Citrus Sinensis ID: 013329

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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-----
Protein Sequence
MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLVASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTSGTAAVEPIDASECGPDVPGISDRRTGQFSAGPKKIELRIGESSAFFTYVKSNMPRDSSPRIVNVDDSAAQNVRMEEKCQPCCQQVVSDTRIHENGEAWENYSQGEDFRSSSSVPDSLSMERSSTPPTDFPQNRNFKDEKFFQPQMPPTRNEPPQATYQYYMSGAMNQVMLPSSSAQMYQKNLHELQNHSMLPQYNHLPQCVPHVNGMASFPYYPINMCLQPGQVSANSWPSYGNSPSTEVKMNKVDRREAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVRKVNGVNVDLNGQPSSVDYDEDEDEEEEMASRDSSPDNDTSGN
Secondary Structure (PSIPRED)
cccccHHHHHHHHHHHccccHHcccccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccHHccHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHcccccccEEccccccccccccccccccccccHHHHHHHHccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccHHHHHHHHHHcHHHHHccHHHHHHHHHHHHHHHHHHHHcccccccccccccHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHccccccccccccccccccccccccEEEcccccccccccccccccccccccccccccccccccHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHcccccEEEHHHHHHHHHHccccccEEEEEEcccccccccccccccccccHcHHHHHcccccccccccccc
Coil and Loop (DISEMBL)
MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILsydfdlvasdpsdantnsttlfsddtddksrrstnpeigmsthqetesvpVATATVVAstsgtaavepidasecgpdvpgisdrrtgqfsagpkkielrigesSAFFTYVksnmprdssprivnvddsaaqnvrmeekcqpccqqvvsdtrihengeawenysqgedfrssssvpdslsmersstpptdfpqnrnfkdekffqpqmpptrneppqatYQYYMSGamnqvmlpsssaQMYQKNLHElqnhsmlpqynhlpqcvphvngmasfpyypinmclqpgqvsanswpsygnspstevkmnKVDRREAALIKFRQKRKERCFDKKIRYVNRKrlaerrprvrgqfvrkvngvnvdlngqpssvdydededeeeemasrdsspdndtsgn
Flexible Loop (DISEMBL)
MSAQDEVSVVVKCLRlgaadylvkplrtneLLNLWTHMWRRRRMLGLAEKNILSYDFDLVasdpsdantnsttlfsddtddksrrstnpeigmsthqetesvpVATATVVASTSgtaavepidasecgpdvpgisdrrtgqfsagpkkielrigeSSAFFTYVKSnmprdssprivNVDDSAAQNVRMEEKCQPCCQQVVSDTRIHENGEAwenysqgedfrsSSSVPDSLSMErsstpptdfpqnrNFKDEKffqpqmpptrnePPQATYQYYMSGAMNQVMLPSSSAQMYQKNLHELQNHSMLPQYNHLPQCVPHVNGMASFPYYPINMCLQPGQVSANSWPSYGNSpstevkmnkvdRREAALIKfrqkrkercfdkkiryvnrkrlaerrprvrgqfvrkvngvnvdlngqpssvdYDEDEDEEeemasrdsspdndtsgn
Low Complexity Region (SEG)
MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLVASDPSDANTNSTTLFsddtddksrrstNPEIGMSTHQetesvpvatatvvastsgtaavePIDASECGPDVPGISDRRTGQFSAGPKKIELRIGESSAFFTYVKSNMPRDSSPRIVNVDDSAAQNVRMEEKCQPCCQQVVSDTRIHENGEAWENYSQGEDFRSSSSVPDSLSMERSSTPPTDFPQNRNFKDEKFFQPQMPPTRNEPPQATYQYYMSGAMNQVMLPSSSAQMYQKNLHELQNHSMLPQYNHLPQCVPHVNGMASFPYYPINMCLQPGQVSANSWPSYGNSPSTEVKMNKVDRREAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVRKVNGVNVDLNGQPssvdydededeeeemasrdssPDNDTSGN
Disordered region (IsUnstruct)
******VSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLVA*******************************************************************************************IG*SSAFFTYV****************************CQPCCQQVVSDT*********************************************************************YY****************************SMLPQYNHLPQCVPHVNGMASFPYYPINMCLQPGQV**************************ALIKFRQKRKERCFDKKIRYVNRKRLAER*PRVRGQFVRKVNGVN************************************
Disordered Region (DISOPRED)
******V***VKCLRLGAADYLVKPLRTNELLNLWTHMWR**************************************************************************************************************************************************************************************************************************************YQYYMSG*************************************************************SANSWPSYGNSPSTEVKMNKVDRR*AALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFV*******************************************
Disordered Region (DISEMBL)
********VVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLVASDPSDANTNSTTLFS**********TNPEIGMSTHQETESVPVATATVVASTSGTAAVEPIDASECGPDVPGISDRRTGQFSAGPKKIELRIGESSAFFTYVKSNMPRDSSPRIVNVDDSAAQNVRMEEKCQPCCQQVVSDTRIHENGEAWENY**************************DFPQNRNFKDEKFFQPQMPPTRNEPPQATYQYYMSGAMNQVMLPSSSAQMYQKNLHELQNHSMLPQYNHLPQCVPHVNGMASFPYYPINMCLQPGQVSANSWPSYGNSPSTEVKMNKVDRREAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVRKVNGVNVDLNGQPSS***************************
Disordered Region (DISPRO)
*****EVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRML**************************************************************************************************************SSAF************************************************************************************************************QATYQYYMSGAMNQVMLPSSSAQM**KNLHELQNHSMLPQYNHLPQCVPHVNGMASFPYYP*******************************DRREAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVRKVN***************************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLVASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTSGTAAVEPIDASECGPDVPGISDRRTGQFSAGPKKIELRIGESSAFFTYVKSNMPRDSSPRIVNVDDSAAQNVRMEEKCQPCCQQVVSDTRIHENGEAWENYSQGEDFRSSSSVPDSLSMERSSTPPTDFPQNRNFKDEKFFQPQMPPTRNEPPQATYQYYMSGAMNQVMLPSSSAQMYQKNLHELQNHSMLPQYNHLPQCVPHVNGMASFPYYPINMCLQPGQVSANSWPSYGNSPSTEVKMNKVDRREAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVRKVNGVNVDLNGQPSSVDYDEDEDEEEEMASRDSSPDNDTSGN
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	445	2.2.26 [Sep-21-2011]
Q9LKL2	618	Two-component response re	yes	no	0.957	0.689	0.477	1e-112
Q689G9	518	Two-component response re	yes	no	0.820	0.704	0.401	4e-73
Q93WK5	727	Two-component response re	no	no	0.110	0.067	0.775	3e-16
Q8L500	468	Two-component response re	no	no	0.103	0.098	0.760	1e-14
Q9LVG4	495	Two-component response re	no	no	0.098	0.088	0.727	3e-13
Q689G6	623	Two-component response re	no	no	0.119	0.085	0.641	4e-13
Q6LA42	558	Two-component response re	no	no	0.114	0.091	0.627	9e-13
Q0D3B6	742	Two-component response re	no	no	0.103	0.061	0.739	1e-12
A2YQ93	742	Two-component response re	N/A	no	0.103	0.061	0.739	1e-12
A2XFB7	767	Two-component response re	N/A	no	0.134	0.078	0.588	1e-12

>sp|Q9LKL2|APRR1_ARATH Two-component response regulator-like APRR1 OS=Arabidopsis thaliana GN=APRR1 PE=1 SV=1

 Score =  405 bits (1041), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 256/536 (47%), Positives = 309/536 (57%), Gaps = 110/536 (20%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLV 60
           MS QDEV VVVKCL+LGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKN+LSYDFDLV
Sbjct: 100 MSRQDEVPVVVKCLKLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNMLSYDFDLV 159

Query: 61  ASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETE----SVPV--------ATAT 108
            SD SD NTNST LFSDDTDD+S RSTNP+ G  +HQE E    + PV        A  T
Sbjct: 160 GSDQSDPNTNSTNLFSDDTDDRSLRSTNPQRGNLSHQENEWSVATAPVHARDGGLGADGT 219

Query: 109 VVASTSGTAAVEPIDASECGPDVPGISDRRTGQFSAGPKKIELRIGESSAFFTYVKSNMP 168
             +S + TA   P+D        P   +    QFS+ PKK  L+IGESSAFFTYVKS + 
Sbjct: 220 ATSSLAVTAIEPPLDHLAGSHHEPMKRNSNPAQFSSAPKKSRLKIGESSAFFTYVKSTVL 279

Query: 169 RDSS----------------------------------------------------PRIV 176
           R +                                                     P +V
Sbjct: 280 RTNGQDPPLVDGNGSLHLHRGLAEKFQVVASEGINNTKQARRATPKSTVLRTNGQDPPLV 339

Query: 177 NVDDSAAQNVRMEEKCQPCCQQVVSDTRIHENGEAWENY-SQGEDFRSSSSVPDSLSMER 235
           N + S   +    EK Q    + +++T+        E Y SQGE  ++ +S P SL  ER
Sbjct: 340 NGNGSHHLHRGAAEKFQVVASEGINNTKQAHRSRGTEQYHSQGETLQNGASYPHSL--ER 397

Query: 236 SSTPPTDF-PQNRNFKDEKFFQPQMPPTRNE-----------PPQATYQYYMSGAMNQVM 283
           S T PT      RN+++     PQ+   R++            P A Y YYM G MNQVM
Sbjct: 398 SRTLPTSMESHGRNYQEGNMNIPQVAMNRSKDSSQVDGSGFSAPNA-YPYYMHGVMNQVM 456

Query: 284 LPSSSAQMYQKNLHELQNHSMLPQYNH-LPQCVP-HVNGMASFPYY--PIN-------MC 332
           + S+               +M+PQY H +P C P H NGM  +PYY  P+N       M 
Sbjct: 457 MQSA---------------AMMPQYGHQIPHCQPNHPNGMTGYPYYHHPMNTSLQHSQMS 501

Query: 333 LQPGQVSA--NSWPSYGNSPSTEVKMNKVDRREAALIKFRQKRKERCFDKKIRYVNRKRL 390
           LQ GQ+S   +SW   GN PS EV++NK+DRRE AL+KFR+KR +RCFDKKIRYVNRKRL
Sbjct: 502 LQNGQMSMVHHSWSPAGNPPSNEVRVNKLDRREEALLKFRRKRNQRCFDKKIRYVNRKRL 561

Query: 391 AERRPRVRGQFVRKVNGVNVDLNGQPSSVDYDE--DEDEEEEMASRDSSPDNDTSG 444
           AERRPRV+GQFVRK+NGVNVDLNGQP S DYD+  +E+EEEE  +RDSSP +D  G
Sbjct: 562 AERRPRVKGQFVRKMNGVNVDLNGQPDSADYDDEEEEEEEEEEENRDSSPQDDALG 617

Controls photoperiodic flowering response. 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. Positive regulator of CCA1 and LHY expression.
Arabidopsis thaliana (taxid: 3702)

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

 Score =  275 bits (704), Expect = 4e-73,   Method: Compositional matrix adjust.
 Identities = 175/436 (40%), Positives = 230/436 (52%), Gaps = 71/436 (16%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLV 60
           MS +DEVSVVVKCLRLGAA+YLVKPLR NELLNLWTH+WRRRRMLGL+EKN  + +F+L 
Sbjct: 109 MSNRDEVSVVVKCLRLGAAEYLVKPLRMNELLNLWTHVWRRRRMLGLSEKNFFNDNFELA 168

Query: 61  ASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVP---------VATATVVA 111
            S+PSDANTNSTTL SDDTDDK + + N E   S   E ES P              +V+
Sbjct: 169 LSEPSDANTNSTTLLSDDTDDKPKENINQETSTSNQHEYESNPSDAEPKQKGTPEGLLVS 228

Query: 112 STSGTAAVEPIDASECGPDVPGISDRRTGQFSAGPKKIELRIGESSAFFTYVKSNMPRDS 171
           +  G  A  P                  G   + P K  LR+ ESSAF  YVKS+ P  S
Sbjct: 229 TEGGDQASSP------------------GVMFSRPIKTNLRVAESSAFLAYVKSSTPTTS 270

Query: 172 SPRIVNVDDSAAQNVRMEEKCQPCCQQVVSDTRIHENGEAWENYSQGEDFRSSSSVPDS- 230
           S                             D+ + + G   ++     +F S++   D+ 
Sbjct: 271 S----------------------------FDSELQKGGNRLDSSDHRGNFSSTTDRSDTG 302

Query: 231 ----LSMERSSTPPTDFP----QNRNFKDEKFFQPQMPPTRNEPPQATYQYYMSGAMNQV 282
               +  + +   P  +P     + N   E+  + Q   +   PP   + +Y  G M+  
Sbjct: 303 TDVNIRDKEAFEMPVQYPVVCFSSSNLHLERSNEGQNDAS-GTPPVYHFPFYYPGMMDHG 361

Query: 283 MLPSSSAQMYQKNLHELQNH---SMLPQYNHLPQCVPHVNGMASFPYYPINMCLQPGQV- 338
           M      Q +Q N++  Q H   ++LPQYN  PQC   V+ M  F Y P  M +Q  Q+ 
Sbjct: 362 MT-HPPVQNFQGNINNAQVHTPQTLLPQYNVYPQC-HGVSMMPPFQYNPAGMSIQSNQLP 419

Query: 339 SANSWPSYGNSPSTEVKMNKVDRREAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVR 398
           + N WP   ++P  E   ++ +RR AAL KFR KRKERCFDKK+RYVNRK+LAE RPRVR
Sbjct: 420 TQNMWPQASSTPMPEETCSRSERRAAALAKFRLKRKERCFDKKVRYVNRKKLAETRPRVR 479

Query: 399 GQFVRKVNGVNVDLNG 414
           GQFVR+ N  ++   G
Sbjct: 480 GQFVRQANYTDITSTG 495

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

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score = 86.7 bits (213), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 38/49 (77%), Positives = 44/49 (89%)

Query: 357 NKVDRREAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVRKV 405
           NK+ +REAAL KFRQKRKERCF KK+RY +RK+LAE+RPRVRGQFVRK 
Sbjct: 664 NKISQREAALTKFRQKRKERCFRKKVRYQSRKKLAEQRPRVRGQFVRKT 712

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

 Score = 81.6 bits (200), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 35/46 (76%), Positives = 43/46 (93%)

Query: 361 RREAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVRKVN 406
           +REAAL+KFR KRK+RCFDKK+RY +RK+LAE+RPRV+GQFVR VN
Sbjct: 416 QREAALMKFRLKRKDRCFDKKVRYQSRKKLAEQRPRVKGQFVRTVN 461

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 = 76.6 bits (187), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 32/44 (72%), Positives = 41/44 (93%)

Query: 361 RREAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVRK 404
           +REAAL+KFR KRKERCF+KK+RY +RK+LAE+RP V+GQF+RK
Sbjct: 441 QREAALMKFRLKRKERCFEKKVRYHSRKKLAEQRPHVKGQFIRK 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|Q689G6|PRR95_ORYSJ Two-component response regulator-like PRR95 OS=Oryza sativa subsp. japonica GN=PRR95 PE=2 SV=1

 Score = 76.6 bits (187), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 34/53 (64%), Positives = 45/53 (84%)

Query: 356 MNKVDRREAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVRKVNGV 408
           +  + +REAAL KFR KRK+RCF+KK+RY +RK LAE+RPRV+GQFVR+ +GV
Sbjct: 568 LRHLSQREAALNKFRLKRKDRCFEKKVRYQSRKLLAEQRPRVKGQFVRQDHGV 620

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

 Score = 75.1 bits (183), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 32/51 (62%), Positives = 45/51 (88%)

Query: 355 KMNKVDRREAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVRKV 405
           K+ +  +REAAL KFR KRK+RC++KK+RY +RK+LAE+RPR++GQFVR+V
Sbjct: 502 KIQQSLQREAALTKFRMKRKDRCYEKKVRYESRKKLAEQRPRIKGQFVRQV 552

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

 Score = 75.1 bits (183), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 34/46 (73%), Positives = 40/46 (86%)

Query: 360 DRREAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVRKV 405
           + R AA+IKFRQKRKER F KK+RY +RKRLAE+RPRVRGQFVR+ 
Sbjct: 680 EHRVAAVIKFRQKRKERNFGKKVRYQSRKRLAEQRPRVRGQFVRQA 725

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

 Score = 75.1 bits (183), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 34/46 (73%), Positives = 40/46 (86%)

Query: 360 DRREAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVRKV 405
           + R AA+IKFRQKRKER F KK+RY +RKRLAE+RPRVRGQFVR+ 
Sbjct: 680 EHRVAAVIKFRQKRKERNFGKKVRYQSRKRLAEQRPRVRGQFVRQA 725

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

 Score = 74.7 bits (182), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 40/68 (58%), Positives = 46/68 (67%), Gaps = 8/68 (11%)

Query: 357 NKVDRREAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVRKVNGVNVDLNGQP 416
           N V  REAAL KFRQKRK R F KK+RY +RKRLAE+RPR+RGQFVR+        +GQ 
Sbjct: 707 NGVCYREAALNKFRQKRKVRNFGKKVRYQSRKRLAEQRPRIRGQFVRQ--------SGQE 758

Query: 417 SSVDYDED 424
                DED
Sbjct: 759 DQAGQDED 766

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	445
359491315	556	PREDICTED: two-component response regula	0.968	0.775	0.699	1e-167
51980216	545	timing of CAB expression 1 protein [Cast	0.903	0.737	0.697	1e-165
224124202	541	pseudo response regulator [Populus trich	0.946	0.778	0.669	1e-161
255547335	550	sensory transduction histidine kinase, p	0.973	0.787	0.667	1e-158
297733942	533	unnamed protein product [Vitis vinifera]	0.907	0.757	0.666	1e-158
356508533	560	PREDICTED: two-component response regula	0.966	0.767	0.627	1e-157
356513521	559	PREDICTED: two-component response regula	0.970	0.772	0.652	1e-154
351722597	558	timing of CAB expression 1 [Glycine max]	0.964	0.768	0.619	1e-153
356565113	565	PREDICTED: two-component response regula	0.968	0.762	0.632	1e-151
327533492	561	TOC1 [Phaseolus vulgaris]	0.961	0.762	0.629	1e-146

>gi|359491315|ref|XP_002281757.2| PREDICTED: two-component response regulator-like APRR1-like [Vitis vinifera]

 Score =  593 bits (1528), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 319/456 (69%), Positives = 371/456 (81%), Gaps = 25/456 (5%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLV 60
           MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNIL+YDFD+ 
Sbjct: 108 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILNYDFDVA 167

Query: 61  ASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTSGTAAVE 120
           ASDPSDANTNST +FSDDTDDKSR S NPE+ +S HQE E V ++ AT+    S   A E
Sbjct: 168 ASDPSDANTNST-MFSDDTDDKSRMSANPEMVVSVHQEDE-VSLSNATI---DSTDVAAE 222

Query: 121 P--IDASECGPDVPGISDRRTGQFSAGPKKIELRIGESSAFFTYVKSNMPRDSSPRIVNV 178
           P  ++  EC PDVPGISDRRTGQ  +GPKK EL++GESSAFFTYVKS+M + +S  I N+
Sbjct: 223 PPVVNQLECRPDVPGISDRRTGQLLSGPKKSELKVGESSAFFTYVKSSMIKTNSQGIPNI 282

Query: 179 DDSAAQNVRMEEKCQPCCQQVVSDTRIHENGEAWENYSQGEDFRSSSSVPDSLSMERSST 238
           ++SA Q+ RMEE+ Q   ++ V+DT+ HENGEAWENYSQG+DF SS+S+PDSLS+E S T
Sbjct: 283 NESAPQHSRMEERVQAWSEKGVNDTQEHENGEAWENYSQGDDFPSSNSIPDSLSVEMSCT 342

Query: 239 PPT--DFPQNRNFKDEKFFQPQMPPTRNE--------PPQATYQYYMSGAMNQVMLPSSS 288
           PP   +F Q RN K E+F Q  + P RNE        P    Y Y MSG MNQVM+PSS 
Sbjct: 343 PPAPIEFVQGRNSKGEEFSQVPIHP-RNEHQVDISGFPGHTAYPYCMSGVMNQVMMPSS- 400

Query: 289 AQMYQKNLHELQNHS----MLPQYNHLPQCVPHVNGMASFPYYPINMCLQPGQVSA-NSW 343
           AQ+Y K+LH++QN++    MLPQYNHLPQC PHV G+ASFPYYP+++CLQPGQ+S  + W
Sbjct: 401 AQLYPKSLHDMQNNATTSAMLPQYNHLPQCPPHVPGVASFPYYPVSICLQPGQMSTTHPW 460

Query: 344 PSYGNSPSTEVKMNKVDRREAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVR 403
           PSYGNS STEVK+ KVDRREAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVR
Sbjct: 461 PSYGNSSSTEVKLGKVDRREAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVR 520

Query: 404 KVNGVNVDLNGQPSSVDYDEDEDEEEEM-ASRDSSP 438
           K+NGVNVDLNG+P+SVD+DEDE+E EE  ASRDS+P
Sbjct: 521 KMNGVNVDLNGRPASVDFDEDEEEYEEENASRDSTP 556

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|51980216|gb|AAU20772.1| timing of CAB expression 1 protein [Castanea sativa]

 Score =  589 bits (1518), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 304/436 (69%), Positives = 352/436 (80%), Gaps = 34/436 (7%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLV 60
           MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTH+WRRRRMLGLAEKNIL+YDFDLV
Sbjct: 113 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHVWRRRRMLGLAEKNILNYDFDLV 172

Query: 61  ASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTSGTAAVE 120
           ASDPSDANTNSTTLFSDDTDD+S RSTNPE+G+S H+E ES               AAVE
Sbjct: 173 ASDPSDANTNSTTLFSDDTDDRSCRSTNPEMGLSVHEEDES-------------AGAAVE 219

Query: 121 P--IDASECGPDVPGISDRRTGQFSAGPKKIELRIGESS-AFFTYVKSNMPRDSSPRIVN 177
           P  I+  E  PDVP ISDRRTGQFS+GPKK EL+IGESS AFFTYVK++  + SSP + N
Sbjct: 220 PPYIELDEYRPDVPKISDRRTGQFSSGPKKSELKIGESSSAFFTYVKTSTLQKSSPGVAN 279

Query: 178 VDDSAAQNVRMEEKCQPCCQQVVSDTRIHENGEAWENYSQGEDFRSSSSVPDSLSMERSS 237
           V+++ AQ VRM E  Q C QQVV+D +I+++GE WE+YSQG++F SS+S+PDS S+ERSS
Sbjct: 280 VEENVAQ-VRMGENHQACVQQVVNDPQINDSGEVWESYSQGDEFPSSNSMPDSFSIERSS 338

Query: 238 TPPT--DFPQNRNFKDEKFFQPQMPPTRNE--------PPQATYQYYMSGAMNQVMLPSS 287
           TP    + PQ R+ KDE+F Q    P RNE        P Q  + Y MSG +NQVM+PS+
Sbjct: 339 TPSASMELPQQRDLKDERFSQVLSHP-RNEHQLDASGLPAQTAFPYCMSGVVNQVMMPSA 397

Query: 288 SAQMYQKNLHELQNHS---MLPQYNHLPQCVPHVNGMASFPYYPINMCLQPGQVSA-NSW 343
            AQ+Y KNLH+LQNHS   M+ QY+HLPQC PHVNGMA FPYYP+N+CLQPGQ+SA +SW
Sbjct: 398 -AQLYHKNLHDLQNHSPKAMMSQYHHLPQCPPHVNGMAPFPYYPVNICLQPGQMSASHSW 456

Query: 344 PSYGNSPSTEVKMNKVDRREAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVR 403
           P +G+  S+EV ++KVDRREAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVR
Sbjct: 457 P-FGSPSSSEVNLSKVDRREAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVR 515

Query: 404 KVNGVNVDLNGQPSSV 419
           KVNGVNVDLNG P+SV
Sbjct: 516 KVNGVNVDLNGHPTSV 531

Source: Castanea sativa

Species: Castanea sativa

Genus: Castanea

Family: Fagaceae

Order: Fagales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224124202|ref|XP_002330130.1| pseudo response regulator [Populus trichocarpa] gi|222871264|gb|EEF08395.1| pseudo response regulator [Populus trichocarpa]

 Score =  573 bits (1477), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 308/460 (66%), Positives = 364/460 (79%), Gaps = 39/460 (8%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLV 60
           MSAQDEVS+VVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR MLGLAEKNIL+YDFD V
Sbjct: 106 MSAQDEVSIVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRHMLGLAEKNILNYDFDPV 165

Query: 61  ASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTSGTAAVE 120
           ASDPSDANTNSTTLFSDDTDD SRRSTNPE+GMSTHQE E                    
Sbjct: 166 ASDPSDANTNSTTLFSDDTDDLSRRSTNPEMGMSTHQEDEP------------------S 207

Query: 121 PIDASECGPDVPGISDRRTGQFSAGPKKIELRIGESSAFFTYVKSNMPRDSSPRIVNVDD 180
           P D  +  PDVPGISDRRTG  S+GPKK EL+IGESSAFFTYVK +  +++S  +  ++D
Sbjct: 208 PGDPQKYRPDVPGISDRRTGHLSSGPKKSELKIGESSAFFTYVKPSTVKNNSQGVALIED 267

Query: 181 SAAQNVRMEEKCQPCCQQVVSDTRIHENGEAWENYSQGEDFRSSSSVPDSLSMERSSTPP 240
           +  QN+RMEEK Q C +Q+++D  + ENGEA E +SQ +DFRSSSS+PDSLS+ERS TPP
Sbjct: 268 NTNQNLRMEEKLQVCGEQMLNDAHLQENGEALEIHSQVDDFRSSSSIPDSLSLERSCTPP 327

Query: 241 T--DFPQNRNFKDEKFFQPQMPPTRNEP--------PQATYQYYMSGAMNQVMLPSSSAQ 290
              +FPQ RNFKD++    Q     NEP         Q+ Y Y+MSG +NQVM+ SSSAQ
Sbjct: 328 MSREFPQ-RNFKDDRVLMHQT----NEPQLDASSLSTQSVYPYFMSGVVNQVMM-SSSAQ 381

Query: 291 MYQKNLHELQN---HSMLPQYNHLPQCVPHVNGMASFPYYPINMCLQPGQV-SANSWPSY 346
           +YQKNLHELQ+    +MLP YNHLPQC PH++GMASFPYYP+++CLQPGQ+ +  SWPS+
Sbjct: 382 LYQKNLHELQSLGTSAMLPGYNHLPQCPPHMSGMASFPYYPVSICLQPGQMPTTPSWPSF 441

Query: 347 GNSPSTEVKMNKVDRREAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVRKVN 406
           G+S S +VK+NKVDRREAAL KFRQKRKERCFDKKIRYVNRK+LAERRPRVRGQFVRKVN
Sbjct: 442 GSSTSADVKLNKVDRREAALNKFRQKRKERCFDKKIRYVNRKKLAERRPRVRGQFVRKVN 501

Query: 407 GVNVDLNGQPSSV-DYDEDEDEEEEMASRDSSPDNDTSGN 445
           GVNVDLNGQP+S    +++E++ +E ASRDSSP++D SG+
Sbjct: 502 GVNVDLNGQPASTDYDEDEEEDGDEQASRDSSPEDDASGS 541

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255547335|ref|XP_002514725.1| sensory transduction histidine kinase, putative [Ricinus communis] gi|223546329|gb|EEF47831.1| sensory transduction histidine kinase, putative [Ricinus communis]

 Score =  565 bits (1455), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 307/460 (66%), Positives = 360/460 (78%), Gaps = 27/460 (5%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLV 60
           MSAQDEVS+VVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNIL YDFDLV
Sbjct: 103 MSAQDEVSIVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILIYDFDLV 162

Query: 61  ASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTSGTAAVE 120
           ASDPSDANTNSTTLFSDDTDDKSR+  NPEIG+STHQE          VV   SGTAA E
Sbjct: 163 ASDPSDANTNSTTLFSDDTDDKSRKCLNPEIGVSTHQE---------DVVNRGSGTAADE 213

Query: 121 --PIDASECGPDVPGISDRRTGQFSAGPKKIELRIGESSAFFTYVKSNMPRDSSPRIVNV 178
             P +  E  PDVPGISDRRT Q S+GPKK EL+IGESSAFFTYVKS+  ++ S      
Sbjct: 214 PPPCNRLEYRPDVPGISDRRTAQLSSGPKKSELKIGESSAFFTYVKSSTIKNDSQGFPTT 273

Query: 179 DDSAAQNVRMEEKCQPCCQQVVSDTRIHENGEAWENYSQGEDFRSSSSVPDSLSMERSST 238
           +D    ++R EE  Q C QQVV+D ++HEN E W++Y Q +DFRSSSS+PDS+S+ERS T
Sbjct: 274 EDYTVPSLRAEENLQACAQQVVNDAQLHENRETWQSYPQ-DDFRSSSSIPDSISLERSCT 332

Query: 239 PP--TDFPQNRNFKDEKFFQPQMPP-------TRNEPPQATYQYYMSGAMNQVMLPSSSA 289
           PP  ++FPQ RNFKD+K  Q    P       T     Q+ Y YYMSG +NQV++P  SA
Sbjct: 333 PPMSSEFPQ-RNFKDDKLPQVFTNPINELQLDTSGLSTQSMYPYYMSGVVNQVIMP-PSA 390

Query: 290 QMYQKNLHELQNHS---MLPQYNHLPQCVPHVNGMASFPYYPINMCLQPGQV-SANSWPS 345
           Q+YQKNLHELQN++   MLPQYNHL QC PHV  MASFPYYP+N+CLQPGQ+   + WPS
Sbjct: 391 QLYQKNLHELQNNAPSPMLPQYNHLSQCSPHVASMASFPYYPVNLCLQPGQMPPTHPWPS 450

Query: 346 YGNSPSTEVKMNKVDRREAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVRKV 405
           +G S S +VK+ K+DRREAAL+KFRQKRKERCFDKKIRYVNRK+LAERRPRVRGQFVRK+
Sbjct: 451 FGGSSSPDVKIKKLDRREAALMKFRQKRKERCFDKKIRYVNRKKLAERRPRVRGQFVRKL 510

Query: 406 NGVNVDLNGQPSSVDYDEDEDEEEEMASRDSSPDNDTSGN 445
           NGVNVDLNGQP++   +++E++E+E+A R SS + D SG+
Sbjct: 511 NGVNVDLNGQPAADYDEDEEEDEDELALRGSSLEEDASGS 550

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297733942|emb|CBI15189.3| unnamed protein product [Vitis vinifera]

 Score =  563 bits (1451), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 294/441 (66%), Positives = 342/441 (77%), Gaps = 37/441 (8%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLV 60
           MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNIL+YDFD+ 
Sbjct: 106 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILNYDFDVA 165

Query: 61  ASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTSGTAAVE 120
           ASDPSDANTNST +FSDDTDDKSR S NPE+ +S HQE ES     +T VA+       E
Sbjct: 166 ASDPSDANTNST-MFSDDTDDKSRMSANPEMVVSVHQEDESNATIDSTDVAA-------E 217

Query: 121 P--IDASECGPDVPGISDRRTGQFSAGPKKIELRIGESSAFFTYVKSNMPRDSSPRIVNV 178
           P  ++  EC PDVPGISDRRTGQ  +GPKK EL++GESSAFFTYVKS+M + +S  I N+
Sbjct: 218 PPVVNQLECRPDVPGISDRRTGQLLSGPKKSELKVGESSAFFTYVKSSMIKTNSQGIPNI 277

Query: 179 DDSAAQNVRMEEKCQPCCQQVVSDTRIHENGEAWENYSQGEDFRSSSSVPDSLSMERSST 238
           ++SA Q+ RMEE+ Q   ++ V+DT+ HENGEAWENYSQG+DF S          E S  
Sbjct: 278 NESAPQHSRMEERVQAWSEKGVNDTQEHENGEAWENYSQGDDFPSK---------EFSQV 328

Query: 239 PPTDFPQNRNFKDEKFFQPQMPPTRNEPPQATYQYYMSGAMNQVMLPSSSAQMYQKNLHE 298
           P    P+N +  D   F          P    Y Y MSG MNQVM+PSS AQ+Y K+LH+
Sbjct: 329 PI--HPRNEHQVDISGF----------PGHTAYPYCMSGVMNQVMMPSS-AQLYPKSLHD 375

Query: 299 LQNHS----MLPQYNHLPQCVPHVNGMASFPYYPINMCLQPGQVSANS-WPSYGNSPSTE 353
           +QN++    MLPQYNHLPQC PHV G+ASFPYYP+++CLQPGQ+S    WPSYGNS STE
Sbjct: 376 MQNNATTSAMLPQYNHLPQCPPHVPGVASFPYYPVSICLQPGQMSTTHPWPSYGNSSSTE 435

Query: 354 VKMNKVDRREAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVRKVNGVNVDLN 413
           VK+ KVDRREAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVRK+NGVNVDLN
Sbjct: 436 VKLGKVDRREAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVRKMNGVNVDLN 495

Query: 414 GQPSSVDYDEDEDEEEEMASR 434
           G+P+SVD+DEDE+E+ +  S+
Sbjct: 496 GRPASVDFDEDEEEKADGFSK 516

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356508533|ref|XP_003523010.1| PREDICTED: two-component response regulator-like APRR1-like [Glycine max]

 Score =  560 bits (1443), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 288/459 (62%), Positives = 352/459 (76%), Gaps = 29/459 (6%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLV 60
           MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGL EKNIL+YDFDLV
Sbjct: 111 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLVEKNILNYDFDLV 170

Query: 61  ASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTSGTAAVE 120
            SDPSDANTNSTTLFSDDTDDKS+RSTNPE+G+S  QE ES  +A A  V         E
Sbjct: 171 VSDPSDANTNSTTLFSDDTDDKSKRSTNPEVGISVQQEQEST-IAIAAAVE--------E 221

Query: 121 PIDA--SECGPDVPGISDRRTGQFSAGPKKIELRIGESSAFFTYVKSNMPRDSSPRIVNV 178
           P DA  SECGPDV G++D +T  FS+GPKK ELRIGESSAFFTYVK+++ + +   +VNV
Sbjct: 222 PPDAHASECGPDVDGVNDHQTAHFSSGPKKSELRIGESSAFFTYVKASILKSNLEGVVNV 281

Query: 179 DDSAAQNVRMEEKCQPCCQQVVSDTRIHENGEAWENYSQGEDFRSSSSVPDSLSMERSST 238
           D + A +VRME   Q C QQ V+D +I ENGEA+E+ SQ +D  SS+S+PDSLS+ERS T
Sbjct: 282 DKNGATHVRMEVMHQTCAQQGVNDLQIRENGEAYESQSQ-DDLPSSTSIPDSLSIERSCT 340

Query: 239 PPT--DFPQNRNFKDEKFFQPQMPP----------TRNEPPQATYQYYMSGAMNQVMLPS 286
           PP   +  Q +++++E   Q  M P                Q  Y YY+SG +N VM+PS
Sbjct: 341 PPASMEVSQQKHYREENLHQGVMHPRNGTHCSELEVSGMASQQVYPYYISGVVNHVMMPS 400

Query: 287 SSAQMYQKNLHELQNH---SMLPQYNHLPQCVPHVNGMASFPYYPINMCLQPGQV-SANS 342
           S+   +QKN+ +LQNH   +M+ QY+HLPQ  PH  GM SFPYYP+++CLQPGQ+ + +S
Sbjct: 401 SAQMYHQKNIQDLQNHPSSAMISQYSHLPQGGPHGTGMTSFPYYPMSICLQPGQIPNPHS 460

Query: 343 WPSYGNSPSTEVKMNKVDRREAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFV 402
           W S+GNS S+E K++KVDRREAAL+KFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFV
Sbjct: 461 WQSFGNSSSSEAKLSKVDRREAALMKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFV 520

Query: 403 RKVNGVNVDLNGQPSSV-DYDEDEDEEEEMASRDSSPDN 440
           RK+ G N DLNGQP+S+   ++DE++E++  +RDSSP++
Sbjct: 521 RKLKGANADLNGQPASIDYDEDDEEDEDDQGARDSSPED 559

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356513521|ref|XP_003525462.1| PREDICTED: two-component response regulator-like APRR1-like [Glycine max]

 Score =  550 bits (1418), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 293/449 (65%), Positives = 349/449 (77%), Gaps = 17/449 (3%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLV 60
           MSAQDEVS+VVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGL E NIL+YDFDLV
Sbjct: 118 MSAQDEVSIVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLVENNILTYDFDLV 177

Query: 61  ASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTSGTAAVE 120
           ASDPSDANTNSTTLFSDDTDDKS+RSTNPE G+S  QE E+     A VV          
Sbjct: 178 ASDPSDANTNSTTLFSDDTDDKSKRSTNPETGVSIQQEQEASIATIAAVVVELPNALL-- 235

Query: 121 PIDASECGPDVPGISDRRTGQFSAGPKKIELRIGESSAFFTYVKSNMPRDSSPRIVNVDD 180
               SE  PDVPGISDRRTG F +GPKK EL+IGESSAFFTYVK+   + +     +VD+
Sbjct: 236 ----SEYQPDVPGISDRRTGHFLSGPKKSELKIGESSAFFTYVKATTLKRNVEESAHVDN 291

Query: 181 SAAQNVRMEEKCQPCCQQVVSDTRIHENGEAWENYSQGEDFRSSSSVPDSLSMERSSTPP 240
           +    VR+E+  Q C +Q  +D + HEN E +EN+SQ +D  SS+S+PDS S+ERS TPP
Sbjct: 292 TTTTEVRVEDMNQACTEQGGNDLKTHENEEMFENHSQ-DDLPSSNSIPDSFSIERSCTPP 350

Query: 241 --TDFPQNRNFKDEK---FFQPQMPPTRNEPPQATYQYYMSGAMNQVMLPSSSAQMYQKN 295
             T+  Q +++K+E       P+     + P Q  Y YY+SG +N VM+PSS AQ+YQKN
Sbjct: 351 ASTEVSQQKHYKEEHSQGVVHPRNGSHGSGPAQHAYPYYISGVVNHVMMPSS-AQLYQKN 409

Query: 296 LHELQNH---SMLPQYNHLPQCVPHVNGMASFPYYPINMCLQPGQVSANSWPSYGNSPST 352
           + +LQ+H   SM+ QYNHLPQC PH NGM SFPYYP+++CLQPGQ+S NSWPS G+S S 
Sbjct: 410 IQDLQSHAGSSMIAQYNHLPQCPPHANGMTSFPYYPMSICLQPGQISTNSWPSLGSSSSC 469

Query: 353 EVKMNKVDRREAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVRKVNGVNVDL 412
           EVK++KVDRREAAL+KFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVRK+NG+NVDL
Sbjct: 470 EVKISKVDRREAALVKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVRKLNGINVDL 529

Query: 413 NGQPSSVDYDEDEDEEEE-MASRDSSPDN 440
           NGQP+S DYDED++EEE+   +RDSSP++
Sbjct: 530 NGQPASTDYDEDDEEEEDNHGARDSSPED 558

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351722597|ref|NP_001235202.1| timing of CAB expression 1 [Glycine max] gi|158999372|gb|ABW87010.1| timing of CAB expression 1 [Glycine max]

 Score =  549 bits (1414), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 285/460 (61%), Positives = 351/460 (76%), Gaps = 31/460 (6%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLV 60
           MSAQDEVS+VVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGL EKNIL+YDFDLV
Sbjct: 109 MSAQDEVSIVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLVEKNILNYDFDLV 168

Query: 61  ASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTSGTAAVE 120
            SDPSDANTNSTTLFSDDTDDKS+RSTNPE G+S  QE ES          + +  AAVE
Sbjct: 169 VSDPSDANTNSTTLFSDDTDDKSKRSTNPEAGISVQQEQES----------TIANAAAVE 218

Query: 121 -PIDA--SECGPDVPGISDRRTGQFSAGPKKIELRIGESSAFFTYVKSNMPRDSSPRIVN 177
            P DA  SECGPDV G++D +T  FS+GPKK ELRIGESSAFFTYVK+++ + +   +VN
Sbjct: 219 GPPDAHASECGPDVDGVNDHQTAHFSSGPKKSELRIGESSAFFTYVKASILKSNFEGVVN 278

Query: 178 VDDSAAQNVRMEEKCQPCCQQVVSDTRIHENGEAWENYSQGEDFRSSSSVPDSLSMERSS 237
           VD++ A +V ME   Q C QQ V+  +I ENGEA E+ SQ +D  SS+S+PDSLS+ERS 
Sbjct: 279 VDNNGATHVGMEVMHQACAQQGVNSLQILENGEACESQSQ-DDLPSSTSIPDSLSIERSC 337

Query: 238 TPPT--DFPQNRNFKDEKFFQPQMPP----------TRNEPPQATYQYYMSGAMNQVMLP 285
           TPP   +  Q +++++E   Q  M P                Q  Y YY+SG +N VM+P
Sbjct: 338 TPPASMEVSQQKHYREENSQQGVMHPRNGTHCSEHEVSGMASQHAYPYYISGVVNHVMMP 397

Query: 286 SSSAQMYQKNLHELQNHS---MLPQYNHLPQCVPHVNGMASFPYYPINMCLQPGQV-SAN 341
           SS+   +QKN+ +LQNH+   M+ QYNHLPQ  PH  GM SFPYYP+++CLQPGQ+ + +
Sbjct: 398 SSAQMYHQKNIQDLQNHTSTAMISQYNHLPQGGPHGTGMTSFPYYPMSICLQPGQIPNPH 457

Query: 342 SWPSYGNSPSTEVKMNKVDRREAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQF 401
           SW S+GNS  +E K++KVDRREAAL+KFRQKRKERCFDKKIRY+NRKRLAERRPRVRGQF
Sbjct: 458 SWQSFGNSSPSEAKLSKVDRREAALMKFRQKRKERCFDKKIRYINRKRLAERRPRVRGQF 517

Query: 402 VRKVNGVNVDLNGQPSSV-DYDEDEDEEEEMASRDSSPDN 440
           VRK+NG NVDLNG+P+S+   ++DE++E++  +RDSSP++
Sbjct: 518 VRKLNGANVDLNGEPASIDYDEDDEEDEDDQGARDSSPED 557

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356565113|ref|XP_003550789.1| PREDICTED: two-component response regulator-like APRR1-like [Glycine max]

 Score =  540 bits (1390), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 287/454 (63%), Positives = 342/454 (75%), Gaps = 23/454 (5%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLV 60
           MSAQDEVS+VVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGL E NIL+YDFDLV
Sbjct: 118 MSAQDEVSIVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLVENNILNYDFDLV 177

Query: 61  ASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTSGTAAVE 120
           ASDPSDANTNSTTLFSDDTDDKS+R TNPE G+   QE E+     A VV          
Sbjct: 178 ASDPSDANTNSTTLFSDDTDDKSKRGTNPETGVLIQQEQEASIATIAAVVVELPSYLV-- 235

Query: 121 PIDASECGPDVPGISDRRTGQFSAGPKKIELRIGESSAFFTYVKSNMPRDSSPRIVNVDD 180
               S+  PDVPGISDRRTG FS+GPKK EL+IGESSAFFTYVK+   + +     +VD+
Sbjct: 236 ----SQYQPDVPGISDRRTGHFSSGPKKSELKIGESSAFFTYVKATTLKSNIEESAHVDN 291

Query: 181 S-------AAQNVRMEEKCQPCCQQVVSDTRIHENGEAWENYSQGEDFRSSSSVPDSLSM 233
           S           VRME+  Q C +Q  +  + H+NGE + N+SQ +D  SS+S+ DS S+
Sbjct: 292 SNNTTTTTTTTEVRMEDMNQACIEQGDNGLKTHKNGEMFGNHSQ-DDLPSSNSILDSFSI 350

Query: 234 ERSSTPPT--DFPQNRNFKDEK---FFQPQMPPTRNEPPQATYQYYMSGAMNQVMLPSSS 288
           ERS TPP   +  Q +++K+E       P+     + P Q  Y YY+SG +N VM+PSS 
Sbjct: 351 ERSCTPPASMEVSQQKHYKEEHSQGVVHPRNGSHGSVPAQHAYPYYISGVVNHVMMPSS- 409

Query: 289 AQMYQKNLHELQNH---SMLPQYNHLPQCVPHVNGMASFPYYPINMCLQPGQVSANSWPS 345
           AQ+YQKN+ +LQ H   SM+ QYNHLPQC PH NGM +FPYYP+N+CLQPGQ+S NSWPS
Sbjct: 410 AQLYQKNIQDLQIHAGSSMIAQYNHLPQCPPHANGMTNFPYYPMNICLQPGQISTNSWPS 469

Query: 346 YGNSPSTEVKMNKVDRREAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVRKV 405
            G+S S EV+++KVDRREAAL+KFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVRK+
Sbjct: 470 LGSSSSCEVQISKVDRREAALMKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVRKL 529

Query: 406 NGVNVDLNGQPSSVDYDEDEDEEEEMASRDSSPD 439
           NG+NVDLNGQP+S DYDED++EE+   +RDSSP+
Sbjct: 530 NGINVDLNGQPASTDYDEDDEEEDNHRARDSSPE 563

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|327533492|gb|AEA92684.1| TOC1 [Phaseolus vulgaris]

 Score =  525 bits (1351), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 290/461 (62%), Positives = 345/461 (74%), Gaps = 33/461 (7%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLV 60
           MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLW HMW RRRMLGL EKNILSY+FD+V
Sbjct: 112 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWMHMWGRRRMLGLVEKNILSYEFDIV 171

Query: 61  ASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTSGTAAVE 120
           ASDPSDANTNSTTLFSDDTDDKS+RS NPE+G+   QE ES         +   G A VE
Sbjct: 172 ASDPSDANTNSTTLFSDDTDDKSKRSNNPEVGLPVQQEQES---------SIAIGAAVVE 222

Query: 121 PID--ASECGPDVPGISDRRTGQFSAGPKKIELRIGESSAFFTYVKSNMPRDSSPRIVNV 178
           P+D  ASE  PDV G +D RT  FS+GPKK ELRIGESSAFFT VK+++ + +   +VNV
Sbjct: 223 PLDAHASEHRPDVDGFNDHRTAHFSSGPKKSELRIGESSAFFTCVKASILKSNFEGVVNV 282

Query: 179 DDSAAQNVRMEEKCQPCCQQVVSDTRIHENGEAWENYSQGEDFRSSSSVPDSLSMERSST 238
           D++ A +VRME   Q C QQ V+D +  ENGE  E+ SQ +D  S SSVPDSLS+ERS T
Sbjct: 283 DNNGAAHVRMEAMHQACAQQGVNDLQTRENGETCESQSQ-DDLPSCSSVPDSLSIERSCT 341

Query: 239 PPTDF---PQNRNFKDEKFFQPQMPP----------TRNEPPQATYQYYMSGAMNQVMLP 285
           PP      PQ    KD+ F Q  M P                Q TY YY+SG  N VM+P
Sbjct: 342 PPASMEVSPQKH--KDKNFHQGVMHPRNGTHCSEHEVSGMASQHTYPYYISGGFNHVMMP 399

Query: 286 SSSAQMYQKNLHELQNH---SMLPQYNHLPQCVPHVNGMASFPYYPINMCLQPGQV-SAN 341
           SS+   +QKN+ +LQNH   +M+ QY+HLPQ  PH  GMASFPYYP+++CLQPGQV   +
Sbjct: 400 SSAQMYHQKNMQDLQNHHSAAMIAQYSHLPQGGPHGTGMASFPYYPMSICLQPGQVPQPH 459

Query: 342 SWPSYGNSPSTEVKMNKVDRREAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQF 401
           SWPS+G+S S+E K++KVDRREAAL+KFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQF
Sbjct: 460 SWPSFGSSSSSEAKLSKVDRREAALMKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQF 519

Query: 402 VRKVNGVNVDLNGQPSSV--DYDEDEDEEEEMASRDSSPDN 440
           VRK+NG N+DLNGQP+S+  D D+DE++E++  +RDSSP++
Sbjct: 520 VRKLNGANMDLNGQPASIDYDEDDDEEDEDDQGARDSSPED 560

Source: Phaseolus vulgaris

Species: Phaseolus vulgaris

Genus: Phaseolus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	445
TAIR|locus:2163198	618	TOC1 "TIMING OF CAB EXPRESSION	0.528	0.380	0.455	3e-93
TAIR|locus:2044376	468	PRR9 "pseudo-response regulato	0.152	0.145	0.563	1.3e-24
TAIR|locus:2151206	727	PRR7 "pseudo-response regulato	0.566	0.346	0.285	3.1e-23
TAIR|locus:2062749	183	AT2G46670 "AT2G46670" [Arabido	0.152	0.371	0.563	9.9e-15
TAIR|locus:2007482	195	AT1G07050 "AT1G07050" [Arabido	0.125	0.287	0.465	2.7e-07
TAIR|locus:2090374	251	ASML2 "activator of spomin::LU	0.222	0.394	0.339	1.6e-06
TAIR|locus:2172545	355	COL5 "CONSTANS-like 5" [Arabid	0.240	0.301	0.309	1.8e-06
TAIR|locus:2047246	294	COL3 "CONSTANS-like 3" [Arabid	0.130	0.197	0.406	2.5e-06
TAIR|locus:2074587	347	COL2 "CONSTANS-like 2" [Arabid	0.130	0.167	0.423	4.8e-06
TAIR|locus:2143221	355	COL1 "CONSTANS-like 1" [Arabid	0.096	0.121	0.511	1.4e-05

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

 Score = 503 (182.1 bits), Expect = 3.0e-93, Sum P(2) = 3.0e-93
 Identities = 128/281 (45%), Positives = 165/281 (58%)

Query:   164 KSNMPRDSS--PRIVNVDDSAAQNVRMEEKCQPCCQQVVSDTRIHENGEAWENY-SQGED 220
             KS + R +   P +VN + S   +    EK Q    + +++T+        E Y SQGE 
Sbjct:   325 KSTVLRTNGQDPPLVNGNGSHHLHRGAAEKFQVVASEGINNTKQAHRSRGTEQYHSQGET 384

Query:   221 FRSSSSVPDSLSMERSSTPPTDFPQN-RNFKDEKFFQPQMPPTRNEP-----------PQ 268
              ++ +S P SL  ERS T PT    + RN+++     PQ+   R++            P 
Sbjct:   385 LQNGASYPHSL--ERSRTLPTSMESHGRNYQEGNMNIPQVAMNRSKDSSQVDGSGFSAPN 442

Query:   269 ATYQYYMSGAMNQVMLPSSSAQMYQKNLHELQNHSMLPQYNH-LPQCVP-HVNGMASFPY 326
             A Y YYM G MNQVM+ S++               M+PQY H +P C P H NGM  +PY
Sbjct:   443 A-YPYYMHGVMNQVMMQSAA---------------MMPQYGHQIPHCQPNHPNGMTGYPY 486

Query:   327 Y--PIN-------MCLQPGQVSA--NSWPSYGNSPSTEVKMNKVDRREAALIKFRQKRKE 375
             Y  P+N       M LQ GQ+S   +SW   GN PS EV++NK+DRRE AL+KFR+KR +
Sbjct:   487 YHHPMNTSLQHSQMSLQNGQMSMVHHSWSPAGNPPSNEVRVNKLDRREEALLKFRRKRNQ 546

Query:   376 RCFDKKIRYVNRKRLAERRPRVRGQFVRKVNGVNVDLNGQP 416
             RCFDKKIRYVNRKRLAERRPRV+GQFVRK+NGVNVDLNGQP
Sbjct:   547 RCFDKKIRYVNRKRLAERRPRVKGQFVRKMNGVNVDLNGQP 587

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

 Score = 193 (73.0 bits), Expect = 1.3e-24, Sum P(2) = 1.3e-24
 Identities = 40/71 (56%), Positives = 53/71 (74%)

Query:   336 GQVSANSWPSYGNSPSTEVKMNKVDRREAALIKFRQKRKERCFDKKIRYVNRKRLAERRP 395
             GQ S+   P      S + + ++  +REAAL+KFR KRK+RCFDKK+RY +RK+LAE+RP
Sbjct:   394 GQSSSTEKPK--EEESAKQRWSR-SQREAALMKFRLKRKDRCFDKKVRYQSRKKLAEQRP 450

Query:   396 RVRGQFVRKVN 406
             RV+GQFVR VN
Sbjct:   451 RVKGQFVRTVN 461

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 = 207 (77.9 bits), Expect = 3.1e-23, Sum P(2) = 3.1e-23
 Identities = 78/273 (28%), Positives = 123/273 (45%)

Query:   151 LRIGESSAFFTY-VKSNMPRDSSPRI--VNVDDSAAQNVRMEEKCQPCCQQVVSDTRIHE 207
             LR  E SAF  Y   SN  + S   +   ++ D+ +Q++  + +    C   ++++  H 
Sbjct:   455 LRRSEGSAFSRYNPASNANKISGGNLGSTSLQDNNSQDLIKKTEAAYDCHSNMNESLPHN 514

Query:   208 NGEAWENYSQGEDFRSSSSVPDSLSMERSSTPPTDFPQNRNFKDEKFFQPQMPPTRNEPP 267
             +     ++    +F  SS+  ++ +  +   P      + + K   F QP   P  +   
Sbjct:   515 H----RSHVGSNNFDMSSTTENN-AFTKPGAPKVSSAGSSSVKHSSF-QPL--PCDHHNN 566

Query:   268 QATYQYYMSGAMNQVMLPSSSAQMYQKNLHELQNHSMLPQYNHLPQCVPH-VNG----MA 322
              A+Y         ++     S+ +Y + + E  N+++    N       H  NG      
Sbjct:   567 HASYNLVHVAERKKLPPQCGSSNVYNETI-EGNNNTVNYSVNGSVSGSGHGSNGPYGSSN 625

Query:   323 SFPYYPINMCLQPGQ-VSAN---SWPSYGNSPSTEVKMNKVDRREAALIKFRQKRKERCF 378
                   +NM    G   + N   S    G+        NK+ +REAAL KFRQKRKERCF
Sbjct:   626 GMNAGGMNMGSDNGAGKNGNGDGSGSGSGSGSGNLADENKISQREAALTKFRQKRKERCF 685

Query:   379 DKKIRYVNRKRLAERRPRVRGQFVRKVNGVNVD 411
              KK+RY +RK+LAE+RPRVRGQFVRK      D
Sbjct:   686 RKKVRYQSRKKLAEQRPRVRGQFVRKTAAATDD 718

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:2062749 AT2G46670 "AT2G46670" [Arabidopsis thaliana (taxid:3702)]

 Score = 193 (73.0 bits), Expect = 9.9e-15, P = 9.9e-15
 Identities = 40/71 (56%), Positives = 53/71 (74%)

Query:   336 GQVSANSWPSYGNSPSTEVKMNKVDRREAALIKFRQKRKERCFDKKIRYVNRKRLAERRP 395
             GQ S+   P      S + + ++  +REAAL+KFR KRK+RCFDKK+RY +RK+LAE+RP
Sbjct:   109 GQSSSTEKPK--EEESAKQRWSR-SQREAALMKFRLKRKDRCFDKKVRYQSRKKLAEQRP 165

Query:   396 RVRGQFVRKVN 406
             RV+GQFVR VN
Sbjct:   166 RVKGQFVRTVN 176

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 135 (52.6 bits), Expect = 2.7e-07, P = 2.7e-07
 Identities = 27/58 (46%), Positives = 41/58 (70%)

Query:   347 GNSPSTEVKMNKVDRREAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVRK 404
             G  P  E K N   RREA+++++++KR+ R F KKIRY  RK  A++RPR +G+FV++
Sbjct:   138 GEVPVIEEKRNM--RREASVLRYKEKRQSRLFSKKIRYQVRKLNADKRPRFKGRFVKR 193

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0007623 "circadian rhythm" evidence=RCA

TAIR|locus:2090374 ASML2 "activator of spomin::LUC2" [Arabidopsis thaliana (taxid:3702)]

 Score = 134 (52.2 bits), Expect = 1.6e-06, Sum P(2) = 1.6e-06
 Identities = 38/112 (33%), Positives = 61/112 (54%)

Query:   305 LPQYNHLPQCVPHVNGMASF------PYYPINMCLQPGQVSANSWPSYGNS-------PS 351
             +P+YN+  Q +   N    F       YY  +  ++P    A    S+GNS       P+
Sbjct:    69 VPEYNNYYQKMSVNNATHYFHGGDHQEYYGFSPEIKPLFRPATGEQSWGNSEGGIQAEPN 128

Query:   352 TEVKMNKVDRREAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVR 403
             T+V    V+ R+  ++++ +K+ +R F+K I+YV RK LA+RR RVRG+F R
Sbjct:   129 TKVGRYSVEERKDRIMRYLKKKNQRNFNKTIKYVCRKTLADRRVRVRGRFAR 180

GO:0005739 "mitochondrion" evidence=ISM

GO:0010182 "sugar mediated signaling pathway" evidence=IMP

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IDA

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

 Score = 138 (53.6 bits), Expect = 1.8e-06, P = 1.8e-06
 Identities = 34/110 (30%), Positives = 60/110 (54%)

Query:   303 SMLPQYNHLPQCVPHVNGMASFPYYPINMCLQPGQVSANSWPSYGNSPSTEVKMNKVDRR 362
             S L  + +  Q V H    +S  Y  +        V+ ++  S  ++   + + + +DR 
Sbjct:   229 SKLSAFTYPSQSVSHSVSTSSIEYGVVPDGNTNNSVNRSTITS--STTGGDHQASSMDR- 285

Query:   363 EAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVRKVNGVNVDL 412
             EA ++++R+KRK R F+K IRY +RK  AE RPR++G+F ++    N D+
Sbjct:   286 EARVLRYREKRKNRKFEKTIRYASRKAYAESRPRIKGRFAKRTETENDDI 335

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:2047246 COL3 "CONSTANS-like 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 135 (52.6 bits), Expect = 2.5e-06, P = 2.5e-06
 Identities = 24/59 (40%), Positives = 43/59 (72%)

Query:   348 NSPSTEVKMNKVDRREAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVRKVN 406
             N+ +  V+++  +R EA ++++R+KRK R F+K IRY +RK  AE RPR++G+F ++ +
Sbjct:   216 NTETPAVQLSPAER-EARVLRYREKRKNRKFEKTIRYASRKAYAEMRPRIKGRFAKRTD 273

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IDA

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

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

GO:0005515 "protein binding" evidence=IPI

GO:0010099 "regulation of photomorphogenesis" evidence=IMP

GO:0010161 "red light signaling pathway" evidence=IMP

GO:0009637 "response to blue light" evidence=RCA

GO:0009644 "response to high light intensity" evidence=RCA

GO:0009744 "response to sucrose stimulus" evidence=RCA

GO:0010114 "response to red light" evidence=RCA

GO:0010155 "regulation of proton transport" evidence=RCA

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

GO:0032880 "regulation of protein localization" evidence=RCA

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

 Score = 134 (52.2 bits), Expect = 4.8e-06, P = 4.8e-06
 Identities = 25/59 (42%), Positives = 40/59 (67%)

Query:   348 NSPSTEVKMNKVD-RREAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVRKV 405
             + P T+V        REA ++++R+K+K R FDK IRY +RK  AE RPR++G+F +++
Sbjct:   263 SGPPTQVVQQLTPMEREARVLRYREKKKTRKFDKTIRYASRKAYAEIRPRIKGRFAKRI 321

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:2143221 COL1 "CONSTANS-like 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 130 (50.8 bits), Expect = 1.4e-05, P = 1.4e-05
 Identities = 22/43 (51%), Positives = 35/43 (81%)

Query:   362 REAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVRK 404
             REA ++++R+K+K R F+K IRY +RK  AE+RPR++G+F +K
Sbjct:   286 REARVLRYREKKKMRKFEKTIRYASRKAYAEKRPRIKGRFAKK 328

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:0007623 "circadian rhythm" evidence=IMP

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

GO:0005515 "protein binding" evidence=IPI

GO:0042802 "identical protein binding" evidence=IPI

GO:0006281 "DNA repair" evidence=RCA

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

GO:0048608 "reproductive structure development" 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:
	PtpRR9	pseudo response regulator (541 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	estExt_Genewise1_v1.C_LG_XIV1950	hypothetical protein (750 aa)					•		•		0.787
	estExt_fgenesh4_pg.C_LG_X0958	hypothetical protein (587 aa)					•		•		0.747
	estExt_fgenesh4_pg.C_LG_V1131	hypothetical protein (1171 aa)					•		•		0.734
	estExt_fgenesh4_pm.C_LG_VI0700	hypothetical protein (664 aa)				•			•		0.724
	fgenesh4_pg.C_scaffold_122000043	hypothetical protein (472 aa)							•		0.702
	estExt_fgenesh4_pg.C_LG_III0902	hypothetical protein (662 aa)							•		0.683
	estExt_fgenesh4_pg.C_1680018	hypothetical protein (922 aa)							•		0.683

---

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	445
pfam06203	45	pfam06203, CCT, CCT motif	3e-19
cd00156	113	cd00156, REC, Signal receiver domain; originally t	5e-05
pfam00072	111	pfam00072, Response_reg, Response regulator receiv	2e-04
COG0745	229	COG0745, OmpR, Response regulators consisting of a	0.004

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

 Score = 80.7 bits (200), Expect = 3e-19
 Identities = 27/43 (62%), Positives = 38/43 (88%)

Query: 362 REAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVRK 404
           REAAL+++++KRK R FDKKIRY +RK +AE RPRV+G+FV++
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 = 42.2 bits (100), Expect = 5e-05
 Identities = 13/32 (40%), Positives = 18/32 (56%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELL 32
           ++A  +    V+ L+ GA DYL KP    ELL
Sbjct: 75  LTAHGDDEDAVEALKAGADDYLTKPFSPEELL 106

Length = 113

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

 Score = 40.3 bits (95), Expect = 2e-04
 Identities = 11/33 (33%), Positives = 18/33 (54%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLN 33
           ++A  +    V+ L+ 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

>gnl|CDD|223816 COG0745, OmpR, Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]

 Score = 38.4 bits (90), Expect = 0.004
 Identities = 14/32 (43%), Positives = 18/32 (56%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELL 32
           ++A+D+    V  L  GA DYL KP    ELL
Sbjct: 78  LTARDDEEDRVLGLEAGADDYLTKPFSPRELL 109

Length = 229

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	445
PF06203	45	CCT: CCT motif; InterPro: IPR010402 The CCT (CONST	99.73
COG0745	229	OmpR Response regulators consisting of a CheY-like	99.19
COG3706	435	PleD Response regulator containing a CheY-like rec	99.09
PRK09836	227	DNA-binding transcriptional activator CusR; Provis	98.29
PRK10766	221	DNA-binding transcriptional regulator TorR; Provis	98.28
PRK11173	237	two-component response regulator; Provisional	98.24
PRK09468	239	ompR osmolarity response regulator; Provisional	98.24
PRK10529	225	DNA-binding transcriptional activator KdpE; Provis	98.18
PRK10701	240	DNA-binding transcriptional regulator RstA; Provis	98.17
PRK10816	223	DNA-binding transcriptional regulator PhoP; Provis	98.16
PRK13856	241	two-component response regulator VirG; Provisional	98.13
TIGR03787	227	marine_sort_RR proteobacterial dedicated sortase s	97.98
PRK10161	229	transcriptional regulator PhoB; Provisional	97.97
PRK11517	223	transcriptional regulatory protein YedW; Provision	97.94
TIGR01387	218	cztR_silR_copR heavy metal response regulator. Mem	97.81
CHL00148	240	orf27 Ycf27; Reviewed	97.75
PRK10955	232	DNA-binding transcriptional regulator CpxR; Provis	97.66
PRK11083	228	DNA-binding response regulator CreB; Provisional	97.64
TIGR02154	226	PhoB phosphate regulon transcriptional regulatory	97.63
PRK09581	457	pleD response regulator PleD; Reviewed	97.59
PRK10643	222	DNA-binding transcriptional regulator BasR; Provis	97.53
PRK10336	219	DNA-binding transcriptional regulator QseB; Provis	97.52
PRK15479	221	transcriptional regulatory protein TctD; Provision	97.42
PRK10710	240	DNA-binding transcriptional regulator BaeR; Provis	97.13
COG2199	181	c-di-GMP synthetase (diguanylate cyclase, GGDEF do	96.95
COG4565	224	CitB Response regulator of citrate/malate metaboli	96.68
COG4566	202	TtrR Response regulator [Signal transduction mecha	96.55
COG2204	464	AtoC Response regulator containing CheY-like recei	96.45
PRK15426	570	putative diguanylate cyclase YedQ; Provisional	96.03
KOG1601	340	consensus GATA-4/5/6 transcription factors [Transc	95.01
PRK10245	366	adrA diguanylate cyclase AdrA; Provisional	94.87
COG3437	360	Response regulator containing a CheY-like receiver	94.74
PRK11059	640	regulatory protein CsrD; Provisional	94.69
PRK10046	225	dpiA two-component response regulator DpiA; Provis	94.59
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	94.12
PF09425	27	CCT_2: Divergent CCT motif; InterPro: IPR018467 Th	93.77
PRK10360	196	DNA-binding transcriptional activator UhpA; Provis	93.75
PRK09958	204	DNA-binding transcriptional activator EvgA; Provis	93.67
PRK10693	303	response regulator of RpoS; Provisional	93.67
PRK10430	239	DNA-binding transcriptional activator DcuR; Provis	93.33
PRK10610	129	chemotaxis regulatory protein CheY; Provisional	93.26
PRK09935	210	transcriptional regulator FimZ; Provisional	93.03
COG4567	182	Response regulator consisting of a CheY-like recei	92.97
PRK13561	651	putative diguanylate cyclase; Provisional	92.92
PRK10840	216	transcriptional regulator RcsB; Provisional	92.86
PRK11829	660	biofilm formation regulator HmsP; Provisional	92.81
TIGR02875	262	spore_0_A sporulation transcription factor Spo0A.	92.43
PRK09894	296	diguanylate cyclase; Provisional	92.26
PLN03029	222	type-a response regulator protein; Provisional	92.18
PRK09581	457	pleD response regulator PleD; Reviewed	91.86
PRK09776	1092	putative diguanylate cyclase; Provisional	91.77
COG4753	475	Response regulator containing CheY-like receiver d	91.65
PRK09966	407	putative inner membrane diguanylate cyclase; Provi	91.35
PRK11475	207	DNA-binding transcriptional activator BglJ; Provis	90.96
PRK09483	217	response regulator; Provisional	90.95
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	90.01
COG2197	211	CitB Response regulator containing a CheY-like rec	89.99
COG0784	130	CheY FOG: CheY-like receiver [Signal transduction	89.97
PRK10403	215	transcriptional regulator NarP; Provisional	89.93
PRK15369	211	two component system sensor kinase SsrB; Provision	89.9
PRK10060	663	RNase II stability modulator; Provisional	89.83
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	89.31
PRK10651	216	transcriptional regulator NarL; Provisional	89.3
PRK15115	444	response regulator GlrR; Provisional	88.19
PRK11107	919	hybrid sensory histidine kinase BarA; Provisional	88.18
PRK11359	799	cyclic-di-GMP phosphodiesterase; Provisional	88.17
PRK15347	921	two component system sensor kinase SsrA; Provision	88.06
PF00990	161	GGDEF: GGDEF domain; InterPro: IPR000160 This doma	87.93
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	87.39
COG3707	194	AmiR Response regulator with putative antiterminat	86.59
PRK13435	145	response regulator; Provisional	86.08
PRK11697	238	putative two-component response-regulatory protein	86.04
PRK14084	246	two-component response regulator; Provisional	85.79
PRK09390	202	fixJ response regulator FixJ; Provisional	85.72
PRK10365	441	transcriptional regulatory protein ZraR; Provision	85.71
TIGR02956	968	TMAO_torS TMAO reductase sytem sensor TorS. This p	85.24
PRK11466	914	hybrid sensory histidine kinase TorS; Provisional	83.78
PRK09959	1197	hybrid sensory histidine kinase in two-component r	83.06
cd00156	113	REC Signal receiver domain; originally thought to	82.25
PRK07239	381	bifunctional uroporphyrinogen-III synthetase/respo	81.19
COG5001	663	Predicted signal transduction protein containing a	81.11

>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=99.73  E-value=1.3e-18  Score=129.81  Aligned_cols=45  Identities=56%  Similarity=0.995  Sum_probs=42.8

Q ss_pred             HHHHHHHHHHhhcccCCCcccchhhhhhhhhhCCCCCcceecccC
Q 013329          362 REAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRGQFVRKVN  406 (445)
Q Consensus       362 R~~~~~ry~eKr~~R~f~kkirY~~RK~~A~~RpRvkGrFvk~~~  406 (445)
                      |+++|+||++||++|+|+|+|+|+|||.+|+.|||||||||+..+
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            678999999999999999999999999999999999999999753

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

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

Probab=99.19  E-value=1.7e-11  Score=117.94  Aligned_cols=101  Identities=27%  Similarity=0.319  Sum_probs=80.9

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhh-hCccccccccccchhhccccccC---CCCeEEEEe
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRM-LGLAEKNILSYDFDLVASDPSDA---NTNSTTLFS   76 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~rL-Tgl~nr~iL~~gLdl~Ld~asr~---n~~slaLL~   76 (445)
                      ||+.++..+.+.++++||||||+|||++.||++||+++++|... +.......+..+ ++.++...+.   ++..+.|+.
T Consensus        78 Lta~~~~~d~v~gl~~GADDYl~KPf~~~EL~ARi~a~lRR~~~~~~~~~~~~~~~g-~l~id~~~~~v~~~~~~i~Lt~  156 (229)
T COG0745          78 LTARDDEEDRVLGLEAGADDYLTKPFSPRELLARLRALLRRNAGASRAEASEVLVFG-DLTLDPDTRTVTLNGRELTLTP  156 (229)
T ss_pred             EECCCcHHHHHHHHhCcCCeeeeCCCCHHHHHHHHHHHHCcCcCcccccccceeEEC-CEEEEcCcCEEEECCEEecCCh
Confidence            58899999999999999999999999999999999999998642 111122344444 4555543332   345778889


Q ss_pred             ecccchhhhhcCCCcccChHHHHhhc
Q 013329           77 DDTDDKSRRSTNPEIGMSTHQETESV  102 (445)
Q Consensus        77 lDLD~FKlINdn~g~vvSreQl~d~~  102 (445)
                      .+++.+..+..|+++++|++++++.+
T Consensus       157 ~Ef~lL~~L~~~~g~v~sR~~L~~~v  182 (229)
T COG0745         157 KEFELLELLARHPGRVLSREQLLEAV  182 (229)
T ss_pred             HHHHHHHHHHhCCCccCCHHHHHHHh
Confidence            99999999999999999999999986

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

Probab=99.09  E-value=6.5e-11  Score=124.01  Aligned_cols=108  Identities=22%  Similarity=0.301  Sum_probs=92.6

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh--------------------hhCccccccccccchhh
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR--------------------MLGLAEKNILSYDFDLV   60 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r--------------------LTgl~nr~iL~~gLdl~   60 (445)
                      +++.++......|++.|++|||+||+...+|.+||+..+++.+                    +||+.|++.|...+...
T Consensus       212 ~~~~~d~~~~~~Af~~G~~Dyi~kPi~~~~l~~Rl~~~l~~~~~~~~L~~~~~~~~~l~~~D~LTGL~NRR~~~~~L~~~  291 (435)
T COG3706         212 LSSKDDDELVVRAFELGVNDYITKPIEEGELRARLRRQLRRKRYERQLRESLERLQELALVDGLTGLFNRRYFDEHLADL  291 (435)
T ss_pred             EecccchHHHHHHHHcCCcceEecCCCHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhhccccccCcccHHHHHHHHHHH
Confidence            3667788899999999999999999999999999999998653                    36677777777767777


Q ss_pred             ccccccCCCCeEEEEeecccchhhhhcCCCcccChHHHHhhcchhhhhhhhccc
Q 013329           61 ASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTS  114 (445)
Q Consensus        61 Ld~asr~n~~slaLL~lDLD~FKlINdn~g~vvSreQl~d~~l~~~A~~~a~~~  114 (445)
                      +.++.+. +.+++++++|+|+||.+|+++||.     .+|.||+.||..|..+.
T Consensus       292 ~~ra~~~-~~pls~~m~DID~FK~iNDt~GH~-----~GDevLr~vA~~L~~~v  339 (435)
T COG3706         292 WKRALRE-GRPLSLLMLDIDDFKEINDTYGHD-----VGDEVLRQVARRLRQTV  339 (435)
T ss_pred             HHHHHhc-CCCeeEEEEecccccccccccCCc-----cHHHHHHHHHHHHHhhc
Confidence            7776665 458999999999999999999655     89999999999999988

>PRK09836 DNA-binding transcriptional activator CusR; Provisional

Probab=98.29  E-value=1.1e-06  Score=79.95  Aligned_cols=98  Identities=26%  Similarity=0.221  Sum_probs=72.8

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhhhCccccccccccchhhcccccc---CCCCeEEEEeec
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLVASDPSD---ANTNSTTLFSDD   78 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~rLTgl~nr~iL~~gLdl~Ld~asr---~n~~slaLL~lD   78 (445)
                      |+..+.+....++++||++||.||++..+|.++|+.++++..  .......+..+ ++.++...+   .++..+.|+..+
T Consensus        79 s~~~~~~~~~~~~~~Ga~~~l~kp~~~~~l~~~i~~~~~~~~--~~~~~~~~~~~-~~~~~~~~~~~~~~~~~i~Lt~~E  155 (227)
T PRK09836         79 TALGTIEHRVKGLELGADDYLVKPFAFAELLARVRTLLRRGA--AVIIESQFQVA-DLMVDLVSRKVTRSGTRITLTSKE  155 (227)
T ss_pred             EcCCCHHHHHHHHhCCCCEEEeCCCCHHHHHHHHHHHHhccc--ccCCCCcEEEc-CEEEEcccCEEEECCEEEecCHHH
Confidence            556777888899999999999999999999999999887632  11111122222 223332211   233467899999


Q ss_pred             ccchhhhhcCCCcccChHHHHhhc
Q 013329           79 TDDKSRRSTNPEIGMSTHQETESV  102 (445)
Q Consensus        79 LD~FKlINdn~g~vvSreQl~d~~  102 (445)
                      ++.+..+..|+++++|++++++.+
T Consensus       156 ~~ll~~l~~~~g~~~sr~~l~~~~  179 (227)
T PRK09836        156 FTLLEFFLRHQGEVLPRSLIASQV  179 (227)
T ss_pred             HHHHHHHHhCCCeeEcHHHHHHHH
Confidence            999999999999999999999986

>PRK10766 DNA-binding transcriptional regulator TorR; Provisional

Probab=98.28  E-value=1e-06  Score=79.62  Aligned_cols=100  Identities=21%  Similarity=0.228  Sum_probs=73.4

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhhhCcc------ccccccccchhhcccccc---CCCCeE
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLA------EKNILSYDFDLVASDPSD---ANTNST   72 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~rLTgl~------nr~iL~~gLdl~Ld~asr---~n~~sl   72 (445)
                      ++..+......++++||+|||.||++..+|..+|+.++++.......      ....+..+ +..++...+   .++..+
T Consensus        80 ~~~~~~~~~~~~l~~Ga~d~l~kP~~~~~L~~~i~~~~~r~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~v  158 (221)
T PRK10766         80 TGRTDSIDRIVGLEMGADDYVTKPLELRELLVRVKNLLWRISLARQAQPHAQEEDNCYRFA-GYCLNVSRRTLERNGEPI  158 (221)
T ss_pred             ECCCcHHHHHHHHHcCCCcEEeCCCCHHHHHHHHHHHHhhhcccccccccccCCCCceEEC-CEEEEcccCEEEECCEEe
Confidence            45667777889999999999999999999999999998774321100      01122222 223332222   234577


Q ss_pred             EEEeecccchhhhhcCCCcccChHHHHhhc
Q 013329           73 TLFSDDTDDKSRRSTNPEIGMSTHQETESV  102 (445)
Q Consensus        73 aLL~lDLD~FKlINdn~g~vvSreQl~d~~  102 (445)
                      .|+..+++.+..+..|+++++|++++++.+
T Consensus       159 ~Lt~~E~~ll~~l~~~~~~v~sr~~l~~~v  188 (221)
T PRK10766        159 KLTKAEYELLVAFVTNPGQVLSRERLLRML  188 (221)
T ss_pred             cCCHHHHHHHHHHHHCCCceEcHHHHHHHh
Confidence            899999999999999999999999999986

>PRK11173 two-component response regulator; Provisional

Probab=98.24  E-value=1.8e-06  Score=79.63  Aligned_cols=100  Identities=18%  Similarity=0.181  Sum_probs=74.1

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhhhC--cc---ccccccccchhhcccccc----CCCCeE
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLG--LA---EKNILSYDFDLVASDPSD----ANTNST   72 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~rLTg--l~---nr~iL~~gLdl~Ld~asr----~n~~sl   72 (445)
                      |+..+......+++.||++||.||++..+|..+|++++++.....  ..   ....+..+ +..++...+    .++..+
T Consensus        81 t~~~~~~~~~~~~~~ga~d~l~kP~~~~eL~~~i~~~l~r~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~  159 (237)
T PRK11173         81 TGRDNEVDKILGLEIGADDYITKPFNPRELTIRARNLLSRTMNLGTVSEERRSVESYKFN-GWELDINSRSLISPDGEQY  159 (237)
T ss_pred             ECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHhccccccccccccccccceEEC-CEEEecccceEEecCCeEE
Confidence            556677778889999999999999999999999999998743111  00   01122223 333433222    244578


Q ss_pred             EEEeecccchhhhhcCCCcccChHHHHhhc
Q 013329           73 TLFSDDTDDKSRRSTNPEIGMSTHQETESV  102 (445)
Q Consensus        73 aLL~lDLD~FKlINdn~g~vvSreQl~d~~  102 (445)
                      .|+..+++.+..+..|+|+++|++++.+.+
T Consensus       160 ~Lt~~E~~ll~~l~~~~g~v~sr~~l~~~v  189 (237)
T PRK11173        160 KLPRSEFRAMLHFCENPGKIQSRAELLKKM  189 (237)
T ss_pred             eCCHHHHHHHHHHHhCCCccCcHHHHHHHh
Confidence            899999999999999999999999999985

>PRK09468 ompR osmolarity response regulator; Provisional

Probab=98.24  E-value=1.5e-06  Score=79.89  Aligned_cols=100  Identities=20%  Similarity=0.270  Sum_probs=73.3

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhhh--Cc--cccccccccchhhcccccc---CCCCeEEE
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRML--GL--AEKNILSYDFDLVASDPSD---ANTNSTTL   74 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~rLT--gl--~nr~iL~~gLdl~Ld~asr---~n~~slaL   74 (445)
                      ++..+......++++|+++||.||++..+|.++|+.++++....  ..  .....+..+ +..++...+   .++..+.|
T Consensus        84 s~~~~~~~~~~~l~~Ga~~~l~kP~~~~~L~~~i~~~~~r~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~i~L  162 (239)
T PRK09468         84 TAKGEEVDRIVGLEIGADDYLPKPFNPRELLARIRAVLRRQAPELPGAPSQEEEVIAFG-KFKLNLGTRELFRGDEPMPL  162 (239)
T ss_pred             ECCCcHHHHHHHHhcCCCeEEECCCCHHHHHHHHHHHhccccccccccccCCCceEEEC-cEEEEcCcCEEEECCEEeec
Confidence            45566777888999999999999999999999999988764210  00  011122222 333333222   23457889


Q ss_pred             EeecccchhhhhcCCCcccChHHHHhhc
Q 013329           75 FSDDTDDKSRRSTNPEIGMSTHQETESV  102 (445)
Q Consensus        75 L~lDLD~FKlINdn~g~vvSreQl~d~~  102 (445)
                      +..+++.|.++..|+++++|+++|++.+
T Consensus       163 t~~E~~lL~~L~~~~~~~~sr~~l~~~v  190 (239)
T PRK09468        163 TTGEFAVLKALVSHPREPLSRDKLMNLA  190 (239)
T ss_pred             CHHHHHHHHHHHhCCCccCcHHHHHHHH
Confidence            9999999999999999999999999985

>PRK10529 DNA-binding transcriptional activator KdpE; Provisional

Probab=98.18  E-value=2.6e-06  Score=77.16  Aligned_cols=99  Identities=21%  Similarity=0.202  Sum_probs=72.5

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhhhCccccccccccchhhcccccc---CCCCeEEEEeec
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLVASDPSD---ANTNSTTLFSDD   78 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~rLTgl~nr~iL~~gLdl~Ld~asr---~n~~slaLL~lD   78 (445)
                      |+..+......++++||++||.||++..+|..+|+.++++...... ....+..+ +..++...+   .++..+.|...+
T Consensus        79 t~~~~~~~~~~~~~~ga~~~l~kP~~~~~l~~~i~~~~~~~~~~~~-~~~~~~~~-~~~~~~~~~~v~~~~~~~~Lt~~E  156 (225)
T PRK10529         79 SARSEESDKIAALDAGADDYLSKPFGIGELQARLRVALRRHSATPA-PDPLVKFS-DVTVDLAARVIHRGEEEVHLTPIE  156 (225)
T ss_pred             ECCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHhhcccccC-CCcceeEC-CEEEEcccCEEEECCEEEECCHHH
Confidence            5666777888999999999999999999999999998876431110 11112222 222222221   234467889999


Q ss_pred             ccchhhhhcCCCcccChHHHHhhc
Q 013329           79 TDDKSRRSTNPEIGMSTHQETESV  102 (445)
Q Consensus        79 LD~FKlINdn~g~vvSreQl~d~~  102 (445)
                      ++.+..+..|+++++|++++++.+
T Consensus       157 ~~ll~~L~~~~~~~~s~~~l~~~v  180 (225)
T PRK10529        157 FRLLAVLLNNAGKVLTQRQLLNQV  180 (225)
T ss_pred             HHHHHHHHhCCCeeEcHHHHHHHh
Confidence            999999999999999999999986

>PRK10701 DNA-binding transcriptional regulator RstA; Provisional

Probab=98.17  E-value=3.2e-06  Score=77.90  Aligned_cols=100  Identities=17%  Similarity=0.147  Sum_probs=72.8

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhhhCcc---------ccccccccchhhcccccc---CCC
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLA---------EKNILSYDFDLVASDPSD---ANT   69 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~rLTgl~---------nr~iL~~gLdl~Ld~asr---~n~   69 (445)
                      ++..+......++++|+++||.||++..+|..+|+.++++.......         ....+..+ .+.++...+   .++
T Consensus        79 ~~~~~~~~~~~~~~~Ga~d~l~kP~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~  157 (240)
T PRK10701         79 TSLDSDMNHILALEMGACDYILKTTPPAVLLARLRLHLRQNEQATQTKGLQETSLTPYKALHFG-TLTIDPVNRQVTLAG  157 (240)
T ss_pred             ECCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHHhccccccccccccccccccccceEec-CEEEEcccCEEEECC
Confidence            44556667788999999999999999999999999988764311000         01112222 233333222   244


Q ss_pred             CeEEEEeecccchhhhhcCCCcccChHHHHhhc
Q 013329           70 NSTTLFSDDTDDKSRRSTNPEIGMSTHQETESV  102 (445)
Q Consensus        70 ~slaLL~lDLD~FKlINdn~g~vvSreQl~d~~  102 (445)
                      ..+.|+..+++.+..+..|+++++|++++.+.+
T Consensus       158 ~~i~Lt~~E~~lL~~l~~~~~~v~sr~~l~~~v  190 (240)
T PRK10701        158 EEISLSTADFDLLWELATHAGQIMDRDALLKNL  190 (240)
T ss_pred             eEeecCHHHHHHHHHHHhCCCccCcHHHHHHHh
Confidence            578899999999999999999999999999986

>PRK10816 DNA-binding transcriptional regulator PhoP; Provisional

Probab=98.16  E-value=2.8e-06  Score=77.14  Aligned_cols=97  Identities=20%  Similarity=0.224  Sum_probs=72.1

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhhhCccccccccccchhhcccccc---CCCCeEEEEeec
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLVASDPSD---ANTNSTTLFSDD   78 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~rLTgl~nr~iL~~gLdl~Ld~asr---~n~~slaLL~lD   78 (445)
                      |+..+......++++||++||.||++..+|.++|+.++++..  .. ....+..+ +..++...+   .++..+.|+..+
T Consensus        79 s~~~~~~~~~~~l~~Ga~d~l~kp~~~~eL~~~i~~~~~~~~--~~-~~~~~~~~-~~~~~~~~~~~~~~~~~i~Lt~~E  154 (223)
T PRK10816         79 TARESWQDKVEVLSAGADDYVTKPFHIEEVMARMQALMRRNS--GL-ASQVISLP-PFQVDLSRRELSINDEVIKLTAFE  154 (223)
T ss_pred             EcCCCHHHHHHHHHcCCCeeEeCCCCHHHHHHHHHHHHhccc--cC-CCCeEEEC-CEEEEcccCEEEECCEEEeCCHHH
Confidence            556677788899999999999999999999999999887642  11 11122222 222222111   134477899999


Q ss_pred             ccchhhhhcCCCcccChHHHHhhc
Q 013329           79 TDDKSRRSTNPEIGMSTHQETESV  102 (445)
Q Consensus        79 LD~FKlINdn~g~vvSreQl~d~~  102 (445)
                      ++.+..+..|+++++|++++.+.+
T Consensus       155 ~~ll~~L~~~~~~vvs~~~l~~~~  178 (223)
T PRK10816        155 YTIMETLIRNNGKVVSKDSLMLQL  178 (223)
T ss_pred             HHHHHHHHhCCCeeEcHHHHHHHh
Confidence            999999999999999999999875

>PRK13856 two-component response regulator VirG; Provisional

Probab=98.13  E-value=4.7e-06  Score=77.45  Aligned_cols=96  Identities=20%  Similarity=0.185  Sum_probs=69.9

Q ss_pred             cHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhhhC-ccccccccccchhhcccccc----CCCCeEEEEeeccc
Q 013329            6 EVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLG-LAEKNILSYDFDLVASDPSD----ANTNSTTLFSDDTD   80 (445)
Q Consensus         6 d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~rLTg-l~nr~iL~~gLdl~Ld~asr----~n~~slaLL~lDLD   80 (445)
                      +......++++||++||.||++..+|.++|+.++++..... ......+..+ ++.++...+    ..+..+.|+..+++
T Consensus        84 ~~~~~~~~l~~Ga~~yl~kP~~~~eL~~~i~~~l~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~i~Lt~~E~~  162 (241)
T PRK13856         84 EEADKVVALELGATDFIAKPFGTREFLARIRVALRVRPNVVRTKDRRSFCFA-DWTLNLRQRRLISEAGGEVKLTAGEFN  162 (241)
T ss_pred             cHHHHHHHHhcCcCeEEeCCCCHHHHHHHHHHHHhhcccccccccccceecC-ceEEehhhCEEEeCCCcEeecCHHHHH
Confidence            45567789999999999999999999999999887643111 1111222222 333332221    23457889999999


Q ss_pred             chhhhhcCCCcccChHHHHhhc
Q 013329           81 DKSRRSTNPEIGMSTHQETESV  102 (445)
Q Consensus        81 ~FKlINdn~g~vvSreQl~d~~  102 (445)
                      .|..+..++++++|++++++.+
T Consensus       163 lL~~l~~~~~~v~sr~~l~~~~  184 (241)
T PRK13856        163 LLVAFLEKPRDVLSREQLLIAS  184 (241)
T ss_pred             HHHHHHhCCCCccCHHHHHHHh
Confidence            9999999999999999999875

>TIGR03787 marine_sort_RR proteobacterial dedicated sortase system response regulator

Probab=97.98  E-value=1.3e-05  Score=72.76  Aligned_cols=100  Identities=23%  Similarity=0.242  Sum_probs=70.5

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhhhC--ccccccccccchhhcccccc---CCCCeEEEE
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLG--LAEKNILSYDFDLVASDPSD---ANTNSTTLF   75 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~rLTg--l~nr~iL~~gLdl~Ld~asr---~n~~slaLL   75 (445)
                      +|+..+......++++||++||.||++..+|..+|+.++++.....  ......+..+ .+.++....   .++..+.|+
T Consensus        80 ls~~~~~~~~~~~~~~Ga~~~l~kp~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~Lt  158 (227)
T TIGR03787        80 LTARDSDFDTVSGLRLGADDYLTKDISLPHLLARITALFRRAEALQKPQKQDDLITRG-PLTLDSDRMTVFWQDQPIDLT  158 (227)
T ss_pred             EECCCCHHHHHHHHhcCCCEEEECCCCHHHHHHHHHHHHHhhhhccccccccceEEEC-CEEEEcccCEEEECCEEecCC
Confidence            3566777788899999999999999999999999999987653111  0111122211 122221111   123356799


Q ss_pred             eecccchhhhhcCCCcccChHHHHhh
Q 013329           76 SDDTDDKSRRSTNPEIGMSTHQETES  101 (445)
Q Consensus        76 ~lDLD~FKlINdn~g~vvSreQl~d~  101 (445)
                      ..+++.+.++..|+|+++|++++.+.
T Consensus       159 ~~E~~il~~l~~~~g~v~s~~~i~~~  184 (227)
T TIGR03787       159 VTEFWMVHALAKHPGHVKSRQQLMDA  184 (227)
T ss_pred             HHHHHHHHHHHhCCCccccHHHHHHH
Confidence            99999999999999999999999776

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.

>PRK10161 transcriptional regulator PhoB; Provisional

Probab=97.97  E-value=1.4e-05  Score=72.88  Aligned_cols=98  Identities=24%  Similarity=0.259  Sum_probs=70.1

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhhhCccccccccccchhhcccccc---CCCCeEEEEeec
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLVASDPSD---ANTNSTTLFSDD   78 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~rLTgl~nr~iL~~gLdl~Ld~asr---~n~~slaLL~lD   78 (445)
                      |+..+......++++||++||.||++..+|..+|+.++++..  .......+..+ ...++....   .++....|...+
T Consensus        83 s~~~~~~~~~~~~~~Ga~~~l~kp~~~~~L~~~i~~~~~~~~--~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~Lt~~E  159 (229)
T PRK10161         83 TARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRRIS--PMAVEEVIEMQ-GLSLDPTSHRVMAGEEPLEMGPTE  159 (229)
T ss_pred             ECCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHHhccc--ccCcCceeEEC-CEEEEcCcCEEEECCEEEEcCHHH
Confidence            456677788899999999999999999999999999887632  11111122211 222222111   123356788899


Q ss_pred             ccchhhhhcCCCcccChHHHHhhc
Q 013329           79 TDDKSRRSTNPEIGMSTHQETESV  102 (445)
Q Consensus        79 LD~FKlINdn~g~vvSreQl~d~~  102 (445)
                      ++.+.++..|+++++|++++.+.+
T Consensus       160 ~~ll~~l~~~~~~~~s~~~l~~~~  183 (229)
T PRK10161        160 FKLLHFFMTHPERVYSREQLLNHV  183 (229)
T ss_pred             HHHHHHHHhCCCceEcHHHHHHHh
Confidence            999999999999999999998874

>PRK11517 transcriptional regulatory protein YedW; Provisional

Probab=97.94  E-value=1.4e-05  Score=71.88  Aligned_cols=96  Identities=25%  Similarity=0.241  Sum_probs=70.8

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhhhCccccccccccchhhcccccc---CCCCeEEEEeec
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLVASDPSD---ANTNSTTLFSDD   78 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~rLTgl~nr~iL~~gLdl~Ld~asr---~n~~slaLL~lD   78 (445)
                      |+..+......++++||++||.||++..+|..+|+.++++...  .  ...+..+ ...++...+   .++..+.|+..+
T Consensus        78 s~~~~~~~~~~a~~~Ga~~~l~kp~~~~~l~~~i~~~~~~~~~--~--~~~~~~~-~~~~~~~~~~~~~~~~~~~Lt~~E  152 (223)
T PRK11517         78 TARDSVDDRVRGLDSGANDYLVKPFSFSELLARVRAQLRQHHA--L--NSTLEIS-GLRMDSVSQSVSRDNISITLTRKE  152 (223)
T ss_pred             ECCCCHHHHHHHHhcCCCEEEECCCCHHHHHHHHHHHHccccC--c--CCeEEEC-CEEEEcCCCEEEECCEEEeCCHHH
Confidence            4566777888999999999999999999999999988865421  1  1112111 122221111   233467899999


Q ss_pred             ccchhhhhcCCCcccChHHHHhhc
Q 013329           79 TDDKSRRSTNPEIGMSTHQETESV  102 (445)
Q Consensus        79 LD~FKlINdn~g~vvSreQl~d~~  102 (445)
                      ++.+..+..++++++|++++.+.+
T Consensus       153 ~~il~~l~~~~g~~~s~~~i~~~~  176 (223)
T PRK11517        153 FQLLWLLASRAGEIIPRTVIASEI  176 (223)
T ss_pred             HHHHHHHHhCCCccCCHHHHHHHh
Confidence            999999999999999999999985

>TIGR01387 cztR_silR_copR heavy metal response regulator

Probab=97.81  E-value=2.9e-05  Score=69.28  Aligned_cols=97  Identities=28%  Similarity=0.268  Sum_probs=70.4

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhhhCccccccccccchhhcccccc---CCCCeEEEEeec
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLVASDPSD---ANTNSTTLFSDD   78 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~rLTgl~nr~iL~~gLdl~Ld~asr---~n~~slaLL~lD   78 (445)
                      |+..+......++++||++||.||++..+|..+|+.++++...  . ....+..+ +..++...+   ..+..+.|+..+
T Consensus        77 s~~~~~~~~~~~~~~Ga~~~l~kp~~~~~l~~~i~~~~~~~~~--~-~~~~~~~~-~~~~~~~~~~~~~~~~~~~Lt~~E  152 (218)
T TIGR01387        77 TARDSVADKVKGLDLGADDYLVKPFSFSELLARVRTLLRRSHS--L-NSTVLEIA-DLRMDSVRHRVSRGNIRITLTRKE  152 (218)
T ss_pred             EcCCCHHHHHHHHHcCCCeEEECCCCHHHHHHHHHHHhccccc--C-CCCeEEEC-CEEEEcccCEEEECCEEEeCCHHH
Confidence            4566777788899999999999999999999999998876431  1 11111111 222221111   133456789999


Q ss_pred             ccchhhhhcCCCcccChHHHHhhc
Q 013329           79 TDDKSRRSTNPEIGMSTHQETESV  102 (445)
Q Consensus        79 LD~FKlINdn~g~vvSreQl~d~~  102 (445)
                      ++.+..+..++++++|++++.+.+
T Consensus       153 ~~il~~l~~~~~~~~sr~~i~~~~  176 (218)
T TIGR01387       153 FQLLWLLMRRTGEVLPRTVIASLV  176 (218)
T ss_pred             HHHHHHHHhCCCeeEcHHHHHHHh
Confidence            999999999999999999999985

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.

>CHL00148 orf27 Ycf27; Reviewed

Probab=97.75  E-value=5.3e-05  Score=69.01  Aligned_cols=100  Identities=22%  Similarity=0.192  Sum_probs=70.0

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhhhC----ccccccccccchhhcccccc---CCCCeEEE
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLG----LAEKNILSYDFDLVASDPSD---ANTNSTTL   74 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~rLTg----l~nr~iL~~gLdl~Ld~asr---~n~~slaL   74 (445)
                      |+..+......++++||++||.||++..+|..+|+.++++.....    ......+..+ ...++....   .++....|
T Consensus        84 s~~~~~~~~~~~~~~Ga~~~l~kp~~~~~L~~~i~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~L  162 (240)
T CHL00148         84 TALGDVSDRITGLELGADDYVVKPFSPKELEARIRSVLRRTNKKSFSSKIPNSSIIRIG-FLKIDLNKKQVYKNNERIRL  162 (240)
T ss_pred             ECCCCHHhHHHHHHCCCCEEEeCCCCHHHHHHHHHHHHhhccccccccccCCCceEEEC-CEEEEcCCCEEEECCEEEEc
Confidence            556677777899999999999999999999999999887643110    0011111111 112211111   12335678


Q ss_pred             EeecccchhhhhcCCCcccChHHHHhhc
Q 013329           75 FSDDTDDKSRRSTNPEIGMSTHQETESV  102 (445)
Q Consensus        75 L~lDLD~FKlINdn~g~vvSreQl~d~~  102 (445)
                      +..+++.++++..+++.++|++++.+..
T Consensus       163 t~~E~~il~~l~~~~~~~~s~~~i~~~l  190 (240)
T CHL00148        163 TGMEFSLLELLISKSGEIFSRATILKEV  190 (240)
T ss_pred             CHHHHHHHHHHHHCCCEEEcHHHHHHHh
Confidence            8899999999999999999999999875

>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional

Probab=97.66  E-value=7e-05  Score=67.86  Aligned_cols=100  Identities=21%  Similarity=0.171  Sum_probs=69.6

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhhhCcc-----ccccccccchhhcccccc---CCCCeEE
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLA-----EKNILSYDFDLVASDPSD---ANTNSTT   73 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~rLTgl~-----nr~iL~~gLdl~Ld~asr---~n~~sla   73 (445)
                      |+..+......++++|+++||.||++..+|..+|+.++++.......     ....+..+ ...++...+   .++....
T Consensus        78 t~~~~~~~~~~~~~~ga~~~l~kp~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~  156 (232)
T PRK10955         78 TARGSELDRVLGLELGADDYLPKPFNDRELVARIRAILRRSHWSEQQQNNDNGSPTLEVD-ALSLNPGRQEASFDGQTLE  156 (232)
T ss_pred             ECCCCHHHHHHHHHcCCCEEEcCCCCHHHHHHHHHHHHhccccccccccccCCCceEEEC-CEEEecCCCEEEECCEEec
Confidence            55666777788999999999999999999999999988764321100     00111111 112221111   1223456


Q ss_pred             EEeecccchhhhhcCCCcccChHHHHhhc
Q 013329           74 LFSDDTDDKSRRSTNPEIGMSTHQETESV  102 (445)
Q Consensus        74 LL~lDLD~FKlINdn~g~vvSreQl~d~~  102 (445)
                      |+..+++.+.++..+++.++|++++.+..
T Consensus       157 Lt~~E~~~l~~l~~~~~~v~sr~~l~~~~  185 (232)
T PRK10955        157 LTGTEFTLLYLLAQHLGQVVSREHLSQEV  185 (232)
T ss_pred             CCHHHHHHHHHHHhCCCceEcHHHHHHHH
Confidence            88999999999999999999999999885

>PRK11083 DNA-binding response regulator CreB; Provisional

Probab=97.64  E-value=7.3e-05  Score=67.17  Aligned_cols=99  Identities=18%  Similarity=0.193  Sum_probs=68.8

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhhhCccccccccccchhhcccccc---CCCCeEEEEeec
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLVASDPSD---ANTNSTTLFSDD   78 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~rLTgl~nr~iL~~gLdl~Ld~asr---~n~~slaLL~lD   78 (445)
                      |+..+......++++||++||.||++..+|..+|+.++++...... .......+ ...++....   ..+....|+..+
T Consensus        82 s~~~~~~~~~~a~~~Ga~~~l~kp~~~~~l~~~i~~~~~~~~~~~~-~~~~~~~~-~~~~~~~~~~~~~~~~~~~Lt~~E  159 (228)
T PRK11083         82 TARSDEVDRLVGLEIGADDYVAKPFSPREVAARVRTILRRVKKFAA-PSPVIRIG-HFELDEPAARISYFGTPLTLTRYE  159 (228)
T ss_pred             EcCCcHHHHHHHhhcCCCeEEECCCCHHHHHHHHHHHHCccccccC-CCceeEEC-CEEEecCccEEEECCEEeecCHHH
Confidence            4556667778899999999999999999999999988876432100 01111111 112221111   122356789999


Q ss_pred             ccchhhhhcCCCcccChHHHHhhc
Q 013329           79 TDDKSRRSTNPEIGMSTHQETESV  102 (445)
Q Consensus        79 LD~FKlINdn~g~vvSreQl~d~~  102 (445)
                      ++.+.++..++++++|++++.+.+
T Consensus       160 ~~il~~l~~~~~~~~s~~~i~~~l  183 (228)
T PRK11083        160 FLLLKTLLLSPGRVFSRQQLMDIV  183 (228)
T ss_pred             HHHHHHHHhCCCceECHHHHHHHh
Confidence            999999999999999999999875

>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB

Probab=97.63  E-value=8.6e-05  Score=66.45  Aligned_cols=98  Identities=27%  Similarity=0.275  Sum_probs=68.6

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhhhCccccccccccchhhcccccc---CCCCeEEEEeec
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLVASDPSD---ANTNSTTLFSDD   78 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~rLTgl~nr~iL~~gLdl~Ld~asr---~n~~slaLL~lD   78 (445)
                      |+..+......++++||++||.||++..+|..+|+.++++... .. ....+..+ ...++....   ..+....|+..+
T Consensus        83 s~~~~~~~~~~~~~~Ga~~~l~kp~~~~~l~~~i~~~~~~~~~-~~-~~~~~~~~-~~~~~~~~~~~~~~~~~~~Lt~~E  159 (226)
T TIGR02154        83 TARGEEEDRVRGLETGADDYITKPFSPRELLARIKAVLRRIRP-QL-SDEVIEVG-DLSLDPVAHRVFRGGQPLSLGPTE  159 (226)
T ss_pred             ecCCCHHHHHHHHhcCcceEEeCCCCHHHHHHHHHHHhccccc-cc-ccCceEEC-CEEEEcCccEEEECCEEEEcCHHH
Confidence            5566677788899999999999999999999999988866421 11 11111111 111221111   122345788999


Q ss_pred             ccchhhhhcCCCcccChHHHHhhc
Q 013329           79 TDDKSRRSTNPEIGMSTHQETESV  102 (445)
Q Consensus        79 LD~FKlINdn~g~vvSreQl~d~~  102 (445)
                      ++.+.++..++++++|++++.+.+
T Consensus       160 ~~il~~l~~~~~~~~s~~~i~~~~  183 (226)
T TIGR02154       160 FRLLHFFMTHPERVYSREQLLDRV  183 (226)
T ss_pred             HHHHHHHHhCCCceEcHHHHHHHh
Confidence            999999999999999999998764

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.

>PRK09581 pleD response regulator PleD; Reviewed

Probab=97.59  E-value=7.5e-05  Score=74.52  Aligned_cols=109  Identities=23%  Similarity=0.357  Sum_probs=72.1

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh--------------------hhCccccccccccchhh
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR--------------------MLGLAEKNILSYDFDLV   60 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r--------------------LTgl~nr~iL~~gLdl~   60 (445)
                      +|+..+.+...++++.||+|||.||+++++|..+|...+...+                    ++++.++..+...+...
T Consensus       234 ls~~~~~~~~~~a~~~Ga~d~l~kp~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~d~lt~l~n~~~~~~~l~~~  313 (457)
T PRK09581        234 LVDEDDDPRLVKALELGVNDYLMRPIDKNELLARVRTQIRRKRYQDALRNNLEQSIEMAVTDGLTGLHNRRYFDMHLKNL  313 (457)
T ss_pred             EeCCCChHHHHHHHHccchhhhhCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCccccccCHHHHHHHHHHH
Confidence            4677788889999999999999999999999999987665321                    11222222221111111


Q ss_pred             ccccccCCCCeEEEEeecccchhhhhcCCCcccChHHHHhhcchhhhhhhhcccC
Q 013329           61 ASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTSG  115 (445)
Q Consensus        61 Ld~asr~n~~slaLL~lDLD~FKlINdn~g~vvSreQl~d~~l~~~A~~~a~~~~  115 (445)
                      +...... ...+.++.++++.|..++...+     +..++..|+.++..|...+.
T Consensus       314 ~~~~~~~-~~~~~~l~i~i~~~~~i~~~~g-----~~~~~~~l~~i~~~l~~~~~  362 (457)
T PRK09581        314 IERANER-GKPLSLMMIDIDHFKKVNDTYG-----HDAGDEVLREFAKRLRNNIR  362 (457)
T ss_pred             HHHHHhc-CCcEEEEEEecchhhHhHHhhC-----hhhHHHHHHHHHHHHHhhCC
Confidence            2211111 2346788899999999988764     44666777788888877664

>PRK10643 DNA-binding transcriptional regulator BasR; Provisional

Probab=97.53  E-value=0.00018  Score=64.32  Aligned_cols=96  Identities=23%  Similarity=0.208  Sum_probs=68.0

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhhhCccccccccccchhhcccccc---CCCCeEEEEeec
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLVASDPSD---ANTNSTTLFSDD   78 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~rLTgl~nr~iL~~gLdl~Ld~asr---~n~~slaLL~lD   78 (445)
                      |+..+......++++||++||.||++..+|..+|+.++++...  . ....+..+ +..+.....   .+.....|+..+
T Consensus        79 s~~~~~~~~~~~~~~ga~~~l~kp~~~~~l~~~i~~~~~~~~~--~-~~~~~~~~-~~~~~~~~~~~~~~~~~~~Lt~~E  154 (222)
T PRK10643         79 TARDTLEDRVAGLDVGADDYLVKPFALEELHARIRALIRRHQG--Q-GENELQVG-NLTLNLGRQQVWLDGQELILTPKE  154 (222)
T ss_pred             ECCCCHHHHHHHHhcCCCeEEeCCCCHHHHHHHHHHHHhhhcc--c-cCCceEEC-CEEEEcCCCEEEECCEEEecCHHH
Confidence            5566777888999999999999999999999999998876431  1 11111111 111111111   122356788889


Q ss_pred             ccchhhhhcCCCcccChHHHHhh
Q 013329           79 TDDKSRRSTNPEIGMSTHQETES  101 (445)
Q Consensus        79 LD~FKlINdn~g~vvSreQl~d~  101 (445)
                      ++.+..+..++|..++++.+.+.
T Consensus       155 ~~il~~l~~~~g~~~~~~~~~~~  177 (222)
T PRK10643        155 FALLSRLMLKAGSPVHREILYQD  177 (222)
T ss_pred             HHHHHHHHhCCCceEcHHHHHHH
Confidence            99999999999999999999874

>PRK10336 DNA-binding transcriptional regulator QseB; Provisional

Probab=97.52  E-value=0.00017  Score=64.54  Aligned_cols=97  Identities=25%  Similarity=0.257  Sum_probs=69.0

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhhhCccccccccccchhhccccc---cCCCCeEEEEeec
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLVASDPS---DANTNSTTLFSDD   78 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~rLTgl~nr~iL~~gLdl~Ld~as---r~n~~slaLL~lD   78 (445)
                      |+..+......++++||++||.||++..+|..+|+.++++..  +.. ...+..+ +..++...   ...+..+.|+..+
T Consensus        79 t~~~~~~~~~~~~~~ga~~~i~kp~~~~~l~~~i~~~~~~~~--~~~-~~~~~~~-~~~~~~~~~~~~~~~~~~~Lt~~E  154 (219)
T PRK10336         79 TARDALAERVEGLRLGADDYLCKPFALIEVAARLEALMRRTN--GQA-SNELRHG-NVMLDPGKRIATLAGEPLTLKPKE  154 (219)
T ss_pred             ECCCCHHHHHHHHhCCCCeEEECCCCHHHHHHHHHHHHhccc--cCC-CCceeEC-CEEEEcccCEEEECCEEEecCHHH
Confidence            556667777889999999999999999999999999887542  111 1111111 11221111   1123356789999


Q ss_pred             ccchhhhhcCCCcccChHHHHhhc
Q 013329           79 TDDKSRRSTNPEIGMSTHQETESV  102 (445)
Q Consensus        79 LD~FKlINdn~g~vvSreQl~d~~  102 (445)
                      ++.|..+..++++++|++++.+..
T Consensus       155 ~~il~~l~~~~~~~~s~~~i~~~l  178 (219)
T PRK10336        155 FALLELLMRNAGRVLPRKLIEEKL  178 (219)
T ss_pred             HHHHHHHHhCCCccCcHHHHHHHh
Confidence            999999999999999999998874

>PRK15479 transcriptional regulatory protein TctD; Provisional

Probab=97.42  E-value=0.00032  Score=62.76  Aligned_cols=97  Identities=24%  Similarity=0.218  Sum_probs=68.3

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhhhCccccccccccchhhcccc--ccCCCCeEEEEeecc
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLVASDP--SDANTNSTTLFSDDT   79 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~rLTgl~nr~iL~~gLdl~Ld~a--sr~n~~slaLL~lDL   79 (445)
                      |+..+.....+++++|+++||.||++..+|..+++.++++...  .... ....+ .+.+...  ....+..+.|+..++
T Consensus        79 t~~~~~~~~~~~~~~g~~~~i~kp~~~~~l~~~i~~~~~~~~~--~~~~-~~~~~-~~~~~~~~~~~~~~~~~~Lt~~E~  154 (221)
T PRK15479         79 TARSAVADRVKGLNVGADDYLPKPFELEELDARLRALLRRSAG--QVQE-VQQLG-ELIFHDEGYFLLQGQPLALTPREQ  154 (221)
T ss_pred             ECCCCHHHHHHHHHcCCCeeEeCCCCHHHHHHHHHHHHhhhcc--CcCc-cEEEC-CEEEccCCeEEECCEEEecCHHHH
Confidence            4556667778899999999999999999999999988876431  1111 11111 1111110  011223567999999


Q ss_pred             cchhhhhcCCCcccChHHHHhhc
Q 013329           80 DDKSRRSTNPEIGMSTHQETESV  102 (445)
Q Consensus        80 D~FKlINdn~g~vvSreQl~d~~  102 (445)
                      +.+.++..+++.++++.++.+..
T Consensus       155 ~il~~l~~~~~~~~~~~~i~~~l  177 (221)
T PRK15479        155 ALLTVLMYRRTRPVSRQQLFEQV  177 (221)
T ss_pred             HHHHHHHhCCCCcCcHHHHHHHh
Confidence            99999999999999999999874

>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional

Probab=97.13  E-value=0.0008  Score=61.30  Aligned_cols=99  Identities=18%  Similarity=0.146  Sum_probs=67.2

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhhhCccccccccccchhhccccc---cCCCCeEEEEeec
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLVASDPS---DANTNSTTLFSDD   78 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~rLTgl~nr~iL~~gLdl~Ld~as---r~n~~slaLL~lD   78 (445)
                      ++..+......++.+|+++||.||++..+|..+|+.++++........ .....+ ...++...   ...+..+.|+..+
T Consensus        88 ~~~~~~~~~~~~~~~ga~~~l~kp~~~~~L~~~i~~~~~~~~~~~~~~-~~~~~~-~~~~~~~~~~~~~~~~~~~Lt~~e  165 (240)
T PRK10710         88 TAKIEEIDRLLGLEIGADDYICKPYSPREVVARVKTILRRCKPQRELQ-QQDAES-PLIIDESRFQASWRGKMLDLTPAE  165 (240)
T ss_pred             EcCCCHHHHHHHHhcCCCeEEECCCCHHHHHHHHHHHHhhccccCCCc-cceEeC-CEEEEcCceEEEECCEEeecCHHH
Confidence            344556667789999999999999999999999999887643211100 001111 11111111   1122355688889


Q ss_pred             ccchhhhhcCCCcccChHHHHhhc
Q 013329           79 TDDKSRRSTNPEIGMSTHQETESV  102 (445)
Q Consensus        79 LD~FKlINdn~g~vvSreQl~d~~  102 (445)
                      ++.+.++..+++.++|++++.+..
T Consensus       166 ~~il~~l~~~~~~~~s~~~i~~~~  189 (240)
T PRK10710        166 FRLLKTLSHEPGKVFSREQLLNHL  189 (240)
T ss_pred             HHHHHHHHhCCCceEcHHHHHHHh
Confidence            999999999999999999998874

>COG2199 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]

Probab=96.95  E-value=0.00055  Score=61.49  Aligned_cols=69  Identities=13%  Similarity=0.120  Sum_probs=54.7

Q ss_pred             hhhCccccccccccchhhccccccCCCCeEEEEeecccchhhhhcCCCcccChHHHHhhcchhhhhhhhcccCCc
Q 013329           43 RMLGLAEKNILSYDFDLVASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTSGTA  117 (445)
Q Consensus        43 rLTgl~nr~iL~~gLdl~Ld~asr~n~~slaLL~lDLD~FKlINdn~g~vvSreQl~d~~l~~~A~~~a~~~~~~  117 (445)
                      .+|++.|+..+...+...+...... ...++|+++|+|+||.||+..|     |+.+|.+|+.+|..|...+...
T Consensus        24 ~LTgl~NR~~~~~~l~~~~~~~~~~-~~~~~l~~iDiD~Fk~iND~~G-----h~~GD~vL~~va~~L~~~~~~~   92 (181)
T COG2199          24 PLTGLPNRRAFEERLERALARARRH-GEPLALLLLDLDHFKQINDTYG-----HAAGDEVLREVARRLRSNLREG   92 (181)
T ss_pred             cccCCHHHHHHHHHHHHHHHHhhcc-CCCeEEEEEeCcCCcccccccc-----chHHHHHHHHHHHHHHHhcCCC
Confidence            5678888877765555555544332 2368999999999999999994     8999999999999999888765

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

Probab=96.68  E-value=0.0017  Score=63.38  Aligned_cols=101  Identities=17%  Similarity=0.299  Sum_probs=65.5

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhhhCccccccccccchhhccccccC---CCCeEEEEee
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLVASDPSDA---NTNSTTLFSD   77 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~rLTgl~nr~iL~~gLdl~Ld~asr~---n~~slaLL~l   77 (445)
                      +||..+.+.+.++++.||.|||.|||..+.|..++....+++..... +...-+..+|..+......   ...+-+|...
T Consensus        80 iTAA~d~~tI~~alr~Gv~DYLiKPf~~eRl~~aL~~y~~~r~~l~~-~~~~sQ~~lD~l~~~~~k~~~~~~LPkGi~~~  158 (224)
T COG4565          80 ITAASDMETIKEALRYGVVDYLIKPFTFERLQQALTRYRQKRHALES-HQQLSQKELDQLFNIQSKEQPPDDLPKGLDEL  158 (224)
T ss_pred             EeccchHHHHHHHHhcCchhheecceeHHHHHHHHHHHHHHHHHHhh-hcccCHHHHHHHHhccccccCcccCCCCcCHH
Confidence            57888999999999999999999999999999999888776543211 1111122234433322221   1122334444


Q ss_pred             cccchhhhhcCCCcccChHHHHhhc
Q 013329           78 DTDDKSRRSTNPEIGMSTHQETESV  102 (445)
Q Consensus        78 DLD~FKlINdn~g~vvSreQl~d~~  102 (445)
                      .+......-..++..+|-+++.+.+
T Consensus       159 Tl~~i~~~~~~~~~~~Taeela~~~  183 (224)
T COG4565         159 TLQKVREALKEPDQELTAEELAQAL  183 (224)
T ss_pred             HHHHHHHHHhCcCCccCHHHHHHHh
Confidence            4444444445788899999988875

>COG4566 TtrR Response regulator [Signal transduction mechanisms]

Probab=96.55  E-value=0.0017  Score=62.55  Aligned_cols=42  Identities=24%  Similarity=0.555  Sum_probs=39.8

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      ||++.+....+++++.||.|||.|||+..+|+..|+.++++.
T Consensus        82 iTGhgDIpmaV~AmK~GAvDFLeKP~~~q~Lldav~~Al~~~  123 (202)
T COG4566          82 LTGHGDIPMAVQAMKAGAVDFLEKPFSEQDLLDAVERALARD  123 (202)
T ss_pred             EeCCCChHHHHHHHHcchhhHHhCCCchHHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999999764

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

Probab=96.45  E-value=0.0039  Score=66.80  Aligned_cols=44  Identities=32%  Similarity=0.586  Sum_probs=41.1

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhh
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRM   44 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~rL   44 (445)
                      ||++.+.+..++|++.||.|||.|||+++.|+..|++++...++
T Consensus        82 ~Tg~g~i~~AV~A~k~GA~Dfl~KP~~~~~L~~~v~ral~~~~~  125 (464)
T COG2204          82 MTGHGDIDTAVEALRLGAFDFLEKPFDLDRLLAIVERALELREL  125 (464)
T ss_pred             EeCCCCHHHHHHHHhcCcceeeeCCCCHHHHHHHHHHHHHHhhh
Confidence            68999999999999999999999999999999999999987653

>PRK15426 putative diguanylate cyclase YedQ; Provisional

Probab=96.03  E-value=0.0036  Score=65.98  Aligned_cols=67  Identities=15%  Similarity=0.096  Sum_probs=51.3

Q ss_pred             hhCccccccccccchhhccccccCCCCeEEEEeecccchhhhhcCCCcccChHHHHhhcchhhhhhhhcccCC
Q 013329           44 MLGLAEKNILSYDFDLVASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTSGT  116 (445)
Q Consensus        44 LTgl~nr~iL~~gLdl~Ld~asr~n~~slaLL~lDLD~FKlINdn~g~vvSreQl~d~~l~~~A~~~a~~~~~  116 (445)
                      +|++.|+..|...++..+....... ..++|+++|+|+||.||+..     +|+.+|.+|+.+|..|...+..
T Consensus       403 LTgl~Nr~~f~~~l~~~~~~~~~~~-~~~~l~~idid~fk~iNd~~-----G~~~GD~~L~~~a~~l~~~~~~  469 (570)
T PRK15426        403 LTRLYNRGALFEKARALAKRCQRDQ-QPFSVIQLDLDHFKSINDRF-----GHQAGDRVLSHAAGLISSSLRA  469 (570)
T ss_pred             CCCCccHHHHHHHHHHHHHHHHhcC-CcEEEEEEECcccCHhhHhh-----ChHHHHHHHHHHHHHHHHhCCC
Confidence            5677777666555454444433322 36899999999999999999     7889999999999999887653

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

Probab=95.01  E-value=0.0097  Score=55.03  Aligned_cols=41  Identities=46%  Similarity=0.799  Sum_probs=39.1

Q ss_pred             HHHHHHHHHHHHHhhcccCCCcccchhhhhhhhhhCCCCCc
Q 013329          359 VDRREAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVRG  399 (445)
Q Consensus       359 ~~~R~~~~~ry~eKr~~R~f~kkirY~~RK~~A~~RpRvkG  399 (445)
                      ...|++.+.||+++++.|.|.++++|..||..|+.|+|+||
T Consensus       290 ~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  330 (340)
T KOG1601|consen  290 SHQRVAEVRRYRESRDGRYFDKGIRYASRKSNAESRPRLKG  330 (340)
T ss_pred             cchHHHHHhhccCccCCcccccccccccccccchhcccccc
Confidence            45699999999999999999999999999999999999999

>PRK10245 adrA diguanylate cyclase AdrA; Provisional

Probab=94.87  E-value=0.015  Score=59.68  Aligned_cols=68  Identities=15%  Similarity=0.026  Sum_probs=51.2

Q ss_pred             hhhCccccccccccchhhccccccCCCCeEEEEeecccchhhhhcCCCcccChHHHHhhcchhhhhhhhcccCC
Q 013329           43 RMLGLAEKNILSYDFDLVASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTSGT  116 (445)
Q Consensus        43 rLTgl~nr~iL~~gLdl~Ld~asr~n~~slaLL~lDLD~FKlINdn~g~vvSreQl~d~~l~~~A~~~a~~~~~  116 (445)
                      .+|++.|+..+...++..+....+. ....+|+.+|+|+||.||+..     +++.+|.+|+.+|..|...+..
T Consensus       209 ~LTGL~NR~~f~~~l~~~l~~~~~~-~~~~~ll~idId~Fk~INd~~-----Gh~~GD~lL~~vA~~L~~~l~~  276 (366)
T PRK10245        209 GMTGVYNRRHWETLLRNEFDNCRRH-HRDATLLIIDIDHFKSINDTW-----GHDVGDEAIVALTRQLQITLRG  276 (366)
T ss_pred             CccCCCCHHHHHHHHHHHHHHHHhc-CCCEEEEEEECCcchHHHHhh-----CchHHHHHHHHHHHHHHHhCCC
Confidence            3467777776655555555543332 236789999999999999999     7788999999999999887654

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

Probab=94.74  E-value=0.022  Score=59.27  Aligned_cols=43  Identities=28%  Similarity=0.431  Sum_probs=39.0

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      +|+..+.+...+++++||+|||.||+++.+|..++...++.++
T Consensus        95 lT~~~d~~~~~~~~~~g~~dyl~KP~~~~~l~~rv~~~~q~k~  137 (360)
T COG3437          95 LTAYADSEDRQRALEAGADDYLSKPISPKELVARVSSHLQLKR  137 (360)
T ss_pred             EeecCChHHHHHHHHhhHHHHhcCCCCHHHHHHHHHHHHHHHH
Confidence            5788999999999999999999999999999999998876553

>PRK11059 regulatory protein CsrD; Provisional

Probab=94.69  E-value=0.019  Score=62.59  Aligned_cols=67  Identities=7%  Similarity=0.024  Sum_probs=52.6

Q ss_pred             hhhCccccccccccchhhccccccCCCCeEEEEeecccchhhhhcCCCcccChHHHHhhcchhhhhhhhcccC
Q 013329           43 RMLGLAEKNILSYDFDLVASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTSG  115 (445)
Q Consensus        43 rLTgl~nr~iL~~gLdl~Ld~asr~n~~slaLL~lDLD~FKlINdn~g~vvSreQl~d~~l~~~A~~~a~~~~  115 (445)
                      .+||+.||..|...++..+....+.. ...+|+++|+|+||.||+..     +|+.+|.+|+.+|..|...+.
T Consensus       232 ~LTGL~NR~~f~~~l~~~l~~~~~~~-~~~~ll~idid~fk~iNd~~-----Gh~~gD~~L~~va~~L~~~~~  298 (640)
T PRK11059        232 AKTGLGNRLFFDNQLATLLEDQEMVG-AHGVVMLIRLPDFDLLQEEW-----GESQVEELLFELINLLSTFVM  298 (640)
T ss_pred             cccCCccHHHHHHHHHHHHHHHhhcC-CcEEEEEEECchHHHHHHhc-----ChHHHHHHHHHHHHHHHHHHh
Confidence            45778888777666665665443322 25789999999999999999     688999999999999988765

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=94.59  E-value=0.064  Score=50.28  Aligned_cols=43  Identities=28%  Similarity=0.501  Sum_probs=37.0

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      +|+..+.....+++++||++||.||++.++|...|+.++....
T Consensus        84 ls~~~~~~~~~~al~~Ga~~yl~Kp~~~~~L~~~i~~~~~~~~  126 (225)
T PRK10046         84 TTAASDMETVSEAVRCGVFDYLIKPIAYERLGQTLTRFRQRKH  126 (225)
T ss_pred             EEcCCCHHHHHHHHHcCccEEEECCcCHHHHHHHHHHHHHHHH
Confidence            3566777888899999999999999999999999998876544

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=94.12  E-value=0.067  Score=55.22  Aligned_cols=42  Identities=24%  Similarity=0.395  Sum_probs=36.7

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      +|+..+.+...+++++||+|||.||++.++|..+|+.++...
T Consensus        79 lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~~~~~  120 (445)
T TIGR02915        79 ITGNDDRENAVKAIGLGAYDFYQKPIDPDVLKLIVDRAFHLY  120 (445)
T ss_pred             EecCCCHHHHHHHHHCCccEEEeCCCCHHHHHHHHhhhhhhh
Confidence            466777888999999999999999999999999998877643

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=93.77  E-value=0.036  Score=37.90  Aligned_cols=24  Identities=42%  Similarity=0.574  Sum_probs=9.9

Q ss_pred             HHHHHHHHHHHhhcccCCCcccchh
Q 013329          361 RREAALIKFRQKRKERCFDKKIRYV  385 (445)
Q Consensus       361 ~R~~~~~ry~eKr~~R~f~kkirY~  385 (445)
                      .|.+.|+||.||||.|... +.-|.
T Consensus         3 aRK~SLqRFLeKRK~R~~~-~~PY~   26 (27)
T PF09425_consen    3 ARKASLQRFLEKRKDRLAA-KSPYQ   26 (27)
T ss_dssp             ---HHHHHHHHHH------------
T ss_pred             hHHHHHHHHHHHHHHhhcc-CCCCC
Confidence            4899999999999999987 55553

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.

>PRK10360 DNA-binding transcriptional activator UhpA; Provisional

Probab=93.75  E-value=0.11  Score=46.04  Aligned_cols=40  Identities=25%  Similarity=0.319  Sum_probs=34.5

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      |...+......+++.|+++||.||++..+|..+|+.+++.
T Consensus        79 s~~~~~~~~~~~~~~ga~~~i~kp~~~~~l~~~i~~~~~~  118 (196)
T PRK10360         79 SVHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVATG  118 (196)
T ss_pred             ECCCCHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHcC
Confidence            4556677778899999999999999999999999888754

>PRK09958 DNA-binding transcriptional activator EvgA; Provisional

Probab=93.67  E-value=0.11  Score=46.24  Aligned_cols=40  Identities=18%  Similarity=0.199  Sum_probs=34.8

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      |+..+......++..|+++||.||++..+|..+|+.+++.
T Consensus        80 s~~~~~~~~~~~~~~ga~~~i~kp~~~~~l~~~i~~~~~~  119 (204)
T PRK09958         80 SAKNDHFYGKHCADAGANGFVSKKEGMNNIIAAIEAAKNG  119 (204)
T ss_pred             eCCCCHHHHHHHHHCCCCEEEecCCCHHHHHHHHHHHHcC
Confidence            4556677788999999999999999999999999988754

>PRK10693 response regulator of RpoS; Provisional

Probab=93.67  E-value=0.1  Score=52.05  Aligned_cols=41  Identities=32%  Similarity=0.463  Sum_probs=34.6

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCC-CHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPL-RTNELLNLWTHMWRR   41 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPf-d~eELLaRVra~LrR   41 (445)
                      +|+..+.+...+++++||+|||.||+ +.++|..+|...++.
T Consensus        51 lt~~~~~~~~~~al~~Ga~dyl~KP~~~~~~L~~~i~~~l~~   92 (303)
T PRK10693         51 ISATENMADIAKALRLGVQDVLLKPVKDLNRLREMVFACLYP   92 (303)
T ss_pred             EECCCCHHHHHHHHHCCCcEEEECCCCcHHHHHHHHHHHhhh
Confidence            35667778888999999999999999 589999998877643

>PRK10430 DNA-binding transcriptional activator DcuR; Provisional

Probab=93.33  E-value=0.16  Score=48.05  Aligned_cols=42  Identities=21%  Similarity=0.493  Sum_probs=36.1

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      +|+..+......++..|+++||.||++.++|...|..++.+.
T Consensus        83 ls~~~~~~~~~~al~~Ga~~yl~Kp~~~~~l~~~i~~~~~~~  124 (239)
T PRK10430         83 ISSAADAATIKDSLHYGVVDYLIKPFQASRFEEALTGWRQKK  124 (239)
T ss_pred             EECCCcHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHHHH
Confidence            356677788889999999999999999999999998876544

>PRK10610 chemotaxis regulatory protein CheY; Provisional

Probab=93.26  E-value=0.2  Score=39.16  Aligned_cols=38  Identities=18%  Similarity=0.439  Sum_probs=32.3

Q ss_pred             CCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            4 QDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         4 ~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      .........+++.|+++||.||++..+|..+++.++++
T Consensus        89 ~~~~~~~~~~~~~g~~~~i~~p~~~~~l~~~l~~~~~~  126 (129)
T PRK10610         89 EAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK  126 (129)
T ss_pred             CCCHHHHHHHHHhCCCeEEECCCCHHHHHHHHHHHHHH
Confidence            34456677889999999999999999999999888765

>PRK09935 transcriptional regulator FimZ; Provisional

Probab=93.03  E-value=0.15  Score=45.28  Aligned_cols=91  Identities=13%  Similarity=0.181  Sum_probs=56.2

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhhhCccccccccccchhhccccccCCCCeEEEEeecccc
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLVASDPSDANTNSTTLFSDDTDD   81 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~rLTgl~nr~iL~~gLdl~Ld~asr~n~~slaLL~lDLD~   81 (445)
                      |+..+......++..|+++|+.||++..+|...|+.++.+...  .... .+... . .... .........|...++..
T Consensus        84 s~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~l~~~~~--~~~~-~~~~~-~-~~~~-~~~~~~~~~lt~re~~v  157 (210)
T PRK09935         84 SSKSECFYAGRAIQAGANGFVSKCNDQNDIFHAVQMILSGYTF--FPSE-TLNYI-K-SNKC-STNSSTDTVLSNREVTI  157 (210)
T ss_pred             ECCCcHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHcCCce--eCHH-HHHHH-H-hccc-ccCccccccCCHHHHHH
Confidence            4556667778899999999999999999999999888765321  1011 11000 0 0000 00111244577777777


Q ss_pred             hhhhhcCCCcccChHHHHhhc
Q 013329           82 KSRRSTNPEIGMSTHQETESV  102 (445)
Q Consensus        82 FKlINdn~g~vvSreQl~d~~  102 (445)
                      +..+..+    +|++++.+..
T Consensus       158 l~~l~~g----~s~~eIa~~l  174 (210)
T PRK09935        158 LRYLVSG----LSNKEIADQL  174 (210)
T ss_pred             HHHHHcC----CCHHHHHHHh
Confidence            7776544    6777777653

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

Probab=92.97  E-value=0.065  Score=50.65  Aligned_cols=37  Identities=27%  Similarity=0.592  Sum_probs=32.9

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTH   37 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra   37 (445)
                      ||+..+....++|+++||++||.||-+.+++++.+..
T Consensus        87 LTGy~sIATAV~AvKlGA~~YLaKPAdaDdi~aAl~~  123 (182)
T COG4567          87 LTGYASIATAVEAVKLGACDYLAKPADADDILAALLR  123 (182)
T ss_pred             EecchHHHHHHHHHHhhhhhhcCCCCChHHHHHHHhh
Confidence            5888999999999999999999999999998876543

>PRK13561 putative diguanylate cyclase; Provisional

Probab=92.92  E-value=0.084  Score=57.22  Aligned_cols=64  Identities=13%  Similarity=0.100  Sum_probs=50.9

Q ss_pred             hhhCccccccccccchhhccccccCCCCeEEEEeecccchhhhhcCCCcccChHHHHhhcchhhhhhhhcccCC
Q 013329           43 RMLGLAEKNILSYDFDLVASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTSGT  116 (445)
Q Consensus        43 rLTgl~nr~iL~~gLdl~Ld~asr~n~~slaLL~lDLD~FKlINdn~g~vvSreQl~d~~l~~~A~~~a~~~~~  116 (445)
                      .+|+++|+..|...++..+.     .....+|+++|+|+|+.+|+..     +++.+|.+|+.+|..|...+..
T Consensus       235 ~lTgL~NR~~f~~~l~~~l~-----~~~~~~l~~idld~f~~in~~~-----G~~~gD~lL~~ia~~L~~~~~~  298 (651)
T PRK13561        235 PVSDLPNKALLMALLEQVVA-----RKQTTALMIITCETLRDTAGVL-----KEAQREILLLTLVEKLKSVLSP  298 (651)
T ss_pred             CCcCCccHHHHHHHHHHHHh-----cCCCeEEEEEECCchHHHHHhh-----ChHHHHHHHHHHHHHHHHhCCC
Confidence            35777888777655555554     2236789999999999999988     7889999999999999887754

>PRK10840 transcriptional regulator RcsB; Provisional

Probab=92.86  E-value=0.17  Score=46.78  Aligned_cols=40  Identities=10%  Similarity=0.176  Sum_probs=34.3

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      |+..+......++++||++||.||+++.+|+..|+.++..
T Consensus        87 s~~~~~~~~~~a~~~Ga~~yl~K~~~~~~l~~ai~~v~~g  126 (216)
T PRK10840         87 TMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQKG  126 (216)
T ss_pred             EecCCHHHHHHHHHCCCeEEEECCCCHHHHHHHHHHHHCC
Confidence            5566777778899999999999999999999999887643

>PRK11829 biofilm formation regulator HmsP; Provisional

Probab=92.81  E-value=0.088  Score=56.97  Aligned_cols=67  Identities=4%  Similarity=0.060  Sum_probs=52.3

Q ss_pred             hhhCccccccccccchhhccccccCCCCeEEEEeecccchhhhhcCCCcccChHHHHhhcchhhhhhhhcccCC
Q 013329           43 RMLGLAEKNILSYDFDLVASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTSGT  116 (445)
Q Consensus        43 rLTgl~nr~iL~~gLdl~Ld~asr~n~~slaLL~lDLD~FKlINdn~g~vvSreQl~d~~l~~~A~~~a~~~~~  116 (445)
                      .+|+++|+..|...++..+......  ...+|+.+|+|+|+.+|+..     +++.+|.+|+.+|..|...+..
T Consensus       236 ~lTgL~NR~~f~~~l~~~l~~~~~~--~~~~l~~idid~f~~in~~~-----G~~~gD~lL~~va~~l~~~~~~  302 (660)
T PRK11829        236 PVTELPNRSLFISLLEKEIASSTRT--DHFHLLVIGIETLQEVSGAM-----SEAQHQQLLLTIVQRIEQCIDD  302 (660)
T ss_pred             CccCchhHHHHHHHHHHHHHhhccC--CCEEEEEEECCcHHHHHHhh-----ChHHHHHHHHHHHHHHHHhCCC
Confidence            4578888887766666666543332  25789999999999999999     7889999999999999876643

>TIGR02875 spore_0_A sporulation transcription factor Spo0A

Probab=92.43  E-value=0.2  Score=47.70  Aligned_cols=41  Identities=22%  Similarity=0.307  Sum_probs=35.0

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      +|+.........+++.|+++||.|||+..+|..+|+.++..
T Consensus        84 lt~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~i~~~~~~  124 (262)
T TIGR02875        84 LSAFGQEKITQRAVALGADYYVLKPFDLEILAARIRQLAWG  124 (262)
T ss_pred             EeCCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHcc
Confidence            35666777788899999999999999999999999887654

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.

>PRK09894 diguanylate cyclase; Provisional

Probab=92.26  E-value=0.16  Score=48.81  Aligned_cols=65  Identities=22%  Similarity=0.156  Sum_probs=47.9

Q ss_pred             hhCccccccccccchhhccccccCCCCeEEEEeecccchhhhhcCCCcccChHHHHhhcchhhhhhhhcccCC
Q 013329           44 MLGLAEKNILSYDFDLVASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTSGT  116 (445)
Q Consensus        44 LTgl~nr~iL~~gLdl~Ld~asr~n~~slaLL~lDLD~FKlINdn~g~vvSreQl~d~~l~~~A~~~a~~~~~  116 (445)
                      +|+++|+..|...++..+..  + ....++|+.+|+|+|+.||+..     +++.+|.+|+.+|..|...+..
T Consensus       134 lTgL~Nr~~~~~~l~~~~~~--~-~~~~~~l~~i~id~f~~in~~~-----G~~~gd~~L~~ia~~l~~~~~~  198 (296)
T PRK09894        134 LTGLPGRRVLDESFDHQLRN--R-EPQNLYLALLDIDRFKLVNDTY-----GHLIGDVVLRTLATYLASWTRD  198 (296)
T ss_pred             ccCCCcHHHHHHHHHHHHHH--c-cCCcEEEEEEECccccHHHHcc-----CcHHHHHHHHHHHHHHHHhCCC
Confidence            46777776665544322221  1 2236789999999999999998     6778999999999999887654

>PLN03029 type-a response regulator protein; Provisional

Probab=92.18  E-value=0.23  Score=47.37  Aligned_cols=40  Identities=30%  Similarity=0.611  Sum_probs=32.4

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      |+........+++++|+++||.||+...+|...+..+++.
T Consensus       109 s~~~~~~~~~~al~~Ga~dyl~KP~~~~~L~~l~~~~~~~  148 (222)
T PLN03029        109 SSENVPSRITRCLEEGAEEFFLKPVQLSDLNRLKPHMMKT  148 (222)
T ss_pred             eCCCCHHHHHHHHHhCchheEECCCCHHHHHHHHHHHHHH
Confidence            5566677788999999999999999999987666655543

>PRK09581 pleD response regulator PleD; Reviewed

Probab=91.86  E-value=0.3  Score=48.91  Aligned_cols=41  Identities=29%  Similarity=0.408  Sum_probs=35.4

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      |+..+.....++++.|+++||.||++.++|..+|+.+++..
T Consensus        83 s~~~~~~~~~~~~~~ga~~~l~kp~~~~~l~~~i~~~~~~~  123 (457)
T PRK09581         83 TALDDPEDRVRGLEAGADDFLTKPINDVALFARVKSLTRLK  123 (457)
T ss_pred             ECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHH
Confidence            45566777889999999999999999999999999887654

>PRK09776 putative diguanylate cyclase; Provisional

Probab=91.77  E-value=0.085  Score=59.75  Aligned_cols=68  Identities=12%  Similarity=0.111  Sum_probs=52.2

Q ss_pred             hhhCccccccccccchhhccccccCCCCeEEEEeecccchhhhhcCCCcccChHHHHhhcchhhhhhhhcccCC
Q 013329           43 RMLGLAEKNILSYDFDLVASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTSGT  116 (445)
Q Consensus        43 rLTgl~nr~iL~~gLdl~Ld~asr~n~~slaLL~lDLD~FKlINdn~g~vvSreQl~d~~l~~~A~~~a~~~~~  116 (445)
                      .+|++.|+..|...+...+......+ ....|+++|+|+||.+|+..     +++.+|.+|+.+|..|...+.+
T Consensus       669 ~lTgl~nr~~f~~~l~~~~~~~~~~~-~~~~l~~idid~fk~in~~~-----G~~~gd~~L~~~a~~l~~~~~~  736 (1092)
T PRK09776        669 ALTHLANRASFEKQLRRLLQTVNSTH-QRHALVFIDLDRFKAVNDSA-----GHAAGDALLRELASLMLSMLRS  736 (1092)
T ss_pred             cccCCccHHHHHHHHHHHHHHHHhcC-CcEEEEEEECcchHHHHHhh-----ChhhHHHHHHHHHHHHHHhCCC
Confidence            46788887776655555554433333 36889999999999999999     7788999999999999877654

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

Probab=91.65  E-value=0.2  Score=54.24  Aligned_cols=42  Identities=31%  Similarity=0.511  Sum_probs=37.9

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      |||.++-+.+.+|+.+|+.|||.||++-.+|...+..+....
T Consensus        82 LSGy~eFeYak~Am~lGV~dYLLKP~~k~eL~~~L~ki~~kl  123 (475)
T COG4753          82 LSGYDEFEYAKKAMKLGVKDYLLKPVDKAELEEALKKIIGKL  123 (475)
T ss_pred             EeccchhHHHHHHHhcCchhheeCcCCHHHHHHHHHHHHHHH
Confidence            578889999999999999999999999999999888887654

>PRK09966 putative inner membrane diguanylate cyclase; Provisional

Probab=91.35  E-value=0.22  Score=50.44  Aligned_cols=64  Identities=16%  Similarity=0.207  Sum_probs=47.4

Q ss_pred             hhCccccccccccchhhccccccCCCCeEEEEeecccchhhhhcCCCcccChHHHHhhcchhhhhhhhccc
Q 013329           44 MLGLAEKNILSYDFDLVASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTS  114 (445)
Q Consensus        44 LTgl~nr~iL~~gLdl~Ld~asr~n~~slaLL~lDLD~FKlINdn~g~vvSreQl~d~~l~~~A~~~a~~~  114 (445)
                      +|++.|+..|...++..+....  ......|+.+|+|+|+.+|+..     +++.+|.+|+.+|..|....
T Consensus       253 lTgl~nr~~f~~~l~~~~~~~~--~~~~~~l~~i~id~f~~in~~~-----G~~~gd~~l~~~a~~L~~~~  316 (407)
T PRK09966        253 LTGLANRAAFRSGINTLMNNSD--ARKTSALLFLDGDNFKYINDTW-----GHATGDRVLIEIAKRLAEFG  316 (407)
T ss_pred             ccCCccHHHHHHHHHHHHHHhh--cCCceEEEEEECccchHHHhhh-----chHHHHHHHHHHHHHHHHhC
Confidence            4666676666555554444322  1235689999999999999999     68899999999999997644

>PRK11475 DNA-binding transcriptional activator BglJ; Provisional

Probab=90.96  E-value=0.33  Score=46.37  Aligned_cols=42  Identities=12%  Similarity=-0.029  Sum_probs=33.6

Q ss_pred             CCCCCcHHHHHHHH-HcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCL-RLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         1 LTA~~d~e~iveAL-eaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      +|+..+......++ ++||++||.||+++++|+..|+.++...
T Consensus        74 lt~~~~~~~~~~~~~~~Ga~gyl~K~~~~~eL~~aI~~v~~G~  116 (207)
T PRK11475         74 IADDDIEARLIGSLSPSPLDGVLSKASTLEILQQELFLSLNGV  116 (207)
T ss_pred             EeCCCCHHHHHHHHHHcCCeEEEecCCCHHHHHHHHHHHHCCC
Confidence            35656565566655 7999999999999999999999987643

>PRK09483 response regulator; Provisional

Probab=90.95  E-value=0.43  Score=42.90  Aligned_cols=40  Identities=23%  Similarity=0.320  Sum_probs=34.2

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      |...+......++..|+++||.||++..+|...|+.++..
T Consensus        82 s~~~~~~~~~~~~~~g~~~~l~k~~~~~~l~~~i~~~~~g  121 (217)
T PRK09483         82 TVHTENPLPAKVMQAGAAGYLSKGAAPQEVVSAIRSVHSG  121 (217)
T ss_pred             eCCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHCC
Confidence            4556667778899999999999999999999999887754

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=90.01  E-value=0.32  Score=50.25  Aligned_cols=42  Identities=36%  Similarity=0.517  Sum_probs=36.2

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      +|+..+.+....+++.|++|||.||++..+|...|+.++...
T Consensus        82 lt~~~~~~~~~~a~~~Ga~d~l~KP~~~~~L~~~i~~~l~~~  123 (457)
T PRK11361         82 MTAYAEVETAVEALRCGAFDYVIKPFDLDELNLIVQRALQLQ  123 (457)
T ss_pred             EeCCCCHHHHHHHHHCCccEEEecccCHHHHHHHHhhhcccc
Confidence            356777888899999999999999999999999998877543

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

Probab=89.99  E-value=0.51  Score=45.07  Aligned_cols=42  Identities=29%  Similarity=0.453  Sum_probs=37.9

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      +|+..+...+..++++||+.||.|..++++|...|+.++...
T Consensus        80 lt~~~~~~~v~~al~~Ga~Gyl~K~~~~~~l~~ai~~v~~G~  121 (211)
T COG2197          80 LTAHDDPAYVIRALRAGADGYLLKDASPEELVEAIRAVAAGG  121 (211)
T ss_pred             EeccCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHCCC
Confidence            477888999999999999999999999999999999987543

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

Probab=89.97  E-value=0.57  Score=38.77  Aligned_cols=40  Identities=33%  Similarity=0.448  Sum_probs=29.7

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHH-HHHHHHHHHHH
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNE-LLNLWTHMWRR   41 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eE-LLaRVra~LrR   41 (445)
                      |+.........++..|+++||.||+...+ |...|+..+..
T Consensus        86 t~~~~~~~~~~~~~~g~~~~l~kP~~~~~~l~~~i~~~~~~  126 (130)
T COG0784          86 TAYADEADRERALAAGADDYLTKPIFLEEELLAALRRLLAR  126 (130)
T ss_pred             EcCcCHHHHHHHHHcCCCeEEcCCCCcHHHHHHHHHHHHHh
Confidence            55556655667789999999999977776 77777755543

>PRK10403 transcriptional regulator NarP; Provisional

Probab=89.93  E-value=0.57  Score=41.28  Aligned_cols=40  Identities=25%  Similarity=0.242  Sum_probs=33.4

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      +...+......+++.|+++||.||++..+|..+|+.++..
T Consensus        87 ~~~~~~~~~~~~~~~g~~~~i~kp~~~~~l~~~i~~~~~~  126 (215)
T PRK10403         87 TVSDASSDVFALIDAGADGYLLKDSDPEVLLEAIRAGAKG  126 (215)
T ss_pred             eCCCChHHHHHHHHcCCCeEEecCCCHHHHHHHHHHHhCC
Confidence            3445666777889999999999999999999999887654

>PRK15369 two component system sensor kinase SsrB; Provisional

Probab=89.90  E-value=0.56  Score=40.83  Aligned_cols=40  Identities=23%  Similarity=0.245  Sum_probs=33.9

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      |+..+......++..|+++||.||++..+|...|+..+..
T Consensus        84 s~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~~~~  123 (211)
T PRK15369         84 TARQEEHMASRTLAAGALGYVLKKSPQQILLAAIQTVAVG  123 (211)
T ss_pred             eCCCCHHHHHHHHHhCCCEEEeCCCCHHHHHHHHHHHHCC
Confidence            4556667778899999999999999999999999887654

>PRK10060 RNase II stability modulator; Provisional

Probab=89.83  E-value=0.28  Score=53.99  Aligned_cols=67  Identities=13%  Similarity=0.130  Sum_probs=52.0

Q ss_pred             HhhhCccccccccccchhhccccccCCCCeEEEEeecccchhhhhcCCCcccChHHHHhhcchhhhhhhhcccCC
Q 013329           42 RRMLGLAEKNILSYDFDLVASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTSGT  116 (445)
Q Consensus        42 ~rLTgl~nr~iL~~gLdl~Ld~asr~n~~slaLL~lDLD~FKlINdn~g~vvSreQl~d~~l~~~A~~~a~~~~~  116 (445)
                      -.+|+++|+..|...++..+..  . ....++|+++|+|+|+.+|+..     ++..+|.+|+.+|..|...+..
T Consensus       240 D~LTGL~NR~~f~~~l~~~l~~--~-~~~~~~ll~idld~fk~iNd~~-----G~~~gD~lL~~va~~L~~~~~~  306 (663)
T PRK10060        240 DSITGLPNRNAIQELIDHAINA--A-DNNQVGIVYLDLDNFKKVNDAY-----GHMFGDQLLQDVSLAILSCLEE  306 (663)
T ss_pred             CccCCCcCHHHHHHHHHHHHHh--C-CCCcEEEEEEECcchhHHHHhh-----CcHHHHHHHHHHHHHHHHhCCC
Confidence            3578888988877766666622  2 2346789999999999999999     6677899999999999876643

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

Probab=89.31  E-value=0.6  Score=48.73  Aligned_cols=42  Identities=29%  Similarity=0.449  Sum_probs=36.4

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      +|+..+.+....++++|+.+||.||++..+|...|..++...
T Consensus        81 lt~~~~~~~~~~a~~~Ga~~~l~KP~~~~~L~~~i~~~l~~~  122 (469)
T PRK10923         81 MTAHSDLDAAVSAYQQGAFDYLPKPFDIDEAVALVERAISHY  122 (469)
T ss_pred             EECCCCHHHHHHHHhcCcceEEecCCcHHHHHHHHHHHHHHH
Confidence            356677778889999999999999999999999999887653

>PRK10651 transcriptional regulator NarL; Provisional

Probab=89.30  E-value=0.71  Score=40.82  Aligned_cols=40  Identities=28%  Similarity=0.388  Sum_probs=33.9

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      +...+......++..|+++||.||++..+|...|+.++..
T Consensus        87 ~~~~~~~~~~~~~~~g~~~~i~k~~~~~~l~~~i~~~~~~  126 (216)
T PRK10651         87 SVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALQQAAAG  126 (216)
T ss_pred             eCCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHCC
Confidence            3455666777899999999999999999999999988754

>PRK15115 response regulator GlrR; Provisional

Probab=88.19  E-value=0.49  Score=48.91  Aligned_cols=42  Identities=17%  Similarity=0.333  Sum_probs=36.4

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      +|+..+.....+++++|+++||.||++..+|...|..++...
T Consensus        83 lt~~~~~~~~~~a~~~Ga~~~l~KP~~~~~L~~~l~~~~~~~  124 (444)
T PRK15115         83 LTAHGSIPDAVAATQQGVFSFLTKPVDRDALYKAIDDALEQS  124 (444)
T ss_pred             EECCCCHHHHHHHHhcChhhhccCCCCHHHHHHHHHHHHHhh
Confidence            356667778889999999999999999999999999888654

>PRK11107 hybrid sensory histidine kinase BarA; Provisional

Probab=88.18  E-value=0.55  Score=52.25  Aligned_cols=41  Identities=22%  Similarity=0.273  Sum_probs=36.0

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      +|+........+++++|+++||.||++..+|...|+..+..
T Consensus       747 lt~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~~~~  787 (919)
T PRK11107        747 VTAHAMAGERERLLSAGMDDYLAKPIDEAMLKQVLLRYKPG  787 (919)
T ss_pred             EeCCCCHHHHHHHHHcCCCeEeeCCCCHHHHHHHHHHHccc
Confidence            46777788889999999999999999999999999887654

>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional

Probab=88.17  E-value=0.36  Score=52.75  Aligned_cols=64  Identities=13%  Similarity=0.079  Sum_probs=49.8

Q ss_pred             hhhCccccccccccchhhccccccCCCCeEEEEeecccchhhhhcCCCcccChHHHHhhcchhhhhhhhcccCC
Q 013329           43 RMLGLAEKNILSYDFDLVASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTSGT  116 (445)
Q Consensus        43 rLTgl~nr~iL~~gLdl~Ld~asr~n~~slaLL~lDLD~FKlINdn~g~vvSreQl~d~~l~~~A~~~a~~~~~  116 (445)
                      .+|+++|+..|...++..+    . .....+|+++|+|+|+.+|+..     +++.+|.+|+++|..|...+.+
T Consensus       380 ~lTgl~Nr~~~~~~l~~~~----~-~~~~~~l~~i~i~~~~~in~~~-----G~~~~d~ll~~~a~~l~~~~~~  443 (799)
T PRK11359        380 PLTGLPNRNNLHNYLDDLV----D-KAVSPVVYLIGVDHFQDVIDSL-----GYAWADQALLEVVNRFREKLKP  443 (799)
T ss_pred             CCCCCccHHHHHHHHHHHH----h-cCCCEEEEEEECCcHHHHHHHh-----CcHHHHHHHHHHHHHHHHhCCC
Confidence            3477888877766555555    1 2236789999999999999999     5889999999999999877653

>PRK15347 two component system sensor kinase SsrA; Provisional

Probab=88.06  E-value=0.73  Score=51.41  Aligned_cols=41  Identities=20%  Similarity=0.344  Sum_probs=35.5

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      +|+.........++++|+++||.||++..+|...|..++..
T Consensus       772 lt~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~~~~  812 (921)
T PRK15347        772 LTANAAPEEIHRCKKAGMNHYLTKPVTLAQLARALELAAEY  812 (921)
T ss_pred             EeCCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHhh
Confidence            46677788888999999999999999999999999877653

>PF00990 GGDEF: GGDEF domain; InterPro: IPR000160 This domain appears to be ubiquitous in bacteria and is often linked to a regulatory domain, such as a phosphorylation receiver or oxygen sensing domain

Probab=87.93  E-value=0.17  Score=42.84  Aligned_cols=67  Identities=10%  Similarity=0.104  Sum_probs=53.8

Q ss_pred             hhCccccccccccchhhccccccCCCCeEEEEeecccchhhhhcCCCcccChHHHHhhcchhhhhhhhcccCC
Q 013329           44 MLGLAEKNILSYDFDLVASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTSGT  116 (445)
Q Consensus        44 LTgl~nr~iL~~gLdl~Ld~asr~n~~slaLL~lDLD~FKlINdn~g~vvSreQl~d~~l~~~A~~~a~~~~~  116 (445)
                      +|++.++..|...+...+....+.. ..++|+.++++.|..++...     +.+.++.+|+.+|..|...+..
T Consensus         6 ~TgL~nr~~f~~~l~~~~~~~~~~~-~~~~l~~i~i~~~~~l~~~~-----G~~~~~~~l~~i~~~L~~~~~~   72 (161)
T PF00990_consen    6 LTGLPNRRYFEEKLESLLERASREG-EPFALVLIDIDNLDELNEKY-----GYEVGDEILRQIAKRLKKQLRE   72 (161)
T ss_dssp             TTSSBEHHHHHHHHHHHHHHHHHHT-SEEEEEEEEETTHHHHHHHH-----HHHHHHHHHHHHHHHHHHHCCT
T ss_pred             CCCCcHHHHHHHHHHHHHHHHhhcC-CCceEEEEeccccccccccc-----cccccccccccccccccccccc
Confidence            5788888777766666666653322 47899999999999999877     7889999999999999987766

Its function is to synthesize cyclic di-GMP, which is used as an intracellular signalling molecule in a wide variety of bacteria [,]. Enzymatic activity can be strongly influenced by the adjacent domains. Processes regulated by this domain include exopolysaccharide synthesis, biofilm formation, motility and cell differentiation. Structural studies of PleD from Caulobacter crescentus show that this domain forms a five-stranded beta sheet surrounded by helices, similar to the catalytic core of adenylate cyclase [].; PDB: 3IGN_A 3BRE_B 3EZU_A 3ICL_B 3PJX_A 3PJW_A 3HVW_A 3HVA_B 3I5C_B 3I5B_B ....

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=87.39  E-value=0.82  Score=47.45  Aligned_cols=42  Identities=26%  Similarity=0.439  Sum_probs=36.0

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      +|+..+.....+++++|+++||.||+..++|...|+.++...
T Consensus        76 lt~~~~~~~~~~a~~~Ga~~~l~KP~~~~~L~~~i~~~l~~~  117 (463)
T TIGR01818        76 MTAHSDLDTAVAAYQRGAFEYLPKPFDLDEAVTLVERALAHA  117 (463)
T ss_pred             EeCCCCHHHHHHHHHcCcceeecCCCCHHHHHHHHHHHHHHH
Confidence            356667778889999999999999999999999998887643

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.

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

Probab=86.59  E-value=0.95  Score=43.89  Aligned_cols=42  Identities=24%  Similarity=0.423  Sum_probs=36.9

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      +|+..+...+.+++++|+..||+||++..-|+..|.-+..+.
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            478889999999999999999999999999998887776654

>PRK13435 response regulator; Provisional

Probab=86.08  E-value=1.1  Score=38.44  Aligned_cols=33  Identities=21%  Similarity=0.180  Sum_probs=28.5

Q ss_pred             HHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329           11 VKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus        11 veALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      ..++..|+++||.||++..+|...|+.++.+..
T Consensus        91 ~~~~~~ga~~~l~kp~~~~~l~~~i~~~~~~~~  123 (145)
T PRK13435         91 VPHDFAGALGVIAKPYSPRGVARALSYLSARRV  123 (145)
T ss_pred             HHHHhcCcceeEeCCCCHHHHHHHHHHHHhcCc
Confidence            467889999999999999999999988876543

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

Probab=86.04  E-value=1.5  Score=40.54  Aligned_cols=34  Identities=24%  Similarity=0.413  Sum_probs=29.5

Q ss_pred             HHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            8 SVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         8 e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      +....+++.|+.+||.||++.++|...|..++..
T Consensus        85 ~~~~~a~~~~~~~yl~KP~~~~~l~~~l~~~~~~  118 (238)
T PRK11697         85 EYAIKAFEEHAFDYLLKPIDPARLAKTLARLRQE  118 (238)
T ss_pred             HHHHHHHhcCCcEEEECCCCHHHHHHHHHHHHHh
Confidence            4567889999999999999999999999887654

>PRK14084 two-component response regulator; Provisional

Probab=85.79  E-value=1.5  Score=40.92  Aligned_cols=35  Identities=23%  Similarity=0.465  Sum_probs=30.0

Q ss_pred             HHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            8 SVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         8 e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      ....++++.|+.+||.||+...+|...|..++...
T Consensus        85 ~~~~~~~~~~~~~yl~KP~~~~~l~~~l~~~~~~~  119 (246)
T PRK14084         85 QFAVKAFELNATDYILKPFEQKRIEQAVNKVRATK  119 (246)
T ss_pred             HHHHHHHhcCCcEEEECCCCHHHHHHHHHHHHHhh
Confidence            34568899999999999999999999998877543

>PRK09390 fixJ response regulator FixJ; Provisional

Probab=85.72  E-value=0.68  Score=40.12  Aligned_cols=41  Identities=22%  Similarity=0.523  Sum_probs=34.7

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      |+..+......+++.|+.+|+.||+...+|..++..++...
T Consensus        82 ~~~~~~~~~~~~~~~g~~~~l~~p~~~~~l~~~l~~~~~~~  122 (202)
T PRK09390         82 TGHGDVPLAVEAMKLGAVDFIEKPFEDERLIGAIERALAQA  122 (202)
T ss_pred             ECCCCHHHHHHHHHcChHHHhhCCCCHHHHHHHHHHHHHhh
Confidence            45566777788999999999999999999999998877653

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=85.71  E-value=0.67  Score=47.59  Aligned_cols=42  Identities=33%  Similarity=0.502  Sum_probs=36.2

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      +|+..+.+....+++.|+.+||.||++..+|...|..++...
T Consensus        83 lt~~~~~~~~~~a~~~ga~~~l~Kp~~~~~L~~~l~~~l~~~  124 (441)
T PRK10365         83 MTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAHT  124 (441)
T ss_pred             EECCCCHHHHHHHHHhhhHHHhcCCCCHHHHHHHHHHHHHHH
Confidence            356667788889999999999999999999999999887653

>TIGR02956 TMAO_torS TMAO reductase sytem sensor TorS

Probab=85.24  E-value=1.2  Score=50.25  Aligned_cols=41  Identities=22%  Similarity=0.254  Sum_probs=35.7

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      +|+.........++++|+++||.||++..+|...|..++..
T Consensus       783 lta~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~~~~  823 (968)
T TIGR02956       783 FSAHVFNEDVAQYLAAGFDGFLAKPVVEEQLTAMIAVILAG  823 (968)
T ss_pred             EECCCCHHHHHHHHHCCCCEEEeCCCCHHHHHHHHHHHhcc
Confidence            35667778888999999999999999999999999888754

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).

>PRK11466 hybrid sensory histidine kinase TorS; Provisional

Probab=83.78  E-value=1.3  Score=49.72  Aligned_cols=41  Identities=17%  Similarity=0.058  Sum_probs=35.6

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      +|+........++++.|+++||.||++.++|...|..++..
T Consensus       760 ~t~~~~~~~~~~~~~~g~~~~l~KP~~~~~L~~~i~~~~~~  800 (914)
T PRK11466        760 FSAHVIDETLRQRTSSLFRGIIPKPVPREVLGQLLAHYLQL  800 (914)
T ss_pred             EeCCCchhhHHHHHhcCcCCEEeCCCCHHHHHHHHHHHhhh
Confidence            35666777788899999999999999999999999988764

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

Probab=83.06  E-value=1.6  Score=50.69  Aligned_cols=41  Identities=22%  Similarity=0.248  Sum_probs=35.4

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      +|+..+.....+++++|+++||.||++..+|...|+.++..
T Consensus      1036 lt~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~~~~ 1076 (1197)
T PRK09959       1036 LTANAQANEREKGLSCGMNLCLFKPLTLDVLKTHLSQLHQV 1076 (1197)
T ss_pred             EECCCCHHHHHHHHHCCCCEEEeCCCCHHHHHHHHHHHhhc
Confidence            36677788888999999999999999999999999876643

>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=82.25  E-value=1.1  Score=32.86  Aligned_cols=33  Identities=36%  Similarity=0.563  Sum_probs=26.9

Q ss_pred             cHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHH
Q 013329            6 EVSVVVKCLRLGAADYLVKPLRTNELLNLWTHM   38 (445)
Q Consensus         6 d~e~iveALeaGAdDYLtKPfd~eELLaRVra~   38 (445)
                      .......++..|+.+|+.||+...+|...++.+
T Consensus        80 ~~~~~~~~~~~~~~~~i~~p~~~~~l~~~l~~~  112 (113)
T cd00156          80 DDEDAVEALKAGADDYLTKPFSPEELLARIRAL  112 (113)
T ss_pred             cHHHHHHHHHcChhhHccCCCCHHHHHHHHHhh
Confidence            445566788999999999999999988877643

>PRK07239 bifunctional uroporphyrinogen-III synthetase/response regulator domain protein; Validated

Probab=81.19  E-value=2.3  Score=43.78  Aligned_cols=87  Identities=14%  Similarity=0.056  Sum_probs=58.5

Q ss_pred             HHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhhhCccccccccccchhhcccccc---CCCCeEEEEeecccchhhh
Q 013329            9 VVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLVASDPSD---ANTNSTTLFSDDTDDKSRR   85 (445)
Q Consensus         9 ~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~rLTgl~nr~iL~~gLdl~Ld~asr---~n~~slaLL~lDLD~FKlI   85 (445)
                      ....+-+.|...++.+.++.+.|+..|...+.-.+-      ..+..+ ++.++....   .++..+.|...+++.+..+
T Consensus       246 Ta~al~~~G~~~~vp~~~t~~~Lv~~i~~~~~~~~~------~~~~~~-~~~l~~~~~~l~~~~~~i~Lt~~E~~lL~~L  318 (381)
T PRK07239        246 TAAPLVRAGVPTSAPERMRLGALARHITEELPLRRA------RTLRAA-GHVLEIRGHAVVVDGEVKPLSPAPMALLRAL  318 (381)
T ss_pred             HHHHHHHcCCCccCCCCCCHHHHHHHHHHHhhhhcC------ceEEEC-CEEEECCCCEEEECCEEEEcCHHHHHHHHHH
Confidence            334455677665667768888888888766544331      122222 222322221   1345788999999999999


Q ss_pred             hcCCCcccChHHHHhhc
Q 013329           86 STNPEIGMSTHQETESV  102 (445)
Q Consensus        86 Ndn~g~vvSreQl~d~~  102 (445)
                      ..|+++++|++++++.+
T Consensus       319 ~~~~~~vvsr~~L~~~v  335 (381)
T PRK07239        319 AARPGRVVSREDLLAAL  335 (381)
T ss_pred             HhCCCceEeHHHHHHHh
Confidence            99999999999999985

>COG5001 Predicted signal transduction protein containing a membrane domain, an EAL and a GGDEF domain [Signal transduction mechanisms]

Probab=81.11  E-value=0.74  Score=49.71  Aligned_cols=54  Identities=11%  Similarity=0.030  Sum_probs=40.5

Q ss_pred             hhCccccccccccchhhccccccCCCCeEEEEeecccchhhhhcCCCcccChHHH
Q 013329           44 MLGLAEKNILSYDFDLVASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQE   98 (445)
Q Consensus        44 LTgl~nr~iL~~gLdl~Ld~asr~n~~slaLL~lDLD~FKlINdn~g~vvSreQl   98 (445)
                      +|+++|+..+...++.++..+...+ ..+.+..+|+|.||.+|+..|+-...--+
T Consensus       233 LTgLpNRr~ffa~Ldarlaaar~~g-~rl~lgvIDLDgFKpvND~~GH~~GDrLL  286 (663)
T COG5001         233 LTGLPNRRRFFAELDARLAAARQSG-RRLVLGVIDLDGFKPVNDAFGHATGDRLL  286 (663)
T ss_pred             hcCCcchhHHHHHHHHHHhhhhhcC-CceEEEEEeccCCeeccccccccchhHHH
Confidence            4677887777777777777654433 47899999999999999999776544333

---

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	445
3hdg_A	137	Uncharacterized protein; two-component sensor acti	4e-06
3snk_A	135	Response regulator CHEY-like protein; P-loop conta	7e-06
1srr_A	124	SPO0F, sporulation response regulatory protein; as	7e-06
2qxy_A	142	Response regulator; regulation of transcription, N	1e-05
4dad_A	146	Putative pilus assembly-related protein; response	2e-05
2qvg_A	143	Two component response regulator; NYSGXRC, PSI-2,	3e-05
3cfy_A	137	Putative LUXO repressor protein; structural genomi	3e-05
3hdv_A	136	Response regulator; PSI-II, structural genomics, P	4e-05
3bre_A	358	Probable two-component response regulator; protein	5e-05
3luf_A	259	Two-component system response regulator/ggdef doma	9e-05
3eq2_A	394	Probable two-component response regulator; adaptor	1e-04
1w25_A	459	Stalked-cell differentiation controlling protein;	1e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-04
1k66_A	149	Phytochrome response regulator RCPB; CHEY homologu	2e-04
1ys7_A	233	Transcriptional regulatory protein PRRA; response	3e-04
1yio_A	208	Response regulatory protein; transcription regulat	3e-04
3eod_A	130	Protein HNR; response regulator, phosphoprotein, t	4e-04
3rqi_A	184	Response regulator protein; structural genomics, s	5e-04

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

 Score = 45.2 bits (108), Expect = 4e-06
 Identities = 10/33 (30%), Positives = 17/33 (51%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLN 33
           +SA  E+   +K + LG   +L KP+    L+ 
Sbjct: 85  ISAFSEMKYFIKAIELGVHLFLPKPIEPGRLME 117

>3snk_A Response regulator CHEY-like protein; P-loop containing nucleoside triphosphate hydrolases, struct genomics; 2.02A {Mesorhizobium loti} Length = 135

 Score = 44.6 bits (106), Expect = 7e-06
 Identities = 11/32 (34%), Positives = 17/32 (53%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELL 32
           +S +         +R+ A+D+L KPL   ELL
Sbjct: 93  VSDELTSEQTRVLVRMNASDWLHKPLDGKELL 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 = 44.0 bits (105), Expect = 7e-06
 Identities = 9/34 (26%), Positives = 18/34 (52%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNL 34
           M+A  E+ ++ +   LGA  +  KP   +E+ + 
Sbjct: 81  MTAYGELDMIQESKELGALTHFAKPFDIDEIRDA 114

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

 Score = 43.7 bits (104), Expect = 1e-05
 Identities = 11/32 (34%), Positives = 21/32 (65%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELL 32
           +SA  +  +++  ++ GA DY++KP R + LL
Sbjct: 81  LSAYVDKDLIINSVKAGAVDYILKPFRLDYLL 112

>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 = 43.6 bits (103), Expect = 2e-05
 Identities = 7/34 (20%), Positives = 13/34 (38%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNL 34
           ++       ++  +R G  D L  PL    L + 
Sbjct: 101 VTTDASSQTLLDAMRAGVRDVLRWPLEPRALDDA 134

>2qvg_A Two component response regulator; NYSGXRC, PSI-2, structural genomics, protein structure initiative; 1.50A {Legionella pneumophila subsp} Length = 143

 Score = 42.6 bits (101), Expect = 3e-05
 Identities = 9/46 (19%), Positives = 15/46 (32%), Gaps = 3/46 (6%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNL---WTHMWRRRR 43
           ++A       +    L    +L+KPL   E + L      M     
Sbjct: 95  LTAAYTSKDKLAFESLNIRGHLIKPLDYGEAIKLFWILQSMEGHHH 140

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

 Score = 42.5 bits (101), Expect = 3e-05
 Identities = 11/44 (25%), Positives = 21/44 (47%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRM 44
            +A   V + V  ++ GA D+L KP+  + L        +R ++
Sbjct: 82  ATAHGSVDLAVNLIQKGAEDFLEKPINADRLKTSVALHLKRAKL 125

>3hdv_A Response regulator; PSI-II, structural genomics, Pro structure initiative, NEW YORK SGX research center for STRU genomics, nysgxrc; 2.09A {Pseudomonas putida} Length = 136

 Score = 42.2 bits (100), Expect = 4e-05
 Identities = 12/44 (27%), Positives = 20/44 (45%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRM 44
           +S   +V   V  + LG  D+L+KP+   +LL L     +    
Sbjct: 87  VSGDTDVEEAVDVMHLGVVDFLLKPVDLGKLLELVNKELKIGEG 130

>3bre_A Probable two-component response regulator; protein-nucleotide complex, signaling protein; HET: C2E; 2.40A {Pseudomonas aeruginosa} PDB: 3i5a_A* Length = 358

 Score = 44.3 bits (105), Expect = 5e-05
 Identities = 14/52 (26%), Positives = 21/52 (40%), Gaps = 1/52 (1%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLN-LWTHMWRRRRMLGLAEKN 51
           +S ++E +V       GA DYLVK     EL+  +  H      +    E  
Sbjct: 99  LSTKEEPTVKSAAFAAGANDYLVKLPDAIELVARIRYHSRSYIALQQRDEAY 150

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

 Score = 43.0 bits (102), Expect = 9e-05
 Identities = 11/45 (24%), Positives = 19/45 (42%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRML 45
           +S  D+  +  + L+ GA D+L +P    EL    +H        
Sbjct: 205 ISVSDKRGLSARYLKQGANDFLNQPFEPEELQCRVSHNLEALEQF 249

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

 Score = 43.3 bits (102), Expect = 1e-04
 Identities = 18/45 (40%), Positives = 23/45 (51%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRML 45
           +S    +S  V+ LRLGAADYL+KPL    +L         R  L
Sbjct: 83  LSGAGVMSDAVEALRLGAADYLIKPLEDLAVLEHSVRRALDRAYL 127

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

 Score = 42.9 bits (101), Expect = 1e-04
 Identities = 14/85 (16%), Positives = 31/85 (36%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLV 60
           ++A D     ++ L  GA+D+L KP+    L      + R + ++    +   S     V
Sbjct: 81  ITALDGRGDRIQGLESGASDFLTKPIDDVMLFARVRSLTRFKLVIDELRQREASGRRMGV 140

Query: 61  ASDPSDANTNSTTLFSDDTDDKSRR 85
            +  +              D++ + 
Sbjct: 141 IAGAAARLDGLGGRVLIVDDNERQA 165

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

 Score = 43.3 bits (101), Expect = 2e-04
 Identities = 48/384 (12%), Positives = 104/384 (27%), Gaps = 94/384 (24%)

Query: 1   MSAQDEVSVVV-------K-CLRLGAA-DYLVKPLRTNELLNLWTHMWRRRRMLGLAEK- 50
           +  +   +V++       K  + L     Y V+     ++   W ++        + E  
Sbjct: 145 LELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIF--WLNLKNCNSPETVLEML 202

Query: 51  NILSYDFDLVASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESV----PVAT 106
             L Y  D   +  SD ++N   L       + RR       + +      +     V  
Sbjct: 203 QKLLYQIDPNWTSRSDHSSN-IKLRIHSIQAELRRL------LKSKPYENCLLVLLNVQN 255

Query: 107 ATVVAS---------TSGTAAVEPIDASECGPDVPGISDRRTGQFSAGPKKIELRIGESS 157
           A    +         T+    V   D          +S   T   S     + L   E  
Sbjct: 256 AKAWNAFNLSCKILLTTRFKQV--TDF---------LSAATTTHISLDHHSMTLTPDEVK 304

Query: 158 AFF-TYVKSNMPRDSSPRIVNVDDSAAQNVRMEEKCQ--PCCQQVVS--DTRIHENGEAW 212
           +    Y+  +      PR               E     P   + +S     I +    W
Sbjct: 305 SLLLKYL--DCRPQDLPR---------------EVLTTNP---RRLSIIAESIRDGLATW 344

Query: 213 ENYSQGEDFRSSSSVPDSLSMERSSTPPTDFPQNRNFKDEKFFQPQMP-PTR------NE 265
           +N+      + ++ +  SL    +   P ++   + F     F P    PT        +
Sbjct: 345 DNWKHVNCDKLTTIIESSL----NVLEPAEY--RKMFDRLSVFPPSAHIPTILLSLIWFD 398

Query: 266 PPQATYQYYMSGAMNQVMLPSSSAQMYQKNLHELQNHSMLPQYNHLPQCVPH---VNGMA 322
             ++     ++      ++     +    ++  +    +  +  +      H   V+   
Sbjct: 399 VIKSDVMVVVNKLHKYSLV-EKQPKESTISIPSIY-LELKVKLENEYAL--HRSIVD--- 451

Query: 323 SFPYYPINMCLQPGQVSANSWPSY 346
              +Y I        +       Y
Sbjct: 452 ---HYNIPKTFDSDDLIPPYLDQY 472

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

 Score = 41.0 bits (95), Expect = 8e-04
 Identities = 28/165 (16%), Positives = 54/165 (32%), Gaps = 41/165 (24%)

Query: 268 QATYQYYMSGAMNQVMLPSSSAQMYQKNLHELQN-HSMLPQYN------------HLPQC 314
           +  Y++ MS    +   PS   +MY +    L N + +  +YN             L + 
Sbjct: 88  RINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLEL 147

Query: 315 VPH----VNGMASF----------PYYPINMCLQPGQVSANSWPSYGN--SPSTEVKM-- 356
            P     ++G+               Y +  C    ++    W +  N  SP T ++M  
Sbjct: 148 RPAKNVLIDGVLGSGKTWVALDVCLSYKV-QCKMDFKI---FWLNLKNCNSPETVLEMLQ 203

Query: 357 ---NKVDRREAALIKFRQKRKERCFDKKIRYVNRKRLAERRPRVR 398
               ++D    +        K R    +      +RL + +P   
Sbjct: 204 KLLYQIDPNWTSRSDHSSNIKLRIHSIQAE---LRRLLKSKPYEN 245

>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 Length = 149

 Score = 40.3 bits (95), Expect = 2e-04
 Identities = 9/42 (21%), Positives = 15/42 (35%), Gaps = 3/42 (7%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNL---WTHMW 39
           M+       +  C     + Y+VKPL  + L      +   W
Sbjct: 98  MTTSSNPKDIEICYSYSISSYIVKPLEIDRLTETVQTFIKYW 139

>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 Length = 233

 Score = 41.3 bits (98), Expect = 3e-04
 Identities = 19/60 (31%), Positives = 26/60 (43%), Gaps = 1/60 (1%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLV 60
           +SA+  V   V  L  GA DYLVKP    EL+     + RRR     +    ++    L 
Sbjct: 85  LSARSSVDDRVAGLEAGADDYLVKPFVLAELVARVKALLRRRGSTATSSSETITVG-PLE 143

>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 Length = 208

 Score = 40.7 bits (96), Expect = 3e-04
 Identities = 9/32 (28%), Positives = 19/32 (59%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELL 32
           ++A  ++ + V+ ++ GA ++L KP     LL
Sbjct: 82  ITAHGDIPMTVRAMKAGAIEFLPKPFEEQALL 113

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

 Score = 39.1 bits (92), Expect = 4e-04
 Identities = 13/32 (40%), Positives = 20/32 (62%), Gaps = 1/32 (3%)

Query: 2   SAQDEVSVVVKCLRLGAADYLVKPLRT-NELL 32
           SA + ++ + K LRLG  D L+KP++  N L 
Sbjct: 86  SATENMADIAKALRLGVEDVLLKPVKDLNRLR 117

>3rqi_A Response regulator protein; structural genomics, seattle structural genomics center for infectious disease, ssgcid; HET: PHD CIT; 1.70A {Burkholderia pseudomallei} Length = 184

 Score = 40.0 bits (94), Expect = 5e-04
 Identities = 12/57 (21%), Positives = 23/57 (40%), Gaps = 1/57 (1%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEK-NILSYD 56
           ++    ++  V+ ++ GA +YL KP     +L          +     E   +LS D
Sbjct: 85  LTGYASIATAVQAVKDGADNYLAKPANVESILAALQTNASEVQAEEALENPVVLSVD 141

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	445
1w25_A	459	Stalked-cell differentiation controlling protein;	98.8
3bre_A	358	Probable two-component response regulator; protein	98.54
3r0j_A	250	Possible two component system response transcript	98.26
3q9s_A	249	DNA-binding response regulator; DNA binding protei	97.77
1p2f_A	220	Response regulator; DRRB, OMPR/PHOB, transcription	97.61
1kgs_A	225	DRRD, DNA binding response regulator D; DNA-bindin	97.57
2hqr_A	223	Putative transcriptional regulator; phosporylation	97.53
1ys7_A	233	Transcriptional regulatory protein PRRA; response	97.48
2gwr_A	238	DNA-binding response regulator MTRA; two-component	97.41
2oqr_A	230	Sensory transduction protein REGX3; response regul	97.36
3f6p_A	120	Transcriptional regulatory protein YYCF; unphospho	97.24
3gl9_A	122	Response regulator; beta-sheet, surrounded by alph	97.21
3tvk_A	179	DGC, diguanylate cyclase YDEH; putative zinc senso	97.18
3t6k_A	136	Response regulator receiver; flavodoxin-like, stru	97.17
3h1g_A	129	Chemotaxis protein CHEY homolog; sulfate-bound CHE	97.12
2pl1_A	121	Transcriptional regulatory protein PHOP; CHEY-like	97.1
1zgz_A	122	Torcad operon transcriptional regulatory protein;	97.06
1jbe_A	128	Chemotaxis protein CHEY; signaling protein; 1.08A	97.04
3crn_A	132	Response regulator receiver domain protein, CHEY-;	96.99
1xhf_A	123	DYE resistance, aerobic respiration control protei	96.99
2a9o_A	120	Response regulator; essential protein, YYCF/YYCG h	96.94
1zh2_A	121	KDP operon transcriptional regulatory protein KDPE	96.94
3kto_A	136	Response regulator receiver protein; PSI-II,struct	96.92
3cfy_A	137	Putative LUXO repressor protein; structural genomi	96.89
3kht_A	144	Response regulator; PSI-II, 11023K, structural gen	96.89
3jte_A	143	Response regulator receiver protein; structural ge	96.88
1dbw_A	126	Transcriptional regulatory protein FIXJ; doubly wo	96.88
2qzj_A	136	Two-component response regulator; 11017X, PSI-II,	96.87
1p6q_A	129	CHEY2; chemotaxis, signal transduction, response r	96.83
3hdg_A	137	Uncharacterized protein; two-component sensor acti	96.81
1dcf_A	136	ETR1 protein; beta-alpha five sandwich, transferas	96.8
1k68_A	140	Phytochrome response regulator RCPA; phosphorylate	96.8
1i3c_A	149	Response regulator RCP1; phytochrome, signaling pr	96.79
2r25_B	133	Osmosensing histidine protein kinase SLN1; alpha5-	96.76
1tmy_A	120	CHEY protein, TMY; chemotaxis, phosphoryl transfer	96.75
3lua_A	140	Response regulator receiver protein; two-component	96.74
3b2n_A	133	Uncharacterized protein Q99UF4; structural genomic	96.71
1k66_A	149	Phytochrome response regulator RCPB; CHEY homologu	96.7
3cnb_A	143	DNA-binding response regulator, MERR family; signa	96.67
3gt7_A	154	Sensor protein; structural genomics, signal receiv	96.67
1dz3_A	130	Stage 0 sporulation protein A; response regulator,	96.66
2zay_A	147	Response regulator receiver protein; structural ge	96.65
3hv2_A	153	Response regulator/HD domain protein; PSI-2, NYSGX	96.65
3rqi_A	184	Response regulator protein; structural genomics, s	96.57
3cg0_A	140	Response regulator receiver modulated diguanylate	96.56
3m6m_D	143	Sensory/regulatory protein RPFC; RPFF, REC, enoyl-	96.53
3hdv_A	136	Response regulator; PSI-II, structural genomics, P	96.53
4e7p_A	150	Response regulator; DNA binding, cytosol, transcri	96.51
2jba_A	127	Phosphate regulon transcriptional regulatory PROT;	96.5
3heb_A	152	Response regulator receiver domain protein (CHEY);	96.47
1qkk_A	155	DCTD, C4-dicarboxylate transport transcriptional r	96.46
3eul_A	152	Possible nitrate/nitrite response transcriptional	96.45
1srr_A	124	SPO0F, sporulation response regulatory protein; as	96.43
1mb3_A	124	Cell division response regulator DIVK; signal tran	96.42
2qxy_A	142	Response regulator; regulation of transcription, N	96.42
1qo0_D	196	AMIR; binding protein, gene regulator, receptor; 2	96.41
3nhm_A	133	Response regulator; protein structure initiative I	96.4
3eod_A	130	Protein HNR; response regulator, phosphoprotein, t	96.39
3n53_A	140	Response regulator receiver modulated diguanylate;	96.37
3kcn_A	151	Adenylate cyclase homolog; SGX, PSI 2, structural	96.36
1a04_A	215	Nitrate/nitrite response regulator protein NARL; s	96.34
1mvo_A	136	PHOP response regulator; phosphate regulon, transc	96.3
2qr3_A	140	Two-component system response regulator; structura	96.26
3grc_A	140	Sensor protein, kinase; protein structure initiati	96.25
3cu5_A	141	Two component transcriptional regulator, ARAC FAM;	96.24
3h5i_A	140	Response regulator/sensory box protein/ggdef domai	96.22
3f6c_A	134	Positive transcription regulator EVGA; structural	96.21
1s8n_A	205	Putative antiterminator; RV1626, structural genomi	96.1
2rjn_A	154	Response regulator receiver:metal-dependent phosph	96.1
3lte_A	132	Response regulator; structural genomics, PSI, prot	96.03
2jk1_A	139	HUPR, hydrogenase transcriptional regulatory prote	96.03
3cz5_A	153	Two-component response regulator, LUXR family; str	96.02
3i5c_A	206	Fusion of general control protein GCN4 and WSPR R	95.97
1dc7_A	124	NTRC, nitrogen regulation protein; receiver domain	95.94
1yio_A	208	Response regulatory protein; transcription regulat	95.92
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	95.9
1w25_A	459	Stalked-cell differentiation controlling protein;	95.87
3qyy_A	167	Response regulator; C-DI-GMP, DGC, ggdef, competit	95.86
3cg4_A	142	Response regulator receiver domain protein (CHEY-;	95.75
3icl_A	171	EAL/ggdef domain protein; structural genomics, PSI	95.74
3klo_A	225	Transcriptional regulator VPST; REC domain, HTH do	95.72
2qsj_A	154	DNA-binding response regulator, LUXR family; struc	95.67
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	95.66
3mtk_A	178	Diguanylate cyclase/phosphodiesterase; structural	95.65
2gkg_A	127	Response regulator homolog; social motility, recei	95.47
3ign_A	177	Diguanylate cyclase; ggdef domain, A1U3W3_marav, N	95.47
3i42_A	127	Response regulator receiver domain protein (CHEY-	95.43
2qvg_A	143	Two component response regulator; NYSGXRC, PSI-2,	95.4
3hva_A	177	Protein FIMX; ggdef diguanylate cyclase, biofilm,	95.37
2qv0_A	143	Protein MRKE; structural genomics, transcription,	95.37
3ezu_A	342	Ggdef domain protein; multidomain protein of unkno	95.28
3eqz_A	135	Response regulator; structural genomics, unknown f	95.27
3eq2_A	394	Probable two-component response regulator; adaptor	95.0
3c3m_A	138	Response regulator receiver protein; structural ge	94.68
3c3w_A	225	Two component transcriptional regulatory protein;	94.65
3hvb_A	437	Protein FIMX; EAL phosphodiesterase, biofilm, C-DI	94.36
3kyj_B	145	CHEY6 protein, putative histidine protein kinase;	94.32
2vyc_A	755	Biodegradative arginine decarboxylase; pyridoxal p	94.02
3pjx_A	430	Cyclic dimeric GMP binding protein; ggdef-EAL tand	93.95
3hvw_A	176	Diguanylate-cyclase (DGC); alpha-beta protein., st	93.24
3a10_A	116	Response regulator; phosphoacceptor, signaling pro	92.91
3sy8_A	400	ROCR; TIM barrel phosphodiesterase-A, transcriptio	92.16
3ogl_Q	21	JAZ1 incomplete degron peptide; leucine-rich repea	92.01
2rdm_A	132	Response regulator receiver protein; structural ge	91.68
3c97_A	140	Signal transduction histidine kinase; structural g	91.05
2lpm_A	123	Two-component response regulator; transcription re	90.41
2j48_A	119	Two-component sensor kinase; pseudo-receiver, circ	90.2
3ogk_Q	22	JAZ1 incomplete degron peptide; leucine rich repea	90.06
3t8y_A	164	CHEB, chemotaxis response regulator protein-glutam	88.77
3luf_A	259	Two-component system response regulator/ggdef doma	88.74
1a2o_A	349	CHEB methylesterase; bacterial chemotaxis, adaptat	88.19
3cwo_X	237	Beta/alpha-barrel protein based on 1THF and 1TMY;	85.86
2pln_A	137	HP1043, response regulator; signaling protein; 1.8	85.06
3q7r_A	121	Transcriptional regulatory protein; CHXR, receiver	81.68

>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=98.80  E-value=4.5e-09  Score=105.03  Aligned_cols=108  Identities=20%  Similarity=0.251  Sum_probs=85.3

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh--------------------hhCccccccccccchhhc
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR--------------------MLGLAEKNILSYDFDLVA   61 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r--------------------LTgl~nr~iL~~gLdl~L   61 (445)
                      |+.........++++|++||+.||+...+|..++..++++.+                    +|++.|+..|...++..+
T Consensus       231 t~~~~~~~~~~~l~~Ga~d~~~kp~~~~~l~~~v~~~~~~~~~~~~l~~~~~~~~~~~~~D~lTgl~nr~~~~~~l~~~~  310 (459)
T 1w25_A          231 VDPDDRGRMVKALEIGVNDILSRPIDPQELSARVKTQIQRKRYTDYLRNNLDHSLELAVTDQLTGLHNRRYMTGQLDSLV  310 (459)
T ss_dssp             ECTTCHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHHHHHHHHHHHHSSSSCCSTTCCBCTTTCCBCHHHHHHHHHHHH
T ss_pred             cCCCchHHHHHHHhccccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhcCccccCcCHHHHHHHHHHHH
Confidence            455666677889999999999999999999999988876532                    355666666655555555


Q ss_pred             cccccCCCCeEEEEeecccchhhhhcCCCcccChHHHHhhcchhhhhhhhcccC
Q 013329           62 SDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTSG  115 (445)
Q Consensus        62 d~asr~n~~slaLL~lDLD~FKlINdn~g~vvSreQl~d~~l~~~A~~~a~~~~  115 (445)
                      ....+.+ ..++|+++|+|+||.||++.     +|+.+|.+|+.+|..|...+.
T Consensus       311 ~~~~~~~-~~~~l~~idid~fk~iNd~~-----Gh~~gD~~L~~~a~~l~~~~~  358 (459)
T 1w25_A          311 KRATLGG-DPVSALLIDIDFFKKINDTF-----GHDIGDEVLREFALRLASNVR  358 (459)
T ss_dssp             HHHHTSS-CCCEEEEEEETTHHHHHHHS-----CHHHHHHHHHHHHHHHHHTSC
T ss_pred             HHHhhcC-CcEEEEEEEchhhchhhhcc-----ChhhHHHHHHHHHHHHHHhCC
Confidence            5443333 36889999999999999999     788999999999999988764

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

Probab=98.54  E-value=4.2e-08  Score=94.22  Aligned_cols=108  Identities=19%  Similarity=0.172  Sum_probs=76.0

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH----------------------------------hhhC
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR----------------------------------RMLG   46 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~----------------------------------rLTg   46 (445)
                      +|+..+......++++||++||.||++..+|+.+|+.+++..                                  .+|+
T Consensus        99 ~s~~~~~~~~~~a~~~Ga~~~l~Kp~~~~~l~~~v~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~l~~~~~~D~lTg  178 (358)
T 3bre_A           99 LSTKEEPTVKSAAFAAGANDYLVKLPDAIELVARIRYHSRSYIALQQRDEAYRALRESQQQLLETNLVLQRLMNSDGLTG  178 (358)
T ss_dssp             EESSCCHHHHHHHHHTTCSEEEESCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHBCTTTC
T ss_pred             EeCCCCHHHHHHHHhcChheEeeccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCC
Confidence            467778888899999999999999999999999998764210                                  1123


Q ss_pred             ccccccccccchhhccccccCCCCeEEEEeecccchhhhhcCCCcccChHHHHhhcchhhhhhhhccc
Q 013329           47 LAEKNILSYDFDLVASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTS  114 (445)
Q Consensus        47 l~nr~iL~~gLdl~Ld~asr~n~~slaLL~lDLD~FKlINdn~g~vvSreQl~d~~l~~~A~~~a~~~  114 (445)
                      +.++..|...+...+....+. ...++|+++|+|+|+.+|+..     ++..+|.+|+.+|..|...+
T Consensus       179 l~nr~~~~~~l~~~~~~~~~~-~~~~~l~~idid~fk~ind~~-----G~~~gD~~L~~va~~l~~~~  240 (358)
T 3bre_A          179 LSNRRHFDEYLEMEWRRSLRE-QSQLSLLMIDVDYFKSYNDTF-----GHVAGDEALRQVAGAIREGC  240 (358)
T ss_dssp             SBCHHHHHHHHHHHHHHHHHH-TCCEEEEEEEETTHHHHHHHH-----CHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCHHHHHHHHHHHHHHHHhc-CCcEEEEEEEchhhhHHHHhc-----ChHHHHHHHHHHHHHHHHhc
Confidence            333332222222222221111 236789999999999999987     67889999999998887654

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

Probab=98.26  E-value=8.1e-07  Score=81.64  Aligned_cols=101  Identities=18%  Similarity=0.230  Sum_probs=72.6

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhhhCc-cccccccccchhhcccccc---CCCCeEEEEe
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGL-AEKNILSYDFDLVASDPSD---ANTNSTTLFS   76 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~rLTgl-~nr~iL~~gLdl~Ld~asr---~n~~slaLL~   76 (445)
                      +|+..+.....+++++||++||.||++.++|+.+|+.++++...... .....+..+ +..++....   ..+..+.|+.
T Consensus       101 lt~~~~~~~~~~~~~~Ga~~yl~Kp~~~~~L~~~i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~LT~  179 (250)
T 3r0j_A          101 LTARDSLQDKIAGLTLGGDDYVTKPFSLEEVVARLRVILRRAGKGNKEPRNVRLTFA-DIELDEETHEVWKAGQPVSLSP  179 (250)
T ss_dssp             EECSTTHHHHHHHHTSTTCEEEESSCCHHHHHHHHHHHHHHHCC------CCEEEET-TEEEETTTCCEEETTEEECCCH
T ss_pred             EECCCCHHHHHHHHHcCCcEEEeCCCCHHHHHHHHHHHHHhhccccccccceEEEEC-CEEEeccccEEEECCEEEecCH
Confidence            46777888899999999999999999999999999999987532111 011111111 222222111   1234567899


Q ss_pred             ecccchhhhhcCCCcccChHHHHhhc
Q 013329           77 DDTDDKSRRSTNPEIGMSTHQETESV  102 (445)
Q Consensus        77 lDLD~FKlINdn~g~vvSreQl~d~~  102 (445)
                      .+++.+.++..++++++|++++.+..
T Consensus       180 rE~~iL~~l~~~~~~~~s~~~i~~~l  205 (250)
T 3r0j_A          180 TEFTLLRYFVINAGTVLSKPKILDHV  205 (250)
T ss_dssp             HHHHHHHHHHHTTTCCBCHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCceEcHHHHHHHH
Confidence            99999999999999999999999875

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

Probab=97.77  E-value=1.3e-05  Score=74.25  Aligned_cols=94  Identities=28%  Similarity=0.318  Sum_probs=69.1

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhhhCccccccccccchhhccccc---cCCCCeEEEEee
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLVASDPS---DANTNSTTLFSD   77 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~rLTgl~nr~iL~~gLdl~Ld~as---r~n~~slaLL~l   77 (445)
                      +|+..+.+...+++++||++||.||++.++|+.+|+.++++......      ... +..++...   ........|+..
T Consensus       114 lt~~~~~~~~~~a~~~Ga~~yl~Kp~~~~~L~~~i~~~l~~~~~~~~------~~~-~~~~~~~~~~~~~~~~~~~LT~r  186 (249)
T 3q9s_A          114 LTARDTVEEKVRLLGLGADDYLIKPFHPDELLARVKVQLRQRTSESL------SMG-DLTLDPQKRLVTYKGEELRLSPK  186 (249)
T ss_dssp             EESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHHCCCCSCCE------EET-TEEEETTTTEEEETTEEECCCHH
T ss_pred             EECCCCHHHHHHHHHCCCcEEEECCCCHHHHHHHHHHHHhhcccCce------eEC-CEEEecccCEEEECCEEeecCHH
Confidence            46777888899999999999999999999999999998865431110      000 11111111   112234568889


Q ss_pred             cccchhhhhcCCCcccChHHHHhh
Q 013329           78 DTDDKSRRSTNPEIGMSTHQETES  101 (445)
Q Consensus        78 DLD~FKlINdn~g~vvSreQl~d~  101 (445)
                      +++.+.++..++++++|+.++.+.
T Consensus       187 E~evL~ll~~g~~~~~s~~eIa~~  210 (249)
T 3q9s_A          187 EFDILALLIRQPGRVYSRQEIGQE  210 (249)
T ss_dssp             HHHHHHHHHHSTTCCCCHHHHHHH
T ss_pred             HHHHHHHHHHCCCceEcHHHHHHH
Confidence            999999999999999999999985

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

Probab=97.61  E-value=3.9e-05  Score=68.35  Aligned_cols=95  Identities=17%  Similarity=0.211  Sum_probs=68.4

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhhhCccccccccccchhhcccccc---CCCCeEEEEee
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLVASDPSD---ANTNSTTLFSD   77 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~rLTgl~nr~iL~~gLdl~Ld~asr---~n~~slaLL~l   77 (445)
                      +|+..+.+...+++++||++||.||++.++|..+|+.++++..  .    ..+..+ .+.++....   ..+....|+..
T Consensus        77 lt~~~~~~~~~~~~~~ga~~~l~Kp~~~~~L~~~i~~~~~~~~--~----~~~~~~-~~~~~~~~~~~~~~~~~~~Lt~r  149 (220)
T 1p2f_A           77 LTLLSDDESVLKGFEAGADDYVTKPFNPEILLARVKRFLEREK--K----GLYDFG-DLKIDATGFTVFLKGKRIHLPKK  149 (220)
T ss_dssp             EESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHHHHCC--C----SEEEET-TEEEETTTTEEEETTEECCCCHH
T ss_pred             EEcCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHHcccc--c----cCcccc-cEEEECCCCEEEECCEEEecCHH
Confidence            3566778888999999999999999999999999999987643  0    111101 111111110   11223457888


Q ss_pred             cccchhhhhcCCCcccChHHHHhhc
Q 013329           78 DTDDKSRRSTNPEIGMSTHQETESV  102 (445)
Q Consensus        78 DLD~FKlINdn~g~vvSreQl~d~~  102 (445)
                      +++.+.++..++++++|+.++.+..
T Consensus       150 E~~vl~~l~~~~~~~~s~~~Ia~~l  174 (220)
T 1p2f_A          150 EFEILLFLAENAGKVVTREKLLETF  174 (220)
T ss_dssp             HHHHHHHHHHTTTSCEEHHHHHHHH
T ss_pred             HHHHHHHHHHCCCceEcHHHHHHHH
Confidence            8999999999999999999998875

>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=97.57  E-value=3.6e-05  Score=68.50  Aligned_cols=98  Identities=22%  Similarity=0.282  Sum_probs=69.5

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhhhCccccccccccchhhcccccc---CCCCeEEEEee
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLVASDPSD---ANTNSTTLFSD   77 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~rLTgl~nr~iL~~gLdl~Ld~asr---~n~~slaLL~l   77 (445)
                      +|+..+......++++||++||.||++.++|..+|+.++++.....   ...+..+ ++.++....   .......|+..
T Consensus        80 ls~~~~~~~~~~~~~~ga~~~l~Kp~~~~~l~~~i~~~~~~~~~~~---~~~~~~~-~~~~~~~~~~~~~~~~~~~Lt~r  155 (225)
T 1kgs_A           80 LTALSDVEYRVKGLNMGADDYLPKPFDLRELIARVRALIRRKSESK---STKLVCG-DLILDTATKKAYRGSKEIDLTKK  155 (225)
T ss_dssp             EESSCHHHHHHHTCCCCCSEEEESSCCHHHHHHHHHHHHHHHCCSC---SSEEEET-TEEEETTTTEEEETTEEECCCHH
T ss_pred             EeCCCCHHHHHHHHhCCccEEEeCCCCHHHHHHHHHHHHhhccccc---CceEEEC-CEEEecccCEEEECCEEEecCHH
Confidence            3566777788899999999999999999999999999988754211   1111111 111111111   12224567888


Q ss_pred             cccchhhhhcCCCcccChHHHHhhc
Q 013329           78 DTDDKSRRSTNPEIGMSTHQETESV  102 (445)
Q Consensus        78 DLD~FKlINdn~g~vvSreQl~d~~  102 (445)
                      +.+.+..+..+++.++|+.++.+..
T Consensus       156 E~~vL~~l~~~~~~~~s~~eIa~~l  180 (225)
T 1kgs_A          156 EYQILEYLVMNKNRVVTKEELQEHL  180 (225)
T ss_dssp             HHHHHHHHHHTTTSCEEHHHHHHHC
T ss_pred             HHHHHHHHHhCCCcccCHHHHHHHh
Confidence            8999999999999999999999875

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

Probab=97.53  E-value=4.1e-05  Score=68.38  Aligned_cols=95  Identities=17%  Similarity=0.189  Sum_probs=68.9

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCC-CHHHHHHHHHHHHHHHhhhCccccccccccchhhcccccc---CCCCeEEEEe
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPL-RTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLVASDPSD---ANTNSTTLFS   76 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPf-d~eELLaRVra~LrR~rLTgl~nr~iL~~gLdl~Ld~asr---~n~~slaLL~   76 (445)
                      +|+..+.+....++++||++||.||+ +.++|..+|+.++++..      ...+..+ ...++....   .++....|+.
T Consensus        74 lt~~~~~~~~~~~~~~Ga~~~l~Kp~~~~~~L~~~i~~~~~~~~------~~~~~~~-~~~~~~~~~~~~~~~~~~~Lt~  146 (223)
T 2hqr_A           74 SSDNPTSEEEVHAFEQGADDYIAKPYRSIKALVARIEARLRFWG------SNVIEIG-DLTISPDEEKIIYKGREVEVKG  146 (223)
T ss_dssp             EESSCCHHHHHHHHHHTCSEEEETTCSCTHHHHHHHHHHTSSCC------CCSEEET-TEEEETTTTEEEETTEEECCCS
T ss_pred             EECCCCHHHHHHHHHcCCCEEEECCCCCHHHHHHHHHHHhcccc------CCeEEEC-CEEEecccCEEEECCEEEecCH
Confidence            46777888889999999999999999 99999999999876530      0111111 111111111   1223456888


Q ss_pred             ecccchhhhhcCCCcccChHHHHhhc
Q 013329           77 DDTDDKSRRSTNPEIGMSTHQETESV  102 (445)
Q Consensus        77 lDLD~FKlINdn~g~vvSreQl~d~~  102 (445)
                      .+++.+.++..+++.++|+.++.+..
T Consensus       147 rE~~vL~~l~~~~~~~~s~~~Ia~~l  172 (223)
T 2hqr_A          147 KPFEVLTHLARHRDQIVSKEQLLDAI  172 (223)
T ss_dssp             TTTHHHHHHHHTCSEEEEHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCcCCHHHHHHHh
Confidence            89999999999999999999999985

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

Probab=97.48  E-value=2.1e-05  Score=70.33  Aligned_cols=100  Identities=27%  Similarity=0.260  Sum_probs=67.4

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhhhCccccccccccchhhcccccc---CCCCeEEEEeec
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLVASDPSD---ANTNSTTLFSDD   78 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~rLTgl~nr~iL~~gLdl~Ld~asr---~n~~slaLL~lD   78 (445)
                      |+..+......++++||++||.||++.++|..+|+.++++...........+..+ .+.++...+   .+.....|+..+
T Consensus        86 t~~~~~~~~~~~~~~ga~~~l~Kp~~~~~L~~~i~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~Lt~rE  164 (233)
T 1ys7_A           86 SARSSVDDRVAGLEAGADDYLVKPFVLAELVARVKALLRRRGSTATSSSETITVG-PLEVDIPGRRARVNGVDVDLTKRE  164 (233)
T ss_dssp             ECCCTTTCCCTTTTTTCSEEEESSCCHHHHHHHHHHHHHHHHCCCCCCCCEEEET-TEEEETTTTEEEETTEECCCCHHH
T ss_pred             EcCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHhhccccccccCcccccC-CeEEccCccEEEECCEEeccCHHH
Confidence            4455555667789999999999999999999999999987542111101111111 111111111   112234588889


Q ss_pred             ccchhhhhcCCCcccChHHHHhhc
Q 013329           79 TDDKSRRSTNPEIGMSTHQETESV  102 (445)
Q Consensus        79 LD~FKlINdn~g~vvSreQl~d~~  102 (445)
                      .+.+.++..+++.++|+.++.+..
T Consensus       165 ~~vL~~l~~g~~~~~s~~~Ia~~l  188 (233)
T 1ys7_A          165 FDLLAVLAEHKTAVLSRAQLLELV  188 (233)
T ss_dssp             HHHHHHHHHTTTCCBCHHHHHHHH
T ss_pred             HHHHHHHHhCCCCeEcHHHHHHHh
Confidence            999999999999999999998874

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

Probab=97.41  E-value=3e-05  Score=70.44  Aligned_cols=97  Identities=25%  Similarity=0.280  Sum_probs=67.2

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhhhCccccccccccchhhcccccc---CCCCeEEEEeec
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLVASDPSD---ANTNSTTLFSDD   78 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~rLTgl~nr~iL~~gLdl~Ld~asr---~n~~slaLL~lD   78 (445)
                      |+..+......++++||++||.||++.++|+.+|+.++++...  . ....+..+ ++.++...+   .......|+..+
T Consensus        83 t~~~~~~~~~~~~~~Ga~~~l~Kp~~~~~L~~~i~~~~~~~~~--~-~~~~~~~~-~~~~~~~~~~~~~~~~~~~LT~rE  158 (238)
T 2gwr_A           83 TAKTDTVDVVLGLESGADDYIMKPFKPKELVARVRARLRRNDD--E-PAEMLSIA-DVEIDVPAHKVTRNGEQISLTPLE  158 (238)
T ss_dssp             EETTCCSCHHHHHHTTCCEEEEESCCHHHHHHHHHHHCCCCSS--C-CCCEEEET-TEEEETTTTEEEETTEEECCCHHH
T ss_pred             eCCCCHHHHHHHHHCCCCEEEeCCCCHHHHHHHHHHHHhhccc--C-cccceecC-ceEEcccccEEEECCEEcccCHHH
Confidence            4455556678899999999999999999999999988765421  1 11111111 111111111   122245688889


Q ss_pred             ccchhhhhcCCCcccChHHHHhhc
Q 013329           79 TDDKSRRSTNPEIGMSTHQETESV  102 (445)
Q Consensus        79 LD~FKlINdn~g~vvSreQl~d~~  102 (445)
                      ++.+.++..++++++|+.++.+..
T Consensus       159 ~~vL~~l~~~~~~~~s~~eIa~~l  182 (238)
T 2gwr_A          159 FDLLVALARKPRQVFTRDVLLEQV  182 (238)
T ss_dssp             HHHHHHHHHSTTCCBCHHHHHHHH
T ss_pred             HHHHHHHHHCCCceecHHHHHHHH
Confidence            999999999999999999999875

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

Probab=97.36  E-value=4.4e-05  Score=68.35  Aligned_cols=100  Identities=23%  Similarity=0.194  Sum_probs=67.9

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhhhCcc-ccccccccchhhcccccc---CCCCeEEEEee
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLA-EKNILSYDFDLVASDPSD---ANTNSTTLFSD   77 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~rLTgl~-nr~iL~~gLdl~Ld~asr---~n~~slaLL~l   77 (445)
                      |+..+......++++||++||.||++.++|..+|+.++++....... ....+..+ .+.++....   .++....|+..
T Consensus        82 t~~~~~~~~~~~~~~ga~~~l~Kp~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~Lt~r  160 (230)
T 2oqr_A           82 TARDSEIDKVVGLELGADDYVTKPYSARELIARIRAVLRRGGDDDSEMSDGVLESG-PVRMDVERHVVSVNGDTITLPLK  160 (230)
T ss_dssp             ECCHHHHHHHHHHHHCCSCCCCSSCCHHHHHHHHHHHHTTTTCTTSTTCCSCEEET-TEEEETTTTEEEESSBCCCCCHH
T ss_pred             eCCCcHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHhhcccccccccccceeec-CEEEeccccEEEECCeeeecCHH
Confidence            55666777888999999999999999999999999998764210100 01111111 111111110   11223468888


Q ss_pred             cccchhhhhcCCCcccChHHHHhhc
Q 013329           78 DTDDKSRRSTNPEIGMSTHQETESV  102 (445)
Q Consensus        78 DLD~FKlINdn~g~vvSreQl~d~~  102 (445)
                      +++.+.++..++++++|+.++.+..
T Consensus       161 E~~vL~~l~~~~~~~~s~~~Ia~~l  185 (230)
T 2oqr_A          161 EFDLLEYLMRNSGRVLTRGQLIDRV  185 (230)
T ss_dssp             HHHHHHHHHHTTTSCEEHHHHHHHH
T ss_pred             HHHHHHHHHhCCCceEcHHHHHHHh
Confidence            9999999999999999999998864

>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=97.24  E-value=0.00018  Score=58.04  Aligned_cols=41  Identities=39%  Similarity=0.505  Sum_probs=35.6

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      +|+..+.....+++++||++||.||++.++|+.+|+.++++
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            35667777888999999999999999999999999988753

>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=97.21  E-value=0.0003  Score=57.02  Aligned_cols=40  Identities=20%  Similarity=0.326  Sum_probs=35.5

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWR   40 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~Lr   40 (445)
                      +|+..+.....+++++||++||.||++.++|..+|+++++
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            3667778888999999999999999999999999998763

>3tvk_A DGC, diguanylate cyclase YDEH; putative zinc sensor, C-DI-GMP, transfe; HET: C2E; 1.80A {Escherichia coli}

Probab=97.18  E-value=9.7e-05  Score=67.17  Aligned_cols=66  Identities=21%  Similarity=0.144  Sum_probs=52.8

Q ss_pred             hhhCccccccccccchhhccccccCCCCeEEEEeecccchhhhhcCCCcccChHHHHhhcchhhhhhhhcccCC
Q 013329           43 RMLGLAEKNILSYDFDLVASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTSGT  116 (445)
Q Consensus        43 rLTgl~nr~iL~~gLdl~Ld~asr~n~~slaLL~lDLD~FKlINdn~g~vvSreQl~d~~l~~~A~~~a~~~~~  116 (445)
                      .||+++|+..|...++..+....   ...++|+++|+|+||.||+..     +++.+|.+|+.+|..|...+..
T Consensus         8 ~LTgL~NR~~f~~~l~~~l~~~~---~~~~~l~~iDiD~FK~INd~~-----Gh~~GD~vL~~va~~L~~~~~~   73 (179)
T 3tvk_A            8 VLTGLPGRRVLDESFDHQLRNAE---PLNLYLMLLDIDRFKLVNDTY-----GHLIGDVVLRTLATYLASWTRD   73 (179)
T ss_dssp             TTTCSCBHHHHHHHHHHHHHTCT---TSEEEEEEEEETTHHHHHHHH-----CHHHHHHHHHHHHHHHHHTSCT
T ss_pred             cccCchhHHHHHHHHHHHHHhcC---CCCEEEEEEECCCCcHHHhcc-----CchhHHHHHHHHHHHhHhcCCc
Confidence            36888888877666555554422   236899999999999999999     6889999999999999987754

>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=97.17  E-value=0.00035  Score=57.66  Aligned_cols=43  Identities=30%  Similarity=0.521  Sum_probs=36.9

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      +|+..+.....+++++||++||.||++.++|+.+|+.++++..
T Consensus        84 ~t~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~i~~~l~~~~  126 (136)
T 3t6k_A           84 LTAQGDISAKIAGFEAGANDYLAKPFEPQELVYRVKNILARTT  126 (136)
T ss_dssp             EECTTCHHHHHHHHHHTCSEEEETTCCHHHHHHHHHHHHHC--
T ss_pred             EecCCCHHHHHHHHhcCcceEEeCCCCHHHHHHHHHHHHhccC
Confidence            3667778888899999999999999999999999999987653

>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=97.12  E-value=0.00048  Score=56.04  Aligned_cols=40  Identities=23%  Similarity=0.413  Sum_probs=35.6

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWR   40 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~Lr   40 (445)
                      +|+..+.....+++++||++||.||++.++|..+|+.++.
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            3667778888899999999999999999999999998874

>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=97.10  E-value=0.00073  Score=53.55  Aligned_cols=41  Identities=29%  Similarity=0.494  Sum_probs=36.2

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      |+..+.....++++.|+++||.||++.++|..+|+.++++.
T Consensus        79 s~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~~~~~  119 (121)
T 2pl1_A           79 TARESWQDKVEVLSAGADDYVTKPFHIEEVMARMQALMRRN  119 (121)
T ss_dssp             ESCCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHHHHH
T ss_pred             ecCCCHHHHHHHHHcCccceEECCCCHHHHHHHHHHHHHhh
Confidence            56667778889999999999999999999999999988764

>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=97.06  E-value=0.0007  Score=53.89  Aligned_cols=41  Identities=27%  Similarity=0.394  Sum_probs=36.1

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      |+..+......++++|+++||.||++.++|..+|+.++++.
T Consensus        80 s~~~~~~~~~~~~~~ga~~~l~Kp~~~~~l~~~i~~~~~~~  120 (122)
T 1zgz_A           80 TGRSDRIDRIVGLEMGADDYVTKPLELRELVVRVKNLLWRI  120 (122)
T ss_dssp             ESSCCHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHHHHH
T ss_pred             ECCCChhhHHHHHHhCHHHHccCCCCHHHHHHHHHHHHHHh
Confidence            56667777889999999999999999999999999988764

>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=97.04  E-value=0.00087  Score=53.78  Aligned_cols=41  Identities=20%  Similarity=0.421  Sum_probs=36.2

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      |+..+.....++++.|+++||.||++.++|..+|+.++++.
T Consensus        86 s~~~~~~~~~~~~~~ga~~~l~KP~~~~~l~~~i~~~~~~~  126 (128)
T 1jbe_A           86 TAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEKL  126 (128)
T ss_dssp             ESSCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHHHHH
T ss_pred             ecCccHHHHHHHHHhCcCceeecCCCHHHHHHHHHHHHHHh
Confidence            56667778889999999999999999999999999988654

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

Probab=96.99  E-value=0.001  Score=54.32  Aligned_cols=43  Identities=21%  Similarity=0.357  Sum_probs=37.3

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      +|+..+.....+++++||++||.||++..+|..+|+.++++..
T Consensus        81 ~s~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~i~~~~~~~~  123 (132)
T 3crn_A           81 VTGYASLENSVFSLNAGADAYIMKPVNPRDLLEKIKEKLDEQE  123 (132)
T ss_dssp             EESCCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHHHHHH
T ss_pred             EeccccHHHHHHHHhccchhhccCCCCHHHHHHHHHHHHhccc
Confidence            3566777788899999999999999999999999999887653

>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=96.99  E-value=0.00091  Score=53.30  Aligned_cols=41  Identities=27%  Similarity=0.411  Sum_probs=35.7

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      |+..+......++++|+++||.||++.++|..+|+.++++.
T Consensus        81 s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~~~~  121 (123)
T 1xhf_A           81 TGRDNEVDKILGLEIGADDYITKPFNPRELTIRARNLLSRT  121 (123)
T ss_dssp             ESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHHHHH
T ss_pred             ECCCChHHHHHHHhcCcceEEeCCCCHHHHHHHHHHHHHHh
Confidence            55667777888999999999999999999999999988653

>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=96.94  E-value=0.00084  Score=52.94  Aligned_cols=40  Identities=40%  Similarity=0.480  Sum_probs=34.9

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      |+..+......++++|+++||.||++.++|..+|+.++++
T Consensus        79 s~~~~~~~~~~~~~~g~~~~l~Kp~~~~~l~~~i~~~~~~  118 (120)
T 2a9o_A           79 SAKDSEFDKVIGLELGADDYVTKPFSNRELQARVKALLRR  118 (120)
T ss_dssp             ESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHHHC
T ss_pred             ecCCchHHHHHHHhCCHhheEeCCCCHHHHHHHHHHHHcc
Confidence            5566677788899999999999999999999999988754

>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=96.94  E-value=0.0011  Score=52.35  Aligned_cols=41  Identities=39%  Similarity=0.461  Sum_probs=36.0

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      |+..+.....++++.|+++||.||++.++|..+|+.++++.
T Consensus        79 s~~~~~~~~~~~~~~g~~~~l~Kp~~~~~l~~~i~~~~~~~  119 (121)
T 1zh2_A           79 SARSEESDKIAALDAGADDYLSKPFGIGELQARLRVALRRH  119 (121)
T ss_dssp             ESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHHHHH
T ss_pred             ECCCCHHHHHHHHhcCCCeEEeCCcCHHHHHHHHHHHHHhh
Confidence            56667777889999999999999999999999999988653

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

Probab=96.92  E-value=0.0011  Score=54.30  Aligned_cols=43  Identities=21%  Similarity=0.432  Sum_probs=38.0

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      +|+..+.+...+++++||++||.||++.++|+.+|++++....
T Consensus        86 ~s~~~~~~~~~~~~~~ga~~~l~KP~~~~~l~~~i~~~~~~~~  128 (136)
T 3kto_A           86 MASSSDIPTAVRAMRASAADFIEKPFIEHVLVHDVQQIINGAK  128 (136)
T ss_dssp             EESSCCHHHHHHHHHTTCSEEEESSBCHHHHHHHHHHHHHHHC
T ss_pred             EEcCCCHHHHHHHHHcChHHheeCCCCHHHHHHHHHHHHhccC
Confidence            3567778888999999999999999999999999999987654

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

Probab=96.89  E-value=0.0014  Score=54.17  Aligned_cols=42  Identities=26%  Similarity=0.461  Sum_probs=36.8

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      |+..+.+....+++.||++||.||++.++|..+|+.++++.+
T Consensus        83 s~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~i~~~~~~~~  124 (137)
T 3cfy_A           83 TAHGSVDLAVNLIQKGAEDFLEKPINADRLKTSVALHLKRAK  124 (137)
T ss_dssp             ESSCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHHHHHH
T ss_pred             EecCcHHHHHHHHHCCccEEEeCCCCHHHHHHHHHHHHHHHH
Confidence            556677788899999999999999999999999999887653

>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=96.89  E-value=0.0013  Score=54.06  Aligned_cols=43  Identities=9%  Similarity=0.152  Sum_probs=38.3

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCC-CHHHHHHHHHHHHHHHh
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPL-RTNELLNLWTHMWRRRR   43 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPf-d~eELLaRVra~LrR~r   43 (445)
                      +|+..+.+...+++++||++||.||+ +.++|..+|+.++++..
T Consensus        87 ~s~~~~~~~~~~~~~~ga~~~l~Kp~~~~~~l~~~i~~~l~~~~  130 (144)
T 3kht_A           87 LTDNVSDDRAKQCMAAGASSVVDKSSNNVTDFYGRIYAIFSYWL  130 (144)
T ss_dssp             EETTCCHHHHHHHHHTTCSEEEECCTTSHHHHHHHHHHHHHHHH
T ss_pred             EeCCCCHHHHHHHHHcCCCEEEECCCCcHHHHHHHHHHHHHHHH
Confidence            35667788888999999999999999 99999999999998764

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

Probab=96.88  E-value=0.0014  Score=53.67  Aligned_cols=44  Identities=18%  Similarity=0.435  Sum_probs=38.5

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhh
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRM   44 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~rL   44 (445)
                      +|+..+.....+++++||++||.||++.++|..+|+.++++.++
T Consensus        83 ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~l~~~~~~~~~  126 (143)
T 3jte_A           83 LTGHGDLDNAILAMKEGAFEYLRKPVTAQDLSIAINNAINRKKL  126 (143)
T ss_dssp             EECTTCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHHHHHHH
T ss_pred             EECCCCHHHHHHHHHhCcceeEeCCCCHHHHHHHHHHHHHHHHH
Confidence            35667777888999999999999999999999999999987653

>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=96.88  E-value=0.00098  Score=53.64  Aligned_cols=41  Identities=17%  Similarity=0.456  Sum_probs=35.7

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      +|+..+.....++++.||++||.||++.++|..+|+.++++
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            35667777888999999999999999999999999988754

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

Probab=96.87  E-value=0.0014  Score=53.97  Aligned_cols=41  Identities=29%  Similarity=0.441  Sum_probs=36.3

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      |+..+......+++.||++||.||++.++|..+|+.++++.
T Consensus        82 s~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~l~~~~~~~  122 (136)
T 2qzj_A           82 TYINEDQSILNALNSGGDDYLIKPLNLEILYAKVKAILRRM  122 (136)
T ss_dssp             ESCCCHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHHHHH
T ss_pred             EcCCCHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHh
Confidence            55667778889999999999999999999999999988764

>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=96.83  E-value=0.0012  Score=53.08  Aligned_cols=41  Identities=24%  Similarity=0.400  Sum_probs=36.0

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      +|+..+.....++++.|+++||.||++.++|..+|+.++++
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            46677778888999999999999999999999999988754

>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=96.81  E-value=0.0015  Score=53.16  Aligned_cols=43  Identities=23%  Similarity=0.405  Sum_probs=38.4

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      +|+..+.+...+++++||++||.||++..+|..+|+.+++...
T Consensus        85 ~s~~~~~~~~~~~~~~g~~~~l~kP~~~~~l~~~i~~~~~~~~  127 (137)
T 3hdg_A           85 ISAFSEMKYFIKAIELGVHLFLPKPIEPGRLMETLEDFRHIKL  127 (137)
T ss_dssp             CCCCCCHHHHHHHHHHCCSEECCSSCCHHHHHHHHHHHHHHHH
T ss_pred             EecCcChHHHHHHHhCCcceeEcCCCCHHHHHHHHHHHHHHHh
Confidence            4667778888899999999999999999999999999987754

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

Probab=96.80  E-value=0.0015  Score=53.25  Aligned_cols=40  Identities=20%  Similarity=0.449  Sum_probs=34.8

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      |+..+.....+++++||++||.||++.++|..+|+.+++.
T Consensus        90 s~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~l~~~~~~  129 (136)
T 1dcf_A           90 SGNTDKSTKEKCMSFGLDGVLLKPVSLDNIRDVLSDLLEP  129 (136)
T ss_dssp             ESCCSHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHHSC
T ss_pred             eCCCCHHHHHHHHHcCCCeEEECCCCHHHHHHHHHHHhch
Confidence            5666777788899999999999999999999999887643

>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=96.80  E-value=0.0018  Score=52.09  Aligned_cols=42  Identities=12%  Similarity=0.085  Sum_probs=37.2

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      |+..+.+...+++++|+++||.||++.++|...|+.++++..
T Consensus        92 s~~~~~~~~~~~~~~g~~~~l~kP~~~~~l~~~i~~~~~~~~  133 (140)
T 1k68_A           92 STSINEDDIFHSYDLHVNCYITKSANLSQLFQIVKGIEEFWL  133 (140)
T ss_dssp             ESCCCHHHHHHHHHTTCSEEEECCSSHHHHHHHHHHHHHHHH
T ss_pred             ecCCcHHHHHHHHHhchhheecCCCCHHHHHHHHHHHHHHHc
Confidence            556677788899999999999999999999999999987754

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

Probab=96.79  E-value=0.0017  Score=54.21  Aligned_cols=41  Identities=15%  Similarity=0.161  Sum_probs=36.0

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      |+..+.....++++.||++||.||++.++|..+|+.+++..
T Consensus        98 s~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~i~~~~~~~  138 (149)
T 1i3c_A           98 TTSHNEDDVIASYELHVNCYLTKSRNLKDLFKMVQGIESFW  138 (149)
T ss_dssp             ESCCCHHHHHHHHHTTCSEEEECCSSHHHHHHHHHHHHHHH
T ss_pred             ECCCChHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Confidence            56667778889999999999999999999999999987654

>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=96.76  E-value=0.0012  Score=54.15  Aligned_cols=41  Identities=24%  Similarity=0.464  Sum_probs=35.7

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      +|+..+.....+++++||++||.||++.++|...|+.++..
T Consensus        87 lt~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~l~~~~~~  127 (133)
T 2r25_B           87 LTAFADDSNIKECLESGMNGFLSKPIKRPKLKTILTEFCAA  127 (133)
T ss_dssp             EESCCSHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHCTT
T ss_pred             EECCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHHh
Confidence            46777788889999999999999999999999999887643

>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=96.75  E-value=0.0013  Score=52.18  Aligned_cols=38  Identities=24%  Similarity=0.539  Sum_probs=33.3

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHH
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMW   39 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~L   39 (445)
                      |+..+.....++++.|+++||.||++.++|..+|+.++
T Consensus        82 s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~  119 (120)
T 1tmy_A           82 SAMGQQAMVIEAIKAGAKDFIVKPFQPSRVVEALNKVS  119 (120)
T ss_dssp             ECTTCHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHC
T ss_pred             eCCCCHHHHHHHHHhCcceeEeCCCCHHHHHHHHHHHh
Confidence            56667778889999999999999999999999998764

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

Probab=96.74  E-value=0.00096  Score=54.67  Aligned_cols=43  Identities=21%  Similarity=0.309  Sum_probs=36.8

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      +|+..+.+...+++++||++||.||++.++|..+|+.++++..
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            3566778888999999999999999999999999999987653

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

Probab=96.71  E-value=0.0015  Score=53.34  Aligned_cols=42  Identities=12%  Similarity=0.128  Sum_probs=35.5

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      +|+..+.....++++.||++||.||++.++|..+|+.+++..
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            356677778889999999999999999999999999887543

>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=96.70  E-value=0.0023  Score=52.19  Aligned_cols=42  Identities=17%  Similarity=0.305  Sum_probs=37.1

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      |+..+......+++.|+++||.||++.++|...|+.++++..
T Consensus        99 t~~~~~~~~~~~~~~g~~~~l~kP~~~~~l~~~i~~~~~~~~  140 (149)
T 1k66_A           99 TTSSNPKDIEICYSYSISSYIVKPLEIDRLTETVQTFIKYWL  140 (149)
T ss_dssp             ESCCCHHHHHHHHHTTCSEEEECCSSHHHHHHHHHHHHHHHH
T ss_pred             eCCCCHHHHHHHHHCCCCEEEeCCCCHHHHHHHHHHHHHHhh
Confidence            556677888899999999999999999999999999987753

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

Probab=96.67  E-value=0.0021  Score=52.22  Aligned_cols=42  Identities=19%  Similarity=0.222  Sum_probs=36.9

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      |+..+.....+++++|+++||.||++.++|..+|+.++++..
T Consensus        91 s~~~~~~~~~~~~~~g~~~~l~kP~~~~~l~~~i~~~~~~~~  132 (143)
T 3cnb_A           91 TGALTDDNVSRIVALGAETCFGKPLNFTLLEKTIKQLVEQKK  132 (143)
T ss_dssp             ESSCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHHHTTC
T ss_pred             eCCCCHHHHHHHHhcCCcEEEeCCCCHHHHHHHHHHHHHhhc
Confidence            556677778899999999999999999999999999987653

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

Probab=96.67  E-value=0.0019  Score=54.35  Aligned_cols=42  Identities=21%  Similarity=0.324  Sum_probs=37.5

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      |+..+.....+++++||++||.||++..+|+.+|+.++...+
T Consensus        88 s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~l~~~~  129 (154)
T 3gt7_A           88 TILSDPRDVVRSLECGADDFITKPCKDVVLASHVKRLLSGVK  129 (154)
T ss_dssp             ECCCSHHHHHHHHHHCCSEEEESSCCHHHHHHHHHHHHHHTC
T ss_pred             ECCCChHHHHHHHHCCCCEEEeCCCCHHHHHHHHHHHHHHHH
Confidence            566777888899999999999999999999999999997754

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

Probab=96.66  E-value=0.00092  Score=54.11  Aligned_cols=41  Identities=22%  Similarity=0.428  Sum_probs=35.6

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      |+..+.....+++++||++||.||++.++|..+|+.++++.
T Consensus        84 s~~~~~~~~~~~~~~ga~~~l~KP~~~~~l~~~i~~~~~~~  124 (130)
T 1dz3_A           84 TAFGQEDVTKKAVELGASYFILKPFDMENLAHHIRQVYGKT  124 (130)
T ss_dssp             EETTCHHHHHHHHHTTCEEEEECSSCCTTHHHHHHHHHHCC
T ss_pred             ecCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHhcCC
Confidence            55667778889999999999999999999999999987653

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

Probab=96.65  E-value=0.0022  Score=52.74  Aligned_cols=42  Identities=17%  Similarity=0.238  Sum_probs=37.1

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      |+..+......++++|+++||.||++..+|..+|+.++++.+
T Consensus        89 s~~~~~~~~~~~~~~g~~~~l~kp~~~~~L~~~i~~~~~~~~  130 (147)
T 2zay_A           89 SGRATAKEEAQLLDMGFIDFIAKPVNAIRLSARIKRVLKLLY  130 (147)
T ss_dssp             ESSCCHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHHHHHC
T ss_pred             eCCCCHHHHHHHHhCCCCEEEeCCCCHHHHHHHHHHHHHHHH
Confidence            566677788899999999999999999999999999987654

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

Probab=96.65  E-value=0.0026  Score=53.13  Aligned_cols=43  Identities=21%  Similarity=0.409  Sum_probs=38.4

Q ss_pred             CCCCCcHHHHHHHHHcC-CcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            1 MSAQDEVSVVVKCLRLG-AADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         1 LTA~~d~e~iveALeaG-AdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      +|+..+.....++++.| |++||.||++..+|..+|+.++++.+
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            46677788889999999 99999999999999999999998764

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

Probab=96.57  E-value=0.0012  Score=57.75  Aligned_cols=43  Identities=19%  Similarity=0.352  Sum_probs=38.2

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      +|+..+.+...+++++||++||.||++.++|..+|+.++.+..
T Consensus        85 lt~~~~~~~~~~a~~~Ga~~~l~KP~~~~~L~~~i~~~~~~~~  127 (184)
T 3rqi_A           85 LTGYASIATAVQAVKDGADNYLAKPANVESILAALQTNASEVQ  127 (184)
T ss_dssp             EESSCCHHHHHHHHHHTCSEEEESSCCHHHHHHHTSTTHHHHH
T ss_pred             EeCCCCHHHHHHHHHhCHHHheeCCCCHHHHHHHHHHHHHHhh
Confidence            4677888889999999999999999999999999998887653

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

Probab=96.56  E-value=0.0026  Score=51.62  Aligned_cols=42  Identities=17%  Similarity=0.355  Sum_probs=37.1

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      |+..+......+++.|+++||.||++.++|..+|+.+++...
T Consensus        89 s~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~~~~~~  130 (140)
T 3cg0_A           89 TSSQDVETFQRAKRVNPFGYLAKPVAADTLHRSIEMAIHKKK  130 (140)
T ss_dssp             ECCCCHHHHHHHHTTCCSEEEEESCCHHHHHHHHHHHHHHHH
T ss_pred             ecCCCHHHHHHHHhcCCCEEEeCCCCHHHHHHHHHHHHhccc
Confidence            566677788899999999999999999999999999987654

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

Probab=96.53  E-value=0.0021  Score=53.49  Aligned_cols=41  Identities=24%  Similarity=0.400  Sum_probs=34.4

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      +|+..+.+...+++++||++||.||++.++|+..|+.++..
T Consensus        96 ~s~~~~~~~~~~~~~~Ga~~~l~KP~~~~~L~~~l~~~~~~  136 (143)
T 3m6m_D           96 LSADVTPEAIRACEQAGARAFLAKPVVAAKLLDTLADLAVS  136 (143)
T ss_dssp             EESCCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHC--
T ss_pred             EeCCCCHHHHHHHHHcChhheeeCCCCHHHHHHHHHHHHHh
Confidence            35667778888999999999999999999999999887644

>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=96.53  E-value=0.003  Score=51.26  Aligned_cols=42  Identities=29%  Similarity=0.509  Sum_probs=35.5

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      +|+..+.+...+++++|+++||.||++.++|..+|++++...
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            356677788889999999999999999999999999887543

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

Probab=96.51  E-value=0.0024  Score=53.15  Aligned_cols=42  Identities=12%  Similarity=0.284  Sum_probs=37.0

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      +|+..+.+...+++++||++||.||++.++|..+|+.+++..
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            356677788889999999999999999999999999988654

>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=96.50  E-value=0.0008  Score=53.76  Aligned_cols=40  Identities=33%  Similarity=0.445  Sum_probs=34.4

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      |+..+.....++++.|+++||.||++.++|..+|+.++++
T Consensus        83 s~~~~~~~~~~~~~~ga~~~l~Kp~~~~~l~~~i~~~~~~  122 (127)
T 2jba_A           83 TARGEEEDRVRGLETGADDCITKPFSPKELVARIKAVMRR  122 (127)
T ss_dssp             EETTHHHHHHTTCCCSCSEEEEESCCHHHHHHHHHHHHHC
T ss_pred             eCCCCHHHHHHHHhcCCCeEEeCCCCHHHHHHHHHHHHhc
Confidence            4555666778889999999999999999999999988765

>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=96.47  E-value=0.0038  Score=51.93  Aligned_cols=43  Identities=21%  Similarity=0.389  Sum_probs=37.0

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      +|+..+.....+++++|+++||.||++.++|...|+.+.+...
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            3566777888899999999999999999999999999876543

>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=96.46  E-value=0.0037  Score=52.17  Aligned_cols=42  Identities=21%  Similarity=0.481  Sum_probs=36.9

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      |+..+......+++.|+++||.||++..+|...|+.++++.+
T Consensus        82 s~~~~~~~~~~~~~~g~~~~l~kP~~~~~L~~~i~~~~~~~~  123 (155)
T 1qkk_A           82 TGHGDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRAEEKRR  123 (155)
T ss_dssp             ECGGGHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHHHHHH
T ss_pred             ECCCChHHHHHHHhcCCCeEEeCCCCHHHHHHHHHHHHHHHH
Confidence            455667778899999999999999999999999999987654

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

Probab=96.45  E-value=0.0032  Score=52.40  Aligned_cols=43  Identities=30%  Similarity=0.435  Sum_probs=37.2

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      +|+..+.....+++++||++||.||++.++|..+|+.++.+..
T Consensus        95 ~s~~~~~~~~~~~~~~g~~~~l~Kp~~~~~l~~~i~~~~~~~~  137 (152)
T 3eul_A           95 ISAHDEPAIVYQALQQGAAGFLLKDSTRTEIVKAVLDCAKGRD  137 (152)
T ss_dssp             EESCCCHHHHHHHHHTTCSEEEETTCCHHHHHHHHHHHHHCC-
T ss_pred             EEccCCHHHHHHHHHcCCCEEEecCCCHHHHHHHHHHHHcCCe
Confidence            3566777888899999999999999999999999999987643

>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=96.43  E-value=0.0022  Score=51.24  Aligned_cols=40  Identities=23%  Similarity=0.356  Sum_probs=34.4

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWR   40 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~Lr   40 (445)
                      +|+..+.....++++.|+++||.||++.++|..+|+.+++
T Consensus        81 ~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~~  120 (124)
T 1srr_A           81 MTAYGELDMIQESKELGALTHFAKPFDIDEIRDAVKKYLP  120 (124)
T ss_dssp             EESSCCHHHHHHHHHHTCCCEEESSCCHHHHHHHHHHHSC
T ss_pred             EEccCchHHHHHHHhcChHhhccCCCCHHHHHHHHHHHhc
Confidence            3566677788899999999999999999999999987653

>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=96.42  E-value=0.0014  Score=52.15  Aligned_cols=39  Identities=15%  Similarity=0.185  Sum_probs=29.5

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHH
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWR   40 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~Lr   40 (445)
                      |+..+......+++.|+++||.||++..+|..+|+.++.
T Consensus        82 s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~~  120 (124)
T 1mb3_A           82 TAFAMKGDEERIREGGCEAYISKPISVVHFLETIKRLLE  120 (124)
T ss_dssp             C------CHHHHHHHTCSEEECSSCCHHHHHHHHHHHHS
T ss_pred             ECCCCHHHHHHHHhCCCCEEEeCCCCHHHHHHHHHHHHh
Confidence            455556667788999999999999999999999988764

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

Probab=96.42  E-value=0.0026  Score=51.98  Aligned_cols=42  Identities=26%  Similarity=0.474  Sum_probs=35.9

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      |+..+.+....+++.|+++||.||++.++|..+|+.++++.+
T Consensus        82 s~~~~~~~~~~~~~~g~~~~l~kP~~~~~l~~~i~~~~~~~~  123 (142)
T 2qxy_A           82 SAYVDKDLIINSVKAGAVDYILKPFRLDYLLERVKKIISSTP  123 (142)
T ss_dssp             ESCCCHHHHHHHHHHTCSCEEESSCCHHHHHHHHHHHHHC--
T ss_pred             ECCCCHHHHHHHHHCCcceeEeCCCCHHHHHHHHHHHHhhcc
Confidence            556677788899999999999999999999999999987643

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

Probab=96.41  E-value=0.0029  Score=55.36  Aligned_cols=42  Identities=14%  Similarity=0.283  Sum_probs=37.3

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      +|+..+.+....+++.|+++||.||++..+|...|+.++.+.
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            467777888899999999999999999999999999988654

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

Probab=96.40  E-value=0.0019  Score=52.16  Aligned_cols=41  Identities=20%  Similarity=0.188  Sum_probs=31.5

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      |+..+... ..+++.|+++||.||++.++|+.+|+.++.+..
T Consensus        84 s~~~~~~~-~~~~~~g~~~~l~KP~~~~~l~~~i~~~l~~~~  124 (133)
T 3nhm_A           84 SGYAPRTE-GPADQPVPDAYLVKPVKPPVLIAQLHALLARAE  124 (133)
T ss_dssp             ESCCC------TTSCCCSEEEESSCCHHHHHHHHHHHHHHHC
T ss_pred             eCCCcHhH-HHHhhcCCceEEeccCCHHHHHHHHHHHHhhhc
Confidence            44445555 788999999999999999999999999998764

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

Probab=96.39  E-value=0.0021  Score=51.75  Aligned_cols=42  Identities=31%  Similarity=0.452  Sum_probs=33.4

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCC-CHHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPL-RTNELLNLWTHMWRRR   42 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPf-d~eELLaRVra~LrR~   42 (445)
                      +|+..+.....++++.|+++||.||+ +.++|...|+.++.+.
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            35667777888999999999999999 8999999999888653

>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=96.37  E-value=0.0011  Score=54.42  Aligned_cols=42  Identities=31%  Similarity=0.473  Sum_probs=33.3

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      |+..+.+...+++++||++||.||++.++|..+|+.++++..
T Consensus        83 s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~~~~~  124 (140)
T 3n53_A           83 FSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQN  124 (140)
T ss_dssp             ECC----CTTTTTTCCCSEEEESSCCHHHHHHHHHHHHHHHH
T ss_pred             ecCCCHHHHHHHHhcCCCeeeeCCCCHHHHHHHHHHHHhhHH
Confidence            445555666778999999999999999999999999998764

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

Probab=96.36  E-value=0.0041  Score=51.81  Aligned_cols=42  Identities=10%  Similarity=0.248  Sum_probs=37.1

Q ss_pred             CCCCcHHHHHHHHHcC-CcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            2 SAQDEVSVVVKCLRLG-AADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         2 TA~~d~e~iveALeaG-AdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      |+..+.....++++.| +++||.||++.++|..+|+.++++.+
T Consensus        83 s~~~~~~~~~~~~~~g~~~~~l~KP~~~~~L~~~i~~~l~~~~  125 (151)
T 3kcn_A           83 TGNQDLTTAMEAVNEGQVFRFLNKPCQMSDIKAAINAGIKQYD  125 (151)
T ss_dssp             ECGGGHHHHHHHHHHTCCSEEEESSCCHHHHHHHHHHHHHHHH
T ss_pred             ECCCCHHHHHHHHHcCCeeEEEcCCCCHHHHHHHHHHHHHHHH
Confidence            5566777888999999 99999999999999999999998754

>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=96.34  E-value=0.0037  Score=55.29  Aligned_cols=42  Identities=26%  Similarity=0.383  Sum_probs=37.2

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      +|+..+.+....++++||++||.||++..+|..+|+.++++.
T Consensus        85 ls~~~~~~~~~~~~~~Ga~~~l~Kp~~~~~L~~~i~~~~~~~  126 (215)
T 1a04_A           85 FSVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALHQAAAGE  126 (215)
T ss_dssp             EECCCCHHHHHHHHHTTCSEEEETTCCHHHHHHHHHHHHHSC
T ss_pred             EECCCCHHHHHHHHHcCCcEEEeCCCCHHHHHHHHHHHHcCC
Confidence            356677888899999999999999999999999999988754

>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=96.30  E-value=0.0022  Score=51.95  Aligned_cols=41  Identities=37%  Similarity=0.462  Sum_probs=34.0

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      |+..+......++++|+++||.||++..+|..+|+.++++.
T Consensus        82 s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~~~~  122 (136)
T 1mvo_A           82 TAKDEEFDKVLGLELGADDYMTKPFSPREVNARVKAILRRS  122 (136)
T ss_dssp             ECTTCCCCHHHHHHTTCCEEEESSCCHHHHHHHHHHHHHTC
T ss_pred             ECCCCHHHHHHHHhCCCCEEEECCCCHHHHHHHHHHHHHhh
Confidence            44445555678899999999999999999999999988654

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

Probab=96.26  E-value=0.0027  Score=51.46  Aligned_cols=41  Identities=24%  Similarity=0.468  Sum_probs=35.4

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      |+..+......++++|+++||.||++..+|..+|+.++++.
T Consensus        87 s~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~l~~~~~~~  127 (140)
T 2qr3_A           87 TAYADIDLAVRGIKEGASDFVVKPWDNQKLLETLLNAASQA  127 (140)
T ss_dssp             EEGGGHHHHHHHHHTTCCEEEEESCCHHHHHHHHHHHHTCC
T ss_pred             ECCCCHHHHHHHHHcCchheeeCCCCHHHHHHHHHHHHHhc
Confidence            45566777889999999999999999999999999988654

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

Probab=96.25  E-value=0.002  Score=52.64  Aligned_cols=42  Identities=19%  Similarity=0.184  Sum_probs=34.6

Q ss_pred             CCCCcHHHHH-HHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            2 SAQDEVSVVV-KCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         2 TA~~d~e~iv-eALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      |+..+..... .++++|+++||.||++.++|..+|+.++++..
T Consensus        87 s~~~~~~~~~~~~~~~g~~~~l~kP~~~~~l~~~i~~~l~~~~  129 (140)
T 3grc_A           87 SANAREGELEFNSQPLAVSTWLEKPIDENLLILSLHRAIDNMA  129 (140)
T ss_dssp             CTTHHHHHHHHCCTTTCCCEEECSSCCHHHHHHHHHHHHHHHC
T ss_pred             ecCCChHHHHHHhhhcCCCEEEeCCCCHHHHHHHHHHHHHhcC
Confidence            4444444555 78899999999999999999999999998764

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

Probab=96.24  E-value=0.0017  Score=53.85  Aligned_cols=42  Identities=14%  Similarity=0.290  Sum_probs=29.7

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      |+..+.....++++.|+++||.||++..+|...|+.++++..
T Consensus        84 s~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~i~~~~~~~~  125 (141)
T 3cu5_A           84 SGYSDKEYLKAAIKFRAIRYVEKPIDPSEIMDALKQSIQTVL  125 (141)
T ss_dssp             CCSTTTCCC------CCCEEECSSCCHHHHHHHHHHHHHHHH
T ss_pred             eCCCcHHHHHHHHhCCccEEEeCCCCHHHHHHHHHHHHHHHH
Confidence            455555566788999999999999999999999999887653

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

Probab=96.22  E-value=0.00094  Score=55.03  Aligned_cols=42  Identities=24%  Similarity=0.252  Sum_probs=34.9

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      |+..+.+...+++++||++||.||++.++|..+|+.++++.+
T Consensus        85 s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~l~~~~  126 (140)
T 3h5i_A           85 TAHTEPAVVEKIRSVTAYGYVMKSATEQVLITIVEMALRLYE  126 (140)
T ss_dssp             ESSSSCCCCGGGGGSCEEEEEETTCCHHHHHHHHHHHHHHHH
T ss_pred             ECCCCHHHHHHHHhCCCcEEEeCCCCHHHHHHHHHHHHHHHH
Confidence            444444555678899999999999999999999999998765

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

Probab=96.21  E-value=0.0016  Score=52.54  Aligned_cols=42  Identities=17%  Similarity=0.158  Sum_probs=33.8

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      |+..+.....++++.|+++||.||++.++|..+|+.++++..
T Consensus        81 s~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~~~~~~  122 (134)
T 3f6c_A           81 SAKNDHFYGKHCADAGANGFVSKKEGMNNIIAAIEAAKNGYC  122 (134)
T ss_dssp             ECC---CTHHHHHHTTCSEEEEGGGCTHHHHHHHHHHHTTCC
T ss_pred             eCCCChHHHHHHHHhCCCEEEeCCCCHHHHHHHHHHHHCCCE
Confidence            455566677889999999999999999999999999886643

>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=96.10  E-value=0.0027  Score=55.92  Aligned_cols=42  Identities=29%  Similarity=0.376  Sum_probs=36.7

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      |+..+.+....+++.||++||.||++..+|..+|+.++++.+
T Consensus        92 t~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~i~~~~~~~~  133 (205)
T 1s8n_A           92 TAFSQRDLVERARDAGAMAYLVKPFSISDLIPAIELAVSRFR  133 (205)
T ss_dssp             EEGGGHHHHHTTGGGSCEEEEEESCCHHHHHHHHHHHHHHHH
T ss_pred             ecCCCHHHHHHHHhcCCcEEEeCCCCHHHHHHHHHHHHHHHH
Confidence            556677778889999999999999999999999999987653

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

Probab=96.10  E-value=0.0076  Score=50.17  Aligned_cols=42  Identities=12%  Similarity=0.279  Sum_probs=36.4

Q ss_pred             CCCCcHHHHHHHHHcC-CcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            2 SAQDEVSVVVKCLRLG-AADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         2 TA~~d~e~iveALeaG-AdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      |+..+......+++.| +++||.||++..+|...|+.++++.+
T Consensus        86 s~~~~~~~~~~~~~~g~~~~~l~kP~~~~~L~~~i~~~~~~~~  128 (154)
T 2rjn_A           86 SGYADAQATIDAVNRGKISRFLLKPWEDEDVFKVVEKGLQLAF  128 (154)
T ss_dssp             ECGGGHHHHHHHHHTTCCSEEEESSCCHHHHHHHHHHHHHHHH
T ss_pred             ecCCCHHHHHHHHhccchheeeeCCCCHHHHHHHHHHHHHHHH
Confidence            5556677788899998 99999999999999999999987654

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

Probab=96.03  E-value=0.0053  Score=49.39  Aligned_cols=35  Identities=26%  Similarity=0.425  Sum_probs=30.3

Q ss_pred             HHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            7 VSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         7 ~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      .....+++++|+++||.||++.++|+.+|+..+..
T Consensus        91 ~~~~~~~~~~g~~~~l~kP~~~~~l~~~i~~~~~~  125 (132)
T 3lte_A           91 KAKLQQAVTEGADDYLEKPFDNDALLDRIHDLVNE  125 (132)
T ss_dssp             SHHHHHHHHHTCCEEECSSCCHHHHHHHHHHHHC-
T ss_pred             hHHHHHHHHhChHHHhhCCCCHHHHHHHHHHHcCC
Confidence            33677899999999999999999999999887754

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

Probab=96.03  E-value=0.0071  Score=49.50  Aligned_cols=42  Identities=17%  Similarity=0.259  Sum_probs=34.1

Q ss_pred             CCCCcHHHHHHHHHc-CCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            2 SAQDEVSVVVKCLRL-GAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         2 TA~~d~e~iveALea-GAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      |+..+......++.. ||++||.||++..+|..+|+.+++...
T Consensus        79 s~~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~i~~~~~~~~  121 (139)
T 2jk1_A           79 TGYTDSASMMAAINDAGIHQFLTKPWHPEQLLSSARNAARMFT  121 (139)
T ss_dssp             ESCTTCHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHHHHHH
T ss_pred             eCCCChHHHHHHHHhhchhhhccCCCCHHHHHHHHHHHHHHHH
Confidence            455566667778876 599999999999999999999887643

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

Probab=96.02  E-value=0.0041  Score=51.77  Aligned_cols=41  Identities=20%  Similarity=0.335  Sum_probs=35.9

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      |+..+......++++|+++||.||++..+|..+|+.++++.
T Consensus        86 s~~~~~~~~~~~~~~g~~~~l~kp~~~~~L~~~i~~~~~~~  126 (153)
T 3cz5_A           86 TMHQGSAFALKAFEAGASGYVTKSSDPAELVQAIEAILAGR  126 (153)
T ss_dssp             ESCCSHHHHHHHHHTTCSEEEETTSCTTHHHHHHHHHTTTC
T ss_pred             ECCCCHHHHHHHHHCCCcEEEecCCCHHHHHHHHHHHHhCC
Confidence            55667778889999999999999999999999999887654

>3i5c_A Fusion of general control protein GCN4 and WSPR R regulator protein; C-DI-GMP, ggdef, leucine zipper, signaling protein; HET: C2E; 1.94A {Pseudomonas aeruginosa PAO1} PDB: 3i5b_A*

Probab=95.97  E-value=0.0029  Score=55.63  Aligned_cols=66  Identities=11%  Similarity=0.084  Sum_probs=51.0

Q ss_pred             hhhCccccccccccchhhccccccCCCCeEEEEeecccchhhhhcCCCcccChHHHHhhcchhhhhhhhccc
Q 013329           43 RMLGLAEKNILSYDFDLVASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTS  114 (445)
Q Consensus        43 rLTgl~nr~iL~~gLdl~Ld~asr~n~~slaLL~lDLD~FKlINdn~g~vvSreQl~d~~l~~~A~~~a~~~  114 (445)
                      .+|+++|+..|...++..+......+ ..++|+.+|+|+|+.||+..     +++.+|.+|+.+|..|...+
T Consensus        34 ~lTgL~Nr~~f~~~l~~~~~~~~~~~-~~~~l~~idid~f~~in~~~-----G~~~gd~~L~~ia~~L~~~~   99 (206)
T 3i5c_A           34 GLTGLSNRRHFDEYLEMEWRRSLREQ-SQLSLLMIDVDYFKSYNDTF-----GHVAGDEALRQVAGAIREGC   99 (206)
T ss_dssp             TTTCSBCHHHHHHHHHHHHHHHHHHT-CCEEEEEEEETTHHHHHHHH-----CHHHHHHHHHHHHHHHHTTC
T ss_pred             cccCCCCHHHHHHHHHHHHHHHHhcC-CcEEEEEEECcchhHHHhcc-----ChhHHHHHHHHHHHHHHHhc
Confidence            35778887777665555554433333 36889999999999999998     67899999999999998755

>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=95.94  E-value=0.00091  Score=52.88  Aligned_cols=41  Identities=27%  Similarity=0.425  Sum_probs=33.8

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      |+..+......+++.|+++||.||++.++|..+|+.++++.
T Consensus        82 s~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~~~~~  122 (124)
T 1dc7_A           82 TAHSDLDAAVSAYQQGAFDYLPKPFDIDEAVALVERAISHY  122 (124)
T ss_dssp             CCSTTSTTTTSSCTTCCCCCBCSSCCHHHHHHHHHHHHHHT
T ss_pred             ecCCCHHHHHHHHhcCcceEeeCCCCHHHHHHHHHHHHHhh
Confidence            44455556667889999999999999999999999988653

>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=95.92  E-value=0.0029  Score=55.52  Aligned_cols=41  Identities=22%  Similarity=0.485  Sum_probs=35.2

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      |+..+......+++.||++||.||++.++|..+|+.++++.
T Consensus        83 s~~~~~~~~~~a~~~Ga~~~l~Kp~~~~~L~~~i~~~~~~~  123 (208)
T 1yio_A           83 TAHGDIPMTVRAMKAGAIEFLPKPFEEQALLDAIEQGLQLN  123 (208)
T ss_dssp             ESCTTSCCCHHHHHTTEEEEEESSCCHHHHHHHHHHHHHHH
T ss_pred             eCCCCHHHHHHHHHCCCcEEEeCCCCHHHHHHHHHHHHhhh
Confidence            45556666788999999999999999999999999998764

>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=95.90  E-value=0.0064  Score=60.62  Aligned_cols=43  Identities=23%  Similarity=0.457  Sum_probs=38.8

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      +|+..+.+...+++++||++||.||++.++|+..|+.++....
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            4777888889999999999999999999999999999987754

>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=95.87  E-value=0.0079  Score=59.88  Aligned_cols=42  Identities=26%  Similarity=0.351  Sum_probs=37.9

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      +|+..+.....+++++||++||.||++..+|+.+|+.+++..
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            467788888999999999999999999999999999988754

>3qyy_A Response regulator; C-DI-GMP, DGC, ggdef, competitive inhibition, xanthomonas Ca signaling protein-inhibitor complex; HET: C2E; 1.90A {Xanthomonas campestris PV}

Probab=95.86  E-value=0.00062  Score=58.29  Aligned_cols=68  Identities=12%  Similarity=0.010  Sum_probs=52.7

Q ss_pred             hhhCccccccccccchhhccccccCCCCeEEEEeecccchhhhhcCCCcccChHHHHhhcchhhhhhhhcccCC
Q 013329           43 RMLGLAEKNILSYDFDLVASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTSGT  116 (445)
Q Consensus        43 rLTgl~nr~iL~~gLdl~Ld~asr~n~~slaLL~lDLD~FKlINdn~g~vvSreQl~d~~l~~~A~~~a~~~~~  116 (445)
                      .+|+++|+..|...++..+....+.+ ..++|+.+|+|+|+.||+..     +++.+|.+|+.+|..|...+.+
T Consensus        15 ~lTgL~Nr~~f~~~l~~~~~~~~~~~-~~~~l~~idid~f~~in~~~-----G~~~gd~~L~~ia~~L~~~~~~   82 (167)
T 3qyy_A           15 PLTEALNRRGCEQAMRDSVTAAQREG-WPFVLFVLDMDNLKPINDRF-----GHLAGDRVLVRLVESAYGWLGA   82 (167)
T ss_dssp             TTTCSBCHHHHHHHHHHHHHHHHHHC-CCCEEEEEEESSHHHHHHHH-----CHHHHHHHHHHHHHHHTTTCCT
T ss_pred             cccCCCcHHHHHHHHHHHHHHHHhhC-CcEEEEEEechhhhHHHhhc-----CcHHHHHHHHHHHHHHHHhcCC
Confidence            56788888777666565555443333 36789999999999999998     6789999999999999877643

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

Probab=95.75  E-value=0.0015  Score=53.39  Aligned_cols=41  Identities=22%  Similarity=0.287  Sum_probs=33.8

Q ss_pred             CCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            3 AQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         3 A~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      +..+......++++|+++||.||++.++|..+|+.++++.+
T Consensus        89 ~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~~~~~~  129 (142)
T 3cg4_A           89 AKNAPDAKMIGLQEYVVDYITKPFDNEDLIEKTTFFMGFVR  129 (142)
T ss_dssp             CTTCCCCSSTTGGGGEEEEEESSCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHhcCccEEEeCCCCHHHHHHHHHHHHHHHh
Confidence            33444455667899999999999999999999999998765

>3icl_A EAL/ggdef domain protein; structural genomics, PSI-2, protein structure initiative, northeast structural genomics, consortium, NESG; HET: MSE; 2.00A {Methylococcus capsulatus}

Probab=95.74  E-value=0.002  Score=55.00  Aligned_cols=67  Identities=15%  Similarity=0.147  Sum_probs=52.3

Q ss_pred             hhCccccccccccchhhccccccCCCCeEEEEeecccchhhhhcCCCcccChHHHHhhcchhhhhhhhcccCC
Q 013329           44 MLGLAEKNILSYDFDLVASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTSGT  116 (445)
Q Consensus        44 LTgl~nr~iL~~gLdl~Ld~asr~n~~slaLL~lDLD~FKlINdn~g~vvSreQl~d~~l~~~A~~~a~~~~~  116 (445)
                      +|++.|+..|...+...+....+.. ..++|+.+|+|+|+.||+..     +++.+|.+|+.+|..|...+..
T Consensus         4 lTgL~Nr~~f~~~l~~~l~~~~~~~-~~~~l~~i~id~f~~in~~~-----G~~~gd~~L~~~a~~L~~~~~~   70 (171)
T 3icl_A            4 VTGLPNRQLFCDRLLQALAAHERDG-NPVVLLFLDVDNFKSINDSL-----GHLVGDRLLRATAERIRTAVRD   70 (171)
T ss_dssp             TTCCCCHHHHHHHHHHHHHHCCCTT-SCCEEEEEEETTHHHHHHHH-----CHHHHHHHHHHHHHHHHHHSCT
T ss_pred             ccCCccHHHHHHHHHHHHHHHHhcC-CcEEEEEEEChHhhHHHHHh-----ChHHHHHHHHHHHHHHHHhcCC
Confidence            5777777777665555555544333 36789999999999999998     6788999999999999987754

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

Probab=95.72  E-value=0.0024  Score=57.40  Aligned_cols=41  Identities=5%  Similarity=0.004  Sum_probs=35.3

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      |+..+......++++||++||.||+++++|..+|+.++++.
T Consensus        90 t~~~~~~~~~~~~~~Ga~~~l~Kp~~~~~L~~~i~~~~~~~  130 (225)
T 3klo_A           90 NCPQDIEHKLLFKWNNLAGVFYIDDDMDTLIKGMSKILQDE  130 (225)
T ss_dssp             EECTTCCHHHHTTSTTEEEEEETTCCHHHHHHHHHHHHTTC
T ss_pred             ECCcchhHHHHHHHhCCCEEEecCCCHHHHHHHHHHHHCCC
Confidence            55566667788899999999999999999999999998754

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

Probab=95.67  E-value=0.0053  Score=51.00  Aligned_cols=42  Identities=14%  Similarity=0.282  Sum_probs=33.1

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      +|+..+......+++.|+++||.||++.++|...|+.++++.
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            355566677888999999999999999999999999988654

>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=95.66  E-value=0.0084  Score=59.97  Aligned_cols=43  Identities=21%  Similarity=0.425  Sum_probs=38.3

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      +|+..+.+...++++.||+|||.|||+.++|..+|+++++...
T Consensus        78 lT~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~l~~~~  120 (387)
T 1ny5_A           78 ITGHGTIKTAVEAMKMGAYDFLTKPCMLEEIELTINKAIEHRK  120 (387)
T ss_dssp             EEETTCHHHHHHHHTTTCCEEEEESCCHHHHHHHHHHHHHHHH
T ss_pred             EeCCCCHHHHHHHHhcCceEEecCCCCHHHHHHHHHHHHHHHH
Confidence            4677788889999999999999999999999999999987654

>3mtk_A Diguanylate cyclase/phosphodiesterase; structural genomics, PSI-2, protein structure initiative; 2.24A {Caldicellulosiruptor saccharolyticus}

Probab=95.65  E-value=0.0023  Score=55.65  Aligned_cols=71  Identities=15%  Similarity=0.114  Sum_probs=55.3

Q ss_pred             HHHHHhhhCccccccccccchhhccccccCCCCeEEEEeecccchhhhhcCCCcccChHHHHhhcchhhhhhhhcccCC
Q 013329           38 MWRRRRMLGLAEKNILSYDFDLVASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTSGT  116 (445)
Q Consensus        38 ~LrR~rLTgl~nr~iL~~gLdl~Ld~asr~n~~slaLL~lDLD~FKlINdn~g~vvSreQl~d~~l~~~A~~~a~~~~~  116 (445)
                      +...=.+|++.|+..|...++..+....   ...++|+.+|+|+|+.||+..     +++.+|.+|+.+|..|...+..
T Consensus         6 ~a~~D~lTgL~Nr~~f~~~l~~~~~~~~---~~~~~l~~idid~f~~in~~~-----G~~~gd~lL~~ia~~L~~~~~~   76 (178)
T 3mtk_A            6 LAFYDELTGLPNKNSLIRWLNLKVSQMD---CIDTYLIFLEVRDLEKLNVTY-----GYDLVDELIIHISKRIKDIAGE   76 (178)
T ss_dssp             HHHBCTTTCSBCHHHHHHHHHHHHHSSC---CTTEEEEEEEETTHHHHHHHH-----CHHHHHHHHHHHHHHHHHHHCS
T ss_pred             HhHcCcccCCccHHHHHHHHHHHHHhcc---CCceEEEEEEhhHhhHHHHHh-----ChHHHHHHHHHHHHHHHHhcCC
Confidence            3333457888888877766665555433   346889999999999999998     6888999999999999887644

>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=95.47  E-value=0.013  Score=46.18  Aligned_cols=35  Identities=17%  Similarity=0.264  Sum_probs=30.5

Q ss_pred             cHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHH
Q 013329            6 EVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWR   40 (445)
Q Consensus         6 d~e~iveALeaGAdDYLtKPfd~eELLaRVra~Lr   40 (445)
                      +......+++.|+++||.||++..+|..+|+.+++
T Consensus        90 ~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~~~  124 (127)
T 2gkg_A           90 DGFAQHRKLKAHADEYVAKPVDADQLVERAGALIG  124 (127)
T ss_dssp             GGHHHHHHSTTCCSEEEESSCCHHHHHHHHHHHHC
T ss_pred             CchhHHHHHHhCcchheeCCCCHHHHHHHHHHHHc
Confidence            44566788999999999999999999999988764

>3ign_A Diguanylate cyclase; ggdef domain, A1U3W3_marav, NESG, MQR89A, structural genomics, PSI-2, protein structure initiative; HET: C2E; 1.83A {Marinobacter aquaeolei VT8}

Probab=95.47  E-value=0.0024  Score=54.98  Aligned_cols=68  Identities=19%  Similarity=0.106  Sum_probs=52.5

Q ss_pred             hhhCccccccccccchhhccccccCCCCeEEEEeecccchhhhhcCCCcccChHHHHhhcchhhhhhhhcccCC
Q 013329           43 RMLGLAEKNILSYDFDLVASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTSGT  116 (445)
Q Consensus        43 rLTgl~nr~iL~~gLdl~Ld~asr~n~~slaLL~lDLD~FKlINdn~g~vvSreQl~d~~l~~~A~~~a~~~~~  116 (445)
                      .+|++.|+..|...++..+....+.+ ..++|+.+|+|+|+.||+..     +++.+|.+|+.+|..|...+..
T Consensus        12 ~lTgL~Nr~~f~~~l~~~~~~~~~~~-~~~~l~~i~id~f~~in~~~-----G~~~gd~~L~~ia~~L~~~~~~   79 (177)
T 3ign_A           12 RLTGLLNRGTWENLVDAEYERFRRYG-QATSLVMFDIDHFKPVNDTY-----GHLAGDEVIRHTADVTRNNIRQ   79 (177)
T ss_dssp             TTTCSEEHHHHHHHHHHHHHHHHHHC-CCEEEEEEEETTHHHHHHHH-----CHHHHHHHHHHHHHHHHTTSCT
T ss_pred             CccCCCcHHHHHHHHHHHHHHHHhhC-CceEEEEEEchhhHHHHHhh-----ChHHHHHHHHHHHHHHHHhCCC
Confidence            45778887777665555555433333 36889999999999999988     6789999999999999887654

>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=95.43  E-value=0.0035  Score=50.27  Aligned_cols=40  Identities=18%  Similarity=0.031  Sum_probs=29.9

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      |+..+... ..++..|+++||.||++.++|+.+|+..+...
T Consensus        84 s~~~~~~~-~~~~~~g~~~~l~KP~~~~~L~~~i~~~~~~~  123 (127)
T 3i42_A           84 SGFAKNDL-GKEACELFDFYLEKPIDIASLEPILQSIEGHH  123 (127)
T ss_dssp             ECC-CTTC-CHHHHHHCSEEEESSCCHHHHHHHHHHHC---
T ss_pred             ECCcchhH-HHHHHHhhHHheeCCCCHHHHHHHHHHhhccC
Confidence            33444444 67889999999999999999999998876553

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

Probab=95.40  E-value=0.015  Score=47.27  Aligned_cols=37  Identities=22%  Similarity=0.223  Sum_probs=31.5

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHH
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHM   38 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~   38 (445)
                      |+..+......++++|+++||.||++.++|+.++...
T Consensus        96 s~~~~~~~~~~~~~~g~~~~l~kP~~~~~L~~~~~~~  132 (143)
T 2qvg_A           96 TAAYTSKDKLAFESLNIRGHLIKPLDYGEAIKLFWIL  132 (143)
T ss_dssp             ESCCCHHHHHHHTTTTCCEEEESSCCHHHHHHHHHHH
T ss_pred             eCCCCHHHHHHHHhcCCCeEEECCCCHHHHHHHHHHH
Confidence            4556677888999999999999999999999886554

>3hva_A Protein FIMX; ggdef diguanylate cyclase, biofilm, C-DI-GMP, transferase; 2.04A {Pseudomonas aeruginosa PAO1}

Probab=95.37  E-value=0.0026  Score=54.63  Aligned_cols=68  Identities=12%  Similarity=0.057  Sum_probs=53.8

Q ss_pred             hhhCccccccccccchhhccccccCCCCeEEEEeecccchhhhhcCCCcccChHHHHhhcchhhhhhhhcccCC
Q 013329           43 RMLGLAEKNILSYDFDLVASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTSGT  116 (445)
Q Consensus        43 rLTgl~nr~iL~~gLdl~Ld~asr~n~~slaLL~lDLD~FKlINdn~g~vvSreQl~d~~l~~~A~~~a~~~~~  116 (445)
                      .+|+++|+..|...++..+....+.+ ..++|+.+|+|+|+.||+..     +++.+|.+|+.+|..|...+..
T Consensus        17 ~lTgL~Nr~~f~~~l~~~~~~~~~~~-~~~~l~~i~id~f~~in~~~-----G~~~gd~~L~~~a~~L~~~~~~   84 (177)
T 3hva_A           17 PVTGLYNRSHFLDLMDAAVQQAVTAR-KPSTLAYIHLNGYPSLQADH-----GLSGIDLLLGQLAGLMREQFGE   84 (177)
T ss_dssp             TTTCSEEHHHHHHHHHHHHHHHHHTC-CCEEEEEEEETTHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHGG
T ss_pred             cccccchHHHHHHHHHHHHHHHHhCC-CCeEEEEEeCCCHHHHHHHh-----CchhHHHHHHHHHHHHHHhCCC
Confidence            46788888777666565555543333 37899999999999999988     7889999999999999887754

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

Probab=95.37  E-value=0.022  Score=46.43  Aligned_cols=35  Identities=23%  Similarity=0.467  Sum_probs=31.5

Q ss_pred             HHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            9 VVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         9 ~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      ...++++.|+++||.||++..+|...|+.+++..+
T Consensus        95 ~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~~~~~  129 (143)
T 2qv0_A           95 HAVEAFELEAFDYILKPYQESRIINMLQKLTTAWE  129 (143)
T ss_dssp             THHHHHHTTCSEEEESSCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCCcceEEeCCCCHHHHHHHHHHHHHHHH
Confidence            45678999999999999999999999999987764

>3ezu_A Ggdef domain protein; multidomain protein of unknown function with GG domain, structural genomics, joint center for structural GE JCSG; 1.95A {Geobacter sulfurreducens}

Probab=95.28  E-value=0.0049  Score=60.68  Aligned_cols=68  Identities=13%  Similarity=0.076  Sum_probs=49.7

Q ss_pred             hhhCccccccccccchhhccccccCCCCeEEEEeecccchhhhhcCCCcccChHHHHhhcchhhhhhhhcccCC
Q 013329           43 RMLGLAEKNILSYDFDLVASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTSGT  116 (445)
Q Consensus        43 rLTgl~nr~iL~~gLdl~Ld~asr~n~~slaLL~lDLD~FKlINdn~g~vvSreQl~d~~l~~~A~~~a~~~~~  116 (445)
                      .+|++.|+..|...++..+....+.. ..++|+++|+|+|+.||+..     +++.+|.+|+.+|..|...+..
T Consensus       186 ~LTGL~NR~~f~~~l~~~l~~~~~~~-~~~all~idId~fk~INd~~-----G~~~gD~lL~~va~~L~~~~~~  253 (342)
T 3ezu_A          186 ALTGVMTRAGFFKTVGSLAYAAQRSG-SNVGIMLIDLDYFKLVGDNY-----GHQTGDRILQLVAETITSHLRR  253 (342)
T ss_dssp             TTTCSBCHHHHHHHHHHHHHHHHHHT-CEEEEEEEEEEECCCCC----------CHHHHHHHHHHHHHHHTCCT
T ss_pred             CCCCcCCHHHHHHHHHHHHHHhhhcC-CcEEEEEEECCcHHHHHHhh-----ChHHHHHHHHHHHHHHHHHCCC
Confidence            46888888877666666655444433 37899999999999999999     6778999999999999887754

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

Probab=95.27  E-value=0.0076  Score=48.34  Aligned_cols=34  Identities=21%  Similarity=0.276  Sum_probs=29.5

Q ss_pred             HHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            8 SVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         8 e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      +...+++.+|+++||.||++.++|...|+.++..
T Consensus        92 ~~~~~~~~~g~~~~l~KP~~~~~l~~~l~~~~~~  125 (135)
T 3eqz_A           92 ETLALSCGLNVINTFTKPINTEVLTCFLTSLSNR  125 (135)
T ss_dssp             HHHHHHTTCEEEEEEESSCCHHHHHHHHHHHSCC
T ss_pred             HHHHHHcCCCcceeeCCCCCHHHHHHHHHHHHhh
Confidence            5566788999999999999999999999887654

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

Probab=95.00  E-value=0.018  Score=56.51  Aligned_cols=43  Identities=40%  Similarity=0.489  Sum_probs=35.2

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCC-CHHHHHHHHHHHHHHHh
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPL-RTNELLNLWTHMWRRRR   43 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPf-d~eELLaRVra~LrR~r   43 (445)
                      +|+..+.+...++++.||++||.||+ ..++|...|+.++++..
T Consensus        83 lt~~~~~~~~~~a~~~ga~~yl~KP~~~~~~l~~~i~~~~~~~~  126 (394)
T 3eq2_A           83 LSGAGVMSDAVEALRLGAADYLIKPLEDLAVLEHSVRRALDRAY  126 (394)
T ss_dssp             C---CHHHHHHHHHHHTCSEECCSSCSCTHHHHHHHHHHHHHHH
T ss_pred             EEcCCCHHHHHHHHhcChhhEEECCCChHHHHHHHHHHHHhhhh
Confidence            57778888899999999999999999 68899999999887653

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

Probab=94.68  E-value=0.019  Score=46.94  Aligned_cols=40  Identities=20%  Similarity=0.254  Sum_probs=30.2

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      |+.........++.+|+++||.||++.++|..+|+.++.+
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            3444444444556677899999999999999999988754

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

Probab=94.65  E-value=0.0053  Score=55.34  Aligned_cols=43  Identities=19%  Similarity=0.288  Sum_probs=38.3

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      +|+..+.+...+++++||++||.||++.++|..+|+.++++..
T Consensus        81 lt~~~~~~~~~~~~~~Ga~~~l~Kp~~~~~L~~~i~~~~~~~~  123 (225)
T 3c3w_A           81 LTSYTSDEAMLDAILAGASGYVVKDIKGMELARAVKDVGAGRS  123 (225)
T ss_dssp             GGGSSSHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHHGG
T ss_pred             EECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHcCCe
Confidence            4667778888999999999999999999999999999987653

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

Probab=94.32  E-value=0.0069  Score=49.93  Aligned_cols=38  Identities=16%  Similarity=-0.054  Sum_probs=24.9

Q ss_pred             CCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            4 QDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         4 ~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      ..+.+...+++++||++||.||++..+|..+++.....
T Consensus        98 ~~~~~~~~~~~~~ga~~~l~KP~~~~~l~~~i~~~~~l  135 (145)
T 3kyj_B           98 VSGSPHAARARELGADGVVAKPSGTVSHDLEEKTGGEL  135 (145)
T ss_dssp             STTSSHHHHHHHTTCSCCCBCCCSCC------CTTHHH
T ss_pred             cCChHHHHHHHhCCCCEEEeCCCCHHHHHHHHHHHHHH
Confidence            44455677899999999999999988888776654443

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

Probab=94.02  E-value=0.012  Score=64.07  Aligned_cols=41  Identities=7%  Similarity=-0.006  Sum_probs=35.8

Q ss_pred             CCCCc-HHHHHHHHHcCCcEEEECCCCHHH-HHHHHHHHHHHH
Q 013329            2 SAQDE-VSVVVKCLRLGAADYLVKPLRTNE-LLNLWTHMWRRR   42 (445)
Q Consensus         2 TA~~d-~e~iveALeaGAdDYLtKPfd~eE-LLaRVra~LrR~   42 (445)
                      |+..+ .++++.++..||+|||+|||+..| |++||+++++|.
T Consensus        92 Ta~~~~~~d~~~~l~~gaddyi~kpf~~~efl~~ri~a~~rr~  134 (755)
T 2vyc_A           92 GDREKALAAMDRDLLELVDEFAWILEDTADFIAGRAVAAMTRY  134 (755)
T ss_dssp             ECHHHHHHTCSHHHHHHCSEEEETTTSCHHHHHHHHHHHHHHH
T ss_pred             ecCCcchhhccHhHhhcCCceEeCCCCCHHHHHHHHHHHHHHh
Confidence            45555 667788999999999999999999 999999999886

>3pjx_A Cyclic dimeric GMP binding protein; ggdef-EAL tandem domain, C-DI-GMP receptor, lyase; 2.00A {Pseudomonas fluorescens} PDB: 3pjw_A 3pju_A* 3pjt_A* 3pfm_A

Probab=93.95  E-value=0.024  Score=56.60  Aligned_cols=67  Identities=16%  Similarity=0.219  Sum_probs=53.3

Q ss_pred             hhhCccccccccccchhhccccccCCCCeEEEEeecccchhhhhcCCCcccChHHHHhhcchhhhhhhhcccCC
Q 013329           43 RMLGLAEKNILSYDFDLVASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTSGT  116 (445)
Q Consensus        43 rLTgl~nr~iL~~gLdl~Ld~asr~n~~slaLL~lDLD~FKlINdn~g~vvSreQl~d~~l~~~A~~~a~~~~~  116 (445)
                      .+|++.|+..|...++..+.....  .....|+.+|+|+|+.||+..     +++.+|.+|+.+|..|...+..
T Consensus        22 ~LTGL~NR~~f~~~l~~~~~~~~~--~~~~~l~~idid~fk~iNd~~-----G~~~gD~lL~~va~~L~~~~~~   88 (430)
T 3pjx_A           22 NLTGLANRRYFEMQLNARVSNPEQ--ASSGYLLLLRVKDLAGLNQRL-----GGQRTDELLKAVGEQLSRECAK   88 (430)
T ss_dssp             TTTSSBCHHHHHHHHHHTTTCTTS--CSCEEEEEEEETTHHHHHHHH-----CHHHHHHHHHHHHHHHHHHHHT
T ss_pred             cccCCccHHHHHHHHHHHHhhccc--cCceEEEEEEchhhhHHHHhc-----ChHHHHHHHHHHHHHHHHHHHh
Confidence            678999988877666665554322  235679999999999999998     6889999999999999876654

>3hvw_A Diguanylate-cyclase (DGC); alpha-beta protein., structural genomics, PSI-2, protein structure initiative; 1.70A {Pseudomonas aeruginosa}

Probab=93.24  E-value=0.013  Score=50.96  Aligned_cols=63  Identities=11%  Similarity=0.017  Sum_probs=45.7

Q ss_pred             hhCccccccccccchhhccccccCCCCeEEEEeecc---cchhhhhcCCCcccChHHHHhhcchhhhhhhhcccCC
Q 013329           44 MLGLAEKNILSYDFDLVASDPSDANTNSTTLFSDDT---DDKSRRSTNPEIGMSTHQETESVPVATATVVASTSGT  116 (445)
Q Consensus        44 LTgl~nr~iL~~gLdl~Ld~asr~n~~slaLL~lDL---D~FKlINdn~g~vvSreQl~d~~l~~~A~~~a~~~~~  116 (445)
                      +|+++|+..|...++..+..     ....+|+.+++   |+|+.||+..     +++.+|.+|+.+|..|...+..
T Consensus         5 lTgL~Nr~~f~~~l~~~~~~-----~~~~~l~~i~i~~id~f~~in~~~-----G~~~gD~~L~~ia~~L~~~~~~   70 (176)
T 3hvw_A            5 PTGLYNRLRLQEDVSLRLQR-----DGALTVIAADLLPLALLNTIIRTL-----GYPFSNDLMLEARDRIRAELPD   70 (176)
T ss_dssp             ----CCHHHHHHHHHHHHHH-----HSEEEEEEEECSCHHHHHHHHHHH-----CHHHHHHHHHHHHHHHHHHCTT
T ss_pred             cCCChhHHHHHHHHHHHHhc-----CCCceEEEEEecCHHHHHHHHHHh-----CcHHHHHHHHHHHHHHHHHCCC
Confidence            56777776665554444433     23577888888   9999999998     7788999999999999887764

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

Probab=92.91  E-value=0.044  Score=42.90  Aligned_cols=29  Identities=21%  Similarity=0.281  Sum_probs=25.3

Q ss_pred             HHHHHcCCcEEEECCCCHHHHHHHHHHHH
Q 013329           11 VKCLRLGAADYLVKPLRTNELLNLWTHMW   39 (445)
Q Consensus        11 veALeaGAdDYLtKPfd~eELLaRVra~L   39 (445)
                      ..+++.|+++||.||++.++|..+|+.++
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            45678999999999999999999998764

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

Probab=92.16  E-value=0.064  Score=53.17  Aligned_cols=35  Identities=29%  Similarity=0.398  Sum_probs=31.4

Q ss_pred             HHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            8 SVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         8 e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      ....+++++||++||.|||+.++|...|+.++...
T Consensus        95 ~~~~~a~~~ga~~yl~KP~~~~~L~~~i~~~~~~~  129 (400)
T 3sy8_A           95 ISMIECLGLNFLGDLGKPFSLERITALLTRYNARR  129 (400)
T ss_dssp             HHHHHTTTCEEEEECCSSCCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHcCCeeccCcCCCcCHHHHHHHHHHHHHhh
Confidence            56678899999999999999999999999998764

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

Probab=91.68  E-value=0.09  Score=41.89  Aligned_cols=39  Identities=15%  Similarity=0.207  Sum_probs=29.6

Q ss_pred             CCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            2 SAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         2 TA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      |+..+......++..|  +||.||++.++|..+|++++...
T Consensus        86 s~~~~~~~~~~~~~~~--~~l~kP~~~~~l~~~i~~~~~~~  124 (132)
T 2rdm_A           86 SGHAALEWASNGVPDS--IILEKPFTSAQLITAVSQLLNAR  124 (132)
T ss_dssp             ESSCCTTHHHHSCTTC--EEEESSCCHHHHHHHHHHHHHTT
T ss_pred             eCCccHHHHHhhcCCc--ceEeCCCCHHHHHHHHHHHHhcC
Confidence            4444555556666665  79999999999999999988654

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

Probab=91.05  E-value=0.16  Score=41.34  Aligned_cols=28  Identities=21%  Similarity=0.318  Sum_probs=23.9

Q ss_pred             HcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329           15 RLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus        15 eaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      .+|+++||.||++.++|...|+.++...
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            6799999999999999999999887543

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

Probab=90.41  E-value=0.026  Score=48.40  Aligned_cols=27  Identities=22%  Similarity=0.252  Sum_probs=22.8

Q ss_pred             HHHcCCcEEEECCCCHHHHHHHHHHHH
Q 013329           13 CLRLGAADYLVKPLRTNELLNLWTHMW   39 (445)
Q Consensus        13 ALeaGAdDYLtKPfd~eELLaRVra~L   39 (445)
                      +.++|+++||+|||++++|.++|++++
T Consensus        94 ~~~~g~~~yl~KP~~~~~L~~~l~~~~  120 (123)
T 2lpm_A           94 DTRYSNIPLLTKPFLDSELEAVLVQIS  120 (123)
T ss_dssp             CSSSCSCSCBCSSSSHHHHHHHHSTTC
T ss_pred             HHhCCCCcEEECCCCHHHHHHHHHHHH
Confidence            346799999999999999999887654

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

Probab=90.20  E-value=0.064  Score=41.18  Aligned_cols=28  Identities=29%  Similarity=0.292  Sum_probs=24.8

Q ss_pred             HHHHcCCcEEEECCCCHHHHHHHHHHHH
Q 013329           12 KCLRLGAADYLVKPLRTNELLNLWTHMW   39 (445)
Q Consensus        12 eALeaGAdDYLtKPfd~eELLaRVra~L   39 (445)
                      .+++.|+++||.||++..+|..+|+.++
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            6788999999999999999999887654

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

Probab=90.06  E-value=0.077  Score=33.82  Aligned_cols=19  Identities=47%  Similarity=0.695  Sum_probs=15.9

Q ss_pred             HHHHHHHHHHhhcccCCCc
Q 013329          362 REAALIKFRQKRKERCFDK  380 (445)
Q Consensus       362 R~~~~~ry~eKr~~R~f~k  380 (445)
                      |.+.|+||.||||.|...+
T Consensus         1 Rk~SLqRFleKRk~R~~~~   19 (22)
T 3ogk_Q            1 RRASLHRFLEKRKDRVTSK   19 (26)
T ss_pred             CchhHHHHHHHHHHHhhcc
Confidence            5678999999999987654

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

Probab=88.77  E-value=0.077  Score=45.06  Aligned_cols=27  Identities=30%  Similarity=0.455  Sum_probs=23.5

Q ss_pred             HHHHHHHcCCcEEEECCCCHHHHHHHH
Q 013329            9 VVVKCLRLGAADYLVKPLRTNELLNLW   35 (445)
Q Consensus         9 ~iveALeaGAdDYLtKPfd~eELLaRV   35 (445)
                      ...+++++||++||.||++..+|..++
T Consensus       114 ~~~~~~~~ga~~~l~KP~~~~~l~~r~  140 (164)
T 3t8y_A          114 ITIEALRNGAVDFITKPHGSISLTFRQ  140 (164)
T ss_dssp             HHHHHHHTTCCEEEECSSSSSCGGGGG
T ss_pred             HHHHHHHcCcCEEEeCCCCHHHHHHHh
Confidence            566899999999999999998887655

>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=88.74  E-value=0.5  Score=43.89  Aligned_cols=28  Identities=25%  Similarity=0.299  Sum_probs=23.8

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRT   28 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~   28 (445)
                      +|+..+.+...+++++||+|||+||+..
T Consensus        80 lt~~~~~~~~~~a~~~Ga~dyl~Kp~~~  107 (259)
T 3luf_A           80 LTADISEDKREAWLEAGVLDYVMKDSRH  107 (259)
T ss_dssp             EECC-CHHHHHHHHHTTCCEEEECSSHH
T ss_pred             EEccCCHHHHHHHHHCCCcEEEeCCchh
Confidence            4788889999999999999999999643

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

Probab=88.19  E-value=0.36  Score=47.76  Aligned_cols=33  Identities=27%  Similarity=0.398  Sum_probs=26.2

Q ss_pred             HHHHHHHHcCCcEEEECCCCH---------HHHHHHHHHHHH
Q 013329            8 SVVVKCLRLGAADYLVKPLRT---------NELLNLWTHMWR   40 (445)
Q Consensus         8 e~iveALeaGAdDYLtKPfd~---------eELLaRVra~Lr   40 (445)
                      +...++++.||+|||.||++.         ++|+.+|+.+++
T Consensus        91 ~~~~~al~~Ga~d~l~KP~~~~~~~l~~~~~~L~~~I~~~~~  132 (349)
T 1a2o_A           91 EVTLRALELGAIDFVTKPQLGIREGMLAYSEMIAEKVRTAAR  132 (349)
T ss_dssp             HHHHHHHHHTCCEEEECSSSSCSSCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCceEEEECCCCccchhHHHHHHHHHHHHHHHHh
Confidence            447889999999999999984         667777766654

>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=85.86  E-value=0.39  Score=42.35  Aligned_cols=37  Identities=16%  Similarity=0.456  Sum_probs=30.3

Q ss_pred             CcHHHHHHHHHcCCcEEEECC--CCHHHHHHHHHHHHHH
Q 013329            5 DEVSVVVKCLRLGAADYLVKP--LRTNELLNLWTHMWRR   41 (445)
Q Consensus         5 ~d~e~iveALeaGAdDYLtKP--fd~eELLaRVra~LrR   41 (445)
                      ...+...++++.|+++||.||  ++..+|+..+...+..
T Consensus        63 ~~~~~~~~~~~~Ga~~~l~kp~~~~~~~l~~~i~~~~~~  101 (237)
T 3cwo_X           63 GQQAMVIEAIKAGAKDFIVNTAAVENPSLITQIAQTFGS  101 (237)
T ss_dssp             STHHHHHHHHHTTCCEEEESHHHHHCTHHHHHHHHHHTG
T ss_pred             CCHHHHHHHHHCCHHheEeCCcccChHHHHHHHHHHhCC
Confidence            346778899999999999999  7888888888776643

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

Probab=85.06  E-value=0.57  Score=37.72  Aligned_cols=28  Identities=32%  Similarity=0.503  Sum_probs=23.2

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRT   28 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~   28 (445)
                      +|+..+......+++.|+++||.||+..
T Consensus        92 ls~~~~~~~~~~~~~~g~~~~l~kP~~~  119 (137)
T 2pln_A           92 SSDNPTSEEEVHAFEQGADDYIAKPYRS  119 (137)
T ss_dssp             EESSCCHHHHHHHHHTTCSEEEESSCSC
T ss_pred             EeCCCCHHHHHHHHHcCCceeeeCCCCC
Confidence            3566677888899999999999999753

>3q7r_A Transcriptional regulatory protein; CHXR, receiver domain, transcription factor, OMPR, chlamydia transcription; 1.60A {Chlamydia trachomatis} PDB: 3q7s_A* 3q7t_A

Probab=81.68  E-value=2  Score=37.09  Aligned_cols=36  Identities=19%  Similarity=0.301  Sum_probs=32.4

Q ss_pred             cHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            6 EVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         6 d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      +++..++.++.||. ||..|+.+..|-+.|++.|+..
T Consensus        84 ~EEa~v~vLd~Ga~-yLlrPIT~kvldAvIraFLrqh  119 (121)
T 3q7r_A           84 DEETSVDLLDRGFW-YLIRPITPRILKSAISLFLSQH  119 (121)
T ss_dssp             CHHHHHHHHHTTCE-EEESCCCHHHHHHHHHHHHHHC
T ss_pred             chHHHHHHHhCCce-eEeccCcHHHHHHHHHHHHhcc
Confidence            56788899999999 9999999999999999988753

---

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	445
d1ny5a1	137	c.23.1.1 (A:1-137) Transcriptional activator sigm5	3e-07
d1ys7a2	121	c.23.1.1 (A:7-127) Transcriptional regulatory prot	4e-07
d1dcfa_	134	c.23.1.2 (A:) Receiver domain of the ethylene rece	5e-07
d1jbea_	128	c.23.1.1 (A:) CheY protein {Escherichia coli [TaxI	6e-07
d1qkka_	140	c.23.1.1 (A:) Transcriptional regulatory protein D	8e-07
d1zesa1	121	c.23.1.1 (A:3-123) PhoB receiver domain {Escherich	8e-07
d2a9pa1	117	c.23.1.1 (A:2-118) DNA-binding response regulator	2e-06
d1yioa2	128	c.23.1.1 (A:3-130) Response regulatory protein Sty	3e-06
d2ayxa1	133	c.23.1.1 (A:817-949) Sensor kinase protein RcsC, C	3e-06
d1p2fa2	120	c.23.1.1 (A:1-120) Response regulator DrrB {Thermo	3e-06
d1xhfa1	121	c.23.1.1 (A:2-122) Aerobic respiration control pro	5e-06
d2pl1a1	119	c.23.1.1 (A:1-119) PhoP receiver domain {Escherich	6e-06
d1mvoa_	121	c.23.1.1 (A:) PhoP receiver domain {Bacillus subti	6e-06
d1zgza1	120	c.23.1.1 (A:2-121) TorCAD operon transcriptional r	7e-06
d1zh2a1	119	c.23.1.1 (A:2-120) Transcriptional regulatory prot	7e-06
d1kgsa2	122	c.23.1.1 (A:2-123) PhoB receiver domain {Thermotog	7e-06
d1w25a1	139	c.23.1.1 (A:2-140) Response regulator PleD, receiv	8e-06
d1u0sy_	118	c.23.1.1 (Y:) CheY protein {Thermotoga maritima [T	8e-06
d1p6qa_	129	c.23.1.1 (A:) CheY protein {Sinorhizobium meliloti	9e-06
d1mb3a_	123	c.23.1.1 (A:) Cell division response regulator Div	1e-05
d1peya_	119	c.23.1.1 (A:) Sporulation response regulator Spo0F	1e-05
d1krwa_	123	c.23.1.1 (A:) NTRC receiver domain {Salmonella typ	1e-05
d1k68a_	140	c.23.1.1 (A:) Response regulator for cyanobacteria	1e-05
d1dz3a_	123	c.23.1.1 (A:) Sporulation response regulator Spo0A	1e-05
d1a04a2	138	c.23.1.1 (A:5-142) Nitrate/nitrite response regula	1e-05
d2r25b1	128	c.23.1.1 (B:1087-1214) Response regulator Sin1 {Ba	2e-05
d1dbwa_	123	c.23.1.1 (A:) Transcriptional regulatory protein F	2e-05
d1s8na_	190	c.23.1.1 (A:) Probable two-component system transc	2e-05
d1i3ca_	144	c.23.1.1 (A:) Response regulator for cyanobacteria	1e-04
d1k66a_	149	c.23.1.1 (A:) Response regulator for cyanobacteria	3e-04
d1w25a2	153	c.23.1.1 (A:141-293) Response regulator PleD, rece	3e-04

>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 = 47.3 bits (112), Expect = 3e-07
 Identities = 9/44 (20%), Positives = 20/44 (45%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRM 44
           ++    +   V+ +++GA D+L KP    E+          R++
Sbjct: 78  ITGHGTIKTAVEAMKMGAYDFLTKPCMLEEIELTINKAIEHRKL 121

>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 = 46.6 bits (110), Expect = 4e-07
 Identities = 18/42 (42%), Positives = 22/42 (52%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR 42
           +SA+  V   V  L  GA DYLVKP    EL+     + RRR
Sbjct: 79  LSARSSVDDRVAGLEAGADDYLVKPFVLAELVARVKALLRRR 120

>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 = 46.5 bits (110), Expect = 5e-07
 Identities = 9/44 (20%), Positives = 21/44 (47%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRM 44
           +S   + S   KC+  G    L+KP+  + + ++ + +   R +
Sbjct: 89  LSGNTDKSTKEKCMSFGLDGVLLKPVSLDNIRDVLSDLLEPRVL 132

>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 = 46.1 bits (109), Expect = 6e-07
 Identities = 9/44 (20%), Positives = 21/44 (47%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRM 44
           ++A+ +   ++   + GA+ Y+VKP     L      ++ +  M
Sbjct: 85  VTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEKLGM 128

>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 = 46.2 bits (109), Expect = 8e-07
 Identities = 9/45 (20%), Positives = 24/45 (53%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRML 45
           ++   ++ + V+ ++ GA D++ KP   + L+        +RR++
Sbjct: 78  VTGHGDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRAEEKRRLV 122

>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 = 45.7 bits (108), Expect = 8e-07
 Identities = 14/41 (34%), Positives = 21/41 (51%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR 41
           ++A+ E    V+ L  GA DY+ KP    EL+     + RR
Sbjct: 80  LTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRR 120

>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 = 44.6 bits (105), Expect = 2e-06
 Identities = 16/41 (39%), Positives = 20/41 (48%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR 41
           +SA+D     V  L LGA DY+ KP    EL      + RR
Sbjct: 77  LSAKDSEFDKVIGLELGADDYVTKPFSNRELQARVKALLRR 117

>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 = 44.3 bits (104), Expect = 3e-06
 Identities = 9/43 (20%), Positives = 21/43 (48%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR 43
           ++A  ++ + V+ ++ GA ++L KP     LL+      +   
Sbjct: 80  ITAHGDIPMTVRAMKAGAIEFLPKPFEEQALLDAIEQGLQLNA 122

>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 = 44.3 bits (104), Expect = 3e-06
 Identities = 10/43 (23%), Positives = 16/43 (37%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR 43
           ++A        +CL  G    L KP+  + +    T    R R
Sbjct: 86  VTANALAEEKQRCLESGMDSCLSKPVTLDVIKQTLTLYAERVR 128

>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 = 43.9 bits (103), Expect = 3e-06
 Identities = 11/43 (25%), Positives = 17/43 (39%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR 43
           ++   +   V+K    GA DY+ KP     LL        R +
Sbjct: 77  LTLLSDDESVLKGFEAGADDYVTKPFNPEILLARVKRFLEREK 119

>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 = 43.1 bits (101), Expect = 5e-06
 Identities = 11/41 (26%), Positives = 19/41 (46%)

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

>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 = 43.2 bits (101), Expect = 6e-06
 Identities = 12/41 (29%), Positives = 21/41 (51%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR 41
           ++A++     V+ L  GA DY+ KP    E++     + RR
Sbjct: 78  LTARESWQDKVEVLSAGADDYVTKPFHIEEVMARMQALMRR 118

>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 = 43.1 bits (101), Expect = 6e-06
 Identities = 15/41 (36%), Positives = 21/41 (51%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR 41
           ++A+DE    V  L LGA 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 = 43.1 bits (101), Expect = 7e-06
 Identities = 11/41 (26%), Positives = 21/41 (51%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR 41
           ++ + +    +  L +GA DY+ KPL   EL+    ++  R
Sbjct: 78  VTGRSDRIDRIVGLEMGADDYVTKPLELRELVVRVKNLLWR 118

>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 = 42.8 bits (100), Expect = 7e-06
 Identities = 16/42 (38%), Positives = 19/42 (45%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR 42
           +SA+ E S  +  L  GA DYL KP    EL        RR 
Sbjct: 77  LSARSEESDKIAALDAGADDYLSKPFGIGELQARLRVALRRH 118

>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 = 42.8 bits (100), Expect = 7e-06
 Identities = 16/42 (38%), Positives = 23/42 (54%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR 42
           ++A  +V   VK L +GA DYL KP    EL+     + RR+
Sbjct: 79  LTALSDVEYRVKGLNMGADDYLPKPFDLRELIARVRALIRRK 120

>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 = 43.3 bits (101), Expect = 8e-06
 Identities = 11/45 (24%), Positives = 22/45 (48%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRML 45
           ++A D     ++ L  GA+D+L KP+    L      + R + ++
Sbjct: 81  ITALDGRGDRIQGLESGASDFLTKPIDDVMLFARVRSLTRFKLVI 125

>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 = 42.6 bits (100), Expect = 8e-06
 Identities = 9/33 (27%), Positives = 22/33 (66%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLN 33
            SA  + ++V++ ++ GA D++VKP + + ++ 
Sbjct: 80  CSAMGQQAMVIEAIKAGAKDFIVKPFQPSRVVE 112

>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 = 42.7 bits (100), Expect = 9e-06
 Identities = 11/46 (23%), Positives = 20/46 (43%), Gaps = 6/46 (13%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLG 46
           ++AQ + ++V K   LGA + L KP    ++            + G
Sbjct: 87  LTAQGDRALVQKAAALGANNVLAKPFTIEKMKA------AIEAVFG 126

>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 = 42.3 bits (99), Expect = 1e-05
 Identities = 7/42 (16%), Positives = 14/42 (33%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR 42
           ++A        +    G   Y+ KP+     L     +  R+
Sbjct: 81  VTAFAMKGDEERIREGGCEAYISKPISVVHFLETIKRLLERQ 122

>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 = 42.2 bits (99), Expect = 1e-05
 Identities = 11/47 (23%), Positives = 22/47 (46%), Gaps = 6/47 (12%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGL 47
           M+A  E+ ++ +   LGA  +  KP   +E+ +        ++ L L
Sbjct: 79  MTAYGELDMIQESKELGALTHFAKPFDIDEIRD------AVKKYLPL 119

>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 = 42.4 bits (99), Expect = 1e-05
 Identities = 12/43 (27%), Positives = 19/43 (44%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR 43
           M+A  ++   V   + GA DYL KP   +E + L        +
Sbjct: 81  MTAHSDLDAAVSAYQQGAFDYLPKPFDIDEAVALVERAISHYQ 123

>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 = 5/42 (11%), Positives = 12/42 (28%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR 42
           +S       +     L    Y+ K    ++L  +   +    
Sbjct: 91  LSTSINEDDIFHSYDLHVNCYITKSANLSQLFQIVKGIEEFW 132

>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 = 42.1 bits (99), Expect = 1e-05
 Identities = 9/41 (21%), Positives = 21/41 (51%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR 41
           ++A  +  V  K + LGA+ +++KP     L +    ++ +
Sbjct: 82  LTAFGQEDVTKKAVELGASYFILKPFDMENLAHHIRQVYGK 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 = 42.6 bits (100), Expect = 1e-05
 Identities = 12/45 (26%), Positives = 18/45 (40%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRML 45
            S  +    VV  L+ GA  YL+K +   +LL           +L
Sbjct: 82  FSVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALHQAAAGEMVL 126

>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 = 41.9 bits (98), Expect = 2e-05
 Identities = 9/34 (26%), Positives = 19/34 (55%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNL 34
           ++A  + S + +CL  G   +L KP++  +L  +
Sbjct: 86  LTAFADDSNIKECLESGMNGFLSKPIKRPKLKTI 119

>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 = 41.6 bits (97), Expect = 2e-05
 Identities = 7/33 (21%), Positives = 18/33 (54%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLN 33
           ++   +V + V+ ++ GA D++ KP     ++ 
Sbjct: 81  ITGHGDVPMAVEAMKAGAVDFIEKPFEDTVIIE 113

>d1s8na_ c.23.1.1 (A:) Probable two-component system transcriptional regulator Rv1626 {Mycobacterium tuberculosis [TaxId: 1773]} Length = 190

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Probable two-component system transcriptional regulator Rv1626
species: Mycobacterium tuberculosis [TaxId: 1773]

 Score = 42.9 bits (100), Expect = 2e-05
 Identities = 14/59 (23%), Positives = 25/59 (42%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDL 59
           ++A  +  +V +    GA  YLVKP   ++L+        R R +   E  + +    L
Sbjct: 81  LTAFSQRDLVERARDAGAMAYLVKPFSISDLIPAIELAVSRFREITALEGEVATLSERL 139

>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 = 6/42 (14%), Positives = 12/42 (28%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR 42
           ++       V+    L    YL K     +L  +   +    
Sbjct: 92  LTTSHNEDDVIASYELHVNCYLTKSRNLKDLFKMVQGIESFW 133

>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 = 38.6 bits (89), Expect = 3e-04
 Identities = 8/41 (19%), Positives = 14/41 (34%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR 41
           M+       +  C     + Y+VKPL  + L        + 
Sbjct: 98  MTTSSNPKDIEICYSYSISSYIVKPLEIDRLTETVQTFIKY 138

>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 = 38.9 bits (90), Expect = 3e-04
 Identities = 17/63 (26%), Positives = 27/63 (42%), Gaps = 1/63 (1%)

Query: 1   MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRMLGLAEKNILSYDFDLV 60
           M   D+   +VK L +G  D L +P+   EL        +R+R       N L +  +L 
Sbjct: 91  MVDPDDRGRMVKALEIGVNDILSRPIDPQELSARVKTQIQRKRYTDYLRNN-LDHSLELA 149

Query: 61  ASD 63
            +D
Sbjct: 150 VTD 152

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	445
d1zgza1	120	TorCAD operon transcriptional regulator TorD, N-te	98.06
d2pl1a1	119	PhoP receiver domain {Escherichia coli [TaxId: 562	98.03
d1xhfa1	121	Aerobic respiration control protein ArcA, N-termin	98.03
d1zh2a1	119	Transcriptional regulatory protein KdpE, N-termina	98.02
d1p2fa2	120	Response regulator DrrB {Thermotoga maritima [TaxI	97.99
d2a9pa1	117	DNA-binding response regulator MicA, N-terminal do	97.98
d1kgsa2	122	PhoB receiver domain {Thermotoga maritima [TaxId:	97.87
d1w25a2	153	Response regulator PleD, receiver domain {Caulobac	97.87
d1w25a1	139	Response regulator PleD, receiver domain {Caulobac	97.86
d1zesa1	121	PhoB receiver domain {Escherichia coli [TaxId: 562	97.82
d1mvoa_	121	PhoP receiver domain {Bacillus subtilis [TaxId: 14	97.81
d1krwa_	123	NTRC receiver domain {Salmonella typhimurium [TaxI	97.8
d1qkka_	140	Transcriptional regulatory protein DctD, receiver	97.8
d1ys7a2	121	Transcriptional regulatory protein PrrA, N-termina	97.77
d1ny5a1	137	Transcriptional activator sigm54 (NtrC1), N-termin	97.67
d1dbwa_	123	Transcriptional regulatory protein FixJ, receiver	97.64
d1jbea_	128	CheY protein {Escherichia coli [TaxId: 562]}	97.6
d1i3ca_	144	Response regulator for cyanobacterial phytochrome	97.52
d1yioa2	128	Response regulatory protein StyR, N-terminal domai	97.51
d2ayxa1	133	Sensor kinase protein RcsC, C-terminal domain {Esc	97.51
d1peya_	119	Sporulation response regulator Spo0F {Bacillus sub	97.51
d1p6qa_	129	CheY protein {Sinorhizobium meliloti, CheY2 [TaxId	97.5
d1k68a_	140	Response regulator for cyanobacterial phytochrome	97.42
d1k66a_	149	Response regulator for cyanobacterial phytochrome	97.41
d1s8na_	190	Probable two-component system transcriptional regu	97.41
d1dz3a_	123	Sporulation response regulator Spo0A {Bacillus ste	97.36
d1mb3a_	123	Cell division response regulator DivK {Caulobacter	97.34
d1qo0d_	189	Positive regulator of the amidase operon AmiR {Pse	97.31
d2r25b1	128	Response regulator Sin1 {Baker's yeast (Saccharomy	97.3
d1a04a2	138	Nitrate/nitrite response regulator (NarL), receive	97.18
d1dcfa_	134	Receiver domain of the ethylene receptor {Thale cr	97.04
d1w25a3	162	Response regulator PleD, C-terminal domain {Caulob	95.25
d2b4aa1	118	Hypothetical protein BH3024 {Bacillus halodurans [	92.48
d1a2oa1	140	Methylesterase CheB, N-terminal domain {Salmonella	91.88

>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=98.06  E-value=1.7e-06  Score=70.82  Aligned_cols=42  Identities=26%  Similarity=0.397  Sum_probs=39.0

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      +|+..+.....+|+++||+|||+|||++.+|+++|+++|+|.
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            478888999999999999999999999999999999999874

>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=98.03  E-value=2.6e-06  Score=70.21  Aligned_cols=41  Identities=29%  Similarity=0.514  Sum_probs=38.3

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      +|+..+.+...+++++||++||+|||+.++|+++|+++++|
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            47888889999999999999999999999999999999976

>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=98.03  E-value=2.2e-06  Score=70.87  Aligned_cols=41  Identities=27%  Similarity=0.435  Sum_probs=38.4

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      +|+..+.....+++++||+|||+|||++++|+++|+++|+|
T Consensus        79 lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~v~~~l~R  119 (121)
T d1xhfa1          79 LTGRDNEVDKILGLEIGADDYITKPFNPRELTIRARNLLSR  119 (121)
T ss_dssp             EESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHHHH
T ss_pred             EECCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHhc
Confidence            47888899999999999999999999999999999999976

>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=98.02  E-value=2.5e-06  Score=70.20  Aligned_cols=42  Identities=38%  Similarity=0.472  Sum_probs=38.8

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      ||+..+.+...+|+++||+|||+|||+.++|+++|+++|+|+
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            477888899999999999999999999999999999999874

>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=97.99  E-value=2.5e-06  Score=70.36  Aligned_cols=43  Identities=26%  Similarity=0.433  Sum_probs=39.4

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      +|+.++.+...+|+++||+|||+|||++++|+.+|+++|++.+
T Consensus        77 it~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~l~r~r  119 (120)
T d1p2fa2          77 LTLLSDDESVLKGFEAGADDYVTKPFNPEILLARVKRFLEREK  119 (120)
T ss_dssp             EESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHHHHCC
T ss_pred             EecCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHcc
Confidence            4778889999999999999999999999999999999998753

>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=97.98  E-value=2.6e-06  Score=69.87  Aligned_cols=41  Identities=39%  Similarity=0.491  Sum_probs=37.7

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      +|+..+.....+++++||+|||+|||++++|+++|+++|+|
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            47788888999999999999999999999999999999864

>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=97.87  E-value=3.4e-06  Score=69.50  Aligned_cols=42  Identities=38%  Similarity=0.578  Sum_probs=39.0

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      +|+..+.....+++++||++||+|||++++|+++|+++++++
T Consensus        79 lt~~~~~~~~~~~~~~Ga~~yl~KP~~~~~L~~~i~~~l~r~  120 (122)
T d1kgsa2          79 LTALSDVEYRVKGLNMGADDYLPKPFDLRELIARVRALIRRK  120 (122)
T ss_dssp             EESSCHHHHHHHTCCCCCSEEEESSCCHHHHHHHHHHHHHHH
T ss_pred             EcCCCCHHHHHHHHHcCCceeecCCCCHHHHHHHHHHHHHHh
Confidence            478888999999999999999999999999999999999875

>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=97.87  E-value=6.9e-06  Score=70.55  Aligned_cols=44  Identities=30%  Similarity=0.458  Sum_probs=40.5

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhh
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRM   44 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~rL   44 (445)
                      +|+..+.....+|+++||+|||+|||++.+|+++|+.+|++.+.
T Consensus        91 lt~~~~~~~~~~a~~~Ga~d~l~KP~~~~~L~~~i~~~l~~~~~  134 (153)
T d1w25a2          91 MVDPDDRGRMVKALEIGVNDILSRPIDPQELSARVKTQIQRKRY  134 (153)
T ss_dssp             EECTTCHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHHHHHHH
T ss_pred             eecCCCHHHHHHHHhcCcceEEECCCCHHHHHHHHHHHHHHHHH
Confidence            47888999999999999999999999999999999999987753

>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=97.86  E-value=7.1e-06  Score=69.07  Aligned_cols=43  Identities=26%  Similarity=0.326  Sum_probs=39.6

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      +|+..+.....+|+++||+|||.|||+..+|+++|+++++++.
T Consensus        81 lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~lr~~~  123 (139)
T d1w25a1          81 ITALDGRGDRIQGLESGASDFLTKPIDDVMLFARVRSLTRFKL  123 (139)
T ss_dssp             EECSSCHHHHHHHHHHTCCEEEESSCCHHHHHHHHHHHHHHHH
T ss_pred             EEcCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHHHHHH
Confidence            4788899999999999999999999999999999999997754

>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=97.82  E-value=7.8e-06  Score=67.15  Aligned_cols=41  Identities=34%  Similarity=0.524  Sum_probs=38.2

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      +|+..+.....+|+++||+|||+|||+.++|+++|+.+|+|
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            47888999999999999999999999999999999999875

>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=97.81  E-value=4.2e-06  Score=68.66  Aligned_cols=41  Identities=37%  Similarity=0.486  Sum_probs=36.5

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      +|+..+.+...+|+++||++||.|||++++|+++|+++|+|
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            36667777788999999999999999999999999999975

>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=97.80  E-value=5.3e-06  Score=68.49  Aligned_cols=42  Identities=29%  Similarity=0.449  Sum_probs=39.5

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      +|+..+.+...+|+++||++||.|||+.++|+.+|+++|+++
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            688899999999999999999999999999999999999875

>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=97.80  E-value=1e-05  Score=68.26  Aligned_cols=44  Identities=20%  Similarity=0.493  Sum_probs=40.7

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhh
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRM   44 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~rL   44 (445)
                      +|+..+.+...+|+++||+|||+|||+.++|+.+|++++++.++
T Consensus        78 lT~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~~~~~~~  121 (140)
T d1qkka_          78 VTGHGDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRAEEKRRL  121 (140)
T ss_dssp             EECGGGHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHHHHHHH
T ss_pred             EECCCCHHHHHHHHHcCCCEeecCCCCHHHHHHHHHHHHHHHHH
Confidence            57889999999999999999999999999999999999987654

>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=97.77  E-value=2.1e-06  Score=71.01  Aligned_cols=42  Identities=43%  Similarity=0.559  Sum_probs=37.9

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      +|+..+.+...+|+++||+|||+|||++++|+++|+++|+|+
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            467777788889999999999999999999999999999875

>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=97.67  E-value=1.6e-05  Score=66.69  Aligned_cols=44  Identities=20%  Similarity=0.437  Sum_probs=40.1

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHhh
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRRM   44 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~rL   44 (445)
                      ||+..+.+...+|+++||+|||+|||++++|..+|++++++.++
T Consensus        78 lT~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~l~~~~~  121 (137)
T d1ny5a1          78 ITGHGTIKTAVEAMKMGAYDFLTKPCMLEEIELTINKAIEHRKL  121 (137)
T ss_dssp             EEETTCHHHHHHHHTTTCCEEEEESCCHHHHHHHHHHHHHHHHH
T ss_pred             EECCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHHHHHH
Confidence            57888999999999999999999999999999999999877653

>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=97.64  E-value=2e-05  Score=65.10  Aligned_cols=41  Identities=17%  Similarity=0.456  Sum_probs=37.5

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      +|+..+.+...+|+++||++||.|||+.++|+.+|++++++
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            57888999999999999999999999999999999988753

>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=97.60  E-value=3.5e-05  Score=63.75  Aligned_cols=42  Identities=19%  Similarity=0.423  Sum_probs=39.2

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      ||+..+.+...+++++|+++||+|||+..+|..+|+.++++.
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            578889999999999999999999999999999999999875

>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=97.52  E-value=4.8e-05  Score=64.29  Aligned_cols=42  Identities=14%  Similarity=0.180  Sum_probs=38.4

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      ||+..+.+...+|+++||++||+|||+.++|+++|+.+++..
T Consensus        92 lT~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~i~~l~~~~  133 (144)
T d1i3ca_          92 LTTSHNEDDVIASYELHVNCYLTKSRNLKDLFKMVQGIESFW  133 (144)
T ss_dssp             EESCCCHHHHHHHHHTTCSEEEECCSSHHHHHHHHHHHHHHH
T ss_pred             EECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHH
Confidence            578889999999999999999999999999999999887654

>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=97.51  E-value=1.5e-05  Score=65.87  Aligned_cols=43  Identities=21%  Similarity=0.478  Sum_probs=37.9

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      ||+.++.+...+++++||+|||+|||+.++|+.+|+++|++.+
T Consensus        80 lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~l~~~~  122 (128)
T d1yioa2          80 ITAHGDIPMTVRAMKAGAIEFLPKPFEEQALLDAIEQGLQLNA  122 (128)
T ss_dssp             EESCTTSCCCHHHHHTTEEEEEESSCCHHHHHHHHHHHHHHHH
T ss_pred             EEEECCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHHH
Confidence            4677777778899999999999999999999999999997654

>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=97.51  E-value=4.3e-05  Score=63.78  Aligned_cols=43  Identities=23%  Similarity=0.302  Sum_probs=39.0

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      +|+..+.+...+++++||++||+|||+.++|..+|+.++++.+
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            4778888899999999999999999999999999999987765

>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=97.51  E-value=3.6e-05  Score=63.08  Aligned_cols=39  Identities=23%  Similarity=0.373  Sum_probs=35.9

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMW   39 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~L   39 (445)
                      +|+..+.+...+|+++||++||+|||+.++|+.+|+++|
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            478888999999999999999999999999999998865

>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=97.50  E-value=4.1e-05  Score=63.51  Aligned_cols=41  Identities=24%  Similarity=0.400  Sum_probs=38.1

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      +|+..+.+...+++++|+++||+|||+.++|+++|++++.+
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            58888999999999999999999999999999999998864

>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=97.42  E-value=7.7e-05  Score=62.72  Aligned_cols=42  Identities=12%  Similarity=0.124  Sum_probs=38.2

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      +|+..+.+...+|+++||++||+||++..+|+.+|+.+++..
T Consensus        91 ls~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~i~~i~~~~  132 (140)
T d1k68a_          91 LSTSINEDDIFHSYDLHVNCYITKSANLSQLFQIVKGIEEFW  132 (140)
T ss_dssp             EESCCCHHHHHHHHHTTCSEEEECCSSHHHHHHHHHHHHHHH
T ss_pred             EeCCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHH
Confidence            477888999999999999999999999999999999987654

>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=97.41  E-value=7.8e-05  Score=63.29  Aligned_cols=43  Identities=19%  Similarity=0.331  Sum_probs=39.5

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      +|+..+.+...+++++||++||+||++..+|..+|+.+++...
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            4788899999999999999999999999999999999998653

>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=97.41  E-value=2.9e-05  Score=67.88  Aligned_cols=43  Identities=28%  Similarity=0.389  Sum_probs=39.5

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHHh
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRRR   43 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~r   43 (445)
                      +|+.++.+...+|+++||+|||+||+++++|+.+|+.++.+.+
T Consensus        81 lTa~~~~~~~~~al~~Ga~~yl~KP~~~~~L~~~i~~~~~~~~  123 (190)
T d1s8na_          81 LTAFSQRDLVERARDAGAMAYLVKPFSISDLIPAIELAVSRFR  123 (190)
T ss_dssp             EEEGGGHHHHHTTGGGSCEEEEEESCCHHHHHHHHHHHHHHHH
T ss_pred             EeCCCCHHHHHHHHHcCCCEeccCCCCHHHHHHHHHHHHHhhH
Confidence            5788999999999999999999999999999999999887654

>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=97.36  E-value=3.9e-05  Score=63.10  Aligned_cols=41  Identities=22%  Similarity=0.452  Sum_probs=36.8

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      +|+..+.....+++++||++||.|||+.++|+.+|+.++++
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            46778888889999999999999999999999999988753

>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=97.34  E-value=3.3e-05  Score=63.23  Aligned_cols=41  Identities=17%  Similarity=0.227  Sum_probs=31.9

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      +|+........+++++|+++||.|||+..+|+.+|+++|++
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            46667777788899999999999999999999999999864

>d1qo0d_ c.23.1.3 (D:) Positive regulator of the amidase operon AmiR {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: Positive regulator of the amidase operon AmiR
domain: Positive regulator of the amidase operon AmiR
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=97.31  E-value=8.5e-05  Score=63.90  Aligned_cols=42  Identities=14%  Similarity=0.283  Sum_probs=38.4

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      ||+..+.+...+|+++||+|||+|||+..+|+..|+.++...
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            578899999999999999999999999999999999887654

>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=97.30  E-value=6.5e-05  Score=62.50  Aligned_cols=40  Identities=25%  Similarity=0.481  Sum_probs=36.5

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWR   40 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~Lr   40 (445)
                      +|+..+.....+++++||++||+|||+..+|...|+.++.
T Consensus        86 lT~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~~~  125 (128)
T d2r25b1          86 LTAFADDSNIKECLESGMNGFLSKPIKRPKLKTILTEFCA  125 (128)
T ss_dssp             EESCCSHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHCT
T ss_pred             EECCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHHH
Confidence            4788899999999999999999999999999999987754

>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=97.18  E-value=0.00019  Score=59.70  Aligned_cols=42  Identities=26%  Similarity=0.383  Sum_probs=37.8

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRRR   42 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR~   42 (445)
                      +|+..+.+...+++++||++||.||+++++|+..|+++++..
T Consensus        82 lt~~~~~~~~~~a~~~Ga~~yl~Kp~~~~~L~~~i~~v~~g~  123 (138)
T d1a04a2          82 FSVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALHQAAAGE  123 (138)
T ss_dssp             EECCCCHHHHHHHHHTTCSEEEETTCCHHHHHHHHHHHHHSC
T ss_pred             EEEECCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHHCCC
Confidence            467788889999999999999999999999999999988653

>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=97.04  E-value=0.00019  Score=59.72  Aligned_cols=41  Identities=20%  Similarity=0.461  Sum_probs=37.0

Q ss_pred             CCCCCcHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Q 013329            1 MSAQDEVSVVVKCLRLGAADYLVKPLRTNELLNLWTHMWRR   41 (445)
Q Consensus         1 LTA~~d~e~iveALeaGAdDYLtKPfd~eELLaRVra~LrR   41 (445)
                      +|+..+.+...+++++|+++||.|||+.++|...|+.+++.
T Consensus        89 lT~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~l~~  129 (134)
T d1dcfa_          89 LSGNTDKSTKEKCMSFGLDGVLLKPVSLDNIRDVLSDLLEP  129 (134)
T ss_dssp             EESCCSHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHHSC
T ss_pred             EeCCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHhhh
Confidence            47788888999999999999999999999999999988754

>d1w25a3 d.58.29.2 (A:294-455) Response regulator PleD, C-terminal domain {Caulobacter crescentus [TaxId: 155892]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: Nucleotide cyclase
family: GGDEF domain
domain: Response regulator PleD, C-terminal domain
species: Caulobacter crescentus [TaxId: 155892]

Probab=95.25  E-value=0.002  Score=53.21  Aligned_cols=67  Identities=15%  Similarity=0.127  Sum_probs=54.4

Q ss_pred             hhCccccccccccchhhccccccCCCCeEEEEeecccchhhhhcCCCcccChHHHHhhcchhhhhhhhcccCC
Q 013329           44 MLGLAEKNILSYDFDLVASDPSDANTNSTTLFSDDTDDKSRRSTNPEIGMSTHQETESVPVATATVVASTSGT  116 (445)
Q Consensus        44 LTgl~nr~iL~~gLdl~Ld~asr~n~~slaLL~lDLD~FKlINdn~g~vvSreQl~d~~l~~~A~~~a~~~~~  116 (445)
                      |||++|+..|...++..+.+..+.. ..++|+.+++|+|+.||+..     +++.++..|+.+|..|...+.+
T Consensus         1 LTGL~Nr~~f~~~l~~~l~~~~~~~-~~~~l~~i~id~~~~in~~~-----G~~~~d~ll~~~a~~l~~~~~~   67 (162)
T d1w25a3           1 LTGLHNRRYMTGQLDSLVKRATLGG-DPVSALLIDIDFFKKINDTF-----GHDIGDEVLREFALRLASNVRA   67 (162)
T ss_dssp             TTCCBCHHHHHHHHHHHHHHHHTSS-CCCEEEEEEETTHHHHHHHS-----CHHHHHHHHHHHHHHHHHTSCT
T ss_pred             CCCchHHHHHHHHHHHHHHHHHhcC-CCEEEEEeccccchhccccc-----cccccchhhhhhhhhhhhccCC
Confidence            5788888888777777776655444 37889999999999999888     6778899999999999988754

>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=92.48  E-value=0.017  Score=46.70  Aligned_cols=26  Identities=23%  Similarity=0.243  Sum_probs=21.2

Q ss_pred             HHHHcCCcEEEECCCCHHHHHHHHHHH
Q 013329           12 KCLRLGAADYLVKPLRTNELLNLWTHM   38 (445)
Q Consensus        12 eALeaGAdDYLtKPfd~eELLaRVra~   38 (445)
                      +++..|+ |||+|||++++|+++|+.+
T Consensus        90 ~~~~~~~-dyl~KP~~~~eL~~~i~~~  115 (118)
T d2b4aa1          90 ESSEHNL-SYLQKPFAISELRAAIDYH  115 (118)
T ss_dssp             CCSSSCE-EEEESSCCHHHHHHHHHHT
T ss_pred             HHhhcCC-CEEECCCCHHHHHHHHHHH
Confidence            4445666 8999999999999999763

>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=91.88  E-value=0.077  Score=43.47  Aligned_cols=21  Identities=38%  Similarity=0.680  Sum_probs=17.8

Q ss_pred             HHHHHHHHHcCCcEEEECCCC
Q 013329            7 VSVVVKCLRLGAADYLVKPLR   27 (445)
Q Consensus         7 ~e~iveALeaGAdDYLtKPfd   27 (445)
                      .+...+|+++||++||.||+.
T Consensus        90 ~~~~~~al~~Ga~~yl~KP~~  110 (140)
T d1a2oa1          90 SEVTLRALELGAIDFVTKPQL  110 (140)
T ss_dssp             HHHHHHHHHHTCCEEEECSSS
T ss_pred             hHHHHHHHHcCCCEEEECCCC
Confidence            346678999999999999964