RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780334|ref|YP_003064747.1| DNA repair protein RadA [Candidatus Liberibacter asiaticus str. psy62] (479 letters) >gnl|CDD|183326 PRK11823, PRK11823, DNA repair protein RadA; Provisional. Length = 446 Score = 716 bits (1852), Expect = 0.0 Identities = 242/457 (52%), Positives = 320/457 (70%), Gaps = 14/457 (3%) Query: 1 MVKIRSQYFCQSCGEIHSRWIGKCDSCNAWNTIIEDSSRKESDQRFSKTIKQGHSISLFM 60 M K ++ Y CQ CG +W+G+C C AWNT++E K G S + Sbjct: 1 MAKKKTAYVCQECGAESPKWLGRCPECGAWNTLVE----------EVAASKAGSSKPVQP 50 Query: 61 LSEESIEEESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHR 120 LS+ EEE RI T I ELDRV GGG V GSV+L+GGDPGIGKSTLL+Q AA LA + Sbjct: 51 LSDIEAEEEPRISTGIGELDRVLGGGLVPGSVVLIGGDPGIGKSTLLLQVAARLAAAGGK 110 Query: 121 ITYVSGEEAIGQIRLRAQRLNTINSSVYIAIETNVEDIIATLITNEKPDLVIIDSIQTLW 180 + YVSGEE+ QI+LRA+RL + ++Y+ ETN+E I+AT I EKPDLV+IDSIQT++ Sbjct: 111 VLYVSGEESASQIKLRAERLGLPSDNLYLLAETNLEAILAT-IEEEKPDLVVIDSIQTMY 169 Query: 181 SQTAESSPGTVIQVRTSVQAMIQYAKKNGVAMVLVGHVTKEGQIAGPRVIEHMVDAVLYF 240 S ES+PG+V QVR +++ AK+ G+A+ LVGHVTKEG IAGPRV+EHMVD VLYF Sbjct: 170 SPELESAPGSVSQVRECAAELMRLAKQRGIAVFLVGHVTKEGAIAGPRVLEHMVDTVLYF 229 Query: 241 EGGTRNTQYDYRILRSVKNRFGPTDEIGVFEMSDKGLQEVSDPSKIFLSDRDSTSPGTAV 300 EG + YRILR+VKNRFG T+EIGVFEM+++GL+EVS+PS++FLS+RD PG+AV Sbjct: 230 EG---DRHSRYRILRAVKNRFGATNEIGVFEMTEQGLREVSNPSELFLSERDENVPGSAV 286 Query: 301 FAGIEGTRALLVEIQSLVVPTSLGMPRRTVVGWDSSRLAMILAVLEARCNIKFGNHDVHL 360 +EGTR LLVEIQ+LV PTS G PRRT VG DS+RLAM+LAVLE R + G+ DV++ Sbjct: 287 TVTMEGTRPLLVEIQALVSPTSFGNPRRTAVGLDSNRLAMLLAVLEKRLGLPLGDQDVYV 346 Query: 361 NIAGGYRISEPAADVAVAAALISSILSIPLPSDFVYFGEVSLSGSVRAVGHMQQRLKEAE 420 N+ GG +I+EPAAD+AVA A+ SS+ PLP D V FGEV L+G +R V +++RLKEA Sbjct: 347 NVVGGLKITEPAADLAVALAIASSLRDRPLPPDTVVFGEVGLTGEIRPVPRIERRLKEAA 406 Query: 421 KIGFLSGVFPESAKGECKIGMLDRQYIKNLSDLVKKI 457 K+GF + P+ + ++ +K L++ ++ + Sbjct: 407 KLGFKRAIVPKGNLPKKPPKGIEVIGVKTLAEALELL 443 >gnl|CDD|161868 TIGR00416, sms, DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)). Length = 454 Score = 487 bits (1256), Expect = e-138 Identities = 217/460 (47%), Positives = 295/460 (64%), Gaps = 12/460 (2%) Query: 1 MVKIRSQYFCQSCGEIHSRWIGKCDSCNAWNTIIED------SSRKESDQRFSKTIKQGH 54 M K +S++ CQ CG +W GKC +C+AWNTI E+ ++K I Q Sbjct: 1 MAKAKSKFVCQHCGADSPKWQGKCPACHAWNTITEERLHRSLGAQKNRRNSGKAGIPQAQ 60 Query: 55 SISLFMLSEESIEEESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASL 114 +S +EE R + ELDRV GGG V GS+IL+GGDPGIGKSTLL+Q A L Sbjct: 61 KSQ--TISAIELEEVPRFSSGFGELDRVLGGGIVPGSLILIGGDPGIGKSTLLLQVACQL 118 Query: 115 AYKKHRITYVSGEEAIGQIRLRAQRLNTINSSVYIAIETNVEDIIATLITNEKPDLVIID 174 A + ++ YVSGEE++ QI++RA RL ++Y+ ETN E I A I E P +ID Sbjct: 119 AKNQMKVLYVSGEESLQQIKMRAIRLGLPEPNLYVLSETNWEQICA-NIEEENPQACVID 177 Query: 175 SIQTLWSQTAESSPGTVIQVRTSVQAMIQYAKKNGVAMVLVGHVTKEGQIAGPRVIEHMV 234 SIQTL+S S+PG+V QVR +++ AK G+A+ +VGHVTKEG IAGP+V+EHMV Sbjct: 178 SIQTLYSPDISSAPGSVSQVRECTAELMRLAKTRGIAIFIVGHVTKEGSIAGPKVLEHMV 237 Query: 235 DAVLYFEGGTRNTQYDYRILRSVKNRFGPTDEIGVFEMSDKGLQEVSDPSKIFLSDRDST 294 D VLYFEG + +RILRSVKNRFG T+EIG+FEM+++GL+EV +PS IFLS R+ Sbjct: 238 DTVLYFEGDRDSR---FRILRSVKNRFGATNEIGIFEMTEQGLREVLNPSAIFLSRREEP 294 Query: 295 SPGTAVFAGIEGTRALLVEIQSLVVPTSLGMPRRTVVGWDSSRLAMILAVLEARCNIKFG 354 G+++ EGTR LLVEIQ+LV PTS PRR G D +RLA++LAVLE R + Sbjct: 295 MSGSSITVTWEGTRPLLVEIQALVSPTSFANPRRVATGLDQNRLALLLAVLEKRLGLPLA 354 Query: 355 NHDVHLNIAGGYRISEPAADVAVAAALISSILSIPLPSDFVYFGEVSLSGSVRAVGHMQQ 414 + DV LN+AGG ++SEPAAD+A+ A++SS PL D V+ GEV L+G +R V +++ Sbjct: 355 DQDVFLNVAGGVKVSEPAADLALLIAIVSSFRDRPLDPDLVFLGEVGLAGEIRPVPSLEE 414 Query: 415 RLKEAEKIGFLSGVFPESAKGECKIGMLDRQYIKNLSDLV 454 RLKEA K+GF + P++ + + +K + D + Sbjct: 415 RLKEAAKLGFKRAIVPKANSPKTAPEGIKVIGVKKVGDAL 454 >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 = 69.4 bits (170), Expect = 2e-12 Identities = 35/114 (30%), Positives = 65/114 (57%), Gaps = 2/114 (1%) Query: 312 VEIQSLVVPTSLGMPRRTVVGWDSSRLAM--ILAVLEARCNIKFGNHDVHLNIAGGYRIS 369 + + ++ +G ++V S+R ++ +LAVL + I N+D+H+N GG + Sbjct: 381 INVTGIIEEEEIGGSGKSVRRKSSARGSVENVLAVLRSVFGINPQNYDIHINFPGGIPVD 440 Query: 370 EPAADVAVAAALISSILSIPLPSDFVYFGEVSLSGSVRAVGHMQQRLKEAEKIG 423 P+A VA+A A+ S+I P+ + GE+SL+G V+ VG + +++ A+K G Sbjct: 441 GPSAGVAIAVAIYSAIFKCPIDNKVAMTGEISLNGLVKPVGGVPSKIEAAKKAG 494 >gnl|CDD|181771 PRK09302, PRK09302, circadian clock protein KaiC; Reviewed. Length = 509 Score = 68.0 bits (167), Expect = 4e-12 Identities = 46/176 (26%), Positives = 75/176 (42%), Gaps = 26/176 (14%) Query: 54 HSISLFMLSEESIEEES---RIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQT 110 IS+ L+ + + S RI + + +LD + GGGF RGS+ILV G G GK+ L + Sbjct: 234 DGISVLPLTAMRLTQRSSNERISSGVPDLDEMLGGGFFRGSIILVSGATGTGKTLLASKF 293 Query: 111 AASLAYKKHRITYVSGEEAIGQI------------RLRAQRLNTINSSVYIAIETNVED- 157 A + + R + EE+ Q+ ++ + L I + +ED Sbjct: 294 AEAACRRGERCLLFAFEESRAQLIRNARSWGIDLEKMEEKGLLKIICAR--PESYGLEDH 351 Query: 158 --IIATLITNEKPDLVIIDSIQTLWSQTAESSPGTVIQVRTSVQAMIQYAKKNGVA 211 II I KP V ID + +A + G++ + R V + Y K + Sbjct: 352 LIIIKREIEEFKPSRVAIDPL------SALARGGSLNEFRQFVIRLTDYLKSEEIT 401 Score = 46.4 bits (111), Expect = 1e-05 Identities = 50/227 (22%), Positives = 83/227 (36%), Gaps = 35/227 (15%) Query: 60 MLSEESIEEESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQ-TAASLAYKK 118 M + ++ T I+ D +T GG +G LV G G GK+ +Q + Sbjct: 1 MNQPSASPGIEKLPTGIEGFDDITHGGLPKGRPTLVSGTAGTGKTLFALQFLVNGIKRFD 60 Query: 119 HRITYVSGEEAIGQIRLRAQRLN------------------TINSSVYIAIETNVEDIIA 160 +V+ EE+ I S A E ++E + Sbjct: 61 EPGVFVTFEESPEDIIRNVASFGWDLQKLIDEGKLFILDASPDPSEQEEAGEYDLEALFI 120 Query: 161 TL---ITNEKPDLVIIDSIQTLWSQTAESSPGTVIQVRTSVQAMIQYAKKNGVAMVLVGH 217 + I V++DSI+ L+S + + VR ++ + + K+ GV V+ G Sbjct: 121 RIEYAIDKIGAKRVVLDSIEALFSGFSNEAV-----VRRELRRLFAWLKQKGVTAVITGE 175 Query: 218 VTKE-GQIAGPRVIEHMVDAVLYFEGGTRNT---QYDYRILRSVKNR 260 E G + V E + D V+ RN + R LR +K R Sbjct: 176 RGDEYGPLTRYGVEEFVSDCVIIL----RNRLEGEKRTRTLRILKYR 218 >gnl|CDD|148381 pfam06745, KaiC, KaiC. This family represents a conserved region within bacterial and archaeal proteins, most of which are hypothetical. More than one copy is sometimes found in each protein. This family includes KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria. Length = 231 Score = 63.4 bits (155), Expect = 1e-10 Identities = 59/234 (25%), Positives = 94/234 (40%), Gaps = 38/234 (16%) Query: 72 IQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRIT-YVSGEEAI 130 ++T I LD + GG G V+L+ G PG GK+ +Q + A + YV+ EE Sbjct: 1 VKTGIPGLDEILKGGIPEGRVVLITGGPGTGKTIFGLQFLYNGALEYGEPGVYVTLEEPP 60 Query: 131 GQIRLRAQRLN----TINSSVYIAI---------------ETNVEDIIATL---ITNEKP 168 +R A+ + +AI ++E++I L I Sbjct: 61 EDLRENAKSFGWDLEKLEEEGKLAIIDASTSGIGIAEVKGRFDLEELIERLREAIREIGA 120 Query: 169 DLVIIDSIQTLWSQTAESSPGTVIQVRTSVQAMIQYAKKNGVAMVLVGHVTK-EGQIAGP 227 V+IDSI TL P R ++ + + KK GV + EG I G Sbjct: 121 KRVVIDSITTL---FYLLKPA---MAREILRRLKRVLKKLGVTAIFTSEKPSGEGGIGGY 174 Query: 228 RVIEHMVDAVLYFEGGTRNTQYDYRILRS---VKNRFGPTD-EIGVFEMSDKGL 277 V E +VD V+ + + ++R+ VK R P + FE++D G+ Sbjct: 175 GVEEFVVDGVIRL----DLKEIEGELVRTIEIVKMRGTPHSMKRYPFEITDNGI 224 >gnl|CDD|163066 TIGR02903, spore_lon_C, ATP-dependent protease, Lon family. Members of this protein family resemble the widely distributed ATP-dependent protease La, also called Lon and LonA. It resembles even more closely LonB, which is a LonA paralog found in genomes if and only if the species is capable of endospore formation (as in Bacillus subtilis, Clostridium tetani, and select other members of the Firmicutes) and expressed specifically in the forespore compartment. Members of this family are restricted to a subset of spore-forming species, and are very likely to participate in the program of endospore formation. We propose the designation LonC. Length = 615 Score = 62.9 bits (153), Expect = 2e-10 Identities = 31/106 (29%), Positives = 60/106 (56%), Gaps = 2/106 (1%) Query: 355 NHDVHLNIAGGYRISEPAADVAVAAALISSILSIPLPSDFVYFGEVSLSGSVRAVGHMQQ 414 N+D+H+N+ GG RI P+A A+ +IS+IL P+ D GE+SL G ++ VG + + Sbjct: 510 NYDIHVNVIGGGRIDGPSAGAAITLCMISAILGKPIRQDVAITGEISLRGKIKPVGGIFE 569 Query: 415 RLKEAEKIGFLSGVFPESAKGECKIGMLDRQ--YIKNLSDLVKKIT 458 ++ A++ G + V PE + G+ + ++ + +L++ + Sbjct: 570 KIYGAKQAGIKTVVIPEENLKDVPQGLPGIEVKFVSTIEELMRIVF 615 >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 = 59.7 bits (144), Expect = 2e-09 Identities = 31/153 (20%), Positives = 65/153 (42%), Gaps = 8/153 (5%) Query: 89 RGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRLRAQRLNTINSSVY 148 G VIL+ G PG GK+TL A L + Y+ GE+ + ++ + + Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS 60 Query: 149 IAIETNVEDIIATLITNEKPDLVIIDSIQTLWSQTAESSPGTVIQVRTSVQAMIQYAKKN 208 + E + +A L KPD++I+D I +L ++ ++ + ++ ++ + Sbjct: 61 GSGELRLRLALA-LARKLKPDVLILDEITSL----LDAEQEALLLLLEELRLLLLLKSEK 115 Query: 209 GVAMVLVGHVTKEGQIAGPRVIEHMVDAVLYFE 241 + ++L + K GP ++ D + Sbjct: 116 NLTVILTTNDEK---DLGPALLRRRFDRRIVLL 145 >gnl|CDD|162777 TIGR02237, recomb_radB, DNA repair and recombination protein RadB. This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236). Length = 209 Score = 59.7 bits (145), Expect = 2e-09 Identities = 50/216 (23%), Positives = 94/216 (43%), Gaps = 25/216 (11%) Query: 79 LDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGE----EAIGQI- 133 +D + GGG RG++ + G PG GK+ + M A + A + ++ Y+ E E QI Sbjct: 1 IDELLGGGVERGTITQIYGPPGSGKTNICMILAVNAARQGKKVVYIDTEGLSPERFKQIA 60 Query: 134 RLRAQRLNTINSSVYIAIETNVEDII----ATLITNEKPDLVIIDSIQTLW-SQTAESSP 188 R +R + N V+ + + + + + I + LV++DS L+ + ++ Sbjct: 61 EDRPERALS-NFIVFEVFDFDEQGVAIQKTSKFIDRDSASLVVVDSFTALYRLELSDDRI 119 Query: 189 GTVIQVRTSVQAMIQYAKKNGVAMVLVGHV---TKEGQIA--GPRVIEHMVDAVLYFE-- 241 ++ + ++ A+K +A+V+ V G + G ++EH +L E Sbjct: 120 SRNRELARQLTLLLSLARKKNLAVVITNQVYTDVNNGTLRPLGGHLLEHWSKVILRLEKF 179 Query: 242 GGTRNTQYDYRILRSVKNRFGPTDEIGVFEMSDKGL 277 G R L K+R P E F ++D G+ Sbjct: 180 RGRRLA-----TLE--KHRSRPEGESVYFRITDDGI 208 >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 = 56.0 bits (135), Expect = 2e-08 Identities = 28/124 (22%), Positives = 62/124 (50%), Gaps = 6/124 (4%) Query: 355 NHDVHLNIAGGY-RISEPAADVAVAAALISSILSIPLPSDFVYFGEVSLSGSVRAVGHMQ 413 N+D+H+ Y + +A ++VA A+IS++ IP+ D G +S+ G V VG + Sbjct: 484 NYDIHIQFLQTYEGVEGDSASISVATAVISALEEIPVDQDVAMTGSLSVRGEVLPVGGVT 543 Query: 414 QRLKEAEKIGFLSGVFPESAKGECKI-----GMLDRQYIKNLSDLVKKITALQKKDKKTV 468 ++++ A + G + P+S + + G ++ ++ L ++++ + L KK + Sbjct: 544 EKIEAAIEAGIKKVIIPKSNMIDVILEKETEGKIEIIPVETLDEVLEHVLDLDKKKGSLI 603 Query: 469 HKTR 472 + Sbjct: 604 ERFN 607 >gnl|CDD|181799 PRK09361, radB, DNA repair and recombination protein RadB; Provisional. Length = 225 Score = 54.5 bits (132), Expect = 6e-08 Identities = 52/237 (21%), Positives = 97/237 (40%), Gaps = 35/237 (14%) Query: 68 EESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGE 127 + R+ T LD + GGGF RG++ + G PG GK+ + +Q A A ++ Y+ E Sbjct: 1 MDERLPTGCKMLDELLGGGFERGTITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYIDTE 60 Query: 128 ----EAIGQIRLRAQRLNTINSSVYI-----------AIETNVEDIIATLITNEKPDLVI 172 E QI + + S++ I AI E + E L++ Sbjct: 61 GLSPERFKQI--AGEDFEELLSNIIIFEPSSFEEQSEAIR-KAEKLAK-----ENVGLIV 112 Query: 173 IDSIQTLW---SQTAESSPGTVIQVRTSVQAMIQYAKKNGVAMVLVGHV---TKEGQI-- 224 +DS +L+ + E + ++ + +++ A+K+ +A+V+ V + Sbjct: 113 LDSATSLYRLELEDEEDNSKLNRELGRQLTHLLKLARKHDLAVVITNQVYSDIDSDGLRP 172 Query: 225 AGPRVIEHMVDAVLYFEGGTRNTQYDYRILRSVKNRFGPTDEIGVFEMSDKGLQEVS 281 G +EH +L E R K+R P E F ++D+G++ + Sbjct: 173 LGGHTLEHWSKTILRLEKFRNGK----RRATLEKHRSRPEGESAEFRITDRGIEIID 225 >gnl|CDD|163593 TIGR03881, KaiC_arch_4, KaiC domain protein, PAE1156 family. Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain. Length = 229 Score = 49.7 bits (119), Expect = 2e-06 Identities = 32/141 (22%), Positives = 57/141 (40%), Gaps = 20/141 (14%) Query: 71 RIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAI 130 R+ T ++ LD++ GG RG + V G+PG GK+ + A + YV+ EE+ Sbjct: 1 RLSTGVEGLDKLLEGGIPRGFFVAVTGEPGTGKTIFCLHFAYKGLRDGDPVIYVTTEESR 60 Query: 131 GQIRLRAQRLNTINSSVYIAIETNVEDIIATLITNEKPDLVIIDSIQTLWSQTAESSPGT 190 I +A + ++ I E+ LVIID+ L + + Sbjct: 61 ESIIRQAAQFG-MDFEKAI----------------EEGKLVIIDA---LMKEKEDEWSLR 100 Query: 191 VIQVRTSVQAMIQYAKKNGVA 211 + + + +I+ K G Sbjct: 101 ELSIEELLNKVIEAKKYLGYG 121 >gnl|CDD|181459 PRK08533, PRK08533, flagellar accessory protein FlaH; Reviewed. Length = 230 Score = 49.7 bits (119), Expect = 2e-06 Identities = 40/135 (29%), Positives = 61/135 (45%), Gaps = 16/135 (11%) Query: 67 EEESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSG 126 E ++I+ DEL + GGG GS+IL+ GD GKS L + A + ++YVS Sbjct: 1 MELAKIELSRDELHKRLGGGIPAGSLILIEGDESTGKSILSQRLAYGFLQNGYSVSYVST 60 Query: 127 E----EAIGQIR-LRAQRLNTINS------SVYIAIETNVE--DIIATLITNEK---PDL 170 + E I Q+ L + S VY + N E + L+ + D+ Sbjct: 61 QLTTTEFIKQMMSLGYDINKKLISGKLLYIPVYPLLSGNSEKRKFLKKLMNTRRFYEKDV 120 Query: 171 VIIDSIQTLWSQTAE 185 +IIDS+ +L S A Sbjct: 121 IIIDSLSSLISNDAS 135 >gnl|CDD|163590 TIGR03878, thermo_KaiC_2, KaiC domain protein, AF_0795 family. This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles. Length = 259 Score = 46.6 bits (111), Expect = 1e-05 Identities = 52/238 (21%), Positives = 92/238 (38%), Gaps = 42/238 (17%) Query: 81 RVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEE----AIGQIRLR 136 R GG SVI + G GKS ++ Q A + A + + + +V+ E ++ R Sbjct: 27 RKPLGGIPAYSVINITGVSDTGKSLMVEQFAVTQASRGNPVLFVTVESPANFVYTSLKER 86 Query: 137 AQRLNT----INSSVYI-------AIETNVEDIIATL---ITNEKPDLVIIDSIQTLWSQ 182 A+ + I ++ + + NV +++ATL I K +IDSI L+ Sbjct: 87 AKAMGVDFDKIEENIILIDAASSTELRENVPNLLATLAYAIKEYKVKNTVIDSITGLYE- 145 Query: 183 TAESSPGTVIQVRTSVQAMIQYAKKNGVAMVLV-----GHVTKEGQIAGPRVIEHMVDAV 237 + R V+ + + KK + V GH + AG + H+VD Sbjct: 146 ------AKEMMAREIVRQLFNFMKKWYQTALFVSQKRSGHEELSAEAAGGYAVSHIVDGT 199 Query: 238 LYFEGGTRNTQYD-----------YRILRSVKNRFGPTD-EIGVFEMSDKGLQEVSDP 283 + +++D R+ R R D + V E+ + GL ++ P Sbjct: 200 IVLAKQLIMSRFDASLYKKPIGEIVRLFRIDGCRMCGHDTKTHVLEIDETGLVKIGPP 257 >gnl|CDD|132639 TIGR03600, phage_DnaB, phage replicative helicase, DnaB family, HK022 subfamily. Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model. Length = 421 Score = 45.1 bits (107), Expect = 4e-05 Identities = 43/193 (22%), Positives = 86/193 (44%), Gaps = 36/193 (18%) Query: 72 IQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKK-HRITYVSGEEAI 130 + T + +LDR+T G V+G +I++G P +GK+TL + A ++A ++ + + S E + Sbjct: 177 LSTGLPKLDRLTNG-LVKGDLIVIGARPSMGKTTLALNIAENVALREGKPVLFFSLEMSA 235 Query: 131 GQI--RLRAQRLNTINSSVYIAIETNVE--DIIATLITNEKPDLVIIDSIQTLWSQTAES 186 Q+ RL A + ++ + + ++ + + DL I D+ Sbjct: 236 EQLGERLLASKSGINTGNIRTGRFNDSDFNRLLNAVDRLSEKDLYIDDTGGL-------- 287 Query: 187 SPGTVIQVRTSVQAMIQYAKKNGVAMVLVGHVTKEGQIAGPRVIEHMVDAVLYFEGGTRN 246 TV Q+R+ + + + KK G+ +++V ++ +A R G RN Sbjct: 288 ---TVAQIRSIARRIKR--KKGGLDLIVVDYIQL---MAPTR-------------GRDRN 326 Query: 247 TQYDYRILRSVKN 259 + I R +K Sbjct: 327 EELGG-ISRGLKA 338 >gnl|CDD|184312 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional. Length = 637 Score = 44.6 bits (106), Expect = 6e-05 Identities = 28/129 (21%), Positives = 63/129 (48%), Gaps = 12/129 (9%) Query: 355 NHDVHLNIAGGYRISE-PAADVAVAAALISSILSIPLPSDFVYFGEVSLSGSVRAVGHMQ 413 N+D+H+ Y E +A ++VA A+IS++ +IP+ G +S+ G V VG + Sbjct: 493 NYDIHIQFVQTYEGVEGDSASISVATAVISALENIPVDQSVAMTGSLSVRGDVLPVGGVT 552 Query: 414 QRLKEAEKIGFLSGVFPESAKGECKIGMLDRQY--------IKNLSDLVKKITALQKKDK 465 +++ A + G + P+S + + M++ +Y + +S++++ + Sbjct: 553 YKIEAAAEAGIKKVIIPKSNEQDV---MIEDEYEDKIEIIPVSTISEVLEHALVGGPEKD 609 Query: 466 KTVHKTRSL 474 + K +S+ Sbjct: 610 SLLDKLKSI 618 >gnl|CDD|131703 TIGR02655, circ_KaiC, circadian clock protein KaiC. Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. Length = 484 Score = 44.6 bits (105), Expect = 6e-05 Identities = 37/142 (26%), Positives = 62/142 (43%), Gaps = 16/142 (11%) Query: 54 HSISLFMLSEESIEEES---RIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQT 110 H I++F L + + S R+ + + LD + GGGF + S+IL G G GK+ L+ + Sbjct: 224 HGINIFPLGAMRLTQRSSNVRVSSGVVRLDEMCGGGFFKDSIILATGATGTGKTLLVSKF 283 Query: 111 AASLAYKKHRITYVSGEEAIGQIRLRA----------QRLNTINSSVYIAIETNVED--- 157 + K R + EE+ Q+ A ++ + +ED Sbjct: 284 LENACANKERAILFAYEESRAQLLRNAYSWGIDFEEMEQQGLLKIICAYPESAGLEDHLQ 343 Query: 158 IIATLITNEKPDLVIIDSIQTL 179 II + I + KP + IDS+ L Sbjct: 344 IIKSEIADFKPARIAIDSLSAL 365 Score = 28.8 bits (64), Expect = 3.7 Identities = 14/40 (35%), Positives = 22/40 (55%) Query: 70 SRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQ 109 ++I+T I+ D ++ GG G LV G G GK+ +Q Sbjct: 1 AKIRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQ 40 >gnl|CDD|163592 TIGR03880, KaiC_arch_3, KaiC domain protein, AF_0351 family. This model represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself. Length = 224 Score = 43.9 bits (104), Expect = 9e-05 Identities = 63/223 (28%), Positives = 98/223 (43%), Gaps = 30/223 (13%) Query: 76 IDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRL 135 I LD + GGGF G VI+V G+ G GK+T +Q + Y+S EE +I Sbjct: 2 IPGLDEMLGGGFPEGHVIVVIGEYGTGKTTFSLQFLYQGLKNGEKAMYISLEEREERILG 61 Query: 136 RAQRL-----NTINSSVYIAIETNVEDIIATL--ITNEKPDL--------VIIDSI---Q 177 A+ + I+ S+YI + + D +L I NE P L V+ID I + Sbjct: 62 YAKSKGWDLEDYIDKSLYI-VRLDPSDFKTSLNRIKNELPILIKELGASRVVIDPISLLE 120 Query: 178 TLWSQTAESSPGTVIQVRTSVQAMIQYAKKNGVAMVLVGHVTKEGQIAGPR-VIEHMVDA 236 TL+ AE RT + ++ GV +L K A +IE++ D Sbjct: 121 TLFDDDAER--------RTELFRFYSSLRETGVTTILTSEADKTNVFASKYGLIEYLADG 172 Query: 237 VLYFEGGTRNTQYDYRI-LRSVKNRFGP-TDEIGVFEMSDKGL 277 V+ + + D R+ + VK R + EI +E++D G+ Sbjct: 173 VIILKYVRNSDLRDVRLAVEVVKMRRSKHSREIKPYEITDSGI 215 >gnl|CDD|180381 PRK06067, PRK06067, flagellar accessory protein FlaH; Validated. Length = 234 Score = 43.8 bits (104), Expect = 1e-04 Identities = 32/141 (22%), Positives = 56/141 (39%), Gaps = 23/141 (16%) Query: 72 IQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIG 131 I T +ELDR GGG S+IL+ GD G GKS L Q + ++ ++ E Sbjct: 7 ISTGNEELDRKLGGGIPFPSLILIEGDHGTGKSVLSQQFVYGALKQGKKVYVITTENTSK 66 Query: 132 QIRLRAQRLNTINSSVYIAI------ETNVE-------------DIIATLITNEKPDLVI 172 + + + I+ S + N E ++I I +++ D++I Sbjct: 67 SYLKQMESV-KIDISDFFLWGYLRIFPLNTEGFEWNSTLANKLLELIIEFIKSKREDVII 125 Query: 173 IDSIQTLWSQTAESSPGTVIQ 193 IDS+ + ++ Sbjct: 126 IDSLTIF---ATYAEEDDILN 143 >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 = 42.7 bits (101), Expect = 2e-04 Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 1/81 (1%) Query: 353 FGNHDVHLNI-AGGYRISEPAADVAVAAALISSILSIPLPSDFVYFGEVSLSGSVRAVGH 411 F D+HL++ G P+A + +A AL+S P+ D GE++L G V +G Sbjct: 663 FEKADIHLHVPEGATPKDGPSAGITMATALLSLATGKPVRPDVAMTGEITLRGKVLPIGG 722 Query: 412 MQQRLKEAEKIGFLSGVFPES 432 ++++ A++ G + + PE Sbjct: 723 LKEKTIAAKRAGIKTIILPEK 743 >gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La; Provisional. Length = 784 Score = 42.2 bits (99), Expect = 3e-04 Identities = 32/127 (25%), Positives = 62/127 (48%), Gaps = 15/127 (11%) Query: 342 LAVLEARCNIKFG-------NHDVHLNIAGGYRISE-PAADVAVAAALISSILSIPLPSD 393 L V+ AR K G D+H+++ G + P+A +A+ AL+S + P+ +D Sbjct: 642 LTVVRARAE-KLGINPDFYEKRDIHVHVPEGATPKDGPSAGIAMCTALVSCLTGNPVRAD 700 Query: 394 FVYFGEVSLSGSVRAVGHMQQRLKEAEKIGFLSGVFPESAKGECK------IGMLDRQYI 447 GE++L G V +G ++++L A + G + + P K + + I LD + Sbjct: 701 VAMTGEITLRGQVLPIGGLKEKLLAAHRGGIKTVLIPFENKRDLEEIPDNVIADLDIHPV 760 Query: 448 KNLSDLV 454 K + +++ Sbjct: 761 KRIEEVL 767 >gnl|CDD|168322 PRK05973, PRK05973, replicative DNA helicase; Provisional. Length = 237 Score = 40.4 bits (95), Expect = 0.001 Identities = 36/142 (25%), Positives = 62/142 (43%), Gaps = 20/142 (14%) Query: 87 FVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGE----------EAIGQIRLR 136 G ++L+G PG GK+ L ++ A + + E A+G R + Sbjct: 61 LKPGDLVLLGARPGHGKTLLGLELAVEAMKSGRTGVFFTLEYTEQDVRDRLRALGADRAQ 120 Query: 137 AQRLNTINSSVYIAIETNVEDIIATLITNEKPDLVIIDSIQTLWSQTAESSPGTVIQVRT 196 L ++S I + IIA L + + LV+ID +Q L Q E +V QVR Sbjct: 121 FADLFEFDTSDAIC----ADYIIARLASAPRGTLVVIDYLQLL-DQRREKPDLSV-QVR- 173 Query: 197 SVQAMIQYAKKNGVAMVLVGHV 218 A+ +A++ G+ +V + + Sbjct: 174 ---ALKSFARERGLIIVFISQI 192 >gnl|CDD|181111 PRK07773, PRK07773, replicative DNA helicase; Validated. Length = 886 Score = 39.3 bits (92), Expect = 0.002 Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 7/65 (10%) Query: 78 ELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYV--SGEEAIGQIRL 135 ELD +T G G +I+V P +GK+T + A + A +HR+ S E + Q+ Sbjct: 206 ELDAMTNG-LHPGQLIIVAARPSMGKTTFGLDFARNCA-IRHRLAVAIFSLEMSKEQL-- 261 Query: 136 RAQRL 140 RL Sbjct: 262 -VMRL 265 >gnl|CDD|161985 TIGR00665, DnaB, replicative DNA helicase. This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of > 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites. Length = 434 Score = 38.9 bits (92), Expect = 0.003 Identities = 12/47 (25%), Positives = 24/47 (51%), Gaps = 1/47 (2%) Query: 72 IQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKK 118 + T +LD++T G +I++ P +GK+ + A + A K+ Sbjct: 178 VPTGFTDLDKLTSG-LQPSDLIILAARPSMGKTAFALNIAENAAIKE 223 >gnl|CDD|162659 TIGR02012, tigrfam_recA, protein RecA. This model describes orthologs of the recA protein. RecA promotes hybridization of homolgous regions of DNA. A segment of ssDNA can be hybridized to another ssDNA region, or to a dsDNA region. ATP is hydrolyzed in the process. Part of the SOS respones, it is regulated by LexA via autocatalytic cleavage. Length = 321 Score = 35.8 bits (83), Expect = 0.026 Identities = 38/155 (24%), Positives = 67/155 (43%), Gaps = 14/155 (9%) Query: 57 SLFMLSEESIEEESRIQTHIDELDRVTG-GGFVRGSVILVGGDPGIGKSTLLMQTAASLA 115 S+ L E+S+ + I T LD G GG RG +I + G GK+TL + A Sbjct: 21 SIMRLGEKSVMDVETISTGSLSLDLALGVGGLPRGRIIEIYGPESSGKTTLALHAIAEAQ 80 Query: 116 YKKHRITYVSGEEAIGQIRLRAQRLNTINSSVYIAIETNVE---DIIATLITNEKPDLVI 172 ++ E A+ + R ++ N + ++ E +I TL+ + D+++ Sbjct: 81 KAGGTAAFIDAEHALDPVYARKLGVDIDN--LLVSQPDTGEQALEIAETLVRSGAVDIIV 138 Query: 173 IDSIQTLWSQT------AESSPGTVIQVRTSVQAM 201 +DS+ L + +S G +Q R QA+ Sbjct: 139 VDSVAALVPKAEIEGEMGDSHVG--LQARLMSQAL 171 >gnl|CDD|131701 TIGR02653, Lon_rel_chp, conserved hypothetical protein. This model describes a protein family of unknown function, about 690 residues in length, in which some members show C-terminal sequence similarity to Pfam model pfam05362, which is the Lon protease C-terminal proteolytic domain, from MEROPS family S16. However, the annotated catalytic sites of E. coli Lon protease are not conserved in members of this family. Members have a motif GP[RK][GS]TGKS, similar to the ATP-binding P-loop motif GxxGxGK[ST]. Length = 675 Score = 35.2 bits (81), Expect = 0.037 Identities = 23/88 (26%), Positives = 39/88 (44%), Gaps = 3/88 (3%) Query: 351 IKFGNHDVHLNIAG--GYRISEPAADVAVAAALISSILSIPLPSDFVYFGEVSLSGSVRA 408 KF HD HL++ S A+ +A AL S++L P+ V G +++ G + Sbjct: 558 AKFSEHDYHLHVVDLHNTGPSTEAS-LAALIALCSALLKRPVQEQMVILGSMTIGGVINP 616 Query: 409 VGHMQQRLKEAEKIGFLSGVFPESAKGE 436 V + L+ A G + P S+ + Sbjct: 617 VQDLAGSLQLAMDSGAKRVLIPMSSARD 644 >gnl|CDD|181451 PRK08506, PRK08506, replicative DNA helicase; Provisional. Length = 472 Score = 35.0 bits (81), Expect = 0.043 Identities = 22/97 (22%), Positives = 43/97 (44%), Gaps = 7/97 (7%) Query: 47 SKTIKQGHSI--SLFMLSEESIEEESRIQTHID----ELDRVTGGGFVRGSVILVGGDPG 100 S+ K + S ++ ++ +D EL+++T G F +G +I++ P Sbjct: 144 SEDFKDSKEVIESTMEHIKKQKRLGNKDIIGLDTGFVELNKMTKG-FNKGDLIIIAARPS 202 Query: 101 IGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRLRA 137 +GK+TL + A + + + S E Q+ LR Sbjct: 203 MGKTTLCLNMALKALNQDKGVAFFSLEMPAEQLMLRM 239 >gnl|CDD|77219 PRK09519, recA, DNA recombination protein RecA; Reviewed. Length = 790 Score = 34.3 bits (78), Expect = 0.078 Identities = 35/127 (27%), Positives = 57/127 (44%), Gaps = 6/127 (4%) Query: 57 SLFMLSEESIEEESRIQTHIDELDRVTG-GGFVRGSVILVGGDPGIGKSTLLMQTAASLA 115 S+ L +E+ + S I T LD G GG RG VI + G GK+T+ + A+ Sbjct: 26 SVMRLGDEARQPISVIPTGSIALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQ 85 Query: 116 YKKHRITYVSGEEAIGQIRLRAQRLNTINSSVYIAIETNVE---DIIATLITNEKPDLVI 172 ++ E A+ A++L S+ ++ E +I LI + D+V+ Sbjct: 86 AAGGVAAFIDAEHALDPD--YAKKLGVDTDSLLVSQPDTGEQALEIADMLIRSGALDIVV 143 Query: 173 IDSIQTL 179 IDS+ L Sbjct: 144 IDSVAAL 150 >gnl|CDD|179826 PRK04328, PRK04328, hypothetical protein; Provisional. Length = 249 Score = 33.5 bits (77), Expect = 0.11 Identities = 15/39 (38%), Positives = 22/39 (56%) Query: 71 RIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQ 109 R++T I +D + GG +V+L+ G PG GKS Q Sbjct: 4 RVKTGIPGMDEILYGGIPERNVVLLSGGPGTGKSIFSQQ 42 >gnl|CDD|183452 PRK12337, PRK12337, 2-phosphoglycerate kinase; Provisional. Length = 475 Score = 33.6 bits (77), Expect = 0.11 Identities = 19/50 (38%), Positives = 30/50 (60%), Gaps = 6/50 (12%) Query: 88 VRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRLRA 137 R +L+GG G+GKS L A++LAY+ IT + +A+ ++ LRA Sbjct: 253 PRPLHVLIGGVSGVGKSVL----ASALAYRLG-ITRIVSTDAVREV-LRA 296 >gnl|CDD|131290 TIGR02236, recomb_radA, DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein. Length = 310 Score = 33.2 bits (76), Expect = 0.14 Identities = 33/129 (25%), Positives = 55/129 (42%), Gaps = 26/129 (20%) Query: 71 RIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHR------ITYV 124 +I T ELD + GGG ++ V G+ G GK+ + Q A ++ + + Y+ Sbjct: 76 KITTGSKELDELLGGGIETQAITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYI 135 Query: 125 SGE-----EAIGQIRLRAQRLN------------TINSSVYIAIETNVEDIIATLITNEK 167 E E I Q+ A+ L+ NS+ + + ED+I L K Sbjct: 136 DTENTFRPERIMQM-AEARGLDPDEVLKNIYVARAYNSNHQMLLVEKAEDLIKELNNPVK 194 Query: 168 PDLVIIDSI 176 L+I+DS+ Sbjct: 195 --LLIVDSL 201 >gnl|CDD|163589 TIGR03877, thermo_KaiC_1, KaiC domain protein, Ph0284 family. Members of this family contain a single copy of the KaiC domain (pfam06745) that occurs in two copies of the circadian clock protein kinase KaiC itself. Members occur primarily in thermophilic archaea and in Thermotoga. Length = 237 Score = 33.2 bits (76), Expect = 0.15 Identities = 15/39 (38%), Positives = 22/39 (56%) Query: 71 RIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQ 109 R++T I +D + GG +V+L+ G PG GKS Q Sbjct: 2 RVKTGIPGMDEILHGGIPERNVVLLSGGPGTGKSIFSQQ 40 >gnl|CDD|129465 TIGR00368, TIGR00368, Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain. Length = 499 Score = 32.1 bits (73), Expect = 0.36 Identities = 30/137 (21%), Positives = 55/137 (40%), Gaps = 21/137 (15%) Query: 306 GTRALLVEIQSLVVPTSLGMPRRTVVGWDSSRLAMILAVLEAR---------CNIKFGNH 356 G A L+ I+ V S G+P T+VG + V E+R F Sbjct: 8 GVEAPLITIE---VDISKGLPGITIVGLPET------TVKESRERVKSAIKNSGFHFPAK 58 Query: 357 DVHLNIA-GGYRISEPAADVAVAAALI--SSILSIPLPSDFVYFGEVSLSGSVRAVGHMQ 413 + +N+A D+ +A ++ S L ++++ GE++L G +R + + Sbjct: 59 RITINLAPADLPKEGGRFDLPIAIGILAASEQLDAKNLGEYLFLGELALDGKLRGIKGVL 118 Query: 414 QRLKEAEKIGFLSGVFP 430 + A+K G + P Sbjct: 119 PAIALAQKSGRKFIIVP 135 >gnl|CDD|177377 PHA02542, 41, 41 helicase; Provisional. Length = 473 Score = 31.6 bits (72), Expect = 0.42 Identities = 20/76 (26%), Positives = 39/76 (51%), Gaps = 4/76 (5%) Query: 69 ESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVS--- 125 ++I ++ L+++T GG R ++ ++ +GKS L AA + + + Y+S Sbjct: 169 ANKIPFKLEILNKITKGGAERKTLNVLLAGVNVGKSLGLCSLAADYLQQGYNVLYISMEM 228 Query: 126 GEEAIGQIRLRAQRLN 141 EE I + R+ A L+ Sbjct: 229 AEEVIAK-RIDANLLD 243 >gnl|CDD|180232 PRK05748, PRK05748, replicative DNA helicase; Provisional. Length = 448 Score = 31.5 bits (72), Expect = 0.48 Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 1/49 (2%) Query: 72 IQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHR 120 I T +LD++T G +I+V P +GK+ + A ++A K + Sbjct: 186 IPTGFTDLDKMTSG-LQPNDLIIVAARPSVGKTAFALNIAQNVATKTDK 233 >gnl|CDD|183314 PRK11788, PRK11788, tetratricopeptide repeat protein; Provisional. Length = 389 Score = 31.3 bits (72), Expect = 0.51 Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 4/34 (11%) Query: 2 VKIRSQYFCQSCG-EIHSR-WIGKCDSCNAWNTI 33 +K + +Y C++CG + W C SC AW TI Sbjct: 349 LKRKPRYRCRNCGFTARTLYW--HCPSCKAWETI 380 >gnl|CDD|150510 pfam09848, DUF2075, Uncharacterized conserved protein (DUF2075). This domain, found in various prokaryotic proteins (including putative ATP/GTP binding proteins), has no known function. Length = 348 Score = 31.0 bits (71), Expect = 0.65 Identities = 24/102 (23%), Positives = 40/102 (39%), Gaps = 19/102 (18%) Query: 91 SVILVGGDPGIGKSTLLMQTAASLAYKKHRIT--YVSGEEAIGQIRLR---AQRLNTINS 145 +V LV G PG GK+ + + A L+ T ++SG + + L A L Sbjct: 2 AVFLVTGGPGTGKTVVALNLFAELSDSDLGRTAVFLSGNHPLVLV-LYEALAGDLKVRKK 60 Query: 146 SVYIAIETNVEDIIATLITNEKP-----DLVIIDSIQTLWSQ 182 ++ + I N D+VI+D LW++ Sbjct: 61 KLFRK--------PTSFINNLHKAPPHEDVVIVDEAHRLWTK 94 >gnl|CDD|183905 PRK13233, nifH, nitrogenase reductase; Reviewed. Length = 275 Score = 30.9 bits (70), Expect = 0.81 Identities = 14/34 (41%), Positives = 20/34 (58%) Query: 93 ILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSG 126 I + G GIGKST TAA++AY + ++ G Sbjct: 5 IAIYGKGGIGKSTTTQNTAAAMAYFHDKKVFIHG 38 >gnl|CDD|180177 PRK05636, PRK05636, replicative DNA helicase; Provisional. Length = 505 Score = 30.6 bits (69), Expect = 0.91 Identities = 18/49 (36%), Positives = 26/49 (53%), Gaps = 1/49 (2%) Query: 69 ESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYK 117 + I T +LD +T G G +I+V PG+GKSTL + S + K Sbjct: 245 ATGIPTGFKDLDDLTNG-LRGGQMIIVAARPGVGKSTLALDFMRSASIK 292 >gnl|CDD|181547 PRK08760, PRK08760, replicative DNA helicase; Provisional. Length = 476 Score = 30.3 bits (68), Expect = 1.2 Identities = 22/81 (27%), Positives = 36/81 (44%), Gaps = 11/81 (13%) Query: 72 IQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYK-KHRITYVSGEEAI 130 + T ++ D +T G +I++ P +GK+T + A A K K + S E + Sbjct: 212 LPTGYNDFDAMTAG-LQPTDLIILAARPAMGKTTFALNIAEYAAIKSKKGVAVFSMEMSA 270 Query: 131 GQIRLR---------AQRLNT 142 Q+ +R AQRL T Sbjct: 271 SQLAMRLISSNGRINAQRLRT 291 >gnl|CDD|184251 PRK13695, PRK13695, putative NTPase; Provisional. Length = 174 Score = 30.3 bits (69), Expect = 1.2 Identities = 10/29 (34%), Positives = 20/29 (68%) Query: 93 ILVGGDPGIGKSTLLMQTAASLAYKKHRI 121 I + G PG+GK+TL+++ A L + +++ Sbjct: 3 IGITGPPGVGKTTLVLKIAELLKEEGYKV 31 >gnl|CDD|117696 pfam09140, MipZ, ATPase MipZ. MipZ is an ATPase that forms a complex with the chromosome partitioning protein ParB near the chromosomal origin of replication. It is responsible for the temporal and spatial regulation of FtsZ ring formation. Length = 261 Score = 30.4 bits (69), Expect = 1.2 Identities = 13/31 (41%), Positives = 18/31 (58%), Gaps = 1/31 (3%) Query: 92 VILVGGDPG-IGKSTLLMQTAASLAYKKHRI 121 VI+VG + G GKST + A +L Y R+ Sbjct: 2 VIVVGNEKGGSGKSTTAVHVAVALLYLGARV 32 >gnl|CDD|139909 PRK13849, PRK13849, putative crown gall tumor protein VirC1; Provisional. Length = 231 Score = 30.2 bits (68), Expect = 1.3 Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 4/57 (7%) Query: 100 GIGKSTLLMQTAASLAYKKHRITYVSGEE--AIGQIRLRAQRLNTINSS--VYIAIE 152 G GK+T LM A+LA R+ +E + + + A R NT + + VY A E Sbjct: 12 GAGKTTALMGLCAALASDGKRVALFEADENRPLTRWKENALRSNTWDPACEVYAADE 68 >gnl|CDD|148602 pfam07088, GvpD, GvpD gas vesicle protein. This family consists of several archaeal GvpD gas vesicle proteins. GvpD is thought to be involved in the regulation of gas vesicle formation. Length = 484 Score = 29.9 bits (67), Expect = 1.4 Identities = 10/28 (35%), Positives = 18/28 (64%) Query: 68 EESRIQTHIDELDRVTGGGFVRGSVILV 95 +++ T I +LD++ GG RGSV+ + Sbjct: 236 DKAEFSTGIGDLDKILSGGTNRGSVVHL 263 >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 = 30.0 bits (68), Expect = 1.4 Identities = 18/69 (26%), Positives = 28/69 (40%), Gaps = 9/69 (13%) Query: 91 SVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSG------EEAIGQIRLRAQRLNTIN 144 V+LVG PG GKS L + AA A + YV E+ G+ + + ++ Sbjct: 1 GVLLVG-PPGTGKSELAERLAA--ALSNRPVFYVQLTRDTTEEDLKGRRNIANGTTSWVD 57 Query: 145 SSVYIAIET 153 + A Sbjct: 58 GPLVRAARE 66 >gnl|CDD|162286 TIGR01287, nifH, nitrogenase iron protein. This model describes nitrogenase (EC 1.18.6.1) iron protein, also called nitrogenase reductase or nitrogenase component II. This model includes molybdenum-iron nitrogenase reductase (nifH), vanadium-iron nitrogenase reductase (vnfH), and iron-iron nitrogenase reductase (anfH). The model excludes the homologous protein from the light-independent protochlorophyllide reductase. Length = 275 Score = 29.7 bits (67), Expect = 1.8 Identities = 13/32 (40%), Positives = 17/32 (53%) Query: 93 ILVGGDPGIGKSTLLMQTAASLAYKKHRITYV 124 I + G GIGKST AA+LA ++ V Sbjct: 3 IAIYGKGGIGKSTTTQNIAAALAEMGKKVMIV 34 >gnl|CDD|179154 PRK00885, PRK00885, phosphoribosylamine--glycine ligase; Provisional. Length = 420 Score = 29.6 bits (68), Expect = 1.8 Identities = 7/21 (33%), Positives = 16/21 (76%) Query: 196 TSVQAMIQYAKKNGVAMVLVG 216 T ++A++ +AK+ G+ + +VG Sbjct: 49 TDIEALVAFAKEEGIDLTVVG 69 >gnl|CDD|162131 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family protein. Length = 1394 Score = 29.3 bits (66), Expect = 2.0 Identities = 23/72 (31%), Positives = 30/72 (41%), Gaps = 16/72 (22%) Query: 90 GSVILVGGDPGIGKSTLLMQTAA----SLAYKKHRITY--VSGEEAIGQIRLRAQRLNTI 143 G + +V G PG G STLL A+ + ITY ++ EE R Sbjct: 87 GELTVVLGRPGSGCSTLLKTIASNTDGFHIGVEGVITYDGITPEEIKKHYR--------- 137 Query: 144 NSSVYIAIETNV 155 VY A ET+V Sbjct: 138 GDVVYNA-ETDV 148 >gnl|CDD|181894 PRK09480, slmA, division inhibitor protein; Provisional. Length = 194 Score = 29.0 bits (66), Expect = 2.7 Identities = 11/47 (23%), Positives = 25/47 (53%), Gaps = 1/47 (2%) Query: 172 IIDSIQTLWSQTAESSPGTVIQVRTSVQAMIQYAKKN-GVAMVLVGH 217 I +S+ + +Q + T+ + R + ++ +A++N G+ VL G Sbjct: 65 IEESLFSRINQILKDEKDTLARARLILLLLLGFAERNPGMTRVLTGD 111 >gnl|CDD|147840 pfam05907, DUF866, Eukaryotic protein of unknown function (DUF866). This family consists of a number of hypothetical eukaryotic proteins of unknown function with an average length of around 165 residues. Length = 161 Score = 28.9 bits (65), Expect = 2.9 Identities = 18/66 (27%), Positives = 24/66 (36%), Gaps = 26/66 (39%) Query: 10 CQSCGEIHSRWIG--------------------KCDSCNAWNTI--IEDSSRK---ESDQ 44 C +CGE+ +WI KC C+ N+I I S E Sbjct: 33 CSNCGEVSDKWIYITLSETVPLPGGKGTANLVQKCKLCSRENSIDIIPGSGSPYTAEDSG 92 Query: 45 RFSKTI 50 +F KTI Sbjct: 93 KF-KTI 97 >gnl|CDD|179771 PRK04182, PRK04182, cytidylate kinase; Provisional. Length = 180 Score = 28.6 bits (65), Expect = 3.2 Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 5/35 (14%) Query: 92 VILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSG 126 +I + G PG GK+T+ A LA +K + +VS Sbjct: 2 IITISGPPGSGKTTV----ARLLA-EKLGLKHVSA 31 >gnl|CDD|149060 pfam07786, DUF1624, Protein of unknown function (DUF1624). These sequences are found in hypothetical proteins of unknown function expressed by bacterial and archaeal species. The region in question is approximately 230 residues long. Length = 222 Score = 28.7 bits (65), Expect = 3.3 Identities = 10/24 (41%), Positives = 14/24 (58%) Query: 375 VAVAAALISSILSIPLPSDFVYFG 398 + AA LI++ I P F+YFG Sbjct: 79 IFAAALLITAATYIVFPDSFIYFG 102 >gnl|CDD|148565 pfam07015, VirC1, VirC1 protein. This family consists of several bacterial VirC1 proteins. In Agrobacterium tumefaciens, a cis-active 24-base-pair sequence adjacent to the right border of the T-DNA, called overdrive, stimulates tumour formation by increasing the level of T-DNA processing. It is thought that the virC operon which enhances T-DNA processing probably does so because the VirC1 protein interacts with overdrive. It has now been shown that the virC1 gene product binds to overdrive but not to the right border of T-DNA. Length = 231 Score = 28.7 bits (64), Expect = 3.8 Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 4/57 (7%) Query: 100 GIGKSTLLMQTAASLAYKKHRITYVSGEE--AIGQIRLRAQRLNTINS--SVYIAIE 152 G GK+T LM ++LA R+ +E + + R A R T + ++ A E Sbjct: 12 GAGKTTALMGLCSALASDGKRVALFEADENRPLTKWRENALRKGTWDPACEIFNADE 68 >gnl|CDD|179814 PRK04301, radA, DNA repair and recombination protein RadA; Validated. Length = 317 Score = 28.7 bits (65), Expect = 3.9 Identities = 15/41 (36%), Positives = 21/41 (51%) Query: 71 RIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTA 111 +I T ELD + GGG S+ G+ G GK+ + Q A Sbjct: 83 KITTGSKELDELLGGGIETQSITEFYGEFGSGKTQICHQLA 123 >gnl|CDD|163585 TIGR03873, F420-0_ABC_ATP, proposed F420-0 ABC transporter, ATP-binding protein. This small clade of ABC-type transporter ATP-binding protein components is found as a three gene cassette along with a periplasmic substrate-binding protein (TIGR03868) and a permease (TIGR03869). The organisms containing this cassette are all Actinobacteria and all contain numerous genes requiring the coenzyme F420. This model was defined based on five such organisms, four of which are lacking all F420 biosynthetic capability save the final side-chain polyglutamate attachment step (via the gene cofE: TIGR01916). In Jonesia denitrificans DSM 20603 and marine actinobacterium PHSC20C1 this cassette is in an apparent operon with the cofE gene and, in PHSC20C1, also with a F420-dependent glucose-6-phosphate dehydrogenase (TIGR03554). Based on these observations we propose that this ATP-binding protein is a component of an F420-0 (that is, F420 lacking only the polyglutamate tail) transporter. Length = 256 Score = 28.6 bits (64), Expect = 3.9 Identities = 20/71 (28%), Positives = 31/71 (43%) Query: 90 GSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRLRAQRLNTINSSVYI 149 GS+ + G G GKSTLL A +L + + R RA+R+ + Sbjct: 27 GSLTGLLGPNGSGKSTLLRLLAGALRPDAGTVDLAGVDLHGLSRRARARRVALVEQDSDT 86 Query: 150 AIETNVEDIIA 160 A+ V D++A Sbjct: 87 AVPLTVRDVVA 97 >gnl|CDD|149480 pfam08433, KTI12, Chromatin associated protein KTI12. This is a family of chromatin associated proteins which interact with the Elongator complex, a component of the elongating form of RNA polymerase II. The Elongator complex has histone acetyltransferase activity. Length = 266 Score = 28.4 bits (64), Expect = 4.2 Identities = 20/86 (23%), Positives = 40/86 (46%), Gaps = 14/86 (16%) Query: 93 ILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIR---LRAQRLNTINSSVYI 149 I++ G P GKST + A L K + + +S +E++G +++ + S+ Sbjct: 2 IILTGLPSSGKSTRAKELAKYLEEKGYDVIVIS-DESLGIESDDYKDSKKEKFLRGSLRS 60 Query: 150 AIETNVEDIIATLITNEKPDLVIIDS 175 A++ ++ K +VI+DS Sbjct: 61 AVKRDL----------SKNTIVIVDS 76 >gnl|CDD|136670 PRK08181, PRK08181, transposase; Validated. Length = 269 Score = 28.4 bits (63), Expect = 4.4 Identities = 26/99 (26%), Positives = 47/99 (47%), Gaps = 16/99 (16%) Query: 89 RGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRLRAQRLNTINSSVY 148 +G+ +L+ G PG GKS L +L R+ + + + ++++ A+R Sbjct: 105 KGANLLLFGPPGGGKSHLAAAIGLALIENGWRVLFTRTTDLVQKLQV-ARR--------- 154 Query: 149 IAIETNVEDIIATLITNEKPDLVIIDSIQTLWSQTAESS 187 E +E IA L +K DL+I+D + + AE+S Sbjct: 155 ---ELQLESAIAKL---DKFDLLILDDLAYVTKDQAETS 187 >gnl|CDD|163451 TIGR03739, PRTRC_D, PRTRC system protein D. A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family is designated PRTRC system protein D. The gray zone, between trusted and noise, includes proteins found in the same genomes as other proteins of the PRTRC systems, but not in the same contiguous gene region. Length = 320 Score = 28.2 bits (63), Expect = 4.4 Identities = 14/53 (26%), Positives = 22/53 (41%), Gaps = 6/53 (11%) Query: 69 ESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRI 121 E+ Q + + G +++LVGG L + A A+ KHRI Sbjct: 254 ETVAQQAVSTMMTWIGAPESIQNIVLVGG------GAFLFKKAVKAAFPKHRI 300 >gnl|CDD|183453 PRK12338, PRK12338, hypothetical protein; Provisional. Length = 319 Score = 28.2 bits (63), Expect = 4.8 Identities = 13/26 (50%), Positives = 17/26 (65%) Query: 92 VILVGGDPGIGKSTLLMQTAASLAYK 117 VIL+G GIGKST+ + A +L K Sbjct: 6 VILIGSASGIGKSTIASELARTLNIK 31 >gnl|CDD|147929 pfam06032, DUF917, Protein of unknown function (DUF917). This family consists of hypothetical bacterial and archaeal proteins of unknown function. Length = 352 Score = 28.3 bits (64), Expect = 4.8 Identities = 11/35 (31%), Positives = 17/35 (48%) Query: 75 HIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQ 109 I +++R T GGF G V + G + T+ Q Sbjct: 241 KIVDVERRTRGGFDVGEVTIEGLEYLGRTLTIPFQ 275 >gnl|CDD|128644 smart00350, MCM, minichromosome maintenance proteins. Length = 509 Score = 28.4 bits (64), Expect = 4.8 Identities = 13/28 (46%), Positives = 17/28 (60%), Gaps = 1/28 (3%) Query: 81 RVTGGGFVRGSV-ILVGGDPGIGKSTLL 107 + G +RG + IL+ GDPG KS LL Sbjct: 226 NLPDGMKIRGDINILLLGDPGTAKSQLL 253 >gnl|CDD|163179 TIGR03185, DNA_S_dndD, DNA sulfur modification protein DndD. This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. Length = 650 Score = 28.1 bits (63), Expect = 5.4 Identities = 17/42 (40%), Positives = 23/42 (54%), Gaps = 3/42 (7%) Query: 92 VILVGGDPGIGKSTLLMQTAASLA-YKKHRITYVSGEEAIGQ 132 +IL+GG G GK+TLL A LA Y K + G ++ Q Sbjct: 30 IILIGGLNGAGKTTLL--DAIQLALYGKRALCSGRGNKSYEQ 69 >gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional. Length = 602 Score = 27.9 bits (63), Expect = 6.4 Identities = 12/23 (52%), Positives = 14/23 (60%), Gaps = 4/23 (17%) Query: 93 ILVGGDPGIGKSTLLMQTAASLA 115 IL+ G PG GKST A +LA Sbjct: 260 ILIAGAPGAGKSTF----AQALA 278 >gnl|CDD|105560 PRK12339, PRK12339, 2-phosphoglycerate kinase; Provisional. Length = 197 Score = 27.8 bits (62), Expect = 6.6 Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 4/61 (6%) Query: 92 VILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRLRAQRLNTINSSVYIAI 151 + +GG PG+GK+++ + +A + +SG+ +R + SVY A Sbjct: 5 IHFIGGIPGVGKTSI----SGYIARHRAIDIVLSGDYLREFLRPYVDDEPVLAKSVYDAW 60 Query: 152 E 152 E Sbjct: 61 E 61 >gnl|CDD|162807 TIGR02323, CP_lyasePhnK, phosphonate C-P lyase system protein PhnK. Members of this family are the PhnK protein of C-P lyase systems for utilization of phosphonates. These systems resemble phosphonatase-based systems in having a three component ABC transporter, where TIGR01097 is the permease, TIGR01098 is the phosphonates binding protein, and TIGR02315 is the ATP-binding cassette (ABC) protein. They differ, however, in having, typically, ten or more additional genes, many of which are believed to form a membrane-associated complex. This protein (PhnK) and the adjacent-encoded PhnL resemble transporter ATP-binding proteins but are suggested, based on mutatgenesis studies, to be part of this complex rather than part of a transporter per se. Length = 253 Score = 27.5 bits (61), Expect = 7.1 Identities = 15/36 (41%), Positives = 19/36 (52%) Query: 90 GSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVS 125 G V+ + G+ G GKSTLL A LA TY+ Sbjct: 29 GEVLGIVGESGSGKSTLLGCLAGRLAPDHGTATYIM 64 >gnl|CDD|184129 PRK13543, PRK13543, cytochrome c biogenesis protein CcmA; Provisional. Length = 214 Score = 27.5 bits (61), Expect = 8.2 Identities = 11/18 (61%), Positives = 13/18 (72%) Query: 90 GSVILVGGDPGIGKSTLL 107 G +LV GD G GK+TLL Sbjct: 37 GEALLVQGDNGAGKTTLL 54 >gnl|CDD|181676 PRK09165, PRK09165, replicative DNA helicase; Provisional. Length = 497 Score = 27.5 bits (62), Expect = 8.3 Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 5/47 (10%) Query: 70 SRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAY 116 S I T + +LD GG +I++ G P +GK+ L A ++A+ Sbjct: 198 SGISTGLRDLDSKLGG-LHPSDLIILAGRPSMGKTAL----ATNIAF 239 >gnl|CDD|150847 pfam10236, DAP3, Mitochondrial ribosomal death-associated protein 3. This is a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29). Length = 274 Score = 27.2 bits (61), Expect = 8.7 Identities = 9/20 (45%), Positives = 12/20 (60%) Query: 93 ILVGGDPGIGKSTLLMQTAA 112 ++ G+ G GKS LL Q A Sbjct: 26 FVLTGERGSGKSVLLAQAMA 45 >gnl|CDD|180157 PRK05595, PRK05595, replicative DNA helicase; Provisional. Length = 444 Score = 27.1 bits (60), Expect = 9.5 Identities = 14/34 (41%), Positives = 20/34 (58%), Gaps = 1/34 (2%) Query: 78 ELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTA 111 ELD T G F +G +IL+ P +GK+T + A Sbjct: 190 ELDAKTSG-FQKGDMILIAARPSMGKTTFALNIA 222 >gnl|CDD|180538 PRK06349, PRK06349, homoserine dehydrogenase; Provisional. Length = 426 Score = 27.4 bits (62), Expect = 9.5 Identities = 8/30 (26%), Positives = 16/30 (53%), Gaps = 1/30 (3%) Query: 197 SVQAMIQYAKKNGVA-MVLVGHVTKEGQIA 225 S+++++Q A +V+V H T E + Sbjct: 375 SIESILQKGAGGEGAEIVIVTHETSEAALR 404 >gnl|CDD|178352 PLN02751, PLN02751, glutamyl-tRNA(Gln) amidotransferase. Length = 544 Score = 27.1 bits (60), Expect = 9.7 Identities = 10/16 (62%), Positives = 11/16 (68%) Query: 223 QIAGPRVIEHMVDAVL 238 QI+ P IE MVD VL Sbjct: 480 QISDPAEIEAMVDKVL 495 >gnl|CDD|148176 pfam06414, Zeta_toxin, Zeta toxin. This family consists of several bacterial zeta toxin proteins. Zeta toxin is thought to be part of a postregulational killing system in bacteria. It relies on antitoxin/toxin systems that secure stable inheritance of low and medium copy number plasmids during cell division and kill cells that have lost the plasmid. Length = 191 Score = 27.2 bits (61), Expect = 10.0 Identities = 9/25 (36%), Positives = 12/25 (48%) Query: 92 VILVGGDPGIGKSTLLMQTAASLAY 116 +L+GG PG GK+ L L Sbjct: 14 AVLLGGQPGAGKTELARALLEELGG 38 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 0.133 0.378 Gapped Lambda K H 0.267 0.0669 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 7,575,960 Number of extensions: 495210 Number of successful extensions: 1478 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1458 Number of HSP's successfully gapped: 96 Length of query: 479 Length of database: 5,994,473 Length adjustment: 97 Effective length of query: 382 Effective length of database: 3,898,497 Effective search space: 1489225854 Effective search space used: 1489225854 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 (26.6 bits)