RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780399|ref|YP_003064812.1| DNA mismatch repair protein [Candidatus Liberibacter asiaticus str. psy62] (594 letters) >gnl|CDD|178860 PRK00095, mutL, DNA mismatch repair protein; Reviewed. Length = 617 Score = 698 bits (1805), Expect = 0.0 Identities = 255/622 (40%), Positives = 379/622 (60%), Gaps = 34/622 (5%) Query: 1 MKIRKLSEKIINQIAAGEIIERPSIAIKELIENSLDAESSRVETVIAGGGKSFFQITDNG 60 M I+ L ++ NQIAAGE++ERP+ +KEL+EN+LDA ++R++ I GG ++ DNG Sbjct: 1 MPIQLLPPQLANQIAAGEVVERPASVVKELVENALDAGATRIDIEIEEGGLKLIRVRDNG 60 Query: 61 FGMTSEEIPMAVQRHCTSKIS--DDFSNIHTFGFRGEALPSIGAVSHLTLMSRPPQNNTG 118 G++ E++ +A+ RH TSKI+ DD I T GFRGEALPSI +VS LTL SR G Sbjct: 61 CGISKEDLALALARHATSKIASLDDLEAIRTLGFRGEALPSIASVSRLTLTSRTADAAEG 120 Query: 119 AQIAISGEKISSVRPVAMNPGTIVEVRDLFFTIPARLNFLKSEQVETNLITDVIRRMAIA 178 QI G +I V+P A GT +EVRDLFF PAR FLKSE+ E I DV+ R+A+A Sbjct: 121 WQIVYEGGEIVEVKPAAHPVGTTIEVRDLFFNTPARRKFLKSEKTELGHIDDVVNRLALA 180 Query: 179 YPKVSFTFSTIKSNRYKMNFQ-STNGNFPERISQVIGEDFINNAVELNEKSNEITLQGYT 237 +P V+FT + N K+ Q G +R++ ++G +F NA+ ++ + ++ L GY Sbjct: 181 HPDVAFTLT---HNG-KLVLQTRGAGQLLQRLAAILGREFAENALPIDAEHGDLRLSGYV 236 Query: 238 GIPTFNRGNANQFYVFINGRTVQDKFILSTIRTAYAETIPLGRYPVVVLLLEIDPRQVDV 297 G+PT +R N + Y+F+NGR V+DK + IR AY + +P GRYP VL LE+DP QVDV Sbjct: 237 GLPTLSRANRDYQYLFVNGRYVRDKLLNHAIRQAYHDLLPRGRYPAFVLFLELDPHQVDV 296 Query: 298 NVHPAKSYIRFRNPTIIRNFIIQSIQKAINKKGISTSSVLSKKMISSFHQDNAPKTHLPK 357 NVHPAK +RFR+ ++ + I+Q+IQ+A+ + G+ ++ + +++ + P P Sbjct: 297 NVHPAKHEVRFRDERLVHDLIVQAIQEALAQSGLIPAAAGANQVLEPAEPEPLPLQQTPL 356 Query: 358 YA---------------TSLTNTQEKLFLQENRLSTNDLLPSDDPTYSED---------- 392 YA +QE+ ++N L N S + Sbjct: 357 YASGSSPPASSPSSAPPEQSEESQEESSAEKNPLQPNASQSEAAAAASAEAAAAAPAAAP 416 Query: 393 NDPVEESEATHYQLGIACAQIHQNYIISQTTDGLVIVDQHAAHERLIFEKMRQDFNSTKI 452 EA + LG A Q+H YI+++ DGL +VDQHAAHERL++E+++ + Sbjct: 417 EPAEAAEEADSFPLGYALGQLHGTYILAENEDGLYLVDQHAAHERLLYEQLKDKLAEVGL 476 Query: 453 TSQTLLTPEIIDLLEGECALIMEHDEDLHRLGIKAERFGPNAIAIREIPAILSKKNIPQL 512 SQ LL P +++L E E + EH E L RLG++ E FGPN+ A+RE+PA+L ++ + +L Sbjct: 477 ASQPLLIPLVLELSEDEADRLEEHKELLARLGLELEPFGPNSFAVREVPALLGQQELEEL 536 Query: 513 LRDIIDEIIDSSTTYTLQDRIENILATMACYGSIRSGRKMQSIEMNRLLREMEKNPNSSQ 572 +RD++DE+ + + TL++R +LATMAC+G+IR+GR++ EMN LLR++E N Sbjct: 537 IRDLLDELAEEGDSDTLKER--ELLATMACHGAIRAGRRLTLEEMNALLRQLEATENPGT 594 Query: 573 CNHGRPTFIKLKLSDIEKLFGR 594 C HGRPT+I+L LSD+EKLF R Sbjct: 595 CPHGRPTYIELSLSDLEKLFKR 616 >gnl|CDD|161941 TIGR00585, mutl, DNA mismatch repair protein MutL. All proteins in this family for which the functions are known are involved in the process of generalized mismatch repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Length = 312 Score = 299 bits (769), Expect = 1e-81 Identities = 126/312 (40%), Positives = 182/312 (58%), Gaps = 5/312 (1%) Query: 1 MKIRKLSEKIINQIAAGEIIERPSIAIKELIENSLDAESSRVETVIAGGGKSFFQITDNG 60 M I+ L +++N+IAAGE+IERP+ +KEL+ENSLDA ++R++ I GG +++DNG Sbjct: 1 MTIKPLPPELVNKIAAGEVIERPASVVKELVENSLDAGATRIDVEIEEGGLKLIEVSDNG 60 Query: 61 FGMTSEEIPMAVQRHCTSKISD--DFSNIHTFGFRGEALPSIGAVSHLTLMSRPPQNN-T 117 G+ E++P+A +RH TSKI D I T GFRGEAL SI +VS LT+ ++ + Sbjct: 61 SGIDKEDLPLACERHATSKIQSFEDLERIETLGFRGEALASISSVSRLTITTKTSAADGL 120 Query: 118 GAQIAISGEKISSVRPVAMNPGTIVEVRDLFFTIPARLNFLKSEQVETNLITDVIRRMAI 177 Q + G I ++P GT VEVRDLF+ +P R FLKS + E I D++ R A+ Sbjct: 121 AWQALLEGGMIEEIKPAPRPVGTTVEVRDLFYNLPVRRKFLKSPKKEFRKILDLLNRYAL 180 Query: 178 AYPKVSFTFSTIKSNRYKMNFQSTNGNFPERISQVIGEDFINNAVELNE-KSNEITLQGY 236 +P VSF+ + +++ + RI V G ++ L E + ++ L+G+ Sbjct: 181 IHPDVSFSLTHDGKKVLQLSTKPNQSLKERRIRSVFGTAVLSKLFPLLEWEDGDLQLEGF 240 Query: 237 TGIPTFNRGNA-NQFYVFINGRTVQDKFILSTIRTAYAETIPLGRYPVVVLLLEIDPRQV 295 P R ++FINGR V+ K +L IR Y E +P G+YPV VL LEIDP V Sbjct: 241 ISEPNVTRSRRSGWQFLFINGRPVELKLLLKAIREVYHEYLPKGQYPVFVLNLEIDPELV 300 Query: 296 DVNVHPAKSYIR 307 DVNVHP K +R Sbjct: 301 DVNVHPDKKEVR 312 >gnl|CDD|149660 pfam08676, MutL_C, MutL C terminal dimerization domain. MutL and MutS are key components of the DNA repair machinery that corrects replication errors. MutS recognizes mispaired or unpaired bases in a DNA duplex and in the presence of ATP, recruits MutL to form a DNA signaling complex for repair. The N terminal region of MutL contains the ATPase domain and the C terminal is involved in dimerization. Length = 142 Score = 172 bits (438), Expect = 3e-43 Identities = 62/147 (42%), Positives = 101/147 (68%), Gaps = 6/147 (4%) Query: 406 LGIACAQIHQNYIISQTTDGLVIVDQHAAHERLIFEKMRQDFNSTKITSQTLLTPEIIDL 465 LG A Q+H YI+++ DGL +VDQHAAHER+++EK++ + SQ LL P ++L Sbjct: 2 LGKALGQVHGTYILAENEDGLYLVDQHAAHERILYEKLKSKLKE-GLQSQPLLIPLTLEL 60 Query: 466 LEGECALIMEHDEDLHRLGIKAERFGPNAIAIREIPAILSKKNIPQLLRDIIDEIIDSST 525 E AL+ EH E L RLG + E FGPN++ +R +PA+L ++N+ +L+R+++DE+ + Sbjct: 61 SPEEAALLEEHKELLARLGFELEEFGPNSLIVRSVPALLRQQNLEELIRELLDELAEKG- 119 Query: 526 TYTLQDRIENILATMACYGSIRSGRKM 552 ++ +E +LATMAC+ +IR+GR++ Sbjct: 120 ----EELLEELLATMACHSAIRAGRRL 142 >gnl|CDD|129086 smart00853, MutL_C, MutL C terminal dimerisation domain. MutL and MutS are key components of the DNA repair machinery that corrects replication errors. MutS recognises mispaired or unpaired bases in a DNA duplex and in the presence of ATP, recruits MutL to form a DNA signaling complex for repair. The N terminal region of MutL contains the ATPase domain and the C terminal is involved in dimerisation. Length = 136 Score = 150 bits (380), Expect = 1e-36 Identities = 52/137 (37%), Positives = 92/137 (67%), Gaps = 2/137 (1%) Query: 406 LGIACAQIHQNYIISQTTDGLVIVDQHAAHERLIFEKMRQDFNSTKIT-SQTLLTPEIID 464 LG Q+H YI++++ DGLV++DQHAAHER+++E+++ + + SQ LL P I++ Sbjct: 1 LGRVLGQVHGTYILAESEDGLVLIDQHAAHERILYEQLKAKLQAGLLEKSQPLLIPVILE 60 Query: 465 LLEGECALIMEHDEDLHRLGIKAERFGPNAIAIREIPAILSKKNIPQLLRDIIDEIIDSS 524 L E AL+ EH E L RLG + E FG ++ +R +PA+L ++N+ +L+ +++D + + Sbjct: 61 LSPEEAALLEEHQELLARLGFELEIFGGQSVILRSVPALLRQQNLQELIPELLDLLAEGG 120 Query: 525 TTYTLQDRIENILATMA 541 +T +L +E +LA++A Sbjct: 121 ST-SLPQLVEALLASLA 136 >gnl|CDD|179773 PRK04184, PRK04184, DNA topoisomerase VI subunit B; Validated. Length = 535 Score = 38.7 bits (91), Expect = 0.005 Identities = 21/56 (37%), Positives = 31/56 (55%), Gaps = 9/56 (16%) Query: 25 IAIKELIENSLDA-ESS------RVETVIAGGGKSFFQIT--DNGFGMTSEEIPMA 71 +KEL++NSLDA E + ++E GK +++T DNG G+ EEIP Sbjct: 39 TTVKELVDNSLDACEEAGILPDIKIEIKRVDEGKDHYRVTVEDNGPGIPPEEIPKV 94 >gnl|CDD|184494 PRK14083, PRK14083, HSP90 family protein; Provisional. Length = 601 Score = 36.8 bits (86), Expect = 0.014 Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 14/58 (24%) Query: 23 PSIAIKELIENSLDAESSR------------VETVIAGGGKSFFQITDNGFGMTSEEI 68 P + ++EL++N++DA ++R +E AGGG + DNG G+T EE+ Sbjct: 24 PRVYVRELLQNAVDAITARRALDPTAPGRIRIELTDAGGGT--LIVEDNGIGLTEEEV 79 >gnl|CDD|128669 smart00387, HATPase_c, Histidine kinase-like ATPases. Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases. Length = 111 Score = 31.9 bits (73), Expect = 0.44 Identities = 11/47 (23%), Positives = 22/47 (46%), Gaps = 3/47 (6%) Query: 26 AIKELIENSLDA--ESSRVE-TVIAGGGKSFFQITDNGFGMTSEEIP 69 + L++N++ E R+ T+ G + DNG G+ E++ Sbjct: 9 VLSNLLDNAIKYTPEGGRITVTLERDGDHLEITVEDNGPGIPPEDLE 55 >gnl|CDD|162176 TIGR01052, top6b, DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase). Length = 488 Score = 30.9 bits (70), Expect = 0.91 Identities = 18/54 (33%), Positives = 22/54 (40%), Gaps = 7/54 (12%) Query: 25 IAIKELIENSLDAESS-------RVETVIAGGGKSFFQITDNGFGMTSEEIPMA 71 I EL+ NSLDA +VE G + DNG G+ E IP Sbjct: 31 TVIHELVTNSLDACEEAGILPDIKVEIEKIGKDHYKVTVEDNGPGIPEEYIPKV 84 >gnl|CDD|173589 PTZ00398, PTZ00398, phosphoenolpyruvate carboxylase; Provisional. Length = 974 Score = 30.5 bits (69), Expect = 1.3 Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 4/75 (5%) Query: 58 DNGFGMTSEEIPMAVQRHCTSKISDDFS-NIHTFGFRGEALPSIGAVSHLTLMSRPPQN- 115 D G ++ E+ A + S I+ + I F RG ++ G HL ++S+PP Sbjct: 631 DGGRLTSAWELYKAQE--RLSNIARQYGVEIRFFHGRGGSVSRGGGPQHLAILSQPPNTI 688 Query: 116 NTGAQIAISGEKISS 130 + +I I GE I+ Sbjct: 689 KSYLRITIQGETITQ 703 >gnl|CDD|163071 TIGR02916, PEP_his_kin, putative PEP-CTERM system histidine kinase. Members of this protein family have a novel N-terminal domain, a single predicted membrane-spanning helix, and a predicted cystosolic histidine kinase domain. We designate this protein PrsK, and its companion DNA-binding response regulator protein (TIGR02915) PrsR. These predicted signal-transducing proteins appear to enable enhancer-dependent transcriptional activation. The prsK gene is often associated with exopolysaccharide biosynthesis genes. Length = 679 Score = 29.7 bits (67), Expect = 2.3 Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 3/51 (5%) Query: 21 ERPSIAIKELIENSLDA--ESSRVE-TVIAGGGKSFFQITDNGFGMTSEEI 68 ER + L++N+L+A RV V G + +I D+G GM+ I Sbjct: 578 ERLERVLGHLVQNALEATPGEGRVAIRVERECGAARIEIEDSGCGMSPAFI 628 >gnl|CDD|184870 PRK14868, PRK14868, DNA topoisomerase VI subunit B; Provisional. Length = 795 Score = 29.0 bits (65), Expect = 3.3 Identities = 19/52 (36%), Positives = 27/52 (51%), Gaps = 10/52 (19%) Query: 26 AIKELIENSLDAESSR-------VETVIAGGGKSF-FQITDNGFGMTSEEIP 69 A+KE ++N+LDA VE I G + + DNG G+T E+IP Sbjct: 50 AVKEAVDNALDATEEAGILPDIYVE--IEEVGDYYRLVVEDNGPGITKEQIP 99 >gnl|CDD|179965 PRK05218, PRK05218, heat shock protein 90; Provisional. Length = 613 Score = 28.9 bits (66), Expect = 3.4 Identities = 21/61 (34%), Positives = 28/61 (45%), Gaps = 17/61 (27%) Query: 25 IAIKELIENSLDA------ESSRVETVIAGGGK-----SF------FQITDNGFGMTSEE 67 I ++ELI N+ DA E+ + G G SF I+DNG GMT EE Sbjct: 29 IFLRELISNASDAIDKLRFEALTDPALYEGDGDLKIRISFDKEARTLTISDNGIGMTREE 88 Query: 68 I 68 + Sbjct: 89 V 89 >gnl|CDD|181750 PRK09277, PRK09277, aconitate hydratase; Validated. Length = 888 Score = 28.6 bits (65), Expect = 4.3 Identities = 8/17 (47%), Positives = 12/17 (70%) Query: 322 IQKAINKKGISTSSVLS 338 I+KAIN + ++VLS Sbjct: 510 IEKAINDNDLVVTAVLS 526 >gnl|CDD|179380 PRK02190, PRK02190, agmatinase; Provisional. Length = 301 Score = 27.9 bits (63), Expect = 7.3 Identities = 15/64 (23%), Positives = 24/64 (37%), Gaps = 16/64 (25%) Query: 489 RFGPNAIAIREIPAILSKKNIP-QLLRDIIDE--IID-----------SSTTYTLQDRIE 534 RFGP AIR+ L+ ++ D+ + ++D L+ E Sbjct: 47 RFGPA--AIRQASTNLAWEDRRYPWNFDLFERLAVVDYGDLVFDYGDAEDFPEALEAHAE 104 Query: 535 NILA 538 ILA Sbjct: 105 KILA 108 >gnl|CDD|185569 PTZ00345, PTZ00345, glycerol-3-phosphate dehydrogenase; Provisional. Length = 365 Score = 28.1 bits (63), Expect = 7.6 Identities = 9/37 (24%), Positives = 16/37 (43%) Query: 486 KAERFGPNAIAIREIPAILSKKNIPQLLRDIIDEIID 522 + +A AI I+ + P L D+I+E + Sbjct: 115 ENNNLKKHARAISLTKGIIVENGKPVLCSDVIEEELG 151 >gnl|CDD|161754 TIGR00189, tesB, acyl-CoA thioesterase II. Subunit: homotetramer. Length = 271 Score = 27.7 bits (62), Expect = 9.0 Identities = 13/61 (21%), Positives = 20/61 (32%), Gaps = 5/61 (8%) Query: 315 RNFIIQSIQKAINKKGISTSSVLSKKMISSF-HQDNAPKTHLPK----YATSLTNTQEKL 369 R+FI + ++ + K I T + S HQ PK P+ L Sbjct: 74 RSFITRRVKAVQHGKTIFTLQASFQAEESGIEHQSTMPKVPAPESELPRENQLATKYPAT 133 Query: 370 F 370 Sbjct: 134 L 134 >gnl|CDD|177398 PHA02569, 39, DNA topoisomerase II large subunit; Provisional. Length = 602 Score = 27.4 bits (61), Expect = 10.0 Identities = 15/57 (26%), Positives = 27/57 (47%), Gaps = 11/57 (19%) Query: 162 QVETNLITDVIRRMAIAYPKVSFTFSTIKSNRYKMNFQSTNGNFPERISQVIGEDFI 218 Q ++I D ++ +A+ +P + FTF N + +G F + Q G+D I Sbjct: 196 QQYLDIILDRLQTLAVVFPDIKFTF----------NGKKVSGKFKKYAKQ-FGDDTI 241 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 0.134 0.372 Gapped Lambda K H 0.267 0.0679 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 9,676,415 Number of extensions: 638959 Number of successful extensions: 1319 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1304 Number of HSP's successfully gapped: 28 Length of query: 594 Length of database: 5,994,473 Length adjustment: 99 Effective length of query: 495 Effective length of database: 3,855,281 Effective search space: 1908364095 Effective search space used: 1908364095 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: 60 (27.0 bits)