Citrus Sinensis ID: 043479

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530----
Protein Sequence
VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDDLKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPKVAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAEQGASAMGKTLALRSSFASGHVSMMLQEAHEFSQVRDQQQQMRTSAFLPGYASGVSALNGTTFGSIGFPSLGASSSSSVPQPGLMGNQANFPQSLFGNTRNPLYQANSAGKTCGSSGSNATEANPLSRGGLAAGLMNQMYQQKSQLRPNPYDNYNIGASSSKGFGTSGWSSSSNTSGLDQNMGTIKNNTYSNYAGIRLNDDGELIPAGQTSLINGNGLNGGYGFISGTSGIMANAAFGHLTPGASSSSARFDNATYQIPSAFAGVNEQENTSMLSQLSSQQQYGPGNNAQNDFTNFAPINNASVNGNTAQPERLGE
Secondary Structure (PSIPRED)
cccccHHHHHHHHHHcccccEEEEEcccccccHHHHHHHHHHHcccccEEEEEccccHHHHHHHHHccccEEEEccccHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHcccccccHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccHHHHHHHHHHHHHccHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHHHcccccEEEEEcccccccHHHHHHHHHHHHccccEEEEEccccccHHHHHHHccHHHHEEccccHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEcHHHHHHHHHHHHHHcccccccHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccHcccccccccccccccccccccccHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHcc
Coil and Loop (DISEMBL)
VTVTRPVEALATVRIQRDIDLVVtdlhmpemngIELQKEINEEfthlpvmvmssdDRESVIMKALASGVAfyilkplnpddlKNVWQYAMTYKKAksisideigsfelagfsagkfslddivsrssvnernknnkdskrkaskkdkgkqtkqnatapkkpkvawTDSLHNRFLQAIRHIGLEKAVPKKILEfmnvpgltreNVASHLQKYRIFLKRVAEQGASAMGKTLALRSSFASGHVSMMLQEAHEFSQVRDQQQQMRtsaflpgyasgvsalngttfgsigfpslgasssssvpqpglmgnqanfpqslfgntrnplyqansagktcgssgsnateanplsrgGLAAGLMNQMYQqksqlrpnpydnynigassskgfgtsgwssssntsgldqnmgtiknntysnyagirlnddgelipagqtslingnglnggygfisgtsgimanaafghltpgassssarfdnatyqipsafagvneqeNTSMLSQLssqqqygpgnnaqndftnfapinnasvngntaqperlge
Flexible Loop (DISEMBL)
vtvtrpvealatvriqrdidlVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDDLKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKfslddivsrssvnernknnkdskrkaskkdkgkqtkqnatapkkpkvawtDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAEQGASAMGKTLALRSSFASGHVSMMLQEAHEFSQVRDQQQQMRTSAFLPGYASGVSALNGTTFGSIGFPSLGASSSSSVPQPGLMGNQANFPQSLFGNTRNPLYQANSAGKTCGSSGSNATEANPLSRGGLAAGLMNQMYQQKSQLRPNPYDNYNIGASSSKGFGTSGWSSSSNTSGLDQNMGTIKNNTYSNYAGIRLNDDGELIPAGQTSLINGNGLNGGYGFISGTSGIMANAAFGHLTPGASSSSARFDNATYQIPSAFAGVNEQENTSMLSQLSSQQQYGPGNNAQNDFTNFAPINNasvngntaqperlge
Low Complexity Region (SEG)
VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDDLKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNErnknnkdskrkaskkdkgkQTKQNATAPKKPKVAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAEQGASAMGKTLALRSSFASGHVSMMLQEAHEFSQVRDQQQQMRTSAFLPGYASGVSALNGTTFGsigfpslgasssssvpqpgLMGNQANFPQSLFGNTRNPLYQANSAGKTCGSSGSNATEANPLSRGGLAAGLMNQMYQQKSQLRPNPYDNYNIGAssskgfgtsgwssssntsgLDQNMGTIKNNTYSNYAGIRLNDDGELIPAGQTslingnglnggygfisgTSGIMANAAFGHLTPGASSSSARFDNATYQIPSAFAGVNEQENTsmlsqlssqqqYGPGNNAQNDFTNFAPINNASVNGNTAQPERLGE
Disordered region (IsUnstruct)
*******EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDDLKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDI****************************************VAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAEQGA******L***********************************FLPGYASGVSALNGTTFGSIGF********************************************************************************************************************IKNNTYSNYAGIRLNDDGELIPAGQTSLINGNGLNGGYGFISGTSGIMANAAFGHL****************************************************************************
Disordered Region (DISOPRED)
VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDDLKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSL***************NKDSKRKASKKDKGKQTKQNATAPKKPKVAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKY***********************************************************************************************************************************************************************************************************************************************************************************************************DFTNFA*******************
Disordered Region (DISEMBL)
VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDDLKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSV**********************************VAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAEQGASAMGKTLALRSSFASGHVSMMLQEAH***********MRTSAFLPGYASGVSALNGTTFGSIGFPSL*********QPGLMGNQANFPQSLFGNTRNPLYQAN****************NPLSRGGLAAGLMNQMYQQKSQLRPNPYDNYNIGASSSK**************GLDQNMGTIKNNTYSNYAGIRLNDDGELIPAGQTSLINGNGLNGGYGFISGTSGIMANAAFGHLTPGASSSSARFDNATYQIPSAFAGVNEQENTSMLSQLSSQQQYGPGNNAQNDFTNFAPINNASVNGN*********
Disordered Region (DISPRO)
VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDDLKNVWQYAMTYKKA**************************************************************KKPKVAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAEQ**************************************************SGVS*L*****************S***************PQ*L***********************************************************************************DQNMGTIKNNTYSNYAGI*********************LNGGYGFISGTSG**A*************SSARFDNATYQIPSAFAGVN*QENTSMLSQLSSQQQ*GPG*NAQNDFTNF********************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDDLKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPKVAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAEQGASAMGKTLALRSSFASGHVSMMLQEAHEFSQVRDQQQQMRTSAFLPGYASGVSALNGTTFGSIGFPSLGASSSSSVPQPGLMGNQANFPQSLFGNTRNPLYQANSAGKTCGSSGSNATEANPLSRGGLAAGLMNQMYQQKSQLRPNPYDNYNIGASSSKGFGTSGWSSSSNTSGLDQNMGTIKNNTYSNYAGIRLNDDGELIPAGQTSLINGNGLNGGYGFISGTSGIMANAAFGHLTPGASSSSARFDNATYQIPSAFAGVNEQENTSMLSQLSSQQQYGPGNNAQNDFTNFAPINNASVNGNTAQPERLGE
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	534	2.2.26 [Sep-21-2011]
Q9LYP5	613	Putative two-component re	yes	no	0.440	0.383	0.432	4e-50
Q9ZVD3	572	Putative two-component re	no	no	0.438	0.409	0.408	2e-44
Q9ZWJ9	664	Two-component response re	no	no	0.398	0.320	0.418	1e-42
Q940D0	690	Two-component response re	no	no	0.385	0.298	0.400	2e-42
Q8L9Y3	382	Two-component response re	no	no	0.387	0.541	0.377	1e-35
O49397	552	Two-component response re	no	no	0.400	0.387	0.362	2e-33
P62598	596	Two-component response re	no	no	0.391	0.350	0.353	2e-31
Q9FXD6	521	Two-component response re	no	no	0.378	0.387	0.367	1e-30
Q9FGT7	635	Two-component response re	no	no	0.387	0.325	0.343	2e-29
Q9LZJ8	426	Putative two-component re	no	no	0.355	0.446	0.342	1e-24

>sp|Q9LYP5|ARR21_ARATH Putative two-component response regulator ARR21 OS=Arabidopsis thaliana GN=ARR21 PE=2 SV=3

 Score =  199 bits (507), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 115/266 (43%), Positives = 158/266 (59%), Gaps = 31/266 (11%)

Query: 1   VTVTRPVEALATVRIQRD-IDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRES 59
           + V  P +AL+T++IQRD IDL++TD +MP MNG++L+K+I +EF +LPV+VMSSD  + 
Sbjct: 43  IAVDDPKKALSTLKIQRDNIDLIITDYYMPGMNGLQLKKQITQEFGNLPVLVMSSDTNKE 102

Query: 60  VIMKALASGVAFYILKPLNPDDLKNVWQYAMTYK-------------KAKSISIDEIGSF 106
              ++L+ G   +I KP++P DL  ++Q+A++ K             K   +S+ +  + 
Sbjct: 103 --EESLSCGAMGFIPKPIHPTDLTKIYQFALSNKRNGKSTLSTEQNHKDADVSVPQQITL 160

Query: 107 ELAGFSAGKFSLDDIVSRSSVNERNKNN-----KDSKRKASKK-------DKGKQTKQNA 154
                   K    +   +S     N  N      D  RK  K+       D G+   Q A
Sbjct: 161 VPEQADVLKTKRKNCSFKSDSRTVNSTNGSCVSTDGSRKNRKRKPNGGPSDDGESMSQPA 220

Query: 155 TAPKKPKVAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFL 214
              KK K+ WTDSLH+ FLQAIRHIGL+KAVPKKIL FM+VP LTRENVASHLQKYRIFL
Sbjct: 221 ---KKKKIQWTDSLHDLFLQAIRHIGLDKAVPKKILAFMSVPYLTRENVASHLQKYRIFL 277

Query: 215 KRVAEQGASAMGKTLALRSSFASGHV 240
           +RVAEQG  +M     + S F   H+
Sbjct: 278 RRVAEQGLYSMLSDRGIDSMFRQTHI 303

Putative transcriptional activator that binds specifically to the DNA sequence 5'-[AG]GATT-3'. Functions as response regulator involved in His-to-Asp phosphorelay signal transduction system. Phosphorylation of the Asp residue in the receiver domain activates the ability of the protein to promote the transcription of target genes. Could directly activate some type-A response regulators in response to cytokinins.
Arabidopsis thaliana (taxid: 3702)

>sp|Q9ZVD3|ARR13_ARATH Putative two-component response regulator ARR13 OS=Arabidopsis thaliana GN=ARR13 PE=2 SV=2

 Score =  180 bits (457), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 109/267 (40%), Positives = 149/267 (55%), Gaps = 33/267 (12%)

Query: 1   VTVTRPVEALATVRIQRD-IDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRES 59
           + V  P +AL+T++ QRD IDL++TD +MP MNG++L+K+I +EF +L V+VMSSD  + 
Sbjct: 46  IAVDYPKKALSTLKNQRDNIDLIITDYYMPGMNGLQLKKQITQEFGNLSVLVMSSDPNKE 105

Query: 60  VIMKALASGVAFYILKPLNPDDLKNVWQYAMTYKK-------------------AKSISI 100
              ++L+ G   +I KP+ P DL  ++Q+A+TYK+                    + I +
Sbjct: 106 --EESLSCGAMGFIPKPIAPTDLPKIYQFALTYKRNGKSTLSTEQNQKDANVSVPQQIML 163

Query: 101 DEIGSFELAGFSAGKFSLDDI-------VSRSSVNERNKNNKDSKRKASKKDKGKQTKQN 153
               ++ L        S  D        VS  S N   KN K  K K    D G+   Q 
Sbjct: 164 VPEQAYVLKTKKKNCSSKSDTRTVNSTNVSHVSTNGSRKNRK-RKPKGGPSDDGESLSQ- 221

Query: 154 ATAPKKPKVAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIF 213
              PKK K+ WT+ L + FLQAI+HIG +K VPKKIL  MNVP LTRENVASHLQKYR+F
Sbjct: 222 --PPKKKKIWWTNPLQDLFLQAIQHIGYDKVVPKKILAIMNVPYLTRENVASHLQKYRLF 279

Query: 214 LKRVAEQGASAMGKTLALRSSFASGHV 240
           +KRV  QG  +M       S F   H+
Sbjct: 280 VKRVVHQGRFSMLSDRGKDSMFRQTHI 306

Putative transcriptional activator that binds specifically to the DNA sequence 5'-[AG]GATT-3'. Functions as response regulator involved in His-to-Asp phosphorelay signal transduction system. Phosphorylation of the Asp residue in the receiver domain activates the ability of the protein to promote the transcription of target genes. Could directly activate some type-A response regulators in response to cytokinins.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9ZWJ9|ARR2_ARATH Two-component response regulator ARR2 OS=Arabidopsis thaliana GN=ARR2 PE=1 SV=1

 Score =  174 bits (442), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 92/220 (41%), Positives = 143/220 (65%), Gaps = 7/220 (3%)

Query: 3   VTRPVEALATVRIQRD-IDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVI 61
             R   AL+ +R  ++  D+V++D+HMP+M+G +L + +  E   LPV++MS+DD +SV+
Sbjct: 57  CNRAESALSLLRKNKNGFDIVISDVHMPDMDGFKLLEHVGLEMD-LPVIMMSADDSKSVV 115

Query: 62  MKALASGVAFYILKPLNPDDLKNVWQYAMTYKKAK-SISIDEIGSFELAGFSAGK---FS 117
           +K +  G   Y++KP+  + LKN+WQ+ +  K+ + ++S    GS E  G    +     
Sbjct: 116 LKGVTHGAVDYLIKPVRIEALKNIWQHVVRKKRNEWNVSEHSGGSIEDTGGDRDRQQQHR 175

Query: 118 LDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPKVAWTDSLHNRFLQAIR 177
            D   + SSVNE N  +   KRK  + D     K+++++ KKP+V W+  LH +F+ A+ 
Sbjct: 176 EDADNNSSSVNEGNGRSS-RKRKEEEVDDQGDDKEDSSSLKKPRVVWSVELHQQFVAAVN 234

Query: 178 HIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRV 217
            +G++KAVPKKILE MNVPGLTRENVASHLQKYRI+L+R+
Sbjct: 235 QLGVDKAVPKKILEMMNVPGLTRENVASHLQKYRIYLRRL 274

Transcriptional activator that binds specifically to the DNA sequence 5'-[AG]GATT-3'. Functions as a response regulator involved in His-to-Asp phosphorelay signal transduction system. Phosphorylation of the Asp residue in the receiver domain activates the ability of the protein to promote the transcription of target genes. Could directly activate some type-A response regulators in response to cytokinins. Involved in the expression of nuclear genes for components of mitochondrial complex I. Promotes cytokinin-mediated leaf longevity. Involved in the ethylene signaling pathway in an ETR1-dependent manner and in the cytokinin signaling pathway.

Arabidopsis thaliana (taxid: 3702)

>sp|Q940D0|ARR1_ARATH Two-component response regulator ARR1 OS=Arabidopsis thaliana GN=ARR1 PE=1 SV=2

 Score =  174 bits (440), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 91/227 (40%), Positives = 146/227 (64%), Gaps = 21/227 (9%)

Query: 9   ALATVRIQRD-IDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
           AL+ +R  +   D+V++D+HMP+M+G +L + +  E   LPV++MS+DD +SV++K +  
Sbjct: 72  ALSLLRKNKHGFDIVISDVHMPDMDGFKLLEHVGLEMD-LPVIMMSADDSKSVVLKGVTH 130

Query: 68  GVAFYILKPLNPDDLKNVWQYAMTYKKAKSISIDEIGSFELAG---------------FS 112
           G   Y++KP+  + LKN+WQ+ +  ++++    +  GS E  G                S
Sbjct: 131 GAVDYLIKPVRMEALKNIWQHVVRKRRSEWSVPEHSGSIEETGERQQQQHRGGGGGAAVS 190

Query: 113 AGKFSLDDIVSRSSVNERNKNNKDSKRKASKK--DKGKQTKQNATAPKKPKVAWTDSLHN 170
            G+ ++DD  + SSVNE N     S+++  ++  ++G    ++A+  KKP+V W+  LH 
Sbjct: 191 GGEDAVDD--NSSSVNEGNNWRSSSRKRKDEEGEEQGDDKDEDASNLKKPRVVWSVELHQ 248

Query: 171 RFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRV 217
           +F+ A+  +G+EKAVPKKILE MNVPGLTRENVASHLQKYRI+L+R+
Sbjct: 249 QFVAAVNQLGVEKAVPKKILELMNVPGLTRENVASHLQKYRIYLRRL 295

Transcriptional activator that binds specifically to the DNA sequence 5'-[AG]GATT-3'. Functions as a response regulator involved in His-to-Asp phosphorelay signal transduction system. Phosphorylation of the Asp residue in the receiver domain activates the ability of the protein to promote the transcription of target genes. Could directly activate some type-A response regulators in response to cytokinins.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8L9Y3|ARR14_ARATH Two-component response regulator ARR14 OS=Arabidopsis thaliana GN=ARR14 PE=1 SV=2

 Score =  151 bits (381), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 82/217 (37%), Positives = 130/217 (59%), Gaps = 10/217 (4%)

Query: 9   ALATVRIQRD-IDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
           AL  +R ++D  DLV++D+HMP MNG  L +++      LPV++MS D R + +M  +  
Sbjct: 46  ALTILRERKDSFDLVLSDVHMPGMNGYNLLQQVGLLEMDLPVIMMSVDGRTTTVMTGINH 105

Query: 68  GVAFYILKPLNPDDLKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIV----- 122
           G   Y++KP+ P++LKN+WQ+ +   + K +   E+ S +    +    SL+ +V     
Sbjct: 106 GACDYLIKPIRPEELKNIWQHVV---RRKCVMKKELRSSQALEDNKNSGSLETVVVSVSE 162

Query: 123 -SRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPKVAWTDSLHNRFLQAIRHIGL 181
            S  S+ +     K  KR   + D       +    KK +V W+  LH +F+ A+  +G+
Sbjct: 163 CSEESLMKCRNKKKKKKRSVDRDDNEDDLLLDPGNSKKSRVVWSIELHQQFVNAVNKLGI 222

Query: 182 EKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVA 218
           +KAVPK+ILE MNVPGL+RENVASHLQK+R++LKR++
Sbjct: 223 DKAVPKRILELMNVPGLSRENVASHLQKFRLYLKRLS 259

Transcriptional activator that binds specifically to the DNA sequence 5'-[AG]GATT-3'. Functions as a response regulator involved in His-to-Asp phosphorelay signal transduction system. Phosphorylation of the Asp residue in the receiver domain activates the ability of the protein to promote the transcription of target genes. Could directly activate some type-A response regulators in response to cytokinins.

Arabidopsis thaliana (taxid: 3702)

>sp|O49397|ARR10_ARATH Two-component response regulator ARR10 OS=Arabidopsis thaliana GN=ARR10 PE=1 SV=1

 Score =  144 bits (362), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 86/237 (36%), Positives = 136/237 (57%), Gaps = 23/237 (9%)

Query: 1   VTVTRPVE-ALATVRIQRD-IDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRE 58
           VT T   + AL  +R  ++  DLV++D+ MP+M+G +L + +  E   LPV+++S+    
Sbjct: 43  VTTTNQAQTALELLRENKNKFDLVISDVDMPDMDGFKLLELVGLEMD-LPVIMLSAHSDP 101

Query: 59  SVIMKALASGVAFYILKPLNPDDLKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSL 118
             +MK +  G   Y+LKP+  ++LKN+WQ+ +   K K            +  S G  + 
Sbjct: 102 KYVMKGVKHGACDYLLKPVRIEELKNIWQHVVRKSKLKKNK---------SNVSNGSGNC 152

Query: 119 DDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPKVAWTDSLHNRFLQAIRH 178
           D         + N+  K+   +  ++++G     + TA KKP+V WT  LHN+FL A+ H
Sbjct: 153 D---------KANRKRKEQYEEEEEEERGNDND-DPTAQKKPRVLWTHELHNKFLAAVDH 202

Query: 179 IGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAEQGASAMGKTLALRSSF 235
           +G+E+AVPKKIL+ MNV  LTRENVASHLQK+R+ LK+V++       +  A+ S F
Sbjct: 203 LGVERAVPKKILDLMNVDKLTRENVASHLQKFRVALKKVSDDAIQQANRA-AIDSHF 258

Transcriptional activator that binds specifically to the DNA sequence 5'-[AG]GATT-3'. Functions as a response regulator involved in His-to-Asp phosphorelay signal transduction system. Phosphorylation of the Asp residue in the receiver domain activates the ability of the protein to promote the transcription of target genes. Could directly activate some type-A response regulators in response to cytokinins.

Arabidopsis thaliana (taxid: 3702)

>sp|P62598|ARR12_ARATH Two-component response regulator ARR12 OS=Arabidopsis thaliana GN=ARR12 PE=2 SV=2

 Score =  137 bits (346), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 77/218 (35%), Positives = 125/218 (57%), Gaps = 9/218 (4%)

Query: 2   TVTRPVEALATVRIQRD-IDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESV 60
           T  +  +AL  +R  ++  DLV++D+ MP+M+G +L + +  E   LPV+++S+      
Sbjct: 45  TTNQAQKALELLRENKNKFDLVISDVDMPDMDGFKLLELVGLEMD-LPVIMLSAHSDPKY 103

Query: 61  IMKALASGVAFYILKPLNPDDLKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDD 120
           +MK +  G   Y+LKP+  ++LKN+WQ+ +  +  K+   +  G       + G      
Sbjct: 104 VMKGVTHGACDYLLKPVRIEELKNIWQHVVRSRFDKNRGSNNNGDKRDGSGNEG------ 157

Query: 121 IVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPKVAWTDSLHNRFLQAIRHIG 180
            V  S  N    N K   +    +D+ +    ++ A KK +V WT  LH +F+ A+  +G
Sbjct: 158 -VGNSDQNNGKGNRKRKDQYNEDEDEDRDDNDDSCAQKKQRVVWTVELHKKFVAAVNQLG 216

Query: 181 LEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVA 218
            EKA+PKKIL+ MNV  LTRENVASHLQK+R++LKR++
Sbjct: 217 YEKAMPKKILDLMNVEKLTRENVASHLQKFRLYLKRIS 254

Transcriptional activator that binds specifically to the DNA sequence 5'-[AG]GATT-3'. Functions as a response regulator involved in His-to-Asp phosphorelay signal transduction system. Phosphorylation of the Asp residue in the receiver domain activates the ability of the protein to promote the transcription of target genes. Could directly activate some type-A response regulators in response to cytokinins.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FXD6|ARR11_ARATH Two-component response regulator ARR11 OS=Arabidopsis thaliana GN=ARR11 PE=1 SV=1

 Score =  135 bits (339), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 82/223 (36%), Positives = 127/223 (56%), Gaps = 21/223 (9%)

Query: 8   EALATVRIQRD-IDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALA 66
           EAL  +R ++D  D+V++D++MP+M+G +L + +  E   LPV++MS D   S +MK + 
Sbjct: 45  EALRLLRERKDGYDIVISDVNMPDMDGFKLLEHVGLELD-LPVIMMSVDGETSRVMKGVQ 103

Query: 67  SGVAFYILKPLNPDDLKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSS 126
            G   Y+LKP+   +LK +WQ+ +  K      + E+   E  G+  G     D ++R  
Sbjct: 104 HGACDYLLKPIRMKELKIIWQHVLRKK------LQEVRDIEGCGYEGGA----DWITRYD 153

Query: 127 VNERNKNNKDSKRKASKKDKG--KQTKQNATAPKK-----PKVAWTDSLHNRFLQAIRHI 179
                   +D      +KD    K+  Q+ + P        +V W+  LH++F+ A+  I
Sbjct: 154 EAHFLGGGEDVSFGKKRKDFDFEKKLLQDESDPSSSSSKKARVVWSFELHHKFVNAVNQI 213

Query: 180 GLE-KAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAEQG 221
           G + KA PKKIL+ MNVP LTRENVASHLQKYR++L R+ E+G
Sbjct: 214 GCDHKAGPKKILDLMNVPWLTRENVASHLQKYRLYLSRL-EKG 255

Transcriptional activator that binds specifically to the DNA sequence 5'-[AG]GATT-3'. Functions as a response regulator involved in His-to-Asp phosphorelay signal transduction system. Phosphorylation of the Asp residue in the receiver domain activates the ability of the protein to promote the transcription of target genes. Could directly activate some type-A response regulators in response to cytokinins.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FGT7|ARR18_ARATH Two-component response regulator ARR18 OS=Arabidopsis thaliana GN=ARR18 PE=2 SV=2

 Score =  131 bits (329), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 76/221 (34%), Positives = 127/221 (57%), Gaps = 14/221 (6%)

Query: 3   VTRPVEALATVRIQRD----IDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRE 58
           VT+ +E+   + + R+     DLV++D+ MP+ +G +L  EI  E   LPV+++S+    
Sbjct: 44  VTKTMESRKALEMLRENSNMFDLVISDVEMPDTDGFKLL-EIGLEMD-LPVIMLSAHSDY 101

Query: 59  SVIMKALASGVAFYILKPLNPDDLKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSL 118
             +MK +  G   Y++KP+   +L+N+W + +  K  KS +   +   E     +     
Sbjct: 102 DSVMKGIIHGACDYLVKPVGLKELQNIWHHVVK-KNIKSYA-KLLPPSESDSVPSASRKR 159

Query: 119 DDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPKVAWTDSLHNRFLQAIRH 178
            D V+ S   + +   +D    + +   G  T+      KKP+V W+  LH +F+ A++ 
Sbjct: 160 KDKVNDSGDEDDSDREEDDGEGSEQDGDGSGTR------KKPRVVWSQELHQKFVSAVQQ 213

Query: 179 IGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAE 219
           +GL+KAVPKKIL+ M++ GLTRENVASHLQKYR++LK++ E
Sbjct: 214 LGLDKAVPKKILDLMSIEGLTRENVASHLQKYRLYLKKIDE 254

Transcriptional activator that binds specifically to the DNA sequence 5'-[AG]GATT-3'. Functions as a response regulator involved in His-to-Asp phosphorelay signal transduction system. Phosphorylation of the Asp residue in the receiver domain activates the ability of the protein to promote the transcription of target genes. Could directly activate some type-A response regulators in response to cytokinins.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LZJ8|ARR20_ARATH Putative two-component response regulator ARR20 OS=Arabidopsis thaliana GN=ARR20 PE=2 SV=1

 Score =  114 bits (286), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 72/210 (34%), Positives = 120/210 (57%), Gaps = 20/210 (9%)

Query: 8   EALA-TVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALA 66
           EA+A  ++ + +IDLV+ D HMP++NG++    I ++   LPV++MS + ++  +M+++ 
Sbjct: 73  EAMAFLMKNKHEIDLVIWDFHMPDINGLDALNIIGKQMD-LPVVIMSHEYKKETVMESIK 131

Query: 67  SGVAFYILKPLNPDDLKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSS 126
            G   +++KP++ + +  +W++    + +KS  +D+ G  E     +     DD+     
Sbjct: 132 YGACDFLVKPVSKEVIAVLWRHVYRKRMSKS-GLDKPG--ESGTVESDPDEYDDL---EQ 185

Query: 127 VNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPKVAWTDSLHNRFLQAIRHIG-LEKAV 185
            N    N + SK     K++   TK       KP++ WT  LH++F  A+  +G LEKA 
Sbjct: 186 DNLYESNEEGSKNTCDHKEEKSPTK-------KPRMQWTPELHHKFEVAVEKMGSLEKAF 238

Query: 186 PKKILEFM----NVPGLTRENVASHLQKYR 211
           PK IL++M    NV GLTR NVASHLQKYR
Sbjct: 239 PKTILKYMQEELNVQGLTRNNVASHLQKYR 268

Putative transcriptional activator that binds specifically to the DNA sequence 5'-[AG]GATT-3'. Functions as response regulator involved in His-to-Asp phosphorelay signal transduction system. Phosphorylation of the Asp residue in the receiver domain activates the ability of the protein to promote the transcription of target genes. Could directly activate some type-A response regulators in response to cytokinins.

Arabidopsis thaliana (taxid: 3702)

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	534
255539557	754	two-component system sensor histidine ki	0.971	0.688	0.437	2e-93
147775384	609	hypothetical protein VITISV_031283 [Viti	0.895	0.784	0.435	5e-88
224136878	716	type-b response regulator [Populus trich	0.777	0.579	0.471	3e-85
297741112	592	unnamed protein product [Vitis vinifera]	0.833	0.751	0.423	7e-82
147765741	659	hypothetical protein VITISV_019100 [Viti	0.833	0.675	0.423	1e-81
297741111	520	unnamed protein product [Vitis vinifera]	0.846	0.869	0.432	4e-81
224120138	658	type-b response regulator [Populus trich	0.958	0.778	0.384	1e-75
224120142	623	predicted protein [Populus trichocarpa]	0.958	0.821	0.384	1e-75
147782854	594	hypothetical protein VITISV_003290 [Viti	0.829	0.745	0.370	2e-69
449528748	631	PREDICTED: uncharacterized protein LOC10	0.593	0.502	0.430	3e-56

>gi|255539557|ref|XP_002510843.1| two-component system sensor histidine kinase/response regulator, putative [Ricinus communis] gi|223549958|gb|EEF51445.1| two-component system sensor histidine kinase/response regulator, putative [Ricinus communis]

 Score =  349 bits (896), Expect = 2e-93,   Method: Compositional matrix adjust.
 Identities = 259/592 (43%), Positives = 336/592 (56%), Gaps = 73/592 (12%)

Query: 1   VTVTRPVEALATVRIQRD-IDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRES 59
           VTV  P++AL++++      DLV+TDLHMP MNGI+LQK+I+EEF  +PV++MSSD + S
Sbjct: 48  VTVKNPLDALSSLQSSDGAFDLVITDLHMPGMNGIQLQKQIDEEF-KIPVVIMSSDGKRS 106

Query: 60  VIMKALASGVAFYILKPLNPDDLKNVWQYAMTYKKAKSISIDEI--GSFELAGFSAGKFS 117
            I+++L SG  +Y++KP+N  DLKNVWQYAM  KK K + + E    +   A  S  K S
Sbjct: 107 AILESLESGAVYYMVKPVNLRDLKNVWQYAMASKKGKEVVVAEEPENNDGEASASTEKDS 166

Query: 118 LDD--IVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPKVAWTDSLHNRFLQA 175
            +D    S S+  E N   K  K++A   D+G+      +APKK KV WT+SLHNRFLQA
Sbjct: 167 CEDNNSASVSANEESNNKKKKGKKRARDHDQGEDA---PSAPKKAKVVWTNSLHNRFLQA 223

Query: 176 IRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAEQG--ASAMGKTLALRS 233
           I HIGL+KAVPK+ILEFMNVPGLTRENVASHLQKYR+FLK+VAE+G  +S      A+RS
Sbjct: 224 INHIGLDKAVPKRILEFMNVPGLTRENVASHLQKYRLFLKKVAERGLWSSQALSERAMRS 283

Query: 234 SFASGHVSMMLQEAH-EFSQVRDQQQQMRTSAFLPGYASGVSALNGTTFGSIGFPSLGAS 292
           SFASG+ SM L+ AH ++SQ+   QQ   T  F PGY   +S L  + FG  G  S  AS
Sbjct: 284 SFASGYSSMFLKNAHQDYSQLPGLQQLRPT--FQPGYGGNISGLGTSKFGFSGCHSQEAS 341

Query: 293 SSSSVP-----QPGLMG-NQANFPQ-SLFGNTRNPLYQANSAGKTCGSSGSNATEANPLS 345
           SS+S+P     Q  L G N ++F Q S+FGNT +PLY +N      G S +N    N   
Sbjct: 342 SSNSLPQIRFGQSSLFGSNLSSFQQRSMFGNT-SPLYSSNDTRP--GLSTTNTAGLNMSP 398

Query: 346 RGGLAAGLMN-------------QMYQQKSQLRPNPYDNYNIGASSSKGFGTSGWSSSSN 392
            G    GLMN             QM+QQ++Q R  P   +  G+    G  +S ++SS  
Sbjct: 399 NGATTFGLMNDAANGLSNCTSPKQMHQQQNQSRSTPLPFFQFGS----GLSSSNYASSIG 454

Query: 393 TSGLDQNMGTIKNNTYSNYAGIRLNDDGELIPAGQTSLINGN-----GLNGGY-----GF 442
            +G   N      N   NYAGIRL ++GELI +GQ    NGN     G NGGY      +
Sbjct: 455 GTGTSSNSYLSSLNPNGNYAGIRLTNEGELIGSGQVRF-NGNELTSTGFNGGYDSSLLNW 513

Query: 443 ISGTSGIMANA-----AFGHLTPGASSSSARFDN------------ATYQIPSAFAGVNE 485
                 + +NA      FG+L P   SSSA F N             T    S+  G   
Sbjct: 514 NISNDNLNSNAQTGGDIFGYLPPQGGSSSATFGNYLAQGASSSTGFGTANPFSSILGAFN 573

Query: 486 QENTSMLSQLSSQQQYGPGNNAQ--NDFTNFAPINNASV-NGNTAQPERLGE 534
           QENTS LS LS Q       NA+  NDF  F  +N+AS+ + N    + LGE
Sbjct: 574 QENTSALSPLSQQHINASLGNAEEDNDFA-FNLLNDASIFDNNFNNQQELGE 624

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147775384|emb|CAN78184.1| hypothetical protein VITISV_031283 [Vitis vinifera]

 Score =  331 bits (849), Expect = 5e-88,   Method: Compositional matrix adjust.
 Identities = 238/547 (43%), Positives = 304/547 (55%), Gaps = 69/547 (12%)

Query: 1   VTVTRPVEALATVRIQRDI-DLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRES 59
           VTV    +AL T+R + +   L+VTD+HMPEM+G E Q+ ++EEF HLPV++MS+DD+ES
Sbjct: 48  VTVNSAQDALTTLRTRSNFFHLIVTDVHMPEMDGFEFQRLVHEEF-HLPVVMMSADDKES 106

Query: 60  VIMKALASGVAFYILKPLNPDDLKNVWQYAMTYKKAKS-ISIDEIGSFELAGFSAGKFSL 118
            +++ L +G AFYI+KP+N DDLKN+WQYA+  KK KS I + EI   + A     K S 
Sbjct: 107 SMLRGLEAGAAFYIVKPVNYDDLKNLWQYAVGXKKGKSHIVMQEIERTQGAS-XLEKTSN 165

Query: 119 DDIVSRSSVNERNKNNKDSKRKASKKDK---GKQTKQNATAPKKPKVAWTDSLHNRFLQA 175
           +++   S +NE   N +DSKRK  KK     GK+ K    APKK KV WT +LHNRFL+A
Sbjct: 166 NEV--ESLMNEEKHNKRDSKRKTLKKTNEGNGKE-KSETVAPKKAKVIWTSALHNRFLEA 222

Query: 176 IRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAEQGASA--MGKTLA--- 230
            R IGLE+AVPK+ILE MNVPGLTRENVASHLQKYRIFLKRV E  +S    GK ++   
Sbjct: 223 ARKIGLERAVPKRILEIMNVPGLTRENVASHLQKYRIFLKRVMETSSSGTITGKNISERT 282

Query: 231 LRSSFASGHVSMMLQEAHE-FSQVRDQQQQMRTSAFLPGYASGVSALNGTTFGSIGFPSL 289
           LRSSFA+GH S+M+      F Q  D  QQ+  S   P +   +   N ++  S  FP+ 
Sbjct: 283 LRSSFATGHPSLMVNALQRGFPQFLD-HQQVGASQLQPRFLGNLPIANASSLSSTIFPNQ 341

Query: 290 GASSSSSVPQPGL-----MGNQANFPQSLFGNTRNPLYQANSAGKTCGSSGSNATEANPL 344
            ASS + +PQ G      M   A   Q  FGNT+  LYQAN AG        NAT  NP+
Sbjct: 342 QASSGNPIPQLGYGQAHSMNKHAYLQQPTFGNTK-ALYQANGAGM-------NAT--NPM 391

Query: 345 SRGGLAAGLMNQMYQQKSQLRPNPYDNYNIGASSSKGFGTSGWSSSSNTSGLDQNMGTIK 404
                      QMYQQK+Q R     N    A S   F   G S  +N  G+ QN G   
Sbjct: 392 -----------QMYQQKTQARSELVPN----AMSKNTFTALGVSDPNNIHGI-QNNGVNN 435

Query: 405 NNTYSNYAGIRLNDDGELIPAGQTSLINGNGLNGGYGFISGTSGI----MANAAFGHLTP 460
           ++   N AG      G++  AG   L   NG NGGYG   G +GI    + N   G+   
Sbjct: 436 SDMTLNIAG-----SGQIGFAGGGIL---NGFNGGYGLFDGNNGITHASLRNVNSGYYAE 487

Query: 461 GASSSSARFDNATYQIPSAFAGVNEQENTSMLSQLSSQQQYGPGNNAQNDF-----TNFA 515
           GA SS+      T QIP  F+ V +QEN  ML  L  Q   G G    +        N A
Sbjct: 488 GACSSAGF--GGTNQIPPRFSNVIQQENNPML--LPQQNNLGEGGEDNSYLLDQXRNNTA 543

Query: 516 PINNASV 522
           P+ N S+
Sbjct: 544 PMENXSI 550

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224136878|ref|XP_002322438.1| type-b response regulator [Populus trichocarpa] gi|222869434|gb|EEF06565.1| type-b response regulator [Populus trichocarpa]

 Score =  322 bits (825), Expect = 3e-85,   Method: Compositional matrix adjust.
 Identities = 212/450 (47%), Positives = 279/450 (62%), Gaps = 35/450 (7%)

Query: 1   VTVTRPVEALATVRIQRDI-DLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRES 59
           VTV  P +AL+T+R+++ + DLVVTDLHMPEMNG+ELQ++++EEF  LPV++MSSDD E 
Sbjct: 53  VTVKNPFDALSTLRLKKGLFDLVVTDLHMPEMNGMELQQQVDEEFK-LPVIIMSSDDSEK 111

Query: 60  VIMKALASGVAFYILKPLNPDDLKNVWQYAMTYKKAK-SISIDEIGSFELAGFSA---GK 115
           VI++ L  G AFYI+KP+N DDLKNVWQYA+  K  K S+SI EIG  + +  S     K
Sbjct: 112 VILRTLEGGAAFYIVKPINKDDLKNVWQYAVATKTGKYSLSIKEIGGSQESSSSTVFDQK 171

Query: 116 FSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPKVAWTDSLHNRFLQA 175
            S+D++ S  S N +  N KD   K  K+ K  Q   +  APKKPKV WT+SLH+RFLQA
Sbjct: 172 ISVDEVSSAKSTNIKICNEKDRINKNRKRTKEDQEVDSQLAPKKPKVVWTNSLHSRFLQA 231

Query: 176 IRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAEQGASAMGKTL---ALR 232
           I HIGL+KAVPK+ILEFM+VPGL+RENVASHLQKYRIFLK+VAE+G S+  K L   AL+
Sbjct: 232 INHIGLDKAVPKRILEFMSVPGLSRENVASHLQKYRIFLKKVAERGTSS-SKNLSGRALK 290

Query: 233 SSFASGHVSMMLQE-AHEFSQVRDQQQQMRTSAFLPGYASGV--SALNGTTFGSIGFPSL 289
           S+FAS   S+ML+    E+SQ   QQQ +R S    G+      +   G+ FGS+  P+ 
Sbjct: 291 SNFASSQPSLMLKNFQQEYSQFSRQQQVLRASV-QAGFGGNTIPTPDGGSNFGSLHSPNQ 349

Query: 290 GASSSSSVPQPGL-----MGNQANFPQSLFGNTRNPLYQANSAGKTCGSSGSNATEAN-P 343
            A +++S  Q         GN   F Q  FGN      QAN   K  G   +N T  N P
Sbjct: 350 QAPNNNSALQSPYKQSRSFGNPTGFQQLSFGNAN----QANK--KRSGLESNNNTGTNPP 403

Query: 344 LSRGGLAAGLMN-----QMYQQKSQLRPNPYDNYNIGASSSKGFGTSGWSSSSNTS-GLD 397
            SR  +  GL +     Q+YQ ++Q R N     +  +S    FG+ G  +++  S   +
Sbjct: 404 ASRESVPNGLTHGKSPMQIYQPQNQGRSNL---QSFDSSEHNKFGSIGVQATNYRSGVGN 460

Query: 398 QNMGTIKNNTYSNYAGIRLNDDGELIPAGQ 427
                   NT +NYAGIR+N DG+LI AGQ
Sbjct: 461 IGNNNNSLNTNNNYAGIRVNTDGQLIGAGQ 490

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297741112|emb|CBI31843.3| unnamed protein product [Vitis vinifera]

 Score =  311 bits (796), Expect = 7e-82,   Method: Compositional matrix adjust.
 Identities = 217/512 (42%), Positives = 291/512 (56%), Gaps = 67/512 (13%)

Query: 1   VTVTRPVEALATVRIQRDI-DLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRES 59
           VTV  P++ALAT+R   D   LVVTD+HMPE++G E QK++ EEF  LPV++MS+DD+ES
Sbjct: 49  VTVKNPLDALATLRSGSDFFHLVVTDVHMPELDGFEFQKKVQEEF-QLPVVMMSADDKES 107

Query: 60  VIMKALASGVAFYILKPLNPDDLKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLD 119
            ++K L +G AFYI+KP+N DDLKN+WQYA+  +K  S+ + ++G          K   D
Sbjct: 108 SMLKGLEAGAAFYIVKPVNYDDLKNIWQYAVGPRKDNSVDMQDVGPAPEEESPVEKTPDD 167

Query: 120 --DIVSRSSVNERNKNNKDSKRKASKK---DKGKQTKQNATAPKKPKVAWTDSLHNRFLQ 174
             DI S SSVNE N++ +D K+KASK+   D GK+   +A +PK+ KV WT +LH RFL+
Sbjct: 168 PVDIESVSSVNEVNQSKRDPKKKASKRVIEDSGKENS-DAVSPKRTKVVWTSALHTRFLE 226

Query: 175 AIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAEQG---ASAMGKTLA- 230
           A+R IGLE+AVPK+ILE MN+PGLTRENVASHLQKYRIFL+RVAE      S+ GK +A 
Sbjct: 227 AVRKIGLERAVPKRILELMNMPGLTRENVASHLQKYRIFLRRVAEASNSTGSSTGKRIAE 286

Query: 231 --LRSSFASGHVSMMLQEAHE-FSQVRDQQQQMRTSAFLPGYASGVSALNGTTFGSIGFP 287
             LRSSFA+GH S+++    + F Q+ +  QQ+  S   PG+   +   + T  G+I FP
Sbjct: 287 RTLRSSFATGHPSLLISALQQGFPQLLN--QQLVGSLLQPGFPGNIQINDPTLRGAI-FP 343

Query: 288 SLGASSSSSVPQPGL-----MGNQANFPQSLFGNTRNPLYQANSAGKTCGSSGSNATEAN 342
           +  ASSS+  PQ G      M NQA   Q  FGNT N L +AN         G     AN
Sbjct: 344 NQQASSSNPRPQLGHGQGHSMNNQAYLQQQPFGNT-NALPEAN---------GGVMNGAN 393

Query: 343 PLSRGGLAAGLMNQMYQQKSQLRPNPYDNYNIGASSSKGFGTSGWSSSSNTSGLDQNMGT 402
           P+        +  Q  Q +S+L PN   N N             +  S N  G+ QNM +
Sbjct: 394 PMQ-------MNQQQTQARSELVPNAMSNNNFTV----------FEGSGNIHGV-QNMES 435

Query: 403 IKNNTYSNYAGIRLNDDGELIPAGQTSLINGNGLNGGYGFISGTSGIMANAAF------G 456
             N      + +  N D     AG   +   NG NG YG I+G   I  N A       G
Sbjct: 436 FNN------SHLPPNFDCNNNIAGSGPMGLSNGFNGNYGSIAGN--INGNLALSESVNSG 487

Query: 457 HLTPGASSSSARFDNATYQIPSAFAGVNEQEN 488
           +   GA SS      +T Q P+ F+ + +Q N
Sbjct: 488 YYAQGAYSSVGL--RSTNQPPTRFSNITQQNN 517

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147765741|emb|CAN73375.1| hypothetical protein VITISV_019100 [Vitis vinifera]

 Score =  310 bits (795), Expect = 1e-81,   Method: Compositional matrix adjust.
 Identities = 217/512 (42%), Positives = 291/512 (56%), Gaps = 67/512 (13%)

Query: 1   VTVTRPVEALATVRIQRDI-DLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRES 59
           VTV  P++ALAT+R   D   LVVTD+HMPE++G E QK++ EEF  LPV++MS+DD+ES
Sbjct: 49  VTVKNPLDALATLRSGSDFFHLVVTDVHMPELDGFEFQKKVQEEF-QLPVVMMSADDKES 107

Query: 60  VIMKALASGVAFYILKPLNPDDLKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLD 119
            ++K L +G AFYI+KP+N DDLKN+WQYA+  +K  S+ + ++G          K   D
Sbjct: 108 SMLKGLEAGAAFYIVKPVNYDDLKNIWQYAVGPRKDNSVDMQDVGPAPEEESPVEKTPDD 167

Query: 120 --DIVSRSSVNERNKNNKDSKRKASKK---DKGKQTKQNATAPKKPKVAWTDSLHNRFLQ 174
             DI S SSVNE N++ +D K+KASK+   D GK+   +A +PK+ KV WT +LH RFL+
Sbjct: 168 PVDIESVSSVNEVNQSKRDPKKKASKRVIEDSGKENS-DAVSPKRTKVVWTSALHTRFLE 226

Query: 175 AIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAEQG---ASAMGKTLA- 230
           A+R IGLE+AVPK+ILE MN+PGLTRENVASHLQKYRIFL+RVAE      S+ GK +A 
Sbjct: 227 AVRKIGLERAVPKRILELMNMPGLTRENVASHLQKYRIFLRRVAEASNSTGSSTGKRIAE 286

Query: 231 --LRSSFASGHVSMMLQEAHE-FSQVRDQQQQMRTSAFLPGYASGVSALNGTTFGSIGFP 287
             LRSSFA+GH S+++    + F Q+ +  QQ+  S   PG+   +   + T  G+I FP
Sbjct: 287 RTLRSSFATGHPSLLISALQQGFPQLLN--QQLVGSLLQPGFPGNIQINDPTLRGAI-FP 343

Query: 288 SLGASSSSSVPQPGL-----MGNQANFPQSLFGNTRNPLYQANSAGKTCGSSGSNATEAN 342
           +  ASSS+  PQ G      M NQA   Q  FGNT N L +AN         G     AN
Sbjct: 344 NQQASSSNPRPQLGHGQGHSMNNQAYLQQQPFGNT-NALPEAN---------GGVMNGAN 393

Query: 343 PLSRGGLAAGLMNQMYQQKSQLRPNPYDNYNIGASSSKGFGTSGWSSSSNTSGLDQNMGT 402
           P+        +  Q  Q +S+L PN   N N             +  S N  G+ QNM +
Sbjct: 394 PMQ-------MNQQQTQARSELVPNAMSNNNFTV----------FEGSGNIHGV-QNMES 435

Query: 403 IKNNTYSNYAGIRLNDDGELIPAGQTSLINGNGLNGGYGFISGTSGIMANAAF------G 456
             N      + +  N D     AG   +   NG NG YG I+G   I  N A       G
Sbjct: 436 FNN------SHLPPNFDCNNNIAGSGPMGLSNGFNGNYGSIAGN--INGNLALSESVNSG 487

Query: 457 HLTPGASSSSARFDNATYQIPSAFAGVNEQEN 488
           +   GA SS      +T Q P+ F+ + +Q N
Sbjct: 488 YYAQGAYSSVGL--RSTNQPPTRFSNITQQNN 517

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297741111|emb|CBI31842.3| unnamed protein product [Vitis vinifera]

 Score =  308 bits (790), Expect = 4e-81,   Method: Compositional matrix adjust.
 Identities = 224/518 (43%), Positives = 286/518 (55%), Gaps = 66/518 (12%)

Query: 28  MPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDDLKNVWQ 87
           MPEM+G E Q+ ++EEF HLPV++MS+DD+ES +++ L +G AFYI+KP+N DDLKN+WQ
Sbjct: 1   MPEMDGFEFQRLVHEEF-HLPVVMMSADDKESSMLRGLEAGAAFYIVKPVNYDDLKNLWQ 59

Query: 88  YAMTYKKAKS-ISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKK-- 144
           YA+  KK KS I + EI   + A     K S +++   S +NE   N +DSKRK  KK  
Sbjct: 60  YAVGPKKGKSHIVMQEIERTQGAS-QLEKTSNNEV--ESLMNEEKHNKRDSKRKTLKKAN 116

Query: 145 DKGKQTKQNATAPKKPKVAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVA 204
           +   + K    APKK KV WT +LHNRFL+A R IGLE+AVPK+ILE MNVPGLTRENVA
Sbjct: 117 EGNGKEKSETVAPKKAKVIWTSALHNRFLEAARKIGLERAVPKRILEIMNVPGLTRENVA 176

Query: 205 SHLQKYRIFLKRVAEQGASA--MGKTLA---LRSSFASGHVSMMLQEAHE-FSQVRDQQQ 258
           SHLQKYRIFLKRV E  +S    GK ++   LRSSFA+GH S+M+      F Q  D  Q
Sbjct: 177 SHLQKYRIFLKRVMETSSSGTITGKNISERTLRSSFATGHPSLMVNALQRGFPQFLD-HQ 235

Query: 259 QMRTSAFLPGYASGVSALNGTTFGSIGFPSLGASSSSSVPQPGL-----MGNQANFPQSL 313
           Q+  S   P +   +   N ++  S  FP+  ASS + +PQ G      M   A   Q  
Sbjct: 236 QVGASQLQPRFLGNLPIANASSLSSTIFPNQQASSGNPIPQLGYGQAHSMNKHAYLQQPT 295

Query: 314 FGNTRNPLYQANSAGKTCGSSGSNATEANPLSRGGLAAGLMNQMYQQKSQLRPNPYDNYN 373
           FGNT+  LYQAN AG        NAT  NP+           QMYQQK+Q R     N  
Sbjct: 296 FGNTK-ALYQANGAGM-------NAT--NPM-----------QMYQQKTQARSELVPN-- 332

Query: 374 IGASSSKGFGTSGWSSSSNTSGLDQNMGTIKNNTYSNYAGIRLNDDGELIPAGQTSLING 433
             A S+  F   G S  +N  G+ QN G   ++   N AG      G++  AG   L   
Sbjct: 333 --AMSNNTFTAFGVSDPNNIHGI-QNNGVNNSDMTLNIAG-----SGQIGFAGGGIL--- 381

Query: 434 NGLNGGYGFISGTSGI----MANAAFGHLTPGASSSSARFDNATYQIPSAFAGVNEQENT 489
           NG NGGYG   G +GI    + N   G+   GA SS+      T QIP  F+ V +QEN 
Sbjct: 382 NGFNGGYGLFDGNNGITHASLRNVNSGYYAEGACSSAGF--GGTNQIPPRFSNVIQQENN 439

Query: 490 SMLSQLSSQQQYGPGNNAQNDF-----TNFAPINNASV 522
            ML  L  Q   G G    +        N AP+ N S+
Sbjct: 440 PML--LPQQNNLGEGGEDNSYLLDQLRNNTAPMENTSI 475

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224120138|ref|XP_002318254.1| type-b response regulator [Populus trichocarpa] gi|222858927|gb|EEE96474.1| type-b response regulator [Populus trichocarpa]

 Score =  290 bits (743), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 219/569 (38%), Positives = 319/569 (56%), Gaps = 57/569 (10%)

Query: 1   VTVTRPVEALATVRIQRDI-DLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRES 59
           VTV +P +AL+ +R+++ + DLVV+DLHMPEMNG+ELQK++ EEF  LPV++MSSD+ ++
Sbjct: 52  VTVKKPFDALSILRLKKGLFDLVVSDLHMPEMNGMELQKQVEEEFK-LPVIIMSSDESKN 110

Query: 60  VIMKALASGVAFYILKPLNPDDLKNVWQYAMTYKKAKSISIDEIGSFELAGFSAG---KF 116
           VI ++L  G AFYI+KP N  DLKNVW YA+  K   S+SI EI       +S+    + 
Sbjct: 111 VISRSLEGGAAFYIVKPANKVDLKNVWHYAVAIKTGNSLSIKEIEGSREPSYSSTLVERL 170

Query: 117 SLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPKVAWTDSLHNRFLQAI 176
           SL+D+ S +S+N+  +  K+ +++  K  K  Q   +  A KKPKV WT+SLHNRFL A+
Sbjct: 171 SLEDVNSATSINDEKRYRKNGRKEERKSTKDDQEVDSQPASKKPKVVWTNSLHNRFLLAL 230

Query: 177 RHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAEQGASAMGKTLA----LR 232
            HIGL+KAVPK+ILE M+V GL+REN+ASHLQKYRIFLK+VAE+G  +  K L+    LR
Sbjct: 231 NHIGLDKAVPKRILECMSVRGLSRENIASHLQKYRIFLKKVAERGGCS-SKNLSGRDDLR 289

Query: 233 SSFASGHVSMMLQEAHEFSQVRDQQQQMRTSAFLPGYASG-VSALNGTTFGSIGFPSLGA 291
           ++FA     MM +   +     +  Q++  ++  PG     + AL G++F ++  P+  A
Sbjct: 290 TNFAPSQPFMMFKNVQQ-----EYSQRVTRASIQPGLGGNTIPALGGSSFRNLHSPNQQA 344

Query: 292 SSSSSVPQPGLMGNQANFPQS-LFG--NTRNPLYQANSAGKTCGSSGSNATEANPLSRGG 348
            S++S+        Q+ + QS LFG  N+ N   Q  S  ++  S G N      +   G
Sbjct: 345 PSNNSIL-------QSPYGQSRLFGNANSANQANQIRSGLESNYSIGENMPSYGGVIPNG 397

Query: 349 LAAGLMN-QMYQQKSQLRPNPYDNY--NIGASS-SKGFGTSGWSSSSNTSGL-DQNMGTI 403
           L  G    QMY  ++Q R     +Y  N G+      FG  G  +++  SG+ D  +   
Sbjct: 398 LTHGTRPMQMYHPQNQAR-----SYLQNFGSPPLINRFGAVGIQATNYGSGVGDIGIINN 452

Query: 404 KNNTYSNYAGIRLNDDGELIPAGQTSLINGNGLNGGYGFISGTSGIMANAAFGHLTPGA- 462
             NT +NY GIR+  DG LI +GQ  L N N L+ G+    G   +M  A  G++   + 
Sbjct: 453 SLNTNNNYVGIRVTTDGRLIGSGQMQL-NTNELSNGFS-DGGHPCLMNWARNGNMNVASI 510

Query: 463 -------------SSSSARFDNAT-YQIPSAFAGVNEQENT-SMLSQLSSQQQYGPGNNA 507
                         S SA F+ A  +  P+ F  V    +T  +L     Q Q G GN  
Sbjct: 511 GFNIASENYVARRGSFSAGFEGANQFFPPTPFTSVYHGNSTPMLLPPPPPQHQLGLGNGG 570

Query: 508 QNDFTNFAPINNAS--VNGNTAQPERLGE 534
           QNDF  F  +NN+   + GN+ Q  ++GE
Sbjct: 571 QNDFV-FGLMNNSPPILGGNSNQQPQIGE 598

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224120142|ref|XP_002318255.1| predicted protein [Populus trichocarpa] gi|222858928|gb|EEE96475.1| predicted protein [Populus trichocarpa]

 Score =  290 bits (743), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 219/569 (38%), Positives = 319/569 (56%), Gaps = 57/569 (10%)

Query: 1   VTVTRPVEALATVRIQRDI-DLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRES 59
           VTV +P +AL+ +R+++ + DLVV+DLHMPEMNG+ELQK++ EEF  LPV++MSSD+ ++
Sbjct: 17  VTVKKPFDALSILRLKKGLFDLVVSDLHMPEMNGMELQKQVEEEFK-LPVIIMSSDESKN 75

Query: 60  VIMKALASGVAFYILKPLNPDDLKNVWQYAMTYKKAKSISIDEIGSFELAGFSAG---KF 116
           VI ++L  G AFYI+KP N  DLKNVW YA+  K   S+SI EI       +S+    + 
Sbjct: 76  VISRSLEGGAAFYIVKPANKVDLKNVWHYAVAIKTGNSLSIKEIEGSREPSYSSTLVERL 135

Query: 117 SLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPKVAWTDSLHNRFLQAI 176
           SL+D+ S +S+N+  +  K+ +++  K  K  Q   +  A KKPKV WT+SLHNRFL A+
Sbjct: 136 SLEDVNSATSINDEKRYRKNGRKEERKSTKDDQEVDSQPASKKPKVVWTNSLHNRFLLAL 195

Query: 177 RHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAEQGASAMGKTLA----LR 232
            HIGL+KAVPK+ILE M+V GL+REN+ASHLQKYRIFLK+VAE+G  +  K L+    LR
Sbjct: 196 NHIGLDKAVPKRILECMSVRGLSRENIASHLQKYRIFLKKVAERGGCS-SKNLSGRDDLR 254

Query: 233 SSFASGHVSMMLQEAHEFSQVRDQQQQMRTSAFLPGYASG-VSALNGTTFGSIGFPSLGA 291
           ++FA     MM +   +     +  Q++  ++  PG     + AL G++F ++  P+  A
Sbjct: 255 TNFAPSQPFMMFKNVQQ-----EYSQRVTRASIQPGLGGNTIPALGGSSFRNLHSPNQQA 309

Query: 292 SSSSSVPQPGLMGNQANFPQS-LFG--NTRNPLYQANSAGKTCGSSGSNATEANPLSRGG 348
            S++S+        Q+ + QS LFG  N+ N   Q  S  ++  S G N      +   G
Sbjct: 310 PSNNSIL-------QSPYGQSRLFGNANSANQANQIRSGLESNYSIGENMPSYGGVIPNG 362

Query: 349 LAAGLMN-QMYQQKSQLRPNPYDNY--NIGASS-SKGFGTSGWSSSSNTSGL-DQNMGTI 403
           L  G    QMY  ++Q R     +Y  N G+      FG  G  +++  SG+ D  +   
Sbjct: 363 LTHGTRPMQMYHPQNQAR-----SYLQNFGSPPLINRFGAVGIQATNYGSGVGDIGIINN 417

Query: 404 KNNTYSNYAGIRLNDDGELIPAGQTSLINGNGLNGGYGFISGTSGIMANAAFGHLTPGA- 462
             NT +NY GIR+  DG LI +GQ  L N N L+ G+    G   +M  A  G++   + 
Sbjct: 418 SLNTNNNYVGIRVTTDGRLIGSGQMQL-NTNELSNGFS-DGGHPCLMNWARNGNMNVASI 475

Query: 463 -------------SSSSARFDNAT-YQIPSAFAGVNEQENT-SMLSQLSSQQQYGPGNNA 507
                         S SA F+ A  +  P+ F  V    +T  +L     Q Q G GN  
Sbjct: 476 GFNIASENYVARRGSFSAGFEGANQFFPPTPFTSVYHGNSTPMLLPPPPPQHQLGLGNGG 535

Query: 508 QNDFTNFAPINNAS--VNGNTAQPERLGE 534
           QNDF  F  +NN+   + GN+ Q  ++GE
Sbjct: 536 QNDFV-FGLMNNSPPILGGNSNQQPQIGE 563

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147782854|emb|CAN61302.1| hypothetical protein VITISV_003290 [Vitis vinifera]

 Score =  269 bits (688), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 202/545 (37%), Positives = 281/545 (51%), Gaps = 102/545 (18%)

Query: 1   VTVTRPVEALATVRIQRDI-DLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRES 59
           V+V    +AL T+R + +   LVVTD+HMP+M+G E QK++ EEF +LPV++MS+DD+ES
Sbjct: 81  VSVKNAEDALITLRTRSNFFHLVVTDVHMPKMDGFEFQKQVREEF-NLPVVMMSADDKES 139

Query: 60  VIMKALASGVAFYILKPLNPDDLKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLD 119
            I++ L +G AFYI+KP+N DDLK++WQYA++ +K                         
Sbjct: 140 SILRGLEAGAAFYIVKPVNYDDLKDLWQYALSPRKG------------------------ 175

Query: 120 DIVSRSSVNERNKNNKDSKRKASKK--DKGKQTKQNATAPKKPKVAWTDSLHNRFLQAIR 177
              S S  +E  +N +DSK+KA KK  +  +Q K  A  P+K KV WT +LHN FL+AIR
Sbjct: 176 ---SVSVXHEEMQNKRDSKKKAGKKVNEGNEQEKSEAIVPRKSKVVWTTALHNDFLEAIR 232

Query: 178 HIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAEQGA---SAMGKTL---AL 231
            IGLE+AVPK+ILE MN PGLTRENVASHLQKYRIFLKRV E  +   S+ GK +    L
Sbjct: 233 KIGLERAVPKRILEHMNEPGLTRENVASHLQKYRIFLKRVTEASSSDGSSTGKNIIEKTL 292

Query: 232 RSSFASGHVSMMLQEAHEFSQVRDQQQQMRTSAFLPGYASGVSALNGTTFGSIGFPSLGA 291
           RSSFA+GH S+++           Q++ +      P            + G+  F +  A
Sbjct: 293 RSSFATGHPSLVINAL--------QKRMLGNLQITP------------SLGATIFSNQQA 332

Query: 292 SSSSSVPQPGL-----MGNQANFPQSLFGNTRNPLYQANSAGKTCGSSGSNATEANPLSR 346
           SSS+ +P+ G      + N A F Q  FGNT + LYQ+N      G++G N         
Sbjct: 333 SSSNPIPELGYGQSHSVDNSAYFQQPTFGNT-SALYQSNGG----GTNGKNPK------- 380

Query: 347 GGLAAGLMNQMYQQKSQLRPNPYDNYNIGASSSKGFGTSGWSSSSNTSGLDQNMGTIKNN 406
                    QMY+Q++Q R     +      S   F   G   S++   + QNMG + N+
Sbjct: 381 ---------QMYKQETQARSERVPD----TMSKNNFPACGILGSNDIHDI-QNMGXLNNS 426

Query: 407 TYS-NYAGIRLNDDGELIPAGQTSLINGNGLNGGYGFISGTSGIMANAAFGHLTPGASSS 465
             + N+       D      G+ S    NG NG Y  I   +G M +  +     G + S
Sbjct: 427 ILTPNFNCNYSIADQVGFSGGEVS----NGFNGSYDLIHENNGNMNSGYYS----GGAYS 478

Query: 466 SARFDNATYQIPSAFAGVNEQENTSMLSQLSSQQQYGPGNNAQNDFTNFAPINNASVNGN 525
            A F   T Q+   F  VN+QEN  ML  LS Q   G G +    F +    NN +   N
Sbjct: 479 PAGF-GRTNQLSPRFPNVNQQENNPML--LSQQNNLGNGGDMNYLFDHLT--NNTTPXEN 533

Query: 526 TAQPE 530
              P+
Sbjct: 534 AFHPQ 538

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449528748|ref|XP_004171365.1| PREDICTED: uncharacterized protein LOC101224737 [Cucumis sativus]

 Score =  226 bits (575), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 154/358 (43%), Positives = 215/358 (60%), Gaps = 41/358 (11%)

Query: 1   VTVTRPVEALATVRIQRD-IDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRES 59
           VT+  P+EAL T+R ++   DLVVTDLHMP+MNG++LQK++ +EF  LPV++MS+D++ S
Sbjct: 36  VTLKDPMEALDTLRARKGYFDLVVTDLHMPQMNGLQLQKKVMQEFK-LPVIMMSADEKPS 94

Query: 60  VIMKALASGVAFYILKPLNPDDLKNVWQYAMTYK-----KAKSISIDEIGSFELAGFSAG 114
           VI+K+L  GVAFY++KP++ DD+K+VWQYA+T K     +  +  I    S + +  S+ 
Sbjct: 95  VILKSLEEGVAFYMVKPISLDDVKHVWQYAITPKNVIPNQTTTTVIQRQLSIDKSSSSST 154

Query: 115 KFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPKVAWTDSLHNRFLQ 174
             S  +I+   S + + KNNK            KQ   N    +K KV WT+SLHNRFLQ
Sbjct: 155 PCSEKEIIKSKSRSSKFKNNK-----------AKQNSINIPI-RKSKVIWTNSLHNRFLQ 202

Query: 175 AIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAEQGASAMG----KTLA 230
           AI+ IGL KAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAE+G  ++      TL+
Sbjct: 203 AIKLIGLHKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAEKGTHSINIYSDYTLS 262

Query: 231 LRSSFASGHVSMMLQEAHEFSQVRDQQQQMRTSAFLPGYASGVSALN----GTTFGSIGF 286
             S+FA+   S    ++H F+    + Q   + +FL      +++LN             
Sbjct: 263 -TSNFANSSHSQF--QSHLFT---PKFQPQNSHSFLQNKLHLMTSLNFQCPNPNLEGHSL 316

Query: 287 PSLGASSSSSVPQPGLMGNQANFP---QSLFGNTRNPLYQA--NSAGKTCGSSGSNAT 339
           P LG  + SS     L+ N+ NFP    S+  +T+N  + A   +    C S G+  T
Sbjct: 317 PYLGNQNHSS---HLLILNKPNFPSNMNSISSSTQNDQHIAPMENENPKCSSDGTGMT 371

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	534
TAIR|locus:2130095	664	RR2 "response regulator 2" [Ar	0.395	0.317	0.399	3.3e-39
TAIR|locus:2093668	690	RR1 "response regulator 1" [Ar	0.415	0.321	0.389	1e-36
TAIR|locus:2065398	382	RR14 "response regulator 14" [	0.413	0.578	0.353	9.5e-34
TAIR|locus:2008585	521	ARR11 "response regulator 11"	0.385	0.395	0.351	1e-29
TAIR|locus:2116587	552	RR10 "response regulator 10" [	0.149	0.144	0.567	1.5e-29
TAIR|locus:2040194	596	RR12 "response regulator 12" [	0.393	0.352	0.345	3.5e-29
UNIPROTKB|Q7Y0W3	341	Q7Y0W3 "Two-component response	0.391	0.612	0.306	1.5e-24
UNIPROTKB|Q7Y0W5	341	EHD1 "Two-component response r	0.391	0.612	0.306	1.5e-24
TAIR|locus:2155954	292	APRR4 "pseudo-response regulat	0.380	0.695	0.323	1e-21
TAIR|locus:2058445	248	MYBC1 "AT2G40970" [Arabidopsis	0.129	0.278	0.549	3.4e-17

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

 Score = 404 (147.3 bits), Expect = 3.3e-39, Sum P(2) = 3.3e-39
 Identities = 87/218 (39%), Positives = 136/218 (62%)

Query:     5 RPVEALATVRIQRD-IDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMK 63
             R   AL+ +R  ++  D+V++D+HMP+M+G +L + +  E   LPV++MS+DD +SV++K
Sbjct:    59 RAESALSLLRKNKNGFDIVISDVHMPDMDGFKLLEHVGLEMD-LPVIMMSADDSKSVVLK 117

Query:    64 ALASGVAFYILKPLNPDDLKNVWQYAMTYKKAK-SISIDEIGSFELAGFSAGKFSL---D 119
              +  G   Y++KP+  + LKN+WQ+ +  K+ + ++S    GS E  G    +      D
Sbjct:   118 GVTHGAVDYLIKPVRIEALKNIWQHVVRKKRNEWNVSEHSGGSIEDTGGDRDRQQQHRED 177

Query:   120 DIVSRSSVNEXXXXXXXXXXXXXXXXXXXQTKQNATAPKKPKVAWTDSLHNRFLQAIRHI 179
                + SSVNE                     K+++++ KKP+V W+  LH +F+ A+  +
Sbjct:   178 ADNNSSSVNEGNGRSSRKRKEEEVDDQGDD-KEDSSSLKKPRVVWSVELHQQFVAAVNQL 236

Query:   180 GLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRV 217
             G++KAVPKKILE MNVPGLTRENVASHLQKYRI+L+R+
Sbjct:   237 GVDKAVPKKILEMMNVPGLTRENVASHLQKYRIYLRRL 274

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

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

GO:0005634 "nucleus" evidence=ISM;IDA

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

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

GO:0005515 "protein binding" evidence=IPI

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

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

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

GO:0010150 "leaf senescence" evidence=IMP

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

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

GO:0007623 "circadian rhythm" evidence=RCA

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

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

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

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

 Score = 401 (146.2 bits), Expect = 1.0e-36, P = 1.0e-36
 Identities = 97/249 (38%), Positives = 149/249 (59%)

Query:     9 ALATVRIQRD-IDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
             AL+ +R  +   D+V++D+HMP+M+G +L + +  E   LPV++MS+DD +SV++K +  
Sbjct:    72 ALSLLRKNKHGFDIVISDVHMPDMDGFKLLEHVGLEMD-LPVIMMSADDSKSVVLKGVTH 130

Query:    68 GVAFYILKPLNPDDLKNVWQYAMTYKKAK-SI-----SIDEIGSFEL---------AGFS 112
             G   Y++KP+  + LKN+WQ+ +  ++++ S+     SI+E G  +          A  S
Sbjct:   131 GAVDYLIKPVRMEALKNIWQHVVRKRRSEWSVPEHSGSIEETGERQQQQHRGGGGGAAVS 190

Query:   113 AGKFSLDDIVSRSSVNEXXX--XXXXXXXXXXXXXXXXQTKQNATAPKKPKVAWTDSLHN 170
              G+ ++DD  + SSVNE                        ++A+  KKP+V W+  LH 
Sbjct:   191 GGEDAVDD--NSSSVNEGNNWRSSSRKRKDEEGEEQGDDKDEDASNLKKPRVVWSVELHQ 248

Query:   171 RFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAEQGASA-MGKTL 229
             +F+ A+  +G+EKAVPKKILE MNVPGLTRENVASHLQKYRI+L+R+   G S   G   
Sbjct:   249 QFVAAVNQLGVEKAVPKKILELMNVPGLTRENVASHLQKYRIYLRRLG--GVSQHQGN-- 304

Query:   230 ALRSSFASG 238
              L +SF +G
Sbjct:   305 -LNNSFMTG 312

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

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

GO:0005634 "nucleus" evidence=ISM;IDA

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

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

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

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

GO:0005515 "protein binding" evidence=IPI

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

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

GO:0048367 "shoot system development" evidence=IGI

GO:0080022 "primary root development" evidence=IGI

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

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

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

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

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

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

TAIR|locus:2065398 RR14 "response regulator 14" [Arabidopsis thaliana (taxid:3702)]

 Score = 367 (134.2 bits), Expect = 9.5e-34, P = 9.5e-34
 Identities = 82/232 (35%), Positives = 134/232 (57%)

Query:     1 VTVTRPVE-ALATVRIQRD-IDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRE 58
             VT+    + AL  +R ++D  DLV++D+HMP MNG  L +++      LPV++MS D R 
Sbjct:    37 VTICSQADVALTILRERKDSFDLVLSDVHMPGMNGYNLLQQVGLLEMDLPVIMMSVDGRT 96

Query:    59 SVIMKALASGVAFYILKPLNPDDLKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSL 118
             + +M  +  G   Y++KP+ P++LKN+WQ+ +   + K +   E+ S +    +    SL
Sbjct:    97 TTVMTGINHGACDYLIKPIRPEELKNIWQHVV---RRKCVMKKELRSSQALEDNKNSGSL 153

Query:   119 DDIV-SRSSVNEXXXXXXXXXXXXXXXXXXXQTKQNATA--P---KKPKVAWTDSLHNRF 172
             + +V S S  +E                      ++     P   KK +V W+  LH +F
Sbjct:   154 ETVVVSVSECSEESLMKCRNKKKKKKRSVDRDDNEDDLLLDPGNSKKSRVVWSIELHQQF 213

Query:   173 LQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAEQGASA 224
             + A+  +G++KAVPK+ILE MNVPGL+RENVASHLQK+R++LKR++ + + +
Sbjct:   214 VNAVNKLGIDKAVPKRILELMNVPGLSRENVASHLQKFRLYLKRLSGEASQS 265

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

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

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

GO:0005515 "protein binding" evidence=IPI

GO:0042802 "identical protein binding" evidence=IPI

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

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

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

TAIR|locus:2008585 ARR11 "response regulator 11" [Arabidopsis thaliana (taxid:3702)]

 Score = 332 (121.9 bits), Expect = 1.0e-29, P = 1.0e-29
 Identities = 77/219 (35%), Positives = 124/219 (56%)

Query:     8 EALATVRIQRD-IDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALA 66
             EAL  +R ++D  D+V++D++MP+M+G +L + +  E   LPV++MS D   S +MK + 
Sbjct:    45 EALRLLRERKDGYDIVISDVNMPDMDGFKLLEHVGLELD-LPVIMMSVDGETSRVMKGVQ 103

Query:    67 SGVAFYILKPLNPDDLKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSL---DDIVS 123
              G   Y+LKP+   +LK +WQ+ +  K      + E+   E  G+  G   +   D+   
Sbjct:   104 HGACDYLLKPIRMKELKIIWQHVLRKK------LQEVRDIEGCGYEGGADWITRYDEAHF 157

Query:   124 RSSVNEXXXXXXXXXXXXXXXXXXXQTKQNATAPKKPKVAWTDSLHNRFLQAIRHIGLE- 182
                  +                   ++  ++++ KK +V W+  LH++F+ A+  IG + 
Sbjct:   158 LGGGEDVSFGKKRKDFDFEKKLLQDESDPSSSSSKKARVVWSFELHHKFVNAVNQIGCDH 217

Query:   183 KAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAEQG 221
             KA PKKIL+ MNVP LTRENVASHLQKYR++L R+ E+G
Sbjct:   218 KAGPKKILDLMNVPWLTRENVASHLQKYRLYLSRL-EKG 255

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

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

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

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

GO:0005515 "protein binding" evidence=IPI

TAIR|locus:2116587 RR10 "response regulator 10" [Arabidopsis thaliana (taxid:3702)]

 Score = 239 (89.2 bits), Expect = 1.5e-29, Sum P(2) = 1.5e-29
 Identities = 46/81 (56%), Positives = 60/81 (74%)

Query:   155 TAPKKPKVAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFL 214
             TA KKP+V WT  LHN+FL A+ H+G+E+AVPKKIL+ MNV  LTRENVASHLQK+R+ L
Sbjct:   179 TAQKKPRVLWTHELHNKFLAAVDHLGVERAVPKKILDLMNVDKLTRENVASHLQKFRVAL 238

Query:   215 KRVAEQGASAMGKTLALRSSF 235
             K+V++       +  A+ S F
Sbjct:   239 KKVSDDAIQQANRA-AIDSHF 258

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

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

GO:0005634 "nucleus" evidence=ISM;IDA

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

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

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

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

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

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

GO:0048367 "shoot system development" evidence=IGI

GO:0080022 "primary root development" evidence=IGI

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

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

TAIR|locus:2040194 RR12 "response regulator 12" [Arabidopsis thaliana (taxid:3702)]

 Score = 330 (121.2 bits), Expect = 3.5e-29, P = 3.5e-29
 Identities = 76/220 (34%), Positives = 119/220 (54%)

Query:     1 VTVTRPVE-ALATVRIQRD-IDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRE 58
             VT T   + AL  +R  ++  DLV++D+ MP+M+G +L + +  E   LPV+++S+    
Sbjct:    43 VTTTNQAQKALELLRENKNKFDLVISDVDMPDMDGFKLLELVGLEMD-LPVIMLSAHSDP 101

Query:    59 SVIMKALASGVAFYILKPLNPDDLKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSL 118
               +MK +  G   Y+LKP+  ++LKN+WQ+ +  +  K+   +  G       + G    
Sbjct:   102 KYVMKGVTHGACDYLLKPVRIEELKNIWQHVVRSRFDKNRGSNNNGDKRDGSGNEG---- 157

Query:   119 DDIVSRSSVNEXXXXXXXXXXXXXXXXXXXQTKQNATAPKKPKVAWTDSLHNRFLQAIRH 178
                V  S  N                        ++ A KK +V WT  LH +F+ A+  
Sbjct:   158 ---VGNSDQNNGKGNRKRKDQYNEDEDEDRDDNDDSCAQKKQRVVWTVELHKKFVAAVNQ 214

Query:   179 IGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVA 218
             +G EKA+PKKIL+ MNV  LTRENVASHLQK+R++LKR++
Sbjct:   215 LGYEKAMPKKILDLMNVEKLTRENVASHLQKFRLYLKRIS 254

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

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

GO:0005634 "nucleus" evidence=ISM;IDA

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

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

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

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

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

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

GO:0048367 "shoot system development" evidence=IGI

GO:0080022 "primary root development" evidence=IGI

UNIPROTKB|Q7Y0W3 Q7Y0W3 "Two-component response regulator EHD1" [Oryza sativa Indica Group (taxid:39946)]

 Score = 283 (104.7 bits), Expect = 1.5e-24, P = 1.5e-24
 Identities = 66/215 (30%), Positives = 110/215 (51%)

Query:    19 IDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLN 78
             +DLV++D   P  +G+ + +E+  +F  +P ++M+S    + +MK +A+G   ++LKP+ 
Sbjct:    57 VDLVISDAFFPTEDGLLILQEVTSKFG-IPTVIMASSGDTNTVMKYVANGAFDFLLKPVR 115

Query:    79 PDDLKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSL---DDIVSRSSVNEXXXXXX 135
              ++L N+WQ+    +     + + +G+ E  G      ++       +RS+  E      
Sbjct:   116 IEELSNIWQHIFRKQMQDHKNNNMVGNLEKPGHPPSILAMARATPATTRSTATEASLAPL 175

Query:   136 XXXXXXXXXXXXXQTKQNATAPKKPKVAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNV 195
                          +        K  ++ WT  LH +F+ A+ H+G +KAVPKKIL  M V
Sbjct:   176 ENEVRDDMVNYNGEITDIRDLGKS-RLTWTTQLHRQFIAAVNHLGEDKAVPKKILGIMKV 234

Query:   196 PGLTRENVASHLQKYRIFLKRVAEQGASAMGKTLA 230
               LTRE VASHLQKYR+ LK+      S  G TL+
Sbjct:   235 KHLTREQVASHLQKYRMQLKKSIPT-TSKHGATLS 268

GO:0003677 "DNA binding" evidence=IDA

GO:0048576 "positive regulation of short-day photoperiodism, flowering" evidence=IMP

UNIPROTKB|Q7Y0W5 EHD1 "Two-component response regulator EHD1" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 283 (104.7 bits), Expect = 1.5e-24, P = 1.5e-24
 Identities = 66/215 (30%), Positives = 110/215 (51%)

Query:    19 IDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLN 78
             +DLV++D   P  +G+ + +E+  +F  +P ++M+S    + +MK +A+G   ++LKP+ 
Sbjct:    57 VDLVISDAFFPTEDGLLILQEVTSKFG-IPTVIMASSGDTNTVMKYVANGAFDFLLKPVR 115

Query:    79 PDDLKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSL---DDIVSRSSVNEXXXXXX 135
              ++L N+WQ+    +     + + +G+ E  G      ++       +RS+  E      
Sbjct:   116 IEELSNIWQHIFRKQMQDHKNNNMVGNLEKPGHPPSILAMARATPATTRSTATEASLAPL 175

Query:   136 XXXXXXXXXXXXXQTKQNATAPKKPKVAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNV 195
                          +        K  ++ WT  LH +F+ A+ H+G +KAVPKKIL  M V
Sbjct:   176 ENEVRDDMVNYNGEITDIRDLGKS-RLTWTTQLHRQFIAAVNHLGEDKAVPKKILGIMKV 234

Query:   196 PGLTRENVASHLQKYRIFLKRVAEQGASAMGKTLA 230
               LTRE VASHLQKYR+ LK+      S  G TL+
Sbjct:   235 KHLTREQVASHLQKYRMQLKKSIPT-TSKHGATLS 268

GO:0048576 "positive regulation of short-day photoperiodism, flowering" evidence=IMP

TAIR|locus:2155954 APRR4 "pseudo-response regulator 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 258 (95.9 bits), Expect = 1.0e-21, P = 1.0e-21
 Identities = 68/210 (32%), Positives = 108/210 (51%)

Query:     1 VTVTRPV-EALATVRIQRD-IDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRE 58
             VT+   V +A+ T+R  R+  DL +  ++  E +      EI  E   LP++++S DD  
Sbjct:    68 VTICNEVNKAMHTLRNHRNRFDLAMIQVNNAEGDIFRFLSEIGSEMD-LPIIIISEDDSV 126

Query:    59 SVIMKALASGVAFYILKPLNPDDLKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSL 118
               + K + +G A Y++KP+ P+DL+ V+++ +  KK +       G  E A       S+
Sbjct:   127 KSVKKWMINGAADYLIKPIRPEDLRIVFKHLV--KKMRERRSVVTGEAEKAAGEKSS-SV 183

Query:   119 DDIVSRSSVNEXXXXXXXXXXXXXXXXXXXQTKQNATAPKKPKVAWTDSLHNRFLQAIRH 178
              D   R+  N+                     +  A++ KK +V W + LH  FL A+  
Sbjct:   184 GDSTIRNP-NKSKRSSCLEAEVNEEDRHDHNDRACASSAKKRRVVWDEELHQNFLNAVDF 242

Query:   179 IGLEKAVPKKILEFMNVPGLTRENVASHLQ 208
             +GLE+AVPKKIL+ M V  ++RENVASHLQ
Sbjct:   243 LGLERAVPKKILDVMKVDYISRENVASHLQ 272

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

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

TAIR|locus:2058445 MYBC1 "AT2G40970" [Arabidopsis thaliana (taxid:3702)]

 Score = 217 (81.4 bits), Expect = 3.4e-17, P = 3.4e-17
 Identities = 39/71 (54%), Positives = 55/71 (77%)

Query:   158 KKPKVAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRV 217
             K+P++ WT  LH RF+ A+ H+G++ AVPK I++ M+V GLTRENVASHLQKYR++L+R+
Sbjct:   104 KRPRLVWTPQLHKRFVDAVGHLGIKNAVPKTIMQLMSVEGLTRENVASHLQKYRLYLRRM 163

Query:   218 AEQGASAMGKT 228
               QG +  G T
Sbjct:   164 --QGGNGNGIT 172

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM;IDA

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

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

GO:0009409 "response to cold" evidence=IMP

---

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:
	PtRR20	type-b response regulator (716 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	gw1.XIII.278.1	type-a response regulator (128 aa)							•		0.501

---

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	534
TIGR01557	57	TIGR01557, myb_SHAQKYF, myb-like DNA-binding domai	1e-24
cd00156	113	cd00156, REC, Signal receiver domain; originally t	2e-21
COG0784	130	COG0784, CheY, FOG: CheY-like receiver [Signal tra	6e-20
PLN03162	526	PLN03162, PLN03162, golden-2 like transcription fa	1e-17
pfam00072	111	pfam00072, Response_reg, Response regulator receiv	2e-17
COG2197	211	COG2197, CitB, Response regulator containing a Che	3e-15
COG0745	229	COG0745, OmpR, Response regulators consisting of a	1e-11
COG2204	464	COG2204, AtoC, Response regulator containing CheY-	2e-11
COG4753	475	COG4753, COG4753, Response regulator containing Ch	4e-11
COG3437	360	COG3437, COG3437, Response regulator containing a	3e-10
COG4565	224	COG4565, CitB, Response regulator of citrate/malat	7e-09
COG3706	435	COG3706, PleD, Response regulator containing a Che	8e-09
PRK10365	441	PRK10365, PRK10365, transcriptional regulatory pro	4e-08
PRK11361	457	PRK11361, PRK11361, acetoacetate metabolism regula	6e-08
PRK10651	216	PRK10651, PRK10651, transcriptional regulator NarL	5e-07
PRK10693	303	PRK10693, PRK10693, response regulator of RpoS; Pr	7e-07
PRK10610	129	PRK10610, PRK10610, chemotaxis regulatory protein	1e-06
TIGR01818	463	TIGR01818, ntrC, nitrogen regulation protein NR(I)	2e-06
PLN03029	222	PLN03029, PLN03029, type-a response regulator prot	2e-06
PRK09959	1197	PRK09959, PRK09959, hybrid sensory histidine kinas	5e-06
TIGR02875	262	TIGR02875, spore_0_A, sporulation transcription fa	1e-05
pfam00249	47	pfam00249, Myb_DNA-binding, Myb-like DNA-binding d	1e-05
PRK09390	202	PRK09390, fixJ, response regulator FixJ; Provision	2e-05
PRK09581	457	PRK09581, pleD, response regulator PleD; Reviewed	3e-05
COG3947	361	COG3947, COG3947, Response regulator containing Ch	3e-05
COG3707	194	COG3707, AmiR, Response regulator with putative an	5e-05
PRK11083	228	PRK11083, PRK11083, DNA-binding response regulator	7e-05
PRK10430	239	PRK10430, PRK10430, DNA-binding transcriptional ac	1e-04
PRK15115	444	PRK15115, PRK15115, response regulator GlrR; Provi	2e-04
PRK10529	225	PRK10529, PRK10529, DNA-binding transcriptional ac	2e-04
COG4566	202	COG4566, TtrR, Response regulator [Signal transduc	2e-04
PRK10710	240	PRK10710, PRK10710, DNA-binding transcriptional re	3e-04
PRK10923	469	PRK10923, glnG, nitrogen regulation protein NR(I);	3e-04
CHL00148	240	CHL00148, orf27, Ycf27; Reviewed	3e-04
PRK11173	237	PRK11173, PRK11173, two-component response regulat	6e-04
PRK09581	457	PRK09581, pleD, response regulator PleD; Reviewed	8e-04
PRK13557	540	PRK13557, PRK13557, histidine kinase; Provisional	0.001
COG2201	350	COG2201, CheB, Chemotaxis response regulator conta	0.001
TIGR01387	218	TIGR01387, cztR_silR_copR, heavy metal response re	0.001
PRK15369	211	PRK15369, PRK15369, two component system sensor ki	0.002
TIGR02154	226	TIGR02154, PhoB, phosphate regulon transcriptional	0.003
PRK00742	354	PRK00742, PRK00742, chemotaxis-specific methyleste	0.003
PRK10161	229	PRK10161, PRK10161, transcriptional regulator PhoB	0.004
PRK10955	232	PRK10955, PRK10955, DNA-binding transcriptional re	0.004

>gnl|CDD|130620 TIGR01557, myb_SHAQKYF, myb-like DNA-binding domain, SHAQKYF class

 Score = 96.7 bits (241), Expect = 1e-24
 Identities = 34/57 (59%), Positives = 44/57 (77%), Gaps = 1/57 (1%)

Query: 159 KPKVAWTDSLHNRFLQAIRHIG-LEKAVPKKILEFMNVPGLTRENVASHLQKYRIFL 214
           KP+V WT+ LH+RFLQA++ +G  + A PK+ILE M V GLTR+ VASHLQKYR+  
Sbjct: 1   KPRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRLKQ 57

This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif. Length = 57

>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 = 89.2 bits (222), Expect = 2e-21
 Identities = 24/90 (26%), Positives = 49/90 (54%), Gaps = 1/90 (1%)

Query: 1   VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESV 60
           V      EALA +  +   DL++ D+ MP M+G+EL + I +    +P++ +++   +  
Sbjct: 25  VEAEDGEEALALLA-EEKPDLILLDIMMPGMDGLELLRRIRKRGPDIPIIFLTAHGDDED 83

Query: 61  IMKALASGVAFYILKPLNPDDLKNVWQYAM 90
            ++AL +G   Y+ KP +P++L    +  +
Sbjct: 84  AVEALKAGADDYLTKPFSPEELLARIRALL 113

Length = 113

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

 Score = 85.7 bits (212), Expect = 6e-20
 Identities = 24/77 (31%), Positives = 46/77 (59%)

Query: 6   PVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKAL 65
             EAL  +R     DL++ D++MP M+GIEL + +     ++PV+++++   E+   +AL
Sbjct: 39  EEEALELLRELPQPDLILLDINMPGMDGIELLRRLRARGPNIPVILLTAYADEADRERAL 98

Query: 66  ASGVAFYILKPLNPDDL 82
           A+G   Y+ KP+  ++ 
Sbjct: 99  AAGADDYLTKPIFLEEE 115

Length = 130

>gnl|CDD|178707 PLN03162, PLN03162, golden-2 like transcription factor; Provisional

 Score = 85.2 bits (210), Expect = 1e-17
 Identities = 51/148 (34%), Positives = 76/148 (51%), Gaps = 8/148 (5%)

Query: 81  DLKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRK 140
           DL  + + +   ++  S+  +E+G  E    +    +  D+VS S   E +  ++   + 
Sbjct: 165 DLGELLEGS---ERLDSVPGNEVGEEEALLLAEAAKATGDVVSASDSGECSSVDRKDNQA 221

Query: 141 ASKKDKGKQTKQNATAPKKPKVAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTR 200
           + K       K  A   KK KV WT  LH RF+ A+  +G+EKA P +ILE M V  LTR
Sbjct: 222 SPK-----SCKNAAPGKKKAKVDWTPELHRRFVHAVEQLGVEKAFPSRILELMGVQCLTR 276

Query: 201 ENVASHLQKYRIFLKRVAEQGASAMGKT 228
            N+ASHLQKYR   + +A + A A   T
Sbjct: 277 HNIASHLQKYRSHRRHLAAREAEAASWT 304

Length = 526

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

 Score = 77.6 bits (192), Expect = 2e-17
 Identities = 24/83 (28%), Positives = 46/83 (55%), Gaps = 1/83 (1%)

Query: 2   TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVI 61
                 EAL  ++ ++  DL++ D+ MP M+G+EL + I       PV+V+++   E   
Sbjct: 27  EADDGEEALELLK-EKRPDLILLDIRMPGMDGLELLRRIRRRPPTTPVIVLTAHGDEEDA 85

Query: 62  MKALASGVAFYILKPLNPDDLKN 84
           ++AL +G   ++ KP +P++L  
Sbjct: 86  VEALKAGANDFLSKPFDPEELVA 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|225107 COG2197, CitB, Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]

 Score = 74.6 bits (184), Expect = 3e-15
 Identities = 25/81 (30%), Positives = 47/81 (58%), Gaps = 1/81 (1%)

Query: 2   TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVI 61
             +   EAL   R +   D+V+ DL MP M+G+E  K++      + V+V+++ D  + +
Sbjct: 31  EASNGEEALDLAR-ELKPDVVLLDLSMPGMDGLEALKQLRARGPDIKVVVLTAHDDPAYV 89

Query: 62  MKALASGVAFYILKPLNPDDL 82
           ++AL +G   Y+LK  +P++L
Sbjct: 90  IRALRAGADGYLLKDASPEEL 110

Length = 211

>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 = 64.6 bits (158), Expect = 1e-11
 Identities = 23/83 (27%), Positives = 45/83 (54%), Gaps = 3/83 (3%)

Query: 1   VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEI-NEEFTHLPVMVMSSDDRES 59
                  EAL     +   DLV+ DL +P+++G+EL + +  ++ +  P++V+++ D E 
Sbjct: 28  DVAADGEEALE--AAREQPDLVLLDLMLPDLDGLELCRRLRAKKGSGPPIIVLTARDDEE 85

Query: 60  VIMKALASGVAFYILKPLNPDDL 82
             +  L +G   Y+ KP +P +L
Sbjct: 86  DRVLGLEAGADDYLTKPFSPREL 108

Length = 229

>gnl|CDD|225114 COG2204, AtoC, Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]

 Score = 65.8 bits (161), Expect = 2e-11
 Identities = 31/83 (37%), Positives = 46/83 (55%), Gaps = 3/83 (3%)

Query: 1   VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSD-DRES 59
           VT     EAL  +  +   DLV+ D+ MP M+G+EL KEI      LPV+VM+   D ++
Sbjct: 32  VTAESAEEALEALS-ESPFDLVLLDIRMPGMDGLELLKEIKSRDPDLPVIVMTGHGDIDT 90

Query: 60  VIMKALASGVAFYILKPLNPDDL 82
            + +AL  G   ++ KP + D L
Sbjct: 91  AV-EALRLGAFDFLEKPFDLDRL 112

Length = 464

>gnl|CDD|227095 COG4753, COG4753, Response regulator containing CheY-like receiver domain and AraC-type DNA-binding domain [Signal transduction mechanisms]

 Score = 64.7 bits (158), Expect = 4e-11
 Identities = 27/80 (33%), Positives = 48/80 (60%), Gaps = 3/80 (3%)

Query: 7   VEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSS-DDRESVIMKAL 65
            EAL  ++ +   D+V+TD++MP M+G++L K I E+      +++S  D+ E    KA+
Sbjct: 38  KEALELIQ-ETQPDIVITDINMPGMDGLDLIKAIKEQSPDTEFIILSGYDEFEYA-KKAM 95

Query: 66  ASGVAFYILKPLNPDDLKNV 85
             GV  Y+LKP++  +L+  
Sbjct: 96  KLGVKDYLLKPVDKAELEEA 115

Length = 475

>gnl|CDD|225971 COG3437, COG3437, Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]

 Score = 61.6 bits (150), Expect = 3e-10
 Identities = 23/74 (31%), Positives = 42/74 (56%), Gaps = 5/74 (6%)

Query: 16  QRDIDLVVTDLHMPEMNGIEL---QKEINEEFTHLPVMVMSS-DDRESVIMKALASGVAF 71
           +   DLV+ D+ MPEM+G E+    K ++     +PV+++++  D E    +AL +G   
Sbjct: 56  EEPPDLVLLDVRMPEMDGAEVLNKLKAMSPSTRRIPVILLTAYADSEDRQ-RALEAGADD 114

Query: 72  YILKPLNPDDLKNV 85
           Y+ KP++P +L   
Sbjct: 115 YLSKPISPKELVAR 128

Length = 360

>gnl|CDD|226931 COG4565, CitB, Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]

 Score = 55.7 bits (135), Expect = 7e-09
 Identities = 27/100 (27%), Positives = 49/100 (49%), Gaps = 5/100 (5%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
           EA   +      DL++ D++MP+ NGIEL  E+  +   + V+V+++      I +AL  
Sbjct: 37  EAKMIIEEF-KPDLILLDIYMPDGNGIELLPELRSQHYPVDVIVITAASDMETIKEALRY 95

Query: 68  GVAFYILKPLNPDDLKNVW----QYAMTYKKAKSISIDEI 103
           GV  Y++KP   + L+       Q     +  + +S  E+
Sbjct: 96  GVVDYLIKPFTFERLQQALTRYRQKRHALESHQQLSQKEL 135

Length = 224

>gnl|CDD|226229 COG3706, PleD, Response regulator containing a CheY-like receiver domain and a GGDEF domain [Signal transduction mechanisms]

 Score = 57.3 bits (139), Expect = 8e-09
 Identities = 27/82 (32%), Positives = 47/82 (57%), Gaps = 3/82 (3%)

Query: 3   VTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMSSDDRESV 60
            T   EAL  +  +   DLV+ D +MP+M+G+EL   +   E    +P++++SS D + +
Sbjct: 162 ATDGEEALLQL-AELPPDLVLLDANMPDMDGLELCTRLRQLERTRDIPIILLSSKDDDEL 220

Query: 61  IMKALASGVAFYILKPLNPDDL 82
           +++A   GV  YI KP+   +L
Sbjct: 221 VVRAFELGVNDYITKPIEEGEL 242

Length = 435

>gnl|CDD|182412 PRK10365, PRK10365, transcriptional regulatory protein ZraR; Provisional

 Score = 55.0 bits (132), Expect = 4e-08
 Identities = 29/87 (33%), Positives = 51/87 (58%), Gaps = 1/87 (1%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
           +AL  VR ++  DLV+ D+ M EM+GI   KEI      +PV++M++       ++AL +
Sbjct: 40  QALEQVR-EQVFDLVLCDVRMAEMDGIATLKEIKALNPAIPVLIMTAYSSVETAVEALKT 98

Query: 68  GVAFYILKPLNPDDLKNVWQYAMTYKK 94
           G   Y++KPL+ D+L+   + A+ +  
Sbjct: 99  GALDYLIKPLDFDNLQATLEKALAHTH 125

Length = 441

>gnl|CDD|183099 PRK11361, PRK11361, acetoacetate metabolism regulatory protein AtoC; Provisional

 Score = 54.9 bits (132), Expect = 6e-08
 Identities = 31/102 (30%), Positives = 50/102 (49%), Gaps = 5/102 (4%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
            AL         D+V+ D+ MPEM+GI+  KE+    T  PV++M++       ++AL  
Sbjct: 39  TALHLFADIH-PDVVLMDIRMPEMDGIKALKEMRSHETRTPVILMTAYAEVETAVEALRC 97

Query: 68  GVAFYILKPLNPDDLKNVWQYAMTYKKAKSISIDEIGSFELA 109
           G   Y++KP + D+L  + Q A+  +  K     EI     A
Sbjct: 98  GAFDYVIKPFDLDELNLIVQRALQLQSMK----KEIRHLHQA 135

Length = 457

>gnl|CDD|182619 PRK10651, PRK10651, transcriptional regulator NarL; Provisional

 Score = 50.4 bits (121), Expect = 5e-07
 Identities = 28/89 (31%), Positives = 45/89 (50%), Gaps = 2/89 (2%)

Query: 16  QRDIDLVVTDLHMPEMNGIELQKEINE-EFTHLPVMVMSSDDRESVIMKALASGVAFYIL 74
             D DL++ DL+MP MNG+E   ++ E   +   V+   S+  E V+  AL  G   Y+L
Sbjct: 50  SLDPDLILLDLNMPGMNGLETLDKLREKSLSGRIVVFSVSNHEEDVV-TALKRGADGYLL 108

Query: 75  KPLNPDDLKNVWQYAMTYKKAKSISIDEI 103
           K + P+DL    Q A   +   S ++  +
Sbjct: 109 KDMEPEDLLKALQQAAAGEMVLSEALTPV 137

Length = 216

>gnl|CDD|182652 PRK10693, PRK10693, response regulator of RpoS; Provisional

 Score = 50.8 bits (122), Expect = 7e-07
 Identities = 27/71 (38%), Positives = 40/71 (56%), Gaps = 1/71 (1%)

Query: 7  VEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALA 66
          V+AL  +      DL++ DL MP MNGIE  + +       PV+V+S+ +  + I KAL 
Sbjct: 7  VDALELLGGFT-PDLIICDLAMPRMNGIEFVEHLRNRGDQTPVLVISATENMADIAKALR 65

Query: 67 SGVAFYILKPL 77
           GV   +LKP+
Sbjct: 66 LGVQDVLLKPV 76

Length = 303

>gnl|CDD|170568 PRK10610, PRK10610, chemotaxis regulatory protein CheY; Provisional

 Score = 47.3 bits (112), Expect = 1e-06
 Identities = 23/79 (29%), Positives = 47/79 (59%), Gaps = 3/79 (3%)

Query: 7   VEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKA 64
           V+AL  ++       V++D +MP M+G+EL K I  +   + LPV++++++ ++  I+ A
Sbjct: 40  VDALNKLQ-AGGFGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAA 98

Query: 65  LASGVAFYILKPLNPDDLK 83
             +G + Y++KP     L+
Sbjct: 99  AQAGASGYVVKPFTAATLE 117

Length = 129

>gnl|CDD|233585 TIGR01818, ntrC, nitrogen regulation protein NR(I)

 Score = 50.1 bits (120), Expect = 2e-06
 Identities = 21/76 (27%), Positives = 41/76 (53%)

Query: 20  DLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP 79
           DL++TD+ MP  +G++L  +I +    LPV+VM++       + A   G   Y+ KP + 
Sbjct: 44  DLLITDVRMPGEDGLDLLPQIKKRHPQLPVIVMTAHSDLDTAVAAYQRGAFEYLPKPFDL 103

Query: 80  DDLKNVWQYAMTYKKA 95
           D+   + + A+ + + 
Sbjct: 104 DEAVTLVERALAHAQE 119

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 [Central intermediary metabolism, Nitrogen metabolism, Regulatory functions, DNA interactions, Signal transduction, Two-component systems]. Length = 463

>gnl|CDD|215544 PLN03029, PLN03029, type-a response regulator protein; Provisional

 Score = 48.5 bits (115), Expect = 2e-06
 Identities = 27/78 (34%), Positives = 45/78 (57%), Gaps = 2/78 (2%)

Query: 18  DIDLVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILK 75
           +++L++TD  MP M G +L K+I E     ++PV++MSS++  S I + L  G   + LK
Sbjct: 72  EVNLIITDYCMPGMTGYDLLKKIKESSSLRNIPVVIMSSENVPSRITRCLEEGAEEFFLK 131

Query: 76  PLNPDDLKNVWQYAMTYK 93
           P+   DL  +  + M  K
Sbjct: 132 PVQLSDLNRLKPHMMKTK 149

Length = 222

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

 Score = 49.3 bits (117), Expect = 5e-06
 Identities = 28/80 (35%), Positives = 50/80 (62%), Gaps = 1/80 (1%)

Query: 4    TRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMK 63
            T  V+AL  V +Q   DL++TD++MP M+G EL +++ E+ + LP+  ++++ + +   K
Sbjct: 989  TDGVQALHKVSMQH-YDLLITDVNMPNMDGFELTRKLREQNSSLPIWGLTANAQANEREK 1047

Query: 64   ALASGVAFYILKPLNPDDLK 83
             L+ G+   + KPL  D LK
Sbjct: 1048 GLSCGMNLCLFKPLTLDVLK 1067

Length = 1197

>gnl|CDD|131922 TIGR02875, spore_0_A, sporulation transcription factor Spo0A

 Score = 47.1 bits (112), Expect = 1e-05
 Identities = 26/74 (35%), Positives = 50/74 (67%), Gaps = 3/74 (4%)

Query: 7   VEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINE-EFTHLP-VMVMSSDDRESVIMKA 64
           V+AL  ++ Q+  D+VV D+ MP ++GI + +++NE E +  P V+++S+  +E +  +A
Sbjct: 38  VDALELIKEQQP-DVVVLDIIMPHLDGIGVLEKLNEIELSARPRVIMLSAFGQEKITQRA 96

Query: 65  LASGVAFYILKPLN 78
           +A G  +Y+LKP +
Sbjct: 97  VALGADYYVLKPFD 110

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 [Cellular processes, Sporulation and germination]. Length = 262

>gnl|CDD|215818 pfam00249, Myb_DNA-binding, Myb-like DNA-binding domain

 Score = 42.1 bits (100), Expect = 1e-05
 Identities = 10/51 (19%), Positives = 18/51 (35%), Gaps = 4/51 (7%)

Query: 161 KVAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYR 211
           +  WT       ++A++  G       KI + +  PG T     +    Y 
Sbjct: 1   RGPWTPEEDELLIEAVKKHG--NGNWSKIAKHL--PGRTDNQCKNRWNNYL 47

This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family. Length = 47

>gnl|CDD|181815 PRK09390, fixJ, response regulator FixJ; Provisional

 Score = 45.8 bits (109), Expect = 2e-05
 Identities = 21/61 (34%), Positives = 35/61 (57%)

Query: 22  VVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD 81
           VVTD+ MP ++GIEL + +    + LPV+VM+      + ++A+  G   +I KP   + 
Sbjct: 51  VVTDVRMPGIDGIELLRRLKARGSPLPVIVMTGHGDVPLAVEAMKLGAVDFIEKPFEDER 110

Query: 82  L 82
           L
Sbjct: 111 L 111

Length = 202

>gnl|CDD|236577 PRK09581, pleD, response regulator PleD; Reviewed

 Score = 46.4 bits (111), Expect = 3e-05
 Identities = 25/81 (30%), Positives = 47/81 (58%), Gaps = 5/81 (6%)

Query: 1   VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEI--NEEFTHLPV-MVMSSDDR 57
           +T +   EA+A    ++  D+++ D+ MP M+G E+ + +  +   TH+PV MV + DD 
Sbjct: 30  LTASSGAEAIAICEREQ-PDIILLDVMMPGMDGFEVCRRLKSDPATTHIPVVMVTALDDP 88

Query: 58  ESVIMKALASGVAFYILKPLN 78
           E  + + L +G   ++ KP+N
Sbjct: 89  EDRV-RGLEAGADDFLTKPIN 108

Length = 457

>gnl|CDD|226456 COG3947, COG3947, Response regulator containing CheY-like receiver and SARP domains [Signal transduction mechanisms]

 Score = 46.0 bits (109), Expect = 3e-05
 Identities = 23/84 (27%), Positives = 43/84 (51%), Gaps = 3/84 (3%)

Query: 2   TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVI 61
           + + PVEAL  +      DL+  D+ MP MNGIE  +++ +  + +P++ +SS    +  
Sbjct: 29  SCSHPVEALDLL-EVFKPDLIFLDIVMPYMNGIEFAEQVRDIESAVPIIFISSHAEYAD- 86

Query: 62  MKALASGVAFYILKPLNPDDLKNV 85
             +    +  Y+ KP+ P+ L   
Sbjct: 87  -DSFGMNLDDYLPKPVTPEKLNRA 109

Length = 361

>gnl|CDD|226230 COG3707, AmiR, Response regulator with putative antiterminator output domain [Signal transduction mechanisms]

 Score = 44.2 bits (105), Expect = 5e-05
 Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 20  DLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP 79
           D+V+ D+ MP  + IE     +E      V + +  D   +I  A+ +GV  YI+KPL+ 
Sbjct: 52  DVVILDIEMPRRDIIEALLLASENVARPIVALTAYSDPA-LIEAAIEAGVMAYIVKPLDE 110

Query: 80  DDLKNVWQYAM 90
             L  +   A+
Sbjct: 111 SRLLPILDVAV 121

Length = 194

>gnl|CDD|236838 PRK11083, PRK11083, DNA-binding response regulator CreB; Provisional

 Score = 44.2 bits (105), Expect = 7e-05
 Identities = 23/78 (29%), Positives = 42/78 (53%), Gaps = 1/78 (1%)

Query: 2   TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVI 61
              R + AL  +R Q+  DLV+ D+ +P+++G EL +++      LPV+ +++   E   
Sbjct: 32  WFERGLPALDKLR-QQPPDLVILDVGLPDISGFELCRQLLAFHPALPVIFLTARSDEVDR 90

Query: 62  MKALASGVAFYILKPLNP 79
           +  L  G   Y+ KP +P
Sbjct: 91  LVGLEIGADDYVAKPFSP 108

Length = 228

>gnl|CDD|182454 PRK10430, PRK10430, DNA-binding transcriptional activator DcuR; Provisional

 Score = 43.6 bits (103), Expect = 1e-04
 Identities = 20/61 (32%), Positives = 35/61 (57%)

Query: 16  QRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILK 75
              IDL++ D++M + NG++L   ++E      V+V+SS    + I  +L  GV  Y++K
Sbjct: 47  DTPIDLILLDIYMQQENGLDLLPVLHEAGCKSDVIVISSAADAATIKDSLHYGVVDYLIK 106

Query: 76  P 76
           P
Sbjct: 107 P 107

Length = 239

>gnl|CDD|185070 PRK15115, PRK15115, response regulator GlrR; Provisional

 Score = 44.1 bits (104), Expect = 2e-04
 Identities = 32/117 (27%), Positives = 61/117 (52%), Gaps = 17/117 (14%)

Query: 15  IQRD-IDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYI 73
           + R+ +DLV++DL M EM+G++L  EI +    +PV+++++       + A   GV  ++
Sbjct: 45  LNREKVDLVISDLRMDEMDGMQLFAEIQKVQPGMPVIILTAHGSIPDAVAATQQGVFSFL 104

Query: 74  LKPLNPDDLKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNER 130
            KP++ D L         YK     +ID+  + E +  +  +   + IV+RS +  R
Sbjct: 105 TKPVDRDAL---------YK-----AIDD--ALEQSAPATDERWREAIVTRSPLMLR 145

Length = 444

>gnl|CDD|182522 PRK10529, PRK10529, DNA-binding transcriptional activator KdpE; Provisional

 Score = 42.5 bits (100), Expect = 2e-04
 Identities = 21/60 (35%), Positives = 39/60 (65%), Gaps = 1/60 (1%)

Query: 17  RDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKP 76
           R  DL++ DL +P+ +GIE  +++  +++ +PV+V+S+   ES  + AL +G   Y+ KP
Sbjct: 44  RKPDLIILDLGLPDGDGIEFIRDL-RQWSAIPVIVLSARSEESDKIAALDAGADDYLSKP 102

Length = 225

>gnl|CDD|226932 COG4566, TtrR, Response regulator [Signal transduction mechanisms]

 Score = 42.3 bits (100), Expect = 2e-04
 Identities = 21/72 (29%), Positives = 40/72 (55%), Gaps = 4/72 (5%)

Query: 22  VVTDLHMPEMNGIELQKEINEEFTHLPVMVMS--SDDRESVIMKALASGVAFYILKPLNP 79
           ++ D+ MP M+G+ELQ  + E    LPV+ ++   D   +V  +A+ +G   ++ KP + 
Sbjct: 52  LLLDVRMPGMSGLELQDRLAERGIRLPVIFLTGHGDIPMAV--QAMKAGAVDFLEKPFSE 109

Query: 80  DDLKNVWQYAMT 91
            DL +  + A+ 
Sbjct: 110 QDLLDAVERALA 121

Length = 202

>gnl|CDD|182665 PRK10710, PRK10710, DNA-binding transcriptional regulator BaeR; Provisional

 Score = 42.4 bits (100), Expect = 3e-04
 Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 2/77 (2%)

Query: 3   VTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIM 62
           ++   E L  VR Q   DL++ DL +P  +G+ L +EI   F+ +P++++++   E   +
Sbjct: 40  LSHGDEVLPYVR-QTPPDLILLDLMLPGTDGLTLCREI-RRFSDIPIVMVTAKIEEIDRL 97

Query: 63  KALASGVAFYILKPLNP 79
             L  G   YI KP +P
Sbjct: 98  LGLEIGADDYICKPYSP 114

Length = 240

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

 Score = 42.9 bits (101), Expect = 3e-04
 Identities = 19/62 (30%), Positives = 36/62 (58%)

Query: 20  DLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP 79
           D++++D+ MP M+G+ L K+I +    LPV++M++       + A   G   Y+ KP + 
Sbjct: 49  DVLLSDIRMPGMDGLALLKQIKQRHPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDI 108

Query: 80  DD 81
           D+
Sbjct: 109 DE 110

Length = 469

>gnl|CDD|214376 CHL00148, orf27, Ycf27; Reviewed

 Score = 42.0 bits (99), Expect = 3e-04
 Identities = 29/113 (25%), Positives = 59/113 (52%), Gaps = 4/113 (3%)

Query: 1   VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESV 60
           +T +   EAL   R ++  DLV+ D+ MP+++G  + +EI +E + +P++++++    S 
Sbjct: 34  ITASDGEEALKLFRKEQ-PDLVILDVMMPKLDGYGVCQEIRKE-SDVPIIMLTALGDVSD 91

Query: 61  IMKALASGVAFYILKPLNPDDLKNVWQYAM--TYKKAKSISIDEIGSFELAGF 111
            +  L  G   Y++KP +P +L+   +  +  T KK+ S  I       +   
Sbjct: 92  RITGLELGADDYVVKPFSPKELEARIRSVLRRTNKKSFSSKIPNSSIIRIGFL 144

Length = 240

>gnl|CDD|183013 PRK11173, PRK11173, two-component response regulator; Provisional

 Score = 41.2 bits (97), Expect = 6e-04
 Identities = 34/122 (27%), Positives = 59/122 (48%), Gaps = 12/122 (9%)

Query: 18  DIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPL 77
           DI+LV+ D+++P  NG+ L +E+ E+  ++ +M ++  D E   +  L  G   YI KP 
Sbjct: 47  DINLVIMDINLPGKNGLLLARELREQ-ANVALMFLTGRDNEVDKILGLEIGADDYITKPF 105

Query: 78  NPDDL----KNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKN 133
           NP +L    +N+    M      S     + S++  G+        DI SRS ++   + 
Sbjct: 106 NPRELTIRARNLLSRTMN-LGTVSEERRSVESYKFNGWEL------DINSRSLISPDGEQ 158

Query: 134 NK 135
            K
Sbjct: 159 YK 160

Length = 237

>gnl|CDD|236577 PRK09581, pleD, response regulator PleD; Reviewed

 Score = 41.4 bits (98), Expect = 8e-04
 Identities = 22/84 (26%), Positives = 46/84 (54%), Gaps = 3/84 (3%)

Query: 1   VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIEL--QKEINEEFTHLPVMVMSSDDRE 58
           V V+ P EAL     + + DLV+   +    + + L  Q    E   ++P++++  +D +
Sbjct: 182 VVVSDPSEALFNA-AETNYDLVIVSANFENYDPLRLCSQLRSKERTRYVPILLLVDEDDD 240

Query: 59  SVIMKALASGVAFYILKPLNPDDL 82
             ++KAL  GV  Y+++P++ ++L
Sbjct: 241 PRLVKALELGVNDYLMRPIDKNEL 264

Length = 457

>gnl|CDD|237425 PRK13557, PRK13557, histidine kinase; Provisional

 Score = 41.2 bits (97), Expect = 0.001
 Identities = 26/83 (31%), Positives = 39/83 (46%), Gaps = 3/83 (3%)

Query: 2   TVTRPVEALATVRIQRDIDLVVTDLHMP-EMNGIELQKEINEEFTHLPVMVMSSDDRESV 60
             +   EAL  +    ++DL+ TDL MP  MNG+ L +E       + V++ +     S 
Sbjct: 444 VASNGREALEILDSHPEVDLLFTDLIMPGGMNGVMLAREARRRQPKIKVLLTTGYAEAS- 502

Query: 61  IMKALASGVAFYIL-KPLNPDDL 82
           I +  A G  F IL KP    +L
Sbjct: 503 IERTDAGGSEFDILNKPYRRAEL 525

Length = 540

>gnl|CDD|225111 COG2201, CheB, Chemotaxis response regulator containing a CheY-like receiver domain and a methylesterase domain [Cell motility and secretion / Signal transduction mechanisms]

 Score = 40.7 bits (96), Expect = 0.001
 Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 3/59 (5%)

Query: 20  DLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRES--VIMKALASGVAFYILKP 76
           D++  D+ MP M+G+E  ++I      LPV+++SS   E     ++AL  G   +I KP
Sbjct: 49  DVITLDVEMPVMDGLEALRKIMRLRP-LPVIMVSSLTEEGAEATLEALELGAVDFIAKP 106

Length = 350

>gnl|CDD|130454 TIGR01387, cztR_silR_copR, heavy metal response regulator

 Score = 40.2 bits (94), Expect = 0.001
 Identities = 16/61 (26%), Positives = 34/61 (55%)

Query: 16  QRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILK 75
           + D DL++ D+ +P M+G ++ + +       PV+ +++ D  +  +K L  G   Y++K
Sbjct: 40  KDDYDLIILDVMLPGMDGWQILQTLRRSGKQTPVLFLTARDSVADKVKGLDLGADDYLVK 99

Query: 76  P 76
           P
Sbjct: 100 P 100

Members of this family contain a response regulator receiver domain (pfam00072) and an associated transcriptional regulatory region (pfam00486). This group is separated phylogenetically from related proteins with similar architecture and contains a number of proteins associated with heavy metal resistance efflux systems for copper, silver, cadmium, and/or zinc. Most members encoded by genes adjacent to genes for encoding a member of the heavy metal sensor histidine kinase family (TIGRFAMs:TIGR01386), its partner in the two-component response regulator system. Length = 218

>gnl|CDD|185267 PRK15369, PRK15369, two component system sensor kinase SsrB; Provisional

 Score = 39.3 bits (92), Expect = 0.002
 Identities = 16/56 (28%), Positives = 37/56 (66%)

Query: 20  DLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILK 75
           D+V+ DL +P MNG+++  ++++ +  + ++V+++   E +  + LA+G   Y+LK
Sbjct: 51  DIVILDLGLPGMNGLDVIPQLHQRWPAMNILVLTARQEEHMASRTLAAGALGYVLK 106

Length = 211

>gnl|CDD|131209 TIGR02154, PhoB, phosphate regulon transcriptional regulatory protein PhoB

 Score = 38.8 bits (91), Expect = 0.003
 Identities = 26/102 (25%), Positives = 51/102 (50%), Gaps = 7/102 (6%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMSSDDRESVIMKAL 65
           EAL  +  +R  DL++ D  +P  +GIEL + +    E   +P++++++   E   ++ L
Sbjct: 37  EALTLIN-ERGPDLILLDWMLPGTSGIELCRRLRRRPETRAIPIIMLTARGEEEDRVRGL 95

Query: 66  ASGVAFYILKPLNPDDL----KNVWQYAMTYKKAKSISIDEI 103
            +G   YI KP +P +L    K V +        + I + ++
Sbjct: 96  ETGADDYITKPFSPRELLARIKAVLRRIRPQLSDEVIEVGDL 137

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 [Regulatory functions, DNA interactions, Signal transduction, Two-component systems]. Length = 226

>gnl|CDD|234828 PRK00742, PRK00742, chemotaxis-specific methylesterase; Provisional

 Score = 39.7 bits (94), Expect = 0.003
 Identities = 19/77 (24%), Positives = 40/77 (51%), Gaps = 4/77 (5%)

Query: 2   TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRE--S 59
           T    +EA   ++ + + D++  D+ MP M+G++  ++I       PV+++SS       
Sbjct: 34  TAPDGLEAREKIK-KLNPDVITLDVEMPVMDGLDALEKIMRL-RPTPVVMVSSLTERGAE 91

Query: 60  VIMKALASGVAFYILKP 76
           + ++AL  G   ++ KP
Sbjct: 92  ITLRALELGAVDFVTKP 108

Length = 354

>gnl|CDD|182277 PRK10161, PRK10161, transcriptional regulator PhoB; Provisional

 Score = 38.9 bits (90), Expect = 0.004
 Identities = 24/95 (25%), Positives = 50/95 (52%), Gaps = 6/95 (6%)

Query: 20  DLVVTDLHMPEMNGIELQKEINEEFT--HLPVMVMSSDDRESVIMKALASGVAFYILKPL 77
           DL++ D  +P  +GI+  K +  E     +PV+++++   E   ++ L +G   YI KP 
Sbjct: 48  DLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPF 107

Query: 78  NPDDLKNVWQYAMTYKKAKSISIDEIGSFELAGFS 112
           +P +L  V +     ++   ++++E+   E+ G S
Sbjct: 108 SPKEL--VARIKAVMRRISPMAVEEV--IEMQGLS 138

Length = 229

>gnl|CDD|182864 PRK10955, PRK10955, DNA-binding transcriptional regulator CpxR; Provisional

 Score = 38.6 bits (90), Expect = 0.004
 Identities = 21/64 (32%), Positives = 36/64 (56%), Gaps = 1/64 (1%)

Query: 19  IDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLN 78
           IDL++ D+ MP+ NGI+  KE+ +     PV+++++   E   +  L  G   Y+ KP N
Sbjct: 45  IDLLLLDVMMPKKNGIDTLKELRQTH-QTPVIMLTARGSELDRVLGLELGADDYLPKPFN 103

Query: 79  PDDL 82
             +L
Sbjct: 104 DREL 107

Length = 232

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	534
COG2197	211	CitB Response regulator containing a CheY-like rec	99.73
COG4566	202	TtrR Response regulator [Signal transduction mecha	99.67
PRK11475	207	DNA-binding transcriptional activator BglJ; Provis	99.67
PLN03162	526	golden-2 like transcription factor; Provisional	99.65
PRK10840	216	transcriptional regulator RcsB; Provisional	99.63
PRK09483	217	response regulator; Provisional	99.6
PRK10046	225	dpiA two-component response regulator DpiA; Provis	99.59
COG0745	229	OmpR Response regulators consisting of a CheY-like	99.58
COG4565	224	CitB Response regulator of citrate/malate metaboli	99.57
PRK10430	239	DNA-binding transcriptional activator DcuR; Provis	99.51
PRK09958	204	DNA-binding transcriptional activator EvgA; Provis	99.5
PRK10100	216	DNA-binding transcriptional regulator CsgD; Provis	99.49
COG4753	475	Response regulator containing CheY-like receiver d	99.49
PRK15411	207	rcsA colanic acid capsular biosynthesis activation	99.46
PRK09935	210	transcriptional regulator FimZ; Provisional	99.46
PRK10651	216	transcriptional regulator NarL; Provisional	99.45
COG2204	464	AtoC Response regulator containing CheY-like recei	99.44
PRK10360	196	DNA-binding transcriptional activator UhpA; Provis	99.43
PRK10643	222	DNA-binding transcriptional regulator BasR; Provis	99.43
PF00072	112	Response_reg: Response regulator receiver domain;	99.43
PRK10403	215	transcriptional regulator NarP; Provisional	99.43
PRK15369	211	two component system sensor kinase SsrB; Provision	99.4
PRK11083	228	DNA-binding response regulator CreB; Provisional	99.4
TIGR03787	227	marine_sort_RR proteobacterial dedicated sortase s	99.39
PRK10336	219	DNA-binding transcriptional regulator QseB; Provis	99.38
TIGR01387	218	cztR_silR_copR heavy metal response regulator. Mem	99.34
PRK10816	223	DNA-binding transcriptional regulator PhoP; Provis	99.31
PRK10955	232	DNA-binding transcriptional regulator CpxR; Provis	99.31
TIGR01557	57	myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF c	99.31
PRK09836	227	DNA-binding transcriptional activator CusR; Provis	99.3
TIGR02154	226	PhoB phosphate regulon transcriptional regulatory	99.28
PRK09390	202	fixJ response regulator FixJ; Provisional	99.28
PRK10161	229	transcriptional regulator PhoB; Provisional	99.28
PRK15479	221	transcriptional regulatory protein TctD; Provision	99.28
CHL00148	240	orf27 Ycf27; Reviewed	99.27
PRK11517	223	transcriptional regulatory protein YedW; Provision	99.25
PRK09468	239	ompR osmolarity response regulator; Provisional	99.21
PRK10766	221	DNA-binding transcriptional regulator TorR; Provis	99.2
PRK10710	240	DNA-binding transcriptional regulator BaeR; Provis	99.17
PRK10693	303	response regulator of RpoS; Provisional	99.15
COG3437	360	Response regulator containing a CheY-like receiver	99.13
COG0784	130	CheY FOG: CheY-like receiver [Signal transduction	99.12
COG3947	361	Response regulator containing CheY-like receiver a	99.11
PRK10529	225	DNA-binding transcriptional activator KdpE; Provis	99.1
PRK11173	237	two-component response regulator; Provisional	99.08
TIGR02875	262	spore_0_A sporulation transcription factor Spo0A.	99.05
PRK09581	457	pleD response regulator PleD; Reviewed	99.04
COG3706	435	PleD Response regulator containing a CheY-like rec	99.03
PRK14084	246	two-component response regulator; Provisional	99.03
KOG0519	786	consensus Sensory transduction histidine kinase [S	99.01
PRK10701	240	DNA-binding transcriptional regulator RstA; Provis	99.01
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	99.01
PLN03029	222	type-a response regulator protein; Provisional	98.99
PRK10841	924	hybrid sensory kinase in two-component regulatory	98.98
COG4567	182	Response regulator consisting of a CheY-like recei	98.97
PRK11466	914	hybrid sensory histidine kinase TorS; Provisional	98.97
PRK13856	241	two-component response regulator VirG; Provisional	98.97
PRK11107	919	hybrid sensory histidine kinase BarA; Provisional	98.92
PRK15115	444	response regulator GlrR; Provisional	98.91
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	98.9
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	98.9
PRK10365	441	transcriptional regulatory protein ZraR; Provision	98.9
PRK15347	921	two component system sensor kinase SsrA; Provision	98.89
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	98.89
PRK11697	238	putative two-component response-regulatory protein	98.87
TIGR02956	968	TMAO_torS TMAO reductase sytem sensor TorS. This p	98.86
PRK10610	129	chemotaxis regulatory protein CheY; Provisional	98.82
PRK09959	1197	hybrid sensory histidine kinase in two-component r	98.81
PRK09581	457	pleD response regulator PleD; Reviewed	98.79
PRK12555	337	chemotaxis-specific methylesterase; Provisional	98.75
PRK11091	779	aerobic respiration control sensor protein ArcB; P	98.73
PRK13435	145	response regulator; Provisional	98.7
cd00156	113	REC Signal receiver domain; originally thought to	98.69
PRK13558	665	bacterio-opsin activator; Provisional	98.64
PRK00742	354	chemotaxis-specific methylesterase; Provisional	98.64
COG3707	194	AmiR Response regulator with putative antiterminat	98.53
PRK09191	261	two-component response regulator; Provisional	98.52
COG2201	350	CheB Chemotaxis response regulator containing a Ch	98.48
PRK13557	540	histidine kinase; Provisional	98.37
PRK13837	828	two-component VirA-like sensor kinase; Provisional	98.32
COG3279	244	LytT Response regulator of the LytR/AlgR family [T	98.22
PRK15029	755	arginine decarboxylase; Provisional	97.7
COG3706	435	PleD Response regulator containing a CheY-like rec	97.54
PRK15320	251	transcriptional activator SprB; Provisional	95.82
PF03709	115	OKR_DC_1_N: Orn/Lys/Arg decarboxylase, N-terminal	95.01
PRK11107	919	hybrid sensory histidine kinase BarA; Provisional	94.71
cd02071	122	MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 bin	93.36
PF00196	58	GerE: Bacterial regulatory proteins, luxR family;	93.2
TIGR03815	322	CpaE_hom_Actino helicase/secretion neighborhood Cp	92.84
PRK00043	212	thiE thiamine-phosphate pyrophosphorylase; Reviewe	92.14
PRK13719	217	conjugal transfer transcriptional regulator TraJ;	92.02
TIGR00640	132	acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal	91.52
PRK02261	137	methylaspartate mutase subunit S; Provisional	91.44
PRK06704	228	RNA polymerase factor sigma-70; Validated	90.97
TIGR02311	249	HpaI 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldola	90.15
PRK13870	234	transcriptional regulator TraR; Provisional	89.98
PRK15201	198	fimbriae regulatory protein FimW; Provisional	89.56
TIGR01501	134	MthylAspMutase methylaspartate mutase, S subunit.	89.05
PRK10188	240	DNA-binding transcriptional activator SdiA; Provis	88.54
PF06490	109	FleQ: Flagellar regulatory protein FleQ; InterPro:	88.28
COG2771	65	CsgD DNA-binding HTH domain-containing proteins [T	88.03
PF00249	48	Myb_DNA-binding: Myb-like DNA-binding domain; Inte	87.94
TIGR03239	249	GarL 2-dehydro-3-deoxyglucarate aldolase. In E. co	87.78
PRK10128	267	2-keto-3-deoxy-L-rhamnonate aldolase; Provisional	87.78
cd02067	119	B12-binding B12 binding domain (B12-BD). This doma	87.64
PRK10558	256	alpha-dehydro-beta-deoxy-D-glucarate aldolase; Pro	87.28
cd04724	242	Tryptophan_synthase_alpha Ttryptophan synthase (TR	84.03
cd04728	248	ThiG Thiazole synthase (ThiG) is the tetrameric en	84.01
PRK00208	250	thiG thiazole synthase; Reviewed	83.31
TIGR03020	247	EpsA transcriptional regulator EpsA. Proteins in t	82.86
PRK09642	160	RNA polymerase sigma factor SigW; Reviewed	82.47
TIGR00262	256	trpA tryptophan synthase, alpha subunit. Tryptopha	82.44
PRK05458	326	guanosine 5'-monophosphate oxidoreductase; Provisi	82.31
PF03328	221	HpcH_HpaI: HpcH/HpaI aldolase/citrate lyase family	82.05
PRK13111	258	trpA tryptophan synthase subunit alpha; Provisiona	81.53
PRK12514	179	RNA polymerase sigma factor; Provisional	81.18
PRK12516	187	RNA polymerase sigma factor; Provisional	80.77
TIGR03541	232	reg_near_HchA LuxR family transcriptional regulato	80.71
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	80.63
PRK11923	193	algU RNA polymerase sigma factor AlgU; Provisional	80.53
TIGR00693	196	thiE thiamine-phosphate pyrophosphorylase. This mo	80.36
PRK12520	191	RNA polymerase sigma factor; Provisional	80.3

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

Probab=99.73  E-value=7.7e-17  Score=157.94  Aligned_cols=156  Identities=24%  Similarity=0.341  Sum_probs=127.0

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.+++++++.++. ..||+||+|+.||+++|+++++.|++..|+++||++|.+.+...+.+++++||++|+.|..++++
T Consensus        31 ~a~~~~~~l~~~~~-~~pdvvl~Dl~mP~~~G~e~~~~l~~~~p~~~vvvlt~~~~~~~v~~al~~Ga~Gyl~K~~~~~~  109 (211)
T COG2197          31 EASNGEEALDLARE-LKPDVVLLDLSMPGMDGLEALKQLRARGPDIKVVVLTAHDDPAYVIRALRAGADGYLLKDASPEE  109 (211)
T ss_pred             EeCCHHHHHHHhhh-cCCCEEEEcCCCCCCChHHHHHHHHHHCCCCcEEEEeccCCHHHHHHHHHcCCCEEEeCCCCHHH
Confidence            46679999999877 89999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccCCCCCC
Q 043479           82 LKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPK  161 (534)
Q Consensus        82 L~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss~kKpr  161 (534)
                      |..+|+.++.+..+.++.....                  +.   .... .               .. .+.       .
T Consensus       110 l~~ai~~v~~G~~~~~~~~~~~------------------~~---~~~~-~---------------~~-~~~-------~  144 (211)
T COG2197         110 LVEAIRAVAAGGTYLPPDIARK------------------LA---GLLP-S---------------SS-AEA-------P  144 (211)
T ss_pred             HHHHHHHHHCCCeEeCHHHHHH------------------HH---hhcc-c---------------cc-ccc-------c
Confidence            9999999998876554322110                  00   0000 0               00 000       0


Q ss_pred             ccCCchhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHH
Q 043479          162 VAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQK  209 (534)
Q Consensus       162 v~Wt~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQK  209 (534)
                      ..  ..|++|+.++++.+..+.. +|+|++.|+   +|..||+.|+..
T Consensus       145 ~~--~~LT~RE~eVL~lla~G~s-nkeIA~~L~---iS~~TVk~h~~~  186 (211)
T COG2197         145 LA--ELLTPRELEVLRLLAEGLS-NKEIAEELN---LSEKTVKTHVSN  186 (211)
T ss_pred             cc--CCCCHHHHHHHHHHHCCCC-HHHHHHHHC---CCHhHHHHHHHH
Confidence            00  4699999999999986666 999999999   999999999765

>COG4566 TtrR Response regulator [Signal transduction mechanisms]

Probab=99.67  E-value=7.6e-16  Score=147.28  Aligned_cols=146  Identities=22%  Similarity=0.309  Sum_probs=119.1

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++.++|..... ..|-++|+|++||+++|+++.++|.+.....|||++|++.|.....++++.||.|||.||++...
T Consensus        33 ~~~s~~~fL~~~~~-~~pGclllDvrMPg~sGlelq~~L~~~~~~~PVIfiTGhgDIpmaV~AmK~GAvDFLeKP~~~q~  111 (202)
T COG4566          33 CFASAEEFLAAAPL-DRPGCLLLDVRMPGMSGLELQDRLAERGIRLPVIFLTGHGDIPMAVQAMKAGAVDFLEKPFSEQD  111 (202)
T ss_pred             eecCHHHHHhhccC-CCCCeEEEecCCCCCchHHHHHHHHhcCCCCCEEEEeCCCChHHHHHHHHcchhhHHhCCCchHH
Confidence            56788888888654 78999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccCCCCCC
Q 043479           82 LKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPK  161 (534)
Q Consensus        82 L~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss~kKpr  161 (534)
                      |.++|+++++...........               ..++      .                                 
T Consensus       112 Lldav~~Al~~~~~~~~~~~~---------------~~~~------~---------------------------------  137 (202)
T COG4566         112 LLDAVERALARDASRRAEADR---------------QAAI------R---------------------------------  137 (202)
T ss_pred             HHHHHHHHHHHHHHHHHhHHH---------------HHHH------H---------------------------------
Confidence            999999999764422110000               0000      0                                 


Q ss_pred             ccCCchhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHH
Q 043479          162 VAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHL  207 (534)
Q Consensus       162 v~Wt~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHL  207 (534)
                       .-...|++|+.+++..+-.+.. +|.|+..|+   ++..||+.|-
T Consensus       138 -~~l~tLT~RERqVl~~vV~G~~-NKqIA~dLg---iS~rTVe~HR  178 (202)
T COG4566         138 -ARLATLTPRERQVLDLVVRGLM-NKQIAFDLG---ISERTVELHR  178 (202)
T ss_pred             -HHHHhcCHHHHHHHHHHHcCcc-cHHHHHHcC---CchhhHHHHH
Confidence             0113488999999999975555 999999999   8899999883

>PRK11475 DNA-binding transcriptional activator BglJ; Provisional

Probab=99.67  E-value=1.8e-15  Score=148.16  Aligned_cols=148  Identities=12%  Similarity=0.137  Sum_probs=119.3

Q ss_pred             eecCHHHHHHHHHhcCCceEEE---EeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHH-HcCCcEEEeCCC
Q 043479            2 TVTRPVEALATVRIQRDIDLVV---TDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKAL-ASGVAFYILKPL   77 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVL---LDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL-~aGA~dyL~KP~   77 (534)
                      ++.+++++++.+.. ..||+||   +|+.||+++|++++++|++..|.+|||++|+.++......++ ++||.+||.||.
T Consensus        22 ~~~~~~~~l~~~~~-~~pd~vl~dl~d~~mp~~~Gl~~~~~l~~~~p~~~iIvlt~~~~~~~~~~~~~~~Ga~gyl~K~~  100 (207)
T PRK11475         22 TFSSQSSFQDAMSR-ISFSAVIFSLSAMRSERREGLSCLTELAIKFPRMRRLVIADDDIEARLIGSLSPSPLDGVLSKAS  100 (207)
T ss_pred             EeCCHHHHHHHhcc-CCCCEEEeeccccCCCCCCHHHHHHHHHHHCCCCCEEEEeCCCCHHHHHHHHHHcCCeEEEecCC
Confidence            46789999998876 6799998   688899999999999999999999999999988777666655 799999999999


Q ss_pred             ChHHHHHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccCC
Q 043479           78 NPDDLKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAP  157 (534)
Q Consensus        78 s~eeL~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss~  157 (534)
                      +.++|.++|+.++++.........                     .      .         .           ..   .
T Consensus       101 ~~~eL~~aI~~v~~G~~~~~~~~~---------------------~------~---------~-----------~~---~  130 (207)
T PRK11475        101 TLEILQQELFLSLNGVRQATDRLN---------------------N------Q---------W-----------YI---N  130 (207)
T ss_pred             CHHHHHHHHHHHHCCCcccCHHHH---------------------H------H---------h-----------hc---c
Confidence            999999999999876543321100                     0      0         0           00   0


Q ss_pred             CCCCccCCchhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHH
Q 043479          158 KKPKVAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKY  210 (534)
Q Consensus       158 kKprv~Wt~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKy  210 (534)
                         .   ...|+.|+.++++.+..++. +|+|++.|+   +|..||+.|+.+.
T Consensus       131 ---~---~~~LT~RE~eVL~ll~~G~s-nkeIA~~L~---iS~~TV~~h~~~I  173 (207)
T PRK11475        131 ---Q---SRMLSPTEREILRFMSRGYS-MPQIAEQLE---RNIKTIRAHKFNV  173 (207)
T ss_pred             ---C---cCCCCHHHHHHHHHHHCCCC-HHHHHHHHC---CCHHHHHHHHHHH
Confidence               0   12499999999999986655 999999999   9999999997765

>PLN03162 golden-2 like transcription factor; Provisional

Probab=99.65  E-value=1.3e-16  Score=163.44  Aligned_cols=91  Identities=44%  Similarity=0.616  Sum_probs=75.0

Q ss_pred             ccCCCCCCccCCchhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHH----HHhhhcccCC---
Q 043479          154 ATAPKKPKVAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKR----VAEQGASAMG---  226 (534)
Q Consensus       154 ~ss~kKprv~Wt~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~lkr----~a~~~~~~~~---  226 (534)
                      ....||+|++||.+||++|+++|++||.++++||+|+++|+|+|||+++|+|||||||+++++    .+++..+...   
T Consensus       230 ~~g~KKpRLrWTpELH~rFVeAV~qLG~dKATPK~ILelMnV~GLTRenVKSHLQKYRl~rk~l~~rEaEa~swt~kr~~  309 (526)
T PLN03162        230 APGKKKAKVDWTPELHRRFVHAVEQLGVEKAFPSRILELMGVQCLTRHNIASHLQKYRSHRRHLAAREAEAASWTHRRAY  309 (526)
T ss_pred             CCCCCCCcccCCHHHHHHHHHHHHHhCcCccchHHHHHHcCCCCcCHHHHHHHHHHHHHhcccccchhhhhccchhhhhh
Confidence            456899999999999999999999999999999999999999999999999999999999984    4444433321   


Q ss_pred             -chhHhhhhhcccchHHHH
Q 043479          227 -KTLALRSSFASGHVSMML  244 (534)
Q Consensus       227 -~~~~lr~~~~sg~~~~~~  244 (534)
                       ..-..|+++++|.+.+|=
T Consensus       310 ~~~P~~rs~~~~g~p~~~p  328 (526)
T PLN03162        310 TQAPWPRSSRRDGLPYLVP  328 (526)
T ss_pred             ccCCcccCCCCCCCccccc
Confidence             112467777877777654

>PRK10840 transcriptional regulator RcsB; Provisional

Probab=99.63  E-value=1.5e-14  Score=139.74  Aligned_cols=155  Identities=18%  Similarity=0.237  Sum_probs=122.6

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCC---CCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCC
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPE---MNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLN   78 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPd---mdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s   78 (534)
                      ++.++.++++.+.. ..|||||+|+.||+   .+|++++++|++..|.+|||++|...+......+++.||++||.||.+
T Consensus        34 ~~~~~~~~~~~~~~-~~~DlvllD~~l~~~~~~~g~~~~~~l~~~~~~~~iIvls~~~~~~~~~~a~~~Ga~~yl~K~~~  112 (216)
T PRK10840         34 EFEDSTALINNLPK-LDAHVLITDLSMPGDKYGDGITLIKYIKRHFPSLSIIVLTMNNNPAILSAVLDLDIEGIVLKQGA  112 (216)
T ss_pred             EECCHHHHHHHHHh-CCCCEEEEeCcCCCCCCCCHHHHHHHHHHHCCCCcEEEEEecCCHHHHHHHHHCCCeEEEECCCC
Confidence            36789999998876 68999999999999   599999999998889999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccCCC
Q 043479           79 PDDLKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPK  158 (534)
Q Consensus        79 ~eeL~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss~k  158 (534)
                      .++|..+|+.++.++...+...                  ..++..     . .     .             ..     
T Consensus       113 ~~~l~~ai~~v~~g~~~~~~~~------------------~~~~~~-----~-~-----~-------------~~-----  145 (216)
T PRK10840        113 PTDLPKALAALQKGKKFTPESV------------------SRLLEK-----I-S-----A-------------GG-----  145 (216)
T ss_pred             HHHHHHHHHHHHCCCeecCHHH------------------HHHHHH-----h-c-----c-------------CC-----
Confidence            9999999999886654322100                  000000     0 0     0             00     


Q ss_pred             CCCccCCchhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHH
Q 043479          159 KPKVAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRI  212 (534)
Q Consensus       159 Kprv~Wt~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl  212 (534)
                       .   -...|+.|+.+++..+..+.. .|+|++.|+   +|..||++|+.+.-.
T Consensus       146 -~---~~~~Lt~rE~evl~~~~~G~s-~~eIA~~l~---iS~~TV~~h~~~i~~  191 (216)
T PRK10840        146 -Y---GDKRLSPKESEVLRLFAEGFL-VTEIAKKLN---RSIKTISSQKKSAMM  191 (216)
T ss_pred             -C---ccccCCHHHHHHHHHHHCCCC-HHHHHHHHC---CCHHHHHHHHHHHHH
Confidence             0   012499999999999985544 999999999   999999999876433

>PRK09483 response regulator; Provisional

Probab=99.60  E-value=3.8e-14  Score=134.40  Aligned_cols=159  Identities=18%  Similarity=0.235  Sum_probs=124.9

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.+..++++.+.. ..||+||+|+.+++.+|+++++.+++..+.+|||+++...+......++..|+++|+.||++.++
T Consensus        32 ~~~~~~~~~~~~~~-~~~dlvi~d~~~~~~~g~~~~~~l~~~~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~k~~~~~~  110 (217)
T PRK09483         32 EACCGEDAVKWCRT-NAVDVVLMDMNMPGIGGLEATRKILRYTPDVKIIMLTVHTENPLPAKVMQAGAAGYLSKGAAPQE  110 (217)
T ss_pred             EeCCHHHHHHHHHh-cCCCEEEEeCCCCCCCHHHHHHHHHHHCCCCeEEEEeCCCCHHHHHHHHHcCCCEEEeCCCCHHH
Confidence            36788999998887 78999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccCCCCCC
Q 043479           82 LKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPK  161 (534)
Q Consensus        82 L~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss~kKpr  161 (534)
                      |..+|++++++.........                     ........     .               ..       .
T Consensus       111 l~~~i~~~~~g~~~~~~~~~---------------------~~~~~~~~-----~---------------~~-------~  142 (217)
T PRK09483        111 VVSAIRSVHSGQRYIASDIA---------------------QQMALSQI-----E---------------PA-------T  142 (217)
T ss_pred             HHHHHHHHHCCCcccCHHHH---------------------HHHHHhhc-----c---------------cC-------C
Confidence            99999998866543221100                     00000000     0               00       0


Q ss_pred             ccCCchhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHH
Q 043479          162 VAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIF  213 (534)
Q Consensus       162 v~Wt~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~  213 (534)
                      -.....|+.|+.+++..+..++. .|+|++.|+   ++..||+.|+++++..
T Consensus       143 ~~~~~~Lt~rE~~vl~~~~~G~~-~~~Ia~~l~---is~~TV~~~~~~i~~K  190 (217)
T PRK09483        143 ENPFASLSERELQIMLMITKGQK-VNEISEQLN---LSPKTVNSYRYRMFSK  190 (217)
T ss_pred             CccccccCHHHHHHHHHHHCCCC-HHHHHHHhC---CCHHHHHHHHHHHHHH
Confidence            01223589999999999975554 899999998   8999999998887664

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=99.59  E-value=9.7e-14  Score=135.57  Aligned_cols=165  Identities=14%  Similarity=0.157  Sum_probs=119.1

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.++++.+.. ..|||||+|+.||+++|+++++.|++..+.++||++|+..+.....++++.||++||.||++.++
T Consensus        35 ~a~~~~~al~~~~~-~~pdlvllD~~mp~~~gle~~~~l~~~~~~~~iivls~~~~~~~~~~al~~Ga~~yl~Kp~~~~~  113 (225)
T PRK10046         35 LAGNLAQARMMIER-FKPGLILLDNYLPDGRGINLLHELVQAHYPGDVVFTTAASDMETVSEAVRCGVFDYLIKPIAYER  113 (225)
T ss_pred             EECCHHHHHHHHHh-cCCCEEEEeCCCCCCcHHHHHHHHHhcCCCCCEEEEEcCCCHHHHHHHHHcCccEEEECCcCHHH
Confidence            46789999999987 78999999999999999999999998777799999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccCCCCCC
Q 043479           82 LKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPK  161 (534)
Q Consensus        82 L~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss~kKpr  161 (534)
                      |..+|+++..++.........           .....+......    . .                 . +.    +.+.
T Consensus       114 L~~~i~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~----~-~-----------------~-~~----~~~~  155 (225)
T PRK10046        114 LGQTLTRFRQRKHMLESIDSA-----------SQKQIDEMFNAY----A-R-----------------G-EP----KDEL  155 (225)
T ss_pred             HHHHHHHHHHHHHHHhccCcc-----------CHHHHHHHHhhc----c-c-----------------c-cc----cccC
Confidence            999999988776543210000           000000000000    0 0                 0 00    0000


Q ss_pred             ccCCchhhHHHHHHHHHhccC--CCcHHHHHHHcCCCCCCHHHHHHHHHHH
Q 043479          162 VAWTDSLHNRFLQAIRHIGLE--KAVPKKILEFMNVPGLTRENVASHLQKY  210 (534)
Q Consensus       162 v~Wt~eLh~RFleaLe~LGle--kAvpK~ILe~M~V~GLT~~tVaSHLQKy  210 (534)
                      ..-...|+.+  ++++.+...  ....|+|++.|+   |++.||+.|+...
T Consensus       156 ~~~~~~Lt~r--~Vl~~~~~g~~g~s~~eIa~~l~---iS~~Tv~~~~~~~  201 (225)
T PRK10046        156 PTGIDPLTLN--AVRKLFKEPGVQHTAETVAQALT---ISRTTARRYLEYC  201 (225)
T ss_pred             CCCCCHHHHH--HHHHHHHcCCCCcCHHHHHHHhC---ccHHHHHHHHHHH
Confidence            0001246666  677777533  356999999999   9999999998654

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

Probab=99.58  E-value=4.4e-14  Score=140.47  Aligned_cols=91  Identities=26%  Similarity=0.455  Sum_probs=84.1

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhh-CCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEE-FTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPD   80 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~-~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~e   80 (534)
                      ++.++++|++.+.. . ||+||+|++||+++|++++++||+. ...+|||++|+..+......++++||+|||.|||++.
T Consensus        29 ~~~~~~~a~~~~~~-~-~dlviLD~~lP~~dG~~~~~~iR~~~~~~~PIi~Lta~~~~~d~v~gl~~GADDYl~KPf~~~  106 (229)
T COG0745          29 VAADGEEALEAARE-Q-PDLVLLDLMLPDLDGLELCRRLRAKKGSGPPIIVLTARDDEEDRVLGLEAGADDYLTKPFSPR  106 (229)
T ss_pred             EECCHHHHHHHHhc-C-CCEEEEECCCCCCCHHHHHHHHHhhcCCCCcEEEEECCCcHHHHHHHHhCcCCeeeeCCCCHH
Confidence            57789999999987 6 9999999999999999999999953 5568999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhh
Q 043479           81 DLKNVWQYAMTYKK   94 (534)
Q Consensus        81 eL~~aI~~aL~~k~   94 (534)
                      ||...|+.++++..
T Consensus       107 EL~ARi~a~lRR~~  120 (229)
T COG0745         107 ELLARLRALLRRNA  120 (229)
T ss_pred             HHHHHHHHHHCcCc
Confidence            99999999997754

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

Probab=99.57  E-value=2.7e-14  Score=138.99  Aligned_cols=94  Identities=28%  Similarity=0.366  Sum_probs=88.1

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      +|.+.+||...++. ..|||||+|+.||+.+|++++.+++..+..+-||++|+..+.+.+.++++.||.|||.|||..+.
T Consensus        31 ~A~~~~ea~~~i~~-~~pDLILLDiYmPd~~Gi~lL~~ir~~~~~~DVI~iTAA~d~~tI~~alr~Gv~DYLiKPf~~eR  109 (224)
T COG4565          31 TAGTLEEAKMIIEE-FKPDLILLDIYMPDGNGIELLPELRSQHYPVDVIVITAASDMETIKEALRYGVVDYLIKPFTFER  109 (224)
T ss_pred             eeccHHHHHHHHHh-hCCCEEEEeeccCCCccHHHHHHHHhcCCCCCEEEEeccchHHHHHHHHhcCchhheecceeHHH
Confidence            57899999999997 78999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhc
Q 043479           82 LKNVWQYAMTYKKAK   96 (534)
Q Consensus        82 L~~aI~~aL~~k~~~   96 (534)
                      |..++.+..+++...
T Consensus       110 l~~aL~~y~~~r~~l  124 (224)
T COG4565         110 LQQALTRYRQKRHAL  124 (224)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999988776543

>PRK10430 DNA-binding transcriptional activator DcuR; Provisional

Probab=99.51  E-value=4.8e-13  Score=131.68  Aligned_cols=92  Identities=25%  Similarity=0.325  Sum_probs=82.3

Q ss_pred             eecCHHHHHHHHHh-cCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChH
Q 043479            2 TVTRPVEALATVRI-QRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPD   80 (534)
Q Consensus         2 tass~~EALe~L~~-~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~e   80 (534)
                      .+.+..++++.+.. ...||+||+|+.||+++|+++++.+++..+.+|||++|+..+.....+++..|+++||.||++.+
T Consensus        32 ~~~~~~~a~~~~~~~~~~~DlvilD~~~p~~~G~eli~~l~~~~~~~~vI~ls~~~~~~~~~~al~~Ga~~yl~Kp~~~~  111 (239)
T PRK10430         32 TASTLEQAKEIIFNSDTPIDLILLDIYMQQENGLDLLPVLHEAGCKSDVIVISSAADAATIKDSLHYGVVDYLIKPFQAS  111 (239)
T ss_pred             EeCCHHHHHHHHHhcCCCCCEEEEecCCCCCCcHHHHHHHHhhCCCCCEEEEECCCcHHHHHHHHHcCCCEEEeCCCCHH
Confidence            35678889888752 25699999999999999999999999988899999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHh
Q 043479           81 DLKNVWQYAMTYK   93 (534)
Q Consensus        81 eL~~aI~~aL~~k   93 (534)
                      +|..+|++++...
T Consensus       112 ~l~~~i~~~~~~~  124 (239)
T PRK10430        112 RFEEALTGWRQKK  124 (239)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999998876543

>PRK09958 DNA-binding transcriptional activator EvgA; Provisional

Probab=99.50  E-value=1.3e-12  Score=122.67  Aligned_cols=157  Identities=18%  Similarity=0.186  Sum_probs=122.7

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.+..++++.+.. ..||+||+|+.+|+++|+++++.++...+..|||++++..+......++..|+++||.||++.++
T Consensus        30 ~~~~~~~~~~~~~~-~~~dlvi~d~~~~~~~g~~~~~~l~~~~~~~~ii~ls~~~~~~~~~~~~~~ga~~~i~kp~~~~~  108 (204)
T PRK09958         30 ELTEGGSAVQRVET-LKPDIVIIDVDIPGVNGIQVLETLRKRQYSGIIIIVSAKNDHFYGKHCADAGANGFVSKKEGMNN  108 (204)
T ss_pred             EeCCHHHHHHHHHc-cCCCEEEEeCCCCCCCHHHHHHHHHhhCCCCeEEEEeCCCCHHHHHHHHHCCCCEEEecCCCHHH
Confidence            36788999998886 78999999999999999999999998888899999999999899999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccCCCCCC
Q 043479           82 LKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPK  161 (534)
Q Consensus        82 L~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss~kKpr  161 (534)
                      |..+|+.++++....+.                  .......    ...                          ....+
T Consensus       109 l~~~i~~~~~~~~~~~~------------------~~~~~~~----~~~--------------------------~~~~~  140 (204)
T PRK09958        109 IIAAIEAAKNGYCYFPF------------------SLNRFVG----SLT--------------------------SDQQK  140 (204)
T ss_pred             HHHHHHHHHcCCcccCH------------------HHHHHHH----hcc--------------------------CCCcc
Confidence            99999998755322110                  0000000    000                          00001


Q ss_pred             ccCCchhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHH
Q 043479          162 VAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFL  214 (534)
Q Consensus       162 v~Wt~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~l  214 (534)
                         ...|+.++.+++..+.... ..++|++.++   ++..+|+.|+.+.|..+
T Consensus       141 ---~~~lt~~E~~vl~~l~~g~-~~~~I~~~l~---~s~~tv~~~~~~l~~Kl  186 (204)
T PRK09958        141 ---LDSLSKQEISVMRYILDGK-DNNDIAEKMF---ISNKTVSTYKSRLMEKL  186 (204)
T ss_pred             ---cccCCHHHHHHHHHHHcCC-CHHHHHHHhC---CCHHHHHHHHHHHHHHc
Confidence               1348889999999996444 4899999998   99999999998887744

>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional

Probab=99.49  E-value=3.4e-13  Score=132.85  Aligned_cols=155  Identities=8%  Similarity=0.121  Sum_probs=114.6

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHH-HHHHhhCCCCcEEEEecCCCHHHHHHHHH--cCCcEEEeCCCC
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQ-KEINEEFTHLPVMVMSSDDRESVIMKALA--SGVAFYILKPLN   78 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL-~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~--aGA~dyL~KP~s   78 (534)
                      .+.++.++++.+.   +|||||+|+.||+++|++++ +.+++..|.++||++|+.++.  ...++.  +||.+||.|+.+
T Consensus        39 ~~~~~~~~~~~~~---~~DvvllDi~~p~~~G~~~~~~~i~~~~p~~~vvvlt~~~~~--~~~~~~~~~Ga~G~l~K~~~  113 (216)
T PRK10100         39 KLHNIQRSLDDIS---SGSIILLDMMEADKKLIHYWQDTLSRKNNNIKILLLNTPEDY--PYREIENWPHINGVFYAMED  113 (216)
T ss_pred             EEcCHHHhhccCC---CCCEEEEECCCCCccHHHHHHHHHHHhCCCCcEEEEECCchh--HHHHHHHhcCCeEEEECCCC
Confidence            3567788887643   49999999999999999997 568888999999999998763  334454  599999999999


Q ss_pred             hHHHHHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccCCC
Q 043479           79 PDDLKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPK  158 (534)
Q Consensus        79 ~eeL~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss~k  158 (534)
                      .++|.++|+.+++++.+.++....                 .+...     . ...   .              .   ..
T Consensus       114 ~~~L~~aI~~v~~G~~~~~~~~~~-----------------~l~~~-----~-~~~---~--------------~---~~  150 (216)
T PRK10100        114 QERVVNGLQGVLRGECYFTQKLAS-----------------YLITH-----S-GNY---R--------------Y---NS  150 (216)
T ss_pred             HHHHHHHHHHHHcCCcccCHHHHH-----------------HHHHh-----h-ccc---c--------------c---CC
Confidence            999999999999876655422110                 00000     0 000   0              0   00


Q ss_pred             CCCccCCchhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHH
Q 043479          159 KPKVAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRI  212 (534)
Q Consensus       159 Kprv~Wt~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl  212 (534)
                      ++    ...|+.|+.+++..+..+.. .|+|++.|+   ++..||+.|+.+...
T Consensus       151 ~~----~~~Lt~rE~~Vl~l~~~G~s-~~eIA~~L~---iS~~TVk~~~~~i~~  196 (216)
T PRK10100        151 TE----SALLTHREKEILNKLRIGAS-NNEIARSLF---ISENTVKTHLYNLFK  196 (216)
T ss_pred             Cc----cCCCCHHHHHHHHHHHcCCC-HHHHHHHhC---CCHHHHHHHHHHHHH
Confidence            00    12489999999999986555 999999999   999999999877644

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

Probab=99.49  E-value=1.1e-13  Score=149.14  Aligned_cols=90  Identities=30%  Similarity=0.472  Sum_probs=86.9

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      +|.++.||++.+.+ .+|||||+|+.||+|||+++++.+++..|++.+||+|+.++.+++.+|++.|+.+||+||++.++
T Consensus        33 tA~NG~eAleli~e-~~pDiviTDI~MP~mdGLdLI~~ike~~p~~~~IILSGy~eFeYak~Am~lGV~dYLLKP~~k~e  111 (475)
T COG4753          33 TAANGKEALELIQE-TQPDIVITDINMPGMDGLDLIKAIKEQSPDTEFIILSGYDEFEYAKKAMKLGVKDYLLKPVDKAE  111 (475)
T ss_pred             ecccHHHHHHHHHh-cCCCEEEEecCCCCCcHHHHHHHHHHhCCCceEEEEeccchhHHHHHHHhcCchhheeCcCCHHH
Confidence            58899999999998 89999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHH
Q 043479           82 LKNVWQYAMTY   92 (534)
Q Consensus        82 L~~aI~~aL~~   92 (534)
                      |..++.++...
T Consensus       112 L~~~L~ki~~k  122 (475)
T COG4753         112 LEEALKKIIGK  122 (475)
T ss_pred             HHHHHHHHHHH
Confidence            99999998765

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

Probab=99.46  E-value=1.7e-12  Score=126.72  Aligned_cols=144  Identities=12%  Similarity=0.059  Sum_probs=114.1

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCC--CCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcE-EEeCCCC
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLH--MPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAF-YILKPLN   78 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~--mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~d-yL~KP~s   78 (534)
                      .+.+++++++.+.. .+|||||+|+.  ++..+|.+++++|++..|.++||++|+..+..... ++..++.. |+.|+.+
T Consensus        32 ~~~~~~~~~~~~~~-~~pDlvLlDl~~~l~~~~g~~~i~~i~~~~p~~~iivlt~~~~~~~~~-~~~~~~~~~~~~K~~~  109 (207)
T PRK15411         32 DIETVDDLAIACDS-LRPSVVFINEDCFIHDASNSQRIKQIINQHPNTLFIVFMAIANIHFDE-YLLVRKNLLISSKSIK  109 (207)
T ss_pred             ecCCHHHHHHHHhc-cCCCEEEEeCcccCCCCChHHHHHHHHHHCCCCeEEEEECCCchhHHH-HHHHHhhceeeeccCC
Confidence            36789999998876 68999999966  88889999999999999999999999988776543 55555544 8899999


Q ss_pred             hHHHHHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccCCC
Q 043479           79 PDDLKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPK  158 (534)
Q Consensus        79 ~eeL~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss~k  158 (534)
                      +++|..+|+.++.++...+.                               . .                        ..
T Consensus       110 ~~~L~~aI~~v~~g~~~~~~-------------------------------~-~------------------------~~  133 (207)
T PRK15411        110 PESLDDLLGDILKKETTITS-------------------------------F-L------------------------NL  133 (207)
T ss_pred             HHHHHHHHHHHHcCCcccCc-------------------------------c-c------------------------cC
Confidence            99999999999765432210                               0 0                        00


Q ss_pred             CCCccCCchhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHH
Q 043479          159 KPKVAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRI  212 (534)
Q Consensus       159 Kprv~Wt~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl  212 (534)
                      .+     ..|++|+.+++..+..+.. .|+|++.|+   +|..||+.|+.+...
T Consensus       134 ~~-----~~LT~RE~eVL~lla~G~s-nkeIA~~L~---iS~~TVk~h~~~I~~  178 (207)
T PRK15411        134 PT-----LSLSRTESSMLRMWMAGQG-TIQISDQMN---IKAKTVSSHKGNIKR  178 (207)
T ss_pred             Cc-----ccCCHHHHHHHHHHHcCCC-HHHHHHHcC---CCHHHHHHHHHHHHH
Confidence            00     1389999999999986666 999999999   999999999876544

>PRK09935 transcriptional regulator FimZ; Provisional

Probab=99.46  E-value=2.7e-12  Score=120.45  Aligned_cols=158  Identities=18%  Similarity=0.209  Sum_probs=121.5

Q ss_pred             ecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHHH
Q 043479            3 VTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDDL   82 (534)
Q Consensus         3 ass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~eeL   82 (534)
                      +.+..++++.+.. ..||+||+|+.+|+++|+++++.++...+.+|||++++..+.....++++.|+++|+.||++.++|
T Consensus        35 ~~~~~~~~~~~~~-~~~dlvild~~l~~~~g~~~~~~l~~~~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~l  113 (210)
T PRK09935         35 TDDYRITIDYLRT-RPVDLIIMDIDLPGTDGFTFLKRIKQIQSTVKVLFLSSKSECFYAGRAIQAGANGFVSKCNDQNDI  113 (210)
T ss_pred             eCCHHHHHHHHHh-cCCCEEEEeCCCCCCCHHHHHHHHHHhCCCCcEEEEECCCcHHHHHHHHHcCCCEEEeCCCCHHHH
Confidence            5678888888876 789999999999999999999999988888999999999998889999999999999999999999


Q ss_pred             HHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccCCCCCCc
Q 043479           83 KNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPKV  162 (534)
Q Consensus        83 ~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss~kKprv  162 (534)
                      ..+|+.++.+......                     +.+.......  ..                  .        ..
T Consensus       114 ~~~i~~~l~~~~~~~~---------------------~~~~~~~~~~--~~------------------~--------~~  144 (210)
T PRK09935        114 FHAVQMILSGYTFFPS---------------------ETLNYIKSNK--CS------------------T--------NS  144 (210)
T ss_pred             HHHHHHHHcCCceeCH---------------------HHHHHHHhcc--cc------------------c--------Cc
Confidence            9999988765321100                     0000000000  00                  0        00


Q ss_pred             cCCchhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHH
Q 043479          163 AWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFL  214 (534)
Q Consensus       163 ~Wt~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~l  214 (534)
                      .-...|+.++++++..+..+ ...++|++.++   ++.++|+.|+.+.|..+
T Consensus       145 ~~~~~lt~re~~vl~~l~~g-~s~~eIa~~l~---~s~~tv~~~~~~~~~kl  192 (210)
T PRK09935        145 STDTVLSNREVTILRYLVSG-LSNKEIADQLL---LSNKTVSAHKSNIYGKL  192 (210)
T ss_pred             cccccCCHHHHHHHHHHHcC-CCHHHHHHHhC---CCHHHHHHHHHHHHHHc
Confidence            01134889999999998544 44899999998   89999999999887754

>PRK10651 transcriptional regulator NarL; Provisional

Probab=99.45  E-value=4.4e-12  Score=118.94  Aligned_cols=161  Identities=23%  Similarity=0.303  Sum_probs=123.1

Q ss_pred             ecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHHH
Q 043479            3 VTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDDL   82 (534)
Q Consensus         3 ass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~eeL   82 (534)
                      +.+..+++..+.. ..||+||+|+.+++++|+++++.+++..+..|+|+++...+......+++.|+++|+.||++.++|
T Consensus        38 ~~~~~~~~~~~~~-~~~dlvl~d~~l~~~~~~~~~~~l~~~~~~~~vi~l~~~~~~~~~~~~~~~g~~~~i~k~~~~~~l  116 (216)
T PRK10651         38 ASNGEQGIELAES-LDPDLILLDLNMPGMNGLETLDKLREKSLSGRIVVFSVSNHEEDVVTALKRGADGYLLKDMEPEDL  116 (216)
T ss_pred             eCCHHHHHHHHHh-CCCCEEEEeCCCCCCcHHHHHHHHHHhCCCCcEEEEeCCCCHHHHHHHHHcCCCEEEeCCCCHHHH
Confidence            5688899998876 689999999999999999999999988888999999999998989999999999999999999999


Q ss_pred             HHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccCCCCCCc
Q 043479           83 KNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPKV  162 (534)
Q Consensus        83 ~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss~kKprv  162 (534)
                      ..+|+.++.+.......                  ..+.... ...+.      ..                     ..-
T Consensus       117 ~~~i~~~~~~~~~~~~~------------------~~~~~~~-~~~~~------~~---------------------~~~  150 (216)
T PRK10651        117 LKALQQAAAGEMVLSEA------------------LTPVLAA-SLRAN------RA---------------------TTE  150 (216)
T ss_pred             HHHHHHHHCCCcccCHH------------------HHHHHHH-Hhhcc------cC---------------------ccc
Confidence            99999988653322110                  0000000 00000      00                     000


Q ss_pred             cCCchhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHH
Q 043479          163 AWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFL  214 (534)
Q Consensus       163 ~Wt~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~l  214 (534)
                      .....|+.++.++++.+... ...+.|++.++   ++..||+.|+.+.|..|
T Consensus       151 ~~~~~Lt~rE~~vl~~l~~g-~~~~~ia~~l~---is~~tV~~~~~~l~~Kl  198 (216)
T PRK10651        151 RDVNQLTPRERDILKLIAQG-LPNKMIARRLD---ITESTVKVHVKHMLKKM  198 (216)
T ss_pred             cccccCCHHHHHHHHHHHcC-CCHHHHHHHcC---CCHHHHHHHHHHHHHHc
Confidence            11234899999999999744 34899999998   89999999999887744

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

Probab=99.44  E-value=5.1e-13  Score=144.19  Aligned_cols=93  Identities=32%  Similarity=0.484  Sum_probs=88.4

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++++|++.+.. ..+||||+|+.||++||+++++++++..|++|||++|++.+.+.+..|++.||.|||.|||+++.
T Consensus        33 ~a~~~~~al~~i~~-~~~~lvl~Di~mp~~~Gl~ll~~i~~~~~~~pVI~~Tg~g~i~~AV~A~k~GA~Dfl~KP~~~~~  111 (464)
T COG2204          33 TAESAEEALEALSE-SPFDLVLLDIRMPGMDGLELLKEIKSRDPDLPVIVMTGHGDIDTAVEALRLGAFDFLEKPFDLDR  111 (464)
T ss_pred             EeCCHHHHHHHHhc-CCCCEEEEecCCCCCchHHHHHHHHhhCCCCCEEEEeCCCCHHHHHHHHhcCcceeeeCCCCHHH
Confidence            57899999999998 58999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhh
Q 043479           82 LKNVWQYAMTYKKA   95 (534)
Q Consensus        82 L~~aI~~aL~~k~~   95 (534)
                      |..+|++++...+.
T Consensus       112 L~~~v~ral~~~~~  125 (464)
T COG2204         112 LLAIVERALELREL  125 (464)
T ss_pred             HHHHHHHHHHHhhh
Confidence            99999999987554

>PRK10360 DNA-binding transcriptional activator UhpA; Provisional

Probab=99.43  E-value=4.7e-12  Score=118.22  Aligned_cols=149  Identities=22%  Similarity=0.289  Sum_probs=117.4

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.++++.+.. ..||+||+|+.+++.+|+++++.++   +.+|||+++...+......+++.|+++|+.||++.++
T Consensus        32 ~~~~~~~~l~~~~~-~~~dlvi~d~~~~~~~g~~~~~~l~---~~~~vi~~s~~~~~~~~~~~~~~ga~~~i~kp~~~~~  107 (196)
T PRK10360         32 EFGSGREALAGLPG-RGVQVCICDISMPDISGLELLSQLP---KGMATIMLSVHDSPALVEQALNAGARGFLSKRCSPDE  107 (196)
T ss_pred             EECCHHHHHHHHhc-CCCCEEEEeCCCCCCCHHHHHHHHc---cCCCEEEEECCCCHHHHHHHHHcCCcEEEECCCCHHH
Confidence            35688999998876 6899999999999999999999886   3589999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccCCCCCC
Q 043479           82 LKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPK  161 (534)
Q Consensus        82 L~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss~kKpr  161 (534)
                      |..+|+.++++......                     +.....    .                     ..        
T Consensus       108 l~~~i~~~~~~~~~~~~---------------------~~~~~~----~---------------------~~--------  133 (196)
T PRK10360        108 LIAAVHTVATGGCYLTP---------------------DIAIKL----A---------------------SG--------  133 (196)
T ss_pred             HHHHHHHHHcCCeeeCH---------------------HHHHHH----H---------------------hc--------
Confidence            99999999864321100                     000000    0                     00        


Q ss_pred             ccCCchhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHH
Q 043479          162 VAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFL  214 (534)
Q Consensus       162 v~Wt~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~l  214 (534)
                        ....|+.++.++++.+... ...+.|++.|+   ++..+|+.|+.+.|..+
T Consensus       134 --~~~~Lt~~E~~il~~l~~g-~~~~~Ia~~l~---~s~~tv~~~~~~l~~Kl  180 (196)
T PRK10360        134 --RQDPLTKRERQVAEKLAQG-MAVKEIAAELG---LSPKTVHVHRANLMEKL  180 (196)
T ss_pred             --cccCCCHHHHHHHHHHHCC-CCHHHHHHHhC---CCHHHHHHHHHHHHHHh
Confidence              0124788999999999644 45899999997   89999999998887743

>PRK10643 DNA-binding transcriptional regulator BasR; Provisional

Probab=99.43  E-value=4.3e-12  Score=120.06  Aligned_cols=168  Identities=17%  Similarity=0.229  Sum_probs=120.5

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.+..++++.+.. ..||+||+|+.||+++|+++++.++...+.+|||+++...+......+++.||++|+.||++.++
T Consensus        29 ~~~~~~~~~~~~~~-~~~d~illd~~~~~~~g~~~~~~l~~~~~~~pii~ls~~~~~~~~~~~~~~ga~~~l~kp~~~~~  107 (222)
T PRK10643         29 CASTAREAEALLES-GHYSLVVLDLGLPDEDGLHLLRRWRQKKYTLPVLILTARDTLEDRVAGLDVGADDYLVKPFALEE  107 (222)
T ss_pred             EeCCHHHHHHHHHh-CCCCEEEEECCCCCCCHHHHHHHHHhcCCCCcEEEEECCCCHHHHHHHHhcCCCeEEeCCCCHHH
Confidence            35688899998876 67999999999999999999999998878899999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccCCCCCC
Q 043479           82 LKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPK  161 (534)
Q Consensus        82 L~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss~kKpr  161 (534)
                      |..+++.++++.........               ...++          ......+      ..    ...    .+  
T Consensus       108 l~~~i~~~~~~~~~~~~~~~---------------~~~~~----------~~~~~~~------~~----~~~----~~--  146 (222)
T PRK10643        108 LHARIRALIRRHQGQGENEL---------------QVGNL----------TLNLGRQ------QV----WLD----GQ--  146 (222)
T ss_pred             HHHHHHHHHhhhccccCCce---------------EECCE----------EEEcCCC------EE----EEC----CE--
Confidence            99999988765432111000               00000          0000000      00    000    00  


Q ss_pred             ccCCchhhHHHHHHHHHhc--cCCCcHHHHHHH-cC--CCCCCHHHHHHHHHHHHHHH
Q 043479          162 VAWTDSLHNRFLQAIRHIG--LEKAVPKKILEF-MN--VPGLTRENVASHLQKYRIFL  214 (534)
Q Consensus       162 v~Wt~eLh~RFleaLe~LG--lekAvpK~ILe~-M~--V~GLT~~tVaSHLQKyRl~l  214 (534)
                         ...|+.++.+++..+.  ....+.++|+.. +-  ..+.+..+|+.|+.+.|..+
T Consensus       147 ---~~~Lt~~E~~il~~l~~~~g~~~~~~~~~~~~~~~~~~~~~~tv~~~i~~lr~Kl  201 (222)
T PRK10643        147 ---ELILTPKEFALLSRLMLKAGSPVHREILYQDIYNWDDEPSSNTLEVHIHNLRDKV  201 (222)
T ss_pred             ---EEecCHHHHHHHHHHHhCCCceEcHHHHHHHhcCCCCCCCcCCHHHHHHHHHHhC
Confidence               1247889999999874  556666777753 21  12367899999999988855

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

Probab=99.43  E-value=1.5e-12  Score=111.43  Aligned_cols=85  Identities=28%  Similarity=0.565  Sum_probs=80.9

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.++++.++. ..||+||+|+.+++++|+++++.|+...+.+|||++|...+.....+++++|+++||.||++.++
T Consensus        28 ~~~~~~~~~~~~~~-~~~d~iiid~~~~~~~~~~~~~~i~~~~~~~~ii~~t~~~~~~~~~~~~~~g~~~~l~kp~~~~~  106 (112)
T PF00072_consen   28 TASSGEEALELLKK-HPPDLIIIDLELPDGDGLELLEQIRQINPSIPIIVVTDEDDSDEVQEALRAGADDYLSKPFSPEE  106 (112)
T ss_dssp             EESSHHHHHHHHHH-STESEEEEESSSSSSBHHHHHHHHHHHTTTSEEEEEESSTSHHHHHHHHHTTESEEEESSSSHHH
T ss_pred             EECCHHHHHHHhcc-cCceEEEEEeeeccccccccccccccccccccEEEecCCCCHHHHHHHHHCCCCEEEECCCCHHH
Confidence            57899999999987 78999999999999999999999999989999999999999999999999999999999999999


Q ss_pred             HHHHHH
Q 043479           82 LKNVWQ   87 (534)
Q Consensus        82 L~~aI~   87 (534)
                      |.++|+
T Consensus       107 l~~~i~  112 (112)
T PF00072_consen  107 LRAAIN  112 (112)
T ss_dssp             HHHHHH
T ss_pred             HHHhhC
Confidence            999875

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

>PRK10403 transcriptional regulator NarP; Provisional

Probab=99.43  E-value=1e-11  Score=116.18  Aligned_cols=158  Identities=18%  Similarity=0.252  Sum_probs=120.1

Q ss_pred             ecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHHH
Q 043479            3 VTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDDL   82 (534)
Q Consensus         3 ass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~eeL   82 (534)
                      +.+..+++..+.. ..||+||+|+.+++++|+++++.+++..+..|+|+++...+......+++.|+++|+.||++.++|
T Consensus        38 ~~~~~~~~~~~~~-~~~dlvi~d~~~~~~~~~~~~~~l~~~~~~~~ii~l~~~~~~~~~~~~~~~g~~~~i~kp~~~~~l  116 (215)
T PRK10403         38 AGDGASAIDLANR-LDPDVILLDLNMKGMSGLDTLNALRRDGVTAQIIILTVSDASSDVFALIDAGADGYLLKDSDPEVL  116 (215)
T ss_pred             eCCHHHHHHHHHh-cCCCEEEEecCCCCCcHHHHHHHHHHhCCCCeEEEEeCCCChHHHHHHHHcCCCeEEecCCCHHHH
Confidence            5688889888876 689999999999999999999999988888999999998888888899999999999999999999


Q ss_pred             HHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccCCCCCCc
Q 043479           83 KNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPKV  162 (534)
Q Consensus        83 ~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss~kKprv  162 (534)
                      ..+++.++.+......                  ...+.+.     .. ..              .   .     .  ..
T Consensus       117 ~~~i~~~~~~~~~~~~------------------~~~~~~~-----~~-~~--------------~---~-----~--~~  148 (215)
T PRK10403        117 LEAIRAGAKGSKVFSE------------------RVNQYLR-----ER-EM--------------F---G-----A--EE  148 (215)
T ss_pred             HHHHHHHhCCCeecCH------------------HHHHHHH-----hh-hc--------------c---C-----C--CC
Confidence            9999988744221100                  0000000     00 00              0   0     0  00


Q ss_pred             cCCchhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHH
Q 043479          163 AWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIF  213 (534)
Q Consensus       163 ~Wt~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~  213 (534)
                      .-...|+.++.+++..+... ...++|++.++   ++..||+.|+.+.|..
T Consensus       149 ~~~~~Lt~~e~~vl~~~~~g-~s~~~ia~~l~---~s~~tv~~~~~~i~~k  195 (215)
T PRK10403        149 DPFSVLTERELDVLHELAQG-LSNKQIASVLN---ISEQTVKVHIRNLLRK  195 (215)
T ss_pred             cccccCCHHHHHHHHHHHCC-CCHHHHHHHcC---CCHHHHHHHHHHHHHH
Confidence            00135889999999998644 55899999997   8999999999988764

>PRK15369 two component system sensor kinase SsrB; Provisional

Probab=99.40  E-value=1.2e-11  Score=114.58  Aligned_cols=158  Identities=22%  Similarity=0.292  Sum_probs=119.3

Q ss_pred             ecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHHH
Q 043479            3 VTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDDL   82 (534)
Q Consensus         3 ass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~eeL   82 (534)
                      +.++.++++.+.. ..||+||+|+.+++++|+++++.+++..+.+|+|+++...+......++..|+.+|+.||++.++|
T Consensus        35 ~~~~~~~~~~~~~-~~~dlvl~d~~~~~~~~~~~~~~l~~~~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~l  113 (211)
T PRK15369         35 VDNGLEVYNACRQ-LEPDIVILDLGLPGMNGLDVIPQLHQRWPAMNILVLTARQEEHMASRTLAAGALGYVLKKSPQQIL  113 (211)
T ss_pred             ECCHHHHHHHHHh-cCCCEEEEeCCCCCCCHHHHHHHHHHHCCCCcEEEEeCCCCHHHHHHHHHhCCCEEEeCCCCHHHH
Confidence            4677888888776 779999999999999999999999988888999999999998989999999999999999999999


Q ss_pred             HHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccCCCCCCc
Q 043479           83 KNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPKV  162 (534)
Q Consensus        83 ~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss~kKprv  162 (534)
                      ..+++.++++.......                  ..    .......                 .   ..   ...   
T Consensus       114 ~~~i~~~~~~~~~~~~~------------------~~----~~~~~~~-----------------~---~~---~~~---  145 (211)
T PRK15369        114 LAAIQTVAVGKRYIDPA------------------LN----REAILAL-----------------L---NA---DDT---  145 (211)
T ss_pred             HHHHHHHHCCCceeCHH------------------HH----HHHHHHh-----------------c---cC---CCC---
Confidence            99998876442211000                  00    0000000                 0   00   000   


Q ss_pred             cCCchhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHH
Q 043479          163 AWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFL  214 (534)
Q Consensus       163 ~Wt~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~l  214 (534)
                       -...|++++.+++..+. +....++|++.|+   ++.++|+.|+++.+..+
T Consensus       146 -~~~~lt~~e~~vl~l~~-~g~~~~~Ia~~l~---~s~~tv~~~~~~~~~kl  192 (211)
T PRK15369        146 -NPPLLTPRERQILKLIT-EGYTNRDIAEQLS---ISIKTVETHRLNMMRKL  192 (211)
T ss_pred             -cccCCCHHHHHHHHHHH-CCCCHHHHHHHhC---CCHHHHHHHHHHHHHHh
Confidence             01248889999999986 4445899999998   89999999998876643

>PRK11083 DNA-binding response regulator CreB; Provisional

Probab=99.40  E-value=6.6e-12  Score=119.26  Aligned_cols=168  Identities=18%  Similarity=0.299  Sum_probs=121.9

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.+..+++..+.. ..||+||+|+.+|+.+|+++++.+++..+.+|||+++...+......+++.||++||.||++.++
T Consensus        32 ~~~~~~~~~~~~~~-~~~dlvl~d~~~~~~~g~~~~~~l~~~~~~~~ii~ls~~~~~~~~~~a~~~Ga~~~l~kp~~~~~  110 (228)
T PRK11083         32 WFERGLPALDKLRQ-QPPDLVILDVGLPDISGFELCRQLLAFHPALPVIFLTARSDEVDRLVGLEIGADDYVAKPFSPRE  110 (228)
T ss_pred             EEcCHHHHHHHHhc-CCCCEEEEeCCCCCCCHHHHHHHHHhhCCCCCEEEEEcCCcHHHHHHHhhcCCCeEEECCCCHHH
Confidence            35678888888876 67999999999999999999999998888899999999998888889999999999999999999


Q ss_pred             HHHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccCCCCCC
Q 043479           82 LKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPK  161 (534)
Q Consensus        82 L~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss~kKpr  161 (534)
                      |..+|+.++++....... ..   ...         ...    ......                            ...
T Consensus       111 l~~~i~~~~~~~~~~~~~-~~---~~~---------~~~----~~~~~~----------------------------~~~  145 (228)
T PRK11083        111 VAARVRTILRRVKKFAAP-SP---VIR---------IGH----FELDEP----------------------------AAR  145 (228)
T ss_pred             HHHHHHHHHCccccccCC-Cc---eeE---------ECC----EEEecC----------------------------ccE
Confidence            999998887653221000 00   000         000    000000                            000


Q ss_pred             ccC---CchhhHHHHHHHHHhccC---CCcHHHHHHHcCCCCC--CHHHHHHHHHHHHHHHH
Q 043479          162 VAW---TDSLHNRFLQAIRHIGLE---KAVPKKILEFMNVPGL--TRENVASHLQKYRIFLK  215 (534)
Q Consensus       162 v~W---t~eLh~RFleaLe~LGle---kAvpK~ILe~M~V~GL--T~~tVaSHLQKyRl~lk  215 (534)
                      +.|   ...|+.++.++++.+...   ....++|++.+.....  +..+|+.|+.+.|..+.
T Consensus       146 ~~~~~~~~~Lt~~E~~il~~l~~~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~l~~Kl~  207 (228)
T PRK11083        146 ISYFGTPLTLTRYEFLLLKTLLLSPGRVFSRQQLMDIVWEDAQDSYDRTVDTHIKTLRAKLR  207 (228)
T ss_pred             EEECCEEeecCHHHHHHHHHHHhCCCceECHHHHHHHhcCCCCCCCccCHHHHHHHHHHHhc
Confidence            001   124899999999999532   2446889999985433  47899999988887654

>TIGR03787 marine_sort_RR proteobacterial dedicated sortase system response regulator

Probab=99.39  E-value=1.4e-11  Score=117.89  Aligned_cols=170  Identities=16%  Similarity=0.206  Sum_probs=120.1

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCC--CCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPE--MNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPd--mdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      .+.+..+++..+.. ..||+||+|+.||+  .+|+++++.++...+.+|||++|+..+......++++||++|+.||++.
T Consensus        29 ~~~~~~~~~~~~~~-~~~dlvild~~l~~~~~~g~~~~~~i~~~~~~~pii~ls~~~~~~~~~~~~~~Ga~~~l~kp~~~  107 (227)
T TIGR03787        29 TYADRPSAMQAFRQ-RLPDLAIIDIGLGEEIDGGFMLCQDLRSLSATLPIIFLTARDSDFDTVSGLRLGADDYLTKDISL  107 (227)
T ss_pred             EecCHHHHHHHHHh-CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCCCCEEEEECCCCHHHHHHHHhcCCCEEEECCCCH
Confidence            35688899998876 78999999999998  5899999999987788999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccCCCC
Q 043479           80 DDLKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKK  159 (534)
Q Consensus        80 eeL~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss~kK  159 (534)
                      ++|..+|+.++++...........          ......         .. .  ....                    .
T Consensus       108 ~~l~~~i~~~~~~~~~~~~~~~~~----------~~~~~~---------~~-~--~~~~--------------------~  145 (227)
T TIGR03787       108 PHLLARITALFRRAEALQKPQKQD----------DLITRG---------PL-T--LDSD--------------------R  145 (227)
T ss_pred             HHHHHHHHHHHHhhhhcccccccc----------ceEEEC---------CE-E--EEcc--------------------c
Confidence            999999999887643221100000          000000         00 0  0000                    0


Q ss_pred             CCccC---CchhhHHHHHHHHHhcc--CC-CcHHHHHHHcCCCCCCHHHHHHHHHHHHHHHH
Q 043479          160 PKVAW---TDSLHNRFLQAIRHIGL--EK-AVPKKILEFMNVPGLTRENVASHLQKYRIFLK  215 (534)
Q Consensus       160 prv~W---t~eLh~RFleaLe~LGl--ek-AvpK~ILe~M~V~GLT~~tVaSHLQKyRl~lk  215 (534)
                      ..+.|   ...|+.++.+++..+..  ++ ...++|++... ..++..+|..|+.+.|..|.
T Consensus       146 ~~~~~~~~~~~Lt~~E~~il~~l~~~~g~v~s~~~i~~~~~-~~~~~~tv~~~v~rlr~Kl~  206 (227)
T TIGR03787       146 MTVFWQDQPIDLTVTEFWMVHALAKHPGHVKSRQQLMDAAK-IVVDDSTITSHIKRIRKKFQ  206 (227)
T ss_pred             CEEEECCEEecCCHHHHHHHHHHHhCCCccccHHHHHHHhh-hcCCccCHHHHHHHHHHHhc
Confidence            00111   12499999999999964  33 24566743322 23688999999999888654

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.

>PRK10336 DNA-binding transcriptional regulator QseB; Provisional

Probab=99.38  E-value=1.7e-11  Score=115.97  Aligned_cols=168  Identities=17%  Similarity=0.203  Sum_probs=120.6

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.+..+++..+.. ..||+||+|+.+|+++|+++++.+++..+.+|||++|...+.....+++++||++|+.||++.++
T Consensus        29 ~~~~~~~~~~~~~~-~~~dlvild~~l~~~~g~~~~~~i~~~~~~~~ii~lt~~~~~~~~~~~~~~ga~~~i~kp~~~~~  107 (219)
T PRK10336         29 WFTQGRQGKEALYS-APYDAVILDLTLPGMDGRDILREWREKGQREPVLILTARDALAERVEGLRLGADDYLCKPFALIE  107 (219)
T ss_pred             EeCCHHHHHHHHhh-CCCCEEEEECCCCCCCHHHHHHHHHhcCCCCcEEEEECCCCHHHHHHHHhCCCCeEEECCCCHHH
Confidence            35678888888876 67999999999999999999999998888899999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccCCCCCC
Q 043479           82 LKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPK  161 (534)
Q Consensus        82 L~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss~kKpr  161 (534)
                      |..+|+.++++......   .            .....+         .   ...+.....  .  .         ..  
T Consensus       108 l~~~i~~~~~~~~~~~~---~------------~~~~~~---------~---~~~~~~~~~--~--~---------~~--  145 (219)
T PRK10336        108 VAARLEALMRRTNGQAS---N------------ELRHGN---------V---MLDPGKRIA--T--L---------AG--  145 (219)
T ss_pred             HHHHHHHHHhccccCCC---C------------ceeECC---------E---EEEcccCEE--E--E---------CC--
Confidence            99999988754321100   0            000000         0   000000000  0  0         00  


Q ss_pred             ccCCchhhHHHHHHHHHhccCC---CcHHHHHHHcCC--CCCCHHHHHHHHHHHHHHH
Q 043479          162 VAWTDSLHNRFLQAIRHIGLEK---AVPKKILEFMNV--PGLTRENVASHLQKYRIFL  214 (534)
Q Consensus       162 v~Wt~eLh~RFleaLe~LGlek---AvpK~ILe~M~V--~GLT~~tVaSHLQKyRl~l  214 (534)
                        -...|+.++.+++..+....   ...++|++.+.-  ..++..+|+.|+.+.|..+
T Consensus       146 --~~~~Lt~~E~~il~~l~~~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~lr~Kl  201 (219)
T PRK10336        146 --EPLTLKPKEFALLELLMRNAGRVLPRKLIEEKLYTWDEEVTSNAVEVHVHHLRRKL  201 (219)
T ss_pred             --EEEecCHHHHHHHHHHHhCCCccCcHHHHHHHhcCCCCCCCccCHHHHHHHHHHhc
Confidence              01248899999999995331   457889888741  2368899999998887754

>TIGR01387 cztR_silR_copR heavy metal response regulator

Probab=99.34  E-value=3.5e-11  Score=113.48  Aligned_cols=169  Identities=15%  Similarity=0.236  Sum_probs=120.3

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.+..++++.+.. ..||+||+|+.||+++|+++++.++...+.+|||+++...+......++.+||++|+.||++.++
T Consensus        27 ~~~~~~~~~~~~~~-~~~dlvl~d~~~~~~~g~~~~~~l~~~~~~~~iivls~~~~~~~~~~~~~~Ga~~~l~kp~~~~~  105 (218)
T TIGR01387        27 AASNGRDGLHLALK-DDYDLIILDVMLPGMDGWQILQTLRRSGKQTPVLFLTARDSVADKVKGLDLGADDYLVKPFSFSE  105 (218)
T ss_pred             EECCHHHHHHHHhc-CCCCEEEEeCCCCCCCHHHHHHHHHccCCCCcEEEEEcCCCHHHHHHHHHcCCCeEEECCCCHHH
Confidence            45688899998876 78999999999999999999999998888899999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccCCCCCC
Q 043479           82 LKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPK  161 (534)
Q Consensus        82 L~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss~kKpr  161 (534)
                      |..+++.++++..........               ..+.    ....      ..+      ..          .   .
T Consensus       106 l~~~i~~~~~~~~~~~~~~~~---------------~~~~----~~~~------~~~------~~----------~---~  141 (218)
T TIGR01387       106 LLARVRTLLRRSHSLNSTVLE---------------IADL----RMDS------VRH------RV----------S---R  141 (218)
T ss_pred             HHHHHHHHhcccccCCCCeEE---------------ECCE----EEEc------ccC------EE----------E---E
Confidence            999999887654322110000               0000    0000      000      00          0   0


Q ss_pred             ccCCchhhHHHHHHHHHhc--cCCCcH-HHHHHHcCCCC--CCHHHHHHHHHHHHHHHH
Q 043479          162 VAWTDSLHNRFLQAIRHIG--LEKAVP-KKILEFMNVPG--LTRENVASHLQKYRIFLK  215 (534)
Q Consensus       162 v~Wt~eLh~RFleaLe~LG--lekAvp-K~ILe~M~V~G--LT~~tVaSHLQKyRl~lk  215 (534)
                      -.+...|+.++.+++..+.  ..+.+. ..|++.+--..  .+..+|..|+.+.|..++
T Consensus       142 ~~~~~~Lt~~E~~il~~l~~~~~~~~sr~~i~~~~~~~~~~~~~~~~~~~i~~lr~kl~  200 (218)
T TIGR01387       142 GNIRITLTRKEFQLLWLLMRRTGEVLPRTVIASLVWGMNFDSDTNVVDVAIRRLRAKVD  200 (218)
T ss_pred             CCEEEeCCHHHHHHHHHHHhCCCeeEcHHHHHHHhcCCCCCCCcCCHHHHHHHHHHhhc
Confidence            0123458999999999994  334444 45666663212  246889999999888653

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.

>PRK10816 DNA-binding transcriptional regulator PhoP; Provisional

Probab=99.31  E-value=6e-11  Score=113.43  Aligned_cols=90  Identities=20%  Similarity=0.323  Sum_probs=83.3

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.++++.+.. ..||+||+|+.+|+++|+++++.+++..+.+|||++++..+......+++.||++||.||++.++
T Consensus        29 ~~~~~~~~l~~~~~-~~~dlvild~~l~~~~g~~l~~~lr~~~~~~pii~ls~~~~~~~~~~~l~~Ga~d~l~kp~~~~e  107 (223)
T PRK10816         29 AAEDAKEADYYLNE-HLPDIAIVDLGLPDEDGLSLIRRWRSNDVSLPILVLTARESWQDKVEVLSAGADDYVTKPFHIEE  107 (223)
T ss_pred             EECCHHHHHHHHhh-CCCCEEEEECCCCCCCHHHHHHHHHhcCCCCCEEEEEcCCCHHHHHHHHHcCCCeeEeCCCCHHH
Confidence            46788999998876 78999999999999999999999998888899999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHH
Q 043479           82 LKNVWQYAMTY   92 (534)
Q Consensus        82 L~~aI~~aL~~   92 (534)
                      |...++.++++
T Consensus       108 L~~~i~~~~~~  118 (223)
T PRK10816        108 VMARMQALMRR  118 (223)
T ss_pred             HHHHHHHHHhc
Confidence            99999988765

>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional

Probab=99.31  E-value=2.9e-11  Score=115.65  Aligned_cols=90  Identities=26%  Similarity=0.391  Sum_probs=80.7

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.++++.+.  ..||+||+|+.||+++|+++++.+++..+ +|||++|+..+......+++.|+++||.||++.++
T Consensus        30 ~~~~~~~~~~~~~--~~~d~vl~d~~~~~~~g~~~~~~l~~~~~-~~ii~lt~~~~~~~~~~~~~~ga~~~l~kp~~~~~  106 (232)
T PRK10955         30 VAHDGEQALDLLD--DSIDLLLLDVMMPKKNGIDTLKELRQTHQ-TPVIMLTARGSELDRVLGLELGADDYLPKPFNDRE  106 (232)
T ss_pred             EeCCHHHHHHHhh--cCCCEEEEeCCCCCCcHHHHHHHHHhcCC-CcEEEEECCCCHHHHHHHHHcCCCEEEcCCCCHHH
Confidence            3568889998875  36999999999999999999999998776 99999999998888899999999999999999999


Q ss_pred             HHHHHHHHHHHhh
Q 043479           82 LKNVWQYAMTYKK   94 (534)
Q Consensus        82 L~~aI~~aL~~k~   94 (534)
                      |..+++.++++..
T Consensus       107 l~~~i~~~~~~~~  119 (232)
T PRK10955        107 LVARIRAILRRSH  119 (232)
T ss_pred             HHHHHHHHHhccc
Confidence            9999999886543

>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class

Probab=99.31  E-value=3.4e-12  Score=100.75  Aligned_cols=54  Identities=63%  Similarity=1.073  Sum_probs=51.7

Q ss_pred             CCCccCCchhhHHHHHHHHHhcc-CCCcHHHHHHHcCCCCCCHHHHHHHHHHHHH
Q 043479          159 KPKVAWTDSLHNRFLQAIRHIGL-EKAVPKKILEFMNVPGLTRENVASHLQKYRI  212 (534)
Q Consensus       159 Kprv~Wt~eLh~RFleaLe~LGl-ekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl  212 (534)
                      |+|+.||.++|.+|+++++.+|. +.++||.|++.|++.+||+.+|+||+||||+
T Consensus         1 k~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~   55 (57)
T TIGR01557         1 KPRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRL   55 (57)
T ss_pred             CCCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHc
Confidence            56899999999999999999997 8899999999999999999999999999997

This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.

>PRK09836 DNA-binding transcriptional activator CusR; Provisional

Probab=99.30  E-value=6.6e-11  Score=113.46  Aligned_cols=90  Identities=17%  Similarity=0.325  Sum_probs=82.7

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.++++.+.. ..||+||+|+.+|+++|+++++.+++..+.+|||+++...+.....+++++||++||.||++.++
T Consensus        29 ~~~~~~~~~~~~~~-~~~dlvild~~~~~~~g~~~~~~lr~~~~~~pii~ls~~~~~~~~~~~~~~Ga~~~l~kp~~~~~  107 (227)
T PRK09836         29 LADNGLNGYHLAMT-GDYDLIILDIMLPDVNGWDIVRMLRSANKGMPILLLTALGTIEHRVKGLELGADDYLVKPFAFAE  107 (227)
T ss_pred             EECCHHHHHHHHhh-CCCCEEEEECCCCCCCHHHHHHHHHhcCCCCCEEEEEcCCCHHHHHHHHhCCCCEEEeCCCCHHH
Confidence            46788899988876 68999999999999999999999998878899999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHH
Q 043479           82 LKNVWQYAMTY   92 (534)
Q Consensus        82 L~~aI~~aL~~   92 (534)
                      |..+++.++++
T Consensus       108 l~~~i~~~~~~  118 (227)
T PRK09836        108 LLARVRTLLRR  118 (227)
T ss_pred             HHHHHHHHHhc
Confidence            99999988754

>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB

Probab=99.28  E-value=4.1e-11  Score=113.44  Aligned_cols=90  Identities=24%  Similarity=0.434  Sum_probs=81.6

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhh--CCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~--~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      .+.+..+++..+.. ..||+||+|+.||+++|+++++.++..  .+.+|||++++..+.....++++.||++||.||++.
T Consensus        31 ~~~~~~~~~~~~~~-~~~d~vi~d~~~~~~~g~~~~~~l~~~~~~~~~~ii~ls~~~~~~~~~~~~~~Ga~~~l~kp~~~  109 (226)
T TIGR02154        31 EAGDGDEALTLINE-RGPDLILLDWMLPGTSGIELCRRLRRRPETRAIPIIMLTARGEEEDRVRGLETGADDYITKPFSP  109 (226)
T ss_pred             EEcCHHHHHHHHHh-cCCCEEEEECCCCCCcHHHHHHHHHccccCCCCCEEEEecCCCHHHHHHHHhcCcceEEeCCCCH
Confidence            35688899998876 789999999999999999999999875  467999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHH
Q 043479           80 DDLKNVWQYAMTY   92 (534)
Q Consensus        80 eeL~~aI~~aL~~   92 (534)
                      ++|..+|+.++++
T Consensus       110 ~~l~~~i~~~~~~  122 (226)
T TIGR02154       110 RELLARIKAVLRR  122 (226)
T ss_pred             HHHHHHHHHHhcc
Confidence            9999999988765

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.

>PRK09390 fixJ response regulator FixJ; Provisional

Probab=99.28  E-value=7.2e-11  Score=108.83  Aligned_cols=154  Identities=21%  Similarity=0.264  Sum_probs=118.1

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.+..++++.+.. ..||+||+|+.+++++|+++++.+++..+.+|+|+++...+......+++.|+.+|+.||+..++
T Consensus        32 ~~~~~~~~~~~~~~-~~~d~ii~d~~~~~~~~~~~~~~l~~~~~~~~ii~l~~~~~~~~~~~~~~~g~~~~l~~p~~~~~  110 (202)
T PRK09390         32 LFESAQAFLDALPG-LRFGCVVTDVRMPGIDGIELLRRLKARGSPLPVIVMTGHGDVPLAVEAMKLGAVDFIEKPFEDER  110 (202)
T ss_pred             EeCCHHHHHHHhcc-CCCCEEEEeCCCCCCcHHHHHHHHHhcCCCCCEEEEECCCCHHHHHHHHHcChHHHhhCCCCHHH
Confidence            35677888888876 67999999999999999999999998888899999999999899999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccCCCCCC
Q 043479           82 LKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPK  161 (534)
Q Consensus        82 L~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss~kKpr  161 (534)
                      |..+++.++........                   ......            ..+                       
T Consensus       111 l~~~l~~~~~~~~~~~~-------------------~~~~~~------------~~~-----------------------  136 (202)
T PRK09390        111 LIGAIERALAQAPEAAK-------------------SEAVAA------------DIR-----------------------  136 (202)
T ss_pred             HHHHHHHHHHhhhhccc-------------------chhHHH------------HHH-----------------------
Confidence            99999887754221100                   000000            000                       


Q ss_pred             ccCCchhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHHH
Q 043479          162 VAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLK  215 (534)
Q Consensus       162 v~Wt~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~lk  215 (534)
                       .....|.+++.++++.+-. ....+.|++.|+   ++..+|+.|+.+.|..++
T Consensus       137 -~~~~~l~~~e~~vl~~~~~-~~~~~~ia~~l~---~s~~tv~~~~~~~~~kl~  185 (202)
T PRK09390        137 -ARIASLSERERQVMDGLVA-GLSNKVIARDLD---ISPRTVEVYRANVMTKMQ  185 (202)
T ss_pred             -HHHHhhhhhHHHHHHHHHc-cCchHHHHHHcC---CCHHHHHHHHHHHHHHHc
Confidence             0123467777888886532 334799999998   899999999999887653

>PRK10161 transcriptional regulator PhoB; Provisional

Probab=99.28  E-value=4.6e-11  Score=114.69  Aligned_cols=90  Identities=23%  Similarity=0.372  Sum_probs=81.6

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhh--CCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~--~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      .+.+..++++.+.. ..||+||+|+.||+++|+++++.+++.  .+.+|||++++..+.....+++++||++||.||++.
T Consensus        31 ~~~~~~~~~~~~~~-~~~dlvild~~l~~~~g~~~~~~l~~~~~~~~~pvi~ls~~~~~~~~~~~~~~Ga~~~l~kp~~~  109 (229)
T PRK10161         31 EAEDYDSAVNQLNE-PWPDLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSP  109 (229)
T ss_pred             EECCHHHHHHHHhc-cCCCEEEEeCCCCCCCHHHHHHHHHhccccCCCCEEEEECCCCHHHHHHHHHcCCCEEEECCCCH
Confidence            46788899998876 789999999999999999999999875  367999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHH
Q 043479           80 DDLKNVWQYAMTY   92 (534)
Q Consensus        80 eeL~~aI~~aL~~   92 (534)
                      ++|..+|+.++++
T Consensus       110 ~~L~~~i~~~~~~  122 (229)
T PRK10161        110 KELVARIKAVMRR  122 (229)
T ss_pred             HHHHHHHHHHHhc
Confidence            9999999988764

>PRK15479 transcriptional regulatory protein TctD; Provisional

Probab=99.28  E-value=2.1e-10  Score=108.45  Aligned_cols=167  Identities=17%  Similarity=0.232  Sum_probs=120.6

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.++++.+.. ..||+||+|+.+|+.+|+++++.++...+++|+|+++...+.....++++.|+++|+.||++.++
T Consensus        29 ~~~~~~~~~~~~~~-~~~d~vild~~~~~~~~~~~~~~i~~~~~~~~ii~lt~~~~~~~~~~~~~~g~~~~i~kp~~~~~  107 (221)
T PRK15479         29 CVFDGLAADHLLQS-EMYALAVLDINMPGMDGLEVLQRLRKRGQTLPVLLLTARSAVADRVKGLNVGADDYLPKPFELEE  107 (221)
T ss_pred             EeCCHHHHHHHHhh-CCCCEEEEeCCCCCCcHHHHHHHHHhcCCCCCEEEEECCCCHHHHHHHHHcCCCeeEeCCCCHHH
Confidence            35678888887776 67999999999999999999999998888899999999999888899999999999999999999


Q ss_pred             HHHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccCCCCCC
Q 043479           82 LKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPK  161 (534)
Q Consensus        82 L~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss~kKpr  161 (534)
                      |..+++.++++.........+               ..         ..   .......   .     ..+.     +  
T Consensus       108 l~~~i~~~~~~~~~~~~~~~~---------------~~---------~~---~~~~~~~---~-----~~~~-----~--  145 (221)
T PRK15479        108 LDARLRALLRRSAGQVQEVQQ---------------LG---------EL---IFHDEGY---F-----LLQG-----Q--  145 (221)
T ss_pred             HHHHHHHHHhhhccCcCccEE---------------EC---------CE---EEccCCe---E-----EECC-----E--
Confidence            999999887654321111000               00         00   0000000   0     0000     0  


Q ss_pred             ccCCchhhHHHHHHHHHhcc--CC-CcHHHHHHHcCC--CCCCHHHHHHHHHHHHHHH
Q 043479          162 VAWTDSLHNRFLQAIRHIGL--EK-AVPKKILEFMNV--PGLTRENVASHLQKYRIFL  214 (534)
Q Consensus       162 v~Wt~eLh~RFleaLe~LGl--ek-AvpK~ILe~M~V--~GLT~~tVaSHLQKyRl~l  214 (534)
                         ...|+.++.+++..+..  .. ...++|++.+.-  .+++..+|+.|+.+.|..+
T Consensus       146 ---~~~Lt~~E~~il~~l~~~~~~~~~~~~i~~~l~~~~~~~~~~tv~~~i~~ir~kl  200 (221)
T PRK15479        146 ---PLALTPREQALLTVLMYRRTRPVSRQQLFEQVFSLNDEVSPESIELYIHRLRKKL  200 (221)
T ss_pred             ---EEecCHHHHHHHHHHHhCCCCcCcHHHHHHHhcCCCCCCCcccHHHHHHHHHHhc
Confidence               12489999999999843  22 246778877641  2368899999999988865

>CHL00148 orf27 Ycf27; Reviewed

Probab=99.27  E-value=1.3e-10  Score=111.80  Aligned_cols=171  Identities=22%  Similarity=0.281  Sum_probs=119.2

Q ss_pred             ecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHHH
Q 043479            3 VTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDDL   82 (534)
Q Consensus         3 ass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~eeL   82 (534)
                      +.+..+++..+.. ..||+||+|+.+|+.+|+++++.+++. +.+|||++++..+......+++.||++||.||++.++|
T Consensus        36 ~~~~~~~l~~~~~-~~~d~illd~~~~~~~g~~~~~~l~~~-~~~~ii~ls~~~~~~~~~~~~~~Ga~~~l~kp~~~~~L  113 (240)
T CHL00148         36 ASDGEEALKLFRK-EQPDLVILDVMMPKLDGYGVCQEIRKE-SDVPIIMLTALGDVSDRITGLELGADDYVVKPFSPKEL  113 (240)
T ss_pred             eCCHHHHHHHHHh-cCCCEEEEeCCCCCCCHHHHHHHHHhc-CCCcEEEEECCCCHHhHHHHHHCCCCEEEeCCCCHHHH
Confidence            5688889988876 689999999999999999999999975 67999999999998888999999999999999999999


Q ss_pred             HHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccCCCCCCc
Q 043479           83 KNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPKV  162 (534)
Q Consensus        83 ~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss~kKprv  162 (534)
                      ..+|+.++++..........       . .........+          ..  ..                    .+..+
T Consensus       114 ~~~i~~~~~~~~~~~~~~~~-------~-~~~~~~~~~~----------~~--~~--------------------~~~~~  153 (240)
T CHL00148        114 EARIRSVLRRTNKKSFSSKI-------P-NSSIIRIGFL----------KI--DL--------------------NKKQV  153 (240)
T ss_pred             HHHHHHHHhhcccccccccc-------C-CCceEEECCE----------EE--Ec--------------------CCCEE
Confidence            99999887654321100000       0 0000000000          00  00                    00001


Q ss_pred             cC---CchhhHHHHHHHHHhcc---CCCcHHHHHHHcCC----CCCCHHHHHHHHHHHHHHHH
Q 043479          163 AW---TDSLHNRFLQAIRHIGL---EKAVPKKILEFMNV----PGLTRENVASHLQKYRIFLK  215 (534)
Q Consensus       163 ~W---t~eLh~RFleaLe~LGl---ekAvpK~ILe~M~V----~GLT~~tVaSHLQKyRl~lk  215 (534)
                      .+   ...|+.++.++++.+..   .....++|++.+--    ..++..+|..|+.+.|..|.
T Consensus       154 ~~~~~~~~Lt~~E~~il~~l~~~~~~~~s~~~i~~~l~~~~~~~~~~~~tv~~~i~~lr~KL~  216 (240)
T CHL00148        154 YKNNERIRLTGMEFSLLELLISKSGEIFSRATILKEVWGYTPERHIDTRVVDVHISRLRAKLE  216 (240)
T ss_pred             EECCEEEEcCHHHHHHHHHHHHCCCEEEcHHHHHHHhcCCCcccCCCcccHHHHHHHHHHHhc
Confidence            01   12488999999998842   12446788887731    13688899999999888654

>PRK11517 transcriptional regulatory protein YedW; Provisional

Probab=99.25  E-value=1.9e-10  Score=109.27  Aligned_cols=167  Identities=14%  Similarity=0.281  Sum_probs=117.4

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.+..+++..+.. ..||+||+|+.||+++|+++++.+++. +.+|||++++..+.....+++++||++||.||++.++
T Consensus        29 ~~~~~~~~l~~~~~-~~~dlvi~d~~~~~~~g~~~~~~l~~~-~~~~ii~ls~~~~~~~~~~a~~~Ga~~~l~kp~~~~~  106 (223)
T PRK11517         29 AVSDGRDGLYLALK-DDYALIILDIMLPGMDGWQILQTLRTA-KQTPVICLTARDSVDDRVRGLDSGANDYLVKPFSFSE  106 (223)
T ss_pred             EECCHHHHHHHHhc-CCCCEEEEECCCCCCCHHHHHHHHHcC-CCCCEEEEECCCCHHHHHHHHhcCCCEEEECCCCHHH
Confidence            45688899988876 789999999999999999999999875 4699999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccCCCCCC
Q 043479           82 LKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPK  161 (534)
Q Consensus        82 L~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss~kKpr  161 (534)
                      |..+|+.++++.........                ..+.    .....       ++..  .   .         ..  
T Consensus       107 l~~~i~~~~~~~~~~~~~~~----------------~~~~----~~~~~-------~~~~--~---~---------~~--  143 (223)
T PRK11517        107 LLARVRAQLRQHHALNSTLE----------------ISGL----RMDSV-------SQSV--S---R---------DN--  143 (223)
T ss_pred             HHHHHHHHHccccCcCCeEE----------------ECCE----EEEcC-------CCEE--E---E---------CC--
Confidence            99999988754321110000                0000    00000       0000  0   0         00  


Q ss_pred             ccCCchhhHHHHHHHHHhcc--CCCc-HHHHHHHc-CCC-CCCHHHHHHHHHHHHHHHH
Q 043479          162 VAWTDSLHNRFLQAIRHIGL--EKAV-PKKILEFM-NVP-GLTRENVASHLQKYRIFLK  215 (534)
Q Consensus       162 v~Wt~eLh~RFleaLe~LGl--ekAv-pK~ILe~M-~V~-GLT~~tVaSHLQKyRl~lk  215 (534)
                        -...|+.++.+++..+..  .+.+ -++|++.+ +.. ..+..+|..|+.+.|..++
T Consensus       144 --~~~~Lt~~E~~il~~l~~~~g~~~s~~~i~~~~w~~~~~~~~~tv~~~i~rlr~Kl~  200 (223)
T PRK11517        144 --ISITLTRKEFQLLWLLASRAGEIIPRTVIASEIWGINFDSDTNTVDVAIRRLRAKVD  200 (223)
T ss_pred             --EEEeCCHHHHHHHHHHHhCCCccCCHHHHHHHhcCCCCCCCcCCHHHHHHHHHHhhc
Confidence              012489999999999942  3333 45566665 321 2357899999999998764

>PRK09468 ompR osmolarity response regulator; Provisional

Probab=99.21  E-value=3.6e-10  Score=109.37  Aligned_cols=91  Identities=18%  Similarity=0.345  Sum_probs=83.2

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.++++.+.. ..||+||+|+.+|+++|+++++.+++..+.+|||++++..+......+++.|+++||.||++.++
T Consensus        34 ~~~~~~~~~~~~~~-~~~dlvild~~l~~~~g~~~~~~lr~~~~~~pii~ls~~~~~~~~~~~l~~Ga~~~l~kP~~~~~  112 (239)
T PRK09468         34 SAANAEQMDRLLTR-ESFHLMVLDLMLPGEDGLSICRRLRSQNNPTPIIMLTAKGEEVDRIVGLEIGADDYLPKPFNPRE  112 (239)
T ss_pred             EECCHHHHHHHHhc-CCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCCEEEEECCCcHHHHHHHHhcCCCeEEECCCCHHH
Confidence            46788889988876 78999999999999999999999998778899999999999998999999999999999999999


Q ss_pred             HHHHHHHHHHHh
Q 043479           82 LKNVWQYAMTYK   93 (534)
Q Consensus        82 L~~aI~~aL~~k   93 (534)
                      |...|+.++++.
T Consensus       113 L~~~i~~~~~r~  124 (239)
T PRK09468        113 LLARIRAVLRRQ  124 (239)
T ss_pred             HHHHHHHHhccc
Confidence            999999988653

>PRK10766 DNA-binding transcriptional regulator TorR; Provisional

Probab=99.20  E-value=5.2e-10  Score=106.61  Aligned_cols=90  Identities=16%  Similarity=0.289  Sum_probs=81.6

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.++++.+.. ..||+||+|+.||+++|+++++.+++. +.+|||++++..+.....++++.||++||.||++.++
T Consensus        31 ~~~~~~~~~~~~~~-~~~dlvild~~l~~~~g~~~~~~lr~~-~~~~ii~l~~~~~~~~~~~~l~~Ga~d~l~kP~~~~~  108 (221)
T PRK10766         31 EAASGAGMREIMQN-QHVDLILLDINLPGEDGLMLTRELRSR-STVGIILVTGRTDSIDRIVGLEMGADDYVTKPLELRE  108 (221)
T ss_pred             EECCHHHHHHHHhc-CCCCEEEEeCCCCCCCHHHHHHHHHhC-CCCCEEEEECCCcHHHHHHHHHcCCCcEEeCCCCHHH
Confidence            46788999988876 679999999999999999999999975 5799999999999998999999999999999999999


Q ss_pred             HHHHHHHHHHHh
Q 043479           82 LKNVWQYAMTYK   93 (534)
Q Consensus        82 L~~aI~~aL~~k   93 (534)
                      |...|..++++.
T Consensus       109 L~~~i~~~~~r~  120 (221)
T PRK10766        109 LLVRVKNLLWRI  120 (221)
T ss_pred             HHHHHHHHHhhh
Confidence            999999887653

>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional

Probab=99.17  E-value=1.1e-09  Score=105.25  Aligned_cols=170  Identities=19%  Similarity=0.276  Sum_probs=118.4

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.+++..+.. ..||+||+|+.+|+++|+++++.++. .+.+|||+++...+......++.+|+++|+.||++.++
T Consensus        39 ~~~~~~~~~~~~~~-~~~dlvl~d~~~~~~~g~~~~~~l~~-~~~~pii~l~~~~~~~~~~~~~~~ga~~~l~kp~~~~~  116 (240)
T PRK10710         39 LLSHGDEVLPYVRQ-TPPDLILLDLMLPGTDGLTLCREIRR-FSDIPIVMVTAKIEEIDRLLGLEIGADDYICKPYSPRE  116 (240)
T ss_pred             EeCCHHHHHHHHhh-CCCCEEEEeCCCCCCCHHHHHHHHHh-cCCCCEEEEEcCCCHHHHHHHHhcCCCeEEECCCCHHH
Confidence            35688889998876 67999999999999999999999986 45799999999988888889999999999999999999


Q ss_pred             HHHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccCCCCCC
Q 043479           82 LKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPK  161 (534)
Q Consensus        82 L~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss~kKpr  161 (534)
                      |..+|+.++++....... ..            ......+    ....      ...      ..   ...         
T Consensus       117 L~~~i~~~~~~~~~~~~~-~~------------~~~~~~~----~~~~------~~~------~~---~~~---------  155 (240)
T PRK10710        117 VVARVKTILRRCKPQREL-QQ------------QDAESPL----IIDE------SRF------QA---SWR---------  155 (240)
T ss_pred             HHHHHHHHHhhccccCCC-cc------------ceEeCCE----EEEc------Cce------EE---EEC---------
Confidence            999998887643211100 00            0000000    0000      000      00   000         


Q ss_pred             ccCCchhhHHHHHHHHHhcc--C-CCcHHHHHHHcCC--CCCCHHHHHHHHHHHHHHHH
Q 043479          162 VAWTDSLHNRFLQAIRHIGL--E-KAVPKKILEFMNV--PGLTRENVASHLQKYRIFLK  215 (534)
Q Consensus       162 v~Wt~eLh~RFleaLe~LGl--e-kAvpK~ILe~M~V--~GLT~~tVaSHLQKyRl~lk  215 (534)
                       .....|+.++.+++..+..  . ....+.|++.|.-  ..++.++|..|+.+.|..+.
T Consensus       156 -~~~~~Lt~~e~~il~~l~~~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~lr~kl~  213 (240)
T PRK10710        156 -GKMLDLTPAEFRLLKTLSHEPGKVFSREQLLNHLYDDYRVVTDRTIDSHIKNLRRKLE  213 (240)
T ss_pred             -CEEeecCHHHHHHHHHHHhCCCceEcHHHHHHHhcCcCcCCCccCHHHHHHHHHHHhh
Confidence             0113488899999999843  2 2334678888752  33688999999998887653

>PRK10693 response regulator of RpoS; Provisional

Probab=99.15  E-value=3.2e-10  Score=116.76  Aligned_cols=91  Identities=31%  Similarity=0.426  Sum_probs=83.6

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCC-ChH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPL-NPD   80 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~-s~e   80 (534)
                      ++.++++|++.+.. ..||+||+|+.||+++|+++++++++..+.+|||++|+..+.+...++++.||++||.||+ +.+
T Consensus         2 ~a~~g~~al~~l~~-~~pDlVL~D~~mp~~~Gle~~~~ir~~~~~ipiI~lt~~~~~~~~~~al~~Ga~dyl~KP~~~~~   80 (303)
T PRK10693          2 LAANGVDALELLGG-FTPDLIICDLAMPRMNGIEFVEHLRNRGDQTPVLVISATENMADIAKALRLGVQDVLLKPVKDLN   80 (303)
T ss_pred             EeCCHHHHHHHHhc-CCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCcEEEEECCCCHHHHHHHHHCCCcEEEECCCCcHH
Confidence            57899999999987 7899999999999999999999999888889999999999999999999999999999999 589


Q ss_pred             HHHHHHHHHHHHh
Q 043479           81 DLKNVWQYAMTYK   93 (534)
Q Consensus        81 eL~~aI~~aL~~k   93 (534)
                      +|..+|+++++..
T Consensus        81 ~L~~~i~~~l~~~   93 (303)
T PRK10693         81 RLREMVFACLYPS   93 (303)
T ss_pred             HHHHHHHHHhhhh
Confidence            9999998877543

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

Probab=99.13  E-value=1.4e-10  Score=120.63  Aligned_cols=92  Identities=26%  Similarity=0.434  Sum_probs=82.4

Q ss_pred             CeecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCC---CCcEEEEecCCCHHHHHHHHHcCCcEEEeCCC
Q 043479            1 VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFT---HLPVMVMSSDDRESVIMKALASGVAFYILKPL   77 (534)
Q Consensus         1 vtass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p---~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~   77 (534)
                      ++|.+++++++.... .++|+||+|++||+|+|++++.+|+...|   .+|||++|+..+.+...+++.+||++||.||+
T Consensus        42 ~~ae~g~~a~kl~~~-~~~dlvllD~~mp~mdg~ev~~~lk~~~p~t~~ip~i~lT~~~d~~~~~~~~~~g~~dyl~KP~  120 (360)
T COG3437          42 IEAENGEEALKLLQE-EPPDLVLLDVRMPEMDGAEVLNKLKAMSPSTRRIPVILLTAYADSEDRQRALEAGADDYLSKPI  120 (360)
T ss_pred             eeecCchHHHHHhcc-cCCceEEeeccCCCccHHHHHHHHHhcCCcccccceEEEeecCChHHHHHHHHhhHHHHhcCCC
Confidence            367899999999887 77999999999999999999999998544   58999999999999999999999999999999


Q ss_pred             ChHHHHHHHHHHHHHh
Q 043479           78 NPDDLKNVWQYAMTYK   93 (534)
Q Consensus        78 s~eeL~~aI~~aL~~k   93 (534)
                      ++.+|...+...+..+
T Consensus       121 ~~~~l~~rv~~~~q~k  136 (360)
T COG3437         121 SPKELVARVSSHLQLK  136 (360)
T ss_pred             CHHHHHHHHHHHHHHH
Confidence            9999999997655444

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

Probab=99.12  E-value=6.7e-10  Score=97.30  Aligned_cols=89  Identities=28%  Similarity=0.455  Sum_probs=76.0

Q ss_pred             eecCHH-HHHHHHHhcC-CceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPV-EALATVRIQR-DIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~-EALe~L~~~~-~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      .+.++. +|++.++. . .||+|++|+.||+++|+++++.+++..+.+|||++|+........+++..|+++|+.||+..
T Consensus        34 ~a~~g~~~al~~~~~-~~~~dlii~D~~mp~~~G~~~~~~l~~~~~~~pvv~~t~~~~~~~~~~~~~~g~~~~l~kP~~~  112 (130)
T COG0784          34 EAADGEEEALELLRE-LPQPDLILLDINMPGMDGIELLRRLRARGPNIPVILLTAYADEADRERALAAGADDYLTKPIFL  112 (130)
T ss_pred             EeCChHHHHHHHHHh-CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCCCCEEEEEcCcCHHHHHHHHHcCCCeEEcCCCCc
Confidence            466885 99999987 6 49999999999999999999999987677888999999888777778999999999999776


Q ss_pred             HH-HHHHHHHHHH
Q 043479           80 DD-LKNVWQYAMT   91 (534)
Q Consensus        80 ee-L~~aI~~aL~   91 (534)
                      .+ |..++.+.+.
T Consensus       113 ~~~l~~~i~~~~~  125 (130)
T COG0784         113 EEELLAALRRLLA  125 (130)
T ss_pred             HHHHHHHHHHHHH
Confidence            66 7777775543

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

Probab=99.11  E-value=8.1e-10  Score=112.23  Aligned_cols=86  Identities=27%  Similarity=0.504  Sum_probs=78.9

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      +|..+.||++.++. ..||||++|+.||+|+|++++++++...+.+|||++|++.  ++...++..-+++||+||++++.
T Consensus        29 ~~~~~~eal~~Le~-~kpDLifldI~mp~~ngiefaeQvr~i~~~v~iifIssh~--eya~dsf~~n~~dYl~KPvt~ek  105 (361)
T COG3947          29 SCSHPVEALDLLEV-FKPDLIFLDIVMPYMNGIEFAEQVRDIESAVPIIFISSHA--EYADDSFGMNLDDYLPKPVTPEK  105 (361)
T ss_pred             ccCCHHHHHHHHHh-cCCCEEEEEeecCCccHHHHHHHHHHhhccCcEEEEecch--hhhhhhcccchHhhccCCCCHHH
Confidence            46789999999997 8999999999999999999999999999999999999986  55567777788999999999999


Q ss_pred             HHHHHHHHH
Q 043479           82 LKNVWQYAM   90 (534)
Q Consensus        82 L~~aI~~aL   90 (534)
                      |-++|.++.
T Consensus       106 LnraIdr~~  114 (361)
T COG3947         106 LNRAIDRRL  114 (361)
T ss_pred             HHHHHHHHh
Confidence            999999987

>PRK10529 DNA-binding transcriptional activator KdpE; Provisional

Probab=99.10  E-value=8.6e-10  Score=105.39  Aligned_cols=90  Identities=27%  Similarity=0.481  Sum_probs=80.7

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.+..+++..+.. ..||+||+|+.||+++|+++++.+++ .+.+|||++++..+.....+++++||++||.||++.++
T Consensus        30 ~~~~~~~~~~~~~~-~~~dlvild~~l~~~~g~~~~~~lr~-~~~~pvi~lt~~~~~~~~~~~~~~ga~~~l~kP~~~~~  107 (225)
T PRK10529         30 EAETLQRGLLEAAT-RKPDLIILDLGLPDGDGIEFIRDLRQ-WSAIPVIVLSARSEESDKIAALDAGADDYLSKPFGIGE  107 (225)
T ss_pred             EeCCHHHHHHHHhc-CCCCEEEEeCCCCCCCHHHHHHHHHc-CCCCCEEEEECCCCHHHHHHHHHcCCCEEEeCCCCHHH
Confidence            35678888888776 67999999999999999999999997 45799999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHh
Q 043479           82 LKNVWQYAMTYK   93 (534)
Q Consensus        82 L~~aI~~aL~~k   93 (534)
                      |...++.++++.
T Consensus       108 l~~~i~~~~~~~  119 (225)
T PRK10529        108 LQARLRVALRRH  119 (225)
T ss_pred             HHHHHHHHHhhc
Confidence            999999887653

>PRK11173 two-component response regulator; Provisional

Probab=99.08  E-value=9.8e-10  Score=106.60  Aligned_cols=90  Identities=28%  Similarity=0.457  Sum_probs=81.6

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.++++.+.. ..||+||+|+.||+++|+++++.+++. +.+|||++++..+......+++.||++||.||++.++
T Consensus        32 ~~~~~~~~~~~~~~-~~~dlvild~~l~~~~g~~~~~~lr~~-~~~pii~lt~~~~~~~~~~~~~~ga~d~l~kP~~~~e  109 (237)
T PRK11173         32 EATDGAEMHQILSE-NDINLVIMDINLPGKNGLLLARELREQ-ANVALMFLTGRDNEVDKILGLEIGADDYITKPFNPRE  109 (237)
T ss_pred             EECCHHHHHHHHhh-CCCCEEEEcCCCCCCCHHHHHHHHhcC-CCCCEEEEECCCCHHHHHHHHHCCCCEEEECCCCHHH
Confidence            46788999998876 789999999999999999999999975 5799999999999888889999999999999999999


Q ss_pred             HHHHHHHHHHHh
Q 043479           82 LKNVWQYAMTYK   93 (534)
Q Consensus        82 L~~aI~~aL~~k   93 (534)
                      |...++.++++.
T Consensus       110 L~~~i~~~l~r~  121 (237)
T PRK11173        110 LTIRARNLLSRT  121 (237)
T ss_pred             HHHHHHHHHhcc
Confidence            999999888653

>TIGR02875 spore_0_A sporulation transcription factor Spo0A

Probab=99.05  E-value=1.5e-09  Score=107.90  Aligned_cols=90  Identities=27%  Similarity=0.407  Sum_probs=81.9

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCC--CcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTH--LPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~--ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      ++.++.++++.+.. ..||+||+|+.||+++|+++++.+++..+.  +|||++|+..+.....++++.|+++|+.||++.
T Consensus        33 ~a~~~~eal~~l~~-~~~DlvllD~~mp~~dG~~~l~~i~~~~~~~~~~iI~lt~~~~~~~~~~~~~~G~~~~l~KP~~~  111 (262)
T TIGR02875        33 VAHNGVDALELIKE-QQPDVVVLDIIMPHLDGIGVLEKLNEIELSARPRVIMLSAFGQEKITQRAVALGADYYVLKPFDL  111 (262)
T ss_pred             EeCCHHHHHHHHHh-cCCCEEEEeCCCCCCCHHHHHHHHHhhccccCCeEEEEeCCCCHHHHHHHHHCCCCEEEECCCCH
Confidence            36789999999987 789999999999999999999999986655  899999999999989999999999999999999


Q ss_pred             HHHHHHHHHHHHH
Q 043479           80 DDLKNVWQYAMTY   92 (534)
Q Consensus        80 eeL~~aI~~aL~~   92 (534)
                      ++|...|++++..
T Consensus       112 ~~L~~~i~~~~~~  124 (262)
T TIGR02875       112 EILAARIRQLAWG  124 (262)
T ss_pred             HHHHHHHHHHHcc
Confidence            9999999987654

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.

>PRK09581 pleD response regulator PleD; Reviewed

Probab=99.04  E-value=6.2e-10  Score=117.15  Aligned_cols=90  Identities=21%  Similarity=0.433  Sum_probs=81.9

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhh--CCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~--~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      .+.++.+|+..+.+ .+|||||+|+.||+++|+++++.+++.  .+++|||++|+..+.+.+.++++.||++||.||+++
T Consensus       183 ~~~~~~~a~~~~~~-~~~d~vi~d~~~p~~~g~~l~~~i~~~~~~~~~~ii~ls~~~~~~~~~~a~~~Ga~d~l~kp~~~  261 (457)
T PRK09581        183 VVSDPSEALFNAAE-TNYDLVIVSANFENYDPLRLCSQLRSKERTRYVPILLLVDEDDDPRLVKALELGVNDYLMRPIDK  261 (457)
T ss_pred             eecChHHHHHhccc-CCCCEEEecCCCCCchHhHHHHHHHhccccCCCcEEEEeCCCChHHHHHHHHccchhhhhCCCcH
Confidence            46788899998876 789999999999999999999999974  478999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHH
Q 043479           80 DDLKNVWQYAMTY   92 (534)
Q Consensus        80 eeL~~aI~~aL~~   92 (534)
                      ++|...|...+..
T Consensus       262 ~~l~~~i~~~~~~  274 (457)
T PRK09581        262 NELLARVRTQIRR  274 (457)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999876654

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

Probab=99.03  E-value=1.3e-09  Score=117.29  Aligned_cols=93  Identities=29%  Similarity=0.497  Sum_probs=85.8

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhh--CCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~--~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      .+.++.+|+..+.+ .+||+||+|+.||++||+++++++|..  ...+|||++++.++.....+|++.|+.|||.||+..
T Consensus       161 ~a~~~~~Al~~~~e-~~~dlil~d~~mp~~dg~el~~~lr~~~~t~~ipii~~~~~~d~~~~~~Af~~G~~Dyi~kPi~~  239 (435)
T COG3706         161 EATDGEEALLQLAE-LPPDLVLLDANMPDMDGLELCTRLRQLERTRDIPIILLSSKDDDELVVRAFELGVNDYITKPIEE  239 (435)
T ss_pred             eecCHHHHHHHHhc-CCCcEEEEecCCCccCHHHHHHHHhcccccccccEEEEecccchHHHHHHHHcCCcceEecCCCH
Confidence            57799999999988 699999999999999999999999974  456999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhh
Q 043479           80 DDLKNVWQYAMTYKKA   95 (534)
Q Consensus        80 eeL~~aI~~aL~~k~~   95 (534)
                      .+|...+++.+++.+.
T Consensus       240 ~~l~~Rl~~~l~~~~~  255 (435)
T COG3706         240 GELRARLRRQLRRKRY  255 (435)
T ss_pred             HHHHHHHHHHHHhhhH
Confidence            9999999999887664

>PRK14084 two-component response regulator; Provisional

Probab=99.03  E-value=2.1e-09  Score=105.39  Aligned_cols=89  Identities=21%  Similarity=0.347  Sum_probs=78.4

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++.++++.+.. ..||+||+|+.||+++|+++++.|++..+..+||++|+..  ....++++.|+.+||.||++.++
T Consensus        31 ~~~~~~~~l~~~~~-~~~dlv~lDi~m~~~~G~~~~~~i~~~~~~~~iI~~t~~~--~~~~~~~~~~~~~yl~KP~~~~~  107 (246)
T PRK14084         31 EAENVKETLEALLI-NQYDIIFLDINLMDESGIELAAKIQKMKEPPAIIFATAHD--QFAVKAFELNATDYILKPFEQKR  107 (246)
T ss_pred             EECCHHHHHHHHHh-cCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCEEEEEecCh--HHHHHHHhcCCcEEEECCCCHHH
Confidence            46788999998876 6899999999999999999999999877778888888865  35678999999999999999999


Q ss_pred             HHHHHHHHHHHh
Q 043479           82 LKNVWQYAMTYK   93 (534)
Q Consensus        82 L~~aI~~aL~~k   93 (534)
                      |..+++++++..
T Consensus       108 l~~~l~~~~~~~  119 (246)
T PRK14084        108 IEQAVNKVRATK  119 (246)
T ss_pred             HHHHHHHHHHhh
Confidence            999999987653

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

Probab=99.01  E-value=9.9e-10  Score=126.68  Aligned_cols=89  Identities=29%  Similarity=0.492  Sum_probs=81.3

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhC-CCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEF-THLPVMVMSSDDRESVIMKALASGVAFYILKPLNPD   80 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~-p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~e   80 (534)
                      ++.++.||++.+.....||+||+|++||.|||++..++||+.. .++|||.+|+..+.....+|++.|.++||.||++.+
T Consensus       695 ~~~sg~e~l~~~~~~~~y~~ifmD~qMP~mDG~e~~~~irk~~~~~~pIvAlTa~~~~~~~~~c~~~Gmd~yl~KP~~~~  774 (786)
T KOG0519|consen  695 EVNSGQEALDKLKPPHSYDVIFMDLQMPEMDGYEATREIRKKERWHLPIVALTADADPSTEEECLEVGMDGYLSKPFTLE  774 (786)
T ss_pred             eecCcHHHHHhcCCCCcccEEEEEcCCcccchHHHHHHHHHhhcCCCCEEEEecCCcHHHHHHHHHhCCceEEcccccHH
Confidence            4568999999998447899999999999999999999999743 569999999999999999999999999999999999


Q ss_pred             HHHHHHHHHH
Q 043479           81 DLKNVWQYAM   90 (534)
Q Consensus        81 eL~~aI~~aL   90 (534)
                      .|+.++++.+
T Consensus       775 ~l~~~l~~~~  784 (786)
T KOG0519|consen  775 KLVKILREFL  784 (786)
T ss_pred             HHHHHHHHHh
Confidence            9999998876

>PRK10701 DNA-binding transcriptional regulator RstA; Provisional

Probab=99.01  E-value=3.3e-09  Score=102.89  Aligned_cols=90  Identities=24%  Similarity=0.362  Sum_probs=80.5

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.++++.+.. ..||+||+|+.||+++|+++++.+++.. ..|||++++..+......++++|+++||.||++.++
T Consensus        30 ~~~~~~~~l~~~~~-~~~dlvild~~l~~~~g~~~~~~ir~~~-~~pii~l~~~~~~~~~~~~~~~Ga~d~l~kP~~~~~  107 (240)
T PRK10701         30 VEPRGDRAEATILR-EQPDLVLLDIMLPGKDGMTICRDLRPKW-QGPIVLLTSLDSDMNHILALEMGACDYILKTTPPAV  107 (240)
T ss_pred             EeCCHHHHHHHHhh-CCCCEEEEeCCCCCCCHHHHHHHHHhcC-CCCEEEEECCCCHHHHHHHHHcCCCEEEECCCCHHH
Confidence            35688999998876 7899999999999999999999999854 589999999888888889999999999999999999


Q ss_pred             HHHHHHHHHHHh
Q 043479           82 LKNVWQYAMTYK   93 (534)
Q Consensus        82 L~~aI~~aL~~k   93 (534)
                      |..+++.++++.
T Consensus       108 l~~~i~~~l~~~  119 (240)
T PRK10701        108 LLARLRLHLRQN  119 (240)
T ss_pred             HHHHHHHHHhcc
Confidence            999999887653

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=99.01  E-value=2.2e-09  Score=115.19  Aligned_cols=90  Identities=26%  Similarity=0.361  Sum_probs=83.5

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCC-----CCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCC
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPE-----MNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKP   76 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPd-----mdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP   76 (534)
                      ++.++.+|++.+.. ..||+||+|+.||+     ++|+++++.+++..+++|||++|+..+.+...++++.||++||.||
T Consensus        25 ~a~~~~~al~~l~~-~~~dlvllD~~mp~~~~~~~~g~~~l~~i~~~~~~~piI~lt~~~~~~~~~~a~~~Ga~dyl~KP  103 (445)
T TIGR02915        25 VAADRESAIALVRR-HEPAVVTLDLGLPPDADGASEGLAALQQILAIAPDTKVIVITGNDDRENAVKAIGLGAYDFYQKP  103 (445)
T ss_pred             EeCCHHHHHHHHhh-CCCCEEEEeCCCCCCcCCCCCHHHHHHHHHhhCCCCCEEEEecCCCHHHHHHHHHCCccEEEeCC
Confidence            56889999999987 78999999999996     8999999999998999999999999999999999999999999999


Q ss_pred             CChHHHHHHHHHHHHH
Q 043479           77 LNPDDLKNVWQYAMTY   92 (534)
Q Consensus        77 ~s~eeL~~aI~~aL~~   92 (534)
                      ++.++|..+|++++..
T Consensus       104 ~~~~~L~~~i~~~~~~  119 (445)
T TIGR02915       104 IDPDVLKLIVDRAFHL  119 (445)
T ss_pred             CCHHHHHHHHhhhhhh
Confidence            9999999999887753

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).

>PLN03029 type-a response regulator protein; Provisional

Probab=98.99  E-value=3.5e-09  Score=104.41  Aligned_cols=92  Identities=34%  Similarity=0.540  Sum_probs=79.3

Q ss_pred             eecCHHHHHHHHHhc-------------------CCceEEEEeCCCCCCCHHHHHHHHHhhC--CCCcEEEEecCCCHHH
Q 043479            2 TVTRPVEALATVRIQ-------------------RDIDLVVTDLHMPEMNGIELQKEINEEF--THLPVMVMSSDDRESV   60 (534)
Q Consensus         2 tass~~EALe~L~~~-------------------~~pDLVLLDi~mPdmdGleLL~~Lr~~~--p~ipVIVLSs~~d~~~   60 (534)
                      ++.++.++++.+...                   ..+||||+|+.||+++|+++++.|++..  +++|||++|+..+...
T Consensus        37 ~a~sg~~al~~l~~~~~d~~~p~~~~~~~~~~~~~~~dlVllD~~mp~~~G~e~l~~ir~~~~~~~ipvIils~~~~~~~  116 (222)
T PLN03029         37 TVDSGSKALKFLGLHEDDRSNPDTPSVSPNSHQEVEVNLIITDYCMPGMTGYDLLKKIKESSSLRNIPVVIMSSENVPSR  116 (222)
T ss_pred             EECCHHHHHHHHHhccccccccccccccccccccccCCEEEEcCCCCCCCHHHHHHHHHhccccCCCcEEEEeCCCCHHH
Confidence            467889999888541                   1367999999999999999999999753  5799999999999999


Q ss_pred             HHHHHHcCCcEEEeCCCChHHHHHHHHHHHHHh
Q 043479           61 IMKALASGVAFYILKPLNPDDLKNVWQYAMTYK   93 (534)
Q Consensus        61 ~~~AL~aGA~dyL~KP~s~eeL~~aI~~aL~~k   93 (534)
                      ..+++++|+++||.||+...+|...+.+++..+
T Consensus       117 ~~~al~~Ga~dyl~KP~~~~~L~~l~~~~~~~~  149 (222)
T PLN03029        117 ITRCLEEGAEEFFLKPVQLSDLNRLKPHMMKTK  149 (222)
T ss_pred             HHHHHHhCchheEECCCCHHHHHHHHHHHHHHH
Confidence            999999999999999999999988887776544

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

Probab=98.98  E-value=2.8e-09  Score=125.08  Aligned_cols=91  Identities=26%  Similarity=0.391  Sum_probs=84.7

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.+|++.+.. ..||+||+|+.||+|+|+++++.|++..+.+|||++|+..+.+...+++++|+++||.||++.++
T Consensus       830 ~a~~g~eal~~l~~-~~~DlVl~D~~mP~mdG~el~~~ir~~~~~~pII~lTa~~~~~~~~~~~~aG~d~~L~KPv~~~~  908 (924)
T PRK10841        830 TANDGVDALNVLSK-NHIDIVLTDVNMPNMDGYRLTQRLRQLGLTLPVIGVTANALAEEKQRCLEAGMDSCLSKPVTLDV  908 (924)
T ss_pred             EECCHHHHHHHHHh-CCCCEEEEcCCCCCCCHHHHHHHHHhcCCCCCEEEEECCCCHHHHHHHHHCCCCEEEeCCCCHHH
Confidence            57899999999987 78999999999999999999999999888899999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHh
Q 043479           82 LKNVWQYAMTYK   93 (534)
Q Consensus        82 L~~aI~~aL~~k   93 (534)
                      |..+|.++....
T Consensus       909 L~~~L~~~~~~~  920 (924)
T PRK10841        909 LKQTLTVYAERV  920 (924)
T ss_pred             HHHHHHHHHHHh
Confidence            999999876543

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

Probab=98.97  E-value=1.6e-09  Score=100.90  Aligned_cols=87  Identities=22%  Similarity=0.323  Sum_probs=81.9

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.+.+|+|..++. ..|+..++|+.|.+.+|+++++.|++..++..|||+|++.+.....+|++.||++||.||.+.++
T Consensus        38 ~a~~~~eal~~art-~~PayAvvDlkL~~gsGL~~i~~lr~~~~d~rivvLTGy~sIATAV~AvKlGA~~YLaKPAdaDd  116 (182)
T COG4567          38 TAESVEEALAAART-APPAYAVVDLKLGDGSGLAVIEALRERRADMRIVVLTGYASIATAVEAVKLGACDYLAKPADADD  116 (182)
T ss_pred             eeccHHHHHHHHhc-CCCceEEEEeeecCCCchHHHHHHHhcCCcceEEEEecchHHHHHHHHHHhhhhhhcCCCCChHH
Confidence            57899999999998 88999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHH
Q 043479           82 LKNVWQYA   89 (534)
Q Consensus        82 L~~aI~~a   89 (534)
                      +..++.+.
T Consensus       117 i~aAl~~~  124 (182)
T COG4567         117 ILAALLRR  124 (182)
T ss_pred             HHHHHhhc
Confidence            98777543

>PRK11466 hybrid sensory histidine kinase TorS; Provisional

Probab=98.97  E-value=2.7e-09  Score=123.66  Aligned_cols=92  Identities=17%  Similarity=0.305  Sum_probs=84.3

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++.+|++.+....+|||||+|+.||+++|+++++.|++..+.+|||++|+........++++.|+++||.||++.++
T Consensus       710 ~a~~~~~al~~~~~~~~~Dlvl~D~~mp~~~G~~~~~~lr~~~~~~~ii~~t~~~~~~~~~~~~~~g~~~~l~KP~~~~~  789 (914)
T PRK11466        710 AVGNAAQALETLQNSEPFAAALVDFDLPDYDGITLARQLAQQYPSLVLIGFSAHVIDETLRQRTSSLFRGIIPKPVPREV  789 (914)
T ss_pred             EeCCHHHHHHHHHcCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCCCCEEEEeCCCchhhHHHHHhcCcCCEEeCCCCHHH
Confidence            47899999998864356899999999999999999999999889999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHh
Q 043479           82 LKNVWQYAMTYK   93 (534)
Q Consensus        82 L~~aI~~aL~~k   93 (534)
                      |..+|.++++..
T Consensus       790 L~~~i~~~~~~~  801 (914)
T PRK11466        790 LGQLLAHYLQLQ  801 (914)
T ss_pred             HHHHHHHHhhhc
Confidence            999999988653

>PRK13856 two-component response regulator VirG; Provisional

Probab=98.97  E-value=5.8e-09  Score=101.80  Aligned_cols=90  Identities=21%  Similarity=0.411  Sum_probs=78.5

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCC-CHHHHHHHHHcCCcEEEeCCCChH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDD-RESVIMKALASGVAFYILKPLNPD   80 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~-d~~~~~~AL~aGA~dyL~KP~s~e   80 (534)
                      .+.++.++++.+.. ..||+||+|+.||+++|+++++.++.. +.+|+|++++.. +.....+++++||++||.||++.+
T Consensus        30 ~~~~~~~~~~~~~~-~~~dlvi~d~~l~~~~g~~l~~~i~~~-~~~pii~lt~~~~~~~~~~~~l~~Ga~~yl~kP~~~~  107 (241)
T PRK13856         30 AVADSQQFNRVLAS-ETVDVVVVDLNLGREDGLEIVRSLATK-SDVPIIIISGDRLEEADKVVALELGATDFIAKPFGTR  107 (241)
T ss_pred             EECCHHHHHHHHhh-CCCCEEEEeCCCCCCCHHHHHHHHHhc-CCCcEEEEECCCCcHHHHHHHHhcCcCeEEeCCCCHH
Confidence            45788899988876 789999999999999999999999875 469999999854 566677899999999999999999


Q ss_pred             HHHHHHHHHHHHh
Q 043479           81 DLKNVWQYAMTYK   93 (534)
Q Consensus        81 eL~~aI~~aL~~k   93 (534)
                      +|...|+.++++.
T Consensus       108 eL~~~i~~~l~~~  120 (241)
T PRK13856        108 EFLARIRVALRVR  120 (241)
T ss_pred             HHHHHHHHHHhhc
Confidence            9999999887653

>PRK11107 hybrid sensory histidine kinase BarA; Provisional

Probab=98.92  E-value=5.5e-09  Score=120.66  Aligned_cols=90  Identities=22%  Similarity=0.350  Sum_probs=82.7

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhh--CCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~--~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      ++.++.+|++.+.. ..||+||+|+.||+++|+++++.|++.  .+++|||++|+..+.....++++.|+++||.||++.
T Consensus       696 ~~~~~~~al~~~~~-~~~dlil~D~~mp~~~g~~~~~~lr~~~~~~~~pii~lt~~~~~~~~~~~~~~G~~~~l~KP~~~  774 (919)
T PRK11107        696 LCDSGHQAVEQAKQ-RPFDLILMDIQMPGMDGIRACELIRQLPHNQNTPIIAVTAHAMAGERERLLSAGMDDYLAKPIDE  774 (919)
T ss_pred             EECCHHHHHHHHHh-CCCCEEEEeCCCCCCcHHHHHHHHHhcccCCCCCEEEEeCCCCHHHHHHHHHcCCCeEeeCCCCH
Confidence            46799999999987 789999999999999999999999973  567999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHH
Q 043479           80 DDLKNVWQYAMTY   92 (534)
Q Consensus        80 eeL~~aI~~aL~~   92 (534)
                      ++|..+|++++..
T Consensus       775 ~~L~~~l~~~~~~  787 (919)
T PRK11107        775 AMLKQVLLRYKPG  787 (919)
T ss_pred             HHHHHHHHHHccc
Confidence            9999999988754

>PRK15115 response regulator GlrR; Provisional

Probab=98.91  E-value=5.4e-09  Score=112.15  Aligned_cols=91  Identities=29%  Similarity=0.445  Sum_probs=84.2

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.+|++.+.. ..||+||+|+.||+++|+++++.+++..+.+|||++|+..+.....+++++|+.+||.||++.++
T Consensus        34 ~~~~~~eal~~l~~-~~~dlvilD~~lp~~~g~~ll~~l~~~~~~~pvIvlt~~~~~~~~~~a~~~Ga~~~l~KP~~~~~  112 (444)
T PRK15115         34 TAESGQEALRVLNR-EKVDLVISDLRMDEMDGMQLFAEIQKVQPGMPVIILTAHGSIPDAVAATQQGVFSFLTKPVDRDA  112 (444)
T ss_pred             EeCCHHHHHHHHhc-CCCCEEEEcCCCCCCCHHHHHHHHHhcCCCCcEEEEECCCCHHHHHHHHhcChhhhccCCCCHHH
Confidence            46789999999886 78999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHh
Q 043479           82 LKNVWQYAMTYK   93 (534)
Q Consensus        82 L~~aI~~aL~~k   93 (534)
                      |..+|.+++...
T Consensus       113 L~~~l~~~~~~~  124 (444)
T PRK15115        113 LYKAIDDALEQS  124 (444)
T ss_pred             HHHHHHHHHHhh
Confidence            999999887653

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

Probab=98.90  E-value=9.8e-09  Score=111.04  Aligned_cols=90  Identities=26%  Similarity=0.459  Sum_probs=83.7

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++.+++..+.. ..||+||+|+.||+++|+++++.+++..+.+|||++|+..+......+++.|+.+||.||++.++
T Consensus        32 ~~~s~~~al~~l~~-~~~DlvllD~~lp~~dgl~~l~~ir~~~~~~pvIvlt~~~~~~~~~~a~~~Ga~~~l~KP~~~~~  110 (469)
T PRK10923         32 TFENGNEVLEALAS-KTPDVLLSDIRMPGMDGLALLKQIKQRHPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDIDE  110 (469)
T ss_pred             EECCHHHHHHHHhc-CCCCEEEECCCCCCCCHHHHHHHHHhhCCCCeEEEEECCCCHHHHHHHHhcCcceEEecCCcHHH
Confidence            46789999999987 78999999999999999999999999888899999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHH
Q 043479           82 LKNVWQYAMTY   92 (534)
Q Consensus        82 L~~aI~~aL~~   92 (534)
                      |...|.+++..
T Consensus       111 L~~~i~~~l~~  121 (469)
T PRK10923        111 AVALVERAISH  121 (469)
T ss_pred             HHHHHHHHHHH
Confidence            99999988764

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=98.90  E-value=9.5e-09  Score=110.74  Aligned_cols=91  Identities=25%  Similarity=0.432  Sum_probs=83.6

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.+|+..+.. ..||+||+|+.||+++|+++++.+++..+.+|||++|+..+.....++++.|+.+||.||++.++
T Consensus        27 ~~~~~~~al~~~~~-~~~DlVllD~~~p~~~g~~ll~~l~~~~~~~~vIvlt~~~~~~~~~~a~~~Ga~~~l~KP~~~~~  105 (463)
T TIGR01818        27 TFGNAASVLRALAR-GQPDLLITDVRMPGEDGLDLLPQIKKRHPQLPVIVMTAHSDLDTAVAAYQRGAFEYLPKPFDLDE  105 (463)
T ss_pred             EECCHHHHHHHHhc-CCCCEEEEcCCCCCCCHHHHHHHHHHhCCCCeEEEEeCCCCHHHHHHHHHcCcceeecCCCCHHH
Confidence            46688999998876 78999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHh
Q 043479           82 LKNVWQYAMTYK   93 (534)
Q Consensus        82 L~~aI~~aL~~k   93 (534)
                      |..+|++++...
T Consensus       106 L~~~i~~~l~~~  117 (463)
T TIGR01818       106 AVTLVERALAHA  117 (463)
T ss_pred             HHHHHHHHHHHH
Confidence            999999887643

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.

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=98.90  E-value=6.2e-09  Score=111.26  Aligned_cols=91  Identities=32%  Similarity=0.480  Sum_probs=83.7

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++.++++.+.. ..||+||+|+.||+++|+++++.+++..+.+|||++|++.+.....++++.|+.+||.||++.++
T Consensus        34 ~~~~~~~al~~l~~-~~~DlvilD~~m~~~~G~~~~~~ir~~~~~~~vi~lt~~~~~~~~~~a~~~ga~~~l~Kp~~~~~  112 (441)
T PRK10365         34 LANSGRQALEQVRE-QVFDLVLCDVRMAEMDGIATLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDN  112 (441)
T ss_pred             EeCCHHHHHHHHhc-CCCCEEEEeCCCCCCCHHHHHHHHHhhCCCCeEEEEECCCCHHHHHHHHHhhhHHHhcCCCCHHH
Confidence            46789999998876 77999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHh
Q 043479           82 LKNVWQYAMTYK   93 (534)
Q Consensus        82 L~~aI~~aL~~k   93 (534)
                      |..+|++++...
T Consensus       113 L~~~l~~~l~~~  124 (441)
T PRK10365        113 LQATLEKALAHT  124 (441)
T ss_pred             HHHHHHHHHHHH
Confidence            999999887643

>PRK15347 two component system sensor kinase SsrA; Provisional

Probab=98.89  E-value=9.1e-09  Score=119.05  Aligned_cols=89  Identities=22%  Similarity=0.390  Sum_probs=81.8

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhh----CCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCC
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEE----FTHLPVMVMSSDDRESVIMKALASGVAFYILKPL   77 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~----~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~   77 (534)
                      ++.++.+|++.++. ..||+||+|+.||+++|+++++.+++.    .+.+|||++|+..+.....+++++|+++||.||+
T Consensus       719 ~a~~~~~al~~~~~-~~~dlil~D~~mp~~~G~~~~~~ir~~~~~~~~~~pii~lt~~~~~~~~~~~~~~G~~~~l~KP~  797 (921)
T PRK15347        719 TAASGTEALELGRQ-HRFDLVLMDIRMPGLDGLETTQLWRDDPNNLDPDCMIVALTANAAPEEIHRCKKAGMNHYLTKPV  797 (921)
T ss_pred             EECCHHHHHHHHhc-CCCCEEEEeCCCCCCCHHHHHHHHHhchhhcCCCCcEEEEeCCCCHHHHHHHHHCCCCEEEECCC
Confidence            57799999999987 789999999999999999999999863    3679999999999999999999999999999999


Q ss_pred             ChHHHHHHHHHHHH
Q 043479           78 NPDDLKNVWQYAMT   91 (534)
Q Consensus        78 s~eeL~~aI~~aL~   91 (534)
                      +.++|..++.+++.
T Consensus       798 ~~~~L~~~l~~~~~  811 (921)
T PRK15347        798 TLAQLARALELAAE  811 (921)
T ss_pred             CHHHHHHHHHHHHh
Confidence            99999999988764

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=98.89  E-value=8.4e-09  Score=110.87  Aligned_cols=90  Identities=30%  Similarity=0.439  Sum_probs=83.1

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++.++++.+.. ..||+||+|+.||+++|+++++.+++..+.+|||++|+..+.....++++.|+.+||.||++.++
T Consensus        33 ~~~~~~~al~~l~~-~~~dlillD~~~p~~~g~~ll~~i~~~~~~~pvI~lt~~~~~~~~~~a~~~Ga~d~l~KP~~~~~  111 (457)
T PRK11361         33 CANNGRTALHLFAD-IHPDVVLMDIRMPEMDGIKALKEMRSHETRTPVILMTAYAEVETAVEALRCGAFDYVIKPFDLDE  111 (457)
T ss_pred             EECCHHHHHHHHhc-CCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCCEEEEeCCCCHHHHHHHHHCCccEEEecccCHHH
Confidence            46789999999886 78999999999999999999999998888899999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHH
Q 043479           82 LKNVWQYAMTY   92 (534)
Q Consensus        82 L~~aI~~aL~~   92 (534)
                      |...|++++..
T Consensus       112 L~~~i~~~l~~  122 (457)
T PRK11361        112 LNLIVQRALQL  122 (457)
T ss_pred             HHHHHhhhccc
Confidence            99999887654

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

Probab=98.87  E-value=1.7e-08  Score=98.13  Aligned_cols=86  Identities=23%  Similarity=0.396  Sum_probs=73.2

Q ss_pred             ecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHHH
Q 043479            3 VTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDDL   82 (534)
Q Consensus         3 ass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~eeL   82 (534)
                      +.++.++++.+.. ..||+||+|+.||+++|+++++.++.. ...+||++|+..  +...++++.|+.+||.||++.++|
T Consensus        33 ~~~~~~~l~~~~~-~~~dlv~lDi~~~~~~G~~~~~~l~~~-~~~~ii~vt~~~--~~~~~a~~~~~~~yl~KP~~~~~l  108 (238)
T PRK11697         33 CSNAIEAIGAIHR-LKPDVVFLDIQMPRISGLELVGMLDPE-HMPYIVFVTAFD--EYAIKAFEEHAFDYLLKPIDPARL  108 (238)
T ss_pred             eCCHHHHHHHHHh-cCCCEEEEeCCCCCCCHHHHHHHhccc-CCCEEEEEeccH--HHHHHHHhcCCcEEEECCCCHHHH
Confidence            5788999998876 689999999999999999999998643 335678888765  466789999999999999999999


Q ss_pred             HHHHHHHHHH
Q 043479           83 KNVWQYAMTY   92 (534)
Q Consensus        83 ~~aI~~aL~~   92 (534)
                      ..++.++...
T Consensus       109 ~~~l~~~~~~  118 (238)
T PRK11697        109 AKTLARLRQE  118 (238)
T ss_pred             HHHHHHHHHh
Confidence            9999998754

>TIGR02956 TMAO_torS TMAO reductase sytem sensor TorS

Probab=98.86  E-value=1.2e-08  Score=118.94  Aligned_cols=90  Identities=17%  Similarity=0.309  Sum_probs=83.3

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCC---CcEEEEecCCCHHHHHHHHHcCCcEEEeCCCC
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTH---LPVMVMSSDDRESVIMKALASGVAFYILKPLN   78 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~---ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s   78 (534)
                      ++.++.+|++.+.. ..||+||+|+.||+++|+++++.|++..+.   +|||++|+..+.....++++.|+++||.||++
T Consensus       731 ~~~~~~~a~~~l~~-~~~dlvl~D~~mp~~~g~~~~~~ir~~~~~~~~~pii~lta~~~~~~~~~~~~~G~~~~l~KP~~  809 (968)
T TIGR02956       731 LAESGQSALECFHQ-HAFDLALLDINLPDGDGVTLLQQLRAIYGAKNEVKFIAFSAHVFNEDVAQYLAAGFDGFLAKPVV  809 (968)
T ss_pred             EECCHHHHHHHHHC-CCCCEEEECCCCCCCCHHHHHHHHHhCccccCCCeEEEEECCCCHHHHHHHHHCCCCEEEeCCCC
Confidence            56899999999987 789999999999999999999999986655   89999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHH
Q 043479           79 PDDLKNVWQYAMTY   92 (534)
Q Consensus        79 ~eeL~~aI~~aL~~   92 (534)
                      .++|..+|.+++..
T Consensus       810 ~~~L~~~l~~~~~~  823 (968)
T TIGR02956       810 EEQLTAMIAVILAG  823 (968)
T ss_pred             HHHHHHHHHHHhcc
Confidence            99999999988754

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).

>PRK10610 chemotaxis regulatory protein CheY; Provisional

Probab=98.82  E-value=8e-08  Score=80.56  Aligned_cols=89  Identities=26%  Similarity=0.503  Sum_probs=78.3

Q ss_pred             ecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhC--CCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChH
Q 043479            3 VTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEF--THLPVMVMSSDDRESVIMKALASGVAFYILKPLNPD   80 (534)
Q Consensus         3 ass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~--p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~e   80 (534)
                      +.+..+++..+.. ..+|+|++|+.+++++++++++.+++..  +.+|+|+++...+.....++++.|+.+|+.||++.+
T Consensus        36 ~~~~~~~~~~~~~-~~~di~l~d~~~~~~~~~~~~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~~g~~~~i~~p~~~~  114 (129)
T PRK10610         36 AEDGVDALNKLQA-GGFGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAA  114 (129)
T ss_pred             eCCHHHHHHHhhc-cCCCEEEEcCCCCCCCHHHHHHHHHhCCCcCCCcEEEEECCCCHHHHHHHHHhCCCeEEECCCCHH
Confidence            4578888888776 6799999999999999999999998753  568999999888888888999999999999999999


Q ss_pred             HHHHHHHHHHHH
Q 043479           81 DLKNVWQYAMTY   92 (534)
Q Consensus        81 eL~~aI~~aL~~   92 (534)
                      ++...+++++++
T Consensus       115 ~l~~~l~~~~~~  126 (129)
T PRK10610        115 TLEEKLNKIFEK  126 (129)
T ss_pred             HHHHHHHHHHHH
Confidence            999999887643

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

Probab=98.81  E-value=2.1e-08  Score=119.88  Aligned_cols=89  Identities=30%  Similarity=0.524  Sum_probs=83.1

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++.+|++.+.. ..|||||+|+.||+++|+++++.|++..+.+|||++|+..+.....++++.|+++||.||++.++
T Consensus       987 ~~~~~~~al~~~~~-~~~dlil~D~~mp~~~g~~~~~~i~~~~~~~pii~lt~~~~~~~~~~~~~~G~~~~l~KP~~~~~ 1065 (1197)
T PRK09959        987 EATDGVQALHKVSM-QHYDLLITDVNMPNMDGFELTRKLREQNSSLPIWGLTANAQANEREKGLSCGMNLCLFKPLTLDV 1065 (1197)
T ss_pred             EECCHHHHHHHhhc-CCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCCEEEEECCCCHHHHHHHHHCCCCEEEeCCCCHHH
Confidence            46789999999986 78999999999999999999999999888899999999999999999999999999999999999


Q ss_pred             HHHHHHHHHH
Q 043479           82 LKNVWQYAMT   91 (534)
Q Consensus        82 L~~aI~~aL~   91 (534)
                      |..+|++++.
T Consensus      1066 L~~~l~~~~~ 1075 (1197)
T PRK09959       1066 LKTHLSQLHQ 1075 (1197)
T ss_pred             HHHHHHHHhh
Confidence            9999988764

>PRK09581 pleD response regulator PleD; Reviewed

Probab=98.79  E-value=4.8e-08  Score=102.86  Aligned_cols=92  Identities=25%  Similarity=0.405  Sum_probs=82.5

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhC--CCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEF--THLPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~--p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      ++.+..+++..+.. ..||+||+|+.+|+.+|+++++.+++..  +.+|||+++...+.....+++..|+++||.||++.
T Consensus        31 ~~~~~~~~~~~~~~-~~~dlvi~d~~~~~~~g~~l~~~i~~~~~~~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~kp~~~  109 (457)
T PRK09581         31 TASSGAEAIAICER-EQPDIILLDVMMPGMDGFEVCRRLKSDPATTHIPVVMVTALDDPEDRVRGLEAGADDFLTKPIND  109 (457)
T ss_pred             EeCCHHHHHHHHhh-cCCCEEEEeCCCCCCCHHHHHHHHHcCcccCCCCEEEEECCCCHHHHHHHHHCCCCEEEECCCCH
Confidence            46788999999886 7899999999999999999999998743  46899999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhh
Q 043479           80 DDLKNVWQYAMTYKK   94 (534)
Q Consensus        80 eeL~~aI~~aL~~k~   94 (534)
                      ++|..+++++++.+.
T Consensus       110 ~~l~~~i~~~~~~~~  124 (457)
T PRK09581        110 VALFARVKSLTRLKM  124 (457)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999998876543

>PRK12555 chemotaxis-specific methylesterase; Provisional

Probab=98.75  E-value=5.7e-08  Score=101.15  Aligned_cols=88  Identities=22%  Similarity=0.333  Sum_probs=73.6

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCC--HHHHHHHHHcCCcEEEeCCC--
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDR--ESVIMKALASGVAFYILKPL--   77 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d--~~~~~~AL~aGA~dyL~KP~--   77 (534)
                      .+.++.++++.+.. ..||+|++|+.||+++|++++++|++..+ +|||++++..+  .....++++.|+.+||.||+  
T Consensus        31 ~a~~~~eal~~l~~-~~pDlVllD~~mp~~~G~e~l~~l~~~~~-~pvivvs~~~~~~~~~~~~al~~Ga~d~l~KP~~~  108 (337)
T PRK12555         31 VATDGAQAVERCAA-QPPDVILMDLEMPRMDGVEATRRIMAERP-CPILIVTSLTERNASRVFEAMGAGALDAVDTPTLG  108 (337)
T ss_pred             EECCHHHHHHHHhc-cCCCEEEEcCCCCCCCHHHHHHHHHHHCC-CcEEEEeCCCCcCHHHHHHHHhcCceEEEECCCCC
Confidence            36789999999987 78999999999999999999999988665 89999998754  45677899999999999999  


Q ss_pred             -------ChHHHHHHHHHHHH
Q 043479           78 -------NPDDLKNVWQYAMT   91 (534)
Q Consensus        78 -------s~eeL~~aI~~aL~   91 (534)
                             ..++|...|+.+.+
T Consensus       109 ~~~~~~~~~~~l~~~i~~~~~  129 (337)
T PRK12555        109 IGAGLEEYAAELLAKIDQIGR  129 (337)
T ss_pred             cchhHHHHHHHHHHHHHHHhh
Confidence                   45566666665543

>PRK11091 aerobic respiration control sensor protein ArcB; Provisional

Probab=98.73  E-value=5.8e-08  Score=111.21  Aligned_cols=89  Identities=21%  Similarity=0.378  Sum_probs=77.9

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhC--CC-CcEEEEecCCCHHHHHHHHHcCCcEEEeCCCC
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEF--TH-LPVMVMSSDDRESVIMKALASGVAFYILKPLN   78 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~--p~-ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s   78 (534)
                      ++.++.+|++.+.. ..||+||+|+.||+++|+++++.|++..  +. +|||++|+.... ...++++.|+++||.||++
T Consensus       554 ~a~~~~eal~~~~~-~~~Dlvl~D~~mp~~~G~e~~~~ir~~~~~~~~~~ii~~ta~~~~-~~~~~~~~G~~~~l~KP~~  631 (779)
T PRK11091        554 VAMTGKEALEMFDP-DEYDLVLLDIQLPDMTGLDIARELRERYPREDLPPLVALTANVLK-DKKEYLDAGMDDVLSKPLS  631 (779)
T ss_pred             EECCHHHHHHHhhc-CCCCEEEEcCCCCCCCHHHHHHHHHhccccCCCCcEEEEECCchH-hHHHHHHCCCCEEEECCCC
Confidence            47899999999986 7899999999999999999999999865  45 488888887654 4578899999999999999


Q ss_pred             hHHHHHHHHHHHHH
Q 043479           79 PDDLKNVWQYAMTY   92 (534)
Q Consensus        79 ~eeL~~aI~~aL~~   92 (534)
                      .++|..+|++++..
T Consensus       632 ~~~L~~~l~~~~~~  645 (779)
T PRK11091        632 VPALTAMIKKFWDT  645 (779)
T ss_pred             HHHHHHHHHHHhcc
Confidence            99999999988754

>PRK13435 response regulator; Provisional

Probab=98.70  E-value=1.2e-07  Score=85.33  Aligned_cols=89  Identities=19%  Similarity=0.332  Sum_probs=74.4

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCC-CCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMP-EMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPD   80 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mP-dmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~e   80 (534)
                      .+.+..++++.+.. ..||+||+|+.++ +.+|+++++.+++. +.+|+|+++...+.   ..++..|+++|+.||++.+
T Consensus        35 ~~~~~~~~~~~~~~-~~~dliivd~~~~~~~~~~~~~~~l~~~-~~~pii~ls~~~~~---~~~~~~ga~~~l~kp~~~~  109 (145)
T PRK13435         35 IAMSSEQAIALGRR-RQPDVALVDVHLADGPTGVEVARRLSAD-GGVEVVFMTGNPER---VPHDFAGALGVIAKPYSPR  109 (145)
T ss_pred             eeCCHHHHHHHhhh-cCCCEEEEeeecCCCCcHHHHHHHHHhC-CCCCEEEEeCCHHH---HHHHhcCcceeEeCCCCHH
Confidence            46788889888876 6799999999998 58999999999764 57999999876432   4677899999999999999


Q ss_pred             HHHHHHHHHHHHhhh
Q 043479           81 DLKNVWQYAMTYKKA   95 (534)
Q Consensus        81 eL~~aI~~aL~~k~~   95 (534)
                      +|..+|++++.++..
T Consensus       110 ~l~~~i~~~~~~~~~  124 (145)
T PRK13435        110 GVARALSYLSARRVG  124 (145)
T ss_pred             HHHHHHHHHHhcCcc
Confidence            999999998765544

>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=98.69  E-value=1.5e-07  Score=74.88  Aligned_cols=86  Identities=27%  Similarity=0.483  Sum_probs=75.7

Q ss_pred             ecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHHH
Q 043479            3 VTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDDL   82 (534)
Q Consensus         3 ass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~eeL   82 (534)
                      +.+..+++..+.. ..+|+||+|..+++.+++++++.++...+.+|+++++..........++..|+.+|+.||+..++|
T Consensus        27 ~~~~~~~~~~~~~-~~~~~ii~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~i~~p~~~~~l  105 (113)
T cd00156          27 AEDGEEALALLAE-EKPDLILLDIMMPGMDGLELLRRIRKRGPDIPIIFLTAHGDDEDAVEALKAGADDYLTKPFSPEEL  105 (113)
T ss_pred             ecCHHHHHHHHHh-CCCCEEEEecCCCCCchHHHHHHHHHhCCCCCEEEEEecccHHHHHHHHHcChhhHccCCCCHHHH
Confidence            4567788888776 689999999999999999999999987778999999988777888889999999999999999999


Q ss_pred             HHHHHHH
Q 043479           83 KNVWQYA   89 (534)
Q Consensus        83 ~~aI~~a   89 (534)
                      ..+++++
T Consensus       106 ~~~l~~~  112 (113)
T cd00156         106 LARIRAL  112 (113)
T ss_pred             HHHHHhh
Confidence            9888754

>PRK13558 bacterio-opsin activator; Provisional

Probab=98.64  E-value=1.3e-07  Score=106.48  Aligned_cols=90  Identities=21%  Similarity=0.279  Sum_probs=78.8

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh--
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP--   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~--   79 (534)
                      .+.++.+++..+.. ..|||||+|+.||+++|+++++.|+...+.+|||++|+..+.....+++..|+.+||.||...  
T Consensus        36 ~~~~~~~al~~~~~-~~~Dlvl~d~~lp~~~g~~~l~~l~~~~~~~piI~lt~~~~~~~~~~al~~Ga~dyl~k~~~~~~  114 (665)
T PRK13558         36 QIRDFVAARDRVEA-GEIDCVVADHEPDGFDGLALLEAVRQTTAVPPVVVVPTAGDEAVARRAVDADAAAYVPAVSDDAT  114 (665)
T ss_pred             eeCCHHHHHHHhhc-cCCCEEEEeccCCCCcHHHHHHHHHhcCCCCCEEEEECCCCHHHHHHHHhcCcceEEeccchhHH
Confidence            46788999998876 779999999999999999999999998889999999999999999999999999999999754  


Q ss_pred             HHHHHHHHHHHHH
Q 043479           80 DDLKNVWQYAMTY   92 (534)
Q Consensus        80 eeL~~aI~~aL~~   92 (534)
                      ..+..+++.++..
T Consensus       115 ~~l~~~i~~~~~~  127 (665)
T PRK13558        115 AAIAERIESAVPE  127 (665)
T ss_pred             HHHHHHHHHhhhc
Confidence            3666667666654

>PRK00742 chemotaxis-specific methylesterase; Provisional

Probab=98.64  E-value=1.9e-07  Score=97.72  Aligned_cols=75  Identities=25%  Similarity=0.413  Sum_probs=65.8

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCC--CHHHHHHHHHcCCcEEEeCCCC
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDD--RESVIMKALASGVAFYILKPLN   78 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~--d~~~~~~AL~aGA~dyL~KP~s   78 (534)
                      .+.+..++++.+.. ..||+|++|+.||+++|++++++|++..+ +|||++++..  ......++++.|+++||.||+.
T Consensus        34 ~a~~~~~al~~~~~-~~~DlVllD~~mp~~dgle~l~~i~~~~~-~piIvls~~~~~~~~~~~~al~~Ga~d~l~kP~~  110 (354)
T PRK00742         34 TAPDGLEAREKIKK-LNPDVITLDVEMPVMDGLDALEKIMRLRP-TPVVMVSSLTERGAEITLRALELGAVDFVTKPFL  110 (354)
T ss_pred             EECCHHHHHHHHhh-hCCCEEEEeCCCCCCChHHHHHHHHHhCC-CCEEEEecCCCCCHHHHHHHHhCCCcEEEeCCcc
Confidence            45689999998876 78999999999999999999999998877 9999999754  3456678999999999999994

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

Probab=98.53  E-value=4.1e-07  Score=88.02  Aligned_cols=91  Identities=24%  Similarity=0.368  Sum_probs=73.2

Q ss_pred             ecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHHH
Q 043479            3 VTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDDL   82 (534)
Q Consensus         3 ass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~eeL   82 (534)
                      +.++.++.+.+.. ..||+||+|+.+|..|-.+-+ .+....+..|||++|+++++..+..++++||.+||+||++...|
T Consensus        36 ~~~~~~~~~~~~~-~~pDvVildie~p~rd~~e~~-~~~~~~~~~piv~lt~~s~p~~i~~a~~~Gv~ayivkpi~~~rl  113 (194)
T COG3707          36 AADGLEAVEVCER-LQPDVVILDIEMPRRDIIEAL-LLASENVARPIVALTAYSDPALIEAAIEAGVMAYIVKPLDESRL  113 (194)
T ss_pred             ecccccchhHHHh-cCCCEEEEecCCCCccHHHHH-HHhhcCCCCCEEEEEccCChHHHHHHHHcCCeEEEecCcchhhh
Confidence            3455566667766 789999999999998833333 23334455899999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhh
Q 043479           83 KNVWQYAMTYKKA   95 (534)
Q Consensus        83 ~~aI~~aL~~k~~   95 (534)
                      +.++.-+..+...
T Consensus       114 ~p~L~vA~srf~~  126 (194)
T COG3707         114 LPILDVAVSRFEE  126 (194)
T ss_pred             hHHHHHHHHHHHH
Confidence            9999888766543

>PRK09191 two-component response regulator; Provisional

Probab=98.52  E-value=8.2e-07  Score=87.57  Aligned_cols=87  Identities=23%  Similarity=0.421  Sum_probs=73.1

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCC-CCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPE-MNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPD   80 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPd-mdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~e   80 (534)
                      .+.+..++++.+.. ..||+||+|+.||+ ++|+++++.++... .+|||++|+..+....  +...++.+|+.||++.+
T Consensus       167 ~~~~~~~~l~~l~~-~~~dlvi~d~~~~~~~~g~e~l~~l~~~~-~~pii~ls~~~~~~~~--~~~~~~~~~l~kP~~~~  242 (261)
T PRK09191        167 IARTRAEAVALAKK-TRPGLILADIQLADGSSGIDAVNDILKTF-DVPVIFITAFPERLLT--GERPEPAFLITKPFQPD  242 (261)
T ss_pred             EECCHHHHHHHHhc-cCCCEEEEecCCCCCCCHHHHHHHHHHhC-CCCEEEEeCCCcHHHH--HHhcccCceEECCCCHH
Confidence            35678889998876 78999999999995 89999999998876 7999999997765433  34467889999999999


Q ss_pred             HHHHHHHHHHHH
Q 043479           81 DLKNVWQYAMTY   92 (534)
Q Consensus        81 eL~~aI~~aL~~   92 (534)
                      +|..+|++++..
T Consensus       243 ~l~~~i~~~~~~  254 (261)
T PRK09191        243 TVKAAISQALFF  254 (261)
T ss_pred             HHHHHHHHHHhc
Confidence            999999987654

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

Probab=98.48  E-value=7.2e-07  Score=93.83  Aligned_cols=75  Identities=31%  Similarity=0.438  Sum_probs=66.8

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCC--HHHHHHHHHcCCcEEEeCCCC
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDR--ESVIMKALASGVAFYILKPLN   78 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d--~~~~~~AL~aGA~dyL~KP~s   78 (534)
                      ++.++.+|++.+.+ ..||+|.+|+.||.|||+++++.|....| +|||++|+...  .+...+++++||.||+.||..
T Consensus        32 ~a~ng~~a~~~~~~-~~PDVi~ld~emp~mdgl~~l~~im~~~p-~pVimvsslt~~g~~~t~~al~~gAvD~i~kp~~  108 (350)
T COG2201          32 TARNGREAIDKVKK-LKPDVITLDVEMPVMDGLEALRKIMRLRP-LPVIMVSSLTEEGAEATLEALELGAVDFIAKPSG  108 (350)
T ss_pred             ecCCHHHHHHHHHh-cCCCEEEEecccccccHHHHHHHHhcCCC-CcEEEEeccccccHHHHHHHHhcCcceeecCCCc
Confidence            46799999999998 89999999999999999999999998855 99999987654  456788999999999999974

>PRK13557 histidine kinase; Provisional

Probab=98.37  E-value=1.8e-06  Score=92.95  Aligned_cols=91  Identities=22%  Similarity=0.297  Sum_probs=80.5

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCC-CCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPE-MNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPD   80 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPd-mdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~e   80 (534)
                      .+.+..++++.+.....||+||+|..+++ ++|+++++.|+...+.+|||+++...+......++..|+.+|+.||++.+
T Consensus       444 ~~~~~~~~~~~~~~~~~~d~vi~d~~~~~~~~~~~~~~~l~~~~~~~~ii~~~~~~~~~~~~~~~~~g~~~~l~kp~~~~  523 (540)
T PRK13557        444 VASNGREALEILDSHPEVDLLFTDLIMPGGMNGVMLAREARRRQPKIKVLLTTGYAEASIERTDAGGSEFDILNKPYRRA  523 (540)
T ss_pred             EeCCHHHHHHHHhcCCCceEEEEeccCCCCCCHHHHHHHHHHhCCCCcEEEEcCCCchhhhhhhccccCCceeeCCCCHH
Confidence            35788899998865236999999999997 99999999999988889999999998888888889999999999999999


Q ss_pred             HHHHHHHHHHHH
Q 043479           81 DLKNVWQYAMTY   92 (534)
Q Consensus        81 eL~~aI~~aL~~   92 (534)
                      +|..+++.++..
T Consensus       524 ~l~~~l~~~~~~  535 (540)
T PRK13557        524 ELARRVRMVLDG  535 (540)
T ss_pred             HHHHHHHHHhcC
Confidence            999999887643

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

Probab=98.32  E-value=2.4e-06  Score=99.21  Aligned_cols=89  Identities=17%  Similarity=0.194  Sum_probs=79.7

Q ss_pred             eecCHHHHHHHHHhc-CCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChH
Q 043479            2 TVTRPVEALATVRIQ-RDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPD   80 (534)
Q Consensus         2 tass~~EALe~L~~~-~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~e   80 (534)
                      .+.++.++++.+... ..||+||+  .||+++|+++++.|+...+.+|||+++...+.....+++..| ++||.||++.+
T Consensus       726 ~~~s~~~al~~l~~~~~~~DlVll--~~~~~~g~~l~~~l~~~~~~ipIIvls~~~~~~~~~~~~~~G-~d~L~KP~~~~  802 (828)
T PRK13837        726 GFSTLAAAIAWISKGPERFDLVLV--DDRLLDEEQAAAALHAAAPTLPIILGGNSKTMALSPDLLASV-AEILAKPISSR  802 (828)
T ss_pred             EeCCHHHHHHHHHhCCCCceEEEE--CCCCCCHHHHHHHHHhhCCCCCEEEEeCCCchhhhhhHhhcc-CcEEeCCCCHH
Confidence            467899999998753 34799999  689999999999999989999999999999988889999999 99999999999


Q ss_pred             HHHHHHHHHHHHh
Q 043479           81 DLKNVWQYAMTYK   93 (534)
Q Consensus        81 eL~~aI~~aL~~k   93 (534)
                      +|..+|+++++..
T Consensus       803 ~L~~~l~~~l~~~  815 (828)
T PRK13837        803 TLAYALRTALATA  815 (828)
T ss_pred             HHHHHHHHHHccc
Confidence            9999999988643

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

Probab=98.22  E-value=2.8e-06  Score=85.44  Aligned_cols=87  Identities=26%  Similarity=0.401  Sum_probs=76.2

Q ss_pred             ecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHHH
Q 043479            3 VTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDDL   82 (534)
Q Consensus         3 ass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~eeL   82 (534)
                      +.++.++++.++. ..+|++++|+.||+++|+++...|+...+..+|+++|++.  +.+..+++..|.+||.||+..+.|
T Consensus        33 ~~~~~~~~~~~~~-~~~~~~fldI~~~~~~G~ela~~i~~~~~~~~Ivfvt~~~--~~a~~afev~a~d~i~kp~~~~~l  109 (244)
T COG3279          33 AENGEEALQLLQG-LRPDLVFLDIAMPDINGIELAARIRKGDPRPAIVFVTAHD--EYAVAAFEVEALDYLLKPISEERL  109 (244)
T ss_pred             eccchhhHHHHhc-cCCCeEEEeeccCccchHHHHHHhcccCCCCeEEEEEehH--HHHHHHHhHHHHhhhcCcchHHHH
Confidence            5677888888887 6899999999999999999999999887778899999976  556677889999999999999999


Q ss_pred             HHHHHHHHHH
Q 043479           83 KNVWQYAMTY   92 (534)
Q Consensus        83 ~~aI~~aL~~   92 (534)
                      ...+.+..+.
T Consensus       110 ~~~l~~~~~~  119 (244)
T COG3279         110 AKTLERLRRY  119 (244)
T ss_pred             HHHHHHHHHH
Confidence            9999876543

>PRK15029 arginine decarboxylase; Provisional

Probab=97.70  E-value=0.00016  Score=83.40  Aligned_cols=90  Identities=17%  Similarity=0.178  Sum_probs=67.4

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHH----HHHHHHHhhCCCCcEEEEecCCC--HHHHHHHHHcCCcEEEeC
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGI----ELQKEINEEFTHLPVMVMSSDDR--ESVIMKALASGVAFYILK   75 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGl----eLL~~Lr~~~p~ipVIVLSs~~d--~~~~~~AL~aGA~dyL~K   75 (534)
                      .+.++++|++.+.....||+||+|+.||+++|+    +++++||+..+++|||++|+..+  +......+ --+.+|+.+
T Consensus        37 ~a~s~~dAl~~l~~~~~~DlVLLD~~LPd~dG~~~~~ell~~IR~~~~~iPIIlLTar~~~~~~~~~~~~-~~~~~~~~~  115 (755)
T PRK15029         37 KSTSFDDGFAILSSNEAIDCLMFSYQMEHPDEHQNVRQLIGKLHERQQNVPVFLLGDREKALAAMDRDLL-ELVDEFAWI  115 (755)
T ss_pred             EECCHHHHHHHHHhcCCCcEEEEECCCCCCccchhHHHHHHHHHhhCCCCCEEEEEcCCcccccCCHHHH-HhhheEEEe
Confidence            577899999999752479999999999999997    89999998888899999999986  33333322 336788887


Q ss_pred             CCChHHH-HHHHHHHHHH
Q 043479           76 PLNPDDL-KNVWQYAMTY   92 (534)
Q Consensus        76 P~s~eeL-~~aI~~aL~~   92 (534)
                      -.+..++ ...|...+++
T Consensus       116 ~~~~~~~~~~~~~~~~~~  133 (755)
T PRK15029        116 LEDTADFIAGRAVAAMTR  133 (755)
T ss_pred             cCCCHHHHHHHHHHHHHH
Confidence            6554444 3445555444

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

Probab=97.54  E-value=0.00012  Score=79.53  Aligned_cols=88  Identities=24%  Similarity=0.334  Sum_probs=76.1

Q ss_pred             ecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHHH
Q 043479            3 VTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDDL   82 (534)
Q Consensus         3 ass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~eeL   82 (534)
                      +..+.+++..+.. +++|.+++|+.||+++|+++++.+++.-.  .++++|...+.....+.+++|++++|.||+....+
T Consensus        18 a~~g~~~l~~~~~-~~~~~~lld~~m~~~~~~~~~~~lk~~~~--~~v~~t~~~~~~~~~~~~~~~~~~~l~~~~~~~~~   94 (435)
T COG3706          18 AKKGLIALAILLD-HKPDYKLLDVMMPGMDGFELCRRLKAEPA--TVVMVTALDDSAPRVRGLKAGADDFLTKPVNDSQL   94 (435)
T ss_pred             ccchHHHHHHHhc-CCCCeEEeecccCCcCchhHHHHHhcCCc--ceEEEEecCCCCcchhHHhhhhhhhccCCCChHHH
Confidence            5678888988887 89999999999999999999999987532  38888888888888899999999999999999888


Q ss_pred             HHHHHHHHHHh
Q 043479           83 KNVWQYAMTYK   93 (534)
Q Consensus        83 ~~aI~~aL~~k   93 (534)
                      ......+.+.+
T Consensus        95 ~~r~~~l~~~k  105 (435)
T COG3706          95 FLRAKSLVRLK  105 (435)
T ss_pred             HHhhhhhccch
Confidence            88777766543

>PRK15320 transcriptional activator SprB; Provisional

Probab=95.82  E-value=0.085  Score=52.02  Aligned_cols=46  Identities=9%  Similarity=0.091  Sum_probs=38.7

Q ss_pred             cCC--chhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHH
Q 043479          163 AWT--DSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRI  212 (534)
Q Consensus       163 ~Wt--~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl  212 (534)
                      .|.  +.|++++.+++..|..+.. .++|++.|+   ++..+|+.|+.+.+.
T Consensus       158 ~~~~~~~LSdREIEVL~LLAkG~S-NKEIAekL~---LS~KTVSTYKnRLLe  205 (251)
T PRK15320        158 WWNLPPGVTQAKYALLILLSSGHP-AIELAKKFG---LGTKTVSIYRKKVMY  205 (251)
T ss_pred             eecCCCCCCHHHHHHHHHHHcCCC-HHHHHHHhc---cchhhHHHHHHHHHH
Confidence            454  4599999999999985555 999999999   999999999777655

>PF03709 OKR_DC_1_N: Orn/Lys/Arg decarboxylase, N-terminal domain; InterPro: IPR005308 This domain has a flavodoxin-like fold, and is termed the "wing" domain because of its position in the overall 3D structure

Probab=95.01  E-value=0.064  Score=47.95  Aligned_cols=90  Identities=20%  Similarity=0.172  Sum_probs=66.7

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCC--CCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCC-C
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPE--MNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPL-N   78 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPd--mdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~-s   78 (534)
                      .+.+.+|++..++....++.||+||. ++  ....++++.++.....+||.+++.....+.+-..+-.-+++|+.... +
T Consensus        22 ~~~~~dd~~~~i~~~~~i~avvi~~d-~~~~~~~~~ll~~i~~~~~~iPVFl~~~~~~~~~l~~~~l~~v~~~i~l~~~t  100 (115)
T PF03709_consen   22 DADSTDDALAIIESFTDIAAVVISWD-GEEEDEAQELLDKIRERNFGIPVFLLAERDTTEDLPAEVLGEVDGFIWLFEDT  100 (115)
T ss_dssp             EESSHHHHHHHHHCTTTEEEEEEECH-HHHHHHHHHHHHHHHHHSTT-EEEEEESCCHHHCCCHHHHCCESEEEETTTTT
T ss_pred             EeCChHHHHHHHHhCCCeeEEEEEcc-cccchhHHHHHHHHHHhCCCCCEEEEecCCCcccCCHHHHhhccEEEEecCCC
Confidence            46788999999987567889999987 21  23567999999999999999999877555444455566889987764 5


Q ss_pred             hHHHHHHHHHHHHH
Q 043479           79 PDDLKNVWQYAMTY   92 (534)
Q Consensus        79 ~eeL~~aI~~aL~~   92 (534)
                      ++.+...|..+.++
T Consensus       101 ~~fia~rI~~Aa~~  114 (115)
T PF03709_consen  101 AEFIARRIEAAARR  114 (115)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHh
Confidence            56666777776643

Ornithine decarboxylase from Lactobacillus 30a (L30a OrnDC, P43099 from SWISSPROT) is representative of the large, pyridoxal-5'-phosphate-dependent decarboxylases that act on lysine, arginine or ornithine. The crystal structure of the L30a OrnDC has been solved to 3.0 A resolution. Six dimers related by C6 symmetry compose the enzymatically active dodecamer (approximately 106 Da). Each monomer of L30a OrnDC can be described in terms of five sequential folding domains. The amino-terminal domain, residues 1 to 107, consists of a five-stranded beta-sheet termed the "wing" domain. Two wing domains of each dimer project inward towards the centre of the dodecamer and contribute to dodecamer stabilisation [].; GO: 0016831 carboxy-lyase activity; PDB: 3Q16_C 3N75_A 1C4K_A 1ORD_A 2VYC_D.

>PRK11107 hybrid sensory histidine kinase BarA; Provisional

Probab=94.71  E-value=0.15  Score=59.53  Aligned_cols=74  Identities=11%  Similarity=0.062  Sum_probs=59.5

Q ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhh--CCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHHHHHHHHHHH
Q 043479           17 RDIDLVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDDLKNVWQYAM   90 (534)
Q Consensus        17 ~~pDLVLLDi~mPdmdGleLL~~Lr~~--~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~eeL~~aI~~aL   90 (534)
                      ..||++|+|+.+|+..+...+......  ....++|+++...+......+.+.|+++|+.||+...+|..++....
T Consensus       575 ~~~d~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~l~~~~  650 (919)
T PRK11107        575 AHYDILLLGLPVTFREPLTMLHERLAKAKSMTDFLILALPCHEQVLAEQLKQDGADACLSKPLSHTRLLPALLEPC  650 (919)
T ss_pred             CCCCEEEecccCCCCCCHHHHHHHHHhhhhcCCcEEEEeCCcchhhHHHHhhCCCceEECCCCCHHHHHHHHHHhh
Confidence            579999999999987776655554432  22356778888888888889999999999999999999998887654

>cd02071 MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 binding domain

Probab=93.36  E-value=0.75  Score=41.32  Aligned_cols=82  Identities=12%  Similarity=-0.071  Sum_probs=59.4

Q ss_pred             CHHHHHHHHHhcCCceEEEEeCCCCCC--CHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHHH
Q 043479            5 RPVEALATVRIQRDIDLVVTDLHMPEM--NGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDDL   82 (534)
Q Consensus         5 s~~EALe~L~~~~~pDLVLLDi~mPdm--dGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~eeL   82 (534)
                      ..++.++.+.+ ..+|+|.+-..+...  .--++++.|++..+....|++.+....+...++.++|++.|+..-.+.+++
T Consensus        38 p~e~~~~~a~~-~~~d~V~iS~~~~~~~~~~~~~~~~L~~~~~~~i~i~~GG~~~~~~~~~~~~~G~d~~~~~~~~~~~~  116 (122)
T cd02071          38 TPEEIVEAAIQ-EDVDVIGLSSLSGGHMTLFPEVIELLRELGAGDILVVGGGIIPPEDYELLKEMGVAEIFGPGTSIEEI  116 (122)
T ss_pred             CHHHHHHHHHH-cCCCEEEEcccchhhHHHHHHHHHHHHhcCCCCCEEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHH
Confidence            46777888877 789999998776532  234567777776554444556655556667788899999999988888888


Q ss_pred             HHHHH
Q 043479           83 KNVWQ   87 (534)
Q Consensus        83 ~~aI~   87 (534)
                      ...|+
T Consensus       117 ~~~~~  121 (122)
T cd02071         117 IDKIR  121 (122)
T ss_pred             HHHHh
Confidence            76654

This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom with a group attached to a neighboring carbon atom. This family is present in both mammals and bacteria. Bacterial members are heterodimers and involved in the fermentation of pyruvate to propionate. Mammalian members are homodimers and responsible for the conversion of odd-chain fatty acids and branched-chain amino acids via propionyl CoA to succinyl CoA for further degradation.

>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators

Probab=93.20  E-value=0.2  Score=39.10  Aligned_cols=45  Identities=27%  Similarity=0.327  Sum_probs=36.9

Q ss_pred             chhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHH
Q 043479          166 DSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFL  214 (534)
Q Consensus       166 ~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~l  214 (534)
                      ..|++++.+++..+..+.. +++|++.|+   ++..+|..|+.+.+..+
T Consensus         2 ~~LT~~E~~vl~~l~~G~~-~~eIA~~l~---is~~tV~~~~~~i~~Kl   46 (58)
T PF00196_consen    2 PSLTERELEVLRLLAQGMS-NKEIAEELG---ISEKTVKSHRRRIMKKL   46 (58)
T ss_dssp             GSS-HHHHHHHHHHHTTS--HHHHHHHHT---SHHHHHHHHHHHHHHHH
T ss_pred             CccCHHHHHHHHHHHhcCC-cchhHHhcC---cchhhHHHHHHHHHHHh
Confidence            3589999999999976666 999999999   89999999988776643

The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....

>TIGR03815 CpaE_hom_Actino helicase/secretion neighborhood CpaE-like protein

Probab=92.84  E-value=0.21  Score=51.92  Aligned_cols=67  Identities=16%  Similarity=0.086  Sum_probs=46.9

Q ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEe-cCCCHHHHHHHHHcCCcEEEeCCCChHHHHHHHHHHH
Q 043479           18 DIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMS-SDDRESVIMKALASGVAFYILKPLNPDDLKNVWQYAM   90 (534)
Q Consensus        18 ~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLS-s~~d~~~~~~AL~aGA~dyL~KP~s~eeL~~aI~~aL   90 (534)
                      .-.+||+|..+-.    .++......++  .++++. ...+......++++|+.+||.+|++.++|.+++.++.
T Consensus        19 ~~~~v~~~~~~~~----~~~~~~~p~~~--~vv~v~~~~~~~~~~~~a~~~Ga~~~l~~P~~~~~l~~~l~~~~   86 (322)
T TIGR03815        19 RAPLVLVDADMAE----ACAAAGLPRRR--RVVLVGGGEPGGALWRAAAAVGAEHVAVLPEAEGWLVELLADLD   86 (322)
T ss_pred             cCCeEEECchhhh----HHHhccCCCCC--CEEEEeCCCCCHHHHHHHHHhChhheeeCCCCHHHHHHHHHhhc
Confidence            3688999864411    12222222233  355444 4557888999999999999999999999999998764

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

>PRK00043 thiE thiamine-phosphate pyrophosphorylase; Reviewed

Probab=92.14  E-value=1.9  Score=41.48  Aligned_cols=69  Identities=19%  Similarity=0.215  Sum_probs=52.3

Q ss_pred             ecCHHHHHHHHHhcCCceEEEEeCCCCCC--------CHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEe
Q 043479            3 VTRPVEALATVRIQRDIDLVVTDLHMPEM--------NGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYIL   74 (534)
Q Consensus         3 ass~~EALe~L~~~~~pDLVLLDi~mPdm--------dGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~   74 (534)
                      +.+..|+.+...  ..+|+|.+....|..        .|++.++++++..+++||++..+- +.+.+..++++||+++..
T Consensus       111 ~~t~~e~~~a~~--~gaD~v~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~v~a~GGI-~~~~i~~~~~~Ga~gv~~  187 (212)
T PRK00043        111 THTLEEAAAALA--AGADYVGVGPIFPTPTKKDAKAPQGLEGLREIRAAVGDIPIVAIGGI-TPENAPEVLEAGADGVAV  187 (212)
T ss_pred             CCCHHHHHHHhH--cCCCEEEECCccCCCCCCCCCCCCCHHHHHHHHHhcCCCCEEEECCc-CHHHHHHHHHcCCCEEEE
Confidence            456677777665  468999987555532        358999999887766998887766 577788999999999874

>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional

Probab=92.02  E-value=0.54  Score=47.01  Aligned_cols=71  Identities=7%  Similarity=0.029  Sum_probs=52.4

Q ss_pred             chhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHhhhcccCCchhHhhhhhcccchHHHHH
Q 043479          166 DSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAEQGASAMGKTLALRSSFASGHVSMMLQ  245 (534)
Q Consensus       166 ~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~lkr~a~~~~~~~~~~~~lr~~~~sg~~~~~~~  245 (534)
                      ..|++|+.++++.++.+.. .++|++.|+   ++..||+.|+.+...   |..     ...+....+-++..|-+.++++
T Consensus       142 ~~LS~RE~eVL~Lia~G~S-nkEIA~~L~---IS~~TVk~hvs~I~~---KLg-----v~sR~eLv~~A~~~gli~~~~~  209 (217)
T PRK13719        142 NKVTKYQNDVFILYSFGFS-HEYIAQLLN---ITVGSSKNKISEILK---FFG-----ISSRDELLIILHTSEMIFYLYK  209 (217)
T ss_pred             CCCCHHHHHHHHHHHCCCC-HHHHHHHhC---CCHHHHHHHHHHHHH---HhC-----CCCHHHHHHHHHHcCChHHHHH
Confidence            5699999999999986655 999999999   999999999776533   221     2233345566666677777776


Q ss_pred             Hhh
Q 043479          246 EAH  248 (534)
Q Consensus       246 ~~~  248 (534)
                      .+-
T Consensus       210 ~~~  212 (217)
T PRK13719        210 KVF  212 (217)
T ss_pred             HHH
Confidence            653

>TIGR00640 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain

Probab=91.52  E-value=2.2  Score=39.24  Aligned_cols=86  Identities=13%  Similarity=-0.036  Sum_probs=59.0

Q ss_pred             cCHHHHHHHHHhcCCceEEEEeCCCCC-CC-HHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            4 TRPVEALATVRIQRDIDLVVTDLHMPE-MN-GIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         4 ss~~EALe~L~~~~~pDLVLLDi~mPd-md-GleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+++++++.+.+ ..+|+|.+-..+.. +. --++++.|++.......|++-+....+...+..++|+++|+..-.+..+
T Consensus        40 ~s~e~~v~aa~e-~~adii~iSsl~~~~~~~~~~~~~~L~~~g~~~i~vivGG~~~~~~~~~l~~~Gvd~~~~~gt~~~~  118 (132)
T TIGR00640        40 QTPEEIARQAVE-ADVHVVGVSSLAGGHLTLVPALRKELDKLGRPDILVVVGGVIPPQDFDELKEMGVAEIFGPGTPIPE  118 (132)
T ss_pred             CCHHHHHHHHHH-cCCCEEEEcCchhhhHHHHHHHHHHHHhcCCCCCEEEEeCCCChHhHHHHHHCCCCEEECCCCCHHH
Confidence            467888888877 78999888665543 22 2345666666544333344454444555677889999999988888888


Q ss_pred             HHHHHHHHH
Q 043479           82 LKNVWQYAM   90 (534)
Q Consensus        82 L~~aI~~aL   90 (534)
                      +...+...+
T Consensus       119 i~~~l~~~~  127 (132)
T TIGR00640       119 SAIFLLKKL  127 (132)
T ss_pred             HHHHHHHHH
Confidence            888887754

Methylmalonyl-CoA mutase (EC 5.4.99.2) catalyzes a reversible isomerization between L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an adenosylcobalamin cofactor. It may be a homodimer, as in mitochondrion, or a heterodimer with partially homologous beta chain that does not bind the adenosylcobalamin cofactor, as in Propionibacterium freudenreichii. The most similar archaeal sequences are separate chains, such as AF2215 and AF2219 of Archaeoglobus fulgidus, that correspond roughly to the first 500 and last 130 residues, respectively of known methylmalonyl-CoA mutases. This model describes the C-terminal domain subfamily. In a neighbor-joining tree (methylaspartate mutase S chain as the outgroup), AF2219 branches with a coenzyme B12-dependent enzyme known not to be 5.4.99.2.

>PRK02261 methylaspartate mutase subunit S; Provisional

Probab=91.44  E-value=2  Score=39.78  Aligned_cols=85  Identities=12%  Similarity=0.069  Sum_probs=62.1

Q ss_pred             CHHHHHHHHHhcCCceEEEEeCCCCCC--CHHHHHHHHHhh-CCCCcEEEEecCC------CHHHHHHHHHcCCcEEEeC
Q 043479            5 RPVEALATVRIQRDIDLVVTDLHMPEM--NGIELQKEINEE-FTHLPVMVMSSDD------RESVIMKALASGVAFYILK   75 (534)
Q Consensus         5 s~~EALe~L~~~~~pDLVLLDi~mPdm--dGleLL~~Lr~~-~p~ipVIVLSs~~------d~~~~~~AL~aGA~dyL~K   75 (534)
                      ..++.++.+.+ ..+|+|.+-..+...  .-.++++.|++. .++++|+ +.+..      ..+...++.+.|++.++..
T Consensus        42 p~e~i~~~a~~-~~~d~V~lS~~~~~~~~~~~~~~~~L~~~~~~~~~i~-vGG~~~~~~~~~~~~~~~l~~~G~~~vf~~  119 (137)
T PRK02261         42 SQEEFIDAAIE-TDADAILVSSLYGHGEIDCRGLREKCIEAGLGDILLY-VGGNLVVGKHDFEEVEKKFKEMGFDRVFPP  119 (137)
T ss_pred             CHHHHHHHHHH-cCCCEEEEcCccccCHHHHHHHHHHHHhcCCCCCeEE-EECCCCCCccChHHHHHHHHHcCCCEEECc
Confidence            56788888877 789999999877642  345677788776 3455544 44432      2345567889999999998


Q ss_pred             CCChHHHHHHHHHHHH
Q 043479           76 PLNPDDLKNVWQYAMT   91 (534)
Q Consensus        76 P~s~eeL~~aI~~aL~   91 (534)
                      ..+.+++...|++.+.
T Consensus       120 ~~~~~~i~~~l~~~~~  135 (137)
T PRK02261        120 GTDPEEAIDDLKKDLN  135 (137)
T ss_pred             CCCHHHHHHHHHHHhc
Confidence            8999999998888763

>PRK06704 RNA polymerase factor sigma-70; Validated

Probab=90.97  E-value=0.76  Score=46.15  Aligned_cols=78  Identities=15%  Similarity=0.121  Sum_probs=61.1

Q ss_pred             hhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHhhhcccC---CchhHhhhhhcccchHHH
Q 043479          167 SLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAEQGASAM---GKTLALRSSFASGHVSMM  243 (534)
Q Consensus       167 eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~lkr~a~~~~~~~---~~~~~lr~~~~sg~~~~~  243 (534)
                      .|..+..+++...-.+...-++|++.|+   ++..+|+++|.+-|..|+...+.+-...   ....++-.+|+...|.++
T Consensus       116 ~Lp~~~R~v~lL~~~eg~S~~EIAe~Lg---iS~~tVksrL~Rark~Lr~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~  192 (228)
T PRK06704        116 SLNVQQSAILLLKDVFQYSIADIAKVCS---VSEGAVKASLFRSRNRLKTVSEEGIEIVEFTDDMEVVVTSIREERPELL  192 (228)
T ss_pred             hCCHHHhhHhhhHHhhCCCHHHHHHHHC---cCHHHHHHHHHHHHHHHHHHHHhcCCCCCccccHHHHHHHHHhcCHHHH
Confidence            4677777777776555666899999999   8999999999999999998887643322   224578888999999988


Q ss_pred             HHHh
Q 043479          244 LQEA  247 (534)
Q Consensus       244 ~~~~  247 (534)
                      ++-+
T Consensus       193 ~~~~  196 (228)
T PRK06704        193 TKLL  196 (228)
T ss_pred             HHHh
Confidence            8755

>TIGR02311 HpaI 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase

Probab=90.15  E-value=2.2  Score=43.37  Aligned_cols=82  Identities=9%  Similarity=-0.042  Sum_probs=61.8

Q ss_pred             HHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhh-CCCCcEEEEecCCCHHHHHHHHHcCCcEEE-eCCCChHHHHHH
Q 043479            8 EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEE-FTHLPVMVMSSDDRESVIMKALASGVAFYI-LKPLNPDDLKNV   85 (534)
Q Consensus         8 EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~-~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL-~KP~s~eeL~~a   85 (534)
                      ..++.+.. ..+|.|++|++....+.-++...++.. ...+.++|=....+...+.++++.|+++++ +|--+.+++.++
T Consensus        24 ~~~e~~~~-~g~D~v~iDlEH~~~~~~~~~~~~~a~~~~g~~~~VRv~~~~~~~i~~~Ld~Ga~gIivP~v~s~e~a~~~  102 (249)
T TIGR02311        24 YAAEICAG-AGFDWLLIDGEHAPNDVRTILSQLQALAPYPSSPVVRPAIGDPVLIKQLLDIGAQTLLVPMIETAEQAEAA  102 (249)
T ss_pred             HHHHHHHh-cCCCEEEEeccCCCCCHHHHHHHHHHHHhcCCCcEEECCCCCHHHHHHHhCCCCCEEEecCcCCHHHHHHH
Confidence            44555555 569999999998888888887777653 223455666666777889999999999986 666788888877


Q ss_pred             HHHHH
Q 043479           86 WQYAM   90 (534)
Q Consensus        86 I~~aL   90 (534)
                      ++.+.
T Consensus       103 v~~~~  107 (249)
T TIGR02311       103 VAATR  107 (249)
T ss_pred             HHHcC
Confidence            77654

This model represents the aldolase which performs the final step unique to the 4-hydroxyphenylacetic acid catabolism pathway in which 2,4-dihydroxyhept-2-ene-1,7-dioic acid is split into pyruvate and succinate-semialdehyde. The gene for enzyme is generally found adjacent to other genes for this pathway organized into an operon.

>PRK13870 transcriptional regulator TraR; Provisional

Probab=89.98  E-value=0.52  Score=47.29  Aligned_cols=45  Identities=16%  Similarity=0.143  Sum_probs=40.4

Q ss_pred             chhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHH
Q 043479          166 DSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFL  214 (534)
Q Consensus       166 ~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~l  214 (534)
                      ..|+.|+.|+|.....+|. .++|+..|+   +|.+||+-||...|..|
T Consensus       172 ~~LT~RE~E~L~W~A~GKT-~~EIa~ILg---ISe~TV~~Hl~na~~KL  216 (234)
T PRK13870        172 AWLDPKEATYLRWIAVGKT-MEEIADVEG---VKYNSVRVKLREAMKRF  216 (234)
T ss_pred             CCCCHHHHHHHHHHHcCCC-HHHHHHHHC---CCHHHHHHHHHHHHHHc
Confidence            3599999999999987777 999999999   99999999999887743

>PRK15201 fimbriae regulatory protein FimW; Provisional

Probab=89.56  E-value=0.75  Score=44.84  Aligned_cols=45  Identities=11%  Similarity=0.015  Sum_probs=38.4

Q ss_pred             CCchhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHH
Q 043479          164 WTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRI  212 (534)
Q Consensus       164 Wt~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl  212 (534)
                      .+..|++|+.+++..++.++. .++|++.|+   ++.+||+.|+.+...
T Consensus       130 ~~~~LSpRErEVLrLLAqGkT-nKEIAe~L~---IS~rTVkth~srImk  174 (198)
T PRK15201        130 TTRHFSVTERHLLKLIASGYH-LSETAALLS---LSEEQTKSLRRSIMR  174 (198)
T ss_pred             CCCCCCHHHHHHHHHHHCCCC-HHHHHHHhC---CCHHHHHHHHHHHHH
Confidence            345599999999999986666 999999999   999999999876544

>TIGR01501 MthylAspMutase methylaspartate mutase, S subunit

Probab=89.05  E-value=4.4  Score=37.63  Aligned_cols=87  Identities=8%  Similarity=-0.001  Sum_probs=61.0

Q ss_pred             cCHHHHHHHHHhcCCceEEEEeCCCCC-CC-HHHHHHHHHhhCCCCcEEEEecCC---CHH---HHHHHHHcCCcEEEeC
Q 043479            4 TRPVEALATVRIQRDIDLVVTDLHMPE-MN-GIELQKEINEEFTHLPVMVMSSDD---RES---VIMKALASGVAFYILK   75 (534)
Q Consensus         4 ss~~EALe~L~~~~~pDLVLLDi~mPd-md-GleLL~~Lr~~~p~ipVIVLSs~~---d~~---~~~~AL~aGA~dyL~K   75 (534)
                      .++++.++.+.+ ..+|+|.+...|.. +. --++.+.|++....-++|++-+..   ..+   ...++.+.|++..+..
T Consensus        39 v~~e~~v~aa~~-~~adiVglS~l~~~~~~~~~~~~~~l~~~gl~~~~vivGG~~vi~~~d~~~~~~~l~~~Gv~~vF~p  117 (134)
T TIGR01501        39 SPQEEFIKAAIE-TKADAILVSSLYGHGEIDCKGLRQKCDEAGLEGILLYVGGNLVVGKQDFPDVEKRFKEMGFDRVFAP  117 (134)
T ss_pred             CCHHHHHHHHHH-cCCCEEEEecccccCHHHHHHHHHHHHHCCCCCCEEEecCCcCcChhhhHHHHHHHHHcCCCEEECc
Confidence            467888888887 78999999887754 22 334666777655434455565531   112   2446788999999998


Q ss_pred             CCChHHHHHHHHHHHH
Q 043479           76 PLNPDDLKNVWQYAMT   91 (534)
Q Consensus        76 P~s~eeL~~aI~~aL~   91 (534)
                      ...++++...|++.++
T Consensus       118 gt~~~~iv~~l~~~~~  133 (134)
T TIGR01501       118 GTPPEVVIADLKKDLN  133 (134)
T ss_pred             CCCHHHHHHHHHHHhc
Confidence            8899999999988763

This model represents the S (sigma) subunit of methylaspartate mutase (glutamate mutase), a cobalamin-dependent enzyme that catalyzes the first step in a pathway of glutamate fermentation.

>PRK10188 DNA-binding transcriptional activator SdiA; Provisional

Probab=88.54  E-value=0.83  Score=45.98  Aligned_cols=44  Identities=11%  Similarity=0.196  Sum_probs=39.1

Q ss_pred             hhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHH
Q 043479          167 SLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFL  214 (534)
Q Consensus       167 eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~l  214 (534)
                      .|+.|+.+++..+..++. .++|++.|+   ++.+||+.|+.+.+..|
T Consensus       179 ~LT~rE~evl~~~a~G~t-~~eIa~~l~---is~~TV~~h~~~~~~KL  222 (240)
T PRK10188        179 NFSKREKEILKWTAEGKT-SAEIAMILS---ISENTVNFHQKNMQKKF  222 (240)
T ss_pred             CCCHHHHHHHHHHHcCCC-HHHHHHHhC---CCHHHHHHHHHHHHHHh
Confidence            599999999999976666 999999999   99999999999877643

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

Probab=88.28  E-value=2.4  Score=37.56  Aligned_cols=67  Identities=21%  Similarity=0.227  Sum_probs=48.3

Q ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHHHHHHHHHH
Q 043479           17 RDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDDLKNVWQYA   89 (534)
Q Consensus        17 ~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~eeL~~aI~~a   89 (534)
                      ...+.+++-..-.. ...++++.+.+..|.+||+++.........     ..+.+-|..|++..+|.++++++
T Consensus        41 ~~~~~~~v~~g~~~-~~~~~l~~l~~~~~~~Pvlllg~~~~~~~~-----~nvvg~Le~Pl~Y~qLt~~L~~c  107 (109)
T PF06490_consen   41 SPWEACAVILGSCS-KLAELLKELLKWAPHIPVLLLGEHDSPEEL-----PNVVGELEEPLNYPQLTDALHRC  107 (109)
T ss_pred             cCCcEEEEEecCch-hHHHHHHHHHhhCCCCCEEEECCCCccccc-----cCeeEecCCCCCHHHHHHHHHHh
Confidence            34454444332222 556788999999999999999887765111     12778899999999999999886

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

>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]

Probab=88.03  E-value=1.5  Score=33.95  Aligned_cols=43  Identities=23%  Similarity=0.352  Sum_probs=36.2

Q ss_pred             chhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHH
Q 043479          166 DSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRI  212 (534)
Q Consensus       166 ~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl  212 (534)
                      ..|+.++.+++..+..++. +++|+..++   ++..+|..|+.+...
T Consensus         3 ~~Lt~rE~~v~~l~~~G~s-~~eia~~l~---is~~tV~~h~~~i~~   45 (65)
T COG2771           3 ADLTPREREILRLVAQGKS-NKEIARILG---ISEETVKTHLRNIYR   45 (65)
T ss_pred             ccCCHHHHHHHHHHHCCCC-HHHHHHHHC---CCHHHHHHHHHHHHH
Confidence            3578999999999976644 999999999   999999999877544

>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins

Probab=87.94  E-value=1.2  Score=33.36  Aligned_cols=47  Identities=28%  Similarity=0.386  Sum_probs=39.1

Q ss_pred             ccCCchhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHH
Q 043479          162 VAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYR  211 (534)
Q Consensus       162 v~Wt~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyR  211 (534)
                      -.|+.+-...|++++..+|..  .-+.|++.|. .+-|...+++|.++|+
T Consensus         2 ~~Wt~eE~~~l~~~v~~~g~~--~W~~Ia~~~~-~~Rt~~qc~~~~~~~~   48 (48)
T PF00249_consen    2 GPWTEEEDEKLLEAVKKYGKD--NWKKIAKRMP-GGRTAKQCRSRYQNLL   48 (48)
T ss_dssp             -SS-HHHHHHHHHHHHHSTTT--HHHHHHHHHS-SSSTHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHHHhCCc--HHHHHHHHcC-CCCCHHHHHHHHHhhC
Confidence            369999999999999999854  3588999987 7889999999988773

These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....

>TIGR03239 GarL 2-dehydro-3-deoxyglucarate aldolase

Probab=87.78  E-value=4.2  Score=41.41  Aligned_cols=81  Identities=7%  Similarity=0.075  Sum_probs=60.5

Q ss_pred             HHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhh-CCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCC-ChHHHHHH
Q 043479            8 EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEE-FTHLPVMVMSSDDRESVIMKALASGVAFYILKPL-NPDDLKNV   85 (534)
Q Consensus         8 EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~-~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~-s~eeL~~a   85 (534)
                      .+.+.+.. ..+|.|++|++....+--++...++.. ...++.+|=....+...+.++++.|+++++.--+ +.++.+++
T Consensus        24 ~~~e~~a~-~G~D~v~iD~EHg~~~~~~~~~~~~a~~~~g~~~~VRvp~~~~~~i~r~LD~Ga~gIivP~v~taeea~~~  102 (249)
T TIGR03239        24 ITTEVLGL-AGFDWLLLDGEHAPNDVLTFIPQLMALKGSASAPVVRPPWNEPVIIKRLLDIGFYNFLIPFVESAEEAERA  102 (249)
T ss_pred             HHHHHHHh-cCCCEEEEecccCCCCHHHHHHHHHHHhhcCCCcEEECCCCCHHHHHHHhcCCCCEEEecCcCCHHHHHHH
Confidence            45555655 569999999999988887777777653 2335566667777889999999999999987444 56777766


Q ss_pred             HHHH
Q 043479           86 WQYA   89 (534)
Q Consensus        86 I~~a   89 (534)
                      ++.+
T Consensus       103 v~a~  106 (249)
T TIGR03239       103 VAAT  106 (249)
T ss_pred             HHHc
Confidence            6554

In E. coli this enzyme (GarL, ) 2-dehydro-3-deoxyglucarate aldolase acts in the catabolism of several sugars including D-galactarate, D-glucarate and L-idarate. In fact, 5-dehydro-4-deoxy-D-glucarate aldolase is a synonym for this enzyme as it is unclear in the literature whether the enzyme acts on only one of these or, as seems likely, has no preference. (Despite the apparent large difference in substrate stucture indicated by their names, 2-DH-3DO- and 5-DH-4DO-glucarate differ only by the chirality of most central hydroxyl-bearing carbon and is alternately named 2-DH-3DO-galactarate.) The reported product of D-galactarate dehydratase (4.2.1.42) is the 5DH-4DO-glucarate isomer and this enzyme is found proximal to the aldolase in many genomes (GenProp0714) where no epimerase is known. Similarly, the product of D-glucarate dehydratase (4.2.1.40) is again the 5-DH-4DO isomer, so the provenance of the 2-DH-3DO-glucarate isomer for which

>PRK10128 2-keto-3-deoxy-L-rhamnonate aldolase; Provisional

Probab=87.78  E-value=4.1  Score=41.96  Aligned_cols=81  Identities=9%  Similarity=0.075  Sum_probs=59.4

Q ss_pred             HHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhh-CCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCC-ChHHHHHH
Q 043479            8 EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEE-FTHLPVMVMSSDDRESVIMKALASGVAFYILKPL-NPDDLKNV   85 (534)
Q Consensus         8 EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~-~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~-s~eeL~~a   85 (534)
                      .+.+.+.. ..||.|++|++....+--++...++.. ...+..++-....+...+.++++.||.+++.--+ +.++.+.+
T Consensus        30 ~~~E~~a~-~GfD~v~iD~EHg~~~~~~l~~~i~a~~~~g~~~lVRvp~~~~~~i~r~LD~GA~GIivP~V~saeeA~~~  108 (267)
T PRK10128         30 YMAEIAAT-SGYDWLLIDGEHAPNTIQDLYHQLQAIAPYASQPVIRPVEGSKPLIKQVLDIGAQTLLIPMVDTAEQARQV  108 (267)
T ss_pred             HHHHHHHH-cCCCEEEEccccCCCCHHHHHHHHHHHHhcCCCeEEECCCCCHHHHHHHhCCCCCeeEecCcCCHHHHHHH
Confidence            44555555 569999999999888877777777653 2335556666777888999999999999998655 55666666


Q ss_pred             HHHH
Q 043479           86 WQYA   89 (534)
Q Consensus        86 I~~a   89 (534)
                      ++.+
T Consensus       109 V~a~  112 (267)
T PRK10128        109 VSAT  112 (267)
T ss_pred             HHhc
Confidence            6554

>cd02067 B12-binding B12 binding domain (B12-BD)

Probab=87.64  E-value=2.7  Score=37.10  Aligned_cols=69  Identities=17%  Similarity=0.126  Sum_probs=48.2

Q ss_pred             CHHHHHHHHHhcCCceEEEEeCCCCC--CCHHHHHHHHHhhCC-CCcEEEEecCCCHHHHHHHHHcCCcEEEeC
Q 043479            5 RPVEALATVRIQRDIDLVVTDLHMPE--MNGIELQKEINEEFT-HLPVMVMSSDDRESVIMKALASGVAFYILK   75 (534)
Q Consensus         5 s~~EALe~L~~~~~pDLVLLDi~mPd--mdGleLL~~Lr~~~p-~ipVIVLSs~~d~~~~~~AL~aGA~dyL~K   75 (534)
                      +.++.++.+.+ .+||+|.+-..+..  ....++++.+++..+ +++|+ +.+..-......+.+.|++.|+..
T Consensus        38 ~~~~l~~~~~~-~~pdvV~iS~~~~~~~~~~~~~i~~l~~~~~~~~~i~-vGG~~~~~~~~~~~~~G~D~~~~~  109 (119)
T cd02067          38 PPEEIVEAAKE-EDADAIGLSGLLTTHMTLMKEVIEELKEAGLDDIPVL-VGGAIVTRDFKFLKEIGVDAYFGP  109 (119)
T ss_pred             CHHHHHHHHHH-cCCCEEEEeccccccHHHHHHHHHHHHHcCCCCCeEE-EECCCCChhHHHHHHcCCeEEECC
Confidence            46677888877 78999999877554  345678888888776 56554 455444444457788999877763

This domain binds different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide, it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins.

>PRK10558 alpha-dehydro-beta-deoxy-D-glucarate aldolase; Provisional

Probab=87.28  E-value=4.4  Score=41.42  Aligned_cols=81  Identities=9%  Similarity=0.084  Sum_probs=60.3

Q ss_pred             HHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhh-CCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCC-ChHHHHHH
Q 043479            8 EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEE-FTHLPVMVMSSDDRESVIMKALASGVAFYILKPL-NPDDLKNV   85 (534)
Q Consensus         8 EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~-~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~-s~eeL~~a   85 (534)
                      .+.+.+.. ..+|.|++|++....|--++...++.. ...++.+|=....+...+.++++.|+.+++.--+ +.++.+.+
T Consensus        31 ~~~e~~a~-~G~D~v~iD~EHg~~~~~~~~~~i~a~~~~g~~~lVRvp~~~~~~i~r~LD~Ga~giivP~v~tae~a~~~  109 (256)
T PRK10558         31 ITTEVLGL-AGFDWLVLDGEHAPNDVSTFIPQLMALKGSASAPVVRVPTNEPVIIKRLLDIGFYNFLIPFVETAEEARRA  109 (256)
T ss_pred             HHHHHHHh-cCCCEEEEccccCCCCHHHHHHHHHHHhhcCCCcEEECCCCCHHHHHHHhCCCCCeeeecCcCCHHHHHHH
Confidence            45555655 569999999999988877777777653 2335666667777889999999999999986443 56777766


Q ss_pred             HHHH
Q 043479           86 WQYA   89 (534)
Q Consensus        86 I~~a   89 (534)
                      ++.+
T Consensus       110 v~a~  113 (256)
T PRK10558        110 VAST  113 (256)
T ss_pred             HHHc
Confidence            6655

>cd04724 Tryptophan_synthase_alpha Ttryptophan synthase (TRPS) alpha subunit (TSA)

Probab=84.03  E-value=11  Score=37.83  Aligned_cols=82  Identities=23%  Similarity=0.355  Sum_probs=55.8

Q ss_pred             HHHHHHHhcCCceEEEEeCCC--CCCC--------------------HHHHHHHHHhhCCCCcEEEEecCCC------HH
Q 043479            8 EALATVRIQRDIDLVVTDLHM--PEMN--------------------GIELQKEINEEFTHLPVMVMSSDDR------ES   59 (534)
Q Consensus         8 EALe~L~~~~~pDLVLLDi~m--Pdmd--------------------GleLL~~Lr~~~p~ipVIVLSs~~d------~~   59 (534)
                      +.++.+.+ ...|++=+|+=.  |-+|                    ++++++++|+.. ++|+++|+-...      ..
T Consensus        18 ~~~~~l~~-~Gad~iel~iPfsdPv~DG~~I~~a~~~al~~g~~~~~~~~~~~~vr~~~-~~pv~lm~y~n~~~~~G~~~   95 (242)
T cd04724          18 EILKALVE-AGADIIELGIPFSDPVADGPVIQAASERALANGVTLKDVLELVKEIRKKN-TIPIVLMGYYNPILQYGLER   95 (242)
T ss_pred             HHHHHHHH-CCCCEEEECCCCCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHhhcC-CCCEEEEEecCHHHHhCHHH
Confidence            44444554 468888888522  1233                    456666666554 689888877543      56


Q ss_pred             HHHHHHHcCCcEEEeCCCChHHHHHHHHHHHH
Q 043479           60 VIMKALASGVAFYILKPLNPDDLKNVWQYAMT   91 (534)
Q Consensus        60 ~~~~AL~aGA~dyL~KP~s~eeL~~aI~~aL~   91 (534)
                      .+.++.++|+++++.-.+.++++...+..+.+
T Consensus        96 fi~~~~~aG~~giiipDl~~ee~~~~~~~~~~  127 (242)
T cd04724          96 FLRDAKEAGVDGLIIPDLPPEEAEEFREAAKE  127 (242)
T ss_pred             HHHHHHHCCCcEEEECCCCHHHHHHHHHHHHH
Confidence            68889999999999977778877766666643

TPRS is a bifunctional tetrameric enzyme (2 alpha and 2 beta subunits) that catalyzes the last two steps of L-tryptophan biosynthesis. Alpha and beta subunit catalyze two distinct reactions which are both strongly stimulated by the formation of the complex. The alpha subunit catalyzes the cleavage of indole 3-glycerol phosphate (IGP) to indole and d-glyceraldehyde 3-phosphate (G3P). Indole is then channeled to the active site of the beta subunit, a PLP-dependent enzyme that catalyzes a replacement reaction to convert L-serine into L-tryptophan.

>cd04728 ThiG Thiazole synthase (ThiG) is the tetrameric enzyme that is involved in the formation of the thiazole moiety of thiamin pyrophosphate, an essential ubiquitous cofactor that plays an important role in carbohydrate and amino acid metabolism

Probab=84.01  E-value=9.9  Score=38.87  Aligned_cols=60  Identities=18%  Similarity=0.198  Sum_probs=48.6

Q ss_pred             HHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEE-----eCCCChHHHHHHHHHHHHHhh
Q 043479           34 IELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYI-----LKPLNPDDLKNVWQYAMTYKK   94 (534)
Q Consensus        34 leLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL-----~KP~s~eeL~~aI~~aL~~k~   94 (534)
                      .++++.|++. .++|||+=..-..++.+.++++.||++++     .|.-++..+.+++..++...+
T Consensus       164 ~~~I~~I~e~-~~vpVI~egGI~tpeda~~AmelGAdgVlV~SAIt~a~dP~~ma~af~~Av~aGr  228 (248)
T cd04728         164 PYNLRIIIER-ADVPVIVDAGIGTPSDAAQAMELGADAVLLNTAIAKAKDPVAMARAFKLAVEAGR  228 (248)
T ss_pred             HHHHHHHHHh-CCCcEEEeCCCCCHHHHHHHHHcCCCEEEEChHhcCCCCHHHHHHHHHHHHHHHH
Confidence            6888988887 56999998888999999999999999996     455567777777777765443

ThiG catalyzes the formation of thiazole from 1-deoxy-D-xylulose 5-phosphate (DXP) and dehydroglycine, with the help of the sulfur carrier protein ThiS that carries the sulfur needed for thiazole assembly on its carboxy terminus (ThiS-COSH).

>PRK00208 thiG thiazole synthase; Reviewed

Probab=83.31  E-value=11  Score=38.69  Aligned_cols=59  Identities=17%  Similarity=0.153  Sum_probs=48.0

Q ss_pred             HHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEE-----eCCCChHHHHHHHHHHHHHh
Q 043479           34 IELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYI-----LKPLNPDDLKNVWQYAMTYK   93 (534)
Q Consensus        34 leLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL-----~KP~s~eeL~~aI~~aL~~k   93 (534)
                      .++++.|++. .++|||+=..-..++.+.++++.|+++++     .|.-++..+.+++..++...
T Consensus       164 ~~~i~~i~e~-~~vpVIveaGI~tpeda~~AmelGAdgVlV~SAItka~dP~~ma~af~~Av~aG  227 (250)
T PRK00208        164 PYNLRIIIEQ-ADVPVIVDAGIGTPSDAAQAMELGADAVLLNTAIAVAGDPVAMARAFKLAVEAG  227 (250)
T ss_pred             HHHHHHHHHh-cCCeEEEeCCCCCHHHHHHHHHcCCCEEEEChHhhCCCCHHHHHHHHHHHHHHH
Confidence            6788888887 57999999999999999999999999996     45556777777777766543

>TIGR03020 EpsA transcriptional regulator EpsA

Probab=82.86  E-value=2.3  Score=43.26  Aligned_cols=45  Identities=18%  Similarity=0.190  Sum_probs=38.2

Q ss_pred             chhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHH
Q 043479          166 DSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFL  214 (534)
Q Consensus       166 ~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~l  214 (534)
                      ..|++|+.+++..+..++. .++|++.|+   ++..||+.|+.+.+..+
T Consensus       189 ~~LT~RE~evl~l~a~G~s-~~eIA~~L~---IS~~TVk~hl~~i~~KL  233 (247)
T TIGR03020       189 GLITAREAEILAWVRDGKT-NEEIAAILG---ISSLTVKNHLQHIFKKL  233 (247)
T ss_pred             cCCCHHHHHHHHHHHCCCC-HHHHHHHHC---cCHHHHHHHHHHHHHHh
Confidence            4689999999999864444 999999999   99999999998876643

Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.

>PRK09642 RNA polymerase sigma factor SigW; Reviewed

Probab=82.47  E-value=3.4  Score=37.98  Aligned_cols=52  Identities=15%  Similarity=0.162  Sum_probs=43.2

Q ss_pred             chhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHhh
Q 043479          166 DSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAEQ  220 (534)
Q Consensus       166 ~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~lkr~a~~  220 (534)
                      ..|+++..+++...-.+....++|++.|+   ++..+|++||.+-|..|++..+.
T Consensus       105 ~~Lp~~~r~v~~l~~~~g~s~~EIA~~lg---is~~tV~~~l~Rar~~Lr~~l~~  156 (160)
T PRK09642        105 RELPENYRDVVLAHYLEEKSYQEIALQEK---IEVKTVEMKLYRARKWIKKHWKE  156 (160)
T ss_pred             HhCCHHHHHHHHHHHHhCCCHHHHHHHHC---CCHHHHHHHHHHHHHHHHHHHhh
Confidence            34777778888776556666899999999   99999999999999998887643

>TIGR00262 trpA tryptophan synthase, alpha subunit

Probab=82.44  E-value=13  Score=37.93  Aligned_cols=57  Identities=18%  Similarity=0.266  Sum_probs=44.0

Q ss_pred             HHHHHHHHhhCCCCcEEEEecCCC------HHHHHHHHHcCCcEEEeCCCChHHHHHHHHHHH
Q 043479           34 IELQKEINEEFTHLPVMVMSSDDR------ESVIMKALASGVAFYILKPLNPDDLKNVWQYAM   90 (534)
Q Consensus        34 leLL~~Lr~~~p~ipVIVLSs~~d------~~~~~~AL~aGA~dyL~KP~s~eeL~~aI~~aL   90 (534)
                      +++++++|+...++|+++|+-...      ...+.++.++|+++++.-....++....+..+.
T Consensus        75 ~~~v~~ir~~~~~~plv~m~Y~Npi~~~G~e~f~~~~~~aGvdgviipDlp~ee~~~~~~~~~  137 (256)
T TIGR00262        75 FELLKKVRQKHPNIPIGLLTYYNLIFRKGVEEFYAKCKEVGVDGVLVADLPLEESGDLVEAAK  137 (256)
T ss_pred             HHHHHHHHhcCCCCCEEEEEeccHHhhhhHHHHHHHHHHcCCCEEEECCCChHHHHHHHHHHH
Confidence            566777776556789887776654      567888999999999998888888877666654

Tryptophan synthase catalyzes the last step in the biosynthesis of tryptophan. The alpha chain is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate. In bacteria and plants each domain is found on a separate subunit (alpha and beta chains), while in fungi the two domains are fused together on a single multifunctional protein. The signature pattern for trpA contains three conserved acidic residues. [LIVM]-E-[LIVM]-G-x(2)-[FYC]-[ST]-[DE]-[PA]-[LIVMY]-[AGLI]-[DE]-G and this is located between residues 43-58 of the model. The Sulfolobus solfataricus trpA is known to be quite divergent from other known trpA sequences.

>PRK05458 guanosine 5'-monophosphate oxidoreductase; Provisional

Probab=82.31  E-value=4  Score=43.33  Aligned_cols=66  Identities=8%  Similarity=-0.020  Sum_probs=48.0

Q ss_pred             HHHHHHHHhcCCceEEEEeCCCCCC-CHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEE
Q 043479            7 VEALATVRIQRDIDLVVTDLHMPEM-NGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYI   73 (534)
Q Consensus         7 ~EALe~L~~~~~pDLVLLDi~mPdm-dGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL   73 (534)
                      +++.++++....+|+|.+|+..+.. .-.+++++|++.+|+++||+= ...+.+.+..+.++||+..+
T Consensus       100 ~~~~~Lv~ag~~~d~i~iD~a~gh~~~~~e~I~~ir~~~p~~~vi~g-~V~t~e~a~~l~~aGad~i~  166 (326)
T PRK05458        100 DFVDQLAAEGLTPEYITIDIAHGHSDSVINMIQHIKKHLPETFVIAG-NVGTPEAVRELENAGADATK  166 (326)
T ss_pred             HHHHHHHhcCCCCCEEEEECCCCchHHHHHHHHHHHhhCCCCeEEEE-ecCCHHHHHHHHHcCcCEEE
Confidence            4445555431135999999998764 456789999999988877652 23367788899999999875

>PF03328 HpcH_HpaI: HpcH/HpaI aldolase/citrate lyase family; InterPro: IPR005000 This family includes 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase (4

Probab=82.05  E-value=9.1  Score=37.67  Aligned_cols=84  Identities=18%  Similarity=0.146  Sum_probs=54.0

Q ss_pred             HHHHHHHHHhcCCceEEEEeCCCCC---------CCHHHHHHHHHh-hCCCCcEEEEecCCCHHHHHH---HHHcCCcEE
Q 043479            6 PVEALATVRIQRDIDLVVTDLHMPE---------MNGIELQKEINE-EFTHLPVMVMSSDDRESVIMK---ALASGVAFY   72 (534)
Q Consensus         6 ~~EALe~L~~~~~pDLVLLDi~mPd---------mdGleLL~~Lr~-~~p~ipVIVLSs~~d~~~~~~---AL~aGA~dy   72 (534)
                      -.+.++.+.. ..+|.|++|++-..         .+-.+++..++. ......+++=....+.....+   +++.|++++
T Consensus        10 ~~~~~~~a~~-~g~D~vilDlEd~~~~~~K~~ar~~~~~~~~~~~~~~~~~~~~~VRvn~~~~~~~~~Dl~~l~~g~~gI   88 (221)
T PF03328_consen   10 SPKMLEKAAA-SGADFVILDLEDGVPPDEKDEAREDLAEALRSIRAARAAGSEIIVRVNSLDSPHIERDLEALDAGADGI   88 (221)
T ss_dssp             SHHHHHHHHT-TCSSEEEEESSTTSSGGGHHHHHHHHHHHHHHHHHHTTSSSEEEEE-SSTTCHHHHHHHHHHHTTSSEE
T ss_pred             CHHHHHHHHh-cCCCEEEEeCcccCCcccchhhHHHHHHHHHhhcccccccccceecCCCCCcchhhhhhhhcccCCCee
Confidence            3455666665 68999999998755         334455555554 222356666666666666666   999999998


Q ss_pred             Ee-CCCChHHHHHHHHHHH
Q 043479           73 IL-KPLNPDDLKNVWQYAM   90 (534)
Q Consensus        73 L~-KP~s~eeL~~aI~~aL   90 (534)
                      +. |--+.+++..+++.+.
T Consensus        89 ~lP~ves~~~~~~~~~~~~  107 (221)
T PF03328_consen   89 VLPKVESAEDARQAVAALR  107 (221)
T ss_dssp             EETT--SHHHHHHHHHHHS
T ss_pred             eccccCcHHHHHHHHHHHh
Confidence            75 4446777777766553

1.2 from EC) and 4-hydroxy-2-oxovalerate aldolase (4.1.2 from EC). ; GO: 0016830 carbon-carbon lyase activity, 0006725 cellular aromatic compound metabolic process; PDB: 1DXF_B 1DXE_A 3QZ6_A 3QLL_C 3QQW_F 3OYZ_A 3PUG_A 3OYX_A 1IZC_A 2V5K_B ....

>PRK13111 trpA tryptophan synthase subunit alpha; Provisional

Probab=81.53  E-value=5.2  Score=41.00  Aligned_cols=57  Identities=26%  Similarity=0.391  Sum_probs=44.7

Q ss_pred             HHHHHHHHhhCCCCcEEEEecCC------CHHHHHHHHHcCCcEEEeCCCChHHHHHHHHHHH
Q 043479           34 IELQKEINEEFTHLPVMVMSSDD------RESVIMKALASGVAFYILKPLNPDDLKNVWQYAM   90 (534)
Q Consensus        34 leLL~~Lr~~~p~ipVIVLSs~~------d~~~~~~AL~aGA~dyL~KP~s~eeL~~aI~~aL   90 (534)
                      +++++++|+..+++|+|+|+=..      -+....+|.++|+++.|.-.+.+++....+..+.
T Consensus        77 ~~~~~~~r~~~~~~p~vlm~Y~N~i~~~G~e~f~~~~~~aGvdGviipDLp~ee~~~~~~~~~  139 (258)
T PRK13111         77 FELVREIREKDPTIPIVLMTYYNPIFQYGVERFAADAAEAGVDGLIIPDLPPEEAEELRAAAK  139 (258)
T ss_pred             HHHHHHHHhcCCCCCEEEEecccHHhhcCHHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHH
Confidence            66777777666789999888443      3456888999999999998898888887776664

>PRK12514 RNA polymerase sigma factor; Provisional

Probab=81.18  E-value=3.4  Score=38.74  Aligned_cols=50  Identities=18%  Similarity=0.202  Sum_probs=41.9

Q ss_pred             chhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHH
Q 043479          166 DSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVA  218 (534)
Q Consensus       166 ~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~lkr~a  218 (534)
                      ..|..+..+++...-++....++|++.|+   ++..+|+++|.+-|..|++..
T Consensus       128 ~~L~~~~r~i~~l~~~~g~s~~eIA~~lg---is~~tV~~~l~Rar~~Lr~~l  177 (179)
T PRK12514        128 EELEKDRAAAVRRAYLEGLSYKELAERHD---VPLNTMRTWLRRSLLKLRECL  177 (179)
T ss_pred             HhCCHHHHHHHHHHHHcCCCHHHHHHHHC---CChHHHHHHHHHHHHHHHHHh
Confidence            34777888877777566667899999999   999999999999999888764

>PRK12516 RNA polymerase sigma factor; Provisional

Probab=80.77  E-value=4.2  Score=39.00  Aligned_cols=53  Identities=15%  Similarity=0.147  Sum_probs=44.9

Q ss_pred             hhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHhhhc
Q 043479          167 SLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAEQGA  222 (534)
Q Consensus       167 eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~lkr~a~~~~  222 (534)
                      .|+++..+++...-.+...-++|++.|+   ++..+|++||.+-|..|++......
T Consensus       116 ~Lp~~~r~i~~L~~~~g~s~~EIA~~Lg---is~~tVk~~l~Rar~~Lr~~l~~~~  168 (187)
T PRK12516        116 QLPDDQREAIILVGASGFAYEEAAEICG---CAVGTIKSRVNRARQRLQEILQIEG  168 (187)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHC---CCHHHHHHHHHHHHHHHHHHHHhhc
Confidence            4778888888886556666899999999   9999999999999999998887643

>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated

Probab=80.71  E-value=3.2  Score=41.40  Aligned_cols=45  Identities=20%  Similarity=0.254  Sum_probs=38.4

Q ss_pred             hhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHHH
Q 043479          167 SLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLK  215 (534)
Q Consensus       167 eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~lk  215 (534)
                      .|+.|+.+++..+..+ ...++|++.|+   ++..||+.||.+.+..|.
T Consensus       171 ~Lt~re~evl~~~a~G-~t~~eIa~~l~---is~~Tv~~~l~~~~~kl~  215 (232)
T TIGR03541       171 VLSEREREVLAWTALG-RRQADIAAILG---ISERTVENHLRSARRKLG  215 (232)
T ss_pred             cCCHHHHHHHHHHHCC-CCHHHHHHHHC---cCHHHHHHHHHHHHHHHC
Confidence            5899999999998644 44999999999   999999999998876543

Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.

>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=80.63  E-value=5.5  Score=30.19  Aligned_cols=44  Identities=16%  Similarity=0.143  Sum_probs=33.2

Q ss_pred             hhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHH
Q 043479          167 SLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIF  213 (534)
Q Consensus       167 eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~  213 (534)
                      .|+++..+++...-++...-++|++.|+   +|..+|+.|+.+-|..
T Consensus        10 ~L~~~~r~i~~l~~~~g~s~~eIa~~l~---~s~~~v~~~l~ra~~~   53 (54)
T PF08281_consen   10 QLPERQREIFLLRYFQGMSYAEIAEILG---ISESTVKRRLRRARKK   53 (54)
T ss_dssp             CS-HHHHHHHHHHHTS---HHHHHHHCT---S-HHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHCcCHHHHHHHHC---cCHHHHHHHHHHHHhh
Confidence            4778888888887666777899999998   9999999999987764

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.

>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional

Probab=80.53  E-value=4.1  Score=38.72  Aligned_cols=51  Identities=14%  Similarity=0.134  Sum_probs=42.3

Q ss_pred             hhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHhh
Q 043479          167 SLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAEQ  220 (534)
Q Consensus       167 eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~lkr~a~~  220 (534)
                      .|+++..+++...-++....++|++.|+   ++..+|++++.+-|..|++..+.
T Consensus       138 ~L~~~~r~v~~l~~~~g~s~~eIA~~lg---is~~tv~~~l~Rar~~Lr~~l~~  188 (193)
T PRK11923        138 QLPEDLRTALTLREFDGLSYEDIASVMQ---CPVGTVRSRIFRAREAIDKALQP  188 (193)
T ss_pred             hCCHHHhHHHhhHHhcCCCHHHHHHHHC---CCHHHHHHHHHHHHHHHHHHHHH
Confidence            3677777777775456666899999999   89999999999999999988764

>TIGR00693 thiE thiamine-phosphate pyrophosphorylase

Probab=80.36  E-value=10  Score=36.18  Aligned_cols=70  Identities=17%  Similarity=0.199  Sum_probs=51.1

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCC--------CCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEE
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPE--------MNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYI   73 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPd--------mdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL   73 (534)
                      ++.+.+|+.+..+  ..+|+|.++-..+.        ..|++.++++.+..+++||+++.+- +.+.+.++++.|++++.
T Consensus       102 s~h~~~e~~~a~~--~g~dyi~~~~v~~t~~k~~~~~~~g~~~l~~~~~~~~~~pv~a~GGI-~~~~~~~~~~~G~~gva  178 (196)
T TIGR00693       102 STHNLEELAEAEA--EGADYIGFGPIFPTPTKKDPAPPAGVELLREIAATSIDIPIVAIGGI-TLENAAEVLAAGADGVA  178 (196)
T ss_pred             eCCCHHHHHHHhH--cCCCEEEECCccCCCCCCCCCCCCCHHHHHHHHHhcCCCCEEEECCc-CHHHHHHHHHcCCCEEE
Confidence            4566777766444  46899998765542        2378999999877667898877665 57778888899999875


Q ss_pred             e
Q 043479           74 L   74 (534)
Q Consensus        74 ~   74 (534)
                      .
T Consensus       179 ~  179 (196)
T TIGR00693       179 V  179 (196)
T ss_pred             E
Confidence            4

This model includes ThiE from Bacillus subtilis but excludes its paralog, the regulatory protein TenI, and neighbors of TenI.

>PRK12520 RNA polymerase sigma factor; Provisional

Probab=80.30  E-value=4.4  Score=38.53  Aligned_cols=52  Identities=15%  Similarity=0.077  Sum_probs=43.0

Q ss_pred             hhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHhhh
Q 043479          167 SLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAEQG  221 (534)
Q Consensus       167 eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~lkr~a~~~  221 (534)
                      .|+++..+++...-++...-++|++.|+   ++..+|+++|.+-|..|++...+.
T Consensus       131 ~Lp~~~r~v~~l~~~~g~s~~EIA~~lg---is~~tV~~~l~Rar~~Lr~~l~~~  182 (191)
T PRK12520        131 RLPPRTGRVFMMREWLELETEEICQELQ---ITATNAWVLLYRARMRLRECLDLH  182 (191)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHC---CCHHHHHHHHHHHHHHHHHHHHHH
Confidence            3777777887776556666899999999   999999999999999888876654

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	534
1irz_A	64	Solution Structure Of Arr10-B Belonging To The Garp		7e-21
3to5_A	134	High Resolution Structure Of Chey3 From Vibrio Chol		3e-09
3gwg_A	129	Crystal Structure Of Chey Of Helicobacter Pylori Le		8e-09
3h1g_A	129	Crystal Structure Of Chey Mutant T84a Of Helicobact		9e-09
3h1f_A	129	Crystal Structure Of Chey Mutant D53a Of Helicobact		7e-08
3eq2_A	394	Structure Of Hexagonal Crystal Form Of Pseudomonas		2e-05
3eod_A	130	Crystal Structure Of N-Terminal Domain Of E. Coli R		2e-05
1u0s_Y	118	Chemotaxis Kinase Chea P2 Domain In Complex With Re		2e-05
3tmy_A	120	Chey From Thermotoga Maritima (Mn-Iii) Length = 120		2e-05
3f7a_A	394	Structure Of Orthorhombic Crystal Form Of Pseudomon		3e-05
1mvo_A	136	Crystal Structure Of The Phop Receiver Domain From		4e-05
3jte_A	143	Crystal Structure Of Response Regulator Receiver Do		6e-05
1dz3_A	130	Domain-Swapping In The Sporulation Response Regulat		8e-05
3myy_A	128	Structure Of E. Coli Chey Mutant A113p Bound To Ber		8e-05
1xhe_A	123	Crystal Structure Of The Receiver Domain Of Redox R		9e-05
3oo0_A	129	Structure Of Apo Chey A113p Length = 129		1e-04
1dc7_A	124	Structure Of A Transiently Phosphorylated "switch"		2e-04
1krw_A	124	Solution Structure And Backbone Dynamics Of Beryllo		2e-04
1j56_A	124	Minimized Average Structure Of Beryllofluoride-Acti		2e-04
1zh2_A	121	Crystal Structure Of The Calcium-Bound Receiver Dom		2e-04
3nhz_A	125	Structure Of N-Terminal Domain Of Mtra Length = 125		3e-04
1hey_A	128	Investigating The Structural Determinants Of The P2		3e-04
3olx_A	129	Structural And Functional Effects Of Substitution A		4e-04
3m6m_D	143	Crystal Structure Of Rpff Complexed With Rec Domain		4e-04
1mih_A	129	A Role For Chey Glu 89 In Chez-Mediated Dephosphory		5e-04
1ymv_A	129	Signal Transduction Protein Chey Mutant With Phe 14		5e-04
1xhf_A	123	Crystal Structure Of The Bef3-Activated Receiver Do		5e-04
3q9s_A	249	Crystal Structure Of Rra(1-215) From Deinococcus Ra		6e-04
1ab5_A	125	Structure Of Chey Mutant F14n, V21t Length = 125		6e-04
1qmp_A	130	Phosphorylated Aspartate In The Crystal Structure O		6e-04
1e6k_A	130	Two-Component Signal Transduction System D12a Mutan		6e-04
1ymu_A	130	Signal Transduction Protein Chey Mutant With Met 17		6e-04
1ehc_A	128	Structure Of Signal Transduction Protein Chey Lengt		7e-04
1e6l_A	127	Two-Component Signal Transduction System D13a Mutan		7e-04
1cye_A	129	Three Dimensional Structure Of Chemotactic Che Y Pr		7e-04
1eay_A	128	Chey-Binding (P2) Domain Of Chea In Complex With Ch		7e-04
3olw_A	129	Structural And Functional Effects Of Substitution A		8e-04
1cey_A	128	Assignments, Secondary Structure, Global Fold, And		8e-04
1djm_A	129	Solution Structure Of Bef3-Activated Chey From Esch		8e-04
2chy_A	128	Three-Dimensional Structure Of Chey, The Response R		9e-04
3olv_A	129	Structural And Functional Effects Of Substitution A		9e-04

>pdb|1IRZ|A Chain A, Solution Structure Of Arr10-B Belonging To The Garp Family Of Plant Myb-Related Dna Binding Motifs Of The Arabidopsis Response Regulators Length = 64

Iteration: 1
 Score = 98.6 bits (244), Expect = 7e-21,   Method: Composition-based stats.
 Identities = 43/64 (67%), Positives = 54/64 (84%)
Query: 155 TAPKKPKVAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFL 214
           TA KKP+V WT  LHN+FL A+ H+G+E+AVPKKIL+ MNV  LTRENVASHLQK+R+ L
Sbjct: 1   TAQKKPRVLWTHELHNKFLAAVDHLGVERAVPKKILDLMNVDKLTRENVASHLQKFRVAL 60
Query: 215 KRVA 218
           K+V+
Sbjct: 61  KKVS 64

>pdb|3TO5|A Chain A, High Resolution Structure Of Chey3 From Vibrio Cholerae Length = 134

Iteration: 1
 Score = 60.1 bits (144), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 30/68 (44%), Positives = 44/68 (64%), Gaps = 2/68 (2%)
Query: 18  DIDLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMSSDDRESVIMKALASGVAFYILK 75
           D D VVTD +MP M GI+L K I  +EE  HLPV++++++ +   I++A  +GV  YI+K
Sbjct: 57  DFDFVVTDWNMPGMQGIDLLKNIRADEELKHLPVLMITAEAKREQIIEAAQAGVNGYIVK 116
Query: 76  PLNPDDLK 83
           P     LK
Sbjct: 117 PFTAATLK 124

>pdb|3GWG|A Chain A, Crystal Structure Of Chey Of Helicobacter Pylori Length = 129

Iteration: 1
 Score = 58.9 bits (141), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 27/79 (34%), Positives = 51/79 (64%), Gaps = 2/79 (2%)
Query: 7   VEALATVRIQRDIDLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMSSDDRESVIMKA 64
           VEA   +    D  +++TD +MPEMNG++L K++  +  F  +P+++++++  ++ ++ A
Sbjct: 40  VEAWEKLDANADTKVLITDWNMPEMNGLDLVKKVRSDSRFKEIPIIMITTEGGKAEVITA 99
Query: 65  LASGVAFYILKPLNPDDLK 83
           L +GV  YI+KP  P  LK
Sbjct: 100 LKAGVNNYIVKPFTPQVLK 118

>pdb|3H1G|A Chain A, Crystal Structure Of Chey Mutant T84a Of Helicobacter Pylori Length = 129

Iteration: 1
 Score = 58.5 bits (140), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 27/79 (34%), Positives = 51/79 (64%), Gaps = 2/79 (2%)
Query: 7   VEALATVRIQRDIDLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMSSDDRESVIMKA 64
           VEA   +    D  +++TD +MPEMNG++L K++  +  F  +P+++++++  ++ ++ A
Sbjct: 40  VEAWEKLDANADTKVLITDWNMPEMNGLDLVKKVRSDSRFKEIPIIMITAEGGKAEVITA 99
Query: 65  LASGVAFYILKPLNPDDLK 83
           L +GV  YI+KP  P  LK
Sbjct: 100 LKAGVNNYIVKPFTPQVLK 118

>pdb|3H1F|A Chain A, Crystal Structure Of Chey Mutant D53a Of Helicobacter Pylori Length = 129

Iteration: 1
 Score = 55.5 bits (132), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 26/79 (32%), Positives = 50/79 (63%), Gaps = 2/79 (2%)
Query: 7   VEALATVRIQRDIDLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMSSDDRESVIMKA 64
           VEA   +    D  +++T  +MPEMNG++L K++  +  F  +P+++++++  ++ ++ A
Sbjct: 40  VEAWEKLDANADTKVLITAWNMPEMNGLDLVKKVRSDSRFKEIPIIMITTEGGKAEVITA 99
Query: 65  LASGVAFYILKPLNPDDLK 83
           L +GV  YI+KP  P  LK
Sbjct: 100 LKAGVNNYIVKPFTPQVLK 118

>pdb|3EQ2|A Chain A, Structure Of Hexagonal Crystal Form Of Pseudomonas Aeruginosa Rssb Length = 394

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 37/59 (62%)
Query: 20  DLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLN 78
           DLV+ DL  P+++G+EL + I +  +  P++V+S     S  ++AL  G A Y++KPL 
Sbjct: 51  DLVICDLRXPQIDGLELIRRIRQTASETPIIVLSGAGVXSDAVEALRLGAADYLIKPLE 109

>pdb|3EOD|A Chain A, Crystal Structure Of N-Terminal Domain Of E. Coli Rssb Length = 130

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 23/58 (39%), Positives = 36/58 (62%)
Query: 20  DLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPL 77
           DL++ D+ MP MNG++L + I       PV+V+S+ +  + I KAL  GV   +LKP+
Sbjct: 53  DLMICDIAMPRMNGLKLLEHIRNRGDQTPVLVISATENMADIAKALRLGVEDVLLKPV 110

>pdb|1U0S|Y Chain Y, Chemotaxis Kinase Chea P2 Domain In Complex With Response Regulator Chey From The Thermophile Thermotoga Maritima Length = 118

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 21/60 (35%), Positives = 40/60 (66%)
Query: 20  DLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP 79
           D+V  D+ MPEMNGI+  KEI +   +  ++V S+  +++++++A+ +G   +I+KP  P
Sbjct: 48  DIVTMDITMPEMNGIDAIKEIMKIDPNAKIIVCSAMGQQAMVIEAIKAGAKDFIVKPFQP 107

>pdb|3TMY|A Chain A, Chey From Thermotoga Maritima (Mn-Iii) Length = 120

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 21/60 (35%), Positives = 40/60 (66%)
Query: 20  DLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP 79
           D+V  D+ MPEMNGI+  KEI +   +  ++V S+  +++++++A+ +G   +I+KP  P
Sbjct: 49  DIVTMDITMPEMNGIDAIKEIMKIDPNAKIIVCSAMGQQAMVIEAIKAGAKDFIVKPFQP 108

>pdb|3F7A|A Chain A, Structure Of Orthorhombic Crystal Form Of Pseudomonas Aeruginosa Rssb Length = 394

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 37/59 (62%)
Query: 20  DLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLN 78
           DLV+ DL  P+++G+EL + I +  +  P++V+S     S  ++AL  G A Y++KPL 
Sbjct: 51  DLVICDLRXPQIDGLELIRRIRQTASETPIIVLSGAGVMSDAVEALRLGAADYLIKPLE 109

>pdb|1MVO|A Chain A, Crystal Structure Of The Phop Receiver Domain From Bacillus Subtilis Length = 136

Iteration: 1
 Score = 46.2 bits (108), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 22/82 (26%), Positives = 48/82 (58%), Gaps = 1/82 (1%)
Query: 1   VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESV 60
           +T +   EAL     ++  DL+V D+ +P+++GIE+ K++ ++    P++++++ D E  
Sbjct: 31  ITASDGEEALKKAETEKP-DLIVLDVMLPKLDGIEVCKQLRQQKLMFPILMLTAKDEEFD 89
Query: 61  IMKALASGVAFYILKPLNPDDL 82
            +  L  G   Y+ KP +P ++
Sbjct: 90  KVLGLELGADDYMTKPFSPREV 111

>pdb|3JTE|A Chain A, Crystal Structure Of Response Regulator Receiver Domain Protein From Clostridium Thermocellum Length = 143

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 24/77 (31%), Positives = 47/77 (61%), Gaps = 2/77 (2%)
Query: 19  IDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSD-DRESVIMKALASGVAFYILKPL 77
           ID+V+TD+ MP+++G+++ +EI +   H+ V++++   D ++ I+ A+  G   Y+ KP+
Sbjct: 50  IDVVITDMKMPKLSGMDILREIKKITPHMAVIILTGHGDLDNAIL-AMKEGAFEYLRKPV 108
Query: 78  NPDDLKNVWQYAMTYKK 94
              DL      A+  KK
Sbjct: 109 TAQDLSIAINNAINRKK 125

>pdb|1DZ3|A Chain A, Domain-Swapping In The Sporulation Response Regulator Spo0a Length = 130

Iteration: 1
 Score = 45.4 bits (106), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 20/64 (31%), Positives = 42/64 (65%), Gaps = 1/64 (1%)
Query: 20  DLVVTDLHMPEMNGIELQKEINEEFTHLP-VMVMSSDDRESVIMKALASGVAFYILKPLN 78
           D+++ D+ MP ++G+ + + I   F H P V+++++  +E V  KA+  G +++ILKP +
Sbjct: 50  DILLLDIIMPHLDGLAVLERIRAGFEHQPNVIMLTAFGQEDVTKKAVELGASYFILKPFD 109
Query: 79  PDDL 82
            ++L
Sbjct: 110 MENL 113

>pdb|3MYY|A Chain A, Structure Of E. Coli Chey Mutant A113p Bound To Beryllium Fluoride Length = 128

Iteration: 1
 Score = 45.4 bits (106), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 21/65 (32%), Positives = 42/65 (64%), Gaps = 2/65 (3%)
Query: 21  LVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPLN 78
            V++D +MP M+G+EL K I  +   + LPV++++++ ++  I+ A  +G + Y++KP  
Sbjct: 52  FVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFT 111
Query: 79  PDDLK 83
           P  L+
Sbjct: 112 PATLE 116

>pdb|1XHE|A Chain A, Crystal Structure Of The Receiver Domain Of Redox Response Regulator Arca Length = 123

Iteration: 1
 Score = 45.1 bits (105), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 23/67 (34%), Positives = 40/67 (59%), Gaps = 1/67 (1%)
Query: 16  QRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILK 75
           + DI+LV+ D+++P  NG+ L +E+ E+  ++ +M ++  D E   +  L  G   YI K
Sbjct: 45  EYDINLVIMDINLPGKNGLLLARELREQ-ANVALMFLTGRDNEVDKILGLEIGADDYITK 103
Query: 76  PLNPDDL 82
           P NP +L
Sbjct: 104 PFNPREL 110

>pdb|3OO0|A Chain A, Structure Of Apo Chey A113p Length = 129

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/65 (32%), Positives = 42/65 (64%), Gaps = 2/65 (3%)
Query: 21  LVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPLN 78
            V++D +MP M+G+EL K I  +   + LPV++++++ ++  I+ A  +G + Y++KP  
Sbjct: 53  FVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFT 112
Query: 79  PDDLK 83
           P  L+
Sbjct: 113 PATLE 117

>pdb|1DC7|A Chain A, Structure Of A Transiently Phosphorylated "switch" In Bacterial Signal Transduction Length = 124

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 20/73 (27%), Positives = 42/73 (57%)
Query: 20  DLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP 79
           D++++D+ MP M+G+ L K+I +    LPV++M++       + A   G   Y+ KP + 
Sbjct: 49  DVLLSDIRMPGMDGLALLKQIKQRHPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDI 108
Query: 80  DDLKNVWQYAMTY 92
           D+   + + A+++
Sbjct: 109 DEAVALVERAISH 121

>pdb|1KRW|A Chain A, Solution Structure And Backbone Dynamics Of Beryllofluoride- Activated Ntrc Receiver Domain Length = 124

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 20/73 (27%), Positives = 42/73 (57%)
Query: 20  DLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP 79
           D++++D+ MP M+G+ L K+I +    LPV++M++       + A   G   Y+ KP + 
Sbjct: 49  DVLLSDIRMPGMDGLALLKQIKQRHPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDI 108
Query: 80  DDLKNVWQYAMTY 92
           D+   + + A+++
Sbjct: 109 DEAVALVERAISH 121

>pdb|1J56|A Chain A, Minimized Average Structure Of Beryllofluoride-Activated Ntrc Receiver Domain: Model Structure Incorporating Active Site Contacts Length = 124

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 20/73 (27%), Positives = 42/73 (57%)
Query: 20  DLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP 79
           D++++D+ MP M+G+ L K+I +    LPV++M++       + A   G   Y+ KP + 
Sbjct: 49  DVLLSDIRMPGMDGLALLKQIKQRHPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDI 108
Query: 80  DDLKNVWQYAMTY 92
           D+   + + A+++
Sbjct: 109 DEAVALVERAISH 121

>pdb|1ZH2|A Chain A, Crystal Structure Of The Calcium-Bound Receiver Domain Of Kdp Potassium Transport System Response Regulator Kdpe Length = 121

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 22/67 (32%), Positives = 42/67 (62%), Gaps = 1/67 (1%)
Query: 17  RDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKP 76
           R  DL++ DL +P+ +GIE  +++  +++ +PV+V+S+   ES  + AL +G   Y+ KP
Sbjct: 44  RKPDLIILDLGLPDGDGIEFIRDL-RQWSAVPVIVLSARSEESDKIAALDAGADDYLSKP 102
Query: 77  LNPDDLK 83
               +L+
Sbjct: 103 FGIGELQ 109

>pdb|3NHZ|A Chain A, Structure Of N-Terminal Domain Of Mtra Length = 125

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 24/74 (32%), Positives = 44/74 (59%), Gaps = 2/74 (2%)
Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
           +AL  VR  R  DLV+ DL +P MNGI++ + +  + + +P++++++      ++  L S
Sbjct: 40  QALTAVRELRP-DLVLLDLMLPGMNGIDVCRVLRAD-SGVPIVMLTAKTDTVDVVLGLES 97
Query: 68  GVAFYILKPLNPDD 81
           G   YI+KP  P +
Sbjct: 98  GADDYIMKPFKPKE 111

>pdb|1HEY|A Chain A, Investigating The Structural Determinants Of The P21-Like Triphosphate And Mg2+ Binding Site Length = 128

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/65 (30%), Positives = 41/65 (63%), Gaps = 2/65 (3%)
Query: 21  LVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPLN 78
            V++D +MP M+G+EL K I  +   + LPV++++++ ++  I+ A  +G + Y++KP  
Sbjct: 52  FVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFT 111
Query: 79  PDDLK 83
              L+
Sbjct: 112 AATLE 116

>pdb|3OLX|A Chain A, Structural And Functional Effects Of Substitution At Position T+1 In Chey: Cheya88s-Bef3-Mn Complex Length = 129

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 20/59 (33%), Positives = 39/59 (66%), Gaps = 2/59 (3%)
Query: 21  LVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPL 77
            V++D +MP M+G+EL K I  +   + LPV++++S+ ++  I+ A  +G + Y++KP 
Sbjct: 53  FVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTSEAKKENIIAAAQAGASGYVVKPF 111

>pdb|3M6M|D Chain D, Crystal Structure Of Rpff Complexed With Rec Domain Of Rpfc Length = 143

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 21/66 (31%), Positives = 36/66 (54%), Gaps = 4/66 (6%)
Query: 16  QRDIDLVVTDLHMPEMNGIELQKEIN----EEFTHLPVMVMSSDDRESVIMKALASGVAF 71
           + D D V+ DLHMP MNG+++ K++         + PV+V+S+D     I     +G   
Sbjct: 56  EEDYDAVIVDLHMPGMNGLDMLKQLRVMQASGMRYTPVVVLSADVTPEAIRACEQAGARA 115
Query: 72  YILKPL 77
           ++ KP+
Sbjct: 116 FLAKPV 121

>pdb|1MIH|A Chain A, A Role For Chey Glu 89 In Chez-Mediated Dephosphorylation Of The E. Coli Chemotaxis Response Regulator Chey Length = 129

Iteration: 1
 Score = 42.7 bits (99), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 20/65 (30%), Positives = 40/65 (61%), Gaps = 2/65 (3%)
Query: 21  LVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPLN 78
            V++D  MP M+G+EL K I  +   + LPV++++++ ++  I+ A  +G + Y++KP  
Sbjct: 53  FVISDWRMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFT 112
Query: 79  PDDLK 83
              L+
Sbjct: 113 AATLE 117

>pdb|1YMV|A Chain A, Signal Transduction Protein Chey Mutant With Phe 14 Replaced By Gly, Ser 15 Replaced By Gly, And Met 17 Replaced By Gly Length = 129

Iteration: 1
 Score = 42.7 bits (99), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 20/65 (30%), Positives = 41/65 (63%), Gaps = 2/65 (3%)
Query: 21  LVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPLN 78
            V++D +MP M+G+EL K I  +   + LPV++++++ ++  I+ A  +G + Y++KP  
Sbjct: 53  FVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFT 112
Query: 79  PDDLK 83
              L+
Sbjct: 113 AATLE 117

>pdb|1XHF|A Chain A, Crystal Structure Of The Bef3-Activated Receiver Domain Of Redox Response Regulator Arca Length = 123

Iteration: 1
 Score = 42.7 bits (99), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 22/67 (32%), Positives = 39/67 (58%), Gaps = 1/67 (1%)
Query: 16  QRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILK 75
           + DI+LV+ D+++P  NG+ L +E+ E+  ++ +  ++  D E   +  L  G   YI K
Sbjct: 45  EYDINLVIXDINLPGKNGLLLARELREQ-ANVALXFLTGRDNEVDKILGLEIGADDYITK 103
Query: 76  PLNPDDL 82
           P NP +L
Sbjct: 104 PFNPREL 110

>pdb|3Q9S|A Chain A, Crystal Structure Of Rra(1-215) From Deinococcus Radiodurans Length = 249

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/80 (25%), Positives = 48/80 (60%), Gaps = 1/80 (1%)
Query: 20  DLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP 79
           DL++ DL +P+ +G ++ + + +  + LP++V+++ D     ++ L  G   Y++KP +P
Sbjct: 83  DLILLDLGLPDFDGGDVVQRLRKN-SALPIIVLTARDTVEEKVRLLGLGADDYLIKPFHP 141
Query: 80  DDLKNVWQYAMTYKKAKSIS 99
           D+L    +  +  + ++S+S
Sbjct: 142 DELLARVKVQLRQRTSESLS 161

>pdb|1AB5|A Chain A, Structure Of Chey Mutant F14n, V21t Length = 125

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/65 (30%), Positives = 41/65 (63%), Gaps = 2/65 (3%)
Query: 21  LVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPLN 78
            V++D +MP M+G+EL K I  +   + LPV++++++ ++  I+ A  +G + Y++KP  
Sbjct: 49  FVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFT 108
Query: 79  PDDLK 83
              L+
Sbjct: 109 AATLE 113

>pdb|1QMP|A Chain A, Phosphorylated Aspartate In The Crystal Structure Of The Sporulation Response Regulator, Spo0a Length = 130

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 19/64 (29%), Positives = 41/64 (64%), Gaps = 1/64 (1%)
Query: 20  DLVVTDLHMPEMNGIELQKEINEEFTHLP-VMVMSSDDRESVIMKALASGVAFYILKPLN 78
           D+++  + MP ++G+ + + I   F H P V+++++  +E V  KA+  G +++ILKP +
Sbjct: 50  DILLLXIIMPHLDGLAVLERIRAGFEHQPNVIMLTAFGQEDVTKKAVELGASYFILKPFD 109
Query: 79  PDDL 82
            ++L
Sbjct: 110 MENL 113

>pdb|1E6K|A Chain A, Two-Component Signal Transduction System D12a Mutant Of Chey Length = 130

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/65 (30%), Positives = 41/65 (63%), Gaps = 2/65 (3%)
Query: 21  LVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPLN 78
            V++D +MP M+G+EL K I  +   + LPV++++++ ++  I+ A  +G + Y++KP  
Sbjct: 54  FVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFT 113
Query: 79  PDDLK 83
              L+
Sbjct: 114 AATLE 118

>pdb|1YMU|A Chain A, Signal Transduction Protein Chey Mutant With Met 17 Replaced By Gly (M17g) Length = 130

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 19/59 (32%), Positives = 39/59 (66%), Gaps = 2/59 (3%)
Query: 21  LVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPL 77
            V++D +MP M+G+EL K I  +   + LPV++++++ ++  I+ A  +G + Y++KP 
Sbjct: 54  FVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPF 112

>pdb|1EHC|A Chain A, Structure Of Signal Transduction Protein Chey Length = 128

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 20/65 (30%), Positives = 41/65 (63%), Gaps = 2/65 (3%)
Query: 21  LVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPLN 78
            V++D +MP M+G+EL K I  +   + LPV++++++ ++  I+ A  +G + Y++KP  
Sbjct: 52  FVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFT 111
Query: 79  PDDLK 83
              L+
Sbjct: 112 AATLE 116

>pdb|1E6L|A Chain A, Two-Component Signal Transduction System D13a Mutant Of Chey Length = 127

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 20/65 (30%), Positives = 41/65 (63%), Gaps = 2/65 (3%)
Query: 21  LVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPLN 78
            V++D +MP M+G+EL K I  +   + LPV++++++ ++  I+ A  +G + Y++KP  
Sbjct: 51  FVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFT 110
Query: 79  PDDLK 83
              L+
Sbjct: 111 AATLE 115

>pdb|1CYE|A Chain A, Three Dimensional Structure Of Chemotactic Che Y Protein In Aqueous Solution By Nuclear Magnetic Resonance Methods Length = 129

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 19/59 (32%), Positives = 39/59 (66%), Gaps = 2/59 (3%)
Query: 21  LVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPL 77
            V++D +MP M+G+EL K I  +   + LPV++++++ ++  I+ A  +G + Y++KP 
Sbjct: 53  FVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPF 111

>pdb|1EAY|A Chain A, Chey-Binding (P2) Domain Of Chea In Complex With Chey From Escherichia Coli Length = 128

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 19/59 (32%), Positives = 39/59 (66%), Gaps = 2/59 (3%)
Query: 21  LVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPL 77
            V++D +MP M+G+EL K I  +   + LPV++++++ ++  I+ A  +G + Y++KP 
Sbjct: 52  FVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPF 110

>pdb|3OLW|A Chain A, Structural And Functional Effects Of Substitution At Position T+1 In Chey: Cheya88t-Bef3-Mn Complex Length = 129

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 19/59 (32%), Positives = 39/59 (66%), Gaps = 2/59 (3%)
Query: 21  LVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPL 77
            V++D +MP M+G+EL K I  +   + LPV++++++ ++  I+ A  +G + Y++KP 
Sbjct: 53  FVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTTEAKKENIIAAAQAGASGYVVKPF 111

>pdb|1CEY|A Chain A, Assignments, Secondary Structure, Global Fold, And Dynamics Of Chemotaxis Y Protein Using Three-And Four-Dimensional Heteronuclear (13c,15n) Nmr Spectroscopy Length = 128

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 19/59 (32%), Positives = 39/59 (66%), Gaps = 2/59 (3%)
Query: 21  LVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPL 77
            V++D +MP M+G+EL K I  +   + LPV++++++ ++  I+ A  +G + Y++KP 
Sbjct: 52  FVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPF 110

>pdb|1DJM|A Chain A, Solution Structure Of Bef3-Activated Chey From Escherichia Coli Length = 129

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 19/59 (32%), Positives = 39/59 (66%), Gaps = 2/59 (3%)
Query: 21  LVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPL 77
            V++D +MP M+G+EL K I  +   + LPV++++++ ++  I+ A  +G + Y++KP 
Sbjct: 53  FVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPF 111

>pdb|2CHY|A Chain A, Three-Dimensional Structure Of Chey, The Response Regulator Of Bacterial Chemotaxis Length = 128

Iteration: 1
 Score = 42.0 bits (97), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 19/65 (29%), Positives = 40/65 (61%), Gaps = 2/65 (3%)
Query: 21  LVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLN 78
            ++ D +MP M+G+EL K I  +   + LPV++++++ ++  I+ A  +G + Y++KP  
Sbjct: 52  FIICDWNMPNMDGLELLKTIRADSAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFT 111
Query: 79  PDDLK 83
              L+
Sbjct: 112 AATLE 116

>pdb|3OLV|A Chain A, Structural And Functional Effects Of Substitution At Position T+1 In Chey: Cheya88v-Bef3-Mg Complex Length = 129

Iteration: 1
 Score = 42.0 bits (97), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 20/65 (30%), Positives = 40/65 (61%), Gaps = 2/65 (3%)
Query: 21  LVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPLN 78
            V++D +MP M+G+EL K I  +   + LPV++++ + ++  I+ A  +G + Y++KP  
Sbjct: 53  FVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTVEAKKENIIAAAQAGASGYVVKPFT 112
Query: 79  PDDLK 83
              L+
Sbjct: 113 AATLE 117

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	534
1irz_A	64	ARR10-B; helix-turn-helix, DNA binding protein; NM	1e-27
3luf_A	259	Two-component system response regulator/ggdef doma	2e-19
3luf_A	259	Two-component system response regulator/ggdef doma	3e-15
3hdg_A	137	Uncharacterized protein; two-component sensor acti	3e-19
3kcn_A	151	Adenylate cyclase homolog; SGX, PSI 2, structural	1e-18
3cu5_A	141	Two component transcriptional regulator, ARAC FAM;	5e-18
3hv2_A	153	Response regulator/HD domain protein; PSI-2, NYSGX	6e-18
2jk1_A	139	HUPR, hydrogenase transcriptional regulatory prote	1e-17
1jbe_A	128	Chemotaxis protein CHEY; signaling protein; 1.08A	1e-17
2rjn_A	154	Response regulator receiver:metal-dependent phosph	2e-17
4dad_A	146	Putative pilus assembly-related protein; response	1e-16
1srr_A	124	SPO0F, sporulation response regulatory protein; as	1e-16
1tmy_A	120	CHEY protein, TMY; chemotaxis, phosphoryl transfer	2e-16
2qvg_A	143	Two component response regulator; NYSGXRC, PSI-2,	2e-16
3hdv_A	136	Response regulator; PSI-II, structural genomics, P	2e-16
1k66_A	149	Phytochrome response regulator RCPB; CHEY homologu	3e-16
2qsj_A	154	DNA-binding response regulator, LUXR family; struc	6e-16
3bre_A	358	Probable two-component response regulator; protein	7e-16
3h1g_A	129	Chemotaxis protein CHEY homolog; sulfate-bound CHE	8e-16
1dc7_A	124	NTRC, nitrogen regulation protein; receiver domain	9e-16
3ilh_A	146	Two component response regulator; NYSGXRC, PSI-II,	1e-15
1w25_A	459	Stalked-cell differentiation controlling protein;	1e-15
1w25_A	459	Stalked-cell differentiation controlling protein;	5e-15
1i3c_A	149	Response regulator RCP1; phytochrome, signaling pr	2e-15
1p6q_A	129	CHEY2; chemotaxis, signal transduction, response r	2e-15
3cfy_A	137	Putative LUXO repressor protein; structural genomi	3e-15
1yio_A	208	Response regulatory protein; transcription regulat	4e-15
3heb_A	152	Response regulator receiver domain protein (CHEY);	4e-15
3jte_A	143	Response regulator receiver protein; structural ge	5e-15
2qxy_A	142	Response regulator; regulation of transcription, N	6e-15
1s8n_A	205	Putative antiterminator; RV1626, structural genomi	1e-14
3eq2_A	394	Probable two-component response regulator; adaptor	2e-14
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	2e-14
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	2e-14
3b2n_A	133	Uncharacterized protein Q99UF4; structural genomic	6e-14
1qkk_A	155	DCTD, C4-dicarboxylate transport transcriptional r	1e-13
3i42_A	127	Response regulator receiver domain protein (CHEY-	1e-13
3hzh_A	157	Chemotaxis response regulator (CHEY-3); phosphatas	2e-13
1dz3_A	130	Stage 0 sporulation protein A; response regulator,	2e-13
2rdm_A	132	Response regulator receiver protein; structural ge	3e-13
3crn_A	132	Response regulator receiver domain protein, CHEY-;	6e-13
3cnb_A	143	DNA-binding response regulator, MERR family; signa	7e-13
1dbw_A	126	Transcriptional regulatory protein FIXJ; doubly wo	8e-13
3f6c_A	134	Positive transcription regulator EVGA; structural	9e-13
1mb3_A	124	Cell division response regulator DIVK; signal tran	1e-12
2ayx_A	254	Sensor kinase protein RCSC; two independent struct	1e-12
3cg0_A	140	Response regulator receiver modulated diguanylate	2e-12
3lua_A	140	Response regulator receiver protein; two-component	2e-12
3eqz_A	135	Response regulator; structural genomics, unknown f	4e-12
3h5i_A	140	Response regulator/sensory box protein/ggdef domai	4e-12
3m6m_D	143	Sensory/regulatory protein RPFC; RPFF, REC, enoyl-	5e-12
2qr3_A	140	Two-component system response regulator; structura	5e-12
3eod_A	130	Protein HNR; response regulator, phosphoprotein, t	6e-12
3snk_A	135	Response regulator CHEY-like protein; P-loop conta	9e-12
4e7p_A	150	Response regulator; DNA binding, cytosol, transcri	1e-11
3grc_A	140	Sensor protein, kinase; protein structure initiati	1e-11
3kht_A	144	Response regulator; PSI-II, 11023K, structural gen	2e-11
1dcf_A	136	ETR1 protein; beta-alpha five sandwich, transferas	4e-11
3kyj_B	145	CHEY6 protein, putative histidine protein kinase;	6e-11
3nhm_A	133	Response regulator; protein structure initiative I	7e-11
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	1e-10
1qo0_D	196	AMIR; binding protein, gene regulator, receptor; 2	1e-10
3rqi_A	184	Response regulator protein; structural genomics, s	1e-10
3cz5_A	153	Two-component response regulator, LUXR family; str	2e-10
1k68_A	140	Phytochrome response regulator RCPA; phosphorylate	4e-10
3kto_A	136	Response regulator receiver protein; PSI-II,struct	5e-10
3n53_A	140	Response regulator receiver modulated diguanylate;	5e-10
3eul_A	152	Possible nitrate/nitrite response transcriptional	1e-09
3gt7_A	154	Sensor protein; structural genomics, signal receiv	1e-09
3gl9_A	122	Response regulator; beta-sheet, surrounded by alph	2e-09
2zay_A	147	Response regulator receiver protein; structural ge	3e-09
2r25_B	133	Osmosensing histidine protein kinase SLN1; alpha5-	3e-09
3t8y_A	164	CHEB, chemotaxis response regulator protein-glutam	3e-09
3klo_A	225	Transcriptional regulator VPST; REC domain, HTH do	4e-09
3c3w_A	225	Two component transcriptional regulatory protein;	4e-09
1a04_A	215	Nitrate/nitrite response regulator protein NARL; s	6e-09
3c3m_A	138	Response regulator receiver protein; structural ge	8e-09
3r0j_A	250	Possible two component system response transcript	1e-08
1zh2_A	121	KDP operon transcriptional regulatory protein KDPE	2e-08
3cg4_A	142	Response regulator receiver domain protein (CHEY-;	2e-08
2b4a_A	138	BH3024; flavodoxin-like fold, structural genomics,	2e-08
1a2o_A	349	CHEB methylesterase; bacterial chemotaxis, adaptat	3e-08
3c97_A	140	Signal transduction histidine kinase; structural g	4e-08
3a10_A	116	Response regulator; phosphoacceptor, signaling pro	6e-08
2j48_A	119	Two-component sensor kinase; pseudo-receiver, circ	1e-07
2qzj_A	136	Two-component response regulator; 11017X, PSI-II,	1e-07
3lte_A	132	Response regulator; structural genomics, PSI, prot	1e-07
1p2f_A	220	Response regulator; DRRB, OMPR/PHOB, transcription	2e-07
1mvo_A	136	PHOP response regulator; phosphate regulon, transc	4e-07
3t6k_A	136	Response regulator receiver; flavodoxin-like, stru	7e-07
2qv0_A	143	Protein MRKE; structural genomics, transcription,	7e-07
2a9o_A	120	Response regulator; essential protein, YYCF/YYCG h	7e-07
2yum_A	75	ZZZ3 protein, zinc finger ZZ-type-containing prote	9e-07
1xhf_A	123	DYE resistance, aerobic respiration control protei	2e-06
3f6p_A	120	Transcriptional regulatory protein YYCF; unphospho	4e-06
2jba_A	127	Phosphate regulon transcriptional regulatory PROT;	5e-06
2cu7_A	72	KIAA1915 protein; nuclear protein, SANT domain, DN	1e-05
1zgz_A	122	Torcad operon transcriptional regulatory protein;	1e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-05
3sy8_A	400	ROCR; TIM barrel phosphodiesterase-A, transcriptio	3e-05
3mm4_A	206	Histidine kinase homolog; receiver domain, CKI1, c	3e-05
2gwr_A	238	DNA-binding response regulator MTRA; two-component	1e-04
2oqr_A	230	Sensory transduction protein REGX3; response regul	1e-04
3q9s_A	249	DNA-binding response regulator; DNA binding protei	2e-04
1kgs_A	225	DRRD, DNA binding response regulator D; DNA-bindin	2e-04
1ys7_A	233	Transcriptional regulatory protein PRRA; response	3e-04

>1irz_A ARR10-B; helix-turn-helix, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: a.4.1.11 Length = 64

 Score =  104 bits (261), Expect = 1e-27
 Identities = 43/64 (67%), Positives = 54/64 (84%)

Query: 155 TAPKKPKVAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFL 214
           TA KKP+V WT  LHN+FL A+ H+G+E+AVPKKIL+ MNV  LTRENVASHLQK+R+ L
Sbjct: 1   TAQKKPRVLWTHELHNKFLAAVDHLGVERAVPKKILDLMNVDKLTRENVASHLQKFRVAL 60

Query: 215 KRVA 218
           K+V+
Sbjct: 61  KKVS 64

>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 = 87.0 bits (216), Expect = 2e-19
 Identities = 23/77 (29%), Positives = 41/77 (53%), Gaps = 2/77 (2%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMSSDDRESVIMKAL 65
           EALAT+     I LV+ D +MPE++GI L + +        L ++ +S  D+  +  + L
Sbjct: 159 EALATLEQHPAIRLVLVDYYMPEIDGISLVRMLRERYSKQQLAIIGISVSDKRGLSARYL 218

Query: 66  ASGVAFYILKPLNPDDL 82
             G   ++ +P  P++L
Sbjct: 219 KQGANDFLNQPFEPEEL 235

>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 = 74.6 bits (184), Expect = 3e-15
 Identities = 17/82 (20%), Positives = 34/82 (41%), Gaps = 3/82 (3%)

Query: 1   VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESV 60
           +     +E     +   +  + + DL +P+    E  K + E    LPV+++++D  E  
Sbjct: 32  IDAFDTLEGARHCQ-GDEYVVALVDLTLPDAPSGEAVKVLLER--GLPVVILTADISEDK 88

Query: 61  IMKALASGVAFYILKPLNPDDL 82
               L +GV  Y++K       
Sbjct: 89  REAWLEAGVLDYVMKDSRHSLQ 110

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

 Score = 83.4 bits (207), Expect = 3e-19
 Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 3/79 (3%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSS-DDRESVIMKALA 66
           E           D+++TD+ MP++ G+E+   I        V+V+S+  + +  I KA+ 
Sbjct: 42  EGERLFG-LHAPDVIITDIRMPKLGGLEMLDRIKAGGAKPYVIVISAFSEMKYFI-KAIE 99

Query: 67  SGVAFYILKPLNPDDLKNV 85
            GV  ++ KP+ P  L   
Sbjct: 100 LGVHLFLPKPIEPGRLMET 118

>3kcn_A Adenylate cyclase homolog; SGX, PSI 2, structural genomics, protein structure initiative; 2.45A {Rhodopirellula baltica} Length = 151

 Score = 81.9 bits (203), Expect = 1e-18
 Identities = 19/87 (21%), Positives = 40/87 (45%), Gaps = 3/87 (3%)

Query: 1   VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSS-DDRES 59
            T     EALA ++      +++ D+ MP M G E+ ++      +   ++++   D  +
Sbjct: 31  TTCESGPEALACIKKSDPFSVIMVDMRMPGMEGTEVIQKARLISPNSVYLMLTGNQDLTT 90

Query: 60  VIMKALASGVAF-YILKPLNPDDLKNV 85
            + +A+  G  F ++ KP    D+K  
Sbjct: 91  AM-EAVNEGQVFRFLNKPCQMSDIKAA 116

>3cu5_A Two component transcriptional regulator, ARAC FAM; structural genomics, protein structure initiative; 2.60A {Clostridium phytofermentans isdg} Length = 141

 Score = 79.9 bits (198), Expect = 5e-18
 Identities = 21/80 (26%), Positives = 42/80 (52%), Gaps = 3/80 (3%)

Query: 7   VEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSS-DDRESVIMKAL 65
           + A+     +   ++++TD+ MP M+GIEL   I + +    V+ MS   D+E +   A+
Sbjct: 39  INAIQIAL-KHPPNVLLTDVRMPRMDGIELVDNILKLYPDCSVIFMSGYSDKEYL-KAAI 96

Query: 66  ASGVAFYILKPLNPDDLKNV 85
                 Y+ KP++P ++ + 
Sbjct: 97  KFRAIRYVEKPIDPSEIMDA 116

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

 Score = 79.9 bits (198), Expect = 6e-18
 Identities = 20/87 (22%), Positives = 44/87 (50%), Gaps = 4/87 (4%)

Query: 1   VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSS-DDRES 59
                  +AL  +   R++DLV++  H+P+M+G  L   I++++     ++++   D + 
Sbjct: 42  HFARDATQALQLLA-SREVDLVISAAHLPQMDGPTLLARIHQQYPSTTRILLTGDPDLKL 100

Query: 60  VIMKALASGVAF-YILKPLNPDDLKNV 85
           +  KA+  G  + Y+ KP +  +L   
Sbjct: 101 IA-KAINEGEIYRYLSKPWDDQELLLA 126

>2jk1_A HUPR, hydrogenase transcriptional regulatory protein HU; nucleotide-binding, transcription regulation; 2.10A {Rhodobacter capsulatus} PDB: 2vui_B 2vuh_B Length = 139

 Score = 78.7 bits (195), Expect = 1e-17
 Identities = 16/87 (18%), Positives = 40/87 (45%), Gaps = 4/87 (4%)

Query: 1   VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSS-DDRES 59
           +T      A+A +  +  + +++ D  MP   G++   E+ E +     ++++   D  S
Sbjct: 28  LTAQGAEAAIAILE-EEWVQVIICDQRMPGRTGVDFLTEVRERWPETVRIIITGYTDSAS 86

Query: 60  VIMKALASGVAF-YILKPLNPDDLKNV 85
           ++  A+       ++ KP +P+ L + 
Sbjct: 87  MM-AAINDAGIHQFLTKPWHPEQLLSS 112

>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 ... Length = 128

 Score = 78.4 bits (194), Expect = 1e-17
 Identities = 23/79 (29%), Positives = 46/79 (58%), Gaps = 3/79 (3%)

Query: 7   VEALATVRIQRDIDLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMSSDDRESVIMKA 64
           V+AL  ++       V++D +MP M+G+EL K I      + LPV++++++ ++  I+ A
Sbjct: 39  VDALNKLQ-AGGYGFVISDWNMPNMDGLELLKTIRAXXAMSALPVLMVTAEAKKENIIAA 97

Query: 65  LASGVAFYILKPLNPDDLK 83
             +G + Y++KP     L+
Sbjct: 98  AQAGASGYVVKPFTAATLE 116

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

 Score = 78.8 bits (195), Expect = 2e-17
 Identities = 24/87 (27%), Positives = 48/87 (55%), Gaps = 4/87 (4%)

Query: 1   VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSS-DDRES 59
           +T T P++AL  ++    + LV++D+ MPEM G    +++ + +  +  +V+S   D ++
Sbjct: 35  ITFTSPLDALEALK-GTSVQLVISDMRMPEMGGEVFLEQVAKSYPDIERVVISGYADAQA 93

Query: 60  VIMKALASGVAF-YILKPLNPDDLKNV 85
            I  A+  G    ++LKP   +D+  V
Sbjct: 94  TI-DAVNRGKISRFLLKPWEDEDVFKV 119

>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 = 76.3 bits (188), Expect = 1e-16
 Identities = 11/78 (14%), Positives = 33/78 (42%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
           + +         D+++ D    +   +   ++++     L  +++++D     ++ A+ +
Sbjct: 57  QIVQRTDGLDAFDILMIDGAALDTAELAAIEKLSRLHPGLTCLLVTTDASSQTLLDAMRA 116

Query: 68  GVAFYILKPLNPDDLKNV 85
           GV   +  PL P  L + 
Sbjct: 117 GVRDVLRWPLEPRALDDA 134

>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 = 75.2 bits (186), Expect = 1e-16
 Identities = 21/79 (26%), Positives = 44/79 (55%), Gaps = 3/79 (3%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
           +AL  V  +   DLV+ D+ +P M+GIE+ K +     ++ V++M++     +I ++   
Sbjct: 38  QALDIVT-KERPDLVLLDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKEL 96

Query: 68  GVAF-YILKPLNPDDLKNV 85
           G A  +  KP + D++++ 
Sbjct: 97  G-ALTHFAKPFDIDEIRDA 114

>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 Length = 120

 Score = 74.8 bits (185), Expect = 2e-16
 Identities = 23/75 (30%), Positives = 46/75 (61%), Gaps = 1/75 (1%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
           EA+   +  +  D+V  D+ MPEMNGI+  KEI +   +  ++V S+  +++++++A+ +
Sbjct: 38  EAVEKYKELKP-DIVTMDITMPEMNGIDAIKEIMKIDPNAKIIVCSAMGQQAMVIEAIKA 96

Query: 68  GVAFYILKPLNPDDL 82
           G   +I+KP  P  +
Sbjct: 97  GAKDFIVKPFQPSRV 111

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

 Score = 75.3 bits (186), Expect = 2e-16
 Identities = 19/95 (20%), Positives = 46/95 (48%), Gaps = 7/95 (7%)

Query: 7   VEALATVRIQRD-----IDLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMSSDDRES 59
            +AL  +  +         L++ D+++P+MNGIE  KE+  +  FT + V V+++     
Sbjct: 43  NQALDMLYGRNKENKIHPKLILLDINIPKMNGIEFLKELRDDSSFTDIEVFVLTAAYTSK 102

Query: 60  VIMKALASGVAFYILKPLNPDDLKNVWQYAMTYKK 94
             +   +  +  +++KPL+  +   ++    + + 
Sbjct: 103 DKLAFESLNIRGHLIKPLDYGEAIKLFWILQSMEG 137

>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 = 74.9 bits (185), Expect = 2e-16
 Identities = 24/80 (30%), Positives = 42/80 (52%), Gaps = 3/80 (3%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINE-EFTHLPVMVMSS-DDRESVIMKAL 65
           EA   +  Q+ I L++TDL M   +G++L + I   E   L ++V+S   D E  +   +
Sbjct: 42  EARLYLHYQKRIGLMITDLRMQPESGLDLIRTIRASERAALSIIVVSGDTDVEEAV-DVM 100

Query: 66  ASGVAFYILKPLNPDDLKNV 85
             GV  ++LKP++   L  +
Sbjct: 101 HLGVVDFLLKPVDLGKLLEL 120

>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 = 75.0 bits (185), Expect = 3e-16
 Identities = 22/96 (22%), Positives = 42/96 (43%), Gaps = 11/96 (11%)

Query: 1   VTVTRPVEALATVR---------IQRDIDLVVTDLHMPEMNGIELQKEI--NEEFTHLPV 49
                  +AL  +          I     +++ DL++P  +G E+ +EI  +E    +PV
Sbjct: 36  YRCITGDQALDFLYQTGSYCNPDIAPRPAVILLDLNLPGTDGREVLQEIKQDEVLKKIPV 95

Query: 50  MVMSSDDRESVIMKALASGVAFYILKPLNPDDLKNV 85
           ++M++      I    +  ++ YI+KPL  D L   
Sbjct: 96  VIMTTSSNPKDIEICYSYSISSYIVKPLEIDRLTET 131

>2qsj_A DNA-binding response regulator, LUXR family; structural genomics, PSI-2, protein structure initiative; 2.10A {Silicibacter pomeroyi dss-3} Length = 154

 Score = 74.2 bits (183), Expect = 6e-16
 Identities = 18/75 (24%), Positives = 36/75 (48%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
           +ALA +     +DL++ D+++P+   I+    +        V ++S +    +I  AL +
Sbjct: 40  DALAFLEADNTVDLILLDVNLPDAEAIDGLVRLKRFDPSNAVALISGETDHELIRAALEA 99

Query: 68  GVAFYILKPLNPDDL 82
           G   +I K  +P  L
Sbjct: 100 GADGFIPKSADPQVL 114

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

 Score = 78.2 bits (193), Expect = 7e-16
 Identities = 21/85 (24%), Positives = 42/85 (49%), Gaps = 3/85 (3%)

Query: 1   VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMSSDDRE 58
              + P +A+A    Q    +++ DL MP ++G+ L      N     +P++V+S+ +  
Sbjct: 47  HFCSDPQQAVAVAN-QIKPTVILQDLVMPGVDGLTLLAAYRGNPATRDIPIIVLSTKEEP 105

Query: 59  SVIMKALASGVAFYILKPLNPDDLK 83
           +V   A A+G   Y++K  +  +L 
Sbjct: 106 TVKSAAFAAGANDYLVKLPDAIELV 130

>3h1g_A Chemotaxis protein CHEY homolog; sulfate-bound CHEY, cytoplasm, flagellar rotatio magnesium, metal-binding, phosphoprotein; 1.70A {Helicobacter pylori} PDB: 3gwg_A 3h1e_A 3h1f_A Length = 129

 Score = 72.9 bits (180), Expect = 8e-16
 Identities = 27/79 (34%), Positives = 51/79 (64%), Gaps = 2/79 (2%)

Query: 7   VEALATVRIQRDIDLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMSSDDRESVIMKA 64
           VEA   +    D  +++TD +MPEMNG++L K++  +  F  +P+++++++  ++ ++ A
Sbjct: 40  VEAWEKLDANADTKVLITDWNMPEMNGLDLVKKVRSDSRFKEIPIIMITAEGGKAEVITA 99

Query: 65  LASGVAFYILKPLNPDDLK 83
           L +GV  YI+KP  P  LK
Sbjct: 100 LKAGVNNYIVKPFTPQVLK 118

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

 Score = 72.5 bits (179), Expect = 9e-16
 Identities = 29/96 (30%), Positives = 53/96 (55%), Gaps = 7/96 (7%)

Query: 2   TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMS--SDDRES 59
           T     E LA +   +  D++++D+ MP M+G+ L K+I +    LPV++M+  SD   +
Sbjct: 32  TFENGNEVLAALA-SKTPDVLLSDIRMPGMDGLALLKQIKQRHPMLPVIIMTAHSDLDAA 90

Query: 60  VIMKALASGVAF-YILKPLNPDDLKNVWQYAMTYKK 94
           V   A   G AF Y+ KP + D+   + + A+++ +
Sbjct: 91  V--SAYQQG-AFDYLPKPFDIDEAVALVERAISHYQ 123

>3ilh_A Two component response regulator; NYSGXRC, PSI-II, protein S initiative, structural genomics; 2.59A {Cytophaga hutchinsonii} Length = 146

 Score = 73.2 bits (180), Expect = 1e-15
 Identities = 21/94 (22%), Positives = 36/94 (38%), Gaps = 9/94 (9%)

Query: 1   VTVTRPVEALATVRIQRDI----DLVVTDLHMPEMNGIELQKEI----NEEFTHLPV-MV 51
            +VT    A+  +           ++  D++MP +NG EL                V ++
Sbjct: 39  QSVTSGNAAINKLNELYAAGRWPSIICIDINMPGINGWELIDLFKQHFQPMKNKSIVCLL 98

Query: 52  MSSDDRESVIMKALASGVAFYILKPLNPDDLKNV 85
            SS D         +  V +Y+ KPL  + L N+
Sbjct: 99  SSSLDPRDQAKAEASDWVDYYVSKPLTANALNNL 132

>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 = 77.9 bits (192), Expect = 1e-15
 Identities = 20/85 (23%), Positives = 44/85 (51%), Gaps = 3/85 (3%)

Query: 1   VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMSSDDRE 58
            T      ALA    +   D+++ D+ MP M+G  + +++  +    H+PV+++++ D  
Sbjct: 29  STAMDGPTALAMAA-RDLPDIILLDVMMPGMDGFTVCRKLKDDPTTRHIPVVLITALDGR 87

Query: 59  SVIMKALASGVAFYILKPLNPDDLK 83
              ++ L SG + ++ KP++   L 
Sbjct: 88  GDRIQGLESGASDFLTKPIDDVMLF 112

>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 = 76.4 bits (188), Expect = 5e-15
 Identities = 20/84 (23%), Positives = 35/84 (41%), Gaps = 2/84 (2%)

Query: 2   TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMSSDDRES 59
            V       A +     +DLV+ +      +G+     +   E    LPV+ M   D   
Sbjct: 178 PVIESDPEKAKISAGGPVDLVIVNAAAKNFDGLRFTAALRSEERTRQLPVLAMVDPDDRG 237

Query: 60  VIMKALASGVAFYILKPLNPDDLK 83
            ++KAL  GV   + +P++P +L 
Sbjct: 238 RMVKALEIGVNDILSRPIDPQELS 261

>1i3c_A Response regulator RCP1; phytochrome, signaling protein; 1.90A {Synechocystis SP} SCOP: c.23.1.1 PDB: 1jlk_A Length = 149

 Score = 72.7 bits (179), Expect = 2e-15
 Identities = 22/94 (23%), Positives = 48/94 (51%), Gaps = 12/94 (12%)

Query: 7   VEALATVRIQRDI------DLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMSSDDRE 58
           + A+A ++ Q +       +L++ DL++P+ +G E+  EI  N +   +PV+V+++   E
Sbjct: 44  LAAMAFLQQQGEYENSPRPNLILLDLNLPKKDGREVLAEIKQNPDLKRIPVVVLTTSHNE 103

Query: 59  SVIMKALASGVAFYILKPLNPDDL----KNVWQY 88
             ++ +    V  Y+ K  N  DL    + +  +
Sbjct: 104 DDVIASYELHVNCYLTKSRNLKDLFKMVQGIESF 137

>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 Length = 129

 Score = 72.2 bits (178), Expect = 2e-15
 Identities = 17/79 (21%), Positives = 39/79 (49%), Gaps = 3/79 (3%)

Query: 7   VEALATVRIQRDIDLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMSSDDRESVIMKA 64
            + +  +  Q    LV++D +MP+M+G+ L + +  N        +++++    +++ KA
Sbjct: 41  EQGMKIMA-QNPHHLVISDFNMPKMDGLGLLQAVRANPATKKAAFIILTAQGDRALVQKA 99

Query: 65  LASGVAFYILKPLNPDDLK 83
            A G    + KP   + +K
Sbjct: 100 AALGANNVLAKPFTIEKMK 118

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

 Score = 71.8 bits (177), Expect = 3e-15
 Identities = 18/80 (22%), Positives = 40/80 (50%), Gaps = 5/80 (6%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSS-DDRESVIMKALA 66
           +A+  +  +    L++ DL +P+M+G ++   IN+      V++ ++    +  +   + 
Sbjct: 39  DAIQFIE-RSKPQLIILDLKLPDMSGEDVLDWINQNDIPTSVIIATAHGSVDLAV-NLIQ 96

Query: 67  SGVAF-YILKPLNPDDLKNV 85
            G A  ++ KP+N D LK  
Sbjct: 97  KG-AEDFLEKPINADRLKTS 115

>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 = 73.5 bits (181), Expect = 4e-15
 Identities = 18/75 (24%), Positives = 39/75 (52%), Gaps = 1/75 (1%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
             L   R ++    +V D+ MP M+GIELQ+++      +P++ +++     + ++A+ +
Sbjct: 39  TFLEHRRPEQH-GCLVLDMRMPGMSGIELQEQLTAISDGIPIVFITAHGDIPMTVRAMKA 97

Query: 68  GVAFYILKPLNPDDL 82
           G   ++ KP     L
Sbjct: 98  GAIEFLPKPFEEQAL 112

>3heb_A Response regulator receiver domain protein (CHEY); NYSGXRC, PSI-II, respose regulator, structure initiative, structural genomics; 2.40A {Rhodospirillum rubrum} Length = 152

 Score = 72.0 bits (177), Expect = 4e-15
 Identities = 22/96 (22%), Positives = 43/96 (44%), Gaps = 14/96 (14%)

Query: 7   VEALATVRIQRD--------IDLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMSSDD 56
             AL  +               LV+ DL++P+M GI++ K +  N      PV+++++ D
Sbjct: 40  TSALNYLFGDDKSGRVSAGRAQLVLLDLNLPDMTGIDILKLVKENPHTRRSPVVILTTTD 99

Query: 57  RESVIMKALASGVAFYILKPLNPDDL----KNVWQY 88
            +  I +    G   YI KP+N ++     + +  +
Sbjct: 100 DQREIQRCYDLGANVYITKPVNYENFANAIRQLGLF 135

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

 Score = 71.4 bits (176), Expect = 5e-15
 Identities = 27/90 (30%), Positives = 49/90 (54%), Gaps = 9/90 (10%)

Query: 1   VTVTRPVEALATVRIQ-RDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSS-DDRE 58
           +T +   E L         ID+V+TD+ MP+++G+++ +EI +   H+ V++++   D +
Sbjct: 31  LTASSSTEGLRIFTENCNSIDVVITDMKMPKLSGMDILREIKKITPHMAVIILTGHGDLD 90

Query: 59  SVI--MKALASGVAF-YILKPLNPDDLKNV 85
           + I  MK    G AF Y+ KP+   DL   
Sbjct: 91  NAILAMKE---G-AFEYLRKPVTAQDLSIA 116

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

 Score = 71.1 bits (175), Expect = 6e-15
 Identities = 26/77 (33%), Positives = 39/77 (50%), Gaps = 4/77 (5%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
           EA   +R +  IDLV  D+       + L + I EEF    V V+S+   + +I+ ++ +
Sbjct: 39  EAFTFLR-REKIDLVFVDV-FEGEESLNLIRRIREEFPDTKVAVLSAYVDKDLIINSVKA 96

Query: 68  GVAF-YILKPLNPDDLK 83
           G A  YILKP   D L 
Sbjct: 97  G-AVDYILKPFRLDYLL 112

>1s8n_A Putative antiterminator; RV1626, structural genomics, transcriptional antiterminator, component system, PSI; 1.48A {Mycobacterium tuberculosis} SCOP: c.23.1.1 PDB: 1sd5_A Length = 205

 Score = 72.0 bits (177), Expect = 1e-14
 Identities = 21/78 (26%), Positives = 42/78 (53%), Gaps = 2/78 (2%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
           EA+    + +  DLV+ D+ MP  +GI+   EI  +    P++V+++  +  ++ +A  +
Sbjct: 49  EAVELAELHKP-DLVIMDVKMPRRDGIDAASEIASKR-IAPIVVLTAFSQRDLVERARDA 106

Query: 68  GVAFYILKPLNPDDLKNV 85
           G   Y++KP +  DL   
Sbjct: 107 GAMAYLVKPFSISDLIPA 124

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

 Score = 74.2 bits (182), Expect = 2e-14
 Identities = 24/82 (29%), Positives = 43/82 (52%), Gaps = 1/82 (1%)

Query: 1   VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESV 60
           +     ++ L         DLV+ DL MP+++G+EL + I +  +  P++V+S     S 
Sbjct: 33  LQALNGLQGLQIFE-SEQPDLVICDLRMPQIDGLELIRRIRQTASETPIIVLSGAGVMSD 91

Query: 61  IMKALASGVAFYILKPLNPDDL 82
            ++AL  G A Y++KPL    +
Sbjct: 92  AVEALRLGAADYLIKPLEDLAV 113

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

 Score = 74.0 bits (183), Expect = 2e-14
 Identities = 22/99 (22%), Positives = 53/99 (53%), Gaps = 5/99 (5%)

Query: 1   VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSS-DDRES 59
            +  R  EA   +  ++  ++V+ DL +P++NG+E+ K I E      V+V++     ++
Sbjct: 28  ESAERGKEAYKLLS-EKHFNVVLLDLLLPDVNGLEILKWIKERSPETEVIVITGHGTIKT 86

Query: 60  VIMKALASGVAF-YILKPLNPDDLKNVWQYAMTYKKAKS 97
            + +A+  G A+ ++ KP   ++++     A+ ++K + 
Sbjct: 87  AV-EAMKMG-AYDFLTKPCMLEEIELTINKAIEHRKLRK 123

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

 Score = 73.7 bits (182), Expect = 2e-14
 Identities = 20/99 (20%), Positives = 44/99 (44%), Gaps = 5/99 (5%)

Query: 1   VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSS-DDRES 59
            T     EA   ++ +    ++V D+ MP+ +G+     I E      V+V++     ++
Sbjct: 28  DTAKTLREAEKKIK-ELFFPVIVLDVWMPDGDGVNFIDFIKENSPDSVVIVITGHGSVDT 86

Query: 60  VIMKALASGVAF-YILKPLNPDDLKNVWQYAMTYKKAKS 97
            + KA+  G A+ ++ KP + +      ++A      K+
Sbjct: 87  AV-KAIKKG-AYEFLEKPFSVERFLLTIKHAFEEYSKKA 123

>3b2n_A Uncharacterized protein Q99UF4; structural genomics, PSI-2, protein structure initiative, NE SGX research center for structural genomics; 2.04A {Staphylococcus aureus} Length = 133

 Score = 67.9 bits (167), Expect = 6e-14
 Identities = 19/75 (25%), Positives = 43/75 (57%), Gaps = 1/75 (1%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
           +A+  +      ++V+ D+ MP M G+E+  EI ++  ++ V+++++  R     KA+ +
Sbjct: 40  DAMKLIEEYN-PNVVILDIEMPGMTGLEVLAEIRKKHLNIKVIIVTTFKRPGYFEKAVVN 98

Query: 68  GVAFYILKPLNPDDL 82
            V  Y+LK  + ++L
Sbjct: 99  DVDAYVLKERSIEEL 113

>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 Length = 155

 Score = 67.6 bits (166), Expect = 1e-13
 Identities = 24/88 (27%), Positives = 44/88 (50%), Gaps = 7/88 (7%)

Query: 1   VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMS--SDDRE 58
            +     EALA +       +V++D+ MP M+G+ L ++I      LP+++++   D   
Sbjct: 31  SSFASATEALAGLS-ADFAGIVISDIRMPGMDGLALFRKILALDPDLPMILVTGHGDIPM 89

Query: 59  SVIMKALASGVAF-YILKPLNPDDLKNV 85
           +V  +A+  G A+ +I KP   D L   
Sbjct: 90  AV--QAIQDG-AYDFIAKPFAADRLVQS 114

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

 Score = 66.8 bits (164), Expect = 1e-13
 Identities = 19/83 (22%), Positives = 36/83 (43%), Gaps = 10/83 (12%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMS---SDDRESVIM 62
           +AL  +   R  D V  DL++P+ +G+ L K++           + +S    +D      
Sbjct: 38  DALHAMS-TRGYDAVFIDLNLPDTSGLALVKQLRALPMEKTSKFVAVSGFAKNDLG---- 92

Query: 63  KALASGVAFYILKPLNPDDLKNV 85
           K       FY+ KP++   L+ +
Sbjct: 93  KEACELFDFYLEKPIDIASLEPI 115

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

 Score = 66.8 bits (163), Expect = 2e-13
 Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 8   EALATVRIQR-DIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALA 66
           EA+   +    +ID+V   + MP+M+GI     I E   +  V+++S+  +E ++   L 
Sbjct: 72  EAVIKYKNHYPNIDIVTLXITMPKMDGITCLSNIMEFDKNARVIMISALGKEQLVKDCLI 131

Query: 67  SGVAFYILKPLNPDDL 82
            G   +I+KPL+   +
Sbjct: 132 KGAKTFIVKPLDRAKV 147

>1dz3_A Stage 0 sporulation protein A; response regulator, domain swapping; 1.65A {Bacillus stearothermophilus} SCOP: c.23.1.1 PDB: 1qmp_A* Length = 130

 Score = 66.0 bits (162), Expect = 2e-13
 Identities = 22/77 (28%), Positives = 47/77 (61%), Gaps = 2/77 (2%)

Query: 7   VEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLP-VMVMSSDDRESVIMKAL 65
            + L  +  +R  D+++ D+ MP ++G+ + + I   F H P V+++++  +E V  KA+
Sbjct: 38  QDCLQMLEEKR-PDILLLDIIMPHLDGLAVLERIRAGFEHQPNVIMLTAFGQEDVTKKAV 96

Query: 66  ASGVAFYILKPLNPDDL 82
             G +++ILKP + ++L
Sbjct: 97  ELGASYFILKPFDMENL 113

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

 Score = 66.1 bits (162), Expect = 3e-13
 Identities = 14/76 (18%), Positives = 32/76 (42%), Gaps = 3/76 (3%)

Query: 8   EALATVRIQRDIDLVVTDLHMPE-MNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALA 66
           +A+  ++    ID VVTD+   +  +G ++ +   E   ++P++ +S           + 
Sbjct: 40  KAIEMLKSGAAIDGVVTDIRFCQPPDGWQVARVAREIDPNMPIVYISGHAALEWASNGVP 99

Query: 67  SGVAFYILKPLNPDDL 82
             +   + KP     L
Sbjct: 100 DSI--ILEKPFTSAQL 113

>3crn_A Response regulator receiver domain protein, CHEY-; structural genomics, signal regulator receiver domain; HET: PHD; 1.58A {Methanospirillum hungatei jf-1} Length = 132

 Score = 64.8 bits (158), Expect = 6e-13
 Identities = 19/76 (25%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
           E LA +      +L +  + +P+M G EL ++ ++    +  ++++        + +L +
Sbjct: 38  EGLAKIE-NEFFNLALFXIKLPDMEGTELLEKAHKLRPGMKKIMVTGYASLENSVFSLNA 96

Query: 68  GVAFYILKPLNPDDLK 83
           G   YI+KP+NP DL 
Sbjct: 97  GADAYIMKPVNPRDLL 112

>3cnb_A DNA-binding response regulator, MERR family; signal receiver domain, DNA binding protein, protein structu initiative, PSI-2; 2.00A {Colwellia psychrerythraea} Length = 143

 Score = 64.9 bits (159), Expect = 7e-13
 Identities = 18/78 (23%), Positives = 33/78 (42%), Gaps = 3/78 (3%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMSSDDRESVIMKAL 65
           +A   +      D+V+ DL M  M+G  +   I       ++ V+ M+    +  + + +
Sbjct: 45  DAGDLLH-TVKPDVVMLDLMMVGMDGFSICHRIKSTPATANIIVIAMTGALTDDNVSRIV 103

Query: 66  ASGVAFYILKPLNPDDLK 83
           A G      KPLN   L+
Sbjct: 104 ALGAETCFGKPLNFTLLE 121

>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* Length = 126

 Score = 64.4 bits (158), Expect = 8e-13
 Identities = 23/84 (27%), Positives = 43/84 (51%), Gaps = 7/84 (8%)

Query: 2   TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMS--SDDRES 59
                   LA     R+  ++VTDL MP+M+G+EL + + +   ++P +V++   D   +
Sbjct: 32  MHQSAEAFLAFAPDVRN-GVLVTDLRMPDMSGVELLRNLGDLKINIPSIVITGHGDVPMA 90

Query: 60  VIMKALASGVAF-YILKPLNPDDL 82
           V  +A+ +G A  +I KP     +
Sbjct: 91  V--EAMKAG-AVDFIEKPFEDTVI 111

>3f6c_A Positive transcription regulator EVGA; structural genomics, PSI-2, protein structure initiative, PO transcription regulator EVGA; 1.45A {Escherichia coli k-12} Length = 134

 Score = 64.4 bits (158), Expect = 9e-13
 Identities = 12/75 (16%), Positives = 35/75 (46%), Gaps = 1/75 (1%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
            A+  V      D+V+ D+ +P +NGI++ + + +      ++++S+ +          +
Sbjct: 37  SAVQRVE-TLKPDIVIIDVDIPGVNGIQVLETLRKRQYSGIIIIVSAKNDHFYGKHCADA 95

Query: 68  GVAFYILKPLNPDDL 82
           G   ++ K    +++
Sbjct: 96  GANGFVSKKEGMNNI 110

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

 Score = 64.1 bits (157), Expect = 1e-12
 Identities = 21/84 (25%), Positives = 42/84 (50%), Gaps = 11/84 (13%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMS----SDDRESVI 61
            AL+  R +   DL++ D+ +PE++G+E+ K +  +++  H+PV+ ++      D E   
Sbjct: 36  SALSIAR-ENKPDLILMDIQLPEISGLEVTKWLKEDDDLAHIPVVAVTAFAMKGDEE--- 91

Query: 62  MKALASGVAFYILKPLNPDDLKNV 85
            +    G   YI KP++       
Sbjct: 92  -RIREGGCEAYISKPISVVHFLET 114

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

 Score = 67.1 bits (164), Expect = 1e-12
 Identities = 23/83 (27%), Positives = 47/83 (56%), Gaps = 9/83 (10%)

Query: 7   VEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMS----SDDRESVIM 62
           V+AL  +  +  ID+V++D++MP M+G  L + I +    LPV+ ++    +++++    
Sbjct: 163 VDALNVLS-KNHIDIVLSDVNMPNMDGYRLTQRIRQLGLTLPVIGVTANALAEEKQ---- 217

Query: 63  KALASGVAFYILKPLNPDDLKNV 85
           + L SG+   + KP+  D +K  
Sbjct: 218 RCLESGMDSCLSKPVTLDVIKQT 240

>3cg0_A Response regulator receiver modulated diguanylate with PAS/PAC sensor; signal receiver domain, diguanylate cyclase; 2.15A {Desulfovibrio desulfuricans subsp} Length = 140

 Score = 63.7 bits (156), Expect = 2e-12
 Identities = 15/77 (19%), Positives = 32/77 (41%), Gaps = 3/77 (3%)

Query: 8   EALATVRIQRDIDLVVTDLHM-PEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALA 66
           EA+         D+ + D+ +   ++G+E    +     +LP++ ++S        +A  
Sbjct: 45  EAVRCAP-DLRPDIALVDIMLCGALDGVETAARLAAGC-NLPIIFITSSQDVETFQRAKR 102

Query: 67  SGVAFYILKPLNPDDLK 83
                Y+ KP+  D L 
Sbjct: 103 VNPFGYLAKPVAADTLH 119

>3lua_A Response regulator receiver protein; two-component signal transduction system, histidine kinase, phosphorelay, receiver domain, nysgxrc; 2.40A {Clostridium thermocellum} Length = 140

 Score = 63.5 bits (155), Expect = 2e-12
 Identities = 21/79 (26%), Positives = 35/79 (44%), Gaps = 3/79 (3%)

Query: 8   EALATVRIQRDIDLVVTDLHMP-EMNGIELQKEI--NEEFTHLPVMVMSSDDRESVIMKA 64
           +  +  +    I L++ D+  P E  G+E+   I  N    + PV++ +  D       A
Sbjct: 40  KFYSIFKDLDSITLIIMDIAFPVEKEGLEVLSAIRNNSRTANTPVIIATKSDNPGYRHAA 99

Query: 65  LASGVAFYILKPLNPDDLK 83
           L   V+ YILKP     L+
Sbjct: 100 LKFKVSDYILKPYPTKRLE 118

>3eqz_A Response regulator; structural genomics, unknown function, PSI-2, protein struct initiative; 2.15A {Colwellia psychrerythraea} Length = 135

 Score = 62.6 bits (153), Expect = 4e-12
 Identities = 20/87 (22%), Positives = 39/87 (44%), Gaps = 6/87 (6%)

Query: 1   VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESV 60
           V   +   A  T+      D+++ DL MP+M+GIE+ + + E  +   ++++S  D   +
Sbjct: 30  VEAFQHPRAFLTLS-LNKQDIIILDLMMPDMDGIEVIRHLAEHKSPASLILISGYDSGVL 88

Query: 61  IM-----KALASGVAFYILKPLNPDDL 82
                   +    V     KP+N + L
Sbjct: 89  HSAETLALSCGLNVINTFTKPINTEVL 115

>3h5i_A Response regulator/sensory box protein/ggdef domain protein; structural genomics, transcription, PSI-2; 1.90A {Carboxydothermus hydrogenoformans z-2901} Length = 140

 Score = 63.0 bits (154), Expect = 4e-12
 Identities = 17/76 (22%), Positives = 35/76 (46%), Gaps = 2/76 (2%)

Query: 8   EALATVRIQRDIDLVVTDLHMPE-MNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALA 66
            A+  V      DL++ D+ + E M+G++    I +    LPV+ +++    +V+ K  +
Sbjct: 40  AAVEKVSGGWYPDLILMDIELGEGMDGVQTALAIQQIS-ELPVVFLTAHTEPAVVEKIRS 98

Query: 67  SGVAFYILKPLNPDDL 82
                Y++K      L
Sbjct: 99  VTAYGYVMKSATEQVL 114

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

 Score = 62.6 bits (153), Expect = 5e-12
 Identities = 21/86 (24%), Positives = 39/86 (45%), Gaps = 13/86 (15%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEI----NEEFTHLPVMVMS----SDDRES 59
           + L  +  + D D V+ DLHMP MNG+++ K++         + PV+V+S     +    
Sbjct: 49  QVLDAMA-EEDYDAVIVDLHMPGMNGLDMLKQLRVMQASGMRYTPVVVLSADVTPEAIR- 106

Query: 60  VIMKALASGVAFYILKPLNPDDLKNV 85
                  +G   ++ KP+    L + 
Sbjct: 107 ---ACEQAGARAFLAKPVVAAKLLDT 129

>2qr3_A Two-component system response regulator; structural genomics, signal receiver, PSI-2, protein structu initiative; 1.80A {Bacteroides fragilis} Length = 140

 Score = 62.6 bits (153), Expect = 5e-12
 Identities = 20/103 (19%), Positives = 47/103 (45%), Gaps = 10/103 (9%)

Query: 1   VTVTRPVEALATVRIQRDIDLVVTDLHMPE-----MNGIELQKEINEEFTHLPVMVMSS- 54
           +T++ PV     +R + + ++V+ D++          G+    EI  ++  LPV++ ++ 
Sbjct: 31  ITLSSPVSLSTVLR-EENPEVVLLDMNFTSGINNGNEGLFWLHEIKRQYRDLPVVLFTAY 89

Query: 55  DDRESVIMKALASGVAF-YILKPLNPDDLKNVWQYAMTYKKAK 96
            D +  + + +  G A  +++KP +   L      A +  K  
Sbjct: 90  ADIDLAV-RGIKEG-ASDFVVKPWDNQKLLETLLNAASQAKDG 130

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

 Score = 61.8 bits (151), Expect = 6e-12
 Identities = 25/72 (34%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
           +AL  +      DL++ D+ MP MNG++L + I       PV+V+S+ +  + I KAL  
Sbjct: 42  DALELLG-GFTPDLMICDIAMPRMNGLKLLEHIRNRGDQTPVLVISATENMADIAKALRL 100

Query: 68  GVAFYILKPLNP 79
           GV   +LKP+  
Sbjct: 101 GVEDVLLKPVKD 112

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

 Score = 61.5 bits (150), Expect = 9e-12
 Identities = 11/75 (14%), Positives = 27/75 (36%), Gaps = 1/75 (1%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
                        +V+ DL   ++ G     E    +  +P++ +S +         +  
Sbjct: 50  FLKGPPA-DTRPGIVILDLGGGDLLGKPGIVEARALWATVPLIAVSDELTSEQTRVLVRM 108

Query: 68  GVAFYILKPLNPDDL 82
             + ++ KPL+  +L
Sbjct: 109 NASDWLHKPLDGKEL 123

>4e7p_A Response regulator; DNA binding, cytosol, transcription regulator; 1.89A {Streptococcus pneumoniae} PDB: 4e7o_A Length = 150

 Score = 61.8 bits (151), Expect = 1e-11
 Identities = 21/75 (28%), Positives = 40/75 (53%), Gaps = 1/75 (1%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
           EA+  +  +  +D+ + D+ MP   G+E+ + I  E     V+V+++  R     +A+ +
Sbjct: 57  EAIQLLEKES-VDIAILDVEMPVKTGLEVLEWIRSEKLETKVVVVTTFKRAGYFERAVKA 115

Query: 68  GVAFYILKPLNPDDL 82
           GV  Y+LK  +  DL
Sbjct: 116 GVDAYVLKERSIADL 130

>3grc_A Sensor protein, kinase; protein structure initiative II(PSI II), NYSGXRC, 11025B, structural genomics; 2.21A {Polaromonas SP} Length = 140

 Score = 61.4 bits (150), Expect = 1e-11
 Identities = 17/79 (21%), Positives = 40/79 (50%), Gaps = 6/79 (7%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMS--SDDRESVIMK 63
           +AL  V  +R    +  DL++P+ +G+ L + +  +     L ++V+S  + + E     
Sbjct: 41  QALEQVA-RRPYAAMTVDLNLPDQDGVSLIRALRRDSRTRDLAIVVVSANAREGELEF-N 98

Query: 64  ALASGVAFYILKPLNPDDL 82
           +    V+ ++ KP++ + L
Sbjct: 99  SQPLAVSTWLEKPIDENLL 117

>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} Length = 144

 Score = 60.7 bits (148), Expect = 2e-11
 Identities = 19/81 (23%), Positives = 37/81 (45%), Gaps = 11/81 (13%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVM----SSDDRESVI 61
           +AL  V+ Q   DL++ D+ +P  NG E+   +       H P++++    S D  +   
Sbjct: 42  KALYQVQ-QAKYDLIILDIGLPIANGFEVMSAVRKPGANQHTPIVILTDNVSDDRAK--- 97

Query: 62  MKALASGVAFYILKPLNPDDL 82
            + +A+G +  + K  N    
Sbjct: 98  -QCMAAGASSVVDKSSNNVTD 117

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

 Score = 59.9 bits (146), Expect = 4e-11
 Identities = 17/87 (19%), Positives = 39/87 (44%), Gaps = 15/87 (17%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIEL-----QKEINEEFTHLPVMVMS----SDDRE 58
           E L  V    +  +V  D+ MP +   ++     +K   +      ++ +S       +E
Sbjct: 42  ECLRVV--SHEHKVVFMDVCMPGVENYQIALRIHEKFTKQRHQRPLLVALSGNTDKSTKE 99

Query: 59  SVIMKALASGVAFYILKPLNPDDLKNV 85
               K ++ G+   +LKP++ D++++V
Sbjct: 100 ----KCMSFGLDGVLLKPVSLDNIRDV 122

>3kyj_B CHEY6 protein, putative histidine protein kinase; protein-protein interaction, histidine kinase, response regulator, phosphorylation; 1.40A {Rhodobacter sphaeroides} PDB: 3kyi_B* Length = 145

 Score = 59.5 bits (145), Expect = 6e-11
 Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 3/73 (4%)

Query: 6   PVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRE--SVIMK 63
             EAL  +  Q ++DL++ D+ MP M+G+E  +    +     + ++SS          +
Sbjct: 48  GQEALDKLAAQPNVDLILLDIEMPVMDGMEFLRHAKLKT-RAKICMLSSVAVSGSPHAAR 106

Query: 64  ALASGVAFYILKP 76
           A   G    + KP
Sbjct: 107 ARELGADGVVAKP 119

>3nhm_A Response regulator; protein structure initiative II(PSI II), NYSGXRC, structural genomics; 2.19A {Myxococcus xanthus} Length = 133

 Score = 59.1 bits (144), Expect = 7e-11
 Identities = 17/78 (21%), Positives = 31/78 (39%), Gaps = 4/78 (5%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMSSDDRESVIMKAL 65
             L         D++++D++M  M+G  L           H+PV+ +S     +    A 
Sbjct: 38  SGLQQAL-AHPPDVLISDVNMDGMDGYALCGHFRSEPTLKHIPVIFVSGYAPRTEG-PAD 95

Query: 66  ASGVAFYILKPLNPDDLK 83
                 Y++KP+ P  L 
Sbjct: 96  QPVPDAYLVKPVKPPVLI 113

>3n0r_A Response regulator; sigma factor, receiver, two-component SI transduction, signaling protein; HET: MSE GOL; 1.25A {Caulobacter vibrioides} PDB: 3t0y_A Length = 286

 Score = 61.3 bits (149), Expect = 1e-10
 Identities = 21/78 (26%), Positives = 36/78 (46%), Gaps = 7/78 (8%)

Query: 8   EALATVRIQRDIDLVVTDLHMP-EMNGIELQKEINEEFTHLPV-MVMSSDDRESVIMKAL 65
           EAL  V  +R   LV+ D+ +    +GI+  K+I      +PV  + +  +R   ++   
Sbjct: 196 EALEAVT-RRTPGLVLADIQLADGSSGIDAVKDILGRM-DVPVIFITAFPER---LLTGE 250

Query: 66  ASGVAFYILKPLNPDDLK 83
                F I KP  P+ +K
Sbjct: 251 RPEPTFLITKPFQPETVK 268

>1qo0_D AMIR; binding protein, gene regulator, receptor; 2.25A {Pseudomonas aeruginosa} SCOP: c.23.1.3 Length = 196

 Score = 60.1 bits (145), Expect = 1e-10
 Identities = 12/104 (11%), Positives = 31/104 (29%), Gaps = 6/104 (5%)

Query: 6   PVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKAL 65
           P EA         +D+V T +     +                ++ +   +  +V+ + +
Sbjct: 45  PPEAFDV-----PVDVVFTSIFQNRHHDEIAALLAAGT-PRTTLVALVEYESPAVLSQII 98

Query: 66  ASGVAFYILKPLNPDDLKNVWQYAMTYKKAKSISIDEIGSFELA 109
                  I +PL+   +  V   A    +  +    +    +  
Sbjct: 99  ELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQDR 142

>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 = 59.6 bits (145), Expect = 1e-10
 Identities = 14/75 (18%), Positives = 32/75 (42%), Gaps = 1/75 (1%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
           EAL         + +   LH+   +G+ L   + +      ++V++     +  ++A+  
Sbjct: 42  EALKLAG-AEKFEFITVXLHLGNDSGLSLIAPLCDLQPDARILVLTGYASIATAVQAVKD 100

Query: 68  GVAFYILKPLNPDDL 82
           G   Y+ KP N + +
Sbjct: 101 GADNYLAKPANVESI 115

>3cz5_A Two-component response regulator, LUXR family; structural genomics, protein structure initiative; 2.70A {Aurantimonas SP} Length = 153

 Score = 58.7 bits (143), Expect = 2e-10
 Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 1/75 (1%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
           EA    R +   D+VV DL +P   GIE  + I +      +++ +     +  +KA  +
Sbjct: 42  EAYRLYR-ETTPDIVVMDLTLPGPGGIEATRHIRQWDGAARILIFTMHQGSAFALKAFEA 100

Query: 68  GVAFYILKPLNPDDL 82
           G + Y+ K  +P +L
Sbjct: 101 GASGYVTKSSDPAEL 115

>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 Length = 140

 Score = 57.2 bits (138), Expect = 4e-10
 Identities = 25/94 (26%), Positives = 46/94 (48%), Gaps = 12/94 (12%)

Query: 7   VEALATVRIQRDI------DLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMSSDDRE 58
           +EA+A +R + +       DL++  L++P+ +G E+  EI  +     +PV+V+S+   E
Sbjct: 38  MEAMAYLRQEGEYANASRPDLILLXLNLPKKDGREVLAEIKSDPTLKRIPVVVLSTSINE 97

Query: 59  SVIMKALASGVAFYILKPLNPDDL----KNVWQY 88
             I  +    V  YI K  N   L    K + ++
Sbjct: 98  DDIFHSYDLHVNCYITKSANLSQLFQIVKGIEEF 131

>3kto_A Response regulator receiver protein; PSI-II,structural genomics, protein structure initiative; 1.98A {Pseudoalteromonas atlantica T6C} Length = 136

 Score = 56.8 bits (138), Expect = 5e-10
 Identities = 20/80 (25%), Positives = 37/80 (46%), Gaps = 9/80 (11%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEM--NGIELQKEINEEFTHLPVMVMS--SDDRESVIMK 63
             +       D   ++ + H+ +   +GIEL + + +   HLP +VM+  SD   +V  +
Sbjct: 41  SFMRQQI-SDDAIGMIIEAHLEDKKDSGIELLETLVKRGFHLPTIVMASSSDIPTAV--R 97

Query: 64  ALASGVAF-YILKPLNPDDL 82
           A+ +  A  +I KP     L
Sbjct: 98  AMRAS-AADFIEKPFIEHVL 116

>3n53_A Response regulator receiver modulated diguanylate; diguanylate cyclase, protein structure I II(PSI II), NYSGXRC, structural genomics; 2.20A {Pelobacter carbinolicus} Length = 140

 Score = 56.8 bits (138), Expect = 5e-10
 Identities = 21/77 (27%), Positives = 40/77 (51%), Gaps = 3/77 (3%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMSSDDRESVIMKAL 65
           EAL  +      DLV+ D+ +   N   L  ++  ++   ++P++++ S + +  I+  L
Sbjct: 37  EALEQID-HHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGL 95

Query: 66  ASGVAFYILKPLNPDDL 82
            SG   Y+ KP N +DL
Sbjct: 96  HSGADDYLTKPFNRNDL 112

>3eul_A Possible nitrate/nitrite response transcriptional regulatory protein NARL (DNA-binding...; central beta strand flanked by alpha helices; 1.90A {Mycobacterium tuberculosis} Length = 152

 Score = 56.4 bits (137), Expect = 1e-09
 Identities = 17/75 (22%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
            AL  ++     D+ + D  MP M+G ++   +        V+++S+ D  +++ +AL  
Sbjct: 52  AALELIKAHLP-DVALLDYRMPGMDGAQVAAAVRSYELPTRVLLISAHDEPAIVYQALQQ 110

Query: 68  GVAFYILKPLNPDDL 82
           G A ++LK     ++
Sbjct: 111 GAAGFLLKDSTRTEI 125

>3gt7_A Sensor protein; structural genomics, signal receiver domain, kinase, PSI-2, protein structure initiative; 2.30A {Syntrophus aciditrophicus SB} Length = 154

 Score = 56.1 bits (136), Expect = 1e-09
 Identities = 21/78 (26%), Positives = 40/78 (51%), Gaps = 5/78 (6%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMSS-DDRESVIMKA 64
           EA+  +      DL+++D+ MPEM+G  L + +    +   +PV++++   D   V+ ++
Sbjct: 42  EAVRFLS-LTRPDLIISDVLMPEMDGYALCRWLKGQPDLRTIPVILLTILSDPRDVV-RS 99

Query: 65  LASGVAFYILKPLNPDDL 82
           L  G   +I KP     L
Sbjct: 100 LECGADDFITKPCKDVVL 117

>3gl9_A Response regulator; beta-sheet, surrounded by alpha helices, BOTH sides, signaling protein; HET: BFD; 1.80A {Thermotoga maritima} PDB: 3dgf_C 3dge_C Length = 122

 Score = 54.4 bits (131), Expect = 2e-09
 Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 3/77 (3%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMSSDDRESVIMKAL 65
            AL  +  +   DL+V  + MP M+G  + K++   EE+  +PV+V+++   E     AL
Sbjct: 37  IALEKLS-EFTPDLIVLXIMMPVMDGFTVLKKLQEKEEWKRIPVIVLTAKGGEEDESLAL 95

Query: 66  ASGVAFYILKPLNPDDL 82
           + G    + KP +P   
Sbjct: 96  SLGARKVMRKPFSPSQF 112

>2zay_A Response regulator receiver protein; structural genomics, NYSGXRC, target 11006U, protein structure initiative; 2.00A {Desulfuromonas acetoxidans} Length = 147

 Score = 54.9 bits (133), Expect = 3e-09
 Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 3/77 (3%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMSSDDRESVIMKAL 65
           EA+     +    L++T+ +MP+++G++L   +  N +   +PV+ +S         + L
Sbjct: 43  EAVPVAV-KTHPHLIITEANMPKISGMDLFNSLKKNPQTASIPVIALSGRATAKEEAQLL 101

Query: 66  ASGVAFYILKPLNPDDL 82
             G   +I KP+N   L
Sbjct: 102 DMGFIDFIAKPVNAIRL 118

>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 Length = 133

 Score = 54.5 bits (132), Expect = 3e-09
 Identities = 17/87 (19%), Positives = 40/87 (45%), Gaps = 13/87 (14%)

Query: 8   EALATVR----IQRDIDLVVTDLHMPEMNGIELQKEI-NEEFTHLPVMVMS----SDDRE 58
           EA   V+       + +++  D+ MP+++G+   K I  +     P++ ++      + +
Sbjct: 38  EAFDKVKELTSKGENYNMIFMDVQMPKVDGLLSTKMIRRDLGYTSPIVALTAFADDSNIK 97

Query: 59  SVIMKALASGVAFYILKPLNPDDLKNV 85
               + L SG+  ++ KP+    LK +
Sbjct: 98  ----ECLESGMNGFLSKPIKRPKLKTI 120

>3t8y_A CHEB, chemotaxis response regulator protein-glutamate methylesterase; CHEA, hydrolase; 1.90A {Thermotoga maritima} Length = 164

 Score = 55.4 bits (134), Expect = 3e-09
 Identities = 22/73 (30%), Positives = 40/73 (54%), Gaps = 4/73 (5%)

Query: 6   PVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRE--SVIMK 63
            +EA+     +   D++  D+ MP +NGIE  K I ++     V+++SS   E  ++ ++
Sbjct: 60  GLEAVEKAI-ELKPDVITMDIEMPNLNGIEALKLIMKKAP-TRVIMVSSLTEEGAAITIE 117

Query: 64  ALASGVAFYILKP 76
           AL +G   +I KP
Sbjct: 118 ALRNGAVDFITKP 130

>3klo_A Transcriptional regulator VPST; REC domain, HTH domain, DNA-binding, transcription regulation; HET: C2E TAR; 2.80A {Vibrio cholerae} PDB: 3kln_A* Length = 225

 Score = 56.1 bits (136), Expect = 4e-09
 Identities = 7/76 (9%), Positives = 20/76 (26%), Gaps = 2/76 (2%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIE-LQKEINEEFTHLPVMVMSSDDRESVIMKALA 66
                    R I ++V D      + +       +        ++++        +    
Sbjct: 45  LEENKPE-SRSIQMLVIDYSRISDDVLTDYSSFKHISCPDAKEVIINCPQDIEHKLLFKW 103

Query: 67  SGVAFYILKPLNPDDL 82
           + +A       + D L
Sbjct: 104 NNLAGVFYIDDDMDTL 119

>3c3w_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 2.20A {Mycobacterium tuberculosis} Length = 225

 Score = 56.0 bits (136), Expect = 4e-09
 Identities = 21/75 (28%), Positives = 43/75 (57%), Gaps = 1/75 (1%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
           EA+A V   R  D+ V D+ +P+ NGIEL +++      L  ++++S   +  ++ A+ +
Sbjct: 38  EAMARVPAARP-DVAVLDVRLPDGNGIELCRDLLSRMPDLRCLILTSYTSDEAMLDAILA 96

Query: 68  GVAFYILKPLNPDDL 82
           G + Y++K +   +L
Sbjct: 97  GASGYVVKDIKGMEL 111

>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 Length = 215

 Score = 55.6 bits (135), Expect = 6e-09
 Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 1/75 (1%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
           + +         DL++ DL+MP MNG+E   ++ E+     ++V S  + E  ++ AL  
Sbjct: 42  QGIELAESLDP-DLILLDLNMPGMNGLETLDKLREKSLSGRIVVFSVSNHEEDVVTALKR 100

Query: 68  GVAFYILKPLNPDDL 82
           G   Y+LK + P+DL
Sbjct: 101 GADGYLLKDMEPEDL 115

>3c3m_A Response regulator receiver protein; structural genomics, unknown function, PSI-2, protein struct initiative; HET: MSE; 1.70A {Methanoculleus marisnigri JR1} Length = 138

 Score = 53.3 bits (129), Expect = 8e-09
 Identities = 20/77 (25%), Positives = 33/77 (42%), Gaps = 3/77 (3%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMSSDDRESVIMKAL 65
           E L  +      DLV+ D+ M  M+G E  + I  +     +PV+++++           
Sbjct: 38  ECLEALN-ATPPDLVLLDIMMEPMDGWETLERIKTDPATRDIPVLMLTAKPLTPEEANEY 96

Query: 66  ASGVAFYILKPLNPDDL 82
            S +  YILKP     L
Sbjct: 97  GSYIEDYILKPTTHHQL 113

>3r0j_A Possible two component system response transcript positive regulator PHOP; beta-alpha fold, winged helix-turn-helix; 2.50A {Mycobacterium tuberculosis} Length = 250

 Score = 54.7 bits (131), Expect = 1e-08
 Identities = 17/76 (22%), Positives = 36/76 (47%), Gaps = 1/76 (1%)

Query: 7   VEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALA 66
            +AL   R +   D V+ D+ MP M+G  + + +  +    P + +++ D     +  L 
Sbjct: 57  AQALDRAR-ETRPDAVILDVXMPGMDGFGVLRRLRADGIDAPALFLTARDSLQDKIAGLT 115

Query: 67  SGVAFYILKPLNPDDL 82
            G   Y+ KP + +++
Sbjct: 116 LGGDDYVTKPFSLEEV 131

>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 Length = 121

 Score = 52.1 bits (126), Expect = 2e-08
 Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 2/75 (2%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
             L      R  DL++ DL +P+ +GIE  +++  +++ +PV+V+S+   ES  + AL +
Sbjct: 36  RGLLEAA-TRKPDLIILDLGLPDGDGIEFIRDL-RQWSAVPVIVLSARSEESDKIAALDA 93

Query: 68  GVAFYILKPLNPDDL 82
           G   Y+ KP    +L
Sbjct: 94  GADDYLSKPFGIGEL 108

>3cg4_A Response regulator receiver domain protein (CHEY-; structural genomics, unknown function; HET: MSE; 1.61A {Methanospirillum hungatei jf-1} Length = 142

 Score = 52.2 bits (126), Expect = 2e-08
 Identities = 17/77 (22%), Positives = 38/77 (49%), Gaps = 3/77 (3%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMSSDDRESVIMKAL 65
           + +  ++ +    +V+ D+ MP M+G +  + I  N     + ++++++ +     M  L
Sbjct: 42  QCIDLLK-KGFSGVVLLDIMMPGMDGWDTIRAILDNSLEQGIAIVMLTAKNAPDAKMIGL 100

Query: 66  ASGVAFYILKPLNPDDL 82
              V  YI KP + +DL
Sbjct: 101 QEYVVDYITKPFDNEDL 117

>2b4a_A BH3024; flavodoxin-like fold, structural genomics, joint center for structural genomics, JCSG, protein structure initiative; 2.42A {Bacillus halodurans} SCOP: c.23.1.1 Length = 138

 Score = 51.8 bits (125), Expect = 2e-08
 Identities = 10/75 (13%), Positives = 27/75 (36%), Gaps = 3/75 (4%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
                       DL++    + +++   L   + E+     V+++++   E +     + 
Sbjct: 50  AFFQHRSQLSTCDLLIVSDQLVDLSIFSLLDIVKEQTKQPSVLILTTGRHELI---ESSE 106

Query: 68  GVAFYILKPLNPDDL 82
               Y+ KP    +L
Sbjct: 107 HNLSYLQKPFAISEL 121

>1a2o_A CHEB methylesterase; bacterial chemotaxis, adaptation, serine hydrolase; 2.40A {Salmonella typhimurium} SCOP: c.23.1.1 c.40.1.1 Length = 349

 Score = 54.4 bits (132), Expect = 3e-08
 Identities = 19/74 (25%), Positives = 42/74 (56%), Gaps = 6/74 (8%)

Query: 6   PVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRE--SVIMK 63
           P+ A   ++ + + D++  D+ MP M+G++  +++      +PV+++SS   +   V ++
Sbjct: 38  PLVARDLIK-KFNPDVLTLDVEMPRMDGLDFLEKLMRLRP-MPVVMVSSLTGKGSEVTLR 95

Query: 64  ALASGVAF-YILKP 76
           AL  G A  ++ KP
Sbjct: 96  ALELG-AIDFVTKP 108

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

 Score = 51.4 bits (124), Expect = 4e-08
 Identities = 22/87 (25%), Positives = 40/87 (45%), Gaps = 17/87 (19%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIE-----LQKEINEEFTHLPVMVMS----SDDRE 58
           +AL   +  R  D+++ D+ MP M+G+E        E         ++ ++     DDR 
Sbjct: 45  QALQAYQ-NRQFDVIIMDIQMPVMDGLEAVSEIRNYERTHNTKRASIIAITADTIDDDRP 103

Query: 59  SVIMKALASGVAFYILKPLNPDDLKNV 85
                   + +  Y+ KPLNP+ L++V
Sbjct: 104 -------GAELDEYVSKPLNPNQLRDV 123

>3a10_A Response regulator; phosphoacceptor, signaling protein; HET: MSE PG4; 1.63A {Thermotoga maritima} PDB: 3a0r_B* 3a0u_A* Length = 116

 Score = 50.1 bits (121), Expect = 6e-08
 Identities = 18/75 (24%), Positives = 37/75 (49%), Gaps = 3/75 (4%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
           EAL       + DLV+ D+ MP ++G+E+  EI ++     ++++++           + 
Sbjct: 36  EALKKFF-SGNYDLVILDIEMPGISGLEVAGEIRKKKKDAKIILLTA--YSHYRSDMSSW 92

Query: 68  GVAFYILKPLNPDDL 82
               Y++K  N D+L
Sbjct: 93  AADEYVVKSFNFDEL 107

>2j48_A Two-component sensor kinase; pseudo-receiver, circadian clock, transferase, response regulator, histidine protein kinase; NMR {Synechococcus elongatus} Length = 119

 Score = 49.4 bits (119), Expect = 1e-07
 Identities = 12/78 (15%), Positives = 33/78 (42%), Gaps = 8/78 (10%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEI--NEEFTHLPV-MVMSSDDRESVIMKA 64
            AL  + + +   +++     P+ + + L + +  ++   H P+ + +     +      
Sbjct: 36  TALDQLDLLQ-PIVILMAWPPPDQSCLLLLQHLREHQADPHPPLVLFLGEPPVD----PL 90

Query: 65  LASGVAFYILKPLNPDDL 82
           L +  +  + KPL+P  L
Sbjct: 91  LTAQASAILSKPLDPQLL 108

>2qzj_A Two-component response regulator; 11017X, PSI-II, structural genomics; 2.89A {Clostridium difficile} Length = 136

 Score = 49.8 bits (120), Expect = 1e-07
 Identities = 22/75 (29%), Positives = 40/75 (53%), Gaps = 2/75 (2%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
           EA+  +      DL+  ++ + + +G  L K+I    T  P++ M+  + +  I+ AL S
Sbjct: 39  EAIGKIF-SNKYDLIFLEIILSDGDGWTLCKKIRNV-TTCPIVYMTYINEDQSILNALNS 96

Query: 68  GVAFYILKPLNPDDL 82
           G   Y++KPLN + L
Sbjct: 97  GGDDYLIKPLNLEIL 111

>3lte_A Response regulator; structural genomics, PSI, protein structure initiative, NYSG YORK structural genomix research consortium, nysgxrc; 2.00A {Bermanella marisrubri} Length = 132

 Score = 49.5 bits (119), Expect = 1e-07
 Identities = 15/76 (19%), Positives = 40/76 (52%), Gaps = 2/76 (2%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEI-NEEFTHLPVMVMSSDDRESVIMKALA 66
           +A   +    +  ++  DL MP+++G+++ + +   +  + P +++ S   ++ + +A+ 
Sbjct: 41  DAGIKLS-TFEPAIMTLDLSMPKLDGLDVIRSLRQNKVANQPKILVVSGLDKAKLQQAVT 99

Query: 67  SGVAFYILKPLNPDDL 82
            G   Y+ KP + D L
Sbjct: 100 EGADDYLEKPFDNDAL 115

>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* Length = 220

 Score = 50.9 bits (123), Expect = 2e-07
 Identities = 19/74 (25%), Positives = 35/74 (47%), Gaps = 7/74 (9%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMS--SDDRESVIMKAL 65
           + L     +    +VV D+ +P+ +G E+ + I E      V++++  SDD   +     
Sbjct: 36  DFLND---EEAFHVVVLDVMLPDYSGYEICRMIKETRPETWVILLTLLSDDESVLK--GF 90

Query: 66  ASGVAFYILKPLNP 79
            +G   Y+ KP NP
Sbjct: 91  EAGADDYVTKPFNP 104

>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 Length = 136

 Score = 48.3 bits (116), Expect = 4e-07
 Identities = 21/72 (29%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
           EAL         DL+V D+ +P+++GIE+ K++ ++    P++++++ D E   +  L  
Sbjct: 38  EALKKAE-TEKPDLIVLDVMLPKLDGIEVCKQLRQQKLMFPILMLTAKDEEFDKVLGLEL 96

Query: 68  GVAFYILKPLNP 79
           G   Y+ KP +P
Sbjct: 97  GADDYMTKPFSP 108

>3t6k_A Response regulator receiver; flavodoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: MSE; 1.86A {Chloroflexus aurantiacus} Length = 136

 Score = 47.5 bits (114), Expect = 7e-07
 Identities = 18/77 (23%), Positives = 38/77 (49%), Gaps = 3/77 (3%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMSSDDRESVIMKAL 65
           EAL  +  +   D ++ D+ +P ++G  L K +  +     LP++++++    S  +   
Sbjct: 39  EALQQIY-KNLPDALICDVLLPGIDGYTLCKRVRQHPLTKTLPILMLTAQGDISAKIAGF 97

Query: 66  ASGVAFYILKPLNPDDL 82
            +G   Y+ KP  P +L
Sbjct: 98  EAGANDYLAKPFEPQEL 114

>2qv0_A Protein MRKE; structural genomics, transcription, PSI-2, protein structure initiative; 2.40A {Klebsiella pneumoniae} Length = 143

 Score = 47.6 bits (114), Expect = 7e-07
 Identities = 22/100 (22%), Positives = 46/100 (46%), Gaps = 19/100 (19%)

Query: 6   PVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSS--DDRESVIMK 63
            ++ L  ++    +D +  D+++P ++G+ L + I+ +F H P +V  +   +       
Sbjct: 44  GLDVLKFLQ-HNKVDAIFLDINIPSLDGVLLAQNIS-QFAHKPFIVFITAWKEH------ 95

Query: 64  ALASGVAF------YILKPLNPDDLKNVWQYAMTYKKAKS 97
           A+    AF      YILKP     + N+ Q   T  + ++
Sbjct: 96  AVE---AFELEAFDYILKPYQESRIINMLQKLTTAWEQQN 132

>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* Length = 120

 Score = 47.0 bits (113), Expect = 7e-07
 Identities = 21/72 (29%), Positives = 40/72 (55%), Gaps = 2/72 (2%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
           EAL         D+++ DL +PE++G+E+ K I +  + +P++++S+ D E   +  L  
Sbjct: 36  EALEQFE-AEQPDIIILDLMLPEIDGLEVAKTIRKT-SSVPILMLSAKDSEFDKVIGLEL 93

Query: 68  GVAFYILKPLNP 79
           G   Y+ KP + 
Sbjct: 94  GADDYVTKPFSN 105

>2yum_A ZZZ3 protein, zinc finger ZZ-type-containing protein 3; transcription, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 75

 Score = 45.7 bits (108), Expect = 9e-07
 Identities = 15/66 (22%), Positives = 26/66 (39%), Gaps = 5/66 (7%)

Query: 154 ATAPKKPKVAWTDSLHNRFLQAIRHIGLEKAVP---KKILEFMNVPGLTRENVASHLQKY 210
            ++       WT     +  Q +     E+      +KI +   +   T + VAS +QKY
Sbjct: 1   GSSGSSGNQLWTVEEQKKLEQLLIKYPPEEVESRRWQKIAD--ELGNRTAKQVASQVQKY 58

Query: 211 RIFLKR 216
            I L +
Sbjct: 59  FIKLTK 64

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

 Score = 45.9 bits (110), Expect = 2e-06
 Identities = 21/74 (28%), Positives = 41/74 (55%), Gaps = 6/74 (8%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMS--SDDRESVIMKAL 65
           E    +  + DI+LV+ D+++P  NG+ L +E+  E  ++ +M ++   ++ + ++   L
Sbjct: 38  EMHQILS-EYDINLVIMDINLPGKNGLLLAREL-REQANVALMFLTGRDNEVDKIL--GL 93

Query: 66  ASGVAFYILKPLNP 79
             G   YI KP NP
Sbjct: 94  EIGADDYITKPFNP 107

>3f6p_A Transcriptional regulatory protein YYCF; unphosphorelated, receiver domain, cytoplasm, DNA-binding, phosphoprotein, transcription regulation; 1.95A {Bacillus subtilis} PDB: 2zwm_A Length = 120

 Score = 45.1 bits (108), Expect = 4e-06
 Identities = 18/72 (25%), Positives = 40/72 (55%), Gaps = 2/72 (2%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
           EA+  V  +   DL++ D+ +P  +G+E+ +E+  +   +P++++++ D E   +  L  
Sbjct: 37  EAVEMVE-ELQPDLILLDIMLPNKDGVEVCREV-RKKYDMPIIMLTAKDSEIDKVIGLEI 94

Query: 68  GVAFYILKPLNP 79
           G   Y+ KP + 
Sbjct: 95  GADDYVTKPFST 106

>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 Length = 127

 Score = 45.2 bits (108), Expect = 5e-06
 Identities = 16/74 (21%), Positives = 35/74 (47%), Gaps = 3/74 (4%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMSSDDRESVIMKAL 65
            A+  +  +   DL++    +P  +GI+  K +        +PV+++++   E   ++ L
Sbjct: 37  SAVNQLN-EPWPDLILLAWMLPGGSGIQFIKHLRRESMTRDIPVVMLTARGEEEDRVRGL 95

Query: 66  ASGVAFYILKPLNP 79
            +G    I KP +P
Sbjct: 96  ETGADDCITKPFSP 109

>2cu7_A KIAA1915 protein; nuclear protein, SANT domain, DNA binding, regulation of transcription, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.3 Length = 72

 Score = 42.5 bits (100), Expect = 1e-05
 Identities = 14/75 (18%), Positives = 25/75 (33%), Gaps = 5/75 (6%)

Query: 154 ATAPKKPKVAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIF 213
           ++      V WT      F Q +   G  +    KI +   +   T   V S+ ++Y   
Sbjct: 2   SSGSSGYSVKWTIEEKELFEQGLAKFG--RRW-TKISKL--IGSRTVLQVKSYARQYFKN 56

Query: 214 LKRVAEQGASAMGKT 228
             +      +   KT
Sbjct: 57  KVKCGLDKETPNQKT 71

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

 Score = 43.6 bits (104), Expect = 1e-05
 Identities = 18/73 (24%), Positives = 37/73 (50%), Gaps = 4/73 (5%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPV-MVMSSDDRESVIMKALA 66
                ++  + +DL++ D+++P+ NG+ L + +  E + + + +V    DR   I+  L 
Sbjct: 37  GLREIMQ-NQSVDLILLDINLPDENGLMLTRAL-RERSTVGIILVTGRSDRIDRIV-GLE 93

Query: 67  SGVAFYILKPLNP 79
            G   Y+ KPL  
Sbjct: 94  MGADDYVTKPLEL 106

>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 = 47.2 bits (111), Expect = 1e-05
 Identities = 53/317 (16%), Positives = 100/317 (31%), Gaps = 75/317 (23%)

Query: 1   VTVTRP---VEAL-ATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDD 56
           +T TR     + L A       +D     L   E+  + L K ++     LP        
Sbjct: 270 LT-TRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSL-LLKYLDCRPQDLP-------- 319

Query: 57  RESVIMKALASGVAFYILKPLNPDDLKNVWQYAMTYKKAKSI--SIDEIGSFEL-AGFSA 113
           RE +        +    ++        N W++    K    I  S++ +   E    F  
Sbjct: 320 REVLTTNPRRLSIIAESIRD-GLATWDN-WKHVNCDKLTTIIESSLNVLEPAEYRKMFDR 377

Query: 114 -GKFSLD-DIVSR---------SSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPKV 162
              F     I +             +     NK  K    +K            PK+  +
Sbjct: 378 LSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQ-----------PKESTI 426

Query: 163 AWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTREN---VASHLQKYRIF------ 213
               S+ + +L+    +  E A+ + I++  N+P  T ++   +  +L +Y  +      
Sbjct: 427 ----SIPSIYLELKVKLENEYALHRSIVDHYNIP-KTFDSDDLIPPYLDQY-FYSHIGHH 480

Query: 214 LKRVAEQGASAMGKTLALRSSF-------------ASGHVSMMLQEAHEFSQ---VRDQQ 257
           LK +       + + + L   F             ASG +   LQ+   +       D +
Sbjct: 481 LKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPK 540

Query: 258 QQMRTSA---FLPGYAS 271
            +   +A   FLP    
Sbjct: 541 YERLVNAILDFLPKIEE 557

>3sy8_A ROCR; TIM barrel phosphodiesterase-A, transcription regulator; HET: EPE; 2.50A {Pseudomonas aeruginosa} Length = 400

 Score = 45.4 bits (108), Expect = 3e-05
 Identities = 18/90 (20%), Positives = 37/90 (41%), Gaps = 7/90 (7%)

Query: 2   TVTRP--VEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDD--- 56
            +      EA+A +     +D+ + DL M  M+G+   +  +       V++ S  D   
Sbjct: 31  ILEAADGKEAVAILESCGHVDIAICDLQMSGMDGLAFLRHASLSGKVHSVILSSEVDPIL 90

Query: 57  RESVIMKALASGVAFY--ILKPLNPDDLKN 84
           R++ I      G+ F   + KP + + +  
Sbjct: 91  RQATISMIECLGLNFLGDLGKPFSLERITA 120

>3mm4_A Histidine kinase homolog; receiver domain, CKI1, cytokinin signaling, ROS fold, CHEY-like, transferase; 2.00A {Arabidopsis thaliana} PDB: 3mmn_A Length = 206

 Score = 44.0 bits (104), Expect = 3e-05
 Identities = 18/75 (24%), Positives = 32/75 (42%), Gaps = 15/75 (20%)

Query: 20  DLVVTDLHMPEMNGIELQKEI----NEEFTHLPV--M---VMSSDDRESVIMKALASGVA 70
           D +  D  MPEM+G E  +EI           P+  +      S++      + + +G+ 
Sbjct: 121 DYIFMDCQMPEMDGYEATREIRKVEKSYGVRTPIIAVSGHDPGSEEAR----ETIQAGMD 176

Query: 71  FYILKPLNPDDLKNV 85
            ++ K L  + L NV
Sbjct: 177 AFLDKSL--NQLANV 189

>2gwr_A DNA-binding response regulator MTRA; two-component regulatory system, transcription regulation, phosphorylation, OMPR family; 2.10A {Mycobacterium tuberculosis} PDB: 3nhz_A Length = 238

 Score = 42.9 bits (102), Expect = 1e-04
 Identities = 26/73 (35%), Positives = 43/73 (58%), Gaps = 4/73 (5%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPV-MVMSSDDRESVIMKALA 66
           +AL  VR +   DLV+ DL +P MNGI++ + +  + + +P+ M+ +  D   V++  L 
Sbjct: 40  QALTAVR-ELRPDLVLLDLMLPGMNGIDVCRVLRAD-SGVPIVMLTAKTDTVDVVL-GLE 96

Query: 67  SGVAFYILKPLNP 79
           SG   YI+KP  P
Sbjct: 97  SGADDYIMKPFKP 109

>2oqr_A Sensory transduction protein REGX3; response regulator, winged-helix-turn-helix, DNA-binding, 3D swapping, two component system; 2.03A {Mycobacterium tuberculosis H37RV} Length = 230

 Score = 42.9 bits (102), Expect = 1e-04
 Identities = 20/72 (27%), Positives = 39/72 (54%), Gaps = 2/72 (2%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
            ALA    +   D+V+ DL +P M+G ++ K++    + +PV+++++ D E   +  L  
Sbjct: 39  AALAEFD-RAGADIVLLDLMLPGMSGTDVCKQLRAR-SSVPVIMVTARDSEIDKVVGLEL 96

Query: 68  GVAFYILKPLNP 79
           G   Y+ KP + 
Sbjct: 97  GADDYVTKPYSA 108

>3q9s_A DNA-binding response regulator; DNA binding protein; 2.40A {Deinococcus radiodurans} Length = 249

 Score = 42.5 bits (101), Expect = 2e-04
 Identities = 20/75 (26%), Positives = 43/75 (57%), Gaps = 2/75 (2%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
             L   R +   DL++ DL +P+ +G ++ + + +  + LP++V+++ D     ++ L  
Sbjct: 72  NGLIKAR-EDHPDLILLDLGLPDFDGGDVVQRLRKN-SALPIIVLTARDTVEEKVRLLGL 129

Query: 68  GVAFYILKPLNPDDL 82
           G   Y++KP +PD+L
Sbjct: 130 GADDYLIKPFHPDEL 144

>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* Length = 225

 Score = 41.7 bits (99), Expect = 2e-04
 Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 1/70 (1%)

Query: 7   VEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALA 66
            E +         D+V+ D+ +P  +G E+ K + E   + PV+++++       +K L 
Sbjct: 36  EEGMYMAL-NEPFDVVILDIMLPVHDGWEILKSMRESGVNTPVLMLTALSDVEYRVKGLN 94

Query: 67  SGVAFYILKP 76
            G   Y+ KP
Sbjct: 95  MGADDYLPKP 104

>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 = 18/70 (25%), Positives = 35/70 (50%), Gaps = 1/70 (1%)

Query: 7   VEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALA 66
            EAL +   +   D +V D++MP ++G+ +   +      +PV V+S+       +  L 
Sbjct: 41  AEALRSAT-ENRPDAIVLDINMPVLDGVSVVTALRAMDNDVPVCVLSARSSVDDRVAGLE 99

Query: 67  SGVAFYILKP 76
           +G   Y++KP
Sbjct: 100 AGADDYLVKP 109

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	534
1irz_A	64	ARR10-B; helix-turn-helix, DNA binding protein; NM	99.75
1a04_A	215	Nitrate/nitrite response regulator protein NARL; s	99.72
3to5_A	134	CHEY homolog; alpha(5)beta(5), chemotaxis, FLIM, p	99.7
1yio_A	208	Response regulatory protein; transcription regulat	99.68
3r0j_A	250	Possible two component system response transcript	99.66
3rqi_A	184	Response regulator protein; structural genomics, s	99.65
3q9s_A	249	DNA-binding response regulator; DNA binding protei	99.64
1kgs_A	225	DRRD, DNA binding response regulator D; DNA-bindin	99.64
3c3w_A	225	Two component transcriptional regulatory protein;	99.63
3klo_A	225	Transcriptional regulator VPST; REC domain, HTH do	99.63
1p2f_A	220	Response regulator; DRRB, OMPR/PHOB, transcription	99.59
1ys7_A	233	Transcriptional regulatory protein PRRA; response	99.59
2oqr_A	230	Sensory transduction protein REGX3; response regul	99.58
3gl9_A	122	Response regulator; beta-sheet, surrounded by alph	99.57
2gwr_A	238	DNA-binding response regulator MTRA; two-component	99.57
3t6k_A	136	Response regulator receiver; flavodoxin-like, stru	99.56
3f6p_A	120	Transcriptional regulatory protein YYCF; unphospho	99.54
3b2n_A	133	Uncharacterized protein Q99UF4; structural genomic	99.54
3crn_A	132	Response regulator receiver domain protein, CHEY-;	99.53
2pl1_A	121	Transcriptional regulatory protein PHOP; CHEY-like	99.53
1dbw_A	126	Transcriptional regulatory protein FIXJ; doubly wo	99.53
3h1g_A	129	Chemotaxis protein CHEY homolog; sulfate-bound CHE	99.53
4e7p_A	150	Response regulator; DNA binding, cytosol, transcri	99.52
2r25_B	133	Osmosensing histidine protein kinase SLN1; alpha5-	99.51
3jte_A	143	Response regulator receiver protein; structural ge	99.51
3hv2_A	153	Response regulator/HD domain protein; PSI-2, NYSGX	99.5
3eul_A	152	Possible nitrate/nitrite response transcriptional	99.5
1srr_A	124	SPO0F, sporulation response regulatory protein; as	99.5
3hdg_A	137	Uncharacterized protein; two-component sensor acti	99.5
3f6c_A	134	Positive transcription regulator EVGA; structural	99.5
1tmy_A	120	CHEY protein, TMY; chemotaxis, phosphoryl transfer	99.5
3cfy_A	137	Putative LUXO repressor protein; structural genomi	99.49
3eod_A	130	Protein HNR; response regulator, phosphoprotein, t	99.49
3kto_A	136	Response regulator receiver protein; PSI-II,struct	99.49
3kht_A	144	Response regulator; PSI-II, 11023K, structural gen	99.49
1zgz_A	122	Torcad operon transcriptional regulatory protein;	99.49
1jbe_A	128	Chemotaxis protein CHEY; signaling protein; 1.08A	99.48
1xhf_A	123	DYE resistance, aerobic respiration control protei	99.48
1dz3_A	130	Stage 0 sporulation protein A; response regulator,	99.48
3gt7_A	154	Sensor protein; structural genomics, signal receiv	99.48
3heb_A	152	Response regulator receiver domain protein (CHEY);	99.47
3m6m_D	143	Sensory/regulatory protein RPFC; RPFF, REC, enoyl-	99.47
2a9o_A	120	Response regulator; essential protein, YYCF/YYCG h	99.47
3hdv_A	136	Response regulator; PSI-II, structural genomics, P	99.46
3cu5_A	141	Two component transcriptional regulator, ARAC FAM;	99.46
3cnb_A	143	DNA-binding response regulator, MERR family; signa	99.46
3grc_A	140	Sensor protein, kinase; protein structure initiati	99.46
3nhm_A	133	Response regulator; protein structure initiative I	99.46
3kcn_A	151	Adenylate cyclase homolog; SGX, PSI 2, structural	99.46
3lua_A	140	Response regulator receiver protein; two-component	99.46
1i3c_A	149	Response regulator RCP1; phytochrome, signaling pr	99.46
2jk1_A	139	HUPR, hydrogenase transcriptional regulatory prote	99.46
1mvo_A	136	PHOP response regulator; phosphate regulon, transc	99.45
2qzj_A	136	Two-component response regulator; 11017X, PSI-II,	99.45
4dad_A	146	Putative pilus assembly-related protein; response	99.45
2zay_A	147	Response regulator receiver protein; structural ge	99.45
3hzh_A	157	Chemotaxis response regulator (CHEY-3); phosphatas	99.45
1p6q_A	129	CHEY2; chemotaxis, signal transduction, response r	99.45
2lpm_A	123	Two-component response regulator; transcription re	99.44
3n53_A	140	Response regulator receiver modulated diguanylate;	99.44
1zh2_A	121	KDP operon transcriptional regulatory protein KDPE	99.44
1mb3_A	124	Cell division response regulator DIVK; signal tran	99.44
3cg0_A	140	Response regulator receiver modulated diguanylate	99.44
3ilh_A	146	Two component response regulator; NYSGXRC, PSI-II,	99.43
3cz5_A	153	Two-component response regulator, LUXR family; str	99.43
3i42_A	127	Response regulator receiver domain protein (CHEY-	99.43
3snk_A	135	Response regulator CHEY-like protein; P-loop conta	99.43
2qr3_A	140	Two-component system response regulator; structura	99.43
2qxy_A	142	Response regulator; regulation of transcription, N	99.43
3luf_A	259	Two-component system response regulator/ggdef doma	99.43
1k68_A	140	Phytochrome response regulator RCPA; phosphorylate	99.43
3sy8_A	400	ROCR; TIM barrel phosphodiesterase-A, transcriptio	99.42
2hqr_A	223	Putative transcriptional regulator; phosporylation	99.42
2rjn_A	154	Response regulator receiver:metal-dependent phosph	99.42
3h5i_A	140	Response regulator/sensory box protein/ggdef domai	99.41
1k66_A	149	Phytochrome response regulator RCPB; CHEY homologu	99.41
1qkk_A	155	DCTD, C4-dicarboxylate transport transcriptional r	99.4
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	99.4
2jba_A	127	Phosphate regulon transcriptional regulatory PROT;	99.39
3mm4_A	206	Histidine kinase homolog; receiver domain, CKI1, c	99.39
3a10_A	116	Response regulator; phosphoacceptor, signaling pro	99.39
2ayx_A	254	Sensor kinase protein RCSC; two independent struct	99.39
3cg4_A	142	Response regulator receiver domain protein (CHEY-;	99.39
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	99.39
3c3m_A	138	Response regulator receiver protein; structural ge	99.38
3lte_A	132	Response regulator; structural genomics, PSI, prot	99.38
2qsj_A	154	DNA-binding response regulator, LUXR family; struc	99.37
2qv0_A	143	Protein MRKE; structural genomics, transcription,	99.37
1s8n_A	205	Putative antiterminator; RV1626, structural genomi	99.36
3eq2_A	394	Probable two-component response regulator; adaptor	99.35
3eqz_A	135	Response regulator; structural genomics, unknown f	99.35
2qvg_A	143	Two component response regulator; NYSGXRC, PSI-2,	99.34
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	99.34
1dcf_A	136	ETR1 protein; beta-alpha five sandwich, transferas	99.33
1w25_A	459	Stalked-cell differentiation controlling protein;	99.33
2gkg_A	127	Response regulator homolog; social motility, recei	99.32
3t8y_A	164	CHEB, chemotaxis response regulator protein-glutam	99.32
3bre_A	358	Probable two-component response regulator; protein	99.32
2rdm_A	132	Response regulator receiver protein; structural ge	99.31
3kyj_B	145	CHEY6 protein, putative histidine protein kinase;	99.29
1dc7_A	124	NTRC, nitrogen regulation protein; receiver domain	99.27
3c97_A	140	Signal transduction histidine kinase; structural g	99.26
2j48_A	119	Two-component sensor kinase; pseudo-receiver, circ	99.23
2pln_A	137	HP1043, response regulator; signaling protein; 1.8	99.23
1qo0_D	196	AMIR; binding protein, gene regulator, receptor; 2	99.1
1a2o_A	349	CHEB methylesterase; bacterial chemotaxis, adaptat	99.09
2b4a_A	138	BH3024; flavodoxin-like fold, structural genomics,	99.08
3luf_A	259	Two-component system response regulator/ggdef doma	98.99
3cwo_X	237	Beta/alpha-barrel protein based on 1THF and 1TMY;	98.96
2vyc_A	755	Biodegradative arginine decarboxylase; pyridoxal p	98.92
1w25_A	459	Stalked-cell differentiation controlling protein;	98.29
3cwo_X	237	Beta/alpha-barrel protein based on 1THF and 1TMY;	95.74
3n75_A	715	LDC, lysine decarboxylase, inducible; pyridoxal-5'	95.46
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	91.74
3c57_A	95	Two component transcriptional regulatory protein;	90.98
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	90.77
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	90.69
2yxb_A	161	Coenzyme B12-dependent mutase; alpha/beta, structu	89.91
2ekc_A	262	AQ_1548, tryptophan synthase alpha chain; structur	89.71
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	88.43
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	87.91
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	87.78
1qop_A	268	Tryptophan synthase alpha chain; lyase, carbon-oxy	87.7
3szt_A	237	QCSR, quorum-sensing control repressor; quorum sen	87.52
3vnd_A	267	TSA, tryptophan synthase alpha chain; psychrophili	87.21
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	87.21
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	86.9
3q7r_A	121	Transcriptional regulatory protein; CHXR, receiver	86.56
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	86.53
2q0o_A	236	Probable transcriptional activator protein TRAR; h	86.39
1l3l_A	234	Transcriptional activator protein TRAR; helix-turn	86.32
1xsv_A	113	Hypothetical UPF0122 protein SAV1236; helix-turn-h	85.97
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	85.8
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	84.68
1geq_A	248	Tryptophan synthase alpha-subunit; hyperthermophIl	84.52
3nav_A	271	Tryptophan synthase alpha chain; alpha subunit, st	84.46
3qp6_A	265	CVIR transcriptional regulator; quorum sensing, ag	83.8
1s7o_A	113	Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP	83.2
3o63_A	243	Probable thiamine-phosphate pyrophosphorylase; thi	82.86
3clo_A	258	Transcriptional regulator; NP_811094.1, bacterial	82.73
3q58_A	229	N-acetylmannosamine-6-phosphate 2-epimerase; TIM b	82.59
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	82.55
1ujp_A	271	Tryptophan synthase alpha chain; riken structural	82.1
1xi3_A	215	Thiamine phosphate pyrophosphorylase; structural g	82.06
1yad_A	221	Regulatory protein TENI; TIM barrel, transcription	81.88
1or7_A	194	Sigma-24, RNA polymerase sigma-E factor; regulatio	81.21
3qz6_A	261	HPCH/HPAI aldolase; structural genomics, PSI-biolo	81.19

>1irz_A ARR10-B; helix-turn-helix, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: a.4.1.11

Probab=99.75  E-value=1.5e-18  Score=138.22  Aligned_cols=62  Identities=68%  Similarity=1.090  Sum_probs=59.1

Q ss_pred             CCCCCCccCCchhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHH
Q 043479          156 APKKPKVAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRV  217 (534)
Q Consensus       156 s~kKprv~Wt~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~lkr~  217 (534)
                      ..+|+|++|+++||.+|++++++||.++++||.|++.|+|+|||+++|+|||||||+.++|.
T Consensus         2 ~~~k~r~~WT~elH~~Fv~Av~~LG~~~AtPk~Il~~M~v~gLT~~~VkSHLQKYR~~l~r~   63 (64)
T 1irz_A            2 AQKKPRVLWTHELHNKFLAAVDHLGVERAVPKKILDLMNVDKLTRENVASHLQKFRVALKKV   63 (64)
T ss_dssp             CCCCSSCSSCHHHHHHHHHHHHHHCTTTCCHHHHHHHHCCTTCCHHHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHHhCCCCCCcHHHHHHcCCCCCCHHHHHHHHHHHHHHHHcc
Confidence            46889999999999999999999999999999999999999999999999999999998863

>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=99.72  E-value=1.2e-16  Score=150.79  Aligned_cols=162  Identities=22%  Similarity=0.310  Sum_probs=125.8

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++.+|++.+.. ..||+||+|+.||+++|+++++.|++..+.+|||++|+..+.+...++++.||++||.||++.++
T Consensus        36 ~~~~~~~al~~~~~-~~~dlvllD~~lp~~~g~~~~~~lr~~~~~~~ii~ls~~~~~~~~~~~~~~Ga~~~l~Kp~~~~~  114 (215)
T 1a04_A           36 EASNGEQGIELAES-LDPDLILLDLNMPGMNGLETLDKLREKSLSGRIVVFSVSNHEEDVVTALKRGADGYLLKDMEPED  114 (215)
T ss_dssp             EESSHHHHHHHHHH-HCCSEEEEETTSTTSCHHHHHHHHHHSCCCSEEEEEECCCCHHHHHHHHHTTCSEEEETTCCHHH
T ss_pred             EeCCHHHHHHHHHh-cCCCEEEEeCCCCCCcHHHHHHHHHHhCCCCcEEEEECCCCHHHHHHHHHcCCcEEEeCCCCHHH
Confidence            46799999999987 68999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccCCCCCC
Q 043479           82 LKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPK  161 (534)
Q Consensus        82 L~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss~kKpr  161 (534)
                      |..+|+.++++.......                  ....+.. .....       .             ..    ..  
T Consensus       115 L~~~i~~~~~~~~~~~~~------------------~~~~~~~-~~~~~-------~-------------~~----~~--  149 (215)
T 1a04_A          115 LLKALHQAAAGEMVLSEA------------------LTPVLAA-SLRAN-------R-------------AT----TE--  149 (215)
T ss_dssp             HHHHHHHHHHSCCCCCTT------------------THHHHHH-HC-------------------------------C--
T ss_pred             HHHHHHHHHcCCeecCHH------------------HHHHHHH-Hhccc-------c-------------cC----CC--
Confidence            999999998764322110                  0000000 00000       0             00    00  


Q ss_pred             ccCCchhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHH
Q 043479          162 VAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFL  214 (534)
Q Consensus       162 v~Wt~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~l  214 (534)
                       .....|+.++.+++..+.... ..++|++.++   ++..||+.|+.+.|..+
T Consensus       150 -~~~~~Lt~rE~~vl~~l~~g~-s~~~Ia~~l~---is~~TV~~hi~~i~~Kl  197 (215)
T 1a04_A          150 -RDVNQLTPRERDILKLIAQGL-PNKMIARRLD---ITESTVKVHVKHMLKKM  197 (215)
T ss_dssp             -CCGGGSCHHHHHHHHHHHTTC-CHHHHHHHHT---CCHHHHHHHHHHHHHHH
T ss_pred             -ccccCCCHHHHHHHHHHHcCC-CHHHHHHHHC---CCHHHHHHHHHHHHHHc
Confidence             012358999999999996544 4899999997   89999999998887744

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

Probab=99.70  E-value=6.8e-17  Score=146.30  Aligned_cols=89  Identities=35%  Similarity=0.604  Sum_probs=83.3

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHh--hCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINE--EFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~--~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      +|.++.+|++.+++ .+|||||+|+.||+|||++++++||+  ..+++|||++|+..+.+...+++++||++||.||++.
T Consensus        42 ~a~~g~~al~~~~~-~~~DlillD~~MP~mdG~el~~~ir~~~~~~~ipvI~lTa~~~~~~~~~~~~~Ga~~yl~KP~~~  120 (134)
T 3to5_A           42 EADDGLTALPMLKK-GDFDFVVTDWNMPGMQGIDLLKNIRADEELKHLPVLMITAEAKREQIIEAAQAGVNGYIVKPFTA  120 (134)
T ss_dssp             EESSHHHHHHHHHH-HCCSEEEEESCCSSSCHHHHHHHHHHSTTTTTCCEEEEESSCCHHHHHHHHHTTCCEEEESSCCH
T ss_pred             EECCHHHHHHHHHh-CCCCEEEEcCCCCCCCHHHHHHHHHhCCCCCCCeEEEEECCCCHHHHHHHHHCCCCEEEECCCCH
Confidence            47899999999987 78999999999999999999999996  4578999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHH
Q 043479           80 DDLKNVWQYAMT   91 (534)
Q Consensus        80 eeL~~aI~~aL~   91 (534)
                      ++|..+|+++++
T Consensus       121 ~~L~~~i~~~l~  132 (134)
T 3to5_A          121 ATLKEKLDKIFE  132 (134)
T ss_dssp             HHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHh
Confidence            999999998874

>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=99.68  E-value=1.8e-16  Score=148.69  Aligned_cols=152  Identities=18%  Similarity=0.256  Sum_probs=122.8

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.+|++.+.. ..||+||+|+.||+++|+++++.|++..+.+|||++|+..+.....++++.||++||.||++.++
T Consensus        33 ~~~~~~~al~~~~~-~~~dlvl~D~~lp~~~g~~~~~~l~~~~~~~~ii~ls~~~~~~~~~~a~~~Ga~~~l~Kp~~~~~  111 (208)
T 1yio_A           33 TFDCASTFLEHRRP-EQHGCLVLDMRMPGMSGIELQEQLTAISDGIPIVFITAHGDIPMTVRAMKAGAIEFLPKPFEEQA  111 (208)
T ss_dssp             EESSHHHHHHHCCT-TSCEEEEEESCCSSSCHHHHHHHHHHTTCCCCEEEEESCTTSCCCHHHHHTTEEEEEESSCCHHH
T ss_pred             EcCCHHHHHHhhhc-cCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCCEEEEeCCCCHHHHHHHHHCCCcEEEeCCCCHHH
Confidence            46789999999876 78999999999999999999999999889999999999998888899999999999999999999


Q ss_pred             HHHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccCCCCCC
Q 043479           82 LKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPK  161 (534)
Q Consensus        82 L~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss~kKpr  161 (534)
                      |..+|++++++........                   .   .  ....                     .         
T Consensus       112 L~~~i~~~~~~~~~~~~~~-------------------~---~--~~~~---------------------~---------  137 (208)
T 1yio_A          112 LLDAIEQGLQLNAERRQAR-------------------E---T--QDQL---------------------E---------  137 (208)
T ss_dssp             HHHHHHHHHHHHHHHHHHH-------------------H---H--HHHH---------------------H---------
T ss_pred             HHHHHHHHHhhhhhhHHHH-------------------H---H--HHHH---------------------H---------
Confidence            9999999987644221000                   0   0  0000                     0         


Q ss_pred             ccCCchhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHH
Q 043479          162 VAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIF  213 (534)
Q Consensus       162 v~Wt~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~  213 (534)
                       .....|+.++.+++..+... ...++|++.++   ++..+|+.|+.+.|..
T Consensus       138 -~~~~~Lt~rE~~vl~~l~~g-~s~~~Ia~~l~---is~~TV~~~~~~i~~K  184 (208)
T 1yio_A          138 -QLFSSLTGREQQVLQLTIRG-LMNKQIAGELG---IAEVTVKVHRHNIMQK  184 (208)
T ss_dssp             -HHHHTSCHHHHHHHHHHTTT-CCHHHHHHHHT---CCHHHHHHHHHHHHHH
T ss_pred             -HHHHhcCHHHHHHHHHHHcC-CcHHHHHHHcC---CCHHHHHHHHHHHHHH
Confidence             00124778899999998543 45899999998   8999999998887764

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

Probab=99.66  E-value=1.5e-15  Score=147.57  Aligned_cols=173  Identities=19%  Similarity=0.228  Sum_probs=124.8

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++.+|++.+.. ..|||||+|+.||+++|++++++|++..+.+|||++|+..+.....+++++||++||.||++.++
T Consensus        52 ~~~~~~~al~~~~~-~~~dlvllD~~lp~~~g~~~~~~lr~~~~~~~ii~lt~~~~~~~~~~~~~~Ga~~yl~Kp~~~~~  130 (250)
T 3r0j_A           52 TATNGAQALDRARE-TRPDAVILDVXMPGMDGFGVLRRLRADGIDAPALFLTARDSLQDKIAGLTLGGDDYVTKPFSLEE  130 (250)
T ss_dssp             EESSHHHHHHHHHH-HCCSEEEEESCCSSSCHHHHHHHHHHTTCCCCEEEEECSTTHHHHHHHHTSTTCEEEESSCCHHH
T ss_pred             EECCHHHHHHHHHh-CCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCCEEEEECCCCHHHHHHHHHcCCcEEEeCCCCHHH
Confidence            57899999999987 68999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccCCCCCC
Q 043479           82 LKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPK  161 (534)
Q Consensus        82 L~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss~kKpr  161 (534)
                      |..+|+.++++...........           .....++    .....      .+           .. .    ..  
T Consensus       131 L~~~i~~~~~~~~~~~~~~~~~-----------~~~~~~~----~~~~~------~~-----------~~-~----~~--  171 (250)
T 3r0j_A          131 VVARLRVILRRAGKGNKEPRNV-----------RLTFADI----ELDEE------TH-----------EV-W----KA--  171 (250)
T ss_dssp             HHHHHHHHHHHHCC------CC-----------EEEETTE----EEETT------TC-----------CE-E----ET--
T ss_pred             HHHHHHHHHHhhccccccccce-----------EEEECCE----EEecc------cc-----------EE-E----EC--
Confidence            9999999987643221100000           0000000    00000      00           00 0    00  


Q ss_pred             ccCCchhhHHHHHHHHHhc--c-CCCcHHHHHHHcCC--CCCCHHHHHHHHHHHHHHHH
Q 043479          162 VAWTDSLHNRFLQAIRHIG--L-EKAVPKKILEFMNV--PGLTRENVASHLQKYRIFLK  215 (534)
Q Consensus       162 v~Wt~eLh~RFleaLe~LG--l-ekAvpK~ILe~M~V--~GLT~~tVaSHLQKyRl~lk  215 (534)
                       .-...|+.++.+++..+.  . .-...++|++.+--  .+.+..+|+.|+.+.|..|.
T Consensus       172 -~~~~~LT~rE~~iL~~l~~~~~~~~s~~~i~~~lw~~~~~~~~~tv~~~i~~lr~KL~  229 (250)
T 3r0j_A          172 -GQPVSLSPTEFTLLRYFVINAGTVLSKPKILDHVWRYDFGGDVNVVESYVSYLRRKID  229 (250)
T ss_dssp             -TEEECCCHHHHHHHHHHHHTTTCCBCHHHHHHHHTTTSCCSCTHHHHHHHHHHHHHHC
T ss_pred             -CEEEecCHHHHHHHHHHHHCCCceEcHHHHHHHHcCCCCCCCccCHHHHHHHHHHhhc
Confidence             001248999999999992  1 22446789888732  23688999999999887553

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

Probab=99.65  E-value=3.7e-16  Score=145.04  Aligned_cols=92  Identities=16%  Similarity=0.264  Sum_probs=86.0

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++.+|++.+.. ..|||||+|+.||+++|++++++|++..+++|||++|+..+.+...++++.||++||.||++.++
T Consensus        36 ~~~~~~~al~~~~~-~~~dlvl~D~~lp~~~g~~~~~~l~~~~~~~~ii~lt~~~~~~~~~~a~~~Ga~~~l~KP~~~~~  114 (184)
T 3rqi_A           36 QAHNKDEALKLAGA-EKFEFITVXLHLGNDSGLSLIAPLCDLQPDARILVLTGYASIATAVQAVKDGADNYLAKPANVES  114 (184)
T ss_dssp             EECSHHHHHHHHTT-SCCSEEEECSEETTEESHHHHHHHHHHCTTCEEEEEESSCCHHHHHHHHHHTCSEEEESSCCHHH
T ss_pred             EeCCHHHHHHHHhh-CCCCEEEEeccCCCccHHHHHHHHHhcCCCCCEEEEeCCCCHHHHHHHHHhCHHHheeCCCCHHH
Confidence            57899999999987 78999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhh
Q 043479           82 LKNVWQYAMTYKK   94 (534)
Q Consensus        82 L~~aI~~aL~~k~   94 (534)
                      |..+|+++++...
T Consensus       115 L~~~i~~~~~~~~  127 (184)
T 3rqi_A          115 ILAALQTNASEVQ  127 (184)
T ss_dssp             HHHHTSTTHHHHH
T ss_pred             HHHHHHHHHHHhh
Confidence            9999998876543

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

Probab=99.64  E-value=9.8e-16  Score=149.87  Aligned_cols=164  Identities=17%  Similarity=0.282  Sum_probs=122.1

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++.+|++.+.. ..|||||+|+.||+++|++++++|++ .+.+|||++|+..+.+.+.+++++||++||.||++.++
T Consensus        66 ~~~~~~~al~~~~~-~~~DlvllD~~lp~~~G~~l~~~lr~-~~~~~iI~lt~~~~~~~~~~a~~~Ga~~yl~Kp~~~~~  143 (249)
T 3q9s_A           66 HADSAMNGLIKARE-DHPDLILLDLGLPDFDGGDVVQRLRK-NSALPIIVLTARDTVEEKVRLLGLGADDYLIKPFHPDE  143 (249)
T ss_dssp             EESSHHHHHHHHHH-SCCSEEEEECCSCHHHHHHHHHHHHT-TCCCCEEEEESCCSHHHHHHHHHHTCSEEEESSCCHHH
T ss_pred             EeCCHHHHHHHHhc-CCCCEEEEcCCCCCCCHHHHHHHHHc-CCCCCEEEEECCCCHHHHHHHHHCCCcEEEECCCCHHH
Confidence            47799999999987 78999999999999999999999998 68899999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccCCCCCC
Q 043479           82 LKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPK  161 (534)
Q Consensus        82 L~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss~kKpr  161 (534)
                      |..+|+.++++..........                  ..    ...      ..+ .     ...   .         
T Consensus       144 L~~~i~~~l~~~~~~~~~~~~------------------~~----~~~------~~~-~-----~~~---~---------  177 (249)
T 3q9s_A          144 LLARVKVQLRQRTSESLSMGD------------------LT----LDP------QKR-L-----VTY---K---------  177 (249)
T ss_dssp             HHHHHHHHHCCCCSCCEEETT------------------EE----EET------TTT-E-----EEE---T---------
T ss_pred             HHHHHHHHHhhcccCceeECC------------------EE----Eec------ccC-E-----EEE---C---------
Confidence            999999998654322110000                  00    000      000 0     000   0         


Q ss_pred             ccCCchhhHHHHHHHHHhccC---CCcHHHHHHHcCC--CCCCHHHHHHHHHHHHHHH
Q 043479          162 VAWTDSLHNRFLQAIRHIGLE---KAVPKKILEFMNV--PGLTRENVASHLQKYRIFL  214 (534)
Q Consensus       162 v~Wt~eLh~RFleaLe~LGle---kAvpK~ILe~M~V--~GLT~~tVaSHLQKyRl~l  214 (534)
                       .-...|+.|+.+++..+...   ....++|++.+..  -+++..+|+.|+.+.|..|
T Consensus       178 -~~~~~LT~rE~evL~ll~~g~~~~~s~~eIa~~l~~~~l~~s~~TV~~hi~~lr~KL  234 (249)
T 3q9s_A          178 -GEELRLSPKEFDILALLIRQPGRVYSRQEIGQEIWQGRLPEGSNVVDVHMANLRAKL  234 (249)
T ss_dssp             -TEEECCCHHHHHHHHHHHHSTTCCCCHHHHHHHHHTTCSCTTCSHHHHHHHHHHHHH
T ss_pred             -CEEeecCHHHHHHHHHHHHCCCceEcHHHHHHHhcCCCCCCCccCHHHHHHHHHHHh
Confidence             00124899999999999433   2447889985332  2267899999998887744

>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=99.64  E-value=3e-15  Score=141.71  Aligned_cols=169  Identities=17%  Similarity=0.222  Sum_probs=125.3

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.+|++.+.. ..||+||+|+.||+++|+++++.|++..+++|||++|+..+.....++++.||++||.||++.++
T Consensus        31 ~~~~~~~a~~~~~~-~~~dlvllD~~l~~~~g~~~~~~lr~~~~~~~ii~ls~~~~~~~~~~~~~~ga~~~l~Kp~~~~~  109 (225)
T 1kgs_A           31 VCYDGEEGMYMALN-EPFDVVILDIMLPVHDGWEILKSMRESGVNTPVLMLTALSDVEYRVKGLNMGADDYLPKPFDLRE  109 (225)
T ss_dssp             EESSHHHHHHHHHH-SCCSEEEEESCCSSSCHHHHHHHHHHTTCCCCEEEEESSCHHHHHHHTCCCCCSEEEESSCCHHH
T ss_pred             EECCHHHHHHHHhc-CCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCCEEEEeCCCCHHHHHHHHhCCccEEEeCCCCHHH
Confidence            46789999999987 78999999999999999999999999889999999999999889999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccCCCCCC
Q 043479           82 LKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPK  161 (534)
Q Consensus        82 L~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss~kKpr  161 (534)
                      |..+|+.++++..........               ..++.    ...      ..+ .   .   .  ..       . 
T Consensus       110 l~~~i~~~~~~~~~~~~~~~~---------------~~~~~----~~~------~~~-~---~---~--~~-------~-  147 (225)
T 1kgs_A          110 LIARVRALIRRKSESKSTKLV---------------CGDLI----LDT------ATK-K---A---Y--RG-------S-  147 (225)
T ss_dssp             HHHHHHHHHHHHCCSCSSEEE---------------ETTEE----EET------TTT-E---E---E--ET-------T-
T ss_pred             HHHHHHHHHhhcccccCceEE---------------ECCEE----Eec------ccC-E---E---E--EC-------C-
Confidence            999999998775432110000               00000    000      000 0   0   0  00       0 


Q ss_pred             ccCCchhhHHHHHHHHHhccC---CCcHHHHHHHcCC--CCCCHHHHHHHHHHHHHHHH
Q 043479          162 VAWTDSLHNRFLQAIRHIGLE---KAVPKKILEFMNV--PGLTRENVASHLQKYRIFLK  215 (534)
Q Consensus       162 v~Wt~eLh~RFleaLe~LGle---kAvpK~ILe~M~V--~GLT~~tVaSHLQKyRl~lk  215 (534)
                        ....|+.++.+++..+...   ....++|++.+.-  ..++..+|+.|+.+.|..+.
T Consensus       148 --~~~~Lt~rE~~vL~~l~~~~~~~~s~~eIa~~l~~~~~~~s~~tv~~hi~~l~~Kl~  204 (225)
T 1kgs_A          148 --KEIDLTKKEYQILEYLVMNKNRVVTKEELQEHLWSFDDEVFSDVLRSHIKNLRKKVD  204 (225)
T ss_dssp             --EEECCCHHHHHHHHHHHHTTTSCEEHHHHHHHCC-----CHHHHHHHHHHHHHHHHH
T ss_pred             --EEEecCHHHHHHHHHHHhCCCcccCHHHHHHHhcCCCCCCCcchHHHHHHHHHHHhh
Confidence              0124889999999988432   1457899999862  23789999999998887553

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

Probab=99.63  E-value=3.9e-16  Score=149.56  Aligned_cols=159  Identities=17%  Similarity=0.242  Sum_probs=125.4

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++.+|++.+.. ..||+||+|+.||+++|+++++.|++..+.+|||++|+..+.....++++.||++||.||++.++
T Consensus        32 ~~~~~~~al~~l~~-~~~dlvllD~~lp~~~g~~~~~~lr~~~~~~~ii~lt~~~~~~~~~~~~~~Ga~~~l~Kp~~~~~  110 (225)
T 3c3w_A           32 EAGSVAEAMARVPA-ARPDVAVLDVRLPDGNGIELCRDLLSRMPDLRCLILTSYTSDEAMLDAILAGASGYVVKDIKGME  110 (225)
T ss_dssp             EESSHHHHHHHHHH-HCCSEEEECSEETTEEHHHHHHHHHHHCTTCEEEEGGGSSSHHHHHHHHHHTCCCHHHHHHHHHH
T ss_pred             EECCHHHHHHHHhh-cCCCEEEEeCCCCCCCHHHHHHHHHHhCCCCcEEEEECCCCHHHHHHHHHCCCCEEEECCCCHHH
Confidence            47899999999987 67999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccCCCCCC
Q 043479           82 LKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPK  161 (534)
Q Consensus        82 L~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss~kKpr  161 (534)
                      |..+|+.++++.........                 ...+....           . ..      .   ..     .  
T Consensus       111 L~~~i~~~~~~~~~~~~~~~-----------------~~~~~~~~-----------~-~~------~---~~-----~--  145 (225)
T 3c3w_A          111 LARAVKDVGAGRSLLDNRAA-----------------AALMAKLR-----------G-AA------E---KQ-----D--  145 (225)
T ss_dssp             HHHHHHHHHHHGGGSCHHHH-----------------HHHHHHHH-----------H-HH------H---HS-----C--
T ss_pred             HHHHHHHHHcCCeeeCHHHH-----------------HHHHHhcc-----------c-cc------c---cc-----c--
Confidence            99999999987553321100                 00000000           0 00      0   00     0  


Q ss_pred             ccCCchhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHH
Q 043479          162 VAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRI  212 (534)
Q Consensus       162 v~Wt~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl  212 (534)
                        ....|+.++.+++..+... ...++|++.++   ++..||+.|+.+.|.
T Consensus       146 --~~~~LT~rE~~vL~~l~~g-~s~~eIa~~l~---is~~TV~~hi~~l~~  190 (225)
T 3c3w_A          146 --PLSGLTDQERTLLGLLSEG-LTNKQIADRMF---LAEKTVKNYVSRLLA  190 (225)
T ss_dssp             --TTTTSCHHHHHHHHHHHTT-CCHHHHHHHHT---CCHHHHHHHHHHHHH
T ss_pred             --ccCCCCHHHHHHHHHHHCC-CCHHHHHHHhC---CCHHHHHHHHHHHHH
Confidence              1134899999999999644 45899999997   899999999987765

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

Probab=99.63  E-value=2e-16  Score=151.07  Aligned_cols=159  Identities=11%  Similarity=0.024  Sum_probs=119.1

Q ss_pred             cCHHHHHH-HHHhcCCceEEEEeCCCCCCCHHHHHHHHHh-hCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            4 TRPVEALA-TVRIQRDIDLVVTDLHMPEMNGIELQKEINE-EFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         4 ss~~EALe-~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~-~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+..+++. .+.. ..|||||+|+.||+++|++++++|++ ..+++|||++|+..+......+++.||++||.||+++++
T Consensus        40 ~~~~~~~~~~~~~-~~~dlvllD~~mp~~~G~~~~~~lr~~~~~~~~ii~lt~~~~~~~~~~~~~~Ga~~~l~Kp~~~~~  118 (225)
T 3klo_A           40 FSELWLEENKPES-RSIQMLVIDYSRISDDVLTDYSSFKHISCPDAKEVIINCPQDIEHKLLFKWNNLAGVFYIDDDMDT  118 (225)
T ss_dssp             GGGHHHHTTCSGG-GGCCEEEEEGGGCCHHHHHHHHHHHHHHCTTCEEEEEEECTTCCHHHHTTSTTEEEEEETTCCHHH
T ss_pred             CCcHHHHHHHhhc-cCCCEEEEeCCCCCCCHHHHHHHHHHhhCCCCcEEEEECCcchhHHHHHHHhCCCEEEecCCCHHH
Confidence            34455554 3554 67999999999999999999999999 799999999999999888899999999999999999999


Q ss_pred             HHHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccCCCCCC
Q 043479           82 LKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPK  161 (534)
Q Consensus        82 L~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss~kKpr  161 (534)
                      |..+|++++++.........                 ...+..... ..                     .   ..   .
T Consensus       119 L~~~i~~~~~~~~~~~~~~~-----------------~~~~~~~~~-~~---------------------~---~~---~  153 (225)
T 3klo_A          119 LIKGMSKILQDEMWLTRKLA-----------------QEYILHYRA-GN---------------------S---VV---T  153 (225)
T ss_dssp             HHHHHHHHHTTCCBCCHHHH-----------------HHHHHHHHT-TC---------------------C---CC---C
T ss_pred             HHHHHHHHHCCCEeeCHHHH-----------------HHHHHHhhc-cc---------------------c---cc---c
Confidence            99999999876543221100                 000000000 00                     0   00   0


Q ss_pred             ccCCchhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHH
Q 043479          162 VAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRI  212 (534)
Q Consensus       162 v~Wt~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl  212 (534)
                      -.....|+.++.+++..+..+ ...++|++.++   ++..||+.|+.+.|.
T Consensus       154 ~~~~~~Lt~rE~~vL~~l~~g-~s~~~Ia~~l~---~s~~Tv~~~i~~l~~  200 (225)
T 3klo_A          154 SQMYAKLTKREQQIIKLLGSG-ASNIEIADKLF---VSENTVKTHLHNVFK  200 (225)
T ss_dssp             CHHHHTSCHHHHHHHHHHTTT-CCHHHHHHHTT---CCHHHHHHHHHHHTT
T ss_pred             ccccccCCHHHHHHHHHHHcC-CCHHHHHHHhC---CCHHHHHHHHHHHHH
Confidence            011235899999999999754 45899999998   899999999988765

>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=99.59  E-value=1.4e-14  Score=137.08  Aligned_cols=163  Identities=17%  Similarity=0.221  Sum_probs=122.3

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++.+|++.+   ..||+||+|+.||+++|+++++.|++..+.+|||++|+..+.....++++.||++||.||++.++
T Consensus        30 ~~~~~~~al~~~---~~~dlvllD~~lp~~~g~~~~~~lr~~~~~~~ii~lt~~~~~~~~~~~~~~ga~~~l~Kp~~~~~  106 (220)
T 1p2f_A           30 TFLTGEDFLNDE---EAFHVVVLDVMLPDYSGYEICRMIKETRPETWVILLTLLSDDESVLKGFEAGADDYVTKPFNPEI  106 (220)
T ss_dssp             EESSHHHHHHCC---SCCSEEEEESBCSSSBHHHHHHHHHHHCTTSEEEEEESCCSHHHHHHHHHHTCSEEEESSCCHHH
T ss_pred             EECCHHHHHHhc---CCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCcEEEEEcCCCHHHHHHHHHcCCCEEEECCCCHHH
Confidence            467889998877   36999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccCCCCCC
Q 043479           82 LKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPK  161 (534)
Q Consensus        82 L~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss~kKpr  161 (534)
                      |..+|++++++..  .....                ..++.    ...      ..+ .     ...   .       . 
T Consensus       107 L~~~i~~~~~~~~--~~~~~----------------~~~~~----~~~------~~~-~-----~~~---~-------~-  141 (220)
T 1p2f_A          107 LLARVKRFLEREK--KGLYD----------------FGDLK----IDA------TGF-T-----VFL---K-------G-  141 (220)
T ss_dssp             HHHHHHHHHHHCC--CSEEE----------------ETTEE----EET------TTT-E-----EEE---T-------T-
T ss_pred             HHHHHHHHHcccc--ccCcc----------------cccEE----EEC------CCC-E-----EEE---C-------C-
Confidence            9999999987643  10000                00000    000      000 0     000   0       0 


Q ss_pred             ccCCchhhHHHHHHHHHhccC---CCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHH
Q 043479          162 VAWTDSLHNRFLQAIRHIGLE---KAVPKKILEFMNVPGLTRENVASHLQKYRIFL  214 (534)
Q Consensus       162 v~Wt~eLh~RFleaLe~LGle---kAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~l  214 (534)
                        ....|+.++.++++.+...   ....++|++.+.-..++..+|+.|+.+.|..+
T Consensus       142 --~~~~Lt~rE~~vl~~l~~~~~~~~s~~~Ia~~l~~~~~s~~tv~~~i~~l~~Kl  195 (220)
T 1p2f_A          142 --KRIHLPKKEFEILLFLAENAGKVVTREKLLETFWEDPVSPRVVDTVIKRIRKAI  195 (220)
T ss_dssp             --EECCCCHHHHHHHHHHHHTTTSCEEHHHHHHHHCSSCCCTHHHHHHHHHHHHHH
T ss_pred             --EEEecCHHHHHHHHHHHHCCCceEcHHHHHHHHhCCCCCcchHHHHHHHHHHHH
Confidence              0124889999999998533   25689999998633378999999999888754

>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=99.59  E-value=8.5e-15  Score=139.31  Aligned_cols=172  Identities=17%  Similarity=0.240  Sum_probs=124.9

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.+|++.+.. ..||+||+|+.||+++|+++++.|++..+.+|||++|+..+.....++++.||++||.||++.++
T Consensus        36 ~~~~~~~a~~~~~~-~~~dlvllD~~l~~~~g~~~~~~l~~~~~~~~ii~lt~~~~~~~~~~~~~~ga~~~l~Kp~~~~~  114 (233)
T 1ys7_A           36 TAVDGAEALRSATE-NRPDAIVLDINMPVLDGVSVVTALRAMDNDVPVCVLSARSSVDDRVAGLEAGADDYLVKPFVLAE  114 (233)
T ss_dssp             EESSHHHHHHHHHH-SCCSEEEEESSCSSSCHHHHHHHHHHTTCCCCEEEEECCCTTTCCCTTTTTTCSEEEESSCCHHH
T ss_pred             EECCHHHHHHHHHh-CCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCCEEEEEcCCCHHHHHHHHHcCCCEEEeCCCCHHH
Confidence            57789999999987 78999999999999999999999999888999999999998888889999999999999999999


Q ss_pred             HHHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccCCCCCC
Q 043479           82 LKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPK  161 (534)
Q Consensus        82 L~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss~kKpr  161 (534)
                      |..+|++++++..........            ......+    ...      ...+ .   .   .  ..         
T Consensus       115 L~~~i~~~~~~~~~~~~~~~~------------~~~~~~~----~~~------~~~~-~---~---~--~~---------  154 (233)
T 1ys7_A          115 LVARVKALLRRRGSTATSSSE------------TITVGPL----EVD------IPGR-R---A---R--VN---------  154 (233)
T ss_dssp             HHHHHHHHHHHHHCCCCCCCC------------EEEETTE----EEE------TTTT-E---E---E--ET---------
T ss_pred             HHHHHHHHHhhccccccccCc------------ccccCCe----EEc------cCcc-E---E---E--EC---------
Confidence            999999998775432110000            0000000    000      0000 0   0   0  00         


Q ss_pred             ccCCchhhHHHHHHHHHhccC--C-CcHHHHHHHcCCC--CCCHHHHHHHHHHHHHHHH
Q 043479          162 VAWTDSLHNRFLQAIRHIGLE--K-AVPKKILEFMNVP--GLTRENVASHLQKYRIFLK  215 (534)
Q Consensus       162 v~Wt~eLh~RFleaLe~LGle--k-AvpK~ILe~M~V~--GLT~~tVaSHLQKyRl~lk  215 (534)
                       .....|+.++.+++..+...  + ...++|++.+.-.  .++..+|+.|+.+.|..+.
T Consensus       155 -~~~~~Lt~rE~~vL~~l~~g~~~~~s~~~Ia~~l~~~~~~~s~~tv~~hi~~l~~Kl~  212 (233)
T 1ys7_A          155 -GVDVDLTKREFDLLAVLAEHKTAVLSRAQLLELVWGYDFAADTNVVDVFIGYLRRKLE  212 (233)
T ss_dssp             -TEECCCCHHHHHHHHHHHHTTTCCBCHHHHHHHHHCCCCC-CCCHHHHHHHHHHHHHH
T ss_pred             -CEEeccCHHHHHHHHHHHhCCCCeEcHHHHHHHhcCcccCCCccCHHHHHHHHHHHhc
Confidence             00124899999999998433  2 4578999988522  2678999999998887554

>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=99.58  E-value=1.3e-14  Score=138.04  Aligned_cols=171  Identities=17%  Similarity=0.232  Sum_probs=122.5

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.+|++.+.. ..||+||+|+.||+++|+++++.|++. +.+|||++|+..+.....++++.||++||.||++.++
T Consensus        33 ~~~~~~~al~~~~~-~~~dlvllD~~l~~~~g~~~~~~l~~~-~~~~ii~lt~~~~~~~~~~~~~~ga~~~l~Kp~~~~~  110 (230)
T 2oqr_A           33 VVTDGPAALAEFDR-AGADIVLLDLMLPGMSGTDVCKQLRAR-SSVPVIMVTARDSEIDKVVGLELGADDYVTKPYSARE  110 (230)
T ss_dssp             EECSHHHHHHHHHH-HCCSEEEEESSCSSSCHHHHHHHHHHH-CSCSEEEEECCHHHHHHHHHHHHCCSCCCCSSCCHHH
T ss_pred             EECCHHHHHHHHhc-cCCCEEEEECCCCCCCHHHHHHHHHcC-CCCCEEEEeCCCcHHHHHHHHHcCCCEEEeCCCCHHH
Confidence            46789999999987 679999999999999999999999986 7899999999998888999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccCCCCCC
Q 043479           82 LKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPK  161 (534)
Q Consensus        82 L~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss~kKpr  161 (534)
                      |..+|++++++..........           .......+          ..  ...         ......     .. 
T Consensus       111 l~~~i~~~~~~~~~~~~~~~~-----------~~~~~~~~----------~~--~~~---------~~~~~~-----~~-  152 (230)
T 2oqr_A          111 LIARIRAVLRRGGDDDSEMSD-----------GVLESGPV----------RM--DVE---------RHVVSV-----NG-  152 (230)
T ss_dssp             HHHHHHHHHTTTTCTTSTTCC-----------SCEEETTE----------EE--ETT---------TTEEEE-----SS-
T ss_pred             HHHHHHHHHhhcccccccccc-----------cceeecCE----------EE--ecc---------ccEEEE-----CC-
Confidence            999999998664211100000           00000000          00  000         000000     00 


Q ss_pred             ccCCchhhHHHHHHHHHhccC---CCcHHHHHHHcCC--CCCCHHHHHHHHHHHHHHH
Q 043479          162 VAWTDSLHNRFLQAIRHIGLE---KAVPKKILEFMNV--PGLTRENVASHLQKYRIFL  214 (534)
Q Consensus       162 v~Wt~eLh~RFleaLe~LGle---kAvpK~ILe~M~V--~GLT~~tVaSHLQKyRl~l  214 (534)
                        ....|+.++.++++.+...   ....++|++.+--  .+++..+|+.|+.+.|..+
T Consensus       153 --~~~~Lt~rE~~vL~~l~~~~~~~~s~~~Ia~~lw~~~~~~s~~tv~~hi~~i~~Kl  208 (230)
T 2oqr_A          153 --DTITLPLKEFDLLEYLMRNSGRVLTRGQLIDRVWGADYVGDTKTLDVHVKRLRSKI  208 (230)
T ss_dssp             --BCCCCCHHHHHHHHHHHHTTTSCEEHHHHHHHHTSSCCTTHHHHHHHHHHHHHHHH
T ss_pred             --eeeecCHHHHHHHHHHHhCCCceEcHHHHHHHhcCCCCCCCCcCHHHHHHHHHHHH
Confidence              0134899999999998533   2557899998811  1378999999998887744

>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=99.57  E-value=1.4e-14  Score=124.94  Aligned_cols=89  Identities=24%  Similarity=0.369  Sum_probs=82.6

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhh--CCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~--~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      ++.++.+|++.++. ..||+||+|+.||+++|++++++|++.  .+.+|||++|+..+.....++++.||++||.||++.
T Consensus        31 ~~~~~~~al~~l~~-~~~dlvllD~~~p~~~g~~~~~~l~~~~~~~~~pii~~s~~~~~~~~~~~~~~Ga~~~l~KP~~~  109 (122)
T 3gl9_A           31 EAENGQIALEKLSE-FTPDLIVLXIMMPVMDGFTVLKKLQEKEEWKRIPVIVLTAKGGEEDESLALSLGARKVMRKPFSP  109 (122)
T ss_dssp             EESSHHHHHHHHTT-BCCSEEEECSCCSSSCHHHHHHHHHTSTTTTTSCEEEEESCCSHHHHHHHHHTTCSEEEESSCCH
T ss_pred             EeCCHHHHHHHHHh-cCCCEEEEeccCCCCcHHHHHHHHHhcccccCCCEEEEecCCchHHHHHHHhcChhhhccCCCCH
Confidence            57899999999987 789999999999999999999999875  467999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHH
Q 043479           80 DDLKNVWQYAMT   91 (534)
Q Consensus        80 eeL~~aI~~aL~   91 (534)
                      ++|..+|+++++
T Consensus       110 ~~L~~~i~~~l~  121 (122)
T 3gl9_A          110 SQFIEEVKHLLN  121 (122)
T ss_dssp             HHHHHHHHHHHC
T ss_pred             HHHHHHHHHHhc
Confidence            999999998863

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

Probab=99.57  E-value=1.3e-14  Score=139.60  Aligned_cols=167  Identities=21%  Similarity=0.313  Sum_probs=120.9

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.+|++.+.. ..||+||+|+.||+++|+++++.|++.. .+|||++|+..+.....++++.||++||.||++.++
T Consensus        34 ~~~~~~~al~~l~~-~~~dlvilD~~l~~~~g~~~~~~lr~~~-~~~ii~lt~~~~~~~~~~~~~~Ga~~~l~Kp~~~~~  111 (238)
T 2gwr_A           34 VIGDGTQALTAVRE-LRPDLVLLDLMLPGMNGIDVCRVLRADS-GVPIVMLTAKTDTVDVVLGLESGADDYIMKPFKPKE  111 (238)
T ss_dssp             EECCGGGHHHHHHH-HCCSEEEEESSCSSSCHHHHHHHHHTTC-CCCEEEEEETTCCSCHHHHHHTTCCEEEEESCCHHH
T ss_pred             EECCHHHHHHHHHh-CCCCEEEEeCCCCCCCHHHHHHHHHhCC-CCcEEEEeCCCCHHHHHHHHHCCCCEEEeCCCCHHH
Confidence            46789999999987 6899999999999999999999999864 799999999999888899999999999999999999


Q ss_pred             HHHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccCCCCCC
Q 043479           82 LKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKKPK  161 (534)
Q Consensus        82 L~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss~kKpr  161 (534)
                      |..+|+.++++........               ....++    ....      ..+ .          ...     .. 
T Consensus       112 L~~~i~~~~~~~~~~~~~~---------------~~~~~~----~~~~------~~~-~----------~~~-----~~-  149 (238)
T 2gwr_A          112 LVARVRARLRRNDDEPAEM---------------LSIADV----EIDV------PAH-K----------VTR-----NG-  149 (238)
T ss_dssp             HHHHHHHHCCCCSSCCCCE---------------EEETTE----EEET------TTT-E----------EEE-----TT-
T ss_pred             HHHHHHHHHhhcccCcccc---------------eecCce----EEcc------ccc-E----------EEE-----CC-
Confidence            9999999875532210000               000000    0000      000 0          000     00 


Q ss_pred             ccCCchhhHHHHHHHHHhccC---CCcHHHHHHHcC-C-CCCCHHHHHHHHHHHHHHH
Q 043479          162 VAWTDSLHNRFLQAIRHIGLE---KAVPKKILEFMN-V-PGLTRENVASHLQKYRIFL  214 (534)
Q Consensus       162 v~Wt~eLh~RFleaLe~LGle---kAvpK~ILe~M~-V-~GLT~~tVaSHLQKyRl~l  214 (534)
                        ....|+.++.+++..+...   ....++|++.+- . .+++..+|+.|+.+.|..+
T Consensus       150 --~~~~LT~rE~~vL~~l~~~~~~~~s~~eIa~~lw~~~~~~s~~tV~~hi~~lr~KL  205 (238)
T 2gwr_A          150 --EQISLTPLEFDLLVALARKPRQVFTRDVLLEQVWGYRHPADTRLVNVHVQRLRAKV  205 (238)
T ss_dssp             --EEECCCHHHHHHHHHHHHSTTCCBCHHHHHHHHTCCC--CCTHHHHHHHHHHHHHH
T ss_pred             --EEcccCHHHHHHHHHHHHCCCceecHHHHHHHHcCCCCCCCcccHHHHHHHHHHHh
Confidence              0134899999999998533   255889999881 1 1378999999999888754

>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=99.56  E-value=3.3e-14  Score=124.90  Aligned_cols=93  Identities=19%  Similarity=0.365  Sum_probs=84.1

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhh--CCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~--~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      ++.++.+|++.+.. ..||+||+|+.||+++|++++++|++.  .+.+|||++|+..+.....++++.||++||.||++.
T Consensus        33 ~~~~~~~al~~~~~-~~~dlvl~D~~lp~~~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~~~~~ga~~~l~KP~~~  111 (136)
T 3t6k_A           33 RAASGEEALQQIYK-NLPDALICDVLLPGIDGYTLCKRVRQHPLTKTLPILMLTAQGDISAKIAGFEAGANDYLAKPFEP  111 (136)
T ss_dssp             EESSHHHHHHHHHH-SCCSEEEEESCCSSSCHHHHHHHHHHSGGGTTCCEEEEECTTCHHHHHHHHHHTCSEEEETTCCH
T ss_pred             EeCCHHHHHHHHHh-CCCCEEEEeCCCCCCCHHHHHHHHHcCCCcCCccEEEEecCCCHHHHHHHHhcCcceEEeCCCCH
Confidence            57899999999987 789999999999999999999999874  567999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhh
Q 043479           80 DDLKNVWQYAMTYKKA   95 (534)
Q Consensus        80 eeL~~aI~~aL~~k~~   95 (534)
                      ++|..+|++++++...
T Consensus       112 ~~L~~~i~~~l~~~~~  127 (136)
T 3t6k_A          112 QELVYRVKNILARTTI  127 (136)
T ss_dssp             HHHHHHHHHHHHC---
T ss_pred             HHHHHHHHHHHhccCC
Confidence            9999999999876543

>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=99.54  E-value=2.8e-14  Score=122.44  Aligned_cols=89  Identities=21%  Similarity=0.421  Sum_probs=82.3

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++.+|++.++. ..||+||+|+.||+++|++++++|++.. .+|||++|+..+.....++++.||++||.||++.++
T Consensus        31 ~~~~~~~al~~~~~-~~~dlii~D~~~p~~~g~~~~~~lr~~~-~~~ii~~t~~~~~~~~~~~~~~ga~~~l~KP~~~~~  108 (120)
T 3f6p_A           31 CAHDGNEAVEMVEE-LQPDLILLDIMLPNKDGVEVCREVRKKY-DMPIIMLTAKDSEIDKVIGLEIGADDYVTKPFSTRE  108 (120)
T ss_dssp             EESSHHHHHHHHHT-TCCSEEEEETTSTTTHHHHHHHHHHTTC-CSCEEEEEESSCHHHHHHHHHTTCCEEEEESCCHHH
T ss_pred             EeCCHHHHHHHHhh-CCCCEEEEeCCCCCCCHHHHHHHHHhcC-CCCEEEEECCCChHHHHHHHhCCcceeEcCCCCHHH
Confidence            47799999999987 7899999999999999999999999754 699999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHH
Q 043479           82 LKNVWQYAMTY   92 (534)
Q Consensus        82 L~~aI~~aL~~   92 (534)
                      |..+|++++++
T Consensus       109 l~~~i~~~l~~  119 (120)
T 3f6p_A          109 LLARVKANLRR  119 (120)
T ss_dssp             HHHHHHHHHTC
T ss_pred             HHHHHHHHHhc
Confidence            99999988753

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

Probab=99.54  E-value=3.9e-14  Score=123.49  Aligned_cols=93  Identities=22%  Similarity=0.369  Sum_probs=84.0

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.+|++.++. ..||+||+|+.||+++|++++++|++..+.+|||++|+..+.....++++.||++||.||++.++
T Consensus        34 ~~~~~~~al~~~~~-~~~dlvilD~~lp~~~g~~~~~~l~~~~~~~~ii~ls~~~~~~~~~~~~~~ga~~~l~Kp~~~~~  112 (133)
T 3b2n_A           34 DTDNGLDAMKLIEE-YNPNVVILDIEMPGMTGLEVLAEIRKKHLNIKVIIVTTFKRPGYFEKAVVNDVDAYVLKERSIEE  112 (133)
T ss_dssp             EESCHHHHHHHHHH-HCCSEEEECSSCSSSCHHHHHHHHHHTTCSCEEEEEESCCCHHHHHHHHHTTCSEEEETTSCHHH
T ss_pred             EcCCHHHHHHHHhh-cCCCEEEEecCCCCCCHHHHHHHHHHHCCCCcEEEEecCCCHHHHHHHHHcCCcEEEECCCCHHH
Confidence            46789999999987 67999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhh
Q 043479           82 LKNVWQYAMTYKKA   95 (534)
Q Consensus        82 L~~aI~~aL~~k~~   95 (534)
                      |..+|+++++++..
T Consensus       113 L~~~i~~~~~~~~~  126 (133)
T 3b2n_A          113 LVETINKVNNGEKE  126 (133)
T ss_dssp             HHHHHHHHHC----
T ss_pred             HHHHHHHHHcCCCc
Confidence            99999999866543

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

Probab=99.53  E-value=6.6e-14  Score=121.82  Aligned_cols=94  Identities=20%  Similarity=0.330  Sum_probs=87.1

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.++++.+.. ..||+||+|+.||+++|+++++.|++..+.+|||++|+..+.....++++.||++||.||++.++
T Consensus        32 ~~~~~~~al~~~~~-~~~dlvl~D~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~KP~~~~~  110 (132)
T 3crn_A           32 IAATAGEGLAKIEN-EFFNLALFXIKLPDMEGTELLEKAHKLRPGMKKIMVTGYASLENSVFSLNAGADAYIMKPVNPRD  110 (132)
T ss_dssp             EESSHHHHHHHHHH-SCCSEEEECSBCSSSBHHHHHHHHHHHCTTSEEEEEESCCCHHHHHHHHHTTCSEEEESSCCHHH
T ss_pred             EeCCHHHHHHHHhc-CCCCEEEEecCCCCCchHHHHHHHHhhCCCCcEEEEeccccHHHHHHHHhccchhhccCCCCHHH
Confidence            46789999999987 78999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhc
Q 043479           82 LKNVWQYAMTYKKAK   96 (534)
Q Consensus        82 L~~aI~~aL~~k~~~   96 (534)
                      |..+|++++++....
T Consensus       111 L~~~i~~~~~~~~~~  125 (132)
T 3crn_A          111 LLEKIKEKLDEQEKE  125 (132)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcccCC
Confidence            999999998776543

>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=99.53  E-value=1.1e-13  Score=117.35  Aligned_cols=91  Identities=20%  Similarity=0.321  Sum_probs=84.7

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.+|++.+.. ..||+||+|+.||+++|+++++.+++..+.+|||++|+..+.....++++.|+++||.||++.++
T Consensus        29 ~~~~~~~a~~~~~~-~~~dlil~D~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~kp~~~~~  107 (121)
T 2pl1_A           29 DAEDAKEADYYLNE-HIPDIAIVDLGLPDEDGLSLIRRWRSNDVSLPILVLTARESWQDKVEVLSAGADDYVTKPFHIEE  107 (121)
T ss_dssp             EESSHHHHHHHHHH-SCCSEEEECSCCSSSCHHHHHHHHHHTTCCSCEEEEESCCCHHHHHHHHHTTCSEEEESSCCHHH
T ss_pred             EeCCHHHHHHHHhc-cCCCEEEEecCCCCCCHHHHHHHHHhcCCCCCEEEEecCCCHHHHHHHHHcCccceEECCCCHHH
Confidence            46789999999987 78999999999999999999999998888899999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHh
Q 043479           82 LKNVWQYAMTYK   93 (534)
Q Consensus        82 L~~aI~~aL~~k   93 (534)
                      |..+|++++++.
T Consensus       108 l~~~i~~~~~~~  119 (121)
T 2pl1_A          108 VMARMQALMRRN  119 (121)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhh
Confidence            999999988653

>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=99.53  E-value=8.4e-14  Score=119.72  Aligned_cols=90  Identities=22%  Similarity=0.340  Sum_probs=83.9

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.++++.+.. ..||+||+|+.||+++|++++++|++..+.+|||++|+..+.....++++.||++||.||++.++
T Consensus        32 ~~~~~~~~~~~~~~-~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~Kp~~~~~  110 (126)
T 1dbw_A           32 MHQSAEAFLAFAPD-VRNGVLVTDLRMPDMSGVELLRNLGDLKINIPSIVITGHGDVPMAVEAMKAGAVDFIEKPFEDTV  110 (126)
T ss_dssp             EESCHHHHHHHGGG-CCSEEEEEECCSTTSCHHHHHHHHHHTTCCCCEEEEECTTCHHHHHHHHHTTCSEEEESSCCHHH
T ss_pred             EeCCHHHHHHHHhc-CCCCEEEEECCCCCCCHHHHHHHHHhcCCCCCEEEEECCCCHHHHHHHHHhCHHHheeCCCCHHH
Confidence            46789999999887 78999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHH
Q 043479           82 LKNVWQYAMTY   92 (534)
Q Consensus        82 L~~aI~~aL~~   92 (534)
                      |..+|++++++
T Consensus       111 l~~~i~~~~~~  121 (126)
T 1dbw_A          111 IIEAIERASEH  121 (126)
T ss_dssp             HHHHHHHHHTT
T ss_pred             HHHHHHHHHHh
Confidence            99999998753

>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=99.53  E-value=6e-14  Score=121.63  Aligned_cols=90  Identities=30%  Similarity=0.626  Sum_probs=81.9

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhh--CCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~--~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      .+.++.++++.+.....||+||+|+.||+++|++++++|++.  .+.+|||++|+..+.....++++.||++||.||++.
T Consensus        35 ~~~~~~~a~~~~~~~~~~dlvi~D~~~p~~~g~~~~~~lr~~~~~~~~pii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~  114 (129)
T 3h1g_A           35 EAEHGVEAWEKLDANADTKVLITDWNMPEMNGLDLVKKVRSDSRFKEIPIIMITAEGGKAEVITALKAGVNNYIVKPFTP  114 (129)
T ss_dssp             EESSHHHHHHHHHHCTTCCEEEECSCCSSSCHHHHHHHHHTSTTCTTCCEEEEESCCSHHHHHHHHHHTCCEEEESCCCH
T ss_pred             EeCCHHHHHHHHHhCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCCCeEEEEeCCCChHHHHHHHHcCccEEEeCCCCH
Confidence            467899999988763479999999999999999999999973  478999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHH
Q 043479           80 DDLKNVWQYAMT   91 (534)
Q Consensus        80 eeL~~aI~~aL~   91 (534)
                      ++|..+|+.++.
T Consensus       115 ~~L~~~l~~~l~  126 (129)
T 3h1g_A          115 QVLKEKLEVVLG  126 (129)
T ss_dssp             HHHHHHHHHHHC
T ss_pred             HHHHHHHHHHhc
Confidence            999999999874

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

Probab=99.52  E-value=6.1e-14  Score=124.67  Aligned_cols=94  Identities=23%  Similarity=0.341  Sum_probs=87.9

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++.+|++.+.. ..|||||+|+.||+++|+++++.|++..+.+|||++|+..+.....++++.||++||.||++.++
T Consensus        51 ~~~~~~~al~~l~~-~~~dlii~D~~l~~~~g~~~~~~l~~~~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~Kp~~~~~  129 (150)
T 4e7p_A           51 QAKNGQEAIQLLEK-ESVDIAILDVEMPVKTGLEVLEWIRSEKLETKVVVVTTFKRAGYFERAVKAGVDAYVLKERSIAD  129 (150)
T ss_dssp             EESSHHHHHHHHTT-SCCSEEEECSSCSSSCHHHHHHHHHHTTCSCEEEEEESCCCHHHHHHHHHTTCSEEEETTSCHHH
T ss_pred             EECCHHHHHHHhhc-cCCCEEEEeCCCCCCcHHHHHHHHHHhCCCCeEEEEeCCCCHHHHHHHHHCCCcEEEecCCCHHH
Confidence            47799999999987 78999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhc
Q 043479           82 LKNVWQYAMTYKKAK   96 (534)
Q Consensus        82 L~~aI~~aL~~k~~~   96 (534)
                      |..+|+++++++...
T Consensus       130 l~~~i~~~~~~~~~~  144 (150)
T 4e7p_A          130 LMQTLHTVLEGRKEY  144 (150)
T ss_dssp             HHHHHHHHHTTCCEE
T ss_pred             HHHHHHHHHcCCEEc
Confidence            999999999776543

>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=99.51  E-value=8.2e-14  Score=121.86  Aligned_cols=91  Identities=21%  Similarity=0.342  Sum_probs=81.5

Q ss_pred             eecCHHHHHHHHHh----cCCceEEEEeCCCCCCCHHHHHHHHHhh-CCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCC
Q 043479            2 TVTRPVEALATVRI----QRDIDLVVTDLHMPEMNGIELQKEINEE-FTHLPVMVMSSDDRESVIMKALASGVAFYILKP   76 (534)
Q Consensus         2 tass~~EALe~L~~----~~~pDLVLLDi~mPdmdGleLL~~Lr~~-~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP   76 (534)
                      ++.++.+|++.++.    ...||+||+|+.||+++|+++++.|++. .+.+|||++|+..+.....++++.||++||.||
T Consensus        32 ~~~~~~~al~~~~~~~~~~~~~dlvllD~~mp~~~G~~~~~~lr~~~~~~~~ii~lt~~~~~~~~~~~~~~ga~~~l~KP  111 (133)
T 2r25_B           32 LACDGQEAFDKVKELTSKGENYNMIFMDVQMPKVDGLLSTKMIRRDLGYTSPIVALTAFADDSNIKECLESGMNGFLSKP  111 (133)
T ss_dssp             EESSHHHHHHHHHHHHHHTCCCSEEEECSCCSSSCHHHHHHHHHHHSCCCSCEEEEESCCSHHHHHHHHHTTCSEEEESS
T ss_pred             EECCHHHHHHHHHHHHhcCCCCCEEEEeCCCCCCChHHHHHHHHhhcCCCCCEEEEECCCCHHHHHHHHHcCCCEEEeCC
Confidence            46789999998864    1469999999999999999999999974 567899999999999999999999999999999


Q ss_pred             CChHHHHHHHHHHHHH
Q 043479           77 LNPDDLKNVWQYAMTY   92 (534)
Q Consensus        77 ~s~eeL~~aI~~aL~~   92 (534)
                      ++.++|..+|++++..
T Consensus       112 ~~~~~L~~~l~~~~~~  127 (133)
T 2r25_B          112 IKRPKLKTILTEFCAA  127 (133)
T ss_dssp             CCHHHHHHHHHHHCTT
T ss_pred             CCHHHHHHHHHHHHHh
Confidence            9999999999988643

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

Probab=99.51  E-value=1.5e-13  Score=120.41  Aligned_cols=96  Identities=26%  Similarity=0.442  Sum_probs=88.4

Q ss_pred             eecCHHHHHHHHHh-cCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChH
Q 043479            2 TVTRPVEALATVRI-QRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPD   80 (534)
Q Consensus         2 tass~~EALe~L~~-~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~e   80 (534)
                      ++.+..+|++.+.. ...||+||+|+.||+++|+++++.|++..+.+|||++|+..+.....++++.||++||.||++.+
T Consensus        32 ~~~~~~~a~~~~~~~~~~~dlvi~d~~l~~~~g~~~~~~l~~~~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~kp~~~~  111 (143)
T 3jte_A           32 TASSSTEGLRIFTENCNSIDVVITDMKMPKLSGMDILREIKKITPHMAVIILTGHGDLDNAILAMKEGAFEYLRKPVTAQ  111 (143)
T ss_dssp             EESSHHHHHHHHHHTTTTCCEEEEESCCSSSCHHHHHHHHHHHCTTCEEEEEECTTCHHHHHHHHHTTCSEEEESSCCHH
T ss_pred             EeCCHHHHHHHHHhCCCCCCEEEEeCCCCCCcHHHHHHHHHHhCCCCeEEEEECCCCHHHHHHHHHhCcceeEeCCCCHH
Confidence            57789999999983 16899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhhcc
Q 043479           81 DLKNVWQYAMTYKKAKS   97 (534)
Q Consensus        81 eL~~aI~~aL~~k~~~s   97 (534)
                      +|..+|++++++++...
T Consensus       112 ~l~~~l~~~~~~~~~~~  128 (143)
T 3jte_A          112 DLSIAINNAINRKKLLM  128 (143)
T ss_dssp             HHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            99999999998776543

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

Probab=99.50  E-value=1.3e-13  Score=122.90  Aligned_cols=94  Identities=23%  Similarity=0.453  Sum_probs=88.0

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcC-CcEEEeCCCChH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASG-VAFYILKPLNPD   80 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aG-A~dyL~KP~s~e   80 (534)
                      ++.++.+|++.+.. ..|||||+|+.||+++|+++++.|++..+.+|||++|+..+.....++++.| |++||.||++.+
T Consensus        43 ~~~~~~~a~~~l~~-~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~~l~KP~~~~  121 (153)
T 3hv2_A           43 FARDATQALQLLAS-REVDLVISAAHLPQMDGPTLLARIHQQYPSTTRILLTGDPDLKLIAKAINEGEIYRYLSKPWDDQ  121 (153)
T ss_dssp             EESSHHHHHHHHHH-SCCSEEEEESCCSSSCHHHHHHHHHHHCTTSEEEEECCCCCHHHHHHHHHTTCCSEEECSSCCHH
T ss_pred             EECCHHHHHHHHHc-CCCCEEEEeCCCCcCcHHHHHHHHHhHCCCCeEEEEECCCCHHHHHHHHhCCCcceEEeCCCCHH
Confidence            57799999999987 7899999999999999999999999999999999999999999999999999 999999999999


Q ss_pred             HHHHHHHHHHHHhhhc
Q 043479           81 DLKNVWQYAMTYKKAK   96 (534)
Q Consensus        81 eL~~aI~~aL~~k~~~   96 (534)
                      +|..+|++++++....
T Consensus       122 ~l~~~i~~~l~~~~~~  137 (153)
T 3hv2_A          122 ELLLALRQALEHQHSE  137 (153)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhHHH
Confidence            9999999999876543

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

Probab=99.50  E-value=1.2e-13  Score=122.86  Aligned_cols=95  Identities=18%  Similarity=0.280  Sum_probs=86.7

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++.+|++.++. ..|||||+|+.||+++|+++++.|++..+.+|||++|+..+.....++++.||++||.||++.++
T Consensus        46 ~~~~~~~a~~~l~~-~~~dlii~d~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~Kp~~~~~  124 (152)
T 3eul_A           46 EADDGAAALELIKA-HLPDVALLDYRMPGMDGAQVAAAVRSYELPTRVLLISAHDEPAIVYQALQQGAAGFLLKDSTRTE  124 (152)
T ss_dssp             EESSHHHHHHHHHH-HCCSEEEEETTCSSSCHHHHHHHHHHTTCSCEEEEEESCCCHHHHHHHHHTTCSEEEETTCCHHH
T ss_pred             EeCCHHHHHHHHHh-cCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCeEEEEEccCCHHHHHHHHHcCCCEEEecCCCHHH
Confidence            47899999999987 68999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhcc
Q 043479           82 LKNVWQYAMTYKKAKS   97 (534)
Q Consensus        82 L~~aI~~aL~~k~~~s   97 (534)
                      |..+|+++++++...+
T Consensus       125 l~~~i~~~~~~~~~~~  140 (152)
T 3eul_A          125 IVKAVLDCAKGRDVVA  140 (152)
T ss_dssp             HHHHHHHHHHCC----
T ss_pred             HHHHHHHHHcCCeeeC
Confidence            9999999998766554

>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=99.50  E-value=7.5e-14  Score=119.45  Aligned_cols=89  Identities=22%  Similarity=0.375  Sum_probs=83.1

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++.+|++.++. ..||+||+|+.||+++|+++++.+++..+.+|||++|+..+.....++++.|+++||.||++.++
T Consensus        32 ~~~~~~~a~~~~~~-~~~dlvl~D~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~  110 (124)
T 1srr_A           32 QAANGLQALDIVTK-ERPDLVLLDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFAKPFDIDE  110 (124)
T ss_dssp             EESSHHHHHHHHHH-HCCSEEEEESCCTTCCHHHHHHHHHHHCTTCEEEEEESSCCHHHHHHHHHHTCCCEEESSCCHHH
T ss_pred             EeCCHHHHHHHHhc-cCCCEEEEecCCCCCCHHHHHHHHHHhCCCCCEEEEEccCchHHHHHHHhcChHhhccCCCCHHH
Confidence            46789999999987 68999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHH
Q 043479           82 LKNVWQYAMT   91 (534)
Q Consensus        82 L~~aI~~aL~   91 (534)
                      |..+|+++++
T Consensus       111 l~~~i~~~~~  120 (124)
T 1srr_A          111 IRDAVKKYLP  120 (124)
T ss_dssp             HHHHHHHHSC
T ss_pred             HHHHHHHHhc
Confidence            9999988764

>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=99.50  E-value=7.9e-14  Score=121.36  Aligned_cols=95  Identities=24%  Similarity=0.372  Sum_probs=88.8

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.+|++.++. ..|||||+|+.||+++|+++++.|++..+.+|||++|+..+.+...++++.||++||.||++.++
T Consensus        36 ~~~~~~~a~~~l~~-~~~dlvi~d~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~kP~~~~~  114 (137)
T 3hdg_A           36 SAGDGEEGERLFGL-HAPDVIITDIRMPKLGGLEMLDRIKAGGAKPYVIVISAFSEMKYFIKAIELGVHLFLPKPIEPGR  114 (137)
T ss_dssp             EESSHHHHHHHHHH-HCCSEEEECSSCSSSCHHHHHHHHHHTTCCCEEEECCCCCCHHHHHHHHHHCCSEECCSSCCHHH
T ss_pred             EECCHHHHHHHHhc-cCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCcEEEEecCcChHHHHHHHhCCcceeEcCCCCHHH
Confidence            57799999999987 68999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhcc
Q 043479           82 LKNVWQYAMTYKKAKS   97 (534)
Q Consensus        82 L~~aI~~aL~~k~~~s   97 (534)
                      |..+|+++++++....
T Consensus       115 l~~~i~~~~~~~~~~~  130 (137)
T 3hdg_A          115 LMETLEDFRHIKLAKE  130 (137)
T ss_dssp             HHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHhcCC
Confidence            9999999998876543

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

Probab=99.50  E-value=3.8e-14  Score=122.64  Aligned_cols=95  Identities=15%  Similarity=0.166  Sum_probs=85.5

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++++|++.+.. ..||+||+|+.||+++|+++++.|++..+.+|||++|+..+.....++++.|+++||.||++.++
T Consensus        31 ~~~~~~~a~~~~~~-~~~dlii~d~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~kp~~~~~  109 (134)
T 3f6c_A           31 ELTEGGSAVQRVET-LKPDIVIIDVDIPGVNGIQVLETLRKRQYSGIIIIVSAKNDHFYGKHCADAGANGFVSKKEGMNN  109 (134)
T ss_dssp             EESSSTTHHHHHHH-HCCSEEEEETTCSSSCHHHHHHHHHHTTCCSEEEEEECC---CTHHHHHHTTCSEEEEGGGCTHH
T ss_pred             EcCCHHHHHHHHHh-cCCCEEEEecCCCCCChHHHHHHHHhcCCCCeEEEEeCCCChHHHHHHHHhCCCEEEeCCCCHHH
Confidence            46788999999987 78999999999999999999999999999999999999999888999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhcc
Q 043479           82 LKNVWQYAMTYKKAKS   97 (534)
Q Consensus        82 L~~aI~~aL~~k~~~s   97 (534)
                      |..+|+++++++...+
T Consensus       110 l~~~i~~~~~~~~~~~  125 (134)
T 3f6c_A          110 IIAAIEAAKNGYCYFP  125 (134)
T ss_dssp             HHHHHHHHHTTCCBCC
T ss_pred             HHHHHHHHHCCCEEeC
Confidence            9999999998776554

>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=99.50  E-value=1e-13  Score=117.63  Aligned_cols=88  Identities=27%  Similarity=0.433  Sum_probs=82.3

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.+|++.+.. ..||+||+|+.||+++|+++++++++..+.+|||++|+..+.....++++.|+++||.||++.++
T Consensus        32 ~~~~~~~a~~~~~~-~~~dlil~D~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~  110 (120)
T 1tmy_A           32 EATNGREAVEKYKE-LKPDIVTMDITMPEMNGIDAIKEIMKIDPNAKIIVCSAMGQQAMVIEAIKAGAKDFIVKPFQPSR  110 (120)
T ss_dssp             EESSHHHHHHHHHH-HCCSEEEEECSCGGGCHHHHHHHHHHHCTTCCEEEEECTTCHHHHHHHHHTTCCEEEESSCCHHH
T ss_pred             EECCHHHHHHHHHh-cCCCEEEEeCCCCCCcHHHHHHHHHhhCCCCeEEEEeCCCCHHHHHHHHHhCcceeEeCCCCHHH
Confidence            46789999999987 68999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             HHHHHHHHH
Q 043479           82 LKNVWQYAM   90 (534)
Q Consensus        82 L~~aI~~aL   90 (534)
                      |..+|++++
T Consensus       111 l~~~i~~~~  119 (120)
T 1tmy_A          111 VVEALNKVS  119 (120)
T ss_dssp             HHHHHHHHC
T ss_pred             HHHHHHHHh
Confidence            999998764

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

Probab=99.49  E-value=1.5e-13  Score=120.71  Aligned_cols=92  Identities=21%  Similarity=0.358  Sum_probs=85.6

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.+|++.+.. ..||+||+|+.||+++|+++++.|++..+.+|||++|+..+.....++++.||++||.||++.++
T Consensus        33 ~~~~~~~a~~~l~~-~~~dlvllD~~l~~~~g~~l~~~l~~~~~~~~ii~ls~~~~~~~~~~~~~~ga~~~l~KP~~~~~  111 (137)
T 3cfy_A           33 HVETGRDAIQFIER-SKPQLIILDLKLPDMSGEDVLDWINQNDIPTSVIIATAHGSVDLAVNLIQKGAEDFLEKPINADR  111 (137)
T ss_dssp             EESSHHHHHHHHHH-HCCSEEEECSBCSSSBHHHHHHHHHHTTCCCEEEEEESSCCHHHHHHHHHTTCSEEEESSCCHHH
T ss_pred             EeCCHHHHHHHHHh-cCCCEEEEecCCCCCCHHHHHHHHHhcCCCCCEEEEEecCcHHHHHHHHHCCccEEEeCCCCHHH
Confidence            46789999999987 68999999999999999999999999888899999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhh
Q 043479           82 LKNVWQYAMTYKK   94 (534)
Q Consensus        82 L~~aI~~aL~~k~   94 (534)
                      |..+|++++++..
T Consensus       112 L~~~i~~~~~~~~  124 (137)
T 3cfy_A          112 LKTSVALHLKRAK  124 (137)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999987654

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

Probab=99.49  E-value=9.3e-14  Score=119.83  Aligned_cols=91  Identities=30%  Similarity=0.412  Sum_probs=77.7

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCC-ChH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPL-NPD   80 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~-s~e   80 (534)
                      .+.++.+|++.++. .+||+||+|+.+|+++|+++++.|++..+.+|||++|+..+.....++++.|+++||.||+ +.+
T Consensus        36 ~~~~~~~a~~~l~~-~~~dlvi~d~~l~~~~g~~~~~~l~~~~~~~~ii~~t~~~~~~~~~~~~~~g~~~~l~KP~~~~~  114 (130)
T 3eod_A           36 LAADGVDALELLGG-FTPDLMICDIAMPRMNGLKLLEHIRNRGDQTPVLVISATENMADIAKALRLGVEDVLLKPVKDLN  114 (130)
T ss_dssp             EESCHHHHHHHHTT-CCCSEEEECCC-----CHHHHHHHHHTTCCCCEEEEECCCCHHHHHHHHHHCCSEEEESCC---C
T ss_pred             EeCCHHHHHHHHhc-CCCCEEEEecCCCCCCHHHHHHHHHhcCCCCCEEEEEcCCCHHHHHHHHHcCCCEEEeCCCCcHH
Confidence            46799999999987 7899999999999999999999999999999999999999999999999999999999999 899


Q ss_pred             HHHHHHHHHHHHh
Q 043479           81 DLKNVWQYAMTYK   93 (534)
Q Consensus        81 eL~~aI~~aL~~k   93 (534)
                      +|..+|++++.++
T Consensus       115 ~l~~~i~~~l~~~  127 (130)
T 3eod_A          115 RLREMVFACLYPS  127 (130)
T ss_dssp             HHHHHHHHHHC--
T ss_pred             HHHHHHHHHhchh
Confidence            9999999998654

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

Probab=99.49  E-value=5e-14  Score=123.25  Aligned_cols=94  Identities=21%  Similarity=0.230  Sum_probs=86.8

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCC--CCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPE--MNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPd--mdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      ++.++.+|++.++. ..||+||+|+.||+  ++|++++++|++..+.+|||++|+..+.....++++.||++||.||++.
T Consensus        35 ~~~~~~~a~~~l~~-~~~dlvi~D~~l~~~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~KP~~~  113 (136)
T 3kto_A           35 CFASAESFMRQQIS-DDAIGMIIEAHLEDKKDSGIELLETLVKRGFHLPTIVMASSSDIPTAVRAMRASAADFIEKPFIE  113 (136)
T ss_dssp             EESSHHHHTTSCCC-TTEEEEEEETTGGGBTTHHHHHHHHHHHTTCCCCEEEEESSCCHHHHHHHHHTTCSEEEESSBCH
T ss_pred             EeCCHHHHHHHHhc-cCCCEEEEeCcCCCCCccHHHHHHHHHhCCCCCCEEEEEcCCCHHHHHHHHHcChHHheeCCCCH
Confidence            57789999999876 78999999999999  9999999999999899999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhhc
Q 043479           80 DDLKNVWQYAMTYKKAK   96 (534)
Q Consensus        80 eeL~~aI~~aL~~k~~~   96 (534)
                      ++|..+|++++.+....
T Consensus       114 ~~l~~~i~~~~~~~~~~  130 (136)
T 3kto_A          114 HVLVHDVQQIINGAKEG  130 (136)
T ss_dssp             HHHHHHHHHHHHHHC--
T ss_pred             HHHHHHHHHHHhccCCC
Confidence            99999999999876543

>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=99.49  E-value=2e-13  Score=119.99  Aligned_cols=93  Identities=20%  Similarity=0.331  Sum_probs=86.8

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHh--hCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCC-C
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINE--EFTHLPVMVMSSDDRESVIMKALASGVAFYILKPL-N   78 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~--~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~-s   78 (534)
                      .+.++.+|++.+.. ..||+||+|+.||+++|+++++.|++  ..+.+|||++|+..+.....++++.||++||.||+ +
T Consensus        36 ~~~~~~~a~~~l~~-~~~dlii~D~~l~~~~g~~~~~~lr~~~~~~~~pii~~s~~~~~~~~~~~~~~ga~~~l~Kp~~~  114 (144)
T 3kht_A           36 FVDNGAKALYQVQQ-AKYDLIILDIGLPIANGFEVMSAVRKPGANQHTPIVILTDNVSDDRAKQCMAAGASSVVDKSSNN  114 (144)
T ss_dssp             EESSHHHHHHHHTT-CCCSEEEECTTCGGGCHHHHHHHHHSSSTTTTCCEEEEETTCCHHHHHHHHHTTCSEEEECCTTS
T ss_pred             EECCHHHHHHHhhc-CCCCEEEEeCCCCCCCHHHHHHHHHhcccccCCCEEEEeCCCCHHHHHHHHHcCCCEEEECCCCc
Confidence            46799999999987 78999999999999999999999998  67889999999999999999999999999999999 9


Q ss_pred             hHHHHHHHHHHHHHhhh
Q 043479           79 PDDLKNVWQYAMTYKKA   95 (534)
Q Consensus        79 ~eeL~~aI~~aL~~k~~   95 (534)
                      .++|..+|+++++++..
T Consensus       115 ~~~l~~~i~~~l~~~~~  131 (144)
T 3kht_A          115 VTDFYGRIYAIFSYWLT  131 (144)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHh
Confidence            99999999999987654

>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=99.49  E-value=3.5e-13  Score=114.72  Aligned_cols=89  Identities=17%  Similarity=0.307  Sum_probs=82.5

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.++++.+.. ..||+||+|+.||+++|+++++.+++ .+.+|||++|+..+.....++++.|+++||.||++.++
T Consensus        31 ~~~~~~~~~~~~~~-~~~dlvi~d~~l~~~~g~~~~~~l~~-~~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~Kp~~~~~  108 (122)
T 1zgz_A           31 VTASGAGLREIMQN-QSVDLILLDINLPDENGLMLTRALRE-RSTVGIILVTGRSDRIDRIVGLEMGADDYVTKPLELRE  108 (122)
T ss_dssp             EESSHHHHHHHHHH-SCCSEEEEESCCSSSCHHHHHHHHHT-TCCCEEEEEESSCCHHHHHHHHHHTCSEEEESSCCHHH
T ss_pred             EecCHHHHHHHHhc-CCCCEEEEeCCCCCCChHHHHHHHHh-cCCCCEEEEECCCChhhHHHHHHhCHHHHccCCCCHHH
Confidence            46788999999887 78999999999999999999999998 67899999999999998999999999999999999999


Q ss_pred             HHHHHHHHHHH
Q 043479           82 LKNVWQYAMTY   92 (534)
Q Consensus        82 L~~aI~~aL~~   92 (534)
                      |..+|++++++
T Consensus       109 l~~~i~~~~~~  119 (122)
T 1zgz_A          109 LVVRVKNLLWR  119 (122)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999998764

>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=99.48  E-value=3.5e-13  Score=115.62  Aligned_cols=90  Identities=26%  Similarity=0.506  Sum_probs=82.9

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHh--hCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINE--EFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~--~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      .+.++.++++.+.. ..||+||+|+.||+++|+++++.|++  ..+.+|||++|+..+.....++++.|+++||.||++.
T Consensus        34 ~~~~~~~a~~~~~~-~~~dlvi~D~~l~~~~g~~l~~~l~~~~~~~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~KP~~~  112 (128)
T 1jbe_A           34 EAEDGVDALNKLQA-GGYGFVISDWNMPNMDGLELLKTIRAXXAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFTA  112 (128)
T ss_dssp             EESSHHHHHHHHTT-CCCCEEEEESCCSSSCHHHHHHHHHC--CCTTCCEEEEESSCCHHHHHHHHHTTCSEEEESSCCH
T ss_pred             eeCCHHHHHHHHHh-cCCCEEEEeCCCCCCCHHHHHHHHHhhcccCCCcEEEEecCccHHHHHHHHHhCcCceeecCCCH
Confidence            46789999999976 78999999999999999999999997  4577999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHH
Q 043479           80 DDLKNVWQYAMTY   92 (534)
Q Consensus        80 eeL~~aI~~aL~~   92 (534)
                      ++|..+|+++++.
T Consensus       113 ~~l~~~i~~~~~~  125 (128)
T 1jbe_A          113 ATLEEKLNKIFEK  125 (128)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999998754

>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=99.48  E-value=3.8e-13  Score=114.60  Aligned_cols=89  Identities=28%  Similarity=0.454  Sum_probs=82.8

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.++++.+.. ..||+||+|+.||+++|+++++.|++. +.+|||++|+..+.....++++.|+++||.||++.++
T Consensus        32 ~~~~~~~a~~~~~~-~~~dlvi~D~~l~~~~g~~~~~~l~~~-~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~  109 (123)
T 1xhf_A           32 EATDGAEMHQILSE-YDINLVIMDINLPGKNGLLLARELREQ-ANVALMFLTGRDNEVDKILGLEIGADDYITKPFNPRE  109 (123)
T ss_dssp             EESSHHHHHHHHHH-SCCSEEEECSSCSSSCHHHHHHHHHHH-CCCEEEEEESCCSHHHHHHHHHHTCSEEEESSCCHHH
T ss_pred             EeCCHHHHHHHHhc-CCCCEEEEcCCCCCCCHHHHHHHHHhC-CCCcEEEEECCCChHHHHHHHhcCcceEEeCCCCHHH
Confidence            46789999999987 789999999999999999999999987 7899999999999988999999999999999999999


Q ss_pred             HHHHHHHHHHH
Q 043479           82 LKNVWQYAMTY   92 (534)
Q Consensus        82 L~~aI~~aL~~   92 (534)
                      |..+|++++++
T Consensus       110 l~~~i~~~~~~  120 (123)
T 1xhf_A          110 LTIRARNLLSR  120 (123)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999998765

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

Probab=99.48  E-value=1.7e-13  Score=118.47  Aligned_cols=91  Identities=21%  Similarity=0.391  Sum_probs=83.4

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhh-CCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEE-FTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPD   80 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~-~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~e   80 (534)
                      ++.++.+|++.+.. ..||+||+|+.||+++|++++++|++. .+.+|||++|+..+.....++++.||++||.||++.+
T Consensus        33 ~~~~~~~a~~~~~~-~~~dlvllD~~l~~~~g~~~~~~l~~~~~~~~~ii~ls~~~~~~~~~~~~~~ga~~~l~KP~~~~  111 (130)
T 1dz3_A           33 TAYNGQDCLQMLEE-KRPDILLLDIIMPHLDGLAVLERIRAGFEHQPNVIMLTAFGQEDVTKKAVELGASYFILKPFDME  111 (130)
T ss_dssp             EESSHHHHHHHHHH-HCCSEEEEESCCSSSCHHHHHHHHHHHCSSCCEEEEEEETTCHHHHHHHHHTTCEEEEECSSCCT
T ss_pred             EeCCHHHHHHHHhc-CCCCEEEEecCCCCCCHHHHHHHHHhcCCCCCcEEEEecCCCHHHHHHHHHcCCCEEEeCCCCHH
Confidence            46799999999987 679999999999999999999999986 5778999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHh
Q 043479           81 DLKNVWQYAMTYK   93 (534)
Q Consensus        81 eL~~aI~~aL~~k   93 (534)
                      +|..+|++++++.
T Consensus       112 ~l~~~i~~~~~~~  124 (130)
T 1dz3_A          112 NLAHHIRQVYGKT  124 (130)
T ss_dssp             THHHHHHHHHHCC
T ss_pred             HHHHHHHHHhcCC
Confidence            9999999987543

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

Probab=99.48  E-value=3.3e-13  Score=120.88  Aligned_cols=93  Identities=23%  Similarity=0.358  Sum_probs=86.0

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhh--CCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~--~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      ++.++.+|++.+.. ..||+||+|+.||+++|+++++.|++.  .+.+|||++|+..+.....++++.||++||.||++.
T Consensus        36 ~~~~~~~al~~l~~-~~~dlii~D~~l~~~~g~~~~~~lr~~~~~~~~pii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~  114 (154)
T 3gt7_A           36 HVRNGREAVRFLSL-TRPDLIISDVLMPEMDGYALCRWLKGQPDLRTIPVILLTILSDPRDVVRSLECGADDFITKPCKD  114 (154)
T ss_dssp             EESSHHHHHHHHTT-CCCSEEEEESCCSSSCHHHHHHHHHHSTTTTTSCEEEEECCCSHHHHHHHHHHCCSEEEESSCCH
T ss_pred             EeCCHHHHHHHHHh-CCCCEEEEeCCCCCCCHHHHHHHHHhCCCcCCCCEEEEECCCChHHHHHHHHCCCCEEEeCCCCH
Confidence            57799999999987 789999999999999999999999985  378999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhh
Q 043479           80 DDLKNVWQYAMTYKKA   95 (534)
Q Consensus        80 eeL~~aI~~aL~~k~~   95 (534)
                      ++|..+|++++++.+.
T Consensus       115 ~~l~~~i~~~l~~~~~  130 (154)
T 3gt7_A          115 VVLASHVKRLLSGVKR  130 (154)
T ss_dssp             HHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHHHHHh
Confidence            9999999999977543

>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=99.47  E-value=5e-13  Score=118.76  Aligned_cols=95  Identities=25%  Similarity=0.416  Sum_probs=86.2

Q ss_pred             eecCHHHHHHHHH--------hcCCceEEEEeCCCCCCCHHHHHHHHHh--hCCCCcEEEEecCCCHHHHHHHHHcCCcE
Q 043479            2 TVTRPVEALATVR--------IQRDIDLVVTDLHMPEMNGIELQKEINE--EFTHLPVMVMSSDDRESVIMKALASGVAF   71 (534)
Q Consensus         2 tass~~EALe~L~--------~~~~pDLVLLDi~mPdmdGleLL~~Lr~--~~p~ipVIVLSs~~d~~~~~~AL~aGA~d   71 (534)
                      .+.++.+|++.++        ....|||||+|+.||+++|+++++.|++  ..+.+|||++|+..+.....++++.|+++
T Consensus        35 ~~~~~~~al~~l~~~~~~~~~~~~~~dliilD~~l~~~~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~~~~~g~~~  114 (152)
T 3heb_A           35 AFTDGTSALNYLFGDDKSGRVSAGRAQLVLLDLNLPDMTGIDILKLVKENPHTRRSPVVILTTTDDQREIQRCYDLGANV  114 (152)
T ss_dssp             EESSHHHHHHHHHCTTSSSGGGTTCBEEEEECSBCSSSBHHHHHHHHHHSTTTTTSCEEEEESCCCHHHHHHHHHTTCSE
T ss_pred             EeCCHHHHHHHHhccccccccccCCCCEEEEeCCCCCCcHHHHHHHHHhcccccCCCEEEEecCCCHHHHHHHHHCCCcE
Confidence            4679999999995        2267999999999999999999999998  67889999999999999999999999999


Q ss_pred             EEeCCCChHHHHHHHHHHHHHhhhc
Q 043479           72 YILKPLNPDDLKNVWQYAMTYKKAK   96 (534)
Q Consensus        72 yL~KP~s~eeL~~aI~~aL~~k~~~   96 (534)
                      ||.||++.++|..+|+++.+.+...
T Consensus       115 ~l~KP~~~~~l~~~i~~~~~~~~~~  139 (152)
T 3heb_A          115 YITKPVNYENFANAIRQLGLFFSVM  139 (152)
T ss_dssp             EEECCSSHHHHHHHHHHHHHHHTTS
T ss_pred             EEeCCCCHHHHHHHHHHHHHHHHHc
Confidence            9999999999999999997766543

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

Probab=99.47  E-value=2.7e-13  Score=120.20  Aligned_cols=90  Identities=27%  Similarity=0.412  Sum_probs=81.0

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhh----CCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCC
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEE----FTHLPVMVMSSDDRESVIMKALASGVAFYILKPL   77 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~----~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~   77 (534)
                      ++.++++|++.+.. ..||+||+|+.||+++|++++++|++.    .+.+|||++|+..+.+...++++.||++||.||+
T Consensus        43 ~~~~~~~al~~~~~-~~~dlvl~D~~mp~~~g~~~~~~lr~~~~~~~~~~pii~~s~~~~~~~~~~~~~~Ga~~~l~KP~  121 (143)
T 3m6m_D           43 CVNGAEQVLDAMAE-EDYDAVIVDLHMPGMNGLDMLKQLRVMQASGMRYTPVVVLSADVTPEAIRACEQAGARAFLAKPV  121 (143)
T ss_dssp             EESSHHHHHHHHHH-SCCSEEEEESCCSSSCHHHHHHHHHHHHHTTCCCCCEEEEESCCCHHHHHHHHHTTCSEEEESSC
T ss_pred             EeCCHHHHHHHHhc-CCCCEEEEeCCCCCCCHHHHHHHHHhchhccCCCCeEEEEeCCCCHHHHHHHHHcChhheeeCCC
Confidence            46789999999987 789999999999999999999999853    4568999999999999999999999999999999


Q ss_pred             ChHHHHHHHHHHHHH
Q 043479           78 NPDDLKNVWQYAMTY   92 (534)
Q Consensus        78 s~eeL~~aI~~aL~~   92 (534)
                      +.++|..+|+++...
T Consensus       122 ~~~~L~~~l~~~~~~  136 (143)
T 3m6m_D          122 VAAKLLDTLADLAVS  136 (143)
T ss_dssp             CHHHHHHHHHHHC--
T ss_pred             CHHHHHHHHHHHHHh
Confidence            999999999987644

>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=99.47  E-value=3.3e-13  Score=113.97  Aligned_cols=89  Identities=26%  Similarity=0.452  Sum_probs=81.7

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.++++.+.. ..||+||+|+.||+++|+++++++++. +.+|||++|+..+.....++++.|+++||.||++.++
T Consensus        30 ~~~~~~~a~~~~~~-~~~dlvl~D~~l~~~~g~~~~~~l~~~-~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~Kp~~~~~  107 (120)
T 2a9o_A           30 TAFNGREALEQFEA-EQPDIIILDLMLPEIDGLEVAKTIRKT-SSVPILMLSAKDSEFDKVIGLELGADDYVTKPFSNRE  107 (120)
T ss_dssp             EESSHHHHHHHHHH-HCCSEEEECSSCSSSCHHHHHHHHHHH-CCCCEEEEESCCSHHHHHHHHHHTCSEEEESSCCHHH
T ss_pred             EecCHHHHHHHHHh-CCCCEEEEeccCCCCCHHHHHHHHHhC-CCCCEEEEecCCchHHHHHHHhCCHhheEeCCCCHHH
Confidence            46789999999887 689999999999999999999999974 6799999999999888899999999999999999999


Q ss_pred             HHHHHHHHHHH
Q 043479           82 LKNVWQYAMTY   92 (534)
Q Consensus        82 L~~aI~~aL~~   92 (534)
                      |..+|++++++
T Consensus       108 l~~~i~~~~~~  118 (120)
T 2a9o_A          108 LQARVKALLRR  118 (120)
T ss_dssp             HHHHHHHHHHC
T ss_pred             HHHHHHHHHcc
Confidence            99999988754

>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=99.46  E-value=3.8e-13  Score=116.86  Aligned_cols=94  Identities=23%  Similarity=0.365  Sum_probs=83.4

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhh-CCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEE-FTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPD   80 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~-~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~e   80 (534)
                      .+.+..+++..+.....||+||+|+.||+++|+++++.|++. .+.+|||++|+..+.....++++.|+++||.||++.+
T Consensus        36 ~~~~~~~a~~~~~~~~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~  115 (136)
T 3hdv_A           36 GADGAEEARLYLHYQKRIGLMITDLRMQPESGLDLIRTIRASERAALSIIVVSGDTDVEEAVDVMHLGVVDFLLKPVDLG  115 (136)
T ss_dssp             EESSHHHHHHHHHHCTTEEEEEECSCCSSSCHHHHHHHHHTSTTTTCEEEEEESSCCHHHHHHHHHTTCSEEEESSCCHH
T ss_pred             EeCCHHHHHHHHHhCCCCcEEEEeccCCCCCHHHHHHHHHhcCCCCCCEEEEeCCCChHHHHHHHhCCcceEEeCCCCHH
Confidence            467899999998873349999999999999999999999987 6889999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhh
Q 043479           81 DLKNVWQYAMTYKKA   95 (534)
Q Consensus        81 eL~~aI~~aL~~k~~   95 (534)
                      +|..+|++++.+...
T Consensus       116 ~l~~~i~~~~~~~~~  130 (136)
T 3hdv_A          116 KLLELVNKELKIGEG  130 (136)
T ss_dssp             HHHHHHHHHHC----
T ss_pred             HHHHHHHHHhcCchh
Confidence            999999999876554

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

Probab=99.46  E-value=1.6e-13  Score=121.26  Aligned_cols=92  Identities=21%  Similarity=0.370  Sum_probs=79.2

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.++++.+.. ..||+||+|+.||+++|+++++.|++..+.+|||++|+..+.....++++.|+++||.||++.++
T Consensus        34 ~~~~~~~al~~~~~-~~~dlvllD~~lp~~~g~~l~~~l~~~~~~~~ii~ls~~~~~~~~~~~~~~ga~~~l~KP~~~~~  112 (141)
T 3cu5_A           34 QADDGINAIQIALK-HPPNVLLTDVRMPRMDGIELVDNILKLYPDCSVIFMSGYSDKEYLKAAIKFRAIRYVEKPIDPSE  112 (141)
T ss_dssp             EESSHHHHHHHHTT-SCCSEEEEESCCSSSCHHHHHHHHHHHCTTCEEEEECCSTTTCCC------CCCEEECSSCCHHH
T ss_pred             ecccHHHHHHHHhc-CCCCEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEeCCCcHHHHHHHHhCCccEEEeCCCCHHH
Confidence            57789999999976 78999999999999999999999999889999999999988888889999999999999999999


Q ss_pred             HHHHHHHHHHHhh
Q 043479           82 LKNVWQYAMTYKK   94 (534)
Q Consensus        82 L~~aI~~aL~~k~   94 (534)
                      |..+|+++++...
T Consensus       113 L~~~i~~~~~~~~  125 (141)
T 3cu5_A          113 IMDALKQSIQTVL  125 (141)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999887644

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

Probab=99.46  E-value=5.5e-13  Score=116.06  Aligned_cols=93  Identities=24%  Similarity=0.286  Sum_probs=85.8

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHh--hCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINE--EFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~--~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      .+.++.+|++.++. ..||+||+|+.+|+++|+++++.|++  ..+.+|||++|+..+.....++++.|+++||.||++.
T Consensus        39 ~~~~~~~a~~~l~~-~~~dlii~d~~l~~~~g~~~~~~l~~~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~kP~~~  117 (143)
T 3cnb_A           39 IAYNPFDAGDLLHT-VKPDVVMLDLMMVGMDGFSICHRIKSTPATANIIVIAMTGALTDDNVSRIVALGAETCFGKPLNF  117 (143)
T ss_dssp             EECSHHHHHHHHHH-TCCSEEEEETTCTTSCHHHHHHHHHTSTTTTTSEEEEEESSCCHHHHHHHHHTTCSEEEESSCCH
T ss_pred             EECCHHHHHHHHHh-cCCCEEEEecccCCCcHHHHHHHHHhCccccCCcEEEEeCCCCHHHHHHHHhcCCcEEEeCCCCH
Confidence            46789999999987 78999999999999999999999998  6788999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhh
Q 043479           80 DDLKNVWQYAMTYKKA   95 (534)
Q Consensus        80 eeL~~aI~~aL~~k~~   95 (534)
                      ++|..+|++++++...
T Consensus       118 ~~l~~~i~~~~~~~~~  133 (143)
T 3cnb_A          118 TLLEKTIKQLVEQKKA  133 (143)
T ss_dssp             HHHHHHHHHHHHTTC-
T ss_pred             HHHHHHHHHHHHhhcc
Confidence            9999999999876554

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

Probab=99.46  E-value=1.3e-13  Score=120.41  Aligned_cols=94  Identities=21%  Similarity=0.350  Sum_probs=85.1

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHh--hCCCCcEEEEecCCCHHHHH-HHHHcCCcEEEeCCCC
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINE--EFTHLPVMVMSSDDRESVIM-KALASGVAFYILKPLN   78 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~--~~p~ipVIVLSs~~d~~~~~-~AL~aGA~dyL~KP~s   78 (534)
                      ++.++.+|++.++. ..||+||+|+.||+++|++++++|++  ..+.+|||++|+..+..... .+++.||++||.||++
T Consensus        35 ~~~~~~~a~~~l~~-~~~dlvi~d~~l~~~~g~~~~~~l~~~~~~~~~~ii~~s~~~~~~~~~~~~~~~g~~~~l~kP~~  113 (140)
T 3grc_A           35 MVHSAAQALEQVAR-RPYAAMTVDLNLPDQDGVSLIRALRRDSRTRDLAIVVVSANAREGELEFNSQPLAVSTWLEKPID  113 (140)
T ss_dssp             EECSHHHHHHHHHH-SCCSEEEECSCCSSSCHHHHHHHHHTSGGGTTCEEEEECTTHHHHHHHHCCTTTCCCEEECSSCC
T ss_pred             EECCHHHHHHHHHh-CCCCEEEEeCCCCCCCHHHHHHHHHhCcccCCCCEEEEecCCChHHHHHHhhhcCCCEEEeCCCC
Confidence            57899999999987 78999999999999999999999998  67889999999988777776 8899999999999999


Q ss_pred             hHHHHHHHHHHHHHhhhc
Q 043479           79 PDDLKNVWQYAMTYKKAK   96 (534)
Q Consensus        79 ~eeL~~aI~~aL~~k~~~   96 (534)
                      .++|..+|+++++++...
T Consensus       114 ~~~l~~~i~~~l~~~~~~  131 (140)
T 3grc_A          114 ENLLILSLHRAIDNMAEG  131 (140)
T ss_dssp             HHHHHHHHHHHHHHHC--
T ss_pred             HHHHHHHHHHHHHhcCCC
Confidence            999999999999876644

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

Probab=99.46  E-value=2.6e-13  Score=117.24  Aligned_cols=93  Identities=22%  Similarity=0.312  Sum_probs=80.1

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhh--CCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~--~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      ++.++.+|++.+.. ..||+||+|+.||+++|+++++.|++.  .+.+|||++|+..+... .++++.|+++||.||++.
T Consensus        32 ~~~~~~~a~~~l~~-~~~dlvi~d~~l~~~~g~~~~~~l~~~~~~~~~pii~~s~~~~~~~-~~~~~~g~~~~l~KP~~~  109 (133)
T 3nhm_A           32 TAADGASGLQQALA-HPPDVLISDVNMDGMDGYALCGHFRSEPTLKHIPVIFVSGYAPRTE-GPADQPVPDAYLVKPVKP  109 (133)
T ss_dssp             EESSHHHHHHHHHH-SCCSEEEECSSCSSSCHHHHHHHHHHSTTTTTCCEEEEESCCC------TTSCCCSEEEESSCCH
T ss_pred             EECCHHHHHHHHhc-CCCCEEEEeCCCCCCCHHHHHHHHHhCCccCCCCEEEEeCCCcHhH-HHHhhcCCceEEeccCCH
Confidence            57899999999987 789999999999999999999999986  56899999999988777 889999999999999999


Q ss_pred             HHHHHHHHHHHHHhhhc
Q 043479           80 DDLKNVWQYAMTYKKAK   96 (534)
Q Consensus        80 eeL~~aI~~aL~~k~~~   96 (534)
                      ++|..+|+++++++...
T Consensus       110 ~~l~~~i~~~l~~~~~~  126 (133)
T 3nhm_A          110 PVLIAQLHALLARAEAE  126 (133)
T ss_dssp             HHHHHHHHHHHHHHC--
T ss_pred             HHHHHHHHHHHhhhccc
Confidence            99999999999876543

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

Probab=99.46  E-value=4.7e-13  Score=119.03  Aligned_cols=94  Identities=20%  Similarity=0.315  Sum_probs=86.4

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcC-CcEEEeCCCChH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASG-VAFYILKPLNPD   80 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aG-A~dyL~KP~s~e   80 (534)
                      .+.++.+|++.+.+..+||+||+|+.||+++|+++++.|++..+.+|||++|+..+.....++++.| +++||.||++.+
T Consensus        32 ~~~~~~~a~~~l~~~~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~~l~KP~~~~  111 (151)
T 3kcn_A           32 TCESGPEALACIKKSDPFSVIMVDMRMPGMEGTEVIQKARLISPNSVYLMLTGNQDLTTAMEAVNEGQVFRFLNKPCQMS  111 (151)
T ss_dssp             EESSHHHHHHHHHHSCCCSEEEEESCCSSSCHHHHHHHHHHHCSSCEEEEEECGGGHHHHHHHHHHTCCSEEEESSCCHH
T ss_pred             EeCCHHHHHHHHHcCCCCCEEEEeCCCCCCcHHHHHHHHHhcCCCcEEEEEECCCCHHHHHHHHHcCCeeEEEcCCCCHH
Confidence            5789999999998733469999999999999999999999999999999999999999999999999 999999999999


Q ss_pred             HHHHHHHHHHHHhhh
Q 043479           81 DLKNVWQYAMTYKKA   95 (534)
Q Consensus        81 eL~~aI~~aL~~k~~   95 (534)
                      +|..+|++++++...
T Consensus       112 ~L~~~i~~~l~~~~~  126 (151)
T 3kcn_A          112 DIKAAINAGIKQYDL  126 (151)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999987654

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

Probab=99.46  E-value=1e-13  Score=121.35  Aligned_cols=95  Identities=23%  Similarity=0.332  Sum_probs=84.9

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCC-CCCHHHHHHHHHh--hCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCC
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMP-EMNGIELQKEINE--EFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLN   78 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mP-dmdGleLL~~Lr~--~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s   78 (534)
                      ++.++.+|++.+.+...|||||+|+.|| +++|++++++|++  ..+.+|||++|+..+.....++++.||++||.||++
T Consensus        34 ~~~~~~~a~~~l~~~~~~dlvi~D~~l~~~~~g~~~~~~l~~~~~~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~KP~~  113 (140)
T 3lua_A           34 EVENLKKFYSIFKDLDSITLIIMDIAFPVEKEGLEVLSAIRNNSRTANTPVIIATKSDNPGYRHAALKFKVSDYILKPYP  113 (140)
T ss_dssp             EECSHHHHHTTTTTCCCCSEEEECSCSSSHHHHHHHHHHHHHSGGGTTCCEEEEESCCCHHHHHHHHHSCCSEEEESSCC
T ss_pred             EECCHHHHHHHHhcCCCCcEEEEeCCCCCCCcHHHHHHHHHhCcccCCCCEEEEeCCCCHHHHHHHHHcCCCEEEECCCC
Confidence            5788999999887425799999999999 9999999999999  889999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHHhhhc
Q 043479           79 PDDLKNVWQYAMTYKKAK   96 (534)
Q Consensus        79 ~eeL~~aI~~aL~~k~~~   96 (534)
                      .++|..+|++++++....
T Consensus       114 ~~~l~~~i~~~~~~~~~~  131 (140)
T 3lua_A          114 TKRLENSVRSVLKICQRF  131 (140)
T ss_dssp             TTHHHHHHHHHHCC----
T ss_pred             HHHHHHHHHHHHHhcccc
Confidence            999999999999776544

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

Probab=99.46  E-value=6.1e-13  Score=118.30  Aligned_cols=92  Identities=24%  Similarity=0.375  Sum_probs=82.6

Q ss_pred             eecCHHHHHHHHHhc------CCceEEEEeCCCCCCCHHHHHHHHHhhC--CCCcEEEEecCCCHHHHHHHHHcCCcEEE
Q 043479            2 TVTRPVEALATVRIQ------RDIDLVVTDLHMPEMNGIELQKEINEEF--THLPVMVMSSDDRESVIMKALASGVAFYI   73 (534)
Q Consensus         2 tass~~EALe~L~~~------~~pDLVLLDi~mPdmdGleLL~~Lr~~~--p~ipVIVLSs~~d~~~~~~AL~aGA~dyL   73 (534)
                      .+.++.+|++.++..      ..||+||+|+.||+++|+++++.|++..  +.+|||++|+..+...+.++++.||++||
T Consensus        39 ~~~~~~~al~~l~~~~~~~~~~~~dlillD~~lp~~~g~~l~~~l~~~~~~~~~piiils~~~~~~~~~~~~~~ga~~~l  118 (149)
T 1i3c_A           39 ILRDGLAAMAFLQQQGEYENSPRPNLILLDLNLPKKDGREVLAEIKQNPDLKRIPVVVLTTSHNEDDVIASYELHVNCYL  118 (149)
T ss_dssp             EECSHHHHHHHHTTCGGGTTCCCCSEEEECSCCSSSCHHHHHHHHHHCTTTTTSCEEEEESCCCHHHHHHHHHTTCSEEE
T ss_pred             EeCCHHHHHHHHHhccccccCCCCCEEEEeCCCCCCcHHHHHHHHHhCcCcCCCeEEEEECCCChHHHHHHHHcCCcEEE
Confidence            467899999998741      3699999999999999999999999753  67999999999999999999999999999


Q ss_pred             eCCCChHHHHHHHHHHHHHh
Q 043479           74 LKPLNPDDLKNVWQYAMTYK   93 (534)
Q Consensus        74 ~KP~s~eeL~~aI~~aL~~k   93 (534)
                      .||++.++|..+|+++++.+
T Consensus       119 ~KP~~~~~L~~~i~~~~~~~  138 (149)
T 1i3c_A          119 TKSRNLKDLFKMVQGIESFW  138 (149)
T ss_dssp             ECCSSHHHHHHHHHHHHHHH
T ss_pred             ECCCCHHHHHHHHHHHHHHH
Confidence            99999999999999987654

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

Probab=99.46  E-value=6.6e-13  Score=116.23  Aligned_cols=92  Identities=18%  Similarity=0.365  Sum_probs=83.5

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHc-CCcEEEeCCCChH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS-GVAFYILKPLNPD   80 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~a-GA~dyL~KP~s~e   80 (534)
                      ++.++.++++.+.. ..||+||+|+.||+++|+++++.|++..+.+|||++|+..+.....+++.. ||++||.||++.+
T Consensus        29 ~~~~~~~a~~~~~~-~~~dlvl~D~~lp~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~~ga~~~l~KP~~~~  107 (139)
T 2jk1_A           29 TAQGAEAAIAILEE-EWVQVIICDQRMPGRTGVDFLTEVRERWPETVRIIITGYTDSASMMAAINDAGIHQFLTKPWHPE  107 (139)
T ss_dssp             EESSHHHHHHHHHH-SCEEEEEEESCCSSSCHHHHHHHHHHHCTTSEEEEEESCTTCHHHHHHHHHTTCCEEEESSCCHH
T ss_pred             EcCCHHHHHHHHhc-CCCCEEEEeCCCCCCcHHHHHHHHHHhCCCCcEEEEeCCCChHHHHHHHHhhchhhhccCCCCHH
Confidence            46789999999987 789999999999999999999999998889999999999888888888876 5999999999999


Q ss_pred             HHHHHHHHHHHHhh
Q 043479           81 DLKNVWQYAMTYKK   94 (534)
Q Consensus        81 eL~~aI~~aL~~k~   94 (534)
                      +|..+|+++++...
T Consensus       108 ~L~~~i~~~~~~~~  121 (139)
T 2jk1_A          108 QLLSSARNAARMFT  121 (139)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999999887644

>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=99.45  E-value=3.2e-13  Score=117.10  Aligned_cols=92  Identities=24%  Similarity=0.442  Sum_probs=84.0

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.++++.+.. ..||+||+|+.||+++|+++++.|++..+.+|||++|+..+......+++.|+++||.||++.++
T Consensus        32 ~~~~~~~a~~~~~~-~~~dlvl~D~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~  110 (136)
T 1mvo_A           32 TASDGEEALKKAET-EKPDLIVLDVMLPKLDGIEVCKQLRQQKLMFPILMLTAKDEEFDKVLGLELGADDYMTKPFSPRE  110 (136)
T ss_dssp             EESSHHHHHHHHHH-HCCSEEEEESSCSSSCHHHHHHHHHHTTCCCCEEEEECTTCCCCHHHHHHTTCCEEEESSCCHHH
T ss_pred             EecCHHHHHHHHhh-cCCCEEEEecCCCCCCHHHHHHHHHcCCCCCCEEEEECCCCHHHHHHHHhCCCCEEEECCCCHHH
Confidence            46789999999887 67999999999999999999999999888899999999988888889999999999999999999


Q ss_pred             HHHHHHHHHHHhh
Q 043479           82 LKNVWQYAMTYKK   94 (534)
Q Consensus        82 L~~aI~~aL~~k~   94 (534)
                      |..+|++++++..
T Consensus       111 l~~~i~~~~~~~~  123 (136)
T 1mvo_A          111 VNARVKAILRRSE  123 (136)
T ss_dssp             HHHHHHHHHHTC-
T ss_pred             HHHHHHHHHHhhc
Confidence            9999999886543

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

Probab=99.45  E-value=4.2e-13  Score=117.74  Aligned_cols=91  Identities=23%  Similarity=0.306  Sum_probs=83.9

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++.+|++.+.. ..||+||+|+.||+++|+++++.|++.. .+|||++|+..+.....++++.||++||.||++.++
T Consensus        33 ~~~~~~~al~~~~~-~~~dlvllD~~l~~~~g~~l~~~l~~~~-~~~ii~ls~~~~~~~~~~~~~~ga~~~l~KP~~~~~  110 (136)
T 2qzj_A           33 LAYNCEEAIGKIFS-NKYDLIFLEIILSDGDGWTLCKKIRNVT-TCPIVYMTYINEDQSILNALNSGGDDYLIKPLNLEI  110 (136)
T ss_dssp             EESSHHHHHHHHHH-CCCSEEEEESEETTEEHHHHHHHHHTTC-CCCEEEEESCCCHHHHHHHHHTTCCEEEESSCCHHH
T ss_pred             EECCHHHHHHHHHh-cCCCEEEEeCCCCCCCHHHHHHHHccCC-CCCEEEEEcCCCHHHHHHHHHcCCcEEEECCCCHHH
Confidence            46789999999987 7899999999999999999999999765 799999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhh
Q 043479           82 LKNVWQYAMTYKK   94 (534)
Q Consensus        82 L~~aI~~aL~~k~   94 (534)
                      |..+|++++++..
T Consensus       111 L~~~l~~~~~~~~  123 (136)
T 2qzj_A          111 LYAKVKAILRRMN  123 (136)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhh
Confidence            9999999887644

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

Probab=99.45  E-value=1.2e-13  Score=121.71  Aligned_cols=92  Identities=13%  Similarity=0.211  Sum_probs=83.6

Q ss_pred             eecCHHHHHHHHHhc-CCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChH
Q 043479            2 TVTRPVEALATVRIQ-RDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPD   80 (534)
Q Consensus         2 tass~~EALe~L~~~-~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~e   80 (534)
                      .+.+..+++..+.+. ..|||||+|+.||+++|+++++.|++..+.+|||++|+..+.+...++++.||++||.||++.+
T Consensus        50 ~~~~~~~~~~~~~~~~~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~ii~lt~~~~~~~~~~~~~~ga~~~l~Kp~~~~  129 (146)
T 4dad_A           50 RTVGRAAQIVQRTDGLDAFDILMIDGAALDTAELAAIEKLSRLHPGLTCLLVTTDASSQTLLDAMRAGVRDVLRWPLEPR  129 (146)
T ss_dssp             EECCCHHHHTTCHHHHTTCSEEEEECTTCCHHHHHHHHHHHHHCTTCEEEEEESCCCHHHHHHHHTTTEEEEEESSCCHH
T ss_pred             EeCCHHHHHHHHHhcCCCCCEEEEeCCCCCccHHHHHHHHHHhCCCCcEEEEeCCCCHHHHHHHHHhCCceeEcCCCCHH
Confidence            456777788776543 5799999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHh
Q 043479           81 DLKNVWQYAMTYK   93 (534)
Q Consensus        81 eL~~aI~~aL~~k   93 (534)
                      +|..+|+++++++
T Consensus       130 ~L~~~i~~~~~~~  142 (146)
T 4dad_A          130 ALDDALKRAAAQC  142 (146)
T ss_dssp             HHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHhhh
Confidence            9999999998764

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

Probab=99.45  E-value=6.5e-13  Score=116.90  Aligned_cols=92  Identities=20%  Similarity=0.343  Sum_probs=85.6

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHh--hCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINE--EFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~--~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      .+.++.+|++.+.. ..||+||+|+.||+++|+++++.|++  ..+.+|||++|+..+.....++++.|+++||.||++.
T Consensus        37 ~~~~~~~a~~~l~~-~~~dlii~d~~l~~~~g~~~~~~l~~~~~~~~~pii~ls~~~~~~~~~~~~~~g~~~~l~kp~~~  115 (147)
T 2zay_A           37 QCGNAIEAVPVAVK-THPHLIITEANMPKISGMDLFNSLKKNPQTASIPVIALSGRATAKEEAQLLDMGFIDFIAKPVNA  115 (147)
T ss_dssp             EESSHHHHHHHHHH-HCCSEEEEESCCSSSCHHHHHHHHHTSTTTTTSCEEEEESSCCHHHHHHHHHHTCSEEEESSCCH
T ss_pred             EeCCHHHHHHHHHc-CCCCEEEEcCCCCCCCHHHHHHHHHcCcccCCCCEEEEeCCCCHHHHHHHHhCCCCEEEeCCCCH
Confidence            47789999999987 68999999999999999999999998  6788999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhh
Q 043479           80 DDLKNVWQYAMTYKK   94 (534)
Q Consensus        80 eeL~~aI~~aL~~k~   94 (534)
                      ++|..+|+++++...
T Consensus       116 ~~L~~~i~~~~~~~~  130 (147)
T 2zay_A          116 IRLSARIKRVLKLLY  130 (147)
T ss_dssp             HHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999987654

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

Probab=99.45  E-value=3.1e-13  Score=121.49  Aligned_cols=89  Identities=25%  Similarity=0.370  Sum_probs=83.8

Q ss_pred             eecCHHHHHHHHHhcC--CceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQR--DIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~--~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      ++.++.+|++.+.+ .  .|||||+|+.||+++|+++++.|++..+.+|||++|+..+.....++++.||++||.||++.
T Consensus        66 ~~~~~~~al~~l~~-~~~~~dliilD~~l~~~~g~~~~~~lr~~~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~KP~~~  144 (157)
T 3hzh_A           66 TAADGEEAVIKYKN-HYPNIDIVTLXITMPKMDGITCLSNIMEFDKNARVIMISALGKEQLVKDCLIKGAKTFIVKPLDR  144 (157)
T ss_dssp             EESSHHHHHHHHHH-HGGGCCEEEECSSCSSSCHHHHHHHHHHHCTTCCEEEEESCCCHHHHHHHHHTTCSEEEESSCCH
T ss_pred             EECCHHHHHHHHHh-cCCCCCEEEEeccCCCccHHHHHHHHHhhCCCCcEEEEeccCcHHHHHHHHHcCCCEEEeCCCCH
Confidence            57899999999987 5  78999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHH
Q 043479           80 DDLKNVWQYAMT   91 (534)
Q Consensus        80 eeL~~aI~~aL~   91 (534)
                      ++|..+|+++++
T Consensus       145 ~~l~~~i~~~l~  156 (157)
T 3hzh_A          145 AKVLQRVMSVFV  156 (157)
T ss_dssp             HHHHHHHHHTTC
T ss_pred             HHHHHHHHHHhc
Confidence            999999998763

>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=99.45  E-value=2.7e-13  Score=116.49  Aligned_cols=89  Identities=17%  Similarity=0.355  Sum_probs=81.8

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhh--CCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~--~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      .+.++.++++.+.. ..||+||+|+.||+++|++++++|++.  .+.+|||++|+..+.....++++.|+++||.||++.
T Consensus        36 ~~~~~~~a~~~~~~-~~~dlvl~D~~l~~~~g~~~~~~l~~~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~  114 (129)
T 1p6q_A           36 AAGDGEQGMKIMAQ-NPHHLVISDFNMPKMDGLGLLQAVRANPATKKAAFIILTAQGDRALVQKAAALGANNVLAKPFTI  114 (129)
T ss_dssp             CCSSHHHHHHHHHT-SCCSEEEECSSSCSSCHHHHHHHHTTCTTSTTCEEEECCSCCCHHHHHHHHHHTCSCEECCCSSH
T ss_pred             ecCCHHHHHHHHHc-CCCCEEEEeCCCCCCCHHHHHHHHhcCccccCCCEEEEeCCCCHHHHHHHHHcCCCEEEECCCCH
Confidence            35789999999987 789999999999999999999999875  578999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHH
Q 043479           80 DDLKNVWQYAMT   91 (534)
Q Consensus        80 eeL~~aI~~aL~   91 (534)
                      ++|..+|+++++
T Consensus       115 ~~l~~~i~~~~~  126 (129)
T 1p6q_A          115 EKMKAAIEAVFG  126 (129)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            999999998874

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

Probab=99.44  E-value=8.4e-15  Score=130.91  Aligned_cols=83  Identities=17%  Similarity=0.240  Sum_probs=73.5

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      +|.++++|++.+++ .+||+||+|+.||+++|++++++|++.  ++|||++|++.+...   +.++|+.+||.||++.++
T Consensus        38 ~a~~g~eAl~~~~~-~~~DlvllDi~mP~~~G~el~~~lr~~--~ipvI~lTa~~~~~~---~~~~g~~~yl~KP~~~~~  111 (123)
T 2lpm_A           38 TASRMQEALDIARK-GQFDIAIIDVNLDGEPSYPVADILAER--NVPFIFATGYGSKGL---DTRYSNIPLLTKPFLDSE  111 (123)
T ss_dssp             CSCCHHHHHHHHHH-CCSSEEEECSSSSSCCSHHHHHHHHHT--CCSSCCBCTTCTTSC---CSSSCSCSCBCSSSSHHH
T ss_pred             EECCHHHHHHHHHh-CCCCEEEEecCCCCCCHHHHHHHHHcC--CCCEEEEecCccHHH---HHhCCCCcEEECCCCHHH
Confidence            46899999999988 899999999999999999999999974  699999999887653   346799999999999999


Q ss_pred             HHHHHHHHH
Q 043479           82 LKNVWQYAM   90 (534)
Q Consensus        82 L~~aI~~aL   90 (534)
                      |..+|++++
T Consensus       112 L~~~l~~~~  120 (123)
T 2lpm_A          112 LEAVLVQIS  120 (123)
T ss_dssp             HHHHHSTTC
T ss_pred             HHHHHHHHH
Confidence            999987764

>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=99.44  E-value=1e-13  Score=121.34  Aligned_cols=95  Identities=23%  Similarity=0.351  Sum_probs=78.3

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhC--CCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEF--THLPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~--p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      ++.++.+|++.+.. ..|||||+|+.||+++|+++++.|++..  +.+|||++|+..+.+...++++.||++||.||++.
T Consensus        31 ~~~~~~~a~~~~~~-~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~  109 (140)
T 3n53_A           31 ESKNEKEALEQIDH-HHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNR  109 (140)
T ss_dssp             EESSHHHHHHHHHH-HCCSEEEEETTC------CHHHHHHTSTTCTTCCEEEEECC----CTTTTTTCCCSEEEESSCCH
T ss_pred             EeCCHHHHHHHHhc-CCCCEEEEeCCCCCCcHHHHHHHHHcCcccCCCCEEEEecCCCHHHHHHHHhcCCCeeeeCCCCH
Confidence            57899999999987 6899999999999999999999999876  88999999999988888899999999999999999


Q ss_pred             HHHHHHHHHHHHHhhhcc
Q 043479           80 DDLKNVWQYAMTYKKAKS   97 (534)
Q Consensus        80 eeL~~aI~~aL~~k~~~s   97 (534)
                      ++|..+|+++++++...+
T Consensus       110 ~~l~~~i~~~~~~~~~~~  127 (140)
T 3n53_A          110 NDLLSRIEIHLRTQNYYS  127 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhHHHHH
Confidence            999999999998877654

>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=99.44  E-value=4.4e-13  Score=113.40  Aligned_cols=90  Identities=27%  Similarity=0.477  Sum_probs=82.1

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.+++..+.. ..||+||+|+.||+++|+++++.+++ .+.+|||++|+..+.....++++.|+++||.||++.++
T Consensus        30 ~~~~~~~~~~~~~~-~~~dlvi~D~~l~~~~g~~~~~~l~~-~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~Kp~~~~~  107 (121)
T 1zh2_A           30 EAETLQRGLLEAAT-RKPDLIILDLGLPDGDGIEFIRDLRQ-WSAVPVIVLSARSEESDKIAALDAGADDYLSKPFGIGE  107 (121)
T ss_dssp             EESSHHHHHHHHHH-HCCSEEEEESEETTEEHHHHHHHHHT-TCCCCEEEEESCCSHHHHHHHHHHTCSEEEESSCCHHH
T ss_pred             EeCCHHHHHHHHhc-CCCCEEEEeCCCCCCcHHHHHHHHHh-CCCCcEEEEECCCCHHHHHHHHhcCCCeEEeCCcCHHH
Confidence            46788999998876 67999999999999999999999994 67899999999999998999999999999999999999


Q ss_pred             HHHHHHHHHHHh
Q 043479           82 LKNVWQYAMTYK   93 (534)
Q Consensus        82 L~~aI~~aL~~k   93 (534)
                      |..+|++++++.
T Consensus       108 l~~~i~~~~~~~  119 (121)
T 1zh2_A          108 LQARLRVALRRH  119 (121)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhh
Confidence            999999988653

>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=99.44  E-value=2.4e-13  Score=115.82  Aligned_cols=90  Identities=22%  Similarity=0.405  Sum_probs=76.2

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhh--CCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~--~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      .+.++.+|++.+.. ..||+||+|+.||+++|++++++|++.  .+.+|||++|+..+.....++++.|+++||.||++.
T Consensus        30 ~~~~~~~a~~~~~~-~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~  108 (124)
T 1mb3_A           30 QTREGLSALSIARE-NKPDLILMDIQLPEISGLEVTKWLKEDDDLAHIPVVAVTAFAMKGDEERIREGGCEAYISKPISV  108 (124)
T ss_dssp             EESCHHHHHHHHHH-HCCSEEEEESBCSSSBHHHHHHHHHHSTTTTTSCEEEEC------CHHHHHHHTCSEEECSSCCH
T ss_pred             EeCCHHHHHHHHhc-CCCCEEEEeCCCCCCCHHHHHHHHHcCccccCCcEEEEECCCCHHHHHHHHhCCCCEEEeCCCCH
Confidence            46789999999887 679999999999999999999999974  467999999999888888899999999999999999


Q ss_pred             HHHHHHHHHHHHH
Q 043479           80 DDLKNVWQYAMTY   92 (534)
Q Consensus        80 eeL~~aI~~aL~~   92 (534)
                      ++|..+|++++.+
T Consensus       109 ~~l~~~i~~~~~~  121 (124)
T 1mb3_A          109 VHFLETIKRLLER  121 (124)
T ss_dssp             HHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHhc
Confidence            9999999988743

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

Probab=99.44  E-value=9e-13  Score=114.55  Aligned_cols=94  Identities=19%  Similarity=0.297  Sum_probs=86.8

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCC-CCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMP-EMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPD   80 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mP-dmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~e   80 (534)
                      ++.+..+|++.+.. ..||+||+|+.+| +++|+++++.|++. +.+|||++|+..+.....++++.|+++||.||++.+
T Consensus        39 ~~~~~~~a~~~~~~-~~~dlii~d~~~~~~~~g~~~~~~l~~~-~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~kp~~~~  116 (140)
T 3cg0_A           39 VFDNGEEAVRCAPD-LRPDIALVDIMLCGALDGVETAARLAAG-CNLPIIFITSSQDVETFQRAKRVNPFGYLAKPVAAD  116 (140)
T ss_dssp             EESSHHHHHHHHHH-HCCSEEEEESSCCSSSCHHHHHHHHHHH-SCCCEEEEECCCCHHHHHHHHTTCCSEEEEESCCHH
T ss_pred             EECCHHHHHHHHHh-CCCCEEEEecCCCCCCCHHHHHHHHHhC-CCCCEEEEecCCCHHHHHHHHhcCCCEEEeCCCCHH
Confidence            37899999999987 6799999999998 79999999999988 889999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhhcc
Q 043479           81 DLKNVWQYAMTYKKAKS   97 (534)
Q Consensus        81 eL~~aI~~aL~~k~~~s   97 (534)
                      +|..+|+++++++...+
T Consensus       117 ~l~~~i~~~~~~~~~~~  133 (140)
T 3cg0_A          117 TLHRSIEMAIHKKKLEE  133 (140)
T ss_dssp             HHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHhccccCC
Confidence            99999999998776543

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

Probab=99.43  E-value=7.4e-13  Score=115.65  Aligned_cols=94  Identities=27%  Similarity=0.334  Sum_probs=83.8

Q ss_pred             eecCHHHHHHHHHhc----CCceEEEEeCCCCCCCHHHHHHHHHh----hCCCCcEEEEecCCCHHHHHHHHHcC-CcEE
Q 043479            2 TVTRPVEALATVRIQ----RDIDLVVTDLHMPEMNGIELQKEINE----EFTHLPVMVMSSDDRESVIMKALASG-VAFY   72 (534)
Q Consensus         2 tass~~EALe~L~~~----~~pDLVLLDi~mPdmdGleLL~~Lr~----~~p~ipVIVLSs~~d~~~~~~AL~aG-A~dy   72 (534)
                      ++.++.+|++.+++.    ..|||||+|+.||+++|+++++.|++    ..+.+|||++|+..+.....+++..| +++|
T Consensus        40 ~~~~~~~a~~~l~~~~~~~~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~~~~~ii~~t~~~~~~~~~~~~~~g~~~~~  119 (146)
T 3ilh_A           40 SVTSGNAAINKLNELYAAGRWPSIICIDINMPGINGWELIDLFKQHFQPMKNKSIVCLLSSSLDPRDQAKAEASDWVDYY  119 (146)
T ss_dssp             EESSHHHHHHHHHHHHTSSCCCSEEEEESSCSSSCHHHHHHHHHHHCGGGTTTCEEEEECSSCCHHHHHHHHHCSSCCEE
T ss_pred             ecCCHHHHHHHHHHhhccCCCCCEEEEcCCCCCCCHHHHHHHHHHhhhhccCCCeEEEEeCCCChHHHHHHHhcCCccee
Confidence            467999999998751    57999999999999999999999998    67889999999999999999999999 9999


Q ss_pred             EeCCCChHHHHHHHHHHHHHhhh
Q 043479           73 ILKPLNPDDLKNVWQYAMTYKKA   95 (534)
Q Consensus        73 L~KP~s~eeL~~aI~~aL~~k~~   95 (534)
                      |.||++.++|..+|+++...+..
T Consensus       120 l~KP~~~~~L~~~i~~~~~~~~~  142 (146)
T 3ilh_A          120 VSKPLTANALNNLYNKVLNEGHH  142 (146)
T ss_dssp             ECSSCCHHHHHHHHHHHHCC---
T ss_pred             eeCCCCHHHHHHHHHHHHHhccC
Confidence            99999999999999998865543

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

Probab=99.43  E-value=7.2e-13  Score=117.85  Aligned_cols=94  Identities=22%  Similarity=0.332  Sum_probs=87.1

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.+|++.+.. ..||+||+|+.|++++|+++++.|++..+.+|||++|+..+.....++++.|+++||.||++.++
T Consensus        36 ~~~~~~~a~~~l~~-~~~dlii~D~~l~~~~g~~~~~~l~~~~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~  114 (153)
T 3cz5_A           36 EAADAGEAYRLYRE-TTPDIVVMDLTLPGPGGIEATRHIRQWDGAARILIFTMHQGSAFALKAFEAGASGYVTKSSDPAE  114 (153)
T ss_dssp             EESSHHHHHHHHHT-TCCSEEEECSCCSSSCHHHHHHHHHHHCTTCCEEEEESCCSHHHHHHHHHTTCSEEEETTSCTTH
T ss_pred             EeCCHHHHHHHHhc-CCCCEEEEecCCCCCCHHHHHHHHHHhCCCCeEEEEECCCCHHHHHHHHHCCCcEEEecCCCHHH
Confidence            57899999999987 78999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhc
Q 043479           82 LKNVWQYAMTYKKAK   96 (534)
Q Consensus        82 L~~aI~~aL~~k~~~   96 (534)
                      |..+|+++++++...
T Consensus       115 L~~~i~~~~~~~~~~  129 (153)
T 3cz5_A          115 LVQAIEAILAGRRAM  129 (153)
T ss_dssp             HHHHHHHHTTTCCEE
T ss_pred             HHHHHHHHHhCCccC
Confidence            999999998765443

>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=99.43  E-value=2e-13  Score=117.20  Aligned_cols=90  Identities=22%  Similarity=0.316  Sum_probs=80.4

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhh--CCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~--~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      .+.++.+|++.++. ..||+||+|+.||+++|++++++|++.  .+.+|||++|+..+... .+++..|+++||.||++.
T Consensus        32 ~~~~~~~a~~~l~~-~~~dlii~D~~l~~~~g~~~~~~l~~~~~~~~~~ii~~s~~~~~~~-~~~~~~g~~~~l~KP~~~  109 (127)
T 3i42_A           32 YVMSGTDALHAMST-RGYDAVFIDLNLPDTSGLALVKQLRALPMEKTSKFVAVSGFAKNDL-GKEACELFDFYLEKPIDI  109 (127)
T ss_dssp             EESSHHHHHHHHHH-SCCSEEEEESBCSSSBHHHHHHHHHHSCCSSCCEEEEEECC-CTTC-CHHHHHHCSEEEESSCCH
T ss_pred             EECCHHHHHHHHHh-cCCCEEEEeCCCCCCCHHHHHHHHHhhhccCCCCEEEEECCcchhH-HHHHHHhhHHheeCCCCH
Confidence            57899999999987 789999999999999999999999987  78899999999988887 889999999999999999


Q ss_pred             HHHHHHHHHHHHHh
Q 043479           80 DDLKNVWQYAMTYK   93 (534)
Q Consensus        80 eeL~~aI~~aL~~k   93 (534)
                      ++|.+++++.....
T Consensus       110 ~~L~~~i~~~~~~~  123 (127)
T 3i42_A          110 ASLEPILQSIEGHH  123 (127)
T ss_dssp             HHHHHHHHHHC---
T ss_pred             HHHHHHHHHhhccC
Confidence            99999999887554

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

Probab=99.43  E-value=4.4e-14  Score=123.16  Aligned_cols=90  Identities=14%  Similarity=0.099  Sum_probs=82.7

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++.+|++.+.. ..||+||+|+.||+++|+++++.|++..+.+|||++|+..+.....++++.||++||.||++.++
T Consensus        44 ~~~~~~~a~~~l~~-~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~  122 (135)
T 3snk_A           44 VSETDDFLKGPPAD-TRPGIVILDLGGGDLLGKPGIVEARALWATVPLIAVSDELTSEQTRVLVRMNASDWLHKPLDGKE  122 (135)
T ss_dssp             EECGGGGGGCCCTT-CCCSEEEEEEETTGGGGSTTHHHHHGGGTTCCEEEEESCCCHHHHHHHHHTTCSEEEESSCCHHH
T ss_pred             EeccHHHHHHHHhc-cCCCEEEEeCCCCCchHHHHHHHHHhhCCCCcEEEEeCCCCHHHHHHHHHcCcHhhccCCCCHHH
Confidence            46788899988876 78999999999999999999999999988999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHH
Q 043479           82 LKNVWQYAMTY   92 (534)
Q Consensus        82 L~~aI~~aL~~   92 (534)
                      |..+|++++++
T Consensus       123 L~~~i~~~~~~  133 (135)
T 3snk_A          123 LLNAVTFHDTG  133 (135)
T ss_dssp             HHHHHHHTC--
T ss_pred             HHHHHHHHhcc
Confidence            99999987654

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

Probab=99.43  E-value=8.1e-13  Score=114.83  Aligned_cols=93  Identities=19%  Similarity=0.391  Sum_probs=84.5

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCC-----CCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCC
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMP-----EMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKP   76 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mP-----dmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP   76 (534)
                      .+.+..+|++.+.. ..||+||+|+.++     +++|+++++.|++..+.+|||++|+..+.....++++.|+++||.||
T Consensus        32 ~~~~~~~a~~~l~~-~~~dlvi~d~~~~~~~~~~~~g~~~~~~l~~~~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~kp  110 (140)
T 2qr3_A           32 TLSSPVSLSTVLRE-ENPEVVLLDMNFTSGINNGNEGLFWLHEIKRQYRDLPVVLFTAYADIDLAVRGIKEGASDFVVKP  110 (140)
T ss_dssp             EECCHHHHHHHHHH-SCEEEEEEETTTTC-----CCHHHHHHHHHHHCTTCCEEEEEEGGGHHHHHHHHHTTCCEEEEES
T ss_pred             EeCCHHHHHHHHHc-CCCCEEEEeCCcCCCCCCCccHHHHHHHHHhhCcCCCEEEEECCCCHHHHHHHHHcCchheeeCC
Confidence            46789999999987 7899999999999     99999999999999999999999999999999999999999999999


Q ss_pred             CChHHHHHHHHHHHHHhhh
Q 043479           77 LNPDDLKNVWQYAMTYKKA   95 (534)
Q Consensus        77 ~s~eeL~~aI~~aL~~k~~   95 (534)
                      ++.++|..+|++++++...
T Consensus       111 ~~~~~l~~~l~~~~~~~~~  129 (140)
T 2qr3_A          111 WDNQKLLETLLNAASQAKD  129 (140)
T ss_dssp             CCHHHHHHHHHHHHTCC--
T ss_pred             CCHHHHHHHHHHHHHhccc
Confidence            9999999999999876543

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

Probab=99.43  E-value=5.3e-13  Score=116.81  Aligned_cols=93  Identities=27%  Similarity=0.368  Sum_probs=84.3

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.+|++.+.. ..||+||+|+ +|+++|+++++.|++..+.+|||++|+..+.....++++.|+++||.||++.++
T Consensus        33 ~~~~~~~a~~~l~~-~~~dlvi~d~-~~~~~g~~~~~~l~~~~~~~pii~ls~~~~~~~~~~~~~~g~~~~l~kP~~~~~  110 (142)
T 2qxy_A           33 WAKNEQEAFTFLRR-EKIDLVFVDV-FEGEESLNLIRRIREEFPDTKVAVLSAYVDKDLIINSVKAGAVDYILKPFRLDY  110 (142)
T ss_dssp             EESSHHHHHHHHTT-SCCSEEEEEC-TTTHHHHHHHHHHHHHCTTCEEEEEESCCCHHHHHHHHHHTCSCEEESSCCHHH
T ss_pred             EECCHHHHHHHHhc-cCCCEEEEeC-CCCCcHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHCCcceeEeCCCCHHH
Confidence            46789999999987 7899999999 999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhc
Q 043479           82 LKNVWQYAMTYKKAK   96 (534)
Q Consensus        82 L~~aI~~aL~~k~~~   96 (534)
                      |..+|+++++++...
T Consensus       111 l~~~i~~~~~~~~~~  125 (142)
T 2qxy_A          111 LLERVKKIISSTPRV  125 (142)
T ss_dssp             HHHHHHHHHHC----
T ss_pred             HHHHHHHHHhhcccc
Confidence            999999998766544

>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=99.43  E-value=7.5e-13  Score=130.59  Aligned_cols=93  Identities=26%  Similarity=0.470  Sum_probs=84.2

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCC--CCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFT--HLPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p--~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      ++.++.+|++.++....|||||+|+.||+++|++++++|++..+  .+|||++|+..+.....+++++||++||.||++.
T Consensus       153 ~a~~~~eal~~l~~~~~~dlvllD~~mP~~dG~~l~~~lr~~~~~~~~~ii~~s~~~~~~~~~~a~~~Ga~~yl~KP~~~  232 (259)
T 3luf_A          153 EASHAREALATLEQHPAIRLVLVDYYMPEIDGISLVRMLRERYSKQQLAIIGISVSDKRGLSARYLKQGANDFLNQPFEP  232 (259)
T ss_dssp             EESSHHHHHHHHHHCTTEEEEEECSCCSSSCHHHHHHHHHHHCCTTTSEEEEEECSSSSSHHHHHHHTTCSEEEESSCCH
T ss_pred             EeCCHHHHHHHHhcCCCCCEEEEcCCCCCCCHHHHHHHHHhccCCCCCeEEEEEccCCHHHHHHHHhcChhheEcCCCCH
Confidence            57899999999986224899999999999999999999998754  5899999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhh
Q 043479           80 DDLKNVWQYAMTYKK   94 (534)
Q Consensus        80 eeL~~aI~~aL~~k~   94 (534)
                      ++|..+|+++++...
T Consensus       233 ~~L~~~i~~~l~~~~  247 (259)
T 3luf_A          233 EELQCRVSHNLEALE  247 (259)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhHh
Confidence            999999999987654

>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=99.43  E-value=1.4e-12  Score=112.62  Aligned_cols=93  Identities=28%  Similarity=0.378  Sum_probs=84.7

Q ss_pred             eecCHHHHHHHHHhc------CCceEEEEeCCCCCCCHHHHHHHHHhhC--CCCcEEEEecCCCHHHHHHHHHcCCcEEE
Q 043479            2 TVTRPVEALATVRIQ------RDIDLVVTDLHMPEMNGIELQKEINEEF--THLPVMVMSSDDRESVIMKALASGVAFYI   73 (534)
Q Consensus         2 tass~~EALe~L~~~------~~pDLVLLDi~mPdmdGleLL~~Lr~~~--p~ipVIVLSs~~d~~~~~~AL~aGA~dyL   73 (534)
                      .+.++.+|++.+...      ..||+||+|+.||+++|+++++.|++..  +.+|||++|+..+.....++++.|+++||
T Consensus        33 ~~~~~~~a~~~l~~~~~~~~~~~~dlvi~d~~~~~~~g~~~~~~l~~~~~~~~~pii~ls~~~~~~~~~~~~~~g~~~~l  112 (140)
T 1k68_A           33 TVRDGMEAMAYLRQEGEYANASRPDLILLXLNLPKKDGREVLAEIKSDPTLKRIPVVVLSTSINEDDIFHSYDLHVNCYI  112 (140)
T ss_dssp             EECSHHHHHHHHTTCGGGGSCCCCSEEEECSSCSSSCHHHHHHHHHHSTTGGGSCEEEEESCCCHHHHHHHHHTTCSEEE
T ss_pred             EECCHHHHHHHHHcccccccCCCCcEEEEecCCCcccHHHHHHHHHcCcccccccEEEEecCCcHHHHHHHHHhchhhee
Confidence            467899999998751      4799999999999999999999999865  78999999999999999999999999999


Q ss_pred             eCCCChHHHHHHHHHHHHHhh
Q 043479           74 LKPLNPDDLKNVWQYAMTYKK   94 (534)
Q Consensus        74 ~KP~s~eeL~~aI~~aL~~k~   94 (534)
                      .||++.++|..+|+++++...
T Consensus       113 ~kP~~~~~l~~~i~~~~~~~~  133 (140)
T 1k68_A          113 TKSANLSQLFQIVKGIEEFWL  133 (140)
T ss_dssp             ECCSSHHHHHHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHHHHHHHHc
Confidence            999999999999999987654

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

Probab=99.42  E-value=1.4e-13  Score=143.94  Aligned_cols=167  Identities=16%  Similarity=0.160  Sum_probs=116.7

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCH-----HHHHHHHHcCCcEEEeCC
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRE-----SVIMKALASGVAFYILKP   76 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~-----~~~~~AL~aGA~dyL~KP   76 (534)
                      ++.++.+|++.++....|||||+|+.||+++|+++++++++..+.++||++|+..+.     ..+.++++.||++||.||
T Consensus        33 ~a~~g~eal~~l~~~~~~DlvllDi~mP~~dG~ell~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~~a~~~ga~~yl~KP  112 (400)
T 3sy8_A           33 EAADGKEAVAILESCGHVDIAICDLQMSGMDGLAFLRHASLSGKVHSVILSSEVDPILRQATISMIECLGLNFLGDLGKP  112 (400)
T ss_dssp             EESSHHHHHHHHHHHSCEEEEEECSSCSSSCHHHHHHHHHHHTCEEEEEESCCCCGGGHHHHHHHHHTTTCEEEEECCSS
T ss_pred             EecCHHHHHHHHhhCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEcCchHHHHHHHHHHHHHcCCeeccCcCCC
Confidence            578999999999762379999999999999999999999998887888888877766     567788999999999999


Q ss_pred             CChHHHHHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccC
Q 043479           77 LNPDDLKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATA  156 (534)
Q Consensus        77 ~s~eeL~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss  156 (534)
                      ++.++|..+|++++..........       .   ........++.......+. ...++|..  ........+.|.   
T Consensus       113 ~~~~~L~~~i~~~~~~~~~~~~~~-------~---~~~~~~~~~l~~al~~~~~-~~~~QPiv--~~~~~~~~g~Ea---  176 (400)
T 3sy8_A          113 FSLERITALLTRYNARRQDLPRQI-------E---VAELPSVADVVRGLDNGEF-EAYYQPKV--ALDGGGLIGAEV---  176 (400)
T ss_dssp             CCHHHHHHHHHHHHHHTTSCCCC-------------CCCCCHHHHHHHHHTTCE-EEEEEEEE--ESSSCCEEEEEE---
T ss_pred             cCHHHHHHHHHHHHHhhhhhhhhh-------h---hhcccHHHHHHHHHHCCcE-EEEEeCeE--EcCCCCEEEEEE---
Confidence            999999999999987654321110       0   0111223444444444444 45555542  122233444555   


Q ss_pred             CCCCCccCCch-----hhHHHHHHHHHhccCCCcHHH
Q 043479          157 PKKPKVAWTDS-----LHNRFLQAIRHIGLEKAVPKK  188 (534)
Q Consensus       157 ~kKprv~Wt~e-----Lh~RFleaLe~LGlekAvpK~  188 (534)
                          .++|.++     .+..|+.+++..|+...+...
T Consensus       177 ----L~R~~~~~~~~i~p~~fi~~ae~~~l~~~l~~~  209 (400)
T 3sy8_A          177 ----LARWNHPHLGVLPPSHFLYVMETYNLVDKLFWQ  209 (400)
T ss_dssp             ----EEEEEETTTEEECGGGTHHHHHHTTCHHHHHHH
T ss_pred             ----EEEEecCCCCEECHHHHHHHHHHCCCHHHHHHH
Confidence                6677664     478888888888765443333

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

Probab=99.42  E-value=1e-12  Score=124.52  Aligned_cols=161  Identities=17%  Similarity=0.272  Sum_probs=116.8

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCC-CCcEEEEecCCCHHHHHHHHHcCCcEEEeCCC-Ch
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFT-HLPVMVMSSDDRESVIMKALASGVAFYILKPL-NP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p-~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~-s~   79 (534)
                      .+.++.+|++.+.. ..||+||    ||+++|+++++.|++. + ++|||++|+..+.....++++.||++||.||+ +.
T Consensus        29 ~~~~~~~al~~l~~-~~~dlvi----lp~~~g~~~~~~lr~~-~~~~~ii~lt~~~~~~~~~~~~~~Ga~~~l~Kp~~~~  102 (223)
T 2hqr_A           29 VTESLEDGEYLMDI-RNYDLVM----VSDKNALSFVSRIKEK-HSSIVVLVSSDNPTSEEEVHAFEQGADDYIAKPYRSI  102 (223)
T ss_dssp             EESSHHHHHHHHTT-SCCSEEE----ECCTTHHHHHHHHHHH-CTTSEEEEEESSCCHHHHHHHHHHTCSEEEETTCSCT
T ss_pred             EECCHHHHHHHHhc-CCCCEEE----eCCCCHHHHHHHHHhC-CCCCcEEEEECCCCHHHHHHHHHcCCCEEEECCCCCH
Confidence            57899999999987 7899999    8999999999999988 7 89999999999999999999999999999999 99


Q ss_pred             HHHHHHHHHHHHHhhhcccccccccceeecCCcCCccchhhHhhhhcccccccccccchhhhccccccccccccccCCCC
Q 043479           80 DDLKNVWQYAMTYKKAKSISIDEIGSFELAGFSAGKFSLDDIVSRSSVNERNKNNKDSKRKASKKDKGKQTKQNATAPKK  159 (534)
Q Consensus        80 eeL~~aI~~aL~~k~~~s~~i~e~~~~~~~~~s~~k~sl~dii~~s~~~e~~q~~k~~Krk~~~~~~~~~~~E~~ss~kK  159 (534)
                      ++|..+|+.++++..  ....                ...++.    ...      ..+ ..  .   .   ..      
T Consensus       103 ~~L~~~i~~~~~~~~--~~~~----------------~~~~~~----~~~------~~~-~~--~---~---~~------  139 (223)
T 2hqr_A          103 KALVARIEARLRFWG--SNVI----------------EIGDLT----ISP------DEE-KI--I---Y---KG------  139 (223)
T ss_dssp             HHHHHHHHHHTSSCC--CCSE----------------EETTEE----EET------TTT-EE--E---E---TT------
T ss_pred             HHHHHHHHHHhcccc--CCeE----------------EECCEE----Eec------ccC-EE--E---E---CC------
Confidence            999999999886530  0000                000000    000      000 00  0   0   00      


Q ss_pred             CCccCCchhhHHHHHHHHHhccC---CCcHHHHHHHcC-CCC-CCHHHHHHHHHHHHHHHH
Q 043479          160 PKVAWTDSLHNRFLQAIRHIGLE---KAVPKKILEFMN-VPG-LTRENVASHLQKYRIFLK  215 (534)
Q Consensus       160 prv~Wt~eLh~RFleaLe~LGle---kAvpK~ILe~M~-V~G-LT~~tVaSHLQKyRl~lk  215 (534)
                          ....|+.++.+++..+...   ....++|++.+. .+. ++..+|+.|+.+.|..|.
T Consensus       140 ----~~~~Lt~rE~~vL~~l~~~~~~~~s~~~Ia~~l~~~~~~~s~~tv~~~i~~lr~KL~  196 (223)
T 2hqr_A          140 ----REVEVKGKPFEVLTHLARHRDQIVSKEQLLDAIWEEPEMVTPNVIEVAINQIRQKMD  196 (223)
T ss_dssp             ----EEECCCSTTTHHHHHHHHTCSEEEEHHHHHHHHCCSSCSCGGGTHHHHHHHHHHHHH
T ss_pred             ----EEEecCHHHHHHHHHHHhCCCCcCCHHHHHHHhcCCccCCCCcCHHHHHHHHHHHHh
Confidence                0113667777888888433   145899999885 222 689999999999888654

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

Probab=99.42  E-value=1.6e-12  Score=115.78  Aligned_cols=93  Identities=24%  Similarity=0.475  Sum_probs=86.3

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcC-CcEEEeCCCChH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASG-VAFYILKPLNPD   80 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aG-A~dyL~KP~s~e   80 (534)
                      .+.++.+|++.+.. ..||+||+|+.+|+++|+++++.|++..+.+|||++|+..+.....++++.| +++||.||++.+
T Consensus        36 ~~~~~~~a~~~l~~-~~~dlvi~d~~l~~~~g~~~~~~l~~~~~~~~ii~ls~~~~~~~~~~~~~~g~~~~~l~kP~~~~  114 (154)
T 2rjn_A           36 TFTSPLDALEALKG-TSVQLVISDMRMPEMGGEVFLEQVAKSYPDIERVVISGYADAQATIDAVNRGKISRFLLKPWEDE  114 (154)
T ss_dssp             EESCHHHHHHHHTT-SCCSEEEEESSCSSSCHHHHHHHHHHHCTTSEEEEEECGGGHHHHHHHHHTTCCSEEEESSCCHH
T ss_pred             EeCCHHHHHHHHhc-CCCCEEEEecCCCCCCHHHHHHHHHHhCCCCcEEEEecCCCHHHHHHHHhccchheeeeCCCCHH
Confidence            47789999999987 7899999999999999999999999998999999999999988999999998 999999999999


Q ss_pred             HHHHHHHHHHHHhhh
Q 043479           81 DLKNVWQYAMTYKKA   95 (534)
Q Consensus        81 eL~~aI~~aL~~k~~   95 (534)
                      +|..+|++++++...
T Consensus       115 ~L~~~i~~~~~~~~~  129 (154)
T 2rjn_A          115 DVFKVVEKGLQLAFL  129 (154)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999877654

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

Probab=99.41  E-value=4.2e-13  Score=117.88  Aligned_cols=94  Identities=20%  Similarity=0.288  Sum_probs=84.5

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCC-CCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPE-MNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPD   80 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPd-mdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~e   80 (534)
                      ++.++.+|++.+.....|||||+|+.||+ ++|+++++.|++. +.+|||++|+..+.....++++.||++||.||++.+
T Consensus        34 ~~~~~~~a~~~l~~~~~~dlvi~D~~l~~~~~g~~~~~~l~~~-~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~KP~~~~  112 (140)
T 3h5i_A           34 IALTGEAAVEKVSGGWYPDLILMDIELGEGMDGVQTALAIQQI-SELPVVFLTAHTEPAVVEKIRSVTAYGYVMKSATEQ  112 (140)
T ss_dssp             EESSHHHHHHHHHTTCCCSEEEEESSCSSSCCHHHHHHHHHHH-CCCCEEEEESSSSCCCCGGGGGSCEEEEEETTCCHH
T ss_pred             EecChHHHHHHHhcCCCCCEEEEeccCCCCCCHHHHHHHHHhC-CCCCEEEEECCCCHHHHHHHHhCCCcEEEeCCCCHH
Confidence            57789999999975357999999999995 9999999999986 789999999999888888899999999999999999


Q ss_pred             HHHHHHHHHHHHhhhc
Q 043479           81 DLKNVWQYAMTYKKAK   96 (534)
Q Consensus        81 eL~~aI~~aL~~k~~~   96 (534)
                      +|..+|++++++.+..
T Consensus       113 ~l~~~i~~~l~~~~~~  128 (140)
T 3h5i_A          113 VLITIVEMALRLYEAN  128 (140)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhh
Confidence            9999999999876543

>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=99.41  E-value=2e-12  Score=112.97  Aligned_cols=93  Identities=24%  Similarity=0.366  Sum_probs=84.7

Q ss_pred             eecCHHHHHHHHHhc---------CCceEEEEeCCCCCCCHHHHHHHHHhhC--CCCcEEEEecCCCHHHHHHHHHcCCc
Q 043479            2 TVTRPVEALATVRIQ---------RDIDLVVTDLHMPEMNGIELQKEINEEF--THLPVMVMSSDDRESVIMKALASGVA   70 (534)
Q Consensus         2 tass~~EALe~L~~~---------~~pDLVLLDi~mPdmdGleLL~~Lr~~~--p~ipVIVLSs~~d~~~~~~AL~aGA~   70 (534)
                      .+.++.+|++.+...         ..||+||+|+.||+++|+++++.|++..  +.+|||++|+..+.....++++.|++
T Consensus        37 ~~~~~~~al~~l~~~~~~~~~~~~~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~~~ii~~t~~~~~~~~~~~~~~g~~  116 (149)
T 1k66_A           37 RCITGDQALDFLYQTGSYCNPDIAPRPAVILLDLNLPGTDGREVLQEIKQDEVLKKIPVVIMTTSSNPKDIEICYSYSIS  116 (149)
T ss_dssp             EECSHHHHHHHHHTCCSSSCGGGCCCCSEEEECSCCSSSCHHHHHHHHTTSTTGGGSCEEEEESCCCHHHHHHHHHTTCS
T ss_pred             EECCHHHHHHHHHhcccccCcccCCCCcEEEEECCCCCCCHHHHHHHHHhCcccCCCeEEEEeCCCCHHHHHHHHHCCCC
Confidence            467899999999751         4799999999999999999999999865  78999999999999999999999999


Q ss_pred             EEEeCCCChHHHHHHHHHHHHHhh
Q 043479           71 FYILKPLNPDDLKNVWQYAMTYKK   94 (534)
Q Consensus        71 dyL~KP~s~eeL~~aI~~aL~~k~   94 (534)
                      +||.||++.++|..+|+++++.+.
T Consensus       117 ~~l~kP~~~~~l~~~i~~~~~~~~  140 (149)
T 1k66_A          117 SYIVKPLEIDRLTETVQTFIKYWL  140 (149)
T ss_dssp             EEEECCSSHHHHHHHHHHHHHHHH
T ss_pred             EEEeCCCCHHHHHHHHHHHHHHhh
Confidence            999999999999999999987654

>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=99.40  E-value=1.3e-12  Score=116.49  Aligned_cols=93  Identities=24%  Similarity=0.389  Sum_probs=86.3

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.+|++.+.. ..||+||+|+.||+++|+++++.|++..+.+|||++|+..+......+++.|+++||.||++.++
T Consensus        32 ~~~~~~~a~~~l~~-~~~dliild~~l~~~~g~~~~~~l~~~~~~~pii~ls~~~~~~~~~~~~~~g~~~~l~kP~~~~~  110 (155)
T 1qkk_A           32 SFASATEALAGLSA-DFAGIVISDIRMPGMDGLALFRKILALDPDLPMILVTGHGDIPMAVQAIQDGAYDFIAKPFAADR  110 (155)
T ss_dssp             EESCHHHHHHTCCT-TCCSEEEEESCCSSSCHHHHHHHHHHHCTTSCEEEEECGGGHHHHHHHHHTTCCEEEESSCCHHH
T ss_pred             EECCHHHHHHHHHh-CCCCEEEEeCCCCCCCHHHHHHHHHhhCCCCCEEEEECCCChHHHHHHHhcCCCeEEeCCCCHHH
Confidence            46789999999876 78999999999999999999999999999999999999999899999999999999999999999


Q ss_pred             HHHHHHHHHHHhhh
Q 043479           82 LKNVWQYAMTYKKA   95 (534)
Q Consensus        82 L~~aI~~aL~~k~~   95 (534)
                      |..+|++++++++.
T Consensus       111 L~~~i~~~~~~~~~  124 (155)
T 1qkk_A          111 LVQSARRAEEKRRL  124 (155)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999999876553

>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=99.40  E-value=5.2e-13  Score=139.25  Aligned_cols=93  Identities=19%  Similarity=0.249  Sum_probs=87.5

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++.+|++.+.. ..|||||+|+.||+++|++++++|++..+++|||++|++.+.+.+.++++.||++||.||++.++
T Consensus        29 ~a~~~~eal~~l~~-~~~DlvllDi~mP~~dG~ell~~lr~~~~~~pvI~lT~~~~~~~~~~a~~~Ga~~yl~KP~~~~~  107 (368)
T 3dzd_A           29 TAKTLREAEKKIKE-LFFPVIVLDVWMPDGDGVNFIDFIKENSPDSVVIVITGHGSVDTAVKAIKKGAYEFLEKPFSVER  107 (368)
T ss_dssp             EESSHHHHHHHHHH-BCCSEEEEESEETTEETTTHHHHHHHHCTTCEEEEEECSSCCHHHHHHHHHTCCEEEESSCCHHH
T ss_pred             EECCHHHHHHHHHh-CCCCEEEEeCCCCCCCHHHHHHHHHhhCCCCeEEEEeCCCCHHHHHHHHhcCcceEEeCCCCHHH
Confidence            57899999999987 78999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhh
Q 043479           82 LKNVWQYAMTYKKA   95 (534)
Q Consensus        82 L~~aI~~aL~~k~~   95 (534)
                      |..+|++++.....
T Consensus       108 L~~~i~~~l~~~~~  121 (368)
T 3dzd_A          108 FLLTIKHAFEEYSK  121 (368)
T ss_dssp             HHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHhhh
Confidence            99999999876543

>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=99.39  E-value=1.7e-13  Score=117.24  Aligned_cols=90  Identities=21%  Similarity=0.319  Sum_probs=82.2

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhC--CCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEF--THLPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~--p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      .+.++.++++.+.. ..||+||+|+.||+++|++++++|++..  +.+|||++|+..+.....++++.|+++||.||++.
T Consensus        31 ~~~~~~~a~~~~~~-~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~Kp~~~  109 (127)
T 2jba_A           31 EAEDYDSAVNQLNE-PWPDLILLAWMLPGGSGIQFIKHLRRESMTRDIPVVMLTARGEEEDRVRGLETGADDCITKPFSP  109 (127)
T ss_dssp             EECSHHHHHTTCSS-SCCSEEEEESEETTEEHHHHHHHHHTSTTTTTSCEEEEEETTHHHHHHTTCCCSCSEEEEESCCH
T ss_pred             EeCCHHHHHHHHhc-cCCCEEEEecCCCCCCHHHHHHHHHhCcccCCCCEEEEeCCCCHHHHHHHHhcCCCeEEeCCCCH
Confidence            46788999998876 6899999999999999999999999764  78999999999988888899999999999999999


Q ss_pred             HHHHHHHHHHHHH
Q 043479           80 DDLKNVWQYAMTY   92 (534)
Q Consensus        80 eeL~~aI~~aL~~   92 (534)
                      ++|..+|++++++
T Consensus       110 ~~l~~~i~~~~~~  122 (127)
T 2jba_A          110 KELVARIKAVMRR  122 (127)
T ss_dssp             HHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHhc
Confidence            9999999998754

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

Probab=99.39  E-value=9.7e-13  Score=124.79  Aligned_cols=91  Identities=26%  Similarity=0.371  Sum_probs=79.0

Q ss_pred             eecCHHHHHHHHHhc------------CCceEEEEeCCCCCCCHHHHHHHHHhh----CCCCcEEEEecCC-CHHHHHHH
Q 043479            2 TVTRPVEALATVRIQ------------RDIDLVVTDLHMPEMNGIELQKEINEE----FTHLPVMVMSSDD-RESVIMKA   64 (534)
Q Consensus         2 tass~~EALe~L~~~------------~~pDLVLLDi~mPdmdGleLL~~Lr~~----~p~ipVIVLSs~~-d~~~~~~A   64 (534)
                      .+.++.+|++.++..            ..|||||+|+.||+++|++++++|++.    .+.+|||++|+.. +.+...++
T Consensus        91 ~a~~~~eal~~l~~~~~~~~~~~~~~~~~~dlillD~~lp~~~G~el~~~lr~~~~~~~~~~piI~ls~~~~~~~~~~~~  170 (206)
T 3mm4_A           91 QCDSGKEALRLVTEGLTQREEQGSVDKLPFDYIFMDCQMPEMDGYEATREIRKVEKSYGVRTPIIAVSGHDPGSEEARET  170 (206)
T ss_dssp             EESSHHHHHHHHHHHHHHHHHHTCSSCCSCSEEEEESCCSSSCHHHHHHHHHHHHHTTTCCCCEEEEESSCCCHHHHHHH
T ss_pred             eeCCHHHHHHHHHhhcccccccccccCCCCCEEEEcCCCCCCCHHHHHHHHHhhhhhcCCCCcEEEEECCCCcHHHHHHH
Confidence            578999999999762            279999999999999999999999985    5889999999998 77888899


Q ss_pred             HHcCCcEEEeCCCChHHHHHHHHHHHHHhh
Q 043479           65 LASGVAFYILKPLNPDDLKNVWQYAMTYKK   94 (534)
Q Consensus        65 L~aGA~dyL~KP~s~eeL~~aI~~aL~~k~   94 (534)
                      ++.|+++||.||++  +|..+|+++++.+.
T Consensus       171 ~~~Ga~~~l~KP~~--~L~~~i~~~l~~~~  198 (206)
T 3mm4_A          171 IQAGMDAFLDKSLN--QLANVIREIESKRH  198 (206)
T ss_dssp             HHHTCSEEEETTCT--THHHHHHHHC----
T ss_pred             HhCCCCEEEcCcHH--HHHHHHHHHHhhhH
Confidence            99999999999998  89999999886654

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

Probab=99.39  E-value=7.6e-13  Score=111.59  Aligned_cols=86  Identities=23%  Similarity=0.347  Sum_probs=78.1

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++.++++.+.. ..||+||+|+.||+++|+++++.+++..+.+|||++|+..+..  .++++.|+++||.||++.++
T Consensus        30 ~~~~~~~a~~~~~~-~~~dlvl~D~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~--~~~~~~g~~~~l~Kp~~~~~  106 (116)
T 3a10_A           30 TAENGEEALKKFFS-GNYDLVILDIEMPGISGLEVAGEIRKKKKDAKIILLTAYSHYR--SDMSSWAADEYVVKSFNFDE  106 (116)
T ss_dssp             EESSHHHHHHHHHH-SCCSEEEECSCCSSSCHHHHHHHHHHHCTTCCEEEEESCGGGG--GCGGGGGSSEEEECCSSTHH
T ss_pred             EeCCHHHHHHHHhc-CCCCEEEEECCCCCCCHHHHHHHHHccCCCCeEEEEECCcchH--HHHHhccccceEECCCCHHH
Confidence            46789999999987 7899999999999999999999999988899999999987655  67889999999999999999


Q ss_pred             HHHHHHHHH
Q 043479           82 LKNVWQYAM   90 (534)
Q Consensus        82 L~~aI~~aL   90 (534)
                      |..+|++++
T Consensus       107 l~~~i~~~~  115 (116)
T 3a10_A          107 LKEKVKKLL  115 (116)
T ss_dssp             HHHHHHHHT
T ss_pred             HHHHHHHHh
Confidence            999998764

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

Probab=99.39  E-value=9.9e-13  Score=129.02  Aligned_cols=92  Identities=26%  Similarity=0.400  Sum_probs=85.9

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.+|++.++. ..||+||+|+.||+++|++++++|++..+.+|||++|+..+.....++++.|+++||.||++.++
T Consensus       158 ~a~~~~eal~~l~~-~~~dlvl~D~~mp~~~G~~l~~~ir~~~~~~piI~lt~~~~~~~~~~~~~~G~~~~l~KP~~~~~  236 (254)
T 2ayx_A          158 TANDGVDALNVLSK-NHIDIVLSDVNMPNMDGYRLTQRIRQLGLTLPVIGVTANALAEEKQRCLESGMDSCLSKPVTLDV  236 (254)
T ss_dssp             EECCSHHHHHHHHH-SCCSEEEEEESSCSSCCHHHHHHHHHHHCCSCEEEEESSTTSHHHHHHHHCCCEEEEESSCCHHH
T ss_pred             EECCHHHHHHHHHh-CCCCEEEEcCCCCCCCHHHHHHHHHhcCCCCcEEEEECCCCHHHHHHHHHcCCceEEECCCCHHH
Confidence            57889999999987 78999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhh
Q 043479           82 LKNVWQYAMTYKK   94 (534)
Q Consensus        82 L~~aI~~aL~~k~   94 (534)
                      |..+|+++++..+
T Consensus       237 L~~~l~~~~~~~~  249 (254)
T 2ayx_A          237 IKQTLTLYAERVR  249 (254)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhh
Confidence            9999999886644

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

Probab=99.39  E-value=5.2e-13  Score=116.59  Aligned_cols=94  Identities=18%  Similarity=0.309  Sum_probs=86.0

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHh--hCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINE--EFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~--~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      .+.+.++|++.++. ..||+||+|+.+|+++|+++++.|++  ..+.+|||++|+..+.....++++.|+++||.||++.
T Consensus        36 ~~~~~~~a~~~l~~-~~~dlii~d~~l~~~~g~~~~~~l~~~~~~~~~pii~~s~~~~~~~~~~~~~~g~~~~l~kp~~~  114 (142)
T 3cg4_A           36 SADSGGQCIDLLKK-GFSGVVLLDIMMPGMDGWDTIRAILDNSLEQGIAIVMLTAKNAPDAKMIGLQEYVVDYITKPFDN  114 (142)
T ss_dssp             EESSHHHHHHHHHT-CCCEEEEEESCCSSSCHHHHHHHHHHTTCCTTEEEEEEECTTCCCCSSTTGGGGEEEEEESSCCH
T ss_pred             EeCCHHHHHHHHHh-cCCCEEEEeCCCCCCCHHHHHHHHHhhcccCCCCEEEEECCCCHHHHHHHHhcCccEEEeCCCCH
Confidence            46789999999987 78999999999999999999999998  6788999999999888888889999999999999999


Q ss_pred             HHHHHHHHHHHHHhhhc
Q 043479           80 DDLKNVWQYAMTYKKAK   96 (534)
Q Consensus        80 eeL~~aI~~aL~~k~~~   96 (534)
                      ++|..+|++++++.+..
T Consensus       115 ~~l~~~i~~~~~~~~~~  131 (142)
T 3cg4_A          115 EDLIEKTTFFMGFVRNQ  131 (142)
T ss_dssp             HHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHhhc
Confidence            99999999998776543

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

Probab=99.39  E-value=2.1e-13  Score=137.33  Aligned_cols=89  Identities=24%  Similarity=0.396  Sum_probs=81.2

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCC-CCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMP-EMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPD   80 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mP-dmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~e   80 (534)
                      ++.++.+|++.+.. ..|||||+|+.|| +|||+++++.||+.. ++|||++|+..+  ...+++++|+++||.||++++
T Consensus       190 ~a~~g~eAl~~~~~-~~~dlvl~D~~MPd~mdG~e~~~~ir~~~-~~piI~lT~~~~--~~~~~~~~G~~~~l~KP~~~~  265 (286)
T 3n0r_A          190 IAATRGEALEAVTR-RTPGLVLADIQLADGSSGIDAVKDILGRM-DVPVIFITAFPE--RLLTGERPEPTFLITKPFQPE  265 (286)
T ss_dssp             EESSHHHHHHHHHH-CCCSEEEEESCCTTSCCTTTTTHHHHHHT-TCCEEEEESCGG--GGCCSSSCCCSSEEESSCCHH
T ss_pred             EeCCHHHHHHHHHh-CCCCEEEEcCCCCCCCCHHHHHHHHHhcC-CCCEEEEeCCHH--HHHHHHhCCCcEEEeCCCCHH
Confidence            58899999999987 7899999999999 799999999999887 899999999853  456789999999999999999


Q ss_pred             HHHHHHHHHHHHhh
Q 043479           81 DLKNVWQYAMTYKK   94 (534)
Q Consensus        81 eL~~aI~~aL~~k~   94 (534)
                      +|..+|++++....
T Consensus       266 ~L~~~i~~~l~~~~  279 (286)
T 3n0r_A          266 TVKAAIGQALFFHP  279 (286)
T ss_dssp             HHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHhCC
Confidence            99999999997643

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

Probab=99.38  E-value=1.6e-12  Score=113.88  Aligned_cols=91  Identities=23%  Similarity=0.330  Sum_probs=79.2

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhh--CCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~--~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      .+.++.+|++.+.. ..||+||+|+.||+++|+++++.|++.  .+.+|||++|+..+......++.+|+++||.||++.
T Consensus        32 ~~~~~~~al~~l~~-~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~~~ii~ls~~~~~~~~~~~~~~~~~~~l~KP~~~  110 (138)
T 3c3m_A           32 TAFSGEECLEALNA-TPPDLVLLDIMMEPMDGWETLERIKTDPATRDIPVLMLTAKPLTPEEANEYGSYIEDYILKPTTH  110 (138)
T ss_dssp             EESSHHHHHHHHHH-SCCSEEEEESCCSSSCHHHHHHHHHHSTTTTTSCEEEEESSCCCHHHHHHTTTTCSEEEECCCHH
T ss_pred             EeCCHHHHHHHHhc-cCCCEEEEeCCCCCCCHHHHHHHHHcCcccCCCCEEEEECCCChHHHHHHhhcCHhheEeCCCCH
Confidence            46789999999987 789999999999999999999999975  357999999998766655666677789999999999


Q ss_pred             HHHHHHHHHHHHHh
Q 043479           80 DDLKNVWQYAMTYK   93 (534)
Q Consensus        80 eeL~~aI~~aL~~k   93 (534)
                      ++|..+|++++.++
T Consensus       111 ~~L~~~i~~~~~~~  124 (138)
T 3c3m_A          111 HQLYEAIEHVLARR  124 (138)
T ss_dssp             HHHHHHHHHHHSCC
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999988543

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

Probab=99.38  E-value=2.8e-12  Score=110.52  Aligned_cols=91  Identities=18%  Similarity=0.329  Sum_probs=76.5

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhC--CCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEF--THLPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~--p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      ++.++.+|++.+.. ..||+||+|+.||+++|++++++|++..  +.++||+++...+. ...++++.||++||.||++.
T Consensus        35 ~~~~~~~a~~~l~~-~~~dlii~d~~l~~~~g~~~~~~l~~~~~~~~~~ii~~~~~~~~-~~~~~~~~g~~~~l~kP~~~  112 (132)
T 3lte_A           35 IAHNGFDAGIKLST-FEPAIMTLDLSMPKLDGLDVIRSLRQNKVANQPKILVVSGLDKA-KLQQAVTEGADDYLEKPFDN  112 (132)
T ss_dssp             EESSHHHHHHHHHH-TCCSEEEEESCBTTBCHHHHHHHHHTTTCSSCCEEEEECCSCSH-HHHHHHHHTCCEEECSSCCH
T ss_pred             EeCCHHHHHHHHHh-cCCCEEEEecCCCCCCHHHHHHHHHhcCccCCCeEEEEeCCChH-HHHHHHHhChHHHhhCCCCH
Confidence            57789999999987 7899999999999999999999999865  44555555555444 77899999999999999999


Q ss_pred             HHHHHHHHHHHHHhh
Q 043479           80 DDLKNVWQYAMTYKK   94 (534)
Q Consensus        80 eeL~~aI~~aL~~k~   94 (534)
                      ++|..+|+++..+..
T Consensus       113 ~~l~~~i~~~~~~~~  127 (132)
T 3lte_A          113 DALLDRIHDLVNEGH  127 (132)
T ss_dssp             HHHHHHHHHHHC---
T ss_pred             HHHHHHHHHHcCCCC
Confidence            999999999886654

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

Probab=99.37  E-value=9.5e-13  Score=116.97  Aligned_cols=96  Identities=19%  Similarity=0.254  Sum_probs=76.8

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.+..+|++.+.....||+||+|+.||+++|+++++.|++..+.+|||++|+..+.....++++.|+++||.||++.++
T Consensus        34 ~~~~~~~a~~~l~~~~~~dlvi~d~~l~~~~g~~~~~~l~~~~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~  113 (154)
T 2qsj_A           34 GAETVSDALAFLEADNTVDLILLDVNLPDAEAIDGLVRLKRFDPSNAVALISGETDHELIRAALEAGADGFIPKSADPQV  113 (154)
T ss_dssp             EESSHHHHHHHHHTTCCCSEEEECC------CHHHHHHHHHHCTTSEEEEC-----CHHHHHHHHTTCCBBCCTTSCHHH
T ss_pred             EecCHHHHHHHHhccCCCCEEEEeCCCCCCchHHHHHHHHHhCCCCeEEEEeCCCCHHHHHHHHHccCCEEEeCCCCHHH
Confidence            46789999999975257999999999999999999999999999999999999998889999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhcc
Q 043479           82 LKNVWQYAMTYKKAKS   97 (534)
Q Consensus        82 L~~aI~~aL~~k~~~s   97 (534)
                      |..+|+++++++...+
T Consensus       114 L~~~l~~~~~~~~~~~  129 (154)
T 2qsj_A          114 LIHAVSLILEGEIFLP  129 (154)
T ss_dssp             HHHHHHHHHTTCCBCC
T ss_pred             HHHHHHHHHcCCEEcC
Confidence            9999999997765544

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

Probab=99.37  E-value=3.5e-12  Score=111.65  Aligned_cols=91  Identities=18%  Similarity=0.284  Sum_probs=81.1

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.+|++.+.. ..|||||+|+.||+++|+++++.|++..+.++||++|+..+  ...++++.|+++||.||++.++
T Consensus        40 ~~~~~~~al~~l~~-~~~dlvi~d~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~--~~~~~~~~g~~~~l~KP~~~~~  116 (143)
T 2qv0_A           40 SFDDGLDVLKFLQH-NKVDAIFLDINIPSLDGVLLAQNISQFAHKPFIVFITAWKE--HAVEAFELEAFDYILKPYQESR  116 (143)
T ss_dssp             EESCHHHHHHHHHH-CCCSEEEECSSCSSSCHHHHHHHHTTSTTCCEEEEEESCCT--THHHHHHTTCSEEEESSCCHHH
T ss_pred             EeCCHHHHHHHHHh-CCCCEEEEecCCCCCCHHHHHHHHHccCCCceEEEEeCCHH--HHHHHHhCCcceEEeCCCCHHH
Confidence            46789999999987 78999999999999999999999998777788999998743  5678899999999999999999


Q ss_pred             HHHHHHHHHHHhhh
Q 043479           82 LKNVWQYAMTYKKA   95 (534)
Q Consensus        82 L~~aI~~aL~~k~~   95 (534)
                      |..+|+++++.++.
T Consensus       117 l~~~i~~~~~~~~~  130 (143)
T 2qv0_A          117 IINMLQKLTTAWEQ  130 (143)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999877654

>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=99.36  E-value=2e-12  Score=121.20  Aligned_cols=91  Identities=24%  Similarity=0.428  Sum_probs=84.0

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++.+|++.+.. ..||+||+|+.||+++|+++++.|++..+ .|||++|+..+.....++++.||++||.||++.++
T Consensus        43 ~~~~~~~al~~~~~-~~~dlvi~D~~~p~~~g~~~~~~l~~~~~-~pii~lt~~~~~~~~~~~~~~ga~~~l~KP~~~~~  120 (205)
T 1s8n_A           43 EAGDGQEAVELAEL-HKPDLVIMDVKMPRRDGIDAASEIASKRI-APIVVLTAFSQRDLVERARDAGAMAYLVKPFSISD  120 (205)
T ss_dssp             EESSHHHHHHHHHH-HCCSEEEEESSCSSSCHHHHHHHHHHTTC-SCEEEEEEGGGHHHHHTTGGGSCEEEEEESCCHHH
T ss_pred             EeCCHHHHHHHHhh-cCCCEEEEeCCCCCCChHHHHHHHHhcCC-CCEEEEecCCCHHHHHHHHhcCCcEEEeCCCCHHH
Confidence            57899999999987 68999999999999999999999998766 59999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhh
Q 043479           82 LKNVWQYAMTYKK   94 (534)
Q Consensus        82 L~~aI~~aL~~k~   94 (534)
                      |..+|++++++..
T Consensus       121 L~~~i~~~~~~~~  133 (205)
T 1s8n_A          121 LIPAIELAVSRFR  133 (205)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999987654

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

Probab=99.35  E-value=1.6e-12  Score=134.94  Aligned_cols=92  Identities=28%  Similarity=0.445  Sum_probs=82.3

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCC-ChH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPL-NPD   80 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~-s~e   80 (534)
                      ++.++.+|++.++. ..|||||+|+.||+++|++++++|++..+++|||++|+..+.+...++++.||++||.||+ ..+
T Consensus        34 ~a~~~~~al~~~~~-~~~dlvllD~~mp~~~G~~~~~~lr~~~~~~pii~lt~~~~~~~~~~a~~~ga~~yl~KP~~~~~  112 (394)
T 3eq2_A           34 QALNGLQGLQIFES-EQPDLVICDLRMPQIDGLELIRRIRQTASETPIIVLSGAGVMSDAVEALRLGAADYLIKPLEDLA  112 (394)
T ss_dssp             ECSSHHHHHHHHHH-SCCSEEEECCCSSSSCTHHHHHHHHHTTCCCCEEEC---CHHHHHHHHHHHTCSEECCSSCSCTH
T ss_pred             EECCHHHHHHHHhh-CCCCEEEEcCCCCCCCHHHHHHHHHhhCCCCcEEEEEcCCCHHHHHHHHhcChhhEEECCCChHH
Confidence            57899999999987 7899999999999999999999999998999999999999999999999999999999999 689


Q ss_pred             HHHHHHHHHHHHhh
Q 043479           81 DLKNVWQYAMTYKK   94 (534)
Q Consensus        81 eL~~aI~~aL~~k~   94 (534)
                      +|..+|+++++...
T Consensus       113 ~l~~~i~~~~~~~~  126 (394)
T 3eq2_A          113 VLEHSVRRALDRAY  126 (394)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhh
Confidence            99999998886543

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

Probab=99.35  E-value=7e-13  Score=114.28  Aligned_cols=92  Identities=21%  Similarity=0.313  Sum_probs=80.8

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCH-----HHHHHHHHcCCcEEEeCC
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRE-----SVIMKALASGVAFYILKP   76 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~-----~~~~~AL~aGA~dyL~KP   76 (534)
                      .+.+.+++++.+.. . ||+||+|+.||+++|+++++.|++..+.+|||++|+..+.     ....++++.|+++||.||
T Consensus        32 ~~~~~~~~~~~~~~-~-~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~~~~~~g~~~~l~KP  109 (135)
T 3eqz_A           32 AFQHPRAFLTLSLN-K-QDIIILDLMMPDMDGIEVIRHLAEHKSPASLILISGYDSGVLHSAETLALSCGLNVINTFTKP  109 (135)
T ss_dssp             EESCHHHHTTSCCC-T-TEEEEEECCTTTTHHHHHHHHHHHTTCCCEEEEEESSCHHHHHHHHHHHHHTTCEEEEEEESS
T ss_pred             eecCHHHHHHhhcc-C-CCEEEEeCCCCCCCHHHHHHHHHhCCCCCCEEEEEeccchhHHHHHHHHHHcCCCcceeeCCC
Confidence            46788888888776 5 9999999999999999999999999999999999998875     666778899999999999


Q ss_pred             CChHHHHHHHHHHHHHhhh
Q 043479           77 LNPDDLKNVWQYAMTYKKA   95 (534)
Q Consensus        77 ~s~eeL~~aI~~aL~~k~~   95 (534)
                      ++.++|..+|++++.++..
T Consensus       110 ~~~~~l~~~l~~~~~~~~~  128 (135)
T 3eqz_A          110 INTEVLTCFLTSLSNRQAE  128 (135)
T ss_dssp             CCHHHHHHHHHHHSCCC--
T ss_pred             CCHHHHHHHHHHHHhhccc
Confidence            9999999999998765543

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

Probab=99.34  E-value=6.6e-12  Score=109.66  Aligned_cols=91  Identities=20%  Similarity=0.303  Sum_probs=81.6

Q ss_pred             eecCHHHHHHHHHh-----cCCceEEEEeCCCCCCCHHHHHHHHHhhC--CCCcEEEEecCCCHHHHHHHHHcCCcEEEe
Q 043479            2 TVTRPVEALATVRI-----QRDIDLVVTDLHMPEMNGIELQKEINEEF--THLPVMVMSSDDRESVIMKALASGVAFYIL   74 (534)
Q Consensus         2 tass~~EALe~L~~-----~~~pDLVLLDi~mPdmdGleLL~~Lr~~~--p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~   74 (534)
                      .+.++.+|++.++.     ...||+||+|+.||+++|+++++.|++..  +.+|||++|+..+.....++++.|+++||.
T Consensus        38 ~~~~~~~a~~~l~~~~~~~~~~~dlii~D~~l~~~~g~~~~~~l~~~~~~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~  117 (143)
T 2qvg_A           38 IAKSGNQALDMLYGRNKENKIHPKLILLDINIPKMNGIEFLKELRDDSSFTDIEVFVLTAAYTSKDKLAFESLNIRGHLI  117 (143)
T ss_dssp             EESSHHHHHHHHHTCTTCCCCCCSEEEEETTCTTSCHHHHHHHHTTSGGGTTCEEEEEESCCCHHHHHHHTTTTCCEEEE
T ss_pred             EECCHHHHHHHHHhcccccCCCCCEEEEecCCCCCCHHHHHHHHHcCccccCCcEEEEeCCCCHHHHHHHHhcCCCeEEE
Confidence            46789999999974     14699999999999999999999999865  789999999999999999999999999999


Q ss_pred             CCCChHHHHHHHHHHHHH
Q 043479           75 KPLNPDDLKNVWQYAMTY   92 (534)
Q Consensus        75 KP~s~eeL~~aI~~aL~~   92 (534)
                      ||++.++|..++......
T Consensus       118 kP~~~~~L~~~~~~~~~~  135 (143)
T 2qvg_A          118 KPLDYGEAIKLFWILQSM  135 (143)
T ss_dssp             SSCCHHHHHHHHHHHHHC
T ss_pred             CCCCHHHHHHHHHHHHHh
Confidence            999999999998776544

>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=99.34  E-value=4.3e-12  Score=132.98  Aligned_cols=92  Identities=23%  Similarity=0.368  Sum_probs=86.2

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++.+|++.+.. ..|||||+|+.||+++|++++++|++..+++|||++|+..+.+.+.++++.||++||.||++.++
T Consensus        29 ~a~~~~eal~~l~~-~~~DlvllD~~mp~~dG~ell~~lr~~~~~~pvIvlT~~~~~~~~~~a~~~Ga~dyl~KP~~~~~  107 (387)
T 1ny5_A           29 SAERGKEAYKLLSE-KHFNVVLLDLLLPDVNGLEILKWIKERSPETEVIVITGHGTIKTAVEAMKMGAYDFLTKPCMLEE  107 (387)
T ss_dssp             EESSHHHHHHHHHH-SCCSEEEEESBCSSSBHHHHHHHHHHHCTTSEEEEEEETTCHHHHHHHHTTTCCEEEEESCCHHH
T ss_pred             EECCHHHHHHHHHh-CCCCEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEeCCCCHHHHHHHHhcCceEEecCCCCHHH
Confidence            57899999999987 78999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhh
Q 043479           82 LKNVWQYAMTYKK   94 (534)
Q Consensus        82 L~~aI~~aL~~k~   94 (534)
                      |..+|+++++...
T Consensus       108 L~~~i~~~l~~~~  120 (387)
T 1ny5_A          108 IELTINKAIEHRK  120 (387)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999886543

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

Probab=99.33  E-value=4e-12  Score=110.59  Aligned_cols=89  Identities=25%  Similarity=0.390  Sum_probs=77.4

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCC----C-CcEEEEecCCCHHHHHHHHHcCCcEEEeCC
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFT----H-LPVMVMSSDDRESVIMKALASGVAFYILKP   76 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p----~-ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP   76 (534)
                      ++.++.+|++.+.. .. |+||+|+.||+++|+++++.|++..+    . .+||++|+..+.....++++.||++||.||
T Consensus        36 ~~~~~~~a~~~~~~-~~-dlvllD~~lp~~~g~~~~~~l~~~~~~~~~~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~KP  113 (136)
T 1dcf_A           36 TVSSNEECLRVVSH-EH-KVVFMDVCMPGVENYQIALRIHEKFTKQRHQRPLLVALSGNTDKSTKEKCMSFGLDGVLLKP  113 (136)
T ss_dssp             EESSHHHHHHHCCT-TC-SEEEEECCSSTTTTTHHHHHHHHHHC-CCSCCCEEEEEESCCSHHHHHHHHHTTCCEEEESS
T ss_pred             EeCCHHHHHHHHhc-cC-CEEEEeCCCCCCcHHHHHHHHHHhhhhccCCCceEEEEeCCCCHHHHHHHHHcCCCeEEECC
Confidence            46789999998865 44 99999999999999999999985432    2 357889999999889999999999999999


Q ss_pred             CChHHHHHHHHHHHHH
Q 043479           77 LNPDDLKNVWQYAMTY   92 (534)
Q Consensus        77 ~s~eeL~~aI~~aL~~   92 (534)
                      ++.++|..+|++++++
T Consensus       114 ~~~~~L~~~l~~~~~~  129 (136)
T 1dcf_A          114 VSLDNIRDVLSDLLEP  129 (136)
T ss_dssp             CCHHHHHHHHHHHHSC
T ss_pred             CCHHHHHHHHHHHhch
Confidence            9999999999998754

>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=99.33  E-value=6.1e-12  Score=132.56  Aligned_cols=92  Identities=23%  Similarity=0.366  Sum_probs=84.4

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhh--CCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~--~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      ++.++.+|++.+.. ..|||||+|+.||+++|+++++.|++.  .+.+|||++|+..+.....+++++||++||.||++.
T Consensus        30 ~a~~~~~al~~~~~-~~~dlvllD~~mp~~~G~~~~~~l~~~~~~~~~pii~lt~~~~~~~~~~a~~~Ga~~~l~KP~~~  108 (459)
T 1w25_A           30 TAMDGPTALAMAAR-DLPDIILLDVMMPGMDGFTVCRKLKDDPTTRHIPVVLITALDGRGDRIQGLESGASDFLTKPIDD  108 (459)
T ss_dssp             EESSHHHHHHHHHH-HCCSEEEEESCCSSSCHHHHHHHHHHSTTTTTSCEEEEECSSCHHHHHHHHHHTCCEEEESSCCH
T ss_pred             EECCHHHHHHHHhc-CCCCEEEEcCCCCCCCHHHHHHHHhcCcccCCCCEEEEECCCCHHHHHHHHHcCCCEEEeCCCCH
Confidence            57899999999987 689999999999999999999999974  467999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhh
Q 043479           80 DDLKNVWQYAMTYKK   94 (534)
Q Consensus        80 eeL~~aI~~aL~~k~   94 (534)
                      ++|..+|+++++...
T Consensus       109 ~~l~~~i~~~~~~~~  123 (459)
T 1w25_A          109 VMLFARVRSLTRFKL  123 (459)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHh
Confidence            999999999886543

>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=99.32  E-value=4.5e-12  Score=107.50  Aligned_cols=88  Identities=17%  Similarity=0.304  Sum_probs=80.9

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCC-CCCHHHHHHHHHhh--CCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCC
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMP-EMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPLN   78 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mP-dmdGleLL~~Lr~~--~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s   78 (534)
                      .+.++.+|++.+.. ..||+||+|+.+| +++|+++++.|++.  .+.+|||++ +..+.....++++.|+++||.||++
T Consensus        34 ~~~~~~~a~~~~~~-~~~dlvi~d~~~~~~~~g~~~~~~l~~~~~~~~~~ii~~-~~~~~~~~~~~~~~g~~~~l~kp~~  111 (127)
T 2gkg_A           34 ETTDGKGSVEQIRR-DRPDLVVLAVDLSAGQNGYLICGKLKKDDDLKNVPIVII-GNPDGFAQHRKLKAHADEYVAKPVD  111 (127)
T ss_dssp             EECCHHHHHHHHHH-HCCSEEEEESBCGGGCBHHHHHHHHHHSTTTTTSCEEEE-ECGGGHHHHHHSTTCCSEEEESSCC
T ss_pred             EecCHHHHHHHHHh-cCCCEEEEeCCCCCCCCHHHHHHHHhcCccccCCCEEEE-ecCCchhHHHHHHhCcchheeCCCC
Confidence            46789999999987 6799999999999 99999999999987  688999999 8888888889999999999999999


Q ss_pred             hHHHHHHHHHHHH
Q 043479           79 PDDLKNVWQYAMT   91 (534)
Q Consensus        79 ~eeL~~aI~~aL~   91 (534)
                      .++|..+|+++++
T Consensus       112 ~~~l~~~i~~~~~  124 (127)
T 2gkg_A          112 ADQLVERAGALIG  124 (127)
T ss_dssp             HHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHc
Confidence            9999999998874

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

Probab=99.32  E-value=5.8e-12  Score=114.31  Aligned_cols=89  Identities=28%  Similarity=0.369  Sum_probs=77.5

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHH--HHHHHHHcCCcEEEeCCCC-
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRES--VIMKALASGVAFYILKPLN-   78 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~--~~~~AL~aGA~dyL~KP~s-   78 (534)
                      ++.++.+|++.+.. ..|||||+|+.||+++|+++++.|++..+ +|||++++..+..  .+.++++.||++||.||++ 
T Consensus        56 ~~~~~~~al~~l~~-~~~dlvilD~~l~~~~g~~l~~~lr~~~~-~~ii~~s~~~~~~~~~~~~~~~~ga~~~l~KP~~~  133 (164)
T 3t8y_A           56 FAKDGLEAVEKAIE-LKPDVITMDIEMPNLNGIEALKLIMKKAP-TRVIMVSSLTEEGAAITIEALRNGAVDFITKPHGS  133 (164)
T ss_dssp             EESSHHHHHHHHHH-HCCSEEEECSSCSSSCHHHHHHHHHHHSC-CEEEEEESSCCTTCHHHHHHHHTTCCEEEECSSSS
T ss_pred             ecCCHHHHHHHhcc-CCCCEEEEeCCCCCCCHHHHHHHHHhcCC-ceEEEEecCCccchHHHHHHHHcCcCEEEeCCCCH
Confidence            47799999999987 68999999999999999999999999888 9999999977654  6778999999999999999 


Q ss_pred             --------hHHHHHHHHHHHHH
Q 043479           79 --------PDDLKNVWQYAMTY   92 (534)
Q Consensus        79 --------~eeL~~aI~~aL~~   92 (534)
                              .++|.++|++++..
T Consensus       134 ~~l~~r~~~~~l~~~i~~~~~~  155 (164)
T 3t8y_A          134 ISLTFRQVAPELLEKIRQAMNV  155 (164)
T ss_dssp             SCGGGGGGHHHHHHHHHHHTTS
T ss_pred             HHHHHHhhhHHHHHHHHHHhCC
Confidence                    56777777766543

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

Probab=99.32  E-value=6.3e-12  Score=127.61  Aligned_cols=89  Identities=22%  Similarity=0.383  Sum_probs=82.2

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhh--CCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~--~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      ++.++.+|++.+.. ..|||||+|+.||+++|+++++.|++.  .+.+|||++|+..+.....++++.||++||.||++.
T Consensus        48 ~~~~~~~al~~~~~-~~~dlvl~D~~mp~~~G~~~~~~l~~~~~~~~~~ii~~s~~~~~~~~~~a~~~Ga~~~l~Kp~~~  126 (358)
T 3bre_A           48 FCSDPQQAVAVANQ-IKPTVILQDLVMPGVDGLTLLAAYRGNPATRDIPIIVLSTKEEPTVKSAAFAAGANDYLVKLPDA  126 (358)
T ss_dssp             EECCHHHHHHHHHH-HCCSEEEEESBCSSSBHHHHHHHHTTSTTTTTSCEEEEESSCCHHHHHHHHHTTCSEEEESCCCH
T ss_pred             EeCCHHHHHHHHHh-CCCCEEEEeCCCCCCCHHHHHHHHhcCcccCCCcEEEEeCCCCHHHHHHHHhcChheEeeccCCH
Confidence            47899999999987 689999999999999999999999874  567999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHH
Q 043479           80 DDLKNVWQYAMT   91 (534)
Q Consensus        80 eeL~~aI~~aL~   91 (534)
                      ++|..+|+.+++
T Consensus       127 ~~l~~~v~~~~~  138 (358)
T 3bre_A          127 IELVARIRYHSR  138 (358)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            999999988754

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

Probab=99.31  E-value=8.7e-12  Score=107.17  Aligned_cols=91  Identities=16%  Similarity=0.264  Sum_probs=81.0

Q ss_pred             eecCHHHHHHHHHhcC-CceEEEEeCCCCC-CCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQR-DIDLVVTDLHMPE-MNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~-~pDLVLLDi~mPd-mdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      .+.++.+|++.+.. . .||+||+|+.+|+ ++|+++++.|++..+.+|||++|+..+......++..|  +||.||++.
T Consensus        34 ~~~~~~~a~~~l~~-~~~~dlvi~d~~l~~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~~--~~l~kP~~~  110 (132)
T 2rdm_A           34 AVSSGAKAIEMLKS-GAAIDGVVTDIRFCQPPDGWQVARVAREIDPNMPIVYISGHAALEWASNGVPDS--IILEKPFTS  110 (132)
T ss_dssp             EESSHHHHHHHHHT-TCCCCEEEEESCCSSSSCHHHHHHHHHHHCTTCCEEEEESSCCTTHHHHSCTTC--EEEESSCCH
T ss_pred             EECCHHHHHHHHHc-CCCCCEEEEeeeCCCCCCHHHHHHHHHhcCCCCCEEEEeCCccHHHHHhhcCCc--ceEeCCCCH
Confidence            46789999999987 5 7999999999998 99999999999988899999999999888777777665  899999999


Q ss_pred             HHHHHHHHHHHHHhhh
Q 043479           80 DDLKNVWQYAMTYKKA   95 (534)
Q Consensus        80 eeL~~aI~~aL~~k~~   95 (534)
                      ++|..+|++++.++..
T Consensus       111 ~~l~~~i~~~~~~~~~  126 (132)
T 2rdm_A          111 AQLITAVSQLLNAREG  126 (132)
T ss_dssp             HHHHHHHHHHHHTTC-
T ss_pred             HHHHHHHHHHHhcCCC
Confidence            9999999999876543

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

Probab=99.29  E-value=4.3e-12  Score=111.84  Aligned_cols=84  Identities=20%  Similarity=0.268  Sum_probs=68.9

Q ss_pred             eecCHHHHHHHHHhcC-CceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEec--CCCHHHHHHHHHcCCcEEEeCCCC
Q 043479            2 TVTRPVEALATVRIQR-DIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSS--DDRESVIMKALASGVAFYILKPLN   78 (534)
Q Consensus         2 tass~~EALe~L~~~~-~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs--~~d~~~~~~AL~aGA~dyL~KP~s   78 (534)
                      ++.++.+|++.+.. . .|||||+|+.||+++|++++++|++..+ .|||+++.  ..+...+.++++.||++||.||++
T Consensus        44 ~~~~~~~al~~l~~-~~~~dlvilD~~l~~~~g~~~~~~lr~~~~-~~iiil~~~~~~~~~~~~~~~~~ga~~~l~KP~~  121 (145)
T 3kyj_B           44 QAANGQEALDKLAA-QPNVDLILLDIEMPVMDGMEFLRHAKLKTR-AKICMLSSVAVSGSPHAARARELGADGVVAKPSG  121 (145)
T ss_dssp             EESSHHHHHHHHHH-CTTCCEEEECTTSCCCTTCHHHHHHHHHCC-CEEC-CBSSCSTTSSHHHHHHHTTCSCCCBCCCS
T ss_pred             EECCHHHHHHHHhc-CCCCCEEEEeCCCCCCCHHHHHHHHHhcCC-CCeEEEEEeccCChHHHHHHHhCCCCEEEeCCCC
Confidence            57899999999987 6 7999999999999999999999998877 89999987  556667889999999999999999


Q ss_pred             hHHHHHHHH
Q 043479           79 PDDLKNVWQ   87 (534)
Q Consensus        79 ~eeL~~aI~   87 (534)
                      .++|...++
T Consensus       122 ~~~l~~~i~  130 (145)
T 3kyj_B          122 TVSHDLEEK  130 (145)
T ss_dssp             CC------C
T ss_pred             HHHHHHHHH
Confidence            666555443

>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=99.27  E-value=2.1e-13  Score=115.66  Aligned_cols=91  Identities=26%  Similarity=0.455  Sum_probs=82.9

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+.++.++++.+.. ..||+||+|+.||+++|+++++.+++..+.+|||++|+..+.....++++.|+++||.||++.++
T Consensus        32 ~~~~~~~~~~~~~~-~~~dlvi~d~~~~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~kp~~~~~  110 (124)
T 1dc7_A           32 TFENGNEVLAALAS-KTPDVLLSDIRMPGMDGLALLKQIKQRHPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDIDE  110 (124)
T ss_dssp             ECCCTTHHHHHSSS-CCCSCEEECSCSSHHHHCSTHHHHHHHCTTSCCCCBCCSTTSTTTTSSCTTCCCCCBCSSCCHHH
T ss_pred             EeCCHHHHHHHHhc-CCCCEEEEeeecCCCCHHHHHHHHHhhCCCCCEEEEecCCCHHHHHHHHhcCcceEeeCCCCHHH
Confidence            45678899999876 78999999999999999999999999888999999999988888888999999999999999999


Q ss_pred             HHHHHHHHHHHh
Q 043479           82 LKNVWQYAMTYK   93 (534)
Q Consensus        82 L~~aI~~aL~~k   93 (534)
                      |..+|+++++++
T Consensus       111 l~~~i~~~~~~~  122 (124)
T 1dc7_A          111 AVALVERAISHY  122 (124)
T ss_dssp             HHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhh
Confidence            999999988653

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

Probab=99.26  E-value=1e-11  Score=108.72  Aligned_cols=90  Identities=26%  Similarity=0.440  Sum_probs=75.1

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhh-----CCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCC
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEE-----FTHLPVMVMSSDDRESVIMKALASGVAFYILKP   76 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~-----~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP   76 (534)
                      .+.++.+|++.+.. ..||+||+|+.||+++|+++++.|++.     .+.+|||++|+........   ++|+++||.||
T Consensus        39 ~~~~~~~al~~l~~-~~~dlvllD~~lp~~~g~~~~~~l~~~~~~~~~~~~~ii~~s~~~~~~~~~---~~g~~~~l~KP  114 (140)
T 3c97_A           39 VVTNGLQALQAYQN-RQFDVIIMDIQMPVMDGLEAVSEIRNYERTHNTKRASIIAITADTIDDDRP---GAELDEYVSKP  114 (140)
T ss_dssp             EESSHHHHHHHHHH-SCCSEEEECTTCCSSCHHHHHHHHHHHHHHHTCCCCCCEEEESSCCSCCCC---CSSCSEEEESS
T ss_pred             EECCHHHHHHHHhc-CCCCEEEEeCCCCCCcHHHHHHHHHhhhhhcCCCceEEEEEeCccchhHHH---hCChhheEeCC
Confidence            46789999999987 789999999999999999999999874     4778999999876544322   78999999999


Q ss_pred             CChHHHHHHHHHHHHHhhh
Q 043479           77 LNPDDLKNVWQYAMTYKKA   95 (534)
Q Consensus        77 ~s~eeL~~aI~~aL~~k~~   95 (534)
                      ++.++|..+|++++.+...
T Consensus       115 ~~~~~L~~~i~~~~~~~~~  133 (140)
T 3c97_A          115 LNPNQLRDVVLTCHSEGAE  133 (140)
T ss_dssp             CCHHHHHHHHHHHHC----
T ss_pred             CCHHHHHHHHHHHhCCCCC
Confidence            9999999999999866544

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

Probab=99.23  E-value=7.8e-12  Score=104.06  Aligned_cols=85  Identities=16%  Similarity=0.215  Sum_probs=76.9

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhC--CCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEF--THLPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~--p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      .+.+..++++.+.. ..||+||+|+.+++++|+++++.+++..  +.+|||+++...+..   .+++.|+++||.||++.
T Consensus        30 ~~~~~~~~~~~l~~-~~~dlii~d~~~~~~~~~~~~~~l~~~~~~~~~~ii~~~~~~~~~---~~~~~g~~~~l~kp~~~  105 (119)
T 2j48_A           30 WLVDGSTALDQLDL-LQPIVILMAWPPPDQSCLLLLQHLREHQADPHPPLVLFLGEPPVD---PLLTAQASAILSKPLDP  105 (119)
T ss_dssp             EESCHHHHHHHHHH-HCCSEEEEECSTTCCTHHHHHHHHHHTCCCSSCCCEEEESSCCSS---HHHHHHCSEECSSCSTT
T ss_pred             EecCHHHHHHHHHh-cCCCEEEEecCCCCCCHHHHHHHHHhccccCCCCEEEEeCCCCch---hhhhcCHHHhccCCCCH
Confidence            46789999999987 6899999999999999999999999875  789999999987766   88999999999999999


Q ss_pred             HHHHHHHHHHH
Q 043479           80 DDLKNVWQYAM   90 (534)
Q Consensus        80 eeL~~aI~~aL   90 (534)
                      ++|..+|++++
T Consensus       106 ~~l~~~l~~~~  116 (119)
T 2j48_A          106 QLLLTTLQGLC  116 (119)
T ss_dssp             HHHHHHHHTTC
T ss_pred             HHHHHHHHHHh
Confidence            99999998765

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

Probab=99.23  E-value=5.4e-11  Score=103.51  Aligned_cols=86  Identities=21%  Similarity=0.301  Sum_probs=78.6

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCC-CCcEEEEecCCCHHHHHHHHHcCCcEEEeCCC-Ch
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFT-HLPVMVMSSDDRESVIMKALASGVAFYILKPL-NP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p-~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~-s~   79 (534)
                      .+.++.+|++.+.. ..||+||    ||+++|+++++.|++. + .+|||++|+..+.....++++.|+++||.||+ +.
T Consensus        47 ~~~~~~~al~~l~~-~~~dlvi----~~~~~g~~~~~~l~~~-~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~kP~~~~  120 (137)
T 2pln_A           47 VTESLEDGEYLMDI-RNYDLVM----VSDKNALSFVSRIKEK-HSSIVVLVSSDNPTSEEEVHAFEQGADDYIAKPYRSI  120 (137)
T ss_dssp             EESCHHHHHHHHHH-SCCSEEE----ECSTTHHHHHHHHHHH-STTSEEEEEESSCCHHHHHHHHHTTCSEEEESSCSCH
T ss_pred             EeCCHHHHHHHHHc-CCCCEEE----EcCccHHHHHHHHHhc-CCCccEEEEeCCCCHHHHHHHHHcCCceeeeCCCCCH
Confidence            46789999999987 7899999    8999999999999988 8 89999999999999999999999999999999 99


Q ss_pred             HHHHHHHHHHHHHh
Q 043479           80 DDLKNVWQYAMTYK   93 (534)
Q Consensus        80 eeL~~aI~~aL~~k   93 (534)
                      ++|..+|+++++++
T Consensus       121 ~~l~~~i~~~~~~~  134 (137)
T 2pln_A          121 KALVARIEARLRFW  134 (137)
T ss_dssp             HHHHHHHHHHTC--
T ss_pred             HHHHHHHHHHHhhh
Confidence            99999999987543

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

Probab=99.10  E-value=1.8e-10  Score=106.95  Aligned_cols=77  Identities=12%  Similarity=0.141  Sum_probs=70.1

Q ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHHHHHHHHHHHHHhh
Q 043479           17 RDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDDLKNVWQYAMTYKK   94 (534)
Q Consensus        17 ~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~eeL~~aI~~aL~~k~   94 (534)
                      ..||+||+|+.||+++|+ +++.++...+.+|||++|+..+.+...++++.||++||.||++.++|..+|+.++....
T Consensus        51 ~~~dlvl~D~~mp~~~g~-l~~~~~~~~~~~~ii~lt~~~~~~~~~~a~~~ga~~~l~KP~~~~~L~~~l~~~~~~~~  127 (196)
T 1qo0_D           51 VPVDVVFTSIFQNRHHDE-IAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISE  127 (196)
T ss_dssp             SCCSEEEEECCSSTHHHH-HHHHHHHSCTTCEEEEEECCCSHHHHHHHHHHTCSEEEESSCCGGGHHHHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCccchH-HHHHHhccCCCCCEEEEEcCCChHHHHHHHHcCCCeeEecCcCHHHHHHHHHHHHHHHH
Confidence            469999999999999998 88888765588999999999999999999999999999999999999999999886644

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

Probab=99.09  E-value=2.9e-10  Score=117.84  Aligned_cols=90  Identities=22%  Similarity=0.359  Sum_probs=79.4

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCH--HHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRE--SVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~--~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      ++.++.+|++.++. ..|||||+|+.||+++|++++++|++..+ +|||++|+..+.  +...++++.||++||.||++.
T Consensus        34 ~a~~~~eAl~~l~~-~~pDlVllDi~mp~~dGlell~~l~~~~p-~pVIvlS~~~~~~~~~~~~al~~Ga~d~l~KP~~~  111 (349)
T 1a2o_A           34 TAPDPLVARDLIKK-FNPDVLTLDVEMPRMDGLDFLEKLMRLRP-MPVVMVSSLTGKGSEVTLRALELGAIDFVTKPQLG  111 (349)
T ss_dssp             EESSHHHHHHHHHH-HCCSEEEEECCCSSSCHHHHHHHHHHSSC-CCEEEEECCTHHHHHHHHHHHHHTCCEEEECSSSS
T ss_pred             EeCCHHHHHHHHhc-cCCCEEEEECCCCCCCHHHHHHHHHhcCC-CcEEEEECCCcccHHHHHHHHhCCceEEEECCCCc
Confidence            46789999999987 68999999999999999999999998887 999999998775  447889999999999999984


Q ss_pred             ---------HHHHHHHHHHHHHh
Q 043479           80 ---------DDLKNVWQYAMTYK   93 (534)
Q Consensus        80 ---------eeL~~aI~~aL~~k   93 (534)
                               ++|...|+.+.+.+
T Consensus       112 ~~~~l~~~~~~L~~~I~~~~~~~  134 (349)
T 1a2o_A          112 IREGMLAYSEMIAEKVRTAARAR  134 (349)
T ss_dssp             CSSCHHHHHHHHHHHHHHHHHCC
T ss_pred             cchhHHHHHHHHHHHHHHHHhhh
Confidence                     78888888876543

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

Probab=99.08  E-value=5.3e-11  Score=103.66  Aligned_cols=87  Identities=11%  Similarity=0.154  Sum_probs=73.8

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEe-cCCCHHHHHHHHHcCCcEEEeCCCChH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMS-SDDRESVIMKALASGVAFYILKPLNPD   80 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLS-s~~d~~~~~~AL~aGA~dyL~KP~s~e   80 (534)
                      .+.++.+|++.++....||+||+|+.||+++|+++++.|++..+.+|||++| +..+... .+++   +++||.||++.+
T Consensus        44 ~~~~~~~al~~l~~~~~~dlvilD~~l~~~~g~~~~~~l~~~~~~~~ii~ls~~~~~~~~-~~~~---~~~~l~KP~~~~  119 (138)
T 2b4a_A           44 VHPSGSAFFQHRSQLSTCDLLIVSDQLVDLSIFSLLDIVKEQTKQPSVLILTTGRHELIE-SSEH---NLSYLQKPFAIS  119 (138)
T ss_dssp             EESSHHHHHHTGGGGGSCSEEEEETTCTTSCHHHHHHHHTTSSSCCEEEEEESCC--CCC-CSSS---CEEEEESSCCHH
T ss_pred             EeCCHHHHHHHHHhCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCCCCEEEEECCCCCHHH-HHHH---HHheeeCCCCHH
Confidence            4678999999886413699999999999999999999999988899999999 8776665 5555   999999999999


Q ss_pred             HHHHHHHHHHHH
Q 043479           81 DLKNVWQYAMTY   92 (534)
Q Consensus        81 eL~~aI~~aL~~   92 (534)
                      +|..+|+++++.
T Consensus       120 ~L~~~i~~~~~~  131 (138)
T 2b4a_A          120 ELRAAIDYHKPS  131 (138)
T ss_dssp             HHHHHHHHTCCC
T ss_pred             HHHHHHHHHHHh
Confidence            999999887643

>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=98.99  E-value=4.4e-10  Score=110.73  Aligned_cols=82  Identities=22%  Similarity=0.266  Sum_probs=65.5

Q ss_pred             ecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHHH
Q 043479            3 VTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDDL   82 (534)
Q Consensus         3 ass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~eeL   82 (534)
                      +.++.+++..+.. ..||+||+|+.||+++|+++++++++.  .+|||++|+..+.+...+++++||++||.||... .+
T Consensus        34 ~~~~~~~~~~~~~-~~~dlvllD~~mP~~~G~~~~~~lr~~--~~pvi~lt~~~~~~~~~~a~~~Ga~dyl~Kp~~~-~~  109 (259)
T 3luf_A           34 AFDTLEGARHCQG-DEYVVALVDLTLPDAPSGEAVKVLLER--GLPVVILTADISEDKREAWLEAGVLDYVMKDSRH-SL  109 (259)
T ss_dssp             EESSTGGGTTCCT-TTEEEEEEESCBTTBTTSHHHHHHHHT--TCCEEEEECC-CHHHHHHHHHTTCCEEEECSSHH-HH
T ss_pred             EeChHHHHHHhhc-CCCcEEEEeCCCCCCCHHHHHHHHHhC--CCCEEEEEccCCHHHHHHHHHCCCcEEEeCCchh-HH
Confidence            3445555555544 679999999999999999999999874  5899999999999999999999999999999643 34


Q ss_pred             HHHHHH
Q 043479           83 KNVWQY   88 (534)
Q Consensus        83 ~~aI~~   88 (534)
                      ..++..
T Consensus       110 ~~~~~~  115 (259)
T 3luf_A          110 QYAVGL  115 (259)
T ss_dssp             HHHHHH
T ss_pred             HHHHHh
Confidence            434433

>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=98.96  E-value=6.2e-10  Score=105.42  Aligned_cols=90  Identities=24%  Similarity=0.355  Sum_probs=78.9

Q ss_pred             ecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCC--CChH
Q 043479            3 VTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKP--LNPD   80 (534)
Q Consensus         3 ass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP--~s~e   80 (534)
                      +.++.+|++.+.. ..|||||+|+.||+++|++++++|++..+..++++++.....+...++++.|+++|+.||  ++..
T Consensus        11 ~~~~~~a~~~~~~-~~~dlvl~D~~~p~~~g~~~~~~l~~~~~~~~i~vi~~~~~~~~~~~~~~~Ga~~~l~kp~~~~~~   89 (237)
T 3cwo_X           11 ATNGREAVEKYKE-LKPDIVTMDITMPEMNGIDAIKEIMKIDPNAKIIVCSAMGQQAMVIEAIKAGAKDFIVNTAAVENP   89 (237)
T ss_dssp             CCSSSTTHHHHHH-HCCSCEEEECCSTTSSHHHHHHHHHHHSSSCCEEEECCSSTHHHHHHHHHTTCCEEEESHHHHHCT
T ss_pred             CCCHHHHHHHHHh-cCCCEEEEeCCCCCCCHHHHHHHHHHhCCCCCEEEEECCCCHHHHHHHHHCCHHheEeCCcccChH
Confidence            5678899999887 679999999999999999999999988877788888877778888999999999999999  7788


Q ss_pred             HHHHHHHHHHHHh
Q 043479           81 DLKNVWQYAMTYK   93 (534)
Q Consensus        81 eL~~aI~~aL~~k   93 (534)
                      ++...+.+.+...
T Consensus        90 ~l~~~i~~~~~~~  102 (237)
T 3cwo_X           90 SLITQIAQTFGSQ  102 (237)
T ss_dssp             HHHHHHHHHHTGG
T ss_pred             HHHHHHHHHhCCC
Confidence            8888888776443

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

Probab=98.92  E-value=8.6e-10  Score=125.07  Aligned_cols=92  Identities=17%  Similarity=0.180  Sum_probs=82.7

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCC----CCHHHHHHHHHhhCCCCcEEEEecCCC-HHHHHHHHHcCCcEEEeCC
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPE----MNGIELQKEINEEFTHLPVMVMSSDDR-ESVIMKALASGVAFYILKP   76 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPd----mdGleLL~~Lr~~~p~ipVIVLSs~~d-~~~~~~AL~aGA~dyL~KP   76 (534)
                      .+.++++|++.+.....+|+||+|++||+    ++|++++++||+..+++|||++|+..+ .+.....+..||++||.||
T Consensus        37 ~a~~g~~al~~~~~~~~~d~vilDi~lp~~~~~~~G~~ll~~iR~~~~~iPIi~lTa~~~~~~d~~~~l~~gaddyi~kp  116 (755)
T 2vyc_A           37 KSTSFDDGFAILSSNEAIDCLMFSYQMEHPDEHQNVRQLIGKLHERQQNVPVFLLGDREKALAAMDRDLLELVDEFAWIL  116 (755)
T ss_dssp             EESSHHHHHHHHTTTCCCSEEEEECCCCSHHHHHHHHHHHHHHHHHSTTCCEEEEECHHHHHHTCSHHHHHHCSEEEETT
T ss_pred             EECCHHHHHHHHhcCCCCcEEEEeCCCCcccccccHHHHHHHHHHhCCCCCEEEEecCCcchhhccHhHhhcCCceEeCC
Confidence            57899999999986235999999999999    999999999999988899999999876 6667788999999999999


Q ss_pred             CChHH-HHHHHHHHHHHh
Q 043479           77 LNPDD-LKNVWQYAMTYK   93 (534)
Q Consensus        77 ~s~ee-L~~aI~~aL~~k   93 (534)
                      ++..+ |...|++++++.
T Consensus       117 f~~~efl~~ri~a~~rr~  134 (755)
T 2vyc_A          117 EDTADFIAGRAVAAMTRY  134 (755)
T ss_dssp             TSCHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHh
Confidence            99999 888999988775

>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=98.29  E-value=4.6e-06  Score=87.58  Aligned_cols=89  Identities=24%  Similarity=0.421  Sum_probs=75.0

Q ss_pred             cCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhh--CCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            4 TRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         4 ss~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~--~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      .+..+++ .+.. ..||+|++|+.||+|+|+++++.++..  ...+|||++|+..+.....++++.|+++|+.||+..++
T Consensus       182 ~~~~~~~-~~~~-~~~dlil~D~~mp~~dG~~~~~~ir~~~~~~~~pii~lt~~~~~~~~~~~l~~Ga~d~~~kp~~~~~  259 (459)
T 1w25_A          182 SDPEKAK-ISAG-GPVDLVIVNAAAKNFDGLRFTAALRSEERTRQLPVLAMVDPDDRGRMVKALEIGVNDILSRPIDPQE  259 (459)
T ss_dssp             CCHHHHH-HHHH-SSCSEEEEETTCSSSCHHHHHHHHHTSGGGTTCCEEEEECTTCHHHHHHHHHTTCCEEEESSCCHHH
T ss_pred             cCHHHHh-hhcc-CCCCEEEEecCCCCCcHHHHHHHHHhCccccCCcEEEEcCCCchHHHHHHHhccccccccCCCCHHH
Confidence            3555554 2333 579999999999999999999999863  45689999999999998899999999999999999999


Q ss_pred             HHHHHHHHHHHhh
Q 043479           82 LKNVWQYAMTYKK   94 (534)
Q Consensus        82 L~~aI~~aL~~k~   94 (534)
                      +...+..+++.+.
T Consensus       260 l~~~v~~~~~~~~  272 (459)
T 1w25_A          260 LSARVKTQIQRKR  272 (459)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            9988888776544

>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=95.74  E-value=0.049  Score=50.68  Aligned_cols=82  Identities=12%  Similarity=0.229  Sum_probs=61.3

Q ss_pred             CHHHHHHHHHhcCCceEEEEeC-CCCCCCHH--HHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEE------eC
Q 043479            5 RPVEALATVRIQRDIDLVVTDL-HMPEMNGI--ELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYI------LK   75 (534)
Q Consensus         5 s~~EALe~L~~~~~pDLVLLDi-~mPdmdGl--eLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL------~K   75 (534)
                      +..+.++.+......++++.++ .++.++|+  +++++++... ++|||++++....+...++++.|+++++      .+
T Consensus       131 ~~~~~i~~~~~~~~~~vli~~~~~~g~~~g~~~~~i~~~~~~~-~~Pvia~~g~~~~~~~~~~~~~G~~~~~vg~a~~~~  209 (237)
T 3cwo_X          131 LLRDWVVEVEKRGAGEILLTSIDRDGTKSGYDTEMIRFVRPLT-TLPIIASGGAGKMEHFLEAFLAGADAALAASVFHFR  209 (237)
T ss_dssp             EHHHHHHHHHHHTCSEEEEEETTTTTCCSCCCHHHHHHHGGGC-CSCEEEESCCCSHHHHHHHHHHTCSEEEESHHHHTT
T ss_pred             CHHHHHHHHhhcCCCeEEEEecCCCCccccccHHHHHHHHHhc-CCCEEecCCCCCHHHHHHHHHcCcHHHhhhHHHHcC
Confidence            4556666665534567999987 55656664  4666666543 6999999999999999999999999995      68


Q ss_pred             CCChHHHHHHHH
Q 043479           76 PLNPDDLKNVWQ   87 (534)
Q Consensus        76 P~s~eeL~~aI~   87 (534)
                      |++..++++.++
T Consensus       210 ~~~~~~~~~~l~  221 (237)
T 3cwo_X          210 EIDVRELKEYLK  221 (237)
T ss_dssp             SSCHHHHHHHHH
T ss_pred             CCCHHHHHHHHH
Confidence            888888876543

>3n75_A LDC, lysine decarboxylase, inducible; pyridoxal-5'-phosphate dependent decarboxylase, acid stress stringent response; HET: LLP G4P P6G; 2.00A {Escherichia coli} PDB: 3q16_A*

Probab=95.46  E-value=0.0089  Score=67.53  Aligned_cols=89  Identities=13%  Similarity=0.060  Sum_probs=67.2

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCC-ChH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPL-NPD   80 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~-s~e   80 (534)
                      .+.+.+||+..+++...+++||+|++++   +.+++++||+..+++||++++...+...+......++++|+.+.. +.+
T Consensus        35 ~a~s~~Da~~~i~~~~~i~avIld~d~~---~~~ll~~Ir~~~~~iPVFl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  111 (715)
T 3n75_A           35 YPNDRDDLLKLIENNARLCGVIFDWDKY---NLELCEEISKMNENLPLYAFANTYSTLDVSLNDLRLQISFFEYALGAAE  111 (715)
T ss_dssp             CCSSHHHHHHHHHHCTTEEEEEEEHHHH---HHHHHHHHHHHCTTCEEEEECCTTCCCCGGGTTSCCEEEEECCCTTCHH
T ss_pred             EeCCHHHHHHHHHhCCCceEEEEecccc---HHHHHHHHHHhCCCCCEEEEecCCcccccchhhhhccCeEEEeCCCCHH
Confidence            5689999999998755699999999885   689999999999999999999885433221112357889998875 456


Q ss_pred             HHHHHHHHHHHHh
Q 043479           81 DLKNVWQYAMTYK   93 (534)
Q Consensus        81 eL~~aI~~aL~~k   93 (534)
                      .+...|.++.+..
T Consensus       112 ~~~~~~~~~~~~y  124 (715)
T 3n75_A          112 DIANKIKQTTDEY  124 (715)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            6666666665543

>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis}

Probab=91.74  E-value=0.42  Score=39.14  Aligned_cols=53  Identities=13%  Similarity=0.033  Sum_probs=44.3

Q ss_pred             chhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHhhh
Q 043479          166 DSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAEQG  221 (534)
Q Consensus       166 ~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~lkr~a~~~  221 (534)
                      ..|..+..+++...-.+....++|++.|+   ++..+|++|+.+-|..|++.....
T Consensus        36 ~~L~~~~r~vl~l~~~~g~s~~eIA~~lg---is~~tV~~~l~ra~~~Lr~~l~~~   88 (92)
T 3hug_A           36 AQLSAEHRAVIQRSYYRGWSTAQIATDLG---IAEGTVKSRLHYAVRALRLTLQEL   88 (92)
T ss_dssp             HTSCHHHHHHHHHHHTSCCCHHHHHHHHT---SCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHcCCCHHHHHHHHC---cCHHHHHHHHHHHHHHHHHHHHHh
Confidence            34888888999885455666899999999   999999999999999988876543

>3c57_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 1.70A {Mycobacterium tuberculosis} PDB: 1zlk_A 1zlj_A

Probab=90.98  E-value=0.3  Score=40.63  Aligned_cols=47  Identities=17%  Similarity=0.134  Sum_probs=38.9

Q ss_pred             CchhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHHH
Q 043479          165 TDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLK  215 (534)
Q Consensus       165 t~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~lk  215 (534)
                      ...|+.+..+++..+ .+....++|++.|+   ++..+|+.|+.+.+..|+
T Consensus        25 l~~Lt~~e~~vl~l~-~~g~s~~eIA~~l~---is~~tV~~~l~r~~~kL~   71 (95)
T 3c57_A           25 LSGLTDQERTLLGLL-SEGLTNKQIADRMF---LAEKTVKNYVSRLLAKLG   71 (95)
T ss_dssp             --CCCHHHHHHHHHH-HTTCCHHHHHHHHT---CCHHHHHHHHHHHHHHHT
T ss_pred             HhcCCHHHHHHHHHH-HcCCCHHHHHHHHC---cCHHHHHHHHHHHHHHHc
Confidence            345899999999998 56666999999999   899999999988776543

>3ulq_B Transcriptional regulatory protein COMA; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis} PDB: 2krf_A

Probab=90.77  E-value=0.31  Score=40.43  Aligned_cols=44  Identities=14%  Similarity=0.192  Sum_probs=36.9

Q ss_pred             CchhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHH
Q 043479          165 TDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRI  212 (534)
Q Consensus       165 t~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl  212 (534)
                      ...|+.++.+++..+. +....++|++.|+   ++..+|+.|+.+.+.
T Consensus        27 ~~~Lt~rE~~Vl~l~~-~G~s~~eIA~~L~---iS~~TV~~~~~~i~~   70 (90)
T 3ulq_B           27 QDVLTPRECLILQEVE-KGFTNQEIADALH---LSKRSIEYSLTSIFN   70 (90)
T ss_dssp             --CCCHHHHHHHHHHH-TTCCHHHHHHHHT---CCHHHHHHHHHHHHH
T ss_pred             ccCCCHHHHHHHHHHH-cCCCHHHHHHHHC---cCHHHHHHHHHHHHH
Confidence            3569999999999997 4455999999999   999999999988655

>1je8_A Nitrate/nitrite response regulator protein NARL; protein-DNA complex, two-component response regulator, helix-turn-helix, DNA bending; 2.12A {Escherichia coli} SCOP: a.4.6.2 PDB: 1zg1_A 1zg5_A

Probab=90.69  E-value=0.36  Score=38.97  Aligned_cols=48  Identities=19%  Similarity=0.176  Sum_probs=39.9

Q ss_pred             CCchhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHHH
Q 043479          164 WTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLK  215 (534)
Q Consensus       164 Wt~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~lk  215 (534)
                      ....|++++.+++..+ .+....++|++.|+   ++..+|+.|+.+.+..|+
T Consensus        18 ~~~~Lt~~e~~vl~l~-~~g~s~~eIA~~l~---is~~tV~~~l~r~~~kL~   65 (82)
T 1je8_A           18 DVNQLTPRERDILKLI-AQGLPNKMIARRLD---ITESTVKVHVKHMLKKMK   65 (82)
T ss_dssp             CGGGSCHHHHHHHHHH-TTTCCHHHHHHHHT---SCHHHHHHHHHHHHHHTT
T ss_pred             HHccCCHHHHHHHHHH-HcCCCHHHHHHHHC---cCHHHHHHHHHHHHHHHc
Confidence            4456999999999998 45566999999999   899999999988766443

>2yxb_A Coenzyme B12-dependent mutase; alpha/beta, structural genomics, NPPSFA, national project on structural and functional analyses; 1.80A {Aeropyrum pernix}

Probab=89.91  E-value=2.2  Score=38.87  Aligned_cols=88  Identities=11%  Similarity=0.082  Sum_probs=59.7

Q ss_pred             CHHHHHHHHHhcCCceEEEEeCCCCC-C-CHHHHHHHHHhhC-CCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            5 RPVEALATVRIQRDIDLVVTDLHMPE-M-NGIELQKEINEEF-THLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         5 s~~EALe~L~~~~~pDLVLLDi~mPd-m-dGleLL~~Lr~~~-p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      +.++.++.+++ ..+|+|.+-..+.. + .--++++.|++.. ++++|++ .+..-......+.+.|++.++..-.+.++
T Consensus        57 p~e~lv~aa~~-~~~diV~lS~~~~~~~~~~~~~i~~L~~~g~~~i~v~v-GG~~~~~~~~~l~~~G~d~v~~~~~~~~~  134 (161)
T 2yxb_A           57 TPEQVAMAAVQ-EDVDVIGVSILNGAHLHLMKRLMAKLRELGADDIPVVL-GGTIPIPDLEPLRSLGIREIFLPGTSLGE  134 (161)
T ss_dssp             CHHHHHHHHHH-TTCSEEEEEESSSCHHHHHHHHHHHHHHTTCTTSCEEE-EECCCHHHHHHHHHTTCCEEECTTCCHHH
T ss_pred             CHHHHHHHHHh-cCCCEEEEEeechhhHHHHHHHHHHHHhcCCCCCEEEE-eCCCchhcHHHHHHCCCcEEECCCCCHHH
Confidence            56788888887 78999999877653 2 2345666777654 3677665 44444444445678999987766566677


Q ss_pred             HHHHHHHHHHHhh
Q 043479           82 LKNVWQYAMTYKK   94 (534)
Q Consensus        82 L~~aI~~aL~~k~   94 (534)
                      ....++.++..++
T Consensus       135 ~~~~~~~~~~~~~  147 (161)
T 2yxb_A          135 IIEKVRKLAEEKR  147 (161)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhh
Confidence            7777777776543

>2ekc_A AQ_1548, tryptophan synthase alpha chain; structural genomics, lyase, NPPSFA, national project on PROT structural and functional analyses; 2.00A {Aquifex aeolicus}

Probab=89.71  E-value=1.2  Score=43.90  Aligned_cols=80  Identities=16%  Similarity=0.332  Sum_probs=55.7

Q ss_pred             HHHHHhcCCceEEEEeCCCCC--CC--------------------HHHHHHHHHhhCCCCcEEEEecCCC------HHHH
Q 043479           10 LATVRIQRDIDLVVTDLHMPE--MN--------------------GIELQKEINEEFTHLPVMVMSSDDR------ESVI   61 (534)
Q Consensus        10 Le~L~~~~~pDLVLLDi~mPd--md--------------------GleLL~~Lr~~~p~ipVIVLSs~~d------~~~~   61 (534)
                      ++.+.+ ...|+|.+++-..+  .|                    .+++++++|+..|++|+++++-...      ...+
T Consensus        37 ~~~l~~-~G~D~IElG~P~sdP~adgp~i~~a~~~al~~G~~~~~~~~~v~~ir~~~~~~Pi~~m~y~n~v~~~g~~~f~  115 (262)
T 2ekc_A           37 FKEVLK-NGTDILEIGFPFSDPVADGPTIQVAHEVALKNGIRFEDVLELSETLRKEFPDIPFLLMTYYNPIFRIGLEKFC  115 (262)
T ss_dssp             HHHHHH-TTCSEEEEECCCSCCTTSCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTSCEEEECCHHHHHHHCHHHHH
T ss_pred             HHHHHH-cCCCEEEECCCCCCcccccHHHHHHHHHHHHcCCCHHHHHHHHHHHHhhcCCCCEEEEecCcHHHHhhHHHHH
Confidence            334444 56899999875433  22                    3466888888766899999853321      3456


Q ss_pred             HHHHHcCCcEEEeCCCChHHHHHHHHHHH
Q 043479           62 MKALASGVAFYILKPLNPDDLKNVWQYAM   90 (534)
Q Consensus        62 ~~AL~aGA~dyL~KP~s~eeL~~aI~~aL   90 (534)
                      ..+.++|+++++.-.+..+++...+..+.
T Consensus       116 ~~~~~aG~dgvii~dl~~ee~~~~~~~~~  144 (262)
T 2ekc_A          116 RLSREKGIDGFIVPDLPPEEAEELKAVMK  144 (262)
T ss_dssp             HHHHHTTCCEEECTTCCHHHHHHHHHHHH
T ss_pred             HHHHHcCCCEEEECCCCHHHHHHHHHHHH
Confidence            77889999999998888888766665543

>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2

Probab=88.43  E-value=0.81  Score=35.20  Aligned_cols=47  Identities=15%  Similarity=0.164  Sum_probs=38.6

Q ss_pred             CCchhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHH
Q 043479          164 WTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFL  214 (534)
Q Consensus       164 Wt~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~l  214 (534)
                      ....|+++..+++..+ .+....++|++.|+   ++..+|..|+.+.+..+
T Consensus         8 ~~~~L~~~e~~il~~~-~~g~s~~eIA~~l~---is~~tV~~~~~~~~~kl   54 (74)
T 1fse_A            8 SKPLLTKREREVFELL-VQDKTTKEIASELF---ISEKTVRNHISNAMQKL   54 (74)
T ss_dssp             CCCCCCHHHHHHHHHH-TTTCCHHHHHHHHT---SCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHH-HcCCCHHHHHHHHC---CCHHHHHHHHHHHHHHH
Confidence            3456889999999998 45556899999999   89999999998876644

>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti}

Probab=87.91  E-value=0.75  Score=36.00  Aligned_cols=46  Identities=17%  Similarity=0.178  Sum_probs=38.4

Q ss_pred             chhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHHH
Q 043479          166 DSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLK  215 (534)
Q Consensus       166 ~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~lk  215 (534)
                      ..|+++..+++..+ .+....++|++.|+   ++..+|..|+.+.+..++
T Consensus        15 ~~L~~~e~~vl~l~-~~g~s~~eIA~~l~---is~~tV~~~~~r~~~kl~   60 (79)
T 1x3u_A           15 QTLSERERQVLSAV-VAGLPNKSIAYDLD---ISPRTVEVHRANVMAKMK   60 (79)
T ss_dssp             HHHCHHHHHHHHHH-TTTCCHHHHHHHTT---SCHHHHHHHHHHHHHHTT
T ss_pred             HhCCHHHHHHHHHH-HcCCCHHHHHHHHC---cCHHHHHHHHHHHHHHHc
Confidence            45889999999998 56666899999999   899999999988766443

>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2

Probab=87.78  E-value=0.77  Score=38.80  Aligned_cols=44  Identities=14%  Similarity=0.143  Sum_probs=36.6

Q ss_pred             chhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHH
Q 043479          166 DSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIF  213 (534)
Q Consensus       166 ~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~  213 (534)
                      ..|++++.+++..+. +....++|++.|+   ++..+|+.|+.+.+..
T Consensus        33 ~~Lt~re~~Vl~l~~-~G~s~~EIA~~L~---iS~~TV~~~l~ri~~K   76 (99)
T 1p4w_A           33 KRLSPKESEVLRLFA-EGFLVTEIAKKLN---RSIKTISSQKKSAMMK   76 (99)
T ss_dssp             SSCCHHHHHHHHHHH-HTCCHHHHHHHHT---SCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHH-cCCCHHHHHHHHC---cCHHHHHHHHHHHHHH
Confidence            458999999998885 4445899999999   8999999998876553

>1qop_A Tryptophan synthase alpha chain; lyase, carbon-oxygen lyase, tryptophan biosynthesis, pyridoxal phosphate; HET: IPL PLP; 1.4A {Salmonella typhimurium} SCOP: c.1.2.4 PDB: 1k8x_A* 1wbj_A* 2clk_A* 2j9z_A* 3cep_A* 1k8y_A* 1a5s_A* 1a50_A* 1c29_A* 1c8v_A* 1c9d_A* 1bks_A* 1cx9_A* 1fuy_A* 1cw2_A* 1k7e_A* 1k7f_A* 1k7x_A* 1k3u_A* 1k8z_A* ...

Probab=87.70  E-value=1.8  Score=42.63  Aligned_cols=81  Identities=12%  Similarity=0.184  Sum_probs=56.5

Q ss_pred             HHHHHHhcCCceEEEEeCCCCC--CC--------------------HHHHHHHHHhhCCCCcEEEEecCC------CHHH
Q 043479            9 ALATVRIQRDIDLVVTDLHMPE--MN--------------------GIELQKEINEEFTHLPVMVMSSDD------RESV   60 (534)
Q Consensus         9 ALe~L~~~~~pDLVLLDi~mPd--md--------------------GleLL~~Lr~~~p~ipVIVLSs~~------d~~~   60 (534)
                      .++.+.+ ...|+|-+|+-..+  +|                    ++++++++|+...++||++++-..      ....
T Consensus        36 ~~~~l~~-~GaD~ieig~P~sdp~~DG~~i~~a~~~al~~G~~~~~~~~~v~~ir~~~~~~Pv~lm~y~n~v~~~g~~~~  114 (268)
T 1qop_A           36 IIDTLID-AGADALELGVPFSDPLADGPTIQNANLRAFAAGVTPAQCFEMLAIIREKHPTIPIGLLMYANLVFNNGIDAF  114 (268)
T ss_dssp             HHHHHHH-TTCSSEEEECCCSCCTTCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCSSSCEEEEECHHHHHTTCHHHH
T ss_pred             HHHHHHH-CCCCEEEECCCCCCccCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCEEEEEcccHHHHhhHHHH
Confidence            3444444 56899999984432  33                    346688888775679998876322      1466


Q ss_pred             HHHHHHcCCcEEEeCCCChHHHHHHHHHHH
Q 043479           61 IMKALASGVAFYILKPLNPDDLKNVWQYAM   90 (534)
Q Consensus        61 ~~~AL~aGA~dyL~KP~s~eeL~~aI~~aL   90 (534)
                      +..+.++|+++++.-.+..+++...+..+.
T Consensus       115 ~~~~~~aGadgii~~d~~~e~~~~~~~~~~  144 (268)
T 1qop_A          115 YARCEQVGVDSVLVADVPVEESAPFRQAAL  144 (268)
T ss_dssp             HHHHHHHTCCEEEETTCCGGGCHHHHHHHH
T ss_pred             HHHHHHcCCCEEEEcCCCHHHHHHHHHHHH
Confidence            778999999999998888887776665553

>3szt_A QCSR, quorum-sensing control repressor; quorum sensing acyl-homoserine lactone, helix-turn-helix, transcription factor, 3-OXO-C12 HSL; HET: OHN; 2.55A {Pseudomonas aeruginosa}

Probab=87.52  E-value=0.56  Score=45.13  Aligned_cols=43  Identities=14%  Similarity=0.125  Sum_probs=37.2

Q ss_pred             chhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHH
Q 043479          166 DSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRI  212 (534)
Q Consensus       166 ~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl  212 (534)
                      ..|++++.+++..+..++. .|+|++.|+   +|..||+.|+.+.+.
T Consensus       174 ~~Lt~re~~vl~~~~~G~s-~~eIa~~l~---is~~tV~~~~~~~~~  216 (237)
T 3szt_A          174 VRLTARETEMLKWTAVGKT-YGEIGLILS---IDQRTVKFHIVNAMR  216 (237)
T ss_dssp             CCCCHHHHHHHHHHHTTCC-HHHHHHHHT---SCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHcCCC-HHHHHHHHC---CCHHHHHHHHHHHHH
Confidence            4599999999999964444 999999999   999999999988755

>3vnd_A TSA, tryptophan synthase alpha chain; psychrophilic enzyme, cold adaptation; HET: PE8; 2.60A {Shewanella frigidimarina}

Probab=87.21  E-value=1.7  Score=43.23  Aligned_cols=83  Identities=12%  Similarity=0.235  Sum_probs=58.5

Q ss_pred             HHHHHHHHhcCCceEEEEeCCCCC--CCH--------------------HHHHHHHHhhCCCCcEEEEecCCC------H
Q 043479            7 VEALATVRIQRDIDLVVTDLHMPE--MNG--------------------IELQKEINEEFTHLPVMVMSSDDR------E   58 (534)
Q Consensus         7 ~EALe~L~~~~~pDLVLLDi~mPd--mdG--------------------leLL~~Lr~~~p~ipVIVLSs~~d------~   58 (534)
                      .+.++.+.+ ...|+|=+++-..|  +||                    +++++++|+...++||++|+-...      .
T Consensus        35 ~~~~~~l~~-~GaD~iElgiPfSDP~aDGp~Iq~a~~~AL~~G~~~~~~~~~v~~ir~~~~~~Pivlm~Y~npv~~~g~e  113 (267)
T 3vnd_A           35 LKIIQTLVD-NGADALELGFPFSDPLADGPVIQGANLRSLAAGTTSSDCFDIITKVRAQHPDMPIGLLLYANLVFANGID  113 (267)
T ss_dssp             HHHHHHHHH-TTCSSEEEECCCSCCTTCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTCCEEEEECHHHHHHHCHH
T ss_pred             HHHHHHHHH-cCCCEEEECCCCCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCEEEEecCcHHHHhhHH
Confidence            344555555 56899988864422  333                    677777887767899999875332      4


Q ss_pred             HHHHHHHHcCCcEEEeCCCChHHHHHHHHHHH
Q 043479           59 SVIMKALASGVAFYILKPLNPDDLKNVWQYAM   90 (534)
Q Consensus        59 ~~~~~AL~aGA~dyL~KP~s~eeL~~aI~~aL   90 (534)
                      ..+.++.++|+++++.-.+.+++....+..+.
T Consensus       114 ~f~~~~~~aGvdgvii~Dlp~ee~~~~~~~~~  145 (267)
T 3vnd_A          114 EFYTKAQAAGVDSVLIADVPVEESAPFSKAAK  145 (267)
T ss_dssp             HHHHHHHHHTCCEEEETTSCGGGCHHHHHHHH
T ss_pred             HHHHHHHHcCCCEEEeCCCCHhhHHHHHHHHH
Confidence            56888999999999998888888666555543

>2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding domain, activator, antibiotic resistance, cytoplasm, DNA-binding; NMR {Staphylococcus aureus}

Probab=87.21  E-value=0.46  Score=38.91  Aligned_cols=47  Identities=17%  Similarity=0.161  Sum_probs=38.9

Q ss_pred             CCchhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHH
Q 043479          164 WTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFL  214 (534)
Q Consensus       164 Wt~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~l  214 (534)
                      +...|+.+..+++..+ .+....++|++.|+   ++..+|+.|+.+.+..|
T Consensus        26 ~l~~Lt~~e~~vl~l~-~~g~s~~eIA~~l~---is~~tV~~~l~r~~~kL   72 (91)
T 2rnj_A           26 LYEMLTEREMEILLLI-AKGYSNQEIASASH---ITIKTVKTHVSNILSKL   72 (91)
T ss_dssp             TGGGCCSHHHHHHHHH-HTTCCTTHHHHHHT---CCHHHHHHHHHHHHHHT
T ss_pred             HHhcCCHHHHHHHHHH-HcCCCHHHHHHHHC---cCHHHHHHHHHHHHHHH
Confidence            4456899999999998 45556899999999   89999999998876644

>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium}

Probab=86.90  E-value=0.78  Score=34.18  Aligned_cols=40  Identities=23%  Similarity=0.191  Sum_probs=31.0

Q ss_pred             HHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHH
Q 043479          171 RFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFL  214 (534)
Q Consensus       171 RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~l  214 (534)
                      ++.+++..+. +....++|++.|+   ++..+|+.|+.+.+..+
T Consensus         2 re~~vl~l~~-~g~s~~eIA~~l~---is~~tV~~~~~~~~~kl   41 (61)
T 2jpc_A            2 RERQVLKLID-EGYTNHGISEKLH---ISIKTVETHRMNMMRKL   41 (61)
T ss_dssp             HHHHHHHHHH-TSCCSHHHHHHTC---SCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHH-cCCCHHHHHHHhC---CCHHHHHHHHHHHHHHH
Confidence            4567777764 3445899999999   89999999998876643

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

Probab=86.56  E-value=1.9  Score=37.20  Aligned_cols=66  Identities=26%  Similarity=0.407  Sum_probs=51.7

Q ss_pred             CceEEEEeCCC-CCCCHHHHHHHHH--hhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHHHHHHHHHHHHH
Q 043479           18 DIDLVVTDLHM-PEMNGIELQKEIN--EEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDDLKNVWQYAMTY   92 (534)
Q Consensus        18 ~pDLVLLDi~m-PdmdGleLL~~Lr--~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~eeL~~aI~~aL~~   92 (534)
                      ..|+|+|+..+ |.        .+.  +..+..-+||+-..-+++.+.+.+..||. ||.+|+++.-|..+|+..++.
T Consensus        50 ~AdlIfCEYlLLPe--------~ifS~k~~~~~dliVLfD~F~EEa~v~vLd~Ga~-yLlrPIT~kvldAvIraFLrq  118 (121)
T 3q7r_A           50 SADLVVCEYSLLPR--------EIRSPKSLEGSFVLVLLDFFDEETSVDLLDRGFW-YLIRPITPRILKSAISLFLSQ  118 (121)
T ss_dssp             TEEEEEEEGGGSCT--------TCCCCTTCCSCEEEEEESSCCHHHHHHHHHTTCE-EEESCCCHHHHHHHHHHHHHH
T ss_pred             cceeEEEeeecChH--------HhcCCCCCCcccEEEEehhhchHHHHHHHhCCce-eEeccCcHHHHHHHHHHHHhc
Confidence            35888888754 32        111  22344678888888899999999999999 999999999999999998864

>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}

Probab=86.53  E-value=1.2  Score=33.74  Aligned_cols=51  Identities=16%  Similarity=0.001  Sum_probs=40.4

Q ss_pred             chhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHh
Q 043479          166 DSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAE  219 (534)
Q Consensus       166 ~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~lkr~a~  219 (534)
                      ..|+++..+++...-.+....++|++.|+   ++..+|..++.+.+..+++...
T Consensus        14 ~~L~~~~r~il~l~~~~g~s~~eIA~~lg---is~~tv~~~~~ra~~~l~~~l~   64 (70)
T 2o8x_A           14 ADLTTDQREALLLTQLLGLSYADAAAVCG---CPVGTIRSRVARARDALLADAE   64 (70)
T ss_dssp             TSSCHHHHHHHHHHHTSCCCHHHHHHHHT---SCHHHHHHHHHHHHHHHHC---
T ss_pred             HhCCHHHHHHHHHHHHcCCCHHHHHHHHC---cCHHHHHHHHHHHHHHHHHHhh
Confidence            34778888888876455666899999999   8999999999999888776554

>2q0o_A Probable transcriptional activator protein TRAR; helix-turn-helix, two-helix coiled coil; HET: LAE; 2.00A {Rhizobium SP}

Probab=86.39  E-value=0.88  Score=43.44  Aligned_cols=44  Identities=14%  Similarity=0.114  Sum_probs=37.7

Q ss_pred             chhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHH
Q 043479          166 DSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIF  213 (534)
Q Consensus       166 ~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~  213 (534)
                      ..|++++.+++..+. +....++|++.|+   ++..||+.|+.+.+..
T Consensus       174 ~~Lt~~e~~vl~~~~-~g~s~~eIa~~l~---is~~tV~~~~~~~~~k  217 (236)
T 2q0o_A          174 QMLSPREMLCLVWAS-KGKTASVTANLTG---INARTVQHYLDKARAK  217 (236)
T ss_dssp             GSCCHHHHHHHHHHH-TTCCHHHHHHHHC---CCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHH-cCCCHHHHHHHHC---cCHHHHHHHHHHHHHH
Confidence            459999999999986 4445999999998   9999999999887664

>1l3l_A Transcriptional activator protein TRAR; helix-turn-helix DNA binding motif, alpha/beta/alpha sandwich; HET: LAE; 1.66A {Agrobacterium tumefaciens} SCOP: a.4.6.2 d.110.5.1 PDB: 1h0m_A*

Probab=86.32  E-value=0.91  Score=43.29  Aligned_cols=44  Identities=14%  Similarity=0.070  Sum_probs=37.7

Q ss_pred             chhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHH
Q 043479          166 DSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIF  213 (534)
Q Consensus       166 ~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~  213 (534)
                      ..|++++.+++..+. +....++|++.|+   ++..||+.|+.+.+..
T Consensus       172 ~~Lt~~e~~vl~~~~-~g~s~~eIa~~l~---is~~tV~~~~~~~~~k  215 (234)
T 1l3l_A          172 AWLDPKEATYLRWIA-VGKTMEEIADVEG---VKYNSVRVKLREAMKR  215 (234)
T ss_dssp             CCCCHHHHHHHHHHT-TTCCHHHHHHHHT---CCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHH-cCCCHHHHHHHHC---cCHHHHHHHHHHHHHH
Confidence            459999999999986 4445999999998   9999999999987664

>1xsv_A Hypothetical UPF0122 protein SAV1236; helix-turn-helix, putative DNA-binding protein, signal recognition particle, unknown function; 1.70A {Staphylococcus aureus subsp} SCOP: a.4.13.3

Probab=85.97  E-value=1.8  Score=37.26  Aligned_cols=53  Identities=15%  Similarity=0.176  Sum_probs=44.2

Q ss_pred             chhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHhhh
Q 043479          166 DSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAEQG  221 (534)
Q Consensus       166 ~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~lkr~a~~~  221 (534)
                      ..|+++..+++...-.+....++|++.|+   ++..+|+.|+.+-|..|++.....
T Consensus        24 ~~L~~~~r~vl~l~~~~g~s~~EIA~~lg---iS~~tV~~~l~ra~~kLr~~l~~~   76 (113)
T 1xsv_A           24 SLLTNKQRNYLELFYLEDYSLSEIADTFN---VSRQAVYDNIRRTGDLVEDYEKKL   76 (113)
T ss_dssp             GGSCHHHHHHHHHHHTSCCCHHHHHHHTT---CCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hcCCHHHHHHHHHHHHcCCCHHHHHHHHC---cCHHHHHHHHHHHHHHHHHHHHHH
Confidence            34788888999887556666899999999   899999999999999888776543

>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma 70, sigma 70 domain 4, transcription, regulation, helix-turn-helix; 2.60A {Escherichia coli} SCOP: a.4.13.2

Probab=85.80  E-value=1.2  Score=34.29  Aligned_cols=48  Identities=17%  Similarity=0.075  Sum_probs=39.5

Q ss_pred             chhhHHHHHHHHHhc----cCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHH
Q 043479          166 DSLHNRFLQAIRHIG----LEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKR  216 (534)
Q Consensus       166 ~eLh~RFleaLe~LG----lekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~lkr  216 (534)
                      ..|+++..+++...-    .+....++|++.|+   +|..+|+.|+.+-+..++.
T Consensus         4 ~~L~~~er~il~l~~~l~~~~g~s~~eIA~~lg---is~~tV~~~~~ra~~kLr~   55 (68)
T 2p7v_B            4 AGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFD---VTRERIRQIEAKALRKLRH   55 (68)
T ss_dssp             CCCCHHHHHHHHHHTTTTSSSCCCHHHHHHHHT---CCHHHHHHHHHHHHHGGGS
T ss_pred             HcCCHHHHHHHHHHHccCCCCCCCHHHHHHHHC---cCHHHHHHHHHHHHHHHHH
Confidence            458889999998874    46777999999999   9999999999887765543

>3mzy_A RNA polymerase sigma-H factor; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative; 2.50A {Fusobacterium nucleatum subsp}

Probab=84.68  E-value=1.7  Score=37.67  Aligned_cols=51  Identities=6%  Similarity=0.051  Sum_probs=43.0

Q ss_pred             hhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHhhh
Q 043479          167 SLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAEQG  221 (534)
Q Consensus       167 eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~lkr~a~~~  221 (534)
                      .|+++..+++. +-++....++|++.|+   +|..+|++++.+-|..|++.....
T Consensus       109 ~L~~~~r~v~~-~~~~g~s~~EIA~~lg---is~~tV~~~~~ra~~~Lr~~l~~~  159 (164)
T 3mzy_A          109 NFSKFEKEVLT-YLIRGYSYREIATILS---KNLKSIDNTIQRIRKKSEEWIKEE  159 (164)
T ss_dssp             HSCHHHHHHHH-HHTTTCCHHHHHHHHT---CCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHH-HHHcCCCHHHHHHHHC---CCHHHHHHHHHHHHHHHHHHHHHc
Confidence            57788888888 5556667999999999   999999999999999988877653

>1geq_A Tryptophan synthase alpha-subunit; hyperthermophIle, pyrococ furiosus, X-RAY analysis, stability, calorimetry, lyase; 2.00A {Pyrococcus furiosus} SCOP: c.1.2.4 PDB: 1wdw_A* 2dzu_A 2dzp_A 2e09_A 2dzw_A 2dzs_A 2dzv_A 2dzt_A 2dzx_A

Probab=84.52  E-value=3.4  Score=39.43  Aligned_cols=78  Identities=19%  Similarity=0.184  Sum_probs=52.5

Q ss_pred             HHHHHHhcCCceEEEEeCC--CCCCCH--------------------HHHHHHHHhhCCCCcEEEEecCCC------HHH
Q 043479            9 ALATVRIQRDIDLVVTDLH--MPEMNG--------------------IELQKEINEEFTHLPVMVMSSDDR------ESV   60 (534)
Q Consensus         9 ALe~L~~~~~pDLVLLDi~--mPdmdG--------------------leLL~~Lr~~~p~ipVIVLSs~~d------~~~   60 (534)
                      .++.+.+ . .|.|-+|+-  -|.+||                    +++++++++.. ++||++++....      .+.
T Consensus        24 ~a~~~~~-~-ad~iel~~p~sdp~~DG~~~~~~~~~al~~g~~~~~~~~~i~~i~~~~-~~pv~~~~~~~~~~~~~~~~~  100 (248)
T 1geq_A           24 FLLALDE-Y-AGAIELGIPFSDPIADGKTIQESHYRALKNGFKLREAFWIVKEFRRHS-STPIVLMTYYNPIYRAGVRNF  100 (248)
T ss_dssp             HHHHHGG-G-BSCEEEECCCSCCTTSCHHHHHHHHHHHHTTCCHHHHHHHHHHHHTTC-CCCEEEEECHHHHHHHCHHHH
T ss_pred             HHHHHHH-c-CCEEEECCCCCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHhhC-CCCEEEEeccchhhhcCHHHH
Confidence            3344444 5 888888842  234554                    67788888764 589988874332      467


Q ss_pred             HHHHHHcCCcEEEeCCCChHHHHHHHHHH
Q 043479           61 IMKALASGVAFYILKPLNPDDLKNVWQYA   89 (534)
Q Consensus        61 ~~~AL~aGA~dyL~KP~s~eeL~~aI~~a   89 (534)
                      +..++++||+.++.-....++....++.+
T Consensus       101 ~~~~~~~Gad~v~~~~~~~~~~~~~~~~~  129 (248)
T 1geq_A          101 LAEAKASGVDGILVVDLPVFHAKEFTEIA  129 (248)
T ss_dssp             HHHHHHHTCCEEEETTCCGGGHHHHHHHH
T ss_pred             HHHHHHCCCCEEEECCCChhhHHHHHHHH
Confidence            78899999999999777666655544443

>3nav_A Tryptophan synthase alpha chain; alpha subunit, structural genomics, CSG center for structural genomics of infectious diseases; 2.10A {Vibrio cholerae o1 biovar el tor} SCOP: c.1.2.4

Probab=84.46  E-value=3.3  Score=41.27  Aligned_cols=81  Identities=11%  Similarity=0.156  Sum_probs=56.0

Q ss_pred             HHHHHHHhcCCceEEEEeCCCCC--CC--------------------HHHHHHHHHhhCCCCcEEEEecC------CCHH
Q 043479            8 EALATVRIQRDIDLVVTDLHMPE--MN--------------------GIELQKEINEEFTHLPVMVMSSD------DRES   59 (534)
Q Consensus         8 EALe~L~~~~~pDLVLLDi~mPd--md--------------------GleLL~~Lr~~~p~ipVIVLSs~------~d~~   59 (534)
                      +.++.+.+ ...|+|=+.+-..|  .|                    .+++++++|+..+++||++|+-.      .-..
T Consensus        38 ~~~~~l~~-~GaD~iElGiPfSDP~aDGpvIq~a~~rAL~~G~~~~~~~~~v~~~r~~~~~~Pivlm~Y~n~v~~~g~~~  116 (271)
T 3nav_A           38 AIMQTLID-AGADALELGMPFSDPLADGPTIQGANLRALAAKTTPDICFELIAQIRARNPETPIGLLMYANLVYARGIDD  116 (271)
T ss_dssp             HHHHHHHH-TTCSSEEEECCCCCGGGCCSHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTSCEEEEECHHHHHHTCHHH
T ss_pred             HHHHHHHH-cCCCEEEECCCCCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCEEEEecCcHHHHHhHHH
Confidence            33444444 46898888764422  22                    35677888877678999999733      2245


Q ss_pred             HHHHHHHcCCcEEEeCCCChHHHHHHHHHH
Q 043479           60 VIMKALASGVAFYILKPLNPDDLKNVWQYA   89 (534)
Q Consensus        60 ~~~~AL~aGA~dyL~KP~s~eeL~~aI~~a   89 (534)
                      .+.+|.++|++++|.-.+.+++....+..+
T Consensus       117 f~~~~~~aGvdGvIipDlp~ee~~~~~~~~  146 (271)
T 3nav_A          117 FYQRCQKAGVDSVLIADVPTNESQPFVAAA  146 (271)
T ss_dssp             HHHHHHHHTCCEEEETTSCGGGCHHHHHHH
T ss_pred             HHHHHHHCCCCEEEECCCCHHHHHHHHHHH
Confidence            688899999999999888888865554444

>3qp6_A CVIR transcriptional regulator; quorum sensing, agonist, antagonist, LUXR, acylated homoseri lactone, transcription factor; HET: HL6; 2.00A {Chromobacterium violaceum} PDB: 3qp5_A*

Probab=83.80  E-value=1.1  Score=44.11  Aligned_cols=44  Identities=14%  Similarity=0.135  Sum_probs=38.0

Q ss_pred             chhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHH
Q 043479          166 DSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIF  213 (534)
Q Consensus       166 ~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~  213 (534)
                      ..|+.++.+++..+. +....++|++.|+   ++..||+.|+.+.+..
T Consensus       196 ~~Lt~re~~vl~~~~-~G~s~~eIA~~l~---is~~TV~~~~~~~~~k  239 (265)
T 3qp6_A          196 MPLSQREYDIFHWMS-RGKTNWEIATILN---ISERTVKFHVANVIRK  239 (265)
T ss_dssp             CCCCHHHHHHHHHHH-TTCCHHHHHHHHT---SCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHH-cCCCHHHHHHHHC---cCHHHHHHHHHHHHHH
Confidence            469999999999996 4445999999999   9999999999887663

>1s7o_A Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SPS1042/SPYM18_1152; putative DNA binding protein, structural genomics; 2.31A {Streptococcus pyogenes serotype M3} SCOP: a.4.13.3

Probab=83.20  E-value=2.5  Score=36.41  Aligned_cols=52  Identities=12%  Similarity=0.154  Sum_probs=43.1

Q ss_pred             chhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHhh
Q 043479          166 DSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAEQ  220 (534)
Q Consensus       166 ~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~lkr~a~~  220 (534)
                      ..|+++..+++...-.+....++|++.|+   +|..+|..|+.+-|..+++....
T Consensus        21 ~~L~~~~r~vl~l~y~~g~s~~EIA~~lg---iS~~tV~~~l~ra~~kLr~~l~~   72 (113)
T 1s7o_A           21 ALLTDKQMNYIELYYADDYSLAEIADEFG---VSRQAVYDNIKRTEKILETYEMK   72 (113)
T ss_dssp             GGSCHHHHHHHHHHHHTCCCHHHHHHHHT---CCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hcCCHHHHHHHHHHHHcCCCHHHHHHHHC---cCHHHHHHHHHHHHHHHHHHHHH
Confidence            35788888999887445566899999999   99999999999999888876544

>3o63_A Probable thiamine-phosphate pyrophosphorylase; thiamin biosynthesis, TIM barrel, transferase; 2.35A {Mycobacterium tuberculosis}

Probab=82.86  E-value=5.5  Score=38.88  Aligned_cols=85  Identities=15%  Similarity=0.174  Sum_probs=59.1

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCC-------CCHHHHHHHHHhhC-CCCcEEEEecCCCHHHHHHHHHcCCcEEE
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPE-------MNGIELQKEINEEF-THLPVMVMSSDDRESVIMKALASGVAFYI   73 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPd-------mdGleLL~~Lr~~~-p~ipVIVLSs~~d~~~~~~AL~aGA~dyL   73 (534)
                      ++.+.+|+.+..+  ..+|.|.+.-..|.       .-|++.++++++.. .++||+.+.+- +.+.+.+++++||+++.
T Consensus       141 S~ht~~Ea~~A~~--~GaDyI~vgpvf~T~tK~~~~~~gl~~l~~~~~~~~~~iPvvAiGGI-~~~ni~~~~~aGa~gva  217 (243)
T 3o63_A          141 STHDPDQVAAAAA--GDADYFCVGPCWPTPTKPGRAAPGLGLVRVAAELGGDDKPWFAIGGI-NAQRLPAVLDAGARRIV  217 (243)
T ss_dssp             EECSHHHHHHHHH--SSCSEEEECCSSCCCC-----CCCHHHHHHHHTC---CCCEEEESSC-CTTTHHHHHHTTCCCEE
T ss_pred             eCCCHHHHHHHhh--CCCCEEEEcCccCCCCCCCcchhhHHHHHHHHHhccCCCCEEEecCC-CHHHHHHHHHcCCCEEE
Confidence            4678888877665  46899998654432       24788888888753 47999999877 66778889999999986


Q ss_pred             e-----CCCChHHHHHHHHHH
Q 043479           74 L-----KPLNPDDLKNVWQYA   89 (534)
Q Consensus        74 ~-----KP~s~eeL~~aI~~a   89 (534)
                      .     +.-++.+..+.+...
T Consensus       218 v~sai~~a~dp~~a~~~l~~~  238 (243)
T 3o63_A          218 VVRAITSADDPRAAAEQLRSA  238 (243)
T ss_dssp             ESHHHHTCSSHHHHHHHHHHH
T ss_pred             EeHHHhCCCCHHHHHHHHHHH
Confidence            5     444555544444443

>3clo_A Transcriptional regulator; NP_811094.1, bacterial regulatory proteins, LUXR family, structural genomics; 2.04A {Bacteroides thetaiotaomicron vpi-5482}

Probab=82.73  E-value=1.1  Score=43.38  Aligned_cols=47  Identities=21%  Similarity=0.176  Sum_probs=40.7

Q ss_pred             chhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHH
Q 043479          166 DSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKR  216 (534)
Q Consensus       166 ~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~lkr  216 (534)
                      ..|+++..+++... .+....++|++.|+   ++..+|++|+.+.|..|+.
T Consensus       196 ~~L~~~erevl~L~-~~G~s~~EIA~~L~---iS~~TVk~~l~ra~~kL~~  242 (258)
T 3clo_A          196 NILSEREKEILRCI-RKGLSSKEIAATLY---ISVNTVNRHRQNILEKLSV  242 (258)
T ss_dssp             TSSCHHHHHHHHHH-HTTCCHHHHHHHHT---CCHHHHHHHHHHHHHHTTC
T ss_pred             ccCCHHHHHHHHHH-HcCCCHHHHHHHHC---cCHHHHHHHHHHHHHHHcC
Confidence            45999999999998 57777999999999   9999999999998876543

>3q58_A N-acetylmannosamine-6-phosphate 2-epimerase; TIM beta/alpha barrel, ribulose-phosphate binding barrel, carbohydrate metabolic process; HET: BTB; 1.80A {Salmonella enterica subsp}

Probab=82.59  E-value=3.7  Score=39.67  Aligned_cols=70  Identities=11%  Similarity=0.194  Sum_probs=53.6

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCC------CCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeC
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLH------MPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILK   75 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~------mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~K   75 (534)
                      .+.+.+++.+..+  ..+|+|.+..+      ......+++++++++.  ++|||.-.+-.+.+.+.+++++||++++.=
T Consensus       135 ~v~t~eea~~a~~--~Gad~Ig~~~~g~t~~~~~~~~~~~li~~l~~~--~ipvIA~GGI~t~~d~~~~~~~GadgV~VG  210 (229)
T 3q58_A          135 DCSTVNEGISCHQ--KGIEFIGTTLSGYTGPITPVEPDLAMVTQLSHA--GCRVIAEGRYNTPALAANAIEHGAWAVTVG  210 (229)
T ss_dssp             ECSSHHHHHHHHH--TTCSEEECTTTTSSSSCCCSSCCHHHHHHHHTT--TCCEEEESSCCSHHHHHHHHHTTCSEEEEC
T ss_pred             ecCCHHHHHHHHh--CCCCEEEecCccCCCCCcCCCCCHHHHHHHHHc--CCCEEEECCCCCHHHHHHHHHcCCCEEEEc
Confidence            3567788877665  46898865322      1234568999999875  799999988889999999999999999863

>1ku3_A Sigma factor SIGA; helix-turn-helix, transcription; 1.80A {Thermus aquaticus} SCOP: a.4.13.2 PDB: 1ku7_A 1rio_H 3n97_A*

Probab=82.55  E-value=3.1  Score=32.32  Aligned_cols=48  Identities=17%  Similarity=0.122  Sum_probs=39.9

Q ss_pred             CchhhHHHHHHHHHhcc----CCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHHH
Q 043479          165 TDSLHNRFLQAIRHIGL----EKAVPKKILEFMNVPGLTRENVASHLQKYRIFLK  215 (534)
Q Consensus       165 t~eLh~RFleaLe~LGl----ekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~lk  215 (534)
                      -..|+++..+++...-.    +....++|++.|+   +|..+|+.|+.+-+..++
T Consensus         8 l~~L~~~er~il~l~~~l~~~~~~s~~eIA~~l~---is~~tV~~~~~ra~~kLr   59 (73)
T 1ku3_A            8 LSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFG---VTRERIRQIENKALRKLK   59 (73)
T ss_dssp             TTTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHT---CCHHHHHHHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHhcccCCCCCHHHHHHHHC---CCHHHHHHHHHHHHHHHH
Confidence            34588899999988743    5667899999999   999999999998877666

>1ujp_A Tryptophan synthase alpha chain; riken structural genomics/P initiative, RSGI, structural genomics, lyase; HET: CIT; 1.34A {Thermus thermophilus} SCOP: c.1.2.4 PDB: 1wxj_A*

Probab=82.10  E-value=2.9  Score=41.51  Aligned_cols=80  Identities=24%  Similarity=0.271  Sum_probs=55.0

Q ss_pred             HHHHHHHhcCCceEEEEeCCCCC--CC--------------------HHHHHHHHHhhCCCCcEEEEecCC------CHH
Q 043479            8 EALATVRIQRDIDLVVTDLHMPE--MN--------------------GIELQKEINEEFTHLPVMVMSSDD------RES   59 (534)
Q Consensus         8 EALe~L~~~~~pDLVLLDi~mPd--md--------------------GleLL~~Lr~~~p~ipVIVLSs~~------d~~   59 (534)
                      +.++.+.+ . .|+|.+++-..|  .|                    .+++++++|+. .++||++|+-..      ...
T Consensus        34 ~~~~~l~~-~-aD~IElG~PfsdP~adGp~Iq~a~~~Al~~G~~~~~~~~~v~~ir~~-~~~Pii~m~y~n~v~~~g~~~  110 (271)
T 1ujp_A           34 QAVEEVLP-Y-ADLLEIGLPYSDPLGDGPVIQRASELALRKGMSVQGALELVREVRAL-TEKPLFLMTYLNPVLAWGPER  110 (271)
T ss_dssp             HHHHHHGG-G-CSSEEEECCCCC----CHHHHHHHHHHHHTTCCHHHHHHHHHHHHHH-CCSCEEEECCHHHHHHHCHHH
T ss_pred             HHHHHHHh-c-CCEEEECCCCCCcccccHHHHHHHHHHHHcCCCHHHHHHHHHHHHhc-CCCCEEEEecCcHHHHhhHHH
Confidence            34455555 5 999999875432  12                    35678888877 679999984222      134


Q ss_pred             HHHHHHHcCCcEEEeCCCChHHHHHHHHHHH
Q 043479           60 VIMKALASGVAFYILKPLNPDDLKNVWQYAM   90 (534)
Q Consensus        60 ~~~~AL~aGA~dyL~KP~s~eeL~~aI~~aL   90 (534)
                      .+..+.++|++++|.-.+..+++...+..+.
T Consensus       111 f~~~~~~aG~dGviv~Dl~~ee~~~~~~~~~  141 (271)
T 1ujp_A          111 FFGLFKQAGATGVILPDLPPDEDPGLVRLAQ  141 (271)
T ss_dssp             HHHHHHHHTCCEEECTTCCGGGCHHHHHHHH
T ss_pred             HHHHHHHcCCCEEEecCCCHHHHHHHHHHHH
Confidence            5677899999999998888877766665543

>1xi3_A Thiamine phosphate pyrophosphorylase; structural genomics, southeast collaboratory for structural genomics, hyperthermophIle; 1.70A {Pyrococcus furiosus} SCOP: c.1.3.1

Probab=82.06  E-value=7  Score=36.04  Aligned_cols=68  Identities=22%  Similarity=0.300  Sum_probs=49.2

Q ss_pred             ecCHHHHHHHHHhcCCceEEEEeCCCCC-------CCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEe
Q 043479            3 VTRPVEALATVRIQRDIDLVVTDLHMPE-------MNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYIL   74 (534)
Q Consensus         3 ass~~EALe~L~~~~~pDLVLLDi~mPd-------mdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~   74 (534)
                      +.+..|+.+...  ..+|.|+++...|.       ..+++.++++++.. ++||++..+-. .+.+.++++.|++++..
T Consensus       115 ~~t~~e~~~~~~--~g~d~i~~~~~~~~~~~~~~~~~~~~~l~~l~~~~-~~pvia~GGI~-~~nv~~~~~~Ga~gv~v  189 (215)
T 1xi3_A          115 VYSLEEALEAEK--KGADYLGAGSVFPTKTKEDARVIGLEGLRKIVESV-KIPVVAIGGIN-KDNAREVLKTGVDGIAV  189 (215)
T ss_dssp             ESSHHHHHHHHH--HTCSEEEEECSSCC----CCCCCHHHHHHHHHHHC-SSCEEEESSCC-TTTHHHHHTTTCSEEEE
T ss_pred             cCCHHHHHHHHh--cCCCEEEEcCCccCCCCCCCCCcCHHHHHHHHHhC-CCCEEEECCcC-HHHHHHHHHcCCCEEEE
Confidence            567777766544  35899998754442       35788888888765 58988776665 67777888999999853

>1yad_A Regulatory protein TENI; TIM barrel, transcription; 2.10A {Bacillus subtilis} PDB: 3qh2_A*

Probab=81.88  E-value=7.7  Score=36.37  Aligned_cols=69  Identities=17%  Similarity=0.265  Sum_probs=50.2

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCC-------CCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEe
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPE-------MNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYIL   74 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPd-------mdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~   74 (534)
                      .+.+.+++.+...  ...|.|+++...+.       .-+++.++.+++.. ++||++..+- +.+.+.+++++||+++..
T Consensus       116 sv~t~~~~~~a~~--~gaD~i~~~~~f~~~~~~g~~~~~~~~l~~~~~~~-~~pvia~GGI-~~~nv~~~~~~Ga~gv~v  191 (221)
T 1yad_A          116 SVHSLEEAVQAEK--EDADYVLFGHVFETDCKKGLEGRGVSLLSDIKQRI-SIPVIAIGGM-TPDRLRDVKQAGADGIAV  191 (221)
T ss_dssp             EECSHHHHHHHHH--TTCSEEEEECCC----------CHHHHHHHHHHHC-CSCEEEESSC-CGGGHHHHHHTTCSEEEE
T ss_pred             EcCCHHHHHHHHh--CCCCEEEECCccccCCCCCCCCCCHHHHHHHHHhC-CCCEEEECCC-CHHHHHHHHHcCCCEEEE
Confidence            4567788776665  45899999764332       23678888887655 5898887777 788888999999998864

>1or7_A Sigma-24, RNA polymerase sigma-E factor; regulation, DNA-binding, transmembrane, transcription; 2.00A {Escherichia coli} SCOP: a.4.13.2 a.177.1.1 PDB: 2h27_A

Probab=81.21  E-value=2.6  Score=37.98  Aligned_cols=50  Identities=20%  Similarity=0.166  Sum_probs=41.7

Q ss_pred             hhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHh
Q 043479          167 SLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAE  219 (534)
Q Consensus       167 eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~lkr~a~  219 (534)
                      .|+++..+++...-.+....++|++.|+   ++..+|++++.+-|..|++...
T Consensus       140 ~L~~~~r~vl~l~~~~g~s~~EIA~~lg---is~~tV~~~l~ra~~~Lr~~l~  189 (194)
T 1or7_A          140 SLPEDLRMAITLRELDGLSYEEIAAIMD---CPVGTVRSRIFRAREAIDNKVQ  189 (194)
T ss_dssp             HSCHHHHHHHHHHHTTCCCHHHHHHHTT---SCHHHHHHHHHHHHHHHHHHHC
T ss_pred             hCCHHHHHHhHHHHHcCCCHHHHHHHHC---CCHHHHHHHHHHHHHHHHHHHH
Confidence            4778888888775455666899999999   9999999999999998887654

>3qz6_A HPCH/HPAI aldolase; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics, MCSG; 2.00A {Desulfitobacterium hafniense} SCOP: c.1.12.0

Probab=81.19  E-value=6.5  Score=38.65  Aligned_cols=81  Identities=10%  Similarity=0.134  Sum_probs=57.9

Q ss_pred             HHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhh-CCCCcEEEEecCCCHHHHHHHHHcCCcEEE-eCCCChHHHHHH
Q 043479            8 EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEE-FTHLPVMVMSSDDRESVIMKALASGVAFYI-LKPLNPDDLKNV   85 (534)
Q Consensus         8 EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~-~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL-~KP~s~eeL~~a   85 (534)
                      +.++.+.. ..+|.|++|++....+.-++...++.. ...++++|=....+...+..+++.|+++++ +|--+.+++..+
T Consensus        28 ~~~e~a~~-~g~D~vilDlEhav~~~~k~~~~l~a~~~~~~~~~VRVn~~~~~di~~~ld~G~~gI~lP~v~saed~~~~  106 (261)
T 3qz6_A           28 DIVRIYAE-AGLDYFIVDCEHAAYTFREINHLVSVAKNAGVSVLVRIPQVDRAHVQRLLDIGAEGFMIPGVQSAETMRET  106 (261)
T ss_dssp             THHHHHHH-TTCSEEEEESSSSCCCHHHHHHHHHHHHHHTCEEEEECSSCCHHHHHHHHHHTCCEEEETTCCSHHHHHHH
T ss_pred             HHHHHHhc-CCcCEEEEeccCCCCCHHHHHHHHHHHhhcCCeEEEEeCCCCHHHHHHHHhcCCCEEEECCcCCHHHHHHH
Confidence            44555554 579999999998777766666666542 223566666666777888899999999876 555678888877


Q ss_pred             HHHH
Q 043479           86 WQYA   89 (534)
Q Consensus        86 I~~a   89 (534)
                      ++.+
T Consensus       107 ~~~~  110 (261)
T 3qz6_A          107 VRLA  110 (261)
T ss_dssp             HHHH
T ss_pred             HHHh
Confidence            6655

---

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	534
d1irza_	64	a.4.1.11 (A:) Arr10-B {Thale cress (Arabidopsis th	1e-28
d1dz3a_	123	c.23.1.1 (A:) Sporulation response regulator Spo0A	7e-18
d1u0sy_	118	c.23.1.1 (Y:) CheY protein {Thermotoga maritima [T	3e-16
d1a04a2	138	c.23.1.1 (A:5-142) Nitrate/nitrite response regula	3e-15
d2b4aa1	118	c.23.1.1 (A:2-119) Hypothetical protein BH3024 {Ba	4e-15
d1peya_	119	c.23.1.1 (A:) Sporulation response regulator Spo0F	2e-14
d1jbea_	128	c.23.1.1 (A:) CheY protein {Escherichia coli [TaxI	2e-14
d1krwa_	123	c.23.1.1 (A:) NTRC receiver domain {Salmonella typ	4e-14
d1a2oa1	140	c.23.1.1 (A:1-140) Methylesterase CheB, N-terminal	6e-14
d1k68a_	140	c.23.1.1 (A:) Response regulator for cyanobacteria	2e-13
d2r25b1	128	c.23.1.1 (B:1087-1214) Response regulator Sin1 {Ba	3e-13
d1zesa1	121	c.23.1.1 (A:3-123) PhoB receiver domain {Escherich	8e-13
d2ayxa1	133	c.23.1.1 (A:817-949) Sensor kinase protein RcsC, C	2e-12
d1dcfa_	134	c.23.1.2 (A:) Receiver domain of the ethylene rece	5e-12
d1i3ca_	144	c.23.1.1 (A:) Response regulator for cyanobacteria	1e-11
d1ny5a1	137	c.23.1.1 (A:1-137) Transcriptional activator sigm5	4e-11
d1qkka_	140	c.23.1.1 (A:) Transcriptional regulatory protein D	5e-11
d1s8na_	190	c.23.1.1 (A:) Probable two-component system transc	8e-11
d2a9pa1	117	c.23.1.1 (A:2-118) DNA-binding response regulator	1e-10
d1k66a_	149	c.23.1.1 (A:) Response regulator for cyanobacteria	1e-10
d1mb3a_	123	c.23.1.1 (A:) Cell division response regulator Div	2e-10
d1p2fa2	120	c.23.1.1 (A:1-120) Response regulator DrrB {Thermo	2e-10
d1p6qa_	129	c.23.1.1 (A:) CheY protein {Sinorhizobium meliloti	2e-10
d1dbwa_	123	c.23.1.1 (A:) Transcriptional regulatory protein F	3e-10
d1yioa2	128	c.23.1.1 (A:3-130) Response regulatory protein Sty	6e-10
d1xhfa1	121	c.23.1.1 (A:2-122) Aerobic respiration control pro	4e-09
d1mvoa_	121	c.23.1.1 (A:) PhoP receiver domain {Bacillus subti	7e-09
d1ys7a2	121	c.23.1.1 (A:7-127) Transcriptional regulatory prot	8e-09
d1kgsa2	122	c.23.1.1 (A:2-123) PhoB receiver domain {Thermotog	1e-08
d1qo0d_	189	c.23.1.3 (D:) Positive regulator of the amidase op	3e-08
d1w25a2	153	c.23.1.1 (A:141-293) Response regulator PleD, rece	3e-08
d2pl1a1	119	c.23.1.1 (A:1-119) PhoP receiver domain {Escherich	6e-08
d1zgza1	120	c.23.1.1 (A:2-121) TorCAD operon transcriptional r	3e-07
d1zh2a1	119	c.23.1.1 (A:2-120) Transcriptional regulatory prot	3e-07
d1w25a1	139	c.23.1.1 (A:2-140) Response regulator PleD, receiv	5e-06

>d1irza_ a.4.1.11 (A:) Arr10-B {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 64

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: GARP response regulators
domain: Arr10-B
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score =  105 bits (264), Expect = 1e-28
 Identities = 43/64 (67%), Positives = 54/64 (84%)

Query: 155 TAPKKPKVAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFL 214
           TA KKP+V WT  LHN+FL A+ H+G+E+AVPKKIL+ MNV  LTRENVASHLQK+R+ L
Sbjct: 1   TAQKKPRVLWTHELHNKFLAAVDHLGVERAVPKKILDLMNVDKLTRENVASHLQKFRVAL 60

Query: 215 KRVA 218
           K+V+
Sbjct: 61  KKVS 64

>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 = 77.5 bits (191), Expect = 7e-18
 Identities = 22/82 (26%), Positives = 48/82 (58%), Gaps = 2/82 (2%)

Query: 2   TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLP-VMVMSSDDRESV 60
           T     + L  +  ++  D+++ D+ MP ++G+ + + I   F H P V+++++  +E V
Sbjct: 32  TAYNGQDCLQMLE-EKRPDILLLDIIMPHLDGLAVLERIRAGFEHQPNVIMLTAFGQEDV 90

Query: 61  IMKALASGVAFYILKPLNPDDL 82
             KA+  G +++ILKP + ++L
Sbjct: 91  TKKAVELGASYFILKPFDMENL 112

>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 = 72.6 bits (178), Expect = 3e-16
 Identities = 24/84 (28%), Positives = 47/84 (55%), Gaps = 1/84 (1%)

Query: 2   TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVI 61
             T   EA+   + +   D+V  D+ MPEMNGI+  KEI +   +  ++V S+  +++++
Sbjct: 31  EATNGREAVEKYK-ELKPDIVTMDITMPEMNGIDAIKEIMKIDPNAKIIVCSAMGQQAMV 89

Query: 62  MKALASGVAFYILKPLNPDDLKNV 85
           ++A+ +G   +I+KP  P  +   
Sbjct: 90  IEAIKAGAKDFIVKPFQPSRVVEA 113

>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 = 70.7 bits (173), Expect = 3e-15
 Identities = 26/96 (27%), Positives = 47/96 (48%), Gaps = 1/96 (1%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
           + +       D DL++ DL+MP MNG+E   ++ E+     ++V S  + E  ++ AL  
Sbjct: 39  QGIELAE-SLDPDLILLDLNMPGMNGLETLDKLREKSLSGRIVVFSVSNHEEDVVTALKR 97

Query: 68  GVAFYILKPLNPDDLKNVWQYAMTYKKAKSISIDEI 103
           G   Y+LK + P+DL      A   +   S ++  +
Sbjct: 98  GADGYLLKDMEPEDLLKALHQAAAGEMVLSEALTPV 133

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

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

 Score = 69.5 bits (170), Expect = 4e-15
 Identities = 10/82 (12%), Positives = 28/82 (34%), Gaps = 3/82 (3%)

Query: 1   VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESV 60
                              DL++    + +++   L   + E+     V+++++   E +
Sbjct: 30  TVHPSGSAFFQHRSQLSTCDLLIVSDQLVDLSIFSLLDIVKEQTKQPSVLILTTGRHELI 89

Query: 61  IMKALASGVAFYILKPLNPDDL 82
             ++       Y+ KP    +L
Sbjct: 90  --ESSEHN-LSYLQKPFAISEL 108

>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 = 68.0 bits (166), Expect = 2e-14
 Identities = 17/70 (24%), Positives = 39/70 (55%)

Query: 16  QRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILK 75
           +   DLV+ D+ +P M+GIE+ K +     ++ V++M++     +I ++   G   +  K
Sbjct: 43  KERPDLVLLDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFAK 102

Query: 76  PLNPDDLKNV 85
           P + D++++ 
Sbjct: 103 PFDIDEIRDA 112

>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 = 66.7 bits (162), Expect = 4e-14
 Identities = 20/79 (25%), Positives = 44/79 (55%)

Query: 16  QRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILK 75
            +  D++++D+ MP M+G+ L K+I +    LPV++M++       + A   G   Y+ K
Sbjct: 45  SKTPDVLLSDIRMPGMDGLALLKQIKQRHPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPK 104

Query: 76  PLNPDDLKNVWQYAMTYKK 94
           P + D+   + + A+++ +
Sbjct: 105 PFDIDEAVALVERAISHYQ 123

>d1a2oa1 c.23.1.1 (A:1-140) Methylesterase CheB, N-terminal domain {Salmonella typhimurium [TaxId: 90371]} Length = 140

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Methylesterase CheB, N-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

 Score = 66.9 bits (163), Expect = 6e-14
 Identities = 19/82 (23%), Positives = 38/82 (46%), Gaps = 2/82 (2%)

Query: 2   TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMS-SDDRESV 60
           T   P+ A   ++ + + D++  D+ MP M+G++  +++        VMV S +     V
Sbjct: 34  TAPDPLVARDLIK-KFNPDVLTLDVEMPRMDGLDFLEKLMRLRPMPVVMVSSLTGKGSEV 92

Query: 61  IMKALASGVAFYILKPLNPDDL 82
            ++AL  G   ++ KP      
Sbjct: 93  TLRALELGAIDFVTKPQLGIRE 114

>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 = 65.1 bits (158), Expect = 2e-13
 Identities = 29/103 (28%), Positives = 52/103 (50%), Gaps = 12/103 (11%)

Query: 1   VTVTRPVEALATVRIQRDI------DLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVM 52
           VTV   +EA+A +R + +       DL++ DL++P+ +G E+  EI  +     +PV+V+
Sbjct: 32  VTVRDGMEAMAYLRQEGEYANASRPDLILLDLNLPKKDGREVLAEIKSDPTLKRIPVVVL 91

Query: 53  SSDDRESVIMKALASGVAFYILKPLNPDDL----KNVWQYAMT 91
           S+   E  I  +    V  YI K  N   L    K + ++ ++
Sbjct: 92  STSINEDDIFHSYDLHVNCYITKSANLSQLFQIVKGIEEFWLS 134

>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 = 64.6 bits (157), Expect = 3e-13
 Identities = 16/70 (22%), Positives = 38/70 (54%), Gaps = 1/70 (1%)

Query: 17  RDIDLVVTDLHMPEMNGIELQKEINEEFT-HLPVMVMSSDDRESVIMKALASGVAFYILK 75
            + +++  D+ MP+++G+   K I  +     P++ +++   +S I + L SG+  ++ K
Sbjct: 50  ENYNMIFMDVQMPKVDGLLSTKMIRRDLGYTSPIVALTAFADDSNIKECLESGMNGFLSK 109

Query: 76  PLNPDDLKNV 85
           P+    LK +
Sbjct: 110 PIKRPKLKTI 119

>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 = 63.0 bits (153), Expect = 8e-13
 Identities = 20/84 (23%), Positives = 40/84 (47%), Gaps = 3/84 (3%)

Query: 1   VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMSSDDRE 58
           V       A+  +  +   DL++ D  +P  +GI+  K +        +PV+++++   E
Sbjct: 28  VEAEDYDSAVNQLN-EPWPDLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLTARGEE 86

Query: 59  SVIMKALASGVAFYILKPLNPDDL 82
              ++ L +G   YI KP +P +L
Sbjct: 87  EDRVRGLETGADDYITKPFSPKEL 110

>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 = 62.4 bits (151), Expect = 2e-12
 Identities = 21/85 (24%), Positives = 40/85 (47%)

Query: 1   VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESV 60
                       V  +  ID+V++D++MP M+G  L + I +    LPV+ ++++     
Sbjct: 35  CKTANDGVDALNVLSKNHIDIVLSDVNMPNMDGYRLTQRIRQLGLTLPVIGVTANALAEE 94

Query: 61  IMKALASGVAFYILKPLNPDDLKNV 85
             + L SG+   + KP+  D +K  
Sbjct: 95  KQRCLESGMDSCLSKPVTLDVIKQT 119

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

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

 Score = 61.2 bits (148), Expect = 5e-12
 Identities = 21/92 (22%), Positives = 46/92 (50%), Gaps = 7/92 (7%)

Query: 1   VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFT-----HLPVMVMSSD 55
            TV+   E L    +  +  +V  D+ MP +   ++   I+E+FT        ++ +S +
Sbjct: 35  TTVSSNEECLR--VVSHEHKVVFMDVCMPGVENYQIALRIHEKFTKQRHQRPLLVALSGN 92

Query: 56  DRESVIMKALASGVAFYILKPLNPDDLKNVWQ 87
             +S   K ++ G+   +LKP++ D++++V  
Sbjct: 93  TDKSTKEKCMSFGLDGVLLKPVSLDNIRDVLS 124

>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 = 60.5 bits (146), Expect = 1e-11
 Identities = 22/100 (22%), Positives = 49/100 (49%), Gaps = 12/100 (12%)

Query: 1   VTVTRPVEALATVRIQR------DIDLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVM 52
           + +   + A+A ++ Q         +L++ DL++P+ +G E+  EI  N +   +PV+V+
Sbjct: 33  IILRDGLAAMAFLQQQGEYENSPRPNLILLDLNLPKKDGREVLAEIKQNPDLKRIPVVVL 92

Query: 53  SSDDRESVIMKALASGVAFYILKPLNPDDL----KNVWQY 88
           ++   E  ++ +    V  Y+ K  N  DL    + +  +
Sbjct: 93  TTSHNEDDVIASYELHVNCYLTKSRNLKDLFKMVQGIESF 132

>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 = 58.5 bits (141), Expect = 4e-11
 Identities = 21/96 (21%), Positives = 48/96 (50%), Gaps = 1/96 (1%)

Query: 1   VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESV 60
            +  R  EA   +  +   ++V+ DL +P++NG+E+ K I E      V+V++       
Sbjct: 28  ESAERGKEAYKLLSEKHF-NVVLLDLLLPDVNGLEILKWIKERSPETEVIVITGHGTIKT 86

Query: 61  IMKALASGVAFYILKPLNPDDLKNVWQYAMTYKKAK 96
            ++A+  G   ++ KP   ++++     A+ ++K +
Sbjct: 87  AVEAMKMGAYDFLTKPCMLEEIELTINKAIEHRKLR 122

>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 = 58.5 bits (141), Expect = 5e-11
 Identities = 18/81 (22%), Positives = 39/81 (48%)

Query: 16  QRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILK 75
                +V++D+ MP M+G+ L ++I      LP+++++      + ++A+  G   +I K
Sbjct: 42  ADFAGIVISDIRMPGMDGLALFRKILALDPDLPMILVTGHGDIPMAVQAIQDGAYDFIAK 101

Query: 76  PLNPDDLKNVWQYAMTYKKAK 96
           P   D L    + A   ++  
Sbjct: 102 PFAADRLVQSARRAEEKRRLV 122

>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 = 59.1 bits (142), Expect = 8e-11
 Identities = 23/96 (23%), Positives = 50/96 (52%), Gaps = 2/96 (2%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
           EA+    + +  DLV+ D+ MP  +GI+   EI  +    P++V+++  +  ++ +A  +
Sbjct: 39  EAVELAELHK-PDLVIMDVKMPRRDGIDAASEIASKR-IAPIVVLTAFSQRDLVERARDA 96

Query: 68  GVAFYILKPLNPDDLKNVWQYAMTYKKAKSISIDEI 103
           G   Y++KP +  DL    + A++  +  +    E+
Sbjct: 97  GAMAYLVKPFSISDLIPAIELAVSRFREITALEGEV 132

>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 = 56.9 bits (137), Expect = 1e-10
 Identities = 24/82 (29%), Positives = 44/82 (53%), Gaps = 2/82 (2%)

Query: 1   VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESV 60
           VT     EAL         D+++ DL +PE++G+E+ K I +  + +P++++S+ D E  
Sbjct: 28  VTAFNGREALEQFE-AEQPDIIILDLMLPEIDGLEVAKTIRKT-SSVPILMLSAKDSEFD 85

Query: 61  IMKALASGVAFYILKPLNPDDL 82
            +  L  G   Y+ KP +  +L
Sbjct: 86  KVIGLELGADDYVTKPFSNREL 107

>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 = 57.5 bits (138), Expect = 1e-10
 Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 2/76 (2%)

Query: 19  IDLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKP 76
             +++ DL++P  +G E+ +EI  +E    +PV++M++      I    +  ++ YI+KP
Sbjct: 63  PAVILLDLNLPGTDGREVLQEIKQDEVLKKIPVVIMTTSSNPKDIEICYSYSISSYIVKP 122

Query: 77  LNPDDLKNVWQYAMTY 92
           L  D L    Q  + Y
Sbjct: 123 LEIDRLTETVQTFIKY 138

>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 = 56.2 bits (135), Expect = 2e-10
 Identities = 19/92 (20%), Positives = 46/92 (50%), Gaps = 3/92 (3%)

Query: 1   VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMSSDDRE 58
           +     + AL+  R +   DL++ D+ +PE++G+E+ K +  +++  H+PV+ +++   +
Sbjct: 29  LQTREGLSALSIAR-ENKPDLILMDIQLPEISGLEVTKWLKEDDDLAHIPVVAVTAFAMK 87

Query: 59  SVIMKALASGVAFYILKPLNPDDLKNVWQYAM 90
               +    G   YI KP++        +  +
Sbjct: 88  GDEERIREGGCEAYISKPISVVHFLETIKRLL 119

>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 = 55.8 bits (134), Expect = 2e-10
 Identities = 19/82 (23%), Positives = 38/82 (46%), Gaps = 3/82 (3%)

Query: 1   VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESV 60
            T     + L     +    +VV D+ +P+ +G E+ + I E      V++++    +  
Sbjct: 29  KTFLTGEDFLND---EEAFHVVVLDVMLPDYSGYEICRMIKETRPETWVILLTLLSDDES 85

Query: 61  IMKALASGVAFYILKPLNPDDL 82
           ++K   +G   Y+ KP NP+ L
Sbjct: 86  VLKGFEAGADDYVTKPFNPEIL 107

>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 = 56.1 bits (135), Expect = 2e-10
 Identities = 19/87 (21%), Positives = 40/87 (45%), Gaps = 2/87 (2%)

Query: 1   VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMSSDDRE 58
           +T     E    +  Q    LV++D +MP+M+G+ L + +  N        +++++    
Sbjct: 34  ITAAGDGEQGMKIMAQNPHHLVISDFNMPKMDGLGLLQAVRANPATKKAAFIILTAQGDR 93

Query: 59  SVIMKALASGVAFYILKPLNPDDLKNV 85
           +++ KA A G    + KP   + +K  
Sbjct: 94  ALVQKAAALGANNVLAKPFTIEKMKAA 120

>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 = 55.8 bits (134), Expect = 3e-10
 Identities = 21/90 (23%), Positives = 44/90 (48%)

Query: 1   VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESV 60
           V + +  EA           ++VTDL MP+M+G+EL + + +   ++P +V++      +
Sbjct: 30  VKMHQSAEAFLAFAPDVRNGVLVTDLRMPDMSGVELLRNLGDLKINIPSIVITGHGDVPM 89

Query: 61  IMKALASGVAFYILKPLNPDDLKNVWQYAM 90
            ++A+ +G   +I KP     +    + A 
Sbjct: 90  AVEAMKAGAVDFIEKPFEDTVIIEAIERAS 119

>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 = 55.1 bits (132), Expect = 6e-10
 Identities = 18/75 (24%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALAS 67
             L   R       +V D+ MP M+GIELQ+++      +P++ +++     + ++A+ +
Sbjct: 37  TFLEHRR-PEQHGCLVLDMRMPGMSGIELQEQLTAISDGIPIVFITAHGDIPMTVRAMKA 95

Query: 68  GVAFYILKPLNPDDL 82
           G   ++ KP     L
Sbjct: 96  GAIEFLPKPFEEQAL 110

>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 = 52.7 bits (126), Expect = 4e-09
 Identities = 25/82 (30%), Positives = 43/82 (52%), Gaps = 2/82 (2%)

Query: 1   VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESV 60
              T   E    +  + DI+LV+ D+++P  NG+ L +E+ E+  ++ +M ++  D E  
Sbjct: 30  FEATDGAEMHQILS-EYDINLVIMDINLPGKNGLLLARELREQ-ANVALMFLTGRDNEVD 87

Query: 61  IMKALASGVAFYILKPLNPDDL 82
            +  L  G   YI KP NP +L
Sbjct: 88  KILGLEIGADDYITKPFNPREL 109

>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 = 51.6 bits (123), Expect = 7e-09
 Identities = 18/67 (26%), Positives = 40/67 (59%)

Query: 16  QRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILK 75
               DL+V D+ +P+++GIE+ K++ ++    P++++++ D E   +  L  G   Y+ K
Sbjct: 44  TEKPDLIVLDVMLPKLDGIEVCKQLRQQKLMFPILMLTAKDEEFDKVLGLELGADDYMTK 103

Query: 76  PLNPDDL 82
           P +P ++
Sbjct: 104 PFSPREV 110

>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 = 51.6 bits (123), Expect = 8e-09
 Identities = 20/82 (24%), Positives = 38/82 (46%), Gaps = 1/82 (1%)

Query: 1   VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESV 60
            T     EAL +   +   D +V D++MP ++G+ +   +      +PV V+S+      
Sbjct: 29  ATAVDGAEALRSAT-ENRPDAIVLDINMPVLDGVSVVTALRAMDNDVPVCVLSARSSVDD 87

Query: 61  IMKALASGVAFYILKPLNPDDL 82
            +  L +G   Y++KP    +L
Sbjct: 88  RVAGLEAGADDYLVKPFVLAEL 109

>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 = 51.3 bits (122), Expect = 1e-08
 Identities = 18/90 (20%), Positives = 38/90 (42%), Gaps = 1/90 (1%)

Query: 1   VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESV 60
                  E +         D+V+ D+ +P  +G E+ K + E   + PV+++++      
Sbjct: 29  DVCYDGEEGMYMAL-NEPFDVVILDIMLPVHDGWEILKSMRESGVNTPVLMLTALSDVEY 87

Query: 61  IMKALASGVAFYILKPLNPDDLKNVWQYAM 90
            +K L  G   Y+ KP +  +L    +  +
Sbjct: 88  RVKGLNMGADDYLPKPFDLRELIARVRALI 117

>d1qo0d_ c.23.1.3 (D:) Positive regulator of the amidase operon AmiR {Pseudomonas aeruginosa [TaxId: 287]} Length = 189

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: Positive regulator of the amidase operon AmiR
domain: Positive regulator of the amidase operon AmiR
species: Pseudomonas aeruginosa [TaxId: 287]

 Score = 51.6 bits (122), Expect = 3e-08
 Identities = 9/77 (11%), Positives = 24/77 (31%), Gaps = 1/77 (1%)

Query: 16  QRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILK 75
              +D+V T +     +                ++ +   +  +V+ + +       I +
Sbjct: 49  DVPVDVVFTSIFQNRHHDEIAALLA-AGTPRTTLVALVEYESPAVLSQIIELECHGVITQ 107

Query: 76  PLNPDDLKNVWQYAMTY 92
           PL+   +  V   A   
Sbjct: 108 PLDAHRVLPVLVSARRI 124

>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 = 50.8 bits (121), Expect = 3e-08
 Identities = 20/91 (21%), Positives = 37/91 (40%), Gaps = 3/91 (3%)

Query: 8   EALATVRIQRDIDLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMSSDDRESVIMKAL 65
           E          +DLV+ +      +G+     +   E    LPV+ M   D    ++KAL
Sbjct: 46  EKAKISA-GGPVDLVIVNAAAKNFDGLRFTAALRSEERTRQLPVLAMVDPDDRGRMVKAL 104

Query: 66  ASGVAFYILKPLNPDDLKNVWQYAMTYKKAK 96
             GV   + +P++P +L    +  +  K+  
Sbjct: 105 EIGVNDILSRPIDPQELSARVKTQIQRKRYT 135

>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 = 49.0 bits (116), Expect = 6e-08
 Identities = 16/82 (19%), Positives = 40/82 (48%), Gaps = 1/82 (1%)

Query: 1   VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESV 60
                  EA   +  +   D+ + DL +P+ +G+ L +        LP++V+++ +    
Sbjct: 28  DDAEDAKEADYYLN-EHIPDIAIVDLGLPDEDGLSLIRRWRSNDVSLPILVLTARESWQD 86

Query: 61  IMKALASGVAFYILKPLNPDDL 82
            ++ L++G   Y+ KP + +++
Sbjct: 87  KVEVLSAGADDYVTKPFHIEEV 108

>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 = 47.3 bits (112), Expect = 3e-07
 Identities = 16/82 (19%), Positives = 37/82 (45%), Gaps = 2/82 (2%)

Query: 1   VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESV 60
                       ++  + +DL++ D+++P+ NG+ L + + E  T   +++++       
Sbjct: 29  SVTASGAGLREIMQ-NQSVDLILLDINLPDENGLMLTRALRERSTV-GIILVTGRSDRID 86

Query: 61  IMKALASGVAFYILKPLNPDDL 82
            +  L  G   Y+ KPL   +L
Sbjct: 87  RIVGLEMGADDYVTKPLELREL 108

>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 = 47.0 bits (111), Expect = 3e-07
 Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 1/75 (1%)

Query: 16  QRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILK 75
            R  DL++ DL +P+ +GIE  +++ +     PV+V+S+   ES  + AL +G   Y+ K
Sbjct: 42  TRKPDLIILDLGLPDGDGIEFIRDLRQWSAV-PVIVLSARSEESDKIAALDAGADDYLSK 100

Query: 76  PLNPDDLKNVWQYAM 90
           P    +L+   + A+
Sbjct: 101 PFGIGELQARLRVAL 115

>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 = 44.1 bits (103), Expect = 5e-06
 Identities = 18/97 (18%), Positives = 46/97 (47%), Gaps = 2/97 (2%)

Query: 1   VTVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEI--NEEFTHLPVMVMSSDDRE 58
           V+          +  +   D+++ D+ MP M+G  + +++  +    H+PV+++++ D  
Sbjct: 28  VSTAMDGPTALAMAARDLPDIILLDVMMPGMDGFTVCRKLKDDPTTRHIPVVLITALDGR 87

Query: 59  SVIMKALASGVAFYILKPLNPDDLKNVWQYAMTYKKA 95
              ++ L SG + ++ KP++   L    +    +K  
Sbjct: 88  GDRIQGLESGASDFLTKPIDDVMLFARVRSLTRFKLV 124

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	534
d2pl1a1	119	PhoP receiver domain {Escherichia coli [TaxId: 562	99.72
d1qkka_	140	Transcriptional regulatory protein DctD, receiver	99.71
d1dbwa_	123	Transcriptional regulatory protein FixJ, receiver	99.7
d1peya_	119	Sporulation response regulator Spo0F {Bacillus sub	99.7
d1ys7a2	121	Transcriptional regulatory protein PrrA, N-termina	99.7
d1a04a2	138	Nitrate/nitrite response regulator (NarL), receive	99.69
d1ny5a1	137	Transcriptional activator sigm54 (NtrC1), N-termin	99.69
d1krwa_	123	NTRC receiver domain {Salmonella typhimurium [TaxI	99.69
d1kgsa2	122	PhoB receiver domain {Thermotoga maritima [TaxId:	99.68
d1u0sy_	118	CheY protein {Thermotoga maritima [TaxId: 2336]}	99.68
d1mvoa_	121	PhoP receiver domain {Bacillus subtilis [TaxId: 14	99.67
d1zh2a1	119	Transcriptional regulatory protein KdpE, N-termina	99.67
d2a9pa1	117	DNA-binding response regulator MicA, N-terminal do	99.66
d1irza_	64	Arr10-B {Thale cress (Arabidopsis thaliana) [TaxId	99.66
d1p2fa2	120	Response regulator DrrB {Thermotoga maritima [TaxI	99.66
d1zesa1	121	PhoB receiver domain {Escherichia coli [TaxId: 562	99.66
d1dz3a_	123	Sporulation response regulator Spo0A {Bacillus ste	99.66
d1xhfa1	121	Aerobic respiration control protein ArcA, N-termin	99.65
d2ayxa1	133	Sensor kinase protein RcsC, C-terminal domain {Esc	99.65
d1jbea_	128	CheY protein {Escherichia coli [TaxId: 562]}	99.64
d1s8na_	190	Probable two-component system transcriptional regu	99.63
d1yioa2	128	Response regulatory protein StyR, N-terminal domai	99.62
d1mb3a_	123	Cell division response regulator DivK {Caulobacter	99.62
d1i3ca_	144	Response regulator for cyanobacterial phytochrome	99.62
d2r25b1	128	Response regulator Sin1 {Baker's yeast (Saccharomy	99.62
d1w25a1	139	Response regulator PleD, receiver domain {Caulobac	99.62
d1p6qa_	129	CheY protein {Sinorhizobium meliloti, CheY2 [TaxId	99.62
d1zgza1	120	TorCAD operon transcriptional regulator TorD, N-te	99.61
d1k66a_	149	Response regulator for cyanobacterial phytochrome	99.61
d1w25a2	153	Response regulator PleD, receiver domain {Caulobac	99.61
d1k68a_	140	Response regulator for cyanobacterial phytochrome	99.6
d1dcfa_	134	Receiver domain of the ethylene receptor {Thale cr	99.53
d1a2oa1	140	Methylesterase CheB, N-terminal domain {Salmonella	99.44
d2b4aa1	118	Hypothetical protein BH3024 {Bacillus halodurans [	99.42
d1qo0d_	189	Positive regulator of the amidase operon AmiR {Pse	99.29
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	95.25
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	94.68
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	94.54
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	93.51
d1p4wa_	87	Transcriptional regulator RcsB {Erwinia amylovora	92.46
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	90.87
d1dxea_	253	2-dehydro-3-deoxy-galactarate aldolase {Escherichi	89.31
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	88.71
d1s7oa_	106	Hypothetical protein SPy1201 {Streptococcus pyogen	86.65
d1izca_	299	Macrophomate synthase {Macrophoma commelinae [TaxI	86.12
d1xsva_	106	Hypothetical protein SAV1236 {Staphylococcus aureu	85.97
d1xrsb1	160	D-lysine 5,6-aminomutase beta subunit KamE, C-term	84.23
d1ccwa_	137	Glutamate mutase, small subunit {Clostridium cochl	82.05

>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=99.72  E-value=2.3e-17  Score=143.80  Aligned_cols=90  Identities=20%  Similarity=0.321  Sum_probs=86.3

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++++|++.+++ ..||+||+|+.||+++|++++++|++..+.+|||++|+..+.+...+++++||++||.||++.++
T Consensus        29 ~a~~g~eal~~l~~-~~~dliilD~~mP~~~G~e~~~~i~~~~~~~pvi~lt~~~~~~~~~~a~~~Ga~~yl~KP~~~~~  107 (119)
T d2pl1a1          29 DAEDAKEADYYLNE-HIPDIAIVDLGLPDEDGLSLIRRWRSNDVSLPILVLTARESWQDKVEVLSAGADDYVTKPFHIEE  107 (119)
T ss_dssp             EESSHHHHHHHHHH-SCCSEEEECSCCSSSCHHHHHHHHHHTTCCSCEEEEESCCCHHHHHHHHHTTCSEEEESSCCHHH
T ss_pred             EECCHHHHHHHHHh-cccceeehhccCCCchhHHHHHHHHhcCcccceEeeeccCCHHHHHHHHHcCCCEEEECCCCHHH
Confidence            58899999999998 88999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHH
Q 043479           82 LKNVWQYAMTY   92 (534)
Q Consensus        82 L~~aI~~aL~~   92 (534)
                      |..+|++++++
T Consensus       108 L~~~v~~~lrR  118 (119)
T d2pl1a1         108 VMARMQALMRR  118 (119)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHcc
Confidence            99999999864

>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=99.71  E-value=1.9e-17  Score=148.29  Aligned_cols=93  Identities=24%  Similarity=0.389  Sum_probs=88.2

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++.+|++.+++ ..||+||+|+.||+++|++++++|++..+++|||++|++.+.+.+.+|+++||++||.||++.++
T Consensus        29 ~~~~~~~al~~l~~-~~~dlil~D~~mP~~~G~el~~~lr~~~~~~pvI~lT~~~~~~~~~~a~~~Ga~dyl~KP~~~~~  107 (140)
T d1qkka_          29 SFASATEALAGLSA-DFAGIVISDIRMPGMDGLALFRKILALDPDLPMILVTGHGDIPMAVQAIQDGAYDFIAKPFAADR  107 (140)
T ss_dssp             EESCHHHHHHTCCT-TCCSEEEEESCCSSSCHHHHHHHHHHHCTTSCEEEEECGGGHHHHHHHHHTTCCEEEESSCCHHH
T ss_pred             EeCChHHHHHHHhc-cCcchHHHhhccCCCCHHHHHHHHHHhCCCCcEEEEECCCCHHHHHHHHHcCCCEeecCCCCHHH
Confidence            57899999999987 89999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhh
Q 043479           82 LKNVWQYAMTYKKA   95 (534)
Q Consensus        82 L~~aI~~aL~~k~~   95 (534)
                      |..+|+++++.++.
T Consensus       108 L~~~i~~~~~~~~~  121 (140)
T d1qkka_         108 LVQSARRAEEKRRL  121 (140)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999999877653

>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=99.70  E-value=4.9e-17  Score=142.47  Aligned_cols=89  Identities=22%  Similarity=0.352  Sum_probs=85.2

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++++|++.+++ .+||+||+|+.||+++|++++++|++..+++|||++|++.+.+...+|+++||++||.||++.++
T Consensus        32 ~a~~~~~al~~~~~-~~~dlvi~D~~mp~~~G~e~~~~lr~~~~~~~iI~lt~~~~~~~~~~a~~~Ga~~yl~KP~~~~~  110 (123)
T d1dbwa_          32 MHQSAEAFLAFAPD-VRNGVLVTDLRMPDMSGVELLRNLGDLKINIPSIVITGHGDVPMAVEAMKAGAVDFIEKPFEDTV  110 (123)
T ss_dssp             EESCHHHHHHHGGG-CCSEEEEEECCSTTSCHHHHHHHHHHTTCCCCEEEEECTTCHHHHHHHHHTTCSEEEESSCCHHH
T ss_pred             EECCHHHHHHHHhh-cCCcEEEEeccCccccchHHHHHHHhcCCCCeEEEEEeeCCHHHHHHHHHCCCCEEEECCCCHHH
Confidence            57899999999987 78999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHH
Q 043479           82 LKNVWQYAMT   91 (534)
Q Consensus        82 L~~aI~~aL~   91 (534)
                      |..+|+++++
T Consensus       111 L~~~i~~a~e  120 (123)
T d1dbwa_         111 IIEAIERASE  120 (123)
T ss_dssp             HHHHHHHHHT
T ss_pred             HHHHHHHHHH
Confidence            9999999874

>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=99.70  E-value=3.2e-17  Score=142.89  Aligned_cols=88  Identities=23%  Similarity=0.379  Sum_probs=84.3

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++.+|++.+++ .+||+||+|+.||+++|++++++||+..+++|||++|++.+.+...+|+++||++||.||++.++
T Consensus        30 ~a~~g~eal~~~~~-~~~dlillD~~mP~~~G~el~~~lr~~~~~~pvi~lt~~~~~~~~~~a~~~Ga~~yl~KP~~~~~  108 (119)
T d1peya_          30 QAANGLQALDIVTK-ERPDLVLLDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFAKPFDIDE  108 (119)
T ss_dssp             EESSHHHHHHHHHH-HCCSEEEEESCCTTCCHHHHHHHHHHHCTTCEEEEEESSCCHHHHHHHHHTTCCEEEESSCCHHH
T ss_pred             EeCCHHHHHHHHHh-CCCCEEEEeccCCCCCHHHHHHHHHHhCCCCcEEEEecCCCHHHHHHHHHCCCCEEEECCCCHHH
Confidence            57899999999988 78999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHH
Q 043479           82 LKNVWQYAM   90 (534)
Q Consensus        82 L~~aI~~aL   90 (534)
                      |..+|++++
T Consensus       109 L~~~v~~~L  117 (119)
T d1peya_         109 IRDAVKKYL  117 (119)
T ss_dssp             HHHHHHHHS
T ss_pred             HHHHHHHHC
Confidence            999999875

>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=99.70  E-value=1.2e-17  Score=146.12  Aligned_cols=91  Identities=22%  Similarity=0.338  Sum_probs=86.7

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++.+|++.+++ ..||+||+|+.||+++|++++++||+..+++|||++|+..+.+...+++++||++||.||++.++
T Consensus        30 ~a~~~~eal~~~~~-~~~dlvl~D~~mP~~~G~el~~~ir~~~~~~piI~lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~~  108 (121)
T d1ys7a2          30 TAVDGAEALRSATE-NRPDAIVLDINMPVLDGVSVVTALRAMDNDVPVCVLSARSSVDDRVAGLEAGADDYLVKPFVLAE  108 (121)
T ss_dssp             EESSHHHHHHHHHH-SCCSEEEEESSCSSSCHHHHHHHHHHTTCCCCEEEEECCCTTTCCCTTTTTTCSEEEESSCCHHH
T ss_pred             EECCHHHHHHHHHh-CCCCEEEEEeeccCcccHHHHHHHHhcCCCCEEEEEEeeCCHHHHHHHHHCCCCEEEECCCCHHH
Confidence            57899999999998 78999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHh
Q 043479           82 LKNVWQYAMTYK   93 (534)
Q Consensus        82 L~~aI~~aL~~k   93 (534)
                      |..+|+++++++
T Consensus       109 L~~~i~~~l~rr  120 (121)
T d1ys7a2         109 LVARVKALLRRR  120 (121)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcC
Confidence            999999998764

>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=99.69  E-value=4.8e-17  Score=144.85  Aligned_cols=95  Identities=27%  Similarity=0.404  Sum_probs=89.3

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++.+|++.+++ ..|||||+|+.||+++|++++++||+..+++|||++|+..+.+...+++++||++||.||++.++
T Consensus        33 ~a~~~~~al~~~~~-~~~DlvllD~~mP~~~G~el~~~ir~~~~~~~vivlt~~~~~~~~~~a~~~Ga~~yl~Kp~~~~~  111 (138)
T d1a04a2          33 EASNGEQGIELAES-LDPDLILLDLNMPGMNGLETLDKLREKSLSGRIVVFSVSNHEEDVVTALKRGADGYLLKDMEPED  111 (138)
T ss_dssp             EESSHHHHHHHHHH-HCCSEEEEETTSTTSCHHHHHHHHHHSCCCSEEEEEECCCCHHHHHHHHHTTCSEEEETTCCHHH
T ss_pred             EECCHHHHHHHHHh-cCCCEEEEecCCCCCCHHHHHHHHHhhCCCCCEEEEEEECCHHHHHHHHHcCCCEEEECCCCHHH
Confidence            47899999999987 78999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhcc
Q 043479           82 LKNVWQYAMTYKKAKS   97 (534)
Q Consensus        82 L~~aI~~aL~~k~~~s   97 (534)
                      |..+|+++++++...+
T Consensus       112 L~~~i~~v~~g~~~~~  127 (138)
T d1a04a2         112 LLKALHQAAAGEMVLS  127 (138)
T ss_dssp             HHHHHHHHHHSCCCCC
T ss_pred             HHHHHHHHHCCCCcCC
Confidence            9999999998766544

>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=99.69  E-value=4.8e-17  Score=144.97  Aligned_cols=93  Identities=23%  Similarity=0.359  Sum_probs=88.1

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      +|.++++|++.+.+ ..||+||+|+.||+++|++++++|++..+++|||++|++.+.....+|+++||++||.||++.++
T Consensus        29 ~a~~~~eAl~~l~~-~~~dlvilD~~mp~~~G~e~~~~lr~~~~~~piI~lT~~~~~~~~~~a~~~Ga~dyl~KP~~~~~  107 (137)
T d1ny5a1          29 SAERGKEAYKLLSE-KHFNVVLLDLLLPDVNGLEILKWIKERSPETEVIVITGHGTIKTAVEAMKMGAYDFLTKPCMLEE  107 (137)
T ss_dssp             EESSHHHHHHHHHH-SCCSEEEEESBCSSSBHHHHHHHHHHHCTTSEEEEEEETTCHHHHHHHHTTTCCEEEEESCCHHH
T ss_pred             EECCHHHHHHHhhc-cccccchHHHhhhhhhHHHHHHHHHHhCCCCCEEEEECCCCHHHHHHHHHcCCCEEEeCCCCHHH
Confidence            57899999999998 78999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhh
Q 043479           82 LKNVWQYAMTYKKA   95 (534)
Q Consensus        82 L~~aI~~aL~~k~~   95 (534)
                      |..+|+++++.++.
T Consensus       108 L~~~i~~~l~~~~~  121 (137)
T d1ny5a1         108 IELTINKAIEHRKL  121 (137)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999999876543

>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=99.69  E-value=1.4e-17  Score=145.77  Aligned_cols=91  Identities=26%  Similarity=0.455  Sum_probs=87.1

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++.+|++.+++ ..||+||+|+.||+++|++++++|++..+++|||++|+..+.+...+|++.||++||.||++.++
T Consensus        32 ~a~~~~~a~~~l~~-~~~dlii~D~~mp~~~G~el~~~l~~~~~~~piI~~t~~~~~~~~~~a~~~Ga~dyl~KP~~~~e  110 (123)
T d1krwa_          32 TFENGNEVLAALAS-KTPDVLLSDIRMPGMDGLALLKQIKQRHPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDIDE  110 (123)
T ss_dssp             EESSSHHHHHHHTT-CCCSEEEECCSSSSSTTHHHHHHHHHHSSSCCEEESCCCSCHHHHHHHHHHTEEEECSSCCHHHH
T ss_pred             EeCCHHHHHHHHHh-CCCCEEEehhhcCCchHHHHHHHHHHhCCCCeEEEEecCCCHHHHHHHHHcCCCeEEeCcCCHHH
Confidence            57899999999987 88999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHh
Q 043479           82 LKNVWQYAMTYK   93 (534)
Q Consensus        82 L~~aI~~aL~~k   93 (534)
                      |..+|+++++++
T Consensus       111 L~~~i~~~l~~~  122 (123)
T d1krwa_         111 AVALVERAISHY  122 (123)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcc
Confidence            999999999764

>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=99.68  E-value=5.1e-17  Score=141.89  Aligned_cols=91  Identities=21%  Similarity=0.292  Sum_probs=86.9

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      +|.++++|++.+++ ..||+||+|+.||+++|+++++++|+..+.+|||++|+..+.....+++++||++||.||++.++
T Consensus        30 ~a~~~~~al~~l~~-~~~dlillD~~mp~~~g~~~~~~lr~~~~~~piI~lt~~~~~~~~~~~~~~Ga~~yl~KP~~~~~  108 (122)
T d1kgsa2          30 VCYDGEEGMYMALN-EPFDVVILDIMLPVHDGWEILKSMRESGVNTPVLMLTALSDVEYRVKGLNMGADDYLPKPFDLRE  108 (122)
T ss_dssp             EESSHHHHHHHHHH-SCCSEEEEESCCSSSCHHHHHHHHHHTTCCCCEEEEESSCHHHHHHHTCCCCCSEEEESSCCHHH
T ss_pred             EEcchHHHHHHHHh-hCccccccccccccchhHHHHHHHHhcCCCCcEEEEcCCCCHHHHHHHHHcCCceeecCCCCHHH
Confidence            57899999999998 89999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHh
Q 043479           82 LKNVWQYAMTYK   93 (534)
Q Consensus        82 L~~aI~~aL~~k   93 (534)
                      |..+|+++++++
T Consensus       109 L~~~i~~~l~r~  120 (122)
T d1kgsa2         109 LIARVRALIRRK  120 (122)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHh
Confidence            999999998765

>d1u0sy_ c.23.1.1 (Y:) CheY protein {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: CheY protein
species: Thermotoga maritima [TaxId: 2336]

Probab=99.68  E-value=9.8e-17  Score=139.54  Aligned_cols=87  Identities=28%  Similarity=0.443  Sum_probs=83.1

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      +|.++.+|++.+++ ..||+||+|+.||+++|++++++|++..+++|||++|++.+.....++++.||++||.||++.++
T Consensus        31 ~a~~~~~al~~~~~-~~~dliilD~~mp~~~G~e~~~~ir~~~~~~pvi~ls~~~~~~~~~~a~~~Ga~~yl~KP~~~~~  109 (118)
T d1u0sy_          31 EATNGREAVEKYKE-LKPDIVTMDITMPEMNGIDAIKEIMKIDPNAKIIVCSAMGQQAMVIEAIKAGAKDFIVKPFQPSR  109 (118)
T ss_dssp             EESSHHHHHHHHHH-HCCSEEEEECSCGGGCHHHHHHHHHHHCTTCCEEEEECTTCHHHHHHHHHTTCCEEEESSCCHHH
T ss_pred             EECCHHHHHHHHHh-ccCCEEEEecCCCCCCHHHHHHHHHHhCCCCcEEEEEccCCHHHHHHHHHcCCCEEEECCCCHHH
Confidence            46899999999988 78999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHH
Q 043479           82 LKNVWQYA   89 (534)
Q Consensus        82 L~~aI~~a   89 (534)
                      |.++|+++
T Consensus       110 L~~~l~~v  117 (118)
T d1u0sy_         110 VVEALNKV  117 (118)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHh
Confidence            99999875

>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=99.67  E-value=1.1e-16  Score=139.36  Aligned_cols=90  Identities=24%  Similarity=0.447  Sum_probs=85.4

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      +|.++.+|++.+++ .+||+||+|+.||+++|++++++++...+.+|||++|+..+.+...+++++||++||.||+++++
T Consensus        31 ~a~~~~~al~~l~~-~~~dlillD~~mp~~~G~~~~~~~r~~~~~~~ii~lt~~~~~~~~~~~~~~Ga~~yl~KP~~~~~  109 (121)
T d1mvoa_          31 TASDGEEALKKAET-EKPDLIVLDVMLPKLDGIEVCKQLRQQKLMFPILMLTAKDEEFDKVLGLELGADDYMTKPFSPRE  109 (121)
T ss_dssp             EESSHHHHHHHHHH-HCCSEEEEESSCSSSCHHHHHHHHHHTTCCCCEEEEECTTCCCCHHHHHHTTCCEEEESSCCHHH
T ss_pred             EECCHHHHHHHHhc-ccccEEEecccccCCCCchhhhhhhccCCCCEEEEEEeeCCHHHHHHHHHCCCCEEEECCCCHHH
Confidence            57899999999988 78999999999999999999999999989999999999999998999999999999999999999


Q ss_pred             HHHHHHHHHHH
Q 043479           82 LKNVWQYAMTY   92 (534)
Q Consensus        82 L~~aI~~aL~~   92 (534)
                      |..+|+.++++
T Consensus       110 L~~~i~~~lrR  120 (121)
T d1mvoa_         110 VNARVKAILRR  120 (121)
T ss_dssp             HHHHHHHHHHT
T ss_pred             HHHHHHHHHcc
Confidence            99999999864

>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=99.67  E-value=9.9e-17  Score=139.59  Aligned_cols=90  Identities=27%  Similarity=0.448  Sum_probs=84.4

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++++|++.+++ ..||+||+|+.||+++|++++++||+. +.+|||++|+..+.+...++++.||++||.||++.++
T Consensus        29 ~a~~~~eal~~l~~-~~~dliilD~~mP~~~G~e~~~~ir~~-~~~piI~lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~~  106 (119)
T d1zh2a1          29 EAETLQRGLLEAAT-RKPDLIILDLGLPDGDGIEFIRDLRQW-SAVPVIVLSARSEESDKIAALDAGADDYLSKPFGIGE  106 (119)
T ss_dssp             EESSHHHHHHHHHH-HCCSEEEEESEETTEEHHHHHHHHHTT-CCCCEEEEESCCSHHHHHHHHHHTCSEEEESSCCHHH
T ss_pred             EeCCHHHHHHHHHh-cCCCEEEeccccCCCCCchHHHHHHhc-cCCcEEEEeccCCHHHHHHHHHcCCCEEEECCCCHHH
Confidence            57899999999988 789999999999999999999999875 5689999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHh
Q 043479           82 LKNVWQYAMTYK   93 (534)
Q Consensus        82 L~~aI~~aL~~k   93 (534)
                      |..+|+++++++
T Consensus       107 L~~~i~~~lrr~  118 (119)
T d1zh2a1         107 LQARLRVALRRH  118 (119)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhh
Confidence            999999999754

>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=99.66  E-value=1.7e-16  Score=137.71  Aligned_cols=89  Identities=26%  Similarity=0.452  Sum_probs=83.5

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++++|++.+++ ..||+||+|+.||+++|+++++++++. +++|||++|+..+.....+++++||++||.||++.++
T Consensus        29 ~a~~~~eal~~~~~-~~~dlillD~~mp~~~G~~~~~~i~~~-~~~pvI~lt~~~~~~~~~~a~~~Ga~d~l~KP~~~~~  106 (117)
T d2a9pa1          29 TAFNGREALEQFEA-EQPDIIILDLMLPEIDGLEVAKTIRKT-SSVPILMLSAKDSEFDKVIGLELGADDYVTKPFSNRE  106 (117)
T ss_dssp             EESSHHHHHHHHHH-HCCSEEEECSSCSSSCHHHHHHHHHTT-CCCCEEEEESCCSHHHHHHHHHHTCSEEEESSCCHHH
T ss_pred             EECCHHHHHHHHHh-cCCCEEEeccccCCCCccHHHHHHHhC-CCCCEEEEecCCCHHHHHHHHHcCCCEEEECCCCHHH
Confidence            57899999999988 789999999999999999999999874 6799999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHH
Q 043479           82 LKNVWQYAMTY   92 (534)
Q Consensus        82 L~~aI~~aL~~   92 (534)
                      |..+|++++++
T Consensus       107 L~~~i~~~lrR  117 (117)
T d2a9pa1         107 LQARVKALLRR  117 (117)
T ss_dssp             HHHHHHHHHHC
T ss_pred             HHHHHHHHhCC
Confidence            99999998853

>d1irza_ a.4.1.11 (A:) Arr10-B {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: GARP response regulators
domain: Arr10-B
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.66  E-value=5e-17  Score=127.70  Aligned_cols=62  Identities=68%  Similarity=1.090  Sum_probs=58.9

Q ss_pred             CCCCCCccCCchhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHH
Q 043479          156 APKKPKVAWTDSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRV  217 (534)
Q Consensus       156 s~kKprv~Wt~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~lkr~  217 (534)
                      ..+|+|++||+|+|.+|+++++.||.+.+.||.|++.|+|+++|+++|+|||||||+.+++.
T Consensus         2 ~~kk~R~~WT~elH~~Fv~Av~~lG~~~atpk~I~~~m~v~~lT~~qV~SHlQKYrl~l~k~   63 (64)
T d1irza_           2 AQKKPRVLWTHELHNKFLAAVDHLGVERAVPKKILDLMNVDKLTRENVASHLQKFRVALKKV   63 (64)
T ss_dssp             CCCCSSCSSCHHHHHHHHHHHHHHCTTTCCHHHHHHHHCCTTCCHHHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHhCccccchHHHHHHcCCCCCCHHHHHHHHHHHHHHHHhc
Confidence            46889999999999999999999999999999999999999999999999999999988763

>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=99.66  E-value=1.8e-16  Score=138.25  Aligned_cols=90  Identities=22%  Similarity=0.341  Sum_probs=82.5

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++.+|++.  . ..|||||+|+.||+++|+++++++|...+.+|||++|+..+.+...+|+++||++||.||+++++
T Consensus        30 ~~~~~~~al~~--~-~~~dlillD~~mP~~~G~~~~~~lr~~~~~~~ii~it~~~~~~~~~~a~~~Ga~dyl~KP~~~~~  106 (120)
T d1p2fa2          30 TFLTGEDFLND--E-EAFHVVVLDVMLPDYSGYEICRMIKETRPETWVILLTLLSDDESVLKGFEAGADDYVTKPFNPEI  106 (120)
T ss_dssp             EESSHHHHHHC--C-SCCSEEEEESBCSSSBHHHHHHHHHHHCTTSEEEEEESCCSHHHHHHHHHHTCSEEEESSCCHHH
T ss_pred             EECCHHHHHhc--C-CCCCEEEEeCcccccchhHHHHHHhhcCCCCcEEEEecCCCHHHHHHHHHCCCCEEEECCCCHHH
Confidence            56788888762  2 57999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhh
Q 043479           82 LKNVWQYAMTYKK   94 (534)
Q Consensus        82 L~~aI~~aL~~k~   94 (534)
                      |..+|++++++++
T Consensus       107 L~~~i~~~l~r~r  119 (120)
T d1p2fa2         107 LLARVKRFLEREK  119 (120)
T ss_dssp             HHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHcc
Confidence            9999999987653

>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=99.66  E-value=1.9e-16  Score=138.02  Aligned_cols=90  Identities=22%  Similarity=0.352  Sum_probs=84.0

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHh--hCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINE--EFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~--~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      +|.++++|++.+++ ..||+||+|+.||+++|++++++||+  ..+++|||++|+..+.....++++.||++||.||++.
T Consensus        29 ~a~~~~~al~~l~~-~~~dlil~D~~mp~~~G~~l~~~lr~~~~~~~~pvi~lt~~~~~~~~~~~~~~G~~d~l~KP~~~  107 (121)
T d1zesa1          29 EAEDYDSAVNQLNE-PWPDLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSP  107 (121)
T ss_dssp             EECSHHHHHHHSSS-SCCSEEEECSSCTTSCHHHHHHHHHHSTTTTTSCEEEEESCCSHHHHHHHHHHTCSEEEESSCCH
T ss_pred             EECChHHHHHHHHc-cCCCEEEeecCCCCCCHHHHHHHHHhCccCCCCeEEEEECCCCHHHHHHHHHCCCCEEEECCCCH
Confidence            57899999999987 88999999999999999999999986  4567999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHH
Q 043479           80 DDLKNVWQYAMTY   92 (534)
Q Consensus        80 eeL~~aI~~aL~~   92 (534)
                      ++|..+|++++++
T Consensus       108 ~~L~~~v~~~lrR  120 (121)
T d1zesa1         108 KELVARIKAVMRR  120 (121)
T ss_dssp             HHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHcC
Confidence            9999999998853

>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=99.66  E-value=1.8e-16  Score=138.67  Aligned_cols=89  Identities=24%  Similarity=0.466  Sum_probs=82.4

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCC-CcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTH-LPVMVMSSDDRESVIMKALASGVAFYILKPLNPD   80 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~-ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~e   80 (534)
                      +|.++++|++.+++ ..||+||+|+.||++||++++++||+..+. +|||++|+..+.....+++++||++||.||++.+
T Consensus        32 ~a~~g~~al~~~~~-~~~dlillD~~mP~~dG~e~~~~ir~~~~~~~~ii~~t~~~~~~~~~~a~~~Ga~~~l~KP~~~~  110 (123)
T d1dz3a_          32 TAYNGQDCLQMLEE-KRPDILLLDIIMPHLDGLAVLERIRAGFEHQPNVIMLTAFGQEDVTKKAVELGASYFILKPFDME  110 (123)
T ss_dssp             EESSHHHHHHHHHH-HCCSEEEEESCCSSSCHHHHHHHHHHHCSSCCEEEEEEETTCHHHHHHHHHTTCEEEEECSSCCT
T ss_pred             EECCHHHHHHHHHh-cCCCEEEEcCCCCCCCHHHHHHHHHhcCCCCCeEEEEECcCCHHHHHHHHHCCCCEEEECCCCHH
Confidence            47899999999987 789999999999999999999999986655 4699999999999999999999999999999999


Q ss_pred             HHHHHHHHHHH
Q 043479           81 DLKNVWQYAMT   91 (534)
Q Consensus        81 eL~~aI~~aL~   91 (534)
                      +|..+|+++++
T Consensus       111 ~L~~~i~~v~~  121 (123)
T d1dz3a_         111 NLAHHIRQVYG  121 (123)
T ss_dssp             THHHHHHHHHH
T ss_pred             HHHHHHHHHHc
Confidence            99999999875

>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=99.65  E-value=4.1e-16  Score=136.11  Aligned_cols=89  Identities=28%  Similarity=0.454  Sum_probs=84.1

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++++|++.+.+ ..||+||+|+.||+++|+++++++++. +++|||++|+..+.....+++++||++||.||+++++
T Consensus        31 ~a~~~~~al~~l~~-~~~dlii~D~~mp~~~G~~~~~~~r~~-~~~pii~lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~~  108 (121)
T d1xhfa1          31 EATDGAEMHQILSE-YDINLVIMDINLPGKNGLLLARELREQ-ANVALMFLTGRDNEVDKILGLEIGADDYITKPFNPRE  108 (121)
T ss_dssp             EESSHHHHHHHHHH-SCCSEEEECSSCSSSCHHHHHHHHHHH-CCCEEEEEESCCSHHHHHHHHHHTCSEEEESSCCHHH
T ss_pred             EECChHHHHHHHHh-cCCCEEEeecccCCccCcHHHHHHHhc-CCCcEEEEECCCCHHHHHHHHHcCCCEEEeCCCCHHH
Confidence            57899999999998 899999999999999999999999875 5799999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHH
Q 043479           82 LKNVWQYAMTY   92 (534)
Q Consensus        82 L~~aI~~aL~~   92 (534)
                      |..+|++++++
T Consensus       109 L~~~v~~~l~R  119 (121)
T d1xhfa1         109 LTIRARNLLSR  119 (121)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHhc
Confidence            99999999864

>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=99.65  E-value=2.6e-16  Score=139.53  Aligned_cols=92  Identities=26%  Similarity=0.400  Sum_probs=86.8

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++.+|++.+.. .+||+||+|+.||+++|++++++||+..+.+|||++|+..+.+...+++++||++||.||++.++
T Consensus        37 ~a~~g~ea~~~~~~-~~~dlillD~~mP~~dG~el~~~ir~~~~~~pii~lt~~~~~~~~~~~~~~G~~~~l~KP~~~~~  115 (133)
T d2ayxa1          37 TANDGVDALNVLSK-NHIDIVLSDVNMPNMDGYRLTQRIRQLGLTLPVIGVTANALAEEKQRCLESGMDSCLSKPVTLDV  115 (133)
T ss_dssp             EECCSHHHHHHHHH-SCCSEEEEEESSCSSCCHHHHHHHHHHHCCSCEEEEESSTTSHHHHHHHHCCCEEEEESSCCHHH
T ss_pred             EECcHHHHHHHHhc-cCceEEEEeccCCCCCHHHHHHHHHHhCCCCCEEEEeccCCHHHHHHHHHcCCCEEEECCCCHHH
Confidence            57899999999988 78999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhh
Q 043479           82 LKNVWQYAMTYKK   94 (534)
Q Consensus        82 L~~aI~~aL~~k~   94 (534)
                      |..+|++++++.+
T Consensus       116 L~~~l~~~~~r~r  128 (133)
T d2ayxa1         116 IKQTLTLYAERVR  128 (133)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999886543

>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=99.63  E-value=2.6e-16  Score=146.79  Aligned_cols=93  Identities=24%  Similarity=0.417  Sum_probs=86.1

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      +|.++.||++.++. ..|||||+|++||++||++++++|++. +.+|||++|++++.+.+.+|+++||++||.||+++++
T Consensus        33 ~a~~g~eal~~~~~-~~pDlvllDi~mP~~dG~e~~~~ir~~-~~~pIi~lTa~~~~~~~~~al~~Ga~~yl~KP~~~~~  110 (190)
T d1s8na_          33 EAGDGQEAVELAEL-HKPDLVIMDVKMPRRDGIDAASEIASK-RIAPIVVLTAFSQRDLVERARDAGAMAYLVKPFSISD  110 (190)
T ss_dssp             EESSHHHHHHHHHH-HCCSEEEEESSCSSSCHHHHHHHHHHT-TCSCEEEEEEGGGHHHHHTTGGGSCEEEEEESCCHHH
T ss_pred             EECCHHHHHHHHhc-CCCCEEEEeccccCcchHHHHHHHHhc-CCCCEEEEeCCCCHHHHHHHHHcCCCEeccCCCCHHH
Confidence            47899999999998 789999999999999999999999986 4599999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhc
Q 043479           82 LKNVWQYAMTYKKAK   96 (534)
Q Consensus        82 L~~aI~~aL~~k~~~   96 (534)
                      |..+|+.++.+.+..
T Consensus       111 L~~~i~~~~~~~~~~  125 (190)
T d1s8na_         111 LIPAIELAVSRFREI  125 (190)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhHhh
Confidence            999999988765543

>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=99.62  E-value=3.5e-16  Score=137.41  Aligned_cols=92  Identities=21%  Similarity=0.379  Sum_probs=86.7

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++++|++.+++ ..||+||+|+.||+++|+++++++++..+.+|||++|+..+.+...++++.||++||.||++.++
T Consensus        31 ~a~~~~~al~~~~~-~~~dliilD~~mp~~~G~~~~~~i~~~~~~~~ii~lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~~  109 (128)
T d1yioa2          31 TFDCASTFLEHRRP-EQHGCLVLDMRMPGMSGIELQEQLTAISDGIPIVFITAHGDIPMTVRAMKAGAIEFLPKPFEEQA  109 (128)
T ss_dssp             EESSHHHHHHHCCT-TSCEEEEEESCCSSSCHHHHHHHHHHTTCCCCEEEEESCTTSCCCHHHHHTTEEEEEESSCCHHH
T ss_pred             ccccHHHHHHHHHh-cCCCEeehhhhcccchhHHHHHHHHhhCCCCeEEEEEEECCHHHHHHHHHCCCCEEEECCCCHHH
Confidence            57899999999987 78999999999999999999999999999999999999999888999999999999999999999


Q ss_pred             HHHHHHHHHHHhh
Q 043479           82 LKNVWQYAMTYKK   94 (534)
Q Consensus        82 L~~aI~~aL~~k~   94 (534)
                      |..+|+++++...
T Consensus       110 L~~~i~~~l~~~~  122 (128)
T d1yioa2         110 LLDAIEQGLQLNA  122 (128)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999987654

>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=99.62  E-value=3.3e-16  Score=136.58  Aligned_cols=90  Identities=22%  Similarity=0.405  Sum_probs=77.9

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhh--CCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~--~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      ++.++.+|++.+++ .+||+||+|+.||++||++++++||+.  .+++|||++|+..+.....+++++|+++||.||++.
T Consensus        30 ~a~~~~~al~~~~~-~~~dlil~D~~mp~~dG~el~~~ir~~~~~~~iPii~lt~~~~~~~~~~~~~~G~~~~l~KP~~~  108 (123)
T d1mb3a_          30 QTREGLSALSIARE-NKPDLILMDIQLPEISGLEVTKWLKEDDDLAHIPVVAVTAFAMKGDEERIREGGCEAYISKPISV  108 (123)
T ss_dssp             EESCHHHHHHHHHH-HCCSEEEEESBCSSSBHHHHHHHHHHSTTTTTSCEEEEC------CHHHHHHHTCSEEECSSCCH
T ss_pred             EECCHHHHHHHHHh-CCCCEEEEEeccCCCcHHHHHHHHHhCCCcCCCCeEEEEEecCHHHHHHHHHcCCCEEEECCCCH
Confidence            57899999999987 789999999999999999999999974  467899999999988888999999999999999999


Q ss_pred             HHHHHHHHHHHHH
Q 043479           80 DDLKNVWQYAMTY   92 (534)
Q Consensus        80 eeL~~aI~~aL~~   92 (534)
                      ++|..+|++++++
T Consensus       109 ~~L~~~i~~~l~r  121 (123)
T d1mb3a_         109 VHFLETIKRLLER  121 (123)
T ss_dssp             HHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHhC
Confidence            9999999999853

>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=99.62  E-value=1.3e-15  Score=136.72  Aligned_cols=93  Identities=24%  Similarity=0.384  Sum_probs=83.9

Q ss_pred             eecCHHHHHHHHHhc------CCceEEEEeCCCCCCCHHHHHHHHHhh--CCCCcEEEEecCCCHHHHHHHHHcCCcEEE
Q 043479            2 TVTRPVEALATVRIQ------RDIDLVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYI   73 (534)
Q Consensus         2 tass~~EALe~L~~~------~~pDLVLLDi~mPdmdGleLL~~Lr~~--~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL   73 (534)
                      ++.++.+|++++++.      ..||+||+|+.||+++|++++++||+.  ..++|||++|+..+.....+|+++||++||
T Consensus        34 ~a~~g~~Al~~l~~~~~~~~~~~pdlIllD~~mP~~~G~el~~~ir~~~~~~~iPvi~lT~~~~~~~~~~a~~~Ga~~yl  113 (144)
T d1i3ca_          34 ILRDGLAAMAFLQQQGEYENSPRPNLILLDLNLPKKDGREVLAEIKQNPDLKRIPVVVLTTSHNEDDVIASYELHVNCYL  113 (144)
T ss_dssp             EECSHHHHHHHHTTCGGGTTCCCCSEEEECSCCSSSCHHHHHHHHHHCTTTTTSCEEEEESCCCHHHHHHHHHTTCSEEE
T ss_pred             EECCHHHHHHHHHhchhhhccCCCCEEEEECccccccchHHHHHHHhCcccCCCeEEEEECCCCHHHHHHHHHCCCCEEE
Confidence            578999999999751      259999999999999999999999973  467999999999999999999999999999


Q ss_pred             eCCCChHHHHHHHHHHHHHhh
Q 043479           74 LKPLNPDDLKNVWQYAMTYKK   94 (534)
Q Consensus        74 ~KP~s~eeL~~aI~~aL~~k~   94 (534)
                      .||++.++|.++|+++++.+.
T Consensus       114 ~KP~~~~~L~~~i~~l~~~~~  134 (144)
T d1i3ca_         114 TKSRNLKDLFKMVQGIESFWL  134 (144)
T ss_dssp             ECCSSHHHHHHHHHHHHHHHT
T ss_pred             ECCCCHHHHHHHHHHHHHHHH
Confidence            999999999999998877654

>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=99.62  E-value=1.2e-15  Score=134.72  Aligned_cols=90  Identities=21%  Similarity=0.354  Sum_probs=81.7

Q ss_pred             eecCHHHHHHHHHh----cCCceEEEEeCCCCCCCHHHHHHHHHhh-CCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCC
Q 043479            2 TVTRPVEALATVRI----QRDIDLVVTDLHMPEMNGIELQKEINEE-FTHLPVMVMSSDDRESVIMKALASGVAFYILKP   76 (534)
Q Consensus         2 tass~~EALe~L~~----~~~pDLVLLDi~mPdmdGleLL~~Lr~~-~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP   76 (534)
                      +|.+++||++.+++    ..+||+||+|+.||++||++++++||+. .+.+|||++|+..+.....+++++||++||.||
T Consensus        31 ~a~~g~eAl~~l~~~~~~~~~~dlillD~~mP~~dG~el~~~ir~~~~~~~piI~lT~~~~~~~~~~~~~~G~~~~l~KP  110 (128)
T d2r25b1          31 LACDGQEAFDKVKELTSKGENYNMIFMDVQMPKVDGLLSTKMIRRDLGYTSPIVALTAFADDSNIKECLESGMNGFLSKP  110 (128)
T ss_dssp             EESSHHHHHHHHHHHHHHTCCCSEEEECSCCSSSCHHHHHHHHHHHSCCCSCEEEEESCCSHHHHHHHHHTTCSEEEESS
T ss_pred             EEcChHHHHHHHHhhhhccCCCCEEEEEeCCCCCCHHHHHHHHHHccCCCCeEEEEECCCCHHHHHHHHHcCCCEEEECC
Confidence            47899999998863    2579999999999999999999999864 556899999999999999999999999999999


Q ss_pred             CChHHHHHHHHHHHH
Q 043479           77 LNPDDLKNVWQYAMT   91 (534)
Q Consensus        77 ~s~eeL~~aI~~aL~   91 (534)
                      ++.++|..+|++++.
T Consensus       111 ~~~~~L~~~l~~~~~  125 (128)
T d2r25b1         111 IKRPKLKTILTEFCA  125 (128)
T ss_dssp             CCHHHHHHHHHHHCT
T ss_pred             CCHHHHHHHHHHHHH
Confidence            999999999998764

>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=99.62  E-value=1.3e-15  Score=135.78  Aligned_cols=92  Identities=23%  Similarity=0.356  Sum_probs=85.5

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHh--hCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINE--EFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~--~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      +|.++.+|++.+.+ ..|||||+|+.||+++|+++++.++.  ..+++|||++|++.+.....+|+++||++||.||++.
T Consensus        30 ~a~~~~eal~~~~~-~~~dlil~D~~~p~~~G~~~~~~ir~~~~~~~~piI~lt~~~~~~~~~~a~~~Ga~dyl~KP~~~  108 (139)
T d1w25a1          30 TAMDGPTALAMAAR-DLPDIILLDVMMPGMDGFTVCRKLKDDPTTRHIPVVLITALDGRGDRIQGLESGASDFLTKPIDD  108 (139)
T ss_dssp             EESSHHHHHHHHHH-HCCSEEEEESCCSSSCHHHHHHHHHHSTTTTTSCEEEEECSSCHHHHHHHHHHTCCEEEESSCCH
T ss_pred             EEccchhhhhhhhc-ccceeeeeeccccCCCchHHHHHhhhcccccCCCEEEEEcCCCHHHHHHHHHcCCCEEEECCCCH
Confidence            57899999999988 78999999999999999999999987  4567999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhh
Q 043479           80 DDLKNVWQYAMTYKK   94 (534)
Q Consensus        80 eeL~~aI~~aL~~k~   94 (534)
                      ++|...|+.+++.+.
T Consensus       109 ~~L~~~i~~~lr~~~  123 (139)
T d1w25a1         109 VMLFARVRSLTRFKL  123 (139)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999998887654

>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=99.62  E-value=6.4e-16  Score=136.19  Aligned_cols=89  Identities=17%  Similarity=0.351  Sum_probs=83.2

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHh--hCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCCh
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINE--EFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNP   79 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~--~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~   79 (534)
                      .+.++++|++.+++ .+||+||+|+.||+++|+++++.||+  ..+++|||++|+..+.+...+++++|+++||.||++.
T Consensus        36 ~a~~~~~al~~l~~-~~~dlii~D~~mP~~~G~el~~~lr~~~~~~~~pii~lt~~~~~~~~~~a~~~G~~~~l~KP~~~  114 (129)
T d1p6qa_          36 AAGDGEQGMKIMAQ-NPHHLVISDFNMPKMDGLGLLQAVRANPATKKAAFIILTAQGDRALVQKAAALGANNVLAKPFTI  114 (129)
T ss_dssp             CCSSHHHHHHHHHT-SCCSEEEECSSSCSSCHHHHHHHHTTCTTSTTCEEEECCSCCCHHHHHHHHHHTCSCEECCCSSH
T ss_pred             EECCHHHHHHHHHh-CCCCeEEeeeecCCCChHHHHHHHHhCcccCCCeEEEEEecCCHHHHHHHHHCCCCEEEECCCCH
Confidence            36789999999998 78999999999999999999999987  4567999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHH
Q 043479           80 DDLKNVWQYAMT   91 (534)
Q Consensus        80 eeL~~aI~~aL~   91 (534)
                      ++|..+|++++.
T Consensus       115 ~~L~~~i~~vl~  126 (129)
T d1p6qa_         115 EKMKAAIEAVFG  126 (129)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            999999999875

>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=99.61  E-value=2.6e-15  Score=130.26  Aligned_cols=89  Identities=17%  Similarity=0.321  Sum_probs=83.0

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++++|++.+.+ ..||+||+|+.||+++|+++++.++.. +.+|||++|+..+.....+|+++||++||.||++.++
T Consensus        30 ~a~~~~~a~~~~~~-~~~dliilD~~mp~~~g~~~~~~~~~~-~~~piI~lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~~  107 (120)
T d1zgza1          30 VTASGAGLREIMQN-QSVDLILLDINLPDENGLMLTRALRER-STVGIILVTGRSDRIDRIVGLEMGADDYVTKPLELRE  107 (120)
T ss_dssp             EESSHHHHHHHHHH-SCCSEEEEESCCSSSCHHHHHHHHHTT-CCCEEEEEESSCCHHHHHHHHHHTCSEEEESSCCHHH
T ss_pred             EECCHHHHHHHHHh-cCCCEEeeehhhccchhHHHHHHHhcc-CCCeEEEEEccCCHHHHHHHHHCCCCEEEECCCCHHH
Confidence            57899999999988 889999999999999999999998764 5699999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHH
Q 043479           82 LKNVWQYAMTY   92 (534)
Q Consensus        82 L~~aI~~aL~~   92 (534)
                      |..+|++++++
T Consensus       108 L~~~i~~~lrR  118 (120)
T d1zgza1         108 LVVRVKNLLWR  118 (120)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHcc
Confidence            99999999865

>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=99.61  E-value=1.5e-15  Score=137.02  Aligned_cols=93  Identities=24%  Similarity=0.387  Sum_probs=84.5

Q ss_pred             eecCHHHHHHHHHhc---------CCceEEEEeCCCCCCCHHHHHHHHHhh--CCCCcEEEEecCCCHHHHHHHHHcCCc
Q 043479            2 TVTRPVEALATVRIQ---------RDIDLVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVA   70 (534)
Q Consensus         2 tass~~EALe~L~~~---------~~pDLVLLDi~mPdmdGleLL~~Lr~~--~p~ipVIVLSs~~d~~~~~~AL~aGA~   70 (534)
                      +|.++.+|++++++.         ..||+||+|+.||++||++++++||+.  .+.+|||++|+..+.+...+++++||+
T Consensus        37 ~a~~g~eAl~~l~~~~~~~~~~~~~~pdlillD~~mP~~~G~el~~~ir~~~~~~~ipiI~lT~~~~~~~~~~~~~~Ga~  116 (149)
T d1k66a_          37 RCITGDQALDFLYQTGSYCNPDIAPRPAVILLDLNLPGTDGREVLQEIKQDEVLKKIPVVIMTTSSNPKDIEICYSYSIS  116 (149)
T ss_dssp             EECSHHHHHHHHHTCCSSSCGGGCCCCSEEEECSCCSSSCHHHHHHHHTTSTTGGGSCEEEEESCCCHHHHHHHHHTTCS
T ss_pred             EECChHHHHHHHHhhccccccccccCCCeEEccccccCCCcHHHHHHHHhccccCCCeEEEEeCCCCHHHHHHHHHCCCC
Confidence            578999999999752         259999999999999999999999863  467999999999999999999999999


Q ss_pred             EEEeCCCChHHHHHHHHHHHHHhh
Q 043479           71 FYILKPLNPDDLKNVWQYAMTYKK   94 (534)
Q Consensus        71 dyL~KP~s~eeL~~aI~~aL~~k~   94 (534)
                      +||.||++.++|.++|+++++.+.
T Consensus       117 ~~l~KP~~~~~L~~~i~~~l~~~~  140 (149)
T d1k66a_         117 SYIVKPLEIDRLTETVQTFIKYWL  140 (149)
T ss_dssp             EEEECCSSHHHHHHHHHHHHHHHH
T ss_pred             EEEECCCCHHHHHHHHHHHHHHHh
Confidence            999999999999999999997654

>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=99.61  E-value=1.8e-15  Score=137.29  Aligned_cols=92  Identities=21%  Similarity=0.364  Sum_probs=82.6

Q ss_pred             ecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHh--hCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChH
Q 043479            3 VTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINE--EFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPD   80 (534)
Q Consensus         3 ass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~--~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~e   80 (534)
                      +.++.++++.+.. .+|||||+|+.||++||++++++||.  ..+++|||++|+..+.....+|+++||++||.||++.+
T Consensus        41 ~~~~~~~~~~~~~-~~~DlillD~~mP~~dG~el~~~ir~~~~~~~iPiI~lt~~~~~~~~~~a~~~Ga~d~l~KP~~~~  119 (153)
T d1w25a2          41 IESDPEKAKISAG-GPVDLVIVNAAAKNFDGLRFTAALRSEERTRQLPVLAMVDPDDRGRMVKALEIGVNDILSRPIDPQ  119 (153)
T ss_dssp             EECCHHHHHHHHH-SSCSEEEEETTCSSSCHHHHHHHHHTSGGGTTCCEEEEECTTCHHHHHHHHHTTCCEEEESSCCHH
T ss_pred             EEccHHHHHHHhc-CCCCEEEEECccccccchHHHHHHHhccccccceeEEeecCCCHHHHHHHHhcCcceEEECCCCHH
Confidence            3456778887776 78999999999999999999999985  45789999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhh
Q 043479           81 DLKNVWQYAMTYKKA   95 (534)
Q Consensus        81 eL~~aI~~aL~~k~~   95 (534)
                      +|..+|+.+++.++.
T Consensus       120 ~L~~~i~~~l~~~~~  134 (153)
T d1w25a2         120 ELSARVKTQIQRKRY  134 (153)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999876553

>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=99.60  E-value=2.1e-15  Score=134.80  Aligned_cols=93  Identities=29%  Similarity=0.414  Sum_probs=83.6

Q ss_pred             eecCHHHHHHHHHhc------CCceEEEEeCCCCCCCHHHHHHHHHhh--CCCCcEEEEecCCCHHHHHHHHHcCCcEEE
Q 043479            2 TVTRPVEALATVRIQ------RDIDLVVTDLHMPEMNGIELQKEINEE--FTHLPVMVMSSDDRESVIMKALASGVAFYI   73 (534)
Q Consensus         2 tass~~EALe~L~~~------~~pDLVLLDi~mPdmdGleLL~~Lr~~--~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL   73 (534)
                      ++.++.+|++++++.      ..||+||+|++||+++|++++++||..  .+++|||++|+..+.....+|+++||++||
T Consensus        33 ~a~~g~eAl~~l~~~~~~~~~~~pdlillD~~mP~~dG~el~~~ir~~~~~~~iPvI~ls~~~~~~~~~~a~~~Ga~~yl  112 (140)
T d1k68a_          33 TVRDGMEAMAYLRQEGEYANASRPDLILLDLNLPKKDGREVLAEIKSDPTLKRIPVVVLSTSINEDDIFHSYDLHVNCYI  112 (140)
T ss_dssp             EECSHHHHHHHHTTCGGGGSCCCCSEEEECSSCSSSCHHHHHHHHHHSTTGGGSCEEEEESCCCHHHHHHHHHTTCSEEE
T ss_pred             EECCHHHHHHHHHHhHHhhccCCCCEEEEeeccccccChHHHHHHHhCcccCCCcEEEEeCCCCHHHHHHHHHCCCCEEE
Confidence            578999999998641      358999999999999999999999873  457999999999999999999999999999


Q ss_pred             eCCCChHHHHHHHHHHHHHhh
Q 043479           74 LKPLNPDDLKNVWQYAMTYKK   94 (534)
Q Consensus        74 ~KP~s~eeL~~aI~~aL~~k~   94 (534)
                      .||++.++|..+|+.+++.+.
T Consensus       113 ~KP~~~~~L~~~i~~i~~~~~  133 (140)
T d1k68a_         113 TKSANLSQLFQIVKGIEEFWL  133 (140)
T ss_dssp             ECCSSHHHHHHHHHHHHHHHH
T ss_pred             ECCCCHHHHHHHHHHHHHHHh
Confidence            999999999999999887653

>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=99.53  E-value=1.1e-14  Score=128.97  Aligned_cols=89  Identities=22%  Similarity=0.362  Sum_probs=80.5

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhh-----CCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCC
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEE-----FTHLPVMVMSSDDRESVIMKALASGVAFYILKP   76 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~-----~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP   76 (534)
                      +|.++.+|++.++  ..||+||+|+.||++||++++++||+.     .+.+|||++|++.+.+...+++++|+++||.||
T Consensus        36 ~a~~g~eal~~l~--~~~dlillD~~mP~~dG~el~~~ir~~~~~~~~~~~~ii~lT~~~~~~~~~~~~~~G~~~~l~KP  113 (134)
T d1dcfa_          36 TVSSNEECLRVVS--HEHKVVFMDVCMPGVENYQIALRIHEKFTKQRHQRPLLVALSGNTDKSTKEKCMSFGLDGVLLKP  113 (134)
T ss_dssp             EESSHHHHHHHCC--TTCSEEEEECCSSTTTTTHHHHHHHHHHC-CCSCCCEEEEEESCCSHHHHHHHHHTTCCEEEESS
T ss_pred             EECCHHHHHHHhh--cCCCeEEEEeccCCCchHHHHHHHHHhcccccCCCCeEEEEeCCCCHHHHHHHHHcCCCEEEECC
Confidence            5789999999875  479999999999999999999999853     345789999999999999999999999999999


Q ss_pred             CChHHHHHHHHHHHHH
Q 043479           77 LNPDDLKNVWQYAMTY   92 (534)
Q Consensus        77 ~s~eeL~~aI~~aL~~   92 (534)
                      ++.++|..+|+++++.
T Consensus       114 ~~~~~L~~~l~~~l~~  129 (134)
T d1dcfa_         114 VSLDNIRDVLSDLLEP  129 (134)
T ss_dssp             CCHHHHHHHHHHHHSC
T ss_pred             CCHHHHHHHHHHHhhh
Confidence            9999999999998854

>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=99.44  E-value=2.2e-13  Score=121.21  Aligned_cols=76  Identities=25%  Similarity=0.378  Sum_probs=66.2

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCC-HHHHHHHHHcCCcEEEeCCCC
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDR-ESVIMKALASGVAFYILKPLN   78 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d-~~~~~~AL~aGA~dyL~KP~s   78 (534)
                      ++.++.+|++.+++ ..|||||+|+.||++||++++++|++..+..+|++++...+ .+...+|+++||++||.||+.
T Consensus        34 ~a~~g~~al~~~~~-~~pDlvllDi~MP~~dG~e~~~~ir~~~~~~~i~i~~~~~~~~~~~~~al~~Ga~~yl~KP~~  110 (140)
T d1a2oa1          34 TAPDPLVARDLIKK-FNPDVLTLDVEMPRMDGLDFLEKLMRLRPMPVVMVSSLTGKGSEVTLRALELGAIDFVTKPQL  110 (140)
T ss_dssp             EESSHHHHHHHHHH-HCCSEEEEECCCSSSCHHHHHHHHHHSSCCCEEEEECCTHHHHHHHHHHHHHTCCEEEECSSS
T ss_pred             EECCHHHHHHHHHh-cCCCEEEEcCCCCCCCHHHHHHHHHHhCCCCcEEEEEecCCChHHHHHHHHcCCCEEEECCCC
Confidence            47899999999987 78999999999999999999999999888777777776543 356778999999999999964

>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=99.42  E-value=4.8e-14  Score=122.58  Aligned_cols=84  Identities=13%  Similarity=0.255  Sum_probs=71.0

Q ss_pred             eecCHHHHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHH
Q 043479            2 TVTRPVEALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDD   81 (534)
Q Consensus         2 tass~~EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~ee   81 (534)
                      ++.++.+|++.+.+...||+||+|+.||+++|++++++||+..+++|||++|+..+..  .++...|+ |||.||++.++
T Consensus        31 ~~~~~~~al~~l~~~~~~dliilD~~lp~~~G~el~~~ir~~~~~~pii~lt~~~~~~--~~~~~~~~-dyl~KP~~~~e  107 (118)
T d2b4aa1          31 VHPSGSAFFQHRSQLSTCDLLIVSDQLVDLSIFSLLDIVKEQTKQPSVLILTTGRHEL--IESSEHNL-SYLQKPFAISE  107 (118)
T ss_dssp             EESSHHHHHHTGGGGGSCSEEEEETTCTTSCHHHHHHHHTTSSSCCEEEEEESCC--C--CCCSSSCE-EEEESSCCHHH
T ss_pred             EECCHHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCcEEEEECCccHH--HHHhhcCC-CEEECCCCHHH
Confidence            5789999998775435799999999999999999999999988899999999876543  34556666 89999999999


Q ss_pred             HHHHHHH
Q 043479           82 LKNVWQY   88 (534)
Q Consensus        82 L~~aI~~   88 (534)
                      |..+|++
T Consensus       108 L~~~i~~  114 (118)
T d2b4aa1         108 LRAAIDY  114 (118)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9998875

>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=99.29  E-value=1.4e-12  Score=120.10  Aligned_cols=78  Identities=12%  Similarity=0.111  Sum_probs=68.9

Q ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCCChHHHHHHHHHHHHHhhh
Q 043479           17 RDIDLVVTDLHMPEMNGIELQKEINEEFTHLPVMVMSSDDRESVIMKALASGVAFYILKPLNPDDLKNVWQYAMTYKKA   95 (534)
Q Consensus        17 ~~pDLVLLDi~mPdmdGleLL~~Lr~~~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~s~eeL~~aI~~aL~~k~~   95 (534)
                      ..||+||+|++||+++|..+ .+++...|++|||++|++.+.+.+.+|++.||++||.||++.++|..+|+.++.....
T Consensus        50 ~~~Dlvl~D~~mp~~~~~~~-~~~~~~~p~~pvI~lta~~~~~~~~~al~~Ga~~yL~KP~~~~~L~~~i~~~~~~~~~  127 (189)
T d1qo0d_          50 VPVDVVFTSIFQNRHHDEIA-ALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISEE  127 (189)
T ss_dssp             SCCSEEEEECCSSTHHHHHH-HHHHHSCTTCEEEEEECCCSHHHHHHHHHHTCSEEEESSCCGGGHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEcCCCCCcHHHHH-HHHHHcCCCCCEEEEeccchHHHHHHHHHcCCcEEEEecchhhHHHHHHhhccccccc
Confidence            46999999999998877655 4566678899999999999999999999999999999999999999999988766543

>d1l3la1 a.4.6.2 (A:170-234) Quorum-sensing transcription factor TraR, C-terminal domain {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Quorum-sensing transcription factor TraR, C-terminal domain
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=95.25  E-value=0.015  Score=43.74  Aligned_cols=44  Identities=16%  Similarity=0.132  Sum_probs=38.1

Q ss_pred             chhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHH
Q 043479          166 DSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIF  213 (534)
Q Consensus       166 ~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~  213 (534)
                      ..|++|+.+++..+..+.. .++|++.|+   ++..||+.|+.+....
T Consensus         3 ~~Lt~rE~~vl~l~~~G~s-~~eIA~~l~---iS~~TV~~~~~~i~~K   46 (65)
T d1l3la1           3 AWLDPKEATYLRWIAVGKT-MEEIADVEG---VKYNSVRVKLREAMKR   46 (65)
T ss_dssp             CCCCHHHHHHHHHHTTTCC-HHHHHHHHT---CCHHHHHHHHHHHHHH
T ss_pred             cccCHHHHHHHHHHHhcCC-HHHHHHHHC---CCHHHHHHHHHHHHHH
Confidence            3589999999999986555 999999999   9999999999876553

>d1fsea_ a.4.6.2 (A:) Germination protein GerE {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Germination protein GerE
species: Bacillus subtilis [TaxId: 1423]

Probab=94.68  E-value=0.025  Score=42.63  Aligned_cols=42  Identities=17%  Similarity=0.193  Sum_probs=36.8

Q ss_pred             hhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHH
Q 043479          167 SLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRI  212 (534)
Q Consensus       167 eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl  212 (534)
                      .|++++.+++..+..+.. .++|++.|+   ++..||+.|+.+.+.
T Consensus         4 ~LT~rE~~vl~l~~~G~s-~~eIA~~L~---is~~TV~~~~~~i~~   45 (67)
T d1fsea_           4 LLTKREREVFELLVQDKT-TKEIASELF---ISEKTVRNHISNAMQ   45 (67)
T ss_dssp             CCCHHHHHHHHHHTTTCC-HHHHHHHHT---SCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHccCC-HHHHHHHHC---CCHHHHHHHHHHHHH
Confidence            489999999999975555 999999999   999999999887655

>d1a04a1 a.4.6.2 (A:150-216) Nitrate/nitrite response regulator (NarL) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Nitrate/nitrite response regulator (NarL)
species: Escherichia coli [TaxId: 562]

Probab=94.54  E-value=0.031  Score=42.23  Aligned_cols=43  Identities=19%  Similarity=0.215  Sum_probs=37.4

Q ss_pred             chhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHH
Q 043479          166 DSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRI  212 (534)
Q Consensus       166 ~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl  212 (534)
                      ..|++++.+++..+..+.. .++|++.|+   ++..+|+.|+.+...
T Consensus         5 ~~LT~rE~~vl~ll~~G~s-~~eIA~~l~---iS~~TV~~~~~~i~~   47 (67)
T d1a04a1           5 NQLTPRERDILKLIAQGLP-NKMIARRLD---ITESTVKVHVKHMLK   47 (67)
T ss_dssp             GGSCHHHHHHHHHHHTTCC-HHHHHHHHT---CCHHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHhCCC-HHHHHHHHC---CCHHHHHHHHHHHHH
Confidence            4699999999999975554 999999999   999999999887655

>d1yioa1 a.4.6.2 (A:131-200) Response regulatory protein StyR, C-terminal domain {Pseudomonas fluorescens [TaxId: 294]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Response regulatory protein StyR, C-terminal domain
species: Pseudomonas fluorescens [TaxId: 294]

Probab=93.51  E-value=0.05  Score=41.45  Aligned_cols=42  Identities=19%  Similarity=0.088  Sum_probs=36.8

Q ss_pred             hhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHH
Q 043479          167 SLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRI  212 (534)
Q Consensus       167 eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl  212 (534)
                      .|++++.+++..+..+.. .++|++.|+   ++..||+.|+.+...
T Consensus        12 ~LT~rE~~vl~~l~~G~s-~~eIA~~l~---iS~~TV~~~~~~i~~   53 (70)
T d1yioa1          12 SLTGREQQVLQLTIRGLM-NKQIAGELG---IAEVTVKVHRHNIMQ   53 (70)
T ss_dssp             TSCHHHHHHHHHHTTTCC-HHHHHHHHT---CCHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHcCCC-HHHHHHHHC---CCHHHHHHHHHHHHH
Confidence            589999999999975555 999999999   999999999887654

>d1p4wa_ a.4.6.2 (A:) Transcriptional regulator RcsB {Erwinia amylovora [TaxId: 552]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Transcriptional regulator RcsB
species: Erwinia amylovora [TaxId: 552]

Probab=92.46  E-value=0.082  Score=41.87  Aligned_cols=42  Identities=12%  Similarity=0.092  Sum_probs=37.3

Q ss_pred             hhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHH
Q 043479          167 SLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRI  212 (534)
Q Consensus       167 eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl  212 (534)
                      .|+.++.+++..+..+.. .++|++.|+   +|..+|+.|++..+.
T Consensus        22 ~LT~rE~~vl~ll~~G~s-~~eIA~~l~---iS~~TV~~~~~~i~~   63 (87)
T d1p4wa_          22 RLSPKESEVLRLFAEGFL-VTEIAKKLN---RSIKTISSQKKSAMM   63 (87)
T ss_dssp             SCCHHHHHHHHHHHHTCC-HHHHHHHHT---SCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHcCCC-HHHHHHHhC---CCHHHHHHHHHHHHH
Confidence            589999999999976666 999999999   999999999887655

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=90.87  E-value=0.3  Score=36.16  Aligned_cols=50  Identities=18%  Similarity=0.121  Sum_probs=43.6

Q ss_pred             chhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHH
Q 043479          166 DSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVA  218 (534)
Q Consensus       166 ~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~lkr~a  218 (534)
                      ..|+++..+++...-.+...-++|++.|+   +|..+|++|+.+-|..|++..
T Consensus        20 ~~L~~~~r~v~~l~~~~~~s~~eIA~~lg---is~~tv~~~~~ra~~~Lr~~L   69 (71)
T d1rp3a2          20 SKLPEREKLVIQLIFYEELPAKEVAKILE---TSVSRVSQLKAKALERLREML   69 (71)
T ss_dssp             TTSCHHHHHHHHHHHTSCCCHHHHHHHTT---SCHHHHHHHHHHHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHhHhCCHHHHHHHHC---CCHHHHHHHHHHHHHHHHHHc
Confidence            35888889999888667777999999999   999999999999999888764

>d1dxea_ c.1.12.5 (A:) 2-dehydro-3-deoxy-galactarate aldolase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Phosphoenolpyruvate/pyruvate domain
family: HpcH/HpaI aldolase
domain: 2-dehydro-3-deoxy-galactarate aldolase
species: Escherichia coli [TaxId: 562]

Probab=89.31  E-value=1.3  Score=41.28  Aligned_cols=81  Identities=9%  Similarity=0.058  Sum_probs=61.8

Q ss_pred             HHHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHhh-CCCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCC-ChHHHHHH
Q 043479            8 EALATVRIQRDIDLVVTDLHMPEMNGIELQKEINEE-FTHLPVMVMSSDDRESVIMKALASGVAFYILKPL-NPDDLKNV   85 (534)
Q Consensus         8 EALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~~-~p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~-s~eeL~~a   85 (534)
                      ...+.+.. ..+|.|++|++....+--++...++.. ...+..+|=....+...+.++++.||.+++.--+ +.++..++
T Consensus        28 ~~~ei~a~-~G~Dfv~iD~EHg~~~~~~~~~~i~a~~~~g~~~~VRvp~~~~~~i~~~LD~Ga~GIivP~v~s~eea~~~  106 (253)
T d1dxea_          28 ISTEVLGL-AGFDWLVLDGEHAPNDISTFIPQLMALKGSASAPVVRVPTNEPVIIKRLLDIGFYNFLIPFVETKEEAELA  106 (253)
T ss_dssp             HHHHHHTT-SCCSEEEEESSSSSCCHHHHHHHHHHTTTCSSEEEEECSSSCHHHHHHHHHTTCCEEEESCCCSHHHHHHH
T ss_pred             HHHHHHHc-CCCCEEEEecccCCCChhHHHHHHHHHhccCCCceecCCCCCHHHHHHHHhcCccEEEecccCCHHHHHHH
Confidence            44555555 569999999999888877777777753 3346667777888999999999999999998655 56777666


Q ss_pred             HHHH
Q 043479           86 WQYA   89 (534)
Q Consensus        86 I~~a   89 (534)
                      ++.+
T Consensus       107 v~~~  110 (253)
T d1dxea_         107 VAST  110 (253)
T ss_dssp             HHTT
T ss_pred             HHhh
Confidence            6554

>d1or7a1 a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaE factor (RpoE)
species: Escherichia coli [TaxId: 562]

Probab=88.71  E-value=0.48  Score=35.03  Aligned_cols=50  Identities=20%  Similarity=0.173  Sum_probs=42.8

Q ss_pred             chhhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHH
Q 043479          166 DSLHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVA  218 (534)
Q Consensus       166 ~eLh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~lkr~a  218 (534)
                      ..|+++..+++...-.+....++|++.|+   ++..+|++++.+-|..|++..
T Consensus        17 ~~Lp~~~r~v~~l~~~~~~s~~eIA~~lg---is~~tv~~~l~ra~~~Lr~~l   66 (68)
T d1or7a1          17 ESLPEDLRMAITLRELDGLSYEEIAAIMD---CPVGTVRSRIFRAREAIDNKV   66 (68)
T ss_dssp             HHSCHHHHHHHHHHHTTCCCHHHHHHHTT---SCHHHHHHHHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHhCCCHHHHHHHHC---cCHHHHHHHHHHHHHHHHHHc
Confidence            45788888888888666677999999999   999999999999998887754

>d1s7oa_ a.4.13.3 (A:) Hypothetical protein SPy1201 {Streptococcus pyogenes [TaxId: 1314]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: YlxM/p13-like
domain: Hypothetical protein SPy1201
species: Streptococcus pyogenes [TaxId: 1314]

Probab=86.65  E-value=0.62  Score=38.17  Aligned_cols=50  Identities=12%  Similarity=0.176  Sum_probs=43.9

Q ss_pred             hhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHhh
Q 043479          168 LHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVAEQ  220 (534)
Q Consensus       168 Lh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~lkr~a~~  220 (534)
                      |+++..+++...-.+.-..++|++.|+   +|+.+|++||.+-|..|+.+-.+
T Consensus        17 Lp~~qR~v~~L~y~~~ls~~EIA~~lg---iS~~aV~~~l~RA~~~L~~~e~k   66 (106)
T d1s7oa_          17 LTDKQMNYIELYYADDYSLAEIADEFG---VSRQAVYDNIKRTEKILETYEMK   66 (106)
T ss_dssp             SCHHHHHHHHHHHHTCCCHHHHHHHHT---CCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHHC---cCHHHHHHHHHHHHHHHHHHHHH
Confidence            889999999998667777999999999   99999999999999999875433

>d1izca_ c.1.12.5 (A:) Macrophomate synthase {Macrophoma commelinae [TaxId: 108330]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Phosphoenolpyruvate/pyruvate domain
family: HpcH/HpaI aldolase
domain: Macrophomate synthase
species: Macrophoma commelinae [TaxId: 108330]

Probab=86.12  E-value=2.9  Score=39.82  Aligned_cols=81  Identities=17%  Similarity=0.215  Sum_probs=57.6

Q ss_pred             HHHHHHhcCCceEEEEeCCCCCCCHHHHHHHHHh---hC-CCCcEEEEecCCCHHHHHHHHHcCCcEEEeCCC-ChHHHH
Q 043479            9 ALATVRIQRDIDLVVTDLHMPEMNGIELQKEINE---EF-THLPVMVMSSDDRESVIMKALASGVAFYILKPL-NPDDLK   83 (534)
Q Consensus         9 ALe~L~~~~~pDLVLLDi~mPdmdGleLL~~Lr~---~~-p~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~-s~eeL~   83 (534)
                      ..+.+.. ..+|.|++|++....|--++...++.   .. ..++.||=....+...+.++|+.||.+++.--+ +.++..
T Consensus        54 ~~e~~a~-~g~D~v~iD~EHg~~~~~~~~~~i~a~~~~~~~~~~~iVRvp~~~~~~I~~~LD~Ga~GIivP~V~s~eea~  132 (299)
T d1izca_          54 VTKVLAA-TKPDFVWIDVEHGMFNRLELHDAIHAAQHHSEGRSLVIVRVPKHDEVSLSTALDAGAAGIVIPHVETVEEVR  132 (299)
T ss_dssp             HHHHHHH-TCCSEEEEETTTSCCCHHHHHHHHHHHHHHTTTCSEEEEECCTTCHHHHHHHHHHTCSEEEETTCCCHHHHH
T ss_pred             HHHHHHc-CCCCEEEEcCCCCCCCHHHHHHHHHHHHHhCCCCCCeEEeCCCCChHHHHHHHHhCcCeeeccccccHHHHH
Confidence            3455554 57999999999887776565544443   22 234556666777888999999999999987544 567777


Q ss_pred             HHHHHHH
Q 043479           84 NVWQYAM   90 (534)
Q Consensus        84 ~aI~~aL   90 (534)
                      ++++.+.
T Consensus       133 ~~v~~~r  139 (299)
T d1izca_         133 EFVKEMY  139 (299)
T ss_dssp             HHHHHHS
T ss_pred             HHHHhhh
Confidence            7777663

>d1xsva_ a.4.13.3 (A:) Hypothetical protein SAV1236 {Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: YlxM/p13-like
domain: Hypothetical protein SAV1236
species: Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]

Probab=85.97  E-value=0.85  Score=37.30  Aligned_cols=48  Identities=17%  Similarity=0.217  Sum_probs=43.4

Q ss_pred             hhHHHHHHHHHhccCCCcHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHH
Q 043479          168 LHNRFLQAIRHIGLEKAVPKKILEFMNVPGLTRENVASHLQKYRIFLKRVA  218 (534)
Q Consensus       168 Lh~RFleaLe~LGlekAvpK~ILe~M~V~GLT~~tVaSHLQKyRl~lkr~a  218 (534)
                      |+++..+++...-.+....++|++.|+   +|+.+|.+|+.+-|..|+.+.
T Consensus        19 Lpe~QR~vl~L~~~e~ls~~EIA~~lg---iS~~aV~~~l~Ra~~~L~~ye   66 (106)
T d1xsva_          19 LTNKQRNYLELFYLEDYSLSEIADTFN---VSRQAVYDNIRRTGDLVEDYE   66 (106)
T ss_dssp             SCHHHHHHHHHHHTSCCCHHHHHHHTT---CCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhCCcHHHHHHHHC---cCHHHHHHHHHHHHHHHHHHH
Confidence            889999999998777777999999999   999999999999999888754

>d1xrsb1 c.23.6.1 (B:102-261) D-lysine 5,6-aminomutase beta subunit KamE, C-terminal domain {Clostridium sticklandii [TaxId: 1511]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: Cobalamin (vitamin B12)-binding domain
family: Cobalamin (vitamin B12)-binding domain
domain: D-lysine 5,6-aminomutase beta subunit KamE, C-terminal domain
species: Clostridium sticklandii [TaxId: 1511]

Probab=84.23  E-value=3.1  Score=36.04  Aligned_cols=85  Identities=11%  Similarity=0.018  Sum_probs=58.5

Q ss_pred             CHHHHHHHHHhcCCceEEEEeCCCCCCCH-H----HHHHHHHhhCC--CCcEEEEecCCCHHHHHHHHHcCCcEEEeCCC
Q 043479            5 RPVEALATVRIQRDIDLVVTDLHMPEMNG-I----ELQKEINEEFT--HLPVMVMSSDDRESVIMKALASGVAFYILKPL   77 (534)
Q Consensus         5 s~~EALe~L~~~~~pDLVLLDi~mPdmdG-l----eLL~~Lr~~~p--~ipVIVLSs~~d~~~~~~AL~aGA~dyL~KP~   77 (534)
                      ++++.++.+.+ ..+|+|-+...|..... +    ++++.+++...  .++||+=-...+.+   .+.+.||+.|...-.
T Consensus        67 p~e~~v~~a~e-~~~d~VglS~l~t~~~~h~~~~~~~i~~l~~~g~~d~v~vivGG~~~~~~---~a~~~GaD~~f~~g~  142 (160)
T d1xrsb1          67 ANEDFIKKAVE-LEADVLLVSQTVTQKNVHIQNMTHLIELLEAEGLRDRFVLLCGGPRINNE---IAKELGYDAGFGPGR  142 (160)
T ss_dssp             CHHHHHHHHHH-TTCSEEEEECCCCTTSHHHHHHHHHHHHHHHTTCGGGSEEEEECTTCCHH---HHHTTTCSEEECTTC
T ss_pred             CHHHHHHHHHh-cCCCEEEEeecccccchhHHHHHHHHHHHHHcCCCCceEEEEcCCCCCHH---HHHHcCCCEEcCCCC
Confidence            67888888887 88999999998875432 2    45566666543  24444333333333   356789999998778


Q ss_pred             ChHHHHHHHHHHHHHh
Q 043479           78 NPDDLKNVWQYAMTYK   93 (534)
Q Consensus        78 s~eeL~~aI~~aL~~k   93 (534)
                      ...++...+...++.+
T Consensus       143 ~a~~~a~~l~~~l~~r  158 (160)
T d1xrsb1         143 FADDVATFAVKTLNDR  158 (160)
T ss_dssp             CHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHh
Confidence            8888888887777543

>d1ccwa_ c.23.6.1 (A:) Glutamate mutase, small subunit {Clostridium cochlearium [TaxId: 1494]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: Cobalamin (vitamin B12)-binding domain
family: Cobalamin (vitamin B12)-binding domain
domain: Glutamate mutase, small subunit
species: Clostridium cochlearium [TaxId: 1494]

Probab=82.05  E-value=2.3  Score=35.80  Aligned_cols=86  Identities=8%  Similarity=-0.071  Sum_probs=59.8

Q ss_pred             cCHHHHHHHHHhcCCceEEEEeCCCCCCC--HHHHHHHHHhhC-CCCcEEEEecCC----C-HHHHHHHHHcCCcEEEeC
Q 043479            4 TRPVEALATVRIQRDIDLVVTDLHMPEMN--GIELQKEINEEF-THLPVMVMSSDD----R-ESVIMKALASGVAFYILK   75 (534)
Q Consensus         4 ss~~EALe~L~~~~~pDLVLLDi~mPdmd--GleLL~~Lr~~~-p~ipVIVLSs~~----d-~~~~~~AL~aGA~dyL~K   75 (534)
                      ...++.++.+.+ ..||+|.+-..+....  --++++.|++.. .++||++=-...    + .....+..+.|++.++..
T Consensus        41 ~p~e~iv~a~~~-~~~d~v~lS~~~~~~~~~~~~~~~~l~~~~~~~i~iivGG~~~~~~~~~~~~~~~l~~~Gv~~if~~  119 (137)
T d1ccwa_          41 SPQELFIKAAIE-TKADAILVSSLYGQGEIDCKGLRQKCDEAGLEGILLYVGGNIVVGKQHWPDVEKRFKDMGYDRVYAP  119 (137)
T ss_dssp             ECHHHHHHHHHH-HTCSEEEEEECSSTHHHHHTTHHHHHHHTTCTTCEEEEEESCSSSSCCHHHHHHHHHHTTCSEECCT
T ss_pred             cCHHHHHHHHHh-cCCCEEEEeeccccchHHHHHHHHHHHHhccCCCEEEEeCCcCCCccccHHHHHHHHHcCCCEEECC
Confidence            467888888887 7899999998887521  123556666543 467766443321    2 334555668899999988


Q ss_pred             CCChHHHHHHHHHHH
Q 043479           76 PLNPDDLKNVWQYAM   90 (534)
Q Consensus        76 P~s~eeL~~aI~~aL   90 (534)
                      ..+++++.+.+++.+
T Consensus       120 ~t~~~~~~~~l~~~l  134 (137)
T d1ccwa_         120 GTPPEVGIADLKKDL  134 (137)
T ss_dssp             TCCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHh
Confidence            899999999888766