RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780877|ref|YP_003065290.1| ATP-dependent Clp protease, ATP-binding subunit protein [Candidatus Liberibacter asiaticus str. psy62] (853 letters) >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 = 1319 bits (3416), Expect = 0.0 Identities = 519/844 (61%), Positives = 656/844 (77%), Gaps = 7/844 (0%) Query: 14 LQSAQTYALAQGHQNLVPEHVLHIFLEDEQGAVYSLIQCSGGDIAQLKDYNQTVLSKIPK 73 LQ+AQ+ AL + HQ + PEH+L L+ E G L+Q +G ++ L+ + L K+PK Sbjct: 9 LQAAQSLALGRDHQQIEPEHLLKALLDQEGGLARRLLQKAGVNVGALRQALEKELEKLPK 68 Query: 74 VTGGGAQVYLSQPLAVILSKSEEIAKKSGDSFVTAEKFLLAMVMETGGIGESLKKCGLKF 133 V+G G QVYLS L +L+ +E++A+K GD F+++E LLA++ + G +G+ LK+ G Sbjct: 69 VSGPGGQVYLSPELNRLLNLAEKLAQKRGDEFISSEHLLLALLDDKGTLGKLLKEAGATA 128 Query: 134 SRLEESIKKLRKGRVADSVNAEQGFDALKKYCRDLTEEARNGKLDPVIGRDDEMRRAIQV 193 LE +I +R G+ S NAE ++AL+KY RDLTE AR GKLDPVIGRD+E+RR IQV Sbjct: 129 DALEAAINAVRGGQKVTSANAEDQYEALEKYARDLTERAREGKLDPVIGRDEEIRRTIQV 188 Query: 194 LSRRTKNNPVLIGDPGVGKTAIIEGLASRIINGDIPESLKGKRLMALDMGALIAGAKFRG 253 LSRRTKNNPVLIG+PGVGKTAI+EGLA RI+NGD+PESLK KRL+ALDMGALIAGAK+RG Sbjct: 189 LSRRTKNNPVLIGEPGVGKTAIVEGLAQRIVNGDVPESLKNKRLLALDMGALIAGAKYRG 248 Query: 254 EFEERLKSLLCEIRSEDGEIILFIDELHVLVGAGKTDGAMDASNLLKPSLARGELHCIGA 313 EFEERLK++L E+ +G+IILFIDELH LVGAGK +GAMDA N+LKP+LARGELHCIGA Sbjct: 249 EFEERLKAVLNEVTKSEGQIILFIDELHTLVGAGKAEGAMDAGNMLKPALARGELHCIGA 308 Query: 314 TTLDEYRKYIEKDPALARRFQSLLVGEPTVTDTISILRGLKERYEQHHKVRISDSALVSA 373 TTLDEYRKYIEKD AL RRFQ + V EPTV DTISILRGLKERYE HH VRI+D A+V+A Sbjct: 309 TTLDEYRKYIEKDAALERRFQPVFVDEPTVEDTISILRGLKERYEVHHGVRITDPAIVAA 368 Query: 374 AVLSNRYITDRFLPDKAIDLMDEASARVRMQIDTKPEVLDELDRRIICLKIEKEALKKEK 433 A LS+RYITDRFLPDKAIDL+DEA+AR+RM+ID+KPE LDELDRRII L+IE+EALKKEK Sbjct: 369 ATLSHRYITDRFLPDKAIDLIDEAAARIRMEIDSKPEELDELDRRIIQLEIEREALKKEK 428 Query: 434 DSFSKGRLIELEKELSSLEEKSHSLTLRWQEGQRKILYVADLKKRLESMRNELAIAQRQG 493 D SK RL +LEKEL+ LEE+ L +W+ + I + +K+ +E +R EL A+R+G Sbjct: 429 DEASKERLEDLEKELAELEEEYADLEEQWKAEKAAIQGIQQIKEEIEQVRLELEQAEREG 488 Query: 494 HFERAGELAYGLIPKTEKELDEAEKADS--TAEDMVQEVVTSDNIANIVSRWTGIPVDKM 551 +A EL YG +P+ EK L AE T +++E VT++ IA +VSRWTGIPV KM Sbjct: 489 DLAKAAELQYGKLPELEKRLQAAEAKLGEETKPRLLREEVTAEEIAEVVSRWTGIPVSKM 548 Query: 552 LESDREKFLRIETEISKSVIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGK 611 LE +REK L +E + + V+GQ AVE+VS+A+RR RAGL DP RP+GSF+FLGPTGVGK Sbjct: 549 LEGEREKLLHMEEVLHERVVGQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGK 608 Query: 612 TELVKSLARLLFDDENSMIRIDMSEYMEKHSVSRLIGSPPGYVGYEEGGALTEAVRRHPY 671 TEL K+LA LFDDE++M+RIDMSEYMEKHSV+RLIG+PPGYVGYEEGG LTEAVRR PY Sbjct: 609 TELAKALAEFLFDDEDAMVRIDMSEYMEKHSVARLIGAPPGYVGYEEGGQLTEAVRRKPY 668 Query: 672 QVVLFDEIEKAHSDVHNILLQVLDDGRLTDSQGRTVDFRNTLIIMTSNLGAEYLIEDGD- 730 VVLFDE+EKAH DV N+LLQVLDDGRLTD QGRTVDFRNT+IIMTSNLG++++ E Sbjct: 669 SVVLFDEVEKAHPDVFNVLLQVLDDGRLTDGQGRTVDFRNTVIIMTSNLGSQFIQELAGG 728 Query: 731 ----SVHDKVMGIVRSAFKPEFLNRLDEIILFEKLRKEDMAKIVRIQLGRVLSLIKERNI 786 + + VM ++R+ F+PEFLNR+DEI++F L +E +A+IV IQLGR+ + ER I Sbjct: 729 DDYEEMREAVMEVLRAHFRPEFLNRIDEIVVFHPLGREQIARIVEIQLGRLRKRLAERKI 788 Query: 787 SMDFDDQVIDWLSCRGYDPSYGARPLKRVIQRYIQNPLAERVLSQTISDGDSIEVFVDDD 846 +++ D +D+L+ GYDP YGARPLKR IQR I+NPLA+++L+ ++DGD+I V V+ Sbjct: 789 TLELSDAALDFLAEAGYDPVYGARPLKRAIQREIENPLAKKILAGEVADGDTIVVDVEGG 848 Query: 847 NLNF 850 L F Sbjct: 849 RLVF 852 >gnl|CDD|182791 PRK10865, PRK10865, protein disaggregation chaperone; Provisional. Length = 857 Score = 1002 bits (2592), Expect = 0.0 Identities = 470/853 (55%), Positives = 620/853 (72%), Gaps = 5/853 (0%) Query: 1 MNSDKYSDLMRNVLQSAQTYALAQGHQNLVPEHVLHIFLEDEQGAVYSLIQCSGGDIAQL 60 M D+ ++ + L AQ+ AL +Q + P H++ L E G+V L+ +G + QL Sbjct: 1 MRLDRLTNKFQLALADAQSLALGHDNQFIEPLHLMSALLNQEGGSVRPLLTSAGINAGQL 60 Query: 61 KDYNQTVLSKIPKVTGGGAQVYLSQPLAVILSKSEEIAKKSGDSFVTAEKFLLAMVMETG 120 + LS++P+V G G V SQ L +L+ +++A+K GD+F+++E F+LA + G Sbjct: 61 RTDINQALSRLPQVEGTGGDVQPSQDLVRVLNLCDKLAQKRGDNFISSELFVLAALESRG 120 Query: 121 GIGESLKKCGLKFSRLEESIKKLRKGRVADSVNAEQGFDALKKYCRDLTEEARNGKLDPV 180 + + LK G + + ++I+++R G + AE ALKKY DLTE A GKLDPV Sbjct: 121 TLADILKAAGATTANITQAIEQMRGGESVNDQGAEDQRQALKKYTIDLTERAEQGKLDPV 180 Query: 181 IGRDDEMRRAIQVLSRRTKNNPVLIGDPGVGKTAIIEGLASRIINGDIPESLKGKRLMAL 240 IGRD+E+RR IQVL RRTKNNPVLIG+PGVGKTAI+EGLA RIING++PE LKG+R++AL Sbjct: 181 IGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLAL 240 Query: 241 DMGALIAGAKFRGEFEERLKSLLCEIRSEDGEIILFIDELHVLVGAGKTDGAMDASNLLK 300 DMGAL+AGAK+RGEFEERLK +L ++ ++G +ILFIDELH +VGAGK DGAMDA N+LK Sbjct: 241 DMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLK 300 Query: 301 PSLARGELHCIGATTLDEYRKYIEKDPALARRFQSLLVGEPTVTDTISILRGLKERYEQH 360 P+LARGELHC+GATTLDEYR+YIEKD AL RRFQ + V EP+V DTI+ILRGLKERYE H Sbjct: 301 PALARGELHCVGATTLDEYRQYIEKDAALERRFQKVFVAEPSVEDTIAILRGLKERYELH 360 Query: 361 HKVRISDSALVSAAVLSNRYITDRFLPDKAIDLMDEASARVRMQIDTKPEVLDELDRRII 420 H V+I+D A+V+AA LS+RYI DR LPDKAIDL+DEA++ +RMQID+KPE LD LDRRII Sbjct: 361 HHVQITDPAIVAAATLSHRYIADRQLPDKAIDLIDEAASSIRMQIDSKPEELDRLDRRII 420 Query: 421 CLKIEKEALKKEKDSFSKGRLIELEKELSSLEEKSHSLTLRWQEGQRKILYVADLKKRLE 480 LK+E++AL KE D SK RL L +ELS E + L W+ + + +K LE Sbjct: 421 QLKLEQQALMKESDEASKKRLDMLNEELSDKERQYSELEEEWKAEKASLSGTQTIKAELE 480 Query: 481 SMRNELAIAQRQGHFERAGELAYGLIPKTEKELDEAEKADSTAEDMVQEVVTSDNIANIV 540 + + A+R G R EL YG IP+ EK+L A + + +++ VT IA ++ Sbjct: 481 QAKIAIEQARRVGDLARMSELQYGKIPELEKQLAAATQLEGKTMRLLRNKVTDAEIAEVL 540 Query: 541 SRWTGIPVDKMLESDREKFLRIETEISKSVIGQSAAVESVSNALRRFRAGLQDPQRPMGS 600 +RWTGIPV +MLES+REK LR+E E+ VIGQ+ AVE+VSNA+RR RAGL DP RP+GS Sbjct: 541 ARWTGIPVSRMLESEREKLLRMEQELHHRVIGQNEAVEAVSNAIRRSRAGLSDPNRPIGS 600 Query: 601 FMFLGPTGVGKTELVKSLARLLFDDENSMIRIDMSEYMEKHSVSRLIGSPPGYVGYEEGG 660 F+FLGPTGVGKTEL K+LA +FD +++M+RIDMSE+MEKHSVSRL+G+PPGYVGYEEGG Sbjct: 601 FLFLGPTGVGKTELCKALANFMFDSDDAMVRIDMSEFMEKHSVSRLVGAPPGYVGYEEGG 660 Query: 661 ALTEAVRRHPYQVVLFDEIEKAHSDVHNILLQVLDDGRLTDSQGRTVDFRNTLIIMTSNL 720 LTEAVRR PY V+L DE+EKAH DV NILLQVLDDGRLTD QGRTVDFRNT++IMTSNL Sbjct: 661 YLTEAVRRRPYSVILLDEVEKAHPDVFNILLQVLDDGRLTDGQGRTVDFRNTVVIMTSNL 720 Query: 721 GAEYLIE-----DGDSVHDKVMGIVRSAFKPEFLNRLDEIILFEKLRKEDMAKIVRIQLG 775 G++ + E D + + V+G+V F+PEF+NR+DE+++F L ++ +A I +IQL Sbjct: 721 GSDLIQERFGELDYAHMKELVLGVVSHNFRPEFINRIDEVVVFHPLGEQHIASIAQIQLQ 780 Query: 776 RVLSLIKERNISMDFDDQVIDWLSCRGYDPSYGARPLKRVIQRYIQNPLAERVLSQTISD 835 R+ ++ER + D+ + LS GYDP YGARPLKR IQ+ I+NPLA+++LS + Sbjct: 781 RLYKRLEERGYEIHISDEALKLLSENGYDPVYGARPLKRAIQQQIENPLAQQILSGELVP 840 Query: 836 GDSIEVFVDDDNL 848 G I + V+DD + Sbjct: 841 GKVIRLEVNDDRI 853 >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 = 737 bits (1904), Expect = 0.0 Identities = 331/868 (38%), Positives = 503/868 (57%), Gaps = 48/868 (5%) Query: 7 SDLMRNVLQSAQTYALAQGHQNLVPEHVLHIFLEDEQGAVYSLIQCSGGDIAQLKDYNQT 66 + R L+ A +A+GH + EH L L+ + ++++ G D+ +LK Sbjct: 2 NPTSRRALEQAAALCVARGHPEVELEHWLLALLDQPDSDLAAILRHFGVDLGRLKADLAR 61 Query: 67 VLSKIPKVTGGGAQVYLSQPLAVILSKSEEIAK-KSGDSFVTAEKFLLAMVMETGGIGES 125 L K+P G S L +L ++ +A + GD + + LLA++ + Sbjct: 62 ALDKLP--RGNTRTPVFSPHLVELLQEAWLLASLELGDGRIRSGHLLLALLTDPELRRLL 119 Query: 126 LKKCGLKFSRLE-ESIKKLRKGRVADSVNAEQ---------------GFDALKKYCRDLT 169 ++++ E++++ V S A G AL +Y DLT Sbjct: 120 GSISPE-LAKIDREALREALPALVEGSAEASAAAADAGPAAAAAGAAGTSALDQYTTDLT 178 Query: 170 EEARNGKLDPVIGRDDEMRRAIQVLSRRTKNNPVLIGDPGVGKTAIIEGLASRIINGDIP 229 +AR GK+DPV+GRDDE+R+ I +L RR +NNP+L G+ GVGKTA++EGLA RI GD+P Sbjct: 179 AQAREGKIDPVLGRDDEIRQMIDILLRRRQNNPILTGEAGVGKTAVVEGLALRIAAGDVP 238 Query: 230 ESLKGKRLMALDMGALIAGAKFRGEFEERLKSLLCEIRSEDGEIILFIDELHVLVGAGKT 289 +L+ RL++LD+G L AGA +GEFE RLKS++ E+++ IILFIDE H L+GAG Sbjct: 239 PALRNVRLLSLDLGLLQAGASVKGEFENRLKSVIDEVKASPQPIILFIDEAHTLIGAGGQ 298 Query: 290 DGAMDASNLLKPSLARGELHCIGATTLDEYRKYIEKDPALARRFQSLLVGEPTVTDTISI 349 G DA+NLLKP+LARGEL I ATT EY+KY EKDPAL RRFQ + V EP I + Sbjct: 299 AGQGDAANLLKPALARGELRTIAATTWAEYKKYFEKDPALTRRFQVVKVEEPDEETAIRM 358 Query: 350 LRGLKERYEQHHKVRISDSALVSAAVLSNRYITDRFLPDKAIDLMDEASARVRMQIDTKP 409 LRGL E+HH V I D A+V+A LS+RYI R LPDKA+ L+D A ARV + + P Sbjct: 359 LRGLAPVLEKHHGVLILDEAVVAAVELSHRYIPGRQLPDKAVSLLDTACARVALSQNATP 418 Query: 410 EVLDELDRRIICLKIEKEALKKE--KDSFSKGRLIELEKELSSLEEKSHSLTLRWQEGQR 467 L++L RRI L++E +AL++E + RL EL EL++LE + +L RWQ+ + Sbjct: 419 AALEDLRRRIAALELELDALEREAALGADHDERLAELRAELAALEAELAALEARWQQEK- 477 Query: 468 KILYVADLKKRLESMRNELAIAQRQGHFERAGELAYGLIPKTEKELDEAEKADSTAEDMV 527 +L + + ++R EL + + E L A E +V Sbjct: 478 ------ELVEAILALRAELEADADA--PADDDAALRAQLAELEAALASA----QGEEPLV 525 Query: 528 QEVVTSDNIANIVSRWTGIPVDKMLESDREKFLRIETEISKSVIGQSAAVESVSNALRRF 587 V + +A +V+ WTGIPV +M+ + E L + +++ VIGQ A+E+++ +R Sbjct: 526 FPEVDAQAVAEVVADWTGIPVGRMVRDEIEAVLSLPDRLAERVIGQDHALEAIAERIRTA 585 Query: 588 RAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLLFDDENSMIRIDMSEYMEKHSVSRLI 647 RAGL+DP++P+G F+ +GP+GVGKTE +LA LL+ E ++I I+MSE+ E H+VSRL Sbjct: 586 RAGLEDPRKPLGVFLLVGPSGVGKTETALALAELLYGGEQNLITINMSEFQEAHTVSRLK 645 Query: 648 GSPPGYVGYEEGGALTEAVRRHPYQVVLFDEIEKAHSDVHNILLQVLDDGRLTDSQGRTV 707 GSPPGYVGY EGG LTEAVRR PY VVL DE+EKAH DV + QV D G + D +GR + Sbjct: 646 GSPPGYVGYGEGGVLTEAVRRKPYSVVLLDEVEKAHPDVLELFYQVFDKGVMEDGEGREI 705 Query: 708 DFRNTLIIMTSNLGAEYLIE---------DGDSVHDKVMGIVRSAFKPEFLNRLDEIILF 758 DF+NT+I++TSN G++ ++ D +++ + + + FKP FL R+ +I + Sbjct: 706 DFKNTVILLTSNAGSDLIMALCADPETAPDPEALLEALRPELLKVFKPAFLGRM-TVIPY 764 Query: 759 EKLRKEDMAKIVRIQLGRVLSLIKER-NISMDFDDQVIDWLSCRGYDPSYGARPLKRVIQ 817 L + +A IVR++L R+ +KE + + + +++ + R + GAR + ++ Sbjct: 765 LPLDDDVLAAIVRLKLDRIARRLKENHGAELVYSEALVEHIVARCTEVESGARNIDAILN 824 Query: 818 RYIQNPLAERVLSQTISDGDSIE-VFVD 844 + + L+ ++L + ++ G+ IE + +D Sbjct: 825 QTLLPELSRQILER-LAAGEPIERIHLD 851 >gnl|CDD|162958 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit clpA. Length = 731 Score = 394 bits (1015), Expect = e-110 Identities = 193/463 (41%), Positives = 280/463 (60%), Gaps = 25/463 (5%) Query: 6 YSDLMRNVLQSAQTYALAQGHQNLVPEHVLHIFLEDEQGAVYSLIQCSGGDI----AQLK 61 S+ + +L +A A + H+ + EH+L L D +++ GGD+ L+ Sbjct: 1 ISEELERILDAALEEAKKRRHEFVTLEHILLALLFDSDAI--EILEECGGDVEALRKDLE 58 Query: 62 DYNQTVLSKIPKVTGGGAQVYLSQPLAVILSKSEEIAKKSGDSFVTAEKFLLAMVMETGG 121 DY + L I A + + +L ++ K +G + L+A+ E Sbjct: 59 DYLENNLPSIT--EENEADPEQTVGVQRVLQRALLHVKSAGKKEIGIGDILVALFDEEDS 116 Query: 122 IGE-SLKKCGLKFSRLEESI--------KKLRKGRVADSVNAEQGFDALKKYCRDLTEEA 172 LK G+ + E I K R A A++ DAL+KY DLTE+A Sbjct: 117 HASYFLKSQGITRLDILEYISHGIPKDDGKNRDAEEAGKEEAKKQEDALEKYTVDLTEKA 176 Query: 173 RNGKLDPVIGRDDEMRRAIQVLSRRTKNNPVLIGDPGVGKTAIIEGLASRIINGDIPESL 232 +NGK+DP+IGR+DE+ R IQVL RR KNNP+L+G+PGVGKTAI EGLA RI G +PE+L Sbjct: 177 KNGKIDPLIGREDELERTIQVLCRRKKNNPLLVGEPGVGKTAIAEGLALRIAEGKVPENL 236 Query: 233 KGKRLMALDMGALIAGAKFRGEFEERLKSLLCEIRSEDGEIILFIDELHVLVGAGKT-DG 291 K ++ +LDMG+L+AG K+RG+FEERLK+++ EI ++ ILFIDE+H +VGAG T G Sbjct: 237 KNAKIYSLDMGSLLAGTKYRGDFEERLKAVVSEI-EKEPNAILFIDEIHTIVGAGATSGG 295 Query: 292 AMDASNLLKPSLARGELHCIGATTLDEYRKYIEKDPALARRFQSLLVGEPTVTDTISILR 351 +MDASNLLKP+L+ G+L CIG+TT +EY+ + EKD AL+RRFQ + VGEP++ +T+ IL+ Sbjct: 296 SMDASNLLKPALSSGKLRCIGSTTYEEYKNHFEKDRALSRRFQKIDVGEPSIEETVKILK 355 Query: 352 GLKERYEQHHKVRISDSALVSAAVLSNRYITDRFLPDKAIDLMDEASARVRMQIDTKPEV 411 GLKE+YE+ H V+ SD AL +A LS RYI DRFLPDKAID++DEA A R++ K + Sbjct: 356 GLKEKYEEFHHVKYSDEALEAAVELSARYINDRFLPDKAIDVIDEAGASFRLRPKAKKKA 415 Query: 412 ---LDELDRRIICLKIEKEALKKEKDSFSKGRLIELEKELSSL 451 + +++ + K+ +K + +L LEK L + Sbjct: 416 NVSVKDIEN--VVAKMAHIPVKTVSVD-DREKLKNLEKNLKAK 455 Score = 353 bits (907), Expect = 1e-97 Identities = 149/316 (47%), Positives = 209/316 (66%), Gaps = 8/316 (2%) Query: 531 VTSDNIANIVSRWTGIPVDKMLESDREKFLRIETEISKSVIGQSAAVESVSNALRRFRAG 590 V+ +I N+V++ IPV + DREK +E + + GQ A++S+ ++++R RAG Sbjct: 417 VSVKDIENVVAKMAHIPVKTVSVDDREKLKNLEKNLKAKIFGQDEAIDSLVSSIKRSRAG 476 Query: 591 LQDPQRPMGSFMFLGPTGVGKTELVKSLARLLFDDENSMIRIDMSEYMEKHSVSRLIGSP 650 L +P +P+GSF+F GPTGVGKTEL K LA L + R DMSEYMEKH+VSRLIG+P Sbjct: 477 LGNPNKPVGSFLFTGPTGVGKTELAKQLAEAL---GVHLERFDMSEYMEKHTVSRLIGAP 533 Query: 651 PGYVGYEEGGALTEAVRRHPYQVVLFDEIEKAHSDVHNILLQVLDDGRLTDSQGRTVDFR 710 PGYVG+E+GG LTEAVR+HP+ V+L DEIEKAH D++NILLQV+D LTD+ GR DFR Sbjct: 534 PGYVGFEQGGLLTEAVRKHPHCVLLLDEIEKAHPDIYNILLQVMDYATLTDNNGRKADFR 593 Query: 711 NTLIIMTSNLGAEYLIED-----GDSVHDKVMGIVRSAFKPEFLNRLDEIILFEKLRKED 765 N ++IMTSN GA + + ++V K ++ F PEF NRLD II F L +E Sbjct: 594 NVILIMTSNAGASEMSKPPIGFGSENVESKSDKAIKKLFSPEFRNRLDAIIHFNPLSEEV 653 Query: 766 MAKIVRIQLGRVLSLIKERNISMDFDDQVIDWLSCRGYDPSYGARPLKRVIQRYIQNPLA 825 + KIV+ + + + E+NI ++ D +L+ +GYD +GARPL RVIQ I+ PL+ Sbjct: 654 LEKIVQKFVDELSKQLNEKNIKLELTDDAKKYLAEKGYDEEFGARPLARVIQEEIKKPLS 713 Query: 826 ERVLSQTISDGDSIEV 841 + +L + G S++V Sbjct: 714 DEILFGKLKKGGSVKV 729 >gnl|CDD|182917 PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit; Provisional. Length = 758 Score = 288 bits (738), Expect = 5e-78 Identities = 126/257 (49%), Positives = 182/257 (70%), Gaps = 4/257 (1%) Query: 150 DSVNAEQ--GFDALKKYCRDLTEEARNGKLDPVIGRDDEMRRAIQVLSRRTKNNPVLIGD 207 + EQ G + ++ + +L + AR G +DP+IGR+ E+ RAIQVL RR KNNP+L+G+ Sbjct: 156 QPNSEEQAGGEERMENFTTNLNQLARVGGIDPLIGREKELERAIQVLCRRRKNNPLLVGE 215 Query: 208 PGVGKTAIIEGLASRIINGDIPESLKGKRLMALDMGALIAGAKFRGEFEERLKSLLCEIR 267 GVGKTAI EGLA RI+ GD+PE + + +LD+G+L+AG K+RG+FE+R K+LL ++ Sbjct: 216 SGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKALLKQLE 275 Query: 268 SEDGEIILFIDELHVLVGAGKTDGA-MDASNLLKPSLARGELHCIGATTLDEYRKYIEKD 326 + ILFIDE+H ++GAG G +DA+NL+KP L+ G++ IG+TT E+ EKD Sbjct: 276 QDT-NSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSSGKIRVIGSTTYQEFSNIFEKD 334 Query: 327 PALARRFQSLLVGEPTVTDTISILRGLKERYEQHHKVRISDSALVSAAVLSNRYITDRFL 386 ALARRFQ + + EP++ +T+ I+ GLK +YE HH VR + A+ +A L+ +YI DR L Sbjct: 335 RALARRFQKIDITEPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAVELAVKYINDRHL 394 Query: 387 PDKAIDLMDEASARVRM 403 PDKAID++DEA AR R+ Sbjct: 395 PDKAIDVIDEAGARARL 411 Score = 287 bits (735), Expect = 1e-77 Identities = 136/330 (41%), Positives = 209/330 (63%), Gaps = 12/330 (3%) Query: 528 QEVVTSDNIANIVSRWTGIPVDKMLESDREKFLRIETEISKSVIGQSAAVESVSNALRRF 587 ++ V +I ++V+R IP + +SDR+ + + V GQ A+E+++ A++ Sbjct: 418 KKTVNVADIESVVARIARIPEKSVSQSDRDTLKNLGDRLKMLVFGQDKAIEALTEAIKMS 477 Query: 588 RAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLLFDDENSMIRIDMSEYMEKHSVSRLI 647 RAGL +P+GSF+F GPTGVGKTE+ L++ L ++R DMSEYME+H+VSRLI Sbjct: 478 RAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKAL---GIELLRFDMSEYMERHTVSRLI 534 Query: 648 GSPPGYVGYEEGGALTEAVRRHPYQVVLFDEIEKAHSDVHNILLQVLDDGRLTDSQGRTV 707 G+PPGYVG+++GG LT+AV +HP+ V+L DEIEKAH DV N+LLQV+D+G LTD+ GR Sbjct: 535 GAPPGYVGFDQGGLLTDAVIKHPHAVLLLDEIEKAHPDVFNLLLQVMDNGTLTDNNGRKA 594 Query: 708 DFRNTLIIMTSNLGAEY-------LIEDGDSVHDKVMGIVRSAFKPEFLNRLDEIILFEK 760 DFRN +++MT+N G LI D+ D M ++ F PEF NRLD II F+ Sbjct: 595 DFRNVVLVMTTNAGVRETERKSIGLIHQ-DNSTD-AMEEIKKIFTPEFRNRLDNIIWFDH 652 Query: 761 LRKEDMAKIVRIQLGRVLSLIKERNISMDFDDQVIDWLSCRGYDPSYGARPLKRVIQRYI 820 L + + ++V + + + + ++ +S++ + DWL+ +GYD + GARP+ RVIQ + Sbjct: 653 LSTDVIHQVVDKFIVELQAQLDQKGVSLEVSQEARDWLAEKGYDRAMGARPMARVIQDNL 712 Query: 821 QNPLAERVLSQTISDGDSIEVFVDDDNLNF 850 + PLA +L ++ DG + V +D + Sbjct: 713 KKPLANELLFGSLVDGGQVTVALDKEKNEL 742 >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 = 286 bits (734), Expect = 2e-77 Identities = 109/168 (64%), Positives = 128/168 (76%), Gaps = 8/168 (4%) Query: 596 RPMGSFMFLGPTGVGKTELVKSLARLLFDDENSMIRIDMSEYMEKHSVSRLIGSPPGYVG 655 RP+GSF+FLGPTGVGKTEL K+LA LLF DE ++IRIDMSEYME+HSVSRLIG+PPGYVG Sbjct: 1 RPIGSFLFLGPTGVGKTELAKALAELLFGDERALIRIDMSEYMEEHSVSRLIGAPPGYVG 60 Query: 656 YEEGGALTEAVRRHPYQVVLFDEIEKAHSDVHNILLQVLDDGRLTDSQGRTVDFRNTLII 715 YEEGG LTEAVRR PY +VL DEIEKAH V N LLQ+L+ G LTD QGR VDFRNTL I Sbjct: 61 YEEGGQLTEAVRRKPYSIVLIDEIEKAHPGVQNDLLQILEGGTLTDKQGRKVDFRNTLFI 120 Query: 716 MTSNLGAEYLIE--------DGDSVHDKVMGIVRSAFKPEFLNRLDEI 755 MT N G+E + + D + + + VM +++ F 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 = 108 bits (272), Expect = 7e-24 Identities = 42/87 (48%), Positives = 61/87 (70%) Query: 761 LRKEDMAKIVRIQLGRVLSLIKERNISMDFDDQVIDWLSCRGYDPSYGARPLKRVIQRYI 820 L KE++ +IV +QL R+ + ER I+++ D DWL+ +GYDP YGARPL+R IQR I Sbjct: 1 LSKEELRQIVDLQLKRLQKRLAERGITLELTDAAKDWLAEKGYDPEYGARPLRRAIQREI 60 Query: 821 QNPLAERVLSQTISDGDSIEVFVDDDN 847 ++PLAE +LS + +GD++ V VDD Sbjct: 61 EDPLAEEILSGELKEGDTVRVDVDDKL 87 >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 = 70.5 bits (172), Expect = 2e-12 Identities = 33/133 (24%), Positives = 53/133 (39%), Gaps = 7/133 (5%) Query: 597 PMGSFMFLGPTGVGKTELVKSLARLLFDDENSMIRIDMSEYMEKHSVSRLIGSPPGYVGY 656 P + +GP G GKT L ++LAR L +I ID + +E+ L+ G Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS 60 Query: 657 EEGGA----LTEAVRRHPYQVVLFDEIEKAHSDVHNILLQVLDDGRLTDSQGRTVDFRNT 712 G R+ V++ DEI LL +L++ RL +N Sbjct: 61 GSGELRLRLALALARKLKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLKS---EKNL 117 Query: 713 LIIMTSNLGAEYL 725 +I+T+N + Sbjct: 118 TVILTTNDEKDLG 130 Score = 41.2 bits (96), Expect = 0.001 Identities = 33/152 (21%), Positives = 56/152 (36%), Gaps = 20/152 (13%) Query: 198 TKNNPVLIGDPGVGKTAIIEGLASRI---------INGDIPESLKGKRLMALDMGALIAG 248 +++G PG GKT + LA + I+G+ ++ + ++ G Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILE----EVLDQLLLIIVGG 56 Query: 249 AKFRGEFEERLKSLLCEIRSEDGEIILFIDELHVLVGAGKTDGAMDA--SNLLKPSLARG 306 K G E RL+ L R +L +DE+ L+ A + + LL + Sbjct: 57 KKASGSGELRLRLALALARKLKP-DVLILDEITSLLDAEQEALLLLLEELRLLLLLKSEK 115 Query: 307 ELHCIGATTLDEYRKYIEKDPALARRFQSLLV 338 L I T ++ L RRF +V Sbjct: 116 NLTVILTTNDEK----DLGPALLRRRFDRRIV 143 >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 = 62.3 bits (152), Expect = 5e-10 Identities = 33/129 (25%), Positives = 54/129 (41%), Gaps = 16/129 (12%) Query: 600 SFMFLGPTGVGKTELVKSLARLLFDDENSMIRIDMSEYMEKHSVSRLIGS--PPGYVGYE 657 + +GP G GK+EL + LA L + ++ ++ + L G Sbjct: 1 GVLLVGPPGTGKSELAERLAAALSNRPVFYVQ--LTRDTTE---EDLKGRRNIANGTTSW 55 Query: 658 EGGALTEAVRRHPYQVVLFDEIEKAHSDVHNILLQVLDDGRLTDSQGRTVD-------FR 710 G L A R ++ + DEI +A+ DV N LL +LD+ RL +G + + Sbjct: 56 VDGPLVRAAREG--EIAVLDEINRANPDVLNSLLSLLDERRLLLPEGGELVKVAPDDFAK 113 Query: 711 NTLIIMTSN 719 +I T N Sbjct: 114 RFRLIATMN 122 Score = 30.7 bits (70), Expect = 1.5 Identities = 10/23 (43%), Positives = 16/23 (69%) Query: 203 VLIGDPGVGKTAIIEGLASRIIN 225 +L+G PG GK+ + E LA+ + N Sbjct: 3 LLVGPPGTGKSELAERLAAALSN 25 >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 = 44.8 bits (106), Expect = 9e-05 Identities = 35/94 (37%), Positives = 52/94 (55%), Gaps = 10/94 (10%) Query: 562 IETEISKSVIGQSAAVESVSNALR-RFR-----AGLQDPQRPMGSFMFLGPTGVGKTELV 615 I E+ K +IGQ A +SV+ ALR R+R L+D P M +GPTGVGKTE+ Sbjct: 6 IVAELDKYIIGQDNAKKSVAIALRNRYRRSQLNEELKDEVTPKNILM-IGPTGVGKTEIA 64 Query: 616 KSLARLLFDDENSMIRIDMSEYMEKHSVSRLIGS 649 + LA+L I+++ +++ E V R + S Sbjct: 65 RRLAKLA---NAPFIKVEATKFTEVGYVGRDVES 95 >gnl|CDD|179962 PRK05201, hslU, ATP-dependent protease ATP-binding subunit HslU; Provisional. Length = 443 Score = 42.4 bits (101), Expect = 6e-04 Identities = 28/63 (44%), Positives = 38/63 (60%), Gaps = 7/63 (11%) Query: 565 EISKSVIGQSAAVESVSNALR-RFR-----AGLQDPQRPMGSFMFLGPTGVGKTELVKSL 618 E+ K +IGQ A +V+ ALR R+R L+D P M +GPTGVGKTE+ + L Sbjct: 12 ELDKYIIGQDDAKRAVAIALRNRWRRMQLPEELRDEVTPKNILM-IGPTGVGKTEIARRL 70 Query: 619 ARL 621 A+L Sbjct: 71 AKL 73 >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 = 39.8 bits (93), Expect = 0.003 Identities = 55/195 (28%), Positives = 85/195 (43%), Gaps = 45/195 (23%) Query: 573 QSAAVESV-SNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLAR-------LLFD 624 ++ AV+ V S ALR ++G P+ GP G GKT L +AR L+ Sbjct: 3 ETDAVKRVTSRALRYLKSG-----YPV---HLRGPAGTGKTTLAMHVARKRDRPVMLING 54 Query: 625 DE---NSMIRIDMSEYMEKHSVSRLIGSPPGYVGYEE-------GGALTEAVRRHPYQVV 674 D S + + Y K + I + V E+ LT AV R + +V Sbjct: 55 DAELTTSDLVGSYAGYTRKKVHDQFIHN---VVKLEDIVRQNWVDNRLTLAV-REGFTLV 110 Query: 675 LFDEIEKAHSDVHNILLQVLDDGRL----TDSQGRTVD----FRNTLIIMTSNLGAEY-- 724 +DE ++ + +N+LL V ++G L R VD FR +I TSN EY Sbjct: 111 -YDEFTRSKPETNNVLLSVFEEGVLELPGKRGTSRYVDVHPEFR---VIFTSN-PVEYAG 165 Query: 725 LIEDGDSVHDKVMGI 739 + E D++ D+++ I Sbjct: 166 VHETQDALLDRLITI 180 >gnl|CDD|179675 PRK03918, PRK03918, chromosome segregation protein; Provisional. Length = 880 Score = 39.7 bits (93), Expect = 0.003 Identities = 38/136 (27%), Positives = 64/136 (47%), Gaps = 16/136 (11%) Query: 410 EVLDELDRRIICLKIEKEA---LKKEKDSFSKGRLIELEKELSSLEEKSHSLTLRWQEGQ 466 E L+E + + LK + E L + + + L E+EK LS LEE+ + + R +E + Sbjct: 276 EELEEKVKELKELKEKAEEYIKLSEFYEEYLD-ELREIEKRLSRLEEEINGIEERIKELE 334 Query: 467 RKILYVADLKKRLESMRNELA-IAQRQGHFERA-----------GELAYGLIPKTEKELD 514 K + +LKK+L+ + L + +R +E A L K EKEL+ Sbjct: 335 EKEERLEELKKKLKELEKRLEELEERHELYEEAKAKKEELERLKKRLTGLTPEKLEKELE 394 Query: 515 EAEKADSTAEDMVQEV 530 E EKA E+ + ++ Sbjct: 395 ELEKAKEEIEEEISKI 410 Score = 32.0 bits (73), Expect = 0.64 Identities = 48/222 (21%), Positives = 85/222 (38%), Gaps = 45/222 (20%) Query: 388 DKAIDLMDEASARVRMQIDTKPEVLDELDRRIICLKIEKEALKKEKDSFS--KGRLIELE 445 ++ I ++ V +I+ L EL + L+ E + L++ K+ + L LE Sbjct: 192 EELIKEKEKELEEVLREINEISSELPELREELEKLEKEVKELEELKEEIEELEKELESLE 251 Query: 446 KELSSLEEKSHSLTLRWQEGQRKI------------------LYVA-------------D 474 LEEK L R +E +++I Y+ + Sbjct: 252 GSKRKLEEKIRELEERIEELKKEIEELEEKVKELKELKEKAEEYIKLSEFYEEYLDELRE 311 Query: 475 LKKRLESMRNELAIAQRQ-----GHFERAGELAYGLIPKTEKELDEAEKADSTAEDMVQE 529 ++KRL + E+ + + ER EL + + EK L+E E+ E+ + Sbjct: 312 IEKRLSRLEEEINGIEERIKELEEKEERLEELK-KKLKELEKRLEELEERHELYEEAKAK 370 Query: 530 VVTSDNIANIVSRWTGIPVDK---MLESDREKFLRIETEISK 568 + + + R TG+ +K LE + IE EISK Sbjct: 371 K---EELERLKKRLTGLTPEKLEKELEELEKAKEEIEEEISK 409 Score = 28.9 bits (65), Expect = 6.3 Identities = 26/128 (20%), Positives = 58/128 (45%), Gaps = 18/128 (14%) Query: 410 EVLDELDRRIICLK--IEKEALKKEKDSFSKGRLIELEKELSSLEEKSHSLTLRWQEGQR 467 EV+ E+ RRI L+ I++ +E + L E+ +E++ + + L + Sbjct: 169 EVIKEIKRRIERLEKFIKRTENIEELIKEKEKELEEVLREINEISSELPEL-------RE 221 Query: 468 KILYVADLKKRLESMRNELAIAQRQ-----GHFERAGELAYGLIPKTEKELDEAEKADST 522 ++ + K LE ++ E+ +++ G + E I + E+ ++E +K Sbjct: 222 ELEKLEKEVKELEELKEEIEELEKELESLEGSKRKLEE----KIRELEERIEELKKEIEE 277 Query: 523 AEDMVQEV 530 E+ V+E+ Sbjct: 278 LEEKVKEL 285 >gnl|CDD|162545 TIGR01818, ntrC, nitrogen regulation protein NR(I). This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc. Length = 463 Score = 39.0 bits (91), Expect = 0.005 Identities = 64/231 (27%), Positives = 94/231 (40%), Gaps = 62/231 (26%) Query: 563 ETEISKSVIGQSAAVESVSNALRRF-RAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARL 621 E E S +IG++ A++ V A+ R R+ + + + G +G GK ELV AR Sbjct: 129 EAEDSAELIGEAPAMQEVFRAIGRLSRSDI--------TVLINGESGTGK-ELV---ARA 176 Query: 622 LFDD----ENSMIRIDMS----EYMEKHSVSRLIGSPPGYVGYEEGGALTEAVRRHPYQV 673 L I ++M+ + +E S L G E GA T A R + Sbjct: 177 LHRHSPRANGPFIALNMAAIPKDLIE----SELFG--------HEKGAFTGANTRRQGRF 224 Query: 674 ------VLF-DEIEKAHSDVHNILLQVLDDGRLTDSQGRT---VDFRNTLIIMTSNLGAE 723 LF DEI D LL+VL DG GRT VD R I+ ++ E Sbjct: 225 EQADGGTLFLDEIGDMPLDAQTRLLRVLADGEFYRVGGRTPIKVDVR---IVAATHQNLE 281 Query: 724 YLIEDGDSVHDKVMGIVRSAFKPEFLNRLDEI-ILFEKL--RKEDMAKIVR 771 L+ G F+ + +RL+ I I L R+ED+ ++ R Sbjct: 282 ALVRQG-------------KFREDLFHRLNVIRIHLPPLRERREDIPRLAR 319 >gnl|CDD|178741 PLN03200, PLN03200, cellulose synthase-interactive protein; Provisional. Length = 2102 Score = 38.5 bits (90), Expect = 0.007 Identities = 17/42 (40%), Positives = 25/42 (59%) Query: 189 RAIQVLSRRTKNNPVLIGDPGVGKTAIIEGLASRIINGDIPE 230 +AI++LSR ++ PV++GD + I LA RIIN E Sbjct: 850 KAIEILSRLCRDQPVVLGDLIANASKCISSLADRIINSSSLE 891 >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 = 38.3 bits (89), Expect = 0.007 Identities = 74/284 (26%), Positives = 117/284 (41%), Gaps = 62/284 (21%) Query: 203 VLIGDPGVGKTAIIEGLASRIINGDIPESLKGKRLMALDMGALIAGAKFRGEFEERLKSL 262 +L G PG GKT + + +A+ G S+ G +M +K+ GE EERL+ + Sbjct: 216 LLYGPPGTGKTLLAKAVANEA--GAYFISINGPEIM----------SKYYGESEERLREI 263 Query: 263 LCEIRSEDGEIILFIDELHVLV-----GAGKTDGAMDAS--NLLKPSLARGELHCIGATT 315 E E+ I+FIDE+ + G+ + + A L+ RG + IGAT Sbjct: 264 FKEAE-ENAPSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVIVIGATN 322 Query: 316 LDEYRKYIEKDPALAR--RF-QSLLVGEPTVTDTISILR------------GLKERYEQH 360 + DPAL R RF + +++ P IL+ L + E Sbjct: 323 RPD-----ALDPALRRPGRFDREIVIRVPDKRARKEILKVHTRNMPLAEDVDLDKLAEVT 377 Query: 361 HKVRISDSALVS--AAVLSNRYITDRFLPDKAIDLMDEASARVRMQIDTKPEVLDELDRR 418 H +D A ++ AA+ + R RF+ + I+ E EVL EL Sbjct: 378 HGFVGADLAALAKEAAMAALR----RFIREGKINFEAEEIPA---------EVLKELK-- 422 Query: 419 IICLKIEKEALKKEKDSFSKGRLIELEK----ELSSLEEKSHSL 458 + +K EALK + S + L+E+ ++ LEE L Sbjct: 423 -VTMKDFMEALKMVEPSAIREVLVEVPNVRWSDIGGLEEVKQEL 465 >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 = 38.3 bits (90), Expect = 0.008 Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 12/55 (21%) Query: 568 KSVIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622 + VIGQ V+++ NA++ R +++F GP G GKT S+AR+ Sbjct: 14 EDVIGQEHIVQTLKNAIKN--------GRIAHAYLFSGPRGTGKT----SIARIF 56 >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 = 38.0 bits (89), Expect = 0.010 Identities = 32/100 (32%), Positives = 46/100 (46%), Gaps = 15/100 (15%) Query: 603 FLGPTGVGKTELVKSLARLLFDDENSMIRIDMSEYMEKHSVSRLIGSPPGYVGYEEG--- 659 +GP GVGKT L KS+A+ L +R + + + G YVG G Sbjct: 352 LVGPPGVGKTSLGKSIAKAL---NRKFVRFSLGGV---RDEAEIRGHRRTYVGAMPGRII 405 Query: 660 GALTEAVRRHPYQVVLFDEIEKAHSDVH----NILLQVLD 695 L +A ++P + L DEI+K S + LL+VLD Sbjct: 406 QGLKKAKTKNP--LFLLDEIDKIGSSFRGDPASALLEVLD 443 >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 = 37.8 bits (88), Expect = 0.012 Identities = 72/316 (22%), Positives = 125/316 (39%), Gaps = 84/316 (26%) Query: 570 VIGQSAAVESVSNA-------LRRFRAGLQDPQRPMG--SFMFLGPTGVGKTELVKSLAR 620 VIGQ A + +S A L + D + + + +GPTG GKT L ++LAR Sbjct: 79 VIGQEQAKKVLSVAVYNHYKRLNFEKNKKSDNGVELSKSNILLIGPTGSGKTLLAQTLAR 138 Query: 621 LLFDDENSMIRI-DMSEYMEKHSVSRLIGSPPGYVGYEEGGALTEAVRRHPYQV------ 673 +L N I D + E GYVG + L + ++ Y V Sbjct: 139 IL----NVPFAIADATTLTEA-----------GYVGEDVENILLKLLQAADYDVEKAQKG 183 Query: 674 -VLFDEIEK--------------AHSDVHNILLQVLDDGRLTD---SQGRTVDFRNTLII 715 + DEI+K + V LL+++ +G + + GR ++ + I Sbjct: 184 IIYIDEIDKISRKSENPSITRDVSGEGVQQALLKII-EGTVANVPPQGGRKHPYQEFIQI 242 Query: 716 MTSNL---------GAEYLI--------------------EDGDSVHDKVM-GIVRSAFK 745 TSN+ G E +I E D + +V+ Sbjct: 243 DTSNILFICGGAFVGLEKIIKKRTGKSSIGFGAEVKKKSKEKADLLRQVEPEDLVKFGLI 302 Query: 746 PEFLNRLDEIILFEKLRKEDMAKIVRIQLGRVL----SLIKERNISMDFDDQVIDWLSCR 801 PEF+ RL I EKL +E + I+ ++ +L K N+ +DF+++ + ++ + Sbjct: 303 PEFIGRLPVIATLEKLDEEALIAILTKPKNALVKQYQALFKMDNVELDFEEEALKAIAKK 362 Query: 802 GYDPSYGARPLKRVIQ 817 + GAR L+ +++ Sbjct: 363 ALERKTGARGLRSIVE 378 >gnl|CDD|184934 PRK14970, PRK14970, DNA polymerase III subunits gamma and tau; Provisional. Length = 367 Score = 37.5 bits (87), Expect = 0.013 Identities = 33/137 (24%), Positives = 57/137 (41%), Gaps = 27/137 (19%) Query: 568 KSVIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL----F 623 V+GQS ++ NA+ + +F GP GVGKT + LAR + + Sbjct: 17 DDVVGQSHITNTLLNAIEN--------NHLAQALLFCGPRGVGKTTCARILARKINQPGY 68 Query: 624 DDENSMIRIDMSEYMEKHSVSRLIGSPPGYVGYEEGGALTEAVRRHP----YQVVLFDEI 679 DD N ++ E ++ S + ++ L + VR P Y++ + DE+ Sbjct: 69 DDPNEDFSFNIFE-LDAASNN----------SVDDIRNLIDQVRIPPQTGKYKIYIIDEV 117 Query: 680 EKAHSDVHNILLQVLDD 696 S N L+ L++ Sbjct: 118 HMLSSAAFNAFLKTLEE 134 >gnl|CDD|183985 PRK13341, PRK13341, recombination factor protein RarA/unknown domain fusion protein; Reviewed. Length = 725 Score = 37.3 bits (87), Expect = 0.015 Identities = 51/167 (30%), Positives = 70/167 (41%), Gaps = 40/167 (23%) Query: 178 DPVIGRDDEMRRAIQV--LSRRTKNNPVLIGDPGVGKTAIIEGLASRIINGDIPESLKGK 235 D ++G +RRAI+ + + +L G PGVGKT LA I N Sbjct: 34 DHILGEGRLLRRAIKADRVG-----SLILYGPPGVGKTT----LARIIANH--------T 76 Query: 236 RLMALDMGALIAGAK-FRGEFEERLKSLLCEIRSEDGEIILFIDELHVLVGAGKTDGAMD 294 R + A++AG K R E + + L ILFIDE+H A + D Sbjct: 77 RAHFSSLNAVLAGVKDLRAEVDRAKERL----ERHGKRTILFIDEVHRFNKAQQ-----D 127 Query: 295 ASNLLKPSLARGELHCIGATTLDEYRKYIEKDPALARR-----FQSL 336 A L P + G + IGATT + Y E + AL R +SL Sbjct: 128 A---LLPWVENGTITLIGATTEN---PYFEVNKALVSRSRLFRLKSL 168 Score = 30.0 bits (68), Expect = 2.9 Identities = 12/25 (48%), Positives = 17/25 (68%), Gaps = 4/25 (16%) Query: 598 MGSFMFLGPTGVGKTELVKSLARLL 622 +GS + GP GVGKT +LAR++ Sbjct: 52 VGSLILYGPPGVGKT----TLARII 72 >gnl|CDD|184920 PRK14956, PRK14956, DNA polymerase III subunits gamma and tau; Provisional. Length = 484 Score = 36.5 bits (84), Expect = 0.028 Identities = 20/72 (27%), Positives = 35/72 (48%), Gaps = 8/72 (11%) Query: 551 MLESDREKFLRIETEISKSVIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVG 610 M + + + + VI Q A+ ++ NAL+ + G +++F GP GVG Sbjct: 1 MSGTHEVLSRKYRPQFFRDVIHQDLAIGALQNALKSGKIG--------HAYIFFGPRGVG 52 Query: 611 KTELVKSLARLL 622 KT + + LA+ L Sbjct: 53 KTTIARILAKRL 64 >gnl|CDD|165554 PHA03297, PHA03297, envelope glycoprotein L; Provisional. Length = 185 Score = 36.2 bits (83), Expect = 0.036 Identities = 15/32 (46%), Positives = 21/32 (65%) Query: 210 VGKTAIIEGLASRIINGDIPESLKGKRLMALD 241 V A+I+GLA + NG++P+ K K L ALD Sbjct: 98 VNPFAVIQGLAEDVTNGNMPQDFKEKLLFALD 129 >gnl|CDD|162740 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type. SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. Length = 1164 Score = 36.2 bits (84), Expect = 0.040 Identities = 34/184 (18%), Positives = 78/184 (42%), Gaps = 23/184 (12%) Query: 394 MDEASARVRMQIDTKPEVLDELDRRIICLKIEKEALKKEKDSFSKGRLIELEKELSSLEE 453 +E A++ +ID ++EL+R I + ++ L +E K L +L EL +++ Sbjct: 320 AEERLAKLEAEIDKLLAEIEELEREIEEERKRRDKLTEEYAE-LKEELEDLRAELEEVDK 378 Query: 454 KSHSLTLRWQEGQRKILYVADLKKRLESMRNELA--------IAQRQGHFERAGELAYGL 505 + ++ + K+ LK+ + ++ EL +++ A Sbjct: 379 EFAETRDELKDYREKL---EKLKREINELKRELDRLQEELQRLSEELADLNAAIAGIEAK 435 Query: 506 IPKTEKELDEAEKADSTAEDMVQEVVTSDNIANIVSRWTGIPVDKMLESDREKFLRIETE 565 I + E+E ++ E +++ +A +S+ ++ L +E++ R+E E Sbjct: 436 INELEEEKEDKALEIKKQEWKLEQ------LAADLSK-----YEQELYDLKEEYDRVEKE 484 Query: 566 ISKS 569 +SK Sbjct: 485 LSKL 488 Score = 31.6 bits (72), Expect = 0.79 Identities = 33/134 (24%), Positives = 64/134 (47%), Gaps = 8/134 (5%) Query: 391 IDLMDEASARVRMQIDTKPEVLDELDRRIICLKIEKEALKKEKDSFSKGRLIELEKELSS 450 + +++ V+ ++ ++EL+ + L+ EAL + S R+ E++ ELS Sbjct: 746 LSSLEQEIENVKSELKELEARIEELEEDLHKLE---EALNDLEARLSHSRIPEIQAELSK 802 Query: 451 LEEKSHSLTLRWQEGQRKILYVADLKKRLESMRNEL-----AIAQRQGHFERAGELAYGL 505 LEE+ + R +E ++K+ + K+ LE EL + ++ E+ E G Sbjct: 803 LEEEVSRIEARLREIEQKLNRLTLEKEYLEKEIQELQEQRIDLKEQIKSIEKEIENLNGK 862 Query: 506 IPKTEKELDEAEKA 519 + E+EL+E E A Sbjct: 863 KEELEEELEELEAA 876 Score = 31.2 bits (71), Expect = 1.3 Identities = 30/145 (20%), Positives = 59/145 (40%), Gaps = 23/145 (15%) Query: 409 PEVLDELDRRIICLKIEKEALKKEKDSF-------------SKGRLIELEKELSSLEEKS 455 P L L R+ LK E +L+ E + ++ E+EKE+ LE++ Sbjct: 673 PAELQRLRERLEGLKRELSSLQSELRRIENRLDELSQELSDASRKIGEIEKEIEQLEQEE 732 Query: 456 HSLTLRWQEGQRKILY----VADLKKRLESMRNELAIAQRQGHFERA------GELAYGL 505 L R +E + + + ++K L+ + + + H L++ Sbjct: 733 EKLKERLEELEEDLSSLEQEIENVKSELKELEARIEELEEDLHKLEEALNDLEARLSHSR 792 Query: 506 IPKTEKELDEAEKADSTAEDMVQEV 530 IP+ + EL + E+ S E ++E+ Sbjct: 793 IPEIQAELSKLEEEVSRIEARLREI 817 >gnl|CDD|180213 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated. Length = 424 Score = 35.6 bits (83), Expect = 0.053 Identities = 12/41 (29%), Positives = 18/41 (43%), Gaps = 1/41 (2%) Query: 573 QSAAVESVSNALRRF-RAGLQDPQRPMGSFMFLGPTGVGKT 612 + A + L ++D + G +GPTGVGKT Sbjct: 195 ERTAWRYLLELLANMIPVRVEDILKQGGVVALVGPTGVGKT 235 >gnl|CDD|180029 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX; Provisional. Length = 412 Score = 35.5 bits (83), Expect = 0.056 Identities = 12/19 (63%), Positives = 16/19 (84%) Query: 604 LGPTGVGKTELVKSLARLL 622 +GPTG GKT L ++LAR+L Sbjct: 114 IGPTGSGKTLLAQTLARIL 132 >gnl|CDD|178596 PLN03025, PLN03025, replication factor C subunit; Provisional. Length = 319 Score = 35.5 bits (82), Expect = 0.058 Identities = 24/53 (45%), Positives = 32/53 (60%), Gaps = 4/53 (7%) Query: 170 EEARNGKLDPVIGRDDEMRRAIQVLSRRTKNNPVLI--GDPGVGKTAIIEGLA 220 E+ R KLD ++G +D + R +QV++R N P LI G PG GKT I LA Sbjct: 5 EKYRPTKLDDIVGNEDAVSR-LQVIAR-DGNMPNLILSGPPGTGKTTSILALA 55 >gnl|CDD|184917 PRK14953, PRK14953, DNA polymerase III subunits gamma and tau; Provisional. Length = 486 Score = 35.2 bits (81), Expect = 0.067 Identities = 20/55 (36%), Positives = 30/55 (54%), Gaps = 8/55 (14%) Query: 568 KSVIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622 K VIGQ V + NA++ QR +++F GP G GKT + + LA++L Sbjct: 16 KEVIGQEIVVRILKNAVKL--------QRVSHAYIFAGPRGTGKTTIARILAKVL 62 >gnl|CDD|183088 PRK11331, PRK11331, 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional. Length = 459 Score = 35.1 bits (80), Expect = 0.074 Identities = 26/86 (30%), Positives = 43/86 (50%), Gaps = 8/86 (9%) Query: 605 GPTGVGKTELVKSLARLLFDDENSMIRIDMSEYMEKHSVSRLI-GSPPGYVGYEEGGAL- 662 GP GVGKT + + LA LL E + R++M ++ + +S I G P VG+ + Sbjct: 201 GPPGVGKTFVARRLAYLL-TGEKAPQRVNMVQFHQSYSYEDFIQGYRPNGVGFRRKDGIF 259 Query: 663 ---TEAVRRHPYQVVLF--DEIEKAH 683 + + P + +F DEI +A+ Sbjct: 260 YNFCQQAKEQPEKKYVFIIDEINRAN 285 >gnl|CDD|149505 pfam08477, Miro, Miro-like protein. Mitochondrial Rho proteins (Miro-1 and Miro-2), are atypical Rho GTPases. They have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains (pfam00036), that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis. Length = 118 Score = 35.1 bits (81), Expect = 0.079 Identities = 17/78 (21%), Positives = 34/78 (43%), Gaps = 4/78 (5%) Query: 203 VLIGDPGVGKTAIIEGLASRIINGDIPESLKGKRLMALDMGALIAGAKFR----GEFEER 258 V+IGD G GK++++ L +IPE ++G L + G EE Sbjct: 3 VVIGDKGSGKSSLLSQLVGGEFPPEIPEEIQGDTLAVDTLEVDGDTELLHIWDFGGREEL 62 Query: 259 LKSLLCEIRSEDGEIILF 276 + +++ D ++++ Sbjct: 63 KFEHIIFMKTADAILLVY 80 >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 = 34.8 bits (80), Expect = 0.088 Identities = 21/57 (36%), Positives = 31/57 (54%), Gaps = 11/57 (19%) Query: 570 VIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLLFDDE 626 VIGQ AVE + A ++ R + + +G GVGK+ L K++A LL D+E Sbjct: 20 VIGQEEAVEIIKKAAKQKR-----------NVLLIGEPGVGKSMLAKAMAELLPDEE 65 Score = 33.3 bits (76), Expect = 0.31 Identities = 16/46 (34%), Positives = 31/46 (67%), Gaps = 6/46 (13%) Query: 177 LDPVIGRDDEMRRAIQVLSRRTKN--NPVLIGDPGVGKTAIIEGLA 220 +D VIG+++ A++++ + K N +LIG+PGVGK+ + + +A Sbjct: 17 IDQVIGQEE----AVEIIKKAAKQKRNVLLIGEPGVGKSMLAKAMA 58 >gnl|CDD|184922 PRK14958, PRK14958, DNA polymerase III subunits gamma and tau; Provisional. Length = 509 Score = 34.7 bits (79), Expect = 0.089 Identities = 21/55 (38%), Positives = 31/55 (56%), Gaps = 8/55 (14%) Query: 568 KSVIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622 + VIGQ+ V ++SNAL D Q +++F G GVGKT + + LA+ L Sbjct: 16 QEVIGQAPVVRALSNAL--------DQQYLHHAYLFTGTRGVGKTTISRILAKCL 62 >gnl|CDD|184935 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau; Provisional. Length = 614 Score = 34.0 bits (78), Expect = 0.16 Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 8/52 (15%) Query: 569 SVIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLAR 620 SV+GQ A ++ NA+ + +++F GP GVGKT + A+ Sbjct: 18 SVVGQEALTTTLKNAIAT--------NKLAHAYLFCGPRGVGKTTCARIFAK 61 >gnl|CDD|162739 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type. SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. Length = 1179 Score = 33.9 bits (78), Expect = 0.17 Identities = 31/154 (20%), Positives = 60/154 (38%), Gaps = 25/154 (16%) Query: 395 DEASARVRMQIDTKPEVLDELDRRIICLKIEKEALKKEKDSF------------------ 436 E A + Q++ L+EL+ ++ L E L+++ + Sbjct: 308 RERLANLERQLEELEAQLEELESKLDELAEELAELEEKLEELKEELESLEAELEELEAEL 367 Query: 437 --SKGRLIELEKELSSLEEKSHSLTLRWQEGQRKILYVADLKKRLESMRNELAIAQRQGH 494 + RL ELE++L +L K L L+ +I + +RLE R L + + Sbjct: 368 EELESRLEELEEQLETLRSKVAQLELQIASLNNEIERLEARLERLEDRRERL-QQEIEEL 426 Query: 495 FERAGELAY----GLIPKTEKELDEAEKADSTAE 524 ++ E + + E+EL+E ++ E Sbjct: 427 LKKLEEAELKELQAELEELEEELEELQEELERLE 460 Score = 31.2 bits (71), Expect = 1.1 Identities = 29/123 (23%), Positives = 54/123 (43%), Gaps = 9/123 (7%) Query: 412 LDELDRRIICLKIEKEALKKEKDSFSKGRLIELEKELSSLEEKSHSLTLRWQEGQRKILY 471 L+EL + + E E L E + +L EL E+S LEE+ L +I Sbjct: 241 LEELQEELKEAEEELEELTAELQE-LEEKLEELRLEVSELEEEIEELQKELYALANEI-- 297 Query: 472 VADLKKRLESMRNELAIAQRQGHFERAGELAYGLIPKTEKELDEAEKADSTAE-DMVQEV 530 + L+++ + +R LA +RQ E L +++ + E A+ + + ++E Sbjct: 298 -SRLEQQKQILRERLANLERQ--LEELEAQLEEL--ESKLDELAEELAELEEKLEELKEE 352 Query: 531 VTS 533 + S Sbjct: 353 LES 355 >gnl|CDD|184914 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau; Provisional. Length = 585 Score = 34.0 bits (78), Expect = 0.18 Identities = 18/53 (33%), Positives = 28/53 (52%), Gaps = 12/53 (22%) Query: 570 VIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622 ++GQ V+++ NA+ R +++F GP GVGKT S AR+L Sbjct: 18 LVGQEHVVQTLRNAIAEGRVA--------HAYLFTGPRGVGKT----STARIL 58 >gnl|CDD|184915 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional. Length = 618 Score = 33.2 bits (76), Expect = 0.26 Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 8/52 (15%) Query: 571 IGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622 +GQ V++++NAL + QR +++F G GVGKT + + LA+ L Sbjct: 19 VGQEHVVQALTNALTQ--------QRLHHAYLFTGTRGVGKTTVSRILAKSL 62 >gnl|CDD|183503 PRK12402, PRK12402, replication factor C small subunit 2; Reviewed. Length = 337 Score = 33.4 bits (77), Expect = 0.27 Identities = 16/55 (29%), Positives = 30/55 (54%) Query: 169 TEEARNGKLDPVIGRDDEMRRAIQVLSRRTKNNPVLIGDPGVGKTAIIEGLASRI 223 TE+ R L+ ++G+D+ + R + + + ++ G PG GKTA + LA + Sbjct: 6 TEKYRPALLEDILGQDEVVERLSRAVDSPNLPHLLVQGPPGSGKTAAVRALAREL 60 Score = 31.5 bits (72), Expect = 0.97 Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 11/72 (15%) Query: 570 VIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLLFDD--EN 627 ++GQ VE L R + P P + GP G GKT V++LAR L+ D EN Sbjct: 17 ILGQDEVVER----LSRA---VDSPNLP--HLLVQGPPGSGKTAAVRALARELYGDPWEN 67 Query: 628 SMIRIDMSEYME 639 + +++++ + Sbjct: 68 NFTEFNVADFFD 79 >gnl|CDD|182809 PRK10884, PRK10884, SH3 domain-containing protein; Provisional. Length = 206 Score = 33.1 bits (76), Expect = 0.28 Identities = 15/61 (24%), Positives = 34/61 (55%), Gaps = 8/61 (13%) Query: 440 RLIELEKELSSLEEK----SHSLTLRWQEGQRKIL----YVADLKKRLESMRNELAIAQR 491 R+ +LE ++ +L +K ++ R E Q+K+ + LK+ + ++N+L +AQ+ Sbjct: 94 RVPDLENQVKTLTDKLNNIDNTWNQRTAEMQQKVAQSDSVINGLKEENQKLKNQLIVAQK 153 Query: 492 Q 492 + Sbjct: 154 K 154 >gnl|CDD|184913 PRK14949, PRK14949, DNA polymerase III subunits gamma and tau; Provisional. Length = 944 Score = 32.4 bits (74), Expect = 0.44 Identities = 20/51 (39%), Positives = 29/51 (56%), Gaps = 12/51 (23%) Query: 571 IGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARL 621 +GQS + +++NAL + QR +++F G GVGKT SLARL Sbjct: 19 VGQSHVLHALTNALTQ--------QRLHHAYLFTGTRGVGKT----SLARL 57 >gnl|CDD|183438 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau; Provisional. Length = 700 Score = 32.5 bits (74), Expect = 0.45 Identities = 18/54 (33%), Positives = 31/54 (57%), Gaps = 8/54 (14%) Query: 569 SVIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622 +++GQ V ++++AL + QR +++F G GVGKT L + LA+ L Sbjct: 17 TLVGQEHVVRALTHAL--------EQQRLHHAYLFTGTRGVGKTTLSRILAKSL 62 >gnl|CDD|163452 TIGR03740, galliderm_ABC, gallidermin-class lantibiotic protection ABC transporter, ATP-binding subunit. Model TIGR03731 represents the family of all lantibiotics related to gallidermin, including epidermin, mutatin, and nisin. This protein family describes the ATP-binding subunit of a gallidermin/epidermin class lantibiotic protection transporter. It is largely restricted to gallidermin-family lantibiotic biosynthesis and export cassettes, but also occurs in orphan transporter cassettes in species that lack candidate lantibiotic precursor and synthetase genes. Length = 223 Score = 32.4 bits (74), Expect = 0.53 Identities = 25/94 (26%), Positives = 39/94 (41%), Gaps = 14/94 (14%) Query: 562 IETEISKSVIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARL 621 +ET+ G+ AV ++S + + + LGP G GK+ L+K + + Sbjct: 1 LETKNLSKRFGKQTAVNNISLTVPKNSV-----------YGLLGPNGAGKSTLLKMITGI 49 Query: 622 LFDDENSMIRIDMSEYMEK--HSVSRLIGSPPGY 653 L I D + K H + LI SPP Y Sbjct: 50 LRPTSGE-IIFDGHPWTRKDLHKIGSLIESPPLY 82 >gnl|CDD|163576 TIGR03864, PQQ_ABC_ATP, ABC transporter, ATP-binding subunit, PQQ-dependent alcohol dehydrogenase system. Members of this protein family are the ATP-binding subunit of an ABC transporter system that is associated with PQQ biosynthesis and PQQ-dependent alcohol dehydrogenases. While this family shows homology to several efflux ABC transporter subunits, the presence of a periplasmic substrate-binding protein and association with systems for catabolism of alcohols suggests a role in import rather than detoxification. Length = 236 Score = 32.3 bits (74), Expect = 0.55 Identities = 18/62 (29%), Positives = 26/62 (41%), Gaps = 14/62 (22%) Query: 572 GQSAAVESVSNALRRFRAGLQDPQRPMGSFM-FLGPTGVGKTELVKSLARLLFDDENSMI 630 G A++ VS +R G F+ LGP G GK+ L L R L+ + I Sbjct: 12 GARRALDDVSFTVRP------------GEFVALLGPNGAGKSTLFSLLTR-LYVAQEGQI 58 Query: 631 RI 632 + Sbjct: 59 SV 60 >gnl|CDD|184312 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional. Length = 637 Score = 32.3 bits (74), Expect = 0.56 Identities = 19/53 (35%), Positives = 26/53 (49%), Gaps = 11/53 (20%) Query: 570 VIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622 VIGQ AVE + A ++ R M +G G GK+ L K++A LL Sbjct: 33 VIGQEHAVEVIKKAAKQRR-----------HVMMIGSPGTGKSMLAKAMAELL 74 >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 = 32.1 bits (73), Expect = 0.57 Identities = 45/151 (29%), Positives = 64/151 (42%), Gaps = 36/151 (23%) Query: 568 KSVIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKT-------ELVKSLAR 620 +IGQ ++++ AL G +PQ + GP GVGKT E K Sbjct: 65 DEIIGQEEGIKALKAAL----CG-PNPQH----VIIYGPPGVGKTAAARLVLEEAKKNPA 115 Query: 621 LLFDDENSMIRIDMS--EYMEKHSVSRLIGS----------PPGYVGYEE--GGALTEAV 666 F + + + ID + + E+ LIGS P G G + GA+T A Sbjct: 116 SPFKEGAAFVEIDATTARFDERGIADPLIGSVHDPIYQGAGPLGIAGIPQPKPGAVTRA- 174 Query: 667 RRHPYQVVLF-DEIEKAHSDVHNILLQVLDD 696 + VLF DEI + H N LL+VL+D Sbjct: 175 ----HGGVLFIDEIGELHPVQMNKLLKVLED 201 Score = 30.9 bits (70), Expect = 1.5 Identities = 15/47 (31%), Positives = 26/47 (55%) Query: 168 LTEEARNGKLDPVIGRDDEMRRAIQVLSRRTKNNPVLIGDPGVGKTA 214 L+E+ R D +IG+++ ++ L + ++ G PGVGKTA Sbjct: 55 LSEKTRPKSFDEIIGQEEGIKALKAALCGPNPQHVIIYGPPGVGKTA 101 >gnl|CDD|180523 PRK06305, PRK06305, DNA polymerase III subunits gamma and tau; Validated. Length = 451 Score = 32.1 bits (73), Expect = 0.66 Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 8/55 (14%) Query: 568 KSVIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622 ++GQ A V + NALR R +++F G G GKT L + A+ L Sbjct: 17 SEILGQDAVVAVLKNALRF--------NRAAHAYLFSGIRGTGKTTLARIFAKAL 63 >gnl|CDD|179026 PRK00440, rfc, replication factor C small subunit; Reviewed. Length = 319 Score = 31.8 bits (73), Expect = 0.71 Identities = 17/56 (30%), Positives = 27/56 (48%), Gaps = 9/56 (16%) Query: 570 VIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLLFDD 625 ++GQ VE L+ + ++ M +F GP G GKT +LAR L+ + Sbjct: 19 IVGQEEIVER----LKSYVK-----EKNMPHLLFAGPPGTGKTTAALALARELYGE 65 >gnl|CDD|185633 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like protein; Provisional. Length = 398 Score = 32.0 bits (73), Expect = 0.72 Identities = 18/49 (36%), Positives = 28/49 (57%), Gaps = 6/49 (12%) Query: 593 DPQRPMGSFMFLGPTGVGKTELVKSLARLLFDDENSMIRIDMSEYMEKH 641 DP P G ++ GP G GKT L K++A + IR+ SE+++K+ Sbjct: 177 DP--PRGVLLY-GPPGTGKTMLAKAVAH---HTTATFIRVVGSEFVQKY 219 >gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional. Length = 880 Score = 31.9 bits (73), Expect = 0.78 Identities = 29/126 (23%), Positives = 54/126 (42%), Gaps = 25/126 (19%) Query: 405 IDTKPEVLDELDRRIICLKIEKEALKKEKDSFSKGRLIELEKELSSLEEKSHSLTLRWQE 464 I+ E ++EL+ + L+ E E +++ + L+E E + LEE+ L Sbjct: 470 IEEDRERVEELEAELEDLEEEVEEVEERLERAED--LVEAEDRIERLEERREDLEEL--- 524 Query: 465 GQRKILYVADLKKRLESMRNELAIAQRQGHFERAGELAYGLIPKTEKELDEAEKADSTAE 524 +A+ ++ +E R + + ERA EL E E +E +A + AE Sbjct: 525 -------IAERRETIEEKRE-----RAEELRERAAEL--------EAEAEEKREAAAEAE 564 Query: 525 DMVQEV 530 + +E Sbjct: 565 EEAEEA 570 >gnl|CDD|184929 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau; Provisional. Length = 576 Score = 31.6 bits (72), Expect = 0.78 Identities = 18/52 (34%), Positives = 24/52 (46%), Gaps = 12/52 (23%) Query: 571 IGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622 GQ ++ NA+ D R +F+F G GVGKT S AR+L Sbjct: 19 TGQEHVSRTLQNAI--------DTGRVAHAFLFTGARGVGKT----STARIL 58 >gnl|CDD|169554 PRK08691, PRK08691, DNA polymerase III subunits gamma and tau; Validated. Length = 709 Score = 31.6 bits (71), Expect = 0.82 Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 8/53 (15%) Query: 570 VIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622 ++GQ V+++ NAL D R +++ G GVGKT + + LA+ L Sbjct: 18 LVGQEHVVKALQNAL--------DEGRLHHAYLLTGTRGVGKTTIARILAKSL 62 >gnl|CDD|163294 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. Length = 282 Score = 31.5 bits (72), Expect = 0.89 Identities = 16/46 (34%), Positives = 21/46 (45%), Gaps = 4/46 (8%) Query: 592 QDPQRPMGSFMFLGPTGVGK-TELVKSLARLLFDDENS---MIRID 633 + G +GPTGVGK T L K AR + + N +I D Sbjct: 188 DEILEQGGVIALVGPTGVGKTTTLAKLAARFVLEHGNKKVALITTD 233 >gnl|CDD|184927 PRK14963, PRK14963, DNA polymerase III subunits gamma and tau; Provisional. Length = 504 Score = 31.3 bits (71), Expect = 1.0 Identities = 20/53 (37%), Positives = 28/53 (52%), Gaps = 12/53 (22%) Query: 570 VIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622 V+GQ E + ALR+ R G +++F GP GVGKT + ARL+ Sbjct: 16 VVGQEHVKEVLLAALRQGRLG--------HAYLFSGPRGVGKT----TTARLI 56 >gnl|CDD|184921 PRK14957, PRK14957, DNA polymerase III subunits gamma and tau; Provisional. Length = 546 Score = 31.2 bits (70), Expect = 1.2 Identities = 38/149 (25%), Positives = 61/149 (40%), Gaps = 43/149 (28%) Query: 570 VIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL------- 622 V GQ A+ S+ +AL + Q+ +++F G GVGKT L + LA+ L Sbjct: 18 VAGQQHALNSLVHAL--------ETQKVHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGVT 69 Query: 623 -----------FDDENSMIRIDMSEYMEKHSVSRLIGSPPGYVGYEEGGALTEAVRRHP- 670 + NS I + +E + SR G EE + + ++ P Sbjct: 70 AEPCNKCENCVAINNNSFI-----DLIEIDAASR--------TGVEETKEILDNIQYMPS 116 Query: 671 ---YQVVLFDEIEKAHSDVHNILLQVLDD 696 Y+V L DE+ N LL+ L++ Sbjct: 117 QGRYKVYLIDEVHMLSKQSFNALLKTLEE 145 >gnl|CDD|180249 PRK05771, PRK05771, V-type ATP synthase subunit I; Validated. Length = 646 Score = 31.1 bits (71), Expect = 1.2 Identities = 28/147 (19%), Positives = 57/147 (38%), Gaps = 21/147 (14%) Query: 427 EALKKEKDSFSKGRLIELEKELSSLEEKSHSLTLRWQEGQRKILYVADLKKRLESMRN-- 484 E L K+ + L ++EKE+ LEE+ L + +++ +RLE N Sbjct: 85 EELIKDVEEE----LEKIEKEIKELEEEISEL----ENEIKELE---QEIERLEPWGNFD 133 Query: 485 -ELAIAQRQGHFERAGELAYGLIPKTEKELDEAEKADSTAEDMVQEVVTSDNIANIVSRW 543 +L++ + G +P+ + E + E E + + +V + Sbjct: 134 LDLSLLLGFKYVSV----FVGTVPEDKLEELKLESDVENVEY-ISTDKGYVYVVVVVLKE 188 Query: 544 TGIPVDKMLESDREKFLRIETEISKSV 570 V++ L+ + F R+E E + Sbjct: 189 LSDEVEEELK--KLGFERLELEEEGTP 213 >gnl|CDD|183986 PRK13342, PRK13342, recombination factor protein RarA; Reviewed. Length = 413 Score = 31.2 bits (72), Expect = 1.2 Identities = 29/105 (27%), Positives = 40/105 (38%), Gaps = 25/105 (23%) Query: 180 VIGRDDEMRRAIQVLSRRTKNNPVLI--GDPGVGKTAIIEGLASRIINGDIPESLKGKRL 237 ++G +RR I+ +I G PG GKT + +A Sbjct: 20 LLGPGKPLRRMIE-----AGRLSSMILWGPPGTGKTTLARIIAGAT----------DAPF 64 Query: 238 MALDMGALIAGAK-FRGEFEERLKSLLCEIRSEDGEIILFIDELH 281 AL A+ +G K R EE + RS ILFIDE+H Sbjct: 65 EALS--AVTSGVKDLREVIEE-----ARQRRSAGRRTILFIDEIH 102 Score = 31.2 bits (72), Expect = 1.3 Identities = 18/54 (33%), Positives = 25/54 (46%), Gaps = 12/54 (22%) Query: 570 VIGQSAAVESVSNALRR-FRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622 V+GQ + LRR AG + S + GP G GKT +LAR++ Sbjct: 14 VVGQEHLLGPGK-PLRRMIEAGR------LSSMILWGPPGTGKT----TLARII 56 >gnl|CDD|181191 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau; Validated. Length = 647 Score = 31.0 bits (71), Expect = 1.3 Identities = 19/53 (35%), Positives = 29/53 (54%), Gaps = 12/53 (22%) Query: 570 VIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622 V+GQ + +++NAL D R +++F G GVGKT ++ARLL Sbjct: 18 VVGQEHVLTALANAL--------DLGRLHHAYLFSGTRGVGKT----TIARLL 58 >gnl|CDD|184933 PRK14969, PRK14969, DNA polymerase III subunits gamma and tau; Provisional. Length = 527 Score = 30.9 bits (70), Expect = 1.3 Identities = 19/52 (36%), Positives = 29/52 (55%), Gaps = 8/52 (15%) Query: 571 IGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622 +GQ V +++NAL + QR +++F G GVGKT L + LA+ L Sbjct: 19 VGQEHVVRALTNALEQ--------QRLHHAYLFTGTRGVGKTTLARILAKSL 62 >gnl|CDD|181656 PRK09111, PRK09111, DNA polymerase III subunits gamma and tau; Validated. Length = 598 Score = 31.0 bits (71), Expect = 1.4 Identities = 21/52 (40%), Positives = 27/52 (51%), Gaps = 12/52 (23%) Query: 571 IGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622 IGQ A V +++NA F G R +FM G GVGKT + AR+L Sbjct: 27 IGQEAMVRTLTNA---FETG-----RIAQAFMLTGVRGVGKT----TTARIL 66 >gnl|CDD|182459 PRK10436, PRK10436, hypothetical protein; Provisional. Length = 462 Score = 30.7 bits (70), Expect = 1.7 Identities = 15/32 (46%), Positives = 17/32 (53%), Gaps = 3/32 (9%) Query: 581 SNALRRFRAGLQDPQRPMGSFMFLGPTGVGKT 612 L +FR LQ PQ G + GPTG GKT Sbjct: 204 PAQLAQFRQALQQPQ---GLILVTGPTGSGKT 232 >gnl|CDD|163043 TIGR02858, spore_III_AA, stage III sporulation protein AA. Members of this protein are the stage III sporulation protein AA, encoded by one of several genes in the spoIIIA locus. It seems that this protein is found in a species if and only if that species is capable of endospore formation. Length = 270 Score = 30.8 bits (70), Expect = 1.7 Identities = 16/49 (32%), Positives = 26/49 (53%) Query: 200 NNPVLIGDPGVGKTAIIEGLASRIINGDIPESLKGKRLMALDMGALIAG 248 N ++I P GKT ++ LA + G L+GK++ +D + IAG Sbjct: 112 LNTLIISPPQCGKTTLLRDLARILSTGISQLGLRGKKVGIVDERSEIAG 160 >gnl|CDD|184916 PRK14952, PRK14952, DNA polymerase III subunits gamma and tau; Provisional. Length = 584 Score = 30.6 bits (69), Expect = 1.9 Identities = 20/53 (37%), Positives = 27/53 (50%), Gaps = 8/53 (15%) Query: 570 VIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622 V+GQ E +S+AL D R +++F GP G GKT + LAR L Sbjct: 15 VVGQEHVTEPLSSAL--------DAGRINHAYLFSGPRGCGKTSSARILARSL 59 >gnl|CDD|184302 PRK13752, PRK13752, putative transcriptional regulator MerR; Provisional. Length = 144 Score = 30.6 bits (69), Expect = 1.9 Identities = 26/86 (30%), Positives = 39/86 (45%), Gaps = 5/86 (5%) Query: 562 IETEISKSVIGQSAAVESVSNALRRF--RAGL-QDPQRPMGSFMFLGPTGVGKTELVKSL 618 +E + IG A V+ RF R GL +P +P GS G V + VKS Sbjct: 1 MENNLENLTIGVFAKAAGVNVETIRFYQRKGLLPEPDKPYGSIRRYGEADVTRVRFVKSA 60 Query: 619 ARLLF--DDENSMIRIDMSEYMEKHS 642 RL F D+ ++R++ + E+ S Sbjct: 61 QRLGFSLDEIAELLRLEDGTHCEEAS 86 >gnl|CDD|179778 PRK04195, PRK04195, replication factor C large subunit; Provisional. Length = 482 Score = 30.7 bits (70), Expect = 1.9 Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 5/51 (9%) Query: 570 VIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLAR 620 V+G A E + + + G P++ + + GP GVGKT L +LA Sbjct: 16 VVGNEKAKEQLREWIESWLKG--KPKKAL---LLYGPPGVGKTSLAHALAN 61 Score = 29.1 bits (66), Expect = 4.9 Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 4/58 (6%) Query: 167 DLTEEARNGKLDPVIGRDDEMRRAIQVLSRRTKNNP----VLIGDPGVGKTAIIEGLA 220 E+ R L V+G + + + + K P +L G PGVGKT++ LA Sbjct: 3 PWVEKYRPKTLSDVVGNEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALA 60 >gnl|CDD|184214 PRK13657, PRK13657, cyclic beta-1,2-glucan ABC transporter; Provisional. Length = 588 Score = 30.3 bits (69), Expect = 1.9 Identities = 21/62 (33%), Positives = 29/62 (46%), Gaps = 12/62 (19%) Query: 572 GQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLLFDDENSMIR 631 VE VS F A +P + +GPTG GK+ L+ L R +FD ++ I Sbjct: 346 NSRQGVEDVS-----FEA------KPGQTVAIVGPTGAGKSTLINLLQR-VFDPQSGRIL 393 Query: 632 ID 633 ID Sbjct: 394 ID 395 >gnl|CDD|183313 PRK11784, PRK11784, tRNA 2-selenouridine synthase; Provisional. Length = 345 Score = 30.6 bits (70), Expect = 2.0 Identities = 10/17 (58%), Positives = 13/17 (76%) Query: 605 GPTGVGKTELVKSLARL 621 G TG GKTEL+++LA Sbjct: 148 GNTGSGKTELLQALANA 164 >gnl|CDD|165505 PHA03246, PHA03246, large tegument protein UL36; Provisional. Length = 3095 Score = 30.3 bits (68), Expect = 2.1 Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 6/42 (14%) Query: 455 SHSLTLRWQEGQRKILY------VADLKKRLESMRNELAIAQ 490 SH LT+R E +Y + L+ RL +++ELA+A+ Sbjct: 1756 SHDLTVRIDESGPMTIYAERIDALVRLENRLAELKSELALAE 1797 >gnl|CDD|178861 PRK00098, PRK00098, GTPase RsgA; Reviewed. Length = 298 Score = 30.2 bits (69), Expect = 2.4 Identities = 19/56 (33%), Positives = 26/56 (46%), Gaps = 13/56 (23%) Query: 203 VLIGDPGVGKT----AIIEGLASRIINGDIPESL-KGK------RLMALDMGALIA 247 VL G GVGK+ A+ L + G+I E+L +GK L L G L+ Sbjct: 168 VLAGQSGVGKSTLLNALAPDLELKT--GEISEALGRGKHTTTHVELYDLPGGGLLI 221 >gnl|CDD|183114 PRK11388, PRK11388, DNA-binding transcriptional regulator DhaR; Provisional. Length = 638 Score = 30.0 bits (68), Expect = 2.4 Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 7/59 (11%) Query: 675 LF-DEIEKAHSDVHNILLQVLDDGRLTDSQGR---TVDFRNTLIIMTSNLGAEYLIEDG 729 LF +++E ++ + LLQVL G +T R VD R +I T+ L+E Sbjct: 420 LFLEKVEYLSPELQSALLQVLKTGVITRLDSRRLIPVDVR---VIATTTADLAMLVEQN 475 >gnl|CDD|150950 pfam10359, Fmp27_WPPW, RNA pol II promoter Fmp27 protein domain. Fmp27_WPPW is a conserved domain of a family of proteins involved in RNA polymerase II transcription initiation. It contains characteristic HQR and WPPW sequence motifs. and is towards the C-terminal in members which contain Fmp27_SW pfam10305. Length = 470 Score = 30.0 bits (68), Expect = 2.5 Identities = 18/52 (34%), Positives = 27/52 (51%), Gaps = 5/52 (9%) Query: 440 RLIELEKELSSLEEKSHSLTLRWQEGQRKIL-----YVADLKKRLESMRNEL 486 RL +LE+++ LEEK L L E + L ++ LK+RLE + L Sbjct: 169 RLKQLEEQIKKLEEKLGDLELNDDEELQSDLEELEKELSVLKERLEFLEKLL 220 >gnl|CDD|152161 pfam11725, AvrE, Pathogenicity factor. This family is secreted by gram-negative Gammaproteobacteria such as Pseudomonas syringae of tomato and the fire blight plant pathogen Erwinia amylovora, amongst others. It is an essential pathogenicity factor of approximately 198 kDa. Its injection into the host-plant is dependent upon the bacterial type III or Hrp secretion system. The family is long and carries a number of predicted functional regions, including an ERMS or endoplasmic reticulum membrane retention signal at both the C- and the N-termini, a leucine-zipper motif from residues 539-560, and a nuclear localisation signal at 1358-1361. this conserved AvrE-family of effectors is among the few that are required for full virulence of many phytopathogenic pseudomonads, erwinias and pantoeas. Length = 1771 Score = 30.1 bits (68), Expect = 2.7 Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 9/67 (13%) Query: 473 ADLKKRLESMRNEL---------AIAQRQGHFERAGELAYGLIPKTEKELDEAEKADSTA 523 A+L K LE R EL + Q+QG GE+ PK K L ++ + + Sbjct: 964 AELVKDLEQFREELENHSTTAAILLGQQQGVLNSHGEINKPFKPKKSKALGQSFNVNRSG 1023 Query: 524 EDMVQEV 530 D+ +E+ Sbjct: 1024 HDLSKEL 1030 >gnl|CDD|180790 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau; Validated. Length = 830 Score = 29.8 bits (67), Expect = 2.8 Identities = 18/54 (33%), Positives = 29/54 (53%), Gaps = 8/54 (14%) Query: 569 SVIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622 S++GQ V ++++AL D R +++F G GVGKT L + A+ L Sbjct: 17 SLVGQEHVVRALTHAL--------DGGRLHHAYLFTGTRGVGKTTLSRIFAKAL 62 >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 = 29.9 bits (68), Expect = 2.8 Identities = 29/107 (27%), Positives = 45/107 (42%), Gaps = 20/107 (18%) Query: 603 FLGPTGVGKTELVKSLARLLFDDENSMIRIDMSEYMEKHSVSRLI--GSPPGYVGYE-EG 659 F GP GVGK L +LA+ L ++ E + RLI G+ P E EG Sbjct: 19 FAGPEGVGKELLALALAKALLCEQPGGG-----EPCGECPSCRLIEAGNHPDLHRLEPEG 73 Query: 660 GALT-EAVRRH-----------PYQVVLFDEIEKAHSDVHNILLQVL 694 ++ + VR +VV+ ++ E+ + N LL+ L Sbjct: 74 QSIKVDQVRELVEFLSRTPQESGRRVVIIEDAERMNEAAANALLKTL 120 >gnl|CDD|183044 PRK11231, fecE, iron-dicitrate transporter ATP-binding subunit; Provisional. Length = 255 Score = 30.0 bits (68), Expect = 2.9 Identities = 11/19 (57%), Positives = 14/19 (73%) Query: 604 LGPTGVGKTELVKSLARLL 622 +GP G GK+ L+K ARLL Sbjct: 34 IGPNGCGKSTLLKCFARLL 52 >gnl|CDD|182120 PRK09862, PRK09862, putative ATP-dependent protease; Provisional. Length = 506 Score = 29.9 bits (67), Expect = 3.0 Identities = 34/121 (28%), Positives = 59/121 (48%), Gaps = 24/121 (19%) Query: 177 LDPVIGRDDEMRRAIQVLSRRTKNNPVLIGDPGVGKTAIIEGLASRIINGDIPESLKGKR 236 L VIG++ + +R +++ + +N +LIG PG GKT LASR ING +P+ + Sbjct: 190 LSDVIGQE-QGKRGLEI-TAAGGHNLLLIGPPGTGKTM----LASR-INGLLPDLSNEEA 242 Query: 237 LMALDMGALIAGAKFRGEFEER------LKSLLCEIRS-----EDGEI------ILFIDE 279 L + + +L+ + ++ +R + L + GEI +LF+DE Sbjct: 243 LESAAILSLVNAESVQKQWRQRPFRSPHHSASLTAMVGGGAIPGPGEISLAHNGVLFLDE 302 Query: 280 L 280 L Sbjct: 303 L 303 >gnl|CDD|163225 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. Length = 1169 Score = 29.6 bits (67), Expect = 3.2 Identities = 15/65 (23%), Positives = 22/65 (33%), Gaps = 16/65 (24%) Query: 168 LTEEARNGKLDPVIGRDDE-------MRRAIQVLSRRTKNNP---------VLIGDPGVG 211 L A KL + E A+ +L R ++IG PG G Sbjct: 64 LAALAAPTKLKADAAAEAEIRELRARFNEALALLKRSRLGGRRYLYDLPWYLVIGPPGSG 123 Query: 212 KTAII 216 KT ++ Sbjct: 124 KTTLL 128 >gnl|CDD|131585 TIGR02533, type_II_gspE, general secretory pathway protein E. This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis. Length = 486 Score = 29.7 bits (67), Expect = 3.6 Identities = 21/55 (38%), Positives = 28/55 (50%), Gaps = 4/55 (7%) Query: 584 LRRFRAGLQDPQRPMGSFMFLGPTGVGK-TELVKSLARLLFDDENSMIRIDMSEY 637 L RF ++ RP G + GPTG GK T L +L+RL + N + D EY Sbjct: 231 LSRFERLIR---RPHGIILVTGPTGSGKTTTLYAALSRLNTPERNILTVEDPVEY 282 >gnl|CDD|130256 TIGR01188, drrA, daunorubicin resistance ABC transporter ATP-binding subunit. This model describes daunorubicin resistance ABC transporter, ATP binding subunit in bacteria and archaea. This model is restricted in its scope to preferentially recognize the ATP binding subunit associated with effux of the drug, daunorubicin. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporter is the obligatory coupling of ATP hydrolysis to substrate translocation. The minimal configuration of bacterial ABC transport system: an ATPase or ATP binding subunit; An integral membrane protein; a hydrophilic polypetpide, which likely functions as substrate binding protein. In eukaryotes proteins of similar function include p-gyco proteins, multidrug resistance protein etc. Length = 302 Score = 29.7 bits (67), Expect = 3.6 Identities = 12/22 (54%), Positives = 14/22 (63%) Query: 601 FMFLGPTGVGKTELVKSLARLL 622 F FLGP G GKT ++ L LL Sbjct: 22 FGFLGPNGAGKTTTIRMLTTLL 43 >gnl|CDD|184912 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau; Provisional. Length = 620 Score = 29.5 bits (67), Expect = 4.0 Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 12/53 (22%) Query: 570 VIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622 ++GQ A ++ NAL R +++F GP G GKT S AR+L Sbjct: 18 LVGQEAIATTLKNALIS--------NRIAPAYLFTGPRGTGKT----SSARIL 58 >gnl|CDD|151168 pfam10662, PduV-EutP, Ethanolamine utilisation - propanediol utilisation. Members of this family function in ethanolamine and propanediol degradation pathways, however the exact roles of these proteins is poorly understood. Length = 143 Score = 29.5 bits (67), Expect = 4.0 Identities = 9/21 (42%), Positives = 13/21 (61%) Query: 598 MGSFMFLGPTGVGKTELVKSL 618 M M +G +G GKT L ++L Sbjct: 1 MKKIMLIGRSGCGKTTLTQAL 21 >gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La; Provisional. Length = 784 Score = 29.5 bits (66), Expect = 4.0 Identities = 31/98 (31%), Positives = 48/98 (48%), Gaps = 11/98 (11%) Query: 603 FLGPTGVGKTELVKSLARLLFDDENSMIRIDMSEYMEKHSVSR-LIGSPPGYVGYEEGGA 661 +GP GVGKT L +S+A+ M + + E R IGS PG + + Sbjct: 354 LVGPPGVGKTSLGQSIAKATGRKYVRMALGGVRDEAEIRGHRRTYIGSMPGKLIQK---- 409 Query: 662 LTEAVRRHPYQVVLFDEIEKAHSDVH----NILLQVLD 695 + + ++P + L DEI+K SD+ + LL+VLD Sbjct: 410 MAKVGVKNP--LFLLDEIDKMSSDMRGDPASALLEVLD 445 >gnl|CDD|184251 PRK13695, PRK13695, putative NTPase; Provisional. Length = 174 Score = 29.5 bits (67), Expect = 4.1 Identities = 12/18 (66%), Positives = 13/18 (72%) Query: 605 GPTGVGKTELVKSLARLL 622 GP GVGKT LV +A LL Sbjct: 7 GPPGVGKTTLVLKIAELL 24 >gnl|CDD|184596 PRK14267, PRK14267, phosphate ABC transporter ATP-binding protein; Provisional. Length = 253 Score = 29.0 bits (65), Expect = 4.5 Identities = 14/32 (43%), Positives = 21/32 (65%), Gaps = 2/32 (6%) Query: 591 LQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622 L+ PQ G F +GP+G GK+ L+++ RLL Sbjct: 25 LKIPQN--GVFALMGPSGCGKSTLLRTFNRLL 54 >gnl|CDD|178968 PRK00300, gmk, guanylate kinase; Provisional. Length = 205 Score = 29.3 bits (67), Expect = 4.8 Identities = 10/44 (22%), Positives = 20/44 (45%), Gaps = 14/44 (31%) Query: 601 FMFLGPTGVGKTELVKSLARLLFDDENSMIRIDMSEYMEKHSVS 644 + GP+G GK+ +L + L + + ++ + SVS Sbjct: 8 IVLSGPSGAGKS----TLVKALLERDPNL----------QLSVS 37 >gnl|CDD|180308 PRK05896, PRK05896, DNA polymerase III subunits gamma and tau; Validated. Length = 605 Score = 29.0 bits (65), Expect = 4.8 Identities = 15/55 (27%), Positives = 27/55 (49%), Gaps = 8/55 (14%) Query: 568 KSVIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622 K +IGQ + + NA+ + +++F GP G+GKT + K A+ + Sbjct: 16 KQIIGQELIKKILVNAILN--------NKLTHAYIFSGPRGIGKTSIAKIFAKAI 62 >gnl|CDD|182342 PRK10261, PRK10261, glutathione transporter ATP-binding protein; Provisional. Length = 623 Score = 29.1 bits (65), Expect = 4.8 Identities = 22/66 (33%), Positives = 32/66 (48%), Gaps = 9/66 (13%) Query: 775 GR-VLSLIKERNISMDFDDQVIDWLSCRGYDPSYGARPLKRVIQRYIQNPLAERVLSQTI 833 GR +L L++ + + F+ Q ID L + L+R IQ Q+P A QT+ Sbjct: 367 GRALLRLVESQGGEIIFNGQRIDTL------SPGKLQALRRDIQFIFQDPYASLDPRQTV 420 Query: 834 SDGDSI 839 GDSI Sbjct: 421 --GDSI 424 >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 = 29.1 bits (66), Expect = 4.9 Identities = 12/50 (24%), Positives = 27/50 (54%), Gaps = 4/50 (8%) Query: 178 DPVIGRDDE---MRRAIQ-VLSRRTKNNPVLIGDPGVGKTAIIEGLASRI 223 D ++ RD++ + +A++ +L +N + G G GKTA+ + + + Sbjct: 15 DRIVHRDEQIEELAKALRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKEL 64 >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 = 29.1 bits (66), Expect = 5.0 Identities = 10/17 (58%), Positives = 12/17 (70%) Query: 605 GPTGVGKTELVKSLARL 621 G TG GKTEL+ +LA Sbjct: 134 GMTGSGKTELLHALANA 150 >gnl|CDD|163064 TIGR02894, DNA_bind_RsfA, transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO. Length = 161 Score = 29.0 bits (65), Expect = 5.2 Identities = 18/64 (28%), Positives = 35/64 (54%), Gaps = 5/64 (7%) Query: 422 LKIEKEALKKEKDSFSKGRLIELEKELSSLEEKSHSLTLRWQEGQRKILYVADLKKRLES 481 L+ E E LK + +S K R ELEKEL L ++ ++ +E + ++ + D ++L Sbjct: 102 LQKENERLKNQNESLQK-RNEELEKELEKLRQRLSTI----EEDYQTLIDIMDRARKLAV 156 Query: 482 MRNE 485 + ++ Sbjct: 157 VEDD 160 >gnl|CDD|180644 PRK06647, PRK06647, DNA polymerase III subunits gamma and tau; Validated. Length = 563 Score = 29.0 bits (65), Expect = 5.5 Identities = 16/54 (29%), Positives = 28/54 (51%), Gaps = 8/54 (14%) Query: 569 SVIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622 S+ GQ VE++ +++ + +++F GP GVGKT ++ AR L Sbjct: 17 SLEGQDFVVETLKHSIESNKIA--------NAYIFSGPRGVGKTSSARAFARCL 62 >gnl|CDD|180787 PRK06995, flhF, flagellar biosynthesis regulator FlhF; Validated. Length = 484 Score = 28.8 bits (65), Expect = 5.8 Identities = 12/21 (57%), Positives = 13/21 (61%) Query: 599 GSFMFLGPTGVGKTELVKSLA 619 G F +GPTGVGKT LA Sbjct: 257 GVFALMGPTGVGKTTTTAKLA 277 >gnl|CDD|179742 PRK04123, PRK04123, ribulokinase; Provisional. Length = 548 Score = 28.7 bits (65), Expect = 6.1 Identities = 12/44 (27%), Positives = 16/44 (36%), Gaps = 4/44 (9%) Query: 651 PGYVGYEEG----GALTEAVRRHPYQVVLFDEIEKAHSDVHNIL 690 PG +GYE G G + R DE E + +L Sbjct: 322 PGLIGYEAGQSAVGDIFAWFARLLVPPEYKDEAEARGKQLLELL 365 >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 = 28.7 bits (65), Expect = 6.2 Identities = 9/18 (50%), Positives = 12/18 (66%) Query: 605 GPTGVGKTELVKSLARLL 622 G G+ KT L ++LAR L Sbjct: 6 GVPGLAKTLLARTLARSL 23 >gnl|CDD|184901 PRK14908, PRK14908, glycyl-tRNA synthetase; Provisional. Length = 1000 Score = 28.8 bits (65), Expect = 6.3 Identities = 21/74 (28%), Positives = 30/74 (40%), Gaps = 15/74 (20%) Query: 470 LYVADLKKRLESMRNELA----------IAQRQGHFERAGELAYGLIPKTEKE-LDEAE- 517 L+ ADLK LE+ +L +A + + E L+P + +E LD A Sbjct: 647 LFKADLKTPLETFVEKLKSVTYFEALGSLADKVERIKAHAEELAALLPLSARETLDRAAE 706 Query: 518 --KADSTAEDMVQE 529 K D MV E Sbjct: 707 LCKFD-LVSQMVNE 719 >gnl|CDD|184924 PRK14960, PRK14960, DNA polymerase III subunits gamma and tau; Provisional. Length = 702 Score = 28.9 bits (64), Expect = 6.4 Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 8/53 (15%) Query: 570 VIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622 ++GQ+ ++S+AL R R +++F G GVGKT + + LA+ L Sbjct: 17 LVGQNHVSRALSSALERGRL--------HHAYLFTGTRGVGKTTIARILAKCL 61 >gnl|CDD|185619 PTZ00440, PTZ00440, reticulocyte binding protein 2-like protein; Provisional. Length = 2722 Score = 28.6 bits (64), Expect = 6.6 Identities = 14/53 (26%), Positives = 22/53 (41%) Query: 90 ILSKSEEIAKKSGDSFVTAEKFLLAMVMETGGIGESLKKCGLKFSRLEESIKK 142 I SE+I K+ +S AE+F E +K+ K + +E K Sbjct: 1292 ISIDSEKILKEILNSTKKAEEFSNDAKKELEKTDNLIKQVEAKIEQAKEHKNK 1344 >gnl|CDD|130260 TIGR01192, chvA, glucan exporter ATP-binding protein. This model describes glucan exporter ATP binding protein in bacteria. It belongs to the larger ABC transporter superfamily with the characteristic ATP binding motif. The In general, this protein is in some ways implicated in osmoregulation and suggested to participate in the export of glucan from the cytoplasm to periplasm. The cyclic beta-1,2-glucan in the bactrerial periplasmic space is suggested to confer the property of high osmolority. It has also been demonstrated that mutants in this loci have lost functions of virulence and motility. It is unclear as to how virulence and osmoadaptaion are related. Length = 585 Score = 28.7 bits (64), Expect = 6.6 Identities = 14/30 (46%), Positives = 18/30 (60%), Gaps = 1/30 (3%) Query: 604 LGPTGVGKTELVKSLARLLFDDENSMIRID 633 +GPTG GKT L+ L R ++D I ID Sbjct: 367 VGPTGAGKTTLINLLQR-VYDPTVGQILID 395 >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 = 28.8 bits (65), Expect = 6.8 Identities = 34/130 (26%), Positives = 52/130 (40%), Gaps = 27/130 (20%) Query: 571 IGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLLFDDENSMI 630 IGQ E V L+ F + Q + + GP G+GKT +LA ++ ++ + Sbjct: 7 IGQ----EKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKT----TLAHIIANEMGVNL 58 Query: 631 RIDMSEYMEKHSVSRLIGSPPGYVGYEEGGALTEAVRRHPYQVVLF-DEIEKAHSDVHNI 689 +I +EK PG + LT VLF DEI + V + Sbjct: 59 KITSGPALEK----------PG----DLAAILTNLEEGD----VLFIDEIHRLSPAVEEL 100 Query: 690 LLQVLDDGRL 699 L ++D RL Sbjct: 101 LYPAMEDFRL 110 >gnl|CDD|181314 PRK08241, PRK08241, RNA polymerase factor sigma-70; Validated. Length = 339 Score = 28.7 bits (65), Expect = 6.9 Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 9/37 (24%) Query: 570 VIGQSAA---------VESVSNALRRFRAGLQDPQRP 597 V+G SAA V +V++AL+R RA L + Sbjct: 167 VLGWSAAEVAELLDTSVAAVNSALQRARATLAERGPS 203 >gnl|CDD|152140 pfam11704, Folliculin, Vesicle coat protein involved in Golgi to plasma membrane transport. In yeast cells this family functions in the regulated delivery of Gap1p (a general amino acid permease) to the cell surface, perhaps as a component of a post-Golgi secretory-vesicle coat complex. Birt-Hogg-Dube (BHD)4 syndrome is an autosomal dominant disorder characterized by hamartomas of skin follicles, lung cysts, spontaneous pneumothorax, and renal cell carcinoma. Folliculin is the protein from the BHD4 gene and is found to have no significant homology to any other human proteins. It is expressed in most tissues. These same symptoms also occur in TSC or tuberous sclerosis complex, suggesting that the same pathway is involved, and it is likely that the target is the down-stream Tor2 - an essential gene. Folliculin appears to bind Tor2, and down-regulation of Tor2 activity leads to up-regulation of nitrogen responsive genes including membrane transporters and amino acid permeases. Length = 168 Score = 28.4 bits (64), Expect = 7.1 Identities = 21/82 (25%), Positives = 32/82 (39%), Gaps = 14/82 (17%) Query: 259 LKSLLCEIRSEDGEIILFIDEL--HVLVGAGKTDGAMDASNLLKPSLARG--ELHCIGAT 314 ++SL CE DG + F D + +VL K LK ARG + + Sbjct: 24 VRSLSCETMGYDGGPLFFGDAIRGYVLSYGFK----------LKDPNARGNERRYSLIVL 73 Query: 315 TLDEYRKYIEKDPALARRFQSL 336 D+ K + P +A F + Sbjct: 74 ADDKMSKLLNNWPFIAEYFGKI 95 >gnl|CDD|132269 TIGR03225, benzo_boxB, benzoyl-CoA oxygenase, B subunit. Members of this protein family are BoxB, the B subunit of benzoyl-CoA oxygenase. This oxygen-requiring enzyme acts in an aerobic pathway of benzoate catabolism via coenzyme A ligation. Length = 471 Score = 28.6 bits (64), Expect = 7.7 Identities = 24/69 (34%), Positives = 36/69 (52%), Gaps = 4/69 (5%) Query: 144 RKGRVADSVNAEQGFDALKKYCR-DLTEEARNGKL-DPVIGRDDEMRRAIQVLSRRTKNN 201 R G++ + AE GFD L + CR LTEEA + + + +GR + R QV+ ++ Sbjct: 211 RDGKMQLAALAESGFDPLSRTCRFMLTEEAHHMFVGESGVGR--VIERTCQVMKENGTDD 268 Query: 202 PVLIGDPGV 210 P I GV Sbjct: 269 PYRIRALGV 277 >gnl|CDD|177536 PHA03132, PHA03132, thymidine kinase; Provisional. Length = 580 Score = 28.6 bits (64), Expect = 8.1 Identities = 12/25 (48%), Positives = 16/25 (64%), Gaps = 1/25 (4%) Query: 601 FMFL-GPTGVGKTELVKSLARLLFD 624 F+FL G GVGKT L+ + +L D Sbjct: 259 FLFLEGVMGVGKTTLLNHMRGILGD 283 >gnl|CDD|173186 PRK14723, flhF, flagellar biosynthesis regulator FlhF; Provisional. Length = 767 Score = 28.2 bits (63), Expect = 8.3 Identities = 11/21 (52%), Positives = 12/21 (57%) Query: 599 GSFMFLGPTGVGKTELVKSLA 619 G +GPTGVGKT LA Sbjct: 186 GVLALVGPTGVGKTTTTAKLA 206 >gnl|CDD|130254 TIGR01186, proV, glycine betaine/L-proline transport ATP binding subunit. This model describes the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporter is the obligatory coupling of ATP hydrolysis to substrate translocation. The minimal configuration of bacterial ABC transport system: an ATPase or ATP binding subunit; An integral membrane protein; a hydrophilic polypetpide, which likely functions as substrate binding protein. Functionally, this transport system is involved in osmoregulation. Under conditions of stress, the organism recruits these transport system to accumulate glycine betaine and other solutes which offer osmo-protection. It has been demonstrated that glycine betaine uptake is accompanied by symport with sodium ions. The locus has been named variously as proU or opuA. A gene library from L.lactis functionally complements an E.coli proU mutant. The comlementing locus is similar to a opuA locus in B.sutlis. This clarifies the differences in nomenclature. Length = 363 Score = 28.3 bits (63), Expect = 8.7 Identities = 9/22 (40%), Positives = 15/22 (68%) Query: 601 FMFLGPTGVGKTELVKSLARLL 622 F+ +G +G GK+ V+ L RL+ Sbjct: 22 FVIMGLSGSGKSTTVRMLNRLI 43 >gnl|CDD|129208 TIGR00101, ureG, urease accessory protein UreG. This model represents UreG, a GTP hydrolase that acts in the assembly of the nickel metallocenter of urease. It is found only in urease-positive species, although some urease-positive species (e.g. Bacillus subtilis) lack this protein. A similar protein, hypB, is an accessory protein for expression of hydrogenase, which also uses nickel. Length = 199 Score = 28.3 bits (63), Expect = 8.8 Identities = 21/69 (30%), Positives = 32/69 (46%), Gaps = 10/69 (14%) Query: 605 GPTGVGKTELVKSLARLLFDD------ENSMIRIDMSEYMEKHSVSRLIGSPPGYVGYEE 658 GP G GKT L+++L R L N + + +E++ K+S P +G E Sbjct: 8 GPVGSGKTALIEALTRALRQKYQLAVITNDIYTQEDAEFLVKNSAL----PPERILGVET 63 Query: 659 GGALTEAVR 667 GG A+R Sbjct: 64 GGCPHTAIR 72 >gnl|CDD|184315 PRK13768, PRK13768, GTPase; Provisional. Length = 253 Score = 28.3 bits (64), Expect = 8.9 Identities = 11/20 (55%), Positives = 13/20 (65%) Query: 603 FLGPTGVGKTELVKSLARLL 622 FLG G GKT L K+L+ L Sbjct: 7 FLGTAGSGKTTLTKALSDWL 26 >gnl|CDD|181856 PRK09436, thrA, bifunctional aspartokinase I/homoserine dehydrogenase I; Provisional. Length = 819 Score = 28.2 bits (64), Expect = 9.4 Identities = 21/64 (32%), Positives = 29/64 (45%), Gaps = 9/64 (14%) Query: 385 FLPDKAIDLMDEASARVRMQIDTKPEVLDELDRRIICLKIEKEALKKEKDSFSKGRLIEL 444 +L K IDL RV +++ +LDE I L +E L + + F RLI L Sbjct: 490 WLKKKNIDL------RVCGIANSRKMLLDE---HGIDLDNWREELAEAGEPFDLDRLIRL 540 Query: 445 EKEL 448 KE Sbjct: 541 VKEY 544 >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 = 28.0 bits (63), Expect = 9.5 Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 3/55 (5%) Query: 568 KSVIGQSAAVESVSNALRRFRAGLQDPQRPMGSFMFLGPTGVGKTELVKSLARLL 622 G A+E N + GL++ ++ LGP G GK+ LV+ L R L Sbjct: 51 HDFFGMEEAIERFVNYFKSAAQGLEERKQ---ILYLLGPVGGGKSSLVECLKRGL 102 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 0.136 0.375 Gapped Lambda K H 0.267 0.0738 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 14,199,078 Number of extensions: 990255 Number of successful extensions: 3141 Number of sequences better than 10.0: 1 Number of HSP's gapped: 3059 Number of HSP's successfully gapped: 226 Length of query: 853 Length of database: 5,994,473 Length adjustment: 102 Effective length of query: 751 Effective length of database: 3,790,457 Effective search space: 2846633207 Effective search space used: 2846633207 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 (27.3 bits)