RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12150
(456 letters)
>gnl|CDD|234763 PRK00440, rfc, replication factor C small subunit; Reviewed.
Length = 319
Score = 300 bits (771), Expect = 1e-99
Identities = 121/288 (42%), Positives = 172/288 (59%), Gaps = 14/288 (4%)
Query: 34 PWVEKYRPKTIDDVIEQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQLFGD 93
WVEKYRP+T+D+++ Q+E+V LK + ++PH LF GPPGTGKT+ +A +L+G+
Sbjct: 6 IWVEKYRPRTLDEIVGQEEIVERLKSYVKEKNMPHLLFAGPPGTGKTTAALALARELYGE 65
Query: 94 MYRERILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPPFKIVILDEADSMTHAA 153
+RE LELNASD+RGI VIR+K+K FA+ G PFKI+ LDEAD++T A
Sbjct: 66 DWRENFLELNASDERGIDVIRNKIKEFARTAPVG-------GAPFKIIFLDEADNLTSDA 118
Query: 154 QAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLAENTMLTRLQYICEQES 213
Q ALRRTME +++TRF L CNY S II P+ SRC+ FRF PL + + RL+YI E E
Sbjct: 119 QQALRRTMEMYSQNTRFILSCNYSSKIIDPIQSRCAVFRFSPLKKEAVAERLRYIAENEG 178
Query: 214 VMCDFKALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVTGVIPKPWIEKLLK 273
+ ALE + S GDMR+AI LQ+ A G+ + E V ++TG I ++++
Sbjct: 179 IEITDDALEAIYYVSEGDMRKAINALQAAAAT--GKEVTEEAVYKITGTARPEEIREMIE 236
Query: 274 V---DSFQVLEKYIEDL-ILEAYSATQLFDQFHDIVMLASSLSDKQKA 317
+ F + + DL I S + Q H V + + ++ K
Sbjct: 237 LALNGDFTEAREKLRDLMIDYGLSGEDIIKQIHREV-WSLDIPEELKV 283
Score = 71.1 bits (175), Expect = 1e-13
Identities = 36/126 (28%), Positives = 63/126 (50%), Gaps = 7/126 (5%)
Query: 320 KALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVTGVIPNPWIEKLLKV---D 376
ALE + S GDMR+AI LQ+ A G+ + E V ++TG I +++++
Sbjct: 184 DALEAIYYVSEGDMRKAINALQAAAAT--GKEVTEEAVYKITGTARPEEIREMIELALNG 241
Query: 377 SFQVLEKYIEDL-ILEAYSATQLFDQFHDIVMSASSLSDKQKALILEKLAECNARLQDGA 435
F + + DL I S + Q H V S + ++ K +++ + E + R+ +GA
Sbjct: 242 DFTEAREKLRDLMIDYGLSGEDIIKQIHREVWS-LDIPEELKVELIDAIGEADFRITEGA 300
Query: 436 SEYIQI 441
+E IQ+
Sbjct: 301 NERIQL 306
>gnl|CDD|178596 PLN03025, PLN03025, replication factor C subunit; Provisional.
Length = 319
Score = 241 bits (616), Expect = 2e-76
Identities = 108/230 (46%), Positives = 149/230 (64%), Gaps = 14/230 (6%)
Query: 33 VPWVEKYRPKTIDDVIEQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQLFG 92
+PWVEKYRP +DD++ ++ VS L+ ++P+ + GPPGTGKT++++A H+L G
Sbjct: 1 LPWVEKYRPTKLDDIVGNEDAVSRLQVIARDGNMPNLILSGPPGTGKTTSILALAHELLG 60
Query: 93 DMYRERILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPP--FKIVILDEADSMT 150
Y+E +LELNASDDRGI V+R+K+K FAQ+ + PP KIVILDEADSMT
Sbjct: 61 PNYKEAVLELNASDDRGIDVVRNKIKMFAQKKVT--------LPPGRHKIVILDEADSMT 112
Query: 151 HAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLAENTMLTRLQYICE 210
AQ ALRRTME + +TRF L CN S II+P+ SRC+ RF L++ +L RL + E
Sbjct: 113 SGAQQALRRTMEIYSNTTRFALACNTSSKIIEPIQSRCAIVRFSRLSDQEILGRLMKVVE 172
Query: 211 QESVMCDFKALETLVETSGGDMRRAITCLQSCARLKGGEGIVN-EDVLEV 259
E V + LE ++ T+ GDMR+A+ LQ+ G G VN E+V +V
Sbjct: 173 AEKVPYVPEGLEAIIFTADGDMRQALNNLQATH---SGFGFVNQENVFKV 219
Score = 37.4 bits (87), Expect = 0.010
Identities = 35/139 (25%), Positives = 60/139 (43%), Gaps = 28/139 (20%)
Query: 320 KALETLVETSGGDMRRAITCLQSCARLKGGEGIVN-EDVLEVTGVIPNPWIEKLLKVDSF 378
+ LE ++ T+ GDMR+A+ LQ+ G G VN E+V +V P+P K
Sbjct: 181 EGLEAIIFTADGDMRQALNNLQATH---SGFGFVNQENVFKVCDQ-PHPLHVK------- 229
Query: 379 QVLEKYIEDLILEAYSATQLFDQFHDIVMSASSL----------SDKQKALILEKLAE-- 426
++ ++ +A + Q +D+ S + + D + L LE L E
Sbjct: 230 NIVRNCLKGKFDDACDGLK---QLYDLGYSPTDIITTLFRVVKNYDMPEFLKLEYLREIG 286
Query: 427 -CNARLQDGASEYIQILDL 444
+ R+ DG +Q+ L
Sbjct: 287 FAHMRICDGVGSLLQLSGL 305
>gnl|CDD|237090 PRK12402, PRK12402, replication factor C small subunit 2; Reviewed.
Length = 337
Score = 170 bits (433), Expect = 4e-49
Identities = 89/298 (29%), Positives = 141/298 (47%), Gaps = 33/298 (11%)
Query: 35 WVEKYRPKTIDDVIEQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQLFGDM 94
W EKYRP ++D++ Q EVV L + + +LPH L GPPG+GKT+ + A +L+GD
Sbjct: 5 WTEKYRPALLEDILGQDEVVERLSRAVDSPNLPHLLVQGPPGSGKTAAVRALARELYGDP 64
Query: 95 YRERILELNASD--DRGIQVIR---------DKVKTFAQQTASGFNQ-----------DG 132
+ E N +D D+G + + K F
Sbjct: 65 WENNFTEFNVADFFDQGKKYLVEDPRFAHFLGTDKRIRSSKIDNFKHVLKEYASYRPLSA 124
Query: 133 KPCPPFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFR 192
+K ++LD A+++ AQ ALRR ME+ +++ RF + S +I P+ SRC
Sbjct: 125 ----DYKTILLDNAEALREDAQQALRRIMEQYSRTCRFIIATRQPSKLIPPIRSRCLPLF 180
Query: 193 FKPLAENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCLQSCARLKGGEGIV 252
F+ ++ ++ L+ I E E V D LE + +GGD+R+AI LQ+ A L GE I
Sbjct: 181 FRAPTDDELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTLQTAA-LAAGE-IT 238
Query: 253 NEDVLEVTGVIP-KPWIEKLL---KVDSFQVLEKYIEDLIL-EAYSATQLFDQFHDIV 305
E E G + IE LL + F K ++DL++ E S ++ ++ +
Sbjct: 239 MEAAYEALGDVGTDEVIESLLDAAEAGDFTDARKTLDDLLIDEGLSGGEVLEELLRVA 296
Score = 53.1 bits (128), Expect = 1e-07
Identities = 39/126 (30%), Positives = 62/126 (49%), Gaps = 9/126 (7%)
Query: 321 ALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVTGVIP-NPWIEKLL---KVD 376
LE + +GGD+R+AI LQ+ A L GE I E E G + + IE LL +
Sbjct: 208 GLELIAYYAGGDLRKAILTLQTAA-LAAGE-ITMEAAYEALGDVGTDEVIESLLDAAEAG 265
Query: 377 SFQVLEKYIEDLIL-EAYSATQLFDQFHDIVMSASSLSDKQKALILEKLAECNARLQDGA 435
F K ++DL++ E S ++ ++ + S A + A+ +ARL DGA
Sbjct: 266 DFTDARKTLDDLLIDEGLSGGEVLEELLRVA--RSRYRGDNLARLHRLAADADARLTDGA 323
Query: 436 SEYIQI 441
++ IQ+
Sbjct: 324 NDRIQL 329
>gnl|CDD|235223 PRK04132, PRK04132, replication factor C small subunit;
Provisional.
Length = 846
Score = 166 bits (421), Expect = 2e-44
Identities = 93/227 (40%), Positives = 130/227 (57%), Gaps = 13/227 (5%)
Query: 80 TSTMIAACHQLFGDMYRERILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPPFK 139
T+ +A +LFG+ +R LELNASD+RGI VIR+KVK FA+ G FK
Sbjct: 580 TTAALALARELFGENWRHNFLELNASDERGINVIREKVKEFARTKPIG-------GASFK 632
Query: 140 IVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLAEN 199
I+ LDEAD++T AQ ALRRTME + + RF L CNY S II+P+ SRC+ FRF+PL +
Sbjct: 633 IIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDE 692
Query: 200 TMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEV 259
+ RL+YI E E + + L+ ++ + GDMRRAI LQ+ A L + I +E+V V
Sbjct: 693 DIAKRLRYIAENEGLELTEEGLQAILYIAEGDMRRAINILQAAAALD--DKITDENVFLV 750
Query: 260 TGVIPKPWIEKL----LKVDSFQVLEKYIEDLILEAYSATQLFDQFH 302
I ++ LK + + EK E L+ + S + Q H
Sbjct: 751 ASRARPEDIREMMLLALKGNFLKAREKLREILLKQGLSGEDVLVQMH 797
Score = 69.5 bits (170), Expect = 1e-12
Identities = 25/49 (51%), Positives = 33/49 (67%)
Query: 34 PWVEKYRPKTIDDVIEQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTST 82
PWVEKYRP+ +DD++ Q+ +V LK + +PH LF GPPG GK T
Sbjct: 8 PWVEKYRPQRLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKCLT 56
Score = 47.5 bits (113), Expect = 1e-05
Identities = 38/124 (30%), Positives = 63/124 (50%), Gaps = 7/124 (5%)
Query: 322 LETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVTGVIPNPWIEKL----LKVDS 377
L+ ++ + GDMRRAI LQ+ A L + I +E+V V I ++ LK +
Sbjct: 714 LQAILYIAEGDMRRAINILQAAAALD--DKITDENVFLVASRARPEDIREMMLLALKGNF 771
Query: 378 FQVLEKYIEDLILEAYSATQLFDQFHDIVMSASSLSDKQKALILEKLAECNARLQDGASE 437
+ EK E L+ + S + Q H V + + + +K + +K+ E N RL +GA+E
Sbjct: 772 LKAREKLREILLKQGLSGEDVLVQMHREVFNL-PIDEPKKVELADKIGEYNFRLVEGANE 830
Query: 438 YIQI 441
IQ+
Sbjct: 831 MIQL 834
>gnl|CDD|222866 PHA02544, 44, clamp loader, small subunit; Provisional.
Length = 316
Score = 140 bits (355), Expect = 4e-38
Identities = 75/232 (32%), Positives = 108/232 (46%), Gaps = 27/232 (11%)
Query: 35 WVEKYRPKTIDDVIEQQEVVSVLKKCLSGADLPHFLFYGP-PGTGKTSTMIAACHQLFGD 93
W +KYRP TID+ I K + +P+ L + P PGTGKT+ A C+++ +
Sbjct: 11 WEQKYRPSTIDECILPAADKETFKSIVKKGRIPNMLLHSPSPGTGKTTVAKALCNEVGAE 70
Query: 94 MYRERILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPPFKIVILDEAD-SMTHA 152
+ +N SD R I +R+++ FA S + G K++I+DE D
Sbjct: 71 VLF-----VNGSDCR-IDFVRNRLTRFA----STVSLTGGG----KVIIIDEFDRLGLAD 116
Query: 153 AQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRF-KPLAEN------TMLTRL 205
AQ LR ME +K+ F + N + II+PL SRC F P E M+ R
Sbjct: 117 AQRHLRSFMEAYSKNCSFIITANNKNGIIEPLRSRCRVIDFGVPTKEEQIEMMKQMIVRC 176
Query: 206 QYICEQESVMCDFKALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVL 257
+ I E E V D K L LV+ + D RR I LQ A G ++ +L
Sbjct: 177 KGILEAEGVEVDMKVLAALVKKNFPDFRRTINELQRYAS----TGKIDAGIL 224
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 139 bits (353), Expect = 2e-36
Identities = 76/237 (32%), Positives = 113/237 (47%), Gaps = 21/237 (8%)
Query: 32 PVPWVEKYRPKTIDDVIEQQEVVSVLKK----CLSGADLPHFLFYGPPGTGKTSTMIAAC 87
+PWVEKYRPKT+ DV+ ++ L++ L G L YGPPG GKTS A
Sbjct: 1 MMPWVEKYRPKTLSDVVGNEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALA 60
Query: 88 HQLFGDMYRERILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPPFKIVILDEAD 147
+ D E ++ELNASD R VI A + S F K+++LDE D
Sbjct: 61 N----DYGWE-VIELNASDQRTADVIERVAGE-AATSGSLFGARR------KLILLDEVD 108
Query: 148 SMTHAAQAALRRTMEKETKSTRFCLIC---NYVSCIIQPLTSRCSKFRFKPLAENTMLTR 204
+ R + + K + +I + ++ L + C FK L+ +++
Sbjct: 109 GIHGNEDRGGARAILELIKKAKQPIILTANDPYDPSLRELRNACLMIEFKRLSTRSIVPV 168
Query: 205 LQYICEQESVMCDFKALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVTG 261
L+ IC +E + CD +AL+ + E SGGD+R AI LQ+ A G + EDV +
Sbjct: 169 LKRICRKEGIECDDEALKEIAERSGGDLRSAINDLQAIAE--GYGKLTLEDVKTLGR 223
Score = 34.9 bits (81), Expect = 0.080
Identities = 17/43 (39%), Positives = 24/43 (55%), Gaps = 2/43 (4%)
Query: 320 KALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVTG 362
+AL+ + E SGGD+R AI LQ+ A G + EDV +
Sbjct: 183 EALKEIAERSGGDLRSAINDLQAIAE--GYGKLTLEDVKTLGR 223
>gnl|CDD|237867 PRK14953, PRK14953, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 486
Score = 118 bits (296), Expect = 8e-29
Identities = 85/305 (27%), Positives = 136/305 (44%), Gaps = 51/305 (16%)
Query: 33 VPWVEKYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTSTM-IAA---- 86
+P+ KYRPK +VI Q+ VV +LK + + H ++F GP GTGKT+ I A
Sbjct: 4 IPFARKYRPKFFKEVIGQEIVVRILKNAVKLQRVSHAYIFAGPRGTGKTTIARILAKVLN 63
Query: 87 ---------CHQL----------FGDMYRERILELNASDDRGI---QVIRDKVKTFAQQT 124
C + F D+ E++A+ +RGI + +RD V +
Sbjct: 64 CLNPQEGEPCGKCENCVEIDKGSFPDLI-----EIDAASNRGIDDIRALRDAVSYTPIK- 117
Query: 125 ASGFNQDGKPCPPFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPL 184
GK +K+ I+DEA +T A AL +T+E+ T F L I +
Sbjct: 118 -------GK----YKVYIIDEAHMLTKEAFNALLKTLEEPPPRTIFILCTTEYDKIPPTI 166
Query: 185 TSRCSKFRFKPLAENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCLQSCAR 244
SRC +F F + + L+ IC +E + + KAL+ L + S G MR A + L +
Sbjct: 167 LSRCQRFIFSKPTKEQIKEYLKRICNEEKIEYEEKALDLLAQASEGGMRDAASLLDQAST 226
Query: 245 LKGGEGIVNEDVLE-VTGVIPKPWIEK---LLKVDSFQVLEKYIEDLILEAYSATQLFDQ 300
GEG V V+E G++ + + K LL K++ L + Y+ + + Q
Sbjct: 227 Y--GEGKVTIKVVEEFLGIVSQESVRKFLNLLLESDVDEAIKFLRTLEEKGYNLNKFWKQ 284
Query: 301 FHDIV 305
+ +
Sbjct: 285 LEEEI 289
Score = 32.5 bits (74), Expect = 0.49
Identities = 24/91 (26%), Positives = 40/91 (43%), Gaps = 6/91 (6%)
Query: 320 KALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLE-VTGVIPNPWIEK---LLKV 375
KAL+ L + S G MR A + L + GEG V V+E G++ + K LL
Sbjct: 201 KALDLLAQASEGGMRDAASLLDQASTY--GEGKVTIKVVEEFLGIVSQESVRKFLNLLLE 258
Query: 376 DSFQVLEKYIEDLILEAYSATQLFDQFHDIV 406
K++ L + Y+ + + Q + +
Sbjct: 259 SDVDEAIKFLRTLEEKGYNLNKFWKQLEEEI 289
>gnl|CDD|233847 TIGR02397, dnaX_nterm, DNA polymerase III, subunit gamma and tau.
This model represents the well-conserved first ~ 365
amino acids of the translation of the dnaX gene. The
full-length product of the dnaX gene in the model
bacterium E. coli is the DNA polymerase III tau subunit.
A translational frameshift leads to early termination
and a truncated protein subunit gamma, about 1/3 shorter
than tau and present in roughly equal amounts. This
frameshift mechanism is not necessarily universal for
species with DNA polymerase III but appears conserved in
the exterme thermophile Thermus thermophilis [DNA
metabolism, DNA replication, recombination, and repair].
Length = 355
Score = 115 bits (290), Expect = 1e-28
Identities = 91/366 (24%), Positives = 161/366 (43%), Gaps = 77/366 (21%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTST--MIA--------- 85
KYRP+T +DVI Q+ +V LK + + H +LF GP GTGKTS + A
Sbjct: 7 KYRPQTFEDVIGQEHIVQTLKNAIKNGRIAHAYLFSGPRGTGKTSIARIFAKALNCQNGP 66
Query: 86 ---------ACHQLFGDMYRERILELNASDDRG---IQVIRDKVKTFAQQTASGFNQDGK 133
+C ++ + ++E++A+ + G I+ I D VK GK
Sbjct: 67 DGEPCNECESCKEINSGSSLD-VIEIDAASNNGVDDIREILDNVKYAPSS--------GK 117
Query: 134 PCPPFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLT--SRCSKF 191
+K+ I+DE ++ +A AL +T+E+ + F L I P T SRC +F
Sbjct: 118 ----YKVYIIDEVHMLSKSAFNALLKTLEEPPEHVVFILATTEPHKI--PATILSRCQRF 171
Query: 192 RFKPLAENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCLQSCARLKGGEGI 251
FK + ++ RL+ I ++E + + +ALE + + G +R A++ L G I
Sbjct: 172 DFKRIPLEDIVERLKKILDKEGIKIEDEALELIARAADGSLRDALSLLDQLISFGNGN-I 230
Query: 252 VNEDVLEVTGVIPKPWIEKLLK-------VDSFQVLEKYIE-----------------DL 287
EDV E+ G++ + +LL+ ++ ++L++ +E DL
Sbjct: 231 TYEDVNELLGLVDDEKLIELLEAILNKDTAEALKILDEILESGVDPEKFLEDLIEILRDL 290
Query: 288 ILEAYSATQLFDQFHDIVMLASSLSDK--QKALFKALETLVETSGGDMRRA--------I 337
+L + + L L+ K + L + L+ L+E + D+R + +
Sbjct: 291 LLIKKTPSNLLAVLESEQEFLKELALKLSLEFLLRLLDILLE-ALKDLRFSNDPRIWLEM 349
Query: 338 TCLQSC 343
T L+
Sbjct: 350 TLLRLL 355
Score = 36.4 bits (85), Expect = 0.022
Identities = 40/175 (22%), Positives = 74/175 (42%), Gaps = 23/175 (13%)
Query: 293 SATQLFD----QFHDIVMLASSLSDKQKALF--KALETLVETSGGDMRRAITCLQSCARL 346
S Q FD DIV + DK+ +ALE + + G +R A++ L
Sbjct: 166 SRCQRFDFKRIPLEDIVERLKKILDKEGIKIEDEALELIARAADGSLRDALSLLDQLISF 225
Query: 347 KGGEGIVNEDVLEVTGVIPNPWIEKLLKV----DSFQVLEKYIEDLILEAYS----ATQL 398
G I EDV E+ G++ + + +LL+ D+ + L K +++++ L
Sbjct: 226 GNGN-ITYEDVNELLGLVDDEKLIELLEAILNKDTAEAL-KILDEILESGVDPEKFLEDL 283
Query: 399 FDQFHDIVMSASSLSDKQKALILEKLAECNARLQDGASEY--IQILDLGSIVIKA 451
+ D++ L K + +L L L++ A + +L L I+++A
Sbjct: 284 IEILRDLL-----LIKKTPSNLLAVLESEQEFLKELALKLSLEFLLRLLDILLEA 333
>gnl|CDD|237869 PRK14962, PRK14962, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 472
Score = 110 bits (277), Expect = 3e-26
Identities = 72/289 (24%), Positives = 125/289 (43%), Gaps = 41/289 (14%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTST-------------- 82
KYRPKT +V+ Q V ++ L + H ++F GP GTGKT+
Sbjct: 7 KYRPKTFSEVVGQDHVKKLIINALKKNSISHAYIFAGPRGTGKTTVARILAKSLNCENRK 66
Query: 83 ------MIAACHQL----FGDMYRERILELNASDDRGIQVIRDKVKTFAQQTASGFNQDG 132
AC + F D ++EL+A+ +RGI IR + G
Sbjct: 67 GVEPCNECRACRSIDEGTFMD-----VIELDAASNRGIDEIRKIRDAVGYRPMEG----- 116
Query: 133 KPCPPFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFR 192
+K+ I+DE +T A AL +T+E+ F L + + + SRC
Sbjct: 117 ----KYKVYIIDEVHMLTKEAFNALLKTLEEPPSHVVFVLATTNLEKVPPTIISRCQVIE 172
Query: 193 FKPLAENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCLQSCARLKGGEGIV 252
F+ +++ ++ RLQ + E E + D +AL + + + G +R A+T L+ + G+ I
Sbjct: 173 FRNISDELIIKRLQEVAEAEGIEIDREALSFIAKRASGGLRDALTMLEQVWKFSEGK-IT 231
Query: 253 NEDVLEVTGVIPKPWIEKLLKVDSFQVLEKYIEDLILEAYSATQLFDQF 301
E V E G+IP + + F K + ++ + Y + + ++
Sbjct: 232 LETVHEALGLIPIEVVRDYINA-IFNGDVKRVFTVLDDVYYSGKDYEVL 279
Score = 34.4 bits (79), Expect = 0.11
Identities = 18/82 (21%), Positives = 37/82 (45%), Gaps = 2/82 (2%)
Query: 321 ALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVTGVIPNPWIEKLLKVDSFQV 380
AL + + + G +R A+T L+ + G+ I E V E G+IP + + F
Sbjct: 200 ALSFIAKRASGGLRDALTMLEQVWKFSEGK-ITLETVHEALGLIPIEVVRDYINA-IFNG 257
Query: 381 LEKYIEDLILEAYSATQLFDQF 402
K + ++ + Y + + ++
Sbjct: 258 DVKRVFTVLDDVYYSGKDYEVL 279
>gnl|CDD|225369 COG2812, DnaX, DNA polymerase III, gamma/tau subunits [DNA
replication, recombination, and repair].
Length = 515
Score = 102 bits (256), Expect = 2e-23
Identities = 78/325 (24%), Positives = 135/325 (41%), Gaps = 48/325 (14%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTST--MIAACH------ 88
KYRPKT DDV+ Q+ VV L L + H +LF GP G GKT+ ++A
Sbjct: 9 KYRPKTFDDVVGQEHVVKTLSNALENGRIAHAYLFSGPRGVGKTTIARILAKALNCENGP 68
Query: 89 --QLFGDMYRER---------ILELNASDDRGIQVIR---DKVKTFAQQTASGFNQDGKP 134
+ G + ++E++A+ + G+ IR +KV S
Sbjct: 69 TAEPCGKCISCKEINEGSLIDVIEIDAASNTGVDDIREIIEKVNY----APSEGR----- 119
Query: 135 CPPFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLT--SRCSKFR 192
+K+ I+DE ++ A AL +T+E+ +F L I P T SRC +F
Sbjct: 120 ---YKVYIIDEVHMLSKQAFNALLKTLEEPPSHVKFILATTEPQKI--PNTILSRCQRFD 174
Query: 193 FKPLAENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCLQSCARLKGGEGIV 252
FK L + L I ++E + + AL + + G +R A++ L A G I
Sbjct: 175 FKRLDLEEIAKHLAAILDKEGINIEEDALSLIARAAEGSLRDALSLL-DQAIAFGEGEIT 233
Query: 253 NEDVLEVTGVIPKPWIEKLLKV-------DSFQVLEKYIEDLILEAYSATQLFDQFHD-I 304
E V ++ G+ + LL+ ++ +++ + IE+ L + D +
Sbjct: 234 LESVRDMLGLTDIEKLLSLLEAILKGDAKEALRLINELIEEGKDPEAFLEDLLNFLRDLL 293
Query: 305 VMLASSLSDKQKALFKALETLVETS 329
+ + ++ Q + E E +
Sbjct: 294 LFKQTVPNELQLNTTEIEERTKELA 318
>gnl|CDD|235943 PRK07133, PRK07133, DNA polymerase III subunits gamma and tau;
Validated.
Length = 725
Score = 98.0 bits (244), Expect = 1e-21
Identities = 82/305 (26%), Positives = 147/305 (48%), Gaps = 44/305 (14%)
Query: 29 RNKPVPWVEKYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTST----- 82
R K KYRPKT DD++ Q +V LK + + H +LF GP GTGKTS
Sbjct: 2 RMKYKALYRKYRPKTFDDIVGQDHIVQTLKNIIKSNKISHAYLFSGPRGTGKTSVAKIFA 61
Query: 83 ----------MIAACHQLFGDMYRE-RILELNASDDRGIQVIR---DKVKTFAQQTASGF 128
++ C + ++ I+E++A+ + G+ IR + VK Q+
Sbjct: 62 NALNCSHKTDLLEPCQECIENVNNSLDIIEMDAASNNGVDEIRELIENVKNLPTQS---- 117
Query: 129 NQDGKPCPPFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLT--S 186
+KI I+DE ++ +A AL +T+E+ K F L V I PLT S
Sbjct: 118 --------KYKIYIIDEVHMLSKSAFNALLKTLEEPPKHVIFILATTEVHKI--PLTILS 167
Query: 187 RCSKFRFKPLAENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCLQSCARLK 246
R +F F+ ++E+ +++RL++I E+E++ + AL+ + + S G +R A++ + +
Sbjct: 168 RVQRFNFRRISEDEIVSRLEFILEKENISYEKNALKLIAKLSSGSLRDALSIAEQVSIFG 227
Query: 247 GGEGIVNEDVLEVTGVIPKPWIEKLLKVDSFQVLEKYIEDLILEAYSATQLFDQFHDIVM 306
+ I ++V E+ G++ + LL + + +++ + L Q+ +Q D +
Sbjct: 228 NNK-ITLKNVEELFGLVSNENLINLLNLLYSKDIKEVLNIL-------NQIKEQGIDPEL 279
Query: 307 LASSL 311
L SL
Sbjct: 280 LLISL 284
>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 94.4 bits (236), Expect = 4e-21
Identities = 62/233 (26%), Positives = 103/233 (44%), Gaps = 34/233 (14%)
Query: 37 EKYRPKTIDDVIEQQEVV---SVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQLFGD 93
E+ RPKT+D+V+ Q+ ++ L++ + L + +GPPGTGKT+ +A ++
Sbjct: 4 ERMRPKTLDEVVGQEHLLGPGKPLRRMIEAGRLSSMILWGPPGTGKTT--LA---RIIAG 58
Query: 94 MYRERILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPPFKIVILDEADSMTHAA 153
L+A G++ +R+ ++ A+Q S + I+ +DE A
Sbjct: 59 ATDAPFEALSAVTS-GVKDLREVIEE-ARQRRSAGRR--------TILFIDEIHRFNKAQ 108
Query: 154 QAALRRTMEKETKSTRFCLIC----N-YVSCIIQPLTSRCSKFRFKPLAENTMLTRLQYI 208
Q AL +E T LI N + L SR F KPL+E + L+
Sbjct: 109 QDALLPHVEDGT----ITLIGATTENPSFE-VNPALLSRAQVFELKPLSEEDIEQLLKRA 163
Query: 209 CEQES---VMCDFKALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLE 258
E + V D +AL+ L + GD RRA+ L+ A + ++LE
Sbjct: 164 LEDKERGLVELDDEALDALARLANGDARRALNLLELAALG---VDSITLELLE 213
Score = 34.7 bits (81), Expect = 0.086
Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 7/53 (13%)
Query: 311 LSDKQKALFK----ALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLE 359
L DK++ L + AL+ L + GD RRA+ L+ A + ++LE
Sbjct: 164 LEDKERGLVELDDEALDALARLANGDARRALNLLELAALG---VDSITLELLE 213
>gnl|CDD|235505 PRK05563, PRK05563, DNA polymerase III subunits gamma and tau;
Validated.
Length = 559
Score = 93.0 bits (232), Expect = 3e-20
Identities = 77/301 (25%), Positives = 133/301 (44%), Gaps = 68/301 (22%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTSTM-IAA----CHQLF 91
K+RP+T +DV+ Q+ + LK + + H +LF GP GTGKTS I A C
Sbjct: 9 KWRPQTFEDVVGQEHITKTLKNAIKQGKISHAYLFSGPRGTGKTSAAKIFAKAVNCLNPP 68
Query: 92 G-------DMYRE-------RILELNASDDRG---IQVIRDKVKTFAQQTASGFNQDGKP 134
++ + ++E++A+ + G I+ IRDKVK +A A
Sbjct: 69 DGEPCNECEICKAITNGSLMDVIEIDAASNNGVDEIRDIRDKVK-YAPSEA--------- 118
Query: 135 CPPFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCL-------ICNYVSCIIQPLT-- 185
+K+ I+DE ++ A AL +T+E+ F L I P T
Sbjct: 119 --KYKVYIIDEVHMLSTGAFNALLKTLEEPPAHVIFILATTEPHKI---------PATIL 167
Query: 186 SRCSKFRFKPLAENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCLQSCARL 245
SRC +F FK ++ ++ RL+YI ++E + + +AL + + G MR A++ L
Sbjct: 168 SRCQRFDFKRISVEDIVERLKYILDKEGIEYEDEALRLIARAAEGGMRDALSILDQAISF 227
Query: 246 KGGEGIVNEDVLEVTGVIPKPWIEKLLKVDSFQVLEKYIEDLILEAYSATQLFDQFHDIV 305
G+ + ED LEVTG + S + L+ ++ ++ + +++
Sbjct: 228 GDGK-VTYEDALEVTGSV------------SQEALDDLVDAIV--EGDVAKALKILEELL 272
Query: 306 M 306
Sbjct: 273 D 273
Score = 34.8 bits (81), Expect = 0.097
Identities = 23/132 (17%), Positives = 45/132 (34%), Gaps = 41/132 (31%)
Query: 293 SATQLFDQFHDIVMLASSLSDKQKALFKALETLVETSG----------------GDMRRA 336
S Q FD F I + + + L+ +++ G G MR A
Sbjct: 168 SRCQRFD-FKRI---------SVEDIVERLKYILDKEGIEYEDEALRLIARAAEGGMRDA 217
Query: 337 ITCLQSCARLKGGEGIVNEDVLEVTGVIPNPWIEKLLKVDSFQVLEKYIEDLILEAYSAT 396
++ L G+ + ED LEVTG + S + L+ ++ ++
Sbjct: 218 LSILDQAISFGDGK-VTYEDALEVTGSV------------SQEALDDLVDAIV--EGDVA 262
Query: 397 QLFDQFHDIVMS 408
+ +++
Sbjct: 263 KALKILEELLDE 274
>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of
cellular Activities) superfamily represents an ancient
group of ATPases belonging to the ASCE (for additional
strand, catalytic E) division of the P-loop NTPase fold.
The ASCE division also includes ABC, RecA-like,
VirD4-like, PilT-like, and SF1/2 helicases. Members of
the AAA+ ATPases function as molecular chaperons, ATPase
subunits of proteases, helicases, or nucleic-acid
stimulated ATPases. The AAA+ proteins contain several
distinct features in addition to the conserved
alpha-beta-alpha core domain structure and the Walker A
and B motifs of the P-loop NTPases.
Length = 151
Score = 85.7 bits (212), Expect = 6e-20
Identities = 41/157 (26%), Positives = 66/157 (42%), Gaps = 15/157 (9%)
Query: 48 IEQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQLFGDMYRERILELNASDD 107
+ Q+E + L++ L + L YGPPGTGKT+ A ++LF L LNASD
Sbjct: 1 VGQEEAIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELF--RPGAPFLYLNASDL 58
Query: 108 RGIQVIRDKVKTFAQQTASGFNQDGKPCPPFKIVILDEADSMTHAAQAALRRTME----- 162
V+ + F + + KP ++ +DE DS++ AQ AL R +E
Sbjct: 59 LEGLVVAELFGHFLVRLLFELAEKAKPG----VLFIDEIDSLSRGAQNALLRVLETLNDL 114
Query: 163 -KETKSTRFCLICNYVSC--IIQPLTSRC-SKFRFKP 195
+ ++ R N + + L R +
Sbjct: 115 RIDRENVRVIGATNRPLLGDLDRALYDRLDIRIVIPL 151
>gnl|CDD|184925 PRK14961, PRK14961, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 363
Score = 82.9 bits (205), Expect = 2e-17
Identities = 67/285 (23%), Positives = 129/285 (45%), Gaps = 48/285 (16%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTST--MIAA-------- 86
K+RP+ D+I Q+ +V+ + LS + H +L G G GKT+ ++A
Sbjct: 9 KWRPQYFRDIIGQKHIVTAISNGLSLGRIHHAWLLSGTRGVGKTTIARLLAKSLNCQNGI 68
Query: 87 ----CHQ----------LFGDMYRERILELNASDDRGIQVIRDKVKTFAQQTASGFNQDG 132
C + L D+ E++A+ ++ +R+ + +
Sbjct: 69 TSNPCRKCIICKEIEKGLCLDLI-----EIDAASRTKVEEMREILDNIYYSPSKS----- 118
Query: 133 KPCPPFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFR 192
FK+ ++DE ++ + AL +T+E+ + +F L V I + + SRC +F+
Sbjct: 119 ----RFKVYLIDEVHMLSRHSFNALLKTLEEPPQHIKFILATTDVEKIPKTILSRCLQFK 174
Query: 193 FKPLAENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCLQSCARLKGGEGIV 252
K ++E + L+YI +ES+ D AL+ + + G MR A+ L+ L G+G +
Sbjct: 175 LKIISEEKIFNFLKYILIKESIDTDEYALKLIAYHAHGSMRDALNLLEHAINL--GKGNI 232
Query: 253 NE-DVLEVTGVIPKPWI----EKLLKVDSFQVLE--KYIEDLILE 290
N +V ++ G++ + + LLK DS + + I + +E
Sbjct: 233 NIKNVTDMLGLLNEKQSFLLTDALLKKDSKKTMLLLNKISSIGIE 277
>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the
Holliday junction resolvase [DNA replication,
recombination, and repair].
Length = 436
Score = 83.4 bits (207), Expect = 3e-17
Identities = 62/245 (25%), Positives = 107/245 (43%), Gaps = 38/245 (15%)
Query: 34 PWVEKYRPKTIDDVIEQQEVV---SVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQL 90
P E+ RPK++D+V+ Q+ ++ L++ + L + +GPPGTGKT+ +A +L
Sbjct: 13 PLAERLRPKSLDEVVGQEHLLGEGKPLRRAVEAGHLHSMILWGPPGTGKTT--LA---RL 67
Query: 91 FGDMYRERILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPPFKIVILDEADSMT 150
L+A G++ +R+ ++ A++ + I+ LDE
Sbjct: 68 IAGTTNAAFEALSAVTS-GVKDLREIIEE-ARKN---RLLGRRT-----ILFLDEIHRFN 117
Query: 151 HAAQAALRRTMEKETKSTRFCLIC------NYVSCIIQPLTSRCSKFRFKPLAENTMLTR 204
A Q AL +E T LI ++ + L SR F KPL+ +
Sbjct: 118 KAQQDALLPHVENGT----IILIGATTENPSFE--LNPALLSRARVFELKPLSSEDIKKL 171
Query: 205 LQYICEQES-------VMCDFKALETLVETSGGDMRRAITCLQSCARL-KGGEGIVNEDV 256
L+ E ++ D +AL+ LV S GD RRA+ L+ A + E ++ E +
Sbjct: 172 LKRALLDEERGLGGQIIVLDEEALDYLVRLSNGDARRALNLLELAALSAEPDEVLILELL 231
Query: 257 LEVTG 261
E+
Sbjct: 232 EEILQ 236
Score = 28.4 bits (64), Expect = 8.0
Identities = 15/43 (34%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 321 ALETLVETSGGDMRRAITCLQSCARL-KGGEGIVNEDVLEVTG 362
AL+ LV S GD RRA+ L+ A + E ++ E + E+
Sbjct: 194 ALDYLVRLSNGDARRALNLLELAALSAEPDEVLILELLEEILQ 236
>gnl|CDD|237871 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 576
Score = 83.3 bits (206), Expect = 5e-17
Identities = 83/344 (24%), Positives = 143/344 (41%), Gaps = 57/344 (16%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTSTM-IAA----CHQLF 91
KYRP+T D+ Q+ V L+ + + H FLF G G GKTST I A C Q
Sbjct: 9 KYRPQTFSDLTGQEHVSRTLQNAIDTGRVAHAFLFTGARGVGKTSTARILAKALNCEQ-- 66
Query: 92 GDMYRE-----------------RILELNASDDRG---IQVIRDKVKTFAQQTASGFNQD 131
+ E + E++ + + G I+ +R+ VK ++
Sbjct: 67 -GLTAEPCNVCPPCVEITEGRSVDVFEIDGASNTGVDDIRELRENVKYLPSRSR------ 119
Query: 132 GKPCPPFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKF 191
+KI I+DE ++ A AL +T+E+ +F + + SRC +F
Sbjct: 120 ------YKIFIIDEVHMLSTNAFNALLKTLEEPPPHVKFIFATTEPHKVPITILSRCQRF 173
Query: 192 RFKPLAENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCLQSCARLKGGEGI 251
F+ + ++ RL+YI +QE + AL + G MR +++ L G+ +
Sbjct: 174 DFRRIPLQKIVDRLRYIADQEGISISDAALALVARKGDGSMRDSLSTLDQ-VLAFCGDAV 232
Query: 252 VNEDVLEVTGVIPKPWI----EKLLKVDSFQVLEKYIEDLILEAYSATQ----LFDQFHD 303
++DV E+ GV+ + + + D+ +LE +E + Y+ Q L D +
Sbjct: 233 GDDDVAELLGVVDRRLLLDISAAVFGRDTRALLEI-VERVDEFGYNMRQFCQELIDHLRN 291
Query: 304 IVML-----ASSLSDKQKALFKALETLVET-SGGDMRRAITCLQ 341
+V+L L D +A L D++R +T L
Sbjct: 292 LVVLRAVGEPGDLLDLSEAELAELRAQAAAADAADLQRHLTLLL 335
>gnl|CDD|184927 PRK14963, PRK14963, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 504
Score = 81.4 bits (201), Expect = 1e-16
Identities = 60/223 (26%), Positives = 97/223 (43%), Gaps = 28/223 (12%)
Query: 37 EKYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTST-----MIAACH-- 88
++ RP T D+V+ Q+ V VL L L H +LF GP G GKT+T M C
Sbjct: 6 QRARPITFDEVVGQEHVKEVLLAALRQGRLGHAYLFSGPRGVGKTTTARLIAMAVNCSGE 65
Query: 89 -----------QLFGDMYRERILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPP 137
+LE++A+ + ++ +RD + G
Sbjct: 66 DPKPCGECESCLAVRRGAHPDVLEIDAASNNSVEDVRDLREKVLLAPLRG---------G 116
Query: 138 FKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLA 197
K+ ILDEA M+ +A AL +T+E+ + F L + + SR FRF+ L
Sbjct: 117 RKVYILDEAHMMSKSAFNALLKTLEEPPEHVIFILATTEPEKMPPTILSRTQHFRFRRLT 176
Query: 198 ENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCLQ 240
E + +L+ + E E + +AL+ + + G MR A + L+
Sbjct: 177 EEEIAGKLRRLLEAEGREAEPEALQLVARLADGAMRDAESLLE 219
>gnl|CDD|184934 PRK14970, PRK14970, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 367
Score = 80.7 bits (199), Expect = 1e-16
Identities = 80/309 (25%), Positives = 128/309 (41%), Gaps = 39/309 (12%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTSTMIAACHQLFGDMYR 96
KYRP+T DDV+ Q + + L + L LF GP G GKT+ C ++
Sbjct: 10 KYRPQTFDDVVGQSHITNTLLNAIENNHLAQALLFCGPRGVGKTT-----CARILARKIN 64
Query: 97 ER------------ILELNASDDRGIQVIRDKVKT--FAQQTASGFNQDGKPCPPFKIVI 142
+ I EL+A+ + + IR+ + QT GK +KI I
Sbjct: 65 QPGYDDPNEDFSFNIFELDAASNNSVDDIRNLIDQVRIPPQT-------GK----YKIYI 113
Query: 143 LDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLAENTML 202
+DE ++ AA A +T+E+ F L II + SRC F FK + +
Sbjct: 114 IDEVHMLSSAAFNAFLKTLEEPPAHAIFILATTEKHKIIPTILSRCQIFDFKRITIKDIK 173
Query: 203 TRLQYICEQESVMCDFKALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVTGV 262
L I +E + + AL + + + G +R A++ G+ I + V E +
Sbjct: 174 EHLAGIAVKEGIKFEDDALHIIAQKADGALRDALSIFDRVVTFC-GKNITRQAVTENLNI 232
Query: 263 IPKPWIEKLLKVDSFQVLEKYIEDLILEAYS--ATQLFDQFHDIVMLASSLSDKQKALFK 320
+ + + V +LE I +L+L A++ + FD H I LAS D +
Sbjct: 233 LD---YDTYINVTDL-ILENKIPELLL-AFNEILRKGFDGHHFIAGLASHFRDLMVSKTP 287
Query: 321 ALETLVETS 329
A L+E
Sbjct: 288 ATIALLEVG 296
>gnl|CDD|180643 PRK06645, PRK06645, DNA polymerase III subunits gamma and tau;
Validated.
Length = 507
Score = 81.1 bits (200), Expect = 2e-16
Identities = 71/302 (23%), Positives = 127/302 (42%), Gaps = 44/302 (14%)
Query: 30 NKPVPWVEKYRPKTIDDVIEQQEVVSVL-----KKCLSGADLPHFLFYGPPGTGKT---- 80
N+ +P+ KYRP ++ Q+ +V VL L+G +L G G GKT
Sbjct: 6 NQYIPFARKYRPSNFAELQGQEVLVKVLSYTILNDRLAGG----YLLTGIRGVGKTTSAR 61
Query: 81 --------------STMIAACHQL-----FGDMYRERILELNASDDRGIQVIRDKVKTFA 121
+T I C Q F + I+E++A+ + IR +++
Sbjct: 62 IIAKAVNCSALITENTTIKTCEQCTNCISFNNHNHPDIIEIDAASKTSVDDIRRIIESAE 121
Query: 122 QQTASGFNQDGKPCPPFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCII 181
+ G KI I+DE ++ A AL +T+E+ F V I
Sbjct: 122 YKPLQG---------KHKIFIIDEVHMLSKGAFNALLKTLEEPPPHIIFIFATTEVQKIP 172
Query: 182 QPLTSRCSKFRFKPLAENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCLQS 241
+ SRC ++ + L+ + L+YI +QE++ D +AL + S G R A++ L
Sbjct: 173 ATIISRCQRYDLRRLSFEEIFKLLEYITKQENLKTDIEALRIIAYKSEGSARDAVSILDQ 232
Query: 242 CARL--KGGEGIVNEDVLEVTGVIPKPWIEKLLKVDSFQVLEKYIEDLILEAYSATQLFD 299
A + K I + + ++ G++ I + ++ + EK I +LI + Y ++ +
Sbjct: 233 AASMSAKSDNIISPQVINQMLGLVDSSVIIEFVEYIIHRETEKAI-NLINKLYGSSVNLE 291
Query: 300 QF 301
F
Sbjct: 292 IF 293
>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 585
Score = 78.7 bits (194), Expect = 1e-15
Identities = 61/236 (25%), Positives = 102/236 (43%), Gaps = 36/236 (15%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTST--MIAACHQLFGDM 94
K+R +T +++ Q+ VV L+ ++ + H +LF GP G GKTST ++A +
Sbjct: 9 KWRSQTFAELVGQEHVVQTLRNAIAEGRVAHAYLFTGPRGVGKTSTARILAKAVNCTTND 68
Query: 95 YRER------------------ILELNASDDRG---IQVIRDKVKTFAQQTASGFNQDGK 133
+ R ++E++A+ + I ++V+ F A
Sbjct: 69 PKGRPCGTCEMCRAIAEGSAVDVIEMDAASHTSVDDAREIIERVQ-FRPALAR------- 120
Query: 134 PCPPFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRF 193
+K+ I+DE ++ AA AL +T+E+ F L V + + SRC +F F
Sbjct: 121 ----YKVYIIDEVHMLSTAAFNALLKTLEEPPPHAIFILATTEVHKVPATILSRCQRFDF 176
Query: 194 KPLAENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCLQSCARLKGGE 249
+ M L+ I E + + ALE + + G MR A LQ A GGE
Sbjct: 177 HRHSVADMAAHLRKIAAAEGINLEPGALEAIARAATGSMRDAENLLQQLATTYGGE 232
>gnl|CDD|223546 COG0470, HolB, ATPase involved in DNA replication [DNA replication,
recombination, and repair].
Length = 230
Score = 74.3 bits (182), Expect = 4e-15
Identities = 48/149 (32%), Positives = 70/149 (46%), Gaps = 21/149 (14%)
Query: 165 TKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLAENTMLTRLQYICEQESVMCDFKALETL 224
K+TRF LI N S I+ + SRC + RFKP +RL+ I E + LE +
Sbjct: 42 PKNTRFILITNDPSKILPTIRSRCQRIRFKP------PSRLEAIAWLED-----QGLEEI 90
Query: 225 VETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVTGVIPKPW----IEKLLKV---DSF 277
+ GD R+AI LQ+ A L+ GE + E +L +P+ +LLK+
Sbjct: 91 AAVAEGDARKAINPLQALAALEIGEESIYEALLL---ALPESLAQLAALELLKLAENKFL 147
Query: 278 QVLEKYIEDLILEAYSATQLFDQFHDIVM 306
+ LEK L+LE L DQ ++
Sbjct: 148 EALEKLWLLLLLEGLLGEDLLDQLQRELL 176
Score = 47.3 bits (112), Expect = 4e-06
Identities = 39/140 (27%), Positives = 63/140 (45%), Gaps = 12/140 (8%)
Query: 311 LSDKQKALFKALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVTGVIPNPW-- 368
L + LE + + GD R+AI LQ+ A L+ GE + E +L +P
Sbjct: 76 LEAIAWLEDQGLEEIAAVAEGDARKAINPLQALAALEIGEESIYEALLL---ALPESLAQ 132
Query: 369 --IEKLLKV---DSFQVLEKYIEDLILEAYSATQLFDQFHDIVMS--ASSLSDKQKALIL 421
+LLK+ + LEK L+LE L DQ ++ + + +++ A +L
Sbjct: 133 LAALELLKLAENKFLEALEKLWLLLLLEGLLGEDLLDQLQRELLKLDKALIQEEKAAELL 192
Query: 422 EKLAECNARLQDGASEYIQI 441
+ LA+ RL DG IQ+
Sbjct: 193 DALAQARRRLLDGLLALIQL 212
>gnl|CDD|236267 PRK08451, PRK08451, DNA polymerase III subunits gamma and tau;
Validated.
Length = 535
Score = 75.5 bits (186), Expect = 1e-14
Identities = 76/234 (32%), Positives = 109/234 (46%), Gaps = 53/234 (22%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTSTM-IAA----CHQLF 91
KYRPK D++I Q+ V L L L H +LF G G+GKTS+ I A C Q
Sbjct: 7 KYRPKHFDELIGQESVSKTLSLALDNNRLAHAYLFSGLRGSGKTSSARIFARALVCEQGP 66
Query: 92 GDMYRER--------------ILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPP 137
+ I+E++A+ +RGI IR+ + +QT K P
Sbjct: 67 SSTPCDTCIQCQSALENRHIDIIEMDAASNRGIDDIRELI----EQT--------KYKPS 114
Query: 138 ---FKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQ-------PLT-- 185
FKI I+DE +T A AL +T+E E S YV I+ P T
Sbjct: 115 MARFKIFIIDEVHMLTKEAFNALLKTLE-EPPS--------YVKFILATTDPLKLPATIL 165
Query: 186 SRCSKFRFKPLAENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCL 239
SR FRFK + +N++++ L+ I E+E V + +ALE L + G +R +T L
Sbjct: 166 SRTQHFRFKQIPQNSIISHLKTILEKEGVSYEPEALEILARSGNGSLRDTLTLL 219
>gnl|CDD|236333 PRK08691, PRK08691, DNA polymerase III subunits gamma and tau;
Validated.
Length = 709
Score = 75.1 bits (184), Expect = 2e-14
Identities = 65/256 (25%), Positives = 120/256 (46%), Gaps = 32/256 (12%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTST-------------- 82
K+RPKT D++ Q+ VV L+ L L H +L G G GKT+
Sbjct: 9 KWRPKTFADLVGQEHVVKALQNALDEGRLHHAYLLTGTRGVGKTTIARILAKSLNCENAQ 68
Query: 83 ------MIAACHQLFGDMYRERILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCP 136
+ +C Q+ Y + +LE++A+ + GI IR+ ++ AQ + GK
Sbjct: 69 HGEPCGVCQSCTQIDAGRYVD-LLEIDAASNTGIDNIREVLEN-AQYAPTA----GK--- 119
Query: 137 PFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPL 196
+K+ I+DE ++ +A A+ +T+E+ + +F L + + SRC +F + +
Sbjct: 120 -YKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILATTDPHKVPVTVLSRCLQFVLRNM 178
Query: 197 AENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDV 256
+ L ++ + E + + AL+ L + G MR A++ L L G+ + DV
Sbjct: 179 TAQQVADHLAHVLDSEKIAYEPPALQLLGRAAAGSMRDALSLLDQAIALGSGK-VAENDV 237
Query: 257 LEVTGVIPKPWIEKLL 272
++ G + K ++ +LL
Sbjct: 238 RQMIGAVDKQYLYELL 253
>gnl|CDD|180523 PRK06305, PRK06305, DNA polymerase III subunits gamma and tau;
Validated.
Length = 451
Score = 74.0 bits (182), Expect = 3e-14
Identities = 63/221 (28%), Positives = 100/221 (45%), Gaps = 34/221 (15%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTS-TMIAA--------- 86
KYRP+T +++ Q VV+VLK L H +LF G GTGKT+ I A
Sbjct: 10 KYRPQTFSEILGQDAVVAVLKNALRFNRAAHAYLFSGIRGTGKTTLARIFAKALNCQNPT 69
Query: 87 -----CHQLFGDMYRE-------RILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKP 134
C+Q +E +LE++ + RGI+ IR +T +
Sbjct: 70 EDQEPCNQCA--SCKEISSGTSLDVLEIDGASHRGIEDIRQINETVLFTPSKS------- 120
Query: 135 CPPFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFK 194
+KI I+DE +T A +L +T+E+ + +F L + I + SRC K K
Sbjct: 121 --RYKIYIIDEVHMLTKEAFNSLLKTLEEPPQHVKFFLATTEIHKIPGTILSRCQKMHLK 178
Query: 195 PLAENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRA 235
+ E T++ +L I +QE + +AL + + G +R A
Sbjct: 179 RIPEETIIDKLALIAKQEGIETSREALLPIARAAQGSLRDA 219
>gnl|CDD|237873 PRK14969, PRK14969, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 527
Score = 71.3 bits (175), Expect = 3e-13
Identities = 72/266 (27%), Positives = 125/266 (46%), Gaps = 52/266 (19%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTST-------------- 82
K+RPK+ +++ Q+ VV L L L H +LF G G GKT+
Sbjct: 9 KWRPKSFSELVGQEHVVRALTNALEQQRLHHAYLFTGTRGVGKTTLARILAKSLNCETGV 68
Query: 83 ------MIAACHQL----FGDMYRERILELNASDDRGIQVIRDKVKT--FAQQTASGFNQ 130
+ +AC ++ F D+ +E++A+ + + +R+ + +A
Sbjct: 69 TATPCGVCSACLEIDSGRFVDL-----IEVDAASNTQVDAMRELLDNAQYAPTRGR---- 119
Query: 131 DGKPCPPFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLT--SRC 188
FK+ I+DE ++ +A A+ +T+E+ + +F L I P+T SRC
Sbjct: 120 -------FKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILATTDPQKI--PVTVLSRC 170
Query: 189 SKFRFKPLAENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCL-QSCARLKG 247
+F K + +++ LQ+I EQE++ D AL+ L + G MR A++ L Q+ A
Sbjct: 171 LQFNLKQMPPPLIVSHLQHILEQENIPFDATALQLLARAAAGSMRDALSLLDQAIAY--- 227
Query: 248 GEGIVNE-DVLEVTGVIPKPWIEKLL 272
G G VNE +V + G I + ++ LL
Sbjct: 228 GGGTVNESEVRAMLGAIDQDYLFALL 253
>gnl|CDD|233087 TIGR00678, holB, DNA polymerase III, delta' subunit. This model
describes the N-terminal half of the delta' subunit of
DNA polymerase III. Delta' is homologous to the gamma
and tau subunits, which form an outgroup for
phylogenetic comparison. The gamma/tau branch of the
tree is much more tighly conserved than the delta'
branch, and some members of that branch score more
highly against this model than some proteins
classisified as delta'. The noise cutoff is set to
detect weakly scoring delta' subunits rather than to
exclude gamma/tau subunits. At position 126-127 of the
seed alignment, this family lacks the HM motif of
gamma/tau; at 132 it has a near-invariant A vs. an
invariant F in gamma/tau [DNA metabolism, DNA
replication, recombination, and repair].
Length = 188
Score = 66.9 bits (164), Expect = 5e-13
Identities = 46/171 (26%), Positives = 70/171 (40%), Gaps = 30/171 (17%)
Query: 57 LKKCLSGADLPH-FLFYGPPGTGKTST---MIAA--CHQLFGDMYRE------RILELNA 104
LK+ L L H +LF GP G GK + A C Q G I N
Sbjct: 4 LKRALEKGRLAHAYLFAGPEGVGKELLALALAKALLCEQPGGGEPCGECPSCRLIEAGNH 63
Query: 105 SDDR---------GIQVIRDKVKTFAQQTASGFNQDGKPCPPFKIVILDEADSMTHAAQA 155
D + +R+ + F +T Q+ ++VI+++A+ M AA
Sbjct: 64 PDLHRLEPEGQSIKVDQVRE-LVEFLSRTP----QES----GRRVVIIEDAERMNEAAAN 114
Query: 156 ALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLAENTMLTRLQ 206
AL +T+E+ +T F LI ++ + SRC F PL+E +L L
Sbjct: 115 ALLKTLEEPPPNTLFILITPSPEKLLPTIRSRCQVLPFPPLSEEALLQWLI 165
>gnl|CDD|237870 PRK14964, PRK14964, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 491
Score = 69.0 bits (169), Expect = 1e-12
Identities = 65/284 (22%), Positives = 125/284 (44%), Gaps = 43/284 (15%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTST--MIAAC-HQLFG- 92
KYRP + D++ Q +V +L+ + +P L G G GKT+ +I+ C + G
Sbjct: 6 KYRPSSFKDLVGQDVLVRILRNAFTLNKIPQSILLVGASGVGKTTCARIISLCLNCSNGP 65
Query: 93 ---------------DMYRERILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPP 137
+ ++E++A+ + + I+ ++ S
Sbjct: 66 TSDPCGTCHNCISIKNSNHPDVIEIDAASNTSVDDIKVILENSCYLPISS---------K 116
Query: 138 FKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLA 197
FK+ I+DE ++++A AL +T+E+ +F L V I + SRC +F + +
Sbjct: 117 FKVYIIDEVHMLSNSAFNALLKTLEEPAPHVKFILATTEVKKIPVTIISRCQRFDLQKIP 176
Query: 198 ENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVL 257
+ ++ L I ++E++ D ++L+ + E S G MR A+ L+ A I + + +
Sbjct: 177 TDKLVEHLVDIAKKENIEHDEESLKLIAENSSGSMRNALFLLEQAA-------IYSNNKI 229
Query: 258 EVTGVIPKPWIEKLLKVDSFQVLEKYIEDLIL-EAYSATQLFDQ 300
V LL +LE +E ++L +A SA +F +
Sbjct: 230 SEKSV------RDLLGCVDKHILEDLVEAILLGDAQSALNVFRE 267
Score = 29.0 bits (65), Expect = 5.8
Identities = 25/107 (23%), Positives = 45/107 (42%), Gaps = 19/107 (17%)
Query: 296 QLFDQFHDIVMLASSLSDKQKALFKALETLVETSGGDMRRAITCLQSCARLKGGEGIVNE 355
+L + DI + D++ +L+ + E S G MR A+ L+ A I +
Sbjct: 179 KLVEHLVDIAKKENIEHDEE-----SLKLIAENSSGSMRNALFLLEQAA-------IYSN 226
Query: 356 DVLEVTGVIPNPWIEKLLKVDSFQVLEKYIEDLIL-EAYSATQLFDQ 401
+ + V LL +LE +E ++L +A SA +F +
Sbjct: 227 NKISEKSV------RDLLGCVDKHILEDLVEAILLGDAQSALNVFRE 267
>gnl|CDD|235638 PRK05896, PRK05896, DNA polymerase III subunits gamma and tau;
Validated.
Length = 605
Score = 68.7 bits (168), Expect = 2e-12
Identities = 70/289 (24%), Positives = 124/289 (42%), Gaps = 39/289 (13%)
Query: 37 EKYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTS--TMIAA------- 86
KYRP +I Q+ + +L + L H ++F GP G GKTS + A
Sbjct: 8 RKYRPHNFKQIIGQELIKKILVNAILNNKLTHAYIFSGPRGIGKTSIAKIFAKAINCLNP 67
Query: 87 -----CHQ-----LFGDMYRERILELNASDDRGIQVIRDKVKT--FAQQTASGFNQDGKP 134
C+ I+EL+A+ + G+ IR+ + + T
Sbjct: 68 KDGDCCNSCSVCESINTNQSVDIVELDAASNNGVDEIRNIIDNINYLPTTFK-------- 119
Query: 135 CPPFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLT--SRCSKFR 192
+K+ I+DEA ++ +A AL +T+E+ K F I PLT SRC ++
Sbjct: 120 ---YKVYIIDEAHMLSTSAWNALLKTLEEPPKHVVFIFATTEFQKI--PLTIISRCQRYN 174
Query: 193 FKPLAENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCLQSCARLKGGEGIV 252
FK L + + L+ I ++E + + A++ + + + G +R ++ L + K E I
Sbjct: 175 FKKLNNSELQELLKSIAKKEKIKIEDNAIDKIADLADGSLRDGLSILDQLSTFKNSE-ID 233
Query: 253 NEDVLEVTGVIPKPWIEKLLKVDSFQVLEKYIEDLILEAYSATQLFDQF 301
ED+ + G++ L+++ +E+ LI E S F+ F
Sbjct: 234 IEDINKTFGLVDNNKKINLIELIQKNDIEELRN-LINELESKGINFEAF 281
>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 614
Score = 67.5 bits (165), Expect = 5e-12
Identities = 63/235 (26%), Positives = 105/235 (44%), Gaps = 36/235 (15%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTS------------TMI 84
KYRP T + V+ Q+ + + LK ++ L H +LF GP G GKT+ +
Sbjct: 10 KYRPSTFESVVGQEALTTTLKNAIATNKLAHAYLFCGPRGVGKTTCARIFAKTINCQNLT 69
Query: 85 A---ACHQL-----FGDMYRERILELNASDDRGIQVIR---DKVKTFAQQTASGFNQDGK 133
A AC++ F + I EL+A+ + + IR ++V+ Q GK
Sbjct: 70 ADGEACNECESCVAFNEQRSYNIHELDAASNNSVDDIRNLIEQVRIPPQI--------GK 121
Query: 134 PCPPFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRF 193
+KI I+DE ++ AA A +T+E+ F L I+ + SRC F F
Sbjct: 122 ----YKIYIIDEVHMLSQAAFNAFLKTLEEPPSYAIFILATTEKHKILPTILSRCQIFDF 177
Query: 194 KPLAENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCLQSCARLKGG 248
+ ++ LQY+ +E + + +AL + + + G MR A++ GG
Sbjct: 178 NRIQVADIVNHLQYVASKEGITAEPEALNVIAQKADGGMRDALSIFDQVVSFTGG 232
>gnl|CDD|203973 pfam08542, Rep_fac_C, Replication factor C C-terminal domain. This
is the C-terminal domain of RFC (replication factor-C)
protein of the clamp loader complex which binds to the
DNA sliding clamp (proliferating cell nuclear antigen,
PCNA). The five modules of RFC assemble into a
right-handed spiral, which results in only three of the
five RFC subunits (RFC-A, RFC-B and RFC-C) making
contact with PCNA, leaving a wedge-shaped gap between
RFC-E and the PCNA clamp-loader complex. The C-terminal
is vital for the correct orientation of RFC-E with
respect to RFC-A.
Length = 89
Score = 61.0 bits (149), Expect = 7e-12
Identities = 24/81 (29%), Positives = 43/81 (53%), Gaps = 4/81 (4%)
Query: 369 IEKLLKV---DSFQVLEKYIEDLILEAYSATQLFDQFHDIVMSASSLSDKQKALILEKLA 425
I+++L F + + +L++E SA + Q H++++ + D K I+++LA
Sbjct: 8 IKEILDSILKGDFDEARETLYELLVEGISAEDILKQLHEVLIR-LDIPDSLKLEIIKELA 66
Query: 426 ECNARLQDGASEYIQILDLGS 446
E RL DGA E IQ+ L +
Sbjct: 67 EIEHRLSDGAKEIIQLEALIA 87
Score = 29.8 bits (68), Expect = 0.77
Identities = 13/62 (20%), Positives = 27/62 (43%), Gaps = 4/62 (6%)
Query: 261 GVIPKPWIEKLLKV---DSFQVLEKYIEDLILEAYSATQLFDQFHDIVMLASSLSDKQKA 317
G P I+++L F + + +L++E SA + Q H++++ + D K
Sbjct: 1 GWPPPEDIKEILDSILKGDFDEARETLYELLVEGISAEDILKQLHEVLI-RLDIPDSLKL 59
Query: 318 LF 319
Sbjct: 60 EI 61
>gnl|CDD|184920 PRK14956, PRK14956, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 484
Score = 66.5 bits (162), Expect = 1e-11
Identities = 57/220 (25%), Positives = 97/220 (44%), Gaps = 37/220 (16%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTSTM------------- 83
KYRP+ DVI Q + L+ L + H ++F+GP G GKT+
Sbjct: 11 KYRPQFFRDVIHQDLAIGALQNALKSGKIGHAYIFFGPRGVGKTTIARILAKRLNCENPI 70
Query: 84 -------IAACHQLFGDMYRERILELNASDDRGIQVIR---DKVKTFAQQTASGFNQDGK 133
+C ++ + + +LE++A+ +RGI+ IR D VK F G
Sbjct: 71 GNEPCNECTSCLEITKGISSD-VLEIDAASNRGIENIRELRDNVK---------FAPMGG 120
Query: 134 PCPPFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRF 193
+K+ I+DE +T + AL +T+E+ F L I + + SRC F F
Sbjct: 121 K---YKVYIIDEVHMLTDQSFNALLKTLEEPPAHIVFILATTEFHKIPETILSRCQDFIF 177
Query: 194 KPLAENTMLTRLQYICEQESVMCDFKALETLVETSGGDMR 233
K + + + + +C+ E+V D + L + + G +R
Sbjct: 178 KKVPLSVLQDYSEKLCKIENVQYDQEGLFWIAKKGDGSVR 217
>gnl|CDD|215649 pfam00004, AAA, ATPase family associated with various cellular
activities (AAA). AAA family proteins often perform
chaperone-like functions that assist in the assembly,
operation, or disassembly of protein complexes.
Length = 131
Score = 61.8 bits (151), Expect = 1e-11
Identities = 28/143 (19%), Positives = 49/143 (34%), Gaps = 29/143 (20%)
Query: 70 LFYGPPGTGKTSTMIAACHQLFGDMYRERILELNASDDRGIQVIRDK-VKTFAQQTASGF 128
L YGPPGTGKT+ + ++ +E++ S+ + K V ++ F
Sbjct: 2 LLYGPPGTGKTTL----AKAVAKELGA-PFIEISGSE------LVSKYVGESEKRLRELF 50
Query: 129 NQDGKPCPPFKIVILDEADSMTHA-----------AQAALRRTMEKETKSTR---FCLIC 174
K P ++ +DE D++ + L ++ T S
Sbjct: 51 EAAKKLAPC--VIFIDEIDALAGSRGSGGDSESRRVVNQLLTELDGFTSSLSKVIVIAAT 108
Query: 175 NYVSCIIQPL-TSRCSKFRFKPL 196
N + L R + PL
Sbjct: 109 NRPDKLDPALLRGRFDRIIEFPL 131
>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 618
Score = 66.3 bits (162), Expect = 1e-11
Identities = 66/233 (28%), Positives = 108/233 (46%), Gaps = 50/233 (21%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKT--STMIA--------- 85
KYRP++ +++ Q+ VV L L+ L H +LF G G GKT S ++A
Sbjct: 9 KYRPRSFSEMVGQEHVVQALTNALTQQRLHHAYLFTGTRGVGKTTVSRILAKSLNCQGPD 68
Query: 86 --------------ACHQL----FGDMYRERILELNASDDRGIQVIRDKVKTFAQQTASG 127
AC + F D Y EL+A+ +RG+ D+V+ +Q
Sbjct: 69 GQGGITATPCGVCQACRDIDSGRFVD-Y----TELDAASNRGV----DEVQQLLEQAVY- 118
Query: 128 FNQDGKPCPP-FKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLT- 185
KP FK+ ++DE +T+ A A+ +T+E+ + +F L + P+T
Sbjct: 119 -----KPVQGRFKVFMIDEVHMLTNTAFNAMLKTLEEPPEYLKFVLATTDPQKV--PVTV 171
Query: 186 -SRCSKFRFKPLAENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAIT 237
SRC +F +P+A T+L L + E+V + +AL L + G MR A++
Sbjct: 172 LSRCLQFNLRPMAPETVLEHLTQVLAAENVPAEPQALRLLARAARGSMRDALS 224
>gnl|CDD|237866 PRK14952, PRK14952, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 584
Score = 65.7 bits (160), Expect = 2e-11
Identities = 76/325 (23%), Positives = 129/325 (39%), Gaps = 50/325 (15%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTST-------------- 82
KYRP T +V+ Q+ V L L + H +LF GP G GKTS+
Sbjct: 6 KYRPATFAEVVGQEHVTEPLSSALDAGRINHAYLFSGPRGCGKTSSARILARSLNCAQGP 65
Query: 83 ------MIAACHQLF----GDMYRERILELNASDDRGI---QVIRDKVKTFAQQTASGFN 129
+ +C L G + ++EL+A+ G+ + +RD+ Q+
Sbjct: 66 TATPCGVCESCVALAPNGPGSI---DVVELDAASHGGVDDTRELRDRAFYAPAQSR---- 118
Query: 130 QDGKPCPPFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCS 189
++I I+DEA +T A AL + +E+ + F ++ + SR
Sbjct: 119 --------YRIFIVDEAHMVTTAGFNALLKIVEEPPEHLIFIFATTEPEKVLPTIRSRTH 170
Query: 190 KFRFKPLAENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCLQSCARLKGGE 249
+ F+ L TM + ICEQE V+ D ++ GG R ++ L
Sbjct: 171 HYPFRLLPPRTMRALIARICEQEGVVVDDAVYPLVIRAGGGSPRDTLSVLDQLLAGAADT 230
Query: 250 GIVNEDVLEVTGVIPKPWIEKL---LKVDSFQVLEKYIEDLILEAYS----ATQLFDQFH 302
+ + L + G I+ L D L IE +I + AT L ++F
Sbjct: 231 HVTYQRALGLLGATDVALIDDAVDALAADDAAALFGAIESVIDAGHDPRRFATDLLERFR 290
Query: 303 DIVMLASSLSDKQKALFKALETLVE 327
D+++L + + + A E ++E
Sbjct: 291 DLIVLQAVPDAAARGVVDAPEDVLE 315
>gnl|CDD|184919 PRK14955, PRK14955, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 397
Score = 63.4 bits (154), Expect = 7e-11
Identities = 72/310 (23%), Positives = 121/310 (39%), Gaps = 50/310 (16%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTSTM-----IAACHQLF 91
KYRPK D+ Q+ + ++ L + H ++F G G GKT+ C ++
Sbjct: 9 KYRPKKFADITAQEHITRTIQNSLRMGRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMI 68
Query: 92 GDM-YRERILE----------------LNASD-DRGIQVIRDKVKTFAQQTASGFNQDGK 133
D Y + + E LN S+ D D ++ + G Q G+
Sbjct: 69 DDADYLQEVTEPCGECESCRDFDAGTSLNISEFDAASNNSVDDIRLLRENVRYG-PQKGR 127
Query: 134 PCPPFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRF 193
+++ I+DE ++ AA A +T+E+ F + I + SRC +F F
Sbjct: 128 ----YRVYIIDEVHMLSIAAFNAFLKTLEEPPPHAIFIFATTELHKIPATIASRCQRFNF 183
Query: 194 KPLAENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCLQSC---ARLKGGEG 250
K + + +LQ ICE E + D AL+ + + G MR A + L + GEG
Sbjct: 184 KRIPLEEIQQQLQGICEAEGISVDADALQLIGRKAQGSMRDAQSILDQVIAFSVESEGEG 243
Query: 251 -------------IVNEDVLEVTGVIPKPWIEKLLKVDSFQVLEKYIEDLILEAYSATQL 297
I +E VT + +L V F + Y E LE +L
Sbjct: 244 SIRYDKVAELLNYIDDEHFFAVTDAVADGDAVAMLDVAQFVIRNGYDEQDFLE-----KL 298
Query: 298 FDQFHDIVML 307
+ + +++
Sbjct: 299 IEHLRNFLVV 308
>gnl|CDD|184918 PRK14954, PRK14954, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 620
Score = 63.4 bits (154), Expect = 1e-10
Identities = 75/310 (24%), Positives = 127/310 (40%), Gaps = 50/310 (16%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTSTM-----IAACHQLF 91
KYRP D+ Q+ + ++ L + H ++F G G GKT+ C ++
Sbjct: 9 KYRPSKFADITAQEHITHTIQNSLRMDRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMI 68
Query: 92 GD-MYRERILE----------------LNASD-DRGIQVIRDKVKTFAQQTASGFNQDGK 133
D +Y + + E LN S+ D D ++ + G Q G+
Sbjct: 69 DDPVYLQEVTEPCGECESCRDFDAGTSLNISEFDAASNNSVDDIRQLRENVRYG-PQKGR 127
Query: 134 PCPPFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRF 193
+++ I+DE ++ AA A +T+E+ F + I + SRC +F F
Sbjct: 128 ----YRVYIIDEVHMLSTAAFNAFLKTLEEPPPHAIFIFATTELHKIPATIASRCQRFNF 183
Query: 194 KPLAENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCL-QSCARLKGGEG-- 250
K + + + ++LQ IC E + D AL+ + + G MR A + L Q A G E
Sbjct: 184 KRIPLDEIQSQLQMICRAEGIQIDADALQLIARKAQGSMRDAQSILDQVIAFSVGSEAEK 243
Query: 251 -------------IVNEDVLEVTGVIPKPWIEKLLKVDSFQVLEKYIEDLILEAYSATQL 297
I +E +VT I + K+L+V F + Y E LE +L
Sbjct: 244 VIAYQGVAELLNYIDDEQFFDVTDAIAENDAVKMLEVARFVIDNGYDEQDFLE-----KL 298
Query: 298 FDQFHDIVML 307
+ F + ++L
Sbjct: 299 IEHFRNFLVL 308
>gnl|CDD|237354 PRK13341, PRK13341, recombination factor protein RarA/unknown
domain fusion protein; Reviewed.
Length = 725
Score = 63.5 bits (155), Expect = 1e-10
Identities = 52/223 (23%), Positives = 95/223 (42%), Gaps = 36/223 (16%)
Query: 34 PWVEKYRPKTIDDVIEQQEVVS---VLKKCLSGADLPHFLFYGPPGTGKTS--TMIAACH 88
P ++ RP+T+++ + Q ++ +L++ + + + YGPPG GKT+ +IA
Sbjct: 17 PLADRLRPRTLEEFVGQDHILGEGRLLRRAIKADRVGSLILYGPPGVGKTTLARIIA--- 73
Query: 89 QLFGDMYRERILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPPFKIVILDEADS 148
+ R LNA G++ +R +V A++ + I+ +DE
Sbjct: 74 ----NHTRAHFSSLNAV-LAGVKDLRAEVDR-AKERLERHGKR-------TILFIDEVHR 120
Query: 149 MTHAAQAALRRTMEKETKSTRFCLIC----NYVSCIIQPLTSRCSKFRFKPLAENTMLTR 204
A Q AL +E T LI N + + L SR FR K L++ +
Sbjct: 121 FNKAQQDALLPWVENGT----ITLIGATTENPYFEVNKALVSRSRLFRLKSLSDEDLHQL 176
Query: 205 LQYICEQE-------SVMCDFKALETLVETSGGDMRRAITCLQ 240
L+ + + V + +A + LV+ + GD R + L+
Sbjct: 177 LKRALQDKERGYGDRKVDLEPEAEKHLVDVANGDARSLLNALE 219
>gnl|CDD|221959 pfam13177, DNA_pol3_delta2, DNA polymerase III, delta subunit. DNA
polymerase III, delta subunit (EC 2.7.7.7) is required
for, along with delta' subunit, the assembly of the
processivity factor beta(2) onto primed DNA in the DNA
polymerase III holoenzyme-catalyzed reaction. The delta
subunit is also known as HolA.
Length = 161
Score = 59.5 bits (145), Expect = 1e-10
Identities = 44/168 (26%), Positives = 71/168 (42%), Gaps = 30/168 (17%)
Query: 50 QQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTST-----MIAACHQLFGDMYRE------ 97
Q +V+ +LK + L H +LF GP G GK C D
Sbjct: 2 QPKVIKLLKNSIKKNKLSHAYLFSGPDGVGKLELALEFAKALFCENPQDDEPCGECKSCK 61
Query: 98 RILELNASDDR---------GIQVIRDKVKTFAQQTASGFNQDGKPCPPFKIVILDEADS 148
RI N D I IR+ ++ F++ F K+ I+++A+
Sbjct: 62 RIENGNHPDVIIIEPEGKSIKIDQIRELIEEFSK---KPFEG------KKKVYIIEDAEK 112
Query: 149 MTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPL 196
MT +A AL +T+E+ ++T F L+ + + ++ + SRC FKPL
Sbjct: 113 MTESAANALLKTLEEPPENTYFILLTSNPNKLLPTIRSRCQVINFKPL 160
>gnl|CDD|184923 PRK14959, PRK14959, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 624
Score = 61.6 bits (149), Expect = 4e-10
Identities = 51/227 (22%), Positives = 92/227 (40%), Gaps = 31/227 (13%)
Query: 34 PWVEKYRPKTIDDVIEQQEVVSVLKKCLSGADL-PHFLFYGPPGTGKTS----------- 81
+YRP+T +V Q+ V ++L + + P +LF G G GKT+
Sbjct: 5 SLTARYRPQTFAEVAGQETVKAILSRAAQENRVAPAYLFSGTRGVGKTTIARIFAKALNC 64
Query: 82 ---------TMIAACHQLFGDMYRERILELNASDDRGIQVIRDKVKTFAQQTASGFNQDG 132
C ++ M+ + ++E++ + +RGI + + G
Sbjct: 65 ETAPTGEPCNTCEQCRKVTQGMHVD-VVEIDGASNRGIDDAKRLKEAIGYAPMEG----- 118
Query: 133 KPCPPFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFR 192
+K+ I+DEA +T A AL +T+E+ F L + SRC F
Sbjct: 119 ----RYKVFIIDEAHMLTREAFNALLKTLEEPPARVTFVLATTEPHKFPVTIVSRCQHFT 174
Query: 193 FKPLAENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCL 239
F L+E + L + +E V D A+ + + G +R +++ L
Sbjct: 175 FTRLSEAGLEAHLTKVLGREGVDYDPAAVRLIARRAAGSVRDSMSLL 221
>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 700
Score = 61.0 bits (148), Expect = 7e-10
Identities = 57/232 (24%), Positives = 100/232 (43%), Gaps = 48/232 (20%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKT--STMIA--------- 85
K+RP+ ++ Q+ VV L L L H +LF G G GKT S ++A
Sbjct: 9 KWRPRDFTTLVGQEHVVRALTHALEQQRLHHAYLFTGTRGVGKTTLSRILAKSLNCTGAD 68
Query: 86 --------------ACHQL----FGDMYRERILELNASDDRGIQVIRDKVKTFAQQTASG 127
AC ++ F D +E++A+ +RG+ + + +G
Sbjct: 69 GEGGITAQPCGQCRACTEIDAGRFVDY-----IEMDAASNRGVDEMAQLLDKAVYAPTAG 123
Query: 128 FNQDGKPCPPFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLT-- 185
FK+ ++DE +T+ A A+ +T+E+ + +F L I P+T
Sbjct: 124 ---------RFKVYMIDEVHMLTNHAFNAMLKTLEEPPEHVKFILATTDPQKI--PVTVL 172
Query: 186 SRCSKFRFKPLAENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAIT 237
SRC +F K + +++ L I +E + + AL L + + G MR A++
Sbjct: 173 SRCLQFNLKQMPPGHIVSHLDAILGEEGIAHEVNALRLLAQAAQGSMRDALS 224
>gnl|CDD|237868 PRK14960, PRK14960, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 702
Score = 60.8 bits (147), Expect = 7e-10
Identities = 63/246 (25%), Positives = 112/246 (45%), Gaps = 12/246 (4%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTST--MIAACHQLFGDM 94
KYRP+ ++++ Q V L L L H +LF G G GKT+ ++A C +
Sbjct: 8 KYRPRNFNELVGQNHVSRALSSALERGRLHHAYLFTGTRGVGKTTIARILAKCLNCETGV 67
Query: 95 YR---ERILELNASDD-RGIQVIRDKVKTFAQQTASGFNQDGKPCPP----FKIVILDEA 146
E A ++ R I +I + + + D P P FK+ ++DE
Sbjct: 68 TSTPCEVCATCKAVNEGRFIDLIEIDAASRTKVEDTRELLDNVPYAPTQGRFKVYLIDEV 127
Query: 147 DSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLAENTMLTRLQ 206
++ + AL +T+E+ + +F + + SRC +F +PLA + + L
Sbjct: 128 HMLSTHSFNALLKTLEEPPEHVKFLFATTDPQKLPITVISRCLQFTLRPLAVDEITKHLG 187
Query: 207 YICEQESVMCDFKALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVTGVIPKP 266
I E+E + D A+ + E++ G +R A++ L A G + ++DV E+ G+I +
Sbjct: 188 AILEKEQIAADQDAIWQIAESAQGSLRDALS-LTDQAIAYGQGAVHHQDVKEMLGLIDRT 246
Query: 267 WIEKLL 272
I L+
Sbjct: 247 IIYDLI 252
>gnl|CDD|236011 PRK07399, PRK07399, DNA polymerase III subunit delta'; Validated.
Length = 314
Score = 58.8 bits (143), Expect = 1e-09
Identities = 51/225 (22%), Positives = 92/225 (40%), Gaps = 29/225 (12%)
Query: 45 DDVIEQQEVVSVLKKCLSGADL-PHFLFYGPPGTGKTSTMIAACHQLF-----GDMYRER 98
++I Q + +L + + P +LF GP G G+ + L R R
Sbjct: 4 ANLIGQPLAIELLTAAIKQNRIAPAYLFAGPEGVGRKLAALCFIEGLLSQGSPSKNIRRR 63
Query: 99 ILELNASDDRGIQ---VIRDKVKTFAQQTASGFNQDGKPC---------------PPF-- 138
+ E N D ++ + K+ T ++ +G + P PP
Sbjct: 64 LEEGNHPDLLWVEPTYQHQGKLITASEAEEAGLKRKAPPQIRLEQIREIKRFLSRPPLEA 123
Query: 139 --KIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPL 196
K+V++++A++M AA AL +T+E+ T LI ++ + SRC F L
Sbjct: 124 PRKVVVIEDAETMNEAAANALLKTLEEPGNGT-LILIAPSPESLLPTIVSRCQIIPFYRL 182
Query: 197 AENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCLQS 241
++ + L+ + ++E + +F L L + S G I LQS
Sbjct: 183 SDEQLEQVLKRLGDEEILNINFPELLALAQGSPGAAIANIEQLQS 227
>gnl|CDD|184921 PRK14957, PRK14957, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 546
Score = 59.7 bits (144), Expect = 1e-09
Identities = 63/291 (21%), Positives = 128/291 (43%), Gaps = 35/291 (12%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTS--TMIAACHQLFGDM 94
KYRP++ +V QQ ++ L L + H +LF G G GKT+ ++A C +
Sbjct: 9 KYRPQSFAEVAGQQHALNSLVHALETQKVHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGV 68
Query: 95 YRE-----------------RILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPP 137
E ++E++A+ G++ ++ + + G
Sbjct: 69 TAEPCNKCENCVAINNNSFIDLIEIDAASRTGVEETKEILDNIQYMPSQG---------R 119
Query: 138 FKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLA 197
+K+ ++DE ++ + AL +T+E+ + +F L I + SRC + K ++
Sbjct: 120 YKVYLIDEVHMLSKQSFNALLKTLEEPPEYVKFILATTDYHKIPVTILSRCIQLHLKHIS 179
Query: 198 ENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVL 257
+ + +L+ I +E++ D ++LE + + G +R A++ L GGE + +
Sbjct: 180 QADIKDQLKIILAKENINSDEQSLEYIAYHAKGSLRDALSLLDQAISFCGGE-LKQAQIK 238
Query: 258 EVTGVIPKP----WIEKLLKVDSFQVLEKYIEDLILEAYSATQLFDQFHDI 304
++ G+I I ++ D +L I++L L SA + D+ +I
Sbjct: 239 QMLGIIDSEEVYSIINAIIDNDPKAILPA-IKNLALTESSADAVLDRIAEI 288
>gnl|CDD|235906 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau;
Validated.
Length = 830
Score = 56.8 bits (137), Expect = 2e-08
Identities = 59/225 (26%), Positives = 102/225 (45%), Gaps = 39/225 (17%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKT--STMIA--------- 85
K+RPK ++ Q+ VV L L G L H +LF G G GKT S + A
Sbjct: 9 KWRPKDFASLVGQEHVVRALTHALDGGRLHHAYLFTGTRGVGKTTLSRIFAKALNCETGV 68
Query: 86 ---------ACHQL----FGDMYRERILELNASDDRGIQVIRDKVKTFAQQTASGFNQDG 132
AC ++ F D +E++A+ +RG+ D++ ++ A D
Sbjct: 69 TSQPCGVCRACREIDEGRFVDY-----VEMDAASNRGV----DEMAALLER-AVYAPVDA 118
Query: 133 KPCPPFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFR 192
+ FK+ ++DE +T+ A A+ +T+E+ +F L I + SRC +F
Sbjct: 119 R----FKVYMIDEVHMLTNHAFNAMLKTLEEPPPHVKFILATTDPQKIPVTVLSRCLQFN 174
Query: 193 FKPLAENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAIT 237
K + +++ L+ I +E + + +AL L + G MR A++
Sbjct: 175 LKQMPAGHIVSHLERILGEERIAFEPQALRLLARAAQGSMRDALS 219
>gnl|CDD|184922 PRK14958, PRK14958, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 509
Score = 55.9 bits (134), Expect = 2e-08
Identities = 79/330 (23%), Positives = 135/330 (40%), Gaps = 58/330 (17%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKT--STMIAACHQL---- 90
K+RP+ +VI Q VV L L L H +LF G G GKT S ++A C
Sbjct: 9 KWRPRCFQEVIGQAPVVRALSNALDQQYLHHAYLFTGTRGVGKTTISRILAKCLNCEKGV 68
Query: 91 ------------------FGDMYRERILELNASDDRGIQVIRDKVKTFAQQTASGFNQDG 132
F D++ E++A+ ++ R+ + G
Sbjct: 69 SANPCNDCENCREIDEGRFPDLF-----EVDAASRTKVEDTRELLDNIPYAPTKG----- 118
Query: 133 KPCPPFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFR 192
FK+ ++DE ++ + AL +T+E+ +F L + + SRC +F
Sbjct: 119 ----RFKVYLIDEVHMLSGHSFNALLKTLEEPPSHVKFILATTDHHKLPVTVLSRCLQFH 174
Query: 193 FKPLAENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCL-QSCARLKGGEGI 251
L + Q++ ++E+V + AL+ L + G +R A++ L QS A G I
Sbjct: 175 LAQLPPLQIAAHCQHLLKEENVEFENAALDLLARAANGSVRDALSLLDQSIAYGNGKVLI 234
Query: 252 VNEDVLEVTGVIPKPWIEKLLKVDSFQVLEKYIEDLILEAYSATQLFDQFHDIVMLASSL 311
+ + T IE LL D + L D +L T+L +Q D +++L
Sbjct: 235 ADVKTMLGT-------IEPLLLFDILEALAAKAGDRLLGC--VTRLVEQGVD---FSNAL 282
Query: 312 SD-----KQKALFKAL-ETLVETSGGDMRR 335
+D Q A+ + + E L+E +R+
Sbjct: 283 ADLLSLLHQIAIIQTVPEALIENDSEQLRQ 312
>gnl|CDD|235845 PRK06647, PRK06647, DNA polymerase III subunits gamma and tau;
Validated.
Length = 563
Score = 55.2 bits (133), Expect = 3e-08
Identities = 53/254 (20%), Positives = 103/254 (40%), Gaps = 30/254 (11%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTST-------------- 82
K RP+ + + Q VV LK + + + ++F GP G GKTS+
Sbjct: 9 KRRPRDFNSLEGQDFVVETLKHSIESNKIANAYIFSGPRGVGKTSSARAFARCLNCVNGP 68
Query: 83 MIAACHQLFGDMYRER-----ILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPP 137
C + + ++E++ + + +Q +R + AS
Sbjct: 69 TPMPCGECSSCKSIDNDNSLDVIEIDGASNTSVQDVRQIKEEIMFPPASS---------R 119
Query: 138 FKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLA 197
+++ I+DE ++++A AL +T+E+ F V + + SRC F F+ L+
Sbjct: 120 YRVYIIDEVHMLSNSAFNALLKTIEEPPPYIVFIFATTEVHKLPATIKSRCQHFNFRLLS 179
Query: 198 ENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVL 257
+ L+ +C ++ + + +AL+ + S G +R A T I E +
Sbjct: 180 LEKIYNMLKKVCLEDQIKYEDEALKWIAYKSTGSVRDAYTLFDQVVSFSDS-DITLEQIR 238
Query: 258 EVTGVIPKPWIEKL 271
G+ ++EKL
Sbjct: 239 SKMGLTGDEFLEKL 252
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 51.6 bits (123), Expect = 5e-08
Identities = 34/140 (24%), Positives = 45/140 (32%), Gaps = 15/140 (10%)
Query: 68 HFLFYGPPGTGKTSTMIAACHQLFGDMYR------ERILELNASDDRGIQVIRDKVKTFA 121
L GPPG+GKT+ A +L E ILE I V K
Sbjct: 4 VILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSG 63
Query: 122 QQTASGFNQDGKPCPPFKIVILDEADSMTHAAQAALRR--------TMEKETKSTRFCLI 173
+ + P ++ILDE S+ A Q AL + K K+ L
Sbjct: 64 ELRLRLALALARKLKP-DVLILDEITSLLDAEQEALLLLLEELRLLLLLKSEKNLTVILT 122
Query: 174 CNYVSCIIQPLTSRCSKFRF 193
N + L R R
Sbjct: 123 TNDEKDLGPALLRRRFDRRI 142
>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 620
Score = 53.0 bits (128), Expect = 2e-07
Identities = 71/253 (28%), Positives = 117/253 (46%), Gaps = 41/253 (16%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCL-SGADLPHFLFYGPPGTGKT-STMIAA--------- 86
KYRP+ D+++ Q+ + + LK L S P +LF GP GTGKT S I A
Sbjct: 9 KYRPQRFDELVGQEAIATTLKNALISNRIAPAYLFTGPRGTGKTSSARILAKSLNCLNSD 68
Query: 87 ------------CHQLFGDMYRERILELNASDDRGIQVIRDKVK--TFAQQTASGFNQDG 132
C + ++E++A+ + G+ IR+ ++ FA A
Sbjct: 69 KPTPEPCGKCELCRAI-AAGNALDVIEIDAASNTGVDNIRELIERAQFAPVQAR------ 121
Query: 133 KPCPPFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFR 192
+K+ ++DE ++ AA AL +T+E+ F L ++ + SRC +F
Sbjct: 122 -----WKVYVIDECHMLSTAAFNALLKTLEEPPPRVVFVLATTDPQRVLPTIISRCQRFD 176
Query: 193 FKPLAENTMLTRLQYICEQESVMCDFKALETLV-ETSGGDMRRAITCLQSCARLKGGEGI 251
F+ + M+ L I E+ES+ + +AL TLV + S G +R A + L + L G I
Sbjct: 177 FRRIPLEAMVQHLSEIAEKESIEIEPEAL-TLVAQRSQGGLRDAESLLDQLSLLPG--PI 233
Query: 252 VNEDVLEVTGVIP 264
E V ++ G +P
Sbjct: 234 TPEAVWDLLGAVP 246
>gnl|CDD|131948 TIGR02902, spore_lonB, ATP-dependent protease LonB. Members of
this protein are LonB, a paralog of the ATP-dependent
protease La (LonA, TIGR00763). LonB proteins are found
strictly, and almost universally, in endospore-forming
bacteria. This protease was shown, in Bacillus subtilis,
to be expressed specifically in the forespore, during
sporulation, under control of sigma(F). The lonB gene,
despite location immediately upstream of lonA, was shown
to be monocistronic. LonB appears able to act on
sigma(H) for post-translation control, but lonB mutation
did not produce an obvious sporulation defect under the
conditions tested. Note that additional paralogs of LonA
and LonB occur in the Clostridium lineage and this model
selects only one per species as the protein that
corresponds to LonB in B. subtilis [Protein fate,
Degradation of proteins, peptides, and glycopeptides,
Cellular processes, Sporulation and germination].
Length = 531
Score = 52.9 bits (127), Expect = 2e-07
Identities = 23/48 (47%), Positives = 31/48 (64%)
Query: 34 PWVEKYRPKTIDDVIEQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTS 81
P EK RPK+ D++I Q+E + LK L G + H + YGPPG GKT+
Sbjct: 54 PLSEKTRPKSFDEIIGQEEGIKALKAALCGPNPQHVIIYGPPGVGKTA 101
Score = 29.7 bits (67), Expect = 3.2
Identities = 25/80 (31%), Positives = 40/80 (50%), Gaps = 6/80 (7%)
Query: 184 LTSRCSKFRFKPLAENTMLTRLQYICEQESVMCDFKALETLVE-TSGGDMRRAITCLQSC 242
L SRC + F+PL + + + E+ + + ALE +V+ S G R A+ +Q
Sbjct: 251 LRSRCVEIFFRPLLDEEIKEIAKNAAEKIGINLEKHALELIVKYASNG--REAVNIVQLA 308
Query: 243 ARLKGGEG---IVNEDVLEV 259
A + GEG I+ ED+ V
Sbjct: 309 AGIALGEGRKRILAEDIEWV 328
>gnl|CDD|169667 PRK09112, PRK09112, DNA polymerase III subunit delta'; Validated.
Length = 351
Score = 52.0 bits (125), Expect = 3e-07
Identities = 37/130 (28%), Positives = 60/130 (46%), Gaps = 13/130 (10%)
Query: 109 GIQV--IRDKVKTFAQQTASGFNQDGKPCPPFKIVILDEADSMTHAAQAALRRTMEKETK 166
I V IR F QT+ N ++IVI+D AD M A A+ +T+E+
Sbjct: 120 AITVDEIRRVGH-FLSQTSGDGN--------WRIVIIDPADDMNRNAANAILKTLEEPPA 170
Query: 167 STRFCLICNYVSCIIQPLTSRCSKFRFKPLAENTMLTRLQYICEQESVMCDFKALETLVE 226
F LI + ++ + SRC KPL ++ + L ++ S D + E L++
Sbjct: 171 RALFILISHSSGRLLPTIRSRCQPISLKPLDDDELKKALSHL--GSSQGSDGEITEALLQ 228
Query: 227 TSGGDMRRAI 236
S G +R+A+
Sbjct: 229 RSKGSVRKAL 238
>gnl|CDD|129690 TIGR00602, rad24, checkpoint protein rad24. All proteins in this
family for which functions are known are involved in DNA
damage tolerance (likely cell cycle checkpoints).This
family is based on the phylogenomic analysis of JA Eisen
(1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 637
Score = 52.7 bits (126), Expect = 3e-07
Identities = 49/258 (18%), Positives = 87/258 (33%), Gaps = 56/258 (21%)
Query: 34 PWVEKYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-----FLFYGPPGTGKTSTMIAACH 88
PWVEKY+P+T ++ ++ + ++ L L + L GP G GK ST I
Sbjct: 73 PWVEKYKPETQHELAVHKKKIEEVETWLKAQVLENAPKRILLITGPSGCGK-STTIKILS 131
Query: 89 QLFGDMYRERI----LELNASDDRGIQVIRDKVKTFAQQTAS---------------GFN 129
+ G +E + +D + + F Q G +
Sbjct: 132 KELGIQVQEWSNPTLPDFQKNDHKVTLSLESCFSNFQSQIEVFSEFLLRATNKLQMLGDD 191
Query: 130 QDGKPCPPFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTS--- 186
KI+++++ + + AL + + S C + ++ ++ +
Sbjct: 192 LMTDK----KIILVEDLPNQFYRDTRALHEILRWKYVSIGRCPLVFIITESLEGDNNQRR 247
Query: 187 -----------------RCSKFRFKPLAENTMLTRLQYICEQESVM-------CDFKALE 222
R S F P+A M L I E+ ++E
Sbjct: 248 LLFPAETIMNKEILEEPRVSNISFNPIAPTIMKKFLNRIVTIEAKKNGEKIKVPKKTSVE 307
Query: 223 TLVETSGGDMRRAITCLQ 240
L + GD+R AI LQ
Sbjct: 308 LLCQGCSGDIRSAINSLQ 325
>gnl|CDD|234619 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 51.7 bits (125), Expect = 3e-07
Identities = 21/47 (44%), Positives = 28/47 (59%), Gaps = 5/47 (10%)
Query: 40 RPKTIDDVIEQQEVVSVLKKCLSGAD-----LPHFLFYGPPGTGKTS 81
RPK++D+ I Q++V LK + A L H L YGPPG GKT+
Sbjct: 20 RPKSLDEFIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTT 66
>gnl|CDD|217429 pfam03215, Rad17, Rad17 cell cycle checkpoint protein.
Length = 490
Score = 52.3 bits (125), Expect = 3e-07
Identities = 52/250 (20%), Positives = 92/250 (36%), Gaps = 44/250 (17%)
Query: 34 PWVEKYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-----FLFYGPPGTGKTSTMIAACH 88
W EKY+P+ D++ ++ ++ + L L L GP G GK++T+
Sbjct: 8 LWTEKYKPRRRDELAIHKKKIAEVDHWLKAVFLESNKQLILLLTGPSGCGKSTTVKVLSK 67
Query: 89 QLFGDMYRERI---------LELNASDDRGIQVIRD--KVKTFAQ--QTASGFNQDGKPC 135
+L G E E D RG ++ +++ F + + +
Sbjct: 68 EL-GIEIIEWSNPEYLHNPDNECQKPDFRGDCIVNSLSQMEQFREFLLRGARYGSLQGGG 126
Query: 136 PPFKIVILDEADSMTHAAQAALRRTMEKETKSTR-----FCL-ICNYVSCIIQP------ 183
K+++++E + ++ R + + +S FCL CN +
Sbjct: 127 LKKKLILVEELPNQFYSDAEKFREVIREVLQSIWHLPLIFCLTECNSLEGDNNQDRFGID 186
Query: 184 ----------LTSRCSKFRFKPLAENTMLTRLQYICEQESVMCDFK---ALETLVETSGG 230
+ R F P+A M L I QE + K LE + + +GG
Sbjct: 187 AETIMTKDILIMPRIDTITFNPIAPTFMKKALVRISVQEGKLKSPKSDSKLEVICQEAGG 246
Query: 231 DMRRAITCLQ 240
D+R AI LQ
Sbjct: 247 DLRSAINSLQ 256
>gnl|CDD|203260 pfam05496, RuvB_N, Holliday junction DNA helicase ruvB
N-terminus. The RuvB protein makes up part of the
RuvABC revolvasome which catalyzes the resolution of
Holliday junctions that arise during genetic
recombination and DNA repair. Branch migration is
catalyzed by the RuvB protein that is targeted to the
Holliday junction by the structure specific RuvA
protein. This family contains the N-terminal region of
the protein.
Length = 231
Score = 48.2 bits (116), Expect = 3e-06
Identities = 22/54 (40%), Positives = 29/54 (53%), Gaps = 6/54 (11%)
Query: 40 RPKTIDDVIEQQEVVSVLKKCLSGAD-----LPHFLFYGPPGTGKTS-TMIAAC 87
RP+ +D+ I Q++V LK + A L H L YGPPG GKT+ I A
Sbjct: 19 RPRRLDEYIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLANIIAN 72
>gnl|CDD|225164 COG2255, RuvB, Holliday junction resolvasome, helicase subunit
[DNA replication, recombination, and repair].
Length = 332
Score = 48.7 bits (117), Expect = 3e-06
Identities = 20/47 (42%), Positives = 28/47 (59%), Gaps = 5/47 (10%)
Query: 40 RPKTIDDVIEQQEVVSVLKKCLSGAD-----LPHFLFYGPPGTGKTS 81
RPKT+D+ I Q++V L+ + A L H L +GPPG GKT+
Sbjct: 21 RPKTLDEFIGQEKVKEQLQIFIKAAKKRGEALDHVLLFGPPGLGKTT 67
>gnl|CDD|236022 PRK07471, PRK07471, DNA polymerase III subunit delta'; Validated.
Length = 365
Score = 48.5 bits (116), Expect = 4e-06
Identities = 30/112 (26%), Positives = 50/112 (44%), Gaps = 11/112 (9%)
Query: 139 KIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLAE 198
++VI+D AD M A AL + +E+ + F L+ + + ++ + SRC K R +PLA
Sbjct: 143 RVVIVDTADEMNANAANALLKVLEEPPARSLFLLVSHAPARLLPTIRSRCRKLRLRPLAP 202
Query: 199 NTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCLQSCARLKGGEG 250
++ L L + G + RA+ RL GG+G
Sbjct: 203 EDVIDAL----AAAGPDLPDDPRAALAALAEGSVGRAL-------RLAGGDG 243
>gnl|CDD|224391 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA
replication, recombination, and repair /
Posttranslational modification, protein turnover,
chaperones].
Length = 366
Score = 47.7 bits (114), Expect = 6e-06
Identities = 60/291 (20%), Positives = 104/291 (35%), Gaps = 41/291 (14%)
Query: 49 EQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQLFGDMYRERILELNASDDR 108
E ++ S L L G + + YGP GTGKT+T+ +L ++ +N + R
Sbjct: 25 EINQLASFLAPALRGERPSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELR 84
Query: 109 G-IQVIRDKVKTFAQQTASG-------------FNQDGKPCPPFKIVILDEADSMTHAAQ 154
QV+ + + +G ++ GK IVILDE D++
Sbjct: 85 TPYQVLSKILNKLGKVPLTGDSSLEILKRLYDNLSKKGKTV----IVILDEVDALVDKDG 140
Query: 155 AALR---RTMEKETKSTRFCLICN---YVSCIIQPLTSRCSKFR--FKPLAENTMLTRLQ 206
L R + + N ++ + + S F P + L+
Sbjct: 141 EVLYSLLRAPGENKVKVSIIAVSNDDKFLDYLDPRVKSSLGPSEIVFPPYTAEELYDILR 200
Query: 207 Y---ICEQESVMCDFKALE---TLVETSGGDMRRAITCLQSCARLKGGEG---IVNEDVL 257
V D L+ LV GD R+AI L+ + EG + + V
Sbjct: 201 ERVEEGFSAGV-IDDDVLKLIAALVAAESGDARKAIDILRRAGEIAEREGSRKVSEDHVR 259
Query: 258 EVTGVIPKPWIEKLLKVDSFQVLEKYIEDLILEAYSAT---QLFDQFHDIV 305
E I + +E++LK +K + I+E +L+D + +
Sbjct: 260 EAQEEIERDVLEEVLKTLPLH--QKIVLLAIVELTVEISTGELYDVYESLC 308
>gnl|CDD|221912 pfam13086, AAA_11, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins.
Length = 220
Score = 43.5 bits (103), Expect = 8e-05
Identities = 18/44 (40%), Positives = 28/44 (63%), Gaps = 2/44 (4%)
Query: 57 LKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQLFGDMYRERIL 100
+KK LS +D+ L GPPGTGKT+T++ QL + +++L
Sbjct: 10 IKKALSSSDI--TLIQGPPGTGKTTTIVEIIKQLLSNAPGKKVL 51
>gnl|CDD|180132 PRK05564, PRK05564, DNA polymerase III subunit delta'; Validated.
Length = 313
Score = 43.9 bits (104), Expect = 1e-04
Identities = 18/69 (26%), Positives = 36/69 (52%)
Query: 139 KIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLAE 198
K++I+ ++ MT AQ A +T+E+ K L+C + I+ + SRC ++ L++
Sbjct: 95 KVIIIYNSEKMTEQAQNAFLKTIEEPPKGVFIILLCENLEQILDTIKSRCQIYKLNRLSK 154
Query: 199 NTMLTRLQY 207
+ + Y
Sbjct: 155 EEIEKFISY 163
>gnl|CDD|180738 PRK06871, PRK06871, DNA polymerase III subunit delta'; Validated.
Length = 325
Score = 42.8 bits (101), Expect = 2e-04
Identities = 37/137 (27%), Positives = 59/137 (43%), Gaps = 20/137 (14%)
Query: 107 DRGIQVIRD---KVKTFAQQTASGFNQDGKPCPPFKIVILDEADSMTHAAQAALRRTMEK 163
D G+ +R+ KV AQQ G N K+V + A+ +T AA AL +T+E+
Sbjct: 86 DIGVDQVREINEKVSQHAQQ---GGN---------KVVYIQGAERLTEAAANALLKTLEE 133
Query: 164 ETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLAENTMLTRLQYICEQESVMCDFKALET 223
+T F L + + ++ + SRC + P E L LQ E + T
Sbjct: 134 PRPNTYFLLQADLSAALLPTIYSRCQTWLIHPPEEQQALDWLQAQSSAEI-----SEILT 188
Query: 224 LVETSGGDMRRAITCLQ 240
+ + G A+T L+
Sbjct: 189 ALRINYGRPLLALTFLE 205
>gnl|CDD|180215 PRK05707, PRK05707, DNA polymerase III subunit delta'; Validated.
Length = 328
Score = 42.4 bits (100), Expect = 3e-04
Identities = 52/210 (24%), Positives = 87/210 (41%), Gaps = 47/210 (22%)
Query: 107 DRGIQV--IRDKVKTFAQQTASGFNQDGKPCPPFKIVILDEADSMTHAAQAALRRTMEKE 164
D+ I+V +R+ V +F QTA G K+V+++ A++M A AL +++E+
Sbjct: 83 DKTIKVDQVRELV-SFVVQTA---QLGG-----RKVVLIEPAEAMNRNAANALLKSLEEP 133
Query: 165 TKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLAENTMLTRLQYICEQESVMCDFKALETL 224
+ T LI + S ++ + SRC + + L LQ Q D + L
Sbjct: 134 SGDTVLLLISHQPSRLLPTIKSRCQQQACPLPSNEESLQWLQ----QALPESDERERIEL 189
Query: 225 VETSGGDMRRAITCLQSCARLKGGEGIVNEDVLE-----VTGVIPKPWIEKLLK--VDSF 277
+ +GG RA+ +L + V E + GV KLLK +
Sbjct: 190 LTLAGGSPLRAL-------QLHE------QGVREQRARVLDGVK------KLLKQQQSAS 230
Query: 278 QVLEKYIEDLILEAYSATQLFDQFHDIVML 307
Q+ E +++ +L LFD F D
Sbjct: 231 QLAESWLKVPLLL------LFDWFCDWAHD 254
>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau;
Validated.
Length = 824
Score = 43.1 bits (102), Expect = 3e-04
Identities = 20/46 (43%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTST 82
+YRP T +VI Q+ V L L + H +LF GP G GKTS+
Sbjct: 8 RYRPATFAEVIGQEHVTEPLSTALDSGRINHAYLFSGPRGCGKTSS 53
>gnl|CDD|144608 pfam01078, Mg_chelatase, Magnesium chelatase, subunit ChlI.
Magnesium-chelatase is a three-component enzyme that
catalyzes the insertion of Mg2+ into protoporphyrin IX.
This is the first unique step in the synthesis of
(bacterio)chlorophyll. Due to this, it is thought that
Mg-chelatase has an important role in channelling inter-
mediates into the (bacterio)chlorophyll branch in
response to conditions suitable for photosynthetic
growth. ChlI and BchD have molecular weight between
38-42 kDa.
Length = 207
Score = 40.2 bits (95), Expect = 7e-04
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 5/60 (8%)
Query: 46 DVIEQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAAC-HQLFGDMYRERILELNA 104
DV Q++ L+ +G + L GPPG+GK TM+A + + + LE+ A
Sbjct: 4 DVKGQEQAKRALEIAAAGGH--NLLMIGPPGSGK--TMLAKRLPGILPPLTEQEALEVTA 59
>gnl|CDD|129721 TIGR00635, ruvB, Holliday junction DNA helicase, RuvB subunit.
All proteins in this family for which functions are
known are 5'-3' DNA helicases that, as part of a
complex with RuvA homologs serve as a 5'-3' Holliday
junction helicase. RuvA specifically binds Holliday
junctions as a sandwich of two tetramers and maintains
the configuration of the junction. It forms a complex
with two hexameric rings of RuvB, the subunit that
contains helicase activity. The complex drives
ATP-dependent branch migration of the Holliday junction
recombination intermediate. The endonuclease RuvC
resolves junctions [DNA metabolism, DNA replication,
recombination, and repair].
Length = 305
Score = 40.7 bits (96), Expect = 0.001
Identities = 19/52 (36%), Positives = 26/52 (50%), Gaps = 6/52 (11%)
Query: 42 KTIDDVIEQQEVVSVLKKCLSGAD-----LPHFLFYGPPGTGKTS-TMIAAC 87
K + + I Q++V L+ + A L H L YGPPG GKT+ I A
Sbjct: 1 KLLAEFIGQEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIAN 52
>gnl|CDD|129465 TIGR00368, TIGR00368, Mg chelatase-related protein. The N-terminal
end matches very strongly a pfam Mg_chelatase domain
[Unknown function, General].
Length = 499
Score = 40.2 bits (94), Expect = 0.002
Identities = 23/80 (28%), Positives = 36/80 (45%), Gaps = 7/80 (8%)
Query: 28 TRNKPVPWVEKYRPKTID--DVIEQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIA 85
T KP + K +D D+ QQ L+ +G + L +GPPG+GK TM+A
Sbjct: 173 TNTKPKSIINKSYIIDLDLKDIKGQQHAKRALEIAAAGGH--NLLLFGPPGSGK--TMLA 228
Query: 86 ACHQ-LFGDMYRERILELNA 104
+ Q + + E +E
Sbjct: 229 SRLQGILPPLTNEEAIETAR 248
>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 368
Score = 39.8 bits (93), Expect = 0.002
Identities = 38/147 (25%), Positives = 62/147 (42%), Gaps = 26/147 (17%)
Query: 15 PSSSKTSVSTSG-KTRNKPVPWVEKYRPKTIDDVIEQQEV---VSVLKKCLSGADL---- 66
PS ST+ E T+DDVI Q+E ++ + L +
Sbjct: 90 PSGGGIITSTTIFVLETPREEDREIISDITLDDVIGQEEAKRKCRLIMEYLENPERFGDW 149
Query: 67 --PHFLFYGPPGTGKTSTMIAACHQLFGDMYRERILELNASDDRGIQVIRDKVKTFAQQT 124
+ LFYGPPGTGKT A ++ + +L + A+ ++I + V A++
Sbjct: 150 APKNVLFYGPPGTGKTMMAKALANEA-----KVPLLLVKAT-----ELIGEHVGDGARRI 199
Query: 125 ASGFNQDGK--PCPPFKIVILDEADSM 149
+ + K PC IV +DE D++
Sbjct: 200 HELYERARKAAPC----IVFIDELDAI 222
>gnl|CDD|234063 TIGR02928, TIGR02928, orc1/cdc6 family replication initiation
protein. Members of this protein family are found
exclusively in the archaea. This set of DNA binding
proteins shows homology to the origin recognition
complex subunit 1/cell division control protein 6
family in eukaryotes. Several members may be found in
genome and interact with each other [DNA metabolism,
DNA replication, recombination, and repair].
Length = 365
Score = 38.8 bits (91), Expect = 0.004
Identities = 18/57 (31%), Positives = 25/57 (43%), Gaps = 5/57 (8%)
Query: 37 EKYRPKTI---DDVIEQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQL 90
Y P I D+ IE E+ L+ L G+ + YG GTGKT+ +L
Sbjct: 10 PDYVPDRIVHRDEQIE--ELAKALRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKEL 64
>gnl|CDD|236134 PRK07940, PRK07940, DNA polymerase III subunit delta'; Validated.
Length = 394
Score = 38.7 bits (91), Expect = 0.006
Identities = 39/177 (22%), Positives = 73/177 (41%), Gaps = 46/177 (25%)
Query: 45 DDVIEQQEVVSVLKKCLSGAD---------LPH-FLFYGPPGTGKTSTMIA--------- 85
DD++ Q+ VV+ L+ A + H +LF GPPG+G++ A
Sbjct: 5 DDLVGQEAVVAELRAAARAARADVAAAGSGMTHAWLFTGPPGSGRSVAARAFAAALQCTD 64
Query: 86 ----------ACHQL----FGDMYRERILELNASDDRGIQVIRDKVKTFAQQTASGFNQD 131
AC + D+ L+ G+ +R+ V A++ ++G
Sbjct: 65 PDEPGCGECRACRTVLAGTHPDVRVVAPEGLSI----GVDEVRELVTIAARRPSTG---- 116
Query: 132 GKPCPPFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRC 188
++IV++++AD +T A AL + +E+ T + L ++ + SRC
Sbjct: 117 -----RWRIVVIEDADRLTERAANALLKAVEEPPPRTVWLLCAPSPEDVLPTIRSRC 168
>gnl|CDD|214386 CHL00176, ftsH, cell division protein; Validated.
Length = 638
Score = 38.1 bits (89), Expect = 0.008
Identities = 38/112 (33%), Positives = 51/112 (45%), Gaps = 31/112 (27%)
Query: 49 EQQEVVSVLKK----CLSGADLPH-FLFYGPPGTGKT--STMIA--ACHQLF---GDMYR 96
E +EVVS LKK GA +P L GPPGTGKT + IA A F G +
Sbjct: 194 EFEEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGEAEVPFFSISGSEFV 253
Query: 97 ERILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPPFKIVILDEADS 148
E + + A+ +RD K A++ + PC IV +DE D+
Sbjct: 254 EMFVGVGAAR------VRDLFKK-AKENS--------PC----IVFIDEIDA 286
>gnl|CDD|234203 TIGR03420, DnaA_homol_Hda, DnaA regulatory inactivator Hda.
Members of this protein family are Hda (Homologous to
DnaA). These proteins are about half the length of DnaA
and homologous over length of Hda. In the model species
Escherichia coli, the initiation of DNA replication
requires DnaA bound to ATP rather than ADP; Hda helps
facilitate the conversion of DnaA-ATP to DnaA-ADP [DNA
metabolism, DNA replication, recombination, and repair].
Length = 226
Score = 37.6 bits (88), Expect = 0.008
Identities = 13/62 (20%), Positives = 25/62 (40%)
Query: 52 EVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQLFGDMYRERILELNASDDRGIQ 111
E+++ L++ +G +G G+GK+ + AAC L L +
Sbjct: 24 ELLAALRQLAAGKGDRFLYLWGESGSGKSHLLQAACAAAEERGKSAIYLPLAELAQADPE 83
Query: 112 VI 113
V+
Sbjct: 84 VL 85
>gnl|CDD|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau;
Validated.
Length = 647
Score = 37.5 bits (88), Expect = 0.012
Identities = 20/49 (40%), Positives = 29/49 (59%), Gaps = 3/49 (6%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTSTMIA 85
K+RP+T +V+ Q+ V++ L L L H +LF G G GKT+ IA
Sbjct: 9 KWRPQTFAEVVGQEHVLTALANALDLGRLHHAYLFSGTRGVGKTT--IA 55
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the AAA
superfamily.
Length = 154
Score = 36.0 bits (83), Expect = 0.014
Identities = 24/126 (19%), Positives = 45/126 (35%), Gaps = 9/126 (7%)
Query: 49 EQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQLFGDMYRERILELNASDDR 108
E + ++ L++ SG P L GP GTGKTS + L + E N
Sbjct: 8 ELERLLDALRRARSGG-PPSVLLTGPSGTGKTSLLRELLEGLLVAAGKCDQAERN-PPYA 65
Query: 109 GIQVIRDKVKTFAQQTASGFNQDGKPCPPFKIVILDEADSMTHAAQAALRRTMEKETKST 168
Q +R+ ++ ++ A+ + +L + L +E+
Sbjct: 66 FSQALRELLRQLLRELAAELLLLREA-------LLAALGAELIEGLQDLVELLERLLARA 118
Query: 169 RFCLIC 174
R ++
Sbjct: 119 RPLVLV 124
>gnl|CDD|236382 PRK09111, PRK09111, DNA polymerase III subunits gamma and tau;
Validated.
Length = 598
Score = 37.6 bits (88), Expect = 0.014
Identities = 18/46 (39%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTST 82
KYRP+T DD+I Q+ +V L + F+ G G GKT+T
Sbjct: 17 KYRPQTFDDLIGQEAMVRTLTNAFETGRIAQAFMLTGVRGVGKTTT 62
>gnl|CDD|181190 PRK07993, PRK07993, DNA polymerase III subunit delta'; Validated.
Length = 334
Score = 36.6 bits (85), Expect = 0.023
Identities = 23/83 (27%), Positives = 40/83 (48%), Gaps = 15/83 (18%)
Query: 109 GIQVIRD---KVKTFAQQTASGFNQDGKPCPPFKIVILDEADSMTHAAQAALRRTMEKET 165
G+ +R+ K+ A+ + K+V L +A +T AA AL +T+E+
Sbjct: 89 GVDAVREVTEKLYEHARLGGA------------KVVWLPDAALLTDAAANALLKTLEEPP 136
Query: 166 KSTRFCLICNYVSCIIQPLTSRC 188
++T F L C + ++ L SRC
Sbjct: 137 ENTWFFLACREPARLLATLRSRC 159
>gnl|CDD|181214 PRK08058, PRK08058, DNA polymerase III subunit delta'; Validated.
Length = 329
Score = 36.4 bits (85), Expect = 0.024
Identities = 51/179 (28%), Positives = 76/179 (42%), Gaps = 32/179 (17%)
Query: 50 QQEVVSVLKKCLSGADLPH-FLFYGPPGTGK--TSTMIAA---CHQLFGDM----YRE-- 97
Q VV +L+ ++ L H +LF G GTGK T+ +A C + G
Sbjct: 11 QPVVVKMLQNSIAKNRLSHAYLFEGAKGTGKKATALWLAKSLFCLERNGVEPCGTCTNCK 70
Query: 98 RILELN-------ASDDRGIQV--IRDKVKTFAQQTASGFNQDGKPCPPFKIVILDEADS 148
RI N A D + I+ IR + F + SG + K+ I++ AD
Sbjct: 71 RIDSGNHPDVHLVAPDGQSIKKDQIRYLKEEF---SKSGVESNK------KVYIIEHADK 121
Query: 149 MT-HAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLAENTMLTRLQ 206
MT AA + L+ E +T L N I+ + SRC F+PL +++ RLQ
Sbjct: 122 MTASAANSLLKFLEEPSGGTTAILLTENK-HQILPTILSRCQVVEFRPLPPESLIQRLQ 179
>gnl|CDD|234053 TIGR02903, spore_lon_C, ATP-dependent protease, Lon family.
Members of this protein family resemble the widely
distributed ATP-dependent protease La, also called Lon
and LonA. It resembles even more closely LonB, which is
a LonA paralog found in genomes if and only if the
species is capable of endospore formation (as in
Bacillus subtilis, Clostridium tetani, and select other
members of the Firmicutes) and expressed specifically in
the forespore compartment. Members of this family are
restricted to a subset of spore-forming species, and are
very likely to participate in the program of endospore
formation. We propose the designation LonC [Protein
fate, Degradation of proteins, peptides, and
glycopeptides, Cellular processes, Sporulation and
germination].
Length = 615
Score = 36.7 bits (85), Expect = 0.024
Identities = 13/42 (30%), Positives = 23/42 (54%)
Query: 40 RPKTIDDVIEQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTS 81
RP+ +++ Q+ + L ++ H + YGPPG GKT+
Sbjct: 149 RPRAFSEIVGQERAIKALLAKVASPFPQHIILYGPPGVGKTT 190
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 34.6 bits (80), Expect = 0.026
Identities = 22/117 (18%), Positives = 42/117 (35%), Gaps = 22/117 (18%)
Query: 70 LFYGPPGTGKTSTMIAACHQLFGDMYRERILELNASDDRGIQVIRDKVKTFAQQTASGFN 129
+ G G+GKT+ +L + R++ + A + + K+ SG
Sbjct: 8 VLTGESGSGKTT----LLRRLARQLPNRRVVYVEAPSLGTPKDLLRKILRALGLPLSGGT 63
Query: 130 QD-------------GKPCPPFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLI 173
G+P ++I+DEA ++ A LR + K + L+
Sbjct: 64 TAELLEAILDALKRRGRP-----LLIIDEAQHLSLEALEELRDLYDLSEKGIQVILV 115
>gnl|CDD|237863 PRK14949, PRK14949, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 944
Score = 36.2 bits (84), Expect = 0.033
Identities = 31/103 (30%), Positives = 57/103 (55%), Gaps = 8/103 (7%)
Query: 138 FKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQ--PLT--SRCSKFRF 193
FK+ ++DE ++ ++ AL +T+E+ + +F L + Q P+T SRC +F
Sbjct: 120 FKVYLIDEVHMLSRSSFNALLKTLEEPPEHVKFLL----ATTDPQKLPVTVLSRCLQFNL 175
Query: 194 KPLAENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAI 236
K L ++ + T+L +I QE + + +AL L + + G MR A+
Sbjct: 176 KSLTQDEIGTQLNHILTQEQLPFEAEALTLLAKAANGSMRDAL 218
Score = 32.4 bits (74), Expect = 0.63
Identities = 18/45 (40%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 38 KYRPKTIDDVIEQQEVVSVLKKCLSGADLPH-FLFYGPPGTGKTS 81
K+RP T + ++ Q V+ L L+ L H +LF G G GKTS
Sbjct: 9 KWRPATFEQMVGQSHVLHALTNALTQQRLHHAYLFTGTRGVGKTS 53
>gnl|CDD|181538 PRK08699, PRK08699, DNA polymerase III subunit delta'; Validated.
Length = 325
Score = 35.6 bits (82), Expect = 0.038
Identities = 35/171 (20%), Positives = 62/171 (36%), Gaps = 45/171 (26%)
Query: 69 FLFYGPPGTGKTSTM---------------------IAACHQLFG-----DMYRERILEL 102
+LF G G GKT+ +CH LFG D Y I L
Sbjct: 24 WLFAGKKGIGKTAFARFAAQALLCETPAPGHKPCGECMSCH-LFGQGSHPDFY--EITPL 80
Query: 103 NASDDRG-------IQVIRDKVKTFAQQTASGFNQDGKPCPPFKIVILDEADSMTHAAQA 155
+ + G I +R+ + T+ + G +++++ A+SM A
Sbjct: 81 SDEPENGRKLLQIKIDAVREIID-NVYLTS---VRGGL-----RVILIHPAESMNLQAAN 131
Query: 156 ALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPLAENTMLTRLQ 206
+L + +E+ F L+ + ++ + SRC K + L L+
Sbjct: 132 SLLKVLEEPPPQVVFLLVSHAADKVLPTIKSRCRKMVLPAPSHEEALAYLR 182
>gnl|CDD|223679 COG0606, COG0606, Predicted ATPase with chaperone activity
[Posttranslational modification, protein turnover,
chaperones].
Length = 490
Score = 36.1 bits (84), Expect = 0.039
Identities = 20/60 (33%), Positives = 30/60 (50%), Gaps = 5/60 (8%)
Query: 46 DVIEQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAAC-HQLFGDMYRERILELNA 104
DV Q++ L+ +G + L GPPGTGK TM+A+ L + LE++A
Sbjct: 180 DVKGQEQAKRALEIAAAGGH--NLLLVGPPGTGK--TMLASRLPGLLPPLSIPEALEVSA 235
>gnl|CDD|237495 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
Length = 637
Score = 35.7 bits (83), Expect = 0.044
Identities = 21/58 (36%), Positives = 29/58 (50%), Gaps = 10/58 (17%)
Query: 28 TRNKPVPWVEKYRPKTIDDVIEQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIA 85
T + VP + ID VI Q+ V V+KK + H + G PGTGK +M+A
Sbjct: 20 TSDIEVP------ERLIDQVIGQEHAVEVIKK--AAKQRRHVMMIGSPGTGK--SMLA 67
>gnl|CDD|188437 TIGR03922, T7SS_EccA, type VII secretion AAA-ATPase EccA. This
model represents the AAA family ATPase, EccA, of the
actinobacterial flavor of type VII secretion systems.
Species such as Mycobacterium tuberculosis have several
instances of this system per genome, designated EccA1,
EccA2, etc [Protein fate, Protein and peptide secretion
and trafficking].
Length = 557
Score = 35.6 bits (82), Expect = 0.053
Identities = 14/41 (34%), Positives = 21/41 (51%), Gaps = 2/41 (4%)
Query: 68 HFLFYGPPGTGKTSTMIAACHQL--FGDMYRERILELNASD 106
H LF GPPGTGKT+ G + + + E++ +D
Sbjct: 314 HMLFAGPPGTGKTTIARVVAKIYCGLGVLRKPLVREVSRAD 354
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 35.6 bits (82), Expect = 0.060
Identities = 22/91 (24%), Positives = 34/91 (37%), Gaps = 30/91 (32%)
Query: 68 HFLFYGPPGTGKTSTMIAACHQLFGDMYRERILELNASDD---------RGIQVIRDKVK 118
L YGPPGTGKT A + R R + + S+ + I+ + +K +
Sbjct: 278 GVLLYGPPGTGKTLLAKAVALES-----RSRFISVKGSELLSKWVGESEKNIRELFEKAR 332
Query: 119 TFAQQTASGFNQDGKPCPPFKIVILDEADSM 149
P I+ +DE DS+
Sbjct: 333 ------------KLAPS----IIFIDEIDSL 347
>gnl|CDD|181551 PRK08769, PRK08769, DNA polymerase III subunit delta'; Validated.
Length = 319
Score = 34.9 bits (80), Expect = 0.061
Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 2/62 (3%)
Query: 139 KIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFK--PL 196
++VI+D AD++ AA AL +T+E+ + LI + + + SRC + FK P
Sbjct: 115 QVVIVDPADAINRAACNALLKTLEEPSPGRYLWLISAQPARLPATIRSRCQRLEFKLPPA 174
Query: 197 AE 198
E
Sbjct: 175 HE 176
>gnl|CDD|224383 COG1466, HolA, DNA polymerase III, delta subunit [DNA replication,
recombination, and repair].
Length = 334
Score = 35.0 bits (81), Expect = 0.065
Identities = 44/204 (21%), Positives = 87/204 (42%), Gaps = 21/204 (10%)
Query: 139 KIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCI---------IQPLTSRCS 189
++V+L A+ + + + ST L+ + + ++ L
Sbjct: 76 RLVVLKNAEKKPNKDKNLALLELAALLPSTDLLLL-VESNKLDKAKKLTKWLKKLAKAVV 134
Query: 190 KFRFKPLAENTMLTRLQYICEQESVMCDFKALETLVETSGGDMRRAITCLQSCARLKGGE 249
KPL E + ++ ++ + D +A++ L+E GG++ ++ A G +
Sbjct: 135 -VECKPLDEAELPQWIKKRAKELGLKIDQEAIQLLLEALGGNLLAIAQEIEKLALYAGDK 193
Query: 250 GIVNEDVLEVTGVIPKP----WIEKLLKVDSFQVLEKYIEDLILEAYS----ATQLFDQF 301
I EDV EV + + + LLK D + L + + DL+LE L QF
Sbjct: 194 EITLEDVEEVVSDVAEFNIFDLADALLKGDVKKAL-RLLRDLLLEGEEPLKLLAALTRQF 252
Query: 302 HDIVMLASSLSDKQKALFKALETL 325
++ L +L++K K+L +A ++L
Sbjct: 253 RLLLQLK-ALAEKGKSLQQAAKSL 275
>gnl|CDD|234751 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 35.2 bits (82), Expect = 0.067
Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 6/60 (10%)
Query: 39 YRPKTIDDVIEQ-QEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQLFGDMYRE 97
Y P+ + EQ +E+ L+ L G+ + L YGPPGTGKT+T+ + + E
Sbjct: 27 YVPENLPHREEQIEELAFALRPALRGSRPLNVLIYGPPGTGKTTTV-----KKVFEELEE 81
>gnl|CDD|234175 TIGR03348, VI_IcmF, type VI secretion protein IcmF. Members of
this protein family are IcmF homologs and tend to be
associated with type VI secretion systems [Cellular
processes, Pathogenesis].
Length = 1169
Score = 35.4 bits (82), Expect = 0.080
Identities = 15/36 (41%), Positives = 22/36 (61%), Gaps = 5/36 (13%)
Query: 51 QEVVSVLKKCLSG-----ADLPHFLFYGPPGTGKTS 81
E +++LK+ G DLP +L GPPG+GKT+
Sbjct: 91 NEALALLKRSRLGGRRYLYDLPWYLVIGPPGSGKTT 126
>gnl|CDD|180394 PRK06090, PRK06090, DNA polymerase III subunit delta'; Validated.
Length = 319
Score = 34.8 bits (80), Expect = 0.082
Identities = 14/58 (24%), Positives = 33/58 (56%)
Query: 138 FKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKP 195
+++ +++ AD+M +A AL +T+E+ + F L+ + ++ + SRC ++ P
Sbjct: 109 YRLFVIEPADAMNESASNALLKTLEEPAPNCLFLLVTHNQKRLLPTIVSRCQQWVVTP 166
>gnl|CDD|215253 PLN02459, PLN02459, probable adenylate kinase.
Length = 261
Score = 34.4 bits (79), Expect = 0.087
Identities = 31/138 (22%), Positives = 51/138 (36%), Gaps = 25/138 (18%)
Query: 68 HFLFYGPPGTGK------TSTMIAACHQLFGDMYRERILELNA---------------SD 106
+++F G PG GK S ++ H GD+ RE I D
Sbjct: 31 NWVFLGCPGVGKGTYASRLSKLLGVPHIATGDLVREEIKSSGPLGAQLKEIVNQGKLVPD 90
Query: 107 DRGIQVIRDKVKTFAQQTASGFNQDGKPCPPFKIVILDEADSMTHAAQAALRRTMEKET- 165
+ ++ +++ ++ SGF DG P + IL+ + LR + E
Sbjct: 91 EIIFSLLSKRLEAGEEEGESGFILDGFPRTVRQAEILEGVTDIDLVVNLKLREEVLVEKC 150
Query: 166 KSTRFCLIC--NY-VSCI 180
R C C N+ V+ I
Sbjct: 151 LGRRICSECGKNFNVADI 168
>gnl|CDD|221955 pfam13173, AAA_14, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily.
Length = 127
Score = 32.9 bits (76), Expect = 0.088
Identities = 19/79 (24%), Positives = 30/79 (37%), Gaps = 17/79 (21%)
Query: 70 LFYGPPGTGKTSTMIAACHQLFGDMYRERILELNASDDRGIQVIR--DKVKTFAQQTASG 127
+ GP GKT+ + Q ++ E IL +N D R + D ++ F + G
Sbjct: 6 VITGPRQVGKTTLL----LQFLKELLSENILYINLDDPR-FLRLALLDLLEEFLKLLLPG 60
Query: 128 FNQDGKPCPPFKIVILDEA 146
K + LDE
Sbjct: 61 ----------KKYLFLDEI 69
>gnl|CDD|232945 TIGR00376, TIGR00376, DNA helicase, putative. The gene product may
represent a DNA helicase. Eukaryotic members of this
family have been characterized as binding certain
single-stranded G-rich DNA sequences (GGGGT and GGGCT).
A number of related proteins are characterized as
helicases [DNA metabolism, DNA replication,
recombination, and repair].
Length = 637
Score = 34.8 bits (80), Expect = 0.10
Identities = 21/54 (38%), Positives = 27/54 (50%), Gaps = 7/54 (12%)
Query: 57 LKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQLFGDMYRERIL---ELNASDD 107
+ LS DL FL +GPPGTGKT T++ QL R+L N + D
Sbjct: 166 VLFALSSKDL--FLIHGPPGTGKTRTLVELIRQLV--KRGLRVLVTAPSNIAVD 215
>gnl|CDD|235898 PRK06964, PRK06964, DNA polymerase III subunit delta'; Validated.
Length = 342
Score = 34.0 bits (78), Expect = 0.16
Identities = 16/53 (30%), Positives = 31/53 (58%)
Query: 139 KIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKF 191
++V+L A+++ AA AL +T+E+ T F L+ + ++ + SRC +F
Sbjct: 134 RVVVLYPAEALNVAAANALLKTLEEPPPGTVFLLVSARIDRLLPTILSRCRQF 186
>gnl|CDD|116340 pfam07726, AAA_3, ATPase family associated with various cellular
activities (AAA). This Pfam entry includes some of the
AAA proteins not detected by the pfam00004 model.
Length = 131
Score = 32.1 bits (74), Expect = 0.17
Identities = 29/99 (29%), Positives = 41/99 (41%), Gaps = 16/99 (16%)
Query: 68 HFLFYGPPGTGKTSTMIAACHQLFGDMYRERIL---ELNASDDRGIQVIRDKVKTFAQQT 124
H L G PG KT + + G +R RI +L SD G +V K + F
Sbjct: 1 HVLLEGVPGLAKT-LLARTLARSLGLDFR-RIQFTPDLLPSDITGTEVYDQKTREF---- 54
Query: 125 ASGFNQDGKPCPPFKIVIL-DEADSMTHAAQAALRRTME 162
+ +P P F V+L DE + Q+AL M+
Sbjct: 55 ------EFRPGPIFANVLLADEINRAPPKTQSALLEAMQ 87
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 33.3 bits (77), Expect = 0.23
Identities = 11/16 (68%), Positives = 13/16 (81%), Gaps = 2/16 (12%)
Query: 70 LFYGPPGTGKTSTMIA 85
L YGPPGTGK T++A
Sbjct: 169 LLYGPPGTGK--TLLA 182
>gnl|CDD|222005 pfam13245, AAA_19, Part of AAA domain.
Length = 73
Score = 30.8 bits (70), Expect = 0.24
Identities = 11/28 (39%), Positives = 14/28 (50%), Gaps = 2/28 (7%)
Query: 73 GPPGTGKTSTMIAACHQLFGDMYRERIL 100
G PGTGKT+T A +L +L
Sbjct: 17 GGPGTGKTATAAAIIARLL--AAGRSVL 42
>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 32.8 bits (75), Expect = 0.27
Identities = 10/28 (35%), Positives = 13/28 (46%)
Query: 69 FLFYGPPGTGKTSTMIAACHQLFGDMYR 96
+ GPPG GKT IA ++L
Sbjct: 108 LVLLGPPGVGKTHLAIAIGNELLKAGIS 135
>gnl|CDD|233327 TIGR01241, FtsH_fam, ATP-dependent metalloprotease FtsH.
HflB(FtsH) is a pleiotropic protein required for correct
cell division in bacteria. It has ATP-dependent zinc
metalloprotease activity. It was formerly designated
cell division protein FtsH [Cellular processes, Cell
division, Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 495
Score = 33.0 bits (76), Expect = 0.31
Identities = 25/68 (36%), Positives = 32/68 (47%), Gaps = 16/68 (23%)
Query: 26 GKTRNKPVPWVEKYRPK-TIDDVI-------EQQEVVSVLKKCLS----GADLPH-FLFY 72
GK++ K + + +PK T DV E E+V LK GA +P L
Sbjct: 38 GKSKAK---LLNEEKPKVTFKDVAGIDEAKEELMEIVDFLKNPSKFTKLGAKIPKGVLLV 94
Query: 73 GPPGTGKT 80
GPPGTGKT
Sbjct: 95 GPPGTGKT 102
>gnl|CDD|233369 TIGR01351, adk, adenylate kinase. Adenylate kinase (EC 2.7.4.3)
converts ATP + AMP to ADP + ADP, that is, uses ATP as a
phosphate donor for AMP. Most members of this family are
known or believed to be adenylate kinase. However, some
members accept other nucleotide triphosphates as donors,
may be unable to use ATP, and may fail to complement
adenylate kinase mutants. An example of a
nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10)
is a GTP:AMP phosphotransferase. This family is
designated subfamily rather than equivalog for this
reason [Purines, pyrimidines, nucleosides, and
nucleotides, Nucleotide and nucleoside
interconversions].
Length = 210
Score = 32.2 bits (74), Expect = 0.33
Identities = 22/87 (25%), Positives = 37/87 (42%), Gaps = 22/87 (25%)
Query: 69 FLFYGPPGTGK--TSTMIAACHQLF----GDMYRERI-------LELNASDDRG------ 109
+ GPPG+GK + IA + L GD+ R I + ++G
Sbjct: 2 LVLLGPPGSGKGTQAKRIAEKYGLPHISTGDLLRAEIKAGTPLGKKAKEYMEKGELVPDE 61
Query: 110 --IQVIRDKVKTFAQQTASGFNQDGKP 134
Q++++++ T Q +GF DG P
Sbjct: 62 IVNQLVKERL-TQNQDNENGFILDGFP 87
>gnl|CDD|130674 TIGR01613, primase_Cterm, phage/plasmid primase, P4 family,
C-terminal domain. This model represents a clade within
a larger family of proteins from viruses of bacteria and
animals. Members of this family are found in phage and
plasmids of bacteria and archaea only. The model
describes a domain of about 300 residues, found
generally toward the protein C-terminus [DNA metabolism,
DNA replication, recombination, and repair, Mobile and
extrachromosomal element functions, Prophage functions].
Length = 304
Score = 32.7 bits (75), Expect = 0.35
Identities = 27/92 (29%), Positives = 34/92 (36%), Gaps = 4/92 (4%)
Query: 5 LRTGKLGKDAPSSSKTSVSTSGKTRNKPVPWVEKYRPKTIDDVIEQQEVV-SVLKKCLSG 63
LRTG+L P T T+ P + +T E E + V+ L+G
Sbjct: 12 LRTGQLEPHDPDEIHTRKITTEYDPKADCPTWNGFLLETFGGDNELIEYLQRVIGYSLTG 71
Query: 64 ADLPHFLF--YGPPGTGKTSTMIAACHQLFGD 93
LF YG G GK ST L GD
Sbjct: 72 NYTEQKLFFLYGNGGNGK-STFQNLLSNLLGD 102
>gnl|CDD|238660 cd01364, KISc_BimC_Eg5, Kinesin motor domain, BimC/Eg5 spindle pole
proteins, participate in spindle assembly and chromosome
segregation during cell division. This catalytic (head)
domain has ATPase activity and belongs to the larger
group of P-loop NTPases. Kinesins are
microtubule-dependent molecular motors that play
important roles in intracellular transport and in cell
division. In most kinesins, the motor domain is found at
the N-terminus (N-type), N-type kinesins are (+)
end-directed motors, i.e. they transport cargo towards
the (+) end of the microtubule. Kinesin motor domains
hydrolyze ATP at a rate of about 80 per second, and move
along the microtubule at a speed of about 6400 Angstroms
per second. To achieve that, kinesin head groups work in
pairs. Upon replacing ADP with ATP, a kinesin motor
domain increases its affinity for microtubule binding
and locks in place. Also, the neck linker binds to the
motor domain, which repositions the other head domain
through the coiled-coil domain close to a second tubulin
dimer, about 80 Angstroms along the microtubule.
Meanwhile, ATP hydrolysis takes place, and when the
second head domain binds to the microtubule, the first
domain again replaces ADP with ATP, triggering a
conformational change that pulls the first domain
forward.
Length = 352
Score = 32.6 bits (75), Expect = 0.37
Identities = 21/72 (29%), Positives = 28/72 (38%), Gaps = 8/72 (11%)
Query: 39 YRPKTIDDVIEQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQLFGDMYRER 98
+ P+ + Q V +L + L G + F YG GTGKT TM GD +
Sbjct: 56 FGPEADQIEVYSQVVSPILDEVLMGYNCTIFA-YGQTGTGKTYTME-------GDRTDNK 107
Query: 99 ILELNASDDRGI 110
S GI
Sbjct: 108 GSTWELSPHAGI 119
>gnl|CDD|180855 PRK07132, PRK07132, DNA polymerase III subunit delta'; Validated.
Length = 299
Score = 32.4 bits (74), Expect = 0.41
Identities = 16/56 (28%), Positives = 30/56 (53%)
Query: 139 KIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFK 194
KI+I+ + +++ AL +T+E+ K T F L ++ ++ + SRC F K
Sbjct: 92 KILIIKNIEKTSNSLLNALLKTIEEPPKDTYFLLTTKNINKVLPTIVSRCQVFNVK 147
>gnl|CDD|233120 TIGR00764, lon_rel, lon-related putative ATP-dependent protease.
This model represents a set of proteins with extensive
C-terminal homology to the ATP-dependent protease La,
product of the lon gene of E. coli. The model is based
on a seed alignment containing only archaeal members,
but several bacterial proteins match the model well.
Because several species, including Thermotoga maritima
and Treponema pallidum, contain both a close homolog of
the lon protease and nearly full-length homolog of the
members of this family, we suggest there may also be a
functional division between the two families. Members of
this family from Pyrococcus horikoshii and Pyrococcus
abyssi each contain a predicted intein [Protein fate,
Degradation of proteins, peptides, and glycopeptides].
Length = 608
Score = 32.9 bits (75), Expect = 0.41
Identities = 28/87 (32%), Positives = 38/87 (43%), Gaps = 9/87 (10%)
Query: 28 TRNKPVPWVEKYRPKTIDDVIEQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAAC 87
T PVP + ID VI Q+E V ++KK + + L G PG GK S + A
Sbjct: 7 TEEIPVP------ERLIDQVIGQEEAVEIIKK--AAKQKRNVLLIGEPGVGK-SMLAKAM 57
Query: 88 HQLFGDMYRERILELNASDDRGIQVIR 114
+L D E IL +D + I
Sbjct: 58 AELLPDEELEDILVYPNPEDPNMPRIV 84
>gnl|CDD|102059 PRK05917, PRK05917, DNA polymerase III subunit delta'; Validated.
Length = 290
Score = 32.1 bits (73), Expect = 0.57
Identities = 19/96 (19%), Positives = 34/96 (35%), Gaps = 15/96 (15%)
Query: 137 PFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPL 196
P+KI I+ EAD MT A +A + +E + L + + SR
Sbjct: 95 PYKIYIIHEADRMTLDAISAFLKVLEDPPQHGVIILTSAKPQRLPPTIRSRSLSI----- 149
Query: 197 AENTMLTRLQYICEQESVMCDFKALETLVETSGGDM 232
+I +E + + + L+ + G
Sbjct: 150 ----------HIPMEEKTLVSKEDIAYLIGYAQGKE 175
>gnl|CDD|206692 cd04107, Rab32_Rab38, Rab GTPase families 18 (Rab18) and 32
(Rab32). Rab38/Rab32 subfamily. Rab32 and Rab38 are
members of the Rab family of small GTPases. Human Rab32
was first identified in platelets but it is expressed
in a variety of cell types, where it functions as an
A-kinase anchoring protein (AKAP). Rab38 has been shown
to be melanocyte-specific. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab
proteins.
Length = 201
Score = 31.5 bits (72), Expect = 0.63
Identities = 10/27 (37%), Positives = 13/27 (48%)
Query: 73 GPPGTGKTSTMIAACHQLFGDMYRERI 99
G G GKTS + H +F Y+ I
Sbjct: 7 GDLGVGKTSIIKRYVHGVFSQHYKATI 33
>gnl|CDD|211576 TIGR00459, aspS_bact, aspartyl-tRNA synthetase, bacterial type.
Asparate--tRNA ligases in this family may be
discriminating (6.1.1.12) or nondiscriminating
(6.1.1.23). In a multiple sequence alignment of
representative asparaginyl-tRNA synthetases (asnS),
archaeal/eukaryotic type aspartyl-tRNA synthetases
(aspS_arch), and bacterial type aspartyl-tRNA
synthetases (aspS_bact), there is a striking similarity
between asnS and aspS_arch in gap pattern and in
sequence, and a striking divergence of aspS_bact.
Consequently, a separate model was built for each of the
three groups. This model, aspS_bact, represents
aspartyl-tRNA synthetases from the Bacteria and from
mitochondria. In some species, this enzyme aminoacylates
tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently
transamidated to Asn-tRNA(asn). This model generates
very low scores for the archaeal type of aspS and for
asnS; scores between the trusted and noise cutoffs
represent fragmentary sequences [Protein synthesis, tRNA
aminoacylation].
Length = 583
Score = 32.0 bits (73), Expect = 0.69
Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 2/61 (3%)
Query: 236 ITCLQSCARLKGGEGIVNEDVLEVTG-VIPKPWIEKLLKVDSFQVLEKYIEDLILEAYSA 294
+ C LK +G+ NEDV++V G V +P +D+ ++ E E + L S
Sbjct: 47 VVCDPDADALKLAKGLRNEDVVQVKGKVSARPEGNINRNLDTGEI-EILAESITLLNKSK 105
Query: 295 T 295
T
Sbjct: 106 T 106
Score = 31.2 bits (71), Expect = 1.4
Identities = 17/63 (26%), Positives = 27/63 (42%), Gaps = 6/63 (9%)
Query: 337 ITCLQSCARLKGGEGIVNEDVLEVTGVI---PNPWIEKLLKVDSFQVLEKYIEDLILEAY 393
+ C LK +G+ NEDV++V G + P I + L ++ E + L
Sbjct: 47 VVCDPDADALKLAKGLRNEDVVQVKGKVSARPEGNINRNLDTGEIEI---LAESITLLNK 103
Query: 394 SAT 396
S T
Sbjct: 104 SKT 106
>gnl|CDD|234172 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family.
Members of this protein family are homologs of ClpB, an
ATPase associated with chaperone-related functions.
These ClpB homologs, designated ClpV1, are a key
component of the bacterial pathogenicity-associated type
VI secretion system [Protein fate, Protein and peptide
secretion and trafficking, Cellular processes,
Pathogenesis].
Length = 852
Score = 32.2 bits (74), Expect = 0.73
Identities = 12/24 (50%), Positives = 14/24 (58%)
Query: 69 FLFYGPPGTGKTSTMIAACHQLFG 92
FL GP G GKT T +A L+G
Sbjct: 599 FLLVGPSGVGKTETALALAELLYG 622
>gnl|CDD|233793 TIGR02237, recomb_radB, DNA repair and recombination protein
RadB. This family consists exclusively of archaeal
RadB protein, a homolog of bacterial RecA (TIGR02012),
eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and
archaeal RadA (TIGR02236).
Length = 209
Score = 31.2 bits (71), Expect = 0.76
Identities = 11/18 (61%), Positives = 13/18 (72%), Gaps = 1/18 (5%)
Query: 71 FYGPPGTGKTS-TMIAAC 87
YGPPG+GKT+ MI A
Sbjct: 17 IYGPPGSGKTNICMILAV 34
>gnl|CDD|222163 pfam13479, AAA_24, AAA domain. This AAA domain is found in a
wide variety of presumed phage proteins.
Length = 201
Score = 31.1 bits (71), Expect = 0.83
Identities = 10/14 (71%), Positives = 10/14 (71%)
Query: 69 FLFYGPPGTGKTST 82
L YGPPG GKTS
Sbjct: 6 VLIYGPPGIGKTSL 19
>gnl|CDD|233959 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA. [Protein fate, Degradation of proteins, peptides,
and glycopeptides].
Length = 730
Score = 31.9 bits (73), Expect = 0.83
Identities = 17/41 (41%), Positives = 24/41 (58%), Gaps = 7/41 (17%)
Query: 45 DDVIEQQEVVSVLKKCLSGADLPH-----FLFYGPPGTGKT 80
D+ I+Q +VS +K+ +G P+ FLF GP G GKT
Sbjct: 459 DEAIDQ--LVSAIKRSRAGLGDPNKPVGSFLFVGPTGVGKT 497
>gnl|CDD|220440 pfam09848, DUF2075, Uncharacterized conserved protein (DUF2075).
This domain, found in various prokaryotic proteins
(including putative ATP/GTP binding proteins), has no
known function.
Length = 348
Score = 31.4 bits (72), Expect = 0.87
Identities = 22/92 (23%), Positives = 31/92 (33%), Gaps = 21/92 (22%)
Query: 69 FLFYGPPGTGKTSTMIAACHQLFG-DMYRERIL-------------ELNASDDRGIQVIR 114
FL G PGTGKT + +L D+ R + L + +
Sbjct: 4 FLVTGGPGTGKTVVALNLFAELSDSDLGRTAVFLSGNHPLVLVLYEALAGDLKVRKKKLF 63
Query: 115 DKVKTFAQQTASGFNQDGKPCPPFKIVILDEA 146
K +F K P +VI+DEA
Sbjct: 64 RKPTSFINNLH-------KAPPHEDVVIVDEA 88
>gnl|CDD|236347 PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated.
Length = 227
Score = 31.1 bits (71), Expect = 0.89
Identities = 26/121 (21%), Positives = 46/121 (38%), Gaps = 28/121 (23%)
Query: 41 PKTIDDVI--EQQEVVSVLKKCLSG--ADLPHFLFYGPPGTGKTSTMIAACHQLFGDMYR 96
P T D+ + E E+V+ L++ +G AD F +G G+G++ + A
Sbjct: 14 PPTFDNFVAGENAELVARLRELAAGPVAD-RFFYLWGEAGSGRSHLLQALVADASYGGRN 72
Query: 97 ERILELNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPPFKIVILDEADSMTHAAQAA 156
R L+ A F+ D P ++ +D+ + + A Q A
Sbjct: 73 ARYLD-------------------AASPLLAFDFD----PEAELYAVDDVERLDDAQQIA 109
Query: 157 L 157
L
Sbjct: 110 L 110
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 30.9 bits (70), Expect = 1.0
Identities = 27/158 (17%), Positives = 44/158 (27%), Gaps = 39/158 (24%)
Query: 50 QQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQLFGDMYRERIL------EL- 102
Q+E + L L + P G+GKT + + R+L EL
Sbjct: 13 QKEAIEALLSGLR-----DVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRELA 67
Query: 103 --------NASDDRGIQVI----RDKVKTFAQQTASG---------------FNQDGKPC 135
G++V+ D + ++ SG D
Sbjct: 68 EQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDKLSL 127
Query: 136 PPFKIVILDEADSMTHAAQAALRRTMEKETKSTRFCLI 173
+VILDEA + + K L+
Sbjct: 128 SNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLL 165
>gnl|CDD|214526 smart00129, KISc, Kinesin motor, catalytic domain. ATPase.
Microtubule-dependent molecular motors that play
important roles in intracellular transport of organelles
and in cell division.
Length = 335
Score = 31.0 bits (71), Expect = 1.1
Identities = 17/73 (23%), Positives = 26/73 (35%), Gaps = 28/73 (38%)
Query: 72 YGPPGTGKTSTMIA----------ACHQLFGDM------------------YRERILELN 103
YG G+GKT TMI A LF + Y E+I +L
Sbjct: 86 YGQTGSGKTYTMIGTPDSPGIIPRALKDLFEKIDKREEGWQFSVKVSYLEIYNEKIRDLL 145
Query: 104 ASDDRGIQVIRDK 116
+ +++ D+
Sbjct: 146 NPSSKKLEIREDE 158
>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 406
Score = 31.1 bits (71), Expect = 1.2
Identities = 10/11 (90%), Positives = 10/11 (90%)
Query: 70 LFYGPPGTGKT 80
L YGPPGTGKT
Sbjct: 189 LLYGPPGTGKT 199
>gnl|CDD|238054 cd00106, KISc, Kinesin motor domain. This catalytic (head) domain
has ATPase activity and belongs to the larger group of
P-loop NTPases. Kinesins are microtubule-dependent
molecular motors that play important roles in
intracellular transport and in cell division. In most
kinesins, the motor domain is found at the N-terminus
(N-type), in some its is found in the middle (M-type),
or C-terminal (C-type). N-type and M-type kinesins are
(+) end-directed motors, while C-type kinesins are (-)
end-directed motors, i.e. they transport cargo towards
the (-) end of the microtubule. Kinesin motor domains
hydrolyze ATP at a rate of about 80 per second, and move
along the microtubule at a speed of about 6400 Angstroms
per second. To achieve that, kinesin head groups work in
pairs. Upon replacing ADP with ATP, a kinesin motor
domain increases its affinity for microtubule binding
and locks in place. Also, the neck linker binds to the
motor domain, which repositions the other head domain
through the coiled-coil domain close to a second tubulin
dimer, about 80 Angstroms along the microtubule.
Meanwhile, ATP hydrolysis takes place, and when the
second head domain binds to the microtubule, the first
domain again replaces ADP with ATP, triggering a
conformational change that pulls the first domain
forward.
Length = 328
Score = 31.1 bits (71), Expect = 1.2
Identities = 15/57 (26%), Positives = 24/57 (42%), Gaps = 7/57 (12%)
Query: 45 DDVIEQQEVVS-----VLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQLFGDMYR 96
D Q++V +++ L G + YG G+GKT TM + G + R
Sbjct: 54 DPNSTQEDVYETTAKPLVESVLEGYNGT-IFAYGQTGSGKTYTMFGSPKDP-GIIPR 108
>gnl|CDD|213221 cd03254, ABCC_Glucan_exporter_like, ATP-binding cassette domain of
glucan transporter and related proteins, subfamily C.
Glucan exporter ATP-binding protein. In A. tumefaciens
cyclic beta-1, 2-glucan must be transported into the
periplasmic space to exert its action as a virulence
factor. This subfamily belongs to the MRP-like family
and is involved in drug, peptide, and lipid export. The
MRP-like family, similar to all ABC proteins, have a
common four-domain core structure constituted by two
membrane-spanning domains each composed of six
transmembrane (TM) helices and two nucleotide-binding
domains (NBD). ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 229
Score = 30.7 bits (70), Expect = 1.2
Identities = 14/32 (43%), Positives = 18/32 (56%), Gaps = 5/32 (15%)
Query: 139 KIVILDEA----DSMTHAA-QAALRRTMEKET 165
KI+ILDEA D+ T Q AL + M+ T
Sbjct: 159 KILILDEATSNIDTETEKLIQEALEKLMKGRT 190
>gnl|CDD|172992 PRK14526, PRK14526, adenylate kinase; Provisional.
Length = 211
Score = 30.6 bits (69), Expect = 1.3
Identities = 25/87 (28%), Positives = 36/87 (41%), Gaps = 23/87 (26%)
Query: 69 FLFYGPPGTGK------TSTMIAACHQLFGDMYRERIL-------ELNASDDRG------ 109
+F GPPG+GK S + H GD++RE IL E+ + G
Sbjct: 3 LVFLGPPGSGKGTIAKILSNELNYYHISTGDLFRENILNSTPLGKEIKQIVENGQLVPDS 62
Query: 110 --IQVIRDKVKTFAQQTASGFNQDGKP 134
I+++ DK+ T F DG P
Sbjct: 63 ITIKIVEDKINTIKNN--DNFILDGFP 87
>gnl|CDD|223666 COG0593, DnaA, ATPase involved in DNA replication initiation [DNA
replication, recombination, and repair].
Length = 408
Score = 31.1 bits (71), Expect = 1.3
Identities = 10/38 (26%), Positives = 17/38 (44%)
Query: 69 FLFYGPPGTGKTSTMIAACHQLFGDMYRERILELNASD 106
YG G GKT + A ++ + R++ L + D
Sbjct: 116 LFIYGGVGLGKTHLLQAIGNEALANGPNARVVYLTSED 153
>gnl|CDD|236153 PRK08116, PRK08116, hypothetical protein; Validated.
Length = 268
Score = 30.8 bits (70), Expect = 1.4
Identities = 18/65 (27%), Positives = 24/65 (36%), Gaps = 15/65 (23%)
Query: 69 FLFYGPPGTGKTSTMIAACHQLFGDMYRERILELNASDDRGIQVIRDKVKTFAQQTASGF 128
L +G GTGKT AAC I N ++G+ VI + S +
Sbjct: 117 LLLWGSVGTGKTYL--AAC-----------I--ANELIEKGVPVIFVNFPQLLNRIKSTY 161
Query: 129 NQDGK 133
GK
Sbjct: 162 KSSGK 166
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 29.1 bits (66), Expect = 1.5
Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 10/52 (19%)
Query: 50 QQEVV-SVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQLFGDMYRERIL 100
Q+E + +L+K L G+GKT T A +L ++++L
Sbjct: 8 QEEAIERLLEK-------KRGLIVMATGSGKTLTAAALIARLAKG--KKKVL 50
>gnl|CDD|236482 PRK09361, radB, DNA repair and recombination protein RadB;
Provisional.
Length = 225
Score = 30.2 bits (69), Expect = 1.5
Identities = 9/19 (47%), Positives = 12/19 (63%), Gaps = 1/19 (5%)
Query: 71 FYGPPGTGKTS-TMIAACH 88
YGPPG+GKT+ + A
Sbjct: 28 IYGPPGSGKTNICLQLAVE 46
>gnl|CDD|185364 PRK15467, PRK15467, ethanolamine utilization protein EutP;
Provisional.
Length = 158
Score = 29.9 bits (67), Expect = 1.5
Identities = 13/45 (28%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 84 IAACHQLFGDM-YRERILELNASDDRGIQVIRDKVKTFAQQTASG 127
+AA +L + + E I ELN+ D + +Q + D + + +Q +G
Sbjct: 108 VAATRKLLLETGFEEPIFELNSHDPQSVQQLVDYLASLTKQEEAG 152
>gnl|CDD|235871 PRK06835, PRK06835, DNA replication protein DnaC; Validated.
Length = 329
Score = 30.6 bits (70), Expect = 1.7
Identities = 11/32 (34%), Positives = 17/32 (53%), Gaps = 2/32 (6%)
Query: 51 QEVVSVLKKCLSGADLPH--FLFYGPPGTGKT 80
++++ K + D + LFYG GTGKT
Sbjct: 166 EKILEKCKNFIENFDKNNENLLFYGNTGTGKT 197
>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 30.5 bits (69), Expect = 1.8
Identities = 15/27 (55%), Positives = 15/27 (55%), Gaps = 1/27 (3%)
Query: 63 GADLPH-FLFYGPPGTGKTSTMIAACH 88
G D P L YGPPGTGKT A H
Sbjct: 175 GIDPPRGVLLYGPPGTGKTMLAKAVAH 201
>gnl|CDD|221803 pfam12846, AAA_10, AAA-like domain. This family of domains
contain a P-loop motif that is characteristic of the
AAA superfamily. Many of the proteins in this family
are conjugative transfer proteins.
Length = 316
Score = 30.5 bits (69), Expect = 1.8
Identities = 8/24 (33%), Positives = 14/24 (58%)
Query: 67 PHFLFYGPPGTGKTSTMIAACHQL 90
P+ L GP G+GK++ + +L
Sbjct: 2 PNMLIVGPSGSGKSTLLKLLALRL 25
>gnl|CDD|240262 PTZ00088, PTZ00088, adenylate kinase 1; Provisional.
Length = 229
Score = 30.2 bits (68), Expect = 2.0
Identities = 29/128 (22%), Positives = 46/128 (35%), Gaps = 22/128 (17%)
Query: 70 LFYGPPGTGK-TSTMIAA-----CHQLFGDMYRERI-------LELNASDDRG------- 109
+ +G PG GK T I + H G++ RE I E+ G
Sbjct: 10 VLFGAPGVGKGTFAEILSKKENLKHINMGNILREEIKAKTTIGKEIQKVVTSGNLVPDNL 69
Query: 110 -IQVIRDKVKTFAQQTASGFNQDGKPCPPFKIVILDEADSMTHAAQAAL-RRTMEKETKS 167
I +++D++ GF DG P + L + ++ L R + K+
Sbjct: 70 VIAIVKDEIAKVTDDCFKGFILDGFPRNLKQCKELGKITNIDLFVNIYLPRNILIKKLLG 129
Query: 168 TRFCLICN 175
R C CN
Sbjct: 130 RRICNTCN 137
>gnl|CDD|222258 pfam13604, AAA_30, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins. There is a Walker A and
Walker B.
Length = 195
Score = 29.8 bits (68), Expect = 2.0
Identities = 23/90 (25%), Positives = 38/90 (42%), Gaps = 10/90 (11%)
Query: 73 GPPGTGKTSTMIAACHQLFGDMYRERILELNASDDRGIQVIRDKVKTFAQQTAS--GFNQ 130
GP GTGKT+++ AA YR L + +V+ +++ A+ AS
Sbjct: 25 GPAGTGKTTSLKAAREAWEAAGYRVIGLAPTG---KAAKVLGEELGIEARTLASLLHRWD 81
Query: 131 DGKPCPPF----KIVILDEADSMTHAAQAA 156
G+ ++++DEA M Q A
Sbjct: 82 KGEDPGRVLDAGTLLVVDEA-GMVGTRQMA 110
>gnl|CDD|107339 cd06344, PBP1_ABC_ligand_binding_like_9, Type I periplasmic
ligand-binding domain of uncharacterized ABC (ATPase
Binding Cassette)-type active transport systems that are
predicted to be involved in uptake of amino acids,
peptides, or inorganic ions. This subgroup includes the
type I periplasmic ligand-binding domain of
uncharacterized ABC (ATPase Binding Cassette)-type
active transport systems that are predicted to be
involved in uptake of amino acids, peptides, or
inorganic ions. Members of this group are
sequence-similar to members of the family of ABC-type
hydrophobic amino acid transporters, such as
leucine/isoleucine/valine binding protein (LIVBP);
however their ligand specificity has not been determined
experimentally.
Length = 332
Score = 30.0 bits (68), Expect = 2.3
Identities = 9/36 (25%), Positives = 14/36 (38%)
Query: 121 AQQTASGFNQDGKPCPPFKIVILDEADSMTHAAQAA 156
AQ Q G K+VI ++ + A + A
Sbjct: 23 AQAQTEINLQGGINGKLLKVVIANDGNDPEIAKKVA 58
>gnl|CDD|225327 COG2607, COG2607, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 287
Score = 30.0 bits (68), Expect = 2.5
Identities = 14/61 (22%), Positives = 30/61 (49%), Gaps = 4/61 (6%)
Query: 64 ADLP--HFLFYGPPGTGKTSTMIAACHQLFGDMYRERILELNASDDRGIQVIRDKVKTFA 121
LP + L +G GTGK S+++ A + D R++E++ D + + + ++
Sbjct: 81 EGLPANNVLLWGARGTGK-SSLVKALLNEYADEGL-RLVEVDKEDLATLPDLVELLRARP 138
Query: 122 Q 122
+
Sbjct: 139 E 139
>gnl|CDD|240274 PTZ00112, PTZ00112, origin recognition complex 1 protein;
Provisional.
Length = 1164
Score = 30.3 bits (68), Expect = 2.5
Identities = 55/222 (24%), Positives = 93/222 (41%), Gaps = 40/222 (18%)
Query: 73 GPPGTGKTSTMIAACHQLFGDMYRERIL-ELNASDDRGIQVIRDKV--KTFAQQTASG-- 127
G PGTGKT+T+ + QL ++++L N + G+ V+ + +Q +
Sbjct: 788 GMPGTGKTATVYSVI-QLLQHKTKQKLLPSFNVFEINGMNVVHPNAAYQVLYKQLFNKKP 846
Query: 128 -------------FNQDGKPCPPFKIVILDEADSMTHAAQAALRRTMEKETK-STRFCLI 173
FNQ+ K I+I+DE D + Q L + TK +++ LI
Sbjct: 847 PNALNSFKILDRLFNQNKKDNRNVSILIIDEIDYLITKTQKVLFTLFDWPTKINSKLVLI 906
Query: 174 C--NYVSCIIQPLTSRC-SKFRFKPLA---------ENTMLTRLQYICEQESVMCDFKAL 221
N + + + L RC S+ F L E + RL+ C++ + D A+
Sbjct: 907 AISNTMD-LPERLIPRCRSRLAFGRLVFSPYKGDEIEKIIKERLEN-CKE---IIDHTAI 961
Query: 222 ETL---VETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVT 260
+ V GD+R+A+ + K G+ IV D+ E T
Sbjct: 962 QLCARKVANVSGDIRKALQICRKAFENKRGQKIVPRDITEAT 1003
>gnl|CDD|214688 smart00483, POLXc, DNA polymerase X family. includes vertebrate
polymerase beta and terminal
deoxynucleotidyltransferases.
Length = 334
Score = 30.0 bits (68), Expect = 2.6
Identities = 28/128 (21%), Positives = 50/128 (39%), Gaps = 22/128 (17%)
Query: 309 SSLSDKQKALFKALETLVETSGGDMRRAITCLQSCARLKGGEGIVNEDVLEVTG------ 362
L+ +QKA K E +++ + RA + I+ + ++ +TG
Sbjct: 122 LKLTKQQKAGLKYYEDILKK----VSRAEAFAVEYIVKRAVRKILPDAIVTLTGSFRRGK 177
Query: 363 ----------VIPNPWIEKLLKVDSFQVLEKYIEDLILEAYSATQL--FDQFHDIVMSAS 410
P+P EK L+V +LE E+L L + L + I+ +
Sbjct: 178 ETGHDVDFLITSPHPAKEKELEVLDLLLLESTFEELQLPSIRVATLDHGQKKFMILKLSP 237
Query: 411 SLSDKQKA 418
S DK+K+
Sbjct: 238 SREDKEKS 245
>gnl|CDD|216186 pfam00910, RNA_helicase, RNA helicase. This family includes RNA
helicases thought to be involved in duplex unwinding
during viral RNA replication. Members of this family
are found in a variety of single stranded RNA viruses.
Length = 105
Score = 28.4 bits (64), Expect = 2.7
Identities = 8/21 (38%), Positives = 10/21 (47%)
Query: 70 LFYGPPGTGKTSTMIAACHQL 90
YGPPG GK++ L
Sbjct: 2 WLYGPPGCGKSTLAKYLARAL 22
>gnl|CDD|181224 PRK08084, PRK08084, DNA replication initiation factor;
Provisional.
Length = 235
Score = 29.6 bits (67), Expect = 2.8
Identities = 8/42 (19%), Positives = 19/42 (45%)
Query: 49 EQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQL 90
+ +++ L+ L + + G G++ + AAC +L
Sbjct: 28 DNDSLLAALQNALRQEHSGYIYLWSREGAGRSHLLHAACAEL 69
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 29.8 bits (67), Expect = 2.9
Identities = 12/20 (60%), Positives = 13/20 (65%)
Query: 70 LFYGPPGTGKTSTMIAACHQ 89
L YGPPGTGKT A H+
Sbjct: 160 LLYGPPGTGKTLLAKAVAHE 179
>gnl|CDD|236128 PRK07908, PRK07908, hypothetical protein; Provisional.
Length = 349
Score = 30.0 bits (68), Expect = 3.0
Identities = 11/62 (17%), Positives = 24/62 (38%), Gaps = 3/62 (4%)
Query: 102 LNASDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPPFKIVILDEADSMTHAAQA---ALR 158
+ + ++ D+ + A A G PF +V + +A+ + + A+R
Sbjct: 252 VAEAAADAARLAADRAEMVAGLRAVGARVVDPAAAPFVLVRVPDAELLRKRLRERGIAVR 311
Query: 159 RT 160
R
Sbjct: 312 RG 313
>gnl|CDD|219538 pfam07728, AAA_5, AAA domain (dynein-related subfamily). This Pfam
entry includes some of the AAA proteins not detected by
the pfam00004 model.
Length = 135
Score = 28.8 bits (65), Expect = 3.1
Identities = 19/92 (20%), Positives = 31/92 (33%), Gaps = 8/92 (8%)
Query: 68 HFLFYGPPGTGKTSTMIAACHQLFGDMYRERIL--ELNASDDRGIQVIRDKVKTFAQQTA 125
L GPPGTGK+ L L + D +G + I ++
Sbjct: 1 GVLLVGPPGTGKSELAERLAAALSNRPVFYVQLTRDTTEEDLKGRRNIDPGGASWVDGPL 60
Query: 126 SGFNQDGKPCPPFKIVILDEADSMTHAAQAAL 157
++G +I +LDE + +L
Sbjct: 61 VRAAREG------EIAVLDEINRANPDVLNSL 86
>gnl|CDD|178279 PLN02674, PLN02674, adenylate kinase.
Length = 244
Score = 29.5 bits (66), Expect = 3.1
Identities = 34/108 (31%), Positives = 45/108 (41%), Gaps = 24/108 (22%)
Query: 59 KCLSGADLPHFLFYGPPGTGK--TSTMI----AACHQLFGDMYRERI-----LELNA--- 104
KC S D + GPPG+GK S +I CH GDM R + L + A
Sbjct: 25 KCSSKPD-KRLILIGPPGSGKGTQSPIIKDEYCLCHLATGDMLRAAVAAKTPLGIKAKEA 83
Query: 105 -------SDDRGIQVIRDKVKTFAQQTASGFNQDGKPCPPFKIVILDE 145
SDD + +I + +K + Q GF DG P + LDE
Sbjct: 84 MDKGELVSDDLVVGIIDEAMKKPSCQ--KGFILDGFPRTVVQAQKLDE 129
>gnl|CDD|205495 pfam13315, DUF4085, Protein of unknown function (DUF4085). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are typically between 101 and 269 amino
acids in length.
Length = 208
Score = 29.4 bits (66), Expect = 3.5
Identities = 11/43 (25%), Positives = 20/43 (46%)
Query: 398 LFDQFHDIVMSASSLSDKQKALILEKLAECNARLQDGASEYIQ 440
+ HD +++ S+K K L+LE + R + EY +
Sbjct: 63 IHPYVHDGTLNSEYPSEKLKKLVLEWSQDYEKRFEQLDQEYNE 105
>gnl|CDD|235833 PRK06581, PRK06581, DNA polymerase III subunit delta'; Validated.
Length = 263
Score = 29.4 bits (66), Expect = 3.6
Identities = 17/64 (26%), Positives = 32/64 (50%), Gaps = 2/64 (3%)
Query: 138 FKIVILDEADSMT-HAAQAALRRTMEKETKSTRFCLICNYVSCIIQPLTSRCSKFRFKPL 196
+K+ I+ A+ M +AA + L+ +E K++ LI + + II + SRC K +
Sbjct: 90 YKVAIIYSAELMNLNAANSCLK-ILEDAPKNSYIFLITSRAASIISTIRSRCFKINVRSS 148
Query: 197 AENT 200
+
Sbjct: 149 ILHA 152
>gnl|CDD|223616 COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ
chaperones [Posttranslational modification, protein
turnover, chaperones].
Length = 786
Score = 29.9 bits (68), Expect = 3.6
Identities = 14/25 (56%), Positives = 14/25 (56%)
Query: 69 FLFYGPPGTGKTSTMIAACHQLFGD 93
FLF GP G GKT A LFGD
Sbjct: 524 FLFLGPTGVGKTELAKALAEALFGD 548
>gnl|CDD|223022 PHA03248, PHA03248, DNA packaging tegument protein UL25;
Provisional.
Length = 583
Score = 29.6 bits (67), Expect = 3.7
Identities = 10/14 (71%), Positives = 10/14 (71%)
Query: 232 MRRAITCLQSCARL 245
M AIT LQSC RL
Sbjct: 213 MTTAITSLQSCGRL 226
Score = 29.6 bits (67), Expect = 3.7
Identities = 10/14 (71%), Positives = 10/14 (71%)
Query: 333 MRRAITCLQSCARL 346
M AIT LQSC RL
Sbjct: 213 MTTAITSLQSCGRL 226
>gnl|CDD|233119 TIGR00763, lon, ATP-dependent protease La. This protein is induced
by heat shock and other stresses in E. coli, B.
subtilis, and other species. The yeast member,
designated PIM1, is located in the mitochondrial matrix,
required for mitochondrial function, and also induced by
heat shock [Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 775
Score = 30.0 bits (68), Expect = 3.7
Identities = 12/28 (42%), Positives = 14/28 (50%), Gaps = 3/28 (10%)
Query: 54 VSVLKKCLSGADLPHFLFYGPPGTGKTS 81
V L+ + G L GPPG GKTS
Sbjct: 338 VQKLRGKMKGPIL---CLVGPPGVGKTS 362
>gnl|CDD|223542 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 29.8 bits (68), Expect = 3.9
Identities = 8/12 (66%), Positives = 8/12 (66%)
Query: 70 LFYGPPGTGKTS 81
GPPG GKTS
Sbjct: 354 CLVGPPGVGKTS 365
>gnl|CDD|238672 cd01376, KISc_KID_like, Kinesin motor domain, KIF22/Kid-like
subgroup. Members of this group might play a role in
regulating chromosomal movement along microtubules in
mitosis. This catalytic (head) domain has ATPase
activity and belongs to the larger group of P-loop
NTPases. Kinesins are microtubule-dependent molecular
motors that play important roles in intracellular
transport and in cell division. In most kinesins, the
motor domain is found at the N-terminus (N-type). N-type
kinesins are (+) end-directed motors, i.e. they
transport cargo towards the (+) end of the microtubule.
Kinesin motor domains hydrolyze ATP at a rate of about
80 per second, and move along the microtubule at a speed
of about 6400 Angstroms per second. To achieve that,
kinesin head groups work in pairs. Upon replacing ADP
with ATP, a kinesin motor domain increases its affinity
for microtubule binding and locks in place. Also, the
neck linker binds to the motor domain, which repositions
the other head domain through the coiled-coil domain
close to a second tubulin dimer, about 80 Angstroms
along the microtubule. Meanwhile, ATP hydrolysis takes
place, and when the second head domain binds to the
microtubule, the first domain again replaces ADP with
ATP, triggering a conformational change that pulls the
first domain forward.
Length = 319
Score = 29.4 bits (66), Expect = 3.9
Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 4/58 (6%)
Query: 48 IEQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQLFGDMYR--ERILELN 103
I +EV ++ LSG + F YG G GKT TM+ ++ G + R +L +
Sbjct: 64 IFSREVKPIVPHLLSGQNATVFA-YGSTGAGKTHTMLGDPNE-PGLIPRTLSDLLRMG 119
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 28.7 bits (65), Expect = 4.5
Identities = 11/46 (23%), Positives = 17/46 (36%), Gaps = 4/46 (8%)
Query: 68 HFLFYGPPGTGKTSTMIAACHQLFGDMYRE---RILELNASDDRGI 110
+ G P TGKT T++ A + E +E +D
Sbjct: 1 RIVITGGPSTGKT-TLLEALAARGYPVVPEYGREYIEEQLADGGDA 45
>gnl|CDD|238687 cd01393, recA_like, RecA is a bacterial enzyme which has roles
in homologous recombination, DNA repair, and the
induction of the SOS response. RecA couples ATP
hydrolysis to DNA strand exchange. While prokaryotes
have a single RecA protein, eukaryotes have multiple
RecA homologs such as Rad51, DMC1 and Rad55/57.
Archaea have the RecA-like homologs radA and radB.
Length = 226
Score = 29.1 bits (66), Expect = 4.6
Identities = 9/26 (34%), Positives = 14/26 (53%), Gaps = 2/26 (7%)
Query: 71 FYGPPGTGKT--STMIAACHQLFGDM 94
+G G+GKT +A QL G++
Sbjct: 24 IFGEFGSGKTQLCLQLAVEAQLPGEL 49
>gnl|CDD|200312 TIGR03689, pup_AAA, proteasome ATPase. In the Actinobacteria, as
shown for Mycobacterium tuberculosis, some proteins are
modified by ligation between an epsilon-amino group of a
lysine side chain and the C-terminal carboxylate of the
ubiquitin-like protein Pup. This modification leads to
protein degradation by the archaeal-like proteasome
found in the Actinobacteria. Members of this protein
family belong to the AAA family of ATPases and tend to
be clustered with the genes for Pup, the Pup ligase
PafA, and structural components of the proteasome. This
protein forms hexameric rings with ATPase activity
[Protein fate, Degradation of proteins, peptides, and
glycopeptides].
Length = 512
Score = 29.3 bits (66), Expect = 5.1
Identities = 11/16 (68%), Positives = 12/16 (75%), Gaps = 2/16 (12%)
Query: 70 LFYGPPGTGKTSTMIA 85
L YGPPG GK T+IA
Sbjct: 220 LLYGPPGCGK--TLIA 233
>gnl|CDD|223637 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
transport and metabolism].
Length = 178
Score = 28.4 bits (64), Expect = 5.8
Identities = 12/35 (34%), Positives = 16/35 (45%), Gaps = 6/35 (17%)
Query: 69 FLFYGPPGTGKT--STMIAACHQLF----GDMYRE 97
L GPPG GK+ + +A L GD+ R
Sbjct: 3 ILILGPPGAGKSTLAKKLAKKLGLPHLDTGDILRA 37
>gnl|CDD|222165 pfam13481, AAA_25, AAA domain. This AAA domain is found in a
wide variety of presumed DNA repair proteins.
Length = 154
Score = 28.0 bits (63), Expect = 5.8
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 70 LFYGPPGTGKTSTMIAAC 87
L G PGTGK++ +
Sbjct: 37 LLAGAPGTGKSTLALDLA 54
>gnl|CDD|223703 COG0630, VirB11, Type IV secretory pathway, VirB11 components, and
related ATPases involved in archaeal flagella
biosynthesis [Cell motility and secretion /
Intracellular trafficking and secretion].
Length = 312
Score = 28.9 bits (65), Expect = 5.9
Identities = 12/53 (22%), Positives = 20/53 (37%), Gaps = 6/53 (11%)
Query: 38 KYRPKTIDDVIEQ----QEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAA 86
P T +D+IE E + L + + G +GKT+ + A
Sbjct: 113 SDEPITPEDLIEYGTISPEQAAYLWLAIEAR--KSIIICGGTASGKTTLLNAL 163
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 27.6 bits (61), Expect = 5.9
Identities = 13/53 (24%), Positives = 20/53 (37%), Gaps = 6/53 (11%)
Query: 70 LFYGPPGTGKTSTMIAACHQL------FGDMYRERILELNASDDRGIQVIRDK 116
L GPPG+GK++ +L D+ RE L + I +
Sbjct: 3 LITGPPGSGKSTLAKKLAEKLGIPVISLDDLLREEGLAELDDGELDDIDIDLE 55
>gnl|CDD|225363 COG2804, PulE, Type II secretory pathway, ATPase PulE/Tfp pilus
assembly pathway, ATPase PilB [Cell motility and
secretion / Intracellular trafficking and secretion].
Length = 500
Score = 28.8 bits (65), Expect = 6.0
Identities = 16/53 (30%), Positives = 24/53 (45%), Gaps = 11/53 (20%)
Query: 50 QQEVVSVLKKCLSGADL---------PH--FLFYGPPGTGKTSTMIAACHQLF 91
Q ++ + K +S L P L GP G+GKT+T+ AA +L
Sbjct: 231 DQVILDLEKLGMSPFQLARLLRLLNRPQGLILVTGPTGSGKTTTLYAALSELN 283
>gnl|CDD|235244 PRK04182, PRK04182, cytidylate kinase; Provisional.
Length = 180
Score = 28.2 bits (64), Expect = 6.4
Identities = 14/45 (31%), Positives = 22/45 (48%), Gaps = 13/45 (28%)
Query: 73 GPPGTGKTST--MIAACHQL--------FGDMYRER---ILELNA 104
GPPG+GKT+ ++A L F ++ +ER + E N
Sbjct: 7 GPPGSGKTTVARLLAEKLGLKHVSAGEIFRELAKERGMSLEEFNK 51
>gnl|CDD|238549 cd01129, PulE-GspE, PulE/GspE The type II secretory pathway is the
main terminal branch of the general secretory pathway
(GSP). It is responsible for the export the majority of
Gram-negative bacterial exoenzymes and toxins. PulE is a
cytoplasmic protein of the GSP, which contains an ATP
binding site and a tetracysteine motif. This subgroup
also includes PillB and HofB.
Length = 264
Score = 28.4 bits (64), Expect = 6.6
Identities = 11/22 (50%), Positives = 15/22 (68%), Gaps = 2/22 (9%)
Query: 67 PH--FLFYGPPGTGKTSTMIAA 86
PH L GP G+GKT+T+ +A
Sbjct: 79 PHGIILVTGPTGSGKTTTLYSA 100
>gnl|CDD|234340 TIGR03744, traC_PFL_4706, conjugative transfer ATPase, PFL_4706
family. Members of this protein family are predicted
ATP-binding proteins apparently associated with DNA
conjugal transfer. Members are found both in plasmids
and in bacterial chromosomal regions that appear to
derive from integrative elements such as conjugative
transposons. More distant homologs, outside the scope of
this family, include type IV secretion/conjugal transfer
proteins such as TraC, VirB4 and TrsE. The granularity
of this protein family definition is chosen so as to
represent one distinctive clade and act as a marker
through which to define and recognize the class of
mobile element it serves [Mobile and extrachromosomal
element functions, Plasmid functions].
Length = 893
Score = 28.9 bits (65), Expect = 6.6
Identities = 11/32 (34%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 68 HFLFYGPPGTGKTSTMIAACHQLFGDMYRERI 99
H L GP G GK++T+ Q+ ++R R+
Sbjct: 477 HLLILGPTGAGKSATLTNLLMQVMA-VHRPRL 507
>gnl|CDD|183521 PRK12422, PRK12422, chromosomal replication initiation protein;
Provisional.
Length = 445
Score = 28.6 bits (64), Expect = 6.7
Identities = 14/24 (58%), Positives = 16/24 (66%), Gaps = 1/24 (4%)
Query: 67 PHFLFYGPPGTGKTSTMIAACHQL 90
P +LF GP G+GKT M AA H L
Sbjct: 143 PIYLF-GPEGSGKTHLMQAAVHAL 165
>gnl|CDD|226581 COG4096, HsdR, Type I site-specific restriction-modification
system, R (restriction) subunit and related helicases
[Defense mechanisms].
Length = 875
Score = 28.9 bits (65), Expect = 7.3
Identities = 16/46 (34%), Positives = 20/46 (43%), Gaps = 3/46 (6%)
Query: 67 PHFLFYGPPGTGKTSTMIAACHQLFGDMYRERILELNASDDRGIQV 112
L GTGKT T IA +L + +R+L L DR V
Sbjct: 186 NRALLVMATGTGKTRTAIAIIDRLIKSGWVKRVLFLA---DRNALV 228
>gnl|CDD|181180 PRK07952, PRK07952, DNA replication protein DnaC; Validated.
Length = 244
Score = 28.2 bits (63), Expect = 7.7
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 69 FLFYGPPGTGKTSTMIAACHQL 90
F+F G PGTGK A C++L
Sbjct: 102 FIFSGKPGTGKNHLAAAICNEL 123
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 28.6 bits (64), Expect = 7.7
Identities = 24/117 (20%), Positives = 35/117 (29%), Gaps = 22/117 (18%)
Query: 50 QQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAACHQLFGD-------------MYR 96
Q+E + L K + P G GKT A +L
Sbjct: 41 QEEALDALVKNRRTERR--GVIVLPTGAGKTVVAAEAIAELKRSTLVLVPTKELLDQWAE 98
Query: 97 ERILELNASDDRGI-----QVIRDKVKTFAQ-QTASGF-NQDGKPCPPFKIVILDEA 146
L +D+ GI + + T A QT + D F ++I DE
Sbjct: 99 ALKKFLLLNDEIGIYGGGEKELEPAKVTVATVQTLARRQLLDEFLGNEFGLIIFDEV 155
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 28.6 bits (64), Expect = 8.1
Identities = 30/126 (23%), Positives = 45/126 (35%), Gaps = 18/126 (14%)
Query: 45 DDVIEQQEVVSVLKKC-LSGADLPHFLFYGPPGTGKTSTMIAACHQLFGDMYRERIL--E 101
V+ +EV+ + L+G H L GPPG GKT + A + G + +
Sbjct: 24 KVVVGDEEVIELALLALLAGG---HVLLEGPPGVGKT-LLARALARALGLPFVRIQCTPD 79
Query: 102 LNASDDRGIQVIRDKVKTFAQQTASGFNQDGK-PCPPFKIVILDE---ADSMTHAAQAAL 157
L SD G + + G I++LDE A Q AL
Sbjct: 80 LLPSDLLGTYAYAALLLEPGEF----RFVPGPLFAAVRVILLLDEINRAPPEV---QNAL 132
Query: 158 RRTMEK 163
+E+
Sbjct: 133 LEALEE 138
>gnl|CDD|216270 pfam01057, Parvo_NS1, Parvovirus non-structural protein NS1. This
family also contains the NS2 protein. Parvoviruses
encode two non-structural proteins, NS1 and NS2. The
mRNA for NS2 contains the coding sequence for the first
87 amino acids of NS1, then by an alternative splicing
mechanism mRNA from a different reading frame, encoding
the last 78 amino acids, makes up the full length of the
NS2 mRNA. NS1, is the major non-structural protein. It
is essential for DNA replication. It is an 83-kDa
nuclear phosphoprotein. It has DNA helicase and ATPase
activity.
Length = 271
Score = 28.1 bits (63), Expect = 8.9
Identities = 12/25 (48%), Positives = 14/25 (56%), Gaps = 2/25 (8%)
Query: 70 LFYGPPGTGKT--STMIAACHQLFG 92
FYGP TGKT + IA L+G
Sbjct: 117 WFYGPASTGKTNLAQAIAHAVPLYG 141
>gnl|CDD|182120 PRK09862, PRK09862, putative ATP-dependent protease; Provisional.
Length = 506
Score = 28.4 bits (63), Expect = 8.9
Identities = 21/58 (36%), Positives = 30/58 (51%), Gaps = 4/58 (6%)
Query: 29 RNKPVPWVEKYRPKTIDDVIEQQEVVSVLKKCLSGADLPHFLFYGPPGTGKTSTMIAA 86
R KP V + + DVI Q++ L+ +G + L GPPGTGK TM+A+
Sbjct: 175 RPKPTDAVSRALQHDLSDVIGQEQGKRGLEITAAGGH--NLLLIGPPGTGK--TMLAS 228
>gnl|CDD|238543 cd01123, Rad51_DMC1_radA, Rad51_DMC1_radA,B. This group of
recombinases includes the eukaryotic proteins RAD51,
RAD55/57 and the meiosis-specific protein DMC1, and the
archaeal proteins radA and radB. They are closely
related to the bacterial RecA group. Rad51 proteins
catalyze a similiar recombination reaction as RecA,
using ATP-dependent DNA binding activity and a
DNA-dependent ATPase. However, this reaction is less
efficient and requires accessory proteins such as
RAD55/57 .
Length = 235
Score = 27.9 bits (63), Expect = 9.4
Identities = 9/20 (45%), Positives = 12/20 (60%), Gaps = 4/20 (20%)
Query: 71 FYGPPGTGKTSTMIAACHQL 90
+G G+GK T + CHQL
Sbjct: 24 IFGEFGSGK--TQL--CHQL 39
>gnl|CDD|222160 pfam13476, AAA_23, AAA domain.
Length = 204
Score = 27.9 bits (62), Expect = 10.0
Identities = 17/56 (30%), Positives = 25/56 (44%), Gaps = 2/56 (3%)
Query: 69 FLFYGPPGTGKTSTMIAACHQLFGDMYR--ERILELNASDDRGIQVIRDKVKTFAQ 122
L YGP G+GKT+ + A L+G R + D I+ K KT+ +
Sbjct: 22 TLIYGPNGSGKTTILDAIRWALYGKTSRLKKSKGRGIVKGDIEIEKDEGKKKTYVE 77
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.134 0.385
Gapped
Lambda K H
0.267 0.0643 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,708,151
Number of extensions: 2204519
Number of successful extensions: 2714
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2602
Number of HSP's successfully gapped: 253
Length of query: 456
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 356
Effective length of database: 6,502,202
Effective search space: 2314783912
Effective search space used: 2314783912
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: 61 (27.5 bits)