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= psy4730
(1513 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3VKH|A Chain A, X-Ray Structure Of A Functional Full-Length Dynein Motor
Domain
pdb|3VKH|B Chain B, X-Ray Structure Of A Functional Full-Length Dynein Motor
Domain
Length = 3367
Score = 339 bits (869), Expect = 9e-93, Method: Compositional matrix adjust.
Identities = 176/444 (39%), Positives = 271/444 (61%), Gaps = 38/444 (8%)
Query: 1084 IGTKMDEFLKNKITDKTISADDLRSLFFGNFLGNTIIFPGAWACFDEFNRIELEVLSVVA 1143
+G+++ F+ D+ + +F G + GAW CFDEFNR+E +LS V+
Sbjct: 624 LGSQLGRFVLVFCCDEGFDLQAMSRIFVG------LCQCGAWGCFDEFNRLEERILSAVS 677
Query: 1144 QQVQSIQLATIAKLKKF-MFEGTEISLNPTSMIFITMNPGYAGRTELPDNLKVLFRSVAM 1202
QQ+Q+IQ+A K+ + G ISL+ IF+TMNPGYAGR+ LPDNLK LFRS+AM
Sbjct: 678 QQIQTIQVALKENSKEVELLGGKNISLHQDMGIFVTMNPGYAGRSNLPDNLKKLFRSMAM 737
Query: 1203 MVPDYAMIGEISLYSMGFQNAKILAEKIVYTYKLCSEQLSSQSHYDYGMRAVKSVLNAAG 1262
+ PD MI ++ LYS GF+ A++LA KIV +KLC EQLS+QSHYD+G+RA+KSVL +AG
Sbjct: 738 IKPDREMIAQVMLYSQGFKTAEVLAGKIVPLFKLCQEQLSAQSHYDFGLRALKSVLVSAG 797
Query: 1263 SLKIKY------PEKD--------------EFVIVLRAIIDVNMPKFLVQDLPLFIGIYK 1302
+K K P D E ++L +I D +PK + D+PL +
Sbjct: 798 GIKRKCQPPQLPPITDAESKTKADQIYCQYEIGVLLNSINDTMIPKLVADDIPLIQSLLL 857
Query: 1303 DLFPGIELPPTDRDELIEQIKINLAKRNAQATDWYIEKIIQVYEMILVRHGLMVVGESFG 1362
D+FPG +L P D+L ++I+ +R+ ++EKI+Q+++++ + HG+M+VG S G
Sbjct: 858 DVFPGSQLQPIQMDQLRKKIQEIAKQRHLVTKQEWVEKILQLHQILNINHGVMMVGPSGG 917
Query: 1363 GKTTAYQTLADSLTDIAAKKSATMKEFKTGYKIINPKSITMGQLYGEFDSASHEWRDGIL 1422
GKTT+++ +++ + KS +++PK+IT QL+G D + EW DG+
Sbjct: 918 GKTTSWEVYLEAIEQVDNIKSEA--------HVMDPKAITKDQLFGSLDLTTREWTDGLF 969
Query: 1423 AKTFREM---AVSTTPDRKWIMFDGPIDAVWIENMNTVLDDNKKLCLINGEIIKMSNTMN 1479
T R + + R WI+FDG +D W+EN+N++LDDNK L L NGE + + N +
Sbjct: 970 TATLRRIIDNVRGESTKRHWIIFDGDVDPEWVENLNSLLDDNKLLTLPNGERLALPNNVR 1029
Query: 1480 LIFECENLEFASPATVSRVGMIYF 1503
++FE ++L++A+ AT+SR GM++F
Sbjct: 1030 VMFEVQDLKYATLATISRCGMVWF 1053
Score = 256 bits (654), Expect = 7e-68, Method: Compositional matrix adjust.
Identities = 178/556 (32%), Positives = 285/556 (51%), Gaps = 31/556 (5%)
Query: 166 DLTRSKLESFRKEVPILQCISNPGMEERHWKILSDELGQDITPNDQTSLKNMLDLGIRNI 225
D ++ ++ + K I+ + + +++RHWKIL L + + T L ++ D +
Sbjct: 89 DHAQNLIKIYLKGNAIITDLHSEAIKDRHWKILKKRLNTNWIITELT-LGSIWDSDLARN 147
Query: 226 LPKLEEVSLSASKEAELSQSLNKMVTEWSDIKLDVVPYRDTGTYIIQGTDEIQVMLDDHI 285
EV +A E L + L + W+ ++LD+V Y+ +++G D++ L +H+
Sbjct: 148 ENIYREVITAAQGEIALEEFLKGVREFWTTLELDLVNYQ-RKCKLVRGWDDLFNKLAEHL 206
Query: 286 LRAQTMRGSPYIKPFETEMEAWESKLINMQDILDIWLQVQGTWMYLEPIFS-SEDIMRQM 344
M+ SPY K FE E W+ +L ++ +LD+W+ VQ W+YLE IFS S DI + +
Sbjct: 207 NSISAMKMSPYYKVFEEEANHWDDRLNKVRSLLDVWIDVQRRWVYLEGIFSGSGDINQLL 266
Query: 345 PEESRNFKTVDQIWKTIMLFVNKDPHILQATEMEDMLKNFNKCNLMLELIQKGLNDYLEX 404
P ES FK+++ + I+ V+ P IL+ +E + + + + +L +QK L +YLE
Sbjct: 267 PAESTRFKSINSEFIAILKKVSGAPLILEVLAIERIQQTMERLSDLLGKVQKALGEYLER 326
Query: 405 XXXXXXXXXXXSNDELLEILSETKDPLRVQPHLKKIFEGI-NLLEYSDSLEIIGMISLEG 463
+++LLEI+ +KD +++Q H +K+F G+ NL + IIGM S EG
Sbjct: 327 QRSAFARFYFVGDEDLLEIIGNSKDIIKIQKHFRKMFAGLANLTLDDEKTTIIGMSSAEG 386
Query: 464 EKVALSGLIR-PNDAKGLVEKWLQQVEDLMIKSLQDICMMALGAYYK------SERVVWV 516
E V I N K + +WL VE M +L + +L + + S+ WV
Sbjct: 387 ETVTFKKPISIANGPK--IHEWLTMVESEMKSTLATLLSESLQHFNQVDVNDHSKYSEWV 444
Query: 517 TKWPGMVVICVSSITWTAEVEKAIQG-----RKLDAMLDKSVKQIDIMVIK-----VRGK 566
+P +V+ S I W+ +V++A+ G K+ L +S++Q M++ V
Sbjct: 445 DNYPTQLVLLTSQIVWSTQVDQALGGGTLQQSKIQEQL-QSIEQTTQMILNNLADSVLQD 503
Query: 567 LLMSERITICALIVIDVHAKEVVASLVESK-VTQVEDFAWMSQLRYYXXXXXXXXC---- 621
L +R LI VH ++VV L + K +T +DF W+ +RYY
Sbjct: 504 LSAQKRKKFEHLITELVHQRDVVRQLQKCKNLTGNKDFDWLYHMRYYYDATQENVLHKLV 563
Query: 622 --MITTTVQYGYEYLGNSDRLVITPLTDRCYRTLMSALKLHLGGAPEGPAGTGKTETSKD 679
M T YG+EYLG +RLV TPLTDRCY TL AL+ +GG P GPAGTGKTET K
Sbjct: 564 IHMANATFYYGFEYLGIGERLVQTPLTDRCYLTLTQALESRMGGNPFGPAGTGKTETVKA 623
Query: 680 LAKAVAKQCIVFNCSD 695
L + + +VF C +
Sbjct: 624 LGSQLGRFVLVFCCDE 639
Score = 78.2 bits (191), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 49/191 (25%), Positives = 97/191 (50%), Gaps = 16/191 (8%)
Query: 889 MILDDLNMPQKETYGAQPAVELLRQIIDHKHLYDFQTVTRVDLVDIIYITAMIPTMNT-- 946
+ D++N+P + YG Q + +RQ+++ + T + L I ++ A P +
Sbjct: 1378 VFCDEINLPSTDKYGTQRVITFIRQMVEKGGFWRTSDHTWIKLDKIQFVGACNPPTDAGR 1437
Query: 947 --ITGRLLRHMNIISIDSFNEATLSKIFTSVLDWHFSKGFAD---SIVKLSKNIVAATFH 1001
+T R LRH I+ +D + ++L++I+ + F++ ++ + N+ A
Sbjct: 1438 VQLTHRFLRHAPILLVDFPSTSSLTQIYGT-----FNRALMKLLPNLRSFADNLTDAMVE 1492
Query: 1002 VYSESTKVFLPIPSKSHYVFNLRDFAKVIMGLTQLPAS--HCKAPDKMYKLWTHEILRVF 1059
YSES K F P ++HY+++ R+ ++ L + + C + + +LW HE LR+F
Sbjct: 1493 FYSESQKRFTP-DIQAHYIYSPRELSRWDRALLEAIQTMDGCTL-EGLVRLWAHEALRLF 1550
Query: 1060 SDRLVDEADKQ 1070
DRLV+ +K+
Sbjct: 1551 QDRLVETEEKE 1561
Score = 49.3 bits (116), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 37/148 (25%), Positives = 72/148 (48%), Gaps = 9/148 (6%)
Query: 815 EFVIVLRAIIDVNMPKFLVQDLPLFIGIYKDLFPGIELPPTDRDELIEQIKINLAKRNAQ 874
E ++L +I D +PK + D+PL + D+FPG +L P D+L ++I+ +R+
Sbjct: 828 EIGVLLNSINDTMIPKLVADDIPLIQSLLLDVFPGSQLQPIQMDQLRKKIQEIAKQRHLV 887
Query: 875 ATDWYIEKIIQVYEMI-LDDLNMPQKETYGAQP--------AVELLRQIIDHKHLYDFQT 925
++EKI+Q+++++ ++ M + G + A+E + I H+ D +
Sbjct: 888 TKQEWVEKILQLHQILNINHGVMMVGPSGGGKTTSWEVYLEAIEQVDNIKSEAHVMDPKA 947
Query: 926 VTRVDLVDIIYITAMIPTMNTITGRLLR 953
+T+ L + +T T T L R
Sbjct: 948 ITKDQLFGSLDLTTREWTDGLFTATLRR 975
Score = 37.7 bits (86), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 38/164 (23%), Positives = 68/164 (41%), Gaps = 25/164 (15%)
Query: 707 DLIIPTNVTCMQNFFINLYLQNDVPMMFVGPTGTGKSTIVLNLLLNLSKDKYLPNIINFS 766
D++IPT T ++ +L P++ GP G+GK+ + + L + P+ S
Sbjct: 1282 DVVIPTVDTTRHVDVLHAWLSEHRPLILCGPPGSGKTMTLTSTL------RAFPDFEVVS 1335
Query: 767 ARTSSNITQEMIMAKLDRRRKGVYGPA---------MGKKYIVFIAGSLKIKYPEKDEF- 816
SS T E+++ D + P+ +GK +VF +I P D++
Sbjct: 1336 LNFSSATTPELLLKTFDHHCEYKRTPSGETVLRPTQLGKWLVVFCD---EINLPSTDKYG 1392
Query: 817 ----VIVLRAIIDVNMPKFLVQDLPLFIGIYKDLFPGIELPPTD 856
+ +R +++ F +I + K F G PPTD
Sbjct: 1393 TQRVITFIRQMVEKG--GFWRTSDHTWIKLDKIQFVGACNPPTD 1434
>pdb|3VKG|A Chain A, X-Ray Structure Of An Mtbd Truncation Mutant Of Dynein Motor
Domain
pdb|3VKG|B Chain B, X-Ray Structure Of An Mtbd Truncation Mutant Of Dynein Motor
Domain
Length = 3245
Score = 338 bits (868), Expect = 1e-92, Method: Compositional matrix adjust.
Identities = 176/444 (39%), Positives = 271/444 (61%), Gaps = 38/444 (8%)
Query: 1084 IGTKMDEFLKNKITDKTISADDLRSLFFGNFLGNTIIFPGAWACFDEFNRIELEVLSVVA 1143
+G+++ F+ D+ + +F G + GAW CFDEFNR+E +LS V+
Sbjct: 624 LGSQLGRFVLVFCCDEGFDLQAMSRIFVG------LCQCGAWGCFDEFNRLEERILSAVS 677
Query: 1144 QQVQSIQLATIAKLKKF-MFEGTEISLNPTSMIFITMNPGYAGRTELPDNLKVLFRSVAM 1202
QQ+Q+IQ+A K+ + G ISL+ IF+TMNPGYAGR+ LPDNLK LFRS+AM
Sbjct: 678 QQIQTIQVALKENSKEVELLGGKNISLHQDMGIFVTMNPGYAGRSNLPDNLKKLFRSMAM 737
Query: 1203 MVPDYAMIGEISLYSMGFQNAKILAEKIVYTYKLCSEQLSSQSHYDYGMRAVKSVLNAAG 1262
+ PD MI ++ LYS GF+ A++LA KIV +KLC EQLS+QSHYD+G+RA+KSVL +AG
Sbjct: 738 IKPDREMIAQVMLYSQGFKTAEVLAGKIVPLFKLCQEQLSAQSHYDFGLRALKSVLVSAG 797
Query: 1263 SLKIKY------PEKD--------------EFVIVLRAIIDVNMPKFLVQDLPLFIGIYK 1302
+K K P D E ++L +I D +PK + D+PL +
Sbjct: 798 GIKRKCQPPQLPPITDAESKTKADQIYCQYEIGVLLNSINDTMIPKLVADDIPLIQSLLL 857
Query: 1303 DLFPGIELPPTDRDELIEQIKINLAKRNAQATDWYIEKIIQVYEMILVRHGLMVVGESFG 1362
D+FPG +L P D+L ++I+ +R+ ++EKI+Q+++++ + HG+M+VG S G
Sbjct: 858 DVFPGSQLQPIQMDQLRKKIQEIAKQRHLVTKQEWVEKILQLHQILNINHGVMMVGPSGG 917
Query: 1363 GKTTAYQTLADSLTDIAAKKSATMKEFKTGYKIINPKSITMGQLYGEFDSASHEWRDGIL 1422
GKTT+++ +++ + KS +++PK+IT QL+G D + EW DG+
Sbjct: 918 GKTTSWEVYLEAIEQVDNIKSEA--------HVMDPKAITKDQLFGSLDLTTREWTDGLF 969
Query: 1423 AKTFREM---AVSTTPDRKWIMFDGPIDAVWIENMNTVLDDNKKLCLINGEIIKMSNTMN 1479
T R + + R WI+FDG +D W+EN+N++LDDNK L L NGE + + N +
Sbjct: 970 TATLRRIIDNVRGESTKRHWIIFDGDVDPEWVENLNSLLDDNKLLTLPNGERLALPNNVR 1029
Query: 1480 LIFECENLEFASPATVSRVGMIYF 1503
++FE ++L++A+ AT+SR GM++F
Sbjct: 1030 VMFEVQDLKYATLATISRCGMVWF 1053
Score = 256 bits (654), Expect = 7e-68, Method: Compositional matrix adjust.
Identities = 178/556 (32%), Positives = 285/556 (51%), Gaps = 31/556 (5%)
Query: 166 DLTRSKLESFRKEVPILQCISNPGMEERHWKILSDELGQDITPNDQTSLKNMLDLGIRNI 225
D ++ ++ + K I+ + + +++RHWKIL L + + T L ++ D +
Sbjct: 89 DHAQNLIKIYLKGNAIITDLHSEAIKDRHWKILKKRLNTNWIITELT-LGSIWDSDLARN 147
Query: 226 LPKLEEVSLSASKEAELSQSLNKMVTEWSDIKLDVVPYRDTGTYIIQGTDEIQVMLDDHI 285
EV +A E L + L + W+ ++LD+V Y+ +++G D++ L +H+
Sbjct: 148 ENIYREVITAAQGEIALEEFLKGVREFWTTLELDLVNYQ-RKCKLVRGWDDLFNKLAEHL 206
Query: 286 LRAQTMRGSPYIKPFETEMEAWESKLINMQDILDIWLQVQGTWMYLEPIFS-SEDIMRQM 344
M+ SPY K FE E W+ +L ++ +LD+W+ VQ W+YLE IFS S DI + +
Sbjct: 207 NSISAMKMSPYYKVFEEEANHWDDRLNKVRSLLDVWIDVQRRWVYLEGIFSGSGDINQLL 266
Query: 345 PEESRNFKTVDQIWKTIMLFVNKDPHILQATEMEDMLKNFNKCNLMLELIQKGLNDYLEX 404
P ES FK+++ + I+ V+ P IL+ +E + + + + +L +QK L +YLE
Sbjct: 267 PAESTRFKSINSEFIAILKKVSGAPLILEVLAIERIQQTMERLSDLLGKVQKALGEYLER 326
Query: 405 XXXXXXXXXXXSNDELLEILSETKDPLRVQPHLKKIFEGI-NLLEYSDSLEIIGMISLEG 463
+++LLEI+ +KD +++Q H +K+F G+ NL + IIGM S EG
Sbjct: 327 QRSAFARFYFVGDEDLLEIIGNSKDIIKIQKHFRKMFAGLANLTLDDEKTTIIGMSSAEG 386
Query: 464 EKVALSGLIR-PNDAKGLVEKWLQQVEDLMIKSLQDICMMALGAYYK------SERVVWV 516
E V I N K + +WL VE M +L + +L + + S+ WV
Sbjct: 387 ETVTFKKPISIANGPK--IHEWLTMVESEMKSTLATLLSESLQHFNQVDVNDHSKYSEWV 444
Query: 517 TKWPGMVVICVSSITWTAEVEKAIQG-----RKLDAMLDKSVKQIDIMVIK-----VRGK 566
+P +V+ S I W+ +V++A+ G K+ L +S++Q M++ V
Sbjct: 445 DNYPTQLVLLTSQIVWSTQVDQALGGGTLQQSKIQEQL-QSIEQTTQMILNNLADSVLQD 503
Query: 567 LLMSERITICALIVIDVHAKEVVASLVESK-VTQVEDFAWMSQLRYYXXXXXXXXC---- 621
L +R LI VH ++VV L + K +T +DF W+ +RYY
Sbjct: 504 LSAQKRKKFEHLITELVHQRDVVRQLQKCKNLTGNKDFDWLYHMRYYYDATQENVLHKLV 563
Query: 622 --MITTTVQYGYEYLGNSDRLVITPLTDRCYRTLMSALKLHLGGAPEGPAGTGKTETSKD 679
M T YG+EYLG +RLV TPLTDRCY TL AL+ +GG P GPAGTGKTET K
Sbjct: 564 IHMANATFYYGFEYLGIGERLVQTPLTDRCYLTLTQALESRMGGNPFGPAGTGKTETVKA 623
Query: 680 LAKAVAKQCIVFNCSD 695
L + + +VF C +
Sbjct: 624 LGSQLGRFVLVFCCDE 639
Score = 78.2 bits (191), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 50/191 (26%), Positives = 97/191 (50%), Gaps = 16/191 (8%)
Query: 889 MILDDLNMPQKETYGAQPAVELLRQIIDHKHLYDFQTVTRVDLVDIIYITAMIPTMNT-- 946
+ D++N+P + YG Q + +RQ+++ + T + L I ++ A P +
Sbjct: 1378 VFCDEINLPSTDKYGTQRVITFIRQMVEKGGFWRTSDHTWIKLDKIQFVGACNPPTDAGR 1437
Query: 947 --ITGRLLRHMNIISIDSFNEATLSKIFTSVLDWHFSKGFADSIVKL---SKNIVAATFH 1001
+T R LRH I+ +D + ++L++I+ + F++ + L + N+ A
Sbjct: 1438 VQLTHRFLRHAPILLVDFPSTSSLTQIYGT-----FNRALMKLLPNLRSFADNLTDAMVE 1492
Query: 1002 VYSESTKVFLPIPSKSHYVFNLRDFAKVIMGLTQLPAS--HCKAPDKMYKLWTHEILRVF 1059
YSES K F P ++HY+++ R+ ++ L + + C + + +LW HE LR+F
Sbjct: 1493 FYSESQKRFTP-DIQAHYIYSPRELSRWDRALLEAIQTMDGCTL-EGLVRLWAHEALRLF 1550
Query: 1060 SDRLVDEADKQ 1070
DRLV+ +K+
Sbjct: 1551 QDRLVETEEKE 1561
Score = 49.3 bits (116), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 37/148 (25%), Positives = 72/148 (48%), Gaps = 9/148 (6%)
Query: 815 EFVIVLRAIIDVNMPKFLVQDLPLFIGIYKDLFPGIELPPTDRDELIEQIKINLAKRNAQ 874
E ++L +I D +PK + D+PL + D+FPG +L P D+L ++I+ +R+
Sbjct: 828 EIGVLLNSINDTMIPKLVADDIPLIQSLLLDVFPGSQLQPIQMDQLRKKIQEIAKQRHLV 887
Query: 875 ATDWYIEKIIQVYEMI-LDDLNMPQKETYGAQP--------AVELLRQIIDHKHLYDFQT 925
++EKI+Q+++++ ++ M + G + A+E + I H+ D +
Sbjct: 888 TKQEWVEKILQLHQILNINHGVMMVGPSGGGKTTSWEVYLEAIEQVDNIKSEAHVMDPKA 947
Query: 926 VTRVDLVDIIYITAMIPTMNTITGRLLR 953
+T+ L + +T T T L R
Sbjct: 948 ITKDQLFGSLDLTTREWTDGLFTATLRR 975
Score = 37.7 bits (86), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 38/164 (23%), Positives = 68/164 (41%), Gaps = 25/164 (15%)
Query: 707 DLIIPTNVTCMQNFFINLYLQNDVPMMFVGPTGTGKSTIVLNLLLNLSKDKYLPNIINFS 766
D++IPT T ++ +L P++ GP G+GK+ + + L + P+ S
Sbjct: 1282 DVVIPTVDTTRHVDVLHAWLSEHRPLILCGPPGSGKTMTLTSTL------RAFPDFEVVS 1335
Query: 767 ARTSSNITQEMIMAKLDRRRKGVYGPA---------MGKKYIVFIAGSLKIKYPEKDEF- 816
SS T E+++ D + P+ +GK +VF +I P D++
Sbjct: 1336 LNFSSATTPELLLKTFDHHCEYKRTPSGETVLRPTQLGKWLVVFCD---EINLPSTDKYG 1392
Query: 817 ----VIVLRAIIDVNMPKFLVQDLPLFIGIYKDLFPGIELPPTD 856
+ +R +++ F +I + K F G PPTD
Sbjct: 1393 TQRVITFIRQMVEKG--GFWRTSDHTWIKLDKIQFVGACNPPTD 1434
>pdb|4AI6|A Chain A, Dynein Motor Domain - Adp Complex
pdb|4AI6|B Chain B, Dynein Motor Domain - Adp Complex
pdb|4AKG|A Chain A, Dynein Motor Domain - Atp Complex
pdb|4AKG|B Chain B, Dynein Motor Domain - Atp Complex
pdb|4AKH|A Chain A, Dynein Motor Domain - Amppnp Complex
pdb|4AKH|B Chain B, Dynein Motor Domain - Amppnp Complex
pdb|4AKI|A Chain A, Dynein Motor Domain - Luac Derivative
pdb|4AKI|B Chain B, Dynein Motor Domain - Luac Derivative
Length = 2695
Score = 226 bits (577), Expect = 6e-59, Method: Compositional matrix adjust.
Identities = 128/391 (32%), Positives = 208/391 (53%), Gaps = 15/391 (3%)
Query: 1123 GAWACFDEFNRIELEVLSVVAQQVQSIQLATIAKLKKFMFEGTEISLNPTSMIFITMNPG 1182
GAW CFDEFNR++ +VLS V+ +Q IQ E L+P + +FIT+NPG
Sbjct: 698 GAWGCFDEFNRLDEKVLSAVSANIQQIQNGLQVGKSHITLLEEETPLSPHTAVFITLNPG 757
Query: 1183 YAGRTELPDNLKVLFRSVAMMVPDYAMIGEISLYSMGFQNAKILAEKIVYTYKLCSEQLS 1242
Y GR+ELP+NLK FR +M P I E+ L MGF+++K LA KIV+ +L S + S
Sbjct: 758 YNGRSELPENLKKSFREFSMKSPQSGTIAEMILQIMGFEDSKSLASKIVHFLELLSSKCS 817
Query: 1243 SQSHYDYGMRAVKSVLNAAGSLKIKYPEKDEFVIVLRAIIDVNMPKFLVQDLPLFIGIYK 1302
S +HY +G+R +K VL L ++ E ++ V+ ++ V +P D +F
Sbjct: 818 SMNHYHFGLRTLKGVLRNCSPLISEFGEGEKTVV--ESLKRVILPSLGDTDELVFKDELS 875
Query: 1303 DLFPGIELPPTDRDELIEQIKINLAKRNAQATDWYIEKIIQVYEMILVRHGLMVVGESFG 1362
+F P + +++ +K + ++ +++K +Q Y M + L++VG++
Sbjct: 876 KIFDSAGTPLNSK-AIVQCLKDAGQRSGFSMSEEFLKKCMQFYYMQKTQQALILVGKAGC 934
Query: 1363 GKTTAYQTLADSLTDIAAKKSATMKEFKTGYKIINPKSITMGQLYGEFDSASHEWRDGIL 1422
GKT ++T+ D++ + +I+ K +T LYG A+ EWRDG+
Sbjct: 935 GKTATWKTVIDAMAIFDGHANVVY--------VIDTKVLTKESLYGSMLKATLEWRDGLF 986
Query: 1423 AKTFREMAVSTTP----DRKWIMFDGPIDAVWIENMNTVLDDNKKLCLINGEIIKMSNTM 1478
R + T R W++FD +D ++E MN+VLDDNK L L NGE + +
Sbjct: 987 TSILRRVNDDITGTFKNSRIWVVFDSDLDPEYVEAMNSVLDDNKILTLPNGERLPIPPNF 1046
Query: 1479 NLIFECENLEFASPATVSRVGMIYFELKCIS 1509
++FE +NL+ +PAT++R G+++F S
Sbjct: 1047 RILFETDNLDHTTPATITRCGLLWFSTDVCS 1077
Score = 134 bits (336), Expect = 5e-31, Method: Compositional matrix adjust.
Identities = 120/470 (25%), Positives = 214/470 (45%), Gaps = 18/470 (3%)
Query: 237 SKEAELSQSLNKMVTEWSDIKLDVVPYRDTGTYIIQGTDEIQVMLDDHILRAQTMRGSPY 296
S E + +SLN++ W + + +V+ + +G +++ D ++ + + +M+ S Y
Sbjct: 218 SDEFVIEKSLNRIKKFWKEAQYEVIEH-SSGLKLVREWDVLEQACKEDLEELVSMKASNY 276
Query: 297 IKPFETEMEAWESKLINMQDILDIWLQVQGTWMYLEPIFSSE-DIMRQMPEESRNFKTVD 355
K FE + ESKL + +I W++VQ W+ L I DI +P E+ FK++
Sbjct: 277 YKIFEQDCLDLESKLTKLSEIQVNWVEVQFYWLDLYGILGENLDIQNFLPLETSKFKSLT 336
Query: 356 QIWKTIMLFVNKDPHILQATEMEDMLKNFNKCNLMLELIQKGLNDYLEXXXXXXXXXXXX 415
+K I + ++ + + L++I+ L+ +LE
Sbjct: 337 SEYKMITTRAFQLDTTIEVIHIPNFDTTLKLTIDSLKMIKSSLSTFLERQRRQFPRFYFL 396
Query: 416 SNDELLEILSETKDPLRVQPHLKKIFEGINLLEYSDSLEIIGMISLEGEKVALSGLIRPN 475
ND+LL+I+ K +V +KK+F I + + + I G+ S+EGE + L+ I
Sbjct: 397 GNDDLLKIIGSGKHHDQVSKFMKKMFGSIESIIFLEDF-ITGVRSVEGEVLNLNEKIELK 455
Query: 476 DAKGLVEKWLQQVEDLMIKSLQDICMMALGAYYKSERV-VWVTKWPGMVVICVSSITWTA 534
D+ ++WL ++ + S+ LG + V V+K+ ++ + + WT
Sbjct: 456 DSIQ-AQEWLNILDTEIKLSVFTQFRDCLGQIKDGTDIEVVVSKYIFQAILLSAQVMWTE 514
Query: 535 EVEKAIQGRKLDAMLDKSVKQIDIMVIKVRGKLLMSE---RITICALIVIDVHAKEVVAS 591
VEK +Q + K K++D+ + + KL S + I AL+V +H V+
Sbjct: 515 LVEKCLQTNQFS----KYWKEVDMKIKGLLDKLNKSSDNVKKKIEALLVEYLHFNNVIGQ 570
Query: 592 LVESKVTQVEDFAWMSQLRYYXXXXXX---XXCMITTT---VQYGYEYLGNSDRLVITPL 645
L + W ++Y I+ + +QY +EY+G +RL+ TPL
Sbjct: 571 LKNCSTKEEARLLWAKVQKFYQKNDTLDDLNSVFISQSGYLLQYKFEYIGIPERLIYTPL 630
Query: 646 TDRCYRTLMSALKLHLGGAPEGPAGTGKTETSKDLAKAVAKQCIVFNCSD 695
+ TL +L GG GPAGTGKTET K + + + +VFNC D
Sbjct: 631 LLIGFATLTDSLHQKYGGCFFGPAGTGKTETVKAFGQNLGRVVVVFNCDD 680
Score = 63.2 bits (152), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 48/212 (22%), Positives = 99/212 (46%), Gaps = 16/212 (7%)
Query: 889 MILDDLNMPQKETYGAQPAVELLRQIIDHKHLYDFQTVTRVDLVDIIYITAMIPTMNT-- 946
+ D++N+P+ + YG+Q V LRQ+++ + + V + I + A P +
Sbjct: 1340 LFCDEINLPKLDKYGSQNVVLFLRQLMEKQGFWKTPENKWVTIERIHIVGACNPPTDPGR 1399
Query: 947 --ITGRLLRHMNIISIDSFNEATLSKIFTSVLDWHFSKGFADSIVKLSKNIVAATFHVYS 1004
++ R RH I+ + + +LS+I+ F ++ A+ H+Y+
Sbjct: 1400 IPMSERFTRHAAILYLGYPSGKSLSQIYEIYYKAIFK--LVPEFRSYTEPFARASVHLYN 1457
Query: 1005 ESTKVFLPIPSKSHYVFNLRDFAKVIMGL-TQLPASHCKAPDKMYKLWTHEILRVFSDRL 1063
E K +SHY+F+ R+ +++ G+ T + + + +LW +E R+F+DRL
Sbjct: 1458 E-CKARYSTGLQSHYLFSPRELTRLVRGVYTAINTGPRQTLRSLIRLWAYEAWRIFADRL 1516
Query: 1064 VDEADKQSLLDMMKYACQNIIGTKMDEFLKNK 1095
V +K S + ++ +D++L N+
Sbjct: 1517 VGVKEKNSF--------EQLLYETVDKYLPNQ 1540
Score = 34.3 bits (77), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 32/97 (32%), Positives = 45/97 (46%), Gaps = 11/97 (11%)
Query: 693 CSDRPTFPPN----LRPSDLIIPTNVTCMQNFFINLYLQNDVPMMFVGPTGTGKSTIVLN 748
CS+ P+ +RP D++IPT T L + ++ GP G+GK+ I+ N
Sbjct: 1228 CSEIPSVSLEAHEVMRP-DIVIPTIDTIKHEKIFYDLLNSKRGIILCGPPGSGKTMIMNN 1286
Query: 749 LLLNLSKDKYLPNIINFSARTSSNITQEMIMAKLDRR 785
L N S Y INFS T T E I++ L R
Sbjct: 1287 ALRNSS--LYDVVGINFSKDT----TTEHILSALHRH 1317
>pdb|3QMZ|A Chain A, Crystal Structure Of The Cytoplasmic Dynein Heavy Chain
Motor Domain
pdb|3QMZ|B Chain B, Crystal Structure Of The Cytoplasmic Dynein Heavy Chain
Motor Domain
Length = 2486
Score = 226 bits (576), Expect = 7e-59, Method: Compositional matrix adjust.
Identities = 128/391 (32%), Positives = 208/391 (53%), Gaps = 15/391 (3%)
Query: 1123 GAWACFDEFNRIELEVLSVVAQQVQSIQLATIAKLKKFMFEGTEISLNPTSMIFITMNPG 1182
GAW CFDEFNR++ +VLS V+ +Q IQ E L+P + +FIT+NPG
Sbjct: 479 GAWGCFDEFNRLDEKVLSAVSANIQQIQNGLQVGKSHITLLEEETPLSPHTAVFITLNPG 538
Query: 1183 YAGRTELPDNLKVLFRSVAMMVPDYAMIGEISLYSMGFQNAKILAEKIVYTYKLCSEQLS 1242
Y GR+ELP+NLK FR +M P I E+ L MGF+++K LA KIV+ +L S + S
Sbjct: 539 YNGRSELPENLKKSFREFSMKSPQSGTIAEMILQIMGFEDSKSLASKIVHFLELLSSKCS 598
Query: 1243 SQSHYDYGMRAVKSVLNAAGSLKIKYPEKDEFVIVLRAIIDVNMPKFLVQDLPLFIGIYK 1302
S +HY +G+R +K VL L ++ E ++ V+ ++ V +P D +F
Sbjct: 599 SMNHYHFGLRTLKGVLRNCSPLISEFGEGEKTVV--ESLKRVILPSLGDTDELVFKDELS 656
Query: 1303 DLFPGIELPPTDRDELIEQIKINLAKRNAQATDWYIEKIIQVYEMILVRHGLMVVGESFG 1362
+F P + +++ +K + ++ +++K +Q Y M + L++VG++
Sbjct: 657 KIFDSAGTPLNSK-AIVQCLKDAGQRSGFSMSEEFLKKCMQFYYMQKTQQALILVGKAGC 715
Query: 1363 GKTTAYQTLADSLTDIAAKKSATMKEFKTGYKIINPKSITMGQLYGEFDSASHEWRDGIL 1422
GKT ++T+ D++ + +I+ K +T LYG A+ EWRDG+
Sbjct: 716 GKTATWKTVIDAMAIFDGHANVVY--------VIDTKVLTKESLYGSMLKATLEWRDGLF 767
Query: 1423 AKTFREMAVSTTP----DRKWIMFDGPIDAVWIENMNTVLDDNKKLCLINGEIIKMSNTM 1478
R + T R W++FD +D ++E MN+VLDDNK L L NGE + +
Sbjct: 768 TSILRRVNDDITGTFKNSRIWVVFDSDLDPEYVEAMNSVLDDNKILTLPNGERLPIPPNF 827
Query: 1479 NLIFECENLEFASPATVSRVGMIYFELKCIS 1509
++FE +NL+ +PAT++R G+++F S
Sbjct: 828 RILFETDNLDHTTPATITRCGLLWFSTDVCS 858
Score = 132 bits (333), Expect = 1e-30, Method: Compositional matrix adjust.
Identities = 119/468 (25%), Positives = 213/468 (45%), Gaps = 18/468 (3%)
Query: 239 EAELSQSLNKMVTEWSDIKLDVVPYRDTGTYIIQGTDEIQVMLDDHILRAQTMRGSPYIK 298
E + +SLN++ W + + +V+ + +G +++ D ++ + + +M+ S Y K
Sbjct: 1 EFVIEKSLNRIKKFWKEAQYEVIEH-SSGLKLVREWDVLEQACKEDLEELVSMKASNYYK 59
Query: 299 PFETEMEAWESKLINMQDILDIWLQVQGTWMYLEPIFSSE-DIMRQMPEESRNFKTVDQI 357
FE + ESKL + +I W++VQ W+ L I DI +P E+ FK++
Sbjct: 60 IFEQDCLDLESKLTKLSEIQVNWVEVQFYWLDLYGILGENLDIQNFLPLETSKFKSLTSE 119
Query: 358 WKTIMLFVNKDPHILQATEMEDMLKNFNKCNLMLELIQKGLNDYLEXXXXXXXXXXXXSN 417
+K I + ++ + + L++I+ L+ +LE N
Sbjct: 120 YKMITTRAFQLDTTIEVIHIPNFDTTLKLTIDSLKMIKSSLSTFLERQRRQFPRFYFLGN 179
Query: 418 DELLEILSETKDPLRVQPHLKKIFEGINLLEYSDSLEIIGMISLEGEKVALSGLIRPNDA 477
D+LL+I+ K +V +KK+F I + + + I G+ S+EGE + L+ I D+
Sbjct: 180 DDLLKIIGSGKHHDQVSKFMKKMFGSIESIIFFEDF-ITGVRSVEGEVLNLNEKIELKDS 238
Query: 478 KGLVEKWLQQVEDLMIKSLQDICMMALGAYYKSERV-VWVTKWPGMVVICVSSITWTAEV 536
++WL ++ + S+ LG + V V+K+ ++ + + WT V
Sbjct: 239 IQ-AQEWLNILDTEIKLSVFTQFRDCLGQLKDGTDIEVVVSKYIFQAILLSAQVMWTELV 297
Query: 537 EKAIQGRKLDAMLDKSVKQIDIMVIKVRGKLLMSE---RITICALIVIDVHAKEVVASLV 593
EK +Q + K K++D+ + + KL S + I AL+V +H V+ L
Sbjct: 298 EKCLQTNEFS----KYWKEVDMKIKGLLDKLNKSSDNVKKKIEALLVEYLHFNNVIGQLK 353
Query: 594 ESKVTQVEDFAWMSQLRYYXXXXXX---XXCMITTT---VQYGYEYLGNSDRLVITPLTD 647
+ W ++Y I+ + +QY +EY+G +RL+ TPL
Sbjct: 354 NCSTKEEARLLWAKVQKFYQKNDTLDDLNSVFISQSGYLLQYKFEYIGIPERLIYTPLLL 413
Query: 648 RCYRTLMSALKLHLGGAPEGPAGTGKTETSKDLAKAVAKQCIVFNCSD 695
+ TL +L GG GPAGTGKTET K + + + +VFNC D
Sbjct: 414 IGFATLTDSLHQKYGGCFFGPAGTGKTETVKAFGQNLGRVVVVFNCDD 461
Score = 62.8 bits (151), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 48/212 (22%), Positives = 99/212 (46%), Gaps = 16/212 (7%)
Query: 889 MILDDLNMPQKETYGAQPAVELLRQIIDHKHLYDFQTVTRVDLVDIIYITAMIPTMNT-- 946
+ D++N+P+ + YG+Q V LRQ+++ + + V + I + A P +
Sbjct: 1121 LFCDEINLPKLDKYGSQNVVLFLRQLMEKQGFWKTPENKWVTIERIHIVGACNPPTDPGR 1180
Query: 947 --ITGRLLRHMNIISIDSFNEATLSKIFTSVLDWHFSKGFADSIVKLSKNIVAATFHVYS 1004
++ R RH I+ + + +LS+I+ F ++ A+ H+Y+
Sbjct: 1181 IPMSERFTRHAAILYLGYPSGKSLSQIYEIYYKAIFK--LVPEFRSYTEPFARASVHLYN 1238
Query: 1005 ESTKVFLPIPSKSHYVFNLRDFAKVIMGL-TQLPASHCKAPDKMYKLWTHEILRVFSDRL 1063
E K +SHY+F+ R+ +++ G+ T + + + +LW +E R+F+DRL
Sbjct: 1239 E-CKARYSTGLQSHYLFSPRELTRLVRGVYTAINTGPRQTLRSLIRLWAYEAWRIFADRL 1297
Query: 1064 VDEADKQSLLDMMKYACQNIIGTKMDEFLKNK 1095
V +K S + ++ +D++L N+
Sbjct: 1298 VGVKEKNSF--------EQLLYETVDKYLPNQ 1321
Score = 34.3 bits (77), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 32/97 (32%), Positives = 45/97 (46%), Gaps = 11/97 (11%)
Query: 693 CSDRPTFPPN----LRPSDLIIPTNVTCMQNFFINLYLQNDVPMMFVGPTGTGKSTIVLN 748
CS+ P+ +RP D++IPT T L + ++ GP G+GK+ I+ N
Sbjct: 1009 CSEIPSVSLEAHEVMRP-DIVIPTIDTIKHEKIFYDLLNSKRGIILCGPPGSGKTMIMNN 1067
Query: 749 LLLNLSKDKYLPNIINFSARTSSNITQEMIMAKLDRR 785
L N S Y INFS T T E I++ L R
Sbjct: 1068 ALRNSS--LYDVVGINFSKDT----TTEHILSALHRH 1098
>pdb|1VL0|A Chain A, Crystal Structure Of A Dtdp-4-Dehydrorhamnose Reductase,
Rfbd Ortholog (Ca_c2315) From Clostridium Acetobutylicum
Atcc 824 At 2.05 A Resolution
pdb|1VL0|B Chain B, Crystal Structure Of A Dtdp-4-Dehydrorhamnose Reductase,
Rfbd Ortholog (Ca_c2315) From Clostridium Acetobutylicum
Atcc 824 At 2.05 A Resolution
pdb|1VL0|C Chain C, Crystal Structure Of A Dtdp-4-Dehydrorhamnose Reductase,
Rfbd Ortholog (Ca_c2315) From Clostridium Acetobutylicum
Atcc 824 At 2.05 A Resolution
Length = 292
Score = 33.9 bits (76), Expect = 0.63, Method: Composition-based stats.
Identities = 21/55 (38%), Positives = 33/55 (60%), Gaps = 1/55 (1%)
Query: 14 LTAIEKSVTGNTTEEFKK-AHKEEHSKMLTAIEKSVTGNTTEEFKKAHKEVLTLL 67
LT I+ VT TTEEF + A + ++S + + TG+ T E+K++ KE + LL
Sbjct: 236 LTGIDVKVTPCTTEEFPRPAKRPKYSVLRNYXLELTTGDITREWKESLKEYIDLL 290
>pdb|1LV5|A Chain A, Crystal Structure Of The Closed Conformation Of Bacillus
Dna Polymerase I Fragment Bound To Dna And Dctp
pdb|1LV5|B Chain B, Crystal Structure Of The Closed Conformation Of Bacillus
Dna Polymerase I Fragment Bound To Dna And Dctp
Length = 580
Score = 33.9 bits (76), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 41/82 (50%), Gaps = 4/82 (4%)
Query: 86 LLKMVRTNYETVDEMLERLEPFDQLWSIILEFRESSDL---WMEGPFKGLNADEIKDKTD 142
+LK +T Y T ++LE+L P+ ++ IL +R+ L ++EG K + D K T
Sbjct: 250 VLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPDTKKVHTI 309
Query: 143 FMFRELNQLARKMTRAPGCKMV 164
F + L Q R + P + +
Sbjct: 310 FN-QALTQTGRLSSTEPNLQNI 330
>pdb|1U45|A Chain A, 8oxoguanine At The Pre-Insertion Site Of The Polymerase
Active Site
pdb|1U47|A Chain A, Cytosine-8-Oxoguanine Base Pair At The Polymerase Active
Site
pdb|1U48|A Chain A, Extension Of A Cytosine-8-Oxoguanine Base Pair
pdb|1U49|A Chain A, Adenine-8oxoguanine Mismatch At The Polymerase Active Site
pdb|1U4B|A Chain A, Extension Of An Adenine-8oxoguanine Mismatch
pdb|1UA0|A Chain A, Aminofluorene Dna Adduct At The Pre-Insertion Site Of A
Dna Polymerase
pdb|1UA1|A Chain A, Structure Of Aminofluorene Adduct Paired Opposite Cytosine
At The Polymerase Active Site
Length = 580
Score = 33.9 bits (76), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 41/82 (50%), Gaps = 4/82 (4%)
Query: 86 LLKMVRTNYETVDEMLERLEPFDQLWSIILEFRESSDL---WMEGPFKGLNADEIKDKTD 142
+LK +T Y T ++LE+L P+ ++ IL +R+ L ++EG K + D K T
Sbjct: 250 VLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPDTKKVHTI 309
Query: 143 FMFRELNQLARKMTRAPGCKMV 164
F + L Q R + P + +
Sbjct: 310 FN-QALTQTGRLSSTEPNLQNI 330
>pdb|3EYZ|A Chain A, Cocrystal Structure Of Bacillus Fragment Dna Polymerase I
With Duplex Dna (Open Form)
Length = 580
Score = 33.9 bits (76), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 41/82 (50%), Gaps = 4/82 (4%)
Query: 86 LLKMVRTNYETVDEMLERLEPFDQLWSIILEFRESSDL---WMEGPFKGLNADEIKDKTD 142
+LK +T Y T ++LE+L P+ ++ IL +R+ L ++EG K + D K T
Sbjct: 250 VLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPDTKKVHTI 309
Query: 143 FMFRELNQLARKMTRAPGCKMV 164
F + L Q R + P + +
Sbjct: 310 FN-QALTQTGRLSSTEPNLQNI 330
>pdb|3HPO|A Chain A, Crystal Structure Of Fragment Dna Polymerase I From
Bacillus Stearothermophilus Y714s Mutant Bound To G:t
Mismatch
Length = 580
Score = 33.9 bits (76), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 41/82 (50%), Gaps = 4/82 (4%)
Query: 86 LLKMVRTNYETVDEMLERLEPFDQLWSIILEFRESSDL---WMEGPFKGLNADEIKDKTD 142
+LK +T Y T ++LE+L P+ ++ IL +R+ L ++EG K + D K T
Sbjct: 250 VLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPDTKKVHTI 309
Query: 143 FMFRELNQLARKMTRAPGCKMV 164
F + L Q R + P + +
Sbjct: 310 FN-QALTQTGRLSSTEPNLQNI 330
>pdb|2HHQ|A Chain A, O6-Methyl-Guanine:t Pair In The Polymerase-10 Basepair
Position
pdb|2HHS|A Chain A, O6-Methyl:c Pair In The Polymerase-10 Basepair Position
pdb|2HHT|A Chain A, C:o6-Methyl-Guanine Pair In The Polymerase-2 Basepair
Position
pdb|2HHU|A Chain A, C:o6-Methyl-Guanine In The Polymerase Postinsertion Site
(- 1 Basepair Position)
pdb|2HHV|A Chain A, T:o6-Methyl-Guanine In The Polymerase-2 Basepair Position
pdb|2HHX|A Chain A, O6-Methyl-Guanine In The Polymerase Template Preinsertion
Site
pdb|2HW3|A Chain A, T:o6-Methyl-Guanine Pair In The Polymerase Postinsertion
Site (-1 Basepair Position)
Length = 580
Score = 33.9 bits (76), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 41/82 (50%), Gaps = 4/82 (4%)
Query: 86 LLKMVRTNYETVDEMLERLEPFDQLWSIILEFRESSDL---WMEGPFKGLNADEIKDKTD 142
+LK +T Y T ++LE+L P+ ++ IL +R+ L ++EG K + D K T
Sbjct: 250 VLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPDTKKVHTI 309
Query: 143 FMFRELNQLARKMTRAPGCKMV 164
F + L Q R + P + +
Sbjct: 310 FN-QALTQTGRLSSTEPNLQNI 330
>pdb|1L3S|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Fragment
Complexed To 9 Base Pairs Of Duplex Dna.
pdb|1L3T|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Fragment
Product Complex With 10 Base Pairs Of Duplex Dna
Following Addition Of A Single Dttp Residue
pdb|1L3U|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Fragment
Product Complex With 11 Base Pairs Of Duplex Dna
Following Addition Of A Dttp And A Datp Residue.
pdb|1L3V|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Fragment
Product Complex With 15 Base Pairs Of Duplex Dna
Following Addition Of Dttp, Datp, Dctp, And Dgtp
Residues.
pdb|1L5U|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Fragment
Product Complex With 12 Base Pairs Of Duplex Dna
Following Addition Of A Dttp, A Datp, And A Dctp
Residue.
pdb|1NJW|A Chain A, Guanine-Thymine Mismatch At The Polymerase Active Site
pdb|1NJX|A Chain A, Thymine-Guanine Mismatch At The Polymerase Active Site
pdb|1NJY|A Chain A, Thymine-Thymine Mismatch At The Polymerase Active Site
pdb|1NJZ|A Chain A, Cytosine-thymine Mismatch At The Polymerase Active Site
pdb|1NK0|A Chain A, Adenine-Guanine Mismatch At The Polymerase Active Site
pdb|1NK4|A Chain A, Guanine-Guanine Mismatch At The Polymerase Active Site
pdb|1NK5|A Chain A, Adenine-Adenine Mismatch At The Polymerase Active Site
pdb|1NK6|A Chain A, Cytosine-Cytosine Mismatch At The Polymerase Active Site
pdb|1NK7|A Chain A, Guanine-Adenine Mismatch At The Polymerase Active Site
pdb|1NK8|A Chain A, A Bacillus Dna Polymerase I Product Complex Bound To A
Guanine-Thymine Mismatch After A Single Round Of Primer
Extension, Following Incorporation Of Dctp.
pdb|1NK9|A Chain A, A Bacillus Dna Polymerase I Product Complex Bound To A
Guanine-Thymine Mismatch After Two Rounds Of Primer
Extension, Following Incorporation Of Dctp And Dgtp.
pdb|1NKB|A Chain A, A Bacillus Dna Polymerase I Product Complex Bound To A
Guanine-Thymine Mismatch After Three Rounds Of Primer
Extension, Following Incorporation Of Dctp, Dgtp, And
Dttp.
pdb|1NKC|A Chain A, A Bacillus Dna Polymerase I Product Complex Bound To A
Guanine-Thymine Mismatch After Five Rounds Of Primer
Extension, Following Incorporation Of Dctp, Dgtp, Dttp,
And Datp.
pdb|1NKE|A Chain A, A Bacillus Dna Polymerase I Product Complex Bound To A
Cytosine-Thymine Mismatch After A Single Round Of Primer
Extension, Following Incorporation Of Dctp.
pdb|1XC9|A Chain A, Structure Of A High-Fidelity Polymerase Bound To A
Benzo[a]pyrene Adduct That Blocks Replication
pdb|1XWL|A Chain A, Bacillus Stearothermophilus (Newly Identified Strain As
Yet Unnamed) Dna Polymerase Fragment
Length = 580
Score = 33.9 bits (76), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 41/82 (50%), Gaps = 4/82 (4%)
Query: 86 LLKMVRTNYETVDEMLERLEPFDQLWSIILEFRESSDL---WMEGPFKGLNADEIKDKTD 142
+LK +T Y T ++LE+L P+ ++ IL +R+ L ++EG K + D K T
Sbjct: 250 VLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPDTKKVHTI 309
Query: 143 FMFRELNQLARKMTRAPGCKMV 164
F + L Q R + P + +
Sbjct: 310 FN-QALTQTGRLSSTEPNLQNI 330
>pdb|3BDP|A Chain A, Dna Polymerase IDNA COMPLEX
pdb|4BDP|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Fragment
Complexed To 11 Base Pairs Of Duplex Dna After Addition
Of Two Datp Residues
pdb|2BDP|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Fragment
Complexed To 9 Base Pairs Of Duplex Dna
Length = 580
Score = 33.9 bits (76), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 41/82 (50%), Gaps = 4/82 (4%)
Query: 86 LLKMVRTNYETVDEMLERLEPFDQLWSIILEFRESSDL---WMEGPFKGLNADEIKDKTD 142
+LK +T Y T ++LE+L P+ ++ IL +R+ L ++EG K + D K T
Sbjct: 250 VLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPDTKKVHTI 309
Query: 143 FMFRELNQLARKMTRAPGCKMV 164
F + L Q R + P + +
Sbjct: 310 FN-QALTQTGRLSSTEPNLQNI 330
>pdb|2Y1I|A Chain A, Crystal Structure Of A S-Diastereomer Analogue Of The
Spore Photoproduct In Complex With Fragment Dna
Polymerase I From Bacillus Stearothermophilus
pdb|2Y1J|A Chain A, Crystal Structure Of A R-Diastereomer Analogue Of The
Spore Photoproduct In Complex With Fragment Dna
Polymerase I From Bacillus Stearothermophilus
Length = 580
Score = 33.9 bits (76), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 41/82 (50%), Gaps = 4/82 (4%)
Query: 86 LLKMVRTNYETVDEMLERLEPFDQLWSIILEFRESSDL---WMEGPFKGLNADEIKDKTD 142
+LK +T Y T ++LE+L P+ ++ IL +R+ L ++EG K + D K T
Sbjct: 250 VLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPDTKKVHTI 309
Query: 143 FMFRELNQLARKMTRAPGCKMV 164
F + L Q R + P + +
Sbjct: 310 FN-QALTQTGRLSSTEPNLQNI 330
>pdb|3TAN|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Duplex Dna With Cytosine-Adenine
Mismatch At (N-1) Position
pdb|3TAP|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Duplex Dna With Cytosine-Adenine
Mismatch At (N-3) Position
pdb|3TAQ|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Duplex Dna With Cytosine-Adenine
Mismatch At (N-4) Position
pdb|3TAR|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Duplex Dna With Cytosine-Adenine
Mismatch At (N-6) Position
pdb|4DQS|A Chain A, Binary Complex Of Bacillus Dna Polymerase I Large Fragment
And Duplex Dna With Rc In Primer Terminus Paired With Dg
Of Template
Length = 592
Score = 33.9 bits (76), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 41/82 (50%), Gaps = 4/82 (4%)
Query: 86 LLKMVRTNYETVDEMLERLEPFDQLWSIILEFRESSDL---WMEGPFKGLNADEIKDKTD 142
+LK +T Y T ++LE+L P+ ++ IL +R+ L ++EG K + D K T
Sbjct: 262 VLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPDTKKVHTI 321
Query: 143 FMFRELNQLARKMTRAPGCKMV 164
F + L Q R + P + +
Sbjct: 322 FN-QALTQTGRLSSTEPNLQNI 342
>pdb|3C41|J Chain J, Abc Protein Artp In Complex With Amp-PnpMG2+
pdb|3C41|K Chain K, Abc Protein Artp In Complex With Amp-PnpMG2+
Length = 242
Score = 33.5 bits (75), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 34/52 (65%), Gaps = 2/52 (3%)
Query: 722 INLYLQNDVPMMFVGPTGTGKSTIV--LNLLLNLSKDKYLPNIINFSARTSS 771
IN++++ ++ +GP+G+GKST + LNLL + + + + + IN A+ ++
Sbjct: 22 INVHIREGEVVVVIGPSGSGKSTFLRCLNLLEDFDEGEIIIDGINLKAKDTN 73
>pdb|2OLJ|A Chain A, Abc Protein Artp In Complex With AdpMG2+
pdb|2OLJ|B Chain B, Abc Protein Artp In Complex With AdpMG2+
pdb|2OLK|A Chain A, Abc Protein Artp In Complex With Adp-Beta-S
pdb|2OLK|B Chain B, Abc Protein Artp In Complex With Adp-Beta-S
pdb|2OLK|C Chain C, Abc Protein Artp In Complex With Adp-Beta-S
pdb|2OLK|D Chain D, Abc Protein Artp In Complex With Adp-Beta-S
pdb|2OUK|A Chain A, Abc Protein Artp In Complex With Sulphate
pdb|2OUK|B Chain B, Abc Protein Artp In Complex With Sulphate
pdb|2OUK|C Chain C, Abc Protein Artp In Complex With Sulphate
pdb|2OUK|D Chain D, Abc Protein Artp In Complex With Sulphate
pdb|2Q0H|A Chain A, Abc Protein Artp In Complex With AdpMG2+, ATP-Gamma-S
Hydrolyzed
pdb|2Q0H|B Chain B, Abc Protein Artp In Complex With AdpMG2+, ATP-Gamma-S
Hydrolyzed
pdb|3C4J|A Chain A, Abc Protein Artp In Complex With Atp-Gamma-S
pdb|3C4J|B Chain B, Abc Protein Artp In Complex With Atp-Gamma-S
Length = 263
Score = 33.5 bits (75), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 34/52 (65%), Gaps = 2/52 (3%)
Query: 722 INLYLQNDVPMMFVGPTGTGKSTIV--LNLLLNLSKDKYLPNIINFSARTSS 771
IN++++ ++ +GP+G+GKST + LNLL + + + + + IN A+ ++
Sbjct: 43 INVHIREGEVVVVIGPSGSGKSTFLRCLNLLEDFDEGEIIIDGINLKAKDTN 94
>pdb|2XY7|A Chain A, Crystal Structure Of A Salicylic Aldehyde Base In The
Pre-Insertion Site Of Fragment Dna Polymerase I From
Bacillus Stearothermophilus
Length = 580
Score = 33.1 bits (74), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 41/82 (50%), Gaps = 4/82 (4%)
Query: 86 LLKMVRTNYETVDEMLERLEPFDQLWSIILEFRESSDL---WMEGPFKGLNADEIKDKTD 142
+LK +T Y T ++LE+L P+ ++ IL +R+ L ++EG K + D K T
Sbjct: 250 VLKKSKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPDTKKVHTI 309
Query: 143 FMFRELNQLARKMTRAPGCKMV 164
F + L Q R + P + +
Sbjct: 310 FN-QALTQTGRLSSTEPNLQNI 330
>pdb|2XY5|A Chain A, Crystal Structure Of An Artificial Salen-Copper Basepair
In Complex With Fragment Dna Polymerase I From Bacillus
Stearothermophilus
Length = 581
Score = 33.1 bits (74), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 41/82 (50%), Gaps = 4/82 (4%)
Query: 86 LLKMVRTNYETVDEMLERLEPFDQLWSIILEFRESSDL---WMEGPFKGLNADEIKDKTD 142
+LK +T Y T ++LE+L P+ ++ IL +R+ L ++EG K + D K T
Sbjct: 251 VLKKSKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPDTKKVHTI 310
Query: 143 FMFRELNQLARKMTRAPGCKMV 164
F + L Q R + P + +
Sbjct: 311 FN-QALTQTGRLSSTEPNLQNI 331
>pdb|2XO7|A Chain A, Crystal Structure Of A Da:o-Allylhydroxylamine-Dc Basepair
In Complex With Fragment Dna Polymerase I From Bacillus
Stearothermophilus
Length = 580
Score = 33.1 bits (74), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 41/82 (50%), Gaps = 4/82 (4%)
Query: 86 LLKMVRTNYETVDEMLERLEPFDQLWSIILEFRESSDL---WMEGPFKGLNADEIKDKTD 142
+LK +T Y T ++LE+L P+ ++ IL +R+ L ++EG K + D K T
Sbjct: 250 VLKKSKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPDTKKVHTI 309
Query: 143 FMFRELNQLARKMTRAPGCKMV 164
F + L Q R + P + +
Sbjct: 310 FN-QALTQTGRLSSTEPNLQNI 330
>pdb|2XY6|A Chain A, Crystal Structure Of A Salicylic Aldehyde Basepair In
Complex With Fragment Dna Polymerase I From Bacillus
Stearothermophilus
Length = 581
Score = 33.1 bits (74), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 41/82 (50%), Gaps = 4/82 (4%)
Query: 86 LLKMVRTNYETVDEMLERLEPFDQLWSIILEFRESSDL---WMEGPFKGLNADEIKDKTD 142
+LK +T Y T ++LE+L P+ ++ IL +R+ L ++EG K + D K T
Sbjct: 251 VLKKSKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPDTKKVHTI 310
Query: 143 FMFRELNQLARKMTRAPGCKMV 164
F + L Q R + P + +
Sbjct: 311 FN-QALTQTGRLSSTEPNLQNI 331
>pdb|3JVV|A Chain A, Crystal Structure Of P. Aeruginosa Pilt With Bound Amp-Pcp
pdb|3JVV|B Chain B, Crystal Structure Of P. Aeruginosa Pilt With Bound Amp-Pcp
pdb|3JVV|C Chain C, Crystal Structure Of P. Aeruginosa Pilt With Bound Amp-Pcp
pdb|3JVU|A Chain A, Crystal Structure Of Unliganded P. Aeruginosa Pilt
pdb|3JVU|B Chain B, Crystal Structure Of Unliganded P. Aeruginosa Pilt
pdb|3JVU|C Chain C, Crystal Structure Of Unliganded P. Aeruginosa Pilt
Length = 356
Score = 33.1 bits (74), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 30/54 (55%), Gaps = 5/54 (9%)
Query: 710 IPTNVTCMQNFFINLYLQ--NDVP---MMFVGPTGTGKSTIVLNLLLNLSKDKY 758
IP+ V M+ + + +DVP ++ GPTG+GKST + +L L+ KY
Sbjct: 99 IPSKVLTMEELGMGEVFKRVSDVPRGLVLVTGPTGSGKSTTLAAMLDYLNNTKY 152
>pdb|3KX2|B Chain B, Crystal Structure Of Prp43p In Complex With Adp
pdb|3KX2|A Chain A, Crystal Structure Of Prp43p In Complex With Adp
Length = 767
Score = 32.7 bits (73), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 25/38 (65%), Gaps = 1/38 (2%)
Query: 714 VTCMQNFFINLYLQNDVPMMFVGPTGTGKSTIVLNLLL 751
V ++ F+ LY QN+ M+FVG TG+GK+T + +L
Sbjct: 95 VHAQRDEFLKLY-QNNQIMVFVGETGSGKTTQIPQFVL 131
>pdb|2XAU|A Chain A, Crystal Structure Of The Prp43p Deah-Box Rna Helicase In
Complex With Adp
pdb|2XAU|B Chain B, Crystal Structure Of The Prp43p Deah-Box Rna Helicase In
Complex With Adp
Length = 773
Score = 32.7 bits (73), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 25/38 (65%), Gaps = 1/38 (2%)
Query: 714 VTCMQNFFINLYLQNDVPMMFVGPTGTGKSTIVLNLLL 751
V ++ F+ LY QN+ M+FVG TG+GK+T + +L
Sbjct: 95 VHAQRDEFLKLY-QNNQIMVFVGETGSGKTTQIPQFVL 131
>pdb|4F4J|A Chain A, Conversion Of The Enzyme Guanylate Kinase Into A Mitotic
Spindle Orienting Protein By A Single Mutation That
Inhibits Gmp- Induced Closing
pdb|4F4J|B Chain B, Conversion Of The Enzyme Guanylate Kinase Into A Mitotic
Spindle Orienting Protein By A Single Mutation That
Inhibits Gmp- Induced Closing
Length = 202
Score = 32.0 bits (71), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 14/30 (46%), Positives = 20/30 (66%), Gaps = 2/30 (6%)
Query: 723 NLYLQNDV--PMMFVGPTGTGKSTIVLNLL 750
NLY Q + P++ GP+GTGKST++ L
Sbjct: 9 NLYFQGSMSRPIVISGPSGTGKSTLLKKLF 38
>pdb|4A5Q|A Chain A, Crystal Structure Of The Chitinase Chi1 Fitted Into The 3d
Structure Of The Yersinia Entomophaga Toxin Complex
pdb|4A5Q|B Chain B, Crystal Structure Of The Chitinase Chi1 Fitted Into The 3d
Structure Of The Yersinia Entomophaga Toxin Complex
pdb|4A5Q|C Chain C, Crystal Structure Of The Chitinase Chi1 Fitted Into The 3d
Structure Of The Yersinia Entomophaga Toxin Complex
pdb|4A5Q|D Chain D, Crystal Structure Of The Chitinase Chi1 Fitted Into The 3d
Structure Of The Yersinia Entomophaga Toxin Complex
pdb|4A5Q|E Chain E, Crystal Structure Of The Chitinase Chi1 Fitted Into The 3d
Structure Of The Yersinia Entomophaga Toxin Complex
Length = 546
Score = 31.6 bits (70), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 28/55 (50%), Gaps = 8/55 (14%)
Query: 967 TLSKIFTSVLDW--------HFSKGFADSIVKLSKNIVAATFHVYSESTKVFLPI 1013
TL SVL+W F KG + KL + VA ++YSE+TKVF+ +
Sbjct: 412 TLGSFEYSVLEWTDIICHYMDFEKGEGRNGYKLVHDKVAKADYLYSEATKVFISL 466
>pdb|3OA5|A Chain A, The Structure Of Chi1, A Chitinase From Yersinia Entomophaga
pdb|3OA5|B Chain B, The Structure Of Chi1, A Chitinase From Yersinia Entomophaga
Length = 574
Score = 31.6 bits (70), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 28/55 (50%), Gaps = 8/55 (14%)
Query: 967 TLSKIFTSVLDW--------HFSKGFADSIVKLSKNIVAATFHVYSESTKVFLPI 1013
TL SVL+W F KG + KL + VA ++YSE+TKVF+ +
Sbjct: 440 TLGSFEYSVLEWTDIICHYMDFEKGEGRNGYKLVHDKVAKADYLYSEATKVFISL 494
>pdb|2HHW|A Chain A, Ddttp:o6-Methyl-Guanine Pair In The Polymerase Active
Site, In The Closed Conformation
pdb|2HHW|D Chain D, Ddttp:o6-Methyl-Guanine Pair In The Polymerase Active
Site, In The Closed Conformation
Length = 580
Score = 31.2 bits (69), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 40/82 (48%), Gaps = 4/82 (4%)
Query: 86 LLKMVRTNYETVDEMLERLEPFDQLWSIILEFRESSDL---WMEGPFKGLNADEIKDKTD 142
+LK +T Y T ++LE+L P+ ++ IL +R+ L ++EG K + K T
Sbjct: 250 VLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPATKKVHTI 309
Query: 143 FMFRELNQLARKMTRAPGCKMV 164
F + L Q R + P + +
Sbjct: 310 FN-QALTQTGRLSSTEPNLQNI 330
>pdb|2HVH|A Chain A, Ddctp:o6meg Pair In The Polymerase Active Site (0
Position)
pdb|2HVH|D Chain D, Ddctp:o6meg Pair In The Polymerase Active Site (0
Position)
pdb|2HVI|A Chain A, Ddctp:g Pair In The Polymerase Active Site (0 Position)
pdb|2HVI|D Chain D, Ddctp:g Pair In The Polymerase Active Site (0 Position)
pdb|3EZ5|A Chain A, Cocrystal Structure Of Bacillus Fragment Dna Polymerase I
With Duplex Dna , Dctp, And Zinc (Closed Form).
pdb|3EZ5|D Chain D, Cocrystal Structure Of Bacillus Fragment Dna Polymerase I
With Duplex Dna , Dctp, And Zinc (Closed Form)
Length = 580
Score = 31.2 bits (69), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 40/82 (48%), Gaps = 4/82 (4%)
Query: 86 LLKMVRTNYETVDEMLERLEPFDQLWSIILEFRESSDL---WMEGPFKGLNADEIKDKTD 142
+LK +T Y T ++LE+L P+ ++ IL +R+ L ++EG K + K T
Sbjct: 250 VLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPATKKVHTI 309
Query: 143 FMFRELNQLARKMTRAPGCKMV 164
F + L Q R + P + +
Sbjct: 310 FN-QALTQTGRLSSTEPNLQNI 330
>pdb|3HP6|A Chain A, Crystal Structure Of Fragment Dna Polymerase I From
Bacillus Stearothermophilus F710y Mutant Bound To G:t
Mismatch
pdb|3HP6|D Chain D, Crystal Structure Of Fragment Dna Polymerase I From
Bacillus Stearothermophilus F710y Mutant Bound To G:t
Mismatch
Length = 580
Score = 30.8 bits (68), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 40/82 (48%), Gaps = 4/82 (4%)
Query: 86 LLKMVRTNYETVDEMLERLEPFDQLWSIILEFRESSDL---WMEGPFKGLNADEIKDKTD 142
+LK +T Y T ++LE+L P+ ++ IL +R+ L ++EG K + K T
Sbjct: 250 VLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPATKKVHTI 309
Query: 143 FMFRELNQLARKMTRAPGCKMV 164
F + L Q R + P + +
Sbjct: 310 FN-QALTQTGRLSSTEPNLQNI 330
>pdb|3HT3|A Chain A, Crystal Structure Of Fragment Dna Polymerase I From
Bacillus Stearothermophilus V713p Mutant Bound To G:dctp
pdb|3HT3|D Chain D, Crystal Structure Of Fragment Dna Polymerase I From
Bacillus Stearothermophilus V713p Mutant Bound To G:dctp
Length = 579
Score = 30.8 bits (68), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 40/82 (48%), Gaps = 4/82 (4%)
Query: 86 LLKMVRTNYETVDEMLERLEPFDQLWSIILEFRESSDL---WMEGPFKGLNADEIKDKTD 142
+LK +T Y T ++LE+L P+ ++ IL +R+ L ++EG K + K T
Sbjct: 249 VLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPATKKVHTI 308
Query: 143 FMFRELNQLARKMTRAPGCKMV 164
F + L Q R + P + +
Sbjct: 309 FN-QALTQTGRLSSTEPNLQNI 329
>pdb|4DQQ|A Chain A, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment E658a, Dna Duplex, And Rctp (Paired With Dg Of
Template) In Presence Of Mg2+
pdb|4DQQ|D Chain D, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment E658a, Dna Duplex, And Rctp (Paired With Dg Of
Template) In Presence Of Mg2+
pdb|4DQR|A Chain A, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment E658a, Dna Duplex, And Rctp (Paired With Dg Of
Template) In Presence Of Mn2+
pdb|4DQR|D Chain D, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment E658a, Dna Duplex, And Rctp (Paired With Dg Of
Template) In Presence Of Mn2+
pdb|4E0D|A Chain A, Binary Complex Of Bacillus Dna Polymerase I Large Fragment
E658a And Duplex Dna
Length = 592
Score = 30.8 bits (68), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 40/82 (48%), Gaps = 4/82 (4%)
Query: 86 LLKMVRTNYETVDEMLERLEPFDQLWSIILEFRESSDL---WMEGPFKGLNADEIKDKTD 142
+LK +T Y T ++LE+L P+ ++ IL +R+ L ++EG K + K T
Sbjct: 262 VLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPATKKVHTI 321
Query: 143 FMFRELNQLARKMTRAPGCKMV 164
F + L Q R + P + +
Sbjct: 322 FN-QALTQTGRLSSTEPNLQNI 342
>pdb|3PV8|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddttp-Da In Closed
Conformation
pdb|3PV8|D Chain D, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddttp-Da In Closed
Conformation
pdb|3PX0|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Dctp-Da Mismatch (Tautomer) In
Closed Conformation
pdb|3PX0|D Chain D, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Dctp-Da Mismatch (Tautomer) In
Closed Conformation
pdb|3PX4|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddctp-Da Mismatch (Wobble) In
Ajar Conformation
pdb|3PX4|D Chain D, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddctp-Da Mismatch (Wobble) In
Ajar Conformation
pdb|3PX6|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddctp-Da Mismatch (Tautomer)
In Closed Conformation
pdb|3PX6|D Chain D, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddctp-Da Mismatch (Tautomer)
In Closed Conformation
pdb|3THV|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddatp-Dt In Closed
Conformation
pdb|3THV|D Chain D, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddatp-Dt In Closed
Conformation
pdb|3TI0|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddgtp-Dc In Closed
Conformation
pdb|3TI0|D Chain D, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddgtp-Dc In Closed
Conformation
pdb|4DSE|A Chain A, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment F710y, Dna Duplex, And Rctp (Paired With Dg Of
Template) In Presence Of Mg2+
pdb|4DSE|D Chain D, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment F710y, Dna Duplex, And Rctp (Paired With Dg Of
Template) In Presence Of Mg2+
pdb|4DSF|A Chain A, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment F710y, Dna Duplex, And Rctp (Paired With Dg Of
Template) In Presence Of Mn2+
pdb|4DSF|D Chain D, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment F710y, Dna Duplex, And Rctp (Paired With Dg Of
Template) In Presence Of Mn2+
Length = 592
Score = 30.8 bits (68), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 40/82 (48%), Gaps = 4/82 (4%)
Query: 86 LLKMVRTNYETVDEMLERLEPFDQLWSIILEFRESSDL---WMEGPFKGLNADEIKDKTD 142
+LK +T Y T ++LE+L P+ ++ IL +R+ L ++EG K + K T
Sbjct: 262 VLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPATKKVHTI 321
Query: 143 FMFRELNQLARKMTRAPGCKMV 164
F + L Q R + P + +
Sbjct: 322 FN-QALTQTGRLSSTEPNLQNI 342
>pdb|4DQI|A Chain A, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment, Dna Duplex, And Dctp (Paired With Dg Of
Template)
pdb|4DQI|D Chain D, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment, Dna Duplex, And Dctp (Paired With Dg Of
Template)
pdb|4DQP|A Chain A, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment, Dna Duplex, And Ddctp (Paired With Dg Of
Template)
pdb|4DQP|D Chain D, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment, Dna Duplex, And Ddctp (Paired With Dg Of
Template)
pdb|4DS4|A Chain A, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment, Dna Duplex, And Rctp In Presence Of Mn2+
pdb|4DS4|D Chain D, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment, Dna Duplex, And Rctp In Presence Of Mn2+
pdb|4DS5|A Chain A, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment, Dna Duplex, And Rctp In Presence Of Mg2+
pdb|4DS5|D Chain D, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment, Dna Duplex, And Rctp In Presence Of Mg2+
Length = 592
Score = 30.8 bits (68), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 40/82 (48%), Gaps = 4/82 (4%)
Query: 86 LLKMVRTNYETVDEMLERLEPFDQLWSIILEFRESSDL---WMEGPFKGLNADEIKDKTD 142
+LK +T Y T ++LE+L P+ ++ IL +R+ L ++EG K + K T
Sbjct: 262 VLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPATKKVHTI 321
Query: 143 FMFRELNQLARKMTRAPGCKMV 164
F + L Q R + P + +
Sbjct: 322 FN-QALTQTGRLSSTEPNLQNI 342
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.320 0.136 0.395
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 42,462,485
Number of Sequences: 62578
Number of extensions: 1731148
Number of successful extensions: 5195
Number of sequences better than 100.0: 46
Number of HSP's better than 100.0 without gapping: 21
Number of HSP's successfully gapped in prelim test: 25
Number of HSP's that attempted gapping in prelim test: 5101
Number of HSP's gapped (non-prelim): 75
length of query: 1513
length of database: 14,973,337
effective HSP length: 111
effective length of query: 1402
effective length of database: 8,027,179
effective search space: 11254104958
effective search space used: 11254104958
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 58 (26.9 bits)