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= psy9396
(1149 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2HNH|A Chain A, Crystal Structure Of The Catalytic Alpha Subunit Of E.
Coli Replicative Dna Polymerase Iii
Length = 910
Score = 834 bits (2155), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 425/918 (46%), Positives = 603/918 (65%), Gaps = 22/918 (2%)
Query: 3 PQFIHLRLHSEYSIIDGLLRINDVIEAAANDYQPALAITDLSNLFGIIKFYKSAYNKGIK 62
P+F+HLR+HS+YS+IDGL + +++ AA PALAITD +NL G++KFY + + GIK
Sbjct: 4 PRFVHLRVHSDYSMIDGLAKTAPLVKKAAALGMPALAITDFTNLCGLVKFYGAGHGAGIK 63
Query: 63 PIIGCDVWITNEIENKKPSRLLLLVKNNNGYLQLCELLSKAYIENINYGRAEIRIEWLEK 122
PI+G D + ++ + + L +L NN GY L L+SKAY I +WL
Sbjct: 64 PIVGADFNVQCDLLGDELTHLTVLAANNTGYQNLTLLISKAYQRGYGAAGPIIDRDWL-- 121
Query: 123 NKYQDGLIALSGAHLGDIGIAVQNGRNDIAENFARRWSKIFPDNFYIEIQRFKQPNMNFQ 182
+ +GLI LSG +GD+G ++ G + + + + + FPD +++E+ R +P+
Sbjct: 122 IELNEGLILLSGGRMGDVGRSLLRGNSALVDECVAFYEEHFPDRYFLELIRTGRPDEESY 181
Query: 183 IQQFINIASNINLPIVATHPIQFLKKTEFLAHEVRTCIAEGEILSNTKRIKKFTKEQNFK 242
+ + +A LP+VAT+ ++F+ ++F AHE+R I +G L + KR + ++ +Q +
Sbjct: 182 LHAAVELAEARGLPVVATNDVRFIDSSDFDAHEIRVAIHDGFTLDDPKRPRNYSPQQYMR 241
Query: 243 TQSEMIKLFYDIPSAIQNTIEIAKRCNLKLEFGKPKLPKFPTPKNININDFLISKSKHGL 302
++ EM +LF DIP A+ NT+EIAKRCN+ + G+ LP+FPT +++ D+L+ ++K GL
Sbjct: 242 SEEEMCELFADIPEALANTVEIAKRCNVTVRLGEYFLPQFPT-GDMSTEDYLVKRAKEGL 300
Query: 303 KKRLLNLYKDPEIYKCEKLRYKKRLQFEIETIIKMNFSGYFLIVSDFIQWAKNNSIPVGP 362
++RL L+ D E + Y +RL+ E++ I +M F GYFLIV +FIQW+K+N +PVGP
Sbjct: 301 EERLAFLFPDEEERLKRRPEYDERLETELQVINQMGFPGYFLIVMEFIQWSKDNGVPVGP 360
Query: 363 GRGSGASSLVAYSLSITDIDPLSYNLLFERFLNPNRISMPDFDIDFCPEGRDRVIQYVKD 422
GRGSGA SLVAY+L ITD+DPL ++LLFERFLNP R+SMPDFD+DFC E RD+VI++V D
Sbjct: 361 GRGSGAGSLVAYALKITDLDPLEFDLLFERFLNPERVSMPDFDVDFCMEKRDQVIEHVAD 420
Query: 423 RYGKDAVSQIVTFGTMAAKGAIRDVGRVLDLRYSFCDSISKLIPFKPGKLITLSNAIKEE 482
YG+DAVSQI+TFGTMAAK IRDVGRVL Y F D ISKLIP PG +TL+ A + E
Sbjct: 421 MYGRDAVSQIITFGTMAAKAVIRDVGRVLGHPYGFVDRISKLIPPDPG--MTLAKAFEAE 478
Query: 483 PQLAERIKNEEEVRQLIELAKQVEGIIRNVGMHAGGVLIAPSKLINFCPLYKQEGMTGII 542
PQL E + +EEV+ LI++A+++EG+ RN G HAGGV+IAP+K+ +F PLY E +
Sbjct: 479 PQLPEIYEADEEVKALIDMARKLEGVTRNAGKHAGGVVIAPTKITDFAPLYCDEEGKHPV 538
Query: 543 SQYDKDDIEEIGLIKFDFLGLTTLSILDKTIYFIKKINTKTTNFSLN--KLPLNDKDTYN 600
+Q+DK D+E GL+KFDFLGL TL+I++ + I K K L+ +PL+DK +++
Sbjct: 539 TQFDKSDVEYAGLVKFDFLGLRTLTIINWALEMINKRRAKNGEPPLDIAAIPLDDKKSFD 598
Query: 601 LLKKANTVAVFQLESQGMKNMLKEAKPDYFEEIIALISLYRPGPMD--LIKNFCRRKHG- 657
+L+++ T AVFQLES+GMK+++K +PD FE++IAL++L+RPGP+ ++ NF RKHG
Sbjct: 599 MLQRSETTAVFQLESRGMKDLIKRLQPDCFEDMIALVALFRPGPLQSGMVDNFIDRKHGR 658
Query: 658 EYFNYPDPR-----TKDVLSETYGIMVYQEQVMQIAQILGGYSLGQADLLRRAIGKKKTS 712
E +YPD + K VL TYGI++YQEQVMQIAQ+L GY+LG AD+LRRA+GKKK
Sbjct: 659 EEISYPDVQWQHESLKPVLEPTYGIILYQEQVMQIAQVLSGYTLGGADMLRRAMGKKKPE 718
Query: 713 EMIEHRKFFQNGAIKYGLSKHKANEIFNEIEKFAGYGFNKSHXXXXXXXXXXXXXXXXHY 772
EM + R F GA K G++ A +IF+ +EKFAGYGFNKSH HY
Sbjct: 719 EMAKQRSVFAEGAEKNGINAELAMKIFDLVEKFAGYGFNKSHSAAYALVSYQTLWLKAHY 778
Query: 773 SSFFMAANLSLSMDDTNKIKILVKDAIKTCGLSILPPNINLSKYYFFPIIESDGKHKKIR 832
+ FMAA ++ MD+T K+ LV + + GL ILPP+IN Y+F + DG +I
Sbjct: 779 PAEFMAAVMTADMDNTEKVVGLVDECWRM-GLKILPPDINSGLYHFH--VNDDG---EIV 832
Query: 833 YGLGAIKGTGKSTIEAIVTER-KFGFFTNLFDFTKRIDKKYXXXXXXXXXXXXGAFDCFN 891
YG+GAIKG G+ IEAI+ R K G+F LFD R D K GAFD
Sbjct: 833 YGIGAIKGVGEGPIEAIIEARNKGGYFRELFDLCARTDTKKLNRRVLEKLIMSGAFDRLG 892
Query: 892 EKRYMLVASIDVALKNAE 909
R L+ S+ ALK A+
Sbjct: 893 PHRAALMNSLGDALKAAD 910
>pdb|2HQA|A Chain A, Crystal Structure Of The Catalytic Alpha Subunit Of E.
Coli Replicative Dna Polymerase Iii
Length = 917
Score = 786 bits (2029), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 418/922 (45%), Positives = 585/922 (63%), Gaps = 22/922 (2%)
Query: 3 PQFIHLRLHSEYSIIDGLLRINDVIEAAANDYQPALAITDLSNLFGIIKFYKSAYNKGIK 62
P+F+HLR+HS+YS IDGL + +++ AA PALAITD +NL G++KFY + + GIK
Sbjct: 4 PRFVHLRVHSDYSXIDGLAKTAPLVKKAAALGXPALAITDFTNLCGLVKFYGAGHGAGIK 63
Query: 63 PIIGCDVWITNEIENKKPSRLLLLVKNNNGYLQLCELLSKAYIENINYGRAEIRIEWLEK 122
PI+G D + ++ + + L +L NN GY L L+SKAY I +WL
Sbjct: 64 PIVGADFNVQCDLLGDELTHLTVLAANNTGYQNLTLLISKAYQRGYGAAGPIIDRDWL-- 121
Query: 123 NKYQDGLIALSGAHLGDIGIAVQNGRNDIAENFARRWSKIFPDNFYIEIQRFKQPNMNFQ 182
+ +GLI LSG GD+G ++ G + + + + + FPD +++E+ R +P+
Sbjct: 122 IELNEGLILLSGGRXGDVGRSLLRGNSALVDECVAFYEEHFPDRYFLELIRTGRPDEESY 181
Query: 183 IQQFINIASNINLPIVATHPIQFLKKTEFLAHEVRTCIAEGEILSNTKRIKKFTKEQNFK 242
+ + +A LP+VAT+ ++F+ ++F AHE+R I +G L + KR + ++ +Q +
Sbjct: 182 LHAAVELAEARGLPVVATNDVRFIDSSDFDAHEIRVAIHDGFTLDDPKRPRNYSPQQYXR 241
Query: 243 TQSEMIKLFYDIPSAIQNTIEIAKRCNLKLEFGKPKLPKFPTPKNININDFLISKSKHGL 302
++ E +LF DIP A+ NT+EIAKRCN+ + G+ LP+FPT + + D+L+ ++K GL
Sbjct: 242 SEEEXCELFADIPEALANTVEIAKRCNVTVRLGEYFLPQFPT-GDXSTEDYLVKRAKEGL 300
Query: 303 KKRLLNLYKDPEIYKCEKLRYKKRLQFEIETIIKMNFSGYFLIVSDFIQWAKNNSIPVGP 362
++RL L+ D E + Y +RL+ E++ I + F GYFLIV +FIQW+K+N +PVGP
Sbjct: 301 EERLAFLFPDEEERLKRRPEYDERLETELQVINQXGFPGYFLIVXEFIQWSKDNGVPVGP 360
Query: 363 GRGSGASSLVAYSLSITDIDPLSYNLLFERFLNPNRISMPDFDIDFCPEGRDRVIQYVKD 422
GRGSGA SLVAY+L ITD+DPL ++LLFERFLNP R+S PDFD+DFC E RD+VI++V D
Sbjct: 361 GRGSGAGSLVAYALKITDLDPLEFDLLFERFLNPERVSXPDFDVDFCXEKRDQVIEHVAD 420
Query: 423 RYGKDAVSQIVTFGTMAAKGAIRDVGRVLDLRYSFCDSISKLIPFKPGKLITLSNAIKEE 482
YG+DAVSQI+TFGT AAK IRDVGRVL Y F D ISKLIP PG TL+ A + E
Sbjct: 421 XYGRDAVSQIITFGTXAAKAVIRDVGRVLGHPYGFVDRISKLIPPDPGX--TLAKAFEAE 478
Query: 483 PQLAERIKNEEEVRQLIELAKQVEGIIRNVGMHAGGVLIAPSKLINFCPLYKQEGMTGII 542
PQL E + +EEV+ LI+ A+++EG+ RN G HAGGV+IAP+K+ +F PLY E +
Sbjct: 479 PQLPEIYEADEEVKALIDXARKLEGVTRNAGKHAGGVVIAPTKITDFAPLYCDEEGKHPV 538
Query: 543 SQYDKDDIEEIGLIKFDFLGLTTLSILDKTIYFIKKINTKTTNFSLN--KLPLNDKDTYN 600
+Q+DK D+E GL+KFDFLGL TL+I++ + I K K L+ +PL+DK +++
Sbjct: 539 TQFDKSDVEYAGLVKFDFLGLRTLTIINWALEXINKRRAKNGEPPLDIAAIPLDDKKSFD 598
Query: 601 LLKKANTVAVFQLESQGMKNMLKEAKPDYFEEIIALISLYRPGPMD--LIKNFCRRKHG- 657
L+++ T AVFQLES+G K+++K +PD FE+ IAL++L+RPGP+ + NF RKHG
Sbjct: 599 XLQRSETTAVFQLESRGXKDLIKRLQPDCFEDXIALVALFRPGPLQSGXVDNFIDRKHGR 658
Query: 658 EYFNYPDPR-----TKDVLSETYGIMVYQEQVMQIAQILGGYSLGQADLLRRAIGKKKTS 712
E +YPD + K VL TYGI++YQEQV QIAQ+L GY+LG AD LRRA GKKK
Sbjct: 659 EEISYPDVQWQHESLKPVLEPTYGIILYQEQVXQIAQVLSGYTLGGADXLRRAXGKKKPE 718
Query: 713 EMIEHRKFFQNGAIKYGLSKHKANEIFNEIEKFAGYGFNKSHXXXXXXXXXXXXXXXXHY 772
E + R F GA K G++ A +IF+ +EKFAGYGFNKSH HY
Sbjct: 719 EXAKQRSVFAEGAEKNGINAELAXKIFDLVEKFAGYGFNKSHSAAYALVSYQTLWLKAHY 778
Query: 773 SSFFMAANLSLSMDDTNKIKILVKDAIKTCGLSILPPNINLSKYYFFPIIESDGKHKKIR 832
+ F AA + D+T K+ LV + + GL ILPP+IN Y+F + DG +I
Sbjct: 779 PAEFXAAVXTADXDNTEKVVGLVDECWRX-GLKILPPDINSGLYHFH--VNDDG---EIV 832
Query: 833 YGLGAIKGTGKSTIEAIVTER-KFGFFTNLFDFTKRIDKKYXXXXXXXXXXXXGAFDCFN 891
YG+GAIKG G+ IEAI+ R K G+F LFD R D K GAFD
Sbjct: 833 YGIGAIKGVGEGPIEAIIEARNKGGYFRELFDLCARTDTKKLNRRVLEKLIXSGAFDRLG 892
Query: 892 EKRYMLVASIDVALKNAEKTKK 913
R L S+ ALK A++ K
Sbjct: 893 PHRAALXNSLGDALKAADQHAK 914
>pdb|2HPI|A Chain A, Eubacterial And Eukaryotic Replicative Dna Polymerases Are
Not Homologous: X-Ray Structure Of Dna Polymerase Iii
pdb|2HPM|A Chain A, Eubacterial And Eukaryotic Replicative Dna Polymerases Are
Not Homologous: X-ray Structure Of Dna Polymerase Iii
Length = 1220
Score = 645 bits (1664), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 409/1150 (35%), Positives = 612/1150 (53%), Gaps = 120/1150 (10%)
Query: 4 QFIHLRLHSEYSIIDGLLRINDVI----EAAANDYQPALAITDLSNLFGIIKFYKSAYNK 59
+F HL H+++S++DG ++ D++ E D PALA+TD NLFG ++FYK A
Sbjct: 6 KFAHLHQHTQFSLLDGAAKLQDLLKWVKETTPED--PALAMTDHGNLFGAVEFYKKATAM 63
Query: 60 GIKPIIGCDVWITNEIE-NKKPSR--------LLLLVKNNNGYLQLCELLSKAYIENINY 110
G+KPIIG + ++ E ++K + L LL K+ GY L L S+AY+E Y
Sbjct: 64 GVKPIIGYEAYVAAESRFDRKRGKGLDGGYFHLTLLAKDFTGYQNLVRLASRAYLEGF-Y 122
Query: 111 GRAEIRIEWLEKNKYQDGLIALSGAHLGDIGIAVQNGRNDIAENFARRWSKIFPDNFYIE 170
+ I E L ++ GLIALSG +I + R D+AE IF D F+IE
Sbjct: 123 EKPRIDREIL--REHAQGLIALSGCLGAEIPQFILQDRLDLAEARLNEDLSIFGDRFFIE 180
Query: 171 IQRFKQPNMNFQIQQFINIASNINLPIVATHPIQFLKKTEFLAHEVRTCIAEGEILSNTK 230
IQ P Q A L +VAT+ +++K + AHEV I L + +
Sbjct: 181 IQNHGLPEQKKVNQVLKEFARKYGLGMVATNDGHYVRKEDARAHEVLLAIQSKTTLDDPE 240
Query: 231 RIKKFTKEQNFKTQSEMIKLFYDIPSA------IQNTIEIAKRCNLKLEFGKP---KLPK 281
R + E KT EM + +P A NT+EIA+ C++ L G ++P+
Sbjct: 241 RWRFPCDEFYVKTPEEMRAM---LPEAEWGDEPFDNTVEIARMCDVDLPIGDKMVYRIPR 297
Query: 282 FPTPKNININDFL---------------ISKS-------------KHGLKKRLLNLYKDP 313
FP P+ +L I+++ HG ++ L
Sbjct: 298 FPLPEGRTEAQYLRELTFLGLLRRYPDRITEAFYREVLRLLGTMPPHGDERALAEALARV 357
Query: 314 EIYKCEKLRYK----------------KRLQFEIETIIKMNFSGYFLIVSDFIQWAKNNS 357
E E+LR + R +E+ I +M F GYFLIV D+I WA+ +
Sbjct: 358 EEKAWEELRKRLPPLEGVREWTAEAILHRALYELSVIERMGFPGYFLIVQDYINWARGHG 417
Query: 358 IPVGPGRGSGASSLVAYSLSITDIDPLSYNLLFERFLNPNRISMPDFDIDFCPEGRDRVI 417
+ VGPGRGS A SLVAY++ IT+IDPL + LLFERFLNP R+SMPD D DF RDRVI
Sbjct: 418 VSVGPGRGSAAGSLVAYAVGITNIDPLRFGLLFERFLNPERVSMPDIDTDFSDRERDRVI 477
Query: 418 QYVKDRYGKDAVSQIVTFGTMAAKGAIRDVGRVLDLRYSFCDSISKLIPFKPGKLITLSN 477
QYV++RYG+D V+QI TFG++A+K A++DV RV + + + ++KLIP + GK L
Sbjct: 478 QYVRERYGEDKVAQIGTFGSLASKAALKDVARVYGIPHKKAEELAKLIPVQFGKPKPLQE 537
Query: 478 AIKEEPQLAERIKNEEEVRQLIELAKQVEGIIRNVGMHAGGVLIAPSKLINFCPLYK-QE 536
AI+ P+L ++ +E +RQ+IE+A ++EG+ R+ +HA GV+IA L + PL + QE
Sbjct: 538 AIQVVPELRAEMEKDERIRQVIEVAMRLEGLNRHASVHAAGVVIAAEPLTDLVPLMRDQE 597
Query: 537 GMTGIISQYDKDDIEEIGLIKFDFLGLTTLSILDKTIYFIKKINTKTTNFSLNKLPLNDK 596
G ++QYD +E +GL+K DFLGL TL+ LD+ +K+ +K ++LPL+D
Sbjct: 598 GRP--VTQYDMGAVEALGLLKMDFLGLRTLTFLDEARRIVKE--SKGVELDYDRLPLDDP 653
Query: 597 DTYNLLKKANTVAVFQLESQGMKNMLKEAKPDYFEEIIALISLYRPGPMDLIKNFCRRKH 656
T+ LL + T VFQLES GM ++ KP E+IIAL+SLYRPGPM+ I + RR H
Sbjct: 654 KTFELLSRGETKGVFQLESGGMTATVRGLKPRRLEDIIALVSLYRPGPMEHIPTYIRRHH 713
Query: 657 GE----YFNYPDPRT--KDVLSETYGIMVYQEQVMQIAQILGGYSLGQADLLRRAIGKKK 710
G+ Y +P + +L ETYGI VYQEQ+MQIA + GYSLG+ADLLRRA+GKK+
Sbjct: 714 GQEPVSYAEFPHAEKYLRPILDETYGIPVYQEQIMQIASQVAGYSLGEADLLRRAMGKKR 773
Query: 711 TSEMIEHRKFFQNGAIKYGLSKHKANEIFNEIEKFAGYGFNKSHXXXXXXXXXXXXXXXX 770
EM +HR+ F GA + G+ + +AN +F+ +E FA YGFNKSH
Sbjct: 774 VEEMQKHRERFVRGAKERGVPEEEANRLFDMLEAFANYGFNKSHAAAYSLLSYQTAYVKA 833
Query: 771 HYSSFFMAANLSLSMDDTNKIKILVKDAIKTCGLSILPPNINLSKYYFFPIIESDGKHKK 830
HY FMAA LS+ D++K+ ++DA + G+ +LPP++N S + F + E +
Sbjct: 834 HYPVEFMAALLSVERHDSDKVAEYIRDA-RALGIPVLPPDVNRSGFDFKVVGE------E 886
Query: 831 IRYGLGAIKGTGKSTIEAIVTER-KFGFFTNLFDFTKRIDKKYXXXXXXXXXXXXGAFDC 889
I +GL A+K G+ AI+ ER + G F +L DF KR+ ++ GA D
Sbjct: 887 ILFGLSAVKNVGEMAARAILEERERGGPFKSLGDFLKRLPEQVVNKRALESLVKAGALDA 946
Query: 890 FNEKRYMLVASIDVALKNAEKTKKFINQ--LSLFKNDDNNNLKEYLNYVKVPSWSKKQEL 947
F + R L+AS++ L+ A +T++ + LF + L V+ + L
Sbjct: 947 FGD-RARLLASLEPLLRWAAETRERGRSGLVGLFAEVEEPPL------VEASPLDEITML 999
Query: 948 IEEKKVLGFCLSEHIFCIYE----------TEIRQFIPIYLSELKPTYSCTVSGIITELK 997
EK+ LG +S H Y E+ +F+ EL +SG++ E+
Sbjct: 1000 RYEKEALGIYVSGHPVLRYPGLREVASCTIEELSEFV----RELPGKPKVLLSGMVEEVV 1055
Query: 998 LKTTYRGKILI-IVIDDNSNSVEVIINNQLYEKNKNILKENELLIVSGKVLEDRFLKNIR 1056
K T G ++ + D + ++EV++ + YE LKE+ L+V +V + + +R
Sbjct: 1056 RKPTRSGGMMARFTLSDETGALEVVVFGRAYEGVSPKLKEDIPLLVLAEVEKG---EELR 1112
Query: 1057 INAEKIFDIN 1066
+ A+ ++ +
Sbjct: 1113 VLAQAVWTLE 1122
>pdb|3E0D|A Chain A, Insights Into The Replisome From The Crystral Structure Of
The Ternary Complex Of The Eubacterial Dna Polymerase Iii
Alpha-Subunit
pdb|3E0D|B Chain B, Insights Into The Replisome From The Crystral Structure Of
The Ternary Complex Of The Eubacterial Dna Polymerase Iii
Alpha-Subunit
Length = 1220
Score = 644 bits (1661), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 408/1150 (35%), Positives = 612/1150 (53%), Gaps = 120/1150 (10%)
Query: 4 QFIHLRLHSEYSIIDGLLRINDVI----EAAANDYQPALAITDLSNLFGIIKFYKSAYNK 59
+F HL H+++S+++G ++ D++ E D PALA+TD NLFG ++FYK A
Sbjct: 6 KFAHLHQHTQFSLLNGAAKLQDLLKWVKETTPED--PALAMTDHGNLFGAVEFYKKATAM 63
Query: 60 GIKPIIGCDVWITNEIE-NKKPSR--------LLLLVKNNNGYLQLCELLSKAYIENINY 110
G+KPIIG + ++ E ++K + L LL K+ GY L L S+AY+E Y
Sbjct: 64 GVKPIIGYEAYVAAESRFDRKRGKGLDGGYFHLTLLAKDFTGYQNLVRLASRAYLEGF-Y 122
Query: 111 GRAEIRIEWLEKNKYQDGLIALSGAHLGDIGIAVQNGRNDIAENFARRWSKIFPDNFYIE 170
+ I E L ++ GLIALSG +I + R D+AE IF D F+IE
Sbjct: 123 EKPRIDREIL--REHAQGLIALSGCLGAEIPQFILQDRLDLAEARLNEDLSIFGDRFFIE 180
Query: 171 IQRFKQPNMNFQIQQFINIASNINLPIVATHPIQFLKKTEFLAHEVRTCIAEGEILSNTK 230
IQ P Q A L +VAT+ +++K + AHEV I L + +
Sbjct: 181 IQNHGLPEQKKVNQVLKEFARKYGLGMVATNNGHYVRKEDARAHEVLLAIQSKTTLDDPE 240
Query: 231 RIKKFTKEQNFKTQSEMIKLFYDIPSA------IQNTIEIAKRCNLKLEFGKP---KLPK 281
R + E KT EM + +P A NT+EIA+ C++ L G ++P+
Sbjct: 241 RWRFPCDEFYVKTPEEMRAM---LPEAEWGDEPFDNTVEIARMCDVDLPIGDKMVYRIPR 297
Query: 282 FPTPKNININDFL---------------ISKS-------------KHGLKKRLLNLYKDP 313
FP P+ +L I+++ HG ++ L
Sbjct: 298 FPLPEGRTEAQYLRELTFLGLLRRYPDRITEAFYREVLRLLGTMPPHGDERALAEALARV 357
Query: 314 EIYKCEKLRYK----------------KRLQFEIETIIKMNFSGYFLIVSDFIQWAKNNS 357
E E+LR + R +E+ I +M F GYFLIV D+I WA+ +
Sbjct: 358 EEKAWEELRKRLPPLEGVREWTAEAILHRALYELSVIERMGFPGYFLIVQDYINWARGHG 417
Query: 358 IPVGPGRGSGASSLVAYSLSITDIDPLSYNLLFERFLNPNRISMPDFDIDFCPEGRDRVI 417
+ VGPGRGS A SLVAY++ IT+IDPL + LLFERFLNP R+SMPD D DF RDRVI
Sbjct: 418 VSVGPGRGSAAGSLVAYAVGITNIDPLRFGLLFERFLNPERVSMPDIDTDFSDRERDRVI 477
Query: 418 QYVKDRYGKDAVSQIVTFGTMAAKGAIRDVGRVLDLRYSFCDSISKLIPFKPGKLITLSN 477
QYV++RYG+D V+QI TFG++A+K A++DV RV + + + ++KLIP + GK L
Sbjct: 478 QYVRERYGEDKVAQIGTFGSLASKAALKDVARVYGIPHKKAEELAKLIPVQFGKPKPLQE 537
Query: 478 AIKEEPQLAERIKNEEEVRQLIELAKQVEGIIRNVGMHAGGVLIAPSKLINFCPLYK-QE 536
A + EP+L ++ +E +RQ+IE+A ++EG+ R+ +HA GV+IA L + PL + QE
Sbjct: 538 AFEAEPELRAEMEKDERIRQVIEVAMRLEGLNRHASVHAAGVVIAAEPLTDLVPLMRDQE 597
Query: 537 GMTGIISQYDKDDIEEIGLIKFDFLGLTTLSILDKTIYFIKKINTKTTNFSLNKLPLNDK 596
G ++QYD +E +GL+K DFLGL TL+ LD+ +K+ +K ++LPL+D
Sbjct: 598 GRP--VTQYDMGAVEALGLLKMDFLGLRTLTFLDEARRIVKE--SKGVELDYDRLPLDDP 653
Query: 597 DTYNLLKKANTVAVFQLESQGMKNMLKEAKPDYFEEIIALISLYRPGPMDLIKNFCRRKH 656
T+ LL + T VFQLES GM ++ KP E+IIAL+SLYRPGPM+ I + RR H
Sbjct: 654 KTFELLSRGETKGVFQLESGGMTATVRGLKPRRLEDIIALVSLYRPGPMEHIPTYIRRHH 713
Query: 657 GE----YFNYPDPRT--KDVLSETYGIMVYQEQVMQIAQILGGYSLGQADLLRRAIGKKK 710
G+ Y +P + +L ETYGI VYQEQ+MQIA + GYSLG+ADLLRRA+GKK+
Sbjct: 714 GQEPVSYAEFPHAEKYLRPILDETYGIPVYQEQIMQIASQVAGYSLGEADLLRRAMGKKR 773
Query: 711 TSEMIEHRKFFQNGAIKYGLSKHKANEIFNEIEKFAGYGFNKSHXXXXXXXXXXXXXXXX 770
EM +HR+ F GA + G+ + +AN +F+ +E FA YGFNKSH
Sbjct: 774 VEEMQKHRERFVRGAKERGVPEEEANRLFDMLEAFANYGFNKSHAAAYSLLSYQTAYVKA 833
Query: 771 HYSSFFMAANLSLSMDDTNKIKILVKDAIKTCGLSILPPNINLSKYYFFPIIESDGKHKK 830
HY FMAA LS+ D++K+ ++DA + G+ +LPP++N S + F + E +
Sbjct: 834 HYPVEFMAALLSVERHDSDKVAEYIRDA-RALGIPVLPPDVNRSGFDFKVVGE------E 886
Query: 831 IRYGLGAIKGTGKSTIEAIVTER-KFGFFTNLFDFTKRIDKKYXXXXXXXXXXXXGAFDC 889
I +GL A+K G+ AI+ ER + G F +L DF KR+ ++ GA D
Sbjct: 887 ILFGLSAVKNVGEMAARAILEERERGGPFKSLGDFLKRLPEQVVNKRALESLVKAGALDA 946
Query: 890 FNEKRYMLVASIDVALKNAEKTKKFINQ--LSLFKNDDNNNLKEYLNYVKVPSWSKKQEL 947
F + R L+AS++ L+ A +T++ + LF + L V+ + L
Sbjct: 947 FGD-RARLLASLEPLLRWAAETRERGRSGLVGLFAEVEEPPL------VEASPLDEITML 999
Query: 948 IEEKKVLGFCLSEHIFCIYE----------TEIRQFIPIYLSELKPTYSCTVSGIITELK 997
EK+ LG +S H Y E+ +F+ EL +SG++ E+
Sbjct: 1000 RYEKEALGIYVSGHPVLRYPGLREVASCTIEELSEFV----RELPGKPKVLLSGMVEEVV 1055
Query: 998 LKTTYRGKILI-IVIDDNSNSVEVIINNQLYEKNKNILKENELLIVSGKVLEDRFLKNIR 1056
K T G ++ + D + ++EV++ + YE LKE+ L+V +V + + +R
Sbjct: 1056 RKPTRSGGMMARFTLSDETGALEVVVFGRAYEGVSPKLKEDIPLLVLAEVEKG---EELR 1112
Query: 1057 INAEKIFDIN 1066
+ A+ ++ +
Sbjct: 1113 VLAQAVWTLE 1122
>pdb|3F2B|A Chain A, Dna Polymerase Polc From Geobacillus Kaustophilus Complex
With Dna, Dgtp, Mg And Zn
pdb|3F2C|A Chain A, Dna Polymerase Polc From Geobacillus Kaustophilus Complex
With Dna, Dgtp And Mn
pdb|3F2D|A Chain A, Dna Polymerase Polc From Geobacillus Kaustophilus Complex
With Dna, Dgtp, Mn And Zn
Length = 1041
Score = 113 bits (283), Expect = 5e-25, Method: Compositional matrix adjust.
Identities = 158/717 (22%), Positives = 277/717 (38%), Gaps = 146/717 (20%)
Query: 6 IHLRLHSEYSIIDGLLRINDVIEAAANDYQPALAITDLSNLFGIIKFYKSAYNKGIKPII 65
+ L LH+ S +D + + +IE A PA+A+TD + + + Y +A G+K I
Sbjct: 117 VELHLHTPMSQMDAVTSVTKLIEQAKKWGHPAIAVTDHAVVQSFPEAYSAAKKHGMKVIY 176
Query: 66 GCDVWIT--------NEIENK-----KPSRLLLLVKNNNGYLQLCELLSKAYIENINYGR 112
G + I NE + P + LL +N G L +L+S + +I Y
Sbjct: 177 GLEANIVDDGVPIAYNETHRRLGSGSGPFHVTLLAQNETGLKNLFKLVS---LSHIQYFH 233
Query: 113 AEIRIEWLEKNKYQDGLIALSGAHLGDIGIAVQNGRNDIAENFARRWS--KIFPDNFY-- 168
RI K++DGL+ SG G++ + + E+ AR + ++ P + Y
Sbjct: 234 RVPRIPRSVLVKHRDGLLVGSGCDKGELFDNLIQKAPEEVEDIARFYDFLEVHPPDVYKP 293
Query: 169 -IEIQRFKQPNM-NFQIQQFINIASNINLPIVATHPIQFLKKTEFLAHEVRTCIAEGEIL 226
IE+ K M I+ + + +++P+VAT + +L + + ++ G
Sbjct: 294 LIEMDYVKDEEMIKNIIRSIVALGEKLDIPVVATGNVHYLNPEDKIYRKILIHSQGGANP 353
Query: 227 SNTKRIKKFTKEQNFKTQSEMIKLFYDIPSAIQNTIEIAKRCNLKLEFG--KPKLPKFPT 284
N + F+T +EM+ F + I + + G KP + T
Sbjct: 354 LNRHELPDVY----FRTTNEMLDCFSFLGPEKAKEIVVDNTQKIASLIGDVKPIKDELYT 409
Query: 285 PKNININDFLISKSKHGLKKRLLNLYKDPEIYKCEKLRYKKRLQFEIETIIKMNFSGYFL 344
P+ I D I + + +R +Y DP KL ++RL+ E+++II F+ +L
Sbjct: 410 PR-IEGADEEIREMSY---RRAKEIYGDP----LPKL-VEERLEKELKSIIGHGFAVIYL 460
Query: 345 IVSDFIQWAKNNSIPVGPGRGSGASSLVAYSLSITDIDPL-------------------- 384
I ++ + ++ VG RGS SS VA IT+++PL
Sbjct: 461 ISHKLVKKSLDDGYLVG-SRGSVGSSFVATMTEITEVNPLPPHYVCPNCKHSEFFNDGSV 519
Query: 385 ---------------------SYNLLFERFLNPNRISMPDFDIDFCPEGRDRVIQYVKDR 423
+++ FE FL +PD D++F E + R Y K
Sbjct: 520 GSGFDLPDKNCPRCGTKYKKDGHDIPFETFLGFKGDKVPDIDLNFSGEYQPRAHNYTKVL 579
Query: 424 YGKDAVSQIVTFGTMAAKGAIRDVGRVLDLRYSFCDSISKLIPFKPGKLITLSNAIKEEP 483
+G+D V + T GT+A K A Y F + + + L A
Sbjct: 580 FGEDNVYRAGTIGTVADKTA-----------YGFVKA------YASDHNLELRGA----- 617
Query: 484 QLAERIKNEEEVRQLIELAKQVEGIIRNVGMHAGGVLIAPS--KLINFCPLYKQEGMTGI 541
++ LA G+ R G H GG+++ P ++ +F P+
Sbjct: 618 -------------EIDRLAAGCTGVKRTTGQHPGGIIVVPDYMEIYDFTPI--------- 655
Query: 542 ISQYDKDDI-EEIGLIKFDFLG----LTTLSILDKTIYFIKKINTKTTNFSLNKLPLNDK 596
QY DD E FDF L L IL + ++ + +P +D
Sbjct: 656 --QYPADDTSSEWRTTHFDFHSIHDNLLKLDILGHDDPTVIRMLQDLSGIDPKTIPTDDP 713
Query: 597 DTYNLLKKA--------------NTVAVFQLESQGMKNMLKEAKPDYFEEIIALISL 639
D + T+ + + ++ ++ ML+E +P F E++ + L
Sbjct: 714 DVMGIFSSTEPLGVTPEQIMCNVGTIGIPEFGTRFVRQMLEETRPKTFSELVQISGL 770
>pdb|4EUF|A Chain A, Crystal Structure Of Clostridium Acetobutulicum
Trans-2-Enoyl-Coa Reductase In Complex With Nad
Length = 418
Score = 30.8 bits (68), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 39/88 (44%), Gaps = 5/88 (5%)
Query: 344 LIVSDFIQWAKNNSIPVGPGRGSGASSLVAYSLSITD--IDPLSY--NLLFERFLNPNRI 399
LIV + I V G + V+Y TD I + N+ F+ F +
Sbjct: 64 LIVGASSGFGLATRISVAFGGPEAHTIGVSYETGATDRRIGTAGWYNNIFFKEFAKKKGL 123
Query: 400 SMPDFDID-FCPEGRDRVIQYVKDRYGK 426
+F D F E +D+VI+Y+KD +GK
Sbjct: 124 VAKNFIEDAFSNETKDKVIKYIKDEFGK 151
>pdb|4EUE|A Chain A, Crystal Structure Of Clostridium Acetobutulicum
Trans-2-Enoyl-Coa Reductase In Complex With Nadh
pdb|4EUH|A Chain A, Crystal Structure Of Clostridium Acetobutulicum
Trans-2-Enoyl-Coa Reductase Apo Form
Length = 418
Score = 30.4 bits (67), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 39/88 (44%), Gaps = 5/88 (5%)
Query: 344 LIVSDFIQWAKNNSIPVGPGRGSGASSLVAYSLSITD--IDPLSY--NLLFERFLNPNRI 399
LIV + I V G + V+Y TD I + N+ F+ F +
Sbjct: 64 LIVGASSGFGLATRISVAFGGPEAHTIGVSYETGATDRRIGTAGWYNNIFFKEFAKKKGL 123
Query: 400 SMPDFDID-FCPEGRDRVIQYVKDRYGK 426
+F D F E +D+VI+Y+KD +GK
Sbjct: 124 VAKNFIEDAFSNETKDKVIKYIKDEFGK 151
>pdb|1KJZ|A Chain A, Structure Of The Large Gamma Subunit Of Initiation Factor
Eif2 From Pyrococcus Abyssi-G235d Mutant
pdb|1KK1|A Chain A, Structure Of The Large Gamma Subunit Of Initiation Factor
Eif2 From Pyrococcus Abyssi-G235d Mutant Complexed With
Gdpnp-Mg2+
pdb|1KK2|A Chain A, Structure Of The Large Gamma Subunit Of Initiation Factor
Eif2 From Pyrococcus Abyssi-G235d Mutant Complexed With
Gdp-Mg2+
Length = 410
Score = 29.6 bits (65), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 42/76 (55%), Gaps = 3/76 (3%)
Query: 439 AAKGAIRDVGRVLDLRYSFCDSISKLIPFKPGKLITLSNAIKEEPQLAER-IKNEEEVRQ 497
A G + VG LD + D ++ + KPGKL + ++++ E L ER + E+E++
Sbjct: 285 AYPGGLVGVGTKLDPYLTKGDLMAGNVVGKPGKLPPVWDSLRLEVHLLERVVGTEQELK- 343
Query: 498 LIELAKQVEGIIRNVG 513
+E K+ E ++ NVG
Sbjct: 344 -VEPIKRKEVLLLNVG 358
>pdb|1KK3|A Chain A, Structure Of The Wild-Type Large Gamma Subunit Of
Initiation Factor Eif2 From Pyrococcus Abyssi Complexed
With Gdp-Mg2+
Length = 410
Score = 29.6 bits (65), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 42/76 (55%), Gaps = 3/76 (3%)
Query: 439 AAKGAIRDVGRVLDLRYSFCDSISKLIPFKPGKLITLSNAIKEEPQLAER-IKNEEEVRQ 497
A G + VG LD + D ++ + KPGKL + ++++ E L ER + E+E++
Sbjct: 285 AYPGGLVGVGTKLDPYLTKGDLMAGNVVGKPGKLPPVWDSLRLEVHLLERVVGTEQELK- 343
Query: 498 LIELAKQVEGIIRNVG 513
+E K+ E ++ NVG
Sbjct: 344 -VEPIKRKEVLLLNVG 358
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
0.321 0.140 0.404
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 33,052,915
Number of Sequences: 62578
Number of extensions: 1411310
Number of successful extensions: 4164
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 4105
Number of HSP's gapped (non-prelim): 21
length of query: 1149
length of database: 14,973,337
effective HSP length: 109
effective length of query: 1040
effective length of database: 8,152,335
effective search space: 8478428400
effective search space used: 8478428400
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 57 (26.6 bits)