Citrus Sinensis ID: 011208

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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-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-
Protein Sequence
MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSSMVSGNETQDESVGQQKIEATSENDAASNHSSGYMACIQSKGEFIEKGSDEQSSCTKPDFEAESAHVEDMPDLSRQLWGKSLQNDVKMQNHEARVNYGQKSLVPVTEAQGSEVAACKEANTRAHFDEDTELETHRSDVILTSEVCNVPVNSPRQVIDFMSAFNNHKPPSNNGASRFDSSPQLDLSLRRTHPDGFENQVERKFILRHSNASAFTRYTNKPSEPQHSSLSGVCNQQKEFETDSEKNFSNILTACNSYTPAATLSTQRSVNSLATGHSKQSELAVSYPQQRPCPVPVSVKVNSTNQAMHKLDHKLDSLEDLGHISPATDQSASSSFCNGAVSRLNSMGYGSACGSNSNLDQVTAGRAAAESKNEEGLFPSNGNLRSIQREAALNKFRLKRKDRCYDKKVRYESRKKLAEQRPRVKGQFVRQVHSETLPLESENHSGNISDG
Secondary Structure (PSIPRED)
ccccccHHHHHHHHHHcccHHHcccccHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHccccccccccccccccHHHcccccccccccccccccHHHHHHcccccccccHHHHHHcccccccccccccccccccHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHcccccccEEEccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccHHHHHHHHHHcHHHHEccHHcHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHcccccccccccccHHHcccccccccccccccccccccccccccEEEcEcccccccccccccccccccccccHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHcccccEEEHHHHHHHHHHccccccEEEEEEccccccccccccccccccc
Coil and Loop (DISEMBL)
MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRqssmvsgnetqdesvgqqkieatsendaasnhssgyMACIQSKGEfiekgsdeqssctkpdfeaesahvedmpdlSRQLWGKSLQNDVKMQNHEARVNYGQKSLVPVTEAQGSEVAACKeantrahfdedtelethrsdviltsevcnvpvnsprQVIDFMSAfnnhkppsnngasrfdsspqldlslrrthpdgfenQVERKFILRHsnasaftrytnkpsepqhsslsgvcnqqkefetdsekNFSNILTAcnsytpaatlstqrsvnslatghskqselavsypqqrpcpvpvsvkvnstnqamhkldhkldsledlghispatdqsasssfCNGAVSRLnsmgygsacgsnsnldqvTAGRAAaeskneeglfpsngnlRSIQREAALNKFRLkrkdrcydkKVRYESRKKLAeqrprvkgqfvrqvhsetlplesenhsgnisdg
Flexible Loop (DISEMBL)
MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRrqssmvsgnetqdesVGQQKIEATsendaasnhSSGYMACIQSKGEFIEKGSDEQSSCTKPDFEAESAHVEDMPDLSRQLWGKSLQNDVKMQNHEARVNYGQKSLVPVTEAQGSEVAACKEAntrahfdedtelethrsdviltsevcnvpvNSPRQVIDFMSAFNNHKPPSNNGASRFDSSPQLDLSLRRTHPDGFENQVERKFILRHSNASAFTRYTNKPSEPQHSSLSGVCNQQKEFETDSEKNFSNILTACNSYTPAATLSTQRSVNSLATGHSKQSELAVSYPQQRPCPVPVSVKVNSTNQAMHKLDHKLDSLEDLGHISPATDQSASSSFCNGAVSRLNSMGYGSACGSNSNLDQVTAGRAAAEskneeglfpsngnlrsIQREAALnkfrlkrkdrcydkkvryesrkklaeqrprvkgqfvrqvhsetlplesenhsgnisdg
Low Complexity Region (SEG)
MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSSMVSGNETQDESVGQQKIEATSENDAASNHSSGYMACIQSKGEFIEKGSDEQSSCTKPDFEAESAHVEDMPDLSRQLWGKSLQNDVKMQNHEARVNYGQKSLVPVTEAQGSEVAACKEANTRAHFDEDTELETHRSDVILTSEVCNVPVNSPRQVIDFMSAFNNHKPPSNNGASRFDSSPQLDLSLRRTHPDGFENQVERKFILRHSNASAFTRYTNKPSEPQHSSLSGVCNQQKEFETDSEKNFSNILTACNSYTPAATLSTQRSVNSLATGHSKQSELAVSYPQQRPCPVPVSVKVNSTNQAMHKLDHKLDSLEDLGHISPATDQSASSSFCNGAVSRLNSMGYGSACGSNSNLDQVTAGRAAAESKNEEGLFPSNGNLRSIQREAALNKFRLKRKDRCYDKKVRYESRKKLAEQRPRVKGQFVRQVHSETLPLESENHSGNISDG
Disordered region (IsUnstruct)
********TVYKCMMRGAADYLVKPVRRNELRNLWQHVWR******************************************************************************************************************************************SDVILTSEVCNVPVNSPRQVIDFM******************************************FI*******************************************NILTACNSY*************************************************************************************************************************************************CY**********************************************
Disordered Region (DISOPRED)
**********YKCMMRGAADYLVKPVRRNELRNLWQHVW***********************************************************************************************************************************************************************************************************************************************************************************************YPQQ****************************************************RLNSMGYGSACGSNSNLDQVTAGRAAAESKNEEGLFPSNGNLRSIQREAALN*FRLKRKDRCYDKKVRYESRKKLAEQRPRVKG*************************
Disordered Region (DISEMBL)
********TVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQS*****************************HSSGYMACIQSKGEFIE**********************DMPDLSRQLWGKSLQNDVKMQNHEARVNYGQKSLVPVTEAQGSEVAACKEANTRAHFDEDTELETHRSDVILTSEVCNVPVNSPRQVIDFMSAFNNHKPPSNNGASRFDSSPQLDLSLRRTHPDGFENQVERKFILRHSNASAFTRYT******************KEFETDSEKNFSNILTACNSYTPAATLS************************QRPCPVPVSVKVNSTNQAMHKLDHKLDSLEDLGHISP*********FCNGAVSRLNSMGYGSACGSNSNLDQ************EEGLFPSNGNLRSIQREAALNKFRLKRKDRCYDKKVRYESRKKLAEQRPRVKGQFVRQVHSETLP*************
Disordered Region (DISPRO)
*****SVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQS************************************************************************************************************************************************************************************QLDL*L**T***************************************************************************************************************************************************************************************************QREAALNKFRLKRKDRCYDKKVRYESRKKLAEQRPRVKGQFVRQVHS*****************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSSMVSGNETQDESVGQQKIEATSENDAASNHSSGYMACIQSKGEFIEKGSDEQSSCTKPDFEAESAHVEDMPDLSRQLWGKSLQNDVKMQNHEARVNYGQKSLVPVTEAQGSEVAACKEANTRAHFDEDTELETHRSDVILTSEVCNVPVNSPRQVIDFMSAFNNHKPPSNNGASRFDSSPQLDLSLRRTHPDGFENQVERKFILRHSNASAFTRYTNKPSEPQHSSLSGVCNQQKEFETDSEKNFSNILTACNSYTPAATLSTQRSVNSLATGHSKQSELAVSYPQQRPCPVPVSVKxxxxxxxxxxxxxxxxxxxxxGHISPATDQSASSSFCNGAVSRLNSMGYGSACGSNSNLDQVTAGRAAAESKNEEGLFPSNGNLRSIQREAALNKFRLKRKDRCYDKKVRYESRKKLAEQRPRVKGQFVRQVHSETLPLESENHSGNISDG
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	491	2.2.26 [Sep-21-2011]
Q6LA42	558	Two-component response re	no	no	0.820	0.722	0.353	4e-57
Q689G6	623	Two-component response re	yes	no	0.201	0.158	0.566	8e-22
Q8L500	468	Two-component response re	no	no	0.419	0.440	0.345	7e-20
Q9LVG4	495	Two-component response re	no	no	0.091	0.090	0.75	1e-15
Q93WK5	727	Two-component response re	no	no	0.120	0.081	0.650	7e-15
A2YQ93	742	Two-component response re	N/A	no	0.515	0.340	0.287	2e-14
Q689G9	518	Two-component response re	no	no	0.099	0.094	0.755	2e-14
Q0D3B6	742	Two-component response re	no	no	0.515	0.340	0.284	4e-14
Q10N34	767	Two-component response re	no	no	0.083	0.053	0.707	2e-13
A2XFB7	767	Two-component response re	N/A	no	0.083	0.053	0.707	2e-13

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

 Score =  222 bits (566), Expect = 4e-57,   Method: Compositional matrix adjust.
 Identities = 178/503 (35%), Positives = 244/503 (48%), Gaps = 100/503 (19%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSSMVSGNETQDESVGQQK 60
           MS+QDSV+TVYKCM++GAADYLVKP+RRNELRNLWQHVWRRQ+S+   +   +ESVGQQK
Sbjct: 131 MSTQDSVNTVYKCMLKGAADYLVKPLRRNELRNLWQHVWRRQTSLAPDSFPWNESVGQQK 190

Query: 61  IEATSENDAASNHSSGYMACIQSKGEFIEKGSDEQSSCTKPDFEAESAHVEDMPDLSRQL 120
            E  S N++        ++           G D QSSCT+P+ E ESA            
Sbjct: 191 AEGASANNSNGKRDDHVVSG---------NGGDAQSSCTRPEMEGESA------------ 229

Query: 121 WGKSLQNDVKMQNHEARVNYGQKSLVPVTEAQGSEVAACKEANTRAHFDEDTELETHRSD 180
                  DV++   +A                                    ++E  +S 
Sbjct: 230 -------DVEVSARDA-----------------------------------VQMECAKSQ 247

Query: 181 VILTSEVCNVPVNSPRQVIDFMSAFNNHKPPSNN--GASRFDSSPQLDLSLRRTHPDGFE 238
              T  + N   +   + IDFM A        N     ++++S  +LDLSLRR  P+  E
Sbjct: 248 FNETRLLANELQSKQAEAIDFMGASFRRTGRRNREESVAQYESRIELDLSLRR--PNASE 305

Query: 239 NQVE-RKFILRHSNASAFTRYTNKPSEPQHSSLSGVCNQQKEFETDSEKNFSNILTACNS 297
           NQ    +  L  S+ASAFTRY ++P + Q S+   V +Q+K      + N   ++   N+
Sbjct: 306 NQSSGDRPSLHPSSASAFTRYVHRPLQTQCSASPVVTDQRKNVAASQDDNIV-LMNQYNT 364

Query: 298 YTPAATLSTQRSVNSLATGHSKQ----SELAVSYPQQ--RPCPVPVS-VKVNSTNQAM-- 348
             P    + +R+  S  TG        S    S+P Q   P P P++ ++    N A   
Sbjct: 365 SEPPPN-APRRNDTSFYTGADSPGPPFSNQLNSWPGQSSYPTPTPINNIQFRDPNTAYTS 423

Query: 349 ------------HKLDHKLDSLEDLGHISPATDQSASSSFCNGAVSRLNSMGYGSACGSN 396
                           H+  S+    +  P   Q    S        ++S    SA G++
Sbjct: 424 AMAPASLSPSPSSVSPHEYSSMFHPFNSKPEGLQDRDCSMDVDERRYVSSATEHSAIGNH 483

Query: 397 SNLDQVTAGRAAAESKNEEGLFPSNGNLR-SIQREAALNKFRLKRKDRCYDKKVRYESRK 455
             +DQ+       E KNE+G   S G ++ S+QREAAL KFR+KRKDRCY+KKVRYESRK
Sbjct: 484 --IDQLI------EKKNEDGYSLSVGKIQQSLQREAALTKFRMKRKDRCYEKKVRYESRK 535

Query: 456 KLAEQRPRVKGQFVRQVHSETLP 478
           KLAEQRPR+KGQFVRQV S   P
Sbjct: 536 KLAEQRPRIKGQFVRQVQSTQAP 558

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 =  105 bits (262), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 64/113 (56%), Positives = 76/113 (67%), Gaps = 14/113 (12%)

Query: 363 HISPATDQSASSSFCNGAVSRLNSMGYGSACGSNSNLDQVTAGRAAAESKNEEGLFPSNG 422
           H+SP T +S SS+  + A   L+    GS C S+SN        A  ES N   + P N 
Sbjct: 518 HVSPTTGESGSSTVLDSARKTLS----GSVCDSSSN-----HMIAPTESSN---VVPENP 565

Query: 423 N-LRSI-QREAALNKFRLKRKDRCYDKKVRYESRKKLAEQRPRVKGQFVRQVH 473
           + LR + QREAALNKFRLKRKDRC++KKVRY+SRK LAEQRPRVKGQFVRQ H
Sbjct: 566 DGLRHLSQREAALNKFRLKRKDRCFEKKVRYQSRKLLAEQRPRVKGQFVRQDH 618

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 = 99.0 bits (245), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 88/255 (34%), Positives = 126/255 (49%), Gaps = 49/255 (19%)

Query: 223 PQLDLSLRRTHPDGFENQVERKF-ILRHSNASAFTRYT-NKPSEPQHSSLSGVCNQQKEF 280
           P+L LSL+R+    FENQ E K   L  S+ASAF+R+  +K +E    +L    + + + 
Sbjct: 256 PELGLSLKRSCSVSFENQDESKHQKLSLSDASAFSRFEESKSAEKAVVALEESTSGEPKT 315

Query: 281 ETDSEKNFSNILTACNSYTPAATLSTQRSVNSLATGHSKQSELAVSYPQQRPCPVPVSVK 340
            T+S +    + +   S   A T S Q ++ S +     Q   +    Q++  P+P  V+
Sbjct: 316 PTESHEKLRKVTSDQGS---ATTSSNQENIGSSSVSFRNQVLQSTVTNQKQDSPIP--VE 370

Query: 341 VNSTNQAMHKLDHKLDSLEDLGHISPATDQSASSSFCNGAVSRLNSMGYGSACGSNSNLD 400
            N    A  +++                                         GS S  +
Sbjct: 371 SNREKAASKEVE----------------------------------------AGSQST-N 389

Query: 401 QVTAGRAAAESKNEEGLFPSNGNLRSIQREAALNKFRLKRKDRCYDKKVRYESRKKLAEQ 460
           +  AG++++  K +E         RS QREAAL KFRLKRKDRC+DKKVRY+SRKKLAEQ
Sbjct: 390 EGIAGQSSSTEKPKEEESAKQRWSRS-QREAALMKFRLKRKDRCFDKKVRYQSRKKLAEQ 448

Query: 461 RPRVKGQFVRQVHSE 475
           RPRVKGQFVR V+S+
Sbjct: 449 RPRVKGQFVRTVNSD 463

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

 Score = 84.7 bits (208), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 39/52 (75%), Positives = 46/52 (88%)

Query: 420 SNGNLRSIQREAALNKFRLKRKDRCYDKKVRYESRKKLAEQRPRVKGQFVRQ 471
           S+G+ R  QREAAL KFRLKRK+RC++KKVRY SRKKLAEQRP VKGQF+R+
Sbjct: 433 SSGSDRWAQREAALMKFRLKRKERCFEKKVRYHSRKKLAEQRPHVKGQFIRK 484

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

 Score = 82.4 bits (202), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 41/63 (65%), Positives = 48/63 (76%), Gaps = 4/63 (6%)

Query: 428 QREAALNKFRLKRKDRCYDKKVRYESRKKLAEQRPRVKGQFVRQVHSETLPLESENHSGN 487
           QREAAL KFR KRK+RC+ KKVRY+SRKKLAEQRPRV+GQFVR+  + T     +N   N
Sbjct: 668 QREAALTKFRQKRKERCFRKKVRYQSRKKLAEQRPRVRGQFVRKTAAAT----DDNDIKN 723

Query: 488 ISD 490
           I D
Sbjct: 724 IED 726

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 = 80.9 bits (198), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 99/344 (28%), Positives = 135/344 (39%), Gaps = 91/344 (26%)

Query: 209 KPPSNNGASRFDSSPQLDLSLRR---THPDGFENQVERKFILRHSNASAFTRY-TNKPSE 264
           K P     +R +  P L+LSL+R   T  D    Q E++ +LR S+ SAFTRY T   S 
Sbjct: 391 KVPEGKDKNRDNIMPSLELSLKRSRSTGDDANAIQEEQRNVLRRSDLSAFTRYHTPVASN 450

Query: 265 PQHSSLSGVC----NQQKEFETDSEKNFSNILTACNSYTPAATLSTQRSVNSLATGHSKQ 320
              +   G C    N  +  +TDS  N  +     NS        +  S N+   G + +
Sbjct: 451 QGGTGFVGSCSPHDNISEAMKTDSAYNMKS-----NSDAAPIKQGSNGSSNNNDMGSTTK 505

Query: 321 SELAVSYPQQRPCPVPVSVKVNSTNQAMHKLDHKLDSLEDLGHISPATDQSASSS----- 375
           + +      +     P +VK N    A H   H        G     TD+ A+++     
Sbjct: 506 NVVTKPSTNKERVMSPSAVKANGHTSAFHPAQHWTSPANTTG--KEKTDEVANNAAKRAQ 563

Query: 376 -----------------FCNGAVSRLNSMGYGSACGSNSNLDQVTAGRAA---------- 408
                            + +  VSR N       CGS++  D    G AA          
Sbjct: 564 PGEVQSNLVQHPRPILHYVHFDVSRENGGSGAPQCGSSNVFDPPVEGHAANYGVNGSNSG 623

Query: 409 ----------------AESKNEEGLFPSNGNL----------------------RSIQRE 430
                           AE  N E    +NG +                      R  QRE
Sbjct: 624 SNNGSNGQNGSTTAVNAERPNME---IANGTINKSGPGGGNGSGSGSGNDMYLKRFTQRE 680

Query: 431 ---AALNKFRLKRKDRCYDKKVRYESRKKLAEQRPRVKGQFVRQ 471
              AA+ KFR KRK+R + KKVRY+SRK+LAEQRPRV+GQFVRQ
Sbjct: 681 HRVAAVIKFRQKRKERNFGKKVRYQSRKRLAEQRPRVRGQFVRQ 724

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|Q689G9|PRR1_ORYSJ Two-component response regulator-like PRR1 OS=Oryza sativa subsp. japonica GN=PRR1 PE=2 SV=2

 Score = 80.9 bits (198), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 37/49 (75%), Positives = 43/49 (87%)

Query: 425 RSIQREAALNKFRLKRKDRCYDKKVRYESRKKLAEQRPRVKGQFVRQVH 473
           RS +R AAL KFRLKRK+RC+DKKVRY +RKKLAE RPRV+GQFVRQ +
Sbjct: 439 RSERRAAALAKFRLKRKERCFDKKVRYVNRKKLAETRPRVRGQFVRQAN 487

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

 Score = 80.1 bits (196), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 98/344 (28%), Positives = 135/344 (39%), Gaps = 91/344 (26%)

Query: 209 KPPSNNGASRFDSSPQLDLSLRRTHPDGFEN---QVERKFILRHSNASAFTRY-TNKPSE 264
           K P     +R +  P L+LSL+R+   G      Q E++ +LR S+ SAFTRY T   S 
Sbjct: 391 KVPEGKDKNRDNIMPSLELSLKRSRSTGDGANAIQEEQRNVLRRSDLSAFTRYHTPVASN 450

Query: 265 PQHSSLSGVC----NQQKEFETDSEKNFSNILTACNSYTPAATLSTQRSVNSLATGHSKQ 320
              +   G C    N  +  +TDS  N  +     NS        +  S N+   G + +
Sbjct: 451 QGGTGFMGSCSLHDNSSEAMKTDSAYNMKS-----NSDAAPIKQGSNGSSNNNDMGSTTK 505

Query: 321 SELAVSYPQQRPCPVPVSVKVNSTNQAMHKLDHKLDSLEDLGHISPATDQSASSS----- 375
           + +      +     P +VK N    A H   H        G     TD+ A+++     
Sbjct: 506 NVVTKPSTNKERVMSPSAVKANGHTSAFHPAQHWTSPANTTG--KEKTDEVANNAAKRAQ 563

Query: 376 -----------------FCNGAVSRLNSMGYGSACGSNSNLDQVTAGRAA---------- 408
                            + +  VSR N       CGS++  D    G AA          
Sbjct: 564 PGEVQSNLVQHPRPILHYVHFDVSRENGGSGAPQCGSSNVFDPPVEGHAANYGVNGSNSG 623

Query: 409 ----------------AESKNEEGLFPSNGNL----------------------RSIQRE 430
                           AE  N E    +NG +                      R  QRE
Sbjct: 624 SNNGSNGQNGSTTAVNAERPNME---IANGTINKSGPGGGNGSGSGSGNDMYLKRFTQRE 680

Query: 431 ---AALNKFRLKRKDRCYDKKVRYESRKKLAEQRPRVKGQFVRQ 471
              AA+ KFR KRK+R + KKVRY+SRK+LAEQRPRV+GQFVRQ
Sbjct: 681 HRVAAVIKFRQKRKERNFGKKVRYQSRKRLAEQRPRVRGQFVRQ 724

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

 Score = 77.8 bits (190), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 29/41 (70%), Positives = 37/41 (90%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR 41
           MSS DS+ TV+KC+ +GA D+LVKP+R+NEL+NLWQHVWRR
Sbjct: 162 MSSNDSMGTVFKCLSKGAVDFLVKPIRKNELKNLWQHVWRR 202

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

 Score = 77.8 bits (190), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 29/41 (70%), Positives = 37/41 (90%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR 41
           MSS DS+ TV+KC+ +GA D+LVKP+R+NEL+NLWQHVWRR
Sbjct: 162 MSSNDSMGTVFKCLSKGAVDFLVKPIRKNELKNLWQHVWRR 202

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)

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	491
302143985	747	unnamed protein product [Vitis vinifera]	0.995	0.654	0.569	1e-144
157399680	698	pseudo-response regulator 5 [Castanea sa	0.985	0.693	0.522	1e-142
224132554	687	pseudo response regulator [Populus trich	0.975	0.697	0.508	1e-132
356518667	700	PREDICTED: two-component response regula	0.953	0.668	0.472	1e-115
356509155	655	PREDICTED: two-component response regula	0.934	0.700	0.460	1e-107
357464211	685	Two-component response regulator-like PR	0.953	0.683	0.434	1e-96
449497396	696	PREDICTED: two-component response regula	0.959	0.676	0.412	8e-92
224132558	477	response regulator [Populus trichocarpa]	0.784	0.807	0.467	9e-92
449456441	696	PREDICTED: two-component response regula	0.959	0.676	0.410	2e-90
359490833	688	PREDICTED: two-component response regula	0.690	0.492	0.531	3e-89

>gi|302143985|emb|CBI23090.3| unnamed protein product [Vitis vinifera]

 Score =  520 bits (1338), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 286/502 (56%), Positives = 340/502 (67%), Gaps = 13/502 (2%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSSMVSGNETQDESVGQQK 60
           MSS  S++TVYKCM+RGAAD+LVKPVRRNEL+NLWQHVWRRQSS VSGN  QDESV QQK
Sbjct: 121 MSSHGSINTVYKCMLRGAADFLVKPVRRNELKNLWQHVWRRQSSTVSGNGPQDESVAQQK 180

Query: 61  IEATSENDAASNHSSGYMACIQSKGEFIEKGSDEQSSCTKPDFEAESAHVEDMPDLSRQL 120
           +EATSEN+  SNHSS ++ACIQ   E + K SD QSSC+KPD EAESA++E M D S   
Sbjct: 181 VEATSENNPTSNHSSDHVACIQKNKEALNKVSDAQSSCSKPDLEAESAYMETMQDFSNPT 240

Query: 121 WGKSLQNDVKMQNHEARVNYGQKSLVPVTEAQGSEVAACKEANTRAHFDEDTELETHRSD 180
           W +SL +D KMQ +E     G K L+   EA G+  AAC++ NT     E  E E     
Sbjct: 241 WSRSLVSDTKMQKNEECAKLGPKFLMHNKEAGGTLEAACRDVNTMTQ-PEAVEPENDGQG 299

Query: 181 VILTSEVCN---VPVNSPRQVIDFMSAFNNHKP------PSNNGASRFDSSPQLDLSLRR 231
               SE C    +  +S R+ ID +  F+N K        SNNG  + DS PQLDLSLRR
Sbjct: 300 ANAPSEACGNNAILGSSSREAIDLIGVFDNSKKCTYGNSSSNNGTKKSDSIPQLDLSLRR 359

Query: 232 THPDGFENQV-ERKFILRHSNASAFTRYTNKPSEPQHSSLSGVCNQQKEFETDSEKNFSN 290
           +HP   ENQV + +  L HSN SAF+RY N+  +P H   +GV NQQK F  DS+K  S 
Sbjct: 360 SHPSSPENQVADERHTLNHSNGSAFSRYINRSLQPPHLPSTGVFNQQKNFGADSDKRLSQ 419

Query: 291 ILTACNSYTPAATLSTQRSVNSLATGHSKQSELAVSYPQQRPCPVPVSVKV-NSTNQAMH 349
           ++T  NS   + TLSTQRSV SLAT  S + E+A+  PQQR  P PV     NST+Q  H
Sbjct: 420 LVTGYNSDITSPTLSTQRSVISLATSPSGRVEIALCGPQQRAFPAPVPQNANNSTSQTNH 479

Query: 350 KLDHKLDSLEDLGHISPATDQSASSSFCNGAVSRLNSMGYGSACGSNSNLDQVTAGRAAA 409
           K +HKLDSLE  GH SPATDQ++SSSF NG  S LNS G GS CGSN N + V   +AAA
Sbjct: 480 KPEHKLDSLEGQGHFSPATDQNSSSSFGNGGASNLNSFGCGSICGSNGNANTVAVVQAAA 539

Query: 410 ESKNEEGLFPSNGN-LRSIQREAALNKFRLKRKDRCYDKKVRYESRKKLAEQRPRVKGQF 468
           E KNEEG+F   G+  RSIQREAAL KFRLKRKDRC++KKVRYESRKKLAEQRPRVKGQF
Sbjct: 540 EGKNEEGIFSHEGHSQRSIQREAALTKFRLKRKDRCFEKKVRYESRKKLAEQRPRVKGQF 599

Query: 469 VRQVHSETLPLESENHSGNISD 490
           VRQVH+   P E + + G+  D
Sbjct: 600 VRQVHTIPPPAEPDTYYGSSFD 621

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|157399680|gb|ABV53464.1| pseudo-response regulator 5 [Castanea sativa]

 Score =  510 bits (1313), Expect = e-142,   Method: Compositional matrix adjust.
 Identities = 294/563 (52%), Positives = 356/563 (63%), Gaps = 79/563 (14%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSSMVSGNETQDESVGQQK 60
           MS+QDSVSTVYKCM+RGAADYLVKP+RRNEL+NLWQHVWR+QSS +  N+ QDESV QQ+
Sbjct: 143 MSAQDSVSTVYKCMLRGAADYLVKPIRRNELKNLWQHVWRKQSSNLGINDPQDESVAQQQ 202

Query: 61  IEATSENDAASNHSSGYMACIQSKGEFIEKGSDEQSSCTKPDFEAESAHVEDMPDLSRQL 120
           +EATSEN+AAS  S+G MACIQ   E IEKGSDEQSSCTKP+ EAES  VE+M + S+  
Sbjct: 203 LEATSENNAASKRSNGRMACIQRNTEQIEKGSDEQSSCTKPEVEAESVRVENMQEFSQPK 262

Query: 121 WGKSLQNDVKMQNHEARVNYGQKSLVPVTEAQGSEVAACKEANTRAHFDEDTELETHRSD 180
           WGKS  +D+  QN E  +N+GQK L   +EA+GSEV  CK+ NT     +D   E+H  D
Sbjct: 263 WGKSFPSDIISQNKEEYLNFGQKFLTHGSEAEGSEVDTCKDDNTTPP-GKDIRPESHNRD 321

Query: 181 VILTSEVCN---VPVNSPRQVIDFMSAFNNHKPPSNNGASRFDSSPQLDLSLRRTHPDGF 237
            I+T+E  +   V VNS R+ ID + +F+N+   S+ G S+FDS PQLDLSLRR+H  GF
Sbjct: 322 AIITNEDFDNNYVLVNSSRKAIDLIGSFHNYPNCSSEGTSKFDSLPQLDLSLRRSHFSGF 381

Query: 238 ENQ-VERKFILRHSNASAFTRYTNKPSEPQHSSLSGVCNQQKEFETDSEKNFSNILTACN 296
            N   E +  L  SNASAFTRYTN+ S+   + ++  CN QKE+ T+SE+  SN  T+C+
Sbjct: 382 CNSYTEERRTLGTSNASAFTRYTNRASQTPQTKIANACNHQKEYGTNSEQMLSNTFTSCS 441

Query: 297 SYTPAATLSTQRSVNSL----------ATGHSKQSELAVSYP------------------ 328
           S  P  T   QRS+ SL          AT  S+Q    V  P                  
Sbjct: 442 SDNPGIT---QRSIISLAAGHSKESEVATSCSQQKVFPVPIPVKGIRVNNLYTGFGSALP 498

Query: 329 -----QQRPCPVPVSVKV----------------------------------NSTNQAMH 349
                Q    P P S  V                                  ++ NQ ++
Sbjct: 499 PMFCTQSGSSPTPSSNSVPQQEPSFQMNILYQSSLENNNFEQQCDPHGQNTNDAANQNVY 558

Query: 350 KLDHKLDSLEDLGHISPATDQSASSSFCNGAVSRLNSMGYGSACGSNSNLDQVTAGRAAA 409
           K +HKLD LED GH+S ATDQSASSSFCNG VS  NS+GYGS CGSNSN+D V    AA 
Sbjct: 559 KQEHKLDPLEDRGHLSSATDQSASSSFCNGGVSHHNSIGYGSGCGSNSNVDHVAFVGAAP 618

Query: 410 ESKNEEGLFPSNGNL-RSIQREAALNKFRLKRKDRCYDKKVRYESRKKLAEQRPRVKGQF 468
           ESKNEEG +P NG+  RS QREAAL KFRLKRK+RCY+KKVRYESRKKLAEQRPRVKGQF
Sbjct: 619 ESKNEEGFYPQNGSAHRSFQREAALAKFRLKRKERCYEKKVRYESRKKLAEQRPRVKGQF 678

Query: 469 VRQVHSETLPLESENHSGNISDG 491
           VRQVH +  P E +   GN  DG
Sbjct: 679 VRQVHIDPSPSEID---GNSYDG 698

Source: Castanea sativa

Species: Castanea sativa

Genus: Castanea

Family: Fagaceae

Order: Fagales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224132554|ref|XP_002321349.1| pseudo response regulator [Populus trichocarpa] gi|222868345|gb|EEF05476.1| pseudo response regulator [Populus trichocarpa]

 Score =  479 bits (1232), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 276/543 (50%), Positives = 334/543 (61%), Gaps = 64/543 (11%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSSMVSGNETQDESVGQQK 60
           MSSQDS+ TVYKCM+RGAADYLVKP+R+NELRNLWQHVWR+QSS+  GN   DESVGQ K
Sbjct: 147 MSSQDSIKTVYKCMLRGAADYLVKPIRKNELRNLWQHVWRKQSSLGGGNGPHDESVGQDK 206

Query: 61  IEATSENDAASNHSSGYMACIQSKGEFIEKGSDEQSSCTKPDFEAESAHVEDMPDLSRQL 120
            EATSEN+A  NHSSG MA IQ   E   K SD QSSCTKP  EAE AH+E+M +  + +
Sbjct: 207 TEATSENNADGNHSSGEMASIQRSKEQAVKRSDSQSSCTKPGLEAEGAHMENMQEFLQPV 266

Query: 121 WGKSLQNDVKMQNHEARVNYGQKSLVPVTEAQGSEVAACKEANTRAHFDEDTELETHRSD 180
           W K    D  MQ HE  VN GQK LV  +EA+GS  A C+++N +   D++    + R  
Sbjct: 267 WSKFSLTDTNMQKHEEHVNLGQKLLVRDSEAEGSATAVCEDSN-KITVDKEITPGSGRVT 325

Query: 181 VILTSEVCN---VPVNSPRQVIDFMSAFNNHKPPSNNGASRFDSSPQLDLSLRRTHPDGF 237
             +  E C+      NSPR+ IDFM A  NH    NN    F SSP LDLSLRR+HP GF
Sbjct: 326 ANIAIEGCDKIGALANSPREAIDFMGASTNHS-SFNNVEIHFCSSPHLDLSLRRSHPSGF 384

Query: 238 ENQV-ERKFILRHSNASAFTRYTNKPSEPQHSSLSGVCNQQKEFETDSEKNFSNILTACN 296
           E QV E +  LRHSNASAFT YTN+ S+  HS+L+   NQ+ EF  + +   S+ +   N
Sbjct: 385 ETQVTEERHTLRHSNASAFTWYTNRASQLPHSALANTGNQE-EFRANYDGKISSNVNGYN 443

Query: 297 SYTPAATLSTQRSVNSLATGHSKQSELAVSYPQQRPCPVPVSVKVNSTN----------- 345
           S   +   ST+RS  SLA G +K+ E+  S   ++  P+ + VK    N           
Sbjct: 444 SDALSLAPSTRRSAISLAAGQTKEYEIVTSSSGEKVFPIHIPVKDTRFNNLCNSYGAVLP 503

Query: 346 -----------QAMHKL----------------------------------DHKLDSLED 360
                      + +HK+                                  ++KLDSLE 
Sbjct: 504 PMMSQSSASQKEPIHKVNPFQCSNYGSTSVQLCDRLGQNANDSINGSLQKQENKLDSLEG 563

Query: 361 LGHISPATDQSASSSFCNGAVSRLNSMGYGSACGSNSNLDQVTAGRAAAESKNEEGLFPS 420
             HIS ATDQSASSSFCNGA S  NS+GYGSA GS SN DQ+    AA+ESKNEEG+F  
Sbjct: 564 REHISSATDQSASSSFCNGAASHFNSIGYGSASGSYSNADQIATVSAASESKNEEGVFTH 623

Query: 421 NGNL-RSIQREAALNKFRLKRKDRCYDKKVRYESRKKLAEQRPRVKGQFVRQVHSETLPL 479
           N N  RSIQREAAL KFRLKRK+RCY+KKVRYESRKKLAEQRPRVKGQFVRQVH +  P 
Sbjct: 624 NSNSHRSIQREAALTKFRLKRKERCYEKKVRYESRKKLAEQRPRVKGQFVRQVHIDPSPA 683

Query: 480 ESE 482
           E++
Sbjct: 684 ETD 686

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356518667|ref|XP_003528000.1| PREDICTED: two-component response regulator-like PRR95-like [Glycine max]

 Score =  422 bits (1086), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 268/567 (47%), Positives = 334/567 (58%), Gaps = 99/567 (17%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSSMVSGNETQDESVGQQK 60
           MSSQDS+STVYKCM+RGAADYLVKP+R+NELRNLWQHVWRRQSS    N  QDESV QQK
Sbjct: 131 MSSQDSISTVYKCMLRGAADYLVKPIRKNELRNLWQHVWRRQSSTTGINGPQDESVAQQK 190

Query: 61  IEATSENDAASNHSSGYMACIQSKGEFIEKGSDEQSSCTKPDFEAESA---HVEDMPDLS 117
           +EAT+EN+AASN SSG  ACIQ   E IEKGSD QSSCTKPD EAES    +++++ + S
Sbjct: 191 VEATAENNAASNRSSGDAACIQRNMELIEKGSDAQSSCTKPDCEAESGPVDNIDNIQEFS 250

Query: 118 RQLWGKSLQNDVKMQNHEARVNYGQKSLVPVTEAQGSEVAACK--EANTR----AHFDED 171
               G++  +  + Q  E  +  GQ  ++  + A G  V+ CK  EA+T      HF   
Sbjct: 251 PLKCGEAYPSGTETQQVETSIRLGQTLMMHASHAGGLNVSICKNGEASTTDADPEHFGNG 310

Query: 172 TELETHRSDVILTSEVCNVPVNSPRQVIDFMSAFNNH-----KPPSNNGASRFDSSPQLD 226
              E H +          V +NS ++ IDF+ AF+ H     K  + N   +FD SPQLD
Sbjct: 311 ISGEAHDNHY--------VQMNSSKEAIDFIGAFHTHPICTLKNSTVNCTGKFDLSPQLD 362

Query: 227 LSLRRTHPDGFENQV-ERKFILRHSNASAFTRYTNKP---SEPQHSSLSGVCNQQKEFET 282
           LSLRR+ P  FEN++ E +  L HSNASAF RYTN+    S P  + L    +QQ++   
Sbjct: 363 LSLRRSRPSSFENELTEERHTLMHSNASAFKRYTNRQLQISTP--AVLINFSDQQRQQIA 420

Query: 283 DSEKNFSNILTACNSYTPAATLSTQRSVNS----------LATGHSKQ------------ 320
           + EKN S I T CNS   ++T S QR + S          LAT HS+             
Sbjct: 421 NCEKNISRIATGCNS--DSSTPSMQRCIVSPTTVQSKEPELATSHSQPGHSLPIPVKGVR 478

Query: 321 -SELAVSYPQQRP-----------CPVPVSVKV--------------------------- 341
            ++L  +Y    P            P P SV +                           
Sbjct: 479 FNDLCTTYGSVFPSVFRAQSGSPAMPSPNSVMLLEPNFQVNAFYQSNMKESSSEQLYEPG 538

Query: 342 ----NST-NQAMHKLDHKLDSLEDLGHISPATDQSASSSFCNGAVSRLNSMGYGSACGSN 396
               N+T N  ++  +HK ++ ED GHISP TDQS SSSFCNG  S LNS+GYGS CGS+
Sbjct: 539 GPNGNTTQNHIVYTQEHKSENAEDQGHISPTTDQSVSSSFCNGNASHLNSIGYGSNCGSS 598

Query: 397 SNLDQVTAGRAAAESKNEEGLFPSNGNL-RSIQREAALNKFRLKRKDRCYDKKVRYESRK 455
           SN+DQV    AA+E K+++    SN N  RSIQREAALNKFRLKRK+RCY+KKVRYESRK
Sbjct: 599 SNVDQVNTVWAASEGKHKD--LTSNANSHRSIQREAALNKFRLKRKERCYEKKVRYESRK 656

Query: 456 KLAEQRPRVKGQFVRQVHSETLPLESE 482
           KLAEQRPRVKGQFVRQVH + L  E +
Sbjct: 657 KLAEQRPRVKGQFVRQVHPDPLVAEKD 683

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356509155|ref|XP_003523317.1| PREDICTED: two-component response regulator-like APRR9-like [Glycine max]

 Score =  394 bits (1012), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 256/556 (46%), Positives = 310/556 (55%), Gaps = 97/556 (17%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSSMVSGNETQDESVGQQK 60
           MSSQDS+STVYKCM+RGAADYLVKP+R+NELRNLWQHVWRRQSS    N  QDESV QQK
Sbjct: 130 MSSQDSISTVYKCMLRGAADYLVKPIRKNELRNLWQHVWRRQSSTTGINGLQDESVAQQK 189

Query: 61  IEATSENDAASNHSSGYMACIQSKGEFIEKGSDEQSSCTKPDFEAESAHVEDMPDLSRQL 120
           +EAT+EN+AASN SSG  ACIQ   E IEKGSD QSSCTKPD EAES  V +M + S   
Sbjct: 190 VEATAENNAASNRSSGDAACIQRNIELIEKGSDAQSSCTKPDCEAESDPVGNMQEFSLLK 249

Query: 121 WGKSLQNDVKMQNHEARVNYGQKSLVPVTEAQGSEVAACKEANTRAHFDEDTELETHRSD 180
            G++  +  + Q  E     GQ  ++    A G  V+  K        D+DT+ E   + 
Sbjct: 250 CGEAYPSGTETQQVETSFRLGQTLMMHDCHAGGLNVSIRKNGEASTTNDKDTDTEHFGNA 309

Query: 181 VILTSEVCNVPVNSPRQVIDFMSAFNNHKPPSNNGASRFDSSPQLDLSLRRTHPDGFENQ 240
            I                             S N    FD SPQLDLSLRR+ P  FEN+
Sbjct: 310 SI-----------------------------SVNCTGNFDHSPQLDLSLRRSCPGSFENK 340

Query: 241 V-ERKFILRHSNASAFTRYTNKPSEPQHSS-LSGVCNQQKEFETDSEKNFSNILTACNS- 297
           + E +  L HSNASAF RYT +  +    + L    +QQ+E  T+ EKN S+I T  NS 
Sbjct: 341 LTEERHTLMHSNASAFKRYTTRQLQISMPAVLINFSDQQREQITNCEKNISHIATGSNSD 400

Query: 298 -YTP-----AATLSTQRSVNSLATGHSKQ-------------SELAVSYPQQRP------ 332
             TP      +  + Q   + LAT H  Q             ++L  +Y    P      
Sbjct: 401 SSTPMQRCIVSPTTVQSKESELATSHPPQGHSLPIPVKGVRFNDLCTAYGSVLPSVFHTQ 460

Query: 333 -----CPVPVSVKV-------------------------------NST-NQAMHKLDHKL 355
                 P P SV +                               N+T N  ++  +HK 
Sbjct: 461 SGPPAMPSPNSVVLLEPNFQVNAFYQSNMKESSSEQLYESRGPNGNTTQNHIVYTQEHKS 520

Query: 356 DSLEDLGHISPATDQSASSSFCNGAVSRLNSMGYGSACGSNSNLDQVTAGRAAAESKNEE 415
           +  ED GHISP TDQS SSSFCNG  S LNS+GYGS CGS+SN+DQV    AA+E K+E+
Sbjct: 521 EHAEDRGHISPTTDQSVSSSFCNGNASHLNSIGYGSNCGSSSNVDQVNTVWAASEGKHED 580

Query: 416 GLFPSNGNL-RSIQREAALNKFRLKRKDRCYDKKVRYESRKKLAEQRPRVKGQFVRQVHS 474
               +N N  RSIQREAALNKFRLKRK+RCY+KKVRYESRKKLAEQRPRVKGQFVRQVH 
Sbjct: 581 --LTNNANSHRSIQREAALNKFRLKRKERCYEKKVRYESRKKLAEQRPRVKGQFVRQVHP 638

Query: 475 ETLPLESENHSGNISD 490
           + L  E +    + SD
Sbjct: 639 DPLVAEKDGKEYDHSD 654

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357464211|ref|XP_003602387.1| Two-component response regulator-like PRR73 [Medicago truncatula] gi|355491435|gb|AES72638.1| Two-component response regulator-like PRR73 [Medicago truncatula]

 Score =  360 bits (924), Expect = 1e-96,   Method: Compositional matrix adjust.
 Identities = 244/562 (43%), Positives = 323/562 (57%), Gaps = 94/562 (16%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR--QSSMVSG-NETQDESVG 57
           MSSQDSVSTVYKCM+RGAADYLVKP+R NELRNLWQHVWRR  QS+  +G N  QDES  
Sbjct: 137 MSSQDSVSTVYKCMLRGAADYLVKPIRINELRNLWQHVWRRQTQSAATAGINGPQDESDT 196

Query: 58  QQKIEATSENDAASNHSSGYMACIQSKGEFIEKGSDEQSSCTKPDFEAESAHVEDMPDLS 117
           QQK EAT+EN+AASN S G  ACIQ   + IEKGSD QSSCT+P+ EAES  V++M + S
Sbjct: 197 QQKFEATAENNAASNRSGGDAACIQRNKDLIEKGSDAQSSCTRPNMEAESGLVDNMHEFS 256

Query: 118 RQLWGKSLQNDVKMQNHEARVNYGQKSLVPVTEAQGSEVA----------ACKEANTRAH 167
           +    ++  +++K +  E  ++ GQ  +   + A G  VA           CK   T A+
Sbjct: 257 QLKCAEAYPSEIKTR--ELDIHLGQAVIAQDSHAGGLSVANCNNGVASTNNCKNGETGAN 314

Query: 168 FDEDTELETHRSDVILTSEVCN---VPVNS-PRQVIDFMSAFNNH-----KPPSNNGASR 218
             +D + + H  +  ++ EV +   V + S  ++ ID + AF        K  S +   +
Sbjct: 315 NCKDGDDQEHFRNASISGEVHDNHYVQIYSTTKEAIDLIGAFRTDPNCSLKNSSIDCTGK 374

Query: 219 FDSSPQLDLSLRRTHPDGFENQV-ERKFILRHSNASAFTRYTNKPSEPQHSSLSGVCNQQ 277
           FD SPQLDLSLR +HP  FE  + E +  L HSNASAF RYTN+  +   + +    +Q 
Sbjct: 375 FDHSPQLDLSLRSSHPSNFEKDLTEERHTLMHSNASAFKRYTNRQLQASPAVVINFSDQP 434

Query: 278 KEFETDSEKNFSNILTACNSYTPAATLSTQRSVNSLATGHSKQ-------------SELA 324
           +E +T++E + S+           +++ + +  + LAT HS+Q             ++L 
Sbjct: 435 REQKTNNENHNSD-----------SSIPSMQKESELATSHSQQRHSLPIPVKGVRFNDLC 483

Query: 325 VSY---------PQQRPCPVPVSVKV-------------------------------NST 344
           ++Y          Q  P  +P SV                                 NST
Sbjct: 484 MAYGSTLPPGFRTQSGPPSMPGSVVFLEQNFQADAFYQSNVKQNNSEQLYEPRGPNGNST 543

Query: 345 -NQAMHKLDHKLDSLEDLGHISPATDQSASSSFC-NGAVSRLNSMGYGSACGSNSNLDQV 402
            NQ M+  +HK +  ED   ISP TDQS SSSFC NG  S  NS+GYGS CGS+ N++QV
Sbjct: 544 PNQIMYTQEHKSEHPEDQRLISPTTDQSVSSSFCNNGNASNFNSIGYGSNCGSSGNVEQV 603

Query: 403 TAGRAAA--ESKNEEGLFPSNGNLRSIQREAALNKFRLKRKDRCYDKKVRYESRKKLAEQ 460
              R AA  E KNEE L  S  + R++ REAALNKFRLKRK+RCY+KKVRYESRKKLAEQ
Sbjct: 604 ATFRTAAVSEGKNEE-LTNSGYSHRAMLREAALNKFRLKRKERCYEKKVRYESRKKLAEQ 662

Query: 461 RPRVKGQFVRQVHSETLPLESE 482
           RPRVKGQFVRQ + ++L  E +
Sbjct: 663 RPRVKGQFVRQPNPDSLSGEKD 684

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449497396|ref|XP_004160390.1| PREDICTED: two-component response regulator-like PRR95-like [Cucumis sativus]

 Score =  343 bits (881), Expect = 8e-92,   Method: Compositional matrix adjust.
 Identities = 235/570 (41%), Positives = 300/570 (52%), Gaps = 99/570 (17%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSSMVSGNETQDESVGQQK 60
           MSS+DS+STVYKCMM+GAADYLVKP+RRNELRNLWQHVWRRQ+S    N   D    Q+K
Sbjct: 142 MSSEDSISTVYKCMMKGAADYLVKPLRRNELRNLWQHVWRRQAS---SNVRADI---QEK 195

Query: 61  IEATSENDAASNHSSGYMACIQSKGEFIEKGSDEQSSCTKPDFEAESAHVEDMPDLSRQL 120
           +E TSEN+ ASNHS+GY+A +Q   + IEKGSD QSSCTK DFE  +   E+    SRQ 
Sbjct: 196 VEVTSENETASNHSTGYVAGVQRNNKNIEKGSDTQSSCTKVDFEPGNKIQEN--SQSRQ- 252

Query: 121 WGKSLQNDVKMQNHEARVNYGQKSLVPVTEAQGSEVAACKEANTRAHFDEDTELET---- 176
            GK+  ND K Q  E  +N  Q+  +   E  G  +A     NT         LE     
Sbjct: 253 -GKASPNDFKPQKDERHINLSQRLFMHENETGG--LAMSCYVNTDLPITLSMGLEPINDG 309

Query: 177 ----------HRSDVILTSEVCNVPVNSPRQVIDFMSAFNNHKPPSNNGASRFDSSPQLD 226
                     H  D+           N  R  I +   +    P +N  A+ F S+  LD
Sbjct: 310 RSPNIASEAGHDKDLFANPSRDATASNHAR--IKYPDNYQKSSPSNNFAANNFGSALHLD 367

Query: 227 LSLRRTHPDGFENQVERKFILRHSNASAFTRYTNKPSEPQHSSLSGVCNQQKEFETDSEK 286
           LSLRR  P+ FE +   +  L+HS+ASAFTRYT +P +   +  S +C++QK  ET+S  
Sbjct: 368 LSLRRCQPNDFEERAAGQATLKHSSASAFTRYTFRPLQSLQAKSSSICDEQK--ETESNP 425

Query: 287 NFSNILTAC---NSYTPAATLSTQRSVNSLATGHSKQ--------SELAV---------- 325
           +    + A    ++  P   L    +   + T  S Q        SE A+          
Sbjct: 426 DHVGSMGATSTSDTINPTPNLQKSSTSMPMITSQSTQSEVAKSSTSETAIPLQVSGTDLM 485

Query: 326 -----------SYPQQRPC--------PVPVSVK----------VNSTNQAMHKLDHKLD 356
                      S P    C        P   SV           V   N   HKL+  L+
Sbjct: 486 SNNQRSGSGHGSLPSHNFCAQLGSPSSPCRTSVTHPELIFGKQTVYPLNLENHKLEQFLN 545

Query: 357 ------------------SLEDLGHISPATDQSASSSFCNGAVSRLNSMGYGSACGSNSN 398
                             S E+ GHISP TD SA+S+ C G  + + S+GY S CGSNSN
Sbjct: 546 QHRILSSPASRKIENSGQSPENQGHISPTTDHSANSNVCRGNTTHVGSLGYPSPCGSNSN 605

Query: 399 LDQVTAGRAAAESKNEEGLFPSNGN-LRSIQREAALNKFRLKRKDRCYDKKVRYESRKKL 457
           +D+V   R  +ES+NEE LF   G+  RS QREAAL KFRLKRKDRCY+KKVRYESRKKL
Sbjct: 606 VDRVGIARVTSESRNEEALFSQGGDSYRSSQREAALTKFRLKRKDRCYEKKVRYESRKKL 665

Query: 458 AEQRPRVKGQFVRQVHSETLPLESENHSGN 487
           AEQRPRVKGQFVR+V ++ LP E+ +++ N
Sbjct: 666 AEQRPRVKGQFVRRVLTDPLPAETNDNTSN 695

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224132558|ref|XP_002321351.1| response regulator [Populus trichocarpa] gi|222868347|gb|EEF05478.1| response regulator [Populus trichocarpa]

 Score =  343 bits (881), Expect = 9e-92,   Method: Compositional matrix adjust.
 Identities = 210/449 (46%), Positives = 261/449 (58%), Gaps = 64/449 (14%)

Query: 95  QSSCTKPDFEAESAHVEDMPDLSRQLWGKSLQNDVKMQNHEARVNYGQKSLVPVTEAQGS 154
           +SSCTKP  EAE AH+E+M +  + +W K    D  MQ HE  VN GQK LV  +EA+GS
Sbjct: 31  KSSCTKPGLEAEGAHMENMQEFLQPVWSKFSLTDTNMQKHEEHVNLGQKLLVRDSEAEGS 90

Query: 155 EVAACKEANTRAHFDEDTELETHRSDVILTSEVCN---VPVNSPRQVIDFMSAFNNHKPP 211
             A C+++N +   D++    + R    +  E C+      NSPR+ IDFM A  NH   
Sbjct: 91  ATAVCEDSN-KITVDKEITPGSGRVTANIAIEGCDKIGALANSPREAIDFMGASTNHSS- 148

Query: 212 SNNGASRFDSSPQLDLSLRRTHPDGFENQV-ERKFILRHSNASAFTRYTNKPSEPQHSSL 270
            NN    F SSP LDLSLRR+HP GFE QV E +  LRHSNASAFT YTN+ S+  HS+L
Sbjct: 149 FNNVEIHFCSSPHLDLSLRRSHPSGFETQVTEERHTLRHSNASAFTWYTNRASQLPHSAL 208

Query: 271 SGVCNQQKEFETDSEKNFSNILTACNSYTPAATLSTQRSVNSLATGHSKQSELAVSYPQQ 330
           +   NQ+ EF  + +   S+ +   NS   +   ST+RS  SLA G +K+ E+  S   +
Sbjct: 209 ANTGNQE-EFRANYDGKISSNVNGYNSDALSLAPSTRRSAISLAAGQTKEYEIVTSSSGE 267

Query: 331 RPCPVPVSV--------------------------------KVN---------------- 342
           +  P+ + V                                KVN                
Sbjct: 268 KVFPIHIPVKDTRFNNLCNSYGAVLPPMMSQSSASQKEPIHKVNPFQCSNYGSTSVQLCD 327

Query: 343 --------STNQAMHKLDHKLDSLEDLGHISPATDQSASSSFCNGAVSRLNSMGYGSACG 394
                   S N ++ K ++KLDSLE   HIS ATDQSASSSFCNGA S  NS+GYGSA G
Sbjct: 328 RLGQNANDSINGSLQKQENKLDSLEGREHISSATDQSASSSFCNGAASHFNSIGYGSASG 387

Query: 395 SNSNLDQVTAGRAAAESKNEEGLFPSNGNL-RSIQREAALNKFRLKRKDRCYDKKVRYES 453
           S SN DQ+    AA+ESKNEEG+F  N N  RSIQREAAL KFRLKRK+RCY+KKVRYES
Sbjct: 388 SYSNADQIATVSAASESKNEEGVFTHNSNSHRSIQREAALTKFRLKRKERCYEKKVRYES 447

Query: 454 RKKLAEQRPRVKGQFVRQVHSETLPLESE 482
           RKKLAEQRPRVKGQFVRQVH +  P E++
Sbjct: 448 RKKLAEQRPRVKGQFVRQVHIDPSPAETD 476

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449456441|ref|XP_004145958.1| PREDICTED: two-component response regulator-like PRR95-like [Cucumis sativus]

 Score =  339 bits (870), Expect = 2e-90,   Method: Compositional matrix adjust.
 Identities = 234/570 (41%), Positives = 299/570 (52%), Gaps = 99/570 (17%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSSMVSGNETQDESVGQQK 60
           MSS+DS+STVYKCMM+GAADYLVKP+RRNELRNLWQHVWRRQ+S    N   D    Q+K
Sbjct: 142 MSSEDSISTVYKCMMKGAADYLVKPLRRNELRNLWQHVWRRQAS---SNVRADI---QEK 195

Query: 61  IEATSENDAASNHSSGYMACIQSKGEFIEKGSDEQSSCTKPDFEAESAHVEDMPDLSRQL 120
           +E TSEN+ ASNHS+GY+A +Q   + IEKGSD QSSCTK DFE  +   E+    SRQ 
Sbjct: 196 VEVTSENETASNHSTGYVAGVQRNNKNIEKGSDTQSSCTKVDFEPGNKIQEN--SQSRQ- 252

Query: 121 WGKSLQNDVKMQNHEARVNYGQKSLVPVTEAQGSEVAACKEANTRAHFDEDTELET---- 176
            GK+  ND K Q  E  +N  Q+  +   E  G  +A     NT         LE     
Sbjct: 253 -GKASPNDFKPQKDERHINLSQRLFMHENETGG--LAMSCYVNTDLPITLSMGLEPINDG 309

Query: 177 ----------HRSDVILTSEVCNVPVNSPRQVIDFMSAFNNHKPPSNNGASRFDSSPQLD 226
                     H  D+           N  R  I +   +    P +N  A+ F S+  LD
Sbjct: 310 RSPNIASEAGHDKDLFANPSRDATASNHAR--IKYPDNYQKSSPSNNFAANNFGSALHLD 367

Query: 227 LSLRRTHPDGFENQVERKFILRHSNASAFTRYTNKPSEPQHSSLSGVCNQQKEFETDSEK 286
           LSLRR  P+ FE +   +  L+HS+ASAFTRYT +P +   +  S +C++QK  ET+S  
Sbjct: 368 LSLRRCQPNDFEERAAGQATLKHSSASAFTRYTFRPLQSLQAKSSSICDEQK--ETESNP 425

Query: 287 NFSNILTAC---NSYTPAATLSTQRSVNSLATGHSKQ--------SELAV---------- 325
           +    + A    ++  P   L    +   + T  S Q        SE A+          
Sbjct: 426 DHVGSMGATSTSDTINPTPNLQKSSTSMPMITSQSTQSEVAKSSTSETAIPLQVSGTDLM 485

Query: 326 -----------SYPQQRPC--------PVPVSVK----------VNSTNQAMHKLDHKLD 356
                      S P    C        P   SV           V   N   HKL+  L+
Sbjct: 486 SNNQRSGSGHGSLPSHNFCAQLGSPSSPCRTSVTHPELIFGKQTVYPLNLENHKLEQFLN 545

Query: 357 ------------------SLEDLGHISPATDQSASSSFCNGAVSRLNSMGYGSACGSNSN 398
                             S E+ GHISP TD SA+S+   G  + + S+GY S CGSNSN
Sbjct: 546 QHRILSSPASRKIENSGQSPENQGHISPTTDHSANSNVWRGNTTHVGSLGYPSPCGSNSN 605

Query: 399 LDQVTAGRAAAESKNEEGLFPSNGN-LRSIQREAALNKFRLKRKDRCYDKKVRYESRKKL 457
           +D+V   R  +ES+NEE LF   G+  RS QREAAL KFRLKRKDRCY+KKVRYESRKKL
Sbjct: 606 VDRVGIARVTSESRNEEALFSQGGDSYRSSQREAALTKFRLKRKDRCYEKKVRYESRKKL 665

Query: 458 AEQRPRVKGQFVRQVHSETLPLESENHSGN 487
           AEQRPRVKGQFVR+V ++ LP E+ +++ N
Sbjct: 666 AEQRPRVKGQFVRRVLTDPLPAETNDNTSN 695

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359490833|ref|XP_003634174.1| PREDICTED: two-component response regulator-like APRR5-like [Vitis vinifera]

 Score =  335 bits (859), Expect = 3e-89,   Method: Compositional matrix adjust.
 Identities = 186/350 (53%), Positives = 227/350 (64%), Gaps = 11/350 (3%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSSMVSGNETQDESVGQQK 60
           MSS  S++TVYKCM+RGAAD+LVKPVRRNEL+NLWQHVWRRQSS VSGN  QDESV QQK
Sbjct: 121 MSSHGSINTVYKCMLRGAADFLVKPVRRNELKNLWQHVWRRQSSTVSGNGPQDESVAQQK 180

Query: 61  IEATSENDAASNHSSGYMACIQSKGEFIEKGSDEQSSCTKPDFEAESAHVEDMPDLSRQL 120
           +EATSEN+  SNHSS ++ACIQ   E + K SD QSSC+KPD EAESA++E M D S   
Sbjct: 181 VEATSENNPTSNHSSDHVACIQKNKEALNKVSDAQSSCSKPDLEAESAYMETMQDFSNPT 240

Query: 121 WGKSLQNDVKMQNHEARVNYGQKSLVPVTEAQGSEVAACKEANTRAHFDEDTELETHRSD 180
           W +SL +D KMQ +E     G K L+   EA G+  AAC++ NT     E  E E     
Sbjct: 241 WSRSLVSDTKMQKNEECAKLGPKFLMHNKEAGGTLEAACRDVNTMTQ-PEAVEPENDGQG 299

Query: 181 VILTSEVCN---VPVNSPRQVIDFMSAFNNHKP------PSNNGASRFDSSPQLDLSLRR 231
               SE C    +  +S R+ ID +  F+N K        SNNG  + DS PQLDLSLRR
Sbjct: 300 ANAPSEACGNNAILGSSSREAIDLIGVFDNSKKCTYGNSSSNNGTKKSDSIPQLDLSLRR 359

Query: 232 THPDGFENQV-ERKFILRHSNASAFTRYTNKPSEPQHSSLSGVCNQQKEFETDSEKNFSN 290
           +HP   ENQV + +  L HSN SAF+RY N+  +P H   +GV NQQK F  DS+K  S 
Sbjct: 360 SHPSSPENQVADERHTLNHSNGSAFSRYINRSLQPPHLPSTGVFNQQKNFGADSDKRLSQ 419

Query: 291 ILTACNSYTPAATLSTQRSVNSLATGHSKQSELAVSYPQQRPCPVPVSVK 340
           ++T  NS   + TLSTQRSV SLAT  S + E+A+  PQQR  P PV V+
Sbjct: 420 LVTGYNSDITSPTLSTQRSVISLATSPSGRVEIALCGPQQRAFPAPVPVR 469

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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	491
TAIR|locus:2044376	468	PRR9 "pseudo-response regulato	0.162	0.170	0.621	6.1e-39
TAIR|locus:2151206	727	PRR7 "pseudo-response regulato	0.221	0.149	0.467	2.4e-32
TAIR|locus:2163198	618	TOC1 "TIMING OF CAB EXPRESSION	0.128	0.101	0.539	1.3e-21
TAIR|locus:2062749	183	AT2G46670 "AT2G46670" [Arabido	0.162	0.437	0.621	3.5e-20
TAIR|locus:2143206	373	CO "CONSTANS" [Arabidopsis tha	0.105	0.139	0.471	4.7e-07
TAIR|locus:2093668	690	RR1 "response regulator 1" [Ar	0.334	0.237	0.301	5.1e-07
TAIR|locus:2074587	347	COL2 "CONSTANS-like 2" [Arabid	0.105	0.149	0.461	7e-07
TAIR|locus:2172545	355	COL5 "CONSTANS-like 5" [Arabid	0.260	0.360	0.326	3.5e-06
TAIR|locus:2130095	664	RR2 "response regulator 2" [Ar	0.205	0.152	0.357	4.5e-06
TAIR|locus:2007482	195	AT1G07050 "AT1G07050" [Arabido	0.095	0.241	0.446	6.2e-06

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

 Score = 227 (85.0 bits), Expect = 6.1e-39, Sum P(3) = 6.1e-39
 Identities = 51/82 (62%), Positives = 62/82 (75%)

Query:   394 GSNSNLDQVTAGRAAAESKNEEGLFPSNGNLRSIQREAALNKFRLKRKDRCYDKKVRYES 453
             GS S  + + AG++++  K +E         RS QREAAL KFRLKRKDRC+DKKVRY+S
Sbjct:   384 GSQSTNEGI-AGQSSSTEKPKEEESAKQRWSRS-QREAALMKFRLKRKDRCFDKKVRYQS 441

Query:   454 RKKLAEQRPRVKGQFVRQVHSE 475
             RKKLAEQRPRVKGQFVR V+S+
Sbjct:   442 RKKLAEQRPRVKGQFVRTVNSD 463

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

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

 Score = 214 (80.4 bits), Expect = 2.4e-32, Sum P(3) = 2.4e-32
 Identities = 58/124 (46%), Positives = 75/124 (60%)

Query:   378 NGAVSRLN--SMG-YGSACGSNSNLDQVTAGRAAAESKNEEGLFPSNG----NL----RS 426
             NG+VS     S G YGS+ G N+    + +   A ++ N +G    +G    NL    + 
Sbjct:   607 NGSVSGSGHGSNGPYGSSNGMNAGGMNMGSDNGAGKNGNGDGSGSGSGSGSGNLADENKI 666

Query:   427 IQREAALNKFRLKRKDRCYDKKVRYESRKKLAEQRPRVKGQFVRQVHSETLPLESENHSG 486
              QREAAL KFR KRK+RC+ KKVRY+SRKKLAEQRPRV+GQFVR+  + T     +N   
Sbjct:   667 SQREAALTKFRQKRKERCFRKKVRYQSRKKLAEQRPRVRGQFVRKTAAAT----DDNDIK 722

Query:   487 NISD 490
             NI D
Sbjct:   723 NIED 726

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:2163198 TOC1 "TIMING OF CAB EXPRESSION 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 178 (67.7 bits), Expect = 1.3e-21, Sum P(2) = 1.3e-21
 Identities = 34/63 (53%), Positives = 46/63 (73%)

Query:   428 QREAALNKFRLKRKDRCYDKKVRYESRKKLAEQRPRVKGQFVRQVHSETLPLESENHSGN 487
             +RE AL KFR KR  RC+DKK+RY +RK+LAE+RPRVKGQFVR+++   + L  +  S +
Sbjct:   532 RREEALLKFRRKRNQRCFDKKIRYVNRKRLAERRPRVKGQFVRKMNGVNVDLNGQPDSAD 591

Query:   488 ISD 490
               D
Sbjct:   592 YDD 594

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

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

GO:0005634 "nucleus" evidence=ISM;IDA;TAS

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

GO:0007623 "circadian rhythm" evidence=IEP;RCA;TAS

GO:0005515 "protein binding" evidence=IPI

GO:0010031 "circumnutation" evidence=IMP

GO:0006351 "transcription, DNA-dependent" evidence=TAS

GO:0044212 "transcription regulatory region DNA binding" evidence=IDA

GO:0003677 "DNA binding" evidence=IDA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IDA

GO:0010629 "negative regulation of gene expression" 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:2062749 AT2G46670 "AT2G46670" [Arabidopsis thaliana (taxid:3702)]

 Score = 227 (85.0 bits), Expect = 3.5e-20, Sum P(2) = 3.5e-20
 Identities = 51/82 (62%), Positives = 62/82 (75%)

Query:   394 GSNSNLDQVTAGRAAAESKNEEGLFPSNGNLRSIQREAALNKFRLKRKDRCYDKKVRYES 453
             GS S  + + AG++++  K +E         RS QREAAL KFRLKRKDRC+DKKVRY+S
Sbjct:    99 GSQSTNEGI-AGQSSSTEKPKEEESAKQRWSRS-QREAALMKFRLKRKDRCFDKKVRYQS 156

Query:   454 RKKLAEQRPRVKGQFVRQVHSE 475
             RKKLAEQRPRVKGQFVR V+S+
Sbjct:   157 RKKLAEQRPRVKGQFVRTVNSD 178

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2143206 CO "CONSTANS" [Arabidopsis thaliana (taxid:3702)]

 Score = 119 (46.9 bits), Expect = 4.7e-07, Sum P(2) = 4.7e-07
 Identities = 25/53 (47%), Positives = 36/53 (67%)

Query:   424 LRSIQREAALNKFRLKRKDRCYDKKVRYESRKKLAEQRPRVKGQFV-RQVHSE 475
             L  + REA + ++R KRK R ++K +RY SRK  AE RPRV G+F  R++ +E
Sbjct:   301 LSPMDREARVLRYREKRKTRKFEKTIRYASRKAYAEIRPRVNGRFAKREIEAE 353

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IDA;NAS

GO:0008270 "zinc ion binding" evidence=IEA;ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0007623 "circadian rhythm" evidence=IGI

GO:0009909 "regulation of flower development" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0010018 "far-red light signaling pathway" evidence=IMP

GO:0010218 "response to far red light" evidence=IMP

GO:0006281 "DNA repair" evidence=RCA

GO:0010100 "negative regulation of photomorphogenesis" evidence=RCA

GO:0048608 "reproductive structure development" evidence=RCA

TAIR|locus:2093668 RR1 "response regulator 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 149 (57.5 bits), Expect = 5.1e-07, P = 5.1e-07
 Identities = 54/179 (30%), Positives = 78/179 (43%)

Query:     1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSSMVSGNETQD--ESVGQ 58
             MS+ DS S V K +  GA DYL+KPVR   L+N+WQHV R++ S  S  E     E  G+
Sbjct:   115 MSADDSKSVVLKGVTHGAVDYLIKPVRMEALKNIWQHVVRKRRSEWSVPEHSGSIEETGE 174

Query:    59 QKIEATSENDAASNHSSGYMACIQSKGEFIEKGSDEQSSCTK-PDFEAESA---HVEDMP 114
             ++ +        +  S G  A +      + +G++ +SS  K  D E E       ED  
Sbjct:   175 RQQQQHRGGGGGAAVSGGEDA-VDDNSSSVNEGNNWRSSSRKRKDEEGEEQGDDKDEDAS 233

Query:   115 DLS--RQLWGKSLQNDVKMQNHEARVNY-GQKSLVPVTEAQGSEVAACKEANTRAHFDE 170
             +L   R +W   L      Q   A VN  G +  VP    +   V      N  +H  +
Sbjct:   234 NLKKPRVVWSVELH-----QQFVAAVNQLGVEKAVPKKILELMNVPGLTRENVASHLQK 287

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

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS;IDA

GO:0009736 "cytokinin mediated signaling pathway" evidence=IGI;RCA;TAS

GO:0009735 "response to cytokinin stimulus" evidence=IGI;IMP

GO:0005515 "protein binding" evidence=IPI

GO:0010380 "regulation of chlorophyll biosynthetic process" evidence=IGI

GO:0031537 "regulation of anthocyanin metabolic process" evidence=IGI;RCA

GO:0048367 "shoot system development" evidence=IGI

GO:0080022 "primary root development" evidence=IGI

GO:0006487 "protein N-linked glycosylation" evidence=RCA

GO:0006635 "fatty acid beta-oxidation" evidence=RCA

GO:0010029 "regulation of seed germination" evidence=RCA

GO:0010043 "response to zinc ion" evidence=RCA

GO:0016558 "protein import into peroxisome matrix" evidence=RCA

GO:0048831 "regulation of shoot system development" evidence=RCA

TAIR|locus:2074587 COL2 "CONSTANS-like 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 131 (51.2 bits), Expect = 7.0e-07, Sum P(3) = 7.0e-07
 Identities = 24/52 (46%), Positives = 38/52 (73%)

Query:   424 LRSIQREAALNKFRLKRKDRCYDKKVRYESRKKLAEQRPRVKGQFVRQVHSE 475
             L  ++REA + ++R K+K R +DK +RY SRK  AE RPR+KG+F +++ +E
Sbjct:   273 LTPMEREARVLRYREKKKTRKFDKTIRYASRKAYAEIRPRIKGRFAKRIETE 324

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA;ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0009909 "regulation of flower development" evidence=IMP

GO:0009658 "chloroplast organization" evidence=IMP

TAIR|locus:2172545 COL5 "CONSTANS-like 5" [Arabidopsis thaliana (taxid:3702)]

 Score = 137 (53.3 bits), Expect = 3.5e-06, P = 3.5e-06
 Identities = 46/141 (32%), Positives = 68/141 (48%)

Query:   335 VPVSVKVNSTNQAMHKLDHKLDSLEDLGHISPATDQSASSSFCNGAVSRLNSMGYGSACG 394
             VPV  K       +   DH  D       +S  T  S S S    +VS  +S+ YG    
Sbjct:   204 VPVQTKTEPL--PLTNNDHCFDIDFCRSKLSAFTYPSQSVSH---SVST-SSIEYGVVPD 257

Query:   395 SNSNLDQVTAGRAAAESKNEEGLFPSNGNLRSIQREAALNKFRLKRKDRCYDKKVRYESR 454
              N+N    +  R+   S    G    +    S+ REA + ++R KRK+R ++K +RY SR
Sbjct:   258 GNTNN---SVNRSTITSSTTGG----DHQASSMDREARVLRYREKRKNRKFEKTIRYASR 310

Query:   455 KKLAEQRPRVKGQFVRQVHSE 475
             K  AE RPR+KG+F ++  +E
Sbjct:   311 KAYAESRPRIKGRFAKRTETE 331

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA;ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

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

GO:0042631 "cellular response to water deprivation" evidence=RCA

TAIR|locus:2130095 RR2 "response regulator 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 146 (56.5 bits), Expect = 4.5e-06, Sum P(2) = 4.5e-06
 Identities = 40/112 (35%), Positives = 63/112 (56%)

Query:     1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQS-----SMVSGNETQD-- 53
             MS+ DS S V K +  GA DYL+KPVR   L+N+WQHV R++      S  SG   +D  
Sbjct:   106 MSADDSKSVVLKGVTHGAVDYLIKPVRIEALKNIWQHVVRKKRNEWNVSEHSGGSIEDTG 165

Query:    54 -ESVGQQKIEATSENDAAS-NHSSGYMACIQSKGEFIEKGSDEQ--SSCTKP 101
              +   QQ+    ++N+++S N  +G  +  + + E  ++G D++  SS  KP
Sbjct:   166 GDRDRQQQHREDADNNSSSVNEGNGRSSRKRKEEEVDDQGDDKEDSSSLKKP 217

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

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS;IDA

GO:0005515 "protein binding" evidence=IPI

GO:0009736 "cytokinin mediated signaling pathway" evidence=RCA;TAS

GO:0009723 "response to ethylene stimulus" evidence=IMP

GO:0009735 "response to cytokinin stimulus" evidence=IEP;IGI

GO:0010150 "leaf senescence" evidence=IMP

GO:0009873 "ethylene mediated signaling pathway" evidence=IMP

GO:0010119 "regulation of stomatal movement" evidence=IMP

GO:0007623 "circadian rhythm" evidence=RCA

GO:0010029 "regulation of seed germination" evidence=RCA

GO:0031537 "regulation of anthocyanin metabolic process" evidence=RCA

GO:0048831 "regulation of shoot system development" evidence=RCA

TAIR|locus:2007482 AT1G07050 "AT1G07050" [Arabidopsis thaliana (taxid:3702)]

 Score = 121 (47.7 bits), Expect = 6.2e-06, Sum P(2) = 6.2e-06
 Identities = 21/47 (44%), Positives = 38/47 (80%)

Query:   425 RSIQREAALNKFRLKRKDRCYDKKVRYESRKKLAEQRPRVKGQFVRQ 471
             R+++REA++ +++ KR+ R + KK+RY+ RK  A++RPR KG+FV++
Sbjct:   147 RNMRREASVLRYKEKRQSRLFSKKIRYQVRKLNADKRPRFKGRFVKR 193

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0007623 "circadian rhythm" evidence=RCA

---

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

Your Input:
	PtpRR3	response regulator (687 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	ETR7	ethylene receptor 7 (769 aa)							•		0.681
	gw1.I.396.1	histidine phosphotransfer protein (117 aa)							•		0.679
	fgenesh4_pg.C_scaffold_697000003	histidine phosphotransfer protein (146 aa)							•		0.679
	fgenesh4_pg.C_LG_XIV000773	histidine phosphotransfer protein (139 aa)							•		0.679
	fgenesh4_pg.C_LG_X002318	histidine phosphotransfer protein (159 aa)							•		0.679
	fgenesh4_pg.C_LG_VI001633	histidine phosphotransfer protein (147 aa)							•		0.679
	fgenesh4_pg.C_LG_IX000220	histidine phosphotransfer protein (245 aa)							•		0.679
	fgenesh4_pg.C_LG_I003334	histidine phosphotransfer protein (147 aa)							•		0.679
	eugene3.00440046	histidine phosphotransfer protein (192 aa)							•		0.679
	eugene3.00180254	hypothetical protein (137 aa)							•		0.679

---

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	491
pfam06203	45	pfam06203, CCT, CCT motif	4e-19
cd00156	113	cd00156, REC, Signal receiver domain; originally t	5e-04
pfam00072	111	pfam00072, Response_reg, Response regulator receiv	0.004

>gnl|CDD|203407 pfam06203, CCT, CCT motif

 Score = 80.3 bits (199), Expect = 4e-19
 Identities = 28/43 (65%), Positives = 36/43 (83%)

Query: 429 REAALNKFRLKRKDRCYDKKVRYESRKKLAEQRPRVKGQFVRQ 471
           REAAL +++ KRK R +DKK+RY SRK +AE RPRVKG+FV+Q
Sbjct: 1   REAALLRYKEKRKTRKFDKKIRYASRKAVAESRPRVKGRFVKQ 43

This short motif is found in a number of plant proteins. It is rich in basic amino acids and has been called a CCT motif after Co, Col and Toc1. The CCT motif is about 45 amino acids long and contains a putative nuclear localisation signal within the second half of the CCT motif. Toc1 mutants have been identified in this region. Length = 45

>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 = 39.5 bits (93), Expect = 5e-04
 Identities = 9/38 (23%), Positives = 16/38 (42%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHV 38
           +++        + +  GA DYL KP    EL    + +
Sbjct: 75  LTAHGDDEDAVEALKAGADDYLTKPFSPEELLARIRAL 112

Length = 113

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

 Score = 36.8 bits (86), Expect = 0.004
 Identities = 8/33 (24%), Positives = 14/33 (42%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRN 33
           +++        + +  GA D+L KP    EL  
Sbjct: 76  LTAHGDEEDAVEALKAGANDFLSKPFDPEELVA 108

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	491
PF06203	45	CCT: CCT motif; InterPro: IPR010402 The CCT (CONST	99.74
COG4753	475	Response regulator containing CheY-like receiver d	98.3
COG4566	202	TtrR Response regulator [Signal transduction mecha	97.62
COG4565	224	CitB Response regulator of citrate/malate metaboli	97.55
COG2204	464	AtoC Response regulator containing CheY-like recei	97.49
COG0745	229	OmpR Response regulators consisting of a CheY-like	97.28
PRK09581	457	pleD response regulator PleD; Reviewed	96.96
COG4567	182	Response regulator consisting of a CheY-like recei	96.85
PLN03029	222	type-a response regulator protein; Provisional	96.73
PRK10046	225	dpiA two-component response regulator DpiA; Provis	96.44
PRK10529	225	DNA-binding transcriptional activator KdpE; Provis	96.39
PRK10643	222	DNA-binding transcriptional regulator BasR; Provis	96.28
TIGR03787	227	marine_sort_RR proteobacterial dedicated sortase s	96.28
PRK10766	221	DNA-binding transcriptional regulator TorR; Provis	96.26
PRK10336	219	DNA-binding transcriptional regulator QseB; Provis	96.19
PRK10161	229	transcriptional regulator PhoB; Provisional	96.15
PRK11173	237	two-component response regulator; Provisional	96.12
PRK09836	227	DNA-binding transcriptional activator CusR; Provis	96.1
PRK10816	223	DNA-binding transcriptional regulator PhoP; Provis	96.08
CHL00148	240	orf27 Ycf27; Reviewed	96.0
PRK10430	239	DNA-binding transcriptional activator DcuR; Provis	95.91
TIGR02154	226	PhoB phosphate regulon transcriptional regulatory	95.87
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	95.86
PF09425	27	CCT_2: Divergent CCT motif; InterPro: IPR018467 Th	95.8
PRK10955	232	DNA-binding transcriptional regulator CpxR; Provis	95.79
PRK10693	303	response regulator of RpoS; Provisional	95.78
PRK09468	239	ompR osmolarity response regulator; Provisional	95.78
PRK10610	129	chemotaxis regulatory protein CheY; Provisional	95.76
PRK10360	196	DNA-binding transcriptional activator UhpA; Provis	95.65
PRK11517	223	transcriptional regulatory protein YedW; Provision	95.64
TIGR01387	218	cztR_silR_copR heavy metal response regulator. Mem	95.58
PRK11083	228	DNA-binding response regulator CreB; Provisional	95.54
PRK09958	204	DNA-binding transcriptional activator EvgA; Provis	95.47
PRK10840	216	transcriptional regulator RcsB; Provisional	95.42
TIGR02875	262	spore_0_A sporulation transcription factor Spo0A.	95.34
KOG1601	340	consensus GATA-4/5/6 transcription factors [Transc	95.33
PRK10701	240	DNA-binding transcriptional regulator RstA; Provis	95.31
PRK13856	241	two-component response regulator VirG; Provisional	95.28
PRK09935	210	transcriptional regulator FimZ; Provisional	95.17
PRK11697	238	putative two-component response-regulatory protein	95.1
PRK15479	221	transcriptional regulatory protein TctD; Provision	95.02
PRK14084	246	two-component response regulator; Provisional	94.88
PRK10710	240	DNA-binding transcriptional regulator BaeR; Provis	94.58
PRK11475	207	DNA-binding transcriptional activator BglJ; Provis	94.48
PRK10365	441	transcriptional regulatory protein ZraR; Provision	94.24
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	94.24
COG2197	211	CitB Response regulator containing a CheY-like rec	94.19
PRK09483	217	response regulator; Provisional	94.14
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	93.98
PRK15115	444	response regulator GlrR; Provisional	93.97
COG0784	130	CheY FOG: CheY-like receiver [Signal transduction	93.66
PRK09581	457	pleD response regulator PleD; Reviewed	93.65
PRK10403	215	transcriptional regulator NarP; Provisional	93.65
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	93.6
PRK15369	211	two component system sensor kinase SsrB; Provision	93.52
COG3437	360	Response regulator containing a CheY-like receiver	93.48
PRK13435	145	response regulator; Provisional	93.47
COG3707	194	AmiR Response regulator with putative antiterminat	93.26
PRK11107	919	hybrid sensory histidine kinase BarA; Provisional	93.02
PRK10651	216	transcriptional regulator NarL; Provisional	92.58
PRK15347	921	two component system sensor kinase SsrA; Provision	92.43
PRK11466	914	hybrid sensory histidine kinase TorS; Provisional	91.78
COG3706	435	PleD Response regulator containing a CheY-like rec	91.67
cd00156	113	REC Signal receiver domain; originally thought to	91.59
PRK09390	202	fixJ response regulator FixJ; Provisional	91.1
TIGR02956	968	TMAO_torS TMAO reductase sytem sensor TorS. This p	90.57
PRK09959	1197	hybrid sensory histidine kinase in two-component r	89.69
TIGR03815	322	CpaE_hom_Actino helicase/secretion neighborhood Cp	87.93
PRK12555	337	chemotaxis-specific methylesterase; Provisional	86.55
PRK11091	779	aerobic respiration control sensor protein ArcB; P	85.41
COG3947	361	Response regulator containing CheY-like receiver a	82.86
PRK12704	520	phosphodiesterase; Provisional	81.21

>PF06203 CCT: CCT motif; InterPro: IPR010402 The CCT (CONSTANS, CO-like, and TOC1) domain is a highly conserved basic module of ~43 amino acids, which is found near the C terminus of plant proteins often involved in light signal transduction

Probab=99.74  E-value=7.6e-19  Score=132.47  Aligned_cols=45  Identities=56%  Similarity=0.986  Sum_probs=43.1

Q ss_pred             HHHHHHHHHHhhhccCCCCcccchhhhhhhhhCCCCCcceecccC
Q 011208          429 REAALNKFRLKRKDRCYDKKVRYESRKKLAEQRPRVKGQFVRQVH  473 (491)
Q Consensus       429 R~~~l~ryr~Krk~R~f~KkirY~~RK~~A~~RpRvKGrFvk~~~  473 (491)
                      |+++|+||++||+.|+|+|+|+|+|||.+|+.|||||||||+..+
T Consensus         1 R~~~l~Ry~~Kr~~R~f~kkirY~~Rk~~A~~R~RvkGRFvk~~e   45 (45)
T PF06203_consen    1 REEKLQRYREKRKRRNFEKKIRYESRKAVADKRPRVKGRFVKKSE   45 (45)
T ss_pred             CHHHHHHHHHHHHhhcccccCCcchHHHHHhhCCccCCcccCCCC
Confidence            689999999999999999999999999999999999999999764

The CCT domain is found in association with other domains, such as the B-box zinc finger, the GATA-type zinc finger, the ZIM motif or the response regulatory domain. The CCT domain contains a putative nuclear localisation signal within the second half of the CCT motif and has been shown to be involved in nuclear localization and probably also has a role in protein-protein interaction [].; GO: 0005515 protein binding

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

Probab=98.30  E-value=5e-07  Score=97.14  Aligned_cols=45  Identities=29%  Similarity=0.447  Sum_probs=42.3

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHhcc
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSSM   45 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~~~   45 (491)
                      +|||++|+||++||++|+.||||||++..||..++.+++.++-..
T Consensus        82 LSGy~eFeYak~Am~lGV~dYLLKP~~k~eL~~~L~ki~~kl~~~  126 (475)
T COG4753          82 LSGYDEFEYAKKAMKLGVKDYLLKPVDKAELEEALKKIIGKLEEQ  126 (475)
T ss_pred             EeccchhHHHHHHHhcCchhheeCcCCHHHHHHHHHHHHHHHHHH
Confidence            699999999999999999999999999999999999998888543

>COG4566 TtrR Response regulator [Signal transduction mechanisms]

Probab=97.62  E-value=3.9e-05  Score=74.39  Aligned_cols=44  Identities=23%  Similarity=0.443  Sum_probs=41.3

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHhc
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSS   44 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~~   44 (491)
                      ||||++..++.+||+.||+|||-|||+..+|...++.++++...
T Consensus        82 iTGhgDIpmaV~AmK~GAvDFLeKP~~~q~Lldav~~Al~~~~~  125 (202)
T COG4566          82 LTGHGDIPMAVQAMKAGAVDFLEKPFSEQDLLDAVERALARDAS  125 (202)
T ss_pred             EeCCCChHHHHHHHHcchhhHHhCCCchHHHHHHHHHHHHHHHH
Confidence            79999999999999999999999999999999999999887643

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

Probab=97.55  E-value=6.7e-05  Score=73.90  Aligned_cols=42  Identities=19%  Similarity=0.440  Sum_probs=38.1

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      +|+-++.++++.||++||+|||||||..+-|...+..-.+++
T Consensus        80 iTAA~d~~tI~~alr~Gv~DYLiKPf~~eRl~~aL~~y~~~r  121 (224)
T COG4565          80 ITAASDMETIKEALRYGVVDYLIKPFTFERLQQALTRYRQKR  121 (224)
T ss_pred             EeccchHHHHHHHHhcCchhheecceeHHHHHHHHHHHHHHH
Confidence            478899999999999999999999999999999998866555

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

Probab=97.49  E-value=0.00011  Score=79.44  Aligned_cols=43  Identities=21%  Similarity=0.363  Sum_probs=40.6

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHh
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQS   43 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~   43 (491)
                      ||+|++.++|..||+.||+|||.|||+.++|..++.+++....
T Consensus        82 ~Tg~g~i~~AV~A~k~GA~Dfl~KP~~~~~L~~~v~ral~~~~  124 (464)
T COG2204          82 MTGHGDIDTAVEALRLGAFDFLEKPFDLDRLLAIVERALELRE  124 (464)
T ss_pred             EeCCCCHHHHHHHHhcCcceeeeCCCCHHHHHHHHHHHHHHhh
Confidence            7999999999999999999999999999999999999987653

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

Probab=97.28  E-value=0.00023  Score=69.89  Aligned_cols=44  Identities=27%  Similarity=0.413  Sum_probs=41.1

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHhc
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSS   44 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~~   44 (491)
                      ||+.++.+....++..||.|||+|||.+.||..-++-++|+...
T Consensus        78 Lta~~~~~d~v~gl~~GADDYl~KPf~~~EL~ARi~a~lRR~~~  121 (229)
T COG0745          78 LTARDDEEDRVLGLEAGADDYLTKPFSPRELLARLRALLRRNAG  121 (229)
T ss_pred             EECCCcHHHHHHHHhCcCCeeeeCCCCHHHHHHHHHHHHCcCcC
Confidence            58889999999999999999999999999999999999988754

>PRK09581 pleD response regulator PleD; Reviewed

Probab=96.96  E-value=0.00061  Score=68.99  Aligned_cols=41  Identities=29%  Similarity=0.498  Sum_probs=37.0

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR   41 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk   41 (491)
                      ||++++++++.+|+..||.|||+||++.++|...+....++
T Consensus       234 ls~~~~~~~~~~a~~~Ga~d~l~kp~~~~~l~~~i~~~~~~  274 (457)
T PRK09581        234 LVDEDDDPRLVKALELGVNDYLMRPIDKNELLARVRTQIRR  274 (457)
T ss_pred             EeCCCChHHHHHHHHccchhhhhCCCcHHHHHHHHHHHHHH
Confidence            58999999999999999999999999999999888775543

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

Probab=96.85  E-value=0.00071  Score=64.17  Aligned_cols=37  Identities=24%  Similarity=0.440  Sum_probs=34.1

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQH   37 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqh   37 (491)
                      +|||.+..++..||++||||||-||-+.+++...+..
T Consensus        87 LTGy~sIATAV~AvKlGA~~YLaKPAdaDdi~aAl~~  123 (182)
T COG4567          87 LTGYASIATAVEAVKLGACDYLAKPADADDILAALLR  123 (182)
T ss_pred             EecchHHHHHHHHHHhhhhhhcCCCCChHHHHHHHhh
Confidence            5899999999999999999999999999999877654

>PLN03029 type-a response regulator protein; Provisional

Probab=96.73  E-value=0.0019  Score=62.33  Aligned_cols=44  Identities=32%  Similarity=0.636  Sum_probs=39.5

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHhc
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSS   44 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~~   44 (491)
                      ||++...+.+.+|+..||.|||+||++..+|..++.++++....
T Consensus       108 ls~~~~~~~~~~al~~Ga~dyl~KP~~~~~L~~l~~~~~~~~~~  151 (222)
T PLN03029        108 MSSENVPSRITRCLEEGAEEFFLKPVQLSDLNRLKPHMMKTKSK  151 (222)
T ss_pred             EeCCCCHHHHHHHHHhCchheEECCCCHHHHHHHHHHHHHHHHH
Confidence            56788899999999999999999999999999999998776644

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=96.44  E-value=0.0042  Score=59.02  Aligned_cols=42  Identities=24%  Similarity=0.424  Sum_probs=38.1

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      +|++.+.+++.++++.||.+||+||++.++|...++++....
T Consensus        84 ls~~~~~~~~~~al~~Ga~~yl~Kp~~~~~L~~~i~~~~~~~  125 (225)
T PRK10046         84 TTAASDMETVSEAVRCGVFDYLIKPIAYERLGQTLTRFRQRK  125 (225)
T ss_pred             EEcCCCHHHHHHHHHcCccEEEECCcCHHHHHHHHHHHHHHH
Confidence            478889999999999999999999999999999999886544

>PRK10529 DNA-binding transcriptional activator KdpE; Provisional

Probab=96.39  E-value=0.0043  Score=57.02  Aligned_cols=42  Identities=31%  Similarity=0.422  Sum_probs=37.6

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+...+|+..||.|||+||+..++|...++.++++.
T Consensus        78 lt~~~~~~~~~~~~~~ga~~~l~kP~~~~~l~~~i~~~~~~~  119 (225)
T PRK10529         78 LSARSEESDKIAALDAGADDYLSKPFGIGELQARLRVALRRH  119 (225)
T ss_pred             EECCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHhhc
Confidence            467788899999999999999999999999999998887764

>PRK10643 DNA-binding transcriptional regulator BasR; Provisional

Probab=96.28  E-value=0.0054  Score=55.63  Aligned_cols=42  Identities=31%  Similarity=0.479  Sum_probs=37.8

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      +|++.+.+.+.+++..||.|||.||++.++|...++.++++.
T Consensus        78 ls~~~~~~~~~~~~~~ga~~~l~kp~~~~~l~~~i~~~~~~~  119 (222)
T PRK10643         78 LTARDTLEDRVAGLDVGADDYLVKPFALEELHARIRALIRRH  119 (222)
T ss_pred             EECCCCHHHHHHHHhcCCCeEEeCCCCHHHHHHHHHHHHhhh
Confidence            467888999999999999999999999999999998887654

>TIGR03787 marine_sort_RR proteobacterial dedicated sortase system response regulator

Probab=96.28  E-value=0.0059  Score=56.20  Aligned_cols=42  Identities=26%  Similarity=0.344  Sum_probs=38.2

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+.+..++..||.|||.||+..++|...++.++++.
T Consensus        80 ls~~~~~~~~~~~~~~Ga~~~l~kp~~~~~l~~~i~~~~~~~  121 (227)
T TIGR03787        80 LTARDSDFDTVSGLRLGADDYLTKDISLPHLLARITALFRRA  121 (227)
T ss_pred             EECCCCHHHHHHHHhcCCCEEEECCCCHHHHHHHHHHHHHhh
Confidence            467888899999999999999999999999999999988765

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.

>PRK10766 DNA-binding transcriptional regulator TorR; Provisional

Probab=96.26  E-value=0.0054  Score=56.23  Aligned_cols=42  Identities=21%  Similarity=0.263  Sum_probs=37.7

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ++++.+...+.+|+..||.|||.||+...+|...++.++++.
T Consensus        79 l~~~~~~~~~~~~l~~Ga~d~l~kP~~~~~L~~~i~~~~~r~  120 (221)
T PRK10766         79 VTGRTDSIDRIVGLEMGADDYVTKPLELRELLVRVKNLLWRI  120 (221)
T ss_pred             EECCCcHHHHHHHHHcCCCcEEeCCCCHHHHHHHHHHHHhhh
Confidence            356778888999999999999999999999999999988775

>PRK10336 DNA-binding transcriptional regulator QseB; Provisional

Probab=96.19  E-value=0.0061  Score=55.35  Aligned_cols=42  Identities=26%  Similarity=0.427  Sum_probs=37.6

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+.+.+++..||.|||+||+..++|...++.++++.
T Consensus        78 lt~~~~~~~~~~~~~~ga~~~i~kp~~~~~l~~~i~~~~~~~  119 (219)
T PRK10336         78 LTARDALAERVEGLRLGADDYLCKPFALIEVAARLEALMRRT  119 (219)
T ss_pred             EECCCCHHHHHHHHhCCCCeEEECCCCHHHHHHHHHHHHhcc
Confidence            467888899999999999999999999999999998887653

>PRK10161 transcriptional regulator PhoB; Provisional

Probab=96.15  E-value=0.0068  Score=56.03  Aligned_cols=41  Identities=27%  Similarity=0.425  Sum_probs=37.4

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR   41 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk   41 (491)
                      ||++.+...+.+|+..||.|||.||++.++|...++.++++
T Consensus        82 ls~~~~~~~~~~~~~~Ga~~~l~kp~~~~~L~~~i~~~~~~  122 (229)
T PRK10161         82 LTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRR  122 (229)
T ss_pred             EECCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHHhc
Confidence            46778889999999999999999999999999999988876

>PRK11173 two-component response regulator; Provisional

Probab=96.12  E-value=0.0066  Score=56.82  Aligned_cols=43  Identities=23%  Similarity=0.320  Sum_probs=37.9

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHh
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQS   43 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~   43 (491)
                      +|++.+......++..||.|||.||++..+|...++.++++..
T Consensus        80 lt~~~~~~~~~~~~~~ga~d~l~kP~~~~eL~~~i~~~l~r~~  122 (237)
T PRK11173         80 LTGRDNEVDKILGLEIGADDYITKPFNPRELTIRARNLLSRTM  122 (237)
T ss_pred             EECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHhccc
Confidence            3667788888999999999999999999999999998887753

>PRK09836 DNA-binding transcriptional activator CusR; Provisional

Probab=96.10  E-value=0.0071  Score=55.84  Aligned_cols=41  Identities=32%  Similarity=0.428  Sum_probs=37.1

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR   41 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk   41 (491)
                      +|++.+.+...+|+..||.|||.||++.++|...++.++++
T Consensus        78 ls~~~~~~~~~~~~~~Ga~~~l~kp~~~~~l~~~i~~~~~~  118 (227)
T PRK09836         78 LTALGTIEHRVKGLELGADDYLVKPFAFAELLARVRTLLRR  118 (227)
T ss_pred             EEcCCCHHHHHHHHhCCCCEEEeCCCCHHHHHHHHHHHHhc
Confidence            46778889999999999999999999999999999888765

>PRK10816 DNA-binding transcriptional regulator PhoP; Provisional

Probab=96.08  E-value=0.007  Score=55.70  Aligned_cols=41  Identities=27%  Similarity=0.439  Sum_probs=37.0

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR   41 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk   41 (491)
                      +|++.+.+...+++..||.|||.||++..+|...++.++++
T Consensus        78 ls~~~~~~~~~~~l~~Ga~d~l~kp~~~~eL~~~i~~~~~~  118 (223)
T PRK10816         78 LTARESWQDKVEVLSAGADDYVTKPFHIEEVMARMQALMRR  118 (223)
T ss_pred             EEcCCCHHHHHHHHHcCCCeeEeCCCCHHHHHHHHHHHHhc
Confidence            46778889999999999999999999999999999888765

>CHL00148 orf27 Ycf27; Reviewed

Probab=96.00  E-value=0.0091  Score=55.14  Aligned_cols=42  Identities=33%  Similarity=0.462  Sum_probs=37.3

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      +|++.+...+.+++..||.|||+||++.++|...++.++++.
T Consensus        83 ls~~~~~~~~~~~~~~Ga~~~l~kp~~~~~L~~~i~~~~~~~  124 (240)
T CHL00148         83 LTALGDVSDRITGLELGADDYVVKPFSPKELEARIRSVLRRT  124 (240)
T ss_pred             EECCCCHHhHHHHHHCCCCEEEeCCCCHHHHHHHHHHHHhhc
Confidence            467888899999999999999999999999999988877653

>PRK10430 DNA-binding transcriptional activator DcuR; Provisional

Probab=95.91  E-value=0.011  Score=56.43  Aligned_cols=42  Identities=21%  Similarity=0.421  Sum_probs=38.0

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+++.+++..||.+||.||+..++|...+..++.+.
T Consensus        83 ls~~~~~~~~~~al~~Ga~~yl~Kp~~~~~l~~~i~~~~~~~  124 (239)
T PRK10430         83 ISSAADAATIKDSLHYGVVDYLIKPFQASRFEEALTGWRQKK  124 (239)
T ss_pred             EECCCcHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHHHH
Confidence            578889999999999999999999999999999998876654

>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB

Probab=95.87  E-value=0.0096  Score=54.03  Aligned_cols=42  Identities=26%  Similarity=0.397  Sum_probs=37.3

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      +|++.+...+.+++..||.+||.||+..++|...++.++++.
T Consensus        82 ls~~~~~~~~~~~~~~Ga~~~l~kp~~~~~l~~~i~~~~~~~  123 (226)
T TIGR02154        82 LTARGEEEDRVRGLETGADDYITKPFSPRELLARIKAVLRRI  123 (226)
T ss_pred             EecCCCHHHHHHHHhcCcceEEeCCCCHHHHHHHHHHHhccc
Confidence            467788899999999999999999999999999998887653

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.

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=95.86  E-value=0.0089  Score=62.47  Aligned_cols=41  Identities=20%  Similarity=0.360  Sum_probs=37.3

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR   41 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk   41 (491)
                      ||++.+.+.+.+|++.||.|||+||++.++|...++++++.
T Consensus        79 lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~~~~  119 (445)
T TIGR02915        79 ITGNDDRENAVKAIGLGAYDFYQKPIDPDVLKLIVDRAFHL  119 (445)
T ss_pred             EecCCCHHHHHHHHHCCccEEEeCCCCHHHHHHHHhhhhhh
Confidence            57888999999999999999999999999999999887654

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).

>PF09425 CCT_2: Divergent CCT motif; InterPro: IPR018467 The short CCT (CO, COL, TOC1) motif is found in a number of plant proteins, including Constans (CO), Constans-like (COL) and TOC1

Probab=95.80  E-value=0.0049  Score=42.55  Aligned_cols=26  Identities=46%  Similarity=0.645  Sum_probs=10.0

Q ss_pred             HHHHHHHHHHHHHhhhccCCCCcccch
Q 011208          426 SIQREAALNKFRLKRKDRCYDKKVRYE  452 (491)
Q Consensus       426 ~~~R~~~l~ryr~Krk~R~f~KkirY~  452 (491)
                      +..|.+.|+||.||||.|... +..|.
T Consensus         1 P~aRK~SLqRFLeKRK~R~~~-~~PY~   26 (27)
T PF09425_consen    1 PIARKASLQRFLEKRKDRLAA-KSPYQ   26 (27)
T ss_dssp             -----HHHHHHHHHH------------
T ss_pred             CchHHHHHHHHHHHHHHhhcc-CCCCC
Confidence            357999999999999999987 77774

The CCT motif is about 45 amino acids long and contains a putative nuclear localisation signal within the second half of the CCT motif []. The CCT motif is found in the Arabidopsis circadian rhythm protein TOC1, an autoregulatory response regulator homologue the controls the photoperiodic flowering through its clock function []. ; GO: 0005515 protein binding; PDB: 3OGK_V 3OGL_S 3OGM_W.

>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional

Probab=95.79  E-value=0.011  Score=54.20  Aligned_cols=42  Identities=29%  Similarity=0.360  Sum_probs=37.1

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      +|++.+...+.+|+..||.+||.||++.++|...++.++++.
T Consensus        77 lt~~~~~~~~~~~~~~ga~~~l~kp~~~~~l~~~i~~~~~~~  118 (232)
T PRK10955         77 LTARGSELDRVLGLELGADDYLPKPFNDRELVARIRAILRRS  118 (232)
T ss_pred             EECCCCHHHHHHHHHcCCCEEEcCCCCHHHHHHHHHHHHhcc
Confidence            467788889999999999999999999999999998887653

>PRK10693 response regulator of RpoS; Provisional

Probab=95.78  E-value=0.011  Score=59.64  Aligned_cols=42  Identities=26%  Similarity=0.403  Sum_probs=37.3

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCC-CHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPV-RRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv-~~eELk~lwqhv~rk~   42 (491)
                      +|++.+.+.+.+|++.||.|||+||+ +.++|...++.+++..
T Consensus        51 lt~~~~~~~~~~al~~Ga~dyl~KP~~~~~~L~~~i~~~l~~~   93 (303)
T PRK10693         51 ISATENMADIAKALRLGVQDVLLKPVKDLNRLREMVFACLYPS   93 (303)
T ss_pred             EECCCCHHHHHHHHHCCCcEEEECCCCcHHHHHHHHHHHhhhh
Confidence            47888999999999999999999999 5999999998887654

>PRK09468 ompR osmolarity response regulator; Provisional

Probab=95.78  E-value=0.01  Score=55.32  Aligned_cols=42  Identities=31%  Similarity=0.374  Sum_probs=37.1

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      +|++.+.+...+++..||.|||.||++.++|...++.++++.
T Consensus        83 ls~~~~~~~~~~~l~~Ga~~~l~kP~~~~~L~~~i~~~~~r~  124 (239)
T PRK09468         83 LTAKGEEVDRIVGLEIGADDYLPKPFNPRELLARIRAVLRRQ  124 (239)
T ss_pred             EECCCcHHHHHHHHhcCCCeEEECCCCHHHHHHHHHHHhccc
Confidence            356778888999999999999999999999999999887763

>PRK10610 chemotaxis regulatory protein CheY; Provisional

Probab=95.76  E-value=0.018  Score=45.89  Aligned_cols=40  Identities=18%  Similarity=0.390  Sum_probs=35.3

Q ss_pred             CcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            3 SQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         3 ~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      .......+.+++..|+.+|+.||+..++|...++.+++++
T Consensus        88 ~~~~~~~~~~~~~~g~~~~i~~p~~~~~l~~~l~~~~~~~  127 (129)
T PRK10610         88 AEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEKL  127 (129)
T ss_pred             CCCCHHHHHHHHHhCCCeEEECCCCHHHHHHHHHHHHHHc
Confidence            3455677889999999999999999999999999998876

>PRK10360 DNA-binding transcriptional activator UhpA; Provisional

Probab=95.65  E-value=0.015  Score=52.25  Aligned_cols=40  Identities=28%  Similarity=0.288  Sum_probs=35.9

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWR   40 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~r   40 (491)
                      +|.+++.+.+..|+..||.+||.||+..++|...++.+.+
T Consensus        78 ~s~~~~~~~~~~~~~~ga~~~i~kp~~~~~l~~~i~~~~~  117 (196)
T PRK10360         78 LSVHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVAT  117 (196)
T ss_pred             EECCCCHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHc
Confidence            3677888999999999999999999999999999888765

>PRK11517 transcriptional regulatory protein YedW; Provisional

Probab=95.64  E-value=0.014  Score=53.33  Aligned_cols=42  Identities=33%  Similarity=0.462  Sum_probs=36.8

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+.+.+++..||.|||.||+..++|...++.++++.
T Consensus        77 ls~~~~~~~~~~a~~~Ga~~~l~kp~~~~~l~~~i~~~~~~~  118 (223)
T PRK11517         77 LTARDSVDDRVRGLDSGANDYLVKPFSFSELLARVRAQLRQH  118 (223)
T ss_pred             EECCCCHHHHHHHHhcCCCEEEECCCCHHHHHHHHHHHHccc
Confidence            466778899999999999999999999999999988877643

>TIGR01387 cztR_silR_copR heavy metal response regulator

Probab=95.58  E-value=0.015  Score=52.63  Aligned_cols=41  Identities=39%  Similarity=0.515  Sum_probs=36.3

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR   41 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk   41 (491)
                      ||++.+...+.+++..||.|||+||+..++|...++.++++
T Consensus        76 ls~~~~~~~~~~~~~~Ga~~~l~kp~~~~~l~~~i~~~~~~  116 (218)
T TIGR01387        76 LTARDSVADKVKGLDLGADDYLVKPFSFSELLARVRTLLRR  116 (218)
T ss_pred             EEcCCCHHHHHHHHHcCCCeEEECCCCHHHHHHHHHHHhcc
Confidence            46778889999999999999999999999999998887654

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.

>PRK11083 DNA-binding response regulator CreB; Provisional

Probab=95.54  E-value=0.013  Score=53.38  Aligned_cols=42  Identities=21%  Similarity=0.336  Sum_probs=36.6

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      +|++.+......|+..||.|||.||+...+|...++.++++.
T Consensus        81 ls~~~~~~~~~~a~~~Ga~~~l~kp~~~~~l~~~i~~~~~~~  122 (228)
T PRK11083         81 LTARSDEVDRLVGLEIGADDYVAKPFSPREVAARVRTILRRV  122 (228)
T ss_pred             EEcCCcHHHHHHHhhcCCCeEEECCCCHHHHHHHHHHHHCcc
Confidence            466778888999999999999999999999999988877654

>PRK09958 DNA-binding transcriptional activator EvgA; Provisional

Probab=95.47  E-value=0.018  Score=51.96  Aligned_cols=41  Identities=15%  Similarity=0.133  Sum_probs=36.4

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR   41 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk   41 (491)
                      +|++.+...+..++..||.+||+||+..++|...++.+++.
T Consensus        79 ls~~~~~~~~~~~~~~ga~~~i~kp~~~~~l~~~i~~~~~~  119 (204)
T PRK09958         79 VSAKNDHFYGKHCADAGANGFVSKKEGMNNIIAAIEAAKNG  119 (204)
T ss_pred             EeCCCCHHHHHHHHHCCCCEEEecCCCHHHHHHHHHHHHcC
Confidence            46677888999999999999999999999999999888653

>PRK10840 transcriptional regulator RcsB; Provisional

Probab=95.42  E-value=0.018  Score=53.85  Aligned_cols=39  Identities=5%  Similarity=0.056  Sum_probs=34.9

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVW   39 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~   39 (491)
                      +|.+.+..++.+|++.||.+||+||+..++|...++.+.
T Consensus        86 ls~~~~~~~~~~a~~~Ga~~yl~K~~~~~~l~~ai~~v~  124 (216)
T PRK10840         86 LTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQ  124 (216)
T ss_pred             EEecCCHHHHHHHHHCCCeEEEECCCCHHHHHHHHHHHH
Confidence            467888999999999999999999999999998887764

>TIGR02875 spore_0_A sporulation transcription factor Spo0A

Probab=95.34  E-value=0.019  Score=55.29  Aligned_cols=41  Identities=17%  Similarity=0.188  Sum_probs=36.6

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR   41 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk   41 (491)
                      +|++.......+++..||.+||+||++.++|...++++++.
T Consensus        84 lt~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~i~~~~~~  124 (262)
T TIGR02875        84 LSAFGQEKITQRAVALGADYYVLKPFDLEILAARIRQLAWG  124 (262)
T ss_pred             EeCCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHcc
Confidence            47788889999999999999999999999999998887653

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.

>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]

Probab=95.33  E-value=0.0069  Score=56.78  Aligned_cols=42  Identities=50%  Similarity=0.782  Sum_probs=39.9

Q ss_pred             CHHHHHHHHHHHHHhhhccCCCCcccchhhhhhhhhCCCCCc
Q 011208          425 RSIQREAALNKFRLKRKDRCYDKKVRYESRKKLAEQRPRVKG  466 (491)
Q Consensus       425 ~~~~R~~~l~ryr~Krk~R~f~KkirY~~RK~~A~~RpRvKG  466 (491)
                      ....|++.+.||+++++.|.|.++++|..|+..|+.|||++|
T Consensus       289 ~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  330 (340)
T KOG1601|consen  289 SSHQRVAEVRRYRESRDGRYFDKGIRYASRKSNAESRPRLKG  330 (340)
T ss_pred             ccchHHHHHhhccCccCCcccccccccccccccchhcccccc
Confidence            356799999999999999999999999999999999999999

>PRK10701 DNA-binding transcriptional regulator RstA; Provisional

Probab=95.31  E-value=0.022  Score=53.32  Aligned_cols=41  Identities=24%  Similarity=0.232  Sum_probs=35.6

Q ss_pred             CCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            2 SSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         2 S~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      +++.+.....+++..||.|||.||+...+|...+..++++.
T Consensus        79 ~~~~~~~~~~~~~~~Ga~d~l~kP~~~~~l~~~i~~~l~~~  119 (240)
T PRK10701         79 TSLDSDMNHILALEMGACDYILKTTPPAVLLARLRLHLRQN  119 (240)
T ss_pred             ECCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHHhcc
Confidence            55667777889999999999999999999999988877764

>PRK13856 two-component response regulator VirG; Provisional

Probab=95.28  E-value=0.023  Score=53.56  Aligned_cols=38  Identities=18%  Similarity=0.217  Sum_probs=33.3

Q ss_pred             chHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            5 DSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         5 d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      .+.....+++..||.|||+||++.++|...++.++++.
T Consensus        83 ~~~~~~~~~l~~Ga~~yl~kP~~~~eL~~~i~~~l~~~  120 (241)
T PRK13856         83 LEEADKVVALELGATDFIAKPFGTREFLARIRVALRVR  120 (241)
T ss_pred             CcHHHHHHHHhcCcCeEEeCCCCHHHHHHHHHHHHhhc
Confidence            35667789999999999999999999999998888764

>PRK09935 transcriptional regulator FimZ; Provisional

Probab=95.17  E-value=0.026  Score=50.74  Aligned_cols=41  Identities=17%  Similarity=0.203  Sum_probs=35.9

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR   41 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk   41 (491)
                      ||++.+...+.+++..||.+||.||+..++|...++.+++.
T Consensus        83 ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~l~~  123 (210)
T PRK09935         83 LSSKSECFYAGRAIQAGANGFVSKCNDQNDIFHAVQMILSG  123 (210)
T ss_pred             EECCCcHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHcC
Confidence            46777888999999999999999999999999998877553

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

Probab=95.10  E-value=0.029  Score=52.71  Aligned_cols=39  Identities=23%  Similarity=0.361  Sum_probs=33.1

Q ss_pred             CCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            2 SSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         2 S~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      |++.  +++..|+..||.|||+||+..++|...++++.++.
T Consensus        81 t~~~--~~~~~a~~~~~~~yl~KP~~~~~l~~~l~~~~~~~  119 (238)
T PRK11697         81 TAFD--EYAIKAFEEHAFDYLLKPIDPARLAKTLARLRQER  119 (238)
T ss_pred             eccH--HHHHHHHhcCCcEEEECCCCHHHHHHHHHHHHHhh
Confidence            4554  47789999999999999999999999999886543

>PRK15479 transcriptional regulatory protein TctD; Provisional

Probab=95.02  E-value=0.033  Score=50.45  Aligned_cols=42  Identities=31%  Similarity=0.466  Sum_probs=37.1

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+.+.+++..||.+||.||+..++|...++.++++.
T Consensus        78 lt~~~~~~~~~~~~~~g~~~~i~kp~~~~~l~~~i~~~~~~~  119 (221)
T PRK15479         78 LTARSAVADRVKGLNVGADDYLPKPFELEELDARLRALLRRS  119 (221)
T ss_pred             EECCCCHHHHHHHHHcCCCeeEeCCCCHHHHHHHHHHHHhhh
Confidence            456778888999999999999999999999999998887654

>PRK14084 two-component response regulator; Provisional

Probab=94.88  E-value=0.035  Score=52.64  Aligned_cols=39  Identities=21%  Similarity=0.386  Sum_probs=32.9

Q ss_pred             CCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            2 SSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         2 S~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      |++.  +++.+|+..||.+||+||+..++|...+++++++.
T Consensus        81 t~~~--~~~~~~~~~~~~~yl~KP~~~~~l~~~l~~~~~~~  119 (246)
T PRK14084         81 TAHD--QFAVKAFELNATDYILKPFEQKRIEQAVNKVRATK  119 (246)
T ss_pred             ecCh--HHHHHHHhcCCcEEEECCCCHHHHHHHHHHHHHhh
Confidence            4554  36789999999999999999999999999887554

>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional

Probab=94.58  E-value=0.046  Score=50.47  Aligned_cols=41  Identities=22%  Similarity=0.253  Sum_probs=35.8

Q ss_pred             CCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            2 SSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         2 S~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      +++.+......++..||.|||.||+..++|...++.++++.
T Consensus        88 ~~~~~~~~~~~~~~~ga~~~l~kp~~~~~L~~~i~~~~~~~  128 (240)
T PRK10710         88 TAKIEEIDRLLGLEIGADDYICKPYSPREVVARVKTILRRC  128 (240)
T ss_pred             EcCCCHHHHHHHHhcCCCeEEECCCCHHHHHHHHHHHHhhc
Confidence            55667788889999999999999999999999988887754

>PRK11475 DNA-binding transcriptional activator BglJ; Provisional

Probab=94.48  E-value=0.044  Score=53.01  Aligned_cols=40  Identities=10%  Similarity=0.013  Sum_probs=34.2

Q ss_pred             CCCcchHHHHHHHH-HhccceeEeCCCCHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCM-MRGAADYLVKPVRRNELRNLWQHVWR   40 (491)
Q Consensus         1 MS~~d~~e~v~kal-~~GA~DYLlKPv~~eELk~lwqhv~r   40 (491)
                      ||++++..++.+++ +.||.+||.||+..++|...++.|++
T Consensus        74 lt~~~~~~~~~~~~~~~Ga~gyl~K~~~~~eL~~aI~~v~~  114 (207)
T PRK11475         74 IADDDIEARLIGSLSPSPLDGVLSKASTLEILQQELFLSLN  114 (207)
T ss_pred             EeCCCCHHHHHHHHHHcCCeEEEecCCCHHHHHHHHHHHHC
Confidence            57888777777776 69999999999999999999888764

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=94.24  E-value=0.038  Score=57.46  Aligned_cols=42  Identities=29%  Similarity=0.480  Sum_probs=38.0

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+++.++++.||.|||+||+..++|...+++++++.
T Consensus        83 lt~~~~~~~~~~a~~~ga~~~l~Kp~~~~~L~~~l~~~l~~~  124 (441)
T PRK10365         83 MTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAHT  124 (441)
T ss_pred             EECCCCHHHHHHHHHhhhHHHhcCCCCHHHHHHHHHHHHHHH
Confidence            478889999999999999999999999999999999887654

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

Probab=94.24  E-value=0.057  Score=56.97  Aligned_cols=42  Identities=24%  Similarity=0.354  Sum_probs=37.9

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+.+..|++.||.|||.||+..++|...+++++...
T Consensus        81 lt~~~~~~~~~~a~~~Ga~~~l~KP~~~~~L~~~i~~~l~~~  122 (469)
T PRK10923         81 MTAHSDLDAAVSAYQQGAFDYLPKPFDIDEAVALVERAISHY  122 (469)
T ss_pred             EECCCCHHHHHHHHhcCcceEEecCCcHHHHHHHHHHHHHHH
Confidence            578889999999999999999999999999999999887643

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

Probab=94.19  E-value=0.062  Score=51.93  Aligned_cols=40  Identities=25%  Similarity=0.366  Sum_probs=36.6

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWR   40 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~r   40 (491)
                      +|.+++..++.+|++.||..||+|....++|...++.|..
T Consensus        80 lt~~~~~~~v~~al~~Ga~Gyl~K~~~~~~l~~ai~~v~~  119 (211)
T COG2197          80 LTAHDDPAYVIRALRAGADGYLLKDASPEELVEAIRAVAA  119 (211)
T ss_pred             EeccCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHC
Confidence            5789999999999999999999999999999988887753

>PRK09483 response regulator; Provisional

Probab=94.14  E-value=0.063  Score=48.93  Aligned_cols=40  Identities=25%  Similarity=0.266  Sum_probs=35.1

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWR   40 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~r   40 (491)
                      +|.+.+...+.+++..||.+||.||+..++|...++.+++
T Consensus        81 ls~~~~~~~~~~~~~~g~~~~l~k~~~~~~l~~~i~~~~~  120 (217)
T PRK09483         81 LTVHTENPLPAKVMQAGAAGYLSKGAAPQEVVSAIRSVHS  120 (217)
T ss_pred             EeCCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHC
Confidence            3567788889999999999999999999999988887754

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=93.98  E-value=0.047  Score=57.15  Aligned_cols=40  Identities=30%  Similarity=0.458  Sum_probs=36.0

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWR   40 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~r   40 (491)
                      +|++.+.+.+..|+..||.|||+||+..++|...+++++.
T Consensus        82 lt~~~~~~~~~~a~~~Ga~d~l~KP~~~~~L~~~i~~~l~  121 (457)
T PRK11361         82 MTAYAEVETAVEALRCGAFDYVIKPFDLDELNLIVQRALQ  121 (457)
T ss_pred             EeCCCCHHHHHHHHHCCccEEEecccCHHHHHHHHhhhcc
Confidence            4788899999999999999999999999999998887654

>PRK15115 response regulator GlrR; Provisional

Probab=93.97  E-value=0.05  Score=56.92  Aligned_cols=41  Identities=20%  Similarity=0.398  Sum_probs=37.5

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR   41 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk   41 (491)
                      ||++.+.+.+.+++..||.|||+||+..++|...++.+++.
T Consensus        83 lt~~~~~~~~~~a~~~Ga~~~l~KP~~~~~L~~~l~~~~~~  123 (444)
T PRK15115         83 LTAHGSIPDAVAATQQGVFSFLTKPVDRDALYKAIDDALEQ  123 (444)
T ss_pred             EECCCCHHHHHHHHhcChhhhccCCCCHHHHHHHHHHHHHh
Confidence            57888999999999999999999999999999999988764

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

Probab=93.66  E-value=0.1  Score=43.95  Aligned_cols=40  Identities=23%  Similarity=0.364  Sum_probs=32.3

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHH-HHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNE-LRNLWQHVWR   40 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eE-Lk~lwqhv~r   40 (491)
                      +|++.......+++..|+.+||.||+...+ |...+++.+.
T Consensus        85 ~t~~~~~~~~~~~~~~g~~~~l~kP~~~~~~l~~~i~~~~~  125 (130)
T COG0784          85 LTAYADEADRERALAAGADDYLTKPIFLEEELLAALRRLLA  125 (130)
T ss_pred             EEcCcCHHHHHHHHHcCCCeEEcCCCCcHHHHHHHHHHHHH
Confidence            467777777888999999999999987777 7777775543

>PRK09581 pleD response regulator PleD; Reviewed

Probab=93.65  E-value=0.098  Score=53.12  Aligned_cols=42  Identities=21%  Similarity=0.299  Sum_probs=36.5

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      +|+..+...+.+++..||.+||.||++.++|...+..+++..
T Consensus        82 ~s~~~~~~~~~~~~~~ga~~~l~kp~~~~~l~~~i~~~~~~~  123 (457)
T PRK09581         82 VTALDDPEDRVRGLEAGADDFLTKPINDVALFARVKSLTRLK  123 (457)
T ss_pred             EECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHH
Confidence            356778899999999999999999999999999888876543

>PRK10403 transcriptional regulator NarP; Provisional

Probab=93.65  E-value=0.09  Score=47.02  Aligned_cols=40  Identities=23%  Similarity=0.284  Sum_probs=34.8

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWR   40 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~r   40 (491)
                      |+.+.+...+..++..||.+||.||++.++|...++.+++
T Consensus        86 l~~~~~~~~~~~~~~~g~~~~i~kp~~~~~l~~~i~~~~~  125 (215)
T PRK10403         86 LTVSDASSDVFALIDAGADGYLLKDSDPEVLLEAIRAGAK  125 (215)
T ss_pred             EeCCCChHHHHHHHHcCCCeEEecCCCHHHHHHHHHHHhC
Confidence            3566778888999999999999999999999999888764

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=93.60  E-value=0.083  Score=55.50  Aligned_cols=41  Identities=27%  Similarity=0.412  Sum_probs=37.1

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR   41 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk   41 (491)
                      ||++.+...+.+|++.||.|||.||+..++|...+++++..
T Consensus        76 lt~~~~~~~~~~a~~~Ga~~~l~KP~~~~~L~~~i~~~l~~  116 (463)
T TIGR01818        76 MTAHSDLDTAVAAYQRGAFEYLPKPFDLDEAVTLVERALAH  116 (463)
T ss_pred             EeCCCCHHHHHHHHHcCcceeecCCCCHHHHHHHHHHHHHH
Confidence            47788899999999999999999999999999999887654

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.

>PRK15369 two component system sensor kinase SsrB; Provisional

Probab=93.52  E-value=0.11  Score=46.02  Aligned_cols=40  Identities=18%  Similarity=0.214  Sum_probs=35.0

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWR   40 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~r   40 (491)
                      ||++.+...+..++..||.+||.||+...+|...++.+++
T Consensus        83 ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~~~  122 (211)
T PRK15369         83 LTARQEEHMASRTLAAGALGYVLKKSPQQILLAAIQTVAV  122 (211)
T ss_pred             EeCCCCHHHHHHHHHhCCCEEEeCCCCHHHHHHHHHHHHC
Confidence            4667788899999999999999999999999988887654

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

Probab=93.48  E-value=0.059  Score=56.91  Aligned_cols=36  Identities=25%  Similarity=0.384  Sum_probs=33.6

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQ   36 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwq   36 (491)
                      +|++.+.+..++|+..||.|||.|||++.+|+..+.
T Consensus        95 lT~~~d~~~~~~~~~~g~~dyl~KP~~~~~l~~rv~  130 (360)
T COG3437          95 LTAYADSEDRQRALEAGADDYLSKPISPKELVARVS  130 (360)
T ss_pred             EeecCChHHHHHHHHhhHHHHhcCCCCHHHHHHHHH
Confidence            478999999999999999999999999999998884

>PRK13435 response regulator; Provisional

Probab=93.47  E-value=0.078  Score=46.08  Aligned_cols=34  Identities=15%  Similarity=0.138  Sum_probs=29.4

Q ss_pred             HHHHHhccceeEeCCCCHHHHHHHHHHHHHHHhc
Q 011208           11 YKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSS   44 (491)
Q Consensus        11 ~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~~   44 (491)
                      ..++..||.+||+||++.++|..++++++.+...
T Consensus        91 ~~~~~~ga~~~l~kp~~~~~l~~~i~~~~~~~~~  124 (145)
T PRK13435         91 VPHDFAGALGVIAKPYSPRGVARALSYLSARRVG  124 (145)
T ss_pred             HHHHhcCcceeEeCCCCHHHHHHHHHHHHhcCcc
Confidence            4678899999999999999999999999765543

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

Probab=93.26  E-value=0.096  Score=51.22  Aligned_cols=42  Identities=17%  Similarity=0.304  Sum_probs=37.2

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      +++|++.+++.+|+..||..|||||++..-|+-++.-+..+.
T Consensus        83 lt~~s~p~~i~~a~~~Gv~ayivkpi~~~rl~p~L~vA~srf  124 (194)
T COG3707          83 LTAYSDPALIEAAIEAGVMAYIVKPLDESRLLPILDVAVSRF  124 (194)
T ss_pred             EEccCChHHHHHHHHcCCeEEEecCcchhhhhHHHHHHHHHH
Confidence            478999999999999999999999999999998887765443

>PRK11107 hybrid sensory histidine kinase BarA; Provisional

Probab=93.02  E-value=0.087  Score=59.27  Aligned_cols=40  Identities=18%  Similarity=0.312  Sum_probs=36.0

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWR   40 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~r   40 (491)
                      ||++...+...+|+..||.|||.||++.++|...+.+++.
T Consensus       747 lt~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~~~  786 (919)
T PRK11107        747 VTAHAMAGERERLLSAGMDDYLAKPIDEAMLKQVLLRYKP  786 (919)
T ss_pred             EeCCCCHHHHHHHHHcCCCeEeeCCCCHHHHHHHHHHHcc
Confidence            5788999999999999999999999999999888877644

>PRK10651 transcriptional regulator NarL; Provisional

Probab=92.58  E-value=0.17  Score=45.49  Aligned_cols=39  Identities=26%  Similarity=0.350  Sum_probs=34.8

Q ss_pred             CCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHH
Q 011208            2 SSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWR   40 (491)
Q Consensus         2 S~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~r   40 (491)
                      ++..+...+..++..||.+||.||++..+|...++.+++
T Consensus        87 ~~~~~~~~~~~~~~~g~~~~i~k~~~~~~l~~~i~~~~~  125 (216)
T PRK10651         87 SVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALQQAAA  125 (216)
T ss_pred             eCCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHC
Confidence            566778889999999999999999999999999888765

>PRK15347 two component system sensor kinase SsrA; Provisional

Probab=92.43  E-value=0.15  Score=57.50  Aligned_cols=41  Identities=20%  Similarity=0.364  Sum_probs=36.9

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR   41 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk   41 (491)
                      ||++.+.+...+|+..||.|||.||++.++|...+..+++.
T Consensus       772 lt~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~~~~  812 (921)
T PRK15347        772 LTANAAPEEIHRCKKAGMNHYLTKPVTLAQLARALELAAEY  812 (921)
T ss_pred             EeCCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHhh
Confidence            57888899999999999999999999999999998887653

>PRK11466 hybrid sensory histidine kinase TorS; Provisional

Probab=91.78  E-value=0.17  Score=57.32  Aligned_cols=41  Identities=22%  Similarity=0.154  Sum_probs=36.9

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR   41 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk   41 (491)
                      ||++.....+.+++..|+.+||.||+..++|...+.++++.
T Consensus       760 ~t~~~~~~~~~~~~~~g~~~~l~KP~~~~~L~~~i~~~~~~  800 (914)
T PRK11466        760 FSAHVIDETLRQRTSSLFRGIIPKPVPREVLGQLLAHYLQL  800 (914)
T ss_pred             EeCCCchhhHHHHHhcCcCCEEeCCCCHHHHHHHHHHHhhh
Confidence            47788889999999999999999999999999999888753

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

Probab=91.67  E-value=0.2  Score=54.23  Aligned_cols=43  Identities=33%  Similarity=0.538  Sum_probs=35.2

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHh
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQS   43 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~   43 (491)
                      ||+-++.+.+-+|++.||.|||+|||...+|..=+...++++.
T Consensus       212 ~~~~~d~~~~~~Af~~G~~Dyi~kPi~~~~l~~Rl~~~l~~~~  254 (435)
T COG3706         212 LSSKDDDELVVRAFELGVNDYITKPIEEGELRARLRRQLRRKR  254 (435)
T ss_pred             EecccchHHHHHHHHcCCcceEecCCCHHHHHHHHHHHHHhhh
Confidence            4677889999999999999999999998888776555555443

>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=91.59  E-value=0.15  Score=38.19  Aligned_cols=36  Identities=25%  Similarity=0.383  Sum_probs=30.3

Q ss_pred             CcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHH
Q 011208            3 SQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHV   38 (491)
Q Consensus         3 ~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv   38 (491)
                      .........+++..|+.+|+.||+...+|...++++
T Consensus        77 ~~~~~~~~~~~~~~~~~~~i~~p~~~~~l~~~l~~~  112 (113)
T cd00156          77 AHGDDEDAVEALKAGADDYLTKPFSPEELLARIRAL  112 (113)
T ss_pred             ecccHHHHHHHHHcChhhHccCCCCHHHHHHHHHhh
Confidence            344567788999999999999999999998888754

>PRK09390 fixJ response regulator FixJ; Provisional

Probab=91.10  E-value=0.19  Score=44.14  Aligned_cols=40  Identities=20%  Similarity=0.346  Sum_probs=34.7

Q ss_pred             CCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHH
Q 011208            2 SSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR   41 (491)
Q Consensus         2 S~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk   41 (491)
                      ++..+.+.+.+++..||.+||.||+...+|...++.++..
T Consensus        82 ~~~~~~~~~~~~~~~g~~~~l~~p~~~~~l~~~l~~~~~~  121 (202)
T PRK09390         82 TGHGDVPLAVEAMKLGAVDFIEKPFEDERLIGAIERALAQ  121 (202)
T ss_pred             ECCCCHHHHHHHHHcChHHHhhCCCCHHHHHHHHHHHHHh
Confidence            5567788889999999999999999999998888877654

>TIGR02956 TMAO_torS TMAO reductase sytem sensor TorS

Probab=90.57  E-value=0.28  Score=55.81  Aligned_cols=40  Identities=20%  Similarity=0.291  Sum_probs=36.2

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWR   40 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~r   40 (491)
                      ||++...+...+|+..|+.+||.|||+.++|..++..++.
T Consensus       783 lta~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~~~  822 (968)
T TIGR02956       783 FSAHVFNEDVAQYLAAGFDGFLAKPVVEEQLTAMIAVILA  822 (968)
T ss_pred             EECCCCHHHHHHHHHCCCCEEEeCCCCHHHHHHHHHHHhc
Confidence            4778888999999999999999999999999999888764

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).

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

Probab=89.69  E-value=0.36  Score=56.70  Aligned_cols=40  Identities=15%  Similarity=0.225  Sum_probs=35.6

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWR   40 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~r   40 (491)
                      ||++.+...+.+|+..||.|||.||+..++|...++.+.+
T Consensus      1036 lt~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~~~ 1075 (1197)
T PRK09959       1036 LTANAQANEREKGLSCGMNLCLFKPLTLDVLKTHLSQLHQ 1075 (1197)
T ss_pred             EECCCCHHHHHHHHHCCCCEEEeCCCCHHHHHHHHHHHhh
Confidence            4788889999999999999999999999999988877643

>TIGR03815 CpaE_hom_Actino helicase/secretion neighborhood CpaE-like protein

Probab=87.93  E-value=0.59  Score=47.48  Aligned_cols=35  Identities=17%  Similarity=0.082  Sum_probs=31.6

Q ss_pred             cchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHH
Q 011208            4 QDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHV   38 (491)
Q Consensus         4 ~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv   38 (491)
                      ..+.+...+||+.||.|||.+|+...||..++..+
T Consensus        51 ~~~~~~~~~a~~~Ga~~~l~~P~~~~~l~~~l~~~   85 (322)
T TIGR03815        51 EPGGALWRAAAAVGAEHVAVLPEAEGWLVELLADL   85 (322)
T ss_pred             CCCHHHHHHHHHhChhheeeCCCCHHHHHHHHHhh
Confidence            45788999999999999999999999999888765

Members of this protein family belong to the MinD/ParA family of P-loop NTPases, and in particular show homology to the CpaE family of pilus assembly proteins (see PubMed:12370432). Nearly all members are found, not only in a gene context consistent with pilus biogenesis or a pilus-like secretion apparatus, but also near a DEAD/DEAH-box helicase, suggesting an involvement in DNA transfer activity. The model describes a clade restricted to the Actinobacteria.

>PRK12555 chemotaxis-specific methylesterase; Provisional

Probab=86.55  E-value=0.74  Score=46.91  Aligned_cols=21  Identities=33%  Similarity=0.482  Sum_probs=18.9

Q ss_pred             hHHHHHHHHHhccceeEeCCC
Q 011208            6 SVSTVYKCMMRGAADYLVKPV   26 (491)
Q Consensus         6 ~~e~v~kal~~GA~DYLlKPv   26 (491)
                      ..+.+.+|++.||.|||.||+
T Consensus        86 ~~~~~~~al~~Ga~d~l~KP~  106 (337)
T PRK12555         86 NASRVFEAMGAGALDAVDTPT  106 (337)
T ss_pred             CHHHHHHHHhcCceEEEECCC
Confidence            366788999999999999999

>PRK11091 aerobic respiration control sensor protein ArcB; Provisional

Probab=85.41  E-value=0.93  Score=50.89  Aligned_cols=38  Identities=18%  Similarity=0.324  Sum_probs=31.3

Q ss_pred             CCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHH
Q 011208            2 SSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWR   40 (491)
Q Consensus         2 S~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~r   40 (491)
                      |++.. ....+|+..|+.+||.||++.++|...+++++.
T Consensus       607 ta~~~-~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~~~  644 (779)
T PRK11091        607 TANVL-KDKKEYLDAGMDDVLSKPLSVPALTAMIKKFWD  644 (779)
T ss_pred             ECCch-HhHHHHHHCCCCEEEECCCCHHHHHHHHHHHhc
Confidence            44443 456789999999999999999999999888764

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

Probab=82.86  E-value=0.53  Score=49.26  Aligned_cols=43  Identities=23%  Similarity=0.293  Sum_probs=31.6

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHhcc
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSSM   45 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~~~   45 (491)
                      +|+|+++..  .+...-+.|||+|||..+.|...+....++....
T Consensus        78 Issh~eya~--dsf~~n~~dYl~KPvt~ekLnraIdr~~k~ve~~  120 (361)
T COG3947          78 ISSHAEYAD--DSFGMNLDDYLPKPVTPEKLNRAIDRRLKRVELT  120 (361)
T ss_pred             Eecchhhhh--hhcccchHhhccCCCCHHHHHHHHHHHhcccccc
Confidence            466665544  4445556999999999999999988877655444

>PRK12704 phosphodiesterase; Provisional

Probab=81.21  E-value=1.5  Score=48.62  Aligned_cols=42  Identities=14%  Similarity=0.145  Sum_probs=36.7

Q ss_pred             CCCcchHH--HHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVS--TVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e--~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||+++...  .+..+|..|+.||++||++++||....+.-+.+.
T Consensus       255 ls~~~~~rre~a~~~l~~l~~dg~i~P~~iee~~~~~~~~~~~~  298 (520)
T PRK12704        255 LSGFDPIRREIARLALEKLVQDGRIHPARIEEMVEKARKEVDEE  298 (520)
T ss_pred             EecCChhhHHHHHHHHHHHHhcCCcCCCCHHHHHHHHHHHHHHH
Confidence            68888887  9999999999999999999999998887765544

---

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	491
4dad_A	146	Putative pilus assembly-related protein; response	8e-05
3i42_A	127	Response regulator receiver domain protein (CHEY-	7e-04
1srr_A	124	SPO0F, sporulation response regulatory protein; as	7e-04

>4dad_A Putative pilus assembly-related protein; response regulator receiver domain, CHEY-related protein, ST genomics; 2.50A {Burkholderia pseudomallei} PDB: 4dn6_A Length = 146

 Score = 41.6 bits (98), Expect = 8e-05
 Identities = 8/43 (18%), Positives = 17/43 (39%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQS 43
           +++  S  T+   M  G  D L  P+    L +  +    + +
Sbjct: 101 VTTDASSQTLLDAMRAGVRDVLRWPLEPRALDDALKRAAAQCA 143

>3i42_A Response regulator receiver domain protein (CHEY- like); structural genomics, PSI-2, protein structure initiative; 2.15A {Methylobacillus flagellatus KT} Length = 127

 Score = 38.7 bits (91), Expect = 7e-04
 Identities = 7/32 (21%), Positives = 10/32 (31%)

Query: 12  KCMMRGAADYLVKPVRRNELRNLWQHVWRRQS 43
           K        YL KP+    L  + Q +     
Sbjct: 93  KEACELFDFYLEKPIDIASLEPILQSIEGHHH 124

>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 = 7e-04
 Identities = 8/44 (18%), Positives = 20/44 (45%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSS 44
           M++   +  + +    GA  +  KP   +E+R+  +     +S+
Sbjct: 81  MTAYGELDMIQESKELGALTHFAKPFDIDEIRDAVKKYLPLKSN 124

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	491
2pl1_A	121	Transcriptional regulatory protein PHOP; CHEY-like	97.62
3gl9_A	122	Response regulator; beta-sheet, surrounded by alph	97.59
1zgz_A	122	Torcad operon transcriptional regulatory protein;	97.58
3t6k_A	136	Response regulator receiver; flavodoxin-like, stru	97.58
1jbe_A	128	Chemotaxis protein CHEY; signaling protein; 1.08A	97.55
3h1g_A	129	Chemotaxis protein CHEY homolog; sulfate-bound CHE	97.55
3f6p_A	120	Transcriptional regulatory protein YYCF; unphospho	97.55
1xhf_A	123	DYE resistance, aerobic respiration control protei	97.54
1p6q_A	129	CHEY2; chemotaxis, signal transduction, response r	97.52
3cfy_A	137	Putative LUXO repressor protein; structural genomi	97.49
1zh2_A	121	KDP operon transcriptional regulatory protein KDPE	97.49
2r25_B	133	Osmosensing histidine protein kinase SLN1; alpha5-	97.49
3kto_A	136	Response regulator receiver protein; PSI-II,struct	97.48
2qzj_A	136	Two-component response regulator; 11017X, PSI-II,	97.48
3hdg_A	137	Uncharacterized protein; two-component sensor acti	97.46
3crn_A	132	Response regulator receiver domain protein, CHEY-;	97.46
1dbw_A	126	Transcriptional regulatory protein FIXJ; doubly wo	97.44
2a9o_A	120	Response regulator; essential protein, YYCF/YYCG h	97.43
3kht_A	144	Response regulator; PSI-II, 11023K, structural gen	97.43
3jte_A	143	Response regulator receiver protein; structural ge	97.41
1dcf_A	136	ETR1 protein; beta-alpha five sandwich, transferas	97.4
1k68_A	140	Phytochrome response regulator RCPA; phosphorylate	97.4
1dz3_A	130	Stage 0 sporulation protein A; response regulator,	97.39
1tmy_A	120	CHEY protein, TMY; chemotaxis, phosphoryl transfer	97.39
1qo0_D	196	AMIR; binding protein, gene regulator, receptor; 2	97.38
1i3c_A	149	Response regulator RCP1; phytochrome, signaling pr	97.36
3lua_A	140	Response regulator receiver protein; two-component	97.34
3b2n_A	133	Uncharacterized protein Q99UF4; structural genomic	97.34
3rqi_A	184	Response regulator protein; structural genomics, s	97.32
1k66_A	149	Phytochrome response regulator RCPB; CHEY homologu	97.32
3eod_A	130	Protein HNR; response regulator, phosphoprotein, t	97.31
3hv2_A	153	Response regulator/HD domain protein; PSI-2, NYSGX	97.3
2zay_A	147	Response regulator receiver protein; structural ge	97.29
3gt7_A	154	Sensor protein; structural genomics, signal receiv	97.29
1srr_A	124	SPO0F, sporulation response regulatory protein; as	97.24
3cnb_A	143	DNA-binding response regulator, MERR family; signa	97.23
3heb_A	152	Response regulator receiver domain protein (CHEY);	97.23
1mb3_A	124	Cell division response regulator DIVK; signal tran	97.2
3r0j_A	250	Possible two component system response transcript	97.2
4e7p_A	150	Response regulator; DNA binding, cytosol, transcri	97.2
3cg0_A	140	Response regulator receiver modulated diguanylate	97.18
3hdv_A	136	Response regulator; PSI-II, structural genomics, P	97.18
3cu5_A	141	Two component transcriptional regulator, ARAC FAM;	97.16
2jba_A	127	Phosphate regulon transcriptional regulatory PROT;	97.15
3m6m_D	143	Sensory/regulatory protein RPFC; RPFF, REC, enoyl-	97.13
1s8n_A	205	Putative antiterminator; RV1626, structural genomi	97.13
3eul_A	152	Possible nitrate/nitrite response transcriptional	97.12
1qkk_A	155	DCTD, C4-dicarboxylate transport transcriptional r	97.1
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	97.09
2qxy_A	142	Response regulator; regulation of transcription, N	97.09
1mvo_A	136	PHOP response regulator; phosphate regulon, transc	97.08
3f6c_A	134	Positive transcription regulator EVGA; structural	97.07
3kcn_A	151	Adenylate cyclase homolog; SGX, PSI 2, structural	97.06
3grc_A	140	Sensor protein, kinase; protein structure initiati	97.06
1a04_A	215	Nitrate/nitrite response regulator protein NARL; s	97.06
2qr3_A	140	Two-component system response regulator; structura	97.05
3h5i_A	140	Response regulator/sensory box protein/ggdef domai	97.01
3n53_A	140	Response regulator receiver modulated diguanylate;	97.01
1p2f_A	220	Response regulator; DRRB, OMPR/PHOB, transcription	96.97
3q9s_A	249	DNA-binding response regulator; DNA binding protei	96.95
1dc7_A	124	NTRC, nitrogen regulation protein; receiver domain	96.94
3bre_A	358	Probable two-component response regulator; protein	96.91
3i42_A	127	Response regulator receiver domain protein (CHEY-	96.91
1yio_A	208	Response regulatory protein; transcription regulat	96.89
2qvg_A	143	Two component response regulator; NYSGXRC, PSI-2,	96.88
3cz5_A	153	Two-component response regulator, LUXR family; str	96.86
2jk1_A	139	HUPR, hydrogenase transcriptional regulatory prote	96.86
2rjn_A	154	Response regulator receiver:metal-dependent phosph	96.85
3nhm_A	133	Response regulator; protein structure initiative I	96.85
2qsj_A	154	DNA-binding response regulator, LUXR family; struc	96.85
1kgs_A	225	DRRD, DNA binding response regulator D; DNA-bindin	96.82
3lte_A	132	Response regulator; structural genomics, PSI, prot	96.8
3eq2_A	394	Probable two-component response regulator; adaptor	96.79
2hqr_A	223	Putative transcriptional regulator; phosporylation	96.79
1w25_A	459	Stalked-cell differentiation controlling protein;	96.78
2qv0_A	143	Protein MRKE; structural genomics, transcription,	96.78
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	96.74
2oqr_A	230	Sensory transduction protein REGX3; response regul	96.65
3eqz_A	135	Response regulator; structural genomics, unknown f	96.65
3cg4_A	142	Response regulator receiver domain protein (CHEY-;	96.64
3c3w_A	225	Two component transcriptional regulatory protein;	96.45
3klo_A	225	Transcriptional regulator VPST; REC domain, HTH do	96.41
2gkg_A	127	Response regulator homolog; social motility, recei	96.4
1ys7_A	233	Transcriptional regulatory protein PRRA; response	96.38
2gwr_A	238	DNA-binding response regulator MTRA; two-component	96.03
3sy8_A	400	ROCR; TIM barrel phosphodiesterase-A, transcriptio	95.82
3kyj_B	145	CHEY6 protein, putative histidine protein kinase;	95.74
3c3m_A	138	Response regulator receiver protein; structural ge	95.47
2rdm_A	132	Response regulator receiver protein; structural ge	94.71
3a10_A	116	Response regulator; phosphoacceptor, signaling pro	94.6
3ogl_Q	21	JAZ1 incomplete degron peptide; leucine-rich repea	94.52
3luf_A	259	Two-component system response regulator/ggdef doma	94.51
2lpm_A	123	Two-component response regulator; transcription re	93.96
2j48_A	119	Two-component sensor kinase; pseudo-receiver, circ	93.61
1a2o_A	349	CHEB methylesterase; bacterial chemotaxis, adaptat	93.52
3t8y_A	164	CHEB, chemotaxis response regulator protein-glutam	93.47
2pln_A	137	HP1043, response regulator; signaling protein; 1.8	93.4
3c97_A	140	Signal transduction histidine kinase; structural g	92.67
3cwo_X	237	Beta/alpha-barrel protein based on 1THF and 1TMY;	92.09
3ogk_Q	22	JAZ1 incomplete degron peptide; leucine rich repea	91.54
1w25_A	459	Stalked-cell differentiation controlling protein;	88.95
2vyc_A	755	Biodegradative arginine decarboxylase; pyridoxal p	83.88
2b4a_A	138	BH3024; flavodoxin-like fold, structural genomics,	80.84

>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=97.62  E-value=6.3e-05  Score=60.61  Aligned_cols=42  Identities=26%  Similarity=0.434  Sum_probs=38.3

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+.+.+|+..||.|||.||++.++|...++.++++.
T Consensus        78 ~s~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~~~~~  119 (121)
T 2pl1_A           78 LTARESWQDKVEVLSAGADDYVTKPFHIEEVMARMQALMRRN  119 (121)
T ss_dssp             EESCCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHHHHH
T ss_pred             EecCCCHHHHHHHHHcCccceEECCCCHHHHHHHHHHHHHhh
Confidence            467888899999999999999999999999999999988764

>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=97.59  E-value=4.4e-05  Score=62.83  Aligned_cols=40  Identities=13%  Similarity=0.206  Sum_probs=36.7

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWR   40 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~r   40 (491)
                      ||++.+.+.+.+|++.||.+||.||++.++|...++.+++
T Consensus        82 ~s~~~~~~~~~~~~~~Ga~~~l~KP~~~~~L~~~i~~~l~  121 (122)
T 3gl9_A           82 LTAKGGEEDESLALSLGARKVMRKPFSPSQFIEEVKHLLN  121 (122)
T ss_dssp             EESCCSHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHHC
T ss_pred             EecCCchHHHHHHHhcChhhhccCCCCHHHHHHHHHHHhc
Confidence            5788899999999999999999999999999999988764

>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=97.58  E-value=7.1e-05  Score=60.57  Aligned_cols=42  Identities=21%  Similarity=0.260  Sum_probs=38.3

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+.+.+|++.||.+||.||++.++|...++.++++.
T Consensus        79 ~s~~~~~~~~~~~~~~ga~~~l~Kp~~~~~l~~~i~~~~~~~  120 (122)
T 1zgz_A           79 VTGRSDRIDRIVGLEMGADDYVTKPLELRELVVRVKNLLWRI  120 (122)
T ss_dssp             EESSCCHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHHHHH
T ss_pred             EECCCChhhHHHHHHhCHHHHccCCCCHHHHHHHHHHHHHHh
Confidence            467888899999999999999999999999999999988764

>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=97.58  E-value=4.6e-05  Score=63.89  Aligned_cols=42  Identities=29%  Similarity=0.428  Sum_probs=38.1

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+.+.+|+..||.|||.||++.++|...++.++++.
T Consensus        84 ~t~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~i~~~l~~~  125 (136)
T 3t6k_A           84 LTAQGDISAKIAGFEAGANDYLAKPFEPQELVYRVKNILART  125 (136)
T ss_dssp             EECTTCHHHHHHHHHHTCSEEEETTCCHHHHHHHHHHHHHC-
T ss_pred             EecCCCHHHHHHHHhcCcceEEeCCCCHHHHHHHHHHHHhcc
Confidence            578889999999999999999999999999999999987755

>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=97.55  E-value=8.3e-05  Score=60.68  Aligned_cols=42  Identities=17%  Similarity=0.396  Sum_probs=38.5

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+.+.+|++.||.+||.||++.++|...++.++++.
T Consensus        85 ~s~~~~~~~~~~~~~~ga~~~l~KP~~~~~l~~~i~~~~~~~  126 (128)
T 1jbe_A           85 VTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEKL  126 (128)
T ss_dssp             EESSCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHHHHH
T ss_pred             EecCccHHHHHHHHHhCcCceeecCCCHHHHHHHHHHHHHHh
Confidence            477888999999999999999999999999999999988764

>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=97.55  E-value=6.7e-05  Score=62.02  Aligned_cols=40  Identities=20%  Similarity=0.402  Sum_probs=36.6

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWR   40 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~r   40 (491)
                      ||++.+.+.+.+|++.||.+||.||++.++|...++.+++
T Consensus        87 ~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~L~~~l~~~l~  126 (129)
T 3h1g_A           87 ITAEGGKAEVITALKAGVNNYIVKPFTPQVLKEKLEVVLG  126 (129)
T ss_dssp             EESCCSHHHHHHHHHHTCCEEEESCCCHHHHHHHHHHHHC
T ss_pred             EeCCCChHHHHHHHHcCccEEEeCCCCHHHHHHHHHHHhc
Confidence            5788899999999999999999999999999999887754

>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=97.55  E-value=3.2e-05  Score=63.31  Aligned_cols=41  Identities=29%  Similarity=0.350  Sum_probs=36.8

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR   41 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk   41 (491)
                      ||++.+...+.+|+..||.|||.||++.++|...++.++++
T Consensus        79 ~t~~~~~~~~~~~~~~ga~~~l~KP~~~~~l~~~i~~~l~~  119 (120)
T 3f6p_A           79 LTAKDSEIDKVIGLEIGADDYVTKPFSTRELLARVKANLRR  119 (120)
T ss_dssp             EEESSCHHHHHHHHHTTCCEEEEESCCHHHHHHHHHHHHTC
T ss_pred             EECCCChHHHHHHHhCCcceeEcCCCCHHHHHHHHHHHHhc
Confidence            46788889999999999999999999999999998887653

>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=97.54  E-value=8.6e-05  Score=60.16  Aligned_cols=42  Identities=24%  Similarity=0.339  Sum_probs=38.0

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      +|++.+...+.+|++.||.+||.||++.++|...++.++++.
T Consensus        80 ~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~~~~  121 (123)
T 1xhf_A           80 LTGRDNEVDKILGLEIGADDYITKPFNPRELTIRARNLLSRT  121 (123)
T ss_dssp             EESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHHHHH
T ss_pred             EECCCChHHHHHHHhcCcceEEeCCCCHHHHHHHHHHHHHHh
Confidence            467788899999999999999999999999999999988764

>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=97.52  E-value=7.6e-05  Score=60.98  Aligned_cols=41  Identities=22%  Similarity=0.336  Sum_probs=37.8

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR   41 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk   41 (491)
                      ||++.+.+.+.+|++.||.+||.||++.++|...++.++++
T Consensus        87 ~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~~~  127 (129)
T 1p6q_A           87 LTAQGDRALVQKAAALGANNVLAKPFTIEKMKAAIEAVFGA  127 (129)
T ss_dssp             CCSCCCHHHHHHHHHHTCSCEECCCSSHHHHHHHHHHHHHC
T ss_pred             EeCCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHHHh
Confidence            58888999999999999999999999999999999988764

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

Probab=97.49  E-value=0.0001  Score=61.86  Aligned_cols=43  Identities=23%  Similarity=0.409  Sum_probs=38.6

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHh
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQS   43 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~   43 (491)
                      +|++.+.+.+.+|+..||.+||.||++.++|...++.++++..
T Consensus        82 ls~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~i~~~~~~~~  124 (137)
T 3cfy_A           82 ATAHGSVDLAVNLIQKGAEDFLEKPINADRLKTSVALHLKRAK  124 (137)
T ss_dssp             EESSCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHHHHHH
T ss_pred             EEecCcHHHHHHHHHCCccEEEeCCCCHHHHHHHHHHHHHHHH
Confidence            4678888999999999999999999999999999999887653

>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=97.49  E-value=0.00012  Score=58.84  Aligned_cols=42  Identities=31%  Similarity=0.422  Sum_probs=38.0

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+.+.+|++.||.+||.||++.++|...++.++++.
T Consensus        78 ~s~~~~~~~~~~~~~~g~~~~l~Kp~~~~~l~~~i~~~~~~~  119 (121)
T 1zh2_A           78 LSARSEESDKIAALDAGADDYLSKPFGIGELQARLRVALRRH  119 (121)
T ss_dssp             EESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHHHHH
T ss_pred             EECCCCHHHHHHHHhcCCCeEEeCCcCHHHHHHHHHHHHHhh
Confidence            467888899999999999999999999999999999987754

>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=97.49  E-value=8.5e-05  Score=62.02  Aligned_cols=40  Identities=20%  Similarity=0.507  Sum_probs=36.5

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWR   40 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~r   40 (491)
                      ||++.+.+.+.+|++.||.+||.||++.++|..+++.++.
T Consensus        87 lt~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~l~~~~~  126 (133)
T 2r25_B           87 LTAFADDSNIKECLESGMNGFLSKPIKRPKLKTILTEFCA  126 (133)
T ss_dssp             EESCCSHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHCT
T ss_pred             EECCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHH
Confidence            5788999999999999999999999999999999887654

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

Probab=97.48  E-value=9.9e-05  Score=61.51  Aligned_cols=44  Identities=25%  Similarity=0.337  Sum_probs=39.7

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHhc
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSS   44 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~~   44 (491)
                      ||++.+.+.+.+|++.||.+||.||++.++|...++.+++....
T Consensus        86 ~s~~~~~~~~~~~~~~ga~~~l~KP~~~~~l~~~i~~~~~~~~~  129 (136)
T 3kto_A           86 MASSSDIPTAVRAMRASAADFIEKPFIEHVLVHDVQQIINGAKE  129 (136)
T ss_dssp             EESSCCHHHHHHHHHTTCSEEEESSBCHHHHHHHHHHHHHHHC-
T ss_pred             EEcCCCHHHHHHHHHcChHHheeCCCCHHHHHHHHHHHHhccCC
Confidence            57888999999999999999999999999999999999877644

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

Probab=97.48  E-value=0.00011  Score=61.50  Aligned_cols=43  Identities=23%  Similarity=0.411  Sum_probs=38.7

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHh
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQS   43 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~   43 (491)
                      ||++.+.+.+.+|++.||.|||+||++.++|...++.++++..
T Consensus        81 ls~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~l~~~~~~~~  123 (136)
T 2qzj_A           81 MTYINEDQSILNALNSGGDDYLIKPLNLEILYAKVKAILRRMN  123 (136)
T ss_dssp             EESCCCHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHHHHHH
T ss_pred             EEcCCCHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHhh
Confidence            4678888999999999999999999999999999999887653

>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=97.46  E-value=0.00015  Score=59.93  Aligned_cols=45  Identities=16%  Similarity=0.206  Sum_probs=40.8

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHhcc
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSSM   45 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~~~   45 (491)
                      ||++.+.+.+.+|+..||.+||.||++.++|...++.+++.....
T Consensus        85 ~s~~~~~~~~~~~~~~g~~~~l~kP~~~~~l~~~i~~~~~~~~~~  129 (137)
T 3hdg_A           85 ISAFSEMKYFIKAIELGVHLFLPKPIEPGRLMETLEDFRHIKLAK  129 (137)
T ss_dssp             CCCCCCHHHHHHHHHHCCSEECCSSCCHHHHHHHHHHHHHHHHHH
T ss_pred             EecCcChHHHHHHHhCCcceeEcCCCCHHHHHHHHHHHHHHHhcC
Confidence            688899999999999999999999999999999999998776443

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

Probab=97.46  E-value=0.00013  Score=60.55  Aligned_cols=42  Identities=21%  Similarity=0.313  Sum_probs=38.2

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+.+.+|++.||.+||.||++.++|...++.+++..
T Consensus        81 ~s~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~i~~~~~~~  122 (132)
T 3crn_A           81 VTGYASLENSVFSLNAGADAYIMKPVNPRDLLEKIKEKLDEQ  122 (132)
T ss_dssp             EESCCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHHHHH
T ss_pred             EeccccHHHHHHHHhccchhhccCCCCHHHHHHHHHHHHhcc
Confidence            477888999999999999999999999999999999987654

>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=97.44  E-value=8.7e-05  Score=60.73  Aligned_cols=41  Identities=17%  Similarity=0.328  Sum_probs=37.1

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR   41 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk   41 (491)
                      ||++.+.+.+.+|++.||.+||.||++.++|...++.++++
T Consensus        81 ~s~~~~~~~~~~~~~~ga~~~l~Kp~~~~~l~~~i~~~~~~  121 (126)
T 1dbw_A           81 ITGHGDVPMAVEAMKAGAVDFIEKPFEDTVIIEAIERASEH  121 (126)
T ss_dssp             EECTTCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHHTT
T ss_pred             EECCCCHHHHHHHHHhCHHHheeCCCCHHHHHHHHHHHHHh
Confidence            47788899999999999999999999999999999887653

>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=97.43  E-value=0.00011  Score=58.97  Aligned_cols=41  Identities=32%  Similarity=0.416  Sum_probs=36.7

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR   41 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk   41 (491)
                      ||++.+...+.+|++.||.+||.||++.++|...++.++++
T Consensus        78 ~s~~~~~~~~~~~~~~g~~~~l~Kp~~~~~l~~~i~~~~~~  118 (120)
T 2a9o_A           78 LSAKDSEFDKVIGLELGADDYVTKPFSNRELQARVKALLRR  118 (120)
T ss_dssp             EESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHHHC
T ss_pred             EecCCchHHHHHHHhCCHhheEeCCCCHHHHHHHHHHHHcc
Confidence            46778888999999999999999999999999999887654

>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=97.43  E-value=0.00016  Score=60.46  Aligned_cols=45  Identities=13%  Similarity=0.193  Sum_probs=41.0

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCC-CHHHHHHHHHHHHHHHhcc
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPV-RRNELRNLWQHVWRRQSSM   45 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv-~~eELk~lwqhv~rk~~~~   45 (491)
                      ||++.+.+.+.+|+..||.+||.||+ ..++|...++.++++....
T Consensus        87 ~s~~~~~~~~~~~~~~ga~~~l~Kp~~~~~~l~~~i~~~l~~~~~~  132 (144)
T 3kht_A           87 LTDNVSDDRAKQCMAAGASSVVDKSSNNVTDFYGRIYAIFSYWLTV  132 (144)
T ss_dssp             EETTCCHHHHHHHHHTTCSEEEECCTTSHHHHHHHHHHHHHHHHHT
T ss_pred             EeCCCCHHHHHHHHHcCCCEEEECCCCcHHHHHHHHHHHHHHHHhc
Confidence            46788899999999999999999999 9999999999999887554

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

Probab=97.41  E-value=0.00016  Score=60.32  Aligned_cols=42  Identities=24%  Similarity=0.407  Sum_probs=38.6

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+.+.+|+..||.+||.||++.++|...++.++++.
T Consensus        83 ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~l~~~~~~~  124 (143)
T 3jte_A           83 LTGHGDLDNAILAMKEGAFEYLRKPVTAQDLSIAINNAINRK  124 (143)
T ss_dssp             EECTTCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHHHHH
T ss_pred             EECCCCHHHHHHHHHhCcceeEeCCCCHHHHHHHHHHHHHHH
Confidence            467888999999999999999999999999999999998765

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

Probab=97.40  E-value=0.00011  Score=60.80  Aligned_cols=40  Identities=30%  Similarity=0.478  Sum_probs=36.1

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWR   40 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~r   40 (491)
                      ||++.+.+.+.+|++.||.+||.||++.++|...++.+++
T Consensus        89 ~s~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~l~~~~~  128 (136)
T 1dcf_A           89 LSGNTDKSTKEKCMSFGLDGVLLKPVSLDNIRDVLSDLLE  128 (136)
T ss_dssp             EESCCSHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHHS
T ss_pred             EeCCCCHHHHHHHHHcCCCeEEECCCCHHHHHHHHHHHhc
Confidence            4778889999999999999999999999999999888764

>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=97.40  E-value=0.00017  Score=59.04  Aligned_cols=44  Identities=11%  Similarity=0.088  Sum_probs=39.8

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHhc
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSS   44 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~~   44 (491)
                      ||++.+.+.+.+|+..||.+||.||++.++|...+++++++...
T Consensus        91 ls~~~~~~~~~~~~~~g~~~~l~kP~~~~~l~~~i~~~~~~~~~  134 (140)
T 1k68_A           91 LSTSINEDDIFHSYDLHVNCYITKSANLSQLFQIVKGIEEFWLS  134 (140)
T ss_dssp             EESCCCHHHHHHHHHTTCSEEEECCSSHHHHHHHHHHHHHHHHT
T ss_pred             EecCCcHHHHHHHHHhchhheecCCCCHHHHHHHHHHHHHHHcc
Confidence            46778889999999999999999999999999999999887754

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

Probab=97.39  E-value=6e-05  Score=62.03  Aligned_cols=42  Identities=17%  Similarity=0.328  Sum_probs=37.5

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+.+.+|+..||.+||.||++.++|...++.++++.
T Consensus        83 ls~~~~~~~~~~~~~~ga~~~l~KP~~~~~l~~~i~~~~~~~  124 (130)
T 1dz3_A           83 LTAFGQEDVTKKAVELGASYFILKPFDMENLAHHIRQVYGKT  124 (130)
T ss_dssp             EEETTCHHHHHHHHHTTCEEEEECSSCCTTHHHHHHHHHHCC
T ss_pred             EecCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHhcCC
Confidence            467888999999999999999999999999999998887643

>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=97.39  E-value=0.00011  Score=59.25  Aligned_cols=39  Identities=23%  Similarity=0.370  Sum_probs=35.2

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVW   39 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~   39 (491)
                      ||++.+.+.+.+|++.||.+||.||++.++|...++.++
T Consensus        81 ~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~  119 (120)
T 1tmy_A           81 CSAMGQQAMVIEAIKAGAKDFIVKPFQPSRVVEALNKVS  119 (120)
T ss_dssp             EECTTCHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHC
T ss_pred             EeCCCCHHHHHHHHHhCcceeEeCCCCHHHHHHHHHHHh
Confidence            467888999999999999999999999999999887764

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

Probab=97.38  E-value=0.00013  Score=64.90  Aligned_cols=42  Identities=7%  Similarity=0.117  Sum_probs=38.4

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+++.+|+..||.|||+||++.++|...++.++++.
T Consensus        85 lt~~~~~~~~~~a~~~ga~~~l~KP~~~~~L~~~l~~~~~~~  126 (196)
T 1qo0_D           85 LVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRIS  126 (196)
T ss_dssp             EECCCSHHHHHHHHHHTCSEEEESSCCGGGHHHHHHHHHHHH
T ss_pred             EEcCCChHHHHHHHHcCCCeeEecCcCHHHHHHHHHHHHHHH
Confidence            578899999999999999999999999999999999887654

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

Probab=97.36  E-value=0.00018  Score=60.95  Aligned_cols=44  Identities=14%  Similarity=0.063  Sum_probs=39.3

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHhc
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSS   44 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~~   44 (491)
                      ||++.+.+.+.+|++.||.+||.||++.++|...++.+.+....
T Consensus        97 ls~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~i~~~~~~~~~  140 (149)
T 1i3c_A           97 LTTSHNEDDVIASYELHVNCYLTKSRNLKDLFKMVQGIESFWLE  140 (149)
T ss_dssp             EESCCCHHHHHHHHHTTCSEEEECCSSHHHHHHHHHHHHHHHTT
T ss_pred             EECCCChHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhh
Confidence            46778889999999999999999999999999999998776653

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

Probab=97.34  E-value=8.9e-05  Score=61.76  Aligned_cols=43  Identities=19%  Similarity=0.235  Sum_probs=38.0

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHh
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQS   43 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~   43 (491)
                      ||++.+.+.+.+|+..||.+||.||++.++|...++.++++..
T Consensus        87 ls~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~~~~~  129 (140)
T 3lua_A           87 ATKSDNPGYRHAALKFKVSDYILKPYPTKRLENSVRSVLKICQ  129 (140)
T ss_dssp             EESCCCHHHHHHHHHSCCSEEEESSCCTTHHHHHHHHHHCC--
T ss_pred             EeCCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHHHhcc
Confidence            4788899999999999999999999999999999999876653

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

Probab=97.34  E-value=0.00014  Score=60.41  Aligned_cols=42  Identities=14%  Similarity=0.154  Sum_probs=37.0

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+++.+|++.||.+||.||++.++|...++.+++..
T Consensus        83 ls~~~~~~~~~~~~~~ga~~~l~Kp~~~~~L~~~i~~~~~~~  124 (133)
T 3b2n_A           83 VTTFKRPGYFEKAVVNDVDAYVLKERSIEELVETINKVNNGE  124 (133)
T ss_dssp             EESCCCHHHHHHHHHTTCSEEEETTSCHHHHHHHHHHHHC--
T ss_pred             EecCCCHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHcCC
Confidence            477888999999999999999999999999999999887654

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

Probab=97.32  E-value=9.3e-05  Score=65.65  Aligned_cols=42  Identities=21%  Similarity=0.313  Sum_probs=38.8

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+++.+|+..||.|||+||++.++|...++.++++.
T Consensus        85 lt~~~~~~~~~~a~~~Ga~~~l~KP~~~~~L~~~i~~~~~~~  126 (184)
T 3rqi_A           85 LTGYASIATAVQAVKDGADNYLAKPANVESILAALQTNASEV  126 (184)
T ss_dssp             EESSCCHHHHHHHHHHTCSEEEESSCCHHHHHHHTSTTHHHH
T ss_pred             EeCCCCHHHHHHHHHhCHHHheeCCCCHHHHHHHHHHHHHHh
Confidence            588999999999999999999999999999999999887655

>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=97.32  E-value=0.00022  Score=59.06  Aligned_cols=44  Identities=18%  Similarity=0.305  Sum_probs=39.9

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHhc
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSS   44 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~~   44 (491)
                      ||++.+.+.+.+|+..||.+||.||++.++|...++.++++...
T Consensus        98 ~t~~~~~~~~~~~~~~g~~~~l~kP~~~~~l~~~i~~~~~~~~~  141 (149)
T 1k66_A           98 MTTSSNPKDIEICYSYSISSYIVKPLEIDRLTETVQTFIKYWLD  141 (149)
T ss_dssp             EESCCCHHHHHHHHHTTCSEEEECCSSHHHHHHHHHHHHHHHHT
T ss_pred             EeCCCCHHHHHHHHHCCCCEEEeCCCCHHHHHHHHHHHHHHhhh
Confidence            46788889999999999999999999999999999999887754

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

Probab=97.31  E-value=0.00012  Score=60.07  Aligned_cols=42  Identities=26%  Similarity=0.404  Sum_probs=35.2

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCC-CHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPV-RRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv-~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+.+.+|+..||.+||.||+ ..++|..+++.+++..
T Consensus        85 ~t~~~~~~~~~~~~~~g~~~~l~KP~~~~~~l~~~i~~~l~~~  127 (130)
T 3eod_A           85 ISATENMADIAKALRLGVEDVLLKPVKDLNRLREMVFACLYPS  127 (130)
T ss_dssp             EECCCCHHHHHHHHHHCCSEEEESCC---CHHHHHHHHHHC--
T ss_pred             EEcCCCHHHHHHHHHcCCCEEEeCCCCcHHHHHHHHHHHhchh
Confidence            47788899999999999999999999 9999999999988654

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

Probab=97.30  E-value=0.00027  Score=59.97  Aligned_cols=43  Identities=21%  Similarity=0.310  Sum_probs=39.5

Q ss_pred             CCCcchHHHHHHHHHhc-cceeEeCCCCHHHHHHHHHHHHHHHh
Q 011208            1 MSSQDSVSTVYKCMMRG-AADYLVKPVRRNELRNLWQHVWRRQS   43 (491)
Q Consensus         1 MS~~d~~e~v~kal~~G-A~DYLlKPv~~eELk~lwqhv~rk~~   43 (491)
                      ||++.+.+.+.+|+..| |.+||.||+..++|...++.++++..
T Consensus        92 ~s~~~~~~~~~~~~~~g~~~~~l~KP~~~~~l~~~i~~~l~~~~  135 (153)
T 3hv2_A           92 LTGDPDLKLIAKAINEGEIYRYLSKPWDDQELLLALRQALEHQH  135 (153)
T ss_dssp             ECCCCCHHHHHHHHHTTCCSEEECSSCCHHHHHHHHHHHHHHHH
T ss_pred             EECCCCHHHHHHHHhCCCcceEEeCCCCHHHHHHHHHHHHHHhH
Confidence            57889999999999999 99999999999999999999987663

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

Probab=97.29  E-value=0.00025  Score=59.28  Aligned_cols=44  Identities=18%  Similarity=0.240  Sum_probs=39.2

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHhc
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSS   44 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~~   44 (491)
                      ||++.+.+.+.+|+..||.+||.||++.++|...++.++++...
T Consensus        88 ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~L~~~i~~~~~~~~~  131 (147)
T 2zay_A           88 LSGRATAKEEAQLLDMGFIDFIAKPVNAIRLSARIKRVLKLLYE  131 (147)
T ss_dssp             EESSCCHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHHHHHC-
T ss_pred             EeCCCCHHHHHHHHhCCCCEEEeCCCCHHHHHHHHHHHHHHHHh
Confidence            46788899999999999999999999999999999999877643

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

Probab=97.29  E-value=0.00023  Score=60.84  Aligned_cols=43  Identities=16%  Similarity=0.268  Sum_probs=39.2

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHh
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQS   43 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~   43 (491)
                      ||++.+.+.+.+|+..||.+||.||++.++|...++.++++..
T Consensus        87 ~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~l~~~~  129 (154)
T 3gt7_A           87 LTILSDPRDVVRSLECGADDFITKPCKDVVLASHVKRLLSGVK  129 (154)
T ss_dssp             EECCCSHHHHHHHHHHCCSEEEESSCCHHHHHHHHHHHHHHTC
T ss_pred             EECCCChHHHHHHHHCCCCEEEeCCCCHHHHHHHHHHHHHHHH
Confidence            4678889999999999999999999999999999999987764

>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=97.24  E-value=0.00016  Score=58.82  Aligned_cols=39  Identities=18%  Similarity=0.277  Sum_probs=35.4

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVW   39 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~   39 (491)
                      ||++.+.+.+.+|+..||.+||.||++.++|...++.++
T Consensus        81 ~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~  119 (124)
T 1srr_A           81 MTAYGELDMIQESKELGALTHFAKPFDIDEIRDAVKKYL  119 (124)
T ss_dssp             EESSCCHHHHHHHHHHTCCCEEESSCCHHHHHHHHHHHS
T ss_pred             EEccCchHHHHHHHhcChHhhccCCCCHHHHHHHHHHHh
Confidence            477888999999999999999999999999999887764

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

Probab=97.23  E-value=0.00026  Score=58.41  Aligned_cols=43  Identities=16%  Similarity=0.200  Sum_probs=38.6

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHh
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQS   43 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~   43 (491)
                      ||++.+.+.+.+|+..||.+||.||++.++|...++.++++..
T Consensus        90 ~s~~~~~~~~~~~~~~g~~~~l~kP~~~~~l~~~i~~~~~~~~  132 (143)
T 3cnb_A           90 MTGALTDDNVSRIVALGAETCFGKPLNFTLLEKTIKQLVEQKK  132 (143)
T ss_dssp             EESSCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHHHTTC
T ss_pred             EeCCCCHHHHHHHHhcCCcEEEeCCCCHHHHHHHHHHHHHhhc
Confidence            4677888999999999999999999999999999999887653

>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=97.23  E-value=0.00041  Score=58.69  Aligned_cols=43  Identities=23%  Similarity=0.367  Sum_probs=38.6

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHh
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQS   43 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~   43 (491)
                      ||++.+.+.+.+|+..||.+||.||++.++|...++.+.+...
T Consensus        95 ~t~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~~~~~  137 (152)
T 3heb_A           95 LTTTDDQREIQRCYDLGANVYITKPVNYENFANAIRQLGLFFS  137 (152)
T ss_dssp             EESCCCHHHHHHHHHTTCSEEEECCSSHHHHHHHHHHHHHHHT
T ss_pred             EecCCCHHHHHHHHHCCCcEEEeCCCCHHHHHHHHHHHHHHHH
Confidence            4778889999999999999999999999999999999866553

>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=97.20  E-value=0.00014  Score=58.80  Aligned_cols=40  Identities=10%  Similarity=0.155  Sum_probs=30.7

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWR   40 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~r   40 (491)
                      ||++.+.+.+.++++.||.+||.||++.++|...++.+++
T Consensus        81 ~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~~  120 (124)
T 1mb3_A           81 VTAFAMKGDEERIREGGCEAYISKPISVVHFLETIKRLLE  120 (124)
T ss_dssp             EC------CHHHHHHHTCSEEECSSCCHHHHHHHHHHHHS
T ss_pred             EECCCCHHHHHHHHhCCCCEEEeCCCCHHHHHHHHHHHHh
Confidence            4777888889999999999999999999999999887764

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

Probab=97.20  E-value=0.00025  Score=65.81  Aligned_cols=43  Identities=23%  Similarity=0.414  Sum_probs=39.8

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHh
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQS   43 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~   43 (491)
                      ||++++.+++.+|+..||.|||+||++.++|...++.++++..
T Consensus       101 lt~~~~~~~~~~~~~~Ga~~yl~Kp~~~~~L~~~i~~~~~~~~  143 (250)
T 3r0j_A          101 LTARDSLQDKIAGLTLGGDDYVTKPFSLEEVVARLRVILRRAG  143 (250)
T ss_dssp             EECSTTHHHHHHHHTSTTCEEEESSCCHHHHHHHHHHHHHHHC
T ss_pred             EECCCCHHHHHHHHHcCCcEEEeCCCCHHHHHHHHHHHHHhhc
Confidence            5788999999999999999999999999999999999988753

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

Probab=97.20  E-value=0.00022  Score=60.32  Aligned_cols=42  Identities=12%  Similarity=0.197  Sum_probs=38.0

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+.+.+|++.||.+||.||+..++|...++.+++..
T Consensus       100 ls~~~~~~~~~~~~~~g~~~~l~Kp~~~~~l~~~i~~~~~~~  141 (150)
T 4e7p_A          100 VTTFKRAGYFERAVKAGVDAYVLKERSIADLMQTLHTVLEGR  141 (150)
T ss_dssp             EESCCCHHHHHHHHHTTCSEEEETTSCHHHHHHHHHHHHTTC
T ss_pred             EeCCCCHHHHHHHHHCCCcEEEecCCCHHHHHHHHHHHHcCC
Confidence            477889999999999999999999999999999999887653

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

Probab=97.18  E-value=0.00028  Score=58.18  Aligned_cols=44  Identities=20%  Similarity=0.292  Sum_probs=39.4

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHhc
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSS   44 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~~   44 (491)
                      ||++.+.+.+.+++..||.+||.||++.++|...++.+++....
T Consensus        88 ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~~~~~~~  131 (140)
T 3cg0_A           88 ITSSQDVETFQRAKRVNPFGYLAKPVAADTLHRSIEMAIHKKKL  131 (140)
T ss_dssp             EECCCCHHHHHHHHTTCCSEEEEESCCHHHHHHHHHHHHHHHHH
T ss_pred             EecCCCHHHHHHHHhcCCCEEEeCCCCHHHHHHHHHHHHhcccc
Confidence            46778889999999999999999999999999999999876643

>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=97.18  E-value=0.00034  Score=57.71  Aligned_cols=42  Identities=26%  Similarity=0.376  Sum_probs=36.5

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+.+.+|+..||.+||.||+..++|...++.++...
T Consensus        87 ~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~~~~  128 (136)
T 3hdv_A           87 VSGDTDVEEAVDVMHLGVVDFLLKPVDLGKLLELVNKELKIG  128 (136)
T ss_dssp             EESSCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHHC--
T ss_pred             EeCCCChHHHHHHHhCCcceEEeCCCCHHHHHHHHHHHhcCc
Confidence            467888999999999999999999999999999998876544

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

Probab=97.16  E-value=0.00012  Score=61.65  Aligned_cols=43  Identities=16%  Similarity=0.193  Sum_probs=32.6

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHh
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQS   43 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~   43 (491)
                      ||++.+.+++.+|++.||.+||.||++.++|...++.++++..
T Consensus        83 ls~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~i~~~~~~~~  125 (141)
T 3cu5_A           83 MSGYSDKEYLKAAIKFRAIRYVEKPIDPSEIMDALKQSIQTVL  125 (141)
T ss_dssp             ECCSTTTCCC------CCCEEECSSCCHHHHHHHHHHHHHHHH
T ss_pred             EeCCCcHHHHHHHHhCCccEEEeCCCCHHHHHHHHHHHHHHHH
Confidence            4777888889999999999999999999999999999887664

>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=97.15  E-value=8.9e-05  Score=60.21  Aligned_cols=42  Identities=24%  Similarity=0.334  Sum_probs=37.5

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+.+.+|++.||.+||.||++.++|...++.++++.
T Consensus        82 ~s~~~~~~~~~~~~~~ga~~~l~Kp~~~~~l~~~i~~~~~~~  123 (127)
T 2jba_A           82 LTARGEEEDRVRGLETGADDCITKPFSPKELVARIKAVMRRI  123 (127)
T ss_dssp             EEETTHHHHHHTTCCCSCSEEEEESCCHHHHHHHHHHHHHCC
T ss_pred             EeCCCCHHHHHHHHhcCCCeEEeCCCCHHHHHHHHHHHHhcc
Confidence            467788899999999999999999999999999999887653

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

Probab=97.13  E-value=0.00037  Score=59.00  Aligned_cols=40  Identities=23%  Similarity=0.348  Sum_probs=35.3

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWR   40 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~r   40 (491)
                      +|++.+.+.+.+|++.||.+||.||+..++|...+..+..
T Consensus        96 ~s~~~~~~~~~~~~~~Ga~~~l~KP~~~~~L~~~l~~~~~  135 (143)
T 3m6m_D           96 LSADVTPEAIRACEQAGARAFLAKPVVAAKLLDTLADLAV  135 (143)
T ss_dssp             EESCCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHC-
T ss_pred             EeCCCCHHHHHHHHHcChhheeeCCCCHHHHHHHHHHHHH
Confidence            4678889999999999999999999999999998877644

>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=97.13  E-value=0.00017  Score=64.54  Aligned_cols=42  Identities=24%  Similarity=0.250  Sum_probs=38.7

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+++.+|+..||.|||.||++.++|...++.++++.
T Consensus        91 lt~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~i~~~~~~~  132 (205)
T 1s8n_A           91 LTAFSQRDLVERARDAGAMAYLVKPFSISDLIPAIELAVSRF  132 (205)
T ss_dssp             EEEGGGHHHHHTTGGGSCEEEEEESCCHHHHHHHHHHHHHHH
T ss_pred             EecCCCHHHHHHHHhcCCcEEEeCCCCHHHHHHHHHHHHHHH
Confidence            478889999999999999999999999999999999987665

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

Probab=97.12  E-value=0.00043  Score=58.55  Aligned_cols=42  Identities=26%  Similarity=0.444  Sum_probs=38.2

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+.+.+|++.||.+||.||+..++|...++.++++.
T Consensus        95 ~s~~~~~~~~~~~~~~g~~~~l~Kp~~~~~l~~~i~~~~~~~  136 (152)
T 3eul_A           95 ISAHDEPAIVYQALQQGAAGFLLKDSTRTEIVKAVLDCAKGR  136 (152)
T ss_dssp             EESCCCHHHHHHHHHTTCSEEEETTCCHHHHHHHHHHHHHCC
T ss_pred             EEccCCHHHHHHHHHcCCCEEEecCCCHHHHHHHHHHHHcCC
Confidence            478889999999999999999999999999999999887654

>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=97.10  E-value=0.00053  Score=58.18  Aligned_cols=42  Identities=14%  Similarity=0.332  Sum_probs=38.2

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+.+.+|+..||.+||.||++.++|...++.++++.
T Consensus        81 ls~~~~~~~~~~~~~~g~~~~l~kP~~~~~L~~~i~~~~~~~  122 (155)
T 1qkk_A           81 VTGHGDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRAEEKR  122 (155)
T ss_dssp             EECGGGHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHHHHH
T ss_pred             EECCCChHHHHHHHhcCCCeEEeCCCCHHHHHHHHHHHHHHH
Confidence            467888999999999999999999999999999999987654

>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=97.09  E-value=0.00031  Score=71.01  Aligned_cols=43  Identities=26%  Similarity=0.417  Sum_probs=39.9

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHh
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQS   43 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~   43 (491)
                      ||++.+.+++.+|++.||.|||.||++.++|...+++++++..
T Consensus        78 lT~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~i~~~l~~~~  120 (368)
T 3dzd_A           78 ITGHGSVDTAVKAIKKGAYEFLEKPFSVERFLLTIKHAFEEYS  120 (368)
T ss_dssp             EECSSCCHHHHHHHHHTCCEEEESSCCHHHHHHHHHHHHHHHS
T ss_pred             EeCCCCHHHHHHHHhcCcceEEeCCCCHHHHHHHHHHHHHHhh
Confidence            6899999999999999999999999999999999999987653

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

Probab=97.09  E-value=0.00047  Score=57.30  Aligned_cols=42  Identities=21%  Similarity=0.338  Sum_probs=37.5

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+.+.+|+..||.+||.||++.++|...++.++++.
T Consensus        81 ls~~~~~~~~~~~~~~g~~~~l~kP~~~~~l~~~i~~~~~~~  122 (142)
T 2qxy_A           81 LSAYVDKDLIINSVKAGAVDYILKPFRLDYLLERVKKIISST  122 (142)
T ss_dssp             EESCCCHHHHHHHHHHTCSCEEESSCCHHHHHHHHHHHHHC-
T ss_pred             EECCCCHHHHHHHHHCCcceeEeCCCCHHHHHHHHHHHHhhc
Confidence            467788999999999999999999999999999999987654

>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=97.08  E-value=0.00019  Score=59.12  Aligned_cols=42  Identities=24%  Similarity=0.368  Sum_probs=36.5

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+...+.+|++.||.+||.||++.++|...++.++++.
T Consensus        81 ~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~~~~  122 (136)
T 1mvo_A           81 LTAKDEEFDKVLGLELGADDYMTKPFSPREVNARVKAILRRS  122 (136)
T ss_dssp             EECTTCCCCHHHHHHTTCCEEEESSCCHHHHHHHHHHHHHTC
T ss_pred             EECCCCHHHHHHHHhCCCCEEEECCCCHHHHHHHHHHHHHhh
Confidence            356677778889999999999999999999999999887654

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

Probab=97.07  E-value=0.00015  Score=59.49  Aligned_cols=42  Identities=14%  Similarity=0.117  Sum_probs=35.1

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+.+.+|++.||.+||.||+..++|...++.++++.
T Consensus        80 ~s~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~~~~~  121 (134)
T 3f6c_A           80 VSAKNDHFYGKHCADAGANGFVSKKEGMNNIIAAIEAAKNGY  121 (134)
T ss_dssp             EECC---CTHHHHHHTTCSEEEEGGGCTHHHHHHHHHHHTTC
T ss_pred             EeCCCChHHHHHHHHhCCCEEEeCCCCHHHHHHHHHHHHCCC
Confidence            467788889999999999999999999999999999987654

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

Probab=97.06  E-value=0.00061  Score=57.67  Aligned_cols=42  Identities=12%  Similarity=0.309  Sum_probs=38.2

Q ss_pred             CCCcchHHHHHHHHHhc-cceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRG-AADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~G-A~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+.+.+|+..| |.+||.||++.++|...++.++++.
T Consensus        82 ~s~~~~~~~~~~~~~~g~~~~~l~KP~~~~~L~~~i~~~l~~~  124 (151)
T 3kcn_A           82 LTGNQDLTTAMEAVNEGQVFRFLNKPCQMSDIKAAINAGIKQY  124 (151)
T ss_dssp             EECGGGHHHHHHHHHHTCCSEEEESSCCHHHHHHHHHHHHHHH
T ss_pred             EECCCCHHHHHHHHHcCCeeEEEcCCCCHHHHHHHHHHHHHHH
Confidence            46788899999999999 9999999999999999999987665

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

Probab=97.06  E-value=0.00025  Score=58.88  Aligned_cols=45  Identities=13%  Similarity=0.102  Sum_probs=38.2

Q ss_pred             CCCcchHHHHH-HHHHhccceeEeCCCCHHHHHHHHHHHHHHHhcc
Q 011208            1 MSSQDSVSTVY-KCMMRGAADYLVKPVRRNELRNLWQHVWRRQSSM   45 (491)
Q Consensus         1 MS~~d~~e~v~-kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~~~   45 (491)
                      ||++.+.+.+. +|+..||.+||.||++.++|...++.++++....
T Consensus        86 ~s~~~~~~~~~~~~~~~g~~~~l~kP~~~~~l~~~i~~~l~~~~~~  131 (140)
T 3grc_A           86 VSANAREGELEFNSQPLAVSTWLEKPIDENLLILSLHRAIDNMAEG  131 (140)
T ss_dssp             ECTTHHHHHHHHCCTTTCCCEEECSSCCHHHHHHHHHHHHHHHC--
T ss_pred             EecCCChHHHHHHhhhcCCCEEEeCCCCHHHHHHHHHHHHHhcCCC
Confidence            46777777777 8999999999999999999999999998887544

>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=97.06  E-value=0.00048  Score=61.90  Aligned_cols=41  Identities=22%  Similarity=0.326  Sum_probs=37.8

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR   41 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk   41 (491)
                      ||++++.+++.+|+..||.+||.||++.++|...++.+++.
T Consensus        85 ls~~~~~~~~~~~~~~Ga~~~l~Kp~~~~~L~~~i~~~~~~  125 (215)
T 1a04_A           85 FSVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALHQAAAG  125 (215)
T ss_dssp             EECCCCHHHHHHHHHTTCSEEEETTCCHHHHHHHHHHHHHS
T ss_pred             EECCCCHHHHHHHHHcCCcEEEeCCCCHHHHHHHHHHHHcC
Confidence            47888999999999999999999999999999999988764

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

Probab=97.05  E-value=0.00036  Score=57.52  Aligned_cols=42  Identities=17%  Similarity=0.313  Sum_probs=37.6

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+.+.+|++.||.+||.||++.++|...+++++++.
T Consensus        86 ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~l~~~~~~~  127 (140)
T 2qr3_A           86 FTAYADIDLAVRGIKEGASDFVVKPWDNQKLLETLLNAASQA  127 (140)
T ss_dssp             EEEGGGHHHHHHHHHTTCCEEEEESCCHHHHHHHHHHHHTCC
T ss_pred             EECCCCHHHHHHHHHcCchheeeCCCCHHHHHHHHHHHHHhc
Confidence            467788899999999999999999999999999999887654

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

Probab=97.01  E-value=8.6e-05  Score=62.20  Aligned_cols=44  Identities=16%  Similarity=0.162  Sum_probs=38.3

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHhc
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSS   44 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~~   44 (491)
                      ||++.+.+.+.+|+..||.+||.||+..++|...++.++++...
T Consensus        84 ls~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~l~~~~~  127 (140)
T 3h5i_A           84 LTAHTEPAVVEKIRSVTAYGYVMKSATEQVLITIVEMALRLYEA  127 (140)
T ss_dssp             EESSSSCCCCGGGGGSCEEEEEETTCCHHHHHHHHHHHHHHHHH
T ss_pred             EECCCCHHHHHHHHhCCCcEEEeCCCCHHHHHHHHHHHHHHHHh
Confidence            46677777888999999999999999999999999999877643

>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=97.01  E-value=0.00014  Score=60.49  Aligned_cols=42  Identities=31%  Similarity=0.449  Sum_probs=34.5

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+.+.+|+..||.+||.||++.++|...++.++++.
T Consensus        82 ~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~~~~  123 (140)
T 3n53_A           82 LFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQ  123 (140)
T ss_dssp             EECC----CTTTTTTCCCSEEEESSCCHHHHHHHHHHHHHHH
T ss_pred             EecCCCHHHHHHHHhcCCCeeeeCCCCHHHHHHHHHHHHhhH
Confidence            467778888899999999999999999999999999998766

>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=96.97  E-value=0.0007  Score=61.03  Aligned_cols=42  Identities=24%  Similarity=0.323  Sum_probs=38.6

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+++.+|+..||.+||.||++.++|...++.++++.
T Consensus        77 lt~~~~~~~~~~~~~~ga~~~l~Kp~~~~~L~~~i~~~~~~~  118 (220)
T 1p2f_A           77 LTLLSDDESVLKGFEAGADDYVTKPFNPEILLARVKRFLERE  118 (220)
T ss_dssp             EESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHHHHC
T ss_pred             EEcCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHHccc
Confidence            478889999999999999999999999999999999988763

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

Probab=96.95  E-value=0.0005  Score=64.49  Aligned_cols=41  Identities=29%  Similarity=0.464  Sum_probs=37.6

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR   41 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk   41 (491)
                      ||++.+.+++.+|+..||.+||.||+..++|...++.++++
T Consensus       114 lt~~~~~~~~~~a~~~Ga~~yl~Kp~~~~~L~~~i~~~l~~  154 (249)
T 3q9s_A          114 LTARDTVEEKVRLLGLGADDYLIKPFHPDELLARVKVQLRQ  154 (249)
T ss_dssp             EESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHHCC
T ss_pred             EECCCCHHHHHHHHHCCCcEEEECCCCHHHHHHHHHHHHhh
Confidence            57889999999999999999999999999999998887654

>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=96.94  E-value=0.00011  Score=59.03  Aligned_cols=42  Identities=24%  Similarity=0.354  Sum_probs=37.0

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+.+.+|++.||.|||.||++.++|...++.++++.
T Consensus        81 ~s~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~~~~~  122 (124)
T 1dc7_A           81 MTAHSDLDAAVSAYQQGAFDYLPKPFDIDEAVALVERAISHY  122 (124)
T ss_dssp             BCCSTTSTTTTSSCTTCCCCCBCSSCCHHHHHHHHHHHHHHT
T ss_pred             EecCCCHHHHHHHHhcCcceEeeCCCCHHHHHHHHHHHHHhh
Confidence            467777888899999999999999999999999999987653

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

Probab=96.91  E-value=0.00078  Score=65.40  Aligned_cols=40  Identities=28%  Similarity=0.263  Sum_probs=36.8

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWR   40 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~r   40 (491)
                      ||++++++++.+|++.||.|||+||++.++|...++.+++
T Consensus        99 ~s~~~~~~~~~~a~~~Ga~~~l~Kp~~~~~l~~~v~~~~~  138 (358)
T 3bre_A           99 LSTKEEPTVKSAAFAAGANDYLVKLPDAIELVARIRYHSR  138 (358)
T ss_dssp             EESSCCHHHHHHHHHTTCSEEEESCCCHHHHHHHHHHHHH
T ss_pred             EeCCCCHHHHHHHHhcChheEeeccCCHHHHHHHHHHHHH
Confidence            5889999999999999999999999999999999887754

>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=96.91  E-value=0.00019  Score=58.53  Aligned_cols=41  Identities=20%  Similarity=0.088  Sum_probs=32.5

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+. .+++..||.+||.||++.++|...++++++..
T Consensus        83 ~s~~~~~~~-~~~~~~g~~~~l~KP~~~~~L~~~i~~~~~~~  123 (127)
T 3i42_A           83 VSGFAKNDL-GKEACELFDFYLEKPIDIASLEPILQSIEGHH  123 (127)
T ss_dssp             EECC-CTTC-CHHHHHHCSEEEESSCCHHHHHHHHHHHC---
T ss_pred             EECCcchhH-HHHHHHhhHHheeCCCCHHHHHHHHHHhhccC
Confidence            355666666 78999999999999999999999999987654

>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=96.89  E-value=0.0003  Score=62.78  Aligned_cols=42  Identities=17%  Similarity=0.356  Sum_probs=38.0

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+++.+|+..||.|||.||++.++|...++.+++..
T Consensus        82 ls~~~~~~~~~~a~~~Ga~~~l~Kp~~~~~L~~~i~~~~~~~  123 (208)
T 1yio_A           82 ITAHGDIPMTVRAMKAGAIEFLPKPFEEQALLDAIEQGLQLN  123 (208)
T ss_dssp             EESCTTSCCCHHHHHTTEEEEEESSCCHHHHHHHHHHHHHHH
T ss_pred             EeCCCCHHHHHHHHHCCCcEEEeCCCCHHHHHHHHHHHHhhh
Confidence            477888889999999999999999999999999999987654

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

Probab=96.88  E-value=0.00067  Score=56.24  Aligned_cols=37  Identities=14%  Similarity=0.118  Sum_probs=33.0

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQH   37 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqh   37 (491)
                      ||++.+.+.+.+|++.||.+||.||++.++|...+++
T Consensus        95 ls~~~~~~~~~~~~~~g~~~~l~kP~~~~~L~~~~~~  131 (143)
T 2qvg_A           95 LTAAYTSKDKLAFESLNIRGHLIKPLDYGEAIKLFWI  131 (143)
T ss_dssp             EESCCCHHHHHHHTTTTCCEEEESSCCHHHHHHHHHH
T ss_pred             EeCCCCHHHHHHHHhcCCCeEEECCCCHHHHHHHHHH
Confidence            4667788999999999999999999999999988665

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

Probab=96.86  E-value=0.00048  Score=58.31  Aligned_cols=42  Identities=17%  Similarity=0.258  Sum_probs=37.2

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+.+.+|+..||.+||.||++.++|...++.++++.
T Consensus        85 ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~L~~~i~~~~~~~  126 (153)
T 3cz5_A           85 FTMHQGSAFALKAFEAGASGYVTKSSDPAELVQAIEAILAGR  126 (153)
T ss_dssp             EESCCSHHHHHHHHHTTCSEEEETTSCTTHHHHHHHHHTTTC
T ss_pred             EECCCCHHHHHHHHHCCCcEEEecCCCHHHHHHHHHHHHhCC
Confidence            467788899999999999999999999999999998886543

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

Probab=96.86  E-value=0.00091  Score=55.66  Aligned_cols=42  Identities=14%  Similarity=0.227  Sum_probs=36.2

Q ss_pred             CCCcchHHHHHHHHHh-ccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMR-GAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~-GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+...+.+++.. ||.|||.||++.++|...++.+++..
T Consensus        78 ~s~~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~i~~~~~~~  120 (139)
T 2jk1_A           78 ITGYTDSASMMAAINDAGIHQFLTKPWHPEQLLSSARNAARMF  120 (139)
T ss_dssp             EESCTTCHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHHHHH
T ss_pred             EeCCCChHHHHHHHHhhchhhhccCCCCHHHHHHHHHHHHHHH
Confidence            4677788889999987 59999999999999999999887654

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

Probab=96.85  E-value=0.0012  Score=55.91  Aligned_cols=42  Identities=14%  Similarity=0.274  Sum_probs=37.8

Q ss_pred             CCCcchHHHHHHHHHhc-cceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRG-AADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~G-A~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+.+.+|+..| |.+||.||++.++|...++.+++..
T Consensus        85 ls~~~~~~~~~~~~~~g~~~~~l~kP~~~~~L~~~i~~~~~~~  127 (154)
T 2rjn_A           85 ISGYADAQATIDAVNRGKISRFLLKPWEDEDVFKVVEKGLQLA  127 (154)
T ss_dssp             EECGGGHHHHHHHHHTTCCSEEEESSCCHHHHHHHHHHHHHHH
T ss_pred             EecCCCHHHHHHHHhccchheeeeCCCCHHHHHHHHHHHHHHH
Confidence            46778889999999998 9999999999999999999987655

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

Probab=96.85  E-value=0.00041  Score=56.87  Aligned_cols=44  Identities=20%  Similarity=0.165  Sum_probs=32.9

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHhcc
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSSM   45 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~~~   45 (491)
                      ||++.+.+. .+|+..||.+||.||++.++|...++.++++....
T Consensus        83 ~s~~~~~~~-~~~~~~g~~~~l~KP~~~~~l~~~i~~~l~~~~~~  126 (133)
T 3nhm_A           83 VSGYAPRTE-GPADQPVPDAYLVKPVKPPVLIAQLHALLARAEAE  126 (133)
T ss_dssp             EESCCC------TTSCCCSEEEESSCCHHHHHHHHHHHHHHHC--
T ss_pred             EeCCCcHhH-HHHhhcCCceEEeccCCHHHHHHHHHHHHhhhccc
Confidence            356666666 89999999999999999999999999998877543

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

Probab=96.85  E-value=0.00053  Score=57.94  Aligned_cols=42  Identities=12%  Similarity=0.183  Sum_probs=33.8

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+.+.+|+..||.+||.||++.++|...++.+++..
T Consensus        84 ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~L~~~l~~~~~~~  125 (154)
T 2qsj_A           84 ISGETDHELIRAALEAGADGFIPKSADPQVLIHAVSLILEGE  125 (154)
T ss_dssp             C-----CHHHHHHHHTTCCBBCCTTSCHHHHHHHHHHHHTTC
T ss_pred             EeCCCCHHHHHHHHHccCCEEEeCCCCHHHHHHHHHHHHcCC
Confidence            577788899999999999999999999999999999887654

>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=96.82  E-value=0.00056  Score=61.57  Aligned_cols=43  Identities=33%  Similarity=0.385  Sum_probs=39.4

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHh
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQS   43 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~   43 (491)
                      ||++.+.+++.+|+..||.+||.||++.++|...++.++++..
T Consensus        80 ls~~~~~~~~~~~~~~ga~~~l~Kp~~~~~l~~~i~~~~~~~~  122 (225)
T 1kgs_A           80 LTALSDVEYRVKGLNMGADDYLPKPFDLRELIARVRALIRRKS  122 (225)
T ss_dssp             EESSCHHHHHHHTCCCCCSEEEESSCCHHHHHHHHHHHHHHHC
T ss_pred             EeCCCCHHHHHHHHhCCccEEEeCCCCHHHHHHHHHHHHhhcc
Confidence            5788899999999999999999999999999999999987753

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

Probab=96.80  E-value=0.0013  Score=53.81  Aligned_cols=40  Identities=25%  Similarity=0.388  Sum_probs=32.3

Q ss_pred             CCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            2 SSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         2 S~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      |+++.. .+.+|++.||.+||.||+..++|...+++++...
T Consensus        87 ~~~~~~-~~~~~~~~g~~~~l~kP~~~~~l~~~i~~~~~~~  126 (132)
T 3lte_A           87 SGLDKA-KLQQAVTEGADDYLEKPFDNDALLDRIHDLVNEG  126 (132)
T ss_dssp             CCSCSH-HHHHHHHHTCCEEECSSCCHHHHHHHHHHHHC--
T ss_pred             eCCChH-HHHHHHHhChHHHhhCCCCHHHHHHHHHHHcCCC
Confidence            344444 7889999999999999999999999988876543

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

Probab=96.79  E-value=0.0011  Score=66.13  Aligned_cols=42  Identities=29%  Similarity=0.423  Sum_probs=35.5

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCC-CHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPV-RRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv-~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+++.+|++.||.|||+||+ ..++|...++.++++.
T Consensus        83 lt~~~~~~~~~~a~~~ga~~yl~KP~~~~~~l~~~i~~~~~~~  125 (394)
T 3eq2_A           83 LSGAGVMSDAVEALRLGAADYLIKPLEDLAVLEHSVRRALDRA  125 (394)
T ss_dssp             C---CHHHHHHHHHHHTCSEECCSSCSCTHHHHHHHHHHHHHH
T ss_pred             EEcCCCHHHHHHHHhcChhhEEECCCChHHHHHHHHHHHHhhh
Confidence            68999999999999999999999999 6899999988887654

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

Probab=96.79  E-value=0.00067  Score=61.28  Aligned_cols=41  Identities=22%  Similarity=0.250  Sum_probs=37.4

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCC-CHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPV-RRNELRNLWQHVWRR   41 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv-~~eELk~lwqhv~rk   41 (491)
                      ||++.+.+++.+|+..||.+||.||+ +.++|...++.++++
T Consensus        74 lt~~~~~~~~~~~~~~Ga~~~l~Kp~~~~~~L~~~i~~~~~~  115 (223)
T 2hqr_A           74 SSDNPTSEEEVHAFEQGADDYIAKPYRSIKALVARIEARLRF  115 (223)
T ss_dssp             EESSCCHHHHHHHHHHTCSEEEETTCSCTHHHHHHHHHHTSS
T ss_pred             EECCCCHHHHHHHHHcCCCEEEECCCCCHHHHHHHHHHHhcc
Confidence            57889999999999999999999999 999999998887654

>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=96.78  E-value=0.0011  Score=67.10  Aligned_cols=42  Identities=21%  Similarity=0.285  Sum_probs=38.5

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++++.+.+.+|++.||.|||+||++.++|...++.+++..
T Consensus        81 lt~~~~~~~~~~a~~~Ga~~~l~KP~~~~~l~~~i~~~~~~~  122 (459)
T 1w25_A           81 ITALDGRGDRIQGLESGASDFLTKPIDDVMLFARVRSLTRFK  122 (459)
T ss_dssp             EECSSCHHHHHHHHHHTCCEEEESSCCHHHHHHHHHHHHHHH
T ss_pred             EECCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHHHH
Confidence            588999999999999999999999999999999999887644

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

Probab=96.78  E-value=0.0011  Score=55.11  Aligned_cols=37  Identities=19%  Similarity=0.280  Sum_probs=33.3

Q ss_pred             HHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHhcc
Q 011208            9 TVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSSM   45 (491)
Q Consensus         9 ~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~~~   45 (491)
                      .+.+|+..||.+||.||+..++|...+++++++....
T Consensus        95 ~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~~~~~~~  131 (143)
T 2qv0_A           95 HAVEAFELEAFDYILKPYQESRIINMLQKLTTAWEQQ  131 (143)
T ss_dssp             THHHHHHTTCSEEEESSCCHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHhCCcceEEeCCCCHHHHHHHHHHHHHHHHhc
Confidence            6788999999999999999999999999998777544

>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=96.74  E-value=0.00079  Score=68.32  Aligned_cols=42  Identities=21%  Similarity=0.366  Sum_probs=38.9

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+++.+|++.||.|||.||++.++|...++++++..
T Consensus        78 lT~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~l~~~  119 (387)
T 1ny5_A           78 ITGHGTIKTAVEAMKMGAYDFLTKPCMLEEIELTINKAIEHR  119 (387)
T ss_dssp             EEETTCHHHHHHHHTTTCCEEEEESCCHHHHHHHHHHHHHHH
T ss_pred             EeCCCCHHHHHHHHhcCceEEecCCCCHHHHHHHHHHHHHHH
Confidence            578999999999999999999999999999999999987654

>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=96.65  E-value=0.00082  Score=60.84  Aligned_cols=42  Identities=31%  Similarity=0.366  Sum_probs=38.1

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+.+.+|+..||.+||.||+..++|...++.++++.
T Consensus        81 lt~~~~~~~~~~~~~~ga~~~l~Kp~~~~~l~~~i~~~~~~~  122 (230)
T 2oqr_A           81 VTARDSEIDKVVGLELGADDYVTKPYSARELIARIRAVLRRG  122 (230)
T ss_dssp             EECCHHHHHHHHHHHHCCSCCCCSSCCHHHHHHHHHHHHTTT
T ss_pred             EeCCCcHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHhhc
Confidence            477888999999999999999999999999999999987653

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

Probab=96.65  E-value=0.00074  Score=55.13  Aligned_cols=34  Identities=12%  Similarity=0.107  Sum_probs=30.3

Q ss_pred             HHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHH
Q 011208            7 VSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWR   40 (491)
Q Consensus         7 ~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~r   40 (491)
                      .+.+.+++..||.+||.||++.++|...+++++.
T Consensus        91 ~~~~~~~~~~g~~~~l~KP~~~~~l~~~l~~~~~  124 (135)
T 3eqz_A           91 AETLALSCGLNVINTFTKPINTEVLTCFLTSLSN  124 (135)
T ss_dssp             HHHHHHHTTCEEEEEEESSCCHHHHHHHHHHHSC
T ss_pred             HHHHHHHcCCCcceeeCCCCCHHHHHHHHHHHHh
Confidence            3788889999999999999999999999888754

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

Probab=96.64  E-value=0.00022  Score=59.11  Aligned_cols=44  Identities=11%  Similarity=0.144  Sum_probs=37.3

Q ss_pred             CCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHhcc
Q 011208            2 SSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSSM   45 (491)
Q Consensus         2 S~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~~~   45 (491)
                      |++.+.+.+.+++..||.+||.||++.++|...+++++++....
T Consensus        88 s~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~~~~~~~~  131 (142)
T 3cg4_A           88 TAKNAPDAKMIGLQEYVVDYITKPFDNEDLIEKTTFFMGFVRNQ  131 (142)
T ss_dssp             ECTTCCCCSSTTGGGGEEEEEESSCCHHHHHHHHHHHHHHHHHC
T ss_pred             ECCCCHHHHHHHHhcCccEEEeCCCCHHHHHHHHHHHHHHHhhc
Confidence            45566667788999999999999999999999999998776443

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

Probab=96.45  E-value=0.00063  Score=62.31  Aligned_cols=42  Identities=24%  Similarity=0.360  Sum_probs=39.0

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+++.+|+..||.+||.||++.++|...++.+++..
T Consensus        81 lt~~~~~~~~~~~~~~Ga~~~l~Kp~~~~~L~~~i~~~~~~~  122 (225)
T 3c3w_A           81 LTSYTSDEAMLDAILAGASGYVVKDIKGMELARAVKDVGAGR  122 (225)
T ss_dssp             GGGSSSHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHHG
T ss_pred             EECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHcCC
Confidence            578889999999999999999999999999999999988764

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

Probab=96.41  E-value=0.00058  Score=62.22  Aligned_cols=41  Identities=5%  Similarity=-0.011  Sum_probs=36.7

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR   41 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk   41 (491)
                      ||++.+.+++..|+..||.|||.||+..++|...++.+++.
T Consensus        89 lt~~~~~~~~~~~~~~Ga~~~l~Kp~~~~~L~~~i~~~~~~  129 (225)
T 3klo_A           89 INCPQDIEHKLLFKWNNLAGVFYIDDDMDTLIKGMSKILQD  129 (225)
T ss_dssp             EEECTTCCHHHHTTSTTEEEEEETTCCHHHHHHHHHHHHTT
T ss_pred             EECCcchhHHHHHHHhCCCEEEecCCCHHHHHHHHHHHHCC
Confidence            46778888999999999999999999999999999888764

>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=96.40  E-value=0.0017  Score=52.06  Aligned_cols=37  Identities=16%  Similarity=0.152  Sum_probs=32.4

Q ss_pred             cchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHH
Q 011208            4 QDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWR   40 (491)
Q Consensus         4 ~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~r   40 (491)
                      +.+.+.+.+++..||.+||.||++.++|...++++++
T Consensus        88 ~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~~~  124 (127)
T 2gkg_A           88 NPDGFAQHRKLKAHADEYVAKPVDADQLVERAGALIG  124 (127)
T ss_dssp             CGGGHHHHHHSTTCCSEEEESSCCHHHHHHHHHHHHC
T ss_pred             cCCchhHHHHHHhCcchheeCCCCHHHHHHHHHHHHc
Confidence            3456788899999999999999999999999988764

>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=96.38  E-value=0.00052  Score=62.09  Aligned_cols=43  Identities=35%  Similarity=0.447  Sum_probs=38.5

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHh
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQS   43 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~   43 (491)
                      ||++.+.+++.+|+..||.|||.||++.++|...++.++++..
T Consensus        85 lt~~~~~~~~~~~~~~ga~~~l~Kp~~~~~L~~~i~~~~~~~~  127 (233)
T 1ys7_A           85 LSARSSVDDRVAGLEAGADDYLVKPFVLAELVARVKALLRRRG  127 (233)
T ss_dssp             EECCCTTTCCCTTTTTTCSEEEESSCCHHHHHHHHHHHHHHHH
T ss_pred             EEcCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHhhcc
Confidence            4677788888999999999999999999999999999987764

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

Probab=96.03  E-value=0.0012  Score=60.69  Aligned_cols=41  Identities=27%  Similarity=0.426  Sum_probs=35.4

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR   41 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk   41 (491)
                      ||++.+.+.+.+|+..||.+||.||++.++|...++.++++
T Consensus        82 lt~~~~~~~~~~~~~~Ga~~~l~Kp~~~~~L~~~i~~~~~~  122 (238)
T 2gwr_A           82 LTAKTDTVDVVLGLESGADDYIMKPFKPKELVARVRARLRR  122 (238)
T ss_dssp             EEETTCCSCHHHHHHTTCCEEEEESCCHHHHHHHHHHHCCC
T ss_pred             EeCCCCHHHHHHHHHCCCCEEEeCCCCHHHHHHHHHHHHhh
Confidence            46677778899999999999999999999999998877543

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

Probab=95.82  E-value=0.0039  Score=62.76  Aligned_cols=43  Identities=19%  Similarity=0.235  Sum_probs=37.3

Q ss_pred             CCCcchH-----HHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHh
Q 011208            1 MSSQDSV-----STVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQS   43 (491)
Q Consensus         1 MS~~d~~-----e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~   43 (491)
                      +|++++.     ..+.+|+..||.|||.||++.++|..+++.++++..
T Consensus        83 ~s~~~~~~~~~~~~~~~a~~~ga~~yl~KP~~~~~L~~~i~~~~~~~~  130 (400)
T 3sy8_A           83 SSEVDPILRQATISMIECLGLNFLGDLGKPFSLERITALLTRYNARRQ  130 (400)
T ss_dssp             SCCCCGGGHHHHHHHHHTTTCEEEEECCSSCCHHHHHHHHHHHHHHTT
T ss_pred             EcCchHHHHHHHHHHHHHcCCeeccCcCCCcCHHHHHHHHHHHHHhhh
Confidence            4667766     788899999999999999999999999999877653

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

Probab=95.74  E-value=0.0017  Score=54.36  Aligned_cols=31  Identities=13%  Similarity=0.023  Sum_probs=23.2

Q ss_pred             cchHHHHHHHHHhccceeEeCCCCHHHHHHH
Q 011208            4 QDSVSTVYKCMMRGAADYLVKPVRRNELRNL   34 (491)
Q Consensus         4 ~d~~e~v~kal~~GA~DYLlKPv~~eELk~l   34 (491)
                      +.+.+.+.+|+..||.+||.||++.++|...
T Consensus        98 ~~~~~~~~~~~~~ga~~~l~KP~~~~~l~~~  128 (145)
T 3kyj_B           98 VSGSPHAARARELGADGVVAKPSGTVSHDLE  128 (145)
T ss_dssp             STTSSHHHHHHHTTCSCCCBCCCSCC-----
T ss_pred             cCChHHHHHHHhCCCCEEEeCCCCHHHHHHH
Confidence            6667788999999999999999996655444

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

Probab=95.47  E-value=0.0045  Score=51.50  Aligned_cols=40  Identities=20%  Similarity=0.272  Sum_probs=29.2

Q ss_pred             CCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHH
Q 011208            2 SSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR   41 (491)
Q Consensus         2 S~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk   41 (491)
                      |++.+......++..||.+||.||++.++|...++.++++
T Consensus        84 s~~~~~~~~~~~~~~~~~~~l~KP~~~~~L~~~i~~~~~~  123 (138)
T 3c3m_A           84 TAKPLTPEEANEYGSYIEDYILKPTTHHQLYEAIEHVLAR  123 (138)
T ss_dssp             ESSCCCHHHHHHTTTTCSEEEECCCHHHHHHHHHHHHHSC
T ss_pred             ECCCChHHHHHHhhcCHhheEeCCCCHHHHHHHHHHHHHH
Confidence            4444444444445556789999999999999999888654

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

Probab=94.71  E-value=0.011  Score=48.12  Aligned_cols=40  Identities=13%  Similarity=0.114  Sum_probs=32.4

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+.+.+|+..|  +||.||++.++|...++++++..
T Consensus        85 ~s~~~~~~~~~~~~~~~--~~l~kP~~~~~l~~~i~~~~~~~  124 (132)
T 2rdm_A           85 ISGHAALEWASNGVPDS--IILEKPFTSAQLITAVSQLLNAR  124 (132)
T ss_dssp             EESSCCTTHHHHSCTTC--EEEESSCCHHHHHHHHHHHHHTT
T ss_pred             EeCCccHHHHHhhcCCc--ceEeCCCCHHHHHHHHHHHHhcC
Confidence            35667777778887776  79999999999999998886543

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

Probab=94.60  E-value=0.011  Score=47.13  Aligned_cols=29  Identities=21%  Similarity=0.281  Sum_probs=25.0

Q ss_pred             HHHHHhccceeEeCCCCHHHHHHHHHHHH
Q 011208           11 YKCMMRGAADYLVKPVRRNELRNLWQHVW   39 (491)
Q Consensus        11 ~kal~~GA~DYLlKPv~~eELk~lwqhv~   39 (491)
                      .+++..||.+||.||++.++|...++.++
T Consensus        87 ~~~~~~g~~~~l~Kp~~~~~l~~~i~~~~  115 (116)
T 3a10_A           87 SDMSSWAADEYVVKSFNFDELKEKVKKLL  115 (116)
T ss_dssp             GCGGGGGSSEEEECCSSTHHHHHHHHHHT
T ss_pred             HHHHhccccceEECCCCHHHHHHHHHHHh
Confidence            45678899999999999999998887764

>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=94.51  E-value=0.033  Score=52.66  Aligned_cols=37  Identities=22%  Similarity=0.242  Sum_probs=28.4

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHV   38 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv   38 (491)
                      ||++++.+.+.+|++.||.|||+||+.. .+..+...+
T Consensus        80 lt~~~~~~~~~~a~~~Ga~dyl~Kp~~~-~~~~~~~~~  116 (259)
T 3luf_A           80 LTADISEDKREAWLEAGVLDYVMKDSRH-SLQYAVGLV  116 (259)
T ss_dssp             EECC-CHHHHHHHHHTTCCEEEECSSHH-HHHHHHHHH
T ss_pred             EEccCCHHHHHHHHHCCCcEEEeCCchh-HHHHHHHhh
Confidence            5889999999999999999999999754 344444433

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

Probab=93.96  E-value=0.0052  Score=53.44  Aligned_cols=27  Identities=19%  Similarity=0.234  Sum_probs=23.1

Q ss_pred             HHhccceeEeCCCCHHHHHHHHHHHHH
Q 011208           14 MMRGAADYLVKPVRRNELRNLWQHVWR   40 (491)
Q Consensus        14 l~~GA~DYLlKPv~~eELk~lwqhv~r   40 (491)
                      .++||.|||.|||+.++|...++.+.|
T Consensus        95 ~~~g~~~yl~KP~~~~~L~~~l~~~~~  121 (123)
T 2lpm_A           95 TRYSNIPLLTKPFLDSELEAVLVQISK  121 (123)
T ss_dssp             SSSCSCSCBCSSSSHHHHHHHHSTTCS
T ss_pred             HhCCCCcEEECCCCHHHHHHHHHHHHh
Confidence            457999999999999999998876654

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

Probab=93.61  E-value=0.017  Score=45.16  Aligned_cols=28  Identities=21%  Similarity=0.189  Sum_probs=24.8

Q ss_pred             HHHHhccceeEeCCCCHHHHHHHHHHHH
Q 011208           12 KCMMRGAADYLVKPVRRNELRNLWQHVW   39 (491)
Q Consensus        12 kal~~GA~DYLlKPv~~eELk~lwqhv~   39 (491)
                      +++..||.+||.||++.++|...+++++
T Consensus        89 ~~~~~g~~~~l~kp~~~~~l~~~l~~~~  116 (119)
T 2j48_A           89 PLLTAQASAILSKPLDPQLLLTTLQGLC  116 (119)
T ss_dssp             HHHHHHCSEECSSCSTTHHHHHHHHTTC
T ss_pred             hhhhcCHHHhccCCCCHHHHHHHHHHHh
Confidence            6889999999999999999998887654

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

Probab=93.52  E-value=0.061  Score=54.04  Aligned_cols=40  Identities=20%  Similarity=0.258  Sum_probs=30.2

Q ss_pred             CCCcchH--HHHHHHHHhccceeEeCCCCH---------HHHHHHHHHHHH
Q 011208            1 MSSQDSV--STVYKCMMRGAADYLVKPVRR---------NELRNLWQHVWR   40 (491)
Q Consensus         1 MS~~d~~--e~v~kal~~GA~DYLlKPv~~---------eELk~lwqhv~r   40 (491)
                      ||++.+.  +.+.+|++.||.|||.||+..         ++|...++.+.+
T Consensus        82 lS~~~~~~~~~~~~al~~Ga~d~l~KP~~~~~~~l~~~~~~L~~~I~~~~~  132 (349)
T 1a2o_A           82 VSSLTGKGSEVTLRALELGAIDFVTKPQLGIREGMLAYSEMIAEKVRTAAR  132 (349)
T ss_dssp             EECCTHHHHHHHHHHHHHTCCEEEECSSSSCSSCHHHHHHHHHHHHHHHHH
T ss_pred             EECCCcccHHHHHHHHhCCceEEEECCCCccchhHHHHHHHHHHHHHHHHh
Confidence            3556654  568999999999999999983         666666666544

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

Probab=93.47  E-value=0.015  Score=50.32  Aligned_cols=38  Identities=16%  Similarity=0.239  Sum_probs=28.5

Q ss_pred             HHHHHHHHHhccceeEeCCCCHHHHHHH--HHHHHHHHhc
Q 011208            7 VSTVYKCMMRGAADYLVKPVRRNELRNL--WQHVWRRQSS   44 (491)
Q Consensus         7 ~e~v~kal~~GA~DYLlKPv~~eELk~l--wqhv~rk~~~   44 (491)
                      .+.+.+|+..||.|||.||++.++|...  ...+++++..
T Consensus       112 ~~~~~~~~~~ga~~~l~KP~~~~~l~~r~~~~~l~~~i~~  151 (164)
T 3t8y_A          112 AAITIEALRNGAVDFITKPHGSISLTFRQVAPELLEKIRQ  151 (164)
T ss_dssp             CHHHHHHHHTTCCEEEECSSSSSCGGGGGGHHHHHHHHHH
T ss_pred             hHHHHHHHHcCcCEEEeCCCCHHHHHHHhhhHHHHHHHHH
Confidence            3478899999999999999998888532  3455555433

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

Probab=93.40  E-value=0.038  Score=45.48  Aligned_cols=39  Identities=23%  Similarity=0.397  Sum_probs=30.1

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+.+.+|+..||.+||.||+.  ....++.. +++.
T Consensus        92 ls~~~~~~~~~~~~~~g~~~~l~kP~~--~~~~l~~~-i~~~  130 (137)
T 2pln_A           92 SSDNPTSEEEVHAFEQGADDYIAKPYR--SIKALVAR-IEAR  130 (137)
T ss_dssp             EESSCCHHHHHHHHHTTCSEEEESSCS--CHHHHHHH-HHHH
T ss_pred             EeCCCCHHHHHHHHHcCCceeeeCCCC--CHHHHHHH-HHHH
Confidence            467888999999999999999999986  44455444 3444

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

Probab=92.67  E-value=0.064  Score=44.36  Aligned_cols=28  Identities=21%  Similarity=0.347  Sum_probs=23.5

Q ss_pred             HhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208           15 MRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus        15 ~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ..||.+||.||++.++|...++.+++..
T Consensus       104 ~~g~~~~l~KP~~~~~L~~~i~~~~~~~  131 (140)
T 3c97_A          104 GAELDEYVSKPLNPNQLRDVVLTCHSEG  131 (140)
T ss_dssp             CSSCSEEEESSCCHHHHHHHHHHHHC--
T ss_pred             hCChhheEeCCCCHHHHHHHHHHHhCCC
Confidence            5699999999999999999998886543

>3cwo_X Beta/alpha-barrel protein based on 1THF and 1TMY; XRAY, CHEY, HISF, half barrel, de novo protein; 3.10A {Thermotoga maritima} PDB: 2lle_A

Probab=92.09  E-value=0.067  Score=48.02  Aligned_cols=38  Identities=21%  Similarity=0.341  Sum_probs=30.7

Q ss_pred             CCcchHHHHHHHHHhccceeEeCC--CCHHHHHHHHHHHH
Q 011208            2 SSQDSVSTVYKCMMRGAADYLVKP--VRRNELRNLWQHVW   39 (491)
Q Consensus         2 S~~d~~e~v~kal~~GA~DYLlKP--v~~eELk~lwqhv~   39 (491)
                      ++....+.+.+|++.||.+||+||  ++..+|...+..++
T Consensus        60 ~~~~~~~~~~~~~~~Ga~~~l~kp~~~~~~~l~~~i~~~~   99 (237)
T 3cwo_X           60 SAMGQQAMVIEAIKAGAKDFIVNTAAVENPSLITQIAQTF   99 (237)
T ss_dssp             CCSSTHHHHHHHHHTTCCEEEESHHHHHCTHHHHHHHHHH
T ss_pred             ECCCCHHHHHHHHHCCHHheEeCCcccChHHHHHHHHHHh
Confidence            344558899999999999999999  77778877666654

>3ogk_Q JAZ1 incomplete degron peptide; leucine rich repeat, ubiquitin ligase, SCF, protein binding; HET: OGK; 2.80A {Arabidopsis thaliana}

Probab=91.54  E-value=0.051  Score=35.07  Aligned_cols=19  Identities=53%  Similarity=0.716  Sum_probs=16.4

Q ss_pred             HHHHHHHHHHhhhccCCCC
Q 011208          429 REAALNKFRLKRKDRCYDK  447 (491)
Q Consensus       429 R~~~l~ryr~Krk~R~f~K  447 (491)
                      |.+.|+||.||||.|...+
T Consensus         1 Rk~SLqRFleKRk~R~~~~   19 (22)
T 3ogk_Q            1 RRASLHRFLEKRKDRVTSK   19 (26)
T ss_pred             CchhHHHHHHHHHHHhhcc
Confidence            5789999999999997654

>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=88.95  E-value=0.39  Score=48.27  Aligned_cols=42  Identities=24%  Similarity=0.349  Sum_probs=35.3

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||+.+..+...+|+..||.||+.||+..++|...+..++++.
T Consensus       230 lt~~~~~~~~~~~l~~Ga~d~~~kp~~~~~l~~~v~~~~~~~  271 (459)
T 1w25_A          230 MVDPDDRGRMVKALEIGVNDILSRPIDPQELSARVKTQIQRK  271 (459)
T ss_dssp             EECTTCHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHHHHH
T ss_pred             EcCCCchHHHHHHHhccccccccCCCCHHHHHHHHHHHHHHH
Confidence            356677778889999999999999999999988887766544

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

Probab=83.88  E-value=0.34  Score=53.58  Aligned_cols=43  Identities=2%  Similarity=0.057  Sum_probs=34.5

Q ss_pred             CCCcch-HHHHHHHHHhccceeEeCCCCHHH-HHHHHHHHHHHHh
Q 011208            1 MSSQDS-VSTVYKCMMRGAADYLVKPVRRNE-LRNLWQHVWRRQS   43 (491)
Q Consensus         1 MS~~d~-~e~v~kal~~GA~DYLlKPv~~eE-Lk~lwqhv~rk~~   43 (491)
                      ||+.++ .+..-.++..||.|||.||++..| |..-++.++|+..
T Consensus        91 lTa~~~~~~d~~~~l~~gaddyi~kpf~~~efl~~ri~a~~rr~~  135 (755)
T 2vyc_A           91 LGDREKALAAMDRDLLELVDEFAWILEDTADFIAGRAVAAMTRYR  135 (755)
T ss_dssp             EECHHHHHHTCSHHHHHHCSEEEETTTSCHHHHHHHHHHHHHHHH
T ss_pred             EecCCcchhhccHhHhhcCCceEeCCCCCHHHHHHHHHHHHHHhh
Confidence            355555 666778899999999999999999 7777777777754

>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=80.84  E-value=0.44  Score=39.02  Aligned_cols=24  Identities=29%  Similarity=0.268  Sum_probs=20.6

Q ss_pred             cceeEeCCCCHHHHHHHHHHHHHH
Q 011208           18 AADYLVKPVRRNELRNLWQHVWRR   41 (491)
Q Consensus        18 A~DYLlKPv~~eELk~lwqhv~rk   41 (491)
                      |.+||.||++.++|...+++++++
T Consensus       108 ~~~~l~KP~~~~~L~~~i~~~~~~  131 (138)
T 2b4a_A          108 NLSYLQKPFAISELRAAIDYHKPS  131 (138)
T ss_dssp             CEEEEESSCCHHHHHHHHHHTCCC
T ss_pred             HHheeeCCCCHHHHHHHHHHHHHh
Confidence            789999999999999998876543

---

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	491
d1jbea_	128	c.23.1.1 (A:) CheY protein {Escherichia coli [TaxI	7e-06
d2a9pa1	117	c.23.1.1 (A:2-118) DNA-binding response regulator	7e-06
d1zesa1	121	c.23.1.1 (A:3-123) PhoB receiver domain {Escherich	8e-06
d1k66a_	149	c.23.1.1 (A:) Response regulator for cyanobacteria	8e-06
d1k68a_	140	c.23.1.1 (A:) Response regulator for cyanobacteria	1e-05
d1zh2a1	119	c.23.1.1 (A:2-120) Transcriptional regulatory prot	1e-05
d1ys7a2	121	c.23.1.1 (A:7-127) Transcriptional regulatory prot	2e-05
d2pl1a1	119	c.23.1.1 (A:1-119) PhoP receiver domain {Escherich	3e-05
d1mb3a_	123	c.23.1.1 (A:) Cell division response regulator Div	3e-05
d1kgsa2	122	c.23.1.1 (A:2-123) PhoB receiver domain {Thermotog	4e-05
d1dz3a_	123	c.23.1.1 (A:) Sporulation response regulator Spo0A	4e-05
d1xhfa1	121	c.23.1.1 (A:2-122) Aerobic respiration control pro	5e-05
d1mvoa_	121	c.23.1.1 (A:) PhoP receiver domain {Bacillus subti	5e-05
d1zgza1	120	c.23.1.1 (A:2-121) TorCAD operon transcriptional r	5e-05
d1ny5a1	137	c.23.1.1 (A:1-137) Transcriptional activator sigm5	7e-05
d1dcfa_	134	c.23.1.2 (A:) Receiver domain of the ethylene rece	7e-05
d1i3ca_	144	c.23.1.1 (A:) Response regulator for cyanobacteria	1e-04
d1p2fa2	120	c.23.1.1 (A:1-120) Response regulator DrrB {Thermo	1e-04
d1p6qa_	129	c.23.1.1 (A:) CheY protein {Sinorhizobium meliloti	1e-04
d2ayxa1	133	c.23.1.1 (A:817-949) Sensor kinase protein RcsC, C	2e-04
d1dbwa_	123	c.23.1.1 (A:) Transcriptional regulatory protein F	2e-04
d1krwa_	123	c.23.1.1 (A:) NTRC receiver domain {Salmonella typ	2e-04
d1yioa2	128	c.23.1.1 (A:3-130) Response regulatory protein Sty	2e-04
d1a04a2	138	c.23.1.1 (A:5-142) Nitrate/nitrite response regula	3e-04
d2r25b1	128	c.23.1.1 (B:1087-1214) Response regulator Sin1 {Ba	3e-04
d1qkka_	140	c.23.1.1 (A:) Transcriptional regulatory protein D	6e-04
d1u0sy_	118	c.23.1.1 (Y:) CheY protein {Thermotoga maritima [T	6e-04
d1w25a1	139	c.23.1.1 (A:2-140) Response regulator PleD, receiv	7e-04
d1peya_	119	c.23.1.1 (A:) Sporulation response regulator Spo0F	0.001
d1w25a2	153	c.23.1.1 (A:141-293) Response regulator PleD, rece	0.001

>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 = 43.4 bits (102), Expect = 7e-06
 Identities = 7/41 (17%), Positives = 17/41 (41%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR 41
           ++++     +      GA+ Y+VKP     L      ++ +
Sbjct: 85  VTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 125

>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 = 43.1 bits (101), Expect = 7e-06
 Identities = 13/41 (31%), Positives = 21/41 (51%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR 41
           +S++DS       +  GA DY+ KP    EL+   + + RR
Sbjct: 77  LSAKDSEFDKVIGLELGADDYVTKPFSNRELQARVKALLRR 117

>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 = 43.0 bits (101), Expect = 8e-06
 Identities = 11/41 (26%), Positives = 19/41 (46%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR 41
           ++++       + +  GA DY+ KP    EL    + V RR
Sbjct: 80  LTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRR 120

>d1k66a_ c.23.1.1 (A:) Response regulator for cyanobacterial phytochrome {Calothrix sp. pcc 7601, RcpB [TaxId: 1188]} Length = 149

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]

 Score = 43.6 bits (102), Expect = 8e-06
 Identities = 9/47 (19%), Positives = 19/47 (40%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSSMVS 47
           M++  +   +  C     + Y+VKP+  + L    Q   +    +V 
Sbjct: 98  MTTSSNPKDIEICYSYSISSYIVKPLEIDRLTETVQTFIKYWLDIVV 144

>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 = 42.8 bits (100), Expect = 1e-05
 Identities = 5/47 (10%), Positives = 17/47 (36%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSSMVS 47
           +S+  +   ++         Y+ K    ++L  + + +     S  +
Sbjct: 91  LSTSINEDDIFHSYDLHVNCYITKSANLSQLFQIVKGIEEFWLSTAT 137

>d1zh2a1 c.23.1.1 (A:2-120) Transcriptional regulatory protein KdpE, N-terminal domain {Escherichia coli [TaxId: 562]} Length = 119

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]

 Score = 42.0 bits (98), Expect = 1e-05
 Identities = 14/43 (32%), Positives = 20/43 (46%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQS 43
           +S++   S     +  GA DYL KP    EL+   +   RR S
Sbjct: 77  LSARSEESDKIAALDAGADDYLSKPFGIGELQARLRVALRRHS 119

>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 = 41.9 bits (98), Expect = 2e-05
 Identities = 15/42 (35%), Positives = 22/42 (52%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ 42
           +S++ SV      +  GA DYLVKP    EL    + + RR+
Sbjct: 79  LSARSSVDDRVAGLEAGADDYLVKPFVLAELVARVKALLRRR 120

>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 = 41.3 bits (96), Expect = 3e-05
 Identities = 11/41 (26%), Positives = 21/41 (51%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR 41
           +++++S     + +  GA DY+ KP    E+    Q + RR
Sbjct: 78  LTARESWQDKVEVLSAGADDYVTKPFHIEEVMARMQALMRR 118

>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 = 41.2 bits (96), Expect = 3e-05
 Identities = 6/42 (14%), Positives = 14/42 (33%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ 42
           +++        +    G   Y+ KP+         + +  RQ
Sbjct: 81  VTAFAMKGDEERIREGGCEAYISKPISVVHFLETIKRLLERQ 122

>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 = 40.9 bits (95), Expect = 4e-05
 Identities = 14/43 (32%), Positives = 21/43 (48%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQS 43
           +++   V    K +  GA DYL KP    EL    + + RR+S
Sbjct: 79  LTALSDVEYRVKGLNMGADDYLPKPFDLRELIARVRALIRRKS 121

>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 = 40.9 bits (96), Expect = 4e-05
 Identities = 7/41 (17%), Positives = 19/41 (46%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR 41
           +++        K +  GA+ +++KP     L +  + V+ +
Sbjct: 82  LTAFGQEDVTKKAVELGASYFILKPFDMENLAHHIRQVYGK 122

>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 = 40.8 bits (95), Expect = 5e-05
 Identities = 10/41 (24%), Positives = 19/41 (46%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR 41
           ++ +D+       +  GA DY+ KP    EL    +++  R
Sbjct: 79  LTGRDNEVDKILGLEIGADDYITKPFNPRELTIRARNLLSR 119

>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 = 40.4 bits (94), Expect = 5e-05
 Identities = 10/41 (24%), Positives = 19/41 (46%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR 41
           ++++D        +  GA DY+ KP    E+    + + RR
Sbjct: 80  LTAKDEEFDKVLGLELGADDYMTKPFSPREVNARVKAILRR 120

>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 = 40.4 bits (94), Expect = 5e-05
 Identities = 9/41 (21%), Positives = 18/41 (43%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR 41
           ++ +         +  GA DY+ KP+   EL    +++  R
Sbjct: 78  VTGRSDRIDRIVGLEMGADDYVTKPLELRELVVRVKNLLWR 118

>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 = 40.4 bits (94), Expect = 7e-05
 Identities = 9/42 (21%), Positives = 17/42 (40%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ 42
           ++   ++ T  + M  GA D+L KP    E+          +
Sbjct: 78  ITGHGTIKTAVEAMKMGAYDFLTKPCMLEEIELTINKAIEHR 119

>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 = 40.4 bits (94), Expect = 7e-05
 Identities = 12/42 (28%), Positives = 20/42 (47%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ 42
           +S     ST  KCM  G    L+KPV  + +R++   +   +
Sbjct: 89  LSGNTDKSTKEKCMSFGLDGVLLKPVSLDNIRDVLSDLLEPR 130

>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 = 40.1 bits (93), Expect = 1e-04
 Identities = 7/47 (14%), Positives = 15/47 (31%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSSMVS 47
           +++  +   V          YL K     +L  + Q +       V+
Sbjct: 92  LTTSHNEDDVIASYELHVNCYLTKSRNLKDLFKMVQGIESFWLETVT 138

>d1p2fa2 c.23.1.1 (A:1-120) Response regulator DrrB {Thermotoga maritima [TaxId: 2336]} Length = 120

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]

 Score = 39.6 bits (92), Expect = 1e-04
 Identities = 10/42 (23%), Positives = 16/42 (38%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ 42
           ++      +V K    GA DY+ KP     L    +    R+
Sbjct: 77  LTLLSDDESVLKGFEAGADDYVTKPFNPEILLARVKRFLERE 118

>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 = 39.6 bits (92), Expect = 1e-04
 Identities = 9/41 (21%), Positives = 19/41 (46%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR 41
           +++Q   + V K    GA + L KP    +++   + V+  
Sbjct: 87  LTAQGDRALVQKAAALGANNVLAKPFTIEKMKAAIEAVFGA 127

>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 = 39.3 bits (91), Expect = 2e-04
 Identities = 7/41 (17%), Positives = 15/41 (36%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR 41
           +++        +C+  G    L KPV  + ++        R
Sbjct: 86  VTANALAEEKQRCLESGMDSCLSKPVTLDVIKQTLTLYAER 126

>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 = 2e-04
 Identities = 7/41 (17%), Positives = 14/41 (34%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR 41
           ++    V    + M  GA D++ KP     +    +     
Sbjct: 81  ITGHGDVPMAVEAMKAGAVDFIEKPFEDTVIIEAIERASEH 121

>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 = 39.3 bits (91), Expect = 2e-04
 Identities = 10/41 (24%), Positives = 16/41 (39%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR 41
           M++   +        +GA DYL KP   +E   L +     
Sbjct: 81  MTAHSDLDAAVSAYQQGAFDYLPKPFDIDEAVALVERAISH 121

>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 = 39.3 bits (91), Expect = 2e-04
 Identities = 7/43 (16%), Positives = 18/43 (41%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQS 43
           +++   +    + M  GA ++L KP     L +  +   +  +
Sbjct: 80  ITAHGDIPMTVRAMKAGAIEFLPKPFEEQALLDAIEQGLQLNA 122

>d1a04a2 c.23.1.1 (A:5-142) Nitrate/nitrite response regulator (NarL), receiver domain {Escherichia coli [TaxId: 562]} Length = 138

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]

 Score = 38.7 bits (90), Expect = 3e-04
 Identities = 9/43 (20%), Positives = 15/43 (34%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQS 43
            S  +    V   + RGA  YL+K +   +L          + 
Sbjct: 82  FSVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALHQAAAGEM 124

>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 = 38.4 bits (89), Expect = 3e-04
 Identities = 8/34 (23%), Positives = 20/34 (58%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNL 34
           +++    S + +C+  G   +L KP++R +L+ +
Sbjct: 86  LTAFADDSNIKECLESGMNGFLSKPIKRPKLKTI 119

>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 = 37.7 bits (87), Expect = 6e-04
 Identities = 12/66 (18%), Positives = 27/66 (40%), Gaps = 6/66 (9%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSSMVSGNETQDESVGQQK 60
           ++    +    + +  GA D++ KP   + L    +    ++  +V  N +      ++ 
Sbjct: 78  VTGHGDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRAEEKR-RLVMENRSL-----RRA 131

Query: 61  IEATSE 66
            EA SE
Sbjct: 132 AEAASE 137

>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 = 37.6 bits (87), Expect = 6e-04
 Identities = 9/38 (23%), Positives = 18/38 (47%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHV 38
            S+    + V + +  GA D++VKP + + +      V
Sbjct: 80  CSAMGQQAMVIEAIKAGAKDFIVKPFQPSRVVEALNKV 117

>d1w25a1 c.23.1.1 (A:2-140) Response regulator PleD, receiver domain {Caulobacter crescentus [TaxId: 155892]} Length = 139

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 = 37.9 bits (87), Expect = 7e-04
 Identities = 13/59 (22%), Positives = 28/59 (47%), Gaps = 2/59 (3%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSSMVSGNETQDESVGQQ 59
           +++ D      + +  GA+D+L KP+    L    + + R +  +V     Q E+ G++
Sbjct: 81  ITALDGRGDRIQGLESGASDFLTKPIDDVMLFARVRSLTRFK--LVIDELRQREASGRR 137

>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 = 36.8 bits (85), Expect = 0.001
 Identities = 7/33 (21%), Positives = 16/33 (48%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRN 33
           M++   +  + +    GA  +  KP   +E+R+
Sbjct: 79  MTAYGELDMIQESKELGALTHFAKPFDIDEIRD 111

>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 = 37.4 bits (86), Expect = 0.001
 Identities = 10/42 (23%), Positives = 17/42 (40%)

Query: 1   MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ 42
           M   D    + K +  G  D L +P+   EL    +   +R+
Sbjct: 91  MVDPDDRGRMVKALEIGVNDILSRPIDPQELSARVKTQIQRK 132

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	491
d1qkka_	140	Transcriptional regulatory protein DctD, receiver	98.24
d1zh2a1	119	Transcriptional regulatory protein KdpE, N-termina	98.22
d2pl1a1	119	PhoP receiver domain {Escherichia coli [TaxId: 562	98.22
d1xhfa1	121	Aerobic respiration control protein ArcA, N-termin	98.2
d1p2fa2	120	Response regulator DrrB {Thermotoga maritima [TaxI	98.18
d1zgza1	120	TorCAD operon transcriptional regulator TorD, N-te	98.16
d1krwa_	123	NTRC receiver domain {Salmonella typhimurium [TaxI	98.16
d1ny5a1	137	Transcriptional activator sigm54 (NtrC1), N-termin	98.15
d1qo0d_	189	Positive regulator of the amidase operon AmiR {Pse	98.12
d2a9pa1	117	DNA-binding response regulator MicA, N-terminal do	98.12
d1zesa1	121	PhoB receiver domain {Escherichia coli [TaxId: 562	98.12
d1kgsa2	122	PhoB receiver domain {Thermotoga maritima [TaxId:	98.11
d1dbwa_	123	Transcriptional regulatory protein FixJ, receiver	98.09
d1w25a1	139	Response regulator PleD, receiver domain {Caulobac	98.05
d1jbea_	128	CheY protein {Escherichia coli [TaxId: 562]}	98.04
d1mvoa_	121	PhoP receiver domain {Bacillus subtilis [TaxId: 14	98.0
d1dz3a_	123	Sporulation response regulator Spo0A {Bacillus ste	97.97
d1ys7a2	121	Transcriptional regulatory protein PrrA, N-termina	97.95
d1peya_	119	Sporulation response regulator Spo0F {Bacillus sub	97.94
d1s8na_	190	Probable two-component system transcriptional regu	97.93
d2ayxa1	133	Sensor kinase protein RcsC, C-terminal domain {Esc	97.93
d1yioa2	128	Response regulatory protein StyR, N-terminal domai	97.93
d1w25a2	153	Response regulator PleD, receiver domain {Caulobac	97.92
d1p6qa_	129	CheY protein {Sinorhizobium meliloti, CheY2 [TaxId	97.89
d1i3ca_	144	Response regulator for cyanobacterial phytochrome	97.84
d1k68a_	140	Response regulator for cyanobacterial phytochrome	97.8
d2r25b1	128	Response regulator Sin1 {Baker's yeast (Saccharomy	97.76
d1a04a2	138	Nitrate/nitrite response regulator (NarL), receive	97.74
d1k66a_	149	Response regulator for cyanobacterial phytochrome	97.73
d1dcfa_	134	Receiver domain of the ethylene receptor {Thale cr	97.6
d1mb3a_	123	Cell division response regulator DivK {Caulobacter	97.59
d1a2oa1	140	Methylesterase CheB, N-terminal domain {Salmonella	95.83
d2b4aa1	118	Hypothetical protein BH3024 {Bacillus halodurans [	93.19

>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=98.24  E-value=4.1e-07  Score=78.11  Aligned_cols=42  Identities=14%  Similarity=0.332  Sum_probs=39.6

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++++++++.+|++.||.|||+|||+.++|...+++++++.
T Consensus        78 lT~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~~~~~  119 (140)
T d1qkka_          78 VTGHGDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRAEEKR  119 (140)
T ss_dssp             EECGGGHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHHHHH
T ss_pred             EECCCCHHHHHHHHHcCCCEeecCCCCHHHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999987665

>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=98.22  E-value=4.9e-07  Score=75.52  Aligned_cols=42  Identities=31%  Similarity=0.422  Sum_probs=39.8

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++++.+.+.+|++.||.|||+|||+.++|...++.++||.
T Consensus        77 lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~lrr~  118 (119)
T d1zh2a1          77 LSARSEESDKIAALDAGADDYLSKPFGIGELQARLRVALRRH  118 (119)
T ss_dssp             EESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHHHHH
T ss_pred             EeccCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHHhhh
Confidence            588999999999999999999999999999999999999875

>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=98.22  E-value=4.9e-07  Score=75.64  Aligned_cols=41  Identities=27%  Similarity=0.439  Sum_probs=39.3

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR   41 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk   41 (491)
                      ||++++.+.+.+|++.||.|||.|||+.++|...++.++||
T Consensus        78 lt~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~v~~~lrR  118 (119)
T d2pl1a1          78 LTARESWQDKVEVLSAGADDYVTKPFHIEEVMARMQALMRR  118 (119)
T ss_dssp             EESCCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHHHH
T ss_pred             eeccCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHHcc
Confidence            58999999999999999999999999999999999999986

>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=98.20  E-value=5.8e-07  Score=75.39  Aligned_cols=42  Identities=24%  Similarity=0.339  Sum_probs=39.8

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++++.+...+|++.||.|||+|||+.++|...++.+++|.
T Consensus        79 lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~v~~~l~Rs  120 (121)
T d1xhfa1          79 LTGRDNEVDKILGLEIGADDYITKPFNPRELTIRARNLLSRT  120 (121)
T ss_dssp             EESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHHHHH
T ss_pred             EECCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHhcc
Confidence            689999999999999999999999999999999999999874

>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=98.18  E-value=6.4e-07  Score=75.03  Aligned_cols=42  Identities=24%  Similarity=0.323  Sum_probs=39.6

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++++.+.+.+|++.||.|||+|||+.++|...++.++++.
T Consensus        77 it~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~l~r~  118 (120)
T d1p2fa2          77 LTLLSDDESVLKGFEAGADDYVTKPFNPEILLARVKRFLERE  118 (120)
T ss_dssp             EESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHHHHC
T ss_pred             EecCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHc
Confidence            589999999999999999999999999999999999998764

>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=98.16  E-value=7.9e-07  Score=73.88  Aligned_cols=42  Identities=21%  Similarity=0.260  Sum_probs=39.7

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++++.+...+|+++||.|||.|||+.++|...++.++||.
T Consensus        78 lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~lrR~  119 (120)
T d1zgza1          78 VTGRSDRIDRIVGLEMGADDYVTKPLELRELVVRVKNLLWRI  119 (120)
T ss_dssp             EESSCCHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHHHHH
T ss_pred             EEccCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHccc
Confidence            589999999999999999999999999999999999999874

>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=98.16  E-value=6e-07  Score=75.36  Aligned_cols=42  Identities=24%  Similarity=0.354  Sum_probs=39.9

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++++.+++.+|++.||.|||.|||+.++|...+++++++.
T Consensus        81 ~t~~~~~~~~~~a~~~Ga~dyl~KP~~~~eL~~~i~~~l~~~  122 (123)
T d1krwa_          81 MTAHSDLDAAVSAYQQGAFDYLPKPFDIDEAVALVERAISHY  122 (123)
T ss_dssp             SCCCSCHHHHHHHHHHTEEEECSSCCHHHHHHHHHHHHHHHH
T ss_pred             EecCCCHHHHHHHHHcCCCeEEeCcCCHHHHHHHHHHHHHcc
Confidence            799999999999999999999999999999999999998764

>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=98.15  E-value=5.1e-07  Score=77.11  Aligned_cols=42  Identities=21%  Similarity=0.366  Sum_probs=39.2

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||+|++.+++.+|++.||.|||+|||..++|...+++++++.
T Consensus        78 lT~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~l~~~  119 (137)
T d1ny5a1          78 ITGHGTIKTAVEAMKMGAYDFLTKPCMLEEIELTINKAIEHR  119 (137)
T ss_dssp             EEETTCHHHHHHHHTTTCCEEEEESCCHHHHHHHHHHHHHHH
T ss_pred             EECCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999987654

>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=98.12  E-value=7.7e-07  Score=78.21  Aligned_cols=42  Identities=7%  Similarity=0.117  Sum_probs=39.2

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||+|++++++.+|++.||.|||+|||..++|...+++++...
T Consensus        84 lta~~~~~~~~~al~~Ga~~yL~KP~~~~~L~~~i~~~~~~~  125 (189)
T d1qo0d_          84 LVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRIS  125 (189)
T ss_dssp             EECCCSHHHHHHHHHHTCSEEEESSCCGGGHHHHHHHHHHHH
T ss_pred             EeccchHHHHHHHHHcCCcEEEEecchhhHHHHHHhhccccc
Confidence            689999999999999999999999999999999999886655

>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=98.12  E-value=7.8e-07  Score=74.02  Aligned_cols=41  Identities=32%  Similarity=0.416  Sum_probs=38.6

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR   41 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk   41 (491)
                      ||++.+.+...+|++.||.|||+|||+.++|...++.++||
T Consensus        77 lt~~~~~~~~~~a~~~Ga~d~l~KP~~~~~L~~~i~~~lrR  117 (117)
T d2a9pa1          77 LSAKDSEFDKVIGLELGADDYVTKPFSNRELQARVKALLRR  117 (117)
T ss_dssp             EESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHHHC
T ss_pred             EecCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHhCC
Confidence            58899999999999999999999999999999999998875

>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=98.12  E-value=8e-07  Score=74.24  Aligned_cols=41  Identities=27%  Similarity=0.425  Sum_probs=39.3

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR   41 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk   41 (491)
                      ||++++.+.+.+|++.||.|||.|||+.++|...++.++||
T Consensus        80 lt~~~~~~~~~~~~~~G~~d~l~KP~~~~~L~~~v~~~lrR  120 (121)
T d1zesa1          80 LTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRR  120 (121)
T ss_dssp             EESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHHHT
T ss_pred             EECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHcC
Confidence            58999999999999999999999999999999999999986

>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=98.11  E-value=5.4e-07  Score=75.39  Aligned_cols=43  Identities=33%  Similarity=0.385  Sum_probs=40.5

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHh
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQS   43 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~   43 (491)
                      ||++++.+++.+|++.||.|||+|||+.++|...++.++|++.
T Consensus        79 lt~~~~~~~~~~~~~~Ga~~yl~KP~~~~~L~~~i~~~l~r~~  121 (122)
T d1kgsa2          79 LTALSDVEYRVKGLNMGADDYLPKPFDLRELIARVRALIRRKS  121 (122)
T ss_dssp             EESSCHHHHHHHTCCCCCSEEEESSCCHHHHHHHHHHHHHHHC
T ss_pred             EcCCCCHHHHHHHHHcCCceeecCCCCHHHHHHHHHHHHHHhc
Confidence            6899999999999999999999999999999999999998763

>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=98.09  E-value=7.9e-07  Score=74.73  Aligned_cols=41  Identities=17%  Similarity=0.328  Sum_probs=38.5

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR   41 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk   41 (491)
                      ||++++.+++.+|++.||.|||.|||+.++|...+++++.+
T Consensus        81 lt~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~i~~a~e~  121 (123)
T d1dbwa_          81 ITGHGDVPMAVEAMKAGAVDFIEKPFEDTVIIEAIERASEH  121 (123)
T ss_dssp             EECTTCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHHTT
T ss_pred             EEeeCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHh
Confidence            68999999999999999999999999999999999988754

>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=98.05  E-value=1.7e-06  Score=73.90  Aligned_cols=42  Identities=21%  Similarity=0.285  Sum_probs=39.5

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++++.+.+.+|++.||.|||+|||+.++|...++.++|+.
T Consensus        81 lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~lr~~  122 (139)
T d1w25a1          81 ITALDGRGDRIQGLESGASDFLTKPIDDVMLFARVRSLTRFK  122 (139)
T ss_dssp             EECSSCHHHHHHHHHHTCCEEEESSCCHHHHHHHHHHHHHHH
T ss_pred             EEcCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999988765

>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=98.04  E-value=1.9e-06  Score=72.60  Aligned_cols=42  Identities=17%  Similarity=0.396  Sum_probs=40.3

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++++.+.+.+|++.||.|||.|||+..+|...++++++|+
T Consensus        85 lt~~~~~~~~~~a~~~G~~~~l~KP~~~~~L~~~l~~~l~r~  126 (128)
T d1jbea_          85 VTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEKL  126 (128)
T ss_dssp             EESSCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHHHHH
T ss_pred             EECcCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHc
Confidence            589999999999999999999999999999999999999886

>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=98.00  E-value=8.4e-07  Score=73.98  Aligned_cols=41  Identities=24%  Similarity=0.375  Sum_probs=38.2

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR   41 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk   41 (491)
                      ||++++.+...+|++.||.|||.|||+.++|...++.++||
T Consensus        80 lt~~~~~~~~~~~~~~Ga~~yl~KP~~~~~L~~~i~~~lrR  120 (121)
T d1mvoa_          80 LTAKDEEFDKVLGLELGADDYMTKPFSPREVNARVKAILRR  120 (121)
T ss_dssp             EECTTCCCCHHHHHHTTCCEEEESSCCHHHHHHHHHHHHHT
T ss_pred             EEeeCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHcc
Confidence            57888888899999999999999999999999999999886

>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=97.97  E-value=1.1e-06  Score=73.61  Aligned_cols=41  Identities=17%  Similarity=0.336  Sum_probs=38.6

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR   41 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk   41 (491)
                      ||++++.+++.+|+++||.|||+|||+.++|...++++++|
T Consensus        82 ~t~~~~~~~~~~a~~~Ga~~~l~KP~~~~~L~~~i~~v~~k  122 (123)
T d1dz3a_          82 LTAFGQEDVTKKAVELGASYFILKPFDMENLAHHIRQVYGK  122 (123)
T ss_dssp             EEETTCHHHHHHHHHTTCEEEEECSSCCTTHHHHHHHHHHC
T ss_pred             EECcCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHcc
Confidence            58899999999999999999999999999999999998875

>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=97.95  E-value=5.1e-07  Score=75.83  Aligned_cols=42  Identities=36%  Similarity=0.454  Sum_probs=39.7

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++++.+.+.+|++.||.|||+|||+.++|...++.++||+
T Consensus        79 lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~l~rr  120 (121)
T d1ys7a2          79 LSARSSVDDRVAGLEAGADDYLVKPFVLAELVARVKALLRRR  120 (121)
T ss_dssp             EECCCTTTCCCTTTTTTCSEEEESSCCHHHHHHHHHHHHHHH
T ss_pred             EEeeCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHcC
Confidence            588999999999999999999999999999999999999876

>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=97.94  E-value=2.5e-06  Score=71.19  Aligned_cols=39  Identities=18%  Similarity=0.277  Sum_probs=36.2

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVW   39 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~   39 (491)
                      ||++++.+++.+|+++||.|||.|||+.++|...+++++
T Consensus        79 lt~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~v~~~L  117 (119)
T d1peya_          79 MTAYGELDMIQESKELGALTHFAKPFDIDEIRDAVKKYL  117 (119)
T ss_dssp             EESSCCHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHS
T ss_pred             EecCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHC
Confidence            689999999999999999999999999999999887753

>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=97.93  E-value=1.4e-06  Score=77.46  Aligned_cols=42  Identities=24%  Similarity=0.250  Sum_probs=38.7

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||+|++.+++.+|+++||.|||+||++.++|...|..++++.
T Consensus        81 lTa~~~~~~~~~al~~Ga~~yl~KP~~~~~L~~~i~~~~~~~  122 (190)
T d1s8na_          81 LTAFSQRDLVERARDAGAMAYLVKPFSISDLIPAIELAVSRF  122 (190)
T ss_dssp             EEEGGGHHHHHTTGGGSCEEEEEESCCHHHHHHHHHHHHHHH
T ss_pred             EeCCCCHHHHHHHHHcCCCEeccCCCCHHHHHHHHHHHHHhh
Confidence            689999999999999999999999999999999998876554

>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=97.93  E-value=2.8e-06  Score=72.15  Aligned_cols=43  Identities=16%  Similarity=0.279  Sum_probs=39.8

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHh
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQS   43 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~   43 (491)
                      ||++++.+.+.+|+..||.|||+|||+.++|...+++++++..
T Consensus        86 lt~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~~~r~r  128 (133)
T d2ayxa1          86 VTANALAEEKQRCLESGMDSCLSKPVTLDVIKQTLTLYAERVR  128 (133)
T ss_dssp             EESSTTSHHHHHHHHCCCEEEEESSCCHHHHHHHHHHHHHHHH
T ss_pred             EeccCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHHHHHH
Confidence            5889999999999999999999999999999999999887663

>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=97.93  E-value=1.2e-06  Score=73.70  Aligned_cols=42  Identities=17%  Similarity=0.356  Sum_probs=38.9

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++++.+++.+|+.+||.|||.|||+.++|...++++++..
T Consensus        80 lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~l~~~  121 (128)
T d1yioa2          80 ITAHGDIPMTVRAMKAGAIEFLPKPFEEQALLDAIEQGLQLN  121 (128)
T ss_dssp             EESCTTSCCCHHHHHTTEEEEEESSCCHHHHHHHHHHHHHHH
T ss_pred             EEEECCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHH
Confidence            588999999999999999999999999999999999988654

>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=97.92  E-value=3.9e-06  Score=73.09  Aligned_cols=43  Identities=23%  Similarity=0.339  Sum_probs=39.4

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHh
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQS   43 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~   43 (491)
                      ||++++.+.+.+|++.||.|||+|||+.++|...++.++++..
T Consensus        91 lt~~~~~~~~~~a~~~Ga~d~l~KP~~~~~L~~~i~~~l~~~~  133 (153)
T d1w25a2          91 MVDPDDRGRMVKALEIGVNDILSRPIDPQELSARVKTQIQRKR  133 (153)
T ss_dssp             EECTTCHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHHHHHH
T ss_pred             eecCCCHHHHHHHHhcCcceEEECCCCHHHHHHHHHHHHHHHH
Confidence            5899999999999999999999999999999999988876653

>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=97.89  E-value=4.1e-06  Score=70.65  Aligned_cols=41  Identities=22%  Similarity=0.336  Sum_probs=39.0

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR   41 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk   41 (491)
                      ||++++.+.+.+|+..||.|||+|||+.++|...+++++++
T Consensus        87 lt~~~~~~~~~~a~~~G~~~~l~KP~~~~~L~~~i~~vl~~  127 (129)
T d1p6qa_          87 LTAQGDRALVQKAAALGANNVLAKPFTIEKMKAAIEAVFGA  127 (129)
T ss_dssp             CCSCCCHHHHHHHHHHTCSCEECCCSSHHHHHHHHHHHHHC
T ss_pred             EEecCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHh
Confidence            68999999999999999999999999999999999998865

>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=97.84  E-value=7.1e-06  Score=70.51  Aligned_cols=44  Identities=14%  Similarity=0.063  Sum_probs=39.9

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHhc
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSS   44 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~~   44 (491)
                      ||++++.+.+.+|+++||.|||+|||+.++|...++.+.+....
T Consensus        92 lT~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~i~~l~~~~~~  135 (144)
T d1i3ca_          92 LTTSHNEDDVIASYELHVNCYLTKSRNLKDLFKMVQGIESFWLE  135 (144)
T ss_dssp             EESCCCHHHHHHHHHTTCSEEEECCSSHHHHHHHHHHHHHHHTT
T ss_pred             EECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHHHh
Confidence            68999999999999999999999999999999999988766543

>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=97.80  E-value=9.3e-06  Score=69.42  Aligned_cols=44  Identities=11%  Similarity=0.088  Sum_probs=40.2

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHhc
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQSS   44 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~~   44 (491)
                      ||++++.+.+.+|+++||.|||+|||+.++|...++.+++....
T Consensus        91 ls~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~i~~i~~~~~~  134 (140)
T d1k68a_          91 LSTSINEDDIFHSYDLHVNCYITKSANLSQLFQIVKGIEEFWLS  134 (140)
T ss_dssp             EESCCCHHHHHHHHHTTCSEEEECCSSHHHHHHHHHHHHHHHHT
T ss_pred             EeCCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHHhh
Confidence            58899999999999999999999999999999999998776544

>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=97.76  E-value=7.1e-06  Score=69.42  Aligned_cols=39  Identities=21%  Similarity=0.525  Sum_probs=36.4

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVW   39 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~   39 (491)
                      ||++++.+++.+|++.||.+||+|||+.++|..++++++
T Consensus        86 lT~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~~  124 (128)
T d2r25b1          86 LTAFADDSNIKECLESGMNGFLSKPIKRPKLKTILTEFC  124 (128)
T ss_dssp             EESCCSHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHC
T ss_pred             EECCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHH
Confidence            589999999999999999999999999999999988754

>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=97.74  E-value=1.1e-05  Score=68.37  Aligned_cols=40  Identities=23%  Similarity=0.342  Sum_probs=37.4

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWR   40 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~r   40 (491)
                      +|++++.+++.+|++.||.+||+||++.++|...++.+++
T Consensus        82 lt~~~~~~~~~~a~~~Ga~~yl~Kp~~~~~L~~~i~~v~~  121 (138)
T d1a04a2          82 FSVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALHQAAA  121 (138)
T ss_dssp             EECCCCHHHHHHHHHTTCSEEEETTCCHHHHHHHHHHHHH
T ss_pred             EEEECCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHHC
Confidence            5789999999999999999999999999999999988865

>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=97.73  E-value=1.2e-05  Score=69.50  Aligned_cols=43  Identities=19%  Similarity=0.308  Sum_probs=39.8

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHHh
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQS   43 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~~   43 (491)
                      ||++++.+.+.+|++.||.|||+|||+.++|...++.+++...
T Consensus        98 lT~~~~~~~~~~~~~~Ga~~~l~KP~~~~~L~~~i~~~l~~~~  140 (149)
T d1k66a_          98 MTTSSNPKDIEICYSYSISSYIVKPLEIDRLTETVQTFIKYWL  140 (149)
T ss_dssp             EESCCCHHHHHHHHHTTCSEEEECCSSHHHHHHHHHHHHHHHH
T ss_pred             EeCCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHHh
Confidence            5899999999999999999999999999999999999987643

>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=97.60  E-value=1.4e-05  Score=67.80  Aligned_cols=42  Identities=29%  Similarity=0.461  Sum_probs=38.5

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRRQ   42 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk~   42 (491)
                      ||++.+.+...+|+..||.+||.|||+.++|..+++++++.+
T Consensus        89 lT~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~l~~r  130 (134)
T d1dcfa_          89 LSGNTDKSTKEKCMSFGLDGVLLKPVSLDNIRDVLSDLLEPR  130 (134)
T ss_dssp             EESCCSHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHHSCC
T ss_pred             EeCCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHhhhh
Confidence            589999999999999999999999999999999999887543

>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=97.59  E-value=9.9e-06  Score=67.32  Aligned_cols=41  Identities=12%  Similarity=0.190  Sum_probs=32.6

Q ss_pred             CCCcchHHHHHHHHHhccceeEeCCCCHHHHHHHHHHHHHH
Q 011208            1 MSSQDSVSTVYKCMMRGAADYLVKPVRRNELRNLWQHVWRR   41 (491)
Q Consensus         1 MS~~d~~e~v~kal~~GA~DYLlKPv~~eELk~lwqhv~rk   41 (491)
                      ||+++..+...+|+..||.|||.|||+.++|...++.+++|
T Consensus        81 lt~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~i~~~l~r  121 (123)
T d1mb3a_          81 VTAFAMKGDEERIREGGCEAYISKPISVVHFLETIKRLLER  121 (123)
T ss_dssp             EC------CHHHHHHHTCSEEECSSCCHHHHHHHHHHHHSC
T ss_pred             EEEecCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHHhC
Confidence            58888899999999999999999999999999999998865

>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=95.83  E-value=0.0022  Score=54.02  Aligned_cols=22  Identities=23%  Similarity=0.430  Sum_probs=19.4

Q ss_pred             hHHHHHHHHHhccceeEeCCCC
Q 011208            6 SVSTVYKCMMRGAADYLVKPVR   27 (491)
Q Consensus         6 ~~e~v~kal~~GA~DYLlKPv~   27 (491)
                      ..+++.+|++.||.|||+||+.
T Consensus        89 ~~~~~~~al~~Ga~~yl~KP~~  110 (140)
T d1a2oa1          89 GSEVTLRALELGAIDFVTKPQL  110 (140)
T ss_dssp             HHHHHHHHHHHTCCEEEECSSS
T ss_pred             ChHHHHHHHHcCCCEEEECCCC
Confidence            3478999999999999999974

>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=93.19  E-value=0.0096  Score=48.93  Aligned_cols=25  Identities=28%  Similarity=0.335  Sum_probs=20.6

Q ss_pred             HHHHhccceeEeCCCCHHHHHHHHHH
Q 011208           12 KCMMRGAADYLVKPVRRNELRNLWQH   37 (491)
Q Consensus        12 kal~~GA~DYLlKPv~~eELk~lwqh   37 (491)
                      +++..|| |||.|||+.+||...+++
T Consensus        90 ~~~~~~~-dyl~KP~~~~eL~~~i~~  114 (118)
T d2b4aa1          90 ESSEHNL-SYLQKPFAISELRAAIDY  114 (118)
T ss_dssp             CCSSSCE-EEEESSCCHHHHHHHHHH
T ss_pred             HHhhcCC-CEEECCCCHHHHHHHHHH
Confidence            3455677 999999999999988875