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= psy12150
(456 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1SXJ|D Chain D, Crystal Structure Of The Eukaryotic Clamp Loader
(Replication Factor C, Rfc) Bound To The Dna Sliding
Clamp (Proliferating Cell Nuclear Antigen, Pcna)
Length = 353
Score = 292 bits (747), Expect = 3e-79, Method: Compositional matrix adjust.
Identities = 147/281 (52%), Positives = 194/281 (69%), Gaps = 11/281 (3%)
Query: 34 PWVEKYRPKTIDDVIEQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQLFG- 92
PWVEKYRPK +D+V Q V+VLKK L A+LPH LFYGPPGTGKTST++A +L+G
Sbjct: 26 PWVEKYRPKNLDEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGP 85
Query: 93 DMYRERILELNASDDRGIQVIRDKVKTFAQQTASG---FNQDGKPCPPFKIVILDEADSM 149
D+ + RILELNASD+RGI ++R+KVK FA+ T S + + PCPP+KI+ILDEADSM
Sbjct: 86 DLMKSRILELNASDERGISIVREKVKNFARLTVSKPSKHDLENYPCPPYKIIILDEADSM 145
Query: 150 THAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLAENTMLTRLQYIC 209
T AQ+ALRRTME + TRFCLICNYV+ II PL S+CSKFRFK L + + RL++I
Sbjct: 146 TADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKFRFKALDASNAIDRLRFIS 205
Query: 210 EQESVMCDFKALETLVETSGGDMRRAITCLQSCAR----LKGGEGIVNEDVLEVTGVIPK 265
EQE+V CD LE +++ S GD+RR IT LQS ++ L G+ I + V E+ GV+P
Sbjct: 206 EQENVKCDDGVLERILDISAGDLRRGITLLQSASKGAQYLGDGKNITSTQVEELAGVVPH 265
Query: 266 P-WIEKLLKVDS--FQVLEKYIEDLILEAYSATQLFDQFHD 303
IE + KV S F ++KY+ + +SA + +Q H+
Sbjct: 266 DILIEIVEKVKSGDFDEIKKYVNTFMKSGWSAASVVNQLHE 306
Score = 70.5 bits (171), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 43/130 (33%), Positives = 73/130 (56%), Gaps = 7/130 (5%)
Query: 322 LETLVETSGGDMRRAITCLQSCAR----LKGGEGIVNEDVLEVTGVIPNP-WIEKLLKVD 376
LE +++ S GD+RR IT LQS ++ L G+ I + V E+ GV+P+ IE + KV
Sbjct: 217 LERILDISAGDLRRGITLLQSASKGAQYLGDGKNITSTQVEELAGVVPHDILIEIVEKVK 276
Query: 377 S--FQVLEKYIEDLILEAYSATQLFDQFHDIVMSASSLSDKQKALILEKLAECNARLQDG 434
S F ++KY+ + +SA + +Q H+ ++ + K I L ++RL +G
Sbjct: 277 SGDFDEIKKYVNTFMKSGWSAASVVNQLHEYYITNDNFDTNFKNQISWLLFTTDSRLNNG 336
Query: 435 ASEYIQILDL 444
+E+IQ+L+L
Sbjct: 337 TNEHIQLLNL 346
>pdb|2CHQ|A Chain A, Replication Factor C Adpnp Complex
pdb|2CHQ|B Chain B, Replication Factor C Adpnp Complex
pdb|2CHQ|C Chain C, Replication Factor C Adpnp Complex
pdb|2CHV|A Chain A, Replication Factor C Adpnp Complex
pdb|2CHV|B Chain B, Replication Factor C Adpnp Complex
pdb|2CHV|C Chain C, Replication Factor C Adpnp Complex
pdb|2CHV|D Chain D, Replication Factor C Adpnp Complex
pdb|2CHV|E Chain E, Replication Factor C Adpnp Complex
pdb|2CHV|F Chain F, Replication Factor C Adpnp Complex
Length = 319
Score = 231 bits (590), Expect = 5e-61, Method: Compositional matrix adjust.
Identities = 114/227 (50%), Positives = 150/227 (66%), Gaps = 9/227 (3%)
Query: 35 WVEKYRPKTIDDVIEQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQLFGDM 94
WVEKYRP+T+D+V+ Q EV+ LK + ++PH LF GPPGTGKT+T IA LFG+
Sbjct: 7 WVEKYRPRTLDEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGEN 66
Query: 95 YRERILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPPFKIVILDEADSMTHAAQ 154
+R+ +E+NASD+RGI V+R K+K FA+ G PFKI+ LDEAD++T AQ
Sbjct: 67 WRDNFIEMNASDERGIDVVRHKIKEFARTAPIG-------GAPFKIIFLDEADALTADAQ 119
Query: 155 AALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLAENTMLTRLQYICEQESV 214
AALRRTME +KS RF L CNYVS II+P+ SRC+ FRFKP+ + M RL ICE+E V
Sbjct: 120 AALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMKKRLLEICEKEGV 179
Query: 215 MCDFKALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVTG 261
LE L+ SGGD R+AI LQ A + GE + + + ++T
Sbjct: 180 KITEDGLEALIYISGGDFRKAINALQGAAAI--GEVVDADTIYQITA 224
Score = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 36/126 (28%), Positives = 66/126 (52%), Gaps = 9/126 (7%)
Query: 321 ALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVTGVIPNPWIEKLLKV---DS 377
LE L+ SGGD R+AI LQ A + GE + + + ++T + +L++ +
Sbjct: 185 GLEALIYISGGDFRKAINALQGAAAI--GEVVDADTIYQITATARPEEMTELIQTALKGN 242
Query: 378 FQVLEKYIEDLILE-AYSATQLFDQ-FHDIVMSASSLSDKQKALILEKLAECNARLQDGA 435
F + ++ L++E S + Q F +I+ + + D K +++KL E + RL +GA
Sbjct: 243 FMEARELLDRLMVEYGMSGEDIVAQLFREII--SMPIKDSLKVQLIDKLGEVDFRLTEGA 300
Query: 436 SEYIQI 441
+E IQ+
Sbjct: 301 NERIQL 306
>pdb|2CHG|A Chain A, Replication Factor C Domains 1 And 2
pdb|2CHG|B Chain B, Replication Factor C Domains 1 And 2
pdb|2CHG|C Chain C, Replication Factor C Domains 1 And 2
pdb|2CHG|D Chain D, Replication Factor C Domains 1 And 2
Length = 226
Score = 230 bits (586), Expect = 2e-60, Method: Compositional matrix adjust.
Identities = 114/227 (50%), Positives = 150/227 (66%), Gaps = 9/227 (3%)
Query: 35 WVEKYRPKTIDDVIEQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQLFGDM 94
WVEKYRP+T+D+V+ Q EV+ LK + ++PH LF GPPGTGKT+T IA LFG+
Sbjct: 7 WVEKYRPRTLDEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGEN 66
Query: 95 YRERILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPPFKIVILDEADSMTHAAQ 154
+R+ +E+NASD+RGI V+R K+K FA+ G PFKI+ LDEAD++T AQ
Sbjct: 67 WRDNFIEMNASDERGIDVVRHKIKEFARTAPIG-------GAPFKIIFLDEADALTADAQ 119
Query: 155 AALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLAENTMLTRLQYICEQESV 214
AALRRTME +KS RF L CNYVS II+P+ SRC+ FRFKP+ + M RL ICE+E V
Sbjct: 120 AALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMKKRLLEICEKEGV 179
Query: 215 MCDFKALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVTG 261
LE L+ SGGD R+AI LQ A + GE + + + ++T
Sbjct: 180 KITEDGLEALIYISGGDFRKAINALQGAAAI--GEVVDADTIYQITA 224
Score = 32.0 bits (71), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 24/42 (57%), Gaps = 2/42 (4%)
Query: 321 ALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVTG 362
LE L+ SGGD R+AI LQ A + GE + + + ++T
Sbjct: 185 GLEALIYISGGDFRKAINALQGAAAI--GEVVDADTIYQITA 224
>pdb|1IQP|A Chain A, Crystal Structure Of The Clamp Loader Small Subunit From
Pyrococcus Furiosus
pdb|1IQP|B Chain B, Crystal Structure Of The Clamp Loader Small Subunit From
Pyrococcus Furiosus
pdb|1IQP|C Chain C, Crystal Structure Of The Clamp Loader Small Subunit From
Pyrococcus Furiosus
pdb|1IQP|D Chain D, Crystal Structure Of The Clamp Loader Small Subunit From
Pyrococcus Furiosus
pdb|1IQP|E Chain E, Crystal Structure Of The Clamp Loader Small Subunit From
Pyrococcus Furiosus
pdb|1IQP|F Chain F, Crystal Structure Of The Clamp Loader Small Subunit From
Pyrococcus Furiosus
Length = 327
Score = 223 bits (567), Expect = 2e-58, Method: Compositional matrix adjust.
Identities = 117/273 (42%), Positives = 162/273 (59%), Gaps = 13/273 (4%)
Query: 34 PWVEKYRPKTIDDVIEQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQLFGD 93
PWVEKYRP+ +DD++ Q+ +V LK + +PH LF GPPG GKT+ +A +LFG+
Sbjct: 14 PWVEKYRPQRLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELFGE 73
Query: 94 MYRERILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPPFKIVILDEADSMTHAA 153
+R LELNASD+RGI VIR+KVK FA+ G FKI+ LDEAD++T A
Sbjct: 74 NWRHNFLELNASDERGINVIREKVKEFARTKPIG-------GASFKIIFLDEADALTQDA 126
Query: 154 QAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLAENTMLTRLQYICEQES 213
Q ALRRTME + + RF L CNY S II+P+ SRC+ FRF+PL + + RL+YI E E
Sbjct: 127 QQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEG 186
Query: 214 VMCDFKALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVTGVIPKPWIEKL-- 271
+ + L+ ++ + GDMRRAI LQ+ A L + I +E+V V I ++
Sbjct: 187 LELTEEGLQAILYIAEGDMRRAINILQAAAAL--DKKITDENVFMVASRARPEDIREMML 244
Query: 272 --LKVDSFQVLEKYIEDLILEAYSATQLFDQFH 302
LK + + EK E L+ + S + Q H
Sbjct: 245 LALKGNFLKAREKLREILLKQGLSGEDVLVQMH 277
Score = 50.1 bits (118), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 39/126 (30%), Positives = 65/126 (51%), Gaps = 7/126 (5%)
Query: 320 KALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVTGVIPNPWIEKL----LKV 375
+ L+ ++ + GDMRRAI LQ+ A L + I +E+V V I ++ LK
Sbjct: 192 EGLQAILYIAEGDMRRAINILQAAAALD--KKITDENVFMVASRARPEDIREMMLLALKG 249
Query: 376 DSFQVLEKYIEDLILEAYSATQLFDQFHDIVMSASSLSDKQKALILEKLAECNARLQDGA 435
+ + EK E L+ + S + Q H V + + + +K L+ +K+ E N RL +GA
Sbjct: 250 NFLKAREKLREILLKQGLSGEDVLVQMHKEVFNLP-IEEPKKVLLADKIGEYNFRLVEGA 308
Query: 436 SEYIQI 441
+E IQ+
Sbjct: 309 NEIIQL 314
>pdb|1SXJ|C Chain C, Crystal Structure Of The Eukaryotic Clamp Loader
(Replication Factor C, Rfc) Bound To The Dna Sliding
Clamp (Proliferating Cell Nuclear Antigen, Pcna)
Length = 340
Score = 219 bits (558), Expect = 3e-57, Method: Compositional matrix adjust.
Identities = 108/236 (45%), Positives = 156/236 (66%), Gaps = 9/236 (3%)
Query: 33 VPWVEKYRPKTIDDVIEQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQLFG 92
+PWVEKYRP+T+D+V Q EV++ ++K + LPH LFYGPPGTGKTST++A +++G
Sbjct: 13 LPWVEKYRPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIYG 72
Query: 93 DMYRERILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPPFKIVILDEADSMTHA 152
Y +LELNASDDRGI V+R+++K FA T F++ FK++ILDEAD+MT+A
Sbjct: 73 KNYSNMVLELNASDDRGIDVVRNQIKDFA-STRQIFSKG------FKLIILDEADAMTNA 125
Query: 153 AQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLAENTMLTRLQYICEQE 212
AQ ALRR +E+ TK+TRFC++ NY + L S+C++FRF+PL + + R+ + E
Sbjct: 126 AQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQPLPQEAIERRIANVLVHE 185
Query: 213 SVMCDFKALETLVETSGGDMRRAITCLQSC-ARLKG-GEGIVNEDVLEVTGVIPKP 266
+ A + L+E S GDMRR + LQSC A L E +++DV+ P+P
Sbjct: 186 KLKLSPNAEKALIELSNGDMRRVLNVLQSCKATLDNPDEDEISDDVIYECCGAPRP 241
Score = 32.7 bits (73), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 45/159 (28%), Positives = 67/159 (42%), Gaps = 25/159 (15%)
Query: 311 LSDKQKALFKALETLVETSGGDMRRAITCLQSC-ARLKG-GEGIVNEDVLEVTGVIPNPW 368
+ +K K A + L+E S GDMRR + LQSC A L E +++DV+ P P
Sbjct: 183 VHEKLKLSPNAEKALIELSNGDMRRVLNVLQSCKATLDNPDEDEISDDVIYECCGAPRP- 241
Query: 369 IEKLLKVDSFQVLEKYIEDLILEAY---------SATQLFDQFHDIVMSASSL---SDKQ 416
D VL+ +ED A+ L D IV +++
Sbjct: 242 ------SDLKAVLKSILEDDWGTAHYTLNKVRSAKGLALIDLIEGIVKILEDYELQNEET 295
Query: 417 KALILEKLAECNARLQDGASEYIQILDLGSIVIKANKTA 455
+ +L KLA+ + G ++ IQ GS VI A K +
Sbjct: 296 RVHLLTKLADIEYSISKGGNDQIQ----GSAVIGAIKAS 330
>pdb|1SXJ|B Chain B, Crystal Structure Of The Eukaryotic Clamp Loader
(Replication Factor C, Rfc) Bound To The Dna Sliding
Clamp (Proliferating Cell Nuclear Antigen, Pcna)
Length = 323
Score = 201 bits (512), Expect = 5e-52, Method: Compositional matrix adjust.
Identities = 112/269 (41%), Positives = 156/269 (57%), Gaps = 21/269 (7%)
Query: 33 VPWVEKYRPKTIDDVIEQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQLFG 92
+PWVEKYRP+ + D++ +E + L++ ++PH + G PG GKT+++ H+L G
Sbjct: 9 LPWVEKYRPQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELLG 68
Query: 93 DMYRERILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPP--FKIVILDEADSMT 150
Y + +LELNASDDRGI V+R+++K FAQ+ PP KIVILDEADSMT
Sbjct: 69 RSYADGVLELNASDDRGIDVVRNQIKHFAQKKLH--------LPPGKHKIVILDEADSMT 120
Query: 151 HAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLAENTMLTRLQYICE 210
AQ ALRRTME + STRF CN + II+PL S+C+ R+ L++ +L RL I +
Sbjct: 121 AGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDEDVLKRLLQIIK 180
Query: 211 QESVMCDFKALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVTGVIPKPWIEK 270
E V LE ++ T+ GDMR+AI LQS G G+VN D + P P I K
Sbjct: 181 LEDVKYTNDGLEAIIFTAEGDMRQAINNLQSTV---AGHGLVNADNVFKIVDSPHPLIVK 237
Query: 271 LLKV-----DSFQVLEKYIEDLILEAYSA 294
+ + DS Q+L DL + YS+
Sbjct: 238 KMLLASNLEDSIQILR---TDLWKKGYSS 263
Score = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 36/140 (25%), Positives = 68/140 (48%), Gaps = 11/140 (7%)
Query: 321 ALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVTGVIPNPWIEKLLKV----- 375
LE ++ T+ GDMR+AI LQS G G+VN D + P+P I K + +
Sbjct: 190 GLEAIIFTAEGDMRQAINNLQSTV---AGHGLVNADNVFKIVDSPHPLIVKKMLLASNLE 246
Query: 376 DSFQVLEKYIEDLILEAYSATQLFDQFHDIVMSASSLSDKQKALILEKLAECNARLQDGA 435
DS Q+L DL + YS+ + + + + + + + +++++ + R+ +G
Sbjct: 247 DSIQILR---TDLWKKGYSSIDIVTTSFRVTKNLAQVKESVRLEMIKEIGLTHMRILEGV 303
Query: 436 SEYIQILDLGSIVIKANKTA 455
Y+Q+ + + + K N A
Sbjct: 304 GTYLQLASMLAKIHKLNNKA 323
>pdb|1SXJ|E Chain E, Crystal Structure Of The Eukaryotic Clamp Loader
(Replication Factor C, Rfc) Bound To The Dna Sliding
Clamp (Proliferating Cell Nuclear Antigen, Pcna)
Length = 354
Score = 124 bits (310), Expect = 1e-28, Method: Compositional matrix adjust.
Identities = 97/288 (33%), Positives = 150/288 (52%), Gaps = 45/288 (15%)
Query: 35 WVEKYRPKTIDDVIEQQEVVSVLKKCLSGA--DLPHFLFYGPPGTGKTSTMIAACHQLFG 92
WV+KYRPK+++ + +E+ + LK LS DLPH L YGP GTGK + +A +FG
Sbjct: 4 WVDKYRPKSLNALSHNEELTNFLKS-LSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFG 62
Query: 93 -DMYRERI------------LELN---------------ASDDRGIQVIRDKVKTFAQQT 124
+YR +I LELN ++DR VI++ +K AQ
Sbjct: 63 PGVYRLKIDVRQFVTASNRKLELNVVSSPYHLEITPSDMGNNDR--IVIQELLKEVAQME 120
Query: 125 ASGFNQDGKP--CPPFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQ 182
F QD K +K VI++EA+S+T AQAALRRTMEK +K+ R ++C+ +S II
Sbjct: 121 QVDF-QDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIA 179
Query: 183 PLTSRCSKFRFKPLAENTMLTRLQYICEQESVMCDFK-ALETLVETSGGDMRRAITCLQS 241
P+ S+C R +++ + T L + E + + K L+ + + S G++R ++ L+S
Sbjct: 180 PIKSQCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLMLES 239
Query: 242 CARLKGGEGIVNEDVLEVTGVIPKP-WIEKLLKVDSFQVLEKYIEDLI 288
A + NE L+ + I KP WI + K+ V E+ + LI
Sbjct: 240 MA-------LNNELALKSSSPIIKPDWIIVIHKLTRKIVKERSVNSLI 280
>pdb|3U5Z|B Chain B, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4
Clamp, Primer-Template Dna, And Atp Analog
pdb|3U5Z|C Chain C, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4
Clamp, Primer-Template Dna, And Atp Analog
pdb|3U5Z|D Chain D, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4
Clamp, Primer-Template Dna, And Atp Analog
pdb|3U5Z|E Chain E, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4
Clamp, Primer-Template Dna, And Atp Analog
pdb|3U5Z|L Chain L, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4
Clamp, Primer-Template Dna, And Atp Analog
pdb|3U5Z|M Chain M, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4
Clamp, Primer-Template Dna, And Atp Analog
pdb|3U5Z|N Chain N, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4
Clamp, Primer-Template Dna, And Atp Analog
pdb|3U5Z|O Chain O, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4
Clamp, Primer-Template Dna, And Atp Analog
pdb|3U60|B Chain B, Structure Of T4 Bacteriophage Clamp Loader Bound To Open
Clamp, Dna And Atp Analog
pdb|3U60|C Chain C, Structure Of T4 Bacteriophage Clamp Loader Bound To Open
Clamp, Dna And Atp Analog
pdb|3U60|D Chain D, Structure Of T4 Bacteriophage Clamp Loader Bound To Open
Clamp, Dna And Atp Analog
pdb|3U60|E Chain E, Structure Of T4 Bacteriophage Clamp Loader Bound To Open
Clamp, Dna And Atp Analog
pdb|3U61|B Chain B, Structure Of T4 Bacteriophage Clamp Loader Bound To Closed
Clamp, Dna And Atp Analog And Adp
pdb|3U61|C Chain C, Structure Of T4 Bacteriophage Clamp Loader Bound To Closed
Clamp, Dna And Atp Analog And Adp
pdb|3U61|D Chain D, Structure Of T4 Bacteriophage Clamp Loader Bound To Closed
Clamp, Dna And Atp Analog And Adp
pdb|3U61|E Chain E, Structure Of T4 Bacteriophage Clamp Loader Bound To Closed
Clamp, Dna And Atp Analog And Adp
Length = 324
Score = 93.6 bits (231), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 73/233 (31%), Positives = 115/233 (49%), Gaps = 28/233 (12%)
Query: 37 EKYRPKTIDDVIEQQEVVSVLKKCLSGADLPHFLFYGP-PGTGKTSTMIAACHQLFGDMY 95
+KYRP TID+ I K S +PH + + P PGTGKT+ A CH + DM
Sbjct: 18 QKYRPSTIDECILPAFDKETFKSITSKGKIPHIILHSPSPGTGKTTVAKALCHDVNADM- 76
Query: 96 RERILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPPFKIVILDEADSMTHA-AQ 154
+ +N SD + I +R + FA +A+ F DG+ K++++DE D A +Q
Sbjct: 77 ----MFVNGSDCK-IDFVRGPLTNFA--SAASF--DGRQ----KVIVIDEFDRSGLAESQ 123
Query: 155 AALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRF-KPLAENT------MLTRLQY 207
LR ME + + + N + II+PL SRC F +P E+ M+ RL
Sbjct: 124 RHLRSFMEAYSSNCSIIITANNIDGIIKPLQSRCRVITFGQPTDEDKIEMMKQMIRRLTE 183
Query: 208 ICEQESV-MCDFKALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEV 259
IC+ E + + D K + LV+ + D R+ I L S + +G+++ +L +
Sbjct: 184 ICKHEGIAIADMKVVAALVKKNFPDFRKTIGELDSYS----SKGVLDAGILSL 232
>pdb|3GLH|B Chain B, Crystal Structure Of The E. Coli Clamp Loader Bound To Psi
Peptide
pdb|3GLH|C Chain C, Crystal Structure Of The E. Coli Clamp Loader Bound To Psi
Peptide
pdb|3GLH|D Chain D, Crystal Structure Of The E. Coli Clamp Loader Bound To Psi
Peptide
pdb|3GLH|G Chain G, Crystal Structure Of The E. Coli Clamp Loader Bound To Psi
Peptide
pdb|3GLH|H Chain H, Crystal Structure Of The E. Coli Clamp Loader Bound To Psi
Peptide
pdb|3GLH|I Chain I, Crystal Structure Of The E. Coli Clamp Loader Bound To Psi
Peptide
pdb|3GLH|L Chain L, Crystal Structure Of The E. Coli Clamp Loader Bound To Psi
Peptide
pdb|3GLH|M Chain M, Crystal Structure Of The E. Coli Clamp Loader Bound To Psi
Peptide
pdb|3GLH|N Chain N, Crystal Structure Of The E. Coli Clamp Loader Bound To Psi
Peptide
Length = 376
Score = 70.9 bits (172), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 60/236 (25%), Positives = 106/236 (44%), Gaps = 31/236 (13%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTS------------TMI 84
K+RP+T DV+ Q+ V++ L LS + H +LF G G GKTS T I
Sbjct: 12 KWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGI 71
Query: 85 AACHQLFGDMYRE-------RILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPP 137
A D RE ++E++A+ ++ RD + A G
Sbjct: 72 TATPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGR--------- 122
Query: 138 FKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLA 197
FK+ ++DE ++ + AL +T+E+ + +F L + + SRC +F K L
Sbjct: 123 FKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALD 182
Query: 198 ENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCLQSCARLKGGEGIVN 253
+ +L++I +E + + +AL+ L + G +R A++ + G+G V+
Sbjct: 183 VEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQA--IASGDGQVS 236
>pdb|1JR3|A Chain A, Crystal Structure Of The Processivity Clamp Loader Gamma
Complex Of E. Coli Dna Polymerase Iii
pdb|1JR3|B Chain B, Crystal Structure Of The Processivity Clamp Loader Gamma
Complex Of E. Coli Dna Polymerase Iii
pdb|1JR3|C Chain C, Crystal Structure Of The Processivity Clamp Loader Gamma
Complex Of E. Coli Dna Polymerase Iii
pdb|1XXH|B Chain B, Atpgs Bound E. Coli Clamp Loader Complex
pdb|1XXH|C Chain C, Atpgs Bound E. Coli Clamp Loader Complex
pdb|1XXH|D Chain D, Atpgs Bound E. Coli Clamp Loader Complex
pdb|1XXH|G Chain G, Atpgs Bound E. Coli Clamp Loader Complex
pdb|1XXH|H Chain H, Atpgs Bound E. Coli Clamp Loader Complex
pdb|1XXH|I Chain I, Atpgs Bound E. Coli Clamp Loader Complex
Length = 373
Score = 70.5 bits (171), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 60/236 (25%), Positives = 106/236 (44%), Gaps = 31/236 (13%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTS------------TMI 84
K+RP+T DV+ Q+ V++ L LS + H +LF G G GKTS T I
Sbjct: 9 KWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGI 68
Query: 85 AACHQLFGDMYRE-------RILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPP 137
A D RE ++E++A+ ++ RD + A G
Sbjct: 69 TATPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGR--------- 119
Query: 138 FKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLA 197
FK+ ++DE ++ + AL +T+E+ + +F L + + SRC +F K L
Sbjct: 120 FKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALD 179
Query: 198 ENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCLQSCARLKGGEGIVN 253
+ +L++I +E + + +AL+ L + G +R A++ + G+G V+
Sbjct: 180 VEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQA--IASGDGQVS 233
>pdb|3GLF|B Chain B, Crystal Structure Of The Ecoli Clamp Loader Bound To
Primer-template Dna
pdb|3GLF|C Chain C, Crystal Structure Of The Ecoli Clamp Loader Bound To
Primer-template Dna
pdb|3GLF|D Chain D, Crystal Structure Of The Ecoli Clamp Loader Bound To
Primer-template Dna
pdb|3GLF|G Chain G, Crystal Structure Of The Ecoli Clamp Loader Bound To
Primer-template Dna
pdb|3GLF|H Chain H, Crystal Structure Of The Ecoli Clamp Loader Bound To
Primer-template Dna
pdb|3GLF|I Chain I, Crystal Structure Of The Ecoli Clamp Loader Bound To
Primer-template Dna
pdb|3GLI|B Chain B, Crystal Structure Of The E. Coli Clamp Loader Bound To
Primer-template Dna And Psi Peptide
pdb|3GLI|C Chain C, Crystal Structure Of The E. Coli Clamp Loader Bound To
Primer-template Dna And Psi Peptide
pdb|3GLI|D Chain D, Crystal Structure Of The E. Coli Clamp Loader Bound To
Primer-template Dna And Psi Peptide
pdb|3GLI|G Chain G, Crystal Structure Of The E. Coli Clamp Loader Bound To
Primer-template Dna And Psi Peptide
pdb|3GLI|H Chain H, Crystal Structure Of The E. Coli Clamp Loader Bound To
Primer-template Dna And Psi Peptide
pdb|3GLI|I Chain I, Crystal Structure Of The E. Coli Clamp Loader Bound To
Primer-template Dna And Psi Peptide
Length = 395
Score = 70.5 bits (171), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 60/236 (25%), Positives = 106/236 (44%), Gaps = 31/236 (13%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTS------------TMI 84
K+RP+T DV+ Q+ V++ L LS + H +LF G G GKTS T I
Sbjct: 31 KWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGI 90
Query: 85 AACHQLFGDMYRE-------RILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPP 137
A D RE ++E++A+ ++ RD + A G
Sbjct: 91 TATPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGR--------- 141
Query: 138 FKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLA 197
FK+ ++DE ++ + AL +T+E+ + +F L + + SRC +F K L
Sbjct: 142 FKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALD 201
Query: 198 ENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCLQSCARLKGGEGIVN 253
+ +L++I +E + + +AL+ L + G +R A++ + G+G V+
Sbjct: 202 VEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQA--IASGDGQVS 255
>pdb|1XXI|B Chain B, Adp Bound E. Coli Clamp Loader Complex
pdb|1XXI|C Chain C, Adp Bound E. Coli Clamp Loader Complex
pdb|1XXI|D Chain D, Adp Bound E. Coli Clamp Loader Complex
pdb|1XXI|G Chain G, Adp Bound E. Coli Clamp Loader Complex
pdb|1XXI|H Chain H, Adp Bound E. Coli Clamp Loader Complex
pdb|1XXI|I Chain I, Adp Bound E. Coli Clamp Loader Complex
Length = 368
Score = 70.5 bits (171), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 60/236 (25%), Positives = 106/236 (44%), Gaps = 31/236 (13%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTS------------TMI 84
K+RP+T DV+ Q+ V++ L LS + H +LF G G GKTS T I
Sbjct: 9 KWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGI 68
Query: 85 AACHQLFGDMYRE-------RILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPP 137
A D RE ++E++A+ ++ RD + A G
Sbjct: 69 TATPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGR--------- 119
Query: 138 FKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLA 197
FK+ ++DE ++ + AL +T+E+ + +F L + + SRC +F K L
Sbjct: 120 FKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALD 179
Query: 198 ENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCLQSCARLKGGEGIVN 253
+ +L++I +E + + +AL+ L + G +R A++ + G+G V+
Sbjct: 180 VEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQA--IASGDGQVS 233
>pdb|3GLG|B Chain B, Crystal Structure Of A Mutant (Gammat157a) E. Coli Clamp
Loader Bound To Primer-Template Dna
pdb|3GLG|C Chain C, Crystal Structure Of A Mutant (Gammat157a) E. Coli Clamp
Loader Bound To Primer-Template Dna
pdb|3GLG|D Chain D, Crystal Structure Of A Mutant (Gammat157a) E. Coli Clamp
Loader Bound To Primer-Template Dna
pdb|3GLG|G Chain G, Crystal Structure Of A Mutant (Gammat157a) E. Coli Clamp
Loader Bound To Primer-Template Dna
pdb|3GLG|H Chain H, Crystal Structure Of A Mutant (Gammat157a) E. Coli Clamp
Loader Bound To Primer-Template Dna
pdb|3GLG|I Chain I, Crystal Structure Of A Mutant (Gammat157a) E. Coli Clamp
Loader Bound To Primer-Template Dna
Length = 395
Score = 70.1 bits (170), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 60/236 (25%), Positives = 106/236 (44%), Gaps = 31/236 (13%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTS------------TMI 84
K+RP+T DV+ Q+ V++ L LS + H +LF G G GKTS T I
Sbjct: 31 KWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGI 90
Query: 85 AACHQLFGDMYRE-------RILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPP 137
A D RE ++E++A+ ++ RD + A G
Sbjct: 91 TATPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGR--------- 141
Query: 138 FKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLA 197
FK+ ++DE ++ + AL +T+E+ + +F L + + SRC +F K L
Sbjct: 142 FKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATADPQKLPVTILSRCLQFHLKALD 201
Query: 198 ENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCLQSCARLKGGEGIVN 253
+ +L++I +E + + +AL+ L + G +R A++ + G+G V+
Sbjct: 202 VEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQA--IASGDGQVS 255
>pdb|1NJG|A Chain A, Nucleotide-Free Form Of An Isolated E. Coli Clamp Loader
Gamma Subunit
pdb|1NJG|B Chain B, Nucleotide-Free Form Of An Isolated E. Coli Clamp Loader
Gamma Subunit
pdb|1NJF|A Chain A, Nucleotide Bound Form Of An Isolated E. Coli Clamp Loader
Gamma Subunit
pdb|1NJF|B Chain B, Nucleotide Bound Form Of An Isolated E. Coli Clamp Loader
Gamma Subunit
pdb|1NJF|C Chain C, Nucleotide Bound Form Of An Isolated E. Coli Clamp Loader
Gamma Subunit
pdb|1NJF|D Chain D, Nucleotide Bound Form Of An Isolated E. Coli Clamp Loader
Gamma Subunit
Length = 250
Score = 69.7 bits (169), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 57/220 (25%), Positives = 100/220 (45%), Gaps = 29/220 (13%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTS------------TMI 84
K+RP+T DV+ Q+ V++ L LS + H +LF G G GKTS T I
Sbjct: 16 KWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGI 75
Query: 85 AACHQLFGDMYRE-------RILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPP 137
A D RE ++E++A+ ++ RD + A G
Sbjct: 76 TATPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARG---------R 126
Query: 138 FKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLA 197
FK+ ++DE ++ + AL +T+E+ + +F L + + SRC +F K L
Sbjct: 127 FKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALD 186
Query: 198 ENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAIT 237
+ +L++I +E + + +AL+ L + G +R A++
Sbjct: 187 VEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALS 226
>pdb|1SXJ|A Chain A, Crystal Structure Of The Eukaryotic Clamp Loader
(Replication Factor C, Rfc) Bound To The Dna Sliding
Clamp (Proliferating Cell Nuclear Antigen, Pcna)
Length = 516
Score = 69.3 bits (168), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 71/282 (25%), Positives = 118/282 (41%), Gaps = 44/282 (15%)
Query: 35 WVEKYRPKTIDDVIEQQEVVSVLKKCLS-------------GAD----LPHFLFYGPPGT 77
W KY P + V + V LK L+ G D + YGPPG
Sbjct: 29 WTVKYAPTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGI 88
Query: 78 GKTSTMIAACHQLFGDMYRERILELNASDDRGIQVIRDKVKT---------FAQQTASGF 128
GKT+ +L D ILE NASD R ++ VK + +
Sbjct: 89 GKTTAAHLVAQELGYD-----ILEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQ 143
Query: 129 NQDGKPCPPFKIVILDEADSMTHAAQAALRRTMEKETK-STRFCLICNYVSCI-IQPLTS 186
N +GK ++I+DE D M+ + + + + K ST LICN + ++P
Sbjct: 144 NLNGKHF----VIIMDEVDGMSGGDRGGVGQLAQFCRKTSTPLILICNERNLPKMRPFDR 199
Query: 187 RCSKFRFKPLAENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCLQSCARLK 246
C +F+ N++ +RL I +E D ++ L++T+ GD+R+ I L + +
Sbjct: 200 VCLDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRGDIRQVINLLSTISTTT 259
Query: 247 GGEGIVNEDVLEVTGVIPKPWIEKLLKVDSFQVLEKYIEDLI 288
+E++ E++ K W EK + + F + K ++ I
Sbjct: 260 KTIN--HENINEIS----KAW-EKNIALKPFDIAHKMLDGQI 294
>pdb|3PVS|A Chain A, Structure And Biochemical Activities Of Escherichia Coli
Mgsa
pdb|3PVS|B Chain B, Structure And Biochemical Activities Of Escherichia Coli
Mgsa
pdb|3PVS|C Chain C, Structure And Biochemical Activities Of Escherichia Coli
Mgsa
pdb|3PVS|D Chain D, Structure And Biochemical Activities Of Escherichia Coli
Mgsa
Length = 447
Score = 45.8 bits (107), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 51/221 (23%), Positives = 88/221 (39%), Gaps = 27/221 (12%)
Query: 34 PWVEKYRPKTIDDVIEQQEVVSV---LKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQL 90
P + RP+ + I QQ +++ L + + L + +GPPGTGKT+ +A
Sbjct: 15 PLAARMRPENLAQYIGQQHLLAAGKPLPRAIEAGHLHSMILWGPPGTGKTT--LAEVIAR 72
Query: 91 FGDMYRERILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPPFKIVILDEADSMT 150
+ + ERI + + G++ IR+ ++ Q +G I+ +DE
Sbjct: 73 YANADVERISAVTS----GVKEIREAIERARQNRNAGRR---------TILFVDEVHRFN 119
Query: 151 HAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLAENTMLTRLQYICE 210
+ Q A +E T + N + L SR + K L+ + L E
Sbjct: 120 KSQQDAFLPHIEDGTITFIGATTENPSFELNSALLSRARVYLLKSLSTEDIEQVLTQAME 179
Query: 211 --------QESVMCDFKALETLVETSGGDMRRAITCLQSCA 243
Q+ V+ D + + E GD RRA+ L+ A
Sbjct: 180 DKTRGYGGQDIVLPD-ETRRAIAELVNGDARRALNTLEMMA 219
>pdb|1IXR|C Chain C, Ruva-Ruvb Complex
Length = 312
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/56 (39%), Positives = 30/56 (53%), Gaps = 5/56 (8%)
Query: 40 RPKTIDDVIEQQEVVSVLKKCLSGAD-----LPHFLFYGPPGTGKTSTMIAACHQL 90
RPKT+D+ I Q+ + L+ L A L H L +GPPG GKT+ H+L
Sbjct: 7 RPKTLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHEL 62
>pdb|1IXS|B Chain B, Structure Of Ruvb Complexed With Ruva Domain Iii
Length = 318
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/56 (39%), Positives = 30/56 (53%), Gaps = 5/56 (8%)
Query: 40 RPKTIDDVIEQQEVVSVLKKCLSGAD-----LPHFLFYGPPGTGKTSTMIAACHQL 90
RPKT+D+ I Q+ + L+ L A L H L +GPPG GKT+ H+L
Sbjct: 7 RPKTLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHEL 62
>pdb|1HQC|A Chain A, Structure Of Ruvb From Thermus Thermophilus Hb8
pdb|1HQC|B Chain B, Structure Of Ruvb From Thermus Thermophilus Hb8
Length = 324
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/56 (39%), Positives = 30/56 (53%), Gaps = 5/56 (8%)
Query: 40 RPKTIDDVIEQQEVVSVLKKCLSGAD-----LPHFLFYGPPGTGKTSTMIAACHQL 90
RPKT+D+ I Q+ + L+ L A L H L +GPPG GKT+ H+L
Sbjct: 7 RPKTLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHEL 62
>pdb|1J7K|A Chain A, Thermotoga Maritima Ruvb P216g Mutant
Length = 334
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 27/51 (52%), Gaps = 5/51 (9%)
Query: 36 VEKYRPKTIDDVIEQQEVVSVLKKCLSGAD-----LPHFLFYGPPGTGKTS 81
V+ RPK++D+ I Q+ V L L A L H L GPPG GKT+
Sbjct: 16 VQFLRPKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTT 66
>pdb|1IN7|A Chain A, Thermotoga Maritima Ruvb R170a
Length = 334
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 27/51 (52%), Gaps = 5/51 (9%)
Query: 36 VEKYRPKTIDDVIEQQEVVSVLKKCLSGAD-----LPHFLFYGPPGTGKTS 81
V+ RPK++D+ I Q+ V L L A L H L GPPG GKT+
Sbjct: 16 VQFLRPKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTT 66
>pdb|1IN4|A Chain A, Thermotoga Maritima Ruvb Holliday Junction Branch
Migration Motor
Length = 334
Score = 38.5 bits (88), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 27/51 (52%), Gaps = 5/51 (9%)
Query: 36 VEKYRPKTIDDVIEQQEVVSVLKKCLSGAD-----LPHFLFYGPPGTGKTS 81
V+ RPK++D+ I Q+ V L L A L H L GPPG GKT+
Sbjct: 16 VQFLRPKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTT 66
>pdb|1IN8|A Chain A, Thermotoga Maritima Ruvb T158v
Length = 334
Score = 38.5 bits (88), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 27/51 (52%), Gaps = 5/51 (9%)
Query: 36 VEKYRPKTIDDVIEQQEVVSVLKKCLSGAD-----LPHFLFYGPPGTGKTS 81
V+ RPK++D+ I Q+ V L L A L H L GPPG GKT+
Sbjct: 16 VQFLRPKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTT 66
>pdb|1IN5|A Chain A, Thermogota Maritima Ruvb A156s Mutant
Length = 334
Score = 38.5 bits (88), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 27/51 (52%), Gaps = 5/51 (9%)
Query: 36 VEKYRPKTIDDVIEQQEVVSVLKKCLSGAD-----LPHFLFYGPPGTGKTS 81
V+ RPK++D+ I Q+ V L L A L H L GPPG GKT+
Sbjct: 16 VQFLRPKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTT 66
>pdb|1IN6|A Chain A, Thermotoga Maritima Ruvb K64r Mutant
Length = 334
Score = 37.7 bits (86), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 27/51 (52%), Gaps = 5/51 (9%)
Query: 36 VEKYRPKTIDDVIEQQEVVSVLKKCLSGAD-----LPHFLFYGPPGTGKTS 81
V+ RPK++D+ I Q+ V L L A L H L GPPG G+T+
Sbjct: 16 VQFLRPKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGRTT 66
>pdb|4FXK|B Chain B, Human Complement C4
Length = 767
Score = 33.1 bits (74), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 30/55 (54%), Gaps = 7/55 (12%)
Query: 232 MRRAITCLQSCARLKGGEGIVNEDVLEVTGVIPKPWIEKLLKVDSFQVLEKYIED 286
++RA+ LQ E +++ED + V P+ W+ ++ VD FQ+L ++ D
Sbjct: 75 LQRALEILQE-------EDLIDEDDIPVRSFFPENWLWRVETVDRFQILTLWLPD 122
Score = 32.7 bits (73), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 7/55 (12%)
Query: 333 MRRAITCLQSCARLKGGEGIVNEDVLEVTGVIPNPWIEKLLKVDSFQVLEKYIED 387
++RA+ LQ E +++ED + V P W+ ++ VD FQ+L ++ D
Sbjct: 75 LQRALEILQE-------EDLIDEDDIPVRSFFPENWLWRVETVDRFQILTLWLPD 122
>pdb|4FXG|B Chain B, Complement C4 In Complex With Masp-2
pdb|4FXG|E Chain E, Complement C4 In Complex With Masp-2
Length = 767
Score = 33.1 bits (74), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 30/55 (54%), Gaps = 7/55 (12%)
Query: 232 MRRAITCLQSCARLKGGEGIVNEDVLEVTGVIPKPWIEKLLKVDSFQVLEKYIED 286
++RA+ LQ E +++ED + V P+ W+ ++ VD FQ+L ++ D
Sbjct: 75 LQRALEILQE-------EDLIDEDDIPVRSFFPENWLWRVETVDRFQILTLWLPD 122
Score = 32.7 bits (73), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 7/55 (12%)
Query: 333 MRRAITCLQSCARLKGGEGIVNEDVLEVTGVIPNPWIEKLLKVDSFQVLEKYIED 387
++RA+ LQ E +++ED + V P W+ ++ VD FQ+L ++ D
Sbjct: 75 LQRALEILQE-------EDLIDEDDIPVRSFFPENWLWRVETVDRFQILTLWLPD 122
>pdb|3PFI|A Chain A, 2.7 Angstrom Resolution Crystal Structure Of A Probable
Holliday Junction Dna Helicase (Ruvb) From
Campylobacter Jejuni Subsp. Jejuni Nctc 11168 In
Complex With Adenosine-5'-Diphosphate
pdb|3PFI|B Chain B, 2.7 Angstrom Resolution Crystal Structure Of A Probable
Holliday Junction Dna Helicase (Ruvb) From
Campylobacter Jejuni Subsp. Jejuni Nctc 11168 In
Complex With Adenosine-5'-Diphosphate
Length = 338
Score = 32.3 bits (72), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 22/47 (46%), Gaps = 5/47 (10%)
Query: 40 RPKTIDDVIEQQEVVSVLKKCLSGAD-----LPHFLFYGPPGTGKTS 81
RP D I Q+ + L ++ A L H LF GP G GKT+
Sbjct: 24 RPSNFDGYIGQESIKKNLNVFIAAAKKRNECLDHILFSGPAGLGKTT 70
>pdb|3PXI|A Chain A, Structure Of Meca108:clpc
pdb|3PXI|B Chain B, Structure Of Meca108:clpc
pdb|3PXI|C Chain C, Structure Of Meca108:clpc
Length = 758
Score = 32.0 bits (71), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 12/25 (48%), Positives = 14/25 (56%)
Query: 69 FLFYGPPGTGKTSTMIAACHQLFGD 93
F+F GP G GKT A +FGD
Sbjct: 524 FIFLGPTGVGKTELARALAESIFGD 548
>pdb|2XZL|A Chain A, Upf1-Rna Complex
Length = 802
Score = 32.0 bits (71), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 31/64 (48%), Gaps = 12/64 (18%)
Query: 67 PHFLFYGPPGTGKTSTMIAACHQLFGDMYRERILELNASD-----------DRGIQVIRD 115
P L GPPGTGKT T + L ++++RIL S+ D G++V+R
Sbjct: 376 PLSLIQGPPGTGKTVTSATIVYHL-SKIHKDRILVCAPSNVAVDHLAAKLRDLGLKVVRL 434
Query: 116 KVKT 119
K+
Sbjct: 435 TAKS 438
>pdb|3M6A|A Chain A, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
pdb|3M6A|B Chain B, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
pdb|3M6A|C Chain C, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
pdb|3M6A|D Chain D, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
pdb|3M6A|E Chain E, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
pdb|3M6A|F Chain F, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
Length = 543
Score = 32.0 bits (71), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 31/98 (31%), Positives = 41/98 (41%), Gaps = 9/98 (9%)
Query: 54 VSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQLFGDMYRERILEL-NASDDRGIQV 112
V L K L G P GPPG GKTS + L R + + + S+ RG +
Sbjct: 99 VQKLTKSLKG---PILCLAGPPGVGKTSLAKSIAKSLGRKFVRISLGGVRDESEIRGHR- 154
Query: 113 IRDKVKTFAQQTASGFNQDGKPCPPFKIVILDEADSMT 150
R V + G + GK P F +LDE D M+
Sbjct: 155 -RTYVGAMPGRIIQGMKKAGKLNPVF---LLDEIDKMS 188
>pdb|3K1J|A Chain A, Crystal Structure Of Lon Protease From Thermococcus
Onnurineus Na1
pdb|3K1J|B Chain B, Crystal Structure Of Lon Protease From Thermococcus
Onnurineus Na1
Length = 604
Score = 31.6 bits (70), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 21/39 (53%), Gaps = 2/39 (5%)
Query: 42 KTIDDVIEQQEVVSVLKKCLSGADLPHFLFYGPPGTGKT 80
K ID VI Q+ V V+K + H L G PGTGK+
Sbjct: 38 KLIDQVIGQEHAVEVIKTAANQKR--HVLLIGEPGTGKS 74
>pdb|4B4T|K Chain K, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 428
Score = 31.6 bits (70), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 40/94 (42%), Gaps = 25/94 (26%)
Query: 63 GADLPH-FLFYGPPGTGKTSTMIAACHQLFGDMYRERILELNASD------DRGIQVIRD 115
G D P L YGPPGTGKT + A + R +N S+ G +++RD
Sbjct: 202 GIDPPRGVLLYGPPGTGKTMLVKAVANSTKAAFIR-----VNGSEFVHKYLGEGPRMVRD 256
Query: 116 KVKTFAQQTASGFNQDGKPCPPFKIVILDEADSM 149
V A++ A I+ +DE DS+
Sbjct: 257 -VFRLARENAPS------------IIFIDEVDSI 277
>pdb|4B4T|J Chain J, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 405
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 22/48 (45%)
Query: 42 KTIDDVIEQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQ 89
K I +VIE L + L A + YGPPGTGKT A H
Sbjct: 158 KEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAHH 205
>pdb|2R62|A Chain A, Crystal Structure Of Helicobacter Pylori Atp Dependent
Protease, Ftsh
pdb|2R62|B Chain B, Crystal Structure Of Helicobacter Pylori Atp Dependent
Protease, Ftsh
pdb|2R65|A Chain A, Crystal Structure Of Helicobacter Pylori Atp Dependent
Protease, Ftsh Adp Complex
pdb|2R65|B Chain B, Crystal Structure Of Helicobacter Pylori Atp Dependent
Protease, Ftsh Adp Complex
pdb|2R65|C Chain C, Crystal Structure Of Helicobacter Pylori Atp Dependent
Protease, Ftsh Adp Complex
pdb|2R65|D Chain D, Crystal Structure Of Helicobacter Pylori Atp Dependent
Protease, Ftsh Adp Complex
pdb|2R65|E Chain E, Crystal Structure Of Helicobacter Pylori Atp Dependent
Protease, Ftsh Adp Complex
Length = 268
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 30/108 (27%), Positives = 44/108 (40%), Gaps = 21/108 (19%)
Query: 63 GADLPH-FLFYGPPGTGKT---STMIAACHQLFGDMYRERILELNASDDRGIQVIRDKVK 118
GA +P L GPPGTGKT + H F M +E+ G +RD +
Sbjct: 40 GAKIPKGVLLVGPPGTGKTLLAKAVAGEAHVPFFSMGGSSFIEMFVG--LGASRVRDLFE 97
Query: 119 TFAQQTASGFNQDGKPCPPFKIVILDEADSM--THAAQAALRRTMEKE 164
T +Q S I+ +DE D++ + AA + E+E
Sbjct: 98 TAKKQAPS-------------IIFIDEIDAIGKSRAAGGVVSGNDERE 132
>pdb|2L4D|A Chain A, Cytochrome C Domain Of Pp3183 Protein From Pseudomonas
Putida
Length = 110
Score = 30.8 bits (68), Expect = 1.5, Method: Composition-based stats.
Identities = 29/106 (27%), Positives = 48/106 (45%), Gaps = 9/106 (8%)
Query: 328 TSGGDM-RRAITCLQSCARLKGGEGIVNEDVLEVTGVIPNPWIEKLLKVDSFQVLEKYIE 386
TSG + R + + + G+ + D+L VT W+ + LKV + EK
Sbjct: 4 TSGEQIFRTRCSSCHTVGNTEPGQPGIGPDLLGVTRQRDANWLVRWLKVPDQMLAEK--- 60
Query: 387 DLILEAYSATQLFDQFHDIVMSASSLSDKQKALILEKLAECNARLQ 432
D + A LF+Q++ + M L D + + ++ L E ARLQ
Sbjct: 61 DPL-----AMLLFEQYNRLAMPNMRLGDAEVSALISYLEEETARLQ 101
>pdb|3BFN|A Chain A, Crystal Structure Of The Motor Domain Of Human Kinesin
Family Member 22
Length = 388
Score = 30.4 bits (67), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 1/51 (1%)
Query: 39 YRPKTIDDVIEQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQ 89
Y ++ I V +L+ L G + L YGP G GKT TM+ + Q
Sbjct: 73 YGERSTQQDIYAGSVQPILRHLLEGQNA-SVLAYGPTGAGKTHTMLGSPEQ 122
>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 = 29.6 bits (65), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 25/57 (43%), Gaps = 5/57 (8%)
Query: 71 FYGPPGTGKTSTMIAACHQLFGDMYRERILELNASDDRGIQVIRDKVKTFAQQTASG 127
F+GP GTGKT T+ A FG ++ N D QV+ + Q A G
Sbjct: 431 FFGPAGTGKTETVKA-----FGQNLGRVVVVFNCDDSFDYQVLSRLLVGITQIGAWG 482
>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 = 29.6 bits (65), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 25/57 (43%), Gaps = 5/57 (8%)
Query: 71 FYGPPGTGKTSTMIAACHQLFGDMYRERILELNASDDRGIQVIRDKVKTFAQQTASG 127
F+GP GTGKT T+ A FG ++ N D QV+ + Q A G
Sbjct: 650 FFGPAGTGKTETVKA-----FGQNLGRVVVVFNCDDSFDYQVLSRLLVGITQIGAWG 701
>pdb|2PBF|A Chain A, Crystal Structure Of A Putative Protein-L-Isoaspartate O-
Methyltransferase Beta-Aspartate Methyltransferase
(Pcmt) From Plasmodium Falciparum In Complex With
S-Adenosyl-L-Homocysteine
pdb|2PBF|B Chain B, Crystal Structure Of A Putative Protein-L-Isoaspartate O-
Methyltransferase Beta-Aspartate Methyltransferase
(Pcmt) From Plasmodium Falciparum In Complex With
S-Adenosyl-L-Homocysteine
Length = 227
Score = 29.3 bits (64), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 5/72 (6%)
Query: 371 KLLKVDSFQVLEKYIEDLILEAYSATQLFDQFHDIVMSASSLSDKQKALILEKLAECNAR 430
+LLK+D+F+++ K I + E LFD H + SAS L + ++++ LAE
Sbjct: 135 ELLKIDNFKIIHKNIYQVNEEEKKELGLFDAIH-VGASASELPE----ILVDLLAENGKL 189
Query: 431 LQDGASEYIQIL 442
+ +Y Q+L
Sbjct: 190 IIPIEEDYTQVL 201
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 0.135 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,588,198
Number of Sequences: 62578
Number of extensions: 510918
Number of successful extensions: 1673
Number of sequences better than 100.0: 44
Number of HSP's better than 100.0 without gapping: 22
Number of HSP's successfully gapped in prelim test: 22
Number of HSP's that attempted gapping in prelim test: 1614
Number of HSP's gapped (non-prelim): 58
length of query: 456
length of database: 14,973,337
effective HSP length: 102
effective length of query: 354
effective length of database: 8,590,381
effective search space: 3040994874
effective search space used: 3040994874
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: 53 (25.0 bits)