RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780163|ref|YP_003064576.1| ATP-dependent Clp protease
ATP-binding subunit [Candidatus Liberibacter asiaticus str. psy62]
(798 letters)
>gnl|CDD|162958 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA.
Length = 731
Score = 1037 bits (2684), Expect = 0.0
Identities = 420/752 (55%), Positives = 542/752 (72%), Gaps = 21/752 (2%)
Query: 4 FSENLEKVLHQALVLANERNHEYATLEHLLLALIDDSDAAIVMLSCNVDLKVLKNNLLNY 63
SE LE++L AL A +R HE+ TLEH+LLAL+ DSDA ++ C D++ L+ +L +Y
Sbjct: 1 ISEELERILDAALEEAKKRRHEFVTLEHILLALLFDSDAIEILEECGGDVEALRKDLEDY 60
Query: 64 IDNDSSNKLKNGFRVECKPTSSFQRVVQRAVLHVQSTGRGIVTGANILVALFSEPDSHAT 123
++N+ + + + T QRV+QRA+LHV+S G+ + +ILVALF E DSHA+
Sbjct: 61 LENNLP-SITEENEADPEQTVGVQRVLQRALLHVKSAGKKEIGIGDILVALFDEEDSHAS 119
Query: 124 YFLQEQEMTLYDAVNFISHGISKRKEFANFQSKLNVDGSSAGSDGEGFVNDYQAKTDLNL 183
YFL+ Q +T D + +ISHGI K D E + + + D
Sbjct: 120 YFLKSQGITRLDILEYISHGIPK-------------DDGKNRDAEEAGKEEAKKQED--- 163
Query: 184 FPALSAYCVDLTEKVKKGKVDILVGRHEEINRTIQILCRRSKNNPLYVGDPGVGKTAIAE 243
AL Y VDLTEK K GK+D L+GR +E+ RTIQ+LCRR KNNPL VG+PGVGKTAIAE
Sbjct: 164 --ALEKYTVDLTEKAKNGKIDPLIGREDELERTIQVLCRRKKNNPLLVGEPGVGKTAIAE 221
Query: 244 GFAKQIVDGMVPDILLGARIFSLDMGNLIAGTRYRGDFEERIKKIVKEIESYANAILYID 303
G A +I +G VP+ L A+I+SLDMG+L+AGT+YRGDFEER+K +V EIE NAIL+ID
Sbjct: 222 GLALRIAEGKVPENLKNAKIYSLDMGSLLAGTKYRGDFEERLKAVVSEIEKEPNAILFID 281
Query: 304 EIHTLVGAGSASGISVDASNLLKPALSSGAVRCIGSTTYSEYRQFFEKDKALVRRFQKID 363
EIHT+VGAG+ SG S+DASNLLKPALSSG +RCIGSTTY EY+ FEKD+AL RRFQKID
Sbjct: 282 EIHTIVGAGATSGGSMDASNLLKPALSSGKLRCIGSTTYEEYKNHFEKDRALSRRFQKID 341
Query: 364 VSEPSIEDAIEIVKGIKPYFEEHHQLRYSKEAIRAAVQLSVRHFTSRKLPDKAIDVIDEA 423
V EPSIE+ ++I+KG+K +EE H ++YS EA+ AAV+LS R+ R LPDKAIDVIDEA
Sbjct: 342 VGEPSIEETVKILKGLKEKYEEFHHVKYSDEALEAAVELSARYINDRFLPDKAIDVIDEA 401
Query: 424 GASQILQPLSKRRKFITEKDIKKTIASMNRSIHTTSFSRDDDSVLSNLEKNLGTVVYGQE 483
GAS L+P +K++ ++ KDI+ +A M I + S DD L NLEKNL ++GQ+
Sbjct: 402 GASFRLRPKAKKKANVSVKDIENVVAKMAH-IPVKTVSVDDREKLKNLEKNLKAKIFGQD 460
Query: 484 EAIKKLSSSIKIARAGLSDPNKPIGCYVFSGPTGVGKTEISKQLAFALGVQLLRFDMSEY 543
EAI L SSIK +RAGL +PNKP+G ++F+GPTGVGKTE++KQLA ALGV L RFDMSEY
Sbjct: 461 EAIDSLVSSIKRSRAGLGNPNKPVGSFLFTGPTGVGKTELAKQLAEALGVHLERFDMSEY 520
Query: 544 MERHAVSRLIGAPPGYVGFGQGGILADSVDQNPYSVVLLDEIEKSHPDVLNILLQIMDYG 603
ME+H VSRLIGAPPGYVGF QGG+L ++V ++P+ V+LLDEIEK+HPD+ NILLQ+MDY
Sbjct: 521 MEKHTVSRLIGAPPGYVGFEQGGLLTEAVRKHPHCVLLLDEIEKAHPDIYNILLQVMDYA 580
Query: 604 ILTDQSGKKISFRNVILIMTTNAGALEMSKARIGFGSSRNDDADKEALRNFLSPEFLNRL 663
LTD +G+K FRNVILIMT+NAGA EMSK IGFGS + +A++ SPEF NRL
Sbjct: 581 TLTDNNGRKADFRNVILIMTSNAGASEMSKPPIGFGSENVESKSDKAIKKLFSPEFRNRL 640
Query: 664 DSIIPFFPLSSDIIRQVVHKFIMKLELQLQEKGISFHFSEEVINWLVSHGYDVKMGARPL 723
D+II F PLS +++ ++V KF+ +L QL EK I +++ +L GYD + GARPL
Sbjct: 641 DAIIHFNPLSEEVLEKIVQKFVDELSKQLNEKNIKLELTDDAKKYLAEKGYDEEFGARPL 700
Query: 724 ERIIKEHVKVPLADEILFGKLKKGGGVVKVSL 755
R+I+E +K PL+DEILFGKLKK GG VKV L
Sbjct: 701 ARVIQEEIKKPLSDEILFGKLKK-GGSVKVDL 731
>gnl|CDD|182917 PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit;
Provisional.
Length = 758
Score = 862 bits (2229), Expect = 0.0
Identities = 386/755 (51%), Positives = 533/755 (70%), Gaps = 18/755 (2%)
Query: 5 SENLEKVLHQALVLANERNHEYATLEHLLLALIDDSDAAIVMLSCNVDLKVLKNNLLNYI 64
++ LE L+ A A E HE+ T+EHLLLAL+ + A + +C+VDL L+ L +I
Sbjct: 3 NQELELSLNMAFARAREHRHEFMTVEHLLLALLSNPSAREALEACSVDLVALRQELEAFI 62
Query: 65 DNDSSNKLKNGFRVECKPTSSFQRVVQRAVLHVQSTGRGIVTGANILVALFSEPDSHATY 124
+ + + + +PT SFQRV+QRAV HVQS+GR VTGAN+LVA+FSE +S A Y
Sbjct: 63 EQTTPVLPASEEERDTQPTLSFQRVLQRAVFHVQSSGRSEVTGANVLVAIFSEQESQAAY 122
Query: 125 FLQEQEMTLYDAVNFISHGISKRKEFANFQSKLNVDGSSAGSDGEGFVNDYQAKTDLNLF 184
L++ E++ D VNFISHG K + S + G ++ QA +
Sbjct: 123 LLRKHEVSRLDVVNFISHGTRKD------------EPSQSSDPGSQPNSEEQAGGE---- 166
Query: 185 PALSAYCVDLTEKVKKGKVDILVGRHEEINRTIQILCRRSKNNPLYVGDPGVGKTAIAEG 244
+ + +L + + G +D L+GR +E+ R IQ+LCRR KNNPL VG+ GVGKTAIAEG
Sbjct: 167 ERMENFTTNLNQLARVGGIDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEG 226
Query: 245 FAKQIVDGMVPDILLGARIFSLDMGNLIAGTRYRGDFEERIKKIVKEIESYANAILYIDE 304
A +IV G VP+++ I+SLD+G+L+AGT+YRGDFE+R K ++K++E N+IL+IDE
Sbjct: 227 LAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKALLKQLEQDTNSILFIDE 286
Query: 305 IHTLVGAGSASGISVDASNLLKPALSSGAVRCIGSTTYSEYRQFFEKDKALVRRFQKIDV 364
IHT++GAG+ASG VDA+NL+KP LSSG +R IGSTTY E+ FEKD+AL RRFQKID+
Sbjct: 287 IHTIIGAGAASGGQVDAANLIKPLLSSGKIRVIGSTTYQEFSNIFEKDRALARRFQKIDI 346
Query: 365 SEPSIEDAIEIVKGIKPYFEEHHQLRYSKEAIRAAVQLSVRHFTSRKLPDKAIDVIDEAG 424
+EPSIE+ ++I+ G+KP +E HH +RY+ +A+RAAV+L+V++ R LPDKAIDVIDEAG
Sbjct: 347 TEPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAVELAVKYINDRHLPDKAIDVIDEAG 406
Query: 425 ASQILQPLSKRRKFITEKDIKKTIASMNRSIHTTSFSRDDDSVLSNLEKNLGTVVYGQEE 484
A L P+SKR+K + DI+ +A + R I S S+ D L NL L +V+GQ++
Sbjct: 407 ARARLMPVSKRKKTVNVADIESVVARIAR-IPEKSVSQSDRDTLKNLGDRLKMLVFGQDK 465
Query: 485 AIKKLSSSIKIARAGLSDPNKPIGCYVFSGPTGVGKTEISKQLAFALGVQLLRFDMSEYM 544
AI+ L+ +IK++RAGL +KP+G ++F+GPTGVGKTE++ QL+ ALG++LLRFDMSEYM
Sbjct: 466 AIEALTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYM 525
Query: 545 ERHAVSRLIGAPPGYVGFGQGGILADSVDQNPYSVVLLDEIEKSHPDVLNILLQIMDYGI 604
ERH VSRLIGAPPGYVGF QGG+L D+V ++P++V+LLDEIEK+HPDV N+LLQ+MD G
Sbjct: 526 ERHTVSRLIGAPPGYVGFDQGGLLTDAVIKHPHAVLLLDEIEKAHPDVFNLLLQVMDNGT 585
Query: 605 LTDQSGKKISFRNVILIMTTNAGALEMSKARIGFGSSRNDDADKEALRNFLSPEFLNRLD 664
LTD +G+K FRNV+L+MTTNAG E + IG N E ++ +PEF NRLD
Sbjct: 586 LTDNNGRKADFRNVVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRNRLD 645
Query: 665 SIIPFFPLSSDIIRQVVHKFIMKLELQLQEKGISFHFSEEVINWLVSHGYDVKMGARPLE 724
+II F LS+D+I QVV KFI++L+ QL +KG+S S+E +WL GYD MGARP+
Sbjct: 646 NIIWFDHLSTDVIHQVVDKFIVELQAQLDQKGVSLEVSQEARDWLAEKGYDRAMGARPMA 705
Query: 725 RIIKEHVKVPLADEILFGKLKKGGGVVKVSLNPDK 759
R+I++++K PLA+E+LFG L GG V V+L+ +K
Sbjct: 706 RVIQDNLKKPLANELLFGSL-VDGGQVTVALDKEK 739
>gnl|CDD|163223 TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB. Members
of this protein family are the bacterial ATP-dependent
chaperone ClpB. This protein belongs to the AAA family,
ATPases associated with various cellular activities
(pfam00004). This molecular chaperone does not act as a
protease, but rather serves to disaggregate misfolded
and aggregated proteins.
Length = 852
Score = 360 bits (926), Expect = e-100
Identities = 170/427 (39%), Positives = 245/427 (57%), Gaps = 36/427 (8%)
Query: 4 FSENLEKVLHQALVLANERNHEYATLEHLLLALIDDSDAAIVML--SCNVDLKVLKNNLL 61
F+E ++ L A LA R+H+ EHLL AL+D L V++ L+ L
Sbjct: 1 FTEKFQEALQAAQSLALGRDHQQIEPEHLLKALLDQEGGLARRLLQKAGVNVGALRQALE 60
Query: 62 NYIDNDSSNKLKNGFRVECKPTSSFQRVVQRAVLHVQSTGRGIVTGANILVALFSEPDSH 121
++ K+ + + R++ A Q G ++ ++L+AL + +
Sbjct: 61 KELE--KLPKVSGPGG-QVYLSPELNRLLNLAEKLAQKRGDEFISSEHLLLALLDDKGTL 117
Query: 122 ATYFLQEQEMTLYDAVNFISHGISKRKEFANFQSKLN-VDGSSAGSDGEGFVNDYQAKTD 180
+ G + ++ +N V G V A+
Sbjct: 118 GKLLKEA--------------GATA----DALEAAINAVRGGQK-------VTSANAE-- 150
Query: 181 LNLFPALSAYCVDLTEKVKKGKVDILVGRHEEINRTIQILCRRSKNNPLYVGDPGVGKTA 240
+ + AL Y DLTE+ ++GK+D ++GR EEI RTIQ+L RR+KNNP+ +G+PGVGKTA
Sbjct: 151 -DQYEALEKYARDLTERAREGKLDPVIGRDEEIRRTIQVLSRRTKNNPVLIGEPGVGKTA 209
Query: 241 IAEGFAKQIVDGMVPDILLGARIFSLDMGNLIAGTRYRGDFEERIKKIVKEIE-SYANAI 299
I EG A++IV+G VP+ L R+ +LDMG LIAG +YRG+FEER+K ++ E+ S I
Sbjct: 210 IVEGLAQRIVNGDVPESLKNKRLLALDMGALIAGAKYRGEFEERLKAVLNEVTKSEGQII 269
Query: 300 LYIDEIHTLVGAGSASGISVDASNLLKPALSSGAVRCIGSTTYSEYRQFFEKDKALVRRF 359
L+IDE+HTLVGAG A G ++DA N+LKPAL+ G + CIG+TT EYR++ EKD AL RRF
Sbjct: 270 LFIDELHTLVGAGKAEG-AMDAGNMLKPALARGELHCIGATTLDEYRKYIEKDAALERRF 328
Query: 360 QKIDVSEPSIEDAIEIVKGIKPYFEEHHQLRYSKEAIRAAVQLSVRHFTSRKLPDKAIDV 419
Q + V EP++ED I I++G+K +E HH +R + AI AA LS R+ T R LPDKAID+
Sbjct: 329 QPVFVDEPTVEDTISILRGLKERYEVHHGVRITDPAIVAAATLSHRYITDRFLPDKAIDL 388
Query: 420 IDEAGAS 426
IDEA A
Sbjct: 389 IDEAAAR 395
Score = 315 bits (809), Expect = 3e-86
Identities = 134/295 (45%), Positives = 197/295 (66%), Gaps = 4/295 (1%)
Query: 468 LSNLEKNLGTVVYGQEEAIKKLSSSIKIARAGLSDPNKPIGCYVFSGPTGVGKTEISKQL 527
L ++E+ L V GQ+EA++ +S +I+ +RAGLSDPN+PIG ++F GPTGVGKTE++K L
Sbjct: 556 LLHMEEVLHERVVGQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELAKAL 615
Query: 528 A---FALGVQLLRFDMSEYMERHAVSRLIGAPPGYVGFGQGGILADSVDQNPYSVVLLDE 584
A F ++R DMSEYME+H+V+RLIGAPPGYVG+ +GG L ++V + PYSVVL DE
Sbjct: 616 AEFLFDDEDAMVRIDMSEYMEKHSVARLIGAPPGYVGYEEGGQLTEAVRRKPYSVVLFDE 675
Query: 585 IEKSHPDVLNILLQIMDYGILTDQSGKKISFRNVILIMTTNAGALEMSKARIGFGSSRND 644
+EK+HPDV N+LLQ++D G LTD G+ + FRN ++IMT+N G+ + + G
Sbjct: 676 VEKAHPDVFNVLLQVLDDGRLTDGQGRTVDFRNTVIIMTSNLGSQFIQELAGGDDYEEMR 735
Query: 645 DADKEALRNFLSPEFLNRLDSIIPFFPLSSDIIRQVVHKFIMKLELQLQEKGISFHFSEE 704
+A E LR PEFLNR+D I+ F PL + I ++V + +L +L E+ I+ S+
Sbjct: 736 EAVMEVLRAHFRPEFLNRIDEIVVFHPLGREQIARIVEIQLGRLRKRLAERKITLELSDA 795
Query: 705 VINWLVSHGYDVKMGARPLERIIKEHVKVPLADEILFGKLKKGGGVVKVSLNPDK 759
+++L GYD GARPL+R I+ ++ PLA +IL G++ G + V + +
Sbjct: 796 ALDFLAEAGYDPVYGARPLKRAIQREIENPLAKKILAGEVAD-GDTIVVDVEGGR 849
Score = 38.0 bits (89), Expect = 0.009
Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 3/64 (4%)
Query: 3 FFSENLEKVLHQALVLANERNHEYATLEHLLLALIDDSDAAIVMLSCNVDLKVLKNNLLN 62
+ S L ++L+ A LA +R E+ + EHLLLAL+DD +L + + L
Sbjct: 77 YLSPELNRLLNLAEKLAQKRGDEFISSEHLLLALLDDKGTLGKLLK---EAGATADALEA 133
Query: 63 YIDN 66
I+
Sbjct: 134 AINA 137
>gnl|CDD|163222 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.
Length = 852
Score = 344 bits (884), Expect = 7e-95
Identities = 162/439 (36%), Positives = 231/439 (52%), Gaps = 60/439 (13%)
Query: 10 KVLHQALVLANERNHEYATLEHLLLALID--DSDAAIVMLSCNVDLKVLKNNLLNYIDND 67
+ L QA L R H LEH LLAL+D DSD A ++ VDL LK +L +D
Sbjct: 7 RALEQAAALCVARGHPEVELEHWLLALLDQPDSDLAAILRHFGVDLGRLKADLARALDK- 65
Query: 68 SSNKLKNGFRVECKPTSSFQ----RVVQRAVLHVQST--GRGIVTGANILVALFSEPDSH 121
T F ++Q A + S G G + ++L+AL ++P+
Sbjct: 66 --------LPRGNTRTPVFSPHLVELLQEA-WLLASLELGDGRIRSGHLLLALLTDPE-- 114
Query: 122 ATYFLQEQEMTLYDAVNFISHGISKRKEFANFQSKLNVDG--------------SSAGSD 167
L + IS E A K++ + +SA +
Sbjct: 115 -----------LRRLLGSIS------PELA----KIDREALREALPALVEGSAEASAAAA 153
Query: 168 GEGFVNDYQAKTDLNLFPALSAYCVDLTEKVKKGKVDILVGRHEEINRTIQILCRRSKNN 227
G AL Y DLT + ++GK+D ++GR +EI + I IL RR +NN
Sbjct: 154 DAGPAAAAAGAAGT---SALDQYTTDLTAQAREGKIDPVLGRDDEIRQMIDILLRRRQNN 210
Query: 228 PLYVGDPGVGKTAIAEGFAKQIVDGMVPDILLGARIFSLDMGNLIAGTRYRGDFEERIKK 287
P+ G+ GVGKTA+ EG A +I G VP L R+ SLD+G L AG +G+FE R+K
Sbjct: 211 PILTGEAGVGKTAVVEGLALRIAAGDVPPALRNVRLLSLDLGLLQAGASVKGEFENRLKS 270
Query: 288 IVKEI-ESYANAILYIDEIHTLVGAGSASGISVDASNLLKPALSSGAVRCIGSTTYSEYR 346
++ E+ S IL+IDE HTL+GAG +G DA+NLLKPAL+ G +R I +TT++EY+
Sbjct: 271 VIDEVKASPQPIILFIDEAHTLIGAGGQAGQG-DAANLLKPALARGELRTIAATTWAEYK 329
Query: 347 QFFEKDKALVRRFQKIDVSEPSIEDAIEIVKGIKPYFEEHHQLRYSKEAIRAAVQLSVRH 406
++FEKD AL RRFQ + V EP E AI +++G+ P E+HH + EA+ AAV+LS R+
Sbjct: 330 KYFEKDPALTRRFQVVKVEEPDEETAIRMLRGLAPVLEKHHGVLILDEAVVAAVELSHRY 389
Query: 407 FTSRKLPDKAIDVIDEAGA 425
R+LPDKA+ ++D A A
Sbjct: 390 IPGRQLPDKAVSLLDTACA 408
Score = 266 bits (683), Expect = 1e-71
Identities = 111/289 (38%), Positives = 178/289 (61%), Gaps = 13/289 (4%)
Query: 462 RDDDSVLSNLEKNLGTVVYGQEEAIKKLSSSIKIARAGLSDPNKPIGCYVFSGPTGVGKT 521
RD+ + +L L V GQ+ A++ ++ I+ ARAGL DP KP+G ++ GP+GVGKT
Sbjct: 551 RDEIEAVLSLPDRLAERVIGQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKT 610
Query: 522 EISKQLAFAL--GVQ-LLRFDMSEYMERHAVSRLIGAPPGYVGFGQGGILADSVDQNPYS 578
E + LA L G Q L+ +MSE+ E H VSRL G+PPGYVG+G+GG+L ++V + PYS
Sbjct: 611 ETALALAELLYGGEQNLITINMSEFQEAHTVSRLKGSPPGYVGYGEGGVLTEAVRRKPYS 670
Query: 579 VVLLDEIEKSHPDVLNILLQIMDYGILTDQSGKKISFRNVILIMTTNAGALEMSKARIGF 638
VVLLDE+EK+HPDVL + Q+ D G++ D G++I F+N ++++T+NAG+ +
Sbjct: 671 VVLLDEVEKAHPDVLELFYQVFDKGVMEDGEGREIDFKNTVILLTSNAGSDLIMALCA-- 728
Query: 639 GSSRNDDAD--KEALR----NFLSPEFLNRLDSIIPFFPLSSDIIRQVVHKFIMKLELQL 692
D + EALR P FL R+ ++IP+ PL D++ +V + ++ +L
Sbjct: 729 DPETAPDPEALLEALRPELLKVFKPAFLGRM-TVIPYLPLDDDVLAAIVRLKLDRIARRL 787
Query: 693 QEK-GISFHFSEEVINWLVSHGYDVKMGARPLERIIKEHVKVPLADEIL 740
+E G +SE ++ +V+ +V+ GAR ++ I+ + + L+ +IL
Sbjct: 788 KENHGAELVYSEALVEHIVARCTEVESGARNIDAILNQTLLPELSRQIL 836
>gnl|CDD|182791 PRK10865, PRK10865, protein disaggregation chaperone; Provisional.
Length = 857
Score = 307 bits (788), Expect = 8e-84
Identities = 137/250 (54%), Positives = 191/250 (76%), Gaps = 2/250 (0%)
Query: 186 ALSAYCVDLTEKVKKGKVDILVGRHEEINRTIQILCRRSKNNPLYVGDPGVGKTAIAEGF 245
AL Y +DLTE+ ++GK+D ++GR EEI RTIQ+L RR+KNNP+ +G+PGVGKTAI EG
Sbjct: 160 ALKKYTIDLTERAEQGKLDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGL 219
Query: 246 AKQIVDGMVPDILLGARIFSLDMGNLIAGTRYRGDFEERIKKIVKEI-ESYANAILYIDE 304
A++I++G VP+ L G R+ +LDMG L+AG +YRG+FEER+K ++ ++ + N IL+IDE
Sbjct: 220 AQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDE 279
Query: 305 IHTLVGAGSASGISVDASNLLKPALSSGAVRCIGSTTYSEYRQFFEKDKALVRRFQKIDV 364
+HT+VGAG A G ++DA N+LKPAL+ G + C+G+TT EYRQ+ EKD AL RRFQK+ V
Sbjct: 280 LHTMVGAGKADG-AMDAGNMLKPALARGELHCVGATTLDEYRQYIEKDAALERRFQKVFV 338
Query: 365 SEPSIEDAIEIVKGIKPYFEEHHQLRYSKEAIRAAVQLSVRHFTSRKLPDKAIDVIDEAG 424
+EPS+ED I I++G+K +E HH ++ + AI AA LS R+ R+LPDKAID+IDEA
Sbjct: 339 AEPSVEDTIAILRGLKERYELHHHVQITDPAIVAAATLSHRYIADRQLPDKAIDLIDEAA 398
Query: 425 ASQILQPLSK 434
+S +Q SK
Sbjct: 399 SSIRMQIDSK 408
Score = 272 bits (698), Expect = 2e-73
Identities = 130/284 (45%), Positives = 192/284 (67%), Gaps = 5/284 (1%)
Query: 468 LSNLEKNLGTVVYGQEEAIKKLSSSIKIARAGLSDPNKPIGCYVFSGPTGVGKTEISKQL 527
L +E+ L V GQ EA++ +S++I+ +RAGLSDPN+PIG ++F GPTGVGKTE+ K L
Sbjct: 559 LLRMEQELHHRVIGQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELCKAL 618
Query: 528 A---FALGVQLLRFDMSEYMERHAVSRLIGAPPGYVGFGQGGILADSVDQNPYSVVLLDE 584
A F ++R DMSE+ME+H+VSRL+GAPPGYVG+ +GG L ++V + PYSV+LLDE
Sbjct: 619 ANFMFDSDDAMVRIDMSEFMEKHSVSRLVGAPPGYVGYEEGGYLTEAVRRRPYSVILLDE 678
Query: 585 IEKSHPDVLNILLQIMDYGILTDQSGKKISFRNVILIMTTNAGALEMSKARIG-FGSSRN 643
+EK+HPDV NILLQ++D G LTD G+ + FRN ++IMT+N G+ ++ + R G +
Sbjct: 679 VEKAHPDVFNILLQVLDDGRLTDGQGRTVDFRNTVVIMTSNLGS-DLIQERFGELDYAHM 737
Query: 644 DDADKEALRNFLSPEFLNRLDSIIPFFPLSSDIIRQVVHKFIMKLELQLQEKGISFHFSE 703
+ + + PEF+NR+D ++ F PL I + + +L +L+E+G H S+
Sbjct: 738 KELVLGVVSHNFRPEFINRIDEVVVFHPLGEQHIASIAQIQLQRLYKRLEERGYEIHISD 797
Query: 704 EVINWLVSHGYDVKMGARPLERIIKEHVKVPLADEILFGKLKKG 747
E + L +GYD GARPL+R I++ ++ PLA +IL G+L G
Sbjct: 798 EALKLLSENGYDPVYGARPLKRAIQQQIENPLAQQILSGELVPG 841
>gnl|CDD|116338 pfam07724, AAA_2, AAA domain (Cdc48 subfamily). This Pfam entry
includes some of the AAA proteins not detected by the
pfam00004 model.
Length = 168
Score = 223 bits (571), Expect = 1e-58
Identities = 87/168 (51%), Positives = 115/168 (68%), Gaps = 6/168 (3%)
Query: 505 KPIGCYVFSGPTGVGKTEISKQLAFALGVQ---LLRFDMSEYMERHAVSRLIGAPPGYVG 561
+PIG ++F GPTGVGKTE++K LA L L+R DMSEYME H+VSRLIGAPPGYVG
Sbjct: 1 RPIGSFLFLGPTGVGKTELAKALAELLFGDERALIRIDMSEYMEEHSVSRLIGAPPGYVG 60
Query: 562 FGQGGILADSVDQNPYSVVLLDEIEKSHPDVLNILLQIMDYGILTDQSGKKISFRNVILI 621
+ +GG L ++V + PYS+VL+DEIEK+HP V N LLQI++ G LTD+ G+K+ FRN + I
Sbjct: 61 YEEGGQLTEAVRRKPYSIVLIDEIEKAHPGVQNDLLQILEGGTLTDKQGRKVDFRNTLFI 120
Query: 622 MTTNAGALEMSKARIGFGSSRNDDADK---EALRNFLSPEFLNRLDSI 666
MT N G+ ++S A S + + + L+ PEFL RL I
Sbjct: 121 MTGNFGSEKISDASRLGKSPDYELLKELVMDLLKKGFIPEFLGRLPII 168
>gnl|CDD|151009 pfam10431, ClpB_D2-small, C-terminal, D2-small domain, of ClpB
protein. This is the C-terminal domain of ClpB protein,
referred to as the D2-small domain, and is a mixed
alpha-beta structure. Compared with the D1-small domain
(included in AAA, pfam00004) it lacks the long
coiled-coil insertion, and instead of helix C4 contains
a beta-strand (e3) that is part of a three stranded
beta-pleated sheet. In Thermophilus the whole protein
forms a hexamer with the D1-small and D2-small domains
located on the outside of the hexamer, with the long
coiled-coil being exposed on the surface. The D2-small
domain is essential for oligomerisation, forming a tight
interface with the D2-large domain of a neighbouring
subunit and thereby providing enough binding energy to
stabilize the functional assembly. The domain is
associated with two Clp_N, pfam02861, at the N-terminus
as well as AAA, pfam00004 and AAA_2, pfam07724.
Length = 89
Score = 104 bits (262), Expect = 1e-22
Identities = 34/87 (39%), Positives = 56/87 (64%), Gaps = 1/87 (1%)
Query: 672 LSSDIIRQVVHKFIMKLELQLQEKGISFHFSEEVINWLVSHGYDVKMGARPLERIIKEHV 731
LS + +RQ+V + +L+ +L E+GI+ ++ +WL GYD + GARPL R I+ +
Sbjct: 1 LSKEELRQIVDLQLKRLQKRLAERGITLELTDAAKDWLAEKGYDPEYGARPLRRAIQREI 60
Query: 732 KVPLADEILFGKLKKGGGVVKVSLNPD 758
+ PLA+EIL G+LK+ G V+V ++
Sbjct: 61 EDPLAEEILSGELKE-GDTVRVDVDDK 86
>gnl|CDD|128665 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 = 54.3 bits (130), Expect = 1e-07
Identities = 29/134 (21%), Positives = 48/134 (35%), Gaps = 10/134 (7%)
Query: 508 GCYVFSGPTGVGKTEISKQLAFAL---GVQLLRFDMSEYMERHAVSRLIGAPPGYVGFGQ 564
+ GP G GKT +++ LA L G ++ D + +E L+ G G
Sbjct: 3 EVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGS 62
Query: 565 GG----ILADSVDQNPYSVVLLDEIEKSHPDVLNILLQIMDYGILTDQSGKKISFRNVIL 620
G + + V++LDEI LL ++ S +N+ +
Sbjct: 63 GELRLRLALALARKLKPDVLILDEITSLLDAEQEALLLLL---EELRLLLLLKSEKNLTV 119
Query: 621 IMTTNAGALEMSKA 634
I+TTN
Sbjct: 120 ILTTNDEKDLGPAL 133
Score = 50.1 bits (119), Expect = 2e-06
Identities = 29/138 (21%), Positives = 54/138 (39%), Gaps = 10/138 (7%)
Query: 231 VGDPGVGKTAIAEGFAKQIVDGMVPDILLGARIFSLDMGN-----LIAGTRYRGDFEERI 285
VG PG GKT +A A+++ I + ++ + ++ G + G E R+
Sbjct: 8 VGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRL 67
Query: 286 KKIVKEIESYANAILYIDEIHTLVGAGSASGISVDA-SNLLKPALSSGAVRCIGSTTYSE 344
+ + +L +DEI +L+ A + + + LL S + I +T
Sbjct: 68 RLALALARKLKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLKSEKNLTVILTTN--- 124
Query: 345 YRQFFEKDKALVRRFQKI 362
+ L RRF +
Sbjct: 125 -DEKDLGPALLRRRFDRR 141
>gnl|CDD|149019 pfam07728, AAA_5, AAA domain (dynein-related subfamily). This Pfam
entry includes some of the AAA proteins not detected by
the pfam00004 model.
Length = 139
Score = 53.5 bits (129), Expect = 2e-07
Identities = 31/124 (25%), Positives = 50/124 (40%), Gaps = 19/124 (15%)
Query: 514 GPTGVGKTEISKQLAFAL-GVQLLRFDMSEYMERHAVSRLIGAPPGYVGFGQGGILADSV 572
GP G GK+E++++LA AL + ++ L G D
Sbjct: 6 GPPGTGKSELAERLAAALSNRPVFYVQLTRDTTE---EDLKG---RRNIANGTTSWVDGP 59
Query: 573 ----DQNPYSVVLLDEIEKSHPDVLNILLQIMDYGIL-TDQSGKKISFRN------VILI 621
+ + +LDEI +++PDVLN LL ++D L + G+ + LI
Sbjct: 60 LVRAAREGE-IAVLDEINRANPDVLNSLLSLLDERRLLLPEGGELVKVAPDDFAKRFRLI 118
Query: 622 MTTN 625
T N
Sbjct: 119 ATMN 122
Score = 33.4 bits (77), Expect = 0.22
Identities = 34/144 (23%), Positives = 47/144 (32%), Gaps = 20/144 (13%)
Query: 229 LYVGDPGVGKTAIAEGFAKQIVDGMVPDILLGARIFSLDMGNLIAGTRYRGDFEERIKKI 288
L VG PG GK+ +AE A + + V + L D L +
Sbjct: 3 LLVGPPGTGKSELAERLAAALSNRPVFYVQLTRDTTEED---LKGRRNIANGTTSWVDGP 59
Query: 289 VKEI--ESYANAILYIDEIHTLVGAGSASGISV---------DASNLLKPALSSGA--VR 335
+ E I +DEI+ S +S+ + L+K A A R
Sbjct: 60 LVRAAREG---EIAVLDEINRANPDVLNSLLSLLDERRLLLPEGGELVKVAPDDFAKRFR 116
Query: 336 CIGSTTYSEYRQFFEKDKALVRRF 359
I T R E AL RF
Sbjct: 117 LIA-TMNPLDRGLNELSPALRSRF 139
>gnl|CDD|162267 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily. This
subfamily of the AAA family ATPases includes two members
each from three archaeal species. It also includes yeast
CDC48 (cell division control protein 48) and the human
ortholog, transitional endoplasmic reticulum ATPase
(valosin-containing protein). These proteins in
eukaryotes are involved in the budding and transfer of
membrane from the transitional endoplasmic reticulum to
the Golgi apparatus.
Length = 733
Score = 49.5 bits (118), Expect = 4e-06
Identities = 34/114 (29%), Positives = 56/114 (49%), Gaps = 16/114 (14%)
Query: 193 DLTEKVKKGKVDI-LVGRHEEINRTIQILCRRSKNNPLYVGDPGVGKTAIAEGFAKQIVD 251
L E +K + + L +H E+ + I L G PG GKT +A+ A +
Sbjct: 182 GLKEAKEKIREMVELPMKHPELFEHLGI---EPPKGVLLYGPPGTGKTLLAKAVANEA-- 236
Query: 252 GMVPDILLGARIFSLDMGNLIAGTRYRGDFEERIKKIVKEIESYANAILYIDEI 305
GA S++ ++ ++Y G+ EER+++I KE E A +I++IDEI
Sbjct: 237 --------GAYFISINGPEIM--SKYYGESEERLREIFKEAEENAPSIIFIDEI 280
Score = 35.3 bits (81), Expect = 0.069
Identities = 29/107 (27%), Positives = 47/107 (43%), Gaps = 15/107 (14%)
Query: 209 RHEEINRTIQILCRRSKNNPLYVGDPGVGKTAIAEGFAKQIVDGMVPDILLGARIFSLDM 268
+H EI + I R L G PG GKT +A+ A + + + G I S
Sbjct: 474 KHPEIFEKMGI---RPPKGVLLFGPPGTGKTLLAKAVATESGANFIA--VRGPEILS--- 525
Query: 269 GNLIAGTRYRGDFEERIKKIVKEIESYANAILYIDEIHTLVGAGSAS 315
++ G+ E+ I++I ++ A AI++ DEI + A A
Sbjct: 526 -------KWVGESEKAIREIFRKARQAAPAIIFFDEIDAIAPARGAR 565
Score = 28.3 bits (63), Expect = 7.6
Identities = 32/142 (22%), Positives = 58/142 (40%), Gaps = 37/142 (26%)
Query: 481 GQEEAIKKLSSSIKIA--------RAGLSDPNKPIGCYVFSGPTGVGKTEISKQLAFALG 532
G +EA +K+ +++ G+ +P K + Y GP G GKT ++K +A G
Sbjct: 182 GLKEAKEKIREMVELPMKHPELFEHLGI-EPPKGVLLY---GPPGTGKTLLAKAVANEAG 237
Query: 533 VQLLRFDMSEYMERHAVSRLIGAPPGYVGFGQGGI--LADSVDQNPYSVVLLDEIEKSHP 590
+ + E M + Y G + + + ++N S++ +DEI+ P
Sbjct: 238 AYFISINGPEIMSK------------YYGESEERLREIFKEAEENAPSIIFIDEIDAIAP 285
Query: 591 D-----------VLNILLQIMD 601
V+ LL +MD
Sbjct: 286 KREEVTGEVEKRVVAQLLTLMD 307
>gnl|CDD|161849 TIGR00382, clpX, endopeptidase Clp ATP-binding regulatory subunit
(clpX). A member of the ATP-dependent proteases, ClpX
has ATP-dependent chaperone activity and is required for
specific ATP-dependent proteolytic activities expressed
by ClpPX. The gene is also found to be involved in
stress tolerance in Bacillus subtilis and is essential
for the efficient acquisition of genes specifying type
IA and IB restriction.
Length = 413
Score = 47.5 bits (113), Expect = 1e-05
Identities = 78/320 (24%), Positives = 119/320 (37%), Gaps = 72/320 (22%)
Query: 471 LEKNLGTVVYGQEEAIKKLSSS-------IKIARAGLSDPNKPIG--CYVFSGPTGVGKT 521
++ +L V GQE+A K LS + + + SD + + GPTG GKT
Sbjct: 71 IKAHLDEYVIGQEQAKKVLSVAVYNHYKRLNFEKNKKSDNGVELSKSNILLIGPTGSGKT 130
Query: 522 EISKQLAFALGVQLLRFDMSEYMERHAVSRLIGAPPGYVGFGQGGILADSVDQNPYSV-- 579
+++ LA L V D + E GYVG IL + Y V
Sbjct: 131 LLAQTLARILNVPFAIADATTLTE-----------AGYVGEDVENILLKLLQAADYDVEK 179
Query: 580 -----VLLDEIEK--------------SHPDVLNILLQIMDYGI--LTDQSGKKISFRNV 618
+ +DEI+K S V LL+I++ + + Q G+K ++
Sbjct: 180 AQKGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKIIEGTVANVPPQGGRKHPYQEF 239
Query: 619 ILIMTTN-----AGAL---------EMSKARIGFGSS--RNDDADKEALRNF-------- 654
I I T+N GA K+ IGFG+ + + LR
Sbjct: 240 IQIDTSNILFICGGAFVGLEKIIKKRTGKSSIGFGAEVKKKSKEKADLLRQVEPEDLVKF 299
Query: 655 -LSPEFLNRLDSIIPFFPLSSDIIRQVVHKFIMKLELQLQE----KGISFHFSEEVINWL 709
L PEF+ RL I L + + ++ K L Q Q + F EE + +
Sbjct: 300 GLIPEFIGRLPVIATLEKLDEEALIAILTKPKNALVKQYQALFKMDNVELDFEEEALKAI 359
Query: 710 VSHGYDVKMGARPLERIIKE 729
+ K GAR L I++
Sbjct: 360 AKKALERKTGARGLRSIVEG 379
Score = 29.0 bits (65), Expect = 5.2
Identities = 26/106 (24%), Positives = 51/106 (48%), Gaps = 20/106 (18%)
Query: 205 ILVGRHEEINRTIQILCRRSKNNPLYVGDPGVGKTAIAEGFAKQIVDGMVPDILLGARIF 264
+ ++++ + +++ SK+N L +G G GKT +A+ A+ + VP F
Sbjct: 100 LNFEKNKKSDNGVEL----SKSNILLIGPTGSGKTLLAQTLARIL---NVP--------F 144
Query: 265 SLDMGNLIAGTRYRG-DFEERIKKIVK----EIESYANAILYIDEI 305
++ + Y G D E + K+++ ++E I+YIDEI
Sbjct: 145 AIADATTLTEAGYVGEDVENILLKLLQAADYDVEKAQKGIIYIDEI 190
>gnl|CDD|162028 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.
Length = 775
Score = 43.8 bits (104), Expect = 2e-04
Identities = 38/106 (35%), Positives = 53/106 (50%), Gaps = 20/106 (18%)
Query: 506 PIGCYVFSGPTGVGKTEISKQLAFALGVQLLRF------DMSEYMERHAVSRLIGAPPGY 559
PI C GP GVGKT + K +A AL + +RF D +E R +GA PG
Sbjct: 348 PILC--LVGPPGVGKTSLGKSIAKALNRKFVRFSLGGVRDEAEI--RGHRRTYVGAMPGR 403
Query: 560 VGFGQGGILADSVDQNPYSVVLLDEIEK----SHPDVLNILLQIMD 601
+ QG L + +NP + LLDEI+K D + LL+++D
Sbjct: 404 I--IQG--LKKAKTKNP--LFLLDEIDKIGSSFRGDPASALLEVLD 443
Score = 30.0 bits (68), Expect = 2.8
Identities = 27/94 (28%), Positives = 40/94 (42%), Gaps = 26/94 (27%)
Query: 219 ILCRRSKNNPLYVGDPGVGKTAIAEGFAKQIVDGMVPDILLGARIFSLDMGNL-----IA 273
ILC VG PGVGKT++ + AK L + +G + I
Sbjct: 349 ILC--------LVGPPGVGKTSLGKSIAKA----------LNRKFVRFSLGGVRDEAEIR 390
Query: 274 GTR--YRGDFEERIKKIVKEIESYANAILYIDEI 305
G R Y G RI + +K+ ++ N + +DEI
Sbjct: 391 GHRRTYVGAMPGRIIQGLKKAKT-KNPLFLLDEI 423
>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.
Length = 531
Score = 41.7 bits (98), Expect = 8e-04
Identities = 47/146 (32%), Positives = 65/146 (44%), Gaps = 39/146 (26%)
Query: 481 GQEEAIKKLSSSIKIARAGLSDPNKPIGCYVFSGPTGVGKT-------EISKQLAF---- 529
GQEE IK L +A L PN P ++ GP GVGKT E +K+
Sbjct: 69 GQEEGIKAL-------KAALCGPN-PQHVIIY-GPPGVGKTAAARLVLEEAKKNPASPFK 119
Query: 530 --ALGVQL----LRFDMSEYMERHAVSRLIGA--PPGYVG---FGQGGI---LADSVDQN 575
A V++ RFD ER LIG+ P Y G G GI +V +
Sbjct: 120 EGAAFVEIDATTARFD-----ERGIADPLIGSVHDPIYQGAGPLGIAGIPQPKPGAVTRA 174
Query: 576 PYSVVLLDEIEKSHPDVLNILLQIMD 601
V+ +DEI + HP +N LL++++
Sbjct: 175 HGGVLFIDEIGELHPVQMNKLLKVLE 200
Score = 31.3 bits (71), Expect = 0.93
Identities = 21/52 (40%), Positives = 27/52 (51%), Gaps = 6/52 (11%)
Query: 194 LTEKVKKGKVDILVGRHEEINRTIQILCRRSKNNPLYV---GDPGVGKTAIA 242
L+EK + D ++G+ E I LC NP +V G PGVGKTA A
Sbjct: 55 LSEKTRPKSFDEIIGQEEGIKALKAALC---GPNPQHVIIYGPPGVGKTAAA 103
>gnl|CDD|162839 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.
Length = 355
Score = 39.1 bits (92), Expect = 0.005
Identities = 22/56 (39%), Positives = 30/56 (53%), Gaps = 14/56 (25%)
Query: 479 VYGQEEAIKKLSSSI---KIARAGLSDPNKPIGCYVFSGPTGVGKTEISKQLAFAL 531
V GQE ++ L ++I +IA A Y+FSGP G GKT I++ A AL
Sbjct: 16 VIGQEHIVQTLKNAIKNGRIAHA-----------YLFSGPRGTGKTSIARIFAKAL 60
>gnl|CDD|147949 pfam06068, TIP49, TIP49 C-terminus. This family consists of the
C-terminal region of several eukaryotic and archaeal
RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin
or TIP49b) proteins. The N-terminal domain contains the
pfam00004 domain. In zebrafish, the liebeskummer (lik)
mutation, causes development of hyperplastic embryonic
hearts. lik encodes Reptin, a component of a
DNA-stimulated ATPase complex. Beta-catenin and Pontin,
a DNA-stimulated ATPase that is often part of complexes
with Reptin, are in the same genetic pathways. The
Reptin/Pontin ratio serves to regulate heart growth
during development, at least in part via the
beta-catenin pathway. TBP-interacting protein 49 (TIP49)
was originally identified as a TBP-binding protein, and
two related proteins are encoded by individual genes,
tip49a and b. Although the function of this gene family
has not been elucidated, they are supposed to play a
critical role in nuclear events because they interact
with various kinds of nuclear factors and have DNA
helicase activities.TIP49a has been suggested to act as
an autoantigen in some patients with autoimmune
diseases.
Length = 395
Score = 38.8 bits (91), Expect = 0.006
Identities = 21/66 (31%), Positives = 34/66 (51%), Gaps = 1/66 (1%)
Query: 229 LYVGDPGVGKTAIAEGFAKQIVDGMVPDILLGARIFSLDMGNLIAGTRY-RGDFEERIKK 287
L G PG GKTA+A +K++ + + G+ ++SL+M A T+ R RIK+
Sbjct: 54 LIAGPPGTGKTALAIAISKELGEDTPFCPISGSEVYSLEMKKTEALTQAFRKAIGVRIKE 113
Query: 288 IVKEIE 293
+ E
Sbjct: 114 EKEVYE 119
>gnl|CDD|129721 TIGR00635, ruvB, Holliday junction DNA helicase, RuvB subunit.
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.
Length = 305
Score = 37.7 bits (88), Expect = 0.012
Identities = 27/121 (22%), Positives = 49/121 (40%), Gaps = 22/121 (18%)
Query: 481 GQEEAIKKLSSSIKIARAGLSDPNKPIGCYVFSGPTGVGKTEISKQLAFALGVQLLRFDM 540
GQE+ ++L I+ A+ + + + GP G+GKT ++ +A +GV L
Sbjct: 8 GQEKVKEQLQLFIEAAK----MRQEALDHLLLYGPPGLGKTTLAHIIANEMGVNL----- 58
Query: 541 SEYMERHAVSRLIGAPPGYVGFGQGGILADSVDQNPYSVVLLDEIEKSHPDVLNILLQIM 600
++ P G + A + V+ +DEI + P V +L M
Sbjct: 59 ----------KITSGP---ALEKPGDLAAILTNLEEGDVLFIDEIHRLSPAVEELLYPAM 105
Query: 601 D 601
+
Sbjct: 106 E 106
Score = 28.4 bits (64), Expect = 8.1
Identities = 25/110 (22%), Positives = 38/110 (34%), Gaps = 38/110 (34%)
Query: 211 EEINRTIQILCRRSKNNP------LYVGDPGVGKTAIAEGFAK------QIVDGMVPDIL 258
E++ +Q+ +K L G PG+GKT +A A +I G
Sbjct: 10 EKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIANEMGVNLKITSG------ 63
Query: 259 LGARIFSLDMGNLIAGTRYRGDFEERIKKIVKEIESYANAILYIDEIHTL 308
A D+ ++ GD +L+IDEIH L
Sbjct: 64 -PALEKPGDLAAILTNLE-EGD------------------VLFIDEIHRL 93
>gnl|CDD|179962 PRK05201, hslU, ATP-dependent protease ATP-binding subunit HslU;
Provisional.
Length = 443
Score = 37.0 bits (87), Expect = 0.019
Identities = 12/15 (80%), Positives = 15/15 (100%)
Query: 514 GPTGVGKTEISKQLA 528
GPTGVGKTEI+++LA
Sbjct: 57 GPTGVGKTEIARRLA 71
>gnl|CDD|180644 PRK06647, PRK06647, DNA polymerase III subunits gamma and tau;
Validated.
Length = 563
Score = 36.7 bits (85), Expect = 0.022
Identities = 21/54 (38%), Positives = 27/54 (50%), Gaps = 14/54 (25%)
Query: 481 GQEEAIKKLSSSI---KIARAGLSDPNKPIGCYVFSGPTGVGKTEISKQLAFAL 531
GQ+ ++ L SI KIA A Y+FSGP GVGKT ++ A L
Sbjct: 20 GQDFVVETLKHSIESNKIANA-----------YIFSGPRGVGKTSSARAFARCL 62
>gnl|CDD|184927 PRK14963, PRK14963, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 504
Score = 36.7 bits (85), Expect = 0.026
Identities = 19/56 (33%), Positives = 30/56 (53%), Gaps = 8/56 (14%)
Query: 479 VYGQEEAIKKLSSSIKIARAGLSDPNKPIGCYVFSGPTGVGKTEISKQLAFALGVQ 534
V GQE + L ++++ R G + Y+FSGP GVGKT ++ +A A+
Sbjct: 16 VVGQEHVKEVLLAALRQGRLGHA--------YLFSGPRGVGKTTTARLIAMAVNCS 63
>gnl|CDD|184917 PRK14953, PRK14953, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 486
Score = 36.3 bits (84), Expect = 0.030
Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 8/53 (15%)
Query: 479 VYGQEEAIKKLSSSIKIARAGLSDPNKPIGCYVFSGPTGVGKTEISKQLAFAL 531
V GQE ++ L +++K+ R + Y+F+GP G GKT I++ LA L
Sbjct: 18 VIGQEIVVRILKNAVKLQRVSHA--------YIFAGPRGTGKTTIARILAKVL 62
>gnl|CDD|180308 PRK05896, PRK05896, DNA polymerase III subunits gamma and tau;
Validated.
Length = 605
Score = 35.2 bits (81), Expect = 0.059
Identities = 21/53 (39%), Positives = 28/53 (52%), Gaps = 8/53 (15%)
Query: 479 VYGQEEAIKKLSSSIKIARAGLSDPNKPIGCYVFSGPTGVGKTEISKQLAFAL 531
+ GQE K L ++I NK Y+FSGP G+GKT I+K A A+
Sbjct: 18 IIGQELIKKILVNAI--------LNNKLTHAYIFSGPRGIGKTSIAKIFAKAI 62
>gnl|CDD|180959 PRK07399, PRK07399, DNA polymerase III subunit delta'; Validated.
Length = 314
Score = 35.3 bits (82), Expect = 0.064
Identities = 18/54 (33%), Positives = 26/54 (48%), Gaps = 14/54 (25%)
Query: 481 GQEEAIKKLSSSIK---IARAGLSDPNKPIGCYVFSGPTGVGKTEISKQLAFAL 531
GQ AI+ L+++IK IA A Y+F+GP GVG+ + L
Sbjct: 8 GQPLAIELLTAAIKQNRIAPA-----------YLFAGPEGVGRKLAALCFIEGL 50
>gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La;
Provisional.
Length = 784
Score = 34.9 bits (80), Expect = 0.076
Identities = 34/106 (32%), Positives = 52/106 (49%), Gaps = 20/106 (18%)
Query: 506 PIGCYVFSGPTGVGKTEISKQLAFALGVQLLRFDM----SEYMERHAVSRLIGAPPGYV- 560
PI C V GP GVGKT + + +A A G + +R + E R IG+ PG +
Sbjct: 350 PILCLV--GPPGVGKTSLGQSIAKATGRKYVRMALGGVRDEAEIRGHRRTYIGSMPGKLI 407
Query: 561 -GFGQGGILADSVDQNPYSVVLLDEIEKSHPDV----LNILLQIMD 601
+ G+ +NP + LLDEI+K D+ + LL+++D
Sbjct: 408 QKMAKVGV------KNP--LFLLDEIDKMSSDMRGDPASALLEVLD 445
>gnl|CDD|163401 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.
Length = 512
Score = 34.7 bits (80), Expect = 0.082
Identities = 52/221 (23%), Positives = 95/221 (42%), Gaps = 29/221 (13%)
Query: 229 LYVGDPGVGKTAIAEGFAKQIVDGMVPDILLGARIFSLDMGNLIAGTRYRGDFEERIKKI 288
LY G PG GKT IA+ A + + + + ++ L+ +Y G+ E +I+ I
Sbjct: 221 LY-GPPGCGKTLIAKAVANSLAQRIGAETGDKSYFLNIKGPELL--NKYVGETERQIRLI 277
Query: 289 VKEIESYAN----AILYIDEIHTLVGAGSASGISVDASNLLKPALSS--------GAVRC 336
+ A+ I++ DE+ ++ SG+S D + P L S V
Sbjct: 278 FQRAREKASDGRPVIVFFDEMDSIFRT-RGSGVSSDVETTVVPQLLSELDGVESLDNVIV 336
Query: 337 IGSTTYSEYRQFFEKDKALVR--RFQ-KIDVSEPSIEDAIEIV-KGIK---PYFEEHHQL 389
IG++ + D A++R R KI + P E A +I K + P + +
Sbjct: 337 IGASNREDM-----IDPAILRPGRLDVKIRIERPDAEAAADIFSKYLTDSLPLDADLAEF 391
Query: 390 RYSKEA-IRAAVQLSVRHFTSRKLPDKAIDVIDEAGASQIL 429
+EA A +Q +V H + ++ ++V G++++L
Sbjct: 392 DGDREATAAALIQRAVDHLYATSEENRYVEVTYANGSTEVL 432
>gnl|CDD|183986 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 34.7 bits (81), Expect = 0.097
Identities = 29/120 (24%), Positives = 45/120 (37%), Gaps = 44/120 (36%)
Query: 232 GDPGVGKTAIAEGFAKQIVDGMVPDILLGARIFSLDMGNLIAGTRYRGDFEERIKKIVKE 291
G PG GKT +A A A +L + +G + ++++++E
Sbjct: 43 GPPGTGKTTLARIIAGA----------TDAPFEALSA--VTSGV-------KDLREVIEE 83
Query: 292 IESYANA----ILYIDEIHTLVGAGSASGISVDASN------LLKPALSSGAVRCIGSTT 341
+A IL+IDEIH N LL P + G + IG+TT
Sbjct: 84 ARQRRSAGRRTILFIDEIHRF--------------NKAQQDALL-PHVEDGTITLIGATT 128
>gnl|CDD|183985 PRK13341, PRK13341, recombination factor protein RarA/unknown
domain fusion protein; Reviewed.
Length = 725
Score = 34.6 bits (80), Expect = 0.10
Identities = 40/134 (29%), Positives = 60/134 (44%), Gaps = 35/134 (26%)
Query: 229 LYVGDPGVGKTAIAEGFAKQIVDGMVPDILLGARIFS---LDMGNLIAGTRYRGDFEERI 285
LY G PGVGKT +A +I+ A + ++AG + D +
Sbjct: 57 LY-GPPGVGKTTLA-----RII----------ANHTRAHFSSLNAVLAGVK---DLRAEV 97
Query: 286 KKIVKEIESYA-NAILYIDEIHTLVGAGSASGISVDASNLLKPALSSGAVRCIGSTTYSE 344
+ + +E + IL+IDE+H A DA L P + +G + IG+TT +
Sbjct: 98 DRAKERLERHGKRTILFIDEVHRFNKAQQ------DA---LLPWVENGTITLIGATTENP 148
Query: 345 YRQFFEKDKALVRR 358
Y FE +KALV R
Sbjct: 149 Y---FEVNKALVSR 159
>gnl|CDD|163294 TIGR03499, FlhF, flagellar biosynthetic protein FlhF.
Length = 282
Score = 33.8 bits (78), Expect = 0.16
Identities = 22/153 (14%), Positives = 50/153 (32%), Gaps = 24/153 (15%)
Query: 392 SKEAIRAAVQLSVRHFTSRKLPDKAIDVIDEAGASQILQPLSKRRKFITEKDIKKTIASM 451
+ + + ++ KL A + A + P ++ + + ++++K + ++
Sbjct: 57 ATASTEEEAKKALEPADPAKLSATAEPLELPAPLEEPAAPAAQAAEPLLPEELRKELEAL 116
Query: 452 NRSIHTTSFSRDD---DSVLSNLEKNL------GTVV----------YGQEEAIKKLSSS 492
+ D + L + L + E+A + L +
Sbjct: 117 RELLERLLAGLAWLQRDPEGAKLLERLLRAGVSPELARELLEKLPERADAEDAWRWLREA 176
Query: 493 I--KIARAGLSDP--NKPIGCYVFSGPTGVGKT 521
+ + D + G GPTGVGKT
Sbjct: 177 LEKMLPVKPEEDEILEQG-GVIALVGPTGVGKT 208
>gnl|CDD|161852 TIGR00390, hslU, ATP-dependent protease HslVU, ATPase subunit.
This model represents the ATPase subunit of HslVU, while
the proteasome-related peptidase subunit is HslV.
Residues 54-61 of the model contain a P-loop ATP-binding
motif. Cys-287 of E. coli (position 308 in the seed
alignment), studied in PubMed:98389714, is Ser in other
members of the seed alignment.
Length = 441
Score = 33.6 bits (77), Expect = 0.18
Identities = 15/38 (39%), Positives = 24/38 (63%)
Query: 514 GPTGVGKTEISKQLAFALGVQLLRFDMSEYMERHAVSR 551
GPTGVGKTEI+++LA ++ + +++ E V R
Sbjct: 54 GPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGR 91
>gnl|CDD|184916 PRK14952, PRK14952, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 584
Score = 33.3 bits (76), Expect = 0.24
Identities = 20/53 (37%), Positives = 28/53 (52%), Gaps = 8/53 (15%)
Query: 479 VYGQEEAIKKLSSSIKIARAGLSDPNKPIGCYVFSGPTGVGKTEISKQLAFAL 531
V GQE + LSS++ R + Y+FSGP G GKT ++ LA +L
Sbjct: 15 VVGQEHVTEPLSSALDAGRINHA--------YLFSGPRGCGKTSSARILARSL 59
>gnl|CDD|184914 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 585
Score = 33.2 bits (76), Expect = 0.25
Identities = 18/50 (36%), Positives = 27/50 (54%), Gaps = 8/50 (16%)
Query: 481 GQEEAIKKLSSSIKIARAGLSDPNKPIGCYVFSGPTGVGKTEISKQLAFA 530
GQE ++ L ++I R + Y+F+GP GVGKT ++ LA A
Sbjct: 20 GQEHVVQTLRNAIAEGRVAHA--------YLFTGPRGVGKTSTARILAKA 61
>gnl|CDD|184923 PRK14959, PRK14959, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 624
Score = 33.1 bits (75), Expect = 0.27
Identities = 22/53 (41%), Positives = 26/53 (49%), Gaps = 8/53 (15%)
Query: 479 VYGQEEAIKKLSSSIKIARAGLSDPNKPIGCYVFSGPTGVGKTEISKQLAFAL 531
V GQE LS RA + P Y+FSG GVGKT I++ A AL
Sbjct: 18 VAGQETVKAILS------RAAQENRVAP--AYLFSGTRGVGKTTIARIFAKAL 62
>gnl|CDD|180615 PRK06547, PRK06547, hypothetical protein; Provisional.
Length = 172
Score = 33.2 bits (76), Expect = 0.31
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 514 GPTGVGKTEISKQLAFALGVQLLRFD 539
G +G GKT ++ LA G QL+ D
Sbjct: 22 GRSGSGKTTLAGALAARTGFQLVHLD 47
>gnl|CDD|184929 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 576
Score = 32.8 bits (75), Expect = 0.32
Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 14/54 (25%)
Query: 481 GQEEAIKKLSSSIK---IARAGLSDPNKPIGCYVFSGPTGVGKTEISKQLAFAL 531
GQE + L ++I +A A ++F+G GVGKT ++ LA AL
Sbjct: 20 GQEHVSRTLQNAIDTGRVAHA-----------FLFTGARGVGKTSTARILAKAL 62
>gnl|CDD|163168 TIGR03167, tRNA_sel_U_synt, tRNA 2-selenouridine synthase. The
Escherichia coli YbbB protein was shown to encode a
selenophosphate-dependent tRNA 2-selenouridine synthase,
essential for modification of some tRNAs to replace a
sulfur atom with selenium. This enzyme works with SelD,
the selenium donor protein, which also acts in
selenocysteine incorporation. Although the members of
this protein family show a fairly deep split, sequences
from both sides of the split are supported by
co-occurence with, and often proximity to, the selD
gene.
Length = 311
Score = 32.6 bits (75), Expect = 0.38
Identities = 13/26 (50%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 511 VFSGPTGVGKTEISKQLAFALGVQLL 536
V G TG GKTE+ LA G Q+L
Sbjct: 131 VLGGMTGSGKTELLHALA-NAGAQVL 155
>gnl|CDD|184925 PRK14961, PRK14961, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 363
Score = 32.5 bits (74), Expect = 0.46
Identities = 16/57 (28%), Positives = 29/57 (50%), Gaps = 8/57 (14%)
Query: 479 VYGQEEAIKKLSSSIKIARAGLSDPNKPIGCYVFSGPTGVGKTEISKQLAFALGVQL 535
+ GQ+ + +S+ + + R + ++ SG GVGKT I++ LA +L Q
Sbjct: 18 IIGQKHIVTAISNGLSLGRIHHA--------WLLSGTRGVGKTTIARLLAKSLNCQN 66
>gnl|CDD|183438 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 700
Score = 32.5 bits (74), Expect = 0.48
Identities = 18/55 (32%), Positives = 31/55 (56%), Gaps = 8/55 (14%)
Query: 477 TVVYGQEEAIKKLSSSIKIARAGLSDPNKPIGCYVFSGPTGVGKTEISKQLAFAL 531
T + GQE ++ L+ +++ R + Y+F+G GVGKT +S+ LA +L
Sbjct: 16 TTLVGQEHVVRALTHALEQQRLHHA--------YLFTGTRGVGKTTLSRILAKSL 62
>gnl|CDD|184915 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 618
Score = 32.4 bits (74), Expect = 0.51
Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 15/65 (23%)
Query: 473 KNLGTVVYGQEEAIKKLSSSIKIAR---AGLSDPNKPIGCYVFSGPTGVGKTEISKQLAF 529
++ +V GQE ++ L++++ R A Y+F+G GVGKT +S+ LA
Sbjct: 13 RSFSEMV-GQEHVVQALTNALTQQRLHHA-----------YLFTGTRGVGKTTVSRILAK 60
Query: 530 ALGVQ 534
+L Q
Sbjct: 61 SLNCQ 65
>gnl|CDD|180131 PRK05563, PRK05563, DNA polymerase III subunits gamma and tau;
Validated.
Length = 559
Score = 32.1 bits (74), Expect = 0.56
Identities = 22/56 (39%), Positives = 28/56 (50%), Gaps = 14/56 (25%)
Query: 479 VYGQEEAIKKLSSSI---KIARAGLSDPNKPIGCYVFSGPTGVGKTEISKQLAFAL 531
V GQE K L ++I KI+ A Y+FSGP G GKT +K A A+
Sbjct: 18 VVGQEHITKTLKNAIKQGKISHA-----------YLFSGPRGTGKTSAAKIFAKAV 62
>gnl|CDD|162029 TIGR00764, lon_rel, lon-related putative ATP-dependent protease.
Members of this family from Pyrococcus horikoshii and
Pyrococcus abyssi each contain a predicted intein.
Length = 608
Score = 31.7 bits (72), Expect = 0.69
Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 4/75 (5%)
Query: 223 RSKNNPLYVGDPGVGKTAIAEGFAKQIVDGMVPDILLGARIFSLDM---GNLIAGTRYRG 279
+ K N L +G+PGVGK+ +A+ A+ + D + DIL+ +M + AG R
Sbjct: 35 KQKRNVLLIGEPGVGKSMLAKAMAELLPDEELEDILVYPNPEDPNMPRIVEVPAG-EGRE 93
Query: 280 DFEERIKKIVKEIES 294
E+ KK K+ S
Sbjct: 94 IVEDYKKKAFKQPSS 108
>gnl|CDD|183313 PRK11784, PRK11784, tRNA 2-selenouridine synthase; Provisional.
Length = 345
Score = 31.7 bits (73), Expect = 0.76
Identities = 13/26 (50%), Positives = 16/26 (61%), Gaps = 1/26 (3%)
Query: 511 VFSGPTGVGKTEISKQLAFALGVQLL 536
V G TG GKTE+ + LA G Q+L
Sbjct: 145 VLGGNTGSGKTELLQALA-NAGAQVL 169
>gnl|CDD|179026 PRK00440, rfc, replication factor C small subunit; Reviewed.
Length = 319
Score = 31.8 bits (73), Expect = 0.76
Identities = 16/55 (29%), Positives = 29/55 (52%)
Query: 195 TEKVKKGKVDILVGRHEEINRTIQILCRRSKNNPLYVGDPGVGKTAIAEGFAKQI 249
EK + +D +VG+ E + R + ++ + L+ G PG GKT A A+++
Sbjct: 8 VEKYRPRTLDEIVGQEEIVERLKSYVKEKNMPHLLFAGPPGTGKTTAALALAREL 62
Score = 31.8 bits (73), Expect = 0.79
Identities = 15/43 (34%), Positives = 23/43 (53%), Gaps = 9/43 (20%)
Query: 479 VYGQEEAIKKLSSSIKIARAGLSDPNKPIGCYVFSGPTGVGKT 521
+ GQEE +++L S +K K + +F+GP G GKT
Sbjct: 19 IVGQEEIVERLKSYVK---------EKNMPHLLFAGPPGTGKT 52
>gnl|CDD|163066 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.
Length = 615
Score = 31.7 bits (72), Expect = 0.78
Identities = 37/161 (22%), Positives = 66/161 (40%), Gaps = 30/161 (18%)
Query: 367 PSIEDAIEIVKGIKPYFEEHHQLRYSKEAIRAAVQLSVRHFTSRKLPDKAIDVIDEAGAS 426
P + EI++ + + + R + I V+ ++ ++ L + + V+ E
Sbjct: 61 PDPRELPEILEDTEDHIADILARRTVENRIERKVETRMQERQNKYLEEIRLQVLKEEKGP 120
Query: 427 QILQPLSK--RRKFITEKDIKKTIASMNRSIHTTSFSRDDDSVLSNLEKNLGTVVYGQEE 484
+ L K R + + +K + K+ S+ R +FS + GQE
Sbjct: 121 ENSSTLKKLERLEKLEKKKLHKSAQSLLRP---RAFSE----------------IVGQER 161
Query: 485 AIKKLSSSIKIARAGLSDPNKPIGCYVFSGPTGVGKTEISK 525
AIK L + K+A S + I Y GP GVGKT ++
Sbjct: 162 AIKALLA--KVA----SPFPQHIILY---GPPGVGKTTAAR 193
>gnl|CDD|184920 PRK14956, PRK14956, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 484
Score = 31.5 bits (71), Expect = 0.80
Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 9/57 (15%)
Query: 478 VVYGQEEAIKKLSSSIKIARAGLSDPNKPIGCYVFSGPTGVGKTEISKQLAFALGVQ 534
V++ Q+ AI L +++K + G + Y+F GP GVGKT I++ LA L +
Sbjct: 20 VIH-QDLAIGALQNALKSGKIGHA--------YIFFGPRGVGKTTIARILAKRLNCE 67
>gnl|CDD|129002 smart00763, AAA_PrkA, PrkA AAA domain. This is a family of PrkA
bacterial and archaeal serine kinases approximately 630
residues long. This is the N-terminal AAA domain.
Length = 361
Score = 31.5 bits (72), Expect = 0.82
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 3/49 (6%)
Query: 479 VYGQEEAIKKLSSSIKIARAGLSDPNKPIGCYVFSGPTGVGKTEISKQL 527
+G EEAI++ + K A GL + K I GP G GK+ + + L
Sbjct: 53 FFGMEEAIERFVNYFKSAAQGL-EERKQI--LYLLGPVGGGKSSLVECL 98
>gnl|CDD|183088 PRK11331, PRK11331, 5-methylcytosine-specific restriction enzyme
subunit McrB; Provisional.
Length = 459
Score = 31.6 bits (71), Expect = 0.82
Identities = 27/102 (26%), Positives = 52/102 (50%), Gaps = 10/102 (9%)
Query: 511 VFSGPTGVGKTEISKQLAFALGVQLL--RFDMSEYMERHAVSRLI-GAPPGYVGF-GQGG 566
+ GP GVGKT ++++LA+ L + R +M ++ + ++ I G P VGF + G
Sbjct: 198 ILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSYEDFIQGYRPNGVGFRRKDG 257
Query: 567 ILADSVDQNPYS-----VVLLDEIEKSH-PDVLNILLQIMDY 602
I + Q V ++DEI +++ V ++ +M++
Sbjct: 258 IFYNFCQQAKEQPEKKYVFIIDEINRANLSKVFGEVMMLMEH 299
>gnl|CDD|184926 PRK14962, PRK14962, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 472
Score = 31.7 bits (72), Expect = 0.86
Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 9/59 (15%)
Query: 473 KNLGTVVYGQEEAIKKLSSSIKIARAGLSDPNKPIGCYVFSGPTGVGKTEISKQLAFAL 531
K VV GQ+ K + +++K N Y+F+GP G GKT +++ LA +L
Sbjct: 11 KTFSEVV-GQDHVKKLIINALKK--------NSISHAYIFAGPRGTGKTTVARILAKSL 60
>gnl|CDD|180523 PRK06305, PRK06305, DNA polymerase III subunits gamma and tau;
Validated.
Length = 451
Score = 31.7 bits (72), Expect = 0.86
Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 8/56 (14%)
Query: 479 VYGQEEAIKKLSSSIKIARAGLSDPNKPIGCYVFSGPTGVGKTEISKQLAFALGVQ 534
+ GQ+ + L ++++ RA + Y+FSG G GKT +++ A AL Q
Sbjct: 19 ILGQDAVVAVLKNALRFNRAAHA--------YLFSGIRGTGKTTLARIFAKALNCQ 66
>gnl|CDD|180855 PRK07132, PRK07132, DNA polymerase III subunit delta'; Validated.
Length = 299
Score = 31.6 bits (72), Expect = 0.91
Identities = 13/49 (26%), Positives = 27/49 (55%), Gaps = 6/49 (12%)
Query: 571 SVDQNPYSVVLLDEIEKSHPDVLNILLQIMD------YGILTDQSGKKI 613
S Q+ ++++ IEK+ +LN LL+ ++ Y +LT ++ K+
Sbjct: 85 SFVQSQKKILIIKNIEKTSNSLLNALLKTIEEPPKDTYFLLTTKNINKV 133
>gnl|CDD|178968 PRK00300, gmk, guanylate kinase; Provisional.
Length = 205
Score = 31.2 bits (72), Expect = 0.94
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 510 YVFSGPTGVGKTEISKQL 527
V SGP+G GK+ + K L
Sbjct: 8 IVLSGPSGAGKSTLVKAL 25
>gnl|CDD|165405 PHA03133, PHA03133, thymidine kinase; Provisional.
Length = 368
Score = 31.4 bits (71), Expect = 0.96
Identities = 18/44 (40%), Positives = 24/44 (54%), Gaps = 5/44 (11%)
Query: 514 GPTGVGKTEISKQLAFALGVQLLRFDMSEYM-ERHAVSRLIGAP 556
GP G+GKT + LA ALG R D EY+ E A +++G
Sbjct: 47 GPHGLGKTTTAAALAAALG----RRDDIEYVPEPMAYWQVLGGS 86
>gnl|CDD|129690 TIGR00602, rad24, checkpoint protein rad24. This family is based
on the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University).
Length = 637
Score = 31.1 bits (70), Expect = 1.1
Identities = 33/144 (22%), Positives = 49/144 (34%), Gaps = 16/144 (11%)
Query: 400 VQLSVRHFTSRKLPDKAIDVIDEAGASQILQPLSKRRKFITEKDIKKTIASMNRSIHTTS 459
V V+ L I I + S S RRK DI R S
Sbjct: 3 VTDWVKPSFDDFLLSSLISTITKW--SLSRPTSSHRRKNSPSTDIHA------RKRGFLS 54
Query: 460 FSRDDDSVLSNLEKNLGTVVYGQ-------EEAI-KKLSSSIKIARAGLSDPNKPIGCYV 511
+D LS+ + + E A+ KK ++ N P +
Sbjct: 55 LEQDTGLELSSENLDGNEPWVEKYKPETQHELAVHKKKIEEVETWLKAQVLENAPKRILL 114
Query: 512 FSGPTGVGKTEISKQLAFALGVQL 535
+GP+G GK+ K L+ LG+Q+
Sbjct: 115 ITGPSGCGKSTTIKILSKELGIQV 138
>gnl|CDD|181818 PRK09393, ftrA, transcriptional activator FtrA; Provisional.
Length = 322
Score = 31.1 bits (71), Expect = 1.1
Identities = 28/88 (31%), Positives = 39/88 (44%), Gaps = 23/88 (26%)
Query: 250 VDGMVPDILL---------GARIFSLDMG-------NLIAG----TRYRGDFEERIKKIV 289
D VP+ LL GAR+ S+ G L+ G T +R + ER++
Sbjct: 87 PDAPVPEPLLEALRAAHARGARLCSICSGVFVLAAAGLLDGRRATTHWR--YAERLQARY 144
Query: 290 KEIESYANAILYIDEIHTLVGAGSASGI 317
I + LY+DE L AGSA+GI
Sbjct: 145 PAIRVDPDV-LYVDEGQILTSAGSAAGI 171
>gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed.
Length = 644
Score = 31.2 bits (70), Expect = 1.3
Identities = 29/91 (31%), Positives = 41/91 (45%), Gaps = 15/91 (16%)
Query: 229 LYVGDPGVGKTAIAEGFAKQIVDGMVPDILLGARIFSLDMGNLIAGTRYRGDFEERIKKI 288
L VG PG GKT +A+ A + VP + F ++M + +R R FE+ K
Sbjct: 189 LMVGPPGTGKTLLAKAIAGE---AKVPFFTISGSDF-VEMFVGVGASRVRDMFEQAKKA- 243
Query: 289 VKEIESYANAILYIDEIHTL---VGAGSASG 316
A I++IDEI + GAG G
Sbjct: 244 -------APCIIFIDEIDAVGRQRGAGLGGG 267
>gnl|CDD|183922 PRK13256, PRK13256, thiopurine S-methyltransferase; Reviewed.
Length = 226
Score = 30.8 bits (69), Expect = 1.3
Identities = 26/83 (31%), Positives = 41/83 (49%), Gaps = 6/83 (7%)
Query: 642 RNDDAD--KEALRNFLSPEF--LNRLDSIIPFFPLSSDIIRQV--VHKFIMKLELQLQEK 695
+NDD +E+ FL F LN DS + P+ I + + K + + ++L EK
Sbjct: 17 QNDDVGFCQESPNEFLVKHFSKLNINDSSVCLIPMCGCSIDMLFFLSKGVKVIGIELSEK 76
Query: 696 GISFHFSEEVINWLVSHGYDVKM 718
+ FS+ IN+ V HG D K+
Sbjct: 77 AVLSFFSQNTINYEVIHGNDYKL 99
>gnl|CDD|179638 PRK03731, aroL, shikimate kinase II; Reviewed.
Length = 171
Score = 31.1 bits (71), Expect = 1.3
Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 4/36 (11%)
Query: 514 GPTGVGKTEISKQLAFALGVQLLRF-DMSEYMERHA 548
G G GKT + LA ALG RF D ++++ +
Sbjct: 9 GARGCGKTTVGMALAQALG---YRFVDTDQWLQSTS 41
>gnl|CDD|161993 TIGR00678, holB, DNA polymerase III, delta' subunit. 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.
Length = 188
Score = 30.7 bits (70), Expect = 1.5
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 229 LYVGDPGVGKTAIAEGFAKQI 249
L+ G GVGK +A AK +
Sbjct: 18 LFAGPEGVGKELLALALAKAL 38
>gnl|CDD|182710 PRK10765, PRK10765, nitroreductase A; Provisional.
Length = 240
Score = 30.7 bits (70), Expect = 1.7
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 6/51 (11%)
Query: 403 SVRHFTSRKLPDKAIDVIDEAG----ASQILQPLSKRRKFITEKDIKKTIA 449
S+RHFT + + + I A +S LQ S R IT+K +++ +
Sbjct: 13 SIRHFTDEPISEAQREAIINAARAASSSSFLQCSSIIR--ITDKALREALV 61
>gnl|CDD|161985 TIGR00665, DnaB, replicative DNA helicase. This model describes
the helicase DnaB, a homohexameric protein required for
DNA replication. The homohexamer can form a ring around
a single strand of DNA near a replication fork. An
intein of > 400 residues is found at a conserved
location in DnaB of Synechocystis PCC6803, Rhodothermus
marinus (both experimentally confirmed), and
Mycobacterium tuberculosis. The intein removes itself by
a self-splicing reaction. The seed alignment contains
inteins so that the model built from the seed alignment
will model a low cost at common intein insertion sites.
Length = 434
Score = 30.5 bits (70), Expect = 1.8
Identities = 19/85 (22%), Positives = 31/85 (36%), Gaps = 18/85 (21%)
Query: 234 PGVGKTAIAEGFAKQIVDGMVPDILLGARIFSLDMGNL------------IAGTRYR-GD 280
P +GKTA A A+ + + FSL+M + + R G
Sbjct: 204 PSMGKTAFALNIAENA--AIKEGKPVA--FFSLEMSAEQLAMRMLSSESRVDSQKLRTGK 259
Query: 281 FEER-IKKIVKEIESYANAILYIDE 304
+ +K+ + A LYID+
Sbjct: 260 LSDEDWEKLTSAAGKLSEAPLYIDD 284
>gnl|CDD|179778 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 30.3 bits (69), Expect = 1.8
Identities = 32/106 (30%), Positives = 47/106 (44%), Gaps = 13/106 (12%)
Query: 473 KNLGTVVYGQEEAIKKLSSSIKIARAGLSDPNKPIGCYVFSGPTGVGKTEISKQLAFALG 532
K L VV G E+A ++L I+ G P K + + GP GVGKT ++ LA G
Sbjct: 11 KTLSDVV-GNEKAKEQLREWIESWLKG--KPKKAL---LLYGPPGVGKTSLAHALANDYG 64
Query: 533 VQLLRFDMSEYMERHAVSRLIGAPPGYVG---FGQGG--ILADSVD 573
+++ + S+ + R+ G FG IL D VD
Sbjct: 65 WEVIELNASDQRTADVIERVAGE--AATSGSLFGARRKLILLDEVD 108
>gnl|CDD|178847 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 30.5 bits (70), Expect = 1.8
Identities = 15/55 (27%), Positives = 28/55 (50%), Gaps = 4/55 (7%)
Query: 481 GQEEAIKKLSSSIKIARAGLSDPNKPIGCYVFSGPTGVGKTEISKQLAFALGVQL 535
GQE+ + L I+ A+ + + + GP G+GKT ++ +A +GV +
Sbjct: 29 GQEKVKENLKIFIEAAKK----RGEALDHVLLYGPPGLGKTTLANIIANEMGVNI 79
>gnl|CDD|184935 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 614
Score = 30.5 bits (69), Expect = 1.9
Identities = 19/52 (36%), Positives = 25/52 (48%), Gaps = 9/52 (17%)
Query: 477 TVVYGQEEAIKKLSSSIKIARAGLSDPNKPIGCYVFSGPTGVGKTEISKQLA 528
+VV GQE L ++I NK Y+F GP GVGKT ++ A
Sbjct: 18 SVV-GQEALTTTLKNAIA--------TNKLAHAYLFCGPRGVGKTTCARIFA 60
>gnl|CDD|184919 PRK14955, PRK14955, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 397
Score = 30.2 bits (68), Expect = 1.9
Identities = 19/64 (29%), Positives = 34/64 (53%), Gaps = 9/64 (14%)
Query: 482 QEEAIKKLSSSIKIARAGLSDPNKPIGCYVFSGPTGVGKTEISKQLAFALGVQLLRFDMS 541
QE + + +S+++ R G Y+FSG GVGKT ++ A A+ Q + D +
Sbjct: 21 QEHITRTIQNSLRMGRVGHG--------YIFSGLRGVGKTTAARVFAKAVNCQRM-IDDA 71
Query: 542 EYME 545
+Y++
Sbjct: 72 DYLQ 75
Score = 28.3 bits (63), Expect = 8.7
Identities = 18/42 (42%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 210 HEEINRTIQILCR--RSKNNPLYVGDPGVGKTAIAEGFAKQI 249
E I RTIQ R R + ++ G GVGKT A FAK +
Sbjct: 21 QEHITRTIQNSLRMGRVGHGYIFSGLRGVGKTTAARVFAKAV 62
>gnl|CDD|132307 TIGR03263, guanyl_kin, guanylate kinase. Members of this family
are the enzyme guanylate kinase, also called GMP kinase.
This enzyme transfers a phosphate from ATP to GMP,
yielding ADP and GDP.
Length = 180
Score = 30.1 bits (69), Expect = 2.1
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 510 YVFSGPTGVGKTEISKQL 527
V SGP+GVGK+ + K L
Sbjct: 4 IVISGPSGVGKSTLVKAL 21
>gnl|CDD|184933 PRK14969, PRK14969, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 527
Score = 30.1 bits (68), Expect = 2.1
Identities = 18/59 (30%), Positives = 34/59 (57%), Gaps = 9/59 (15%)
Query: 473 KNLGTVVYGQEEAIKKLSSSIKIARAGLSDPNKPIGCYVFSGPTGVGKTEISKQLAFAL 531
K+ +V GQE ++ L+++++ R + Y+F+G GVGKT +++ LA +L
Sbjct: 13 KSFSELV-GQEHVVRALTNALEQQRLHHA--------YLFTGTRGVGKTTLARILAKSL 62
>gnl|CDD|184918 PRK14954, PRK14954, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 620
Score = 29.9 bits (67), Expect = 2.3
Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 8/53 (15%)
Query: 482 QEEAIKKLSSSIKIARAGLSDPNKPIGCYVFSGPTGVGKTEISKQLAFALGVQ 534
QE + +S+++ R G Y+FSG GVGKT ++ A A+ Q
Sbjct: 21 QEHITHTIQNSLRMDRVGHG--------YIFSGLRGVGKTTAARVFAKAVNCQ 65
Score = 28.0 bits (62), Expect = 9.0
Identities = 17/42 (40%), Positives = 21/42 (50%), Gaps = 2/42 (4%)
Query: 210 HEEINRTIQILCR--RSKNNPLYVGDPGVGKTAIAEGFAKQI 249
E I TIQ R R + ++ G GVGKT A FAK +
Sbjct: 21 QEHITHTIQNSLRMDRVGHGYIFSGLRGVGKTTAARVFAKAV 62
>gnl|CDD|161743 TIGR00174, miaA, tRNA isopentenyltransferase (miaA). Catalyzes the
first step in the modification of an adenosine near the
anticodon to 2-methylthio-N6-isopentyladenosine.
Length = 287
Score = 30.1 bits (68), Expect = 2.5
Identities = 13/36 (36%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 511 VFSGPTGVGKTEISKQLAFALGVQLLRFD-MSEYME 545
GPT VGK++++ QLA L +++ D M Y
Sbjct: 3 FIMGPTAVGKSQLAIQLAKKLNAEIISVDSMQIYKG 38
>gnl|CDD|173186 PRK14723, flhF, flagellar biosynthesis regulator FlhF; Provisional.
Length = 767
Score = 30.2 bits (68), Expect = 2.5
Identities = 11/21 (52%), Positives = 13/21 (61%)
Query: 508 GCYVFSGPTGVGKTEISKQLA 528
G GPTGVGKT + +LA
Sbjct: 186 GVLALVGPTGVGKTTTTAKLA 206
>gnl|CDD|130205 TIGR01135, glmS, glucosamine--fructose-6-phosphate aminotransferase
(isomerizing). The member from Methanococcus jannaschii
contains an intein.
Length = 607
Score = 29.9 bits (68), Expect = 2.5
Identities = 17/41 (41%), Positives = 25/41 (60%), Gaps = 1/41 (2%)
Query: 276 RYRGDFEERIKKIVKEIE-SYANAILYIDEIHTLVGAGSAS 315
R GD E ++K +K++ +YA A+L+ D TLV A S S
Sbjct: 137 REGGDLLEAVQKALKQLRGAYALAVLHADHPETLVAARSGS 177
>gnl|CDD|180213 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 424
Score = 29.9 bits (68), Expect = 2.6
Identities = 13/41 (31%), Positives = 18/41 (43%), Gaps = 1/41 (2%)
Query: 482 QEEAIKKLSSSI-KIARAGLSDPNKPIGCYVFSGPTGVGKT 521
+ A + L + + + D K G GPTGVGKT
Sbjct: 195 ERTAWRYLLELLANMIPVRVEDILKQGGVVALVGPTGVGKT 235
>gnl|CDD|180790 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau;
Validated.
Length = 830
Score = 29.8 bits (67), Expect = 2.7
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 510 YVFSGPTGVGKTEISKQLAFAL 531
Y+F+G GVGKT +S+ A AL
Sbjct: 41 YLFTGTRGVGKTTLSRIFAKAL 62
>gnl|CDD|179793 PRK04220, PRK04220, 2-phosphoglycerate kinase; Provisional.
Length = 301
Score = 29.9 bits (68), Expect = 2.9
Identities = 14/40 (35%), Positives = 24/40 (60%), Gaps = 3/40 (7%)
Query: 514 GPTGVGKTEISKQLAFALGVQ-LLRFDM-SEYMERHAVSR 551
G +GVG + I+ +LA LG++ ++ D E M R +S+
Sbjct: 99 GASGVGTSTIAFELASRLGIRSVIGTDSIREVM-RKIISK 137
>gnl|CDD|180787 PRK06995, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 484
Score = 29.9 bits (68), Expect = 2.9
Identities = 16/45 (35%), Positives = 21/45 (46%), Gaps = 12/45 (26%)
Query: 508 GCYVFSGPTGVGKTEISKQLAFALGVQLLRFDMSEYMERHAVSRL 552
G + GPTGVGKT + +LA R M RH S++
Sbjct: 257 GVFALMGPTGVGKTTTTAKLA-------ARCVM-----RHGASKV 289
>gnl|CDD|173184 PRK14721, flhF, flagellar biosynthesis regulator FlhF; Provisional.
Length = 420
Score = 29.9 bits (67), Expect = 2.9
Identities = 12/21 (57%), Positives = 14/21 (66%)
Query: 508 GCYVFSGPTGVGKTEISKQLA 528
G Y GPTGVGKT + +LA
Sbjct: 192 GVYALIGPTGVGKTTTTAKLA 212
>gnl|CDD|107157 PHA02244, PHA02244, ATPase-like protein.
Length = 383
Score = 29.7 bits (66), Expect = 3.2
Identities = 50/204 (24%), Positives = 78/204 (38%), Gaps = 40/204 (19%)
Query: 514 GPTGVGKTEISKQLAFALGVQLLRFDMSEYMERHAVSRLIGA------PPGYVGFGQGGI 567
G G GK I++Q+A AL + + M+ M+ + I A P Y F +GG+
Sbjct: 126 GGAGSGKNHIAEQIAEALDLDF--YFMNAIMDEFELKGFIDANGKFHETPFYEAFKKGGL 183
Query: 568 LADSVDQNPYSVVLLDEIEKSHPDVLNIL-----LQIMDYGILTDQSGKKISFRNVILIM 622
+DEI+ S P+ L I+ + D+ + + FR +
Sbjct: 184 F------------FIDEIDASIPEALIIINSAIANKFFDFADERVTAHE--DFRVISAGN 229
Query: 623 TTNAGALEMSKARIGFGSSRNDDADKEALRNFLSPEFLNRLDSIIPFFPLSSDIIRQVVH 682
T GA + AR + D L F EF D I + D +V+
Sbjct: 230 TLGKGADHIYVAR--------NKIDGATLDRFAPIEF--DYDEKIEHLISNGD--EDLVN 277
Query: 683 KFIMKLELQLQEKGISFHFSEEVI 706
F+ L ++ EKG+ FS I
Sbjct: 278 -FVALLRHEMAEKGLDHVFSMRAI 300
>gnl|CDD|183503 PRK12402, PRK12402, replication factor C small subunit 2; Reviewed.
Length = 337
Score = 29.6 bits (67), Expect = 3.2
Identities = 15/55 (27%), Positives = 29/55 (52%)
Query: 195 TEKVKKGKVDILVGRHEEINRTIQILCRRSKNNPLYVGDPGVGKTAIAEGFAKQI 249
TEK + ++ ++G+ E + R + + + + L G PG GKTA A+++
Sbjct: 6 TEKYRPALLEDILGQDEVVERLSRAVDSPNLPHLLVQGPPGSGKTAAVRALAREL 60
>gnl|CDD|181191 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau;
Validated.
Length = 647
Score = 29.5 bits (67), Expect = 3.6
Identities = 13/22 (59%), Positives = 16/22 (72%)
Query: 510 YVFSGPTGVGKTEISKQLAFAL 531
Y+FSG GVGKT I++ LA L
Sbjct: 41 YLFSGTRGVGKTTIARLLAKGL 62
>gnl|CDD|181111 PRK07773, PRK07773, replicative DNA helicase; Validated.
Length = 886
Score = 29.3 bits (66), Expect = 3.7
Identities = 12/38 (31%), Positives = 15/38 (39%), Gaps = 4/38 (10%)
Query: 232 GDPGVGKTAIAEGFAKQIVDGMVPDILLGARIFSLDMG 269
P +GKT FA+ L IFSL+M
Sbjct: 224 ARPSMGKTTFGLDFARNCAIRHR----LAVAIFSLEMS 257
>gnl|CDD|178433 PLN02840, PLN02840, tRNA dimethylallyltransferase.
Length = 421
Score = 29.4 bits (66), Expect = 3.8
Identities = 12/29 (41%), Positives = 19/29 (65%)
Query: 511 VFSGPTGVGKTEISKQLAFALGVQLLRFD 539
V SGPTG GK+ ++ +LA L +++ D
Sbjct: 25 VISGPTGAGKSRLALELAKRLNGEIISAD 53
>gnl|CDD|168777 PRK07036, PRK07036, hypothetical protein; Provisional.
Length = 466
Score = 29.3 bits (66), Expect = 3.9
Identities = 20/66 (30%), Positives = 29/66 (43%), Gaps = 19/66 (28%)
Query: 215 RTIQILCRRSKNNPLYVGDPGVGKTA---IAEGFAKQIVDGMVPDIL------------L 259
++ +CRR + LY+ D V T + FA + V G+ PDI+ L
Sbjct: 244 ARMREICRR--YDILYISDEVV--TGFGRLGHFFASEAVFGIQPDIITFAKGLTSGYQPL 299
Query: 260 GARIFS 265
GA I S
Sbjct: 300 GAVIIS 305
>gnl|CDD|163076 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.
Length = 365
Score = 29.5 bits (67), Expect = 3.9
Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 4/50 (8%)
Query: 204 DILVGRHEEINRTIQIL---CRRSK-NNPLYVGDPGVGKTAIAEGFAKQI 249
D +V R E+I + L R S+ +N G G GKTA+ + K++
Sbjct: 15 DRIVHRDEQIEELAKALRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKEL 64
Score = 29.1 bits (66), Expect = 5.0
Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 7/46 (15%)
Query: 481 GQEEAIKKLSSSIKIARAGLSDPNKPIGCYVF-SGPTGVGKTEISK 525
++E I++L+ +++ G N VF G TG GKT ++K
Sbjct: 19 HRDEQIEELAKALRPILRGSRPSN------VFIYGKTGTGKTAVTK 58
>gnl|CDD|179744 PRK04132, PRK04132, replication factor C small subunit;
Provisional.
Length = 846
Score = 29.4 bits (66), Expect = 4.1
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 2/62 (3%)
Query: 196 EKVKKGKVDILVGRHEEINRTIQILCRRSKNNPLYVGDPGVGKTAIAEGFAKQIVDGMVP 255
EK + ++D +VG+ + R + S + L+ G PGVGK G K I +G +
Sbjct: 11 EKYRPQRLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKCLT--GDTKVIANGELF 68
Query: 256 DI 257
+I
Sbjct: 69 EI 70
>gnl|CDD|180856 PRK07133, PRK07133, DNA polymerase III subunits gamma and tau;
Validated.
Length = 725
Score = 29.4 bits (66), Expect = 4.2
Identities = 20/53 (37%), Positives = 28/53 (52%), Gaps = 8/53 (15%)
Query: 479 VYGQEEAIKKLSSSIKIARAGLSDPNKPIGCYVFSGPTGVGKTEISKQLAFAL 531
+ GQ+ ++ L + IK NK Y+FSGP G GKT ++K A AL
Sbjct: 20 IVGQDHIVQTLKNIIKS--------NKISHAYLFSGPRGTGKTSVAKIFANAL 64
>gnl|CDD|179010 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 29.0 bits (66), Expect = 4.5
Identities = 42/165 (25%), Positives = 73/165 (44%), Gaps = 43/165 (26%)
Query: 483 EEAIKKLSSSIKIARAGLSDPNKPIGCYVFSGPTGVGKT--------EISKQLAFALGVQ 534
EE I++L+ +++ A G ++P+ + GP G GKT E+ + A+ V
Sbjct: 36 EEQIEELAFALRPALRG----SRPLNVLI-YGPPGTGKTTTVKKVFEELEEI---AVKVV 87
Query: 535 LLRFDMSEYMERHAV-----SRLIGAPPGYVG------FGQGGILADSVDQ-NPYSVVLL 582
+ + R+A+ +L G PP G F + +A+ +D+ + +V L
Sbjct: 88 YVYINCQIDRTRYAIFSEIARQLFGHPPPSSGLSFDELFDK---IAEYLDERDRVLIVAL 144
Query: 583 DEI----EKSHPDVLNILLQIMDYGILTDQSGKKISFRNVILIMT 623
D+I EK DVL LL+ + + G +I VI I +
Sbjct: 145 DDINYLFEKEGNDVLYSLLRAHE-----EYPGARIG---VIGISS 181
>gnl|CDD|184151 PRK13570, PRK13570, anthranilate synthase component I; Provisional.
Length = 455
Score = 29.2 bits (66), Expect = 4.6
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 268 MGNLIAGTRYRGDFEERIKKIVKEIES 294
N IAGTR RG +E + + KE+ S
Sbjct: 273 TTNPIAGTRPRGKTKEEDEALAKELLS 299
>gnl|CDD|178865 PRK00104, scpA, segregation and condensation protein A; Reviewed.
Length = 242
Score = 29.0 bits (66), Expect = 4.7
Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 3/49 (6%)
Query: 345 YRQFFEKDKALVRRFQKIDVSEPSIEDAIEIVKGIKPYFEEHHQLRYSK 393
+ + E+ KA R KI+ E IED + + + E +L +S+
Sbjct: 151 FSKLMERKKANKPRHTKIERDEYKIEDRMLYILEL---LESKKRLSFSE 196
>gnl|CDD|181214 PRK08058, PRK08058, DNA polymerase III subunit delta'; Validated.
Length = 329
Score = 29.1 bits (66), Expect = 4.9
Identities = 14/50 (28%), Positives = 21/50 (42%), Gaps = 14/50 (28%)
Query: 482 QEEAIKKLSSSI---KIARAGLSDPNKPIGCYVFSGPTGVGKTEISKQLA 528
Q +K L +SI +++ A Y+F G G GK + LA
Sbjct: 11 QPVVVKMLQNSIAKNRLSHA-----------YLFEGAKGTGKKATALWLA 49
>gnl|CDD|181106 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau;
Validated.
Length = 824
Score = 28.8 bits (65), Expect = 5.0
Identities = 9/12 (75%), Positives = 10/12 (83%)
Query: 510 YVFSGPTGVGKT 521
Y+FSGP G GKT
Sbjct: 40 YLFSGPRGCGKT 51
>gnl|CDD|178452 PLN02861, PLN02861, long-chain-fatty-acid-CoA ligase.
Length = 660
Score = 29.0 bits (65), Expect = 5.1
Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 7/63 (11%)
Query: 709 LVSHGYDVKMGARPLERIIKEHVKVPLADEILFGKLKKG-GGVVKVSLNPDKSASSPIFF 767
L Y+ K+G L + +K+ P D ++F K+K+G GG V++ L S ++P+
Sbjct: 344 LFDFAYNYKLGN--LRKGLKQEEASPRLDRLVFDKIKEGLGGRVRLLL----SGAAPLPR 397
Query: 768 EIE 770
+E
Sbjct: 398 HVE 400
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 29.0 bits (65), Expect = 5.1
Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 13/77 (16%)
Query: 229 LYVGDPGVGKTAIAEGFAKQIVDGMVPDILLGARIFSLDMGNLIAGTRYRGDFEERIKKI 288
LY G PG GKT +A+ A + A + LI +Y GD + ++++
Sbjct: 222 LY-GPPGTGKTLLAKAVANET----------SATFLRVVGSELI--QKYLGDGPKLVREL 268
Query: 289 VKEIESYANAILYIDEI 305
+ E A +I++IDEI
Sbjct: 269 FRVAEENAPSIVFIDEI 285
>gnl|CDD|184922 PRK14958, PRK14958, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 509
Score = 28.9 bits (64), Expect = 5.4
Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 8/56 (14%)
Query: 479 VYGQEEAIKKLSSSIKIARAGLSDPNKPIGCYVFSGPTGVGKTEISKQLAFALGVQ 534
V GQ ++ LS+++ D Y+F+G GVGKT IS+ LA L +
Sbjct: 18 VIGQAPVVRALSNAL--------DQQYLHHAYLFTGTRGVGKTTISRILAKCLNCE 65
>gnl|CDD|178856 PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase;
Reviewed.
Length = 307
Score = 28.9 bits (66), Expect = 5.5
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 514 GPTGVGKTEISKQLAFALGV 533
GPT GKT ++ +LA L
Sbjct: 11 GPTASGKTALAIELAKRLNG 30
>gnl|CDD|185633 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 28.6 bits (64), Expect = 5.8
Identities = 34/139 (24%), Positives = 61/139 (43%), Gaps = 38/139 (27%)
Query: 502 DPNKPIGCYVFSGPTGVGKTEISKQLAFALGVQLLRFDMSEYMERHAVSRLIGAPPGYVG 561
DP P G ++ GP G GKT ++K +A +R SE+++++
Sbjct: 177 DP--PRGVLLY-GPPGTGKTMLAKAVAHHTTATFIRVVGSEFVQKY-------------- 219
Query: 562 FGQGGILADSV----DQNPYSVVLLDEIEK-----------SHPDVLNILLQIMDYGILT 606
G+G + V +N S++ +DE++ + +V ILL++++
Sbjct: 220 LGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGADREVQRILLELLNQMDGF 279
Query: 607 DQSGKKISFRNVILIMTTN 625
DQ+ NV +IM TN
Sbjct: 280 DQT------TNVKVIMATN 292
>gnl|CDD|150510 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 = 28.7 bits (65), Expect = 6.5
Identities = 22/88 (25%), Positives = 35/88 (39%), Gaps = 15/88 (17%)
Query: 232 GDPGVGKTAIAEGFAKQIVDGMVPDILLGARIFSLDMGNLIAGTRY--RGDFEERIKKIV 289
G PG GKT +A ++ D L +F L+ GD + R KK+
Sbjct: 8 GGPGTGKTVVALNLFAELSD----SDLGRTAVFLSGNHPLVLVLYEALAGDLKVRKKKLF 63
Query: 290 KEIESYANA---------ILYIDEIHTL 308
++ S+ N ++ +DE H L
Sbjct: 64 RKPTSFINNLHKAPPHEDVVIVDEAHRL 91
>gnl|CDD|184924 PRK14960, PRK14960, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 702
Score = 28.5 bits (63), Expect = 6.8
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 8/51 (15%)
Query: 481 GQEEAIKKLSSSIKIARAGLSDPNKPIGCYVFSGPTGVGKTEISKQLAFAL 531
GQ + LSS+++ R + Y+F+G GVGKT I++ LA L
Sbjct: 19 GQNHVSRALSSALERGRLHHA--------YLFTGTRGVGKTTIARILAKCL 61
>gnl|CDD|148316 pfam06638, Strabismus, Strabismus protein. This family consists of
several strabismus (STB) or Van Gogh-like (VANGL)
proteins 1 and 2. The exact function of this family is
unknown. It is thought, however that STB1 gene and STB2
may be potent tumour suppressor gene candidates.
Length = 507
Score = 28.5 bits (64), Expect = 7.0
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 667 IPFFPLSSDIIRQVVHKFIMKL 688
IPFF LS + + HKF++KL
Sbjct: 480 IPFFNLSEEFVDPKSHKFVLKL 501
>gnl|CDD|185588 PTZ00385, PTZ00385, lysyl-tRNA synthetase; Provisional.
Length = 659
Score = 28.5 bits (63), Expect = 7.3
Identities = 15/52 (28%), Positives = 24/52 (46%)
Query: 642 RNDDADKEALRNFLSPEFLNRLDSIIPFFPLSSDIIRQVVHKFIMKLELQLQ 693
RN+DAD+ F S EF + P++ DI RQ+ + +Q+
Sbjct: 312 RNEDADRSHNPEFTSCEFYAAYHTYEDLMPMTEDIFRQLAMRVNGTTVVQIY 363
>gnl|CDD|162667 TIGR02031, BchD-ChlD, magnesium chelatase ATPase subunit D. This
model represents one of two ATPase subunits of the
trimeric magnesium chelatase responsible for insertion
of magnesium ion into protoporphyrin IX. This is an
essential step in the biosynthesis of both chlorophyll
and bacteriochlorophyll. This subunit is found in green
plants, photosynthetic algae, cyanobacteria and other
photosynthetic bacteria. Unlike subunit I (TIGR02030),
this subunit is not found in archaea.
Length = 589
Score = 28.2 bits (63), Expect = 7.6
Identities = 43/189 (22%), Positives = 67/189 (35%), Gaps = 36/189 (19%)
Query: 502 DPNKPIGCYVFSGPTGVGKTEISKQLAFAL--GVQLLRF--DMSEYMERHAVSRLIGA-- 555
DP+ +G G GKT +++ LA L + + ++E RLIG
Sbjct: 13 DPS--LGGVAIRARAGTGKTALARALAEILPPIMPFVELPLGVTE-------DRLIGGID 63
Query: 556 ----PPGYVGFGQGGILADSVDQNPYSVVLLDEIEKSHPDVLNILLQIMDYGILTDQSGK 611
G Q G+L ++ P V+ +D + N LLQ +D G++ + +
Sbjct: 64 VEESLAGGQRVTQPGLLDEA----PRGVLYVDMANLLDDGLSNRLLQALDEGVVIVER-E 118
Query: 612 KISFR---NVILIMTTNA----GALEMSKA-RIGFGSSRND----DADKEALRNFLSPEF 659
IS LI T + G L R+ S D D E +R E
Sbjct: 119 GISVVHPAKFALIATYDPAEGGGGLPDHLLDRLALHVSLEDVASQDLRVEIVRRERCNEV 178
Query: 660 LNRLDSIIP 668
D +
Sbjct: 179 FRMNDELEL 187
>gnl|CDD|178596 PLN03025, PLN03025, replication factor C subunit; Provisional.
Length = 319
Score = 28.5 bits (64), Expect = 7.7
Identities = 17/43 (39%), Positives = 23/43 (53%), Gaps = 9/43 (20%)
Query: 479 VYGQEEAIKKLSSSIKIARAGLSDPNKPIGCYVFSGPTGVGKT 521
+ G E+A+ +L IAR G + PN + SGP G GKT
Sbjct: 15 IVGNEDAVSRLQV---IARDG-NMPN-----LILSGPPGTGKT 48
>gnl|CDD|184912 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 620
Score = 28.4 bits (64), Expect = 8.0
Identities = 17/45 (37%), Positives = 23/45 (51%), Gaps = 16/45 (35%)
Query: 481 GQEEAIKK-LSSSI---KIARAGLSDPNKPIGCYVFSGPTGVGKT 521
GQE AI L +++ +IA A Y+F+GP G GKT
Sbjct: 20 GQE-AIATTLKNALISNRIAPA-----------YLFTGPRGTGKT 52
>gnl|CDD|148114 pfam06309, Torsin, Torsin. This family consists of several
eukaryotic torsin proteins. Torsion dystonia is an
autosomal dominant movement disorder characterized by
involuntary, repetitive muscle contractions and twisted
postures. The most severe early-onset form of dystonia
has been linked to mutations in the human DYT1 (TOR1A)
gene encoding a protein termed torsinA. While causative
genetic alterations have been identified, the function
of torsin proteins and the molecular mechanism
underlying dystonia remain unknown. Phylogenetic
analysis of the torsin protein family indicates these
proteins share distant sequence similarity with the
large and diverse family of (pfam00004) proteins. It has
been suggested that torsins play a role in effectively
managing protein folding and that possible breakdown in
a neuroprotective mechanism that is, in part, mediated
by torsins may be responsible for the neuronal
dysfunction associated with dystonia.
Length = 127
Score = 28.1 bits (63), Expect = 8.4
Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 6/60 (10%)
Query: 471 LEKNLGTVVYGQEEAIKKLSSSIKIARAGLSDPN--KPIGCYVFSGPTGVGKTEISKQLA 528
LE++L ++GQ + + S+K +P KP+ F G TG GK +++ +A
Sbjct: 19 LERDLARRLFGQHLVKQLVVRSVK---GHWENPKPRKPL-VLSFHGWTGTGKNFVAEIIA 74
>gnl|CDD|173185 PRK14722, flhF, flagellar biosynthesis regulator FlhF; Provisional.
Length = 374
Score = 28.1 bits (62), Expect = 8.5
Identities = 29/94 (30%), Positives = 43/94 (45%), Gaps = 11/94 (11%)
Query: 508 GCYVFSGPTGVGKTEISKQLAF-------ALGVQLLRFD---MSEYMERHAVSRLIGAPP 557
G + GPTGVGKT + +LA A V LL D + + + +++G P
Sbjct: 138 GVFALMGPTGVGKTTTTAKLAARCVMRFGASKVALLTTDSYRIGGHEQLRIFGKILGVPV 197
Query: 558 GYVGFGQGGILADSVDQNPYSVVLLDEIEKSHPD 591
V G LA + +N + +VL+D I S D
Sbjct: 198 HAVKDGGDLQLALAELRNKH-MVLIDTIGMSQRD 230
>gnl|CDD|131688 TIGR02640, gas_vesic_GvpN, gas vesicle protein GvpN. Members of
this family are the GvpN protein associated with the
production of gas vesicles produced in some prokaryotes
to give cells buoyancy. This family belongs to a larger
family of ATPases (pfam07728).
Length = 262
Score = 28.2 bits (63), Expect = 8.8
Identities = 29/121 (23%), Positives = 43/121 (35%), Gaps = 39/121 (32%)
Query: 512 FSGPTGVGKTEISKQLAFALG--VQLLRFDMSEYMERHAVSRLIGAPPGYVGFGQGGILA 569
GP G GKT ++ +A V L+ D S L+G+ GY
Sbjct: 26 LRGPAGTGKTTLAMHVARKRDRPVMLINGD-----AELTTSDLVGSYAGYTR-------K 73
Query: 570 DSVDQNPYSVVLL-------------------------DEIEKSHPDVLNILLQIMDYGI 604
DQ ++VV L DE +S P+ N+LL + + G+
Sbjct: 74 KVHDQFIHNVVKLEDIVRQNWVDNRLTLAVREGFTLVYDEFTRSKPETNNVLLSVFEEGV 133
Query: 605 L 605
L
Sbjct: 134 L 134
>gnl|CDD|131926 TIGR02880, cbbX_cfxQ, probable Rubsico expression protein CbbX.
Proteins in this family are now designated CbbX. Some
previously were CfxQ (carbon fixation Q). Its gene is
often found immmediately downstream of the Rubisco large
and small chain genes, and it is suggested to be
necessary for Rubisco expression. CbbX has been shown to
be necessary for photoautotrophic growth. This protein
belongs to the larger family of pfam00004, ATPase family
Associated with various cellular Activities. Within that
larger family, members of this family are most closely
related to the stage V sporulation protein K, or SpoVK,
in endospore-forming bacteria such as Bacillus subtilis.
Length = 284
Score = 28.3 bits (63), Expect = 9.4
Identities = 25/85 (29%), Positives = 39/85 (45%), Gaps = 20/85 (23%)
Query: 230 YVGDPGVGKTAIAEGFAKQIVDGMVPDILLGARIFSLDMGNLIAGTR------YRGDFEE 283
+ G+PG GKT +A A IL R+ + G+L++ TR Y G
Sbjct: 63 FTGNPGTGKTTVALRMA---------QIL--HRLGYVRKGHLVSVTRDDLVGQYIGHTAP 111
Query: 284 RIKKIVKEIESYANAILYIDEIHTL 308
+ K+I+K +L+IDE + L
Sbjct: 112 KTKEILKRAMG---GVLFIDEAYYL 133
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 27.8 bits (62), Expect = 9.8
Identities = 42/161 (26%), Positives = 69/161 (42%), Gaps = 29/161 (18%)
Query: 229 LYVGDPGVGKTAIAEGFAKQIVDGMVPDILLGARIFSLDMGNLIAGTRYRGDFEERIKKI 288
L G PG GKT +A+ A + + R+ ++ +Y G+ +++I
Sbjct: 160 LLYGPPGTGKTLLAKAVAHETNATFI-------RVVGSELVR-----KYIGEGARLVREI 207
Query: 289 VKEIESYANAILYIDEIHTLVGAGSASGISVD--ASNLLKPAL-------SSGAVRCIGS 339
+ + A +I++IDEI + + SG S D L L G V+ I +
Sbjct: 208 FELAKEKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAELDGFDPRGNVKVIAA 267
Query: 340 TTYSEYRQFFEKDKALVR--RFQK-IDVSEPSIEDAIEIVK 377
T + D AL+R RF + I+V P E +EI+K
Sbjct: 268 TNRPDIL-----DPALLRPGRFDRIIEVPLPDFEGRLEILK 303
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.317 0.135 0.375
Gapped
Lambda K H
0.267 0.0662 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 13,021,955
Number of extensions: 883545
Number of successful extensions: 2555
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2511
Number of HSP's successfully gapped: 160
Length of query: 798
Length of database: 5,994,473
Length adjustment: 101
Effective length of query: 697
Effective length of database: 3,812,065
Effective search space: 2657009305
Effective search space used: 2657009305
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 61 (27.4 bits)