RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1361
(1274 letters)
>1qht_A Protein (DNA polymerase); archaea, hyperthermostable, family B
polymer alpha family polymerase, transferase; 2.10A
{Thermococcus SP} SCOP: c.55.3.5 e.8.1.1 PDB: 1tgo_A
2xhb_A* 2vwj_A* 2vwk_A* 1wns_A* 1wn7_A 1qqc_A* 4ahc_A*
4ail_C* 3a2f_A* 2jgu_A* 1d5a_A
Length = 775
Score = 476 bits (1227), Expect = e-152
Identities = 128/455 (28%), Positives = 209/455 (45%), Gaps = 41/455 (9%)
Query: 562 ITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNKKEGEETGEANKGKGR 621
++ + G L E+ LL ++++ + P+K + R
Sbjct: 333 LSRLIGQSLWDVSRSSTGNLVEWFLLRKAYKRNELAPNKPD-------------ERELAR 379
Query: 622 KKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCE 681
++ Y+GG V EP++G +D I+ +DF SLYPSII +N+ T+ ++ D+
Sbjct: 380 RRGGYAGGYVKEPERGLWDN-IVYLDFRSLYPSIIITHNVSPDTLNREGCKEYDVAPEVG 438
Query: 682 YLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGC 741
+ G +PS + L+E R+++K MK + D RQ+A+K+ ANS YG
Sbjct: 439 HKFCKDFP-GFIPSLLGDLLEERQKIKRKMKAT-VDPLEKKLLDYRQRAIKILANSFYGY 496
Query: 742 LGFPNSRFFAQPLAALVTAKGREILLNTKSLV-ENLNYEVIYGDTDSLMISCNVNDYDSV 800
G+ +R++ + A VTA GRE + + E ++V+Y DTD L + D ++V
Sbjct: 497 YGYAKARWYCKECAESVTAWGREYIEMVIRELEEKFGFKVLYADTDGLHATIPGADAETV 556
Query: 801 FKIGNQIKSECN-KLYKQLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGV 859
K + N KL LEL+ +G Y + KKKYA + GK+ +G+
Sbjct: 557 KKKAKEFLKYINPKLPGLLELEYEGFYVRGFFVTKKKYAVID----EEGKI----TTRGL 608
Query: 860 DVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTL 919
++VRRDWS++A E V+ IL ++ +K++ L VP
Sbjct: 609 EIVRRDWSEIAKETQARVLEAILKHGD---------VEEAVRIVKEVTEKLSKYEVPPEK 659
Query: 920 LEITKQLTKAPEEYTDRKALPHVQVALRLNNTNSKKLKQGDTISYIICEDGTSEAATQRA 979
L I +Q+T+ +Y PHV VA RL K++ G ISYI+ + RA
Sbjct: 660 LVIHEQITRDLRDYK--ATGPHVAVAKRLAARG-VKIRPGTVISYIVLKGSGR--IGDRA 714
Query: 980 YNIEELKNNSKLKIDVNYYLSQQIHPVVTRLLEPI 1014
+E K + D YY+ Q+ P V R+L+
Sbjct: 715 IPADEFDPT-KHRYDAEYYIENQVLPAVERILKAF 748
>3iay_A DNA polymerase delta catalytic subunit; protein-DNA complex, DNA
replication, DNA-BI DNA-directed DNA polymerase,
exonuclease, hydrolase; HET: DNA DOC DCP; 2.00A
{Saccharomyces cerevisiae}
Length = 919
Score = 444 bits (1143), Expect = e-138
Identities = 124/481 (25%), Positives = 208/481 (43%), Gaps = 57/481 (11%)
Query: 560 IRITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNKKEGEETGEANKGK 619
+ V G S L G+ + L E V+P+ Q
Sbjct: 472 TEMARVTGVPFSYLLARGQQIKVVSQLFRKCLEIDTVIPNMQSQ---------------- 515
Query: 620 GRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTI---------PVRM 670
Y G V+EP +G+YD I +DFNSLYPSI+ +N+C+TT+ +++
Sbjct: 516 -ASDDQYEGATVIEPIRGYYDVPIATLDFNSLYPSIMMAHNLCYTTLCNKATVERLNLKI 574
Query: 671 LQDSDITTLCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKA 730
+D IT +Y + GILP + +L+ +R++ K ++ + RQ A
Sbjct: 575 DEDYVITPNGDYFVTTKRRRGILPIILDELISARKRAKKDLRDEK-DPFKRDVLNGRQLA 633
Query: 731 LKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVE---------NLNYEVI 781
LK++ANS+YG G + +++ VTA GR ++L TK+ V+ + V+
Sbjct: 634 LKISANSVYGFTGATVGKLPCLAISSSVTAYGRTMILKTKTAVQEKYCIKNGYKHDAVVV 693
Query: 782 YGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYKQ-LELDIDGVYKYMLLLKKKKYAAL 840
YGDTDS+M+ D +G + + L+K + L+ + Y LL+ KK+YA L
Sbjct: 694 YGDTDSVMVKFGTTDLKEAMDLGTEAAKYVSTLFKHPINLEFEKAYFPYLLINKKRYAGL 753
Query: 841 SISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIH 900
+N + KG+ VRRD L S V+ +IL E++ +
Sbjct: 754 FW---TNPDKFDKLDQKGLASVRRDSCSLVSIVMNKVLKKILIERN---------VDGAL 801
Query: 901 EHMKKIRTDLDNGFVPLTLLEITKQLTKAPEEYTDRKALPHVQVALRLNNTNSKKLKQGD 960
+++ D+ + V ++ L I+K L YT+ PH +A R+ GD
Sbjct: 802 AFVRETINDILHNRVDISKLIISKTLAP---NYTNP--QPHAVLAERMKRREGVGPNVGD 856
Query: 961 TISYIICEDGTSEAATQRAYNIEELKNNSKLKIDVNYYLSQQIHPVVTRLLEPIEGTDAV 1020
+ Y+I RA + + N +++D YYL+ Q+ + ++ PI G
Sbjct: 857 RVDYVIIGGNDK--LYNRAEDPLFVLEN-NIQVDSRYYLTNQLQNPIISIVAPIIGDKQA 913
Query: 1021 R 1021
Sbjct: 914 N 914
Score = 66.9 bits (163), Expect = 4e-11
Identities = 36/242 (14%), Positives = 80/242 (33%), Gaps = 35/242 (14%)
Query: 346 EWEAIQTEPSTSEPQVHSRTADDSLPLATDHENKK-VFRMFFLDAFEDIY-----KQPGT 399
E + Q E ++ + H ++ + L TD + +DA + + + T
Sbjct: 10 EQDVSQMEHDMADQEEHDLSSFERKKLPTDFDPSLYDISFQQIDAEQSVLNGIKDENTST 69
Query: 400 V-YLFGKVFVKENNSHSSCCVIVQNIDRKIYLLPRSEHLKTKEPVSIAQVYSEFDQIATQ 458
V FG + S V +Y+ + + Q+ +
Sbjct: 70 VVRFFGV-----TSEGHSVLCNVTGFKNYLYVPAPNSS----DANDQEQINKFVHYLNET 120
Query: 459 YKILDFKSRKIEKK--YAFNLPGVPDLSEYLEV--RYSAKCPALPSDL--SGDTFSHVFG 512
+ + K+ + ++ + ++ Y L + +F+ F
Sbjct: 121 FDHAIDSIEVVSKQSIWGYS---GDTKLPFWKIYVTYPHMVNKLRTAFERGHLSFNSWFS 177
Query: 513 TKSSFLEN------LLLERKIKGPSWLEFPEAE----KFPSRISWCKYEVQCNQMEKIRI 562
++ +N L+++ I G SW+ P+ + + +R+S C+ EV N I
Sbjct: 178 NGTTTYDNIAYTLRLMVDCGIVGMSWITLPKGKYSMIEPNNRVSSCQLEVSINYRNLIAH 237
Query: 563 TN 564
Sbjct: 238 PA 239
>1s5j_A DNA polymerase I; replication, disulfide bonds, transferase; HET:
DNA; 2.40A {Sulfolobus solfataricus} SCOP: c.55.3.5
e.8.1.1
Length = 847
Score = 438 bits (1127), Expect = e-137
Identities = 117/528 (22%), Positives = 209/528 (39%), Gaps = 55/528 (10%)
Query: 519 ENLLLERKIKGPSWLEFPEAEKF----------PSRI-SWCKYEVQCNQMEKIRITNVCG 567
+ LL K+K + + F + EK ++ ++ + RI+ +
Sbjct: 349 KALLGTSKVKVDTLISFLDVEKLIEYNFRDAEITLQLTTFNNDLTMKLIVLFSRISRLGI 408
Query: 568 NVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNKKEGEETGEANKGKGRKKAAYS 627
L+RT S + L ++++++P K ++ ++ K Y
Sbjct: 409 EELTRT---EISTWVKNLYYWEHRKRNWLIPLK-----EEILAKSSNIRTSALIKGKGYK 460
Query: 628 GGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLPEHQ 687
G +V++P G + I ++DF SLYPSII+ +N+ + T+ ++ + H
Sbjct: 461 GAVVIDPPAGIFFN-ITVLDFASLYPSIIRTWNLSYETVDIQQCKKPYEVKDETGEVLHI 519
Query: 688 V---DTGILPSEIKKLVESRRQVKA-LMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLG 743
V GI L + R ++ K PN S + + YD+ Q+A+K+ N+ YG G
Sbjct: 520 VCMDRPGITAVITGLLRDFRVKIYKKKAKNPNNSEEQKLLYDVVQRAMKVFINATYGVFG 579
Query: 744 FPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKI 803
+A +A VTA GR ++ +T V+YGDTDSL + +
Sbjct: 580 AETFPLYAPRVAESVTALGRYVITSTVKKAREEGLTVLYGDTDSLFLLNPPKN------S 633
Query: 804 GNQIKSECNKLYKQLELDIDGVYKYMLLL-KKKKYAALSISKLSNGKMICSQEIKGVDVV 862
I + L+L++D YK++ KK Y + +GK+ +IKG+ V
Sbjct: 634 LENIIKWVKTTFN-LDLEVDKTYKFVAFSGLKKNYFGV----YQDGKV----DIKGMLVK 684
Query: 863 RRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEI 922
+R+ + + V ++ S D + + + I + +K L N L L
Sbjct: 685 KRNTPEFVKKVFNEVKELMISINSPND--VKEIKRKIVDVVKGSYEKLKNKGYNLDELAF 742
Query: 923 TKQLTKAPEEYTDRKALPHVQVALRLNNTNSKKLKQGDTISYIICEDGTSEAATQRAYNI 982
L+K + Y + HV+ AL+L + D I Y+ Q A
Sbjct: 743 KVMLSKPLDAY-KKNTPQHVKAALQLRPFG-VNVLPRDIIYYVKVRSKDGVKPVQLAKVT 800
Query: 983 EELKNNSKLKIDVNYYLSQQIHPVVTRLLEPIEGTDAVRIAECLGLDT 1030
E ID YL + + ++L G IA + +D+
Sbjct: 801 E---------IDAEKYL-EALRSTFEQILRAF-GVSWDEIAATMSIDS 837
Score = 59.1 bits (143), Expect = 8e-09
Identities = 17/176 (9%), Positives = 40/176 (22%), Gaps = 26/176 (14%)
Query: 377 ENKKVFRMFFLDAFEDIYKQPGTVYLFGKVFVKENNSHSSCCVIVQNIDRKIYLLPRSEH 436
E ++ F L D K LF K + +
Sbjct: 9 EAQENKIYFLLQVDYDGKKGKAVCKLFDKE-----TQKIYALYDNTGHKPYFLVDLEPDK 63
Query: 437 LKTKEPVSIAQVYSEFDQIATQYKILDFKSRKIEKKYAFNLPGVPDLSEYLEVRYSAKCP 496
+ K P + + + ++ + K+ K + V L +
Sbjct: 64 VG-KIPKIVRDPSFDHIETVSKIDPYTWNKFKLTKIVVRDPLAVRRLRNDVP-------- 114
Query: 497 ALPSDLSGDTFSHVFGTKSSFLENLLLERKIKGPSWLEFPEAEKFPSRISWCKYEV 552
+ + N + + + + +S + +V
Sbjct: 115 ------------KAYEAHIKYFNNYMYDIGLIPGMPYVVKNGKLESVYLSLDEKDV 158
>3k59_A POL II, DNA polymerase II; protein-DNA complex, DNA damage, DNA
repair, DNA-binding; HET: DNA DOC DCP; 1.92A {Escherichia
coli} PDB: 3k57_A* 3k58_A* 3k5l_A* 3k5m_A* 3k5n_A*
3k5o_A* 3maq_A* 1q8i_A*
Length = 786
Score = 412 bits (1062), Expect = e-128
Identities = 115/489 (23%), Positives = 187/489 (38%), Gaps = 79/489 (16%)
Query: 560 IRITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNKKEGEETGEANKGK 619
+ V G + R GG L H YV P+
Sbjct: 356 LERATVNGLPVDRH--GGSVAAFGHLYFPRMHRAGYVAPNL------------------G 395
Query: 620 GRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTL 679
A GG V++ + G YD ++++D+ SLYPSII+ + I + M Q +
Sbjct: 396 EVPPHASPGGYVMDSRPGLYDS-VLVLDYKSLYPSIIRTFLIDPVGLVEGMAQPDPEHST 454
Query: 680 CEYLPEH-QVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSM 738
+L + LP + + R + K +ALK+ N+
Sbjct: 455 EGFLDAWFSREKHCLPEIVTNIWHGRDEAKRQG------------NKPLSQALKIIMNAF 502
Query: 739 YGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMISC-NVNDY 797
YG LG RFF LA+ +T +G +I+ TK+L+E Y+VIYGDTDS + +
Sbjct: 503 YGVLGTTACRFFDPRLASSITMRGHQIMRQTKALIEAQGYDVIYGDTDSTFVWLKGAHSE 562
Query: 798 DSVFKIGNQIKSECNKLYKQ----------LELDIDGVYKYMLLLKKKKYAALSISK--- 844
+ KIG + N + + LEL+ + + L+ + S +
Sbjct: 563 EEAAKIGRALVQHVNAWWAETLQKQRLTSALELEYETHFCRFLMPTIRGADTGSKKRYAG 622
Query: 845 LSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMK 904
L KG++ VR DW+ LA + + + +I + E+++
Sbjct: 623 LIQEGDKQRMVFKGLETVRTDWTPLAQQFQQELYLRIFRN------------EPYQEYVR 670
Query: 905 KIRTDLDNGFVPLTLLEITKQLTKAPEEYTDRKALPHVQVALRLNNTNSK-----KLKQG 959
+ L G + L K+L + EY R PHV+ A + N K + +
Sbjct: 671 ETIDKLMAGELDA-RLVYRKRLRRPLSEY-QRNVPPHVRAARLADEENQKRGRPLQYQNR 728
Query: 960 DTISYIICEDGTSEAATQRAYNIEELKNNSKLKIDVNYYLSQQIHPVVTRLLEPIEGTDA 1019
TI Y+ +G QR+ +D +YL++Q+ PV +L IE A
Sbjct: 729 GTIKYVWTTNGPEPLDYQRS------------PLDYEHYLTRQLQPVAEGILPFIEDNFA 776
Query: 1020 VRIAECLGL 1028
+ LGL
Sbjct: 777 TLMTGQLGL 785
Score = 53.6 bits (129), Expect = 4e-07
Identities = 21/164 (12%), Positives = 43/164 (26%), Gaps = 31/164 (18%)
Query: 399 TVYLFGKVFVKENNSHSSCCVIVQNIDRKIYLLPRSEHLKTKEPVSIAQVYSEFDQIATQ 458
V + + V + + +P + + + I Q F
Sbjct: 23 EVSFWLA------TDNGPLQVTLAP-QESVAFIPADQVPRAQH---ILQGEQGFRLTPLA 72
Query: 459 YKILDFKSRKIEKKYAFNLPGVPDLSEYLEVRYSAKCPALPSDLSGDTFSHVFGTKSSFL 518
K DF + + Y + + + L + V+
Sbjct: 73 LK--DFHRQPVYGLYCRAHRQLMNYEKRLR----------------EGGVTVYEADVRPP 114
Query: 519 ENLLLERKIKGPSWLEFPEAEKFPSRISWCKYEVQCNQMEKIRI 562
E L+ER I P W+E I + + + ++
Sbjct: 115 ERYLMERFITSPVWVEGDMHNG---TIVNARLKPHPDYRPPLKW 155
>2gv9_A DNA polymerase; polymerase alpha fold, transferase; HET: DNA; 2.68A
{Human herpesvirus 1} PDB: 1dml_B*
Length = 1193
Score = 403 bits (1036), Expect = e-121
Identities = 116/558 (20%), Positives = 212/558 (37%), Gaps = 95/558 (17%)
Query: 558 EKIRITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNKKEG-------- 609
E + + G ++RT+ G+ R LL +K ++LPD Q G
Sbjct: 555 ELSAVARLAGINITRTIYDGQQIRVFTCLLRLADQKGFILPDTQGRFRGAGGEAPKRPAA 614
Query: 610 -----------------------EETGEANKGKGRKKAAYSGGLVLEPKKGFYDKFIILM 646
E E + + Y G VL+P GF+ +++
Sbjct: 615 AREDEERPEEEGEDEDEREEGGGEREPEGARETAGRHVGYQGAKVLDPTSGFHVNPVVVF 674
Query: 647 DFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYL-----------PEHQVDTGILPS 695
DF SLYPSIIQ +N+CF+T+ +R + + +YL + V +L
Sbjct: 675 DFASLYPSIIQAHNLCFSTLSLRADAVAHLEAGKDYLEIEVGGRRLFFVKAHVRESLLSI 734
Query: 696 EIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLA 755
++ + R+Q+++ + Q S + + D +Q A+K+ NS+YG G + +A
Sbjct: 735 LLRDWLAMRKQIRSRIPQ--SSPEEAVLLDKQQAAIKVVCNSVYGFTGVQHGLLPCLHVA 792
Query: 756 ALVTAKGREILLNTKSLVEN-----------------------LNYEVIYGDTDSLMISC 792
A VT GRE+LL T+ V + +IYGDTDS+ + C
Sbjct: 793 ATVTTIGREMLLATREYVHARWAAFEQLLADFPEAADMRAPGPYSMRIIYGDTDSIFVLC 852
Query: 793 NVNDYDSVFKIGNQIKSECNKLY--KQLELDIDGVYKYMLLLKKKKYAALSISKLSNGKM 850
+ +G+++ S ++ ++L+ + + +LL+ KKKY + + GKM
Sbjct: 853 RGLTAAGLTAMGDKMASHISRALFLPPIKLECEKTFTKLLLIAKKKYIGV----IYGGKM 908
Query: 851 ICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQS---------------YTDYSLDDR 895
IKGVD+VR++ + + ++ + + + + L +
Sbjct: 909 ----LIKGVDLVRKNNCAFINRTSRALVDLLFYDDTVSGAAAALAERPAEEWLARPLPEG 964
Query: 896 LQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPEEYTDRKALPHVQVALRLNNTNSKK 955
LQ + + + + +T +L++ P YT+ K L H+ V +L ++
Sbjct: 965 LQAFGAVLVDAHRRITDPERDIQDFVLTAELSRHPRAYTN-KRLAHLTVYYKLMARRAQV 1023
Query: 956 LKQGDTISYIIC--EDGTSEAATQRAYNIEELKNNSKLKIDVNYYLSQQIHPVVTRLLEP 1013
D I Y+I E + A E + L
Sbjct: 1024 PSIKDRIPYVIVAQTREVEETVARLAALRELDAAAPGDEPAPPAALPSPAKRPRETPSHA 1083
Query: 1014 IEGTDAVRIAECLGLDTS 1031
A + + L + +
Sbjct: 1084 DPPGGASKPRKLLVSELA 1101
>3flo_B DNA polymerase alpha catalytic subunit A; protein-protein complex,
phosphoesterase fold, OB fold, zinc-binding motif, DNA
replication; HET: DNA; 2.50A {Saccharomyces cerevisiae}
Length = 206
Score = 132 bits (333), Expect = 4e-35
Identities = 41/198 (20%), Positives = 73/198 (36%), Gaps = 25/198 (12%)
Query: 1056 EVKYQFCDKFEFTCMNPSCKQVNTVEAPTRLSTHGVVFVLDECINPECKVPPYTYLPHLI 1115
+++ E +C PSC + + + V + +C + E P L
Sbjct: 12 VERFKDTVTLELSC--PSCDKRFPFGGIVSSNYYRVSYNGLQCKHCEQLFTPLQ----LT 65
Query: 1116 NKLSQDMNKYIVKYYEGWLKCEDPGCSDLTRRCPLGLKTRLCTTCHKYKLHRVYTELQLY 1175
+++ + +I YY GWL+C+D C +TR+ + K L C + Y++ QLY
Sbjct: 66 SQIEHSIRAHISLYYAGWLQCDDSTCGIVTRQVSVFGKRCLNDGC-TGVMRYKYSDKQLY 124
Query: 1176 QQLSFFHYICDITKALTKSDTPSIKFDSETYMG------------------YCKMKQHVE 1217
QL +F + D K + P D Y + V+
Sbjct: 125 NQLLYFDSLFDCEKNKKQELKPIYLPDDLDYPKEQLTESSIKALTEQNRELMETGRSVVQ 184
Query: 1218 RFLESSAYNIVDLKKLFS 1235
++L VD+ +F
Sbjct: 185 KYLNDCGRRYVDMTSIFD 202
>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 = 75.3 bits (184), Expect = 1e-13
Identities = 104/740 (14%), Positives = 212/740 (28%), Gaps = 247/740 (33%)
Query: 390 FEDIYKQPGTVYLFGKVFVKENNSHSSCCVIVQNIDRKIYLLPRSEHLKTKEPVSIAQVY 449
++DI + +F FV + C VQ++ + I +H+ +++
Sbjct: 18 YKDI------LSVFEDAFVDNFD-----CKDVQDMPKSILSKEEIDHI-IMSKDAVSGTL 65
Query: 450 SEFDQIATQYK--ILDFKSRKIEKKYAFNLPGVPDLSEYLEVRYSAKCPALPSDLSGDTF 507
F + ++ + + F + Y F L ++ + P++ + + +
Sbjct: 66 RLFWTLLSKQEEMVQKFVEEVLRINYKF-------LMS--PIKTEQRQPSMMTRMYIEQR 116
Query: 508 SHVFGTKSSF-------------LENLLLE-RKIK----------GPSWL------EFPE 537
++ F L LLE R K G +W+ +
Sbjct: 117 DRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKV 176
Query: 538 AEKFPSRISWCKYEVQCNQMEKI--RITNVCGNVLSRTLMGGRSERNEFLLLHAF-HEKS 594
K +I W + CN E + + + + N L +H+ E
Sbjct: 177 QCKMDFKIFWLNLK-NCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELR 235
Query: 595 YVLPDKQYGKNKKEGEETGEANKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPS 654
+L K Y + L ++L++ +
Sbjct: 236 RLLKSKPY-------------------ENC-------L----------LVLLNVQN--AK 257
Query: 655 IIQEYNI-C---FTTIPVRMLQDSDITTLCEYLPEHQVDTGILPSEIKKLVESRRQVKAL 710
+N+ C TT + +T L + + L
Sbjct: 258 AWNAFNLSCKILLTT------RFKQVTD-------------FLSAATTTHISLDHHSMTL 298
Query: 711 MKQPNLSSDLLMQY-DIRQKALKLTANSMYGCLGFPNSRFFAQPLA-ALVTAKGREILLN 768
S LL++Y D R + L P +++ R+ L
Sbjct: 299 TPDEVKS--LLLKYLDCRPQDLPREV-----LTTNP--------RRLSIIAESIRDGLAT 343
Query: 769 TKSLVENLNYEVIYGDTDSLMISCNVND---------YD--SVFKIGNQIKSE------C 811
N++ + D + +I ++N +D SVF I +
Sbjct: 344 WD------NWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWF 397
Query: 812 NKLYKQLELDIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLAS 871
+ + + + ++ ++KY L+ K+ K + +SI + + +++ + R
Sbjct: 398 DVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIY---LELKVKLENEYALHR------- 447
Query: 872 EAGKFVISQILDE-QSYTDYSLDDRLQN---------IHEHMKKIR-TDLDNGFVPLTLL 920
I+D + DD + I H+K I + F
Sbjct: 448 --------SIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLF------ 493
Query: 921 EITKQLTKAPEEYTDRKALPHVQVALRLNNTNSKKLKQGDTISYIICEDGTSEAATQRAY 980
+ D R L+Q I D T+ A+
Sbjct: 494 ---------RMVFLD----------FRF-------LEQK------IRHDSTAWNASGSIL 521
Query: 981 NIEELKNNSKLKIDVNYYLS--QQIHPVVTRLLEPIEGTDAVRIAECLGLDTSLYRSQIK 1038
N + +Y P RL+ I D + E +L S+
Sbjct: 522 N---------TLQQLKFYKPYICDNDPKYERLVNAIL--DFLPKIE-----ENLICSKYT 565
Query: 1039 ESIQ---QSEENILGVGEAE 1055
+ ++ +E+ + EA
Sbjct: 566 DLLRIALMAEDEAI-FEEAH 584
Score = 56.4 bits (135), Expect = 6e-08
Identities = 87/567 (15%), Positives = 164/567 (28%), Gaps = 170/567 (29%)
Query: 764 EILLNTKSLVENLNYEVIYGDTDSLMISCN-VNDY-DSVFKIGNQIKSECNKLYKQLELD 821
E K ++ + + + D C V D S+ K E + + +
Sbjct: 13 EHQYQYKDILS-VFEDAFVDNFD-----CKDVQDMPKSILS-----KEEIDHIIMSKD-A 60
Query: 822 IDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQI 881
+ G + L LS + + + ++ +V+R ++ L S
Sbjct: 61 VSGTLRLFWTL------------LSKQEEMVQKFVE--EVLRINYKFLMSPIKTEQRQPS 106
Query: 882 LDEQSYTDYSLDDRLQN-----------IHEHMKKIRTDL----DNGFVPL--------T 918
+ + Y + DRL N + K+R L V + T
Sbjct: 107 MMTRMYIEQR--DRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKT 164
Query: 919 LLEITKQLTKAPEEYTDRKALPHV--QVA-LRLNNTNSKK--LKQGDTISYIICEDGTSE 973
+ A + K + ++ L L N NS + L+ + Y I + TS
Sbjct: 165 WV--------ALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSR 216
Query: 974 AATQRAYNIEELKNNSKLKIDVNYYLSQQIHPVVTRLLEPIEGTDAVRIAECLGLDTSLY 1033
+ + NI+ ++ + ++ L + + CL L
Sbjct: 217 S--DHSSNIKLRIHSIQAEL--RRLLKSKPYE------------------NCL-----L- 248
Query: 1034 RSQIKESIQQSEENIL-GVGEAEEVKYQFCDKFEFTC---MNPSCKQV-NTVEAPTR--- 1085
+L V A+ F +C + KQV + + A T
Sbjct: 249 --------------VLLNVQNAKAWNA-----FNLSCKILLTTRFKQVTDFLSAATTTHI 289
Query: 1086 -LSTHGVVFVLDE-------CIN------PE--CKVPPYTYLPHLINKLSQDMNKYIVKY 1129
L H + DE ++ P P +I + +D +
Sbjct: 290 SLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPR--RLSIIAESIRDG----LAT 343
Query: 1130 YEGWLKCEDPGCSDLTRRCPLGLKTRLCTTCHKYKLHRVYTELQLYQQLSFFHYICDIT- 1188
++ W C LT + +R +++ +LS F I
Sbjct: 344 WDNWKH---VNCDKLTT------IIESSLNVLEPAEYR-----KMFDRLSVFPPSAHIPT 389
Query: 1189 KALTKSDTPSIKFDSETYMGYCKMKQHVERFLESSAYNIVDLKKLFSCE-EKQPKLSRGV 1247
L+ IK D + VE+ + S +I + + E + L
Sbjct: 390 ILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYAL---- 445
Query: 1248 EREHVTVAEGEGDDYEFDFDLEYSDLS 1274
H ++ D Y + DL
Sbjct: 446 ---HRSIV----DHYNIPKTFDSDDLI 465
Score = 55.2 bits (132), Expect = 1e-07
Identities = 86/570 (15%), Positives = 163/570 (28%), Gaps = 156/570 (27%)
Query: 1 QLVHHFVSE----HRKWRVE----ELNVKEGKSTRARSACSSFCVGTQKMEGGRAKR-QK 51
++V FV E + K+ + E + Q R Q
Sbjct: 77 EMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQP 136
Query: 52 IDKTNKFAAFQKLKD--------LKGQGVK----------HKYEFTADENVY-EEVSEKE 92
K + A +L+ + G G K +K + D ++ +
Sbjct: 137 YLKLRQ--ALLELRPAKNVLIDGVLGSG-KTWVALDVCLSYKVQCKMDFKIFWLNLKNCN 193
Query: 93 YTERVLKRQEDDWIDDDGGDGYVEDGREIFDDDIEDVPQKKEKHDKRKKNK-------NI 145
E VL+ + D D I + + + K K + N+
Sbjct: 194 SPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNV 253
Query: 146 QNPN-AKG-DIQ-KLLANMPVKKKKKEEVQLNNDDVLADLLSEVNTTIAPTLKLNTKTNE 202
QN ++ K+L + D LS TT
Sbjct: 254 QNAKAWNAFNLSCKILL-------------TTRFKQVTDFLSAATTT------------H 288
Query: 203 IVIPKEEPPAPTAKEYLANFSKPIKVEKKIEKPIKKEPSPLKDEIKSNDSVMEVEMNVAE 262
I + T E + K + + +P + + + +AE
Sbjct: 289 ISL-DHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRR-----------LSI-IAE 335
Query: 263 QSKEEPVDDGLWEQMQIDDWDNSQQTQ-DVL-PEQAKVELQIEAI--ESQSIEEKV---- 314
++ W+ + D ++ +VL P + + ++ S I +
Sbjct: 336 SIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLI 395
Query: 315 --DVTNVESVSSAVELSTSPPPQVVEK--KEHKCAEWEAIQTE---PSTSEPQVHSR--- 364
DV + + +L +VEK KE +I E +E +H
Sbjct: 396 WFDVIKSDVMVVVNKLHKY---SLVEKQPKESTI-SIPSIYLELKVKLENEYALHRSIVD 451
Query: 365 --------TADDSLPLATD---------H-------ENKKVFRMFFLDAFEDIYKQPGTV 400
+DD +P D H E +FRM FLD
Sbjct: 452 HYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLD------------ 499
Query: 401 YLFGKVFVKENNSHSSCCVIVQN--IDRKIYL------LPRSEH--------LKTKEPVS 444
+ F + ++ +++ + + N K Y P+ E L E
Sbjct: 500 FRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENL 559
Query: 445 IAQVYSEFDQIATQYK---ILDFKSRKIEK 471
I Y++ +IA + I + +++++
Sbjct: 560 ICSKYTDLLRIALMAEDEAIFEEAHKQVQR 589
>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 = 67.4 bits (164), Expect = 3e-11
Identities = 95/575 (16%), Positives = 175/575 (30%), Gaps = 197/575 (34%)
Query: 243 LKDEIKSNDSVMEVEMNVAEQSKEEPVDD-GLWEQ-----MQIDDWDNSQQTQDVLPEQA 296
L+++ + E A +EP L + + + Q VL
Sbjct: 33 LQEQFNK--ILPEPTEGFAAD--DEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVL---- 84
Query: 297 KVELQIEAIESQSIEEKVDVTNVESVSSAVELSTSPPPQVVEKKEH-KCAEWEAIQTEPS 355
L + E+ +E ++ ++ A +L +V+ KE K A
Sbjct: 85 --NLCLTEFENCYLEGN----DIHAL--AAKLLQENDTTLVKTKELIKNY-ITARIM--- 132
Query: 356 TSEPQVHSRTADDSLPLATDHENKKVFRMF--------FLDAFEDIYKQPGTVYLFGKVF 407
P + ++ +L A N ++ +F + + D+Y+ Y V
Sbjct: 133 AKRPF--DKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQ----TY---HVL 183
Query: 408 VKENNSHSSCCVIVQNIDRKIYLLPRSEHLKTKEPVSIAQVYSE-FDQIATQYKILDFKS 466
V + +++ + L R+ + +V+++ + + L+ S
Sbjct: 184 VGD---------LIKFSAETLSELIRT-------TLDAEKVFTQGLNILE----WLENPS 223
Query: 467 RKIEKKY----AFNLP--GVPDLSEYLEV-RYSAKCPA-LPSDLSGDTFSHVFG------ 512
+K Y + P GV L+ Y+ + P L S L G T H G
Sbjct: 224 NTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGAT-GHSQGLVTAVA 282
Query: 513 -----TKSSFLENLLLERKIKGPSWL------EFPEA--------------EKFPS---R 544
+ SF ++ + I ++ +P E PS
Sbjct: 283 IAETDSWESFFVSVR--KAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLS 340
Query: 545 ISWCKYEV------QCNQM----EKIRITNVCG---NVLS---RTLMGGRSERNEFLLLH 588
IS E + N +++ I+ V G V+S ++L G L
Sbjct: 341 ISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYG---------LNL 391
Query: 589 AFHEKSYVLPDKQYGKNKKEGEETGEANKGKGRKKAAYSGGLVLEPKKGFYDKFI-ILMD 647
K K A G + + +S E K F ++F+ +
Sbjct: 392 TLR------------KAK--------APSGLDQSRIPFS-----ERKLKFSNRFLPVASP 426
Query: 648 FNSLY-----PSIIQ---EYNICFTT----IPV---------RMLQDSDITTLCEYLPEH 686
F+S I + + N+ F IPV R+L S + + +
Sbjct: 427 FHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRL 486
Query: 687 QVD---------TGIL---P---SEIKKLVESRRQ 706
V T IL P S + L +
Sbjct: 487 PVKWETTTQFKATHILDFGPGGASGLGVLTHRNKD 521
Score = 65.5 bits (159), Expect = 1e-10
Identities = 93/593 (15%), Positives = 166/593 (27%), Gaps = 245/593 (41%)
Query: 305 IESQSIEEKVDV-TNVESVSSAVEL-----STSPPPQVVEKKEHKCAEWEAIQTEPSTSE 358
+ S+E + V T S A +L P P E A EP+ +
Sbjct: 11 LSHGSLEHVLLVPTA--SFFIASQLQEQFNKILPEP----------TEGFAADDEPT-TP 57
Query: 359 PQVHSR----TADDSLPLATDHENKKVFRMFFLDAFEDIYKQPGTVYLFGKVFVKENNSH 414
++ + + P ++ V L FE YL G N+ H
Sbjct: 58 AELVGKFLGYVSSLVEPSKVGQFDQ-VLN-LCLTEFE-------NCYLEG------NDIH 102
Query: 415 SSCCVIVQNIDRKI---------YLLPR--SEHLKTKEPVSI---------AQVYSEFD- 453
+ ++Q D + Y+ R ++ K+ S AQ+ + F
Sbjct: 103 ALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGG 162
Query: 454 Q-IATQYKILDFKS-RKIEKKYAFNLPGVPDL----SEYLE--VRYSAKCPALPSDLSGD 505
Q Y F+ R + + Y V DL +E L +R + +
Sbjct: 163 QGNTDDY----FEELRDLYQTYH---VLVGDLIKFSAETLSELIRTTLDAEKV------- 208
Query: 506 TFSHVFGTKSSFLENLLLERKIKGPSWLEFPEAEKFPSR-------ISW--------CKY 550
F+ N+L WLE P P + IS Y
Sbjct: 209 -FTQGL--------NIL--------EWLENPSNT--PDKDYLLSIPISCPLIGVIQLAHY 249
Query: 551 EVQCNQMEKIRITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYGKNKKEGE 610
V + G + R+ + G + ++ L+ ++
Sbjct: 250 VVTAKLLGFTP-----GEL--RSYLKGATGHSQGLVTAVAIAET---------------- 286
Query: 611 ETGEANKGKGRKKAAYSGGLVLEPKKGFYD---KFIILMDF------------NSLYPSI 655
++ E+ F+ K I ++ F SL PSI
Sbjct: 287 DSWES----------------------FFVSVRKAITVL-FFIGVRCYEAYPNTSLPPSI 323
Query: 656 IQEYNICFTTIPVRMLQ---------DSDITTLCEYLPEHQ-------------VDTGIL 693
+++ +P ML + +LP + V +G
Sbjct: 324 LEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSG-P 382
Query: 694 PSEIKKLVESRRQVKALM-----------KQPNLS-----------SDLL------MQYD 725
P + L + R+ KA ++ S S LL + D
Sbjct: 383 PQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKD 442
Query: 726 IRQKALKLTANSMYGCLGFPNSRFFAQPLAALV--TAKGREILLNTKSLVENL 776
+ + + A + P V T G ++ + + S+ E +
Sbjct: 443 LVKNNVSFNAKD----IQIP------------VYDTFDGSDLRVLSGSISERI 479
Score = 48.9 bits (116), Expect = 1e-05
Identities = 93/582 (15%), Positives = 154/582 (26%), Gaps = 273/582 (46%)
Query: 55 TNKFAAFQKLKDLKGQGVKHKYEFTA-----------DENVYEEVSEKEYTERVLKRQED 103
T F +L++ +F D+ E + E + L
Sbjct: 24 TASFFIASQLQE----------QFNKILPEPTEGFAADD---EPTTPAELVGKFL----- 65
Query: 104 DWIDDDGGDGYVEDGREI-------FDDDI---EDV-------PQKKEKHDKRKKNKNIQ 146
++ V ++ F++ D+ Q+ + K + I+
Sbjct: 66 GYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDT-TLVKTKELIK 124
Query: 147 N-PNAKGDIQKLLANMPVKKK---------KKEEVQL--------NNDD----------- 177
N A+ ++A P KK + QL N DD
Sbjct: 125 NYITAR-----IMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQT 179
Query: 178 ---VLADLLSEVNTTIAPTLKLNTKTNEIVIPK--------EEP-PAPTAKEYLAN--FS 223
++ DL+ T++ ++ ++ + E P P K+YL + S
Sbjct: 180 YHVLVGDLIKFSAETLSELIRTTLDAEKV-FTQGLNILEWLENPSNTP-DKDYLLSIPIS 237
Query: 224 KPIKVEKKIE-----------KPIKKEPSPLKDEIK-----SNDSVMEVEMNVAEQSKEE 267
P+ I K + P L+ +K S V V +
Sbjct: 238 CPL-----IGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAET------ 286
Query: 268 PVDDGLWEQMQIDDWDN------------------SQQT--QDVLPE---QAKVE----- 299
D W++ + LP + +E
Sbjct: 287 ------------DSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGV 334
Query: 300 ----LQIEAIESQSIEEKVDVTNVE-SVSSAVELS----------TSPPPQ----VVEKK 340
L I + + +++ V+ TN VE+S + PP + +
Sbjct: 335 PSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLR 394
Query: 341 EHKCAEWEAIQTEPSTSEPQVHSRTADDSLPLATDHENKKVFRMFFLDAFEDIYKQPGTV 400
+ K PS + Q SR P + E K F FL P
Sbjct: 395 KAKA---------PSGLD-Q--SRI-----PFS---ERKLKFSNRFL---------PVAS 425
Query: 401 YLFGKVFVKENNSHSSCCVIVQNIDRKIYLLPRSEHLKT---KEPVSIAQ------VYSE 451
F HS L+P S+ + K VS VY
Sbjct: 426 -----PF------HSH------------LLVPASDLINKDLVKNNVSFNAKDIQIPVYDT 462
Query: 452 FD-----------------QI---------ATQYK---ILDF 464
FD I TQ+K ILDF
Sbjct: 463 FDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHILDF 504
Score = 47.0 bits (111), Expect = 4e-05
Identities = 45/282 (15%), Positives = 89/282 (31%), Gaps = 74/282 (26%)
Query: 635 KKG----FYDKFII------LMD--FNSLYP-SIIQ-------EYNICFTTIPVRMLQDS 674
++G Y D F Y SI+ I F + ++++
Sbjct: 1628 EQGMGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIREN 1687
Query: 675 DITTLCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLT 734
+ E + + ++ T + EI + + LL Q AL L
Sbjct: 1688 YSAMIFETIVDGKLKTEKIFKEI-----NEHSTSYTFRSEK---GLLSATQFTQPALTLM 1739
Query: 735 ANSMYGCL----GFPNSRFFA-QPL---AALVTAKGREILLNTKSLVE------NLNYEV 780
+ + L P FA L AAL + +++ +SLVE
Sbjct: 1740 EKAAFEDLKSKGLIPADATFAGHSLGEYAALASLAD---VMSIESLVEVVFYRGMTMQVA 1796
Query: 781 I----YGDTDSLMISCNVN------DYDSVFKIGNQIKSECNKLYKQLEL---------- 820
+ G ++ MI+ N +++ + ++ L +E+
Sbjct: 1797 VPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWL---VEIVNYNVENQQY 1853
Query: 821 ----DIDGVYKYMLLLKKKKYAALSISKLSNGKMICSQEIKG 858
D+ + +L K + I +L K + +E++G
Sbjct: 1854 VAAGDLRALDTVTNVLNFIKLQKIDIIELQ--KSLSLEEVEG 1893
Score = 32.7 bits (74), Expect = 0.96
Identities = 24/155 (15%), Positives = 42/155 (27%), Gaps = 64/155 (41%)
Query: 1175 YQQL--SFFHYICDITKALTKSDTPSIKFDSET-----YMGYCKMK-------------- 1213
QL F + + T+ D P+ + ++GY
Sbjct: 30 ASQLQEQFNKILPEPTEGFAADDEPT----TPAELVGKFLGYVSSLVEPSKVGQFDQVLN 85
Query: 1214 ---QHVER-FL-------------ESSAYNIVDLKKLFSC-------------EEKQPKL 1243
E +L + + +V K+L ++ L
Sbjct: 86 LCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSAL 145
Query: 1244 SRGVEREHVTVA-----EGEGDDYEFDFDLEYSDL 1273
R V + + +G DDY F+ E DL
Sbjct: 146 FRAVGEGNAQLVAIFGGQGNTDDY-FE---ELRDL 176
>3qex_A DNA polymerase, GP43; difluorotoluene nucleoside; HET: DNA DOC DGT;
1.73A {Enterobacteria phage RB69} PDB: 3qei_A* 3qer_A*
3qes_A* 3qet_A* 3qep_A* 3qew_A* 3qev_A* 3s9h_A* 3sq0_A*
3spz_A* 3ne6_A* 3nhg_A* 3si6_A* 3scx_A* 3sjj_A* 3snn_A*
3ngi_A* 3lzi_A* 3lzj_A* 3ndk_A* ...
Length = 903
Score = 60.7 bits (146), Expect = 3e-09
Identities = 76/464 (16%), Positives = 140/464 (30%), Gaps = 123/464 (26%)
Query: 615 ANKGKGRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTI-------P 667
+G+ Y G V EP Y +++ D SLYPSII++ NI TI P
Sbjct: 380 IPQGRSHPVQPYPGAFVKEPIPNRYK-YVMSFDLTSLYPSIIRQVNISPETIAGTFKVAP 438
Query: 668 VRMLQDSDITTLCEYLPE-------HQVDTGILPSEIKKLVESRRQVKALM--------- 711
+ ++ + ++ G++P+EI K+ R++ K M
Sbjct: 439 LHDYINAVAERPSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEI 498
Query: 712 -----------------------------------------KQPNLSSDLLMQYDIRQKA 730
+ + + Q
Sbjct: 499 IKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQIN 558
Query: 731 LKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYE---------VI 781
K N + G LG R++ A +T G+ L + V E V+
Sbjct: 559 RKALINGLAGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFVL 618
Query: 782 YGDTDSLMISCNVNDYDSVFKIGNQIKSECNKLYK----QLELDIDGVYKYM-------- 829
YGDTDS+ +S + + L K ++E ID ++ M
Sbjct: 619 YGDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDKFARERMEPAIDRGFREMCEYMNNKQ 678
Query: 830 ----------------------LLLKKKKYAALSISKLSNGKMICSQEIKGVDVVRRDWS 867
KK+YA +I G++ +
Sbjct: 679 HLMFMDREAIAGPPLGSKGIGGFWTGKKRYALNVWDMEGTRYAEPKLKIMGLETQKSSTP 738
Query: 868 QLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLT 927
+ +A K I ++L E + SL + + + +++ V +
Sbjct: 739 KAVQKALKECIRRMLQE---GEESLQEYFKEFEKEFRQLNYI-SIASV-----SSANNIA 789
Query: 928 KAPEEYTDRKALP-HVQVALRLN-----NTNSKKLKQGDTISYI 965
K P H++ L N N ++ ++ +G+ + +
Sbjct: 790 KYDVGGFPGPKCPFHIRGILTYNRAIKGNIDAPQVVEGEKVYVL 833
>2py5_A DNA polymerase; protein-DNA complex, replication, transferase/DNA
complex; HET: DNA; 1.60A {Bacillus phage PHI29} SCOP:
c.55.3.5 e.8.1.1 PDB: 1xhz_A* 1xhx_A* 2ex3_A* 1xi1_A*
2pyj_A* 2pyl_A* 2pzs_A*
Length = 575
Score = 58.0 bits (139), Expect = 1e-08
Identities = 54/354 (15%), Positives = 101/354 (28%), Gaps = 92/354 (25%)
Query: 623 KAAYSGGLVL--EPKKGFYDKFIILMDFNSLYPSIIQEYNIC---FTTIPVRMLQDSDIT 677
+ AY GG + K ++ D NSLYP+ + + + + D D
Sbjct: 223 RYAYRGGFTWLNDRFKEKEIGEGMVFDVNSLYPAQMYSRLLPYGEPIVFEGKYVWDEDYP 282
Query: 678 TLC-----------EYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDI 726
Y+P Q+ + L S ++ L + YD+
Sbjct: 283 LHIQHIRCEFELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLSNVDLELMKEHYDL 342
Query: 727 R-----------------------------------QKALKLTANSMYGCLGFPNSR--- 748
++ KL NS+YG
Sbjct: 343 YNVEYISGLKFKATTGLFKDFIDKWTYIKTTSEGAIKQLAKLMLNSLYGKFASNPDVTGK 402
Query: 749 ---------------------FFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDS 787
P+ +TA R + + +IY DTDS
Sbjct: 403 VPYLKENGALGFRLGEEETKDPVYTPMGVFITAWARYTTITAA---QACYDRIIYCDTDS 459
Query: 788 LMISCNVNDYDSVFKIGNQIKSECNKLYKQL-ELDIDGVYKYMLLLKKKKYAALSISKLS 846
+ ++ +I + IK + K+L + +K L++K Y K
Sbjct: 460 IHLTGT--------EIPDVIKDIVDP--KKLGYWAHESTFKRAKYLRQKTYIQDIYMKEV 509
Query: 847 NGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIH 900
+GK++ E D +S + + ++ E +S + + +
Sbjct: 510 DGKLV---EGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKVGFSRKMKPKPVQ 560
>1n5g_A 38-MER of DNA polymerase alpha catalytic subunit; zinc finger
protein, DNA binding domain, transferase; NMR {Synthetic}
SCOP: g.67.1.1
Length = 38
Score = 43.9 bits (103), Expect = 4e-06
Identities = 15/37 (40%), Positives = 17/37 (45%), Gaps = 2/37 (5%)
Query: 1133 WLKCEDPGCSDLTRRCPLGL--KTRLCTTCHKYKLHR 1167
WL CE+P C + TR PL LC C K L
Sbjct: 1 WLICEEPTCRNRTRHLPLQFSRTGPLCPACMKATLQP 37
>1k0p_A DNA polymerase alpha catalytic subunit; zinc finger protein, DNA
binding domain, transferase; HET: DNA; NMR {Synthetic}
SCOP: g.67.1.1 PDB: 1k18_A*
Length = 31
Score = 34.2 bits (78), Expect = 0.010
Identities = 12/29 (41%), Positives = 14/29 (48%), Gaps = 2/29 (6%)
Query: 1136 CEDPGCSDLTRRCPLGL--KTRLCTTCHK 1162
CE+P C + TR PL LC C K
Sbjct: 2 CEEPTCRNRTRHLPLQFSRTGPLCPACMK 30
>1vk0_A Hypothetical protein; homohexamer, AT5G06450, struc genomics,
protein structure initiative, center for eukaryot
structural genomics, CESG; 2.10A {Arabidopsis thaliana}
SCOP: c.55.3.5 PDB: 2q3s_A
Length = 206
Score = 34.2 bits (78), Expect = 0.17
Identities = 11/74 (14%), Positives = 24/74 (32%), Gaps = 6/74 (8%)
Query: 799 SVFKIGNQIKSECNKLYKQLELDIDGV----YKYMLLLKKKKYAALSISKLSNGKMICSQ 854
V +G QI+ + + L + L I L +L+ +
Sbjct: 108 FVTFVGVQIEEDLDLLRENHGLVIRNAINVGKLAAEARGTLVLEFLGTRELA--HRVLWS 165
Query: 855 EIKGVDVVRRDWSQ 868
++ +D + W +
Sbjct: 166 DLGQLDSIEAKWEK 179
>3gdb_A Endo-D, putative uncharacterized protein SPR0440;
alpha-beta-barrels, cell WALL, peptidoglycan-anchor,
secreted, hydrolase; HET: PGE; 1.87A {Streptococcus
pneumoniae} PDB: 2xqx_A
Length = 937
Score = 33.8 bits (76), Expect = 0.43
Identities = 16/166 (9%), Positives = 45/166 (27%), Gaps = 9/166 (5%)
Query: 207 KEEPPAPTAKEYLANFSKPIKVEKKIEKPIKKEPSPLKDEIKSNDSVMEVEMNVAEQSKE 266
EE P + V + E + + E + + + E
Sbjct: 21 GEETAVPENSG-----ANTELVSGESEHSTNEADKQNEGEHARENKLEKAEGVATASETA 75
Query: 267 EPVDD---GLWEQMQIDDWDNSQQTQDVLPEQAKVELQIEAIESQSIEEKVDVTNVESVS 323
P + ++ +V+ E E + ++ + + + ES
Sbjct: 76 SPASNEAATTETAEAASAAKPEEKASEVVAETPSAEAKPKSDKETEAKPEATNQGDES-K 134
Query: 324 SAVELSTSPPPQVVEKKEHKCAEWEAIQTEPSTSEPQVHSRTADDS 369
A E + + + ++ + + + ++ E +
Sbjct: 135 PAAEANKTEKEVQPDVPKNTEKTLKPKEIKFNSWEELLKWEPGARE 180
>4dah_A Sporulation kinase D; alpha-beta-alpha structure, structural
genomics, midwest CEN structural genomics (MCSG),
PSI-biology, PAS-like fold; 2.03A {Bacillus subtilis}
PDB: 4dbj_A 4dbi_A 4dak_A 3fos_A
Length = 217
Score = 32.7 bits (74), Expect = 0.61
Identities = 10/38 (26%), Positives = 15/38 (39%), Gaps = 2/38 (5%)
Query: 847 NGKMICS--QEIKGVDVVRRDWSQLASEAGKFVISQIL 882
G + S + V++ R + A E K VIS
Sbjct: 79 KGDVTASTTELKTKVNLADRSFFIKAKETKKTVISDSY 116
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 32.4 bits (73), Expect = 0.65
Identities = 19/107 (17%), Positives = 32/107 (29%), Gaps = 44/107 (41%)
Query: 8 SEH-RKWRVEELNVKEGKSTRARSACSSFCVGTQKMEGGRAKR-QKIDKTNKFAAFQKLK 65
E RKWR EE + KR Q++D +K +
Sbjct: 84 PESIRKWR-EE----------------------------QRKRLQELDAASK----VMEQ 110
Query: 66 DLKGQGVKHKYEFTADENVYEEVSEK------EYTERVLKRQEDDWI 106
+ + + K E+ E EK + ++ + D I
Sbjct: 111 EWREKAKKDLEEWNQR---QSEQVEKNKINNRIADKAFYQQPDADII 154
Score = 30.9 bits (69), Expect = 2.1
Identities = 12/82 (14%), Positives = 35/82 (42%), Gaps = 12/82 (14%)
Query: 233 EKPIKKEPSPLKDEIKSNDSVMEVEMNVAEQSKEEPVDDGLWEQMQ--IDDWDNSQQTQD 290
+ +EP ++ + ++ E++ A + E+ E+ + +++W+ Q Q
Sbjct: 77 ADRLTQEPESIRKWREEQRKRLQ-ELDAASKVMEQ----EWREKAKKDLEEWNQRQSEQV 131
Query: 291 VLPEQAKVELQIEAIESQSIEE 312
E+ K+ +I + ++
Sbjct: 132 ---EKNKINNRIA--DKAFYQQ 148
>3rj1_B Mediator of RNA polymerase II transcription subun; RNA polymeras
II, POL II, head module, head, regulator, helical
bundle; 4.30A {Saccharomyces cerevisiae}
Length = 583
Score = 32.6 bits (73), Expect = 0.97
Identities = 30/154 (19%), Positives = 60/154 (38%), Gaps = 17/154 (11%)
Query: 82 ENVYEEVSEKEYTERVLKRQEDDWIDDDGGDGYVEDGREIFDDDIEDVPQKKEKHDKRKK 141
+ + E+ + E D DG D V+ G + + D ED
Sbjct: 25 KELQNEIKQLGSDSSDGHNSEKK--DTDGADENVQIGEDFMEVDYED-KDNPVDSRNETD 81
Query: 142 NKNIQNPNAKGDIQKLLANMPVKKKKKEEVQLNND---------DVLADLLSEVN----- 187
+K +N +I+ ++ K++++ ++ N + ++ LLS V
Sbjct: 82 HKTNENGETDDNIETVMTQEQFVKRRRDMLEHINLAMNESSLALEFVSLLLSSVKESTGM 141
Query: 188 TTIAPTLKLNTKTNEIVIPKEEPPAPTAKEYLAN 221
++++P L+ K + + K APT KEY+
Sbjct: 142 SSMSPFLRKVVKPSSLNSDKIPYVAPTKKEYIEL 175
>3qi3_A High affinity CGMP-specific 3',5'-cyclic phosphod 9A; mutation,
glutamine switch, hydrolase-hydrolase inhibitor CO; HET:
PDB; 2.30A {Homo sapiens} PDB: 3qi4_A*
Length = 533
Score = 31.5 bits (71), Expect = 2.0
Identities = 22/177 (12%), Positives = 60/177 (33%), Gaps = 9/177 (5%)
Query: 174 NNDDVLADLLSEVNTTIAPTLKLNTKTNEIVIPKEEPPAPTAKEYLANFSKPIKVEKKIE 233
N+ D++ T+ L T + +V PA + + IK + E
Sbjct: 31 NSSDIMDLFCIATGLPRNTTISLLTTDDAMVSIDPTMPANSERTPYKVRPVAIKQLSERE 90
Query: 234 KPIKKEPSPLKDEIKSNDSVMEVEMNVAEQSKEEPVDDGLWEQMQIDDWDNSQQTQDVLP 293
+ I+ + + ++ + E++ VA E+ + + +
Sbjct: 91 ELIQSVLAQVAEQFSRAFKINELKAEVANHLAVL-------EKRVELEGLKVVEIEKCKS 143
Query: 294 EQAKVELQIEAIESQSIE--EKVDVTNVESVSSAVELSTSPPPQVVEKKEHKCAEWE 348
+ K+ ++ A S++ + + N + ++ ++ T P + + +
Sbjct: 144 DIKKMREELAARSSRTNCPCKYSFLDNHKKLTPRRDVPTYPKYLLSPETIEALRKPT 200
>2gre_A Deblocking aminopeptidase; structural genomi protein structure
initiative, midwest center for structural genomics,
MCSG, hydrolase; 2.65A {Bacillus cereus} SCOP: b.49.3.1
c.56.5.4
Length = 349
Score = 30.6 bits (70), Expect = 3.2
Identities = 14/58 (24%), Positives = 23/58 (39%), Gaps = 5/58 (8%)
Query: 34 SFCVGTQKMEGGRAKRQKIDKTNK---FAAFQKLKDLKGQGVKHKYEFTADENVYEEV 88
SF Q E G K + +D +K + +K L+ + V Y + EE+
Sbjct: 167 SFDPRVQITESGYIKSRHLD--DKVSVAILLKLIKRLQDENVTLPYTTHFLISNNEEI 222
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 29.1 bits (64), Expect = 5.5
Identities = 11/50 (22%), Positives = 19/50 (38%), Gaps = 22/50 (44%)
Query: 685 EHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLT 734
E Q +KKL ++ ++ A + S+ L A+K T
Sbjct: 18 EKQ--------ALKKL-QASLKLYA----DD-SAPAL--------AIKAT 45
>2ivf_B Ethylbenzene dehydrogenase beta-subunit; anaerobic hydrocarbon
degradation, MOCO, Fe/S cluster, MO- B enzyme, DMSO
reductase family; HET: MES MGD MD1 HEM; 1.88A
{Aromatoleum aromaticum}
Length = 352
Score = 30.0 bits (67), Expect = 6.1
Identities = 11/55 (20%), Positives = 21/55 (38%), Gaps = 1/55 (1%)
Query: 1046 ENILGVGEAEEVKYQFCDKFEFTCMNPSCKQVNTVEAPTRLSTHGVVFV-LDECI 1099
+ G G+ + + + C NP+C A + +G+V V + C
Sbjct: 131 DEDQGGGKWPNPFFFYLARMCNHCTNPACLAACPTGAIYKREDNGIVLVDQERCK 185
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
0.315 0.133 0.381
Gapped
Lambda K H
0.267 0.0548 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 18,987,754
Number of extensions: 1149362
Number of successful extensions: 1988
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1905
Number of HSP's successfully gapped: 47
Length of query: 1274
Length of database: 6,701,793
Length adjustment: 105
Effective length of query: 1169
Effective length of database: 3,770,088
Effective search space: 4407232872
Effective search space used: 4407232872
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 63 (28.5 bits)