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)