RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254781149|ref|YP_003065562.1| replicative DNA helicase [Candidatus Liberibacter asiaticus str. psy62] (266 letters) >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 = 119 bits (300), Expect = 9e-28 Identities = 71/253 (28%), Positives = 108/253 (42%), Gaps = 36/253 (14%) Query: 5 IISHFESQTKISFSTYLNNLLTLASSISSEVINA---ARRVVQQWAR---ITISQEAKAL 58 + E K+ L L LA ++ S N A V ++ I E L Sbjct: 62 VKEELEKDGKLEEVGGLAYLAELADNVPS-AANIEYYAEIVKEKAILRRLIEAGTEIVEL 120 Query: 59 ALHTSDPTCNTATLIRKSMQSFEDIISEVH-----LTKNQCTGSSCISIANAATTAMKSA 113 A E+++ E + +++ T SI ++ Sbjct: 121 AYDPEG--------------DVEELLDEAEQKIFEIAESR-TSGGFKSIKEILKDTVEEI 165 Query: 114 EQ-QKKEGENPDIKWGLQSVDHLMGGVQLRELILIGARPSMGKTTFALSTALHMAM-SGH 171 E+ ++ G + G +D L G+Q +LI++ ARPSMGKT FAL+ A + A+ G Sbjct: 166 EELYERGGGITGVPTGFTDLDKLTSGLQPSDLIILAARPSMGKTAFALNIAENAAIKEGK 225 Query: 172 GVAFFSLEMDREKLGARALSNLLYPSSSRIPYLNLIRGEINQEQY-RISQGICEKLQDFP 230 VAFFSLEM E+L R LS S SR+ L G+++ E + +++ KL + P Sbjct: 226 PVAFFSLEMSAEQLAMRMLS-----SESRVDSQKLRTGKLSDEDWEKLTSAA-GKLSEAP 279 Query: 231 LIIDDRPSPGIME 243 L IDD P I E Sbjct: 280 LYIDDTPGLTITE 292 >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 = 95.5 bits (238), Expect = 1e-20 Identities = 54/178 (30%), Positives = 80/178 (44%), Gaps = 13/178 (7%) Query: 69 TATLIRKSMQSFEDIISEVHLTKNQCTGSS------CISIANAATTAMKSAEQQ-KKEGE 121 Q+ E + E TG S ++ ++ +++ +GE Sbjct: 114 IDLACSDGGQTAEQKVEEAQAALLALTGMSDGQERGFVTFGEVLEDVVRDLDKRFNPKGE 173 Query: 122 NPDIKWGLQSVDHLMGGVQLRELILIGARPSMGKTTFALSTALHMAMS-GHGVAFFSLEM 180 + GL +D L G+ +LI+IGARPSMGKTT AL+ A ++A+ G V FFSLEM Sbjct: 174 LTGLSTGLPKLDRLTNGLVKGDLIVIGARPSMGKTTLALNIAENVALREGKPVLFFSLEM 233 Query: 181 DREKLGARALSNLLYPSSSRIPYLNLIRGEINQEQYRISQGICEKLQDFPLIIDDRPS 238 E+LG R L+ S S I N+ G N + ++L + L IDD Sbjct: 234 SAEQLGERLLA-----SKSGINTGNIRTGRFNDSDFNRLLNAVDRLSEKDLYIDDTGG 286 >gnl|CDD|181676 PRK09165, PRK09165, replicative DNA helicase; Provisional. Length = 497 Score = 94.2 bits (235), Expect = 3e-20 Identities = 68/247 (27%), Positives = 97/247 (39%), Gaps = 42/247 (17%) Query: 18 STYLNNLLTLASSISSEVINA---ARRVVQQWAR---ITISQEAKALALHTSDPTCNTAT 71 YL L T A +I INA R + R I I ++ A Sbjct: 97 VQYLAKLATEAVTI----INARDYGRIIYDLALRRELINIGEDVVNNAYDAPVD--VAPQ 150 Query: 72 -LIRKSMQSFEDIISEVHLTKNQCTGSSCISIANAATTAMKSAEQQKKEGEN-PDIKWGL 129 I + Q + L + S A T A+ A K + I GL Sbjct: 151 EQIEDAEQKLYE------LAETGRYEGGFQSFGTAITEAVDMANAAFKRDGHLSGISTGL 204 Query: 130 QSVDHLMGGVQLRELILIGARPSMGKTTFALSTALHMAMS---------------GHGVA 174 + +D +GG+ +LI++ RPSMGKT A + A + A + G V Sbjct: 205 RDLDSKLGGLHPSDLIILAGRPSMGKTALATNIAFNAAKAYRREAQPDGSKKAVNGGVVG 264 Query: 175 FFSLEMDREKLGARALSNLLYPSSSRIPYLNLIRGEINQEQYRISQGICEKLQDFPLIID 234 FFSLEM E+L R LS S I + RG+I++E + ++LQ PL ID Sbjct: 265 FFSLEMSAEQLATRILS-----EQSEISSSKIRRGKISEEDFEKLVDASQELQKLPLYID 319 Query: 235 DRPSPGI 241 D +P + Sbjct: 320 D--TPAL 324 >gnl|CDD|181451 PRK08506, PRK08506, replicative DNA helicase; Provisional. Length = 472 Score = 88.9 bits (221), Expect = 1e-18 Identities = 57/177 (32%), Positives = 85/177 (48%), Gaps = 17/177 (9%) Query: 70 ATLIRK----SMQSFEDIISEVHLTKNQCT-GSSCISIANA---ATTAMKSAEQQKKEGE 121 A I + Q DI+ EV T GS+ ++ + M+ ++QK+ G Sbjct: 110 ANTIPEQAVEEDQKSSDILDEVERELYSITNGSNSEDFKDSKEVIESTMEHIKKQKRLG- 168 Query: 122 NPDI---KWGLQSVDHLMGGVQLRELILIGARPSMGKTTFALSTALHMAMSGHGVAFFSL 178 N DI G ++ + G +LI+I ARPSMGKTT L+ AL GVAFFSL Sbjct: 169 NKDIIGLDTGFVELNKMTKGFNKGDLIIIAARPSMGKTTLCLNMALKALNQDKGVAFFSL 228 Query: 179 EMDREKLGARALSNLLYPSSSRIPYLNLIRGEINQEQYRISQGICEKLQDFPLIIDD 235 EM E+L R LS + + IP NL G+++ +++ C++L L + D Sbjct: 229 EMPAEQLMLRMLS-----AKTSIPLQNLRTGDLDDDEWERLSDACDELSKKKLFVYD 280 >gnl|CDD|181111 PRK07773, PRK07773, replicative DNA helicase; Validated. Length = 886 Score = 87.9 bits (218), Expect = 3e-18 Identities = 45/138 (32%), Positives = 75/138 (54%), Gaps = 8/138 (5%) Query: 120 GENPDIKWGLQSVDHLMGGVQLRELILIGARPSMGKTTFALSTALHMAMSGH-GVAFFSL 178 G + G +D + G+ +LI++ ARPSMGKTTF L A + A+ VA FSL Sbjct: 195 GLARGVPTGFTELDAMTNGLHPGQLIIVAARPSMGKTTFGLDFARNCAIRHRLAVAIFSL 254 Query: 179 EMDREKLGARALSNLLYPSSSRIPYLNLIRGEINQEQY-RISQGICEKLQDFPLIIDDRP 237 EM +E+L R LS + ++I ++ G ++ + + R+++ + E + + P+ IDD P Sbjct: 255 EMSKEQLVMRLLS-----AEAKIKLSDMRSGRMSDDDWTRLARAMGE-ISEAPIFIDDTP 308 Query: 238 SPGIMEFVHVANGLRNKH 255 + +ME A LR + Sbjct: 309 NLTVMEIRAKARRLRQEA 326 >gnl|CDD|168658 PRK06749, PRK06749, replicative DNA helicase; Provisional. Length = 428 Score = 76.9 bits (189), Expect = 5e-15 Identities = 46/143 (32%), Positives = 70/143 (48%), Gaps = 5/143 (3%) Query: 114 EQQKKEGENPDIKWGLQSVDHLMGGVQLRELILIGARPSMGKTTFALSTALHMAMSGHGV 173 E + E I+ G S++ + G+Q + +++GARPSMGKT FAL+ LH A SG V Sbjct: 158 ELHQDAKEITGIETGYTSLNKMTCGLQEGDFVVLGARPSMGKTAFALNVGLHAAKSGAAV 217 Query: 174 AFFSLEMDREKLGARALSNLLYPSSSRIPYLNLIRGEINQEQY-RISQGICEKLQDFPLI 232 FSLEM ++L R S + S R L + E + ++S+ E + + PL Sbjct: 218 GLFSLEMSSKQLLKRMASCVGEVSGGR---LKNPKHRFAMEDWEKVSKAFAE-IGELPLE 273 Query: 233 IDDRPSPGIMEFVHVANGLRNKH 255 I D + + L+ KH Sbjct: 274 IYDNAGVTVQDIWMQTRKLKRKH 296 >gnl|CDD|181547 PRK08760, PRK08760, replicative DNA helicase; Provisional. Length = 476 Score = 74.2 bits (182), Expect = 3e-14 Identities = 51/146 (34%), Positives = 76/146 (52%), Gaps = 13/146 (8%) Query: 105 AATTAMKSA-EQQKKEGENPD----IKWGLQSVDHLMGGVQLRELILIGARPSMGKTTFA 159 A A+K A E+ + EN + G D + G+Q +LI++ ARP+MGKTTFA Sbjct: 187 AMPGALKDAFEELRNRFENGGNITGLPTGYNDFDAMTAGLQPTDLIILAARPAMGKTTFA 246 Query: 160 LSTALHMAM-SGHGVAFFSLEMDREKLGARALSNLLYPSSSRIPYLNLIRGEINQEQYRI 218 L+ A + A+ S GVA FS+EM +L R +S S+ RI L G + E + Sbjct: 247 LNIAEYAAIKSKKGVAVFSMEMSASQLAMRLIS-----SNGRINAQRLRTGALEDEDWAR 301 Query: 219 SQGICEKLQDFPLIIDDRP--SPGIM 242 G + L++ + IDD P SP ++ Sbjct: 302 VTGAIKMLKETKIFIDDTPGVSPEVL 327 >gnl|CDD|180157 PRK05595, PRK05595, replicative DNA helicase; Provisional. Length = 444 Score = 71.0 bits (174), Expect = 3e-13 Identities = 44/128 (34%), Positives = 63/128 (49%), Gaps = 6/128 (4%) Query: 117 KKEGENPDIKWGLQSVDHLMGGVQLRELILIGARPSMGKTTFALSTALHMAM-SGHGVAF 175 +GE + G + +D G Q ++ILI ARPSMGKTTFAL+ A + A+ G VA Sbjct: 176 NNKGETTGVASGFRELDAKTSGFQKGDMILIAARPSMGKTTFALNIAEYAALREGKSVAI 235 Query: 176 FSLEMDREKLGARALSNLLYPSSSRIPYLNLIRGEINQEQYRISQGICEKLQDFPLIIDD 235 FSLEM +E+L + L S + + L L G + + + L + IDD Sbjct: 236 FSLEMSKEQLAYKLLC-----SEANVDMLRLRTGNLEDKDWENIARASGPLAAAKIFIDD 290 Query: 236 RPSPGIME 243 +ME Sbjct: 291 TAGVSVME 298 >gnl|CDD|180232 PRK05748, PRK05748, replicative DNA helicase; Provisional. Length = 448 Score = 67.7 bits (166), Expect = 3e-12 Identities = 43/118 (36%), Positives = 61/118 (51%), Gaps = 14/118 (11%) Query: 128 GLQSVDHLMGGVQLRELILIGARPSMGKTTFALSTALHMAMSGH-GVAFFSLEMDREKLG 186 G +D + G+Q +LI++ ARPS+GKT FAL+ A ++A VA FSLEM E L Sbjct: 189 GFTDLDKMTSGLQPNDLIIVAARPSVGKTAFALNIAQNVATKTDKNVAIFSLEMGAESLV 248 Query: 187 ARALSNLLYPSSSRIPYLNLIRGEINQE---QYRISQGICEKLQDFPLIIDDRPSPGI 241 R L + I L G++ + + I+ G L D P+ IDD +PGI Sbjct: 249 MRMLC-----AEGNIDAQRLRTGQLTDDDWPKLTIAMG---SLSDAPIYIDD--TPGI 296 >gnl|CDD|180791 PRK07004, PRK07004, replicative DNA helicase; Provisional. Length = 460 Score = 61.9 bits (150), Expect = 2e-10 Identities = 35/118 (29%), Positives = 60/118 (50%), Gaps = 8/118 (6%) Query: 128 GLQSVDHLMGGVQLRELILIGARPSMGKTTFALSTALHMAM-SGHGVAFFSLEMDREKLG 186 G +D + G+ ELI++ RPSMGKT F+++ ++A+ G VA FS+EM +L Sbjct: 199 GFVDLDRMTSGMHGGELIIVAGRPSMGKTAFSMNIGEYVAVEYGLPVAVFSMEMPGTQLA 258 Query: 187 ARALSNLLYPSSSRIPYLNLIRGEINQEQY-RISQGICEKLQDFPLIIDDRPSPGIME 243 R L S R+ + G + E + +++ + +K+ + L ID+ ME Sbjct: 259 MRMLG-----SVGRLDQHRMRTGRLTDEDWPKLTHAV-QKMSEAQLFIDETGGLNPME 310 >gnl|CDD|181193 PRK08006, PRK08006, replicative DNA helicase; Provisional. Length = 471 Score = 60.8 bits (147), Expect = 4e-10 Identities = 39/110 (35%), Positives = 61/110 (55%), Gaps = 7/110 (6%) Query: 128 GLQSVDHLMGGVQLRELILIGARPSMGKTTFALSTALHMAM-SGHGVAFFSLEMDREKLG 186 G ++ G+Q +LI++ ARPSMGKTTFA++ + AM V FSLEM E++ Sbjct: 210 GYDDLNKKTAGLQPSDLIIVAARPSMGKTTFAMNLCENAAMLQDKPVLIFSLEMPGEQIM 269 Query: 187 ARALSNLLYPSSSRIPYLNLIRGEINQEQY-RISQGICEKLQDFPLIIDD 235 R L++L SR+ + G+++ E + RIS + L+ + IDD Sbjct: 270 MRMLASL-----SRVDQTRIRTGQLDDEDWARISGTMGILLEKRNMYIDD 314 >gnl|CDD|181562 PRK08840, PRK08840, replicative DNA helicase; Provisional. Length = 464 Score = 57.7 bits (139), Expect = 3e-09 Identities = 39/110 (35%), Positives = 61/110 (55%), Gaps = 7/110 (6%) Query: 128 GLQSVDHLMGGVQLRELILIGARPSMGKTTFALSTALHMAMSGHG-VAFFSLEMDREKLG 186 G ++ G+Q +LI++ ARPSMGKTTFA++ + AM V FSLEM E+L Sbjct: 203 GFTDLNKKTAGLQGSDLIIVAARPSMGKTTFAMNLCENAAMDQDKPVLIFSLEMPAEQLM 262 Query: 187 ARALSNLLYPSSSRIPYLNLIRGEINQEQY-RISQGICEKLQDFPLIIDD 235 R L++L SR+ + G+++ E + RIS + ++ + IDD Sbjct: 263 MRMLASL-----SRVDQTKIRTGQLDDEDWARISSTMGILMEKKNMYIDD 307 >gnl|CDD|136106 PRK06904, PRK06904, replicative DNA helicase; Validated. Length = 472 Score = 56.2 bits (135), Expect = 8e-09 Identities = 41/111 (36%), Positives = 59/111 (53%), Gaps = 8/111 (7%) Query: 128 GLQSVDHLMGGVQLRELILIGARPSMGKTTFALSTALHMAM-SGHGVAFFSLEMDREKLG 186 G +D G+Q +LI++ ARPSMGKTTFA++ + AM S V FSLEM E++ Sbjct: 207 GFTDLDKKTAGLQPSDLIIVAARPSMGKTTFAMNLCENAAMASEKPVLVFSLEMPAEQIM 266 Query: 187 ARALSNLLYPSSSRIPYLNLIRGEI--NQEQYRISQGICEKLQDFPLIIDD 235 R L++L SR+ + G+ Q+ +IS + Q L IDD Sbjct: 267 MRMLASL-----SRVDQTKIRTGQNLDQQDWAKISSTVGMFKQKPNLYIDD 312 >gnl|CDD|180177 PRK05636, PRK05636, replicative DNA helicase; Provisional. Length = 505 Score = 54.8 bits (132), Expect = 2e-08 Identities = 35/133 (26%), Positives = 70/133 (52%), Gaps = 14/133 (10%) Query: 128 GLQSVDHLMGGVQLRELILIGARPSMGKTTFAL----STALHMAMSGHGVAFFSLEMDRE 183 G + +D L G++ ++I++ ARP +GK+T AL S ++ + FSLEM + Sbjct: 251 GFKDLDDLTNGLRGGQMIIVAARPGVGKSTLALDFMRSASIKHNKAS---VIFSLEMSKS 307 Query: 184 KLGARALSNLLYPSSSRIPYLNLIRGEINQEQY-RISQGICEKLQDFPLIIDDRPSPGIM 242 ++ R LS + + + ++ G+++++ + ++ Q + K+ P+ IDD + +M Sbjct: 308 EIVMRLLS-----AEAEVRLSDMRGGKMDEDAWEKLVQRL-GKIAQAPIFIDDSANLTMM 361 Query: 243 EFVHVANGLRNKH 255 E A L+ KH Sbjct: 362 EIRSKARRLKQKH 374 >gnl|CDD|180528 PRK06321, PRK06321, replicative DNA helicase; Provisional. Length = 472 Score = 50.6 bits (121), Expect = 4e-07 Identities = 35/132 (26%), Positives = 63/132 (47%), Gaps = 13/132 (9%) Query: 132 VDHLMGGVQLRELILIGARPSMGKTTFALSTALHMAMSGH-GVAFFSLEMDREKLGARAL 190 +D ++ G L+++ ARP+MGKT AL+ A + V FSLEM ++L R + Sbjct: 216 LDKMINGFSPSNLMILAARPAMGKTALALNIAENFCFQNRLPVGIFSLEMTVDQLIHRII 275 Query: 191 SNLLYPSSSRIPYLNLIRGEINQEQYRISQGICEKLQDFPLIIDDRPSPGIMEFVHVANG 250 S S + + G+++ ++ + ++Q+ L+IDD+P I Sbjct: 276 C-----SRSEVESKKISVGDLSGRDFQRIVSVVNEMQEHTLLIDDQPGLKI-------TD 323 Query: 251 LRNKHTKMVQLY 262 LR + +M + Y Sbjct: 324 LRARARRMKESY 335 >gnl|CDD|168322 PRK05973, PRK05973, replicative DNA helicase; Provisional. Length = 237 Score = 48.5 bits (116), Expect = 2e-06 Identities = 19/54 (35%), Positives = 28/54 (51%) Query: 135 LMGGVQLRELILIGARPSMGKTTFALSTALHMAMSGHGVAFFSLEMDREKLGAR 188 L ++ +L+L+GARP GKT L A+ SG FF+LE + + R Sbjct: 57 LFSQLKPGDLVLLGARPGHGKTLLGLELAVEAMKSGRTGVFFTLEYTEQDVRDR 110 >gnl|CDD|177377 PHA02542, 41, 41 helicase; Provisional. Length = 473 Score = 37.4 bits (87), Expect = 0.004 Identities = 18/58 (31%), Positives = 30/58 (51%) Query: 137 GGVQLRELILIGARPSMGKTTFALSTALHMAMSGHGVAFFSLEMDREKLGARALSNLL 194 GG + + L ++ A ++GK+ S A G+ V + S+EM E + R +NLL Sbjct: 185 GGAERKTLNVLLAGVNVGKSLGLCSLAADYLQQGYNVLYISMEMAEEVIAKRIDANLL 242 >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 = 36.3 bits (84), Expect = 0.007 Identities = 37/115 (32%), Positives = 51/115 (44%), Gaps = 10/115 (8%) Query: 121 ENPDIKWGLQSVDH-LMGGVQLRELILIGARPSMGKTTFALSTALHMAMSGHGVAFFSLE 179 E P G +D L GG+ LILIG P +GK+T L A +A + V + S E Sbjct: 72 EVPRFSSGFGELDRVLGGGIVPGSLILIGGDPGIGKSTLLLQVACQLAKNQMKVLYVSGE 131 Query: 180 MDREKLGARALSNLLYPSSSRIPYLNLIRGEINQEQYRISQGICEKLQDFPLIID 234 +++ RA L P P L ++ E N EQ I I E+ +ID Sbjct: 132 ESLQQIKMRA-IRLGLPE----PNLYVL-SETNWEQ--ICANI-EEENPQACVID 177 >gnl|CDD|183326 PRK11823, PRK11823, DNA repair protein RadA; Provisional. Length = 446 Score = 35.5 bits (83), Expect = 0.017 Identities = 26/105 (24%), Positives = 45/105 (42%), Gaps = 23/105 (21%) Query: 137 GGVQLRELILIGARPSMGKTTFALSTALHMAMSGHGVAFFSLE-------MDREKLGARA 189 GG+ ++LIG P +GK+T L A +A +G V + S E + E+LG + Sbjct: 75 GGLVPGSVVLIGGDPGIGKSTLLLQVAARLAAAGGKVLYVSGEESASQIKLRAERLGLPS 134 Query: 190 LSNLLYPSSSRIPYLNLIRGEINQEQYRISQGICEKLQDFPLIID 234 + L ++ L I I +E+ + ++ID Sbjct: 135 DNLYLLAETN----LEAILATIEEEKPDL------------VVID 163 >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 = 32.0 bits (72), Expect = 0.19 Identities = 23/97 (23%), Positives = 36/97 (37%), Gaps = 15/97 (15%) Query: 142 RELILIGARPSMGKTTFALSTALHMAMSGHGVAFFSLEMDREKLGARA---LSNLLYPSS 198 E+ILI P GKTT A + A + G GV + E E++ + + S Sbjct: 2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASG 61 Query: 199 SRIPYLNLIRGEINQEQYRISQGICEKLQDFPLIIDD 235 S L L + + + LI+D+ Sbjct: 62 SGELRLRLALALARKLKPDV------------LILDE 86 >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 = 31.6 bits (72), Expect = 0.22 Identities = 20/67 (29%), Positives = 28/67 (41%), Gaps = 8/67 (11%) Query: 135 LMGGVQLRELILIGARPSMGKTTFALSTALHMAMSGHGVAF-----FSLEMDREKLGA-- 187 L GGV+ + I P GKT + A++ A G V + S E ++ Sbjct: 5 LGGGVERGTITQIYGPPGSGKTNICMILAVNAARQGKKVVYIDTEGLSPERFKQIAEDRP 64 Query: 188 -RALSNL 193 RALSN Sbjct: 65 ERALSNF 71 >gnl|CDD|129627 TIGR00536, hemK_fam, HemK family putative methylases. The gene hemK from E. coli was found to contribute to heme biosynthesis and originally suggested to be protoporphyrinogen oxidase (Medline 95189105). Functional analysis of the nearest homolog in Saccharomyces cerevisiae, YNL063w, finds it is not protoporphyrinogen oxidase and sequence analysis suggests that HemK homologs have S-adenosyl-methionine-dependent methyltransferase activity (Medline 99237242). Homologs are found, usually in a single copy, in nearly all completed genomes, but varying somewhat in apparent domain architecture. Both E. coli and H. influenzae have two members rather than one. The members from the Mycoplasmas have an additional C-terminal domain. Length = 284 Score = 30.4 bits (69), Expect = 0.51 Identities = 12/54 (22%), Positives = 21/54 (38%), Gaps = 8/54 (14%) Query: 67 CNTATLIRKS------MQSFEDIISEVHLTK--NQCTGSSCISIANAATTAMKS 112 N LI + ++ +IS+ + + TGS CI++A A Sbjct: 87 VNEHVLIPRPETEELVEKALASLISQNPILHILDLGTGSGCIALALAYEFPNAE 140 >gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional. Length = 602 Score = 29.8 bits (68), Expect = 0.83 Identities = 9/15 (60%), Positives = 10/15 (66%) Query: 145 ILIGARPSMGKTTFA 159 ILI P GK+TFA Sbjct: 260 ILIAGAPGAGKSTFA 274 >gnl|CDD|183735 PRK12771, PRK12771, putative glutamate synthase (NADPH) small subunit; Provisional. Length = 564 Score = 29.1 bits (66), Expect = 1.4 Identities = 15/40 (37%), Positives = 17/40 (42%), Gaps = 9/40 (22%) Query: 147 IGARPSMGKTTFALSTALHMAMSGHGVAFFSLEMDREKLG 186 IG P+ LS A H+ GH V F E KLG Sbjct: 143 IGGGPA------GLSAAYHLRRMGHAVTIF--EA-GPKLG 173 >gnl|CDD|181799 PRK09361, radB, DNA repair and recombination protein RadB; Provisional. Length = 225 Score = 28.3 bits (64), Expect = 2.2 Identities = 19/58 (32%), Positives = 25/58 (43%), Gaps = 6/58 (10%) Query: 128 GLQSVDHLMGGVQLRELIL-IGARPSMGKTTFALSTALHMAMSGHGVAF-----FSLE 179 G + +D L+GG R I I P GKT L A+ A +G V + S E Sbjct: 8 GCKMLDELLGGGFERGTITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYIDTEGLSPE 65 >gnl|CDD|181823 PRK09401, PRK09401, reverse gyrase; Reviewed. Length = 1176 Score = 28.0 bits (63), Expect = 2.6 Identities = 10/22 (45%), Positives = 14/22 (63%) Query: 149 ARPSMGKTTFALSTALHMAMSG 170 A +GKTTF L +L++A G Sbjct: 102 APTGVGKTTFGLVMSLYLAKKG 123 >gnl|CDD|162097 TIGR00898, 2A0119, cation transport protein. Length = 505 Score = 28.1 bits (63), Expect = 2.6 Identities = 12/52 (23%), Positives = 20/52 (38%), Gaps = 4/52 (7%) Query: 151 PSMGKTTFALSTALHMAMSGHGVAFFSLEMDREKLGARALSNLLYPSSSRIP 202 P++ KTT L M +++ L +D LG +L +P Sbjct: 323 PNLRKTTLCLM----MLWFTTAFSYYGLVLDLGNLGGNIYLDLFISGLVELP 370 >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 = 28.0 bits (63), Expect = 3.0 Identities = 22/86 (25%), Positives = 33/86 (38%), Gaps = 15/86 (17%) Query: 133 DHLMGGVQLRELILIGARPSMGKTTFALSTALHMAMS-GHGVAFFSLE------------ 179 + L GG+ ++LI P GKT F L + A+ G + +LE Sbjct: 10 EILKGGIPEGRVVLITGGPGTGKTIFGLQFLYNGALEYGEPGVYVTLEEPPEDLRENAKS 69 Query: 180 --MDREKLGARALSNLLYPSSSRIPY 203 D EKL ++ S+S I Sbjct: 70 FGWDLEKLEEEGKLAIIDASTSGIGI 95 >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 = 27.7 bits (62), Expect = 3.1 Identities = 18/65 (27%), Positives = 30/65 (46%), Gaps = 1/65 (1%) Query: 128 GLQSVDHLM-GGVQLRELILIGARPSMGKTTFALSTALHMAMSGHGVAFFSLEMDREKLG 186 G+ +D ++ GG +I++ GKTTF+L +G + SLE E++ Sbjct: 1 GIPGLDEMLGGGFPEGHVIVVIGEYGTGKTTFSLQFLYQGLKNGEKAMYISLEEREERIL 60 Query: 187 ARALS 191 A S Sbjct: 61 GYAKS 65 >gnl|CDD|163310 TIGR03533, L3_gln_methyl, protein-(glutamine-N5) methyltransferase, ribosomal protein L3-specific. Members of this protein family methylate ribosomal protein L3 on a glutamine side chain. This family is related to HemK, a protein-glutamine methyltranferase for peptide chain release factors. Length = 284 Score = 27.5 bits (62), Expect = 3.4 Identities = 9/12 (75%), Positives = 10/12 (83%) Query: 94 CTGSSCISIANA 105 CTGS CI+IA A Sbjct: 129 CTGSGCIAIACA 140 >gnl|CDD|181312 PRK08236, PRK08236, hypothetical protein; Provisional. Length = 212 Score = 27.7 bits (62), Expect = 3.5 Identities = 13/34 (38%), Positives = 17/34 (50%) Query: 163 ALHMAMSGHGVAFFSLEMDREKLGARALSNLLYP 196 A+ AM G GVA + L RA+SN + P Sbjct: 156 AVAEAMEGFGVAEAAAAAGLPVLELRAISNPVGP 189 >gnl|CDD|183320 PRK11805, PRK11805, N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional. Length = 307 Score = 27.1 bits (61), Expect = 4.6 Identities = 9/12 (75%), Positives = 10/12 (83%) Query: 94 CTGSSCISIANA 105 CTGS CI+IA A Sbjct: 141 CTGSGCIAIACA 152 >gnl|CDD|162131 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family protein. Length = 1394 Score = 26.6 bits (59), Expect = 6.6 Identities = 7/21 (33%), Positives = 11/21 (52%) Query: 143 ELILIGARPSMGKTTFALSTA 163 EL ++ RP G +T + A Sbjct: 88 ELTVVLGRPGSGCSTLLKTIA 108 >gnl|CDD|184171 PRK13598, hisB, imidazoleglycerol-phosphate dehydratase; Provisional. Length = 193 Score = 26.3 bits (58), Expect = 7.7 Identities = 10/26 (38%), Positives = 17/26 (65%) Query: 168 MSGHGVAFFSLEMDREKLGARALSNL 193 +SG G+AF +L + R ++G A N+ Sbjct: 110 ISGRGMAFVNLNLKRSEIGGLATENI 135 >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 = 26.3 bits (58), Expect = 8.4 Identities = 11/36 (30%), Positives = 22/36 (61%), Gaps = 1/36 (2%) Query: 125 IKWGLQSVDHLM-GGVQLRELILIGARPSMGKTTFA 159 +K G+ +D ++ GG+ R ++L+ P GK+ F+ Sbjct: 3 VKTGIPGMDEILHGGIPERNVVLLSGGPGTGKSIFS 38 >gnl|CDD|163142 TIGR03117, cas_csf4, CRISPR-associated DEAD/DEAH-box helicase Csf4. Members of this family show up near CRISPR repeats in Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens DSM 15236. In the latter two species, the CRISPR/cas locus is found on a plasmid. This family is one of several characteristic of a type of CRISPR-associated (cas) gene cluster we designate Aferr after A. ferrooxidans, where it is both chromosomal and the only type of cas gene cluster found. The gene is designated csf4 (CRISPR/cas Subtype as in A. ferrooxidans protein 1), as it lies farthest (fourth closest) from the repeats in the A. ferrooxidans genome. Length = 636 Score = 26.5 bits (58), Expect = 8.7 Identities = 18/123 (14%), Positives = 43/123 (34%), Gaps = 20/123 (16%) Query: 31 ISSEVINAARRVVQQWARITISQEAKALALHTSDPTCNTATLIRKSMQSFEDIISEVHLT 90 I S + A +Q+ + + + + L L D + + + D S + Sbjct: 250 IVSAAVAAVSHCIQRLRALDVFGDGQTLCL---DAGNKELETLFADLDAALDACS---VG 303 Query: 91 KNQCTGSSCIS----IANAATTAMKSAEQQKKEGE-----NPDIKW-----GLQSVDHLM 136 +N+ +S + A + + + +PD ++ G + + +M Sbjct: 304 RNRDENKKALSVVKDVKKARFILDNAITAIQGKASAVLQFSPDRRFPSLIVGREDLGKVM 363 Query: 137 GGV 139 GG+ Sbjct: 364 GGL 366 >gnl|CDD|151380 pfam10933, DUF2827, Protein of unknown function (DUF2827). This is a family of uncharacterized proteins found in Burkholderia. Length = 364 Score = 26.2 bits (58), Expect = 9.6 Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 4/40 (10%) Query: 230 PLIIDD---RPSPGIMEFVHVANGLRNK-HTKMVQLYRLL 265 P+++ D R P +EFVHV N L K H + V L Sbjct: 208 PMLVADEAYRAQPDAVEFVHVTNTLHLKEHPEFVHFANSL 247 >gnl|CDD|181459 PRK08533, PRK08533, flagellar accessory protein FlaH; Reviewed. Length = 230 Score = 26.2 bits (58), Expect = 9.8 Identities = 14/46 (30%), Positives = 23/46 (50%) Query: 135 LMGGVQLRELILIGARPSMGKTTFALSTALHMAMSGHGVAFFSLEM 180 L GG+ LILI S GK+ + A +G+ V++ S ++ Sbjct: 17 LGGGIPAGSLILIEGDESTGKSILSQRLAYGFLQNGYSVSYVSTQL 62 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 0.318 0.130 0.364 Gapped Lambda K H 0.267 0.0686 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 4,064,687 Number of extensions: 243435 Number of successful extensions: 522 Number of sequences better than 10.0: 1 Number of HSP's gapped: 501 Number of HSP's successfully gapped: 49 Length of query: 266 Length of database: 5,994,473 Length adjustment: 92 Effective length of query: 174 Effective length of database: 4,006,537 Effective search space: 697137438 Effective search space used: 697137438 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: 56 (25.4 bits)