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: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2PMZ|C Chain C, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|G Chain G, Archaeal Rna Polymerase From Sulfolobus Solfataricus
Length = 392
Score = 175 bits (443), Expect = 2e-43, Method: Compositional matrix adjust.
Identities = 120/374 (32%), Positives = 187/374 (50%), Gaps = 64/374 (17%)
Query: 1072 KVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGE 1131
K+ L+ IL+ + + F A K +Y I P A+G +AAQS+GE
Sbjct: 24 KIVDDLKNLILNKEIIVTRDEIDKIFDLAIK------EYSEGLIAPGEAIGIVAAQSVGE 77
Query: 1132 PGTQMTLKTFHFAG-----------EVCEYIEEVFVPDDSFILIKL----DMDRIRLLHL 1176
PGTQMTL+TFHFAG + E ++ VP + I L DR + L +
Sbjct: 78 PGTQMTLRTFHFAGIRELNVTLGLPRLIEIVDAKKVPSTPMMTIYLTDEYKRDRDKALEV 137
Query: 1177 ----------------EVDIDSIRYCIE------RTRGIS--------GHLTVSGHSFLI 1206
+DI S+ ++ + +G++ G L + F+I
Sbjct: 138 ARKLEYTKIENVVSSTSIDIASMSIILQLDNEMLKDKGVTVDDVKKAIGRLKLG--DFMI 195
Query: 1207 LKPKDSSKSFN-------SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVE 1259
+ +DS+ + N + +++++ + + IKG++GI RA++ ++ E Y +L +
Sbjct: 196 EESEDSTLNINFANIDSIAALFKLRDKILNTKIKGIKGIKRAIVQKKGDE----YIILTD 251
Query: 1260 GDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPM 1319
G NL V++ GV K +NN E+ + GIEAAR I+ EI V+ G+ +D RH +
Sbjct: 252 GSNLSGVLSVKGVDVAKVETNNIREIEEVFGIEAAREIIIREISKVLAEQGLDVDIRHIL 311
Query: 1320 LVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECII 1379
L+AD+MT G V I RHG+ K SVL A+FE T HL DAA G + GV E II
Sbjct: 312 LIADVMTRTGIVRQIGRHGVTGEKNSVLARAAFEVTVKHLLDAAARGDVEEFKGVVENII 371
Query: 1380 MGLPMNVGTGLIKL 1393
+G P+ +GTG+++L
Sbjct: 372 IGHPIKLGTGMVEL 385
Score = 106 bits (265), Expect = 8e-23, 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
Score = 36.6 bits (83), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 2/69 (2%)
Query: 636 REGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAAFYGQTDCISGVSECIIMGLPM 695
R G+V + TG L ++ ++ V++ DAA G + GV E II+G P+
Sbjct: 319 RTGIVRQIGRHGVTGEKNSVLARAAFEVTVKH--LLDAAARGDVEEFKGVVENIIIGHPI 376
Query: 696 NVGTGLIKL 704
+GTG+++L
Sbjct: 377 KLGTGMVEL 385
>pdb|3HKZ|C Chain C, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|M Chain M, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 395
Score = 174 bits (442), Expect = 2e-43, Method: Compositional matrix adjust.
Identities = 120/374 (32%), Positives = 187/374 (50%), Gaps = 64/374 (17%)
Query: 1072 KVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGE 1131
K+ L+ IL+ + + F A K +Y I P A+G +AAQS+GE
Sbjct: 27 KIVDDLKNLILNKEIIVTRDEIDKIFDLAIK------EYSEGLIAPGEAIGIVAAQSVGE 80
Query: 1132 PGTQMTLKTFHFAG-----------EVCEYIEEVFVPDDSFILIKL----DMDRIRLLHL 1176
PGTQMTL+TFHFAG + E ++ VP + I L DR + L +
Sbjct: 81 PGTQMTLRTFHFAGIRELNVTLGLPRLIEIVDAKKVPSTPMMTIYLTDEYKRDRDKALEV 140
Query: 1177 ----------------EVDIDSIRYCIE------RTRGIS--------GHLTVSGHSFLI 1206
+DI S+ ++ + +G++ G L + F+I
Sbjct: 141 ARKLEYTKIENVVSSTSIDIASMSIILQLDNEMLKDKGVTVDDVKKAIGRLKLG--DFMI 198
Query: 1207 LKPKDSSKSFN-------SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVE 1259
+ +DS+ + N + +++++ + + IKG++GI RA++ ++ E Y +L +
Sbjct: 199 EESEDSTLNINFANIDSIAALFKLRDKILNTKIKGIKGIKRAIVQKKGDE----YIILTD 254
Query: 1260 GDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPM 1319
G NL V++ GV K +NN E+ + GIEAAR I+ EI V+ G+ +D RH +
Sbjct: 255 GSNLSGVLSVKGVDVAKVETNNIREIEEVFGIEAAREIIIREISKVLAEQGLDVDIRHIL 314
Query: 1320 LVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECII 1379
L+AD+MT G V I RHG+ K SVL A+FE T HL DAA G + GV E II
Sbjct: 315 LIADVMTRTGIVRQIGRHGVTGEKNSVLARAAFEVTVKHLLDAAARGDVEEFKGVVENII 374
Query: 1380 MGLPMNVGTGLIKL 1393
+G P+ +GTG+++L
Sbjct: 375 IGHPIKLGTGMVEL 388
Score = 106 bits (265), Expect = 8e-23, 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
Score = 36.6 bits (83), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 2/69 (2%)
Query: 636 REGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAAFYGQTDCISGVSECIIMGLPM 695
R G+V + TG L ++ ++ V++ DAA G + GV E II+G P+
Sbjct: 322 RTGIVRQIGRHGVTGEKNSVLARAAFEVTVKH--LLDAAARGDVEEFKGVVENIIIGHPI 379
Query: 696 NVGTGLIKL 704
+GTG+++L
Sbjct: 380 KLGTGMVEL 388
>pdb|2WAQ|C Chain C, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|C Chain C, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|Y Chain Y, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
Length = 395
Score = 167 bits (424), Expect = 3e-41, Method: Compositional matrix adjust.
Identities = 110/338 (32%), Positives = 167/338 (49%), Gaps = 58/338 (17%)
Query: 1108 EKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFV 1156
++Y I P A+G +AAQS+GEPGTQMTL+TFHFAG + E ++ V
Sbjct: 57 KEYSEGLIAPGEAIGIVAAQSVGEPGTQMTLRTFHFAGIRELNVTLGLPRLIEIVDAKKV 116
Query: 1157 PDDSFILI------------------KLDMDRIR---------------LLHLE------ 1177
P + I KL+ +I +L L+
Sbjct: 117 PSTPMMTIYLTDEYKHDKEKALEVARKLEYTKIENVVSSTSIDIASMSIILQLDNEMLKD 176
Query: 1178 --VDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGV 1235
V +D ++ I R + G + L ++ + +++++ + + IKG+
Sbjct: 177 KGVTVDDVKKAINRLK--LGEFVIDESEGTTLNISFANIDSIAALFKLRDKILNTKIKGI 234
Query: 1236 QGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAAR 1295
+GI RA++ ++ E Y +L +G NL V++ GV K +NN E+ + GIEAAR
Sbjct: 235 KGIKRAIVQKKGDE----YIILTDGSNLSGVLSVKGVDIAKVETNNIREIEEVFGIEAAR 290
Query: 1296 STIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENT 1355
I+ EI V+ G+ +D RH +LVAD+MT G V I RHG+ K SVL A+FE T
Sbjct: 291 EIIIREISKVLAEQGLDVDMRHILLVADVMTRTGVVRQIGRHGVTGEKNSVLARAAFEVT 350
Query: 1356 SDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
HL DAA G + GV E II+G P+ +GTG+++L
Sbjct: 351 VKHLLDAAARGDVEEFKGVVENIIIGHPIKLGTGMVEL 388
Score = 103 bits (257), Expect = 7e-22, 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
Score = 36.6 bits (83), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 2/69 (2%)
Query: 636 REGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAAFYGQTDCISGVSECIIMGLPM 695
R G+V + TG L ++ ++ V++ DAA G + GV E II+G P+
Sbjct: 322 RTGVVRQIGRHGVTGEKNSVLARAAFEVTVKH--LLDAAARGDVEEFKGVVENIIIGHPI 379
Query: 696 NVGTGLIKL 704
+GTG+++L
Sbjct: 380 KLGTGMVEL 388
>pdb|2Y0S|C Chain C, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|Y Chain Y, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|C Chain C, Rnap At 3.2ang
pdb|4B1O|C Chain C, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|Y Chain Y, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 395
Score = 167 bits (422), Expect = 6e-41, Method: Compositional matrix adjust.
Identities = 110/338 (32%), Positives = 167/338 (49%), Gaps = 58/338 (17%)
Query: 1108 EKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIEEVFV 1156
++Y I P A+G +AAQS+GEPGTQMTL+TFHFAG + E ++ V
Sbjct: 57 KEYSEGLIAPGEAIGIVAAQSVGEPGTQMTLRTFHFAGIRELNVTLGLPRLIEIVDAKKV 116
Query: 1157 PDDSFILI------------------KLDMDRIR---------------LLHLE------ 1177
P + I KL+ +I +L L+
Sbjct: 117 PSTPMMTIYLTDEYKHDKEKALEVARKLEYTKIENVVSSTSIDIASMSIILQLDNEMLKD 176
Query: 1178 --VDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGV 1235
V +D ++ I R + G + L ++ + +++++ + + IKG+
Sbjct: 177 KGVTVDDVKKAINRLK--LGEFVIDESEGNTLNISFANIDSIAALFKLRDKILNTKIKGI 234
Query: 1236 QGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAAR 1295
+GI RA++ ++ E Y +L +G NL V++ GV K +NN E+ + GIEAAR
Sbjct: 235 KGIKRAIVQKKGDE----YIILTDGSNLSGVLSVKGVDIAKVETNNIREIEEVFGIEAAR 290
Query: 1296 STIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENT 1355
I+ EI V+ G+ +D RH +LVAD+MT G V I RHG+ K SVL A+FE T
Sbjct: 291 EIIIREISKVLAEQGLDVDMRHILLVADVMTRTGVVRQIGRHGVTGEKNSVLARAAFEVT 350
Query: 1356 SDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
HL DAA G + GV E II+G P+ +GTG+++L
Sbjct: 351 VKHLLDAAARGDVEEFKGVVENIIIGHPIKLGTGMVEL 388
Score = 102 bits (254), Expect = 1e-21, 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
Score = 36.6 bits (83), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 2/69 (2%)
Query: 636 REGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAAFYGQTDCISGVSECIIMGLPM 695
R G+V + TG L ++ ++ V++ DAA G + GV E II+G P+
Sbjct: 322 RTGVVRQIGRHGVTGEKNSVLARAAFEVTVKH--LLDAAARGDVEEFKGVVENIIIGHPI 379
Query: 696 NVGTGLIKL 704
+GTG+++L
Sbjct: 380 KLGTGMVEL 388
>pdb|2WAQ|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|W Chain W, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2Y0S|A Chain A, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|W Chain W, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|A Chain A, Rnap At 3.2ang
pdb|4B1O|A Chain A, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|W Chain W, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 880
Score = 162 bits (411), Expect = 9e-40, 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-25, 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-17, 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
Score = 33.9 bits (76), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 23/31 (74%), Gaps = 1/31 (3%)
Query: 20 QVLMANKSNLVTPRNGELLIAATQDFITGGY 50
++++ +K N++TPR G +I A QD+I+G Y
Sbjct: 478 EIMLVHK-NIITPRYGGPIIGAAQDYISGAY 507
>pdb|2PMZ|A Chain A, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|Q Chain Q, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|3HKZ|A Chain A, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|I Chain I, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 880
Score = 162 bits (410), Expect = 1e-39, 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 = 8e-24, 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 = 89.4 bits (220), Expect = 1e-17, 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
Score = 33.9 bits (76), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 23/31 (74%), Gaps = 1/31 (3%)
Query: 20 QVLMANKSNLVTPRNGELLIAATQDFITGGY 50
++++ +K N++TPR G +I A QD+I+G Y
Sbjct: 478 EIMLVHK-NIITPRYGGPIIGAAQDYISGAY 507
>pdb|3H0G|A Chain A, Rna Polymerase Ii From Schizosaccharomyces Pombe
pdb|3H0G|M Chain M, Rna Polymerase Ii From Schizosaccharomyces Pombe
Length = 1752
Score = 160 bits (405), Expect = 4e-39, 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-24, 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-20, 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 = 2e-18, 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-14, Method: Compositional matrix adjust.
Identities = 60/209 (28%), Positives = 96/209 (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 ++ K K N Y K+ + K VC G+
Sbjct: 112 CGKL-----KIDSSNPKF-NDTQRYRDPKNRLNAVWNVCKTKMVCD-----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-07, 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
>pdb|4A3C|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid
pdb|4A3B|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid
pdb|4A3D|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid
pdb|4A3E|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid
pdb|4A3L|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid
pdb|4A3I|A Chain A, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|A Chain A, Rna Polymerase Ii Elongation Complex Containing A Cpd
Lesion
Length = 1732
Score = 149 bits (377), Expect = 8e-36, Method: Compositional matrix adjust.
Identities = 89/267 (33%), Positives = 143/267 (53%), Gaps = 36/267 (13%)
Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
DND VLFNRQPSLHK+S+MAHR KV+P+ TFR N V +PYNADFDGDEMN+H+PQ+EE
Sbjct: 438 DNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 497
Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
RAE L A +V+P++ + + QD + G LT ++ F
Sbjct: 498 RAE--------------LSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIEL 543
Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
Q + ++ D G+I P + ++ +W+GKQI S+ + P
Sbjct: 544 DQVL----NMLYWVPDWDGVIP-------TPAI-IKPKPLWSGKQILSVAI------PNG 585
Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
+L+ T +D+ +++ + +++ G ++K T+GS + +++ R+ G V
Sbjct: 586 IHLQRFDEGTTL---LSPKDNGMLIIDGQIIFGVVEKKTVGS-SNGGLIHVVTREKGPQV 641
Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGD 607
+ ++ +F+L++ GFS GIGD
Sbjct: 642 CAKLFGNIQKVVNFWLLHNGFSTGIGD 668
Score = 102 bits (255), Expect = 1e-21, 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 MGGREGL+DTAVKTAETGY+QRRLVK+LED+ V
Sbjct: 791 DYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMV 850
Query: 666 QYD 668
YD
Sbjct: 851 HYD 853
Score = 96.7 bits (239), Expect = 8e-20, Method: Compositional matrix adjust.
Identities = 55/178 (30%), Positives = 97/178 (54%), Gaps = 9/178 (5%)
Query: 1226 LLPSVVIKGVQGINRAVIHEED--VEGVT-------KYKLLVEGDNLRDVMATYGVKGVK 1276
+L ++ ++GV+ I R V+ + D V T ++ L +G NL +VM G+ +
Sbjct: 1267 MLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTR 1326
Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITR 1336
+N+ ++ + LGIEA R+ + E+ V+ + G +++RH L+ D+MT++G + +TR
Sbjct: 1327 IYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTR 1386
Query: 1337 HGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
HG + L SFE T + LF+A + D GVSE +I+G +GTG ++
Sbjct: 1387 HGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVM 1444
Score = 83.2 bits (204), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 73/283 (25%), Positives = 132/283 (46%), Gaps = 53/283 (18%)
Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
GVPR+KEI+N ++N+ TP +T YL+ D + A++++ +E TTL V E + P
Sbjct: 1097 GVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDP 1156
Query: 822 DDSFILIKLDMDRIRLLHLEVDIDS-----------IRYCIER--------TRGISGH-- 860
D +I D + I+L +D ++ +R ++R T G G
Sbjct: 1157 DPRSTVIPEDEEIIQLHFSLLDEEAEQSFDQQSPWLLRLELDRAAMNDKDLTMGQVGERI 1216
Query: 861 -LTVSGHSFLI---------------LKPKDSSKSFNSKMYQM-----KQLLPSVVIKGV 899
T F+I ++PK ++ M +L ++ ++GV
Sbjct: 1217 KQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLRGV 1276
Query: 900 QGINRAVIHEED--VEGVT-------KYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVY 950
+ I R V+ + D V T ++ L +G NL +VM G+ + +N+ ++
Sbjct: 1277 ENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIM 1336
Query: 951 KTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
+ LGIEA R+ + E+ V+ + G +++RH L+ D+MT++G
Sbjct: 1337 EVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQG 1379
Score = 73.6 bits (179), Expect = 7e-13, Method: Compositional matrix adjust.
Identities = 59/218 (27%), Positives = 93/218 (42%), Gaps = 43/218 (19%)
Query: 119 GLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPT 178
GL D R+G+ + C TC + +++C GHFG+IDL PVFH+G+ + + + +C +
Sbjct: 52 GLNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMH-- 109
Query: 179 CARVLLGEEKAAGFRA------KLRNPALSYLVRKSLKKKILETTKKVSVCP-------H 225
C ++LL E +A K R A+ L + K + ET P
Sbjct: 110 CGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCK---TKMVCETDVPSEDDPTQLVSRGG 166
Query: 226 CGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQT 285
CG ++K GL + K T D PE ++
Sbjct: 167 CGNTQPTIRKDGLKLVGSWKKDRATGDAD----------------EPE---------LRV 201
Query: 286 LNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRL 323
L+ E+L +F+ I ++D L N S+P +ILT L
Sbjct: 202 LSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCL 239
Score = 57.0 bits (136), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 24/37 (64%), Positives = 29/37 (78%)
Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
+++R+ + P VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1052 QFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1088
>pdb|1I3Q|A Chain A, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
pdb|1I50|A Chain A, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
pdb|1I6H|A Chain A, Rna Polymerase Ii Elongation Complex
pdb|1K83|A Chain A, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
With The Inhibitor Alpha Amanitin
pdb|1NIK|A Chain A, Wild Type Rna Polymerase Ii
pdb|1NT9|A Chain A, Complete 12-Subunit Rna Polymerase Ii
pdb|1PQV|A Chain A, Rna Polymerase Ii-Tfiis Complex
pdb|1R5U|A Chain A, Rna Polymerase Ii Tfiib Complex
pdb|1SFO|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex
pdb|1R9S|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex,
Matched Nucleotide
pdb|1R9T|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex,
Mismatched Nucleotide
pdb|1TWA|A Chain A, Rna Polymerase Ii Complexed With Atp
pdb|1TWC|A Chain A, Rna Polymerase Ii Complexed With Gtp
pdb|1TWF|A Chain A, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
pdb|1TWG|A Chain A, Rna Polymerase Ii Complexed With Ctp
pdb|1TWH|A Chain A, Rna Polymerase Ii Complexed With 2'datp
pdb|1WCM|A Chain A, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
pdb|1Y1W|A Chain A, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|A Chain A, Complete Rna Polymerase Ii Elongation Complex With
Substrate Analogue Gmpcpp
pdb|1Y1V|A Chain A, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|A Chain A, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|2B63|A Chain A, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2B8K|A Chain A, 12-Subunit Rna Polymerase Ii
pdb|2E2H|A Chain A, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With Gtp
pdb|2E2I|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dgtp
pdb|2E2J|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
Gmpcpp
pdb|2NVQ|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
2'dutp
pdb|2NVT|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Gmpcpp
pdb|2NVX|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dutp
pdb|2NVY|A Chain A, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
pdb|2NVZ|A Chain A, Rna Polymerase Ii Elongation Complex With Utp, Updated
112006
pdb|2JA5|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
A
pdb|2JA6|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
B
pdb|2JA7|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA7|M Chain M, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA8|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
D
pdb|2YU9|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Utp
pdb|2R7Z|A Chain A, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|A Chain A, Elongation Complex Of Rna Polymerase Ii With Artificial
Rdrp Scaffold
pdb|2R93|A Chain A, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|A Chain A, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3CQZ|A Chain A, Crystal Structure Of 10 Subunit Rna Polymerase Ii In
Complex With The Inhibitor Alpha-Amanitin
pdb|3FKI|A Chain A, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3GTG|A Chain A, Backtracked Rna Polymerase Ii Complex With 12mer Rna
pdb|3GTJ|A Chain A, Backtracked Rna Polymerase Ii Complex With 13mer Rna
pdb|3GTK|A Chain A, Backtracked Rna Polymerase Ii Complex With 18mer Rna
pdb|3GTL|A Chain A, Backtracked Rna Polymerase Ii Complex With 13mer With G<>u
Mismatch
pdb|3GTM|A Chain A, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
pdb|3GTO|A Chain A, Backtracked Rna Polymerase Ii Complex With 15mer Rna
pdb|3GTP|A Chain A, Backtracked Rna Polymerase Ii Complex With 24mer Rna
pdb|3GTQ|A Chain A, Backtracked Rna Polymerase Ii Complex Induced By Damage
pdb|3H3V|B Chain B, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|A Chain A, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|M Chain M, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|A Chain A, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3HOW|A Chain A, Complete Rna Polymerase Ii Elongation Complex Iii With A
T-U Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|A Chain A, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|A Chain A, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|A Chain A, Complete Rna Polymerase Ii Elongation Complex Iv With A
T-U Mismatch And A Frayed Rna 3'-Guanine
pdb|3I4M|A Chain A, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex D
pdb|3I4N|A Chain A, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex E
pdb|3K1F|A Chain A, Crystal Structure Of Rna Polymerase Ii In Complex With
Tfiib
pdb|3K7A|A Chain A, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
pdb|3M3Y|A Chain A, Rna Polymerase Ii Elongation Complex C
pdb|3M4O|A Chain A, Rna Polymerase Ii Elongation Complex B
pdb|3PO2|A Chain A, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|A Chain A, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3QT1|A Chain A, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
pdb|3RZD|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
pdb|3RZO|A Chain A, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
pdb|3S14|A Chain A, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
pdb|3S15|A Chain A, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
pdb|3S16|A Chain A, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
pdb|3S17|A Chain A, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
pdb|3S1M|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 1)
pdb|3S1N|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 2)
pdb|3S1Q|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Atp
pdb|3S1R|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Gtp
pdb|3S2D|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
Containing A 5br- U
pdb|3S2H|A Chain A, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
Containing A 2[prime]-Iodo Atp
pdb|4BBR|A Chain A, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|A Chain A, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 1733
Score = 149 bits (377), Expect = 9e-36, Method: Compositional matrix adjust.
Identities = 89/267 (33%), Positives = 143/267 (53%), Gaps = 36/267 (13%)
Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
DND VLFNRQPSLHK+S+MAHR KV+P+ TFR N V +PYNADFDGDEMN+H+PQ+EE
Sbjct: 438 DNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 497
Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
RAE L A +V+P++ + + QD + G LT ++ F
Sbjct: 498 RAE--------------LSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIEL 543
Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
Q + ++ D G+I P + ++ +W+GKQI S+ + P
Sbjct: 544 DQVL----NMLYWVPDWDGVIP-------TPAI-IKPKPLWSGKQILSVAI------PNG 585
Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
+L+ T +D+ +++ + +++ G ++K T+GS + +++ R+ G V
Sbjct: 586 IHLQRFDEGTTL---LSPKDNGMLIIDGQIIFGVVEKKTVGS-SNGGLIHVVTREKGPQV 641
Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGD 607
+ ++ +F+L++ GFS GIGD
Sbjct: 642 CAKLFGNIQKVVNFWLLHNGFSTGIGD 668
Score = 102 bits (255), Expect = 1e-21, 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 MGGREGL+DTAVKTAETGY+QRRLVK+LED+ V
Sbjct: 791 DYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMV 850
Query: 666 QYD 668
YD
Sbjct: 851 HYD 853
Score = 96.7 bits (239), Expect = 8e-20, Method: Compositional matrix adjust.
Identities = 55/178 (30%), Positives = 97/178 (54%), Gaps = 9/178 (5%)
Query: 1226 LLPSVVIKGVQGINRAVIHEED--VEGVT-------KYKLLVEGDNLRDVMATYGVKGVK 1276
+L ++ ++GV+ I R V+ + D V T ++ L +G NL +VM G+ +
Sbjct: 1267 MLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTR 1326
Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITR 1336
+N+ ++ + LGIEA R+ + E+ V+ + G +++RH L+ D+MT++G + +TR
Sbjct: 1327 IYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTR 1386
Query: 1337 HGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
HG + L SFE T + LF+A + D GVSE +I+G +GTG ++
Sbjct: 1387 HGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVM 1444
Score = 83.2 bits (204), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 73/283 (25%), Positives = 132/283 (46%), Gaps = 53/283 (18%)
Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
GVPR+KEI+N ++N+ TP +T YL+ D + A++++ +E TTL V E + P
Sbjct: 1097 GVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDP 1156
Query: 822 DDSFILIKLDMDRIRLLHLEVDIDS-----------IRYCIER--------TRGISGH-- 860
D +I D + I+L +D ++ +R ++R T G G
Sbjct: 1157 DPRSTVIPEDEEIIQLHFSLLDEEAEQSFDQQSPWLLRLELDRAAMNDKDLTMGQVGERI 1216
Query: 861 -LTVSGHSFLI---------------LKPKDSSKSFNSKMYQM-----KQLLPSVVIKGV 899
T F+I ++PK ++ M +L ++ ++GV
Sbjct: 1217 KQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLRGV 1276
Query: 900 QGINRAVIHEED--VEGVT-------KYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVY 950
+ I R V+ + D V T ++ L +G NL +VM G+ + +N+ ++
Sbjct: 1277 ENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIM 1336
Query: 951 KTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
+ LGIEA R+ + E+ V+ + G +++RH L+ D+MT++G
Sbjct: 1337 EVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQG 1379
Score = 73.6 bits (179), Expect = 7e-13, Method: Compositional matrix adjust.
Identities = 59/218 (27%), Positives = 93/218 (42%), Gaps = 43/218 (19%)
Query: 119 GLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPT 178
GL D R+G+ + C TC + +++C GHFG+IDL PVFH+G+ + + + +C +
Sbjct: 52 GLNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMH-- 109
Query: 179 CARVLLGEEKAAGFRA------KLRNPALSYLVRKSLKKKILETTKKVSVCP-------H 225
C ++LL E +A K R A+ L + K + ET P
Sbjct: 110 CGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCK---TKMVCETDVPSEDDPTQLVSRGG 166
Query: 226 CGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQT 285
CG ++K GL + K T D PE ++
Sbjct: 167 CGNTQPTIRKDGLKLVGSWKKDRATGDAD----------------EPE---------LRV 201
Query: 286 LNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRL 323
L+ E+L +F+ I ++D L N S+P +ILT L
Sbjct: 202 LSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCL 239
Score = 57.0 bits (136), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 24/37 (64%), Positives = 29/37 (78%)
Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
+++R+ + P VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1052 QFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1088
>pdb|3J0K|A Chain A, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
Length = 1455
Score = 149 bits (376), Expect = 1e-35, Method: Compositional matrix adjust.
Identities = 89/267 (33%), Positives = 143/267 (53%), Gaps = 36/267 (13%)
Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
DND VLFNRQPSLHK+S+MAHR KV+P+ TFR N V +PYNADFDGDEMN+H+PQ+EE
Sbjct: 438 DNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 497
Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
RAE L A +V+P++ + + QD + G LT ++ F
Sbjct: 498 RAE--------------LSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIEL 543
Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
Q + ++ D G+I P + ++ +W+GKQI S+ + P
Sbjct: 544 DQVL----NMLYWVPDWDGVIP-------TPAI-IKPKPLWSGKQILSVAI------PNG 585
Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGEDV 580
+L+ T +D+ +++ + +++ G ++K T+GS + +++ R+ G V
Sbjct: 586 IHLQRFDEGTTL---LSPKDNGMLIIDGQIIFGVVEKKTVGS-SNGGLIHVVTREKGPQV 641
Query: 581 AVTAMWRLSRMTSFYLMNRGFSIGIGD 607
+ ++ +F+L++ GFS GIGD
Sbjct: 642 CAKLFGNIQKVVNFWLLHNGFSTGIGD 668
Score = 103 bits (256), Expect = 9e-22, 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 MGGREGL+DTAVKTAETGY+QRRLVK+LED+ V
Sbjct: 791 DYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMV 850
Query: 666 QYD 668
YD
Sbjct: 851 HYD 853
Score = 96.7 bits (239), Expect = 8e-20, Method: Compositional matrix adjust.
Identities = 55/178 (30%), Positives = 98/178 (55%), Gaps = 9/178 (5%)
Query: 1226 LLPSVVIKGVQGINRAVIHEEDV-------EGVTKYKLLVEGD--NLRDVMATYGVKGVK 1276
+L ++ ++GV+ I R V+ + D E V + + ++E D NL +VM G+ +
Sbjct: 1267 MLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTR 1326
Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITR 1336
+N+ ++ + LGIEA R+ + E+ V+ + G +++RH L+ D+MT++G + +TR
Sbjct: 1327 IYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTR 1386
Query: 1337 HGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
HG + L SFE T + LF+A + D GVSE +I+G +GTG ++
Sbjct: 1387 HGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVM 1444
Score = 82.8 bits (203), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 73/283 (25%), Positives = 133/283 (46%), Gaps = 53/283 (18%)
Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
GVPR+KEI+N ++N+ TP +T YL+ D + A++++ +E TTL V E + P
Sbjct: 1097 GVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDP 1156
Query: 822 DDSFILIKLDMDRIRLLHLEVDIDS-----------IRYCIER--------TRGISGH-- 860
D +I D + I+L +D ++ +R ++R T G G
Sbjct: 1157 DPRSTVIPEDEEIIQLHFSLLDEEAEQSFDQQSPWLLRLELDRAAMNDKDLTMGQVGERI 1216
Query: 861 -LTVSGHSFLI---------------LKPKDSSKSFNSKMYQM-----KQLLPSVVIKGV 899
T F+I ++PK ++ M +L ++ ++GV
Sbjct: 1217 KQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLRGV 1276
Query: 900 QGINRAVIHEEDV-------EGVTKYKLLVEGD--NLRDVMATYGVKGVKCSSNNTYEVY 950
+ I R V+ + D E V + + ++E D NL +VM G+ + +N+ ++
Sbjct: 1277 ENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIM 1336
Query: 951 KTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
+ LGIEA R+ + E+ V+ + G +++RH L+ D+MT++G
Sbjct: 1337 EVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQG 1379
Score = 73.6 bits (179), Expect = 9e-13, Method: Compositional matrix adjust.
Identities = 58/221 (26%), Positives = 90/221 (40%), Gaps = 49/221 (22%)
Query: 119 GLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPT 178
GL D R+G+ + C TC + +++C GHFG+IDL PVFH+G+ + + + +C +
Sbjct: 52 GLNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMH-- 109
Query: 179 CARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKVSVCP-------------- 224
C ++LL E +L AL+ K I K VC
Sbjct: 110 CGKLLLDEHN------ELMRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQLVS 163
Query: 225 --HCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGL 282
CG ++K GL + K T D PE
Sbjct: 164 RGGCGNTQPTIRKDGLKLVGSWKKDRATGDAD----------------EPE--------- 198
Query: 283 IQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRL 323
++ L+ E+L +F+ I ++D L N S+P +ILT L
Sbjct: 199 LRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCL 239
Score = 57.4 bits (137), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 24/37 (64%), Positives = 29/37 (78%)
Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
+++R+ + P VG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1052 QFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAG 1088
>pdb|3QQC|A Chain A, Crystal Structure Of Archaeal Spt45 BOUND TO THE RNAP
CLAMP DOMAIN
Length = 436
Score = 114 bits (285), Expect = 4e-25, Method: Compositional matrix adjust.
Identities = 82/289 (28%), Positives = 135/289 (46%), Gaps = 43/289 (14%)
Query: 61 RAQTMRIASTLIAGRKVFFRGLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGL 120
+A +R L G KV G IE + +++ S +++ + Y D PI G+
Sbjct: 52 KAMVIRPKLNLSEGGKVI--GSIEFGILSPQEIRKMSAVEVTVPDTY--DDDGYPIEGGV 107
Query: 121 LDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCA 180
+D+RMG C TCG +C GHFG+I+L PV H+G+ + + IL+S C+ C
Sbjct: 108 MDKRMGVIDPGLRCETCGGRAGECPGHFGHIELARPVIHVGFAKTIYRILESTCRE--CG 165
Query: 181 RVLLGEEKAAGFRAKL---RNPALSYLVRKSLKKKILETTKKVSVCPHCGEINGVVKKCG 237
R+ L +E+ + K+ RN + + K+I + K+ VCPHCG +
Sbjct: 166 RIKLTDEEIEEYMKKIELARNRRSEF---NEIIKEIHKKAKERMVCPHCGAPQYPI---- 218
Query: 238 LLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEA 297
K++ T + ++ EY L P EV E
Sbjct: 219 -------KFEKPTIYWEIRKDEQGNEYR------------------HRLMPTEVRDWLEK 253
Query: 298 IPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVI--SDLKSDNDV 344
IP +D+PLL ++ E S+P ++LT L VPP RPS+ + +++++D+
Sbjct: 254 IPDKDLPLLGLDPEKSRPEWMVLTVLPVPPVTARPSITLETGIRAEDDL 302
Score = 36.6 bits (83), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 17/36 (47%), Positives = 25/36 (69%)
Query: 1346 VLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMG 1381
VL A+FE T HLF+AA G+ D ++GV E +++G
Sbjct: 393 VLARAAFEITVQHLFEAAEKGEVDNLNGVIENVLIG 428
>pdb|3IYD|D Chain D, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
Length = 1413
Score = 85.9 bits (211), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 42/109 (38%), Positives = 63/109 (57%), Gaps = 14/109 (12%)
Query: 345 VLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEA 404
VL NR P+LH+L I A ++ + + + VC YNADFDGD+M VH+P T EA+ E
Sbjct: 421 VLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLE- 479
Query: 405 LPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 453
A+ LM + +N+++P NGE +I +QD + G Y +T+
Sbjct: 480 -------------ARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTR 515
Score = 54.7 bits (130), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 31/77 (40%), Positives = 41/77 (53%), Gaps = 13/77 (16%)
Query: 615 VQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAA 674
+ +F GL ++F T G R+GL DTA+KTA +GY+ RRLV +DL V D
Sbjct: 759 ITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTED------ 812
Query: 675 FYGQTDCISGVSECIIM 691
DC G E I+M
Sbjct: 813 -----DC--GTHEGIMM 822
Score = 47.8 bits (112), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 19/31 (61%), Positives = 24/31 (77%)
Query: 1115 IEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
I A+G +AAQSIGEPGTQ+T++TFH G
Sbjct: 909 INKGEAIGVIAAQSIGEPGTQLTMRTFHIGG 939
Score = 42.4 bits (98), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/60 (40%), Positives = 38/60 (63%), Gaps = 2/60 (3%)
Query: 1330 EVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
++LGIT+ LA ES ++ ASF+ T+ L +AA G+ D + G+ E +I+G + GTG
Sbjct: 1305 DLLGITKASLAT--ESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTG 1362
Score = 33.5 bits (75), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 24/35 (68%)
Query: 20 QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 54
+ LM + +N+++P NGE +I +QD + G Y +T+
Sbjct: 481 RALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTR 515
>pdb|3LU0|D Chain D, Molecular Model Of Escherichia Coli Core Rna Polymerase
pdb|4IGC|D Chain D, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
pdb|4IGC|I Chain I, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
Length = 1407
Score = 85.9 bits (211), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 42/109 (38%), Positives = 63/109 (57%), Gaps = 14/109 (12%)
Query: 345 VLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEA 404
VL NR P+LH+L I A ++ + + + VC YNADFDGD+M VH+P T EA+ E
Sbjct: 421 VLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLE- 479
Query: 405 LPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 453
A+ LM + +N+++P NGE +I +QD + G Y +T+
Sbjct: 480 -------------ARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTR 515
Score = 54.7 bits (130), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 31/77 (40%), Positives = 41/77 (53%), Gaps = 13/77 (16%)
Query: 615 VQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAA 674
+ +F GL ++F T G R+GL DTA+KTA +GY+ RRLV +DL V D
Sbjct: 759 ITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTED------ 812
Query: 675 FYGQTDCISGVSECIIM 691
DC G E I+M
Sbjct: 813 -----DC--GTHEGIMM 822
Score = 47.8 bits (112), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 19/31 (61%), Positives = 24/31 (77%)
Query: 1115 IEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
I A+G +AAQSIGEPGTQ+T++TFH G
Sbjct: 909 INKGEAIGVIAAQSIGEPGTQLTMRTFHIGG 939
Score = 42.4 bits (98), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/60 (40%), Positives = 38/60 (63%), Gaps = 2/60 (3%)
Query: 1330 EVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
++LGIT+ LA ES ++ ASF+ T+ L +AA G+ D + G+ E +I+G + GTG
Sbjct: 1305 DLLGITKASLAT--ESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTG 1362
Score = 33.5 bits (75), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 24/35 (68%)
Query: 20 QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 54
+ LM + +N+++P NGE +I +QD + G Y +T+
Sbjct: 481 RALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTR 515
>pdb|4GZY|D Chain D, Crystal Structures Of Bacterial Rna Polymerase Paused
Elongation Complexes
pdb|4GZZ|D Chain D, Crystal Structures Of Bacterial Rna Polymerase Paused
Elongation Complexes
Length = 1534
Score = 80.5 bits (197), Expect = 6e-15, Method: Compositional matrix adjust.
Identities = 41/110 (37%), Positives = 64/110 (58%), Gaps = 14/110 (12%)
Query: 344 VVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAE 403
VVL NR P+LH+L I A + ++ ++ + + VC +NADFDGD+M VH+P + A+AE
Sbjct: 699 VVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAE 758
Query: 404 ALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 453
A++ M + NL++P +GE L ++D I G Y +TQ
Sbjct: 759 --------------ARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQ 794
Score = 65.5 bits (158), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 72/295 (24%), Positives = 136/295 (46%), Gaps = 44/295 (14%)
Query: 1120 AVGALAAQSIGEPGTQMTLKTFHFAG------------EVCEYIEEVFVPDDSFILIKLD 1167
AVG +AAQSIGEPGTQ+T++TFH G V E E P ++ ++D
Sbjct: 1220 AVGIVAAQSIGEPGTQLTMRTFHTGGVAGAADITQGLPRVIELF-EARRPKAKAVISEID 1278
Query: 1168 MDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKD---SSKSFNSKMYQMK 1224
++ +E + + +E + G S + + L++K D + +
Sbjct: 1279 G----VVRIEETEEKLSVFVE-SEGFSKEYKLPKEARLLVKDGDYVEAGQPLTRGAIDPH 1333
Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYE 1284
QLL + KG + + R ++ E+++ V + + + D +++ +K V+ +
Sbjct: 1334 QLLEA---KGPEAVERYLV--EEIQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSR 1388
Query: 1285 VYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKE 1344
+ + +E + E +L+ E G + P+L +G+T+ L+ +
Sbjct: 1389 LLEGQVLEKWDVEALNE-RLIAE--GKTPVAWKPLL-----------MGVTKSALS--TK 1432
Query: 1345 SVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMG--LPMNVGTGLIKLLQAV 1397
S L+ ASF+NT+ L +AA G+ D + G+ E +I+G +P G+ ++ Q V
Sbjct: 1433 SWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVV 1487
Score = 50.4 bits (119), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 22/52 (42%), Positives = 36/52 (69%)
Query: 615 VQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQ 666
V++SF GLT E+F + G R+G DTA++TA++GY+ R+LV ++ V+
Sbjct: 1057 VRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVTHEIVVR 1108
>pdb|1IW7|D Chain D, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1IW7|N Chain N, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1SMY|D Chain D, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1SMY|N Chain N, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1ZYR|D Chain D, Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Streptolydigin
pdb|1ZYR|N Chain N, Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Streptolydigin
pdb|2A68|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A68|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A69|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A69|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A6E|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6E|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6H|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2A6H|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2CW0|D Chain D, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2CW0|N Chain N, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2BE5|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2BE5|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2O5I|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Elongation Complex
pdb|2O5I|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Elongation Complex
pdb|2O5J|D Chain D, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog
pdb|2O5J|N Chain N, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog
pdb|2PPB|D Chain D, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog And
Antibiotic Streptolydigin
pdb|2PPB|N Chain N, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog And
Antibiotic Streptolydigin
pdb|3DXJ|D Chain D, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3DXJ|N Chain N, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3EQL|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3EQL|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3AOH|D Chain D, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOH|I Chain I, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOH|N Chain N, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOI|D Chain D, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|3AOI|I Chain I, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|3AOI|N Chain N, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|4G7H|D Chain D, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7H|N Chain N, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7O|D Chain D, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7O|N Chain N, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7Z|D Chain D, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
pdb|4G7Z|N Chain N, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
Length = 1524
Score = 80.5 bits (197), Expect = 6e-15, Method: Compositional matrix adjust.
Identities = 41/110 (37%), Positives = 64/110 (58%), Gaps = 14/110 (12%)
Query: 344 VVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAE 403
VVL NR P+LH+L I A + ++ ++ + + VC +NADFDGD+M VH+P + A+AE
Sbjct: 699 VVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAE 758
Query: 404 ALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 453
A++ M + NL++P +GE L ++D I G Y +TQ
Sbjct: 759 --------------ARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQ 794
Score = 65.5 bits (158), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 72/295 (24%), Positives = 136/295 (46%), Gaps = 44/295 (14%)
Query: 1120 AVGALAAQSIGEPGTQMTLKTFHFAG------------EVCEYIEEVFVPDDSFILIKLD 1167
AVG +AAQSIGEPGTQ+T++TFH G V E E P ++ ++D
Sbjct: 1220 AVGIVAAQSIGEPGTQLTMRTFHTGGVAGAADITQGLPRVIELF-EARRPKAKAVISEID 1278
Query: 1168 MDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKD---SSKSFNSKMYQMK 1224
++ +E + + +E + G S + + L++K D + +
Sbjct: 1279 G----VVRIEETEEKLSVFVE-SEGFSKEYKLPKEARLLVKDGDYVEAGQPLTRGAIDPH 1333
Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYE 1284
QLL + KG + + R ++ E+++ V + + + D +++ +K V+ +
Sbjct: 1334 QLLEA---KGPEAVERYLV--EEIQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSR 1388
Query: 1285 VYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKE 1344
+ + +E + E +L+ E G + P+L +G+T+ L+ +
Sbjct: 1389 LLEGQVLEKWDVEALNE-RLIAE--GKTPVAWKPLL-----------MGVTKSALS--TK 1432
Query: 1345 SVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMG--LPMNVGTGLIKLLQAV 1397
S L+ ASF+NT+ L +AA G+ D + G+ E +I+G +P G+ ++ Q V
Sbjct: 1433 SWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVV 1487
Score = 50.4 bits (119), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 22/52 (42%), Positives = 36/52 (69%)
Query: 615 VQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQ 666
V++SF GLT E+F + G R+G DTA++TA++GY+ R+LV ++ V+
Sbjct: 1057 VRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVTHEIVVR 1108
>pdb|2GHO|D Chain D, Recombinant Thermus Aquaticus Rna Polymerase For
Structural Studies
Length = 1233
Score = 80.5 bits (197), Expect = 6e-15, Method: Compositional matrix adjust.
Identities = 41/110 (37%), Positives = 64/110 (58%), Gaps = 14/110 (12%)
Query: 344 VVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAE 403
VVL NR P+LH+L I A + ++ ++ + + VC +NADFDGD+M VH+P + A+AE
Sbjct: 408 VVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAE 467
Query: 404 ALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 453
A++ M + NL++P +GE L ++D I G Y +TQ
Sbjct: 468 --------------ARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQ 503
Score = 64.7 bits (156), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 72/300 (24%), Positives = 135/300 (45%), Gaps = 54/300 (18%)
Query: 1120 AVGALAAQSIGEPGTQMTLKTFHFAG------------EVCEYIEEVFVPDDSFILIKLD 1167
AVG +AA+SIGEPGTQ+T++TFH G V E E P ++ ++D
Sbjct: 929 AVGVVAAESIGEPGTQLTMRTFHTGGVAVGTDITQGLPRVIELF-EARRPKAKAVISEID 987
Query: 1168 MDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKD---SSKSFNSKMYQMK 1224
++ +E D + +E + G S + + L++K D + +
Sbjct: 988 G----VVRIEEGEDRLSVFVE-SEGFSKEYKLPKDARLLVKDGDYVEAGQPLTRGAIDPH 1042
Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTY- 1283
QLL + KG + + R ++ E ++ V + + + D +++ +K V+ +
Sbjct: 1043 QLLEA---KGPEAVERYLVDE--IQKVYRAQGVKLHDKHIEIVVRQMLKYVEVTDPGDSR 1097
Query: 1284 ----EVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGL 1339
+V + +EA ++ E K+ P+ L+ +G+T+ L
Sbjct: 1098 LLEGQVLEKWDVEALNERLIAEGKV-------------PVAWKPLL------MGVTKSAL 1138
Query: 1340 AKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMG--LPMNVGTGLIKLLQAV 1397
+ +S L+ ASF+NT+ L +AA G+ D + G+ E +I+G +P G+ ++ Q V
Sbjct: 1139 S--TKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVV 1196
Score = 50.4 bits (119), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 22/52 (42%), Positives = 36/52 (69%)
Query: 615 VQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQ 666
V++SF GLT E+F + G R+G DTA++TA++GY+ R+LV ++ V+
Sbjct: 766 VRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVAHEIVVR 817
>pdb|1L9U|D Chain D, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9U|M Chain M, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9Z|D Chain D, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
pdb|1YNJ|D Chain D, Taq Rna Polymerase-Sorangicin Complex
pdb|1YNJ|J Chain J, Taq Rna Polymerase-Sorangicin Complex
pdb|1YNN|D Chain D, Taq Rna Polymerase-rifampicin Complex
pdb|1YNN|J Chain J, Taq Rna Polymerase-rifampicin Complex
Length = 1524
Score = 80.5 bits (197), Expect = 6e-15, Method: Compositional matrix adjust.
Identities = 41/110 (37%), Positives = 64/110 (58%), Gaps = 14/110 (12%)
Query: 344 VVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAE 403
VVL NR P+LH+L I A + ++ ++ + + VC +NADFDGD+M VH+P + A+AE
Sbjct: 699 VVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAE 758
Query: 404 ALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 453
A++ M + NL++P +GE L ++D I G Y +TQ
Sbjct: 759 --------------ARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQ 794
Score = 64.7 bits (156), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 72/300 (24%), Positives = 135/300 (45%), Gaps = 54/300 (18%)
Query: 1120 AVGALAAQSIGEPGTQMTLKTFHFAG------------EVCEYIEEVFVPDDSFILIKLD 1167
AVG +AA+SIGEPGTQ+T++TFH G V E E P ++ ++D
Sbjct: 1220 AVGVVAAESIGEPGTQLTMRTFHTGGVAVGTDITQGLPRVIELF-EARRPKAKAVISEID 1278
Query: 1168 MDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKD---SSKSFNSKMYQMK 1224
++ +E D + +E + G S + + L++K D + +
Sbjct: 1279 G----VVRIEEGEDRLSVFVE-SEGFSKEYKLPKDARLLVKDGDYVEAGQPLTRGAIDPH 1333
Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTY- 1283
QLL + KG + + R ++ E ++ V + + + D +++ +K V+ +
Sbjct: 1334 QLLEA---KGPEAVERYLVDE--IQKVYRAQGVKLHDKHIEIVVRQMLKYVEVTDPGDSR 1388
Query: 1284 ----EVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGL 1339
+V + +EA ++ E K+ P+ L+ +G+T+ L
Sbjct: 1389 LLEGQVLEKWDVEALNERLIAEGKV-------------PVAWKPLL------MGVTKSAL 1429
Query: 1340 AKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMG--LPMNVGTGLIKLLQAV 1397
+ +S L+ ASF+NT+ L +AA G+ D + G+ E +I+G +P G+ ++ Q V
Sbjct: 1430 S--TKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVV 1487
Score = 50.4 bits (119), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 22/52 (42%), Positives = 36/52 (69%)
Query: 615 VQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQ 666
V++SF GLT E+F + G R+G DTA++TA++GY+ R+LV ++ V+
Sbjct: 1057 VRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVAHEIVVR 1108
>pdb|1I6V|D Chain D, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1264
Score = 80.5 bits (197), Expect = 7e-15, Method: Compositional matrix adjust.
Identities = 41/110 (37%), Positives = 64/110 (58%), Gaps = 14/110 (12%)
Query: 344 VVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAE 403
VVL NR P+LH+L I A + ++ ++ + + VC +NADFDGD+M VH+P + A+AE
Sbjct: 439 VVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAE 498
Query: 404 ALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 453
A++ M + NL++P +GE L ++D I G Y +TQ
Sbjct: 499 --------------ARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQ 534
Score = 65.1 bits (157), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 72/300 (24%), Positives = 135/300 (45%), Gaps = 54/300 (18%)
Query: 1120 AVGALAAQSIGEPGTQMTLKTFHFAG------------EVCEYIEEVFVPDDSFILIKLD 1167
AVG +AA+SIGEPGTQ+T++TFH G V E E P ++ ++D
Sbjct: 960 AVGVVAAESIGEPGTQLTMRTFHTGGVAVGTDITQGLPRVIELF-EARRPKAKAVISEID 1018
Query: 1168 MDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKD---SSKSFNSKMYQMK 1224
++ +E D + +E + G S + + L++K D + +
Sbjct: 1019 G----VVRIEEGEDRLSVFVE-SEGFSKEYKLPKDARLLVKDGDYVEAGQPLTRGAIDPH 1073
Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTY- 1283
QLL + KG + + R ++ E ++ V + + + D +++ +K V+ +
Sbjct: 1074 QLLEA---KGPEAVERYLVDE--IQKVYRAQGVKLHDKHIEIVVRQMLKYVEVTDPGDSR 1128
Query: 1284 ----EVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGL 1339
+V + +EA ++ E K+ P+ L+ +G+T+ L
Sbjct: 1129 LLEGQVLEKWDVEALNERLIAEGKV-------------PVAWKPLL------MGVTKSAL 1169
Query: 1340 AKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMG--LPMNVGTGLIKLLQAV 1397
+ +S L+ ASF+NT+ L +AA G+ D + G+ E +I+G +P G+ ++ Q V
Sbjct: 1170 S--TKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVV 1227
Score = 50.4 bits (119), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 22/52 (42%), Positives = 36/52 (69%)
Query: 615 VQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQ 666
V++SF GLT E+F + G R+G DTA++TA++GY+ R+LV ++ V+
Sbjct: 797 VRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVAHEIVVR 848
>pdb|1HQM|D Chain D, Crystal Structure Of Thermus Aquaticus Core Rna
Polymerase- Includes Complete Structure With Side-Chains
(Except For Disordered Regions)-Further Refined From
Original Deposition-Contains Additional Sequence
Information
Length = 1265
Score = 80.5 bits (197), Expect = 7e-15, Method: Compositional matrix adjust.
Identities = 41/110 (37%), Positives = 64/110 (58%), Gaps = 14/110 (12%)
Query: 344 VVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAE 403
VVL NR P+LH+L I A + ++ ++ + + VC +NADFDGD+M VH+P + A+AE
Sbjct: 439 VVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAE 498
Query: 404 ALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 453
A++ M + NL++P +GE L ++D I G Y +TQ
Sbjct: 499 --------------ARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQ 534
Score = 64.7 bits (156), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 72/300 (24%), Positives = 135/300 (45%), Gaps = 54/300 (18%)
Query: 1120 AVGALAAQSIGEPGTQMTLKTFHFAG------------EVCEYIEEVFVPDDSFILIKLD 1167
AVG +AA+SIGEPGTQ+T++TFH G V E E P ++ ++D
Sbjct: 961 AVGVVAAESIGEPGTQLTMRTFHTGGVAVGTDITQGLPRVIELF-EARRPKAKAVISEID 1019
Query: 1168 MDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKD---SSKSFNSKMYQMK 1224
++ +E D + +E + G S + + L++K D + +
Sbjct: 1020 G----VVRIEEGEDRLSVFVE-SEGFSKEYKLPKDARLLVKDGDYVEAGQPLTRGAIDPH 1074
Query: 1225 QLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTY- 1283
QLL + KG + + R ++ E ++ V + + + D +++ +K V+ +
Sbjct: 1075 QLLEA---KGPEAVERYLVDE--IQKVYRAQGVKLHDKHIEIVVRQMLKYVEVTDPGDSP 1129
Query: 1284 ----EVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGL 1339
+V + +EA ++ E K+ P+ L+ +G+T+ L
Sbjct: 1130 LLEGQVLEKWDVEALNERLIAEGKV-------------PVAWKPLL------MGVTKSAL 1170
Query: 1340 AKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMG--LPMNVGTGLIKLLQAV 1397
+ +S L+ ASF+NT+ L +AA G+ D + G+ E +I+G +P G+ ++ Q V
Sbjct: 1171 S--TKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVV 1228
Score = 50.1 bits (118), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 22/52 (42%), Positives = 36/52 (69%)
Query: 615 VQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQ 666
V++SF GLT E+F + G R+G DTA++TA++GY+ R+LV ++ V+
Sbjct: 798 VRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVAHEIVVR 849
>pdb|1SPX|A Chain A, Crystal Structure Of Glucose Dehydrogenase Of
Caenorhabditis Elegans In The Apo-Form
Length = 278
Score = 33.1 bits (74), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 43/84 (51%), Gaps = 4/84 (4%)
Query: 844 IDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGIN 903
ID I++ I R IS L +G + P+++SK F S M MK+ +P+ V+ Q I
Sbjct: 178 IDLIQHGI-RVNSISPGLVATGFGSAMGMPEETSKKFYSTMATMKECVPAGVMGQPQDIA 236
Query: 904 RAVIHEEDVEG---VTKYKLLVEG 924
+ D + + ++L+V+G
Sbjct: 237 EVIAFLADRKTSSYIIGHQLVVDG 260
Score = 33.1 bits (74), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 43/84 (51%), Gaps = 4/84 (4%)
Query: 1180 IDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGIN 1239
ID I++ I R IS L +G + P+++SK F S M MK+ +P+ V+ Q I
Sbjct: 178 IDLIQHGI-RVNSISPGLVATGFGSAMGMPEETSKKFYSTMATMKECVPAGVMGQPQDIA 236
Query: 1240 RAVIHEEDVEG---VTKYKLLVEG 1260
+ D + + ++L+V+G
Sbjct: 237 EVIAFLADRKTSSYIIGHQLVVDG 260
>pdb|3U3L|C Chain C, Crystal Structure Of The Selenomethionine Derivative Of
Tablysin-15
Length = 233
Score = 32.7 bits (73), Expect = 1.7, Method: Composition-based stats.
Identities = 24/85 (28%), Positives = 38/85 (44%), Gaps = 10/85 (11%)
Query: 733 ERRRDYSVKVTASVKVTLELWNPG--DYKLSQDGVPRIKEIINAS--------RNISTPI 782
+R V T + + T W PG ++K S D +PRIKE+I+ + NI+ I
Sbjct: 82 KRHTKGCVGETHACRNTERFWLPGQLNFKYSGDKLPRIKELIDDAVKKGHLQKHNITREI 141
Query: 783 ITAYLDKDTDLDYARIVKGRLERTT 807
I Y + + D + +R T
Sbjct: 142 IENYRENGPNGDVKELALAISDRVT 166
>pdb|3U3N|C Chain C, Crystal Structure Of Tablysin-15
pdb|3U3U|C Chain C, Crystal Structure Of The Tablysin-15-Leukotriene E4
Complex
Length = 233
Score = 32.0 bits (71), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 36/78 (46%), Gaps = 10/78 (12%)
Query: 740 VKVTASVKVTLELWNPG--DYKLSQDGVPRIKEIINAS--------RNISTPIITAYLDK 789
V T + + T W PG ++K S D +PRIKE+I+ + NI+ II Y +
Sbjct: 89 VGETHACRNTERFWLPGQLNFKYSGDKLPRIKELIDDAVKKGHLQKHNITREIIENYREN 148
Query: 790 DTDLDYARIVKGRLERTT 807
+ D + +R T
Sbjct: 149 GPNGDVKELALAISDRVT 166
>pdb|2RHD|A Chain A, Crystal Structure Of Cryptosporidium Parvum Small Gtpase
Rab1a
Length = 175
Score = 30.8 bits (68), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 28/116 (24%), Positives = 55/116 (47%), Gaps = 13/116 (11%)
Query: 852 ERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEED 911
ER R I+ H +I+ SF++ +KQ + + ++ +N+ ++ +
Sbjct: 69 ERFRTITSSYYRGAHGIIIVYDVTDRDSFDN----VKQWIQEIDRYAMENVNKLLVGNK- 123
Query: 912 VEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIK 967
+ V+K +V D R++ ++G+K ++ S+ N Y V E A T+ EIK
Sbjct: 124 CDLVSK--RVVTSDEGRELADSHGIKFIETSAKNAYNV------EQAFHTMAGEIK 171
Score = 30.8 bits (68), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 28/116 (24%), Positives = 55/116 (47%), Gaps = 13/116 (11%)
Query: 1188 ERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEED 1247
ER R I+ H +I+ SF++ +KQ + + ++ +N+ ++ +
Sbjct: 69 ERFRTITSSYYRGAHGIIIVYDVTDRDSFDN----VKQWIQEIDRYAMENVNKLLVGNK- 123
Query: 1248 VEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIK 1303
+ V+K +V D R++ ++G+K ++ S+ N Y V E A T+ EIK
Sbjct: 124 CDLVSK--RVVTSDEGRELADSHGIKFIETSAKNAYNV------EQAFHTMAGEIK 171
>pdb|1VRA|A Chain A, Crystal Structure Of Arginine Biosynthesis Bifunctional
Protein Argj (10175521) From Bacillus Halodurans At 2.00
A Resolution
Length = 208
Score = 30.4 bits (67), Expect = 8.1, Method: Composition-based stats.
Identities = 13/41 (31%), Positives = 22/41 (53%)
Query: 887 MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 927
++QL P I+G N A++ + VE T Y+ +V G +
Sbjct: 151 IRQLKPEATIEGAHAFNEAILTTDTVEKHTCYQTIVNGKTV 191
Score = 30.4 bits (67), Expect = 8.1, Method: Composition-based stats.
Identities = 13/41 (31%), Positives = 22/41 (53%)
Query: 1223 MKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 1263
++QL P I+G N A++ + VE T Y+ +V G +
Sbjct: 151 IRQLKPEATIEGAHAFNEAILTTDTVEKHTCYQTIVNGKTV 191
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.320 0.136 0.397
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 40,188,265
Number of Sequences: 62578
Number of extensions: 1663069
Number of successful extensions: 3786
Number of sequences better than 100.0: 47
Number of HSP's better than 100.0 without gapping: 21
Number of HSP's successfully gapped in prelim test: 26
Number of HSP's that attempted gapping in prelim test: 3607
Number of HSP's gapped (non-prelim): 155
length of query: 1423
length of database: 14,973,337
effective HSP length: 111
effective length of query: 1312
effective length of database: 8,027,179
effective search space: 10531658848
effective search space used: 10531658848
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: 58 (26.9 bits)