Citrus Sinensis ID: 039733

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------40
Protein Sequence
MCYEQKEVGNGVAGEGHGLGSSEEDESRVDDAVNSNNGPGGTIQVHDGFQISQQQQPQGSVIRWERFLPTRSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESSGSGSGSGSESGTQTKKSAKSKSNNGSENDSSSGDELENGSNGLSIRDGSDNGSGTQSSWTKKAAEVDSPQPISPRYQSADDSICAQVIHTKPESFSNGWVHLNEPKDGLEQDEQPDGVAMHKGLEMQVSENADLKCDCQHEKKSTQQTSKKKIKLPEVDSKPFDNKQLEVDNENICGKRRDQATSTSSANANHANPHAEIRDFDTPSGPSDISHVKETPCLELTLKRMRGVEDDQSAANEDCNVLRHSIFSAFSKYDLNLKALNFRVFSKLK
Secondary Structure (PSIPRED)
ccEEEccccccccccccccccccccccEEcccccccccccccEEEEcccccccccccccccccccccccccccEEEEEEccHHHHHHHHHHHHccccEEEEEccHHHHHHHHHHHcccccEEEEccccccccccccHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHccccccccccccccccccccccccccccccccccccccEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
ccccEEEcccccccccccccccccccccEEEccccccccccEEEccccccccccccccccEEEEEccccccEEEEEEEEcccHHHHHHHHHHHHcccEEEEcccHHHHHHHHHcccccccEEEEEEEccccHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccEEEEEEEcccccccccccccccccccEEEccccccccccccccccHHccccccccccccccccccEcccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHccccHHHHHccccccccccccccccccccEEEcccccccccccccccccHccHcccccccHHHHHHHHHHHHcEEEHcccc
Coil and Loop (DISEMBL)
mcyeqkevgngvageghglgsseedesrvddavnsnngpggtiqvhdgfqisqqqqpqgsvirwerflptrSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIvltessgsgsgsgsesgtqtkksaksksnngsendsssgdelengsnglsirdgsdngsgtqsswtkkaaevdspqpispryqsaddsicaqvihtkpesfsngwvhlnepkdgleqdeqpdgvamhkGLEMQvsenadlkcdcqhekkstqqtskkkiklpevdskpfdnkqlevdnenicgkrrdqatstssananhanphaeirdfdtpsgpsdishvketpclELTLKRmrgveddqsaaneDCNVLRHSIFSAFSKYDLNLKALNFRVFSKLK
Flexible Loop (DISEMBL)
mcyeqkevgngvageghglgsseedESRVDDAVNSNNGPGGTIQVHDGFQISQQQQPQGSVIRWERFLPTRSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTessgsgsgsgsesgtqtkksaksksnngsendsssgdelenGSNGLSIRDGSDNGSGTQSSWTKKAAEVDSPQPISPRYQSADDSICAQVIHTKPESFSNGWVHLNEPKDGLEQDEQPDGVAMHKGLEMQVSENADLKCDCQHekkstqqtskkkiklpevdskpfdnkqlevdnenicgKRRDQAtstssananhanphaEIRDFDTPSGPSDISHVKETPCLELTLKRMRGVEDDQSAANEDCNVLRHSIFSafskydlnlKALNFRVFSKLK
Low Complexity Region (SEG)
MCYEQKEVGNGVAGEGHGLGSSEEDESRVDDAVNSNNGPGGTIQVHDGFqisqqqqpqGSVIRWERFLPTRSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTessgsgsgsgsesgTQTkksaksksnngsendsssgdeLENGSNGLSIRDGSDNGSGTQSSWTKKAAEVDSPQPISPRYQSADDSICAQVIHTKPESFSNGWVHLNEPKDGLEQDEQPDGVAMHKGLEMQVSENADLKCDCQHEkkstqqtskkkIKLPEVDSKPFDNKQLEVDNENICGKRRDQatstssananhanphaEIRDFDTPSGPSDISHVKETPCLELTLKRMRGVEDDQSAANEDCNVLRHSIFSAFSKYDLNLKALNFRVFSKLK
Disordered region (IsUnstruct)
*************************************************************IRWERFLPTRSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVL**************************************************************************************ICAQVIHT****FSNGWVH******************************************************************************************************************************************EDCNVLRHSIFSAFSKYDLNLKALNFRVF****
Disordered Region (DISOPRED)
MCYEQKEVGNGVAG******************************************************PTRSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESSG****************************************************************************************************************************************************************************************************************************ELT*****************CNVLRHSIFSAFSKYDLNLKALNFRVFSKL*
Disordered Region (DISEMBL)
MCYEQKEVGNGVAGEG**************DAVNSNNGPGGTIQVHDGFQI********SVIRWERFLPTRSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTE****************************************GSNGLSIRDG************************SPRYQSADDSICAQVIHTKPESFSNGWVHLNEPKDGLEQDEQPDGVAMHKGLEMQVSENADLKCDCQ**************KLPEVDSKPFDNKQLEVDNENICGK**************HANPHAEIRDFDTPSGPSDISHVKETPCLELTLKRMRGVEDDQSAANEDCNVLRHSIFSAFSKYDLNLKALNFRVFSKLK
Disordered Region (DISPRO)
*CY***EV********************VDD*******PGGTIQV**GFQ******PQGSVIRWERFLPTRSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESSGSGSGSGSESGTQTKKSA**************************************SSWTKKAAEVDSPQ***********SICAQ***********************************************************************************************QATSTS****N*************************************************C**L*HSIFSAFSKYDLNLKALNFRVFSKL*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MCYEQKEVGNGVAGEGHGLGSSEEDESRVDDAVNSNNGPGGTIQVHDGFQISQQQQPQGSVIRWERFLPTRSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESSGSGSGSGSESGTQTKKSAKSKSNNGSENDSSSGDELENGSNGLSIRDGSDNGSGTQSSWTKKAAEVDSPQPISPRYQSADDSICAQVIHTKPESFSNGWVHLNEPKDGLEQDEQPDGVAMHKGLEMQVSENADLKCDCQHEKKSTQQTSKKKIKLPEVDSKPFDNKQLEVDNENICGKRRDQATSTSSANANHANPHAEIRDFDTPSGPSDISHVKETPCLELTLKRMRGVEDDQSAANEDCNVLRHSIFSAFSKYDLNLKALNFRVFSKLK
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	399	2.2.26 [Sep-21-2011]
Q9LVG4	495	Two-component response re	no	no	0.338	0.272	0.550	3e-31
A2XFB7	767	Two-component response re	N/A	no	0.278	0.144	0.52	2e-26
Q10N34	767	Two-component response re	yes	no	0.278	0.144	0.512	6e-26
Q93WK5	727	Two-component response re	no	no	0.248	0.136	0.538	6e-24
A2YQ93	742	Two-component response re	N/A	no	0.581	0.312	0.366	5e-21
Q0D3B6	742	Two-component response re	no	no	0.581	0.312	0.359	4e-19
Q8L500	468	Two-component response re	no	no	0.197	0.168	0.443	1e-16
Q6LA42	558	Two-component response re	no	no	0.162	0.116	0.538	1e-16
Q689G6	623	Two-component response re	no	no	0.157	0.101	0.507	3e-12

>sp|Q9LVG4|APRR3_ARATH Two-component response regulator-like APRR3 OS=Arabidopsis thaliana GN=APRR3 PE=1 SV=1

 Score =  136 bits (342), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 82/149 (55%), Positives = 99/149 (66%), Gaps = 14/149 (9%)

Query: 1   MCYEQKEVGNGVAGEGHGLGSSEEDESRVDD-AVNSNNGPGGTIQVHDGFQISQQQQ-PQ 58
           MC+   E G+ V  E    GSSEEDE RV+D A N+NN            QISQQQQ P 
Sbjct: 1   MCFNNIETGDEVETERQVFGSSEEDEFRVEDTARNTNN-----------VQISQQQQQPL 49

Query: 59  GSVIRWERFLPTRSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNH 118
             V++WER+LP RSLKVLLVENDDSTRH+V+ALL+NCSYEVTAV + L AW+ILED  + 
Sbjct: 50  AHVVKWERYLPVRSLKVLLVENDDSTRHIVTALLKNCSYEVTAVPDVLEAWRILEDEKSC 109

Query: 119 IDIVLTESSGS-GSGSGSESGTQTKKSAK 146
           ID+VLTE      SG+G  S   + K+ K
Sbjct: 110 IDLVLTEVDMPVHSGTGLLSKIMSHKTLK 138

Controls photoperiodic flowering response. Component of the circadian clock. Controls the degradation of APRR1/TOC1 by the SCF(ZTL) complex. Expression of several members of the ARR-like family is controlled by circadian rhythm. The particular coordinated sequential expression of APRR9, APRR7, APRR5, APRR3 and APPR1 result to circadian waves that may be at the basis of the endogenous circadian clock.
Arabidopsis thaliana (taxid: 3702)

>sp|A2XFB7|PRR73_ORYSI Two-component response regulator-like PRR73 OS=Oryza sativa subsp. indica GN=PRR73 PE=2 SV=2

 Score =  120 bits (301), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 65/125 (52%), Positives = 78/125 (62%), Gaps = 14/125 (11%)

Query: 6   KEVGNGVAGEGHGLGSSEEDESRVDDAVNSNNG-----PGGTIQVHDGFQISQQQQPQGS 60
           K  GNG+   GH    SEE+E R        NG     P G     +  Q  +Q++ Q  
Sbjct: 18  KGTGNGILENGHS-HKSEEEEWR--------NGMGEDLPNGHSTPPEPQQTDEQKEHQVR 68

Query: 61  VIRWERFLPTRSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHID 120
           ++RWERFLP ++L+VLLVENDDSTR VVSALLR C YEV    N LHAW+ LEDL NHID
Sbjct: 69  IVRWERFLPVKTLRVLLVENDDSTRQVVSALLRKCCYEVIPAENGLHAWQCLEDLQNHID 128

Query: 121 IVLTE 125
           +VLTE
Sbjct: 129 LVLTE 133

Controls photoperiodic flowering response. Seems to be one of the component of the circadian clock. Expression of several members of the ARR-like family is controlled by circadian rhythm. The particular coordinated sequential expression of PRR73, PRR37, PRR95, PRR59 and PPR1 result to circadian waves that may be at the basis of the endogenous circadian clock.

Oryza sativa subsp. indica (taxid: 39946)

>sp|Q10N34|PRR73_ORYSJ Two-component response regulator-like PRR73 OS=Oryza sativa subsp. japonica GN=PRR73 PE=2 SV=1

 Score =  119 bits (297), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 64/125 (51%), Positives = 77/125 (61%), Gaps = 14/125 (11%)

Query: 6   KEVGNGVAGEGHGLGSSEEDESRVDDAVNSNNG-----PGGTIQVHDGFQISQQQQPQGS 60
           K  GNG+   GH     EE+E R        NG     P G     +  Q  +Q++ Q  
Sbjct: 18  KGTGNGILENGHS-HKPEEEEWR--------NGMGEDLPNGHSTPPEPQQTDEQKEHQVQ 68

Query: 61  VIRWERFLPTRSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHID 120
           ++RWERFLP ++L+VLLVENDDSTR VVSALLR C YEV    N LHAW+ LEDL NHID
Sbjct: 69  IVRWERFLPVKTLRVLLVENDDSTRQVVSALLRKCCYEVIPAENGLHAWQCLEDLQNHID 128

Query: 121 IVLTE 125
           +VLTE
Sbjct: 129 LVLTE 133

Controls photoperiodic flowering response. Seems to be one of the component of the circadian clock. Expression of several members of the ARR-like family is controlled by circadian rhythm. The particular coordinated sequential expression of PRR73, PRR37, PRR95, PRR59 and PPR1 result to circadian waves that may be at the basis of the endogenous circadian clock.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q93WK5|APRR7_ARATH Two-component response regulator-like APRR7 OS=Arabidopsis thaliana GN=APRR7 PE=2 SV=1

 Score =  112 bits (279), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 56/104 (53%), Positives = 69/104 (66%), Gaps = 5/104 (4%)

Query: 26  ESRVDDAVNSNNGPGGTIQVHDG----FQISQQQQPQGSVIRWERFLPTRSLKVLLVEND 81
           ESR +         G T+ V +G     QI   QQ   +V  WERFL  R+++VLLVEND
Sbjct: 28  ESRTEKHSEEEKTNGITMDVRNGSSGGLQIPLSQQTAATVC-WERFLHVRTIRVLLVEND 86

Query: 82  DSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTE 125
           D TR++V+ALLRNCSYEV   +N + AWK+LEDL NHIDIVLTE
Sbjct: 87  DCTRYIVTALLRNCSYEVVEASNGIQAWKVLEDLNNHIDIVLTE 130

Controls photoperiodic flowering response. Seems to be one of the component of the circadian clock. Expression of several members of the ARR-like family is controlled by circadian rhythm. The particular coordinated sequential expression of APRR9, APRR7, APRR5, APRR3 and APPR1 result to circadian waves that may be at the basis of the endogenous circadian clock.

Arabidopsis thaliana (taxid: 3702)

>sp|A2YQ93|PRR37_ORYSI Two-component response regulator-like PRR37 OS=Oryza sativa subsp. indica GN=PRR37 PE=2 SV=2

 Score =  102 bits (254), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 95/259 (36%), Positives = 134/259 (51%), Gaps = 27/259 (10%)

Query: 140 QTKKSAKSKSNNGSENDSSSGDELENGSN----GLSIRDGSDNGSGT--QSSWTKKAAEV 193
           QT+K AKSKS  G E++++SG   ++  +    GL+ RDGSDNGSGT  QSSWTK+A E+
Sbjct: 197 QTQKCAKSKS--GDESNNNSGSNDDDDDDGVIMGLNARDGSDNGSGTQAQSSWTKRAVEI 254

Query: 194 DSPQPISPRYQSAD--DSICAQVIHTKPESFSNGWVHLNEPKDGLEQDEQPDGVAMHKGL 251
           DSPQ +SP  Q AD  DS CAQVIH K +  SN W+     K+  +Q E  D     K L
Sbjct: 255 DSPQAMSPD-QLADPPDSTCAQVIHLKSDICSNRWLPCTSNKNSKKQKETNDDFK-GKDL 312

Query: 252 EMQVSENADLKCDCQHEKKSTQQTSKKKIKLPEVDSKPFDNKQLEVDNENICGKRRDQAT 311
           E+    N +        ++S + T ++       +  P  N   E   EN+  +   +A 
Sbjct: 313 EIGSPRNLNTAYQSSPNERSIKPTDRR-------NEYPLQNNSKEAAMENL-EESSVRAA 364

Query: 312 STSSANANHANPHAEIRDFDTPSGPSDISHVKE------TPCLELTLKRMRGVEDDQSAA 365
               + A + +     R  + P+  S +   K+       P LEL+LKR R   DD +A 
Sbjct: 365 DLIGSMAKNMDAQQAARATNAPNCSSKVPEGKDKNRDNIMPSLELSLKRSRSTGDDANAI 424

Query: 366 NED-CNVLRHSIFSAFSKY 383
            E+  NVLR S  SAF++Y
Sbjct: 425 QEEQRNVLRRSDLSAFTRY 443

Controls photoperiodic flowering response. Seems to be one of the component of the circadian clock. Expression of several members of the ARR-like family is controlled by circadian rhythm. The particular coordinated sequential expression of PRR73, PRR37, PRR95, PRR59 and PPR1 result to circadian waves that may be at the basis of the endogenous circadian clock.

Oryza sativa subsp. indica (taxid: 39946)

>sp|Q0D3B6|PRR37_ORYSJ Two-component response regulator-like PRR37 OS=Oryza sativa subsp. japonica GN=PRR37 PE=2 SV=1

 Score = 96.3 bits (238), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 93/259 (35%), Positives = 133/259 (51%), Gaps = 27/259 (10%)

Query: 140 QTKKSAKSKSNNGSENDSSSGDELENGSN----GLSIRDGSDNGSGT--QSSWTKKAAEV 193
           QT+K AKSKS  G E+++++G   ++  +    GL+ RDGSDNGSGT  QSSWTK+A E+
Sbjct: 197 QTQKCAKSKS--GDESNNNNGSNDDDDDDGVIMGLNARDGSDNGSGTQAQSSWTKRAVEI 254

Query: 194 DSPQPISPRYQSAD--DSICAQVIHTKPESFSNGWVHLNEPKDGLEQDEQPDGVAMHKGL 251
           DSPQ +SP  Q AD  DS CAQVIH K +  SN W+     K+  +Q E  D     K L
Sbjct: 255 DSPQAMSPD-QLADPPDSTCAQVIHLKSDICSNRWLPCTSNKNSKKQKETNDDFK-GKDL 312

Query: 252 EMQVSENADLKCDCQHEKKSTQQTSKKKIKLPEVDSKPFDNKQLEVDNENICGKRRDQAT 311
           E+    N +        ++S + T ++       +  P  N   E   EN+  +   +A 
Sbjct: 313 EIGSPRNLNTAYQSSPNERSIKPTDRR-------NEYPLQNNSKEAAMENL-EESSVRAA 364

Query: 312 STSSANANHANPHAEIRDFDTPSGPSDISHVKE------TPCLELTLKRMRGVEDDQSAA 365
               + A + +     R  + P+  S +   K+       P LEL+LKR R   D  +A 
Sbjct: 365 DLIGSMAKNMDAQQAARAANAPNCSSKVPEGKDKNRDNIMPSLELSLKRSRSTGDGANAI 424

Query: 366 NED-CNVLRHSIFSAFSKY 383
            E+  NVLR S  SAF++Y
Sbjct: 425 QEEQRNVLRRSDLSAFTRY 443

Controls photoperiodic flowering response. Seems to be one of the component of the circadian clock. Expression of several members of the ARR-like family is controlled by circadian rhythm. The particular coordinated sequential expression of PRR73, PRR37, PRR95, PRR59 and PPR1 result to circadian waves that may be at the basis of the endogenous circadian clock.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q8L500|APRR9_ARATH Two-component response regulator-like APRR9 OS=Arabidopsis thaliana GN=APRR9 PE=2 SV=2

 Score = 87.8 bits (216), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 35/79 (44%), Positives = 59/79 (74%)

Query: 47  DGFQISQQQQPQGSVIRWERFLPTRSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSL 106
           DG +  + +     V++WE++LP   L+VLLVE+D STR +++ALLR C Y+V AV++ L
Sbjct: 11  DGMETIKNRVKSSEVVQWEKYLPKTVLRVLLVESDYSTRQIITALLRKCCYKVVAVSDGL 70

Query: 107 HAWKILEDLTNHIDIVLTE 125
            AW++L++ +++ID++LTE
Sbjct: 71  AAWEVLKEKSHNIDLILTE 89

Controls photoperiodic flowering response. Seems to be one of the component of the circadian clock. Expression of several members of the ARR-like family is controlled by circadian rhythm. The particular coordinated sequential expression of APRR9, APRR7, APRR5, APRR3 and APPR1 result to circadian waves that may be at the basis of the endogenous circadian clock.

Arabidopsis thaliana (taxid: 3702)

>sp|Q6LA42|APRR5_ARATH Two-component response regulator-like APRR5 OS=Arabidopsis thaliana GN=APRR5 PE=1 SV=2

 Score = 87.8 bits (216), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 35/65 (53%), Positives = 50/65 (76%)

Query: 61  VIRWERFLPTRSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHID 120
           +++WERFLP  +L+VLLVE DDSTR +++ALLR CSY V AV + L AW++L+     +D
Sbjct: 38  LVKWERFLPKIALRVLLVEADDSTRQIIAALLRKCSYRVAAVPDGLKAWEMLKGKPESVD 97

Query: 121 IVLTE 125
           ++LTE
Sbjct: 98  LILTE 102

Controls photoperiodic flowering response. Seems to be one of the component of the circadian clock. Expression of several members of the ARR-like family is controlled by circadian rhythm. The particular coordinated sequential expression of APRR9, APRR7, APRR5, APRR3 and APPR1 result to circadian waves that may be at the basis of the endogenous circadian clock.

Arabidopsis thaliana (taxid: 3702)

>sp|Q689G6|PRR95_ORYSJ Two-component response regulator-like PRR95 OS=Oryza sativa subsp. japonica GN=PRR95 PE=2 SV=1

 Score = 73.6 bits (179), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 32/63 (50%), Positives = 44/63 (69%)

Query: 63  RWERFLPTRSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIV 122
           R  R LP   ++VLL E DDSTRH++ ALLR C Y V A ++ + AW IL++ + +ID+V
Sbjct: 33  RETRMLPRMPVRVLLAEGDDSTRHIICALLRKCGYRVAAASDGVKAWDILKEKSFNIDLV 92

Query: 123 LTE 125
           LTE
Sbjct: 93  LTE 95

Controls photoperiodic flowering response. Seems to be one of the component of the circadian clock. Expression of several members of the ARR-like family is controlled by circadian rhythm. The particular coordinated sequential expression of PRR73, PRR37, PRR95, PRR59 and PPR1 result to circadian waves that may be at the basis of the endogenous circadian clock.

Oryza sativa subsp. japonica (taxid: 39947)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	399
255582079	807	sensory transduction histidine kinase, p	0.614	0.303	0.571	1e-62
225435163	785	PREDICTED: two-component response regula	0.576	0.292	0.531	5e-61
297746178	482	unnamed protein product [Vitis vinifera]	0.576	0.477	0.531	8e-61
359486449	747	PREDICTED: two-component response regula	0.308	0.164	0.666	6e-41
356542579	777	PREDICTED: LOW QUALITY PROTEIN: two-comp	0.609	0.312	0.449	2e-38
297736458	769	unnamed protein product [Vitis vinifera]	0.601	0.312	0.423	4e-38
224098126	766	pseudo response regulator [Populus trich	0.614	0.319	0.406	6e-37
224098134	711	predicted protein [Populus trichocarpa]	0.614	0.344	0.406	7e-37
357472487	830	Two-component response regulator-like PR	0.596	0.286	0.407	1e-36
356539090	792	PREDICTED: LOW QUALITY PROTEIN: two-comp	0.310	0.156	0.634	5e-36

>gi|255582079|ref|XP_002531836.1| sensory transduction histidine kinase, putative [Ricinus communis] gi|223528532|gb|EEF30556.1| sensory transduction histidine kinase, putative [Ricinus communis]

 Score =  246 bits (628), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 147/257 (57%), Positives = 180/257 (70%), Gaps = 12/257 (4%)

Query: 139 TQTKKSAKSKSNNGSENDSSSGDEL-ENGSNGLSIRDGSDNGSGTQSSWTKKAAEVDSPQ 197
           TQTKKSAK+KSN  SEN+S S DEL + GSNG S RDGSDNGSGTQSSWTK+AA++DSP+
Sbjct: 208 TQTKKSAKTKSNEESENNSDSSDELGDYGSNGPSNRDGSDNGSGTQSSWTKRAADIDSPR 267

Query: 198 PISPRYQSAD--DSICAQVIHTKPESFSNGWVHLNEPKDGLEQDEQPDGVAMHKGLEMQV 255
           P+S  YQ AD  DS CAQVIHTKPE+F N WVH+ + K   E+D++ D  AM K LE+ V
Sbjct: 268 PMSSAYQMADAPDSTCAQVIHTKPETFGNIWVHVTDTKGLQERDDKHDDFAMGKDLEIGV 327

Query: 256 SENADLKCDCQHEKKSTQQTSKKKIKLPEVDSKPFDNKQLEVDNENICGKRRDQATSTSS 315
           S N D + DCQ E  S + TSK++ K+ EVDSKP +N  LE D EN+  K RDQ    +S
Sbjct: 328 SSNLDTRHDCQLENLSPRPTSKRQQKISEVDSKPLENGMLEHDGENLFTKLRDQTPQLAS 387

Query: 316 ANANHANPHAEIRDFDTPSGPSDISHVK--------ETPCLELTLKRMRGVEDDQSAANE 367
            NA+ ANP  EI+   T + P DIS +K        E P  EL+LKR+RGV DD +AA++
Sbjct: 388 TNADSANPRIEIKKVGTSNRP-DISQLKDKACCDSGELPSFELSLKRLRGVGDDGNAADD 446

Query: 368 DCNVLRHSIFSAFSKYD 384
           D NVLRHS  SAFSKY+
Sbjct: 447 DRNVLRHSDLSAFSKYN 463

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225435163|ref|XP_002281776.1| PREDICTED: two-component response regulator-like PRR73-like [Vitis vinifera]

 Score =  241 bits (614), Expect = 5e-61,   Method: Compositional matrix adjust.
 Identities = 136/256 (53%), Positives = 171/256 (66%), Gaps = 26/256 (10%)

Query: 139 TQTKKSAKSKSNNGSENDSSSGDELENGSNGLSIRDGSDNGSGTQSSWTKKAAEVDSPQP 198
           TQTKKS KSKSN+ SEN++ S DE +NGS G SIRDGSDNGSGTQSSWTK+AAEVDSPQP
Sbjct: 229 TQTKKSVKSKSNDESENNTGSSDERDNGSTGPSIRDGSDNGSGTQSSWTKRAAEVDSPQP 288

Query: 199 ISPRYQSAD--DSICAQVIHTKPESFSNGWVHLNEPKDGLEQDEQPDGVAMHKGLEMQVS 256
           +SP  Q AD  DS C QVIHTKP + SN WVH+ E K+   +DEQPD VAM + LE+ V+
Sbjct: 289 LSPLDQLADAPDSTCPQVIHTKPGTLSNQWVHVIETKECQGKDEQPDNVAMGRDLELGVA 348

Query: 257 ENADLKCDCQHEKKSTQQTSKKKIKLPEVDSKPFDNKQLEVDNENICGKRRDQATSTSSA 316
            N  ++ + QHEK ST  T K++ KLPE DSKPFD + LE                 +S 
Sbjct: 349 TNPAVQLEYQHEKFSTYPTCKRQNKLPESDSKPFDKEHLE----------------HNST 392

Query: 317 NANHANPHAEIRDFDTPSGPSDISHVK--------ETPCLELTLKRMRGVEDDQSAANED 368
           +AN  +P  E R F+ P+G SD+S +K        E P L+L+LKR+RG  D  +  ++D
Sbjct: 393 SANCTDPQVESRTFENPNGLSDVSQIKDKGSCETTELPPLDLSLKRLRGAGDVGACVHDD 452

Query: 369 CNVLRHSIFSAFSKYD 384
            ++LRHS  SAFSKY+
Sbjct: 453 RSILRHSDLSAFSKYN 468

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297746178|emb|CBI16234.3| unnamed protein product [Vitis vinifera]

 Score =  240 bits (613), Expect = 8e-61,   Method: Compositional matrix adjust.
 Identities = 136/256 (53%), Positives = 171/256 (66%), Gaps = 26/256 (10%)

Query: 139 TQTKKSAKSKSNNGSENDSSSGDELENGSNGLSIRDGSDNGSGTQSSWTKKAAEVDSPQP 198
           TQTKKS KSKSN+ SEN++ S DE +NGS G SIRDGSDNGSGTQSSWTK+AAEVDSPQP
Sbjct: 229 TQTKKSVKSKSNDESENNTGSSDERDNGSTGPSIRDGSDNGSGTQSSWTKRAAEVDSPQP 288

Query: 199 ISPRYQSAD--DSICAQVIHTKPESFSNGWVHLNEPKDGLEQDEQPDGVAMHKGLEMQVS 256
           +SP  Q AD  DS C QVIHTKP + SN WVH+ E K+   +DEQPD VAM + LE+ V+
Sbjct: 289 LSPLDQLADAPDSTCPQVIHTKPGTLSNQWVHVIETKECQGKDEQPDNVAMGRDLELGVA 348

Query: 257 ENADLKCDCQHEKKSTQQTSKKKIKLPEVDSKPFDNKQLEVDNENICGKRRDQATSTSSA 316
            N  ++ + QHEK ST  T K++ KLPE DSKPFD + LE                 +S 
Sbjct: 349 TNPAVQLEYQHEKFSTYPTCKRQNKLPESDSKPFDKEHLE----------------HNST 392

Query: 317 NANHANPHAEIRDFDTPSGPSDISHVK--------ETPCLELTLKRMRGVEDDQSAANED 368
           +AN  +P  E R F+ P+G SD+S +K        E P L+L+LKR+RG  D  +  ++D
Sbjct: 393 SANCTDPQVESRTFENPNGLSDVSQIKDKGSCETTELPPLDLSLKRLRGAGDVGACVHDD 452

Query: 369 CNVLRHSIFSAFSKYD 384
            ++LRHS  SAFSKY+
Sbjct: 453 RSILRHSDLSAFSKYN 468

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359486449|ref|XP_002275645.2| PREDICTED: two-component response regulator-like PRR73 [Vitis vinifera]

 Score =  174 bits (442), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 84/126 (66%), Positives = 100/126 (79%), Gaps = 3/126 (2%)

Query: 1   MCYEQKEVGNGVAGEGHGLGSSEEDESRVDDAV-NSNNGPGGTIQVHDGFQISQQQQPQG 59
           MCYEQK + + V GEGHGL  SEEDESR+++ V + N+G  G++Q   G     QQQPQG
Sbjct: 1   MCYEQKNIRDKVVGEGHGL--SEEDESRINEDVEDLNDGRIGSVQAVQGVLHGPQQQPQG 58

Query: 60  SVIRWERFLPTRSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHI 119
            ++RWERFLP RSLKVLLVEND+STR VVSALLRNCSYEVTAVAN + AW IL+DLTNH+
Sbjct: 59  PIVRWERFLPLRSLKVLLVENDNSTRQVVSALLRNCSYEVTAVANGVQAWSILDDLTNHV 118

Query: 120 DIVLTE 125
           D+VL E
Sbjct: 119 DLVLAE 124

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356542579|ref|XP_003539744.1| PREDICTED: LOW QUALITY PROTEIN: two-component response regulator-like PRR37-like [Glycine max]

 Score =  166 bits (420), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 120/267 (44%), Positives = 152/267 (56%), Gaps = 24/267 (8%)

Query: 138 GTQTKKSAKSKSNNGSENDSSSGDELENGSNGLSIRDGSDNGSGTQSSWTKKAAEVDSPQ 197
            T T+K AKS+SN+  EN+S S DE + GS GLSIRDGSDNGSGTQSSWTK  A+V SP 
Sbjct: 206 ATLTRKFAKSRSNDAYENNSDSSDENDYGSRGLSIRDGSDNGSGTQSSWTKCLAQVGSPH 265

Query: 198 PISPRYQSAD--DSICAQVIHTKPESFSNGWVHLNEPKDGLEQDEQ----PDGVAMHKGL 251
           P+SP  Q  D  DS CAQV+ TK E  S+ WVH  E K+  E  +     PD VA  K L
Sbjct: 266 PVSPHKQLVDAPDSTCAQVMQTKTEKVSSRWVHATE-KECHELIDLVTFFPDDVARVKDL 324

Query: 252 EMQVSENADLKCDCQHEKKSTQQTSKKKIKLPEVD--------SKPFDNKQLEVDNENIC 303
            M +S N  L+   + E  S     K   K+ +VD        S   +  QLE + +   
Sbjct: 325 AMGISLNMQLEHPLE-ELSSNPIVGKGANKMSDVDDMQIIKRKSNVCEKGQLEYNGDKT- 382

Query: 304 GKRRDQATSTSSANANHANPHAEIRDFDTPSGPSDISHV------KETPCLELTLKRMRG 357
           G + +QA +      +++ P AE RD +TP+G S  S        KE P LELTLKR+  
Sbjct: 383 GTQENQAMNVIDVTDSNS-PQAESRDLNTPNGFSGFSQSKANCCPKEHPSLELTLKRLGE 441

Query: 358 VEDDQSAANEDCNVLRHSIFSAFSKYD 384
           V D ++   E+CNVLRHS  SAFSKY+
Sbjct: 442 VGDAKNVTGEECNVLRHSDQSAFSKYN 468

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297736458|emb|CBI25329.3| unnamed protein product [Vitis vinifera]

 Score =  165 bits (418), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 108/255 (42%), Positives = 153/255 (60%), Gaps = 15/255 (5%)

Query: 140 QTKKSAKSKSNNGSENDSSSGDELENGSNGLSIRDGSDNGSGTQSSWTKKAAEVDSPQPI 199
           +TKKSAKSKS  GS+N++ S DE +NGS GL++RDGSDNGSGTQSSWTK A EVDSP+P+
Sbjct: 231 RTKKSAKSKSVAGSDNNTGSNDE-DNGSIGLNVRDGSDNGSGTQSSWTKMAVEVDSPKPM 289

Query: 200 SPRYQSAD--DSICAQVIHTKPESFSNGWVHLNEPKDGLEQDEQPDGVAMHKGLEMQVSE 257
            P  QSAD  DS CAQV  + PE+F N  V +   KD  EQD++ D V M K L++ V  
Sbjct: 290 QPWDQSADPPDSTCAQVTQSWPEAFGNYQVPMTSSKDYQEQDDELDNVEMGKDLKIGVPR 349

Query: 258 NADLKCDCQHEKKSTQQTSKKKIKLPEVDSKPFDNKQLEVDNENICGKRRDQATSTSSAN 317
           N++L+   Q +     +    ++ L + D K  +N+Q+++++     +   +A    S  
Sbjct: 350 NSNLQ--LQDDVVGANKDKFHELTLKKDDEK-LENRQMDLNSNKPNDELDKEAVDLMSVI 406

Query: 318 ANHANPHAEIRDFDTPSGPSDISHV--------KETPCLELTLKRMRGVEDDQSAANEDC 369
           AN+ NP  +   F TPSG S++           KE P LEL+LKR+R      +  ++  
Sbjct: 407 ANNTNPQKKSMGFKTPSGLSEVPETKDKAMYDKKEIPSLELSLKRLRDTGGTDTNPHDQI 466

Query: 370 NVLRHSIFSAFSKYD 384
            + RHS  SAFS+Y+
Sbjct: 467 -IWRHSDLSAFSRYN 480

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224098126|ref|XP_002311123.1| pseudo response regulator [Populus trichocarpa] gi|222850943|gb|EEE88490.1| pseudo response regulator [Populus trichocarpa]

 Score =  161 bits (407), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 106/261 (40%), Positives = 149/261 (57%), Gaps = 16/261 (6%)

Query: 139 TQTKKSAKSKSNNGSENDSSSGDELENGSNGLSIRDGSDNGSGTQSSWTKKAAEVDSPQP 198
            +T+KS KS   + S+ND+ S D+   GS GL+ RDGSDNGSGTQSSWTK+A EV+SP+P
Sbjct: 226 VRTQKSTKSNGADESDNDTGSNDDDGIGSVGLNARDGSDNGSGTQSSWTKRAVEVESPKP 285

Query: 199 ISPRYQ----SADDSICAQVIHTKPESFSNGWVHLNEPKDGLEQDEQPDGVAMHKGLEMQ 254
           +SP  Q       DS CAQVIH++PE+  N WV L   K   EQD++ D + M K LE+ 
Sbjct: 286 MSPWDQDHLSDPPDSTCAQVIHSRPEACDNSWVPLATMKKCGEQDDELDNIVMGKDLEIG 345

Query: 255 VSENADLKCDCQHEKKSTQQTSKKKIKLPEVDSK----PFDNKQLEVDNENICGKRRDQA 310
           V    +L+     ++  T        K PE+ SK      + +Q E+++E    + R+Q 
Sbjct: 346 VPRIPNLQLKDPIKRVPTNIADNDGEKFPEIKSKHDGGHLEKRQQELNSEKCNTELRNQG 405

Query: 311 TSTSSAN-ANHANPHAEIRDFDTPSGPS-----DISH-VKETPCLELTLKRMRGVEDDQS 363
                    N ANP  +    D P+G S     ++++  KE P  EL+LKR+R +  D  
Sbjct: 406 NDLKGGGITNSANPRMDSLVLDVPNGLSSNRKNEVTYETKEVPSFELSLKRLRDI-GDAG 464

Query: 364 AANEDCNVLRHSIFSAFSKYD 384
           A++ D NVLRHS  SAFS+Y+
Sbjct: 465 ASSHDRNVLRHSDLSAFSRYN 485

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224098134|ref|XP_002311124.1| predicted protein [Populus trichocarpa] gi|222850944|gb|EEE88491.1| predicted protein [Populus trichocarpa]

 Score =  161 bits (407), Expect = 7e-37,   Method: Compositional matrix adjust.
 Identities = 106/261 (40%), Positives = 149/261 (57%), Gaps = 16/261 (6%)

Query: 139 TQTKKSAKSKSNNGSENDSSSGDELENGSNGLSIRDGSDNGSGTQSSWTKKAAEVDSPQP 198
            +T+KS KS   + S+ND+ S D+   GS GL+ RDGSDNGSGTQSSWTK+A EV+SP+P
Sbjct: 171 VRTQKSTKSNGADESDNDTGSNDDDGIGSVGLNARDGSDNGSGTQSSWTKRAVEVESPKP 230

Query: 199 ISPRYQ----SADDSICAQVIHTKPESFSNGWVHLNEPKDGLEQDEQPDGVAMHKGLEMQ 254
           +SP  Q       DS CAQVIH++PE+  N WV L   K   EQD++ D + M K LE+ 
Sbjct: 231 MSPWDQDHLSDPPDSTCAQVIHSRPEACDNSWVPLATMKKCGEQDDELDNIVMGKDLEIG 290

Query: 255 VSENADLKCDCQHEKKSTQQTSKKKIKLPEVDSK----PFDNKQLEVDNENICGKRRDQA 310
           V    +L+     ++  T        K PE+ SK      + +Q E+++E    + R+Q 
Sbjct: 291 VPRIPNLQLKDPIKRVPTNIADNDGEKFPEIKSKHDGGHLEKRQQELNSEKCNTELRNQG 350

Query: 311 TSTSSAN-ANHANPHAEIRDFDTPSGPS-----DISH-VKETPCLELTLKRMRGVEDDQS 363
                    N ANP  +    D P+G S     ++++  KE P  EL+LKR+R +  D  
Sbjct: 351 NDLKGGGITNSANPRMDSLVLDVPNGLSSNRKNEVTYETKEVPSFELSLKRLRDI-GDAG 409

Query: 364 AANEDCNVLRHSIFSAFSKYD 384
           A++ D NVLRHS  SAFS+Y+
Sbjct: 410 ASSHDRNVLRHSDLSAFSRYN 430

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357472487|ref|XP_003606528.1| Two-component response regulator-like PRR73 [Medicago truncatula] gi|355507583|gb|AES88725.1| Two-component response regulator-like PRR73 [Medicago truncatula]

 Score =  160 bits (405), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 108/265 (40%), Positives = 147/265 (55%), Gaps = 27/265 (10%)

Query: 139 TQTKKSAKSKSNNGSENDSSSGDELENGSNGLSIRDGSDNGSGTQSSWTKKAAEV-DSPQ 197
           T T+K AKS+S    +N++ S DE + GS GLS++DGSD GSGTQSSWT   A+V  S +
Sbjct: 257 TNTRKFAKSRSICAFDNNTGSSDENDYGSRGLSVQDGSDKGSGTQSSWTTNLAQVSSSSR 316

Query: 198 PISPRYQSAD--DSICAQVIHTKPESFSNGWVHLNEPKDGLEQDEQPDGVAMHKGLEMQV 255
           P+S   QS D  DS CAQV+HTKPE+  +  VH  E K+  E  + PD +AM K L M +
Sbjct: 317 PVSTHNQSHDAPDSTCAQVVHTKPENIRSMCVHATE-KEFHEPIDHPDDIAMGKDLAMGI 375

Query: 256 SENADLKCDCQHEKKSTQQTSKKKIKLPEVDSKPFDNKQLEVDNENICGK---------- 305
           S N         +K + Q+ S   ++         D  QL     N+C K          
Sbjct: 376 SLNT-------QQKHALQELSNNPMRKGVNKMSDIDGMQLNKGQSNVCEKVQLEEDSDKN 428

Query: 306 RRDQATSTSSANANHANPHAEIRDFDTPSGPSDISHVKETPC------LELTLKRMRGVE 359
           R  +   T+   A+ ++PHAE RD +T +G S  +  K + C      LELTL+RM  V+
Sbjct: 429 RMQENQGTNFGVADSSSPHAESRDLNTSNGFSGFAKTKASCCFKQHPSLELTLERMGEVK 488

Query: 360 DDQSAANEDCNVLRHSIFSAFSKYD 384
           DD+    ++CNVLRHS  SAFSKY+
Sbjct: 489 DDEHVTGDECNVLRHSNLSAFSKYN 513

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356539090|ref|XP_003538033.1| PREDICTED: LOW QUALITY PROTEIN: two-component response regulator-like APRR3-like [Glycine max]

 Score =  158 bits (399), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 80/126 (63%), Positives = 94/126 (74%), Gaps = 2/126 (1%)

Query: 1   MCYEQKEVGNGVAGEGHGLGSSEEDESRVDD-AVNSNNGPGGTIQVHDGFQISQQQQPQG 59
           M + +K + NGV  EG   GSS ED++R +  A + NNG  G IQ+H   QISQQ  PQG
Sbjct: 18  MFFNKKSLNNGVVNEGVSSGSSTEDDTRFNKVAEDGNNGLRGLIQIHGSLQISQQP-PQG 76

Query: 60  SVIRWERFLPTRSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHI 119
            V+ WERFLP RS+KVLLVE+DDSTRHVV ALLRNCSYEVTAV+N L AWK+LED  N I
Sbjct: 77  PVVCWERFLPVRSIKVLLVEDDDSTRHVVRALLRNCSYEVTAVSNGLQAWKVLEDPENGI 136

Query: 120 DIVLTE 125
           D+VLTE
Sbjct: 137 DLVLTE 142

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	399
TAIR|locus:2151206	727	PRR7 "pseudo-response regulato	0.543	0.298	0.329	7.6e-44
TAIR|locus:2044376	468	PRR9 "pseudo-response regulato	0.195	0.166	0.435	1.1e-12

TAIR|locus:2151206 PRR7 "pseudo-response regulator 7" [Arabidopsis thaliana (taxid:3702)]

 Score = 253 (94.1 bits), Expect = 7.6e-44, Sum P(2) = 7.6e-44
 Identities = 77/234 (32%), Positives = 110/234 (47%)

Query:   164 ENGSNGLSIRDGSDNGSGTQSSWTKKAAEVD-SPQPISPRYQSADDSICAQVIHTKPESF 222
             ENGS GL+  DGS +GSG QSSWTKKA +VD SP+ +S       DS CAQV+H+ PE  
Sbjct:   238 ENGSIGLNASDGSSDGSGAQSSWTKKAVDVDDSPRAVS--LWDRVDSTCAQVVHSNPEFP 295

Query:   223 SNGWVHLNEPKDGLEQDEQPDGVAMHKGLEMQVSENADLKCDCQHEXXXXXXXXXXXIKL 282
             SN  V     K+  E D++ + V M + LE+ +  N DL  + + E              
Sbjct:   296 SNQLVAPPAEKETQEHDDKFEDVTMGRDLEISIRRNCDLALEPKDEPLSKTTGIMRQDNS 355

Query:   283 PEVDSKPFDNK----QLEVDNENICGKRRDQXXXXXXXXXXXXXXX--------XEIRDF 330
              E  S  +  K     L++ +E+   K+  +                         ++  
Sbjct:   356 FEKSSSKWKMKVGKGPLDLSSESPSSKQMHEDGGSSFKAMSSHLQDNREPEAPNTHLKTL 415

Query:   331 DTPSGPSDISHVKETPCLELTLKRMRGVEDDQSAANEDCNVLRHSIFSAFSKYD 384
             DT      IS  +E   +E + KR RG +DD +   +D NVLR S  SAFS+Y+
Sbjct:   416 DTNEASVKIS--EELMHVEHSSKRHRGTKDDGTLVRDDRNVLRRSEGSAFSRYN 467

GO:0000156 "phosphorelay response regulator activity" evidence=IEA;ISS

GO:0000160 "phosphorelay signal transduction system" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA;TAS

GO:0007623 "circadian rhythm" evidence=IMP;TAS

GO:0010017 "red or far-red light signaling pathway" evidence=IMP

GO:0005739 "mitochondrion" evidence=IDA

GO:0009266 "response to temperature stimulus" evidence=IGI

GO:0003677 "DNA binding" evidence=IPI

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IDA

GO:0009639 "response to red or far red light" evidence=RCA

GO:0042752 "regulation of circadian rhythm" evidence=RCA

GO:0048574 "long-day photoperiodism, flowering" evidence=RCA

TAIR|locus:2044376 PRR9 "pseudo-response regulator 9" [Arabidopsis thaliana (taxid:3702)]

 Score = 193 (73.0 bits), Expect = 1.1e-12, P = 1.1e-12
 Identities = 34/78 (43%), Positives = 55/78 (70%)

Query:    47 DGFXXXXXXXXXGSVIRWERFLPTRSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSL 106
             DG            V++WE++LP   L+VLLVE+D STR +++ALLR C Y+V AV++ L
Sbjct:    11 DGMETIKNRVKSSEVVQWEKYLPKTVLRVLLVESDYSTRQIITALLRKCCYKVVAVSDGL 70

Query:   107 HAWKILEDLTNHIDIVLT 124
              AW++L++ +++ID++LT
Sbjct:    71 AAWEVLKEKSHNIDLILT 88


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.312   0.131   0.384    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      399       328   0.00088  116 3  11 23  0.48    34
                                                     33  0.45    37


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  2
  No. of states in DFA:  617 (66 KB)
  Total size of DFA:  247 KB (2133 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  26.34u 0.13s 26.47t   Elapsed:  00:00:02
  Total cpu time:  26.34u 0.13s 26.47t   Elapsed:  00:00:02
  Start:  Sat May 11 13:58:59 2013   End:  Sat May 11 13:59:01 2013

GO:0000156 "phosphorelay response regulator activity" evidence=IEA;ISS

GO:0000160 "phosphorelay signal transduction system" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA;TAS

GO:0007623 "circadian rhythm" evidence=IMP;TAS

GO:0005515 "protein binding" evidence=IPI

GO:0009266 "response to temperature stimulus" evidence=IGI

GO:0010017 "red or far-red light signaling pathway" evidence=IMP

GO:0003677 "DNA binding" evidence=IPI

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	399
smart00448	55	smart00448, REC, cheY-homologous receiver domain	3e-06
COG0784	130	COG0784, CheY, FOG: CheY-like receiver [Signal tra	4e-05
cd00156	113	cd00156, REC, Signal receiver domain; originally t	6e-04
pfam00072	111	pfam00072, Response_reg, Response regulator receiv	0.001

>gnl|CDD|214668 smart00448, REC, cheY-homologous receiver domain

 Score = 43.7 bits (104), Expect = 3e-06
 Identities = 14/52 (26%), Positives = 28/52 (53%), Gaps = 2/52 (3%)

Query: 73  LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLT 124
           +++L+V++D   R ++ ALL    YEV    +   A ++L+      D++L 
Sbjct: 1   MRILVVDDDPLLRELLKALLEKEGYEVDEATDGEEALELLK--EEKPDLILL 50

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

>gnl|CDD|223855 COG0784, CheY, FOG: CheY-like receiver [Signal transduction mechanisms]

 Score = 42.5 bits (100), Expect = 4e-05
 Identities = 15/55 (27%), Positives = 29/55 (52%), Gaps = 2/55 (3%)

Query: 71  RSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLH-AWKILEDLTNHIDIVLT 124
             L+VL+V+++   R ++  LL +  YEV   A+    A ++L +     D++L 
Sbjct: 4   SGLRVLVVDDEPVNRRLLKRLLEDLGYEVVEAADGEEEALELLRE-LPQPDLILL 57

Length = 130

>gnl|CDD|238088 cd00156, REC, Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; contains a phosphoacceptor site that is phosphorylated by histidine kinase homologs; usually found N-terminal to a DNA binding effector domain; forms homodimers

 Score = 38.7 bits (91), Expect = 6e-04
 Identities = 13/49 (26%), Positives = 22/49 (44%), Gaps = 2/49 (4%)

Query: 76  LLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLT 124
           L+V++D   R ++  LL    YEV    +   A  +L       D++L 
Sbjct: 1   LIVDDDPLIRELLRRLLEKEGYEVVEAEDGEEALALLA--EEKPDLILL 47

Length = 113

>gnl|CDD|200976 pfam00072, Response_reg, Response regulator receiver domain

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 13/50 (26%), Positives = 24/50 (48%), Gaps = 2/50 (4%)

Query: 75  VLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLT 124
           VL+V++D   R ++  LL    Y V    +   A ++L+      D++L 
Sbjct: 1   VLIVDDDPLIRELLRQLLEKEGYVVAEADDGEEALELLK--EKRPDLILL 48

This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain. Length = 111

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	399
PRK11091	779	aerobic respiration control sensor protein ArcB; P	98.4
PRK11466	914	hybrid sensory histidine kinase TorS; Provisional	98.16
TIGR02956	968	TMAO_torS TMAO reductase sytem sensor TorS. This p	98.12
PRK15347	921	two component system sensor kinase SsrA; Provision	98.07
COG0745	229	OmpR Response regulators consisting of a CheY-like	98.05
PRK09959	1197	hybrid sensory histidine kinase in two-component r	98.05
PF00072	112	Response_reg: Response regulator receiver domain;	97.93
COG0784	130	CheY FOG: CheY-like receiver [Signal transduction	97.92
COG4753	475	Response regulator containing CheY-like receiver d	97.81
PRK13837	828	two-component VirA-like sensor kinase; Provisional	97.73
PRK10841	924	hybrid sensory kinase in two-component regulatory	97.71
PRK13557	540	histidine kinase; Provisional	97.68
COG2204	464	AtoC Response regulator containing CheY-like recei	97.65
PRK10618	894	phosphotransfer intermediate protein in two-compon	97.64
PRK11107	919	hybrid sensory histidine kinase BarA; Provisional	97.56
smart00448	55	REC cheY-homologous receiver domain. CheY regulate	97.49
PRK10701	240	DNA-binding transcriptional regulator RstA; Provis	97.4
TIGR02154	226	PhoB phosphate regulon transcriptional regulatory	97.4
PRK10766	221	DNA-binding transcriptional regulator TorR; Provis	97.39
PRK10161	229	transcriptional regulator PhoB; Provisional	97.38
PRK10529	225	DNA-binding transcriptional activator KdpE; Provis	97.36
PRK13856	241	two-component response regulator VirG; Provisional	97.36
PRK10816	223	DNA-binding transcriptional regulator PhoP; Provis	97.35
PRK11173	237	two-component response regulator; Provisional	97.3
PRK11083	228	DNA-binding response regulator CreB; Provisional	97.29
COG4565	224	CitB Response regulator of citrate/malate metaboli	97.29
COG2197	211	CitB Response regulator containing a CheY-like rec	97.28
PRK13435	145	response regulator; Provisional	97.27
PRK10643	222	DNA-binding transcriptional regulator BasR; Provis	97.27
PRK09468	239	ompR osmolarity response regulator; Provisional	97.27
PRK09836	227	DNA-binding transcriptional activator CusR; Provis	97.25
TIGR03787	227	marine_sort_RR proteobacterial dedicated sortase s	97.25
PLN03029	222	type-a response regulator protein; Provisional	97.23
COG3437	360	Response regulator containing a CheY-like receiver	97.23
PRK10336	219	DNA-binding transcriptional regulator QseB; Provis	97.21
PRK11517	223	transcriptional regulatory protein YedW; Provision	97.2
PRK10046	225	dpiA two-component response regulator DpiA; Provis	97.2
PRK10955	232	DNA-binding transcriptional regulator CpxR; Provis	97.2
PRK15115	444	response regulator GlrR; Provisional	97.17
CHL00148	240	orf27 Ycf27; Reviewed	97.14
PRK09483	217	response regulator; Provisional	97.12
PRK10365	441	transcriptional regulatory protein ZraR; Provision	97.06
PRK09958	204	DNA-binding transcriptional activator EvgA; Provis	97.05
COG4567	182	Response regulator consisting of a CheY-like recei	97.01
PRK15411	207	rcsA colanic acid capsular biosynthesis activation	96.92
PRK15029	755	arginine decarboxylase; Provisional	96.9
PRK09390	202	fixJ response regulator FixJ; Provisional	96.9
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	96.9
PRK11697	238	putative two-component response-regulatory protein	96.86
PRK10710	240	DNA-binding transcriptional regulator BaeR; Provis	96.84
PRK00742	354	chemotaxis-specific methylesterase; Provisional	96.83
PRK12555	337	chemotaxis-specific methylesterase; Provisional	96.83
PRK10360	196	DNA-binding transcriptional activator UhpA; Provis	96.81
PRK10840	216	transcriptional regulator RcsB; Provisional	96.8
TIGR01387	218	cztR_silR_copR heavy metal response regulator. Mem	96.71
PRK10610	129	chemotaxis regulatory protein CheY; Provisional	96.7
COG2201	350	CheB Chemotaxis response regulator containing a Ch	96.67
PRK15479	221	transcriptional regulatory protein TctD; Provision	96.63
PRK10430	239	DNA-binding transcriptional activator DcuR; Provis	96.62
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	96.61
COG4566	202	TtrR Response regulator [Signal transduction mecha	96.6
COG3947	361	Response regulator containing CheY-like receiver a	96.59
COG3706	435	PleD Response regulator containing a CheY-like rec	96.57
PRK14084	246	two-component response regulator; Provisional	96.55
PRK13558	665	bacterio-opsin activator; Provisional	96.5
PRK09581	457	pleD response regulator PleD; Reviewed	96.5
TIGR02875	262	spore_0_A sporulation transcription factor Spo0A.	96.48
KOG0519	786	consensus Sensory transduction histidine kinase [S	96.46
PRK09935	210	transcriptional regulator FimZ; Provisional	96.42
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	96.41
PRK09191	261	two-component response regulator; Provisional	96.26
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	95.99
PRK15369	211	two component system sensor kinase SsrB; Provision	95.94
PRK10403	215	transcriptional regulator NarP; Provisional	95.87
cd00156	113	REC Signal receiver domain; originally thought to	95.76
PRK10651	216	transcriptional regulator NarL; Provisional	95.66
PRK09581	457	pleD response regulator PleD; Reviewed	95.6
COG3707	194	AmiR Response regulator with putative antiterminat	95.27
PRK10100	216	DNA-binding transcriptional regulator CsgD; Provis	94.65
COG3279	244	LytT Response regulator of the LytR/AlgR family [T	86.98
PRK11107	919	hybrid sensory histidine kinase BarA; Provisional	85.81
COG0512	191	PabA Anthranilate/para-aminobenzoate synthases com	85.63
PF06490	109	FleQ: Flagellar regulatory protein FleQ; InterPro:	83.17
PRK07649	195	para-aminobenzoate/anthranilate synthase glutamine	80.03

>PRK11091 aerobic respiration control sensor protein ArcB; Provisional

Probab=98.40  E-value=4.5e-07  Score=98.88  Aligned_cols=109  Identities=20%  Similarity=0.277  Sum_probs=81.8

Q ss_pred             eeccccCCCCchhhhhhccc--ccc--CCCCCCCccccCCCcCCCCCCCCCCccccccccCCCCCcEEEEEeCChhhHHH
Q 039733           12 VAGEGHGLGSSEEDESRVDD--AVN--SNNGPGGTIQVHDGFQISQQQQPQGSVIRWERFLPTRSLKVLLVENDDSTRHV   87 (399)
Q Consensus        12 ~~~~~~~l~~S~e~~~r~~~--~~~--~~~g~~~av~~~~~~~~p~~~~~~~~~~~~e~~lp~~~~rVLLVEDD~~~rei   87 (399)
                      .-|+|.||.+++....+++|  ...  .+.|..|.+..+.......+  ...+..   ...+....+||||||++.++..
T Consensus       466 ~~GtGLGL~i~~~iv~~~gG~i~v~s~~g~Gt~f~i~lP~~~~~~~~--~~~~~~---~~~~~~~~~ILivdD~~~~~~~  540 (779)
T PRK11091        466 ATGTGIGLAVSKRLAQAMGGDITVTSEEGKGSCFTLTIHAPAVAEEV--EDAFDE---DDMPLPALNILLVEDIELNVIV  540 (779)
T ss_pred             CCCcchHHHHHHHHHHHcCCEEEEEecCCCeEEEEEEEecccccccc--cccccc---ccccccccceEEEcCCHHHHHH
Confidence            56899999999999999999  332  34566666665543222111  011111   1123345799999999999999


Q ss_pred             HHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           88 VSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        88 L~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +..+|+..||.+..+.++.+|++.+.  ...||+||+|+.
T Consensus       541 l~~~L~~~g~~v~~a~~~~eal~~~~--~~~~Dlvl~D~~  578 (779)
T PRK11091        541 ARSVLEKLGNSVDVAMTGKEALEMFD--PDEYDLVLLDIQ  578 (779)
T ss_pred             HHHHHHHcCCEEEEECCHHHHHHHhh--cCCCCEEEEcCC
Confidence            99999999999999999999999998  778999999998

>PRK11466 hybrid sensory histidine kinase TorS; Provisional

Probab=98.16  E-value=3.5e-06  Score=93.10  Aligned_cols=108  Identities=18%  Similarity=0.267  Sum_probs=78.1

Q ss_pred             eccccCCCCchhhhhhccc--ccc--CCCCCCCccccCCCcCCCCCCCCCCccccccccCCCCCcEEEEEeCChhhHHHH
Q 039733           13 AGEGHGLGSSEEDESRVDD--AVN--SNNGPGGTIQVHDGFQISQQQQPQGSVIRWERFLPTRSLKVLLVENDDSTRHVV   88 (399)
Q Consensus        13 ~~~~~~l~~S~e~~~r~~~--~~~--~~~g~~~av~~~~~~~~p~~~~~~~~~~~~e~~lp~~~~rVLLVEDD~~~reiL   88 (399)
                      -|+|.||.+.++...+++|  ...  .+.|..|.+..+.....+.++.  .+.    ...+....+||||||++.++..+
T Consensus       624 ~g~GLGL~i~~~l~~~~gG~i~v~s~~~~Gt~f~i~lP~~~~~~~~~~--~~~----~~~~~~~~~vLivdD~~~~~~~l  697 (914)
T PRK11466        624 GGTGLGLTISSRLAQAMGGELSATSTPEVGSCFCLRLPLRVATAPVPK--TVN----QAVRLDGLRLLLIEDNPLTQRIT  697 (914)
T ss_pred             CCCcccHHHHHHHHHHcCCEEEEEecCCCCeEEEEEEEcccccccccc--ccc----cccccCCcceEEEeCCHHHHHHH
Confidence            4889999999999999999  322  3345666665553322111111  110    11122346899999999999999


Q ss_pred             HHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           89 SALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        89 ~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ..+|+..||.|..+.++.+|+..+.. ...||+||+|+.
T Consensus       698 ~~~L~~~g~~v~~a~~~~~al~~~~~-~~~~Dlvl~D~~  735 (914)
T PRK11466        698 AEMLNTSGAQVVAVGNAAQALETLQN-SEPFAAALVDFD  735 (914)
T ss_pred             HHHHHhcCCceEEeCCHHHHHHHHHc-CCCCCEEEEeCC
Confidence            99999999999999999999998862 357899999998

>TIGR02956 TMAO_torS TMAO reductase sytem sensor TorS

Probab=98.12  E-value=4.7e-06  Score=92.44  Aligned_cols=108  Identities=19%  Similarity=0.232  Sum_probs=79.7

Q ss_pred             eeccccCCCCchhhhhhccc--ccc--CCCCCCCccccCCCcCCCCCCCCCCccccccccCCCCCcEEEEEeCChhhHHH
Q 039733           12 VAGEGHGLGSSEEDESRVDD--AVN--SNNGPGGTIQVHDGFQISQQQQPQGSVIRWERFLPTRSLKVLLVENDDSTRHV   87 (399)
Q Consensus        12 ~~~~~~~l~~S~e~~~r~~~--~~~--~~~g~~~av~~~~~~~~p~~~~~~~~~~~~e~~lp~~~~rVLLVEDD~~~rei   87 (399)
                      .-|+|.||.+.++....++|  ...  ...|..|.+..+.....+.....   ..   ...+....+||||||++..+..
T Consensus       644 ~~g~GLGL~i~~~l~~~~gG~i~~~s~~~~Gt~f~~~lp~~~~~~~~~~~---~~---~~~~~~~~~iLvvdd~~~~~~~  717 (968)
T TIGR02956       644 SGGTGLGLAISQRLVEAMDGELGVESELGVGSCFWFTLPLTRGKPAEDSA---TL---TVIDLPPQRVLLVEDNEVNQMV  717 (968)
T ss_pred             CCCccHHHHHHHHHHHHcCCEEEEEecCCCcEEEEEEEEcCCCCcccccc---cc---ccccccccceEEEcCcHHHHHH
Confidence            35889999999999999998  322  33455666655533222111000   00   0112234589999999999999


Q ss_pred             HHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           88 VSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        88 L~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +..+|+..||.|..+.++.+|++.+.  ...||+||+|+.
T Consensus       718 l~~~L~~~g~~v~~~~~~~~a~~~l~--~~~~dlvl~D~~  755 (968)
T TIGR02956       718 AQGFLTRLGHKVTLAESGQSALECFH--QHAFDLALLDIN  755 (968)
T ss_pred             HHHHHHHcCCEEEEECCHHHHHHHHH--CCCCCEEEECCC
Confidence            99999999999999999999999998  788999999998

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).

>PRK15347 two component system sensor kinase SsrA; Provisional

Probab=98.07  E-value=8.7e-06  Score=89.71  Aligned_cols=53  Identities=25%  Similarity=0.449  Sum_probs=50.9

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ++||||||++..+..+..+|+..||.|..+.++.+|++.+.  ...||+||+|+.
T Consensus       691 ~~iLivdd~~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~~--~~~~dlil~D~~  743 (921)
T PRK15347        691 LQILLVDDVETNRDIIGMMLVELGQQVTTAASGTEALELGR--QHRFDLVLMDIR  743 (921)
T ss_pred             CCEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHh--cCCCCEEEEeCC
Confidence            58999999999999999999999999999999999999998  788999999998

>COG0745 OmpR Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]

Probab=98.05  E-value=1.1e-05  Score=77.21  Aligned_cols=52  Identities=27%  Similarity=0.415  Sum_probs=50.0

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ++||||||++.++..|..+|+..||.|..+.++.+|+..+.  .. ||+||+|++
T Consensus         1 ~~ILiveDd~~i~~~l~~~L~~~g~~v~~~~~~~~a~~~~~--~~-~dlviLD~~   52 (229)
T COG0745           1 MRILLVEDDPELAELLKEYLEEEGYEVDVAADGEEALEAAR--EQ-PDLVLLDLM   52 (229)
T ss_pred             CeEEEEcCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh--cC-CCEEEEECC
Confidence            38999999999999999999999999999999999999999  67 999999999

>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional

Probab=98.05  E-value=7e-06  Score=93.63  Aligned_cols=110  Identities=16%  Similarity=0.261  Sum_probs=78.2

Q ss_pred             eccccCCCCchhhhhhccc--ccc--CCCCCCCccccCCCcCCCCCCCCCCccccccccCCCCCcEEEEEeCChhhHHHH
Q 039733           13 AGEGHGLGSSEEDESRVDD--AVN--SNNGPGGTIQVHDGFQISQQQQPQGSVIRWERFLPTRSLKVLLVENDDSTRHVV   88 (399)
Q Consensus        13 ~~~~~~l~~S~e~~~r~~~--~~~--~~~g~~~av~~~~~~~~p~~~~~~~~~~~~e~~lp~~~~rVLLVEDD~~~reiL   88 (399)
                      -|+|.||.+++....+++|  ...  .+.|..|.+..+........ ...  .............+||||||++..+..+
T Consensus       898 ~G~GLGL~i~~~iv~~~gG~i~v~s~~~~Gt~f~i~lP~~~~~~~~-~~~--~~~~~~~~~~~~~~iLivdd~~~~~~~l  974 (1197)
T PRK09959        898 TGSGLGLMICKELIKNMQGDLSLESHPGIGTTFTITIPVEISQQVA-TVE--AKAEQPITLPEKLSILIADDHPTNRLLL  974 (1197)
T ss_pred             CCcCchHHHHHHHHHHcCCEEEEEeCCCCcEEEEEEEEccccchhc-ccc--cccccccccccCceEEEcCCCHHHHHHH
Confidence            4889999999999999998  333  23355555555432211111 000  0000011112346899999999999999


Q ss_pred             HHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           89 SALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        89 ~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ..+|+..||++..+.++.+|+..+.  ...||+||+|+.
T Consensus       975 ~~~L~~~g~~v~~~~~~~~al~~~~--~~~~dlil~D~~ 1011 (1197)
T PRK09959        975 KRQLNLLGYDVDEATDGVQALHKVS--MQHYDLLITDVN 1011 (1197)
T ss_pred             HHHHHHcCCEEEEECCHHHHHHHhh--cCCCCEEEEeCC
Confidence            9999999999999999999999998  788999999988

>PF00072 Response_reg: Response regulator receiver domain; InterPro: IPR001789 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []

Probab=97.93  E-value=3e-05  Score=62.95  Aligned_cols=51  Identities=25%  Similarity=0.524  Sum_probs=48.8

Q ss_pred             EEEEeCChhhHHHHHHHHHcCCC-EEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           75 VLLVENDDSTRHVVSALLRNCSY-EVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        75 VLLVEDD~~~reiL~~lLe~~Gy-eV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ||||||++..+..+..+|+..|| .|..+.++.+|+..+.  ...||+||+|+.
T Consensus         1 Ilivd~~~~~~~~l~~~l~~~~~~~v~~~~~~~~~~~~~~--~~~~d~iiid~~   52 (112)
T PF00072_consen    1 ILIVDDDPEIRELLEKLLERAGYEEVTTASSGEEALELLK--KHPPDLIIIDLE   52 (112)
T ss_dssp             EEEEESSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHH--HSTESEEEEESS
T ss_pred             cEEEECCHHHHHHHHHHHHhCCCCEEEEECCHHHHHHHhc--ccCceEEEEEee
Confidence            79999999999999999999999 8999999999999999  678999999987

Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Bipartite response regulator proteins are involved in a two-component signal transduction system in bacteria, and certain eukaryotes like protozoa, that functions to detect and respond to environmental changes []. These systems have been detected during host invasion, drug resistance, motility, phosphate uptake, osmoregulation, and nitrogen fixation, amongst others []. The two-component system consists of a histidine protein kinase environmental sensor that phosphorylates the receiver domain of a response regulator protein; phosphorylation induces a conformational change in the response regulator, which activates the effector domain, triggering the cellular response []. The domains of the two-component proteins are highly modular, but the core structures and activities are maintained. The response regulators act as phosphorylation-activated switches to affect a cellular response, usually by transcriptional regulation. Most of these proteins consist of two domains, an N-terminal response regulator receiver domain, and a variable C-terminal effector domain with DNA-binding activity. This entry represents the response regulator receiver domain, which belongs to the CheY family, and receives the signal from the sensor partner in the two-component system.; GO: 0000156 two-component response regulator activity, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2QR3_A 2QXY_A 1I3C_A 1JLK_A 2PKX_A 2PL1_A 3H1F_A 3H1E_A 3GWG_A 3H1G_A ....

>COG0784 CheY FOG: CheY-like receiver [Signal transduction mechanisms]

Probab=97.92  E-value=4.7e-05  Score=63.29  Aligned_cols=54  Identities=28%  Similarity=0.508  Sum_probs=50.5

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHH-HHHHHHHhcCC-CccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSL-HAWKILEDLTN-HIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~-eAle~L~~~~~-~pDLIIlDl~  127 (399)
                      ..+||||||++..+..+..+|...||.+..+.++. +|++.+.  .. .||+||+|+.
T Consensus         5 ~~~vLivdD~~~~~~~~~~~l~~~g~~v~~a~~g~~~al~~~~--~~~~~dlii~D~~   60 (130)
T COG0784           5 GLRVLVVDDEPVNRRLLKRLLEDLGYEVVEAADGEEEALELLR--ELPQPDLILLDIN   60 (130)
T ss_pred             CcEEEEEcCCHHHHHHHHHHHHHcCCeEEEeCChHHHHHHHHH--hCCCCCEEEEeCC
Confidence            46999999999999999999999999999999995 9999999  56 4999999999

>COG4753 Response regulator containing CheY-like receiver domain and AraC-type DNA-binding domain [Signal transduction mechanisms]

Probab=97.81  E-value=2.8e-05  Score=81.88  Aligned_cols=54  Identities=28%  Similarity=0.425  Sum_probs=49.4

Q ss_pred             CcEEEEEeCChhhHHHHHHHHH--cCCCE-EEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLR--NCSYE-VTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe--~~Gye-V~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      |.+||||||++.+|+.|+.++.  .+||+ |..|.||.+||+++.  ...|||||+|+.
T Consensus         1 MykVlIVDDE~lIr~GLk~lI~w~~~g~eiVgtA~NG~eAleli~--e~~pDiviTDI~   57 (475)
T COG4753           1 MYKVLIVDDEPLIREGLKSLIDWEALGIEVVGTAANGKEALELIQ--ETQPDIVITDIN   57 (475)
T ss_pred             CeeEEEecChHHHHHHHHHhCChhhcCCeEEEecccHHHHHHHHH--hcCCCEEEEecC
Confidence            4689999999999999999986  46898 558999999999999  789999999999

>PRK13837 two-component VirA-like sensor kinase; Provisional

Probab=97.73  E-value=8.6e-05  Score=82.46  Aligned_cols=111  Identities=22%  Similarity=0.214  Sum_probs=75.3

Q ss_pred             eccccCCCCchhhhhhccc--ccc--CCCCCCCccccCCCcCCCCCCCCCCccccccccCCCCCcEEEEEeCChhhHHHH
Q 039733           13 AGEGHGLGSSEEDESRVDD--AVN--SNNGPGGTIQVHDGFQISQQQQPQGSVIRWERFLPTRSLKVLLVENDDSTRHVV   88 (399)
Q Consensus        13 ~~~~~~l~~S~e~~~r~~~--~~~--~~~g~~~av~~~~~~~~p~~~~~~~~~~~~e~~lp~~~~rVLLVEDD~~~reiL   88 (399)
                      -|+|.||.+.+....+++|  ...  .+.|..|.+..+.....+..+..   .............+||||||++..+..+
T Consensus       637 ~G~GLGL~i~~~iv~~~gG~i~v~s~~g~Gt~f~i~LP~~~~~~~~~~~---~~~~~~~~~~~~~~ILvVddd~~~~~~l  713 (828)
T PRK13837        637 GGTGLGLATVHGIVSAHAGYIDVQSTVGRGTRFDVYLPPSSKVPVAPQA---FFGPGPLPRGRGETVLLVEPDDATLERY  713 (828)
T ss_pred             CCCcchHHHHHHHHHHCCCEEEEEecCCCeEEEEEEEeCCCCCCCCccc---cCCCcccCCCCCCEEEEEcCCHHHHHHH
Confidence            4788899889999888888  222  33456666655533222111110   0011111111345899999999999999


Q ss_pred             HHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcC
Q 039733           89 SALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTES  126 (399)
Q Consensus        89 ~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl  126 (399)
                      ...|...||++..+.++.+++..+......||+||+++
T Consensus       714 ~~~L~~~G~~v~~~~s~~~al~~l~~~~~~~DlVll~~  751 (828)
T PRK13837        714 EEKLAALGYEPVGFSTLAAAIAWISKGPERFDLVLVDD  751 (828)
T ss_pred             HHHHHHCCCEEEEeCCHHHHHHHHHhCCCCceEEEECC
Confidence            99999999999999999999999973123489999943

>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional

Probab=97.71  E-value=8.3e-05  Score=84.05  Aligned_cols=54  Identities=28%  Similarity=0.545  Sum_probs=51.4

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .++||||||++..+..+..+|+..||.|..+.++.+|++.+.  ...||+||+|+.
T Consensus       801 ~~~ILvVdD~~~~~~~l~~~L~~~G~~v~~a~~g~eal~~l~--~~~~DlVl~D~~  854 (924)
T PRK10841        801 DMMILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVLS--KNHIDIVLTDVN  854 (924)
T ss_pred             CCEEEEECCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHH--hCCCCEEEEcCC
Confidence            468999999999999999999999999999999999999998  788999999998

>PRK13557 histidine kinase; Provisional

Probab=97.68  E-value=0.00013  Score=74.44  Aligned_cols=109  Identities=16%  Similarity=0.244  Sum_probs=75.3

Q ss_pred             eccccCCCCchhhhhhccc--cccC--CCCCCCccccCCCcCCCCCCCCCCccccccccCCCCCcEEEEEeCChhhHHHH
Q 039733           13 AGEGHGLGSSEEDESRVDD--AVNS--NNGPGGTIQVHDGFQISQQQQPQGSVIRWERFLPTRSLKVLLVENDDSTRHVV   88 (399)
Q Consensus        13 ~~~~~~l~~S~e~~~r~~~--~~~~--~~g~~~av~~~~~~~~p~~~~~~~~~~~~e~~lp~~~~rVLLVEDD~~~reiL   88 (399)
                      -|+|.||.+.+....+++|  ....  ..|..|.+..+........ .+......   .......+||||++++..+..+
T Consensus       356 ~g~GlGL~i~~~~v~~~gG~i~~~s~~~~G~~f~i~lP~~~~~~~~-~~~~~~~~---~~~~~~~~iliv~~~~~~~~~l  431 (540)
T PRK13557        356 KGTGLGLSMVYGFAKQSGGAVRIYSEVGEGTTVRLYFPASDQAENP-EQEPKARA---IDRGGTETILIVDDRPDVAELA  431 (540)
T ss_pred             CCCCccHHHHHHHHHHCCCEEEEEecCCCceEEEEEeeCCCCccCC-CCCCCCcc---cccCCCceEEEEcCcHHHHHHH
Confidence            3788888888888888888  3333  3355555554432221111 11111111   1112346899999999999999


Q ss_pred             HHHHHcCCCEEEEECCHHHHHHHHHhcCC-CccEEEEcCC
Q 039733           89 SALLRNCSYEVTAVANSLHAWKILEDLTN-HIDIVLTESS  127 (399)
Q Consensus        89 ~~lLe~~GyeV~~A~dg~eAle~L~~~~~-~pDLIIlDl~  127 (399)
                      ..+|+..||.+..+.++.+++..+.  .. .||+||+|+.
T Consensus       432 ~~~l~~~~~~v~~~~~~~~~~~~~~--~~~~~d~vi~d~~  469 (540)
T PRK13557        432 RMILEDFGYRTLVASNGREALEILD--SHPEVDLLFTDLI  469 (540)
T ss_pred             HHHHHhcCCeEEEeCCHHHHHHHHh--cCCCceEEEEecc
Confidence            9999999999999999999999986  44 6999999987

>COG2204 AtoC Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]

Probab=97.65  E-value=0.00012  Score=77.11  Aligned_cols=54  Identities=24%  Similarity=0.417  Sum_probs=51.2

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +.+|||||||..+|..+..+|+..||.|..+.++.+|++.+.  ...||+||+|+.
T Consensus         4 ~~~iLvVDDd~~ir~~l~~~L~~~G~~v~~a~~~~~al~~i~--~~~~~lvl~Di~   57 (464)
T COG2204           4 MARILVVDDDPDIRELLEQALELAGYEVVTAESAEEALEALS--ESPFDLVLLDIR   57 (464)
T ss_pred             cCCEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCHHHHHHHHh--cCCCCEEEEecC
Confidence            347999999999999999999999999999999999999999  568999999999

>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional

Probab=97.64  E-value=6e-05  Score=85.06  Aligned_cols=99  Identities=16%  Similarity=0.163  Sum_probs=70.8

Q ss_pred             eccccCCCCchhhhhhccc--ccc--CCCCCCCccccCCCcCCCCCCCCCCccccccccCCCCCcEEEEEeCChhhHHHH
Q 039733           13 AGEGHGLGSSEEDESRVDD--AVN--SNNGPGGTIQVHDGFQISQQQQPQGSVIRWERFLPTRSLKVLLVENDDSTRHVV   88 (399)
Q Consensus        13 ~~~~~~l~~S~e~~~r~~~--~~~--~~~g~~~av~~~~~~~~p~~~~~~~~~~~~e~~lp~~~~rVLLVEDD~~~reiL   88 (399)
                      -|+|.||.+++....+++|  ...  .+.|..|.+..+.......+  +.    ..+.  .....+||||||++.++..+
T Consensus       634 ~GtGLGLaI~k~Lve~~GG~I~v~S~~g~GT~F~I~LPl~~~~~~~--~~----~~~~--~l~g~~vLlvdD~~~~r~~l  705 (894)
T PRK10618        634 KASGLTFFLCNQLCRKLGGHLTIKSREGLGTRYSIHLKMLAADPEV--EE----EEEK--LLDGVTVLLDITSEEVRKIV  705 (894)
T ss_pred             CCcChhHHHHHHHHHHcCCEEEEEECCCCcEEEEEEEEccCCcccc--cc----cccc--cCCCCEEEEEeCCHHHHHHH
Confidence            4889999999999999999  323  44566666666543211111  00    0011  12346999999999999999


Q ss_pred             HHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           89 SALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        89 ~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ..+|+.+||+|..+.++      +.  ...||+||+|+.
T Consensus       706 ~~~L~~~G~~v~~a~~~------~~--~~~~Dlvl~D~~  736 (894)
T PRK10618        706 TRQLENWGATCITPDER------LI--SQEYDIFLTDNP  736 (894)
T ss_pred             HHHHHHCCCEEEEcCcc------cc--CCCCCEEEECCC
Confidence            99999999999988753      23  467999999987

>PRK11107 hybrid sensory histidine kinase BarA; Provisional

Probab=97.56  E-value=0.00018  Score=79.21  Aligned_cols=54  Identities=19%  Similarity=0.295  Sum_probs=51.3

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .++||||||++..+..+..+|+..||.|..+.++.+|++.+.  ...||+||+|+.
T Consensus       667 ~~~vLivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~al~~~~--~~~~dlil~D~~  720 (919)
T PRK11107        667 PLTVMAVDDNPANLKLIGALLEEQVEHVVLCDSGHQAVEQAK--QRPFDLILMDIQ  720 (919)
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHH--hCCCCEEEEeCC
Confidence            368999999999999999999999999999999999999998  789999999998

>smart00448 REC cheY-homologous receiver domain

Probab=97.49  E-value=0.00078  Score=43.96  Aligned_cols=51  Identities=27%  Similarity=0.507  Sum_probs=46.7

Q ss_pred             EEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcC
Q 039733           74 KVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTES  126 (399)
Q Consensus        74 rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl  126 (399)
                      +|+++++++..+..+...|...|+.+..+.+..+++..+.  ...++++++|+
T Consensus         2 ~i~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~--~~~~~~vi~~~   52 (55)
T smart00448        2 RILVVDDDPLLRELLKALLEREGYEVDEATDGEEALELLK--EEKPDLILLDI   52 (55)
T ss_pred             eEEEEcCCHHHHHHHHHHHhhcCcEEEEeCCHHHHHHHHH--hcCCCEEEEec
Confidence            6999999999999999999999999999999999999887  56799999986

CheY regulates the clockwise rotation of E. coli flagellar motors. This domain contains a phosphoacceptor site that is phosphorylated by histidine kinase homologues.

>PRK10701 DNA-binding transcriptional regulator RstA; Provisional

Probab=97.40  E-value=0.00056  Score=63.02  Aligned_cols=53  Identities=23%  Similarity=0.283  Sum_probs=49.9

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .+||||||++..+..+..+|+..||.+..+.++.+++..+.  ...||+||+|+.
T Consensus         2 ~~iLivedd~~~~~~l~~~L~~~g~~v~~~~~~~~~l~~~~--~~~~dlvild~~   54 (240)
T PRK10701          2 NKIVFVEDDAEVGSLIAAYLAKHDIDVTVEPRGDRAEATIL--REQPDLVLLDIM   54 (240)
T ss_pred             ceEEEEeCCHHHHHHHHHHHHHcCCEEEEeCCHHHHHHHHh--hCCCCEEEEeCC
Confidence            48999999999999999999999999999999999999998  678999999988

>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB

Probab=97.40  E-value=0.00064  Score=60.87  Aligned_cols=53  Identities=19%  Similarity=0.394  Sum_probs=49.6

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .+||||||++.++..+..+|+..||.+..+.++.+++..+.  ...||+||+|+.
T Consensus         3 ~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~--~~~~d~vi~d~~   55 (226)
T TIGR02154         3 RRILVVEDEPAIRELIAYNLEKAGYDVVEAGDGDEALTLIN--ERGPDLILLDWM   55 (226)
T ss_pred             CeEEEEeCCHHHHHHHHHHHHHCCCEEEEEcCHHHHHHHHH--hcCCCEEEEECC
Confidence            58999999999999999999989999999999999999998  678999999987

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.

>PRK10766 DNA-binding transcriptional regulator TorR; Provisional

Probab=97.39  E-value=0.00071  Score=61.14  Aligned_cols=54  Identities=24%  Similarity=0.470  Sum_probs=50.2

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ..+||||||++..+..+...|+..||.|..+.++.+++..+.  ...||+||+|+.
T Consensus         2 ~~~iLlv~d~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~--~~~~dlvild~~   55 (221)
T PRK10766          2 SYHILVVEDEPVTRARLQGYFEQEGYTVSEAASGAGMREIMQ--NQHVDLILLDIN   55 (221)
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHh--cCCCCEEEEeCC
Confidence            358999999999999999999999999999999999999998  678999999987

>PRK10161 transcriptional regulator PhoB; Provisional

Probab=97.38  E-value=0.00066  Score=61.83  Aligned_cols=53  Identities=19%  Similarity=0.290  Sum_probs=49.7

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .+||||||++.++..+...|+..||++..+.++.+++..+.  ...||+||+|+.
T Consensus         3 ~~Ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~~~~~~~--~~~~dlvild~~   55 (229)
T PRK10161          3 RRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLN--EPWPDLILLDWM   55 (229)
T ss_pred             CeEEEEcCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh--ccCCCEEEEeCC
Confidence            58999999999999999999999999999999999999988  678999999987

>PRK10529 DNA-binding transcriptional activator KdpE; Provisional

Probab=97.36  E-value=0.00074  Score=61.18  Aligned_cols=53  Identities=17%  Similarity=0.241  Sum_probs=49.5

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .+||||||++.++..+...|+..||.+..+.++.+++..+.  ...||+||+|+.
T Consensus         2 ~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~~~~~~~--~~~~dlvild~~   54 (225)
T PRK10529          2 TNVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEAA--TRKPDLIILDLG   54 (225)
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHh--cCCCCEEEEeCC
Confidence            48999999999999999999999999999999999999887  678999999998

>PRK13856 two-component response regulator VirG; Provisional

Probab=97.36  E-value=0.0007  Score=62.83  Aligned_cols=53  Identities=28%  Similarity=0.513  Sum_probs=49.8

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .+||||||++..+..+...|+..||.+..+.++.+++..+.  ...||+||+|+.
T Consensus         2 ~~ILived~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~--~~~~dlvi~d~~   54 (241)
T PRK13856          2 KHVLVIDDDVAMRHLIVEYLTIHAFKVTAVADSQQFNRVLA--SETVDVVVVDLN   54 (241)
T ss_pred             CeEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHh--hCCCCEEEEeCC
Confidence            38999999999999999999999999999999999999988  678999999987

>PRK10816 DNA-binding transcriptional regulator PhoP; Provisional

Probab=97.35  E-value=0.00072  Score=61.34  Aligned_cols=52  Identities=25%  Similarity=0.340  Sum_probs=49.4

Q ss_pred             EEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           74 KVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        74 rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +||||||++..+..+...|+..||.+..+.++.+|+..+.  ...||+||+|+.
T Consensus         2 ~iLlv~d~~~~~~~l~~~L~~~g~~v~~~~~~~~~l~~~~--~~~~dlvild~~   53 (223)
T PRK10816          2 RVLVVEDNALLRHHLKVQLQDAGHQVDAAEDAKEADYYLN--EHLPDIAIVDLG   53 (223)
T ss_pred             eEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh--hCCCCEEEEECC
Confidence            7999999999999999999999999999999999999988  678999999987

>PRK11173 two-component response regulator; Provisional

Probab=97.30  E-value=0.001  Score=61.37  Aligned_cols=53  Identities=23%  Similarity=0.452  Sum_probs=50.1

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .+||||||++..+..+...|+..||.+..+.++.+++..+.  ...||+||+|+.
T Consensus         4 ~~iLiv~dd~~~~~~l~~~L~~~g~~v~~~~~~~~~~~~~~--~~~~dlvild~~   56 (237)
T PRK11173          4 PHILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQILS--ENDINLVIMDIN   56 (237)
T ss_pred             CeEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHh--hCCCCEEEEcCC
Confidence            48999999999999999999999999999999999999998  678999999997

>PRK11083 DNA-binding response regulator CreB; Provisional

Probab=97.29  E-value=0.0011  Score=59.59  Aligned_cols=54  Identities=20%  Similarity=0.297  Sum_probs=49.8

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +++||||||++..+..+...|...||.+..+.++.+++..+.  ...||+||+|+.
T Consensus         3 ~~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~--~~~~dlvl~d~~   56 (228)
T PRK11083          3 QPTILLVEDEQAIADTLVYALQSEGFTVEWFERGLPALDKLR--QQPPDLVILDVG   56 (228)
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHHCCCEEEEEcCHHHHHHHHh--cCCCCEEEEeCC
Confidence            358999999999999999999999999999999999999888  678999999987

>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]

Probab=97.29  E-value=0.00063  Score=65.20  Aligned_cols=53  Identities=19%  Similarity=0.314  Sum_probs=48.2

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcC-CCE-EEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNC-SYE-VTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~-Gye-V~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ++|||||||+.+.++-..+++.. ||. |.+|.++++|..++.  ...|||||+|+-
T Consensus         1 i~VLIiEDD~mVaeih~~yv~~~~gF~~vg~A~~~~ea~~~i~--~~~pDLILLDiY   55 (224)
T COG4565           1 INVLIIEDDPMVAEIHRRYVKQIPGFSVVGTAGTLEEAKMIIE--EFKPDLILLDIY   55 (224)
T ss_pred             CcEEEEcCchHHHHHHHHHHHhCCCceEEEeeccHHHHHHHHH--hhCCCEEEEeec
Confidence            47999999999999999999975 898 558999999999999  778899999998

>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]

Probab=97.28  E-value=0.0008  Score=63.50  Aligned_cols=53  Identities=28%  Similarity=0.340  Sum_probs=47.3

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCC-CEEE-EECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCS-YEVT-AVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~G-yeV~-~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ++||||||++.+|..|..+|...+ ++|+ .+.++.++++.+.  ...||+||+|+.
T Consensus         1 ~~vlivDDh~l~r~gl~~~L~~~~~~~vv~~a~~~~~~l~~~~--~~~pdvvl~Dl~   55 (211)
T COG2197           1 IKVLIVDDHPLVREGLRQLLELEPDLEVVGEASNGEEALDLAR--ELKPDVVLLDLS   55 (211)
T ss_pred             CeEEEECCcHHHHHHHHHHHhhCCCCEEEEEeCCHHHHHHHhh--hcCCCEEEEcCC
Confidence            369999999999999999998765 8854 6778999999988  789999999998

>PRK13435 response regulator; Provisional

Probab=97.27  E-value=0.0011  Score=56.82  Aligned_cols=56  Identities=25%  Similarity=0.306  Sum_probs=49.8

Q ss_pred             CCCcEEEEEeCChhhHHHHHHHHHcCCCEEE-EECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           70 TRSLKVLLVENDDSTRHVVSALLRNCSYEVT-AVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        70 ~~~~rVLLVEDD~~~reiL~~lLe~~GyeV~-~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ..+++|||+++++..+..+...|+..||.+. .+.++.+++..+.  ...||+||+|+.
T Consensus         3 ~~~~~iliid~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~--~~~~dliivd~~   59 (145)
T PRK13435          3 LRQLKVLIVEDEALIALELEKLVEEAGHEVVGIAMSSEQAIALGR--RRQPDVALVDVH   59 (145)
T ss_pred             cccceEEEEcCcHHHHHHHHHHHHhcCCeEEEeeCCHHHHHHHhh--hcCCCEEEEeee
Confidence            4467999999999999999999998899976 7899999999887  568999999986

>PRK10643 DNA-binding transcriptional regulator BasR; Provisional

Probab=97.27  E-value=0.0011  Score=59.43  Aligned_cols=53  Identities=23%  Similarity=0.353  Sum_probs=49.3

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ++||||||++..+..+..+|+..||.+..+.++.+++..+.  ...||+||+|+.
T Consensus         1 ~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~--~~~~d~illd~~   53 (222)
T PRK10643          1 MKILIVEDDTLLLQGLILALQTEGYACDCASTAREAEALLE--SGHYSLVVLDLG   53 (222)
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHH--hCCCCEEEEECC
Confidence            37999999999999999999999999999999999999988  678999999987

>PRK09468 ompR osmolarity response regulator; Provisional

Probab=97.27  E-value=0.0012  Score=60.71  Aligned_cols=54  Identities=19%  Similarity=0.358  Sum_probs=50.4

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ..+||||||++.++..+...|+..||.+..+.++.+++..+.  ...||+||+|+.
T Consensus         5 ~~~iLiv~d~~~~~~~l~~~L~~~g~~v~~~~~~~~~~~~~~--~~~~dlvild~~   58 (239)
T PRK09468          5 NYKILVVDDDMRLRALLERYLTEQGFQVRSAANAEQMDRLLT--RESFHLMVLDLM   58 (239)
T ss_pred             CCeEEEEcCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh--cCCCCEEEEeCC
Confidence            358999999999999999999999999999999999999988  678999999987

>PRK09836 DNA-binding transcriptional activator CusR; Provisional

Probab=97.25  E-value=0.0011  Score=60.25  Aligned_cols=52  Identities=21%  Similarity=0.404  Sum_probs=49.0

Q ss_pred             EEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           74 KVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        74 rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +||||||++.++..+...|+..||.|..+.++.+++..+.  ...||+||+|+.
T Consensus         2 ~iliv~d~~~~~~~l~~~L~~~g~~v~~~~~~~~~~~~~~--~~~~dlvild~~   53 (227)
T PRK09836          2 KLLIVEDEKKTGEYLTKGLTEAGFVVDLADNGLNGYHLAM--TGDYDLIILDIM   53 (227)
T ss_pred             eEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh--hCCCCEEEEECC
Confidence            7999999999999999999999999999999999999887  678999999987

>TIGR03787 marine_sort_RR proteobacterial dedicated sortase system response regulator

Probab=97.25  E-value=0.0011  Score=60.23  Aligned_cols=52  Identities=19%  Similarity=0.348  Sum_probs=48.9

Q ss_pred             EEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           74 KVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        74 rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +||||||++.++..+...|+..||.+..+.++.+++..+.  ...||+||+|+.
T Consensus         2 ~iLivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~--~~~~dlvild~~   53 (227)
T TIGR03787         2 RIAIVEDEAAIRENYADALKRQGYQVTTYADRPSAMQAFR--QRLPDLAIIDIG   53 (227)
T ss_pred             eEEEEeCCHHHHHHHHHHHHHCCcEEEEecCHHHHHHHHH--hCCCCEEEEECC
Confidence            6999999999999999999999999999999999999988  678999999987

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.

>PLN03029 type-a response regulator protein; Provisional

Probab=97.23  E-value=0.0011  Score=62.52  Aligned_cols=57  Identities=26%  Similarity=0.427  Sum_probs=49.4

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhc------------------CCCccEEEEcCC
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDL------------------TNHIDIVLTESS  127 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~------------------~~~pDLIIlDl~  127 (399)
                      ..++||||||+...+..+..+|+..||.|..+.++.++++.+...                  ...+||||+|+.
T Consensus         7 ~~~~VLiVdd~~~~~~~l~~~L~~~g~~v~~a~sg~~al~~l~~~~~d~~~p~~~~~~~~~~~~~~~dlVllD~~   81 (222)
T PLN03029          7 SQFHVLAVDDSLIDRKLIEKLLKTSSYQVTTVDSGSKALKFLGLHEDDRSNPDTPSVSPNSHQEVEVNLIITDYC   81 (222)
T ss_pred             CCccEEEEeCCHHHHHHHHHHHHHcCceEEEECCHHHHHHHHHhccccccccccccccccccccccCCEEEEcCC
Confidence            357999999999999999999999999999999999999998621                  113679999998

>COG3437 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]

Probab=97.23  E-value=0.00056  Score=69.70  Aligned_cols=55  Identities=31%  Similarity=0.457  Sum_probs=52.0

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ..++||+|||.+..+..+..+|+..||.|..|.+|++|++++.  .+.+|+||+|++
T Consensus        13 ~~~~vl~vDD~~~~~~~~~~lL~~~~y~v~~ae~g~~a~kl~~--~~~~dlvllD~~   67 (360)
T COG3437          13 EKLTVLLVDDEPDNLEALRQLLRMIGYRVIEAENGEEALKLLQ--EEPPDLVLLDVR   67 (360)
T ss_pred             ccceEEEecCchhHHHHHHHHHHhcccceeeecCchHHHHHhc--ccCCceEEeecc
Confidence            4569999999999999999999999999999999999999998  677999999999

>PRK10336 DNA-binding transcriptional regulator QseB; Provisional

Probab=97.21  E-value=0.0012  Score=59.04  Aligned_cols=53  Identities=17%  Similarity=0.247  Sum_probs=49.1

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ++||||||++.++..+..+|+..||.+..+.++.+++..+.  ...||+||+|+.
T Consensus         1 ~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~--~~~~dlvild~~   53 (219)
T PRK10336          1 MRILLIEDDMLIGDGIKTGLSKMGFSVDWFTQGRQGKEALY--SAPYDAVILDLT   53 (219)
T ss_pred             CeEEEEcCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHh--hCCCCEEEEECC
Confidence            37999999999999999999999999999999999999887  678999999987

>PRK11517 transcriptional regulatory protein YedW; Provisional

Probab=97.20  E-value=0.0014  Score=58.98  Aligned_cols=52  Identities=19%  Similarity=0.358  Sum_probs=49.1

Q ss_pred             EEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           74 KVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        74 rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +||||||++..+..+...|+..||.+..+.++.+++..+.  ...||+||+|+.
T Consensus         2 ~iliv~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~l~~~~--~~~~dlvi~d~~   53 (223)
T PRK11517          2 KILLIEDNQRTQEWVTQGLSEAGYVIDAVSDGRDGLYLAL--KDDYALIILDIM   53 (223)
T ss_pred             EEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh--cCCCCEEEEECC
Confidence            7999999999999999999999999999999999999988  678999999987

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=97.20  E-value=0.0013  Score=61.24  Aligned_cols=54  Identities=17%  Similarity=0.336  Sum_probs=48.8

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcC-CCE-EEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNC-SYE-VTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~-Gye-V~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .++||||||++.++..+..+|+.. +|. |..+.++.+|++.+.  ...||+||+|+.
T Consensus         4 ~~~ilivdd~~~~~~~l~~~L~~~~~~~~v~~a~~~~~al~~~~--~~~pdlvllD~~   59 (225)
T PRK10046          4 PLTLLIVEDETPLAEMHAEYIRHIPGFSQILLAGNLAQARMMIE--RFKPGLILLDNY   59 (225)
T ss_pred             cceEEEECCCHHHHHHHHHHHHhCCCcEEEEEECCHHHHHHHHH--hcCCCEEEEeCC
Confidence            468999999999999999999864 785 678999999999998  678999999998

>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional

Probab=97.20  E-value=0.0013  Score=59.51  Aligned_cols=52  Identities=25%  Similarity=0.429  Sum_probs=47.9

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .+||||||++..+..+..+|+..||.+..+.++.+++..+.  . .||+||+|+.
T Consensus         2 ~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~--~-~~d~vl~d~~   53 (232)
T PRK10955          2 NKILLVDDDRELTSLLKELLEMEGFNVIVAHDGEQALDLLD--D-SIDLLLLDVM   53 (232)
T ss_pred             ceEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHhh--c-CCCEEEEeCC
Confidence            48999999999999999999999999999999999999876  3 6999999987

>PRK15115 response regulator GlrR; Provisional

Probab=97.17  E-value=0.0014  Score=67.20  Aligned_cols=56  Identities=20%  Similarity=0.416  Sum_probs=51.8

Q ss_pred             CCCcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           70 TRSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        70 ~~~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ....+||||||++.++..+..+|+..||.|..+.++.+|+..+.  ...||+||+|+.
T Consensus         3 ~~~~~vLiVdd~~~~~~~l~~~L~~~g~~v~~~~~~~eal~~l~--~~~~dlvilD~~   58 (444)
T PRK15115          3 RKPAHLLLVDDDPGLLKLLGMRLTSEGYSVVTAESGQEALRVLN--REKVDLVISDLR   58 (444)
T ss_pred             CCCCeEEEEECCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHh--cCCCCEEEEcCC
Confidence            34469999999999999999999999999999999999999998  678999999998

>CHL00148 orf27 Ycf27; Reviewed

Probab=97.14  E-value=0.002  Score=58.65  Aligned_cols=54  Identities=22%  Similarity=0.404  Sum_probs=49.9

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +++||||||++..+..+...|+..||.+..+.++.+++..+.  ...||+||+|+.
T Consensus         6 ~~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~~l~~~~--~~~~d~illd~~   59 (240)
T CHL00148          6 KEKILVVDDEAYIRKILETRLSIIGYEVITASDGEEALKLFR--KEQPDLVILDVM   59 (240)
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHH--hcCCCEEEEeCC
Confidence            458999999999999999999999999999999999999888  678999999987

>PRK09483 response regulator; Provisional

Probab=97.12  E-value=0.0016  Score=58.61  Aligned_cols=54  Identities=26%  Similarity=0.376  Sum_probs=48.4

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcC-CCEEE-EECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNC-SYEVT-AVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~-GyeV~-~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      |++||||||++..+..+..+|+.. ++.+. .+.++.+++..+.  ...||+||+|+.
T Consensus         1 m~~ilivd~~~~~~~~l~~~L~~~~~~~~v~~~~~~~~~~~~~~--~~~~dlvi~d~~   56 (217)
T PRK09483          1 MINVLLVDDHELVRAGIRRILEDIKGIKVVGEACCGEDAVKWCR--TNAVDVVLMDMN   56 (217)
T ss_pred             CeEEEEECCcHHHHHHHHHHHccCCCCEEEEEeCCHHHHHHHHH--hcCCCEEEEeCC
Confidence            468999999999999999999874 88865 7899999999998  678999999997

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=97.06  E-value=0.0021  Score=65.56  Aligned_cols=55  Identities=25%  Similarity=0.436  Sum_probs=51.3

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ..++||||||++..+..+..+|+..||.+..+.++.+++..+.  ...||+||+|+.
T Consensus         4 ~~~~Ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~--~~~~DlvilD~~   58 (441)
T PRK10365          4 DNIDILVVDDDISHCTILQALLRGWGYNVALANSGRQALEQVR--EQVFDLVLCDVR   58 (441)
T ss_pred             CcceEEEEECCHHHHHHHHHHHHHCCCeEEEeCCHHHHHHHHh--cCCCCEEEEeCC
Confidence            3469999999999999999999999999999999999999998  678999999998

>PRK09958 DNA-binding transcriptional activator EvgA; Provisional

Probab=97.05  E-value=0.0021  Score=57.24  Aligned_cols=53  Identities=17%  Similarity=0.267  Sum_probs=48.7

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEE-EECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVT-AVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~-~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ++||||||++..+..+...|+..||.+. .+.++.+++..+.  ...||+||+|+.
T Consensus         1 m~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~~--~~~~dlvi~d~~   54 (204)
T PRK09958          1 MNAIIIDDHPLAIAAIRNLLIKNDIEILAELTEGGSAVQRVE--TLKPDIVIIDVD   54 (204)
T ss_pred             CcEEEECCcHHHHHHHHHHHhcCCCEEEEEeCCHHHHHHHHH--ccCCCEEEEeCC
Confidence            3799999999999999999998999987 6899999999998  678999999987

>COG4567 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]

Probab=97.01  E-value=0.0022  Score=58.95  Aligned_cols=54  Identities=15%  Similarity=0.223  Sum_probs=51.7

Q ss_pred             EEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC-CC
Q 039733           74 KVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS-GS  129 (399)
Q Consensus        74 rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~-Gs  129 (399)
                      ..||||||..+...|...|++.||.|.++.+..+++..++  ...|...++|+- |.
T Consensus        11 ~lllvdDD~~f~~~LaRa~e~RGf~v~~a~~~~eal~~ar--t~~PayAvvDlkL~~   65 (182)
T COG4567          11 SLLLVDDDTPFLRTLARAMERRGFAVVTAESVEEALAAAR--TAPPAYAVVDLKLGD   65 (182)
T ss_pred             eeEEecCChHHHHHHHHHHhccCceeEeeccHHHHHHHHh--cCCCceEEEEeeecC
Confidence            6999999999999999999999999999999999999999  889999999999 65

>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional

Probab=96.92  E-value=0.0025  Score=59.71  Aligned_cols=51  Identities=8%  Similarity=0.069  Sum_probs=44.3

Q ss_pred             EEEEEeCChhhHHHHHHHHHcCCC--E-EEEECCHHHHHHHHHhcCCCccEEEEcC
Q 039733           74 KVLLVENDDSTRHVVSALLRNCSY--E-VTAVANSLHAWKILEDLTNHIDIVLTES  126 (399)
Q Consensus        74 rVLLVEDD~~~reiL~~lLe~~Gy--e-V~~A~dg~eAle~L~~~~~~pDLIIlDl  126 (399)
                      .||||||++.++..+..+|+..++  . +..+.++.+++..+.  ...|||||+|+
T Consensus         2 ~~lIvDD~~~~~~gl~~~L~~~~~~~~vv~~~~~~~~~~~~~~--~~~pDlvLlDl   55 (207)
T PRK15411          2 STIIMDLCSYTRLGLTGYLLSRGVKKREINDIETVDDLAIACD--SLRPSVVFINE   55 (207)
T ss_pred             CEEEEcCCHHHHHHHHHHHHhCCCcceEEEecCCHHHHHHHHh--ccCCCEEEEeC
Confidence            599999999999999999987653  3 557899999999888  67899999994

>PRK15029 arginine decarboxylase; Provisional

Probab=96.90  E-value=0.0022  Score=71.45  Aligned_cols=52  Identities=21%  Similarity=0.233  Sum_probs=48.7

Q ss_pred             EEEEEeCChh--------hHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcC-CCccEEEEcCC
Q 039733           74 KVLLVENDDS--------TRHVVSALLRNCSYEVTAVANSLHAWKILEDLT-NHIDIVLTESS  127 (399)
Q Consensus        74 rVLLVEDD~~--------~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~-~~pDLIIlDl~  127 (399)
                      +|||||||..        ++..|...|+..||+|..+.++.+|+..+.  . ..||+||+|++
T Consensus         2 kILIVDDD~~~~~~~~~~i~~~L~~~Le~~G~eV~~a~s~~dAl~~l~--~~~~~DlVLLD~~   62 (755)
T PRK15029          2 KVLIVESEFLHQDTWVGNAVERLADALSQQNVTVIKSTSFDDGFAILS--SNEAIDCLMFSYQ   62 (755)
T ss_pred             eEEEEeCCcccccchhHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHH--hcCCCcEEEEECC
Confidence            7999999996        699999999999999999999999999997  5 58999999998

>PRK09390 fixJ response regulator FixJ; Provisional

Probab=96.90  E-value=0.0042  Score=54.01  Aligned_cols=54  Identities=20%  Similarity=0.273  Sum_probs=49.6

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ..+||||+|++..+..+...|...||.+..+.++.+++..+.  ...||+||+|+.
T Consensus         3 ~~~iliv~~~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~--~~~~d~ii~d~~   56 (202)
T PRK09390          3 KGVVHVVDDDEAMRDSLAFLLDSAGFEVRLFESAQAFLDALP--GLRFGCVVTDVR   56 (202)
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHHCCCeEEEeCCHHHHHHHhc--cCCCCEEEEeCC
Confidence            358999999999999999999999999999999999999888  678999999987

>PRK10923 glnG nitrogen regulation protein NR(I); Provisional

Probab=96.90  E-value=0.0033  Score=65.04  Aligned_cols=53  Identities=23%  Similarity=0.310  Sum_probs=50.4

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .+||||||++.++..+..+|+..||.+..+.++.+|+..+.  ...||+||+|+.
T Consensus         4 ~~ILiVdd~~~~~~~L~~~L~~~g~~v~~~~s~~~al~~l~--~~~~DlvllD~~   56 (469)
T PRK10923          4 GIVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLEALA--SKTPDVLLSDIR   56 (469)
T ss_pred             CeEEEEECCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHh--cCCCCEEEECCC
Confidence            48999999999999999999999999999999999999998  778999999988

>PRK11697 putative two-component response-regulatory protein YehT; Provisional

Probab=96.86  E-value=0.0034  Score=58.01  Aligned_cols=54  Identities=24%  Similarity=0.374  Sum_probs=47.4

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCC-CE-EEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCS-YE-VTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~G-ye-V~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      |++|||+||++..+..+..+|+..+ +. +..+.++.+++..+.  ...||+||+|+.
T Consensus         1 m~~IlIvdd~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~~--~~~~dlv~lDi~   56 (238)
T PRK11697          1 MIKVLIVDDEPLAREELRELLQEEGDIEIVGECSNAIEAIGAIH--RLKPDVVFLDIQ   56 (238)
T ss_pred             CcEEEEECCCHHHHHHHHHHHhhCCCcEEEEEeCCHHHHHHHHH--hcCCCEEEEeCC
Confidence            3689999999999999999999887 34 456889999999988  678999999998

>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional

Probab=96.84  E-value=0.0051  Score=56.00  Aligned_cols=53  Identities=17%  Similarity=0.313  Sum_probs=49.5

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .+||||||++.++..+..+|...||.+..+.++.+++..+.  ...||+||+|+.
T Consensus        11 ~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~--~~~~dlvl~d~~   63 (240)
T PRK10710         11 PRILIVEDEPKLGQLLIDYLQAASYATTLLSHGDEVLPYVR--QTPPDLILLDLM   63 (240)
T ss_pred             CeEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHh--hCCCCEEEEeCC
Confidence            38999999999999999999999999999999999999998  678999999987

>PRK00742 chemotaxis-specific methylesterase; Provisional

Probab=96.83  E-value=0.0037  Score=62.57  Aligned_cols=54  Identities=20%  Similarity=0.382  Sum_probs=49.1

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcC-CCEEE-EECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNC-SYEVT-AVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~-GyeV~-~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +++||||||+..++..+..+|... +|.+. .+.++.+++..+.  ...||+||+|+.
T Consensus         3 ~~~ILiVdd~~~~~~~L~~~L~~~~~~~vv~~a~~~~~al~~~~--~~~~DlVllD~~   58 (354)
T PRK00742          3 KIRVLVVDDSAFMRRLISEILNSDPDIEVVGTAPDGLEAREKIK--KLNPDVITLDVE   58 (354)
T ss_pred             ccEEEEECCCHHHHHHHHHHHhhCCCCEEEEEECCHHHHHHHHh--hhCCCEEEEeCC
Confidence            469999999999999999999876 88876 8899999999998  678999999997

>PRK12555 chemotaxis-specific methylesterase; Provisional

Probab=96.83  E-value=0.0038  Score=62.18  Aligned_cols=53  Identities=13%  Similarity=0.197  Sum_probs=47.8

Q ss_pred             cEEEEEeCChhhHHHHHHHHH-cCCCEEE-EECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLR-NCSYEVT-AVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe-~~GyeV~-~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ++||||||++..+..+..+|+ ..+|++. .+.++.++++.+.  ...||+||+|+.
T Consensus         1 ~~VLvVdd~~~~~~~l~~~L~~~~~~~vv~~a~~~~eal~~l~--~~~pDlVllD~~   55 (337)
T PRK12555          1 MRIGIVNDSPLAVEALRRALARDPDHEVVWVATDGAQAVERCA--AQPPDVILMDLE   55 (337)
T ss_pred             CEEEEEeCCHHHHHHHHHHHhhCCCCEEEEEECCHHHHHHHHh--ccCCCEEEEcCC
Confidence            379999999999999999994 6688876 7899999999998  678999999998

>PRK10360 DNA-binding transcriptional activator UhpA; Provisional

Probab=96.81  E-value=0.0044  Score=54.79  Aligned_cols=53  Identities=17%  Similarity=0.202  Sum_probs=46.8

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcC-CCE-EEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNC-SYE-VTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~-Gye-V~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ++||||||++..+..+..+|... ++. +..+.++.+++..+.  ...||+||+|+.
T Consensus         2 ~~ilivd~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~l~~~~--~~~~dlvi~d~~   56 (196)
T PRK10360          2 ITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLP--GRGVQVCICDIS   56 (196)
T ss_pred             eEEEEECCcHHHHHHHHHHHccCCCcEEEEEECCHHHHHHHHh--cCCCCEEEEeCC
Confidence            58999999999999999999754 676 568899999999998  678999999987

>PRK10840 transcriptional regulator RcsB; Provisional

Probab=96.80  E-value=0.0041  Score=57.18  Aligned_cols=53  Identities=13%  Similarity=0.208  Sum_probs=47.2

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCC-E-EEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSY-E-VTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~Gy-e-V~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ++||||||++.++..+..+|+..++ . +..+.++.+++..+.  ...||+||+|+.
T Consensus         4 ~~Ilivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~~~~~~~--~~~~DlvllD~~   58 (216)
T PRK10840          4 MNVIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLP--KLDAHVLITDLS   58 (216)
T ss_pred             eEEEEECCcHHHHHHHHHHHhcCCCCEEEEEECCHHHHHHHHH--hCCCCEEEEeCc
Confidence            5899999999999999999987665 4 667899999999988  678999999987

>TIGR01387 cztR_silR_copR heavy metal response regulator

Probab=96.71  E-value=0.0052  Score=54.83  Aligned_cols=51  Identities=20%  Similarity=0.358  Sum_probs=47.7

Q ss_pred             EEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           75 VLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        75 VLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ||||||++..+..+...|+..||.+..+.++.+++..+.  ...||+||+|+.
T Consensus         1 iliidd~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~--~~~~dlvl~d~~   51 (218)
T TIGR01387         1 ILVVEDEQKTAEYLQQGLSESGYVVDAASNGRDGLHLAL--KDDYDLIILDVM   51 (218)
T ss_pred             CEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh--cCCCCEEEEeCC
Confidence            689999999999999999999999999999999999998  678999999987

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.

>PRK10610 chemotaxis regulatory protein CheY; Provisional

Probab=96.70  E-value=0.01  Score=46.75  Aligned_cols=54  Identities=22%  Similarity=0.435  Sum_probs=48.2

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCE-EEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYE-VTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~Gye-V~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .++||++++++.....+...|+..|+. +..+.++.+++..+.  ...+|+||+|..
T Consensus         5 ~~~il~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~--~~~~di~l~d~~   59 (129)
T PRK10610          5 ELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQ--AGGFGFVISDWN   59 (129)
T ss_pred             cceEEEEcCCHHHHHHHHHHHHHcCCCeEEEeCCHHHHHHHhh--ccCCCEEEEcCC
Confidence            468999999999999999999988985 778899999999887  678999999976

>COG2201 CheB Chemotaxis response regulator containing a CheY-like receiver domain and a methylesterase domain [Cell motility and secretion / Signal transduction mechanisms]

Probab=96.67  E-value=0.0043  Score=63.48  Aligned_cols=54  Identities=22%  Similarity=0.338  Sum_probs=49.8

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCC-CE-EEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCS-YE-VTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~G-ye-V~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +++||||||...+|..|..+|...+ ++ |..+.|+.+|++.+.  ...||+|+||+.
T Consensus         1 ~irVlvVddsal~R~~i~~~l~~~~~i~vv~~a~ng~~a~~~~~--~~~PDVi~ld~e   56 (350)
T COG2201           1 KIRVLVVDDSALMRKVISDILNSDPDIEVVGTARNGREAIDKVK--KLKPDVITLDVE   56 (350)
T ss_pred             CcEEEEEcCcHHHHHHHHHHHhcCCCeEEEEecCCHHHHHHHHH--hcCCCEEEEecc
Confidence            3699999999999999999999988 55 678999999999999  789999999999

>PRK15479 transcriptional regulatory protein TctD; Provisional

Probab=96.63  E-value=0.0079  Score=53.76  Aligned_cols=52  Identities=19%  Similarity=0.330  Sum_probs=48.4

Q ss_pred             EEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           74 KVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        74 rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +|||+++++..+..+..+|+..|+.+..+.++.+++..+.  ...||+||+|+.
T Consensus         2 ~ilivd~~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~--~~~~d~vild~~   53 (221)
T PRK15479          2 RLLLAEDNRELAHWLEKALVQNGFAVDCVFDGLAADHLLQ--SEMYALAVLDIN   53 (221)
T ss_pred             eEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHh--hCCCCEEEEeCC
Confidence            7999999999999999999999999999999999998887  678999999987

>PRK10430 DNA-binding transcriptional activator DcuR; Provisional

Probab=96.62  E-value=0.0072  Score=56.78  Aligned_cols=55  Identities=16%  Similarity=0.280  Sum_probs=46.0

Q ss_pred             cEEEEEeCChhhHHHHHHHHHc-CCCEE-EEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRN-CSYEV-TAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~-~GyeV-~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ++||||||++.++..+..+|.. .++.+ ..+.++.+++..+......||+||+|+.
T Consensus         2 ~~VLivdd~~~~~~~l~~~L~~~~~~~~~~~~~~~~~a~~~~~~~~~~~DlvilD~~   58 (239)
T PRK10430          2 INVLIVDDDAMVAELNRRYVAQIPGFQCCGTASTLEQAKEIIFNSDTPIDLILLDIY   58 (239)
T ss_pred             eeEEEEcCCHHHHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhcCCCCCEEEEecC
Confidence            5899999999999999999986 47764 4788999999988521357999999997

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=96.61  E-value=0.0073  Score=62.04  Aligned_cols=53  Identities=23%  Similarity=0.418  Sum_probs=50.1

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .+||||||++..+..+...|...||.|..+.++.+|+..+.  ...||+||+|+.
T Consensus         5 ~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~--~~~~dlillD~~   57 (457)
T PRK11361          5 NRILIVDDEDNVRRMLSTAFALQGFETHCANNGRTALHLFA--DIHPDVVLMDIR   57 (457)
T ss_pred             CeEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh--cCCCCEEEEeCC
Confidence            48999999999999999999999999999999999999998  678999999988

>COG4566 TtrR Response regulator [Signal transduction mechanisms]

Probab=96.60  E-value=0.0055  Score=57.97  Aligned_cols=54  Identities=19%  Similarity=0.273  Sum_probs=50.2

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ...|.|||||..+|+.+..+|+..||++..+.++.+.+....  ...|.++|+|+.
T Consensus         4 ~~~V~vVDDD~~vr~al~~Ll~s~G~~v~~~~s~~~fL~~~~--~~~pGclllDvr   57 (202)
T COG4566           4 EPLVHVVDDDESVRDALAFLLESAGFQVKCFASAEEFLAAAP--LDRPGCLLLDVR   57 (202)
T ss_pred             CCeEEEEcCcHHHHHHHHHHHHhCCceeeeecCHHHHHhhcc--CCCCCeEEEecC
Confidence            347999999999999999999999999999999999999876  678999999999

>COG3947 Response regulator containing CheY-like receiver and SARP domains [Signal transduction mechanisms]

Probab=96.59  E-value=0.0029  Score=63.45  Aligned_cols=53  Identities=19%  Similarity=0.403  Sum_probs=50.6

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ++|+|||||..+...|..+|.+.|+.+..+....+|+..|.  ...|||||+|+.
T Consensus         1 ~~~iiVDdd~a~~~~l~~iLs~~~~~~~~~~~~~eal~~Le--~~kpDLifldI~   53 (361)
T COG3947           1 PRIIIVDDDAAIVKLLSVILSRAGHEVRSCSHPVEALDLLE--VFKPDLIFLDIV   53 (361)
T ss_pred             CcEEEEcchHHHHHHHHHHHHhccchhhccCCHHHHHHHHH--hcCCCEEEEEee
Confidence            47999999999999999999999988999999999999999  789999999999

>COG3706 PleD Response regulator containing a CheY-like receiver domain and a GGDEF domain [Signal transduction mechanisms]

Probab=96.57  E-value=0.0055  Score=64.34  Aligned_cols=55  Identities=22%  Similarity=0.332  Sum_probs=52.1

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ...+||||||+...+..+..+|...||.+..+.++.+|+..+.  +..||+||+|+.
T Consensus       131 ~~~kILvvdD~~~~~~~l~~~L~~~g~~v~~a~~~~~Al~~~~--e~~~dlil~d~~  185 (435)
T COG3706         131 APKKILVVDDDATQRERLRRILQVEGFRVVEATDGEEALLQLA--ELPPDLVLLDAN  185 (435)
T ss_pred             cCceEEEEcCcHHHHHHHHHHHHhccceeeeecCHHHHHHHHh--cCCCcEEEEecC
Confidence            3469999999999999999999999999999999999999999  679999999999

>PRK14084 two-component response regulator; Provisional

Probab=96.55  E-value=0.0082  Score=55.98  Aligned_cols=53  Identities=23%  Similarity=0.431  Sum_probs=47.0

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCC-C-EEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCS-Y-EVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~G-y-eV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ++||||||++..+..+..+|+..+ + .+..+.++.+++..+.  ...||+||+|+.
T Consensus         1 ~~ilivdd~~~~~~~l~~~l~~~~~~~~v~~~~~~~~~l~~~~--~~~~dlv~lDi~   55 (246)
T PRK14084          1 MKALIVDDEPLARNELTYLLNEIGGFEEINEAENVKETLEALL--INQYDIIFLDIN   55 (246)
T ss_pred             CEEEEECCCHHHHHHHHHHHHhCCCceEEEEECCHHHHHHHHH--hcCCCEEEEeCC
Confidence            479999999999999999998765 4 4678999999999998  678999999998

>PRK13558 bacterio-opsin activator; Provisional

Probab=96.50  E-value=0.0051  Score=66.19  Aligned_cols=53  Identities=25%  Similarity=0.300  Sum_probs=49.8

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ++||||||++.++..+..+|...||.|..+.++.+++..+.  ...|||||+|+.
T Consensus         8 ~~ILivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~al~~~~--~~~~Dlvl~d~~   60 (665)
T PRK13558          8 RGVLFVGDDPEAGPVDCDLDEDGRLDVTQIRDFVAARDRVE--AGEIDCVVADHE   60 (665)
T ss_pred             eeEEEEccCcchHHHHHHHhhccCcceEeeCCHHHHHHHhh--ccCCCEEEEecc
Confidence            58999999999999999999989999999999999999998  678999999987

>PRK09581 pleD response regulator PleD; Reviewed

Probab=96.50  E-value=0.0088  Score=59.85  Aligned_cols=53  Identities=23%  Similarity=0.301  Sum_probs=49.8

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .+||||++++..+..+..+|...||.+..+.++.+++..+.  ...||+||+|+.
T Consensus         3 ~~ilii~~~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~--~~~~dlvi~d~~   55 (457)
T PRK09581          3 ARILVVDDIPANVKLLEAKLLAEYYTVLTASSGAEAIAICE--REQPDIILLDVM   55 (457)
T ss_pred             CeEEEEeCCHHHHHHHHHHHHhCCCEEEEeCCHHHHHHHHh--hcCCCEEEEeCC
Confidence            48999999999999999999988999999999999999998  678999999997

>TIGR02875 spore_0_A sporulation transcription factor Spo0A

Probab=96.48  E-value=0.0094  Score=56.43  Aligned_cols=54  Identities=13%  Similarity=0.335  Sum_probs=47.4

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcC-CCEE-EEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNC-SYEV-TAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~-GyeV-~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .++||||||++..+..+..+|... ++.+ ..+.++.+++..+.  ...||+||+|+.
T Consensus         2 ~~~vLivdd~~~~~~~l~~~L~~~~~~~~~~~a~~~~eal~~l~--~~~~DlvllD~~   57 (262)
T TIGR02875         2 KIRIVIADDNKEFCNLLKEYLAAQPDMEVVGVAHNGVDALELIK--EQQPDVVVLDII   57 (262)
T ss_pred             CcEEEEEcCCHHHHHHHHHHHhcCCCeEEEEEeCCHHHHHHHHH--hcCCCEEEEeCC
Confidence            358999999999999999999864 5664 47899999999998  678999999988

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.

>KOG0519 consensus Sensory transduction histidine kinase [Signal transduction mechanisms]

Probab=96.46  E-value=0.0037  Score=69.92  Aligned_cols=56  Identities=25%  Similarity=0.418  Sum_probs=52.2

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ...+||||||+...+.+...+|++.|.++..+.+|.+|+..+.. .+.||+||||+-
T Consensus       665 ~g~~iLlvddn~vn~~Va~~~l~~~g~~~~~~~sg~e~l~~~~~-~~~y~~ifmD~q  720 (786)
T KOG0519|consen  665 TGPKILLVDDNPVNRKVATGMLKKLGAEVTEVNSGQEALDKLKP-PHSYDVIFMDLQ  720 (786)
T ss_pred             cCCceEEEecccchHHHHHHHHHHhCCeeEeecCcHHHHHhcCC-CCcccEEEEEcC
Confidence            45699999999999999999999999999999999999999974 578999999998

>PRK09935 transcriptional regulator FimZ; Provisional

Probab=96.42  E-value=0.013  Score=51.90  Aligned_cols=53  Identities=13%  Similarity=0.294  Sum_probs=47.0

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcC-CCEEE-EECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNC-SYEVT-AVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~-GyeV~-~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .+||||+|++..+..+..+|+.. ++.+. .+.++.+++..+.  ...||+||+|+.
T Consensus         4 ~~iliv~d~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~--~~~~dlvild~~   58 (210)
T PRK09935          4 ASVIIMDTHPIIRMSIEVLLQKNSELQIVLKTDDYRITIDYLR--TRPVDLIIMDID   58 (210)
T ss_pred             ceEEEECCcHHHHHHHHHHHhhCCCceEEEEeCCHHHHHHHHH--hcCCCEEEEeCC
Confidence            58999999999999999999876 57865 6789999999888  678999999987

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=96.41  E-value=0.0079  Score=61.98  Aligned_cols=51  Identities=27%  Similarity=0.465  Sum_probs=48.2

Q ss_pred             EEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           75 VLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        75 VLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ||||||++.++..+..+|+..||.|..+.++.+|+..+.  ...||+||+|+.
T Consensus         1 ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~--~~~~DlVllD~~   51 (463)
T TIGR01818         1 VWVVDDDRSIRWVLEKALSRAGYEVRTFGNAASVLRALA--RGQPDLLITDVR   51 (463)
T ss_pred             CEEEECCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHh--cCCCCEEEEcCC
Confidence            689999999999999999999999999999999999998  678999999997

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.

>PRK09191 two-component response regulator; Provisional

Probab=96.26  E-value=0.015  Score=54.51  Aligned_cols=54  Identities=15%  Similarity=0.242  Sum_probs=49.1

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEE-EECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVT-AVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~-~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ..+|||++|++..+..+...|+..|+.+. .+.++.+++..+.  ...||+||+|+.
T Consensus       137 ~~~~liidd~~~~~~~l~~~L~~~~~~~~~~~~~~~~~l~~l~--~~~~dlvi~d~~  191 (261)
T PRK09191        137 ATRVLIIEDEPIIAMDLEQLVESLGHRVTGIARTRAEAVALAK--KTRPGLILADIQ  191 (261)
T ss_pred             CCeEEEEcCcHHHHHHHHHHHhcCCCEEEEEECCHHHHHHHHh--ccCCCEEEEecC
Confidence            35899999999999999999998899977 6889999999998  678999999997

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=95.99  E-value=0.016  Score=59.57  Aligned_cols=49  Identities=18%  Similarity=0.283  Sum_probs=45.7

Q ss_pred             EEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           75 VLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        75 VLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ||||||++.++..+...|  .||.|..+.++.+|++.+.  ...||+||+|+.
T Consensus         1 ILivddd~~~~~~l~~~l--~~~~v~~a~~~~~al~~l~--~~~~dlvllD~~   49 (445)
T TIGR02915         1 LLIVEDDLGLQKQLKWSF--ADYELAVAADRESAIALVR--RHEPAVVTLDLG   49 (445)
T ss_pred             CEEEECCHHHHHHHHHHh--CCCeEEEeCCHHHHHHHHh--hCCCCEEEEeCC
Confidence            689999999999999888  7899999999999999998  678999999987

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).

>PRK15369 two component system sensor kinase SsrB; Provisional

Probab=95.94  E-value=0.031  Score=48.74  Aligned_cols=54  Identities=22%  Similarity=0.383  Sum_probs=46.8

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcC-CCEE-EEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNC-SYEV-TAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~-GyeV-~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .++||||++++..+..+..+|... ++.+ ..+.++.+++..+.  ...||+||+|+.
T Consensus         3 ~~~iliv~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~--~~~~dlvl~d~~   58 (211)
T PRK15369          3 NYKILLVDDHELIINGIKNMLAPYPRYKIVGQVDNGLEVYNACR--QLEPDIVILDLG   58 (211)
T ss_pred             ccEEEEECCcHHHHHHHHHHHccCCCcEEEEEECCHHHHHHHHH--hcCCCEEEEeCC
Confidence            468999999999999999999875 5664 47889999998887  678999999987

>PRK10403 transcriptional regulator NarP; Provisional

Probab=95.87  E-value=0.031  Score=49.28  Aligned_cols=54  Identities=22%  Similarity=0.337  Sum_probs=47.2

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHc-CCCEEE-EECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRN-CSYEVT-AVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~-~GyeV~-~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ..+||||++++..+..+...|+. .+|.+. .+.++.+++..+.  ...||+||+|+.
T Consensus         6 ~~~ilii~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~--~~~~dlvi~d~~   61 (215)
T PRK10403          6 PFQVLIVDDHPLMRRGVRQLLELDPGFEVVAEAGDGASAIDLAN--RLDPDVILLDLN   61 (215)
T ss_pred             eEEEEEEcCCHHHHHHHHHHHhcCCCCEEEEEeCCHHHHHHHHH--hcCCCEEEEecC
Confidence            35899999999999999999975 578865 6889999999887  678999999987

>cd00156 REC Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; contains a phosphoacceptor site that is phosphorylated by histidine kinase homologs; usually found N-terminal to a DNA binding effector domain; forms homodimers

Probab=95.76  E-value=0.038  Score=40.95  Aligned_cols=50  Identities=26%  Similarity=0.439  Sum_probs=45.5

Q ss_pred             EEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           76 LLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        76 LLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      |++++++..+..+...|...|+.+..+.+..+++..+.  ...+|+||+|+.
T Consensus         1 l~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~--~~~~~~ii~~~~   50 (113)
T cd00156           1 LIVDDDPLIRELLRRLLEKEGYEVVEAEDGEEALALLA--EEKPDLILLDIM   50 (113)
T ss_pred             CeecCcHHHHHHHHHHHhhcCceEEEecCHHHHHHHHH--hCCCCEEEEecC
Confidence            57899999999999999988999999999999999888  678999999987

>PRK10651 transcriptional regulator NarL; Provisional

Probab=95.66  E-value=0.047  Score=48.32  Aligned_cols=54  Identities=19%  Similarity=0.290  Sum_probs=46.7

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcC-CCEE-EEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNC-SYEV-TAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~-GyeV-~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ..+||||++++..+..+..+|... ++.+ ..+.++.+++..+.  ...||+||+|+.
T Consensus         6 ~~~iliv~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~--~~~~dlvl~d~~   61 (216)
T PRK10651          6 PATILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAE--SLDPDLILLDLN   61 (216)
T ss_pred             ceEEEEECCCHHHHHHHHHHHccCCCcEEEEEeCCHHHHHHHHH--hCCCCEEEEeCC
Confidence            358999999999999999999864 5664 46889999999998  678999999987

>PRK09581 pleD response regulator PleD; Reviewed

Probab=95.60  E-value=0.024  Score=56.77  Aligned_cols=54  Identities=20%  Similarity=0.375  Sum_probs=48.0

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ...+||||||++..+..+..+|.. .+.+..+.++.+|+..+.  ...||+||+|+.
T Consensus       154 ~~~~vlivdd~~~~~~~l~~~l~~-~~~~~~~~~~~~a~~~~~--~~~~d~vi~d~~  207 (457)
T PRK09581        154 EDGRILLVDDDVSQAERIANILKE-EFRVVVVSDPSEALFNAA--ETNYDLVIVSAN  207 (457)
T ss_pred             cCceEEEEecccchHHHHHHHHhh-cceeeeecChHHHHHhcc--cCCCCEEEecCC
Confidence            346899999999999999999964 577778999999999988  788999999997

>COG3707 AmiR Response regulator with putative antiterminator output domain [Signal transduction mechanisms]

Probab=95.27  E-value=0.022  Score=53.92  Aligned_cols=55  Identities=25%  Similarity=0.360  Sum_probs=49.8

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHcCCCE-EEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRNCSYE-VTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~~Gye-V~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +.++||+++|.+..+..+...|...||. |..+.++..+.+.+.  ...||+||+|+.
T Consensus         4 ~~lrvlv~~d~~i~~~~i~~~l~eag~~~Vg~~~~~~~~~~~~~--~~~pDvVildie   59 (194)
T COG3707           4 MLLRVLVADDEALTRMDIREGLLEAGYQRVGEAADGLEAVEVCE--RLQPDVVILDIE   59 (194)
T ss_pred             cccceeeccccccchhhHHHHHHHcCCeEeeeecccccchhHHH--hcCCCEEEEecC
Confidence            4579999999999999999999999998 557889999999998  789999999998

>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional

Probab=94.65  E-value=0.057  Score=51.28  Aligned_cols=52  Identities=13%  Similarity=0.130  Sum_probs=43.5

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHcCCCE-EEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRNCSYE-VTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~~Gye-V~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .+.+|+||+|++..+..|..+|+ .++. +..+.++.+++..+.    .||+||+|+.
T Consensus         9 ~~~~~~~v~~~~l~~~~l~~~L~-~~~~v~~~~~~~~~~~~~~~----~~DvvllDi~   61 (216)
T PRK10100          9 HGHTLLLITKPSLQATALLQHLK-QSLAITGKLHNIQRSLDDIS----SGSIILLDMM   61 (216)
T ss_pred             cCceEEEEeChHhhhHHHHHHHH-HhCCCeEEEcCHHHhhccCC----CCCEEEEECC
Confidence            34579999999999999999998 4565 556789999888754    4999999999

>COG3279 LytT Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]

Probab=86.98  E-value=1.3  Score=42.97  Aligned_cols=55  Identities=25%  Similarity=0.372  Sum_probs=46.7

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcC-CCE-EEEECCHHHHHHHHHhcCCCccEEEEcCC-C
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNC-SYE-VTAVANSLHAWKILEDLTNHIDIVLTESS-G  128 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~-Gye-V~~A~dg~eAle~L~~~~~~pDLIIlDl~-G  128 (399)
                      +++|+++||++..++.+..++... .++ +..+.++.++++.+.  ...+|++++|+. +
T Consensus         1 m~~i~i~dd~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~fldI~~~   58 (244)
T COG3279           1 MLKVLIVDDEPLAREELRRILNEIPDIEIVGEAENGEEALQLLQ--GLRPDLVFLDIAMP   58 (244)
T ss_pred             CCcEEEecCCHHHHHHHHHHHHhhhhcCeeeeeccchhhHHHHh--ccCCCeEEEeeccC
Confidence            468999999999999999999842 333 337889999999999  679999999999 6

>PRK11107 hybrid sensory histidine kinase BarA; Provisional

Probab=85.81  E-value=1.8  Score=48.13  Aligned_cols=103  Identities=17%  Similarity=0.159  Sum_probs=71.5

Q ss_pred             eeccccCCCCchhhhhhccc--ccc--CCCCCCCccccCCCcCCCCCCCCCCccccccccCCCCCcEEEEEeCChhhHHH
Q 039733           12 VAGEGHGLGSSEEDESRVDD--AVN--SNNGPGGTIQVHDGFQISQQQQPQGSVIRWERFLPTRSLKVLLVENDDSTRHV   87 (399)
Q Consensus        12 ~~~~~~~l~~S~e~~~r~~~--~~~--~~~g~~~av~~~~~~~~p~~~~~~~~~~~~e~~lp~~~~rVLLVEDD~~~rei   87 (399)
                      .-|+|.||.+.++....++|  ...  .+.|..|.+..+........ ....+.      ......+|||+|+++..+..
T Consensus       479 ~~g~GLGL~i~~~i~~~~gG~i~v~s~~~~Gt~f~i~lp~~~~~~~~-~~~~~~------~~~~g~~ili~d~~~~~~~~  551 (919)
T PRK11107        479 HGGTGLGLVITQKLVNEMGGDISFHSQPNRGSTFWFHLPLDLNPNPI-IDGLPT------DCLAGKRLLYVEPNSAAAQA  551 (919)
T ss_pred             CCCcchhHHHHHHHHHHhCCEEEEEecCCCCEEEEEEEEeccCCccc-cccCCc------cccCCCeEEEEeCCHHHHHH
Confidence            34889999999999988988  323  33455555555432211110 000010      11124599999999999999


Q ss_pred             HHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           88 VSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        88 L~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +..+|..+||.+..+.+..+    +.  ...||++|+|+.
T Consensus       552 l~~~L~~~g~~v~~~~~~~~----l~--~~~~d~il~~~~  585 (919)
T PRK11107        552 TLDILSETPLEVTYSPTLSQ----LP--EAHYDILLLGLP  585 (919)
T ss_pred             HHHHHHHCCCEEEEcCCHHH----hc--cCCCCEEEeccc
Confidence            99999999999999988877    44  568999999987

>COG0512 PabA Anthranilate/para-aminobenzoate synthases component II [Amino acid transport and metabolism / Coenzyme metabolism]

Probab=85.63  E-value=1.3  Score=41.98  Aligned_cols=60  Identities=27%  Similarity=0.372  Sum_probs=47.3

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC-CCCCCCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS-GSGSGSG  134 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~-Gsssgs~  134 (399)
                      ++|||||+.+.+-.-|..+|+..|++|.++.+....+..++  ...||+||+--. |.-...|
T Consensus         2 ~~IL~IDNyDSFtyNLv~yl~~lg~~v~V~rnd~~~~~~~~--~~~pd~iviSPGPG~P~d~G   62 (191)
T COG0512           2 MMILLIDNYDSFTYNLVQYLRELGAEVTVVRNDDISLELIE--ALKPDAIVISPGPGTPKDAG   62 (191)
T ss_pred             ceEEEEECccchHHHHHHHHHHcCCceEEEECCccCHHHHh--hcCCCEEEEcCCCCChHHcc
Confidence            58999999999999999999999998887777644444555  567999999777 6444443

>PF06490 FleQ: Flagellar regulatory protein FleQ; InterPro: IPR010518 This domain is found at the N terminus of a subset of sigma54-dependent transcriptional activators that are involved in regulation of flagellar motility e

Probab=83.17  E-value=2.3  Score=36.26  Aligned_cols=50  Identities=18%  Similarity=0.166  Sum_probs=36.0

Q ss_pred             EEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcC
Q 039733           74 KVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTES  126 (399)
Q Consensus        74 rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl  126 (399)
                      ||||||||...++.|..+|+=.|+++..+....- .....  ....+.+++-+
T Consensus         1 kILvIddd~~R~~~L~~ILeFlGe~~~~~~~~~~-~~~~~--~~~~~~~~v~~   50 (109)
T PF06490_consen    1 KILVIDDDAERRQRLSTILEFLGEQCEAVSSSDW-SQADW--SSPWEACAVIL   50 (109)
T ss_pred             CEEEECCcHHHHHhhhhhhhhcCCCeEEecHHHH-HHhhh--hcCCcEEEEEe
Confidence            6999999999999999999988999887765332 23333  34455554433

g. FleQ in Pseudomonas aeruginosa. It is clearly related to IPR001789 from INTERPRO, but lacks the conserved aspartate residue that undergoes phosphorylation in the classic two-component system response regulator (IPR001789 from INTERPRO).

>PRK07649 para-aminobenzoate/anthranilate synthase glutamine amidotransferase component II; Validated

Probab=80.03  E-value=2.4  Score=39.64  Aligned_cols=51  Identities=18%  Similarity=0.223  Sum_probs=39.9

Q ss_pred             EEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           75 VLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        75 VLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      |||||....+-..|...|++.|+++.++......++.+.  ...||.||+--.
T Consensus         2 il~idn~dsft~nl~~~l~~~g~~v~v~~~~~~~~~~~~--~~~~d~iIlsgG   52 (195)
T PRK07649          2 ILMIDNYDSFTFNLVQFLGELGQELVVKRNDEVTISDIE--NMKPDFLMISPG   52 (195)
T ss_pred             EEEEeCCCccHHHHHHHHHHCCCcEEEEeCCCCCHHHHh--hCCCCEEEECCC
Confidence            899999999999999999999999887765543444455  457898887443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	399
3luf_A	259	Two-component system response regulator/ggdef doma	1e-07
2rdm_A	132	Response regulator receiver protein; structural ge	2e-07
3eq2_A	394	Probable two-component response regulator; adaptor	3e-06
3jte_A	143	Response regulator receiver protein; structural ge	5e-06
3hdg_A	137	Uncharacterized protein; two-component sensor acti	7e-05
2rjn_A	154	Response regulator receiver:metal-dependent phosph	7e-05
3hv2_A	153	Response regulator/HD domain protein; PSI-2, NYSGX	9e-05
1dcf_A	136	ETR1 protein; beta-alpha five sandwich, transferas	9e-05
3c97_A	140	Signal transduction histidine kinase; structural g	9e-05
3m6m_D	143	Sensory/regulatory protein RPFC; RPFF, REC, enoyl-	1e-04
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	1e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-04
1dc7_A	124	NTRC, nitrogen regulation protein; receiver domain	1e-04
2qxy_A	142	Response regulator; regulation of transcription, N	2e-04
1mb3_A	124	Cell division response regulator DIVK; signal tran	2e-04
1xhf_A	123	DYE resistance, aerobic respiration control protei	2e-04
2ayx_A	254	Sensor kinase protein RCSC; two independent struct	2e-04
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	2e-04
3hzh_A	157	Chemotaxis response regulator (CHEY-3); phosphatas	3e-04
3cfy_A	137	Putative LUXO repressor protein; structural genomi	4e-04
3eod_A	130	Protein HNR; response regulator, phosphoprotein, t	5e-04
1srr_A	124	SPO0F, sporulation response regulatory protein; as	6e-04
1w25_A	459	Stalked-cell differentiation controlling protein;	7e-04
1zgz_A	122	Torcad operon transcriptional regulatory protein;	7e-04

>3luf_A Two-component system response regulator/ggdef domain protein; structural genomics, ASA_2441, PSI-2, protein structure initiative; HET: MSE; 1.76A {Aeromonas salmonicida} PDB: 3mf4_A* Length = 259

 Score = 51.1 bits (123), Expect = 1e-07
 Identities = 16/60 (26%), Positives = 29/60 (48%), Gaps = 1/60 (1%)

Query: 65  ERFLPTRSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLT 124
            R    + ++VL+V++  ++RH   A LR    +V   +++  A   LE     I +VL 
Sbjct: 117 HRLYLNQQIEVLVVDDSRTSRHRTMAQLRKQLLQVHEASHAREALATLEQ-HPAIRLVLV 175

>2rdm_A Response regulator receiver protein; structural genomics, unknown function, PSI-2, protein struct initiative; HET: MSE; 1.76A {Sinorhizobium medicae} Length = 132

 Score = 49.1 bits (118), Expect = 2e-07
 Identities = 13/57 (22%), Positives = 29/57 (50%), Gaps = 1/57 (1%)

Query: 68  LPTRSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLT 124
           +   ++ +LL +++        + L +  + VTAV++   A ++L+     ID V+T
Sbjct: 1   MSLEAVTILLADDEAILLLDFESTLTDAGFLVTAVSSGAKAIEMLKSGA-AIDGVVT 56

>3eq2_A Probable two-component response regulator; adaptor sigmas, signaling protein; 3.40A {Pseudomonas aeruginosa} PDB: 3f7a_A Length = 394

 Score = 48.0 bits (114), Expect = 3e-06
 Identities = 13/54 (24%), Positives = 28/54 (51%), Gaps = 2/54 (3%)

Query: 71  RSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLT 124
            S  +L++++D+  R  ++A L + +++V    N L   +I E      D+V+ 
Sbjct: 4   VSATLLIIDDDEVVRESLAAYLEDSNFKVLQALNGLQGLQIFES--EQPDLVIC 55

>3jte_A Response regulator receiver protein; structural genomics, nysgrc, response regulator receiver domain, target 11226E, PSI-2; 1.90A {Clostridium thermocellum atcc 27405} Length = 143

 Score = 44.8 bits (107), Expect = 5e-06
 Identities = 13/51 (25%), Positives = 27/51 (52%)

Query: 74  KVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLT 124
           K+L+++++ +    +  LL     EV   ++S    +I  +  N ID+V+T
Sbjct: 5   KILVIDDESTILQNIKFLLEIDGNEVLTASSSTEGLRIFTENCNSIDVVIT 55

>3hdg_A Uncharacterized protein; two-component sensor activity, response regulator, PSI-II, 11227F, NYSGXRC, structural genomics; 2.27A {Wolinella succinogenes} Length = 137

 Score = 41.4 bits (98), Expect = 7e-05
 Identities = 13/53 (24%), Positives = 28/53 (52%), Gaps = 2/53 (3%)

Query: 72  SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLT 124
           +LK+L+VE+D   R  +S ++ N   EV +  +     ++     +  D+++T
Sbjct: 7   ALKILIVEDDTDAREWLSTIISNHFPEVWSAGDGEEGERLFGL--HAPDVIIT 57

>2rjn_A Response regulator receiver:metal-dependent phosphohydrolase, HD subdomain; structural genomics, oceanospirillum SP. MED92; 2.10A {Neptuniibacter caesariensis} Length = 154

 Score = 41.8 bits (99), Expect = 7e-05
 Identities = 9/57 (15%), Positives = 27/57 (47%), Gaps = 2/57 (3%)

Query: 68  LPTRSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLT 124
           L  ++  V+LV+++    + +  L++     +    + L A + L+     + +V++
Sbjct: 3   LNYKNYTVMLVDDEQPILNSLKRLIKRLGCNIITFTSPLDALEALK--GTSVQLVIS 57

>3hv2_A Response regulator/HD domain protein; PSI-2, NYSGXRC, structural genomics, protein structure initiative; 1.50A {Pseudomonas fluorescens pf-5} Length = 153

 Score = 41.4 bits (98), Expect = 9e-05
 Identities = 12/56 (21%), Positives = 28/56 (50%), Gaps = 2/56 (3%)

Query: 69  PTRSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLT 124
            TR  ++LLV++ +     +  LL    Y +    ++  A ++L   +  +D+V++
Sbjct: 11  VTRRPEILLVDSQEVILQRLQQLLSPLPYTLHFARDATQALQLLA--SREVDLVIS 64

>1dcf_A ETR1 protein; beta-alpha five sandwich, transferase; 2.50A {Arabidopsis thaliana} SCOP: c.23.1.2 Length = 136

 Score = 41.0 bits (97), Expect = 9e-05
 Identities = 14/53 (26%), Positives = 27/53 (50%), Gaps = 3/53 (5%)

Query: 71  RSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVL 123
             LKVL+++ +  +R V   LL +   EVT V+++      L  +++   +V 
Sbjct: 6   TGLKVLVMDENGVSRMVTKGLLVHLGCEVTTVSSNEEC---LRVVSHEHKVVF 55

>3c97_A Signal transduction histidine kinase; structural genomics, signaling, PSI-2, protein structure initiative; 1.70A {Aspergillus oryzae RIB40} Length = 140

 Score = 41.0 bits (97), Expect = 9e-05
 Identities = 15/55 (27%), Positives = 27/55 (49%), Gaps = 2/55 (3%)

Query: 69  PTRSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVL 123
               L VL+ E++D  R V +  L  C+ ++T V N L A +  +      D+++
Sbjct: 7   QIMPLSVLIAEDNDICRLVAAKALEKCTNDITVVTNGLQALQAYQ--NRQFDVII 59

>3m6m_D Sensory/regulatory protein RPFC; RPFF, REC, enoyl-COA hydratase, lyase-transferase COMP; 2.50A {Xanthomonas campestris PV} Length = 143

 Score = 41.0 bits (97), Expect = 1e-04
 Identities = 11/55 (20%), Positives = 25/55 (45%), Gaps = 2/55 (3%)

Query: 69  PTRSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVL 123
             RS+++L+ ++ ++ R V+  LL    ++V  V  +      +       D V+
Sbjct: 11  RVRSMRMLVADDHEANRMVLQRLLEKAGHKVLCVNGAEQVLDAMA--EEDYDAVI 63

>1ny5_A Transcriptional regulator (NTRC family); AAA+ ATPase, sigma54 activator, bacterial transcription, DIM transcription; HET: ADP; 2.40A {Aquifex aeolicus} SCOP: c.23.1.1 c.37.1.20 PDB: 1ny6_A* 3m0e_A* 1zy2_A* Length = 387

 Score = 42.8 bits (102), Expect = 1e-04
 Identities = 13/52 (25%), Positives = 26/52 (50%), Gaps = 2/52 (3%)

Query: 73  LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLT 124
           + VL++E+D   R ++   L     +V +      A+K+L +   H ++VL 
Sbjct: 1   MNVLVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLLSE--KHFNVVLL 50

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 43.3 bits (101), Expect = 1e-04
 Identities = 55/385 (14%), Positives = 99/385 (25%), Gaps = 107/385 (27%)

Query: 46  HDGFQISQQQQPQGSVIRWERFLPT--RSLKVLLVENDDSTRHVVSALLRNCSYEVTAVA 103
           H  F+  + Q     ++    F      +     V+  D  + ++S        E+  + 
Sbjct: 6   HMDFETGEHQYQYKDIL--SVFEDAFVDNFDCKDVQ--DMPKSILS------KEEIDHII 55

Query: 104 NSLHAWKILEDLTNHIDIVLTESSGSGSGSGSESGTQTKKSAKSKSNNGSENDSSSGDEL 163
            S  A   +         +L                       SK     +      + L
Sbjct: 56  MSKDA---VSGTLRLFWTLL-----------------------SKQEEMVQ--KFVEEVL 87

Query: 164 ENGSNGLSIRDGSDNGSGTQSSWTKKAAEVDSPQPISPRYQSADDSICAQVIHTKPESFS 223
                 L                +    E   P  ++  Y    D      ++   + F+
Sbjct: 88  RINYKFL---------------MSPIKTEQRQPSMMTRMYIEQRD-----RLYNDNQVFA 127

Query: 224 NGWVHLNEP----KDGLEQDEQPDGVAMH--KG-----LEMQVSENADL----------- 261
              V   +P    +  L +      V +    G     + + V  +  +           
Sbjct: 128 KYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWL 187

Query: 262 ---KCDCQHEKKSTQQTSKKKIKLPEVDSKPFDNKQLEVDNENICGKRRDQATSTSSANA 318
               C+         Q    +I  P   S+   +  +++   +I  + R    S    N 
Sbjct: 188 NLKNCNSPETVLEMLQKLLYQID-PNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENC 246

Query: 319 -----NHANPHAEIRDFDTPSGPSDISHVKETPCLELTLKRMRGVEDDQSAANEDCNVLR 373
                N  N  A    F       ++S      C  L   R + V D  SAA      L 
Sbjct: 247 LLVLLNVQNAKA-WNAF-------NLS------CKILLTTRFKQVTDFLSAATTTHISLD 292

Query: 374 HSI--FSAFSKYDLNLKALNFRVFS 396
           H     +      L LK L+ R   
Sbjct: 293 HHSMTLTPDEVKSLLLKYLDCRPQD 317

>1dc7_A NTRC, nitrogen regulation protein; receiver domain, phosphorylation, signal transduction, conformational rearrangement; NMR {Salmonella typhimurium} SCOP: c.23.1.1 PDB: 1j56_A 1krw_A 1krx_A 1ntr_A 1dc8_A* Length = 124

 Score = 40.2 bits (95), Expect = 1e-04
 Identities = 12/51 (23%), Positives = 19/51 (37%), Gaps = 2/51 (3%)

Query: 74  KVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLT 124
            V +V++D S R V+   L       T   N       L       D++L+
Sbjct: 5   IVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAALAS--KTPDVLLS 53

>2qxy_A Response regulator; regulation of transcription, NYSGXRC, protein structure initiative II (PSI II), structural genomics; 1.95A {Thermotoga maritima} Length = 142

 Score = 40.6 bits (96), Expect = 2e-04
 Identities = 12/55 (21%), Positives = 20/55 (36%), Gaps = 2/55 (3%)

Query: 70  TRSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLT 124
           + +  V++V+    T   V   L    + V    N   A+  L      ID+V  
Sbjct: 2   SLTPTVMVVDESRITFLAVKNALEKDGFNVIWAKNEQEAFTFLRR--EKIDLVFV 54

>1mb3_A Cell division response regulator DIVK; signal transduction protein, structural proteomics in europe, spine, structural genomics; 1.41A {Caulobacter vibrioides} SCOP: c.23.1.1 PDB: 1m5u_A 1mav_A 1mb0_A 1m5t_A Length = 124

 Score = 40.2 bits (95), Expect = 2e-04
 Identities = 15/52 (28%), Positives = 23/52 (44%), Gaps = 2/52 (3%)

Query: 72  SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVL 123
           + KVL+VE+++    +   LL    YE       L A  I     N  D++L
Sbjct: 1   TKKVLIVEDNELNMKLFHDLLEAQGYETLQTREGLSALSIAR--ENKPDLIL 50

>1xhf_A DYE resistance, aerobic respiration control protein ARCA; two-component system, gene regulation, transcription factor, anoxic redox control; 2.15A {Escherichia coli} SCOP: c.23.1.1 PDB: 1xhe_A Length = 123

 Score = 39.7 bits (94), Expect = 2e-04
 Identities = 11/50 (22%), Positives = 26/50 (52%), Gaps = 2/50 (4%)

Query: 74  KVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVL 123
            +L+VE++  TR+ + ++     Y+V    +     +IL +    I++V+
Sbjct: 5   HILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQILSE--YDINLVI 52

>2ayx_A Sensor kinase protein RCSC; two independent structural domains, transferase; NMR {Escherichia coli} SCOP: c.23.1.1 c.23.1.6 PDB: 2ayz_A 2ayy_A Length = 254

 Score = 41.6 bits (98), Expect = 2e-04
 Identities = 14/56 (25%), Positives = 28/56 (50%), Gaps = 2/56 (3%)

Query: 69  PTRSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLT 124
               + +L+V++    R +++  L +  Y+     + + A  +L    NHIDIVL+
Sbjct: 126 DNDDMMILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVLS--KNHIDIVLS 179

>3dzd_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; HET: ADP; 2.40A {Aquifex aeolicus} PDB: 1zit_A 2jrl_A Length = 368

 Score = 41.7 bits (99), Expect = 2e-04
 Identities = 10/51 (19%), Positives = 24/51 (47%), Gaps = 2/51 (3%)

Query: 74  KVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLT 124
           +VL+V++++S    +SA+L    Y          A K +++      +++ 
Sbjct: 2   RVLVVDDEESITSSLSAILEEEGYHPDTAKTLREAEKKIKE--LFFPVIVL 50

>3hzh_A Chemotaxis response regulator (CHEY-3); phosphatase, complex, response regulator, receiver domain, two-component signal transduction; HET: BFD; 1.96A {Borrelia burgdorferi} Length = 157

 Score = 39.9 bits (93), Expect = 3e-04
 Identities = 15/86 (17%), Positives = 31/86 (36%), Gaps = 3/86 (3%)

Query: 41  GTIQVHDGFQISQQQQP--QGSVIRWERFLPTRSLKVLLVENDDSTRHVVSALLRNCSYE 98
           G+   H    I +        S  R   +       VL+V++   T   ++ +  +  + 
Sbjct: 3   GSHHHHHHGSIQKTTIAADSSSKPRGINYDTGIPFNVLIVDDSVFTVKQLTQIFTSEGFN 62

Query: 99  VTAVA-NSLHAWKILEDLTNHIDIVL 123
           +   A +   A    ++   +IDIV 
Sbjct: 63  IIDTAADGEEAVIKYKNHYPNIDIVT 88

>3cfy_A Putative LUXO repressor protein; structural genomics, unknown function, uncharacterized protein, signal receiver domain; 2.50A {Vibrio parahaemolyticus rimd 2210633} Length = 137

 Score = 39.4 bits (93), Expect = 4e-04
 Identities = 10/51 (19%), Positives = 24/51 (47%), Gaps = 2/51 (3%)

Query: 74  KVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLT 124
           +VLLVE+  S   +    +++  Y++  V     A + +E   +   +++ 
Sbjct: 6   RVLLVEDSTSLAILYKQYVKDEPYDIFHVETGRDAIQFIER--SKPQLIIL 54

>3eod_A Protein HNR; response regulator, phosphoprotein, two-component regulatory system, signaling protein; 1.75A {Escherichia coli K12} Length = 130

 Score = 38.7 bits (91), Expect = 5e-04
 Identities = 9/55 (16%), Positives = 25/55 (45%), Gaps = 2/55 (3%)

Query: 69  PTRSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVL 123
           P    ++L+VE++   R ++ +   +        A+ + A ++L       D+++
Sbjct: 4   PLVGKQILIVEDEQVFRSLLDSWFSSLGATTVLAADGVDALELLG--GFTPDLMI 56

>1srr_A SPO0F, sporulation response regulatory protein; aspartate pocket, two component system; 1.90A {Bacillus subtilis} SCOP: c.23.1.1 PDB: 1pey_A 3q15_C 2ftk_E* 1fsp_A 1nat_A 1pux_A 2fsp_A 2jvj_A 2jvk_A 2jvi_A 1f51_E Length = 124

 Score = 38.6 bits (91), Expect = 6e-04
 Identities = 13/51 (25%), Positives = 24/51 (47%), Gaps = 2/51 (3%)

Query: 74  KVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLT 124
           K+L+V++    R +++ +     Y+    AN L A  I+       D+VL 
Sbjct: 5   KILIVDDQSGIRILLNEVFNKEGYQTFQAANGLQALDIVTK--ERPDLVLL 53

>1w25_A Stalked-cell differentiation controlling protein; two-component system, ggdef domain, cyclic dinucleotide, cyclic-digmp; HET: C2E; 2.70A {Caulobacter vibrioides} SCOP: c.23.1.1 c.23.1.1 d.58.29.2 PDB: 2v0n_A* 2wb4_A* Length = 459

 Score = 40.6 bits (95), Expect = 7e-04
 Identities = 11/51 (21%), Positives = 25/51 (49%), Gaps = 2/51 (3%)

Query: 74  KVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLT 124
           ++L+V++ ++   ++ A L    YEV+   +   A  +     +  DI+L 
Sbjct: 3   RILVVDDIEANVRLLEAKLTAEYYEVSTAMDGPTALAMAA--RDLPDIILL 51

>1zgz_A Torcad operon transcriptional regulatory protein; two-component system, gene regulation, transcription factor, respiratory system; 1.80A {Escherichia coli} SCOP: c.23.1.1 Length = 122

 Score = 38.2 bits (90), Expect = 7e-04
 Identities = 9/50 (18%), Positives = 26/50 (52%), Gaps = 2/50 (4%)

Query: 74  KVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVL 123
            +++VE++  T+  + +      Y V+  A+     +I+++    +D++L
Sbjct: 4   HIVIVEDEPVTQARLQSYFTQEGYTVSVTASGAGLREIMQN--QSVDLIL 51

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	399
2lpm_A	123	Two-component response regulator; transcription re	98.69
3to5_A	134	CHEY homolog; alpha(5)beta(5), chemotaxis, FLIM, p	98.6
3mm4_A	206	Histidine kinase homolog; receiver domain, CKI1, c	98.54
3gl9_A	122	Response regulator; beta-sheet, surrounded by alph	98.47
3f6p_A	120	Transcriptional regulatory protein YYCF; unphospho	98.44
3t6k_A	136	Response regulator receiver; flavodoxin-like, stru	98.37
3h5i_A	140	Response regulator/sensory box protein/ggdef domai	98.37
3i42_A	127	Response regulator receiver domain protein (CHEY-	98.35
3eod_A	130	Protein HNR; response regulator, phosphoprotein, t	98.33
3rqi_A	184	Response regulator protein; structural genomics, s	98.32
3gt7_A	154	Sensor protein; structural genomics, signal receiv	98.3
3grc_A	140	Sensor protein, kinase; protein structure initiati	98.3
2rdm_A	132	Response regulator receiver protein; structural ge	98.3
4e7p_A	150	Response regulator; DNA binding, cytosol, transcri	98.28
3cg4_A	142	Response regulator receiver domain protein (CHEY-;	98.28
3m6m_D	143	Sensory/regulatory protein RPFC; RPFF, REC, enoyl-	98.28
3c3m_A	138	Response regulator receiver protein; structural ge	98.26
3a10_A	116	Response regulator; phosphoacceptor, signaling pro	98.26
3hv2_A	153	Response regulator/HD domain protein; PSI-2, NYSGX	98.25
1srr_A	124	SPO0F, sporulation response regulatory protein; as	98.25
3kht_A	144	Response regulator; PSI-II, 11023K, structural gen	98.24
3lua_A	140	Response regulator receiver protein; two-component	98.24
3lte_A	132	Response regulator; structural genomics, PSI, prot	98.23
3crn_A	132	Response regulator receiver domain protein, CHEY-;	98.23
2gkg_A	127	Response regulator homolog; social motility, recei	98.21
3hzh_A	157	Chemotaxis response regulator (CHEY-3); phosphatas	98.21
2qr3_A	140	Two-component system response regulator; structura	98.2
2a9o_A	120	Response regulator; essential protein, YYCF/YYCG h	98.19
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	98.19
2qxy_A	142	Response regulator; regulation of transcription, N	98.19
3c97_A	140	Signal transduction histidine kinase; structural g	98.18
2pl1_A	121	Transcriptional regulatory protein PHOP; CHEY-like	98.18
3jte_A	143	Response regulator receiver protein; structural ge	98.17
3ilh_A	146	Two component response regulator; NYSGXRC, PSI-II,	98.17
1k66_A	149	Phytochrome response regulator RCPB; CHEY homologu	98.17
1xhf_A	123	DYE resistance, aerobic respiration control protei	98.17
1zgz_A	122	Torcad operon transcriptional regulatory protein;	98.17
2r25_B	133	Osmosensing histidine protein kinase SLN1; alpha5-	98.16
3kto_A	136	Response regulator receiver protein; PSI-II,struct	98.16
1tmy_A	120	CHEY protein, TMY; chemotaxis, phosphoryl transfer	98.16
3hdv_A	136	Response regulator; PSI-II, structural genomics, P	98.16
3hdg_A	137	Uncharacterized protein; two-component sensor acti	98.16
3r0j_A	250	Possible two component system response transcript	98.16
2jba_A	127	Phosphate regulon transcriptional regulatory PROT;	98.15
2rjn_A	154	Response regulator receiver:metal-dependent phosph	98.14
3nhm_A	133	Response regulator; protein structure initiative I	98.13
1mvo_A	136	PHOP response regulator; phosphate regulon, transc	98.13
1dbw_A	126	Transcriptional regulatory protein FIXJ; doubly wo	98.13
1mb3_A	124	Cell division response regulator DIVK; signal tran	98.13
2b4a_A	138	BH3024; flavodoxin-like fold, structural genomics,	98.12
3cz5_A	153	Two-component response regulator, LUXR family; str	98.11
2qzj_A	136	Two-component response regulator; 11017X, PSI-II,	98.11
1kgs_A	225	DRRD, DNA binding response regulator D; DNA-bindin	98.11
3h1g_A	129	Chemotaxis protein CHEY homolog; sulfate-bound CHE	98.11
1p6q_A	129	CHEY2; chemotaxis, signal transduction, response r	98.1
3cnb_A	143	DNA-binding response regulator, MERR family; signa	98.08
1k68_A	140	Phytochrome response regulator RCPA; phosphorylate	98.08
1zh2_A	121	KDP operon transcriptional regulatory protein KDPE	98.07
3kyj_B	145	CHEY6 protein, putative histidine protein kinase;	98.07
3cfy_A	137	Putative LUXO repressor protein; structural genomi	98.07
3cg0_A	140	Response regulator receiver modulated diguanylate	98.06
3heb_A	152	Response regulator receiver domain protein (CHEY);	98.05
1jbe_A	128	Chemotaxis protein CHEY; signaling protein; 1.08A	98.05
2j48_A	119	Two-component sensor kinase; pseudo-receiver, circ	98.05
2zay_A	147	Response regulator receiver protein; structural ge	98.04
3f6c_A	134	Positive transcription regulator EVGA; structural	98.04
1dz3_A	130	Stage 0 sporulation protein A; response regulator,	98.04
3n53_A	140	Response regulator receiver modulated diguanylate;	98.04
3snk_A	135	Response regulator CHEY-like protein; P-loop conta	98.03
2gwr_A	238	DNA-binding response regulator MTRA; two-component	98.02
3eq2_A	394	Probable two-component response regulator; adaptor	98.02
2ayx_A	254	Sensor kinase protein RCSC; two independent struct	98.01
1s8n_A	205	Putative antiterminator; RV1626, structural genomi	98.01
2oqr_A	230	Sensory transduction protein REGX3; response regul	97.99
1dcf_A	136	ETR1 protein; beta-alpha five sandwich, transferas	97.99
1yio_A	208	Response regulatory protein; transcription regulat	97.98
3kcn_A	151	Adenylate cyclase homolog; SGX, PSI 2, structural	97.98
2qvg_A	143	Two component response regulator; NYSGXRC, PSI-2,	97.97
3q9s_A	249	DNA-binding response regulator; DNA binding protei	97.96
1i3c_A	149	Response regulator RCP1; phytochrome, signaling pr	97.95
1qkk_A	155	DCTD, C4-dicarboxylate transport transcriptional r	97.94
1ys7_A	233	Transcriptional regulatory protein PRRA; response	97.94
3b2n_A	133	Uncharacterized protein Q99UF4; structural genomic	97.92
2qv0_A	143	Protein MRKE; structural genomics, transcription,	97.92
4dad_A	146	Putative pilus assembly-related protein; response	97.91
2qsj_A	154	DNA-binding response regulator, LUXR family; struc	97.91
2pln_A	137	HP1043, response regulator; signaling protein; 1.8	97.89
3eqz_A	135	Response regulator; structural genomics, unknown f	97.88
3t8y_A	164	CHEB, chemotaxis response regulator protein-glutam	97.87
3cu5_A	141	Two component transcriptional regulator, ARAC FAM;	97.87
3luf_A	259	Two-component system response regulator/ggdef doma	97.84
1a04_A	215	Nitrate/nitrite response regulator protein NARL; s	97.83
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	97.82
3eul_A	152	Possible nitrate/nitrite response transcriptional	97.82
1dc7_A	124	NTRC, nitrogen regulation protein; receiver domain	97.78
2jk1_A	139	HUPR, hydrogenase transcriptional regulatory prote	97.77
3c3w_A	225	Two component transcriptional regulatory protein;	97.74
3sy8_A	400	ROCR; TIM barrel phosphodiesterase-A, transcriptio	97.73
1w25_A	459	Stalked-cell differentiation controlling protein;	97.68
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	97.65
1p2f_A	220	Response regulator; DRRB, OMPR/PHOB, transcription	97.43
2hqr_A	223	Putative transcriptional regulator; phosporylation	97.43
3bre_A	358	Probable two-component response regulator; protein	97.4
1a2o_A	349	CHEB methylesterase; bacterial chemotaxis, adaptat	97.39
2vyc_A	755	Biodegradative arginine decarboxylase; pyridoxal p	97.3
3klo_A	225	Transcriptional regulator VPST; REC domain, HTH do	96.96
1qo0_D	196	AMIR; binding protein, gene regulator, receptor; 2	96.92
3luf_A	259	Two-component system response regulator/ggdef doma	96.81
2ayx_A	254	Sensor kinase protein RCSC; two independent struct	94.47
3rht_A	259	(gatase1)-like protein; structural genomics, PSI-b	80.51

>2lpm_A Two-component response regulator; transcription regulator; NMR {Sinorhizobium meliloti}

Probab=98.69  E-value=6.7e-09  Score=88.92  Aligned_cols=58  Identities=22%  Similarity=0.366  Sum_probs=52.8

Q ss_pred             CCCCCcEEEEEeCChhhHHHHHHHHHcCCCEEE-EECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           68 LPTRSLKVLLVENDDSTRHVVSALLRNCSYEVT-AVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        68 lp~~~~rVLLVEDD~~~reiL~~lLe~~GyeV~-~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      |....+|||||||++.++..+..+|+..||+|+ .|.++.+|++++.  ...||+||+|+.
T Consensus         4 m~~r~~rILiVdD~~~~~~~l~~~L~~~G~~v~~~a~~g~eAl~~~~--~~~~DlvllDi~   62 (123)
T 2lpm_A            4 MTERRLRVLVVEDESMIAMLIEDTLCELGHEVAATASRMQEALDIAR--KGQFDIAIIDVN   62 (123)
T ss_dssp             CCCCCCCEEEESSSTTTSHHHHHHHHHHCCCCCBCSCCHHHHHHHHH--HCCSSEEEECSS
T ss_pred             CCCCCCEEEEEeCCHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHH--hCCCCEEEEecC
Confidence            344567999999999999999999999999976 7899999999999  689999999999

>3to5_A CHEY homolog; alpha(5)beta(5), chemotaxis, FLIM, phosphorylation, motor AC signaling protein; 1.65A {Vibrio cholerae}

Probab=98.60  E-value=5.2e-08  Score=84.28  Aligned_cols=54  Identities=26%  Similarity=0.519  Sum_probs=50.6

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCE-EEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYE-VTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~Gye-V~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .+|||||||++.+|..+..+|+.+||. |..|.+|.+|++++.  ...|||||+|+.
T Consensus        12 ~~rILiVDD~~~~r~~l~~~L~~~G~~~v~~a~~g~~al~~~~--~~~~DlillD~~   66 (134)
T 3to5_A           12 NMKILIVDDFSTMRRIVKNLLRDLGFNNTQEADDGLTALPMLK--KGDFDFVVTDWN   66 (134)
T ss_dssp             TCCEEEECSCHHHHHHHHHHHHHTTCCCEEEESSHHHHHHHHH--HHCCSEEEEESC
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHHcCCcEEEEECCHHHHHHHHH--hCCCCEEEEcCC
Confidence            468999999999999999999999996 778999999999999  678999999999

>3mm4_A Histidine kinase homolog; receiver domain, CKI1, cytokinin signaling, ROS fold, CHEY-like, transferase; 2.00A {Arabidopsis thaliana} PDB: 3mmn_A

Probab=98.54  E-value=1.2e-07  Score=85.28  Aligned_cols=88  Identities=16%  Similarity=0.144  Sum_probs=52.0

Q ss_pred             CCCCCCCccccCCCcCCCCCCCCCCccccccccCCCCCcEEEEEeCChhhHHHHHHHHHcCCC-EEEEECCHHHHHHHHH
Q 039733           35 SNNGPGGTIQVHDGFQISQQQQPQGSVIRWERFLPTRSLKVLLVENDDSTRHVVSALLRNCSY-EVTAVANSLHAWKILE  113 (399)
Q Consensus        35 ~~~g~~~av~~~~~~~~p~~~~~~~~~~~~e~~lp~~~~rVLLVEDD~~~reiL~~lLe~~Gy-eV~~A~dg~eAle~L~  113 (399)
                      .+.|+.|.+..+...+.+.+.. ..+.    ........+||||||++.++..+..+|+..|| .|..+.++.+|++++.
T Consensus        29 ~g~Gs~f~~~lP~~~~~~~~~~-~~~~----~~~~~~~~~ILiVdDd~~~~~~l~~~L~~~g~~~v~~a~~~~eal~~l~  103 (206)
T 3mm4_A           29 TRVKSVRTGRKPIGNPEDEQET-SKPS----DDEFLRGKRVLVVDDNFISRKVATGKLKKMGVSEVEQCDSGKEALRLVT  103 (206)
T ss_dssp             -------------------------------CTTTTTTCEEEEECSCHHHHHHHHHHHHHTTCSEEEEESSHHHHHHHHH
T ss_pred             CCCcceeeeccCCCCCcccccc-cCCC----cccccCCCEEEEEeCCHHHHHHHHHHHHHcCCCeeeeeCCHHHHHHHHH
Confidence            5667888877764332221111 1111    11222456999999999999999999999999 8999999999999998


Q ss_pred             hc-----------CCCccEEEEcCC
Q 039733          114 DL-----------TNHIDIVLTESS  127 (399)
Q Consensus       114 ~~-----------~~~pDLIIlDl~  127 (399)
                      ..           ...|||||+|+.
T Consensus       104 ~~~~~~~~~~~~~~~~~dlillD~~  128 (206)
T 3mm4_A          104 EGLTQREEQGSVDKLPFDYIFMDCQ  128 (206)
T ss_dssp             HHHHHHHHHTCSSCCSCSEEEEESC
T ss_pred             hhcccccccccccCCCCCEEEEcCC
Confidence            31           137999999998

>3gl9_A Response regulator; beta-sheet, surrounded by alpha helices, BOTH sides, signaling protein; HET: BFD; 1.80A {Thermotoga maritima} SCOP: c.23.1.0 PDB: 3dgf_C 3dge_C

Probab=98.47  E-value=3.6e-07  Score=74.39  Aligned_cols=53  Identities=30%  Similarity=0.343  Sum_probs=50.7

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .+||||||++..+..+..+|+..||+|..+.++.+|++.+.  ...||+||+|+.
T Consensus         3 ~~ILivdd~~~~~~~l~~~l~~~g~~v~~~~~~~~al~~l~--~~~~dlvllD~~   55 (122)
T 3gl9_A            3 KKVLLVDDSAVLRKIVSFNLKKEGYEVIEAENGQIALEKLS--EFTPDLIVLXIM   55 (122)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHT--TBCCSEEEECSC
T ss_pred             ceEEEEeCCHHHHHHHHHHHHHCCcEEEEeCCHHHHHHHHH--hcCCCEEEEecc
Confidence            58999999999999999999999999999999999999998  778999999998

>3f6p_A Transcriptional regulatory protein YYCF; unphosphorelated, receiver domain, cytoplasm, DNA-binding, phosphoprotein, transcription regulation; 1.95A {Bacillus subtilis} SCOP: c.23.1.1 PDB: 2zwm_A

Probab=98.44  E-value=6.4e-07  Score=72.54  Aligned_cols=53  Identities=23%  Similarity=0.374  Sum_probs=50.8

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .+||||||++..+..+..+|+..||.|..+.++.+|++.+.  ...||+||+|+.
T Consensus         3 ~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~--~~~~dlii~D~~   55 (120)
T 3f6p_A            3 KKILVVDDEKPIADILEFNLRKEGYEVHCAHDGNEAVEMVE--ELQPDLILLDIM   55 (120)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--TTCCSEEEEETT
T ss_pred             CeEEEEECCHHHHHHHHHHHHhCCEEEEEeCCHHHHHHHHh--hCCCCEEEEeCC
Confidence            58999999999999999999999999999999999999999  788999999998

>3t6k_A Response regulator receiver; flavodoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: MSE; 1.86A {Chloroflexus aurantiacus} SCOP: c.23.1.0

Probab=98.37  E-value=8.5e-07  Score=73.53  Aligned_cols=54  Identities=24%  Similarity=0.398  Sum_probs=51.2

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ..+||||||++.++..+..+|+..||.|..+.++.+|++.+.  ...||+||+|+.
T Consensus         4 ~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~--~~~~dlvl~D~~   57 (136)
T 3t6k_A            4 PHTLLIVDDDDTVAEMLELVLRGAGYEVRRAASGEEALQQIY--KNLPDALICDVL   57 (136)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HSCCSEEEEESC
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHH--hCCCCEEEEeCC
Confidence            458999999999999999999999999999999999999998  678999999998

>3h5i_A Response regulator/sensory box protein/ggdef domain protein; structural genomics, transcription, PSI-2; 1.90A {Carboxydothermus hydrogenoformans z-2901}

Probab=98.37  E-value=1e-06  Score=73.08  Aligned_cols=55  Identities=18%  Similarity=0.282  Sum_probs=50.6

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcC-CCccEEEEcCC
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLT-NHIDIVLTESS  127 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~-~~pDLIIlDl~  127 (399)
                      ..++||||||++..+..+..+|+..||.|..+.++.+|++.+.  . ..||+||+|+.
T Consensus         4 ~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--~~~~~dlvi~D~~   59 (140)
T 3h5i_A            4 KDKKILIVEDSKFQAKTIANILNKYGYTVEIALTGEAAVEKVS--GGWYPDLILMDIE   59 (140)
T ss_dssp             --CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--TTCCCSEEEEESS
T ss_pred             CCcEEEEEeCCHHHHHHHHHHHHHcCCEEEEecChHHHHHHHh--cCCCCCEEEEecc
Confidence            3469999999999999999999999999999999999999998  5 68999999998

>3i42_A Response regulator receiver domain protein (CHEY- like); structural genomics, PSI-2, protein structure initiative; 2.15A {Methylobacillus flagellatus KT} SCOP: c.23.1.0

Probab=98.35  E-value=8e-07  Score=71.93  Aligned_cols=54  Identities=19%  Similarity=0.261  Sum_probs=51.2

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +.+||||||++..+..+..+|+..||.|..+.++.+|++.+.  ...||+||+|+.
T Consensus         3 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--~~~~dlii~D~~   56 (127)
T 3i42_A            3 LQQALIVEDYQAAAETFKELLEMLGFQADYVMSGTDALHAMS--TRGYDAVFIDLN   56 (127)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHHHTTEEEEEESSHHHHHHHHH--HSCCSEEEEESB
T ss_pred             cceEEEEcCCHHHHHHHHHHHHHcCCCEEEECCHHHHHHHHH--hcCCCEEEEeCC
Confidence            468999999999999999999999999999999999999998  678999999998

>3eod_A Protein HNR; response regulator, phosphoprotein, two-component regulatory system, signaling protein; 1.75A {Escherichia coli K12}

Probab=98.33  E-value=1.6e-06  Score=70.40  Aligned_cols=55  Identities=15%  Similarity=0.286  Sum_probs=51.8

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ...+||||||++..+..+..+|+..||.+..+.++.+|++.+.  ...||+||+|+.
T Consensus         6 ~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--~~~~dlvi~d~~   60 (130)
T 3eod_A            6 VGKQILIVEDEQVFRSLLDSWFSSLGATTVLAADGVDALELLG--GFTPDLMICDIA   60 (130)
T ss_dssp             TTCEEEEECSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHHHT--TCCCSEEEECCC
T ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhCCceEEEeCCHHHHHHHHh--cCCCCEEEEecC
Confidence            3469999999999999999999999999999999999999998  788999999998

>3rqi_A Response regulator protein; structural genomics, seattle structural genomics center for infectious disease, ssgcid; HET: PHD CIT; 1.70A {Burkholderia pseudomallei}

Probab=98.32  E-value=1.1e-06  Score=77.02  Aligned_cols=54  Identities=13%  Similarity=0.227  Sum_probs=51.6

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +.+||||||++.++..+..+|+..||.|..+.++.+|++.+.  ...||+||+|+.
T Consensus         7 ~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~--~~~~dlvl~D~~   60 (184)
T 3rqi_A            7 DKNFLVIDDNEVFAGTLARGLERRGYAVRQAHNKDEALKLAG--AEKFEFITVXLH   60 (184)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEECSHHHHHHHHT--TSCCSEEEECSE
T ss_pred             CCeEEEEcCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHh--hCCCCEEEEecc
Confidence            469999999999999999999999999999999999999998  788999999998

>3gt7_A Sensor protein; structural genomics, signal receiver domain, kinase, PSI-2, protein structure initiative; 2.30A {Syntrophus aciditrophicus SB}

Probab=98.30  E-value=1.5e-06  Score=73.47  Aligned_cols=55  Identities=20%  Similarity=0.384  Sum_probs=51.6

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ...+||||||++..+..+..+|+..||.|..+.++.+|++.+.  ...||+||+|+.
T Consensus         6 ~~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~--~~~~dlii~D~~   60 (154)
T 3gt7_A            6 RAGEILIVEDSPTQAEHLKHILEETGYQTEHVRNGREAVRFLS--LTRPDLIISDVL   60 (154)
T ss_dssp             -CCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHT--TCCCSEEEEESC
T ss_pred             CCCcEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHH--hCCCCEEEEeCC
Confidence            3469999999999999999999999999999999999999998  788999999998

>3grc_A Sensor protein, kinase; protein structure initiative II(PSI II), NYSGXRC, 11025B, structural genomics; 2.21A {Polaromonas SP}

Probab=98.30  E-value=1.7e-06  Score=71.22  Aligned_cols=54  Identities=11%  Similarity=0.261  Sum_probs=51.3

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +.+||||||++..+..+..+|+..||.|..+.++.+|++.+.  ...||+||+|+.
T Consensus         6 ~~~iLivdd~~~~~~~l~~~l~~~g~~v~~~~~~~~a~~~l~--~~~~dlvi~d~~   59 (140)
T 3grc_A            6 RPRILICEDDPDIARLLNLMLEKGGFDSDMVHSAAQALEQVA--RRPYAAMTVDLN   59 (140)
T ss_dssp             CSEEEEECSCHHHHHHHHHHHHHTTCEEEEECSHHHHHHHHH--HSCCSEEEECSC
T ss_pred             CCCEEEEcCCHHHHHHHHHHHHHCCCeEEEECCHHHHHHHHH--hCCCCEEEEeCC
Confidence            469999999999999999999999999999999999999998  678999999998

>2rdm_A Response regulator receiver protein; structural genomics, unknown function, PSI-2, protein struct initiative; HET: MSE; 1.76A {Sinorhizobium medicae}

Probab=98.30  E-value=2.4e-06  Score=69.15  Aligned_cols=55  Identities=24%  Similarity=0.352  Sum_probs=51.4

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCC-CccEEEEcCC
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTN-HIDIVLTESS  127 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~-~pDLIIlDl~  127 (399)
                      .+++||||||++..+..+..+|+..||.|..+.++.+|++.+.  .. .||+||+|+.
T Consensus         4 ~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--~~~~~dlvi~d~~   59 (132)
T 2rdm_A            4 EAVTILLADDEAILLLDFESTLTDAGFLVTAVSSGAKAIEMLK--SGAAIDGVVTDIR   59 (132)
T ss_dssp             SSCEEEEECSSHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--TTCCCCEEEEESC
T ss_pred             CCceEEEEcCcHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHH--cCCCCCEEEEeee
Confidence            4569999999999999999999999999999999999999998  66 8999999998

>4e7p_A Response regulator; DNA binding, cytosol, transcription regulator; 1.89A {Streptococcus pneumoniae} PDB: 4e7o_A

Probab=98.28  E-value=1.5e-06  Score=72.88  Aligned_cols=57  Identities=25%  Similarity=0.338  Sum_probs=50.9

Q ss_pred             CCCCcEEEEEeCChhhHHHHHHHHHcCC--CEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           69 PTRSLKVLLVENDDSTRHVVSALLRNCS--YEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        69 p~~~~rVLLVEDD~~~reiL~~lLe~~G--yeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ...+++||||||++.++..+..+|+..|  |.|..+.++.+|++.+.  ...||+||+|+.
T Consensus        17 ~~~m~~iLivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~al~~l~--~~~~dlii~D~~   75 (150)
T 4e7p_A           17 RGSHMKVLVAEDQSMLRDAMCQLLTLQPDVESVLQAKNGQEAIQLLE--KESVDIAILDVE   75 (150)
T ss_dssp             ---CEEEEEECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHHT--TSCCSEEEECSS
T ss_pred             CCCccEEEEEcCCHHHHHHHHHHHHhCCCcEEEEEECCHHHHHHHhh--ccCCCEEEEeCC
Confidence            3456799999999999999999999887  78999999999999998  788999999998

>3cg4_A Response regulator receiver domain protein (CHEY-; structural genomics, unknown function; HET: MSE; 1.61A {Methanospirillum hungatei jf-1}

Probab=98.28  E-value=2.3e-06  Score=70.30  Aligned_cols=55  Identities=16%  Similarity=0.343  Sum_probs=52.0

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .+.+||||||++..+..+..+|+..||+|..+.++.+|++.+.  ...||+||+|+.
T Consensus         6 ~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--~~~~dlii~d~~   60 (142)
T 3cg4_A            6 HKGDVMIVDDDAHVRIAVKTILSDAGFHIISADSGGQCIDLLK--KGFSGVVLLDIM   60 (142)
T ss_dssp             CCCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--TCCCEEEEEESC
T ss_pred             CCCeEEEEcCCHHHHHHHHHHHHHCCeEEEEeCCHHHHHHHHH--hcCCCEEEEeCC
Confidence            4579999999999999999999999999999999999999999  778999999998

>3m6m_D Sensory/regulatory protein RPFC; RPFF, REC, enoyl-COA hydratase, lyase-transferase COMP; 2.50A {Xanthomonas campestris PV}

Probab=98.28  E-value=1.4e-06  Score=72.90  Aligned_cols=55  Identities=20%  Similarity=0.397  Sum_probs=48.8

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ..++||||||++..+..+..+|+..||.+..+.++.+|++.+.  ...||+||+|+.
T Consensus        13 ~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~--~~~~dlvl~D~~   67 (143)
T 3m6m_D           13 RSMRMLVADDHEANRMVLQRLLEKAGHKVLCVNGAEQVLDAMA--EEDYDAVIVDLH   67 (143)
T ss_dssp             --CEEEEECSSHHHHHHHHHHHHC--CEEEEESSHHHHHHHHH--HSCCSEEEEESC
T ss_pred             ccceEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCHHHHHHHHh--cCCCCEEEEeCC
Confidence            3469999999999999999999999999999999999999998  678999999998

>3c3m_A Response regulator receiver protein; structural genomics, unknown function, PSI-2, protein struct initiative; HET: MSE; 1.70A {Methanoculleus marisnigri JR1}

Probab=98.26  E-value=2.2e-06  Score=70.86  Aligned_cols=54  Identities=17%  Similarity=0.243  Sum_probs=50.7

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +.+||||||++.++..+..+|+..||.+..+.++.+|++.+.  ...||+||+|+.
T Consensus         3 ~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~--~~~~dlvi~D~~   56 (138)
T 3c3m_A            3 LYTILVVDDSPMIVDVFVTMLERGGYRPITAFSGEECLEALN--ATPPDLVLLDIM   56 (138)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HSCCSEEEEESC
T ss_pred             cceEEEEeCCHHHHHHHHHHHHHcCceEEEeCCHHHHHHHHh--ccCCCEEEEeCC
Confidence            358999999999999999999999999999999999999998  578999999998

>3a10_A Response regulator; phosphoacceptor, signaling protein; HET: MSE PG4; 1.63A {Thermotoga maritima} PDB: 3a0r_B* 3a0u_A*

Probab=98.26  E-value=2.4e-06  Score=67.81  Aligned_cols=53  Identities=21%  Similarity=0.402  Sum_probs=50.2

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .+||||||++..+..+..+|+..||.+..+.++.+|++.+.  ...||+||+|+.
T Consensus         2 ~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~~~--~~~~dlvl~D~~   54 (116)
T 3a10_A            2 KRILVVDDEPNIRELLKEELQEEGYEIDTAENGEEALKKFF--SGNYDLVILDIE   54 (116)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HSCCSEEEECSC
T ss_pred             cEEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHh--cCCCCEEEEECC
Confidence            48999999999999999999999999999999999999998  578999999998

>3hv2_A Response regulator/HD domain protein; PSI-2, NYSGXRC, structural genomics, protein structure initiative; 1.50A {Pseudomonas fluorescens pf-5}

Probab=98.25  E-value=2.3e-06  Score=71.93  Aligned_cols=55  Identities=20%  Similarity=0.420  Sum_probs=51.7

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .+.+||||||++..+..+..+|+..||.|..+.++.+|++.+.  ...||+||+|+.
T Consensus        13 ~~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--~~~~dlvi~D~~   67 (153)
T 3hv2_A           13 RRPEILLVDSQEVILQRLQQLLSPLPYTLHFARDATQALQLLA--SREVDLVISAAH   67 (153)
T ss_dssp             SCCEEEEECSCHHHHHHHHHHHTTSSCEEEEESSHHHHHHHHH--HSCCSEEEEESC
T ss_pred             CCceEEEECCCHHHHHHHHHHhcccCcEEEEECCHHHHHHHHH--cCCCCEEEEeCC
Confidence            3469999999999999999999999999999999999999998  678999999998

>1srr_A SPO0F, sporulation response regulatory protein; aspartate pocket, two component system; 1.90A {Bacillus subtilis} SCOP: c.23.1.1 PDB: 1pey_A 3q15_C 2ftk_E* 1fsp_A 1nat_A 1pux_A 2fsp_A 2jvj_A 2jvk_A 2jvi_A 1f51_E

Probab=98.25  E-value=1.9e-06  Score=69.39  Aligned_cols=54  Identities=24%  Similarity=0.439  Sum_probs=50.5

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ..+||||||++..+..+..+|+..||.+..+.++.+|+..+.  ...||+||+|+.
T Consensus         3 ~~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~~~--~~~~dlvl~D~~   56 (124)
T 1srr_A            3 NEKILIVDDQSGIRILLNEVFNKEGYQTFQAANGLQALDIVT--KERPDLVLLDMK   56 (124)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHH--HHCCSEEEEESC
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHCCcEEEEeCCHHHHHHHHh--ccCCCEEEEecC
Confidence            358999999999999999999999999999999999999998  568999999998

>3kht_A Response regulator; PSI-II, 11023K, structural genomics, Pro structure initiative, NEW YORK SGX research center for STRU genomics, nysgxrc; 2.10A {Hahella chejuensis} SCOP: c.23.1.0

Probab=98.24  E-value=2.1e-06  Score=71.09  Aligned_cols=55  Identities=20%  Similarity=0.318  Sum_probs=50.9

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHcCCCE--EEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRNCSYE--VTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~~Gye--V~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .+++||||||++..+..+..+|+..||.  |..+.++.+|++.+.  ...||+||+|+.
T Consensus         4 ~~~~ILivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~a~~~l~--~~~~dlii~D~~   60 (144)
T 3kht_A            4 RSKRVLVVEDNPDDIALIRRVLDRKDIHCQLEFVDNGAKALYQVQ--QAKYDLIILDIG   60 (144)
T ss_dssp             -CEEEEEECCCHHHHHHHHHHHHHTTCCEEEEEESSHHHHHHHHT--TCCCSEEEECTT
T ss_pred             CCCEEEEEeCCHHHHHHHHHHHHhcCCCeeEEEECCHHHHHHHhh--cCCCCEEEEeCC
Confidence            4579999999999999999999999987  889999999999998  788999999998

>3lua_A Response regulator receiver protein; two-component signal transduction system, histidine kinase, phosphorelay, receiver domain, nysgxrc; 2.40A {Clostridium thermocellum}

Probab=98.24  E-value=1.6e-06  Score=71.50  Aligned_cols=54  Identities=19%  Similarity=0.348  Sum_probs=51.3

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHc-CCCEEEEECCHHHHHHHHHhcC-CCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRN-CSYEVTAVANSLHAWKILEDLT-NHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~-~GyeV~~A~dg~eAle~L~~~~-~~pDLIIlDl~  127 (399)
                      +.+||||||++..+..+..+|+. .||+|..+.++.+|++.+.  . ..||+||+|+.
T Consensus         4 ~~~ilivdd~~~~~~~l~~~L~~~~~~~v~~~~~~~~a~~~l~--~~~~~dlvi~D~~   59 (140)
T 3lua_A            4 DGTVLLIDYFEYEREKTKIIFDNIGEYDFIEVENLKKFYSIFK--DLDSITLIIMDIA   59 (140)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHHCCCEEEEECSHHHHHTTTT--TCCCCSEEEECSC
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHhccCccEEEECCHHHHHHHHh--cCCCCcEEEEeCC
Confidence            46999999999999999999999 9999999999999999998  7 89999999997

>3lte_A Response regulator; structural genomics, PSI, protein structure initiative, NYSG YORK structural genomix research consortium, nysgxrc; 2.00A {Bermanella marisrubri}

Probab=98.23  E-value=2.6e-06  Score=69.21  Aligned_cols=54  Identities=22%  Similarity=0.299  Sum_probs=50.8

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ..+||||||++..+..+..+|+..||.|..+.++.+|++.+.  ...||+||+|+.
T Consensus         6 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--~~~~dlii~d~~   59 (132)
T 3lte_A            6 SKRILVVDDDQAMAAAIERVLKRDHWQVEIAHNGFDAGIKLS--TFEPAIMTLDLS   59 (132)
T ss_dssp             -CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HTCCSEEEEESC
T ss_pred             CccEEEEECCHHHHHHHHHHHHHCCcEEEEeCCHHHHHHHHH--hcCCCEEEEecC
Confidence            469999999999999999999999999999999999999998  678999999998

>3crn_A Response regulator receiver domain protein, CHEY-; structural genomics, signal regulator receiver domain; HET: PHD; 1.58A {Methanospirillum hungatei jf-1}

Probab=98.23  E-value=2.7e-06  Score=69.78  Aligned_cols=54  Identities=19%  Similarity=0.287  Sum_probs=50.7

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +.+||||||++.++..+..+|+..||.|..+.++.+|++.+.  ...||+||+|+.
T Consensus         3 ~~~Ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~--~~~~dlvl~D~~   56 (132)
T 3crn_A            3 LKRILIVDDDTAILDSTKQILEFEGYEVEIAATAGEGLAKIE--NEFFNLALFXIK   56 (132)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HSCCSEEEECSB
T ss_pred             ccEEEEEeCCHHHHHHHHHHHHHCCceEEEeCCHHHHHHHHh--cCCCCEEEEecC
Confidence            458999999999999999999999999999999999999998  578999999998

>2gkg_A Response regulator homolog; social motility, receiver domain, signalling, high resolutio signaling protein; 1.00A {Myxococcus xanthus} PDB: 2i6f_A 2nt4_A 2nt3_A

Probab=98.21  E-value=1.8e-06  Score=68.96  Aligned_cols=54  Identities=19%  Similarity=0.305  Sum_probs=50.1

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .++||||||++..+..+..+|+..||++..+.++.+|++.+.  ...||+||+|+.
T Consensus         5 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~~~--~~~~dlvi~d~~   58 (127)
T 2gkg_A            5 SKKILIVESDTALSATLRSALEGRGFTVDETTDGKGSVEQIR--RDRPDLVVLAVD   58 (127)
T ss_dssp             -CEEEEECSCHHHHHHHHHHHHHHTCEEEEECCHHHHHHHHH--HHCCSEEEEESB
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCceEEEecCHHHHHHHHH--hcCCCEEEEeCC
Confidence            359999999999999999999999999999999999999998  567999999987

>3hzh_A Chemotaxis response regulator (CHEY-3); phosphatase, complex, response regulator, receiver domain, two-component signal transduction; HET: BFD; 1.96A {Borrelia burgdorferi}

Probab=98.21  E-value=2.3e-06  Score=72.62  Aligned_cols=55  Identities=18%  Similarity=0.274  Sum_probs=50.9

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHcCCCEEE-EECCHHHHHHHHHhcCC--CccEEEEcCC
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRNCSYEVT-AVANSLHAWKILEDLTN--HIDIVLTESS  127 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~~GyeV~-~A~dg~eAle~L~~~~~--~pDLIIlDl~  127 (399)
                      ++++||||||++..+..+..+|+..||.+. .+.++.+|++.+.  ..  .|||||+|+.
T Consensus        35 ~~~~Ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~~al~~l~--~~~~~~dliilD~~   92 (157)
T 3hzh_A           35 IPFNVLIVDDSVFTVKQLTQIFTSEGFNIIDTAADGEEAVIKYK--NHYPNIDIVTLXIT   92 (157)
T ss_dssp             EECEEEEECSCHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHH--HHGGGCCEEEECSS
T ss_pred             CceEEEEEeCCHHHHHHHHHHHHhCCCeEEEEECCHHHHHHHHH--hcCCCCCEEEEecc
Confidence            456999999999999999999999999988 9999999999998  45  7899999998

>2qr3_A Two-component system response regulator; structural genomics, signal receiver, PSI-2, protein structu initiative; 1.80A {Bacteroides fragilis}

Probab=98.20  E-value=3.3e-06  Score=69.05  Aligned_cols=54  Identities=17%  Similarity=0.305  Sum_probs=51.0

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +++||||||++..+..+..+|+..||.|..+.++.+|++.+.  ...||+||+|+.
T Consensus         3 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--~~~~dlvi~d~~   56 (140)
T 2qr3_A            3 LGTIIIVDDNKGVLTAVQLLLKNHFSKVITLSSPVSLSTVLR--EENPEVVLLDMN   56 (140)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHTTTSSEEEEECCHHHHHHHHH--HSCEEEEEEETT
T ss_pred             CceEEEEeCCHHHHHHHHHHHHhCCcEEEEeCCHHHHHHHHH--cCCCCEEEEeCC
Confidence            469999999999999999999999999999999999999998  578999999997

>2a9o_A Response regulator; essential protein, YYCF/YYCG homolog, signaling protein; 1.65A {Streptococcus pneumoniae} SCOP: c.23.1.1 PDB: 1nxo_A 1nxs_A 1nxv_A 1nxw_A 1nxx_A 1nxp_A 2a9p_A 2a9q_A 1nxt_A* 2a9r_A*

Probab=98.19  E-value=3e-06  Score=67.30  Aligned_cols=53  Identities=21%  Similarity=0.373  Sum_probs=49.8

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .+||||||++..+..+..+|+..||.+..+.++.+|+..+.  ...||+||+|+.
T Consensus         2 ~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~~~--~~~~dlvl~D~~   54 (120)
T 2a9o_A            2 KKILIVDDEKPISDIIKFNMTKEGYEVVTAFNGREALEQFE--AEQPDIIILDLM   54 (120)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HHCCSEEEECSS
T ss_pred             ceEEEEcCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHHH--hCCCCEEEEecc
Confidence            48999999999999999999999999999999999999998  568999999998

>3n0r_A Response regulator; sigma factor, receiver, two-component SI transduction, signaling protein; HET: MSE GOL; 1.25A {Caulobacter vibrioides} PDB: 3t0y_A

Probab=98.19  E-value=2.4e-06  Score=81.78  Aligned_cols=60  Identities=23%  Similarity=0.323  Sum_probs=53.9

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEE-EECCHHHHHHHHHhcCCCccEEEEcCC-C-CCCCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVT-AVANSLHAWKILEDLTNHIDIVLTESS-G-SGSGS  133 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~-~A~dg~eAle~L~~~~~~pDLIIlDl~-G-sssgs  133 (399)
                      ..+||||||++.++..+..+|+..||.|. .+.+|.+|++.+.  ...|||||+|+. - ...|-
T Consensus       160 ~~rILvVdD~~~~~~~l~~~L~~~g~~v~~~a~~g~eAl~~~~--~~~~dlvl~D~~MPd~mdG~  222 (286)
T 3n0r_A          160 ATEVLIIEDEPVIAADIEALVRELGHDVTDIAATRGEALEAVT--RRTPGLVLADIQLADGSSGI  222 (286)
T ss_dssp             CCEEEEECCSHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHH--HCCCSEEEEESCCTTSCCTT
T ss_pred             CCcEEEEcCCHHHHHHHHHHhhccCceEEEEeCCHHHHHHHHH--hCCCCEEEEcCCCCCCCCHH
Confidence            35899999999999999999999999999 9999999999999  678999999998 3 44444

>2qxy_A Response regulator; regulation of transcription, NYSGXRC, protein structure initiative II (PSI II), structural genomics; 1.95A {Thermotoga maritima}

Probab=98.19  E-value=3.7e-06  Score=69.31  Aligned_cols=54  Identities=22%  Similarity=0.316  Sum_probs=50.7

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +.+||||||++..+..+..+|+..||+|..+.++.+|++.+.  ...||+||+|+.
T Consensus         4 ~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--~~~~dlvi~d~~   57 (142)
T 2qxy_A            4 TPTVMVVDESRITFLAVKNALEKDGFNVIWAKNEQEAFTFLR--REKIDLVFVDVF   57 (142)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHGGGTCEEEEESSHHHHHHHHT--TSCCSEEEEECT
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHhCCCEEEEECCHHHHHHHHh--ccCCCEEEEeCC
Confidence            468999999999999999999999999999999999999998  678999999984

>3c97_A Signal transduction histidine kinase; structural genomics, signaling, PSI-2, protein structure initiative; 1.70A {Aspergillus oryzae RIB40}

Probab=98.18  E-value=3.8e-06  Score=69.42  Aligned_cols=54  Identities=28%  Similarity=0.562  Sum_probs=50.6

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ..+||||||++..+..+..+|+..||.+..+.++.+|+..+.  ...||+||+|+.
T Consensus        10 ~~~iLivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~al~~l~--~~~~dlvllD~~   63 (140)
T 3c97_A           10 PLSVLIAEDNDICRLVAAKALEKCTNDITVVTNGLQALQAYQ--NRQFDVIIMDIQ   63 (140)
T ss_dssp             CCEEEEECCCHHHHHHHHHHHTTTCSEEEEESSHHHHHHHHH--HSCCSEEEECTT
T ss_pred             CceEEEEcCCHHHHHHHHHHHHHcCCceEEECCHHHHHHHHh--cCCCCEEEEeCC
Confidence            358999999999999999999999999999999999999998  578999999998

>2pl1_A Transcriptional regulatory protein PHOP; CHEY-like fold, response regulator, beryllium fluoride, transcription factor, activated, virulence; 1.90A {Escherichia coli} SCOP: c.23.1.1 PDB: 2pkx_A

Probab=98.18  E-value=4.2e-06  Score=66.70  Aligned_cols=53  Identities=21%  Similarity=0.325  Sum_probs=50.0

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ++||||||++..+..+..+|+..||.|..+.++.+|+..+.  ...||+||+|+.
T Consensus         1 ~~ilivdd~~~~~~~l~~~l~~~g~~v~~~~~~~~a~~~~~--~~~~dlil~D~~   53 (121)
T 2pl1_A            1 MRVLVVEDNALLRHHLKVQIQDAGHQVDDAEDAKEADYYLN--EHIPDIAIVDLG   53 (121)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HSCCSEEEECSC
T ss_pred             CeEEEEeCcHHHHHHHHHHHhhcCCEEEEeCCHHHHHHHHh--ccCCCEEEEecC
Confidence            37999999999999999999999999999999999999998  578999999998

>3jte_A Response regulator receiver protein; structural genomics, nysgrc, response regulator receiver DOM target 11226E, PSI-2; 1.90A {Clostridium thermocellum atcc 27405}

Probab=98.17  E-value=5.6e-06  Score=68.27  Aligned_cols=56  Identities=23%  Similarity=0.375  Sum_probs=51.2

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +.+||||||++..+..+..+|+..||.|..+.++.+|+..+......||+||+|+.
T Consensus         3 ~~~ilivdd~~~~~~~l~~~l~~~g~~v~~~~~~~~a~~~~~~~~~~~dlvi~d~~   58 (143)
T 3jte_A            3 LAKILVIDDESTILQNIKFLLEIDGNEVLTASSSTEGLRIFTENCNSIDVVITDMK   58 (143)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHTTTTCCEEEEESC
T ss_pred             CCEEEEEcCCHHHHHHHHHHHHhCCceEEEeCCHHHHHHHHHhCCCCCCEEEEeCC
Confidence            56999999999999999999999999999999999999999732358999999998

>3ilh_A Two component response regulator; NYSGXRC, PSI-II, protein S initiative, structural genomics; 2.59A {Cytophaga hutchinsonii}

Probab=98.17  E-value=4e-06  Score=68.84  Aligned_cols=55  Identities=20%  Similarity=0.299  Sum_probs=51.2

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHcCCC--EEEEECCHHHHHHHHHhcC-----CCccEEEEcCC
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRNCSY--EVTAVANSLHAWKILEDLT-----NHIDIVLTESS  127 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~~Gy--eV~~A~dg~eAle~L~~~~-----~~pDLIIlDl~  127 (399)
                      .+++||||||++..+..+..+|+..||  .|..+.++.+|++.+.  .     ..||+||+|+.
T Consensus         8 ~~~~iLivdd~~~~~~~l~~~l~~~~~~~~v~~~~~~~~a~~~l~--~~~~~~~~~dlvi~D~~   69 (146)
T 3ilh_A            8 KIDSVLLIDDDDIVNFLNTTIIRMTHRVEEIQSVTSGNAAINKLN--ELYAAGRWPSIICIDIN   69 (146)
T ss_dssp             CEEEEEEECSCHHHHHHHHHHHHTTCCEEEEEEESSHHHHHHHHH--HHHTSSCCCSEEEEESS
T ss_pred             ccceEEEEeCCHHHHHHHHHHHHhcCCCeeeeecCCHHHHHHHHH--HhhccCCCCCEEEEcCC
Confidence            346999999999999999999999999  8999999999999998  5     78999999998

>1k66_A Phytochrome response regulator RCPB; CHEY homologue, homodimer, APO-protein, (beta/alpha)5, signaling protein; 1.75A {Tolypothrix SP} SCOP: c.23.1.1

Probab=98.17  E-value=4.9e-06  Score=68.35  Aligned_cols=56  Identities=16%  Similarity=0.198  Sum_probs=51.8

Q ss_pred             CCCcEEEEEeCChhhHHHHHHHHHcCCC--EEEEECCHHHHHHHHHhcC----------CCccEEEEcCC
Q 039733           70 TRSLKVLLVENDDSTRHVVSALLRNCSY--EVTAVANSLHAWKILEDLT----------NHIDIVLTESS  127 (399)
Q Consensus        70 ~~~~rVLLVEDD~~~reiL~~lLe~~Gy--eV~~A~dg~eAle~L~~~~----------~~pDLIIlDl~  127 (399)
                      .++.+||||||++..+..+..+|+..||  .|..+.++.+|++.+.  .          ..||+||+|+.
T Consensus         4 ~~~~~iLivdd~~~~~~~l~~~L~~~g~~~~v~~~~~~~~al~~l~--~~~~~~~~~~~~~~dlvi~D~~   71 (149)
T 1k66_A            4 NATQPLLVVEDSDEDFSTFQRLLQREGVVNPIYRCITGDQALDFLY--QTGSYCNPDIAPRPAVILLDLN   71 (149)
T ss_dssp             CTTSCEEEECCCHHHHHHHHHHHHHTTBCSCEEEECSHHHHHHHHH--TCCSSSCGGGCCCCSEEEECSC
T ss_pred             CCCccEEEEECCHHHHHHHHHHHHHcCCCceEEEECCHHHHHHHHH--hcccccCcccCCCCcEEEEECC
Confidence            3456899999999999999999999998  8999999999999998  5          68999999998

>1xhf_A DYE resistance, aerobic respiration control protein ARCA; two-component system, gene regulation, transcription factor, anoxic redox control; 2.15A {Escherichia coli} SCOP: c.23.1.1 PDB: 1xhe_A

Probab=98.17  E-value=5.2e-06  Score=66.55  Aligned_cols=53  Identities=21%  Similarity=0.419  Sum_probs=50.1

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .+||||||++..+..+..+|+..||.+..+.++.+|+..+.  ...||+||+|+.
T Consensus         4 ~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~~~--~~~~dlvi~D~~   56 (123)
T 1xhf_A            4 PHILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQILS--EYDINLVIMDIN   56 (123)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHH--HSCCSEEEECSS
T ss_pred             ceEEEEeCCHHHHHHHHHHHhhCCcEEEEeCCHHHHHHHHh--cCCCCEEEEcCC
Confidence            48999999999999999999999999999999999999998  578999999998

>1zgz_A Torcad operon transcriptional regulatory protein; two-component system, gene regulation, transcription factor, respiratory system; 1.80A {Escherichia coli} SCOP: c.23.1.1

Probab=98.17  E-value=4.5e-06  Score=66.78  Aligned_cols=53  Identities=17%  Similarity=0.383  Sum_probs=50.0

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .+||||||++..+..+..+|+..||.+..+.++.+++..+.  ...||+||+|+.
T Consensus         3 ~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~--~~~~dlvi~d~~   55 (122)
T 1zgz_A            3 HHIVIVEDEPVTQARLQSYFTQEGYTVSVTASGAGLREIMQ--NQSVDLILLDIN   55 (122)
T ss_dssp             CEEEEECSSHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HSCCSEEEEESC
T ss_pred             cEEEEEECCHHHHHHHHHHHHHCCCeEEEecCHHHHHHHHh--cCCCCEEEEeCC
Confidence            58999999999999999999999999999999999999998  578999999998

>2r25_B Osmosensing histidine protein kinase SLN1; alpha5-BETA5, response regulator, four helix bundle, histidine phosphotransfer (HPT) protein; 1.70A {Saccharomyces cerevisiae} SCOP: c.23.1.1 PDB: 1oxk_B 1oxb_B

Probab=98.16  E-value=3.7e-06  Score=69.35  Aligned_cols=53  Identities=15%  Similarity=0.385  Sum_probs=48.7

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCE-EEEECCHHHHHHHHHhcC-----CCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYE-VTAVANSLHAWKILEDLT-----NHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~Gye-V~~A~dg~eAle~L~~~~-----~~pDLIIlDl~  127 (399)
                      ++||||||++.++..+..+|+..||. |..+.++.+|++.+.  .     ..||+||+|+.
T Consensus         3 ~~ILivdD~~~~~~~l~~~L~~~g~~~v~~~~~~~~al~~~~--~~~~~~~~~dlvllD~~   61 (133)
T 2r25_B            3 VKILVVEDNHVNQEVIKRMLNLEGIENIELACDGQEAFDKVK--ELTSKGENYNMIFMDVQ   61 (133)
T ss_dssp             SCEEEECSCHHHHHHHHHHHHHTTCCCEEEESSHHHHHHHHH--HHHHHTCCCSEEEECSC
T ss_pred             ceEEEEcCCHHHHHHHHHHHHHcCCceEEEECCHHHHHHHHH--HHHhcCCCCCEEEEeCC
Confidence            58999999999999999999998985 888999999999987  4     67999999998

>3kto_A Response regulator receiver protein; PSI-II,structural genomics, protein structure initiative; 1.98A {Pseudoalteromonas atlantica T6C} SCOP: c.23.1.0

Probab=98.16  E-value=1.4e-06  Score=71.81  Aligned_cols=54  Identities=15%  Similarity=0.164  Sum_probs=50.7

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +.+||||||++..+..+..+|+..||.|..+.++.+|++.+.  ...||+||+|+.
T Consensus         6 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--~~~~dlvi~D~~   59 (136)
T 3kto_A            6 HPIIYLVDHQKDARAALSKLLSPLDVTIQCFASAESFMRQQI--SDDAIGMIIEAH   59 (136)
T ss_dssp             -CEEEEECSCHHHHHHHHHHHTTSSSEEEEESSHHHHTTSCC--CTTEEEEEEETT
T ss_pred             CCeEEEEcCCHHHHHHHHHHHHHCCcEEEEeCCHHHHHHHHh--ccCCCEEEEeCc
Confidence            469999999999999999999999999999999999999998  788999999998

>1tmy_A CHEY protein, TMY; chemotaxis, phosphoryl transfer, signal transduction; 1.90A {Thermotoga maritima} SCOP: c.23.1.1 PDB: 2tmy_A 3tmy_A 4tmy_A 1u0s_Y

Probab=98.16  E-value=3.6e-06  Score=67.19  Aligned_cols=54  Identities=20%  Similarity=0.312  Sum_probs=49.5

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCE-EEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYE-VTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~Gye-V~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ..+||||||++..+..+..+|+..||. +..+.++.+|+..+.  ...||+||+|+.
T Consensus         2 ~~~ilivdd~~~~~~~l~~~l~~~g~~vv~~~~~~~~a~~~~~--~~~~dlil~D~~   56 (120)
T 1tmy_A            2 GKRVLIVDDAAFMRMMLKDIITKAGYEVAGEATNGREAVEKYK--ELKPDIVTMDIT   56 (120)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHH--HHCCSEEEEECS
T ss_pred             CceEEEEcCcHHHHHHHHHHHhhcCcEEEEEECCHHHHHHHHH--hcCCCEEEEeCC
Confidence            358999999999999999999999999 568999999999998  568999999998

>3hdv_A Response regulator; PSI-II, structural genomics, Pro structure initiative, NEW YORK SGX research center for STRU genomics, nysgxrc; 2.09A {Pseudomonas putida} SCOP: c.23.1.0

Probab=98.16  E-value=4.1e-06  Score=68.51  Aligned_cols=55  Identities=16%  Similarity=0.249  Sum_probs=50.2

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +.+||||||++..+..+..+|+..||.|..+.++.+|+..+.. ...||+||+|+.
T Consensus         7 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~~~~-~~~~dlvi~D~~   61 (136)
T 3hdv_A            7 RPLVLVVDDNAVNREALILYLKSRGIDAVGADGAEEARLYLHY-QKRIGLMITDLR   61 (136)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCCEEEESSHHHHHHHHHH-CTTEEEEEECSC
T ss_pred             CCeEEEECCCHHHHHHHHHHHHHcCceEEEeCCHHHHHHHHHh-CCCCcEEEEecc
Confidence            5699999999999999999999999999999999999999983 234999999998

>3hdg_A Uncharacterized protein; two-component sensor activity, response regulator, PSI-II, 11227F, NYSGXRC, structural genomics; 2.27A {Wolinella succinogenes} SCOP: c.23.1.0

Probab=98.16  E-value=2.9e-06  Score=69.49  Aligned_cols=54  Identities=24%  Similarity=0.396  Sum_probs=51.0

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +++||||||++..+..+..+|+..||.+..+.++.+|++.+.  ...||+||+|+.
T Consensus         7 ~~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~a~~~l~--~~~~dlvi~d~~   60 (137)
T 3hdg_A            7 ALKILIVEDDTDAREWLSTIISNHFPEVWSAGDGEEGERLFG--LHAPDVIITDIR   60 (137)
T ss_dssp             CCCEEEECSCHHHHHHHHHHHHTTCSCEEEESSHHHHHHHHH--HHCCSEEEECSS
T ss_pred             ccEEEEEeCCHHHHHHHHHHHHhcCcEEEEECCHHHHHHHHh--ccCCCEEEEeCC
Confidence            469999999999999999999999999999999999999998  578999999998

>3r0j_A Possible two component system response transcript positive regulator PHOP; beta-alpha fold, winged helix-turn-helix; 2.50A {Mycobacterium tuberculosis}

Probab=98.16  E-value=3.2e-06  Score=77.57  Aligned_cols=54  Identities=20%  Similarity=0.310  Sum_probs=51.2

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +++||||||++.++..+..+|+..||.|..+.++.+|++.+.  ...||+||+|+.
T Consensus        23 ~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~--~~~~dlvllD~~   76 (250)
T 3r0j_A           23 EARVLVVDDEANIVELLSVSLKFQGFEVYTATNGAQALDRAR--ETRPDAVILDVX   76 (250)
T ss_dssp             SCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HHCCSEEEEESC
T ss_pred             CceEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHH--hCCCCEEEEeCC
Confidence            469999999999999999999999999999999999999998  568999999998

>2jba_A Phosphate regulon transcriptional regulatory PROT; transcription factor, sensory transduction, phosphate regula transcription regulation; 1.45A {Escherichia coli} PDB: 2jba_B 1b00_A 2iyn_A 2jb9_A 1zes_A

Probab=98.15  E-value=2.5e-06  Score=68.67  Aligned_cols=54  Identities=19%  Similarity=0.275  Sum_probs=50.5

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +.+||||||++..+..+..+|+..||.+..+.++.+|++.+.  ...||+||+|+.
T Consensus         2 ~~~ilivdd~~~~~~~l~~~l~~~g~~v~~~~~~~~a~~~~~--~~~~dlvi~D~~   55 (127)
T 2jba_A            2 ARRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLN--EPWPDLILLAWM   55 (127)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEECSHHHHHTTCS--SSCCSEEEEESE
T ss_pred             CcEEEEEcCCHHHHHHHHHHHHHCCceEEEeCCHHHHHHHHh--ccCCCEEEEecC
Confidence            358999999999999999999999999999999999999988  678999999998

>2rjn_A Response regulator receiver:metal-dependent phosphohydrolase, HD subdomain; structural genomics, oceanospirillum SP. MED92; 2.10A {Neptuniibacter caesariensis}

Probab=98.14  E-value=6.4e-06  Score=69.11  Aligned_cols=55  Identities=15%  Similarity=0.399  Sum_probs=51.6

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .+++||||||++..+..+..+|+..||.|..+.++.+|+..+.  ...||+||+|+.
T Consensus         6 ~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--~~~~dlvi~d~~   60 (154)
T 2rjn_A            6 KNYTVMLVDDEQPILNSLKRLIKRLGCNIITFTSPLDALEALK--GTSVQLVISDMR   60 (154)
T ss_dssp             SCCEEEEECSCHHHHHHHHHHHHTTTCEEEEESCHHHHHHHHT--TSCCSEEEEESS
T ss_pred             CCCeEEEEcCCHHHHHHHHHHHHHcCCeEEEeCCHHHHHHHHh--cCCCCEEEEecC
Confidence            3569999999999999999999999999999999999999998  678999999998

>3nhm_A Response regulator; protein structure initiative II(PSI II), NYSGXRC, structural genomics; 2.19A {Myxococcus xanthus}

Probab=98.13  E-value=5.3e-06  Score=67.37  Aligned_cols=53  Identities=23%  Similarity=0.343  Sum_probs=49.5

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +.+||||||++..+..+..+|+ .||.|..+.++.+|++.+.  ...||+||+|+.
T Consensus         4 ~~~ilivdd~~~~~~~l~~~l~-~~~~v~~~~~~~~a~~~l~--~~~~dlvi~d~~   56 (133)
T 3nhm_A            4 KPKVLIVENSWTMRETLRLLLS-GEFDCTTAADGASGLQQAL--AHPPDVLISDVN   56 (133)
T ss_dssp             -CEEEEECSCHHHHHHHHHHHT-TTSEEEEESSHHHHHHHHH--HSCCSEEEECSS
T ss_pred             CCEEEEEcCCHHHHHHHHHHHh-CCcEEEEECCHHHHHHHHh--cCCCCEEEEeCC
Confidence            4699999999999999999999 8999999999999999998  678999999998

>1mvo_A PHOP response regulator; phosphate regulon, transcriptional regulatory protein, alpha/beta doubly wound fold, phosphorylation; 1.60A {Bacillus subtilis} SCOP: c.23.1.1

Probab=98.13  E-value=4.7e-06  Score=67.94  Aligned_cols=54  Identities=22%  Similarity=0.378  Sum_probs=50.5

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ..+||||||++..+..+..+|+..||.+..+.++.+|+..+.  ...||+||+|+.
T Consensus         3 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~~~--~~~~dlvl~D~~   56 (136)
T 1mvo_A            3 NKKILVVDDEESIVTLLQYNLERSGYDVITASDGEEALKKAE--TEKPDLIVLDVM   56 (136)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HHCCSEEEEESS
T ss_pred             CCEEEEEECCHHHHHHHHHHHHHCCcEEEEecCHHHHHHHHh--hcCCCEEEEecC
Confidence            458999999999999999999999999999999999999998  568999999998

>1dbw_A Transcriptional regulatory protein FIXJ; doubly wound five-stranded beta/alpha fold, nitrogen fixatio regulation; HET: 15P; 1.60A {Sinorhizobium meliloti} SCOP: c.23.1.1 PDB: 1dck_A* 1dcm_A 1d5w_A*

Probab=98.13  E-value=6.4e-06  Score=66.61  Aligned_cols=54  Identities=11%  Similarity=0.201  Sum_probs=50.5

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ..+||||||++..+..+..+|+..||.+..+.++.+++..+.  ...||+||+|+.
T Consensus         3 ~~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~--~~~~dlvi~D~~   56 (126)
T 1dbw_A            3 DYTVHIVDDEEPVRKSLAFMLTMNGFAVKMHQSAEAFLAFAP--DVRNGVLVTDLR   56 (126)
T ss_dssp             CCEEEEEESSHHHHHHHHHHHHHTTCEEEEESCHHHHHHHGG--GCCSEEEEEECC
T ss_pred             CCEEEEEcCCHHHHHHHHHHHHhCCcEEEEeCCHHHHHHHHh--cCCCCEEEEECC
Confidence            358999999999999999999999999999999999999998  678999999998

>1mb3_A Cell division response regulator DIVK; signal transduction protein, structural proteomics in europe, spine, structural genomics; 1.41A {Caulobacter vibrioides} SCOP: c.23.1.1 PDB: 1m5u_A 1mav_A 1mb0_A 1m5t_A

Probab=98.13  E-value=4.7e-06  Score=66.71  Aligned_cols=53  Identities=28%  Similarity=0.419  Sum_probs=49.7

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .+||||||++..+..+..+|+..||.+..+.++.+|+..+.  ...||+||+|+.
T Consensus         2 ~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~a~~~~~--~~~~dlvi~D~~   54 (124)
T 1mb3_A            2 KKVLIVEDNELNMKLFHDLLEAQGYETLQTREGLSALSIAR--ENKPDLILMDIQ   54 (124)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHHHH--HHCCSEEEEESB
T ss_pred             cEEEEEcCCHHHHHHHHHHHHHcCcEEEEeCCHHHHHHHHh--cCCCCEEEEeCC
Confidence            48999999999999999999999999999999999999998  568999999998

>2b4a_A BH3024; flavodoxin-like fold, structural genomics, joint center for structural genomics, JCSG, protein structure initiative; 2.42A {Bacillus halodurans} SCOP: c.23.1.1

Probab=98.12  E-value=3.8e-06  Score=69.07  Aligned_cols=55  Identities=18%  Similarity=0.274  Sum_probs=51.3

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcC-CCccEEEEcCC
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLT-NHIDIVLTESS  127 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~-~~pDLIIlDl~  127 (399)
                      ...+||||||++..+..+..+|+..||.|..+.++.+|++.+.  . ..||+||+|+.
T Consensus        14 ~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~--~~~~~dlvilD~~   69 (138)
T 2b4a_A           14 QPFRVTLVEDEPSHATLIQYHLNQLGAEVTVHPSGSAFFQHRS--QLSTCDLLIVSDQ   69 (138)
T ss_dssp             CCCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHTGG--GGGSCSEEEEETT
T ss_pred             CCCeEEEECCCHHHHHHHHHHHHHcCCEEEEeCCHHHHHHHHH--hCCCCCEEEEeCC
Confidence            3468999999999999999999999999999999999999998  6 68999999998

>3cz5_A Two-component response regulator, LUXR family; structural genomics, protein structure initiative; 2.70A {Aurantimonas SP}

Probab=98.11  E-value=6.9e-06  Score=68.81  Aligned_cols=56  Identities=20%  Similarity=0.362  Sum_probs=51.1

Q ss_pred             CCCcEEEEEeCChhhHHHHHHHHHc-CCCEEE-EECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           70 TRSLKVLLVENDDSTRHVVSALLRN-CSYEVT-AVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        70 ~~~~rVLLVEDD~~~reiL~~lLe~-~GyeV~-~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ..+++||||||++..+..+..+|+. .||.+. .+.++.+|+..+.  ...||+||+|+.
T Consensus         3 ~~~~~ILivdd~~~~~~~l~~~L~~~~~~~v~~~~~~~~~a~~~l~--~~~~dlii~D~~   60 (153)
T 3cz5_A            3 LSTARIMLVDDHPIVREGYRRLIERRPGYAVVAEAADAGEAYRLYR--ETTPDIVVMDLT   60 (153)
T ss_dssp             -CCEEEEEECSCHHHHHHHHHHHTTSTTEEEEEEESSHHHHHHHHH--TTCCSEEEECSC
T ss_pred             CcccEEEEECCcHHHHHHHHHHHhhCCCcEEEEEeCCHHHHHHHHh--cCCCCEEEEecC
Confidence            3457999999999999999999998 799987 8999999999999  678999999998

>2qzj_A Two-component response regulator; 11017X, PSI-II, structural genomics; 2.89A {Clostridium difficile}

Probab=98.11  E-value=6.6e-06  Score=68.05  Aligned_cols=54  Identities=17%  Similarity=0.265  Sum_probs=50.6

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ..+||||||++.++..+..+|+..||.|..+.++.+|++.+.  ...||+||+|+.
T Consensus         4 ~~~Ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~--~~~~dlvllD~~   57 (136)
T 2qzj_A            4 QTKILIIDGDKDNCQKLKGFLEEKGISIDLAYNCEEAIGKIF--SNKYDLIFLEII   57 (136)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHH--HCCCSEEEEESE
T ss_pred             CCeEEEEcCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHH--hcCCCEEEEeCC
Confidence            358999999999999999999999999999999999999998  578999999998

>1kgs_A DRRD, DNA binding response regulator D; DNA-binding protein, ALPH-beta sandwich, winged-helix, helix helix, DNA binding protein; HET: DNA MSE; 1.50A {Thermotoga maritima} SCOP: a.4.6.1 c.23.1.1 PDB: 3nnn_A*

Probab=98.11  E-value=5.4e-06  Score=73.89  Aligned_cols=54  Identities=15%  Similarity=0.306  Sum_probs=51.0

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +++||||||++.++..+..+|+..||.|..+.++.+|+..+.  ...||+||+|+.
T Consensus         2 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~~~--~~~~dlvllD~~   55 (225)
T 1kgs_A            2 NVRVLVVEDERDLADLITEALKKEMFTVDVCYDGEEGMYMAL--NEPFDVVILDIM   55 (225)
T ss_dssp             CCEEEEECSSHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HSCCSEEEEESC
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh--cCCCCEEEEeCC
Confidence            469999999999999999999999999999999999999998  578999999998

>3h1g_A Chemotaxis protein CHEY homolog; sulfate-bound CHEY, cytoplasm, flagellar rotatio magnesium, metal-binding, phosphoprotein; 1.70A {Helicobacter pylori} SCOP: c.23.1.1 PDB: 3gwg_A 3h1e_A 3h1f_A

Probab=98.11  E-value=7.2e-06  Score=66.92  Aligned_cols=55  Identities=24%  Similarity=0.543  Sum_probs=49.2

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCE-EEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYE-VTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~Gye-V~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .++||||||++..+..+..+|+..||. +..+.++.+|+..+.. ...||+||+|+.
T Consensus         5 ~~~iLivdd~~~~~~~l~~~L~~~g~~~v~~~~~~~~a~~~~~~-~~~~dlvi~D~~   60 (129)
T 3h1g_A            5 SMKLLVVDDSSTMRRIIKNTLSRLGYEDVLEAEHGVEAWEKLDA-NADTKVLITDWN   60 (129)
T ss_dssp             -CCEEEECSCHHHHHHHHHHHHHTTCCCEEEESSHHHHHHHHHH-CTTCCEEEECSC
T ss_pred             CcEEEEEeCCHHHHHHHHHHHHHcCCcEEEEeCCHHHHHHHHHh-CCCCCEEEEeCC
Confidence            468999999999999999999999996 8899999999998873 347999999998

>1p6q_A CHEY2; chemotaxis, signal transduction, response regulator, structural proteomics in europe, spine, structural genomics; NMR {Sinorhizobium meliloti} SCOP: c.23.1.1 PDB: 1p6u_A

Probab=98.10  E-value=5.2e-06  Score=67.08  Aligned_cols=54  Identities=22%  Similarity=0.458  Sum_probs=50.3

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCC-EEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSY-EVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~Gy-eV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +++||||||++..+..+..+|+..|| .+..+.++.+|+..+.  ...||+||+|+.
T Consensus         6 ~~~ilivdd~~~~~~~l~~~L~~~g~~~v~~~~~~~~a~~~~~--~~~~dlvl~D~~   60 (129)
T 1p6q_A            6 KIKVLIVDDQVTSRLLLGDALQQLGFKQITAAGDGEQGMKIMA--QNPHHLVISDFN   60 (129)
T ss_dssp             CCCEEEECSSHHHHHHHHHHHHTTTCSCEECCSSHHHHHHHHH--TSCCSEEEECSS
T ss_pred             cCeEEEEcCCHHHHHHHHHHHHHCCCcEEEecCCHHHHHHHHH--cCCCCEEEEeCC
Confidence            45899999999999999999999999 7889999999999998  678999999998

>3cnb_A DNA-binding response regulator, MERR family; signal receiver domain, DNA binding protein, protein structu initiative, PSI-2; 2.00A {Colwellia psychrerythraea}

Probab=98.08  E-value=6.7e-06  Score=67.26  Aligned_cols=54  Identities=22%  Similarity=0.433  Sum_probs=50.4

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHc-CCCE-EEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRN-CSYE-VTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~-~Gye-V~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +++||||||++..+..+..+|+. .||. |..+.++.+|+..+.  ...||+||+|+.
T Consensus         8 ~~~iLivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~a~~~l~--~~~~dlii~d~~   63 (143)
T 3cnb_A            8 DFSILIIEDDKEFADMLTQFLENLFPYAKIKIAYNPFDAGDLLH--TVKPDVVMLDLM   63 (143)
T ss_dssp             -CEEEEECSCHHHHHHHHHHHHHHCTTCEEEEECSHHHHHHHHH--HTCCSEEEEETT
T ss_pred             CceEEEEECCHHHHHHHHHHHHhccCccEEEEECCHHHHHHHHH--hcCCCEEEEecc
Confidence            46999999999999999999999 9999 999999999999998  578999999998

>1k68_A Phytochrome response regulator RCPA; phosphorylated aspartate, CHEY homologue, homodimer, (beta/alpha)5, signaling protein; HET: PHD; 1.90A {Tolypothrix SP} SCOP: c.23.1.1

Probab=98.08  E-value=1e-05  Score=65.47  Aligned_cols=53  Identities=25%  Similarity=0.412  Sum_probs=50.1

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCC--EEEEECCHHHHHHHHHhcC-------CCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSY--EVTAVANSLHAWKILEDLT-------NHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~Gy--eV~~A~dg~eAle~L~~~~-------~~pDLIIlDl~  127 (399)
                      ++||||||++..+..+..+|+..||  .|..+.++.+|++.+.  .       ..||+||+|+.
T Consensus         3 ~~ilivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~a~~~l~--~~~~~~~~~~~dlvi~d~~   64 (140)
T 1k68_A            3 KKIFLVEDNKADIRLIQEALANSTVPHEVVTVRDGMEAMAYLR--QEGEYANASRPDLILLXLN   64 (140)
T ss_dssp             CEEEEECCCHHHHHHHHHHHHTCSSCCEEEEECSHHHHHHHHT--TCGGGGSCCCCSEEEECSS
T ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCCceEEEECCHHHHHHHHH--cccccccCCCCcEEEEecC
Confidence            5899999999999999999999998  8999999999999998  5       68999999998

>1zh2_A KDP operon transcriptional regulatory protein KDPE; two-component system, gene regulation, transcription factor, KDP potassium transport system; 2.00A {Escherichia coli} SCOP: c.23.1.1 PDB: 1zh4_A

Probab=98.07  E-value=6.9e-06  Score=65.28  Aligned_cols=53  Identities=17%  Similarity=0.241  Sum_probs=49.6

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ++||||||++..+..+..+|+..||.+..+.++.+++..+.  ...||+||+|+.
T Consensus         2 ~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~--~~~~dlvi~D~~   54 (121)
T 1zh2_A            2 TNVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEAA--TRKPDLIILDLG   54 (121)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHH--HHCCSEEEEESE
T ss_pred             cEEEEEeCCHHHHHHHHHHHhcCCCEEEEeCCHHHHHHHHh--cCCCCEEEEeCC
Confidence            58999999999999999999999999999999999999887  568999999998

>3kyj_B CHEY6 protein, putative histidine protein kinase; protein-protein interaction, histidine kinase, response regulator, phosphorylation; 1.40A {Rhodobacter sphaeroides} PDB: 3kyi_B*

Probab=98.07  E-value=7.9e-06  Score=67.84  Aligned_cols=55  Identities=18%  Similarity=0.418  Sum_probs=49.8

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHcC-CCEEE-EECCHHHHHHHHHhcCC-CccEEEEcCC
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRNC-SYEVT-AVANSLHAWKILEDLTN-HIDIVLTESS  127 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~~-GyeV~-~A~dg~eAle~L~~~~~-~pDLIIlDl~  127 (399)
                      ...+||||||++.++..+..+|+.. ||.++ .+.++.+|++.+.  .. .||+||+|+.
T Consensus        12 ~~~~vlivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~al~~l~--~~~~~dlvilD~~   69 (145)
T 3kyj_B           12 SPYNVMIVDDAAMMRLYIASFIKTLPDFKVVAQAANGQEALDKLA--AQPNVDLILLDIE   69 (145)
T ss_dssp             CSEEEEEECSCHHHHHHHHHHHTTCTTEEEEEEESSHHHHHHHHH--HCTTCCEEEECTT
T ss_pred             CCCeEEEEcCCHHHHHHHHHHHHhCCCceEEEEECCHHHHHHHHh--cCCCCCEEEEeCC
Confidence            4568999999999999999999988 89864 8999999999998  56 7999999998

>3cfy_A Putative LUXO repressor protein; structural genomics, unknown function, uncharacterized protein, signal receiver domain; 2.50A {Vibrio parahaemolyticus rimd 2210633}

Probab=98.07  E-value=5e-06  Score=68.88  Aligned_cols=53  Identities=19%  Similarity=0.345  Sum_probs=49.9

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .+||||||++..+..+..+|+..||.|..+.++.+|++.+.  ...||+||+|+.
T Consensus         5 ~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--~~~~dlvllD~~   57 (137)
T 3cfy_A            5 PRVLLVEDSTSLAILYKQYVKDEPYDIFHVETGRDAIQFIE--RSKPQLIILDLK   57 (137)
T ss_dssp             CEEEEECSCTTHHHHHHHHTTTSSSEEEEESSHHHHHHHHH--HHCCSEEEECSB
T ss_pred             ceEEEEeCCHHHHHHHHHHHHhcCceEEEeCCHHHHHHHHH--hcCCCEEEEecC
Confidence            48999999999999999999999999999999999999998  568999999998

>3cg0_A Response regulator receiver modulated diguanylate with PAS/PAC sensor; signal receiver domain, diguanylate cyclase; 2.15A {Desulfovibrio desulfuricans subsp}

Probab=98.06  E-value=5.3e-06  Score=67.82  Aligned_cols=55  Identities=22%  Similarity=0.215  Sum_probs=50.6

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHcCCCEEE-EECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRNCSYEVT-AVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~~GyeV~-~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .+++||||||++..+..+..+|+..||.+. .+.++.+|+..+.  ...||+||+|+.
T Consensus         8 ~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~~a~~~~~--~~~~dlii~d~~   63 (140)
T 3cg0_A            8 DLPGVLIVEDGRLAAATLRIQLESLGYDVLGVFDNGEEAVRCAP--DLRPDIALVDIM   63 (140)
T ss_dssp             CCCEEEEECCBHHHHHHHHHHHHHHTCEEEEEESSHHHHHHHHH--HHCCSEEEEESS
T ss_pred             CCceEEEEECCHHHHHHHHHHHHHCCCeeEEEECCHHHHHHHHH--hCCCCEEEEecC
Confidence            356999999999999999999999999998 5999999999998  567999999987

>3heb_A Response regulator receiver domain protein (CHEY); NYSGXRC, PSI-II, respose regulator, structure initiative, structural genomics; 2.40A {Rhodospirillum rubrum} SCOP: c.23.1.0

Probab=98.05  E-value=8.9e-06  Score=68.07  Aligned_cols=56  Identities=18%  Similarity=0.318  Sum_probs=50.0

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCC--EEEEECCHHHHHHHHHh-------cCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSY--EVTAVANSLHAWKILED-------LTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~Gy--eV~~A~dg~eAle~L~~-------~~~~pDLIIlDl~  127 (399)
                      .++||||||++..+..+..+|+..||  .|..+.++.+|++.+..       ....||+||+|+.
T Consensus         4 ~~~ILivddd~~~~~~l~~~L~~~g~~~~v~~~~~~~~al~~l~~~~~~~~~~~~~~dliilD~~   68 (152)
T 3heb_A            4 SVTIVMIEDDLGHARLIEKNIRRAGVNNEIIAFTDGTSALNYLFGDDKSGRVSAGRAQLVLLDLN   68 (152)
T ss_dssp             -CEEEEECCCHHHHHHHHHHHHHTTCCCCEEEESSHHHHHHHHHCTTSSSGGGTTCBEEEEECSB
T ss_pred             CceEEEEeCCHHHHHHHHHHHHhCCCcceEEEeCCHHHHHHHHhccccccccccCCCCEEEEeCC
Confidence            46999999999999999999999998  89999999999999951       1468999999998

>1jbe_A Chemotaxis protein CHEY; signaling protein; 1.08A {Escherichia coli} SCOP: c.23.1.1 PDB: 3chy_A 1a0o_A 1cey_A 1bdj_A 1eay_A 1f4v_A 1ffg_A 1ffs_A 1ffw_A 1fqw_A 2b1j_A 1chn_A 1djm_A 1kmi_Y* 1d4z_A 3olx_A 3olw_A 1cye_A 2che_A 2chf_A ...

Probab=98.05  E-value=1e-05  Score=65.24  Aligned_cols=54  Identities=22%  Similarity=0.425  Sum_probs=50.1

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCC-EEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSY-EVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~Gy-eV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .++||||||++..+..+..+|+..|| .+..+.++.+|++.+.  ...||+||+|+.
T Consensus         4 ~~~ilivdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~--~~~~dlvi~D~~   58 (128)
T 1jbe_A            4 ELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQ--AGGYGFVISDWN   58 (128)
T ss_dssp             TCCEEEECSCHHHHHHHHHHHHHTTCCCEEEESSHHHHHHHHT--TCCCCEEEEESC
T ss_pred             ccEEEEECCCHHHHHHHHHHHHHcCCcEEEeeCCHHHHHHHHH--hcCCCEEEEeCC
Confidence            35899999999999999999999999 6899999999999998  678999999998

>2j48_A Two-component sensor kinase; pseudo-receiver, circadian clock, transferase, response regulator, histidine protein kinase; NMR {Synechococcus elongatus}

Probab=98.05  E-value=9e-06  Score=63.48  Aligned_cols=53  Identities=21%  Similarity=0.296  Sum_probs=50.0

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .+|||||+++..+..+..+|+..||.+..+.++.+++..+.  ...||+||+|+.
T Consensus         2 ~~iliv~~~~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~l~--~~~~dlii~d~~   54 (119)
T 2j48_A            2 GHILLLEEEDEAATVVCEMLTAAGFKVIWLVDGSTALDQLD--LLQPIVILMAWP   54 (119)
T ss_dssp             CEEEEECCCHHHHHHHHHHHHHTTCEEEEESCHHHHHHHHH--HHCCSEEEEECS
T ss_pred             CEEEEEeCCHHHHHHHHHHHHhCCcEEEEecCHHHHHHHHH--hcCCCEEEEecC
Confidence            48999999999999999999999999999999999999998  568999999997

>2zay_A Response regulator receiver protein; structural genomics, NYSGXRC, target 11006U, protein structure initiative; 2.00A {Desulfuromonas acetoxidans}

Probab=98.04  E-value=4.2e-06  Score=69.32  Aligned_cols=55  Identities=15%  Similarity=0.311  Sum_probs=50.9

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ++++||||||++..+..+..+|+..||.|..+.++.+|+..+.  ...||+||+|+.
T Consensus         7 ~~~~iLivd~~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--~~~~dlii~d~~   61 (147)
T 2zay_A            7 KWWRIMLVDTQLPALAASISALSQEGFDIIQCGNAIEAVPVAV--KTHPHLIITEAN   61 (147)
T ss_dssp             -CEEEEEECTTGGGGHHHHHHHHHHTEEEEEESSHHHHHHHHH--HHCCSEEEEESC
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCHHHHHHHHH--cCCCCEEEEcCC
Confidence            3569999999999999999999999999999999999999998  568999999998

>3f6c_A Positive transcription regulator EVGA; structural genomics, PSI-2, protein structure initiative, PO transcription regulator EVGA; 1.45A {Escherichia coli k-12}

Probab=98.04  E-value=3.4e-06  Score=68.61  Aligned_cols=53  Identities=19%  Similarity=0.275  Sum_probs=49.9

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEE-EECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVT-AVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~-~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ++||||||++..+..+..+|+..||.+. .+.++.+|+..+.  ...||+||+|+.
T Consensus         2 ~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~~a~~~~~--~~~~dlii~d~~   55 (134)
T 3f6c_A            2 LNAIIIDDHPLAIAAIRNLLIKNDIEILAELTEGGSAVQRVE--TLKPDIVIIDVD   55 (134)
T ss_dssp             EEEEEECCCHHHHHHHHHHHHHTTEEEEEEESSSTTHHHHHH--HHCCSEEEEETT
T ss_pred             eEEEEEcCCHHHHHHHHHHHhhCCcEEEEEcCCHHHHHHHHH--hcCCCEEEEecC
Confidence            5899999999999999999999999987 8999999999998  578999999998

>1dz3_A Stage 0 sporulation protein A; response regulator, domain swapping; 1.65A {Bacillus stearothermophilus} SCOP: c.23.1.1 PDB: 1qmp_A*

Probab=98.04  E-value=7.4e-06  Score=66.60  Aligned_cols=54  Identities=20%  Similarity=0.324  Sum_probs=48.8

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcC-CCEEE-EECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNC-SYEVT-AVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~-GyeV~-~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .++||||||++..+..+..+|+.. ||.+. .+.++.+|++.+.  ...||+||+|+.
T Consensus         2 ~~~ilivdd~~~~~~~l~~~l~~~~~~~~~~~~~~~~~a~~~~~--~~~~dlvllD~~   57 (130)
T 1dz3_A            2 SIKVCIADDNRELVSLLDEYISSQPDMEVIGTAYNGQDCLQMLE--EKRPDILLLDII   57 (130)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHHH--HHCCSEEEEESC
T ss_pred             ceEEEEEcCCHHHHHHHHHHHHhCCCceEEEEeCCHHHHHHHHh--cCCCCEEEEecC
Confidence            358999999999999999999987 88865 7899999999998  568999999998

>3n53_A Response regulator receiver modulated diguanylate; diguanylate cyclase, protein structure I II(PSI II), NYSGXRC, structural genomics; 2.20A {Pelobacter carbinolicus} SCOP: c.23.1.0

Probab=98.04  E-value=7.8e-06  Score=67.31  Aligned_cols=53  Identities=23%  Similarity=0.374  Sum_probs=49.8

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +.+||||||++..+..+..+|+.. |.|..+.++.+|++.+.  ...||+||+|+.
T Consensus         3 ~~~iLivdd~~~~~~~l~~~l~~~-~~v~~~~~~~~a~~~~~--~~~~dlvi~D~~   55 (140)
T 3n53_A            3 LKKILIIDQQDFSRIELKNFLDSE-YLVIESKNEKEALEQID--HHHPDLVILDMD   55 (140)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHTTT-SEEEEESSHHHHHHHHH--HHCCSEEEEETT
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHhc-ceEEEeCCHHHHHHHHh--cCCCCEEEEeCC
Confidence            469999999999999999999988 99999999999999998  568999999998

>3snk_A Response regulator CHEY-like protein; P-loop containing nucleoside triphosphate hydrolases, struct genomics; 2.02A {Mesorhizobium loti}

Probab=98.03  E-value=1.6e-06  Score=71.30  Aligned_cols=55  Identities=16%  Similarity=0.158  Sum_probs=51.5

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHcCC-CEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRNCS-YEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~~G-yeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .+.+||||||++..+..+..+|+..| |.|..+.++.+|++.+.  ...||+||+|+.
T Consensus        13 ~~~~ilivdd~~~~~~~l~~~L~~~g~~~v~~~~~~~~a~~~l~--~~~~dlvi~D~~   68 (135)
T 3snk_A           13 KRKQVALFSSDPNFKRDVATRLDALAIYDVRVSETDDFLKGPPA--DTRPGIVILDLG   68 (135)
T ss_dssp             CCEEEEEECSCHHHHHHHHHHHHHTSSEEEEEECGGGGGGCCCT--TCCCSEEEEEEE
T ss_pred             CCcEEEEEcCCHHHHHHHHHHHhhcCCeEEEEeccHHHHHHHHh--ccCCCEEEEeCC
Confidence            34699999999999999999999999 99999999999999998  788999999998

>2gwr_A DNA-binding response regulator MTRA; two-component regulatory system, transcription regulation, phosphorylation, OMPR family; 2.10A {Mycobacterium tuberculosis} PDB: 3nhz_A

Probab=98.02  E-value=5.9e-06  Score=75.10  Aligned_cols=55  Identities=18%  Similarity=0.361  Sum_probs=51.2

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ++++||||||++.++..+..+|+..||.|..+.++.+|++.+.  ...||+||+|+.
T Consensus         4 m~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~--~~~~dlvilD~~   58 (238)
T 2gwr_A            4 MRQRILVVDDDASLAEMLTIVLRGEGFDTAVIGDGTQALTAVR--ELRPDLVLLDLM   58 (238)
T ss_dssp             CCCEEEEECSCHHHHHHHHHHHHHTTCEEEEECCGGGHHHHHH--HHCCSEEEEESS
T ss_pred             ccCeEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHH--hCCCCEEEEeCC
Confidence            4569999999999999999999999999999999999999998  568999999998

>3eq2_A Probable two-component response regulator; adaptor sigmas, signaling protein; 3.40A {Pseudomonas aeruginosa} PDB: 3f7a_A

Probab=98.02  E-value=5.8e-06  Score=81.29  Aligned_cols=55  Identities=24%  Similarity=0.492  Sum_probs=51.8

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +..+||||||++.++..+..+|+..||+|..+.++.+|++.+.  ...||+||+|+.
T Consensus         4 ~~~~iLivdD~~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~~--~~~~dlvllD~~   58 (394)
T 3eq2_A            4 VSATLLIIDDDEVVRESLAAYLEDSNFKVLQALNGLQGLQIFE--SEQPDLVICDLR   58 (394)
T ss_dssp             CEEEEEEECSCHHHHHHHHHHHHHTTEEEEECSSHHHHHHHHH--HSCCSEEEECCC
T ss_pred             CCCEEEEEeCCHHHHHHHHHHHHhCCCEEEEECCHHHHHHHHh--hCCCCEEEEcCC
Confidence            3569999999999999999999999999999999999999998  678999999998

>2ayx_A Sensor kinase protein RCSC; two independent structural domains, transferase; NMR {Escherichia coli} SCOP: c.23.1.1 c.23.1.6 PDB: 2ayz_A 2ayy_A

Probab=98.01  E-value=1.3e-05  Score=74.44  Aligned_cols=55  Identities=25%  Similarity=0.527  Sum_probs=51.6

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ..++||||||++.++..+..+|+..||.|..+.++.+|++.+.  ...||+||+|+.
T Consensus       128 ~~~~ILivdd~~~~~~~l~~~L~~~g~~v~~a~~~~eal~~l~--~~~~dlvl~D~~  182 (254)
T 2ayx_A          128 DDMMILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVLS--KNHIDIVLSDVN  182 (254)
T ss_dssp             CCCEEEEEESSHHHHHHHHHHHHHHTSEEEEECCSHHHHHHHH--HSCCSEEEEEES
T ss_pred             CCCEEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHH--hCCCCEEEEcCC
Confidence            3569999999999999999999999999999999999999998  578999999998

>1s8n_A Putative antiterminator; RV1626, structural genomics, transcriptional antiterminator, component system, PSI; 1.48A {Mycobacterium tuberculosis} SCOP: c.23.1.1 PDB: 1sd5_A

Probab=98.01  E-value=9.4e-06  Score=71.75  Aligned_cols=53  Identities=23%  Similarity=0.410  Sum_probs=49.9

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEE-EECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVT-AVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~-~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .+||||||++.++..+..+|+..||.+. .+.++.+|+..+.  ...||+||+|+.
T Consensus        14 ~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~~al~~~~--~~~~dlvi~D~~   67 (205)
T 1s8n_A           14 RRVLIAEDEALIRMDLAEMLREEGYEIVGEAGDGQEAVELAE--LHKPDLVIMDVK   67 (205)
T ss_dssp             CEEEEECSSHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHH--HHCCSEEEEESS
T ss_pred             ccEEEEECCHHHHHHHHHHHHHCCCEEEEEeCCHHHHHHHHh--hcCCCEEEEeCC
Confidence            5899999999999999999999999988 8999999999998  568999999998

>2oqr_A Sensory transduction protein REGX3; response regulator, winged-helix-turn-helix, DNA-binding, 3D swapping, two component system; 2.03A {Mycobacterium tuberculosis H37RV}

Probab=97.99  E-value=9.6e-06  Score=72.66  Aligned_cols=54  Identities=30%  Similarity=0.400  Sum_probs=50.7

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +++||||||++.++..+..+|+..||.|..+.++.+|++.+.  ...||+||+|+.
T Consensus         4 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~--~~~~dlvllD~~   57 (230)
T 2oqr_A            4 ATSVLIVEDEESLADPLAFLLRKEGFEATVVTDGPAALAEFD--RAGADIVLLDLM   57 (230)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEECSHHHHHHHHH--HHCCSEEEEESS
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh--ccCCCEEEEECC
Confidence            469999999999999999999999999999999999999998  568999999998

>1dcf_A ETR1 protein; beta-alpha five sandwich, transferase; 2.50A {Arabidopsis thaliana} SCOP: c.23.1.2

Probab=97.99  E-value=1.3e-05  Score=65.57  Aligned_cols=53  Identities=26%  Similarity=0.480  Sum_probs=48.8

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .++||||||++..+..+..+|+..||.|..+.++.+|++.+.  ... |+||+|+.
T Consensus         7 ~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~~~--~~~-dlvllD~~   59 (136)
T 1dcf_A            7 GLKVLVMDENGVSRMVTKGLLVHLGCEVTTVSSNEECLRVVS--HEH-KVVFMDVC   59 (136)
T ss_dssp             TCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHCC--TTC-SEEEEECC
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCHHHHHHHHh--ccC-CEEEEeCC
Confidence            468999999999999999999999999999999999999887  444 99999998

>1yio_A Response regulatory protein; transcription regulation, DNA binding protein; 2.20A {Pseudomonas fluorescens} SCOP: a.4.6.2 c.23.1.1 PDB: 1zn2_A

Probab=97.98  E-value=1.1e-05  Score=71.19  Aligned_cols=54  Identities=19%  Similarity=0.254  Sum_probs=50.8

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ..+||||||++.++..+..+|+..||.|..+.++.+|++.+.  ...||+||+|+.
T Consensus         4 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~--~~~~dlvl~D~~   57 (208)
T 1yio_A            4 KPTVFVVDDDMSVREGLRNLLRSAGFEVETFDCASTFLEHRR--PEQHGCLVLDMR   57 (208)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHCC--TTSCEEEEEESC
T ss_pred             CCEEEEEcCCHHHHHHHHHHHHhCCceEEEcCCHHHHHHhhh--ccCCCEEEEeCC
Confidence            358999999999999999999999999999999999999988  678999999998

>3kcn_A Adenylate cyclase homolog; SGX, PSI 2, structural genomics, protein structure initiative; 2.45A {Rhodopirellula baltica}

Probab=97.98  E-value=1.6e-05  Score=66.59  Aligned_cols=54  Identities=19%  Similarity=0.341  Sum_probs=48.5

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +.+||||||++..+..+..+|+. ||.|..+.++.+|++.+.. ..+||+||+|+.
T Consensus         4 ~~~ILivdd~~~~~~~l~~~L~~-~~~v~~~~~~~~a~~~l~~-~~~~dlvi~D~~   57 (151)
T 3kcn_A            4 NERILLVDDDYSLLNTLKRNLSF-DFEVTTCESGPEALACIKK-SDPFSVIMVDMR   57 (151)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHTT-TSEEEEESSHHHHHHHHHH-SCCCSEEEEESC
T ss_pred             CCeEEEEeCCHHHHHHHHHHhcc-CceEEEeCCHHHHHHHHHc-CCCCCEEEEeCC
Confidence            46999999999999999999976 9999999999999999983 234699999998

>2qvg_A Two component response regulator; NYSGXRC, PSI-2, structural genomics, protein structure initiative; 1.50A {Legionella pneumophila subsp}

Probab=97.97  E-value=1.3e-05  Score=65.88  Aligned_cols=54  Identities=17%  Similarity=0.296  Sum_probs=50.3

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCC--EEEEECCHHHHHHHHHhcC------CCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSY--EVTAVANSLHAWKILEDLT------NHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~Gy--eV~~A~dg~eAle~L~~~~------~~pDLIIlDl~  127 (399)
                      .++||||||++..+..+..+|+..||  .|..+.++.+|+..+.  .      ..||+||+|+.
T Consensus         7 ~~~ILivdd~~~~~~~l~~~L~~~g~~~~v~~~~~~~~a~~~l~--~~~~~~~~~~dlii~D~~   68 (143)
T 2qvg_A            7 KVDILYLEDDEVDIQSVERVFHKISSLIKIEIAKSGNQALDMLY--GRNKENKIHPKLILLDIN   68 (143)
T ss_dssp             CCSEEEECCCHHHHHHHHHHHHHHCTTCCEEEESSHHHHHHHHH--TCTTCCCCCCSEEEEETT
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHHhCCCceEEEECCHHHHHHHHH--hcccccCCCCCEEEEecC
Confidence            46899999999999999999999898  8999999999999998  5      67999999998

>3q9s_A DNA-binding response regulator; DNA binding protein; 2.40A {Deinococcus radiodurans}

Probab=97.96  E-value=1.4e-05  Score=73.90  Aligned_cols=54  Identities=19%  Similarity=0.377  Sum_probs=51.1

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +++||||||++.++..+..+|+..||.|..+.++.+|+..+.  ...||+||+|+.
T Consensus        37 ~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~--~~~~DlvllD~~   90 (249)
T 3q9s_A           37 EQRILVIEDDHDIANVLRMDLTDAGYVVDHADSAMNGLIKAR--EDHPDLILLDLG   90 (249)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHH--HSCCSEEEEECC
T ss_pred             CCEEEEEECCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHh--cCCCCEEEEcCC
Confidence            469999999999999999999999999999999999999998  678999999998

>1i3c_A Response regulator RCP1; phytochrome, signaling protein; 1.90A {Synechocystis SP} SCOP: c.23.1.1 PDB: 1jlk_A

Probab=97.95  E-value=2.4e-05  Score=65.54  Aligned_cols=56  Identities=20%  Similarity=0.380  Sum_probs=49.2

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCC--EEEEECCHHHHHHHHHhc-----CCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSY--EVTAVANSLHAWKILEDL-----TNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~Gy--eV~~A~dg~eAle~L~~~-----~~~pDLIIlDl~  127 (399)
                      .++||||||++..+..+..+|+..||  .|..+.++.+|++.+...     ...||+||+|+.
T Consensus         8 ~~~ILivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~al~~l~~~~~~~~~~~~dlillD~~   70 (149)
T 1i3c_A            8 PKVILLVEDSKADSRLVQEVLKTSTIDHELIILRDGLAAMAFLQQQGEYENSPRPNLILLDLN   70 (149)
T ss_dssp             CEEEEEECCCHHHHHHHHHHHHSCCSCEEEEEECSHHHHHHHHTTCGGGTTCCCCSEEEECSC
T ss_pred             CCeEEEEECCHHHHHHHHHHHHhcCCCccEEEeCCHHHHHHHHHhccccccCCCCCEEEEeCC
Confidence            35899999999999999999998887  788999999999999720     047999999998

>1qkk_A DCTD, C4-dicarboxylate transport transcriptional regulatory protein; receiver domain, 2-component signal transduction; 1.7A {Sinorhizobium meliloti} SCOP: c.23.1.1 PDB: 1l5z_A 1l5y_A

Probab=97.94  E-value=1.2e-05  Score=67.50  Aligned_cols=54  Identities=20%  Similarity=0.359  Sum_probs=50.4

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .++||||||++..+..+..+|+..||.|..+.++.+|+..+.  ...||+||+|+.
T Consensus         3 ~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--~~~~dliild~~   56 (155)
T 1qkk_A            3 APSVFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGLS--ADFAGIVISDIR   56 (155)
T ss_dssp             -CEEEEECSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHTCC--TTCCSEEEEESC
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHHcCcEEEEECCHHHHHHHHH--hCCCCEEEEeCC
Confidence            358999999999999999999999999999999999999998  678999999998

>1ys7_A Transcriptional regulatory protein PRRA; response regulator, DNA binding domain, phosphorylation; 1.58A {Mycobacterium tuberculosis} SCOP: a.4.6.1 c.23.1.1 PDB: 1ys6_A

Probab=97.94  E-value=1.7e-05  Score=71.01  Aligned_cols=54  Identities=22%  Similarity=0.326  Sum_probs=50.8

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .++||||||++.++..+..+|+..||.|..+.++.+|+..+.  ...||+||+|+.
T Consensus         7 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~~~--~~~~dlvllD~~   60 (233)
T 1ys7_A            7 SPRVLVVDDDSDVLASLERGLRLSGFEVATAVDGAEALRSAT--ENRPDAIVLDIN   60 (233)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HSCCSEEEEESS
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHhCCCEEEEECCHHHHHHHHH--hCCCCEEEEeCC
Confidence            358999999999999999999999999999999999999998  578999999998

>3b2n_A Uncharacterized protein Q99UF4; structural genomics, PSI-2, protein structure initiative, NE SGX research center for structural genomics; 2.04A {Staphylococcus aureus}

Probab=97.92  E-value=1.2e-05  Score=65.85  Aligned_cols=54  Identities=17%  Similarity=0.308  Sum_probs=48.4

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCC--CEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCS--YEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~G--yeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +.+||||||++..+..+..+|+..|  +.+..+.++.+|++.+.  ...||+||+|+.
T Consensus         3 ~~~Ilivdd~~~~~~~l~~~l~~~~~~~~v~~~~~~~~al~~~~--~~~~dlvilD~~   58 (133)
T 3b2n_A            3 LTSLIIAEDQNMLRQAMVQLIKLHGDFEILADTDNGLDAMKLIE--EYNPNVVILDIE   58 (133)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHHHHSSEEEEEEESCHHHHHHHHH--HHCCSEEEECSS
T ss_pred             ceEEEEECCCHHHHHHHHHHHhhCCCcEEEEEcCCHHHHHHHHh--hcCCCEEEEecC
Confidence            4589999999999999999999876  45778999999999998  568999999998

>2qv0_A Protein MRKE; structural genomics, transcription, PSI-2, protein structure initiative; 2.40A {Klebsiella pneumoniae}

Probab=97.92  E-value=2e-05  Score=64.90  Aligned_cols=55  Identities=24%  Similarity=0.417  Sum_probs=48.4

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHcC-CCE-EEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRNC-SYE-VTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~~-Gye-V~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ..++||||||++..+..+..+|+.. ||. +..+.++.+|+..+.  ...||+||+|+.
T Consensus         8 ~~~~iLivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~al~~l~--~~~~dlvi~d~~   64 (143)
T 2qv0_A            8 EKMKVIIVEDEFLAQQELSWLINTHSQMEIVGSFDDGLDVLKFLQ--HNKVDAIFLDIN   64 (143)
T ss_dssp             --CEEEEECSCHHHHHHHHHHHHHHSCCEEEEEESCHHHHHHHHH--HCCCSEEEECSS
T ss_pred             CceEEEEEcCCHHHHHHHHHHHHhCCCceEEEEeCCHHHHHHHHH--hCCCCEEEEecC
Confidence            3569999999999999999999976 888 458999999999998  578999999998

>4dad_A Putative pilus assembly-related protein; response regulator receiver domain, CHEY-related protein, ST genomics; 2.50A {Burkholderia pseudomallei} PDB: 4dn6_A

Probab=97.91  E-value=7.1e-06  Score=68.03  Aligned_cols=56  Identities=18%  Similarity=0.297  Sum_probs=49.9

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHcCC-CEEEEECCHHHHHHHHHhcC-CCccEEEEcCC
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRNCS-YEVTAVANSLHAWKILEDLT-NHIDIVLTESS  127 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~~G-yeV~~A~dg~eAle~L~~~~-~~pDLIIlDl~  127 (399)
                      ...+||||||++..+..+..+|+..| |.|..+.++.+++..+.. . ..|||||+|+.
T Consensus        19 ~~~~ilivdd~~~~~~~l~~~L~~~g~~~v~~~~~~~~~~~~~~~-~~~~~dlvi~D~~   76 (146)
T 4dad_A           19 GMINILVASEDASRLAHLARLVGDAGRYRVTRTVGRAAQIVQRTD-GLDAFDILMIDGA   76 (146)
T ss_dssp             GGCEEEEECSCHHHHHHHHHHHHHHCSCEEEEECCCHHHHTTCHH-HHTTCSEEEEECT
T ss_pred             CCCeEEEEeCCHHHHHHHHHHHhhCCCeEEEEeCCHHHHHHHHHh-cCCCCCEEEEeCC
Confidence            34699999999999999999999998 999999999988887762 3 78999999998

>2qsj_A DNA-binding response regulator, LUXR family; structural genomics, PSI-2, protein structure initiative; 2.10A {Silicibacter pomeroyi dss-3}

Probab=97.91  E-value=2.4e-05  Score=65.41  Aligned_cols=54  Identities=26%  Similarity=0.338  Sum_probs=49.2

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcC-CC-EEEEECCHHHHHHHHHhcC-CCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNC-SY-EVTAVANSLHAWKILEDLT-NHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~-Gy-eV~~A~dg~eAle~L~~~~-~~pDLIIlDl~  127 (399)
                      +++||||||++..+..+..+|+.. || .|..+.++.+|+..+.  . ..||+||+|+.
T Consensus         3 ~~~iLivdd~~~~~~~l~~~L~~~~g~~~v~~~~~~~~a~~~l~--~~~~~dlvi~d~~   59 (154)
T 2qsj_A            3 LTVVLIVDDHHLIRAGAKNLLEGAFSGMRVEGAETVSDALAFLE--ADNTVDLILLDVN   59 (154)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHHHHCTTEEEEEESSHHHHHHHHH--TTCCCSEEEECC-
T ss_pred             ccEEEEEcCCHHHHHHHHHHHHhCCCceEEEEecCHHHHHHHHh--ccCCCCEEEEeCC
Confidence            468999999999999999999987 88 6889999999999999  6 78999999998

>2pln_A HP1043, response regulator; signaling protein; 1.80A {Helicobacter pylori} PDB: 2hqo_A

Probab=97.89  E-value=3e-05  Score=63.51  Aligned_cols=51  Identities=16%  Similarity=0.236  Sum_probs=47.7

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEE
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVL  123 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLII  123 (399)
                      ...+||||||++..+..+..+|+..||.|..+.++.+|+..+.  ...||+||
T Consensus        17 ~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~--~~~~dlvi   67 (137)
T 2pln_A           17 GSMRVLLIEKNSVLGGEIEKGLNVKGFMADVTESLEDGEYLMD--IRNYDLVM   67 (137)
T ss_dssp             TCSEEEEECSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHHHH--HSCCSEEE
T ss_pred             CCCeEEEEeCCHHHHHHHHHHHHHcCcEEEEeCCHHHHHHHHH--cCCCCEEE
Confidence            4569999999999999999999999999999999999999998  57899999

>3eqz_A Response regulator; structural genomics, unknown function, PSI-2, protein struct initiative; 2.15A {Colwellia psychrerythraea} SCOP: c.23.1.0

Probab=97.88  E-value=1e-05  Score=65.53  Aligned_cols=53  Identities=15%  Similarity=0.195  Sum_probs=49.2

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +.+||||||++..+..+..+|+..++.+..+.++.+++..+.  .. ||+||+|+.
T Consensus         3 ~~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~--~~-~dlvi~D~~   55 (135)
T 3eqz_A            3 LNRVFIVDDDTLTCNLLKTIVEPIFGNVEAFQHPRAFLTLSL--NK-QDIIILDLM   55 (135)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHTTTCSCEEEESCHHHHTTSCC--CT-TEEEEEECC
T ss_pred             cceEEEEeCCHHHHHHHHHHHHhhcceeeeecCHHHHHHhhc--cC-CCEEEEeCC
Confidence            469999999999999999999988889999999999999887  56 999999998

>3t8y_A CHEB, chemotaxis response regulator protein-glutamate methylesterase; CHEA, hydrolase; 1.90A {Thermotoga maritima}

Probab=97.87  E-value=2.2e-05  Score=67.22  Aligned_cols=56  Identities=18%  Similarity=0.262  Sum_probs=48.5

Q ss_pred             CCCcEEEEEeCChhhHHHHHHHHHcCC-CE-EEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           70 TRSLKVLLVENDDSTRHVVSALLRNCS-YE-VTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        70 ~~~~rVLLVEDD~~~reiL~~lLe~~G-ye-V~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ..+++||||||++..+..+..+|+..| +. +..+.++.+|++.+.  ...||+||+|+.
T Consensus        23 ~~~~~ILivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~al~~l~--~~~~dlvilD~~   80 (164)
T 3t8y_A           23 DRVIRVLVVDDSAFMRMVLKDIIDSQPDMKVVGFAKDGLEAVEKAI--ELKPDVITMDIE   80 (164)
T ss_dssp             -CCEEEEEECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHHH--HHCCSEEEECSS
T ss_pred             cCccEEEEEcCCHHHHHHHHHHHhcCCCeEEEEecCCHHHHHHHhc--cCCCCEEEEeCC
Confidence            345799999999999999999999875 44 457999999999998  568999999998

>3cu5_A Two component transcriptional regulator, ARAC FAM; structural genomics, protein structure initiative; 2.60A {Clostridium phytofermentans isdg}

Probab=97.87  E-value=2.1e-05  Score=65.41  Aligned_cols=54  Identities=22%  Similarity=0.364  Sum_probs=48.6

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHc--CCCEEE-EECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRN--CSYEVT-AVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~--~GyeV~-~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +++||||||++..+..+..+|..  .||.+. .+.++.+|+..+.  ...||+||+|+.
T Consensus         2 ~~~ILivdd~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~al~~~~--~~~~dlvllD~~   58 (141)
T 3cu5_A            2 SLRILIVDDEKLTRDGLIANINWKALSFDQIDQADDGINAIQIAL--KHPPNVLLTDVR   58 (141)
T ss_dssp             CCEEEEECSCHHHHHHHHHHCCGGGSCCSEEEEESSHHHHHHHHT--TSCCSEEEEESC
T ss_pred             cceEEEEeCCHHHHHHHHHHHHHccCCcEEeeecccHHHHHHHHh--cCCCCEEEEeCC
Confidence            46899999999999999999973  688877 8999999999998  678999999998

>3luf_A Two-component system response regulator/ggdef domain protein; structural genomics, ASA_2441, PSI-2, protein structure initiative; HET: MSE; 1.76A {Aeromonas salmonicida} PDB: 3mf4_A*

Probab=97.84  E-value=3.3e-05  Score=72.21  Aligned_cols=55  Identities=27%  Similarity=0.392  Sum_probs=50.3

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ..+||||||++.++..+..+|+..||.|..+.++.+|++.+.. ...||+||+|+.
T Consensus       124 ~~~ILivDD~~~~~~~l~~~L~~~~~~v~~a~~~~eal~~l~~-~~~~dlvllD~~  178 (259)
T 3luf_A          124 QIEVLVVDDSRTSRHRTMAQLRKQLLQVHEASHAREALATLEQ-HPAIRLVLVDYY  178 (259)
T ss_dssp             TCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHHH-CTTEEEEEECSC
T ss_pred             CCcEEEEeCCHHHHHHHHHHHHHcCcEEEEeCCHHHHHHHHhc-CCCCCEEEEcCC
Confidence            4699999999999999999999999999999999999999983 234899999998

>1a04_A Nitrate/nitrite response regulator protein NARL; signal transduction protein, response regulators, two- component systems; 2.20A {Escherichia coli} SCOP: a.4.6.2 c.23.1.1 PDB: 1rnl_A

Probab=97.83  E-value=2.3e-05  Score=69.57  Aligned_cols=54  Identities=19%  Similarity=0.290  Sum_probs=49.1

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcC-CCEE-EEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNC-SYEV-TAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~-GyeV-~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +++||||||++.++..+..+|+.. +|.+ ..+.++.+|++.+.  ...||+||+|+.
T Consensus         5 ~~~ilivdd~~~~~~~l~~~L~~~~~~~vv~~~~~~~~al~~~~--~~~~dlvllD~~   60 (215)
T 1a04_A            5 PATILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAE--SLDPDLILLDLN   60 (215)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHTTCTTEEEEEEESSHHHHHHHHH--HHCCSEEEEETT
T ss_pred             ceEEEEECCCHHHHHHHHHHHhcCCCcEEEEEeCCHHHHHHHHH--hcCCCEEEEeCC
Confidence            469999999999999999999987 4887 68999999999998  568999999998

>3dzd_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; HET: ADP; 2.40A {Aquifex aeolicus} PDB: 1zit_A 2jrl_A

Probab=97.82  E-value=2.5e-05  Score=77.60  Aligned_cols=52  Identities=19%  Similarity=0.299  Sum_probs=50.1

Q ss_pred             EEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           74 KVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        74 rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +||||||++.++..+..+|+..||.|..+.++.+|++.+.  ...||+||+|+.
T Consensus         2 ~ILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~eal~~l~--~~~~DlvllDi~   53 (368)
T 3dzd_A            2 RVLVVDDEESITSSLSAILEEEGYHPDTAKTLREAEKKIK--ELFFPVIVLDVW   53 (368)
T ss_dssp             EEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HBCCSEEEEESE
T ss_pred             EEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHH--hCCCCEEEEeCC
Confidence            7999999999999999999999999999999999999998  678999999998

>3eul_A Possible nitrate/nitrite response transcriptional regulatory protein NARL (DNA-binding...; central beta strand flanked by alpha helices; 1.90A {Mycobacterium tuberculosis}

Probab=97.82  E-value=2.5e-05  Score=65.26  Aligned_cols=55  Identities=15%  Similarity=0.183  Sum_probs=49.3

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHcCCCE--EEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRNCSYE--VTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~~Gye--V~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ...+||||||++..+..+..+|+..|+.  +..+.++.+|++.+.  ...||+||+|+.
T Consensus        14 ~~~~iLivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~a~~~l~--~~~~dlii~d~~   70 (152)
T 3eul_A           14 EKVRVVVGDDHPLFREGVVRALSLSGSVNVVGEADDGAAALELIK--AHLPDVALLDYR   70 (152)
T ss_dssp             CCEEEEEECSSHHHHHHHHHHHHHHSSEEEEEEESSHHHHHHHHH--HHCCSEEEEETT
T ss_pred             ceEEEEEEcCCHHHHHHHHHHHhhCCCeEEEEEeCCHHHHHHHHH--hcCCCEEEEeCC
Confidence            3469999999999999999999998854  558999999999998  568999999998

>1dc7_A NTRC, nitrogen regulation protein; receiver domain, phosphorylation, signal transduction, conformational rearrangement; NMR {Salmonella typhimurium} SCOP: c.23.1.1 PDB: 1j56_A 1krw_A 1krx_A 1ntr_A 1dc8_A*

Probab=97.78  E-value=9.5e-06  Score=64.56  Aligned_cols=53  Identities=23%  Similarity=0.300  Sum_probs=49.8

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .+||||||++..+..+..+|+..||.+..+.++.+++..+.  ...||+||+|+.
T Consensus         4 ~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~--~~~~dlvi~d~~   56 (124)
T 1dc7_A            4 GIVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAALA--SKTPDVLLSDIR   56 (124)
T ss_dssp             CCCEEECSSSSHHHHHHHHHTTTTCCCEECCCTTHHHHHSS--SCCCSCEEECSC
T ss_pred             cEEEEEeCCHHHHHHHHHHHHhCCcEEEEeCCHHHHHHHHh--cCCCCEEEEeee
Confidence            47999999999999999999999999999999999999998  678999999998

>2jk1_A HUPR, hydrogenase transcriptional regulatory protein HU; nucleotide-binding, transcription regulation; 2.10A {Rhodobacter capsulatus} PDB: 2vui_B 2vuh_B

Probab=97.77  E-value=4.4e-05  Score=62.81  Aligned_cols=52  Identities=17%  Similarity=0.355  Sum_probs=48.1

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .+||||||++..+..+..+|+.. |.|..+.++.+|+..+.  ...||+||+|+.
T Consensus         2 ~~Ilivdd~~~~~~~l~~~l~~~-~~v~~~~~~~~a~~~~~--~~~~dlvl~D~~   53 (139)
T 2jk1_A            2 PAILLVDDEPHSLAAMKLALEDD-FDVLTAQGAEAAIAILE--EEWVQVIICDQR   53 (139)
T ss_dssp             CEEEEECSSHHHHHHHHHHHTTT-SCEEEESSHHHHHHHHH--HSCEEEEEEESC
T ss_pred             CeEEEEcCCHHHHHHHHHHhhcC-ceEEEcCCHHHHHHHHh--cCCCCEEEEeCC
Confidence            37999999999999999999875 99999999999999998  568999999998

>3c3w_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 2.20A {Mycobacterium tuberculosis}

Probab=97.74  E-value=3.9e-05  Score=69.33  Aligned_cols=54  Identities=19%  Similarity=0.265  Sum_probs=48.7

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCC-CEE-EEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCS-YEV-TAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~G-yeV-~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +++||||||++.++..+..+|+..| |.+ ..+.++.+|++.+.  ...||+||+|+.
T Consensus         1 m~~ILivdd~~~~~~~l~~~L~~~~~~~vv~~~~~~~~al~~l~--~~~~dlvllD~~   56 (225)
T 3c3w_A            1 MVKVFLVDDHEVVRRGLVDLLGADPELDVVGEAGSVAEAMARVP--AARPDVAVLDVR   56 (225)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHHTCTTEEEEEEESSHHHHHHHHH--HHCCSEEEECSE
T ss_pred             CcEEEEEcCCHHHHHHHHHHHhcCCCcEEEEEECCHHHHHHHHh--hcCCCEEEEeCC
Confidence            3589999999999999999999886 884 57999999999998  567999999998

>3sy8_A ROCR; TIM barrel phosphodiesterase-A, transcription regulator; HET: EPE; 2.50A {Pseudomonas aeruginosa}

Probab=97.73  E-value=4.5e-05  Score=75.66  Aligned_cols=54  Identities=28%  Similarity=0.428  Sum_probs=49.9

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHc-CCCEEEEECCHHHHHHHHHhcC-CCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRN-CSYEVTAVANSLHAWKILEDLT-NHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~-~GyeV~~A~dg~eAle~L~~~~-~~pDLIIlDl~  127 (399)
                      +++||||||++.++..+..+|+. .||.|..+.++.+|++.+.  . ..||+||+|+.
T Consensus         3 ~~~ILivDD~~~~~~~l~~~L~~~~~~~v~~a~~g~eal~~l~--~~~~~DlvllDi~   58 (400)
T 3sy8_A            3 DLNVLVLEDEPFQRLVAVTALKKVVPGSILEAADGKEAVAILE--SCGHVDIAICDLQ   58 (400)
T ss_dssp             CEEEEEECSSHHHHHHHHHHHHHHCSEEEEEESSHHHHHHHHH--HHSCEEEEEECSS
T ss_pred             CceEEEEcCCHHHHHHHHHHHHhcCCcEEEEecCHHHHHHHHh--hCCCCCEEEEeCC
Confidence            46999999999999999999998 6889999999999999998  5 58999999999

>1w25_A Stalked-cell differentiation controlling protein; two-component system, ggdef domain, cyclic dinucleotide, cyclic-digmp; HET: C2E; 2.70A {Caulobacter vibrioides} SCOP: c.23.1.1 c.23.1.1 d.58.29.2 PDB: 2v0n_A* 2wb4_A*

Probab=97.68  E-value=4.8e-05  Score=75.81  Aligned_cols=53  Identities=21%  Similarity=0.327  Sum_probs=50.2

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .+||||||++.++..+..+|+..||.|..+.++.+|++.+.  ...|||||+|+.
T Consensus         2 ~~iLivdD~~~~~~~l~~~L~~~~~~v~~a~~~~~al~~~~--~~~~dlvllD~~   54 (459)
T 1w25_A            2 ARILVVDDIEANVRLLEAKLTAEYYEVSTAMDGPTALAMAA--RDLPDIILLDVM   54 (459)
T ss_dssp             CEEEEECSSTTHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HHCCSEEEEESC
T ss_pred             CeEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHh--cCCCCEEEEcCC
Confidence            48999999999999999999999999999999999999998  568999999998

>1ny5_A Transcriptional regulator (NTRC family); AAA+ ATPase, sigma54 activator, bacterial transcription, DIM transcription; HET: ADP; 2.40A {Aquifex aeolicus} SCOP: c.23.1.1 c.37.1.20 PDB: 1ny6_A* 3m0e_A* 1zy2_A*

Probab=97.65  E-value=5.5e-05  Score=75.41  Aligned_cols=53  Identities=25%  Similarity=0.431  Sum_probs=50.2

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ++||||||++.++..+..+|+..||.|..+.++.+|++.+.  ...||+||+|+.
T Consensus         1 m~ILIVDDd~~~~~~l~~~L~~~g~~v~~a~~~~eal~~l~--~~~~DlvllD~~   53 (387)
T 1ny5_A            1 MNVLVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLLS--EKHFNVVLLDLL   53 (387)
T ss_dssp             CEEEEECCCHHHHHHHHHHHHHHTCEEEEESSHHHHHHHHH--HSCCSEEEEESB
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHH--hCCCCEEEEeCC
Confidence            37999999999999999999999999999999999999998  678999999998

>1p2f_A Response regulator; DRRB, OMPR/PHOB, transcription; HET: MSE; 1.80A {Thermotoga maritima} SCOP: a.4.6.1 c.23.1.1 PDB: 3nns_A*

Probab=97.43  E-value=0.00014  Score=64.74  Aligned_cols=52  Identities=15%  Similarity=0.157  Sum_probs=47.2

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      |+++||||||++.++..+..+|+..| .|..+.++.+|++.+    ..||+||+|+.
T Consensus         1 Mm~~ilivdd~~~~~~~l~~~L~~~~-~v~~~~~~~~al~~~----~~~dlvllD~~   52 (220)
T 1p2f_A            1 MMWKIAVVDDDKNILKKVSEKLQQLG-RVKTFLTGEDFLNDE----EAFHVVVLDVM   52 (220)
T ss_dssp             CCEEEEEECSCHHHHHHHHHHHTTTE-EEEEESSHHHHHHCC----SCCSEEEEESB
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHhCC-CEEEECCHHHHHHhc----CCCCEEEEeCC
Confidence            35699999999999999999999988 899999999998876    37999999998

>2hqr_A Putative transcriptional regulator; phosporylation-independent response regulator, H. pylori, SY dimer, signaling protein; NMR {Helicobacter pylori}

Probab=97.43  E-value=0.00018  Score=64.09  Aligned_cols=49  Identities=14%  Similarity=0.238  Sum_probs=46.3

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEE
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVL  123 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLII  123 (399)
                      ++||||||++.++..+..+|+..||.|..+.++.+|+..+.  ...||+||
T Consensus         1 m~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~--~~~~dlvi   49 (223)
T 2hqr_A            1 MRVLLIEKNSVLGGEIEKGLNVKGFMADVTESLEDGEYLMD--IRNYDLVM   49 (223)
T ss_dssp             CCEEEECSCHHHHHHHHHHHGGGTCCEEEESSHHHHHHHHT--TSCCSEEE
T ss_pred             CEEEEEcCCHHHHHHHHHHHHHCCcEEEEECCHHHHHHHHh--cCCCCEEE
Confidence            37999999999999999999999999999999999999998  67899999

>3bre_A Probable two-component response regulator; protein-nucleotide complex, signaling protein; HET: C2E; 2.40A {Pseudomonas aeruginosa} PDB: 3i5a_A*

Probab=97.40  E-value=8.3e-05  Score=71.27  Aligned_cols=54  Identities=15%  Similarity=0.218  Sum_probs=49.1

Q ss_pred             CcEEEEEeCChhhHHHHHHHHH-cCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLR-NCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe-~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ..+||||||++.++..+..+|. ..||.|..+.++.+|++.+.  ...||+||+|+.
T Consensus        18 ~~~ilivdD~~~~~~~l~~~l~~~~~~~v~~~~~~~~al~~~~--~~~~dlvl~D~~   72 (358)
T 3bre_A           18 AVMVLLVDDQAMIGEAVRRSLASEAGIDFHFCSDPQQAVAVAN--QIKPTVILQDLV   72 (358)
T ss_dssp             CEEEEEECSCTTHHHHHHTTSSSCTTEEEEEECCHHHHHHHHH--HHCCSEEEEESB
T ss_pred             CceEEEEECCHHHHHHHHHHHHhccCcEEEEeCCHHHHHHHHH--hCCCCEEEEeCC
Confidence            3579999999999999999997 46999999999999999998  568999999998

>1a2o_A CHEB methylesterase; bacterial chemotaxis, adaptation, serine hydrolase; 2.40A {Salmonella typhimurium} SCOP: c.23.1.1 c.40.1.1

Probab=97.39  E-value=0.00021  Score=70.53  Aligned_cols=54  Identities=17%  Similarity=0.374  Sum_probs=49.5

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcC-CCE-EEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNC-SYE-VTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~-Gye-V~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +++||||||++.++..+..+|+.. ||+ +..+.++.+|++.+.  ...||+||+|+.
T Consensus         3 ~~rVLIVDD~~~~r~~L~~~L~~~~g~~vv~~a~~~~eAl~~l~--~~~pDlVllDi~   58 (349)
T 1a2o_A            3 KIRVLSVDDSALMRQIMTEIINSHSDMEMVATAPDPLVARDLIK--KFNPDVLTLDVE   58 (349)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHHH--HHCCSEEEEECC
T ss_pred             CCEEEEEECCHHHHHHHHHHHhcCCCcEEEEEeCCHHHHHHHHh--ccCCCEEEEECC
Confidence            469999999999999999999986 898 568999999999998  568999999998

>2vyc_A Biodegradative arginine decarboxylase; pyridoxal phosphate, PLP-dependent E lyase, acid resistance; HET: LLP; 2.4A {Escherichia coli}

Probab=97.30  E-value=0.00031  Score=76.20  Aligned_cols=52  Identities=23%  Similarity=0.260  Sum_probs=49.2

Q ss_pred             EEEEEeCCh-hh-------HHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCC-CccEEEEcCC
Q 039733           74 KVLLVENDD-ST-------RHVVSALLRNCSYEVTAVANSLHAWKILEDLTN-HIDIVLTESS  127 (399)
Q Consensus        74 rVLLVEDD~-~~-------reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~-~pDLIIlDl~  127 (399)
                      +||||||+. .+       +..|...|+..||+|..+.++.+|+..+.  .. .||+||+|++
T Consensus         2 ~ILiVdDd~~~~~~~~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~~~--~~~~~d~vilDi~   62 (755)
T 2vyc_A            2 KVLIVESEFLHQDTWVGNAVERLADALSQQNVTVIKSTSFDDGFAILS--SNEAIDCLMFSYQ   62 (755)
T ss_dssp             EEEEECCTTSTTSHHHHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHT--TTCCCSEEEEECC
T ss_pred             eEEEEeCCccccccccHHHHHHHHHHHHhCCCEEEEECCHHHHHHHHh--cCCCCcEEEEeCC
Confidence            899999999 89       99999999999999999999999999998  55 4999999999

>3klo_A Transcriptional regulator VPST; REC domain, HTH domain, DNA-binding, transcription regulation; HET: C2E TAR; 2.80A {Vibrio cholerae} PDB: 3kln_A*

Probab=96.96  E-value=0.00025  Score=63.72  Aligned_cols=55  Identities=13%  Similarity=0.143  Sum_probs=44.8

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHc-CCCEEEE-ECCHHHHHHH-HHhcCCCccEEEEcCC
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRN-CSYEVTA-VANSLHAWKI-LEDLTNHIDIVLTESS  127 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~-~GyeV~~-A~dg~eAle~-L~~~~~~pDLIIlDl~  127 (399)
                      .+++||||||++.++..+..+|+. .||.+.. +.++.+++.. +.  ...||+||+|+.
T Consensus         6 ~~~~IlivdD~~~~~~~l~~~L~~~~~~~v~~~~~~~~~~~~~~~~--~~~~dlvllD~~   63 (225)
T 3klo_A            6 NKLNVRMLSDVCMQSRLLKEALESKLPLALEITPFSELWLEENKPE--SRSIQMLVIDYS   63 (225)
T ss_dssp             SSEEEEEESCCSHHHHHHHHHHHHHSSEEEEEECGGGHHHHTTCSG--GGGCCEEEEEGG
T ss_pred             CceEEEEEcCcHHHHHHHHHHHhhCCCceEEEEeCCcHHHHHHHhh--ccCCCEEEEeCC
Confidence            356999999999999999999994 6898754 4566666653 55  568999999998

>1qo0_D AMIR; binding protein, gene regulator, receptor; 2.25A {Pseudomonas aeruginosa} SCOP: c.23.1.3

Probab=96.92  E-value=0.00036  Score=61.03  Aligned_cols=50  Identities=18%  Similarity=0.217  Sum_probs=44.1

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .++||||||++..+..+..+|+..||.|..+.++.+|+   .   ..||+||+|+.
T Consensus        12 ~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al---~---~~~dlvl~D~~   61 (196)
T 1qo0_D           12 ELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAF---D---VPVDVVFTSIF   61 (196)
T ss_dssp             GCEEEEESCTTHHHHHHHHHHHHHTCEEEEECSCCSSC---S---SCCSEEEEECC
T ss_pred             CCeEEEEcCChhHHHHHHHHHHHcCCeEEEecCchhhC---C---CCCCEEEEeCC
Confidence            45899999999999999999999999999888877655   2   47999999998

>3luf_A Two-component system response regulator/ggdef domain protein; structural genomics, ASA_2441, PSI-2, protein structure initiative; HET: MSE; 1.76A {Aeromonas salmonicida} PDB: 3mf4_A*

Probab=96.81  E-value=0.00027  Score=65.95  Aligned_cols=52  Identities=17%  Similarity=0.319  Sum_probs=42.4

Q ss_pred             cEEEEEeCChhhHHHHHHHHHc-CCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRN-CSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~-~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .+||||||++.++..+..+|.. .||.+..+ ++.+++..+.  ...||+||+|+.
T Consensus         5 ~~ILiVdD~~~~~~~l~~~L~~~~~~~v~~~-~~~~~~~~~~--~~~~dlvllD~~   57 (259)
T 3luf_A            5 QKILIVEDSMTIRRMLIQAIAQQTGLEIDAF-DTLEGARHCQ--GDEYVVALVDLT   57 (259)
T ss_dssp             CEEEEECCCHHHHHHHHHHHHHHHCCEEEEE-SSTGGGTTCC--TTTEEEEEEESC
T ss_pred             CeEEEEECCHHHHHHHHHHHHhcCCeEEEEe-ChHHHHHHhh--cCCCcEEEEeCC
Confidence            5899999999999999999976 47887654 5556666555  568999999999

>2ayx_A Sensor kinase protein RCSC; two independent structural domains, transferase; NMR {Escherichia coli} SCOP: c.23.1.1 c.23.1.6 PDB: 2ayz_A 2ayy_A

Probab=94.47  E-value=0.035  Score=51.16  Aligned_cols=47  Identities=17%  Similarity=0.217  Sum_probs=41.2

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ..+||||||++.++..+..+|+.+|++|..+.+       ..  ...+|+||+|+.
T Consensus        11 ~~~vlvv~d~~~~~~~l~~~L~~~g~~v~~~~~-------~~--~~~~~~ii~d~~   57 (254)
T 2ayx_A           11 GKRCWLAVRNASLCQFLETSLQRSGIVVTTYEG-------QE--PTPEDVLITDEV   57 (254)
T ss_dssp             TEEEEEECCCHHHHHHHHHHHTTTTEEEEECSS-------CC--CCTTCEEEEESS
T ss_pred             CCEEEEEcCCHHHHHHHHHHHHHCCCEEEEecC-------CC--CCcCcEEEEcCC
Confidence            459999999999999999999999999988764       12  467999999998

>3rht_A (gatase1)-like protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, unknown function; HET: MSE; 1.83A {Planctomyces limnophilus}

Probab=80.51  E-value=0.82  Score=43.55  Aligned_cols=50  Identities=14%  Similarity=0.309  Sum_probs=36.7

Q ss_pred             CcEEEEEeCC--hhhHHHHHHHHHcCCCEEEEECCHHH--HHHHHHhcCCCccEEEEc
Q 039733           72 SLKVLLVEND--DSTRHVVSALLRNCSYEVTAVANSLH--AWKILEDLTNHIDIVLTE  125 (399)
Q Consensus        72 ~~rVLLVEDD--~~~reiL~~lLe~~GyeV~~A~dg~e--Ale~L~~~~~~pDLIIlD  125 (399)
                      |.+||||+++  +.....|..+|+..||+|.......-  -.+.|.    .||+||++
T Consensus         4 m~~vLiV~g~~~~~~a~~l~~aL~~~g~~V~~i~~~~~~~~~~~L~----~yDvIIl~   57 (259)
T 3rht_A            4 MTRVLYCGDTSLETAAGYLAGLMTSWQWEFDYIPSHVGLDVGELLA----KQDLVILS   57 (259)
T ss_dssp             --CEEEEESSCTTTTHHHHHHHHHHTTCCCEEECTTSCBCSSHHHH----TCSEEEEE
T ss_pred             CceEEEECCCCchhHHHHHHHHHHhCCceEEEecccccccChhHHh----cCCEEEEc
Confidence            4589999988  66788899999999999887654321  123444    79999886

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	399
d2b4aa1	118	c.23.1.1 (A:2-119) Hypothetical protein BH3024 {Ba	1e-05
d1dcfa_	134	c.23.1.2 (A:) Receiver domain of the ethylene rece	3e-05
d1zgza1	120	c.23.1.1 (A:2-121) TorCAD operon transcriptional r	3e-05
d2r25b1	128	c.23.1.1 (B:1087-1214) Response regulator Sin1 {Ba	4e-05
d2pl1a1	119	c.23.1.1 (A:1-119) PhoP receiver domain {Escherich	6e-05
d1qo0d_	189	c.23.1.3 (D:) Positive regulator of the amidase op	7e-05
d1peya_	119	c.23.1.1 (A:) Sporulation response regulator Spo0F	8e-05
d1mb3a_	123	c.23.1.1 (A:) Cell division response regulator Div	1e-04
d1xhfa1	121	c.23.1.1 (A:2-122) Aerobic respiration control pro	1e-04
d1dbwa_	123	c.23.1.1 (A:) Transcriptional regulatory protein F	1e-04
d2a9pa1	117	c.23.1.1 (A:2-118) DNA-binding response regulator	1e-04
d1s8na_	190	c.23.1.1 (A:) Probable two-component system transc	2e-04
d1ys7a2	121	c.23.1.1 (A:7-127) Transcriptional regulatory prot	3e-04
d1dz3a_	123	c.23.1.1 (A:) Sporulation response regulator Spo0A	3e-04
d1k68a_	140	c.23.1.1 (A:) Response regulator for cyanobacteria	3e-04
d1zesa1	121	c.23.1.1 (A:3-123) PhoB receiver domain {Escherich	3e-04
d1a2oa1	140	c.23.1.1 (A:1-140) Methylesterase CheB, N-terminal	5e-04
d1ny5a1	137	c.23.1.1 (A:1-137) Transcriptional activator sigm5	6e-04
d1krwa_	123	c.23.1.1 (A:) NTRC receiver domain {Salmonella typ	6e-04
d1p6qa_	129	c.23.1.1 (A:) CheY protein {Sinorhizobium meliloti	7e-04
d1i3ca_	144	c.23.1.1 (A:) Response regulator for cyanobacteria	0.001
d1u0sy_	118	c.23.1.1 (Y:) CheY protein {Thermotoga maritima [T	0.001
d1kgsa2	122	c.23.1.1 (A:2-123) PhoB receiver domain {Thermotog	0.001
d1mvoa_	121	c.23.1.1 (A:) PhoP receiver domain {Bacillus subti	0.001
d1qkka_	140	c.23.1.1 (A:) Transcriptional regulatory protein D	0.001
d1jbea_	128	c.23.1.1 (A:) CheY protein {Escherichia coli [TaxI	0.001
d1w25a2	153	c.23.1.1 (A:141-293) Response regulator PleD, rece	0.002
d1yioa2	128	c.23.1.1 (A:3-130) Response regulatory protein Sty	0.003
d2ayxa1	133	c.23.1.1 (A:817-949) Sensor kinase protein RcsC, C	0.004

>d2b4aa1 c.23.1.1 (A:2-119) Hypothetical protein BH3024 {Bacillus halodurans [TaxId: 86665]} Length = 118

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Hypothetical protein BH3024
species: Bacillus halodurans [TaxId: 86665]

 Score = 41.8 bits (98), Expect = 1e-05
 Identities = 10/60 (16%), Positives = 23/60 (38%), Gaps = 1/60 (1%)

Query: 71  RSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESSGSG 130
           +  +V LVE++ S   ++   L     EVT   +    ++      +  D+++       
Sbjct: 1   QPFRVTLVEDEPSHATLIQYHLNQLGAEVTVHPSGSAFFQHRSQ-LSTCDLLIVSDQLVD 59

>d1dcfa_ c.23.1.2 (A:) Receiver domain of the ethylene receptor {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 134

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: Receiver domain of the ethylene receptor
domain: Receiver domain of the ethylene receptor
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 41.5 bits (97), Expect = 3e-05
 Identities = 14/60 (23%), Positives = 29/60 (48%), Gaps = 3/60 (5%)

Query: 71  RSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESSGSG 130
             LKVL+++ +  +R V   LL +   EVT V+++    +++    +   +V  +    G
Sbjct: 6   TGLKVLVMDENGVSRMVTKGLLVHLGCEVTTVSSNEECLRVVS---HEHKVVFMDVCMPG 62

>d1zgza1 c.23.1.1 (A:2-121) TorCAD operon transcriptional regulator TorD, N-terminal domain {Escherichia coli [TaxId: 562]} Length = 120

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: TorCAD operon transcriptional regulator TorD, N-terminal domain
species: Escherichia coli [TaxId: 562]

 Score = 40.8 bits (95), Expect = 3e-05
 Identities = 8/50 (16%), Positives = 25/50 (50%), Gaps = 2/50 (4%)

Query: 73  LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIV 122
             +++VE++  T+  + +      Y V+  A+     +I+++    +D++
Sbjct: 2   HHIVIVEDEPVTQARLQSYFTQEGYTVSVTASGAGLREIMQN--QSVDLI 49

>d2r25b1 c.23.1.1 (B:1087-1214) Response regulator Sin1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 128

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator Sin1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 40.7 bits (95), Expect = 4e-05
 Identities = 11/63 (17%), Positives = 25/63 (39%), Gaps = 4/63 (6%)

Query: 72  SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANS----LHAWKILEDLTNHIDIVLTESS 127
           S+K+L+VE++   + V+  +L     E   +A          K L     + +++  +  
Sbjct: 1   SVKILVVEDNHVNQEVIKRMLNLEGIENIELACDGQEAFDKVKELTSKGENYNMIFMDVQ 60

Query: 128 GSG 130
              
Sbjct: 61  MPK 63

>d2pl1a1 c.23.1.1 (A:1-119) PhoP receiver domain {Escherichia coli [TaxId: 562]} Length = 119

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: PhoP receiver domain
species: Escherichia coli [TaxId: 562]

 Score = 40.1 bits (93), Expect = 6e-05
 Identities = 11/49 (22%), Positives = 25/49 (51%)

Query: 73  LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDI 121
           ++VL+VE++   RH +   +++  ++V    ++  A   L +    I I
Sbjct: 1   MRVLVVEDNALLRHHLKVQIQDAGHQVDDAEDAKEADYYLNEHIPDIAI 49

>d1qo0d_ c.23.1.3 (D:) Positive regulator of the amidase operon AmiR {Pseudomonas aeruginosa [TaxId: 287]} Length = 189

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: Positive regulator of the amidase operon AmiR
domain: Positive regulator of the amidase operon AmiR
species: Pseudomonas aeruginosa [TaxId: 287]

 Score = 41.2 bits (95), Expect = 7e-05
 Identities = 8/45 (17%), Positives = 15/45 (33%)

Query: 71  RSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDL 115
           R L+VL++         +   L      V        A+ +  D+
Sbjct: 10  RELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDVPVDV 54

>d1peya_ c.23.1.1 (A:) Sporulation response regulator Spo0F {Bacillus subtilis [TaxId: 1423]} Length = 119

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Sporulation response regulator Spo0F
species: Bacillus subtilis [TaxId: 1423]

 Score = 39.5 bits (92), Expect = 8e-05
 Identities = 11/55 (20%), Positives = 25/55 (45%)

Query: 74  KVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESSG 128
           K+L+V++    R +++ +     Y+    AN L A  I+      + ++  +  G
Sbjct: 3   KILIVDDQSGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLLDMKIPG 57

>d1mb3a_ c.23.1.1 (A:) Cell division response regulator DivK {Caulobacter crescentus [TaxId: 155892]} Length = 123

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Cell division response regulator DivK
species: Caulobacter crescentus [TaxId: 155892]

 Score = 39.6 bits (92), Expect = 1e-04
 Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 2/52 (3%)

Query: 74  KVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTE 125
           KVL+VE+++    +   LL    YE       L A  I  +  N  D++L +
Sbjct: 3   KVLIVEDNELNMKLFHDLLEAQGYETLQTREGLSALSIARE--NKPDLILMD 52

>d1xhfa1 c.23.1.1 (A:2-122) Aerobic respiration control protein ArcA, N-terminal domain {Escherichia coli [TaxId: 562]} Length = 121

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Aerobic respiration control protein ArcA, N-terminal domain
species: Escherichia coli [TaxId: 562]

 Score = 39.2 bits (91), Expect = 1e-04
 Identities = 9/46 (19%), Positives = 23/46 (50%)

Query: 74  KVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHI 119
            +L+VE++  TR+ + ++     Y+V    +     +IL +   ++
Sbjct: 4   HILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQILSEYDINL 49

>d1dbwa_ c.23.1.1 (A:) Transcriptional regulatory protein FixJ, receiver domain {Rhizobium meliloti [TaxId: 382]} Length = 123

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional regulatory protein FixJ, receiver domain
species: Rhizobium meliloti [TaxId: 382]

 Score = 39.2 bits (91), Expect = 1e-04
 Identities = 7/50 (14%), Positives = 21/50 (42%)

Query: 73  LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIV 122
             V +V++++  R  ++ +L    + V    ++        D+ N + + 
Sbjct: 4   YTVHIVDDEEPVRKSLAFMLTMNGFAVKMHQSAEAFLAFAPDVRNGVLVT 53

>d2a9pa1 c.23.1.1 (A:2-118) DNA-binding response regulator MicA, N-terminal domain {Streptococcus pneumoniae [TaxId: 1313]} Length = 117

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: DNA-binding response regulator MicA, N-terminal domain
species: Streptococcus pneumoniae [TaxId: 1313]

 Score = 38.8 bits (90), Expect = 1e-04
 Identities = 11/57 (19%), Positives = 23/57 (40%), Gaps = 2/57 (3%)

Query: 74  KVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESSGSG 130
           K+L+V+++     ++   +    YEV    N   A +  E      DI++ +     
Sbjct: 2   KILIVDDEKPISDIIKFNMTKEGYEVVTAFNGREALEQFE--AEQPDIIILDLMLPE 56

>d1s8na_ c.23.1.1 (A:) Probable two-component system transcriptional regulator Rv1626 {Mycobacterium tuberculosis [TaxId: 1773]} Length = 190

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Probable two-component system transcriptional regulator Rv1626
species: Mycobacterium tuberculosis [TaxId: 1773]

 Score = 39.8 bits (92), Expect = 2e-04
 Identities = 13/51 (25%), Positives = 26/51 (50%), Gaps = 3/51 (5%)

Query: 74  KVLLVENDDSTRHVVSALLRNCSYEVTAVANS-LHAWKILEDLTNHIDIVL 123
           +VL+ E++   R  ++ +LR   YE+   A     A ++ E   +  D+V+
Sbjct: 5   RVLIAEDEALIRMDLAEMLREEGYEIVGEAGDGQEAVELAEL--HKPDLVI 53

>d1ys7a2 c.23.1.1 (A:7-127) Transcriptional regulatory protein PrrA, N-terminal domain {Mycobacterium tuberculosis [TaxId: 1773]} Length = 121

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional regulatory protein PrrA, N-terminal domain
species: Mycobacterium tuberculosis [TaxId: 1773]

 Score = 38.1 bits (88), Expect = 3e-04
 Identities = 10/48 (20%), Positives = 19/48 (39%)

Query: 72  SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHI 119
           S +VL+V++D      +   LR   +EV    +   A +   +     
Sbjct: 1   SPRVLVVDDDSDVLASLERGLRLSGFEVATAVDGAEALRSATENRPDA 48

>d1dz3a_ c.23.1.1 (A:) Sporulation response regulator Spo0A {Bacillus stearothermophilus [TaxId: 1422]} Length = 123

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Sporulation response regulator Spo0A
species: Bacillus stearothermophilus [TaxId: 1422]

 Score = 38.3 bits (89), Expect = 3e-04
 Identities = 9/55 (16%), Positives = 23/55 (41%), Gaps = 4/55 (7%)

Query: 72  SLKVLLVENDDSTRHVVSALLRNCS--YEVTAVANSLHAWKILEDLTNHIDIVLT 124
           S+KV + +++     ++   + +      +    N     ++LE+     DI+L 
Sbjct: 1   SIKVCIADDNRELVSLLDEYISSQPDMEVIGTAYNGQDCLQMLEE--KRPDILLL 53

>d1k68a_ c.23.1.1 (A:) Response regulator for cyanobacterial phytochrome {Calothrix sp. pcc 7601, RcpA [TaxId: 1188]} Length = 140

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator for cyanobacterial phytochrome
species: Calothrix sp. pcc 7601, RcpA [TaxId: 1188]

 Score = 38.5 bits (89), Expect = 3e-04
 Identities = 13/59 (22%), Positives = 26/59 (44%), Gaps = 7/59 (11%)

Query: 74  KVLLVENDDSTRHVVSALLRN--CSYEVTAVANSLHAWKILED-----LTNHIDIVLTE 125
           K+ LVE++ +   ++   L N    +EV  V + + A   L         +  D++L +
Sbjct: 4   KIFLVEDNKADIRLIQEALANSTVPHEVVTVRDGMEAMAYLRQEGEYANASRPDLILLD 62

>d1zesa1 c.23.1.1 (A:3-123) PhoB receiver domain {Escherichia coli [TaxId: 562]} Length = 121

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: PhoB receiver domain
species: Escherichia coli [TaxId: 562]

 Score = 38.0 bits (88), Expect = 3e-04
 Identities = 8/46 (17%), Positives = 20/46 (43%)

Query: 74  KVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHI 119
           ++L+VE++   R +V  +L    ++     +   A   L +    +
Sbjct: 2   RILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDL 47

>d1a2oa1 c.23.1.1 (A:1-140) Methylesterase CheB, N-terminal domain {Salmonella typhimurium [TaxId: 90371]} Length = 140

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Methylesterase CheB, N-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

 Score = 38.0 bits (88), Expect = 5e-04
 Identities = 8/54 (14%), Positives = 25/54 (46%), Gaps = 4/54 (7%)

Query: 73  LKVLLVENDDSTRHVVSALLR--NCSYEVTAVANSLHAWKILEDLTNHIDIVLT 124
           ++VL V++    R +++ ++   +    V    + L A  +++    + D++  
Sbjct: 4   IRVLSVDDSALMRQIMTEIINSHSDMEMVATAPDPLVARDLIKK--FNPDVLTL 55

>d1ny5a1 c.23.1.1 (A:1-137) Transcriptional activator sigm54 (NtrC1), N-terminal domain {Aquifex aeolicus [TaxId: 63363]} Length = 137

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional activator sigm54 (NtrC1), N-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

 Score = 37.3 bits (86), Expect = 6e-04
 Identities = 9/39 (23%), Positives = 19/39 (48%)

Query: 73  LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKI 111
           + VL++E+D   R ++   L     +V +      A+K+
Sbjct: 1   MNVLVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKL 39

>d1krwa_ c.23.1.1 (A:) NTRC receiver domain {Salmonella typhimurium [TaxId: 90371]} Length = 123

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: NTRC receiver domain
species: Salmonella typhimurium [TaxId: 90371]

 Score = 37.4 bits (86), Expect = 6e-04
 Identities = 12/52 (23%), Positives = 20/52 (38%), Gaps = 2/52 (3%)

Query: 74  KVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTE 125
            V +V++D S R V+   L       T   N       L       D++L++
Sbjct: 5   IVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAALAS--KTPDVLLSD 54

>d1p6qa_ c.23.1.1 (A:) CheY protein {Sinorhizobium meliloti, CheY2 [TaxId: 382]} Length = 129

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: CheY protein
species: Sinorhizobium meliloti, CheY2 [TaxId: 382]

 Score = 37.3 bits (86), Expect = 7e-04
 Identities = 12/50 (24%), Positives = 28/50 (56%), Gaps = 1/50 (2%)

Query: 73  LKVLLVENDDSTRHVVSALLRNCSYE-VTAVANSLHAWKILEDLTNHIDI 121
           +KVL+V++  ++R ++   L+   ++ +TA  +     KI+    +H+ I
Sbjct: 7   IKVLIVDDQVTSRLLLGDALQQLGFKQITAAGDGEQGMKIMAQNPHHLVI 56

>d1i3ca_ c.23.1.1 (A:) Response regulator for cyanobacterial phytochrome {Synechocystis sp. PCC 6803, RCP1 [TaxId: 1148]} Length = 144

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator for cyanobacterial phytochrome
species: Synechocystis sp. PCC 6803, RCP1 [TaxId: 1148]

 Score = 37.0 bits (85), Expect = 0.001
 Identities = 11/59 (18%), Positives = 27/59 (45%), Gaps = 7/59 (11%)

Query: 74  KVLLVENDDSTRHVVSALLR--NCSYEVTAVANSLHAWKILED-----LTNHIDIVLTE 125
            +LLVE+  +   +V  +L+     +E+  + + L A   L+       +   +++L +
Sbjct: 5   VILLVEDSKADSRLVQEVLKTSTIDHELIILRDGLAAMAFLQQQGEYENSPRPNLILLD 63

>d1u0sy_ c.23.1.1 (Y:) CheY protein {Thermotoga maritima [TaxId: 2336]} Length = 118

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: CheY protein
species: Thermotoga maritima [TaxId: 2336]

 Score = 36.4 bits (84), Expect = 0.001
 Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 4/59 (6%)

Query: 74  KVLLVENDDSTRHVVSALLRNCSYEVTAVA-NSLHAWKILEDLTNHI---DIVLTESSG 128
           +VL+V++    R ++  ++    YEV   A N   A +  ++L   I   DI + E +G
Sbjct: 3   RVLIVDDAAFMRMMLKDIITKAGYEVAGEATNGREAVEKYKELKPDIVTMDITMPEMNG 61

>d1kgsa2 c.23.1.1 (A:2-123) PhoB receiver domain {Thermotoga maritima [TaxId: 2336]} Length = 122

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: PhoB receiver domain
species: Thermotoga maritima [TaxId: 2336]

 Score = 36.6 bits (84), Expect = 0.001
 Identities = 7/49 (14%), Positives = 21/49 (42%)

Query: 74  KVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIV 122
           +VL+VE++     +++  L+   + V    +      +  +    + I+
Sbjct: 3   RVLVVEDERDLADLITEALKKEMFTVDVCYDGEEGMYMALNEPFDVVIL 51

>d1mvoa_ c.23.1.1 (A:) PhoP receiver domain {Bacillus subtilis [TaxId: 1423]} Length = 121

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: PhoP receiver domain
species: Bacillus subtilis [TaxId: 1423]

 Score = 36.2 bits (83), Expect = 0.001
 Identities = 10/46 (21%), Positives = 22/46 (47%)

Query: 74  KVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHI 119
           K+L+V++++S   ++   L    Y+V   ++   A K  E     +
Sbjct: 4   KILVVDDEESIVTLLQYNLERSGYDVITASDGEEALKKAETEKPDL 49

>d1qkka_ c.23.1.1 (A:) Transcriptional regulatory protein DctD, receiver domain {Sinorhizobium meliloti [TaxId: 382]} Length = 140

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional regulatory protein DctD, receiver domain
species: Sinorhizobium meliloti [TaxId: 382]

 Score = 36.6 bits (84), Expect = 0.001
 Identities = 12/55 (21%), Positives = 21/55 (38%)

Query: 74  KVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESSG 128
            V L+++D   R  +   L    + V++ A++  A   L      I I      G
Sbjct: 2   SVFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGLSADFAGIVISDIRMPG 56

>d1jbea_ c.23.1.1 (A:) CheY protein {Escherichia coli [TaxId: 562]} Length = 128

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: CheY protein
species: Escherichia coli [TaxId: 562]

 Score = 36.5 bits (84), Expect = 0.001
 Identities = 13/62 (20%), Positives = 25/62 (40%), Gaps = 4/62 (6%)

Query: 71  RSLKVLLVENDDSTRHVVSALLRNCSYE-VTAVANSLHAWKILEDLTNHI---DIVLTES 126
           + LK L+V++  + R +V  LL+   +  V    + + A   L+         D  +   
Sbjct: 3   KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNM 62

Query: 127 SG 128
            G
Sbjct: 63  DG 64

>d1w25a2 c.23.1.1 (A:141-293) Response regulator PleD, receiver domain {Caulobacter crescentus [TaxId: 155892]} Length = 153

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator PleD, receiver domain
species: Caulobacter crescentus [TaxId: 155892]

 Score = 35.8 bits (82), Expect = 0.002
 Identities = 12/58 (20%), Positives = 22/58 (37%), Gaps = 4/58 (6%)

Query: 68  LPTRSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTE 125
           L     +VL+V++++     V+A L      V          KI       +D+V+  
Sbjct: 9   LDGLGGRVLIVDDNERQAQRVAAELGVEHRPVIESDPE--KAKISAG--GPVDLVIVN 62

>d1yioa2 c.23.1.1 (A:3-130) Response regulatory protein StyR, N-terminal domain {Pseudomonas fluorescens [TaxId: 294]} Length = 128

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulatory protein StyR, N-terminal domain
species: Pseudomonas fluorescens [TaxId: 294]

 Score = 35.0 bits (80), Expect = 0.003
 Identities = 11/55 (20%), Positives = 22/55 (40%)

Query: 74  KVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESSG 128
            V +V++D S R  +  LLR+  +EV     +    +      +   ++     G
Sbjct: 4   TVFVVDDDMSVREGLRNLLRSAGFEVETFDCASTFLEHRRPEQHGCLVLDMRMPG 58

>d2ayxa1 c.23.1.1 (A:817-949) Sensor kinase protein RcsC, C-terminal domain {Escherichia coli [TaxId: 562]} Length = 133

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Sensor kinase protein RcsC, C-terminal domain
species: Escherichia coli [TaxId: 562]

 Score = 35.1 bits (80), Expect = 0.004
 Identities = 8/52 (15%), Positives = 22/52 (42%)

Query: 73  LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLT 124
           + +L+V++    R +++  L +  Y+     + + A  +L      I +   
Sbjct: 9   MMILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVLSKNHIDIVLSDV 60

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	399
d1mvoa_	121	PhoP receiver domain {Bacillus subtilis [TaxId: 14	98.82
d2pl1a1	119	PhoP receiver domain {Escherichia coli [TaxId: 562	98.75
d1ys7a2	121	Transcriptional regulatory protein PrrA, N-termina	98.74
d1kgsa2	122	PhoB receiver domain {Thermotoga maritima [TaxId:	98.73
d2a9pa1	117	DNA-binding response regulator MicA, N-terminal do	98.7
d1xhfa1	121	Aerobic respiration control protein ArcA, N-termin	98.69
d1krwa_	123	NTRC receiver domain {Salmonella typhimurium [TaxI	98.69
d1mb3a_	123	Cell division response regulator DivK {Caulobacter	98.68
d1dbwa_	123	Transcriptional regulatory protein FixJ, receiver	98.66
d1zesa1	121	PhoB receiver domain {Escherichia coli [TaxId: 562	98.66
d1yioa2	128	Response regulatory protein StyR, N-terminal domai	98.66
d1zgza1	120	TorCAD operon transcriptional regulator TorD, N-te	98.65
d1peya_	119	Sporulation response regulator Spo0F {Bacillus sub	98.65
d1zh2a1	119	Transcriptional regulatory protein KdpE, N-termina	98.64
d1ny5a1	137	Transcriptional activator sigm54 (NtrC1), N-termin	98.64
d1w25a1	139	Response regulator PleD, receiver domain {Caulobac	98.63
d2ayxa1	133	Sensor kinase protein RcsC, C-terminal domain {Esc	98.59
d1a2oa1	140	Methylesterase CheB, N-terminal domain {Salmonella	98.59
d1u0sy_	118	CheY protein {Thermotoga maritima [TaxId: 2336]}	98.56
d1s8na_	190	Probable two-component system transcriptional regu	98.55
d2b4aa1	118	Hypothetical protein BH3024 {Bacillus halodurans [	98.55
d1dcfa_	134	Receiver domain of the ethylene receptor {Thale cr	98.55
d1p6qa_	129	CheY protein {Sinorhizobium meliloti, CheY2 [TaxId	98.54
d1qkka_	140	Transcriptional regulatory protein DctD, receiver	98.53
d2r25b1	128	Response regulator Sin1 {Baker's yeast (Saccharomy	98.47
d1jbea_	128	CheY protein {Escherichia coli [TaxId: 562]}	98.42
d1dz3a_	123	Sporulation response regulator Spo0A {Bacillus ste	98.39
d1p2fa2	120	Response regulator DrrB {Thermotoga maritima [TaxI	98.3
d1a04a2	138	Nitrate/nitrite response regulator (NarL), receive	98.29
d1k66a_	149	Response regulator for cyanobacterial phytochrome	98.28
d1i3ca_	144	Response regulator for cyanobacterial phytochrome	98.23
d1k68a_	140	Response regulator for cyanobacterial phytochrome	98.21
d1w25a2	153	Response regulator PleD, receiver domain {Caulobac	98.02
d1qo0d_	189	Positive regulator of the amidase operon AmiR {Pse	97.79

>d1mvoa_ c.23.1.1 (A:) PhoP receiver domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: PhoP receiver domain
species: Bacillus subtilis [TaxId: 1423]

Probab=98.82  E-value=2.7e-09  Score=87.91  Aligned_cols=54  Identities=22%  Similarity=0.378  Sum_probs=51.6

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ..|||||||++.++..+..+|+..||+|..|.++.+|++.+.  ...||+||+|+.
T Consensus         2 ~krILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~l~--~~~~dlillD~~   55 (121)
T d1mvoa_           2 NKKILVVDDEESIVTLLQYNLERSGYDVITASDGEEALKKAE--TEKPDLIVLDVM   55 (121)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HHCCSEEEEESS
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh--cccccEEEeccc
Confidence            358999999999999999999999999999999999999999  678999999999

>d2pl1a1 c.23.1.1 (A:1-119) PhoP receiver domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: PhoP receiver domain
species: Escherichia coli [TaxId: 562]

Probab=98.75  E-value=7.8e-09  Score=85.18  Aligned_cols=53  Identities=21%  Similarity=0.325  Sum_probs=51.2

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +|||||||++.++..+..+|+.+||+|..+.++.+|++++.  ...||+||+|+.
T Consensus         1 mrILvVDDd~~~~~~l~~~L~~~G~~v~~a~~g~eal~~l~--~~~~dliilD~~   53 (119)
T d2pl1a1           1 MRVLVVEDNALLRHHLKVQIQDAGHQVDDAEDAKEADYYLN--EHIPDIAIVDLG   53 (119)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HSCCSEEEECSC
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHH--hcccceeehhcc
Confidence            48999999999999999999999999999999999999999  688999999999

>d1ys7a2 c.23.1.1 (A:7-127) Transcriptional regulatory protein PrrA, N-terminal domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional regulatory protein PrrA, N-terminal domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=98.74  E-value=8.4e-09  Score=85.31  Aligned_cols=53  Identities=21%  Similarity=0.318  Sum_probs=51.1

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +|||||||++.++..+..+|+..||+|..|.++.+|++.+.  ...||+||+|+.
T Consensus         2 PkILiVDD~~~~~~~l~~~L~~~g~~v~~a~~~~eal~~~~--~~~~dlvl~D~~   54 (121)
T d1ys7a2           2 PRVLVVDDDSDVLASLERGLRLSGFEVATAVDGAEALRSAT--ENRPDAIVLDIN   54 (121)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HSCCSEEEEESS
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHH--hCCCCEEEEEee
Confidence            48999999999999999999999999999999999999999  688999999998

>d1kgsa2 c.23.1.1 (A:2-123) PhoB receiver domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: PhoB receiver domain
species: Thermotoga maritima [TaxId: 2336]

Probab=98.73  E-value=8.8e-09  Score=84.97  Aligned_cols=53  Identities=15%  Similarity=0.307  Sum_probs=51.3

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +|||||||++.++..++.+|+.+||+|..+.++.+|++.+.  ...||+||+|+.
T Consensus         2 irILiVdDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~l~--~~~~dlillD~~   54 (122)
T d1kgsa2           2 VRVLVVEDERDLADLITEALKKEMFTVDVCYDGEEGMYMAL--NEPFDVVILDIM   54 (122)
T ss_dssp             CEEEEECSSHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HSCCSEEEEESC
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHCCCEEEEEcchHHHHHHHH--hhCccccccccc
Confidence            58999999999999999999999999999999999999999  689999999999

>d2a9pa1 c.23.1.1 (A:2-118) DNA-binding response regulator MicA, N-terminal domain {Streptococcus pneumoniae [TaxId: 1313]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: DNA-binding response regulator MicA, N-terminal domain
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=98.70  E-value=1.1e-08  Score=83.81  Aligned_cols=52  Identities=21%  Similarity=0.394  Sum_probs=50.5

Q ss_pred             EEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           74 KVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        74 rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      |||||||++.++..+..+|+..||+|..+.++.+|++.+.  ...||+||+|+.
T Consensus         2 rILiVdDd~~~~~~l~~~L~~~g~~v~~a~~~~eal~~~~--~~~~dlillD~~   53 (117)
T d2a9pa1           2 KILIVDDEKPISDIIKFNMTKEGYEVVTAFNGREALEQFE--AEQPDIIILDLM   53 (117)
T ss_dssp             EEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HHCCSEEEECSS
T ss_pred             EEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHH--hcCCCEEEeccc
Confidence            8999999999999999999999999999999999999999  679999999998

>d1xhfa1 c.23.1.1 (A:2-122) Aerobic respiration control protein ArcA, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Aerobic respiration control protein ArcA, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=98.69  E-value=1.6e-08  Score=83.44  Aligned_cols=53  Identities=21%  Similarity=0.419  Sum_probs=51.2

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ++||||||++.++..+..+|+.+||+|..+.++.+|++.+.  ...||+||+|+.
T Consensus         3 p~ILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~l~--~~~~dlii~D~~   55 (121)
T d1xhfa1           3 PHILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQILS--EYDINLVIMDIN   55 (121)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHH--HSCCSEEEECSS
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCEEEEECChHHHHHHHH--hcCCCEEEeecc
Confidence            48999999999999999999999999999999999999999  689999999999

>d1krwa_ c.23.1.1 (A:) NTRC receiver domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: NTRC receiver domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=98.69  E-value=1.5e-08  Score=83.73  Aligned_cols=53  Identities=23%  Similarity=0.300  Sum_probs=51.2

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .+||||||++.++..+..+|+..||+|..+.++.+|++.+.  ...||+||+|+.
T Consensus         4 ~~ILIVDDd~~~~~~l~~~L~~~g~~v~~a~~~~~a~~~l~--~~~~dlii~D~~   56 (123)
T d1krwa_           4 GIVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAALA--SKTPDVLLSDIR   56 (123)
T ss_dssp             CEEEEESSSHHHHHHHHHHHHHTTCEEEEESSSHHHHHHHT--TCCCSEEEECCS
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHH--hCCCCEEEehhh
Confidence            47999999999999999999999999999999999999999  789999999998

>d1mb3a_ c.23.1.1 (A:) Cell division response regulator DivK {Caulobacter crescentus [TaxId: 155892]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Cell division response regulator DivK
species: Caulobacter crescentus [TaxId: 155892]

Probab=98.68  E-value=1.2e-08  Score=83.90  Aligned_cols=53  Identities=28%  Similarity=0.419  Sum_probs=50.8

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .|||||||++.++..+..+|+.+||+|..+.++.+|++++.  ...||+||+|+.
T Consensus         2 krILiVDD~~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~~--~~~~dlil~D~~   54 (123)
T d1mb3a_           2 KKVLIVEDNELNMKLFHDLLEAQGYETLQTREGLSALSIAR--ENKPDLILMDIQ   54 (123)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHHHH--HHCCSEEEEESB
T ss_pred             ceEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHH--hCCCCEEEEEec
Confidence            48999999999999999999999999999999999999999  578999999998

>d1dbwa_ c.23.1.1 (A:) Transcriptional regulatory protein FixJ, receiver domain {Rhizobium meliloti [TaxId: 382]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional regulatory protein FixJ, receiver domain
species: Rhizobium meliloti [TaxId: 382]

Probab=98.66  E-value=2.2e-08  Score=82.84  Aligned_cols=54  Identities=11%  Similarity=0.201  Sum_probs=51.7

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ..+||||||++.+|..+..+|+..||+|..+.++.+|++++.  ...||+||+|+.
T Consensus         3 ~~~ILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~~--~~~~dlvi~D~~   56 (123)
T d1dbwa_           3 DYTVHIVDDEEPVRKSLAFMLTMNGFAVKMHQSAEAFLAFAP--DVRNGVLVTDLR   56 (123)
T ss_dssp             CCEEEEEESSHHHHHHHHHHHHHTTCEEEEESCHHHHHHHGG--GCCSEEEEEECC
T ss_pred             CCEEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh--hcCCcEEEEecc
Confidence            469999999999999999999999999999999999999998  688999999999

>d1zesa1 c.23.1.1 (A:3-123) PhoB receiver domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: PhoB receiver domain
species: Escherichia coli [TaxId: 562]

Probab=98.66  E-value=1.7e-08  Score=83.13  Aligned_cols=52  Identities=19%  Similarity=0.310  Sum_probs=50.7

Q ss_pred             EEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           74 KVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        74 rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      |||||||++.++..+..+|+..||+|..+.++.+|++++.  ...||+||+|+.
T Consensus         2 kILiVDD~~~~~~~l~~~L~~~g~~v~~a~~~~~al~~l~--~~~~dlil~D~~   53 (121)
T d1zesa1           2 RILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLN--EPWPDLILLDWM   53 (121)
T ss_dssp             EEEEECSCHHHHHHHHHHHHHTTCEEEEECSHHHHHHHSS--SSCCSEEEECSS
T ss_pred             EEEEEeCCHHHHHHHHHHHHHCCCEEEEECChHHHHHHHH--ccCCCEEEeecC
Confidence            8999999999999999999999999999999999999998  789999999999

>d1yioa2 c.23.1.1 (A:3-130) Response regulatory protein StyR, N-terminal domain {Pseudomonas fluorescens [TaxId: 294]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulatory protein StyR, N-terminal domain
species: Pseudomonas fluorescens [TaxId: 294]

Probab=98.66  E-value=1.7e-08  Score=83.71  Aligned_cols=53  Identities=19%  Similarity=0.258  Sum_probs=51.2

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ++||||||++.++..+..+|+..||+|..+.++.+|++++.  ...||+||+|+.
T Consensus         3 P~ILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~~--~~~~dliilD~~   55 (128)
T d1yioa2           3 PTVFVVDDDMSVREGLRNLLRSAGFEVETFDCASTFLEHRR--PEQHGCLVLDMR   55 (128)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHCC--TTSCEEEEEESC
T ss_pred             CEEEEEECCHHHHHHHHHHHHHcCCCccccccHHHHHHHHH--hcCCCEeehhhh
Confidence            48999999999999999999999999999999999999998  789999999999

>d1zgza1 c.23.1.1 (A:2-121) TorCAD operon transcriptional regulator TorD, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: TorCAD operon transcriptional regulator TorD, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=98.65  E-value=2.3e-08  Score=81.85  Aligned_cols=53  Identities=17%  Similarity=0.383  Sum_probs=51.1

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .|||||||++.++..+..+|+..||+|..+.++.+|++.+.  ...||+||+|+.
T Consensus         2 ~rILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~~a~~~~~--~~~~dliilD~~   54 (120)
T d1zgza1           2 HHIVIVEDEPVTQARLQSYFTQEGYTVSVTASGAGLREIMQ--NQSVDLILLDIN   54 (120)
T ss_dssp             CEEEEECSSHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HSCCSEEEEESC
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHH--hcCCCEEeeehh
Confidence            48999999999999999999999999999999999999999  689999999999

>d1peya_ c.23.1.1 (A:) Sporulation response regulator Spo0F {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Sporulation response regulator Spo0F
species: Bacillus subtilis [TaxId: 1423]

Probab=98.65  E-value=1.8e-08  Score=82.99  Aligned_cols=53  Identities=25%  Similarity=0.441  Sum_probs=50.9

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .|||||||++.++..+..+|+..||+|..+.++.+|++.+.  ...||+||+|+.
T Consensus         2 krILvVDD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~~~--~~~~dlillD~~   54 (119)
T d1peya_           2 EKILIVDDQSGIRILLNEVFNKEGYQTFQAANGLQALDIVT--KERPDLVLLDMK   54 (119)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HHCCSEEEEESC
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHcCCEEEEeCCHHHHHHHHH--hCCCCEEEEecc
Confidence            38999999999999999999999999999999999999999  678999999999

>d1zh2a1 c.23.1.1 (A:2-120) Transcriptional regulatory protein KdpE, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional regulatory protein KdpE, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=98.64  E-value=1.8e-08  Score=82.78  Aligned_cols=52  Identities=17%  Similarity=0.254  Sum_probs=50.4

Q ss_pred             EEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           74 KVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        74 rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +||||||++.++..+..+|+.+||+|..+.++.+|++.+.  ...||+||+|+.
T Consensus         2 nILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~eal~~l~--~~~~dliilD~~   53 (119)
T d1zh2a1           2 NVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEAA--TRKPDLIILDLG   53 (119)
T ss_dssp             EEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHH--HHCCSEEEEESE
T ss_pred             EEEEEECCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHH--hcCCCEEEeccc
Confidence            7999999999999999999999999999999999999999  678999999999

>d1ny5a1 c.23.1.1 (A:1-137) Transcriptional activator sigm54 (NtrC1), N-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional activator sigm54 (NtrC1), N-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=98.64  E-value=1.7e-08  Score=84.89  Aligned_cols=53  Identities=25%  Similarity=0.431  Sum_probs=51.0

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ++||||||++.++..+..+|+..||+|..|.++.+|++++.  .+.||+||+|+.
T Consensus         1 mkILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~eAl~~l~--~~~~dlvilD~~   53 (137)
T d1ny5a1           1 MNVLVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLLS--EKHFNVVLLDLL   53 (137)
T ss_dssp             CEEEEECCCHHHHHHHHHHHHHHTCEEEEESSHHHHHHHHH--HSCCSEEEEESB
T ss_pred             CEEEEEecCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHhh--ccccccchHHHh
Confidence            48999999999999999999999999999999999999999  679999999998

>d1w25a1 c.23.1.1 (A:2-140) Response regulator PleD, receiver domain {Caulobacter crescentus [TaxId: 155892]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator PleD, receiver domain
species: Caulobacter crescentus [TaxId: 155892]

Probab=98.63  E-value=1.9e-08  Score=84.82  Aligned_cols=53  Identities=21%  Similarity=0.327  Sum_probs=50.9

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .|||||||++.++..+..+|+..||+|..+.++.+|++.+.  .+.|||||+|+.
T Consensus         2 arILiVDD~~~~~~~l~~~L~~~g~~v~~a~~~~eal~~~~--~~~~dlil~D~~   54 (139)
T d1w25a1           2 ARILVVDDIEANVRLLEAKLTAEYYEVSTAMDGPTALAMAA--RDLPDIILLDVM   54 (139)
T ss_dssp             CEEEEECSSTTHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HHCCSEEEEESC
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCEEEEEccchhhhhhhh--cccceeeeeecc
Confidence            38999999999999999999999999999999999999999  678999999998

>d2ayxa1 c.23.1.1 (A:817-949) Sensor kinase protein RcsC, C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Sensor kinase protein RcsC, C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=98.59  E-value=2.5e-08  Score=83.52  Aligned_cols=55  Identities=25%  Similarity=0.527  Sum_probs=52.3

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ..++||||||++.++..+..+|+.+||+|..+.++.+|++++.  ...||+||+|+.
T Consensus         7 ~~~~ILiVDD~~~~~~~l~~~L~~~g~~v~~a~~g~ea~~~~~--~~~~dlillD~~   61 (133)
T d2ayxa1           7 DDMMILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVLS--KNHIDIVLSDVN   61 (133)
T ss_dssp             CCCEEEEEESSHHHHHHHHHHHHHHTSEEEEECCSHHHHHHHH--HSCCSEEEEEES
T ss_pred             CCCEEEEEECCHHHHHHHHHHHHHcCCEEEEECcHHHHHHHHh--ccCceEEEEecc
Confidence            3569999999999999999999999999999999999999999  679999999998

>d1a2oa1 c.23.1.1 (A:1-140) Methylesterase CheB, N-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Methylesterase CheB, N-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=98.59  E-value=3.2e-08  Score=83.38  Aligned_cols=54  Identities=17%  Similarity=0.334  Sum_probs=49.7

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCC--EEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSY--EVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~Gy--eV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ++|||||||++.+|..+..+|+..|+  .|..+.||.+|++.+.  ...||+||+|+.
T Consensus         3 kirVLiVDD~~~~r~~l~~~L~~~g~~~~v~~a~~g~~al~~~~--~~~pDlvllDi~   58 (140)
T d1a2oa1           3 KIRVLSVDDSALMRQIMTEIINSHSDMEMVATAPDPLVARDLIK--KFNPDVLTLDVE   58 (140)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHHH--HHCCSEEEEECC
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHhCCCeEEEEEECCHHHHHHHHH--hcCCCEEEEcCC
Confidence            46999999999999999999999884  5778999999999998  679999999999

>d1u0sy_ c.23.1.1 (Y:) CheY protein {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: CheY protein
species: Thermotoga maritima [TaxId: 2336]

Probab=98.56  E-value=4.7e-08  Score=80.22  Aligned_cols=53  Identities=23%  Similarity=0.347  Sum_probs=49.8

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEE-EECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVT-AVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~-~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .|||||||++.++..+..+|+.+||+|. .|.++.+|++.+.  ...||+||+|+.
T Consensus         2 krILivDD~~~~~~~l~~~L~~~g~~v~~~a~~~~~al~~~~--~~~~dliilD~~   55 (118)
T d1u0sy_           2 KRVLIVDDAAFMRMMLKDIITKAGYEVAGEATNGREAVEKYK--ELKPDIVTMDIT   55 (118)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHH--HHCCSEEEEECS
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHcCCceEEEECCHHHHHHHHH--hccCCEEEEecC
Confidence            4899999999999999999999999976 6899999999999  678999999999

>d1s8na_ c.23.1.1 (A:) Probable two-component system transcriptional regulator Rv1626 {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Probable two-component system transcriptional regulator Rv1626
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=98.55  E-value=4.2e-08  Score=86.15  Aligned_cols=53  Identities=23%  Similarity=0.410  Sum_probs=50.1

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEE-EECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVT-AVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~-~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +|||||||++.+|..+..+|+..||+++ .|.++.+|++++.  ...|||||+|+.
T Consensus         4 ~kILiVDD~~~~r~~l~~~L~~~g~~vv~~a~~g~eal~~~~--~~~pDlvllDi~   57 (190)
T d1s8na_           4 RRVLIAEDEALIRMDLAEMLREEGYEIVGEAGDGQEAVELAE--LHKPDLVIMDVK   57 (190)
T ss_dssp             CEEEEECSSHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHH--HHCCSEEEEESS
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHh--cCCCCEEEEecc
Confidence            5899999999999999999999999975 7899999999999  679999999999

>d2b4aa1 c.23.1.1 (A:2-119) Hypothetical protein BH3024 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Hypothetical protein BH3024
species: Bacillus halodurans [TaxId: 86665]

Probab=98.55  E-value=4.5e-08  Score=80.66  Aligned_cols=54  Identities=19%  Similarity=0.265  Sum_probs=50.0

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +|||||||++.++..+..+|+.+||+|..+.++.+|++.+.+ ...||+||+|+.
T Consensus         3 ~rILvVdDd~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~~-~~~~dliilD~~   56 (118)
T d2b4aa1           3 FRVTLVEDEPSHATLIQYHLNQLGAEVTVHPSGSAFFQHRSQ-LSTCDLLIVSDQ   56 (118)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHTGGG-GGSCSEEEEETT
T ss_pred             CEEEEEECCHHHHHHHHHHHHhcCCCeEEECCHHHHHHHHHh-cCCCCEEEEeCC
Confidence            599999999999999999999999999999999999997752 357999999999

>d1dcfa_ c.23.1.2 (A:) Receiver domain of the ethylene receptor {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: Receiver domain of the ethylene receptor
domain: Receiver domain of the ethylene receptor
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=98.55  E-value=5.1e-08  Score=81.73  Aligned_cols=54  Identities=24%  Similarity=0.426  Sum_probs=50.4

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ..+|||||||++.++..+..+|+.+||+|..|.++.+|++.+.   ..||+||+|+.
T Consensus         6 ~g~rILvVDD~~~~~~~l~~~L~~~G~~v~~a~~g~eal~~l~---~~~dlillD~~   59 (134)
T d1dcfa_           6 TGLKVLVMDENGVSRMVTKGLLVHLGCEVTTVSSNEECLRVVS---HEHKVVFMDVC   59 (134)
T ss_dssp             TTCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHCC---TTCSEEEEECC
T ss_pred             CCCEEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHhh---cCCCeEEEEec
Confidence            3469999999999999999999999999999999999999875   57999999999

>d1p6qa_ c.23.1.1 (A:) CheY protein {Sinorhizobium meliloti, CheY2 [TaxId: 382]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: CheY protein
species: Sinorhizobium meliloti, CheY2 [TaxId: 382]

Probab=98.54  E-value=5.2e-08  Score=81.08  Aligned_cols=54  Identities=22%  Similarity=0.455  Sum_probs=50.8

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCE-EEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYE-VTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~Gye-V~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ++|||||||++.++..+..+|+..||. |..+.++.+|++++.  ...||+||+|+.
T Consensus         6 ~~kILiVDD~~~~~~~l~~~L~~~g~~~v~~a~~~~~al~~l~--~~~~dlii~D~~   60 (129)
T d1p6qa_           6 KIKVLIVDDQVTSRLLLGDALQQLGFKQITAAGDGEQGMKIMA--QNPHHLVISDFN   60 (129)
T ss_dssp             CCCEEEECSSHHHHHHHHHHHHTTTCSCEECCSSHHHHHHHHH--TSCCSEEEECSS
T ss_pred             CCEEEEEECCHHHHHHHHHHHHHCCCeEEEEECCHHHHHHHHH--hCCCCeEEeeee
Confidence            468999999999999999999999995 788999999999999  789999999999

>d1qkka_ c.23.1.1 (A:) Transcriptional regulatory protein DctD, receiver domain {Sinorhizobium meliloti [TaxId: 382]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional regulatory protein DctD, receiver domain
species: Sinorhizobium meliloti [TaxId: 382]

Probab=98.53  E-value=4.8e-08  Score=82.50  Aligned_cols=53  Identities=21%  Similarity=0.359  Sum_probs=51.0

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ++||||||++.++..+..+|+..||.|..+.++.+|++.+.  ...||+||+|+.
T Consensus         1 P~ILiVDDd~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~--~~~~dlil~D~~   53 (140)
T d1qkka_           1 PSVFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGLS--ADFAGIVISDIR   53 (140)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHTCC--TTCCSEEEEESC
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCEEEEeCChHHHHHHHh--ccCcchHHHhhc
Confidence            37999999999999999999999999999999999999998  789999999999

>d2r25b1 c.23.1.1 (B:1087-1214) Response regulator Sin1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator Sin1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.47  E-value=1.1e-07  Score=79.20  Aligned_cols=55  Identities=15%  Similarity=0.369  Sum_probs=49.7

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCCCE-EEEECCHHHHHHHHHh---cCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCSYE-VTAVANSLHAWKILED---LTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~Gye-V~~A~dg~eAle~L~~---~~~~pDLIIlDl~  127 (399)
                      +|||||||++.++..+..+|+.+||+ |..|.+|.+|++++..   ....||+||+|+.
T Consensus         2 irVLvVDD~~~~~~~l~~~L~~~g~~~v~~a~~g~eAl~~l~~~~~~~~~~dlillD~~   60 (128)
T d2r25b1           2 VKILVVEDNHVNQEVIKRMLNLEGIENIELACDGQEAFDKVKELTSKGENYNMIFMDVQ   60 (128)
T ss_dssp             SCEEEECSCHHHHHHHHHHHHHTTCCCEEEESSHHHHHHHHHHHHHHTCCCSEEEECSC
T ss_pred             eEEEEEeCCHHHHHHHHHHHHHcCCeEEEEEcChHHHHHHHHhhhhccCCCCEEEEEeC
Confidence            58999999999999999999999996 7889999999998852   1468999999999

>d1jbea_ c.23.1.1 (A:) CheY protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: CheY protein
species: Escherichia coli [TaxId: 562]

Probab=98.42  E-value=1.9e-07  Score=77.29  Aligned_cols=55  Identities=22%  Similarity=0.433  Sum_probs=51.2

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHcCCC-EEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRNCSY-EVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~~Gy-eV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +.+|||||||++..+..++.+|+.+|| .|..+.++.+|++.+.  ...||+||+|+.
T Consensus         3 k~lriLvVDD~~~~r~~i~~~L~~~g~~~v~~a~~g~~a~~~~~--~~~~dlii~D~~   58 (128)
T d1jbea_           3 KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQ--AGGYGFVISDWN   58 (128)
T ss_dssp             TTCCEEEECSCHHHHHHHHHHHHHTTCCCEEEESSHHHHHHHHT--TCCCCEEEEESC
T ss_pred             CCCEEEEEeCCHHHHHHHHHHHHHCCCcEEEEecCchHHHHHHh--cCCCCEEEEecc
Confidence            346899999999999999999999998 5889999999999998  789999999999

>d1dz3a_ c.23.1.1 (A:) Sporulation response regulator Spo0A {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Sporulation response regulator Spo0A
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=98.39  E-value=2e-07  Score=76.73  Aligned_cols=53  Identities=17%  Similarity=0.311  Sum_probs=48.2

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCC-CE-EEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCS-YE-VTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~G-ye-V~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      +|||||||++.++..+..+|+..| +. |..|.+|.+|++.+.  ...||+||+|+.
T Consensus         2 irILivDD~~~~~~~l~~~L~~~~~~~~v~~a~~g~~al~~~~--~~~~dlillD~~   56 (123)
T d1dz3a_           2 IKVCIADDNRELVSLLDEYISSQPDMEVIGTAYNGQDCLQMLE--EKRPDILLLDII   56 (123)
T ss_dssp             EEEEEECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHHH--HHCCSEEEEESC
T ss_pred             cEEEEEeCCHHHHHHHHHHHHhCCCcEEEEEECCHHHHHHHHH--hcCCCEEEEcCC
Confidence            689999999999999999999876 44 557999999999999  678999999999

>d1p2fa2 c.23.1.1 (A:1-120) Response regulator DrrB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator DrrB
species: Thermotoga maritima [TaxId: 2336]

Probab=98.30  E-value=3.4e-07  Score=75.19  Aligned_cols=52  Identities=15%  Similarity=0.201  Sum_probs=46.2

Q ss_pred             CCcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           71 RSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        71 ~~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ++.|||||||++.++..+..+|+..|| +.++.++.+|+.  .  ...||+||+|+.
T Consensus         1 mM~kILiVDDd~~~~~~l~~~L~~~g~-v~~~~~~~~al~--~--~~~~dlillD~~   52 (120)
T d1p2fa2           1 MMWKIAVVDDDKNILKKVSEKLQQLGR-VKTFLTGEDFLN--D--EEAFHVVVLDVM   52 (120)
T ss_dssp             CCEEEEEECSCHHHHHHHHHHHTTTEE-EEEESSHHHHHH--C--CSCCSEEEEESB
T ss_pred             CCCEEEEEECCHHHHHHHHHHHHhCCE-EEEECCHHHHHh--c--CCCCCEEEEeCc
Confidence            467999999999999999999999986 888999999875  2  467999999998

>d1a04a2 c.23.1.1 (A:5-142) Nitrate/nitrite response regulator (NarL), receiver domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Nitrate/nitrite response regulator (NarL), receiver domain
species: Escherichia coli [TaxId: 562]

Probab=98.29  E-value=4e-07  Score=76.11  Aligned_cols=53  Identities=19%  Similarity=0.273  Sum_probs=48.5

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCC--CEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCS--YEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~G--yeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ++||||||++.+|..++.+|+..+  +.|..+.++.+|++++.  ...||+||+|+.
T Consensus         3 i~VLiVDD~~~~r~~l~~~L~~~~~~~~v~~a~~~~~al~~~~--~~~~DlvllD~~   57 (138)
T d1a04a2           3 ATILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAE--SLDPDLILLDLN   57 (138)
T ss_dssp             EEEEEECSCHHHHHHHHHHHTTCTTEEEEEEESSHHHHHHHHH--HHCCSEEEEETT
T ss_pred             CEEEEECCCHHHHHHHHHHHHhCCCcEEEEEECCHHHHHHHHH--hcCCCEEEEecC
Confidence            599999999999999999999876  45778999999999998  678999999999

>d1k66a_ c.23.1.1 (A:) Response regulator for cyanobacterial phytochrome {Calothrix sp. pcc 7601, RcpB [TaxId: 1188]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator for cyanobacterial phytochrome
species: Calothrix sp. pcc 7601, RcpB [TaxId: 1188]

Probab=98.28  E-value=8e-07  Score=75.50  Aligned_cols=56  Identities=16%  Similarity=0.199  Sum_probs=49.6

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCC--EEEEECCHHHHHHHHHhc--------CCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSY--EVTAVANSLHAWKILEDL--------TNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~Gy--eV~~A~dg~eAle~L~~~--------~~~pDLIIlDl~  127 (399)
                      ..+||||||++..+..+..+|+..||  +|..|.+|.+|++++.+.        ...|||||+|+.
T Consensus         6 ~~~ILiVDD~~~~~~~l~~~L~~~g~~~~v~~a~~g~eAl~~l~~~~~~~~~~~~~~pdlillD~~   71 (149)
T d1k66a_           6 TQPLLVVEDSDEDFSTFQRLLQREGVVNPIYRCITGDQALDFLYQTGSYCNPDIAPRPAVILLDLN   71 (149)
T ss_dssp             TSCEEEECCCHHHHHHHHHHHHHTTBCSCEEEECSHHHHHHHHHTCCSSSCGGGCCCCSEEEECSC
T ss_pred             CCcEEEEECCHHHHHHHHHHHHHcCCceEEEEECChHHHHHHHHhhccccccccccCCCeEEcccc
Confidence            34799999999999999999999998  789999999999999731        136999999998

>d1i3ca_ c.23.1.1 (A:) Response regulator for cyanobacterial phytochrome {Synechocystis sp. PCC 6803, RCP1 [TaxId: 1148]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator for cyanobacterial phytochrome
species: Synechocystis sp. PCC 6803, RCP1 [TaxId: 1148]

Probab=98.23  E-value=1.2e-06  Score=73.87  Aligned_cols=55  Identities=20%  Similarity=0.375  Sum_probs=48.1

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCC--CEEEEECCHHHHHHHHHhc-----CCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCS--YEVTAVANSLHAWKILEDL-----TNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~G--yeV~~A~dg~eAle~L~~~-----~~~pDLIIlDl~  127 (399)
                      .+||||||++..+..++.+|+..|  |+|..+.+|.+|++++...     ...||+||+|+.
T Consensus         4 k~ILiVdD~~~~~~~l~~~L~~~g~~~~v~~a~~g~~Al~~l~~~~~~~~~~~pdlIllD~~   65 (144)
T d1i3ca_           4 KVILLVEDSKADSRLVQEVLKTSTIDHELIILRDGLAAMAFLQQQGEYENSPRPNLILLDLN   65 (144)
T ss_dssp             EEEEEECCCHHHHHHHHHHHHSCCSCEEEEEECSHHHHHHHHTTCGGGTTCCCCSEEEECSC
T ss_pred             CEEEEEECCHHHHHHHHHHHHHcCCCeEEEEECCHHHHHHHHHhchhhhccCCCCEEEEECc
Confidence            489999999999999999999876  5789999999999999721     125999999999

>d1k68a_ c.23.1.1 (A:) Response regulator for cyanobacterial phytochrome {Calothrix sp. pcc 7601, RcpA [TaxId: 1188]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator for cyanobacterial phytochrome
species: Calothrix sp. pcc 7601, RcpA [TaxId: 1188]

Probab=98.21  E-value=1.3e-06  Score=73.45  Aligned_cols=55  Identities=24%  Similarity=0.396  Sum_probs=48.5

Q ss_pred             cEEEEEeCChhhHHHHHHHHHcCC--CEEEEECCHHHHHHHHHhc-----CCCccEEEEcCC
Q 039733           73 LKVLLVENDDSTRHVVSALLRNCS--YEVTAVANSLHAWKILEDL-----TNHIDIVLTESS  127 (399)
Q Consensus        73 ~rVLLVEDD~~~reiL~~lLe~~G--yeV~~A~dg~eAle~L~~~-----~~~pDLIIlDl~  127 (399)
                      .|||||||++..+..+..+|+..|  |+|..+.+|.+|++++.+.     ...||+||+|+.
T Consensus         3 krILiVDD~~~~~~~l~~~L~~~g~~~~v~~a~~g~eAl~~l~~~~~~~~~~~pdlillD~~   64 (140)
T d1k68a_           3 KKIFLVEDNKADIRLIQEALANSTVPHEVVTVRDGMEAMAYLRQEGEYANASRPDLILLDLN   64 (140)
T ss_dssp             CEEEEECCCHHHHHHHHHHHHTCSSCCEEEEECSHHHHHHHHTTCGGGGSCCCCSEEEECSS
T ss_pred             CcEEEEECCHHHHHHHHHHHHHcCCCeEEEEECCHHHHHHHHHHhHHhhccCCCCEEEEeec
Confidence            489999999999999999999876  6899999999999999621     246899999999

>d1w25a2 c.23.1.1 (A:141-293) Response regulator PleD, receiver domain {Caulobacter crescentus [TaxId: 155892]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator PleD, receiver domain
species: Caulobacter crescentus [TaxId: 155892]

Probab=98.02  E-value=2.7e-06  Score=72.62  Aligned_cols=55  Identities=20%  Similarity=0.228  Sum_probs=47.0

Q ss_pred             CCCCcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           69 PTRSLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        69 p~~~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      ..+..|||||||++.++..+..+|+..||.|..  ++.+++.++.  ...|||||+|+.
T Consensus        10 ~~~~~rILiVDD~~~~~~~l~~~L~~~g~~v~~--~~~~~~~~~~--~~~~DlillD~~   64 (153)
T d1w25a2          10 DGLGGRVLIVDDNERQAQRVAAELGVEHRPVIE--SDPEKAKISA--GGPVDLVIVNAA   64 (153)
T ss_dssp             SSCSCEEEEECSCHHHHHHHHHHHTTTSEEEEE--CCHHHHHHHH--HSSCSEEEEETT
T ss_pred             cCCCCeEEEEeCCHHHHHHHHHHHHHCCCEEEE--ccHHHHHHHh--cCCCCEEEEECc
Confidence            335569999999999999999999999998754  4567777777  678999999999

>d1qo0d_ c.23.1.3 (D:) Positive regulator of the amidase operon AmiR {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: Positive regulator of the amidase operon AmiR
domain: Positive regulator of the amidase operon AmiR
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=97.79  E-value=3.8e-06  Score=72.44  Aligned_cols=50  Identities=18%  Similarity=0.203  Sum_probs=46.0

Q ss_pred             CcEEEEEeCChhhHHHHHHHHHcCCCEEEEECCHHHHHHHHHhcCCCccEEEEcCC
Q 039733           72 SLKVLLVENDDSTRHVVSALLRNCSYEVTAVANSLHAWKILEDLTNHIDIVLTESS  127 (399)
Q Consensus        72 ~~rVLLVEDD~~~reiL~~lLe~~GyeV~~A~dg~eAle~L~~~~~~pDLIIlDl~  127 (399)
                      .++||||||++.++..|...|+..||+|..+.++.+|+.      ..||+||+|+.
T Consensus        11 ~~~iLvvdd~~~~~~~l~~~L~~~G~~v~~~~~~~~al~------~~~Dlvl~D~~   60 (189)
T d1qo0d_          11 ELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFD------VPVDVVFTSIF   60 (189)
T ss_dssp             GCEEEEESCTTHHHHHHHHHHHHHTCEEEEECSCCSSCS------SCCSEEEEECC
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHHcCCcceecCCHHHhcc------CCCCEEEEcCC
Confidence            469999999999999999999999999999999988762      47999999998