RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780334|ref|YP_003064747.1| DNA repair protein RadA [Candidatus Liberibacter asiaticus str. psy62] (479 letters) >gnl|CDD|31265 COG1066, Sms, Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]. Length = 456 Score = 586 bits (1511), Expect = e-168 Identities = 237/460 (51%), Positives = 320/460 (69%), Gaps = 10/460 (2%) Query: 1 MVKIRSQYFCQSCGEIHSRWIGKCDSCNAWNTIIED---SSRKESDQRFSKTIKQGHSIS 57 M K ++ + CQ CG + +W+GKC +C AWNT++E+ +S + + Sbjct: 1 MAKKKTAFVCQECGYVSPKWLGKCPACGAWNTLVEEVLAASPGGAPNKRRSGKAGSEPSK 60 Query: 58 LFMLSEESIEEESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYK 117 + LS+ +EEE RI T I+ELDRV GGG V GSVIL+GGDPGIGKSTLL+Q AA LA K Sbjct: 61 VLKLSDIELEEEPRISTGIEELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAARLA-K 119 Query: 118 KHRITYVSGEEAIGQIRLRAQRLNTINSSVYIAIETNVEDIIATLITNEKPDLVIIDSIQ 177 + ++ YVSGEE++ QI+LRA RL +++Y+ ETN+EDIIA + EKPDLV+IDSIQ Sbjct: 120 RGKVLYVSGEESLQQIKLRADRLGLPTNNLYLLAETNLEDIIAE-LEQEKPDLVVIDSIQ 178 Query: 178 TLWSQTAESSPGTVIQVRTSVQAMIQYAKKNGVAMVLVGHVTKEGQIAGPRVIEHMVDAV 237 TL+S+ S+PG+V QVR +++ AK +A+ +VGHVTKEG IAGPRV+EHMVD V Sbjct: 179 TLYSEEITSAPGSVSQVREVAAELMRLAKTKNIAIFIVGHVTKEGAIAGPRVLEHMVDTV 238 Query: 238 LYFEGGTRNTQYDYRILRSVKNRFGPTDEIGVFEMSDKGLQEVSDPSKIFLSDRDSTSPG 297 LYFEG + YRILRSVKNRFG T+E+GVFEM++ GL+EVS+PS +FLS+R +PG Sbjct: 239 LYFEG---DRHSRYRILRSVKNRFGATNELGVFEMTENGLREVSNPSALFLSERGEQTPG 295 Query: 298 TAVFAGIEGTRALLVEIQSLVVPTSLGMPRRTVVGWDSSRLAMILAVLEARCNIKFGNHD 357 +AV +EGTR LLVEIQ+LV P+S G PRR VG D +RLAM+LAVLE R + G+ D Sbjct: 296 SAVVVVMEGTRPLLVEIQALVSPSSFGNPRRVAVGLDQNRLAMLLAVLEKRLGLPLGDQD 355 Query: 358 VHLNIAGGYRISEPAADVAVAAALISSILSIPLPSDFVYFGEVSLSGSVRAVGHMQQRLK 417 V++N+AGG +++EPAAD+AVA AL+SS + PLP D V FGEV LSG +R V ++RLK Sbjct: 356 VYVNVAGGVKVTEPAADLAVALALVSSFRNRPLPQDTVVFGEVGLSGEIRPVPRGERRLK 415 Query: 418 EAEKIGFLSGVFPESAKGECKIGMLDRQYIKNLSDLVKKI 457 EA K+GF + P+ + + L++ ++ + Sbjct: 416 EAAKLGFKRAIVPKGNIP--LPEGIKVIGVSTLAEALEVV 453 >gnl|CDD|29987 cd01121, Sms, Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.. Length = 372 Score = 488 bits (1259), Expect = e-138 Identities = 203/377 (53%), Positives = 270/377 (71%), Gaps = 5/377 (1%) Query: 8 YFCQSCGEIHSRWIGKCDSCNAWNTIIEDSSRKESDQRFSKTIKQGHSISLFMLSEESIE 67 Y C CG + +W+GKC C WNT++E+ S ++ S + LS+ E Sbjct: 1 YVCSECGYVSPKWLGKCPECGEWNTLVEEIEPSSSSGSGGRSSGGSAS-KVIPLSDIEAE 59 Query: 68 EESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGE 127 EE RI T I+ELDRV GGG V GSVIL+GGDPGIGKSTLL+Q AA LA + ++ YVSGE Sbjct: 60 EEERIPTGIEELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAARLAKRGGKVLYVSGE 119 Query: 128 EAIGQIRLRAQRLNTINSSVYIAIETNVEDIIATLITNEKPDLVIIDSIQTLWSQTAESS 187 E+ QI+LRA RL ++Y+ ETN+EDI+A+ I KPDLVIIDSIQT++S S+ Sbjct: 120 ESPEQIKLRADRLGISTENLYLLAETNLEDILAS-IEELKPDLVIIDSIQTVYSSELTSA 178 Query: 188 PGTVIQVRTSVQAMIQYAKKNGVAMVLVGHVTKEGQIAGPRVIEHMVDAVLYFEGGTRNT 247 PG+V QVR ++++AK+ + + +VGHVTKEG IAGP+V+EHMVD VLYFEG + Sbjct: 179 PGSVSQVRECTAELMRFAKERNIPIFIVGHVTKEGSIAGPKVLEHMVDTVLYFEGDRHS- 237 Query: 248 QYDYRILRSVKNRFGPTDEIGVFEMSDKGLQEVSDPSKIFLSDRDSTSPGTAVFAGIEGT 307 +YRILRSVKNRFG T+E+GVFEM + GL+EVS+PS++FLS+R+ PG+AV +EG+ Sbjct: 238 --EYRILRSVKNRFGSTNELGVFEMRENGLREVSNPSELFLSEREEDVPGSAVTVVMEGS 295 Query: 308 RALLVEIQSLVVPTSLGMPRRTVVGWDSSRLAMILAVLEARCNIKFGNHDVHLNIAGGYR 367 R LLVE+Q+LV PTS PRR VG+D +RL+M+LAVLE R + + DV +N+AGG + Sbjct: 296 RPLLVEVQALVSPTSYANPRRVAVGFDPNRLSMLLAVLEKRLGLPLADQDVFVNVAGGLK 355 Query: 368 ISEPAADVAVAAALISS 384 I+EPAAD+AVA A++SS Sbjct: 356 ITEPAADLAVALAIVSS 372 >gnl|CDD|29986 cd01120, RecA-like_NTPases, RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.. Length = 165 Score = 73.6 bits (180), Expect = 1e-13 Identities = 39/165 (23%), Positives = 69/165 (41%), Gaps = 14/165 (8%) Query: 92 VILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRLRAQRLNT--INSSVYI 149 +ILV G G GK+TL +Q A ++A K ++ YV EE I ++ R + ++ I Sbjct: 1 LILVFGPTGSGKTTLALQLALNIATKGGKVVYVDIEEEIEELTERLIGESLKGALDNLII 60 Query: 150 AIETNVEDIIAT-------LITNEKPDLVIIDSIQTLWSQTAESSPGTVIQVRTSVQAMI 202 T + A L DL+I+D + L E G ++ ++ ++ Sbjct: 61 VFATADDPAAARLLSKAERLRERGGDDLIILDELTRLVRALREIREGYPGELDEELRELL 120 Query: 203 QYAKKNGVAMVLVGHV-----TKEGQIAGPRVIEHMVDAVLYFEG 242 + A+K GV ++ V G + +E + D V+ Sbjct: 121 ERARKGGVTVIFTLQVPSGDKGDPRLTRGAQNLEDIADTVIVLSR 165 >gnl|CDD|30816 COG0468, RecA, RecA/RadA recombinase [DNA replication, recombination, and repair]. Length = 279 Score = 69.2 bits (169), Expect = 3e-12 Identities = 51/250 (20%), Positives = 95/250 (38%), Gaps = 22/250 (8%) Query: 53 GHSISLFMLSEESIEEESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAA 112 SI + + +E E+ I T LD GGG RG + + G GK+TL +Q A Sbjct: 24 KGSI-MALGGDERREDIEAISTGSLALDEALGGGLPRGRITEIYGPESSGKTTLALQLVA 82 Query: 113 SLAYKKHRITYVSGEEAIGQIRLRAQRLNTINSSVYIAIETNVED---IIATLITN--EK 167 + + ++ E A+ R + ++ + ++ ++ E I L + EK Sbjct: 83 NAQKPGGKAAFIDTEHALDPERAKQLGVDLL-DNLLVSQPDTGEQQLEIAEKLARSGAEK 141 Query: 168 PDLVIIDSIQTLWSQTAESSPGTVI--QVRTSVQA--MIQYAKKNGVAMVLVGHV-TKEG 222 DL+++DS+ L + E G + S + + A K A++ V K G Sbjct: 142 IDLLVVDSVAALV-RAEEIEDGHLGLRARLLSKALRKLTRLANKYNTAVIFTNQVRAKIG 200 Query: 223 -------QIAGPRVIEHMVDAVLYFEGGTRNTQY--DYRILRSVKNRFGPTDEIGVFEMS 273 G ++ L + + R ++ VKN+ P + F+++ Sbjct: 201 VMFGDPETTTGGNALKFYASVRLDLRRIESLKEDVGNKRRVKVVKNKVAPPFKEAEFDIT 260 Query: 274 DKGLQEVSDP 283 G + Sbjct: 261 YGGGIDREGE 270 >gnl|CDD|30815 COG0467, RAD55, RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]. Length = 260 Score = 69.0 bits (168), Expect = 3e-12 Identities = 62/249 (24%), Positives = 98/249 (39%), Gaps = 31/249 (12%) Query: 70 SRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEE- 128 RI T I LD + GGG RGSV+L+ G PG GK+ +Q A + + YVS EE Sbjct: 3 ERIPTGIPGLDEILGGGLPRGSVVLITGPPGTGKTIFALQFLYEGAREGEPVLYVSTEES 62 Query: 129 -------------------AIGQIRLRAQRLNTINSSVYIAIETN----VEDIIATLITN 165 G++ + L+ + + + D I ++ Sbjct: 63 PEELLENARSFGWDLEVYIEKGKLAILDAFLSEKGLVSIVVGDPLDLEELLDRIREIVEK 122 Query: 166 EKPDLVIIDSIQTLWSQTAESSPGTVIQVRTSVQAMIQYAKKNGVAMVLVGHVTKEGQIA 225 E D V+IDSI L + VR + + ++ KK GV +L + Sbjct: 123 EGADRVVIDSITELTLYLNDP-----ALVRRILLLLKRFLKKLGVTSLLT-TEAPVEERG 176 Query: 226 GPRVIEHMVDAVLYFEGGTRNTQYDYRILRSVKNR-FGPTDEIGVFEMSDKGLQEVSDPS 284 V E++VD V+ + D R LR +K R + ++ FE++D V Sbjct: 177 ESGVEEYIVDGVIRLDLKEIEGGGDRRYLRILKMRGTPHSLKVIPFEITDGEGIVVYPEG 236 Query: 285 KIFLSDRDS 293 +I L + Sbjct: 237 RIRLEEERV 245 >gnl|CDD|30003 cd01393, recA_like, RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response. RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs radA and radB.. Length = 226 Score = 59.8 bits (145), Expect = 1e-09 Identities = 50/227 (22%), Positives = 87/227 (38%), Gaps = 34/227 (14%) Query: 72 IQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKH------RITYVS 125 I T LD + GGG G + + G+ G GK+ L +Q A ++ Y+ Sbjct: 1 ISTGSKALDELLGGGIPTGRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYID 60 Query: 126 GEEAIGQIRLRA------QRLNTINSSVYIAIETNVE------DIIATLITNEKPDLVII 173 E A RL + ++Y+A N E + + ++++ + DLV++ Sbjct: 61 TEGAFRPERLVQLAVRFGLDPEEVLDNIYVARPYNGEQQLEIVEELERIMSSGRVDLVVV 120 Query: 174 DSIQTLWSQTAESSPGTVIQVRTS-----VQAMIQYAKKNGVAMVLVGHVT--------K 220 DS+ L+ + E ++ R ++ +++ A K VA+V V Sbjct: 121 DSVAALFRK--EFIGRGMLAERARLLSQALRKLLRLADKFNVAVVFTNQVRAKVDVMFGD 178 Query: 221 EGQIAGPRVIEHMVDAVLYFEGGTRNTQYDYRILRSVKNRFGPTDEI 267 AG + H L G R + RI + VK+ P E Sbjct: 179 PETPAGGNALAHASTTRLDLRKG-RGIIGERRIAKVVKSPALPEAEA 224 >gnl|CDD|30004 cd01394, radB, RadB. The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.. Length = 218 Score = 58.0 bits (140), Expect = 5e-09 Identities = 58/219 (26%), Positives = 93/219 (42%), Gaps = 27/219 (12%) Query: 79 LDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGE----EAIGQI- 133 LD + GGG RG+V V G PG GK+ + +Q A A + ++ Y+ E E QI Sbjct: 8 LDELLGGGVERGTVTQVYGPPGTGKTNIAIQLAVETAGQGKKVAYIDTEGLSSERFRQIA 67 Query: 134 RLRAQRL--NTINSSVYIAIETNVEDIIATLITNEKPDLVIIDSIQTLWSQTAESSPGTV 191 R +R + I E +EK DLV++DS L+ T+ Sbjct: 68 GDRPERAASSIIVFEPMDFNEQGRAIQETETFADEKVDLVVVDSATALYRLELGDDDTTI 127 Query: 192 ---IQVRTSVQAMIQYAKKNGVAMVLVGHVTKEGQ------IAGPRVIEHMVDAVLYFE- 241 ++ + ++ A+K+ VA+V+ V + + G +EH +L E Sbjct: 128 KNYRELAKQLTFLLWLARKHDVAVVITNQVYSDVGSGSVRPLGGH-TLEHWSKVILRLEK 186 Query: 242 --GGTRNTQYDYRILRSVKNRFGPTDEIGVFEMSDKGLQ 278 GTR +L K+RF P F ++DKG++ Sbjct: 187 LRVGTR-----RAVLE--KHRFRPEGSSVYFRITDKGIE 218 >gnl|CDD|29989 cd01123, Rad51_DMC1_radA, Rad51_DMC1_radA,B. This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 .. Length = 235 Score = 56.0 bits (135), Expect = 2e-08 Identities = 54/241 (22%), Positives = 92/241 (38%), Gaps = 42/241 (17%) Query: 72 IQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKH------RITYVS 125 + T LD + GGG GS+ + G+ G GK+ L Q A ++ + Y+ Sbjct: 1 LTTGSKALDELLGGGIETGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYID 60 Query: 126 GEEAIGQIRLRA------QRLNTINSSVYIAIETNVEDII-------ATLITNEKPDLVI 172 E RL + ++Y+A N + + A LI + + LVI Sbjct: 61 TEGTFRPERLVQIAERFGLDPEEVLDNIYVARAYNSDHQLQLLEELEAILIESSRIKLVI 120 Query: 173 IDSIQTLWSQTAESSPGTVIQVRTS-----VQAMIQYAKKNGVAMVLVGHVT-------- 219 +DS+ L+ AE + R ++ + + A + VA+V+ VT Sbjct: 121 VDSVTALFR--AEFDGRGELAERQQHLAKLLRTLKRLADEFNVAVVITNQVTARPDGAAM 178 Query: 220 ---KEGQIAGPRVIEHMVDAVLYFEGGTRNTQYDYRILRSVKNRFGPTDEIGVFEMSDKG 276 + AG + H LY G RI + V + P E VF ++++G Sbjct: 179 FGGDPKKPAGGNIWAHASTTRLYLRKGRGEE----RIAKIVDSPHLPEGEA-VFAITEEG 233 Query: 277 L 277 + Sbjct: 234 I 234 >gnl|CDD|29990 cd01124, KaiC, KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs. A related protein is found in archaea.. Length = 187 Score = 54.9 bits (132), Expect = 5e-08 Identities = 43/197 (21%), Positives = 71/197 (36%), Gaps = 34/197 (17%) Query: 92 VILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRLRAQRL----------- 140 L+ G PG GK+T +Q + + YV+ EE+ ++ A+ L Sbjct: 1 STLLSGGPGTGKTTFALQFLYAGLARGEPGLYVTLEESPEELIENAESLGWDLERLEDEG 60 Query: 141 -------NTINSSVYIA-IETNVEDIIATLITNEKPDLVIIDSIQTLWSQTAESSPGTVI 192 + + + + + I K V+IDS+ L Sbjct: 61 LLAIVDADPDEIGPAESSLRLELIQRLKDAIEEFKAKRVVIDSVSGLLLMEQS------- 113 Query: 193 QVRTSVQAMIQYAKKNGV-AMVLVGHVTKEGQIAGPRVIEHMVDAVL---YFEGGTRNTQ 248 R ++ ++ K+ GV ++ EG G +E++VD V+ E G R Sbjct: 114 TARLEIRRLLFALKRFGVTTLLTSEQSGLEGTGFGGGDVEYLVDGVIRLRLDEEGGRLR- 172 Query: 249 YDYRILRSVKNRFGPTD 265 R L VK R GP D Sbjct: 173 ---RSLSVVKMRGGPHD 186 >gnl|CDD|31266 COG1067, LonB, Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]. Length = 647 Score = 48.8 bits (116), Expect = 3e-06 Identities = 20/82 (24%), Positives = 35/82 (42%), Gaps = 11/82 (13%) Query: 336 SRLAMILAVLEARCNIKFGNHDVHLNIAGGYRISE-------PAADVAVAAALISSILSI 388 ++ MI + N+D+H+ + + +A +A A ALIS++ I Sbjct: 477 NKGMMIKQA----FLMSILNYDIHIPFSASLVFEQSYGEVDGDSASLAEACALISALSKI 532 Query: 389 PLPSDFVYFGEVSLSGSVRAVG 410 P+ D G + G V+ VG Sbjct: 533 PVDQDIAITGSIDQFGEVQPVG 554 >gnl|CDD|32701 COG2874, FlaH, Predicted ATPases involved in biogenesis of archaeal flagella [Cell motility and secretion / Intracellular trafficking and secretion]. Length = 235 Score = 47.5 bits (113), Expect = 7e-06 Identities = 41/128 (32%), Positives = 61/128 (47%), Gaps = 18/128 (14%) Query: 67 EEESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSG 126 E + I++ DELD+ GGG GS+IL+ GD G GKS L + A +R+TYVS Sbjct: 5 ELKKIIKSGNDELDKRLGGGIPVGSLILIEGDNGTGKSVLSQRFAYGFLMNGYRVTYVST 64 Query: 127 E----EAIGQIR-LRAQRLNTINSSVYIAIETNVE-------------DIIATLITNEKP 168 E E I Q+ L + + S + N+E D++ I + Sbjct: 65 ELTVREFIKQMESLSYDVSDFLLSGRLLFFPVNLEPVNWGRRSARKLLDLLLEFIKRWEK 124 Query: 169 DLVIIDSI 176 D++IIDS+ Sbjct: 125 DVIIIDSL 132 >gnl|CDD|37215 KOG2004, KOG2004, KOG2004, Mitochondrial ATP-dependent protease PIM1/LON [Posttranslational modification, protein turnover, chaperones]. Length = 906 Score = 46.5 bits (110), Expect = 2e-05 Identities = 50/178 (28%), Positives = 81/178 (45%), Gaps = 19/178 (10%) Query: 270 FEMSDKGLQEVSDPSKIFLSDR--DSTSPGTAVFAGIE--GTRALLVEIQSLVVPTSLGM 325 E+ + LQ++ P +F S+R + T PG + G L VE SL+ G Sbjct: 692 IEIDESNLQDILGP-PVFTSERMYEVTPPGVVMGLAWTAMGGSTLYVE-TSLMRGLGDGS 749 Query: 326 PRRT----VVGWDSSRLAMILAVLEARCNIK------FGNHDVHLNI-AGGYRISEPAAD 374 T V +S+++A A + K N D+HL++ G P+A Sbjct: 750 LEITGQLGDVMKESAQIA--YTWARAFLSKKEPENKFLENSDIHLHVPEGATPKDGPSAG 807 Query: 375 VAVAAALISSILSIPLPSDFVYFGEVSLSGSVRAVGHMQQRLKEAEKIGFLSGVFPES 432 V + AL+S L P+ D GEV+L+G V VG ++++ A + G + +FPE+ Sbjct: 808 VTMVTALLSLALGKPVRQDLAMTGEVTLTGKVLPVGGIKEKTIAARRSGVKTIIFPEA 865 Score = 28.8 bits (64), Expect = 3.8 Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%) Query: 86 GFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIR 134 G V+G ++ G PG+GK+++ A +L K R + V G + +I+ Sbjct: 434 GSVQGKILCFVGPPGVGKTSIAKSIARALNRKFFRFS-VGGMTDVAEIK 481 >gnl|CDD|30653 COG0305, DnaB, Replicative DNA helicase [DNA replication, recombination, and repair]. Length = 435 Score = 46.0 bits (109), Expect = 2e-05 Identities = 30/150 (20%), Positives = 67/150 (44%), Gaps = 20/150 (13%) Query: 72 IQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHR-ITYVSGEEAI 130 + T +LD +T G F G +I+V PG+GK+ L + A + A + + S E + Sbjct: 179 VPTGFTDLDEITSG-FRPGDLIIVAARPGMGKTALALNIALNAAADGRKPVAIFSLEMSE 237 Query: 131 GQIRLRAQRLNTINSSVYIAIETNVE-DIIATLITNEKPDLVIIDSIQTL--WSQTAESS 187 Q+ +R ++ E+ +E + T ++ +I + L + + Sbjct: 238 EQLVMRL-----------LSSESGIESSKLRTGRLSDDEWERLIKAASELSEAPIFIDDT 286 Query: 188 PG-TVIQVRTSVQAMIQYAKKNGVAMVLVG 216 PG T+ ++R+ + + K+ + ++++ Sbjct: 287 PGLTITEIRSKARRL---KLKHNLGLIVID 313 >gnl|CDD|30814 COG0466, Lon, ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]. Length = 782 Score = 44.4 bits (105), Expect = 6e-05 Identities = 22/80 (27%), Positives = 45/80 (56%), Gaps = 1/80 (1%) Query: 353 FGNHDVHLNIAGGYRISE-PAADVAVAAALISSILSIPLPSDFVYFGEVSLSGSVRAVGH 411 F D+H+++ G + P+A + +A AL+S + P+ +D GE++L G V +G Sbjct: 661 FEKRDIHIHVPEGATPKDGPSAGITMATALVSLLTGKPVRADVAMTGEITLRGRVLPIGG 720 Query: 412 MQQRLKEAEKIGFLSGVFPE 431 ++++L A + G + + P+ Sbjct: 721 LKEKLLAAHRGGIKTVIIPK 740 >gnl|CDD|146436 pfam03796, DnaB_C, DnaB-like helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. Length = 186 Score = 44.5 bits (106), Expect = 6e-05 Identities = 14/49 (28%), Positives = 28/49 (57%), Gaps = 1/49 (2%) Query: 72 IQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHR 120 + T +LD++TGG +G +I++ P +GK+ + A + A K+ + Sbjct: 2 LPTGFTDLDQLTGG-LQKGDLIIIAARPSMGKTAFALNIARNAALKQDK 49 >gnl|CDD|36646 KOG1433, KOG1433, KOG1433, DNA repair protein RAD51/RHP55 [Replication, recombination and repair]. Length = 326 Score = 43.9 bits (103), Expect = 1e-04 Identities = 50/238 (21%), Positives = 91/238 (38%), Gaps = 33/238 (13%) Query: 72 IQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIG 131 + T LD++ GGG GS+ + G PG GK+ L A + + ++ Y+ E Sbjct: 93 LSTGSKALDKLLGGGIETGSLTELVGPPGSGKTQLCHTLAVTCGGGEGKVLYIDTESTFR 152 Query: 132 QIRL------RAQRLNTINSSVYIAIETNVEDIIATLITNE------KPDLVIIDSIQTL 179 RL R S++ +A N++ + + E + L+I+DS L Sbjct: 153 LERLTEIAGRSGLRGRDTLSNLMLARAYNLDHQLQLIQEAEIMINQSRVKLLIVDSATAL 212 Query: 180 WSQT---AESSPGTVIQVRTSVQAMIQYAKKNGVAMVLVGHVT------------KEGQI 224 + T + + ++++ + A + GVA+V+ VT + I Sbjct: 213 YRTTFKGRGELSARQMLLAKFLRSLKKLADEFGVAVVITNQVTAQVDGAIMFGSDPKKPI 272 Query: 225 AGPRVIEHMVDAVLYFEGGTRNTQYDYRILRSVKNRFGPTDEIGVFEMSDKGLQEVSD 282 G H V L G RI + + P E VF +++ G+ + + Sbjct: 273 GGNI-WAHAVTTRLGLRKGKGER----RICKIADSPCLPEAE-AVFAITEDGISDQRE 324 >gnl|CDD|29988 cd01122, GP4d_helicase, GP4d_helicase is a homohexameric 5'-3' helicases. Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.. Length = 271 Score = 43.0 bits (101), Expect = 2e-04 Identities = 47/237 (19%), Positives = 86/237 (36%), Gaps = 57/237 (24%) Query: 77 DELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYK-KHRITYVSGEEA------ 129 L+++T G +G +I++ G+GK+T L + A L + R+ +S EE Sbjct: 18 PVLNKLTKG-LRKGELIILTAGTGVGKTTFLREYALDLITQHGVRVGTISLEEPVVRTAR 76 Query: 130 --IGQI---RLRAQRLNTINSS-----------------VYIAIETN----VEDIIATLI 163 +GQ RL I + +Y + V + + + Sbjct: 77 RLLGQYAGKRLHLPDTVFIYTLEEFDAAFDEFEGTGRLFMYDSFGEYSMDSVLEKVRYMA 136 Query: 164 TNEKPDLVIIDSIQTLWSQTAESSPGTVIQVRTSVQAMIQYAKKNGVAMVLVGHVTKE-- 221 + +IID++ + S S + + + +A ++G+ + LV H+ + Sbjct: 137 VSHGIQHIIIDNLSIMVSDERASG-DERKALDEIMTKLRGFATEHGIHITLVSHLRRPDG 195 Query: 222 ------------GQIAGPRVIEHMVDAVLYFEGGTRNTQYDYRI-----LRSVKNRF 261 G I + D V+ E RN Q + LR +KNRF Sbjct: 196 DKTHEEGGEVSLSDFRGSAAIGQLADNVIALE---RNQQAELDERNTTYLRILKNRF 249 >gnl|CDD|29984 cd00983, recA, RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response. RecA couples ATP hydrolysis to DNA strand exchange.. Length = 325 Score = 42.5 bits (100), Expect = 3e-04 Identities = 39/172 (22%), Positives = 77/172 (44%), Gaps = 21/172 (12%) Query: 40 KESDQRFSKTIKQGHSISLFMLSEESIEEESRIQTHIDELDRVTG-GGFVRGSVILVGGD 98 K+ +++F K S+ L ++++++ I T LD G GG+ +G +I + G Sbjct: 11 KQIEKKFGKG-------SIMKLGDDAVQDVEVIPTGSLSLDIALGIGGYPKGRIIEIYGP 63 Query: 99 PGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRLRAQRLNTINSSVYIAIETNVE-- 156 GK+TL + A + ++ E A+ + A++L ++ I+ E Sbjct: 64 ESSGKTTLALHAIAEAQKLGGTVAFIDAEHALD--PVYAKKLGVDLDNLLISQPDTGEQA 121 Query: 157 -DIIATLITNEKPDLVIIDSIQTLWSQT------AESSPGTVIQVRTSVQAM 201 +I +L+ + DL+++DS+ L + +S G Q R QA+ Sbjct: 122 LEIADSLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGL--QARLMSQAL 171 >gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.. Length = 151 Score = 42.1 bits (99), Expect = 4e-04 Identities = 18/91 (19%), Positives = 34/91 (37%), Gaps = 13/91 (14%) Query: 89 RGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRLRAQRLNTINSSVY 148 +++L G PG GK+TL A L Y++ + + + + Sbjct: 19 PKNLLLYG-PPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVA------------ 65 Query: 149 IAIETNVEDIIATLITNEKPDLVIIDSIQTL 179 + ++ L KP ++ ID I +L Sbjct: 66 ELFGHFLVRLLFELAEKAKPGVLFIDEIDSL 96 >gnl|CDD|36647 KOG1434, KOG1434, KOG1434, Meiotic recombination protein Dmc1 [Energy production and conversion, Replication, recombination and repair]. Length = 335 Score = 40.7 bits (95), Expect = 8e-04 Identities = 40/200 (20%), Positives = 74/200 (37%), Gaps = 34/200 (17%) Query: 47 SKTIKQGHSISLFMLSEESIEEESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTL 106 +K+I G +L +L + + I T LD + GGG S+ + G+ GK+ L Sbjct: 74 NKSISHGFCTALELLEQR--KTVGSITTGSSALDDILGGGIPSMSITEIFGEFRCGKTQL 131 Query: 107 LMQTAAS------LAYKKHRITYVSGEEAIGQIRLR--AQRLN--------------TIN 144 + + + ++ E R++ A+R N Sbjct: 132 SHTLCVTVQLPREMGGVGGKAIFIDTEGTFRPDRIKDIAERFKVDPDFTLDNILYFRAYN 191 Query: 145 SSVYIAIETNVEDIIATLITNEKPDLVIIDSIQTLWSQTAESSPGTVIQVRTSV-----Q 199 S + + + D ++ + K LVI+DSI L+ + + R Q Sbjct: 192 SEEQMELVYLLGDFLS---EHGKYRLVIVDSIMALFRV--DYDGRGELSERQQKLNQMLQ 246 Query: 200 AMIQYAKKNGVAMVLVGHVT 219 + + A++ VA+ L VT Sbjct: 247 KLNKLAEEFNVAVFLTNQVT 266 >gnl|CDD|29985 cd00984, DnaB_C, DnaB helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.. Length = 242 Score = 39.8 bits (93), Expect = 0.002 Identities = 30/134 (22%), Positives = 53/134 (39%), Gaps = 34/134 (25%) Query: 77 DELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYK-KHRITYVSGEEAIGQIRL 135 +LD +TGG G +I++ P +GK+ + A ++A K + + S E + Q+ Sbjct: 1 TDLDNLTGG-LQPGDLIIIAARPSMGKTAFALNIAENIAKKQGKPVLFFSLEMSKEQLLQ 59 Query: 136 R---------AQRLNTINSS------------------VYIAIETN--VEDIIAT---LI 163 R +L T + S +YI ++ V DI + L Sbjct: 60 RLLASESGISLSKLRTGSLSDEDWERLAEAIGELKELPIYIDDSSSLTVSDIRSRARRLK 119 Query: 164 TNEKPDLVIIDSIQ 177 L++ID +Q Sbjct: 120 KEHGLGLIVIDYLQ 133 >gnl|CDD|114104 pfam05362, Lon_C, Lon protease (S16) C-terminal proteolytic domain. The Lon serine proteases must hydrolyse ATP to degrade protein substrates. In Escherichia coli, these proteases are involved in turnover of intracellular proteins, including abnormal proteins following heat-shock. The active site for protease activity resides in a C-terminal domain. The Lon proteases are classified as family S16 in Merops. Length = 205 Score = 39.1 bits (92), Expect = 0.003 Identities = 24/80 (30%), Positives = 45/80 (56%), Gaps = 1/80 (1%) Query: 353 FGNHDVHLNI-AGGYRISEPAADVAVAAALISSILSIPLPSDFVYFGEVSLSGSVRAVGH 411 F D+H+++ G P+A V +A AL+S++ IP+ D GE++L G V +G Sbjct: 91 FEKKDIHIHVPEGATPKDGPSAGVTMATALVSALTGIPVRKDVAMTGEITLRGRVLPIGG 150 Query: 412 MQQRLKEAEKIGFLSGVFPE 431 ++++L A + G + + P+ Sbjct: 151 LKEKLLAAHRAGIKTVIIPK 170 >gnl|CDD|30951 COG0606, COG0606, Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]. Length = 490 Score = 35.6 bits (82), Expect = 0.029 Identities = 36/160 (22%), Positives = 66/160 (41%), Gaps = 22/160 (13%) Query: 309 ALLVEIQSLVVPTSLGMPRRTVVGWDSSRLAMILAVLEAR---------CNIKFGNHDVH 359 A VE++ + S G+P T+VG + AV E+R +F + Sbjct: 2 APPVEVEVDI---SNGLPGFTIVGLPDT------AVKESRERVRAALTNSGFEFPAKRIT 52 Query: 360 LNIA-GGYRISEPAADVAVAAALISSILSIPLP--SDFVYFGEVSLSGSVRAVGHMQQRL 416 +N+A D+ +A ++++ +P + + GE+SL G +R VG + Sbjct: 53 INLAPADLPKEGSRFDLPIALGILAASGQLPADALILYEFLGELSLDGLLRPVGGVLPAA 112 Query: 417 KEAEKIGFLSGVFPESAKGECK-IGMLDRQYIKNLSDLVK 455 A++ G + P+ E IG L + L ++V Sbjct: 113 LAAKEKGKRGLIVPKENAEEASLIGGLPVYGARYLEEVVN 152 >gnl|CDD|144183 pfam00493, MCM, MCM2/3/5 family. Length = 327 Score = 34.8 bits (81), Expect = 0.052 Identities = 19/47 (40%), Positives = 25/47 (53%), Gaps = 5/47 (10%) Query: 81 RVTGGGFVRGSV-ILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSG 126 + G +RG + +L+ GDPG KS LL + A LA R Y SG Sbjct: 47 NLPDGTRLRGDINVLLVGDPGTAKSQLL-KYVAKLA---PRAVYTSG 89 >gnl|CDD|33687 COG3899, COG3899, Predicted ATPase [General function prediction only]. Length = 849 Score = 35.0 bits (80), Expect = 0.052 Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 3/57 (5%) Query: 66 IEEESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRIT 122 E+ + + DRV+ G RG V+LV G+ GIGKS L+ + + ++ Sbjct: 3 YGRETELAQLLAAFDRVSKG---RGEVVLVAGESGIGKSALVNEVHKPITQQRGYFI 56 >gnl|CDD|29991 cd01125, repA, Hexameric Replicative Helicase RepA. RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent.. Length = 239 Score = 34.9 bits (80), Expect = 0.053 Identities = 43/165 (26%), Positives = 74/165 (44%), Gaps = 39/165 (23%) Query: 90 GSVILVGGDPGIGKSTLLMQTAASLAYKKH------------RITYVSGEEAIGQI--RL 135 G V + G GKS+LL+ A ++A K+ R+ Y+S E+ +I RL Sbjct: 1 GYVSALVAPGGTGKSSLLLVLALAMALGKNLFGGGLKVTEPGRVVYLSAEDPREEIHRRL 60 Query: 136 RA--QRLNTINSSVYIAIET------------------NVEDIIATLITNEKPDLVIIDS 175 A Q L ++ + I++ E II L+ + DLV+ID Sbjct: 61 EAILQHLEPDDAGDRLFIDSGRIQPISIAREGRIIVVPEFERIIEQLLI-RRIDLVVIDP 119 Query: 176 IQTLWSQTAESSPGTVIQVRTSVQAMIQYAKKNGVAMVLVGHVTK 220 + + + +E+ G + V ++A+ + A + G A++LV HV K Sbjct: 120 LVS-FHGVSENDNGAMDAV---IKALRRIAAQTGAAILLVHHVRK 160 >gnl|CDD|33398 COG3598, RepA, RecA-family ATPase [DNA replication, recombination, and repair]. Length = 402 Score = 34.6 bits (79), Expect = 0.060 Identities = 36/165 (21%), Positives = 70/165 (42%), Gaps = 32/165 (19%) Query: 87 FVRGSVILVGGDPGIGKSTLLMQTAASLAYKKH----------RITYVSGE----EAIGQ 132 F +G V ++ GD G+GK+TLL+ +LA K+ ++ YVS E + + + Sbjct: 86 FRKGYVSILYGDSGVGKTTLLLYLCIALAAGKNLFGNKVKEPGKVLYVSLELYREDILER 145 Query: 133 IRLRAQRLNTINSSVYIAIETNVE------DIIA------TLITNE--KPDLVIIDSIQT 178 + R+ + V T+V D+++ E +PD V+ID Sbjct: 146 LEPVRARMGLSPADVRNMDLTDVSGAADESDVLSPKLYRRFEKILEQKRPDFVVIDPFVA 205 Query: 179 LWSQTAESSPGTVIQVRTSVQAMIQYAKKNGVAMVLVGHVTKEGQ 223 + + S +QV+ ++ + A+ A++ + H +K Sbjct: 206 FYEGKSISD----VQVKEFIKKTRKLARNLECAIIYIHHTSKSSG 246 >gnl|CDD|36777 KOG1564, KOG1564, KOG1564, DNA repair protein RHP57 [Replication, recombination and repair]. Length = 351 Score = 34.6 bits (79), Expect = 0.066 Identities = 36/182 (19%), Positives = 61/182 (33%), Gaps = 32/182 (17%) Query: 70 SRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKH------RITY 123 S++ T LD GG + + G+ G GK+ LL+Q + + + Y Sbjct: 82 SKLTTGCVALDECLRGGIPTDGITEICGESGCGKTQLLLQLSLCVQLPRSHGGLGGGAVY 141 Query: 124 VSGEEAIGQIRLR----------------------AQRLNTINSSVYIAIETNVEDIIAT 161 + E RL + N + V + Sbjct: 142 ICTESPFPTRRLHQLSHTLPQRPNPEKELNYNDNPGDHIFVENVHDVDHLLHIVNRQLPI 201 Query: 162 LITNEKPDLVIIDSIQTLWSQTAESSPGTVI----QVRTSVQAMIQYAKKNGVAMVLVGH 217 L+ +K LVIIDS+ L+ + +P + + + Q A K +A+V Sbjct: 202 LLNRKKIKLVIIDSVAALFRSEFDYNPSDLKKRARHLFRLAGKLRQLASKFDLAVVCANQ 261 Query: 218 VT 219 VT Sbjct: 262 VT 263 >gnl|CDD|31936 COG1750, COG1750, Archaeal serine proteases [General function prediction only]. Length = 579 Score = 33.8 bits (77), Expect = 0.12 Identities = 27/142 (19%), Positives = 60/142 (42%), Gaps = 10/142 (7%) Query: 302 AGIEGTRALLVEIQSLVVPTS-------LGMPRRTVVGWDSSRLAMILAVLEARCNIKFG 354 + + + V I V T P + S+R+A +A+ A + Sbjct: 40 SVTSQGQGVGVPINISVTVTPGDGRVYVATFPYTQIDMQGSARVAAGVALRLA--GVDMS 97 Query: 355 NHDVHLNI-AGGYRISEPAADVAVAAALISSILSIPLPSDFVYFGEVSLSGSVRAVGHMQ 413 ++DV++ + A + P+A + A+ ++++ + D + G ++ GS+ VG + Sbjct: 98 SYDVYIAVEADSPVVGGPSAGGYMTVAIYAALMGWSIRKDVMMTGMINPDGSIGPVGGIL 157 Query: 414 QRLKEAEKIGFLSGVFPESAKG 435 ++L+ A K G + P + Sbjct: 158 EKLEAAAKAGAKIFLIPVGQRI 179 >gnl|CDD|72971 cd00267, ABC_ATPase, ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.. Length = 157 Score = 33.3 bits (76), Expect = 0.13 Identities = 31/142 (21%), Positives = 55/142 (38%), Gaps = 14/142 (9%) Query: 89 RGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRLRAQRLNTINSSVY 148 G ++ + G G GKSTLL A L I + I ++ L R Sbjct: 24 AGEIVALVGPNGSGKSTLLRAIAGLLKPTSGEILI--DGKDIAKLPLEELRRRIGYVPQL 81 Query: 149 IAIETNVEDIIATLITNEKPDLVIIDSIQTLWSQTAESSPGTVIQVRTSVQAMIQYAKKN 208 + + L+ N PDL+++D E + G R + +++ + Sbjct: 82 SGGQRQRVALARALLLN--PDLLLLD----------EPTSGLDPASRERLLELLRELAEE 129 Query: 209 GVAMVLVGHVTKEGQIAGPRVI 230 G +++V H + ++A RVI Sbjct: 130 GRTVIIVTHDPELAELAADRVI 151 >gnl|CDD|147726 pfam05729, NACHT, NACHT domain. This NTPase domain is found in apoptosis proteins as well as those involved in MHC transcription activation. This family is closely related to pfam00931. Length = 165 Score = 33.4 bits (77), Expect = 0.14 Identities = 17/98 (17%), Positives = 36/98 (36%), Gaps = 22/98 (22%) Query: 91 SVILVGGDPGIGKSTLLMQTAASLA----YKKHRITYVSGEEAIGQIRLRAQRLNTIN-- 144 +++ G+ G GK+TLL + A A + + L + L+ Sbjct: 1 RTVILQGEAGSGKTTLLQKLALLWAQGKLPQDFDFVFF----------LPCRELSRSGEA 50 Query: 145 ------SSVYIAIETNVEDIIATLITNEKPDLVIIDSI 176 S + V ++ A ++ + L+I+D + Sbjct: 51 SLADLLFSQWPEPAAPVSEVWAVILELPERVLLILDGL 88 >gnl|CDD|31058 COG0714, COG0714, MoxR-like ATPases [General function prediction only]. Length = 329 Score = 33.2 bits (75), Expect = 0.15 Identities = 12/36 (33%), Positives = 18/36 (50%) Query: 86 GFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRI 121 + G +L+ G PG+GK+ L A +L RI Sbjct: 39 ALLAGGHVLLEGPPGVGKTLLARALARALGLPFVRI 74 >gnl|CDD|31673 COG1484, DnaC, DNA replication protein [DNA replication, recombination, and repair]. Length = 254 Score = 32.7 bits (74), Expect = 0.23 Identities = 24/176 (13%), Positives = 60/176 (34%), Gaps = 32/176 (18%) Query: 4 IRSQYFCQSCGEIHSRWIGKCDSCNAWNTIIEDSSRKESDQRFSKTIKQGHSISLF---M 60 + C+ G ++ ++ + +RK + S + + F Sbjct: 30 LEQAADCKEWG--YAEFLEYLLEEE----KLAREARKIERRLRSASFPAKKTFEEFDFEF 83 Query: 61 LSEESIEEESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHR 120 + + + ++ +R +++ G PG+GK+ L + L Sbjct: 84 QPGIDKKALEDLASLVEFFERGEN--------LVLLGPPGVGKTHLAIAIGNELLKAGIS 135 Query: 121 ITYVSGEEAIGQIRLRAQRLNTINSSVYIAIETNVEDIIATLITNEKPDLVIIDSI 176 + +++ + + +++ A + E ++ L K DL+IID I Sbjct: 136 VLFITAPDLLSKLK-AAFDEGRLE-----------EKLLRELK---KVDLLIIDDI 176 >gnl|CDD|146080 pfam03266, DUF265, Protein of unknown function, DUF265. Length = 168 Score = 32.6 bits (75), Expect = 0.25 Identities = 25/107 (23%), Positives = 36/107 (33%), Gaps = 25/107 (23%) Query: 92 VILVGGDPGIGKSTLLMQTAASLAY---------------KKHRI-----TYVSGEEAIG 131 I + G PG+GK+TL+ + L RI SGE Sbjct: 1 RIFITGPPGVGKTTLVKKVIELLKSEGVKVGGFYTPEVREGGRRIGFDIVDLASGERGP- 59 Query: 132 QIRLRAQRLNTINSSVYIAIETNVEDIIATLITN--EKPDLVIIDSI 176 R+ Y+ E+I + E+ DL+IID I Sbjct: 60 LARVGGVS--GPRVGKYVVNLEEFEEIALPALRRALEEADLIIIDEI 104 >gnl|CDD|31438 COG1245, COG1245, Predicted ATPase, RNase L inhibitor (RLI) homolog [General function prediction only]. Length = 591 Score = 31.7 bits (72), Expect = 0.41 Identities = 14/64 (21%), Positives = 22/64 (34%), Gaps = 8/64 (12%) Query: 59 FMLSEESIEEESRIQTHIDELDR--------VTGGGFVRGSVILVGGDPGIGKSTLLMQT 110 F ++ +L + V G G VI + G GIGK+T + Sbjct: 328 FEEKPPRDDKARDTLVEYPDLKKTYGDFKLEVEEGEIYDGEVIGILGPNGIGKTTFVKLL 387 Query: 111 AASL 114 A + Sbjct: 388 AGVI 391 >gnl|CDD|35288 KOG0065, KOG0065, KOG0065, Pleiotropic drug resistance proteins (PDR1-15), ABC superfamily [Secondary metabolites biosynthesis, transport and catabolism]. Length = 1391 Score = 31.8 bits (72), Expect = 0.43 Identities = 16/37 (43%), Positives = 18/37 (48%), Gaps = 3/37 (8%) Query: 90 GSVILVGGDPGIGKSTLLMQTAASL---AYKKHRITY 123 G + LV G PG GK+TLL A L ITY Sbjct: 141 GEMTLVLGPPGSGKTTLLKALAGKLDNFLKSSGEITY 177 >gnl|CDD|35701 KOG0480, KOG0480, KOG0480, DNA replication licensing factor, MCM6 component [Replication, recombination and repair]. Length = 764 Score = 31.8 bits (72), Expect = 0.43 Identities = 15/40 (37%), Positives = 19/40 (47%), Gaps = 5/40 (12%) Query: 88 VRGSV-ILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSG 126 +RG + + + GDPG GKS L A R Y SG Sbjct: 375 LRGDINVCIVGDPGTGKSQFLKAVCAFSP----RSVYTSG 410 >gnl|CDD|32257 COG2074, COG2074, 2-phosphoglycerate kinase [Carbohydrate transport and metabolism]. Length = 299 Score = 31.4 bits (71), Expect = 0.57 Identities = 27/94 (28%), Positives = 45/94 (47%), Gaps = 15/94 (15%) Query: 92 VILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRLRA----QRLNTINSSV 147 +IL+GG G+GKST+ + A L I V ++I ++ LR + L T+++S Sbjct: 91 IILIGGASGVGKSTIAGELARRLG-----IRSVISTDSIREV-LRKIISPELLPTLHTSS 144 Query: 148 YIA-----IETNVEDIIATLITNEKPDLVIIDSI 176 Y A T+ IIA +V I+++ Sbjct: 145 YDAWKALRDPTDENPIIAGFEDQASAVMVGIEAV 178 >gnl|CDD|39152 KOG3949, KOG3949, KOG3949, RNA polymerase II elongator complex, subunit ELP4 [Chromatin structure and dynamics, Transcription]. Length = 360 Score = 31.1 bits (70), Expect = 0.60 Identities = 13/65 (20%), Positives = 31/65 (47%) Query: 72 IQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIG 131 + I +LD++ GGG GS +L+ D + ++L++ + + ++ + Sbjct: 29 TSSGIADLDQILGGGLPLGSSVLIEEDRSMIYHSVLLKYFLAEGLVNNHTLLLASPKKDP 88 Query: 132 QIRLR 136 ++ LR Sbjct: 89 KMFLR 93 >gnl|CDD|31434 COG1241, MCM2, Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]. Length = 682 Score = 31.1 bits (70), Expect = 0.61 Identities = 18/44 (40%), Positives = 22/44 (50%), Gaps = 5/44 (11%) Query: 85 GGFVRGSV-ILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGE 127 G +RG + IL+ GDPG KS LL A R Y SG+ Sbjct: 313 GTRIRGDIHILLVGDPGTAKSQLLKYVAKLA----PRGVYTSGK 352 >gnl|CDD|147666 pfam05625, PAXNEB, PAXNEB protein. PAXNEB or PAX6 neighbour is found in several eukaryotic organisms. PAXNED is an RNA polymerase II Elongator protein subunit. It is part of the HAP subcomplex of Elongator, which is a six-subunit component of the RNA polymerase II holoenzyme. The HAP subcomplex is required for Elongator structural integrity and histone acetyltransferase activity. This protein family has a P-loop motif. However its sequence has degraded in many members of the family. Length = 353 Score = 31.1 bits (71), Expect = 0.66 Identities = 24/100 (24%), Positives = 46/100 (46%), Gaps = 2/100 (2%) Query: 144 NSSVYIAIETNVEDIIATLITNEKPDL-VIIDSI-QTLWSQTAESSPGTVIQVRTSVQAM 201 N S Y ++ ++ +IA + N L ++I S+ LW S P ++ S++A+ Sbjct: 170 NESPYASLLKQIQSLIAKSLFNPNNVLRIVIPSLLSPLWYPPECSQPTELLPFLHSLRAL 229 Query: 202 IQYAKKNGVAMVLVGHVTKEGQIAGPRVIEHMVDAVLYFE 241 ++ N VA++ + + R IE + D V+ E Sbjct: 230 LRKYSSNLVAIITLPLSLYPRSSSLVRWIELLADGVIELE 269 >gnl|CDD|35699 KOG0478, KOG0478, KOG0478, DNA replication licensing factor, MCM4 component [Replication, recombination and repair]. Length = 804 Score = 31.1 bits (70), Expect = 0.69 Identities = 18/44 (40%), Positives = 19/44 (43%), Gaps = 4/44 (9%) Query: 83 TGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSG 126 G F IL+ GDPG KS LL Q L R Y SG Sbjct: 455 KSGRFRGDINILLVGDPGTSKSQLL-QYCHRLL---PRGVYTSG 494 >gnl|CDD|58499 cd01822, Lysophospholipase_L1_like, Lysophospholipase L1-like subgroup of SGNH-hydrolases. The best characterized member in this family is TesA, an E. coli periplasmic protein with thioesterase, esterase, arylesterase, protease and lysophospholipase activity.. Length = 177 Score = 30.9 bits (70), Expect = 0.76 Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 15/63 (23%) Query: 159 IATLITNEKPDLVII-----DSIQTLWSQTAESSPGTVIQVRTSVQAMIQYAKKNGVAMV 213 + L+ KPDLVI+ D ++ + P Q R +++ MI+ A+ G ++ Sbjct: 56 LPALLAQHKPDLVILELGGNDGLRGI-------PPD---QTRANLRQMIETAQARGAPVL 105 Query: 214 LVG 216 LVG Sbjct: 106 LVG 108 >gnl|CDD|73290 cd01983, Fer4_NifH, The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.. Length = 99 Score = 30.8 bits (69), Expect = 0.83 Identities = 14/33 (42%), Positives = 21/33 (63%) Query: 92 VILVGGDPGIGKSTLLMQTAASLAYKKHRITYV 124 VI+V G G+GK+TL AA+LA + R+ + Sbjct: 1 VIVVTGKGGVGKTTLAANLAAALAKRGKRVLLI 33 >gnl|CDD|73298 cd02035, ArsA, ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces resistance to the toxic agents. The pump is composed of two subunits, the catalytic ArsA subunit and the membrane subunit ArsB, which are encoded by arsA and arsB genes respectively. Arsenic efflux in bacteria is catalyzed by either ArsB alone or by ArsAB complex. The ATP-coupled pump, however, is more efficient. ArsA is composed of two homologous halves, A1 and A2, connected by a short linker sequence.. Length = 217 Score = 30.6 bits (69), Expect = 0.96 Identities = 17/63 (26%), Positives = 25/63 (39%) Query: 92 VILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRLRAQRLNTINSSVYIAI 151 VI G G+GK+T+ TA LA + ++ VS + A L+ I Sbjct: 1 VIFFTGKGGVGKTTIAAATAVRLAEEGKKVLLVSTDPAHNLSDKGLPNLSDAFIVEDPEI 60 Query: 152 ETN 154 N Sbjct: 61 APN 63 >gnl|CDD|33845 COG4088, COG4088, Predicted nucleotide kinase [Nucleotide transport and metabolism]. Length = 261 Score = 30.7 bits (69), Expect = 0.99 Identities = 26/126 (20%), Positives = 52/126 (41%), Gaps = 13/126 (10%) Query: 92 VILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRLRAQRLNTINSSVYIAI 151 +I++ G PG GK+T + A L + R+ ++ + G + I VY Sbjct: 3 LIILTGYPGSGKTTFAKELAKELRQEIWRVIHLEKDYLRG---ILWDESLPILKEVY--R 57 Query: 152 ETNVEDIIATLITNEKPDLVIIDSIQTLWSQTAE--------SSPGTVIQVRTSVQAMIQ 203 E+ ++ + L + K LVI+D S + + +I +RT + ++ Sbjct: 58 ESFLKSVERLLDSALKNYLVIVDDTNYYKSMRRQLACEAKERKTTWCIIYLRTPLDTCLR 117 Query: 204 YAKKNG 209 ++ G Sbjct: 118 RNRERG 123 >gnl|CDD|143922 pfam00154, RecA, recA bacterial DNA recombination protein. RecA is a DNA-dependent ATPase and functions in DNA repair systems. RecA protein catalyses an ATP-dependent DNA strand-exchange reaction that is the central step in the repair of dsDNA breaks by homologous recombination. Length = 322 Score = 30.3 bits (69), Expect = 1.1 Identities = 29/127 (22%), Positives = 57/127 (44%), Gaps = 6/127 (4%) Query: 57 SLFMLSEESIEEESRIQTHIDELDRVTG-GGFVRGSVILVGGDPGIGKSTLLMQTAASLA 115 S+ L ++++E+ I T LD G GG +G +I + G GK+TL + A Sbjct: 18 SIMRLGDKTVEDVEVISTGSLGLDIALGIGGLPKGRIIEIYGPESSGKTTLALHAIAEAQ 77 Query: 116 YKKHRITYVSGEEAIGQIRLRAQRLNTINSSVYIAIETNVE---DIIATLITNEKPDLVI 172 ++ E A+ + + ++ N + ++ E +I L+ + DL++ Sbjct: 78 KAGGTAAFIDAEHALDPVYAKKLGVDIDN--LLVSQPDTGEQALEIADMLVRSGAVDLIV 135 Query: 173 IDSIQTL 179 +DS+ L Sbjct: 136 VDSVAAL 142 >gnl|CDD|32776 COG2956, COG2956, Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]. Length = 389 Score = 30.3 bits (68), Expect = 1.1 Identities = 12/32 (37%), Positives = 17/32 (53%) Query: 2 VKIRSQYFCQSCGEIHSRWIGKCDSCNAWNTI 33 ++ + +Y CQ+CG C SC AW TI Sbjct: 349 LRRKPRYRCQNCGFTAHTLYWHCPSCRAWETI 380 >gnl|CDD|110677 pfam01695, IstB, IstB-like ATP binding protein. This protein contains an ATP/GTP binding P-loop motif. It is found associated with IS21 family insertion sequences. The function of this protein is unknown, but it may perform a transposase function. Length = 178 Score = 30.3 bits (69), Expect = 1.2 Identities = 21/98 (21%), Positives = 42/98 (42%), Gaps = 25/98 (25%) Query: 84 GGGFV-RGSVILVGGDPGIGKSTLLMQTAASLAYKK----HRITYVSGEEAIGQIRLRAQ 138 G ++ + +L+ G PG+GK+ L A +L ++ + + + + + Q++ RA+ Sbjct: 40 GLDWIEQAENLLLLGPPGVGKTHL----ACALGHQACRAGYSVLFTRTPDLVEQLK-RAR 94 Query: 139 RLNTINSSVYIAIETNVEDIIATLITNEKPDLVIIDSI 176 + TL K DL+I+D I Sbjct: 95 GDGRLAR---------------TLQRLAKADLLILDDI 117 >gnl|CDD|73214 cd00550, ArsA_ATPase, Oxyanion-translocating ATPase (ArsA). This ATPase is involved in transport of arsenite, antimonite or other oxyanions across biological membranes in all three kingdoms of life. ArsA contains a highly conserved AAA motif present in the AAA+ ATPase superfamily associated with a variety of cellular activities. To form a functional ATP-driven pump, ArsA interacts with the permease ArsB, which is a channel-forming integral membrane protein. One of the most interesting features of ArsA is the allosteric activation by its transport substrates. A divalent cation, typically Mg2+, is required for its enzymatic activity.. Length = 254 Score = 30.2 bits (68), Expect = 1.2 Identities = 14/38 (36%), Positives = 21/38 (55%) Query: 92 VILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEA 129 I GG G+GK+T+ TA LA + ++ VS + A Sbjct: 2 YIFFGGKGGVGKTTISAATAVRLAEQGKKVLLVSTDPA 39 >gnl|CDD|72996 cd03237, ABC_RNaseL_inhibitor_domain2, The ATPase domain 2 of RNase L inhibitor. The ABC ATPase, RNase L inhibitor (RLI), is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids. RLI's are not transport proteins and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity of more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.. Length = 246 Score = 30.3 bits (68), Expect = 1.3 Identities = 13/33 (39%), Positives = 16/33 (48%) Query: 82 VTGGGFVRGSVILVGGDPGIGKSTLLMQTAASL 114 V GG VI + G GIGK+T + A L Sbjct: 17 VEGGSISESEVIGILGPNGIGKTTFIKMLAGVL 49 >gnl|CDD|48371 cd02117, NifH_like, This family contains the NifH (iron protein) of nitrogenase, L subunit (BchL/ChlL) of the protochlorophyllide reductase and the BchX subunit of the Chlorophyllide reductase. Members of this family use energey from ATP hydrolysis and transfer electrons through a Fe4-S4 cluster to other subunit for reduction of substrate.. Length = 212 Score = 29.8 bits (67), Expect = 1.8 Identities = 11/30 (36%), Positives = 16/30 (53%) Query: 92 VILVGGDPGIGKSTLLMQTAASLAYKKHRI 121 I + G GIGKST +A+LA ++ Sbjct: 2 QIAIYGKGGIGKSTTSQNLSAALAEMGKKV 31 >gnl|CDD|143913 pfam00142, Fer4_NifH, 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family. Length = 269 Score = 29.6 bits (67), Expect = 1.9 Identities = 12/30 (40%), Positives = 17/30 (56%) Query: 92 VILVGGDPGIGKSTLLMQTAASLAYKKHRI 121 I + G GIGKST T+A+LA ++ Sbjct: 2 KIAIYGKGGIGKSTTSQNTSAALAEMGKKV 31 >gnl|CDD|32733 COG2909, MalT, ATP-dependent transcriptional regulator [Transcription]. Length = 894 Score = 29.5 bits (66), Expect = 2.0 Identities = 21/114 (18%), Positives = 40/114 (35%), Gaps = 20/114 (17%) Query: 76 IDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRL 135 +D L R +IL+ G GK+TLL Q A E R Sbjct: 28 LDRLRRAN-----DYRLILISAPAGFGKTTLLAQWRELAADGAAVAWLSLDESDNDPARF 82 Query: 136 RAQRLNTINSSV---------------YIAIETNVEDIIATLITNEKPDLVIID 174 + + + + Y+++E+ + ++ L + E P +++D Sbjct: 83 LSYLIAALQQATPTLGDEAQTLLQKHQYVSLESLLSSLLNELASYEGPLYLVLD 136 >gnl|CDD|144046 pfam00308, Bac_DnaA, Bacterial dnaA protein. Length = 219 Score = 29.6 bits (67), Expect = 2.0 Identities = 23/86 (26%), Positives = 37/86 (43%), Gaps = 20/86 (23%) Query: 97 GDPGIGKSTLLMQTAASLAYKKH---RITYVSGEEAIGQIRLRAQRLNTINSSVYIAIET 153 G G+GK T L+ + A + R+ Y++ EE + A R N I A + Sbjct: 41 GGVGLGK-THLLHAIGNYALRNFPNLRVVYLTSEE-FLNDFVDALRDNKIE-----AFKK 93 Query: 154 NVEDIIATLITNEKPDLVIIDSIQTL 179 + ++ DL++ID IQ L Sbjct: 94 SYRNV----------DLLLIDDIQFL 109 >gnl|CDD|48369 cd02040, NifH, NifH gene encodes component II (iron protein) of nitrogenase. Nitrogenase is responsible for the biological nitrogen fixation, i.e. reduction of molecular nitrogen to ammonia. NifH consists of two oxygen-sensitive metallosulfur proteins: the mollybdenum-iron (alternatively, vanadium-iron or iron-iron) protein (commonly referred to as component 1), and the iron protein (commonly referred to as component 2). The iron protein is a homodimer, with an Fe4S4 cluster bound between the subunits and two ATP-binding domains. It supplies energy by ATP hydrolysis, and transfers electrons from reduced ferredoxin or flavodoxin to component 1 for the reduction of molecular nitrogen to ammonia.. Length = 270 Score = 29.4 bits (66), Expect = 2.1 Identities = 12/32 (37%), Positives = 17/32 (53%) Query: 93 ILVGGDPGIGKSTLLMQTAASLAYKKHRITYV 124 I + G GIGKST +A+LA ++ V Sbjct: 4 IAIYGKGGIGKSTTTQNLSAALAEMGKKVMIV 35 >gnl|CDD|145008 pfam01637, Arch_ATPase, Archaeal ATPase. This family contain a conserved P-loop motif that is involved in binding ATP. This family is almost exclusively found in archaebacteria and particularly in Methanococcus jannaschii that encodes sixteen members of this family. Length = 223 Score = 29.2 bits (66), Expect = 2.3 Identities = 21/102 (20%), Positives = 35/102 (34%), Gaps = 14/102 (13%) Query: 91 SVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVS--GEEAIGQIRLR------AQRLNT 142 +I+V G GK+ LL + L +R+ Y E ++ A+ L Sbjct: 21 PIIVVYGPRRCGKTALLREFLEELRELGYRVIYYDPLRREFEEKLDRFEEAKRLAEALGD 80 Query: 143 INSSVYIAIETNVEDIIATLI-----TNEKPDLVIIDSIQTL 179 + IA + L +K +IID +Q Sbjct: 81 ALPKIGIAKSKLAFLSLTLLFELLKRKGKKI-AIIIDEVQYA 121 >gnl|CDD|36919 KOG1707, KOG1707, KOG1707, Predicted Ras related/Rac-GTP binding protein [Defense mechanisms]. Length = 625 Score = 29.2 bits (65), Expect = 2.4 Identities = 19/67 (28%), Positives = 29/67 (43%), Gaps = 5/67 (7%) Query: 32 TIIEDSSRKESDQRFSKTIKQGHSISLFML--SEESIEEESRIQTHIDELDRVTGGGFVR 89 +I++ SS + K I++ I L E +++ RI T L R G + Sbjct: 59 SIVDTSSDSDDRLCLRKEIRKADVICLVYAVDDESTVD---RISTKWLPLIRQLFGDYHE 115 Query: 90 GSVILVG 96 VILVG Sbjct: 116 TPVILVG 122 >gnl|CDD|31539 COG1348, NifH, Nitrogenase subunit NifH (ATPase) [Inorganic ion transport and metabolism]. Length = 278 Score = 29.4 bits (66), Expect = 2.5 Identities = 13/32 (40%), Positives = 17/32 (53%) Query: 93 ILVGGDPGIGKSTLLMQTAASLAYKKHRITYV 124 I + G GIGKST AA+LA ++ V Sbjct: 4 IAIYGKGGIGKSTTSQNLAAALAELGKKVLIV 35 >gnl|CDD|111283 pfam02374, ArsA_ATPase, Anion-transporting ATPase. This Pfam family represents a conserved domain, which is sometimes repeated, in an anion-transporting ATPase. The ATPase is involved in the removal of arsenate, antimonite, and arsenate from the cell. Length = 304 Score = 29.2 bits (66), Expect = 2.6 Identities = 13/38 (34%), Positives = 21/38 (55%) Query: 92 VILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEA 129 I GG G+GK+T+ TA L+ + ++ VS + A Sbjct: 3 WIFFGGKGGVGKTTVSCATAVRLSEQGKKVLLVSTDPA 40 >gnl|CDD|143799 pfam00006, ATP-synt_ab, ATP synthase alpha/beta family, nucleotide-binding domain. This family includes the ATP synthase alpha and beta subunits, the ATP synthase associated with flagella and the termination factor Rho. Length = 213 Score = 29.3 bits (67), Expect = 2.6 Identities = 9/24 (37%), Positives = 12/24 (50%) Query: 88 VRGSVILVGGDPGIGKSTLLMQTA 111 +G I + G G GK+ LL A Sbjct: 13 GKGQRIGIFGGSGTGKTVLLGMIA 36 >gnl|CDD|48379 cd03115, SRP, The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes. SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.. Length = 173 Score = 29.3 bits (66), Expect = 2.7 Identities = 23/92 (25%), Positives = 41/92 (44%), Gaps = 9/92 (9%) Query: 91 SVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGE----EAIGQIRLRAQRLNTINSS 146 +VIL+ G G+GK+T + A L K ++ V+ + AI Q+R+ +++ Sbjct: 1 TVILLVGLQGVGKTTTAAKLALYLKKKGKKVLLVAADTYRPAAIEQLRVLGEQVGV--PV 58 Query: 147 VYIAIETNVEDIIATLIT---NEKPDLVIIDS 175 + I I E D+VI+D+ Sbjct: 59 FEEGEGKDPVSIAKRAIEHAREENFDVVIVDT 90 >gnl|CDD|144508 pfam00931, NB-ARC, NB-ARC domain. Length = 285 Score = 29.2 bits (66), Expect = 2.7 Identities = 24/119 (20%), Positives = 42/119 (35%), Gaps = 24/119 (20%) Query: 72 IQTHIDEL-DRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRIT-------- 122 + I+ L +++ G V +VG G+GK+TL A Y + Sbjct: 1 REDMIEALIEKLLEMSENLGVVGIVGM-GGVGKTTL-----AKQIYNDDSVGGHFDSVAW 54 Query: 123 -YVSGEEAIGQI-RLRAQRLNTINSSVYIAIETNVEDIIATLITN---EKPDLVIIDSI 176 VS ++ + Q L +S E +A I K L+++D + Sbjct: 55 VVVSKTYTEFRLQKDILQELGLDDSDWV----EKNESELAVKIKEALLRKRFLLVLDDV 109 >gnl|CDD|30898 COG0552, FtsY, Signal recognition particle GTPase [Intracellular trafficking and secretion]. Length = 340 Score = 29.1 bits (65), Expect = 3.0 Identities = 20/82 (24%), Positives = 36/82 (43%), Gaps = 6/82 (7%) Query: 64 ESIEEESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITY 123 E++ E R +D + + VIL G G+GK+T + + A L + + Sbjct: 115 EALIEILRPVDKVDLPLEIPKEK--KPFVILFVGVNGVGKTTTIAKLAKYLKQQGKSVLL 172 Query: 124 VSGEE----AIGQIRLRAQRLN 141 +G+ AI Q+ + +RL Sbjct: 173 AAGDTFRAAAIEQLEVWGERLG 194 >gnl|CDD|34201 COG4559, COG4559, ABC-type hemin transport system, ATPase component [Inorganic ion transport and metabolism]. Length = 259 Score = 29.1 bits (65), Expect = 3.0 Identities = 15/70 (21%), Positives = 28/70 (40%) Query: 90 GSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRLRAQRLNTINSSVYI 149 G V+ + G G GKSTLL + L+ +T A+ + + + Sbjct: 27 GEVLAILGPNGAGKSTLLKALSGELSPDSGEVTLNGVPLNSWPPEELARHRAVLPQNSSL 86 Query: 150 AIETNVEDII 159 A V++++ Sbjct: 87 AFPFTVQEVV 96 >gnl|CDD|72992 cd03233, ABC_PDR_domain1, The pleiotropic drug resistance (PDR) family of ATP-binding cassette (ABC) transporters. PDR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.. Length = 202 Score = 29.0 bits (65), Expect = 3.2 Identities = 13/24 (54%), Positives = 16/24 (66%), Gaps = 1/24 (4%) Query: 86 GFVR-GSVILVGGDPGIGKSTLLM 108 G V+ G ++LV G PG G STLL Sbjct: 28 GVVKPGEMVLVLGRPGSGCSTLLK 51 >gnl|CDD|36000 KOG0781, KOG0781, KOG0781, Signal recognition particle receptor, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]. Length = 587 Score = 28.4 bits (63), Expect = 4.0 Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 8/61 (13%) Query: 92 VILVGGDPGIGKSTLLMQTAASLAYKKHRI------TYVSGEEAIGQIRLRAQRLNTINS 145 VI G G+GKST L + A L K R+ T+ SG A+ Q+R +RL+ ++ Sbjct: 380 VISFVGVNGVGKSTNLAKIAYWLLQNKFRVLIAACDTFRSG--AVEQLRTHVERLSALHG 437 Query: 146 S 146 + Sbjct: 438 T 438 >gnl|CDD|37891 KOG2680, KOG2680, KOG2680, DNA helicase TIP49, TBP-interacting protein [Transcription]. Length = 454 Score = 28.4 bits (63), Expect = 4.0 Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 1/43 (2%) Query: 86 GFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEE 128 G + G IL+ G PG GK+ + M + SL T +SG E Sbjct: 62 GKIAGRAILIAGQPGTGKTAIAMGMSKSLGDDTPF-TSISGSE 103 >gnl|CDD|38557 KOG3347, KOG3347, KOG3347, Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]. Length = 176 Score = 28.3 bits (63), Expect = 4.2 Identities = 12/25 (48%), Positives = 14/25 (56%) Query: 93 ILVGGDPGIGKSTLLMQTAASLAYK 117 ILV G PG GKSTL + A + Sbjct: 10 ILVTGTPGTGKSTLAERLAEKTGLE 34 >gnl|CDD|35844 KOG0625, KOG0625, KOG0625, Phosphoglucomutase [Carbohydrate transport and metabolism]. Length = 558 Score = 28.3 bits (63), Expect = 4.6 Identities = 23/94 (24%), Positives = 42/94 (44%), Gaps = 13/94 (13%) Query: 195 RTSVQAMIQYAKKNGVAMVLVGHVTKEGQIAGPRVIEHMVDAVLYFEGGTRNTQYDYRIL 254 + ++Q + + A NGV ++VG + G ++ P V ++ + GG IL Sbjct: 68 KEAIQIIAKIAAANGVGRLIVG---QNGILSTPAV-SCIIRKYIKAGGGI--------IL 115 Query: 255 RSVKNRFGPTDEIGV-FEMSDKGLQEVSDPSKIF 287 + N GP + G+ F + + G S KI+ Sbjct: 116 TASHNPGGPEGDFGIKFNLENGGPAPESVTDKIY 149 >gnl|CDD|48378 cd03114, ArgK-like, The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and ornithine (AO system) and lysine, arginine and ornithine (LAO) transport systems.. Length = 148 Score = 28.3 bits (63), Expect = 5.1 Identities = 20/66 (30%), Positives = 32/66 (48%), Gaps = 10/66 (15%) Query: 92 VILVGGDPGIGKSTLLMQTAASLAYKKHRITYV--------SGEEAIGQIRLRAQRLNTI 143 VI + G PG GKSTL+ +L + R+ + SG +G R+R +R + Sbjct: 1 VIGITGVPGAGKSTLIDALITALRARGKRVAVLAIDPSSPFSGGAILGD-RIRMERHAS- 58 Query: 144 NSSVYI 149 + V+I Sbjct: 59 DPGVFI 64 >gnl|CDD|34868 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]. Length = 4600 Score = 28.1 bits (62), Expect = 5.4 Identities = 16/57 (28%), Positives = 24/57 (42%), Gaps = 14/57 (24%) Query: 93 ILVGGDPGIGKSTLLMQTAASLAYKKHRI-------------TYVSGEEAIGQIRLR 136 IL+ G PG+GK++L+ A K RI + + EE G+ R Sbjct: 1546 ILLEGSPGVGKTSLITALARKTGKKLIRINLSEQTDLCDLFGSDLPVEEG-GEFRWM 1601 >gnl|CDD|133282 cd01882, BMS1, Bms1. Bms1 is an essential, evolutionarily conserved, nucleolar protein. Its depletion interferes with processing of the 35S pre-rRNA at sites A0, A1, and A2, and the formation of 40S subunits. Bms1, the putative endonuclease Rc11, and the essential U3 small nucleolar RNA form a stable subcomplex that is believed to control an early step in the formation of the 40S subumit. The C-terminal domain of Bms1 contains a GTPase-activating protein (GAP) that functions intramolecularly. It is believed that Rc11 activates Bms1 by acting as a guanine-nucleotide exchange factor (GEF) to promote GDP/GTP exchange, and that activated (GTP-bound) Bms1 delivers Rc11 to the preribosomes. Length = 225 Score = 28.0 bits (63), Expect = 5.4 Identities = 27/80 (33%), Positives = 39/80 (48%), Gaps = 17/80 (21%) Query: 92 VILVGGDPGIGKSTLLMQTAASLA--YKKHRITYVSGEEAIGQIRLRAQRL------NTI 143 V+ V G PG+GK+TL+ SL Y K I+ + G + + R RL N I Sbjct: 41 VVAVVGPPGVGKTTLI----KSLVKNYTKQNISDIKGPITVVTGKKR--RLTFIECPNDI 94 Query: 144 NSSVYIAIETNVEDIIATLI 163 N+ + IA V D++ LI Sbjct: 95 NAMIDIA---KVADLVLLLI 111 >gnl|CDD|144975 pfam01580, FtsK_SpoIIIE, FtsK/SpoIIIE family. FtsK has extensive sequence similarity to wide variety of proteins from prokaryotes and plasmids, termed the FtsK/SpoIIIE family. This domain contains a putative ATP binding P-loop motif. It is found in the FtsK cell division protein from E. coli and the stage III sporulation protein E SpoIIIE which has roles in regulation of prespore specific gene expression in B. subtilis. A mutation in FtsK causes a temperature sensitive block in cell division and it is involved in peptidoglycan synthesis or modification. The SpoIIIE protein is implicated in intercellular chromosomal DNA transfer. Length = 202 Score = 28.1 bits (63), Expect = 5.5 Identities = 11/27 (40%), Positives = 14/27 (51%) Query: 93 ILVGGDPGIGKSTLLMQTAASLAYKKH 119 +L+ G G GKST L SLA + Sbjct: 41 LLIAGATGSGKSTFLNTLILSLAARHS 67 >gnl|CDD|30352 COG0003, ArsA, Predicted ATPase involved in chromosome partitioning [Cell division and chromosome partitioning]. Length = 322 Score = 28.0 bits (62), Expect = 6.1 Identities = 12/38 (31%), Positives = 20/38 (52%) Query: 92 VILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEA 129 ++ G G+GK+T+ TA LA ++ VS + A Sbjct: 4 IVFFTGKGGVGKTTIAAATAVKLAESGKKVLLVSTDPA 41 >gnl|CDD|30727 COG0378, HypB, Ni2+-binding GTPase involved in regulation of expression and maturation of urease and hydrogenase [Posttranslational modification, protein turnover, chaperones / Transcription]. Length = 202 Score = 27.9 bits (62), Expect = 6.1 Identities = 13/36 (36%), Positives = 23/36 (63%), Gaps = 1/36 (2%) Query: 92 VILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGE 127 I VGG PG GK+ L+ +T +L +++I ++G+ Sbjct: 15 RIGVGGPPGSGKTALIEKTLRALK-DEYKIAVITGD 49 >gnl|CDD|34242 COG4619, COG4619, ABC-type uncharacterized transport system, ATPase component [General function prediction only]. Length = 223 Score = 28.0 bits (62), Expect = 6.1 Identities = 22/88 (25%), Positives = 34/88 (38%), Gaps = 13/88 (14%) Query: 89 RGSVILVGGDPGIGKSTLLMQ-------TAASLAYKKHRITYVSGEEAIGQIRLRAQRLN 141 G I + G G GKSTLL T+ +L ++ ++ + E Q+ AQ Sbjct: 28 AGEFIAITGPSGCGKSTLLKIVASLISPTSGTLLFEGEDVSTLKPEAYRQQVSYCAQTPA 87 Query: 142 TINSSVYIAIETNVEDIIATLITNEKPD 169 +V + I I N +PD Sbjct: 88 LFGDTVEDNL------IFPWQIRNRRPD 109 >gnl|CDD|112137 pfam03308, ArgK, ArgK protein. The ArgK protein acts as an ATPase enzyme and as a kinase, and phosphorylates periplasmic binding proteins involved in the LAO (lysine, arginine, ornithine)/AO transport systems. Length = 267 Score = 27.7 bits (62), Expect = 6.4 Identities = 26/87 (29%), Positives = 37/87 (42%), Gaps = 15/87 (17%) Query: 64 ESIEEESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITY 123 ES E+R + L +TG R + + G PG GKSTL+ L + HR+ Sbjct: 9 ESRRPEAR--ELLRRLMPLTG----RAHRVGITGVPGAGKSTLIEALGMELRRRGHRVAV 62 Query: 124 V--------SGEEAIGQIRLRAQRLNT 142 + +G +G R R QRL Sbjct: 63 LAVDPSSPFTGGSILGD-RTRMQRLAV 88 >gnl|CDD|73302 cd02042, ParA, ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the initiation of DNA replication. ParB regulates the ParA ATPase activity by promoting nucleotide exchange in a fashion reminiscent of the exchange factors of eukaryotic G proteins. ADP-bound ParA binds single-stranded DNA, whereas the ATP-bound form dissociates ParB from its DNA binding sites. Increasing the fraction of ParA-ADP in the cell inhibits cell division, suggesting that this simple nucleotide switch may regulate cytokinesis. ParA shares sequence similarity to a conserved and widespread family of ATPases which includes the repA protein of the repABC operon in R. etli Sym plasmid. This operon is involved in the plasmid replication and partition.. Length = 104 Score = 27.9 bits (62), Expect = 6.9 Identities = 9/22 (40%), Positives = 15/22 (68%) Query: 100 GIGKSTLLMQTAASLAYKKHRI 121 G+GK+T + AA+LA + R+ Sbjct: 10 GVGKTTTAVNLAAALARRGKRV 31 >gnl|CDD|35194 COG5635, COG5635, Predicted NTPase (NACHT family) [Signal transduction mechanisms]. Length = 824 Score = 27.8 bits (61), Expect = 7.1 Identities = 23/109 (21%), Positives = 42/109 (38%), Gaps = 8/109 (7%) Query: 13 CGEIHSRWIGKCDSCNAWNTIIEDSSRKESDQRFSKTIKQGHSISLFM---LSEESIEEE 69 G + I + + +I+ + +E S+ K+ ++ EE + E Sbjct: 147 AGTLLELLI--ARGVQSQDKLIDVNILEEVPLA-SQRSKRIFDLNTKGEKRFDEEFLLEL 203 Query: 70 SRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKK 118 ++ D L + +IL G PG GK+T L + A LA + Sbjct: 204 TQSADDQDALPGLEALEKYAKLLIL--GAPGSGKTTFLQRLALWLAQRT 250 >gnl|CDD|34265 COG4646, COG4646, DNA methylase [Transcription / DNA replication, recombination, and repair]. Length = 637 Score = 27.7 bits (61), Expect = 7.5 Identities = 14/55 (25%), Positives = 22/55 (40%), Gaps = 4/55 (7%) Query: 424 FLSGVFPESAKGECKIGMLDRQYIKNLSDLVKKITALQKKDKKTVHKTRSLNSPW 478 +LSG + K LD + +N+ L +Q D + T L +PW Sbjct: 292 YLSGQVRDKLKAAKAAAALDPVFERNVRAL----VEVQPADLRPSDITARLGAPW 342 >gnl|CDD|133251 cd00157, Rho, Rho (Ras homology) family. Members of the Rho family include RhoA, Cdc42, Rac, Rnd, Wrch1, RhoBTB, and Rop. There are 22 human Rho family members identified currently. These proteins are all involved in the reorganization of the actin cytoskeleton in response to external stimuli. They also have roles in cell transformation by Ras in cytokinesis, in focal adhesion formation and in the stimulation of stress-activated kinase. These various functions are controlled through distinct effector proteins and mediated through a GTP-binding/GTPase cycle involving three classes of regulating proteins: GAPs (GTPase-activating proteins), GEFs (guanine nucleotide exchange factors), and GDIs (guanine nucleotide dissociation inhibitors). Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Since crystal structures often lack C-terminal residues, this feature is not available for annotation in many of the CDs in the hierarchy. Length = 171 Score = 27.5 bits (62), Expect = 7.5 Identities = 11/35 (31%), Positives = 17/35 (48%), Gaps = 13/35 (37%) Query: 93 ILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGE 127 I+V GD +GK+ LL I+Y +G+ Sbjct: 3 IVVVGDGAVGKTCLL-------------ISYTTGK 24 >gnl|CDD|33644 COG3854, SpoIIIAA, ncharacterized protein conserved in bacteria [Function unknown]. Length = 308 Score = 27.6 bits (61), Expect = 7.7 Identities = 22/96 (22%), Positives = 39/96 (40%), Gaps = 12/96 (12%) Query: 91 SVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRLRAQRLNTINS--SVY 148 L+ G P +GK+TLL A L+ ++ +G I R++ +N Sbjct: 138 LNTLIIGPPQVGKTTLLRDIARLLSDGINQFLPKK----VGIIDERSEIAGCLNGVPQHG 193 Query: 149 IAIETNVED------IIATLITNEKPDLVIIDSIQT 178 +V D + I + P+++I+D I T Sbjct: 194 RGRRMDVLDPCPKAEGMMMAIRSMSPEVIIVDEIGT 229 >gnl|CDD|30605 COG0256, RplR, Ribosomal protein L18 [Translation, ribosomal structure and biogenesis]. Length = 125 Score = 27.5 bits (61), Expect = 7.7 Identities = 17/85 (20%), Positives = 41/85 (48%), Gaps = 3/85 (3%) Query: 162 LITNEKPDLVIIDSIQTLWSQTAESSPGTVIQVRTSVQAMIQ-YAKKNGVAMVLVGHVTK 220 L T+ +P LV+ S + +++Q + G + +++ ++ Y KK G ++ Sbjct: 24 LGTSGRPRLVVRRSNRHIYAQIIDDVKGGTLASASTLSKELRKYGKKGGGGNTEAAYLV- 82 Query: 221 EGQIAGPRVIEHMVDAVLYFEGGTR 245 G++ R + ++ V++ GG + Sbjct: 83 -GKLIAERALAKGIEEVVFDRGGYK 106 >gnl|CDD|133293 cd01893, Miro1, Miro1 subfamily. Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms. This CD represents the N-terminal GTPase domain of Miro proteins. These atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis. Most Rho proteins contain a lipid modification site at the C-terminus; however, Miro is one of few Rho subfamilies that lack this feature. Length = 166 Score = 27.7 bits (62), Expect = 8.3 Identities = 9/16 (56%), Positives = 14/16 (87%) Query: 93 ILVGGDPGIGKSTLLM 108 I++ GD G+GKS+L+M Sbjct: 3 IVLIGDEGVGKSSLIM 18 >gnl|CDD|31805 COG1618, COG1618, Predicted nucleotide kinase [Nucleotide transport and metabolism]. Length = 179 Score = 27.5 bits (61), Expect = 8.9 Identities = 11/29 (37%), Positives = 20/29 (68%) Query: 93 ILVGGDPGIGKSTLLMQTAASLAYKKHRI 121 I + G PG+GK+TL+++ A L K +++ Sbjct: 8 IFITGRPGVGKTTLVLKIAEKLREKGYKV 36 >gnl|CDD|145449 pfam02301, HORMA, HORMA domain. The HORMA (for Hop1p, Rev7p and MAD2) domain has been suggested to recognize chromatin states that result from DNA adducts, double stranded breaks or non-attachment to the spindle and acts as an adaptor that recruits other proteins. MAD2 is a spindle checkpoint protein which prevents progression of the cell cycle upon detection of a defect in mitotic spindle integrity. Length = 189 Score = 27.3 bits (61), Expect = 9.1 Identities = 13/56 (23%), Positives = 23/56 (41%), Gaps = 11/56 (19%) Query: 422 IGFLSGVFPESAKGECKIGMLD---------RQYIKNLSDLVKKITALQKKDKKTV 468 I +L G++PE + + K L Y++ + V AL+K K + Sbjct: 20 ILYLRGIYPEESFEDRKKYNLPVLVSEDPQLIDYLEKVLSGVFD--ALEKGYLKKL 73 >gnl|CDD|31385 COG1192, Soj, ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]. Length = 259 Score = 27.5 bits (60), Expect = 9.4 Identities = 16/81 (19%), Positives = 34/81 (41%), Gaps = 14/81 (17%) Query: 100 GIGKSTLLMQTAASLA-YKKHRITYVSGEEAIGQIRLRAQRLNTINSSVYIAIETNVEDI 158 G+GK+T + AA+LA ++ I L Q + + ++ + ++E Sbjct: 13 GVGKTTTAVNLAAALAKRGGKKVLL---------IDLDPQG----SLTSWLGLRPDLEGD 59 Query: 159 IATLITNEKPDLVIIDSIQTL 179 + L++ K I+D + Sbjct: 60 LYNLLSGLKERPDILDYTVVI 80 >gnl|CDD|163626 cd07383, MPP_Dcr2, Saccharomyces cerevisiae DCR2 phosphatase and related proteins, metallophosphatase domain. DCR2 phosphatase (Dosage-dependent Cell Cycle Regulator 2) functions together with DCR1 (Gid8) in a common pathway to accelerate initiation of DNA replication in Saccharomyces cerevisiae. Genetic analysis suggests that DCR1 functions upstream of DCR2. DCR2 interacts with and dephosphorylates Sic1, an inhibitor of mitotic cyclin/cyclin-dependent kinase complexes, which may serve to trigger the initiation of cell division. DCR2 belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. Length = 199 Score = 27.2 bits (61), Expect = 9.5 Identities = 11/60 (18%), Positives = 21/60 (35%), Gaps = 13/60 (21%) Query: 159 IATLITNEKPDLVII--DSIQTLWSQTAESSPGTVIQVRTSVQAMIQYAKKNGV--AMVL 214 I ++ EKPDLV++ D I + T +++ + + A Sbjct: 33 IERVLDAEKPDLVVLTGDLI---------TGENTNDNSTSALDKAVSPMIDRKIPWAATF 83 >gnl|CDD|110632 pfam01645, Glu_synthase, Conserved region in glutamate synthase. This family represents a region of the glutamate synthase protein. This region is expressed as a separate subunit in the glutamate synthase alpha subunit from archaebacteria, or part of a large multidomain enzyme in other organisms. The aligned region of these proteins contains a putative FMN binding site and Fe-S cluster. Length = 367 Score = 27.3 bits (61), Expect = 9.5 Identities = 18/47 (38%), Positives = 20/47 (42%), Gaps = 12/47 (25%) Query: 356 HDVHLNIAGGYRISEPAADVAVAAALISSILSIPLPSDFVYFGEVSL 402 V L GG R ADVA AAA L +D VY G +L Sbjct: 272 DRVSLIADGGLRTG---ADVAKAAA---------LGADAVYIGTAAL 306 >gnl|CDD|34522 COG4913, COG4913, Uncharacterized protein conserved in bacteria [Function unknown]. Length = 1104 Score = 27.3 bits (60), Expect = 9.6 Identities = 23/117 (19%), Positives = 40/117 (34%), Gaps = 35/117 (29%) Query: 93 ILVGGDPGIGKSTL------LMQTAASLAY---------KKHRITYVSG------EEAIG 131 ILV G G GKSTL ++ L + ++ +TY+ G + Sbjct: 40 ILVTGGSGSGKSTLIDAITAVLLPQGKLRFNSAAQANTPRRSLVTYIRGAWRAQEDPLQD 99 Query: 132 QIRLRAQRLNTINSSVYIAIETNVEDIIATLITNEKPDLVIIDSIQTLWSQTAESSP 188 QI R S+ +N E + TL + + ++++ S Sbjct: 100 QIVSTYLR-PRATYSLVGLTYSNGEGVEHTL-------------VAIFYLKSSDISS 142 >gnl|CDD|73300 cd02037, MRP-like, MRP (Multiple Resistance and pH adaptation) is a homologue of the Fer4_NifH superfamily. Like the other members of the superfamily, MRP contains a ATP-binding domain at the N-termini. It is found in bacteria as a membrane-spanning protein and functions as a Na+/H+ antiporter.. Length = 169 Score = 27.4 bits (61), Expect = 9.6 Identities = 12/31 (38%), Positives = 19/31 (61%), Gaps = 1/31 (3%) Query: 92 VILVG-GDPGIGKSTLLMQTAASLAYKKHRI 121 VI V G G+GKST+ + A +LA +++ Sbjct: 1 VIAVMSGKGGVGKSTVAVNLALALAKLGYKV 31 >gnl|CDD|144961 pfam01561, Hanta_G2, Hantavirus glycoprotein G2. The medium (M) genome segment of hantaviruses (family Bunyaviridae) encodes the two virion glycoproteins. G1 and G2, as a precursor protein in the complementary sense RNA. Length = 486 Score = 27.5 bits (61), Expect = 9.6 Identities = 15/52 (28%), Positives = 19/52 (36%) Query: 51 KQGHSISLFMLSEESIEEESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIG 102 K GHS S F + + LDRVTG + + G P G Sbjct: 386 KGGHSGSKFKCCHGTDCSSEGLTAAAPHLDRVTGYNEIDSDKVYDDGAPECG 437 >gnl|CDD|72981 cd03222, ABC_RNaseL_inhibitor, The ABC ATPase RNase L inhibitor (RLI) is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids. RLI's are not transport proteins, and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains, which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.. Length = 177 Score = 27.3 bits (60), Expect = 9.8 Identities = 31/128 (24%), Positives = 41/128 (32%), Gaps = 21/128 (16%) Query: 66 IEEESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASL----------- 114 ++ + V G G VI + G G GK+T + A L Sbjct: 1 QLYPDCVKRYGVFFLLVELGVVKEGEVIGIVGPNGTGKTTAVKILAGQLIPNGDNDEWDG 60 Query: 115 ---AYKKHRITYVSGE---EAIGQIRLRAQRLNTINS-SVYIAIET--NVEDIIATLIT- 164 YK I GE AI LR + S Y+ IE N I L Sbjct: 61 ITPVYKPQYIDLSGGELQRVAIAAALLRNATFYLFDEPSAYLDIEQRLNAARAIRRLSEE 120 Query: 165 NEKPDLVI 172 +K LV+ Sbjct: 121 GKKTALVV 128 >gnl|CDD|39108 KOG3905, KOG3905, KOG3905, Dynein light intermediate chain [Cell motility]. Length = 473 Score = 27.3 bits (60), Expect = 9.8 Identities = 12/31 (38%), Positives = 17/31 (54%) Query: 90 GSVILVGGDPGIGKSTLLMQTAASLAYKKHR 120 G +LV GD G GK++L+ + S KK Sbjct: 52 GKNVLVLGDNGSGKTSLISKLQGSETVKKGS 82 >gnl|CDD|72862 cd04760, BAH_Dnmt1_I, BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.. Length = 124 Score = 27.2 bits (60), Expect = 9.8 Identities = 10/19 (52%), Positives = 12/19 (63%) Query: 273 SDKGLQEVSDPSKIFLSDR 291 SD L E SDP ++FL D Sbjct: 48 SDTVLGETSDPLELFLVDE 66 >gnl|CDD|38036 KOG2825, KOG2825, KOG2825, Putative arsenite-translocating ATPase [Inorganic ion transport and metabolism]. Length = 323 Score = 27.3 bits (60), Expect = 9.9 Identities = 13/37 (35%), Positives = 19/37 (51%) Query: 93 ILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEA 129 I VGG G+GK+T A LA + + +S + A Sbjct: 22 IFVGGKGGVGKTTCSCSLAVQLAKVRESVLIISTDPA 58 >gnl|CDD|31889 COG1703, ArgK, Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]. Length = 323 Score = 27.2 bits (60), Expect = 9.9 Identities = 20/62 (32%), Positives = 28/62 (45%), Gaps = 9/62 (14%) Query: 89 RGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYV--------SGEEAIGQIRLRAQRL 140 VI + G PG GKSTL+ L + HR+ + +G +G R+R QRL Sbjct: 50 NAHVIGITGVPGAGKSTLIEALGRELRERGHRVAVLAVDPSSPFTGGSILGD-RIRMQRL 108 Query: 141 NT 142 Sbjct: 109 AV 110 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.317 0.133 0.378 Gapped Lambda K H 0.267 0.0724 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 5,419,556 Number of extensions: 282818 Number of successful extensions: 1312 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1290 Number of HSP's successfully gapped: 130 Length of query: 479 Length of database: 6,263,737 Length adjustment: 97 Effective length of query: 382 Effective length of database: 4,167,664 Effective search space: 1592047648 Effective search space used: 1592047648 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: 59 (26.5 bits)