RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 000525
(1443 letters)
>4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit,
transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A
2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A
Length = 880
Score = 324 bits (833), Expect = 2e-94
Identities = 217/933 (23%), Positives = 356/933 (38%), Gaps = 150/933 (16%)
Query: 18 TGISLGISTDTEKEKLSVMEI---------GAVSE--VTNPRLGLPNPTNECSSCGAKDR 66
GI GI + E K+SV I G E V +PRLG+ P +C +CG
Sbjct: 7 KGIKFGILSPDEIRKMSVTAIITPDVYDEDGTPIEGSVMDPRLGVIEPGQKCPTCG-NTL 65
Query: 67 KACEGHFGFIKFPFTILHPYFLSDIAKLLNSICPKCKTIRKERQKGAGSSRKEQPRVCKY 126
C GHFG I+ ++H F+ + + L + C +C ++ + SR ++
Sbjct: 66 GNCPGHFGHIELVRPVIHVGFVKHVYEFLKATCRRCGRVKISEDEIEKYSRIYNAIKKRW 125
Query: 127 CVRNPAQWYPRMRFKLSSKDLSGKTAIIVEIDEKLSKKNKKLPDDYWGFIPFDAQQEENS 186
+ + ++ +I K K
Sbjct: 126 PSAARRLTEYVKKTAMKAQVCPHCGEKQFKI-----KLEKPYNFYEER------------ 168
Query: 187 VKPNRKVLSCKQVSYLLKDVDPSIREEFILSKDAP-------FLKCFPVTPNNHRVTEVP 239
K L+ + L+ V + IL D L PV P R P
Sbjct: 169 -KEGVAKLTPSDIRERLEKV--PESDVEILGYDPTTSRPEWMILTVLPVPPITIR----P 221
Query: 240 HAFSHEKKLFFDNWTRHLKKMVDYRGRDIEL------SHLVQDCLKISKLHLDKSSRKDS 293
D+ T L +V R E +++D + + H+ +
Sbjct: 222 SIMIESGIRAEDDLTHKLVDIVRINERLKESIDAGAPQLIIEDLWDLLQYHVATYFDNEI 281
Query: 294 AEVRQKKNIDISNSSGL--RW------IKDVVLGKRNDDCFRMVVTGDPNIKLKEIGIPC 345
+ K+ L R + + GKR D R V++ DPNI + E+G+P
Sbjct: 282 PGLPPSKHRSGRPLRTLAQRLKGKEGRFRGNLSGKRVDFSSRTVISPDPNISIDEVGVPE 341
Query: 346 QVAERLQISERLNSWNWERLSVCIS-FRLLEKGELYVCRKGGLV--------RIRRIDAL 396
+A L + ER+ WN E+L + G YV R G R L
Sbjct: 342 IIARTLTVPERITPWNIEKLRQFVINGPDKWPGANYVIRPDGRRIDLRYVKDRKELASTL 401
Query: 397 ELGDIIYRPLTDGDIVLINRPPSIHPHSLIALTVKVLPISSVVTINPLCCSPFHGDFDGD 456
G ++ R LTDGD+VL NR PS+H S++A V+VL +N L C P++ DFDGD
Sbjct: 402 APGYVVERHLTDGDVVLFNRQPSLHRISMMAHRVRVLK-GLTFRLNLLVCPPYNADFDGD 460
Query: 457 CLHGYIPQAIGARVELTELVALDKQLINQQSGRNLLSLGQDSLTAAHLLMEDSVLLSHLQ 516
++ ++PQ+ A E E++ + K +I + G ++ QD ++ A+LL + LL+ +
Sbjct: 461 EMNLHVPQSEEAIAEAKEIMLVHKNIITPRYGGPIIGAAQDYISGAYLLTVKTTLLTKEE 520
Query: 517 MQQLQMFCPHRFLSPDIFKISKDSVWSGKQLFSMLLPPDFEYTFPSKD------------ 564
QQ+ + + ++ ++GKQ+ S LP DF + +
Sbjct: 521 AQQILGVADVKIDLGEPAILAPREYYTGKQVVSAFLPKDFNFHGQANVSSGPRLCKNEDC 580
Query: 565 -----VYISGGKLIS------AEGSSWLRDYEGNLFQYLIKRY-RDKVLDFLYAAQEVLC 612
V I G L+ A G+ ++ +LIK Y + + V
Sbjct: 581 PHDSYVVIKNGILLEGVFDKKAIGNQ----QPESILHWLIKEYSDEYGKWLMDNLFRVFI 636
Query: 613 EWLSVRGMTVSLSDLYLASHSCSRKILMDEIFYGLREAQDTCNFQQLMVDSHMNFLMSAK 672
++ ++G T+ L D+ L + EI+ + A+ + N + K
Sbjct: 637 RFVELQGFTMRLEDVSL------GDDVKKEIYNEIDRAKVEVD----------NLIQKYK 680
Query: 673 DSESTRSLQGEHL--SYEKQRSAALSQASVDAFKHVFWDIQNLAYKYGSKDNSLLAMFKA 730
+ E + G L S E L + A ++A KY N M +
Sbjct: 681 NGELEP-IPGRTLEESLENYILDTLDKLRSTA--------GDIASKYLDPFNFAYVMART 731
Query: 731 GSKGNLLKLVQHSLCLGLQHSL----APLSFR---FPHELSCAAWNRLRAGDNTECAKSY 783
G++G++L + Q + LG Q S+ + PH + D + A+ +
Sbjct: 732 GARGSVLNITQMAAMLGQQ-SVRGERIKRGYMTRTLPH---------FKPYDISPEARGF 781
Query: 784 IPSAVVENSFLTGLNPLECFIHSVTSRDSSFSDNA---DLPGTLTRRLMFFMRDLCTAYD 840
+ +SF TGL P E F H+ R+ D A G + RRL+ + DL YD
Sbjct: 782 -----IYSSFRTGLKPTELFFHAAGGRE-GLVDTAVRTSQSGYMQRRLINALSDLRAEYD 835
Query: 841 GTVRNAYGNQIVQFSYNIEGTSTPTGEIGDQPV 873
GTVR+ YG ++Q +Y +G P + V
Sbjct: 836 GTVRSLYGE-VIQVAYGDDGVF-PMYSAHGKTV 866
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 328 bits (841), Expect = 7e-92
Identities = 208/943 (22%), Positives = 366/943 (38%), Gaps = 133/943 (14%)
Query: 11 EVPSGILTGISLGISTDTEKEKLSVMEI------------GAVSEVTNPRLGLPNPTNEC 58
VP + + GI + E +SV +I V + +PRLG + +C
Sbjct: 10 SVPLRRVEEVQFGILSPEEIRSMSVAKIEFPETMDESGQRPRVGGLLDPRLGTIDRQFKC 69
Query: 59 SSCGAKDRKACEGHFGFIKFPFTILHPYFLSDIAKLLNSICPKC----------KTIRKE 108
+CG + C GHFG I+ + H FLS I K+L +C C K +
Sbjct: 70 QTCG-ETMADCPGHFGHIELAKPVFHIGFLSKIKKILECVCWNCGKLKIDSSNPKFNDTQ 128
Query: 109 RQKGAGSSRKEQPRVCKYCVRNPAQWYPRMRFKLSSKDLSGKTAIIVEIDEKLSKKNKKL 168
R + + VCK + S + +
Sbjct: 129 RYRDPKNRLNAVWNVCKTKMVCDT------GLSAGSDNFDLSNPSANMGHGGCGAAQPTI 182
Query: 169 PDDYWGFIPFDAQQEENSVKPNRKVLSCKQVSYLLKDVDPSIREEFILSKDAP-----FL 223
D + ++ S P +++LS +V + + L++ +
Sbjct: 183 RKDGLRLWGSWKRGKDESDLPEKRLLSPLEVHTIFTHISSEDLAHLGLNEQYARPDWMII 242
Query: 224 KCFPVTPNNHRVTEVPHAFSHEKKLFFDNWTRHLKKMVDYRGR------DIELSHLVQDC 277
PV P + R P D+ T L ++ + +H+V +
Sbjct: 243 TVLPVPPPSVR----PSISVDGTSRGEDDLTHKLSDIIKANANVRRCEQEGAPAHIVSEY 298
Query: 278 LKISKLHLD-----KSSRKDSAEVRQKKNI-----DISNSSGLRWIKDVVLGKRNDDCFR 327
++ + H+ + + + A + + + + G ++ ++GKR D R
Sbjct: 299 EQLLQFHVATYMDNEIAGQPQALQKSGRPLKSIRARLKGKEGR--LRGNLMGKRVDFSAR 356
Query: 328 MVVTGDPNIKLKEIGIPCQVAERLQISERLNSWNWERLSVCISFRLLEKGE------LYV 381
V+TGDPN+ L E+G+P +A+ L E + +N +L L+ G Y+
Sbjct: 357 TVITGDPNLSLDELGVPRSIAKTLTYPETVTPYNIYQLQ-----ELVRNGPDEHPGAKYI 411
Query: 382 CRKGG------LVRIRRIDALELGDIIYRPLTDGDIVLINRPPSIHPHSLIALTVKVLPI 435
R G + L G + R + DGD+V+ NR PS+H S++ ++V+P
Sbjct: 412 IRDTGERIDLRYHKRAGDIPLRYGWRVERHIRDGDVVIFNRQPSLHKMSMMGHRIRVMP- 470
Query: 436 SSVVTINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQLINQQSGRNLLSLG 495
S +N SP++ DFDGD ++ ++PQ+ R E+ E+ + KQ+++ QS + ++ +
Sbjct: 471 YSTFRLNLSVTSPYNADFDGDEMNMHVPQSEETRAEIQEITMVPKQIVSPQSNKPVMGIV 530
Query: 496 QDSLTAAHLLMEDSVLLSHLQMQQLQMFCPH-RFLSPDIFKISKDSVWSGKQLFSMLLPP 554
QD+L L+ + + ++ P + P + +W+GKQ+ S+++P
Sbjct: 531 QDTLAGVRKFSLRDNFLTRNAVMNIMLWVPDWDGILPPPVILKPKVLWTGKQILSLIIPK 590
Query: 555 DFEYTFPSKD----------VYISGGKLIS-AEGSSWLRDYEGNLFQYLIKRY-RDKVLD 602
+ I G++I + +G L + K +
Sbjct: 591 GINLIRDDDKQSLSNPTDSGMLIENGEIIYGVVDKKTVGASQGGLVHTIWKEKGPEICKG 650
Query: 603 FLYAAQEVLCEWLSVRGMTVSLSDLYLASHSCSRKILMDEIFYGLREAQDTCNFQQLMVD 662
F Q V+ WL G ++ + D M E+ ++EA+ + + D
Sbjct: 651 FFNGIQRVVNYWLLHNGFSIGIGDTIA------DADTMKEVTRTVKEARRQV--AECIQD 702
Query: 663 SHMNFLMSAKDSESTRSLQGEHLSYEKQRSAALSQASVDAFKHVFWDIQNLAYKYGSKDN 722
+ N L E +L+ S+E + S L+QA +A + A N
Sbjct: 703 AQHNRL----KPEPGMTLR---ESFEAKVSRILNQARDNAGRS--------AEHSLKDSN 747
Query: 723 SLLAMFKAGSKGNLLKLVQHSLCLGLQHS---LAPLSFR---FPHELSCAAWNRLRAGDN 776
++ M AGSKG+ + + Q S C+G Q P F+ PH D+
Sbjct: 748 NVKQMVAAGSKGSFINISQMSACVGQQIVEGKRIPFGFKYRTLPH---------FPKDDD 798
Query: 777 TECAKSYIPSAVVENSFLTGLNPLECFIHSVTSRDSSFSDNADLP--GTLTRRLMFFMRD 834
+ ++ + +ENS+L GL P E F H++ R+ G + RRL+ M D
Sbjct: 799 SPESRGF-----IENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKAMED 853
Query: 835 LCTAYDGTVRNAYGNQIVQFSYNIEGTSTPTGEIGDQPVGSLS 877
+ YDGTVRNA G I+QF+Y +G E LS
Sbjct: 854 VMVRYDGTVRNAMG-DIIQFAYGEDGLDATLVEYQVFDSLRLS 895
Score = 81.7 bits (201), Expect = 1e-15
Identities = 58/366 (15%), Positives = 127/366 (34%), Gaps = 56/366 (15%)
Query: 920 TMSLFLSNKLGKRRHGFEYGALEVKNHLECLMLSDIVSTSMIIYSPQTGS---------- 969
+++++L + A V+ +E LS + S + I Y P
Sbjct: 1118 SLTIYLMPWIAANMDL----AKNVQTQIEHTTLSTVTSATEIHYDPDPQDTVIEEDKDFV 1173
Query: 970 --------------MKHFSPWICHFHVRKEIMKRTGLKEHSIIDSLYRQCKAARTELKIS 1015
+ SPW+ + + M K+ S+ D + ++ +L
Sbjct: 1174 EAFFAIPDEEVEENLYKQSPWLLRLELDRAKMLD---KKLSMSDVAGKIAESFERDLFTI 1230
Query: 1016 VPDMLISNKDCSSINMQKECNDAFCVTVMIVENFKRTSIDLETIQMWVMPFLLKTVVKGF 1075
+ N D I + +D + + M L ++G
Sbjct: 1231 WSED---NADKLIIRCRIIRDDDRKAEDDDNMIEEDVFLKTIEGHM-----LESISLRGV 1282
Query: 1076 REIKKVDILWKDKQKASKSHDDSFGELYLRVSMSGQCHITSLWSALMNDCHQIMDMIDWT 1135
I +V + + + + D +F V + ++T + ++ +D T
Sbjct: 1283 PNITRVYM--MEHKIVRQIEDGTFERADEWVLETDGINLTEAMT---------VEGVDAT 1331
Query: 1136 RSHPDNIRSFCLAYGIDAGLQFFLTNLESAISDTGKNILPEHLLIVANTLSATGEFVGLN 1195
R++ ++ GI+A L L + I G + HL ++ + +++ G + +
Sbjct: 1332 RTYSNSFVEILQILGIEATRSALLKELRNVIEFDGSYVNYRHLALLCDVMTSRGHLMAIT 1391
Query: 1196 AKGLALQRKHSSVSSPFVQAFFSNPGASFIKAAKAGAVDNLQGSVDALGWGKVPSVGTGG 1255
G+ + + ++ F + AA +G D+ +G + + G++ +GTG
Sbjct: 1392 RHGIN-----RAETGALMRCSFEETVEILMDAAASGEKDDCKGISENIMLGQLAPMGTGA 1446
Query: 1256 HFDIIY 1261
FDI
Sbjct: 1447 -FDIYL 1451
>1twf_A B220, DNA-directed RNA polymerase II largest subunit;
transcription, mRNA, multiprotein complex; HET: UTP;
2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB:
1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A
1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A*
1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...
Length = 1733
Score = 322 bits (826), Expect = 5e-90
Identities = 205/936 (21%), Positives = 358/936 (38%), Gaps = 123/936 (13%)
Query: 11 EVPSGILTGISLGISTDTEKEKLSVMEI------------GAVSEVTNPRLGLPNPTNEC 58
P + + G+ + E +SV +I + + +PRLG + +C
Sbjct: 8 SAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRNLKC 67
Query: 59 SSCGAKDRKACEGHFGFIKFPFTILHPYFLSDIAKLLNSICPKCKTIRKERQKGAGSSRK 118
+C + C GHFG I + H F++ I K+ +C C + + +
Sbjct: 68 QTCQ-EGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHN---ELMR 123
Query: 119 EQPRVCKYCVRNPAQW-YPRMRFKLSSKDLSGKTAIIVEIDEKLSKKNKKLPDDYWGFIP 177
+ + R A W + + + S + + D +
Sbjct: 124 QALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQLVSRGGCGNTQPTIRKDGLKLVG 183
Query: 178 -FDAQQEENSV-KPNRKVLSCKQVSYLLKDVDPSIREEFILSKDAP-------FLKCFPV 228
+ + +P +VLS +++ + K + S+++ L + L C PV
Sbjct: 184 SWKKDRATGDADEPELRVLSTEEILNIFKHI--SVKDFTSLGFNEVFSRPEWMILTCLPV 241
Query: 229 TPNNHRVTEVPHAFSHEKKLFFDNWTRHLKKMVDYRG--RDIELS----HLVQDCLKISK 282
P R P +E + D+ T L ++ +E + H +++ + +
Sbjct: 242 PPPPVR----PSISFNESQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQ 297
Query: 283 LHLDKSSRKDSAEVRQKKNIDISNSSGLR--------WIKDVVLGKRNDDCFRMVVTGDP 334
H+ D A Q +R I+ ++GKR D R V++GDP
Sbjct: 298 FHVATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDP 357
Query: 335 NIKLKEIGIPCQVAERLQISERLNSWNWERLSVCISFRLLEKGE------LYVCRKGG-- 386
N++L ++G+P +A+ L E + +N +RL+ +L+ G YV R G
Sbjct: 358 NLELDQVGVPKSIAKTLTYPEVVTPYNIDRLT-----QLVRNGPNEHPGAKYVIRDSGDR 412
Query: 387 --LVRIRRIDA--LELGDIIYRPLTDGDIVLINRPPSIHPHSLIALTVKVLPISSVVTIN 442
L +R L+ G + R + D D VL NR PS+H S++A VKV+P S +N
Sbjct: 413 IDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIP-YSTFRLN 471
Query: 443 PLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQLINQQSGRNLLSLGQDSLTAA 502
SP++ DFDGD ++ ++PQ+ R EL++L A+ Q+++ QS + + + QD+L
Sbjct: 472 LSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGI 531
Query: 503 HLLMEDSVLLSHLQMQQLQM-FCPHRFLSPDIFKISKDSVWSGKQLFSMLLPPDFEYTFP 561
L + Q+ + + P I +WSGKQ+ S+ +P
Sbjct: 532 RKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRF 591
Query: 562 SKD----------VYISGGKLISAE-GSSWLRDYEGNLFQYLIKRY-RDKVLDFLYAAQE 609
+ + I G++I + G L + + Q+
Sbjct: 592 DEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQK 651
Query: 610 VLCEWLSVRGMTVSLSDLYLASHSCSRKILMDEIFYGLREAQDTCNFQQLMVDSHMNFLM 669
V+ WL G + + D M EI + EA+ + ++ N L
Sbjct: 652 VVNFWLLHNGFSTGIGDTIA------DGPTMREITETIAEAKKKV--LDVTKEAQANLL- 702
Query: 670 SAKDSESTRSLQGEHLSYEKQRSAALSQASVDAFKHVFWDIQNLAYKYGSKDNSLLAMFK 729
++ +L+ S+E L++A A + LA N++ M
Sbjct: 703 ---TAKHGMTLRE---SFEDNVVRFLNEARDKAGR--------LAEVNLKDLNNVKQMVM 748
Query: 730 AGSKGNLLKLVQHSLCLGLQHS---LAPLSFR---FPHELSCAAWNRLRAGDNTECAKSY 783
AGSKG+ + + Q S C+G Q F PH D + +K +
Sbjct: 749 AGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPH---------FSKDDYSPESKGF 799
Query: 784 IPSAVVENSFLTGLNPLECFIHSVTSRDSSFSDNADLP--GTLTRRLMFFMRDLCTAYDG 841
VENS+L GL P E F H++ R+ G + RRL+ + D+ YD
Sbjct: 800 -----VENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDN 854
Query: 842 TVRNAYGNQIVQFSYNIEGTSTPTGEIGDQPVGSLS 877
T RN+ G ++QF Y +G E S
Sbjct: 855 TTRNSLG-NVIQFIYGEDGMDAAHIEKQSLDTIGGS 889
Score = 79.8 bits (196), Expect = 6e-15
Identities = 48/354 (13%), Positives = 115/354 (32%), Gaps = 65/354 (18%)
Query: 940 ALEVKNHLECLMLSDIVSTSMIIYSPQTGS------------------------MKHFSP 975
A +++ +E L + S I Y P S SP
Sbjct: 1131 AKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEAEQSFDQQSP 1190
Query: 976 WICHFHVRKEIMKRTGLKEHSIIDSLYRQCKAARTELKISVPDMLISNKDCSSINMQKEC 1035
W+ + + M L + + + + K+ + ++
Sbjct: 1191 WLLRLELDRAAMNDKDLTMGQVGERIKQT------------------FKNDLFVIWSEDN 1232
Query: 1036 NDAFCVTVMIVENFKRTSIDLETIQMWVMPF----LLKTVVKGFREIKKVDILWKDKQKA 1091
++ + +V + + L ++G I++V ++ D++
Sbjct: 1233 DEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLRGVENIERVVMMKYDRKVP 1292
Query: 1092 SKSHD-DSFGELYLRVSMSGQCHITSLWSALMNDCHQIMDMIDWTRSHPDNIRSFCLAYG 1150
S + + E L ++ + + + ID TR + ++ G
Sbjct: 1293 SPTGEYVKEPEWVLETDGVN---LSEVMT---------VPGIDPTRIYTNSFIDIMEVLG 1340
Query: 1151 IDAGLQFFLTNLESAISDTGKNILPEHLLIVANTLSATGEFVGLNAKGLALQRKHSSVSS 1210
I+AG + + I+ G + H+ ++ + ++ G + G S +
Sbjct: 1341 IEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFN-----RSNTG 1395
Query: 1211 PFVQAFFSNPGASFIKAAKAGAVDNLQGSVDALGWGKVPSVGTGGHFDIIYSGE 1264
++ F +A + +D+ +G + + G++ +GTG FD++ E
Sbjct: 1396 ALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGA-FDVMIDEE 1448
>2k0m_A Uncharacterized protein; structural genomics, unknown function,
PSI-2, protein structure initiative; NMR {Rhodospirillum
rubrum atcc 11170}
Length = 104
Score = 99 bits (249), Expect = 5e-25
Identities = 27/89 (30%), Positives = 42/89 (47%), Gaps = 2/89 (2%)
Query: 1333 TYNDVLRLSNALKKILHKYSIGQRLSEKDKTTVIRALYFHPRRNEKLGIEPPDIEVTYHP 1392
+ +K +L++Y G +S D ++ AL HP K+G + EV
Sbjct: 13 EFARKADALAFMKVMLNRYRPGDIVSTVDGAFLVEALKRHPDATSKIGPGVRNFEV--RS 70
Query: 1393 EHQNSRCFSLVREDGSIEDFSYHKCVIGA 1421
++CF ++R DGS E FSY KCV+
Sbjct: 71 ADYGTQCFWILRTDGSEERFSYKKCVLEH 99
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 81.1 bits (199), Expect = 2e-15
Identities = 90/680 (13%), Positives = 186/680 (27%), Gaps = 221/680 (32%)
Query: 138 MRFKLSSKDLSGKTAIIVEIDEKLSKKNKKLPDDYWGFIPFDAQQEENSVKPNRKVLSCK 197
M F+ K I+ + E N FD + ++ K +LS +
Sbjct: 7 MDFETGEHQYQYKD--ILSVFEDAFVDN------------FDCKDVQDMPKS---ILSKE 49
Query: 198 QVSYLLKDVDP----------------SIREEFI---LSKDAPFLKCFPVTPNNHRVTEV 238
++ +++ D + ++F+ L + FL T
Sbjct: 50 EIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMT 109
Query: 239 PHAFSHEKKLFFDNWTRHLKKMVDYRGRDIELSHLVQDCLKISK------LHLDKSSRKD 292
+L+ DN + K R ++ ++ L + + S K
Sbjct: 110 RMYIEQRDRLYNDN--QVFAKYNVSR---LQPYLKLRQALLELRPAKNVLIDGVLGSGKT 164
Query: 293 S--AEVRQKKNIDISNSSGLRWIKDVVLGKRNDD----------CFRMVVTGDPNIKLKE 340
+V + + W+ L N +++ DPN
Sbjct: 165 WVALDVCLSYKVQCKMDFKIFWLN---LKNCNSPETVLEMLQKLLYQI----DPNW---- 213
Query: 341 IGIPCQVAERLQ-ISERLNSWNWERLSVCISFRLLEKGELYV----------------CR 383
++ I R++S L + + E L V C+
Sbjct: 214 ----TSRSDHSSNIKLRIHSIQ-AELRRLLKSKPYENC-LLVLLNVQNAKAWNAFNLSCK 267
Query: 384 KGGLV--RIRRI-DALELGDIIYRPLTDGDIVLINR-----------------PP---SI 420
L+ R +++ D L + L + L P +
Sbjct: 268 I--LLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTT 325
Query: 421 HP--HSLIALTVKVLPI------------------SSVVTINP-------LCCSPFHGDF 453
+P S+IA +++ SS+ + P S F
Sbjct: 326 NPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSA 385
Query: 454 DGDCLHGYIPQAIGARV------ELTELVA---LDKQLINQQSGRNLLSLGQDSLTAAHL 504
IP + + + +V L+ +Q + +S+
Sbjct: 386 H-------IPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISI--------PS 430
Query: 505 LMEDSVLLSHLQMQQLQMFCPHRFLSPDIFKISKDSVWSGKQLFSMLLPPDFEYTFPSKD 564
+ + L+++ + HR + + ++ ++ P +Y +
Sbjct: 431 IYLE------LKVKLENEYALHRSI------VDHYNIPKTFDSDDLIPPYLDQYFYS--- 475
Query: 565 VYISGGKLISAEGSSWLRDYEGNLFQYLIKRYRDKVLDFLYAAQEVLCEWLSVRGMTVSL 624
+I G L + E LF R LDF +L + +
Sbjct: 476 -HI-GHHLKNIE-----HPERMTLF-------RMVFLDF---------RFLEQK---IRH 509
Query: 625 SDLYLASHSCSRKILMDEIFYGLREAQDTCNFQQLMVDSHMNFLMSAKD----SESTRSL 680
+ L FY D + +V++ ++FL ++ S+ T L
Sbjct: 510 DSTAWNASGSILNTLQQLKFYK-PYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLL 568
Query: 681 Q------GEHLSYEKQRSAA 694
+ E + E +
Sbjct: 569 RIALMAEDEAIFEEAHKQVQ 588
Score = 62.6 bits (151), Expect = 9e-10
Identities = 93/712 (13%), Positives = 200/712 (28%), Gaps = 221/712 (31%)
Query: 583 DYEGNLFQYLIKRYRDKVLDFLYAAQEVL-CEWL--SVRGMTVS--LSDLYLASHSCSRK 637
D+E QY +Y+D + F A + C+ + + + + + ++ + S
Sbjct: 8 DFETGEHQY---QYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSG- 63
Query: 638 ILMDEIFYGLREAQDTCNFQQLMVDSHM---NFLMSAKDSESTRSLQGEHLSYEKQRSAA 694
+F+ L Q+ Q+ + + FLMS +E R Y +QR
Sbjct: 64 --TLRLFWTLLSKQEEM-VQKFVEEVLRINYKFLMSPIKTE-QRQPSMMTRMYIEQRDRL 119
Query: 695 LSQASVDAFKHV-----FWDIQNLAYK---------YG-------------SKDNSLLAM 727
+ V A +V + ++ + G +
Sbjct: 120 YNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCK 179
Query: 728 FKAG----------SKGNLLKLVQHSLCLGLQHSLAPL---SFRFPHELSCAAWNRLRAG 774
S +L+++Q L + + S + + LR
Sbjct: 180 MDFKIFWLNLKNCNSPETVLEMLQ-KLLYQIDPNWTSRSDHSSNIKLRIH-SIQAELR-- 235
Query: 775 DNTECAKSYIPSAV-----VENSFLTGLNPLECF-IHS---VTSRDSSFSDNADLPGTLT 825
+K Y + + V+N+ F + +T+R +D L T
Sbjct: 236 -RLLKSKPY-ENCLLVLLNVQNA-----KAWNAFNLSCKILLTTRFKQVTD--FLSAATT 286
Query: 826 RRLMFFMRDLCTAYDGTVRNAYGNQIVQFSYNIEGTSTPTGEIGDQPVGSLSACAISEAA 885
+ + T TP D+ L
Sbjct: 287 THI-------------------------SLDHHSMTLTP-----DEVKSLLLKYLDCRPQ 316
Query: 886 YSALDQPISLLETSPLLNLKNVLECGSKKSNADQTMSLFLSNKLGKRRHGFEYGALEVKN 945
D P +L T+P +S+ + + ++
Sbjct: 317 ----DLPREVLTTNPRR------------------LSII-AESIRDGLATWDN-----WK 348
Query: 946 HLECLMLSDIVSTSMIIYSPQTGSMKHFSPWICHFHVRKEIMKRTGLKEHSIIDSLYRQC 1005
H+ C L+ I+ + S+ P ++ ++ +
Sbjct: 349 HVNCDKLTTIIES----------SLNVLEP---------AEYRK-----------MFDRL 378
Query: 1006 KAARTELKISVPDMLIS------NKDCSSINMQKECNDAFCVTVMIVENFKRTSIDLETI 1059
I P +L+S K + + K ++ + K ++I + +I
Sbjct: 379 SVFPPSAHI--PTILLSLIWFDVIKSDVMVVVNK-----LHKYSLVEKQPKESTISIPSI 431
Query: 1060 QMWV------MPFLLKTVVKGFREIKKVD-----ILWKDK----------QKASKSH-DD 1097
+ + L +++V + K D + D+ +
Sbjct: 432 YLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMT 491
Query: 1098 SFGELYLRVSMSGQ--CHITSLWSALMNDCHQIMDMIDW----TRSHPDNIRSFCLAYGI 1151
F ++L Q H ++ W+A + + + + + + P R
Sbjct: 492 LFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNA---- 547
Query: 1152 DAGLQFFLTNLESAISDTGKNILPEHLLIVANTLSATGEFVGLNAKGLALQR 1203
+ FL +E + I ++ ++ L A E + A +QR
Sbjct: 548 ---ILDFLPKIEENL------ICSKYTDLLRIALMAEDEAIFEEAHK-QVQR 589
Score = 44.8 bits (105), Expect = 2e-04
Identities = 69/567 (12%), Positives = 157/567 (27%), Gaps = 154/567 (27%)
Query: 886 YSALDQPISLL---ETSPLLNLKNVLE-----CGSKKSNADQTMSLFLSNKLGKRRHGFE 937
D P S+L E ++ K+ + + S ++ + F+ L
Sbjct: 36 KDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRI-----N 90
Query: 938 YGALEVKNHLECLMLSDIVSTSMIIYSPQTGSMKHFSPWICHFHV-RKEIMK--RTGLKE 994
Y L E S + +Y Q + + + ++V R + R L E
Sbjct: 91 YKFLMSPIKTEQRQPSMM----TRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLE 146
Query: 995 HSIIDSLYRQCKAARTELKISVPDMLISNKDCSSINMQKECNDAFCVTVMIVE----NFK 1050
R + + +L S K ++++ C M + N K
Sbjct: 147 -------------LRPAKNVLIDGVLGSGKTWVALDV---CLSYKVQCKMDFKIFWLNLK 190
Query: 1051 RTSIDLETIQMWVMPFLLKTVVKGFREIKKVDILWKDKQKASKSHDDSFGELYLRVSMSG 1110
+ ++M L+ + +I D K S + LR +
Sbjct: 191 NCNSPETVLEM------LQKL---LYQIDPNWTSRSDHSSNIKLRIHSI-QAELRRLLKS 240
Query: 1111 QCHITSLWSALMNDCHQIMDMID-WTRSHPDNIRSFCLAYGIDAGLQFFLTNLESAISDT 1169
+ + L L ++ + +F + + LT ++D
Sbjct: 241 KPYENCL---L------VLL--NVQNAKA---WNAF------NLSCKILLTTRFKQVTDF 280
Query: 1170 GKNILPEHLLIV--------ANTLSATGEFVGLNAKGLALQRKHSSVSSPFVQAFFSNPG 1221
H+ + S +++ + L + ++ P +
Sbjct: 281 LSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTN---PRRLSII---A 334
Query: 1222 ASFIKAA------KAGAVDNLQGSVDALGWGKVPSVGTGGHFDIIYSGEGRTLSKPVDVY 1275
S K D L +++ S+ +++ E R + +
Sbjct: 335 ESIRDGLATWDNWKHVNCDKLTTIIES-------SL------NVLEPAEYRKM------F 375
Query: 1276 NLLS-----TPVSSKQNEKL---KVCKAQGLISDKCGAKFGDFAFKGLGNLDFETISRGV 1327
+ LS + + + + ++ +K L + +
Sbjct: 376 DRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKL-------HKYSL-------VEKQP 421
Query: 1328 LRKSWTYNDV---LRLSNALKKILHK-----YSIGQRLSEKDKTTVIRALYFHPRRNEKL 1379
+ + + L++ + LH+ Y+I + D YF+ +
Sbjct: 422 KESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFY----SHI 477
Query: 1380 GIEPPDIEVTYH-PEHQNSRCFSLVRE 1405
G +H ++ +L R
Sbjct: 478 G---------HHLKNIEHPERMTLFRM 495
Score = 39.1 bits (90), Expect = 0.013
Identities = 69/440 (15%), Positives = 129/440 (29%), Gaps = 145/440 (32%)
Query: 890 DQPISLLETSPLLNLKNVLECGSKKSNADQTMSLFL---SNKLGKRRHGFEYGALEVKNH 946
+ P ++LE L L ++ + S +D + ++ L S + RR L+ K +
Sbjct: 193 NSPETVLE--MLQKLLYQIDP-NWTSRSDHSSNIKLRIHSIQAELRRL------LKSKPY 243
Query: 947 LECLMLSDIVSTSMIIYSPQTGSMKHFSPWICHFHVRKEIMKRTGLKEHSIIDSLYRQCK 1006
CL++ V + F+ + I+ T + + D L
Sbjct: 244 ENCLLVLLNVQNAKAW--------NAFN-----LSCK--ILLTT--RFKQVTDFL----- 281
Query: 1007 AARTELKISVPD------------MLISNKDCSSINMQKE-CNDAFCVTVMIVENFKRTS 1053
+A T IS+ +L+ DC ++ +E +I E+ +
Sbjct: 282 SAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIR--- 338
Query: 1054 IDLETIQMWVMPFL--LKTVVKGF------REIKK-----------VDI-------LWKD 1087
L T W L T+++ E +K I +W D
Sbjct: 339 DGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFD 398
Query: 1088 KQK------ASKSHDDSFGELYLRVSMSGQCHITSLWSALMNDC------HQIM------ 1129
K +K H S L + I S++ L H+ +
Sbjct: 399 VIKSDVMVVVNKLHKYS---LVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNI 455
Query: 1130 ----DMIDWTRSHPDN-IRSFCLAY---GIDAGLQFFLTN--------LESAISDTGKNI 1173
D D + D S + + I+ + L LE I
Sbjct: 456 PKTFDSDDLIPPYLDQYFYSH-IGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAW 514
Query: 1174 LPE----HLL---------IVANT------LSATGEFVGLNAKGLALQRKHSSVSSPF-- 1212
+ L I N ++A +F+ + + + + S +
Sbjct: 515 NASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFL--------PKIEENLICSKYTD 566
Query: 1213 -VQAFFSNP-GASFIKAAKA 1230
++ A F +A K
Sbjct: 567 LLRIALMAEDEAIFEEAHKQ 586
>4ayb_C DNA-directed RNA polymerase; transferase, multi-subunit,
transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_C
4b1o_C 4b1p_Y 2waq_C 2wb1_C 3hkz_C 2pmz_C
Length = 395
Score = 71.3 bits (174), Expect = 7e-13
Identities = 50/316 (15%), Positives = 109/316 (34%), Gaps = 36/316 (11%)
Query: 948 ECLMLSDIVSTSMIIYSPQTGSMKHFSPWICHFHVRKEIMKRTGLKEHSIIDSLYRQCKA 1007
E + + ST M+ + V +++ T ++ S+ +
Sbjct: 109 EIVDAKKVPSTPMMTIYLTDEYKHDKEKALE---VARKLEY-TKIENVVSSTSIDIASMS 164
Query: 1008 ARTELKISVPDMLISNKD--CSSINMQKECNDAFCVTVMIVENFKRTSIDLETIQMWVMP 1065
+L + D +IN K + N +ID +
Sbjct: 165 IILQLDNEMLKDKGVTVDDVKKAINRLKLGEFVIDESEGNTLNISFANIDSIAALFKLRD 224
Query: 1066 FLLKTVVKGFREIKKVDILWKDKQKASKSHDDSFGELYLRVSMSGQCHITSLWSALMNDC 1125
+L T +KG + IK+ + K + + + +
Sbjct: 225 KILNTKIKGIKGIKRAIVQKKGDEYIILTDGSNLSGVL---------------------- 262
Query: 1126 HQIMDMIDWTRSHPDNIRSFCLAYGIDAGLQFFLTNLESAISDTGKNILPEHLLIVANTL 1185
+ +D + +NIR +GI+A + + + +++ G ++ H+L+VA+ +
Sbjct: 263 --SVKGVDIAKVETNNIREIEEVFGIEAAREIIIREISKVLAEQGLDVDMRHILLVADVM 320
Query: 1186 SATGEFVGLNAKGLALQRKHSSVSSPFVQAFFSNPGASFIKAAKAGAVDNLQGSVDALGW 1245
+ TG + G+ ++ +S +A F + AA G V+ +G V+ +
Sbjct: 321 TRTGVVRQIGRHGVTGEK-----NSVLARAAFEVTVKHLLDAAARGDVEEFKGVVENIII 375
Query: 1246 GKVPSVGTGGHFDIIY 1261
G +GT G ++
Sbjct: 376 GHPIKLGT-GMVELTM 390
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 60.8 bits (147), Expect = 3e-09
Identities = 115/707 (16%), Positives = 210/707 (29%), Gaps = 304/707 (42%)
Query: 393 IDALELGDIIYRPLT--DGDI---VLINRPPSIHPHSLIALTVK-----VLP-------- 434
+DA RPLT G + +L+ P + A ++ +LP
Sbjct: 1 MDAYST-----RPLTLSHGSLEHVLLV--PTASFFI---ASQLQEQFNKILPEPTEGFAA 50
Query: 435 ---ISSVVTINPLCCSPFHGDFDGDCLHGYI-----PQAIGARVELTELVALDKQLINQQ 486
++ L G F L GY+ P +G ++ L L +
Sbjct: 51 DDEPTTPA---ELV-----GKF----L-GYVSSLVEPSKVGQFDQVLNLC-----L--TE 90
Query: 487 SGRNLLSLGQD--SLTAAHLLMED--------SVLLSHLQMQQLQMFCPHRFLSPDIFKI 536
L G D +L AA LL E+ ++ +++ + + + + +F+
Sbjct: 91 FENCYLE-GNDIHAL-AAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFR- 147
Query: 537 SKDSVWSGK-QLFSMLLPPDFEYTFPSKDVYISGGKLISAEGSSWLRDY--EGNLFQYLI 593
+V G QL ++ F GG +G++ DY E + L
Sbjct: 148 ---AVGEGNAQLVAI---------F--------GG-----QGNT--DDYFEE---LRDLY 177
Query: 594 KRYRDKVLDFLYAAQEVLCE--------------------WLSVRGMTVSLSDLYLASHS 633
+ Y V D + + E L E WL T YL S
Sbjct: 178 QTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNT--PDKDYLLSIP 235
Query: 634 CSRKILMDEIFYGLREAQDTCNFQQLMVDSHMNFLMSAKDSEST-----RSLQGEHLSYE 688
S ++ G+ QL +H ++++AK T L+G +
Sbjct: 236 ISCPLI------GV---------IQL---AH--YVVTAKLLGFTPGELRSYLKG--ATGH 273
Query: 689 KQR---SAALSQA-SVDAFKHVFWDIQNLAYKYGSKDNSLLAMFKAGSKGNLLKLVQHSL 744
Q + A+++ S ++F + S ++ +F G +
Sbjct: 274 SQGLVTAVAIAETDSWESF-------------FVSVRKAITVLFFIGVRC---------- 310
Query: 745 CLGLQHSLAPLSFRFPHELSCAAWNRLRAGDNTECAKSYIPSAVVENSFLTGLNP--LEC 802
+ P + P L + +N E S + S ++ L ++
Sbjct: 311 -----YEAYPNTSLPPSILEDSL-------ENNEGVPSPMLS-------ISNLTQEQVQD 351
Query: 803 FIHSVTSRDSSFSDNADLPGTLTRRLMFFMRDLCTAYDGTVRNAYGNQIVQFSYNIEGTS 862
+++ N+ LP + + + + N N +V
Sbjct: 352 YVNKT---------NSHLPAG---------KQVEIS----LVNGAKNLVV---------- 379
Query: 863 TPTGEIGDQPVGSLSACAIS---EAAYSALDQ-----------------PISLLETSPLL 902
+G P SL ++ A S LDQ P++ S LL
Sbjct: 380 --SG-----PPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLL 432
Query: 903 NLKNVLECGSKKSNADQTMSLFLSNKLGKRRHGFEYGALEVKNHLECLMLSDIVSTSMI- 961
A ++ L ++ + A +++ I
Sbjct: 433 ------------VPASDLINKDLV------KNNVSFNAKDIQ----------------IP 458
Query: 962 IYSPQTGS-MKHFS--------PWICHFHVRKEIMKRTGLKEHSIID 999
+Y GS ++ S I V+ E T K I+D
Sbjct: 459 VYDTFDGSDLRVLSGSISERIVDCIIRLPVKWE--TTTQFKATHILD 503
Score = 53.9 bits (129), Expect = 5e-07
Identities = 82/574 (14%), Positives = 157/574 (27%), Gaps = 207/574 (36%)
Query: 51 LPNPT------NECSS-----------CGAKDRKACEGHFG-FIKFPFTILHPYFLS--D 90
LP PT +E ++ + + G F + T +L D
Sbjct: 41 LPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGND 100
Query: 91 I----AKLLNSICPK--------------CKTIRKERQKGAGS-----SRKEQPRVCKYC 127
I AKLL ++ K + S + ++
Sbjct: 101 IHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQL--VA 158
Query: 128 V----RNPAQWYPRMR--FKLSSKDLSGKTAIIVEIDEKLSKKNKKLPDDY-WGFIPFDA 180
+ N ++ +R ++ + E +L + + G +
Sbjct: 159 IFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGL---NI 215
Query: 181 QQ--EENSVKPNRKVLSCKQVSYLLKDVDPSIREEFI--LSKDAPFLKCFPVTPNNHR-- 234
+ E S P++ L +S P I + L+ K TP R
Sbjct: 216 LEWLENPSNTPDKDYLLSIPISC------PLI---GVIQLAHYVVTAKLLGFTPGELRSY 266
Query: 235 -----------VTEVPHAFSHEKKLFFDNWTRHLKKM--VDYRGRD------IELSHLVQ 275
VT V A + + FF + + + + + R + + S +++
Sbjct: 267 LKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPS-ILE 325
Query: 276 DCLK--------------ISKLHLDKSSRKDSAEVRQKKNIDIS--NSSGLRWIKDVVLG 319
D L+ +++ + K ++ + K ++IS N G
Sbjct: 326 DSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVN------------G 373
Query: 320 KRNDDCFRMVVTGDPNIKLKEIGIPCQVAERLQISERLNSWNWERLSVCISFRLLEKGEL 379
+N +VV+G P + L LN L K
Sbjct: 374 AKN-----LVVSGPP--------------QSLY---GLNLT-------------LRK--- 395
Query: 380 YVCRKGGLVRIRRIDALELGDIIYRPLTDGDIVLINRPPSIHPHSLIALTVKVLPISSVV 439
GL + RI P ++ R + LP++
Sbjct: 396 -AKAPSGLDQ-SRI-----------PFSE-------RKLKFS--------NRFLPVA--- 424
Query: 440 TINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQL----INQQSGRNLLSLG 495
SPFH L I + + K + + G +L L
Sbjct: 425 -------SPFHSHL----LVPASDL-INKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVL- 471
Query: 496 QDSLTAAHLLMEDSVLLSHLQMQQLQMFCPHRFL 529
S++ + D ++ ++ + F L
Sbjct: 472 SGSISERIV---DCIIRLPVKWETTTQFKATHIL 502
Score = 50.8 bits (121), Expect = 3e-06
Identities = 52/267 (19%), Positives = 88/267 (32%), Gaps = 90/267 (33%)
Query: 121 PRVCKYCVRN----PAQWYPRMRFKLSSKDLSGKTAIIVEIDEKLSKKNKKLPDDYWGFI 176
P + + + N P+ P M LS +L+ + ++ + ++K N LP I
Sbjct: 321 PSILEDSLENNEGVPS---P-M---LSISNLTQE-----QVQDYVNKTNSHLPAGKQVEI 368
Query: 177 PFDAQQEENSVKPNRKVLS------CKQVSYLLK-----DVDPSIREEFILSKDAP---- 221
N V+S L K +D S R F S+
Sbjct: 369 SL-----VNG--AKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQS-RIPF--SERKLKFSN 418
Query: 222 -FLKCFPVTPNNHRVTEVP-HAFSH-----EKKLFFD------NWTRH-LKKMV------ 261
FL PV P H SH + D ++ ++ V
Sbjct: 419 RFL---PVA--------SPFH--SHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDG 465
Query: 262 -DYRGRDIELSHLVQDCLKISKLHLDKSSRKDSAEVRQKKNIDI--SNSSGLRWIKDVVL 318
D R +S + DC+ + + +++ + + +D +SGL VL
Sbjct: 466 SDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHI-----LDFGPGGASGL-----GVL 515
Query: 319 GKRNDD--CFRMVVTGDPNIKLK-EIG 342
RN D R++V G +I + G
Sbjct: 516 THRNKDGTGVRVIVAGTLDINPDDDYG 542
Score = 50.8 bits (121), Expect = 4e-06
Identities = 88/539 (16%), Positives = 159/539 (29%), Gaps = 199/539 (36%)
Query: 166 KKLPDDYWGFIPFDAQQEENSVKPNRKVLSCKQVSYLLKDVDPSIREEFILSKDAPFLKC 225
K LP+ GF A +E + L K + Y+ V+PS +F L
Sbjct: 39 KILPEPTEGF----AADDEPTTPAE---LVGKFLGYVSSLVEPSKVGQF-----DQVLN- 85
Query: 226 FPVTPNNHRVTEVPHAFSHEKKLFFDNWTRHLKKMVDYRGRDIELSH-LVQDCLKISKLH 284
+ F+ +L G DI H L L+ +
Sbjct: 86 --------------LCLTE-----FE--NCYL------EGNDI---HALAAKLLQENDTT 115
Query: 285 LDKSSRKD------SAEVRQKKNIDISNSSGLRWIKDVVLGKRNDDCFRMVVT----GDP 334
L K K+ +A + K+ D ++S L + ++V G+
Sbjct: 116 LVK--TKELIKNYITARIMAKRPFDKKSNSAL-------FRAVGEGNAQLVAIFGGQGNT 166
Query: 335 NIKLKEIGIPCQVAERLQISERLNSWNWERLSVCISFRLLEKGELYVCRKGGLVR--IRR 392
+ +E L+ +LY LV I+
Sbjct: 167 DDYFEE----------LR-------------------------DLY-QTYHVLVGDLIKF 190
Query: 393 IDALELGDIIYRP------LTDG-DIV-LINRPPSIHPHSLIALTVKV-LPISSVVTINP 443
L ++I T G +I+ + P + + ++ + P+ V+
Sbjct: 191 SAET-LSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLL-SIPISCPLIGVIQ--- 245
Query: 444 LCCSPFHGDFDGDC-LHGYIPQAIGARVELTELVALDKQLINQQSGRNLLSLGQDSLTAA 502
L + L G+ P +L + G Q +TA
Sbjct: 246 LAH------YVVTAKLLGFTP----------------GELRSYLKG--ATGHSQGLVTAV 281
Query: 503 HLLMEDS------------VLLSHLQMQQLQMFCPHRFLSPDIFKISKDSVWSGKQLFS- 549
+ DS +L + ++ + + P+ L P I +DS+ + + + S
Sbjct: 282 AIAETDSWESFFVSVRKAITVLFFIGVRCYEAY-PNTSLPP---SILEDSLENNEGVPSP 337
Query: 550 ML----LPPDF---------EYTFPSKDVYIS----------GGKLISAEG-SSWLRDY- 584
ML L + + K V IS G S G + LR
Sbjct: 338 MLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAK 397
Query: 585 -EGNLFQYLIKRYRDKVLDF---------------LYAAQEVLCEWLSVRGMTVSLSDL 627
L Q I + ++ L F L A +++ + L ++ + D+
Sbjct: 398 APSGLDQSRIP-FSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDI 455
Score = 50.0 bits (119), Expect = 7e-06
Identities = 55/340 (16%), Positives = 105/340 (30%), Gaps = 123/340 (36%)
Query: 59 SSCGAKD-RKACEGHFGFIKFPFTILHPYFLSDIAKLLNSICPKCKTIRKERQKGAGSSR 117
+S A+D + HF + F+IL DI N+ P TI +KG
Sbjct: 1638 TSKAAQDVWNRADNHF-KDTYGFSIL------DIVI--NN--PVNLTIHFGGEKG----- 1681
Query: 118 KEQPRVCKYCVRNPAQWYPRMRFKLSSKDLSGKTAIIVEIDEKLSKKNKKLPDDYWGFIP 177
+ + Y M F+ I EI+E +
Sbjct: 1682 -----------KRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTS------------YT 1718
Query: 178 FDAQQE-----ENSVKPNRKVLSCKQ-----VSY-LLKDVDPSIREEFILSKDAPF---- 222
F +++ + + Q + +D ++ + ++ DA F
Sbjct: 1719 FRSEKGLLSATQFT-----------QPALTLMEKAAFED----LKSKGLIPADATFAGHS 1763
Query: 223 ------LKCFPVTPNNHRVTEVPHAFSHEKKLFFDNWTRHLKKMVDYRGR----DIELSH 272
L + +V + ++ L ++V YRG +
Sbjct: 1764 LGEYAALAS---------LADV---------MSIES----LVEVVFYRGMTMQVAVPRDE 1801
Query: 273 LVQDCLKISKLHLDKSSRKDSAEVRQKKNIDISNSSGLRWIKDVVLGKRNDDC--FRMVV 330
L + + ++ + + S E Q + +G W+ ++V N + + V
Sbjct: 1802 LGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTG--WLVEIV----NYNVENQQYVA 1855
Query: 331 TGDP-----------NIKLKEIGI-PCQVAERLQ-ISERL 357
GD IKL++I I Q + L+ + L
Sbjct: 1856 AGDLRALDTVTNVLNFIKLQKIDIIELQKSLSLEEVEGHL 1895
Score = 49.7 bits (118), Expect = 8e-06
Identities = 59/337 (17%), Positives = 96/337 (28%), Gaps = 135/337 (40%)
Query: 681 QGEHLSYEKQRSAALSQASVDAFKHVFWDI--QNLAYKYG------SKDN--SLLAMFKA 730
QG S E+ L + S A + V W+ + YG +N +L F
Sbjct: 1624 QG---SQEQGMGMDLYKTS-KAAQDV-WNRADNHFKDTYGFSILDIVINNPVNLTIHF-G 1677
Query: 731 GSKG-----NLLKLVQHSLCLG----------LQHSLAPLSFRFPHEL------------ 763
G KG N ++ ++ G + +FR L
Sbjct: 1678 GEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALT 1737
Query: 764 --SCAAWNRLRAGDNTECAKSYIPSAVVENSFLTGLNPLECFIHS-------VTSRDS-S 813
AA+ L+ +K IP ++ G HS + D S
Sbjct: 1738 LMEKAAFEDLK-------SKGLIP----ADATFAG--------HSLGEYAALASLADVMS 1778
Query: 814 FSDNADL------------PGTLTRRLMFFMRDLCTAYDGTVRNAYGNQIVQFSYNIEGT 861
++ P R + M G V ++ + +Q Y +E
Sbjct: 1779 IESLVEVVFYRGMTMQVAVPRDELGRSNYGM---IAINPGRVAASFSQEALQ--YVVERV 1833
Query: 862 STPTGEI---------GDQPV--GSLSACAISEAAYSALDQPISLLETSPLLNLKNVLEC 910
TG + Q V G L ALD ++L + L+ +
Sbjct: 1834 GKRTGWLVEIVNYNVENQQYVAAGDL----------RALDTVTNVLNF---IKLQKI--- 1877
Query: 911 GSKKSNADQTMSLFLSNKLGKRRHGFEYGALEVKNHL 947
+++SL E EV+ HL
Sbjct: 1878 --DIIELQKSLSL-------------E----EVEGHL 1895
Score = 49.3 bits (117), Expect = 1e-05
Identities = 60/367 (16%), Positives = 105/367 (28%), Gaps = 143/367 (38%)
Query: 766 AAWNRLRAGDNTECAKSYIPSAVVENSFLTGLNPLECFIHSVTSRDSSFSDNADLPGTLT 825
WNR A ++ + + +V N NP+ IH + +N
Sbjct: 1644 DVWNR--ADNHFKDTYGFSILDIVIN------NPVNLTIHFGGEKGKRIREN-------- 1687
Query: 826 RRLMFFMRDLCTAYDGTVRNAYGNQIVQF---SYNIEGTSTPTGEIGD----QPVGSLSA 878
+ + T DG ++ + + SY G + QP
Sbjct: 1688 --YSAMIFE--TIVDGKLKTEKIFKEINEHSTSYTFRS---EKGLLSATQFTQP------ 1734
Query: 879 CAI---SEAAYSALDQPISLLETSPLLNLKNVLECGSKKSNADQTMSLF--LSNKLGKRR 933
A+ +AA+ L K + F S LG
Sbjct: 1735 -ALTLMEKAAFEDL-----------------------KSKGLIPADATFAGHS--LG--- 1765
Query: 934 HGFEYGAL----EVKNHLECLMLSDIVSTSMIIYSPQTGSMKHFSPWICHFHVRKEIMKR 989
EY AL +V + + +V V R
Sbjct: 1766 ---EYAALASLADV------MSIESLVEV-----------------------VF----YR 1789
Query: 990 TGLKEHSIIDSLYRQCKAARTELKISVPDMLISNKDCSSINMQKECNDAFCVTV-----M 1044
G + Q R EL S M+ N + + +E V
Sbjct: 1790 -G---------MTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGW 1839
Query: 1045 IVE--NF----KRTSI--DLETIQMWVMPFLLKTVVKGFREIKKVDILWKDKQKASKSHD 1096
+VE N+ ++ DL + + V+ F +++K+DI+ + + S S +
Sbjct: 1840 LVEIVNYNVENQQYVAAGDLRALDT------VTNVLN-FIKLQKIDII---ELQKSLSLE 1889
Query: 1097 DSFGELY 1103
+ G L+
Sbjct: 1890 EVEGHLF 1896
Score = 46.2 bits (109), Expect = 1e-04
Identities = 102/672 (15%), Positives = 172/672 (25%), Gaps = 263/672 (39%)
Query: 750 HSLAPL-----SFRF----PHELSCAAWNRLRAG-------DNTECAKSYIPSAVVE--N 791
+S PL S P A ++L+ A P+ E
Sbjct: 4 YSTRPLTLSHGSLEHVLLVPTASFFIA-SQLQEQFNKILPEPTEGFAADDEPTTPAELVG 62
Query: 792 SFLTGLNPLECFIHSVTSRDSSFSDNADLPGTLTRRLMFFMRD-LCTAYDGTVRNAYGNQ 850
FL ++ S S L L F L GN
Sbjct: 63 KFL-------GYV----SSLVEPSKVGQFDQVLNLCLTEFENCYLE-----------GND 100
Query: 851 IVQFSYNIEGTSTPTGEIGDQPVGSLSACAISEAAYSA---LDQPISLLETSPLLNLKNV 907
I + + + + + + +A +P S L
Sbjct: 101 IHALAAKLLQ---------ENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFR---- 147
Query: 908 LECGSKKSNADQTMSLFLSNKLGKRRHG-------FE--------YGALE---VKNHLEC 949
+ NA Q +++F G G FE Y L +K E
Sbjct: 148 ---AVGEGNA-QLVAIF-----G----GQGNTDDYFEELRDLYQTYHVLVGDLIKFSAET 194
Query: 950 LM-LSDIVSTSMIIYS---------------PQTGSMKH--FS-PWI-----CHFHVRKE 985
L L + +++ P + S P I H+ V
Sbjct: 195 LSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVV--- 251
Query: 986 IMKRTGLKEHSIIDSLYRQCKAARTELKISVPDMLISNKDCSSINMQKECNDAFCVTVMI 1045
K G + L K A + V + I+ D
Sbjct: 252 TAKLLGFTPGELRSYL----KGATGHSQGLVTAVAIAETDSW------------------ 289
Query: 1046 VENFKRTSIDLETIQMWVMPFLLKTVVKGFREIKKVDILWKDKQKASKSHDDSFGELYLR 1105
E+F + T+ ++ G R + +++ L
Sbjct: 290 -ESFFVSVRKAITVLFFI----------GVR-----------------CY-EAYPNTSLP 320
Query: 1106 VSMSGQC------------HITSLWSALMNDCHQIMDMIDWTRSH-PDN----I------ 1142
S+ I++L Q+ D ++ T SH P I
Sbjct: 321 PSILEDSLENNEGVPSPMLSISNL------TQEQVQDYVNKTNSHLPAGKQVEISLVNGA 374
Query: 1143 RSFCLAYGIDAGLQFFLTNLESAISDTGKNILPEHLLIVANTLSATGEFVGLNAKGLALQ 1202
++ ++ G L L A + +G + ++ +
Sbjct: 375 KNLVVS-GPPQSLYGLNLTLRKAKAPSGLD----------------------QSRIPFSE 411
Query: 1203 RK---HSS---VSSPFVQAFFSNPGASFIKAAKAGAVDNLQGSVDALGWG----KVP--S 1250
RK + V+SP F S + A +L + + + ++P
Sbjct: 412 RKLKFSNRFLPVASP----FHS----HLLVPASDLINKDLVK--NNVSFNAKDIQIPVYD 461
Query: 1251 VGTGGHFDIIYSGEGRTLSKPVD---VYNLLSTPVSSKQN-EKLKVCKAQGLISDKCGAK 1306
G D+ R LS + V ++ PV E KA ++ D
Sbjct: 462 TFDGS--DL------RVLSGSISERIVDCIIRLPV----KWETTTQFKATHIL-D----- 503
Query: 1307 FGDFAFKGLGNL 1318
FG GLG L
Sbjct: 504 FGPGGASGLGVL 515
Score = 42.0 bits (98), Expect = 0.002
Identities = 46/355 (12%), Positives = 95/355 (26%), Gaps = 111/355 (31%)
Query: 1051 RTSIDLETIQMWVMPFLLKTVVKGFREI--KKVDILWKDKQKASKSHDDSFGELYLR--- 1105
+ + T + + L+ + F +I + + D + + + EL +
Sbjct: 17 EHVLLVPT-ASFFIASQLQ---EQFNKILPEPTEGFAADDEPTTPA------ELVGKFLG 66
Query: 1106 -----VSMSGQCHITSLWSALM----------NDCHQIM-DMIDWTRSHPDNIRSFCLAY 1149
V S + + + ND H + ++ + + Y
Sbjct: 67 YVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNY 126
Query: 1150 GIDAGLQFFLTNLESAISDTGKNILPEH---LLIVANTLSAT------GEFVGLNAKGLA 1200
+A + + L +A G+ G
Sbjct: 127 --------I-----TARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQ--GNTDDYFE 171
Query: 1201 -LQRKHSSVSSPFVQAFFSNPGASFIKAAKAGAVDN--LQGSVDALGWGKVPSVGTGGHF 1257
L+ + + V + + + ++ L W + PS
Sbjct: 172 ELRDLYQT-YHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPS------- 223
Query: 1258 DIIYSGEGRTLSKPVDVYNLLSTPVSSKQNEKLK------VCKAQGLISDKCGAKFGDFA 1311
+ P D LLS P+S ++ K G G+
Sbjct: 224 -----------NTP-DKDYLLSIPISCPLIGVIQLAHYVVTAKLLGF-------TPGELR 264
Query: 1312 --FKGLGNLDFETISRGVL-------RKSW-TYNDVLRLSNALKKILHKYSIGQR 1356
KG S+G++ SW ++ +R A+ +L + IG R
Sbjct: 265 SYLKGA-----TGHSQGLVTAVAIAETDSWESFFVSVR--KAI-TVL--FFIGVR 309
Score = 37.0 bits (85), Expect = 0.066
Identities = 52/263 (19%), Positives = 85/263 (32%), Gaps = 89/263 (33%)
Query: 1143 RSFCLAYGIDAGLQFFLTNLESAISDTGKNILPEHLLIVANTLSATGEFVG-LNA--KGL 1199
R L++G +LE + +P +A+ L +F L +G
Sbjct: 7 RPLTLSHG----------SLEHVLL------VPTASFFIASQLQE--QFNKILPEPTEGF 48
Query: 1200 ALQRKHSSVSSPFVQAF--FSNPGASFIKAAKAGAVDN-LQGSVDALGWGKVPSVGTGGH 1256
A + ++ + V F + +S ++ +K G D L +
Sbjct: 49 AADDEPTTPAE-LVGKFLGYV---SSLVEPSKVGQFDQVLNLCLT--------------E 90
Query: 1257 F--------DI------IYSGEGRTLSKPVDV---Y----NLLSTPVSSKQNEKLKVCKA 1295
F DI + TL K ++ Y + P K N L
Sbjct: 91 FENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVG 150
Query: 1296 QGLISDKCGAKFGDFA-FKGLGNLD--FETISRGVLRKSW-TYNDVLRLSNALKKILHKY 1351
+G A+ A F G GN D FE LR + TY+ ++ L K
Sbjct: 151 EG------NAQL--VAIFGGQGNTDDYFEE-----LRDLYQTYHVLVG---DLIK----- 189
Query: 1352 SIGQRLSEKDKTTVIRALYFHPR 1374
+ LSE +TT+ A +
Sbjct: 190 FSAETLSELIRTTL-DAEKVFTQ 211
>3qqc_A DNA-directed RNA polymerase subunit B, DNA-direct polymerase
subunit A', DNA-directed...; transcription, fusion
protein, chimera protein, multiprotein; 3.30A
{Pyrococcus furiosus}
Length = 436
Score = 52.8 bits (127), Expect = 6e-07
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 47 PRLGLPNPTNECSSCGAKDRKACEGHFGFIKFPFTILHPYFLSDIAKLLNSICPKC 102
R+G+ +P C +CG C GHFG I+ ++H F I ++L S C +C
Sbjct: 110 KRMGVIDPGLRCETCG-GRAGECPGHFGHIELARPVIHVGFAKTIYRILESTCREC 164
Score = 37.0 bits (86), Expect = 0.040
Identities = 5/52 (9%), Positives = 10/52 (19%), Gaps = 7/52 (13%)
Query: 318 LGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERLQISERLNSWNWERLSVCI 369
G V V + +E+ N + +
Sbjct: 381 SGGAGSGAGSGSVLARAA-------FEITVQHLFEAAEKGEVDNLNGVIENV 425
>1hqm_D DNA-directed RNA polymerase; transferase, transcription, 3D-
structure; 3.30A {Thermus aquaticus} SCOP: i.8.1.1 PDB:
1i6v_D* 2gho_D
Length = 1265
Score = 36.9 bits (86), Expect = 0.061
Identities = 41/147 (27%), Positives = 69/147 (46%), Gaps = 30/147 (20%)
Query: 318 LGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERLQ---ISERLNSWNWERLSVCISF--- 371
LGKR D R V+ P +KL + G+P ++A L + +++ E + +
Sbjct: 359 LGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKM-----EEKAFAPNVKAA 413
Query: 372 -RLLEKGELYVCRKGGLVRIRRIDALELGDIIY-RPLTDGDIVLINRPPSIHPHSLIALT 429
R+LE+ ++ DALE ++I+ + VL+NR P++H + A
Sbjct: 414 RRMLERQRD--------IKDEVWDALE--EVIHGKV------VLLNRAPTLHRLGIQAFQ 457
Query: 430 VKVLPISSVVTINPLCCSPFHGDFDGD 456
VL + ++PL C F+ DFDGD
Sbjct: 458 P-VLVEGQSIQLHPLVCEAFNADFDGD 483
>2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme,
streptolydigin, antibiotic, transcription regulation;
HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2
PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D*
2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D*
3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D
Length = 1524
Score = 36.3 bits (84), Expect = 0.085
Identities = 41/148 (27%), Positives = 70/148 (47%), Gaps = 30/148 (20%)
Query: 317 VLGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERLQ---ISERLNSWNWERLSVCISF-- 371
+LGKR D R V+ P +KL + G+P ++A L + +++ E + +
Sbjct: 618 LLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKM-----EEKGIAPNVKA 672
Query: 372 --RLLEKGELYVCRKGGLVRIRRIDALELGDIIY-RPLTDGDIVLINRPPSIHPHSLIAL 428
R+LE+ ++ DALE ++I+ + VL+NR P++H + A
Sbjct: 673 ARRMLERQRD--------IKDEVWDALE--EVIHGKV------VLLNRAPTLHRLGIQAF 716
Query: 429 TVKVLPISSVVTINPLCCSPFHGDFDGD 456
VL + ++PL C F+ DFDGD
Sbjct: 717 QP-VLVEGQSIQLHPLVCEAFNADFDGD 743
>1gd2_E Transcription factor PAP1; basic leucine zipper, protein-DNA
complex, transcription/DNA complex; HET: DNA; 2.00A
{Schizosaccharomyces pombe} SCOP: h.1.3.1
Length = 70
Score = 29.6 bits (66), Expect = 1.2
Identities = 16/63 (25%), Positives = 24/63 (38%), Gaps = 8/63 (12%)
Query: 106 RKERQKGAGSSRKEQPRVCKYCVRNPAQWYPRMRFKLSSKDLSGKTAIIVEIDEKLSKKN 165
RK + S RK Q R AQ R R + K L + + E+ + +N
Sbjct: 1 RKNSDQEPSSKRKAQNRA--------AQRAFRKRKEDHLKALETQVVTLKELHSSTTLEN 52
Query: 166 KKL 168
+L
Sbjct: 53 DQL 55
>3chv_A Prokaryotic domain of unknown function (DUF849) W barrel fold; TIM
barrel fold, structural genomics, joint center for struc
genomics; HET: MSE; 1.45A {Silicibacter pomeroyi dss-3}
PDB: 3fa5_A
Length = 284
Score = 31.5 bits (71), Expect = 1.7
Identities = 19/183 (10%), Positives = 43/183 (23%), Gaps = 29/183 (15%)
Query: 977 ICHFHVRKEIMKRTGLKEHSIIDSLYRQCKAARTELKISVPDMLISNKDCSSINMQKECN 1036
I H HVR + G S + + P M++ +
Sbjct: 50 IAHCHVRND----DG--TPSSDPDRFARLTEGLHT---HCPGMIVQFSTGGRSGAGQARG 100
Query: 1037 DAFCVTVMIVENFKRTSIDLETI--QMWVMPFLLKTVVKGFREIKKVDILWKDKQKASKS 1094
+ + S+ + + V V +++ + + ++
Sbjct: 101 GMLPLKPDMA------SLSVGSNNFPSRVYENPPDLVDWLAAQMRSYRVTPE-----IEA 149
Query: 1095 HDDSFGELYLRVSMSGQCHITSLWSALM-------NDCHQIMDMIDWTRSHPDNIRSFCL 1147
D S + + G + +M D + R+
Sbjct: 150 FDLSHILRAIDMHGRGLLYGKLYVQFVMGVKNAMPADREVFDFYVRMMRTRAPQAEWCAA 209
Query: 1148 AYG 1150
G
Sbjct: 210 GIG 212
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 30.8 bits (69), Expect = 2.2
Identities = 9/34 (26%), Positives = 13/34 (38%), Gaps = 12/34 (35%)
Query: 98 ICPKCKT----IRKERQKGAGSSRKEQPRVCKYC 127
CP+CK I + +G + VC C
Sbjct: 23 TCPECKVYPPKIVERFSEG------D--VVCALC 48
>3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase,
nucleotidyltransferase, transcription, transferase;
11.20A {Escherichia coli} PDB: 3iyd_D*
Length = 1407
Score = 30.7 bits (70), Expect = 4.4
Identities = 41/162 (25%), Positives = 64/162 (39%), Gaps = 63/162 (38%)
Query: 318 LGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERLQISERLNSWNWERLSVCISF------ 371
LGKR D R V+T P ++L + G+P ++A L F
Sbjct: 343 LGKRVDYSGRSVITVGPYLRLHQCGLPKKMALEL-------------------FKPFIYG 383
Query: 372 RLLEKGELY--------VCRKGGLVRIRRIDALELGDIIY-RPLTDGDIVLINRPPSIH- 421
+L +G V R+ +V D L+ ++I P VL+NR P++H
Sbjct: 384 KLELRGLATTIKAAKKMVEREEAVV----WDILD--EVIREHP------VLLNRAPTLHR 431
Query: 422 -------PHSLIALTVKVLPISSVVTINPLCCSPFHGDFDGD 456
P VL + ++PL C+ ++ DFDGD
Sbjct: 432 LGIQAFEP---------VLIEGKAIQLHPLVCAAYNADFDGD 464
>3mbg_A FAD-linked sulfhydryl oxidase ALR; flavin, flavoprotein, GFER; HET:
FAD; 1.85A {Homo sapiens} PDB: 3r7c_A*
Length = 139
Score = 28.9 bits (64), Expect = 5.9
Identities = 11/60 (18%), Positives = 22/60 (36%), Gaps = 2/60 (3%)
Query: 944 KNHLECLMLSDIVSTSMIIYSPQTGSMKHFSPWICHFHVRKEIMKRTGLKEHSIIDSLYR 1003
C ++ + + P T + F+ W+CH H E+ ++ G + R
Sbjct: 71 SKFYPCEECAEDLRKRLARNHPDTRTRAAFTQWLCHLH--NEVNRKLGKPDFDCSKVDER 128
>3ekg_A Mandelate racemase/muconate lactonizing enzyme; structural
genomics, nysgrc, L-rhamnonate dehydratase,target PSI-2;
HET: TLA; 1.60A {Azotobacter vinelandii avop} PDB:
2oz3_A*
Length = 404
Score = 29.6 bits (67), Expect = 8.6
Identities = 14/61 (22%), Positives = 24/61 (39%), Gaps = 2/61 (3%)
Query: 100 PKCKTIRKERQKGAGSSRKEQPR--VCKYCVRNPAQWYPRMRFKLSSKDLSGKTAIIVEI 157
P K +R +G G+ +Q + P YP R S ++ ++VEI
Sbjct: 6 PTIKQVRAFVLRGGGADYHDQGDGHWIDDHISTPMGKYPEYRQSRRSFGINVLGTLVVEI 65
Query: 158 D 158
+
Sbjct: 66 E 66
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.320 0.136 0.408
Gapped
Lambda K H
0.267 0.0510 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 21,835,317
Number of extensions: 1328832
Number of successful extensions: 2427
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2362
Number of HSP's successfully gapped: 35
Length of query: 1443
Length of database: 6,701,793
Length adjustment: 106
Effective length of query: 1337
Effective length of database: 3,742,167
Effective search space: 5003277279
Effective search space used: 5003277279
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 64 (28.9 bits)