RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12150
(456 letters)
>2chq_A Replication factor C small subunit; DNA-binding protein, DNA
replication, clamp loader, AAA+ ATP ATP-binding,
nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus
fulgidus} PDB: 2chv_A
Length = 319
Score = 376 bits (968), Expect = e-129
Identities = 125/305 (40%), Positives = 178/305 (58%), Gaps = 19/305 (6%)
Query: 34 PWVEKYRPKTIDDVIEQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQLFGD 93
WVEKYRP+T+D+V+ Q EV+ LK + ++PH LF GPPGTGKT+T IA LFG+
Sbjct: 6 IWVEKYRPRTLDEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGE 65
Query: 94 MYRERILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPPFKIVILDEADSMTHAA 153
+R+ +E+NASD+RGI V+R K+K FA+ PFKI+ LDEAD++T A
Sbjct: 66 NWRDNFIEMNASDERGIDVVRHKIKEFARTAPI-------GGAPFKIIFLDEADALTADA 118
Query: 154 QAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLAENTMLTRLQYICEQES 213
QAALRRTME +KS RF L CNYVS II+P+ SRC+ FRFKP+ + M RL ICE+E
Sbjct: 119 QAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMKKRLLEICEKEG 178
Query: 214 VMCDFKALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVTGVIPKPWIEKLLK 273
V LE L+ SGGD R+AI LQ A GE + + + ++T + +L++
Sbjct: 179 VKITEDGLEALIYISGGDFRKAINALQGAAA--IGEVVDADTIYQITATARPEEMTELIQ 236
Query: 274 V---DSFQVLEKYIEDLILEA-YSATQLFDQFHDIVMLASSLSDKQKALFKALETLVETS 329
+F + ++ L++E S + Q ++ + + D K + ++ L E
Sbjct: 237 TALKGNFMEARELLDRLMVEYGMSGEDIVAQLFREII-SMPIKDSLKV--QLIDKLGEV- 292
Query: 330 GGDMR 334
D R
Sbjct: 293 --DFR 295
Score = 110 bits (276), Expect = 3e-27
Identities = 35/129 (27%), Positives = 63/129 (48%), Gaps = 7/129 (5%)
Query: 320 KALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVTGVIPNPWIEKLLKV---D 376
LE L+ SGGD R+AI LQ A GE + + + ++T + +L++
Sbjct: 184 DGLEALIYISGGDFRKAINALQGAAA--IGEVVDADTIYQITATARPEEMTELIQTALKG 241
Query: 377 SFQVLEKYIEDLILEA-YSATQLFDQFHDIVMSASSLSDKQKALILEKLAECNARLQDGA 435
+F + ++ L++E S + Q ++S + D K +++KL E + RL +GA
Sbjct: 242 NFMEARELLDRLMVEYGMSGEDIVAQLFREIIS-MPIKDSLKVQLIDKLGEVDFRLTEGA 300
Query: 436 SEYIQILDL 444
+E IQ+
Sbjct: 301 NERIQLDAY 309
>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA
sliding clamp, AAA+ at polymerase, DNA-binding protein;
HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP:
a.80.1.1 c.37.1.20
Length = 323
Score = 375 bits (965), Expect = e-129
Identities = 107/309 (34%), Positives = 169/309 (54%), Gaps = 14/309 (4%)
Query: 27 KTRNKPVPWVEKYRPKTIDDVIEQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAA 86
KT + +PWVEKYRP+ + D++ +E + L++ ++PH + G PG GKT+++
Sbjct: 3 KTLSLQLPWVEKYRPQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCL 62
Query: 87 CHQLFGDMYRERILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPPFKIVILDEA 146
H+L G Y + +LELNASDDRGI V+R+++K FAQ+ P KIVILDEA
Sbjct: 63 AHELLGRSYADGVLELNASDDRGIDVVRNQIKHFAQKKLH------LPPGKHKIVILDEA 116
Query: 147 DSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLAENTMLTRLQ 206
DSMT AQ ALRRTME + STRF CN + II+PL S+C+ R+ L++ +L RL
Sbjct: 117 DSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDEDVLKRLL 176
Query: 207 YICEQESVMCDFKALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVTGVIPKP 266
I + E V LE ++ T+ GDMR+AI LQS G + ++V ++
Sbjct: 177 QIIKLEDVKYTNDGLEAIIFTAEGDMRQAINNLQSTVA--GHGLVNADNVFKIVDSPHPL 234
Query: 267 WIEKLLKVDSFQ-VLEKYIEDLILEAYSATQLFDQFHDIVMLASSLSDKQKALFKALETL 325
++K+L + + ++ DL + YS+ + + + + + + + ++ +
Sbjct: 235 IVKKMLLASNLEDSIQILRTDLWKKGYSSIDIVTTSFRVTKNLAQVKESVRL--EMIKEI 292
Query: 326 VETSGGDMR 334
T MR
Sbjct: 293 GLT---HMR 298
Score = 119 bits (301), Expect = 1e-30
Identities = 27/137 (19%), Positives = 65/137 (47%), Gaps = 3/137 (2%)
Query: 320 KALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVTGVIPNPWIEKLLKVDSFQ 379
LE ++ T+ GDMR+AI LQS G + ++V ++ ++K+L + +
Sbjct: 189 DGLEAIIFTAEGDMRQAINNLQSTVA--GHGLVNADNVFKIVDSPHPLIVKKMLLASNLE 246
Query: 380 -VLEKYIEDLILEAYSATQLFDQFHDIVMSASSLSDKQKALILEKLAECNARLQDGASEY 438
++ DL + YS+ + + + + + + + +++++ + R+ +G Y
Sbjct: 247 DSIQILRTDLWKKGYSSIDIVTTSFRVTKNLAQVKESVRLEMIKEIGLTHMRILEGVGTY 306
Query: 439 IQILDLGSIVIKANKTA 455
+Q+ + + + K N A
Sbjct: 307 LQLASMLAKIHKLNNKA 323
>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP,
replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP:
a.80.1.1 c.37.1.20
Length = 327
Score = 373 bits (959), Expect = e-128
Identities = 116/297 (39%), Positives = 168/297 (56%), Gaps = 14/297 (4%)
Query: 27 KTRNKPVPWVEKYRPKTIDDVIEQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAA 86
+ + PWVEKYRP+ +DD++ Q+ +V LK + +PH LF GPPG GKT+ +A
Sbjct: 7 EVKVLEKPWVEKYRPQRLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALAL 66
Query: 87 CHQLFGDMYRERILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPPFKIVILDEA 146
+LFG+ +R LELNASD+RGI VIR+KVK FA+ FKI+ LDEA
Sbjct: 67 ARELFGENWRHNFLELNASDERGINVIREKVKEFARTKPI-------GGASFKIIFLDEA 119
Query: 147 DSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLAENTMLTRLQ 206
D++T AQ ALRRTME + + RF L CNY S II+P+ SRC+ FRF+PL + + RL+
Sbjct: 120 DALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLR 179
Query: 207 YICEQESVMCDFKALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVTGVIPKP 266
YI E E + + L+ ++ + GDMRRAI LQ+ A + I +E+V V
Sbjct: 180 YIAENEGLELTEEGLQAILYIAEGDMRRAINILQAAAA--LDKKITDENVFMVASRARPE 237
Query: 267 WIEKLLKV----DSFQVLEKYIEDLILEAYSATQLFDQFHDIVMLASSLSDKQKALF 319
I +++ + + + EK E L+ + S + Q H V + + +K L
Sbjct: 238 DIREMMLLALKGNFLKAREKLREILLKQGLSGEDVLVQMHKEVF-NLPIEEPKKVLL 293
Score = 109 bits (275), Expect = 5e-27
Identities = 38/138 (27%), Positives = 67/138 (48%), Gaps = 7/138 (5%)
Query: 320 KALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVTGVIPNPWIEKLLKV---- 375
+ L+ ++ + GDMRRAI LQ+ A + I +E+V V I +++ +
Sbjct: 192 EGLQAILYIAEGDMRRAINILQAAAA--LDKKITDENVFMVASRARPEDIREMMLLALKG 249
Query: 376 DSFQVLEKYIEDLILEAYSATQLFDQFHDIVMSASSLSDKQKALILEKLAECNARLQDGA 435
+ + EK E L+ + S + Q H V + + + +K L+ +K+ E N RL +GA
Sbjct: 250 NFLKAREKLREILLKQGLSGEDVLVQMHKEVFN-LPIEEPKKVLLADKIGEYNFRLVEGA 308
Query: 436 SEYIQILDLGSIVIKANK 453
+E IQ+ L + K
Sbjct: 309 NEIIQLEALLAQFTLIGK 326
>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA
sliding clamp, AAA+ at polymerase, DNA-binding protein;
HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP:
a.80.1.1 c.37.1.20
Length = 353
Score = 371 bits (955), Expect = e-127
Identities = 143/315 (45%), Positives = 200/315 (63%), Gaps = 11/315 (3%)
Query: 14 APSSSKTSVSTSGKTRNKPVPWVEKYRPKTIDDVIEQQEVVSVLKKCLSGADLPHFLFYG 73
P+ + + + PWVEKYRPK +D+V Q V+VLKK L A+LPH LFYG
Sbjct: 6 GPNKKRKISKLAAEQSLAQQPWVEKYRPKNLDEVTAQDHAVTVLKKTLKSANLPHMLFYG 65
Query: 74 PPGTGKTSTMIAACHQLFG-DMYRERILELNASDDRGIQVIRDKVKTFAQ---QTASGFN 129
PPGTGKTST++A +L+G D+ + RILELNASD+RGI ++R+KVK FA+ S +
Sbjct: 66 PPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKVKNFARLTVSKPSKHD 125
Query: 130 QDGKPCPPFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCS 189
+ PCPP+KI+ILDEADSMT AQ+ALRRTME + TRFCLICNYV+ II PL S+CS
Sbjct: 126 LENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCS 185
Query: 190 KFRFKPLAENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCLQSCAR----L 245
KFRFK L + + RL++I EQE+V CD LE +++ S GD+RR IT LQS ++ L
Sbjct: 186 KFRFKALDASNAIDRLRFISEQENVKCDDGVLERILDISAGDLRRGITLLQSASKGAQYL 245
Query: 246 KGGEGIVNEDVLEVTGVIPKPWIEKLLKV---DSFQVLEKYIEDLILEAYSATQLFDQFH 302
G+ I + V E+ GV+P + ++++ F ++KY+ + +SA + +Q H
Sbjct: 246 GDGKNITSTQVEELAGVVPHDILIEIVEKVKSGDFDEIKKYVNTFMKSGWSAASVVNQLH 305
Query: 303 DIVMLASSLSDKQKA 317
+ + + K
Sbjct: 306 EYYITNDNFDTNFKN 320
Score = 116 bits (292), Expect = 3e-29
Identities = 38/132 (28%), Positives = 72/132 (54%), Gaps = 7/132 (5%)
Query: 320 KALETLVETSGGDMRRAITCLQSCAR----LKGGEGIVNEDVLEVTGVIPNPWIEKLLKV 375
LE +++ S GD+RR IT LQS ++ L G+ I + V E+ GV+P+ + ++++
Sbjct: 215 GVLERILDISAGDLRRGITLLQSASKGAQYLGDGKNITSTQVEELAGVVPHDILIEIVEK 274
Query: 376 ---DSFQVLEKYIEDLILEAYSATQLFDQFHDIVMSASSLSDKQKALILEKLAECNARLQ 432
F ++KY+ + +SA + +Q H+ ++ + K I L ++RL
Sbjct: 275 VKSGDFDEIKKYVNTFMKSGWSAASVVNQLHEYYITNDNFDTNFKNQISWLLFTTDSRLN 334
Query: 433 DGASEYIQILDL 444
+G +E+IQ+L+L
Sbjct: 335 NGTNEHIQLLNL 346
>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA
sliding clamp, AAA+ at polymerase, DNA-binding protein;
HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP:
a.80.1.1 c.37.1.20
Length = 340
Score = 369 bits (948), Expect = e-126
Identities = 110/319 (34%), Positives = 174/319 (54%), Gaps = 19/319 (5%)
Query: 23 STSGKTRNKPVPWVEKYRPKTIDDVIEQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTST 82
+++ K + +PWVEKYRP+T+D+V Q EV++ ++K + LPH LFYGPPGTGKTST
Sbjct: 3 TSTEKRSKENLPWVEKYRPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTST 62
Query: 83 MIAACHQLFGDMYRERILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPPFKIVI 142
++A +++G Y +LELNASDDRGI V+R+++K FA FK++I
Sbjct: 63 IVALAREIYGKNYSNMVLELNASDDRGIDVVRNQIKDFASTRQI-------FSKGFKLII 115
Query: 143 LDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLAENTML 202
LDEAD+MT+AAQ ALRR +E+ TK+TRFC++ NY + L S+C++FRF+PL + +
Sbjct: 116 LDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQPLPQEAIE 175
Query: 203 TRLQYICEQESVMCDFKALETLVETSGGDMRRAITCLQSCARLKG---GEGIVNEDVLEV 259
R+ + E + A + L+E S GDMRR + LQSC + I ++ + E
Sbjct: 176 RRIANVLVHEKLKLSPNAEKALIELSNGDMRRVLNVLQSCKATLDNPDEDEISDDVIYEC 235
Query: 260 TGVIPKPWIEKLLKV---DSFQVLEKYIEDLILEA-YSATQLFDQFHDIVMLASSLSDKQ 315
G ++ +LK D + + + + L + I+ +++
Sbjct: 236 CGAPRPSDLKAVLKSILEDDWGTAHYTLNKVRSAKGLALIDLIEGIVKILEDYELQNEET 295
Query: 316 KALFKALETLVETSGGDMR 334
+ L L + +
Sbjct: 296 RV--HLLTKLADI---EYS 309
Score = 112 bits (282), Expect = 7e-28
Identities = 28/139 (20%), Positives = 56/139 (40%), Gaps = 7/139 (5%)
Query: 320 KALETLVETSGGDMRRAITCLQSCARLKG---GEGIVNEDVLEVTGVIPNPWIEKLLKV- 375
A + L+E S GDMRR + LQSC + I ++ + E G ++ +LK
Sbjct: 192 NAEKALIELSNGDMRRVLNVLQSCKATLDNPDEDEISDDVIYECCGAPRPSDLKAVLKSI 251
Query: 376 --DSFQVLEKYIEDLILEA-YSATQLFDQFHDIVMSASSLSDKQKALILEKLAECNARLQ 432
D + + + + L + I+ +++ + +L KLA+ +
Sbjct: 252 LEDDWGTAHYTLNKVRSAKGLALIDLIEGIVKILEDYELQNEETRVHLLTKLADIEYSIS 311
Query: 433 DGASEYIQILDLGSIVIKA 451
G ++ IQ + + +
Sbjct: 312 KGGNDQIQGSAVIGAIKAS 330
>2chg_A Replication factor C small subunit; DNA-binding protein, DNA
replication, clamp loader, AAA+ ATPase, ATP-binding,
nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus
fulgidus}
Length = 226
Score = 357 bits (918), Expect = e-123
Identities = 113/229 (49%), Positives = 148/229 (64%), Gaps = 9/229 (3%)
Query: 34 PWVEKYRPKTIDDVIEQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQLFGD 93
WVEKYRP+T+D+V+ Q EV+ LK + ++PH LF GPPGTGKT+T IA LFG+
Sbjct: 6 IWVEKYRPRTLDEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGE 65
Query: 94 MYRERILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPPFKIVILDEADSMTHAA 153
+R+ +E+NASD+RGI V+R K+K FA+ PFKI+ LDEAD++T A
Sbjct: 66 NWRDNFIEMNASDERGIDVVRHKIKEFARTAPI-------GGAPFKIIFLDEADALTADA 118
Query: 154 QAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLAENTMLTRLQYICEQES 213
QAALRRTME +KS RF L CNYVS II+P+ SRC+ FRFKP+ + M RL ICE+E
Sbjct: 119 QAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMKKRLLEICEKEG 178
Query: 214 VMCDFKALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVTGV 262
V LE L+ SGGD R+AI LQ A GE + + + ++T
Sbjct: 179 VKITEDGLEALIYISGGDFRKAINALQGAAA--IGEVVDADTIYQITAT 225
Score = 52.6 bits (127), Expect = 5e-08
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 2/44 (4%)
Query: 320 KALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVTGV 363
LE L+ SGGD R+AI LQ A GE + + + ++T
Sbjct: 184 DGLEALIYISGGDFRKAINALQGAAA--IGEVVDADTIYQITAT 225
>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA
sliding clamp, AAA+ at polymerase, DNA-binding protein;
HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP:
a.80.1.1 c.37.1.20
Length = 354
Score = 315 bits (809), Expect = e-105
Identities = 82/319 (25%), Positives = 146/319 (45%), Gaps = 33/319 (10%)
Query: 34 PWVEKYRPKTIDDVIEQQEVVSVLKKCLS-GADLPHFLFYGPPGTGKTSTMIAACHQLFG 92
WV+KYRPK+++ + +E+ + LK DLPH L YGP GTGK + +A +FG
Sbjct: 3 LWVDKYRPKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFG 62
Query: 93 D------------------------MYRERILELNASDDRGI--QVIRDKVKTFAQ-QTA 125
+ LE+ SD VI++ +K AQ +
Sbjct: 63 PGVYRLKIDVRQFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQMEQV 122
Query: 126 SGFNQDGKPCPPFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLT 185
+ +K VI++EA+S+T AQAALRRTMEK +K+ R ++C+ +S II P+
Sbjct: 123 DFQDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIK 182
Query: 186 SRCSKFRFKPLAENTMLTRLQYICEQESVMCDFK-ALETLVETSGGDMRRAITCLQSCAR 244
S+C R +++ + T L + E + + K L+ + + S G++R ++ L+S A
Sbjct: 183 SQCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLMLESMAL 242
Query: 245 LKGGEGIVNEDVLEVT-GVIPKPWIEKLLK---VDSFQVLEKYIEDLILEAYSATQLFDQ 300
+ +++ ++ K++K V+S + DL+ A + +
Sbjct: 243 NNELALKSSSPIIKPDWIIVIHKLTRKIVKERSVNSLIECRAVLYDLLAHCIPANIILKE 302
Query: 301 FHDIVMLASSLSDKQKALF 319
++ +L+ K+
Sbjct: 303 LTFSLLDVETLNTTNKSSI 321
Score = 106 bits (267), Expect = 8e-26
Identities = 22/135 (16%), Positives = 55/135 (40%), Gaps = 4/135 (2%)
Query: 321 ALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVT-GVIPNPWIEKLLK---VD 376
L+ + + S G++R ++ L+S A + +++ ++ + K++K V+
Sbjct: 218 ILKRIAQASNGNLRVSLLMLESMALNNELALKSSSPIIKPDWIIVIHKLTRKIVKERSVN 277
Query: 377 SFQVLEKYIEDLILEAYSATQLFDQFHDIVMSASSLSDKQKALILEKLAECNARLQDGAS 436
S + DL+ A + + ++ +L+ K+ I+E + + RL G
Sbjct: 278 SLIECRAVLYDLLAHCIPANIILKELTFSLLDVETLNTTNKSSIIEYSSVFDERLSLGNK 337
Query: 437 EYIQILDLGSIVIKA 451
+ + V+
Sbjct: 338 AIFHLEGFIAKVMCC 352
>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp
loader, sliding clamp, primer-TEM DNA, DNA binding
protein-DNA complex; HET: DNA ADP 08T; 3.20A
{Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*
Length = 324
Score = 306 bits (787), Expect = e-102
Identities = 77/306 (25%), Positives = 127/306 (41%), Gaps = 39/306 (12%)
Query: 15 PSSSKTSVSTSGKTRNKPVPWVEKYRPKTIDDVIEQQEVVSVLKKCLSGADLPHFLFYGP 74
P S +V+ K +KYRP TID+ I K S +PH + + P
Sbjct: 2 PGGSMITVN------EKEHILEQKYRPSTIDECILPAFDKETFKSITSKGKIPHIILHSP 55
Query: 75 -PGTGKTSTMIAACHQLFGDMYRERILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGK 133
PGTGKT+ A CH + DM + +N SD + I +R + FA +
Sbjct: 56 SPGTGKTTVAKALCHDVNADM-----MFVNGSDCK-IDFVRGPLTNFASAAS-------- 101
Query: 134 PCPPFKIVILDEAD-SMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFR 192
K++++DE D S +Q LR ME + + + N + II+PL SRC
Sbjct: 102 FDGRQKVIVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITANNIDGIIKPLQSRCRVIT 161
Query: 193 FKPLAE-------NTMLTRLQYICEQESV-MCDFKALETLVETSGGDMRRAITCLQSCAR 244
F + M+ RL IC+ E + + D K + LV+ + D R+ I L S +
Sbjct: 162 FGQPTDEDKIEMMKQMIRRLTEICKHEGIAIADMKVVAALVKKNFPDFRKTIGELDSYSS 221
Query: 245 LKGGEGIVNEDVLEVTGVIPKPWIEKL---LKVDSFQVLEKYIEDLILEA-YSATQLFDQ 300
+G+++ +L + I+ + LK + L + + +L ++
Sbjct: 222 ----KGVLDAGILSLVTNDRGA-IDDVLESLKNKDVKQLRALAPKYAADYSWFVGKLAEE 276
Query: 301 FHDIVM 306
+ V
Sbjct: 277 IYSRVT 282
Score = 93.6 bits (233), Expect = 2e-21
Identities = 20/128 (15%), Positives = 46/128 (35%), Gaps = 13/128 (10%)
Query: 320 KALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVTGVIPNPWIEKL---LKVD 376
K + LV+ + D R+ I L S + +G+++ +L + I+ + LK
Sbjct: 196 KVVAALVKKNFPDFRKTIGELDSYSS----KGVLDAGILSLVTNDRGA-IDDVLESLKNK 250
Query: 377 SFQVLEKYIEDLILEAYSATQLFDQFHDIVMSASSLSDKQKALILEKLAECNARLQDGAS 436
+ L + + + + S ++ + + E + E N A+
Sbjct: 251 DVKQLRALAPKYA---ADYSWFVGKLAEEIY--SRVTPQSIIRMYEIVGENNQYHGIAAN 305
Query: 437 EYIQILDL 444
+ + L
Sbjct: 306 TELHLAYL 313
>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA
sliding clamp, AAA+ at polymerase, DNA-binding protein;
HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP:
a.80.1.1 c.37.1.20
Length = 516
Score = 303 bits (778), Expect = 2e-98
Identities = 78/366 (21%), Positives = 133/366 (36%), Gaps = 50/366 (13%)
Query: 8 GKLGKDAPSSSKTSVSTSGKTRNKPVPWVEKYRPKTIDDVIEQQEVVSVLKKCLSGAD-- 65
G SS V G W KY P + V + V LK L+ +
Sbjct: 2 GSSHHHHHHSSGLEVLFQGPHMASDKLWTVKYAPTNLQQVCGNKGSVMKLKNWLANWENS 61
Query: 66 ---------------LPHFLFYGPPGTGKTSTMIAACHQLFGDMYRERILELNASDDRGI 110
+ YGPPG GKT+ +L ILE NASD R
Sbjct: 62 KKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQEL-----GYDILEQNASDVRSK 116
Query: 111 QVIRDKVKTFAQQT-----ASGFNQDGKPCPPFKIVILDEADSMTHAAQAALRRTMEKET 165
++ VK + ++I+DE D M+ + + + +
Sbjct: 117 TLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCR 176
Query: 166 KSTR-FCLICNYVSC-IIQPLTSRCSKFRFKPLAENTMLTRLQYICEQESVMCDFKALET 223
K++ LICN + ++P C +F+ N++ +RL I +E D ++
Sbjct: 177 KTSTPLILICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDR 236
Query: 224 LVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVTGVIPK-----PW--IEKLLKVDS 276
L++T+ GD+R+ I L + + + I +E++ E++ K P+ K+L
Sbjct: 237 LIQTTRGDIRQVINLLSTIS--TTTKTINHENINEISKAWEKNIALKPFDIAHKMLDGQI 294
Query: 277 FQVLEKY------IEDLILEAYSATQLFDQFHDIVMLASSLSDKQKAL---FKALETLVE 327
+ + L + + T L Q + + S L Q L +A +
Sbjct: 295 YSDIGSRNFTLNDKIALYFDDFDFTPLMIQENYLSTRPSVLKPGQSHLEAVAEAANCI-- 352
Query: 328 TSGGDM 333
S GD+
Sbjct: 353 -SLGDI 357
Score = 63.4 bits (154), Expect = 5e-11
Identities = 23/128 (17%), Positives = 49/128 (38%), Gaps = 17/128 (13%)
Query: 320 KALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVTG-----VIPNPW--IEKL 372
++ L++T+ GD+R+ I L + + + I +E++ E++ + P+ K+
Sbjct: 232 NVIDRLIQTTRGDIRQVINLLSTIS--TTTKTINHENINEISKAWEKNIALKPFDIAHKM 289
Query: 373 LKVDSFQVLEKY------IEDLILEAYSATQLFDQFHDIVMSASSLSDKQKALILEKLAE 426
L + + L + + T L + +S K LE +AE
Sbjct: 290 LDGQIYSDIGSRNFTLNDKIALYFDDFDFTPLM--IQENYLSTRPSVLKPGQSHLEAVAE 347
Query: 427 CNARLQDG 434
+ G
Sbjct: 348 AANCISLG 355
>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase
domains, sensor 1, sensor 2, transferase; HET: DNA;
2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*
Length = 250
Score = 99 bits (250), Expect = 4e-24
Identities = 60/254 (23%), Positives = 112/254 (44%), Gaps = 50/254 (19%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTST--MIA--------- 85
K+RP+T DV+ Q+ V++ L LS + H +LF G G GKTS ++A
Sbjct: 16 KWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGI 75
Query: 86 ---------ACHQL----FGDMYRERILELNASDDRGIQVIR---DKVKTFAQQTASGFN 129
C ++ F D ++E++A+ ++ R D V+ +A
Sbjct: 76 TATPCGVCDNCREIEQGRFVD-----LIEIDAASRTKVEDTRDLLDNVQ-YAPARG---- 125
Query: 130 QDGKPCPPFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLT--SR 187
FK+ ++DE ++ + AL +T+E+ + +F L + P+T SR
Sbjct: 126 -------RFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKL--PVTILSR 176
Query: 188 CSKFRFKPLAENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCLQSCARLKG 247
C +F K L + +L++I +E + + +AL+ L + G +R A++
Sbjct: 177 CLQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGD 236
Query: 248 GEGIVNEDVLEVTG 261
G+ + + V + G
Sbjct: 237 GQ-VSTQAVSAMLG 249
>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp,
clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A
{Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B*
3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*
Length = 373
Score = 101 bits (255), Expect = 6e-24
Identities = 68/315 (21%), Positives = 127/315 (40%), Gaps = 73/315 (23%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTST--MIA--------- 85
K+RP+T DV+ Q+ V++ L LS + H +LF G G GKTS ++A
Sbjct: 9 KWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGI 68
Query: 86 ---------ACHQL----FGDMYRERILELNASDDRGIQVIR---DKVKTFAQQTASGFN 129
C ++ F D ++E++A+ ++ R D V+ +A
Sbjct: 69 TATPCGVCDNCREIEQGRFVD-----LIEIDAASRTKVEDTRDLLDNVQ-YAPARG---- 118
Query: 130 QDGKPCPPFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCI-----IQ-- 182
FK+ ++DE ++ + AL +T+E E +V + Q
Sbjct: 119 -------RFKVYLIDEVHMLSRHSFNALLKTLE-EPPE--------HVKFLLATTDPQKL 162
Query: 183 PLT--SRCSKFRFKPLAENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCLQ 240
P+T SRC +F K L + +L++I +E + + +AL+ L + G +R A++
Sbjct: 163 PVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTD 222
Query: 241 SCARLKGGEGIVNEDVLEVTGVIPKPWIEKLLKV----DSFQVLEKYIEDLILEAYSATQ 296
G+ + + V + G + L++ + +V+ I +
Sbjct: 223 QAIASGDGQ-VSTQAVSAMLGTLDDDQALSLVEAMVEANGERVMAL-INEAAARGIEWEA 280
Query: 297 LFDQ----FHDIVML 307
L + H I M+
Sbjct: 281 LLVEMLGLLHRIAMV 295
Score = 38.4 bits (90), Expect = 0.004
Identities = 22/134 (16%), Positives = 46/134 (34%), Gaps = 13/134 (9%)
Query: 320 KALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVTGVIPNPWIEKLLKV---- 375
+AL+ L + G +R A++ G+ + + V + G + + L++
Sbjct: 201 RALQLLARAAEGSLRDALSLTDQAIASGDGQ-VSTQAVSAMLGTLDDDQALSLVEAMVEA 259
Query: 376 DSFQVLEKYIEDLILEAYSATQLFDQ----FHDIVM--SASSLSDKQKALILEKLAECNA 429
+ +V+ I + L + H I M + + A I ++ E
Sbjct: 260 NGERVMAL-INEAAARGIEWEALLVEMLGLLHRIAMVQLSPAALGNDMAAIELRMRELAR 318
Query: 430 RL-QDGASEYIQIL 442
+ Y Q L
Sbjct: 319 TIPPTDIQLYYQTL 332
>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia
coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E*
1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*
Length = 334
Score = 97.9 bits (244), Expect = 7e-23
Identities = 56/313 (17%), Positives = 89/313 (28%), Gaps = 57/313 (18%)
Query: 50 QQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTST--MIA------------------ACH 88
+ L H L PG G + ++ C
Sbjct: 7 LRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQ 66
Query: 89 QL----FGDMYRERILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPPFKIVILD 144
+ D Y + + G+ +R+ V + A + G K+V +
Sbjct: 67 LMQAGTHPDYYT--LAPEKGKNTLGVDAVRE-VTEKLNEHA----RLGG----AKVVWVT 115
Query: 145 EADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLAENTMLTR 204
+A +T AA AL +T+E+ T F L ++ L SRC P E +T
Sbjct: 116 DAALLTDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTW 175
Query: 205 LQYICEQESVMCDFKALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVTGVIP 264
L V AL + S G A+ Q + +P
Sbjct: 176 L-----SREVTMSQDALLAALRLSAGSPGAALALFQG-----DNWQARETLCQALAYSVP 225
Query: 265 KPWIEKLLKV-------DSFQVLEKYIEDLILEAYSATQLF--DQFHDIVMLASSLSDKQ 315
LL L + D + + A Q+ D + LA+ LS
Sbjct: 226 SGDWYSLLAALNHEQAPARLHWLATLLMDALKRHHGAAQVTNVDVPGLVAELANHLS--P 283
Query: 316 KALFKALETLVET 328
L L +
Sbjct: 284 SRLQAILGDVCHI 296
Score = 31.6 bits (72), Expect = 0.44
Identities = 20/125 (16%), Positives = 34/125 (27%), Gaps = 14/125 (11%)
Query: 320 KALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVTGVIPNPWIEKLLKV---- 375
AL + S G A+ Q + +P+ LL
Sbjct: 185 DALLAALRLSAGSPGAALALFQG-----DNWQARETLCQALAYSVPSGDWYSLLAALNHE 239
Query: 376 ---DSFQVLEKYIEDLILEAYSATQLF--DQFHDIVMSASSLSDKQKALILEKLAECNAR 430
L + D + + A Q+ D + A+ LS + IL + +
Sbjct: 240 QAPARLHWLATLLMDALKRHHGAAQVTNVDVPGLVAELANHLSPSRLQAILGDVCHIREQ 299
Query: 431 LQDGA 435
L
Sbjct: 300 LMSVT 304
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 85.7 bits (211), Expect = 8e-18
Identities = 67/465 (14%), Positives = 134/465 (28%), Gaps = 132/465 (28%)
Query: 20 TSVSTSGKTRNKPVPWVEKYRPKTIDDV-------IEQQEVVSVLKKCLSGADLPHFLF- 71
+ + T + + + R + +D + + + L++ L +
Sbjct: 96 SPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLI 155
Query: 72 YGPPGTGKTSTMIAAC-----HQLFGDMYRERILELNASDDRGIQVIRDKVKTFAQQTAS 126
G G+GKT + C +I LN + + + + ++ Q
Sbjct: 156 DGVLGSGKTWVALDVCLSYKVQCKMDF----KIFWLNLKNCNSPETVLEMLQKLLYQIDP 211
Query: 127 GFNQ--DGKPCPPFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLI-----CNYVSC 179
+ D +I H+ QA LRR ++ K CL+ N +
Sbjct: 212 NWTSRSDHSSNIKLRI----------HSIQAELRRLLKS--KPYENCLLVLLNVQN--AK 257
Query: 180 IIQPLTSRCSKFRFKPLAENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCL 239
C K L + TR + V DF + T S +T
Sbjct: 258 AWNAFNLSC-----KIL----LTTR------FKQVT-DFLSAATTTHISLDHHSMTLT-- 299
Query: 240 QSCARLKGGEGIVNEDVLEVTGVIPKPWIEKLLKVDSFQVLEKYIEDLILEAYSATQLFD 299
++V + LLK L+ +DL E +
Sbjct: 300 -------------PDEVKSL-----------LLK-----YLDCRPQDLPREVLTTNPRR- 329
Query: 300 QFHDIVMLASSLSDK-------QKALFKALETLVETS-----GGDMRRAITCLQSCARLK 347
+ ++A S+ D + L T++E+S + R+ +
Sbjct: 330 ----LSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRK---MFDRLS--- 379
Query: 348 GGEGIVNEDVLEVTGVIPNP-----WIEKLLKVDSFQVLEKYIEDLILEAYSATQLFDQF 402
+ IP W + ++K D V+ K + ++E
Sbjct: 380 ----VFPPSAH-----IPTILLSLIWFD-VIKSDVMVVVNKLHKYSLVEKQPKESTI-SI 428
Query: 403 HDIVMSASSLSDKQKAL---ILEKLA-----ECNARLQDGASEYI 439
I + + + AL I++ + + + +Y
Sbjct: 429 PSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYF 473
Score = 43.7 bits (102), Expect = 1e-04
Identities = 55/375 (14%), Positives = 107/375 (28%), Gaps = 115/375 (30%)
Query: 17 SSKTSVSTSGKTRNKPVP---WVEKYRPKTIDDV---IEQQEVVSVLKKCL--SGADLP- 67
S K + T TR K V ++D + EV S+L K L DLP
Sbjct: 265 SCKILL-T---TRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPR 320
Query: 68 ----------------------HFLFYGPPGTGKTSTMIAAC-HQLFGDMYRERILELNA 104
+ + K +T+I + + L YR+ L+
Sbjct: 321 EVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSV 380
Query: 105 -SDDRGI--QVI----RDKVKTFAQQTASGF------NQDGKPCPPFKIVILDEADSMTH 151
I ++ D +K+ + + K I I
Sbjct: 381 FPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKE---STISI--------P 429
Query: 152 AAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLAENTMLTRLQY---I 208
+ L+ +E E R ++ +Y + S P + + + +
Sbjct: 430 SIYLELKVKLENEYALHR-SIVDHY-----NIPKTFDSDDLIPPYLDQYFYSHIGHHLKN 483
Query: 209 CEQESVMCDFKALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVTGVIPKPWI 268
E M F+ + D R L+ K + W
Sbjct: 484 IEHPERMTLFRMVFL-------DFR----FLEQ----K----------IRHDST---AWN 515
Query: 269 EKLLKVDSFQVLEKY--------------IEDLI--LEAYSATQLFDQFHDIVMLASSLS 312
+++ Q L+ Y + ++ L + ++ D++ +A L
Sbjct: 516 ASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIA--LM 573
Query: 313 DKQKALFKALETLVE 327
+ +A+F+ V+
Sbjct: 574 AEDEAIFEEAHKQVQ 588
Score = 34.1 bits (77), Expect = 0.11
Identities = 11/95 (11%), Positives = 33/95 (34%), Gaps = 11/95 (11%)
Query: 355 EDVLEVT-GVIPNPWIEKLLKVDSFQVLEKYIEDLILEAYSATQLFDQF--------HDI 405
+DV ++ ++ I+ ++ + +L ++ +F +
Sbjct: 36 KDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLS--KQEEMVQKFVEEVLRINYKF 93
Query: 406 VMSASSLSDKQKALILEKLAECNARLQDGASEYIQ 440
+MS +Q +++ E RL + + +
Sbjct: 94 LMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAK 128
>3pvs_A Replication-associated recombination protein A; maintenance of
genome stability Pro recombination; 2.50A {Escherichia
coli}
Length = 447
Score = 73.7 bits (182), Expect = 2e-14
Identities = 52/254 (20%), Positives = 99/254 (38%), Gaps = 47/254 (18%)
Query: 28 TRNKPVPWVEKYRPKTIDDVIEQQEVV---SVLKKCLSGADLPHFLFYGPPGTGKTSTMI 84
+ N P + RP+ + I QQ ++ L + + L + +GPPGTGKT+ +
Sbjct: 9 SDNTFQPLAARMRPENLAQYIGQQHLLAAGKPLPRAIEAGHLHSMILWGPPGTGKTT--L 66
Query: 85 AACHQLFGDMYRERILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPPFKIVILD 144
A ++ + ++A G++ IR+ ++ A+Q G+ I+ +D
Sbjct: 67 A---EVIARYANADVERISAVTS-GVKEIREAIER-ARQNR----NAGRRT----ILFVD 113
Query: 145 EADSMTH----AAQAALRRTMEKETKSTRFCLIC----N-YVSCIIQPLTSRCSKFRFKP 195
E H + Q A +E T I N + L SR + K
Sbjct: 114 E----VHRFNKSQQDAFLPHIEDGT----ITFIGATTENPSFE-LNSALLSRARVYLLKS 164
Query: 196 LAEN---TMLTRLQYICEQ----ESVMCDFKALETLVETSGGDMRRAITCLQSCARL--- 245
L+ +LT+ + + ++ + + E GD RRA+ L+ A +
Sbjct: 165 LSTEDIEQVLTQAMEDKTRGYGGQDIVLPDETRRAIAELVNGDARRALNTLEMMADMAEV 224
Query: 246 -KGGEGIVNEDVLE 258
G+ ++ ++L
Sbjct: 225 DDSGKRVLKPELLT 238
Score = 32.5 bits (75), Expect = 0.27
Identities = 10/43 (23%), Positives = 19/43 (44%), Gaps = 4/43 (9%)
Query: 321 ALETLVETSGGDMRRAITCLQSCARL----KGGEGIVNEDVLE 359
+ E GD RRA+ L+ A + G+ ++ ++L
Sbjct: 196 TRRAIAELVNGDARRALNTLEMMADMAEVDDSGKRVLKPELLT 238
>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET:
ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*
Length = 368
Score = 71.1 bits (174), Expect = 1e-13
Identities = 50/321 (15%), Positives = 88/321 (27%), Gaps = 83/321 (25%)
Query: 42 KTIDDVIEQQEVVSVLKKCL----SGADLPH-FLFYGPPGTGKTSTMIA-----ACHQLF 91
+ ++ Q L G L G PGTGKT+ + F
Sbjct: 41 QASQGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTPF 100
Query: 92 G-------------------------------------------DMYRERILELNASDDR 108
D+ R A
Sbjct: 101 TAIAGSEIFSLEMSKTEALTQAFRRSIGVRIKAGAVHTVSLHEIDVINSRTQGFLALFSG 160
Query: 109 GIQVIRDKVKTFAQQTASGFNQDGKPCPPFKIVILDEADSMTHAAQAALRRTMEKETKST 168
I+ +V+ + + ++GK ++ +DE + + + L R +E +
Sbjct: 161 DTGEIKSEVREQINAKVAEWREEGKAEIIPGVLFIDEVHMLDIESFSFLNRALE-SDMAP 219
Query: 169 RFCLICNYVSCIIQ----------PLT--SRCSKFRFKPLAENTMLTRLQYICEQESVMC 216
+ N I+ P+ R P +E L+ CE+E V
Sbjct: 220 VLIMATNRGITRIRGTSYQSPHGIPIDLLDRLLIVSTTPYSEKDTKQILRIRCEEEDVEM 279
Query: 217 DFKALETLVETSG-GDMRRAI---TCLQSCARLKGGEGIVNEDVLEVTGVIPKPWIEKLL 272
A L +R AI T R + G + +D+ V L
Sbjct: 280 SEDAYTVLTRIGLETSLRYAIQLITAASLVCRKRKGTEVQVDDIKRVYS----------L 329
Query: 273 KVD---SFQVLEKYIEDLILE 290
+D S Q +++Y + +
Sbjct: 330 FLDESRSTQYMKEYQDAFLFN 350
>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3;
winged-helix domain, helix-turn-helix, AAA+ ATPase
domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A
{Sulfolobus solfataricus}
Length = 384
Score = 68.6 bits (167), Expect = 8e-13
Identities = 44/285 (15%), Positives = 86/285 (30%), Gaps = 32/285 (11%)
Query: 49 EQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQLFGDMYRE----------- 97
++ ++ + LF G GTGKT +++ +
Sbjct: 28 ILRDAAIAIRYFVKNEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYV 87
Query: 98 RILELNASDDRGIQVIRDKV------KTFAQQTASGFNQDGKPCPPFKIVILDEADSM-- 149
E+ + + + K+ K I+ LDE D++
Sbjct: 88 NCREVGGTPQAVLSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNIRAIIYLDEVDTLVK 147
Query: 150 THAAQAALRRTMEKETKSTRFCLICN---YVSCIIQPLTSRCSK-FRFKPLAENTMLTRL 205
L + + + + +I N + + S FKP + L
Sbjct: 148 RRGGDIVLYQLLRSDANIS-VIMISNDINVRDYMEPRVLSSLGPSVIFKPYDAEQLKFIL 206
Query: 206 QYICEQ--ESVMCDFKALETL---VETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVT 260
E D + L + GD R+A+ L A+L G GI+ ++ V
Sbjct: 207 SKYAEYGLIKGTYDDEILSYIAAISAKEHGDARKAVNLLFRAAQLASGGGIIRKE--HVD 264
Query: 261 GVIPKPWIEKLLKV-DSFQVLEKYIEDLILEAYSATQLFDQFHDI 304
I E+L++ + K ++E+ + D+
Sbjct: 265 KAIVDYEQERLIEAVKALPFHYKLALRSLIESEDVMSAHKMYTDL 309
Score = 39.0 bits (90), Expect = 0.002
Identities = 25/147 (17%), Positives = 48/147 (32%), Gaps = 5/147 (3%)
Query: 285 EDLILEAYSATQLFDQFHDIVMLASSLSDKQKALFKALETLVETSGGDMRRAITCLQSCA 344
+I + Y A QL + + + GD R+A+ L A
Sbjct: 190 PSVIFKPYDAEQLKFILSKYAEYGLIKGTYDDEILSYIAAISAKEHGDARKAVNLLFRAA 249
Query: 345 RLKGGEGIVN-EDVLEVTGVIPNPWIEKLLKVDSFQVLEKYIEDLILEAYSATQLFDQFH 403
+L G GI+ E V + + + V + K ++E+ +
Sbjct: 250 QLASGGGIIRKEHVDKAIVDYEQERLIE--AVKALPFHYKLALRSLIESEDVMSAHKMYT 307
Query: 404 DI--VMSASSLSDKQKALILEKLAECN 428
D+ LS ++ + I+ +L
Sbjct: 308 DLCNKFKQKPLSYRRFSDIISELDMFG 334
>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA
replication initation factor, cell cycle control factor;
HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11
c.37.1.20
Length = 389
Score = 62.1 bits (150), Expect = 1e-10
Identities = 64/390 (16%), Positives = 120/390 (30%), Gaps = 54/390 (13%)
Query: 39 YRPKTI---DDVIEQQEVVSVLKKCL--SGADLPHFLFYGPPGTGKTSTMIAACHQLFGD 93
Y PK + + + Q++ +L L G P G PGTGKT T+ D
Sbjct: 14 YVPKRLPHREQ--QLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELY-KD 70
Query: 94 MYRERILELNASDDRGI-QVIRDKVKTFAQQTASG----------FNQDGKPCPPFKIVI 142
R + +N R +I + ++ + + + ++
Sbjct: 71 KTTARFVYINGFIYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLV 130
Query: 143 LDEADSMTHAAQAALRRTMEK--ETKSTRFCLIC-----NYVSCIIQPLTSRCS--KFRF 193
LD+A ++ + R ++ + + R L+ ++ + RF
Sbjct: 131 LDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNLDPSTRGIMGKYVIRF 190
Query: 194 KPLAENT----MLTRLQYICEQESV-------MCDFKALETLVETSGGDMRRAITCLQSC 242
P ++ +L R + + S + D +T ++T+ GD R AI L
Sbjct: 191 SPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNRGDARLAIDILYRS 250
Query: 243 ARLKGGEGIVNEDVLEVTGVIPKPWIEKLLK-VDSFQVLEKYIEDLILEAYSATQLFDQF 301
A G + +V + + + + EK L L A +
Sbjct: 251 AYAAQQNGRKHIAPEDVRKSSKEVLFGISEEVLIGLPLHEK----LFLLAIVRSLKISHT 306
Query: 302 HDIVMLASSLSDKQKALFKALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVT 361
I ++ + + E G R L +GIV +
Sbjct: 307 PYITF---------GDAEESYKIVCEEYGERPRVHSQLWSYLNDL-REKGIVETRQNKRG 356
Query: 362 GVIPNPWIEKLLKVDSFQVLEKYIEDLILE 391
+ + + LE I LI E
Sbjct: 357 EGVRGRTTLISIGTEPLDTLEAVITKLIKE 386
>2gno_A DNA polymerase III, gamma subunit-related protein; structural
genomics, joint center for structural genomics, J
protein structure initiative; HET: DNA; 2.00A
{Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20
Length = 305
Score = 55.5 bits (134), Expect = 1e-08
Identities = 49/317 (15%), Positives = 106/317 (33%), Gaps = 71/317 (22%)
Query: 50 QQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQLFGDMYRER-------ILEL 102
++ + LK+ + ++ L G + +L Y E+ +LE+
Sbjct: 2 AKDQLETLKRIIEKSEGISILINGEDLSYPRE----VSLEL--PEYVEKFPPKASDVLEI 55
Query: 103 N-ASDDRGIQVIR---DKVKTFAQQTASGFNQDGKPCPPFKIVILDEADSMTHAAQAALR 158
+ ++ GI IR D + ++ + + K VI+ + + MT A A
Sbjct: 56 DPEGENIGIDDIRTIKDFLN-YSPELYT-----------RKYVIVHDCERMTQQAANAFL 103
Query: 159 RTMEKETKSTRFCL-------ICNYVSCIIQPLT--SRCSKFR------FKPLAENTMLT 203
+ +E+ + L + T SR + F+ L + +
Sbjct: 104 KALEEPPEYAVIVLNTRRWHYL---------LPTIKSRVFRVVVNVPKEFRDLVKEKIGD 154
Query: 204 RLQYICE-QESVMCDFKALETLVETSGGDMRRAITCLQSCARLK-----GGEGIVN-EDV 256
+ + + +A + E G + ++ L++ LK G EG + ++
Sbjct: 155 LWEELPLLERDFKTALEAYKLGAEKLSG-LMESLKVLETEKLLKKVLSKGLEGYLACREL 213
Query: 257 LEVTGVIPKPWIEKLLK--------VDSFQVLEKYIEDLILEAYSATQLFDQFHDIVMLA 308
LE + L D+F ++++ I+ + + + + L
Sbjct: 214 LERFSKVESKEFFALFDQVTNTITGKDAFLLIQRLTR--IILHENTWESVEDQKSVSFLD 271
Query: 309 SSLSDKQKALFKALETL 325
S L K L L +
Sbjct: 272 SILRVKIANLNNKLTLM 288
>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1;
winged-helix domain, helix-turn-helix, AAA+ ATPase
domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A
{Sulfolobus solfataricus}
Length = 386
Score = 51.6 bits (123), Expect = 2e-07
Identities = 42/296 (14%), Positives = 94/296 (31%), Gaps = 32/296 (10%)
Query: 49 EQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQLFGDMYRE-RILELNA--- 104
+ +++ S+L + YG GTGKT+ + +L + + + +N
Sbjct: 28 QIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYINTRQI 87
Query: 105 -SDDRGIQVI----RDKVKTFAQQTASGFNQDGKPCPPFK---IVILDEADSM-THAAQA 155
+ R + + KV A + + K + +++LDE D+
Sbjct: 88 DTPYRVLADLLESLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAFVKKYNDD 147
Query: 156 ALRR--TMEKETKSTRFCLIC-----NYVSCIIQPLTSRCSKFR--FKPLAENTMLTRLQ 206
L + + E ++ I +V + + S S+ F P + L
Sbjct: 148 ILYKLSRINSEVNKSKISFIGITNDVKFVDLLDPRVKSSLSEEEIIFPPYNAEELEDILT 207
Query: 207 YICEQ--ESVMCDFKALETL---VETSGGDMRRAITCLQSCARL---KGGEGIVNEDVLE 258
+ + + ++ GD RRA+ L+ + + E V
Sbjct: 208 KRAQMAFKPGVLPDNVIKLCAALAAREHGDARRALDLLRVSGEIAERMKDTKVKEEYVYM 267
Query: 259 VTGVIPKPWIEKLLKVDSFQVLEKYIEDLILEAYSATQLFDQFHDIVMLASSLSDK 314
I + + ++ F K + ++ S + + ++ K
Sbjct: 268 AKEEIERDRVRDIILTLPFH--SKLVLMAVVSISSEENVVSTTGAVYETYLNICKK 321
Score = 27.7 bits (61), Expect = 8.1
Identities = 23/156 (14%), Positives = 54/156 (34%), Gaps = 14/156 (8%)
Query: 285 EDLILEAYSATQLFDQFHDIVMLASSLSDKQKALFKALETLVETSGGDMRRAITCLQSCA 344
E++I Y+A +L D +A + K L GD RRA+ L+
Sbjct: 190 EEIIFPPYNAEELEDILTKRAQMAFKPGVLPDNVIKLCAALAAREHGDARRALDLLRVSG 249
Query: 345 RL---KGGEGIVNEDVLEVTGVIPNPWIEKLLKVDSFQVLEKYIEDLILEAY-------S 394
+ + E V I + ++ F K + ++ +
Sbjct: 250 EIAERMKDTKVKEEYVYMAKEEIERDRVRDIILTLPFH--SKLVLMAVVSISSEENVVST 307
Query: 395 ATQLFDQFHDI--VMSASSLSDKQKALILEKLAECN 428
+++ + +I + +++ ++ + I+ +L
Sbjct: 308 TGAVYETYLNICKKLGVEAVTQRRVSDIINELDMVG 343
>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide,
hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP:
a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*
Length = 324
Score = 47.6 bits (114), Expect = 4e-06
Identities = 22/53 (41%), Positives = 30/53 (56%), Gaps = 7/53 (13%)
Query: 40 RPKTIDDVIEQQEVVSVLKKCLSGAD-----LPHFLFYGPPGTGKT--STMIA 85
RPKT+D+ I Q+ + L+ L A L H L +GPPG GKT + +IA
Sbjct: 7 RPKTLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIA 59
>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase,
winged-helix domain, ATP hydrolysis, walker A, walker
B, sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga
maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A*
1in8_A* 1in7_A* 1j7k_A*
Length = 334
Score = 47.6 bits (114), Expect = 4e-06
Identities = 22/53 (41%), Positives = 28/53 (52%), Gaps = 7/53 (13%)
Query: 40 RPKTIDDVIEQQEVVSVLKKCLSGAD-----LPHFLFYGPPGTGKT--STMIA 85
RPK++D+ I Q+ V L L A L H L GPPG GKT + +IA
Sbjct: 20 RPKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIA 72
>2v1u_A Cell division control protein 6 homolog; DNA replication,
nucleotide-binding, replication, archaea; HET: ADP;
3.10A {Aeropyrum pernix}
Length = 387
Score = 47.5 bits (112), Expect = 5e-06
Identities = 40/248 (16%), Positives = 72/248 (29%), Gaps = 39/248 (15%)
Query: 49 EQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQLFGDMYRE----RILELNA 104
E + + VL L G + L YG GTGKT+ +L + + +NA
Sbjct: 27 ELRRLAEVLAPALRGEKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVNA 86
Query: 105 SDDRGIQVIRDK--------VKTFAQQTASGFNQDGKPCPPFK---IVILDEADSMTHAA 153
+ V + + K + I++LDE D +
Sbjct: 87 RHRETPYRVASAIAEAVGVRVPFTGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFLPKRP 146
Query: 154 QA-----ALRRTMEKETKSTRFCLIC-----NYVSCIIQPLTSRCSKFR--FKPLAENTM 201
+ R ++ L+ +V + + S + F P +
Sbjct: 147 GGQDLLYRITRINQELGDRVWVSLVGITNSLGFVENLEPRVKSSLGEVELVFPPYTAPQL 206
Query: 202 LT----RLQYICEQESVMCDFKALETL---VETSGGDMRRAITCLQSCARL---KGGEGI 251
R + + D + GD RRA+ L+ + + E +
Sbjct: 207 RDILETRAEEAFNPGVL--DPDVVPLCAALAAREHGDARRALDLLRVAGEIAERRREERV 264
Query: 252 VNEDVLEV 259
E V
Sbjct: 265 RREHVYSA 272
>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable
holliday junction DNA helicase; HET: ADP; 2.69A
{Campylobacter jejuni subsp}
Length = 338
Score = 46.8 bits (112), Expect = 8e-06
Identities = 18/53 (33%), Positives = 25/53 (47%), Gaps = 7/53 (13%)
Query: 40 RPKTIDDVIEQQEVVSVLKKCLSGAD-----LPHFLFYGPPGTGKT--STMIA 85
RP D I Q+ + L ++ A L H LF GP G GKT + +I+
Sbjct: 24 RPSNFDGYIGQESIKKNLNVFIAAAKKRNECLDHILFSGPAGLGKTTLANIIS 76
>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain,
PIN-tower interface, coupling hydrolysis to DNA
unwinding, ssDNA; 3.30A {Enterobacteria phage T4}
Length = 459
Score = 43.9 bits (103), Expect = 9e-05
Identities = 21/133 (15%), Positives = 40/133 (30%), Gaps = 20/133 (15%)
Query: 31 KPVPWVEKYRPKTIDDVIEQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQL 90
VP + + Q+ +++ K + H GP GTG T T+ +
Sbjct: 13 GLVPRGSHMTFDDLTE--GQKNAFNIVMKAIKEKK-HHVTINGPAGTGAT-TLTKFIIEA 68
Query: 91 FGDMYRERILELNASDDRGIQVIRDKVKTFAQ--------------QTASGFNQDGKPCP 136
I+ L A +++ A + ++
Sbjct: 69 LISTGETGII-LAAPTHAAKKILSKLSGKEASTIHSILKINPVTYEENVLFEQKEVPDLA 127
Query: 137 PFKIVILDEADSM 149
+++I DE SM
Sbjct: 128 KCRVLICDEV-SM 139
>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR
complex, HMR, HML, TELO AAA+ domain, structural,
nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}
Length = 318
Score = 41.0 bits (95), Expect = 5e-04
Identities = 12/143 (8%), Positives = 42/143 (29%), Gaps = 19/143 (13%)
Query: 49 EQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQL-----FGDMYRERILELN 103
+ + + L + F + K + +L ++ + ++
Sbjct: 28 DFTRIFLPIYDSLMSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHID 87
Query: 104 A----SDDRGIQVIRDKV-------KTFAQQTASGFNQDGKPCPPFKIVILDEADSMTHA 152
A D + I + + K ++++ +++
Sbjct: 88 ALELAGMDALYEKIWFAISKENLCGDISLEALNFYITNVPKAKKRKTLILIQNPENLLS- 146
Query: 153 AQAALRRTMEKET-KSTRFCLIC 174
+ L+ + + K+++ +IC
Sbjct: 147 -EKILQYFEKWISSKNSKLSIIC 168
>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding,
nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A
{Thermococcus onnurineus}
Length = 604
Score = 39.3 bits (92), Expect = 0.002
Identities = 18/46 (39%), Positives = 23/46 (50%), Gaps = 4/46 (8%)
Query: 37 EKYRPKTIDDVIEQQEVVSVLKKCLSGADLP-HFLFYGPPGTGKTS 81
+ K ID VI Q+ V V+K A+ H L G PGTGK+
Sbjct: 33 IEVPEKLIDQVIGQEHAVEVIKT---AANQKRHVLLIGEPGTGKSM 75
>1svm_A Large T antigen; AAA+ fold, viral protein; HET: ATP; 1.94A {Simian
virus 40} SCOP: c.37.1.20 PDB: 1svl_A* 1svo_A 1n25_A
2h1l_A
Length = 377
Score = 38.9 bits (90), Expect = 0.003
Identities = 33/159 (20%), Positives = 57/159 (35%), Gaps = 28/159 (17%)
Query: 53 VVSVLKKCLSGADLPH---FLFYGPPGTGKTSTMIAACHQLFGDMYRERILELNASDDRG 109
V LK + +P +LF GP +GKT+ A G + L +N DR
Sbjct: 155 VYDFLKCMVYN--IPKKRYWLFKGPIDSGKTTLAAALLELCGG-----KALNVNLPLDRL 207
Query: 110 ---IQVIRD-KVKTFAQQTASGFNQDGKPCPPFKIVILDEADSMTHAAQAALRRTMEKET 165
+ V D + F +G P ++ D++ +++ +EK+
Sbjct: 208 NFELGVAIDQFLVVFEDVKGTGGESRDLPSGQG----INNLDNLRDYLDGSVKVNLEKKH 263
Query: 166 KSTR------FCLICNYVSCIIQPLTSRCSK---FRFKP 195
+ R + N + + L +R K FR K
Sbjct: 264 LNKRTQIFPPGIVTMN-EYSVPKTLQARFVKQIDFRPKD 301
>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay,
zinc-finger, ATP-binding, metal-BIN UPF2, UPF1,
helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A
2iyk_A
Length = 800
Score = 38.8 bits (90), Expect = 0.003
Identities = 13/34 (38%), Positives = 15/34 (44%), Gaps = 1/34 (2%)
Query: 67 PHFLFYGPPGTGKTSTMIAACHQLFGDMYRERIL 100
P L GPPGTGKT T + L +L
Sbjct: 372 PLSLIQGPPGTGKTVTSATIVYHLA-RQGNGPVL 404
>2w58_A DNAI, primosome component (helicase loader); ATP-binding,
nucleotide-binding, hydrolase; HET: ADP; 2.50A
{Geobacillus kaustophilus HTA426}
Length = 202
Score = 37.4 bits (87), Expect = 0.004
Identities = 10/62 (16%), Positives = 21/62 (33%), Gaps = 8/62 (12%)
Query: 37 EKYRPKTIDDVIEQQE--------VVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACH 88
+ ++ DV + + + G + +G G GKT + A +
Sbjct: 17 REILRASLSDVDLNDDGRIKAIRFAERFVAEYEPGKKMKGLYLHGSFGVGKTYLLAAIAN 76
Query: 89 QL 90
+L
Sbjct: 77 EL 78
>2qgz_A Helicase loader, putative primosome component; structural genomics,
PSI-2, protein structure initiative; 2.40A
{Streptococcus pyogenes serotype M3}
Length = 308
Score = 37.1 bits (86), Expect = 0.008
Identities = 13/61 (21%), Positives = 22/61 (36%), Gaps = 7/61 (11%)
Query: 37 EKYRPKTIDDVI----EQQEVVSVLKKCLSGADLPH---FLFYGPPGTGKTSTMIAACHQ 89
+ YR + D+ + E S + + YG G GK+ + A H+
Sbjct: 116 KSYRHIHLSDIDVNNASRMEAFSAILDFVEQYPSAEQKGLYLYGDMGIGKSYLLAAMAHE 175
Query: 90 L 90
L
Sbjct: 176 L 176
>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding,
chromatin regulator, growth regulation, hydrolase,
nuclear protein, DNA recombination; HET: ADP; 2.2A
{Homo sapiens} PDB: 2xsz_A*
Length = 456
Score = 37.3 bits (86), Expect = 0.009
Identities = 12/56 (21%), Positives = 20/56 (35%), Gaps = 5/56 (8%)
Query: 40 RPKTIDDVIEQQEVVSVLKKCLSGADLP-----HFLFYGPPGTGKTSTMIAACHQL 90
+ ++ Q+ + L GPPGTGKT+ +A +L
Sbjct: 32 AKQAASGLVGQENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALAIAQEL 87
Score = 30.7 bits (69), Expect = 1.1
Identities = 28/163 (17%), Positives = 54/163 (33%), Gaps = 16/163 (9%)
Query: 113 IRDKVKTFAQQTASGFNQDGKPCPPFKIVILDEADSMTHAAQAALRRTMEKE-------- 164
I DK++ + + + G ++ +DE + L R +E
Sbjct: 271 ITDKLRGEINKVVNKYIDQGIAELVPGVLFVDEVHMLDIECFTYLHRALESSIAPIVIFA 330
Query: 165 TKSTRFCLI--CNYVSC--IIQPLTSRCSKFRFKPLAENTMLTRLQYICEQESVMCDFKA 220
+ + + S I L R R M ++ + E + +A
Sbjct: 331 SNRGNCVIRGTEDITSPHGIPLDLLDRVMIIRTMLYTPQEMKQIIKIRAQTEGINISEEA 390
Query: 221 LETLVET-SGGDMRRA---ITCLQSCARLKGGEGIVNEDVLEV 259
L L E + +R + +T A++ G + I E V E+
Sbjct: 391 LNHLGEIGTKTTLRYSVQLLTPANLLAKINGKDSIEKEHVEEI 433
>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase;
1.90A {Tomato mosaic virus}
Length = 446
Score = 37.1 bits (85), Expect = 0.010
Identities = 18/89 (20%), Positives = 28/89 (31%), Gaps = 7/89 (7%)
Query: 70 LFYGPPGTGKTSTMIAACHQLFGDMY----RERILELNASDDRGIQVIRDKVKTFAQQTA 125
L G PG GKT I + D+ R+ + + ++ K +
Sbjct: 165 LVDGVPGCGKT-KEILSRVNFEEDLILVPGRQAAEMIRRRANASGIIVATKDNVRTVDSF 223
Query: 126 SGFNQDGKPCPPFKIVILDEADSMTHAAQ 154
N FK + +DE M H
Sbjct: 224 -LMNYGKGARCQFKRLFIDEG-LMLHTGC 250
>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA
degradation, allosteric REGU; HET: ADP 1PE; 2.40A
{Saccharomyces cerevisiae}
Length = 802
Score = 37.2 bits (86), Expect = 0.012
Identities = 33/147 (22%), Positives = 54/147 (36%), Gaps = 23/147 (15%)
Query: 49 EQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQLFGDMYRERIL---ELNAS 105
Q V L P L GPPGTGKT T + L ++++RIL N +
Sbjct: 364 SQSNAV---SHVLQR---PLSLIQGPPGTGKTVTSATIVYHLS-KIHKDRILVCAPSNVA 416
Query: 106 DD--------RGIQVIRDKVKT-----FAQQTASGFNQDGKPCPPFKIVILDEADSMTHA 152
D G++V+R K+ + + N G+ +L D +
Sbjct: 417 VDHLAAKLRDLGLKVVRLTAKSREDVESSVSNLALHNLVGRGAKGELKNLLKLKDEVGEL 476
Query: 153 AQAALRRTMEKETKSTRFCLICNYVSC 179
+ + +R ++ K+ L V C
Sbjct: 477 SASDTKRFVKLVRKTEAEILNKADVVC 503
>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein,
calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides}
PDB: 3syk_A 3zuh_A*
Length = 309
Score = 36.6 bits (84), Expect = 0.012
Identities = 26/177 (14%), Positives = 56/177 (31%), Gaps = 29/177 (16%)
Query: 68 HFLFYGPPGTGKTST--MIAACHQLFGDMYRERILELNASDDRGIQVIRDKVKTFAQQTA 125
H F G PGTGKT+ +A G + + ++ + D ++ + A +T
Sbjct: 69 HMSFTGNPGTGKTTVALKMAGLLHRLGYVRKGHLVSVTRDD-----LVGQYIGHTAPKTK 123
Query: 126 SGFNQDGKPCPPFKIVILDEADSMTH---------AAQAALRRTMEKETKSTRFCLICNY 176
+ ++ +DEA + A L + ME + ++ Y
Sbjct: 124 EVLKRAMG-----GVLFIDEAYYLYRPDNERDYGQEAIEILLQVMENN-RDDLVVILAGY 177
Query: 177 VSCIIQPLTSR-------CSKFRFKPLAENTMLTRLQYICEQESVMCDFKALETLVE 226
+ S F ++ + ++ + ++ +A L
Sbjct: 178 ADRMENFFQSNPGFRSRIAHHIEFPDYSDEELFEIAGHMLDDQNYQMTPEAETALRA 234
>3ec2_A DNA replication protein DNAC; helicase loader, replication
initiation factor, ATP-binding, nucleotide-binding; HET:
DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*
Length = 180
Score = 35.4 bits (82), Expect = 0.018
Identities = 18/116 (15%), Positives = 39/116 (33%), Gaps = 16/116 (13%)
Query: 37 EKYRPKTIDDVI----EQQEVVSVLKKCLSGADLPH---FLFYGPPGTGKTSTMIAACHQ 89
++Y +D Q + ++ + + F G PG GKT +A
Sbjct: 2 KRYWNANLDTYHPKNVSQNRALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHLAVATLKA 61
Query: 90 LFGDMYRERILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPPFKIVILDE 145
++ + R + D +I + + F + P +++LD+
Sbjct: 62 IY-EKKGIRGYFFDTKD-----LIFRLKHLMDEGKDTKFLKTVLNSP---VLVLDD 108
>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop,
rossman fold, AAA+, photosynthesis, metal transport;
2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB:
2x31_G
Length = 350
Score = 36.3 bits (84), Expect = 0.018
Identities = 12/61 (19%), Positives = 23/61 (37%), Gaps = 1/61 (1%)
Query: 68 HFLFYGPPGTGKTSTMIAACHQLFGDMYRERILELNASDDRGIQVIRDKVKTFAQQTASG 127
L +G GTGK ST + A L ++ +++ + I + T + +
Sbjct: 47 GVLVFGDRGTGK-STAVRALAALLPEIEAVEGCPVSSPNVEMIPDWATVLSTNVIRKPTP 105
Query: 128 F 128
Sbjct: 106 V 106
>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold,
hydro; HET: ADP; 2.91A {Escherichia coli}
Length = 500
Score = 36.3 bits (84), Expect = 0.019
Identities = 22/124 (17%), Positives = 35/124 (28%), Gaps = 21/124 (16%)
Query: 47 VIEQQEVVSVLKKC-LSGADLPHFLFYGPPGTGKTSTMIAACHQLFGDMYRERIL---EL 102
+ E+ + + LSG GPPG K+ + F + L
Sbjct: 24 LYERSHAIRLCLLAALSGE---SVFLLGPPGIAKS-LIARRLKFAFQNARAFEYLMTRFS 79
Query: 103 NASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPPF-KIVILDE---ADSMTHAAQAALR 158
+ G I+ + + P +IV LDE A A L
Sbjct: 80 TPEEVFGPLSIQALKDEGR------YERLTSGYLPEAEIVFLDEIWKAGP---AILNTLL 130
Query: 159 RTME 162
+
Sbjct: 131 TAIN 134
>2r2a_A Uncharacterized protein; zonular occludens toxin, structural
genomics, APC84050.2, PS protein structure initiative;
HET: MSE; 1.82A {Neisseria meningitidis MC58}
Length = 199
Score = 35.1 bits (80), Expect = 0.023
Identities = 19/98 (19%), Positives = 31/98 (31%), Gaps = 15/98 (15%)
Query: 62 SGADLPHFLFYGPPGTGKTSTMIA---------ACHQLFGDMYRERILELN----ASDDR 108
S A L G PG+GKT M++ I L +
Sbjct: 1 SNAMAEICLITGTPGSGKTLKMVSMMANDEMFKPDENGIRRKVFTNIKGLKIPHTYIETD 60
Query: 109 GIQVIRDKVKTFAQQTASGFNQDGKPCPPFKIVILDEA 146
++ + + + + + P IVI+DEA
Sbjct: 61 AKKLPKSTDEQLSAHDMYEWIKK--PENIGSIVIVDEA 96
>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase,
ATP-binding cassette, ATP-binding, endosome, MEM
nucleotide-binding; 2.70A {Saccharomyces cerevisiae}
PDB: 3eih_A* 2rko_A 3mhv_C
Length = 322
Score = 35.0 bits (81), Expect = 0.035
Identities = 10/17 (58%), Positives = 12/17 (70%), Gaps = 2/17 (11%)
Query: 69 FLFYGPPGTGKTSTMIA 85
L YGPPGTGK + +A
Sbjct: 54 ILLYGPPGTGK--SYLA 68
>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo
sapiens}
Length = 322
Score = 35.0 bits (81), Expect = 0.038
Identities = 9/17 (52%), Positives = 12/17 (70%), Gaps = 2/17 (11%)
Query: 69 FLFYGPPGTGKTSTMIA 85
L +GPPGTGK + +A
Sbjct: 48 ILLFGPPGTGK--SYLA 62
>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo
sapiens}
Length = 389
Score = 35.2 bits (81), Expect = 0.044
Identities = 10/18 (55%), Positives = 12/18 (66%), Gaps = 2/18 (11%)
Query: 70 LFYGPPGTGKTSTMIAAC 87
L +GPPG GK TM+A
Sbjct: 152 LLFGPPGNGK--TMLAKA 167
>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD,
hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A*
2gk7_A 2xzo_A* 2xzp_A
Length = 624
Score = 35.2 bits (81), Expect = 0.046
Identities = 13/34 (38%), Positives = 15/34 (44%), Gaps = 1/34 (2%)
Query: 67 PHFLFYGPPGTGKTSTMIAACHQLFGDMYRERIL 100
P L GPPGTGKT T + L +L
Sbjct: 196 PLSLIQGPPGTGKTVTSATIVYHLA-RQGNGPVL 228
>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD,
CDC48, ATP-binding, lipid-binding, nucle binding,
nucleus, phosphoprotein, transport; HET: ADP; 3.00A
{Mus musculus}
Length = 301
Score = 34.5 bits (80), Expect = 0.047
Identities = 11/17 (64%), Positives = 13/17 (76%), Gaps = 2/17 (11%)
Query: 69 FLFYGPPGTGKTSTMIA 85
LFYGPPG GK T++A
Sbjct: 52 VLFYGPPGCGK--TLLA 66
>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding,
nucleotide-binding, hydrolase; 2.70A {Drosophila
melanogaster}
Length = 297
Score = 34.6 bits (80), Expect = 0.050
Identities = 9/18 (50%), Positives = 12/18 (66%), Gaps = 2/18 (11%)
Query: 70 LFYGPPGTGKTSTMIAAC 87
L +GPPG GK T++A
Sbjct: 58 LLFGPPGNGK--TLLARA 73
>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic;
photosynthesis, rubisco activase, AAA+ protein; 2.95A
{Nicotiana tabacum} PDB: 3zw6_A
Length = 293
Score = 34.4 bits (79), Expect = 0.054
Identities = 13/82 (15%), Positives = 30/82 (36%), Gaps = 14/82 (17%)
Query: 70 LFYGPPGTGKTSTMIAACHQL---FGDMYRERILELNASDDRGIQVIRDKVKTFAQQTAS 126
+G G GK+ ++ M + NA + ++IR + + A+
Sbjct: 40 GIWGGKGQGKSFQCELVFRKMGINPIMMSAGELESGNAGE--PAKLIRQ---RY--REAA 92
Query: 127 GFNQDGKPCPPFKIVILDEADS 148
+ G C + +++ D+
Sbjct: 93 EIIRKGNMC----CLFINDLDA 110
>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A
{Homo sapiens}
Length = 274
Score = 34.5 bits (80), Expect = 0.054
Identities = 9/16 (56%), Positives = 11/16 (68%), Gaps = 2/16 (12%)
Query: 70 LFYGPPGTGKTSTMIA 85
L GPPG GK T++A
Sbjct: 48 LLAGPPGCGK--TLLA 61
>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural
genomics consortium, ATP- hydrolase, magnesium,
metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo
sapiens}
Length = 357
Score = 34.4 bits (79), Expect = 0.061
Identities = 11/18 (61%), Positives = 13/18 (72%), Gaps = 2/18 (11%)
Query: 70 LFYGPPGTGKTSTMIAAC 87
L +GPPGTGK T+I C
Sbjct: 121 LLFGPPGTGK--TLIGKC 136
>1ypw_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD,
CDC48; HET: ADP ANP; 3.50A {Mus musculus} PDB: 1oz4_A*
1yq0_A* 1yqi_A* 1r7r_A* 3cf2_A* 3cf1_A* 3cf3_A*
Length = 806
Score = 34.8 bits (80), Expect = 0.068
Identities = 22/95 (23%), Positives = 34/95 (35%), Gaps = 25/95 (26%)
Query: 63 GADLPH-FLFYGPPGTGKTSTMIAACHQLFGDMYRERILELNASD------DRGIQVIRD 115
G P L YGPPGTGKT A ++ +N + +R
Sbjct: 234 GVKPPRGILLYGPPGTGKTLIARAVANETGA-----FFFLINGPEIMSKLAGESESNLRK 288
Query: 116 KVKTFAQQTASGFNQDGKPCPPFKIVILDEADSMT 150
+ A++ A P I+ +DE D++
Sbjct: 289 AFEE-AEKNA--------PA----IIFIDELDAIA 310
Score = 34.0 bits (78), Expect = 0.10
Identities = 11/17 (64%), Positives = 13/17 (76%), Gaps = 2/17 (11%)
Query: 69 FLFYGPPGTGKTSTMIA 85
LFYGPPG GK T++A
Sbjct: 514 VLFYGPPGCGK--TLLA 528
>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase;
3.20A {Thermus thermophilus} SCOP: c.37.1.20
Length = 278
Score = 33.9 bits (78), Expect = 0.090
Identities = 22/67 (32%), Positives = 28/67 (41%), Gaps = 15/67 (22%)
Query: 26 GKTRNKPVPWVEKYRPKTIDDVI-------EQQEVVSVLKKCLS----GADLPH-FLFYG 73
K+R + + K T DV E +E+V LK GA +P L G
Sbjct: 24 TKSRARVLTEAPKV---TFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVG 80
Query: 74 PPGTGKT 80
PPG GKT
Sbjct: 81 PPGVGKT 87
>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding,
nucleotide-binding, HY; HET: ADP; 3.11A
{Methanocaldococcus jannaschii}
Length = 285
Score = 33.4 bits (77), Expect = 0.14
Identities = 11/16 (68%), Positives = 13/16 (81%), Gaps = 2/16 (12%)
Query: 70 LFYGPPGTGKTSTMIA 85
L YGPPGTGK T++A
Sbjct: 55 LLYGPPGTGK--TLLA 68
>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase;
NMR {Homo sapiens} SCOP: c.37.1.11
Length = 189
Score = 32.8 bits (74), Expect = 0.14
Identities = 20/112 (17%), Positives = 33/112 (29%), Gaps = 9/112 (8%)
Query: 68 HFLFYGPPGTGKTSTMIAACHQL------FGDMYRERILELNASDDRGIQVIRDKVKTFA 121
H GPPG GKT+ + A L Y E + + + + +
Sbjct: 3 HVFLTGPPGVGKTTLIHKASEVLKSSGVPVDGFYTEEVRQGGRRIGFDVVTLSGTRGPLS 62
Query: 122 QQTASGFNQDGKPCPPFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLI 173
+ + +V L + + A LR R C+I
Sbjct: 63 RVGLEPPPGKRECRVGQYVVDLTSFEQL---ALPVLRNADCSSGPGQRVCVI 111
>1e9r_A Conjugal transfer protein TRWB; coupling protein, bacterial
conjugation, F1-ATPase-like quaternary structure, ring
helicases; 2.4A {Escherichia coli} SCOP: c.37.1.11 PDB:
1e9s_A 1gki_A* 1gl7_A* 1gl6_A*
Length = 437
Score = 33.3 bits (76), Expect = 0.15
Identities = 12/58 (20%), Positives = 18/58 (31%), Gaps = 16/58 (27%)
Query: 68 HFLFYGPPGTGKTST---MIAACHQ-------------LFGDMYRERILELNASDDRG 109
H L G GTGK+ + + R++ + LN D R
Sbjct: 55 HLLVNGATGTGKSVLLRELAYTGLLRGDRMVIVDPNGDMLSKFGRDKDIILNPYDQRT 112
>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding,
cell CELL division, hydrolase, membrane, metal-binding;
3.30A {Helicobacter pylori} PDB: 2r65_A*
Length = 268
Score = 32.6 bits (75), Expect = 0.20
Identities = 19/58 (32%), Positives = 26/58 (44%), Gaps = 13/58 (22%)
Query: 36 VEKYRPK-TIDDVI-------EQQEVVSVLK---KCLS-GADLPH-FLFYGPPGTGKT 80
+ +P D+ E E+V LK + + GA +P L GPPGTGKT
Sbjct: 1 INAEKPNVRFKDMAGNEEAKEEVVEIVDFLKYPERYANLGAKIPKGVLLVGPPGTGKT 58
>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET:
ADP; 3.90A {Thermus thermophilus}
Length = 499
Score = 33.0 bits (76), Expect = 0.20
Identities = 22/67 (32%), Positives = 29/67 (43%), Gaps = 15/67 (22%)
Query: 26 GKTRNKPVPWVEKYRPKTIDDVI-------EQQEVVSVLK---KCLS-GADLPH-FLFYG 73
K+R + + K T DV E +E+V LK + GA +P L G
Sbjct: 15 TKSRARVLTEAPKV---TFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVG 71
Query: 74 PPGTGKT 80
PPG GKT
Sbjct: 72 PPGVGKT 78
>2ce7_A Cell division protein FTSH; metalloprotease; HET: ADP; 2.44A
{Thermotoga maritima} SCOP: a.269.1.1 c.37.1.20 PDB:
2cea_A* 3kds_E*
Length = 476
Score = 32.9 bits (76), Expect = 0.23
Identities = 22/57 (38%), Positives = 25/57 (43%), Gaps = 13/57 (22%)
Query: 37 EKYRPK-TIDDVI-------EQQEVVSVLK---KCLS-GADLPH-FLFYGPPGTGKT 80
+ T DV E +EVV LK K GA +P L GPPGTGKT
Sbjct: 7 PSGNKRVTFKDVGGAEEAIEELKEVVEFLKDPSKFNRIGARMPKGILLVGPPGTGKT 63
>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase;
2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB:
1iy0_A* 1iy1_A*
Length = 254
Score = 32.3 bits (74), Expect = 0.26
Identities = 16/37 (43%), Positives = 19/37 (51%), Gaps = 5/37 (13%)
Query: 49 EQQEVVSVLKKCLS----GADLPH-FLFYGPPGTGKT 80
E +E+V LK GA +P L GPPG GKT
Sbjct: 27 ELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKT 63
>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A
{Escherichia coli} SCOP: c.37.1.20
Length = 257
Score = 31.9 bits (73), Expect = 0.31
Identities = 15/37 (40%), Positives = 19/37 (51%), Gaps = 5/37 (13%)
Query: 49 EQQEVVSVLKKCLS----GADLPH-FLFYGPPGTGKT 80
E E+V L++ G +P L GPPGTGKT
Sbjct: 23 EVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKT 59
>2v9p_A Replication protein E1; AAA+ molecular motor, DNA replication, DNA
translocation, nucleotide-binding, DNA-binding; 3.00A
{Bovine papillomavirus type 1} PDB: 2gxa_A*
Length = 305
Score = 32.2 bits (73), Expect = 0.33
Identities = 16/46 (34%), Positives = 21/46 (45%), Gaps = 1/46 (2%)
Query: 48 IEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTSTMIAACHQLFG 92
IE ++ LK L G + F GPP TGK+ + H L G
Sbjct: 107 IELITFINALKLWLKGIPKKNCLAFIGPPNTGKSMLCNSLIHFLGG 152
>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain,
ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus}
SCOP: c.37.1.20 PDB: 1nsf_A*
Length = 272
Score = 32.0 bits (73), Expect = 0.34
Identities = 9/17 (52%), Positives = 11/17 (64%), Gaps = 2/17 (11%)
Query: 70 LFYGPPGTGKTSTMIAA 86
L GPP +GK T +AA
Sbjct: 68 LLEGPPHSGK--TALAA 82
>2kjq_A DNAA-related protein; solution structure, NESG, structural
genomics, PSI-2, protei structure initiative; NMR
{Neisseria meningitidis serogroup B}
Length = 149
Score = 31.1 bits (71), Expect = 0.35
Identities = 11/42 (26%), Positives = 18/42 (42%), Gaps = 4/42 (9%)
Query: 49 EQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQL 90
E E+V VL+ ++ +G G GK+ + A Q
Sbjct: 23 ENAELVYVLR---HKHGQFIYV-WGEEGAGKSHLLQAWVAQA 60
>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics,
structural G consortium, SGC, ATP-binding,
nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo
sapiens}
Length = 262
Score = 31.8 bits (73), Expect = 0.37
Identities = 16/37 (43%), Positives = 18/37 (48%), Gaps = 5/37 (13%)
Query: 49 EQQEVVSVLKKCLS----GADLPH-FLFYGPPGTGKT 80
E +E V LK GA +P L GPPG GKT
Sbjct: 17 EVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKT 53
>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA
replication initiation, DNA BIND protein, AAA+ ATPase;
HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11
c.37.1.20 PDB: 1w5t_A*
Length = 412
Score = 32.2 bits (72), Expect = 0.39
Identities = 41/279 (14%), Positives = 73/279 (26%), Gaps = 66/279 (23%)
Query: 39 YRPKTI---DDVIEQQEVVSVLKKCLSGADLP-----HFLFYGPPGTGKTSTMIAACHQL 90
Y P + E + + + L + G G GKT+ ++
Sbjct: 19 YIPPELRVRRG--EAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRV 76
Query: 91 FGDMYRERILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPPFK----------- 139
+ V + Q G P
Sbjct: 77 ------SEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALV 130
Query: 140 ----------IVILDEADSMTHAAQAA---------LRRTMEKETKSTRFCLIC-----N 175
+VILDE SM + + A + + R +
Sbjct: 131 DNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVR 190
Query: 176 YVSCIIQPLTSRCSKFRFKPLAENTMLTRLQYICEQ------ESVMCDFKALETLVETSG 229
+S + + + S+ FK L I EQ + + + LE + + G
Sbjct: 191 ALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYG 250
Query: 230 ------GDMRRAITCLQSCARL---KGGEGIVNEDVLEV 259
G RRAI L+ + G + + + V +
Sbjct: 251 EDKGGDGSARRAIVALKMACEMAEAMGRDSLSEDLVRKA 289
>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding
mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli}
SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*
Length = 758
Score = 32.2 bits (74), Expect = 0.40
Identities = 16/59 (27%), Positives = 24/59 (40%), Gaps = 9/59 (15%)
Query: 47 VIEQQEVVSVLKKCL----SGADLPH-----FLFYGPPGTGKTSTMIAACHQLFGDMYR 96
V Q + + L + + +G H FLF GP G GKT + L ++ R
Sbjct: 460 VFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALGIELLR 518
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 32.3 bits (73), Expect = 0.41
Identities = 26/155 (16%), Positives = 40/155 (25%), Gaps = 57/155 (36%)
Query: 4 FLRTGKLGKDAP--SS-------------SKTSVSTSGKTRNKPVPWVEKYRPKTIDDV- 47
FL +P S K +VS + K PV Y D+
Sbjct: 420 FLPVA-----SPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPV-----YDTFDGSDLR 469
Query: 48 IEQQEVVSVLKKCL----------SGADLPHFLFYGPPGTGKTSTMIAACHQLFGDMYRE 97
+ + + C+ + H L +GP G +
Sbjct: 470 VLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTH------------ 517
Query: 98 RILELNASDDRGIQVIRDKVKTFAQQTAS--GFNQ 130
R + G++VI T GF Q
Sbjct: 518 RNKDG-----TGVRVI--VAGTLDINPDDDYGFKQ 545
Score = 31.9 bits (72), Expect = 0.47
Identities = 35/202 (17%), Positives = 63/202 (31%), Gaps = 56/202 (27%)
Query: 288 ILEAYSATQLFDQFHDIVMLASSLSDKQKALFKAL-ETLV----ETSGGDMRR------A 336
I E YSA +F+ D K + +FK + E + G + A
Sbjct: 1684 IRENYSA-MIFETIVDG-------KLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPA 1735
Query: 337 ITCLQSCA---RLKGGEGIVNEDVL-------E------VTGVIPNPWIEKLLKVDSFQV 380
+T L A LK +G++ D E + V+ IE L++V V
Sbjct: 1736 LT-LMEKAAFEDLKS-KGLIPADATFAGHSLGEYAALASLADVMS---IESLVEV----V 1786
Query: 381 LE--KYIEDLILEAYSATQLFDQFHDIVMSASSLSDKQKALILEKLAECNARLQDGASEY 438
++ + + M A + + E L R+
Sbjct: 1787 FYRGMTMQVAVPRDELGRSNYG------MIAINPGRVAASFSQEALQYVVERVGKRTGWL 1840
Query: 439 IQI----LDLGSIVIKANKTAV 456
++I ++ V + A+
Sbjct: 1841 VEIVNYNVENQQYVAAGDLRAL 1862
Score = 31.9 bits (72), Expect = 0.59
Identities = 12/59 (20%), Positives = 30/59 (50%), Gaps = 7/59 (11%)
Query: 393 YSATQLFDQFHDIVMSAS---SLSDKQKA---LILEKLAECNARLQDG-ASEYIQILDL 444
+ A+QL +QF+ I+ + + D+ L+ + L ++ ++ ++ Q+L+L
Sbjct: 28 FIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNL 86
Score = 30.4 bits (68), Expect = 1.8
Identities = 32/170 (18%), Positives = 61/170 (35%), Gaps = 47/170 (27%)
Query: 292 YSATQLFDQFHDIVMLAS---SLSDKQK------ALFKA-LETLVETSGGDMRRAI--TC 339
+ A+QL +QF+ I+ + + D+ F + +LVE S + C
Sbjct: 28 FIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLC 87
Query: 340 LQSCAR--LKGGEGIVNEDVLEVTGVIPNPWIEKLLKVDSFQVLEKYIEDLILEAYSATQ 397
L L+G D+ + + L+K ++++ Y +A
Sbjct: 88 LTEFENCYLEG------NDIHALAAKLLQENDTTLVKT--KELIKNY--------ITARI 131
Query: 398 LFDQFHDIVMSASSLSDKQKALILEKLAECNARL------QDGASE-YIQ 440
+ + D S S+L + E NA+L Q G ++ Y +
Sbjct: 132 MAKRPFDK-KSNSAL--------FRAVGEGNAQLVAIFGGQ-GNTDDYFE 171
>1nlf_A Regulatory protein REPA; replicative DNA helicase structural
changes, replication; 1.95A {Escherichia coli} SCOP:
c.37.1.11 PDB: 1g8y_A 1olo_A
Length = 279
Score = 31.6 bits (71), Expect = 0.43
Identities = 14/112 (12%), Positives = 31/112 (27%), Gaps = 14/112 (12%)
Query: 70 LFYGPPGTGKTSTM------IAACHQLFGDMYRE--RILELNASDDRGIQVIRDKVKTFA 121
P G GK+ IA L ++ L A D R
Sbjct: 34 ALVSPGGAGKSMLALQLAAQIAGGPDLLEVGELPTGPVIYLPAEDPPTAIHHR------L 87
Query: 122 QQTASGFNQDGKPCPPFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLI 173
+ + + + ++I S+ + +++ + R ++
Sbjct: 88 HALGAHLSAEERQAVADGLLIQPLIGSLPNIMAPEWFDGLKRAAEGRRLMVL 139
>2r7r_A RNA-dependent RNA polymerase; viral protein, RNA-dependent RNA
polymerase, single subunit polymerase fold, fingers,
PALM, thumb; 2.60A {Simian rotavirus} PDB: 2r7q_A 2r7s_A
2r7t_A 2r7u_A 2r7v_A 2r7w_A* 2r7x_A* 2r7o_A
Length = 1095
Score = 32.1 bits (72), Expect = 0.47
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 270 KLLKVDSFQVLEKYIEDLILEAYSATQLFD 299
K+ D +++LE Y+ +L+ Y QLFD
Sbjct: 979 KIYSRDKYRILESYVYNLLSINYGCYQLFD 1008
Score = 32.1 bits (72), Expect = 0.47
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 371 KLLKVDSFQVLEKYIEDLILEAYSATQLFD 400
K+ D +++LE Y+ +L+ Y QLFD
Sbjct: 979 KIYSRDKYRILESYVYNLLSINYGCYQLFD 1008
>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein;
HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A*
1e32_A* 1s3s_A* 2pjh_B
Length = 489
Score = 31.7 bits (72), Expect = 0.49
Identities = 10/12 (83%), Positives = 10/12 (83%)
Query: 69 FLFYGPPGTGKT 80
L YGPPGTGKT
Sbjct: 241 ILLYGPPGTGKT 252
>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor,
microtubles, motor protein; HET: ADP SPM; 2.81A
{Dictyostelium discoideum} PDB: 3vkh_A* 3vkh_C*
Length = 3245
Score = 31.8 bits (72), Expect = 0.54
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 68 HFLFYGPPGTGKTSTMIAACHQL 90
+ GPPG+GKT T+ +
Sbjct: 1306 PLILCGPPGSGKTMTLTSTLRAF 1328
>3m6a_A ATP-dependent protease LA 1; alpha, beta, ATP-binding, hydrolase,
nucleotide-binding, Pro serine protease, stress
response; HET: ADP; 3.40A {Bacillus subtilis} PDB:
1x37_A
Length = 543
Score = 31.3 bits (72), Expect = 0.72
Identities = 8/11 (72%), Positives = 8/11 (72%)
Query: 71 FYGPPGTGKTS 81
GPPG GKTS
Sbjct: 113 LAGPPGVGKTS 123
>1ye8_A Protein THEP1, hypothetical UPF0334 kinase-like protein AQ_1292;
mixed alpha-beta protein, rossman fold, signaling
protein, transferase; 1.40A {Aquifex aeolicus} SCOP:
c.37.1.11
Length = 178
Score = 30.4 bits (68), Expect = 0.82
Identities = 22/163 (13%), Positives = 49/163 (30%), Gaps = 31/163 (19%)
Query: 68 HFLFYGPPGTGKTSTMIAACHQL---FGDMYRERILELNASDDRGIQV--IRDKVKTFAQ 122
+ G PG GKT+ + +L + E + + G ++ K K F+
Sbjct: 2 KIIITGEPGVGKTTLVKKIVERLGKRAIGFWTEEVRDPETKKRTGFRIITTEGKKKIFSS 61
Query: 123 QTASGFNQDGK-----------------------PCPPFKIVILDE---ADSMTHAAQAA 156
+ + G K++I+DE + + +
Sbjct: 62 KFFTSKKLVGSYGVNVQYFEELAIPILERAYREAKKDRRKVIIIDEIGKMELFSKKFRDL 121
Query: 157 LRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLAEN 199
+R+ M + + V +++ + + EN
Sbjct: 122 VRQIMHDPNVNVVATIPIRDVHPLVKEIRRLPGAVLIELTPEN 164
>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase,
nucleotide excision repair,; 2.20A {Thermoplasma
acidophilum} PDB: 2vsf_A*
Length = 620
Score = 31.2 bits (71), Expect = 0.84
Identities = 15/121 (12%), Positives = 43/121 (35%), Gaps = 5/121 (4%)
Query: 284 IEDLILEAYSATQLFDQFHDIVMLASSLSDKQKALFKALETLVETSGGDMRRAITCLQSC 343
+ D+ S + + A + D + + + L+E +R A+ + S
Sbjct: 216 LPDIGRSIGSFRISVESLNRADREAQAYGDPELSQKIHVSDLIEM----IRSALQSMVSE 271
Query: 344 ARLKGGEGIVNEDVLEVTGVIPNPWIEKLLKVDSF-QVLEKYIEDLILEAYSATQLFDQF 402
KG I ++ +E ++ ++ + ++ + +Y+E+ + +
Sbjct: 272 RCGKGDVRIRFQEFMEYMRIMNKRSEREIRSLLNYLYLFGEYVENEKEKVGKVPFSYCSS 331
Query: 403 H 403
Sbjct: 332 V 332
>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+
protein; 2.10A {Human papillomavirus type 18} SCOP:
c.37.1.20
Length = 212
Score = 30.2 bits (68), Expect = 0.97
Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 1/46 (2%)
Query: 48 IEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTSTMIAACHQLFG 92
IE + LK L G + +F GP TGK+ ++ H + G
Sbjct: 39 IEFITFLGALKSFLKGTPKKNCLVFCGPANTGKSYFGMSFIHFIQG 84
>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and
beta protein; HET: GSP; 1.90A {Methanocaldococcus
jannaschii} PDB: 2hf8_A*
Length = 226
Score = 30.3 bits (69), Expect = 1.1
Identities = 6/22 (27%), Positives = 8/22 (36%)
Query: 73 GPPGTGKTSTMIAACHQLFGDM 94
G G+GKT + L
Sbjct: 45 GAIGSGKTLLIEKLIDNLKDKY 66
>2wbe_C Bipolar kinesin KRP-130; EG5, KLP61F, tubulin, mitosis,
GTP-binding, motor protein, cell division, cell cycle,
microtubule, ATP-binding; HET: GTP ANP GDP TA1; 9.40A
{Drosophila melanogaster}
Length = 373
Score = 30.7 bits (70), Expect = 1.1
Identities = 14/39 (35%), Positives = 16/39 (41%), Gaps = 7/39 (17%)
Query: 72 YGPPGTGKTSTMIAACHQLFGDMYRERILELNASDDRGI 110
YG GTGKT TM+ G+ E D GI
Sbjct: 107 YGQTGTGKTHTMV-------GNETAELKSSWEDDSDIGI 138
>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain
cytoplasmic; motor protein, AAA+ protein, ASCE protein,
P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma
japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A
Length = 2695
Score = 31.0 bits (70), Expect = 1.1
Identities = 16/94 (17%), Positives = 31/94 (32%), Gaps = 14/94 (14%)
Query: 1 MEAFLRTGKLGKDAPSSSKTSVSTSGKTRNKPVPWVEKYRPKTID--DVIEQQEVVS--- 55
+ T G D+ S S + + + +++ +V+ V+
Sbjct: 1194 FIQTINT-YFGHDSQELSDYSTIVIANDKLSFSSFCSEIPSVSLEAHEVMRPDIVIPTID 1252
Query: 56 ------VLKKCLSGADLPHFLFYGPPGTGKTSTM 83
+ L+ + GPPG+GKT M
Sbjct: 1253 TIKHEKIFYDLLNSKR--GIILCGPPGSGKTMIM 1284
>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding
protein; 2.30A {Archaeoglobus fulgidus}
Length = 221
Score = 29.9 bits (68), Expect = 1.2
Identities = 5/22 (22%), Positives = 11/22 (50%)
Query: 73 GPPGTGKTSTMIAACHQLFGDM 94
G G+GKT + ++ ++
Sbjct: 37 GAIGSGKTLLIERTIERIGNEV 58
>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA
helicase, acetyltransferase, GCN5 acetyltransferase;
HET: ACO ADP; 2.35A {Escherichia coli K12}
Length = 671
Score = 30.8 bits (69), Expect = 1.2
Identities = 18/127 (14%), Positives = 36/127 (28%), Gaps = 16/127 (12%)
Query: 25 SGKTRNKPVPWVEKYRPKTIDDVIEQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMI 84
+ + P T EQQ+++ L G G GK++
Sbjct: 155 NQPFSLAHFTPRTDWYPATGAPQPEQQQLLKQLMTMPPGV----AAVTAARGRGKSALAG 210
Query: 85 AACHQLFGDMYRERILELNASDDRGIQVIRDKVKTFAQQTAS--GFNQDGKPCPPFKIVI 142
++ G + A V+ FA + + ++
Sbjct: 211 QLISRIAGRAI------VTAPAKASTDVLAQ----FAGEKFRFIAPDALLASDEQADWLV 260
Query: 143 LDEADSM 149
+DEA ++
Sbjct: 261 VDEAAAI 267
>2bdt_A BH3686; alpha-beta protein, structural genomics, PSI, protein
struct initiative, northeast structural genomics
consortium, NESG, function; 2.40A {Bacillus halodurans}
SCOP: c.37.1.25
Length = 189
Score = 29.9 bits (67), Expect = 1.3
Identities = 11/58 (18%), Positives = 22/58 (37%), Gaps = 9/58 (15%)
Query: 69 FLFYGPPGTGKTST--MIAA----CHQLFGDMYRERI---LELNASDDRGIQVIRDKV 117
++ GP G GK++T +AA + GD+ + D + + +
Sbjct: 5 YIITGPAGVGKSTTCKRLAAQLDNSAYIEGDIINHMVVGGYRPPWESDELLALTWKNI 62
>3euj_A Chromosome partition protein MUKB, linker; MUKB, MUKE, chromosome
condensation, condensin, SMC, N subunit, ABC-type
ATPase, WHD, ATP-binding; HET: AGS; 3.10A {Haemophilus
ducreyi} PDB: 3euk_A*
Length = 483
Score = 30.3 bits (67), Expect = 1.4
Identities = 7/44 (15%), Positives = 19/44 (43%), Gaps = 3/44 (6%)
Query: 120 FAQQTASGFNQDGKPCPPFKIVILDEADSMTHAAQAALRRTMEK 163
+ +++ +D P +++ LD+A + + L E+
Sbjct: 400 WEEESRRMRAKDI---LPCRLLFLDQAARLDAMSINTLFELCER 440
>3bos_A Putative DNA replication factor; P-loop containing nucleoside
triphosphate hydrolases, struct genomics; HET: MSE CDP;
1.75A {Shewanella amazonensis} PDB: 3sc3_A
Length = 242
Score = 29.5 bits (67), Expect = 1.8
Identities = 7/23 (30%), Positives = 14/23 (60%), Gaps = 1/23 (4%)
Query: 69 FLF-YGPPGTGKTSTMIAACHQL 90
++ +GP +G+T + AAC +
Sbjct: 54 AIYLWGPVKSGRTHLIHAACARA 76
>3auy_A DNA double-strand break repair RAD50 ATPase; DNA repair, ABC
transporter ATPase domain-like; HET: DNA ADP; 2.70A
{Methanocaldococcus jannaschii} PDB: 3aux_A* 3av0_B*
Length = 371
Score = 29.4 bits (66), Expect = 2.3
Identities = 25/179 (13%), Positives = 57/179 (31%), Gaps = 15/179 (8%)
Query: 265 KPWIEKLLKVDSFQVLEKYIEDLILEAYSATQLFDQFHDIVMLASSLSDKQKALFKALET 324
+ KLL +D F+ + + +++ E ++ + + LE
Sbjct: 149 LETVAKLLGIDEFEKCYQKMGEIVKEYEKR---LERIEGELNYKEESLKARLKEMSNLEK 205
Query: 325 LVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVTGVIPNPWIEKLLKVDSFQVLEKY 384
E + + + L R+ G G + ++ + K + E
Sbjct: 206 EKE----KLTKFVEYLDKVRRIFGRNGFQAYLREK--------YVPLIQKYLNEAFSEFD 253
Query: 385 IEDLILEAYSATQLFDQFHDIVMSASSLSDKQKALILEKLAECNARLQDGASEYIQILD 443
+ +E ++ + V++ +LS ++ + L A G ILD
Sbjct: 254 LPYSFVELTKDFEVRVHAPNGVLTIDNLSGGEQIAVALSLRLAIANALIGNRVECIILD 312
>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus
abyssi}
Length = 350
Score = 29.3 bits (65), Expect = 2.6
Identities = 40/234 (17%), Positives = 75/234 (32%), Gaps = 45/234 (19%)
Query: 40 RPKT-IDDVIEQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQLFG---DMY 95
RPKT +D+ +++E L++ L P L G GK+S + A ++ G D
Sbjct: 6 RPKTRREDIFDREEESRKLEESLENY--PLTLLLGIRRVGKSSLLRAFLNERPGILIDCR 63
Query: 96 RERILELNASDDRGIQVIRDKVKTFAQQTAS---GFNQDGKPCPPFK------------- 139
+ + + I+ ++ + F + + N P K
Sbjct: 64 ELYAERGHITREELIKELQSTISPFQKFQSKFKISLNLKFLTLEPRKLSLREVFRELNDL 123
Query: 140 -------IVILDEADSMTHAAQAALR------RTMEKETKSTRFCLICNYVSCIIQ---- 182
IV DEA + + + + L + V +
Sbjct: 124 GEELGEFIVAFDEAQYLRFYGSRGGKELLALFAYAYDSLPNLKIILTGSEVGLLHDFLKI 183
Query: 183 -----PLTSRCSK-FRFKPLAENTMLTRLQYICEQESVMCDFKALETLVETSGG 230
PL R + KP ++T + L+ + ++ +E VE G
Sbjct: 184 TDYESPLYGRIAGEVLVKPFDKDTSVEFLKRGFREVNLDVPENEIEEAVELLDG 237
>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus
thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*
Length = 311
Score = 29.1 bits (66), Expect = 2.8
Identities = 11/25 (44%), Positives = 11/25 (44%)
Query: 69 FLFYGPPGTGKTSTMIAACHQLFGD 93
FLF GP G GKT LF
Sbjct: 50 FLFLGPTGVGKTELAKTLAATLFDT 74
>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP
phosphotransferase, myokinase, structural genomics,
structural genomics consortium, SGC; 1.48A {Homo
sapiens} PDB: 2ak3_A*
Length = 227
Score = 28.7 bits (65), Expect = 3.0
Identities = 22/94 (23%), Positives = 37/94 (39%), Gaps = 24/94 (25%)
Query: 62 SGADLPHFLFYGPPGTGK-T-STMIAACHQLF----GDMYRERI-----LELNA------ 104
+ A L + G PG+GK T S+ I +L GD+ R+ + + + A
Sbjct: 3 ASARLLRAVIMGAPGSGKGTVSSRITTHFELKHLSSGDLLRDNMLRGTEIGVLAKAFIDQ 62
Query: 105 ----SDDRGIQVIRDKVKTFAQQTASGFNQDGKP 134
DD ++ ++K T + DG P
Sbjct: 63 GKLIPDDVMTRLALHELK---NLTQYSWLLDGFP 93
>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic
subunit]; helicase, flavivirus, DEAD-BOX, ATPase,
rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP:
c.37.1.14 c.37.1.14 PDB: 1ymf_A*
Length = 440
Score = 29.0 bits (65), Expect = 3.1
Identities = 20/108 (18%), Positives = 28/108 (25%), Gaps = 26/108 (24%)
Query: 73 GPPGTGKTSTMIAACHQLFGDMYRERILELN-----------------------ASDDRG 109
PG GKT R R L L A G
Sbjct: 15 FHPGAGKT-RRFLPQILAECARRRLRTLVLAPTRVVLSEMKEAFHGLDVKFHTQAFSAHG 73
Query: 110 IQVIRDKVKTFAQQTASGFNQDGKPCPPFKIVILDEADSMTHAAQAAL 157
A T + ++++I+DEA + A+ AA
Sbjct: 74 SGREVIDAMCHATLTY--RMLEPTRVVNWEVIIMDEAHFLDPASIAAR 119
>2qis_A Farnesyl pyrophosphate synthetase; trans-prenyltransferase,
structural genomics, structural GEN consortium, SGC,
transferase; HET: RIS; 1.80A {Homo sapiens} PDB: 4dem_F*
1yv5_A* 1yq7_A* 2opm_A* 2opn_A* 3cp6_A* 2rah_A* 2vf6_A*
1zw5_A* 3b7l_A* 3s4j_A* 3rye_A* 3n45_F* 2f89_F* 2f7m_F*
2f8z_F* 2f8c_F* 2f92_F* 2f9k_F* 3n1v_F* ...
Length = 374
Score = 29.0 bits (65), Expect = 3.4
Identities = 11/62 (17%), Positives = 20/62 (32%), Gaps = 2/62 (3%)
Query: 296 QLFDQFHDIVMLASSLSDKQKALFKALETLVETSGGDMRRAITCLQSCARLKGGEGIVNE 355
Q+ + M + D L + LE GG R +T + + L +
Sbjct: 44 QIVRVLTEDEMGHPEIGDAIARLKEVLEYNA--IGGKYNRGLTVVVAFRELVEPRKQDAD 101
Query: 356 DV 357
+
Sbjct: 102 SL 103
>2cvh_A DNA repair and recombination protein RADB; filament formation,
homologous recombination, ATPase domain,
hyperthermophIle; HET: DNA; 2.20A {Thermococcus
kodakarensis} PDB: 2cvf_A*
Length = 220
Score = 28.7 bits (65), Expect = 3.4
Identities = 7/21 (33%), Positives = 10/21 (47%), Gaps = 4/21 (19%)
Query: 70 LFYGPPGTGKTSTMIAACHQL 90
YGP +GK +T+ Q
Sbjct: 24 QVYGPYASGK-TTL---ALQT 40
>2ghi_A Transport protein; multidrug resistance protein, MDR, structural
genomics, structural genomics consortium, SGC; 2.20A
{Plasmodium yoelii yoelii str}
Length = 260
Score = 28.7 bits (65), Expect = 3.5
Identities = 13/35 (37%), Positives = 16/35 (45%), Gaps = 7/35 (20%)
Query: 136 PPFKIVILDEA----DSMT-HAAQAALRRTMEKET 165
P IVI DEA DS T + Q A+ + T
Sbjct: 174 PK--IVIFDEATSSLDSKTEYLFQKAVEDLRKNRT 206
>3bfn_A Kinesin-like protein KIF22; limited proteolysis, structural
genomics consortium domain, ADP, SGC, ATP-binding,
DNA-binding, microtubule, MO protein; HET: ADP; 2.30A
{Homo sapiens}
Length = 388
Score = 28.8 bits (65), Expect = 3.5
Identities = 13/46 (28%), Positives = 15/46 (32%), Gaps = 15/46 (32%)
Query: 72 YGPPGTGKTSTMIA----------ACHQLFGDMYRERILELNASDD 107
YGP G GKT TM+ A L + E A
Sbjct: 105 YGPTGAGKTHTMLGSPEQPGVIPRALMDLL-----QLTREEGAEGR 145
>3nh6_A ATP-binding cassette SUB-family B member 6, mitoc; ABC-transporter,
ABCB6, nucleotide binding domain, heme BIOS transport
protein; 2.00A {Homo sapiens} PDB: 3nh9_A* 3nha_A*
3nhb_A*
Length = 306
Score = 28.7 bits (65), Expect = 3.8
Identities = 12/35 (34%), Positives = 17/35 (48%), Gaps = 7/35 (20%)
Query: 136 PPFKIVILDEA----DSMT-HAAQAALRRTMEKET 165
P I++LDEA D+ A QA+L + T
Sbjct: 209 PG--IILLDEATSALDTSNERAIQASLAKVCANRT 241
>1x88_A Kinesin-like protein KIF11; switch II, motor domain, NECK linker,
cell cycle; HET: ADP NAT; 1.80A {Homo sapiens} SCOP:
c.37.1.9 PDB: 3hqd_A* 3ken_A* 2pg2_A* 1yrs_A* 2fme_A*
2g1q_A* 2gm1_A* 1ii6_A* 2uyi_A* 2uym_A* 2wog_A* 2x2r_A*
2x7c_A* 2x7d_A* 2x7e_A* 2xae_A* 3k3b_A* 3k5e_A* 3l9h_A*
1q0b_A* ...
Length = 359
Score = 28.7 bits (65), Expect = 4.3
Identities = 12/39 (30%), Positives = 13/39 (33%), Gaps = 7/39 (17%)
Query: 72 YGPPGTGKTSTMIAACHQLFGDMYRERILELNASDDRGI 110
YG GTGKT TM G+ GI
Sbjct: 95 YGQTGTGKTFTME-------GERSPNEEYTWEEDPLAGI 126
>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase;
HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A*
3l0p_A*
Length = 223
Score = 28.4 bits (64), Expect = 4.3
Identities = 21/86 (24%), Positives = 35/86 (40%), Gaps = 24/86 (27%)
Query: 70 LFYGPPGTGK-T-STMIAACHQLF----GDMYRERI-----LELNA----------SDDR 108
L +GP G+GK T ++ + L G ++RE I L A DD
Sbjct: 4 LIFGPNGSGKGTQGNLVKDKYSLAHIESGGIFREHIGGGTELGKKAKEFIDRGDLVPDDI 63
Query: 109 GIQVIRDKVKTFAQQTASGFNQDGKP 134
I ++ + ++ + G+ DG P
Sbjct: 64 TIPMVLETLE---SKGKDGWLLDGFP 86
>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA
ATPase, ATP-binding, coiled coil, membrane,
nucleotide-binding, phosphorylation; HET: ATP; 3.00A
{Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A
2jq9_A 2k3w_A 1yxr_A
Length = 444
Score = 28.8 bits (64), Expect = 4.3
Identities = 9/19 (47%), Positives = 12/19 (63%), Gaps = 2/19 (10%)
Query: 69 FLFYGPPGTGKTSTMIAAC 87
L +GPPGTGK + +A
Sbjct: 170 ILLFGPPGTGK--SYLAKA 186
>2rhm_A Putative kinase; P-loop containing nucleoside triphosphate
hydrolases fold, S genomics, joint center for structural
genomics, JCSG; HET: MSE; 1.70A {Chloroflexus
aurantiacus}
Length = 193
Score = 28.0 bits (62), Expect = 4.8
Identities = 11/46 (23%), Positives = 18/46 (39%), Gaps = 7/46 (15%)
Query: 69 FLFYGPPGTGKTSTMIAACHQLFG------DMYRERILELNASDDR 108
+ G P TGK +T+ A D ++E + + DR
Sbjct: 8 IIVTGHPATGK-TTLSQALATGLRLPLLSKDAFKEVMFDGLGWSDR 52
>3p32_A Probable GTPase RV1496/MT1543; structural genomics, seattle
structural genomics center for infectious disease,
ssgcid, MEAB, MMAA; HET: GDP PGE; 1.90A {Mycobacterium
tuberculosis} PDB: 3md0_A* 3nxs_A* 3tk1_A*
Length = 355
Score = 28.3 bits (63), Expect = 5.2
Identities = 12/26 (46%), Positives = 12/26 (46%), Gaps = 5/26 (19%)
Query: 73 GPPGTGKTSTMIAACHQLFGDMYRER 98
G PG GK ST I A G ER
Sbjct: 86 GVPGVGK-STAIEA----LGMHLIER 106
>3fho_A ATP-dependent RNA helicase DBP5; mRNA export, ATPase, translation
termination, binding, hydrolase, membrane, mRNA
transport; 2.80A {Schizosaccharomyces pombe}
Length = 508
Score = 28.3 bits (64), Expect = 5.3
Identities = 7/11 (63%), Positives = 10/11 (90%)
Query: 139 KIVILDEADSM 149
K+ +LDEAD+M
Sbjct: 261 KVFVLDEADNM 271
>1weh_A Conserved hypothetical protein TT1887; rossman fold, structural
genomics, riken structural genomics/proteomics
initiative, RSGI; 1.80A {Thermus thermophilus} SCOP:
c.129.1.1
Length = 171
Score = 27.5 bits (62), Expect = 5.4
Identities = 10/48 (20%), Positives = 16/48 (33%), Gaps = 17/48 (35%)
Query: 348 GGEGI---VNEDVLE----VTGVI----------PNPWIEKLLKVDSF 378
G +G + V V GV PNP+++ L +
Sbjct: 40 GYQGGMEALARGVKAKGGLVVGVTAPAFFPERRGPNPFVDLELPAATL 87
>2p67_A LAO/AO transport system kinase; ARGK, structural GEN PSI-2,
protein structure initiative, NEW YORK SGX research for
structural genomics; 1.80A {Escherichia coli} SCOP:
c.37.1.10
Length = 341
Score = 28.2 bits (63), Expect = 5.5
Identities = 10/26 (38%), Positives = 12/26 (46%), Gaps = 5/26 (19%)
Query: 73 GPPGTGKTSTMIAACHQLFGDMYRER 98
G PG GK ST + A FG +
Sbjct: 63 GTPGAGK-STFLEA----FGMLLIRE 83
>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport
protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo
sapiens}
Length = 349
Score = 28.3 bits (63), Expect = 5.7
Identities = 14/26 (53%), Positives = 14/26 (53%), Gaps = 5/26 (19%)
Query: 73 GPPGTGKTSTMIAACHQLFGDMYRER 98
GPPG GK ST I FG M ER
Sbjct: 81 GPPGAGK-STFIEY----FGKMLTER 101
>1mv5_A LMRA, multidrug resistance ABC transporter ATP-binding and permease
protein; asymmetric dimer, tetramer, P-glycoprotein;
HET: ATP ADP; 3.10A {Lactococcus lactis} SCOP: c.37.1.12
Length = 243
Score = 27.8 bits (63), Expect = 5.8
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 5/32 (15%)
Query: 139 KIVILDEA----DSMT-HAAQAALRRTMEKET 165
KI++LDEA DS + Q AL M+ T
Sbjct: 159 KILMLDEATASLDSESESMVQKALDSLMKGRT 190
>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET:
MSE; 1.70A {Methylobacterium extorquens} SCOP:
c.37.1.10 PDB: 2qm7_A*
Length = 337
Score = 28.2 bits (63), Expect = 5.9
Identities = 10/26 (38%), Positives = 11/26 (42%), Gaps = 5/26 (19%)
Query: 73 GPPGTGKTSTMIAACHQLFGDMYRER 98
G PG GK ST I A G +
Sbjct: 62 GVPGVGK-STTIDA----LGSLLTAA 82
>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A
{Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*
Length = 287
Score = 28.0 bits (61), Expect = 6.8
Identities = 14/97 (14%), Positives = 34/97 (35%), Gaps = 10/97 (10%)
Query: 37 EKYRPKTIDDVIEQQEVVSVLKKCLSGADLPHFLFY-GPPGTGKTSTMIAACHQLFG--- 92
+ K ++ + + + L + + P G PG+GKTS A + G
Sbjct: 5 VNFTDKQFENRLN--DNLEELIQGKKAVESPTAFLLGGQPGSGKTSLRSAIFEETQGNVI 62
Query: 93 ----DMYRERILELNASDDRGIQVIRDKVKTFAQQTA 125
D ++++ + + + V ++ +
Sbjct: 63 VIDNDTFKQQHPNFDELVKLYEKDVVKHVTPYSNRMT 99
>1ltq_A Polynucleotide kinase; phosphatase, alpha/beta, P-loop,
transferase; HET: ADP; 2.33A {Enterobacteria phage T4}
SCOP: c.108.1.9 c.37.1.1 PDB: 1rc8_A* 1rpz_A* 1rrc_A*
2ia5_A
Length = 301
Score = 27.7 bits (61), Expect = 7.7
Identities = 19/83 (22%), Positives = 29/83 (34%), Gaps = 10/83 (12%)
Query: 69 FLFYGPPGTGKTS---TMIAACHQLF---GDMYRERILELNASDDRGIQVIRDK-VKTFA 121
L G PG+GK++ IA + D YR+ I+ D+ ++ V
Sbjct: 5 ILTIGCPGSGKSTWAREFIAKNPGFYNINRDDYRQSIMAHEERDEYKYTKKKEGIVTGMQ 64
Query: 122 QQTASGFNQDGKPCPPFKIVILD 144
TA G VI+
Sbjct: 65 FDTAKSILYGGDSVKG---VIIS 84
>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain,
beta domain, C-terminal helix, ATP-binding, E
nucleotide-binding; 2.90A {Saccharomyces cerevisiae}
PDB: 2qpa_A*
Length = 355
Score = 27.9 bits (62), Expect = 8.5
Identities = 9/12 (75%), Positives = 10/12 (83%)
Query: 69 FLFYGPPGTGKT 80
L YGPPGTGK+
Sbjct: 87 ILLYGPPGTGKS 98
>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET:
AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1
Length = 222
Score = 27.2 bits (61), Expect = 8.9
Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 6/44 (13%)
Query: 62 SGADLPHFLFYGPPGTGK-T-STMIAACHQLF----GDMYRERI 99
+ AD + G P +GK T +I +QL GD+ R I
Sbjct: 1 ALADPLKVMISGAPASGKGTQCELIKTKYQLAHISAGDLLRAEI 44
>1wek_A Hypothetical protein TT1465; rossman fold, structural genomics,
riken structural genomics/proteomics initiative, RSGI,
unknown function; 2.20A {Thermus thermophilus} SCOP:
c.129.1.1
Length = 217
Score = 27.2 bits (61), Expect = 9.2
Identities = 11/46 (23%), Positives = 15/46 (32%), Gaps = 15/46 (32%)
Query: 348 GGEGI---VNEDVLE----VTGVIP--------NPWIEKLLKVDSF 378
GG G+ VN E G+ NP+ L + F
Sbjct: 76 GGPGVMEAVNRGAYEAGGVSVGLNIELPHEQKPNPYQTHALSLRYF 121
>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP;
2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB:
3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A*
3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*
Length = 525
Score = 27.6 bits (61), Expect = 9.3
Identities = 7/21 (33%), Positives = 8/21 (38%)
Query: 70 LFYGPPGTGKTSTMIAACHQL 90
L G GTGKT +
Sbjct: 285 LATGATGTGKTLLVSRFVENA 305
>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling,
archaea, isomeras; 2.35A {Thermotoga maritima} PDB:
3p4y_A 3p4x_A*
Length = 414
Score = 27.8 bits (62), Expect = 9.5
Identities = 4/12 (33%), Positives = 8/12 (66%)
Query: 138 FKIVILDEADSM 149
F V +D+ D++
Sbjct: 140 FDFVFVDDVDAV 151
>1uby_A FPS, farnesyl diphosphate synthase; transferase, isoprene
biosynthesis, cholesterol biosynthesis; HET: DMA; 2.40A
{Gallus gallus} SCOP: a.128.1.1 PDB: 1ubw_A* 1ubv_A*
1ubx_A* 1fps_A
Length = 367
Score = 27.4 bits (61), Expect = 9.5
Identities = 11/62 (17%), Positives = 21/62 (33%), Gaps = 2/62 (3%)
Query: 296 QLFDQFHDIVMLASSLSDKQKALFKALETLVETSGGDMRRAITCLQSCARLKGGEGIVNE 355
Q+ + + + D L + L+ GG R +T + + L G E
Sbjct: 37 QIVRDLTEDGIGHPEVGDAVARLKEVLQYNA--PGGKCNRGLTVVAAYRELSGPGQKDAE 94
Query: 356 DV 357
+
Sbjct: 95 SL 96
>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB,
proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR
binding; 6.93A {Bacillus subtilis}
Length = 758
Score = 27.9 bits (63), Expect = 9.5
Identities = 12/25 (48%), Positives = 14/25 (56%)
Query: 69 FLFYGPPGTGKTSTMIAACHQLFGD 93
F+F GP G GKT A +FGD
Sbjct: 524 FIFLGPTGVGKTELARALAESIFGD 548
>3lre_A Kinesin-like protein KIF18A; motor protein, nucleotide binding,
microtubule binding, ATP- cell projection, cytoskeleton,
glycoprotein, microtubule; HET: ADP; 2.20A {Homo
sapiens}
Length = 355
Score = 27.6 bits (62), Expect = 9.6
Identities = 9/30 (30%), Positives = 11/30 (36%), Gaps = 10/30 (33%)
Query: 72 YGPPGTGKTSTMIA----------ACHQLF 91
YG G GKT TM+ L+
Sbjct: 112 YGATGAGKTHTMLGSADEPGVMYLTMLHLY 141
>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide
biosynthesis, nucleotide-binding, transferase,
structural genomics; 1.80A {Thermus thermophilus}
Length = 186
Score = 27.1 bits (61), Expect = 9.7
Identities = 12/36 (33%), Positives = 19/36 (52%), Gaps = 6/36 (16%)
Query: 70 LFYGPPGTGK-T-STMIAACHQLF----GDMYRERI 99
+F GPPG GK T ++ +A GD+ R+ +
Sbjct: 8 IFLGPPGAGKGTQASRLAQELGFKKLSTGDILRDHV 43
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.319 0.134 0.385
Gapped
Lambda K H
0.267 0.0797 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,861,187
Number of extensions: 419036
Number of successful extensions: 1317
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1256
Number of HSP's successfully gapped: 175
Length of query: 456
Length of database: 6,701,793
Length adjustment: 97
Effective length of query: 359
Effective length of database: 3,993,456
Effective search space: 1433650704
Effective search space used: 1433650704
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 59 (26.4 bits)