RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

Searching..................................................done

Query= gi|254780893|ref|YP_003065306.1| two component response
regulator [Candidatus Liberibacter asiaticus str. psy62]
         (236 letters)



>gnl|CDD|182612 PRK10643, PRK10643, DNA-binding transcriptional regulator BasR;
           Provisional.
          Length = 222

 Score =  167 bits (424), Expect = 3e-42
 Identities = 85/229 (37%), Positives = 129/229 (56%), Gaps = 11/229 (4%)

Query: 1   MRILLIEDDKALAHSIELMLKSENFNVYVTDLGEDGIELCKFYE---FDAIILDLGLTDI 57
           M+IL++EDD  L   + L L++E    Y  D      E     E   +  ++LDLGL D 
Sbjct: 1   MKILIVEDDTLLLQGLILALQTEG---YACDCASTAREAEALLESGHYSLVVLDLGLPDE 57

Query: 58  PGFEVLRALRVAKISTPVCILSGMSSIEDKVRGLQSGADDYISKPFNKEELVARIRAIVR 117
            G  +LR  R  K + PV IL+   ++ED+V GL  GADDY+ KPF  EEL ARIRA++R
Sbjct: 58  DGLHLLRRWRQKKYTLPVLILTARDTLEDRVAGLDVGADDYLVKPFALEELHARIRALIR 117

Query: 118 RSRGHAQSLIVTGDLSVNLDAKTVEVQGHRIHLTGKEYQMIELLSLRKNTTLTKEMFLNH 177
           R +G  ++ +  G+L++NL  + V + G  + LT KE+ ++  L L+  + + +E+    
Sbjct: 118 RHQGQGENELQVGNLTLNLGRQQVWLDGQELILTPKEFALLSRLMLKAGSPVHREILYQD 177

Query: 178 LYDGRDEPEVKIIDVFICKLRKKLSNAAGGKNYIETVWGRGYVLRENAK 226
           +Y+  DEP    ++V I  LR K+     GK+ I TV G GY+L  N +
Sbjct: 178 IYNWDDEPSSNTLEVHIHNLRDKV-----GKDRIRTVRGFGYMLVANEE 221


>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 =  144 bits (365), Expect = 2e-35
 Identities = 75/219 (34%), Positives = 122/219 (55%), Gaps = 1/219 (0%)

Query: 3   ILLIEDDKALAHSIELMLKSENFNVYVTDLGEDGIELCKFYEFDAIILDLGLTDIPGFEV 62
           IL++ED++  A  ++  L    + V     G DG+ L    ++D IILD+ L  + G+++
Sbjct: 1   ILVVEDEQKTAEYLQQGLSESGYVVDAASNGRDGLHLALKDDYDLIILDVMLPGMDGWQI 60

Query: 63  LRALRVAKISTPVCILSGMSSIEDKVRGLQSGADDYISKPFNKEELVARIRAIVRRSRGH 122
           L+ LR +   TPV  L+   S+ DKV+GL  GADDY+ KPF+  EL+AR+R ++RRS   
Sbjct: 61  LQTLRRSGKQTPVLFLTARDSVADKVKGLDLGADDYLVKPFSFSELLARVRTLLRRSHSL 120

Query: 123 AQSLIVTGDLSVNLDAKTVEVQGHRIHLTGKEYQMIELLSLRKNTTLTKEMFLNHLYDGR 182
             +++   DL ++     V     RI LT KE+Q++ LL  R    L + +  + ++   
Sbjct: 121 NSTVLEIADLRMDSVRHRVSRGNIRITLTRKEFQLLWLLMRRTGEVLPRTVIASLVWGMN 180

Query: 183 DEPEVKIIDVFICKLRKKLSNAAGGKNYIETVWGRGYVL 221
            + +  ++DV I +LR K+ +    K  I T+ G GYVL
Sbjct: 181 FDSDTNVVDVAIRRLRAKVDDPFEEK-LIHTIRGMGYVL 218


>gnl|CDD|182950 PRK11083, PRK11083, DNA-binding response regulator CreB;
           Provisional.
          Length = 228

 Score =  142 bits (359), Expect = 1e-34
 Identities = 71/224 (31%), Positives = 118/224 (52%), Gaps = 2/224 (0%)

Query: 1   MRILLIEDDKALAHSIELMLKSENFNVYVTDLGEDGIELCKFYEFDAIILDLGLTDIPGF 60
             ILL+ED++A+A ++   L+SE F V   + G   ++  +    D +ILD+GL DI GF
Sbjct: 4   PTILLVEDEQAIADTLVYALQSEGFTVEWFERGLPALDKLRQQPPDLVILDVGLPDISGF 63

Query: 61  EVLRALRVAKISTPVCILSGMSSIEDKVRGLQSGADDYISKPFNKEELVARIRAIVRRSR 120
           E+ R L     + PV  L+  S   D++ GL+ GADDY++KPF+  E+ AR+R I+RR +
Sbjct: 64  ELCRQLLAFHPALPVIFLTARSDEVDRLVGLEIGADDYVAKPFSPREVAARVRTILRRVK 123

Query: 121 GHA--QSLIVTGDLSVNLDAKTVEVQGHRIHLTGKEYQMIELLSLRKNTTLTKEMFLNHL 178
             A    +I  G   ++  A  +   G  + LT  E+ +++ L L      +++  ++ +
Sbjct: 124 KFAAPSPVIRIGHFELDEPAARISYFGTPLTLTRYEFLLLKTLLLSPGRVFSRQQLMDIV 183

Query: 179 YDGRDEPEVKIIDVFICKLRKKLSNAAGGKNYIETVWGRGYVLR 222
           ++   +   + +D  I  LR KL       + I T  G GY LR
Sbjct: 184 WEDAQDSYDRTVDTHIKTLRAKLRAINPDLSPINTHRGMGYSLR 227


>gnl|CDD|182102 PRK09836, PRK09836, DNA-binding transcriptional activator CusR;
           Provisional.
          Length = 227

 Score =  138 bits (348), Expect = 2e-33
 Identities = 77/222 (34%), Positives = 126/222 (56%), Gaps = 2/222 (0%)

Query: 1   MRILLIEDDKALAHSIELMLKSENFNVYVTDLGEDGIELCKFYEFDAIILDLGLTDIPGF 60
           M++L++ED+K     +   L    F V + D G +G  L    ++D IILD+ L D+ G+
Sbjct: 1   MKLLIVEDEKKTGEYLTKGLTEAGFVVDLADNGLNGYHLAMTGDYDLIILDIMLPDVNGW 60

Query: 61  EVLRALRVAKISTPVCILSGMSSIEDKVRGLQSGADDYISKPFNKEELVARIRAIVRRSR 120
           +++R LR A    P+ +L+ + +IE +V+GL+ GADDY+ KPF   EL+AR+R ++RR  
Sbjct: 61  DIVRMLRSANKGMPILLLTALGTIEHRVKGLELGADDYLVKPFAFAELLARVRTLLRRGA 120

Query: 121 GH-AQSLIVTGDLSVNLDAKTVEVQGHRIHLTGKEYQMIELLSLRKNTTLTKEMFLNHLY 179
               +S     DL V+L ++ V   G RI LT KE+ ++E     +   L + +  + ++
Sbjct: 121 AVIIESQFQVADLMVDLVSRKVTRSGTRITLTSKEFTLLEFFLRHQGEVLPRSLIASQVW 180

Query: 180 DGRDEPEVKIIDVFICKLRKKLSNAAGGKNYIETVWGRGYVL 221
           D   + +   IDV + +LR K+ N    K  I+TV G GY+L
Sbjct: 181 DMNFDSDTNAIDVAVKRLRGKIDNDFEPK-LIQTVRGVGYML 221


>gnl|CDD|185376 PRK15479, PRK15479, transcriptional regulatory protein TctD;
           Provisional.
          Length = 221

 Score =  137 bits (348), Expect = 2e-33
 Identities = 79/224 (35%), Positives = 125/224 (55%), Gaps = 10/224 (4%)

Query: 1   MRILLIEDDKALAHSIELMLKSENFNVYVTDLGEDGI---ELCKFYEFDAIILDLGLTDI 57
           MR+LL ED++ LAH +E  L    F V   D   DG+    L +   +   +LD+ +  +
Sbjct: 1   MRLLLAEDNRELAHWLEKALVQNGFAV---DCVFDGLAADHLLQSEMYALAVLDINMPGM 57

Query: 58  PGFEVLRALRVAKISTPVCILSGMSSIEDKVRGLQSGADDYISKPFNKEELVARIRAIVR 117
            G EVL+ LR    + PV +L+  S++ D+V+GL  GADDY+ KPF  EEL AR+RA++R
Sbjct: 58  DGLEVLQRLRKRGQTLPVLLLTARSAVADRVKGLNVGADDYLPKPFELEELDARLRALLR 117

Query: 118 RSRGHAQSLIVTGDLSVNLDAKTVEVQGHRIHLTGKEYQMIELLSLRKNTTLTKEMFLNH 177
           RS G  Q +   G+L  + D     +QG  + LT +E  ++ +L  R+   ++++     
Sbjct: 118 RSAGQVQEVQQLGELIFH-DEGYFLLQGQPLALTPREQALLTVLMYRRTRPVSRQQLFEQ 176

Query: 178 LYDGRDEPEVKIIDVFICKLRKKLSNAAGGKNYIETVWGRGYVL 221
           ++   DE   + I+++I +LRKKL  +      I T+ G GYVL
Sbjct: 177 VFSLNDEVSPESIELYIHRLRKKLQGSDVR---ITTLRGLGYVL 217


>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 =  134 bits (340), Expect = 2e-32
 Identities = 74/223 (33%), Positives = 120/223 (53%), Gaps = 4/223 (1%)

Query: 2   RILLIEDDKALAHSIELMLKSENFNVYVTDLGEDGIELCKFYEFDAIILDLGLTDIPGFE 61
           RIL++ED+ A+   I   L+   ++V     G++ + L      D I+LD  L    G E
Sbjct: 4   RILVVEDEPAIRELIAYNLEKAGYDVVEAGDGDEALTLINERGPDLILLDWMLPGTSGIE 63

Query: 62  VLRALRVAKI--STPVCILSGMSSIEDKVRGLQSGADDYISKPFNKEELVARIRAIVRRS 119
           + R LR      + P+ +L+     ED+VRGL++GADDYI+KPF+  EL+ARI+A++RR 
Sbjct: 64  LCRRLRRRPETRAIPIIMLTARGEEEDRVRGLETGADDYITKPFSPRELLARIKAVLRRI 123

Query: 120 R-GHAQSLIVTGDLSVNLDAKTVEVQGHRIHLTGKEYQMIELLSLRKNTTLTKEMFLNHL 178
           R   +  +I  GDLS++  A  V   G  + L   E++++           ++E  L+ +
Sbjct: 124 RPQLSDEVIEVGDLSLDPVAHRVFRGGQPLSLGPTEFRLLHFFMTHPERVYSREQLLDRV 183

Query: 179 YDGRDEPEVKIIDVFICKLRKKLSNAAGGKNYIETVWGRGYVL 221
           +      E + +DV I +LRK L N  G ++ ++TV G GY  
Sbjct: 184 WGRDVYVEERTVDVHIRRLRKAL-NPFGLEDPVQTVRGAGYRF 225


>gnl|CDD|182755 PRK10816, PRK10816, DNA-binding transcriptional regulator PhoP;
           Provisional.
          Length = 223

 Score =  131 bits (332), Expect = 1e-31
 Identities = 75/222 (33%), Positives = 120/222 (54%), Gaps = 7/222 (3%)

Query: 1   MRILLIEDDKALAHSIELMLKSENFNVYVTDLGEDGIELCKF---YEFDAIILDLGLTDI 57
           MR+L++ED+  L H +++ L+     V   D  ED  E   +   +  D  I+DLGL D 
Sbjct: 1   MRVLVVEDNALLRHHLKVQLQDAGHQV---DAAEDAKEADYYLNEHLPDIAIVDLGLPDE 57

Query: 58  PGFEVLRALRVAKISTPVCILSGMSSIEDKVRGLQSGADDYISKPFNKEELVARIRAIVR 117
            G  ++R  R   +S P+ +L+   S +DKV  L +GADDY++KPF+ EE++AR++A++R
Sbjct: 58  DGLSLIRRWRSNDVSLPILVLTARESWQDKVEVLSAGADDYVTKPFHIEEVMARMQALMR 117

Query: 118 RSRGHAQSLIVTGDLSVNLDAKTVEVQGHRIHLTGKEYQMIELLSLRKNTTLTKEMFLNH 177
           R+ G A  +I      V+L  + + +    I LT  EY ++E L       ++K+  +  
Sbjct: 118 RNSGLASQVISLPPFQVDLSRRELSINDEVIKLTAFEYTIMETLIRNNGKVVSKDSLMLQ 177

Query: 178 LYDGRDEPEVKIIDVFICKLRKKLSNAAGGKNYIETVWGRGY 219
           LY   +  E   IDV + +LRKK+         I TV G+GY
Sbjct: 178 LYPDAELRESHTIDVLMGRLRKKIQAQYPQ-EVITTVRGQGY 218


>gnl|CDD|182387 PRK10336, PRK10336, DNA-binding transcriptional regulator QseB;
           Provisional.
          Length = 219

 Score =  129 bits (325), Expect = 7e-31
 Identities = 76/223 (34%), Positives = 118/223 (52%), Gaps = 5/223 (2%)

Query: 1   MRILLIEDDKALAHSIELMLKSENFNVYVTDLGEDGIELCKFYEFDAIILDLGLTDIPGF 60
           MRILLIEDD  +   I+  L    F+V     G  G E      +DA+ILDL L  + G 
Sbjct: 1   MRILLIEDDMLIGDGIKTGLSKMGFSVDWFTQGRQGKEALYSAPYDAVILDLTLPGMDGR 60

Query: 61  EVLRALRVAKISTPVCILSGMSSIEDKVRGLQSGADDYISKPFNKEELVARIRAIVRRSR 120
           ++LR  R      PV IL+   ++ ++V GL+ GADDY+ KPF   E+ AR+ A++RR+ 
Sbjct: 61  DILREWREKGQREPVLILTARDALAERVEGLRLGADDYLCKPFALIEVAARLEALMRRTN 120

Query: 121 GHAQSLIVTGDLSVNLDAKTVEVQGHRIHLTGKEYQMIELLSLRKNTTLTKEMFLNHLYD 180
           G A + +  G++ ++   +   + G  + L  KE+ ++ELL       L +++    LY 
Sbjct: 121 GQASNELRHGNVMLDPGKRIATLAGEPLTLKPKEFALLELLMRNAGRVLPRKLIEEKLYT 180

Query: 181 GRDEPEVKIIDVFICKLRKKLSNAAGGKNYIETVWGRGYVLRE 223
             +E     ++V +  LR+KL     G ++I TV G GY L E
Sbjct: 181 WDEEVTSNAVEVHVHHLRRKL-----GSDFIRTVHGIGYTLGE 218


>gnl|CDD|183172 PRK11517, PRK11517, transcriptional regulatory protein YedW;
           Provisional.
          Length = 223

 Score =  129 bits (325), Expect = 8e-31
 Identities = 75/223 (33%), Positives = 127/223 (56%), Gaps = 5/223 (2%)

Query: 1   MRILLIEDDKALAHSIELMLKSENFNV-YVTDLGEDGIELCKFYEFDAIILDLGLTDIPG 59
           M+ILLIED++     +   L    + +  V+D G DG+ L    ++  IILD+ L  + G
Sbjct: 1   MKILLIEDNQRTQEWVTQGLSEAGYVIDAVSD-GRDGLYLALKDDYALIILDIMLPGMDG 59

Query: 60  FEVLRALRVAKISTPVCILSGMSSIEDKVRGLQSGADDYISKPFNKEELVARIRAIVRRS 119
           +++L+ LR AK  TPV  L+   S++D+VRGL SGA+DY+ KPF+  EL+AR+RA +R+ 
Sbjct: 60  WQILQTLRTAK-QTPVICLTARDSVDDRVRGLDSGANDYLVKPFSFSELLARVRAQLRQH 118

Query: 120 RGHAQSLIVTGDLSVNLDAKTVEVQGHRIHLTGKEYQMIELLSLRKNTTLTKEMFLNHLY 179
                +L ++G L ++  +++V      I LT KE+Q++ LL+ R    + + +  + ++
Sbjct: 119 HALNSTLEISG-LRMDSVSQSVSRDNISITLTRKEFQLLWLLASRAGEIIPRTVIASEIW 177

Query: 180 DGRDEPEVKIIDVFICKLRKKLSNAAGGKNYIETVWGRGYVLR 222
               + +   +DV I +LR K+ +    K  I T+ G GY   
Sbjct: 178 GINFDSDTNTVDVAIRRLRAKVDDPFPEK-LIATIRGMGYSFV 219


>gnl|CDD|182864 PRK10955, PRK10955, DNA-binding transcriptional regulator CpxR;
           Provisional.
          Length = 232

 Score =  123 bits (311), Expect = 3e-29
 Identities = 79/228 (34%), Positives = 122/228 (53%), Gaps = 10/228 (4%)

Query: 2   RILLIEDDKALAHSIELMLKSENFNVYVTDLGEDGIELCKFYEFDAIILDLGLTDIPGFE 61
           +ILL++DD+ L   ++ +L+ E FNV V   GE  ++L      D ++LD+ +    G +
Sbjct: 3   KILLVDDDRELTSLLKELLEMEGFNVIVAHDGEQALDLLD-DSIDLLLLDVMMPKKNGID 61

Query: 62  VLRALRVAKISTPVCILSGMSSIEDKVRGLQSGADDYISKPFNKEELVARIRAIVRRSRG 121
            L+ LR     TPV +L+   S  D+V GL+ GADDY+ KPFN  ELVARIRAI+RRS  
Sbjct: 62  TLKELRQTH-QTPVIMLTARGSELDRVLGLELGADDYLPKPFNDRELVARIRAILRRSHW 120

Query: 122 HAQ--------SLIVTGDLSVNLDAKTVEVQGHRIHLTGKEYQMIELLSLRKNTTLTKEM 173
             Q          +    LS+N   +     G  + LTG E+ ++ LL+      +++E 
Sbjct: 121 SEQQQNNDNGSPTLEVDALSLNPGRQEASFDGQTLELTGTEFTLLYLLAQHLGQVVSREH 180

Query: 174 FLNHLYDGRDEPEVKIIDVFICKLRKKLSNAAGGKNYIETVWGRGYVL 221
               +   R  P  + ID+ I  LR+KL +   G  + +T+ GRGY++
Sbjct: 181 LSQEVLGKRLTPFDRAIDMHISNLRRKLPDRKDGHPWFKTLRGRGYLM 228


>gnl|CDD|181883 PRK09468, ompR, osmolarity response regulator; Provisional.
          Length = 239

 Score =  120 bits (303), Expect = 4e-28
 Identities = 70/230 (30%), Positives = 114/230 (49%), Gaps = 15/230 (6%)

Query: 2   RILLIEDDKALAHSIELMLKSENFNVYVTDLGEDGIELCKFYE---FDAIILDLGLTDIP 58
           +IL+++DD  L   +E  L  + F V       +  ++ +      F  ++LDL L    
Sbjct: 7   KILVVDDDMRLRALLERYLTEQGFQVRSA---ANAEQMDRLLTRESFHLMVLDLMLPGED 63

Query: 59  GFEVLRALRVAKISTPVCILSGMSSIEDKVRGLQSGADDYISKPFNKEELVARIRAIVRR 118
           G  + R LR     TP+ +L+      D++ GL+ GADDY+ KPFN  EL+ARIRA++RR
Sbjct: 64  GLSICRRLRSQNNPTPIIMLTAKGEEVDRIVGLEIGADDYLPKPFNPRELLARIRAVLRR 123

Query: 119 -------SRGHAQSLIVTGDLSVNLDAKTVEVQGHRIHLTGKEYQMIELLSLRKNTTLTK 171
                  +    + +I  G   +NL  + +      + LT  E+ +++ L       L++
Sbjct: 124 QAPELPGAPSQEEEVIAFGKFKLNLGTRELFRGDEPMPLTTGEFAVLKALVSHPREPLSR 183

Query: 172 EMFLNHLYDGRD-EPEVKIIDVFICKLRKKLSNAAGGKNYIETVWGRGYV 220
           +  +N L  GR+     + IDV I +LR+ +        YI+TVWG GYV
Sbjct: 184 DKLMN-LARGREYSAMERSIDVQISRLRRLIEEDPAHPRYIQTVWGLGYV 232


>gnl|CDD|182522 PRK10529, PRK10529, DNA-binding transcriptional activator KdpE;
           Provisional.
          Length = 225

 Score =  111 bits (279), Expect = 2e-25
 Identities = 69/219 (31%), Positives = 112/219 (51%), Gaps = 3/219 (1%)

Query: 3   ILLIEDDKALAHSIELMLKSENFNVYVTDLGEDGIELCKFYEFDAIILDLGLTDIPGFEV 62
           +L++ED++A+   +   L+ +   V+  +  + G+      + D IILDLGL D  G E 
Sbjct: 4   VLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEAATRKPDLIILDLGLPDGDGIEF 63

Query: 63  LRALRVAKISTPVCILSGMSSIEDKVRGLQSGADDYISKPFNKEELVARIRAIVRR-SRG 121
           +R LR    + PV +LS  S   DK+  L +GADDY+SKPF   EL AR+R  +RR S  
Sbjct: 64  IRDLRQWS-AIPVIVLSARSEESDKIAALDAGADDYLSKPFGIGELQARLRVALRRHSAT 122

Query: 122 HAQSLIVT-GDLSVNLDAKTVEVQGHRIHLTGKEYQMIELLSLRKNTTLTKEMFLNHLYD 180
            A   +V   D++V+L A+ +      +HLT  E++++ +L       LT+   LN ++ 
Sbjct: 123 PAPDPLVKFSDVTVDLAARVIHRGEEEVHLTPIEFRLLAVLLNNAGKVLTQRQLLNQVWG 182

Query: 181 GRDEPEVKIIDVFICKLRKKLSNAAGGKNYIETVWGRGY 219
                    + +++  LR+KL        +  T  G GY
Sbjct: 183 PNAVEHSHYLRIYMGHLRQKLEQDPARPRHFITETGIGY 221


>gnl|CDD|182665 PRK10710, PRK10710, DNA-binding transcriptional regulator BaeR;
           Provisional.
          Length = 240

 Score = 98.6 bits (246), Expect = 1e-21
 Identities = 64/221 (28%), Positives = 113/221 (51%), Gaps = 5/221 (2%)

Query: 2   RILLIEDDKALAHSIELMLKSENFNVYVTDLGEDGIELCKFYEFDAIILDLGLTDIPGFE 61
           RIL++ED+  L   +   L++ ++   +   G++ +   +    D I+LDL L    G  
Sbjct: 12  RILIVEDEPKLGQLLIDYLQAASYATTLLSHGDEVLPYVRQTPPDLILLDLMLPGTDGLT 71

Query: 62  VLRALRVAKIS-TPVCILSGMSSIEDKVRGLQSGADDYISKPFNKEELVARIRAIVRRSR 120
           + R +R  + S  P+ +++      D++ GL+ GADDYI KP++  E+VAR++ I+RR +
Sbjct: 72  LCREIR--RFSDIPIVMVTAKIEEIDRLLGLEIGADDYICKPYSPREVVARVKTILRRCK 129

Query: 121 --GHAQSLIVTGDLSVNLDAKTVEVQGHRIHLTGKEYQMIELLSLRKNTTLTKEMFLNHL 178
                Q       L ++        +G  + LT  E+++++ LS       ++E  LNHL
Sbjct: 130 PQRELQQQDAESPLIIDESRFQASWRGKMLDLTPAEFRLLKTLSHEPGKVFSREQLLNHL 189

Query: 179 YDGRDEPEVKIIDVFICKLRKKLSNAAGGKNYIETVWGRGY 219
           YD       + ID  I  LR+KL +    +++I  V+G GY
Sbjct: 190 YDDYRVVTDRTIDSHIKNLRRKLESLDAEQSFIRAVYGVGY 230


>gnl|CDD|182277 PRK10161, PRK10161, transcriptional regulator PhoB; Provisional.
          Length = 229

 Score = 98.3 bits (244), Expect = 1e-21
 Identities = 65/221 (29%), Positives = 113/221 (51%), Gaps = 4/221 (1%)

Query: 2   RILLIEDDKALAHSIELMLKSENFNVYVTDLGEDGIELCKFYEFDAIILDLGLTDIPGFE 61
           RIL++ED+  +   +  +L+   F     +  +  +        D I+LD  L    G +
Sbjct: 4   RILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDLILLDWMLPGGSGIQ 63

Query: 62  VLRALRVAKIS--TPVCILSGMSSIEDKVRGLQSGADDYISKPFNKEELVARIRAIVRR- 118
            ++ L+   ++   PV +L+     ED+VRGL++GADDYI+KPF+ +ELVARI+A++RR 
Sbjct: 64  FIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRRI 123

Query: 119 SRGHAQSLIVTGDLSVNLDAKTVEVQGHRIHLTGKEYQMIELLSLRKNTTLTKEMFLNHL 178
           S    + +I    LS++  +  V      + +   E++++           ++E  LNH+
Sbjct: 124 SPMAVEEVIEMQGLSLDPTSHRVMAGEEPLEMGPTEFKLLHFFMTHPERVYSREQLLNHV 183

Query: 179 YDGRDEPEVKIIDVFICKLRKKLSNAAGGKNYIETVWGRGY 219
           +      E + +DV I +LRK L    G    ++TV G GY
Sbjct: 184 WGTNVYVEDRTVDVHIRRLRKALEP-GGHDRMVQTVRGTGY 223


>gnl|CDD|172377 PRK13856, PRK13856, two-component response regulator VirG;
           Provisional.
          Length = 241

 Score = 87.6 bits (217), Expect = 3e-18
 Identities = 69/226 (30%), Positives = 104/226 (46%), Gaps = 9/226 (3%)

Query: 3   ILLIEDDKALAHSIELMLKSENFNVY-VTDLGEDGIELCKFYEFDAIILDLGLTDIPGFE 61
           +L+I+DD A+ H I   L    F V  V D  +    L      D +++DL L    G E
Sbjct: 4   VLVIDDDVAMRHLIVEYLTIHAFKVTAVADSQQFNRVLAS-ETVDVVVVDLNLGREDGLE 62

Query: 62  VLRALRVAKISTPVCILSGMSSIE-DKVRGLQSGADDYISKPFNKEELVARIRAIVRR-- 118
           ++R+L   K   P+ I+SG    E DKV  L+ GA D+I+KPF   E +ARIR  +R   
Sbjct: 63  IVRSL-ATKSDVPIIIISGDRLEEADKVVALELGATDFIAKPFGTREFLARIRVALRVRP 121

Query: 119 --SRGHAQSLIVTGDLSVNLDAKTV-EVQGHRIHLTGKEYQMIELLSLRKNTTLTKEMFL 175
              R   +      D ++NL  + +    G  + LT  E+ ++     +    L++E  L
Sbjct: 122 NVVRTKDRRSFCFADWTLNLRQRRLISEAGGEVKLTAGEFNLLVAFLEKPRDVLSREQLL 181

Query: 176 NHLYDGRDEPEVKIIDVFICKLRKKLSNAAGGKNYIETVWGRGYVL 221
                  +E   + IDV I +LR+KL         I+T  G GY  
Sbjct: 182 IASRVREEEVYDRSIDVLILRLRRKLEQDPANPQLIKTARGAGYFF 227


>gnl|CDD|182711 PRK10766, PRK10766, DNA-binding transcriptional regulator TorR;
           Provisional.
          Length = 221

 Score = 86.6 bits (215), Expect = 5e-18
 Identities = 61/211 (28%), Positives = 102/211 (48%), Gaps = 12/211 (5%)

Query: 2   RILLIEDDKALAHSIELMLKSENFNVYVTDLGEDGIELCKFYEFDAIILDLGLTDIPGFE 61
            IL++ED+      ++   + E + V     G    E+ +    D I+LD+ L    G  
Sbjct: 4   HILVVEDEPVTRARLQGYFEQEGYTVSEAASGAGMREIMQNQHVDLILLDINLPGEDGLM 63

Query: 62  VLRALRVAKISTPVCIL-SGMSSIEDKVRGLQSGADDYISKPFNKEELVARIR------A 114
           + R LR    ST   IL +G +   D++ GL+ GADDY++KP    EL+ R++      +
Sbjct: 64  LTRELR--SRSTVGIILVTGRTDSIDRIVGLEMGADDYVTKPLELRELLVRVKNLLWRIS 121

Query: 115 IVRRSRGHAQ---SLIVTGDLSVNLDAKTVEVQGHRIHLTGKEYQMIELLSLRKNTTLTK 171
           + R+++ HAQ   +        +N+  +T+E  G  I LT  EY+++          L++
Sbjct: 122 LARQAQPHAQEEDNCYRFAGYCLNVSRRTLERNGEPIKLTKAEYELLVAFVTNPGQVLSR 181

Query: 172 EMFLNHLYDGRDEPEVKIIDVFICKLRKKLS 202
           E  L  L    + P  + IDV I +LR KL+
Sbjct: 182 ERLLRMLSHRVENPNDRTIDVLIRRLRHKLN 212


>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 = 85.2 bits (211), Expect = 2e-17
 Identities = 63/229 (27%), Positives = 107/229 (46%), Gaps = 18/229 (7%)

Query: 2   RILLIEDDKALAHSIELMLKSENFNVYVTDLGEDGIELCKFYEFDAIILDLGLTD--IPG 59
           RI ++ED+ A+  +    LK + + V         ++  +    D  I+D+GL +    G
Sbjct: 2   RIAIVEDEAAIRENYADALKRQGYQVTTYADRPSAMQAFRQRLPDLAIIDIGLGEEIDGG 61

Query: 60  FEVLRALRVAKISTPVCILSGMSSIEDKVRGLQSGADDYISKPFNKEELVARIRAIVRRS 119
           F + + LR    + P+  L+   S  D V GL+ GADDY++K  +   L+ARI A+ RR+
Sbjct: 62  FMLCQDLRSLSATLPIIFLTARDSDFDTVSGLRLGADDYLTKDISLPHLLARITALFRRA 121

Query: 120 RGHAQ-----SLIVTGDLSVNLDAKTVEVQGHRIHLTGKEYQMIELLSLRKNTTLTKEMF 174
               +      LI  G L+++ D  TV  Q   I LT  E+ M+  L+       +++  
Sbjct: 122 EALQKPQKQDDLITRGPLTLDSDRMTVFWQDQPIDLTVTEFWMVHALAKHPGHVKSRQQL 181

Query: 175 LNHLYDGRDEPEVKIIDVFIC----KLRKKLSNAAGGKNYIETVWGRGY 219
           +       D  ++ + D  I     ++RKK        + I+TV+G GY
Sbjct: 182 M-------DAAKIVVDDSTITSHIKRIRKKFQAVDDNFDCIQTVYGMGY 223


>gnl|CDD|181966 PRK09581, pleD, response regulator PleD; Reviewed.
          Length = 457

 Score = 83.0 bits (206), Expect = 6e-17
 Identities = 42/118 (35%), Positives = 72/118 (61%), Gaps = 2/118 (1%)

Query: 2   RILLIEDDKALAHSIELMLKSENFNVYVTDLGEDGIELCKFYEFDAIILDLGLTDIPGFE 61
           RIL+++D  A    +E  L +E + V     G + I +C+  + D I+LD+ +  + GFE
Sbjct: 4   RILVVDDIPANVKLLEAKLLAEYYTVLTASSGAEAIAICEREQPDIILLDVMMPGMDGFE 63

Query: 62  VLRALRVAKIST--PVCILSGMSSIEDKVRGLQSGADDYISKPFNKEELVARIRAIVR 117
           V R L+    +T  PV +++ +   ED+VRGL++GADD+++KP N   L AR++++ R
Sbjct: 64  VCRRLKSDPATTHIPVVMVTALDDPEDRVRGLEAGADDFLTKPINDVALFARVKSLTR 121



 Score = 62.2 bits (152), Expect = 1e-10
 Identities = 38/122 (31%), Positives = 61/122 (50%), Gaps = 5/122 (4%)

Query: 2   RILLIEDDKALAHSIELMLKSENFNVYVTDLGEDGIELCKFYEFDAIILDLGLTDIPGFE 61
           RILL++DD + A  I  +LK E   V V+D  E      +   +D +I+     +     
Sbjct: 157 RILLVDDDVSQAERIANILKEEFRVVVVSDPSEALFNAAE-TNYDLVIVSANFENYDPLR 215

Query: 62  VLRALRVAKIST---PVCILSGMSSIEDKVRGLQSGADDYISKPFNKEELVARIRAIVRR 118
           +   LR +K  T   P+ +L         V+ L+ G +DY+ +P +K EL+AR+R  +RR
Sbjct: 216 LCSQLR-SKERTRYVPILLLVDEDDDPRLVKALELGVNDYLMRPIDKNELLARVRTQIRR 274

Query: 119 SR 120
            R
Sbjct: 275 KR 276


>gnl|CDD|129095 smart00862, Trans_reg_C, Transcriptional regulatory protein, C
           terminal.  This domain is almost always found associated
           with the response regulator receiver domain. It may play
           a role in DNA binding.
          Length = 78

 Score = 80.3 bits (199), Expect = 4e-16
 Identities = 28/78 (35%), Positives = 42/78 (53%), Gaps = 1/78 (1%)

Query: 145 GHRIHLTGKEYQMIELLSLRKNTTLTKEMFLNHLYDGR-DEPEVKIIDVFICKLRKKLSN 203
           G  I LT KE++++ELL       +++E  L  ++    D+ +   +DV I +LRKKL +
Sbjct: 1   GEPIKLTPKEFRLLELLLRNPGRVVSREELLEAVWGDDDDDVDDNTLDVHISRLRKKLED 60

Query: 204 AAGGKNYIETVWGRGYVL 221
                  IETV G GY L
Sbjct: 61  DGANPRLIETVRGVGYRL 78


>gnl|CDD|182660 PRK10701, PRK10701, DNA-binding transcriptional regulator RstA;
           Provisional.
          Length = 240

 Score = 73.5 bits (181), Expect = 4e-14
 Identities = 62/243 (25%), Positives = 112/243 (46%), Gaps = 21/243 (8%)

Query: 2   RILLIEDDKALAHSIELMLKSENFNVYVTDLGEDGIELCKFYEFDAIILDLGLTDIPGFE 61
           +I+ +EDD  +   I   L   + +V V   G+         + D ++LD+ L    G  
Sbjct: 3   KIVFVEDDAEVGSLIAAYLAKHDIDVTVEPRGDRAEATILREQPDLVLLDIMLPGKDGMT 62

Query: 62  VLRALRVAKISTPVCILSGMSSIEDKVRGLQSGADDYISKPFNKEELVARIRAIVRRSRG 121
           + R LR  K   P+ +L+ + S  + +  L+ GA DYI K      L+AR+R  +R++  
Sbjct: 63  ICRDLR-PKWQGPIVLLTSLDSDMNHILALEMGACDYILKTTPPAVLLARLRLHLRQNEQ 121

Query: 122 HAQSLIVT------------GDLSVNLDAKTVEVQGHRIHLTGKEYQMIELLSLRKNTTL 169
             Q+  +             G L+++   + V + G  I L+  ++ ++  L+      +
Sbjct: 122 ATQTKGLQETSLTPYKALHFGTLTIDPVNRQVTLAGEEISLSTADFDLLWELATHAGQIM 181

Query: 170 TKEMFLNHL----YDGRDEPEVKIIDVFICKLRKKLSNAAGGKNYIETVWGRGYVLRENA 225
            ++  L +L    YDG D    + +DV I +LRKKL + A     I+TV  +GY+   +A
Sbjct: 182 DRDALLKNLRGVSYDGLD----RSVDVAISRLRKKLLDNAAEPYRIKTVRNKGYLFAPHA 237

Query: 226 KDE 228
            + 
Sbjct: 238 WES 240


>gnl|CDD|183099 PRK11361, PRK11361, acetoacetate metabolism regulatory protein
           AtoC; Provisional.
          Length = 457

 Score = 68.3 bits (167), Expect = 2e-12
 Identities = 30/118 (25%), Positives = 62/118 (52%), Gaps = 4/118 (3%)

Query: 2   RILLIEDDKALAHSIELMLKSENFNVYVTDLGEDGIELCKFYEFDAIILDLGLTDIPGFE 61
           RIL+++D+  +   +      + F  +  + G   + L      D +++D+ + ++ G +
Sbjct: 6   RILIVDDEDNVRRMLSTAFALQGFETHCANNGRTALHLFADIHPDVVLMDIRMPEMDGIK 65

Query: 62  VLRALRVAKISTPVCILSGMSSIEDKVRGLQSGADDYISKPFNKEELVARIRAIVRRS 119
            L+ +R  +  TPV +++  + +E  V  L+ GA DY+ KPF+ +EL      IV+R+
Sbjct: 66  ALKEMRSHETRTPVILMTAYAEVETAVEALRCGAFDYVIKPFDLDEL----NLIVQRA 119


>gnl|CDD|183013 PRK11173, PRK11173, two-component response regulator; Provisional.
          Length = 237

 Score = 65.0 bits (159), Expect = 2e-11
 Identities = 55/228 (24%), Positives = 110/228 (48%), Gaps = 12/228 (5%)

Query: 2   RILLIEDDKALAHSIELMLKSENFNVYVTDLGEDGIELCKFYEFDAIILDLGLTDIPGFE 61
            IL++ED+    ++++ + ++E ++V+    G +  ++    + + +I+D+ L    G  
Sbjct: 5   HILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQILSENDINLVIMDINLPGKNGLL 64

Query: 62  VLRALRVAKISTPVCILSGMSSIEDKVRGLQSGADDYISKPFNKEELVARIRAIVRRSRG 121
           + R LR  + +  +  L+G  +  DK+ GL+ GADDYI+KPFN  EL  R R ++ R+  
Sbjct: 65  LARELR-EQANVALMFLTGRDNEVDKILGLEIGADDYITKPFNPRELTIRARNLLSRTMN 123

Query: 122 HAQSLIVTGDL-SVNLDAKTVEVQGHR-IHLTGKEYQMIE-----LLSLRKN--TTLTKE 172
                     + S   +   +++     I   G++Y++       +L   +N     ++ 
Sbjct: 124 LGTVSEERRSVESYKFNGWELDINSRSLISPDGEQYKLPRSEFRAMLHFCENPGKIQSRA 183

Query: 173 MFLNHLYDGRD-EPEVKIIDVFICKLRKKLSNAAGGKNYIETVWGRGY 219
             L  +  GR+ +P  + +DV I ++RK   +       I T+ G GY
Sbjct: 184 ELLKKM-TGRELKPHDRTVDVTIRRIRKHFESTPDTPEIIATIHGEGY 230


>gnl|CDD|181815 PRK09390, fixJ, response regulator FixJ; Provisional.
          Length = 202

 Score = 64.6 bits (158), Expect = 2e-11
 Identities = 34/127 (26%), Positives = 64/127 (50%)

Query: 6   IEDDKALAHSIELMLKSENFNVYVTDLGEDGIELCKFYEFDAIILDLGLTDIPGFEVLRA 65
           ++DD+A+  S+  +L S  F V + +  +  ++      F  ++ D+ +  I G E+LR 
Sbjct: 9   VDDDEAMRDSLAFLLDSAGFEVRLFESAQAFLDALPGLRFGCVVTDVRMPGIDGIELLRR 68

Query: 66  LRVAKISTPVCILSGMSSIEDKVRGLQSGADDYISKPFNKEELVARIRAIVRRSRGHAQS 125
           L+      PV +++G   +   V  ++ GA D+I KPF  E L+  I   + ++   A+S
Sbjct: 69  LKARGSPLPVIVMTGHGDVPLAVEAMKLGAVDFIEKPFEDERLIGAIERALAQAPEAAKS 128

Query: 126 LIVTGDL 132
             V  D+
Sbjct: 129 EAVAADI 135


>gnl|CDD|182412 PRK10365, PRK10365, transcriptional regulatory protein ZraR;
           Provisional.
          Length = 441

 Score = 63.9 bits (155), Expect = 4e-11
 Identities = 36/160 (22%), Positives = 77/160 (48%), Gaps = 14/160 (8%)

Query: 3   ILLIEDDKALAHSIELMLKSENFNVYVTDLGEDGIELCKFYEFDAIILDLGLTDIPGFEV 62
           IL+++DD +    ++ +L+   +NV + + G   +E  +   FD ++ D+ + ++ G   
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALANSGRQALEQVREQVFDLVLCDVRMAEMDGIAT 67

Query: 63  LRALRVAKISTPVCILSGMSSIEDKVRGLQSGADDYISKPFNKEELVARIRAIVRRSRGH 122
           L+ ++    + PV I++  SS+E  V  L++GA DY+ KP + +     ++A + ++  H
Sbjct: 68  LKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFD----NLQATLEKALAH 123

Query: 123 AQSLIVTGDLSVNLDAKTVEVQGHRIHLTGKEYQMIELLS 162
                +  +      +        +  + GK   M  LLS
Sbjct: 124 TH--SIDAETPAVTAS--------QFGMVGKSPAMQHLLS 153


>gnl|CDD|182619 PRK10651, PRK10651, transcriptional regulator NarL; Provisional.
          Length = 216

 Score = 59.7 bits (145), Expect = 7e-10
 Identities = 29/82 (35%), Positives = 44/82 (53%)

Query: 33  GEDGIELCKFYEFDAIILDLGLTDIPGFEVLRALRVAKISTPVCILSGMSSIEDKVRGLQ 92
           GE GIEL +  + D I+LDL +  + G E L  LR   +S  + + S  +  ED V  L+
Sbjct: 41  GEQGIELAESLDPDLILLDLNMPGMNGLETLDKLREKSLSGRIVVFSVSNHEEDVVTALK 100

Query: 93  SGADDYISKPFNKEELVARIRA 114
            GAD Y+ K    E+L+  ++ 
Sbjct: 101 RGADGYLLKDMEPEDLLKALQQ 122


>gnl|CDD|185070 PRK15115, PRK15115, response regulator GlrR; Provisional.
          Length = 444

 Score = 58.7 bits (142), Expect = 1e-09
 Identities = 29/111 (26%), Positives = 58/111 (52%)

Query: 2   RILLIEDDKALAHSIELMLKSENFNVYVTDLGEDGIELCKFYEFDAIILDLGLTDIPGFE 61
            +LL++DD  L   + + L SE ++V   + G++ + +    + D +I DL + ++ G +
Sbjct: 7   HLLLVDDDPGLLKLLGMRLTSEGYSVVTAESGQEALRVLNREKVDLVISDLRMDEMDGMQ 66

Query: 62  VLRALRVAKISTPVCILSGMSSIEDKVRGLQSGADDYISKPFNKEELVARI 112
           +   ++  +   PV IL+   SI D V   Q G   +++KP +++ L   I
Sbjct: 67  LFAEIQKVQPGMPVIILTAHGSIPDAVAATQQGVFSFLTKPVDRDALYKAI 117


>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 = 57.1 bits (138), Expect = 4e-09
 Identities = 28/122 (22%), Positives = 57/122 (46%), Gaps = 4/122 (3%)

Query: 3   ILLIEDDKALAHSIELMLKSENFNVYVTDLGEDGIELCKFYEFDAIILDLGLTDIPGFEV 62
           + +++DD+++   +E  L    + V         +      + D +I D+ +    G ++
Sbjct: 1   VWVVDDDRSIRWVLEKALSRAGYEVRTFGNAASVLRALARGQPDLLITDVRMPGEDGLDL 60

Query: 63  LRALRVAKISTPVCILSGMSSIEDKVRGLQSGADDYISKPFNKEELVARIRAIVRRSRGH 122
           L  ++      PV +++  S ++  V   Q GA +Y+ KPF+ +E V     +V R+  H
Sbjct: 61  LPQIKKRHPQLPVIVMTAHSDLDTAVAAYQRGAFEYLPKPFDLDEAV----TLVERALAH 116

Query: 123 AQ 124
           AQ
Sbjct: 117 AQ 118


>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 = 54.9 bits (133), Expect = 2e-08
 Identities = 19/54 (35%), Positives = 33/54 (61%)

Query: 1  MRILLIEDDKALAHSIELMLKSENFNVYVTDLGEDGIELCKFYEFDAIILDLGL 54
          MRIL+++DD  L   ++ +L+ E + V     GE+ +EL K  + D I+LD+ +
Sbjct: 1  MRILVVDDDPLLRELLKALLEREGYEVDEATDGEEALELLKEEKPDLILLDIMM 54


>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 = 48.6 bits (116), Expect = 1e-06
 Identities = 39/119 (32%), Positives = 62/119 (52%), Gaps = 8/119 (6%)

Query: 1   MRILLIEDDKALAHSIE--LMLKSENFNVYVTDLGEDGIELCKFYEFDAIILDLGLTDIP 58
           +RI++ +D+K   + ++  L  + +   V V   G D +EL K  + D ++LD+ +  + 
Sbjct: 3   IRIVIADDNKEFCNLLKEYLAAQPDMEVVGVAHNGVDALELIKEQQPDVVVLDIIMPHLD 62

Query: 59  GFEVLRALRVAKISTP--VCILS--GMSSIEDKVRGLQSGADDYISKPFNKEELVARIR 113
           G  VL  L   ++S    V +LS  G   I  +   L  GAD Y+ KPF+ E L ARIR
Sbjct: 63  GIGVLEKLNEIELSARPRVIMLSAFGQEKITQRAVAL--GADYYVLKPFDLEILAARIR 119


>gnl|CDD|182956 PRK11091, PRK11091, aerobic respiration control sensor protein
           ArcB; Provisional.
          Length = 779

 Score = 48.4 bits (116), Expect = 2e-06
 Identities = 37/123 (30%), Positives = 62/123 (50%), Gaps = 20/123 (16%)

Query: 1   MRILLIEDDKALAHSIEL-------MLKSENFNVYVTDLGEDGIELCKFYEFDAIILDLG 53
           + ILL+ED       IEL       +L+    +V V   G++ +E+    E+D ++LD+ 
Sbjct: 526 LNILLVED-------IELNVIVARSVLEKLGNSVDVAMTGKEALEMFDPDEYDLVLLDIQ 578

Query: 54  LTDIPGFEVLRALR----VAKISTPVCILSGMSSIEDKVRGLQSGADDYISKPFNKEELV 109
           L D+ G ++ R LR       +  P+  L+  + ++DK   L +G DD +SKP +   L 
Sbjct: 579 LPDMTGLDIARELRERYPREDL-PPLVALTA-NVLKDKKEYLDAGMDDVLSKPLSVPALT 636

Query: 110 ARI 112
           A I
Sbjct: 637 AMI 639


>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 = 47.5 bits (113), Expect = 3e-06
 Identities = 34/117 (29%), Positives = 55/117 (47%), Gaps = 3/117 (2%)

Query: 2   RILLIEDDKALAHSIELMLKSENFNVYVTDLGEDGIELCKFYEFDAIILDLGLTDIPGFE 61
           R+LL+ED++      +  L      V + + G+  +E    + FD  +LD+ L D  G  
Sbjct: 704 RVLLVEDNEVNQMVAQGFLTRLGHKVTLAESGQSALECFHQHAFDLALLDINLPDGDGVT 763

Query: 62  VLRALRV---AKISTPVCILSGMSSIEDKVRGLQSGADDYISKPFNKEELVARIRAI 115
           +L+ LR    AK        S     ED  + L +G D +++KP  +E+L A I  I
Sbjct: 764 LLQQLRAIYGAKNEVKFIAFSAHVFNEDVAQYLAAGFDGFLAKPVVEEQLTAMIAVI 820


>gnl|CDD|170568 PRK10610, PRK10610, chemotaxis regulatory protein CheY;
           Provisional.
          Length = 129

 Score = 46.9 bits (111), Expect = 4e-06
 Identities = 29/121 (23%), Positives = 59/121 (48%), Gaps = 3/121 (2%)

Query: 1   MRILLIEDDKALAHSIELMLKSENF-NVYVTDLGEDGIELCKFYEFDAIILDLGLTDIPG 59
           ++ L+++D   +   +  +LK   F NV   + G D +   +   F  +I D  + ++ G
Sbjct: 6   LKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGFGFVISDWNMPNMDG 65

Query: 60  FEVLRALRV--AKISTPVCILSGMSSIEDKVRGLQSGADDYISKPFNKEELVARIRAIVR 117
            E+L+ +R   A  + PV +++  +  E+ +   Q+GA  Y+ KPF    L  ++  I  
Sbjct: 66  LELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFE 125

Query: 118 R 118
           +
Sbjct: 126 K 126


>gnl|CDD|182842 PRK10923, glnG, nitrogen regulation protein NR(I); Provisional.
          Length = 469

 Score = 45.6 bits (108), Expect = 1e-05
 Identities = 21/80 (26%), Positives = 40/80 (50%)

Query: 46  DAIILDLGLTDIPGFEVLRALRVAKISTPVCILSGMSSIEDKVRGLQSGADDYISKPFNK 105
           D ++ D+ +  + G  +L+ ++      PV I++  S ++  V   Q GA DY+ KPF+ 
Sbjct: 49  DVLLSDIRMPGMDGLALLKQIKQRHPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDI 108

Query: 106 EELVARIRAIVRRSRGHAQS 125
           +E VA +   +   +   Q 
Sbjct: 109 DEAVALVERAISHYQEQQQP 128


>gnl|CDD|185245 PRK15347, PRK15347, two component system sensor kinase SsrA;
           Provisional.
          Length = 921

 Score = 43.5 bits (103), Expect = 5e-05
 Identities = 24/106 (22%), Positives = 52/106 (49%), Gaps = 4/106 (3%)

Query: 1   MRILLIEDDKALAHSIELMLKSENFNVYVTDLGEDGIELCKFYEFDAIILDLGLTDIPGF 60
           ++ILL++D +     I +ML      V     G + +EL + + FD +++D+ +  + G 
Sbjct: 691 LQILLVDDVETNRDIIGMMLVELGQQVTTAASGTEALELGRQHRFDLVLMDIRMPGLDGL 750

Query: 61  EVLRALR--VAKIST--PVCILSGMSSIEDKVRGLQSGADDYISKP 102
           E  +  R     +     +  L+  ++ E+  R  ++G + Y++KP
Sbjct: 751 ETTQLWRDDPNNLDPDCMIVALTANAAPEEIHRCKKAGMNHYLTKP 796


>gnl|CDD|182652 PRK10693, PRK10693, response regulator of RpoS; Provisional.
          Length = 303

 Score = 43.4 bits (103), Expect = 5e-05
 Identities = 23/75 (30%), Positives = 36/75 (48%)

Query: 28  YVTDLGEDGIELCKFYEFDAIILDLGLTDIPGFEVLRALRVAKISTPVCILSGMSSIEDK 87
            +   G D +EL   +  D II DL +  + G E +  LR     TPV ++S   ++ D 
Sbjct: 1   VLAANGVDALELLGGFTPDLIICDLAMPRMNGIEFVEHLRNRGDQTPVLVISATENMADI 60

Query: 88  VRGLQSGADDYISKP 102
            + L+ G  D + KP
Sbjct: 61  AKALRLGVQDVLLKP 75


>gnl|CDD|185267 PRK15369, PRK15369, two component system sensor kinase SsrB;
           Provisional.
          Length = 211

 Score = 43.1 bits (102), Expect = 7e-05
 Identities = 42/166 (25%), Positives = 78/166 (46%), Gaps = 13/166 (7%)

Query: 2   RILLIEDDKALAHSIELMLKS-ENFN-VYVTDLGEDGIELCKFYEFDAIILDLGLTDIPG 59
           +ILL++D + + + I+ ML     +  V   D G +    C+  E D +ILDLGL  + G
Sbjct: 5   KILLVDDHELIINGIKNMLAPYPRYKIVGQVDNGLEVYNACRQLEPDIVILDLGLPGMNG 64

Query: 60  FEVLRALRVAKISTPVCILSGMSSIEDKVRGLQSGADDYISKPFNKEELVARIRAIVRRS 119
            +V+  L     +  + +L+         R L +GA  Y+ K   ++ L+A I+ +   +
Sbjct: 65  LDVIPQLHQRWPAMNILVLTARQEEHMASRTLAAGALGYVLKKSPQQILLAAIQTV---A 121

Query: 120 RGHAQSLIVTGDLSVNLD---AKTVEVQGHRIHLTGKEYQMIELLS 162
            G     I   D ++N +   A       +   LT +E Q+++L++
Sbjct: 122 VGK--RYI---DPALNREAILALLNADDTNPPLLTPRERQILKLIT 162


>gnl|CDD|182169 PRK09959, PRK09959, hybrid sensory histidine kinase in two-component
            regulatory system with EvgA; Provisional.
          Length = 1197

 Score = 42.0 bits (98), Expect = 1e-04
 Identities = 29/110 (26%), Positives = 50/110 (45%), Gaps = 9/110 (8%)

Query: 4    LLIEDDKALAHSIELMLKSENFNV--YVTDLGEDGIEL---CKFYEFDAIILDLGLTDIP 58
            +LI DD    H    +L     N+  Y  D   DG++         +D +I D+ + ++ 
Sbjct: 961  ILIADD----HPTNRLLLKRQLNLLGYDVDEATDGVQALHKVSMQHYDLLITDVNMPNMD 1016

Query: 59   GFEVLRALRVAKISTPVCILSGMSSIEDKVRGLQSGADDYISKPFNKEEL 108
            GFE+ R LR    S P+  L+  +   ++ +GL  G +  + KP   + L
Sbjct: 1017 GFELTRKLREQNSSLPIWGLTANAQANEREKGLSCGMNLCLFKPLTLDVL 1066


>gnl|CDD|182431 PRK10403, PRK10403, transcriptional regulator NarP; Provisional.
          Length = 215

 Score = 42.1 bits (99), Expect = 1e-04
 Identities = 31/115 (26%), Positives = 57/115 (49%), Gaps = 2/115 (1%)

Query: 2   RILLIEDDKALAHSIELMLKSE-NFNVYV-TDLGEDGIELCKFYEFDAIILDLGLTDIPG 59
           ++L+++D   +   +  +L+ +  F V      G   I+L    + D I+LDL +  + G
Sbjct: 8   QVLIVDDHPLMRRGVRQLLELDPGFEVVAEAGDGASAIDLANRLDPDVILLDLNMKGMSG 67

Query: 60  FEVLRALRVAKISTPVCILSGMSSIEDKVRGLQSGADDYISKPFNKEELVARIRA 114
            + L ALR   ++  + IL+   +  D    + +GAD Y+ K  + E L+  IRA
Sbjct: 68  LDTLNALRRDGVTAQIIILTVSDASSDVFALIDAGADGYLLKDSDPEVLLEAIRA 122


>gnl|CDD|182154 PRK09935, PRK09935, transcriptional regulator FimZ; Provisional.
          Length = 210

 Score = 41.0 bits (96), Expect = 2e-04
 Identities = 26/101 (25%), Positives = 51/101 (50%), Gaps = 2/101 (1%)

Query: 3   ILLIEDDKALAHSIELML-KSENFNVYV-TDLGEDGIELCKFYEFDAIILDLGLTDIPGF 60
           +++++    +  SIE++L K+    + + TD     I+  +    D II+D+ L    GF
Sbjct: 6   VIIMDTHPIIRMSIEVLLQKNSELQIVLKTDDYRITIDYLRTRPVDLIIMDIDLPGTDGF 65

Query: 61  EVLRALRVAKISTPVCILSGMSSIEDKVRGLQSGADDYISK 101
             L+ ++  + +  V  LS  S      R +Q+GA+ ++SK
Sbjct: 66  TFLKRIKQIQSTVKVLFLSSKSECFYAGRAIQAGANGFVSK 106


>gnl|CDD|184495 PRK14084, PRK14084, two-component response regulator; Provisional.
          Length = 246

 Score = 40.1 bits (94), Expect = 5e-04
 Identities = 38/160 (23%), Positives = 76/160 (47%), Gaps = 11/160 (6%)

Query: 1   MRILLIEDDKALAHSIELMLKSENFNVYVTDLGE---DGIELCKFYEFDAIILDLGLTDI 57
           M+ L++ DD+ LA +    L +E       +  E   + +E     ++D I LD+ L D 
Sbjct: 1   MKALIV-DDEPLARNELTYLLNEIGGFEEINEAENVKETLEALLINQYDIIFLDINLMDE 59

Query: 58  PGFEVLRALRVAKISTPVCILSGMSSIEDKVRGLQSGADDYISKPFNK---EELVARIRA 114
            G E+  A ++ K+  P  I+   +  +  V+  +  A DYI KPF +   E+ V ++RA
Sbjct: 60  SGIEL--AAKIQKMKEPPAIIFATAHDQFAVKAFELNATDYILKPFEQKRIEQAVNKVRA 117

Query: 115 IVRRSRGHAQSLIVTGDLSVNLDAKTVEVQGHRIHLTGKE 154
              +   +A ++      + +  +  +E+   +IH+  ++
Sbjct: 118 TKAKDDNNASAIANDMSANFD-QSLPIEID-DKIHMLNQQ 155


>gnl|CDD|179106 PRK00742, PRK00742, chemotaxis-specific methylesterase;
           Provisional.
          Length = 354

 Score = 38.2 bits (90), Expect = 0.002
 Identities = 30/101 (29%), Positives = 47/101 (46%), Gaps = 16/101 (15%)

Query: 33  GEDGIELCKFYEFDAIILDLGLTDIPGFEVLRALRVAKISTPVCILSGMSSIED--KV-- 88
           G +  E  K    D I LD+ +  + G + L  + +    TPV ++S  S  E   ++  
Sbjct: 38  GLEAREKIKKLNPDVITLDVEMPVMDGLDALEKI-MRLRPTPVVMVS--SLTERGAEITL 94

Query: 89  RGLQSGADDYISKPF---------NKEELVARIRAIVRRSR 120
           R L+ GA D+++KPF          KEEL  ++RA  R   
Sbjct: 95  RALELGAVDFVTKPFLGISLGMDEYKEELAEKVRAAARARV 135


>gnl|CDD|182408 PRK10360, PRK10360, DNA-binding transcriptional activator UhpA;
           Provisional.
          Length = 196

 Score = 36.5 bits (84), Expect = 0.006
 Identities = 32/131 (24%), Positives = 59/131 (45%), Gaps = 31/131 (23%)

Query: 36  GIELCKFYEFDAIILDLGLTDIPGFEVLRALRVAKISTPVCILSGMSSIEDKV----RGL 91
           G+++C        I D+ + DI G E+L  L       P  + + M S+ D      + L
Sbjct: 47  GVQVC--------ICDISMPDISGLELLSQL-------PKGMATIMLSVHDSPALVEQAL 91

Query: 92  QSGADDYISKPFNKEELVARIRAIVRRSRGHAQSLIVTGDLSVNLDAKTVEVQGHRIHLT 151
            +GA  ++SK  + +EL+A +  +            +T D+++ L +      G +  LT
Sbjct: 92  NAGARGFLSKRCSPDELIAAVHTVA------TGGCYLTPDIAIKLAS------GRQDPLT 139

Query: 152 GKEYQMIELLS 162
            +E Q+ E L+
Sbjct: 140 KRERQVAEKLA 150


>gnl|CDD|181897 PRK09483, PRK09483, response regulator; Provisional.
          Length = 217

 Score = 36.2 bits (84), Expect = 0.007
 Identities = 26/92 (28%), Positives = 48/92 (52%), Gaps = 8/92 (8%)

Query: 33  GEDGIELCKFYEFDAIILDLGLTDIPGFEVLRALRVAKISTPVCILSGMSSIED----KV 88
           GED ++ C+    D +++D+ +  I G E  R  ++ + +  V I+      E+    KV
Sbjct: 36  GEDAVKWCRTNAVDVVLMDMNMPGIGGLEATR--KILRYTPDVKIIMLTVHTENPLPAKV 93

Query: 89  RGLQSGADDYISKPFNKEELVARIRAIVRRSR 120
             +Q+GA  Y+SK    +E+V+ IR++    R
Sbjct: 94  --MQAGAAGYLSKGAAPQEVVSAIRSVHSGQR 123


>gnl|CDD|182968 PRK11107, PRK11107, hybrid sensory histidine kinase BarA;
           Provisional.
          Length = 919

 Score = 34.4 bits (80), Expect = 0.023
 Identities = 25/104 (24%), Positives = 53/104 (50%), Gaps = 2/104 (1%)

Query: 1   MRILLIEDDKALAHSIELMLKSENFNVYVTDLGEDGIELCKFYEFDAIILDLGLTDIPGF 60
           + ++ ++D+ A    I  +L+ +  +V + D G   +E  K   FD I++D+ +  + G 
Sbjct: 668 LTVMAVDDNPANLKLIGALLEEQVEHVVLCDSGHQAVEQAKQRPFDLILMDIQMPGMDGI 727

Query: 61  EVLRALRVAKI--STPVCILSGMSSIEDKVRGLQSGADDYISKP 102
                +R      +TP+  ++  +   ++ R L +G DDY++KP
Sbjct: 728 RACELIRQLPHNQNTPIIAVTAHAMAGERERLLSAGMDDYLAKP 771



 Score = 29.0 bits (66), Expect = 1.1
 Identities = 28/113 (24%), Positives = 45/113 (39%), Gaps = 12/113 (10%)

Query: 1   MRILLIEDDKALAHSIELMLKSENFNV-YVTDLGEDGIELCKFYEFDAIILDLGLTDIPG 59
            R+L +E + A A +   +L      V Y   L +          +D ++L L +T    
Sbjct: 537 KRLLYVEPNSAAAQATLDILSETPLEVTYSPTLSQLPEA-----HYDILLLGLPVTFREP 591

Query: 60  FEVLRA-LRVAKISTPVCIL---SGMSSIEDKVRGLQSGADDYISKPFNKEEL 108
             +L   L  AK  T   IL        + +++   Q GAD  +SKP +   L
Sbjct: 592 LTMLHERLAKAKSMTDFLILALPCHEQVLAEQL--KQDGADACLSKPLSHTRL 642


>gnl|CDD|182168 PRK09958, PRK09958, DNA-binding transcriptional activator EvgA;
           Provisional.
          Length = 204

 Score = 34.1 bits (78), Expect = 0.029
 Identities = 26/112 (23%), Positives = 51/112 (45%), Gaps = 2/112 (1%)

Query: 5   LIEDDKALAH-SIELMLKSENFNVYVT-DLGEDGIELCKFYEFDAIILDLGLTDIPGFEV 62
           +I DD  LA  +I  +L   +  +      G   ++  +  + D +I+D+ +  + G +V
Sbjct: 4   IIIDDHPLAIAAIRNLLIKNDIEILAELTEGGSAVQRVETLKPDIVIIDVDIPGVNGIQV 63

Query: 63  LRALRVAKISTPVCILSGMSSIEDKVRGLQSGADDYISKPFNKEELVARIRA 114
           L  LR  + S  + I+S  +          +GA+ ++SK      ++A I A
Sbjct: 64  LETLRKRQYSGIIIIVSAKNDHFYGKHCADAGANGFVSKKEGMNNIIAAIEA 115


>gnl|CDD|182772 PRK10841, PRK10841, hybrid sensory kinase in two-component
           regulatory system with RcsB and YojN; Provisional.
          Length = 924

 Score = 33.4 bits (77), Expect = 0.057
 Identities = 31/128 (24%), Positives = 59/128 (46%), Gaps = 13/128 (10%)

Query: 1   MRILLIEDDKALAHSIELML-----KSENFNVYVTDLGEDGIELCKFYEFDAIILDLGLT 55
           M IL+++D     H I   L      S  +     + G D + +      D ++ D+ + 
Sbjct: 802 MMILVVDD-----HPINRRLLADQLGSLGYQCKTANDGVDALNVLSKNHIDIVLTDVNMP 856

Query: 56  DIPGFEVLRALRVAKISTPVCILSGMSSIEDKVRGLQSGADDYISKPFNKEEL---VARI 112
           ++ G+ + + LR   ++ PV  ++  +  E+K R L++G D  +SKP   + L   +   
Sbjct: 857 NMDGYRLTQRLRQLGLTLPVIGVTANALAEEKQRCLEAGMDSCLSKPVTLDVLKQTLTVY 916

Query: 113 RAIVRRSR 120
              VR+SR
Sbjct: 917 AERVRKSR 924


>gnl|CDD|182454 PRK10430, PRK10430, DNA-binding transcriptional activator DcuR;
           Provisional.
          Length = 239

 Score = 33.2 bits (76), Expect = 0.061
 Identities = 17/60 (28%), Positives = 27/60 (45%)

Query: 44  EFDAIILDLGLTDIPGFEVLRALRVAKISTPVCILSGMSSIEDKVRGLQSGADDYISKPF 103
             D I+LD+ +    G ++L  L  A   + V ++S  +        L  G  DY+ KPF
Sbjct: 49  PIDLILLDIYMQQENGLDLLPVLHEAGCKSDVIVISSAADAATIKDSLHYGVVDYLIKPF 108


>gnl|CDD|138914 PRK12370, PRK12370, invasion protein regulator; Provisional.
          Length = 553

 Score = 32.9 bits (75), Expect = 0.069
 Identities = 23/92 (25%), Positives = 45/92 (48%), Gaps = 3/92 (3%)

Query: 128 VTGDLSVNLDAKTVEVQGHRIHLTGKEYQMIELLSLRKNTTLTKEMFLNHLYDGRDEPEV 187
           V  D  +N+D   +     ++++  KEY ++ +L       ++K   L+ ++   +  E 
Sbjct: 15  VFDDFILNMDGSLLR-SEKKVNIPPKEYAVLVILLEAAGEIVSKNTLLDQVWGDAEVNEE 73

Query: 188 KIIDVFICKLRKKLSNAAGGKNYIETVWGRGY 219
            +    I  LR+ LS     + YIET++G+GY
Sbjct: 74  SLTRC-IYALRRILSEDKEHR-YIETLYGQGY 103


>gnl|CDD|182208 PRK10046, dpiA, two-component response regulator DpiA; Provisional.
          Length = 225

 Score = 32.3 bits (73), Expect = 0.11
 Identities = 20/73 (27%), Positives = 29/73 (39%)

Query: 48  IILDLGLTDIPGFEVLRALRVAKISTPVCILSGMSSIEDKVRGLQSGADDYISKPFNKEE 107
           I+LD  L D  G  +L  L  A     V   +  S +E     ++ G  DY+ KP   E 
Sbjct: 54  ILLDNYLPDGRGINLLHELVQAHYPGDVVFTTAASDMETVSEAVRCGVFDYLIKPIAYER 113

Query: 108 LVARIRAIVRRSR 120
           L   +    +R  
Sbjct: 114 LGQTLTRFRQRKH 126


>gnl|CDD|178599 PLN03029, PLN03029, type-a response regulator protein; Provisional.
          Length = 222

 Score = 29.6 bits (66), Expect = 0.70
 Identities = 26/122 (21%), Positives = 52/122 (42%), Gaps = 22/122 (18%)

Query: 3   ILLIEDDKALAHSIELMLKSENFNVYVTDLGEDGIELCKFYEFDA--------------- 47
           +L ++D       IE +LK+ ++ V   D G   ++    +E D                
Sbjct: 11  VLAVDDSLIDRKLIEKLLKTSSYQVTTVDSGSKALKFLGLHEDDRSNPDTPSVSPNSHQE 70

Query: 48  -----IILDLGLTDIPGFEVLRALRVAKI--STPVCILSGMSSIEDKVRGLQSGADDYIS 100
                II D  +  + G+++L+ ++ +    + PV I+S  +      R L+ GA+++  
Sbjct: 71  VEVNLIITDYCMPGMTGYDLLKKIKESSSLRNIPVVIMSSENVPSRITRCLEEGAEEFFL 130

Query: 101 KP 102
           KP
Sbjct: 131 KP 132


>gnl|CDD|177999 PLN02371, PLN02371, phosphoglucosamine mutase family protein.
          Length = 583

 Score = 28.9 bits (65), Expect = 1.2
 Identities = 37/128 (28%), Positives = 53/128 (41%), Gaps = 20/128 (15%)

Query: 93  SGADDYISKPFNKEELVARIRAIVRRSRGHAQSLIVTGDLSVNLDAKT--VEVQGHRIHL 150
           S   D   +  N+  L+A + AIV     H  + IVT   SV  D  T  +E +G + H 
Sbjct: 340 SAVVDSSGREINRNRLIALMSAIVLEE--HPGTTIVTD--SVTSDGLTTFIEKKGGKHHR 395

Query: 151 TGKEY-----QMIELLSLRKNTTLTKE------MFLNHLYDGRDEPEVKIIDVFICKLRK 199
             + Y     + + L S  + T L  E      +  NH  D      VKII   I  +R 
Sbjct: 396 FKRGYKNVIDKGVRLNSDGEETHLMIETSGHGALKENHFLDDGAYLAVKII---IELVRM 452

Query: 200 KLSNAAGG 207
           + + A GG
Sbjct: 453 RAAGAGGG 460


>gnl|CDD|181239 PRK08125, PRK08125, bifunctional UDP-glucuronic acid
           decarboxylase/UDP-4-amino-4-deoxy-L-arabinose
           formyltransferase; Validated.
          Length = 660

 Score = 27.6 bits (62), Expect = 2.7
 Identities = 10/25 (40%), Positives = 15/25 (60%)

Query: 14  HSIELMLKSENFNVYVTDLGEDGIE 38
           H  E +L+ +N+ VY  D+G D I 
Sbjct: 330 HLTERLLRDDNYEVYGLDIGSDAIS 354


>gnl|CDD|184141 PRK13557, PRK13557, histidine kinase; Provisional.
          Length = 540

 Score = 27.7 bits (62), Expect = 2.7
 Identities = 33/128 (25%), Positives = 58/128 (45%), Gaps = 24/128 (18%)

Query: 2   RILLIEDDKALAHSIELMLKSENFNVYVTDLGEDGIELCKFYEFDAIILDLGLTDI--PG 59
            IL+++D   +A    ++L+   +   V   G + +E+          +DL  TD+  PG
Sbjct: 417 TILIVDDRPDVAELARMILEDFGYRTLVASNGREALEILD----SHPEVDLLFTDLIMPG 472

Query: 60  --------FEVLRALRVAKISTPVCILSGM--SSIEDKVRGLQSGAD-DYISKPFNKEEL 108
                    E  R  R  KI   V + +G   +SIE   R    G++ D ++KP+ + EL
Sbjct: 473 GMNGVMLAREARR--RQPKIK--VLLTTGYAEASIE---RTDAGGSEFDILNKPYRRAEL 525

Query: 109 VARIRAIV 116
             R+R ++
Sbjct: 526 ARRVRMVL 533


>gnl|CDD|180904 PRK07239, PRK07239, bifunctional uroporphyrinogen-III
           synthetase/response regulator domain protein; Validated.
          Length = 381

 Score = 27.3 bits (61), Expect = 3.5
 Identities = 30/124 (24%), Positives = 49/124 (39%), Gaps = 24/124 (19%)

Query: 108 LVARIRAIVRR-SRGHAQSLIVTGDLSVNLDAKTVEVQGHRIHLTGKEYQM-------IE 159
           L A  R I        A++L   G          +E++GH + + G+   +       + 
Sbjct: 265 LGALARHITEELPLRRARTLRAAG--------HVLEIRGHAVVVDGEVKPLSPAPMALLR 316

Query: 160 LLSLRKNTTLTKEMFLNHL-YDGRDEPEVKIIDVFICKLRKKLSNAAGGKNYIETVWGRG 218
            L+ R    +++E  L  L   G DE  V   +  + +LR  L    G    ++TV  RG
Sbjct: 317 ALAARPGRVVSREDLLAALPGGGTDEHAV---ETAVARLRTAL----GDPKLVQTVVKRG 369

Query: 219 YVLR 222
           Y L 
Sbjct: 370 YRLA 373


>gnl|CDD|182646 PRK10683, PRK10683, putrescine transporter subunit: membrane
           component of ABC superfamily; Provisional.
          Length = 317

 Score = 27.4 bits (61), Expect = 3.6
 Identities = 18/39 (46%), Positives = 24/39 (61%), Gaps = 6/39 (15%)

Query: 48  IILDLG----LTDIPGF--EVLRALRVAKISTPVCILSG 80
           I L+LG    LTD P +    L++L+VA IST  C+L G
Sbjct: 79  ITLNLGNFLQLTDDPLYFDAYLQSLQVAAISTLCCLLIG 117


>gnl|CDD|149141 pfam07902, Gp58, gp58-like protein.  Sequences found in this family
           are derived from a number of bacteriophage and prophage
           proteins. They are similar to gp58, a minor structural
           protein of Lactococcus delbrueckii bacteriophage LL-H.
          Length = 601

 Score = 27.2 bits (60), Expect = 3.9
 Identities = 23/95 (24%), Positives = 40/95 (42%), Gaps = 21/95 (22%)

Query: 82  SSIEDKVRGLQ---SGADDYISKPFNK-----EELVAR--IRAIVRRS---------RGH 122
           SS+   V GLQ   SG +  I   F +     ++ V R  + +I+ +S            
Sbjct: 292 SSLTQTVAGLQSTVSGPNSKIQSRFTQLAGLIDQKVTRGGVESIISQSGDSIMLAIKAKL 351

Query: 123 AQSLIVTGDL--SVNLDAKTVEVQGHRIHLTGKEY 155
            QS +   ++  ++NL+   V++ G  I L G   
Sbjct: 352 PQSKMSASEIISAINLNRYGVKISGKNIALDGNTT 386


>gnl|CDD|162015 TIGR00735, hisF, imidazoleglycerol phosphate synthase, cyclase
          subunit. 
          Length = 254

 Score = 26.2 bits (58), Expect = 7.4
 Identities = 12/31 (38%), Positives = 19/31 (61%), Gaps = 1/31 (3%)

Query: 67 RVA-KISTPVCILSGMSSIEDKVRGLQSGAD 96
          R A  +  P+ +  G+ SIED  + L++GAD
Sbjct: 68 RTAETVFIPLTVGGGIKSIEDVDKLLRAGAD 98


>gnl|CDD|131814 TIGR02767, TraG-Ti, Ti-type conjugative transfer system protien
           TraG.  This protein is found in the Agrobacterium
           tumefaciens Ti plasmid tra region responsible for
           conjugative transfer of the entire plasmid among
           Agrobacterium strains. The protein is distantly related
           to the F-type conjugation system TraG protein. Both of
           these systems are examples of type IV secretion systems.
          Length = 623

 Score = 26.0 bits (57), Expect = 8.2
 Identities = 17/52 (32%), Positives = 22/52 (42%), Gaps = 4/52 (7%)

Query: 1   MRILLIEDDKALAHSIELMLKSENFNVYVTDLGEDG----IELCKFYEFDAI 48
           MRIL    D+   + I LML  ++        G DG     E C F  + AI
Sbjct: 480 MRILEEARDRGRKYGISLMLIYQSLGQLREHFGRDGASSWFESCSFISYAAI 531


>gnl|CDD|179553 PRK03202, PRK03202, 6-phosphofructokinase; Provisional.
          Length = 320

 Score = 26.2 bits (59), Expect = 8.6
 Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 4/41 (9%)

Query: 90  GLQSGADDYI--SKPFNKEELVARIRAIVRRSRGHAQSLIV 128
           G+  GA+  +    PF+ EEL A+I+    R RG   ++IV
Sbjct: 181 GIAGGAEVILIPEVPFDIEELCAKIKK--GRERGKKHAIIV 219


>gnl|CDD|179939 PRK05111, PRK05111, acetylornithine deacetylase; Provisional.
          Length = 383

 Score = 25.9 bits (58), Expect = 8.8
 Identities = 12/32 (37%), Positives = 17/32 (53%), Gaps = 5/32 (15%)

Query: 52  LGLTDIPGF-----EVLRALRVAKISTPVCIL 78
           LG  D+ GF     E LR + + K+  P+ IL
Sbjct: 107 LGTADMKGFFAFILEALRDIDLTKLKKPLYIL 138


>gnl|CDD|161761 TIGR00200, cinA_nterm, competence/damage-inducible protein CinA
           N-terminal domain.  cinA is a DNA damage- or
           competence-inducible protein that is polycistronic with
           recA in a number of species.
          Length = 413

 Score = 26.0 bits (57), Expect = 8.9
 Identities = 11/32 (34%), Positives = 15/32 (46%)

Query: 111 RIRAIVRRSRGHAQSLIVTGDLSVNLDAKTVE 142
           R++ I+R +   A  LI  G L    D  T E
Sbjct: 48  RLKTIIRIASERADVLIFNGGLGPTSDDLTAE 79


  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
   0.320    0.138    0.391 

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: 3,832,395
Number of extensions: 243790
Number of successful extensions: 605
Number of sequences better than 10.0: 1
Number of HSP's gapped: 560
Number of HSP's successfully gapped: 81
Length of query: 236
Length of database: 5,994,473
Length adjustment: 90
Effective length of query: 146
Effective length of database: 4,049,753
Effective search space: 591263938
Effective search space used: 591263938
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (25.5 bits)