GLTP EF FH MGGR G++DTA KT++TGY+QRRLVKS+E   V YD
Sbjct: 815 RGFCKNSYIAGLTPPEFLFHAMGGRTGIIDTACKTSDTGYIQRRLVKSMESHHVAYD 871



 Score = 84.3 bits (207), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 73/280 (26%), Positives = 129/280 (46%), Gaps = 50/280 (17%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+ E++N +++I TP +T   ++D   D +  + V+ ++E  +  +     E  + P
Sbjct: 1117 GVPRLNELMNLAKHIRTPSVTVEFERDVAKDEEIVKAVRAQIESASFKKFVIKAEIYYDP 1176

Query: 822  DDSFILIKLDMD----RIR---------------LLHLEVD--------IDSIRYCIERT 854
            +    +I+ D      RIR               +L  E++        I+SI   +++ 
Sbjct: 1177 NPEETIIEPDTKWINTRIRYGGVEDRELQDLAPWVLRFEINREEMIASNIESISDIVQKI 1236

Query: 855  RGISGH--LTVSGHSFLILKP----KDSSKSFNSKMYQMK----QLLPSVVIKGVQGINR 904
            +G+ G     +      I++     KD    F   +  ++    Q+  S  +KG+ GI+R
Sbjct: 1237 KGMYGDKFFVIGDDDARIIRMQARLKDEQAEFAMDVKFLRETEQQMYKSFTLKGIPGISR 1296

Query: 905  AVIHEE--------DVEGVTKYK---LLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTL 953
              I+          +  G  K K   L  EG   R++++   V  V   +N+ Y+V   L
Sbjct: 1297 VKINSAAEKMFLNPETHGFDKEKVSCLYTEGTAFREILSLDHVDTVHTITNDIYQVCDVL 1356

Query: 954  GIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
            GIEAAR ++  E+ L+MEN G +++ RH  L+AD MT  G
Sbjct: 1357 GIEAARHSLSYEMMLIMENAGAALNRRHLDLLADTMTQYG 1396



 Score = 55.5 bits (132), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/41 (53%), Positives = 30/41 (73%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            + ++++ R+ + P   VG +A QSIGEP TQMTL TFHFAG
Sbjct: 1068 SIKDRFYRSIVAPGEMVGTIAGQSIGEPSTQMTLNTFHFAG 1108


>gi|413915240|gb|AFW21482.1| RNA polymerase II largest subunit [Balansia obtecta]
          Length = 1760

 Score =  158 bits (400), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 88/276 (31%), Positives = 154/276 (55%), Gaps = 32/276 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D ++FNRQPSLHK S+M HR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQTEE 
Sbjct: 450 DGDYIIFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQTEET 509

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE             R   L+ N  N+V+P+    L+   QD + G Y + +++ F ++
Sbjct: 510 RAEV------------RELCLVPN--NIVSPQKNGPLMGIVQDSLAGAYKICRRDTFIDK 555

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              M     ++    +  G+I +       P + ++    WTGKQ+ S+++   ++  ++
Sbjct: 556 EMVM----NMMLWVPNWDGVIPQ-------PAI-LKPRPRWTGKQLISMVIP--KEISLH 601

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           +   + G+    N +   +D+ +++++ ELL G + K  +GS     + ++   + G D 
Sbjct: 602 SPESSGGQ---DNADIPLKDTGLLIQSGELLYGLLKKKNIGSAA-GGIVHLSYNELGPDG 657

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           A+  +  + ++ +++L+N G SIGIGD  P +  ++
Sbjct: 658 AMAFLNGVQQVVTYWLLNNGHSIGIGDTVPDKQTIE 693



 Score =  107 bits (268), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 78/284 (27%), Positives = 136/284 (47%), Gaps = 39/284 (13%)

Query: 1145 GEVCEYIEEVF-VPDDS--------FILIKLDMDRIRLLHLEVDIDSIRYCI--ERTRGI 1193
             E  + +E  F +PDDS          L+++ +DR +LL  E+ ID +   I  E    +
Sbjct: 1180 AEDMDMVESYFLIPDDSQDTIDQQSRWLLRITLDRQKLLDKEIKIDDVAQRIKEEYPNDL 1239

Query: 1194 SGHLTVSGHSFLIL----------KPKDSSKSFNSKMYQMK---QLLPSVVIKGVQGINR 1240
            +   + +     ++          K +D  K     +   +    LL ++ ++GV G+ R
Sbjct: 1240 AVIFSDNNADEQVIRIRTIRTEDEKDEDGEKKIEDDVMLKRLEAHLLDTLTLRGVPGVER 1299

Query: 1241 AV---------------IHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEV 1285
            A                I ++D +  T++ L   G  LRDV+A  GV   +  +N+ +++
Sbjct: 1300 AFLTKGTRLVIDDDGSEIAKKDSDKCTQWYLDTSGSALRDVLAVEGVDPTRTYTNDLWQI 1359

Query: 1286 YKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKES 1345
             +  GIEAARS ++ E+  V+   G  ++ RH  L+ D+MT +G +  +TRHG+ +    
Sbjct: 1360 VEVFGIEAARSALVKELTNVLAFDGSYVNHRHIALLVDVMTYRGSISAVTRHGINRADTG 1419

Query: 1346 VLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
             L   SFE T + L +AA  G+ D   G+SE +++G    +GTG
Sbjct: 1420 ALMRCSFEETVEILLEAAATGELDDCRGISENVMLGQLAPMGTG 1463



 Score =  103 bits (256), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 46/63 (73%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QRRLVK+LEDL  
Sbjct: 807 DYSPEARGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDLSA 866

Query: 666 QYD 668
           +YD
Sbjct: 867 RYD 869



 Score = 87.8 bits (216), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 74/296 (25%), Positives = 133/296 (44%), Gaps = 68/296 (22%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKD-------------------------TDLDYARI 798
            GVPR+KEI+N +++I TP +  YL+                           T++ Y   
Sbjct: 1114 GVPRLKEILNLAKDIKTPSMAVYLNTHLGTQEQAKKLRSLVEYTNLRSITSVTEIYYDPD 1173

Query: 799  VKGRLERTTLGEVCEYIEEVF-VPDDS--------FILIKLDMDRIRLLHLEVDIDSIRY 849
            ++G    T + E  + +E  F +PDDS          L+++ +DR +LL  E+ ID +  
Sbjct: 1174 IQG----TNIAEDMDMVESYFLIPDDSQDTIDQQSRWLLRITLDRQKLLDKEIKIDDVAQ 1229

Query: 850  CI--ERTRGISGHLTVSGHSFLIL----------KPKDSSKSFNSKMYQMK---QLLPSV 894
             I  E    ++   + +     ++          K +D  K     +   +    LL ++
Sbjct: 1230 RIKEEYPNDLAVIFSDNNADEQVIRIRTIRTEDEKDEDGEKKIEDDVMLKRLEAHLLDTL 1289

Query: 895  VIKGVQGINRAV---------------IHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
             ++GV G+ RA                I ++D +  T++ L   G  LRDV+A  GV   
Sbjct: 1290 TLRGVPGVERAFLTKGTRLVIDDDGSEIAKKDSDKCTQWYLDTSGSALRDVLAVEGVDPT 1349

Query: 940  KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            +  +N+ +++ +  GIEAARS ++ E+  V+   G  ++ RH  L+ D+MT +G +
Sbjct: 1350 RTYTNDLWQIVEVFGIEAARSALVKELTNVLAFDGSYVNHRHIALLVDVMTYRGSI 1405



 Score = 67.0 bits (162), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 33/75 (44%), Positives = 46/75 (61%), Gaps = 3/75 (4%)

Query: 110 DPQRT-PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVIN 168
           D  RT P   GL D  +G+  +   C TC Q +SDC GHFG+I+L  PV+H G+ + V  
Sbjct: 44  DESRTKPRDGGLNDPLLGSIDRGFKCKTCTQAMSDCPGHFGHIELAKPVYHPGFIKKVKK 103

Query: 169 ILQSICKNPTCARVL 183
           IL+ +C N  C++VL
Sbjct: 104 ILEIVCHN--CSKVL 116



 Score = 55.5 bits (132), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/39 (61%), Positives = 29/39 (74%)

Query: 1107 REKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            + ++ R+ + P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1067 QNRWDRSFVSPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1105


>gi|242078217|ref|XP_002443877.1| hypothetical protein SORBIDRAFT_07g003680 [Sorghum bicolor]
 gi|241940227|gb|EES13372.1| hypothetical protein SORBIDRAFT_07g003680 [Sorghum bicolor]
          Length = 1857

 Score =  158 bits (400), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 97/272 (35%), Positives = 149/272 (54%), Gaps = 37/272 (13%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D D VLFNRQPSLHK+SIM HR K++P+ TFR N  V +PYNADFDGDEMN+H+PQ+ E
Sbjct: 449 NDGDFVLFNRQPSLHKMSIMGHRIKIMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSFE 508

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE L             +++M  K  +V+P++   ++   QD + G   +T+++    
Sbjct: 509 TRAEVL-------------ELMMVPKC-IVSPQSNRPVMGIVQDTLLGCRKITKRDTLIE 554

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           +   M I    +    D  G I         P + ++   IWTGKQ+F+LI+      P 
Sbjct: 555 KDVFMNI----LMWWQDFDGKIPA-------PAI-LKPRPIWTGKQVFNLII------PK 596

Query: 520 NANLKTKGRAYTANEE---FCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
             NL  +  A+ + EE       D+ V +   ELL+G++ K +LG+ G  ++ +I+  + 
Sbjct: 597 QINL-IRFSAWHSEEEKGFITPGDTMVRIEKGELLSGTLCKKSLGT-GTGSLIHIIWEEV 654

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           G D A   +     + +++L+  GFSIGIGD 
Sbjct: 655 GPDAARKFLGHTQWLVNYWLLQNGFSIGIGDT 686



 Score =  108 bits (271), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 59/173 (34%), Positives = 96/173 (55%), Gaps = 9/173 (5%)

Query: 1226 LLPSVVIKGVQGINRAVIHE---------EDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 1276
            +L  + ++G+  IN+  I E         E  +   ++ L  EG NL  VM    V   +
Sbjct: 1286 MLTEMALRGIPDINKVFIKEGKVNTFYQDEGFKAANEWMLDTEGVNLLAVMCHEDVDATR 1345

Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITR 1336
             +SN+  EV + LGIEA R +++ E+++V+   G  +++RH  ++ D MT +G ++ ITR
Sbjct: 1346 TTSNHLIEVIEVLGIEAVRRSLLDELRVVISFDGSYVNYRHLAILCDTMTYRGHLMAITR 1405

Query: 1337 HGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
            HG+ +     L   SFE T D L DAA Y ++D + GV+E I++G    +GTG
Sbjct: 1406 HGINRNDTGPLMRCSFEETVDILLDAAVYAESDHLRGVTENIMLGQLAPIGTG 1458



 Score =  100 bits (249), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 42/57 (73%), Positives = 52/57 (91%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKT+ETGY+QRRLVK++ED+ V+YD
Sbjct: 814 RGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDIMVKYD 870



 Score = 87.0 bits (214), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 71/253 (28%), Positives = 130/253 (51%), Gaps = 38/253 (15%)

Query: 82  LIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQR-TPIPHGLLDRRMGTNQKEANCTTCGQN 140
           L++  +   D ++Q S +QI     + +  +R  P P GL D R+GT  ++  C TC   
Sbjct: 17  LVQFGILSPDEIRQMSVVQIE----HAETMERGKPKPGGLSDPRLGTIDRKIKCETCMAG 72

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNP 199
           +++C GHFG+++L  P+FHIG+ + V++I++ +C N  C+++L  E++    +A K+RNP
Sbjct: 73  MAECPGHFGHLELAKPMFHIGFIKTVLSIMRCVCFN--CSKILADEDETKFKQALKIRNP 130

Query: 200 ALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNR----TKKKDA 255
                  K+  K+I +  K   VC    +++  V++    + + E  K R     ++ + 
Sbjct: 131 -------KNRLKRIYDACKSKKVCAGGDDLD--VQE----QDTDEPVKKRGGCGAQQPNI 177

Query: 256 IVE--DLLAEYNEAVKFN------PEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLL 307
            V+   ++AE+    K +      PE    K     Q L+   VL + + I  ED  LL 
Sbjct: 178 TVDGMKMVAEFKAPKKKSDDQDQLPEPVERK-----QILSAERVLNVLKRISDEDCLLLG 232

Query: 308 MNAELSKPSDLIL 320
           +N + ++P  +IL
Sbjct: 233 LNPKYARPDWMIL 245



 Score = 80.9 bits (198), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 74/288 (25%), Positives = 133/288 (46%), Gaps = 54/288 (18%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDL--DYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR++EIIN ++ I TP ++ YL  + +   + A+ V+  LE TTL  V    E  + P
Sbjct: 1115 GVPRLREIINVAKKIKTPSLSVYLKPEVNQKKELAKNVQCALEYTTLRSVTHATEIWYDP 1174

Query: 822  DDSFILIKLDMDRIR----LLHLEVDIDSI-----RYCIERTRGISGHLTVS------GH 866
            D    +I+ D + ++    +   ++D D I     R  + R   +   L+++        
Sbjct: 1175 DPLGTIIEEDAEFVQSYYEMPDEDIDPDKISPWLLRIELNREMMVDKKLSMADIADKINR 1234

Query: 867  SF---------------LILK--------PK----DSSKSFNSKMYQMK-QLLPSVVIKG 898
             F               LIL+        PK    D S   +  + +++  +L  + ++G
Sbjct: 1235 EFDDDLSCIFNDDNADKLILRIRITNDEAPKGEIQDESAEDDVFLKKIEGNMLTEMALRG 1294

Query: 899  VQGINRAVIHE---------EDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEV 949
            +  IN+  I E         E  +   ++ L  EG NL  VM    V   + +SN+  EV
Sbjct: 1295 IPDINKVFIKEGKVNTFYQDEGFKAANEWMLDTEGVNLLAVMCHEDVDATRTTSNHLIEV 1354

Query: 950  YKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             + LGIEA R +++ E+++V+   G  +++RH  ++ D MT +G ++ 
Sbjct: 1355 IEVLGIEAVRRSLLDELRVVISFDGSYVNYRHLAILCDTMTYRGHLMA 1402



 Score = 52.0 bits (123), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 20/37 (54%), Positives = 29/37 (78%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            +++++ + P   +G +AAQSIGEP TQMTL TFH+AG
Sbjct: 1070 RFLQSLVAPGEMIGCVAAQSIGEPATQMTLNTFHYAG 1106


>gi|448589494|ref|ZP_21649653.1| DNA-directed RNA polymerase subunit A' [Haloferax elongans ATCC
           BAA-1513]
 gi|445735922|gb|ELZ87470.1| DNA-directed RNA polymerase subunit A' [Haloferax elongans ATCC
           BAA-1513]
          Length = 973

 Score =  158 bits (400), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 95/268 (35%), Positives = 142/268 (52%), Gaps = 45/268 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 484 DGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQNEEA 543

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR GE +I A QD I+G YLLT  N  F  
Sbjct: 544 RAE--------------ARVLMRVQEQILSPRFGENIIGAIQDHISGTYLLTHDNPHFVE 589

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q + +      DT      +   +    +   +      WTG+QIFS +L      P +
Sbjct: 590 TQALDLLRATRVDT------LPEPAGEDDDGTPY------WTGQQIFSELL------PDD 631

Query: 521 ANLKTKGRAYTANEEFCHR-DSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            N+           EF  +    V++ + +LL G++D+  +G+ G   +  +L +D+ + 
Sbjct: 632 LNM-----------EFTSKVGDTVVIEDGQLLEGTIDEDAVGAFG-GEIVDVLAKDYSKT 679

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            +   +  ++ +    +M+ G SIGI D
Sbjct: 680 RSRIFINEIASLAMRAIMHFGLSIGIDD 707



 Score =  105 bits (263), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 81/296 (27%), Positives = 127/296 (42%), Gaps = 60/296 (20%)

Query: 97  SHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP 156
           S  ++++ + Y  D    PI  GL+D R+G       C TCGQ+   C GHFG+I+L  P
Sbjct: 26  SATKVITADTY--DDDGYPIDMGLMDPRLGVIDPGLQCRTCGQHSGSCNGHFGHIELAAP 83

Query: 157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKL-RNPALSYLVRKSLKKKILE 215
           V H+G+ + +  +L+S C+   C R+ L +E+A  +R KL R   L       +K  + +
Sbjct: 84  VIHVGFTKLIRRLLRSTCRE--CGRLALTQEEADDYRDKLGRTKELGDDWSDVMKSAVRQ 141

Query: 216 TTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVK------ 269
             +K   CPHC      +K        HEK     + ++ +  D      EA++      
Sbjct: 142 -ARKAHRCPHCSSPQHDIK--------HEKPTTYYEVQNVLAGDFSERIAEAMQPDPDDE 192

Query: 270 ----------------------------FNP----EIEAHKKFGL------IQTLNPLEV 291
                                       F P         K  G+      +  L P ++
Sbjct: 193 DDEGISPVDLAEKADLPAERVNQVLAGEFRPVGDDRKALEKALGIDLTEEDMNKLMPSDI 252

Query: 292 LQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDNDVV 345
              FE IP ED+  L ++ E S+P  +ILT L VPP   RPS+  D   +S++D+ 
Sbjct: 253 RDWFEDIPDEDLITLGIDPERSRPEWMILTVLPVPPVTARPSITLDNGQRSEDDLT 308



 Score = 92.8 bits (229), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 44/81 (54%), Positives = 59/81 (72%), Gaps = 7/81 (8%)

Query: 597 MNRGFS------IGIGDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAET 649
           +NRG+          GD++    GFV+NS+ +GLTP EFFFH MGGREGLVDTAV+T+++
Sbjct: 814 INRGYEERTLSHYQKGDLSAEAHGFVENSYCAGLTPREFFFHAMGGREGLVDTAVRTSKS 873

Query: 650 GYMQRRLVKSLEDLCVQYDMS 670
           GY+QRRL+ +L +L  QYD S
Sbjct: 874 GYLQRRLINALSELEAQYDGS 894



 Score = 43.1 bits (100), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 20/46 (43%), Positives = 28/46 (60%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 65
           +VLM  +  +++PR GE +I A QD I+G YLLT  N  F   Q +
Sbjct: 548 RVLMRVQEQILSPRFGENIIGAIQDHISGTYLLTHDNPHFVETQAL 593


>gi|339252982|ref|XP_003371714.1| DNA-directed RNA polymerase II subunit RPB1 [Trichinella spiralis]
 gi|316967997|gb|EFV52341.1| DNA-directed RNA polymerase II subunit RPB1 [Trichinella spiralis]
          Length = 1816

 Score =  158 bits (400), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 94/279 (33%), Positives = 153/279 (54%), Gaps = 39/279 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND+V+FNRQP+LHK+S+M HR +VLP  TFR N  V TPYNADFDGDEMN+HLPQ++EA
Sbjct: 434 DNDIVIFNRQPTLHKMSMMGHRVRVLPWSTFRLNLSVTTPYNADFDGDEMNLHLPQSQEA 493

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE L    +L ++             ++TP+    ++   QD +T    LT+++ F +R
Sbjct: 494 KAEIL----ELCMIPRM----------ILTPQANRPVMGIVQDTLTACRKLTKRDVFIDR 539

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           A              D+  ++ +++ +   P + V+   +WTGKQ+FS+I+      P N
Sbjct: 540 ATMF-----------DLLMLLPKWNGKMPIPTI-VKPKPLWTGKQLFSMII------PGN 581

Query: 521 ANLKTKGRAYTANEE------FCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLR 574
            NL      +  +E+          D+ V++ + +LL+G + K TLG+    ++ +I+  
Sbjct: 582 VNLIRTHSTHPDDEDNGPYKWISPGDTKVLIEHGQLLSGILCKKTLGASA-GSLMHIVTL 640

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQG 613
           + G  +A +    +  + + +L+  G SIGIGD    Q 
Sbjct: 641 ELGCYIAASFYSDIQVVVNTWLLTEGHSIGIGDTIADQA 679



 Score =  101 bits (252), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 42/57 (73%), Positives = 53/57 (92%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NS+ +GLTP+EFFFHTMGGREGL+DTAVKTAETGY+QRRL+K++E + V YD
Sbjct: 802 RGFVENSYLAGLTPSEFFFHTMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVAYD 858



 Score = 83.6 bits (205), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 66/233 (28%), Positives = 114/233 (48%), Gaps = 33/233 (14%)

Query: 119 GLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPT 178
           GL+D R G   + + C TC   ++DC GHFG+++L  PV+H+G+   V+ +L+ +C    
Sbjct: 50  GLMDPRQGVIDRRSRCQTCAGTIADCPGHFGHLELSKPVYHVGFLPKVLKVLRCVCF--Y 107

Query: 179 CARVLLGEE--KAAGFRAKLRNPALSYLVRKSLK--------KKILETTKKV--SVCPHC 226
           C+R+L+ +   K     AK +     Y  RK L         K+I E  +K    +    
Sbjct: 108 CSRLLVNKNSTKVEAALAKTK-----YSCRKRLTTIYDLCKVKRICEGIEKSPEQLAVDR 162

Query: 227 GEI---NGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLI 283
           GE+   NG   +         +Y+   K+   +  +++AE+    K N E++  K     
Sbjct: 163 GELVEENGEDSQQAKAPTGCGRYQPSYKR---VGLEVIAEWK---KTNEEMQEKK----- 211

Query: 284 QTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVIS 336
            TL+   VL++ + I  ED   L  + + S+P  +I+  L VPP  +RP+V++
Sbjct: 212 MTLSAERVLEILKGISDEDAITLGFHPKYSRPDWMIIQVLPVPPLSVRPAVVT 264



 Score = 77.4 bits (189), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 61/195 (31%), Positives = 97/195 (49%), Gaps = 37/195 (18%)

Query: 1218 SKMYQMKQLLPSVVIKGVQGINRAVIHEE-DVEGVTKYKLLVEGDNLRDVMATYGVKGVK 1276
            SK+Y    LLPS   K      R VI+ + + + V+++ L  +G +L  V++   V   +
Sbjct: 1260 SKVYM---LLPSSDDK-----KRFVINADGEYQAVSEWILETDGTSLLKVLSDPAVDATR 1311

Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITR 1336
              SN+  E+++ LGIEA R  +  EIK V+   G  +++RH  L+ D+MT+KG V     
Sbjct: 1312 TYSNHICEIFEVLGIEAVRKAVEKEIKHVISFDGSYVNYRHLALLCDIMTAKGHV----- 1366

Query: 1337 HGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL-- 1394
                                D L +AA + + D + GVSE I++G    +GTG   LL  
Sbjct: 1367 --------------------DILMEAAAHAEEDLLLGVSESIMLGQLARLGTGSFDLLLD 1406

Query: 1395 -QAVPRSEPVPRTLL 1408
             QA  ++  VP +L+
Sbjct: 1407 VQACKQAMEVPMSLV 1421



 Score = 61.2 bits (147), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 40/115 (34%), Positives = 65/115 (56%), Gaps = 9/115 (7%)

Query: 882  SKMYQMKQLLPSVVIKGVQGINRAVIHEE-DVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
            SK+Y    LLPS   K      R VI+ + + + V+++ L  +G +L  V++   V   +
Sbjct: 1260 SKVYM---LLPSSDDK-----KRFVINADGEYQAVSEWILETDGTSLLKVLSDPAVDATR 1311

Query: 941  CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
              SN+  E+++ LGIEA R  +  EIK V+   G  +++RH  L+ D+MT+KG V
Sbjct: 1312 TYSNHICEIFEVLGIEAVRKAVEKEIKHVISFDGSYVNYRHLALLCDIMTAKGHV 1366



 Score = 52.8 bits (125), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 22/33 (66%), Positives = 27/33 (81%)

Query: 1113 AQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            AQ++P   VGAL+A S+GEP TQMTL TFH+AG
Sbjct: 1061 AQVQPGEMVGALSALSLGEPATQMTLNTFHYAG 1093


>gi|225459758|ref|XP_002285900.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB1-like [Vitis
           vinifera]
          Length = 1848

 Score =  158 bits (400), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 95/271 (35%), Positives = 147/271 (54%), Gaps = 35/271 (12%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D D VLFNRQPSLHK+SIM HR K++P+ TFR N  V +PYNADFDGDEMN+H+PQ+ E
Sbjct: 450 NDGDFVLFNRQPSLHKMSIMGHRIKIMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSFE 509

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE L             +++M  K  +V+P++   ++   QD + G   +T+++ F  
Sbjct: 510 TRAEVL-------------ELMMVPKC-IVSPQSNRPVMGIVQDTLLGCRKITKRDTFIE 555

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           +   M I    +    D  G I         P + ++   +WTGKQ+F+LI+      P 
Sbjct: 556 KDVFMNI----LMWWEDFDGKIPA-------PAI-LKPRPLWTGKQVFNLII------PK 597

Query: 520 NANLKTKGRAYTANEE--FCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFG 577
             NL      ++ +E       D+ V +   ELLAG++ K TLG+    ++ +++  + G
Sbjct: 598 QINLLRTSAWHSESETGFITPGDTQVRIEKGELLAGTLCKKTLGT-STGSLIHVIWEEVG 656

Query: 578 EDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
            D A   +     + +++L+  GFSIGIGD 
Sbjct: 657 PDAARKFLGHTQWLVNYWLLQNGFSIGIGDT 687



 Score =  105 bits (262), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 59/173 (34%), Positives = 97/173 (56%), Gaps = 9/173 (5%)

Query: 1226 LLPSVVIKGVQGINRAVIHE------EDVEGV---TKYKLLVEGDNLRDVMATYGVKGVK 1276
            +L  + ++G+  IN+  I        ++ EG     ++ L  EG NL  VM    V   +
Sbjct: 1287 MLTEMALRGIPDINKVFIKSGKVNKFDESEGFKPEVEWMLDTEGVNLLAVMCHEDVDARR 1346

Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITR 1336
             +SN+  EV + LGIEA R +++ E+++V+   G  +++RH  ++ D MT +G ++ ITR
Sbjct: 1347 TTSNHLIEVIEVLGIEAVRRSLLDELRVVISFDGSYVNYRHLAILCDTMTYRGHLMAITR 1406

Query: 1337 HGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
            HG+ +     +   SFE T D L DAA Y +TD + GV+E I++G    +GTG
Sbjct: 1407 HGINRNDTGPMMRCSFEETVDILLDAAVYAETDFLRGVTENIMLGQLAPIGTG 1459



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 42/57 (73%), Positives = 52/57 (91%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKT+ETGY+QRRLVK++ED+ V+YD
Sbjct: 815 RGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDIMVKYD 871



 Score = 98.6 bits (244), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 88/275 (32%), Positives = 140/275 (50%), Gaps = 41/275 (14%)

Query: 82  LIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQR-TPIPHGLLDRRMGTNQKEANCTTCGQN 140
           +++  +   D ++Q S +QI     + +  +R  P P GL D R+GT  ++  C TC  N
Sbjct: 17  MVQFGILSPDEIRQMSVVQIE----HSETTERGKPKPGGLSDPRLGTIDRKMKCETCTAN 72

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNP 199
           +++C GHFG+++L  P+FHIG+ + V++I++ +C N  C+++L  EE     +A K+RNP
Sbjct: 73  MAECPGHFGHLELAKPMFHIGFMKTVLSIMRCVCFN--CSKILADEEDHKFKQAQKIRNP 130

Query: 200 ALSYLVRKSLKKKILETTKKVSVCPHCGEI-------NGVVKK----CGLL--KISHEKY 246
                  K+  KKIL+  K  S C    EI       +  VKK    CG    K++ E  
Sbjct: 131 -------KNRLKKILDACKNKSKCEGGDEIETQALDSDEPVKKSRGGCGAQQPKLTIEGM 183

Query: 247 KNRTKKKDAIVEDLLAEYNEAVKFNPEIEA-HKKFGLIQTLNPLEVLQLFEAIPLEDIPL 305
           K            ++AEY    K N + E   +     Q L+   VL + + I  ED  L
Sbjct: 184 K------------MIAEYKIQRKKNDDPEQLPEPVERKQQLSAERVLNVLKRISDEDCIL 231

Query: 306 LLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKS 340
           L +N + ++P  +IL  L +PP  +RPSV+ D  S
Sbjct: 232 LGLNPKYARPDWMILQVLPIPPPPVRPSVMMDTSS 266



 Score = 75.5 bits (184), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 71/288 (24%), Positives = 132/288 (45%), Gaps = 54/288 (18%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDL--DYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR++EIIN ++ I TP ++ YL  D     + A+ V+  LE TTL  V +  E  + P
Sbjct: 1116 GVPRLREIINVAKKIKTPSLSVYLKPDVSKTKERAKNVQCALEYTTLRSVTQATEVWYDP 1175

Query: 822  DD----------------------------SFILIKLDMDRIRLLHLEVDIDSI--RYCI 851
            D                             S  L++++++R  ++  ++ +  I  +  +
Sbjct: 1176 DPMSTIIEEDVDFVKSYYEMPDEEVAPEKISPWLLRIELNREMMVDKKLSMADIAEKINL 1235

Query: 852  ERTRGISGHLTVSGHSFLILK--------PK----DSSKSFNSKMYQMK-QLLPSVVIKG 898
            E    ++          LIL+        PK    D S   +  + +++  +L  + ++G
Sbjct: 1236 EFDDDLTCIFNDDNAEKLILRIRIMNDEAPKGELQDESAEDDVFLKKIESNMLTEMALRG 1295

Query: 899  VQGINRAVIHE------EDVEGV---TKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEV 949
            +  IN+  I        ++ EG     ++ L  EG NL  VM    V   + +SN+  EV
Sbjct: 1296 IPDINKVFIKSGKVNKFDESEGFKPEVEWMLDTEGVNLLAVMCHEDVDARRTTSNHLIEV 1355

Query: 950  YKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             + LGIEA R +++ E+++V+   G  +++RH  ++ D MT +G ++ 
Sbjct: 1356 IEVLGIEAVRRSLLDELRVVISFDGSYVNYRHLAILCDTMTYRGHLMA 1403



 Score = 52.0 bits (123), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 20/37 (54%), Positives = 29/37 (78%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            +++++ + P   +G +AAQSIGEP TQMTL TFH+AG
Sbjct: 1071 RFLQSLVAPGEMIGCVAAQSIGEPATQMTLNTFHYAG 1107


>gi|289581817|ref|YP_003480283.1| DNA-directed RNA polymerase subunit A' [Natrialba magadii ATCC
           43099]
 gi|448282778|ref|ZP_21474060.1| DNA-directed RNA polymerase subunit A' [Natrialba magadii ATCC
           43099]
 gi|289531370|gb|ADD05721.1| DNA-directed RNA polymerase subunit A' [Natrialba magadii ATCC
           43099]
 gi|445575393|gb|ELY29868.1| DNA-directed RNA polymerase subunit A' [Natrialba magadii ATCC
           43099]
          Length = 976

 Score =  158 bits (400), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 101/275 (36%), Positives = 144/275 (52%), Gaps = 46/275 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 483 DGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQNEEA 542

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR GE +I A QD I+G YLLT  N  FN 
Sbjct: 543 RAE--------------ARVLMRVQEQILSPRFGENIIGAIQDHISGMYLLTHDNPRFNE 588

Query: 461 AQTMR-IASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q +  + +T I +  +  GI                    WTG  +FS +L      P 
Sbjct: 589 TQALDLLRATRIDELPEPSGIDD-------------EGEPFWTGHDVFSELL------PD 629

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           + NL   G   T  E+       VI+ + +L+ G++ +  +G  G   +   + + +G  
Sbjct: 630 DLNLDFTG---TVGEK-------VIIEDGQLIEGTIAEDEVGEFG-GEIVDTITKIYGNT 678

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVT-PGQG 613
            +   +  +S +    +M+ GFSIGI D T PG+ 
Sbjct: 679 RSRIFINEVSTLAMRAIMHFGFSIGIDDETIPGEA 713



 Score =  108 bits (271), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 83/302 (27%), Positives = 136/302 (45%), Gaps = 41/302 (13%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G I   + + +  ++ S  +I++ + Y  D    PI  GL+D R+G       C TCG++
Sbjct: 10  GSINFGLMEPEEYREMSATKIITADTY--DDDGFPIDMGLMDPRLGVIDPGLECKTCGKH 67

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
              C GHFG+I+L  PV H+G+ + +  +L+  C+   C+R+LL E++   F+ ++    
Sbjct: 68  SGSCNGHFGHIELAAPVIHVGFTKLIRRLLRGTCRE--CSRLLLVEDEREEFQDQIEESR 125

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVV---------------------KKCGLL 239
                   + K  +   +K   CP CGE+   +                     +  G +
Sbjct: 126 KLGRDLNDVTKAAIRQARKKDRCPFCGEVQYDIDHEKPTTYYEVQQVLTSEYSQRIAGAM 185

Query: 240 KISHEKYKNRTKKKD--AIVEDLLAEYNEAV--KFNPE------IEAHKKFGLIQT---- 285
           +   E    RT   +  A  E  L   NE +   F P       IE      L +     
Sbjct: 186 QGDEEAGIERTSPDELAAETEIDLTRINEILSGSFRPRESQREAIEKALDIDLTEEDTNK 245

Query: 286 LNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDND 343
           L P ++   FE IP EDI +L ++A+ S+P  +ILT L VPP   RPS+  D   +S++D
Sbjct: 246 LMPSDIRDWFENIPDEDIEVLGIDADRSRPEWMILTVLPVPPVTARPSITLDNGQRSEDD 305

Query: 344 VV 345
           + 
Sbjct: 306 LT 307



 Score = 92.8 bits (229), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 39/58 (67%), Positives = 49/58 (84%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
             GFV+NS+ SGLTP EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 834 AHGFVENSYTSGLTPREFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELEAQYD 891



 Score = 45.4 bits (106), Expect = 0.23,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 29/46 (63%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 65
           +VLM  +  +++PR GE +I A QD I+G YLLT  N  FN  Q +
Sbjct: 547 RVLMRVQEQILSPRFGENIIGAIQDHISGMYLLTHDNPRFNETQAL 592


>gi|214028080|gb|ACJ63309.1| RNA polymerase III large subunit [Illicium parviflorum]
          Length = 546

 Score =  158 bits (400), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 83/221 (37%), Positives = 135/221 (61%), Gaps = 25/221 (11%)

Query: 392 VHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLL 451
           +H+PQTEEAR EAL              +LM  ++NL TP+NG++L+A+TQDF+T  +L+
Sbjct: 1   LHVPQTEEARTEAL--------------MLMGVQNNLCTPKNGDILVASTQDFLTSSFLI 46

Query: 452 TQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLIL 511
           T+K+ F++RA +  +    + D ++   +          P + ++   +WTGKQ+FS+++
Sbjct: 47  TRKDTFYDRA-SFALMCPYMGDATEAIDLP--------TPAI-LKPVELWTGKQLFSVLV 96

Query: 512 KPNRDCPVNANLKTKGRAYT-ANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFY 570
           +PN +  V  NL    + Y+ + E  C  D  V  RNSEL++G + K+TLG+G K  +F 
Sbjct: 97  RPNANMRVFVNLIVMEKNYSKSGETMCRNDGCVCFRNSELISGQIGKATLGNGNKNGLFT 156

Query: 571 ILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPG 611
           +LLRD+    A + M RL+++++ ++ N GFSIGI DV PG
Sbjct: 157 VLLRDYNTHAAASCMNRLAKLSARWIGNHGFSIGIDDVQPG 197



 Score =  105 bits (261), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 59/111 (53%), Positives = 69/111 (62%), Gaps = 7/111 (6%)

Query: 607 DVTPG-QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D TP  +GFV NSF++GLT TEFFFHTMGGREGLVDTAVKTAETGYM RRL+K+LEDL  
Sbjct: 316 DKTPAAKGFVANSFYTGLTATEFFFHTMGGREGLVDTAVKTAETGYMSRRLMKALEDLST 375

Query: 666 QYDMSFDAAFYGQTDCISGVSECIIM------GLPMNVGTGLIKLLQAVPR 710
            YD +   A  G    + G             G P+N+   L+K     PR
Sbjct: 376 HYDGTVRNASGGIVQLLYGDDGMDPAHMEGNDGAPLNMDRLLMKTKATCPR 426



 Score = 55.5 bits (132), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 21/42 (50%), Positives = 36/42 (85%)

Query: 21 VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRA 62
          +LM  ++NL TP+NG++L+A+TQDF+T  +L+T+K+ F++RA
Sbjct: 15 MLMGVQNNLCTPKNGDILVASTQDFLTSSFLITRKDTFYDRA 56


>gi|449524332|ref|XP_004169177.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB1-like
           [Cucumis sativus]
          Length = 1853

 Score =  158 bits (400), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 96/272 (35%), Positives = 151/272 (55%), Gaps = 37/272 (13%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D D VLFNRQPSLHK+SIM HR K++P+ TFR N  V +PYNADFDGDEMN+H+PQ+ E
Sbjct: 450 NDGDFVLFNRQPSLHKMSIMGHRIKIMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSFE 509

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE L             +++M  K  +V+P++   ++   QD + G   +T+++ F  
Sbjct: 510 TRAEVL-------------ELMMVPKC-IVSPQSNRPVMGIVQDTLLGCRKITKRDTFIT 555

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           +   M   +TL+    D  G I         P + ++   +WTGKQ+F+LI+      P 
Sbjct: 556 KDVFM---NTLMW-WEDFDGKIPA-------PAI-LKPQPLWTGKQVFNLII------PK 597

Query: 520 NANLKTKGRAYTANEEFCH---RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
             NL T+  A+ +  E  H    D++V +   ELL+G++ K  LG+    ++ +++  + 
Sbjct: 598 QINL-TRTSAWHSESETGHITPGDTFVRIEKGELLSGTLCKKALGT-STGSLIHVIWEEV 655

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           G D A   +     + +++L+   FSIGIGD 
Sbjct: 656 GPDAARKFLGHTQWLVNYWLLQNAFSIGIGDT 687



 Score =  104 bits (260), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 58/173 (33%), Positives = 95/173 (54%), Gaps = 9/173 (5%)

Query: 1226 LLPSVVIKGVQGINRAVI---------HEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 1276
            +L  + ++G+  IN+  I           E  +   ++ L  EG NL  VM    V   +
Sbjct: 1287 MLTEMALRGIPDINKVFIKCGKVNKFDENEGFKPEMEWMLDTEGVNLLAVMTHEDVDARR 1346

Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITR 1336
             +SN+  EV + LGIEA R +++ E+++V+   G  +++RH  ++ D MT +G ++ ITR
Sbjct: 1347 TTSNHLIEVIEVLGIEAVRRSLLDELRVVISFDGSYVNYRHLAILCDTMTYRGHLMAITR 1406

Query: 1337 HGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
            HG+ +     +   SFE T D L DAA Y +TD + GV+E I++G    +GTG
Sbjct: 1407 HGINRNDTGPMMRCSFEETVDILLDAAVYAETDHLRGVTENIMLGQLAPIGTG 1459



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 42/57 (73%), Positives = 52/57 (91%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKT+ETGY+QRRLVK++ED+ V+YD
Sbjct: 815 RGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDIMVKYD 871



 Score = 96.7 bits (239), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 87/275 (31%), Positives = 139/275 (50%), Gaps = 41/275 (14%)

Query: 82  LIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQR-TPIPHGLLDRRMGTNQKEANCTTCGQN 140
           +++  +   D ++Q S +QI     + +  +R  P   GL D R+GT  ++  C TC  N
Sbjct: 17  MVQFGILSPDEIRQMSVVQIE----HGETTERGKPKVAGLSDPRLGTIDRKMKCETCTAN 72

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNP 199
           +++C GHFG+++L  P+FHIG+ + V+ I++S+C N  C+++L+ EE     +A +++NP
Sbjct: 73  MAECPGHFGHLELAKPMFHIGFMKTVLTIMRSVCFN--CSKILVDEEDPKFKQALRIKNP 130

Query: 200 ALSYLVRKSLKKKILETTKKVSVCPHCGEI-------NGVVKK----CGLL--KISHEKY 246
                  K+  +KIL+  K  + C    EI       +  VKK    CG    KIS E  
Sbjct: 131 -------KNRLRKILDACKNKTKCEGGDEIDVQGQDSDQPVKKSRGGCGAQQPKISIEGM 183

Query: 247 KNRTKKKDAIVEDLLAEYNEAVKFNPEIEA-HKKFGLIQTLNPLEVLQLFEAIPLEDIPL 305
           K            + AEY    K N + E   +     QTL    VL + + I  ED  L
Sbjct: 184 K------------MTAEYKAQRKKNDDPEQLPEPVERKQTLTAERVLGILKRITDEDCKL 231

Query: 306 LLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKS 340
           L +N + ++P  +IL  L +PP  +RPSV+ D  S
Sbjct: 232 LGLNPKYARPDWMILQVLPIPPPPVRPSVMMDTSS 266



 Score = 79.3 bits (194), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 71/288 (24%), Positives = 131/288 (45%), Gaps = 54/288 (18%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDL--DYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR++EIIN ++ I TP ++ YL  + +   + A+ V+  LE TTL  V +  E  + P
Sbjct: 1116 GVPRLREIINVAKRIKTPSLSVYLKPEANKTKERAKTVQCALEYTTLRSVTQATEVWYDP 1175

Query: 822  DDSFILIKLDMDRIR------------------LLHLEVDIDSI------------RYCI 851
            D    +I+ D+D ++                  LL +E++ + +            +  +
Sbjct: 1176 DPMSTIIEEDIDFVKSYYEMPDEEIAPEKISPWLLRIELNREMMVDKKLSMANIAEKINL 1235

Query: 852  ERTRGISGHLTVSGHSFLILK--------PKD--SSKSFNSKMYQMK---QLLPSVVIKG 898
            E    ++          LIL+        PK   + +S    ++  K    +L  + ++G
Sbjct: 1236 EFDDDLTCIFNDDNAEKLILRIRIMNDEAPKGELTDESAEDDVFLKKIESNMLTEMALRG 1295

Query: 899  VQGINRAVI---------HEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEV 949
            +  IN+  I           E  +   ++ L  EG NL  VM    V   + +SN+  EV
Sbjct: 1296 IPDINKVFIKCGKVNKFDENEGFKPEMEWMLDTEGVNLLAVMTHEDVDARRTTSNHLIEV 1355

Query: 950  YKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             + LGIEA R +++ E+++V+   G  +++RH  ++ D MT +G ++ 
Sbjct: 1356 IEVLGIEAVRRSLLDELRVVISFDGSYVNYRHLAILCDTMTYRGHLMA 1403



 Score = 52.0 bits (123), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 20/37 (54%), Positives = 29/37 (78%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            +++++ + P   +G +AAQSIGEP TQMTL TFH+AG
Sbjct: 1071 RFLQSLVAPGEMIGCVAAQSIGEPATQMTLNTFHYAG 1107


>gi|162221|gb|AAA30232.1| RNA polymerase IIB largest subunit [Trypanosoma brucei]
          Length = 1765

 Score =  158 bits (400), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 93/268 (34%), Positives = 144/268 (53%), Gaps = 39/268 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + DVVLFNRQP+LH++S+M HR +VL + TFR N    TPYNADFDGDEMN+H+PQ+   
Sbjct: 443 NGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNLSCTTPYNADFDGDEMNLHVPQSLLT 502

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE +             +++M  K N V+P      +   QD + G Y LT K+ F ++
Sbjct: 503 KAELI-------------EMMMVPK-NFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFLDK 548

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                +A  L     D+        W+   P + ++   +WTGKQ+FSLIL P  + P  
Sbjct: 549 YFVQSVALWL-----DL--------WQLPIPAI-LKPRPLWTGKQVFSLIL-PEVNHPAT 593

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
              +           F H DS V++R  +LL G + KS +G+    ++ +++  + G D 
Sbjct: 594 PQDRPP---------FPHNDSVVMIRRGQLLCGPITKSIVGA-APGSLIHVIFNEHGSDE 643

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
               +  + R+T+F+L+N GFS+G+ D 
Sbjct: 644 VARFINGVQRVTTFFLLNFGFSVGVQDT 671



 Score = 92.8 bits (229), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 67/209 (32%), Positives = 107/209 (51%), Gaps = 29/209 (13%)

Query: 1222 QMKQLLPSVVIKGVQGINRAVIHEE----------DVEGVTKYKLLVEGDNLRDVMATYG 1271
            ++  LL  V ++G+ G+ RA++ +            + G   + +  +G  LR   A  G
Sbjct: 1280 EIPALLARVHLRGIPGVRRALLKDTTEFTVDQATGKMSGNKIWAIDTDGTALR--RAFIG 1337

Query: 1272 VKG---------VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVA 1322
            V G         VK SSN   EV   LGIEAARS ++TE++     +G++I++RH  ++ 
Sbjct: 1338 VVGEDGKNIINAVKTSSNKVPEVCSLLGIEAARSKMLTELREAYLAYGLNINYRHYTILV 1397

Query: 1323 DLMTSKGEVLGITRHGLAKMKES-VLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMG 1381
            D +   G ++ ++R G+ +   S  L   SFE T   L  AA +G+ D + GVS  +++G
Sbjct: 1398 DTICQHGYLMAVSRSGINRSDTSGPLMRCSFEETVKVLMAAASFGECDPVRGVSANLVLG 1457

Query: 1382 LPMNVGTGLIKLL-------QAVPRSEPV 1403
                VGTGL  L+       QAVP++E V
Sbjct: 1458 NQARVGTGLFDLVLNMAALQQAVPQAEAV 1486



 Score = 83.2 bits (204), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 34/57 (59%), Positives = 44/57 (77%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +G     +  GL P EFFFHTM GREGL+DTAVKT++TGY+QR+L+K+LED+   YD
Sbjct: 799 RGMANRGYVEGLKPHEFFFHTMAGREGLIDTAVKTSDTGYLQRKLIKALEDVHAAYD 855



 Score = 83.2 bits (204), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 70/248 (28%), Positives = 110/248 (44%), Gaps = 42/248 (16%)

Query: 115 PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSIC 174
           P+  G+ D RMGT   E  C TC +   +C GHFGYI+L  PVF+IG F  V+ +L+ +C
Sbjct: 49  PVRGGINDLRMGTTDFEFACETCHRKHPECPGHFGYIELAEPVFNIGVFDLVLLVLKCVC 108

Query: 175 KNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPH--------- 225
           K  TC  +LL   +      KL++  ++ L R     K+ E   +VS             
Sbjct: 109 K--TCGALLL-NTREQDVHKKLQH--MTGLNRLRQVAKMAEAKCRVSTSTEDDMGIDGFD 163

Query: 226 -------CGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHK 278
                   G   G  + CG         + R  +   I   L+    +AV    + E H 
Sbjct: 164 SAPFNGGSGMGPGATRGCG-------ASQPRVSRFYGIYPTLVI---KAVHEEQDAEWHA 213

Query: 279 KFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSV-ISD 337
                      +V Q+ + +  +D  L+  + +   P DL+LT L VPP  +RP++    
Sbjct: 214 D----------KVRQVLDRVSDDDARLMGFDPQRCHPRDLVLTVLPVPPPQVRPAISFGG 263

Query: 338 LKSDNDVV 345
           L+SD+++ 
Sbjct: 264 LRSDDELT 271



 Score = 62.8 bits (151), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 67/294 (22%), Positives = 121/294 (41%), Gaps = 62/294 (21%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDY-ARIVKGRLERTTLGEVCEYIEEVFVPD 822
            GVPR+ E++N SRN     +T  L    D    A+  +  +E  TL  +   I+ ++ PD
Sbjct: 1117 GVPRLLELLNVSRNQKHASMTVSLFPPYDEKRNAQKAQHLIEYCTLESITRRIQFIYDPD 1176

Query: 823  DSFILIKLDMDRIRL------------------------LHLEVDIDSIRYCIERTRGIS 858
                +++ D D + L                        + LE+D+D +       + + 
Sbjct: 1177 PRHTVVEADRDILELEWNVMDESDAELRIQEVVAGSPWVVRLELDVDMVTDKALDMKDVK 1236

Query: 859  GHLTVSGHSFLI----------------LKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGI 902
              +     S++I                 +  + + S      ++  LL  V ++G+ G+
Sbjct: 1237 QAILRVDESYIIETGMANNVRQRTIRMRSRYNEGADSIPKLKREIPALLARVHLRGIPGV 1296

Query: 903  NRAVIHEE----------DVEGVTKYKLLVEGDNLRDVMATYGVKG---------VKCSS 943
             RA++ +            + G   + +  +G  LR   A  GV G         VK SS
Sbjct: 1297 RRALLKDTTEFTVDQATGKMSGNKIWAIDTDGTALR--RAFIGVVGEDGKNIINAVKTSS 1354

Query: 944  NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            N   EV   LGIEAARS ++TE++     +G++I++RH  ++ D +   G ++ 
Sbjct: 1355 NKVPEVCSLLGIEAARSKMLTELREAYLAYGLNINYRHYTILVDTICQHGYLMA 1408



 Score = 50.8 bits (120), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 23/39 (58%), Positives = 27/39 (69%)

Query: 1107 REKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            R KY ++   P   +GA+AAQS GEP TQMTL TFH AG
Sbjct: 1070 RTKYHQSLTTPGENIGAIAAQSCGEPATQMTLNTFHNAG 1108


>gi|83320438|gb|ABC02846.1| RNA polymerase II largest subunit, partial [Conidiobolus coronatus]
          Length = 749

 Score =  158 bits (400), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 98/276 (35%), Positives = 147/276 (53%), Gaps = 49/276 (17%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DNDVV+FNRQPSLHK+S+M H  KV+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE+
Sbjct: 368 DNDVVIFNRQPSLHKMSMMGHLIKVMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSEES 427

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE L              + M  +  +V+P++ + ++   QD + G    TQ++AF +R
Sbjct: 428 RAEVL-------------NICMVPRQ-IVSPQSNKPVMGIVQDTLCGIRKFTQRDAFLDR 473

Query: 461 AQTMRIASTLIADTSDICGIIKRFSW-RSWNPVVFVRTAV----IWTGKQIFSLILKPNR 515
           A  M +                   W  +WN V+     +    +WTGKQI SLI+    
Sbjct: 474 ALVMNL-----------------LMWVPNWNGVLPTPAVIAPKPLWTGKQIVSLII---- 512

Query: 516 DCPVNANLKTKGRAYTANEE--FCHRDSYVILRNSELLAGSMDKSTLG--SGGKANVFYI 571
             P   N+ T    +   E       D+ VI+ + +L+AG + K T+G  SGG   + + 
Sbjct: 513 --PKQTNMMTTHSTHPDGENTFISPGDTKVIIHDGDLVAGIVCKKTVGTPSGG---LIHT 567

Query: 572 LLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           +  + G +     +     + +++L+  GFSIGIGD
Sbjct: 568 IFNEHGFEECKKFINGCQAIVNYWLLQNGFSIGIGD 603



 Score = 45.8 bits (107), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 49/197 (24%), Positives = 88/197 (44%), Gaps = 23/197 (11%)

Query: 150 YIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEE--KAAGFRAKLRNPALSYLVRK 207
           +I L  PV+H G+      IL+ +C    C+R+ + E   K    R K        +   
Sbjct: 1   HISLSKPVYHPGFISKAKKILECVCY--ICSRLKVDESHPKMRNIRGKNAKIRFKIVWDV 58

Query: 208 SLKKKILETTKKVSVCPHCGE------INGVVKK-CGLLKISHEKYKNRTKKKDAIVEDL 260
           S  K I E     +  P+         + G  ++ CG        +++ T +K+ +   L
Sbjct: 59  SKTKTICEVDSNENSGPNLDPTDPSSILEGPTREGCG--------HRHPTIRKEGM--KL 108

Query: 261 LAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
            A + +A K   +    +  G I  L P + L++F+ I   D+  + ++ E ++P  +I+
Sbjct: 109 FAVF-KASKQADDSGFGEPEGRI-PLPPSKALEIFKRIDEADVDKMGLSWEFARPEWMII 166

Query: 321 TRLLVPPNCIRPSVISD 337
           T L VPP  +RPS++ D
Sbjct: 167 TALAVPPPAVRPSIMMD 183


>gi|449456849|ref|XP_004146161.1| PREDICTED: LOW QUALITY PROTEIN: DNA-directed RNA polymerase II
           subunit RPB1-like [Cucumis sativus]
          Length = 1832

 Score =  158 bits (400), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 96/272 (35%), Positives = 151/272 (55%), Gaps = 37/272 (13%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D D VLFNRQPSLHK+SIM HR K++P+ TFR N  V +PYNADFDGDEMN+H+PQ+ E
Sbjct: 450 NDGDFVLFNRQPSLHKMSIMGHRIKIMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSFE 509

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE L             +++M  K  +V+P++   ++   QD + G   +T+++ F  
Sbjct: 510 TRAEVL-------------ELMMVPKC-IVSPQSNRPVMGIVQDTLLGCRKITKRDTFIT 555

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           +   M   +TL+    D  G I         P + ++   +WTGKQ+F+LI+      P 
Sbjct: 556 KDVFM---NTLMW-WEDFDGKIPA-------PAI-LKPQPLWTGKQVFNLII------PK 597

Query: 520 NANLKTKGRAYTANEEFCH---RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
             NL T+  A+ +  E  H    D++V +   ELL+G++ K  LG+    ++ +++  + 
Sbjct: 598 QINL-TRTSAWHSESETGHITPGDTFVRIEKGELLSGTLCKKALGT-STGSLIHVIWEEV 655

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           G D A   +     + +++L+   FSIGIGD 
Sbjct: 656 GPDAARKFLGHTQWLVNYWLLQNAFSIGIGDT 687



 Score =  104 bits (260), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 58/173 (33%), Positives = 95/173 (54%), Gaps = 9/173 (5%)

Query: 1226 LLPSVVIKGVQGINRAVI---------HEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 1276
            +L  + ++G+  IN+  I           E  +   ++ L  EG NL  VM    V   +
Sbjct: 1287 MLTEMALRGIPDINKVFIKCGKVNKFDENEGFKPEMEWMLDTEGVNLLAVMTHEDVDARR 1346

Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITR 1336
             +SN+  EV + LGIEA R +++ E+++V+   G  +++RH  ++ D MT +G ++ ITR
Sbjct: 1347 TTSNHLIEVIEVLGIEAVRRSLLDELRVVISFDGSYVNYRHLAILCDTMTYRGHLMAITR 1406

Query: 1337 HGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
            HG+ +     +   SFE T D L DAA Y +TD + GV+E I++G    +GTG
Sbjct: 1407 HGINRNDTGPMMRCSFEETVDILLDAAVYAETDHLRGVTENIMLGQLAPIGTG 1459



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 42/57 (73%), Positives = 52/57 (91%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKT+ETGY+QRRLVK++ED+ V+YD
Sbjct: 815 RGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDIMVKYD 871



 Score = 96.7 bits (239), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 87/275 (31%), Positives = 139/275 (50%), Gaps = 41/275 (14%)

Query: 82  LIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQR-TPIPHGLLDRRMGTNQKEANCTTCGQN 140
           +++  +   D ++Q S +QI     + +  +R  P   GL D R+GT  ++  C TC  N
Sbjct: 17  MVQFGILSPDEIRQMSVVQIE----HGETTERGKPKVAGLSDPRLGTIDRKMKCETCTAN 72

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNP 199
           +++C GHFG+++L  P+FHIG+ + V+ I++S+C N  C+++L+ EE     +A +++NP
Sbjct: 73  MAECPGHFGHLELAKPMFHIGFMKTVLTIMRSVCFN--CSKILVDEEDPKFKQALRIKNP 130

Query: 200 ALSYLVRKSLKKKILETTKKVSVCPHCGEI-------NGVVKK----CGLL--KISHEKY 246
                  K+  +KIL+  K  + C    EI       +  VKK    CG    KIS E  
Sbjct: 131 -------KNRLRKILDACKNKTKCEGGDEIDVQGQDSDQPVKKSRGGCGAQQPKISIEGM 183

Query: 247 KNRTKKKDAIVEDLLAEYNEAVKFNPEIEA-HKKFGLIQTLNPLEVLQLFEAIPLEDIPL 305
           K            + AEY    K N + E   +     QTL    VL + + I  ED  L
Sbjct: 184 K------------MTAEYKAQRKKNDDPEQLPEPVERKQTLTAERVLGILKRITDEDCKL 231

Query: 306 LLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKS 340
           L +N + ++P  +IL  L +PP  +RPSV+ D  S
Sbjct: 232 LGLNPKYARPDWMILQVLPIPPPPVRPSVMMDTSS 266



 Score = 79.3 bits (194), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 71/288 (24%), Positives = 131/288 (45%), Gaps = 54/288 (18%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDL--DYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR++EIIN ++ I TP ++ YL  + +   + A+ V+  LE TTL  V +  E  + P
Sbjct: 1116 GVPRLREIINVAKRIKTPSLSVYLKPEANKTKERAKTVQCALEYTTLRSVTQATEVWYDP 1175

Query: 822  DDSFILIKLDMDRIR------------------LLHLEVDIDSI------------RYCI 851
            D    +I+ D+D ++                  LL +E++ + +            +  +
Sbjct: 1176 DPMSTIIEEDIDFVKSYYEMPDEEIAPEKISPWLLRIELNREMMVDKKLSMANIAEKINL 1235

Query: 852  ERTRGISGHLTVSGHSFLILK--------PKD--SSKSFNSKMYQMK---QLLPSVVIKG 898
            E    ++          LIL+        PK   + +S    ++  K    +L  + ++G
Sbjct: 1236 EFDDDLTCIFNDDNAEKLILRIRIMNDEAPKGELTDESAEDDVFLKKIESNMLTEMALRG 1295

Query: 899  VQGINRAVI---------HEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEV 949
            +  IN+  I           E  +   ++ L  EG NL  VM    V   + +SN+  EV
Sbjct: 1296 IPDINKVFIKCGKVNKFDENEGFKPEMEWMLDTEGVNLLAVMTHEDVDARRTTSNHLIEV 1355

Query: 950  YKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             + LGIEA R +++ E+++V+   G  +++RH  ++ D MT +G ++ 
Sbjct: 1356 IEVLGIEAVRRSLLDELRVVISFDGSYVNYRHLAILCDTMTYRGHLMA 1403



 Score = 52.0 bits (123), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 20/37 (54%), Positives = 29/37 (78%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            +++++ + P   +G +AAQSIGEP TQMTL TFH+AG
Sbjct: 1071 RFLQSLVAPGEMIGCVAAQSIGEPATQMTLNTFHYAG 1107


>gi|110669639|gb|ABG81914.1| RNA polymerase II largest subunit [Bacidia schweinitzii]
          Length = 1016

 Score =  158 bits (400), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 92/270 (34%), Positives = 148/270 (54%), Gaps = 37/270 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D ++FNRQPSLHK S+M HR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 373 DGDYIIFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 432

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    +++L ++            N+V+P+    L+   QD + G Y + +++ F +R
Sbjct: 433 RAE----VNQLCMVP----------LNVVSPQRNGPLMGIVQDTLCGIYKICRRDVFLSR 478

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M I    +    D  G+I +       P + ++   +WTGKQ+ SL++      P  
Sbjct: 479 DQVMNI----LLWVPDWDGVIPQ-------PAI-IKPRAMWTGKQLISLVV------PTG 520

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            NL   G     +  F   D  +++   EL+ G + K+ +G+     + +I+  + G D 
Sbjct: 521 LNLVRPG----DHGFFPLEDDTLVVLGGELMVGLLKKAYVGA-SPGGIIHIIYNEKGSDA 575

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           A++       + +++L++ GFSIGIGD  P
Sbjct: 576 AMSFFNGAQTLVNYWLLHNGFSIGIGDTIP 605



 Score =  100 bits (248), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+  
Sbjct: 725 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDVMC 784

Query: 666 QYD 668
           +YD
Sbjct: 785 KYD 787



 Score = 53.5 bits (127), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 48/195 (24%), Positives = 83/195 (42%), Gaps = 41/195 (21%)

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNPAL 201
           +C GHFG+I+L  PVFH+G+   +  +L+++C N  C ++L+ E   A   A + R+P  
Sbjct: 1   ECPGHFGHIELAAPVFHVGFMTKIKKLLETVCHN--CGKILVDESNPAFADAQRYRDPKR 58

Query: 202 SY--LVRKSLKKKILETT-------------KKVSVCPHCGEINGVVKKCGLLKISHEKY 246
            +  + R    K I E T             K+      CG     +++ GL      K 
Sbjct: 59  RFDAVWRLCKPKLICEATPAAEDDAPTDDPKKQKHDHGGCGNAQPEIRREGLRLTGTWKP 118

Query: 247 KNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLL 306
           +                     K + E EA +     + + P  VL +F  I  EDI  +
Sbjct: 119 Q---------------------KGDDETEAQQPDK--RPITPQMVLNIFRHISNEDIERM 155

Query: 307 LMNAELSKPSDLILT 321
            ++ + ++P  +I+T
Sbjct: 156 GLSNDYARPEWMIIT 170


>gi|72388454|ref|XP_844651.1| RNA polymerase IIA largest subunit [Trypanosoma brucei TREU927]
 gi|62360128|gb|AAX80548.1| RNA polymerase IIA largest subunit [Trypanosoma brucei]
 gi|70801184|gb|AAZ11092.1| RNA polymerase IIA largest subunit [Trypanosoma brucei brucei
           strain 927/4 GUTat10.1]
          Length = 1765

 Score =  158 bits (400), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 93/268 (34%), Positives = 144/268 (53%), Gaps = 39/268 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + DVVLFNRQP+LH++S+M HR +VL + TFR N    TPYNADFDGDEMN+H+PQ+   
Sbjct: 443 NGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNLSCTTPYNADFDGDEMNLHVPQSLLT 502

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE +             +++M  K N V+P      +   QD + G Y LT K+ F ++
Sbjct: 503 KAELI-------------EMMMVPK-NFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFLDK 548

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                +A  L     D+        W+   P + ++   +WTGKQ+FSLIL P  + P  
Sbjct: 549 YFVQSVALWL-----DL--------WQLPIPAI-LKPRPLWTGKQVFSLIL-PEVNHPAT 593

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
              +           F H DS V++R  +LL G + KS +G+    ++ +++  + G D 
Sbjct: 594 PQDRPP---------FPHNDSVVMIRRGQLLCGPITKSIVGA-APGSLIHVIFNEHGSDE 643

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
               +  + R+T+F+L+N GFS+G+ D 
Sbjct: 644 VARFINGVQRVTTFFLLNFGFSVGVQDT 671



 Score = 92.8 bits (229), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 67/209 (32%), Positives = 107/209 (51%), Gaps = 29/209 (13%)

Query: 1222 QMKQLLPSVVIKGVQGINRAVIHEE----------DVEGVTKYKLLVEGDNLRDVMATYG 1271
            ++  LL  V ++G+ G+ RA++ +            + G   + +  +G  LR   A  G
Sbjct: 1280 EIPALLARVHLRGIPGVRRALLKDTTEFTVDQATGKMSGNKIWAIDTDGTALR--RAFIG 1337

Query: 1272 VKG---------VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVA 1322
            V G         VK SSN   EV   LGIEAARS ++TE++     +G++I++RH  ++ 
Sbjct: 1338 VVGEDGKNIINAVKTSSNKVPEVCSLLGIEAARSKMLTELREAYLAYGLNINYRHYTILV 1397

Query: 1323 DLMTSKGEVLGITRHGLAKMKES-VLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMG 1381
            D +   G ++ ++R G+ +   S  L   SFE T   L  AA +G+ D + GVS  +++G
Sbjct: 1398 DTICQHGYLMAVSRSGINRSDTSGPLMRCSFEETVKVLMAAASFGECDPVRGVSANLVLG 1457

Query: 1382 LPMNVGTGLIKLL-------QAVPRSEPV 1403
                VGTGL  L+       QAVP++E V
Sbjct: 1458 NQARVGTGLFDLVLNMAALQQAVPQAEAV 1486



 Score = 84.7 bits (208), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 70/248 (28%), Positives = 110/248 (44%), Gaps = 42/248 (16%)

Query: 115 PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSIC 174
           P+  G+ D RMGT   E  C TC +   +C GHFGYI+L  PVF+IG F  V+ +L+ +C
Sbjct: 49  PVRGGINDLRMGTTDFEFACETCHRKHPECPGHFGYIELAEPVFNIGVFDLVLQVLKCVC 108

Query: 175 KNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPH--------- 225
           K  TC  +LL   +      KL++  ++ L R     K+ E   +VS             
Sbjct: 109 K--TCGALLL-NTREQDVHKKLQH--MTGLNRLRQVAKMAEAKCRVSTSTEDDMGIDGFD 163

Query: 226 -------CGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHK 278
                   G   G  + CG         + R  +   I   L+    +AV    + E H 
Sbjct: 164 SAPFNGGSGMGPGATRGCG-------ASQPRVSRFYGIYPTLVI---KAVHEEQDAEWHA 213

Query: 279 KFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSV-ISD 337
                      +V Q+ + +  +D  L+  + +   P DL+LT L VPP  +RP++    
Sbjct: 214 D----------KVRQVLDRVSDDDARLMGFDPQRCHPRDLVLTVLPVPPPQVRPAISFGG 263

Query: 338 LKSDNDVV 345
           L+SD+++ 
Sbjct: 264 LRSDDELT 271



 Score = 83.2 bits (204), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 34/57 (59%), Positives = 44/57 (77%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +G     +  GL P EFFFHTM GREGL+DTAVKT++TGY+QR+L+K+LED+   YD
Sbjct: 799 RGMANRGYVEGLKPHEFFFHTMAGREGLIDTAVKTSDTGYLQRKLIKALEDVHAAYD 855



 Score = 62.8 bits (151), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 67/294 (22%), Positives = 121/294 (41%), Gaps = 62/294 (21%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDY-ARIVKGRLERTTLGEVCEYIEEVFVPD 822
            GVPR+ E++N SRN     +T  L    D    A+  +  +E  TL  +   I+ ++ PD
Sbjct: 1117 GVPRLLELLNVSRNQKHASMTVSLFPPYDEKRNAQKAQHLIEYCTLESITRRIQFIYDPD 1176

Query: 823  DSFILIKLDMDRIRL------------------------LHLEVDIDSIRYCIERTRGIS 858
                +++ D D + L                        + LE+D+D +       + + 
Sbjct: 1177 PRHTVVEADRDILELEWNVMDESDAELRIQEVVAGSPWVVRLELDVDMVTDKALDMKDVK 1236

Query: 859  GHLTVSGHSFLI----------------LKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGI 902
              +     S++I                 +  + + S      ++  LL  V ++G+ G+
Sbjct: 1237 QAILRVDESYIIETGMANNVRQRTIRMRSRYNEGADSIPKLKREIPALLARVHLRGIPGV 1296

Query: 903  NRAVIHEE----------DVEGVTKYKLLVEGDNLRDVMATYGVKG---------VKCSS 943
             RA++ +            + G   + +  +G  LR   A  GV G         VK SS
Sbjct: 1297 RRALLKDTTEFTVDQATGKMSGNKIWAIDTDGTALR--RAFIGVVGEDGKNIINAVKTSS 1354

Query: 944  NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            N   EV   LGIEAARS ++TE++     +G++I++RH  ++ D +   G ++ 
Sbjct: 1355 NKVPEVCSLLGIEAARSKMLTELREAYLAYGLNINYRHYTILVDTICQHGYLMA 1408



 Score = 50.4 bits (119), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 23/39 (58%), Positives = 27/39 (69%)

Query: 1107 REKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            R KY ++   P   +GA+AAQS GEP TQMTL TFH AG
Sbjct: 1070 RTKYHQSLTTPGENIGAIAAQSCGEPATQMTLNTFHNAG 1108


>gi|448532890|ref|ZP_21621310.1| DNA-directed RNA polymerase subunit A' [Halorubrum hochstenium ATCC
           700873]
 gi|445706124|gb|ELZ58009.1| DNA-directed RNA polymerase subunit A' [Halorubrum hochstenium ATCC
           700873]
          Length = 970

 Score =  158 bits (400), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 96/273 (35%), Positives = 140/273 (51%), Gaps = 55/273 (20%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 476 DGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQNEEA 535

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR G  +I A QD I+G YLLT  N  F+ 
Sbjct: 536 RAE--------------ARVLMRVQEQILSPRFGGNIIGAIQDHISGTYLLTNSNPEFSE 581

Query: 461 AQTM------RIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPN 514
            Q +      R+     AD  D  G  + F                WTG+ +FS +L  +
Sbjct: 582 TQALDLLRATRVDELPEADGVDDDG--REF----------------WTGRTLFSELLPDD 623

Query: 515 RDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLR 574
            D    ++                    V++ + +L+ G++D+  +G+ G   V   L +
Sbjct: 624 LDLSFTSSAGDS----------------VVIEDGQLIEGTIDEDAVGAFG-GEVVDTLTK 666

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           ++GE  +   +  ++ +    +MN GFSIGI D
Sbjct: 667 EYGETRSRVFINEIASLAMRAIMNFGFSIGIDD 699



 Score =  107 bits (267), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 79/294 (26%), Positives = 125/294 (42%), Gaps = 57/294 (19%)

Query: 97  SHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP 156
           S  ++++ + Y  D    PI  GL+D R+G       C TCG +   C GHFG+I+L  P
Sbjct: 19  SATKVITADTY--DDDGYPIDMGLMDPRLGVIDPGLECRTCGSHSGSCNGHFGHIELAAP 76

Query: 157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILET 216
           V H+G+ + +  +L+S C+   C R+ L + +   FR +             + K  +  
Sbjct: 77  VIHVGFTKLIRRLLRSTCRE--CGRLALDDAQRDEFRDRYERAKELGDDEHDVLKAAVRQ 134

Query: 217 TKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDL---------------- 260
            +K S CP CGE    +K        HEK     + +D +  D                 
Sbjct: 135 ARKASTCPFCGEPQADIK--------HEKPTTYYEVQDVLSGDYSERIAAAMQPDEEEDD 186

Query: 261 -------LAEYNE----------AVKFNPEIEAHKKFGL----------IQTLNPLEVLQ 293
                  LAE  +          A +F P  E  +              +  L P ++  
Sbjct: 187 PGTSPQELAEKTDIALDRVNDIMAGEFRPRKEDRRAIEKALDVDLTEEDMNKLMPSDIRD 246

Query: 294 LFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDNDVV 345
            FE IP ED+ +L +++E S+P  +ILT L VPP   RPS+  D   +S++D+ 
Sbjct: 247 WFEDIPDEDLEVLGIDSEHSRPEWMILTVLPVPPVTTRPSITLDNGQRSEDDLT 300



 Score = 91.3 bits (225), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 38/57 (66%), Positives = 48/57 (84%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFV+NS+  GLTP EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 828 HGFVENSYRGGLTPEEFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELEAQYD 884


>gi|72393537|ref|XP_847569.1| RNA polymerase IIA largest subunit [Trypanosoma brucei TREU927]
 gi|62175081|gb|AAX69230.1| RNA polymerase IIA largest subunit [Trypanosoma brucei]
 gi|70803599|gb|AAZ13503.1| RNA polymerase IIA largest subunit [Trypanosoma brucei brucei
           strain 927/4 GUTat10.1]
          Length = 1765

 Score =  158 bits (400), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 93/268 (34%), Positives = 144/268 (53%), Gaps = 39/268 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + DVVLFNRQP+LH++S+M HR +VL + TFR N    TPYNADFDGDEMN+H+PQ+   
Sbjct: 443 NGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNLSCTTPYNADFDGDEMNLHVPQSLLT 502

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE +             +++M  K N V+P      +   QD + G Y LT K+ F ++
Sbjct: 503 KAELI-------------EMMMVPK-NFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFLDK 548

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                +A  L     D+        W+   P + ++   +WTGKQ+FSLIL P  + P  
Sbjct: 549 YFVQSVALWL-----DL--------WQLPIPAI-LKPRPLWTGKQVFSLIL-PEVNHPAT 593

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
              +           F H DS V++R  +LL G + KS +G+    ++ +++  + G D 
Sbjct: 594 PQDRPP---------FPHNDSVVMIRRGQLLCGPITKSIVGA-APGSLIHVIFNEHGSDE 643

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
               +  + R+T+F+L+N GFS+G+ D 
Sbjct: 644 VARFINGVQRVTTFFLLNFGFSVGVQDT 671



 Score = 92.8 bits (229), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 67/209 (32%), Positives = 107/209 (51%), Gaps = 29/209 (13%)

Query: 1222 QMKQLLPSVVIKGVQGINRAVIHEE----------DVEGVTKYKLLVEGDNLRDVMATYG 1271
            ++  LL  V ++G+ G+ RA++ +            + G   + +  +G  LR   A  G
Sbjct: 1280 EIPALLARVHLRGIPGVRRALLKDTTEFTVDQATGKMSGNKIWAIDTDGTALR--RAFIG 1337

Query: 1272 VKG---------VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVA 1322
            V G         VK SSN   EV   LGIEAARS ++TE++     +G++I++RH  ++ 
Sbjct: 1338 VVGEDGKNIINAVKTSSNKVPEVCSLLGIEAARSKMLTELREAYLAYGLNINYRHYTILV 1397

Query: 1323 DLMTSKGEVLGITRHGLAKMKES-VLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMG 1381
            D +   G ++ ++R G+ +   S  L   SFE T   L  AA +G+ D + GVS  +++G
Sbjct: 1398 DTICQHGYLMAVSRSGINRSDTSGPLMRCSFEETVKVLMAAASFGECDPVRGVSANLVLG 1457

Query: 1382 LPMNVGTGLIKLL-------QAVPRSEPV 1403
                VGTGL  L+       QAVP++E V
Sbjct: 1458 NQARVGTGLFDLVLNMAALQQAVPQAEAV 1486



 Score = 84.7 bits (208), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 70/248 (28%), Positives = 110/248 (44%), Gaps = 42/248 (16%)

Query: 115 PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSIC 174
           P+  G+ D RMGT   E  C TC +   +C GHFGYI+L  PVF+IG F  V+ +L+ +C
Sbjct: 49  PVRGGINDLRMGTTDFEFACETCHRKHPECPGHFGYIELAEPVFNIGVFDLVLQVLKCVC 108

Query: 175 KNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPH--------- 225
           K  TC  +LL   +      KL++  ++ L R     K+ E   +VS             
Sbjct: 109 K--TCGALLL-NTREQDVHKKLQH--MTGLNRLRQVAKMAEAKCRVSTSTEDDMGIDGFD 163

Query: 226 -------CGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHK 278
                   G   G  + CG         + R  +   I   L+    +AV    + E H 
Sbjct: 164 SAPFNGGSGMGPGATRGCG-------ASQPRVSRFYGIYPTLVI---KAVHEEQDAEWHA 213

Query: 279 KFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSV-ISD 337
                      +V Q+ + +  +D  L+  + +   P DL+LT L VPP  +RP++    
Sbjct: 214 D----------KVRQVLDRVSDDDARLMGFDPQRCHPRDLVLTVLPVPPPQVRPAISFGG 263

Query: 338 LKSDNDVV 345
           L+SD+++ 
Sbjct: 264 LRSDDELT 271



 Score = 83.2 bits (204), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 34/57 (59%), Positives = 44/57 (77%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +G     +  GL P EFFFHTM GREGL+DTAVKT++TGY+QR+L+K+LED+   YD
Sbjct: 799 RGMANRGYVEGLKPHEFFFHTMAGREGLIDTAVKTSDTGYLQRKLIKALEDVHAAYD 855



 Score = 63.5 bits (153), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 66/294 (22%), Positives = 125/294 (42%), Gaps = 62/294 (21%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDY-ARIVKGRLERTTLGEVCEYIEEVFVPD 822
            GVPR+ E++N SRN     +T  L    D    A+  +  +E  TL  +   I+ ++ PD
Sbjct: 1117 GVPRLLELLNVSRNQKHASMTVSLFPPYDEKRNAQKAQHLIEYCTLESITRRIQFIYDPD 1176

Query: 823  DSFILIKLDMDRIRL------------------------LHLEVDIDSIRYCIERTRGIS 858
                +++ D D + L                        + LE+D+D +       + + 
Sbjct: 1177 PRHTVVEADRDILELEWNVMDESDAELRIQEVVAGSPWVVRLELDVDMVTDKALDMKDVK 1236

Query: 859  GHLTVSGHSFLI------------LKPKDSSKSFNSKMYQMKQLLPSVV----IKGVQGI 902
              +     S++I            ++ +         + Q+K+ +P+++    ++G+ G+
Sbjct: 1237 QAILRVDESYIIETGMANNVRQRTIRMRSRYNEGADSIPQLKREIPALLARVHLRGIPGV 1296

Query: 903  NRAVIHEE----------DVEGVTKYKLLVEGDNLRDVMATYGVKG---------VKCSS 943
             RA++ +            + G   + +  +G  LR   A  GV G         VK SS
Sbjct: 1297 RRALLKDTTEFTVDQATGKMSGNKIWAIDTDGTALR--RAFIGVVGEDGKNIINAVKTSS 1354

Query: 944  NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            N   EV   LGIEAARS ++TE++     +G++I++RH  ++ D +   G ++ 
Sbjct: 1355 NKVPEVCSLLGIEAARSKMLTELREAYLAYGLNINYRHYTILVDTICQHGYLMA 1408



 Score = 50.4 bits (119), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 23/39 (58%), Positives = 27/39 (69%)

Query: 1107 REKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            R KY ++   P   +GA+AAQS GEP TQMTL TFH AG
Sbjct: 1070 RTKYHQSLTTPGENIGAIAAQSCGEPATQMTLNTFHNAG 1108


>gi|340924320|gb|EGS19223.1| hypothetical protein CTHT_0058480 [Chaetomium thermophilum var.
           thermophilum DSM 1495]
          Length = 1756

 Score =  158 bits (399), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 94/271 (34%), Positives = 142/271 (52%), Gaps = 37/271 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D V+FNRQPSLHK S+M HR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQTEE 
Sbjct: 453 DGDYVIFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQTEET 512

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE               K L     N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 513 RAE--------------VKELCMVPLNIVSPQRNGPLMGIVQDTLAGVYKMCRRDVFLTK 558

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPV-VFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q M     L+    D  GII         P+   ++    WTGKQI S+I+      P 
Sbjct: 559 EQVM----NLMLWVPDWDGII---------PIPAILKPRPRWTGKQIVSMII------PK 599

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
             NL     +   N  F  +D  ++++  E++ G + K ++G+ G   + ++   + G  
Sbjct: 600 IINLHMGSDSPDKNHPF--KDDGLLIQQGEIMYGLLSKKSVGASG-GGIVHLCYNELGPQ 656

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
            A+  +    R+ +++L++ G SIGIGD  P
Sbjct: 657 GAMDFLNGCQRVVNYWLLHNGHSIGIGDTIP 687



 Score =  104 bits (259), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 58/186 (31%), Positives = 99/186 (53%), Gaps = 15/186 (8%)

Query: 1224 KQLLPSVVIKGVQGINRAVIHE---------------EDVEGVTKYKLLVEGDNLRDVMA 1268
            K LL ++ ++GV GI RA +++               +D     ++ L  +G  LR+V+ 
Sbjct: 1286 KHLLDNLTLRGVPGIERAFLNKGTKLAVLPDGSQIANKDHPACQEWYLDTQGTALREVLQ 1345

Query: 1269 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK 1328
              GV   + S+N+ Y++    GIEAAR+ ++ E+  V+   G  ++ RH  L+ D+MT +
Sbjct: 1346 IEGVDTRRTSTNDLYQIVDVFGIEAARAALLQELTQVLAFDGSYVNHRHLALLVDVMTYR 1405

Query: 1329 GEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGT 1388
            G +  +TRHG+ +     L   SFE T + L +AA  G+ D   G+SE +++G    +GT
Sbjct: 1406 GSIAAVTRHGINRADTGALMRCSFEETVEILLEAAAVGELDDCRGISENVMLGQMAPMGT 1465

Query: 1389 GLIKLL 1394
            G   +L
Sbjct: 1466 GHFDVL 1471



 Score = 98.2 bits (243), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 52/63 (82%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTP+EFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED   
Sbjct: 807 DYSPEARGFVENSYLRGLTPSEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDAEA 866

Query: 666 QYD 668
            YD
Sbjct: 867 HYD 869



 Score = 87.0 bits (214), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 72/293 (24%), Positives = 132/293 (45%), Gaps = 61/293 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLD-KDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPD 822
            GVPR+KEI+N +++I TP +  YLD ++   + A+ ++ ++E T+L  V    E  + PD
Sbjct: 1116 GVPRLKEILNVAKDIKTPSMVVYLDAENATQEDAKKMRNKVEHTSLRSVTAVTEIYYDPD 1175

Query: 823  DSFILIKLDMDRIR---LLHLEVDIDSI--------RYCIERTRGISGHLTVS--GHSF- 868
             +  +I  D D +    L+    D +SI        R  ++R + +   L V    H   
Sbjct: 1176 ITSTVIPEDFDMVESYFLIPDSSDQESIENQSRWLLRITLDRQKMLDKGLRVEDVAHKIK 1235

Query: 869  -----------------------LILKPKDSSKSFNSKMYQ--------MKQLLPSVVIK 897
                                    +++ +D       K+ +         K LL ++ ++
Sbjct: 1236 EEYKKDVAIIFSDNNAEEMVIRIRVVRQEDDKDEDGHKIIEDDVMLKRLEKHLLDNLTLR 1295

Query: 898  GVQGINRAVIHE---------------EDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCS 942
            GV GI RA +++               +D     ++ L  +G  LR+V+   GV   + S
Sbjct: 1296 GVPGIERAFLNKGTKLAVLPDGSQIANKDHPACQEWYLDTQGTALREVLQIEGVDTRRTS 1355

Query: 943  SNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            +N+ Y++    GIEAAR+ ++ E+  V+   G  ++ RH  L+ D+MT +G +
Sbjct: 1356 TNDLYQIVDVFGIEAARAALLQELTQVLAFDGSYVNHRHLALLVDVMTYRGSI 1408



 Score = 68.6 bits (166), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 46/177 (25%), Positives = 84/177 (47%), Gaps = 28/177 (15%)

Query: 110 DPQRT-PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVIN 168
           D  RT P   GL D  +G+  ++  C TC +N+S+C GHFG+I+L  PV+H G+ +    
Sbjct: 44  DETRTKPRDGGLNDPLLGSVDRQFKCKTCTENMSECPGHFGHIELARPVYHPGFIKRTKK 103

Query: 169 ILQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSY-------LVRKSLKKKILETTKKV 220
           +L+ +C N  C+RVL          A K+R+P + +         ++  +  I +  +  
Sbjct: 104 LLEIVCHN--CSRVLADRSDPQYAAAMKIRDPKIRFKRVWDICKSKRRCENDIPKQAEDG 161

Query: 221 SVCPH-------------CGEINGVVKKCGLLKISHEKYKN----RTKKKDAIVEDL 260
              P+             CG    V+++  L   +H ++++    +TK+K  I  ++
Sbjct: 162 DYNPNGNAQEAPVGGHGGCGNAQPVIRQQALTLWAHYEHRDDDGVKTKEKKIITPEM 218



 Score = 57.4 bits (137), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 24/37 (64%), Positives = 28/37 (75%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            ++ R+ + P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1071 RWARSMVNPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1107


>gi|162215|gb|AAA30229.1| RNA polymerase IIA largest subunit [Trypanosoma brucei]
 gi|261327848|emb|CBH10825.1| RNA polymerase IIA largest subunit, putative [Trypanosoma brucei
           gambiense DAL972]
          Length = 1765

 Score =  158 bits (399), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 93/268 (34%), Positives = 144/268 (53%), Gaps = 39/268 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + DVVLFNRQP+LH++S+M HR +VL + TFR N    TPYNADFDGDEMN+H+PQ+   
Sbjct: 443 NGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNLSCTTPYNADFDGDEMNLHVPQSLLT 502

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE +             +++M  K N V+P      +   QD + G Y LT K+ F ++
Sbjct: 503 KAELI-------------EMMMVPK-NFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFLDK 548

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                +A  L     D+        W+   P + ++   +WTGKQ+FSLIL P  + P  
Sbjct: 549 YFVQSVALWL-----DL--------WQLPIPAI-LKPRPLWTGKQVFSLIL-PEVNHPAT 593

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
              +           F H DS V++R  +LL G + KS +G+    ++ +++  + G D 
Sbjct: 594 PQDRPP---------FPHNDSVVMIRRGQLLCGPITKSIVGA-APGSLIHVIFNEHGSDE 643

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
               +  + R+T+F+L+N GFS+G+ D 
Sbjct: 644 VARFINGVQRVTTFFLLNFGFSVGVQDT 671



 Score = 92.8 bits (229), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 67/209 (32%), Positives = 107/209 (51%), Gaps = 29/209 (13%)

Query: 1222 QMKQLLPSVVIKGVQGINRAVIHEE----------DVEGVTKYKLLVEGDNLRDVMATYG 1271
            ++  LL  V ++G+ G+ RA++ +            + G   + +  +G  LR   A  G
Sbjct: 1280 EIPALLARVHLRGIPGVRRALLKDTTEFTVDQATGKMSGNKIWAIDTDGTALR--RAFIG 1337

Query: 1272 VKG---------VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVA 1322
            V G         VK SSN   EV   LGIEAARS ++TE++     +G++I++RH  ++ 
Sbjct: 1338 VVGEDGKNIINAVKTSSNKVPEVCSLLGIEAARSKMLTELREAYLAYGLNINYRHYTILV 1397

Query: 1323 DLMTSKGEVLGITRHGLAKMKES-VLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMG 1381
            D +   G ++ ++R G+ +   S  L   SFE T   L  AA +G+ D + GVS  +++G
Sbjct: 1398 DTICQHGYLMAVSRSGINRSDTSGPLMRCSFEETVKVLMAAASFGECDPVRGVSANLVLG 1457

Query: 1382 LPMNVGTGLIKLL-------QAVPRSEPV 1403
                VGTGL  L+       QAVP++E V
Sbjct: 1458 NQARVGTGLFDLVLNMAALQQAVPQAEAV 1486



 Score = 83.2 bits (204), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 34/57 (59%), Positives = 44/57 (77%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +G     +  GL P EFFFHTM GREGL+DTAVKT++TGY+QR+L+K+LED+   YD
Sbjct: 799 RGMANRGYVEGLKPHEFFFHTMAGREGLIDTAVKTSDTGYLQRKLIKALEDVHAAYD 855



 Score = 83.2 bits (204), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 70/248 (28%), Positives = 110/248 (44%), Gaps = 42/248 (16%)

Query: 115 PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSIC 174
           P+  G+ D RMGT   E  C TC +   +C GHFGYI+L  PVF+IG F  V+ +L+ +C
Sbjct: 49  PVRGGINDLRMGTTDFEFACETCHRKHPECPGHFGYIELAEPVFNIGVFDLVLLVLKCVC 108

Query: 175 KNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPH--------- 225
           K  TC  +LL   +      KL++  ++ L R     K+ E   +VS             
Sbjct: 109 K--TCGALLL-NTREQDVHKKLQH--MTGLNRLRQVAKMAEAKCRVSTSTEDDMGIDGFD 163

Query: 226 -------CGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHK 278
                   G   G  + CG         + R  +   I   L+    +AV    + E H 
Sbjct: 164 SAPFNGGSGMGPGATRGCG-------ASQPRVSRFYGIYPTLVI---KAVHEEQDAEWHA 213

Query: 279 KFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSV-ISD 337
                      +V Q+ + +  +D  L+  + +   P DL+LT L VPP  +RP++    
Sbjct: 214 D----------KVRQVLDRVSDDDARLMGFDPQRCHPRDLVLTVLPVPPPQVRPAISFGG 263

Query: 338 LKSDNDVV 345
           L+SD+++ 
Sbjct: 264 LRSDDELT 271



 Score = 62.8 bits (151), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 67/294 (22%), Positives = 121/294 (41%), Gaps = 62/294 (21%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDY-ARIVKGRLERTTLGEVCEYIEEVFVPD 822
            GVPR+ E++N SRN     +T  L    D    A+  +  +E  TL  +   I+ ++ PD
Sbjct: 1117 GVPRLLELLNVSRNQKHASMTVSLFPPYDEKRNAQKAQHLIEYCTLESITRRIQFIYDPD 1176

Query: 823  DSFILIKLDMDRIRL------------------------LHLEVDIDSIRYCIERTRGIS 858
                +++ D D + L                        + LE+D+D +       + + 
Sbjct: 1177 PRHTVVEADRDILELEWNVMDESDAELRIQEVVAGSPWVVRLELDVDMVTDKALDMKDVK 1236

Query: 859  GHLTVSGHSFLI----------------LKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGI 902
              +     S++I                 +  + + S      ++  LL  V ++G+ G+
Sbjct: 1237 QAILRVDESYIIETGMANNVRQRTIRMRSRYNEGADSIPKLKREIPALLARVHLRGIPGV 1296

Query: 903  NRAVIHEE----------DVEGVTKYKLLVEGDNLRDVMATYGVKG---------VKCSS 943
             RA++ +            + G   + +  +G  LR   A  GV G         VK SS
Sbjct: 1297 RRALLKDTTEFTVDQATGKMSGNKIWAIDTDGTALR--RAFIGVVGEDGKNIINAVKTSS 1354

Query: 944  NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            N   EV   LGIEAARS ++TE++     +G++I++RH  ++ D +   G ++ 
Sbjct: 1355 NKVPEVCSLLGIEAARSKMLTELREAYLAYGLNINYRHYTILVDTICQHGYLMA 1408



 Score = 50.4 bits (119), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 23/39 (58%), Positives = 27/39 (69%)

Query: 1107 REKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            R KY ++   P   +GA+AAQS GEP TQMTL TFH AG
Sbjct: 1070 RTKYHQSLTTPGENIGAIAAQSCGEPATQMTLNTFHNAG 1108


>gi|119643527|gb|ABL85575.1| RNA polymerase II largest subunit [Flavopunctelia flaventior]
          Length = 995

 Score =  158 bits (399), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 95/278 (34%), Positives = 150/278 (53%), Gaps = 41/278 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D + ++FNRQP  HK S+M HR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 366 DGNYIIFNRQPXXHKESMMGHRVRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 425

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    +++L ++            N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 426 RAE----INQLCMVP----------LNIVSPQRNGPLMGIVQDTLCGIYKMCRRDVFLTK 471

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M I    +    D  G+I +       P + V+   +WTGKQI SL++      P  
Sbjct: 472 EQVMNI----LLWVPDWDGVIPQ-------PAI-VKPLAMWTGKQILSLVI------PTG 513

Query: 521 ANLKTKGRAYTANEEFCH--RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            NL         NEE      D  +++ + EL+ G + K T+G+ G   V +I+  + G 
Sbjct: 514 LNL------LRGNEEGFSPLNDDGLLISSGELMYGLLAKKTVGASG-GGVIHIVFNEKGP 566

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           + A+T       + +++L++ GFSIGIGD  P +  +Q
Sbjct: 567 EAAMTFFNGAQTVVNYWLLHNGFSIGIGDTIPDRHTIQ 604



 Score =  101 bits (251), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+  
Sbjct: 718 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDVMA 777

Query: 666 QYD 668
           +YD
Sbjct: 778 KYD 780


>gi|358387637|gb|EHK25231.1| hypothetical protein TRIVIDRAFT_85034 [Trichoderma virens Gv29-8]
          Length = 1757

 Score =  158 bits (399), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 93/276 (33%), Positives = 147/276 (53%), Gaps = 37/276 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D ++FNRQPSLHK S+M HR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 452 DGDYIIFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 511

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE               K L    +N+V+P+    L+   QD + G Y + +++ F ++
Sbjct: 512 RAE--------------VKELCLVPNNIVSPQKNGPLMGIVQDSLAGAYKICRRDTFLDK 557

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M     L+    +  GII +       P + ++    WTGKQI S+++      P  
Sbjct: 558 NQVM----NLMLWVPNWDGIIPQ-------PAI-LKPRPRWTGKQIISMVI------PKE 599

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            +L     A     E   RD+ ++++  EL+ G M K  +GS     V ++   + G + 
Sbjct: 600 ISL----HAPEDKSESPLRDTGLLIQAGELMYGLMKKKNIGS-ASGGVIHLCYNELGPEG 654

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           A+  +  + ++ S++L+  G SIGIGD  P +  ++
Sbjct: 655 AMAFLNGVQQVVSYWLLQNGHSIGIGDTIPDKQTIE 690



 Score =  103 bits (256), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 46/63 (73%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTP+EFFFH M GREGL+DTAVKTAETGY+QRRLVK+LEDL  
Sbjct: 804 DYSPEARGFVENSYLRGLTPSEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDLNA 863

Query: 666 QYD 668
           QYD
Sbjct: 864 QYD 866



 Score =  102 bits (253), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 76/284 (26%), Positives = 135/284 (47%), Gaps = 39/284 (13%)

Query: 1145 GEVCEYIEEVF-VPDDS--------FILIKLDMDRIRLLHLEVDIDSIRYCI--ERTRGI 1193
             E  + +E  F +PDDS          L+++ +DR +LL  E+ ID +   I  E    +
Sbjct: 1177 AEDVDMVESYFLIPDDSQDTIDQQSRWLLRITLDRQKLLDKEIKIDDVAQRIKEEYPNDL 1236

Query: 1194 SGHLTVSGHSFLIL----------KPKDSSKSFNSKMYQMK---QLLPSVVIKGVQGINR 1240
            +   + +     ++          K +D  K     +   +    LL ++ ++GV G+ R
Sbjct: 1237 AVIFSDNNADEQVIRIRTIRQNDEKDEDGEKKIEDDVMLKRLEAHLLDTLTLRGVPGVER 1296

Query: 1241 AVIHE-----EDVEG----------VTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEV 1285
            A + +     E V+G           T++ L   G  LR+V+A  GV   +  +N+ ++V
Sbjct: 1297 AFLTKGTRLVESVDGSELALKDDIRCTQWYLDTSGSALREVLAVPGVDPTRTYTNDLWQV 1356

Query: 1286 YKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKES 1345
             +  GIE  R+ ++ E+  V+   G  ++ RH  L+ D+MT +G +  +TRHG+ +    
Sbjct: 1357 IEVFGIEGTRAALVKELTAVLAFDGSYVNHRHIALLCDVMTYRGSISAVTRHGINRADTG 1416

Query: 1346 VLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
             L   SFE T + L +AA  G+ D   G+SE +++G    +GTG
Sbjct: 1417 ALMRCSFEETVEILLEAAATGELDDCRGISENVMLGQMAPMGTG 1460



 Score = 87.0 bits (214), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 74/292 (25%), Positives = 133/292 (45%), Gaps = 60/292 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKD-TDLDYARIVKGRLE------------------ 804
            GVPR+KEI+N ++NI TP +  YLD      + A+ ++  +E                  
Sbjct: 1111 GVPRLKEILNLAKNIKTPSMAVYLDTPLAKQEQAKKLRSLVEYTNLRSITSVTEIYYDPD 1170

Query: 805  --RTTLGEVCEYIEEVF-VPDDS--------FILIKLDMDRIRLLHLEVDIDSIRYCI-- 851
               TT+ E  + +E  F +PDDS          L+++ +DR +LL  E+ ID +   I  
Sbjct: 1171 VQSTTIAEDVDMVESYFLIPDDSQDTIDQQSRWLLRITLDRQKLLDKEIKIDDVAQRIKE 1230

Query: 852  ERTRGISGHLTVSGHSFLIL----------KPKDSSKSFNSKMYQMK---QLLPSVVIKG 898
            E    ++   + +     ++          K +D  K     +   +    LL ++ ++G
Sbjct: 1231 EYPNDLAVIFSDNNADEQVIRIRTIRQNDEKDEDGEKKIEDDVMLKRLEAHLLDTLTLRG 1290

Query: 899  VQGINRAVIHE-----EDVEG----------VTKYKLLVEGDNLRDVMATYGVKGVKCSS 943
            V G+ RA + +     E V+G           T++ L   G  LR+V+A  GV   +  +
Sbjct: 1291 VPGVERAFLTKGTRLVESVDGSELALKDDIRCTQWYLDTSGSALREVLAVPGVDPTRTYT 1350

Query: 944  NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            N+ ++V +  GIE  R+ ++ E+  V+   G  ++ RH  L+ D+MT +G +
Sbjct: 1351 NDLWQVIEVFGIEGTRAALVKELTAVLAFDGSYVNHRHIALLCDVMTYRGSI 1402



 Score = 65.5 bits (158), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 29/72 (40%), Positives = 44/72 (61%), Gaps = 2/72 (2%)

Query: 115 PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSIC 174
           P   GL D  +G+  ++  C TC Q + +C GHFG+I+L  PV+H G+ + V  IL+ +C
Sbjct: 50  PRDGGLNDPLLGSIDRQFKCKTCTQAMGECPGHFGHIELAKPVYHPGFIKKVKKILEIVC 109

Query: 175 KNPTCARVLLGE 186
            N  C++VL  E
Sbjct: 110 HN--CSKVLADE 119



 Score = 55.5 bits (132), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/39 (61%), Positives = 29/39 (74%)

Query: 1107 REKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            + ++ R+ + P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1064 QNRWDRSFVNPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1102


>gi|13274097|emb|CAC33855.1| RNA polymerase II largest subunit [Cystosporogenes operophterae]
          Length = 982

 Score =  158 bits (399), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 98/280 (35%), Positives = 156/280 (55%), Gaps = 41/280 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           +ND VLFNRQPSLHK+S+M HRAK++  +TFR N    +PYNADFDGDEMN+H+PQ+  +
Sbjct: 330 NNDEVLFNRQPSLHKMSMMGHRAKIMQGKTFRLNLSATSPYNADFDGDEMNLHMPQSYPS 389

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           ++E L SL  +S               +V+P++ + +I   QD + G +L T +++FF R
Sbjct: 390 KSE-LCSLTSVS-------------KQIVSPQSNKPVIGIVQDTLVGAFLFTIRDSFFKR 435

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAV-----IWTGKQIFSLILKP-- 513
           A+ M +   L             F  ++ + + F++  +     +WTGKQIFS IL    
Sbjct: 436 AEAMSLLYNL-----------NVFGKKNQDFIDFMKPTILEPVELWTGKQIFSAILPRIF 484

Query: 514 -NRDCPVNANLKTKGRAYTANEEF----CHRDSYVILRNSELLAGSMDKSTLGSGGKANV 568
            +R   V  +     R    N+E+    C  DS  I++N  LLAG +D  ++G+  +  +
Sbjct: 485 YDRQANVGIDQDISDR-LNENKEWNTMNC-TDSRTIIKNGVLLAGRIDVVSMGT-KQGGI 541

Query: 569 FYILLRDFGEDVAVTAMWRLSRMTSFYLMN-RGFSIGIGD 607
             I+  D G + A+  +  + R+ +++L++   FSIGIGD
Sbjct: 542 IQIIYNDCGSNAALNFIDSIQRLINYFLLHISSFSIGIGD 581



 Score = 95.1 bits (235), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 40/59 (67%), Positives = 50/59 (84%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
           +GFVQNS+ SG+ P EFFFH MGG EG++DT++KTAETGY+QRRLVK+LED   Q+D S
Sbjct: 722 RGFVQNSYISGMWPDEFFFHAMGGGEGIIDTSIKTAETGYIQRRLVKALEDATAQHDYS 780



 Score = 52.8 bits (125), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 50/198 (25%), Positives = 81/198 (40%), Gaps = 42/198 (21%)

Query: 149 GYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKS 208
           G+++L  P+FH+GY   +   L+ +C    C+++ + + K         +  L +     
Sbjct: 1   GHMELSKPMFHVGYLTKIKKTLECVCF--YCSKIKISKNKL--------DEGLEHCWTAL 50

Query: 209 LKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAV 268
             K I E          CG     +KK GL  I+  K            ED   EYNE  
Sbjct: 51  KFKNICEGEVTSEGKTGCGNKQPSIKKEGLNLIAFMK------------ED---EYNEGK 95

Query: 269 KFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPN 328
                            LN   V  + + IP ED   L  + E  KP  +IL  ++VPP 
Sbjct: 96  ---------------VVLNGERVYNILKKIPEEDYRFLGFHPEFCKPEWMILCAIIVPPP 140

Query: 329 CIRPSVISD--LKSDNDV 344
            +RPS++ +  L+ ++D+
Sbjct: 141 AVRPSIVLNGYLRGEDDL 158


>gi|413917378|gb|AFW57310.1| RNA polymerase II large subunit family protein [Zea mays]
          Length = 1850

 Score =  158 bits (399), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 96/272 (35%), Positives = 149/272 (54%), Gaps = 37/272 (13%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D D VLFNRQPSLHK+SIM HR K++P+ TFR N  V +PYNADFDGDEMN+H+PQ+ E
Sbjct: 449 NDGDFVLFNRQPSLHKMSIMGHRIKIMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSFE 508

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE L             +++M  K  +V+P++   ++   QD + G   +T+++    
Sbjct: 509 TRAEVL-------------ELMMVPKC-IVSPQSNRPVMGIVQDTLLGCRKITKRDTLIE 554

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           +   M I    +    D  G I         P + ++   IWTGKQ+F+LI+      P 
Sbjct: 555 KDVFMNI----LMWWQDFDGKIPA-------PTI-LKPRPIWTGKQVFNLII------PK 596

Query: 520 NANLKTKGRAYTANEE---FCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
             NL  +  A+ + EE       D+ V +   ELL+G++ K +LG+G   ++ +++  + 
Sbjct: 597 QINL-IRFSAWHSEEEKGFITPGDTMVRIEKGELLSGTLCKKSLGTGS-GSLIHVIWEEV 654

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           G D A   +     + +++L+  GFSIGIGD 
Sbjct: 655 GPDAARKFLGHTQWLVNYWLLQNGFSIGIGDT 686



 Score =  108 bits (269), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 59/173 (34%), Positives = 96/173 (55%), Gaps = 9/173 (5%)

Query: 1226 LLPSVVIKGVQGINRAVIHEEDV---------EGVTKYKLLVEGDNLRDVMATYGVKGVK 1276
            +L  + ++G+  IN+  I E  V         +   ++ L  EG NL  VM    V   +
Sbjct: 1286 MLTEMALRGIPDINKVFIKEGKVNTFYQDDGFKAANEWMLDTEGVNLLAVMCHEDVDATR 1345

Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITR 1336
             +SN+  EV + LGIEA R +++ E+++V+   G  +++RH  ++ D MT +G ++ ITR
Sbjct: 1346 TTSNHLIEVIEVLGIEAVRRSLLDELRVVISFDGSYVNYRHLAILCDTMTYRGHLMAITR 1405

Query: 1337 HGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
            HG+ +     L   SFE T D L DAA Y ++D + GV+E I++G    +GTG
Sbjct: 1406 HGINRNDTGPLMRCSFEETVDILLDAAVYAESDHLRGVTENIMLGQLAPIGTG 1458



 Score =  100 bits (249), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 42/57 (73%), Positives = 52/57 (91%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKT+ETGY+QRRLVK++ED+ V+YD
Sbjct: 814 RGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDIMVKYD 870



 Score = 86.3 bits (212), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 68/248 (27%), Positives = 129/248 (52%), Gaps = 28/248 (11%)

Query: 82  LIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQR-TPIPHGLLDRRMGTNQKEANCTTCGQN 140
            ++  +   D ++Q S IQI     + +  +R  P P GL D R+GT  ++  C TC   
Sbjct: 17  FVQFGILSPDEIRQMSVIQIE----HAETMERGKPKPGGLSDPRLGTIDRKIKCETCMAG 72

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNP 199
           +++C GHFG+++L  P+FHIG+ + V++I++ +C N  C+++L  E++    +A K+RNP
Sbjct: 73  MAECPGHFGHLELAKPMFHIGFIKTVLSIMRCVCFN--CSKILADEDETKFKQALKIRNP 130

Query: 200 ALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNR----TKKKDA 255
                  K+  K+I +  K   VC    +++  V++    + + E  K R     ++ + 
Sbjct: 131 -------KNRLKRIYDACKSKKVCAGGDDLD--VQE----QDTDEPIKKRGGCGAQQPNI 177

Query: 256 IVE--DLLAEYNEA-VKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAEL 312
            V+   ++AE+     K + + +  +     Q L+   VL + + I  ED  LL +N + 
Sbjct: 178 TVDGMKMVAEFKAPKKKTDDQDQLPEPVERKQILSAERVLNVLKRISDEDCLLLGLNPKY 237

Query: 313 SKPSDLIL 320
           ++P  +IL
Sbjct: 238 ARPDWMIL 245



 Score = 79.3 bits (194), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 74/288 (25%), Positives = 132/288 (45%), Gaps = 54/288 (18%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDL--DYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR++EIIN ++ I TP ++ YL    +   + A+ V+  LE TTL  V    E  + P
Sbjct: 1115 GVPRLREIINVAKKIKTPSLSVYLKPQVNQKKELAKNVQCALEYTTLRSVTHATEIWYDP 1174

Query: 822  DDSFILIKLDMDRIR----LLHLEVDIDSI-----RYCIERTRGISGHLTVS------GH 866
            D    +I+ D + ++    +   ++D D I     R  + R   +   L+++        
Sbjct: 1175 DPLGTIIEEDTEFVQSYYEMPDEDIDPDKISPWLLRIELNREMMVDKKLSMADIAEKINR 1234

Query: 867  SF---------------LILK--------PK----DSSKSFNSKMYQMK-QLLPSVVIKG 898
             F               LIL+        PK    D S   +  + +++  +L  + ++G
Sbjct: 1235 EFDDDLSCIFNDDNADKLILRIRITNDEAPKGEIQDESAEDDVFLKKIEGNMLTEMALRG 1294

Query: 899  VQGINRAVIHEEDV---------EGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEV 949
            +  IN+  I E  V         +   ++ L  EG NL  VM    V   + +SN+  EV
Sbjct: 1295 IPDINKVFIKEGKVNTFYQDDGFKAANEWMLDTEGVNLLAVMCHEDVDATRTTSNHLIEV 1354

Query: 950  YKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             + LGIEA R +++ E+++V+   G  +++RH  ++ D MT +G ++ 
Sbjct: 1355 IEVLGIEAVRRSLLDELRVVISFDGSYVNYRHLAILCDTMTYRGHLMA 1402



 Score = 52.0 bits (123), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 20/37 (54%), Positives = 29/37 (78%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            +++++ + P   +G +AAQSIGEP TQMTL TFH+AG
Sbjct: 1070 RFLQSLVAPGEMIGCVAAQSIGEPATQMTLNTFHYAG 1106


>gi|133329|sp|P17545.1|RPB1B_TRYBB RecName: Full=DNA-directed RNA polymerase II subunit RPB1-B;
           Short=RNA polymerase II subunit B1-B; AltName:
           Full=DNA-directed RNA polymerase II largest subunit B
 gi|10503|emb|CAA31847.1| unnamed protein product [Trypanosoma brucei]
          Length = 1766

 Score =  158 bits (399), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 93/268 (34%), Positives = 144/268 (53%), Gaps = 39/268 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + DVVLFNRQP+LH++S+M HR +VL + TFR N    TPYNADFDGDEMN+H+PQ+   
Sbjct: 444 NGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNLSCTTPYNADFDGDEMNLHVPQSLLT 503

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE +             +++M  K N V+P      +   QD + G Y LT K+ F ++
Sbjct: 504 KAELI-------------EMMMVPK-NFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFLDK 549

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                +A  L     D+        W+   P + ++   +WTGKQ+FSLIL P  + P  
Sbjct: 550 YFVQSVALWL-----DL--------WQLPIPAI-LKPRPLWTGKQVFSLIL-PEVNHPAT 594

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
              +           F H DS V++R  +LL G + KS +G+    ++ +++  + G D 
Sbjct: 595 PQDRPP---------FPHNDSVVMIRRGQLLCGPITKSIVGA-APGSLIHVIFNEHGSDE 644

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
               +  + R+T+F+L+N GFS+G+ D 
Sbjct: 645 VARFINGVQRVTTFFLLNFGFSVGVQDT 672



 Score = 92.8 bits (229), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 67/209 (32%), Positives = 107/209 (51%), Gaps = 29/209 (13%)

Query: 1222 QMKQLLPSVVIKGVQGINRAVIHEE----------DVEGVTKYKLLVEGDNLRDVMATYG 1271
            ++  LL  V ++G+ G+ RA++ +            + G   + +  +G  LR   A  G
Sbjct: 1281 EIPALLARVHLRGIPGVRRALLKDTTEFTVDQATGKMSGNKIWAIDTDGTALR--RAFIG 1338

Query: 1272 VKG---------VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVA 1322
            V G         VK SSN   EV   LGIEAARS ++TE++     +G++I++RH  ++ 
Sbjct: 1339 VVGEDGKNIINAVKTSSNKVPEVCSLLGIEAARSKMLTELREAYLAYGLNINYRHYTILV 1398

Query: 1323 DLMTSKGEVLGITRHGLAKMKES-VLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMG 1381
            D +   G ++ ++R G+ +   S  L   SFE T   L  AA +G+ D + GVS  +++G
Sbjct: 1399 DTICQHGYLMAVSRSGINRSDTSGPLMRCSFEETVKVLMAAASFGECDPVRGVSANLVLG 1458

Query: 1382 LPMNVGTGLIKLL-------QAVPRSEPV 1403
                VGTGL  L+       QAVP++E V
Sbjct: 1459 NQARVGTGLFDLVLNMAALQQAVPQAEAV 1487



 Score = 83.2 bits (204), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 34/57 (59%), Positives = 44/57 (77%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +G     +  GL P EFFFHTM GREGL+DTAVKT++TGY+QR+L+K+LED+   YD
Sbjct: 800 RGMANRGYVEGLKPHEFFFHTMAGREGLIDTAVKTSDTGYLQRKLIKALEDVHAAYD 856



 Score = 70.9 bits (172), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 62/229 (27%), Positives = 100/229 (43%), Gaps = 42/229 (18%)

Query: 134 CTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFR 193
           C TC +   +C GHFGYI+L  PVF+IG F  V+ +L+ +CK  TC  +LL   +     
Sbjct: 69  CETCHRKHPECPGHFGYIELAEPVFNIGVFDLVLLVLKCVCK--TCGALLL-NTREQDVH 125

Query: 194 AKLRNPALSYLVRKSLKKKILETTKKVSVCPH----------------CGEINGVVKKCG 237
            KL++  ++ L R     K+ E   +VS                     G   G  + CG
Sbjct: 126 KKLQH--MTGLNRLRQVAKMAEAKCRVSTSTEDDMGIDGFDSAPFNGGSGMGPGATRGCG 183

Query: 238 LLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEA 297
                    + R  +   I   L+    +AV    + E H            +V Q+ + 
Sbjct: 184 -------ASQPRVSRFYGIYPTLVI---KAVHEEQDAEWHAD----------KVRQVLDR 223

Query: 298 IPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSV-ISDLKSDNDVV 345
           +  +D  L+  + +   P DL+LT L VPP  +RP++    L+SD+++ 
Sbjct: 224 VSDDDARLMGFDPQRCHPRDLVLTVLPVPPPQVRPAISFGGLRSDDELT 272



 Score = 63.2 bits (152), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 67/294 (22%), Positives = 121/294 (41%), Gaps = 62/294 (21%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDY-ARIVKGRLERTTLGEVCEYIEEVFVPD 822
            GVPR+ E++N SRN     +T  L    D    A+  +  +E  TL  +   I+ ++ PD
Sbjct: 1118 GVPRLLELLNVSRNQKHASMTVSLFPPYDEKRNAQKAQHLIEYCTLESITRRIQFIYDPD 1177

Query: 823  DSFILIKLDMDRIRL------------------------LHLEVDIDSIRYCIERTRGIS 858
                +++ D D + L                        + LE+D+D +       + + 
Sbjct: 1178 PRHTVVEADRDILELEWNVMDESDAELRIQEVVAGSPWVVRLELDVDMVTDKALDMKDVK 1237

Query: 859  GHLTVSGHSFLI----------------LKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGI 902
              +     S++I                 +  + + S      ++  LL  V ++G+ G+
Sbjct: 1238 QAILRVDESYIIETGMANNVRQRTIRMRSRYNEGADSIPKLKREIPALLARVHLRGIPGV 1297

Query: 903  NRAVIHEE----------DVEGVTKYKLLVEGDNLRDVMATYGVKG---------VKCSS 943
             RA++ +            + G   + +  +G  LR   A  GV G         VK SS
Sbjct: 1298 RRALLKDTTEFTVDQATGKMSGNKIWAIDTDGTALR--RAFIGVVGEDGKNIINAVKTSS 1355

Query: 944  NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            N   EV   LGIEAARS ++TE++     +G++I++RH  ++ D +   G ++ 
Sbjct: 1356 NKVPEVCSLLGIEAARSKMLTELREAYLAYGLNINYRHYTILVDTICQHGYLMA 1409



 Score = 50.8 bits (120), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 23/39 (58%), Positives = 27/39 (69%)

Query: 1107 REKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            R KY ++   P   +GA+AAQS GEP TQMTL TFH AG
Sbjct: 1071 RTKYHQSLTTPGENIGAIAAQSCGEPATQMTLNTFHNAG 1109


>gi|397135928|gb|AFO11459.1| RNA polymerase I, partial [Nadsonia fulvescens]
          Length = 872

 Score =  158 bits (399), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 94/281 (33%), Positives = 155/281 (55%), Gaps = 44/281 (15%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND VLFNRQPSLHK+S+MAHR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 251 DNDPVLFNRQPSLHKMSMMAHRVRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 310

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L +L ++  +          +V+P++ + ++   QD + G   +T ++ F + 
Sbjct: 311 RAE----LSQLCMVPLQ----------IVSPQSNKPVMGIVQDTLCGIRKMTLRDTFIDY 356

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVV----FVRTAVIWTGKQIFSLILKPNRD 516
            Q M           +IC     F    W+ VV     ++   +WTGKQ+ SL +     
Sbjct: 357 EQVM-----------NIC-----FWVPGWDGVVPHPAILKPKPLWTGKQMASLCI----- 395

Query: 517 CPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            P   +L+   R   +N     +D+ + + + +++ G +DK T+G+ G   + + ++R+ 
Sbjct: 396 -PKGIHLQ---RFDDSNPIISPKDNGMYIVDGQIIYGVVDKKTIGATG-GGLVHTIMREK 450

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQN 617
           G  +       + +  +F+L++ GFSIGIGD     G +++
Sbjct: 451 GSQICCNFFGSIQKTVNFWLLHNGFSIGIGDTIADAGTMRD 491



 Score =  102 bits (253), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GF++NS+  GLTP EFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+ V
Sbjct: 604 DYSPESKGFIENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDVMV 663

Query: 666 QYD 668
           QYD
Sbjct: 664 QYD 666


>gi|448434392|ref|ZP_21586202.1| DNA-directed RNA polymerase subunit A' [Halorubrum tebenquichense
           DSM 14210]
 gi|445685308|gb|ELZ37663.1| DNA-directed RNA polymerase subunit A' [Halorubrum tebenquichense
           DSM 14210]
          Length = 970

 Score =  158 bits (399), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 92/268 (34%), Positives = 140/268 (52%), Gaps = 45/268 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 476 DGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQNEEA 535

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR G  +I A QD I+G YLLT  N  F+ 
Sbjct: 536 RAE--------------ARVLMRVQEQILSPRFGGNIIGAIQDHISGTYLLTNSNPEFSE 581

Query: 461 AQTMR-IASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q +  + +T + +  +  G+                    WTG+ +FS +L  + D   
Sbjct: 582 TQALDLLRATRVDELPEADGVDD-------------EGQEFWTGRTLFSELLPDDLDLSF 628

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            ++                    V++ + +L+ G++D+  +G+ G   V   L +++GE 
Sbjct: 629 TSSAGDD----------------VVIEDGQLIRGTIDEDAVGAFG-GEVVDTLTKEYGET 671

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            +   +  ++ +    +MN GFSIGI D
Sbjct: 672 RSRVFINEIASLAMRAIMNFGFSIGIDD 699



 Score =  107 bits (268), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 79/294 (26%), Positives = 125/294 (42%), Gaps = 57/294 (19%)

Query: 97  SHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP 156
           S  ++++ + Y  D    PI  GL+D R+G       C TCG +   C GHFG+I+L  P
Sbjct: 19  SATKVITADTY--DDDGYPIDMGLMDPRLGVIDPGLECRTCGSHSGSCNGHFGHIELAAP 76

Query: 157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILET 216
           V H+G+ + +  +L+S C+   C R+ L + +   FR +             + K  +  
Sbjct: 77  VIHVGFTKLIRRLLRSTCRE--CGRLALDDAQRDEFRDRYERAKELGDDEHDVLKAAVRQ 134

Query: 217 TKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDL---------------- 260
            +K S CP CGE    +K        HEK     + +D +  D                 
Sbjct: 135 ARKASTCPFCGEPQADIK--------HEKPTTYYEVQDVLSGDYSERIAAAMQPDEEEDD 186

Query: 261 -------LAEYNE----------AVKFNPEIEAHKKFGL----------IQTLNPLEVLQ 293
                  LAE  +          A +F P  E  +              +  L P ++  
Sbjct: 187 PGTSPQELAEKTDIALDRVNDIMAGEFRPRKEDRRAIETALDVDLTEEDMNKLMPSDIRD 246

Query: 294 LFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDNDVV 345
            FE IP ED+ +L +++E S+P  +ILT L VPP   RPS+  D   +S++D+ 
Sbjct: 247 WFEDIPDEDLEVLGIDSEHSRPEWMILTVLPVPPVTTRPSITLDNGQRSEDDLT 300



 Score = 90.9 bits (224), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 38/57 (66%), Positives = 48/57 (84%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFV+NS+  GLTP EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 828 HGFVENSYRGGLTPEEFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELEAQYD 884


>gi|33326207|gb|AAQ08513.1| RNA polymerase II largest subunit [Pinus nigra]
          Length = 1013

 Score =  158 bits (399), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 93/271 (34%), Positives = 148/271 (54%), Gaps = 35/271 (12%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D D VLFNRQPSLHK+SIM HR K++P+ TFR N  V +PYNADFDGDEMN+H+PQ+ E
Sbjct: 372 NDGDFVLFNRQPSLHKMSIMGHRIKIMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSFE 431

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE L             +++M  K  +V+P++   ++   QD + G   +T+++ F  
Sbjct: 432 TRAEVL-------------ELMMVPKC-IVSPQSNRPVMGIVQDTLLGCRKITKRDTFIE 477

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           +   M I    +    D  G I         P ++ +   IWTGKQ+F+LI+      P 
Sbjct: 478 KDVFMNI----LMWWEDFDGKIP-------APTIY-KPRPIWTGKQVFNLII------PK 519

Query: 520 NANLKTKGRAYTANEE--FCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFG 577
             NL      ++ +E       D+ V +   E+++G++ K TLG+    ++ +++  + G
Sbjct: 520 QINLIRTSAWHSESESGVITPGDTLVRIEKGEVISGTLCKKTLGTSS-GSLIHVIWEEVG 578

Query: 578 EDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
            D A   +     + +++L+ +GFSIGIGD 
Sbjct: 579 PDAARKFLGHTQWLVNYWLLQQGFSIGIGDT 609



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 42/57 (73%), Positives = 52/57 (91%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKT+ETGY+QRRLVK++ED+ V+YD
Sbjct: 737 RGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDIMVKYD 793



 Score = 50.1 bits (118), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 46/182 (25%), Positives = 88/182 (48%), Gaps = 25/182 (13%)

Query: 150 YIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKS 208
           ++ L  P++HIG+ + V++IL+ +C N  C+R+L  E+     +A K++NP       K 
Sbjct: 1   HLXLAKPMYHIGFLKTVLSILRCVCFN--CSRILADEDDHRFKQALKVKNP-------KH 51

Query: 209 LKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVED---LLAEY- 264
             KK+L+  K  + C     I+    + G  ++  +++     ++  I  D   ++AEY 
Sbjct: 52  RLKKVLDCCKNKTKCEGGDVIDEDQGQDGDEEVKKKRHGGCGAQQPKITIDGMKIIAEYK 111

Query: 265 ------NEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDL 318
                 +E  +  PE    K     Q L+   VL + + I  E+  +L +N + ++P  +
Sbjct: 112 APRKKADEQEQLMPEPAERK-----QQLSAERVLNVLKRITDEECQMLGLNPKYARPDWM 166

Query: 319 IL 320
           IL
Sbjct: 167 IL 168


>gi|336126930|gb|AEI17890.1| RNA polymerase II largest subunit [fungal sp. FSU 1945]
          Length = 463

 Score =  158 bits (399), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 87/269 (32%), Positives = 144/269 (53%), Gaps = 33/269 (12%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D+DVV+FNRQPSLHK+S+M HR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQ+ E
Sbjct: 91  NDDDVVIFNRQPSLHKMSMMGHRVRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSLE 150

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE               ++ M  K  +V+P++ + ++   QD + G    T ++ F  
Sbjct: 151 TRAEV-------------TEICMVPKQ-IVSPQSNKPVMGIVQDTLCGIRKFTLRDCFLT 196

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSW-NPVVFVRTAVIWTGKQIFSLILKPNRDCP 518
           +   M I             ++   SW  +  P   ++   +WTGKQI ++++    +C 
Sbjct: 197 KDLVMNI-------------VMWVPSWDGYIPPPAILKPKPMWTGKQILAMVIPKGINCQ 243

Query: 519 VNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
              +    G     +      D+ VI+ N EL+ G + K T+G+ G   + + ++ + G 
Sbjct: 244 TFHSTHPDGETTLISPG----DTRVIIENGELICGIVCKKTVGTAG-GGLIHTIMNELGP 298

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           + A   +    ++ +++L+  GFSIGIGD
Sbjct: 299 EAAKNFLGGTQQVVNYWLLQNGFSIGIGD 327


>gi|397771993|ref|YP_006539539.1| DNA-directed RNA polymerase subunit A' [Natrinema sp. J7-2]
 gi|397681086|gb|AFO55463.1| DNA-directed RNA polymerase subunit A' [Natrinema sp. J7-2]
          Length = 975

 Score =  158 bits (399), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 100/270 (37%), Positives = 143/270 (52%), Gaps = 45/270 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 483 DGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQNEEA 542

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR GE +I A QD I+G YLLT  N  FN 
Sbjct: 543 RAE--------------ARVLMRVQEQMLSPRFGENIIGAIQDHISGMYLLTHDNPRFNE 588

Query: 461 AQTMR-IASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q +  + +T I +  +  GI    +               WTG  +FS +L      P 
Sbjct: 589 TQALDLLRATRIDELPEPSGIDDEGT-------------PFWTGYDVFSELL------PD 629

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           + +L+  G   T  +E       VI+ + +LL G++ +  +G  G   +   + + +G  
Sbjct: 630 DLDLEFTG---TIGDE-------VIIEDGQLLQGTIAEDEVGEFG-GEIVDTITKVYGNT 678

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVT 609
            A   +  +S +    +M+ GFSIGI D T
Sbjct: 679 RARIFVNEVSTLAMRAIMHFGFSIGIDDET 708



 Score =  111 bits (278), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 84/290 (28%), Positives = 131/290 (45%), Gaps = 43/290 (14%)

Query: 94  QQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDL 153
           ++ S  +I++ + Y  D    PI  GL+D R+G       C TCG++   C GHFG+I+L
Sbjct: 23  REMSATKIITADTY--DDDGFPIDMGLMDPRLGVIDPGLECKTCGKHSGSCNGHFGHIEL 80

Query: 154 PLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKI 213
             PV H+G+ + +  +L+  C+   C+++LL E++   FR +L            + K  
Sbjct: 81  AAPVIHVGFTKLIRRLLRGTCRE--CSKLLLTEDERDEFRDQLDESRKLSRDLNDVTKAA 138

Query: 214 LETTKKVSVCPHCGEINGVV---------------------KKCGLLKISHEKYKNRTKK 252
           +   +K   CP CGEI   +                     +  G ++   E+   RT  
Sbjct: 139 IRQARKKDRCPFCGEIQYDIDHEKPTTYYEVQQVLTSEYSQRIAGAMQGDEEEGVERT-T 197

Query: 253 KDAIVEDL---LAEYNEAV--KFNPE------IEAHKKFGLIQT----LNPLEVLQLFEA 297
            D + E     L   NE +   F P       IE      L +     L P ++   FE 
Sbjct: 198 PDELAEQTEIELTRVNEILSGSFRPRESQRKAIEKALDIDLTEEDTNKLMPSDIRDWFEN 257

Query: 298 IPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDNDVV 345
           IP EDI +L +N E S+P  +ILT L VPP   RPS+  D   +S++D+ 
Sbjct: 258 IPDEDIEVLGINPERSRPEWMILTVLPVPPVTARPSITLDNGQRSEDDLT 307



 Score = 92.8 bits (229), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 39/58 (67%), Positives = 49/58 (84%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
             GFV+NS+ SGLTP EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 834 AHGFVENSYTSGLTPREFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELETQYD 891



 Score = 45.8 bits (107), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 29/46 (63%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 65
           +VLM  +  +++PR GE +I A QD I+G YLLT  N  FN  Q +
Sbjct: 547 RVLMRVQEQMLSPRFGENIIGAIQDHISGMYLLTHDNPRFNETQAL 592


>gi|133332|sp|P17546.1|RPB1A_TRYBB RecName: Full=DNA-directed RNA polymerase II subunit RPB1-A;
           Short=RNA polymerase II subunit B1-A; AltName:
           Full=DNA-directed RNA polymerase II largest subunit A
 gi|10505|emb|CAA31846.1| unnamed protein product [Trypanosoma brucei]
          Length = 1766

 Score =  158 bits (399), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 93/267 (34%), Positives = 144/267 (53%), Gaps = 39/267 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + DVVLFNRQP+LH++S+M HR +VL + TFR N    TPYNADFDGDEMN+H+PQ+   
Sbjct: 444 NGDVVLFNRQPTLHRMSMMGHRVRVLNYSTFRLNLSCTTPYNADFDGDEMNLHVPQSLLT 503

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE +             +++M  K N V+P      +   QD + G Y LT K+ F ++
Sbjct: 504 KAELI-------------EMMMVPK-NFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFLDK 549

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                +A  L     D+        W+   P + ++   +WTGKQ+FSLIL P  + P  
Sbjct: 550 YFVQSVALWL-----DL--------WQLPIPAI-LKPRPLWTGKQVFSLIL-PEVNHPAT 594

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
              +           F H DS V++R  +LL G + KS +G+    ++ +++  + G D 
Sbjct: 595 PQDRPP---------FPHNDSVVMIRRGQLLCGPITKSIVGA-APGSLIHVIFNEHGSDE 644

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGD 607
               +  + R+T+F+L+N GFS+G+ D
Sbjct: 645 VARFINGVQRVTTFFLLNFGFSVGVQD 671



 Score = 92.8 bits (229), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 67/209 (32%), Positives = 107/209 (51%), Gaps = 29/209 (13%)

Query: 1222 QMKQLLPSVVIKGVQGINRAVIHEE----------DVEGVTKYKLLVEGDNLRDVMATYG 1271
            ++  LL  V ++G+ G+ RA++ +            + G   + +  +G  LR   A  G
Sbjct: 1281 EIPALLARVHLRGIPGVRRALLKDTTEFTVDQATGKMSGNKIWAIDTDGTALR--RAFIG 1338

Query: 1272 VKG---------VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVA 1322
            V G         VK SSN   EV   LGIEAARS ++TE++     +G++I++RH  ++ 
Sbjct: 1339 VVGEDGKNIINAVKTSSNKVPEVCSLLGIEAARSKMLTELREAYLAYGLNINYRHYTILV 1398

Query: 1323 DLMTSKGEVLGITRHGLAKMKES-VLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMG 1381
            D +   G ++ ++R G+ +   S  L   SFE T   L  AA +G+ D + GVS  +++G
Sbjct: 1399 DTICQHGYLMAVSRSGINRSDTSGPLMRCSFEETVKVLMAAASFGECDPVRGVSANLVLG 1458

Query: 1382 LPMNVGTGLIKLL-------QAVPRSEPV 1403
                VGTGL  L+       QAVP++E V
Sbjct: 1459 NQARVGTGLFDLVLNMAALQQAVPQAEAV 1487



 Score = 83.2 bits (204), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 34/57 (59%), Positives = 44/57 (77%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +G     +  GL P EFFFHTM GREGL+DTAVKT++TGY+QR+L+K+LED+   YD
Sbjct: 800 RGMANRGYVEGLKPHEFFFHTMAGREGLIDTAVKTSDTGYLQRKLIKALEDVHAAYD 856



 Score = 70.1 bits (170), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 62/228 (27%), Positives = 100/228 (43%), Gaps = 42/228 (18%)

Query: 134 CTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFR 193
           C TC +   +C GHFGYI+L  PVF+IG F  V+ +L+ +CK  TC  +LL   +     
Sbjct: 69  CETCHRKHPECPGHFGYIELAEPVFNIGVFDLVLLVLKCVCK--TCGALLL-NTREQDVH 125

Query: 194 AKLRNPALSYLVRKSLKKKILETTKKVSVCPH----------------CGEINGVVKKCG 237
            KL++  ++ L R     K+ E   +VS                     G   G  + CG
Sbjct: 126 KKLQH--VTGLNRLRQVAKMAEAKCRVSTSTEDDMGIDGFDSAPFNGGSGMGPGATRGCG 183

Query: 238 LLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEA 297
                    + R  +   I   L+    +AV    + E H            +V Q+ + 
Sbjct: 184 -------ASQPRVSRFYGIYPTLVI---KAVHEEQDAEWHAD----------KVRQVLDR 223

Query: 298 IPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSV-ISDLKSDNDV 344
           +  +D  L+  + +   P DL+LT L VPP  +RP++    L+SD+++
Sbjct: 224 VSDDDARLMGFDPQRCHPRDLVLTVLPVPPPQVRPAISFGGLRSDDEL 271



 Score = 62.8 bits (151), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 67/294 (22%), Positives = 121/294 (41%), Gaps = 62/294 (21%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDY-ARIVKGRLERTTLGEVCEYIEEVFVPD 822
            GVPR+ E++N SRN     +T  L    D    A+  +  +E  TL  +   I+ ++ PD
Sbjct: 1118 GVPRLLELLNVSRNQKHASMTVSLFPPYDEKRNAQKAQHLIEYCTLESITRRIQFIYDPD 1177

Query: 823  DSFILIKLDMDRIRL------------------------LHLEVDIDSIRYCIERTRGIS 858
                +++ D D + L                        + LE+D+D +       + + 
Sbjct: 1178 PRHTVVEADRDILELEWNVMDESDAELRIQEVVAGSPWVVRLELDVDMVTDKALDMKDVK 1237

Query: 859  GHLTVSGHSFLI----------------LKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGI 902
              +     S++I                 +  + + S      ++  LL  V ++G+ G+
Sbjct: 1238 QAILRVDESYIIETGMANNVRQRTIRMRSRYNEGADSIPKLKREIPALLARVHLRGIPGV 1297

Query: 903  NRAVIHEE----------DVEGVTKYKLLVEGDNLRDVMATYGVKG---------VKCSS 943
             RA++ +            + G   + +  +G  LR   A  GV G         VK SS
Sbjct: 1298 RRALLKDTTEFTVDQATGKMSGNKIWAIDTDGTALR--RAFIGVVGEDGKNIINAVKTSS 1355

Query: 944  NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            N   EV   LGIEAARS ++TE++     +G++I++RH  ++ D +   G ++ 
Sbjct: 1356 NKVPEVCSLLGIEAARSKMLTELREAYLAYGLNINYRHYTILVDTICQHGYLMA 1409



 Score = 50.8 bits (120), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 23/39 (58%), Positives = 27/39 (69%)

Query: 1107 REKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            R KY ++   P   +GA+AAQS GEP TQMTL TFH AG
Sbjct: 1071 RTKYHQSLTTPGENIGAIAAQSCGEPATQMTLNTFHNAG 1109


>gi|188532155|gb|ACD63089.1| RNA polymerase II largest subunit [Persea americana]
          Length = 1009

 Score =  157 bits (398), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 95/271 (35%), Positives = 147/271 (54%), Gaps = 35/271 (12%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D D VLFNRQPSLHK+SIM HR K++P+ TFR N  V +PYNADFDGDEMN+H+PQ+ E
Sbjct: 368 NDGDFVLFNRQPSLHKMSIMGHRIKIMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSFE 427

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE L             +++M  K  +V+P++   ++   QD + G   +T+++ F  
Sbjct: 428 TRAEVL-------------ELMMVPKC-IVSPQSNRPVMGIVQDTLLGCRKITKRDTFIE 473

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           +   M I    +    D  G I         P + ++   +WTGKQ+F+LI+      P 
Sbjct: 474 KDVFMNI----LMWWEDFDGKIP-------APAI-LKPRPLWTGKQVFNLII------PK 515

Query: 520 NANLKTKGRAYTANEE--FCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFG 577
             NL      ++ +E       D+ V +   ELLAG++ K TLG+    ++ +++  + G
Sbjct: 516 QINLIXTSAWHSESETGFITPGDTQVRIEKGELLAGTLCKKTLGT-STGSLIHVIWEEVG 574

Query: 578 EDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
            D A   +     + +++L+  GFSIGIGD 
Sbjct: 575 PDAARKFLGHTQWLVNYWLLQNGFSIGIGDT 605



 Score =  100 bits (249), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 42/57 (73%), Positives = 52/57 (91%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKT+ETGY+QRRLVK++ED+ V+YD
Sbjct: 733 RGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDIMVKYD 789



 Score = 50.1 bits (118), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 51/197 (25%), Positives = 97/197 (49%), Gaps = 13/197 (6%)

Query: 150 YIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKS 208
           +++L  P+FHIG+ + V+ I++ +C N  C+++L+  +     ++ K+RNP       K 
Sbjct: 1   HLELAKPMFHIGFMKTVLTIMRCVCFN--CSKILVDXDDLKFKQSQKIRNP-------KH 51

Query: 209 LKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVE--DLLAEYNE 266
             K++ +  K    C    E++ V  +     +   +     ++    +E   ++AEY  
Sbjct: 52  RLKRVFDACKNKQKCEGGDEMD-VQGQGSEEPVKKSRGGCGAQQPKLTIEGMKMIAEYKG 110

Query: 267 AVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVP 326
           + K N E    +     Q L+   VL + + I  ED  LL +N + ++P  +IL  L +P
Sbjct: 111 SRKKNDEEPLPEPVERKQQLSAERVLSVLKRISDEDCMLLGLNPKYARPDWMILQVLPIP 170

Query: 327 PNCIRPSVISDLKSDND 343
           P  +RPSV+ D  S ++
Sbjct: 171 PPPVRPSVMMDTSSRSE 187


>gi|448342574|ref|ZP_21531522.1| DNA-directed RNA polymerase subunit A' [Natrinema gari JCM 14663]
 gi|445625329|gb|ELY78691.1| DNA-directed RNA polymerase subunit A' [Natrinema gari JCM 14663]
          Length = 975

 Score =  157 bits (398), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 100/270 (37%), Positives = 143/270 (52%), Gaps = 45/270 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 483 DGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQNEEA 542

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR GE +I A QD I+G YLLT  N  FN 
Sbjct: 543 RAE--------------ARVLMRVQEQMLSPRFGENIIGAIQDHISGMYLLTHDNPRFNE 588

Query: 461 AQTMR-IASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q +  + +T I +  +  GI    +               WTG  +FS +L      P 
Sbjct: 589 TQALDLLRATRIDELPEPSGIDDEGT-------------PFWTGYDVFSELL------PD 629

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           + +L+  G   T  +E       VI+ + +LL G++ +  +G  G   +   + + +G  
Sbjct: 630 DLDLEFTG---TIGDE-------VIIEDGQLLQGTIAEDEVGEFG-GEIVDTITKVYGNT 678

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVT 609
            A   +  +S +    +M+ GFSIGI D T
Sbjct: 679 RARIFVNEVSTLAMRAIMHFGFSIGIDDET 708



 Score =  111 bits (278), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 84/290 (28%), Positives = 131/290 (45%), Gaps = 43/290 (14%)

Query: 94  QQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDL 153
           ++ S  +I++ + Y  D    PI  GL+D R+G       C TCG++   C GHFG+I+L
Sbjct: 23  REMSATKIITADTY--DDDGFPIDMGLMDPRLGVIDPGLECKTCGKHSGSCNGHFGHIEL 80

Query: 154 PLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKI 213
             PV H+G+ + +  +L+  C+   C+++LL E++   FR +L            + K  
Sbjct: 81  AAPVIHVGFTKLIRRLLRGTCRE--CSKLLLTEDERDEFRDQLDESRKLSRDLNDVTKAA 138

Query: 214 LETTKKVSVCPHCGEINGVV---------------------KKCGLLKISHEKYKNRTKK 252
           +   +K   CP CGEI   +                     +  G ++   E+   RT  
Sbjct: 139 IRQARKKDRCPFCGEIQYDIDHEKPTTYYEVQQVLTSEYSQRIAGAMQGDEEEGVERT-T 197

Query: 253 KDAIVEDL---LAEYNEAV--KFNPE------IEAHKKFGLIQT----LNPLEVLQLFEA 297
            D + E     L   NE +   F P       IE      L +     L P ++   FE 
Sbjct: 198 PDELAEQTEIELTRVNEILSGSFRPRESQRKAIEKALDIDLTEEDTNKLMPSDIRDWFEN 257

Query: 298 IPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDNDVV 345
           IP EDI +L +N E S+P  +ILT L VPP   RPS+  D   +S++D+ 
Sbjct: 258 IPDEDIEVLGINPERSRPEWMILTVLPVPPVTARPSITLDNGQRSEDDLT 307



 Score = 92.8 bits (229), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 39/58 (67%), Positives = 49/58 (84%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
             GFV+NS+ SGLTP EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 834 AHGFVENSYTSGLTPREFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELETQYD 891



 Score = 45.8 bits (107), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 29/46 (63%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 65
           +VLM  +  +++PR GE +I A QD I+G YLLT  N  FN  Q +
Sbjct: 547 RVLMRVQEQMLSPRFGENIIGAIQDHISGMYLLTHDNPRFNETQAL 592


>gi|345004223|ref|YP_004807076.1| DNA-directed RNA polymerase subunit A'' [halophilic archaeon DL31]
 gi|344319849|gb|AEN04703.1| DNA-directed RNA polymerase, subunit A'' [halophilic archaeon DL31]
          Length = 412

 Score =  157 bits (398), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 115/369 (31%), Positives = 185/369 (50%), Gaps = 67/369 (18%)

Query: 1100 ACKAE------ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-------- 1145
            A KAE      A   +Y   +++    VG ++AQSIGEPGTQ+T+ TFHFAG        
Sbjct: 43   ATKAEVQDIVTAVVNRYEETRVDALDPVGTVSAQSIGEPGTQLTMNTFHFAGVAEIDVTQ 102

Query: 1146 ---EVCEYIEEVFVPDDSFILIKLD------MDRIR--------------------LLHL 1176
                + E ++    PD   + + LD       D+ R                    +  +
Sbjct: 103  GLPRLIELVDARKTPDTPTMTVYLDGEYATDRDKAREVVWQIEATKILALGNVSTNVADM 162

Query: 1177 EVDIDSIRYCIER-------TRGISGHLTVSGHSFLIL--KPKDSSKSFN------SKMY 1221
            +V ID     +++          I+  +  S  S L +  K K ++ +F        ++ 
Sbjct: 163  QVTIDLNEETLQKRWPTYDDVGTIAAEIQESIESNLKVATKRKGTAIAFGPEEPSYRRLL 222

Query: 1222 QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTK-----YKLLVEGDNLRDVMATYGVKGVK 1276
            Q+ + L  V+ KG++ ++R VI +E++    +     + L  EG    DV+   GV   +
Sbjct: 223  QLVEELREVIFKGIEEVSRVVIRKEEIGAEEEEEEEEFVLYTEGSAFGDVLDIEGVDTTR 282

Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMS-IDFRHPMLVADLMTSKGEVLGIT 1335
             + NN +EV+  LGIEAAR TI+ E    +   G+  ++ RH MLVAD+MT++G +  I 
Sbjct: 283  STCNNIHEVHSELGIEAARETIINETNETLAEQGLDDVNVRHLMLVADIMTNRGTIQSIG 342

Query: 1336 RHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQ 1395
            RHG++  K+SVL  A+FE T +HL DAA +G+ D ++GV E +I+G P+++GTG + L  
Sbjct: 343  RHGISGSKDSVLARAAFEVTVNHLLDAAIHGEVDDLNGVIENVIVGKPVSIGTGDVDLRM 402

Query: 1396 AVPRSEPVP 1404
                S+P P
Sbjct: 403  G---SKPTP 408



 Score = 90.1 bits (222), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 75/250 (30%), Positives = 125/250 (50%), Gaps = 24/250 (9%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERT---TLGEVCEYIEEV 818
           G+PR+ E+++A +   TP +T YLD +  TD D AR V  ++E T    LG V   +   
Sbjct: 103 GLPRLIELVDARKTPDTPTMTVYLDGEYATDRDKAREVVWQIEATKILALGNVSTNVA-- 160

Query: 819 FVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGH---SFLILKPKD 875
               D  + I L+ + ++      D D      E    I  +L V+     + +   P++
Sbjct: 161 ----DMQVTIDLNEETLQKRWPTYD-DVGTIAAEIQESIESNLKVATKRKGTAIAFGPEE 215

Query: 876 SSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTK-----YKLLVEGDNLRDV 930
            S     ++ Q+ + L  V+ KG++ ++R VI +E++    +     + L  EG    DV
Sbjct: 216 PSYR---RLLQLVEELREVIFKGIEEVSRVVIRKEEIGAEEEEEEEEFVLYTEGSAFGDV 272

Query: 931 MATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGM-SIDFRHPMLVADLM 989
           +   GV   + + NN +EV+  LGIEAAR TI+ E    +   G+  ++ RH MLVAD+M
Sbjct: 273 LDIEGVDTTRSTCNNIHEVHSELGIEAARETIINETNETLAEQGLDDVNVRHLMLVADIM 332

Query: 990 TSKGEVLGNG 999
           T++G +   G
Sbjct: 333 TNRGTIQSIG 342


>gi|33326211|gb|AAQ08515.1| RNA polymerase II largest subunit [Zea mays]
          Length = 1009

 Score =  157 bits (398), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 96/272 (35%), Positives = 149/272 (54%), Gaps = 37/272 (13%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D D VLFNRQPSLHK+SIM HR K++P+ TFR N  V +PYNADFDGDEMN+H+PQ+ E
Sbjct: 368 NDGDFVLFNRQPSLHKMSIMGHRIKIMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSFE 427

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE L             +++M  K  +V+P++   ++   QD + G   +T+++    
Sbjct: 428 TRAEVL-------------ELMMVPKC-IVSPQSNRPVMGIVQDTLLGCRKITKRDTLIE 473

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           +   M I    +    D  G I         P + ++   IWTGKQ+F+LI+      P 
Sbjct: 474 KDVFMNI----LMWWQDFDGKIP-------APTI-LKPRPIWTGKQVFNLII------PK 515

Query: 520 NANLKTKGRAYTANEE---FCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
             NL  +  A+ + EE       D+ V +   ELL+G++ K +LG+G   ++ +++  + 
Sbjct: 516 QINL-IRFSAWHSEEEKGFITPGDTMVRIEKGELLSGTLCKKSLGTGS-GSLIHVIWEEV 573

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           G D A   +     + +++L+  GFSIGIGD 
Sbjct: 574 GPDAARKFLGHTQWLVNYWLLQNGFSIGIGDT 605



 Score =  100 bits (249), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 42/57 (73%), Positives = 52/57 (91%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKT+ETGY+QRRLVK++ED+ V+YD
Sbjct: 733 RGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDIMVKYD 789



 Score = 46.2 bits (108), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 45/183 (24%), Positives = 81/183 (44%), Gaps = 31/183 (16%)

Query: 150 YIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKS 208
           +++L  P+FHIG+ + V++I++ +C N  C+++L  E++    +A K+RNP       K+
Sbjct: 1   HLELAKPMFHIGFIKTVLSIMRCVCFN--CSKILADEDETKFKQALKIRNP-------KN 51

Query: 209 LKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAV 268
             K+I +  K   VC    +          L +  +      KK+            + +
Sbjct: 52  RLKRIYDACKSKKVCAGGDD----------LDVQEQDTDEPIKKRGGCGAQQPNITVDGM 101

Query: 269 KFNPEIEAHKK-----------FGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSD 317
           K   E +A KK               Q L+   VL + + I  ED  LL +N + ++P  
Sbjct: 102 KMVAEFKAPKKKTDDQDQLPEPVERKQILSAERVLNVLKRISDEDCLLLGLNPKYARPDW 161

Query: 318 LIL 320
           +IL
Sbjct: 162 MIL 164


>gi|448417596|ref|ZP_21579452.1| DNA-directed RNA polymerase subunit A' [Halosarcina pallida JCM
           14848]
 gi|445677550|gb|ELZ30050.1| DNA-directed RNA polymerase subunit A' [Halosarcina pallida JCM
           14848]
          Length = 976

 Score =  157 bits (398), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 97/268 (36%), Positives = 146/268 (54%), Gaps = 45/268 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+++FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  QTEEA
Sbjct: 482 DGDIIIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQTEEA 541

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR G+ +I A QD I+G YLLT  N  F+ 
Sbjct: 542 RAE--------------ARVLMRVQEQILSPRFGQNIIGAIQDHISGTYLLTNGNPHFSE 587

Query: 461 AQTMRIASTLIADT-SDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q + +      DT  +  G  +    R +           WTG+Q+FS +L      P 
Sbjct: 588 TQALDLLRATSIDTLPEPAG--EEADGRPY-----------WTGRQLFSELL------PD 628

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           + NL+     +T++         V++ + +LL G++D+  +G+ G   V   L + + + 
Sbjct: 629 DLNLE-----FTSS-----TGEDVVIEDGQLLEGTIDEDAVGAFG-GEVVDTLAKVYSKT 677

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            A   +  ++ +    +M+ GFSIGI D
Sbjct: 678 RARVFINEVASLAMRAIMHFGFSIGIDD 705



 Score =  106 bits (264), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 83/312 (26%), Positives = 132/312 (42%), Gaps = 60/312 (19%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G I+  +   +  +  S  ++++ + Y  D    PI  GL+D R+G       C TCG +
Sbjct: 8   GAIQFGLMDPETYRDMSATKVITADTY--DDDGYPIDMGLMDPRLGVIDPGLECRTCGSH 65

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKL-RNP 199
              C GHFG+I+L  PV H+G+ + +  +L+S C+   C R+ L +E++  FR+ L R  
Sbjct: 66  SGSCNGHFGHIELAAPVIHVGFTKLIRRLLRSTCRE--CGRLSLTDEESEEFRSGLTRTE 123

Query: 200 ALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVED 259
            L       LK  + +  +K   CPHCG     +K        HEK     + +D +  D
Sbjct: 124 ELGDDWTDVLKSAVRQ-ARKAKRCPHCGAPQHDIK--------HEKPTTYYEVQDVLAGD 174

Query: 260 LLAEYNEAVK----------------------------------FNPEIEAHKKFGL--- 282
                 EA++                                  F P  +  KK      
Sbjct: 175 FSERIAEAMQPDEDEEDDAGIAPATLADETGIALQRVNQILSGEFRPVGDDRKKLEKALD 234

Query: 283 -------IQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVI 335
                  +  L P ++   FE IP EDI  L ++   ++P  +ILT L VPP   RPS+ 
Sbjct: 235 VDLTEEDMNKLMPSDIRDWFEDIPDEDIVTLGVDPSRARPEWMILTVLPVPPVTARPSIT 294

Query: 336 SD--LKSDNDVV 345
            D   +S++D+ 
Sbjct: 295 LDNGQRSEDDLT 306



 Score = 92.8 bits (229), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 39/57 (68%), Positives = 49/57 (85%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFV+NS+  GLTPTEFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 834 HGFVENSYRGGLTPTEFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALTELEAQYD 890



 Score = 42.7 bits (99), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 19/48 (39%), Positives = 30/48 (62%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRI 67
           +VLM  +  +++PR G+ +I A QD I+G YLLT  N  F+  Q + +
Sbjct: 546 RVLMRVQEQILSPRFGQNIIGAIQDHISGTYLLTNGNPHFSETQALDL 593


>gi|110669629|gb|ABG81909.1| RNA polymerase II largest subunit [Roccella fuciformis]
          Length = 1017

 Score =  157 bits (398), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 95/284 (33%), Positives = 139/284 (48%), Gaps = 65/284 (22%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D ++FNRQPSLHK S M HR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 377 DGDYIIFNRQPSLHKESRMGHRVRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 436

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE +               L     N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 437 RAEVMN--------------LCMVPLNIVSPQRNGPLMGIVQDTLCGIYKICRRDVFLTQ 482

Query: 461 AQTMRIASTLIADTSDICGIIKRFSW-RSWNPVV----FVRTAVIWTGKQIFSLILKPN- 514
            Q M +                   W  SW+ V+     V+ +  WTGKQI S+ L P  
Sbjct: 483 EQVMNV-----------------LLWVPSWDGVLPQPAIVKPSPRWTGKQIISMALVPGL 525

Query: 515 --------RDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKA 566
                    DCPVN                   D  +++ N EL+ G   K ++G+ G  
Sbjct: 526 NLVRKGEEGDCPVN-------------------DDGLLIDNGELIYGLFSKKSVGATG-G 565

Query: 567 NVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
            V + +  + G + AV  +     + +++L++ GFSIGIGD  P
Sbjct: 566 GVIHTIFNERGPEAAVAFINGAQTIVNYWLLHNGFSIGIGDTVP 609



 Score = 97.4 bits (241), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 43/63 (68%), Positives = 52/63 (82%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+N +  GLTP EFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+  
Sbjct: 729 DYSPESRGFVENPYLQGLTPAEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDVMA 788

Query: 666 QYD 668
           +YD
Sbjct: 789 KYD 791



 Score = 70.1 bits (170), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 65/228 (28%), Positives = 105/228 (46%), Gaps = 53/228 (23%)

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA--KLRNPA 200
           +C GHFG+I+L +PVFH G+   V  IL+S+C N  C + LL +E+   F+A   +++P 
Sbjct: 1   ECPGHFGHIELAVPVFHAGFVTKVKKILESVCHN--CGK-LLDDERNPHFKAACNIKDPK 57

Query: 201 LSY-LVRKSLKKKIL---------------ETTKKVSVCPH--CGEINGVVKKCGL-LKI 241
             +  + K  K K++                   K+ V  H  CG I   +++  L L  
Sbjct: 58  RRFDAIHKLCKPKMVCEPDIQDDGNDDFGGNPKAKLKVKGHGGCGNIQPEIRRDALRLTG 117

Query: 242 SHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLE 301
           + +  K   +++D                 PE    KK      + P   L +F  I   
Sbjct: 118 TWKLPKGEEQEEDK---------------GPE----KKI-----ITPQMALNVFRNITDR 153

Query: 302 DIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD-----LKSDNDV 344
            + LL  NA+ ++P  LILT L VPP  +RPS+  D     ++S++D+
Sbjct: 154 GLTLLGSNADYARPEWLILTVLPVPPPAVRPSISVDGTSQGMRSEDDL 201


>gi|413915234|gb|AFW21479.1| RNA polymerase II largest subunit [Neotyphodium gansuense var.
           inebrians]
          Length = 1761

 Score =  157 bits (398), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 88/277 (31%), Positives = 151/277 (54%), Gaps = 34/277 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D ++FNRQPSLHK S+M HR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 450 DGDYIIFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 509

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE               K L    +N+V+P+    L+   QD + G Y + +++ F ++
Sbjct: 510 RAE--------------VKELCLVPNNIVSPQKNGPLMGVVQDSLAGAYKICRRDTFIDK 555

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              M     ++    +  G+I +       P + ++    WTGKQ+ S+++      P  
Sbjct: 556 EMVM----NMMLWVPNWDGVIPQ-------PAI-LKPRPRWTGKQLISMVI------PKE 597

Query: 521 ANLKT-KGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            +L + +  A   N +   +D+ +++++ ELL G + K  +GS     + ++   + G D
Sbjct: 598 ISLHSPESSAGQDNADIPLKDTGLLIQSGELLYGLLKKKNIGSAA-GGIVHLSYNELGPD 656

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
            A+  +  + ++ +++L+N G SIGIGD  P +  ++
Sbjct: 657 GAMAFLNGVQQVVTYWLLNNGHSIGIGDTVPDKQTIE 693



 Score =  107 bits (267), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 81/283 (28%), Positives = 136/283 (48%), Gaps = 39/283 (13%)

Query: 1146 EVCEYIEEVF-VPDDS--------FILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGH 1196
            E  + +E  F +PDDS          L+++ +DR +LL  E+ ID +   I+        
Sbjct: 1181 EDMDMVESYFLIPDDSQDTTDQQSRWLLRITLDRQKLLDKEIKIDDVAQRIKEEYPSDLA 1240

Query: 1197 LTVSGHSF---LIL---------KPKDSSKSFNSKMYQMK---QLLPSVVIKGVQGINRA 1241
            +  S ++    +I          K +D  K     +   +    LL ++ ++GV GI RA
Sbjct: 1241 IIFSDNNADEQVIRIRTIRADNEKDEDGEKKIEDDVMLKRLEAHLLDTLTLRGVPGIERA 1300

Query: 1242 V---------------IHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVY 1286
                            I ++D +  T++ L   G  LRDV+A  GV   +  +N+ ++V 
Sbjct: 1301 FLTKGTRLVVDDDGAEIAKKDDDKCTQWYLDTSGSALRDVLAVDGVDPTRTYTNDLWQVV 1360

Query: 1287 KTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESV 1346
            +  GIEAARS ++ E+  V+   G  ++ RH  L+ D+MT +G +  +TRHG+ +     
Sbjct: 1361 EVFGIEAARSALVKELTNVLAFDGSYVNHRHIALLVDVMTYRGTISAVTRHGINRADTGA 1420

Query: 1347 LNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
            L   SFE T + L +AA  G+ D   G+SE +++G    +GTG
Sbjct: 1421 LMRCSFEETVEILLEAAASGELDDCRGISENVMLGQLAPMGTG 1463



 Score =  103 bits (256), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 46/63 (73%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QRRLVK+LEDL  
Sbjct: 807 DYSPEARGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDLSA 866

Query: 666 QYD 668
           +YD
Sbjct: 867 RYD 869



 Score = 86.3 bits (212), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 76/292 (26%), Positives = 133/292 (45%), Gaps = 60/292 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDL-DYARIVKGRLERTTLGEVC---------- 812
            GVPR+KEI+N +++I TP +  YL+      + A+ ++  +E T L  +           
Sbjct: 1114 GVPRLKEILNLAKDIKTPSMAVYLNTHLGTQEQAKKLRSLVEYTNLRSITSVTEIYYDPD 1173

Query: 813  ----------EYIEEVF-VPDDS--------FILIKLDMDRIRLLHLEVDIDSIRYCIER 853
                      + +E  F +PDDS          L+++ +DR +LL  E+ ID +   I+ 
Sbjct: 1174 IQSTSIVEDMDMVESYFLIPDDSQDTTDQQSRWLLRITLDRQKLLDKEIKIDDVAQRIKE 1233

Query: 854  TRGISGHLTVSGHSF---LIL---------KPKDSSKSFNSKMYQMK---QLLPSVVIKG 898
                   +  S ++    +I          K +D  K     +   +    LL ++ ++G
Sbjct: 1234 EYPSDLAIIFSDNNADEQVIRIRTIRADNEKDEDGEKKIEDDVMLKRLEAHLLDTLTLRG 1293

Query: 899  VQGINRAV---------------IHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSS 943
            V GI RA                I ++D +  T++ L   G  LRDV+A  GV   +  +
Sbjct: 1294 VPGIERAFLTKGTRLVVDDDGAEIAKKDDDKCTQWYLDTSGSALRDVLAVDGVDPTRTYT 1353

Query: 944  NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            N+ ++V +  GIEAARS ++ E+  V+   G  ++ RH  L+ D+MT +G +
Sbjct: 1354 NDLWQVVEVFGIEAARSALVKELTNVLAFDGSYVNHRHIALLVDVMTYRGTI 1405



 Score = 66.6 bits (161), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 33/75 (44%), Positives = 46/75 (61%), Gaps = 3/75 (4%)

Query: 110 DPQRT-PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVIN 168
           D  RT P   GL D  +G+  +   C TC Q +SDC GHFG+I+L  PV+H G+ + V  
Sbjct: 44  DETRTKPRDGGLNDPLLGSIDRGFKCKTCTQAMSDCPGHFGHIELAKPVYHPGFIKKVKK 103

Query: 169 ILQSICKNPTCARVL 183
           IL+ +C N  C++VL
Sbjct: 104 ILEIVCHN--CSKVL 116



 Score = 55.5 bits (132), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/39 (61%), Positives = 29/39 (74%)

Query: 1107 REKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            + ++ R+ + P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1067 QNRWDRSFVSPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1105


>gi|448396747|ref|ZP_21569195.1| DNA-directed RNA polymerase subunit A' [Haloterrigena limicola JCM
           13563]
 gi|445673276|gb|ELZ25837.1| DNA-directed RNA polymerase subunit A' [Haloterrigena limicola JCM
           13563]
          Length = 975

 Score =  157 bits (398), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 99/270 (36%), Positives = 142/270 (52%), Gaps = 45/270 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 483 DGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQNEEA 542

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR GE +I A QD I+G YLLT  N  FN 
Sbjct: 543 RAE--------------ARVLMRVQEQILSPRFGENIIGAIQDHISGMYLLTADNPRFNE 588

Query: 461 AQTMR-IASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q +  + +T I +  +  G+                    WTG  +FS +L      P 
Sbjct: 589 TQALDLLRATRIDELPEPSGVDD-------------EGKPFWTGYDVFSELL------PD 629

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           + NL+  G   T  +E       V++ + +LL G++ +  +G  G   +   + + +G  
Sbjct: 630 DLNLEFTG---TVGDE-------VVIEDGQLLQGTIAEDEVGEFG-GEIVDTITKIYGNT 678

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVT 609
            A   +  +S +    +M+ GFSIGI D T
Sbjct: 679 RARIFVNEVSTLAMRAIMHFGFSIGIDDET 708



 Score =  114 bits (285), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 90/297 (30%), Positives = 132/297 (44%), Gaps = 57/297 (19%)

Query: 94  QQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDL 153
           ++ S  +I++ + Y  D    PI  GL+D R+G       C TCG++   C GHFG+I+L
Sbjct: 23  REMSATKIITADTY--DDDGFPIDMGLMDPRLGVIDPGLECKTCGKHSGSCNGHFGHIEL 80

Query: 154 PLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKI 213
             PV H+G+ + +  +L+  C+   C+R+LL E++   FR +L            + K  
Sbjct: 81  AAPVIHVGFTKLIRRLLRGTCRE--CSRLLLTEDERDEFRDQLDESRKLSRDLNDVTKAA 138

Query: 214 LETTKKVSVCPHCGEINGVVKKCGLLKISHEK--------------YKNRTK-----KKD 254
           +   +K   CP CGEI           I HEK              Y  R        ++
Sbjct: 139 IRQARKKDRCPFCGEIQ--------YDIDHEKPTTYYEVQQVLTSEYSQRIAGAMQGDEE 190

Query: 255 AIVE----DLLAEYNE----------AVKFNPE------IEAHKKFGLIQT----LNPLE 290
           A VE    D LAE  E          +  F P       IE      L +     L P +
Sbjct: 191 AGVERTTPDELAEKTEIELTRVNEILSGSFRPRESQRKAIEKALDIDLTEEDTNKLMPSD 250

Query: 291 VLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDNDVV 345
           +   FE IP EDI +L +N E S+P  +ILT L VPP   RPS+  D   +S++D+ 
Sbjct: 251 IRDWFENIPDEDIEVLGINPERSRPEWMILTVLPVPPVTARPSITLDNGQRSEDDLT 307



 Score = 92.8 bits (229), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 39/58 (67%), Positives = 49/58 (84%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
             GFV+NS+ SGLTP EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 834 AHGFVENSYTSGLTPREFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELETQYD 891



 Score = 45.1 bits (105), Expect = 0.34,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 29/46 (63%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 65
           +VLM  +  +++PR GE +I A QD I+G YLLT  N  FN  Q +
Sbjct: 547 RVLMRVQEQILSPRFGENIIGAIQDHISGMYLLTADNPRFNETQAL 592


>gi|328867419|gb|EGG15801.1| RNA polymerase II largest subunit [Dictyostelium fasciculatum]
          Length = 1701

 Score =  157 bits (398), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 100/294 (34%), Positives = 154/294 (52%), Gaps = 48/294 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVV+FNRQPSLHK+S+M HR KV+P+ TFR N  V TPYNADFDGDEMN+H+PQT E 
Sbjct: 415 DGDVVIFNRQPSLHKMSMMGHRIKVMPYSTFRLNLSVTTPYNADFDGDEMNLHVPQTLET 474

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE +             +++M  +  +V+P++   ++   QD + G  L T+++ F  R
Sbjct: 475 RAEVI-------------EIMMVPR-QIVSPQSNRPVMGIVQDSLLGSRLFTKRDTFIER 520

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWN----PVVFVRTAVIWTGKQIFSLILKPNRD 516
              M I   L                 SW+    P    +   +WTGKQIFSLI+ P  +
Sbjct: 521 DLMMNILMWL----------------PSWDGKIPPPAIWKPKKLWTGKQIFSLII-PKIN 563

Query: 517 C---PVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILL 573
                   N K K ++  A+      D+ VI+   EL++G + K +LGS    ++ +++ 
Sbjct: 564 LTRFTSTHNDKEKEKSEMAS------DTVVIIDQGELMSGILCKRSLGSAN-GSIIHVVQ 616

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV---TPGQGFVQNSFFSGLT 624
            + G +     + +   + + +L++ GF++GIGD    +     VQN+  S  T
Sbjct: 617 NEHGHEATRCFIDQTQTVVNSWLISHGFTVGIGDTIADSATMAKVQNAITSAKT 670



 Score =  107 bits (266), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 93/359 (25%), Positives = 172/359 (47%), Gaps = 54/359 (15%)

Query: 1107 REKYVRAQIEPATAVGALAAQSI---GEPGTQMTLKTFHFAGEVCEYIEEVFVPDD---- 1159
            + K V+ Q+E  T     AA  I    EP T +  +   F   V  Y+    +PD+    
Sbjct: 1129 KAKSVQCQLEYTTMARVTAATEIYYDPEPNTTVIEEDLEF---VTRYM---MLPDEEINE 1182

Query: 1160 ---SFILIKLDMDRIRLLHLEVDIDSIRYCIER---------TRGISGHLTVSGHSFLIL 1207
               S  L+++++DR  +   ++ +  I  CI++         +   +  L +   + +  
Sbjct: 1183 GALSPWLLRVELDREMVTDKKLSLYEITQCIKKDFDKLNCIFSDDNADKLIIRIRTIMDN 1242

Query: 1208 KPKDSSK----SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVT----------K 1253
            + K+S+     +F  ++  M  +L  +V+ G+  I +  +  +D   +           +
Sbjct: 1243 ENKESANDDDDTFLRRVESM--MLSQMVLCGIPNIKKVFMRNDDRSMINPDTGAYYTKKE 1300

Query: 1254 YKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSI 1313
            + L  +G NL +VM+   V   +  SN+  E+ + LGIEA R+ ++ E++ V+   G  +
Sbjct: 1301 WVLDTDGVNLLEVMSHPDVDFSRTVSNDIVEIIQVLGIEAVRNALLKELRAVISFDGSYV 1360

Query: 1314 DFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISG 1373
            ++RH  ++AD+MT +G ++ ITRHG+ +++   L   SFE T + L +AA + +TD I G
Sbjct: 1361 NYRHLAMLADVMTYRGHLMAITRHGINRVESGPLMRCSFEETVEILMEAALFSETDNICG 1420

Query: 1374 VSECIIMGLPMNVGTG---------LIKLLQAVPRSEPVPRTLLFDNPEFHTNTLAAVP 1423
            V+E II+G    +GTG         +IK   ++   EP+  T     P+  +NT    P
Sbjct: 1421 VTENIILGQLPPLGTGSFEVYLNQDMIKNAHSISLPEPMAITY----PDTPSNTGGQTP 1475



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 42/59 (71%), Positives = 53/59 (89%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
           +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKT+ETGY+QRRLVK++ED+ V+YD +
Sbjct: 779 RGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDVSVRYDAT 837



 Score = 85.5 bits (210), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 71/287 (24%), Positives = 137/287 (47%), Gaps = 55/287 (19%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEIIN ++N+ TP +T YL  D   D + A+ V+ +LE TT+  V    E  + P
Sbjct: 1096 GVPRLKEIINVAKNVKTPSLTIYLQPDIARDSEKAKSVQCQLEYTTMARVTAATEIYYDP 1155

Query: 822  DDSFILIKLDMDRIR------------------LLHLEVDID----------SIRYCIER 853
            + +  +I+ D++ +                   LL +E+D +           I  CI++
Sbjct: 1156 EPNTTVIEEDLEFVTRYMMLPDEEINEGALSPWLLRVELDREMVTDKKLSLYEITQCIKK 1215

Query: 854  ---------TRGISGHLTVSGHSFLILKPKDSSK----SFNSKMYQMKQLLPSVVIKGVQ 900
                     +   +  L +   + +  + K+S+     +F  ++  M  +L  +V+ G+ 
Sbjct: 1216 DFDKLNCIFSDDNADKLIIRIRTIMDNENKESANDDDDTFLRRVESM--MLSQMVLCGIP 1273

Query: 901  GINRAVIHEEDVEGVT----------KYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVY 950
             I +  +  +D   +           ++ L  +G NL +VM+   V   +  SN+  E+ 
Sbjct: 1274 NIKKVFMRNDDRSMINPDTGAYYTKKEWVLDTDGVNLLEVMSHPDVDFSRTVSNDIVEII 1333

Query: 951  KTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            + LGIEA R+ ++ E++ V+   G  +++RH  ++AD+MT +G ++ 
Sbjct: 1334 QVLGIEAVRNALLKELRAVISFDGSYVNYRHLAMLADVMTYRGHLMA 1380



 Score = 73.2 bits (178), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 40/107 (37%), Positives = 59/107 (55%), Gaps = 12/107 (11%)

Query: 119 GLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPT 178
           GL+D  MGT  K   C TC   +++C GHFG+++L  PVFHIG+   V+ I++ +C +  
Sbjct: 21  GLVDPHMGTIDKHQKCATCSGTMAECPGHFGHLELAKPVFHIGFIDTVLKIVRCVCFH-- 78

Query: 179 CARVLLGEEKAAGFRA--KLRNPALSYLVRKSLKKKILETTKKVSVC 223
           C++ LL +   + FR   K+RNP       K     IL+  K   VC
Sbjct: 79  CSK-LLTDTNDSHFRQALKIRNP-------KRRLNAILDICKTKKVC 117



 Score = 55.1 bits (131), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/37 (64%), Positives = 28/37 (75%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            K++ +   P   VGALAAQSIGEP TQMTL TFH+AG
Sbjct: 1051 KFMTSLANPGEMVGALAAQSIGEPATQMTLNTFHYAG 1087


>gi|320166366|gb|EFW43265.1| polymerase II polypeptide A [Capsaspora owczarzaki ATCC 30864]
          Length = 1792

 Score =  157 bits (398), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 98/275 (35%), Positives = 142/275 (51%), Gaps = 41/275 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D V+FNRQPSLHK+S+M HR +VLP  TFR N  V TPYNADFDGDEMN+H+PQ  E 
Sbjct: 469 DGDPVIFNRQPSLHKMSMMGHRIRVLPWSTFRLNLSVTTPYNADFDGDEMNLHVPQNLET 528

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE                 +M+    ++TP     ++   QD +TG   LT+++ F   
Sbjct: 529 RAEVTE--------------IMSVSRQILTPAGNRPVMGIVQDTLTGSRKLTKRDTFIEM 574

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              M++   L   T  +             P + ++   +WTGKQIFS+I+      P  
Sbjct: 575 DLMMQLLMWLPGWTGHVP-----------QPAI-LKPRPMWTGKQIFSMII------PAE 616

Query: 521 ANLKTKGRAYTANEE----FCH---RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILL 573
            NL T+  +   +EE    + H    D+ V++    LL+G + K TLG      + +IL 
Sbjct: 617 VNL-TRTHSTHDDEEDKGNYVHMSPSDTKVLIEKGRLLSGIICKKTLGPSA-GGLIHILF 674

Query: 574 RDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           +++G +VA        R+ +++LM  G SIGIGD 
Sbjct: 675 KEWGHEVARNFFNACQRVVNYWLMWEGHSIGIGDA 709



 Score = 99.0 bits (245), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 41/57 (71%), Positives = 52/57 (91%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NS+  GLTP+EFFFH MGGREG++DTAVKT+ETGY+QRRLVK +ED+ V+YD
Sbjct: 837 RGFVENSYLKGLTPSEFFFHAMGGREGVIDTAVKTSETGYIQRRLVKCMEDVMVKYD 893



 Score = 95.5 bits (236), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 77/292 (26%), Positives = 141/292 (48%), Gaps = 47/292 (16%)

Query: 1147 VCEYIEEVFVPDDSFIL-------IKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTV 1199
            V +Y E   +PDD  IL       +++++DR ++ +  + ++ +   I    G   H+  
Sbjct: 1209 VNDYYE---MPDDPEILKHISPWLLRMELDRKQMEYRRLTMERVAEKITADFGNDLHVIF 1265

Query: 1200 SGHSF--LILK------------------PKDSSKSFNSKMYQMKQLLPS----VVIKGV 1235
            S  +   LIL+                  P+D  +S  +    +++L+P+    + ++G+
Sbjct: 1266 SDDNADKLILQIRMLKKTSEGDGESGDKNPEDELRSGAADDTFLRKLIPNYLWPLTLQGL 1325

Query: 1236 QGINRAVI------HEEDVEG-------VTKYKLLVEGDNLRDVMATYGVKGVKCSSNNT 1282
            + I +  +      H   V G       V ++ L  +G +L   ++   V   +  SN+ 
Sbjct: 1326 EDIAKVYMTQKNRKHFHPVTGALVNDKNVKEWVLETDGSSLLLALSQPNVDVTRTVSNDI 1385

Query: 1283 YEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKM 1342
             E+ + LG+EA R ++  E+  V   +G+ I++RH  L+ D+MT++G ++ +TRHG+  +
Sbjct: 1386 VEIMRVLGVEAVRQSLFKEMHAVYSLYGIYINYRHLALLCDVMTARGHIMAVTRHGINGL 1445

Query: 1343 KESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
                L   SFE T + L  AA + +TD + G SE II+G    VGTG   LL
Sbjct: 1446 DTGPLMRCSFEETVEILVTAAQHSETDWLRGPSENIILGQLAPVGTGYFDLL 1497



 Score = 87.4 bits (215), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 68/236 (28%), Positives = 106/236 (44%), Gaps = 34/236 (14%)

Query: 119 GLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPT 178
           GL D RMGT +++  C TC  ++ DC GHFG+I+L  PVF++     +   L+S+C +  
Sbjct: 65  GLSDPRMGTVERQFKCQTCTGSMGDCPGHFGHIELVKPVFNVTMMTKIQKTLKSVCYH-- 122

Query: 179 CARVLLGEEKAAGFRAKLRNPALSYLVRKSLK-----------------KKILETTKKVS 221
           C+R+L+  E  A   A+  N       R S                   K  ++ T K  
Sbjct: 123 CSRLLVSPEDMAYKHAQRTNNMSERFRRLSTACFGKTRCGGGTDVDADMKPSIDLTAKAR 182

Query: 222 VCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFG 281
               CG +    K+ G L +++E ++    KKD+           A+             
Sbjct: 183 TG--CGNVQPKYKRDG-LSLTYE-FRLTGAKKDSESTAGGGSGGGALPTG---------- 228

Query: 282 LIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD 337
             QTL+P +  ++ + I  ED   L  N E  +P  +I+T L VPP  +RPSV+ D
Sbjct: 229 -TQTLSPEKAHEILKRISDEDCRALGFNPEQGRPDWMIITVLPVPPMTVRPSVVMD 283



 Score = 84.3 bits (207), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 71/299 (23%), Positives = 138/299 (46%), Gaps = 65/299 (21%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP-- 821
            GVPR++E+IN S++  TP +T YL    D + A+ V  RLE TTL ++  + E  + P  
Sbjct: 1138 GVPRLRELINVSKSPKTPSLTVYLQSGMDQERAKDVACRLEHTTLLKITTHTEIYYDPNP 1197

Query: 822  -------DDSFI-------------------LIKLDMDRIRLLHLEVDIDSIRYCIERTR 855
                   D SF+                   L+++++DR ++ +  + ++ +   I    
Sbjct: 1198 LASVVEEDQSFVNDYYEMPDDPEILKHISPWLLRMELDRKQMEYRRLTMERVAEKITADF 1257

Query: 856  GISGHLTVSGHSF--LILK------------------PKDSSKSFNSKMYQMKQLLPS-- 893
            G   H+  S  +   LIL+                  P+D  +S  +    +++L+P+  
Sbjct: 1258 GNDLHVIFSDDNADKLILQIRMLKKTSEGDGESGDKNPEDELRSGAADDTFLRKLIPNYL 1317

Query: 894  --VVIKGVQGINRAVI------HEEDVEG-------VTKYKLLVEGDNLRDVMATYGVKG 938
              + ++G++ I +  +      H   V G       V ++ L  +G +L   ++   V  
Sbjct: 1318 WPLTLQGLEDIAKVYMTQKNRKHFHPVTGALVNDKNVKEWVLETDGSSLLLALSQPNVDV 1377

Query: 939  VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             +  SN+  E+ + LG+EA R ++  E+  V   +G+ I++RH  L+ D+MT++G ++ 
Sbjct: 1378 TRTVSNDIVEIMRVLGVEAVRQSLFKEMHAVYSLYGIYINYRHLALLCDVMTARGHIMA 1436



 Score = 59.7 bits (143), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 25/37 (67%), Positives = 31/37 (83%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            ++ +A++EP   VGALAAQS+GEP TQMTL TFHFAG
Sbjct: 1093 RFQQAKVEPGEMVGALAAQSLGEPATQMTLNTFHFAG 1129


>gi|302813666|ref|XP_002988518.1| hypothetical protein SELMODRAFT_128226 [Selaginella moellendorffii]
 gi|300143625|gb|EFJ10314.1| hypothetical protein SELMODRAFT_128226 [Selaginella moellendorffii]
          Length = 1797

 Score =  157 bits (398), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 94/270 (34%), Positives = 141/270 (52%), Gaps = 35/270 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D VLFNRQPSLHK+SIM HR +++P+ TFR N  V +PYNADFDGDEMN+H+PQ+ E 
Sbjct: 462 DGDFVLFNRQPSLHKMSIMGHRIRIMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSFET 521

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE                 LM     +V+P++   +I   QD + G   +T+++ F  +
Sbjct: 522 RAE--------------VSELMIVPKCIVSPQSNRPVIGIVQDTLLGCRKVTKRDTFIEK 567

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              M           +I    + F  +   P + V+   IWTGKQIFSLI+      P  
Sbjct: 568 DVFM-----------NILMWWEDFDGKVPTPAI-VKPRPIWTGKQIFSLII------PKQ 609

Query: 521 ANLKTKGRAYTANE--EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            N+      +  +E  +    D+ V +   ELL G++ K TLG+    ++ +++  + G 
Sbjct: 610 INMVRTAAWHNDSETGDNSPGDTMVRIEKGELLTGTLCKKTLGTSS-GSLIHVIWEEVGP 668

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           D A   +     + +++L+  GFSIGIGD 
Sbjct: 669 DAARKFLGHTQWLVNYWLLQHGFSIGIGDT 698



 Score =  103 bits (258), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 59/178 (33%), Positives = 98/178 (55%), Gaps = 9/178 (5%)

Query: 1226 LLPSVVIKGVQGINRAVIHE------EDVEGV---TKYKLLVEGDNLRDVMATYGVKGVK 1276
            +L  + ++G+  I++  I E      ++ EG    T++ L  EG N+  VM    V   +
Sbjct: 1297 MLTEMALRGIPDIHKVFIREHKRQRFDEHEGFKTETEWMLDTEGVNMLAVMCNEDVDATR 1356

Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITR 1336
              SN+  EV + LGIEA R  ++ E++ V+   G  +++RH  ++ D+MT +G ++ ITR
Sbjct: 1357 TVSNHLIEVIEVLGIEAVRQALLKELREVISFDGSYVNYRHLAILCDVMTYRGHLMAITR 1416

Query: 1337 HGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            HG+ +     +   SFE T D L DAA + + D + GV+E I++G    +GTG   LL
Sbjct: 1417 HGINRNDTGPMMRCSFEETVDILLDAAVFAEADHLRGVTENIMLGQLAPIGTGDFGLL 1474



 Score = 99.0 bits (245), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 41/57 (71%), Positives = 52/57 (91%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NS+  GLTP EF+FH MGGREGL+DTAVKT+ETGY+QRRLVK++ED+ V+YD
Sbjct: 826 RGFVENSYLRGLTPQEFYFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDVMVKYD 882



 Score = 75.5 bits (184), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 34/93 (36%), Positives = 57/93 (61%), Gaps = 5/93 (5%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D ++Q S  +I S   Y +     P   GL D R+GT  ++  C TCG ++++C GHFG+
Sbjct: 26  DEIRQMSVCKIESSETYDRG---KPKSGGLSDPRLGTIDRQTKCETCGGSMAECPGHFGH 82

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVL 183
           ++L  P+FHIG+ + V+ +L+ +C N  C+ +L
Sbjct: 83  LELAKPMFHIGFLKTVLALLRCVCYN--CSHIL 113



 Score = 74.3 bits (181), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 71/287 (24%), Positives = 131/287 (45%), Gaps = 53/287 (18%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR++EIIN ++ I TP +  +L  +   + + A+ V+  LE TTL  V +  E  + P
Sbjct: 1127 GVPRLREIINVAKKIKTPSLYVHLKPEVSKEKERAKNVQCALEYTTLRSVTQATEIWYDP 1186

Query: 822  DDSFILIKLDMDRIRLLHLEVDIDS---------IRYCIERTRGISGHLTVS-------- 864
            D    +I+ D++ ++  +   D D          +R  + R   +   L+++        
Sbjct: 1187 DPMSTIIEEDVEFVKSYYEMPDEDVTPDKISPWLLRIELNREMMVDKKLSMADIAEKINL 1246

Query: 865  -------------GHSFLILKPK----DSSKS-----FNSKMYQMK---QLLPSVVIKGV 899
                             LIL+ +    D SK       +  ++  K    +L  + ++G+
Sbjct: 1247 EFVDDLTCIFNDDNAEKLILRVRIMNDDVSKGGEVDQSDDDVFLKKIESNMLTEMALRGI 1306

Query: 900  QGINRAVIHE------EDVEGV---TKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVY 950
              I++  I E      ++ EG    T++ L  EG N+  VM    V   +  SN+  EV 
Sbjct: 1307 PDIHKVFIREHKRQRFDEHEGFKTETEWMLDTEGVNMLAVMCNEDVDATRTVSNHLIEVI 1366

Query: 951  KTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            + LGIEA R  ++ E++ V+   G  +++RH  ++ D+MT +G ++ 
Sbjct: 1367 EVLGIEAVRQALLKELREVISFDGSYVNYRHLAILCDVMTYRGHLMA 1413



 Score = 52.4 bits (124), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 20/37 (54%), Positives = 29/37 (78%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            +++++ + P   +G +AAQSIGEP TQMTL TFH+AG
Sbjct: 1082 RFLQSLVAPGEMIGCVAAQSIGEPATQMTLNTFHYAG 1118


>gi|188532149|gb|ACD63086.1| RNA polymerase II largest subunit [Liriodendron tulipifera]
          Length = 1010

 Score =  157 bits (398), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 98/271 (36%), Positives = 147/271 (54%), Gaps = 35/271 (12%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D D VLFNRQPSLHK+SIM HR K++P+ TFR N  V +PYNADFDGDEMN+H+PQ+ E
Sbjct: 369 NDGDFVLFNRQPSLHKMSIMGHRIKIMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSFE 428

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE L             +++M  K  +V+P++   ++   QD + G   +T+++ F  
Sbjct: 429 TRAEVL-------------ELMMVPKC-IVSPQSNRPVMGIVQDTLLGCRKITKRDTFIE 474

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           +   M I    +    D  G I         P V ++   +WTGKQ+F+LI+      P 
Sbjct: 475 KDVFMNI----LMWWEDFDGKIP-------APAV-LKPRPLWTGKQVFNLII------PK 516

Query: 520 NANL-KTKGRAYTANEEF-CHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFG 577
             NL +T      A   F    D+ V +   ELLAG++ K TLG+    ++ +++  + G
Sbjct: 517 QINLIRTSAWHSEAETGFITPGDTQVRIERGELLAGTLCKKTLGT-STGSLIHVIWEEVG 575

Query: 578 EDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
            D A   +     + +++L+  GFSIGIGD 
Sbjct: 576 PDAARKFLGHTQWLVNYWLLQNGFSIGIGDT 606



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 42/57 (73%), Positives = 52/57 (91%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKT+ETGY+QRRLVK++ED+ V+YD
Sbjct: 734 RGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDIMVKYD 790



 Score = 54.7 bits (130), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 60/200 (30%), Positives = 101/200 (50%), Gaps = 24/200 (12%)

Query: 150 YIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKS 208
           +++L  P+FHIG+ + V++I++ +C N  C+++L+ EE+    +A K+RNP       K 
Sbjct: 1   HLELAKPMFHIGFLKTVLSIMRCVCFN--CSKILVDEEEHKFKQAQKIRNP-------KH 51

Query: 209 LKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNR-----TKKKDAIVE--DLL 261
             +K+L+  K  + C    +I   V+   L     E  K R      ++    VE   ++
Sbjct: 52  RLRKVLDACKNKTRCEGGDDIE--VRDQDL----EEPVKKRRGGCGAQQPKLTVEGMKMI 105

Query: 262 AEYNEAVKFNPEIEA-HKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
           AEY    K N + E   +     Q L+   VL + + I  ED  LL +N + ++P  +IL
Sbjct: 106 AEYKATRKKNDDQEQLPEPVERKQQLSAERVLSVLKRISDEDCLLLGLNPKYARPDWMIL 165

Query: 321 TRLLVPPNCIRPSVISDLKS 340
             L +PP  +RPSV+ D  S
Sbjct: 166 QVLPIPPPPVRPSVMMDTSS 185


>gi|336041421|gb|AEH95288.1| RNA polymerase II largest subunit [Malawimonas californiana]
          Length = 1014

 Score =  157 bits (398), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 94/272 (34%), Positives = 148/272 (54%), Gaps = 37/272 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DVV+FNRQPSLHK+S+M HR ++LP  TFR N  V TPYNADFDGDEMN+H+ Q+ E 
Sbjct: 355 DGDVVIFNRQPSLHKMSMMGHRIRILPWSTFRLNLSVTTPYNADFDGDEMNMHVAQSPET 414

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE               + +M     +V+P+  + ++   QD + G  L T+++ F  R
Sbjct: 415 RAE--------------IEEIMMVPRQIVSPQANKPVMGIVQDSLLGTKLFTKRDTFIER 460

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              M +   L    S   G + + +         ++  V+WTGKQIFS+++      PVN
Sbjct: 461 DLVMNVLMWL----STFEGKVPKPA--------MLKPKVLWTGKQIFSMLIP-----PVN 503

Query: 521 ANLKT-KGRAYTANEEFCHRD----SYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
              K+ +      NEEF + D    S V + N E+++G + K T+GS    ++ +++  +
Sbjct: 504 LLRKSAQAPERELNEEFTYTDTRVCSLVCIENGEVISGIICKQTVGSSS-GSLVHVVWNE 562

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            G +     +  +  + + +L++RGFS+GIGD
Sbjct: 563 HGHEATRNFLDSVQAVVNQWLLSRGFSVGIGD 594



 Score = 99.4 bits (246), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 42/64 (65%), Positives = 54/64 (84%), Gaps = 1/64 (1%)

Query: 606 GDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
            D +P  +GFV+NS+  GL P EFFFH MGGREGL+DTAVKT+ETGY+QRRL+K++ED+ 
Sbjct: 716 ADYSPEARGFVENSYLRGLNPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLIKAMEDVM 775

Query: 665 VQYD 668
           V+YD
Sbjct: 776 VRYD 779


>gi|448320528|ref|ZP_21510014.1| DNA-directed RNA polymerase subunit A' [Natronococcus amylolyticus
           DSM 10524]
 gi|445605430|gb|ELY59352.1| DNA-directed RNA polymerase subunit A' [Natronococcus amylolyticus
           DSM 10524]
          Length = 975

 Score =  157 bits (398), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 99/270 (36%), Positives = 142/270 (52%), Gaps = 45/270 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 483 DGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQNEEA 542

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR GE +I A QD I+G YLLT  N  FN 
Sbjct: 543 RAE--------------ARVLMRVQEQILSPRFGENIIGAIQDHISGMYLLTHDNPRFNE 588

Query: 461 AQTMR-IASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q +  + +T I +  +  GI                    WTG  +FS +L      P 
Sbjct: 589 TQALDLLRATRIDELPEPSGIDD-------------EGEPFWTGYDVFSELL------PD 629

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           + +L+  G   T  ++       V++ N +LL G++ +  +G  G   +   + + +G  
Sbjct: 630 DLDLEFTG---TVGDD-------VVVENGQLLEGTIAEDEVGEFG-GEIVDTITKVYGNT 678

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVT 609
            A   +  +S +    +M+ GFSIGI D T
Sbjct: 679 RARIFINEVSTLAMRAIMHFGFSIGIDDET 708



 Score =  115 bits (288), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 90/310 (29%), Positives = 138/310 (44%), Gaps = 57/310 (18%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G I   + + +  ++ S  +I++ + Y  D    PI  GL+D R+G       C TCG++
Sbjct: 10  GSINFGLMEPEEYREMSATKIITADTY--DDDGFPIDMGLMDPRLGVIDPGLECKTCGKH 67

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
              C GHFG+I+L  PV H+G+ + +  +L+  C+   C+R+LL E++   F  ++    
Sbjct: 68  SGSCNGHFGHIELAAPVIHVGFTKLIRRLLRGTCRE--CSRLLLTEDERGEFYDQIDESR 125

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEK--------------Y 246
                   + K  +   +K   CPHCGE+           I HEK              Y
Sbjct: 126 KLGRDLNDVTKAAIRQARKKDRCPHCGEVQ--------YDIDHEKPTTYYEVQQVLTSEY 177

Query: 247 KNRTK-----KKDAIVE----DLLAEYNE----------AVKFNPE------IEAHKKFG 281
             R        ++A VE    D LAE  E          +  F P       IE      
Sbjct: 178 SQRIAGAMQGDEEAGVERTTPDELAEKTEIDIGRINEILSGSFRPRESQRKAIEKALDID 237

Query: 282 LIQT----LNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD 337
           L +     L P ++   FEAIP ED+ +L +N E S+P  +ILT L VPP   RPS+  D
Sbjct: 238 LTEEDTNKLMPSDIRDWFEAIPDEDMEVLGINPERSRPEWMILTVLPVPPVTARPSITLD 297

Query: 338 --LKSDNDVV 345
              +S++D+ 
Sbjct: 298 NGQRSEDDLT 307



 Score = 92.8 bits (229), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 39/58 (67%), Positives = 49/58 (84%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
             GFV+NS+ SGLTP EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 834 AHGFVENSYTSGLTPREFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELEAQYD 891



 Score = 45.4 bits (106), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 29/46 (63%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 65
           +VLM  +  +++PR GE +I A QD I+G YLLT  N  FN  Q +
Sbjct: 547 RVLMRVQEQILSPRFGENIIGAIQDHISGMYLLTHDNPRFNETQAL 592


>gi|347522776|ref|YP_004780346.1| DNA-directed RNA polymerase subunit A'' [Pyrolobus fumarii 1A]
 gi|343459658|gb|AEM38094.1| DNA-directed RNA polymerase, subunit A'' [Pyrolobus fumarii 1A]
          Length = 424

 Score =  157 bits (398), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 108/324 (33%), Positives = 165/324 (50%), Gaps = 57/324 (17%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG----------------------- 1145
            +Y  + +EP   VG +AAQSIGEPGTQMTL+TFH+AG                       
Sbjct: 66   EYELSLVEPGEPVGTVAAQSIGEPGTQMTLRTFHYAGVREFNVTLGLPRFIELVDAKKEP 125

Query: 1146 ---------------------EVCEYIE---------EVFVPDDSFILIKLDMDRIRLLH 1175
                                  V   IE         EV++ D + + I + +D+  L  
Sbjct: 126  STPMMTVYLDEEHKYDLEKAKAVARAIEYTRVENVASEVYI-DMATLSIVVKLDKTMLED 184

Query: 1176 LEVDIDSIRYCIERTR-GISGHLTVSGHSFLILKPKDSSKSFNS-KMYQMKQLLPSVVIK 1233
              V ++ ++  +E+ + G         ++  I  P +S  + N  ++ + K  + +  IK
Sbjct: 185  KGVTVEQVKRVLEKLKLGTVREDPNDPYTLRIELPIESMGAINIIELQKKKDRVLNAKIK 244

Query: 1234 GVQGINRAVIHEEDV-EGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIE 1292
            G++ I R V+   D+ +G  +Y LL EG +L++V+   GV  V   +NN  E+ + LGIE
Sbjct: 245  GIKKIRRVVVQSVDLPDGRKEYYLLTEGSSLKEVLEVPGVDPVHTITNNIREIEQVLGIE 304

Query: 1293 AARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASF 1352
            AAR  ++ E+K V+++ G+ +D RH +LVAD+MT  G V  I RHG++  K SVL  A+F
Sbjct: 305  AARYALIKEMKGVLDDQGLDVDIRHLILVADIMTQTGRVRQIGRHGVSGEKPSVLARAAF 364

Query: 1353 ENTSDHLFDAAFYGQTDCISGVSE 1376
            E T  HLFDAA  G+ D I GV+E
Sbjct: 365  EMTVQHLFDAAARGEADRILGVTE 388



 Score =  113 bits (283), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 76/237 (32%), Positives = 135/237 (56%), Gaps = 9/237 (3%)

Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PR  E+++A +  STP++T YLD++   DL+ A+ V   +E T +  V     EV++ 
Sbjct: 111 GLPRFIELVDAKKEPSTPMMTVYLDEEHKYDLEKAKAVARAIEYTRVENVAS---EVYI- 166

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTR-GISGHLTVSGHSFLILKPKDSSKSF 880
           D + + I + +D+  L    V ++ ++  +E+ + G         ++  I  P +S  + 
Sbjct: 167 DMATLSIVVKLDKTMLEDKGVTVEQVKRVLEKLKLGTVREDPNDPYTLRIELPIESMGAI 226

Query: 881 NS-KMYQMKQLLPSVVIKGVQGINRAVIHEEDV-EGVTKYKLLVEGDNLRDVMATYGVKG 938
           N  ++ + K  + +  IKG++ I R V+   D+ +G  +Y LL EG +L++V+   GV  
Sbjct: 227 NIIELQKKKDRVLNAKIKGIKKIRRVVVQSVDLPDGRKEYYLLTEGSSLKEVLEVPGVDP 286

Query: 939 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
           V   +NN  E+ + LGIEAAR  ++ E+K V+++ G+ +D RH +LVAD+MT  G V
Sbjct: 287 VHTITNNIREIEQVLGIEAARYALIKEMKGVLDDQGLDVDIRHLILVADIMTQTGRV 343


>gi|33326209|gb|AAQ08514.1| RNA polymerase II largest subunit [Welwitschia mirabilis]
          Length = 1013

 Score =  157 bits (398), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 93/271 (34%), Positives = 149/271 (54%), Gaps = 35/271 (12%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D D+VLFNRQPSLHK+SIM HR K++P+ TFR N  V +PYNADFDGDEMN+H+PQ+ E
Sbjct: 372 NDGDLVLFNRQPSLHKMSIMGHRIKIMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSFE 431

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE +             +++M  K  +V+P++   ++   QD + G   +T+ + F  
Sbjct: 432 TRAEVM-------------ELMMVPKC-IVSPQSNRPVMGIVQDTLLGCRKVTKGDTFTE 477

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           +   M           +I    + F  +  NP + ++   IWTGKQ+F+LI+      P 
Sbjct: 478 KDVFM-----------NILMWWEEFEGKIPNPAI-LKPRPIWTGKQVFNLII------PK 519

Query: 520 NANLKTKGRAYTANEEF--CHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFG 577
             NL      +  +E+      D+ V +   E+L+G++ K TLGS    ++ +++  + G
Sbjct: 520 QINLIRYSAWHNESEKGFPTPGDTVVRIEKGEVLSGTLCKKTLGSSS-GSLIHVIWEEVG 578

Query: 578 EDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
            D A   +     + +++L+ +GFSIGIGD 
Sbjct: 579 PDAARKFLGHTQWLVNYWLLQQGFSIGIGDT 609



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 42/57 (73%), Positives = 52/57 (91%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKT+ETGY+QRRLVK++ED+ V+YD
Sbjct: 737 RGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDIMVKYD 793



 Score = 48.1 bits (113), Expect = 0.041,   Method: Compositional matrix adjust.
 Identities = 62/222 (27%), Positives = 101/222 (45%), Gaps = 53/222 (23%)

Query: 150 YIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKS 208
           +++L  P+FHIG+ + V++IL+ +C N  C+R+L  EE     +A K++NP       K 
Sbjct: 1   HLELAKPMFHIGFMKTVLSILRCVCFN--CSRILADEEDHRFKQALKIKNP-------KH 51

Query: 209 LKKKILETTKKVSVC---------------------PH--CGEINGVVKKCGLLKISHEK 245
             +KIL+  K  + C                     PH  CG     +   G+  I+  +
Sbjct: 52  RLEKILDCCKNKTKCEGGDVIEDDQGQDVDEEVKKKPHGGCGSQQPKITIDGMKIIA--E 109

Query: 246 YKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPL 305
           YK   KK D           E  +  PE    K     Q L+   VL + + I  E+  +
Sbjct: 110 YKAPRKKAD-----------EQEQLMPEPVERK-----QQLSAERVLNILKRISDEECQM 153

Query: 306 LLMNAELSKPSDLILTRLLVPPNCIRPSVI--SDLKSDNDVV 345
           L  N + ++P  +IL  L +PP  +RPSV+  S  +S++D+ 
Sbjct: 154 LGFNPKYARPDWMILQVLPIPPPPVRPSVMMNSTTRSEDDLT 195


>gi|429217660|ref|YP_007175650.1| DNA-directed RNA polymerase subunit A'' [Caldisphaera lagunensis
           DSM 15908]
 gi|429134189|gb|AFZ71201.1| DNA-directed RNA polymerase subunit A'' [Caldisphaera lagunensis
           DSM 15908]
          Length = 888

 Score =  157 bits (398), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 94/268 (35%), Positives = 137/268 (51%), Gaps = 29/268 (10%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + D+VLFNRQPSLH++SIMAH+ +V+P RTFR N   C PYNADFDGDEMN+H+P+    
Sbjct: 423 NGDIVLFNRQPSLHRMSIMAHKVRVMPGRTFRLNLLDCAPYNADFDGDEMNLHVPRL--- 479

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
                            A+ LM  +  +++PR G  +I   QD+I+G YLLT K     +
Sbjct: 480 -----------EEARAEAEELMLVEKQILSPRYGGPIIGGRQDYISGSYLLTVKTNLLTK 528

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q     S L+A  +        +  +   P + ++   +WTGKQ+ SL L   +     
Sbjct: 529 EQV----SLLLAAAN--------YKGKMPEPAI-IKPQPLWTGKQLVSLFLP--KGLSFE 573

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
              K        + E C  DSY I+ N  LL G  DK+ +G+    NV + +  ++G D 
Sbjct: 574 GRAKINAGELKCDNERCFFDSYTIISNGRLLMGVFDKNAIGAEQPENVLHYITLEYGPDK 633

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           A   +  + RM    L  +GFSI + +V
Sbjct: 634 AREFLDNVFRMFIRMLEIKGFSISLKEV 661



 Score = 95.1 bits (235), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 75/262 (28%), Positives = 122/262 (46%), Gaps = 55/262 (20%)

Query: 93  VQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYID 152
           +++ + + +V   +Y  D   TP+  G+ D   G  +    C  CG    DC GHFG ID
Sbjct: 28  IRKMAKVTVVRPEIYEAD--GTPVSGGVRDSHFGAIEPGERCPVCGNTREDCPGHFGKID 85

Query: 153 LPLPVF--HIGYFRCVIN-ILQSICKNPTCARVLLGEEKAAGF-----RAKLRNPALSYL 204
           L  PV   H+G     IN ILQS C+N  C R+LL +EK   +     + K + P L+  
Sbjct: 86  LARPVLLPHLG---DKINVILQSTCRN--CGRILLPDEKITYYTNIYLKLKEKWPVLA-- 138

Query: 205 VRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEY 264
             ++   ++ + T  VS CPHCG               +++YK +  K     E      
Sbjct: 139 --ETFADEVAKQTSSVSECPHCG---------------YKQYKLKFIKPFTFYE------ 175

Query: 265 NEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLL 324
                  PE E          L P E+ +  E +  +DI +L ++ + ++P  ++LT L 
Sbjct: 176 -----VRPEGEIR--------LTPSEIRERLERVQDKDIVVLGVDPKAARPEWMVLTVLP 222

Query: 325 VPPNCIRPSVI--SDLKSDNDV 344
           VPP  +RPS+   S +++++D+
Sbjct: 223 VPPLSVRPSITMESGMRAEDDL 244



 Score = 88.2 bits (217), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 46/101 (45%), Positives = 64/101 (63%), Gaps = 9/101 (8%)

Query: 577 GEDVAVTAMWRL--SRMTSFYLMNRGF------SIGIGDVTP-GQGFVQNSFFSGLTPTE 627
           G D+ +T M  +   +      ++RGF          GD++P  +GF+ ++F  GL P E
Sbjct: 745 GSDINITQMAAMLGQQTVRGKRISRGFRTRTLPQFKPGDLSPEARGFIISNFRLGLKPYE 804

Query: 628 FFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            FFH  GGREGLVDTAVKT+++GYMQRRL+ +L+DL V YD
Sbjct: 805 VFFHAAGGREGLVDTAVKTSQSGYMQRRLINALQDLYVSYD 845


>gi|435845619|ref|YP_007307869.1| DNA-directed RNA polymerase, subunit A' [Natronococcus occultus
           SP4]
 gi|433671887|gb|AGB36079.1| DNA-directed RNA polymerase, subunit A' [Natronococcus occultus
           SP4]
          Length = 975

 Score =  157 bits (398), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 99/270 (36%), Positives = 142/270 (52%), Gaps = 45/270 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 483 DGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQNEEA 542

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR GE +I A QD I+G YLLT  N  FN 
Sbjct: 543 RAE--------------ARVLMRVQEQILSPRFGENIIGAIQDHISGMYLLTHDNPRFNE 588

Query: 461 AQTMR-IASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q +  + +T I +  +  GI                    WTG  +FS +L      P 
Sbjct: 589 TQALDLLRATRIDELPEPSGIDD-------------EGEPFWTGYDVFSELL------PD 629

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           + NL+  G   T  ++       V++ + +LL G++ +  +G  G   +   + + +G  
Sbjct: 630 DLNLEFTG---TVGDD-------VVIEDGQLLEGTIAEDEVGEFG-GEIVDTITKVYGNT 678

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVT 609
            A   +  +S +    +M+ GFSIGI D T
Sbjct: 679 RARIFVNEVSTLAMRAIMHFGFSIGIDDET 708



 Score =  109 bits (273), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 89/310 (28%), Positives = 136/310 (43%), Gaps = 57/310 (18%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G I   + + +  ++ S  +I++ + Y  D    PI  GL+D R+G       C TCG++
Sbjct: 10  GSINFGLMEPEEYREMSATKIITADTY--DDDGFPIDMGLMDPRLGVIDPGLECKTCGKH 67

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
              C GHFG+I+L  PV H+G+ + +  +L+  C+   C+R+LL E++   F  K+    
Sbjct: 68  SGSCNGHFGHIELAAPVIHVGFTKLIRRLLRGTCRE--CSRLLLTEDEREEFYDKIDESR 125

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEK--------------Y 246
                   + K  +   +K   CP C E+           I HEK              Y
Sbjct: 126 KLGRDLNDVTKAAIRQARKKDRCPFCSEVQ--------YDIDHEKPTTYYEVQQVLASEY 177

Query: 247 KNRTK-----KKDAIVE----DLLAEYNE----------AVKFNPE------IEAHKKFG 281
             R        ++A VE    D LAE  E          +  F P       IE      
Sbjct: 178 SQRIAGAMQGDEEAGVERTTPDELAEKTEIDIGRINEILSGSFRPRESQRKAIEKALDID 237

Query: 282 LIQT----LNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD 337
           L +     L P ++   FEAIP ED+ +L +N E S+P  +ILT L VPP   RPS+  D
Sbjct: 238 LTEEDTNKLMPSDIRDWFEAIPDEDMEVLGINPERSRPEWMILTVLPVPPVTARPSITLD 297

Query: 338 --LKSDNDVV 345
              +S++D+ 
Sbjct: 298 NGQRSEDDLT 307



 Score = 92.8 bits (229), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 39/58 (67%), Positives = 49/58 (84%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
             GFV+NS+ SGLTP EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 834 AHGFVENSYTSGLTPREFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELEAQYD 891



 Score = 45.4 bits (106), Expect = 0.23,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 29/46 (63%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 65
           +VLM  +  +++PR GE +I A QD I+G YLLT  N  FN  Q +
Sbjct: 547 RVLMRVQEQILSPRFGENIIGAIQDHISGMYLLTHDNPRFNETQAL 592


>gi|327242121|gb|AEA40839.1| RNA polymerase II largest subunit [Trichomonas sp. RWG-2007-2]
          Length = 1019

 Score =  157 bits (398), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 91/269 (33%), Positives = 146/269 (54%), Gaps = 35/269 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+D+V+FNRQPSLHK+S+M HRA ++  RTFR N C  TPYNADFDGDEMN+H+PQ++ A
Sbjct: 372 DDDIVIFNRQPSLHKMSMMGHRALIMSGRTFRLNLCDTTPYNADFDGDEMNLHVPQSQTA 431

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R E               + +MA    +++P+  + +I   QD + G  LL++++ F  R
Sbjct: 432 RTE--------------VRHIMAVPKQIISPQANKPVIGLVQDALLGCRLLSKRDTFLTR 477

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLIL-KPNRDC-P 518
            Q M +   L      I             P   ++   +W+GKQ+FSL L K + D   
Sbjct: 478 NQVMNLMMWLPTTKDTILP-----------PPCILKPVQLWSGKQVFSLFLPKISHDSYS 526

Query: 519 VNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            +AN   +     A       D +VI+R+  LLAG +DK T+    + ++ ++++  +  
Sbjct: 527 QDANKMDQNSIPLA-------DRHVIIRDGNLLAGILDKKTVAR-SEGSLIHVVINSYNT 578

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           ++A   + +   + + +L +RGFSIG+ D
Sbjct: 579 NIAKDFLNQTQLIVNNWLEHRGFSIGLID 607



 Score = 85.5 bits (210), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 36/57 (63%), Positives = 46/57 (80%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GF +NS+ +GLTP EF FH MGGR G++DTA KT++TGY+QRRLVKS+E   V YD
Sbjct: 736 RGFCKNSYIAGLTPPEFLFHAMGGRTGIIDTACKTSDTGYIQRRLVKSMESHHVAYD 792



 Score = 53.5 bits (127), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 58/212 (27%), Positives = 87/212 (41%), Gaps = 51/212 (24%)

Query: 149 GYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLV-RK 207
           GYI L  P FH+G+      +LQ +C    C RVL              +P + Y+V   
Sbjct: 1   GYIRLAEPFFHVGFLPHCYKLLQMVCHK--CGRVL----------CSYSDPEIQYIVTHY 48

Query: 208 SLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAE---- 263
             K + L+  +K++             K G  K  H        + D  +++   E    
Sbjct: 49  KGKNRFLKLFEKIA------------SKSG--KCQHSPDLKNPNEPDVCLDERFWELVNG 94

Query: 264 --YNEAVKFN-------PEIEAHKKFGLIQT----------LNPLEVLQLFEAIPLEDIP 304
             ++E V+         P IE  K F LI+           L+   VL++FE I  +D+ 
Sbjct: 95  DSHSEHVRVKKPCNATVPAIEQGKDF-LIKLKDVSKTEEDYLSAEVVLRIFENISDQDVR 153

Query: 305 LLLMNAELSKPSDLILTRLLVPPNCIRPSVIS 336
           LL  N + S P  +IL  L VPP  +RP V+S
Sbjct: 154 LLGFNPKRSHPKWMILKILPVPPLAVRPQVVS 185


>gi|210075525|ref|XP_501909.2| YALI0C16566p [Yarrowia lipolytica]
 gi|199425290|emb|CAG82229.2| YALI0C16566p [Yarrowia lipolytica CLIB122]
          Length = 1750

 Score =  157 bits (398), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 92/271 (33%), Positives = 151/271 (55%), Gaps = 44/271 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND VLFNRQPSLHK+S+MAHR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 443 DNDPVLFNRQPSLHKMSMMAHRVRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 502

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L +L ++  +          +V+P++ + ++   QD + G   +T +++F + 
Sbjct: 503 RAE----LSQLCMVPLQ----------IVSPQSNKPVMGIVQDTLCGVRKMTIRDSFIDY 548

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVV----FVRTAVIWTGKQIFSLILKPNRD 516
              M I                 F   +W+ VV     ++   +WTGKQ+ S+ +     
Sbjct: 549 DMVMNIL----------------FWIPNWDGVVPTPAILKPKPLWTGKQMVSMCI----- 587

Query: 517 CPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            P   +L+   R    N   C +D+ + + + +++ G +DK T+G+ G   + + ++R+ 
Sbjct: 588 -PKGIHLQ---RFDDQNPITCPKDNGMYIIDGQIMWGVVDKKTIGATG-GGLVHTIMREK 642

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           G  V       + ++ +F+L++ GFSIGIGD
Sbjct: 643 GSAVCCNFFGTIQKVVNFWLLHYGFSIGIGD 673



 Score =  110 bits (276), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 82/260 (31%), Positives = 135/260 (51%), Gaps = 23/260 (8%)

Query: 1153 EVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSF--LILK-- 1208
            E  + + S  L++L++DR ++L  ++ +  +   I  + G    +  S  +   LI++  
Sbjct: 1186 EATLDNQSPWLLRLELDRAKMLDKQLTMSQVAQKISSSYGEDLFVMWSEDNADKLIIRCR 1245

Query: 1209 ----PKDSSKSFNSKMYQM-----KQLLPSVVIKGVQGINRAVIHE------EDVEGVTK 1253
                PK   +  +++  QM       +L S+ ++G++GI+R  + E      ++V G  K
Sbjct: 1246 VVRDPKTLEEDVDAEEDQMLKRIEGHMLDSISLRGIEGIDRVFMMEHKMSVPDEVTGDYK 1305

Query: 1254 YK----LLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENH 1309
             K    L  +G NL +VMA  GV   +  SN+  EV   LGIEA RS +  EI  V+   
Sbjct: 1306 TKMEWVLETDGINLAEVMAVDGVDPYRTYSNSFVEVLSVLGIEATRSALYREILNVIAFD 1365

Query: 1310 GMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTD 1369
            G  +++RH  L+ D+MTS+G ++ ITRHG+ +     L   SFE T + L +AA   + D
Sbjct: 1366 GSYVNYRHMALLVDVMTSRGYLMAITRHGINRADTGALMRCSFEETVEILLEAAAVAELD 1425

Query: 1370 CISGVSECIIMGLPMNVGTG 1389
               GVSE I++G    +GTG
Sbjct: 1426 DCRGVSENIMLGQLAPLGTG 1445



 Score =  107 bits (266), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 83/289 (28%), Positives = 140/289 (48%), Gaps = 55/289 (19%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N ++NI TP +T YL+     D++ A++V+  +E T+L  V    E  + P
Sbjct: 1101 GVPRLKEILNVAKNIKTPALTVYLEPSVAADIEKAKVVQSAIEHTSLKNVTAATEIYYDP 1160

Query: 822  DDSFILIKLDMDRIRLLH------LEVDIDS-----IRYCIERTRGISGHLTVS------ 864
            D    +I+ D+D +          +E  +D+     +R  ++R + +   LT+S      
Sbjct: 1161 DPRTTVIEEDIDTVDAYFSIPDETVEATLDNQSPWLLRLELDRAKMLDKQLTMSQVAQKI 1220

Query: 865  ----GHSFLIL-----------------KPKDSSKSFNSKMYQM-----KQLLPSVVIKG 898
                G    ++                  PK   +  +++  QM       +L S+ ++G
Sbjct: 1221 SSSYGEDLFVMWSEDNADKLIIRCRVVRDPKTLEEDVDAEEDQMLKRIEGHMLDSISLRG 1280

Query: 899  VQGINRAVIHE------EDVEGVTKYK----LLVEGDNLRDVMATYGVKGVKCSSNNTYE 948
            ++GI+R  + E      ++V G  K K    L  +G NL +VMA  GV   +  SN+  E
Sbjct: 1281 IEGIDRVFMMEHKMSVPDEVTGDYKTKMEWVLETDGINLAEVMAVDGVDPYRTYSNSFVE 1340

Query: 949  VYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            V   LGIEA RS +  EI  V+   G  +++RH  L+ D+MTS+G ++ 
Sbjct: 1341 VLSVLGIEATRSALYREILNVIAFDGSYVNYRHMALLVDVMTSRGYLMA 1389



 Score =  101 bits (252), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GF++NS+  GLTP EFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+ V
Sbjct: 796 DYSPESKGFIENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDVMV 855

Query: 666 QYD 668
           QYD
Sbjct: 856 QYD 858



 Score = 89.4 bits (220), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 67/215 (31%), Positives = 108/215 (50%), Gaps = 20/215 (9%)

Query: 112 QRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQ 171
           ++ P   GL D R+GT  +   C TCG+ +++C GHFG+I+L  PVFHIG+   +  I +
Sbjct: 47  RQRPRVGGLNDPRLGTIDRNFKCQTCGEGMAECPGHFGHIELAKPVFHIGFIAKIKKICE 106

Query: 172 SICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEIN 230
           S+C +  C +VLL E      +A ++R+P   +    SL K     TK V       E +
Sbjct: 107 SVCFH--CGKVLLDENNKQFAQAIRIRDPKRRFNAVWSLCK-----TKMVCETDVPTEDD 159

Query: 231 GVVKKCGLLKISHEKYKN--RTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNP 288
           G     G++K SH    N   T ++D +   L   +      +   ++ +K    + L P
Sbjct: 160 G----SGVVKHSHGGCGNIQPTVRRDGL--KLWGTWKRGKNGDDMGDSPEK----RLLTP 209

Query: 289 LEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRL 323
            E+L +F+ I  ED   L +N + ++P  LI+T L
Sbjct: 210 AEILNVFKHISSEDCQRLGLNEDYARPEWLIITTL 244



 Score = 53.1 bits (126), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 21/37 (56%), Positives = 28/37 (75%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            ++ ++ + P   VG +AAQSIGEP TQMTL TFH+AG
Sbjct: 1056 QFAKSVVHPGEMVGVIAAQSIGEPATQMTLNTFHYAG 1092


>gi|302794771|ref|XP_002979149.1| hypothetical protein SELMODRAFT_110201 [Selaginella moellendorffii]
 gi|300152917|gb|EFJ19557.1| hypothetical protein SELMODRAFT_110201 [Selaginella moellendorffii]
          Length = 1764

 Score =  157 bits (397), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 94/270 (34%), Positives = 141/270 (52%), Gaps = 35/270 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D VLFNRQPSLHK+SIM HR +++P+ TFR N  V +PYNADFDGDEMN+H+PQ+ E 
Sbjct: 470 DGDFVLFNRQPSLHKMSIMGHRIRIMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSFET 529

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE                 LM     +V+P++   +I   QD + G   +T+++ F  +
Sbjct: 530 RAE--------------VSELMIVPKCIVSPQSNRPVIGIVQDTLLGCRKVTKRDTFIEK 575

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              M           +I    + F  +   P + V+   IWTGKQIFSLI+      P  
Sbjct: 576 DVFM-----------NILMWWEDFDGKVPTPAI-VKPRPIWTGKQIFSLII------PKQ 617

Query: 521 ANLKTKGRAYTANE--EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            N+      +  +E  +    D+ V +   ELL G++ K TLG+    ++ +++  + G 
Sbjct: 618 INMVRTAAWHNDSETGDNSPGDTMVRIEKGELLTGTLCKKTLGTSS-GSLIHVIWEEVGP 676

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           D A   +     + +++L+  GFSIGIGD 
Sbjct: 677 DAARKFLGHTQWLVNYWLLQHGFSIGIGDT 706



 Score =  104 bits (260), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 58/178 (32%), Positives = 96/178 (53%), Gaps = 9/178 (5%)

Query: 1226 LLPSVVIKGVQGINRAVIHE---------EDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 1276
            +L  + ++G+  I++  I E         E  +  T++ L  EG N+  VM    V   +
Sbjct: 1305 MLTEMALRGIPDIHKVFIREHKRQRFDEHEGFKAETEWMLDTEGVNMLAVMCNEDVDATR 1364

Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITR 1336
              SN+  EV + LGIEA R  ++ E++ V+   G  +++RH  ++ D+MT +G ++ ITR
Sbjct: 1365 TVSNHLIEVIEVLGIEAVRQALLKELREVISFDGSYVNYRHLAILCDVMTYRGHLMAITR 1424

Query: 1337 HGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
            HG+ +     +   SFE T D L DAA + + D + GV+E I++G    +GTG   LL
Sbjct: 1425 HGINRNDTGPMMRCSFEETVDILLDAAVFAEADHLRGVTENIMLGQLAPIGTGDFGLL 1482



 Score = 99.0 bits (245), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 41/57 (71%), Positives = 52/57 (91%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NS+  GLTP EF+FH MGGREGL+DTAVKT+ETGY+QRRLVK++ED+ V+YD
Sbjct: 834 RGFVENSYLRGLTPQEFYFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDVMVKYD 890



 Score = 75.5 bits (184), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 34/93 (36%), Positives = 57/93 (61%), Gaps = 5/93 (5%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D ++Q S  +I S   Y    +  P   GL D R+GT  ++  C TCG ++++C GHFG+
Sbjct: 26  DEIRQMSVCKIESSETY---DRGKPKSGGLSDPRLGTIDRQTKCETCGGSMAECPGHFGH 82

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVL 183
           ++L  P+FHIG+ + V+ +L+ +C N  C+ +L
Sbjct: 83  LELAKPMFHIGFLKTVLALLRCVCYN--CSHIL 113



 Score = 74.7 bits (182), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 70/287 (24%), Positives = 129/287 (44%), Gaps = 53/287 (18%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR++EIIN ++ I TP +  +L  +   + + A+ V+  LE TTL  V +  E  + P
Sbjct: 1135 GVPRLREIINVAKKIKTPSLYVHLKPEVSKEKERAKNVQCALEYTTLRSVTQATEIWYDP 1194

Query: 822  DDSFILIKLDMDRIRLLHLEVDIDS---------IRYCIERTRGISGHLTVS-------- 864
            D    +I+ D++ ++  +   D D          +R  + R   +   L+++        
Sbjct: 1195 DPMSTIIEEDVEFVKSYYEMPDEDVTPDKISPWLLRIELNREMMVDKKLSMADIAEKINL 1254

Query: 865  -------------GHSFLILKPK----DSSK-----SFNSKMYQMK---QLLPSVVIKGV 899
                             LIL+ +    D SK       +  ++  K    +L  + ++G+
Sbjct: 1255 EFVDDLTCIFNDDNAEKLILRVRIMNDDVSKGGEVDQSDDDVFLKKIESNMLTEMALRGI 1314

Query: 900  QGINRAVIHE---------EDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVY 950
              I++  I E         E  +  T++ L  EG N+  VM    V   +  SN+  EV 
Sbjct: 1315 PDIHKVFIREHKRQRFDEHEGFKAETEWMLDTEGVNMLAVMCNEDVDATRTVSNHLIEVI 1374

Query: 951  KTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            + LGIEA R  ++ E++ V+   G  +++RH  ++ D+MT +G ++ 
Sbjct: 1375 EVLGIEAVRQALLKELREVISFDGSYVNYRHLAILCDVMTYRGHLMA 1421



 Score = 52.4 bits (124), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 20/37 (54%), Positives = 29/37 (78%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            +++++ + P   +G +AAQSIGEP TQMTL TFH+AG
Sbjct: 1090 RFLQSLVAPGEMIGCVAAQSIGEPATQMTLNTFHYAG 1126


>gi|288561071|ref|YP_003424557.1| DNA-directed RNA polymerase subunit A' RpoA1 [Methanobrevibacter
           ruminantium M1]
 gi|288543781|gb|ADC47665.1| DNA-directed RNA polymerase subunit A' RpoA1 [Methanobrevibacter
           ruminantium M1]
          Length = 926

 Score =  157 bits (397), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 100/285 (35%), Positives = 151/285 (52%), Gaps = 46/285 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+VLFNRQPSLH++S+MAH  +VLP++TFR N CVC PYNADFDGDEMN+H+ QT+E+
Sbjct: 423 DGDIVLFNRQPSLHRMSMMAHEVRVLPYKTFRLNLCVCPPYNADFDGDEMNMHVFQTDES 482

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLT-------Q 453
           RAE              AK LM  + ++++PR G  +I A  D I+G YLLT       +
Sbjct: 483 RAE--------------AKSLMRVQEHILSPRFGGPIIGAIHDHISGAYLLTRDGFTVPE 528

Query: 454 KNAFFNRAQTMRIASTLIA----------DTSDICGIIKRFSWRSWNPVVFVRTAVIWTG 503
            +AF    Q +R +  L            D  +    IK ++ +        R    WTG
Sbjct: 529 DDAF----QMIRKSHLLKCPYDEYLKRDLDEKEYKQQIKEYNEK------LKRKHRDWTG 578

Query: 504 KQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGS- 562
           K++FSL+L    +    A +  K     A  E C  DSYV++++ +L  G++D++  GS 
Sbjct: 579 KELFSLLLPSTLNMNYRAEICRKCEECMA--EACEYDSYVVIKDGQLTHGAIDEAAYGSF 636

Query: 563 GGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            GK  +   +++++G   A   + R + +    +M  G +    D
Sbjct: 637 SGK--ILDNIVKEYGPAYAKEFLDRSTDLAICGIMKTGITTSTND 679



 Score =  118 bits (295), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 85/262 (32%), Positives = 129/262 (49%), Gaps = 32/262 (12%)

Query: 91  DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
           D++++ S + I   + Y +D    PI +GL+D R+G       C TCG+   +C GHFG 
Sbjct: 4   DQIREMSVVNITRPDTYDEDG--YPIENGLMDSRLGVIDPSLKCRTCGEKGGECQGHFGM 61

Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
           IDL  PV H+G+   +  IL+S C    C RVLL EE+   +  KL     +    + L 
Sbjct: 62  IDLARPVIHVGFGDDIHKILRSTCNE--CGRVLLDEEEIEEYTEKLNELQEAGESTEDLI 119

Query: 211 K---KILETTKKVSVCPHCG---EINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEY 264
           K   KI +  K   VCPHCG   E   +VK  G++++  E  +N     DA    +  +Y
Sbjct: 120 KEVYKICKAKKAKDVCPHCGAEQEDIKIVKPIGIIEVRKEYDENGELLTDANGNPVTTDY 179

Query: 265 NEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLL 324
           +                    L   EV +  E IP ED  +L +N E+++P  ++LT L 
Sbjct: 180 D--------------------LTASEVREKLERIPDEDAYVLGVNPEVARPEWMVLTVLP 219

Query: 325 VPPNCIRPSVISDL--KSDNDV 344
           VPP  +RPS+  D   +S++D+
Sbjct: 220 VPPVTVRPSITLDTGERSEDDL 241



 Score = 90.5 bits (223), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 39/58 (67%), Positives = 48/58 (82%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            +GFV +S+  GL P EFFFH MGGREGLVDTA++TA++GYMQRRLV +LEDL V+ D
Sbjct: 822 AKGFVHSSYKEGLDPVEFFFHAMGGREGLVDTAIRTAQSGYMQRRLVNALEDLNVRSD 879


>gi|261330838|emb|CBH13823.1| RNA polymerase IIA largest subunit, (fragment) [Trypanosoma brucei
           gambiense DAL972]
          Length = 948

 Score =  157 bits (397), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 93/267 (34%), Positives = 144/267 (53%), Gaps = 39/267 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + DVVLFNRQP+LH++S+M HR +VL + TFR N    TPYNADFDGDEMN+H+PQ+   
Sbjct: 443 NGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNLSCTTPYNADFDGDEMNLHVPQSLLT 502

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE +             +++M  K N V+P      +   QD + G Y LT K+ F ++
Sbjct: 503 KAELI-------------EMMMVPK-NFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFLDK 548

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                +A  L     D+        W+   P + ++   +WTGKQ+FSLIL P  + P  
Sbjct: 549 YFVQSVALWL-----DL--------WQLPIPAI-LKPRPLWTGKQVFSLIL-PEVNHPAT 593

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
              +           F H DS V++R  +LL G + KS +G+    ++ +++  + G D 
Sbjct: 594 PQDRPP---------FPHNDSVVMIRRGQLLCGPITKSIVGA-APGSLIHVIFNEHGSDE 643

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGD 607
               +  + R+T+F+L+N GFS+G+ D
Sbjct: 644 VARFINGVQRVTTFFLLNFGFSVGVQD 670



 Score = 82.4 bits (202), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 34/57 (59%), Positives = 44/57 (77%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +G     +  GL P EFFFHTM GREGL+DTAVKT++TGY+QR+L+K+LED+   YD
Sbjct: 799 RGMANRGYVEGLKPHEFFFHTMAGREGLIDTAVKTSDTGYLQRKLIKALEDVHAAYD 855



 Score = 82.4 bits (202), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 70/247 (28%), Positives = 110/247 (44%), Gaps = 42/247 (17%)

Query: 115 PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSIC 174
           P+  G+ D RMGT   E  C TC +   +C GHFGYI+L  PVF+IG F  V+ +L+ +C
Sbjct: 49  PVRGGINDLRMGTTDFEFACETCHRKHPECPGHFGYIELAEPVFNIGVFDLVLLVLKCVC 108

Query: 175 KNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPH--------- 225
           K  TC  +LL   +      KL++  ++ L R     K+ E   +VS             
Sbjct: 109 K--TCGALLL-NTREQDVHKKLQH--MTGLNRLRQVAKMAEAKCRVSTSTEDDMGIDGFD 163

Query: 226 -------CGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHK 278
                   G   G  + CG         + R  +   I   L+    +AV    + E H 
Sbjct: 164 SAPFNGGSGMGPGATRGCG-------ASQPRVSRFYGIYPTLVI---KAVHEEQDAEWHA 213

Query: 279 KFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSV-ISD 337
                      +V Q+ + +  +D  L+  + +   P DL+LT L VPP  +RP++    
Sbjct: 214 D----------KVRQVLDRVSDDDARLMGFDPQRCHPRDLVLTVLPVPPPQVRPAISFGG 263

Query: 338 LKSDNDV 344
           L+SD+++
Sbjct: 264 LRSDDEL 270


>gi|448579179|ref|ZP_21644456.1| DNA-directed RNA polymerase subunit A' [Haloferax larsenii JCM
           13917]
 gi|445723858|gb|ELZ75494.1| DNA-directed RNA polymerase subunit A' [Haloferax larsenii JCM
           13917]
          Length = 973

 Score =  157 bits (397), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 95/268 (35%), Positives = 141/268 (52%), Gaps = 45/268 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 484 DGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQNEEA 543

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR GE +I A QD I+G YLLT  N  F  
Sbjct: 544 RAE--------------ARVLMRVQEQILSPRFGENIIGAIQDHISGTYLLTHDNPHFVE 589

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q + +      DT      +   +    +   +      WTG QIFS +L      P +
Sbjct: 590 TQALDLLRATRVDT------LPEPAGEDDDGTPY------WTGHQIFSELL------PDD 631

Query: 521 ANLKTKGRAYTANEEFCHR-DSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            N+           EF  +    V++ + +LL G++D+  +G+ G   +  +L +D+ + 
Sbjct: 632 LNM-----------EFTSKVGDTVVIEDGQLLEGTIDEDAVGAFG-GEIVDVLAKDYSKT 679

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            +   +  ++ +    +M+ G SIGI D
Sbjct: 680 RSRIFINEIASLAMRAIMHFGLSIGIDD 707



 Score =  104 bits (260), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 80/296 (27%), Positives = 127/296 (42%), Gaps = 60/296 (20%)

Query: 97  SHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP 156
           S  ++++ + Y  D    PI  GL+D R+G       C TCGQ+   C GHFG+I+L  P
Sbjct: 26  SATKVITADTY--DDDGYPIDMGLMDPRLGVIDPGLQCRTCGQHSGSCNGHFGHIELAAP 83

Query: 157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKL-RNPALSYLVRKSLKKKILE 215
           V H+G+ + +  +L+S C+   C R+ L +E+A  +R KL R   L       +K  + +
Sbjct: 84  VIHVGFTKLIRRLLRSTCRE--CGRLALTQEEADDYRDKLGRTKELGDDWSDVMKSAVRQ 141

Query: 216 TTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVK------ 269
             +K   CPHC      +K        HEK     + ++ +  D      EA++      
Sbjct: 142 -ARKAHRCPHCSSPQHDIK--------HEKPTTYYEVQNVLAGDFSERIAEAMQPDPDDE 192

Query: 270 ----------------------------FNP----EIEAHKKFGL------IQTLNPLEV 291
                                       F P         K  G+      +  L P ++
Sbjct: 193 DDEGISPVDLAEKADLPAERVNQVLAGEFRPVGDDRKALEKALGIDLTEEDMNKLMPSDI 252

Query: 292 LQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDNDVV 345
              FE IP ED+  L ++ + S+P  +ILT L VPP   RPS+  D   +S++D+ 
Sbjct: 253 RDWFEDIPDEDLVTLGIDPDRSRPEWMILTVLPVPPVTARPSITLDNGQRSEDDLT 308



 Score = 92.4 bits (228), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 44/81 (54%), Positives = 59/81 (72%), Gaps = 7/81 (8%)

Query: 597 MNRGFS------IGIGDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAET 649
           +NRG+          GD++    GFV+NS+ +GLTP EFFFH MGGREGLVDTAV+T+++
Sbjct: 814 INRGYEERTLSHYQKGDLSAEAHGFVENSYCAGLTPREFFFHAMGGREGLVDTAVRTSKS 873

Query: 650 GYMQRRLVKSLEDLCVQYDMS 670
           GY+QRRL+ +L +L  QYD S
Sbjct: 874 GYLQRRLINALSELEAQYDGS 894



 Score = 43.1 bits (100), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 20/46 (43%), Positives = 28/46 (60%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 65
           +VLM  +  +++PR GE +I A QD I+G YLLT  N  F   Q +
Sbjct: 548 RVLMRVQEQILSPRFGENIIGAIQDHISGTYLLTHDNPHFVETQAL 593


>gi|448312200|ref|ZP_21501950.1| DNA-directed RNA polymerase subunit A' [Natronolimnobius
           innermongolicus JCM 12255]
 gi|445602707|gb|ELY56679.1| DNA-directed RNA polymerase subunit A' [Natronolimnobius
           innermongolicus JCM 12255]
          Length = 977

 Score =  157 bits (397), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 99/270 (36%), Positives = 142/270 (52%), Gaps = 45/270 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 483 DGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQNEEA 542

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR GE +I A QD I+G YLLT  N  FN 
Sbjct: 543 RAE--------------ARVLMRVQEQILSPRFGENIIGAIQDHISGMYLLTADNPRFNE 588

Query: 461 AQTMR-IASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q +  + +T I +  +  GI                    WTG  +FS +L      P 
Sbjct: 589 TQALDLLRATRIDELPEPSGIDD-------------EGEPFWTGYDVFSELL------PD 629

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           + NL+  G   T  EE       V++ + +L+ G++ +  +G  G   +   + + +G  
Sbjct: 630 DLNLEFTG---TIGEE-------VVIEDGQLIEGTIAEDEVGEFG-GEIVDRITKSYGNT 678

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVT 609
            +   +  +S +    +M+ GFSIGI D T
Sbjct: 679 RSRIFINEVSTLAMRAIMHFGFSIGIDDET 708



 Score =  108 bits (270), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 88/310 (28%), Positives = 136/310 (43%), Gaps = 57/310 (18%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G I   + + +  ++ S  +I++ + Y  D    PI  GL+D R+G       C TCG++
Sbjct: 10  GSISFGLMEPEEYREMSATKIITADTY--DDDGFPIDMGLMDPRLGVIDPGLECKTCGKH 67

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
              C GHFG+I+L  PV H+G+ + +  +L+  C+   C+++LL E++   FR  +    
Sbjct: 68  SGSCNGHFGHIELAAPVIHVGFTKLIRRLLRGTCRE--CSKLLLTEDEREEFRDDITESR 125

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEK--------------Y 246
                   + K  +   +K   CP CGEI           I HEK              Y
Sbjct: 126 KLGRDLNDVTKAAIRQARKKDRCPFCGEIQ--------YDIDHEKPTTYYEVQQVLTSEY 177

Query: 247 KNRTK-----KKDAIVE----DLLAEYNE----------AVKFNPE------IEAHKKFG 281
             R        ++A VE    D LA   E          +  F P       IE      
Sbjct: 178 SQRIAAAMQGDEEAGVERTSPDELAAETEIDLTRINEILSGSFRPRESQRKAIEKALDID 237

Query: 282 LIQT----LNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD 337
           L +     L P ++   FEAIP EDI +L ++ + S+P  +ILT L VPP   RPS+  D
Sbjct: 238 LTEEDTNKLMPSDIRDWFEAIPDEDIQVLGIDPDRSRPEWMILTVLPVPPVTARPSITLD 297

Query: 338 --LKSDNDVV 345
              +S++D+ 
Sbjct: 298 NGQRSEDDLT 307



 Score = 92.8 bits (229), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 39/58 (67%), Positives = 49/58 (84%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
             GFV+NS+ SGLTP EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 834 AHGFVENSYTSGLTPREFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELETQYD 891



 Score = 45.1 bits (105), Expect = 0.32,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 29/46 (63%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 65
           +VLM  +  +++PR GE +I A QD I+G YLLT  N  FN  Q +
Sbjct: 547 RVLMRVQEQILSPRFGENIIGAIQDHISGMYLLTADNPRFNETQAL 592


>gi|359294821|gb|AEV21781.1| RPB1, partial [Mortierella hyalina]
          Length = 459

 Score =  157 bits (397), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 90/271 (33%), Positives = 145/271 (53%), Gaps = 37/271 (13%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D DVV+FNRQPSLHK+S+M H+ +V+P+ TFR N  V +PYNADFDGDEMN+H+PQ+ E
Sbjct: 84  NDGDVVIFNRQPSLHKMSMMGHKIRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSVE 143

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE               ++ M  +  +V+P++ + ++   QD + G    T+++ F  
Sbjct: 144 TRAEI-------------TEICMVPRQ-IVSPQSNKPVMGIVQDTLCGVRKFTKRDCFLT 189

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPV-VFVRTAVIWTGKQIFSLILKPNRDCP 518
           +   M +   +               W  + P    ++   +WTGKQ+ S+I+      P
Sbjct: 190 KEMVMNLVMWVPG-------------WEGFLPTPAILKHKPLWTGKQMISMII------P 230

Query: 519 VNANLKTKGRAYTANEE--FCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
              N  T    +  NEE      D+ VI+ N EL+ G + K T+G+ G   + ++++  +
Sbjct: 231 KGINCITFHSTHPDNEESDISPGDTKVIVENGELICGIVCKKTVGTSGGGWI-HVIMNQY 289

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           G +VA T       + +++L+  GFSIGIGD
Sbjct: 290 GPEVAKTFFNGCQTVVNYWLLQHGFSIGIGD 320


>gi|188532147|gb|ACD63085.1| RNA polymerase II largest subunit [Illicium parviflorum]
          Length = 1013

 Score =  157 bits (397), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 94/271 (34%), Positives = 148/271 (54%), Gaps = 35/271 (12%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D D VLFNRQPSLHK+SIM HR K++P+ TFR N  V +PYNADFDGDEMN+H+PQ+ E
Sbjct: 372 NDGDYVLFNRQPSLHKMSIMGHRIKIMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSFE 431

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE L             +++M  K  +V+P++   ++   QD + G   +T+++ F  
Sbjct: 432 TRAEVL-------------ELMMVPKC-IVSPQSNRPVMGIVQDTLLGCRKITKRDTFIE 477

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           +   M I    +    D  G I         P + ++   +WTGKQ+F+LI+      P 
Sbjct: 478 KDVFMNI----LMWWEDFDGKIP-------APAI-LKPRPLWTGKQVFNLII------PK 519

Query: 520 NANLKTKGRAYTANEE--FCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFG 577
             NL      ++ +E       D++V +   ELL+G++ K TLG+    ++ +++  + G
Sbjct: 520 QINLIRTSAWHSESETGFITPGDTHVRIEKGELLSGTLCKKTLGT-STGSLIHVIWEEVG 578

Query: 578 EDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
            D A   +     + +++L+  GFSIGIGD 
Sbjct: 579 PDAARKFLGHTQWLVNYWLLQNGFSIGIGDT 609



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 42/57 (73%), Positives = 52/57 (91%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKT+ETGY+QRRLVK++ED+ V+YD
Sbjct: 737 RGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDIMVKYD 793



 Score = 55.1 bits (131), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 65/212 (30%), Positives = 102/212 (48%), Gaps = 45/212 (21%)

Query: 150 YIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKS 208
           +++L  P+FHIG+ + V++I++S+C N  C+ +L  +E     +A K+RNP       K 
Sbjct: 1   HLELAKPMFHIGFLKTVLSIMRSVCFN--CSHILADQEDHRFKQALKIRNP-------KH 51

Query: 209 LKKKILETTKKVSVCPHCGEI---------NGVVKK----CGLL--KISHEKYK-----N 248
             +K+L+  K    C    +I         +GV KK    CG    KI+ E  K      
Sbjct: 52  RLRKVLDCCKSKQKCEGGDDIDEDQAQDSEDGVKKKGHGGCGAQQPKITVEGMKMIAEFK 111

Query: 249 RTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLM 308
           +T+KK    E +L E            A +K    Q L+   VL + + I  ED  LL +
Sbjct: 112 QTRKKSDEQEQMLPE-----------PAERK----QQLSAERVLSILKRISDEDCLLLGL 156

Query: 309 NAELSKPSDLILTRLLVPPNCIRPSVISDLKS 340
           N + ++P  +IL  L +PP  +RPSV+ D  S
Sbjct: 157 NPKYARPDWMILQVLPIPPPPVRPSVMMDTSS 188


>gi|448347128|ref|ZP_21536007.1| DNA-directed RNA polymerase subunit A' [Natrinema altunense JCM
           12890]
 gi|445631465|gb|ELY84697.1| DNA-directed RNA polymerase subunit A' [Natrinema altunense JCM
           12890]
          Length = 975

 Score =  157 bits (397), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 99/270 (36%), Positives = 143/270 (52%), Gaps = 45/270 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 483 DGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQNEEA 542

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR GE +I A QD I+G YLLT  N  FN 
Sbjct: 543 RAE--------------ARVLMRVQEQMLSPRFGENIIGAIQDHISGMYLLTHDNPRFNE 588

Query: 461 AQTMR-IASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q +  + +T I +  +  GI    +               WTG  +FS +L      P 
Sbjct: 589 TQALDLLRATRIDELPEPSGIDDEGT-------------PFWTGYDVFSELL------PD 629

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           + +L+  G   T  +E       V++ + +LL G++ +  +G  G   +   + + +G  
Sbjct: 630 DLDLEFTG---TIGDE-------VVIEDGQLLQGTIAEDEVGEFG-GEIVDTITKVYGNT 678

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVT 609
            A   +  +S +    +M+ GFSIGI D T
Sbjct: 679 RARIFVNEVSTLAMRAIMHFGFSIGIDDET 708



 Score =  110 bits (274), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 83/290 (28%), Positives = 131/290 (45%), Gaps = 43/290 (14%)

Query: 94  QQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDL 153
           ++ S  +I++ + Y  D    PI  GL+D R+G       C TCG++   C GHFG+I+L
Sbjct: 23  REMSATKIITADTY--DDDGFPIDMGLMDPRLGVIDPGLECKTCGKHSGSCNGHFGHIEL 80

Query: 154 PLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKI 213
             PV H+G+ + +  +L+  C+   C+++LL E++   FR +L            + K  
Sbjct: 81  AAPVIHVGFTKLIRRLLRGTCRE--CSKLLLTEDERDEFRDQLDESRKLSRDLNDVTKAA 138

Query: 214 LETTKKVSVCPHCGEINGVV---------------------KKCGLLKISHEKYKNRTKK 252
           +   +K   CP CGEI   +                     +  G ++   E+   RT  
Sbjct: 139 IRQARKKDRCPFCGEIQYDIDHEKPTTYYEVQQVLTSEYSQRIAGAMQGDEEEGVERT-T 197

Query: 253 KDAIVEDL---LAEYNEAV--KFNPE------IEAHKKFGLIQT----LNPLEVLQLFEA 297
            D + E     L   NE +   F P       IE      L +     L P ++   FE 
Sbjct: 198 PDELAEQTEIELTRVNEILSGSFRPRESQRKAIEKALDIDLTEEDTNKLMPSDIRDWFEN 257

Query: 298 IPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDNDVV 345
           IP EDI +L +N + S+P  +ILT L VPP   RPS+  D   +S++D+ 
Sbjct: 258 IPDEDIEVLGINPDRSRPEWMILTVLPVPPVTARPSITLDNGQRSEDDLT 307



 Score = 92.8 bits (229), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 39/58 (67%), Positives = 49/58 (84%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
             GFV+NS+ SGLTP EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 834 AHGFVENSYTSGLTPREFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELETQYD 891



 Score = 45.8 bits (107), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 29/46 (63%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 65
           +VLM  +  +++PR GE +I A QD I+G YLLT  N  FN  Q +
Sbjct: 547 RVLMRVQEQMLSPRFGENIIGAIQDHISGMYLLTHDNPRFNETQAL 592


>gi|327242117|gb|AEA40837.1| RNA polymerase II largest subunit [Trichomonas sp. RWG-2007-1]
          Length = 998

 Score =  157 bits (397), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 87/267 (32%), Positives = 146/267 (54%), Gaps = 31/267 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+D+V+FNRQPSLHK+S+M HRA ++  RTFR N C  TPYNADFDGDEMN+H+PQ++ A
Sbjct: 353 DDDIVIFNRQPSLHKMSMMGHRALIMSGRTFRLNLCDTTPYNADFDGDEMNLHVPQSQTA 412

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R E               + +MA    +++P+  + +I   QD + G  LL++++ F  R
Sbjct: 413 RTE--------------VRHIMAVPKQIISPQANKPVIGLVQDALLGCRLLSKRDTFLTR 458

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M +   L + T D           +  P   ++   +W+GKQ+FSL L       ++
Sbjct: 459 NQVMNLMMWLPS-TKDT----------NLPPPCILKPVQLWSGKQVFSLFLP-----KIS 502

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            +  ++             D +VI+R+  LLAG +DK T+    + ++ ++++  +  ++
Sbjct: 503 HDSLSQDATDADKNSLPLNDRHVIIRDGNLLAGILDKRTVAR-SEGSLIHVVINSYNTNI 561

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           A   + +   + + +L +RGFSIG+ D
Sbjct: 562 AKDFLNQTQLIVNNWLEHRGFSIGLID 588



 Score = 82.4 bits (202), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 35/57 (61%), Positives = 44/57 (77%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GF  NS+ +GLTP EF FH MGGR G++DTA KT++TGY+QRRL KS+E   V YD
Sbjct: 717 RGFCVNSYIAGLTPPEFLFHAMGGRTGIIDTACKTSDTGYIQRRLCKSMESHHVAYD 773



 Score = 47.8 bits (112), Expect = 0.045,   Method: Compositional matrix adjust.
 Identities = 61/216 (28%), Positives = 93/216 (43%), Gaps = 61/216 (28%)

Query: 169 ILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRK-SLKKKILETTKKVSVCPHCG 227
           +LQ +C   +C RVL              +P + ++VR    K + L+  +K+S      
Sbjct: 1   LLQMVCH--SCGRVL----------CNYSDPEIQFIVRHYKGKNRFLKLFEKIS------ 42

Query: 228 EINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAE------YNEAVKFN-------PEI 274
             N   +KC     S  + KN  K  D + +D   E      +++ V+         P +
Sbjct: 43  --NKQCQKC-----SSGEDKNSNKDMDCVSDDRFWEIVNGDAHSDHVRIKKPCESTVPAV 95

Query: 275 EAHKKFGLIQTLN---------PLE-VLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLL 324
           E  K F LI+  +         P E VL++FE I  +D+ LL  N + S P  LI+  L 
Sbjct: 96  EQGKHF-LIKYKDSSANEDDYIPAEKVLRIFENISDQDVRLLGFNVKRSHPKWLIIKILP 154

Query: 325 VPPNCIRPSVIS---DLKSDNDVVLFNRQPSLHKLS 357
           VPP  +RP V+S    + S +DV         HKLS
Sbjct: 155 VPPLAVRPQVVSPGQSVPSQDDVT--------HKLS 182


>gi|374724392|gb|EHR76472.1| DNA-directed RNA polymerase subunit A [uncultured marine group II
            euryarchaeote]
          Length = 519

 Score =  157 bits (397), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 108/369 (29%), Positives = 176/369 (47%), Gaps = 67/369 (18%)

Query: 1090 HGRESNPFPSACKAEACREKYV---RAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG- 1145
            H R  N        +   E  V   +A I+P  A G + AQSIGEPGTQMT++TFH+AG 
Sbjct: 148  HARGKNKLTKPQAKKVVEEAVVALDKASIDPYEAAGIITAQSIGEPGTQMTMRTFHYAGV 207

Query: 1146 ----------EVCEYIEEVFVPDDSFILIKLDMDR-------------------IRLLHL 1176
                       + E ++   VP+   + I L  ++                   + +  L
Sbjct: 208  ATVNVTQGLPRIIEIVDARKVPNTPTMTICLLGEKKHDAKEAQKLAAAIEVTTTVNIATL 267

Query: 1177 EVDIDSIRYCIERTRGISGHLTVSG---------HSFLILKPKDSSK------------- 1214
            E D+   R  ++  +G      ++G          + L+++P +                
Sbjct: 268  ETDVAQRRLVLKLNKGNLKQKNMTGLEVKDKLERATRLLVQPDNEKNPGTLTLIPGVHSE 327

Query: 1215 ------SFNSKMY----QMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLR 1264
                  + N   Y    Q+++ +  + +KG+  I RA +  +D  G  +Y L   G NL 
Sbjct: 328  EDLAELAENPPSYTMLLQLEEKIRDMRLKGIPNIERANVQLDDKTG--EYYLSTIGSNLT 385

Query: 1265 DVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADL 1324
             V     +   +  +NN  E+Y  LGIEAAR  I+ E++  ++   + +D RH ++VAD+
Sbjct: 386  RVSEIETIDRTRTYTNNIIEIYDFLGIEAARQAIINELQATLDGARLEVDVRHLLMVADV 445

Query: 1325 MTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPM 1384
            MTS+GEV  I RHG++  K S+L  A+FE T +HL  A   G+ D ++GV+E II+G P+
Sbjct: 446  MTSEGEVRAIGRHGVSGTKHSILARAAFEVTVNHLLKAGIIGERDYLTGVAENIIVGQPI 505

Query: 1385 NVGTGLIKL 1393
            ++GTG ++L
Sbjct: 506  SLGTGSVEL 514



 Score = 77.4 bits (189), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 71/249 (28%), Positives = 119/249 (47%), Gaps = 20/249 (8%)

Query: 764 GVPRIKEIINASRNISTPIITAYL--DKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
           G+PRI EI++A +  +TP +T  L  +K  D   A+ +   +E TT   +     +V   
Sbjct: 215 GLPRIIEIVDARKVPNTPTMTICLLGEKKHDAKEAQKLAAAIEVTTTVNIATLETDVAQR 274

Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGI---------SGHLTV--SGHSFLI 870
                L K ++ +  +  LEV     +  +ER   +          G LT+    HS   
Sbjct: 275 RLVLKLNKGNLKQKNMTGLEV-----KDKLERATRLLVQPDNEKNPGTLTLIPGVHSEED 329

Query: 871 LKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDV 930
           L     +    + + Q+++ +  + +KG+  I RA +  +D  G  +Y L   G NL  V
Sbjct: 330 LAELAENPPSYTMLLQLEEKIRDMRLKGIPNIERANVQLDDKTG--EYYLSTIGSNLTRV 387

Query: 931 MATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMT 990
                +   +  +NN  E+Y  LGIEAAR  I+ E++  ++   + +D RH ++VAD+MT
Sbjct: 388 SEIETIDRTRTYTNNIIEIYDFLGIEAARQAIINELQATLDGARLEVDVRHLLMVADVMT 447

Query: 991 SKGEVLGNG 999
           S+GEV   G
Sbjct: 448 SEGEVRAIG 456


>gi|110669637|gb|ABG81913.1| RNA polymerase II largest subunit [Lecanora hybocarpa]
          Length = 1016

 Score =  157 bits (397), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 93/271 (34%), Positives = 149/271 (54%), Gaps = 39/271 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D ++FNRQPSLHK S+M HR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 373 DGDYIIFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 432

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    +++L ++            N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 433 RAE----VNQLCMVP----------LNIVSPQRNGPLMGIVQDTLCGIYKMCRRDVFLTK 478

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M I    +    D  G+I +       P + ++   +WTGKQI SL++      P  
Sbjct: 479 EQVMNI----LLWVPDWDGVIPQ-------PAI-LKPRPMWTGKQILSLVI------PAG 520

Query: 521 ANLKTKGRAYTANEEFCH-RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
            NL        ++E F    D  +++   EL+ G ++K ++G+ G   V +I+  + G +
Sbjct: 521 LNL-----LRGSDEGFSPLNDDGLLVSGGELMYGLLNKKSVGATG-GGVIHIIFNEKGPE 574

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
            A+        + +++L++ GFSIGIGD  P
Sbjct: 575 AAMNFFNGAQTVVNYWLLHNGFSIGIGDTIP 605



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+  
Sbjct: 725 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDVMA 784

Query: 666 QYD 668
           +YD
Sbjct: 785 KYD 787



 Score = 58.2 bits (139), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 49/195 (25%), Positives = 88/195 (45%), Gaps = 41/195 (21%)

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNPAL 201
           +C GHFG+I+L +PVFH+G+   +  +L+++C N  C ++L+ E   A   A + R+P  
Sbjct: 1   ECPGHFGHIELAVPVFHVGFMTKIKKLLETVCHN--CGKILVDESNPAFVDALRYRDPKR 58

Query: 202 SY--LVRKSLKKKILETT---------KKVSVCPH----CGEINGVVKKCGLLKISHEKY 246
            +  + R    K I ETT         +K     H    CG I   +++ GL      + 
Sbjct: 59  RFDAVWRLCKPKMICETTIAMDDDAPPEKQKEPKHDHGGCGNIQPEIRREGL------RL 112

Query: 247 KNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLL 306
               K +    E+             E++  +K    + + P   L +F  I  EDI  +
Sbjct: 113 NGTWKPQKGDEEN-------------EVQQPEK----KPITPQMALNIFRHITTEDIRRM 155

Query: 307 LMNAELSKPSDLILT 321
            ++ + ++P  +I+T
Sbjct: 156 GLSNDYARPEWMIIT 170


>gi|33326219|gb|AAQ08519.1| RNA polymerase II largest subunit [Psilotum nudum]
          Length = 1013

 Score =  157 bits (397), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 95/270 (35%), Positives = 147/270 (54%), Gaps = 35/270 (12%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D D VLFNRQPSLHK+SIM H+ +++P  TFR N  V +PYNADFDGDEMN+H+PQ+ E
Sbjct: 372 NDGDFVLFNRQPSLHKMSIMGHKIRIMPFSTFRLNLSVTSPYNADFDGDEMNMHVPQSFE 431

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE L             +++M  K  +V+P++   +I   QD + G   +T+++ F  
Sbjct: 432 TRAEVL-------------ELMMVPKC-IVSPQSNRPVIGIVQDTLLGCRKVTKRDTFIE 477

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           +   M I    +    D  G I         P + ++   +WTGKQ+FSLI+      P 
Sbjct: 478 KDVFMNI----LMWWEDFDGKIP-------APTI-LKPKPLWTGKQLFSLII------PK 519

Query: 520 NANLKTKGRAYTANE--EFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFG 577
             NL      +  +E  E    D+ V +   EL++G++ K TLG+ G  ++ +++  + G
Sbjct: 520 QINLIRFSAWHLDSEVGEITPGDTVVRIEKGELISGTLCKKTLGTSG-GSLIHVIWEEVG 578

Query: 578 EDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            D A   +     + +++L+  GFSIGIGD
Sbjct: 579 PDAARKFLGHTQWLVNYWLLQHGFSIGIGD 608



 Score =  100 bits (249), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 42/57 (73%), Positives = 52/57 (91%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKT+ETGY+QRRLVK++ED+ V+YD
Sbjct: 737 RGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDVMVKYD 793



 Score = 67.8 bits (164), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 57/203 (28%), Positives = 102/203 (50%), Gaps = 17/203 (8%)

Query: 150 YIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKS 208
           +++L  P+FHIG  + V+ IL+ +C N  C+R+L  EE     +A K+RNP       K 
Sbjct: 1   HLELAKPMFHIGVLKTVLTILRCVCYN--CSRILADEEDHRFKQARKIRNP-------KH 51

Query: 209 LKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVED---LLAEYN 265
             +++L+  K  S C    +I+             +K+     ++  I  D   ++AE+ 
Sbjct: 52  RLRRMLDCCKTKSKCEGGDDIDEDQGHDNEEAEKKKKHGGCGAQQPKITIDGMKIIAEFK 111

Query: 266 EAVKFNPEIEAH--KKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRL 323
            + K N E + +  +     Q L+  +VL + + I  ED   L +N + ++P  +IL  L
Sbjct: 112 ASKKKNEEQDQYMPEPVERKQQLSAEKVLSILKQISDEDCVTLGLNPKYARPDWMILQVL 171

Query: 324 LVPPNCIRPSVISD--LKSDNDV 344
            +PP  +RPSV+ D   +S++D+
Sbjct: 172 PIPPPSVRPSVMMDTSARSEDDL 194


>gi|413915232|gb|AFW21478.1| RNA polymerase II largest subunit [Neotyphodium gansuense]
          Length = 1761

 Score =  157 bits (397), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 86/276 (31%), Positives = 153/276 (55%), Gaps = 32/276 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D ++FNRQPSLHK S+M HR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 450 DGDYIIFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 509

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE               K L    +N+V+P+    L+   QD + G Y + +++ F ++
Sbjct: 510 RAE--------------VKELCLVPNNIVSPQKNGPLMGVVQDSLAGAYKICRRDTFIDK 555

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              M     ++    +  G+I +       P + ++    WTGKQ+ S+++   ++  ++
Sbjct: 556 EMVM----NMMLWVPNWDGVIPQ-------PAI-LKPRPRWTGKQLISMVIP--KEISLH 601

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           +   + G+    N +   +D+ +++++ ELL G + K  +GS     + ++   + G D 
Sbjct: 602 SPESSGGQ---DNADIPLKDTGLLIQSGELLYGLLKKKNIGSAA-GGIVHLSYNELGPDG 657

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           A+  +  + ++ +++L+N G SIGIGD  P +  ++
Sbjct: 658 AMAFLNGVQQVVTYWLLNNGHSIGIGDTVPDKQTIE 693



 Score =  107 bits (267), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 81/283 (28%), Positives = 136/283 (48%), Gaps = 39/283 (13%)

Query: 1146 EVCEYIEEVF-VPDDS--------FILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGH 1196
            E  + +E  F +PDDS          L+++ +DR +LL  E+ ID +   I+        
Sbjct: 1181 EDMDMVESYFLIPDDSQDTTDQQSRWLLRITLDRQKLLDKEIKIDDVAQRIKEEYPSDLA 1240

Query: 1197 LTVSGHSF---LIL---------KPKDSSKSFNSKMYQMK---QLLPSVVIKGVQGINRA 1241
            +  S ++    +I          K +D  K     +   +    LL ++ ++GV GI RA
Sbjct: 1241 IIFSDNNADEQVIRIRTIRADNEKDEDGEKKIEDDVMLKRLEAHLLDTLTLRGVPGIERA 1300

Query: 1242 V---------------IHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVY 1286
                            I ++D +  T++ L   G  LRDV+A  GV   +  +N+ ++V 
Sbjct: 1301 FLTKGTRLVVDDDGAEIAKKDDDKCTQWYLDTSGSALRDVLAVDGVDPTRTYTNDLWQVV 1360

Query: 1287 KTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESV 1346
            +  GIEAARS ++ E+  V+   G  ++ RH  L+ D+MT +G +  +TRHG+ +     
Sbjct: 1361 EVFGIEAARSALVKELTNVLAFDGSYVNHRHIALLVDVMTYRGTISAVTRHGINRADTGA 1420

Query: 1347 LNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
            L   SFE T + L +AA  G+ D   G+SE +++G    +GTG
Sbjct: 1421 LMRCSFEETVEILLEAAASGELDDCRGISENVMLGQLAPMGTG 1463



 Score =  103 bits (256), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 46/63 (73%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QRRLVK+LEDL  
Sbjct: 807 DYSPEARGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDLSA 866

Query: 666 QYD 668
           +YD
Sbjct: 867 RYD 869



 Score = 86.7 bits (213), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 77/296 (26%), Positives = 134/296 (45%), Gaps = 68/296 (22%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKD-------------------------TDLDYARI 798
            GVPR+KEI+N +++I TP +  YL+                           T++ Y   
Sbjct: 1114 GVPRLKEILNLAKDIKTPSMAVYLNTHLGTQEQAKKLRSLVEYTNLRSITSVTEIYYDPD 1173

Query: 799  VKGRLERTTLGEVCEYIEEVF-VPDDS--------FILIKLDMDRIRLLHLEVDIDSIRY 849
            ++G    T++ E  + +E  F +PDDS          L+++ +DR +LL  E+ ID +  
Sbjct: 1174 IQG----TSIVEDMDMVESYFLIPDDSQDTTDQQSRWLLRITLDRQKLLDKEIKIDDVAQ 1229

Query: 850  CIERTRGISGHLTVSGHSF---LIL---------KPKDSSKSFNSKMYQMK---QLLPSV 894
             I+        +  S ++    +I          K +D  K     +   +    LL ++
Sbjct: 1230 RIKEEYPSDLAIIFSDNNADEQVIRIRTIRADNEKDEDGEKKIEDDVMLKRLEAHLLDTL 1289

Query: 895  VIKGVQGINRAV---------------IHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
             ++GV GI RA                I ++D +  T++ L   G  LRDV+A  GV   
Sbjct: 1290 TLRGVPGIERAFLTKGTRLVVDDDGAEIAKKDDDKCTQWYLDTSGSALRDVLAVDGVDPT 1349

Query: 940  KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            +  +N+ ++V +  GIEAARS ++ E+  V+   G  ++ RH  L+ D+MT +G +
Sbjct: 1350 RTYTNDLWQVVEVFGIEAARSALVKELTNVLAFDGSYVNHRHIALLVDVMTYRGTI 1405



 Score = 66.6 bits (161), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 61/221 (27%), Positives = 101/221 (45%), Gaps = 27/221 (12%)

Query: 110 DPQRT-PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVIN 168
           D  RT P   GL D  +G+  +   C TC Q +SDC GHFG+I+L  PV+H G+ + V  
Sbjct: 44  DETRTKPRDGGLNDPLLGSIDRGFKCKTCTQAMSDCPGHFGHIELAKPVYHPGFIKKVKK 103

Query: 169 ILQSICKNPTCARVLLGEE-----KAAGFR-AKLRNPALSYLVRKSLKKKILETTKK--V 220
           IL+ +C N  C++VL          A   R AKLR   +  + +K  + +  + T+K   
Sbjct: 104 ILEIVCHN--CSKVLADTSDPEFVSAIHTRDAKLRFNRVWAVCKKKRRCENEDRTEKNDE 161

Query: 221 SVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKF 280
              P    +      CG ++    +   + K    +V++   +  E V   PE+ AH   
Sbjct: 162 EFAPGMKPVVNNHGGCGNVQPQVRQAALQLKAAFDVVQEDGPKRRETVPITPEM-AHG-- 218

Query: 281 GLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
                        + + I  ED+  + +N++ ++P  LI+T
Sbjct: 219 -------------ILKRISEEDLRHMGLNSDYARPEWLIIT 246



 Score = 55.5 bits (132), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/39 (61%), Positives = 29/39 (74%)

Query: 1107 REKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            + ++ R+ + P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1067 QNRWDRSFVSPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1105


>gi|120561229|gb|ABM27000.1| RNA polymerase II largest subunit, partial [Blastocladiella
           emersonii]
          Length = 1005

 Score =  157 bits (397), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 98/284 (34%), Positives = 155/284 (54%), Gaps = 38/284 (13%)

Query: 327 PNCIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFD 386
           PN     V+    SDNDV++FNRQPSLHK+S+M H+ KV+P+ TFR N  V +PYNADFD
Sbjct: 345 PNLQPGWVVERHLSDNDVIIFNRQPSLHKMSMMGHKVKVMPYSTFRLNLSVTSPYNADFD 404

Query: 387 GDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFIT 446
           GDEMN+H+PQ+ EARAE    + +L ++  +          +V+P++ + ++   QD + 
Sbjct: 405 GDEMNLHVPQSVEARAE----IQQLCMVPLQ----------IVSPQSNKPVMGIVQDTLC 450

Query: 447 GGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPV-VFVRTAVIWTGKQ 505
           G    T+++ F ++A  M +             ++    W    PV   ++   +WTGKQ
Sbjct: 451 GITKFTRRDTFMDKAMVMNL-------------LMWVPGWDGNVPVPAILKPKPLWTGKQ 497

Query: 506 IFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLG--SG 563
           I SLI+ P  +C    +    G       +    D+ VI+ + ELLAG + K T+G  +G
Sbjct: 498 ILSLII-PKVNCITLHSTHPDGET----TDISPGDTRVIVEDGELLAGIVCKKTVGTSAG 552

Query: 564 GKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           G  +V ++   + G + A   +     + + +L++ GFSIGIGD
Sbjct: 553 GLVHVSWM---EHGPEAAKALLNGCQTIVNHWLLHNGFSIGIGD 593



 Score =  101 bits (251), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GL P EFFFH MGGREGL+DTAVKTAETGY+QRRLVK+LED+ V
Sbjct: 716 DYSPESRGFVENSYLRGLNPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMV 775

Query: 666 QYD 668
           +YD
Sbjct: 776 KYD 778



 Score = 49.3 bits (116), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 47/177 (26%), Positives = 77/177 (43%), Gaps = 24/177 (13%)

Query: 150 YIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSL 209
           +I+L  PV+HI +   V  IL+ IC +  C+R LLG+     F+  +R        R   
Sbjct: 1   HIELARPVYHISFLPRVKKILECICFH--CSR-LLGDPNHPAFKKAVRTRD-----RNRR 52

Query: 210 KKKILETTKKVSVCP-----HCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEY 264
            K++    K ++VCP        E+  +  +  L            K++  I +  L  Y
Sbjct: 53  FKEVHAHCKAINVCPAEDPNKADEMPDLEDRIPLHGCG--------KRQPDIRKKNLTLY 104

Query: 265 NEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
           ++   + P             L P +VLQ+ + IP ED   L +N E ++P  +ILT
Sbjct: 105 SQ---WKPNASDDAALEGRHDLTPDQVLQILKRIPDEDCEALGLNPEYARPEWMILT 158


>gi|123979340|gb|ABM81495.1| RNA polymerase II largest subunit [Tornabea scutellifera]
          Length = 993

 Score =  157 bits (397), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 94/270 (34%), Positives = 146/270 (54%), Gaps = 39/270 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D ++FNRQPSLHK S+M HR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 353 DGDFIIFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 412

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    +++L ++            N+V+P+    L+   QD + G Y + +++ F N 
Sbjct: 413 RAE----VNQLCMVP----------LNIVSPQRNSPLMGIVQDTLCGIYKICRRDVFLNH 458

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M I    +    +  GII +       P V ++   +WTGKQI SL++      P  
Sbjct: 459 EQVMNI----LLWVPEWDGIIPQ-------PAV-LKPKPLWTGKQIVSLVI------PSG 500

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            NL  KG  Y        +D  + +   EL+ G ++K  +G+     + +I+  + G + 
Sbjct: 501 LNL-VKGSDYAP-----LKDEGIFVAGGELMFGLLNKKVVGA-AMGGIIHIVYNEKGSEA 553

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           A+        + +++L++ GFSIGIGD  P
Sbjct: 554 AMNFFNGAQAVVNYWLLHNGFSIGIGDTIP 583



 Score =  101 bits (251), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+  
Sbjct: 703 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDVMA 762

Query: 666 QYD 668
           +YD
Sbjct: 763 KYD 765


>gi|448383941|ref|ZP_21562939.1| DNA-directed RNA polymerase subunit A' [Haloterrigena
           thermotolerans DSM 11522]
 gi|445658930|gb|ELZ11742.1| DNA-directed RNA polymerase subunit A' [Haloterrigena
           thermotolerans DSM 11522]
          Length = 975

 Score =  157 bits (396), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 98/270 (36%), Positives = 142/270 (52%), Gaps = 45/270 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 483 DGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQNEEA 542

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR GE +I A QD I+G YLLT  N  FN 
Sbjct: 543 RAE--------------ARVLMRVQEQMLSPRFGENIIGAIQDHISGMYLLTHDNPRFNE 588

Query: 461 AQTMR-IASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q +  + +T I +  +  G+                    WTG  +FS +L      P 
Sbjct: 589 TQALDLLRATRIDELPEPSGVDD-------------EGEPFWTGHDVFSELL------PD 629

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           + +L+  G   T  +E       V++ + +LL G++ +  +G  G   +   + + +G  
Sbjct: 630 DLDLEFTG---TVGDE-------VVVEDGQLLKGTIAEDEVGEFG-GEIVDTITKVYGNT 678

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVT 609
            A   +  +S +    +M+ GFSIGI D T
Sbjct: 679 RARIFVNEVSTLAMRAIMHFGFSIGIDDET 708



 Score =  112 bits (280), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 86/303 (28%), Positives = 136/303 (44%), Gaps = 43/303 (14%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G I   + + +  ++ S  +I++ + Y  D    PI  GL+D R+G       C TCG++
Sbjct: 10  GAINFGLMEPEEYREMSATKIITADTY--DDDGFPIDMGLMDPRLGVIDPGLECKTCGKH 67

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
              C GHFG+I+L  PV H+G+ + +  +L+  C+   C+R+LL E++   F  +L    
Sbjct: 68  SGSCNGHFGHIELAAPVIHVGFTKLIRRLLRGTCRE--CSRLLLTEDERDEFHDQLDESR 125

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVV---------------------KKCGLL 239
                   + K  +   +K   CP CGEI   +                     +  G +
Sbjct: 126 KLSRDLNDVTKAAIRQARKKDRCPFCGEIQYDIDHEKPTTYYEVQQVLTSEYSQRIAGAM 185

Query: 240 KISHEKYKNRTKKKDAIVEDL---LAEYNEAV--KFNPE------IEAHKKFGLIQT--- 285
           +   E+   RT   D + E     L   NE +   F P       IE      L +    
Sbjct: 186 QGDEEEGIERT-TPDELAEQTEIELTRVNEILSGSFRPRESQRKAIEKALDIDLTEEDTN 244

Query: 286 -LNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDN 342
            L P ++   FEAIP ED+ +L +N E S+P  +ILT L VPP   RPS+  D   +S++
Sbjct: 245 KLMPSDIRDWFEAIPDEDMEVLGINPERSRPEWMILTVLPVPPVTARPSITLDNGQRSED 304

Query: 343 DVV 345
           D+ 
Sbjct: 305 DLT 307



 Score = 92.8 bits (229), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 39/58 (67%), Positives = 49/58 (84%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
             GFV+NS+ SGLTP EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 834 AHGFVENSYTSGLTPREFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELETQYD 891



 Score = 45.8 bits (107), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 29/46 (63%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 65
           +VLM  +  +++PR GE +I A QD I+G YLLT  N  FN  Q +
Sbjct: 547 RVLMRVQEQMLSPRFGENIIGAIQDHISGMYLLTHDNPRFNETQAL 592


>gi|448354757|ref|ZP_21543512.1| DNA-directed RNA polymerase subunit A' [Natrialba hulunbeirensis
           JCM 10989]
 gi|445637088|gb|ELY90244.1| DNA-directed RNA polymerase subunit A' [Natrialba hulunbeirensis
           JCM 10989]
          Length = 976

 Score =  157 bits (396), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 100/275 (36%), Positives = 144/275 (52%), Gaps = 46/275 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 483 DGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQNEEA 542

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR GE +I A QD I+G YLLT  N  FN 
Sbjct: 543 RAE--------------ARVLMRVQEQILSPRFGENIIGAIQDHISGMYLLTHDNPRFNE 588

Query: 461 AQTMR-IASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q +  + +T I +  +  GI                    WTG  +FS +L      P 
Sbjct: 589 TQALDLLRATRIDELPEPSGIDD-------------EDQPFWTGYDVFSELL------PD 629

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           + NL+  G   T  E        V++ + +L+ G++ +  +G  G   +   + + +G  
Sbjct: 630 DLNLEFTG---TIGEP-------VVIEDGQLIEGTIAEDEVGEFG-GEIVDTITKIYGNT 678

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVT-PGQG 613
            +   +  +S +    +M+ GFSIGI D T PG+ 
Sbjct: 679 RSRIFINEVSTLAMRAIMHFGFSIGIDDETIPGEA 713



 Score =  108 bits (271), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 83/302 (27%), Positives = 136/302 (45%), Gaps = 41/302 (13%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G I   + + +  ++ S  +I++ + Y  D    PI  GL+D R+G       C TCG++
Sbjct: 10  GSINFGLMEPEEYREMSATKIITADTY--DDDGFPIDMGLMDPRLGVIDPGLECKTCGKH 67

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
              C GHFG+I+L  PV H+G+ + +  +L+  C+   C+R+LL E++   F+ ++    
Sbjct: 68  SGSCNGHFGHIELAAPVIHVGFTKLIRRLLRGTCRE--CSRLLLVEDEREEFQDQIEESR 125

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVV---------------------KKCGLL 239
                   + K  +   +K   CP CGE+   +                     +  G +
Sbjct: 126 KLGRDLNDVTKAAIRQARKKDRCPFCGEVQYDIDHEKPTTYYEVQQVLTSEYSQRIAGAM 185

Query: 240 KISHEKYKNRTKKKD--AIVEDLLAEYNEAV--KFNPE------IEAHKKFGLIQT---- 285
           +   E    RT   +  A  E  L   NE +   F P       IE      L +     
Sbjct: 186 QGDEEAGIERTSPDELAAETEIDLTRINEILSGSFRPRESQREAIEKALDIDLTEEDTNK 245

Query: 286 LNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDND 343
           L P ++   FE IP EDI +L ++A+ S+P  +ILT L VPP   RPS+  D   +S++D
Sbjct: 246 LMPSDIRDWFENIPDEDIEVLGIDADRSRPEWMILTVLPVPPVTARPSITLDNGQRSEDD 305

Query: 344 VV 345
           + 
Sbjct: 306 LT 307



 Score = 92.8 bits (229), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 39/58 (67%), Positives = 49/58 (84%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
             GFV+NS+ SGLTP EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 834 AHGFVENSYTSGLTPREFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELEAQYD 891



 Score = 45.4 bits (106), Expect = 0.22,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 29/46 (63%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 65
           +VLM  +  +++PR GE +I A QD I+G YLLT  N  FN  Q +
Sbjct: 547 RVLMRVQEQILSPRFGENIIGAIQDHISGMYLLTHDNPRFNETQAL 592


>gi|397135920|gb|AFO11455.1| RNA polymerase I, partial [Nakazawaea holstii]
          Length = 870

 Score =  157 bits (396), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 88/267 (32%), Positives = 145/267 (54%), Gaps = 36/267 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+D VLFNRQPSLHK+S+MAHR KV+P+ TFR N    +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 249 DDDPVLFNRQPSLHKMSMMAHRVKVMPYSTFRMNLSATSPYNADFDGDEMNLHVPQSEET 308

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE                 + A    +V+P++ + ++   QD + G   +T ++ F   
Sbjct: 309 RAE--------------LSQICAVPLQIVSPQSNKPIMGIVQDTLCGVRKMTLRDVFIEY 354

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            + M           +I   I  +  R   P + V+   +WTGKQ+ S+++      P  
Sbjct: 355 DEVM-----------NILYWIPDWDGRIPEPTI-VKPKPLWTGKQMLSMVI------PKG 396

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            N++ K   +T        D+ +++ + E++ G ++K T+G+ G   + + + R+ G   
Sbjct: 397 INIERKDEKFTY---LSKDDTGMLIVDGEIMLGVVNKKTVGATG-GGLIHAVFREKGPQA 452

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGD 607
             T    + ++ +++L++ GFSIGIGD
Sbjct: 453 CATLFGNIQKVVNYWLLHNGFSIGIGD 479



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 53/63 (84%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTP EFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+ V
Sbjct: 602 DYSPESKGFVENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDIMV 661

Query: 666 QYD 668
            YD
Sbjct: 662 HYD 664


>gi|448444629|ref|ZP_21589919.1| DNA-directed RNA polymerase subunit A' [Halorubrum saccharovorum
           DSM 1137]
 gi|445686042|gb|ELZ38383.1| DNA-directed RNA polymerase subunit A' [Halorubrum saccharovorum
           DSM 1137]
          Length = 968

 Score =  157 bits (396), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 96/268 (35%), Positives = 144/268 (53%), Gaps = 45/268 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 476 DGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQNEEA 535

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR G  +I A QD I+G YLLT  N  F  
Sbjct: 536 RAE--------------ARVLMRVQEQILSPRFGGNIIGAIQDHISGTYLLTHSNPEFTE 581

Query: 461 AQTMR-IASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q +  + +T + +  +  G+      R +           WTG+ +FS +L P+ D  +
Sbjct: 582 TQALDLLRATRVDELPEADGVDD--EGREY-----------WTGRTLFSELL-PD-DLSL 626

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           +    T  R              V++ N +L+ G++D+  +G+ G   V   L +++GE 
Sbjct: 627 DFTSSTGDR--------------VLIENGQLVEGTIDEDAVGAFG-GEVVDTLTKEYGET 671

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            +   +  ++ +    +M+ GFSIGI D
Sbjct: 672 RSRVFINEIASLAMRAIMHFGFSIGIDD 699



 Score =  109 bits (272), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 80/294 (27%), Positives = 125/294 (42%), Gaps = 57/294 (19%)

Query: 97  SHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLP 156
           S  ++++ + Y  D    PI  GL+D R+G       C TCG +   C GHFG+I+L  P
Sbjct: 19  SATKVITADTY--DDDGYPIDMGLMDPRLGVIDPGLECRTCGSHSGSCNGHFGHIELAAP 76

Query: 157 VFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILET 216
           V H+G+ + +  +L+S C+   C R+ L E +   FR +             + K  +  
Sbjct: 77  VIHVGFTKLIRRLLRSTCRE--CGRLALDEAQRDEFRDRYERAQELGDDEHDVLKAAVRQ 134

Query: 217 TKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDL---------------- 260
            +K S CP CGE    +K        HEK     + +D +  D                 
Sbjct: 135 ARKASTCPFCGEPQADIK--------HEKPTTYYEVQDVLSGDYSERIAAAMQPDEEEDD 186

Query: 261 -------LAEYNE----------AVKFNPEIEAHKKFGL----------IQTLNPLEVLQ 293
                  LAE  +          A +F P  E  +              +  L P ++  
Sbjct: 187 PGTSPQELAEKTDIALDRINEIMAGEFRPRKEDRRAIEKALDIDLTEEDMNKLMPSDIRD 246

Query: 294 LFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDNDVV 345
            FE IP ED+ +L +++E S+P  +ILT L VPP   RPS+  D   +S++D+ 
Sbjct: 247 WFEDIPDEDLEVLGIDSEHSRPEWMILTVLPVPPVTTRPSITLDNGQRSEDDLT 300



 Score = 91.3 bits (225), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 38/57 (66%), Positives = 48/57 (84%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFV+NS+  GLTP EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 828 HGFVENSYRGGLTPQEFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELEAQYD 884


>gi|448366553|ref|ZP_21554676.1| DNA-directed RNA polymerase subunit A' [Natrialba aegyptia DSM
           13077]
 gi|445654008|gb|ELZ06864.1| DNA-directed RNA polymerase subunit A' [Natrialba aegyptia DSM
           13077]
          Length = 975

 Score =  157 bits (396), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 99/270 (36%), Positives = 144/270 (53%), Gaps = 45/270 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 483 DGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQNEEA 542

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR GE +I A QD I+G YLLT  N  FN 
Sbjct: 543 RAE--------------ARVLMRVQEQILSPRFGENIIGAIQDHISGMYLLTHDNPRFNE 588

Query: 461 AQTMR-IASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q +  + +T I +  +  GI       +  P         WTG  +FS +L      P 
Sbjct: 589 TQALDLLRATRIDELPEPSGIDD-----AGEP--------FWTGYDVFSELL------PD 629

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           + NL+  G   T  +E       V++ + +L+ G++ +  +G  G   +   + + +G  
Sbjct: 630 DLNLEFTG---TVGDE-------VVIEDGQLIEGTVAEDEVGEFG-GEIVDTITKVYGNT 678

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVT 609
            +   +  +S +    +M+ GFSIGI D T
Sbjct: 679 RSRIFINEVSTLAMRAIMHFGFSIGIDDET 708



 Score =  116 bits (291), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 87/303 (28%), Positives = 140/303 (46%), Gaps = 43/303 (14%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G I   + + +  ++ S  +I++ + Y  D    PI  GL+D R+G       C TCG++
Sbjct: 10  GSINFGLMEPEEYREMSATKIITADTY--DDDGFPIDMGLMDPRLGVIDPGLECKTCGKH 67

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
              C GHFG+I+L  PV H+G+ + +  +L+  C+   C+R+LL E++   FR ++    
Sbjct: 68  SGSCNGHFGHIELAAPVIHVGFTKLIRRLLRGTCRE--CSRLLLTEDERGEFRDQIDESR 125

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVV---------------------KKCGLL 239
                   + K  +   +K   CP CGEI   +                     +  G +
Sbjct: 126 KLGRDLNDVTKAAIRQARKKDRCPFCGEIQYDIDHEKPTTYYEVQQVLTSEYSQRIAGAM 185

Query: 240 KISHEKYKNRTKKKDAIVEDL---LAEYNEAV--KFNPE------IEAHKKFGLIQT--- 285
           +   E+   RT   D + E+    L+  NE +   F P       IE      L +    
Sbjct: 186 QGDEEEGIERT-SPDELAEETDIELSRINEILSGSFRPRESQRKAIEKALDIDLTEEDTN 244

Query: 286 -LNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDN 342
            L P ++   FEAIP EDI +L ++AE S+P  +ILT L VPP   RPS+  D   +S++
Sbjct: 245 KLMPSDIRDWFEAIPDEDIEVLGIDAERSRPEWMILTVLPVPPVTARPSITLDNGQRSED 304

Query: 343 DVV 345
           D+ 
Sbjct: 305 DLT 307



 Score = 92.8 bits (229), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 39/58 (67%), Positives = 49/58 (84%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
             GFV+NS+ SGLTP EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 834 AHGFVENSYTSGLTPREFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELEAQYD 891



 Score = 45.4 bits (106), Expect = 0.22,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 29/46 (63%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 65
           +VLM  +  +++PR GE +I A QD I+G YLLT  N  FN  Q +
Sbjct: 547 RVLMRVQEQILSPRFGENIIGAIQDHISGMYLLTHDNPRFNETQAL 592


>gi|123979324|gb|ABM81487.1| RNA polymerase II largest subunit [Cladonia stipitata]
          Length = 984

 Score =  157 bits (396), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 95/280 (33%), Positives = 148/280 (52%), Gaps = 46/280 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D ++FNRQPSLHK S+M HR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 354 DGDFIIFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 413

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE               ++ M   + + + RNG L+    QD + G Y + +++ F  +
Sbjct: 414 RAEV-------------NQLCMVPLNIVSSQRNGPLM-GIVQDTLCGTYKMCRRDVFMTK 459

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              M I    +    D  G+I +       P + ++   +WTGKQI SL++      P  
Sbjct: 460 EAVMNI----LLWVPDWDGVIPQ-------PAI-IKPRPMWTGKQILSLVI------PAG 501

Query: 521 ANL----KTKG-RAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRD 575
            N     +T+G  A T   +F H          EL+ G +DK  +G+  +  V +++  +
Sbjct: 502 LNYMKLDETEGFTALTDEGQFIH--------GGELMFGLLDKKAVGAATQG-VIHLIFNE 552

Query: 576 FGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFV 615
            G D A++       + +++L++ GFSIGIGD  P +G +
Sbjct: 553 LGSDAAMSFFNGAQTVVNYWLLHNGFSIGIGDTIPDRGTI 592



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+  
Sbjct: 707 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDVMA 766

Query: 666 QYD 668
           +YD
Sbjct: 767 KYD 769


>gi|33326213|gb|AAQ08516.1| RNA polymerase II largest subunit [Magnolia x soulangeana]
          Length = 1010

 Score =  157 bits (396), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 97/271 (35%), Positives = 147/271 (54%), Gaps = 35/271 (12%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D D VLFNRQPSLHK+SIM HR K++P+ TFR N  V +PYNADFDGDEMN+H+PQ+ E
Sbjct: 369 NDGDFVLFNRQPSLHKMSIMGHRIKIMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSFE 428

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE L             +++M  K  +V+P++   ++   QD + G   +T+++ F  
Sbjct: 429 TRAEVL-------------ELMMVPKC-IVSPQSNRPVMGIVQDTLLGCRKITKRDTFIE 474

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           +   M I    +    D  G I         P + ++   +WTGKQ+F+LI+      P 
Sbjct: 475 KDVFMNI----LMWWEDFDGKIP-------APTI-LKPRPLWTGKQVFNLII------PK 516

Query: 520 NANL-KTKGRAYTANEEF-CHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFG 577
             NL +T      A   F    D+ V +   ELLAG++ K TLG+    ++ +++  + G
Sbjct: 517 QINLIRTSAWHSEAETGFITPGDTQVRIERGELLAGTLCKKTLGT-STGSLIHVIWEEVG 575

Query: 578 EDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
            D A   +     + +++L+  GFSIGIGD 
Sbjct: 576 PDAARKFLGHTQWLVNYWLLQNGFSIGIGDT 606



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 42/57 (73%), Positives = 52/57 (91%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKT+ETGY+QRRLVK++ED+ V+YD
Sbjct: 734 RGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDIMVKYD 790



 Score = 52.8 bits (125), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 59/200 (29%), Positives = 100/200 (50%), Gaps = 24/200 (12%)

Query: 150 YIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKS 208
           +++L  P+FHIG+ + V++I++ +C N  C+++L+ EE     ++ K+RNP       K 
Sbjct: 1   HLELAKPMFHIGFLKTVLSIMRCVCFN--CSKILVDEEDHKFKQSQKIRNP-------KH 51

Query: 209 LKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNR-----TKKKDAIVE--DLL 261
             +K+L+  K  + C    +I   V+   L     E  K R      ++    VE   ++
Sbjct: 52  RLRKVLDACKNKTKCDGGDDIE--VRDQDL----EEPVKKRRGGCGAQQPKLTVEGMKMI 105

Query: 262 AEYNEAVKFNPEIEA-HKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
           AEY    K N + E   +     Q L+   VL + + I  ED  LL +N + ++P  +IL
Sbjct: 106 AEYKATRKKNDDQEQLPEPVERKQQLSAERVLSVLKRISDEDCLLLGLNPKYARPDWMIL 165

Query: 321 TRLLVPPNCIRPSVISDLKS 340
             L +PP  +RPSV+ D  S
Sbjct: 166 QVLPIPPPPVRPSVMMDTSS 185


>gi|23345055|gb|AAN17722.1| RNA polymerase II largest subunit [Trypanosoma cruzi]
          Length = 1731

 Score =  157 bits (396), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 92/267 (34%), Positives = 143/267 (53%), Gaps = 39/267 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + DVVLFNRQP+LH++S+M HR +VL + TFR N    TPYNADFDGDEMN+H+PQ+   
Sbjct: 427 NGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNLSCTTPYNADFDGDEMNLHVPQSLLT 486

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE +             +++M  K N V+P      +   QD + G Y LT K+ F ++
Sbjct: 487 KAELI-------------EMMMVPK-NFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFLDK 532

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                +A  L     D+        W+   P V ++   +WTGKQ+FSLIL P  + P  
Sbjct: 533 YFVQSVALWL-----DL--------WQLPVPAV-LKPRPLWTGKQVFSLIL-PEVNHPAT 577

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
              +           F H DS +++R  +LL G + K  +G+    ++ +++  + G D 
Sbjct: 578 PQERPP---------FPHNDSSIMIRRGQLLCGPITKGIVGA-APGSLIHVIFNERGSDE 627

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGD 607
               +  + R+T+F+L+N GFS+G+ D
Sbjct: 628 VARFINGVQRITTFFLINFGFSVGVQD 654



 Score = 88.2 bits (217), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 73/281 (25%), Positives = 132/281 (46%), Gaps = 35/281 (12%)

Query: 1150 YIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKP 1209
            +I  + +  D F+   L+M  ++   L VD     Y IE     +G    +    + ++P
Sbjct: 1198 WIARLELDADMFVDKALNMKDVKQAILRVDDG---YVIE-----TGMANDTKERTIRMRP 1249

Query: 1210 K--DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEE----------DVEGVTKYKLL 1257
            K  D   S     + + +LL  V ++G+ G+ +A++ +            + G   + + 
Sbjct: 1250 KKNDGVDSIPRLKHAIPELLARVHLRGIPGVRKALLKDRTTFTVDPATGKMTGEKTWLID 1309

Query: 1258 VEGDNLR-------DVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHG 1310
             +G  LR       D      +   + SSN   EV   LGIEAAR  ++ E++     +G
Sbjct: 1310 TDGTALRRAFIGIVDEKGNNIINATRTSSNKVPEVCSLLGIEAARYKMLHELREAYLAYG 1369

Query: 1311 MSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKES-VLNLASFENTSDHLFDAAFYGQTD 1369
            ++I++RH  ++ D +  +G ++ ++R G+ + + S  L   SFE T   L  AA +G+ D
Sbjct: 1370 LNINYRHYTILVDTICQRGYLMAVSRVGINRSEMSGPLMRCSFEETVKVLMAAAAFGERD 1429

Query: 1370 CISGVSECIIMGLPMNVGTGLIKLL-------QAVPRSEPV 1403
             + GVS  +++G    +GTGL  L+       QAVP+ + V
Sbjct: 1430 PVRGVSANLVLGNQARIGTGLFDLVLNMAALQQAVPQEDAV 1470



 Score = 83.2 bits (204), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 34/57 (59%), Positives = 44/57 (77%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +G     +  GL P EFFFHTM GREGL+DTAVKT++TGY+QR+L+K+LED+   YD
Sbjct: 783 RGMANRGYVEGLKPHEFFFHTMAGREGLIDTAVKTSDTGYLQRKLIKALEDVHAAYD 839



 Score = 80.5 bits (197), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 64/239 (26%), Positives = 106/239 (44%), Gaps = 42/239 (17%)

Query: 115 PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSIC 174
           P+  G+ D RMGT   E  C TC +   +C GHFGYIDL  PVF+IG F  V+ +L+ +C
Sbjct: 49  PVRGGINDLRMGTTDFEFACETCHRKHPECPGHFGYIDLAEPVFNIGVFDIVLQVLKCVC 108

Query: 175 KNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVK 234
           K  +C  +L+                              +  KK+        +  VVK
Sbjct: 109 K--SCGALLMDTNDP-------------------------QVHKKLQHLTGVNRLRQVVK 141

Query: 235 KCGL-LKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVL- 292
            CG+  ++S +     T  ++A+V           +    +  +    +  TL   +++ 
Sbjct: 142 MCGMKCRMSTDA----TTPEEAVVARGCGATQP--RIGRYLGIYPTLIIKATLEEQDMVW 195

Query: 293 ------QLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSV-ISDLKSDNDV 344
                 Q+ + +  ED  ++  +A    P DL+LT L VPP  +RP++    LKSD+++
Sbjct: 196 HADTARQVLDRVSDEDARVMGFDALRCHPRDLVLTVLPVPPPQVRPAISFGSLKSDDEL 254



 Score = 54.3 bits (129), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 66/294 (22%), Positives = 123/294 (41%), Gaps = 62/294 (21%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDY-ARIVKGRLERTTLGEVCEYIEEVFVPD 822
            GVPR+ E++N SR+     +   L    D    A+  +  +E  TL  V + I+ ++ PD
Sbjct: 1101 GVPRLLELLNVSRHQKHASMNVSLYPPWDKKRTAQQAQHLIEYCTLESVTKRIQFIYDPD 1160

Query: 823  DSFILIKLD----------MD----RIRL----------LHLEVDID----------SIR 848
                +++ D          MD    R RL            LE+D D           ++
Sbjct: 1161 PRETVVEADRAILELEWSVMDESDERARLQEVENGSPWIARLELDADMFVDKALNMKDVK 1220

Query: 849  YCIERTRGISGHLTVSGHS------FLILKPK--DSSKSFNSKMYQMKQLLPSVVIKGVQ 900
              I R     G++  +G +       + ++PK  D   S     + + +LL  V ++G+ 
Sbjct: 1221 QAILRVD--DGYVIETGMANDTKERTIRMRPKKNDGVDSIPRLKHAIPELLARVHLRGIP 1278

Query: 901  GINRAVIHEE----------DVEGVTKYKLLVEGDNLR-------DVMATYGVKGVKCSS 943
            G+ +A++ +            + G   + +  +G  LR       D      +   + SS
Sbjct: 1279 GVRKALLKDRTTFTVDPATGKMTGEKTWLIDTDGTALRRAFIGIVDEKGNNIINATRTSS 1338

Query: 944  NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            N   EV   LGIEAAR  ++ E++     +G++I++RH  ++ D +  +G ++ 
Sbjct: 1339 NKVPEVCSLLGIEAARYKMLHELREAYLAYGLNINYRHYTILVDTICQRGYLMA 1392



 Score = 53.5 bits (127), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 23/39 (58%), Positives = 29/39 (74%)

Query: 1107 REKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            R KY+++ + P   +GA+AAQS GEP TQMTL TFH AG
Sbjct: 1054 RTKYLQSLVSPGENIGAIAAQSCGEPATQMTLNTFHNAG 1092


>gi|397135952|gb|AFO11471.1| RNA polymerase I, partial [Yarrowia lipolytica]
          Length = 870

 Score =  157 bits (396), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 92/271 (33%), Positives = 151/271 (55%), Gaps = 44/271 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND VLFNRQPSLHK+S+MAHR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 251 DNDPVLFNRQPSLHKMSMMAHRVRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 310

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L +L ++  +          +V+P++ + ++   QD + G   +T +++F + 
Sbjct: 311 RAE----LSQLCMVPLQ----------IVSPQSNKPVMGIVQDTLCGVRKMTIRDSFIDY 356

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVV----FVRTAVIWTGKQIFSLILKPNRD 516
              M I                 F   +W+ VV     ++   +WTGKQ+ S+ +     
Sbjct: 357 DMVMNIL----------------FWIPNWDGVVPTPAILKPKPLWTGKQMVSMCI----- 395

Query: 517 CPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
            P   +L+   R    N   C +D+ + + + +++ G +DK T+G+ G   + + ++R+ 
Sbjct: 396 -PKGIHLQ---RFDDQNPITCPKDNGMYIIDGQIMWGVVDKKTIGATG-GGLVHTIMREK 450

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           G  V       + ++ +F+L++ GFSIGIGD
Sbjct: 451 GSAVCCNFFGTIQKVVNFWLLHYGFSIGIGD 481



 Score =  102 bits (253), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GF++NS+  GLTP EFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+ V
Sbjct: 604 DYSPESKGFIENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDVMV 663

Query: 666 QYD 668
           QYD
Sbjct: 664 QYD 666


>gi|385804832|ref|YP_005841232.1| DNA-directed RNA polymerase subunit A' (subunit A) [Haloquadratum
           walsbyi C23]
 gi|339730324|emb|CCC41653.1| DNA-directed RNA polymerase subunit A' (subunit A) [Haloquadratum
           walsbyi C23]
          Length = 978

 Score =  157 bits (396), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 100/268 (37%), Positives = 143/268 (53%), Gaps = 45/268 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  QTEE+
Sbjct: 484 DGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQTEES 543

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  L++PR GE +I A QD I+G YLLT  N  F+ 
Sbjct: 544 RAE--------------ARVLMRVQEQLLSPRFGENIIGAIQDHISGTYLLTNGNPQFSE 589

Query: 461 AQTMR-IASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q +  + +T I +     G  +  S               W+G+Q+FS +L      P 
Sbjct: 590 TQALDLLRATSIDNLPPAAGQTEDGS-------------PYWSGRQLFSELL------PD 630

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           N NL+    A             V + + EL+AG++D++ +G+ G   V   L +   + 
Sbjct: 631 NLNLEFTSAA----------GDTVEIVDGELIAGTIDENAVGAFG-GEVVDTLAKVHSKT 679

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            A   +  ++ +    +M+ GFSIGI D
Sbjct: 680 RARVFVNEVASLAMRAIMHFGFSIGIDD 707



 Score =  103 bits (256), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 82/312 (26%), Positives = 136/312 (43%), Gaps = 60/312 (19%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G I+  +   +  +  S  ++++ + Y  D    PI  GL+D R+G       C TCG +
Sbjct: 10  GAIQFGLMDPETYRDMSATKVITADTY--DDDGYPIDMGLMDPRLGVIDPGLECKTCGSH 67

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKL-RNP 199
              C GHFG+I+L  PV H+G+ + +  +L+S C+  +C  + L E +   FR  L RN 
Sbjct: 68  SGSCNGHFGHIELAAPVIHVGFTKLIRRLLRSTCR--SCGHLALTENEREEFREGLQRNE 125

Query: 200 ALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVED 259
            L       LK  + +  +K +VCP CGE    +K        HEK     + +D +  D
Sbjct: 126 ELGEDWTDVLKSAVRQ-ARKTNVCPSCGETQHDIK--------HEKPTTYYEVQDVLAGD 176

Query: 260 LLAEYNEAVK----------------------------------FNP------EIEAHKK 279
              +   A++                                  F P      E+E+   
Sbjct: 177 YPEKIASAMQPDPDDDSDSGLSPNSLADATGINVERINNILSGEFRPVGEDRKELESALD 236

Query: 280 FGLIQT-LNPL---EVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVI 335
             L +  +N L   ++   FE+IP EDI  L ++   ++P  +++T L VPP   RPS+ 
Sbjct: 237 IDLTEEDMNKLMASDIRDWFESIPDEDIRTLGIDPSRARPEWMVMTVLPVPPVTARPSIT 296

Query: 336 SD--LKSDNDVV 345
            D   +S++D+ 
Sbjct: 297 LDNGQRSEDDLT 308



 Score = 90.9 bits (224), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 38/57 (66%), Positives = 48/57 (84%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFV+NS+  GLTP EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 836 HGFVENSYRGGLTPREFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELEAQYD 892



 Score = 44.3 bits (103), Expect = 0.53,   Method: Compositional matrix adjust.
 Identities = 22/51 (43%), Positives = 31/51 (60%)

Query: 15  TRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 65
           +R   +VLM  +  L++PR GE +I A QD I+G YLLT  N  F+  Q +
Sbjct: 543 SRAEARVLMRVQEQLLSPRFGENIIGAIQDHISGTYLLTNGNPQFSETQAL 593


>gi|188532143|gb|ACD63083.1| RNA polymerase II largest subunit [Ceratophyllum demersum]
          Length = 1010

 Score =  157 bits (396), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 97/271 (35%), Positives = 147/271 (54%), Gaps = 35/271 (12%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D D VLFNRQPSLHK+SIM HR K++P+ TFR N  V +PYNADFDGDEMN+H+PQ+ E
Sbjct: 369 NDGDFVLFNRQPSLHKMSIMGHRIKIMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSFE 428

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE L             +++M  K  +V+P++   ++   QD + G   +T+++ F  
Sbjct: 429 TRAEVL-------------ELMMVPKC-IVSPQSNRPVMGIVQDTLLGCRKITKRDTFIE 474

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           +   M I    +    D  G I         P + ++   +WTGKQ+F+LI+      P 
Sbjct: 475 KDVFMNI----LMWWEDFDGKIP-------APTI-LKPRPLWTGKQVFNLII------PK 516

Query: 520 NANL-KTKGRAYTANEEF-CHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFG 577
             NL +T      A   F    D+ V +   ELLAG++ K TLG+    ++ +++  + G
Sbjct: 517 QINLIRTSAWHSEAETGFITPGDTQVRIERGELLAGTLCKKTLGT-STGSLIHVIWEEVG 575

Query: 578 EDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
            D A   +     + +++L+  GFSIGIGD 
Sbjct: 576 PDAARKFLGHTQWLVNYWLLQNGFSIGIGDT 606



 Score =  100 bits (249), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 42/57 (73%), Positives = 52/57 (91%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKT+ETGY+QRRLVK++ED+ V+YD
Sbjct: 734 RGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDIMVKYD 790



 Score = 45.4 bits (106), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 53/196 (27%), Positives = 96/196 (48%), Gaps = 16/196 (8%)

Query: 150 YIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKS 208
           +++L  P+FHIG+ + V N+++ IC N  C+++L  EE     +A K++NP       K 
Sbjct: 1   HLELAKPMFHIGFLKTVCNLMRCICFN--CSKILADEEDHKFKQAVKIKNP-------KH 51

Query: 209 LKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVED---LLAEYN 265
             +K+++  K    C    E++  V+     +   +K      ++  I  +   ++AE+ 
Sbjct: 52  RLRKVMDACKSKQKCEGGDEMD--VQGQDEDEPXKKKRGGCGSQQPKIAVEGMKIIAEFK 109

Query: 266 EAVKFNPEIEA-HKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLL 324
              K + E +   +     Q L+   VL + + I  ED  LL  N + ++P  +IL  L 
Sbjct: 110 APKKRSDEQDQLPEPVERKQQLSAERVLSILKRISDEDCVLLGFNPKYARPDWMILQVLP 169

Query: 325 VPPNCIRPSVISDLKS 340
           +PP  +RPSV+ D  S
Sbjct: 170 IPPPPVRPSVMMDTSS 185


>gi|22002086|gb|AAK97604.2|AF372503_1 RNA polymerase II largest subunit [Trypanosoma cruzi]
          Length = 1731

 Score =  157 bits (396), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 92/267 (34%), Positives = 143/267 (53%), Gaps = 39/267 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + DVVLFNRQP+LH++S+M HR +VL + TFR N    TPYNADFDGDEMN+H+PQ+   
Sbjct: 427 NGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNLSCTTPYNADFDGDEMNLHVPQSLLT 486

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE +             +++M  K N V+P      +   QD + G Y LT K+ F ++
Sbjct: 487 KAELI-------------EMMMVPK-NFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFLDK 532

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                +A  L     D+        W+   P V ++   +WTGKQ+FSLIL P  + P  
Sbjct: 533 YFVQSVALWL-----DL--------WQLPVPAV-LKPRPLWTGKQVFSLIL-PEVNHPAT 577

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
              +           F H DS +++R  +LL G + K  +G+    ++ +++  + G D 
Sbjct: 578 PQERPP---------FPHNDSSIMIRRGQLLCGPITKGIVGA-APGSLIHVIFNERGSDE 627

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGD 607
               +  + R+T+F+L+N GFS+G+ D
Sbjct: 628 VARFINGVQRITTFFLINFGFSVGVQD 654



 Score = 88.2 bits (217), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 73/281 (25%), Positives = 132/281 (46%), Gaps = 35/281 (12%)

Query: 1150 YIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKP 1209
            +I  + +  D F+   L+M  ++   L VD     Y IE     +G    +    + ++P
Sbjct: 1198 WIARLELDADMFVDKALNMKDVKQAILRVDDG---YVIE-----TGMANDTKERTIRMRP 1249

Query: 1210 K--DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEE----------DVEGVTKYKLL 1257
            K  D   S     + + +LL  V ++G+ G+ +A++ +            + G   + + 
Sbjct: 1250 KKNDGVDSIPRLKHAIPELLARVHLRGIPGVRKALLKDRTTFTVDPATGKMTGEKTWLID 1309

Query: 1258 VEGDNLR-------DVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHG 1310
             +G  LR       D      +   + SSN   EV   LGIEAAR  ++ E++     +G
Sbjct: 1310 TDGTALRRAFIGIVDEKGNNIINATRTSSNKVPEVCSLLGIEAARYKMLHELREAYLAYG 1369

Query: 1311 MSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKES-VLNLASFENTSDHLFDAAFYGQTD 1369
            ++I++RH  ++ D +  +G ++ ++R G+ + + S  L   SFE T   L  AA +G+ D
Sbjct: 1370 LNINYRHYTILVDTICQRGYLMAVSRVGINRSEMSGPLMRCSFEETVKVLMAAAAFGERD 1429

Query: 1370 CISGVSECIIMGLPMNVGTGLIKLL-------QAVPRSEPV 1403
             + GVS  +++G    +GTGL  L+       QAVP+ + V
Sbjct: 1430 PVRGVSANLVLGNQARIGTGLFDLVLNMAALQQAVPQEDAV 1470



 Score = 83.2 bits (204), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 34/57 (59%), Positives = 44/57 (77%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +G     +  GL P EFFFHTM GREGL+DTAVKT++TGY+QR+L+K+LED+   YD
Sbjct: 783 RGMANRGYVEGLKPHEFFFHTMAGREGLIDTAVKTSDTGYLQRKLIKALEDVHAAYD 839



 Score = 80.5 bits (197), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 64/239 (26%), Positives = 106/239 (44%), Gaps = 42/239 (17%)

Query: 115 PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSIC 174
           P+  G+ D RMGT   E  C TC +   +C GHFGYIDL  PVF+IG F  V+ +L+ +C
Sbjct: 49  PVRGGINDLRMGTTDFEFACETCHRKHPECPGHFGYIDLAEPVFNIGVFDIVLQVLKCVC 108

Query: 175 KNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVK 234
           K  +C  +L+                              +  KK+        +  VVK
Sbjct: 109 K--SCGALLMDTNDP-------------------------QVHKKLQHLTGVNRLRQVVK 141

Query: 235 KCGL-LKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVL- 292
            CG+  ++S +     T  ++A+V           +    +  +    +  TL   +++ 
Sbjct: 142 MCGMKCRMSTDA----TTPEEAVVARGCGATQP--RIGRYLGIYPTLIIKATLEEQDMVW 195

Query: 293 ------QLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSV-ISDLKSDNDV 344
                 Q+ + +  ED  ++  +A    P DL+LT L VPP  +RP++    LKSD+++
Sbjct: 196 HADTARQVLDRVSDEDARVMGFDALRCHPRDLVLTVLPVPPPQVRPAISFGSLKSDDEL 254



 Score = 53.9 bits (128), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 66/294 (22%), Positives = 123/294 (41%), Gaps = 62/294 (21%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDY-ARIVKGRLERTTLGEVCEYIEEVFVPD 822
            GVPR+ E++N SR+     +   L    D    A+  +  +E  TL  V + I+ ++ PD
Sbjct: 1101 GVPRLLELLNVSRHQKHASMNVSLYPPWDKKRTAQQAQHLIEYCTLESVTKRIQFIYDPD 1160

Query: 823  DSFILIKLD----------MD----RIRL----------LHLEVDID----------SIR 848
                +++ D          MD    R RL            LE+D D           ++
Sbjct: 1161 PRETVVEADRAILELEWSVMDESDERARLQEVENGSPWIARLELDADMFVDKALNMKDVK 1220

Query: 849  YCIERTRGISGHLTVSGHS------FLILKPK--DSSKSFNSKMYQMKQLLPSVVIKGVQ 900
              I R     G++  +G +       + ++PK  D   S     + + +LL  V ++G+ 
Sbjct: 1221 QAILRVD--DGYVIETGMANDTKERTIRMRPKKNDGVDSIPRLKHAIPELLARVHLRGIP 1278

Query: 901  GINRAVIHEE----------DVEGVTKYKLLVEGDNLR-------DVMATYGVKGVKCSS 943
            G+ +A++ +            + G   + +  +G  LR       D      +   + SS
Sbjct: 1279 GVRKALLKDRTTFTVDPATGKMTGEKTWLIDTDGTALRRAFIGIVDEKGNNIINATRTSS 1338

Query: 944  NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            N   EV   LGIEAAR  ++ E++     +G++I++RH  ++ D +  +G ++ 
Sbjct: 1339 NKVPEVCSLLGIEAARYKMLHELREAYLAYGLNINYRHYTILVDTICQRGYLMA 1392



 Score = 53.5 bits (127), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 23/39 (58%), Positives = 29/39 (74%)

Query: 1107 REKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            R KY+++ + P   +GA+AAQS GEP TQMTL TFH AG
Sbjct: 1054 RTKYLQSLVSPGENIGAIAAQSCGEPATQMTLNTFHNAG 1092


>gi|214028074|gb|ACJ63306.1| RNA polymerase III large subunit [Acorus calamus]
          Length = 544

 Score =  157 bits (396), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 83/229 (36%), Positives = 131/229 (57%), Gaps = 37/229 (16%)

Query: 392 VHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLL 451
           +H+PQTEEAR +A+              +LM  ++NL TP+NGE+L+A+TQDF+T  +L+
Sbjct: 1   LHVPQTEEARTDAM--------------ILMGVQNNLCTPKNGEILVASTQDFLTSSFLI 46

Query: 452 TQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPV-----VFVRTAVIWTGKQI 506
           T+K+ F++R              S  C ++  F     +P+       ++   +WTGKQ+
Sbjct: 47  TRKDTFYDR--------------SAFC-LMCSFMGDGMDPIDLPTPALIKPMELWTGKQL 91

Query: 507 FSLILKPNRDCPVNANLKTKGRAY---TANEEFCHRDSYVILRNSELLAGSMDKSTLGSG 563
           FS++L+P     V  NL    ++Y      E  C  D++V  RNS+LL G + K+TLG+G
Sbjct: 92  FSVLLRPYAQMRVFVNLTLMEKSYDKRQGRETMCPNDAFVYFRNSDLLCGQLGKATLGNG 151

Query: 564 GKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
            K  +F +LLRD+    A + M RL+++++ ++ N GFSIGI DV PG 
Sbjct: 152 NKDGLFSVLLRDYNSHAAASCMNRLAKLSARWIGNHGFSIGIDDVQPGH 200



 Score =  100 bits (250), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 47/61 (77%), Positives = 52/61 (85%), Gaps = 1/61 (1%)

Query: 609 TP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQY 667
           TP  +GFV NSF++GLT TEFFFHTM GREGLVDTAV+TAETGYM RRL+KSLEDL   Y
Sbjct: 320 TPSAKGFVANSFYTGLTATEFFFHTMAGREGLVDTAVRTAETGYMSRRLIKSLEDLSTYY 379

Query: 668 D 668
           D
Sbjct: 380 D 380



 Score = 56.6 bits (135), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/42 (50%), Positives = 36/42 (85%)

Query: 21 VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRA 62
          +LM  ++NL TP+NGE+L+A+TQDF+T  +L+T+K+ F++R+
Sbjct: 15 ILMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDRS 56


>gi|113957514|gb|ABI49120.1| RNA polymerase II largest subunit [Anaptychia palmatula]
          Length = 1020

 Score =  157 bits (396), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 96/270 (35%), Positives = 146/270 (54%), Gaps = 39/270 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D ++FNRQPSLHK S+M HR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 378 DGDFIIFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 437

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    +++L ++            N+V+P+    L+   QD + G Y + +++ F N+
Sbjct: 438 RAE----VNQLCMVP----------LNIVSPQRNSPLMGIVQDTLCGIYKICRRDVFLNQ 483

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M I    +    D  GII +       P +   T V WTGKQI SLI+      P  
Sbjct: 484 GQVMNI----LLWVPDWDGIIPQ-------PAILKPTPV-WTGKQIVSLII------PAG 525

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            NL  + + +   +     D   ++   EL+ G + K  +G+   A V +I+  + G + 
Sbjct: 526 LNL-VRDKNHNPLD-----DKGALISGGELMYGLLTKRIVGA-QMAGVIHIVYNEKGPEA 578

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTP 610
           A+        + +++L++ GFSIGIGD  P
Sbjct: 579 AMNFFNGAQAVVNYWLLHNGFSIGIGDTIP 608



 Score = 98.6 bits (244), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 53/63 (84%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPT FFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+  
Sbjct: 728 DYSPESRGFVENSYLRGLTPTGFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDVMA 787

Query: 666 QYD 668
           +YD
Sbjct: 788 KYD 790



 Score = 55.5 bits (132), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 53/200 (26%), Positives = 87/200 (43%), Gaps = 46/200 (23%)

Query: 143 DCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNPAL 201
           +C GHFG+I+L +PVFH+G+   +  +L++IC N  C ++ + E       A ++R+P  
Sbjct: 1   ECPGHFGHIELAVPVFHVGFITKIKKLLETICHN--CGKIKVDESNEHFKDALRIRDPKK 58

Query: 202 SY--LVRKSLKKKILE----------------TTKKVSVCPH--CGEINGVVKKCGLLKI 241
            +  + R S  K I E                   K    PH  CG I   V++ GL  I
Sbjct: 59  RFDAIWRVSKPKGICEMDAPSDESDKDSAKDSPKSKQPRIPHGGCGNIQPEVRRDGLKLI 118

Query: 242 SHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLE 301
              K     +K D        + NE  +  PE          + + P   L +F  +  E
Sbjct: 119 GTWK----PQKGD--------DENEGQQ--PE---------KKPITPAMALAIFLQMSPE 155

Query: 302 DIPLLLMNAELSKPSDLILT 321
           DI  + M+ + ++P  +I+T
Sbjct: 156 DIKTMGMSNDYARPEWMIIT 175



 Score = 42.4 bits (98), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 18/29 (62%), Positives = 21/29 (72%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMT 1137
            ++ RA + P   VG LAAQSIGEP TQMT
Sbjct: 992  RFSRAAVNPGEMVGVLAAQSIGEPATQMT 1020


>gi|33326203|gb|AAQ08511.1| RNA polymerase II largest subunit [Zamia muricata]
          Length = 1013

 Score =  157 bits (396), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 93/271 (34%), Positives = 149/271 (54%), Gaps = 35/271 (12%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D D VLFNRQPSLHK+SIM HR K++P+ TFR N  V +PYNADFDGDEMN+H+PQ+ E
Sbjct: 372 NDGDFVLFNRQPSLHKMSIMGHRIKIMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSFE 431

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE L             +++M  K  +V+P++   ++   QD + G   +T+++ F  
Sbjct: 432 TRAEVL-------------ELMMVPKC-IVSPQSNRPVMGIVQDTLLGCRKITKRDTFIE 477

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           +   M I    +    D  G I        +P + ++   +WTGKQ+F+LI+      P 
Sbjct: 478 KDVFMNI----LMWWEDFDGKIP-------SPTI-LKPRPLWTGKQVFNLII------PR 519

Query: 520 NANLKTKGRAYTANEE--FCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFG 577
             NL      ++ +E       D+ V +   E+L+G++ K TLG+    ++ +++  + G
Sbjct: 520 QINLIRYSAWHSESETGFITPGDTVVRIEKGEVLSGTLCKKTLGTSS-GSLIHVIWEEVG 578

Query: 578 EDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
            D A   +     + +++L+ +GFSIGIGD 
Sbjct: 579 PDAARKFLGHTQWLVNYWLLQQGFSIGIGDT 609



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 42/57 (73%), Positives = 52/57 (91%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKT+ETGY+QRRLVK++ED+ V+YD
Sbjct: 737 RGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDIMVKYD 793



 Score = 65.1 bits (157), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 57/209 (27%), Positives = 104/209 (49%), Gaps = 27/209 (12%)

Query: 150 YIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKS 208
           +++L  P++HIG+ + V++IL+S+C +  C+R+L  EE     +A K++NP       K 
Sbjct: 1   HLELAKPMYHIGFMKTVLSILRSVCFD--CSRILADEEDHRFKQALKIKNP-------KH 51

Query: 209 LKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVED---LLAEY- 264
             +K+L+  K    C    EI     + G      +++     ++  I  D   ++AEY 
Sbjct: 52  RLRKVLDCCKNKVKCEGGDEIEDDQAQDGEETAKKKRHGGCGAQQPKISIDGMKIIAEYK 111

Query: 265 ------NEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDL 318
                 +E  +  PE    K     Q L+  +VL + + I  ED  LL +N + ++P  +
Sbjct: 112 ATRKKADEQEQLMPEPVERK-----QQLSAEKVLDILKRISDEDCQLLGLNPKYARPDWM 166

Query: 319 ILTRLLVPPNCIRPSVI--SDLKSDNDVV 345
           IL  L +P   +RPSV+  +  +S++D+ 
Sbjct: 167 ILQVLPIPSPPVRPSVMMNTTARSEDDLT 195


>gi|448411893|ref|ZP_21576249.1| DNA-directed RNA polymerase subunit A' [Halosimplex carlsbadense
           2-9-1]
 gi|445669827|gb|ELZ22435.1| DNA-directed RNA polymerase subunit A' [Halosimplex carlsbadense
           2-9-1]
          Length = 1004

 Score =  157 bits (396), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 99/277 (35%), Positives = 144/277 (51%), Gaps = 45/277 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 515 DGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTTVCPPYNADFDGDEMNMHALQNEEA 574

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR GE +I A QD ITG YLLT  N  FN 
Sbjct: 575 RAE--------------ARVLMRVQEQMLSPRFGENIIGAIQDHITGTYLLTHTNPQFNE 620

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q + +      D                 P         WTG+ +FS +L      P +
Sbjct: 621 TQALDLLRATRIDELPA-------------PDGEEDGKAYWTGRTLFSELL------PDD 661

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            N++      +A +E       V++ + +LL+G++D+  +G  G   V   + +++ +  
Sbjct: 662 LNVEFTS---SAGDE-------VVIEDGQLLSGTIDEDAVGGFG-GEVVDTIAKEYSKTR 710

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVT-PGQGFVQ 616
           A   +  +S +    +M+ GFSI I D + PG+   Q
Sbjct: 711 ARIFVNEVSTLAMRSIMHFGFSISIDDESIPGEAEGQ 747



 Score =  101 bits (251), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 86/321 (26%), Positives = 138/321 (42%), Gaps = 74/321 (23%)

Query: 94  QQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDL 153
           ++ S  ++++ + Y  D    PI  GL+D R+G       C TCG++   C GHFG+I+L
Sbjct: 24  REMSATKVITADTY--DDDGFPIDMGLMDPRLGVIDPGLECKTCGKHSGSCNGHFGHIEL 81

Query: 154 PLPVFHIGYFRCVINILQSICKNPTCARVL------------LGEEKAAGFRAKL-RNPA 200
             PV H+G+ + +  +L+  C+   C+R+               EE+   +R KL R   
Sbjct: 82  AAPVIHVGFAKLIRRLLRGTCRE--CSRLTPVDGRREADAEQKAEERKREYREKLERTAE 139

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKK------CGLLKISHEKYKNRTKKK- 253
           L+  +   LK  I E  +KV  CP+CG     +K         ++++ H +   R ++  
Sbjct: 140 LNEDMSDVLKSAIRE-CRKVDYCPYCGAKQFDIKHEKPTTYYEIIEVPHGELSKRLERAM 198

Query: 254 ----------DAIVEDLLAEYNEAVK--------FNP---EIEAHKKFGL---------- 282
                       I E+L  +  EA +        + P   +IE  K  G           
Sbjct: 199 DPPEGEAVRPSDIAEELDDDDFEADRIRELLSGTYRPDRNDIERLKNLGRALGRLNDLDE 258

Query: 283 ----------------IQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVP 326
                           +  L P ++   FE IP EDI  L +N E S+P  +ILT L VP
Sbjct: 259 LEEDVSSAAEYLVEEDMDKLMPSDIRDWFEEIPDEDIEALGINPERSRPEWMILTVLPVP 318

Query: 327 PNCIRPSVISD--LKSDNDVV 345
           P   RPS+  D   +S++D+ 
Sbjct: 319 PVTARPSITLDNGQRSEDDLT 339



 Score = 88.6 bits (218), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 37/58 (63%), Positives = 48/58 (82%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
             GFV++S+ SGL P EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 865 AHGFVEHSYRSGLEPREFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELETQYD 922



 Score = 47.4 bits (111), Expect = 0.057,   Method: Compositional matrix adjust.
 Identities = 22/46 (47%), Positives = 29/46 (63%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 65
           +VLM  +  +++PR GE +I A QD ITG YLLT  N  FN  Q +
Sbjct: 579 RVLMRVQEQMLSPRFGENIIGAIQDHITGTYLLTHTNPQFNETQAL 624


>gi|397135942|gb|AFO11466.1| RNA polymerase I, partial [Trichomonascus petasosporus]
          Length = 873

 Score =  157 bits (396), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 94/273 (34%), Positives = 149/273 (54%), Gaps = 46/273 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND VLFNRQPSLHK+S+MAHR KV+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 251 DNDPVLFNRQPSLHKMSMMAHRVKVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 310

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L +L ++  +          +V+P++ + ++   QD + G   +++++ F   
Sbjct: 311 RAE----LSQLCMVPLQ----------IVSPQSNKPVMGIVQDTLCGIRKMSKRDNFLEF 356

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVV----FVRTAVIWTGKQIFSLILKPNRD 516
            Q M I                 F   SW+  V     +R   +WTGKQI S+       
Sbjct: 357 DQVMNIL----------------FWIPSWDGNVPTPTILRPKPLWTGKQIISM------- 393

Query: 517 CPVNANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLG--SGGKANVFYILLR 574
           C  N     +  +   +     +D+ +++   E++ G++DK T+G  SGG   + + ++R
Sbjct: 394 CIPNGIYLQRLDSEGGSAWISPKDTGMLISKGEIMFGAVDKKTVGATSGG---LVHTIMR 450

Query: 575 DFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           + G  VA      + ++ +++L++  FSIGIGD
Sbjct: 451 EKGPQVACNFFGEVQKVVNYWLLHNSFSIGIGD 483



 Score = 99.8 bits (247), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 42/57 (73%), Positives = 50/57 (87%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GF++NS+  GLTP EFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+ V YD
Sbjct: 612 RGFIENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDVMVHYD 668


>gi|120561215|gb|ABM26993.1| RNA polymerase II largest subunit, partial [Furculomyces
           boomerangus]
          Length = 1024

 Score =  157 bits (396), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 90/269 (33%), Positives = 147/269 (54%), Gaps = 35/269 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+DVV+FNRQPSLHK+S+M HR KV+P+ TFR N  V +PYNADFDGDEMN+HLPQ+EE 
Sbjct: 377 DDDVVIFNRQPSLHKMSMMGHRVKVMPYSTFRLNLSVTSPYNADFDGDEMNLHLPQSEET 436

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE               ++ M  K  +V+P++   ++   QD +    + T+++     
Sbjct: 437 RAEV-------------TEICMVPK-QIVSPQSNMPVMGIVQDTLCAINIFTKRDTLLQY 482

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              M +  T+     D  GI+         P + ++   +W+GKQI+S+++      P  
Sbjct: 483 DFVMNLLMTI----PDWDGIVP-------TPCI-LKPQPLWSGKQIYSMVI------PKG 524

Query: 521 ANLKTKGRAYTANE-EFCHR-DSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            N       +  NE  +C   D+ +I+ N ELL+G++ K T+G+   + + +++  + G 
Sbjct: 525 VNCHRYNSTHPDNEYTWCSPGDTRIIIENGELLSGALCKRTVGA-VDSGLIHVIRNELGP 583

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           D A        ++ +++ +  GFS+GIGD
Sbjct: 584 DYAKKFFGGTQKLVNYWFLQTGFSVGIGD 612



 Score =  101 bits (251), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 47/79 (59%), Positives = 59/79 (74%), Gaps = 1/79 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTP EF+FH MGGREGL+DTAVKTAETGY+QRRLVK+LED+ V
Sbjct: 735 DYSPQSRGFVENSYLRGLTPQEFYFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMV 794

Query: 666 QYDMSFDAAFYGQTDCISG 684
            YD +   +     D + G
Sbjct: 795 HYDGTVRNSLGSIIDFVYG 813


>gi|71423780|ref|XP_812569.1| RNA polymerase IIA largest subunit [Trypanosoma cruzi strain CL
           Brener]
 gi|70877365|gb|EAN90718.1| RNA polymerase IIA largest subunit, putative [Trypanosoma cruzi]
          Length = 1731

 Score =  157 bits (396), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 92/267 (34%), Positives = 143/267 (53%), Gaps = 39/267 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + DVVLFNRQP+LH++S+M HR +VL + TFR N    TPYNADFDGDEMN+H+PQ+   
Sbjct: 427 NGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNLSCTTPYNADFDGDEMNLHVPQSLLT 486

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE +             +++M  K N V+P      +   QD + G Y LT K+ F ++
Sbjct: 487 KAELI-------------EMMMVPK-NFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFLDK 532

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                +A  L     D+        W+   P V ++   +WTGKQ+FSLIL P  + P  
Sbjct: 533 YFVQSVALWL-----DL--------WQLPVPAV-LKPRPLWTGKQVFSLIL-PEVNHPAT 577

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
              +           F H DS +++R  +LL G + K  +G+    ++ +++  + G D 
Sbjct: 578 PQERPP---------FPHNDSSIMIRRGQLLCGPITKGIVGA-APGSLIHVIFNERGSDE 627

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGD 607
               +  + R+T+F+L+N GFS+G+ D
Sbjct: 628 VARFINGVQRITTFFLINFGFSVGVQD 654



 Score = 87.8 bits (216), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 73/281 (25%), Positives = 132/281 (46%), Gaps = 35/281 (12%)

Query: 1150 YIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKP 1209
            +I  + +  D F+   L+M  ++   L VD     Y IE     +G    +    + ++P
Sbjct: 1198 WIARLELDADMFVDKALNMKDVKQAILRVDDG---YVIE-----TGMANDTKERTIRMRP 1249

Query: 1210 K--DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEE----------DVEGVTKYKLL 1257
            K  D   S     + + +LL  V ++G+ G+ +A++ +            + G   + + 
Sbjct: 1250 KKNDGVDSIPRLKHAIPELLARVHLRGIPGVRKALLKDRTTFTVDPATGKMTGEKTWLID 1309

Query: 1258 VEGDNLR-------DVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHG 1310
             +G  LR       D      +   + SSN   EV   LGIEAAR  ++ E++     +G
Sbjct: 1310 TDGTALRRAFIGIVDEKGNNIINATRTSSNKVPEVCSLLGIEAARYKMLHELREAYLAYG 1369

Query: 1311 MSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKES-VLNLASFENTSDHLFDAAFYGQTD 1369
            ++I++RH  ++ D +  +G ++ ++R G+ + + S  L   SFE T   L  AA +G+ D
Sbjct: 1370 LNINYRHYTILVDTICQRGYLMAVSRVGINRSEMSGPLMRCSFEETVKVLMAAAAFGERD 1429

Query: 1370 CISGVSECIIMGLPMNVGTGLIKLL-------QAVPRSEPV 1403
             + GVS  +++G    +GTGL  L+       QAVP+ + V
Sbjct: 1430 PVRGVSANLVLGNQARIGTGLFDLVLNMAALQQAVPQEDAV 1470



 Score = 83.2 bits (204), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 34/57 (59%), Positives = 44/57 (77%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +G     +  GL P EFFFHTM GREGL+DTAVKT++TGY+QR+L+K+LED+   YD
Sbjct: 783 RGMANRGYVEGLKPHEFFFHTMAGREGLIDTAVKTSDTGYLQRKLIKALEDVHAAYD 839



 Score = 80.5 bits (197), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 64/239 (26%), Positives = 106/239 (44%), Gaps = 42/239 (17%)

Query: 115 PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSIC 174
           P+  G+ D RMGT   E  C TC +   +C GHFGYIDL  PVF+IG F  V+ +L+ +C
Sbjct: 49  PVRGGINDLRMGTTDFEFACETCHRKHPECPGHFGYIDLAEPVFNIGVFDIVLQVLKCVC 108

Query: 175 KNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVK 234
           K  +C  +L+                              +  KK+        +  VVK
Sbjct: 109 K--SCGALLMDTNDP-------------------------QVHKKLQHLTGVNRLRQVVK 141

Query: 235 KCGL-LKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVL- 292
            CG+  ++S +     T  ++A+V           +    +  +    +  TL   +++ 
Sbjct: 142 MCGMKCRMSTDA----TTPEEAVVARGCGATQP--RIGRYLGIYPTLIIKATLEEQDMVW 195

Query: 293 ------QLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSV-ISDLKSDNDV 344
                 Q+ + +  ED  ++  +A    P DL+LT L VPP  +RP++    LKSD+++
Sbjct: 196 HADTARQVLDRVSDEDARVMGFDALRCHPRDLVLTVLPVPPPQVRPAISFGSLKSDDEL 254



 Score = 53.9 bits (128), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 66/294 (22%), Positives = 123/294 (41%), Gaps = 62/294 (21%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDY-ARIVKGRLERTTLGEVCEYIEEVFVPD 822
            GVPR+ E++N SR+     +   L    D    A+  +  +E  TL  V + I+ ++ PD
Sbjct: 1101 GVPRLLELLNVSRHQKHASMNVSLYPPWDKKRTAQQAQHLIEYCTLESVTKRIQFIYDPD 1160

Query: 823  DSFILIKLD----------MD----RIRL----------LHLEVDID----------SIR 848
                +++ D          MD    R RL            LE+D D           ++
Sbjct: 1161 PRETVVEADRAILELEWSVMDESDERARLQEVENGSPWIARLELDADMFVDKALNMKDVK 1220

Query: 849  YCIERTRGISGHLTVSGHS------FLILKPK--DSSKSFNSKMYQMKQLLPSVVIKGVQ 900
              I R     G++  +G +       + ++PK  D   S     + + +LL  V ++G+ 
Sbjct: 1221 QAILRVD--DGYVIETGMANDTKERTIRMRPKKNDGVDSIPRLKHAIPELLARVHLRGIP 1278

Query: 901  GINRAVIHEE----------DVEGVTKYKLLVEGDNLR-------DVMATYGVKGVKCSS 943
            G+ +A++ +            + G   + +  +G  LR       D      +   + SS
Sbjct: 1279 GVRKALLKDRTTFTVDPATGKMTGEKTWLIDTDGTALRRAFIGIVDEKGNNIINATRTSS 1338

Query: 944  NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            N   EV   LGIEAAR  ++ E++     +G++I++RH  ++ D +  +G ++ 
Sbjct: 1339 NKVPEVCSLLGIEAARYKMLHELREAYLAYGLNINYRHYTILVDTICQRGYLMA 1392



 Score = 53.5 bits (127), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 23/39 (58%), Positives = 29/39 (74%)

Query: 1107 REKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            R KY+++ + P   +GA+AAQS GEP TQMTL TFH AG
Sbjct: 1054 RTKYLQSLVSPGENIGAIAAQSCGEPATQMTLNTFHNAG 1092


>gi|448106653|ref|XP_004200803.1| Piso0_003410 [Millerozyma farinosa CBS 7064]
 gi|448109741|ref|XP_004201434.1| Piso0_003410 [Millerozyma farinosa CBS 7064]
 gi|359382225|emb|CCE81062.1| Piso0_003410 [Millerozyma farinosa CBS 7064]
 gi|359382990|emb|CCE80297.1| Piso0_003410 [Millerozyma farinosa CBS 7064]
          Length = 1639

 Score =  157 bits (396), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 107/297 (36%), Positives = 149/297 (50%), Gaps = 29/297 (9%)

Query: 319 ILTRLLVPPN---CIRPSVISDLKSDNDVVLFNRQPSLHKLSIMAHRAKVLP-HRTFRFN 374
           +  +LL P N    I   V   +K + DVVL NRQPSLHK S+M H+ +VLP  +T R +
Sbjct: 530 LANQLLTPTNGESVINKKVFRHIK-NKDVVLMNRQPSLHKASMMGHKVRVLPGEKTLRLH 588

Query: 375 ECVCTPYNADFDGDEMNVHLPQTEEARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNG 434
                 YNADFDGDEMN+H PQ E A+AEAL               L    S  +TP +G
Sbjct: 589 YANTGAYNADFDGDEMNLHFPQNENAKAEALN--------------LANTDSQYLTPTSG 634

Query: 435 ELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVF 494
             L    QD I+ G  LT K+ FF R +  ++    I       G       ++  P +F
Sbjct: 635 SPLRGLIQDHISAGLWLTNKDTFFTREEYQQLIYGCIRPED---GHTSSAKIQTMPPTIF 691

Query: 495 VRTAVIWTGKQIFSLIL---KPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILRNSELL 551
            +   +WTGKQ+ S IL   KP R+ P   NL +K +           ++ VI RN ELL
Sbjct: 692 -KPVPLWTGKQVISTILLNIKP-RNVP-GVNLISKNKVKNEYWGKYSSENEVIFRNGELL 748

Query: 552 AGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
            G +DKS  G+  K  + + L   +G D+A  A+  L R+ + Y+M   F+ G+ D+
Sbjct: 749 CGILDKSQYGA-SKFGIIHSLHEVYGPDIAGKALSVLGRLFTNYIMKTAFTCGMDDL 804



 Score = 89.4 bits (220), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 59/179 (32%), Positives = 91/179 (50%), Gaps = 4/179 (2%)

Query: 1223 MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYG-VKGVKCSSNN 1281
            +++L   VV+K V  I R +  E  VE  +K  L  EG N + +      +   + +SN+
Sbjct: 1463 IEELCHKVVVKEVPRIGRCLRPE--VEAGSKRVLTTEGVNFKAMWEQDDFIDPNRITSND 1520

Query: 1282 TYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAK 1341
             Y V KT G+EAAR+TI+ EI  V E + +++  RH  L+AD+MT +G  L   R G+  
Sbjct: 1521 IYAVLKTYGVEAARNTIVNEINNVFERYAIAVSSRHLDLIADMMTREGTYLAFNRQGIDS 1580

Query: 1342 MKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAVPRS 1400
               S + + S+E T   L  A   G  + +   S  I++G    VGTG   L   +P +
Sbjct: 1581 STSSFMKM-SYETTCQFLTKAVLDGDRESLDSPSARIVVGKLSKVGTGAFDLFAKIPET 1638



 Score = 77.0 bits (188), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 31/56 (55%), Positives = 43/56 (76%)

Query: 613  GFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            G+++  F+SG+ P E++FH M GREGL+DTAVKT+ +GY+QR L K LE + V YD
Sbjct: 951  GYIKGRFYSGIRPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCLTKQLEGVHVGYD 1006



 Score = 63.5 bits (153), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 41/112 (36%), Positives = 63/112 (56%), Gaps = 3/112 (2%)

Query: 887  MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYG-VKGVKCSSNN 945
            +++L   VV+K V  I R +  E  VE  +K  L  EG N + +      +   + +SN+
Sbjct: 1463 IEELCHKVVVKEVPRIGRCLRPE--VEAGSKRVLTTEGVNFKAMWEQDDFIDPNRITSND 1520

Query: 946  TYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             Y V KT G+EAAR+TI+ EI  V E + +++  RH  L+AD+MT +G  L 
Sbjct: 1521 IYAVLKTYGVEAARNTIVNEINNVFERYAIAVSSRHLDLIADMMTREGTYLA 1572



 Score = 59.3 bits (142), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 25/37 (67%), Positives = 30/37 (81%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            KY+R+ + P  AVG +A+QSIGEP TQMTL TFHFAG
Sbjct: 1149 KYMRSLVNPGEAVGIIASQSIGEPSTQMTLNTFHFAG 1185



 Score = 47.0 bits (110), Expect = 0.088,   Method: Compositional matrix adjust.
 Identities = 33/111 (29%), Positives = 51/111 (45%), Gaps = 5/111 (4%)

Query: 87  VTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVG 146
           V   D +++ S  QI +  ++  D    PI  GL D  +G   +   C TCG +   C G
Sbjct: 18  VLSTDEIRRLSAKQITNPTVF--DNLGHPINGGLYDLALGAFLRNL-CRTCGLDEKFCPG 74

Query: 147 HFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLR 197
           H G+I+LP+P ++  +F      L+S C    C    L   +   +  KLR
Sbjct: 75  HQGHIELPVPAYNPMFFNQFYVFLRSCCL--YCHHFRLNSVEVHRYECKLR 123


>gi|119643929|gb|ABL85595.1| RNA polymerase II largest subunit [Xanthoria polycarpa]
          Length = 1020

 Score =  156 bits (395), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 94/278 (33%), Positives = 149/278 (53%), Gaps = 35/278 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D ++FNRQPSLHK S+M HR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 373 DGDYIIFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 432

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE +  L  +S+             N+V+P+    ++   QD + G Y + +++   + 
Sbjct: 433 RAE-ISQLCMVSL-------------NIVSPQRNWPIMGIVQDTLCGIYKMCRRDVVLSE 478

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
           AQ M I    +    D  G+I +       P + ++    WTGKQI SLIL      P  
Sbjct: 479 AQVMNI----LLWVPDWDGVIPQ-------PAI-LKPQPRWTGKQIISLIL------PAT 520

Query: 521 ANLKTKGRAYTANEEFCH--RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            N +   +     +      +D  V++ + EL+ G + KS +G+  K  + +I+  + G 
Sbjct: 521 LNYRQIEKEKKTEKPLFSPLKDEGVMVDSGELMFGLLKKSAVGA-SKQGIIHIIFNEKGP 579

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           + A+        + +++L++ GFSIGIGD  P +  +Q
Sbjct: 580 EAALNFFNGAQTVVNYWLLHNGFSIGIGDTIPDRKTIQ 617



 Score =  101 bits (252), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+  
Sbjct: 731 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDVMA 790

Query: 666 QYD 668
           +YD
Sbjct: 791 KYD 793



 Score = 43.5 bits (101), Expect = 0.95,   Method: Compositional matrix adjust.
 Identities = 19/29 (65%), Positives = 21/29 (72%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMT 1137
            K+ RA + P   VG LAAQSIGEP TQMT
Sbjct: 992  KFCRAAVNPGEMVGVLAAQSIGEPATQMT 1020


>gi|425770649|gb|EKV09117.1| DNA-directed RNA polymerase [Penicillium digitatum Pd1]
 gi|425771955|gb|EKV10383.1| DNA-directed RNA polymerase [Penicillium digitatum PHI26]
          Length = 1733

 Score =  156 bits (395), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 94/274 (34%), Positives = 140/274 (51%), Gaps = 35/274 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + D +LFNRQPSLHK S+M HR +V+P  TFR N  V +PYNADFDGDEMN+H+PQ EEA
Sbjct: 449 NGDYILFNRQPSLHKESMMGHRVRVMPFSTFRMNLSVTSPYNADFDGDEMNLHVPQGEEA 508

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE    L +L+++            N+V+P+    L+   QD + G Y + +++ F  +
Sbjct: 509 RAE----LAELTLVP----------KNIVSPQRNGPLMGIVQDTLCGIYKICRRDTFLTK 554

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M     L+    D  G I         P   ++    WTGKQ+ S+        P  
Sbjct: 555 DQVM----NLMLWVPDWDGAIP--------PPAILKPRPRWTGKQMISMAF------PSG 596

Query: 521 AN-LKTKGRAYTANEEFCH-RDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGE 578
            N L+         E+F    D  +++   +L+ G + K T+G+ G   V + +  ++G 
Sbjct: 597 LNLLRVDKDGSPLAEKFSPLSDGGLLIHGGQLMYGMLSKKTVGASG-GGVIHTIFNEYGP 655

Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQ 612
           D  V        +  ++L++ GFSIGIGD  P Q
Sbjct: 656 DTCVKFFSGAQTIVGYWLLHNGFSIGIGDTIPDQ 689



 Score =  103 bits (256), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 60/181 (33%), Positives = 98/181 (54%), Gaps = 15/181 (8%)

Query: 1224 KQLLPSVVIKGVQGINRAVIHEED----VEGVT-----------KYKLLVEGDNLRDVMA 1268
            + LL ++ ++GV G++RA I+E+     +E  T           ++ L   G +L  V+ 
Sbjct: 1280 QHLLDTLTLRGVPGVDRAFINEKSKVRVIEDGTLHTSKSDPLCKEWVLETSGSSLAAVLT 1339

Query: 1269 TYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK 1328
              GV   +  SN   E+++  GIEAAR+ ++ E+ LV+   G  ++ RH  L+ D+MT +
Sbjct: 1340 IPGVDASRTYSNQFIEIFEVFGIEAARTAVLRELTLVLAFDGSYVNHRHLALLVDVMTVR 1399

Query: 1329 GEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGT 1388
            G +  +TRHG+ +     L   SFE T + L +AA +G+ D   GVSE +I+G     GT
Sbjct: 1400 GYLTPVTRHGINRADNGALMRCSFEETVEILLEAAAFGELDDCRGVSENLILGQMAPAGT 1459

Query: 1389 G 1389
            G
Sbjct: 1460 G 1460



 Score = 99.4 bits (246), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/63 (69%), Positives = 55/63 (87%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QR+LVK+LE++ V
Sbjct: 807 DYSPESRGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRKLVKALEEVMV 866

Query: 666 QYD 668
           +YD
Sbjct: 867 KYD 869



 Score = 97.8 bits (242), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 64/241 (26%), Positives = 112/241 (46%), Gaps = 40/241 (16%)

Query: 110 DPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINI 169
           D ++ P   G+ D R+GT  ++ NC TC +   +C GHFG+I+L  PVFHIG+   +  +
Sbjct: 45  DQRQRPRTKGINDPRLGTIDRQYNCETCEEGPKECPGHFGHIELASPVFHIGFLTKIKKL 104

Query: 170 LQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKSLKKKIL-------------- 214
           L+++C N  C ++      +    A + R+P   +     L K +L              
Sbjct: 105 LETVCHN--CGKIKANTADSKFTEALRFRDPKRRFDSIWRLSKDVLICEADAPVDDEEFS 162

Query: 215 ETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEI 274
           + ++K      CG     V+K G+  +         K   A++ED +A+  + V      
Sbjct: 163 KDSQKGRSHGGCGNAQPTVRKEGICLV------GTWKPSKAMMEDEMAQPEKKV------ 210

Query: 275 EAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSV 334
                      + P   L +F  I +ED+ ++ ++ + ++P  +ILT L VPP  +RPSV
Sbjct: 211 -----------ITPTMALNIFRNISVEDVRIMGLSNDYARPEWMILTVLPVPPPTVRPSV 259

Query: 335 I 335
           +
Sbjct: 260 V 260



 Score = 87.8 bits (216), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 76/288 (26%), Positives = 134/288 (46%), Gaps = 58/288 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDK--DTDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+KEI+N + NI TP +T Y +     D + A++++  +E T+L  V E  E  + P
Sbjct: 1113 GVPRLKEILNVATNIKTPSMTVYQEGMMTHDKEGAKLLRSLVEHTSLRSVTESTEIYYDP 1172

Query: 822  DDSFILIKLDMDRIRLLHL--EVDIDSI--------RYCIERTRGISGHLTVSGHSFLIL 871
            D    +I+ D D +    +  E + D +        R  + R   +   LTV   +  I 
Sbjct: 1173 DIQSTVIENDRDMVESYFIIPEDNADDVSQQSKWLLRIVLSRRSLLDKGLTVQDVATRIK 1232

Query: 872  K--PKD-----SSKSFNSKMYQMKQ------------------------LLPSVVIKGVQ 900
            +  P+D     S  + + ++ +++Q                        LL ++ ++GV 
Sbjct: 1233 QAYPRDIAVIFSDNNADEQVIRIRQVQDYKDDDDEDVEYDVTLKKLEQHLLDTLTLRGVP 1292

Query: 901  GINRAVIHEED----VEGVT-----------KYKLLVEGDNLRDVMATYGVKGVKCSSNN 945
            G++RA I+E+     +E  T           ++ L   G +L  V+   GV   +  SN 
Sbjct: 1293 GVDRAFINEKSKVRVIEDGTLHTSKSDPLCKEWVLETSGSSLAAVLTIPGVDASRTYSNQ 1352

Query: 946  TYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
              E+++  GIEAAR+ ++ E+ LV+   G  ++ RH  L+ D+MT +G
Sbjct: 1353 FIEIFEVFGIEAARTAVLRELTLVLAFDGSYVNHRHLALLVDVMTVRG 1400



 Score = 58.2 bits (139), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 26/41 (63%), Positives = 28/41 (68%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            A   ++ RA   P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1064 AIESRFARAAANPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1104


>gi|407418760|gb|EKF38234.1| RNA polymerase IIA largest subunit, putative [Trypanosoma cruzi
           marinkellei]
          Length = 1733

 Score =  156 bits (395), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 92/267 (34%), Positives = 143/267 (53%), Gaps = 39/267 (14%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           + DVVLFNRQP+LH++S+M HR +VL + TFR N    TPYNADFDGDEMN+H+PQ+   
Sbjct: 427 NGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNLSCTTPYNADFDGDEMNLHVPQSLLT 486

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           +AE +             +++M  K N V+P      +   QD + G Y LT K+ F ++
Sbjct: 487 KAELI-------------EMMMVPK-NFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFLDK 532

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
                +A  L     D+        W+   P V ++   +WTGKQ+FSLIL P  + P  
Sbjct: 533 YFVQSVALWL-----DL--------WQLPVPAV-LKPRPLWTGKQVFSLIL-PEVNHPAT 577

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
              +           F H DS +++R  +LL G + K  +G+    ++ +++  + G D 
Sbjct: 578 PQERPP---------FPHNDSSIMIRRGQLLCGPITKGIVGA-APGSLIHVIFNERGSDE 627

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGD 607
               +  + R+T+F+L+N GFS+G+ D
Sbjct: 628 VARFINGVQRITTFFLINFGFSVGVQD 654



 Score = 86.7 bits (213), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 73/281 (25%), Positives = 131/281 (46%), Gaps = 35/281 (12%)

Query: 1150 YIEEVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKP 1209
            +I  + +  D F+   L+M  ++   L VD     Y IE     +G    +    + ++P
Sbjct: 1198 WIARLELDADMFVDKALNMKDVKQAILRVDDG---YVIE-----TGMANDTKERTIRMRP 1249

Query: 1210 K--DSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEE----------DVEGVTKYKLL 1257
            K  D   S       + +LL  V ++G+ G+ +A++ +            + G   + + 
Sbjct: 1250 KKNDGVDSIPRLKQAIPELLARVHLRGIPGVRKALLKDRTTFTVDPATGKMTGEKTWLID 1309

Query: 1258 VEGDNLR-------DVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHG 1310
             +G  LR       D      +   + SSN   EV   LGIEAAR  ++ E++     +G
Sbjct: 1310 TDGTALRRAFIGIVDEKGNNIINATRTSSNKVPEVCSLLGIEAARYKMLHELREAYLAYG 1369

Query: 1311 MSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKES-VLNLASFENTSDHLFDAAFYGQTD 1369
            ++I++RH  ++ D +  +G ++ ++R G+ + + S  L   SFE T   L  AA +G+ D
Sbjct: 1370 LNINYRHYTILVDTICQRGYLMAVSRVGINRSEMSGPLMRCSFEETVKVLMAAAAFGERD 1429

Query: 1370 CISGVSECIIMGLPMNVGTGLIKLL-------QAVPRSEPV 1403
             + GVS  +++G    +GTGL  L+       QAVP+ + V
Sbjct: 1430 PVRGVSANLVLGNQARIGTGLFDLVLNMAALQQAVPQEDAV 1470



 Score = 83.2 bits (204), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 34/57 (59%), Positives = 44/57 (77%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +G     +  GL P EFFFHTM GREGL+DTAVKT++TGY+QR+L+K+LED+   YD
Sbjct: 783 RGMANRGYVEGLKPHEFFFHTMAGREGLIDTAVKTSDTGYLQRKLIKALEDVHAAYD 839



 Score = 80.1 bits (196), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 64/239 (26%), Positives = 106/239 (44%), Gaps = 42/239 (17%)

Query: 115 PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSIC 174
           P+  G+ D RMGT   E  C TC +   +C GHFGYIDL  PVF+IG F  V+ +L+ +C
Sbjct: 49  PVRGGINDLRMGTTDFEFACETCHRKHPECPGHFGYIDLAEPVFNIGVFDIVLQVLKCVC 108

Query: 175 KNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVK 234
           K  +C  +L+                              +  KK+        +  VVK
Sbjct: 109 K--SCGALLMDTNDP-------------------------QVHKKLQHLTGVNRLRQVVK 141

Query: 235 KCGL-LKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVL- 292
            CG+  ++S +     T  ++A+V           +    +  +    +  TL   +++ 
Sbjct: 142 MCGMKCRMSTDA----TTPEEAVVARGCGATQP--RIGRYLGIYPTLIIKATLEEQDMVW 195

Query: 293 ------QLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSV-ISDLKSDNDV 344
                 Q+ + +  ED  ++  +A    P DL+LT L VPP  +RP++    LKSD+++
Sbjct: 196 HADTARQVLDRVSDEDARVMGFDALRCHPRDLVLTVLPVPPPQVRPAISFGSLKSDDEL 254



 Score = 53.5 bits (127), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 23/39 (58%), Positives = 29/39 (74%)

Query: 1107 REKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            R KY+++ + P   +GA+AAQS GEP TQMTL TFH AG
Sbjct: 1054 RTKYLQSLVSPGENIGAIAAQSCGEPATQMTLNTFHNAG 1092



 Score = 52.8 bits (125), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 66/294 (22%), Positives = 122/294 (41%), Gaps = 62/294 (21%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDLDY-ARIVKGRLERTTLGEVCEYIEEVFVPD 822
            GVPR+ E++N SR+     +   L    D    A+  +  +E  TL  V + I+ ++ PD
Sbjct: 1101 GVPRLLELLNVSRHQKHASMNVSLYPPWDKKRTAQQAQHLIEYCTLESVTKRIQFIYDPD 1160

Query: 823  DSFILIKLD----------MD----RIRL----------LHLEVDID----------SIR 848
                +++ D          MD    R RL            LE+D D           ++
Sbjct: 1161 PRETVVEADRAILELEWSVMDESDERARLQEVENGSPWIARLELDADMFVDKALNMKDVK 1220

Query: 849  YCIERTRGISGHLTVSGHS------FLILKPK--DSSKSFNSKMYQMKQLLPSVVIKGVQ 900
              I R     G++  +G +       + ++PK  D   S       + +LL  V ++G+ 
Sbjct: 1221 QAILRVD--DGYVIETGMANDTKERTIRMRPKKNDGVDSIPRLKQAIPELLARVHLRGIP 1278

Query: 901  GINRAVIHEE----------DVEGVTKYKLLVEGDNLR-------DVMATYGVKGVKCSS 943
            G+ +A++ +            + G   + +  +G  LR       D      +   + SS
Sbjct: 1279 GVRKALLKDRTTFTVDPATGKMTGEKTWLIDTDGTALRRAFIGIVDEKGNNIINATRTSS 1338

Query: 944  NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
            N   EV   LGIEAAR  ++ E++     +G++I++RH  ++ D +  +G ++ 
Sbjct: 1339 NKVPEVCSLLGIEAARYKMLHELREAYLAYGLNINYRHYTILVDTICQRGYLMA 1392


>gi|413915228|gb|AFW21476.1| RNA polymerase II largest subunit [Epichloe festucae]
          Length = 1756

 Score =  156 bits (395), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 86/276 (31%), Positives = 153/276 (55%), Gaps = 32/276 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D ++FNRQPSLHK S+M HR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 450 DGDYIIFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 509

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE               K L    +N+V+P+    L+   QD + G Y L +++ F ++
Sbjct: 510 RAE--------------VKELCLVPNNIVSPQKNGPLMGVVQDSLAGAYKLCRRDTFIDK 555

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              M     ++    +  G+I +       P + ++    WTGKQ+ S+++   ++  ++
Sbjct: 556 EMVM----NMMLWVPNWDGVIPQ-------PAI-LKPRPRWTGKQLISMVIP--KEISLH 601

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           +   + G+    N +   +D+ +++++ ELL G + K  +GS     + ++   + G + 
Sbjct: 602 SPESSGGQ---DNADIPLKDTGLLIQSGELLYGLLKKKNIGSAA-GGIVHLSYNELGPEG 657

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           A+  +  + ++ +++L+N G SIGIGD  P +  ++
Sbjct: 658 AMAFLNGVQQVVTYWLLNNGHSIGIGDTVPDKQTIE 693



 Score =  106 bits (264), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 79/283 (27%), Positives = 136/283 (48%), Gaps = 39/283 (13%)

Query: 1146 EVCEYIEEVF-VPDDS--------FILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGH 1196
            E  + +E  F +PDDS          L+++ +DR +LL  E+ ID +   I+        
Sbjct: 1181 EDMDMVESYFLIPDDSQDTTDQQSRWLLRITLDRQKLLDKEIKIDDVAQRIKEEYPSDLA 1240

Query: 1197 LTVSGHSF---LIL---------KPKDSSKSFNSKMYQMK---QLLPSVVIKGVQGINRA 1241
            +  S ++    +I          K +D  K     +   +    LL ++ ++GV G+ RA
Sbjct: 1241 IIFSDNNADEQVIRIRTIRTDNEKDEDGEKKIEDDVMLKRLEAHLLDTLTLRGVPGVERA 1300

Query: 1242 V---------------IHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVY 1286
                            I ++D +  T++ L   G  LRDV+A  GV   +  +N+ +++ 
Sbjct: 1301 FLTKGTRLVVDDDGAEIAKKDDDKCTQWYLDTSGSALRDVLAVDGVDPTRTYTNDLWQIV 1360

Query: 1287 KTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESV 1346
            +  GIEAARS ++ E+  V+   G  ++ RH  L+ D+MT +G +  +TRHG+ +     
Sbjct: 1361 EVFGIEAARSALVKELTNVLAFDGSYVNHRHIALLVDVMTYRGTISAVTRHGINRADTGA 1420

Query: 1347 LNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
            L   SFE T + L +AA  G+ D   G+SE +++G    +GTG
Sbjct: 1421 LMRCSFEETVEILLEAAASGELDDCRGISENVMLGQLAPMGTG 1463



 Score =  103 bits (256), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 46/63 (73%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QRRLVK+LEDL  
Sbjct: 807 DYSPEARGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDLSA 866

Query: 666 QYD 668
           +YD
Sbjct: 867 RYD 869



 Score = 85.5 bits (210), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 75/296 (25%), Positives = 134/296 (45%), Gaps = 68/296 (22%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKD-------------------------TDLDYARI 798
            GVPR+KEI+N +++I TP +  YL+                           T++ Y   
Sbjct: 1114 GVPRLKEILNLAKDIKTPSMAVYLNTHLGTQEQAKKLRSLVEYTNLRSITSVTEIYYDPD 1173

Query: 799  VKGRLERTTLGEVCEYIEEVF-VPDDS--------FILIKLDMDRIRLLHLEVDIDSIRY 849
            ++G    T++ E  + +E  F +PDDS          L+++ +DR +LL  E+ ID +  
Sbjct: 1174 IQG----TSIVEDMDMVESYFLIPDDSQDTTDQQSRWLLRITLDRQKLLDKEIKIDDVAQ 1229

Query: 850  CIERTRGISGHLTVSGHSF---LIL---------KPKDSSKSFNSKMYQMK---QLLPSV 894
             I+        +  S ++    +I          K +D  K     +   +    LL ++
Sbjct: 1230 RIKEEYPSDLAIIFSDNNADEQVIRIRTIRTDNEKDEDGEKKIEDDVMLKRLEAHLLDTL 1289

Query: 895  VIKGVQGINRAV---------------IHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
             ++GV G+ RA                I ++D +  T++ L   G  LRDV+A  GV   
Sbjct: 1290 TLRGVPGVERAFLTKGTRLVVDDDGAEIAKKDDDKCTQWYLDTSGSALRDVLAVDGVDPT 1349

Query: 940  KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            +  +N+ +++ +  GIEAARS ++ E+  V+   G  ++ RH  L+ D+MT +G +
Sbjct: 1350 RTYTNDLWQIVEVFGIEAARSALVKELTNVLAFDGSYVNHRHIALLVDVMTYRGTI 1405



 Score = 67.0 bits (162), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 60/221 (27%), Positives = 102/221 (46%), Gaps = 27/221 (12%)

Query: 110 DPQRT-PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVIN 168
           D  RT P   GL D  +G+  +   C TC Q +SDC GHFG+I+L  PV+H G+ + V  
Sbjct: 44  DETRTKPRDGGLNDPLLGSIDRGLKCKTCTQAMSDCPGHFGHIELAKPVYHPGFIKKVKK 103

Query: 169 ILQSICKNPTCARVLL---GEEKAAGFR---AKLRNPALSYLVRKSLKKKILETTKK--V 220
           IL+ +C N  C++VL      E  +  +   AKLR   +  + +K  + +  + T+K   
Sbjct: 104 ILEIVCHN--CSKVLADTSDPEFVSAIQTRDAKLRFNRVWAVCKKKRRCENEDRTEKNDE 161

Query: 221 SVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKF 280
              P    +      CG ++    +   + K    +V++   +  E V   PE+ AH   
Sbjct: 162 EFAPGMKPLVNNHGGCGNVQPQVRQAALQLKAAFDVVQEDGPKRRETVPITPEM-AHG-- 218

Query: 281 GLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
                        + + I  ED+  + +N++ ++P  LI+T
Sbjct: 219 -------------ILKRISEEDLRQMGLNSDYARPEWLIIT 246



 Score = 55.5 bits (132), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/39 (61%), Positives = 29/39 (74%)

Query: 1107 REKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            + ++ R+ + P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1067 QNRWDRSFVSPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1105


>gi|45935327|gb|AAS79685.1| RNA polymerase II large subunit [Taxus canadensis]
          Length = 1013

 Score =  156 bits (395), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 94/272 (34%), Positives = 149/272 (54%), Gaps = 37/272 (13%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D D VLFNRQPSLHK+SIM HR +++P+ TFR N  V +PYNADFDGDEMN+H+PQ+ E
Sbjct: 372 NDGDFVLFNRQPSLHKMSIMGHRIRIMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSFE 431

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE L             +++M  K  +V+P++   ++   QD + G   +T+++ F  
Sbjct: 432 TRAEVL-------------ELMMVPKC-IVSPQSNRPVMGIVQDTLLGCRKITKRDTFIE 477

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           +   M I    +    D  G I         P + ++   +WTGKQ+F+LI+      P 
Sbjct: 478 KDVFMNI----LMWWEDFDGKIP-------APTI-LKPRPLWTGKQVFNLII------PK 519

Query: 520 NANLKTKGRAYTANEE---FCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
             NL  +  A+ A  E       D+ V +   E+L+G++ K TLG+    ++ +++  + 
Sbjct: 520 QINL-IRQSAWHAESETGFITPGDTIVRIEKGEVLSGTLCKKTLGTSS-GSLIHVIWEEV 577

Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
           G D A   +     + +++L+ +GFSIGIGD 
Sbjct: 578 GPDAARKFLGHTQWLVNYWLLQQGFSIGIGDT 609



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 42/57 (73%), Positives = 52/57 (91%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKT+ETGY+QRRLVK++ED+ V+YD
Sbjct: 737 RGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDIMVKYD 793



 Score = 48.1 bits (113), Expect = 0.036,   Method: Compositional matrix adjust.
 Identities = 45/177 (25%), Positives = 87/177 (49%), Gaps = 15/177 (8%)

Query: 150 YIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNPALSYLVRKS 208
           +++L  P++HIG+ + +++IL+ +C N  C+R+L  E+     +A K++NP       K 
Sbjct: 1   HLELAKPMYHIGFLKTILSILRCVCFN--CSRILADEDDHRFKQALKVKNP-------KH 51

Query: 209 LKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVED---LLAEYN 265
             KK+L+  K  + C     I+    + G  ++  ++      ++  I  D   ++AEY 
Sbjct: 52  RLKKVLDCCKNKTKCEGGDVIDEDQGQDGDDEVKKKRQGGCGAQQPKIYIDGMKIIAEYK 111

Query: 266 EAVKF--NPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLIL 320
              K   +PE    +     Q L+   VL + + I  E+  +L +N + S+P  +IL
Sbjct: 112 APRKKADDPEQLMPEPVERKQQLSAERVLSVLKRITDEECQMLGLNPKYSRPDWMIL 168


>gi|448363836|ref|ZP_21552431.1| DNA-directed RNA polymerase subunit A' [Natrialba asiatica DSM
           12278]
 gi|445645420|gb|ELY98424.1| DNA-directed RNA polymerase subunit A' [Natrialba asiatica DSM
           12278]
          Length = 975

 Score =  156 bits (395), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 99/270 (36%), Positives = 143/270 (52%), Gaps = 45/270 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 483 DGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQNEEA 542

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR GE +I A QD I+G YLLT  N  FN 
Sbjct: 543 RAE--------------ARVLMRVQEQILSPRFGENIIGAIQDHISGMYLLTHDNPRFNE 588

Query: 461 AQTMR-IASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q +  + +T I +  +  GI       +  P         WTG  +FS +L      P 
Sbjct: 589 TQALDLLRATRIDELPEPSGIDD-----AGEP--------FWTGYDVFSELL------PD 629

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           + NL+  G   T  +E       V++   +L+ G++ +  +G  G   +   + + +G  
Sbjct: 630 DLNLEFTG---TVGDE-------VVIEEGQLIEGTIAEDEVGEFG-GEIVDTITKVYGNT 678

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVT 609
            +   +  +S +    +M+ GFSIGI D T
Sbjct: 679 RSRIFINEVSTLAMRAIMHFGFSIGIDDET 708



 Score =  116 bits (291), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 87/303 (28%), Positives = 140/303 (46%), Gaps = 43/303 (14%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G I   + + +  ++ S  +I++ + Y  D    PI  GL+D R+G       C TCG++
Sbjct: 10  GSINFGLMEPEEYREMSATKIITADTY--DDDGFPIDMGLMDPRLGVIDPGLECKTCGKH 67

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
              C GHFG+I+L  PV H+G+ + +  +L+  C+   C+R+LL E++   FR ++    
Sbjct: 68  SGSCNGHFGHIELAAPVIHVGFTKLIRRLLRGTCRE--CSRLLLTEDERGEFRDQIDESR 125

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVV---------------------KKCGLL 239
                   + K  +   +K   CP CGEI   +                     +  G +
Sbjct: 126 KLGRDLNDVTKAAIRQARKKDRCPFCGEIQYDIDHEKPTTYYEVQQVLTSEYSQRIAGAM 185

Query: 240 KISHEKYKNRTKKKDAIVEDL---LAEYNEAV--KFNPE------IEAHKKFGLIQT--- 285
           +   E+   RT   D + E+    L+  NE +   F P       IE      L +    
Sbjct: 186 QGDEEEGIERT-SPDELAEETDIELSRINEILSGSFRPRENQRKAIEKALDIDLTEEDTN 244

Query: 286 -LNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDN 342
            L P ++   FEAIP EDI +L ++AE S+P  +ILT L VPP   RPS+  D   +S++
Sbjct: 245 KLMPSDIRDWFEAIPDEDIEVLGIDAERSRPEWMILTVLPVPPVTARPSITLDNGQRSED 304

Query: 343 DVV 345
           D+ 
Sbjct: 305 DLT 307



 Score = 92.8 bits (229), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 39/58 (67%), Positives = 49/58 (84%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
             GFV+NS+ SGLTP EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 834 AHGFVENSYTSGLTPREFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELEAQYD 891



 Score = 45.4 bits (106), Expect = 0.22,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 29/46 (63%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 65
           +VLM  +  +++PR GE +I A QD I+G YLLT  N  FN  Q +
Sbjct: 547 RVLMRVQEQILSPRFGENIIGAIQDHISGMYLLTHDNPRFNETQAL 592


>gi|448683947|ref|ZP_21692567.1| DNA-directed RNA polymerase subunit A' [Haloarcula japonica DSM
           6131]
 gi|189332911|dbj|BAG41983.1| RNA polymerase subunit A [Haloarcula japonica]
 gi|445783520|gb|EMA34349.1| DNA-directed RNA polymerase subunit A' [Haloarcula japonica DSM
           6131]
          Length = 969

 Score =  156 bits (395), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 93/268 (34%), Positives = 140/268 (52%), Gaps = 45/268 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+++FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 480 DGDIIIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTTVCPPYNADFDGDEMNMHALQNEEA 539

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR GE +I A QD I+G YLLT  N  FN 
Sbjct: 540 RAE--------------ARVLMRVQEQMLSPRFGENIIGAIQDHISGTYLLTHTNPKFNE 585

Query: 461 AQTMR-IASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q +  + +T I +  +  G+ +                  WTG+ +FS +L      P 
Sbjct: 586 TQALDLLRATRIDELPEADGVDE-------------NGEEYWTGRSLFSELL------PE 626

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           + NL+    A             V++ + ++  G++D+  +G+ G   +   + +D+   
Sbjct: 627 DLNLEFTSSAGDT----------VVVEDGQMTGGTIDEDAVGAFG-GEIVDTIAKDYSRT 675

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            A   +  +S +    +M+ GFSI I D
Sbjct: 676 RARILVNEVSALAMRSIMHFGFSISIDD 703



 Score =  105 bits (261), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 81/294 (27%), Positives = 125/294 (42%), Gaps = 55/294 (18%)

Query: 94  QQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDL 153
           ++ S  ++++ + Y  D    PI  GL+D R+G       C TCG++   C GHFG+I+L
Sbjct: 24  REMSATKVITADTY--DDDGFPIDMGLMDPRLGVIDPGLECKTCGKHSGSCNGHFGHIEL 81

Query: 154 PLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKL-RNPALSYLVRKSLKKK 212
             PV H+G+ + +  +L+  C+   C+R+ L E +   F  +L R   L   +    K  
Sbjct: 82  AAPVIHVGFAKLIRRLLRGTCRE--CSRLCLDEHERDEFADRLTRTQDLGRDLNDVTKAA 139

Query: 213 ILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDL-------LAEYN 265
           I +  KK   CP CGE            I HEK     + +D +  D        + E  
Sbjct: 140 IRQARKK-DRCPFCGEKQ--------YDIKHEKPTTYYEVQDVLASDYPERIAAAMEESE 190

Query: 266 EAV----------------------KFNPEIEAHKKFGL----------IQTLNPLEVLQ 293
           E +                      +F P  E  K              +  L P ++  
Sbjct: 191 EPISPIDLSEETGIDSSRVQEILSGEFRPRQEDRKALEKALSVDLTEEDMNKLMPSDIRD 250

Query: 294 LFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDNDVV 345
            FE IP +DI +L M    S+P  +ILT L VPP   RPS+  D   +S++D+ 
Sbjct: 251 WFEDIPDQDIEVLGMKPARSRPEWMILTVLPVPPVTARPSITLDNGQRSEDDLT 304



 Score = 87.4 bits (215), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 37/58 (63%), Positives = 47/58 (81%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
             GFV+ S+ SGL P EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 831 AHGFVEASYRSGLGPKEFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELETQYD 888



 Score = 46.2 bits (108), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 29/46 (63%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 65
           +VLM  +  +++PR GE +I A QD I+G YLLT  N  FN  Q +
Sbjct: 544 RVLMRVQEQMLSPRFGENIIGAIQDHISGTYLLTHTNPKFNETQAL 589


>gi|448356450|ref|ZP_21545183.1| DNA-directed RNA polymerase subunit A' [Natrialba chahannaoensis
           JCM 10990]
 gi|445653483|gb|ELZ06354.1| DNA-directed RNA polymerase subunit A' [Natrialba chahannaoensis
           JCM 10990]
          Length = 976

 Score =  156 bits (395), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 100/275 (36%), Positives = 144/275 (52%), Gaps = 46/275 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 483 DGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQNEEA 542

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR GE +I A QD I+G YLLT  N  FN 
Sbjct: 543 RAE--------------ARVLMRVQEQILSPRFGENIIGAIQDHISGMYLLTHDNPRFNE 588

Query: 461 AQTMR-IASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q +  + +T I +  +  GI                    WTG  +FS +L      P 
Sbjct: 589 TQALDLLRATRIDELPEPSGIND-------------EGEPFWTGYDVFSELL------PD 629

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           + NL+  G   T  E        V++ + +L+ G++ +  +G  G   +   + + +G  
Sbjct: 630 DLNLEFTG---TIGEP-------VVIEDGQLIEGTIAEDEVGEFG-GEIVDTITKIYGNT 678

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVT-PGQG 613
            +   +  +S +    +M+ GFSIGI D T PG+ 
Sbjct: 679 RSRIFINEVSTLAMRAIMHFGFSIGIDDETIPGEA 713



 Score =  112 bits (280), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 84/302 (27%), Positives = 137/302 (45%), Gaps = 41/302 (13%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G I   + + +  ++ S  +I++ + Y  D    PI  GL+D R+G       C TCG++
Sbjct: 10  GSINFGLMEPEEYREMSATKIITADTY--DDDGFPIDMGLMDPRLGVIDPGLECKTCGKH 67

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPA 200
              C GHFG+I+L  PV H+G+ + +  +L+  C+   C+R+LL E++   F+ ++    
Sbjct: 68  SGSCNGHFGHIELAAPVIHVGFTKLIRRLLRGTCRE--CSRLLLVEDEREEFQDQIEESR 125

Query: 201 LSYLVRKSLKKKILETTKKVSVCPHCGEINGVV---------------------KKCGLL 239
                   + K  +   +K   CPHCGE+   +                     +  G +
Sbjct: 126 KLGRDLNDVTKAAIRQARKKDRCPHCGEVQYDIDHEKPTTYYEVQQVLTSEYSQRIAGAM 185

Query: 240 KISHEKYKNRTKKKD--AIVEDLLAEYNEAV--KFNPE------IEAHKKFGLIQT---- 285
           +   E    RT   +  A  E  L   NE +   F P       IE      L +     
Sbjct: 186 QGDEEAGIERTSPDELAAETEIDLTRINEILSGSFRPRESQREAIEKALDIDLTEEDTNK 245

Query: 286 LNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDND 343
           L P ++   FE IP EDI +L ++A+ S+P  +ILT L VPP   RPS+  D   +S++D
Sbjct: 246 LMPSDIRDWFENIPDEDIEVLGIDADRSRPEWMILTVLPVPPVTARPSITLDNGQRSEDD 305

Query: 344 VV 345
           + 
Sbjct: 306 LT 307



 Score = 92.8 bits (229), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 39/58 (67%), Positives = 49/58 (84%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
             GFV+NS+ SGLTP EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 834 AHGFVENSYTSGLTPREFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELEAQYD 891



 Score = 45.4 bits (106), Expect = 0.23,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 29/46 (63%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 65
           +VLM  +  +++PR GE +I A QD I+G YLLT  N  FN  Q +
Sbjct: 547 RVLMRVQEQILSPRFGENIIGAIQDHISGMYLLTHDNPRFNETQAL 592


>gi|255579596|ref|XP_002530639.1| DNA-directed RNA polymerase II largest subunit, putative [Ricinus
           communis]
 gi|223529812|gb|EEF31747.1| DNA-directed RNA polymerase II largest subunit, putative [Ricinus
           communis]
          Length = 1855

 Score =  156 bits (395), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 92/271 (33%), Positives = 147/271 (54%), Gaps = 35/271 (12%)

Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
           +D D VLFNRQPSLHK+SIM HR K++P+ TFR N  V +PYNADFDGDEMN+H+PQ+ E
Sbjct: 450 NDGDFVLFNRQPSLHKMSIMGHRIKIMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSFE 509

Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
            RAE L             +++M  K  +V+P++   ++   QD + G   +T+++ F  
Sbjct: 510 TRAEVL-------------ELMMVPKC-IVSPQSNRPVMGIVQDTLLGCRKITKRDTFIE 555

Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
           +   M           +I    + F  +   P + ++   +WTGKQ+F+LI+      P 
Sbjct: 556 KDVFM-----------NILMWWEDFDGKVPAPAI-LKPRPLWTGKQVFNLII------PK 597

Query: 520 NANLKTKGRAYTANEE--FCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFG 577
             NL      ++ +E       D+ V +   ELL+G++ K TLG+    ++ +++  + G
Sbjct: 598 QINLIRTAAWHSDSERGVITPGDTLVRIEKGELLSGTVCKKTLGT-STGSLIHVIWEEVG 656

Query: 578 EDVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
            D A   +     + +++L+  GFSIGIGD 
Sbjct: 657 PDAARKFLGHTQWLVNYWLLQNGFSIGIGDT 687



 Score =  108 bits (269), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 60/173 (34%), Positives = 97/173 (56%), Gaps = 9/173 (5%)

Query: 1226 LLPSVVIKGVQGINRAVIHEEDV------EG---VTKYKLLVEGDNLRDVMATYGVKGVK 1276
            +L  + ++G+  IN+  I +  V      EG   + ++ L  EG NL  VM    V   +
Sbjct: 1287 MLTEMALRGIPDINKVFIKQSKVSKFDENEGFKTIEEWMLDTEGVNLLAVMCNENVDARR 1346

Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITR 1336
             +SN+  EV + LGIEA R +++ E+++V+   G  +++RH  ++ D MT +G ++ ITR
Sbjct: 1347 TTSNHLIEVIEVLGIEAVRRSLLDELRVVISFDGSYVNYRHLAILCDTMTYRGHLMAITR 1406

Query: 1337 HGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
            HG+ +     L   SFE T D L DAA Y + D + GV+E I++G    +GTG
Sbjct: 1407 HGINRNDTGPLMRCSFEETVDILLDAAVYAEADYLRGVTENIMLGQLAPIGTG 1459



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 42/57 (73%), Positives = 52/57 (91%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GFV+NS+  GLTP EFFFH MGGREGL+DTAVKT+ETGY+QRRLVK++ED+ V+YD
Sbjct: 815 RGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDIMVKYD 871



 Score = 97.1 bits (240), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 84/275 (30%), Positives = 139/275 (50%), Gaps = 41/275 (14%)

Query: 82  LIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQR-TPIPHGLLDRRMGTNQKEANCTTCGQN 140
           +++  +   D ++Q S +QI     + +  +R  P P GL D R+GT  ++  C TC  N
Sbjct: 17  MVQFGILSPDEIRQMSVVQIE----FSETTERGKPKPGGLSDLRLGTIDRKMKCETCTAN 72

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNP 199
           +++C GHFG+++L  P+FHIG+ + V++I++ +C N  C+++L  EE     +A K++NP
Sbjct: 73  MAECPGHFGHLELAKPMFHIGFLKTVLSIMRCVCFN--CSKILADEEDHKFKQALKIKNP 130

Query: 200 ALSYLVRKSLKKKILETTKKVSVCP-------HCGEINGVVKK----CGLL--KISHEKY 246
                  K+  KKIL+  K  + C        H  + +  VKK    CG    +++ E  
Sbjct: 131 -------KNRLKKILDACKNKTKCEGGDDIDVHSQDTDEPVKKSRGGCGAQQPRMTIEGM 183

Query: 247 KNRTKKKDAIVEDLLAEYNEAVKFNPEIEA-HKKFGLIQTLNPLEVLQLFEAIPLEDIPL 305
           K            ++AEY    K N + E   +     QTL    VL + + I  +D  L
Sbjct: 184 K------------MIAEYKAQRKKNDDQEQLPEPVERKQTLTAERVLGVLKRISDDDCRL 231

Query: 306 LLMNAELSKPSDLILTRLLVPPNCIRPSVISDLKS 340
           L  N + ++P  +IL  L +PP  +RPSV+ D  S
Sbjct: 232 LGFNPKYARPDWMILQVLPIPPPPVRPSVMMDTSS 266



 Score = 78.2 bits (191), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 72/288 (25%), Positives = 134/288 (46%), Gaps = 54/288 (18%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDTDL--DYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR++EIIN ++ I TP ++ +L  + +   + A+ V+  LE TTL  V +  E  + P
Sbjct: 1116 GVPRLREIINVAKKIKTPSLSIFLIPECNKTKERAKNVQCALEYTTLRSVTQATEVWYDP 1175

Query: 822  DDSFILIKLDMDRIR------------------LLHLEVDIDSI------------RYCI 851
            D    +I+ D+D ++                  LL +E++ + +            +  +
Sbjct: 1176 DPMSTIIEEDVDFVKSYYEMPDEEISPEKISPWLLRIELNREMMVDKKLNMADIAEKINL 1235

Query: 852  ERTRGISGHLTVSGHSFLILK--------PKD--SSKSFNSKMYQMK---QLLPSVVIKG 898
            E    ++          LIL+        PK   + +S    ++  K    +L  + ++G
Sbjct: 1236 EFDDDLTCIFNDDNAEKLILRIRIMNDEAPKGELNDESAEDDVFLKKIESNMLTEMALRG 1295

Query: 899  VQGINRAVIHEEDV------EG---VTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEV 949
            +  IN+  I +  V      EG   + ++ L  EG NL  VM    V   + +SN+  EV
Sbjct: 1296 IPDINKVFIKQSKVSKFDENEGFKTIEEWMLDTEGVNLLAVMCNENVDARRTTSNHLIEV 1355

Query: 950  YKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
             + LGIEA R +++ E+++V+   G  +++RH  ++ D MT +G ++ 
Sbjct: 1356 IEVLGIEAVRRSLLDELRVVISFDGSYVNYRHLAILCDTMTYRGHLMA 1403



 Score = 52.4 bits (124), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 20/37 (54%), Positives = 29/37 (78%)

Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            +++++ + P   +G +AAQSIGEP TQMTL TFH+AG
Sbjct: 1071 RFLQSLVAPGEMIGCVAAQSIGEPATQMTLNTFHYAG 1107


>gi|110669268|ref|YP_659079.1| DNA-directed RNA polymerase subunit A' [Haloquadratum walsbyi DSM
           16790]
 gi|109627015|emb|CAJ53491.1| DNA-directed RNA polymerase subunit A' (subunit A) [Haloquadratum
           walsbyi DSM 16790]
          Length = 978

 Score =  156 bits (395), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 100/268 (37%), Positives = 141/268 (52%), Gaps = 45/268 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+V+FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  QTEE+
Sbjct: 484 DGDIVIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTVVCPPYNADFDGDEMNMHALQTEES 543

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  L++PR GE +I A QD I+G YLLT  N  F+ 
Sbjct: 544 RAE--------------ARVLMRVQEQLLSPRFGENIIGAIQDHISGTYLLTNGNPQFSE 589

Query: 461 AQTMRIASTLIADT-SDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q + +      DT     G  +  S               W+G+Q+FS +L      P 
Sbjct: 590 TQALDLLRATSIDTLPPAAGQTEDGS-------------PYWSGRQLFSELL------PD 630

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           N NL+    A             V + + EL+AG++D++ +G+ G   V   L +   + 
Sbjct: 631 NLNLEFTSAA----------GDTVEIVDGELIAGTIDENAVGAFG-GEVVDTLAKVHSKT 679

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            A   +  ++ +    +M+ GFSIGI D
Sbjct: 680 RARVFVNEVASLAMRAIMHFGFSIGIDD 707



 Score =  105 bits (261), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 83/312 (26%), Positives = 136/312 (43%), Gaps = 60/312 (19%)

Query: 81  GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
           G I+  +   +  +  S  ++++ + Y  D    PI  GL+D R+G       C TCG +
Sbjct: 10  GAIQFGLMDPETYRDMSATKVITADTY--DDDGYPIDMGLMDPRLGVIDPGLECKTCGSH 67

Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKL-RNP 199
              C GHFG+I+L  PV H+G+ + +  +L+S C+N  C  + L E +   FR  L RN 
Sbjct: 68  SGSCNGHFGHIELAAPVIHVGFTKLIRRLLRSTCRN--CGHLALTESEREEFREGLQRNE 125

Query: 200 ALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVED 259
            L       LK  + +  +K +VCP CGE    +K        HEK     + +D +  D
Sbjct: 126 ELGEDWTDVLKSAVRQ-ARKTNVCPSCGETQHDIK--------HEKPTTYYEVQDVLAGD 176

Query: 260 LLAEYNEAVK----------------------------------FNP------EIEAHKK 279
              +   A++                                  F P      E+E+   
Sbjct: 177 YPEKIASAMQPDPDDDSDSGLSPNSLADATGINVERINNILSGEFRPVGEDRKELESALD 236

Query: 280 FGLI-QTLNPL---EVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVI 335
             L  + +N L   ++   FE+IP EDI  L ++   ++P  +++T L VPP   RPS+ 
Sbjct: 237 IDLTEEDMNKLMASDIRDWFESIPDEDIRTLGIDPSRARPEWMVMTVLPVPPVTARPSIT 296

Query: 336 SD--LKSDNDVV 345
            D   +S++D+ 
Sbjct: 297 LDNGQRSEDDLT 308



 Score = 90.9 bits (224), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 38/57 (66%), Positives = 48/57 (84%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
            GFV+NS+  GLTP EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 836 HGFVENSYRGGLTPREFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELEAQYD 892



 Score = 44.3 bits (103), Expect = 0.51,   Method: Compositional matrix adjust.
 Identities = 22/51 (43%), Positives = 31/51 (60%)

Query: 15  TRNCWQVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 65
           +R   +VLM  +  L++PR GE +I A QD I+G YLLT  N  F+  Q +
Sbjct: 543 SRAEARVLMRVQEQLLSPRFGENIIGAIQDHISGTYLLTNGNPQFSETQAL 593


>gi|448627103|ref|ZP_21671778.1| DNA-directed RNA polymerase subunit A' [Haloarcula vallismortis
           ATCC 29715]
 gi|445759731|gb|EMA11007.1| DNA-directed RNA polymerase subunit A' [Haloarcula vallismortis
           ATCC 29715]
          Length = 969

 Score =  156 bits (395), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 94/268 (35%), Positives = 140/268 (52%), Gaps = 45/268 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+++FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 480 DGDIIIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTTVCPPYNADFDGDEMNMHALQNEEA 539

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR GE +I A QD I+G YLLT  N  FN 
Sbjct: 540 RAE--------------ARVLMRVQEQMLSPRFGENIIGAIQDHISGTYLLTHTNPKFNE 585

Query: 461 AQTMR-IASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q +  + +T I +  +  GI +                  WTG+ +FS +L      P 
Sbjct: 586 TQALDLLRATRIDELPEADGIDE-------------DGEEYWTGRSLFSELL------PD 626

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           + NL+    A             V++ + ++  G++D+  +G+ G   +   + +D+   
Sbjct: 627 DLNLEFTSSAGDT----------VVVEDGQMTGGTIDEDAVGAFG-GEIVDTIAKDYSRT 675

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            A   +  +S +    +M+ GFSI I D
Sbjct: 676 RARILVNEVSALAMRSIMHFGFSISIDD 703



 Score =  104 bits (260), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 81/294 (27%), Positives = 126/294 (42%), Gaps = 55/294 (18%)

Query: 94  QQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDL 153
           ++ S  ++++ + Y  D    PI  GL+D R+G       C TCG++   C GHFG+I+L
Sbjct: 24  REMSATKVITADTY--DDDGFPIDMGLMDPRLGVIDPGLECKTCGKHSGSCNGHFGHIEL 81

Query: 154 PLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKL-RNPALSYLVRKSLKKK 212
             PV H+G+ + +  +L+  C++  C+R+ L E +   F  +L R   L   +    K  
Sbjct: 82  AAPVIHVGFAKLIRRLLRGTCRD--CSRLCLDEHEREEFDDRLTRTQDLGRDLNDVTKAA 139

Query: 213 ILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVED----LLAEYNEAV 268
           I +  KK   CP CGE            I HEK     + +D +  D    + A   EA 
Sbjct: 140 IRQARKK-DRCPFCGEKQ--------YDIKHEKPTTYYEVQDVLASDYPERIAAAMEEAE 190

Query: 269 -------------------------KFNPEIEAHKKFGL----------IQTLNPLEVLQ 293
                                    +F P  E  +              +  L P ++  
Sbjct: 191 DPISPIDLSEETGIDSSRVQEILSGEFRPRQEDRRALEKALSVDLTEEDMNKLMPSDIRD 250

Query: 294 LFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDNDVV 345
            FE IP +DI +L M    S+P  +ILT L VPP   RPS+  D   +S++D+ 
Sbjct: 251 WFEDIPDQDIEVLGMKPARSRPEWMILTVLPVPPVTARPSITLDNGQRSEDDLT 304



 Score = 87.4 bits (215), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 37/58 (63%), Positives = 47/58 (81%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
             GFV+ S+ SGL P EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 831 AHGFVEASYRSGLGPKEFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELETQYD 888



 Score = 46.2 bits (108), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 29/46 (63%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 65
           +VLM  +  +++PR GE +I A QD I+G YLLT  N  FN  Q +
Sbjct: 544 RVLMRVQEQMLSPRFGENIIGAIQDHISGTYLLTHTNPKFNETQAL 589


>gi|21280521|gb|AAM45153.1|AF395835_1 RNA polymerase II largest subunit [Cercomonas ATCC50319]
          Length = 1014

 Score =  156 bits (395), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 90/268 (33%), Positives = 141/268 (52%), Gaps = 34/268 (12%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D DV+LFNRQPSLHK+SIMAH+ +V+P  TFR N    TPYNADFDGDEMN+H+PQ+   
Sbjct: 368 DGDVILFNRQPSLHKMSIMAHKIRVMPWSTFRLNLSCTTPYNADFDGDEMNLHVPQSMMT 427

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAEAL               +M     +V+P+  + +I   QD + G    T ++ F ++
Sbjct: 428 RAEALE--------------IMLCPRQIVSPQANKPVIGIVQDTLLGCMKFTYRDNFLDK 473

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPV-VFVRTAVIWTGKQIFSLILKPNRDCPV 519
           A    I             ++   +W    P+   ++   +W+GKQIFSLI+       V
Sbjct: 474 AMVFNI-------------LMHLENWDGTVPIPCILKPVPLWSGKQIFSLIIP-----RV 515

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           N   K  G   + +      D+ V +   +LL G +DK T+G+    ++ +++  + G +
Sbjct: 516 NMERKANGHPDSEHTVMSVNDTRVRIEQGQLLMGVVDKQTVGN-TPGSLIHVIWNECGFE 574

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
                +    ++ +++LM+ GFS+GIGD
Sbjct: 575 ATRQFLAECQKVVNYFLMHYGFSVGIGD 602



 Score =  104 bits (260), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 45/66 (68%), Positives = 57/66 (86%), Gaps = 1/66 (1%)

Query: 606 GDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
           GD++P  +GFV NS+  GLTP EFFFH MGGREGL+DTAVKTAETGY+QRRLVK++ED+ 
Sbjct: 724 GDLSPESKGFVSNSYLQGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKAMEDVM 783

Query: 665 VQYDMS 670
           ++YD +
Sbjct: 784 IKYDAT 789



 Score = 43.5 bits (101), Expect = 0.87,   Method: Compositional matrix adjust.
 Identities = 39/180 (21%), Positives = 80/180 (44%), Gaps = 25/180 (13%)

Query: 144 CVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFR-AKLRNPALS 202
           C GHFG+++L  PV H+ +   ++ +L+ +C +  C+ + +  +       A+++NP   
Sbjct: 1   CPGHFGHLELAKPVIHVSFLPTILKLLRCVCYH--CSALXVSRDNRRFLEAARVKNP--- 55

Query: 203 YLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLA 262
                  KK++      + VC    +  G ++   L  +  E+     KK+      L  
Sbjct: 56  -------KKRL---NAMLEVCRTAKDCGGGLE---LDPVDGERPAEEKKKRTGCGSTLPT 102

Query: 263 EYNEAVKFNPEIEAHKKF---GLI---QTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPS 316
              + +K   E  A+ +F   G +   + L+P ++  +F  I  ED+  L ++   + PS
Sbjct: 103 YRRDGIKIIVEFPANTEFEDAGSVDRKKNLSPQKIYDIFRNITDEDMTALGLDPVNAHPS 162


>gi|397135878|gb|AFO11434.1| RNA polymerase I, partial [Wickerhamia fluorescens]
          Length = 872

 Score =  156 bits (395), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 89/267 (33%), Positives = 146/267 (54%), Gaps = 36/267 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           DND VLFNRQPSLHK+S+MAHR KV+P+ TFR N  V +PYNADFDGDEMN+H+PQ+ E 
Sbjct: 251 DNDPVLFNRQPSLHKMSMMAHRVKVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSPET 310

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R+E                 + A    +V+P++ + ++   QD + G   +T ++ F   
Sbjct: 311 RSE--------------LSQICAVPLQIVSPQSNKPVMGIVQDTLCGVRKMTLRDIFIEY 356

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M     ++    D  G+I         P   ++   +WTGKQ+ S+ +      P  
Sbjct: 357 DQVM----NMLYWIPDWDGVIP--------PPAVIKPKPMWTGKQLLSMAI------PKG 398

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            +L+   R     +    +D+ +++ + E++ G +DK T+G+ G   + + ++R+ G  V
Sbjct: 399 IHLQ---RFDGGKDMLSPKDTGMLIVDGEIMFGVVDKKTVGATG-GGLIHTVMREKGPYV 454

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGD 607
                 R+ ++ +++L++ GFSIGIGD
Sbjct: 455 CAQLFSRIQKVVNYWLLHNGFSIGIGD 481



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 45/63 (71%), Positives = 53/63 (84%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTP EFFFH M GREGL+DTAVKTAETGY+QRRLVK+LED+ V
Sbjct: 604 DYSPESKGFVENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDIMV 663

Query: 666 QYD 668
            YD
Sbjct: 664 HYD 666


>gi|413915230|gb|AFW21477.1| RNA polymerase II largest subunit [Epichloe festucae]
          Length = 1756

 Score =  156 bits (395), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 86/276 (31%), Positives = 153/276 (55%), Gaps = 32/276 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D ++FNRQPSLHK S+M HR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 450 DGDYIIFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 509

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE               K L    +N+V+P+    L+   QD + G Y L +++ F ++
Sbjct: 510 RAE--------------VKELCLVPNNIVSPQKNGPLMGVVQDSLAGAYKLCRRDTFIDK 555

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              M     ++    +  G+I +       P + ++    WTGKQ+ S+++   ++  ++
Sbjct: 556 EMVM----NMMLWVPNWDGVIPQ-------PAI-LKPRPRWTGKQLISMVIP--KEISLH 601

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           +   + G+    N +   +D+ +++++ ELL G + K  +GS     + ++   + G + 
Sbjct: 602 SPESSGGQ---DNADIPLKDTGLLIQSGELLYGLLKKKNIGSAA-GGIVHLSYNELGPEG 657

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           A+  +  + ++ +++L+N G SIGIGD  P +  ++
Sbjct: 658 AMAFLNGVQQVVTYWLLNNGHSIGIGDTVPDKQTIE 693



 Score =  106 bits (264), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 79/283 (27%), Positives = 136/283 (48%), Gaps = 39/283 (13%)

Query: 1146 EVCEYIEEVF-VPDDS--------FILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGH 1196
            E  + +E  F +PDDS          L+++ +DR +LL  E+ ID +   I+        
Sbjct: 1181 EDMDMVESYFLIPDDSQDTTDQQSRWLLRITLDRQKLLDKEIKIDDVAQRIKEEYPSDLA 1240

Query: 1197 LTVSGHSF---LIL---------KPKDSSKSFNSKMYQMK---QLLPSVVIKGVQGINRA 1241
            +  S ++    +I          K +D  K     +   +    LL ++ ++GV G+ RA
Sbjct: 1241 IIFSDNNADEQVIRIRTIRTDNEKDEDGEKKIEDDVMLKRLEAHLLDTLTLRGVPGVERA 1300

Query: 1242 V---------------IHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVY 1286
                            I ++D +  T++ L   G  LRDV+A  GV   +  +N+ +++ 
Sbjct: 1301 FLTKGTRLVVDDDGAEIAKKDDDKCTQWYLDTSGSALRDVLAVDGVDPTRTYTNDLWQIV 1360

Query: 1287 KTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESV 1346
            +  GIEAARS ++ E+  V+   G  ++ RH  L+ D+MT +G +  +TRHG+ +     
Sbjct: 1361 EVFGIEAARSALVKELTNVLAFDGSYVNHRHIALLVDVMTYRGTISAVTRHGINRADTGA 1420

Query: 1347 LNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
            L   SFE T + L +AA  G+ D   G+SE +++G    +GTG
Sbjct: 1421 LMRCSFEETVEILLEAAASGELDDCRGISENVMLGQLAPMGTG 1463



 Score =  103 bits (256), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 46/63 (73%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QRRLVK+LEDL  
Sbjct: 807 DYSPEARGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDLSA 866

Query: 666 QYD 668
           +YD
Sbjct: 867 RYD 869



 Score = 85.5 bits (210), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 75/296 (25%), Positives = 134/296 (45%), Gaps = 68/296 (22%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKD-------------------------TDLDYARI 798
            GVPR+KEI+N +++I TP +  YL+                           T++ Y   
Sbjct: 1114 GVPRLKEILNLAKDIKTPSMAVYLNTHLGTQEQAKKLRSLVEYTNLRSITSVTEIYYDPD 1173

Query: 799  VKGRLERTTLGEVCEYIEEVF-VPDDS--------FILIKLDMDRIRLLHLEVDIDSIRY 849
            ++G    T++ E  + +E  F +PDDS          L+++ +DR +LL  E+ ID +  
Sbjct: 1174 IQG----TSIVEDMDMVESYFLIPDDSQDTTDQQSRWLLRITLDRQKLLDKEIKIDDVAQ 1229

Query: 850  CIERTRGISGHLTVSGHSF---LIL---------KPKDSSKSFNSKMYQMK---QLLPSV 894
             I+        +  S ++    +I          K +D  K     +   +    LL ++
Sbjct: 1230 RIKEEYPSDLAIIFSDNNADEQVIRIRTIRTDNEKDEDGEKKIEDDVMLKRLEAHLLDTL 1289

Query: 895  VIKGVQGINRAV---------------IHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
             ++GV G+ RA                I ++D +  T++ L   G  LRDV+A  GV   
Sbjct: 1290 TLRGVPGVERAFLTKGTRLVVDDDGAEIAKKDDDKCTQWYLDTSGSALRDVLAVDGVDPT 1349

Query: 940  KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            +  +N+ +++ +  GIEAARS ++ E+  V+   G  ++ RH  L+ D+MT +G +
Sbjct: 1350 RTYTNDLWQIVEVFGIEAARSALVKELTNVLAFDGSYVNHRHIALLVDVMTYRGTI 1405



 Score = 67.0 bits (162), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 61/221 (27%), Positives = 101/221 (45%), Gaps = 27/221 (12%)

Query: 110 DPQRT-PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVIN 168
           D  RT P   GL D  +G+  +   C TC Q +SDC GHFG+I+L  PV+H G+ + V  
Sbjct: 44  DETRTKPRDGGLNDPLLGSIDRGLKCKTCTQAMSDCPGHFGHIELAKPVYHPGFIKKVKK 103

Query: 169 ILQSICKNPTCARVLLGEE-----KAAGFR-AKLRNPALSYLVRKSLKKKILETTKK--V 220
           IL+ +C N  C++VL          A   R AKLR   +  + +K  + +  + T+K   
Sbjct: 104 ILEIVCHN--CSKVLADTSDPEFVSAIQTRDAKLRFNRVWAVCKKKRRCENEDRTEKNDE 161

Query: 221 SVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKF 280
              P    +      CG ++    +   + K    +V++   +  E V   PE+ AH   
Sbjct: 162 EFAPGMKPLVNNHGGCGNVQPQVRQAALQLKAAFDVVQEDGPKRRETVPITPEM-AHG-- 218

Query: 281 GLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
                        + + I  ED+  + +N++ ++P  LI+T
Sbjct: 219 -------------ILKRISEEDLRRMGLNSDYARPEWLIIT 246



 Score = 55.5 bits (132), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/39 (61%), Positives = 29/39 (74%)

Query: 1107 REKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            + ++ R+ + P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1067 QNRWDRSFVSPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1105


>gi|1143740|gb|AAB50025.1| RNA polymerase II [Trichomonas vaginalis]
          Length = 1661

 Score =  156 bits (395), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 86/267 (32%), Positives = 142/267 (53%), Gaps = 31/267 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D+D+V+FNRQPSLHK+S+M HRA ++  RTFR N C  TPYNADFDGDEMN+H+PQ++ A
Sbjct: 451 DDDIVIFNRQPSLHKMSMMGHRALIMSGRTFRLNPCDTTPYNADFDGDEMNLHVPQSQTA 510

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           R E               + +MA    +++P+  + +I   QD + G  LL++++ F  R
Sbjct: 511 RTE--------------VRHIMAVPKQIISPQANKPVIGLVQDALLGCRLLSKRDTFLTR 556

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M +   L      I             P   ++   +W+GKQ+FSL L       ++
Sbjct: 557 NQVMNLMMWLPTTKDTILP-----------PPCILKPVQLWSGKQVFSLFLP-----KIS 600

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
            N  ++             D +VI+R+  LLAG + K T+    + ++ ++++  +  ++
Sbjct: 601 HNSYSQDANKMDQNSIPLADRHVIIRDGNLLAGILGKKTVAR-SEGSLIHVVINSYNTNI 659

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGD 607
           A   + +   + + +L +RGFSIG+ D
Sbjct: 660 AKDFLNQTQLIVNNWLEHRGFSIGLID 686



 Score =  115 bits (289), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 90/317 (28%), Positives = 155/317 (48%), Gaps = 38/317 (11%)

Query: 1109 KYVRAQIEPATAVGAL----------AAQSIGEPGTQMTLKTFHFAGEVCEYIEEVFVPD 1158
            K VRAQIE A+    +            ++I EP T+       + G     +E+  + D
Sbjct: 1152 KAVRAQIESASFKKFVIKAEIYYDPNPEETIIEPDTKWINTRIRYGG-----VEDRELQD 1206

Query: 1159 DSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGH--LTVSGHSFLILKP----KDS 1212
             +  +++ +++R  ++    +I+SI   +++ +G+ G     +      I++     KD 
Sbjct: 1207 LAPWVLRFEINREEMI--ASNIESISDIVQKIKGMYGDKFFVIGDDDARIIRMQARLKDE 1264

Query: 1213 SKSFNSKMYQMK----QLLPSVVIKGVQGINRAVIHEE--------DVEGVTKYK---LL 1257
               F   +  ++    Q+  S  +KG+ GI+R  I+          +  G  K K   L 
Sbjct: 1265 QAEFAMDVKFLRETEQQMYKSFTLKGIPGISRVKINSAAEKMFLNPETHGFDKEKVSCLY 1324

Query: 1258 VEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRH 1317
             EG   R++++   V  V   +N+ Y+V   LGIEAAR ++  E+ L+ME  G +++ RH
Sbjct: 1325 TEGTAFREILSLDHVDTVHTITNDIYQVCDVLGIEAARHSLSYEMMLIMEKAGAALNRRH 1384

Query: 1318 PMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSEC 1377
              L+AD MT  G +  ++RHG+ K     L  AS+E T+D  FDAA + + D +  VS  
Sbjct: 1385 LDLLADTMTQYGVLYPVSRHGINKTPTGTLMRASYEMTNDVFFDAAVFSEIDYMRDVSSN 1444

Query: 1378 IIMGLPMNVGTGLIKLL 1394
            II G P   GTG++++L
Sbjct: 1445 IIAGKPSRAGTGIVEVL 1461



 Score = 94.0 bits (232), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 77/246 (31%), Positives = 109/246 (44%), Gaps = 51/246 (20%)

Query: 119 GLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPT 178
           GL D RMGT  +E  C TCG+N  DC GHFGYI L  P FH+G+      +LQ +C    
Sbjct: 50  GLSDLRMGTQTRERLCDTCGRNQEDCPGHFGYIRLAEPFFHVGFLPHCYKLLQMVCHK-- 107

Query: 179 CARVLLGEEKAAGFRAKLRNPALSYLV-RKSLKKKILETTKKVSVCPHCGEINGVVKKCG 237
           C RVL              +P + Y+V     K + L+  +K++             K G
Sbjct: 108 CGRVL----------CSYSDPEIQYIVTHYKGKNRFLKLFEKIA------------SKSG 145

Query: 238 LLKISHEKYKNRTKKKDAIVEDLLAE------YNEAVKFN-------PEIEAHKKFGLIQ 284
             K  H        + D  +++   E      ++E V+         P IE  K F LI+
Sbjct: 146 --KCQHSPDLKNPNEPDVCLDERFWELVNGDSHSEHVRVKKPCNAAVPAIEQGKDF-LIK 202

Query: 285 T----------LNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSV 334
                      L+   VL++FE I  +D+ LL  N + S P  +IL  L VPP  +RP V
Sbjct: 203 LKDVSKTEEDYLSAEVVLRIFENISDQDVRLLGFNPKRSHPKWMILKILPVPPLAVRPQV 262

Query: 335 ISDLKS 340
           +S  +S
Sbjct: 263 VSPGQS 268



 Score = 85.5 bits (210), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 36/57 (63%), Positives = 46/57 (80%)

Query: 612 QGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
           +GF +NS+ +GLTP EF FH MGGR G++DTA KT++TGY+QRRLVKS+E   V YD
Sbjct: 815 RGFCKNSYIAGLTPPEFLFHAMGGRTGIIDTACKTSDTGYIQRRLVKSMESHHVAYD 871



 Score = 82.0 bits (201), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 72/280 (25%), Positives = 128/280 (45%), Gaps = 50/280 (17%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
            GVPR+ E++N +++I TP +T   ++D   D +  + V+ ++E  +  +     E  + P
Sbjct: 1117 GVPRLNELMNLAKHIRTPSVTVEFERDVAKDEEIVKAVRAQIESASFKKFVIKAEIYYDP 1176

Query: 822  DDSFILIKLDMD----RIR---------------LLHLEVD--------IDSIRYCIERT 854
            +    +I+ D      RIR               +L  E++        I+SI   +++ 
Sbjct: 1177 NPEETIIEPDTKWINTRIRYGGVEDRELQDLAPWVLRFEINREEMIASNIESISDIVQKI 1236

Query: 855  RGISGH--LTVSGHSFLILKP----KDSSKSFNSKMYQMK----QLLPSVVIKGVQGINR 904
            +G+ G     +      I++     KD    F   +  ++    Q+  S  +KG+ GI+R
Sbjct: 1237 KGMYGDKFFVIGDDDARIIRMQARLKDEQAEFAMDVKFLRETEQQMYKSFTLKGIPGISR 1296

Query: 905  AVIHEE--------DVEGVTKYK---LLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTL 953
              I+          +  G  K K   L  EG   R++++   V  V   +N+ Y+V   L
Sbjct: 1297 VKINSAAEKMFLNPETHGFDKEKVSCLYTEGTAFREILSLDHVDTVHTITNDIYQVCDVL 1356

Query: 954  GIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
            GIEAAR ++  E+ L+ME  G +++ RH  L+AD MT  G
Sbjct: 1357 GIEAARHSLSYEMMLIMEKAGAALNRRHLDLLADTMTQYG 1396



 Score = 55.5 bits (132), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/41 (53%), Positives = 30/41 (73%)

Query: 1105 ACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            + ++++ R+ + P   VG +A QSIGEP TQMTL TFHFAG
Sbjct: 1068 SIKDRFYRSIVAPGEMVGTIAGQSIGEPSTQMTLNTFHFAG 1108


>gi|448680460|ref|ZP_21690777.1| DNA-directed RNA polymerase subunit A' [Haloarcula argentinensis
           DSM 12282]
 gi|445768904|gb|EMA19981.1| DNA-directed RNA polymerase subunit A' [Haloarcula argentinensis
           DSM 12282]
          Length = 969

 Score =  156 bits (395), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 93/268 (34%), Positives = 140/268 (52%), Gaps = 45/268 (16%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D+++FNRQPSLH++SIMAH   V+P++TFR N  VC PYNADFDGDEMN+H  Q EEA
Sbjct: 480 DGDIIIFNRQPSLHRMSIMAHEVVVMPYKTFRLNTTVCPPYNADFDGDEMNMHALQNEEA 539

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE              A+VLM  +  +++PR GE +I A QD I+G YLLT  N  FN 
Sbjct: 540 RAE--------------ARVLMRVQEQMLSPRFGENIIGAIQDHISGTYLLTHTNPKFNE 585

Query: 461 AQTMR-IASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
            Q +  + +T I +  +  G+ +                  WTG+ +FS +L      P 
Sbjct: 586 TQALDLLRATRIDELPEADGVDE-------------NGEEYWTGRSLFSELL------PD 626

Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
           + NL+    A             V++ + ++  G++D+  +G+ G   +   + +D+   
Sbjct: 627 DLNLEFTSSAGDT----------VVVEDGQMTGGTIDEDAVGAFG-GEIVDTIAKDYSRT 675

Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGD 607
            A   +  +S +    +M+ GFSI I D
Sbjct: 676 RARILVNEVSALAMRSIMHFGFSISIDD 703



 Score =  106 bits (264), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 82/294 (27%), Positives = 125/294 (42%), Gaps = 55/294 (18%)

Query: 94  QQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDL 153
           ++ S  ++++ + Y  D    PI  GL+D R+G       C TCG++   C GHFG+I+L
Sbjct: 24  REMSATKVITADTY--DDDGFPIDMGLMDPRLGVIDPGLECKTCGKHSGSCNGHFGHIEL 81

Query: 154 PLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKL-RNPALSYLVRKSLKKK 212
             PV H+G+ + +  +L+  C+   C+R+ L E +   F  +L R   L   +    K  
Sbjct: 82  AAPVIHVGFAKLIRRLLRGTCRE--CSRLCLDEHERDEFADRLTRTQDLGRDLNDVTKAA 139

Query: 213 ILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDL-------LAEYN 265
           I +  KK   CP CGE            I HEK     + +D +  D        + E  
Sbjct: 140 IRQARKK-DRCPFCGEKQ--------YDIKHEKPTTYYEVQDVLASDYPERIAAAMEESE 190

Query: 266 EAV----------------------KFNPEIEAHKKFGL----------IQTLNPLEVLQ 293
           E +                      +F P  E  K              +  L P ++  
Sbjct: 191 EPISPIELSEETGIDSSRVQEILSGEFRPRQEDRKALEKALSVDLTEEDMNKLMPSDIRD 250

Query: 294 LFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD--LKSDNDVV 345
            FE IP EDI +L M    S+P  +ILT L VPP   RPS+  D   +S++D+ 
Sbjct: 251 WFEDIPDEDIEVLGMKPARSRPEWMILTVLPVPPVTARPSITLDNGQRSEDDLT 304



 Score = 87.4 bits (215), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 37/58 (63%), Positives = 47/58 (81%)

Query: 611 GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
             GFV+ S+ SGL P EFFFH MGGREGLVDTAV+T+++GY+QRRL+ +L +L  QYD
Sbjct: 831 AHGFVEASYRSGLGPKEFFFHAMGGREGLVDTAVRTSKSGYLQRRLINALSELETQYD 888



 Score = 46.2 bits (108), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 29/46 (63%)

Query: 20  QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTM 65
           +VLM  +  +++PR GE +I A QD I+G YLLT  N  FN  Q +
Sbjct: 544 RVLMRVQEQMLSPRFGENIIGAIQDHISGTYLLTHTNPKFNETQAL 589


>gi|358390960|gb|EHK40365.1| hypothetical protein TRIATDRAFT_89498 [Trichoderma atroviride IMI
           206040]
          Length = 1756

 Score =  156 bits (395), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 90/276 (32%), Positives = 148/276 (53%), Gaps = 37/276 (13%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D ++FNRQPSLHK S+M HR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 452 DGDYIIFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 511

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE               K L    +N+V+P+    L+   QD + G Y + +++ F ++
Sbjct: 512 RAE--------------VKELCLVPNNIVSPQKNGPLMGIVQDSLAGAYKICRRDTFLDK 557

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
            Q M     L+    +  GII +       P + ++    WTGKQI S+++   ++  +N
Sbjct: 558 NQVM----NLMLWVPNWDGIIPQ-------PAI-LKPRPRWTGKQIISMVIP--KEISLN 603

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           A                  D+ ++++  EL+ G M K ++GS     V ++   + G + 
Sbjct: 604 APEDKADNPLN--------DTGLLIQAGELMYGLMKKKSIGS-ASGGVIHLCYNELGPEG 654

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           A+  +  + ++T+++L+  G SIGIGD  P +  ++
Sbjct: 655 AMAFLNGVQQVTAYWLLQEGHSIGIGDTIPDKQTIE 690



 Score =  103 bits (256), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 46/63 (73%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTP+EFFFH M GREGL+DTAVKTAETGY+QRRLVK+LEDL  
Sbjct: 804 DYSPEARGFVENSYLRGLTPSEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDLNA 863

Query: 666 QYD 668
           QYD
Sbjct: 864 QYD 866



 Score =  100 bits (250), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 74/283 (26%), Positives = 133/283 (46%), Gaps = 39/283 (13%)

Query: 1146 EVCEYIEEVF-VPDD--------SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGH 1196
            E  + +E  F +PDD        S  L+++ +DR +LL  E+ ID +   I+        
Sbjct: 1178 EDVDMVESYFLIPDDTQDTIDQQSRWLLRITLDRQKLLDKEIKIDDVAQRIKEEYPNDLA 1237

Query: 1197 LTVSGHS-------FLILKPKDSSKSFNSKMYQ--------MKQLLPSVVIKGVQGINRA 1241
            +  S ++          ++  D       K  +           LL ++ ++GV G+ +A
Sbjct: 1238 VIFSDNNADEQVIRIRTIRAGDEKNDDGEKKIEDDVMLKRLEAHLLDTLTLRGVPGVEKA 1297

Query: 1242 VIHE-----EDVEG----------VTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVY 1286
             + +     E  +G           T++ L   G  LR+V+A  GV  ++  +N+ ++V 
Sbjct: 1298 FLTKGTRLVEAADGSELALKDDPRCTQWYLDTSGSALREVLAVPGVDPIRTYTNDLWQVV 1357

Query: 1287 KTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESV 1346
            +  GIE AR+ ++ E+  V+   G  ++ RH  L+ D+MT +G +  +TRHG+ +     
Sbjct: 1358 EVFGIEGARAALVKELTAVLAFDGSYVNHRHIALLCDVMTYRGSISAVTRHGINRADTGA 1417

Query: 1347 LNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
            L   SFE T + L +AA  G+ D   G+SE +++G    +GTG
Sbjct: 1418 LMRCSFEETVEILLEAAATGELDDCRGISENVMLGQMAPMGTG 1460



 Score = 84.0 bits (206), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 72/292 (24%), Positives = 131/292 (44%), Gaps = 60/292 (20%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKD-TDLDYARIVKGRLE------------------ 804
            GVPR+KEI+N ++NI TP +  YLD      + A+ ++  +E                  
Sbjct: 1111 GVPRLKEILNLAKNIKTPGMAVYLDTPLAKQEQAKKLRSLVEYTNLRSITSVTEIYYDPD 1170

Query: 805  --RTTLGEVCEYIEEVF-VPDD--------SFILIKLDMDRIRLLHLEVDIDSIRYCIER 853
               TT+ E  + +E  F +PDD        S  L+++ +DR +LL  E+ ID +   I+ 
Sbjct: 1171 VQSTTIVEDVDMVESYFLIPDDTQDTIDQQSRWLLRITLDRQKLLDKEIKIDDVAQRIKE 1230

Query: 854  TRGISGHLTVSGHS-------FLILKPKDSSKSFNSKMYQ--------MKQLLPSVVIKG 898
                   +  S ++          ++  D       K  +           LL ++ ++G
Sbjct: 1231 EYPNDLAVIFSDNNADEQVIRIRTIRAGDEKNDDGEKKIEDDVMLKRLEAHLLDTLTLRG 1290

Query: 899  VQGINRAVIHE-----EDVEG----------VTKYKLLVEGDNLRDVMATYGVKGVKCSS 943
            V G+ +A + +     E  +G           T++ L   G  LR+V+A  GV  ++  +
Sbjct: 1291 VPGVEKAFLTKGTRLVEAADGSELALKDDPRCTQWYLDTSGSALREVLAVPGVDPIRTYT 1350

Query: 944  NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            N+ ++V +  GIE AR+ ++ E+  V+   G  ++ RH  L+ D+MT +G +
Sbjct: 1351 NDLWQVVEVFGIEGARAALVKELTAVLAFDGSYVNHRHIALLCDVMTYRGSI 1402



 Score = 65.5 bits (158), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 29/72 (40%), Positives = 44/72 (61%), Gaps = 2/72 (2%)

Query: 115 PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSIC 174
           P   GL D  +G+  ++  C TC Q + +C GHFG+I+L  PV+H G+ + V  IL+ +C
Sbjct: 50  PRDGGLNDPLLGSIDRQFKCKTCTQAMGECPGHFGHIELAKPVYHPGFIKKVKKILEIVC 109

Query: 175 KNPTCARVLLGE 186
            N  C++VL  E
Sbjct: 110 HN--CSKVLADE 119



 Score = 55.5 bits (132), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/39 (61%), Positives = 29/39 (74%)

Query: 1107 REKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            + ++ R+ + P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1064 QNRWDRSFVNPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1102


>gi|413915226|gb|AFW21475.1| RNA polymerase II largest subunit [Epichloe amarillans]
          Length = 1752

 Score =  156 bits (395), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 86/276 (31%), Positives = 153/276 (55%), Gaps = 32/276 (11%)

Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
           D D ++FNRQPSLHK S+M HR +V+P+ TFR N  V +PYNADFDGDEMN+H+PQ+EE 
Sbjct: 450 DGDYIIFNRQPSLHKESMMGHRVRVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 509

Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
           RAE               K L    +N+V+P+    L+   QD + G Y L +++ F ++
Sbjct: 510 RAE--------------VKELCLVPNNIVSPQKNGPLMGVVQDSLAGAYKLCRRDTFVDK 555

Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
              M     ++    +  G+I +       P + ++    WTGKQ+ S+++   ++  ++
Sbjct: 556 EMVM----NMMLWVPNWDGVIPQ-------PAI-LKPRPRWTGKQLISMVIP--KEISLH 601

Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
           +   + G+    N +   +D+ +++++ ELL G + K  +GS     + ++   + G + 
Sbjct: 602 SPESSGGQ---DNADIPLKDTGLLIQSGELLYGLLKKKNIGSAA-GGIVHLSYNELGPEG 657

Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGDVTPGQGFVQ 616
           A+  +  + ++ +++L+N G SIGIGD  P +  ++
Sbjct: 658 AMAFLNGVQQVVTYWLLNNGHSIGIGDTVPDKQTIE 693



 Score =  106 bits (264), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 79/283 (27%), Positives = 136/283 (48%), Gaps = 39/283 (13%)

Query: 1146 EVCEYIEEVF-VPDDS--------FILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGH 1196
            E  + +E  F +PDDS          L+++ +DR +LL  E+ ID +   I+        
Sbjct: 1181 EDMDMVESYFLIPDDSQDTTDQQSRWLLRITLDRQKLLDKEIKIDDVAQRIKEEYPSDLA 1240

Query: 1197 LTVSGHSF---LIL---------KPKDSSKSFNSKMYQMK---QLLPSVVIKGVQGINRA 1241
            +  S ++    +I          K +D  K     +   +    LL ++ ++GV G+ RA
Sbjct: 1241 IIFSDNNADEQVIRIRTIRTDNEKDEDGEKKIEDDVMLKRLEAHLLDTLTLRGVPGVERA 1300

Query: 1242 V---------------IHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVY 1286
                            I ++D +  T++ L   G  LRDV+A  GV   +  +N+ +++ 
Sbjct: 1301 FLTKGTRLVVDDDGAEIAKKDDDKCTQWYLDTSGSALRDVLAVDGVDPTRTYTNDLWQIV 1360

Query: 1287 KTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESV 1346
            +  GIEAARS ++ E+  V+   G  ++ RH  L+ D+MT +G +  +TRHG+ +     
Sbjct: 1361 EVFGIEAARSALVKELTNVLAFDGSYVNHRHIALLVDVMTYRGTISAVTRHGINRADTGA 1420

Query: 1347 LNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
            L   SFE T + L +AA  G+ D   G+SE +++G    +GTG
Sbjct: 1421 LMRCSFEETVEILLEAAASGELDDCRGISENVMLGQLAPMGTG 1463



 Score =  103 bits (256), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 46/63 (73%), Positives = 54/63 (85%), Gaps = 1/63 (1%)

Query: 607 DVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
           D +P  +GFV+NS+  GLTPTEFFFH M GREGL+DTAVKTAETGY+QRRLVK+LEDL  
Sbjct: 807 DYSPEARGFVENSYLRGLTPTEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDLSA 866

Query: 666 QYD 668
           +YD
Sbjct: 867 RYD 869



 Score = 85.5 bits (210), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 75/296 (25%), Positives = 134/296 (45%), Gaps = 68/296 (22%)

Query: 764  GVPRIKEIINASRNISTPIITAYLDKD-------------------------TDLDYARI 798
            GVPR+KEI+N +++I TP +  YL+                           T++ Y   
Sbjct: 1114 GVPRLKEILNLAKDIKTPSMAVYLNTHLGTQEQAKKLRSLVEYTNLRSITSVTEIYYDPD 1173

Query: 799  VKGRLERTTLGEVCEYIEEVF-VPDDS--------FILIKLDMDRIRLLHLEVDIDSIRY 849
            ++G    T++ E  + +E  F +PDDS          L+++ +DR +LL  E+ ID +  
Sbjct: 1174 IQG----TSIVEDMDMVESYFLIPDDSQDTTDQQSRWLLRITLDRQKLLDKEIKIDDVAQ 1229

Query: 850  CIERTRGISGHLTVSGHSF---LIL---------KPKDSSKSFNSKMYQMK---QLLPSV 894
             I+        +  S ++    +I          K +D  K     +   +    LL ++
Sbjct: 1230 RIKEEYPSDLAIIFSDNNADEQVIRIRTIRTDNEKDEDGEKKIEDDVMLKRLEAHLLDTL 1289

Query: 895  VIKGVQGINRAV---------------IHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
             ++GV G+ RA                I ++D +  T++ L   G  LRDV+A  GV   
Sbjct: 1290 TLRGVPGVERAFLTKGTRLVVDDDGAEIAKKDDDKCTQWYLDTSGSALRDVLAVDGVDPT 1349

Query: 940  KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
            +  +N+ +++ +  GIEAARS ++ E+  V+   G  ++ RH  L+ D+MT +G +
Sbjct: 1350 RTYTNDLWQIVEVFGIEAARSALVKELTNVLAFDGSYVNHRHIALLVDVMTYRGTI 1405



 Score = 67.4 bits (163), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 61/221 (27%), Positives = 101/221 (45%), Gaps = 27/221 (12%)

Query: 110 DPQRT-PIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVIN 168
           D  RT P   GL D  +G+  +   C TC Q +SDC GHFG+I+L  PV+H G+ + V  
Sbjct: 44  DETRTKPRDGGLNDPLLGSIDRGLKCKTCTQAMSDCPGHFGHIELAKPVYHPGFIKKVKK 103

Query: 169 ILQSICKNPTCARVLLGEE-----KAAGFR-AKLRNPALSYLVRKSLKKKILETTKK--V 220
           IL+ +C N  C++VL          A   R AKLR   +  + +K  + +  + T+K   
Sbjct: 104 ILEIVCHN--CSKVLADTSDPEFVSAIQTRDAKLRFNRVWAVCKKKRRCENEDRTEKNDE 161

Query: 221 SVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKF 280
              P    +      CG ++    +   + K    +V++   +  E V   PE+ AH   
Sbjct: 162 EFAPGMKPVVNNHGGCGNVQPQVRQAALQLKAAFDVVQEDGPKRRETVPITPEM-AHG-- 218

Query: 281 GLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILT 321
                        + + I  ED+  + +N++ ++P  LI+T
Sbjct: 219 -------------ILKRISEEDLRQMGLNSDYARPEWLIIT 246



 Score = 55.5 bits (132), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/39 (61%), Positives = 29/39 (74%)

Query: 1107 REKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
            + ++ R+ + P   VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1067 QNRWDRSFVSPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1105


  Database: nr
    Posted date:  Mar 3, 2013 10:45 PM
  Number of letters in database: 999,999,864
  Number of sequences in database:  2,912,245
  
  Database: /local_scratch/syshi//blastdatabase/nr.01
    Posted date:  Mar 3, 2013 10:52 PM
  Number of letters in database: 999,999,666
  Number of sequences in database:  2,912,720
  
  Database: /local_scratch/syshi//blastdatabase/nr.02
    Posted date:  Mar 3, 2013 10:58 PM
  Number of letters in database: 999,999,938
  Number of sequences in database:  3,014,250
  
  Database: /local_scratch/syshi//blastdatabase/nr.03
    Posted date:  Mar 3, 2013 11:03 PM
  Number of letters in database: 999,999,780
  Number of sequences in database:  2,805,020
  
  Database: /local_scratch/syshi//blastdatabase/nr.04
    Posted date:  Mar 3, 2013 11:08 PM
  Number of letters in database: 999,999,551
  Number of sequences in database:  2,816,253
  
  Database: /local_scratch/syshi//blastdatabase/nr.05
    Posted date:  Mar 3, 2013 11:13 PM
  Number of letters in database: 999,999,897
  Number of sequences in database:  2,981,387
  
  Database: /local_scratch/syshi//blastdatabase/nr.06
    Posted date:  Mar 3, 2013 11:18 PM
  Number of letters in database: 999,999,649
  Number of sequences in database:  2,911,476
  
  Database: /local_scratch/syshi//blastdatabase/nr.07
    Posted date:  Mar 3, 2013 11:24 PM
  Number of letters in database: 999,999,452
  Number of sequences in database:  2,920,260
  
  Database: /local_scratch/syshi//blastdatabase/nr.08
    Posted date:  Mar 3, 2013 11:25 PM
  Number of letters in database: 64,230,274
  Number of sequences in database:  189,558
  
Lambda     K      H
   0.320    0.136    0.396 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,466,494,206
Number of Sequences: 23463169
Number of extensions: 904691738
Number of successful extensions: 2198535
Number of sequences better than 100.0: 1000
Number of HSP's better than 100.0 without gapping: 13204
Number of HSP's successfully gapped in prelim test: 1266
Number of HSP's that attempted gapping in prelim test: 2118553
Number of HSP's gapped (non-prelim): 59731
length of query: 1423
length of database: 8,064,228,071
effective HSP length: 156
effective length of query: 1267
effective length of database: 8,698,941,003
effective search space: 11021558250801
effective search space used: 11021558250801
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 84 (37.0 bits)