RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780476|ref|YP_003064889.1| two component response regulator [Candidatus Liberibacter asiaticus str. psy62] (123 letters) >gnl|CDD|182968 PRK11107, PRK11107, hybrid sensory histidine kinase BarA; Provisional. Length = 919 Score = 94.1 bits (235), Expect = 7e-21 Identities = 39/108 (36%), Positives = 62/108 (57%), Gaps = 8/108 (7%) Query: 4 KVMIVEDNELNMKL----FRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEI 59 VM V+DN N+KL + +E + +G +A+E A+Q D+I+MDIQ+ + Sbjct: 669 TVMAVDDNPANLKLIGALLEEQVEH----VVLCDSGHQAVEQAKQRPFDLILMDIQMPGM 724 Query: 60 SGLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPI 107 G+ + I++ Q P+IAVTA AM G+ ER+ G + Y++KPI Sbjct: 725 DGIRACELIRQLPHNQNTPIIAVTAHAMAGERERLLSAGMDDYLAKPI 772 >gnl|CDD|131209 TIGR02154, PhoB, phosphate regulon transcriptional regulatory protein PhoB. PhoB is a DNA-binding response regulator protein acting with PhoR in a 2-component system responding to phosphate ion. PhoB acts as a positive regulator of gene expression for phosphate-related genes such as phoA, phoS, phoE and ugpAB as well as itself. It is often found proximal to genes for the high-affinity phosphate ABC transporter (pstSCAB; GenProp0190) and presumably regulates these as well. Length = 226 Score = 79.7 bits (197), Expect = 2e-16 Identities = 40/120 (33%), Positives = 71/120 (59%), Gaps = 6/120 (5%) Query: 1 MLKKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEIS 60 M +++++VED +L +E +GY ++ +G EAL L + PD+I++D L S Sbjct: 1 MTRRILVVEDEPAIRELIAYNLEKAGYDVVEAGDGDEALTLINERGPDLILLDWMLPGTS 60 Query: 61 GLEITKQIKEDSELQEIPVIAVTAFAMKGDEE-RIR--KGGCEAYISKPISLSIFMETIK 117 G+E+ ++++ E + IP+I +TA +G+EE R+R + G + YI+KP S + IK Sbjct: 61 GIELCRRLRRRPETRAIPIIMLTA---RGEEEDRVRGLETGADDYITKPFSPRELLARIK 117 >gnl|CDD|185245 PRK15347, PRK15347, two component system sensor kinase SsrA; Provisional. Length = 921 Score = 72.4 bits (178), Expect = 3e-14 Identities = 37/122 (30%), Positives = 69/122 (56%), Gaps = 16/122 (13%) Query: 4 KVMIVEDNELNMKLFRDLIETSGYIALQ-------TRNGMEALELARQHKPDVIIMDIQL 56 ++++V+D E N RD+I G + ++ +G EALEL RQH+ D+++MDI++ Sbjct: 692 QILLVDDVETN----RDII---GMMLVELGQQVTTAASGTEALELGRQHRFDLVLMDIRM 744 Query: 57 QEISGLEITKQIKEDSELQ--EIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFME 114 + GLE T+ ++D + ++A+TA A + R +K G Y++KP++L+ Sbjct: 745 PGLDGLETTQLWRDDPNNLDPDCMIVALTANAAPEEIHRCKKAGMNHYLTKPVTLAQLAR 804 Query: 115 TI 116 + Sbjct: 805 AL 806 >gnl|CDD|182956 PRK11091, PRK11091, aerobic respiration control sensor protein ArcB; Provisional. Length = 779 Score = 71.9 bits (177), Expect = 4e-14 Identities = 37/120 (30%), Positives = 72/120 (60%), Gaps = 2/120 (1%) Query: 5 VMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLEI 64 +++VED ELN+ + R ++E G G EALE+ + D++++DIQL +++GL+I Sbjct: 528 ILLVEDIELNVIVARSVLEKLGNSVDVAMTGKEALEMFDPDEYDLVLLDIQLPDMTGLDI 587 Query: 65 TKQIKEDSELQEI-PVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYIGEA 123 ++++E +++ P++A+TA +K D++ G + +SKP+S+ IKK+ Sbjct: 588 ARELRERYPREDLPPLVALTANVLK-DKKEYLDAGMDDVLSKPLSVPALTAMIKKFWDTQ 646 >gnl|CDD|181966 PRK09581, pleD, response regulator PleD; Reviewed. Length = 457 Score = 70.7 bits (174), Expect = 1e-13 Identities = 32/110 (29%), Positives = 64/110 (58%), Gaps = 4/110 (3%) Query: 1 MLKKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEIS 60 M ++++V+D N+KL + Y L +G EA+ + + +PD+I++D+ + + Sbjct: 1 MTARILVVDDIPANVKLLEAKLLAEYYTVLTASSGAEAIAICEREQPDIILLDVMMPGMD 60 Query: 61 GLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIR--KGGCEAYISKPIS 108 G E+ +++K D IPV+ VT A+ E+R+R + G + +++KPI+ Sbjct: 61 GFEVCRRLKSDPATTHIPVVMVT--ALDDPEDRVRGLEAGADDFLTKPIN 108 Score = 33.0 bits (76), Expect = 0.022 Identities = 16/74 (21%), Positives = 33/74 (44%), Gaps = 6/74 (8%) Query: 37 EALELARQHKPDVIIMDIQLQEISGLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRK 96 EAL A + D++I+ + L + Q++ + +P++ + D+ R+ K Sbjct: 189 EALFNAAETNYDLVIVSANFENYDPLRLCSQLRSKERTRYVPILLLVDE---DDDPRLVK 245 Query: 97 G---GCEAYISKPI 107 G Y+ +PI Sbjct: 246 ALELGVNDYLMRPI 259 >gnl|CDD|163083 TIGR02956, TMAO_torS, TMAO reductase sytem sensor TorS. This protein, TorS, is part of a regulatory system for the torCAD operon that encodes the pterin molybdenum cofactor-containing enzyme trimethylamine-N-oxide (TMAO) reductase (TorA), a cognate chaperone (TorD), and a penta-haem cytochrome (TorC). TorS works together with the inducer-binding protein TorT and the response regulator TorR. TorS contains histidine kinase ATPase (pfam02518), HAMP (pfam00672), phosphoacceptor (pfam00512), and phosphotransfer (pfam01627) domains and a response regulator receiver domain (pfam00072). Length = 968 Score = 62.5 bits (152), Expect = 2e-11 Identities = 29/118 (24%), Positives = 56/118 (47%), Gaps = 1/118 (0%) Query: 4 KVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLE 63 +V++VEDNE+N + + + G+ +G ALE QH D+ ++DI L + G+ Sbjct: 704 RVLLVEDNEVNQMVAQGFLTRLGHKVTLAESGQSALECFHQHAFDLALLDINLPDGDGVT 763 Query: 64 ITKQIKE-DSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120 + +Q++ E+ IA +A D + G + +++KP+ I + Sbjct: 764 LLQQLRAIYGAKNEVKFIAFSAHVFNEDVAQYLAAGFDGFLAKPVVEEQLTAMIAVIL 821 >gnl|CDD|128724 smart00448, REC, cheY-homologous receiver domain. CheY regulates the clockwise rotation of E. coli flagellar motors. This domain contains a phosphoacceptor site that is phosphorylated by histidine kinase homologues. Length = 55 Score = 61.4 bits (150), Expect = 6e-11 Identities = 20/54 (37%), Positives = 37/54 (68%) Query: 3 KKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQL 56 ++++V+D+ L +L + L+E GY + +G EALEL ++ KPD+I++DI + Sbjct: 1 MRILVVDDDPLLRELLKALLEREGYEVDEATDGEEALELLKEEKPDLILLDIMM 54 >gnl|CDD|183099 PRK11361, PRK11361, acetoacetate metabolism regulatory protein AtoC; Provisional. Length = 457 Score = 58.3 bits (141), Expect = 5e-10 Identities = 29/106 (27%), Positives = 51/106 (48%), Gaps = 2/106 (1%) Query: 4 KVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLE 63 +++IV+D + ++ G+ NG AL L PDV++MDI++ E+ G++ Sbjct: 6 RILIVDDEDNVRRMLSTAFALQGFETHCANNGRTALHLFADIHPDVVLMDIRMPEMDGIK 65 Query: 64 ITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISL 109 K+++ PVI +TA+A + G Y+ KP L Sbjct: 66 ALKEMRSHE--TRTPVILMTAYAEVETAVEALRCGAFDYVIKPFDL 109 >gnl|CDD|181686 PRK09191, PRK09191, two-component response regulator; Provisional. Length = 261 Score = 56.8 bits (138), Expect = 1e-09 Identities = 38/112 (33%), Positives = 61/112 (54%), Gaps = 21/112 (18%) Query: 4 KVMIVEDNEL-NMKLFRDLIETSGY----IALQTRNGMEALELARQHKPDVIIMDIQLQE 58 +V+I+ED + M L L+E+ G+ IA R EA+ LA++ +P +I+ DIQL + Sbjct: 139 RVLIIEDEPIIAMDL-EQLVESLGHRVTGIA---RTRAEAVALAKKTRPGLILADIQLAD 194 Query: 59 -ISGLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCE--AY-ISKP 106 SG++ I + ++PVI +TAF ER+ G A+ I+KP Sbjct: 195 GSSGIDAVNDILKTF---DVPVIFITAFP-----ERLLTGERPEPAFLITKP 238 >gnl|CDD|182412 PRK10365, PRK10365, transcriptional regulatory protein ZraR; Provisional. Length = 441 Score = 55.0 bits (132), Expect = 5e-09 Identities = 29/119 (24%), Positives = 60/119 (50%), Gaps = 2/119 (1%) Query: 5 VMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLEI 64 +++V+D+ + + + L+ GY +G +ALE R+ D+++ D+++ E+ G+ Sbjct: 8 ILVVDDDISHCTILQALLRGWGYNVALANSGRQALEQVREQVFDLVLCDVRMAEMDGIAT 67 Query: 65 TKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYIGEA 123 K+IK + IPV+ +TA++ K G Y+ KP+ T++K + Sbjct: 68 LKEIKALNP--AIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAHT 124 >gnl|CDD|179106 PRK00742, PRK00742, chemotaxis-specific methylesterase; Provisional. Length = 354 Score = 54.8 bits (133), Expect = 5e-09 Identities = 30/120 (25%), Positives = 67/120 (55%), Gaps = 8/120 (6%) Query: 4 KVMIVEDNELNMKLFRDLIETSGYI--ALQTRNGMEALELARQHKPDVIIMDIQLQEISG 61 +V++V+D+ +L +++ + I +G+EA E ++ PDVI +D+++ + G Sbjct: 5 RVLVVDDSAFMRRLISEILNSDPDIEVVGTAPDGLEAREKIKKLNPDVITLDVEMPVMDG 64 Query: 62 LEITKQIKEDSELQEIPVIAVTAFAMKGDEERIR--KGGCEAYISKP-ISLSIFMETIKK 118 L+ ++I L+ PV+ V++ +G E +R + G +++KP + +S+ M+ K+ Sbjct: 65 LDALEKIM---RLRPTPVVMVSSLTERGAEITLRALELGAVDFVTKPFLGISLGMDEYKE 121 >gnl|CDD|130454 TIGR01387, cztR_silR_copR, heavy metal response regulator. Members of this family contain a response regulator receiver domain (Pfam:PF00072) and an associated transcriptional regulatory region (Pfam:PF00486). This group is separated phylogenetically from related proteins with similar architecture and contains a number of proteins associated with heavy metal resistance efflux systems for copper, silver, cadmium, and/or zinc. Most members encoded by genes adjacent to genes for encoding a member of the heavy metal sensor histidine kinase family (TIGRFAMs:TIGR01386), its partner in the two-component response regulator system. Length = 218 Score = 54.4 bits (131), Expect = 7e-09 Identities = 29/106 (27%), Positives = 55/106 (51%), Gaps = 2/106 (1%) Query: 5 VMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLEI 64 +++VED + + + + SGY+ NG + L LA + D+II+D+ L + G +I Sbjct: 1 ILVVEDEQKTAEYLQQGLSESGYVVDAASNGRDGLHLALKDDYDLIILDVMLPGMDGWQI 60 Query: 65 TKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLS 110 + ++ ++ PV+ +TA D+ + G + Y+ KP S S Sbjct: 61 LQTLRRSG--KQTPVLFLTARDSVADKVKGLDLGADDYLVKPFSFS 104 >gnl|CDD|182772 PRK10841, PRK10841, hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional. Length = 924 Score = 54.2 bits (131), Expect = 7e-09 Identities = 31/119 (26%), Positives = 71/119 (59%), Gaps = 4/119 (3%) Query: 4 KVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALE-LARQHKPDVIIMDIQLQEISGL 62 +++V+D+ +N +L D + + GY +G++AL L++ H D+++ D+ + + G Sbjct: 803 MILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVLSKNHI-DIVLTDVNMPNMDGY 861 Query: 63 EITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYIG 121 +T+++++ +PVI VTA A+ +++R + G ++ +SKP++L + +T+ Y Sbjct: 862 RLTQRLRQLG--LTLPVIGVTANALAEEKQRCLEAGMDSCLSKPVTLDVLKQTLTVYAE 918 >gnl|CDD|182277 PRK10161, PRK10161, transcriptional regulator PhoB; Provisional. Length = 229 Score = 54.3 bits (130), Expect = 7e-09 Identities = 32/117 (27%), Positives = 64/117 (54%) Query: 1 MLKKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEIS 60 M +++++VED ++ ++E +G+ ++ + A+ + PD+I++D L S Sbjct: 1 MARRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDLILLDWMLPGGS 60 Query: 61 GLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIK 117 G++ K +K +S ++IPV+ +TA + D R + G + YI+KP S + IK Sbjct: 61 GIQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSPKELVARIK 117 >gnl|CDD|182665 PRK10710, PRK10710, DNA-binding transcriptional regulator BaeR; Provisional. Length = 240 Score = 53.2 bits (128), Expect = 2e-08 Identities = 36/108 (33%), Positives = 54/108 (50%), Gaps = 11/108 (10%) Query: 5 VMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLEI 64 ++IVED +L D ++ + Y +G E L RQ PD+I++D+ L GL + Sbjct: 13 ILIVEDEPKLGQLLIDYLQAASYATTLLSHGDEVLPYVRQTPPDLILLDLMLPGTDGLTL 72 Query: 65 TKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEA----YISKPIS 108 ++I+ S +IP++ VTA EE R G E YI KP S Sbjct: 73 CREIRRFS---DIPIVMVTAKI----EEIDRLLGLEIGADDYICKPYS 113 >gnl|CDD|131922 TIGR02875, spore_0_A, sporulation transcription factor Spo0A. Spo0A, the stage 0 sporulation protein A, is a transcription factor critical for the initiation of sporulation. It contains a response regulator receiver domain (pfam00072). In Bacillus subtilis, it works together with response regulator Spo0F and the phosphotransferase Spo0B, both of which are missing from at least some sporulating species and thus not part of the endospore forming bacteria minimal gene set. Spo0A, however, is universal among endospore-forming species. Length = 262 Score = 52.5 bits (126), Expect = 3e-08 Identities = 34/123 (27%), Positives = 65/123 (52%), Gaps = 14/123 (11%) Query: 4 KVMIVEDNELNMKLFRDLIETSGYIALQ--------TRNGMEALELARQHKPDVIIMDIQ 55 +++I +DN K F +L++ Y+A Q NG++ALEL ++ +PDV+++DI Sbjct: 4 RIVIADDN----KEFCNLLKE--YLAAQPDMEVVGVAHNGVDALELIKEQQPDVVVLDII 57 Query: 56 LQEISGLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMET 115 + + G+ + +++ E VI ++AF + +R G + Y+ KP L I Sbjct: 58 MPHLDGIGVLEKLNEIELSARPRVIMLSAFGQEKITQRAVALGADYYVLKPFDLEILAAR 117 Query: 116 IKK 118 I++ Sbjct: 118 IRQ 120 >gnl|CDD|170568 PRK10610, PRK10610, chemotaxis regulatory protein CheY; Provisional. Length = 129 Score = 52.3 bits (125), Expect = 3e-08 Identities = 30/116 (25%), Positives = 59/116 (50%), Gaps = 1/116 (0%) Query: 4 KVMIVEDNELNMKLFRDLIETSGYIALQ-TRNGMEALELARQHKPDVIIMDIQLQEISGL 62 K ++V+D ++ R+L++ G+ ++ +G++AL + +I D + + GL Sbjct: 7 KFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGFGFVISDWNMPNMDGL 66 Query: 63 EITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKK 118 E+ K I+ D + +PV+ VTA A K + + G Y+ KP + + E + K Sbjct: 67 ELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNK 122 >gnl|CDD|182950 PRK11083, PRK11083, DNA-binding response regulator CreB; Provisional. Length = 228 Score = 51.1 bits (123), Expect = 6e-08 Identities = 29/78 (37%), Positives = 47/78 (60%), Gaps = 10/78 (12%) Query: 35 GMEALELARQHKPDVIIMDIQLQEISGLEITKQIKEDSELQEIPVIAVTAFAMKGDE-ER 93 G+ AL+ RQ PD++I+D+ L +ISG E+ +Q+ +PVI +TA + DE +R Sbjct: 36 GLPALDKLRQQPPDLVILDVGLPDISGFELCRQLLA--FHPALPVIFLTA---RSDEVDR 90 Query: 94 IRKG---GCEAYISKPIS 108 + G G + Y++KP S Sbjct: 91 L-VGLEIGADDYVAKPFS 107 >gnl|CDD|183172 PRK11517, PRK11517, transcriptional regulatory protein YedW; Provisional. Length = 223 Score = 50.7 bits (121), Expect = 1e-07 Identities = 30/107 (28%), Positives = 53/107 (49%), Gaps = 3/107 (2%) Query: 4 KVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLE 63 K++++EDN+ + + +GY+ +G + L LA + +II+DI L + G + Sbjct: 2 KILLIEDNQRTQEWVTQGLSEAGYVIDAVSDGRDGLYLALKDDYALIILDIMLPGMDGWQ 61 Query: 64 ITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLS 110 I + ++ ++ PVI +TA D R G Y+ KP S S Sbjct: 62 ILQTLR---TAKQTPVICLTARDSVDDRVRGLDSGANDYLVKPFSFS 105 >gnl|CDD|183278 PRK11697, PRK11697, putative two-component response-regulatory protein YehT; Provisional. Length = 238 Score = 47.9 bits (115), Expect = 6e-07 Identities = 31/88 (35%), Positives = 52/88 (59%), Gaps = 8/88 (9%) Query: 1 MLKKVMIVEDNELNMKLFRDLIETSGYIAL--QTRNGMEALELARQHKPDVIIMDIQLQE 58 M+K V+IV+D L + R+L++ G I + + N +EA+ + KPDV+ +DIQ+ Sbjct: 1 MIK-VLIVDDEPLAREELRELLQEEGDIEIVGECSNAIEAIGAIHRLKPDVVFLDIQMPR 59 Query: 59 ISGLEITKQIKEDSELQEIP-VIAVTAF 85 ISGLE+ + + +P ++ VTAF Sbjct: 60 ISGLELVGMLDPEH----MPYIVFVTAF 83 >gnl|CDD|185267 PRK15369, PRK15369, two component system sensor kinase SsrB; Provisional. Length = 211 Score = 47.8 bits (114), Expect = 8e-07 Identities = 28/116 (24%), Positives = 57/116 (49%), Gaps = 4/116 (3%) Query: 4 KVMIVEDNELNMKLFRDLIET--SGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISG 61 K+++V+D+EL + ++++ I Q NG+E RQ +PD++I+D+ L ++G Sbjct: 5 KILLVDDHELIINGIKNMLAPYPRYKIVGQVDNGLEVYNACRQLEPDIVILDLGLPGMNG 64 Query: 62 LEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIK 117 L++ Q+ + ++ +TA + R G Y+ K I + I+ Sbjct: 65 LDVIPQLH--QRWPAMNILVLTARQEEHMASRTLAAGALGYVLKKSPQQILLAAIQ 118 >gnl|CDD|182522 PRK10529, PRK10529, DNA-binding transcriptional activator KdpE; Provisional. Length = 225 Score = 47.1 bits (112), Expect = 1e-06 Identities = 31/106 (29%), Positives = 53/106 (50%), Gaps = 3/106 (2%) Query: 5 VMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLEI 64 V+IVED + + R +E G + L A KPD+II+D+ L + G+E Sbjct: 4 VLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEAATRKPDLIILDLGLPDGDGIEF 63 Query: 65 TKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLS 110 + +++ S IPVI ++A + + D+ G + Y+SKP + Sbjct: 64 IRDLRQWS---AIPVIVLSARSEESDKIAALDAGADDYLSKPFGIG 106 >gnl|CDD|183591 PRK12555, PRK12555, chemotaxis-specific methylesterase; Provisional. Length = 337 Score = 47.2 bits (113), Expect = 1e-06 Identities = 22/86 (25%), Positives = 45/86 (52%), Gaps = 11/86 (12%) Query: 4 KVMIVEDNELNMKLFRDLIETSG-----YIALQTRNGMEALELARQHKPDVIIMDIQLQE 58 ++ IV D+ L ++ R + ++A +G +A+E PDVI+MD+++ Sbjct: 2 RIGIVNDSPLAVEALRRALARDPDHEVVWVA---TDGAQAVERCAAQPPDVILMDLEMPR 58 Query: 59 ISGLEITKQIKEDSELQEIPVIAVTA 84 + G+E T++I + P++ VT+ Sbjct: 59 MDGVEATRRIMAERPC---PILIVTS 81 >gnl|CDD|182431 PRK10403, PRK10403, transcriptional regulator NarP; Provisional. Length = 215 Score = 46.8 bits (111), Expect = 1e-06 Identities = 29/117 (24%), Positives = 61/117 (52%), Gaps = 4/117 (3%) Query: 4 KVMIVEDNELNMKLFRDLIETSGY--IALQTRNGMEALELARQHKPDVIIMDIQLQEISG 61 +V+IV+D+ L + R L+E + + +G A++LA + PDVI++D+ ++ +SG Sbjct: 8 QVLIVDDHPLMRRGVRQLLELDPGFEVVAEAGDGASAIDLANRLDPDVILLDLNMKGMSG 67 Query: 62 LEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKK 118 L+ ++ D +I ++ V+ + D + G + Y+ K + +E I+ Sbjct: 68 LDTLNALRRDGVTAQIIILTVSDAS--SDVFALIDAGADGYLLKDSDPEVLLEAIRA 122 >gnl|CDD|182711 PRK10766, PRK10766, DNA-binding transcriptional regulator TorR; Provisional. Length = 221 Score = 46.2 bits (110), Expect = 2e-06 Identities = 28/114 (24%), Positives = 53/114 (46%), Gaps = 13/114 (11%) Query: 1 MLKKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEIS 60 M +++VED + + E GY + +G E+ + D+I++DI L Sbjct: 1 MSYHILVVEDEPVTRARLQGYFEQEGYTVSEAASGAGMREIMQNQHVDLILLDINLPGED 60 Query: 61 GLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRK-----GGCEAYISKPISL 109 GL +T++++ S + +I VT G + I + G + Y++KP+ L Sbjct: 61 GLMLTRELRSRS---TVGIILVT-----GRTDSIDRIVGLEMGADDYVTKPLEL 106 >gnl|CDD|182619 PRK10651, PRK10651, transcriptional regulator NarL; Provisional. Length = 216 Score = 45.0 bits (107), Expect = 4e-06 Identities = 21/81 (25%), Positives = 46/81 (56%), Gaps = 2/81 (2%) Query: 5 VMIVEDNELNMKLFRDLIETSGYIAL--QTRNGMEALELARQHKPDVIIMDIQLQEISGL 62 +++++D+ + + LI + I + + NG + +ELA PD+I++D+ + ++GL Sbjct: 9 ILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAESLDPDLILLDLNMPGMNGL 68 Query: 63 EITKQIKEDSELQEIPVIAVT 83 E +++E S I V +V+ Sbjct: 69 ETLDKLREKSLSGRIVVFSVS 89 >gnl|CDD|178599 PLN03029, PLN03029, type-a response regulator protein; Provisional. Length = 222 Score = 44.6 bits (105), Expect = 6e-06 Identities = 34/126 (26%), Positives = 61/126 (48%), Gaps = 20/126 (15%) Query: 5 VMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPD---------------- 48 V+ V+D+ ++ KL L++TS Y +G +AL+ H+ D Sbjct: 11 VLAVDDSLIDRKLIEKLLKTSSYQVTTVDSGSKALKFLGLHEDDRSNPDTPSVSPNSHQE 70 Query: 49 ----VIIMDIQLQEISGLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYIS 104 +II D + ++G ++ K+IKE S L+ IPV+ +++ + R + G E + Sbjct: 71 VEVNLIITDYCMPGMTGYDLLKKIKESSSLRNIPVVIMSSENVPSRITRCLEEGAEEFFL 130 Query: 105 KPISLS 110 KP+ LS Sbjct: 131 KPVQLS 136 >gnl|CDD|184052 PRK13435, PRK13435, response regulator; Provisional. Length = 145 Score = 44.3 bits (105), Expect = 8e-06 Identities = 31/111 (27%), Positives = 57/111 (51%), Gaps = 12/111 (10%) Query: 4 KVMIVEDNELNMKLFRDLIETSGY-IALQTRNGMEALELARQHKPDVIIMDIQLQE-ISG 61 KV+IVED L L+E +G+ + + +A+ L R+ +PDV ++D+ L + +G Sbjct: 7 KVLIVEDEALIALELEKLVEEAGHEVVGIAMSSEQAIALGRRRQPDVALVDVHLADGPTG 66 Query: 62 LEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKG--GCEAYISKPISLS 110 +E+ +++ S + V+ +T G+ ER+ G I+KP S Sbjct: 67 VEVARRL---SADGGVEVVFMT-----GNPERVPHDFAGALGVIAKPYSPR 109 >gnl|CDD|182102 PRK09836, PRK09836, DNA-binding transcriptional activator CusR; Provisional. Length = 227 Score = 44.1 bits (104), Expect = 9e-06 Identities = 30/117 (25%), Positives = 60/117 (51%), Gaps = 8/117 (6%) Query: 4 KVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLE 63 K++IVED + + + +G++ NG+ LA D+II+DI L +++G + Sbjct: 2 KLLIVEDEKKTGEYLTKGLTEAGFVVDLADNGLNGYHLAMTGDYDLIILDIMLPDVNGWD 61 Query: 64 ITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKG---GCEAYISKPISLSIFMETIK 117 I + ++ S + +P++ +TA G E KG G + Y+ KP + + + ++ Sbjct: 62 IVRMLR--SANKGMPILLLTAL---GTIEHRVKGLELGADDYLVKPFAFAELLARVR 113 >gnl|CDD|185070 PRK15115, PRK15115, response regulator GlrR; Provisional. Length = 444 Score = 42.1 bits (99), Expect = 3e-05 Identities = 26/103 (25%), Positives = 58/103 (56%), Gaps = 2/103 (1%) Query: 5 VMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLEI 64 +++V+D+ +KL + + GY + +G EAL + + K D++I D+++ E+ G+++ Sbjct: 8 LLLVDDDPGLLKLLGMRLTSEGYSVVTAESGQEALRVLNREKVDLVISDLRMDEMDGMQL 67 Query: 65 TKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPI 107 +I++ +PVI +TA D + G ++++KP+ Sbjct: 68 FAEIQK--VQPGMPVIILTAHGSIPDAVAATQQGVFSFLTKPV 108 >gnl|CDD|163499 TIGR03787, marine_sort_RR, proteobacterial dedicated sortase system response regulator. This model describes a family of DNA-binding response regulator proteins, associated with an adjacent histidine kinase (TIGR03785) to form a two-component system. This system co-occurs with, and often is adjacent to, a proteobacterial variant form of the protein sorting transpeptidase called sortase (TIGR03784), and a single target protein for the sortase. We give this protein the gene symbol pdsR, for Proteobacterial Dedicated Sortase system Response regulator. Length = 227 Score = 42.0 bits (99), Expect = 4e-05 Identities = 32/109 (29%), Positives = 54/109 (49%), Gaps = 4/109 (3%) Query: 3 KKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQ-EIS- 60 K++ IVED + + D ++ GY + A++ RQ PD+ I+DI L EI Sbjct: 1 KRIAIVEDEAAIRENYADALKRQGYQVTTYADRPSAMQAFRQRLPDLAIIDIGLGEEIDG 60 Query: 61 GLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISL 109 G + + ++ S +P+I +TA D + G + Y++K ISL Sbjct: 61 GFMLCQDLRSLS--ATLPIIFLTARDSDFDTVSGLRLGADDYLTKDISL 107 >gnl|CDD|182652 PRK10693, PRK10693, response regulator of RpoS; Provisional. Length = 303 Score = 40.7 bits (96), Expect = 1e-04 Identities = 20/75 (26%), Positives = 41/75 (54%), Gaps = 2/75 (2%) Query: 34 NGMEALELARQHKPDVIIMDIQLQEISGLEITKQIKEDSELQEIPVIAVTAFAMKGDEER 93 NG++ALEL PD+II D+ + ++G+E + ++ + + PV+ ++A D + Sbjct: 5 NGVDALELLGGFTPDLIICDLAMPRMNGIEFVEHLR--NRGDQTPVLVISATENMADIAK 62 Query: 94 IRKGGCEAYISKPIS 108 + G + + KP+ Sbjct: 63 ALRLGVQDVLLKPVK 77 >gnl|CDD|181897 PRK09483, PRK09483, response regulator; Provisional. Length = 217 Score = 40.5 bits (95), Expect = 1e-04 Identities = 27/103 (26%), Positives = 54/103 (52%), Gaps = 4/103 (3%) Query: 5 VMIVEDNELNMKLFRDLIETSGYIAL--QTRNGMEALELARQHKPDVIIMDIQLQEISGL 62 V++V+D+EL R ++E I + + G +A++ R + DV++MD+ + I GL Sbjct: 4 VLLVDDHELVRAGIRRILEDIKGIKVVGEACCGEDAVKWCRTNAVDVVLMDMNMPGIGGL 63 Query: 63 EITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISK 105 E T++I + ++ +I +T ++ + G Y+SK Sbjct: 64 EATRKILRYTP--DVKIIMLTVHTENPLPAKVMQAGAAGYLSK 104 >gnl|CDD|182842 PRK10923, glnG, nitrogen regulation protein NR(I); Provisional. Length = 469 Score = 40.2 bits (94), Expect = 1e-04 Identities = 25/81 (30%), Positives = 41/81 (50%), Gaps = 2/81 (2%) Query: 4 KVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLE 63 V +V+D+ + + +G NG E LE PDV++ DI++ + GL Sbjct: 5 IVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLEALASKTPDVLLSDIRMPGMDGLA 64 Query: 64 ITKQIKEDSELQEIPVIAVTA 84 + KQIK+ + +PVI +TA Sbjct: 65 LLKQIKQRHPM--LPVIIMTA 83 >gnl|CDD|182864 PRK10955, PRK10955, DNA-binding transcriptional regulator CpxR; Provisional. Length = 232 Score = 39.8 bits (93), Expect = 2e-04 Identities = 25/105 (23%), Positives = 59/105 (56%), Gaps = 4/105 (3%) Query: 2 LKKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISG 61 + K+++V+D+ L ++L+E G+ + +G +AL+L D++++D+ + + +G Sbjct: 1 MNKILLVDDDRELTSLLKELLEMEGFNVIVAHDGEQALDLL-DDSIDLLLLDVMMPKKNG 59 Query: 62 LEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKP 106 ++ K++++ + PVI +TA + D + G + Y+ KP Sbjct: 60 IDTLKELRQT---HQTPVIMLTARGSELDRVLGLELGADDYLPKP 101 >gnl|CDD|162545 TIGR01818, ntrC, nitrogen regulation protein NR(I). This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc. Length = 463 Score = 39.0 bits (91), Expect = 3e-04 Identities = 24/98 (24%), Positives = 44/98 (44%), Gaps = 2/98 (2%) Query: 26 GYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLEITKQIKEDSELQEIPVIAVTAF 85 GY N L + +PD++I D+++ GL++ QIK ++PVI +TA Sbjct: 22 GYEVRTFGNAASVLRALARGQPDLLITDVRMPGEDGLDLLPQIK--KRHPQLPVIVMTAH 79 Query: 86 AMKGDEERIRKGGCEAYISKPISLSIFMETIKKYIGEA 123 + + G Y+ KP L + +++ + A Sbjct: 80 SDLDTAVAAYQRGAFEYLPKPFDLDEAVTLVERALAHA 117 >gnl|CDD|182168 PRK09958, PRK09958, DNA-binding transcriptional activator EvgA; Provisional. Length = 204 Score = 38.0 bits (88), Expect = 6e-04 Identities = 21/101 (20%), Positives = 52/101 (51%), Gaps = 3/101 (2%) Query: 6 MIVEDNELNMKLFRDLIETSGY-IALQTRNGMEALELARQHKPDVIIMDIQLQEISGLEI 64 +I++D+ L + R+L+ + I + G A++ KPD++I+D+ + ++G+++ Sbjct: 4 IIIDDHPLAIAAIRNLLIKNDIEILAELTEGGSAVQRVETLKPDIVIIDVDIPGVNGIQV 63 Query: 65 TKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISK 105 + +++ + I +I V+A + G ++SK Sbjct: 64 LETLRK-RQYSGI-IIIVSAKNDHFYGKHCADAGANGFVSK 102 >gnl|CDD|183013 PRK11173, PRK11173, two-component response regulator; Provisional. Length = 237 Score = 36.9 bits (86), Expect = 0.001 Identities = 17/71 (23%), Positives = 39/71 (54%) Query: 4 KVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLE 63 ++IVED + + + E GY + +G E ++ ++ +++IMDI L +GL Sbjct: 5 HILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQILSENDINLVIMDINLPGKNGLL 64 Query: 64 ITKQIKEDSEL 74 + ++++E + + Sbjct: 65 LARELREQANV 75 >gnl|CDD|185376 PRK15479, PRK15479, transcriptional regulatory protein TctD; Provisional. Length = 221 Score = 37.0 bits (86), Expect = 0.001 Identities = 27/108 (25%), Positives = 57/108 (52%), Gaps = 4/108 (3%) Query: 4 KVMIVEDN-ELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGL 62 ++++ EDN EL L + L++ +G+ +G+ A L + + ++DI + + GL Sbjct: 2 RLLLAEDNRELAHWLEKALVQ-NGFAVDCVFDGLAADHLLQSEMYALAVLDINMPGMDGL 60 Query: 63 EITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLS 110 E+ +++++ Q +PV+ +TA + D + G + Y+ KP L Sbjct: 61 EVLQRLRKRG--QTLPVLLLTARSAVADRVKGLNVGADDYLPKPFELE 106 >gnl|CDD|182612 PRK10643, PRK10643, DNA-binding transcriptional regulator BasR; Provisional. Length = 222 Score = 34.6 bits (80), Expect = 0.007 Identities = 30/112 (26%), Positives = 55/112 (49%), Gaps = 12/112 (10%) Query: 4 KVMIVEDNELNMKLFRDLI---ETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEIS 60 K++IVED+ L L + LI +T GY EA L ++++D+ L + Sbjct: 2 KILIVEDDTL---LLQGLILALQTEGYACDCASTAREAEALLESGHYSLVVLDLGLPDED 58 Query: 61 GLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIR--KGGCEAYISKPISLS 110 GL + ++ ++ + +PV+ +T A E+R+ G + Y+ KP +L Sbjct: 59 GLHLLRRWRQ--KKYTLPVLILT--ARDTLEDRVAGLDVGADDYLVKPFALE 106 >gnl|CDD|183148 PRK11466, PRK11466, hybrid sensory histidine kinase TorS; Provisional. Length = 914 Score = 34.1 bits (78), Expect = 0.010 Identities = 16/69 (23%), Positives = 36/69 (52%), Gaps = 1/69 (1%) Query: 3 KKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALE-LARQHKPDVIIMDIQLQEISG 61 +++++EDN L ++ +++ TSG + N +ALE L ++D L + G Sbjct: 682 LRLLLIEDNPLTQRITAEMLNTSGAQVVAVGNAAQALETLQNSEPFAAALVDFDLPDYDG 741 Query: 62 LEITKQIKE 70 + + +Q+ + Sbjct: 742 ITLARQLAQ 750 >gnl|CDD|182755 PRK10816, PRK10816, DNA-binding transcriptional regulator PhoP; Provisional. Length = 223 Score = 33.9 bits (78), Expect = 0.011 Identities = 25/106 (23%), Positives = 54/106 (50%), Gaps = 2/106 (1%) Query: 4 KVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLE 63 +V++VEDN L + ++ +G+ + EA +H PD+ I+D+ L + GL Sbjct: 2 RVLVVEDNALLRHHLKVQLQDAGHQVDAAEDAKEADYYLNEHLPDIAIVDLGLPDEDGLS 61 Query: 64 ITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISL 109 + ++ + + +P++ +TA D+ + G + Y++KP + Sbjct: 62 LIRRWRSNDV--SLPILVLTARESWQDKVEVLSAGADDYVTKPFHI 105 >gnl|CDD|182454 PRK10430, PRK10430, DNA-binding transcriptional activator DcuR; Provisional. Length = 239 Score = 32.4 bits (74), Expect = 0.028 Identities = 28/122 (22%), Positives = 51/122 (41%), Gaps = 12/122 (9%) Query: 5 VMIVEDN----ELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEIS 60 V+IV+D+ ELN + + T + + D+I++DI +Q+ + Sbjct: 4 VLIVDDDAMVAELNRRYVAQIPGFQCCGTASTLEQAKEIIFNSDTPIDLILLDIYMQQEN 63 Query: 61 GLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKG---GCEAYISKPISLSIFMETIK 117 GL++ + E ++ VI+ A D I+ G Y+ KP S F E + Sbjct: 64 GLDLLPVLHEAGCKSDVIVISSAA-----DAATIKDSLHYGVVDYLIKPFQASRFEEALT 118 Query: 118 KY 119 + Sbjct: 119 GW 120 >gnl|CDD|182154 PRK09935, PRK09935, transcriptional regulator FimZ; Provisional. Length = 210 Score = 31.8 bits (72), Expect = 0.049 Identities = 15/43 (34%), Positives = 22/43 (51%) Query: 28 IALQTRNGMEALELARQHKPDVIIMDIQLQEISGLEITKQIKE 70 I L+T + ++ R D+IIMDI L G K+IK+ Sbjct: 31 IVLKTDDYRITIDYLRTRPVDLIIMDIDLPGTDGFTFLKRIKQ 73 >gnl|CDD|184141 PRK13557, PRK13557, histidine kinase; Provisional. Length = 540 Score = 31.6 bits (72), Expect = 0.054 Identities = 18/51 (35%), Positives = 29/51 (56%), Gaps = 1/51 (1%) Query: 5 VMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQH-KPDVIIMDI 54 ++IV+D +L R ++E GY L NG EALE+ H + D++ D+ Sbjct: 418 ILIVDDRPDVAELARMILEDFGYRTLVASNGREALEILDSHPEVDLLFTDL 468 >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 = 30.5 bits (70), Expect = 0.10 Identities = 20/57 (35%), Positives = 30/57 (52%), Gaps = 16/57 (28%) Query: 38 ALELARQHKPDVIIMD-IQL-----------QEISGLEITKQIKE-DSELQEIPVIA 81 A L R+H +I++D +QL QE+S EI++ +K EL +PVIA Sbjct: 297 ARRLKREHGLGLIVIDYLQLMSGSGRSENRQQEVS--EISRSLKALAKEL-NVPVIA 350 >gnl|CDD|172377 PRK13856, PRK13856, two-component response regulator VirG; Provisional. Length = 241 Score = 30.2 bits (68), Expect = 0.15 Identities = 21/117 (17%), Positives = 54/117 (46%), Gaps = 4/117 (3%) Query: 2 LKKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISG 61 +K V++++D+ L + + + + + + DV+++D+ L G Sbjct: 1 MKHVLVIDDDVAMRHLIVEYLTIHAFKVTAVADSQQFNRVLASETVDVVVVDLNLGREDG 60 Query: 62 LEITKQIKEDSELQEIPVIAVTAFAMKGDEERIR-KGGCEAYISKPISLSIFMETIK 117 LEI + + S ++P+I ++ ++ ++ + + G +I+KP F+ I+ Sbjct: 61 LEIVRSLATKS---DVPIIIISGDRLEEADKVVALELGATDFIAKPFGTREFLARIR 114 >gnl|CDD|181676 PRK09165, PRK09165, replicative DNA helicase; Provisional. Length = 497 Score = 29.5 bits (67), Expect = 0.22 Identities = 24/67 (35%), Positives = 34/67 (50%), Gaps = 20/67 (29%) Query: 29 ALQTRNGMEALELARQHKPDVIIMD-IQL-------------QEISGLEITKQIKEDSEL 74 L+ R A L RQH D++++D +QL QEIS EIT+ +K ++ Sbjct: 328 QLRAR----ARRLKRQHGLDLLVVDYLQLIRGSSKRSSDNRVQEIS--EITQGLKALAKE 381 Query: 75 QEIPVIA 81 IPVIA Sbjct: 382 LNIPVIA 388 >gnl|CDD|162183 TIGR01063, gyrA, DNA gyrase, A subunit. This model describes the common type II DNA topoisomerase (DNA gyrase). Two apparently independently arising families, one in the Proteobacteria and one in Gram-positive lineages, are both designated toposisomerase IV. Length = 800 Score = 28.4 bits (64), Expect = 0.44 Identities = 12/26 (46%), Positives = 18/26 (69%) Query: 51 IMDIQLQEISGLEITKQIKEDSELQE 76 I+D++LQ ++GLE K +E EL E Sbjct: 416 ILDMRLQRLTGLEREKLQEEYKELLE 441 >gnl|CDD|184495 PRK14084, PRK14084, two-component response regulator; Provisional. Length = 246 Score = 27.4 bits (61), Expect = 0.86 Identities = 32/97 (32%), Positives = 50/97 (51%), Gaps = 15/97 (15%) Query: 4 KVMIVED-----NELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQE 58 K +IV+D NEL L + I I + N E LE ++ D+I +DI L + Sbjct: 2 KALIVDDEPLARNELTYLL--NEIGGFEEIN-EAENVKETLEALLINQYDIIFLDINLMD 58 Query: 59 ISGLEITKQIKEDSELQEIP-VIAVTA---FAMKGDE 91 SG+E+ +I+ +++E P +I TA FA+K E Sbjct: 59 ESGIELAAKIQ---KMKEPPAIIFATAHDQFAVKAFE 92 >gnl|CDD|163070 TIGR02915, PEP_resp_reg, putative PEP-CTERM system response regulator. Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158). Length = 445 Score = 27.4 bits (61), Expect = 0.95 Identities = 28/121 (23%), Positives = 47/121 (38%), Gaps = 13/121 (10%) Query: 5 VMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQL-----QEI 59 ++IVED+ K + R A+ L R+H+P V+ +D+ L Sbjct: 1 LLIVEDDLGLQKQLKWSFADYELAVAADRE--SAIALVRRHEPAVVTLDLGLPPDADGAS 58 Query: 60 SGLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAY--ISKPISLSIFMETIK 117 GL +QI + + VI +T E ++ G AY KPI + + Sbjct: 59 EGLAALQQILAIAP--DTKVIVIT--GNDDRENAVKAIGLGAYDFYQKPIDPDVLKLIVD 114 Query: 118 K 118 + Sbjct: 115 R 115 >gnl|CDD|178792 PRK00011, glyA, serine hydroxymethyltransferase; Reviewed. Length = 416 Score = 27.3 bits (62), Expect = 1.0 Identities = 8/15 (53%), Positives = 11/15 (73%) Query: 37 EALELARQHKPDVII 51 E +LA +HKP +II Sbjct: 156 EVEKLALEHKPKLII 170 >gnl|CDD|148851 pfam07478, Dala_Dala_lig_C, D-ala D-ala ligase C-terminus. This family represents the C-terminal, catalytic domain of the D-alanine--D-alanine ligase enzyme EC:6.3.2.4. D-Alanine is one of the central molecules of the cross-linking step of peptidoglycan assembly. There are three enzymes involved in the D-alanine branch of peptidoglycan biosynthesis: the pyridoxal phosphate-dependent D-alanine racemase (Alr), the ATP-dependent D-alanine:D-alanine ligase (Ddl), and the ATP-dependent D-alanine:D-alanine-adding enzyme (MurF). Length = 201 Score = 26.8 bits (60), Expect = 1.4 Identities = 13/47 (27%), Positives = 22/47 (46%), Gaps = 4/47 (8%) Query: 37 EALELARQHKPDVIIMDIQLQEISGLEITKQIKEDSELQEIPVIAVT 83 A+E A Q+ V+I + I G EI + + +L+ PV + Sbjct: 60 SAIEEAFQYDNKVLIE----EAIEGREIECAVLGNEDLEVSPVGEIR 102 >gnl|CDD|179452 PRK02625, rpoC1, DNA-directed RNA polymerase subunit gamma; Provisional. Length = 627 Score = 26.2 bits (58), Expect = 2.0 Identities = 16/34 (47%), Positives = 20/34 (58%), Gaps = 1/34 (2%) Query: 56 LQEISGLEITKQI-KEDSELQEIPVIAVTAFAMK 88 L E LEI QI EDSEL+ V+ + A A+K Sbjct: 162 LTEDQWLEIEDQIYAEDSELEGEEVVGIGAEALK 195 >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 = 26.2 bits (57), Expect = 2.1 Identities = 20/93 (21%), Positives = 38/93 (40%), Gaps = 12/93 (12%) Query: 3 KKVMIVEDNELNMKLFRDLIETSGYIALQTRNGME----ALELARQHKPDVIIMD----- 53 V+ ++ ++ ++ L+ + +G AL LAR+ KPDV+I+D Sbjct: 31 GGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALARKLKPDVLILDEITSL 90 Query: 54 ---IQLQEISGLEITKQIKEDSELQEIPVIAVT 83 Q + LE + + + + VI T Sbjct: 91 LDAEQEALLLLLEELRLLLLLKSEKNLTVILTT 123 >gnl|CDD|183642 PRK12640, flgF, flagellar basal body rod protein FlgF; Reviewed. Length = 246 Score = 26.0 bits (58), Expect = 2.5 Identities = 13/47 (27%), Positives = 23/47 (48%), Gaps = 6/47 (12%) Query: 19 RDL---IETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGL 62 R L ++ G++A+Q +G EA + D + QL+ +GL Sbjct: 76 RPLDVALQGDGWLAVQAPDGSEAYTRNGSLQVDA---NGQLRTANGL 119 >gnl|CDD|163389 TIGR03676, aRF1/eRF1, peptide chain release factor 1, archaeal and eukaryotic forms. Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. This model identifies both archaeal (aRF1) and eukaryotic (eRF1) of the protein. Also known as translation termination factor 1. Length = 403 Score = 26.1 bits (58), Expect = 2.7 Identities = 10/40 (25%), Positives = 23/40 (57%) Query: 2 LKKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALEL 41 LK + ++++ +L + F++L++ G A +ALE+ Sbjct: 263 LKDLELMKEKKLMERFFKELVKDGGLAAYGEEEVRKALEM 302 >gnl|CDD|179082 PRK00652, lpxK, tetraacyldisaccharide 4'-kinase; Reviewed. Length = 328 Score = 26.0 bits (58), Expect = 3.0 Identities = 7/16 (43%), Positives = 9/16 (56%) Query: 38 ALELARQHKPDVIIMD 53 A L H D+II+D Sbjct: 134 ARALLAAHGADIIILD 149 >gnl|CDD|178449 PLN02858, PLN02858, fructose-bisphosphate aldolase. Length = 1378 Score = 25.6 bits (56), Expect = 3.5 Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 6/34 (17%) Query: 65 TKQIKE-----DSELQEIPVIAVTAFAMKGDEER 93 TKQ++E L+ I V +V AMK E R Sbjct: 932 TKQVEELKSQCGQSLRSIEV-SVEKVAMKSSEVR 964 >gnl|CDD|179174 PRK00941, PRK00941, acetyl-CoA decarbonylase/synthase complex subunit alpha; Validated. Length = 781 Score = 25.3 bits (56), Expect = 4.1 Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 13/59 (22%) Query: 41 LARQHK------PDVIIMDIQLQEISGLEITKQIKEDSELQEIPVIAVTAFAMKGDEER 93 L++Q K PDVI++D Q + I E+++ IPVIA G +R Sbjct: 291 LSKQLKFIRSGIPDVIVVDEQC-------VRTDILEEAKKLGIPVIATNDKICLGLPDR 342 >gnl|CDD|180220 PRK05718, PRK05718, keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase; Provisional. Length = 212 Score = 25.2 bits (56), Expect = 4.2 Identities = 7/24 (29%), Positives = 14/24 (58%) Query: 28 IALQTRNGMEALELARQHKPDVII 51 + L+T +EA+ L + P+ +I Sbjct: 46 VTLRTPAALEAIRLIAKEVPEALI 69 >gnl|CDD|185244 PRK15346, PRK15346, outer membrane secretin SsaC; Provisional. Length = 499 Score = 25.0 bits (55), Expect = 4.4 Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 13/58 (22%) Query: 7 IVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLEI 64 IV D NM ++R LI L R M +E++ V I+D+ +I+ L I Sbjct: 248 IVRDRAANMAIYRSLIT-----QLDQRPQM--IEIS------VSIIDVDAGDINQLGI 292 >gnl|CDD|183573 PRK12524, PRK12524, RNA polymerase sigma factor; Provisional. Length = 196 Score = 24.9 bits (54), Expect = 5.0 Identities = 19/61 (31%), Positives = 28/61 (45%), Gaps = 4/61 (6%) Query: 29 ALQTRNGMEALELARQHKPDVIIMDIQLQEISGLEITKQIKEDSELQEIPVIAVTAFAMK 88 AL + M AL+ A P+ + L+ I GL E +E+ EI V AV + + Sbjct: 120 ALIEGDRMRALDAALAALPERQRQAVVLRHIEGL----SNPEIAEVMEIGVEAVESLTAR 175 Query: 89 G 89 G Sbjct: 176 G 176 >gnl|CDD|150734 pfam10094, DUF2332, Uncharacterized protein conserved in bacteria (DUF2332). Members of this family of hypothetical bacterial proteins have no known function. Length = 342 Score = 25.0 bits (55), Expect = 5.2 Identities = 7/16 (43%), Positives = 9/16 (56%) Query: 38 ALELARQHKPDVIIMD 53 A+ LARQ P + D Sbjct: 229 AIALARQAPPQLERGD 244 >gnl|CDD|162241 TIGR01182, eda, Entner-Doudoroff aldolase. 2-deydro-3-deoxyphosphogluconate aldolase (EC 4.1.2.14) is an enzyme of the Entner-Doudoroff pathway. This aldolase has another function, 4-hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16) shown experimentally in Escherichia coli and Pseudomonas putida. Length = 204 Score = 25.0 bits (55), Expect = 5.3 Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 3/50 (6%) Query: 5 VMIVEDNELNMKLFRDLIE---TSGYIALQTRNGMEALELARQHKPDVII 51 V+ ++D + + L + LIE + L+T ++A+ L R+ PD +I Sbjct: 13 VIRIDDVDDALPLAKALIEGGLRVLEVTLRTPVALDAIRLLRKEVPDALI 62 >gnl|CDD|183163 PRK11498, bcsA, cellulose synthase catalytic subunit; Provisional. Length = 852 Score = 24.6 bits (54), Expect = 6.6 Identities = 15/57 (26%), Positives = 25/57 (43%), Gaps = 14/57 (24%) Query: 74 LQEIPVIAV--------TAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYIGE 122 L EI IAV T+ + R+G AY+ P + + E++ +IG+ Sbjct: 430 LDEIGGIAVETVTEDAHTSLRLH------RRGYTSAYMRIPQAAGLATESLSAHIGQ 480 >gnl|CDD|184338 PRK13805, PRK13805, bifunctional acetaldehyde-CoA/alcohol dehydrogenase; Provisional. Length = 862 Score = 24.4 bits (54), Expect = 7.1 Identities = 8/16 (50%), Positives = 9/16 (56%) Query: 36 MEALELARQHKPDVII 51 + EL R KPD II Sbjct: 529 RKGAELMRSFKPDTII 544 >gnl|CDD|132172 TIGR03128, RuMP_HxlA, 3-hexulose-6-phosphate synthase. at the cost of also yielding formaldehyde. These latter species tend usually have a formaldehyde-activating enzyme to attach formaldehyde to the C1 carrier tetrahydromethanopterin. In these species, the enzyme is viewed as a lyase rather than a synthase and is called D-arabino 3-hexulose 6-phosphate formaldehyde lyase. Note that there is some overlap in specificity with the Escherichia coli enzyme 3-keto-L-gulonate 6-phosphate decarboxylase. Length = 206 Score = 24.3 bits (53), Expect = 7.8 Identities = 17/45 (37%), Positives = 25/45 (55%), Gaps = 2/45 (4%) Query: 28 IALQTRNGMEALELARQHKPDVIIMDIQLQEI--SGLEITKQIKE 70 +AL + EALELA + V I++I I G+E K++KE Sbjct: 4 LALDLLDIEEALELAEKVADYVDIIEIGTPLIKNEGIEAVKEMKE 48 >gnl|CDD|181426 PRK08444, PRK08444, hypothetical protein; Provisional. Length = 353 Score = 24.3 bits (53), Expect = 8.4 Identities = 8/21 (38%), Positives = 15/21 (71%) Query: 11 NELNMKLFRDLIETSGYIALQ 31 N L+++ F LI+ SG+I ++ Sbjct: 322 NGLSLEDFIFLIKDSGFIPVE 342 >gnl|CDD|180128 PRK05560, PRK05560, DNA gyrase subunit A; Validated. Length = 805 Score = 24.2 bits (54), Expect = 8.8 Identities = 11/26 (42%), Positives = 16/26 (61%) Query: 51 IMDIQLQEISGLEITKQIKEDSELQE 76 I+D++LQ ++GLE K E EL Sbjct: 419 ILDMRLQRLTGLERDKIEDEYKELLA 444 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 0.136 0.360 Gapped Lambda K H 0.267 0.0664 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 1,984,209 Number of extensions: 119316 Number of successful extensions: 417 Number of sequences better than 10.0: 1 Number of HSP's gapped: 396 Number of HSP's successfully gapped: 105 Length of query: 123 Length of database: 5,994,473 Length adjustment: 82 Effective length of query: 41 Effective length of database: 4,222,617 Effective search space: 173127297 Effective search space used: 173127297 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: 51 (23.6 bits)