Citrus Sinensis ID: 029986

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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----
Protein Sequence
MSPASSSVAVSDQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPFEESDDSYSVNQGNWRTSNRRKDEEEEAEKRDDTSTLKKPRFLVS
Secondary Structure (PSIPRED)
ccccccccccccccccccEEEEEEccHHHHHHHHHHHHHcccEEEEEccHHHHHHHHHHccccccEEEEEcccccccHHHHHHHHHccccccEEEEEcccccHHHHHHccccccEEEcccccHHHHHHHHHHHHHccccccccccccccccccccccccHHHHHHHcccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccEEEEEcccHHHHHHHHHHHHHcccEEEEEccHHHHHHHHHHHcccccEEEEEcccccccHHHHHHHHHHcccccEEEEEEccccccEEEEEEEccccEEEccccHHHHHHHHHHHHHHcccccccccccccccccccEEEEEcccEEEcccccccccccccEEEEc
Coil and Loop (DISEMBL)
mspasssvavsdqfpaglrvlvvdddpIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSkngydivisdvhmpdmdgfklheqvglemdlpvimmsvdgctqdvmKGVTHGAcnyllkpirIKELRNIWQHVaqqpkpfeesddsysvnqgnwrtsnrrkdeeeeaekrddtstlkkprflvs
Flexible Loop (DISEMBL)
mspasssvavsdqfpaglrvlvvDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQqpkpfeesddsysvnqgnwrtsnrrkdeeeeaekrddtstlkkprflvs
Low Complexity Region (SEG)
MSPASSSVAVSDQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPFEESDDSYSVNQGNWRTSNrrkdeeeeaekrddTSTLKKPRFLVS
Disordered region (IsUnstruct)
************QFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVA**************************************************
Disordered Region (DISOPRED)
*****************LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHV*******************************************KKPRFLVS
Disordered Region (DISEMBL)
**********SDQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQP***************************************KKPRFLVS
Disordered Region (DISPRO)
*************FPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKP**********NQGNWRTSNRRKDEEEEAEKRDDTSTLKKPRFLVS
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSPASSSVAVSDQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPFEESDDSYSVNQGNWRTSNRRKDEEEEAEKRDDTSTLKKPRFLVS
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	184	2.2.26 [Sep-21-2011]
Q9ZWJ9	664	Two-component response re	yes	no	0.983	0.272	0.545	5e-57
Q940D0	690	Two-component response re	no	no	0.956	0.255	0.550	2e-56
Q9FXD6	521	Two-component response re	no	no	0.663	0.234	0.754	1e-48
O49397	552	Two-component response re	no	no	0.945	0.315	0.527	2e-46
P62598	596	Two-component response re	no	no	0.869	0.268	0.532	7e-45
Q8L9Y3	382	Two-component response re	no	no	0.690	0.332	0.625	3e-43
Q9FGT7	635	Two-component response re	no	no	0.673	0.195	0.584	9e-34
Q9FJ16	292	Putative two-component re	no	no	0.684	0.431	0.420	2e-24
Q7Y0W5	341	Two-component response re	no	no	0.668	0.360	0.414	1e-22
Q7Y0W3	341	Two-component response re	N/A	no	0.668	0.360	0.414	1e-22

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

 Score =  220 bits (560), Expect = 5e-57,   Method: Compositional matrix adjust.
 Identities = 114/209 (54%), Positives = 142/209 (67%), Gaps = 28/209 (13%)

Query: 2   SPASSSVAVSDQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSK 61
           S  ++  + SD FPA LRVLVVDDDP  L ILE+ML  CLY VTKCNRAE AL +LR +K
Sbjct: 12  SGTAAGGSNSDPFPANLRVLVVDDDPTCLMILERMLMTCLYRVTKCNRAESALSLLRKNK 71

Query: 62  NGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPI 121
           NG+DIVISDVHMPDMDGFKL E VGLEMDLPVIMMS D     V+KGVTHGA +YL+KP+
Sbjct: 72  NGFDIVISDVHMPDMDGFKLLEHVGLEMDLPVIMMSADDSKSVVLKGVTHGAVDYLIKPV 131

Query: 122 RIKELRNIWQHVA--------------------------QQPKPFEESDDSYSVNQGNWR 155
           RI+ L+NIWQHV                           QQ    +  ++S SVN+GN R
Sbjct: 132 RIEALKNIWQHVVRKKRNEWNVSEHSGGSIEDTGGDRDRQQQHREDADNNSSSVNEGNGR 191

Query: 156 TSNRRKDEE--EEAEKRDDTSTLKKPRFL 182
           +S +RK+EE  ++ + ++D+S+LKKPR +
Sbjct: 192 SSRKRKEEEVDDQGDDKEDSSSLKKPRVV 220

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 =  218 bits (555), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 119/216 (55%), Positives = 145/216 (67%), Gaps = 40/216 (18%)

Query: 9   AVSDQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVI 68
            V + FP+GLRVLVVDDDP  L ILE+MLR CLYEVTKCNRAE+AL +LR +K+G+DIVI
Sbjct: 28  TVVEMFPSGLRVLVVDDDPTCLMILERMLRTCLYEVTKCNRAEMALSLLRKNKHGFDIVI 87

Query: 69  SDVHMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRN 128
           SDVHMPDMDGFKL E VGLEMDLPVIMMS D     V+KGVTHGA +YL+KP+R++ L+N
Sbjct: 88  SDVHMPDMDGFKLLEHVGLEMDLPVIMMSADDSKSVVLKGVTHGAVDYLIKPVRMEALKN 147

Query: 129 IWQHVAQQPK----------PFEES-------------------------DDSYSVNQG- 152
           IWQHV ++ +            EE+                         D+S SVN+G 
Sbjct: 148 IWQHVVRKRRSEWSVPEHSGSIEETGERQQQQHRGGGGGAAVSGGEDAVDDNSSSVNEGN 207

Query: 153 NWRTSNR-RKDEEEEAE---KRDDTSTLKKPRFLVS 184
           NWR+S+R RKDEE E +   K +D S LKKPR + S
Sbjct: 208 NWRSSSRKRKDEEGEEQGDDKDEDASNLKKPRVVWS 243

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 =  192 bits (487), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 92/122 (75%), Positives = 103/122 (84%)

Query: 15  PAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMP 74
           P GLRVLVVDDDP WL+ILEKML+KC YEVT C  A  AL +LR  K+GYDIVISDV+MP
Sbjct: 8   PVGLRVLVVDDDPTWLKILEKMLKKCSYEVTTCGLAREALRLLRERKDGYDIVISDVNMP 67

Query: 75  DMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVA 134
           DMDGFKL E VGLE+DLPVIMMSVDG T  VMKGV HGAC+YLLKPIR+KEL+ IWQHV 
Sbjct: 68  DMDGFKLLEHVGLELDLPVIMMSVDGETSRVMKGVQHGACDYLLKPIRMKELKIIWQHVL 127

Query: 135 QQ 136
           ++
Sbjct: 128 RK 129

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 =  184 bits (468), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 96/182 (52%), Positives = 126/182 (69%), Gaps = 8/182 (4%)

Query: 8   VAVSDQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIV 67
           + V DQFP G+RVL VDDD   LRIL+ +L++C Y VT  N+A+ AL++LR +KN +D+V
Sbjct: 7   IEVLDQFPVGMRVLAVDDDQTCLRILQTLLQRCQYHVTTTNQAQTALELLRENKNKFDLV 66

Query: 68  ISDVHMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           ISDV MPDMDGFKL E VGLEMDLPVIM+S     + VMKGV HGAC+YLLKP+RI+EL+
Sbjct: 67  ISDVDMPDMDGFKLLELVGLEMDLPVIMLSAHSDPKYVMKGVKHGACDYLLKPVRIEELK 126

Query: 128 NIWQHVAQQPKPFEESDDSYSVNQGNWRTSNRRKDEE-------EEAEKRDDTSTLKKPR 180
           NIWQHV ++    +++  + S   GN   +NR++ E+       E     DD +  KKPR
Sbjct: 127 NIWQHVVRK-SKLKKNKSNVSNGSGNCDKANRKRKEQYEEEEEEERGNDNDDPTAQKKPR 185

Query: 181 FL 182
            L
Sbjct: 186 VL 187

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 =  179 bits (455), Expect = 7e-45,   Method: Compositional matrix adjust.
 Identities = 90/169 (53%), Positives = 113/169 (66%), Gaps = 9/169 (5%)

Query: 12  DQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDV 71
           DQFP G+RVL VDDD   L+ILE +LR C Y VT  N+A+ AL++LR +KN +D+VISDV
Sbjct: 11  DQFPVGMRVLAVDDDQTCLKILESLLRHCQYHVTTTNQAQKALELLRENKNKFDLVISDV 70

Query: 72  HMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQ 131
            MPDMDGFKL E VGLEMDLPVIM+S     + VMKGVTHGAC+YLLKP+RI+EL+NIWQ
Sbjct: 71  DMPDMDGFKLLELVGLEMDLPVIMLSAHSDPKYVMKGVTHGACDYLLKPVRIEELKNIWQ 130

Query: 132 HVAQQPKPFEESDDSYSVNQGNWRTSNRRKDEEEEAEKRDDTSTLKKPR 180
           HV +           +  N+G+    ++R     E     D +  K  R
Sbjct: 131 HVVR---------SRFDKNRGSNNNGDKRDGSGNEGVGNSDQNNGKGNR 170

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 =  174 bits (441), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 80/128 (62%), Positives = 106/128 (82%), Gaps = 1/128 (0%)

Query: 10  VSDQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVIS 69
           ++DQFP+GLR+LVVDDD   L ILEKML + +Y+VT C++A++AL +LR  K+ +D+V+S
Sbjct: 3   INDQFPSGLRILVVDDDTSCLFILEKMLLRLMYQVTICSQADVALTILRERKDSFDLVLS 62

Query: 70  DVHMPDMDGFKLHEQVG-LEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRN 128
           DVHMP M+G+ L +QVG LEMDLPVIMMSVDG T  VM G+ HGAC+YL+KPIR +EL+N
Sbjct: 63  DVHMPGMNGYNLLQQVGLLEMDLPVIMMSVDGRTTTVMTGINHGACDYLIKPIRPEELKN 122

Query: 129 IWQHVAQQ 136
           IWQHV ++
Sbjct: 123 IWQHVVRR 130

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 =  142 bits (359), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 73/125 (58%), Positives = 94/125 (75%), Gaps = 1/125 (0%)

Query: 12  DQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDV 71
           D+FP G+RVL VDD+P  LR LE++L +C Y VTK   +  AL+MLR + N +D+VISDV
Sbjct: 12  DKFPVGMRVLAVDDNPTCLRKLEELLLRCKYHVTKTMESRKALEMLRENSNMFDLVISDV 71

Query: 72  HMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQ 131
            MPD DGFKL E +GLEMDLPVIM+S       VMKG+ HGAC+YL+KP+ +KEL+NIW 
Sbjct: 72  EMPDTDGFKLLE-IGLEMDLPVIMLSAHSDYDSVMKGIIHGACDYLVKPVGLKELQNIWH 130

Query: 132 HVAQQ 136
           HV ++
Sbjct: 131 HVVKK 135

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|Q9FJ16|APRR4_ARATH Putative two-component response regulator-like APRR4 OS=Arabidopsis thaliana GN=APRR4 PE=3 SV=1

 Score =  111 bits (278), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 53/126 (42%), Positives = 84/126 (66%)

Query: 11  SDQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISD 70
           S  FP GLRVLV D+DP +L ILE+ L+K  Y+VT CN    A+  LR  +N +D+ +  
Sbjct: 35  SSNFPEGLRVLVFDEDPSYLLILERHLQKFQYQVTICNEVNKAMHTLRNHRNRFDLAMIQ 94

Query: 71  VHMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIW 130
           V+  + D F+   ++G EMDLP+I++S D   + V K + +GA +YL+KPIR ++LR ++
Sbjct: 95  VNNAEGDIFRFLSEIGSEMDLPIIIISEDDSVKSVKKWMINGAADYLIKPIRPEDLRIVF 154

Query: 131 QHVAQQ 136
           +H+ ++
Sbjct: 155 KHLVKK 160

Transcriptional activator that binds specifically to the DNA sequence 5'-[AG]GATT-3'.

Arabidopsis thaliana (taxid: 3702)

>sp|Q7Y0W5|EHD1_ORYSJ Two-component response regulator EHD1 OS=Oryza sativa subsp. japonica GN=EHD1 PE=1 SV=1

 Score =  106 bits (264), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 51/123 (41%), Positives = 78/123 (63%)

Query: 14  FPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHM 73
           +P GLRVLV+DDD  +L ++E +L KC Y+VT       A+  +  +    D+VISD   
Sbjct: 7   WPYGLRVLVIDDDCSYLSVMEDLLLKCSYKVTTYKNVREAVPFILDNPQIVDLVISDAFF 66

Query: 74  PDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHV 133
           P  DG  + ++V  +  +P ++M+  G T  VMK V +GA ++LLKP+RI+EL NIWQH+
Sbjct: 67  PTEDGLLILQEVTSKFGIPTVIMASSGDTNTVMKYVANGAFDFLLKPVRIEELSNIWQHI 126

Query: 134 AQQ 136
            ++
Sbjct: 127 FRK 129

Transcriptional activator that acts as floral inducer to promote short-day (SD) flowering pathway. Activates HD3A and other FT-like genes independently from HD1. May also activate MADS-box transcription factors involved in flowering regulation.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q7Y0W3|EHD1_ORYSI Two-component response regulator EHD1 OS=Oryza sativa subsp. indica PE=2 SV=1

 Score =  106 bits (264), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 51/123 (41%), Positives = 78/123 (63%)

Query: 14  FPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHM 73
           +P GLRVLV+DDD  +L ++E +L KC Y+VT       A+  +  +    D+VISD   
Sbjct: 7   WPYGLRVLVIDDDCSYLSVMEDLLLKCSYKVTTYKNVREAVPFILDNPQIVDLVISDAFF 66

Query: 74  PDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHV 133
           P  DG  + ++V  +  +P ++M+  G T  VMK V +GA ++LLKP+RI+EL NIWQH+
Sbjct: 67  PTEDGLLILQEVTSKFGIPTVIMASSGDTNTVMKYVANGAFDFLLKPVRIEELSNIWQHI 126

Query: 134 AQQ 136
            ++
Sbjct: 127 FRK 129

Transcriptional activator that acts as floral inducer to promote short-day (SD) flowering pathway. Activates Hd3a and other FT-like genes independently from Hd1. May also activate MADS-box transcription factors involved in flowering regulation.

Oryza sativa subsp. indica (taxid: 39946)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	184
255556280	682	sensor histidine kinase, putative [Ricin	1.0	0.269	0.661	3e-65
313184318	674	putative type-b response regulator (sens	1.0	0.272	0.652	5e-64
449464732	673	PREDICTED: two-component response regula	0.945	0.258	0.634	2e-63
449432892	660	PREDICTED: two-component response regula	1.0	0.278	0.612	3e-63
33330870	643	type-B response regulator [Catharanthus	0.978	0.279	0.648	4e-63
224106962	634	type-b response regulator [Populus trich	0.994	0.288	0.668	7e-63
359477139	681	PREDICTED: two-component response regula	1.0	0.270	0.647	9e-63
298103716	670	putative B-type response regulator 13 [P	0.994	0.273	0.668	1e-62
296083291	533	unnamed protein product [Vitis vinifera]	1.0	0.345	0.647	2e-62
356521815	679	PREDICTED: two-component response regula	0.945	0.256	0.675	4e-62

>gi|255556280|ref|XP_002519174.1| sensor histidine kinase, putative [Ricinus communis] gi|223541489|gb|EEF43038.1| sensor histidine kinase, putative [Ricinus communis]

 Score =  253 bits (645), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 139/210 (66%), Positives = 155/210 (73%), Gaps = 26/210 (12%)

Query: 1   MSPASSSVA------VSDQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIAL 54
           MS ASSSVA      V DQFPAGLRVLVVDDDP  L ILEKMLR CLYEVTKCNRAE AL
Sbjct: 10  MSTASSSVAWKAGEVVPDQFPAGLRVLVVDDDPTCLMILEKMLRTCLYEVTKCNRAETAL 69

Query: 55  DMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGAC 114
            +LR +KNGYDIVISDVHMPDMDGFKL E +GLEMDLPVIMMS D     VMKGVTHGAC
Sbjct: 70  SLLRENKNGYDIVISDVHMPDMDGFKLLEHIGLEMDLPVIMMSADEAKSVVMKGVTHGAC 129

Query: 115 NYLLKPIRIKELRNIWQHVA--------------------QQPKPFEESDDSYSVNQGNW 154
           +YL+KP+RI+ L+NIWQHV                     +QPK  E++D S S N+GNW
Sbjct: 130 DYLIKPVRIEALKNIWQHVVRKKRNEWKDLEQSGSVEEGDRQPKQSEDADYSSSANEGNW 189

Query: 155 RTSNRRKDEEEEAEKRDDTSTLKKPRFLVS 184
           R S +RKDEEEE ++RDDTSTLKKPR + S
Sbjct: 190 RNSKKRKDEEEEGDERDDTSTLKKPRVVWS 219

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|313184318|emb|CBL94183.1| putative type-b response regulator (sensor histidine kinase) [Malus x domestica]

 Score =  249 bits (635), Expect = 5e-64,   Method: Compositional matrix adjust.
 Identities = 137/210 (65%), Positives = 156/210 (74%), Gaps = 26/210 (12%)

Query: 1   MSPASSSVA------VSDQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIAL 54
           MS ASSS A      V+DQFPAGLRVLVVDDDP  L ILE+MLR CLYEVTKCNRAEIAL
Sbjct: 10  MSTASSSGAWKSGDVVTDQFPAGLRVLVVDDDPTCLMILERMLRTCLYEVTKCNRAEIAL 69

Query: 55  DMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGAC 114
            +LR +KNG+DIVISDVHMPDMDGFKL EQVGLEMDLPVIMMS D     VMKGVTHGAC
Sbjct: 70  SLLRENKNGFDIVISDVHMPDMDGFKLLEQVGLEMDLPVIMMSADDGQSVVMKGVTHGAC 129

Query: 115 NYLLKPIRIKELRNIWQHVA--------------------QQPKPFEESDDSYSVNQGNW 154
           +YL+KP+RI+ L+NIWQHV                     +Q KP E++D S S N+G W
Sbjct: 130 DYLIKPVRIEALKNIWQHVVRKKKNEWKDVEQSGSVEEGDRQQKPSEDADYSSSANEGTW 189

Query: 155 RTSNRRKDEEEEAEKRDDTSTLKKPRFLVS 184
           + S RRKDEEEE ++RDD+STLKKPR + S
Sbjct: 190 KNSKRRKDEEEETDERDDSSTLKKPRVVWS 219

Source: Malus x domestica

Species: Malus x domestica

Genus: Malus

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449464732|ref|XP_004150083.1| PREDICTED: two-component response regulator ARR2-like [Cucumis sativus] gi|449501499|ref|XP_004161384.1| PREDICTED: two-component response regulator ARR2-like [Cucumis sativus]

 Score =  247 bits (630), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 123/194 (63%), Positives = 143/194 (73%), Gaps = 20/194 (10%)

Query: 11  SDQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISD 70
           SDQFPAGLRVLVVDDDP  L+ILEKML+ C Y VTKCNRAEIAL MLR +KNG+DIV+SD
Sbjct: 30  SDQFPAGLRVLVVDDDPTCLKILEKMLQNCCYAVTKCNRAEIALSMLRENKNGFDIVLSD 89

Query: 71  VHMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIW 130
           VHMPDMDGFKL EQVGLEMDLPVIMMS D     VMKGV HGAC+YL+KP+RI+ LRN+W
Sbjct: 90  VHMPDMDGFKLLEQVGLEMDLPVIMMSADDGKNVVMKGVIHGACDYLIKPVRIEALRNLW 149

Query: 131 QHVAQQPKP--------------------FEESDDSYSVNQGNWRTSNRRKDEEEEAEKR 170
           QHV ++ K                      E ++ S S  +G+W +S RR+D EEE E+R
Sbjct: 150 QHVVRKRKTEWKDLEQSGSVDEGDREQNLSEGANYSSSAYEGSWNSSKRRRDAEEEPEER 209

Query: 171 DDTSTLKKPRFLVS 184
           DDTSTLKKPR + S
Sbjct: 210 DDTSTLKKPRVVWS 223

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449432892|ref|XP_004134232.1| PREDICTED: two-component response regulator ARR2-like [Cucumis sativus] gi|449503838|ref|XP_004162202.1| PREDICTED: two-component response regulator ARR2-like [Cucumis sativus]

 Score =  246 bits (628), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 128/209 (61%), Positives = 151/209 (72%), Gaps = 25/209 (11%)

Query: 1   MSPASSSV------AVSDQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIAL 54
           MS ASSS       AV DQFPAGLRVLVVDDDP  L ILEKMLR C Y+VT C+RAE AL
Sbjct: 1   MSTASSSSVRKAGEAVPDQFPAGLRVLVVDDDPTCLMILEKMLRICRYDVTNCSRAEDAL 60

Query: 55  DMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGAC 114
            +LR +KNG+DIV+SDVHMPDMDGFKL E +GLEMDLPVIMMSVD     VMKGVTHGAC
Sbjct: 61  SLLRQNKNGFDIVLSDVHMPDMDGFKLLEYIGLEMDLPVIMMSVDDGKNVVMKGVTHGAC 120

Query: 115 NYLLKPIRIKELRNIWQHVA-------------------QQPKPFEESDDSYSVNQGNWR 155
           +YL+KP+R++ L+NIWQHV                    +Q K  E++D S S N+G+WR
Sbjct: 121 DYLIKPVRMEALKNIWQHVVRKRKNEWKDLEQTCVDDVDRQQKTNEDADYSSSANEGSWR 180

Query: 156 TSNRRKDEEEEAEKRDDTSTLKKPRFLVS 184
            S RRKD+ E+ E+RDD+STLKKPR + S
Sbjct: 181 NSKRRKDDVEDPEERDDSSTLKKPRVVWS 209

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|33330870|gb|AAQ10678.1| type-B response regulator [Catharanthus roseus]

 Score =  246 bits (627), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 131/202 (64%), Positives = 151/202 (74%), Gaps = 22/202 (10%)

Query: 5   SSSVAVSDQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGY 64
           S    VSDQFPAGLRVLVVDDDP  LRILEKML+ CLYEVTKCNRAEIAL +LR ++NGY
Sbjct: 23  SGGDGVSDQFPAGLRVLVVDDDPTCLRILEKMLKNCLYEVTKCNRAEIALKLLRDNRNGY 82

Query: 65  DIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIK 124
           DIVISDVHMPDMDGFKL EQVGLEMDLPVIMMS D     VMKGVTHGAC+YL+KP+RI+
Sbjct: 83  DIVISDVHMPDMDGFKLLEQVGLEMDLPVIMMSADDSKNVVMKGVTHGACDYLIKPVRIE 142

Query: 125 ELRNIWQHVA----------------------QQPKPFEESDDSYSVNQGNWRTSNRRKD 162
            L+NIWQHV                       +Q KP E+ D S S N+GNW+ S +RKD
Sbjct: 143 ALKNIWQHVVRKGKHEWKEKDYEQSGSVEDGERQQKPNEDVDYSSSANEGNWKNSKKRKD 202

Query: 163 EEEEAEKRDDTSTLKKPRFLVS 184
           +EE+ E++DD+STLKKPR + S
Sbjct: 203 DEEDQEEKDDSSTLKKPRVVWS 224

Source: Catharanthus roseus

Species: Catharanthus roseus

Genus: Catharanthus

Family: Apocynaceae

Order: Gentianales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224106962|ref|XP_002314325.1| type-b response regulator [Populus trichocarpa] gi|222863365|gb|EEF00496.1| type-b response regulator [Populus trichocarpa]

 Score =  245 bits (625), Expect = 7e-63,   Method: Compositional matrix adjust.
 Identities = 137/205 (66%), Positives = 154/205 (75%), Gaps = 22/205 (10%)

Query: 1   MSPASSSVAVSDQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMS 60
           MS ASS   VSDQFPAGLRVLVVDDDP  L ILEKMLR CLYEVTKCNRAEIAL +LR +
Sbjct: 11  MSTASSG-GVSDQFPAGLRVLVVDDDPTCLVILEKMLRTCLYEVTKCNRAEIALSLLREN 69

Query: 61  KNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKP 120
           +NGYDIVISDVHMPDMDGFKL E +GLEMDLPVIMMS D     VMKGVTHGAC+YL+KP
Sbjct: 70  RNGYDIVISDVHMPDMDGFKLLELIGLEMDLPVIMMSADDGKNVVMKGVTHGACDYLIKP 129

Query: 121 IRIKELRNIWQHVA---------------------QQPKPFEESDDSYSVNQGNWRTSNR 159
           IRI+ L+NIWQHV                      +Q K  E++D S S N+G+W+ S R
Sbjct: 130 IRIEALKNIWQHVVRKRKNEWKDLEQSGSVEEGGDRQQKQSEDADYSSSANEGSWKNSKR 189

Query: 160 RKDEEEEAEKRDDTSTLKKPRFLVS 184
           RKDEEEEA++RDDTSTLKKPR + S
Sbjct: 190 RKDEEEEADERDDTSTLKKPRVVWS 214

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359477139|ref|XP_002275142.2| PREDICTED: two-component response regulator ARR1-like [Vitis vinifera]

 Score =  244 bits (624), Expect = 9e-63,   Method: Compositional matrix adjust.
 Identities = 136/210 (64%), Positives = 154/210 (73%), Gaps = 26/210 (12%)

Query: 1   MSPASSSVA------VSDQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIAL 54
           MS ASSS A      V DQFPAGLRVLVVDDDP  L ILEKMLR CLYEVTKCNRAE AL
Sbjct: 10  MSTASSSGAWKAGDVVPDQFPAGLRVLVVDDDPTCLMILEKMLRTCLYEVTKCNRAETAL 69

Query: 55  DMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGAC 114
            +LR +K+G+DIVISDVHMPDMDGFKL E +GLEMDLPVIMMS D     VMKGVTHGAC
Sbjct: 70  SLLRGNKSGFDIVISDVHMPDMDGFKLLEHIGLEMDLPVIMMSADDGKHVVMKGVTHGAC 129

Query: 115 NYLLKPIRIKELRNIWQHVA--------------------QQPKPFEESDDSYSVNQGNW 154
           +YL+KP+RI+ L+NIWQHV                     +Q KP E+ D S S N+GNW
Sbjct: 130 DYLIKPVRIEALKNIWQHVVRKRKNEWKDLEQSGSVEDGDRQQKPSEDVDYSSSANEGNW 189

Query: 155 RTSNRRKDEEEEAEKRDDTSTLKKPRFLVS 184
           + S RRKDEE++AE+RDDTSTLKKPR + S
Sbjct: 190 KNSKRRKDEEDDAEERDDTSTLKKPRVVWS 219

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|298103716|emb|CBM42559.1| putative B-type response regulator 13 [Populus x canadensis]

 Score =  244 bits (623), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 137/205 (66%), Positives = 156/205 (76%), Gaps = 22/205 (10%)

Query: 1   MSPASSSVAVSDQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMS 60
           MS ASS   VSDQFPAGLRVLVVDDDP  L ILEKMLR CLYEVTKCNRAEIAL +LR +
Sbjct: 1   MSTASSG-GVSDQFPAGLRVLVVDDDPTCLVILEKMLRTCLYEVTKCNRAEIALSLLREN 59

Query: 61  KNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKP 120
           +NGYDIVISDVHMPDMDGFKL E +GLEMDLPVIMMS D     VMKGVTHGAC+YL+KP
Sbjct: 60  RNGYDIVISDVHMPDMDGFKLLELIGLEMDLPVIMMSADDGKNVVMKGVTHGACDYLIKP 119

Query: 121 IRIKELRNIWQHVAQQPK------------------PFEESDD---SYSVNQGNWRTSNR 159
           IRI+ L+NIWQHV ++ K                  P ++S+D   S S N+G+W+ S R
Sbjct: 120 IRIEALKNIWQHVVRKRKNEWKDLEQSGSVEEGGDRPQKQSEDADYSSSANEGSWKNSKR 179

Query: 160 RKDEEEEAEKRDDTSTLKKPRFLVS 184
           RKDEEEEA++RDDTSTLKKPR + S
Sbjct: 180 RKDEEEEADERDDTSTLKKPRVVWS 204

Source: Populus x canadensis

Species: Populus x canadensis

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296083291|emb|CBI22927.3| unnamed protein product [Vitis vinifera]

 Score =  243 bits (620), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 136/210 (64%), Positives = 154/210 (73%), Gaps = 26/210 (12%)

Query: 1   MSPASSSVA------VSDQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIAL 54
           MS ASSS A      V DQFPAGLRVLVVDDDP  L ILEKMLR CLYEVTKCNRAE AL
Sbjct: 10  MSTASSSGAWKAGDVVPDQFPAGLRVLVVDDDPTCLMILEKMLRTCLYEVTKCNRAETAL 69

Query: 55  DMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGAC 114
            +LR +K+G+DIVISDVHMPDMDGFKL E +GLEMDLPVIMMS D     VMKGVTHGAC
Sbjct: 70  SLLRGNKSGFDIVISDVHMPDMDGFKLLEHIGLEMDLPVIMMSADDGKHVVMKGVTHGAC 129

Query: 115 NYLLKPIRIKELRNIWQHVA--------------------QQPKPFEESDDSYSVNQGNW 154
           +YL+KP+RI+ L+NIWQHV                     +Q KP E+ D S S N+GNW
Sbjct: 130 DYLIKPVRIEALKNIWQHVVRKRKNEWKDLEQSGSVEDGDRQQKPSEDVDYSSSANEGNW 189

Query: 155 RTSNRRKDEEEEAEKRDDTSTLKKPRFLVS 184
           + S RRKDEE++AE+RDDTSTLKKPR + S
Sbjct: 190 KNSKRRKDEEDDAEERDDTSTLKKPRVVWS 219

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356521815|ref|XP_003529546.1| PREDICTED: two-component response regulator ARR2-like [Glycine max]

 Score =  242 bits (618), Expect = 4e-62,   Method: Compositional matrix adjust.
 Identities = 131/194 (67%), Positives = 148/194 (76%), Gaps = 20/194 (10%)

Query: 9   AVSDQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVI 68
           AVSDQFPAGLRVLVVDDDP  L ILEKMLR CLYEVTKCNRAE AL +LR +KNG+DIVI
Sbjct: 24  AVSDQFPAGLRVLVVDDDPTCLMILEKMLRTCLYEVTKCNRAETALSLLRENKNGFDIVI 83

Query: 69  SDVHMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRN 128
           SDVHMPDMDGFKL E +GLEMDLPVIMMS D     VMKGVTHGAC+YL+KP+RI+ L+N
Sbjct: 84  SDVHMPDMDGFKLLEHIGLEMDLPVIMMSADDGKSVVMKGVTHGACDYLIKPVRIEALKN 143

Query: 129 IWQHVA--------------------QQPKPFEESDDSYSVNQGNWRTSNRRKDEEEEAE 168
           IWQHV                     +QPK  +E+D S S N+G+WR S +R+DEEEEAE
Sbjct: 144 IWQHVVRKRKNEWKDAEQSGSAEEGDRQPKASDEADYSSSANEGSWRNSKKRRDEEEEAE 203

Query: 169 KRDDTSTLKKPRFL 182
            RDDTSTLKKPR +
Sbjct: 204 DRDDTSTLKKPRVV 217

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	184
TAIR|locus:2093668	690	RR1 "response regulator 1" [Ar	0.690	0.184	0.716	7.7e-50
TAIR|locus:2130095	664	RR2 "response regulator 2" [Ar	0.695	0.192	0.718	1.3e-49
TAIR|locus:2008585	521	ARR11 "response regulator 11"	0.701	0.247	0.725	2.7e-45
TAIR|locus:2116587	552	RR10 "response regulator 10" [	0.815	0.271	0.576	5.2e-42
TAIR|locus:2040194	596	RR12 "response regulator 12" [	0.673	0.208	0.669	7.5e-41
TAIR|locus:2065398	382	RR14 "response regulator 14" [	0.690	0.332	0.625	4.2e-40
TAIR|locus:2155954	292	APRR4 "pseudo-response regulat	0.684	0.431	0.420	1.4e-23
UNIPROTKB|Q7Y0W3	341	Q7Y0W3 "Two-component response	0.652	0.351	0.425	3.4e-22
UNIPROTKB|Q7Y0W5	341	EHD1 "Two-component response r	0.652	0.351	0.425	3.4e-22
TAIR|locus:2044376	468	PRR9 "pseudo-response regulato	0.625	0.245	0.366	1e-15

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

 Score = 484 (175.4 bits), Expect = 7.7e-50, Sum P(2) = 7.7e-50
 Identities = 91/127 (71%), Positives = 108/127 (85%)

Query:    10 VSDQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVIS 69
             V + FP+GLRVLVVDDDP  L ILE+MLR CLYEVTKCNRAE+AL +LR +K+G+DIVIS
Sbjct:    29 VVEMFPSGLRVLVVDDDPTCLMILERMLRTCLYEVTKCNRAEMALSLLRKNKHGFDIVIS 88

Query:    70 DVHMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNI 129
             DVHMPDMDGFKL E VGLEMDLPVIMMS D     V+KGVTHGA +YL+KP+R++ L+NI
Sbjct:    89 DVHMPDMDGFKLLEHVGLEMDLPVIMMSADDSKSVVLKGVTHGAVDYLIKPVRMEALKNI 148

Query:   130 WQHVAQQ 136
             WQHV ++
Sbjct:   149 WQHVVRK 155

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

 Score = 481 (174.4 bits), Expect = 1.3e-49, Sum P(2) = 1.3e-49
 Identities = 92/128 (71%), Positives = 105/128 (82%)

Query:    11 SDQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISD 70
             SD FPA LRVLVVDDDP  L ILE+ML  CLY VTKCNRAE AL +LR +KNG+DIVISD
Sbjct:    21 SDPFPANLRVLVVDDDPTCLMILERMLMTCLYRVTKCNRAESALSLLRKNKNGFDIVISD 80

Query:    71 VHMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIW 130
             VHMPDMDGFKL E VGLEMDLPVIMMS D     V+KGVTHGA +YL+KP+RI+ L+NIW
Sbjct:    81 VHMPDMDGFKLLEHVGLEMDLPVIMMSADDSKSVVLKGVTHGAVDYLIKPVRIEALKNIW 140

Query:   131 QHVAQQPK 138
             QHV ++ +
Sbjct:   141 QHVVRKKR 148

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

 Score = 476 (172.6 bits), Expect = 2.7e-45, P = 2.7e-45
 Identities = 95/131 (72%), Positives = 106/131 (80%)

Query:    15 PAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMP 74
             P GLRVLVVDDDP WL+ILEKML+KC YEVT C  A  AL +LR  K+GYDIVISDV+MP
Sbjct:     8 PVGLRVLVVDDDPTWLKILEKMLKKCSYEVTTCGLAREALRLLRERKDGYDIVISDVNMP 67

Query:    75 DMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVA 134
             DMDGFKL E VGLE+DLPVIMMSVDG T  VMKGV HGAC+YLLKPIR+KEL+ IWQHV 
Sbjct:    68 DMDGFKLLEHVGLELDLPVIMMSVDGETSRVMKGVQHGACDYLLKPIRMKELKIIWQHVL 127

Query:   135 QQPKPFEESDD 145
             +  K  +E  D
Sbjct:   128 R--KKLQEVRD 136

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 = 445 (161.7 bits), Expect = 5.2e-42, P = 5.2e-42
 Identities = 87/151 (57%), Positives = 113/151 (74%)

Query:     8 VAVSDQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIV 67
             + V DQFP G+RVL VDDD   LRIL+ +L++C Y VT  N+A+ AL++LR +KN +D+V
Sbjct:     7 IEVLDQFPVGMRVLAVDDDQTCLRILQTLLQRCQYHVTTTNQAQTALELLRENKNKFDLV 66

Query:    68 ISDVHMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
             ISDV MPDMDGFKL E VGLEMDLPVIM+S     + VMKGV HGAC+YLLKP+RI+EL+
Sbjct:    67 ISDVDMPDMDGFKLLELVGLEMDLPVIMLSAHSDPKYVMKGVKHGACDYLLKPVRIEELK 126

Query:   128 NIWQHVAQQPKPFEESDDSYSVNQGNWRTSN 158
             NIWQHV ++ K  +++  + S   GN   +N
Sbjct:   127 NIWQHVVRKSK-LKKNKSNVSNGSGNCDKAN 156

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 = 434 (157.8 bits), Expect = 7.5e-41, P = 7.5e-41
 Identities = 83/124 (66%), Positives = 100/124 (80%)

Query:    12 DQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDV 71
             DQFP G+RVL VDDD   L+ILE +LR C Y VT  N+A+ AL++LR +KN +D+VISDV
Sbjct:    11 DQFPVGMRVLAVDDDQTCLKILESLLRHCQYHVTTTNQAQKALELLRENKNKFDLVISDV 70

Query:    72 HMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQ 131
              MPDMDGFKL E VGLEMDLPVIM+S     + VMKGVTHGAC+YLLKP+RI+EL+NIWQ
Sbjct:    71 DMPDMDGFKLLELVGLEMDLPVIMLSAHSDPKYVMKGVTHGACDYLLKPVRIEELKNIWQ 130

Query:   132 HVAQ 135
             HV +
Sbjct:   131 HVVR 134

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

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

 Score = 427 (155.4 bits), Expect = 4.2e-40, P = 4.2e-40
 Identities = 80/128 (62%), Positives = 106/128 (82%)

Query:    10 VSDQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVIS 69
             ++DQFP+GLR+LVVDDD   L ILEKML + +Y+VT C++A++AL +LR  K+ +D+V+S
Sbjct:     3 INDQFPSGLRILVVDDDTSCLFILEKMLLRLMYQVTICSQADVALTILRERKDSFDLVLS 62

Query:    70 DVHMPDMDGFKLHEQVGL-EMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRN 128
             DVHMP M+G+ L +QVGL EMDLPVIMMSVDG T  VM G+ HGAC+YL+KPIR +EL+N
Sbjct:    63 DVHMPGMNGYNLLQQVGLLEMDLPVIMMSVDGRTTTVMTGINHGACDYLIKPIRPEELKN 122

Query:   129 IWQHVAQQ 136
             IWQHV ++
Sbjct:   123 IWQHVVRR 130

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

 Score = 271 (100.5 bits), Expect = 1.4e-23, P = 1.4e-23
 Identities = 53/126 (42%), Positives = 84/126 (66%)

Query:    11 SDQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISD 70
             S  FP GLRVLV D+DP +L ILE+ L+K  Y+VT CN    A+  LR  +N +D+ +  
Sbjct:    35 SSNFPEGLRVLVFDEDPSYLLILERHLQKFQYQVTICNEVNKAMHTLRNHRNRFDLAMIQ 94

Query:    71 VHMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIW 130
             V+  + D F+   ++G EMDLP+I++S D   + V K + +GA +YL+KPIR ++LR ++
Sbjct:    95 VNNAEGDIFRFLSEIGSEMDLPIIIISEDDSVKSVKKWMINGAADYLIKPIRPEDLRIVF 154

Query:   131 QHVAQQ 136
             +H+ ++
Sbjct:   155 KHLVKK 160

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

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

 Score = 258 (95.9 bits), Expect = 3.4e-22, P = 3.4e-22
 Identities = 51/120 (42%), Positives = 76/120 (63%)

Query:    14 FPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHM 73
             +P GLRVLV+DDD  +L ++E +L KC Y+VT       A+  +  +    D+VISD   
Sbjct:     7 WPYGLRVLVIDDDCSYLSVMEDLLLKCSYKVTTYKNVREAVPFILDNPQIVDLVISDAFF 66

Query:    74 PDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHV 133
             P  DG  + ++V  +  +P ++M+  G T  VMK V +GA ++LLKP+RI+EL NIWQH+
Sbjct:    67 PTEDGLLILQEVTSKFGIPTVIMASSGDTNTVMKYVANGAFDFLLKPVRIEELSNIWQHI 126

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 = 258 (95.9 bits), Expect = 3.4e-22, P = 3.4e-22
 Identities = 51/120 (42%), Positives = 76/120 (63%)

Query:    14 FPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHM 73
             +P GLRVLV+DDD  +L ++E +L KC Y+VT       A+  +  +    D+VISD   
Sbjct:     7 WPYGLRVLVIDDDCSYLSVMEDLLLKCSYKVTTYKNVREAVPFILDNPQIVDLVISDAFF 66

Query:    74 PDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHV 133
             P  DG  + ++V  +  +P ++M+  G T  VMK V +GA ++LLKP+RI+EL NIWQH+
Sbjct:    67 PTEDGLLILQEVTSKFGIPTVIMASSGDTNTVMKYVANGAFDFLLKPVRIEELSNIWQHI 126

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

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

 Score = 204 (76.9 bits), Expect = 1.0e-15, P = 1.0e-15
 Identities = 44/120 (36%), Positives = 74/120 (61%)

Query:    18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMD 77
             LRVL+V+ D    +I+  +LRKC Y+V   +    A ++L+   +  D++++++ +P + 
Sbjct:    37 LRVLLVESDYSTRQIITALLRKCCYKVVAVSDGLAAWEVLKEKSHNIDLILTELDLPSIS 96

Query:    78 GFKLHEQVGLEMD----LPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHV 133
             GF L   V +E +    +PVIMMS     + V+K +  GA +YL+KP+R  EL+N+WQHV
Sbjct:    97 GFALLALV-MEHEACKNIPVIMMSSQDSIKMVLKCMLRGAADYLIKPMRKNELKNLWQHV 155

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

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

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0005515 "protein binding" evidence=IPI

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

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

GO:0003677 "DNA binding" evidence=IPI

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	estExt_Genewise1_v1.C_LG_X3573	type-b response regulator (678 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	PtRR11	type-a response regulator (134 aa)							•		0.501
	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	184
cd00156	113	cd00156, REC, Signal receiver domain; originally t	9e-25
pfam00072	111	pfam00072, Response_reg, Response regulator receiv	1e-20
COG2204	464	COG2204, AtoC, Response regulator containing CheY-	4e-20
COG0784	130	COG0784, CheY, FOG: CheY-like receiver [Signal tra	8e-20
COG0745	229	COG0745, OmpR, Response regulators consisting of a	8e-20
CHL00148	240	CHL00148, orf27, Ycf27; Reviewed	3e-15
COG3706	435	COG3706, PleD, Response regulator containing a Che	5e-15
TIGR01818	463	TIGR01818, ntrC, nitrogen regulation protein NR(I)	7e-14
COG3437	360	COG3437, COG3437, Response regulator containing a	1e-13
PRK09581	457	PRK09581, pleD, response regulator PleD; Reviewed	3e-13
PRK10841	924	PRK10841, PRK10841, hybrid sensory kinase in two-c	7e-13
smart00448	55	smart00448, REC, cheY-homologous receiver domain	3e-12
COG2197	211	COG2197, CitB, Response regulator containing a Che	2e-11
PRK10610	129	PRK10610, PRK10610, chemotaxis regulatory protein	3e-11
PRK15115	444	PRK15115, PRK15115, response regulator GlrR; Provi	5e-11
COG4753	475	COG4753, COG4753, Response regulator containing Ch	1e-10
COG3947	361	COG3947, COG3947, Response regulator containing Ch	2e-10
TIGR02956	968	TIGR02956, TMAO_torS, TMAO reductase sytem sensor	2e-10
PRK10365	441	PRK10365, PRK10365, transcriptional regulatory pro	2e-10
PRK11361	457	PRK11361, PRK11361, acetoacetate metabolism regula	2e-09
PRK15479	221	PRK15479, PRK15479, transcriptional regulatory pro	2e-09
TIGR01387	218	TIGR01387, cztR_silR_copR, heavy metal response re	3e-09
PRK10923	469	PRK10923, glnG, nitrogen regulation protein NR(I);	4e-09
PLN03029	222	PLN03029, PLN03029, type-a response regulator prot	6e-09
PRK15347	921	PRK15347, PRK15347, two component system sensor ki	6e-09
TIGR02154	226	TIGR02154, PhoB, phosphate regulon transcriptional	1e-08
PRK09959	1197	PRK09959, PRK09959, hybrid sensory histidine kinas	2e-08
PRK11083	228	PRK11083, PRK11083, DNA-binding response regulator	4e-08
COG4565	224	COG4565, CitB, Response regulator of citrate/malat	5e-08
PRK10955	232	PRK10955, PRK10955, DNA-binding transcriptional re	5e-08
PRK09581	457	PRK09581, pleD, response regulator PleD; Reviewed	7e-08
PRK09468	239	PRK09468, ompR, osmolarity response regulator; Pro	2e-07
PRK09390	202	PRK09390, fixJ, response regulator FixJ; Provision	1e-06
COG4566	202	COG4566, TtrR, Response regulator [Signal transduc	2e-06
PRK10643	222	PRK10643, PRK10643, DNA-binding transcriptional re	3e-06
PRK11107	919	PRK11107, PRK11107, hybrid sensory histidine kinas	5e-06
PRK11517	223	PRK11517, PRK11517, transcriptional regulatory pro	7e-06
PRK10710	240	PRK10710, PRK10710, DNA-binding transcriptional re	1e-05
COG4567	182	COG4567, COG4567, Response regulator consisting of	1e-05
PRK09836	227	PRK09836, PRK09836, DNA-binding transcriptional ac	1e-05
COG2201	350	COG2201, CheB, Chemotaxis response regulator conta	7e-05
PRK10693	303	PRK10693, PRK10693, response regulator of RpoS; Pr	1e-04
PRK10161	229	PRK10161, PRK10161, transcriptional regulator PhoB	5e-04
PRK10816	223	PRK10816, PRK10816, DNA-binding transcriptional re	6e-04
PRK11466	914	PRK11466, PRK11466, hybrid sensory histidine kinas	6e-04
COG3707	194	COG3707, AmiR, Response regulator with putative an	7e-04
PRK10651	216	PRK10651, PRK10651, transcriptional regulator NarL	8e-04
PRK10529	225	PRK10529, PRK10529, DNA-binding transcriptional ac	0.001
PRK10766	221	PRK10766, PRK10766, DNA-binding transcriptional re	0.001
PRK12555	337	PRK12555, PRK12555, chemotaxis-specific methyleste	0.001
TIGR02875	262	TIGR02875, spore_0_A, sporulation transcription fa	0.002

>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 = 92.6 bits (231), Expect = 9e-25
 Identities = 37/115 (32%), Positives = 64/115 (55%), Gaps = 3/115 (2%)

Query: 21  LVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFK 80
           L+VDDDP+   +L ++L K  YEV +    E AL +L   +   D+++ D+ MP MDG +
Sbjct: 1   LIVDDDPLIRELLRRLLEKEGYEVVEAEDGEEALALLA--EEKPDLILLDIMMPGMDGLE 58

Query: 81  LHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVA 134
           L  ++     D+P+I ++  G  +D ++ +  GA +YL KP   +EL    + + 
Sbjct: 59  LLRRIRKRGPDIPIIFLTAHGDDEDAVEALKAGADDYLTKPFSPEELLARIRALL 113

Length = 113

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

 Score = 81.5 bits (202), Expect = 1e-20
 Identities = 36/111 (32%), Positives = 64/111 (57%), Gaps = 3/111 (2%)

Query: 20  VLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGF 79
           VL+VDDDP+   +L ++L K  Y V + +  E AL++L+  +   D+++ D+ MP MDG 
Sbjct: 1   VLIVDDDPLIRELLRQLLEKEGYVVAEADDGEEALELLK--EKRPDLILLDIRMPGMDGL 58

Query: 80  KLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNI 129
           +L  ++       PVI+++  G  +D ++ +  GA ++L KP   +EL   
Sbjct: 59  ELLRRIRRRPPTTPVIVLTAHGDEEDAVEALKAGANDFLSKPFDPEELVAA 109

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

 Score = 86.2 bits (214), Expect = 4e-20
 Identities = 43/125 (34%), Positives = 69/125 (55%), Gaps = 3/125 (2%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           R+LVVDDDP    +LE+ L    YEV     AE AL+ L   ++ +D+V+ D+ MP MDG
Sbjct: 6   RILVVDDDPDIRELLEQALELAGYEVVTAESAEEALEALS--ESPFDLVLLDIRMPGMDG 63

Query: 79  FKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQP 137
            +L +++   + DLPVI+M+  G     ++ +  GA ++L KP  +  L  I +   +  
Sbjct: 64  LELLKEIKSRDPDLPVIVMTGHGDIDTAVEALRLGAFDFLEKPFDLDRLLAIVERALELR 123

Query: 138 KPFEE 142
           +   E
Sbjct: 124 ELQRE 128

Length = 464

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

 Score = 80.3 bits (198), Expect = 8e-20
 Identities = 41/112 (36%), Positives = 69/112 (61%), Gaps = 3/112 (2%)

Query: 17  GLRVLVVDDDPIWLRILEKMLRKCLYEVTKC-NRAEIALDMLRMSKNGYDIVISDVHMPD 75
           GLRVLVVDD+P+  R+L+++L    YEV +  +  E AL++LR      D+++ D++MP 
Sbjct: 5   GLRVLVVDDEPVNRRLLKRLLEDLGYEVVEAADGEEEALELLRELPQ-PDLILLDINMPG 63

Query: 76  MDGFKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
           MDG +L  ++     ++PVI+++      D  + +  GA +YL KPI ++E 
Sbjct: 64  MDGIELLRRLRARGPNIPVILLTAYADEADRERALAAGADDYLTKPIFLEEE 115

Length = 130

>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 = 82.7 bits (205), Expect = 8e-20
 Identities = 35/111 (31%), Positives = 60/111 (54%), Gaps = 5/111 (4%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           R+L+V+DDP    +L++ L +  YEV      E AL+  R      D+V+ D+ +PD+DG
Sbjct: 2   RILLVEDDPELAELLKEYLEEEGYEVDVAADGEEALEAAR---EQPDLVLLDLMLPDLDG 58

Query: 79  FKLHEQV--GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
            +L  ++        P+I+++     +D + G+  GA +YL KP   +EL 
Sbjct: 59  LELCRRLRAKKGSGPPIIVLTARDDEEDRVLGLEAGADDYLTKPFSPRELL 109

Length = 229

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

 Score = 70.9 bits (174), Expect = 3e-15
 Identities = 46/146 (31%), Positives = 75/146 (51%), Gaps = 5/146 (3%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           ++LVVDD+    +ILE  L    YEV   +  E AL + R  K   D+VI DV MP +DG
Sbjct: 8   KILVVDDEAYIRKILETRLSIIGYEVITASDGEEALKLFR--KEQPDLVILDVMMPKLDG 65

Query: 79  FKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHV---AQ 135
           + + +++  E D+P+IM++  G   D + G+  GA +Y++KP   KEL    + V     
Sbjct: 66  YGVCQEIRKESDVPIIMLTALGDVSDRITGLELGADDYVVKPFSPKELEARIRSVLRRTN 125

Query: 136 QPKPFEESDDSYSVNQGNWRTSNRRK 161
           +     +  +S  +  G  +    +K
Sbjct: 126 KKSFSSKIPNSSIIRIGFLKIDLNKK 151

Length = 240

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

 Score = 71.6 bits (176), Expect = 5e-15
 Identities = 37/119 (31%), Positives = 61/119 (51%), Gaps = 5/119 (4%)

Query: 12  DQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDV 71
               A  ++LVVDDD      L ++L+   + V +    E AL  L  ++   D+V+ D 
Sbjct: 127 LPEDAPKKILVVDDDATQRERLRRILQVEGFRVVEATDGEEALLQL--AELPPDLVLLDA 184

Query: 72  HMPDMDGFKLHEQVGLE---MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           +MPDMDG +L  ++       D+P+I++S     + V++    G  +Y+ KPI   ELR
Sbjct: 185 NMPDMDGLELCTRLRQLERTRDIPIILLSSKDDDELVVRAFELGVNDYITKPIEEGELR 243

Length = 435

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

 Score = 68.2 bits (167), Expect = 7e-14
 Identities = 38/121 (31%), Positives = 52/121 (42%), Gaps = 3/121 (2%)

Query: 20  VLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGF 79
           V VVDDD     +LEK L +  YEV     A   L  L   +   D++I+DV MP  DG 
Sbjct: 1   VWVVDDDRSIRWVLEKALSRAGYEVRTFGNAASVLRALARGQP--DLLITDVRMPGEDGL 58

Query: 80  KLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPK 138
            L  Q+      LPVI+M+        +     GA  YL KP  + E   + +      +
Sbjct: 59  DLLPQIKKRHPQLPVIVMTAHSDLDTAVAAYQRGAFEYLPKPFDLDEAVTLVERALAHAQ 118

Query: 139 P 139
            
Sbjct: 119 E 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|225971 COG3437, COG3437, Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]

 Score = 67.4 bits (165), Expect = 1e-13
 Identities = 42/115 (36%), Positives = 61/115 (53%), Gaps = 6/115 (5%)

Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMD 77
           L VL+VDD+P  L  L ++LR   Y V +    E AL +L   +   D+V+ DV MP+MD
Sbjct: 15  LTVLLVDDEPDNLEALRQLLRMIGYRVIEAENGEEALKLL--QEEPPDLVLLDVRMPEMD 72

Query: 78  GF----KLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRN 128
           G     KL         +PVI+++    ++D  + +  GA +YL KPI  KEL  
Sbjct: 73  GAEVLNKLKAMSPSTRRIPVILLTAYADSEDRQRALEAGADDYLSKPISPKELVA 127

Length = 360

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

 Score = 66.5 bits (163), Expect = 3e-13
 Identities = 39/120 (32%), Positives = 64/120 (53%), Gaps = 16/120 (13%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           R+LVVDD P  +++LE  L    Y V   +    A+ +    +   DI++ DV MP MDG
Sbjct: 4   RILVVDDIPANVKLLEAKLLAEYYTVLTASSGAEAIAICEREQ--PDIILLDVMMPGMDG 61

Query: 79  FKLHEQVGLEMD-----LPVIMMSVDGCTQDVMKGVTHGACNYLLKPI-------RIKEL 126
           F++  +  L+ D     +PV+M++     +D ++G+  GA ++L KPI       R+K L
Sbjct: 62  FEVCRR--LKSDPATTHIPVVMVTALDDPEDRVRGLEAGADDFLTKPINDVALFARVKSL 119

Length = 457

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

 Score = 65.4 bits (160), Expect = 7e-13
 Identities = 36/94 (38%), Positives = 54/94 (57%), Gaps = 3/94 (3%)

Query: 2   SPASSSVAVSDQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSK 61
           + A  S   +      + +LVVDD PI  R+L   L    Y+    N    AL++L  SK
Sbjct: 786 ANALPSTDKAVSDNDDMMILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVL--SK 843

Query: 62  NGYDIVISDVHMPDMDGFKLHEQV-GLEMDLPVI 94
           N  DIV++DV+MP+MDG++L +++  L + LPVI
Sbjct: 844 NHIDIVLTDVNMPNMDGYRLTQRLRQLGLTLPVI 877

Length = 924

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

 Score = 58.3 bits (142), Expect = 3e-12
 Identities = 22/57 (38%), Positives = 37/57 (64%), Gaps = 2/57 (3%)

Query: 18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMP 74
          +R+LVVDDDP+   +L+ +L K  YEV +    E AL++L+  +   D+++ D+ MP
Sbjct: 1  MRILVVDDDPLLRELLKALLEKEGYEVDEATDGEEALELLK--EEKPDLILLDIMMP 55

CheY regulates the clockwise rotation of E. coli flagellar motors. This domain contains a phosphoacceptor site that is phosphorylated by histidine kinase homologues. Length = 55

>gnl|CDD|225107 COG2197, CitB, Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]

 Score = 60.0 bits (146), Expect = 2e-11
 Identities = 36/111 (32%), Positives = 59/111 (53%), Gaps = 5/111 (4%)

Query: 19  RVLVVDDDPIWLRILEKMLRK-CLYEVT-KCNRAEIALDMLRMSKNGYDIVISDVHMPDM 76
           +VL+VDD P+    L ++L      EV  + +  E ALD+ R  K   D+V+ D+ MP M
Sbjct: 2   KVLIVDDHPLVREGLRQLLELEPDLEVVGEASNGEEALDLARELK--PDVVLLDLSMPGM 59

Query: 77  DGFKLHEQVGLEM-DLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
           DG +  +Q+     D+ V++++       V++ +  GA  YLLK    +EL
Sbjct: 60  DGLEALKQLRARGPDIKVVVLTAHDDPAYVIRALRAGADGYLLKDASPEEL 110

Length = 211

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

 Score = 57.7 bits (139), Expect = 3e-11
 Identities = 34/107 (31%), Positives = 59/107 (55%), Gaps = 6/107 (5%)

Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD     RI+  +L++  +       AE  +D L ++   G+  VISD +MP+M
Sbjct: 6   LKFLVVDDFSTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGFGFVISDWNMPNM 63

Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKP 120
           DG +L + +   G    LPV+M++ +   ++++     GA  Y++KP
Sbjct: 64  DGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKP 110

Length = 129

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

 Score = 60.2 bits (146), Expect = 5e-11
 Identities = 35/104 (33%), Positives = 55/104 (52%), Gaps = 3/104 (2%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
            +L+VDDDP  L++L   L    Y V      + AL +L   K   D+VISD+ M +MDG
Sbjct: 7   HLLLVDDDPGLLKLLGMRLTSEGYSVVTAESGQEALRVLNREK--VDLVISDLRMDEMDG 64

Query: 79  FKL-HEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPI 121
            +L  E   ++  +PVI+++  G   D +     G  ++L KP+
Sbjct: 65  MQLFAEIQKVQPGMPVIILTAHGSIPDAVAATQQGVFSFLTKPV 108

Length = 444

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

 Score = 59.3 bits (144), Expect = 1e-10
 Identities = 37/123 (30%), Positives = 64/123 (52%), Gaps = 8/123 (6%)

Query: 19  RVLVVDDDPIWLRILEKML--RKCLYEV--TKCNRAEIALDMLRMSKNGYDIVISDVHMP 74
           +VL+VDD+P+    L+ ++       EV  T  N  E AL++++  +   DIVI+D++MP
Sbjct: 3   KVLIVDDEPLIREGLKSLIDWEALGIEVVGTAANGKE-ALELIQ--ETQPDIVITDINMP 59

Query: 75  DMDGFKLHEQVGLEM-DLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHV 133
            MDG  L + +  +  D   I++S     +   K +  G  +YLLKP+   EL    + +
Sbjct: 60  GMDGLDLIKAIKEQSPDTEFIILSGYDEFEYAKKAMKLGVKDYLLKPVDKAELEEALKKI 119

Query: 134 AQQ 136
             +
Sbjct: 120 IGK 122

Length = 475

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

 Score = 58.3 bits (141), Expect = 2e-10
 Identities = 33/105 (31%), Positives = 56/105 (53%), Gaps = 5/105 (4%)

Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMD 77
            R+++VDDD   +++L  +L +  +EV  C+    ALD+L       D++  D+ MP M+
Sbjct: 1   PRIIIVDDDAAIVKLLSVILSRAGHEVRSCSHPVEALDLLE--VFKPDLIFLDIVMPYMN 58

Query: 78  GFKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPI 121
           G +  EQV  +E  +P+I +S      D   G+     +YL KP+
Sbjct: 59  GIEFAEQVRDIESAVPIIFISSHAEYADDSFGMN--LDDYLPKPV 101

Length = 361

>gnl|CDD|234070 TIGR02956, TMAO_torS, TMAO reductase sytem sensor TorS

 Score = 58.3 bits (141), Expect = 2e-10
 Identities = 33/147 (22%), Positives = 68/147 (46%), Gaps = 6/147 (4%)

Query: 2   SPASSSVAVSDQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSK 61
            PA  S  ++       RVL+V+D+ +   + +  L +  ++VT     + AL      +
Sbjct: 687 KPAEDSATLTVIDLPPQRVLLVEDNEVNQMVAQGFLTRLGHKVTLAESGQSAL--ECFHQ 744

Query: 62  NGYDIVISDVHMPDMDGFKLHEQV----GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYL 117
           + +D+ + D+++PD DG  L +Q+    G + ++  I  S     +DV + +  G   +L
Sbjct: 745 HAFDLALLDINLPDGDGVTLLQQLRAIYGAKNEVKFIAFSAHVFNEDVAQYLAAGFDGFL 804

Query: 118 LKPIRIKELRNIWQHVAQQPKPFEESD 144
            KP+  ++L  +   +    K   E+ 
Sbjct: 805 AKPVVEEQLTAMIAVILAGGKSNTEAP 831

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) [Signal transduction, Two-component systems]. Length = 968

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

 Score = 58.1 bits (140), Expect = 2e-10
 Identities = 37/111 (33%), Positives = 60/111 (54%), Gaps = 3/111 (2%)

Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMD 77
           + +LVVDDD     IL+ +LR   Y V   N    AL+ +R  +  +D+V+ DV M +MD
Sbjct: 6   IDILVVDDDISHCTILQALLRGWGYNVALANSGRQALEQVR--EQVFDLVLCDVRMAEMD 63

Query: 78  GFK-LHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           G   L E   L   +PV++M+     +  ++ +  GA +YL+KP+    L+
Sbjct: 64  GIATLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQ 114

Length = 441

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

 Score = 55.6 bits (134), Expect = 2e-09
 Identities = 37/118 (31%), Positives = 57/118 (48%), Gaps = 3/118 (2%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           R+L+VDD+    R+L        +E    N    AL +        D+V+ D+ MP+MDG
Sbjct: 6   RILIVDDEDNVRRMLSTAFALQGFETHCANNGRTALHLFADIHP--DVVLMDIRMPEMDG 63

Query: 79  FK-LHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ 135
            K L E    E   PVI+M+     +  ++ +  GA +Y++KP  + EL  I Q   Q
Sbjct: 64  IKALKEMRSHETRTPVILMTAYAEVETAVEALRCGAFDYVIKPFDLDELNLIVQRALQ 121

Length = 457

>gnl|CDD|185376 PRK15479, PRK15479, transcriptional regulatory protein TctD; Provisional

 Score = 54.3 bits (131), Expect = 2e-09
 Identities = 34/110 (30%), Positives = 61/110 (55%), Gaps = 3/110 (2%)

Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMD 77
           +R+L+ +D+      LEK L +  + V  C    +A D L  S+  Y + + D++MP MD
Sbjct: 1   MRLLLAEDNRELAHWLEKALVQNGFAV-DCVFDGLAADHLLQSEM-YALAVLDINMPGMD 58

Query: 78  GFKLHEQVGLE-MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
           G ++ +++      LPV++++      D +KG+  GA +YL KP  ++EL
Sbjct: 59  GLEVLQRLRKRGQTLPVLLLTARSAVADRVKGLNVGADDYLPKPFELEEL 108

Length = 221

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

 Score = 54.0 bits (130), Expect = 3e-09
 Identities = 34/131 (25%), Positives = 62/131 (47%), Gaps = 8/131 (6%)

Query: 20  VLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGF 79
           +LVV+D+      L++ L +  Y V   +     L +    K+ YD++I DV +P MDG+
Sbjct: 1   ILVVEDEQKTAEYLQQGLSESGYVVDAASNGRDGLHL--ALKDDYDLIILDVMLPGMDGW 58

Query: 80  KLHEQVGLE-MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL-----RNIWQHV 133
           ++ + +       PV+ ++      D +KG+  GA +YL+KP    EL       + +  
Sbjct: 59  QILQTLRRSGKQTPVLFLTARDSVADKVKGLDLGADDYLVKPFSFSELLARVRTLLRRSH 118

Query: 134 AQQPKPFEESD 144
           +      E +D
Sbjct: 119 SLNSTVLEIAD 129

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

 Score = 54.5 bits (131), Expect = 4e-09
 Identities = 35/107 (32%), Positives = 49/107 (45%), Gaps = 3/107 (2%)

Query: 20  VLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGF 79
           V VVDDD     +LE+ L       T        L+ L  +    D+++SD+ MP MDG 
Sbjct: 6   VWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLEAL--ASKTPDVLLSDIRMPGMDGL 63

Query: 80  KLHEQVGLEMD-LPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKE 125
            L +Q+      LPVI+M+        +     GA +YL KP  I E
Sbjct: 64  ALLKQIKQRHPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDIDE 110

Length = 469

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

 Score = 53.1 bits (127), Expect = 6e-09
 Identities = 45/195 (23%), Positives = 83/195 (42%), Gaps = 37/195 (18%)

Query: 7   SVAVSDQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNG--- 63
            +    QF     VL VDD  I  +++EK+L+   Y+VT  +    AL  L + ++    
Sbjct: 2   GITTESQF----HVLAVDDSLIDRKLIEKLLKTSSYQVTTVDSGSKALKFLGLHEDDRSN 57

Query: 64  ---------------YDIVISDVHMPDMDGF----KLHEQVGLEMDLPVIMMSVDGCTQD 104
                           +++I+D  MP M G+    K+ E   L  ++PV++MS +     
Sbjct: 58  PDTPSVSPNSHQEVEVNLIITDYCMPGMTGYDLLKKIKESSSLR-NIPVVIMSSENVPSR 116

Query: 105 VMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPFEESDDSYSVNQGNWRTSNRRKDEE 164
           + + +  GA  + LKP+++ +L  +  H+ +          + S NQ       + K EE
Sbjct: 117 ITRCLEEGAEEFFLKPVQLSDLNRLKPHMMK----------TKSKNQKQENQEKQEKLEE 166

Query: 165 EEAEKRDDTSTLKKP 179
            E +        ++P
Sbjct: 167 SEIQSEKQEQPSQQP 181

Length = 222

>gnl|CDD|237951 PRK15347, PRK15347, two component system sensor kinase SsrA; Provisional

 Score = 53.9 bits (130), Expect = 6e-09
 Identities = 29/117 (24%), Positives = 59/117 (50%), Gaps = 7/117 (5%)

Query: 15  PAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMP 74
           P  L++L+VDD      I+  ML +   +VT       AL++ R  +  +D+V+ D+ MP
Sbjct: 688 PWQLQILLVDDVETNRDIIGMMLVELGQQVTTAASGTEALELGRQHR--FDLVLMDIRMP 745

Query: 75  DMDGFKL-----HEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
            +DG +       +   L+ D  ++ ++ +   +++ +    G  +YL KP+ + +L
Sbjct: 746 GLDGLETTQLWRDDPNNLDPDCMIVALTANAAPEEIHRCKKAGMNHYLTKPVTLAQL 802

Length = 921

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

 Score = 52.3 bits (126), Expect = 1e-08
 Identities = 31/114 (27%), Positives = 60/114 (52%), Gaps = 5/114 (4%)

Query: 16  AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPD 75
              R+LVV+D+P    ++   L K  Y+V +    + AL ++   + G D+++ D  +P 
Sbjct: 1   MTRRILVVEDEPAIRELIAYNLEKAGYDVVEAGDGDEALTLIN--ERGPDLILLDWMLPG 58

Query: 76  MDGFKLHEQVGLE---MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
             G +L  ++        +P+IM++  G  +D ++G+  GA +Y+ KP   +EL
Sbjct: 59  TSGIELCRRLRRRPETRAIPIIMLTARGEEEDRVRGLETGADDYITKPFSPREL 112

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

 Score = 52.8 bits (126), Expect = 2e-08
 Identities = 39/126 (30%), Positives = 65/126 (51%), Gaps = 12/126 (9%)

Query: 14   FPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHM 73
             P  L +L+ DD P    +L++ L    Y+V +      AL   ++S   YD++I+DV+M
Sbjct: 955  LPEKLSILIADDHPTNRLLLKRQLNLLGYDVDEATDGVQALH--KVSMQHYDLLITDVNM 1012

Query: 74   PDMDGF----KLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNI 129
            P+MDGF    KL EQ      LP+  ++ +    +  KG++ G    L KP+ +  L+  
Sbjct: 1013 PNMDGFELTRKLREQ---NSSLPIWGLTANAQANEREKGLSCGMNLCLFKPLTLDVLKT- 1068

Query: 130  WQHVAQ 135
              H++Q
Sbjct: 1069 --HLSQ 1072

Length = 1197

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

 Score = 50.7 bits (122), Expect = 4e-08
 Identities = 35/109 (32%), Positives = 55/109 (50%), Gaps = 3/109 (2%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
            +L+V+D+      L   L+   + V    R   ALD LR  +   D+VI DV +PD+ G
Sbjct: 5   TILLVEDEQAIADTLVYALQSEGFTVEWFERGLPALDKLR--QQPPDLVILDVGLPDISG 62

Query: 79  FKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
           F+L  Q+      LPVI ++      D + G+  GA +Y+ KP   +E+
Sbjct: 63  FELCRQLLAFHPALPVIFLTARSDEVDRLVGLEIGADDYVAKPFSPREV 111

Length = 228

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

 Score = 50.3 bits (121), Expect = 5e-08
 Identities = 26/114 (22%), Positives = 57/114 (50%), Gaps = 5/114 (4%)

Query: 18  LRVLVVDDDPIWLRILEKMLRKCLY--EVTKCNRAEIALDMLRMSKNGYDIVISDVHMPD 75
           + VL+++DDP+   I  + +++      V      E A  ++   K   D+++ D++MPD
Sbjct: 1   INVLIIEDDPMVAEIHRRYVKQIPGFSVVGTAGTLEEAKMIIEEFKP--DLILLDIYMPD 58

Query: 76  MDGFK-LHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRN 128
            +G + L E       + VI+++     + + + + +G  +YL+KP   + L+ 
Sbjct: 59  GNGIELLPELRSQHYPVDVIVITAASDMETIKEALRYGVVDYLIKPFTFERLQQ 112

Length = 224

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

 Score = 50.6 bits (121), Expect = 5e-08
 Identities = 34/108 (31%), Positives = 58/108 (53%), Gaps = 3/108 (2%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           ++L+VDDD     +L+++L    + V   +  E ALD+L    +  D+++ DV MP  +G
Sbjct: 3   KILLVDDDRELTSLLKELLEMEGFNVIVAHDGEQALDLL---DDSIDLLLLDVMMPKKNG 59

Query: 79  FKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
               +++      PVIM++  G   D + G+  GA +YL KP   +EL
Sbjct: 60  IDTLKELRQTHQTPVIMLTARGSELDRVLGLELGADDYLPKPFNDREL 107

Length = 232

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

 Score = 50.7 bits (122), Expect = 7e-08
 Identities = 31/126 (24%), Positives = 60/126 (47%), Gaps = 7/126 (5%)

Query: 4   ASSSVAVSDQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNG 63
           A   +A +++   G R+L+VDDD      +  +L K  + V   +    AL     ++  
Sbjct: 143 ALMIMAYANKDEDG-RILLVDDDVSQAERIANIL-KEEFRVVVVSDPSEALF--NAAETN 198

Query: 64  YDIVISDVHMPDMDGFKLHEQV-GLEMD--LPVIMMSVDGCTQDVMKGVTHGACNYLLKP 120
           YD+VI   +  + D  +L  Q+   E    +P++++  +     ++K +  G  +YL++P
Sbjct: 199 YDLVIVSANFENYDPLRLCSQLRSKERTRYVPILLLVDEDDDPRLVKALELGVNDYLMRP 258

Query: 121 IRIKEL 126
           I   EL
Sbjct: 259 IDKNEL 264

Length = 457

>gnl|CDD|181883 PRK09468, ompR, osmolarity response regulator; Provisional

 Score = 48.8 bits (117), Expect = 2e-07
 Identities = 34/112 (30%), Positives = 59/112 (52%), Gaps = 9/112 (8%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           ++LVVDDD     +LE+ L +  ++V     AE  +D L +++  + +++ D+ +P  DG
Sbjct: 7   KILVVDDDMRLRALLERYLTEQGFQVRSAANAE-QMDRL-LTRESFHLMVLDLMLPGEDG 64

Query: 79  F----KLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
                +L  Q       P+IM++  G   D + G+  GA +YL KP   +EL
Sbjct: 65  LSICRRLRSQ---NNPTPIIMLTAKGEEVDRIVGLEIGADDYLPKPFNPREL 113

Length = 239

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

 Score = 46.5 bits (111), Expect = 1e-06
 Identities = 37/108 (34%), Positives = 52/108 (48%), Gaps = 15/108 (13%)

Query: 20  VLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGF 79
           V VVDDD      L  +L    +EV     A+  LD L   + G   V++DV MP +DG 
Sbjct: 6   VHVVDDDEAMRDSLAFLLDSAGFEVRLFESAQAFLDALPGLRFG--CVVTDVRMPGIDGI 63

Query: 80  KLHEQVG-LEMDLPVIMMSVDGCTQDV------MKGVTHGACNYLLKP 120
           +L  ++      LPVI+M+  G   DV      MK    GA +++ KP
Sbjct: 64  ELLRRLKARGSPLPVIVMTGHG---DVPLAVEAMKL---GAVDFIEKP 105

Length = 202

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

 Score = 45.7 bits (109), Expect = 2e-06
 Identities = 34/117 (29%), Positives = 52/117 (44%), Gaps = 9/117 (7%)

Query: 15  PAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMP 74
           P    V VVDDD      L  +L    ++V     AE  L    + + G   ++ DV MP
Sbjct: 2   PREPLVHVVDDDESVRDALAFLLESAGFQVKCFASAEEFLAAAPLDRPG--CLLLDVRMP 59

Query: 75  DMDGFKLHEQV-GLEMDLPVIMMSVDG---CTQDVMKGVTHGACNYLLKPIRIKELR 127
            M G +L +++    + LPVI ++  G        MK    GA ++L KP   ++L 
Sbjct: 60  GMSGLELQDRLAERGIRLPVIFLTGHGDIPMAVQAMK---AGAVDFLEKPFSEQDLL 113

Length = 202

>gnl|CDD|182612 PRK10643, PRK10643, DNA-binding transcriptional regulator BasR; Provisional

 Score = 45.4 bits (108), Expect = 3e-06
 Identities = 32/110 (29%), Positives = 59/110 (53%), Gaps = 3/110 (2%)

Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMD 77
           +++L+V+DD + L+ L   L+   Y     + A  A  +L      Y +V+ D+ +PD D
Sbjct: 1   MKILIVEDDTLLLQGLILALQTEGYACDCASTAREAEALLESGH--YSLVVLDLGLPDED 58

Query: 78  GFKLHEQVGLE-MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
           G  L  +   +   LPV++++     +D + G+  GA +YL+KP  ++EL
Sbjct: 59  GLHLLRRWRQKKYTLPVLILTARDTLEDRVAGLDVGADDYLVKPFALEEL 108

Length = 222

>gnl|CDD|236848 PRK11107, PRK11107, hybrid sensory histidine kinase BarA; Provisional

 Score = 45.6 bits (109), Expect = 5e-06
 Identities = 22/80 (27%), Positives = 44/80 (55%), Gaps = 5/80 (6%)

Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMD 77
           L V+ VDD+P  L+++  +L + +  V  C+    A++  +  +  +D+++ D+ MP MD
Sbjct: 668 LTVMAVDDNPANLKLIGALLEEQVEHVVLCDSGHQAVEQAK--QRPFDLILMDIQMPGMD 725

Query: 78  GF---KLHEQVGLEMDLPVI 94
           G    +L  Q+    + P+I
Sbjct: 726 GIRACELIRQLPHNQNTPII 745

Length = 919

>gnl|CDD|183172 PRK11517, PRK11517, transcriptional regulatory protein YedW; Provisional

 Score = 44.5 bits (105), Expect = 7e-06
 Identities = 27/110 (24%), Positives = 58/110 (52%), Gaps = 4/110 (3%)

Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMS-KNGYDIVISDVHMPDM 76
           +++L+++D+      + + L +  Y +   +      D L ++ K+ Y ++I D+ +P M
Sbjct: 1   MKILLIEDNQRTQEWVTQGLSEAGYVI---DAVSDGRDGLYLALKDDYALIILDIMLPGM 57

Query: 77  DGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
           DG+++ + +      PVI ++      D ++G+  GA +YL+KP    EL
Sbjct: 58  DGWQILQTLRTAKQTPVICLTARDSVDDRVRGLDSGANDYLVKPFSFSEL 107

Length = 223

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

 Score = 43.5 bits (103), Expect = 1e-05
 Identities = 31/138 (22%), Positives = 66/138 (47%), Gaps = 6/138 (4%)

Query: 13  QFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVH 72
                 R+L+V+D+P   ++L   L+   Y  T  +  +  L  +R  +   D+++ D+ 
Sbjct: 6   IDENTPRILIVEDEPKLGQLLIDYLQAASYATTLLSHGDEVLPYVR--QTPPDLILLDLM 63

Query: 73  MPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL----RN 128
           +P  DG  L  ++    D+P++M++      D + G+  GA +Y+ KP   +E+    + 
Sbjct: 64  LPGTDGLTLCREIRRFSDIPIVMVTAKIEEIDRLLGLEIGADDYICKPYSPREVVARVKT 123

Query: 129 IWQHVAQQPKPFEESDDS 146
           I +    Q +  ++  +S
Sbjct: 124 ILRRCKPQRELQQQDAES 141

Length = 240

>gnl|CDD|226933 COG4567, COG4567, Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]

 Score = 43.2 bits (102), Expect = 1e-05
 Identities = 28/101 (27%), Positives = 49/101 (48%), Gaps = 3/101 (2%)

Query: 21  LVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFK 80
           L+VDDD  +LR L + + +  + V      E AL   R +   Y +V  D+ + D  G  
Sbjct: 13  LLVDDDTPFLRTLARAMERRGFAVVTAESVEEALAAARTAPPAYAVV--DLKLGDGSGLA 70

Query: 81  LHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKP 120
           + E +     D+ +++++        ++ V  GAC+YL KP
Sbjct: 71  VIEALRERRADMRIVVLTGYASIATAVEAVKLGACDYLAKP 111

Length = 182

>gnl|CDD|182102 PRK09836, PRK09836, DNA-binding transcriptional activator CusR; Provisional

 Score = 43.4 bits (102), Expect = 1e-05
 Identities = 29/111 (26%), Positives = 62/111 (55%), Gaps = 5/111 (4%)

Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNG-YDIVISDVHMPDM 76
           +++L+V+D+      L K L +  + V   + A+  L+   ++  G YD++I D+ +PD+
Sbjct: 1   MKLLIVEDEKKTGEYLTKGLTEAGFVV---DLADNGLNGYHLAMTGDYDLIILDIMLPDV 57

Query: 77  DGFKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
           +G+ +   +      +P+++++  G  +  +KG+  GA +YL+KP    EL
Sbjct: 58  NGWDIVRMLRSANKGMPILLLTALGTIEHRVKGLELGADDYLVKPFAFAEL 108

Length = 227

>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 = 41.9 bits (99), Expect = 7e-05
 Identities = 29/82 (35%), Positives = 44/82 (53%), Gaps = 6/82 (7%)

Query: 19 RVLVVDDDPIWLRILEKMLRK--CLYEV-TKCNRAEIALDMLRMSKNGYDIVISDVHMPD 75
          RVLVVDD  +  +++  +L     +  V T  N  E A+D ++  K   D++  DV MP 
Sbjct: 3  RVLVVDDSALMRKVISDILNSDPDIEVVGTARNGRE-AIDKVKKLKP--DVITLDVEMPV 59

Query: 76 MDGFKLHEQVGLEMDLPVIMMS 97
          MDG +   ++     LPVIM+S
Sbjct: 60 MDGLEALRKIMRLRPLPVIMVS 81

Length = 350

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

 Score = 41.5 bits (98), Expect = 1e-04
 Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 1/59 (1%)

Query: 65  DIVISDVHMPDMDGFKLHEQVGLE-MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIR 122
           D++I D+ MP M+G +  E +       PV+++S      D+ K +  G  + LLKP++
Sbjct: 19  DLIICDLAMPRMNGIEFVEHLRNRGDQTPVLVISATENMADIAKALRLGVQDVLLKPVK 77

Length = 303

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

 Score = 39.3 bits (91), Expect = 5e-04
 Identities = 28/111 (25%), Positives = 60/111 (54%), Gaps = 5/111 (4%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           R+LVV+D+     ++  +L +  ++  +    + A++ L  ++   D+++ D  +P   G
Sbjct: 4   RILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQL--NEPWPDLILLDWMLPGGSG 61

Query: 79  FKLHEQVGLEM---DLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
            +  + +  E    D+PV+M++  G  +D ++G+  GA +Y+ KP   KEL
Sbjct: 62  IQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSPKEL 112

Length = 229

>gnl|CDD|182755 PRK10816, PRK10816, DNA-binding transcriptional regulator PhoP; Provisional

 Score = 39.0 bits (91), Expect = 6e-04
 Identities = 32/110 (29%), Positives = 60/110 (54%), Gaps = 3/110 (2%)

Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMD 77
           +RVLVV+D+ +    L+  L+   ++V     A+ A   L   ++  DI I D+ +PD D
Sbjct: 1   MRVLVVEDNALLRHHLKVQLQDAGHQVDAAEDAKEADYYLN--EHLPDIAIVDLGLPDED 58

Query: 78  GFKL-HEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
           G  L       ++ LP+++++     QD ++ ++ GA +Y+ KP  I+E+
Sbjct: 59  GLSLIRRWRSNDVSLPILVLTARESWQDKVEVLSAGADDYVTKPFHIEEV 108

Length = 223

>gnl|CDD|236914 PRK11466, PRK11466, hybrid sensory histidine kinase TorS; Provisional

 Score = 39.5 bits (92), Expect = 6e-04
 Identities = 23/69 (33%), Positives = 38/69 (55%), Gaps = 1/69 (1%)

Query: 17  GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDM 76
           GLR+L+++D+P+  RI  +ML     +V     A  AL+ L+ S+  +   + D  +PD 
Sbjct: 681 GLRLLLIEDNPLTQRITAEMLNTSGAQVVAVGNAAQALETLQNSE-PFAAALVDFDLPDY 739

Query: 77  DGFKLHEQV 85
           DG  L  Q+
Sbjct: 740 DGITLARQL 748

Length = 914

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

 Score = 38.5 bits (90), Expect = 7e-04
 Identities = 23/113 (20%), Positives = 45/113 (39%), Gaps = 3/113 (2%)

Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMD 77
           LRVLV DD+ +    + + L +  Y+        +    +   +   D+VI D+ MP  D
Sbjct: 6   LRVLVADDEALTRMDIREGLLEAGYQRVGEAADGLEAVEVC-ERLQPDVVILDIEMPRRD 64

Query: 78  GFKLHEQVGLEMDLPVIMMSVDGCTQDVM-KGVTHGACNYLLKPIRIKELRNI 129
             +        +  P++ +        ++   +  G   Y++KP+    L  I
Sbjct: 65  IIEALLLASENVARPIVAL-TAYSDPALIEAAIEAGVMAYIVKPLDESRLLPI 116

Length = 194

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

 Score = 38.5 bits (90), Expect = 8e-04
 Identities = 28/116 (24%), Positives = 52/116 (44%), Gaps = 29/116 (25%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGY-----------DIV 67
            +L++DD P        MLR  + ++         + ++  + NG            D++
Sbjct: 8   TILLIDDHP--------MLRTGVKQLI---SMAPDITVVGEASNGEQGIELAESLDPDLI 56

Query: 68  ISDVHMPDMDGF----KLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLK 119
           + D++MP M+G     KL E+    +   +++ SV    +DV+  +  GA  YLLK
Sbjct: 57  LLDLNMPGMNGLETLDKLREK---SLSGRIVVFSVSNHEEDVVTALKRGADGYLLK 109

Length = 216

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

 Score = 38.2 bits (89), Expect = 0.001
 Identities = 21/62 (33%), Positives = 33/62 (53%)

Query: 65  DIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIK 124
           D++I D+ +PD DG +    +     +PVI++S      D +  +  GA +YL KP  I 
Sbjct: 47  DLIILDLGLPDGDGIEFIRDLRQWSAIPVIVLSARSEESDKIAALDAGADDYLSKPFGIG 106

Query: 125 EL 126
           EL
Sbjct: 107 EL 108

Length = 225

>gnl|CDD|182711 PRK10766, PRK10766, DNA-binding transcriptional regulator TorR; Provisional

 Score = 38.1 bits (89), Expect = 0.001
 Identities = 33/135 (24%), Positives = 71/135 (52%), Gaps = 10/135 (7%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLR-MSKNGYDIVISDVHMPDMD 77
            +LVV+D+P+    L+    +  Y V++   A     M   M     D+++ D+++P  D
Sbjct: 4   HILVVEDEPVTRARLQGYFEQEGYTVSE---AASGAGMREIMQNQHVDLILLDINLPGED 60

Query: 78  GFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL----RNI-WQ- 131
           G  L  ++     + +I+++    + D + G+  GA +Y+ KP+ ++EL    +N+ W+ 
Sbjct: 61  GLMLTRELRSRSTVGIILVTGRTDSIDRIVGLEMGADDYVTKPLELRELLVRVKNLLWRI 120

Query: 132 HVAQQPKPFEESDDS 146
            +A+Q +P  + +D+
Sbjct: 121 SLARQAQPHAQEEDN 135

Length = 221

>gnl|CDD|237135 PRK12555, PRK12555, chemotaxis-specific methylesterase; Provisional

 Score = 38.3 bits (90), Expect = 0.001
 Identities = 19/83 (22%), Positives = 41/83 (49%), Gaps = 4/83 (4%)

Query: 19 RVLVVDDDPIWLRILEKML-RKCLYEVTKCNR-AEIALDMLRMSKNGYDIVISDVHMPDM 76
          R+ +V+D P+ +  L + L R   +EV         A++    +    D+++ D+ MP M
Sbjct: 2  RIGIVNDSPLAVEALRRALARDPDHEVVWVATDGAQAVER--CAAQPPDVILMDLEMPRM 59

Query: 77 DGFKLHEQVGLEMDLPVIMMSVD 99
          DG +   ++  E   P+++++  
Sbjct: 60 DGVEATRRIMAERPCPILIVTSL 82

Length = 337

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

 Score = 37.9 bits (88), Expect = 0.002
 Identities = 31/123 (25%), Positives = 61/123 (49%), Gaps = 14/123 (11%)

Query: 18  LRVLVVDDDPIWLRILEKML--RKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPD 75
           +R+++ DD+  +  +L++ L  +  +  V   +    AL++++  +   D+V+ D+ MP 
Sbjct: 3   IRIVIADDNKEFCNLLKEYLAAQPDMEVVGVAHNGVDALELIKEQQP--DVVVLDIIMPH 60

Query: 76  MDGFKLHEQVGLEMDLP---VIMMSVDGCTQDVMKGVTHGACNYLLKPI-------RIKE 125
           +DG  + E++          VIM+S  G  +   + V  GA  Y+LKP        RI++
Sbjct: 61  LDGIGVLEKLNEIELSARPRVIMLSAFGQEKITQRAVALGADYYVLKPFDLEILAARIRQ 120

Query: 126 LRN 128
           L  
Sbjct: 121 LAW 123

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	184
COG0745	229	OmpR Response regulators consisting of a CheY-like	99.92
COG4566	202	TtrR Response regulator [Signal transduction mecha	99.86
COG4753	475	Response regulator containing CheY-like receiver d	99.86
COG4565	224	CitB Response regulator of citrate/malate metaboli	99.86
COG2204	464	AtoC Response regulator containing CheY-like recei	99.84
PF00072	112	Response_reg: Response regulator receiver domain;	99.84
COG2197	211	CitB Response regulator containing a CheY-like rec	99.83
PRK10046	225	dpiA two-component response regulator DpiA; Provis	99.79
COG3947	361	Response regulator containing CheY-like receiver a	99.77
PRK10529	225	DNA-binding transcriptional activator KdpE; Provis	99.77
COG3437	360	Response regulator containing a CheY-like receiver	99.76
PRK11173	237	two-component response regulator; Provisional	99.75
PRK10840	216	transcriptional regulator RcsB; Provisional	99.75
PRK10816	223	DNA-binding transcriptional regulator PhoP; Provis	99.75
COG0784	130	CheY FOG: CheY-like receiver [Signal transduction	99.75
PRK11517	223	transcriptional regulatory protein YedW; Provision	99.75
PRK10766	221	DNA-binding transcriptional regulator TorR; Provis	99.74
PRK09836	227	DNA-binding transcriptional activator CusR; Provis	99.74
PRK10643	222	DNA-binding transcriptional regulator BasR; Provis	99.74
COG3706	435	PleD Response regulator containing a CheY-like rec	99.74
PRK13856	241	two-component response regulator VirG; Provisional	99.73
PRK10161	229	transcriptional regulator PhoB; Provisional	99.73
CHL00148	240	orf27 Ycf27; Reviewed	99.73
PRK10336	219	DNA-binding transcriptional regulator QseB; Provis	99.73
PRK10701	240	DNA-binding transcriptional regulator RstA; Provis	99.73
TIGR02154	226	PhoB phosphate regulon transcriptional regulatory	99.72
PRK10955	232	DNA-binding transcriptional regulator CpxR; Provis	99.72
PLN03029	222	type-a response regulator protein; Provisional	99.72
COG4567	182	Response regulator consisting of a CheY-like recei	99.71
PRK11083	228	DNA-binding response regulator CreB; Provisional	99.71
PRK09468	239	ompR osmolarity response regulator; Provisional	99.71
TIGR03787	227	marine_sort_RR proteobacterial dedicated sortase s	99.71
PRK09958	204	DNA-binding transcriptional activator EvgA; Provis	99.71
PRK10430	239	DNA-binding transcriptional activator DcuR; Provis	99.71
PRK09483	217	response regulator; Provisional	99.7
TIGR01387	218	cztR_silR_copR heavy metal response regulator. Mem	99.69
PRK11107	919	hybrid sensory histidine kinase BarA; Provisional	99.69
PRK10841	924	hybrid sensory kinase in two-component regulatory	99.68
PRK15347	921	two component system sensor kinase SsrA; Provision	99.68
KOG0519	786	consensus Sensory transduction histidine kinase [S	99.68
PRK11697	238	putative two-component response-regulatory protein	99.67
PRK10360	196	DNA-binding transcriptional activator UhpA; Provis	99.67
PRK11466	914	hybrid sensory histidine kinase TorS; Provisional	99.67
PRK09935	210	transcriptional regulator FimZ; Provisional	99.66
PRK14084	246	two-component response regulator; Provisional	99.65
PRK10710	240	DNA-binding transcriptional regulator BaeR; Provis	99.65
TIGR02875	262	spore_0_A sporulation transcription factor Spo0A.	99.65
PRK15479	221	transcriptional regulatory protein TctD; Provision	99.65
PRK10100	216	DNA-binding transcriptional regulator CsgD; Provis	99.65
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	99.64
PRK10365	441	transcriptional regulatory protein ZraR; Provision	99.64
PRK15115	444	response regulator GlrR; Provisional	99.64
TIGR02956	968	TMAO_torS TMAO reductase sytem sensor TorS. This p	99.64
PRK11091	779	aerobic respiration control sensor protein ArcB; P	99.63
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	99.62
PRK09959	1197	hybrid sensory histidine kinase in two-component r	99.61
PRK13435	145	response regulator; Provisional	99.61
PRK11475	207	DNA-binding transcriptional activator BglJ; Provis	99.61
PRK09581	457	pleD response regulator PleD; Reviewed	99.6
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	99.6
PRK09390	202	fixJ response regulator FixJ; Provisional	99.59
PRK15411	207	rcsA colanic acid capsular biosynthesis activation	99.59
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	99.58
PRK12555	337	chemotaxis-specific methylesterase; Provisional	99.58
PRK09581	457	pleD response regulator PleD; Reviewed	99.57
PRK10610	129	chemotaxis regulatory protein CheY; Provisional	99.56
PRK10651	216	transcriptional regulator NarL; Provisional	99.55
PRK13558	665	bacterio-opsin activator; Provisional	99.55
PRK10403	215	transcriptional regulator NarP; Provisional	99.54
PRK15369	211	two component system sensor kinase SsrB; Provision	99.53
PRK00742	354	chemotaxis-specific methylesterase; Provisional	99.52
COG2201	350	CheB Chemotaxis response regulator containing a Ch	99.52
PRK13837	828	two-component VirA-like sensor kinase; Provisional	99.48
COG3707	194	AmiR Response regulator with putative antiterminat	99.48
PRK09191	261	two-component response regulator; Provisional	99.45
cd00156	113	REC Signal receiver domain; originally thought to	99.38
PRK13557	540	histidine kinase; Provisional	99.36
COG3279	244	LytT Response regulator of the LytR/AlgR family [T	99.27
PRK10693	303	response regulator of RpoS; Provisional	99.27
PRK15029	755	arginine decarboxylase; Provisional	99.13
PRK11107	919	hybrid sensory histidine kinase BarA; Provisional	98.61
PF06490	109	FleQ: Flagellar regulatory protein FleQ; InterPro:	98.23
COG3706	435	PleD Response regulator containing a CheY-like rec	98.22
smart00448	55	REC cheY-homologous receiver domain. CheY regulate	97.96
cd02071	122	MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 bin	97.38
PRK02261	137	methylaspartate mutase subunit S; Provisional	96.86
cd02067	119	B12-binding B12 binding domain (B12-BD). This doma	96.86
PF03709	115	OKR_DC_1_N: Orn/Lys/Arg decarboxylase, N-terminal	96.81
TIGR00640	132	acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal	96.52
COG4999	140	Uncharacterized domain of BarA-like signal transdu	96.42
PRK10618	894	phosphotransfer intermediate protein in two-compon	96.17
TIGR03815	322	CpaE_hom_Actino helicase/secretion neighborhood Cp	95.11
PF10087	97	DUF2325: Uncharacterized protein conserved in bact	94.89
PRK15399	713	lysine decarboxylase LdcC; Provisional	94.89
PF02310	121	B12-binding: B12 binding domain; InterPro: IPR0061	94.58
PRK15400	714	lysine decarboxylase CadA; Provisional	94.36
TIGR01501	134	MthylAspMutase methylaspartate mutase, S subunit.	94.3
cd04728	248	ThiG Thiazole synthase (ThiG) is the tetrameric en	94.25
PRK00208	250	thiG thiazole synthase; Reviewed	93.92
cd02069	213	methionine_synthase_B12_BD B12 binding domain of m	93.91
cd02070	201	corrinoid_protein_B12-BD B12 binding domain of cor	93.72
PRK05718	212	keto-hydroxyglutarate-aldolase/keto-deoxy-phosphog	93.61
TIGR00262	256	trpA tryptophan synthase, alpha subunit. Tryptopha	93.01
PRK10128	267	2-keto-3-deoxy-L-rhamnonate aldolase; Provisional	92.99
PRK10558	256	alpha-dehydro-beta-deoxy-D-glucarate aldolase; Pro	92.85
PF07688	283	KaiA: KaiA domain; InterPro: IPR011648 KaiA is a c	92.47
COG2185	143	Sbm Methylmalonyl-CoA mutase, C-terminal domain/su	92.25
TIGR03239	249	GarL 2-dehydro-3-deoxyglucarate aldolase. In E. co	92.2
TIGR01182	204	eda Entner-Doudoroff aldolase. 2-deydro-3-deoxypho	91.9
PRK01130	221	N-acetylmannosamine-6-phosphate 2-epimerase; Provi	91.69
PRK09426	714	methylmalonyl-CoA mutase; Reviewed	91.04
TIGR02370	197	pyl_corrinoid methyltransferase cognate corrinoid	90.91
PRK05749	425	3-deoxy-D-manno-octulosonic-acid transferase; Revi	90.81
cd02072	128	Glm_B12_BD B12 binding domain of glutamate mutase	90.79
cd04724	242	Tryptophan_synthase_alpha Ttryptophan synthase (TR	90.64
TIGR02311	249	HpaI 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldola	90.44
PRK00043	212	thiE thiamine-phosphate pyrophosphorylase; Reviewe	90.39
cd06533	171	Glyco_transf_WecG_TagA The glycosyltransferase Wec	89.97
TIGR01334	277	modD putative molybdenum utilization protein ModD.	89.77
PRK13111	258	trpA tryptophan synthase subunit alpha; Provisiona	89.57
TIGR01305	343	GMP_reduct_1 guanosine monophosphate reductase, eu	89.51
PRK06015	201	keto-hydroxyglutarate-aldolase/keto-deoxy-phosphog	89.47
CHL00200	263	trpA tryptophan synthase alpha subunit; Provisiona	89.16
TIGR03151	307	enACPred_II putative enoyl-(acyl-carrier-protein)	89.07
TIGR02855	283	spore_yabG sporulation peptidase YabG. Members of	89.05
COG0512	191	PabA Anthranilate/para-aminobenzoate synthases com	88.89
PLN02591	250	tryptophan synthase	88.89
PRK01911	292	ppnK inorganic polyphosphate/ATP-NAD kinase; Provi	88.82
PF14097	180	SpoVAE: Stage V sporulation protein AE1	88.7
PF03808	172	Glyco_tran_WecB: Glycosyl transferase WecB/TagA/Cp	88.68
PF05582	287	Peptidase_U57: YabG peptidase U57; InterPro: IPR00	88.66
PRK08385	278	nicotinate-nucleotide pyrophosphorylase; Provision	88.62
PF05690	247	ThiG: Thiazole biosynthesis protein ThiG; InterPro	87.71
cd02068	127	radical_SAM_B12_BD B12 binding domain_like associa	87.31
cd00564	196	TMP_TenI Thiamine monophosphate synthase (TMP synt	87.27
PRK07896	289	nicotinate-nucleotide pyrophosphorylase; Provision	87.21
PF01729	169	QRPTase_C: Quinolinate phosphoribosyl transferase,	87.07
PRK05848	273	nicotinate-nucleotide pyrophosphorylase; Provision	86.98
TIGR00696	177	wecB_tagA_cpsF bacterial polymer biosynthesis prot	86.93
TIGR03088	374	stp2 sugar transferase, PEP-CTERM/EpsH1 system ass	86.83
TIGR00343	287	pyridoxal 5'-phosphate synthase, synthase subunit	86.7
PF01081	196	Aldolase: KDPG and KHG aldolase; InterPro: IPR0008	86.51
COG0157	280	NadC Nicotinate-nucleotide pyrophosphorylase [Coen	86.45
PF03602	183	Cons_hypoth95: Conserved hypothetical protein 95;	86.38
PF01408	120	GFO_IDH_MocA: Oxidoreductase family, NAD-binding R	85.96
PLN02871	465	UDP-sulfoquinovose:DAG sulfoquinovosyltransferase	85.59
PF01596	205	Methyltransf_3: O-methyltransferase; InterPro: IPR	85.28
PRK03708	277	ppnK inorganic polyphosphate/ATP-NAD kinase; Provi	85.27
TIGR00693	196	thiE thiamine-phosphate pyrophosphorylase. This mo	85.12
PRK10669	558	putative cation:proton antiport protein; Provision	84.78
PRK15320	251	transcriptional activator SprB; Provisional	84.74
PF02581	180	TMP-TENI: Thiamine monophosphate synthase/TENI; In	84.55
cd04727	283	pdxS PdxS is a subunit of the pyridoxal 5'-phospha	84.28
CHL00162	267	thiG thiamin biosynthesis protein G; Validated	84.26
PRK03958	176	tRNA 2'-O-methylase; Reviewed	84.15
COG3010	229	NanE Putative N-acetylmannosamine-6-phosphate epim	84.09
TIGR02026	497	BchE magnesium-protoporphyrin IX monomethyl ester	83.62
KOG4175	268	consensus Tryptophan synthase alpha chain [Amino a	83.46
PRK03372	306	ppnK inorganic polyphosphate/ATP-NAD kinase; Provi	82.36
PRK04885	265	ppnK inorganic polyphosphate/ATP-NAD kinase; Provi	82.17
cd04729	219	NanE N-acetylmannosamine-6-phosphate epimerase (Na	82.08
PRK03692	243	putative UDP-N-acetyl-D-mannosaminuronic acid tran	81.74
cd05212	140	NAD_bind_m-THF_DH_Cyclohyd_like NAD(P) binding dom	81.2
PRK14075	256	pnk inorganic polyphosphate/ATP-NAD kinase; Provis	81.17
PRK05458	326	guanosine 5'-monophosphate oxidoreductase; Provisi	81.08
cd04730	236	NPD_like 2-Nitropropane dioxygenase (NPD), one of	80.98
PRK06552	213	keto-hydroxyglutarate-aldolase/keto-deoxy-phosphog	80.91
PRK15484	380	lipopolysaccharide 1,2-N-acetylglucosaminetransfer	80.43
TIGR00007	230	phosphoribosylformimino-5-aminoimidazole carboxami	80.25
COG2022	262	ThiG Uncharacterized enzyme of thiazole biosynthes	80.16
PF04131	192	NanE: Putative N-acetylmannosamine-6-phosphate epi	80.03

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

Probab=99.92  E-value=2.5e-23  Score=158.47  Aligned_cols=119  Identities=29%  Similarity=0.502  Sum_probs=111.3

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc--cCCCCEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL--EMDLPVIM   95 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~--~~~~~iIi   95 (184)
                      ++|+||||++..++.|..+|+..||++..+.++.++++.+.  .. ||+|++|+.||+++|++++++++.  ....|||+
T Consensus         1 ~~ILiveDd~~i~~~l~~~L~~~g~~v~~~~~~~~a~~~~~--~~-~dlviLD~~lP~~dG~~~~~~iR~~~~~~~PIi~   77 (229)
T COG0745           1 MRILLVEDDPELAELLKEYLEEEGYEVDVAADGEEALEAAR--EQ-PDLVLLDLMLPDLDGLELCRRLRAKKGSGPPIIV   77 (229)
T ss_pred             CeEEEEcCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh--cC-CCEEEEECCCCCCCHHHHHHHHHhhcCCCCcEEE
Confidence            47999999999999999999999999999999999999987  55 999999999999999999999983  36789999


Q ss_pred             EEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCC
Q 029986           96 MSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKP  139 (184)
Q Consensus        96 ~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~  139 (184)
                      +|+..+......++++||+||++||+++.+|..+++.++++...
T Consensus        78 Lta~~~~~d~v~gl~~GADDYl~KPf~~~EL~ARi~a~lRR~~~  121 (229)
T COG0745          78 LTARDDEEDRVLGLEAGADDYLTKPFSPRELLARLRALLRRNAG  121 (229)
T ss_pred             EECCCcHHHHHHHHhCcCCeeeeCCCCHHHHHHHHHHHHCcCcC
Confidence            99999999999999999999999999999999999999987653

>COG4566 TtrR Response regulator [Signal transduction mechanisms]

Probab=99.86  E-value=1.3e-21  Score=140.89  Aligned_cols=147  Identities=22%  Similarity=0.287  Sum_probs=120.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhc-ccCCCCEEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVG-LEMDLPVIM   95 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~-~~~~~~iIi   95 (184)
                      ..-|.|||||...++.+..+|++.||.+..+.++++++....  ...|-++++|+.||+++|.++.+.+. ..+..|||+
T Consensus         4 ~~~V~vVDDD~~vr~al~~Ll~s~G~~v~~~~s~~~fL~~~~--~~~pGclllDvrMPg~sGlelq~~L~~~~~~~PVIf   81 (202)
T COG4566           4 EPLVHVVDDDESVRDALAFLLESAGFQVKCFASAEEFLAAAP--LDRPGCLLLDVRMPGMSGLELQDRLAERGIRLPVIF   81 (202)
T ss_pred             CCeEEEEcCcHHHHHHHHHHHHhCCceeeeecCHHHHHhhcc--CCCCCeEEEecCCCCCchHHHHHHHHhcCCCCCEEE
Confidence            446999999999999999999999999999999999999854  45689999999999999999999995 457899999


Q ss_pred             EEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCCCCCCCCCccccCCcccccCCccchhH
Q 029986           96 MSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPFEESDDSYSVNQGNWRTSNRRKDEEE  165 (184)
Q Consensus        96 ~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  165 (184)
                      +|..++-....++++.||.|||.||++...|.+++..++...................+..+++++++-.
T Consensus        82 iTGhgDIpmaV~AmK~GAvDFLeKP~~~q~Lldav~~Al~~~~~~~~~~~~~~~~~~~l~tLT~RERqVl  151 (202)
T COG4566          82 LTGHGDIPMAVQAMKAGAVDFLEKPFSEQDLLDAVERALARDASRRAEADRQAAIRARLATLTPRERQVL  151 (202)
T ss_pred             EeCCCChHHHHHHHHcchhhHHhCCCchHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcCHHHHHHH
Confidence            9999999999999999999999999999999999999887644332222222223334444555544443

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

Probab=99.86  E-value=4.8e-21  Score=156.80  Aligned_cols=116  Identities=29%  Similarity=0.444  Sum_probs=106.9

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhc--CCe-EEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKC--LYE-VTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPV   93 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~--~~~-v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~i   93 (184)
                      .+|+||||++..+++|+.++.+.  |++ |..+.+|.+|++.+.  +..|||||.|+.||+++|+++++.++. .|.+.+
T Consensus         2 ykVlIVDDE~lIr~GLk~lI~w~~~g~eiVgtA~NG~eAleli~--e~~pDiviTDI~MP~mdGLdLI~~ike~~p~~~~   79 (475)
T COG4753           2 YKVLIVDDEPLIREGLKSLIDWEALGIEVVGTAANGKEALELIQ--ETQPDIVITDINMPGMDGLDLIKAIKEQSPDTEF   79 (475)
T ss_pred             eeEEEecChHHHHHHHHHhCChhhcCCeEEEecccHHHHHHHHH--hcCCCEEEEecCCCCCcHHHHHHHHHHhCCCceE
Confidence            58999999999999999999764  765 569999999999998  677999999999999999999999964 578999


Q ss_pred             EEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           94 IMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        94 Ii~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      ||+|+..+.+++.+|++.|+.|||+||++..+|..++.++..
T Consensus        80 IILSGy~eFeYak~Am~lGV~dYLLKP~~k~eL~~~L~ki~~  121 (475)
T COG4753          80 IILSGYDEFEYAKKAMKLGVKDYLLKPVDKAELEEALKKIIG  121 (475)
T ss_pred             EEEeccchhHHHHHHHhcCchhheeCcCCHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999888865

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

Probab=99.86  E-value=1.4e-21  Score=143.29  Aligned_cols=121  Identities=21%  Similarity=0.421  Sum_probs=107.2

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhc-CCe-EEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc-CCCCEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKC-LYE-VTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE-MDLPVI   94 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~-~~~-v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~-~~~~iI   94 (184)
                      ++||||||++..++.-+.+++.. ||. |..+.+.+++..++.  ...||+|++|+.||+++|++++..++.. ..+-||
T Consensus         1 i~VLIiEDD~mVaeih~~yv~~~~gF~~vg~A~~~~ea~~~i~--~~~pDLILLDiYmPd~~Gi~lL~~ir~~~~~~DVI   78 (224)
T COG4565           1 INVLIIEDDPMVAEIHRRYVKQIPGFSVVGTAGTLEEAKMIIE--EFKPDLILLDIYMPDGNGIELLPELRSQHYPVDVI   78 (224)
T ss_pred             CcEEEEcCchHHHHHHHHHHHhCCCceEEEeeccHHHHHHHHH--hhCCCEEEEeeccCCCccHHHHHHHHhcCCCCCEE
Confidence            57999999999999999999986 665 568999999999998  4458999999999999999999999754 577899


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCCC
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPF  140 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~  140 (184)
                      ++|+..+.+.+.+++..|+.||+.||+..+.|.+++....+....+
T Consensus        79 ~iTAA~d~~tI~~alr~Gv~DYLiKPf~~eRl~~aL~~y~~~r~~l  124 (224)
T COG4565          79 VITAASDMETIKEALRYGVVDYLIKPFTFERLQQALTRYRQKRHAL  124 (224)
T ss_pred             EEeccchHHHHHHHHhcCchhheecceeHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999998876654433

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

Probab=99.84  E-value=6.2e-20  Score=150.49  Aligned_cols=119  Identities=35%  Similarity=0.568  Sum_probs=111.4

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhc-ccCCCCEEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVG-LEMDLPVIMM   96 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~-~~~~~~iIi~   96 (184)
                      .+|+||||++..+..+...|+..||.+..+.++.++++.+..  ..+|+|++|+.||+++|+++++.++ ..+.+|||++
T Consensus         5 ~~iLvVDDd~~ir~~l~~~L~~~G~~v~~a~~~~~al~~i~~--~~~~lvl~Di~mp~~~Gl~ll~~i~~~~~~~pVI~~   82 (464)
T COG2204           5 ARILVVDDDPDIRELLEQALELAGYEVVTAESAEEALEALSE--SPFDLVLLDIRMPGMDGLELLKEIKSRDPDLPVIVM   82 (464)
T ss_pred             CCEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCHHHHHHHHhc--CCCCEEEEecCCCCCchHHHHHHHHhhCCCCCEEEE
Confidence            469999999999999999999999999999999999999983  3699999999999999999999995 4579999999


Q ss_pred             EccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCC
Q 029986           97 SVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPK  138 (184)
Q Consensus        97 ~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~  138 (184)
                      |.+.+.+.+..|++.||.||+.||++.+.|..+++.++...+
T Consensus        83 Tg~g~i~~AV~A~k~GA~Dfl~KP~~~~~L~~~v~ral~~~~  124 (464)
T COG2204          83 TGHGDIDTAVEALRLGAFDFLEKPFDLDRLLAIVERALELRE  124 (464)
T ss_pred             eCCCCHHHHHHHHhcCcceeeeCCCCHHHHHHHHHHHHHHhh
Confidence            999999999999999999999999999999999999988644

>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=99.84  E-value=1.4e-19  Score=122.67  Aligned_cols=110  Identities=37%  Similarity=0.618  Sum_probs=102.3

Q ss_pred             EEEEeCCHHHHHHHHHHHHhcCC-eEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc-CCCCEEEEE
Q 029986           20 VLVVDDDPIWLRILEKMLRKCLY-EVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE-MDLPVIMMS   97 (184)
Q Consensus        20 Ilivdd~~~~~~~l~~~L~~~~~-~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~-~~~~iIi~~   97 (184)
                      |+||||++..+..+...|+..|+ .+..+.++.++++.+.  +..||++|+|+.+++.+|.+++++++.. +.+|+|+++
T Consensus         1 Ilivd~~~~~~~~l~~~l~~~~~~~v~~~~~~~~~~~~~~--~~~~d~iiid~~~~~~~~~~~~~~i~~~~~~~~ii~~t   78 (112)
T PF00072_consen    1 ILIVDDDPEIRELLEKLLERAGYEEVTTASSGEEALELLK--KHPPDLIIIDLELPDGDGLELLEQIRQINPSIPIIVVT   78 (112)
T ss_dssp             EEEEESSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHH--HSTESEEEEESSSSSSBHHHHHHHHHHHTTTSEEEEEE
T ss_pred             cEEEECCHHHHHHHHHHHHhCCCCEEEEECCHHHHHHHhc--ccCceEEEEEeeeccccccccccccccccccccEEEec
Confidence            78999999999999999998899 9999999999999997  4559999999999999999999999644 689999999


Q ss_pred             ccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHH
Q 029986           98 VDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQ  131 (184)
Q Consensus        98 ~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~  131 (184)
                      ...+......++++|+++|+.||++.++|.++++
T Consensus        79 ~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~  112 (112)
T PF00072_consen   79 DEDDSDEVQEALRAGADDYLSKPFSPEELRAAIN  112 (112)
T ss_dssp             SSTSHHHHHHHHHTTESEEEESSSSHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHCCCCEEEECCCCHHHHHHhhC
Confidence            9888899999999999999999999999998874

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 ....

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

Probab=99.83  E-value=5.5e-19  Score=133.25  Aligned_cols=125  Identities=30%  Similarity=0.405  Sum_probs=113.3

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcC-Ce-EEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhc-ccCCCCEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCL-YE-VTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVG-LEMDLPVI   94 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~-~~-v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~-~~~~~~iI   94 (184)
                      ++|+|+||++..+..++.+|...+ ++ +..+.+++++++.+.  ...||++++|+.||+++|+++++.++ ..++++|+
T Consensus         1 ~~vlivDDh~l~r~gl~~~L~~~~~~~vv~~a~~~~~~l~~~~--~~~pdvvl~Dl~mP~~~G~e~~~~l~~~~p~~~vv   78 (211)
T COG2197           1 IKVLIVDDHPLVREGLRQLLELEPDLEVVGEASNGEEALDLAR--ELKPDVVLLDLSMPGMDGLEALKQLRARGPDIKVV   78 (211)
T ss_pred             CeEEEECCcHHHHHHHHHHHhhCCCCEEEEEeCCHHHHHHHhh--hcCCCEEEEcCCCCCCChHHHHHHHHHHCCCCcEE
Confidence            479999999999999999998764 66 557778999999876  56799999999999999999999996 55788999


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCCCCCCC
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPFEESD  144 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~~~~~  144 (184)
                      +++...+..+...++++||++|++|..+.++|..+++.+..+..++++..
T Consensus        79 vlt~~~~~~~v~~al~~Ga~Gyl~K~~~~~~l~~ai~~v~~G~~~~~~~~  128 (211)
T COG2197          79 VLTAHDDPAYVIRALRAGADGYLLKDASPEELVEAIRAVAAGGTYLPPDI  128 (211)
T ss_pred             EEeccCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHCCCeEeCHHH
Confidence            99999999999999999999999999999999999999999998877643

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=99.79  E-value=1.2e-17  Score=127.15  Aligned_cols=123  Identities=20%  Similarity=0.308  Sum_probs=108.6

Q ss_pred             CCCCCeEEEEeCCHHHHHHHHHHHHhc-CC-eEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCC
Q 029986           14 FPAGLRVLVVDDDPIWLRILEKMLRKC-LY-EVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMD   90 (184)
Q Consensus        14 ~~~~~~Ilivdd~~~~~~~l~~~L~~~-~~-~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~   90 (184)
                      +|..++|+|+||++..+..+...|... ++ .+..+.++.++++.+.  ...||++++|+.||+.+|+++++.++. .++
T Consensus         1 ~~~~~~ilivdd~~~~~~~l~~~L~~~~~~~~v~~a~~~~~al~~~~--~~~pdlvllD~~mp~~~gle~~~~l~~~~~~   78 (225)
T PRK10046          1 MTAPLTLLIVEDETPLAEMHAEYIRHIPGFSQILLAGNLAQARMMIE--RFKPGLILLDNYLPDGRGINLLHELVQAHYP   78 (225)
T ss_pred             CCCcceEEEECCCHHHHHHHHHHHHhCCCcEEEEEECCHHHHHHHHH--hcCCCEEEEeCCCCCCcHHHHHHHHHhcCCC
Confidence            355789999999999999999999864 67 4678999999999987  566999999999999999999999964 467


Q ss_pred             CCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCC
Q 029986           91 LPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPK  138 (184)
Q Consensus        91 ~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~  138 (184)
                      .+||+++...+.....++++.||++|+.||++.++|..+++.+..+..
T Consensus        79 ~~iivls~~~~~~~~~~al~~Ga~~yl~Kp~~~~~L~~~i~~~~~~~~  126 (225)
T PRK10046         79 GDVVFTTAASDMETVSEAVRCGVFDYLIKPIAYERLGQTLTRFRQRKH  126 (225)
T ss_pred             CCEEEEEcCCCHHHHHHHHHcCccEEEECCcCHHHHHHHHHHHHHHHH
Confidence            899999998888999999999999999999999999999988765433

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

Probab=99.77  E-value=3.4e-18  Score=130.79  Aligned_cols=117  Identities=27%  Similarity=0.437  Sum_probs=106.6

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIMM   96 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi~   96 (184)
                      ++|+||||+......|..+|++.|..+..|++..++++.+.  ...||++|+|+.||+++|++|+++++. .+.+|||++
T Consensus         1 ~~~iiVDdd~a~~~~l~~iLs~~~~~~~~~~~~~eal~~Le--~~kpDLifldI~mp~~ngiefaeQvr~i~~~v~iifI   78 (361)
T COG3947           1 PRIIIVDDDAAIVKLLSVILSRAGHEVRSCSHPVEALDLLE--VFKPDLIFLDIVMPYMNGIEFAEQVRDIESAVPIIFI   78 (361)
T ss_pred             CcEEEEcchHHHHHHHHHHHHhccchhhccCCHHHHHHHHH--hcCCCEEEEEeecCCccHHHHHHHHHHhhccCcEEEE
Confidence            47999999999999999999999999999999999999998  567999999999999999999999964 478999999


Q ss_pred             EccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCC
Q 029986           97 SVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPK  138 (184)
Q Consensus        97 ~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~  138 (184)
                      |++  .++..++++..+.||+.||++.+.|.+++.++.+...
T Consensus        79 ssh--~eya~dsf~~n~~dYl~KPvt~ekLnraIdr~~k~ve  118 (361)
T COG3947          79 SSH--AEYADDSFGMNLDDYLPKPVTPEKLNRAIDRRLKRVE  118 (361)
T ss_pred             ecc--hhhhhhhcccchHhhccCCCCHHHHHHHHHHHhcccc
Confidence            965  6888899999999999999999999999999886543

>PRK10529 DNA-binding transcriptional activator KdpE; Provisional

Probab=99.77  E-value=7.1e-17  Score=121.92  Aligned_cols=118  Identities=25%  Similarity=0.342  Sum_probs=107.7

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMS   97 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi~~   97 (184)
                      .+|+++||++..++.+...|...|+.+..+.++.+++..+.  ...||++|+|+.||+.+|+++++.++..+..|+|+++
T Consensus         2 ~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~~~~~~~--~~~~dlvild~~l~~~~g~~~~~~lr~~~~~pvi~lt   79 (225)
T PRK10529          2 TNVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEAA--TRKPDLIILDLGLPDGDGIEFIRDLRQWSAIPVIVLS   79 (225)
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHh--cCCCCEEEEeCCCCCCCHHHHHHHHHcCCCCCEEEEE
Confidence            47999999999999999999998999999999999988776  4569999999999999999999999876789999999


Q ss_pred             ccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCC
Q 029986           98 VDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQP  137 (184)
Q Consensus        98 ~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~  137 (184)
                      +..+......+++.|+++|+.||++.++|...++.+.++.
T Consensus        80 ~~~~~~~~~~~~~~ga~~~l~kP~~~~~l~~~i~~~~~~~  119 (225)
T PRK10529         80 ARSEESDKIAALDAGADDYLSKPFGIGELQARLRVALRRH  119 (225)
T ss_pred             CCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHhhc
Confidence            8888888999999999999999999999999999887654

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

Probab=99.76  E-value=1.9e-17  Score=130.12  Aligned_cols=120  Identities=34%  Similarity=0.487  Sum_probs=108.0

Q ss_pred             CCCCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cC---
Q 029986           14 FPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EM---   89 (184)
Q Consensus        14 ~~~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~---   89 (184)
                      ....++|++|||.+..+..++..|+..||.+..+.+++++++...  ...||++++|++||+++|++++++++. .+   
T Consensus        11 ~~~~~~vl~vDD~~~~~~~~~~lL~~~~y~v~~ae~g~~a~kl~~--~~~~dlvllD~~mp~mdg~ev~~~lk~~~p~t~   88 (360)
T COG3437          11 PDEKLTVLLVDDEPDNLEALRQLLRMIGYRVIEAENGEEALKLLQ--EEPPDLVLLDVRMPEMDGAEVLNKLKAMSPSTR   88 (360)
T ss_pred             CcccceEEEecCchhHHHHHHHHHHhcccceeeecCchHHHHHhc--ccCCceEEeeccCCCccHHHHHHHHHhcCCccc
Confidence            334678999999999999999999999999999999999999876  445999999999999999999999975 44   


Q ss_pred             CCCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           90 DLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        90 ~~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      .+|++++|...+.+...+++..|+++|+.||++..+|...++..++
T Consensus        89 ~ip~i~lT~~~d~~~~~~~~~~g~~dyl~KP~~~~~l~~rv~~~~q  134 (360)
T COG3437          89 RIPVILLTAYADSEDRQRALEAGADDYLSKPISPKELVARVSSHLQ  134 (360)
T ss_pred             ccceEEEeecCChHHHHHHHHhhHHHHhcCCCCHHHHHHHHHHHHH
Confidence            6799999999999999999999999999999999999888865543

>PRK11173 two-component response regulator; Provisional

Probab=99.75  E-value=1.1e-16  Score=122.23  Aligned_cols=118  Identities=19%  Similarity=0.374  Sum_probs=108.1

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMS   97 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi~~   97 (184)
                      .+|+++||++..+..+...|+..|+.+..+.++.+++..+.  ...||++|+|+.||+.+|+++++.++..+..|+|+++
T Consensus         4 ~~iLiv~dd~~~~~~l~~~L~~~g~~v~~~~~~~~~~~~~~--~~~~dlvild~~l~~~~g~~~~~~lr~~~~~pii~lt   81 (237)
T PRK11173          4 PHILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQILS--ENDINLVIMDINLPGKNGLLLARELREQANVALMFLT   81 (237)
T ss_pred             CeEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHh--hCCCCEEEEcCCCCCCCHHHHHHHHhcCCCCCEEEEE
Confidence            47999999999999999999999999999999999999886  4569999999999999999999999766789999999


Q ss_pred             ccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCC
Q 029986           98 VDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQP  137 (184)
Q Consensus        98 ~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~  137 (184)
                      +..+......+++.|+++|+.||++..+|...++.++++.
T Consensus        82 ~~~~~~~~~~~~~~ga~d~l~kP~~~~eL~~~i~~~l~r~  121 (237)
T PRK11173         82 GRDNEVDKILGLEIGADDYITKPFNPRELTIRARNLLSRT  121 (237)
T ss_pred             CCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHhcc
Confidence            8888888889999999999999999999999998887753

>PRK10840 transcriptional regulator RcsB; Provisional

Probab=99.75  E-value=7.9e-17  Score=121.72  Aligned_cols=124  Identities=20%  Similarity=0.258  Sum_probs=109.7

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCC-e-EEEECCHHHHHHHHHhcCCCccEEEEeCCCCC---CCHHHHHHHhcc-cCC
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLY-E-VTKCNRAEIALDMLRMSKNGYDIVISDVHMPD---MDGFKLHEQVGL-EMD   90 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~-~-v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~---~~g~~l~~~l~~-~~~   90 (184)
                      +++|+|+||++..+..++..|...++ . +..+.++.++++.+.  ...||++|+|+.+++   .+|++++++++. .+.
T Consensus         3 ~~~Ilivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~~~~~~~--~~~~DlvllD~~l~~~~~~~g~~~~~~l~~~~~~   80 (216)
T PRK10840          3 NMNVIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLP--KLDAHVLITDLSMPGDKYGDGITLIKYIKRHFPS   80 (216)
T ss_pred             ceEEEEECCcHHHHHHHHHHHhcCCCCEEEEEECCHHHHHHHHH--hCCCCEEEEeCcCCCCCCCCHHHHHHHHHHHCCC
Confidence            47899999999999999999987654 3 667899999999886  456999999999999   599999999964 478


Q ss_pred             CCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCCCCC
Q 029986           91 LPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPFEE  142 (184)
Q Consensus        91 ~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~~~  142 (184)
                      +|||+++...+......+++.|+++|+.||.+.++|..+++.+..+..++++
T Consensus        81 ~~iIvls~~~~~~~~~~a~~~Ga~~yl~K~~~~~~l~~ai~~v~~g~~~~~~  132 (216)
T PRK10840         81 LSIIVLTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQKGKKFTPE  132 (216)
T ss_pred             CcEEEEEecCCHHHHHHHHHCCCeEEEECCCCHHHHHHHHHHHHCCCeecCH
Confidence            8999999988888889999999999999999999999999999998877654

>PRK10816 DNA-binding transcriptional regulator PhoP; Provisional

Probab=99.75  E-value=1.4e-16  Score=120.31  Aligned_cols=118  Identities=28%  Similarity=0.412  Sum_probs=108.2

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIMM   96 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi~   96 (184)
                      |+|+++||++..+..+...|...|+.+..+.++.+++..+.  ...||++++|+.+|+.+|+++++.++. .+.+|+|++
T Consensus         1 m~iLlv~d~~~~~~~l~~~L~~~g~~v~~~~~~~~~l~~~~--~~~~dlvild~~l~~~~g~~l~~~lr~~~~~~pii~l   78 (223)
T PRK10816          1 MRVLVVEDNALLRHHLKVQLQDAGHQVDAAEDAKEADYYLN--EHLPDIAIVDLGLPDEDGLSLIRRWRSNDVSLPILVL   78 (223)
T ss_pred             CeEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh--hCCCCEEEEECCCCCCCHHHHHHHHHhcCCCCCEEEE
Confidence            57999999999999999999999999999999999999876  456999999999999999999999964 468999999


Q ss_pred             EccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCC
Q 029986           97 SVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQP  137 (184)
Q Consensus        97 ~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~  137 (184)
                      +...+......+++.|+++|+.||++..+|...+..+.++.
T Consensus        79 s~~~~~~~~~~~l~~Ga~d~l~kp~~~~eL~~~i~~~~~~~  119 (223)
T PRK10816         79 TARESWQDKVEVLSAGADDYVTKPFHIEEVMARMQALMRRN  119 (223)
T ss_pred             EcCCCHHHHHHHHHcCCCeeEeCCCCHHHHHHHHHHHHhcc
Confidence            99888888999999999999999999999999999887754

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

Probab=99.75  E-value=2.2e-16  Score=109.49  Aligned_cols=118  Identities=36%  Similarity=0.609  Sum_probs=100.7

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHH-HHHHHHHhcCC-CccEEEEeCCCCCCCHHHHHHHhccc-CCCC
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAE-IALDMLRMSKN-GYDIVISDVHMPDMDGFKLHEQVGLE-MDLP   92 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~-~~~~~l~~~~~-~~dlvilD~~l~~~~g~~l~~~l~~~-~~~~   92 (184)
                      ...+|+++||++..+..++..|...|+.+..+.++. ++++.+.  .. .||++++|+.||+++|+++++.++.. ..+|
T Consensus         4 ~~~~vLivdD~~~~~~~~~~~l~~~g~~v~~a~~g~~~al~~~~--~~~~~dlii~D~~mp~~~G~~~~~~l~~~~~~~p   81 (130)
T COG0784           4 SGLRVLVVDDEPVNRRLLKRLLEDLGYEVVEAADGEEEALELLR--ELPQPDLILLDINMPGMDGIELLRRLRARGPNIP   81 (130)
T ss_pred             CCcEEEEEcCCHHHHHHHHHHHHHcCCeEEEeCChHHHHHHHHH--hCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCCCC
Confidence            467899999999999999999999999999999995 9999987  44 49999999999999999999999765 6778


Q ss_pred             EEEEEccCChHHHHHHHHcCCCceEeCCCCHHH-HHHHHHHHHc
Q 029986           93 VIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKE-LRNIWQHVAQ  135 (184)
Q Consensus        93 iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~-l~~~l~~~~~  135 (184)
                      ++++++.........++..|+++|+.||+...+ +...+.....
T Consensus        82 vv~~t~~~~~~~~~~~~~~g~~~~l~kP~~~~~~l~~~i~~~~~  125 (130)
T COG0784          82 VILLTAYADEADRERALAAGADDYLTKPIFLEEELLAALRRLLA  125 (130)
T ss_pred             EEEEEcCcCHHHHHHHHHcCCCeEEcCCCCcHHHHHHHHHHHHH
Confidence            877777766665677899999999999977666 6777665443

>PRK11517 transcriptional regulatory protein YedW; Provisional

Probab=99.75  E-value=9.5e-17  Score=120.88  Aligned_cols=119  Identities=23%  Similarity=0.441  Sum_probs=108.5

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMS   97 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi~~   97 (184)
                      |+|+++||++..+..+...|...|+.+..+.+..+++..+.  ...||++++|..+++.+|+++++.++..+..|+|+++
T Consensus         1 m~iliv~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~l~~~~--~~~~dlvi~d~~~~~~~g~~~~~~l~~~~~~~ii~ls   78 (223)
T PRK11517          1 MKILLIEDNQRTQEWVTQGLSEAGYVIDAVSDGRDGLYLAL--KDDYALIILDIMLPGMDGWQILQTLRTAKQTPVICLT   78 (223)
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh--cCCCCEEEEECCCCCCCHHHHHHHHHcCCCCCEEEEE
Confidence            57999999999999999999988999999999999998876  4669999999999999999999999766688999999


Q ss_pred             ccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCC
Q 029986           98 VDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPK  138 (184)
Q Consensus        98 ~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~  138 (184)
                      ...+......++..|+++|+.||++.++|...++.+.++..
T Consensus        79 ~~~~~~~~~~a~~~Ga~~~l~kp~~~~~l~~~i~~~~~~~~  119 (223)
T PRK11517         79 ARDSVDDRVRGLDSGANDYLVKPFSFSELLARVRAQLRQHH  119 (223)
T ss_pred             CCCCHHHHHHHHhcCCCEEEECCCCHHHHHHHHHHHHcccc
Confidence            88888889999999999999999999999999998877643

>PRK10766 DNA-binding transcriptional regulator TorR; Provisional

Probab=99.74  E-value=2e-16  Score=119.17  Aligned_cols=118  Identities=20%  Similarity=0.394  Sum_probs=107.7

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMM   96 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi~   96 (184)
                      .++|+++||++..+..+...|...|+.+..+.++.+++..+.  ...||++++|..+|+.+|+++++.++..+..|+|++
T Consensus         2 ~~~iLlv~d~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~--~~~~dlvild~~l~~~~g~~~~~~lr~~~~~~ii~l   79 (221)
T PRK10766          2 SYHILVVEDEPVTRARLQGYFEQEGYTVSEAASGAGMREIMQ--NQHVDLILLDINLPGEDGLMLTRELRSRSTVGIILV   79 (221)
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHh--cCCCCEEEEeCCCCCCCHHHHHHHHHhCCCCCEEEE
Confidence            358999999999999999999999999999999999998876  456999999999999999999999976678899999


Q ss_pred             EccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           97 SVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        97 ~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      +...+......+++.||++|+.||++..+|...+..+.++
T Consensus        80 ~~~~~~~~~~~~l~~Ga~d~l~kP~~~~~L~~~i~~~~~r  119 (221)
T PRK10766         80 TGRTDSIDRIVGLEMGADDYVTKPLELRELLVRVKNLLWR  119 (221)
T ss_pred             ECCCcHHHHHHHHHcCCCcEEeCCCCHHHHHHHHHHHHhh
Confidence            9888888888999999999999999999999999887765

>PRK09836 DNA-binding transcriptional activator CusR; Provisional

Probab=99.74  E-value=2.2e-16  Score=119.44  Aligned_cols=118  Identities=22%  Similarity=0.432  Sum_probs=107.5

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc-CCCCEEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE-MDLPVIMM   96 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~-~~~~iIi~   96 (184)
                      |+|++++|++..+..+...|...|+.+..+.++.++++.+.  ...||++|+|+.+++.+|+++++.++.. +.+|+|++
T Consensus         1 m~iliv~d~~~~~~~l~~~L~~~g~~v~~~~~~~~~~~~~~--~~~~dlvild~~~~~~~g~~~~~~lr~~~~~~pii~l   78 (227)
T PRK09836          1 MKLLIVEDEKKTGEYLTKGLTEAGFVVDLADNGLNGYHLAM--TGDYDLIILDIMLPDVNGWDIVRMLRSANKGMPILLL   78 (227)
T ss_pred             CeEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh--hCCCCEEEEECCCCCCCHHHHHHHHHhcCCCCCEEEE
Confidence            57999999999999999999988999999999999998876  4569999999999999999999999653 68899999


Q ss_pred             EccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCC
Q 029986           97 SVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQP  137 (184)
Q Consensus        97 ~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~  137 (184)
                      +...+......+++.|+++|+.||++.++|...++.+.++.
T Consensus        79 s~~~~~~~~~~~~~~Ga~~~l~kp~~~~~l~~~i~~~~~~~  119 (227)
T PRK09836         79 TALGTIEHRVKGLELGADDYLVKPFAFAELLARVRTLLRRG  119 (227)
T ss_pred             EcCCCHHHHHHHHhCCCCEEEeCCCCHHHHHHHHHHHHhcc
Confidence            99888899999999999999999999999999999887653

>PRK10643 DNA-binding transcriptional regulator BasR; Provisional

Probab=99.74  E-value=3.8e-16  Score=117.31  Aligned_cols=119  Identities=27%  Similarity=0.479  Sum_probs=107.5

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIMM   96 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi~   96 (184)
                      |+|+++||++..+..+...|...|+.+..+.++.+++..+.  ...||++++|+.+++.+|+++++.++. .+..|+|++
T Consensus         1 ~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~--~~~~d~illd~~~~~~~g~~~~~~l~~~~~~~pii~l   78 (222)
T PRK10643          1 MKILIVEDDTLLLQGLILALQTEGYACDCASTAREAEALLE--SGHYSLVVLDLGLPDEDGLHLLRRWRQKKYTLPVLIL   78 (222)
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHH--hCCCCEEEEECCCCCCCHHHHHHHHHhcCCCCcEEEE
Confidence            57999999999999999999998999989999999998876  456999999999999999999999964 367899999


Q ss_pred             EccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCC
Q 029986           97 SVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPK  138 (184)
Q Consensus        97 ~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~  138 (184)
                      +...+......+++.|+++|+.||++.++|...++.+.++..
T Consensus        79 s~~~~~~~~~~~~~~ga~~~l~kp~~~~~l~~~i~~~~~~~~  120 (222)
T PRK10643         79 TARDTLEDRVAGLDVGADDYLVKPFALEELHARIRALIRRHQ  120 (222)
T ss_pred             ECCCCHHHHHHHHhcCCCeEEeCCCCHHHHHHHHHHHHhhhc
Confidence            988888889999999999999999999999999998876543

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

Probab=99.74  E-value=1.1e-16  Score=130.57  Aligned_cols=122  Identities=30%  Similarity=0.435  Sum_probs=112.1

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc---CCCC
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE---MDLP   92 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~---~~~~   92 (184)
                      ...+|+++||+...+..+..+|...|+.+..+.++++++..+.  +..||+||+|+.||+.||++++++++..   ..+|
T Consensus       131 ~~~kILvvdD~~~~~~~l~~~L~~~g~~v~~a~~~~~Al~~~~--e~~~dlil~d~~mp~~dg~el~~~lr~~~~t~~ip  208 (435)
T COG3706         131 APKKILVVDDDATQRERLRRILQVEGFRVVEATDGEEALLQLA--ELPPDLVLLDANMPDMDGLELCTRLRQLERTRDIP  208 (435)
T ss_pred             cCceEEEEcCcHHHHHHHHHHHHhccceeeeecCHHHHHHHHh--cCCCcEEEEecCCCccCHHHHHHHHhccccccccc
Confidence            3568999999999999999999999999999999999999987  5579999999999999999999999643   4789


Q ss_pred             EEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCC
Q 029986           93 VIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKP  139 (184)
Q Consensus        93 iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~  139 (184)
                      +|++++..+.....+||+.|++||+.||+...++...+...+++.++
T Consensus       209 ii~~~~~~d~~~~~~Af~~G~~Dyi~kPi~~~~l~~Rl~~~l~~~~~  255 (435)
T COG3706         209 IILLSSKDDDELVVRAFELGVNDYITKPIEEGELRARLRRQLRRKRY  255 (435)
T ss_pred             EEEEecccchHHHHHHHHcCCcceEecCCCHHHHHHHHHHHHHhhhH
Confidence            99999999999999999999999999999999999988888887654

>PRK13856 two-component response regulator VirG; Provisional

Probab=99.73  E-value=5.3e-16  Score=118.79  Aligned_cols=117  Identities=22%  Similarity=0.371  Sum_probs=105.0

Q ss_pred             eEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEEEEc
Q 029986           19 RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMSV   98 (184)
Q Consensus        19 ~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi~~~   98 (184)
                      +|+++||++..+..+...|...|+.+..+.++.++++.+.  ...||++|+|..+|+.+|+++++.++....+|+++++.
T Consensus         3 ~ILived~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~--~~~~dlvi~d~~l~~~~g~~l~~~i~~~~~~pii~lt~   80 (241)
T PRK13856          3 HVLVIDDDVAMRHLIVEYLTIHAFKVTAVADSQQFNRVLA--SETVDVVVVDLNLGREDGLEIVRSLATKSDVPIIIISG   80 (241)
T ss_pred             eEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHh--hCCCCEEEEeCCCCCCCHHHHHHHHHhcCCCcEEEEEC
Confidence            7999999999999999999999999999999999998876  45699999999999999999999997667889999987


Q ss_pred             cC-ChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCC
Q 029986           99 DG-CTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQP  137 (184)
Q Consensus        99 ~~-~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~  137 (184)
                      .. +......+++.||++|+.||++.++|...++.++++.
T Consensus        81 ~~~~~~~~~~~l~~Ga~~yl~kP~~~~eL~~~i~~~l~~~  120 (241)
T PRK13856         81 DRLEEADKVVALELGATDFIAKPFGTREFLARIRVALRVR  120 (241)
T ss_pred             CCCcHHHHHHHHhcCcCeEEeCCCCHHHHHHHHHHHHhhc
Confidence            43 5566778999999999999999999999999887764

>PRK10161 transcriptional regulator PhoB; Provisional

Probab=99.73  E-value=4.2e-16  Score=118.07  Aligned_cols=117  Identities=25%  Similarity=0.421  Sum_probs=106.9

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc---CCCCEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE---MDLPVI   94 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~---~~~~iI   94 (184)
                      .+|+++||++..+..+...|...|+.+..+.++.+++..+.  ...||++|+|..+++.+|+++++.++..   +.+|+|
T Consensus         3 ~~Ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~~~~~~~--~~~~dlvild~~l~~~~g~~~~~~l~~~~~~~~~pvi   80 (229)
T PRK10161          3 RRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLN--EPWPDLILLDWMLPGGSGIQFIKHLKRESMTRDIPVV   80 (229)
T ss_pred             CeEEEEcCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh--ccCCCEEEEeCCCCCCCHHHHHHHHHhccccCCCCEE
Confidence            57999999999999999999988999999999999999876  4569999999999999999999999643   578999


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      ++++..+......++++|+++|+.||++..+|...+..+.++
T Consensus        81 ~ls~~~~~~~~~~~~~~Ga~~~l~kp~~~~~L~~~i~~~~~~  122 (229)
T PRK10161         81 MLTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRR  122 (229)
T ss_pred             EEECCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHHhc
Confidence            999888888999999999999999999999999999988775

>CHL00148 orf27 Ycf27; Reviewed

Probab=99.73  E-value=4.2e-16  Score=118.61  Aligned_cols=121  Identities=36%  Similarity=0.561  Sum_probs=109.1

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEE
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIM   95 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi   95 (184)
                      +.++|+++||++..+..+...|...|+.+..+.+..+++..+.  ...||++++|+.+++.+|+++++.++..+++|+|+
T Consensus         5 ~~~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~~l~~~~--~~~~d~illd~~~~~~~g~~~~~~l~~~~~~~ii~   82 (240)
T CHL00148          5 SKEKILVVDDEAYIRKILETRLSIIGYEVITASDGEEALKLFR--KEQPDLVILDVMMPKLDGYGVCQEIRKESDVPIIM   82 (240)
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHH--hcCCCEEEEeCCCCCCCHHHHHHHHHhcCCCcEEE
Confidence            3578999999999999999999988999988999999998876  45699999999999999999999997667899999


Q ss_pred             EEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCC
Q 029986           96 MSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPK  138 (184)
Q Consensus        96 ~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~  138 (184)
                      ++...+......+++.|+++|+.||++.++|...++.+.++..
T Consensus        83 ls~~~~~~~~~~~~~~Ga~~~l~kp~~~~~L~~~i~~~~~~~~  125 (240)
T CHL00148         83 LTALGDVSDRITGLELGADDYVVKPFSPKELEARIRSVLRRTN  125 (240)
T ss_pred             EECCCCHHhHHHHHHCCCCEEEeCCCCHHHHHHHHHHHHhhcc
Confidence            9988888888899999999999999999999999998876643

>PRK10336 DNA-binding transcriptional regulator QseB; Provisional

Probab=99.73  E-value=4.1e-16  Score=116.96  Aligned_cols=117  Identities=23%  Similarity=0.382  Sum_probs=106.2

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIMM   96 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi~   96 (184)
                      |+|+++||++..+..+...|...|+.+..+.++.+++..+.  ...||++|+|..+++.+|+++++.++. .+.+|+|++
T Consensus         1 ~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~--~~~~dlvild~~l~~~~g~~~~~~i~~~~~~~~ii~l   78 (219)
T PRK10336          1 MRILLIEDDMLIGDGIKTGLSKMGFSVDWFTQGRQGKEALY--SAPYDAVILDLTLPGMDGRDILREWREKGQREPVLIL   78 (219)
T ss_pred             CeEEEEcCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHh--hCCCCEEEEECCCCCCCHHHHHHHHHhcCCCCcEEEE
Confidence            57999999999999999999988999989999999998876  456999999999999999999999964 467899999


Q ss_pred             EccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           97 SVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        97 ~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      +...+......+++.|+++|+.||++.++|..++..+.++
T Consensus        79 t~~~~~~~~~~~~~~ga~~~i~kp~~~~~l~~~i~~~~~~  118 (219)
T PRK10336         79 TARDALAERVEGLRLGADDYLCKPFALIEVAARLEALMRR  118 (219)
T ss_pred             ECCCCHHHHHHHHhCCCCeEEECCCCHHHHHHHHHHHHhc
Confidence            9888888889999999999999999999999999988764

>PRK10701 DNA-binding transcriptional regulator RstA; Provisional

Probab=99.73  E-value=5.1e-16  Score=118.62  Aligned_cols=118  Identities=20%  Similarity=0.314  Sum_probs=106.7

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMS   97 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi~~   97 (184)
                      .+|+++||++..+..+...|...|+.+..+.++.+++..+.  ...||++|+|+.||+.+|+++++.++.....|+|+++
T Consensus         2 ~~iLivedd~~~~~~l~~~L~~~g~~v~~~~~~~~~l~~~~--~~~~dlvild~~l~~~~g~~~~~~ir~~~~~pii~l~   79 (240)
T PRK10701          2 NKIVFVEDDAEVGSLIAAYLAKHDIDVTVEPRGDRAEATIL--REQPDLVLLDIMLPGKDGMTICRDLRPKWQGPIVLLT   79 (240)
T ss_pred             ceEEEEeCCHHHHHHHHHHHHHcCCEEEEeCCHHHHHHHHh--hCCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCEEEEE
Confidence            37999999999999999999999999999999999999876  4569999999999999999999999766678999998


Q ss_pred             ccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCC
Q 029986           98 VDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQP  137 (184)
Q Consensus        98 ~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~  137 (184)
                      ..........++..|+++|+.||++..+|...++.++++.
T Consensus        80 ~~~~~~~~~~~~~~Ga~d~l~kP~~~~~l~~~i~~~l~~~  119 (240)
T PRK10701         80 SLDSDMNHILALEMGACDYILKTTPPAVLLARLRLHLRQN  119 (240)
T ss_pred             CCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHHhcc
Confidence            8777778889999999999999999999999999877653

>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB

Probab=99.72  E-value=5.6e-16  Score=116.54  Aligned_cols=119  Identities=27%  Similarity=0.514  Sum_probs=107.5

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc---CCCCEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE---MDLPVI   94 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~---~~~~iI   94 (184)
                      .+|+++||++..+..+...|...|+.+..+.+..+++..+.  ...||++++|..+++.+|+++++.++..   +.+|+|
T Consensus         3 ~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~--~~~~d~vi~d~~~~~~~g~~~~~~l~~~~~~~~~~ii   80 (226)
T TIGR02154         3 RRILVVEDEPAIRELIAYNLEKAGYDVVEAGDGDEALTLIN--ERGPDLILLDWMLPGTSGIELCRRLRRRPETRAIPII   80 (226)
T ss_pred             CeEEEEeCCHHHHHHHHHHHHHCCCEEEEEcCHHHHHHHHH--hcCCCEEEEECCCCCCcHHHHHHHHHccccCCCCCEE
Confidence            57999999999999999999988999989999999999886  4569999999999999999999999643   578999


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCC
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPK  138 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~  138 (184)
                      +++...+......+++.|+++|+.||++.++|...+..+.++..
T Consensus        81 ~ls~~~~~~~~~~~~~~Ga~~~l~kp~~~~~l~~~i~~~~~~~~  124 (226)
T TIGR02154        81 MLTARGEEEDRVRGLETGADDYITKPFSPRELLARIKAVLRRIR  124 (226)
T ss_pred             EEecCCCHHHHHHHHhcCcceEEeCCCCHHHHHHHHHHHhcccc
Confidence            99988888888999999999999999999999999999887643

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.

>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional

Probab=99.72  E-value=6.5e-16  Score=116.98  Aligned_cols=118  Identities=29%  Similarity=0.471  Sum_probs=106.2

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMS   97 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi~~   97 (184)
                      .+|+++||++..+..+...|...|+.+..+.++.+++..+.   ..||++++|+.||+.+|+++++.++.....|+|+++
T Consensus         2 ~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~---~~~d~vl~d~~~~~~~g~~~~~~l~~~~~~~ii~lt   78 (232)
T PRK10955          2 NKILLVDDDRELTSLLKELLEMEGFNVIVAHDGEQALDLLD---DSIDLLLLDVMMPKKNGIDTLKELRQTHQTPVIMLT   78 (232)
T ss_pred             ceEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHhh---cCCCEEEEeCCCCCCcHHHHHHHHHhcCCCcEEEEE
Confidence            37999999999999999999988999989999999998764   259999999999999999999999755458999999


Q ss_pred             ccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCC
Q 029986           98 VDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPK  138 (184)
Q Consensus        98 ~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~  138 (184)
                      ...+......+++.|+++|+.||++.++|...++.+.++..
T Consensus        79 ~~~~~~~~~~~~~~ga~~~l~kp~~~~~l~~~i~~~~~~~~  119 (232)
T PRK10955         79 ARGSELDRVLGLELGADDYLPKPFNDRELVARIRAILRRSH  119 (232)
T ss_pred             CCCCHHHHHHHHHcCCCEEEcCCCCHHHHHHHHHHHHhccc
Confidence            88888888899999999999999999999999999887654

>PLN03029 type-a response regulator protein; Provisional

Probab=99.72  E-value=5.4e-16  Score=117.94  Aligned_cols=120  Identities=28%  Similarity=0.560  Sum_probs=104.2

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcC------------------CCccEEEEeCCCCCCC
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSK------------------NGYDIVISDVHMPDMD   77 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~------------------~~~dlvilD~~l~~~~   77 (184)
                      ..++|++|||++..+..+...|...|+.+..+.++.++++.+....                  ..+|+||+|+.||+++
T Consensus         7 ~~~~VLiVdd~~~~~~~l~~~L~~~g~~v~~a~sg~~al~~l~~~~~d~~~p~~~~~~~~~~~~~~~dlVllD~~mp~~~   86 (222)
T PLN03029          7 SQFHVLAVDDSLIDRKLIEKLLKTSSYQVTTVDSGSKALKFLGLHEDDRSNPDTPSVSPNSHQEVEVNLIITDYCMPGMT   86 (222)
T ss_pred             CCccEEEEeCCHHHHHHHHHHHHHcCceEEEECCHHHHHHHHHhccccccccccccccccccccccCCEEEEcCCCCCCC
Confidence            3578999999999999999999999999999999999999885211                  1367999999999999


Q ss_pred             HHHHHHHhccc---CCCCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           78 GFKLHEQVGLE---MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        78 g~~l~~~l~~~---~~~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      |+++++.++..   ..+|+|+++.........+++..|+++|+.||++..+|...+..+.+
T Consensus        87 G~e~l~~ir~~~~~~~ipvIils~~~~~~~~~~al~~Ga~dyl~KP~~~~~L~~l~~~~~~  147 (222)
T PLN03029         87 GYDLLKKIKESSSLRNIPVVIMSSENVPSRITRCLEEGAEEFFLKPVQLSDLNRLKPHMMK  147 (222)
T ss_pred             HHHHHHHHHhccccCCCcEEEEeCCCCHHHHHHHHHhCchheEECCCCHHHHHHHHHHHHH
Confidence            99999999643   47899999988888888899999999999999999999777665443

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

Probab=99.71  E-value=3.4e-16  Score=108.99  Aligned_cols=113  Identities=23%  Similarity=0.393  Sum_probs=105.3

Q ss_pred             eEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEEEE
Q 029986           19 RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIMMS   97 (184)
Q Consensus        19 ~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi~~   97 (184)
                      ..+|||||..+...|...+++.||.+..+++.++++...+  ...|.-.++|+.|.+++|+++++.++. .++..+|++|
T Consensus        11 ~lllvdDD~~f~~~LaRa~e~RGf~v~~a~~~~eal~~ar--t~~PayAvvDlkL~~gsGL~~i~~lr~~~~d~rivvLT   88 (182)
T COG4567          11 SLLLVDDDTPFLRTLARAMERRGFAVVTAESVEEALAAAR--TAPPAYAVVDLKLGDGSGLAVIEALRERRADMRIVVLT   88 (182)
T ss_pred             eeEEecCChHHHHHHHHHHhccCceeEeeccHHHHHHHHh--cCCCceEEEEeeecCCCchHHHHHHHhcCCcceEEEEe
Confidence            6999999999999999999999999999999999999988  567999999999999999999999964 4789999999


Q ss_pred             ccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHH
Q 029986           98 VDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHV  133 (184)
Q Consensus        98 ~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~  133 (184)
                      .+.+-..++.|.+.||++|+.||.+.+.+..++..-
T Consensus        89 Gy~sIATAV~AvKlGA~~YLaKPAdaDdi~aAl~~~  124 (182)
T COG4567          89 GYASIATAVEAVKLGACDYLAKPADADDILAALLRR  124 (182)
T ss_pred             cchHHHHHHHHHHhhhhhhcCCCCChHHHHHHHhhc
Confidence            999999999999999999999999999998877654

>PRK11083 DNA-binding response regulator CreB; Provisional

Probab=99.71  E-value=9.5e-16  Score=115.56  Aligned_cols=120  Identities=30%  Similarity=0.406  Sum_probs=107.9

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc-CCCCEEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE-MDLPVIMM   96 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~-~~~~iIi~   96 (184)
                      ++|+|+||++..++.+...|...|+.+..+.+..+++..+.  ...||++++|+.+++.+|+++++.++.. +.+|+|++
T Consensus         4 ~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~--~~~~dlvl~d~~~~~~~g~~~~~~l~~~~~~~~ii~l   81 (228)
T PRK11083          4 PTILLVEDEQAIADTLVYALQSEGFTVEWFERGLPALDKLR--QQPPDLVILDVGLPDISGFELCRQLLAFHPALPVIFL   81 (228)
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHCCCEEEEEcCHHHHHHHHh--cCCCCEEEEeCCCCCCCHHHHHHHHHhhCCCCCEEEE
Confidence            58999999999999999999988999988999999988876  4569999999999999999999999654 68999999


Q ss_pred             EccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCC
Q 029986           97 SVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKP  139 (184)
Q Consensus        97 ~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~  139 (184)
                      +...+......++..|+++|+.||++.++|..+++.+.++...
T Consensus        82 s~~~~~~~~~~a~~~Ga~~~l~kp~~~~~l~~~i~~~~~~~~~  124 (228)
T PRK11083         82 TARSDEVDRLVGLEIGADDYVAKPFSPREVAARVRTILRRVKK  124 (228)
T ss_pred             EcCCcHHHHHHHhhcCCCeEEECCCCHHHHHHHHHHHHCcccc
Confidence            9888888888999999999999999999999999988876543

>PRK09468 ompR osmolarity response regulator; Provisional

Probab=99.71  E-value=1.3e-15  Score=116.20  Aligned_cols=119  Identities=27%  Similarity=0.459  Sum_probs=108.3

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc-CCCCEEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE-MDLPVIM   95 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~-~~~~iIi   95 (184)
                      ..+|+|++|++..+..+...|...|+.+..+.++.++++.+.  ...||++|+|..+++.+|+++++.++.. +.+|+|+
T Consensus         5 ~~~iLiv~d~~~~~~~l~~~L~~~g~~v~~~~~~~~~~~~~~--~~~~dlvild~~l~~~~g~~~~~~lr~~~~~~pii~   82 (239)
T PRK09468          5 NYKILVVDDDMRLRALLERYLTEQGFQVRSAANAEQMDRLLT--RESFHLMVLDLMLPGEDGLSICRRLRSQNNPTPIIM   82 (239)
T ss_pred             CCeEEEEcCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh--cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCCEEE
Confidence            458999999999999999999999999999999999998876  4669999999999999999999999644 6789999


Q ss_pred             EEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCC
Q 029986           96 MSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQP  137 (184)
Q Consensus        96 ~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~  137 (184)
                      ++...+......++..|+++|+.||++.++|...+..++++.
T Consensus        83 ls~~~~~~~~~~~l~~Ga~~~l~kP~~~~~L~~~i~~~~~r~  124 (239)
T PRK09468         83 LTAKGEEVDRIVGLEIGADDYLPKPFNPRELLARIRAVLRRQ  124 (239)
T ss_pred             EECCCcHHHHHHHHhcCCCeEEECCCCHHHHHHHHHHHhccc
Confidence            998888888889999999999999999999999999887754

>TIGR03787 marine_sort_RR proteobacterial dedicated sortase system response regulator

Probab=99.71  E-value=1.1e-15  Score=115.53  Aligned_cols=118  Identities=23%  Similarity=0.366  Sum_probs=106.3

Q ss_pred             eEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCC--CCHHHHHHHhccc-CCCCEEE
Q 029986           19 RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPD--MDGFKLHEQVGLE-MDLPVIM   95 (184)
Q Consensus        19 ~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~--~~g~~l~~~l~~~-~~~~iIi   95 (184)
                      +|+++||++..+..+...|...|+.+..+.++.+++..+.  ...||++++|+.+++  .+|+++++.++.. +.+|+|+
T Consensus         2 ~iLivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~--~~~~dlvild~~l~~~~~~g~~~~~~i~~~~~~~pii~   79 (227)
T TIGR03787         2 RIAIVEDEAAIRENYADALKRQGYQVTTYADRPSAMQAFR--QRLPDLAIIDIGLGEEIDGGFMLCQDLRSLSATLPIIF   79 (227)
T ss_pred             eEEEEeCCHHHHHHHHHHHHHCCcEEEEecCHHHHHHHHH--hCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCCCCEEE
Confidence            6999999999999999999988999988999999999876  456999999999998  4899999999643 6789999


Q ss_pred             EEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCC
Q 029986           96 MSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPK  138 (184)
Q Consensus        96 ~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~  138 (184)
                      ++...+......++.+|+++|+.||++.++|...++.+.++..
T Consensus        80 ls~~~~~~~~~~~~~~Ga~~~l~kp~~~~~l~~~i~~~~~~~~  122 (227)
T TIGR03787        80 LTARDSDFDTVSGLRLGADDYLTKDISLPHLLARITALFRRAE  122 (227)
T ss_pred             EECCCCHHHHHHHHhcCCCEEEECCCCHHHHHHHHHHHHHhhh
Confidence            9988888889999999999999999999999999999887654

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.

>PRK09958 DNA-binding transcriptional activator EvgA; Provisional

Probab=99.71  E-value=1.2e-15  Score=113.51  Aligned_cols=121  Identities=18%  Similarity=0.248  Sum_probs=108.1

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEE-EECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc-CCCCEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVT-KCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE-MDLPVIM   95 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~-~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~-~~~~iIi   95 (184)
                      |+|+++||++..+..+...|+..|+.+. .+.++.+++..+.  ...||++++|..+++.+|+++++.++.. +..|+|+
T Consensus         1 m~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~~--~~~~dlvi~d~~~~~~~g~~~~~~l~~~~~~~~ii~   78 (204)
T PRK09958          1 MNAIIIDDHPLAIAAIRNLLIKNDIEILAELTEGGSAVQRVE--TLKPDIVIIDVDIPGVNGIQVLETLRKRQYSGIIII   78 (204)
T ss_pred             CcEEEECCcHHHHHHHHHHHhcCCCEEEEEeCCHHHHHHHHH--ccCCCEEEEeCCCCCCCHHHHHHHHHhhCCCCeEEE
Confidence            5799999999999999999998899886 6899999999887  4569999999999999999999999643 5778999


Q ss_pred             EEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCCC
Q 029986           96 MSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPF  140 (184)
Q Consensus        96 ~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~  140 (184)
                      +++..+......++..|+++|+.||++.++|..+++.++++..+.
T Consensus        79 ls~~~~~~~~~~~~~~ga~~~i~kp~~~~~l~~~i~~~~~~~~~~  123 (204)
T PRK09958         79 VSAKNDHFYGKHCADAGANGFVSKKEGMNNIIAAIEAAKNGYCYF  123 (204)
T ss_pred             EeCCCCHHHHHHHHHCCCCEEEecCCCHHHHHHHHHHHHcCCccc
Confidence            998888888899999999999999999999999999998875543

>PRK10430 DNA-binding transcriptional activator DcuR; Provisional

Probab=99.71  E-value=7.8e-16  Score=118.12  Aligned_cols=116  Identities=19%  Similarity=0.326  Sum_probs=101.2

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhc-CCe-EEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKC-LYE-VTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVI   94 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~-~~~-v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iI   94 (184)
                      ++|+|+||++..++.+...|... ++. +..+.++.++++.+......||++|+|+.||+.+|+++++.++. .+.+|+|
T Consensus         2 ~~VLivdd~~~~~~~l~~~L~~~~~~~~~~~~~~~~~a~~~~~~~~~~~DlvilD~~~p~~~G~eli~~l~~~~~~~~vI   81 (239)
T PRK10430          2 INVLIVDDDAMVAELNRRYVAQIPGFQCCGTASTLEQAKEIIFNSDTPIDLILLDIYMQQENGLDLLPVLHEAGCKSDVI   81 (239)
T ss_pred             eeEEEEcCCHHHHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhcCCCCCEEEEecCCCCCCcHHHHHHHHhhCCCCCEE
Confidence            58999999999999999999864 665 45788899998887532355999999999999999999999964 4688999


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHH
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHV  133 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~  133 (184)
                      ++++..+......++..|+++|+.||++.++|..++..+
T Consensus        82 ~ls~~~~~~~~~~al~~Ga~~yl~Kp~~~~~l~~~i~~~  120 (239)
T PRK10430         82 VISSAADAATIKDSLHYGVVDYLIKPFQASRFEEALTGW  120 (239)
T ss_pred             EEECCCcHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHH
Confidence            999988889999999999999999999999999999863

>PRK09483 response regulator; Provisional

Probab=99.70  E-value=1.6e-15  Score=113.81  Aligned_cols=122  Identities=24%  Similarity=0.319  Sum_probs=108.8

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhc-CCeEE-EECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKC-LYEVT-KCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVI   94 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~-~~~v~-~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iI   94 (184)
                      ++|+|+||++..+..+...|... ++.+. .+.+..+++..+.  ...||++|+|+.+++.+|+++++.++. .+.+|+|
T Consensus         2 ~~ilivd~~~~~~~~l~~~L~~~~~~~~v~~~~~~~~~~~~~~--~~~~dlvi~d~~~~~~~g~~~~~~l~~~~~~~~ii   79 (217)
T PRK09483          2 INVLLVDDHELVRAGIRRILEDIKGIKVVGEACCGEDAVKWCR--TNAVDVVLMDMNMPGIGGLEATRKILRYTPDVKII   79 (217)
T ss_pred             eEEEEECCcHHHHHHHHHHHccCCCCEEEEEeCCHHHHHHHHH--hcCCCEEEEeCCCCCCCHHHHHHHHHHHCCCCeEE
Confidence            58999999999999999999874 77765 7889999998887  456999999999999999999999953 5678999


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCCCC
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPFE  141 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~~  141 (184)
                      +++...+......++..|+++|+.||++.++|..+++.+..+..+.+
T Consensus        80 ~ls~~~~~~~~~~~~~~g~~~~l~k~~~~~~l~~~i~~~~~g~~~~~  126 (217)
T PRK09483         80 MLTVHTENPLPAKVMQAGAAGYLSKGAAPQEVVSAIRSVHSGQRYIA  126 (217)
T ss_pred             EEeCCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHCCCcccC
Confidence            99988888888999999999999999999999999999998876554

>TIGR01387 cztR_silR_copR heavy metal response regulator

Probab=99.69  E-value=3.6e-15  Score=111.63  Aligned_cols=119  Identities=27%  Similarity=0.482  Sum_probs=107.3

Q ss_pred             EEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEEEEc
Q 029986           20 VLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIMMSV   98 (184)
Q Consensus        20 Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi~~~   98 (184)
                      |+++||++..+..+...|...|+.+..+.+..+++..+.  ...||++++|+.+++.+|+++++.++. .+.+|+|+++.
T Consensus         1 iliidd~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~--~~~~dlvl~d~~~~~~~g~~~~~~l~~~~~~~~iivls~   78 (218)
T TIGR01387         1 ILVVEDEQKTAEYLQQGLSESGYVVDAASNGRDGLHLAL--KDDYDLIILDVMLPGMDGWQILQTLRRSGKQTPVLFLTA   78 (218)
T ss_pred             CEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh--cCCCCEEEEeCCCCCCCHHHHHHHHHccCCCCcEEEEEc
Confidence            589999999999999999988999999999999998876  456999999999999999999999964 46889999999


Q ss_pred             cCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCCC
Q 029986           99 DGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPF  140 (184)
Q Consensus        99 ~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~  140 (184)
                      ..+......++..|+++|+.||++.+++...++.+.++....
T Consensus        79 ~~~~~~~~~~~~~Ga~~~l~kp~~~~~l~~~i~~~~~~~~~~  120 (218)
T TIGR01387        79 RDSVADKVKGLDLGADDYLVKPFSFSELLARVRTLLRRSHSL  120 (218)
T ss_pred             CCCHHHHHHHHHcCCCeEEECCCCHHHHHHHHHHHhcccccC
Confidence            888889999999999999999999999999999988765543

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.

>PRK11107 hybrid sensory histidine kinase BarA; Provisional

Probab=99.69  E-value=2.1e-15  Score=135.06  Aligned_cols=121  Identities=25%  Similarity=0.496  Sum_probs=110.6

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc---cCCCC
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL---EMDLP   92 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~---~~~~~   92 (184)
                      .+++|+||||++..+..++..|...|+.+..+.++.++++.+.  ...||+||+|+.||+++|+++++.++.   .+.+|
T Consensus       666 ~~~~vLivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~al~~~~--~~~~dlil~D~~mp~~~g~~~~~~lr~~~~~~~~p  743 (919)
T PRK11107        666 LPLTVMAVDDNPANLKLIGALLEEQVEHVVLCDSGHQAVEQAK--QRPFDLILMDIQMPGMDGIRACELIRQLPHNQNTP  743 (919)
T ss_pred             CCCeEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHH--hCCCCEEEEeCCCCCCcHHHHHHHHHhcccCCCCC
Confidence            4679999999999999999999999999999999999999987  567999999999999999999999974   35789


Q ss_pred             EEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCC
Q 029986           93 VIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPK  138 (184)
Q Consensus        93 iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~  138 (184)
                      ||+++..........+++.|+++|+.||++..+|...++.+.....
T Consensus       744 ii~lt~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~~~~~~  789 (919)
T PRK11107        744 IIAVTAHAMAGERERLLSAGMDDYLAKPIDEAMLKQVLLRYKPGPK  789 (919)
T ss_pred             EEEEeCCCCHHHHHHHHHcCCCeEeeCCCCHHHHHHHHHHHccccc
Confidence            9999998888999999999999999999999999999998876543

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

Probab=99.68  E-value=2e-15  Score=135.25  Aligned_cols=119  Identities=32%  Similarity=0.527  Sum_probs=109.2

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc-CCCCEE
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE-MDLPVI   94 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~-~~~~iI   94 (184)
                      .+++|+||||++..+..+...|+..|+.+..+.++.++++.+.  ...||+||+|+.||+++|+++++.++.. +.+|||
T Consensus       800 ~~~~ILvVdD~~~~~~~l~~~L~~~G~~v~~a~~g~eal~~l~--~~~~DlVl~D~~mP~mdG~el~~~ir~~~~~~pII  877 (924)
T PRK10841        800 DDMMILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVLS--KNHIDIVLTDVNMPNMDGYRLTQRLRQLGLTLPVI  877 (924)
T ss_pred             CCCEEEEECCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHH--hCCCCEEEEcCCCCCCCHHHHHHHHHhcCCCCCEE
Confidence            4679999999999999999999999999999999999999987  5669999999999999999999999754 578999


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      ++++....+....+++.|+++|+.||++.++|...+.....+
T Consensus       878 ~lTa~~~~~~~~~~~~aG~d~~L~KPv~~~~L~~~L~~~~~~  919 (924)
T PRK10841        878 GVTANALAEEKQRCLEAGMDSCLSKPVTLDVLKQTLTVYAER  919 (924)
T ss_pred             EEECCCCHHHHHHHHHCCCCEEEeCCCCHHHHHHHHHHHHHH
Confidence            999988888889999999999999999999999999887653

>PRK15347 two component system sensor kinase SsrA; Provisional

Probab=99.68  E-value=1.7e-15  Score=135.79  Aligned_cols=118  Identities=24%  Similarity=0.399  Sum_probs=107.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc-----CC
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE-----MD   90 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~-----~~   90 (184)
                      .+++|+||||++..+..+...|...|+.+..+.++.++++.+.  ...||+||+|+.||+++|+++++.++..     +.
T Consensus       689 ~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~~--~~~~dlil~D~~mp~~~G~~~~~~ir~~~~~~~~~  766 (921)
T PRK15347        689 WQLQILLVDDVETNRDIIGMMLVELGQQVTTAASGTEALELGR--QHRFDLVLMDIRMPGLDGLETTQLWRDDPNNLDPD  766 (921)
T ss_pred             ccCCEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHh--cCCCCEEEEeCCCCCCCHHHHHHHHHhchhhcCCC
Confidence            3579999999999999999999999999999999999999987  5679999999999999999999999642     56


Q ss_pred             CCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           91 LPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        91 ~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      +|||++++.........+++.|+++|+.||++.++|..++..+..
T Consensus       767 ~pii~lt~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~~~  811 (921)
T PRK15347        767 CMIVALTANAAPEEIHRCKKAGMNHYLTKPVTLAQLARALELAAE  811 (921)
T ss_pred             CcEEEEeCCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHh
Confidence            899999998888888999999999999999999999999987654

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

Probab=99.68  E-value=7.6e-16  Score=135.40  Aligned_cols=121  Identities=29%  Similarity=0.529  Sum_probs=109.7

Q ss_pred             CCCCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc--CCC
Q 029986           14 FPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE--MDL   91 (184)
Q Consensus        14 ~~~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~--~~~   91 (184)
                      .-.+.+||++||+...+...+.+|+..|.++..+.++.+|++.+.. ...||+||+|++||.+||++..+.+|+.  .++
T Consensus       663 ~l~g~~iLlvddn~vn~~Va~~~l~~~g~~~~~~~sg~e~l~~~~~-~~~y~~ifmD~qMP~mDG~e~~~~irk~~~~~~  741 (786)
T KOG0519|consen  663 LLTGPKILLVDDNPVNRKVATGMLKKLGAEVTEVNSGQEALDKLKP-PHSYDVIFMDLQMPEMDGYEATREIRKKERWHL  741 (786)
T ss_pred             cccCCceEEEecccchHHHHHHHHHHhCCeeEeecCcHHHHHhcCC-CCcccEEEEEcCCcccchHHHHHHHHHhhcCCC
Confidence            3347799999999999999999999999999999999999999862 4569999999999999999999999754  489


Q ss_pred             CEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           92 PVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        92 ~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      |||.+|+...+....++++.|.++|+.||+..+.+...+.+.+.
T Consensus       742 pIvAlTa~~~~~~~~~c~~~Gmd~yl~KP~~~~~l~~~l~~~~~  785 (786)
T KOG0519|consen  742 PIVALTADADPSTEEECLEVGMDGYLSKPFTLEKLVKILREFLL  785 (786)
T ss_pred             CEEEEecCCcHHHHHHHHHhCCceEEcccccHHHHHHHHHHHhc
Confidence            99999999989999999999999999999999999998887653

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

Probab=99.67  E-value=3.2e-15  Score=114.19  Aligned_cols=115  Identities=27%  Similarity=0.434  Sum_probs=96.9

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcC-Ce-EEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCL-YE-VTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIM   95 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~-~~-v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi   95 (184)
                      ++|+||||++..++.+...|...+ +. +..+.++.+++..+.  ...||++|+|+.||+.+|+++++.++.....++|+
T Consensus         2 ~~IlIvdd~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~~--~~~~dlv~lDi~~~~~~G~~~~~~l~~~~~~~ii~   79 (238)
T PRK11697          2 IKVLIVDDEPLAREELRELLQEEGDIEIVGECSNAIEAIGAIH--RLKPDVVFLDIQMPRISGLELVGMLDPEHMPYIVF   79 (238)
T ss_pred             cEEEEECCCHHHHHHHHHHHhhCCCcEEEEEeCCHHHHHHHHH--hcCCCEEEEeCCCCCCCHHHHHHHhcccCCCEEEE
Confidence            689999999999999999998876 33 457889999998876  45699999999999999999999986433445677


Q ss_pred             EEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           96 MSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        96 ~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      +++.  .+...++++.|+.+|+.||++.++|..++..+...
T Consensus        80 vt~~--~~~~~~a~~~~~~~yl~KP~~~~~l~~~l~~~~~~  118 (238)
T PRK11697         80 VTAF--DEYAIKAFEEHAFDYLLKPIDPARLAKTLARLRQE  118 (238)
T ss_pred             Eecc--HHHHHHHHhcCCcEEEECCCCHHHHHHHHHHHHHh
Confidence            6654  46778999999999999999999999999888653

>PRK10360 DNA-binding transcriptional activator UhpA; Provisional

Probab=99.67  E-value=6e-15  Score=109.00  Aligned_cols=118  Identities=26%  Similarity=0.312  Sum_probs=104.2

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhc-CCe-EEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKC-LYE-VTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIM   95 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~-~~~-v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi   95 (184)
                      ++|+|+||++..+..+...|... ++. +..+.++.+++..+.  ...||++|+|+.+++.+|+++++.++  +..|+++
T Consensus         2 ~~ilivd~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~l~~~~--~~~~dlvi~d~~~~~~~g~~~~~~l~--~~~~vi~   77 (196)
T PRK10360          2 ITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLP--GRGVQVCICDISMPDISGLELLSQLP--KGMATIM   77 (196)
T ss_pred             eEEEEECCcHHHHHHHHHHHccCCCcEEEEEECCHHHHHHHHh--cCCCCEEEEeCCCCCCCHHHHHHHHc--cCCCEEE
Confidence            58999999999999999999754 554 568889999999886  45699999999999999999999885  3579999


Q ss_pred             EEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCC
Q 029986           96 MSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKP  139 (184)
Q Consensus        96 ~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~  139 (184)
                      ++...+......++..|+++|+.||++.+++..+++.+.++...
T Consensus        78 ~s~~~~~~~~~~~~~~ga~~~i~kp~~~~~l~~~i~~~~~~~~~  121 (196)
T PRK10360         78 LSVHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVATGGCY  121 (196)
T ss_pred             EECCCCHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHcCCee
Confidence            99988888889999999999999999999999999999887543

>PRK11466 hybrid sensory histidine kinase TorS; Provisional

Probab=99.67  E-value=4.5e-15  Score=133.03  Aligned_cols=122  Identities=25%  Similarity=0.348  Sum_probs=109.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEE
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVI   94 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iI   94 (184)
                      ++++|+|+||++..+..+...|...|+.+..+.++.++++.+.. ...||+||+|+.||+++|+++++.++. .+++|+|
T Consensus       680 ~~~~vLivdD~~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~~~-~~~~Dlvl~D~~mp~~~G~~~~~~lr~~~~~~~ii  758 (914)
T PRK11466        680 DGLRLLLIEDNPLTQRITAEMLNTSGAQVVAVGNAAQALETLQN-SEPFAAALVDFDLPDYDGITLARQLAQQYPSLVLI  758 (914)
T ss_pred             CCcceEEEeCCHHHHHHHHHHHHhcCCceEEeCCHHHHHHHHHc-CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCCCCEE
Confidence            36789999999999999999999999999999999999998752 345899999999999999999999964 4789999


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCC
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPK  138 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~  138 (184)
                      +++..........++..|+++|+.||++.++|...+..+..+..
T Consensus       759 ~~t~~~~~~~~~~~~~~g~~~~l~KP~~~~~L~~~i~~~~~~~~  802 (914)
T PRK11466        759 GFSAHVIDETLRQRTSSLFRGIIPKPVPREVLGQLLAHYLQLQV  802 (914)
T ss_pred             EEeCCCchhhHHHHHhcCcCCEEeCCCCHHHHHHHHHHHhhhcc
Confidence            99998888888899999999999999999999999999887544

>PRK09935 transcriptional regulator FimZ; Provisional

Probab=99.66  E-value=1.3e-14  Score=108.04  Aligned_cols=121  Identities=21%  Similarity=0.329  Sum_probs=106.4

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhc-CCeEE-EECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKC-LYEVT-KCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPV   93 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~-~~~v~-~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~i   93 (184)
                      +.+|+|++|++..+..+...|... ++.+. .+.++.++...+.  ...||++++|..+++.+|.++++.++. .+.+|+
T Consensus         3 ~~~iliv~d~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~--~~~~dlvild~~l~~~~g~~~~~~l~~~~~~~~i   80 (210)
T PRK09935          3 PASVIIMDTHPIIRMSIEVLLQKNSELQIVLKTDDYRITIDYLR--TRPVDLIIMDIDLPGTDGFTFLKRIKQIQSTVKV   80 (210)
T ss_pred             cceEEEECCcHHHHHHHHHHHhhCCCceEEEEeCCHHHHHHHHH--hcCCCEEEEeCCCCCCCHHHHHHHHHHhCCCCcE
Confidence            468999999999999999999876 57664 6788888888876  456999999999999999999999964 467899


Q ss_pred             EEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCC
Q 029986           94 IMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKP  139 (184)
Q Consensus        94 Ii~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~  139 (184)
                      |++++..+......++..|+++|+.||++.++|..+++.++++...
T Consensus        81 i~ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~l~~~~~  126 (210)
T PRK09935         81 LFLSSKSECFYAGRAIQAGANGFVSKCNDQNDIFHAVQMILSGYTF  126 (210)
T ss_pred             EEEECCCcHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHcCCce
Confidence            9999988888889999999999999999999999999998887554

>PRK14084 two-component response regulator; Provisional

Probab=99.65  E-value=1e-14  Score=112.11  Aligned_cols=115  Identities=24%  Similarity=0.421  Sum_probs=98.0

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcC-C-eEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc-CCCCEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCL-Y-EVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE-MDLPVI   94 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~-~-~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~-~~~~iI   94 (184)
                      ++|+||||++..+..+...|...+ + .+..+.++++++..+.  ...||++|+|+.||+.+|+++++.++.. +..++|
T Consensus         1 ~~ilivdd~~~~~~~l~~~l~~~~~~~~v~~~~~~~~~l~~~~--~~~~dlv~lDi~m~~~~G~~~~~~i~~~~~~~~iI   78 (246)
T PRK14084          1 MKALIVDDEPLARNELTYLLNEIGGFEEINEAENVKETLEALL--INQYDIIFLDINLMDESGIELAAKIQKMKEPPAII   78 (246)
T ss_pred             CEEEEECCCHHHHHHHHHHHHhCCCceEEEEECCHHHHHHHHH--hcCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCEEE
Confidence            579999999999999999998764 4 5668899999999886  4569999999999999999999999754 455677


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      ++++.  .....++++.|+.+|+.||++.++|..+++.+.++
T Consensus        79 ~~t~~--~~~~~~~~~~~~~~yl~KP~~~~~l~~~l~~~~~~  118 (246)
T PRK14084         79 FATAH--DQFAVKAFELNATDYILKPFEQKRIEQAVNKVRAT  118 (246)
T ss_pred             EEecC--hHHHHHHHhcCCcEEEECCCCHHHHHHHHHHHHHh
Confidence            76654  45678899999999999999999999999988654

>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional

Probab=99.65  E-value=1.8e-14  Score=109.58  Aligned_cols=117  Identities=24%  Similarity=0.430  Sum_probs=106.6

Q ss_pred             eEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEEEEc
Q 029986           19 RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMSV   98 (184)
Q Consensus        19 ~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi~~~   98 (184)
                      +|+++||++..+..+...|...|+.+..+.++.+++..+.  ...||++++|..+++.+|+++++.++..+..|+++++.
T Consensus        12 ~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~--~~~~dlvl~d~~~~~~~g~~~~~~l~~~~~~pii~l~~   89 (240)
T PRK10710         12 RILIVEDEPKLGQLLIDYLQAASYATTLLSHGDEVLPYVR--QTPPDLILLDLMLPGTDGLTLCREIRRFSDIPIVMVTA   89 (240)
T ss_pred             eEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHh--hCCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCEEEEEc
Confidence            7999999999999999999988999999999999999886  45699999999999999999999997667899999998


Q ss_pred             cCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCC
Q 029986           99 DGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQP  137 (184)
Q Consensus        99 ~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~  137 (184)
                      ..+......++..|+++|+.||++.++|...++.+.++.
T Consensus        90 ~~~~~~~~~~~~~ga~~~l~kp~~~~~L~~~i~~~~~~~  128 (240)
T PRK10710         90 KIEEIDRLLGLEIGADDYICKPYSPREVVARVKTILRRC  128 (240)
T ss_pred             CCCHHHHHHHHhcCCCeEEECCCCHHHHHHHHHHHHhhc
Confidence            887788889999999999999999999999998887654

>TIGR02875 spore_0_A sporulation transcription factor Spo0A

Probab=99.65  E-value=1.3e-14  Score=112.66  Aligned_cols=118  Identities=26%  Similarity=0.406  Sum_probs=102.9

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhc-CCeE-EEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc-C--CC
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKC-LYEV-TKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE-M--DL   91 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~-~~~v-~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~-~--~~   91 (184)
                      .++|+++||++..+..+...|... ++.+ ..+.++.++++.+.  ...||+|++|+.||+.+|+++++.++.. .  ..
T Consensus         2 ~~~vLivdd~~~~~~~l~~~L~~~~~~~~~~~a~~~~eal~~l~--~~~~DlvllD~~mp~~dG~~~l~~i~~~~~~~~~   79 (262)
T TIGR02875         2 KIRIVIADDNKEFCNLLKEYLAAQPDMEVVGVAHNGVDALELIK--EQQPDVVVLDIIMPHLDGIGVLEKLNEIELSARP   79 (262)
T ss_pred             CcEEEEEcCCHHHHHHHHHHHhcCCCeEEEEEeCCHHHHHHHHH--hcCCCEEEEeCCCCCCCHHHHHHHHHhhccccCC
Confidence            468999999999999999999864 4554 47899999999987  4569999999999999999999999643 2  37


Q ss_pred             CEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           92 PVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        92 ~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      |+|+++..........+++.|+++|+.||++..+|...+..+..+
T Consensus        80 ~iI~lt~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~i~~~~~~  124 (262)
T TIGR02875        80 RVIMLSAFGQEKITQRAVALGADYYVLKPFDLEILAARIRQLAWG  124 (262)
T ss_pred             eEEEEeCCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHcc
Confidence            899999888888888999999999999999999999999988764

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.

>PRK15479 transcriptional regulatory protein TctD; Provisional

Probab=99.65  E-value=2.4e-14  Score=107.42  Aligned_cols=120  Identities=26%  Similarity=0.447  Sum_probs=106.5

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIMM   96 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi~   96 (184)
                      |+|+++|+++.....+...|...|+.+..+.++.++...+.  ...||++++|..+++.+|+++++.++. .+..|+|++
T Consensus         1 ~~ilivd~~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~--~~~~d~vild~~~~~~~~~~~~~~i~~~~~~~~ii~l   78 (221)
T PRK15479          1 MRLLLAEDNRELAHWLEKALVQNGFAVDCVFDGLAADHLLQ--SEMYALAVLDINMPGMDGLEVLQRLRKRGQTLPVLLL   78 (221)
T ss_pred             CeEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHh--hCCCCEEEEeCCCCCCcHHHHHHHHHhcCCCCCEEEE
Confidence            47999999999999999999988999888999999988776  456999999999999999999999964 467899999


Q ss_pred             EccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCC
Q 029986           97 SVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKP  139 (184)
Q Consensus        97 ~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~  139 (184)
                      +...+......++..|+++|+.||++.+++...+..+.++...
T Consensus        79 t~~~~~~~~~~~~~~g~~~~i~kp~~~~~l~~~i~~~~~~~~~  121 (221)
T PRK15479         79 TARSAVADRVKGLNVGADDYLPKPFELEELDARLRALLRRSAG  121 (221)
T ss_pred             ECCCCHHHHHHHHHcCCCeeEeCCCCHHHHHHHHHHHHhhhcc
Confidence            9888888888999999999999999999999999988775443

>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional

Probab=99.65  E-value=6.8e-15  Score=111.33  Aligned_cols=121  Identities=12%  Similarity=0.136  Sum_probs=99.9

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHH-HHhc-ccCCCCEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLH-EQVG-LEMDLPVI   94 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~-~~l~-~~~~~~iI   94 (184)
                      ..+++++||++..+..|+..|......+..+.++.++++.+.    .||+|++|+.||+.+|++++ +.++ ..+.++||
T Consensus        10 ~~~~~~v~~~~l~~~~l~~~L~~~~~v~~~~~~~~~~~~~~~----~~DvvllDi~~p~~~G~~~~~~~i~~~~p~~~vv   85 (216)
T PRK10100         10 GHTLLLITKPSLQATALLQHLKQSLAITGKLHNIQRSLDDIS----SGSIILLDMMEADKKLIHYWQDTLSRKNNNIKIL   85 (216)
T ss_pred             CceEEEEeChHhhhHHHHHHHHHhCCCeEEEcCHHHhhccCC----CCCEEEEECCCCCccHHHHHHHHHHHhCCCCcEE
Confidence            456999999999999999999854444557778888887643    38999999999999999986 5565 45789999


Q ss_pred             EEEccCChHHHHHHHH--cCCCceEeCCCCHHHHHHHHHHHHcCCCCCCCC
Q 029986           95 MMSVDGCTQDVMKGVT--HGACNYLLKPIRIKELRNIWQHVAQQPKPFEES  143 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~--~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~~~~  143 (184)
                      +++...+  ....++.  .||.+|+.|+.+.++|.++++.+..+..++++.
T Consensus        86 vlt~~~~--~~~~~~~~~~Ga~G~l~K~~~~~~L~~aI~~v~~G~~~~~~~  134 (216)
T PRK10100         86 LLNTPED--YPYREIENWPHINGVFYAMEDQERVVNGLQGVLRGECYFTQK  134 (216)
T ss_pred             EEECCch--hHHHHHHHhcCCeEEEECCCCHHHHHHHHHHHHcCCcccCHH
Confidence            9998755  4445555  499999999999999999999999998888754

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=99.64  E-value=1.3e-14  Score=121.08  Aligned_cols=120  Identities=30%  Similarity=0.449  Sum_probs=108.0

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCE
Q 029986           15 PAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPV   93 (184)
Q Consensus        15 ~~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~i   93 (184)
                      ++..+|+|+||++..+..+...|...|+.+..+.++.+++..+.  ...||+|++|+.||+.+|+++++.++. .+.+|+
T Consensus         2 ~~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~--~~~~dlillD~~~p~~~g~~ll~~i~~~~~~~pv   79 (457)
T PRK11361          2 TAINRILIVDDEDNVRRMLSTAFALQGFETHCANNGRTALHLFA--DIHPDVVLMDIRMPEMDGIKALKEMRSHETRTPV   79 (457)
T ss_pred             CCCCeEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh--cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCCE
Confidence            45668999999999999999999999999999999999999886  556999999999999999999999964 467899


Q ss_pred             EEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           94 IMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        94 Ii~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      |+++...+......+++.|+++|+.||++.+++...+..+...
T Consensus        80 I~lt~~~~~~~~~~a~~~Ga~d~l~KP~~~~~L~~~i~~~l~~  122 (457)
T PRK11361         80 ILMTAYAEVETAVEALRCGAFDYVIKPFDLDELNLIVQRALQL  122 (457)
T ss_pred             EEEeCCCCHHHHHHHHHCCccEEEecccCHHHHHHHHhhhccc
Confidence            9999988888999999999999999999999999988876653

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=99.64  E-value=7.3e-15  Score=122.03  Aligned_cols=119  Identities=29%  Similarity=0.534  Sum_probs=107.3

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEE
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVI   94 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iI   94 (184)
                      ..++|+||||++..+..+...|...|+.+..+.++.+++..+.  ...||+||+|+.||+.+|+++++.++. .+.+|+|
T Consensus         4 ~~~~Ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~--~~~~DlvilD~~m~~~~G~~~~~~ir~~~~~~~vi   81 (441)
T PRK10365          4 DNIDILVVDDDISHCTILQALLRGWGYNVALANSGRQALEQVR--EQVFDLVLCDVRMAEMDGIATLKEIKALNPAIPVL   81 (441)
T ss_pred             CcceEEEEECCHHHHHHHHHHHHHCCCeEEEeCCHHHHHHHHh--cCCCCEEEEeCCCCCCCHHHHHHHHHhhCCCCeEE
Confidence            3578999999999999999999999999999999999999876  456999999999999999999999964 4678999


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      +++...+......+++.|+.+|+.||++.++|...+..+..+
T Consensus        82 ~lt~~~~~~~~~~a~~~ga~~~l~Kp~~~~~L~~~l~~~l~~  123 (441)
T PRK10365         82 IMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAH  123 (441)
T ss_pred             EEECCCCHHHHHHHHHhhhHHHhcCCCCHHHHHHHHHHHHHH
Confidence            999888888999999999999999999999999988876653

>PRK15115 response regulator GlrR; Provisional

Probab=99.64  E-value=1.1e-14  Score=121.28  Aligned_cols=118  Identities=30%  Similarity=0.513  Sum_probs=107.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIM   95 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi   95 (184)
                      ..+|+||||++..+..+...|...|+.+..+.++.+++..+.  ...||+||+|+.||+.+|+++++.++. .+.+|+|+
T Consensus         5 ~~~vLiVdd~~~~~~~l~~~L~~~g~~v~~~~~~~eal~~l~--~~~~dlvilD~~lp~~~g~~ll~~l~~~~~~~pvIv   82 (444)
T PRK15115          5 PAHLLLVDDDPGLLKLLGMRLTSEGYSVVTAESGQEALRVLN--REKVDLVISDLRMDEMDGMQLFAEIQKVQPGMPVII   82 (444)
T ss_pred             CCeEEEEECCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHh--cCCCCEEEEcCCCCCCCHHHHHHHHHhcCCCCcEEE
Confidence            468999999999999999999999999999999999999886  456999999999999999999999953 46789999


Q ss_pred             EEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           96 MSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        96 ~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      +++..+......+++.|+++|+.||++.++|...+..+...
T Consensus        83 lt~~~~~~~~~~a~~~Ga~~~l~KP~~~~~L~~~l~~~~~~  123 (444)
T PRK15115         83 LTAHGSIPDAVAATQQGVFSFLTKPVDRDALYKAIDDALEQ  123 (444)
T ss_pred             EECCCCHHHHHHHHhcChhhhccCCCCHHHHHHHHHHHHHh
Confidence            99988888899999999999999999999999999888764

>TIGR02956 TMAO_torS TMAO reductase sytem sensor TorS

Probab=99.64  E-value=1e-14  Score=131.45  Aligned_cols=118  Identities=23%  Similarity=0.355  Sum_probs=108.1

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc-CC---CC
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE-MD---LP   92 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~-~~---~~   92 (184)
                      +.+|+||||++..+..+...|+..|+.+..+.++.++++.+.  ...||+||+|+.||+++|+++++.++.. +.   +|
T Consensus       702 ~~~iLvvdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--~~~~dlvl~D~~mp~~~g~~~~~~ir~~~~~~~~~p  779 (968)
T TIGR02956       702 PQRVLLVEDNEVNQMVAQGFLTRLGHKVTLAESGQSALECFH--QHAFDLALLDINLPDGDGVTLLQQLRAIYGAKNEVK  779 (968)
T ss_pred             ccceEEEcCcHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHH--CCCCCEEEECCCCCCCCHHHHHHHHHhCccccCCCe
Confidence            458999999999999999999999999999999999999987  5679999999999999999999999753 22   89


Q ss_pred             EEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           93 VIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        93 iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      ||+++..........++..|+++|+.||++..+|...+..+...
T Consensus       780 ii~lta~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~~~~  823 (968)
T TIGR02956       780 FIAFSAHVFNEDVAQYLAAGFDGFLAKPVVEEQLTAMIAVILAG  823 (968)
T ss_pred             EEEEECCCCHHHHHHHHHCCCCEEEeCCCCHHHHHHHHHHHhcc
Confidence            99999988888899999999999999999999999999988754

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).

>PRK11091 aerobic respiration control sensor protein ArcB; Provisional

Probab=99.63  E-value=1.8e-14  Score=127.44  Aligned_cols=119  Identities=22%  Similarity=0.389  Sum_probs=104.1

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc---CC-CC
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE---MD-LP   92 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~---~~-~~   92 (184)
                      +++|+||||++..+..+...|+..|+.+..+.++.++++.+.  ...||+||+|+.||+++|+++++.++..   +. .|
T Consensus       525 ~~~ILivdD~~~~~~~l~~~L~~~g~~v~~a~~~~eal~~~~--~~~~Dlvl~D~~mp~~~G~e~~~~ir~~~~~~~~~~  602 (779)
T PRK11091        525 ALNILLVEDIELNVIVARSVLEKLGNSVDVAMTGKEALEMFD--PDEYDLVLLDIQLPDMTGLDIARELRERYPREDLPP  602 (779)
T ss_pred             ccceEEEcCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHhh--cCCCCEEEEcCCCCCCCHHHHHHHHHhccccCCCCc
Confidence            578999999999999999999999999999999999999987  5669999999999999999999999643   34 47


Q ss_pred             EEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCC
Q 029986           93 VIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPK  138 (184)
Q Consensus        93 iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~  138 (184)
                      +|+++.... .....+++.|+++|+.||++..+|...+..+.....
T Consensus       603 ii~~ta~~~-~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~~~~~~  647 (779)
T PRK11091        603 LVALTANVL-KDKKEYLDAGMDDVLSKPLSVPALTAMIKKFWDTQD  647 (779)
T ss_pred             EEEEECCch-HhHHHHHHCCCCEEEECCCCHHHHHHHHHHHhcccc
Confidence            888876554 446788999999999999999999999999876543

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

Probab=99.62  E-value=3.2e-14  Score=119.18  Aligned_cols=116  Identities=30%  Similarity=0.424  Sum_probs=105.9

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIMM   96 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi~   96 (184)
                      .+|+||||++..+..+...|...|+.+..+.++.+++..+.  ...||+||+|+.||+.+|+++++.++. .+.+|+|++
T Consensus         4 ~~ILiVdd~~~~~~~L~~~L~~~g~~v~~~~s~~~al~~l~--~~~~DlvllD~~lp~~dgl~~l~~ir~~~~~~pvIvl   81 (469)
T PRK10923          4 GIVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLEALA--SKTPDVLLSDIRMPGMDGLALLKQIKQRHPMLPVIIM   81 (469)
T ss_pred             CeEEEEECCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHh--cCCCCEEEECCCCCCCCHHHHHHHHHhhCCCCeEEEE
Confidence            48999999999999999999999999999999999999987  456999999999999999999999964 467899999


Q ss_pred             EccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           97 SVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        97 ~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      +...+......+++.|+++|+.||++.+++...+..++.
T Consensus        82 t~~~~~~~~~~a~~~Ga~~~l~KP~~~~~L~~~i~~~l~  120 (469)
T PRK10923         82 TAHSDLDAAVSAYQQGAFDYLPKPFDIDEAVALVERAIS  120 (469)
T ss_pred             ECCCCHHHHHHHHhcCcceEEecCCcHHHHHHHHHHHHH
Confidence            998888889999999999999999999999888887654

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

Probab=99.61  E-value=2.9e-14  Score=131.05  Aligned_cols=119  Identities=29%  Similarity=0.513  Sum_probs=108.7

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCE
Q 029986           15 PAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPV   93 (184)
Q Consensus        15 ~~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~i   93 (184)
                      +..++|+||||++..+..+...|+..|+.+..+.++.++++.+.  ...||+||+|+.||+++|+++++.++. .+.+|+
T Consensus       956 ~~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~--~~~~dlil~D~~mp~~~g~~~~~~i~~~~~~~pi 1033 (1197)
T PRK09959        956 PEKLSILIADDHPTNRLLLKRQLNLLGYDVDEATDGVQALHKVS--MQHYDLLITDVNMPNMDGFELTRKLREQNSSLPI 1033 (1197)
T ss_pred             ccCceEEEcCCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHhh--cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCCE
Confidence            34578999999999999999999999999999999999999987  567999999999999999999999964 467899


Q ss_pred             EEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           94 IMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        94 Ii~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      |+++..........+++.|+++|+.||++.++|...++.+..
T Consensus      1034 i~lt~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~~~ 1075 (1197)
T PRK09959       1034 WGLTANAQANEREKGLSCGMNLCLFKPLTLDVLKTHLSQLHQ 1075 (1197)
T ss_pred             EEEECCCCHHHHHHHHHCCCCEEEeCCCCHHHHHHHHHHHhh
Confidence            999999888899999999999999999999999999987754

>PRK13435 response regulator; Provisional

Probab=99.61  E-value=7.7e-14  Score=98.77  Aligned_cols=120  Identities=20%  Similarity=0.271  Sum_probs=101.1

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEE-EECCHHHHHHHHHhcCCCccEEEEeCCCC-CCCHHHHHHHhcccCCCCEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVT-KCNRAEIALDMLRMSKNGYDIVISDVHMP-DMDGFKLHEQVGLEMDLPVI   94 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~-~~~~~~~~~~~l~~~~~~~dlvilD~~l~-~~~g~~l~~~l~~~~~~~iI   94 (184)
                      .++|+|+++++.....+...|+..|+.+. .+.+..++++.+.  ...||++|+|..++ +.+|+++++.++..+.+|+|
T Consensus         5 ~~~iliid~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~--~~~~dliivd~~~~~~~~~~~~~~~l~~~~~~pii   82 (145)
T PRK13435          5 QLKVLIVEDEALIALELEKLVEEAGHEVVGIAMSSEQAIALGR--RRQPDVALVDVHLADGPTGVEVARRLSADGGVEVV   82 (145)
T ss_pred             cceEEEEcCcHHHHHHHHHHHHhcCCeEEEeeCCHHHHHHHhh--hcCCCEEEEeeecCCCCcHHHHHHHHHhCCCCCEE
Confidence            46899999999999999999998888876 7889999988875  45699999999997 47899999998656688999


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCCCC
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPFE  141 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~~  141 (184)
                      +++...+   ...++..|+++|+.||++.++|...++.+..+...+.
T Consensus        83 ~ls~~~~---~~~~~~~ga~~~l~kp~~~~~l~~~i~~~~~~~~~~~  126 (145)
T PRK13435         83 FMTGNPE---RVPHDFAGALGVIAKPYSPRGVARALSYLSARRVGDR  126 (145)
T ss_pred             EEeCCHH---HHHHHhcCcceeEeCCCCHHHHHHHHHHHHhcCcccc
Confidence            9986432   2467789999999999999999999999887665443

>PRK11475 DNA-binding transcriptional activator BglJ; Provisional

Probab=99.61  E-value=2.7e-14  Score=107.41  Aligned_cols=112  Identities=12%  Similarity=0.116  Sum_probs=94.1

Q ss_pred             HHHHHHHHHHh---cCCeEEEECCHHHHHHHHHhcCCCccEEE---EeCCCCCCCHHHHHHHhc-ccCCCCEEEEEccCC
Q 029986           29 WLRILEKMLRK---CLYEVTKCNRAEIALDMLRMSKNGYDIVI---SDVHMPDMDGFKLHEQVG-LEMDLPVIMMSVDGC  101 (184)
Q Consensus        29 ~~~~l~~~L~~---~~~~v~~~~~~~~~~~~l~~~~~~~dlvi---lD~~l~~~~g~~l~~~l~-~~~~~~iIi~~~~~~  101 (184)
                      .+..+..+|..   .++.+..+.+++++++.+.  ...||+++   +|+.||+++|++++++++ ..+.+|||++|...+
T Consensus         2 ~r~gi~~lL~~~~~~~~~v~~~~~~~~~l~~~~--~~~pd~vl~dl~d~~mp~~~Gl~~~~~l~~~~p~~~iIvlt~~~~   79 (207)
T PRK11475          2 SSIGIESLFRKFPGNPYKLHTFSSQSSFQDAMS--RISFSAVIFSLSAMRSERREGLSCLTELAIKFPRMRRLVIADDDI   79 (207)
T ss_pred             chHHHHHHHhcCCCCeeEEEEeCCHHHHHHHhc--cCCCCEEEeeccccCCCCCCHHHHHHHHHHHCCCCCEEEEeCCCC
Confidence            35678888865   3566778999999999876  45689998   688899999999999995 457899999998776


Q ss_pred             hHHHHHHH-HcCCCceEeCCCCHHHHHHHHHHHHcCCCCCCC
Q 029986          102 TQDVMKGV-THGACNYLLKPIRIKELRNIWQHVAQQPKPFEE  142 (184)
Q Consensus       102 ~~~~~~a~-~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~~~  142 (184)
                      +.....++ +.||.+|+.||.+.++|.++++.+..+..++++
T Consensus        80 ~~~~~~~~~~~Ga~gyl~K~~~~~eL~~aI~~v~~G~~~~~~  121 (207)
T PRK11475         80 EARLIGSLSPSPLDGVLSKASTLEILQQELFLSLNGVRQATD  121 (207)
T ss_pred             HHHHHHHHHHcCCeEEEecCCCHHHHHHHHHHHHCCCcccCH
Confidence            66666655 799999999999999999999999999887654

>PRK09581 pleD response regulator PleD; Reviewed

Probab=99.60  E-value=1.7e-14  Score=119.40  Aligned_cols=117  Identities=22%  Similarity=0.364  Sum_probs=103.3

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc---CCCC
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE---MDLP   92 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~---~~~~   92 (184)
                      ...+|+++||++..+..+...|.+. +.+..+.++.+++..+.  +..||+|++|+.||+++|+++++.++..   +.+|
T Consensus       154 ~~~~vlivdd~~~~~~~l~~~l~~~-~~~~~~~~~~~a~~~~~--~~~~d~vi~d~~~p~~~g~~l~~~i~~~~~~~~~~  230 (457)
T PRK09581        154 EDGRILLVDDDVSQAERIANILKEE-FRVVVVSDPSEALFNAA--ETNYDLVIVSANFENYDPLRLCSQLRSKERTRYVP  230 (457)
T ss_pred             cCceEEEEecccchHHHHHHHHhhc-ceeeeecChHHHHHhcc--cCCCCEEEecCCCCCchHhHHHHHHHhccccCCCc
Confidence            4568999999999999999999764 66667889999998865  5679999999999999999999999642   6899


Q ss_pred             EEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           93 VIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        93 iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      +|+++...+..+...+++.|+.+|+.||++.++|...+....+
T Consensus       231 ii~ls~~~~~~~~~~a~~~Ga~d~l~kp~~~~~l~~~i~~~~~  273 (457)
T PRK09581        231 ILLLVDEDDDPRLVKALELGVNDYLMRPIDKNELLARVRTQIR  273 (457)
T ss_pred             EEEEeCCCChHHHHHHHHccchhhhhCCCcHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999888876543

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=99.60  E-value=4.2e-14  Score=117.74  Aligned_cols=112  Identities=23%  Similarity=0.363  Sum_probs=100.8

Q ss_pred             EEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCC-----CCHHHHHHHhc-ccCCCCE
Q 029986           20 VLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPD-----MDGFKLHEQVG-LEMDLPV   93 (184)
Q Consensus        20 Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~-----~~g~~l~~~l~-~~~~~~i   93 (184)
                      |+||||++..+..+...|  .||.+..+.++.++++.+.  ...||+||+|+.||+     .+|+++++.++ ..+.+||
T Consensus         1 ILivddd~~~~~~l~~~l--~~~~v~~a~~~~~al~~l~--~~~~dlvllD~~mp~~~~~~~~g~~~l~~i~~~~~~~pi   76 (445)
T TIGR02915         1 LLIVEDDLGLQKQLKWSF--ADYELAVAADRESAIALVR--RHEPAVVTLDLGLPPDADGASEGLAALQQILAIAPDTKV   76 (445)
T ss_pred             CEEEECCHHHHHHHHHHh--CCCeEEEeCCHHHHHHHHh--hCCCCEEEEeCCCCCCcCCCCCHHHHHHHHHhhCCCCCE
Confidence            589999999999999888  6899999999999999987  456999999999996     79999999995 4468999


Q ss_pred             EEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           94 IMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        94 Ii~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      |+++...+.+....+++.|+++|+.||++.++|..++..+..
T Consensus        77 I~lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~~~  118 (445)
T TIGR02915        77 IVITGNDDRENAVKAIGLGAYDFYQKPIDPDVLKLIVDRAFH  118 (445)
T ss_pred             EEEecCCCHHHHHHHHHCCccEEEeCCCCHHHHHHHHhhhhh
Confidence            999998888999999999999999999999999988877654

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).

>PRK09390 fixJ response regulator FixJ; Provisional

Probab=99.59  E-value=9.5e-14  Score=102.18  Aligned_cols=119  Identities=29%  Similarity=0.373  Sum_probs=106.1

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEE
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVI   94 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iI   94 (184)
                      +..+|+++++++.....+...|...++.+..+.++.++++.+.  ...||++++|..+++.+|+++++.++. .+.+|+|
T Consensus         2 ~~~~iliv~~~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~--~~~~d~ii~d~~~~~~~~~~~~~~l~~~~~~~~ii   79 (202)
T PRK09390          2 DKGVVHVVDDDEAMRDSLAFLLDSAGFEVRLFESAQAFLDALP--GLRFGCVVTDVRMPGIDGIELLRRLKARGSPLPVI   79 (202)
T ss_pred             CCCEEEEEeCCHHHHHHHHHHHHHCCCeEEEeCCHHHHHHHhc--cCCCCEEEEeCCCCCCcHHHHHHHHHhcCCCCCEE
Confidence            3458999999999999999999988999989999999888876  456999999999999999999999964 4678999


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      +++...+......+++.|+.+|+.||+...++...+..+..+
T Consensus        80 ~l~~~~~~~~~~~~~~~g~~~~l~~p~~~~~l~~~l~~~~~~  121 (202)
T PRK09390         80 VMTGHGDVPLAVEAMKLGAVDFIEKPFEDERLIGAIERALAQ  121 (202)
T ss_pred             EEECCCCHHHHHHHHHcChHHHhhCCCCHHHHHHHHHHHHHh
Confidence            999888888889999999999999999999999988887765

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

Probab=99.59  E-value=9.6e-14  Score=104.50  Aligned_cols=122  Identities=9%  Similarity=-0.041  Sum_probs=99.8

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcC--C-eEEEECCHHHHHHHHHhcCCCccEEEEeCC--CCCCCHHHHHHHhc-ccCCC
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCL--Y-EVTKCNRAEIALDMLRMSKNGYDIVISDVH--MPDMDGFKLHEQVG-LEMDL   91 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~--~-~v~~~~~~~~~~~~l~~~~~~~dlvilD~~--l~~~~g~~l~~~l~-~~~~~   91 (184)
                      |.|+|+||++..++.++.+|...+  + .+..+.++.+++..+.  ...||++++|+.  ++..+|.++++.++ ..+.+
T Consensus         1 ~~~lIvDD~~~~~~gl~~~L~~~~~~~~vv~~~~~~~~~~~~~~--~~~pDlvLlDl~~~l~~~~g~~~i~~i~~~~p~~   78 (207)
T PRK15411          1 MSTIIMDLCSYTRLGLTGYLLSRGVKKREINDIETVDDLAIACD--SLRPSVVFINEDCFIHDASNSQRIKQIINQHPNT   78 (207)
T ss_pred             CCEEEEcCCHHHHHHHHHHHHhCCCcceEEEecCCHHHHHHHHh--ccCCCEEEEeCcccCCCCChHHHHHHHHHHCCCC
Confidence            469999999999999999998654  2 4567899999998876  456999999966  88889999999995 45789


Q ss_pred             CEEEEEccCChHHHHHHHHcCCCc-eEeCCCCHHHHHHHHHHHHcCCCCCCC
Q 029986           92 PVIMMSVDGCTQDVMKGVTHGACN-YLLKPIRIKELRNIWQHVAQQPKPFEE  142 (184)
Q Consensus        92 ~iIi~~~~~~~~~~~~a~~~ga~~-~l~kP~~~~~l~~~l~~~~~~~~~~~~  142 (184)
                      ++|+++...+..... ++..|+.. |+.|+.+.++|..+++.+..+..+++.
T Consensus        79 ~iivlt~~~~~~~~~-~~~~~~~~~~~~K~~~~~~L~~aI~~v~~g~~~~~~  129 (207)
T PRK15411         79 LFIVFMAIANIHFDE-YLLVRKNLLISSKSIKPESLDDLLGDILKKETTITS  129 (207)
T ss_pred             eEEEEECCCchhHHH-HHHHHhhceeeeccCCHHHHHHHHHHHHcCCcccCc
Confidence            999999876665543 55555554 889999999999999999998877653

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=99.58  E-value=6.9e-14  Score=116.94  Aligned_cols=114  Identities=33%  Similarity=0.477  Sum_probs=103.4

Q ss_pred             EEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEEEEc
Q 029986           20 VLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIMMSV   98 (184)
Q Consensus        20 Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi~~~   98 (184)
                      |+|+||++..+..+...|...|+.+..+.++.+++..+.  ...||+|++|+.||+.+|+++++.++. .+.+|+|+++.
T Consensus         1 ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~--~~~~DlVllD~~~p~~~g~~ll~~l~~~~~~~~vIvlt~   78 (463)
T TIGR01818         1 VWVVDDDRSIRWVLEKALSRAGYEVRTFGNAASVLRALA--RGQPDLLITDVRMPGEDGLDLLPQIKKRHPQLPVIVMTA   78 (463)
T ss_pred             CEEEECCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHh--cCCCCEEEEcCCCCCCCHHHHHHHHHHhCCCCeEEEEeC
Confidence            689999999999999999988999999999999999886  456999999999999999999999964 46789999998


Q ss_pred             cCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           99 DGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        99 ~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      ..+......+++.|+++|+.||++.++|...+..+..
T Consensus        79 ~~~~~~~~~a~~~Ga~~~l~KP~~~~~L~~~i~~~l~  115 (463)
T TIGR01818        79 HSDLDTAVAAYQRGAFEYLPKPFDLDEAVTLVERALA  115 (463)
T ss_pred             CCCHHHHHHHHHcCcceeecCCCCHHHHHHHHHHHHH
Confidence            8888888999999999999999999999998887654

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.

>PRK12555 chemotaxis-specific methylesterase; Provisional

Probab=99.58  E-value=8.6e-14  Score=112.06  Aligned_cols=116  Identities=21%  Similarity=0.328  Sum_probs=96.9

Q ss_pred             CeEEEEeCCHHHHHHHHHHHH-hcCCeEE-EECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLR-KCLYEVT-KCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIM   95 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~-~~~~~v~-~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi   95 (184)
                      ++|+|+||++..+..+..+|. ..++.+. .+.++.++++.+.  ...||+|++|+.||+++|+++++.++....+|+++
T Consensus         1 ~~VLvVdd~~~~~~~l~~~L~~~~~~~vv~~a~~~~eal~~l~--~~~pDlVllD~~mp~~~G~e~l~~l~~~~~~pviv   78 (337)
T PRK12555          1 MRIGIVNDSPLAVEALRRALARDPDHEVVWVATDGAQAVERCA--AQPPDVILMDLEMPRMDGVEATRRIMAERPCPILI   78 (337)
T ss_pred             CEEEEEeCCHHHHHHHHHHHhhCCCCEEEEEECCHHHHHHHHh--ccCCCEEEEcCCCCCCCHHHHHHHHHHHCCCcEEE
Confidence            589999999999999999995 5577765 7899999999987  56699999999999999999999997666689999


Q ss_pred             EEccCC--hHHHHHHHHcCCCceEeCCC---------CHHHHHHHHHHHHc
Q 029986           96 MSVDGC--TQDVMKGVTHGACNYLLKPI---------RIKELRNIWQHVAQ  135 (184)
Q Consensus        96 ~~~~~~--~~~~~~a~~~ga~~~l~kP~---------~~~~l~~~l~~~~~  135 (184)
                      ++....  .....++++.|+++|+.||+         ..+++...++.+..
T Consensus        79 vs~~~~~~~~~~~~al~~Ga~d~l~KP~~~~~~~~~~~~~~l~~~i~~~~~  129 (337)
T PRK12555         79 VTSLTERNASRVFEAMGAGALDAVDTPTLGIGAGLEEYAAELLAKIDQIGR  129 (337)
T ss_pred             EeCCCCcCHHHHHHHHhcCceEEEECCCCCcchhHHHHHHHHHHHHHHHhh
Confidence            987543  45667899999999999999         45566666666554

>PRK09581 pleD response regulator PleD; Reviewed

Probab=99.57  E-value=2.2e-13  Score=112.76  Aligned_cols=116  Identities=30%  Similarity=0.491  Sum_probs=105.4

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc---CCCCEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE---MDLPVI   94 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~---~~~~iI   94 (184)
                      .+|+++++++..+..+...|...++.+..+.++.+++..+.  ...||+|++|+.+++.+|+++++.++..   +.+|+|
T Consensus         3 ~~ilii~~~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~--~~~~dlvi~d~~~~~~~g~~l~~~i~~~~~~~~~~ii   80 (457)
T PRK09581          3 ARILVVDDIPANVKLLEAKLLAEYYTVLTASSGAEAIAICE--REQPDIILLDVMMPGMDGFEVCRRLKSDPATTHIPVV   80 (457)
T ss_pred             CeEEEEeCCHHHHHHHHHHHHhCCCEEEEeCCHHHHHHHHh--hcCCCEEEEeCCCCCCCHHHHHHHHHcCcccCCCCEE
Confidence            37999999999999999999888999999999999999887  4569999999999999999999999653   368999


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      ++++..+.....+++..|+++|+.||++.++|..++..+.+
T Consensus        81 ~~s~~~~~~~~~~~~~~ga~~~l~kp~~~~~l~~~i~~~~~  121 (457)
T PRK09581         81 MVTALDDPEDRVRGLEAGADDFLTKPINDVALFARVKSLTR  121 (457)
T ss_pred             EEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHH
Confidence            99998888899999999999999999999999998887765

>PRK10610 chemotaxis regulatory protein CheY; Provisional

Probab=99.56  E-value=9e-13  Score=89.28  Aligned_cols=117  Identities=29%  Similarity=0.542  Sum_probs=102.0

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCC-eEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc---CCCC
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLY-EVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE---MDLP   92 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~-~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~---~~~~   92 (184)
                      .++++++++++.....+...|...++ .+..+.+..+++..+.  ...+|++++|..+++.+|+++++.++..   +..|
T Consensus         5 ~~~il~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~--~~~~di~l~d~~~~~~~~~~~~~~l~~~~~~~~~~   82 (129)
T PRK10610          5 ELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQ--AGGFGFVISDWNMPNMDGLELLKTIRADGAMSALP   82 (129)
T ss_pred             cceEEEEcCCHHHHHHHHHHHHHcCCCeEEEeCCHHHHHHHhh--ccCCCEEEEcCCCCCCCHHHHHHHHHhCCCcCCCc
Confidence            57899999999999999999998887 4777889999988875  4569999999999999999999999643   4678


Q ss_pred             EEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           93 VIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        93 iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      +++++..........++..|+++|+.||++..++...++.+.+
T Consensus        83 ~i~~~~~~~~~~~~~~~~~g~~~~i~~p~~~~~l~~~l~~~~~  125 (129)
T PRK10610         83 VLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFE  125 (129)
T ss_pred             EEEEECCCCHHHHHHHHHhCCCeEEECCCCHHHHHHHHHHHHH
Confidence            9999887777888899999999999999999999998887654

>PRK10651 transcriptional regulator NarL; Provisional

Probab=99.55  E-value=7.6e-13  Score=98.66  Aligned_cols=123  Identities=20%  Similarity=0.386  Sum_probs=106.0

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhc-CCeE-EEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCC
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKC-LYEV-TKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLP   92 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~-~~~v-~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~   92 (184)
                      ...+|+++++++..+..+...|... ++.+ ..+.+..+++..+.  ...||++++|..+++.+|+++++.++. .+..|
T Consensus         5 ~~~~iliv~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~--~~~~dlvl~d~~l~~~~~~~~~~~l~~~~~~~~   82 (216)
T PRK10651          5 EPATILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAE--SLDPDLILLDLNMPGMNGLETLDKLREKSLSGR   82 (216)
T ss_pred             cceEEEEECCCHHHHHHHHHHHccCCCcEEEEEeCCHHHHHHHHH--hCCCCEEEEeCCCCCCcHHHHHHHHHHhCCCCc
Confidence            3468999999999999999999765 4554 46889999998876  456999999999999999999999964 36789


Q ss_pred             EEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCCC
Q 029986           93 VIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPF  140 (184)
Q Consensus        93 iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~  140 (184)
                      +++++..........++..|+++|+.||++..+|...+..+..+....
T Consensus        83 vi~l~~~~~~~~~~~~~~~g~~~~i~k~~~~~~l~~~i~~~~~~~~~~  130 (216)
T PRK10651         83 IVVFSVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALQQAAAGEMVL  130 (216)
T ss_pred             EEEEeCCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHCCCccc
Confidence            999998888888889999999999999999999999999998875443

>PRK13558 bacterio-opsin activator; Provisional

Probab=99.55  E-value=1.6e-13  Score=119.48  Aligned_cols=118  Identities=20%  Similarity=0.178  Sum_probs=102.6

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEE
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVI   94 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iI   94 (184)
                      +.++|+|+||++..+..+...|...|+.+..+.++.+++..+.  ...||+||+|..||+++|+++++.++. .+.+|+|
T Consensus         6 ~~~~ILivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~al~~~~--~~~~Dlvl~d~~lp~~~g~~~l~~l~~~~~~~piI   83 (665)
T PRK13558          6 PTRGVLFVGDDPEAGPVDCDLDEDGRLDVTQIRDFVAARDRVE--AGEIDCVVADHEPDGFDGLALLEAVRQTTAVPPVV   83 (665)
T ss_pred             cceeEEEEccCcchHHHHHHHhhccCcceEeeCCHHHHHHHhh--ccCCCEEEEeccCCCCcHHHHHHHHHhcCCCCCEE
Confidence            3579999999999999999999888999999999999999876  566999999999999999999999964 4689999


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHH--HHHHHHHHHHc
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIK--ELRNIWQHVAQ  135 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~--~l~~~l~~~~~  135 (184)
                      +++...+......++..|+.+|+.||....  .+..++.....
T Consensus        84 ~lt~~~~~~~~~~al~~Ga~dyl~k~~~~~~~~l~~~i~~~~~  126 (665)
T PRK13558         84 VVPTAGDEAVARRAVDADAAAYVPAVSDDATAAIAERIESAVP  126 (665)
T ss_pred             EEECCCCHHHHHHHHhcCcceEEeccchhHHHHHHHHHHHhhh
Confidence            999988889999999999999999997543  55566665554

>PRK10403 transcriptional regulator NarP; Provisional

Probab=99.54  E-value=6.8e-13  Score=98.73  Aligned_cols=121  Identities=25%  Similarity=0.387  Sum_probs=104.0

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHh-cCCeEE-EECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc-CCCCE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRK-CLYEVT-KCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE-MDLPV   93 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~-~~~~v~-~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~-~~~~i   93 (184)
                      .++|+++++++..+..+...|.. .++.+. .+.+..+++..+.  ...||++++|..+++.+|.++++.++.. +..|+
T Consensus         6 ~~~ilii~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~--~~~~dlvi~d~~~~~~~~~~~~~~l~~~~~~~~i   83 (215)
T PRK10403          6 PFQVLIVDDHPLMRRGVRQLLELDPGFEVVAEAGDGASAIDLAN--RLDPDVILLDLNMKGMSGLDTLNALRRDGVTAQI   83 (215)
T ss_pred             eEEEEEEcCCHHHHHHHHHHHhcCCCCEEEEEeCCHHHHHHHHH--hcCCCEEEEecCCCCCcHHHHHHHHHHhCCCCeE
Confidence            46899999999999999999975 467664 6889999988876  4569999999999999999999999644 57789


Q ss_pred             EEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCC
Q 029986           94 IMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKP  139 (184)
Q Consensus        94 Ii~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~  139 (184)
                      ++++..........+++.|+++|+.||++..+|...+..+..+...
T Consensus        84 i~l~~~~~~~~~~~~~~~g~~~~i~kp~~~~~l~~~i~~~~~~~~~  129 (215)
T PRK10403         84 IILTVSDASSDVFALIDAGADGYLLKDSDPEVLLEAIRAGAKGSKV  129 (215)
T ss_pred             EEEeCCCChHHHHHHHHcCCCeEEecCCCHHHHHHHHHHHhCCCee
Confidence            9998887788888999999999999999999999999988776543

>PRK15369 two component system sensor kinase SsrB; Provisional

Probab=99.53  E-value=1e-12  Score=97.17  Aligned_cols=121  Identities=21%  Similarity=0.313  Sum_probs=104.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhc-CCeE-EEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKC-LYEV-TKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPV   93 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~-~~~v-~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~i   93 (184)
                      .++|+++++++..+..+...|... ++.+ ..+.++.+++..+.  ...||++++|..+++.+|+++++.++. .+..|+
T Consensus         3 ~~~iliv~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~--~~~~dlvl~d~~~~~~~~~~~~~~l~~~~~~~~i   80 (211)
T PRK15369          3 NYKILLVDDHELIINGIKNMLAPYPRYKIVGQVDNGLEVYNACR--QLEPDIVILDLGLPGMNGLDVIPQLHQRWPAMNI   80 (211)
T ss_pred             ccEEEEECCcHHHHHHHHHHHccCCCcEEEEEECCHHHHHHHHH--hcCCCEEEEeCCCCCCCHHHHHHHHHHHCCCCcE
Confidence            468999999999999999999875 4554 47888888888776  456999999999999999999999964 467899


Q ss_pred             EEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCC
Q 029986           94 IMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKP  139 (184)
Q Consensus        94 Ii~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~  139 (184)
                      ++++..........++..|+++|+.||++..+|...+..+..+...
T Consensus        81 i~ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~~~~~~~  126 (211)
T PRK15369         81 LVLTARQEEHMASRTLAAGALGYVLKKSPQQILLAAIQTVAVGKRY  126 (211)
T ss_pred             EEEeCCCCHHHHHHHHHhCCCEEEeCCCCHHHHHHHHHHHHCCCce
Confidence            9999888888888999999999999999999999999988776543

>PRK00742 chemotaxis-specific methylesterase; Provisional

Probab=99.52  E-value=7.4e-13  Score=107.30  Aligned_cols=117  Identities=28%  Similarity=0.375  Sum_probs=96.0

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhc-CCeEE-EECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKC-LYEVT-KCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVI   94 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~-~~~v~-~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iI   94 (184)
                      .++|+|+||++..+..+...|... ++.+. .+.++.+++..+.  ...||+|++|+.||+++|++++++++....+|+|
T Consensus         3 ~~~ILiVdd~~~~~~~L~~~L~~~~~~~vv~~a~~~~~al~~~~--~~~~DlVllD~~mp~~dgle~l~~i~~~~~~piI   80 (354)
T PRK00742          3 KIRVLVVDDSAFMRRLISEILNSDPDIEVVGTAPDGLEAREKIK--KLNPDVITLDVEMPVMDGLDALEKIMRLRPTPVV   80 (354)
T ss_pred             ccEEEEECCCHHHHHHHHHHHhhCCCCEEEEEECCHHHHHHHHh--hhCCCEEEEeCCCCCCChHHHHHHHHHhCCCCEE
Confidence            468999999999999999999876 77776 7889999999876  4569999999999999999999999655459999


Q ss_pred             EEEccC--ChHHHHHHHHcCCCceEeCCCCH---------HHHHHHHHHHHc
Q 029986           95 MMSVDG--CTQDVMKGVTHGACNYLLKPIRI---------KELRNIWQHVAQ  135 (184)
Q Consensus        95 i~~~~~--~~~~~~~a~~~ga~~~l~kP~~~---------~~l~~~l~~~~~  135 (184)
                      +++...  .......+++.|+++|+.||+..         .++...++.+.+
T Consensus        81 vls~~~~~~~~~~~~al~~Ga~d~l~kP~~~~~~~~~~~~~~l~~~i~~~~~  132 (354)
T PRK00742         81 MVSSLTERGAEITLRALELGAVDFVTKPFLGISLGMDEYKEELAEKVRAAAR  132 (354)
T ss_pred             EEecCCCCCHHHHHHHHhCCCcEEEeCCcccccchHHHHHHHHHHHHHHHhh
Confidence            998643  33566789999999999999943         445555555433

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

Probab=99.52  E-value=3e-13  Score=107.52  Aligned_cols=103  Identities=29%  Similarity=0.435  Sum_probs=91.4

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcC--CeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCL--YEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIM   95 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~--~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi   95 (184)
                      ++|++|||....+..++..|...+  ..+..+.|+.++++.+.  +..||+|.+|+.||.+||+++++.+-....+|||+
T Consensus         2 irVlvVddsal~R~~i~~~l~~~~~i~vv~~a~ng~~a~~~~~--~~~PDVi~ld~emp~mdgl~~l~~im~~~p~pVim   79 (350)
T COG2201           2 IRVLVVDDSALMRKVISDILNSDPDIEVVGTARNGREAIDKVK--KLKPDVITLDVEMPVMDGLEALRKIMRLRPLPVIM   79 (350)
T ss_pred             cEEEEEcCcHHHHHHHHHHHhcCCCeEEEEecCCHHHHHHHHH--hcCCCEEEEecccccccHHHHHHHHhcCCCCcEEE
Confidence            689999999999999999999987  56678999999999998  67799999999999999999999985457899999


Q ss_pred             EEccCC--hHHHHHHHHcCCCceEeCCCC
Q 029986           96 MSVDGC--TQDVMKGVTHGACNYLLKPIR  122 (184)
Q Consensus        96 ~~~~~~--~~~~~~a~~~ga~~~l~kP~~  122 (184)
                      +++-.+  .+...++++.||.||+.||..
T Consensus        80 vsslt~~g~~~t~~al~~gAvD~i~kp~~  108 (350)
T COG2201          80 VSSLTEEGAEATLEALELGAVDFIAKPSG  108 (350)
T ss_pred             EeccccccHHHHHHHHhcCcceeecCCCc
Confidence            986433  467779999999999999984

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

Probab=99.48  E-value=2.8e-12  Score=114.27  Aligned_cols=118  Identities=19%  Similarity=0.178  Sum_probs=105.1

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIM   95 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi   95 (184)
                      +.+|+|+||++..+..+...|...||.+..+.++.++++.+......||+||+  .+++++|+++++.++. .+.+|||+
T Consensus       697 ~~~ILvVddd~~~~~~l~~~L~~~G~~v~~~~s~~~al~~l~~~~~~~DlVll--~~~~~~g~~l~~~l~~~~~~ipIIv  774 (828)
T PRK13837        697 GETVLLVEPDDATLERYEEKLAALGYEPVGFSTLAAAIAWISKGPERFDLVLV--DDRLLDEEQAAAALHAAAPTLPIIL  774 (828)
T ss_pred             CCEEEEEcCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHHhCCCCceEEEE--CCCCCCHHHHHHHHHhhCCCCCEEE
Confidence            56899999999999999999999999999999999999998643344799999  7899999999999963 46889999


Q ss_pred             EEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCC
Q 029986           96 MSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQP  137 (184)
Q Consensus        96 ~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~  137 (184)
                      ++.........+++..| ++|+.||++..+|..+++.+++..
T Consensus       775 ls~~~~~~~~~~~~~~G-~d~L~KP~~~~~L~~~l~~~l~~~  815 (828)
T PRK13837        775 GGNSKTMALSPDLLASV-AEILAKPISSRTLAYALRTALATA  815 (828)
T ss_pred             EeCCCchhhhhhHhhcc-CcEEeCCCCHHHHHHHHHHHHccc
Confidence            99888888888999999 999999999999999999887643

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

Probab=99.48  E-value=7.6e-13  Score=96.23  Aligned_cols=117  Identities=21%  Similarity=0.264  Sum_probs=97.8

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeE-EEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEV-TKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIM   95 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v-~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi   95 (184)
                      .++|++++|++..+..+...|...||.+ ..+.++......+.  ...||+||+|+.+|..+-.+-.-.....+..|||+
T Consensus         5 ~lrvlv~~d~~i~~~~i~~~l~eag~~~Vg~~~~~~~~~~~~~--~~~pDvVildie~p~rd~~e~~~~~~~~~~~piv~   82 (194)
T COG3707           5 LLRVLVADDEALTRMDIREGLLEAGYQRVGEAADGLEAVEVCE--RLQPDVVILDIEMPRRDIIEALLLASENVARPIVA   82 (194)
T ss_pred             ccceeeccccccchhhHHHHHHHcCCeEeeeecccccchhHHH--hcCCCEEEEecCCCCccHHHHHHHhhcCCCCCEEE
Confidence            5689999999999999999999888864 46666666666665  56699999999999998444444444556789999


Q ss_pred             EEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           96 MSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        96 ~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      ++.+++++....+.++|+.+|++||++...+...+.-+..
T Consensus        83 lt~~s~p~~i~~a~~~Gv~ayivkpi~~~rl~p~L~vA~s  122 (194)
T COG3707          83 LTAYSDPALIEAAIEAGVMAYIVKPLDESRLLPILDVAVS  122 (194)
T ss_pred             EEccCChHHHHHHHHcCCeEEEecCcchhhhhHHHHHHHH
Confidence            9999999999999999999999999999988888877655

>PRK09191 two-component response regulator; Provisional

Probab=99.45  E-value=6.9e-12  Score=97.00  Aligned_cols=116  Identities=19%  Similarity=0.285  Sum_probs=96.5

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEE-EECCHHHHHHHHHhcCCCccEEEEeCCCCC-CCHHHHHHHhcccCCCCEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVT-KCNRAEIALDMLRMSKNGYDIVISDVHMPD-MDGFKLHEQVGLEMDLPVI   94 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~-~~~~~~~~~~~l~~~~~~~dlvilD~~l~~-~~g~~l~~~l~~~~~~~iI   94 (184)
                      ..+|+|+||++..+..+...|+..|+.+. .+.++.+++..+.  ...||+||+|+.+|+ .+|+++++.++...++|+|
T Consensus       137 ~~~~liidd~~~~~~~l~~~L~~~~~~~~~~~~~~~~~l~~l~--~~~~dlvi~d~~~~~~~~g~e~l~~l~~~~~~pii  214 (261)
T PRK09191        137 ATRVLIIEDEPIIAMDLEQLVESLGHRVTGIARTRAEAVALAK--KTRPGLILADIQLADGSSGIDAVNDILKTFDVPVI  214 (261)
T ss_pred             CCeEEEEcCcHHHHHHHHHHHhcCCCEEEEEECCHHHHHHHHh--ccCCCEEEEecCCCCCCCHHHHHHHHHHhCCCCEE
Confidence            34799999999999999999998888876 6888899998876  456999999999995 7899999999644488999


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      ++++..+...  .+...|+.+|+.||++.++|...+..+...
T Consensus       215 ~ls~~~~~~~--~~~~~~~~~~l~kP~~~~~l~~~i~~~~~~  254 (261)
T PRK09191        215 FITAFPERLL--TGERPEPAFLITKPFQPDTVKAAISQALFF  254 (261)
T ss_pred             EEeCCCcHHH--HHHhcccCceEECCCCHHHHHHHHHHHHhc
Confidence            9987655433  334467889999999999999999887664

>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=99.38  E-value=3.6e-11  Score=78.21  Aligned_cols=110  Identities=34%  Similarity=0.593  Sum_probs=95.5

Q ss_pred             EEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEEEEcc
Q 029986           21 LVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIMMSVD   99 (184)
Q Consensus        21 livdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi~~~~   99 (184)
                      +++++++..+..+...+...|+.+..+.+..++...+.  ...||++++|..+++.+|.++++.++. .+..|+++++..
T Consensus         1 l~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~--~~~~~~ii~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~   78 (113)
T cd00156           1 LIVDDDPLIRELLRRLLEKEGYEVVEAEDGEEALALLA--EEKPDLILLDIMMPGMDGLELLRRIRKRGPDIPIIFLTAH   78 (113)
T ss_pred             CeecCcHHHHHHHHHHHhhcCceEEEecCHHHHHHHHH--hCCCCEEEEecCCCCCchHHHHHHHHHhCCCCCEEEEEec
Confidence            47899999999999999888898888888999888876  456999999999999999999999864 467889988877


Q ss_pred             CChHHHHHHHHcCCCceEeCCCCHHHHHHHHHH
Q 029986          100 GCTQDVMKGVTHGACNYLLKPIRIKELRNIWQH  132 (184)
Q Consensus       100 ~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~  132 (184)
                      ........++..|+.+|+.||++..++...+..
T Consensus        79 ~~~~~~~~~~~~~~~~~i~~p~~~~~l~~~l~~  111 (113)
T cd00156          79 GDDEDAVEALKAGADDYLTKPFSPEELLARIRA  111 (113)
T ss_pred             ccHHHHHHHHHcChhhHccCCCCHHHHHHHHHh
Confidence            667777889999999999999999999888764

>PRK13557 histidine kinase; Provisional

Probab=99.36  E-value=4.1e-11  Score=101.23  Aligned_cols=120  Identities=22%  Similarity=0.283  Sum_probs=105.5

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCC-CCHHHHHHHhcc-cCCCCEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPD-MDGFKLHEQVGL-EMDLPVI   94 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~-~~g~~l~~~l~~-~~~~~iI   94 (184)
                      +.+|+|+++++..+..+...|+..|+.+..+.+..++++.+.. ...||++++|..+++ .+|+++++.++. .+.+|++
T Consensus       415 ~~~iliv~~~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~~-~~~~d~vi~d~~~~~~~~~~~~~~~l~~~~~~~~ii  493 (540)
T PRK13557        415 TETILIVDDRPDVAELARMILEDFGYRTLVASNGREALEILDS-HPEVDLLFTDLIMPGGMNGVMLAREARRRQPKIKVL  493 (540)
T ss_pred             CceEEEEcCcHHHHHHHHHHHHhcCCeEEEeCCHHHHHHHHhc-CCCceEEEEeccCCCCCCHHHHHHHHHHhCCCCcEE
Confidence            4589999999999999999999889999999999999998752 235999999999997 899999999964 4678999


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCC
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQP  137 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~  137 (184)
                      +++...+......++..|+.+|+.||++.++|...+..+..+.
T Consensus       494 ~~~~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~l~~~~~~~  536 (540)
T PRK13557        494 LTTGYAEASIERTDAGGSEFDILNKPYRRAELARRVRMVLDGP  536 (540)
T ss_pred             EEcCCCchhhhhhhccccCCceeeCCCCHHHHHHHHHHHhcCC
Confidence            9988877777888899999999999999999999999877643

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

Probab=99.27  E-value=8.4e-11  Score=90.62  Aligned_cols=112  Identities=27%  Similarity=0.444  Sum_probs=93.7

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhc-CC-eEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc-CCCCEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKC-LY-EVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE-MDLPVI   94 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~-~~-~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~-~~~~iI   94 (184)
                      ++|+++||++..++.+...+... .+ .+..+.++.++++.+.  ...||++|+|+.||+++|+++...++.. +..+|+
T Consensus         2 ~~i~i~dd~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~fldI~~~~~~G~ela~~i~~~~~~~~Iv   79 (244)
T COG3279           2 LKVLIVDDEPLAREELRRILNEIPDIEIVGEAENGEEALQLLQ--GLRPDLVFLDIAMPDINGIELAARIRKGDPRPAIV   79 (244)
T ss_pred             CcEEEecCCHHHHHHHHHHHHhhhhcCeeeeeccchhhHHHHh--ccCCCeEEEeeccCccchHHHHHHhcccCCCCeEE
Confidence            68999999999999999999832 22 2237888999999987  4479999999999999999999999764 455566


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHH
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHV  133 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~  133 (184)
                      ++++  ..+++..+++..|.||+.||+..+.|...+...
T Consensus        80 fvt~--~~~~a~~afev~a~d~i~kp~~~~~l~~~l~~~  116 (244)
T COG3279          80 FVTA--HDEYAVAAFEVEALDYLLKPISEERLAKTLERL  116 (244)
T ss_pred             EEEe--hHHHHHHHHhHHHHhhhcCcchHHHHHHHHHHH
Confidence            6664  478888899999999999999999999998753

>PRK10693 response regulator of RpoS; Provisional

Probab=99.27  E-value=9e-11  Score=93.29  Aligned_cols=88  Identities=26%  Similarity=0.411  Sum_probs=77.0

Q ss_pred             EECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc-CCCCEEEEEccCChHHHHHHHHcCCCceEeCCC-CH
Q 029986           46 KCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE-MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPI-RI  123 (184)
Q Consensus        46 ~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~-~~~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~-~~  123 (184)
                      .+.++.++++.+.  ...||+|++|+.||+++|+++++.++.. +.+|+|+++...+.+...++++.|+++|+.||+ +.
T Consensus         2 ~a~~g~~al~~l~--~~~pDlVL~D~~mp~~~Gle~~~~ir~~~~~ipiI~lt~~~~~~~~~~al~~Ga~dyl~KP~~~~   79 (303)
T PRK10693          2 LAANGVDALELLG--GFTPDLIICDLAMPRMNGIEFVEHLRNRGDQTPVLVISATENMADIAKALRLGVQDVLLKPVKDL   79 (303)
T ss_pred             EeCCHHHHHHHHh--cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCcEEEEECCCCHHHHHHHHHCCCcEEEECCCCcH
Confidence            3567888998886  4669999999999999999999999644 678999999998888999999999999999999 48


Q ss_pred             HHHHHHHHHHHc
Q 029986          124 KELRNIWQHVAQ  135 (184)
Q Consensus       124 ~~l~~~l~~~~~  135 (184)
                      +++..++...+.
T Consensus        80 ~~L~~~i~~~l~   91 (303)
T PRK10693         80 NRLREMVFACLY   91 (303)
T ss_pred             HHHHHHHHHHhh
Confidence            899888877664

>PRK15029 arginine decarboxylase; Provisional

Probab=99.13  E-value=1.1e-09  Score=95.71  Aligned_cols=107  Identities=13%  Similarity=0.148  Sum_probs=85.4

Q ss_pred             CeEEEEeCCHH--------HHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHH----HHHHHh
Q 029986           18 LRVLVVDDDPI--------WLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGF----KLHEQV   85 (184)
Q Consensus        18 ~~Ilivdd~~~--------~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~----~l~~~l   85 (184)
                      |+|+||||+..        .++.|...|+..||++..+.++++++..+.. ...||+||+|+.||+++|+    ++++++
T Consensus         1 MkILIVDDD~~~~~~~~~~i~~~L~~~Le~~G~eV~~a~s~~dAl~~l~~-~~~~DlVLLD~~LPd~dG~~~~~ell~~I   79 (755)
T PRK15029          1 MKVLIVESEFLHQDTWVGNAVERLADALSQQNVTVIKSTSFDDGFAILSS-NEAIDCLMFSYQMEHPDEHQNVRQLIGKL   79 (755)
T ss_pred             CeEEEEeCCcccccchhHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHh-cCCCcEEEEECCCCCCccchhHHHHHHHH
Confidence            57999999995        6999999999999999999999999999863 2469999999999999997    899999


Q ss_pred             cc-cCCCCEEEEEccCC--hHHHHHHHHcCCCceEeCCCCHHHH
Q 029986           86 GL-EMDLPVIMMSVDGC--TQDVMKGVTHGACNYLLKPIRIKEL  126 (184)
Q Consensus        86 ~~-~~~~~iIi~~~~~~--~~~~~~a~~~ga~~~l~kP~~~~~l  126 (184)
                      +. .+++|||++|....  .......++ -+++|+.+--...++
T Consensus        80 R~~~~~iPIIlLTar~~~~~~~~~~~~~-~~~~~~~~~~~~~~~  122 (755)
T PRK15029         80 HERQQNVPVFLLGDREKALAAMDRDLLE-LVDEFAWILEDTADF  122 (755)
T ss_pred             HhhCCCCCEEEEEcCCcccccCCHHHHH-hhheEEEecCCCHHH
Confidence            75 46899999998765  333333333 356777766554443

>PRK11107 hybrid sensory histidine kinase BarA; Provisional

Probab=98.61  E-value=1.8e-06  Score=77.88  Aligned_cols=113  Identities=19%  Similarity=0.135  Sum_probs=91.1

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHH-Hhcc--cCCCC
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHE-QVGL--EMDLP   92 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~-~l~~--~~~~~   92 (184)
                      .+.+|+++|+++..+..+..+|...|+.+..+.+...    +.  ...||++++|..+++..+..... .++.  ....+
T Consensus       535 ~g~~ili~d~~~~~~~~l~~~L~~~g~~v~~~~~~~~----l~--~~~~d~il~~~~~~~~~~~~~~~~~~~~~~~~~~~  608 (919)
T PRK11107        535 AGKRLLYVEPNSAAAQATLDILSETPLEVTYSPTLSQ----LP--EAHYDILLLGLPVTFREPLTMLHERLAKAKSMTDF  608 (919)
T ss_pred             CCCeEEEEeCCHHHHHHHHHHHHHCCCEEEEcCCHHH----hc--cCCCCEEEecccCCCCCCHHHHHHHHHhhhhcCCc
Confidence            4679999999999999999999999999998888776    23  45699999999999877655443 3332  22345


Q ss_pred             EEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHH
Q 029986           93 VIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVA  134 (184)
Q Consensus        93 iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~  134 (184)
                      +++++..........+.+.|+++|+.||+...++...+....
T Consensus       609 ~i~~~~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~l~~~~  650 (919)
T PRK11107        609 LILALPCHEQVLAEQLKQDGADACLSKPLSHTRLLPALLEPC  650 (919)
T ss_pred             EEEEeCCcchhhHHHHhhCCCceEECCCCCHHHHHHHHHHhh
Confidence            777777777778888999999999999999999988887654

>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=98.23  E-value=2.3e-05  Score=52.93  Aligned_cols=106  Identities=12%  Similarity=0.178  Sum_probs=73.0

Q ss_pred             eEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHh-cccCCCCEEEEE
Q 029986           19 RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQV-GLEMDLPVIMMS   97 (184)
Q Consensus        19 ~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l-~~~~~~~iIi~~   97 (184)
                      ||+|+|||...+..|+..|+=.|+....++..+ ......  ....+.+++-..-.+ ...+.++.+ +..+++|++++.
T Consensus         1 kILvIddd~~R~~~L~~ILeFlGe~~~~~~~~~-~~~~~~--~~~~~~~~v~~g~~~-~~~~~l~~l~~~~~~~Pvlllg   76 (109)
T PF06490_consen    1 KILVIDDDAERRQRLSTILEFLGEQCEAVSSSD-WSQADW--SSPWEACAVILGSCS-KLAELLKELLKWAPHIPVLLLG   76 (109)
T ss_pred             CEEEECCcHHHHHhhhhhhhhcCCCeEEecHHH-HHHhhh--hcCCcEEEEEecCch-hHHHHHHHHHhhCCCCCEEEEC
Confidence            699999999999999999998888887776433 323222  233455544332222 345566666 556899999997


Q ss_pred             ccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHH
Q 029986           98 VDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHV  133 (184)
Q Consensus        98 ~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~  133 (184)
                      ........     ..+.+-+..|++..+|.+.++..
T Consensus        77 ~~~~~~~~-----~nvvg~Le~Pl~Y~qLt~~L~~c  107 (109)
T PF06490_consen   77 EHDSPEEL-----PNVVGELEEPLNYPQLTDALHRC  107 (109)
T ss_pred             CCCccccc-----cCeeEecCCCCCHHHHHHHHHHh
Confidence            66544111     12556689999999999999875

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).

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

Probab=98.22  E-value=3e-06  Score=69.95  Aligned_cols=93  Identities=28%  Similarity=0.389  Sum_probs=77.9

Q ss_pred             CeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEEEEccCChHHHHHHHHcCCCceEeCCC
Q 029986           42 YEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPI  121 (184)
Q Consensus        42 ~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~  121 (184)
                      +++..+..+..++..+.  ...||++++|..||+++|+++++.+++.+.. +++++...........+++|+++|++||.
T Consensus        13 ~~v~~a~~g~~~l~~~~--~~~~~~~lld~~m~~~~~~~~~~~lk~~~~~-~v~~t~~~~~~~~~~~~~~~~~~~l~~~~   89 (435)
T COG3706          13 KEVATAKKGLIALAILL--DHKPDYKLLDVMMPGMDGFELCRRLKAEPAT-VVMVTALDDSAPRVRGLKAGADDFLTKPV   89 (435)
T ss_pred             hhhhhccchHHHHHHHh--cCCCCeEEeecccCCcCchhHHHHHhcCCcc-eEEEEecCCCCcchhHHhhhhhhhccCCC
Confidence            45666888888888887  6779999999999999999999999866544 77777777778888999999999999999


Q ss_pred             CHHHHHHHHHHHHcCC
Q 029986          122 RIKELRNIWQHVAQQP  137 (184)
Q Consensus       122 ~~~~l~~~l~~~~~~~  137 (184)
                      ....+......+...+
T Consensus        90 ~~~~~~~r~~~l~~~k  105 (435)
T COG3706          90 NDSQLFLRAKSLVRLK  105 (435)
T ss_pred             ChHHHHHhhhhhccch
Confidence            9888877777765543

>smart00448 REC cheY-homologous receiver domain

Probab=97.96  E-value=0.00013  Score=40.20  Aligned_cols=54  Identities=37%  Similarity=0.680  Sum_probs=46.8

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCC
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHM   73 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l   73 (184)
                      ++++++++++.....+...+...|+.+..+.+...+...+.  ...+|++++|..+
T Consensus         1 ~~i~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~--~~~~~~vi~~~~~   54 (55)
T smart00448        1 MRILVVDDDPLLRELLKALLEREGYEVDEATDGEEALELLK--EEKPDLILLDIMM   54 (55)
T ss_pred             CeEEEEcCCHHHHHHHHHHHhhcCcEEEEeCCHHHHHHHHH--hcCCCEEEEeccC
Confidence            46999999999999999999988999888999998888775  4468999999764

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

>cd02071 MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 binding domain

Probab=97.38  E-value=0.015  Score=39.88  Aligned_cols=105  Identities=11%  Similarity=-0.022  Sum_probs=71.7

Q ss_pred             eCCHHHHHHHHHHHHhcCCeEEEEC---CHHHHHHHHHhcCCCccEEEEeCCCCCCC--HHHHHHHhccc-CCCCEEEEE
Q 029986           24 DDDPIWLRILEKMLRKCLYEVTKCN---RAEIALDMLRMSKNGYDIVISDVHMPDMD--GFKLHEQVGLE-MDLPVIMMS   97 (184)
Q Consensus        24 dd~~~~~~~l~~~L~~~~~~v~~~~---~~~~~~~~l~~~~~~~dlvilD~~l~~~~--g~~l~~~l~~~-~~~~iIi~~   97 (184)
                      |.+..-...+..+|+..||++....   ..++..+...  +..||+|.+-..+....  --++++.+++. +....+++.
T Consensus        10 d~H~lG~~~~~~~l~~~G~~vi~lG~~vp~e~~~~~a~--~~~~d~V~iS~~~~~~~~~~~~~~~~L~~~~~~~i~i~~G   87 (122)
T cd02071          10 DGHDRGAKVIARALRDAGFEVIYTGLRQTPEEIVEAAI--QEDVDVIGLSSLSGGHMTLFPEVIELLRELGAGDILVVGG   87 (122)
T ss_pred             ChhHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHH--HcCCCEEEEcccchhhHHHHHHHHHHHHhcCCCCCEEEEE
Confidence            5666677778888899999987554   3666666665  56799999977664322  23455566544 334445555


Q ss_pred             ccCChHHHHHHHHcCCCceEeCCCCHHHHHHHH
Q 029986           98 VDGCTQDVMKGVTHGACNYLLKPIRIKELRNIW  130 (184)
Q Consensus        98 ~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l  130 (184)
                      .....+....+.++|.+.|+..--+.++....+
T Consensus        88 G~~~~~~~~~~~~~G~d~~~~~~~~~~~~~~~~  120 (122)
T cd02071          88 GIIPPEDYELLKEMGVAEIFGPGTSIEEIIDKI  120 (122)
T ss_pred             CCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHH
Confidence            545556677888999999998887777765544

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.

>PRK02261 methylaspartate mutase subunit S; Provisional

Probab=96.86  E-value=0.085  Score=37.04  Aligned_cols=116  Identities=14%  Similarity=0.049  Sum_probs=81.4

Q ss_pred             CCeEEEE----eCCHHHHHHHHHHHHhcCCeEEEEC---CHHHHHHHHHhcCCCccEEEEeCCCCCCC--HHHHHHHhcc
Q 029986           17 GLRVLVV----DDDPIWLRILEKMLRKCLYEVTKCN---RAEIALDMLRMSKNGYDIVISDVHMPDMD--GFKLHEQVGL   87 (184)
Q Consensus        17 ~~~Iliv----dd~~~~~~~l~~~L~~~~~~v~~~~---~~~~~~~~l~~~~~~~dlvilD~~l~~~~--g~~l~~~l~~   87 (184)
                      ..+|++.    |.+..-...+..+|+..||++....   ..++..+.+.  +..||+|.+...+....  .-++++.++.
T Consensus         3 ~~~vl~~~~~gD~H~lG~~iv~~~lr~~G~eVi~LG~~vp~e~i~~~a~--~~~~d~V~lS~~~~~~~~~~~~~~~~L~~   80 (137)
T PRK02261          3 KKTVVLGVIGADCHAVGNKILDRALTEAGFEVINLGVMTSQEEFIDAAI--ETDADAILVSSLYGHGEIDCRGLREKCIE   80 (137)
T ss_pred             CCEEEEEeCCCChhHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHH--HcCCCEEEEcCccccCHHHHHHHHHHHHh
Confidence            3467777    7778788888899999999988654   4677777765  56699999988776432  3445666654


Q ss_pred             c-C-CCCEEEEEccC------ChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           88 E-M-DLPVIMMSVDG------CTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        88 ~-~-~~~iIi~~~~~------~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      . . +++ +++....      ..+....+.+.|++.++...-+.+++...+++.++
T Consensus        81 ~~~~~~~-i~vGG~~~~~~~~~~~~~~~l~~~G~~~vf~~~~~~~~i~~~l~~~~~  135 (137)
T PRK02261         81 AGLGDIL-LYVGGNLVVGKHDFEEVEKKFKEMGFDRVFPPGTDPEEAIDDLKKDLN  135 (137)
T ss_pred             cCCCCCe-EEEECCCCCCccChHHHHHHHHHcCCCEEECcCCCHHHHHHHHHHHhc
Confidence            3 3 444 3443322      23445678889999999988888999888887655

>cd02067 B12-binding B12 binding domain (B12-BD)

Probab=96.86  E-value=0.04  Score=37.45  Aligned_cols=93  Identities=15%  Similarity=0.039  Sum_probs=60.5

Q ss_pred             eCCHHHHHHHHHHHHhcCCeEEEEC---CHHHHHHHHHhcCCCccEEEEeCCCCCC--CHHHHHHHhcccCC-CCEEEEE
Q 029986           24 DDDPIWLRILEKMLRKCLYEVTKCN---RAEIALDMLRMSKNGYDIVISDVHMPDM--DGFKLHEQVGLEMD-LPVIMMS   97 (184)
Q Consensus        24 dd~~~~~~~l~~~L~~~~~~v~~~~---~~~~~~~~l~~~~~~~dlvilD~~l~~~--~g~~l~~~l~~~~~-~~iIi~~   97 (184)
                      |.+..-...+..+|+..||++....   ..++..+.+.  +..||+|.+-..+...  ...++++.+++... -+.|++.
T Consensus        10 e~H~lG~~~~~~~l~~~G~~V~~lg~~~~~~~l~~~~~--~~~pdvV~iS~~~~~~~~~~~~~i~~l~~~~~~~~~i~vG   87 (119)
T cd02067          10 DGHDIGKNIVARALRDAGFEVIDLGVDVPPEEIVEAAK--EEDADAIGLSGLLTTHMTLMKEVIEELKEAGLDDIPVLVG   87 (119)
T ss_pred             chhhHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHH--HcCCCEEEEeccccccHHHHHHHHHHHHHcCCCCCeEEEE
Confidence            5566667778899999999986433   4566667666  5669999998765442  33556667754432 3344555


Q ss_pred             ccCChHHHHHHHHcCCCceEe
Q 029986           98 VDGCTQDVMKGVTHGACNYLL  118 (184)
Q Consensus        98 ~~~~~~~~~~a~~~ga~~~l~  118 (184)
                      ..........+...|++.|+.
T Consensus        88 G~~~~~~~~~~~~~G~D~~~~  108 (119)
T cd02067          88 GAIVTRDFKFLKEIGVDAYFG  108 (119)
T ss_pred             CCCCChhHHHHHHcCCeEEEC
Confidence            544444445678889976665

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.

>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=96.81  E-value=0.015  Score=39.58  Aligned_cols=104  Identities=14%  Similarity=0.140  Sum_probs=71.2

Q ss_pred             HHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCC--CCHHHHHHHhcc-cCCCCEEEEEccCChHHH
Q 029986           29 WLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPD--MDGFKLHEQVGL-EMDLPVIMMSVDGCTQDV  105 (184)
Q Consensus        29 ~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~--~~g~~l~~~l~~-~~~~~iIi~~~~~~~~~~  105 (184)
                      ....|...|...|+++..+.+.++++..+.. .....+|++++. ++  ....++++.++. ..++||.+++.....+.+
T Consensus         5 ~~~~l~~~L~~~~~~vv~~~~~dd~~~~i~~-~~~i~avvi~~d-~~~~~~~~~ll~~i~~~~~~iPVFl~~~~~~~~~l   82 (115)
T PF03709_consen    5 ASRELAEALEQRGREVVDADSTDDALAIIES-FTDIAAVVISWD-GEEEDEAQELLDKIRERNFGIPVFLLAERDTTEDL   82 (115)
T ss_dssp             HHHHHHHHHHHTTTEEEEESSHHHHHHHHHC-TTTEEEEEEECH-HHHHHHHHHHHHHHHHHSTT-EEEEEESCCHHHCC
T ss_pred             HHHHHHHHHHHCCCEEEEeCChHHHHHHHHh-CCCeeEEEEEcc-cccchhHHHHHHHHHHhCCCCCEEEEecCCCcccC
Confidence            3456778888889999999999999999974 356899999986 11  234567888853 468999999875544443


Q ss_pred             HHHHHcCCCceEeCCCCHH-HHHHHHHHHH
Q 029986          106 MKGVTHGACNYLLKPIRIK-ELRNIWQHVA  134 (184)
Q Consensus       106 ~~a~~~ga~~~l~kP~~~~-~l~~~l~~~~  134 (184)
                      -.-.-..+++|+....+.. .+...+..+.
T Consensus        83 ~~~~l~~v~~~i~l~~~t~~fia~rI~~Aa  112 (115)
T PF03709_consen   83 PAEVLGEVDGFIWLFEDTAEFIARRIEAAA  112 (115)
T ss_dssp             CHHHHCCESEEEETTTTTHHHHHHHHHHHH
T ss_pred             CHHHHhhccEEEEecCCCHHHHHHHHHHHH
Confidence            3334445788887766444 4455555543

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.

>TIGR00640 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain

Probab=96.52  E-value=0.14  Score=35.70  Aligned_cols=108  Identities=9%  Similarity=-0.060  Sum_probs=71.9

Q ss_pred             eCCHHHHHHHHHHHHhcCCeEEE---ECCHHHHHHHHHhcCCCccEEEEeCCCCCC-C-HHHHHHHhccc-CCCCEEEEE
Q 029986           24 DDDPIWLRILEKMLRKCLYEVTK---CNRAEIALDMLRMSKNGYDIVISDVHMPDM-D-GFKLHEQVGLE-MDLPVIMMS   97 (184)
Q Consensus        24 dd~~~~~~~l~~~L~~~~~~v~~---~~~~~~~~~~l~~~~~~~dlvilD~~l~~~-~-g~~l~~~l~~~-~~~~iIi~~   97 (184)
                      |.+..-...+..+|+..||+|..   ..+.+++.+...  +..+|+|.+-..+... . --++++.+++. .....+++.
T Consensus        13 D~Hd~g~~iv~~~l~~~GfeVi~lg~~~s~e~~v~aa~--e~~adii~iSsl~~~~~~~~~~~~~~L~~~g~~~i~vivG   90 (132)
T TIGR00640        13 DGHDRGAKVIATAYADLGFDVDVGPLFQTPEEIARQAV--EADVHVVGVSSLAGGHLTLVPALRKELDKLGRPDILVVVG   90 (132)
T ss_pred             CccHHHHHHHHHHHHhCCcEEEECCCCCCHHHHHHHHH--HcCCCEEEEcCchhhhHHHHHHHHHHHHhcCCCCCEEEEe
Confidence            56677778888999999999874   345777777776  4569999986654321 1 12345555443 223344555


Q ss_pred             ccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHH
Q 029986           98 VDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHV  133 (184)
Q Consensus        98 ~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~  133 (184)
                      .....+......++|+++|+..--+..++...+...
T Consensus        91 G~~~~~~~~~l~~~Gvd~~~~~gt~~~~i~~~l~~~  126 (132)
T TIGR00640        91 GVIPPQDFDELKEMGVAEIFGPGTPIPESAIFLLKK  126 (132)
T ss_pred             CCCChHhHHHHHHCCCCEEECCCCCHHHHHHHHHHH
Confidence            434455667789999999998877777777666553

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.

>COG4999 Uncharacterized domain of BarA-like signal transduction histidine kinases [Signal transduction mechanisms]

Probab=96.42  E-value=0.025  Score=38.38  Aligned_cols=110  Identities=15%  Similarity=0.173  Sum_probs=75.1

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHh--cccCCCCEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQV--GLEMDLPVI   94 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l--~~~~~~~iI   94 (184)
                      +.+.+.||.|...+......|...+.+|.......    .+.  ..+||.+++.+-.+-.+...+....  +.-.-.-.+
T Consensus        11 gk~LayiEpNstAA~~t~~iL~~tpleVtyr~t~~----~lp--~~hYD~~Ll~vavtfr~n~tm~~~~l~~Al~mtd~v   84 (140)
T COG4999          11 GKRLAYIEPNSTAAQCTLDILSETPLEVTYRPTFS----ALP--PAHYDMMLLGVAVTFRENLTMQHERLAKALSMTDFV   84 (140)
T ss_pred             cceeEEecCccHHHHHHHHHHhcCCceEEeccccc----ccC--hhhhceeeecccccccCCchHHHHHHHHHHhhhcce
Confidence            55799999999999999999999999987654432    222  3569999999877766654444322  211112233


Q ss_pred             EEEccCCh-HHHHHHHHcCCCceEeCCCCHHHHHHHHHH
Q 029986           95 MMSVDGCT-QDVMKGVTHGACNYLLKPIRIKELRNIWQH  132 (184)
Q Consensus        95 i~~~~~~~-~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~  132 (184)
                      |++-.+.. -.+....+.|+-+++.||++...|...+-.
T Consensus        85 ilalPs~~qv~AeqLkQ~g~~~CllKPls~~rLlptlla  123 (140)
T COG4999          85 ILALPSHAQVNAEQLKQDGAGACLLKPLSSTRLLPTLLA  123 (140)
T ss_pred             EEecCcHHHHhHHHHhhcchHhHhhCcchhhhhHHHHHH
Confidence            44433333 345567888999999999999988775443

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

Probab=96.17  E-value=0.017  Score=52.67  Aligned_cols=50  Identities=20%  Similarity=0.205  Sum_probs=42.4

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCC
Q 029986           15 PAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVH   72 (184)
Q Consensus        15 ~~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~   72 (184)
                      .++.+|+++||++..+..++.+|+..|+.|..+.+.      ..  ...||+||+|..
T Consensus       687 l~g~~vLlvdD~~~~r~~l~~~L~~~G~~v~~a~~~------~~--~~~~Dlvl~D~~  736 (894)
T PRK10618        687 LDGVTVLLDITSEEVRKIVTRQLENWGATCITPDER------LI--SQEYDIFLTDNP  736 (894)
T ss_pred             CCCCEEEEEeCCHHHHHHHHHHHHHCCCEEEEcCcc------cc--CCCCCEEEECCC
Confidence            357899999999999999999999999999887652      12  455999999987

>TIGR03815 CpaE_hom_Actino helicase/secretion neighborhood CpaE-like protein

Probab=95.11  E-value=0.13  Score=41.32  Aligned_cols=85  Identities=14%  Similarity=0.045  Sum_probs=53.7

Q ss_pred             CCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEEEEc-cCChHHHHHHHHcCCCceEeC
Q 029986           41 LYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMSV-DGCTQDVMKGVTHGACNYLLK  119 (184)
Q Consensus        41 ~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi~~~-~~~~~~~~~a~~~ga~~~l~k  119 (184)
                      |.++..+.+..++.....    ...+|++|..+...    .+... .-+...++++.. ..+.+....++..|+.+|+.+
T Consensus         1 ~~~~~~~~~~~~~~~~~~----~~~~v~~~~~~~~~----~~~~~-~p~~~~vv~v~~~~~~~~~~~~a~~~Ga~~~l~~   71 (322)
T TIGR03815         1 GVELDVAPDPEAARRAWA----RAPLVLVDADMAEA----CAAAG-LPRRRRVVLVGGGEPGGALWRAAAAVGAEHVAVL   71 (322)
T ss_pred             CCceEEccCchhhhhccc----cCCeEEECchhhhH----HHhcc-CCCCCCEEEEeCCCCCHHHHHHHHHhChhheeeC
Confidence            345555665554444332    25789998743211    11111 111233554444 555778889999999999999


Q ss_pred             CCCHHHHHHHHHHHH
Q 029986          120 PIRIKELRNIWQHVA  134 (184)
Q Consensus       120 P~~~~~l~~~l~~~~  134 (184)
                      |.+..+|.+.+..+.
T Consensus        72 P~~~~~l~~~l~~~~   86 (322)
T TIGR03815        72 PEAEGWLVELLADLD   86 (322)
T ss_pred             CCCHHHHHHHHHhhc
Confidence            999999999998874

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.

>PF10087 DUF2325: Uncharacterized protein conserved in bacteria (DUF2325); InterPro: IPR016772 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function

Probab=94.89  E-value=0.62  Score=30.46  Aligned_cols=87  Identities=14%  Similarity=0.129  Sum_probs=54.9

Q ss_pred             eEEEEeCCHHHHHHHHHHHHhcCCeEEEE------CCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCC
Q 029986           19 RVLVVDDDPIWLRILEKMLRKCLYEVTKC------NRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLP   92 (184)
Q Consensus        19 ~Ilivdd~~~~~~~l~~~L~~~~~~v~~~------~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~   92 (184)
                      +|+||.........++..+++.|+.....      ......+...   -..+|+||+=...-.=+....++...+..+.|
T Consensus         1 ~vliVGG~~~~~~~~~~~~~~~G~~~~~hg~~~~~~~~~~~l~~~---i~~aD~VIv~t~~vsH~~~~~vk~~akk~~ip   77 (97)
T PF10087_consen    1 SVLIVGGREDRERRYKRILEKYGGKLIHHGRDGGDEKKASRLPSK---IKKADLVIVFTDYVSHNAMWKVKKAAKKYGIP   77 (97)
T ss_pred             CEEEEcCCcccHHHHHHHHHHcCCEEEEEecCCCCccchhHHHHh---cCCCCEEEEEeCCcChHHHHHHHHHHHHcCCc
Confidence            48999998888889999999999988777      2222122221   23479998866544444444455554456788


Q ss_pred             EEEEEccCChHHHHHHH
Q 029986           93 VIMMSVDGCTQDVMKGV  109 (184)
Q Consensus        93 iIi~~~~~~~~~~~~a~  109 (184)
                      +++.-+ .......+++
T Consensus        78 ~~~~~~-~~~~~l~~~l   93 (97)
T PF10087_consen   78 IIYSRS-RGVSSLERAL   93 (97)
T ss_pred             EEEECC-CCHHHHHHHH
Confidence            887643 3344444443

>PRK15399 lysine decarboxylase LdcC; Provisional

Probab=94.89  E-value=0.54  Score=41.88  Aligned_cols=79  Identities=13%  Similarity=0.095  Sum_probs=57.8

Q ss_pred             CeEEEEeCCH-H-----HHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCC
Q 029986           18 LRVLVVDDDP-I-----WLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMD   90 (184)
Q Consensus        18 ~~Ilivdd~~-~-----~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~   90 (184)
                      |+|++++++. .     ....|...|++.|+++..+.+..++...+.. ....+++++++.-.   ..++++.++. ...
T Consensus         1 ~~~~~i~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~---~~~~~~~~~~~~~~   76 (713)
T PRK15399          1 MNIIAIMGPHGVFYKDEPIKELESALQAQGFQTIWPQNSVDLLKFIEH-NPRICGVIFDWDEY---SLDLCSDINQLNEY   76 (713)
T ss_pred             CcEEEEecccccccccHHHHHHHHHHHHCCcEEEEecCHHHHHHHHhc-ccceeEEEEecccc---hHHHHHHHHHhCCC
Confidence            4677887663 1     2455677788889999999999999998863 45589999996432   3457787753 468


Q ss_pred             CCEEEEEccC
Q 029986           91 LPVIMMSVDG  100 (184)
Q Consensus        91 ~~iIi~~~~~  100 (184)
                      +||+++....
T Consensus        77 ~Pv~~~~~~~   86 (713)
T PRK15399         77 LPLYAFINTH   86 (713)
T ss_pred             CCEEEEcCcc
Confidence            9999987643

>PF02310 B12-binding: B12 binding domain; InterPro: IPR006158 The cobalamin (vitamin B12) binding domain can bind two different forms of the cobalamin cofactor, with cobalt bonded either to a methyl group (methylcobalamin) or to 5'-deoxyadenosine (adenosylcobalamin)

Probab=94.58  E-value=0.84  Score=30.69  Aligned_cols=93  Identities=22%  Similarity=0.164  Sum_probs=55.3

Q ss_pred             CHHHHHHHHHHHHhcCCeEEEEC---CHHHHHHHHHhcCCCccEEEEeCCCC-CC-CHHHHHHHhcccCCCCEEEEEccC
Q 029986           26 DPIWLRILEKMLRKCLYEVTKCN---RAEIALDMLRMSKNGYDIVISDVHMP-DM-DGFKLHEQVGLEMDLPVIMMSVDG  100 (184)
Q Consensus        26 ~~~~~~~l~~~L~~~~~~v~~~~---~~~~~~~~l~~~~~~~dlvilD~~l~-~~-~g~~l~~~l~~~~~~~iIi~~~~~  100 (184)
                      ++.-...+..+|++.|+++....   +.++..+.+.  ...||+|.+...+. .. ...++++.++...+-..+++....
T Consensus        13 ~~lGl~~la~~l~~~G~~v~~~d~~~~~~~l~~~~~--~~~pd~V~iS~~~~~~~~~~~~l~~~~k~~~p~~~iv~GG~~   90 (121)
T PF02310_consen   13 HPLGLLYLAAYLRKAGHEVDILDANVPPEELVEALR--AERPDVVGISVSMTPNLPEAKRLARAIKERNPNIPIVVGGPH   90 (121)
T ss_dssp             TSHHHHHHHHHHHHTTBEEEEEESSB-HHHHHHHHH--HTTCSEEEEEESSSTHHHHHHHHHHHHHTTCTTSEEEEEESS
T ss_pred             hhHHHHHHHHHHHHCCCeEEEECCCCCHHHHHHHHh--cCCCcEEEEEccCcCcHHHHHHHHHHHHhcCCCCEEEEECCc
Confidence            45567788999999999987662   3466667666  34699999987433 22 245566666544333344444443


Q ss_pred             ChHHHHHHHH--cCCCceEeCC
Q 029986          101 CTQDVMKGVT--HGACNYLLKP  120 (184)
Q Consensus       101 ~~~~~~~a~~--~ga~~~l~kP  120 (184)
                      -.......++  .|+|..+.-+
T Consensus        91 ~t~~~~~~l~~~~~~D~vv~Ge  112 (121)
T PF02310_consen   91 ATADPEEILREYPGIDYVVRGE  112 (121)
T ss_dssp             SGHHHHHHHHHHHTSEEEEEET
T ss_pred             hhcChHHHhccCcCcceecCCC
Confidence            3333344444  6777555433

Cobalamin-binding domains are mainly found in two families of enzymes present in animals and prokaryotes, which perform distinct kinds of reactions at the cobalt-carbon bond. Enzymes that require methylcobalamin carry out methyl transfer reactions. Enzymes that require adenosylcobalamin catalyse reactions in which the first step is the cleavage of adenosylcobalamin to form cob(II)alamin and the 5'-deoxyadenosyl radical, and thus act as radical generators. In both types of enzymes the B12-binding domain uses a histidine to bind the cobalt atom of cobalamin cofactors. This histidine is embedded in a DXHXXG sequence, the most conserved primary sequence motif of the domain [, , ]. Proteins containing the cobalamin-binding domain include: Animal and prokaryotic methionine synthase (2.1.1.13 from EC), which catalyse the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. Animal and prokaryotic methylmalonyl-CoA mutase (5.4.99.2 from EC), which are involved in the degradation of several amino acids, odd-chain fatty acids and cholesterol via propionyl-CoA to the tricarboxylic acid cycle. Prokaryotic lysine 5,6-aminomutase (5.4.3.4 from EC). Prokaryotic glutamate mutase (5.4.99.1 from EC) []. Prokaryotic methyleneglutarate mutase (5.4.99.4 from EC). Prokaryotic isobutyryl-CoA mutase (5.4.99.13 from EC). The core structure of the cobalamin-binding domain is characterised by a five-stranded alpha/beta (Rossmann) fold, which consists of 5 parallel beta-sheets surrounded by 4-5 alpha helices in three layers (alpha/beta/alpha) []. Upon binding cobalamin, important elements of the binding site appear to become structured, including an alpha-helix that forms on one side of the cleft accommodating the nucleotide 'tail' of the cofactor. In cobalamin, the cobalt atom can be either free (dmb-off) or bound to dimethylbenzimidazole (dmb-on) according to the pH. When bound to the cobalamin-binding domain, the dimethylbenzimidazole ligand is replaced by the active histidine (His-on) of the DXHXXG motif. The replacement of dimethylbenzimidazole by histidine allows switching between the catalytic and activation cycles []. In methionine synthase the cobalamin cofactor is sandwiched between the cobalamin-binding domain and an approximately 90 residues N-terminal domain forming a helical bundle comprising two pairs of antiparallel helices []. In methionine synthase, there is a second, adjacent domain involved in cobalamin binding that forms a 4-helical bundle cap (IPR003759 from INTERPRO); in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO) [].; GO: 0031419 cobalamin binding, 0046872 metal ion binding; PDB: 1Y80_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 3KP1_A 3KOW_A 3KOZ_A ....

>PRK15400 lysine decarboxylase CadA; Provisional

Probab=94.36  E-value=0.71  Score=41.13  Aligned_cols=79  Identities=16%  Similarity=0.226  Sum_probs=57.3

Q ss_pred             CeEEEEeCCH------HHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhc-ccCC
Q 029986           18 LRVLVVDDDP------IWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVG-LEMD   90 (184)
Q Consensus        18 ~~Ilivdd~~------~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~-~~~~   90 (184)
                      |+|++|+++.      .....|...|++.|++|..+.+..++...... ....+++++++.-  . ...+++.++ ....
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~~-~~~~~~~~~~~~~--~-~~~~~~~~~~~~~~   76 (714)
T PRK15400          1 MNVIAILNHMGVYFKEEPIRELHRALERLNFQIVYPNDRDDLLKLIEN-NARLCGVIFDWDK--Y-NLELCEEISKMNEN   76 (714)
T ss_pred             CcEEEEccccccccccHHHHHHHHHHHHCCcEEEEeCCHHHHHHHHhc-ccceeEEEEecch--h-hHHHHHHHHHhCCC
Confidence            4677777662      12455777888889999999999999998763 4558999999632  2 245777775 3468


Q ss_pred             CCEEEEEccC
Q 029986           91 LPVIMMSVDG  100 (184)
Q Consensus        91 ~~iIi~~~~~  100 (184)
                      +||+++....
T Consensus        77 ~Pv~~~~~~~   86 (714)
T PRK15400         77 LPLYAFANTY   86 (714)
T ss_pred             CCEEEEcccc
Confidence            9999987643

>TIGR01501 MthylAspMutase methylaspartate mutase, S subunit

Probab=94.30  E-value=1.2  Score=31.10  Aligned_cols=108  Identities=6%  Similarity=-0.042  Sum_probs=71.1

Q ss_pred             CCHHHHHHHHHHHHhcCCeEEEE---CCHHHHHHHHHhcCCCccEEEEeCCCCCCC--HHHHHHHhccc-CCCCEEEEEc
Q 029986           25 DDPIWLRILEKMLRKCLYEVTKC---NRAEIALDMLRMSKNGYDIVISDVHMPDMD--GFKLHEQVGLE-MDLPVIMMSV   98 (184)
Q Consensus        25 d~~~~~~~l~~~L~~~~~~v~~~---~~~~~~~~~l~~~~~~~dlvilD~~l~~~~--g~~l~~~l~~~-~~~~iIi~~~   98 (184)
                      -+..-...+..+|+..||+|...   -..++..+...  +..+|+|-+...|....  --++.+.+++. ..-+.+++..
T Consensus        13 ~HdiGk~iv~~~l~~~GfeVi~LG~~v~~e~~v~aa~--~~~adiVglS~l~~~~~~~~~~~~~~l~~~gl~~~~vivGG   90 (134)
T TIGR01501        13 CHAVGNKILDHAFTNAGFNVVNLGVLSPQEEFIKAAI--ETKADAILVSSLYGHGEIDCKGLRQKCDEAGLEGILLYVGG   90 (134)
T ss_pred             hhhHhHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHH--HcCCCEEEEecccccCHHHHHHHHHHHHHCCCCCCEEEecC
Confidence            34455567888999999998743   46777887776  45699999987765432  23355556433 2234455554


Q ss_pred             cC---ChH---HHHHHHHcCCCceEeCCCCHHHHHHHHHHHH
Q 029986           99 DG---CTQ---DVMKGVTHGACNYLLKPIRIKELRNIWQHVA  134 (184)
Q Consensus        99 ~~---~~~---~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~  134 (184)
                      ..   ..+   ...++.+.|++..+...-+.+++...++..+
T Consensus        91 ~~vi~~~d~~~~~~~l~~~Gv~~vF~pgt~~~~iv~~l~~~~  132 (134)
T TIGR01501        91 NLVVGKQDFPDVEKRFKEMGFDRVFAPGTPPEVVIADLKKDL  132 (134)
T ss_pred             CcCcChhhhHHHHHHHHHcCCCEEECcCCCHHHHHHHHHHHh
Confidence            21   111   2346888999999988888888888777654

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.

>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=94.25  E-value=0.99  Score=34.82  Aligned_cols=110  Identities=21%  Similarity=0.224  Sum_probs=68.4

Q ss_pred             CeEEEEeCCHHHHHHHH------HHHHhcCCeEE-EE-CCHHHHHHHHHhcCCCccEEEEeCCCC---------CCCHHH
Q 029986           18 LRVLVVDDDPIWLRILE------KMLRKCLYEVT-KC-NRAEIALDMLRMSKNGYDIVISDVHMP---------DMDGFK   80 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~------~~L~~~~~~v~-~~-~~~~~~~~~l~~~~~~~dlvilD~~l~---------~~~g~~   80 (184)
                      +|+=|+.|+....-.+.      +.|-+.|+.+. .+ .|...+..+..   .++++|     ||         +..-.+
T Consensus        94 iKlEVi~d~~~Llpd~~~tv~aa~~L~~~Gf~vlpyc~dd~~~ar~l~~---~G~~~v-----mPlg~pIGsg~Gi~~~~  165 (248)
T cd04728          94 IKLEVIGDDKTLLPDPIETLKAAEILVKEGFTVLPYCTDDPVLAKRLED---AGCAAV-----MPLGSPIGSGQGLLNPY  165 (248)
T ss_pred             EEEEEecCccccccCHHHHHHHHHHHHHCCCEEEEEeCCCHHHHHHHHH---cCCCEe-----CCCCcCCCCCCCCCCHH
Confidence            35555555543332222      23334488776 44 45555555443   468887     34         111256


Q ss_pred             HHHHhcccCCCCEEEEEccCChHHHHHHHHcCCCceE-----eCCCCHHHHHHHHHHHHc
Q 029986           81 LHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYL-----LKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        81 l~~~l~~~~~~~iIi~~~~~~~~~~~~a~~~ga~~~l-----~kP~~~~~l~~~l~~~~~  135 (184)
                      +++.++...++|||+=+.-.+++.+..+++.|+++.+     .|.-++..+.+.+.....
T Consensus       166 ~I~~I~e~~~vpVI~egGI~tpeda~~AmelGAdgVlV~SAIt~a~dP~~ma~af~~Av~  225 (248)
T cd04728         166 NLRIIIERADVPVIVDAGIGTPSDAAQAMELGADAVLLNTAIAKAKDPVAMARAFKLAVE  225 (248)
T ss_pred             HHHHHHHhCCCcEEEeCCCCCHHHHHHHHHcCCCEEEEChHhcCCCCHHHHHHHHHHHHH
Confidence            7787765567899888888889999999999999996     453445566665555543

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=93.92  E-value=1.2  Score=34.36  Aligned_cols=110  Identities=20%  Similarity=0.199  Sum_probs=68.4

Q ss_pred             CeEEEEeCCHHHHHHHH------HHHHhcCCeEE-EEC-CHHHHHHHHHhcCCCccEEEEeCCCC---------CCCHHH
Q 029986           18 LRVLVVDDDPIWLRILE------KMLRKCLYEVT-KCN-RAEIALDMLRMSKNGYDIVISDVHMP---------DMDGFK   80 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~------~~L~~~~~~v~-~~~-~~~~~~~~l~~~~~~~dlvilD~~l~---------~~~g~~   80 (184)
                      +|+=|+.|+....-.+.      +.|-+.|+.+. .+. |...+-.+.   ..+|++|     ||         +..-.+
T Consensus        94 iKlEVi~d~~~llpd~~~tv~aa~~L~~~Gf~vlpyc~~d~~~ak~l~---~~G~~~v-----mPlg~pIGsg~gi~~~~  165 (250)
T PRK00208         94 IKLEVIGDDKTLLPDPIETLKAAEILVKEGFVVLPYCTDDPVLAKRLE---EAGCAAV-----MPLGAPIGSGLGLLNPY  165 (250)
T ss_pred             EEEEEecCCCCCCcCHHHHHHHHHHHHHCCCEEEEEeCCCHHHHHHHH---HcCCCEe-----CCCCcCCCCCCCCCCHH
Confidence            45556665543222222      23334488776 444 555555544   3468887     44         111146


Q ss_pred             HHHHhcccCCCCEEEEEccCChHHHHHHHHcCCCceE-----eCCCCHHHHHHHHHHHHc
Q 029986           81 LHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYL-----LKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        81 l~~~l~~~~~~~iIi~~~~~~~~~~~~a~~~ga~~~l-----~kP~~~~~l~~~l~~~~~  135 (184)
                      +++.++...++|||+=+.-.+++.+..+++.|+++.+     .|--++..+.+.+.....
T Consensus       166 ~i~~i~e~~~vpVIveaGI~tpeda~~AmelGAdgVlV~SAItka~dP~~ma~af~~Av~  225 (250)
T PRK00208        166 NLRIIIEQADVPVIVDAGIGTPSDAAQAMELGADAVLLNTAIAVAGDPVAMARAFKLAVE  225 (250)
T ss_pred             HHHHHHHhcCCeEEEeCCCCCHHHHHHHHHcCCCEEEEChHhhCCCCHHHHHHHHHHHHH
Confidence            6777765567899888888889999999999999996     453445666665555543

>cd02069 methionine_synthase_B12_BD B12 binding domain of methionine synthase

Probab=93.91  E-value=1.6  Score=33.01  Aligned_cols=102  Identities=14%  Similarity=0.184  Sum_probs=66.4

Q ss_pred             CCeEEEE----eCCHHHHHHHHHHHHhcCCeEEEEC---CHHHHHHHHHhcCCCccEEEEeCCCCCC--CHHHHHHHhcc
Q 029986           17 GLRVLVV----DDDPIWLRILEKMLRKCLYEVTKCN---RAEIALDMLRMSKNGYDIVISDVHMPDM--DGFKLHEQVGL   87 (184)
Q Consensus        17 ~~~Iliv----dd~~~~~~~l~~~L~~~~~~v~~~~---~~~~~~~~l~~~~~~~dlvilD~~l~~~--~g~~l~~~l~~   87 (184)
                      .-+|++.    |.+..=...+..+|+..||+|....   ..++..+.+.  +..||+|.+...++..  .--++++.++.
T Consensus        88 ~~~vvl~t~~gd~HdiG~~iv~~~l~~~G~~Vi~LG~~vp~e~~v~~~~--~~~~~~V~lS~~~~~~~~~~~~~i~~L~~  165 (213)
T cd02069          88 KGKIVLATVKGDVHDIGKNLVGVILSNNGYEVIDLGVMVPIEKILEAAK--EHKADIIGLSGLLVPSLDEMVEVAEEMNR  165 (213)
T ss_pred             CCeEEEEeCCCchhHHHHHHHHHHHHhCCCEEEECCCCCCHHHHHHHHH--HcCCCEEEEccchhccHHHHHHHHHHHHh
Confidence            3477777    7777778888899999999998655   3677777766  5679999998877653  23445666654


Q ss_pred             c-CCCCEEEEEccCChHHHHH---HHHcCCCceEeCC
Q 029986           88 E-MDLPVIMMSVDGCTQDVMK---GVTHGACNYLLKP  120 (184)
Q Consensus        88 ~-~~~~iIi~~~~~~~~~~~~---a~~~ga~~~l~kP  120 (184)
                      . .+++|++=...-+.+....   +-..|||.|-.-.
T Consensus       166 ~~~~~~i~vGG~~~~~~~~~~~~~~~~~gad~y~~da  202 (213)
T cd02069         166 RGIKIPLLIGGAATSRKHTAVKIAPEYDGPVVYVKDA  202 (213)
T ss_pred             cCCCCeEEEEChhcCHHHHhhhhccccCCCceEecCH
Confidence            3 3455554433333333332   2346998776533

This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy).

>cd02070 corrinoid_protein_B12-BD B12 binding domain of corrinoid proteins

Probab=93.72  E-value=2.2  Score=31.86  Aligned_cols=97  Identities=18%  Similarity=0.118  Sum_probs=64.1

Q ss_pred             CCeEEEE----eCCHHHHHHHHHHHHhcCCeEEEEC---CHHHHHHHHHhcCCCccEEEEeCCCCCC--CHHHHHHHhcc
Q 029986           17 GLRVLVV----DDDPIWLRILEKMLRKCLYEVTKCN---RAEIALDMLRMSKNGYDIVISDVHMPDM--DGFKLHEQVGL   87 (184)
Q Consensus        17 ~~~Iliv----dd~~~~~~~l~~~L~~~~~~v~~~~---~~~~~~~~l~~~~~~~dlvilD~~l~~~--~g~~l~~~l~~   87 (184)
                      ..+|++.    |.+..=...+..+|+..||++....   ..++..+.+.  +..||+|-+...+...  ..-++++.++.
T Consensus        82 ~~~vl~~~~~gd~H~lG~~~v~~~l~~~G~~vi~lG~~~p~~~l~~~~~--~~~~d~v~lS~~~~~~~~~~~~~i~~lr~  159 (201)
T cd02070          82 KGKVVIGTVEGDIHDIGKNLVATMLEANGFEVIDLGRDVPPEEFVEAVK--EHKPDILGLSALMTTTMGGMKEVIEALKE  159 (201)
T ss_pred             CCeEEEEecCCccchHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHH--HcCCCEEEEeccccccHHHHHHHHHHHHH
Confidence            3477777    6777778888899999999987543   4667777776  5679999998876653  23445666654


Q ss_pred             cC---CCCEEEEEccCChHHHHHHHHcCCCceEe
Q 029986           88 EM---DLPVIMMSVDGCTQDVMKGVTHGACNYLL  118 (184)
Q Consensus        88 ~~---~~~iIi~~~~~~~~~~~~a~~~ga~~~l~  118 (184)
                      .+   +++|++ ....-...  -+-..||+.|-.
T Consensus       160 ~~~~~~~~i~v-GG~~~~~~--~~~~~GaD~~~~  190 (201)
T cd02070         160 AGLRDKVKVMV-GGAPVNQE--FADEIGADGYAE  190 (201)
T ss_pred             CCCCcCCeEEE-ECCcCCHH--HHHHcCCcEEEC
Confidence            43   344444 33322222  456669997765

A family of small methanogenic corrinoid proteins that bind methyl-Co(III) 5-hydroxybenzimidazolylcobamide as a cofactor. They play a role on the methanogenesis from trimethylamine, dimethylamine or monomethylamine, which is initiated by a series of corrinoid-dependent methyltransferases.

>PRK05718 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional

Probab=93.61  E-value=2.4  Score=32.06  Aligned_cols=97  Identities=16%  Similarity=0.194  Sum_probs=63.4

Q ss_pred             HHHHHHhcCC-eEEEECCHHHHHHHHHh-cCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEEEEccCChHHHHHHHH
Q 029986           33 LEKMLRKCLY-EVTKCNRAEIALDMLRM-SKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVT  110 (184)
Q Consensus        33 l~~~L~~~~~-~v~~~~~~~~~~~~l~~-~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi~~~~~~~~~~~~a~~  110 (184)
                      +...|.+.+. -+....+.++++...+. .+.+.+  ++.+.+...++.+.++.+++..+--+|-..+-.+.+.+..+++
T Consensus         8 ~~~~l~~~~~iaV~r~~~~~~a~~i~~al~~~Gi~--~iEitl~~~~~~~~I~~l~~~~p~~~IGAGTVl~~~~a~~a~~   85 (212)
T PRK05718          8 IEEILRAGPVVPVIVINKLEDAVPLAKALVAGGLP--VLEVTLRTPAALEAIRLIAKEVPEALIGAGTVLNPEQLAQAIE   85 (212)
T ss_pred             HHHHHHHCCEEEEEEcCCHHHHHHHHHHHHHcCCC--EEEEecCCccHHHHHHHHHHHCCCCEEEEeeccCHHHHHHHHH
Confidence            3345555543 45566778888877753 234466  5555666778999999996433223344444455688889999


Q ss_pred             cCCCceEeCCCCHHHHHHHHHH
Q 029986          111 HGACNYLLKPIRIKELRNIWQH  132 (184)
Q Consensus       111 ~ga~~~l~kP~~~~~l~~~l~~  132 (184)
                      +||+ |++-|.-..++.+...+
T Consensus        86 aGA~-FivsP~~~~~vi~~a~~  106 (212)
T PRK05718         86 AGAQ-FIVSPGLTPPLLKAAQE  106 (212)
T ss_pred             cCCC-EEECCCCCHHHHHHHHH
Confidence            9998 88888876677665443

>TIGR00262 trpA tryptophan synthase, alpha subunit

Probab=93.01  E-value=1.3  Score=34.51  Aligned_cols=60  Identities=13%  Similarity=0.206  Sum_probs=44.8

Q ss_pred             CHHHHHHHhccc-CCCCEEEEEccCC------hHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           77 DGFKLHEQVGLE-MDLPVIMMSVDGC------TQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        77 ~g~~l~~~l~~~-~~~~iIi~~~~~~------~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      ..+++++.+++. .++|+++++-...      ..+...+.++|+++.+......++....+..+.+.
T Consensus        73 ~~~~~v~~ir~~~~~~plv~m~Y~Npi~~~G~e~f~~~~~~aGvdgviipDlp~ee~~~~~~~~~~~  139 (256)
T TIGR00262        73 KCFELLKKVRQKHPNIPIGLLTYYNLIFRKGVEEFYAKCKEVGVDGVLVADLPLEESGDLVEAAKKH  139 (256)
T ss_pred             HHHHHHHHHHhcCCCCCEEEEEeccHHhhhhHHHHHHHHHHcCCCEEEECCCChHHHHHHHHHHHHC
Confidence            346677777654 6789876654332      46788899999999999988888888887777654

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.

>PRK10128 2-keto-3-deoxy-L-rhamnonate aldolase; Provisional

Probab=92.99  E-value=2.2  Score=33.53  Aligned_cols=100  Identities=15%  Similarity=0.165  Sum_probs=62.7

Q ss_pred             HHHHHHHhcCCe--EEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc--cCCCCEEEEEccCChHHHHH
Q 029986           32 ILEKMLRKCLYE--VTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL--EMDLPVIMMSVDGCTQDVMK  107 (184)
Q Consensus        32 ~l~~~L~~~~~~--v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~--~~~~~iIi~~~~~~~~~~~~  107 (184)
                      .+++.|+.-...  ++.........+.+.  ..++|-|++|.+....+.-++...++.  ...++.++=....+...+.+
T Consensus         8 ~lk~~L~~G~~~~G~~~~~~sp~~~E~~a--~~GfD~v~iD~EHg~~~~~~l~~~i~a~~~~g~~~lVRvp~~~~~~i~r   85 (267)
T PRK10128          8 PFKEGLRKGEVQIGLWLSSTTSYMAEIAA--TSGYDWLLIDGEHAPNTIQDLYHQLQAIAPYASQPVIRPVEGSKPLIKQ   85 (267)
T ss_pred             HHHHHHHcCCceEEEEecCCCcHHHHHHH--HcCCCEEEEccccCCCCHHHHHHHHHHHHhcCCCeEEECCCCCHHHHHH
Confidence            355666553222  222222344555554  456999999999998887777666642  23343343345566788899


Q ss_pred             HHHcCCCceEeCCC-CHHHHHHHHHHH
Q 029986          108 GVTHGACNYLLKPI-RIKELRNIWQHV  133 (184)
Q Consensus       108 a~~~ga~~~l~kP~-~~~~l~~~l~~~  133 (184)
                      +++.||.+.+..-+ +.++...+++..
T Consensus        86 ~LD~GA~GIivP~V~saeeA~~~V~a~  112 (267)
T PRK10128         86 VLDIGAQTLLIPMVDTAEQARQVVSAT  112 (267)
T ss_pred             HhCCCCCeeEecCcCCHHHHHHHHHhc
Confidence            99999999998655 455666665544

>PRK10558 alpha-dehydro-beta-deoxy-D-glucarate aldolase; Provisional

Probab=92.85  E-value=2.1  Score=33.41  Aligned_cols=100  Identities=13%  Similarity=0.076  Sum_probs=63.8

Q ss_pred             HHHHHHHhcCCeE--EEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc--CCCCEEEEEccCChHHHHH
Q 029986           32 ILEKMLRKCLYEV--TKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE--MDLPVIMMSVDGCTQDVMK  107 (184)
Q Consensus        32 ~l~~~L~~~~~~v--~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~--~~~~iIi~~~~~~~~~~~~  107 (184)
                      .+++.|..-...+  +.........+.+.  ..++|.|++|.+....+.-++...++..  ..++.++=....++..+.+
T Consensus         9 ~lk~~l~~g~~~~g~~~~~~sp~~~e~~a--~~G~D~v~iD~EHg~~~~~~~~~~i~a~~~~g~~~lVRvp~~~~~~i~r   86 (256)
T PRK10558          9 KFKAALAAKQVQIGCWSALANPITTEVLG--LAGFDWLVLDGEHAPNDVSTFIPQLMALKGSASAPVVRVPTNEPVIIKR   86 (256)
T ss_pred             HHHHHHHcCCceEEEEEcCCCcHHHHHHH--hcCCCEEEEccccCCCCHHHHHHHHHHHhhcCCCcEEECCCCCHHHHHH
Confidence            4666666532222  22222344555554  4669999999999988877776666422  3344444445567888999


Q ss_pred             HHHcCCCceEeCCC-CHHHHHHHHHHH
Q 029986          108 GVTHGACNYLLKPI-RIKELRNIWQHV  133 (184)
Q Consensus       108 a~~~ga~~~l~kP~-~~~~l~~~l~~~  133 (184)
                      +++.|+++.+..-+ +.++..++++..
T Consensus        87 ~LD~Ga~giivP~v~tae~a~~~v~a~  113 (256)
T PRK10558         87 LLDIGFYNFLIPFVETAEEARRAVAST  113 (256)
T ss_pred             HhCCCCCeeeecCcCCHHHHHHHHHHc
Confidence            99999999987544 566666666654

>PF07688 KaiA: KaiA domain; InterPro: IPR011648 KaiA is a component of the kaiABC clock protein complex, which constitutes the main circadian regulator in cyanobacteria

Probab=92.47  E-value=0.93  Score=35.09  Aligned_cols=77  Identities=17%  Similarity=0.229  Sum_probs=54.4

Q ss_pred             eEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc-CCCCEEEEE
Q 029986           19 RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE-MDLPVIMMS   97 (184)
Q Consensus        19 ~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~-~~~~iIi~~   97 (184)
                      .|.+.-.++...+.+...|....|.+..+.+.++.++.+.......|++++....   ....+..++... --.|+|++.
T Consensus         2 sI~~~v~s~~Laqsl~~~L~~dRY~l~~~~s~~ef~~~le~~~e~iDCLvle~~~---~~~~~~~~L~e~g~LLPaVil~   78 (283)
T PF07688_consen    2 SICLLVSSPALAQSLRQWLPGDRYELVQVDSPEEFLEFLEQHREQIDCLVLEQSP---LLPPLFNQLYEQGILLPAVILG   78 (283)
T ss_dssp             EEEEE-S-HHHHHHHHHHT-STTEEEEEESSCHHHHHHHCCTTTT-SEEEEETTS---TTHHHHHHHHHCT----EEEES
T ss_pred             eEEEEeCCHHHHHHHHHHcccCceEEEEcCcHHHHHHHHHhchhccCEEEEecCC---CcHHHHHHHHHcCccccEEEEe
Confidence            4677778899999999999988899999999999999997556679999998743   344566777533 467998886


Q ss_pred             c
Q 029986           98 V   98 (184)
Q Consensus        98 ~   98 (184)
                      .
T Consensus        79 ~   79 (283)
T PF07688_consen   79 S   79 (283)
T ss_dssp             -
T ss_pred             c
Confidence            5

The kaiABC complex may act as a promoter-nonspecific transcription regulator that represses transcription, possibly by acting on the state of chromosome compaction. In the complex, KaiA enhances the phosphorylation status of kaiC. In contrast, the presence of kaiB in the complex decreases the phosphorylation status of kaiC, suggesting that kaiB acts by antagonising the interaction between kaiA and kaiC. The activity of KaiA activates kaiBC expression, while KaiC represses it. The overall fold of the KaiA monomer is that of a four-helix bundle, which forms a dimer in the known structure []. KaiA functions as a homodimer. Each monomer is composed of three functional domains: the N-terminal amplitude-amplifier domain, the central period-adjuster domain and the C-termianl clock-oscillator domain. The N-terminal domain of KaiA, from cyanobacteria, acts as a psuedo-receiver domain, but lacks the conserved aspartyl residue required for phosphotransfer in response regulators []. The C-terminal domain is responsible for dimer formation, binding to KaiC, enhancing KaiC phosphorylation and generating the circadian oscillations []. The KaiA protein from Anabaena sp. (strain PCC 7120) lacks the N-terminal CheY-like domain.; GO: 0006468 protein phosphorylation, 0007623 circadian rhythm; PDB: 1V2Z_A 1Q6B_B 1Q6A_A 1SV1_B 1SUY_B 1R5Q_A 1M2E_A 1R8J_B 1M2F_A.

>COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism]

Probab=92.25  E-value=3  Score=29.49  Aligned_cols=113  Identities=16%  Similarity=0.053  Sum_probs=74.7

Q ss_pred             CeEEE----EeCCHHHHHHHHHHHHhcCCeEE---EECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHH----HHHhc
Q 029986           18 LRVLV----VDDDPIWLRILEKMLRKCLYEVT---KCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKL----HEQVG   86 (184)
Q Consensus        18 ~~Ili----vdd~~~~~~~l~~~L~~~~~~v~---~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l----~~~l~   86 (184)
                      .||++    .|.+..-.+.+.+.|++.|++|.   .+.+.+++.+..-  +...|+|.+...  .....++    ++.++
T Consensus        13 prvlvak~GlDgHd~gakvia~~l~d~GfeVi~~g~~~tp~e~v~aA~--~~dv~vIgvSsl--~g~h~~l~~~lve~lr   88 (143)
T COG2185          13 PRVLVAKLGLDGHDRGAKVIARALADAGFEVINLGLFQTPEEAVRAAV--EEDVDVIGVSSL--DGGHLTLVPGLVEALR   88 (143)
T ss_pred             ceEEEeccCccccccchHHHHHHHHhCCceEEecCCcCCHHHHHHHHH--hcCCCEEEEEec--cchHHHHHHHHHHHHH
Confidence            35554    47888889999999999999987   4567778777764  455788887543  3333444    44444


Q ss_pred             ccCCCCEE-EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHH
Q 029986           87 LEMDLPVI-MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVA  134 (184)
Q Consensus        87 ~~~~~~iI-i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~  134 (184)
                      +..--.|+ +....-.++......+.|++.++..-....+...-+...+
T Consensus        89 e~G~~~i~v~~GGvip~~d~~~l~~~G~~~if~pgt~~~~~~~~v~~~l  137 (143)
T COG2185          89 EAGVEDILVVVGGVIPPGDYQELKEMGVDRIFGPGTPIEEALSDLLTRL  137 (143)
T ss_pred             HhCCcceEEeecCccCchhHHHHHHhCcceeeCCCCCHHHHHHHHHHHH
Confidence            43322344 4444555566777888999999987777666655544433

>TIGR03239 GarL 2-dehydro-3-deoxyglucarate aldolase

Probab=92.20  E-value=3.3  Score=32.15  Aligned_cols=81  Identities=14%  Similarity=0.095  Sum_probs=56.0

Q ss_pred             HHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc--CCCCEEEEEccCChHHHHHHHHcCCCceEeCCC-CHHHHH
Q 029986           51 EIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE--MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPI-RIKELR  127 (184)
Q Consensus        51 ~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~--~~~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~-~~~~l~  127 (184)
                      ....+.+.  ..++|-|++|.+....+.-++...++..  ..++.++=....+...+.++++.|+++.+..-+ +.++..
T Consensus        23 p~~~e~~a--~~G~D~v~iD~EHg~~~~~~~~~~~~a~~~~g~~~~VRvp~~~~~~i~r~LD~Ga~gIivP~v~taeea~  100 (249)
T TIGR03239        23 PITTEVLG--LAGFDWLLLDGEHAPNDVLTFIPQLMALKGSASAPVVRPPWNEPVIIKRLLDIGFYNFLIPFVESAEEAE  100 (249)
T ss_pred             cHHHHHHH--hcCCCEEEEecccCCCCHHHHHHHHHHHhhcCCCcEEECCCCCHHHHHHHhcCCCCEEEecCcCCHHHHH
Confidence            44555554  4569999999999988877776666422  334433333556678899999999999987544 566666


Q ss_pred             HHHHHH
Q 029986          128 NIWQHV  133 (184)
Q Consensus       128 ~~l~~~  133 (184)
                      ++++..
T Consensus       101 ~~v~a~  106 (249)
T TIGR03239       101 RAVAAT  106 (249)
T ss_pred             HHHHHc
Confidence            666654

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

>TIGR01182 eda Entner-Doudoroff aldolase

Probab=91.90  E-value=4.3  Score=30.55  Aligned_cols=85  Identities=16%  Similarity=0.171  Sum_probs=53.6

Q ss_pred             EEEECCHHHHHHHHHh-cCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEEEEccCChHHHHHHHHcCCCceEeCCCC
Q 029986           44 VTKCNRAEIALDMLRM-SKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIR  122 (184)
Q Consensus        44 v~~~~~~~~~~~~l~~-~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~  122 (184)
                      +....+.+++.+..+. .+.+..  ++.+.+...+..+.++++++..+--+|-..+=.+.+.+..+.++||+ |+..|..
T Consensus        13 Vlr~~~~e~a~~~~~al~~~Gi~--~iEit~~t~~a~~~i~~l~~~~~~~~vGAGTVl~~~~a~~a~~aGA~-FivsP~~   89 (204)
T TIGR01182        13 VIRIDDVDDALPLAKALIEGGLR--VLEVTLRTPVALDAIRLLRKEVPDALIGAGTVLNPEQLRQAVDAGAQ-FIVSPGL   89 (204)
T ss_pred             EEecCCHHHHHHHHHHHHHcCCC--EEEEeCCCccHHHHHHHHHHHCCCCEEEEEeCCCHHHHHHHHHcCCC-EEECCCC
Confidence            4445566666665542 234455  44445556678888888864322223334445567888899999998 8888888


Q ss_pred             HHHHHHHHH
Q 029986          123 IKELRNIWQ  131 (184)
Q Consensus       123 ~~~l~~~l~  131 (184)
                      ..++.+..+
T Consensus        90 ~~~v~~~~~   98 (204)
T TIGR01182        90 TPELAKHAQ   98 (204)
T ss_pred             CHHHHHHHH
Confidence            777766554

2-deydro-3-deoxyphosphogluconate aldolase (EC 4.1.2.14) is an enzyme of the Entner-Doudoroff pathway. This aldolase has another function, 4-hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16) shown experimentally in Escherichia coli and Pseudomonas putida

>PRK01130 N-acetylmannosamine-6-phosphate 2-epimerase; Provisional

Probab=91.69  E-value=4.1  Score=30.74  Aligned_cols=86  Identities=21%  Similarity=0.273  Sum_probs=56.4

Q ss_pred             HHHHHHHHHh-cCCeE-EEECCHHHHHHHHHhcCCCccEEEEeCC-------CCCCCHHHHHHHhcccCCCCEEEEEccC
Q 029986           30 LRILEKMLRK-CLYEV-TKCNRAEIALDMLRMSKNGYDIVISDVH-------MPDMDGFKLHEQVGLEMDLPVIMMSVDG  100 (184)
Q Consensus        30 ~~~l~~~L~~-~~~~v-~~~~~~~~~~~~l~~~~~~~dlvilD~~-------l~~~~g~~l~~~l~~~~~~~iIi~~~~~  100 (184)
                      ...+....++ .+..+ ..+.+.+++....   ..++|++.+...       .....+++++++++...++|++....-.
T Consensus       107 ~~~~i~~~~~~~~i~vi~~v~t~ee~~~a~---~~G~d~i~~~~~g~t~~~~~~~~~~~~~i~~i~~~~~iPvia~GGI~  183 (221)
T PRK01130        107 LAELVKRIKEYPGQLLMADCSTLEEGLAAQ---KLGFDFIGTTLSGYTEETKKPEEPDFALLKELLKAVGCPVIAEGRIN  183 (221)
T ss_pred             HHHHHHHHHhCCCCeEEEeCCCHHHHHHHH---HcCCCEEEcCCceeecCCCCCCCcCHHHHHHHHHhCCCCEEEECCCC
Confidence            3344445555 45443 4566677775543   356898866421       1123346788888655578999887777


Q ss_pred             ChHHHHHHHHcCCCceEe
Q 029986          101 CTQDVMKGVTHGACNYLL  118 (184)
Q Consensus       101 ~~~~~~~a~~~ga~~~l~  118 (184)
                      +.+.+..+++.|+++++.
T Consensus       184 t~~~~~~~l~~GadgV~i  201 (221)
T PRK01130        184 TPEQAKKALELGAHAVVV  201 (221)
T ss_pred             CHHHHHHHHHCCCCEEEE
Confidence            789999999999998864

>PRK09426 methylmalonyl-CoA mutase; Reviewed

Probab=91.04  E-value=5.3  Score=35.89  Aligned_cols=108  Identities=10%  Similarity=-0.084  Sum_probs=68.3

Q ss_pred             CCHHHHHHHHHHHHhcCCeEEE---ECCHHHHHHHHHhcCCCccEEEEeCCCCCC--CHHHHHHHhcccCCCCE-EEEEc
Q 029986           25 DDPIWLRILEKMLRKCLYEVTK---CNRAEIALDMLRMSKNGYDIVISDVHMPDM--DGFKLHEQVGLEMDLPV-IMMSV   98 (184)
Q Consensus        25 d~~~~~~~l~~~L~~~~~~v~~---~~~~~~~~~~l~~~~~~~dlvilD~~l~~~--~g~~l~~~l~~~~~~~i-Ii~~~   98 (184)
                      .+..-...+..+|...|++|..   +.+.+++.+...  +..+|+|.+-..+...  ..-.+++.|+....-.+ +++..
T Consensus       594 ~H~~ra~fv~~~l~~~GfeV~~~~~~~s~e~~v~aa~--~~~a~ivvlcs~d~~~~e~~~~l~~~Lk~~G~~~v~vl~GG  671 (714)
T PRK09426        594 GHDRGAKVIATAFADLGFDVDIGPLFQTPEEAARQAV--ENDVHVVGVSSLAAGHKTLVPALIEALKKLGREDIMVVVGG  671 (714)
T ss_pred             chhHhHHHHHHHHHhCCeeEecCCCCCCHHHHHHHHH--HcCCCEEEEeccchhhHHHHHHHHHHHHhcCCCCcEEEEeC
Confidence            4555666677888888999853   345677777776  4568888875443321  23345666654421124 44443


Q ss_pred             cCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHH
Q 029986           99 DGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVA  134 (184)
Q Consensus        99 ~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~  134 (184)
                      ..-++....+.++|+++|+..-.+..++...+...+
T Consensus       672 ~~~~~~~~~l~~aGvD~~i~~g~d~~~~L~~l~~~l  707 (714)
T PRK09426        672 VIPPQDYDFLYEAGVAAIFGPGTVIADAAIDLLELL  707 (714)
T ss_pred             CCChhhHHHHHhCCCCEEECCCCCHHHHHHHHHHHH
Confidence            312344456788999999998888887776666554

>TIGR02370 pyl_corrinoid methyltransferase cognate corrinoid proteins, Methanosarcina family

Probab=90.91  E-value=5.2  Score=29.79  Aligned_cols=95  Identities=18%  Similarity=0.135  Sum_probs=59.0

Q ss_pred             eEEEE----eCCHHHHHHHHHHHHhcCCeEEEEC---CHHHHHHHHHhcCCCccEEEEeCCCCCCC--HHHHHHHhccc-
Q 029986           19 RVLVV----DDDPIWLRILEKMLRKCLYEVTKCN---RAEIALDMLRMSKNGYDIVISDVHMPDMD--GFKLHEQVGLE-   88 (184)
Q Consensus        19 ~Iliv----dd~~~~~~~l~~~L~~~~~~v~~~~---~~~~~~~~l~~~~~~~dlvilD~~l~~~~--g~~l~~~l~~~-   88 (184)
                      +|++.    |.+..=...+..+|+..||++....   ..++..+.+.  +..||+|-+...++...  --++++.+++. 
T Consensus        86 ~vv~~t~~gd~H~lG~~~v~~~l~~~G~~vi~LG~~vp~e~~v~~~~--~~~pd~v~lS~~~~~~~~~~~~~i~~l~~~~  163 (197)
T TIGR02370        86 KVVCGVAEGDVHDIGKNIVVTMLRANGFDVIDLGRDVPIDTVVEKVK--KEKPLMLTGSALMTTTMYGQKDINDKLKEEG  163 (197)
T ss_pred             eEEEEeCCCchhHHHHHHHHHHHHhCCcEEEECCCCCCHHHHHHHHH--HcCCCEEEEccccccCHHHHHHHHHHHHHcC
Confidence            55544    3455556667788888999988544   4567777776  56799999988776542  23455566543 


Q ss_pred             -C-CCCEEEEEccCChHHHHHHHHcCCCceEe
Q 029986           89 -M-DLPVIMMSVDGCTQDVMKGVTHGACNYLL  118 (184)
Q Consensus        89 -~-~~~iIi~~~~~~~~~~~~a~~~ga~~~l~  118 (184)
                       + +++| ++....-..  .-+...|||.|-.
T Consensus       164 ~~~~v~i-~vGG~~~~~--~~~~~~gad~~~~  192 (197)
T TIGR02370       164 YRDSVKF-MVGGAPVTQ--DWADKIGADVYGE  192 (197)
T ss_pred             CCCCCEE-EEEChhcCH--HHHHHhCCcEEeC
Confidence             2 2444 444332222  2355679998864

This model describes a subfamily of the B12 binding domain (pfam02607, pfam02310) proteins. Members of the seed alignment include corrinoid proteins specific to four different, mutally non-homologous enzymes of the genus Methanosarcina. Three of the four cognate enzymes (trimethylamine, dimethylamine, and monomethylamine methyltransferases) all have the unusual, ribosomally incorporated amino acid pyrrolysine at the active site. All act in systems in which a methyl group is transferred to the corrinoid protein to create methylcobalamin, from which the methyl group is later transferred elsewhere.

>PRK05749 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed

Probab=90.81  E-value=5.7  Score=32.89  Aligned_cols=111  Identities=13%  Similarity=0.110  Sum_probs=63.9

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeE---------------EEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHH
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEV---------------TKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKL   81 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v---------------~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l   81 (184)
                      +.+++|+.+.+.....+.+.+++.|...               .......+...++.  .  .|++++--.+...-|..+
T Consensus       262 ~~~liivG~g~~r~~~l~~~~~~~gl~~~~~~~~~~~~~~~~v~l~~~~~el~~~y~--~--aDi~~v~~S~~e~~g~~~  337 (425)
T PRK05749        262 NLLLILVPRHPERFKEVEELLKKAGLSYVRRSQGEPPSADTDVLLGDTMGELGLLYA--I--ADIAFVGGSLVKRGGHNP  337 (425)
T ss_pred             CcEEEEcCCChhhHHHHHHHHHhCCCcEEEccCCCCCCCCCcEEEEecHHHHHHHHH--h--CCEEEECCCcCCCCCCCH
Confidence            5678888888766566777777666532               22222334444443  1  588777433323334445


Q ss_pred             HHHhcccCCCCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           82 HEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        82 ~~~l~~~~~~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      ++-+.  ..+|||.-....+.....+.+.  ..+++..|-+.++|.+.+..++.
T Consensus       338 lEAma--~G~PVI~g~~~~~~~e~~~~~~--~~g~~~~~~d~~~La~~l~~ll~  387 (425)
T PRK05749        338 LEPAA--FGVPVISGPHTFNFKEIFERLL--QAGAAIQVEDAEDLAKAVTYLLT  387 (425)
T ss_pred             HHHHH--hCCCEEECCCccCHHHHHHHHH--HCCCeEEECCHHHHHHHHHHHhc
Confidence            55442  4678886332233344333332  22566668889999999988865

>cd02072 Glm_B12_BD B12 binding domain of glutamate mutase (Glm)

Probab=90.79  E-value=4.1  Score=28.27  Aligned_cols=103  Identities=11%  Similarity=0.018  Sum_probs=66.6

Q ss_pred             CCHHHHHHHHHHHHhcCCeEEEE---CCHHHHHHHHHhcCCCccEEEEeCCCCCCC--HHHHHHHhccc-C-CCCEEEEE
Q 029986           25 DDPIWLRILEKMLRKCLYEVTKC---NRAEIALDMLRMSKNGYDIVISDVHMPDMD--GFKLHEQVGLE-M-DLPVIMMS   97 (184)
Q Consensus        25 d~~~~~~~l~~~L~~~~~~v~~~---~~~~~~~~~l~~~~~~~dlvilD~~l~~~~--g~~l~~~l~~~-~-~~~iIi~~   97 (184)
                      -+..-...+..+|+..||+|...   -..++..+...  +..+|+|-+..-|...-  .-++.+.++.. . +++ +++.
T Consensus        11 ~HdiGkniv~~~L~~~GfeVidLG~~v~~e~~v~aa~--~~~adiVglS~L~t~~~~~~~~~~~~l~~~gl~~v~-vivG   87 (128)
T cd02072          11 CHAVGNKILDHAFTEAGFNVVNLGVLSPQEEFIDAAI--ETDADAILVSSLYGHGEIDCKGLREKCDEAGLKDIL-LYVG   87 (128)
T ss_pred             hhHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHH--HcCCCEEEEeccccCCHHHHHHHHHHHHHCCCCCCe-EEEE
Confidence            34445567888999999998743   45677777776  45699999987665432  23455566533 2 433 4444


Q ss_pred             ccC-----C-hHHHHHHHHcCCCceEeCCCCHHHHHHHH
Q 029986           98 VDG-----C-TQDVMKGVTHGACNYLLKPIRIKELRNIW  130 (184)
Q Consensus        98 ~~~-----~-~~~~~~a~~~ga~~~l~kP~~~~~l~~~l  130 (184)
                      ...     + .+...++.+.|++..+...-+.+++...+
T Consensus        88 G~~~i~~~d~~~~~~~L~~~Gv~~vf~pgt~~~~i~~~l  126 (128)
T cd02072          88 GNLVVGKQDFEDVEKRFKEMGFDRVFAPGTPPEEAIADL  126 (128)
T ss_pred             CCCCCChhhhHHHHHHHHHcCCCEEECcCCCHHHHHHHH
Confidence            331     1 23445688899999998877777776554

Glutamate mutase catalysis the conversion of (S)-glutamate with (2S,3S)-3-methylaspartate. The rearrangement reaction is initiated by the extraction of a hydrogen from the protein-bound substrate by a 5'-desoxyadenosyl radical, which is generated by the homolytic cleavage of the organometallic bond of the cofactor B12. Glm is a heterotetrameric molecule consisting of two alpha and two epsilon polypeptide chains.

>cd04724 Tryptophan_synthase_alpha Ttryptophan synthase (TRPS) alpha subunit (TSA)

Probab=90.64  E-value=1.8  Score=33.33  Aligned_cols=60  Identities=10%  Similarity=0.190  Sum_probs=43.4

Q ss_pred             CHHHHHHHhcccCCCCEEEEEccCC------hHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           77 DGFKLHEQVGLEMDLPVIMMSVDGC------TQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        77 ~g~~l~~~l~~~~~~~iIi~~~~~~------~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      .++++++.++...++|+++++-...      ...+..+.++|+++.+...+..+++...+..+.+.
T Consensus        63 ~~~~~~~~vr~~~~~pv~lm~y~n~~~~~G~~~fi~~~~~aG~~giiipDl~~ee~~~~~~~~~~~  128 (242)
T cd04724          63 DVLELVKEIRKKNTIPIVLMGYYNPILQYGLERFLRDAKEAGVDGLIIPDLPPEEAEEFREAAKEY  128 (242)
T ss_pred             HHHHHHHHHhhcCCCCEEEEEecCHHHHhCHHHHHHHHHHCCCcEEEECCCCHHHHHHHHHHHHHc
Confidence            3566777776555788877654332      55677889999999999777778887777777654

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.

>TIGR02311 HpaI 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase

Probab=90.44  E-value=6.5  Score=30.44  Aligned_cols=82  Identities=12%  Similarity=0.041  Sum_probs=55.7

Q ss_pred             HHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc--CCCCEEEEEccCChHHHHHHHHcCCCceEe-CCCCHHHHH
Q 029986           51 EIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE--MDLPVIMMSVDGCTQDVMKGVTHGACNYLL-KPIRIKELR  127 (184)
Q Consensus        51 ~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~--~~~~iIi~~~~~~~~~~~~a~~~ga~~~l~-kP~~~~~l~  127 (184)
                      ....+.+.  ..++|.|++|++....+.-++...++..  ....+++=....+...+..+++.|+++.+. |--+.++..
T Consensus        23 p~~~e~~~--~~g~D~v~iDlEH~~~~~~~~~~~~~a~~~~g~~~~VRv~~~~~~~i~~~Ld~Ga~gIivP~v~s~e~a~  100 (249)
T TIGR02311        23 PYAAEICA--GAGFDWLLIDGEHAPNDVRTILSQLQALAPYPSSPVVRPAIGDPVLIKQLLDIGAQTLLVPMIETAEQAE  100 (249)
T ss_pred             cHHHHHHH--hcCCCEEEEeccCCCCCHHHHHHHHHHHHhcCCCcEEECCCCCHHHHHHHhCCCCCEEEecCcCCHHHHH
Confidence            44555554  4569999999998887776666655432  233333333445667889999999999874 455777877


Q ss_pred             HHHHHHH
Q 029986          128 NIWQHVA  134 (184)
Q Consensus       128 ~~l~~~~  134 (184)
                      ++++.+.
T Consensus       101 ~~v~~~~  107 (249)
T TIGR02311       101 AAVAATR  107 (249)
T ss_pred             HHHHHcC
Confidence            7777654

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.

>PRK00043 thiE thiamine-phosphate pyrophosphorylase; Reviewed

Probab=90.39  E-value=5.8  Score=29.40  Aligned_cols=69  Identities=17%  Similarity=0.214  Sum_probs=48.2

Q ss_pred             EECCHHHHHHHHHhcCCCccEEEEeCCCCCC--------CHHHHHHHhcccC-CCCEEEEEccCChHHHHHHHHcCCCce
Q 029986           46 KCNRAEIALDMLRMSKNGYDIVISDVHMPDM--------DGFKLHEQVGLEM-DLPVIMMSVDGCTQDVMKGVTHGACNY  116 (184)
Q Consensus        46 ~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~--------~g~~l~~~l~~~~-~~~iIi~~~~~~~~~~~~a~~~ga~~~  116 (184)
                      .+++..++.+...   .++|.|.+.-..|..        .|++.+++++... ++||++...- +.+.+..+++.|++++
T Consensus       110 ~~~t~~e~~~a~~---~gaD~v~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~v~a~GGI-~~~~i~~~~~~Ga~gv  185 (212)
T PRK00043        110 STHTLEEAAAALA---AGADYVGVGPIFPTPTKKDAKAPQGLEGLREIRAAVGDIPIVAIGGI-TPENAPEVLEAGADGV  185 (212)
T ss_pred             eCCCHHHHHHHhH---cCCCEEEECCccCCCCCCCCCCCCCHHHHHHHHHhcCCCCEEEECCc-CHHHHHHHHHcCCCEE
Confidence            4555566666543   568999987555533        3578888885443 4888877654 5788889999999998


Q ss_pred             Ee
Q 029986          117 LL  118 (184)
Q Consensus       117 l~  118 (184)
                      ..
T Consensus       186 ~~  187 (212)
T PRK00043        186 AV  187 (212)
T ss_pred             EE
Confidence            74

>cd06533 Glyco_transf_WecG_TagA The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins

Probab=89.97  E-value=3.5  Score=29.91  Aligned_cols=76  Identities=20%  Similarity=0.310  Sum_probs=51.9

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhc--CCeEEEEC-------CHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKC--LYEVTKCN-------RAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL   87 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~--~~~v~~~~-------~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~   87 (184)
                      +.+|.++...+...+.+...|++.  +..+..+.       +..+.++.+.  ...||+|++-+.+|..+-+  +...+.
T Consensus        46 ~~~v~llG~~~~~~~~~~~~l~~~yp~l~i~g~~~g~~~~~~~~~i~~~I~--~~~pdiv~vglG~PkQE~~--~~~~~~  121 (171)
T cd06533          46 GLRVFLLGAKPEVLEKAAERLRARYPGLKIVGYHHGYFGPEEEEEIIERIN--ASGADILFVGLGAPKQELW--IARHKD  121 (171)
T ss_pred             CCeEEEECCCHHHHHHHHHHHHHHCCCcEEEEecCCCCChhhHHHHHHHHH--HcCCCEEEEECCCCHHHHH--HHHHHH
Confidence            578999999999999999888876  45554321       1223455555  5569999999999987643  444443


Q ss_pred             cCCCCEEEE
Q 029986           88 EMDLPVIMM   96 (184)
Q Consensus        88 ~~~~~iIi~   96 (184)
                      .-+.++++-
T Consensus       122 ~l~~~v~~~  130 (171)
T cd06533         122 RLPVPVAIG  130 (171)
T ss_pred             HCCCCEEEE
Confidence            334555554

E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common antigen (eca) synthesis. B. subtilis TagA plays a key role in the Wall Teichoic Acid (WTA) biosynthetic pathway, catalyzing the transfer of N-acetylmannosamine to the C4 hydroxyl of a membrane-anchored N-acetylglucosaminyl diphospholipid to make ManNAc-beta-(1,4)-GlcNAc-pp-undecaprenyl. This is the first committed step in this pathway. Also included in this group is Xanthomonas campestris pv. campestris GumM, a glycosyltransferase participating in the biosynthesis of the exopolysaccharide xanthan.

>TIGR01334 modD putative molybdenum utilization protein ModD

Probab=89.77  E-value=3.1  Score=32.86  Aligned_cols=94  Identities=16%  Similarity=0.211  Sum_probs=59.4

Q ss_pred             EEEEeCCHHHHH---HHHHHHHh---c---CCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCC
Q 029986           20 VLVVDDDPIWLR---ILEKMLRK---C---LYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMD   90 (184)
Q Consensus        20 Ilivdd~~~~~~---~l~~~L~~---~---~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~   90 (184)
                      |+|-|.|-....   .+...+..   .   .-....+.+.+++.+.+.   .++|+|++| +|+..+-.+.++.++....
T Consensus       159 ilikdnHi~~~g~~~~i~~av~~~r~~~~~~kIeVEv~tleea~ea~~---~GaDiI~lD-n~~~e~l~~~v~~l~~~~~  234 (277)
T TIGR01334       159 LLVFANHRTFLNDNFDWGGAIGRLKQTAPERKITVEADTIEQALTVLQ---ASPDILQLD-KFTPQQLHHLHERLKFFDH  234 (277)
T ss_pred             heehHHHHHHhCCcccHHHHHHHHHHhCCCCCEEEECCCHHHHHHHHH---cCcCEEEEC-CCCHHHHHHHHHHHhccCC
Confidence            666666655443   34444432   1   123446789999999875   559999999 3444444445555543223


Q ss_pred             CCEEEEEccCChHHHHHHHHcCCCceE
Q 029986           91 LPVIMMSVDGCTQDVMKGVTHGACNYL  117 (184)
Q Consensus        91 ~~iIi~~~~~~~~~~~~a~~~ga~~~l  117 (184)
                      ...+-.+..-+.+.+......|++-+.
T Consensus       235 ~~~leasGGI~~~ni~~ya~~GvD~is  261 (277)
T TIGR01334       235 IPTLAAAGGINPENIADYIEAGIDLFI  261 (277)
T ss_pred             CEEEEEECCCCHHHHHHHHhcCCCEEE
Confidence            335666777788888888899988654

The gene modD for a member of this family is found with molybdenum transport genes modABC in Rhodobacter capsulatus. However, disruption of modD causes only a 4-fold (rather than 500-fold for modA, modB, modC) change in the external molybdenum concentration required to suppress an alternative nitrogenase. ModD proteins are highly similar to nicotinate-nucleotide pyrophosphorylase (also called quinolinate phosphoribosyltransferase). The function unknown.

>PRK13111 trpA tryptophan synthase subunit alpha; Provisional

Probab=89.57  E-value=2.3  Score=33.20  Aligned_cols=59  Identities=12%  Similarity=0.277  Sum_probs=44.6

Q ss_pred             HHHHHHHhc-ccCCCCEEEEEcc------CChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           78 GFKLHEQVG-LEMDLPVIMMSVD------GCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        78 g~~l~~~l~-~~~~~~iIi~~~~------~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      .++++++++ ..+++|+++++-.      .-+.....+.++|+++.+.-.+..++....+..+.+.
T Consensus        76 ~~~~~~~~r~~~~~~p~vlm~Y~N~i~~~G~e~f~~~~~~aGvdGviipDLp~ee~~~~~~~~~~~  141 (258)
T PRK13111         76 VFELVREIREKDPTIPIVLMTYYNPIFQYGVERFAADAAEAGVDGLIIPDLPPEEAEELRAAAKKH  141 (258)
T ss_pred             HHHHHHHHHhcCCCCCEEEEecccHHhhcCHHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHc
Confidence            466777776 4568898877632      3345678899999999999999988888887776553

>TIGR01305 GMP_reduct_1 guanosine monophosphate reductase, eukaryotic

Probab=89.51  E-value=2.7  Score=34.01  Aligned_cols=58  Identities=14%  Similarity=-0.050  Sum_probs=42.6

Q ss_pred             CCccEEEEeCCCCCCC-HHHHHHHhcccCCCCEEEEEccCChHHHHHHHHcCCCceEeC
Q 029986           62 NGYDIVISDVHMPDMD-GFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLK  119 (184)
Q Consensus        62 ~~~dlvilD~~l~~~~-g~~l~~~l~~~~~~~iIi~~~~~~~~~~~~a~~~ga~~~l~k  119 (184)
                      ..+|+|++|+...... -++.+++++...+-+.|+-.+-.+.+.+..+.++||+...+-
T Consensus       120 ~~~d~iviD~AhGhs~~~i~~ik~ir~~~p~~~viaGNV~T~e~a~~Li~aGAD~ikVg  178 (343)
T TIGR01305       120 PQLKFICLDVANGYSEHFVEFVKLVREAFPEHTIMAGNVVTGEMVEELILSGADIVKVG  178 (343)
T ss_pred             CCCCEEEEECCCCcHHHHHHHHHHHHhhCCCCeEEEecccCHHHHHHHHHcCCCEEEEc
Confidence            3589999999765443 366788887543345555555778899999999999988644

A deep split separates two families of GMP reductase. This family includes both eukaryotic and some proteobacterial sequences, while the other family contains other bacterial sequences.

>PRK06015 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional

Probab=89.47  E-value=7.4  Score=29.21  Aligned_cols=63  Identities=10%  Similarity=0.131  Sum_probs=40.4

Q ss_pred             EEeCCCCCCCHHHHHHHhcccCCCCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHH
Q 029986           68 ISDVHMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQ  131 (184)
Q Consensus        68 ilD~~l~~~~g~~l~~~l~~~~~~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~  131 (184)
                      .+.+.|...+.++.++.+++..+--+|=..+=-+.+.+..+.++||. |++.|.-..++.+..+
T Consensus        32 ~iEit~~tp~a~~~I~~l~~~~~~~~vGAGTVl~~e~a~~ai~aGA~-FivSP~~~~~vi~~a~   94 (201)
T PRK06015         32 AIEITLRTPAALDAIRAVAAEVEEAIVGAGTILNAKQFEDAAKAGSR-FIVSPGTTQELLAAAN   94 (201)
T ss_pred             EEEEeCCCccHHHHHHHHHHHCCCCEEeeEeCcCHHHHHHHHHcCCC-EEECCCCCHHHHHHHH
Confidence            44555556667777777753322223333344567788888899888 8888887777766554

>CHL00200 trpA tryptophan synthase alpha subunit; Provisional

Probab=89.16  E-value=2.1  Score=33.56  Aligned_cols=59  Identities=12%  Similarity=0.164  Sum_probs=44.4

Q ss_pred             HHHHHHHhcccCCCCEEEEEcc------CChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           78 GFKLHEQVGLEMDLPVIMMSVD------GCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        78 g~~l~~~l~~~~~~~iIi~~~~------~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      .++++++++....+|+++++-.      .-+....++.++|+++.+...+..++.......+.+.
T Consensus        79 ~~~~~~~~r~~~~~p~vlm~Y~N~i~~~G~e~F~~~~~~aGvdgviipDLP~ee~~~~~~~~~~~  143 (263)
T CHL00200         79 ILSILSEVNGEIKAPIVIFTYYNPVLHYGINKFIKKISQAGVKGLIIPDLPYEESDYLISVCNLY  143 (263)
T ss_pred             HHHHHHHHhcCCCCCEEEEecccHHHHhCHHHHHHHHHHcCCeEEEecCCCHHHHHHHHHHHHHc
Confidence            4667777775578898877533      2245678899999999999999888887777776554

>TIGR03151 enACPred_II putative enoyl-(acyl-carrier-protein) reductase II

Probab=89.07  E-value=8.4  Score=30.86  Aligned_cols=82  Identities=20%  Similarity=0.150  Sum_probs=57.9

Q ss_pred             HHHHHHhcCCeE-EEECCHHHHHHHHHhcCCCccEEEEeCCCC-----CCCHHHHHHHhcccCCCCEEEEEccCChHHHH
Q 029986           33 LEKMLRKCLYEV-TKCNRAEIALDMLRMSKNGYDIVISDVHMP-----DMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVM  106 (184)
Q Consensus        33 l~~~L~~~~~~v-~~~~~~~~~~~~l~~~~~~~dlvilD~~l~-----~~~g~~l~~~l~~~~~~~iIi~~~~~~~~~~~  106 (184)
                      +-..++..|..+ ..+.+.+.+.....   .++|.|++.-.-.     ....+.+++++....++|||.-..-.+...+.
T Consensus       101 ~i~~lk~~g~~v~~~v~s~~~a~~a~~---~GaD~Ivv~g~eagGh~g~~~~~~ll~~v~~~~~iPviaaGGI~~~~~~~  177 (307)
T TIGR03151       101 YIPRLKENGVKVIPVVASVALAKRMEK---AGADAVIAEGMESGGHIGELTTMALVPQVVDAVSIPVIAAGGIADGRGMA  177 (307)
T ss_pred             HHHHHHHcCCEEEEEcCCHHHHHHHHH---cCCCEEEEECcccCCCCCCCcHHHHHHHHHHHhCCCEEEECCCCCHHHHH
Confidence            445566666654 35677777766653   5689999854322     22357888888655578998887777788899


Q ss_pred             HHHHcCCCceE
Q 029986          107 KGVTHGACNYL  117 (184)
Q Consensus       107 ~a~~~ga~~~l  117 (184)
                      .++..||++..
T Consensus       178 ~al~~GA~gV~  188 (307)
T TIGR03151       178 AAFALGAEAVQ  188 (307)
T ss_pred             HHHHcCCCEee
Confidence            99999999875

This oxidoreductase of the 2-nitropropane dioxygenase family (pfam03060) is commonly found in apparent operons with genes involved in fatty acid biosynthesis. Furthermore, this genomic context generally includes the fabG 3-oxoacyl-[ACP] reductase and lacks the fabI enoyl-[ACP] reductase.

>TIGR02855 spore_yabG sporulation peptidase YabG

Probab=89.05  E-value=6.4  Score=30.90  Aligned_cols=104  Identities=23%  Similarity=0.290  Sum_probs=63.0

Q ss_pred             CCCCCeEEEEeCCHHHHHHHHHHHHhcCCeEE-----EECCHHHHHHHHHhcCCCccEEEEeC---CCCC-CCHHH----
Q 029986           14 FPAGLRVLVVDDDPIWLRILEKMLRKCLYEVT-----KCNRAEIALDMLRMSKNGYDIVISDV---HMPD-MDGFK----   80 (184)
Q Consensus        14 ~~~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~-----~~~~~~~~~~~l~~~~~~~dlvilD~---~l~~-~~g~~----   80 (184)
                      |..+-+||=+|.|+...+.....-++.+..+.     .-.-.+...+++.  +..|||+++--   ..-+ .+-.+    
T Consensus       101 f~~PGrVLHiDGD~~YL~~Cl~~Ykql~i~a~G~~~~E~eqp~~i~~Ll~--~~~PDIlViTGHD~~~K~~~d~~dl~~Y  178 (283)
T TIGR02855       101 FGMPGRVLHIDGDPEYLRKCLKLYKKIGVPVVGIHCKEKEMPEKVLDLIE--EVRPDILVITGHDAYSKNKGNYMDLNAY  178 (283)
T ss_pred             CCCCCcEEeecCCHHHHHHHHHHHHHhCCceEEEEecchhchHHHHHHHH--HhCCCEEEEeCchhhhcCCCChhhhhhh
Confidence            44344899999999988887766676654433     3333455566665  56699999832   2211 11111    


Q ss_pred             -----HHHHh---ccc-CCC-CEEEEEccCChHHHHHHHHcCCCceEeCCC
Q 029986           81 -----LHEQV---GLE-MDL-PVIMMSVDGCTQDVMKGVTHGACNYLLKPI  121 (184)
Q Consensus        81 -----l~~~l---~~~-~~~-~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~  121 (184)
                           |++.+   |.. ++. -++|++ .++.......+++||+ |-+.|-
T Consensus       179 rnSkyFVeaVk~aR~y~~~~D~LVIFA-GACQS~yEall~AGAN-FASSP~  227 (283)
T TIGR02855       179 RHSKYFVETVREARKYVPSLDQLVIFA-GACQSHFESLIRAGAN-FASSPS  227 (283)
T ss_pred             hhhHHHHHHHHHHHhcCCCcccEEEEc-chhHHHHHHHHHcCcc-ccCCcc
Confidence                 33333   322 333 255554 4567778888999998 877774

Members of this family are the protein YabG, demonstrated for Bacillus subtilis to be an endopeptidase able to release N-terminal peptides from a number of sporulation proteins, including CotT, CotF, and SpoIVA. It appears to be expressed under control of sigma-K.

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

Probab=88.89  E-value=2.7  Score=31.15  Aligned_cols=75  Identities=19%  Similarity=0.289  Sum_probs=51.1

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCC--CCCC--HHHHHHHhcccCCCCE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHM--PDMD--GFKLHEQVGLEMDLPV   93 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l--~~~~--g~~l~~~l~~~~~~~i   93 (184)
                      ++||++|.-...--.|.++|.+.|.++....+.......+.  ...||.|++.-.-  |...  ..++++++  ...+||
T Consensus         2 ~~IL~IDNyDSFtyNLv~yl~~lg~~v~V~rnd~~~~~~~~--~~~pd~iviSPGPG~P~d~G~~~~~i~~~--~~~~Pi   77 (191)
T COG0512           2 MMILLIDNYDSFTYNLVQYLRELGAEVTVVRNDDISLELIE--ALKPDAIVISPGPGTPKDAGISLELIRRF--AGRIPI   77 (191)
T ss_pred             ceEEEEECccchHHHHHHHHHHcCCceEEEECCccCHHHHh--hcCCCEEEEcCCCCChHHcchHHHHHHHh--cCCCCE
Confidence            57999999999999999999999887776665433333443  3458999997643  3222  34455555  345788


Q ss_pred             EEE
Q 029986           94 IMM   96 (184)
Q Consensus        94 Ii~   96 (184)
                      +-+
T Consensus        78 LGV   80 (191)
T COG0512          78 LGV   80 (191)
T ss_pred             EEE
Confidence            765

>PLN02591 tryptophan synthase

Probab=88.89  E-value=2.4  Score=32.95  Aligned_cols=60  Identities=10%  Similarity=0.235  Sum_probs=44.9

Q ss_pred             CHHHHHHHhcccCCCCEEEEEcc------CChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           77 DGFKLHEQVGLEMDLPVIMMSVD------GCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        77 ~g~~l~~~l~~~~~~~iIi~~~~------~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      +.++++++++...++|+++++-.      .-+....++.++|+++.+.-.+..++.......+.+.
T Consensus        65 ~~~~~~~~~r~~~~~p~ilm~Y~N~i~~~G~~~F~~~~~~aGv~GviipDLP~ee~~~~~~~~~~~  130 (250)
T PLN02591         65 SVISMLKEVAPQLSCPIVLFTYYNPILKRGIDKFMATIKEAGVHGLVVPDLPLEETEALRAEAAKN  130 (250)
T ss_pred             HHHHHHHHHhcCCCCCEEEEecccHHHHhHHHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHHc
Confidence            35777888875567898877532      2234577889999999999999988888877776554

>PRK01911 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional

Probab=88.82  E-value=4.6  Score=32.13  Aligned_cols=105  Identities=15%  Similarity=0.202  Sum_probs=60.8

Q ss_pred             CeEEEEeC--CHH---HHHHHHHHHHhcCCeEEEECCHHHHHHH-------------HHhcCCCccEEEEeCCCCCCCHH
Q 029986           18 LRVLVVDD--DPI---WLRILEKMLRKCLYEVTKCNRAEIALDM-------------LRMSKNGYDIVISDVHMPDMDGF   79 (184)
Q Consensus        18 ~~Ilivdd--~~~---~~~~l~~~L~~~~~~v~~~~~~~~~~~~-------------l~~~~~~~dlvilD~~l~~~~g~   79 (184)
                      |+|.|+-.  .+.   ....+..+|.+.|+++.........+..             .......+|++|+    -++|| 
T Consensus         1 m~igii~~~~~~~~~~~~~~i~~~l~~~g~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dlvi~----lGGDG-   75 (292)
T PRK01911          1 MKIAIFGQTYQESASPYIQELFDELEERGAEVLIEEKFLDFLKQDLKFHPSYDTFSDNEELDGSADMVIS----IGGDG-   75 (292)
T ss_pred             CEEEEEeCCCCHHHHHHHHHHHHHHHHCCCEEEEecchhhhhccccccccccccccchhhcccCCCEEEE----ECCcH-
Confidence            46666632  233   3445566676778887764432221110             0111124688777    36777 


Q ss_pred             HHHHHhcc--cCCCCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCCCC
Q 029986           80 KLHEQVGL--EMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPFE  141 (184)
Q Consensus        80 ~l~~~l~~--~~~~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~~  141 (184)
                      .+++..+.  ...+||+-+-             .|-.+|+. .++.+++...+..++++.....
T Consensus        76 T~L~aa~~~~~~~~PilGIN-------------~G~lGFLt-~~~~~~~~~~l~~i~~g~~~i~  125 (292)
T PRK01911         76 TFLRTATYVGNSNIPILGIN-------------TGRLGFLA-TVSKEEIEETIDELLNGDYTIE  125 (292)
T ss_pred             HHHHHHHHhcCCCCCEEEEe-------------cCCCCccc-ccCHHHHHHHHHHHHcCCceEE
Confidence            34444432  2367877663             36678887 6788999999999998765433

>PF14097 SpoVAE: Stage V sporulation protein AE1

Probab=88.70  E-value=7.5  Score=28.28  Aligned_cols=80  Identities=18%  Similarity=0.174  Sum_probs=55.7

Q ss_pred             EEEEeCCHHHHHHHHHHHHhcCCeEEEEC-------CHHHHHHHHHhcCCCccEEEEeCC-C-CCCCHHHHHHHhcccCC
Q 029986           20 VLVVDDDPIWLRILEKMLRKCLYEVTKCN-------RAEIALDMLRMSKNGYDIVISDVH-M-PDMDGFKLHEQVGLEMD   90 (184)
Q Consensus        20 Ilivdd~~~~~~~l~~~L~~~~~~v~~~~-------~~~~~~~~l~~~~~~~dlvilD~~-l-~~~~g~~l~~~l~~~~~   90 (184)
                      |+|-|.|...+..++..-++.|..+.+.+       ++++..+++......|=+|++|-. . ..+.|-+.++.+...+.
T Consensus         3 IlvTDGD~~A~ravE~aa~~iGgRCIS~S~GNPT~lsG~elV~lIk~a~~DPV~VMfDD~G~~g~G~GE~Al~~v~~h~~   82 (180)
T PF14097_consen    3 ILVTDGDEYAKRAVEIAAKNIGGRCISQSAGNPTPLSGEELVELIKQAPHDPVLVMFDDKGFIGEGPGEQALEYVANHPD   82 (180)
T ss_pred             EEEECChHHHHHHHHHHHHHhCcEEEeccCCCCCcCCHHHHHHHHHhCCCCCEEEEEeCCCCCCCCccHHHHHHHHcCCC
Confidence            55666777777777777777888877654       789999999876666777777653 2 23567788888866666


Q ss_pred             CC---EEEEEcc
Q 029986           91 LP---VIMMSVD   99 (184)
Q Consensus        91 ~~---iIi~~~~   99 (184)
                      +-   +|.+++.
T Consensus        83 IeVLG~iAVASn   94 (180)
T PF14097_consen   83 IEVLGAIAVASN   94 (180)
T ss_pred             ceEEEEEEEEec
Confidence            54   4555543

>PF03808 Glyco_tran_WecB: Glycosyl transferase WecB/TagA/CpsF family; InterPro: IPR004629 The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in Enterobacterial common antigen (eca) synthesis in Escherichia coli

Probab=88.68  E-value=7.4  Score=28.22  Aligned_cols=76  Identities=17%  Similarity=0.234  Sum_probs=52.3

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhc--CCeEEEECC-------HHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKC--LYEVTKCNR-------AEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL   87 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~--~~~v~~~~~-------~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~   87 (184)
                      +.+|.++...+...+.+...|+..  +..+.-+.+       .++.++.+.  ...||+|++-+..|..+-  ++...+.
T Consensus        48 ~~~ifllG~~~~~~~~~~~~l~~~yP~l~ivg~~~g~f~~~~~~~i~~~I~--~~~pdiv~vglG~PkQE~--~~~~~~~  123 (172)
T PF03808_consen   48 GKRIFLLGGSEEVLEKAAANLRRRYPGLRIVGYHHGYFDEEEEEAIINRIN--ASGPDIVFVGLGAPKQER--WIARHRQ  123 (172)
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHHHCCCeEEEEecCCCCChhhHHHHHHHHH--HcCCCEEEEECCCCHHHH--HHHHHHH
Confidence            568999999999999999999876  555553332       344555555  566999999998887663  4555544


Q ss_pred             cCCCCEEEE
Q 029986           88 EMDLPVIMM   96 (184)
Q Consensus        88 ~~~~~iIi~   96 (184)
                      .-+.++++-
T Consensus       124 ~l~~~v~i~  132 (172)
T PF03808_consen  124 RLPAGVIIG  132 (172)
T ss_pred             HCCCCEEEE
Confidence            444554443

Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.; GO: 0009058 biosynthetic process

>PF05582 Peptidase_U57: YabG peptidase U57; InterPro: IPR008764 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families

Probab=88.66  E-value=6  Score=31.20  Aligned_cols=106  Identities=18%  Similarity=0.238  Sum_probs=63.0

Q ss_pred             ccCCCCCeEEEEeCCHHHHHHHHHHHHhcCCeEE--EECC---HHHHHHHHHhcCCCccEEEEeCC---CCCC------C
Q 029986           12 DQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVT--KCNR---AEIALDMLRMSKNGYDIVISDVH---MPDM------D   77 (184)
Q Consensus        12 ~~~~~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~--~~~~---~~~~~~~l~~~~~~~dlvilD~~---l~~~------~   77 (184)
                      .-|..+-|||=+|.|+...+.....-++.|..+.  .+..   .+...+++.  +..|||+++--+   +-+.      +
T Consensus       100 ~~F~~PGkVLHlDGD~~YL~~Cl~~Ykql~i~a~G~~~~E~eqp~~i~~Ll~--~~~PDIlViTGHD~~~K~~~d~~dl~  177 (287)
T PF05582_consen  100 EYFERPGKVLHLDGDEEYLNKCLKVYKQLGIPAVGIHVPEKEQPEKIYRLLE--EYRPDILVITGHDGYLKNKKDYSDLN  177 (287)
T ss_pred             cccCCCCeEEEecCCHHHHHHHHHHHHHcCCceEEEEechHHhhHHHHHHHH--HcCCCEEEEeCchhhhcCCCChhhhh
Confidence            3344455899999999988887777777765443  2332   333445554  566999998322   1111      1


Q ss_pred             H----HHHHHHh---ccc-CCCC-EEEEEccCChHHHHHHHHcCCCceEeCCC
Q 029986           78 G----FKLHEQV---GLE-MDLP-VIMMSVDGCTQDVMKGVTHGACNYLLKPI  121 (184)
Q Consensus        78 g----~~l~~~l---~~~-~~~~-iIi~~~~~~~~~~~~a~~~ga~~~l~kP~  121 (184)
                      .    --|++.+   |.. ++.- .+|++ .++.......+++||+ |-+.|-
T Consensus       178 ~YrnSkyFVeaV~~aR~~ep~~D~LVIfA-GACQS~fEall~AGAN-FASSP~  228 (287)
T PF05582_consen  178 NYRNSKYFVEAVKEARKYEPNLDDLVIFA-GACQSHFEALLEAGAN-FASSPK  228 (287)
T ss_pred             hhhccHHHHHHHHHHHhcCCCcccEEEEc-chhHHHHHHHHHcCcc-ccCCcc
Confidence            1    1134433   322 3332 44454 4567777888999998 877764

Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. The peptidases families associated with clan U- have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported. This is a group of peptidases belong to MEROPS peptidase family U57 (clan U-). The type example is the YabG protein of Bacillus subtilis. This is a protease involved in the synthesis and maturation of the spore coat proteins SpoIVA and YrbA of B. subtilis [].

>PRK08385 nicotinate-nucleotide pyrophosphorylase; Provisional

Probab=88.62  E-value=11  Score=29.90  Aligned_cols=93  Identities=18%  Similarity=0.158  Sum_probs=59.6

Q ss_pred             EEEEeCCHHHHHHHHHHHHhc---C---CeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccC--CC
Q 029986           20 VLVVDDDPIWLRILEKMLRKC---L---YEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEM--DL   91 (184)
Q Consensus        20 Ilivdd~~~~~~~l~~~L~~~---~---~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~--~~   91 (184)
                      |+|-|.+-... .+...+...   .   --...+.+.+++.+.+.   .++|+|.+|-..|. +--+..+.++...  +.
T Consensus       157 vLikdnHi~~~-~i~~av~~~r~~~~~~kIeVEv~~leea~~a~~---agaDiI~LDn~~~e-~l~~~v~~l~~~~~~~~  231 (278)
T PRK08385        157 ILIKDNHLALV-PLEEAIRRAKEFSVYKVVEVEVESLEDALKAAK---AGADIIMLDNMTPE-EIREVIEALKREGLRER  231 (278)
T ss_pred             EEEccCHHHHH-HHHHHHHHHHHhCCCCcEEEEeCCHHHHHHHHH---cCcCEEEECCCCHH-HHHHHHHHHHhcCcCCC
Confidence            78888886655 666666532   1   13346889999999885   55899999954322 2223334443221  23


Q ss_pred             CEEEEEccCChHHHHHHHHcCCCceE
Q 029986           92 PVIMMSVDGCTQDVMKGVTHGACNYL  117 (184)
Q Consensus        92 ~iIi~~~~~~~~~~~~a~~~ga~~~l  117 (184)
                      ..+..+..-+.+.+....+.|+|.+-
T Consensus       232 ~~leaSGGI~~~ni~~yA~tGvD~Is  257 (278)
T PRK08385        232 VKIEVSGGITPENIEEYAKLDVDVIS  257 (278)
T ss_pred             EEEEEECCCCHHHHHHHHHcCCCEEE
Confidence            34555667778888888999998554

>PF05690 ThiG: Thiazole biosynthesis protein ThiG; InterPro: IPR008867 This family consists of several bacterial thiazole biosynthesis protein G sequences

Probab=87.71  E-value=9.3  Score=29.42  Aligned_cols=96  Identities=18%  Similarity=0.137  Sum_probs=57.2

Q ss_pred             HHHHHhcCCeEEEEC--CHHHHHHHHHhcCCCccEEEEeCCCCCCCH-----HHHHHHhcccCCCCEEEEEccCChHHHH
Q 029986           34 EKMLRKCLYEVTKCN--RAEIALDMLRMSKNGYDIVISDVHMPDMDG-----FKLHEQVGLEMDLPVIMMSVDGCTQDVM  106 (184)
Q Consensus        34 ~~~L~~~~~~v~~~~--~~~~~~~~l~~~~~~~dlvilD~~l~~~~g-----~~l~~~l~~~~~~~iIi~~~~~~~~~~~  106 (184)
                      .+.|-+.||.|..+.  |..-|.++..   .+.. .++-+.-|-++|     -..++.+....++|||+=+.-..+..+.
T Consensus       116 ae~Lv~eGF~VlPY~~~D~v~akrL~d---~Gca-avMPlgsPIGSg~Gi~n~~~l~~i~~~~~vPvIvDAGiG~pSdaa  191 (247)
T PF05690_consen  116 AEILVKEGFVVLPYCTDDPVLAKRLED---AGCA-AVMPLGSPIGSGRGIQNPYNLRIIIERADVPVIVDAGIGTPSDAA  191 (247)
T ss_dssp             HHHHHHTT-EEEEEE-S-HHHHHHHHH---TT-S-EBEEBSSSTTT---SSTHHHHHHHHHHGSSSBEEES---SHHHHH
T ss_pred             HHHHHHCCCEEeecCCCCHHHHHHHHH---CCCC-EEEecccccccCcCCCCHHHHHHHHHhcCCcEEEeCCCCCHHHHH
Confidence            356667799987544  4444544433   3333 355566665554     2356666555689999988888899999


Q ss_pred             HHHHcCCCceEe-----CCCCHHHHHHHHHHH
Q 029986          107 KGVTHGACNYLL-----KPIRIKELRNIWQHV  133 (184)
Q Consensus       107 ~a~~~ga~~~l~-----kP~~~~~l~~~l~~~  133 (184)
                      .+++.|+++.++     +--++-.+.+++...
T Consensus       192 ~AMElG~daVLvNTAiA~A~dPv~MA~Af~~A  223 (247)
T PF05690_consen  192 QAMELGADAVLVNTAIAKAKDPVAMARAFKLA  223 (247)
T ss_dssp             HHHHTT-SEEEESHHHHTSSSHHHHHHHHHHH
T ss_pred             HHHHcCCceeehhhHHhccCCHHHHHHHHHHH
Confidence            999999999985     333455555555444

ThiG, together with ThiF and ThiH, is proposed to be involved in the synthesis of 4-methyl-5-(b-hydroxyethyl)thiazole (THZ) which is an intermediate in the thiazole production pathway [].; GO: 0009228 thiamine biosynthetic process; PDB: 1WV2_B 1TYG_C 1XM3_B 2HTM_C 2YZR_C.

>cd02068 radical_SAM_B12_BD B12 binding domain_like associated with radical SAM domain

Probab=87.31  E-value=7.2  Score=26.51  Aligned_cols=106  Identities=8%  Similarity=0.062  Sum_probs=61.9

Q ss_pred             HHHHHHHHHHhcCCeEEEEC--CHHHHHHHHHhcCCCccEEEEeCCCCCC-CHHHHHHHhccc-CCCCEEEEEccCChHH
Q 029986           29 WLRILEKMLRKCLYEVTKCN--RAEIALDMLRMSKNGYDIVISDVHMPDM-DGFKLHEQVGLE-MDLPVIMMSVDGCTQD  104 (184)
Q Consensus        29 ~~~~l~~~L~~~~~~v~~~~--~~~~~~~~l~~~~~~~dlvilD~~l~~~-~g~~l~~~l~~~-~~~~iIi~~~~~~~~~  104 (184)
                      ....+..+|.+.|+++....  ..++..+.+.. ...||+|.+....... ...++++.+++. ++++|++=....+ ..
T Consensus         4 gl~~~aa~l~~~g~~v~~~~~~~~~~~~~~~~~-~~~pdiv~~S~~~~~~~~~~~~~~~ik~~~p~~~iv~GG~~~t-~~   81 (127)
T cd02068           4 GLAYLAAVLEDAGFIVAEHDVLSADDIVEDIKE-LLKPDVVGISLMTSAIYEALELAKIAKEVLPNVIVVVGGPHAT-FF   81 (127)
T ss_pred             hHHHHHHHHHHCCCeeeecCCCCHHHHHHHHHH-hcCCCEEEEeeccccHHHHHHHHHHHHHHCCCCEEEECCcchh-hC
Confidence            34567788888887765433  45556666542 1569999998754443 345577777643 5555554332222 12


Q ss_pred             HHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986          105 VMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus       105 ~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      ....+.....||+..--...-+...++.+.++
T Consensus        82 p~~~~~~~~~D~vv~GEgE~~~~~l~~~l~~g  113 (127)
T cd02068          82 PEEILEEPGVDFVVIGEGEETFLKLLEELEEG  113 (127)
T ss_pred             HHHHhcCCCCCEEEECCcHHHHHHHHHHHHcC
Confidence            22223344456877766666777777776554

This domain shows similarity with B12 (adenosylcobamide) binding domains found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase, but it lacks the signature motif Asp-X-His-X-X-Gly, which contains the histidine that acts as a cobalt ligand. The function of this domain remains unclear.

>cd00564 TMP_TenI Thiamine monophosphate synthase (TMP synthase)/TenI

Probab=87.27  E-value=9.2  Score=27.68  Aligned_cols=68  Identities=19%  Similarity=0.199  Sum_probs=47.0

Q ss_pred             ECCHHHHHHHHHhcCCCccEEEEeCCCCC--------CCHHHHHHHhcccCCCCEEEEEccCChHHHHHHHHcCCCceEe
Q 029986           47 CNRAEIALDMLRMSKNGYDIVISDVHMPD--------MDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLL  118 (184)
Q Consensus        47 ~~~~~~~~~~l~~~~~~~dlvilD~~l~~--------~~g~~l~~~l~~~~~~~iIi~~~~~~~~~~~~a~~~ga~~~l~  118 (184)
                      +++..++.+...   .++|.+++....|.        ..+.+.+++++...++|+++...- +.+.+..+...|++++..
T Consensus       102 ~~t~~~~~~~~~---~g~d~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pv~a~GGi-~~~~i~~~~~~Ga~~i~~  177 (196)
T cd00564         102 THSLEEALRAEE---LGADYVGFGPVFPTPTKPGAGPPLGLELLREIAELVEIPVVAIGGI-TPENAAEVLAAGADGVAV  177 (196)
T ss_pred             CCCHHHHHHHhh---cCCCEEEECCccCCCCCCCCCCCCCHHHHHHHHHhCCCCEEEECCC-CHHHHHHHHHcCCCEEEE
Confidence            445556555543   45899998755442        345677887765567888887654 467888999999998864

TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5- (beta-hydroxyethyl) thiazole phosphate to yield thiamine phosphate. TenI is a enzymatically inactive regulatory protein involved in the regulation of several extracellular enzymes. This superfamily also contains other enzymatically inactive proteins with unknown functions.

>PRK07896 nicotinate-nucleotide pyrophosphorylase; Provisional

Probab=87.21  E-value=7.1  Score=31.04  Aligned_cols=94  Identities=13%  Similarity=0.050  Sum_probs=56.7

Q ss_pred             EEEEeCCHHHHHHHHHHHHhc----C--CeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCE
Q 029986           20 VLVVDDDPIWLRILEKMLRKC----L--YEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPV   93 (184)
Q Consensus        20 Ilivdd~~~~~~~l~~~L~~~----~--~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~i   93 (184)
                      |+|=|.+-...-.+...+++.    .  -....+.+.+++.+.+.   .++|+|.+| +|.-.+--+.++.++.......
T Consensus       173 ilIkdNHi~~~G~i~~ai~~~r~~~~~~kIeVEv~tl~ea~eal~---~gaDiI~LD-nm~~e~vk~av~~~~~~~~~v~  248 (289)
T PRK07896        173 ALIKDNHVAAAGSVVAALRAVRAAAPDLPCEVEVDSLEQLDEVLA---EGAELVLLD-NFPVWQTQEAVQRRDARAPTVL  248 (289)
T ss_pred             eeecHHHHHHhCcHHHHHHHHHHhCCCCCEEEEcCCHHHHHHHHH---cCCCEEEeC-CCCHHHHHHHHHHHhccCCCEE
Confidence            666666644443444444322    2  23457889999999875   558999999 4432222223333332332335


Q ss_pred             EEEEccCChHHHHHHHHcCCCceE
Q 029986           94 IMMSVDGCTQDVMKGVTHGACNYL  117 (184)
Q Consensus        94 Ii~~~~~~~~~~~~a~~~ga~~~l  117 (184)
                      +..+..-+.+.+....+.|+|.+-
T Consensus       249 ieaSGGI~~~ni~~yA~tGvD~Is  272 (289)
T PRK07896        249 LESSGGLTLDTAAAYAETGVDYLA  272 (289)
T ss_pred             EEEECCCCHHHHHHHHhcCCCEEE
Confidence            556667778888888999998553

>PF01729 QRPTase_C: Quinolinate phosphoribosyl transferase, C-terminal domain; InterPro: IPR002638 Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase 2

Probab=87.07  E-value=4.7  Score=29.34  Aligned_cols=94  Identities=17%  Similarity=0.101  Sum_probs=57.7

Q ss_pred             EEEEeCCHHHHHHHHHHHHhc------CC-eEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCC
Q 029986           20 VLVVDDDPIWLRILEKMLRKC------LY-EVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLP   92 (184)
Q Consensus        20 Ilivdd~~~~~~~l~~~L~~~------~~-~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~   92 (184)
                      ++|=|.+-.....+...++..      .. -...+.+.+++.+.+.   .++|+|.+|-.-| .+--+.++.++......
T Consensus        53 ili~~nHi~~~g~i~~av~~~~~~~~~~~~I~VEv~~~ee~~ea~~---~g~d~I~lD~~~~-~~~~~~v~~l~~~~~~v  128 (169)
T PF01729_consen   53 ILIKDNHIAFFGGIEEAVKAARQAAPEKKKIEVEVENLEEAEEALE---AGADIIMLDNMSP-EDLKEAVEELRELNPRV  128 (169)
T ss_dssp             EEE-HHHHHHHSSHHHHHHHHHHHSTTTSEEEEEESSHHHHHHHHH---TT-SEEEEES-CH-HHHHHHHHHHHHHTTTS
T ss_pred             EEehHHHHHHhCCHHHHHHHHHHhCCCCceEEEEcCCHHHHHHHHH---hCCCEEEecCcCH-HHHHHHHHHHhhcCCcE
Confidence            666665555554455544432      22 3447888999999886   4589999996533 22233444444444446


Q ss_pred             EEEEEccCChHHHHHHHHcCCCceE
Q 029986           93 VIMMSVDGCTQDVMKGVTHGACNYL  117 (184)
Q Consensus        93 iIi~~~~~~~~~~~~a~~~ga~~~l  117 (184)
                      .|..+..-+.+.+.+..+.|+|.+-
T Consensus       129 ~ie~SGGI~~~ni~~ya~~gvD~is  153 (169)
T PF01729_consen  129 KIEASGGITLENIAEYAKTGVDVIS  153 (169)
T ss_dssp             EEEEESSSSTTTHHHHHHTT-SEEE
T ss_pred             EEEEECCCCHHHHHHHHhcCCCEEE
Confidence            7777888888888898999987654

4.2.19 from EC is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide [, ]. Unlike IPR004393 from INTERPRO, this domain also includes the molybdenum transport system protein ModD.; GO: 0004514 nicotinate-nucleotide diphosphorylase (carboxylating) activity, 0009435 NAD biosynthetic process; PDB: 3C2O_A 3C2F_A 3C2E_A 3C2R_A 3C2V_A 1QPN_E 1QPO_A 1QPQ_F 1QPR_E 2I14_D ....

>PRK05848 nicotinate-nucleotide pyrophosphorylase; Provisional

Probab=86.98  E-value=5.9  Score=31.22  Aligned_cols=95  Identities=13%  Similarity=0.116  Sum_probs=56.9

Q ss_pred             EEEEeCCHHHHHHHHHHHHh----cCC---eEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCC
Q 029986           20 VLVVDDDPIWLRILEKMLRK----CLY---EVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLP   92 (184)
Q Consensus        20 Ilivdd~~~~~~~l~~~L~~----~~~---~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~   92 (184)
                      |+|=|.+-.....+...++.    ...   -...+.+.+++.+.+.   .++|+|.+|-. .-.+--+.++.++...+-.
T Consensus       155 vlikdnHi~~~g~i~~~v~~~k~~~p~~~~I~VEv~tleea~~A~~---~GaDiI~LDn~-~~e~l~~~v~~~~~~~~~~  230 (273)
T PRK05848        155 LMLKDTHLKHIKDLKEFIQHARKNIPFTAKIEIECESLEEAKNAMN---AGADIVMCDNM-SVEEIKEVVAYRNANYPHV  230 (273)
T ss_pred             hCcCHHHHHHHCcHHHHHHHHHHhCCCCceEEEEeCCHHHHHHHHH---cCCCEEEECCC-CHHHHHHHHHHhhccCCCe
Confidence            66666665555555555543    232   3347889999999875   55899998742 1111112222222211223


Q ss_pred             EEEEEccCChHHHHHHHHcCCCceEe
Q 029986           93 VIMMSVDGCTQDVMKGVTHGACNYLL  118 (184)
Q Consensus        93 iIi~~~~~~~~~~~~a~~~ga~~~l~  118 (184)
                      .+..+..-+.+.+....+.|+|.+.+
T Consensus       231 ~ieAsGgIt~~ni~~ya~~GvD~Isv  256 (273)
T PRK05848        231 LLEASGNITLENINAYAKSGVDAISS  256 (273)
T ss_pred             EEEEECCCCHHHHHHHHHcCCCEEEe
Confidence            45556667889999999999986543

>TIGR00696 wecB_tagA_cpsF bacterial polymer biosynthesis proteins, WecB/TagA/CpsF family

Probab=86.93  E-value=6.9  Score=28.68  Aligned_cols=76  Identities=17%  Similarity=0.201  Sum_probs=50.5

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhc--CCeEEEE----C--CHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKC--LYEVTKC----N--RAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL   87 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~--~~~v~~~----~--~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~   87 (184)
                      .+.+|.++...+...+.+.+.|+..  +..+..+    .  +.++..+.+.  ...||+|++-+..|..+-+  +.+.+.
T Consensus        47 ~~~~vfllG~~~~v~~~~~~~l~~~yP~l~i~g~~g~f~~~~~~~i~~~I~--~s~~dil~VglG~PkQE~~--~~~~~~  122 (177)
T TIGR00696        47 EKLPIFLYGGKPDVLQQLKVKLIKEYPKLKIVGAFGPLEPEERKAALAKIA--RSGAGIVFVGLGCPKQEIW--MRNHRH  122 (177)
T ss_pred             cCCeEEEECCCHHHHHHHHHHHHHHCCCCEEEEECCCCChHHHHHHHHHHH--HcCCCEEEEEcCCcHhHHH--HHHhHH
Confidence            3579999999999999999999865  4554432    1  1233455555  4569999999999988743  444433


Q ss_pred             cCCCCEEE
Q 029986           88 EMDLPVIM   95 (184)
Q Consensus        88 ~~~~~iIi   95 (184)
                      ....++++
T Consensus       123 ~~~~~v~~  130 (177)
T TIGR00696       123 LKPDAVMI  130 (177)
T ss_pred             hCCCcEEE
Confidence            32344443

The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.

>TIGR03088 stp2 sugar transferase, PEP-CTERM/EpsH1 system associated

Probab=86.83  E-value=12  Score=30.02  Aligned_cols=107  Identities=21%  Similarity=0.219  Sum_probs=66.3

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCC--eEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLY--EVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVI   94 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~--~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iI   94 (184)
                      +.+++++.+.+. .+.+...++..+.  .+.......+..+++.  .  .|++++-.. .++-|..+++.+.  ..+|+|
T Consensus       229 ~~~l~i~G~g~~-~~~~~~~~~~~~~~~~v~~~g~~~~~~~~~~--~--adi~v~pS~-~Eg~~~~~lEAma--~G~Pvv  300 (374)
T TIGR03088       229 RLRLVIVGDGPA-RGACEQMVRAAGLAHLVWLPGERDDVPALMQ--A--LDLFVLPSL-AEGISNTILEAMA--SGLPVI  300 (374)
T ss_pred             ceEEEEecCCch-HHHHHHHHHHcCCcceEEEcCCcCCHHHHHH--h--cCEEEeccc-cccCchHHHHHHH--cCCCEE
Confidence            467777776553 3456666665543  2333333344455544  2  577776432 3444666777663  467887


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      ..-.    ....+.+..|..+++..|-+.+++.+.+..++.
T Consensus       301 ~s~~----~g~~e~i~~~~~g~~~~~~d~~~la~~i~~l~~  337 (374)
T TIGR03088       301 ATAV----GGNPELVQHGVTGALVPPGDAVALARALQPYVS  337 (374)
T ss_pred             EcCC----CCcHHHhcCCCceEEeCCCCHHHHHHHHHHHHh
Confidence            6322    224455667888999999999999999998765

Members of this family include a match to the pfam00534 Glycosyl transferases group 1 domain. Nearly all are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria. In particular, these transferases are found proximal to a particular variant of exosortase, EpsH1, which appears to travel with a conserved group of genes summarized by Genome Property GenProp0652. The nature of the sugar transferase reaction catalyzed by members of this clade is unknown and may conceivably be variable with respect to substrate by species, but we hypothesize a conserved substrate.

>TIGR00343 pyridoxal 5'-phosphate synthase, synthase subunit Pdx1

Probab=86.70  E-value=9.7  Score=30.13  Aligned_cols=60  Identities=17%  Similarity=0.065  Sum_probs=44.0

Q ss_pred             CHHHHHHHhcccCCCCEE--EEEccCChHHHHHHHHcCCCceE-----eCCCCHHHHHHHHHHHHcC
Q 029986           77 DGFKLHEQVGLEMDLPVI--MMSVDGCTQDVMKGVTHGACNYL-----LKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        77 ~g~~l~~~l~~~~~~~iI--i~~~~~~~~~~~~a~~~ga~~~l-----~kP~~~~~l~~~l~~~~~~  136 (184)
                      .++++++++.....+||+  ....-.+++.+..+++.|+++++     .|.-++.+..+.+..+..+
T Consensus       184 ~~~elLkei~~~~~iPVV~fAiGGI~TPedAa~~melGAdGVaVGSaI~ks~dP~~~akafv~ai~~  250 (287)
T TIGR00343       184 VPVELLLEVLKLGKLPVVNFAAGGVATPADAALMMQLGADGVFVGSGIFKSSNPEKLAKAIVEATTH  250 (287)
T ss_pred             CCHHHHHHHHHhCCCCEEEeccCCCCCHHHHHHHHHcCCCEEEEhHHhhcCCCHHHHHHHHHHHHHH
Confidence            467888888665678998  55555688999999999999996     4544566666666665543

This protein had been believed to be a singlet oxygen resistance protein. Subsequent work showed that it is a protein of pyridoxine (vitamin B6) biosynthesis, and that pyridoxine quenches the highly toxic singlet form of oxygen produced by light in the presence of certain chemicals.

>PF01081 Aldolase: KDPG and KHG aldolase; InterPro: IPR000887 4-Hydroxy-2-oxoglutarate aldolase (4

Probab=86.51  E-value=3  Score=31.13  Aligned_cols=63  Identities=11%  Similarity=0.116  Sum_probs=41.9

Q ss_pred             EEeCCCCCCCHHHHHHHhccc-CCCCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHH
Q 029986           68 ISDVHMPDMDGFKLHEQVGLE-MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQH  132 (184)
Q Consensus        68 ilD~~l~~~~g~~l~~~l~~~-~~~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~  132 (184)
                      ++.+.+...++.+.++.+++. ++ -+|=..+=.+.+.+..+.++||. |++.|.-.+++.+..++
T Consensus        36 ~iEiT~~t~~a~~~I~~l~~~~p~-~~vGAGTV~~~e~a~~a~~aGA~-FivSP~~~~~v~~~~~~   99 (196)
T PF01081_consen   36 AIEITLRTPNALEAIEALRKEFPD-LLVGAGTVLTAEQAEAAIAAGAQ-FIVSPGFDPEVIEYARE   99 (196)
T ss_dssp             EEEEETTSTTHHHHHHHHHHHHTT-SEEEEES--SHHHHHHHHHHT-S-EEEESS--HHHHHHHHH
T ss_pred             EEEEecCCccHHHHHHHHHHHCCC-CeeEEEeccCHHHHHHHHHcCCC-EEECCCCCHHHHHHHHH
Confidence            566677777888888888543 44 34444555667889999999998 88888877777666553

1.3.16 from EC) (KHG-aldolase) catalyzes the interconversion of 4-hydroxy-2-oxoglutarate into pyruvate and glyoxylate. Phospho-2-dehydro-3-deoxygluconate aldolase (4.1.2.14 from EC) (KDPG-aldolase) catalyzes the interconversion of 6-phospho-2-dehydro-3-deoxy-D-gluconate into pyruvate and glyceraldehyde 3-phosphate. These two enzymes are structurally and functionally related []. They are both homotrimeric proteins of approximately 220 amino-acid residues. They are class I aldolases whose catalytic mechanism involves the formation of a Schiff-base intermediate between the substrate and the epsilon-amino group of a lysine residue. In both enzymes, an arginine is required for catalytic activity.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 3VCR_A 1FQ0_A 1EUN_A 1EUA_B 1FWR_A 2C0A_B 1WBH_A 1WAU_A 2YW3_B 2YW4_A ....

>COG0157 NadC Nicotinate-nucleotide pyrophosphorylase [Coenzyme metabolism]

Probab=86.45  E-value=7.9  Score=30.51  Aligned_cols=92  Identities=16%  Similarity=0.152  Sum_probs=58.6

Q ss_pred             EEEEeCCHHHHHHHHHHHHhc----CCeE---EEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCC
Q 029986           20 VLVVDDDPIWLRILEKMLRKC----LYEV---TKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLP   92 (184)
Q Consensus        20 Ilivdd~~~~~~~l~~~L~~~----~~~v---~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~   92 (184)
                      |+|=|.+-...-.+...+++.    ++..   ..+.+.+++.+++.   .++|+|++|-.-| ..--+.++.++ .....
T Consensus       161 vliKDNHia~~g~i~~Av~~aR~~~~~~~kIEVEvesle~~~eAl~---agaDiImLDNm~~-e~~~~av~~l~-~~~~~  235 (280)
T COG0157         161 VLIKDNHIAAAGSITEAVRRARAAAPFTKKIEVEVESLEEAEEALE---AGADIIMLDNMSP-EELKEAVKLLG-LAGRA  235 (280)
T ss_pred             EEehhhHHHHhccHHHHHHHHHHhCCCCceEEEEcCCHHHHHHHHH---cCCCEEEecCCCH-HHHHHHHHHhc-cCCce
Confidence            677777777666677777643    4422   36888999999886   5599999995333 22223333331 23334


Q ss_pred             EEEEEccCChHHHHHHHHcCCCce
Q 029986           93 VIMMSVDGCTQDVMKGVTHGACNY  116 (184)
Q Consensus        93 iIi~~~~~~~~~~~~a~~~ga~~~  116 (184)
                      ++=.+..-+.+.+......|++.+
T Consensus       236 ~lEaSGgIt~~ni~~yA~tGVD~I  259 (280)
T COG0157         236 LLEASGGITLENIREYAETGVDVI  259 (280)
T ss_pred             EEEEeCCCCHHHHHHHhhcCCCEE
Confidence            455566667777888888888744

>PF03602 Cons_hypoth95: Conserved hypothetical protein 95; InterPro: IPR004398 This entry contains Ribosomal RNA small subunit methyltransferase D as well as the putative rRNA methyltransferase YlbH

Probab=86.38  E-value=5.4  Score=29.38  Aligned_cols=69  Identities=22%  Similarity=0.109  Sum_probs=44.2

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCe---EEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCH-HHHHHHhc
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYE---VTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG-FKLHEQVG   86 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~---v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g-~~l~~~l~   86 (184)
                      -+|..||-++.....+++-++..+..   .....+...++.........+|+||+|-=-..... .++++.+.
T Consensus        66 ~~v~fVE~~~~a~~~i~~N~~~l~~~~~~~v~~~d~~~~l~~~~~~~~~fDiIflDPPY~~~~~~~~~l~~l~  138 (183)
T PF03602_consen   66 KSVVFVEKNRKAIKIIKKNLEKLGLEDKIRVIKGDAFKFLLKLAKKGEKFDIIFLDPPYAKGLYYEELLELLA  138 (183)
T ss_dssp             SEEEEEES-HHHHHHHHHHHHHHT-GGGEEEEESSHHHHHHHHHHCTS-EEEEEE--STTSCHHHHHHHHHHH
T ss_pred             CeEEEEECCHHHHHHHHHHHHHhCCCcceeeeccCHHHHHHhhcccCCCceEEEECCCcccchHHHHHHHHHH
Confidence            47999999999999999999887632   33456666666655333566999999952223333 55666664

They methylate the guanosine in position 966 of 16S rRNA in the assembled 30S particle [].; GO: 0008168 methyltransferase activity, 0031167 rRNA methylation; PDB: 3P9N_A 2ESR_B 2IFT_A 1WS6_A 2FPO_B 2FHP_A.

>PF01408 GFO_IDH_MocA: Oxidoreductase family, NAD-binding Rossmann fold; InterPro: IPR000683 This group of enzymes utilise NADP or NAD, and is known as the GFO/IDH/MOCA family in UniProtKB/Swiss-Prot

Probab=85.96  E-value=8  Score=25.67  Aligned_cols=38  Identities=13%  Similarity=0.231  Sum_probs=30.5

Q ss_pred             CChHHHHHHHHcCCCceEeCCC--CHHHHHHHHHHHHcCC
Q 029986          100 GCTQDVMKGVTHGACNYLLKPI--RIKELRNIWQHVAQQP  137 (184)
Q Consensus       100 ~~~~~~~~a~~~ga~~~l~kP~--~~~~l~~~l~~~~~~~  137 (184)
                      ...+....+++.|.+=|+-||+  +.+++.+.++.+.+.+
T Consensus        74 ~h~~~~~~~l~~g~~v~~EKP~~~~~~~~~~l~~~a~~~~  113 (120)
T PF01408_consen   74 SHAEIAKKALEAGKHVLVEKPLALTLEEAEELVEAAKEKG  113 (120)
T ss_dssp             GHHHHHHHHHHTTSEEEEESSSSSSHHHHHHHHHHHHHHT
T ss_pred             chHHHHHHHHHcCCEEEEEcCCcCCHHHHHHHHHHHHHhC
Confidence            3357788999999999999999  7888888887765543

GFO is a glucose--fructose oxidoreductase, which converts D-glucose and D-fructose into D-gluconolactone and D-glucitol in the sorbitol-gluconate pathway. MOCA is a rhizopine catabolism protein which may catalyse the NADH-dependent dehydrogenase reaction involved in rhizopine catabolism. Other proteins belonging to this family include Gal80, a negative regulator for the expression of lactose and galactose metabolic genes; and several hypothetical proteins from yeast, Escherichia coli and Bacillus subtilis. The oxidoreductase, N-terminal domain is almost always associated with the oxidoreductase, C-terminal domain (see IPR004104 from INTERPRO).; GO: 0016491 oxidoreductase activity; PDB: 1LC0_A 1LC3_A 1GCU_A 3IP3_E 3CEA_C 3EVN_A 3NTQ_A 3NTR_B 3NT5_A 3MZ0_A ....

>PLN02871 UDP-sulfoquinovose:DAG sulfoquinovosyltransferase

Probab=85.59  E-value=20  Score=30.19  Aligned_cols=108  Identities=18%  Similarity=0.249  Sum_probs=64.9

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMM   96 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi~   96 (184)
                      +.+++|+.+.+. .+.+.++.+.......-.-..++...++.  .  .|++++-.. .+.-|..+++.+.  ..+|||..
T Consensus       290 ~~~l~ivG~G~~-~~~l~~~~~~~~V~f~G~v~~~ev~~~~~--~--aDv~V~pS~-~E~~g~~vlEAmA--~G~PVI~s  361 (465)
T PLN02871        290 GARLAFVGDGPY-REELEKMFAGTPTVFTGMLQGDELSQAYA--S--GDVFVMPSE-SETLGFVVLEAMA--SGVPVVAA  361 (465)
T ss_pred             CcEEEEEeCChH-HHHHHHHhccCCeEEeccCCHHHHHHHHH--H--CCEEEECCc-ccccCcHHHHHHH--cCCCEEEc
Confidence            567777777653 34455554433222212223356666654  2  578776443 3334556666663  46888754


Q ss_pred             EccCChHHHHHHHHc---CCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           97 SVDGCTQDVMKGVTH---GACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        97 ~~~~~~~~~~~a~~~---ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      ...    ...+.+..   |-.+++..|-+.+++.+.+..++..
T Consensus       362 ~~g----g~~eiv~~~~~~~~G~lv~~~d~~~la~~i~~ll~~  400 (465)
T PLN02871        362 RAG----GIPDIIPPDQEGKTGFLYTPGDVDDCVEKLETLLAD  400 (465)
T ss_pred             CCC----CcHhhhhcCCCCCceEEeCCCCHHHHHHHHHHHHhC
Confidence            322    23344555   8889999999999999999888753

>PF01596 Methyltransf_3: O-methyltransferase; InterPro: IPR002935 Members of this family are O-methyltransferases

Probab=85.28  E-value=12  Score=28.13  Aligned_cols=60  Identities=20%  Similarity=0.237  Sum_probs=44.6

Q ss_pred             cCCCCCeEEEEeCCHHHHHHHHHHHHhcCC--eE-EEECCHHHHHHHHHhcC--CCccEEEEeCC
Q 029986           13 QFPAGLRVLVVDDDPIWLRILEKMLRKCLY--EV-TKCNRAEIALDMLRMSK--NGYDIVISDVH   72 (184)
Q Consensus        13 ~~~~~~~Ilivdd~~~~~~~l~~~L~~~~~--~v-~~~~~~~~~~~~l~~~~--~~~dlvilD~~   72 (184)
                      ..|++-+|.-+|-++...+.-+..++..|+  .+ ....++.+.+..+....  ..+|+||+|..
T Consensus        66 ~l~~~g~i~tiE~~~~~~~~A~~~~~~ag~~~~I~~~~gda~~~l~~l~~~~~~~~fD~VFiDa~  130 (205)
T PF01596_consen   66 ALPEDGKITTIEIDPERAEIARENFRKAGLDDRIEVIEGDALEVLPELANDGEEGQFDFVFIDAD  130 (205)
T ss_dssp             TSTTTSEEEEEESSHHHHHHHHHHHHHTTGGGGEEEEES-HHHHHHHHHHTTTTTSEEEEEEEST
T ss_pred             hhcccceEEEecCcHHHHHHHHHHHHhcCCCCcEEEEEeccHhhHHHHHhccCCCceeEEEEccc
Confidence            445566999999999999999999998765  23 35567777777665322  36999999985

The family includes also bacterial O-methyltransferases that may be involved in antibiotic production [].; GO: 0008171 O-methyltransferase activity; PDB: 1SUI_C 1SUS_D 3CBG_A 2GPY_B 3TR6_A 2AVD_A 3DUL_B 3DUW_B 2ZTH_A 1VID_A ....

>PRK03708 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional

Probab=85.27  E-value=13  Score=29.29  Aligned_cols=104  Identities=15%  Similarity=0.171  Sum_probs=58.9

Q ss_pred             CeEEEEeC--C---HHHHHHHHHHHHhcCCeEEEECCHHHHHHHH------HhcCCCccEEEEeCCCCCCCHHHHHHHhc
Q 029986           18 LRVLVVDD--D---PIWLRILEKMLRKCLYEVTKCNRAEIALDML------RMSKNGYDIVISDVHMPDMDGFKLHEQVG   86 (184)
Q Consensus        18 ~~Ilivdd--~---~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l------~~~~~~~dlvilD~~l~~~~g~~l~~~l~   86 (184)
                      |||.|+-.  .   ......+..+|++.|+++....+........      ......+|++|+    -++|| .+++.++
T Consensus         1 m~v~iv~~~~k~~~~~~~~~I~~~L~~~g~~v~v~~~~~~~~~~~~~~~~~~~~~~~~d~vi~----iGGDG-TlL~a~~   75 (277)
T PRK03708          1 MRFGIVARRDKEEALKLAYRVYDFLKVSGYEVVVDSETYEHLPEFSEEDVLPLEEMDVDFIIA----IGGDG-TILRIEH   75 (277)
T ss_pred             CEEEEEecCCCHHHHHHHHHHHHHHHHCCCEEEEecchhhhcCcccccccccccccCCCEEEE----EeCcH-HHHHHHH
Confidence            56777732  2   2244556667777788877653221111100      001124787776    26777 2333332


Q ss_pred             -ccCCCCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCCC
Q 029986           87 -LEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPF  140 (184)
Q Consensus        87 -~~~~~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~  140 (184)
                       ....+||+.+..             |-.+|+. .+..+++...+..+.++....
T Consensus        76 ~~~~~~pi~gIn~-------------G~lGFl~-~~~~~~~~~~l~~i~~g~~~~  116 (277)
T PRK03708         76 KTKKDIPILGINM-------------GTLGFLT-EVEPEETFFALSRLLEGDYFI  116 (277)
T ss_pred             hcCCCCeEEEEeC-------------CCCCccc-cCCHHHHHHHHHHHHcCCceE
Confidence             123678877742             4456766 667899999999998876443

>TIGR00693 thiE thiamine-phosphate pyrophosphorylase

Probab=85.12  E-value=13  Score=27.29  Aligned_cols=70  Identities=14%  Similarity=0.217  Sum_probs=47.8

Q ss_pred             EEECCHHHHHHHHHhcCCCccEEEEeCCCCC--------CCHHHHHHHhcc-cCCCCEEEEEccCChHHHHHHHHcCCCc
Q 029986           45 TKCNRAEIALDMLRMSKNGYDIVISDVHMPD--------MDGFKLHEQVGL-EMDLPVIMMSVDGCTQDVMKGVTHGACN  115 (184)
Q Consensus        45 ~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~--------~~g~~l~~~l~~-~~~~~iIi~~~~~~~~~~~~a~~~ga~~  115 (184)
                      .++++.+++.+..   +.++|.+.++-..+.        ..|++.++.+.. .+++||+++..- +.+.+..+.+.|+++
T Consensus       101 ~s~h~~~e~~~a~---~~g~dyi~~~~v~~t~~k~~~~~~~g~~~l~~~~~~~~~~pv~a~GGI-~~~~~~~~~~~G~~g  176 (196)
T TIGR00693       101 VSTHNLEELAEAE---AEGADYIGFGPIFPTPTKKDPAPPAGVELLREIAATSIDIPIVAIGGI-TLENAAEVLAAGADG  176 (196)
T ss_pred             EeCCCHHHHHHHh---HcCCCEEEECCccCCCCCCCCCCCCCHHHHHHHHHhcCCCCEEEECCc-CHHHHHHHHHcCCCE
Confidence            3566667666543   356899998665542        236788888753 346888877544 577888889999988


Q ss_pred             eEe
Q 029986          116 YLL  118 (184)
Q Consensus       116 ~l~  118 (184)
                      +..
T Consensus       177 va~  179 (196)
T TIGR00693       177 VAV  179 (196)
T ss_pred             EEE
Confidence            753

This model includes ThiE from Bacillus subtilis but excludes its paralog, the regulatory protein TenI, and neighbors of TenI.

>PRK10669 putative cation:proton antiport protein; Provisional

Probab=84.78  E-value=25  Score=30.59  Aligned_cols=70  Identities=10%  Similarity=0.052  Sum_probs=37.5

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHhc-ccCCCCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCC
Q 029986           63 GYDIVISDVHMPDMDGFKLHEQVG-LEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPK  138 (184)
Q Consensus        63 ~~dlvilD~~l~~~~g~~l~~~l~-~~~~~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~  138 (184)
                      ..|.+++-..-.+.+ ..++..++ ..++.+++.-+.  +++......+.|++ ++..|-  .++.+.+...+....
T Consensus       481 ~a~~viv~~~~~~~~-~~iv~~~~~~~~~~~iiar~~--~~~~~~~l~~~Gad-~vv~p~--~~~a~~i~~~l~~~~  551 (558)
T PRK10669        481 CARWLLLTIPNGYEA-GEIVASAREKRPDIEIIARAH--YDDEVAYITERGAN-QVVMGE--REIARTMLELLETPP  551 (558)
T ss_pred             ccCEEEEEcCChHHH-HHHHHHHHHHCCCCeEEEEEC--CHHHHHHHHHcCCC-EEEChH--HHHHHHHHHHhcCCC
Confidence            356666644321111 12333333 345677776653  45555556788998 555453  566666666655443

>PRK15320 transcriptional activator SprB; Provisional

Probab=84.74  E-value=4.7  Score=30.27  Aligned_cols=98  Identities=16%  Similarity=0.108  Sum_probs=62.8

Q ss_pred             eEEEEeCCHHHHHHHHHHHHhc--CCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEEE
Q 029986           19 RVLVVDDDPIWLRILEKMLRKC--LYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMM   96 (184)
Q Consensus        19 ~Ilivdd~~~~~~~l~~~L~~~--~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi~   96 (184)
                      +|+|..++=...-.+..++++.  |..+..+.+....+..++   ..||.+++=.--|..--+-|......-++-||+++
T Consensus         3 ~viiyg~~w~~~~a~~~~~~~~~p~~~~~t~~~l~~ll~~l~---~~p~a~lil~l~p~eh~~lf~~l~~~l~~~~v~vv   79 (251)
T PRK15320          3 NVIIYGINWTNCYALQSIFKQKYPEKCVKTCNSLTALLHSLS---DMPDAGLILALNPHEHVYLFHALLTRLQNRKVLVV   79 (251)
T ss_pred             cEEEEeccchHHHHHHHHHHHHCCccchhhhhhHHHHHHHHh---hCCCceEEEeeCchhHHHHHHHHHHHcCCCceEEE
Confidence            4788888888888888888876  677778888888887776   33666665433344433333332223467889999


Q ss_pred             EccCChHHHHHHHHcCCCceEeC
Q 029986           97 SVDGCTQDVMKGVTHGACNYLLK  119 (184)
Q Consensus        97 ~~~~~~~~~~~a~~~ga~~~l~k  119 (184)
                      ++.-......-..-.|.-+|+.|
T Consensus        80 ~d~l~~~dr~vl~~~g~~~~~l~  102 (251)
T PRK15320         80 ADRLYYIDRCVLQYFGVMDYVLK  102 (251)
T ss_pred             ecceeehhhhhhhhhcchhHHHH
Confidence            87654443333344577777765

>PF02581 TMP-TENI: Thiamine monophosphate synthase/TENI; InterPro: IPR003733 Thiamine monophosphate synthase (TMP) (2

Probab=84.55  E-value=13  Score=27.01  Aligned_cols=79  Identities=16%  Similarity=0.130  Sum_probs=53.4

Q ss_pred             HHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCC-------CHHHHHHHhcccCCCCEEEEEccCChHHHHHH
Q 029986           36 MLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDM-------DGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKG  108 (184)
Q Consensus        36 ~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~-------~g~~l~~~l~~~~~~~iIi~~~~~~~~~~~~a  108 (184)
                      .+....+--.++++.+++.....   ..+|.+++.-..+..       -|++.++++.....+||+.+..- +.+....+
T Consensus        91 ~~~~~~~ig~S~h~~~e~~~a~~---~g~dYv~~gpvf~T~sk~~~~~~g~~~l~~~~~~~~~pv~AlGGI-~~~~i~~l  166 (180)
T PF02581_consen   91 LLGPDKIIGASCHSLEEAREAEE---LGADYVFLGPVFPTSSKPGAPPLGLDGLREIARASPIPVYALGGI-TPENIPEL  166 (180)
T ss_dssp             HHTTTSEEEEEESSHHHHHHHHH---CTTSEEEEETSS--SSSSS-TTCHHHHHHHHHHHTSSCEEEESS---TTTHHHH
T ss_pred             hcccceEEEeecCcHHHHHHhhh---cCCCEEEECCccCCCCCccccccCHHHHHHHHHhCCCCEEEEcCC-CHHHHHHH
Confidence            34333344458888888666643   558999998766543       38888888866667999999654 56677788


Q ss_pred             HHcCCCceEe
Q 029986          109 VTHGACNYLL  118 (184)
Q Consensus       109 ~~~ga~~~l~  118 (184)
                      .+.|++++-.
T Consensus       167 ~~~Ga~gvAv  176 (180)
T PF02581_consen  167 REAGADGVAV  176 (180)
T ss_dssp             HHTT-SEEEE
T ss_pred             HHcCCCEEEE
Confidence            9999998753

5.1.3 from EC) catalyzes the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5- (beta-hydroxyethyl)thiazole phosphate to yield thiamine phosphate in the thiamine biosynthesis pathway []. TENI, a protein from Bacillus subtilis that regulates the production of several extracellular enzymes by reducing alkaline protease production belongs to this group [].; GO: 0004789 thiamine-phosphate diphosphorylase activity, 0009228 thiamine biosynthetic process; PDB: 3NL5_A 3NL2_A 3NM1_A 3NM3_C 3NL6_B 3NL3_A 3CEU_A 3O63_B 3QH2_C 1YAD_D ....

>cd04727 pdxS PdxS is a subunit of the pyridoxal 5'-phosphate (PLP) synthase, an important enzyme in deoxyxylulose 5-phosphate (DXP)-independent pathway for de novo biosynthesis of PLP, present in some eubacteria, in archaea, fungi, plants, plasmodia, and some metazoa

Probab=84.28  E-value=15  Score=29.11  Aligned_cols=59  Identities=14%  Similarity=0.081  Sum_probs=41.6

Q ss_pred             CHHHHHHHhcccCCCCEE--EEEccCChHHHHHHHHcCCCceEe-----CCCCHHHHHHHHHHHHc
Q 029986           77 DGFKLHEQVGLEMDLPVI--MMSVDGCTQDVMKGVTHGACNYLL-----KPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        77 ~g~~l~~~l~~~~~~~iI--i~~~~~~~~~~~~a~~~ga~~~l~-----kP~~~~~l~~~l~~~~~  135 (184)
                      .++++++++.+...+||+  ....-.+++.+..+++.|++++++     +.-++.+..+.+...+.
T Consensus       181 ~d~elLk~l~~~~~iPVV~iAeGGI~Tpena~~v~e~GAdgVaVGSAI~~a~dP~~~tk~f~~ai~  246 (283)
T cd04727         181 APYELVKETAKLGRLPVVNFAAGGVATPADAALMMQLGADGVFVGSGIFKSENPEKRARAIVEAVT  246 (283)
T ss_pred             CCHHHHHHHHHhcCCCeEEEEeCCCCCHHHHHHHHHcCCCEEEEcHHhhcCCCHHHHHHHHHHHHH
Confidence            467888888665578997  555555789999999999999963     33345555555555544

Together with PdxT, PdxS forms the PLP synthase, a heteromeric glutamine amidotransferase (GATase), whereby PdxT produces ammonia from glutamine and PdxS combines ammonia with five- and three-carbon phosphosugars to form PLP. PLP is the biologically active form of vitamin B6, an essential cofactor in many biochemical processes. PdxS subunits form two hexameric rings.

>CHL00162 thiG thiamin biosynthesis protein G; Validated

Probab=84.26  E-value=18  Score=28.26  Aligned_cols=98  Identities=15%  Similarity=0.148  Sum_probs=67.3

Q ss_pred             HHHHHhcCCeEEEECC--HHHHHHHHHhcCCCccEEEEeCCCCCCCH-----HHHHHHhcccCCCCEEEEEccCChHHHH
Q 029986           34 EKMLRKCLYEVTKCNR--AEIALDMLRMSKNGYDIVISDVHMPDMDG-----FKLHEQVGLEMDLPVIMMSVDGCTQDVM  106 (184)
Q Consensus        34 ~~~L~~~~~~v~~~~~--~~~~~~~l~~~~~~~dlvilD~~l~~~~g-----~~l~~~l~~~~~~~iIi~~~~~~~~~~~  106 (184)
                      .+.|-+.||.|..+.+  ..-|.++..   .++ ..++-+.-|-++|     -..++.+...+++|||+=+.-..++.+.
T Consensus       130 ae~Lv~eGF~VlPY~~~D~v~a~rLed---~Gc-~aVMPlgsPIGSg~Gl~n~~~l~~i~e~~~vpVivdAGIgt~sDa~  205 (267)
T CHL00162        130 AEFLVKKGFTVLPYINADPMLAKHLED---IGC-ATVMPLGSPIGSGQGLQNLLNLQIIIENAKIPVIIDAGIGTPSEAS  205 (267)
T ss_pred             HHHHHHCCCEEeecCCCCHHHHHHHHH---cCC-eEEeeccCcccCCCCCCCHHHHHHHHHcCCCcEEEeCCcCCHHHHH
Confidence            4566677999986553  444444433   333 3455565554443     2356666667889999998888999999


Q ss_pred             HHHHcCCCceE-----eCCCCHHHHHHHHHHHHc
Q 029986          107 KGVTHGACNYL-----LKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus       107 ~a~~~ga~~~l-----~kP~~~~~l~~~l~~~~~  135 (184)
                      .+++.|+++.+     .|--++.++...+..+.+
T Consensus       206 ~AmElGaDgVL~nSaIakA~dP~~mA~a~~~AV~  239 (267)
T CHL00162        206 QAMELGASGVLLNTAVAQAKNPEQMAKAMKLAVQ  239 (267)
T ss_pred             HHHHcCCCEEeecceeecCCCHHHHHHHHHHHHH
Confidence            99999999986     455567788777776654

>PRK03958 tRNA 2'-O-methylase; Reviewed

Probab=84.15  E-value=14  Score=27.06  Aligned_cols=92  Identities=7%  Similarity=0.049  Sum_probs=62.1

Q ss_pred             eEEEEeCCHHHHHHHHHHHHhcC--CeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHH-HhcccCCCCEEE
Q 029986           19 RVLVVDDDPIWLRILEKMLRKCL--YEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHE-QVGLEMDLPVIM   95 (184)
Q Consensus        19 ~Ilivdd~~~~~~~l~~~L~~~~--~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~-~l~~~~~~~iIi   95 (184)
                      +++|+.+++...+.+...+..+|  |.+....+.+++++.+......|.++.-+....+  .++-++ .+..  .-|+++
T Consensus        33 ~~yiv~~~~~q~~~v~~I~~~WGg~fnv~~~~s~~~~i~~~k~~G~vvhLtmyga~~~~--~~~~ir~~~~~--~~p~LI  108 (176)
T PRK03958         33 KIILASNDEHVKESVEDIVERWGGPFEVEVTKSWKKEIREWKDGGIVVHLTMYGENIQD--VEPEIREAHRK--GEPLLI  108 (176)
T ss_pred             eEEEecCcHHHHHHHHHHHHhcCCceEEEEcCCHHHHHHHHHhCCcEEEEEEecCCccc--hHHHHHHhhcc--CCcEEE
Confidence            68999999999999999999885  6788999999999998732334777777877765  433333 2322  456666


Q ss_pred             EEccCChHHHHHHHHcCCCceEe
Q 029986           96 MSVDGCTQDVMKGVTHGACNYLL  118 (184)
Q Consensus        96 ~~~~~~~~~~~~a~~~ga~~~l~  118 (184)
                      +..  ..+...+.++  ..||.+
T Consensus       109 vvG--g~gvp~evye--~aDynl  127 (176)
T PRK03958        109 VVG--AEKVPREVYE--LADWNV  127 (176)
T ss_pred             EEc--CCCCCHHHHh--hCCEEe
Confidence            654  2333334443  334654

>COG3010 NanE Putative N-acetylmannosamine-6-phosphate epimerase [Carbohydrate transport and metabolism]

Probab=84.09  E-value=16  Score=27.61  Aligned_cols=86  Identities=19%  Similarity=0.268  Sum_probs=62.4

Q ss_pred             eEEEECCHHHHHHHHHhcCCCccEEEEeCCCCC---------CCHHHHHHHhcccCCCCEEEEEccCChHHHHHHHHcCC
Q 029986           43 EVTKCNRAEIALDMLRMSKNGYDIVISDVHMPD---------MDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGA  113 (184)
Q Consensus        43 ~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~---------~~g~~l~~~l~~~~~~~iIi~~~~~~~~~~~~a~~~ga  113 (184)
                      -+.-+++.++++...+   .++|  |+...|.+         ...+++++.+.. ..+++|.=....+++.+.++++.||
T Consensus       130 ~MAD~St~ee~l~a~~---~G~D--~IGTTLsGYT~~~~~~~~pDf~lvk~l~~-~~~~vIAEGr~~tP~~Ak~a~~~Ga  203 (229)
T COG3010         130 AMADCSTFEEGLNAHK---LGFD--IIGTTLSGYTGYTEKPTEPDFQLVKQLSD-AGCRVIAEGRYNTPEQAKKAIEIGA  203 (229)
T ss_pred             EEeccCCHHHHHHHHH---cCCc--EEecccccccCCCCCCCCCcHHHHHHHHh-CCCeEEeeCCCCCHHHHHHHHHhCC
Confidence            4567888999988764   5578  55555543         345889998864 6788988888888999999999999


Q ss_pred             CceEeCCC--CHHHHHHHHHHHH
Q 029986          114 CNYLLKPI--RIKELRNIWQHVA  134 (184)
Q Consensus       114 ~~~l~kP~--~~~~l~~~l~~~~  134 (184)
                      +...+--.  .++++.......+
T Consensus       204 ~aVvVGsAITRp~~It~~F~~~i  226 (229)
T COG3010         204 DAVVVGSAITRPEEITQWFVDAI  226 (229)
T ss_pred             eEEEECcccCCHHHHHHHHHHHH
Confidence            98865433  3466666655544

>TIGR02026 BchE magnesium-protoporphyrin IX monomethyl ester anaerobic oxidative cyclase

Probab=83.62  E-value=27  Score=29.90  Aligned_cols=109  Identities=12%  Similarity=0.139  Sum_probs=65.5

Q ss_pred             CHHHHHHHHHHHHhcC-CeEEEEC------CHHHHHHHHHhcCCCccEEEEeCCCCCC-CHHHHHHHhcc-cCCCCEEEE
Q 029986           26 DPIWLRILEKMLRKCL-YEVTKCN------RAEIALDMLRMSKNGYDIVISDVHMPDM-DGFKLHEQVGL-EMDLPVIMM   96 (184)
Q Consensus        26 ~~~~~~~l~~~L~~~~-~~v~~~~------~~~~~~~~l~~~~~~~dlvilD~~l~~~-~g~~l~~~l~~-~~~~~iIi~   96 (184)
                      .|.-...|...|+..| ++|....      +.++..+.+.  ...||+|.+...-+.. ...++++.+++ .|+++||+=
T Consensus        21 pPlgl~~lAa~L~~~G~~~V~iiD~~~~~~~~~~~~~~l~--~~~pdvVgis~~t~~~~~a~~~~~~~k~~~P~~~iV~G   98 (497)
T TIGR02026        21 PPLWVAYIGGALLDAGYHDVTFLDAMTGPLTDEKLVERLR--AHCPDLVLITAITPAIYIACETLKFARERLPNAIIVLG   98 (497)
T ss_pred             CCHHHHHHHHHHHhcCCcceEEecccccCCCHHHHHHHHH--hcCcCEEEEecCcccHHHHHHHHHHHHHHCCCCEEEEc
Confidence            5667778889998888 5776543      2333444444  4569999997644332 23456666654 356655543


Q ss_pred             EccCChHHHHHHHH-cCCCceEeCCCCHHHHHHHHHHHHcCC
Q 029986           97 SVDGCTQDVMKGVT-HGACNYLLKPIRIKELRNIWQHVAQQP  137 (184)
Q Consensus        97 ~~~~~~~~~~~a~~-~ga~~~l~kP~~~~~l~~~l~~~~~~~  137 (184)
                      .... .....+++. ....||++.--...-+.+.++.+..+.
T Consensus        99 G~h~-t~~~~~~l~~~p~vD~Vv~GEGE~~~~~Ll~~l~~g~  139 (497)
T TIGR02026        99 GIHP-TFMFHQVLTEAPWIDFIVRGEGEETVVKLIAALENHN  139 (497)
T ss_pred             CCCc-CcCHHHHHhcCCCccEEEeCCcHHHHHHHHHHHHcCC
Confidence            3222 222234443 345678888777788888888776543

This model respresents the cobalamin-dependent oxidative cyclase responsible for forming the distinctive E-ring of the chlorin ring system under anaerobic conditions. This step is essential in the biosynthesis of both bacteriochlorophyll and chlorophyll under anaerobic conditions (a separate enzyme, AcsF, acts under aerobic conditions). This model identifies two clades of sequences, one from photosynthetic, non-cyanobacterial bacteria and another including Synechocystis and several non-photosynthetic bacteria. The function of the Synechocystis gene is supported by gene clustering with other photosynthetic genes, so the purpose of the gene in the non-photosynthetic bacteria is uncertain. Note that homologs of this gene are not found in plants which rely solely on the aerobic cyclase.

>KOG4175 consensus Tryptophan synthase alpha chain [Amino acid transport and metabolism]

Probab=83.46  E-value=6.4  Score=29.59  Aligned_cols=49  Identities=14%  Similarity=0.303  Sum_probs=38.0

Q ss_pred             CCCCEEEEEc------cCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCC
Q 029986           89 MDLPVIMMSV------DGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQP  137 (184)
Q Consensus        89 ~~~~iIi~~~------~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~  137 (184)
                      -.+|||+++-      +....++..+.++||++|+.-.+.++|-...-+.+.++.
T Consensus        94 vt~PIiLmgYYNPIl~yG~e~~iq~ak~aGanGfiivDlPpEEa~~~Rne~~k~g  148 (268)
T KOG4175|consen   94 VTCPIILMGYYNPILRYGVENYIQVAKNAGANGFIIVDLPPEEAETLRNEARKHG  148 (268)
T ss_pred             cccceeeeecccHHHhhhHHHHHHHHHhcCCCceEeccCChHHHHHHHHHHHhcC
Confidence            3679988853      344567888999999999999998888877777766553

>PRK03372 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional

Probab=82.36  E-value=21  Score=28.61  Aligned_cols=106  Identities=22%  Similarity=0.275  Sum_probs=61.9

Q ss_pred             CeEEEEeC--CHH---HHHHHHHHHHhcCCeEEEECCHHHHHHH----------------HHhcCCCccEEEEeCCCCCC
Q 029986           18 LRVLVVDD--DPI---WLRILEKMLRKCLYEVTKCNRAEIALDM----------------LRMSKNGYDIVISDVHMPDM   76 (184)
Q Consensus        18 ~~Ilivdd--~~~---~~~~l~~~L~~~~~~v~~~~~~~~~~~~----------------l~~~~~~~dlvilD~~l~~~   76 (184)
                      .+|.|+-.  .+.   ....+..+|...|+.+.........+..                .......+|++|+    -++
T Consensus         6 ~~I~iv~~~~~~~~~~~~~~l~~~L~~~g~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~D~vi~----lGG   81 (306)
T PRK03372          6 RRVLLVAHTGRDEATEAARRVAKQLGDAGIGVRVLDAEAVDLGATHPAPDDFRAMEVVDADPDAADGCELVLV----LGG   81 (306)
T ss_pred             cEEEEEecCCCHHHHHHHHHHHHHHHHCCCEEEEeechhhhhcccccccccccccccccchhhcccCCCEEEE----EcC
Confidence            35777743  222   3455666777778877765432221110                0011123677776    367


Q ss_pred             CHHHHHHHhcc--cCCCCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCCCCC
Q 029986           77 DGFKLHEQVGL--EMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPFEE  142 (184)
Q Consensus        77 ~g~~l~~~l~~--~~~~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~~~  142 (184)
                      || .+++..+.  ...+||+-+.             .|-.+|+. .+..+++...+..++++.....+
T Consensus        82 DG-T~L~aar~~~~~~~PilGIN-------------~G~lGFL~-~~~~~~~~~~l~~i~~g~y~i~~  134 (306)
T PRK03372         82 DG-TILRAAELARAADVPVLGVN-------------LGHVGFLA-EAEAEDLDEAVERVVDRDYRVEE  134 (306)
T ss_pred             CH-HHHHHHHHhccCCCcEEEEe-------------cCCCceec-cCCHHHHHHHHHHHHcCCceEEE
Confidence            87 33333321  2467877653             37778988 57789999999999987654443

>PRK04885 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional

Probab=82.17  E-value=8.2  Score=30.26  Aligned_cols=60  Identities=22%  Similarity=0.203  Sum_probs=41.5

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHhccc----CCCCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCC
Q 029986           63 GYDIVISDVHMPDMDGFKLHEQVGLE----MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPK  138 (184)
Q Consensus        63 ~~dlvilD~~l~~~~g~~l~~~l~~~----~~~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~  138 (184)
                      .+|++|+    -++|| .+++..+..    .++|++-+.             .|-.+|+. .++.+++...+..+.++..
T Consensus        35 ~~Dlvi~----iGGDG-T~L~a~~~~~~~~~~iPilGIN-------------~G~lGFL~-~~~~~~~~~~l~~i~~g~y   95 (265)
T PRK04885         35 NPDIVIS----VGGDG-TLLSAFHRYENQLDKVRFVGVH-------------TGHLGFYT-DWRPFEVDKLVIALAKDPG   95 (265)
T ss_pred             CCCEEEE----ECCcH-HHHHHHHHhcccCCCCeEEEEe-------------CCCceecc-cCCHHHHHHHHHHHHcCCc
Confidence            3788887    36787 444544321    466776553             47788998 6888999999999988765


Q ss_pred             CCC
Q 029986          139 PFE  141 (184)
Q Consensus       139 ~~~  141 (184)
                      ...
T Consensus        96 ~i~   98 (265)
T PRK04885         96 QVV   98 (265)
T ss_pred             eEE
Confidence            433

>cd04729 NanE N-acetylmannosamine-6-phosphate epimerase (NanE) converts N-acetylmannosamine-6-phosphate to N-acetylglucosamine-6-phosphate

Probab=82.08  E-value=19  Score=27.03  Aligned_cols=72  Identities=19%  Similarity=0.304  Sum_probs=49.3

Q ss_pred             EEECCHHHHHHHHHhcCCCccEEEEeCC-C------CCCCHHHHHHHhcccCCCCEEEEEccCChHHHHHHHHcCCCceE
Q 029986           45 TKCNRAEIALDMLRMSKNGYDIVISDVH-M------PDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYL  117 (184)
Q Consensus        45 ~~~~~~~~~~~~l~~~~~~~dlvilD~~-l------~~~~g~~l~~~l~~~~~~~iIi~~~~~~~~~~~~a~~~ga~~~l  117 (184)
                      ..+.+.+++.....   .++|.+.+... .      ....+++.++.++...++|++....-.+.+.+.+++..|+++.+
T Consensus       128 v~v~t~~ea~~a~~---~G~d~i~~~~~g~t~~~~~~~~~~~~~l~~i~~~~~ipvia~GGI~~~~~~~~~l~~GadgV~  204 (219)
T cd04729         128 ADISTLEEALNAAK---LGFDIIGTTLSGYTEETAKTEDPDFELLKELRKALGIPVIAEGRINSPEQAAKALELGADAVV  204 (219)
T ss_pred             EECCCHHHHHHHHH---cCCCEEEccCccccccccCCCCCCHHHHHHHHHhcCCCEEEeCCCCCHHHHHHHHHCCCCEEE
Confidence            35566777655543   56888765321 1      12234678888865557899988777778999999999999887


Q ss_pred             eC
Q 029986          118 LK  119 (184)
Q Consensus       118 ~k  119 (184)
                      .-
T Consensus       205 vG  206 (219)
T cd04729         205 VG  206 (219)
T ss_pred             Ec
Confidence            53

This reaction is part of the pathway that allows the usage of sialic acid as a carbohydrate source. Sialic acids are a family of related sugars that are found as a component of glycoproteins, gangliosides, and other sialoglycoconjugates.

>PRK03692 putative UDP-N-acetyl-D-mannosaminuronic acid transferase; Provisional

Probab=81.74  E-value=16  Score=28.24  Aligned_cols=76  Identities=20%  Similarity=0.244  Sum_probs=50.4

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhc-CCeEEEEC----C---HHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKC-LYEVTKCN----R---AEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL   87 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~-~~~v~~~~----~---~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~   87 (184)
                      .+.+|.++...+...+.+.+.|+.. +..+.-+.    +   .++..+.+.  ..+||++++-+..|..+-+  +.+.+.
T Consensus       104 ~~~~v~llG~~~~v~~~a~~~l~~~y~l~i~g~~~Gyf~~~e~~~i~~~I~--~s~~dil~VglG~PkQE~~--~~~~~~  179 (243)
T PRK03692        104 EGTPVFLVGGKPEVLAQTEAKLRTQWNVNIVGSQDGYFTPEQRQALFERIH--ASGAKIVTVAMGSPKQEIF--MRDCRL  179 (243)
T ss_pred             cCCeEEEECCCHHHHHHHHHHHHHHhCCEEEEEeCCCCCHHHHHHHHHHHH--hcCCCEEEEECCCcHHHHH--HHHHHH
Confidence            3578999999999999999888654 55543222    1   233455555  4569999999999987654  444433


Q ss_pred             cCCCCEEE
Q 029986           88 EMDLPVIM   95 (184)
Q Consensus        88 ~~~~~iIi   95 (184)
                      ....++++
T Consensus       180 ~~~~~v~~  187 (243)
T PRK03692        180 VYPDALYM  187 (243)
T ss_pred             hCCCCEEE
Confidence            33445543

>cd05212 NAD_bind_m-THF_DH_Cyclohyd_like NAD(P) binding domain of methylene-tetrahydrofolate dehydrogenase and methylene-tetrahydrofolate dehydrogenase/cyclohydrolase

Probab=81.20  E-value=11  Score=26.47  Aligned_cols=56  Identities=23%  Similarity=0.274  Sum_probs=42.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHH-HHHHHHHhcCCCccEEEEeCCCCC
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAE-IALDMLRMSKNGYDIVISDVHMPD   75 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~-~~~~~l~~~~~~~dlvilD~~l~~   75 (184)
                      ++.+|.|+.......+.+..+|.+.|..+..++... +..+.++    ..|+|+.-..-+.
T Consensus        27 ~gk~v~VvGrs~~vG~pla~lL~~~gatV~~~~~~t~~l~~~v~----~ADIVvsAtg~~~   83 (140)
T cd05212          27 DGKKVLVVGRSGIVGAPLQCLLQRDGATVYSCDWKTIQLQSKVH----DADVVVVGSPKPE   83 (140)
T ss_pred             CCCEEEEECCCchHHHHHHHHHHHCCCEEEEeCCCCcCHHHHHh----hCCEEEEecCCCC
Confidence            577999999999999999999999999998887322 2222333    2699999876553

NAD(P) binding domains of methylene-tetrahydrofolate dehydrogenase (m-THF DH) and m-THF DH/cyclohydrolase bifunctional enzymes (m-THF DH/cyclohydrolase). M-THF is a versatile carrier of activated one-carbon units. The major one-carbon folate donors are N-5 methyltetrahydrofolate, N5,N10-m-THF, and N10-formayltetrahydrofolate. The oxidation of metabolic intermediate m-THF to m-THF requires the enzyme m-THF DH. In addition, most DHs also have an associated cyclohydrolase activity which catalyzes its hydrolysis to N10-formyltetrahydrofolate. m-THF DH is typically found as part of a multifunctional protein in eukaryotes. NADP-dependent m-THF DH in mammals, birds and yeast are components of a trifunctional enzyme with DH, cyclohydrolase, and synthetase activities. Certain eukaryotic cells also contain homodimeric bifunctional

>PRK14075 pnk inorganic polyphosphate/ATP-NAD kinase; Provisional

Probab=81.17  E-value=24  Score=27.48  Aligned_cols=96  Identities=14%  Similarity=0.180  Sum_probs=60.4

Q ss_pred             CeEEEEeCCH--HHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEE
Q 029986           18 LRVLVVDDDP--IWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIM   95 (184)
Q Consensus        18 ~~Ilivdd~~--~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi   95 (184)
                      |++.++..+.  ...+.+...|.+.|..+....+..       .....+|++|+    -++|| .+++..+.. ++||+-
T Consensus         1 m~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~-------~~~~~~d~vi~----iGGDG-T~L~a~~~~-~~Pilg   67 (256)
T PRK14075          1 MKLGIFYREEKEKEAKFLKEKISKEHEVVEFCEASA-------SGKVTADLIIV----VGGDG-TVLKAAKKV-GTPLVG   67 (256)
T ss_pred             CEEEEEeCccHHHHHHHHHHHHHHcCCeeEeecccc-------cccCCCCEEEE----ECCcH-HHHHHHHHc-CCCEEE
Confidence            3555554333  344556667777777766554322       11345788887    36777 344545433 788876


Q ss_pred             EEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCCC
Q 029986           96 MSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPF  140 (184)
Q Consensus        96 ~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~  140 (184)
                      +.             .|-.+|+. .+..+++...+..+.++....
T Consensus        68 in-------------~G~lGfl~-~~~~~~~~~~l~~~~~g~~~~   98 (256)
T PRK14075         68 FK-------------AGRLGFLS-SYTLEEIDRFLEDLKNWNFRE   98 (256)
T ss_pred             Ee-------------CCCCcccc-ccCHHHHHHHHHHHHcCCcEE
Confidence            63             45577887 688899999999988875443

>PRK05458 guanosine 5'-monophosphate oxidoreductase; Provisional

Probab=81.08  E-value=6.8  Score=31.73  Aligned_cols=54  Identities=15%  Similarity=0.071  Sum_probs=39.6

Q ss_pred             CccEEEEeCCCCCCC-HHHHHHHhccc-CCCCEEEEEccCChHHHHHHHHcCCCceE
Q 029986           63 GYDIVISDVHMPDMD-GFKLHEQVGLE-MDLPVIMMSVDGCTQDVMKGVTHGACNYL  117 (184)
Q Consensus        63 ~~dlvilD~~l~~~~-g~~l~~~l~~~-~~~~iIi~~~~~~~~~~~~a~~~ga~~~l  117 (184)
                      .+|+|.+|...+..+ -.+++++++.. ++.|||. .+-.+.+.+..+.++|++...
T Consensus       111 ~~d~i~iD~a~gh~~~~~e~I~~ir~~~p~~~vi~-g~V~t~e~a~~l~~aGad~i~  166 (326)
T PRK05458        111 TPEYITIDIAHGHSDSVINMIQHIKKHLPETFVIA-GNVGTPEAVRELENAGADATK  166 (326)
T ss_pred             CCCEEEEECCCCchHHHHHHHHHHHhhCCCCeEEE-EecCCHHHHHHHHHcCcCEEE
Confidence            469999999887644 46678888644 4566554 234578899999999999865

>cd04730 NPD_like 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites

Probab=80.98  E-value=22  Score=26.88  Aligned_cols=83  Identities=18%  Similarity=0.172  Sum_probs=51.7

Q ss_pred             HHHHHhcCCeEE-EECCHHHHHHHHHhcCCCccEEEEeCCCCC-------CCHHHHHHHhcccCCCCEEEEEccCChHHH
Q 029986           34 EKMLRKCLYEVT-KCNRAEIALDMLRMSKNGYDIVISDVHMPD-------MDGFKLHEQVGLEMDLPVIMMSVDGCTQDV  105 (184)
Q Consensus        34 ~~~L~~~~~~v~-~~~~~~~~~~~l~~~~~~~dlvilD~~l~~-------~~g~~l~~~l~~~~~~~iIi~~~~~~~~~~  105 (184)
                      ...+...+..+. .+.+.+.+....   +..+|.++++..-.+       ...+++++++++..++|+++...-.+.+.+
T Consensus        95 ~~~~~~~~i~~i~~v~~~~~~~~~~---~~gad~i~~~~~~~~G~~~~~~~~~~~~i~~i~~~~~~Pvi~~GGI~~~~~v  171 (236)
T cd04730          95 VERLKAAGIKVIPTVTSVEEARKAE---AAGADALVAQGAEAGGHRGTFDIGTFALVPEVRDAVDIPVIAAGGIADGRGI  171 (236)
T ss_pred             HHHHHHcCCEEEEeCCCHHHHHHHH---HcCCCEEEEeCcCCCCCCCccccCHHHHHHHHHHHhCCCEEEECCCCCHHHH
Confidence            333444444433 344555544433   245788887653211       135667888765557899888776666888


Q ss_pred             HHHHHcCCCceEeC
Q 029986          106 MKGVTHGACNYLLK  119 (184)
Q Consensus       106 ~~a~~~ga~~~l~k  119 (184)
                      .+++..|+++...-
T Consensus       172 ~~~l~~GadgV~vg  185 (236)
T cd04730         172 AAALALGADGVQMG  185 (236)
T ss_pred             HHHHHcCCcEEEEc
Confidence            89999999988643

NDP is a member of the NAD(P)H-dependent flavin oxidoreductase family that reduce a range of alternative electron acceptors. Most use FAD/FMN as a cofactor and NAD(P)H as electron donor. Some contain 4Fe-4S cluster to transfer electron from FAD to FMN.

>PRK06552 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional

Probab=80.91  E-value=22  Score=26.90  Aligned_cols=94  Identities=17%  Similarity=0.104  Sum_probs=61.1

Q ss_pred             HHHHhcC-CeEEEECCHHHHHHHHHh-cCCCccEEEEeCCCCCCCHHHHHHHhccc-CCCC--EEEEEccCChHHHHHHH
Q 029986           35 KMLRKCL-YEVTKCNRAEIALDMLRM-SKNGYDIVISDVHMPDMDGFKLHEQVGLE-MDLP--VIMMSVDGCTQDVMKGV  109 (184)
Q Consensus        35 ~~L~~~~-~~v~~~~~~~~~~~~l~~-~~~~~dlvilD~~l~~~~g~~l~~~l~~~-~~~~--iIi~~~~~~~~~~~~a~  109 (184)
                      ..|.+.+ .-|....+.+++....+. .+.+..  ++.+.|...++++.++.+++. +.-|  +|=..+=.+.+.+..+.
T Consensus         8 ~~l~~~~vi~vir~~~~~~a~~~~~al~~~Gi~--~iEit~~~~~a~~~i~~l~~~~~~~p~~~vGaGTV~~~~~~~~a~   85 (213)
T PRK06552          8 TKLKANGVVAVVRGESKEEALKISLAVIKGGIK--AIEVTYTNPFASEVIKELVELYKDDPEVLIGAGTVLDAVTARLAI   85 (213)
T ss_pred             HHHHHCCEEEEEECCCHHHHHHHHHHHHHCCCC--EEEEECCCccHHHHHHHHHHHcCCCCCeEEeeeeCCCHHHHHHHH
Confidence            4455444 345556667777766653 233333  666677777788888888543 2222  33334455678889999


Q ss_pred             HcCCCceEeCCCCHHHHHHHHH
Q 029986          110 THGACNYLLKPIRIKELRNIWQ  131 (184)
Q Consensus       110 ~~ga~~~l~kP~~~~~l~~~l~  131 (184)
                      ++||. |++.|....++.+..+
T Consensus        86 ~aGA~-FivsP~~~~~v~~~~~  106 (213)
T PRK06552         86 LAGAQ-FIVSPSFNRETAKICN  106 (213)
T ss_pred             HcCCC-EEECCCCCHHHHHHHH
Confidence            99998 8888988888866654

>PRK15484 lipopolysaccharide 1,2-N-acetylglucosaminetransferase; Provisional

Probab=80.43  E-value=30  Score=28.24  Aligned_cols=110  Identities=14%  Similarity=0.171  Sum_probs=64.5

Q ss_pred             CCeEEEEeCCH--------HHHHHHHHHHHhcCCeEEEEC--CHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhc
Q 029986           17 GLRVLVVDDDP--------IWLRILEKMLRKCLYEVTKCN--RAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVG   86 (184)
Q Consensus        17 ~~~Ilivdd~~--------~~~~~l~~~L~~~~~~v~~~~--~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~   86 (184)
                      ..+.+|+.+.+        ...+.+.......+..+....  ..++..+++.  .  .|++++-....+.-|..+++.+.
T Consensus       224 ~~~lvivG~g~~~~~~~~~~~~~~l~~~~~~l~~~v~~~G~~~~~~l~~~~~--~--aDv~v~pS~~~E~f~~~~lEAma  299 (380)
T PRK15484        224 NLKLVVVGDPTASSKGEKAAYQKKVLEAAKRIGDRCIMLGGQPPEKMHNYYP--L--ADLVVVPSQVEEAFCMVAVEAMA  299 (380)
T ss_pred             CeEEEEEeCCccccccchhHHHHHHHHHHHhcCCcEEEeCCCCHHHHHHHHH--h--CCEEEeCCCCccccccHHHHHHH
Confidence            45677776532        223334444444443443333  3455555554  2  58888755444444555566553


Q ss_pred             ccCCCCEEEEEccCChHHHHHHHHcCCCce-EeCCCCHHHHHHHHHHHHcC
Q 029986           87 LEMDLPVIMMSVDGCTQDVMKGVTHGACNY-LLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        87 ~~~~~~iIi~~~~~~~~~~~~a~~~ga~~~-l~kP~~~~~l~~~l~~~~~~  136 (184)
                        ..+|||.....    ...+.+..|..+| +..|.+.+++.+.+..++..
T Consensus       300 --~G~PVI~s~~g----g~~Eiv~~~~~G~~l~~~~d~~~la~~I~~ll~d  344 (380)
T PRK15484        300 --AGKPVLASTKG----GITEFVLEGITGYHLAEPMTSDSIISDINRTLAD  344 (380)
T ss_pred             --cCCCEEEeCCC----CcHhhcccCCceEEEeCCCCHHHHHHHHHHHHcC
Confidence              46888764322    2344566788888 56789999999999988763

>TIGR00007 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase

Probab=80.25  E-value=15  Score=27.77  Aligned_cols=66  Identities=18%  Similarity=0.289  Sum_probs=45.5

Q ss_pred             HHHHHHHHhcCCCcc-EEEEeCCCCCC---CHHHHHHHhcccCCCCEEEEEccCChHHHHHHHHcCCCceEe
Q 029986           51 EIALDMLRMSKNGYD-IVISDVHMPDM---DGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLL  118 (184)
Q Consensus        51 ~~~~~~l~~~~~~~d-lvilD~~l~~~---~g~~l~~~l~~~~~~~iIi~~~~~~~~~~~~a~~~ga~~~l~  118 (184)
                      .+..+.+.  +.+++ +++.|+.-.+.   -.+++++.+....++|+++=..-.+.+.+..+++.|+++.+.
T Consensus       148 ~~~~~~~~--~~g~~~ii~~~~~~~g~~~g~~~~~i~~i~~~~~ipvia~GGi~~~~di~~~~~~Gadgv~i  217 (230)
T TIGR00007       148 EELAKRLE--ELGLEGIIYTDISRDGTLSGPNFELTKELVKAVNVPVIASGGVSSIDDLIALKKLGVYGVIV  217 (230)
T ss_pred             HHHHHHHH--hCCCCEEEEEeecCCCCcCCCCHHHHHHHHHhCCCCEEEeCCCCCHHHHHHHHHCCCCEEEE
Confidence            44444444  44567 66677743321   226778888665678988877778888888999999999875

Examples of this enzyme in Actinobacteria have been found to be bifunctional, also possessing phosphoribosylanthranilate isomerase activity ; the trusted cutoff here has now been raised to 275.0 to exclude the bifunctional group, now represented by model TIGR01919. HisA from Lactococcus lactis was reported to be inactive (MEDLINE:93322317).

>COG2022 ThiG Uncharacterized enzyme of thiazole biosynthesis [Nucleotide transport and metabolism]

Probab=80.16  E-value=22  Score=27.38  Aligned_cols=97  Identities=20%  Similarity=0.168  Sum_probs=63.0

Q ss_pred             HHHHHhcCCeEEEECCH--HHHHHHHHhcCCCccEEEEeCCCCCCCHH-----HHHHHhcccCCCCEEEEEccCChHHHH
Q 029986           34 EKMLRKCLYEVTKCNRA--EIALDMLRMSKNGYDIVISDVHMPDMDGF-----KLHEQVGLEMDLPVIMMSVDGCTQDVM  106 (184)
Q Consensus        34 ~~~L~~~~~~v~~~~~~--~~~~~~l~~~~~~~dlvilD~~l~~~~g~-----~l~~~l~~~~~~~iIi~~~~~~~~~~~  106 (184)
                      .+.|-+.||.|..+.+.  --+.++..   .++ ..++-+.-|-++|.     ..++.+....++|||+=+.-..+..+.
T Consensus       123 ae~Lv~eGF~VlPY~~dD~v~arrLee---~Gc-aavMPl~aPIGSg~G~~n~~~l~iiie~a~VPviVDAGiG~pSdAa  198 (262)
T COG2022         123 AEQLVKEGFVVLPYTTDDPVLARRLEE---AGC-AAVMPLGAPIGSGLGLQNPYNLEIIIEEADVPVIVDAGIGTPSDAA  198 (262)
T ss_pred             HHHHHhCCCEEeeccCCCHHHHHHHHh---cCc-eEeccccccccCCcCcCCHHHHHHHHHhCCCCEEEeCCCCChhHHH
Confidence            45666779998865543  33333322   232 45666766655543     345666556689999998888899999


Q ss_pred             HHHHcCCCceEeC-----CCCHHHHHHHHHHHH
Q 029986          107 KGVTHGACNYLLK-----PIRIKELRNIWQHVA  134 (184)
Q Consensus       107 ~a~~~ga~~~l~k-----P~~~~~l~~~l~~~~  134 (184)
                      .+++.|+|+.+.-     --++-.+.++...+.
T Consensus       199 ~aMElG~DaVL~NTAiA~A~DPv~MA~Af~~Av  231 (262)
T COG2022         199 QAMELGADAVLLNTAIARAKDPVAMARAFALAV  231 (262)
T ss_pred             HHHhcccceeehhhHhhccCChHHHHHHHHHHH
Confidence            9999999999853     224445555554443

>PF04131 NanE: Putative N-acetylmannosamine-6-phosphate epimerase; InterPro: IPR007260 This family represents a putative ManNAc-6-P-to-GlcNAc-6P epimerase in the N-acetylmannosamine (ManNAc) utilization pathway found mainly in pathogenic bacteria for the reaction: N-acyl-D-glucosamine 6-phosphate = N-acyl-D-mannosamine 6-phosphate It is probably encoded by the yhcJ gene []

Probab=80.03  E-value=12  Score=27.83  Aligned_cols=70  Identities=11%  Similarity=0.038  Sum_probs=49.0

Q ss_pred             CCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCC--CCHHHHHHHhcccCCCCEEEEEccCChHHHHHHHHcCCCceE
Q 029986           41 LYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPD--MDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYL  117 (184)
Q Consensus        41 ~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~--~~g~~l~~~l~~~~~~~iIi~~~~~~~~~~~~a~~~ga~~~l  117 (184)
                      ++.|....+.+++.+.+.   .+.|+|=+|...-.  .+--+++++++...   .+++++-++.+....+.++|+| ++
T Consensus        45 ~~~V~ITPT~~ev~~l~~---aGadIIAlDaT~R~Rp~~l~~li~~i~~~~---~l~MADist~ee~~~A~~~G~D-~I  116 (192)
T PF04131_consen   45 DSDVYITPTLKEVDALAE---AGADIIALDATDRPRPETLEELIREIKEKY---QLVMADISTLEEAINAAELGFD-II  116 (192)
T ss_dssp             TSS--BS-SHHHHHHHHH---CT-SEEEEE-SSSS-SS-HHHHHHHHHHCT---SEEEEE-SSHHHHHHHHHTT-S-EE
T ss_pred             CCCeEECCCHHHHHHHHH---cCCCEEEEecCCCCCCcCHHHHHHHHHHhC---cEEeeecCCHHHHHHHHHcCCC-EE
Confidence            467888888899988876   45899999985532  55677888886544   7788888999999999999976 65

; GO: 0047465 N-acylglucosamine-6-phosphate 2-epimerase activity, 0006051 N-acetylmannosamine metabolic process; PDB: 1Y0E_B 3IGS_A 1YXY_A 3Q58_B.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	184
2ayx_A	254	Solution Structure Of The E.Coli Rcsc C-Terminus (R		7e-12
2ayz_A	133	Solution Structure Of The E.Coli Rcsc C-Terminus (R		8e-12
1ab6_A	125	Structure Of Chey Mutant F14n, V86t Length = 125		7e-11
3olv_A	129	Structural And Functional Effects Of Substitution A		8e-11
1ab5_A	125	Structure Of Chey Mutant F14n, V21t Length = 125		8e-11
1ymv_A	129	Signal Transduction Protein Chey Mutant With Phe 14		9e-11
1d4z_A	128	Crystal Structure Of Chey-95iv, A Hyperactive Chey		1e-10
3fft_A	128	Crystal Structure Of Chey Double Mutant F14e, E89r		1e-10
1cye_A	129	Three Dimensional Structure Of Chemotactic Che Y Pr		2e-10
3ffx_A	128	Crystal Structure Of Chey Triple Mutant F14e, N59r,		2e-10
1ymu_A	130	Signal Transduction Protein Chey Mutant With Met 17		2e-10
3myy_A	128	Structure Of E. Coli Chey Mutant A113p Bound To Ber		2e-10
1eay_A	128	Chey-Binding (P2) Domain Of Chea In Complex With Ch		2e-10
1djm_A	129	Solution Structure Of Bef3-Activated Chey From Esch		2e-10
1cey_A	128	Assignments, Secondary Structure, Global Fold, And		2e-10
3olw_A	129	Structural And Functional Effects Of Substitution A		2e-10
3oo0_A	129	Structure Of Apo Chey A113p Length = 129		2e-10
3oly_A	129	Structural And Functional Effects Of Substitution A		2e-10
1mih_A	129	A Role For Chey Glu 89 In Chez-Mediated Dephosphory		3e-10
3fgz_A	128	Crystal Structure Of Chey Triple Mutant F14e, N59m,		3e-10
3olx_A	129	Structural And Functional Effects Of Substitution A		3e-10
3ffw_A	128	Crystal Structure Of Chey Triple Mutant F14q, N59k,		5e-10
1vlz_A	128	Uncoupled Phosphorylation And Activation In Bacteri		6e-10
3f7n_A	128	Crystal Structure Of Chey Triple Mutant F14e, N59m,		6e-10
5chy_A	128	Structure Of Chemotaxis Protein Chey Length = 128		7e-10
3rvj_A	132	Structure Of The Chey-Bef3 Complex With Substitutio		7e-10
3rvp_A	132	Structure Of The Chey-Bef3 Complex With Substitutio		8e-10
3t6k_A	136	Crystal Structure Of A Hypothetical Response Regula		9e-10
1jbe_A	128	1.08 A Structure Of Apo-Chey Reveals Meta-Active Co		1e-09
1ehc_A	128	Structure Of Signal Transduction Protein Chey Lengt		1e-09
1c4w_A	128	1.9 A Structure Of A-Thiophosphonate Modified Chey		1e-09
1e6m_A	128	Two-Component Signal Transduction System D57a Mutan		1e-09
1e6l_A	127	Two-Component Signal Transduction System D13a Mutan		1e-09
3rvl_A	132	Structure Of The Chey-Bef3 Complex With Substitutio		1e-09
1e6k_A	130	Two-Component Signal Transduction System D12a Mutan		1e-09
1zdm_A	129	Crystal Structure Of Activated Chey Bound To Xe Len		1e-09
3rvn_A	132	Structure Of The Chey-Bef3 Complex With Substitutio		2e-09
1udr_A	129	Chey Mutant With Lys 91 Replaced By Asp, Lys 92 Rep		2e-09
2che_A	128	Structure Of The Mg2+-Bound Form Of Chey And Mechan		3e-09
6chy_A	128	Structure Of Chemotaxis Protein Chey Length = 128		3e-09
2fka_A	129	Crystal Structure Of Mg(2+) And Bef(3)(-)-Bound Che		3e-09
2id7_A	128	1.75 A Structure Of T87i Phosphono-Chey Length = 12		4e-09
1w25_A	459	Response Regulator Pled In Complex With C-digmp Len		8e-09
2wb4_A	459	Activated Diguanylate Cyclase Pled In Complex With		9e-09
3r0j_A	250	Structure Of Phop From Mycobacterium Tuberculosis L		1e-08
2id9_A	128	1.85 A Structure Of T87iY106W PHOSPHONO-Chey Length		2e-08
3m6m_D	143	Crystal Structure Of Rpff Complexed With Rec Domain		2e-08
2chy_A	128	Three-Dimensional Structure Of Chey, The Response R		2e-08
3f6p_A	120	Crystal Structure Of Unphosphorelated Receiver Doma		2e-08
3dge_C	122	Structure Of A Histidine Kinase-response Regulator		2e-08
2zwm_A	130	Crystal Structure Of Yycf Receiver Domain From Baci		3e-08
1hey_A	128	Investigating The Structural Determinants Of The P2		4e-08
3gt7_A	154	Crystal Structure Of Signal Receiver Domain Of Sign		8e-08
1qkk_A	155	Crystal Structure Of The Receiver Domain And Linker		1e-07
1l5y_A	155	Crystal Structure Of Mg2+ / Bef3-bound Receiver Dom		1e-07
3gl9_A	122	The Structure Of A Histidine Kinase-Response Regula		2e-07
1u8t_A	128	Crystal Structure Of Chey D13k Y106w Alone And In C		2e-07
3to5_A	134	High Resolution Structure Of Chey3 From Vibrio Chol		2e-07
3nhz_A	125	Structure Of N-Terminal Domain Of Mtra Length = 125		3e-07
3gwg_A	129	Crystal Structure Of Chey Of Helicobacter Pylori Le		4e-07
3h1g_A	129	Crystal Structure Of Chey Mutant T84a Of Helicobact		4e-07
1nxo_A	120	Micarec Ph7.0 Length = 120		8e-07
2oqr_A	230	The Structure Of The Response Regulator Regx3 From		8e-07
1p6u_A	129	Nmr Structure Of The Bef3-Activated Structure Of Th		3e-06
3h1f_A	129	Crystal Structure Of Chey Mutant D53a Of Helicobact		3e-06
1s8n_A	205	Crystal Structure Of Rv1626 From Mycobacterium Tube		4e-06
1dc7_A	124	Structure Of A Transiently Phosphorylated "switch"		4e-06
1yio_A	208	Crystallographic Structure Of Response Regulator St		4e-06
1krw_A	124	Solution Structure And Backbone Dynamics Of Beryllo		5e-06
1j56_A	124	Minimized Average Structure Of Beryllofluoride-Acti		5e-06
1nxt_A	120	Micarec Ph 4.0 Length = 120		5e-06
1mvo_A	136	Crystal Structure Of The Phop Receiver Domain From		6e-06
1ys6_A	233	Crystal Structure Of The Response Regulatory Protei		8e-06
3eq2_A	394	Structure Of Hexagonal Crystal Form Of Pseudomonas		9e-06
3nnn_A	122	Bef3 Activated Drrd Receiver Domain Length = 122		1e-05
3f7a_A	394	Structure Of Orthorhombic Crystal Form Of Pseudomon		1e-05
3q9s_A	249	Crystal Structure Of Rra(1-215) From Deinococcus Ra		2e-05
1dc8_A	124	Structure Of A Transiently Phosphorylated "switch"		3e-05
1u0s_Y	118	Chemotaxis Kinase Chea P2 Domain In Complex With Re		4e-05
3tmy_A	120	Chey From Thermotoga Maritima (Mn-Iii) Length = 120		4e-05
2pkx_A	121	E.Coli Response Regulator Phop Receiver Domain Leng		6e-05
3jte_A	143	Crystal Structure Of Response Regulator Receiver Do		6e-05
1zh2_A	121	Crystal Structure Of The Calcium-Bound Receiver Dom		1e-04
3mm4_A	206	Crystal Structure Of The Receiver Domain Of The His		1e-04
3eod_A	130	Crystal Structure Of N-Terminal Domain Of E. Coli R		2e-04
1srr_A	124	Crystal Structure Of A Phosphatase Resistant Mutant		2e-04
1f51_E	119	A Transient Interaction Between Two Phosphorelay Pr		2e-04
1m5t_A	124	Crystal Structure Of The Response Regulator Divk Le		2e-04
3cu5_A	141	Crystal Structure Of A Two Component Transcriptiona		2e-04
2jvk_A	132	Nmr Solution Structure Of The Hyper-Sporulation Res		3e-04
1zes_A	125	Bef3- Activated Phob Receiver Domain Length = 125		3e-04
1b00_A	127	Phob Receiver Domain From Escherichia Coli Length =		3e-04
3q15_C	126	Crystal Structure Of Raph Complexed With Spo0f Leng		3e-04
1kgs_A	225	Crystal Structure At 1.50 A Of An OmprPHOB HOMOLOG		3e-04
1dz3_A	130	Domain-Swapping In The Sporulation Response Regulat		4e-04
1pux_A	124	Nmr Solution Structure Of Bef3-Activated Spo0f, 20		4e-04
1dbw_A	126	Crystal Structure Of Fixj-N Length = 126		4e-04
2jvj_A	132	Nmr Solution Structure Of The Hyper-Sporulation Res		8e-04
3c97_A	140	Crystal Structure Of The Response Regulator Receive		9e-04

>pdb|2AYX|A Chain A, Solution Structure Of The E.Coli Rcsc C-Terminus (Residues 700-949) Containing Linker Region And Phosphoreceiver Domain Length = 254

Iteration: 1
 Score = 66.6 bits (161), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 46/140 (32%), Positives = 78/140 (55%), Gaps = 5/140 (3%)
Query: 5   SSSVAVSDQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGY 64
           S+  AVSD     + +LVVDD PI  R+L   L    Y+    N    AL++L  SKN  
Sbjct: 119 STDKAVSDN--DDMMILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVL--SKNHI 174
Query: 65  DIVISDVHMPDMDGFKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRI 123
           DIV+SDV+MP+MDG++L +++  L + LPVI ++ +   ++  + +  G  + L KP+ +
Sbjct: 175 DIVLSDVNMPNMDGYRLTQRIRQLGLTLPVIGVTANALAEEKQRCLESGMDSCLSKPVTL 234
Query: 124 KELRNIWQHVAQQPKPFEES 143
             ++      A++ +   +S
Sbjct: 235 DVIKQTLTLYAERVRKSRDS 254

>pdb|2AYZ|A Chain A, Solution Structure Of The E.Coli Rcsc C-Terminus (Residues 817-949) Containing Phosphoreceiver Domain Length = 133

Iteration: 1
 Score = 66.6 bits (161), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 45/136 (33%), Positives = 76/136 (55%), Gaps = 5/136 (3%)
Query: 9   AVSDQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVI 68
           AVSD     + +LVVDD PI  R+L   L    Y+    N    AL++L  SKN  DIV+
Sbjct: 2   AVSDN--DDMMILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVL--SKNHIDIVL 57
Query: 69  SDVHMPDMDGFKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           SDV+MP+MDG++L +++  L + LPVI ++ +   ++  + +  G  + L KP+ +  ++
Sbjct: 58  SDVNMPNMDGYRLTQRIRQLGLTLPVIGVTANALAEEKQRCLESGMDSCLSKPVTLDVIK 117
Query: 128 NIWQHVAQQPKPFEES 143
                 A++ +   +S
Sbjct: 118 QTLTLYAERVRKSRDS 133

>pdb|1AB6|A Chain A, Structure Of Chey Mutant F14n, V86t Length = 125

Iteration: 1
 Score = 63.5 bits (153), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 36/114 (31%), Positives = 60/114 (52%), Gaps = 6/114 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD+    RI+  +L++  +       AE  +D L ++   GY  VISD +MP+M
Sbjct: 2   LKFLVVDDNSTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISDWNMPNM 59
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           DG +L + +   G    LPV+M + +   ++++     GA  Y++KP     L 
Sbjct: 60  DGLELLKTIRADGAMSALPVLMTTAEAKKENIIAAAQAGASGYVVKPFTAATLE 113

>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 = 63.2 bits (152), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 37/114 (32%), Positives = 61/114 (53%), Gaps = 6/114 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD     RI+  +L++  +       AE  +D L ++   GY  VISD +MP+M
Sbjct: 6   LKFLVVDDFSTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISDWNMPNM 63
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           DG +L + +   G    LPV+M++V+   ++++     GA  Y++KP     L 
Sbjct: 64  DGLELLKTIRADGAMSALPVLMVTVEAKKENIIAAAQAGASGYVVKPFTAATLE 117

>pdb|1AB5|A Chain A, Structure Of Chey Mutant F14n, V21t Length = 125

Iteration: 1
 Score = 63.2 bits (152), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 36/114 (31%), Positives = 60/114 (52%), Gaps = 6/114 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD+    RI   +L++  +       AE  +D L ++   GY  VISD +MP+M
Sbjct: 2   LKFLVVDDNSTMRRITRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISDWNMPNM 59
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           DG +L + +   G    LPV+M++ +   ++++     GA  Y++KP     L 
Sbjct: 60  DGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLE 113

>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 = 63.2 bits (152), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 35/108 (32%), Positives = 59/108 (54%), Gaps = 6/108 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD     RI+  +L++  +       AE  +D L ++   GY  VISD +MP+M
Sbjct: 6   LKFLVVDDGGTGRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISDWNMPNM 63
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPI 121
           DG +L + +   G    LPV+M++ +   ++++     GA  Y++KP 
Sbjct: 64  DGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPF 111

>pdb|1D4Z|A Chain A, Crystal Structure Of Chey-95iv, A Hyperactive Chey Mutant Length = 128

Iteration: 1
 Score = 62.4 bits (150), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 37/114 (32%), Positives = 60/114 (52%), Gaps = 6/114 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD     RI+  +L++  +       AE  +D L ++   GY  VISD +MP+M
Sbjct: 5   LKFLVVDDFSTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISDWNMPNM 62
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           DG +L + +   G    LPV+M++ +   ++V+     GA  Y++KP     L 
Sbjct: 63  DGLELLKTIRADGAMSALPVLMVTAEAKKENVIAAAQAGASGYVVKPFTAATLE 116

>pdb|3FFT|A Chain A, Crystal Structure Of Chey Double Mutant F14e, E89r Complexed With Bef3- And Mn2+ Length = 128

Iteration: 1
 Score = 62.4 bits (150), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 35/108 (32%), Positives = 59/108 (54%), Gaps = 6/108 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD+    RI+  +L++  +       AE  +D L ++   GY  VISD +MP+M
Sbjct: 5   LKFLVVDDESTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISDWNMPNM 62
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPI 121
           DG +L + +   G    LPV+M++     ++++     GA  Y++KP 
Sbjct: 63  DGLELLKTIRADGAMSALPVLMVTARAKKENIIAAAQAGASGYVVKPF 110

>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 = 62.0 bits (149), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 35/108 (32%), Positives = 59/108 (54%), Gaps = 6/108 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD     RI+  +L++  +       AE  +D L ++   GY  VISD +MP+M
Sbjct: 6   LKFLVVDDFSTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISDWNMPNM 63
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPI 121
           DG +L + +   G    LPV+M++ +   ++++     GA  Y++KP 
Sbjct: 64  DGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPF 111

>pdb|3FFX|A Chain A, Crystal Structure Of Chey Triple Mutant F14e, N59r, E89h Complexed With Bef3- And Mn2+ Length = 128

Iteration: 1
 Score = 62.0 bits (149), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 35/108 (32%), Positives = 58/108 (53%), Gaps = 6/108 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD+    RI+  +L++  +       AE  +D L ++   GY  VISD  MP+M
Sbjct: 5   LKFLVVDDESTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISDWRMPNM 62
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPI 121
           DG +L + +   G    LPV+M++     ++++     GA  Y++KP 
Sbjct: 63  DGLELLKTIRADGAMSALPVLMVTAHAKKENIIAAAQAGASGYVVKPF 110

>pdb|1YMU|A Chain A, Signal Transduction Protein Chey Mutant With Met 17 Replaced By Gly (M17g) Length = 130

Iteration: 1
 Score = 62.0 bits (149), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 35/108 (32%), Positives = 59/108 (54%), Gaps = 6/108 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD     RI+  +L++  +       AE  +D L ++   GY  VISD +MP+M
Sbjct: 7   LKFLVVDDFSTGRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISDWNMPNM 64
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPI 121
           DG +L + +   G    LPV+M++ +   ++++     GA  Y++KP 
Sbjct: 65  DGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPF 112

>pdb|3MYY|A Chain A, Structure Of E. Coli Chey Mutant A113p Bound To Beryllium Fluoride Length = 128

Iteration: 1
 Score = 62.0 bits (149), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 35/108 (32%), Positives = 59/108 (54%), Gaps = 6/108 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD     RI+  +L++  +       AE  +D L ++   GY  VISD +MP+M
Sbjct: 5   LKFLVVDDFSTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISDWNMPNM 62
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPI 121
           DG +L + +   G    LPV+M++ +   ++++     GA  Y++KP 
Sbjct: 63  DGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPF 110

>pdb|1EAY|A Chain A, Chey-Binding (P2) Domain Of Chea In Complex With Chey From Escherichia Coli Length = 128

Iteration: 1
 Score = 62.0 bits (149), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 36/114 (31%), Positives = 60/114 (52%), Gaps = 6/114 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD     RI+  +L++  +       AE  +D L ++   GY  VISD +MP+M
Sbjct: 5   LKFLVVDDFSTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISDWNMPNM 62
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           DG +L + +   G    LPV+M++ +   ++++     GA  Y++KP     L 
Sbjct: 63  DGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLE 116

>pdb|1DJM|A Chain A, Solution Structure Of Bef3-Activated Chey From Escherichia Coli Length = 129

Iteration: 1
 Score = 62.0 bits (149), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 36/114 (31%), Positives = 60/114 (52%), Gaps = 6/114 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD     RI+  +L++  +       AE  +D L ++   GY  VISD +MP+M
Sbjct: 6   LKFLVVDDFSTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISDWNMPNM 63
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           DG +L + +   G    LPV+M++ +   ++++     GA  Y++KP     L 
Sbjct: 64  DGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLE 117

>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 = 62.0 bits (149), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 36/114 (31%), Positives = 60/114 (52%), Gaps = 6/114 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD     RI+  +L++  +       AE  +D L ++   GY  VISD +MP+M
Sbjct: 5   LKFLVVDDFSTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISDWNMPNM 62
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           DG +L + +   G    LPV+M++ +   ++++     GA  Y++KP     L 
Sbjct: 63  DGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLE 116

>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 = 62.0 bits (149), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 36/114 (31%), Positives = 60/114 (52%), Gaps = 6/114 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD     RI+  +L++  +       AE  +D L ++   GY  VISD +MP+M
Sbjct: 6   LKFLVVDDFSTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISDWNMPNM 63
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           DG +L + +   G    LPV+M++ +   ++++     GA  Y++KP     L 
Sbjct: 64  DGLELLKTIRADGAMSALPVLMVTTEAKKENIIAAAQAGASGYVVKPFTAATLE 117

>pdb|3OO0|A Chain A, Structure Of Apo Chey A113p Length = 129

Iteration: 1
 Score = 61.6 bits (148), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 35/108 (32%), Positives = 59/108 (54%), Gaps = 6/108 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD     RI+  +L++  +       AE  +D L ++   GY  VISD +MP+M
Sbjct: 6   LKFLVVDDFSTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISDWNMPNM 63
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPI 121
           DG +L + +   G    LPV+M++ +   ++++     GA  Y++KP 
Sbjct: 64  DGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPF 111

>pdb|3OLY|A Chain A, Structural And Functional Effects Of Substitution At Position T+1 In Chey: Cheya88m-Bef3-Mn Complex Length = 129

Iteration: 1
 Score = 61.6 bits (148), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 36/114 (31%), Positives = 61/114 (53%), Gaps = 6/114 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD     RI+  +L++  +       AE  +D L ++   GY  VISD +MP+M
Sbjct: 6   LKFLVVDDFSTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISDWNMPNM 63
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           DG +L + +   G    LPV+M++++   ++++     GA  Y++KP     L 
Sbjct: 64  DGLELLKTIRADGAMSALPVLMVTMEAKKENIIAAAQAGASGYVVKPFTAATLE 117

>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 = 61.2 bits (147), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 35/108 (32%), Positives = 58/108 (53%), Gaps = 6/108 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD     RI+  +L++  +       AE  +D L ++   GY  VISD  MP+M
Sbjct: 6   LKFLVVDDFSTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISDWRMPNM 63
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPI 121
           DG +L + +   G    LPV+M++ +   ++++     GA  Y++KP 
Sbjct: 64  DGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPF 111

>pdb|3FGZ|A Chain A, Crystal Structure Of Chey Triple Mutant F14e, N59m, E89r Complexed With Bef3- And Mn2+ Length = 128

Iteration: 1
 Score = 61.2 bits (147), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 35/108 (32%), Positives = 58/108 (53%), Gaps = 6/108 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD+    RI+  +L++  +       AE  +D L ++   GY  VISD  MP+M
Sbjct: 5   LKFLVVDDESTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISDWMMPNM 62
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPI 121
           DG +L + +   G    LPV+M++     ++++     GA  Y++KP 
Sbjct: 63  DGLELLKTIRADGAMSALPVLMVTARAKKENIIAAAQAGASGYVVKPF 110

>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 = 61.2 bits (147), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 36/114 (31%), Positives = 60/114 (52%), Gaps = 6/114 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD     RI+  +L++  +       AE  +D L ++   GY  VISD +MP+M
Sbjct: 6   LKFLVVDDFSTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISDWNMPNM 63
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           DG +L + +   G    LPV+M++ +   ++++     GA  Y++KP     L 
Sbjct: 64  DGLELLKTIRADGAMSALPVLMVTSEAKKENIIAAAQAGASGYVVKPFTAATLE 117

>pdb|3FFW|A Chain A, Crystal Structure Of Chey Triple Mutant F14q, N59k, E89y Complexed With Bef3- And Mn2+ Length = 128

Iteration: 1
 Score = 60.5 bits (145), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 35/108 (32%), Positives = 57/108 (52%), Gaps = 6/108 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD     RI+  +L++  +       AE  +D L ++   GY  VISD  MP+M
Sbjct: 5   LKFLVVDDQSTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISDWKMPNM 62
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPI 121
           DG +L + +   G    LPV+M++     ++++     GA  Y++KP 
Sbjct: 63  DGLELLKTIRADGAMSALPVLMVTAYAKKENIIAAAQAGASGYVVKPF 110

>pdb|1VLZ|A Chain A, Uncoupled Phosphorylation And Activation In Bacterial Chemotaxis: The 2.1 Angstrom Structure Of A Threonine To Isoleucine Mutant At Position 87 Of Chey Length = 128

Iteration: 1
 Score = 60.1 bits (144), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 35/108 (32%), Positives = 58/108 (53%), Gaps = 6/108 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD     RI+  +L++  +       AE  +D L ++   GY  VISD +MP+M
Sbjct: 5   LKFLVVDDFSTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISDWNMPNM 62
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPI 121
           DG +L + +   G    LPV+M+  +   ++++     GA  Y++KP 
Sbjct: 63  DGLELLKTIRADGAMSALPVLMVIAEAKKENIIAAAQAGASGYVVKPF 110

>pdb|3F7N|A Chain A, Crystal Structure Of Chey Triple Mutant F14e, N59m, E89l Complexed With Bef3- And Mn2+ Length = 128

Iteration: 1
 Score = 60.1 bits (144), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 36/114 (31%), Positives = 59/114 (51%), Gaps = 6/114 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD+    RI+  +L++  +       AE  +D L ++   GY  VISD  MP+M
Sbjct: 5   LKFLVVDDESTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISDWMMPNM 62
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           DG +L + +   G    LPV+M++     ++++     GA  Y++KP     L 
Sbjct: 63  DGLELLKTIRADGAMSALPVLMVTALAKKENIIAAAQAGASGYVVKPFTAATLE 116

>pdb|5CHY|A Chain A, Structure Of Chemotaxis Protein Chey Length = 128

Iteration: 1
 Score = 60.1 bits (144), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 35/114 (30%), Positives = 60/114 (52%), Gaps = 6/114 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD     RI+  +L++  +       AE  +D L ++   GY  VISD +MP+M
Sbjct: 5   LKFLVVDDFSTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISDWNMPNM 62
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           DG +L + +   G    LPV+M++ +   ++++     GA  +++KP     L 
Sbjct: 63  DGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGWVVKPFTAATLE 116

>pdb|3RVJ|A Chain A, Structure Of The Chey-Bef3 Complex With Substitutions At 59 And 89: N59d And E89q Length = 132

Iteration: 1
 Score = 60.1 bits (144), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 36/114 (31%), Positives = 58/114 (50%), Gaps = 6/114 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD     RI+  +L++  +       AE  +D L ++   GY  VISD  MP+M
Sbjct: 9   LKFLVVDDFSTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISDWDMPNM 66
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           DG +L + +   G    LPV+M++     ++++     GA  Y++KP     L 
Sbjct: 67  DGLELLKTIRADGAMSALPVLMVTAQAKKENIIAAAQAGASGYVVKPFTAATLE 120

>pdb|3RVP|A Chain A, Structure Of The Chey-Bef3 Complex With Substitutions At 59 And 89: N59d And E89k Length = 132

Iteration: 1
 Score = 59.7 bits (143), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 36/114 (31%), Positives = 58/114 (50%), Gaps = 6/114 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD     RI+  +L++  +       AE  +D L ++   GY  VISD  MP+M
Sbjct: 9   LKFLVVDDFSTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISDWDMPNM 66
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           DG +L + +   G    LPV+M++     ++++     GA  Y++KP     L 
Sbjct: 67  DGLELLKTIRADGAMSALPVLMVTAKAKKENIIAAAQAGASGYVVKPFTAATLE 120

>pdb|3T6K|A Chain A, Crystal Structure Of A Hypothetical Response Regulator (Caur_3799) From Chloroflexus Aurantiacus J-10-Fl At 1.86 A Resolution Length = 136

Iteration: 1
 Score = 59.7 bits (143), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 39/110 (35%), Positives = 58/110 (52%), Gaps = 5/110 (4%)
Query: 20  VLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGF 79
           +L+VDDD      LE +LR   YEV +    E AL   ++ KN  D +I DV +P +DG+
Sbjct: 7   LLIVDDDDTVAEXLELVLRGAGYEVRRAASGEEALQ--QIYKNLPDALICDVLLPGIDGY 64
Query: 80  KLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
            L ++V    L   LP++ ++  G     + G   GA +YL KP   +EL
Sbjct: 65  TLCKRVRQHPLTKTLPILXLTAQGDISAKIAGFEAGANDYLAKPFEPQEL 114

>pdb|1JBE|A Chain A, 1.08 A Structure Of Apo-Chey Reveals Meta-Active Conformation Length = 128

Iteration: 1
 Score = 59.7 bits (143), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 34/108 (31%), Positives = 58/108 (53%), Gaps = 6/108 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD     RI+  +L++  +       AE  +D L ++   GY  VISD +MP+M
Sbjct: 5   LKFLVVDDFSTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISDWNMPNM 62
Query: 77  DGFKLHEQVGLEM---DLPVIMMSVDGCTQDVMKGVTHGACNYLLKPI 121
           DG +L + +        LPV+M++ +   ++++     GA  Y++KP 
Sbjct: 63  DGLELLKTIRAXXAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPF 110

>pdb|1EHC|A Chain A, Structure Of Signal Transduction Protein Chey Length = 128

Iteration: 1
 Score = 59.7 bits (143), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 34/108 (31%), Positives = 58/108 (53%), Gaps = 6/108 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVD      RI+  +L++  +       AE  +D L ++   GY  VISD +MP+M
Sbjct: 5   LKFLVVDKFSTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISDWNMPNM 62
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPI 121
           DG +L + +   G    LPV+M++ +   ++++     GA  Y++KP 
Sbjct: 63  DGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPF 110

>pdb|1C4W|A Chain A, 1.9 A Structure Of A-Thiophosphonate Modified Chey D57c Length = 128

Iteration: 1
 Score = 59.3 bits (142), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 35/114 (30%), Positives = 59/114 (51%), Gaps = 6/114 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD     RI+  +L++  +       AE  +D L ++   GY  VIS  +MP+M
Sbjct: 5   LKFLVVDDFSTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISXWNMPNM 62
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           DG +L + +   G    LPV+M++ +   ++++     GA  Y++KP     L 
Sbjct: 63  DGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLE 116

>pdb|1E6M|A Chain A, Two-Component Signal Transduction System D57a Mutant Of Chey Length = 128

Iteration: 1
 Score = 59.3 bits (142), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 35/114 (30%), Positives = 59/114 (51%), Gaps = 6/114 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD     RI+  +L++  +       AE  +D L ++   GY  VIS  +MP+M
Sbjct: 5   LKFLVVDDFSTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISAWNMPNM 62
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           DG +L + +   G    LPV+M++ +   ++++     GA  Y++KP     L 
Sbjct: 63  DGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLE 116

>pdb|1E6L|A Chain A, Two-Component Signal Transduction System D13a Mutant Of Chey Length = 127

Iteration: 1
 Score = 59.3 bits (142), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 35/114 (30%), Positives = 59/114 (51%), Gaps = 6/114 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVD      RI+  +L++  +       AE  +D L ++   GY  VISD +MP+M
Sbjct: 4   LKFLVVDAFSTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISDWNMPNM 61
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           DG +L + +   G    LPV+M++ +   ++++     GA  Y++KP     L 
Sbjct: 62  DGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLE 115

>pdb|3RVL|A Chain A, Structure Of The Chey-Bef3 Complex With Substitutions At 59 And 89: N59d And E89r Length = 132

Iteration: 1
 Score = 59.3 bits (142), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 36/113 (31%), Positives = 58/113 (51%), Gaps = 6/113 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD     RI+  +L++  +       AE  +D L ++   GY  VISD  MP+M
Sbjct: 9   LKFLVVDDFSTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISDWDMPNM 66
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
           DG +L + +   G    LPV+M++     ++++     GA  Y++KP     L
Sbjct: 67  DGLELLKTIRADGAMSALPVLMVTARAKKENIIAAAQAGASGYVVKPFTAATL 119

>pdb|1E6K|A Chain A, Two-Component Signal Transduction System D12a Mutant Of Chey Length = 130

Iteration: 1
 Score = 59.3 bits (142), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 34/108 (31%), Positives = 58/108 (53%), Gaps = 6/108 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVV D     RI+  +L++  +       AE  +D L ++   GY  VISD +MP+M
Sbjct: 7   LKFLVVADFSTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISDWNMPNM 64
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPI 121
           DG +L + +   G    LPV+M++ +   ++++     GA  Y++KP 
Sbjct: 65  DGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPF 112

>pdb|1ZDM|A Chain A, Crystal Structure Of Activated Chey Bound To Xe Length = 129

Iteration: 1
 Score = 58.9 bits (141), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 35/114 (30%), Positives = 59/114 (51%), Gaps = 6/114 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD     RI+  +L++  +       AE  +D L ++   GY  VIS  +MP+M
Sbjct: 6   LKFLVVDDFSTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISXWNMPNM 63
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           DG +L + +   G    LPV+M++ +   ++++     GA  Y++KP     L 
Sbjct: 64  DGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLE 117

>pdb|3RVN|A Chain A, Structure Of The Chey-Bef3 Complex With Substitutions At 59 And 89: N59d And E89y Length = 132

Iteration: 1
 Score = 58.9 bits (141), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 36/114 (31%), Positives = 58/114 (50%), Gaps = 6/114 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD     RI+  +L++  +       AE  +D L ++   GY  VISD  MP+M
Sbjct: 9   LKFLVVDDFSTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISDWDMPNM 66
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           DG +L + +   G    LPV+M++     ++++     GA  Y++KP     L 
Sbjct: 67  DGLELLKTIRADGAMSALPVLMVTAYAKKENIIAAAQAGASGYVVKPFTAATLE 120

>pdb|1UDR|A Chain A, Chey Mutant With Lys 91 Replaced By Asp, Lys 92 Replaced By Ala, Ile 96 Replaced By Lys And Ala 98 Replaced By Leu (Stabilizing Mutations In Helix 4) Length = 129

Iteration: 1
 Score = 58.5 bits (140), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 36/123 (29%), Positives = 62/123 (50%), Gaps = 6/123 (4%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD     RI+  +L++  +       AE  +D L ++   GY  VISD +MP+M
Sbjct: 6   LKFLVVDDFSTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISDWNMPNM 63
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHV 133
           DG +L + +   G    LPV+M++ +   +++      GA  Y++KP     L      +
Sbjct: 64  DGLELLKTIRADGAMSALPVLMVTAEADAENIKALAQAGASGYVVKPFTAATLEEKLNKI 123
Query: 134 AQQ 136
            ++
Sbjct: 124 FEK 126

>pdb|2CHE|A Chain A, Structure Of The Mg2+-Bound Form Of Chey And Mechanism Of Phosphoryl Transfer In Bacterial Chemotaxis Length = 128

Iteration: 1
 Score = 58.2 bits (139), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 33/123 (26%), Positives = 63/123 (51%), Gaps = 6/123 (4%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD     RI+  +L++  +       AE  +D L ++   G+  +ISD +MP+M
Sbjct: 5   LKFLVVDDFSTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGFGFIISDWNMPNM 62
Query: 77  DGFKLHEQVGLE---MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHV 133
           DG +L + +  +     LPV+M++ +   ++++     GA  Y++KP     L      +
Sbjct: 63  DGLELLKTIRADSAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKI 122
Query: 134 AQQ 136
            ++
Sbjct: 123 FEK 125

>pdb|6CHY|A Chain A, Structure Of Chemotaxis Protein Chey Length = 128

Iteration: 1
 Score = 58.2 bits (139), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 35/114 (30%), Positives = 59/114 (51%), Gaps = 6/114 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD     RI+  +L++  +       AE  +D L ++   GY  VISD +MP+M
Sbjct: 5   LKFLVVDDFSTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISDWNMPNM 62
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           DG +L + +   G    LPV+M+  +   ++++     GA  +++KP     L 
Sbjct: 63  DGLELLKTIRADGAMSALPVLMVIAEAKKENIIAAAQAGASGWVVKPFTAATLE 116

>pdb|2FKA|A Chain A, Crystal Structure Of Mg(2+) And Bef(3)(-)-Bound Chey In Complex With Chez(200-214) Solved From A F432 Crystal Grown In Caps (Ph 10.5) Length = 129

Iteration: 1
 Score = 58.2 bits (139), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 33/114 (28%), Positives = 60/114 (52%), Gaps = 6/114 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD     RI+  +L++  +       AE  +D L ++   G+  +ISD +MP+M
Sbjct: 6   LKFLVVDDFSTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGFGFIISDWNMPNM 63
Query: 77  DGFKLHEQVGLE---MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           DG +L + +  +     LPV+M++ +   ++++     GA  Y++KP     L 
Sbjct: 64  DGLELLKTIRADSAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLE 117

>pdb|2ID7|A Chain A, 1.75 A Structure Of T87i Phosphono-Chey Length = 128

Iteration: 1
 Score = 57.4 bits (137), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 34/108 (31%), Positives = 57/108 (52%), Gaps = 6/108 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD     RI+  +L++  +       AE  +D L ++   GY  VIS  +MP+M
Sbjct: 5   LKFLVVDDFSTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISXWNMPNM 62
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPI 121
           DG +L + +   G    LPV+M+  +   ++++     GA  Y++KP 
Sbjct: 63  DGLELLKTIRADGAMSALPVLMVIAEAKKENIIAAAQAGASGYVVKPF 110

>pdb|1W25|A Chain A, Response Regulator Pled In Complex With C-digmp Length = 459

Iteration: 1
 Score = 56.6 bits (135), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 36/106 (33%), Positives = 58/106 (54%), Gaps = 5/106 (4%)
Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           R+LVVDD    +R+LE  L    YEV+       AL M   +++  DI++ DV MP MDG
Sbjct: 3   RILVVDDIEANVRLLEAKLTAEYYEVSTAMDGPTALAM--AARDLPDIILLDVMMPGMDG 60
Query: 79  FKLHEQVG---LEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPI 121
           F +  ++        +PV++++      D ++G+  GA ++L KPI
Sbjct: 61  FTVCRKLKDDPTTRHIPVVLITALDGRGDRIQGLESGASDFLTKPI 106

>pdb|2WB4|A Chain A, Activated Diguanylate Cyclase Pled In Complex With C-Di-Gmp Length = 459

Iteration: 1
 Score = 56.2 bits (134), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 36/106 (33%), Positives = 58/106 (54%), Gaps = 5/106 (4%)
Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           R+LVVDD    +R+LE  L    YEV+       AL M   +++  DI++ DV MP MDG
Sbjct: 4   RILVVDDIEANVRLLEAKLTAEYYEVSTAMDGPTALAM--AARDLPDIILLDVMMPGMDG 61
Query: 79  FKLHEQVG---LEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPI 121
           F +  ++        +PV++++      D ++G+  GA ++L KPI
Sbjct: 62  FTVCRKLKDDPTTRHIPVVLITALDGRGDRIQGLESGASDFLTKPI 107

>pdb|3R0J|A Chain A, Structure Of Phop From Mycobacterium Tuberculosis Length = 250

Iteration: 1
 Score = 55.8 bits (133), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 35/109 (32%), Positives = 57/109 (52%), Gaps = 3/109 (2%)
Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           RVLVVDD+   + +L   L+   +EV        ALD  R ++   D VI DV  P  DG
Sbjct: 25  RVLVVDDEANIVELLSVSLKFQGFEVYTATNGAQALDRARETRP--DAVILDVXXPGXDG 82
Query: 79  FKLHEQVGLE-MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
           F +  ++  + +D P + ++     QD + G+T G  +Y+ KP  ++E+
Sbjct: 83  FGVLRRLRADGIDAPALFLTARDSLQDKIAGLTLGGDDYVTKPFSLEEV 131

>pdb|2ID9|A Chain A, 1.85 A Structure Of T87iY106W PHOSPHONO-Chey Length = 128

Iteration: 1
 Score = 55.5 bits (132), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 33/108 (30%), Positives = 57/108 (52%), Gaps = 6/108 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD     RI+  +L++  +       AE  +D L ++   GY  VIS  +MP+M
Sbjct: 5   LKFLVVDDFSTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISXWNMPNM 62
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPI 121
           DG +L + +   G    LPV+M+  +   ++++     GA  +++KP 
Sbjct: 63  DGLELLKTIRADGAMSALPVLMVIAEAKKENIIAAAQAGASGWVVKPF 110

>pdb|3M6M|D Chain D, Crystal Structure Of Rpff Complexed With Rec Domain Of Rpfc Length = 143

Iteration: 1
 Score = 55.5 bits (132), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 38/123 (30%), Positives = 64/123 (52%), Gaps = 9/123 (7%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMD 77
           +R+LV DD      +L+++L K  ++V   N AE  LD   M++  YD VI D+HMP M+
Sbjct: 15  MRMLVADDHEANRMVLQRLLEKAGHKVLCVNGAEQVLDA--MAEEDYDAVIVDLHMPGMN 72
Query: 78  GFKLHEQV------GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQ 131
           G  + +Q+      G+    PV+++S D   + +      GA  +L KP+   +L +   
Sbjct: 73  GLDMLKQLRVMQASGMRYT-PVVVLSADVTPEAIRACEQAGARAFLAKPVVAAKLLDTLA 131
Query: 132 HVA 134
            +A
Sbjct: 132 DLA 134

>pdb|2CHY|A Chain A, Three-Dimensional Structure Of Chey, The Response Regulator Of Bacterial Chemotaxis Length = 128

Iteration: 1
 Score = 55.1 bits (131), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 32/123 (26%), Positives = 62/123 (50%), Gaps = 6/123 (4%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVDD     RI+  +L++  +       AE  +D L ++   G+  +I D +MP+M
Sbjct: 5   LKFLVVDDFSTMRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGFGFIICDWNMPNM 62
Query: 77  DGFKLHEQVGLE---MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHV 133
           DG +L + +  +     LPV+M++ +   ++++     GA  Y++KP     L      +
Sbjct: 63  DGLELLKTIRADSAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKI 122
Query: 134 AQQ 136
            ++
Sbjct: 123 FEK 125

>pdb|3F6P|A Chain A, Crystal Structure Of Unphosphorelated Receiver Domain Of Yycf Length = 120

Iteration: 1
 Score = 55.1 bits (131), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 35/108 (32%), Positives = 62/108 (57%), Gaps = 2/108 (1%)
Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           ++LVVDD+     ILE  LRK  YEV   +    A++M+   +   D+++ D+ +P+ DG
Sbjct: 4   KILVVDDEKPIADILEFNLRKEGYEVHCAHDGNEAVEMVEELQP--DLILLDIMLPNKDG 61
Query: 79  FKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
            ++  +V  + D+P+IM++      D + G+  GA +Y+ KP   +EL
Sbjct: 62  VEVCREVRKKYDMPIIMLTAKDSEIDKVIGLEIGADDYVTKPFSTREL 109

>pdb|3DGE|C Chain C, Structure Of A Histidine Kinase-response Regulator Complex Reveals Insights Into Two-component Signaling And A Novel Cis- Autophosphorylation Mechanism Length = 122

Iteration: 1
 Score = 55.1 bits (131), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 32/106 (30%), Positives = 62/106 (58%), Gaps = 5/106 (4%)
Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           +VL+VDD  +  +I+   L+K  YEV +    +IAL+  ++S+   D+++ D+ MP MDG
Sbjct: 4   KVLLVDDSAVLRKIVSFNLKKEGYEVIEAENGQIALE--KLSEFTPDLIVLDIMMPVMDG 61
Query: 79  FKLHEQVGLEMD---LPVIMMSVDGCTQDVMKGVTHGACNYLLKPI 121
           F + +++  + +   +PVI+++  G  +D    ++ GA   + KP 
Sbjct: 62  FTVLKKLQEKEEWKRIPVIVLTAKGGEEDESLALSLGARKVMRKPF 107

>pdb|2ZWM|A Chain A, Crystal Structure Of Yycf Receiver Domain From Bacillus Subtilis Length = 130

Iteration: 1
 Score = 54.7 bits (130), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 35/108 (32%), Positives = 62/108 (57%), Gaps = 2/108 (1%)
Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           ++LVVDD+     ILE  LRK  YEV   +    A++M+   +   D+++ D+ +P+ DG
Sbjct: 4   KILVVDDEKPIADILEFNLRKEGYEVHCAHDGNEAVEMVEELQP--DLILLDIMLPNKDG 61
Query: 79  FKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
            ++  +V  + D+P+IM++      D + G+  GA +Y+ KP   +EL
Sbjct: 62  VEVCREVRKKYDMPIIMLTAKDSEIDKVIGLEIGADDYVTKPFSTREL 109

>pdb|1HEY|A Chain A, Investigating The Structural Determinants Of The P21-Like Triphosphate And Mg2+ Binding Site Length = 128

Iteration: 1
 Score = 54.3 bits (129), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 32/114 (28%), Positives = 57/114 (50%), Gaps = 6/114 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVV +       +  +L++  +       AE  +D L ++   GY  VISD +MP+M
Sbjct: 5   LKFLVVGNGGTGKSTVRNLLKELGF--NNVEDAEDGVDALNKLQAGGYGFVISDWNMPNM 62
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           DG +L + +   G    LPV+M++ +   ++++     GA  Y++KP     L 
Sbjct: 63  DGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLE 116

>pdb|3GT7|A Chain A, Crystal Structure Of Signal Receiver Domain Of Signal Transduction Histidine Kinase From Syntrophus Aciditrophicus Length = 154

Iteration: 1
 Score = 53.1 bits (126), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 39/139 (28%), Positives = 74/139 (53%), Gaps = 7/139 (5%)
Query: 20  VLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGF 79
           +L+V+D P     L+ +L +  Y+         A+  L +++   D++ISDV MP+MDG+
Sbjct: 10  ILIVEDSPTQAEHLKHILEETGYQTEHVRNGREAVRFLSLTRP--DLIISDVLMPEMDGY 67
Query: 80  KLHEQVGLEMDL---PVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ 136
            L   +  + DL   PVI++++    +DV++ +  GA +++ KP +   L +  + +   
Sbjct: 68  ALCRWLKGQPDLRTIPVILLTILSDPRDVVRSLECGADDFITKPCKDVVLASHVKRLLSG 127
Query: 137 PKPFEE--SDDSYSVNQGN 153
            K  EE  S +S ++  GN
Sbjct: 128 VKRTEERYSRESITLAFGN 146

>pdb|1QKK|A Chain A, Crystal Structure Of The Receiver Domain And Linker Region Of Dctd From Sinorhizobium Meliloti Length = 155

Iteration: 1
 Score = 52.8 bits (125), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 33/108 (30%), Positives = 56/108 (51%), Gaps = 3/108 (2%)
Query: 20  VLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGF 79
           V ++DDD    + +++ L    + V+    A  AL  L  S +   IVISD+ MP MDG 
Sbjct: 6   VFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGL--SADFAGIVISDIRMPGMDGL 63
Query: 80  KLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
            L  ++  L+ DLP+I+++  G     ++ +  GA +++ KP     L
Sbjct: 64  ALFRKILALDPDLPMILVTGHGDIPMAVQAIQDGAYDFIAKPFAADRL 111

>pdb|1L5Y|A Chain A, Crystal Structure Of Mg2+ / Bef3-bound Receiver Domain Of Sinorhizobium Meliloti Dctd Length = 155

Iteration: 1
 Score = 52.8 bits (125), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 33/108 (30%), Positives = 56/108 (51%), Gaps = 3/108 (2%)
Query: 20  VLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGF 79
           V ++DDD    + +++ L    + V+    A  AL  L  S +   IVISD+ MP MDG 
Sbjct: 6   VFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGL--SADFAGIVISDIRMPGMDGL 63
Query: 80  KLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
            L  ++  L+ DLP+I+++  G     ++ +  GA +++ KP     L
Sbjct: 64  ALFRKILALDPDLPMILVTGHGDIPMAVQAIQDGAYDFIAKPFAADRL 111

>pdb|3GL9|A Chain A, The Structure Of A Histidine Kinase-Response Regulator Complex Sheds Light Into Two-Component Signaling And Reveals A Novel Cis Autophosphorylation Mechanism Length = 122

Iteration: 1
 Score = 52.4 bits (124), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 31/106 (29%), Positives = 61/106 (57%), Gaps = 5/106 (4%)
Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           +VL+VDD  +  +I+   L+K  YEV +    +IAL+  ++S+   D+++  + MP MDG
Sbjct: 4   KVLLVDDSAVLRKIVSFNLKKEGYEVIEAENGQIALE--KLSEFTPDLIVLXIMMPVMDG 61
Query: 79  FKLHEQVGLEMD---LPVIMMSVDGCTQDVMKGVTHGACNYLLKPI 121
           F + +++  + +   +PVI+++  G  +D    ++ GA   + KP 
Sbjct: 62  FTVLKKLQEKEEWKRIPVIVLTAKGGEEDESLALSLGARKVMRKPF 107

>pdb|1U8T|A Chain A, Crystal Structure Of Chey D13k Y106w Alone And In Complex With A Flim Peptide Length = 128

Iteration: 1
 Score = 52.0 bits (123), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 30/108 (27%), Positives = 55/108 (50%), Gaps = 6/108 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDML-RMSKNGYDIVISDVHMPDM 76
           L+ LVVD      RI+  +L++  +       AE  +D L ++   GY  VISD + P+ 
Sbjct: 5   LKFLVVDKFSTXRRIVRNLLKELGF--NNVEEAEDGVDALNKLQAGGYGFVISDWNXPNX 62
Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPI 121
           DG +L + +   G    LPV+ ++ +   ++++     GA  +++KP 
Sbjct: 63  DGLELLKTIRADGAXSALPVLXVTAEAKKENIIAAAQAGASGWVVKPF 110

>pdb|3TO5|A Chain A, High Resolution Structure Of Chey3 From Vibrio Cholerae Length = 134

Iteration: 1
 Score = 52.0 bits (123), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 32/114 (28%), Positives = 61/114 (53%), Gaps = 6/114 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNG-YDIVISDVHMPDM 76
           +++L+VDD     RI++ +LR   +  T+   A+  L  L M K G +D V++D +MP M
Sbjct: 13  MKILIVDDFSTMRRIVKNLLRDLGFNNTQ--EADDGLTALPMLKKGDFDFVVTDWNMPGM 70
Query: 77  DGFKLHEQVGLEMD---LPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
            G  L + +  + +   LPV+M++ +   + +++    G   Y++KP     L+
Sbjct: 71  QGIDLLKNIRADEELKHLPVLMITAEAKREQIIEAAQAGVNGYIVKPFTAATLK 124

>pdb|3NHZ|A Chain A, Structure Of N-Terminal Domain Of Mtra Length = 125

Iteration: 1
 Score = 51.2 bits (121), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 32/107 (29%), Positives = 58/107 (54%), Gaps = 2/107 (1%)
Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           R+LVVDDD     +L  +LR   ++         AL  +R  +   D+V+ D+ +P M+G
Sbjct: 7   RILVVDDDASLAEMLTIVLRGEGFDTAVIGDGTQALTAVRELRP--DLVLLDLMLPGMNG 64
Query: 79  FKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKE 125
             +   +  +  +P++M++    T DV+ G+  GA +Y++KP + KE
Sbjct: 65  IDVCRVLRADSGVPIVMLTAKTDTVDVVLGLESGADDYIMKPFKPKE 111

>pdb|3GWG|A Chain A, Crystal Structure Of Chey Of Helicobacter Pylori Length = 129

Iteration: 1
 Score = 50.8 bits (120), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 33/111 (29%), Positives = 63/111 (56%), Gaps = 6/111 (5%)
Query: 15  PAG-LRVLVVDDDPIWLRILEKMLRKCLYE-VTKCNRAEIALDMLRMSKNGYDIVISDVH 72
           P G +++LVVDD     RI++  L +  YE V +      A + L  + +   ++I+D +
Sbjct: 2   PLGSMKLLVVDDSSTMRRIIKNTLSRLGYEDVLEAEHGVEAWEKLDANAD-TKVLITDWN 60
Query: 73  MPDMDGFKLHEQVGLE---MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKP 120
           MP+M+G  L ++V  +    ++P+IM++ +G   +V+  +  G  NY++KP
Sbjct: 61  MPEMNGLDLVKKVRSDSRFKEIPIIMITTEGGKAEVITALKAGVNNYIVKP 111

>pdb|3H1G|A Chain A, Crystal Structure Of Chey Mutant T84a Of Helicobacter Pylori Length = 129

Iteration: 1
 Score = 50.8 bits (120), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 33/111 (29%), Positives = 63/111 (56%), Gaps = 6/111 (5%)
Query: 15  PAG-LRVLVVDDDPIWLRILEKMLRKCLYE-VTKCNRAEIALDMLRMSKNGYDIVISDVH 72
           P G +++LVVDD     RI++  L +  YE V +      A + L  + +   ++I+D +
Sbjct: 2   PLGSMKLLVVDDSSTMRRIIKNTLSRLGYEDVLEAEHGVEAWEKLDANAD-TKVLITDWN 60
Query: 73  MPDMDGFKLHEQVGLE---MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKP 120
           MP+M+G  L ++V  +    ++P+IM++ +G   +V+  +  G  NY++KP
Sbjct: 61  MPEMNGLDLVKKVRSDSRFKEIPIIMITAEGGKAEVITALKAGVNNYIVKP 111

>pdb|1NXO|A Chain A, Micarec Ph7.0 Length = 120

Iteration: 1
 Score = 50.1 bits (118), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 30/109 (27%), Positives = 58/109 (53%), Gaps = 2/109 (1%)
Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           ++L+VDD+     I++  + K  YEV        AL+     +   DI+I D+ +P++DG
Sbjct: 3   KILIVDDEKPISDIIKFNMTKEGYEVVTAFNGREALEQFEAEQP--DIIILDLMLPEIDG 60
Query: 79  FKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
            ++ + +     +P++M+S      D + G+  GA +Y+ KP   +EL+
Sbjct: 61  LEVAKTIRKTSSVPILMLSAKDSEFDKVIGLELGADDYVTKPFSNRELQ 109

>pdb|2OQR|A Chain A, The Structure Of The Response Regulator Regx3 From Mycobacterium Tuberculosis Length = 230

Iteration: 1
 Score = 49.7 bits (117), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 34/107 (31%), Positives = 54/107 (50%), Gaps = 2/107 (1%)
Query: 20  VLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGF 79
           VL+V+D+      L  +LRK  +E T       AL      + G DIV+ D+ +P M G 
Sbjct: 7   VLIVEDEESLADPLAFLLRKEGFEATVVTDGPAAL--AEFDRAGADIVLLDLMLPGMSGT 64
Query: 80  KLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
            + +Q+     +PVIM++      D + G+  GA +Y+ KP   +EL
Sbjct: 65  DVCKQLRARSSVPVIMVTARDSEIDKVVGLELGADDYVTKPYSAREL 111

>pdb|1P6U|A Chain A, Nmr Structure Of The Bef3-Activated Structure Of The Response Regulator Chey2-Mg2+ From Sinorhizobium Meliloti Length = 129

Iteration: 1
 Score = 48.1 bits (113), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 34/120 (28%), Positives = 59/120 (49%), Gaps = 6/120 (5%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLY-EVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDM 76
           ++VL+VDD      +L   L++  + ++T     E  + +  M++N + +VISD +MP M
Sbjct: 7   IKVLIVDDQVTSRLLLGDALQQLGFKQITAAGDGEQGMKI--MAQNPHHLVISDFNMPKM 64
Query: 77  DGFKLHEQVGLE---MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHV 133
           DG  L + V           I+++  G    V K    GA N L KP  I++++   + V
Sbjct: 65  DGLGLLQAVRANPATKKAAFIILTAQGDRALVQKAAALGANNVLAKPFTIEKMKAAIEAV 124

>pdb|3H1F|A Chain A, Crystal Structure Of Chey Mutant D53a Of Helicobacter Pylori Length = 129

Iteration: 1
 Score = 48.1 bits (113), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 32/111 (28%), Positives = 62/111 (55%), Gaps = 6/111 (5%)
Query: 15  PAG-LRVLVVDDDPIWLRILEKMLRKCLYE-VTKCNRAEIALDMLRMSKNGYDIVISDVH 72
           P G +++LVVDD     RI++  L +  YE V +      A + L  + +   ++I+  +
Sbjct: 2   PLGSMKLLVVDDSSTMRRIIKNTLSRLGYEDVLEAEHGVEAWEKLDANAD-TKVLITAWN 60
Query: 73  MPDMDGFKLHEQVGLE---MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKP 120
           MP+M+G  L ++V  +    ++P+IM++ +G   +V+  +  G  NY++KP
Sbjct: 61  MPEMNGLDLVKKVRSDSRFKEIPIIMITTEGGKAEVITALKAGVNNYIVKP 111

>pdb|1S8N|A Chain A, Crystal Structure Of Rv1626 From Mycobacterium Tuberculosis Length = 205

Iteration: 1
 Score = 47.8 bits (112), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 32/109 (29%), Positives = 56/109 (51%), Gaps = 3/109 (2%)
Query: 19  RVLVVDDDPIWLRILEKMLRKCLYE-VTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMD 77
           RVL+ +D+ +    L +MLR+  YE V +    + A+++  + K   D+VI DV MP  D
Sbjct: 15  RVLIAEDEALIRMDLAEMLREEGYEIVGEAGDGQEAVELAELHKP--DLVIMDVKMPRRD 72
Query: 78  GFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
           G     ++  +   P+++++       V +    GA  YL+KP  I +L
Sbjct: 73  GIDAASEIASKRIAPIVVLTAFSQRDLVERARDAGAMAYLVKPFSISDL 121

>pdb|1DC7|A Chain A, Structure Of A Transiently Phosphorylated "switch" In Bacterial Signal Transduction Length = 124

Iteration: 1
 Score = 47.4 bits (111), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 35/107 (32%), Positives = 48/107 (44%), Gaps = 3/107 (2%)
Query: 20  VLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGF 79
           V VVDDD     +LE+ L       T        L  L  +    D+++SD+ MP MDG 
Sbjct: 6   VWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAAL--ASKTPDVLLSDIRMPGMDGL 63
Query: 80  KLHEQVGLEMD-LPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKE 125
            L +Q+      LPVI+M+        +     GA +YL KP  I E
Sbjct: 64  ALLKQIKQRHPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDIDE 110

>pdb|1YIO|A Chain A, Crystallographic Structure Of Response Regulator Styr From Pseudomonas Fluorescens Length = 208

Iteration: 1
 Score = 47.4 bits (111), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 37/134 (27%), Positives = 59/134 (44%), Gaps = 22/134 (16%)
Query: 20  VLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGF 79
           V VVDDD      L  +LR   +EV   + A   L+  R  ++G   ++ D+ MP M G 
Sbjct: 7   VFVVDDDMSVREGLRNLLRSAGFEVETFDCASTFLEHRRPEQHG--CLVLDMRMPGMSGI 64
Query: 80  KLHEQVGLEMD-LPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPK 138
           +L EQ+    D +P++ ++  G     ++ +  GA  +L                   PK
Sbjct: 65  ELQEQLTAISDGIPIVFITAHGDIPMTVRAMKAGAIEFL-------------------PK 105
Query: 139 PFEESDDSYSVNQG 152
           PFEE     ++ QG
Sbjct: 106 PFEEQALLDAIEQG 119

>pdb|1KRW|A Chain A, Solution Structure And Backbone Dynamics Of Beryllofluoride- Activated Ntrc Receiver Domain Length = 124

Iteration: 1
 Score = 47.4 bits (111), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 35/107 (32%), Positives = 48/107 (44%), Gaps = 3/107 (2%)
Query: 20  VLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGF 79
           V VVDDD     +LE+ L       T        L  L  +    D+++SD+ MP MDG 
Sbjct: 6   VWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAAL--ASKTPDVLLSDIRMPGMDGL 63
Query: 80  KLHEQVGLEMD-LPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKE 125
            L +Q+      LPVI+M+        +     GA +YL KP  I E
Sbjct: 64  ALLKQIKQRHPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDIDE 110

>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 = 47.4 bits (111), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 35/107 (32%), Positives = 48/107 (44%), Gaps = 3/107 (2%)
Query: 20  VLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGF 79
           V VVDDD     +LE+ L       T        L  L  +    D+++SD+ MP MDG 
Sbjct: 6   VWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAAL--ASKTPDVLLSDIRMPGMDGL 63
Query: 80  KLHEQVGLEMD-LPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKE 125
            L +Q+      LPVI+M+        +     GA +YL KP  I E
Sbjct: 64  ALLKQIKQRHPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDIDE 110

>pdb|1NXT|A Chain A, Micarec Ph 4.0 Length = 120

Iteration: 1
 Score = 47.0 bits (110), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 29/109 (26%), Positives = 57/109 (52%), Gaps = 2/109 (1%)
Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           ++L+VDD+     I++  + K  YEV        AL+     +   DI+I  + +P++DG
Sbjct: 3   KILIVDDEKPISDIIKFNMTKEGYEVVTAFNGREALEQFEAEQP--DIIILXLMLPEIDG 60
Query: 79  FKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
            ++ + +     +P++M+S      D + G+  GA +Y+ KP   +EL+
Sbjct: 61  LEVAKTIRKTSSVPILMLSAKDSEFDKVIGLELGADDYVTKPFSNRELQ 109

>pdb|1MVO|A Chain A, Crystal Structure Of The Phop Receiver Domain From Bacillus Subtilis Length = 136

Iteration: 1
 Score = 47.0 bits (110), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 30/109 (27%), Positives = 60/109 (55%), Gaps = 3/109 (2%)
Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           ++LVVDD+   + +L+  L +  Y+V   +  E AL      K   D+++ DV +P +DG
Sbjct: 5   KILVVDDEESIVTLLQYNLERSGYDVITASDGEEALKKAETEKP--DLIVLDVMLPKLDG 62
Query: 79  FKLHEQVGLE-MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
            ++ +Q+  + +  P++M++      D + G+  GA +Y+ KP   +E+
Sbjct: 63  IEVCKQLRQQKLMFPILMLTAKDEEFDKVLGLELGADDYMTKPFSPREV 111

>pdb|1YS6|A Chain A, Crystal Structure Of The Response Regulatory Protein Prra From Mycobacterium Tuberculosis Length = 233

Iteration: 1
 Score = 46.6 bits (109), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 30/96 (31%), Positives = 53/96 (55%), Gaps = 5/96 (5%)
Query: 33  LEKMLRKCLYEV-TKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQV-GLEMD 90
           LE+ LR   +EV T  + AE    +   ++N  D ++ D++MP +DG  +   +  ++ D
Sbjct: 23  LERGLRLSGFEVATAVDGAEA---LRSATENRPDAIVLDINMPVLDGVSVVTALRAMDND 79
Query: 91  LPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
           +PV ++S      D + G+  GA +YL+KP  + EL
Sbjct: 80  VPVCVLSARSSVDDRVAGLEAGADDYLVKPFVLAEL 115

>pdb|3EQ2|A Chain A, Structure Of Hexagonal Crystal Form Of Pseudomonas Aeruginosa Rssb Length = 394

Iteration: 1
 Score = 46.2 bits (108), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 27/103 (26%), Positives = 52/103 (50%), Gaps = 3/103 (2%)
Query: 20  VLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGF 79
           +L++DDD +    L   L    ++V +       L +    +   D+VI D+  P +DG 
Sbjct: 8   LLIIDDDEVVRESLAAYLEDSNFKVLQALNGLQGLQIFESEQP--DLVICDLRXPQIDGL 65
Query: 80  KLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPI 121
           +L  ++     + P+I++S  G   D ++ +  GA +YL+KP+
Sbjct: 66  ELIRRIRQTASETPIIVLSGAGVXSDAVEALRLGAADYLIKPL 108

>pdb|3NNN|A Chain A, Bef3 Activated Drrd Receiver Domain Length = 122

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 32/110 (29%), Positives = 62/110 (56%), Gaps = 3/110 (2%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMD 77
           +RVLVV+D+     ++ + L+K ++ V  C   E  + M       +D+VI D+ +P  D
Sbjct: 3   VRVLVVEDERDLADLITEALKKEMFTVDVCYDGEEGMYM--ALNEPFDVVILDIMLPVHD 60
Query: 78  GFKLHEQVGLE-MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
           G+++ + +    ++ PV+M++     +  +KG+  GA +YL KP  ++EL
Sbjct: 61  GWEILKSMRESGVNTPVLMLTALSDVEYRVKGLNMGADDYLPKPFDLREL 110

>pdb|3F7A|A Chain A, Structure Of Orthorhombic Crystal Form Of Pseudomonas Aeruginosa Rssb Length = 394

Iteration: 1
 Score = 45.8 bits (107), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 27/103 (26%), Positives = 52/103 (50%), Gaps = 3/103 (2%)
Query: 20  VLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGF 79
           +L++DDD +    L   L    ++V +       L +    +   D+VI D+  P +DG 
Sbjct: 8   LLIIDDDEVVRESLAAYLEDSNFKVLQALNGLQGLQIFESEQP--DLVICDLRXPQIDGL 65
Query: 80  KLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPI 121
           +L  ++     + P+I++S  G   D ++ +  GA +YL+KP+
Sbjct: 66  ELIRRIRQTASETPIIVLSGAGVMSDAVEALRLGAADYLIKPL 108

>pdb|3Q9S|A Chain A, Crystal Structure Of Rra(1-215) From Deinococcus Radiodurans Length = 249

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 28/108 (25%), Positives = 57/108 (52%), Gaps = 2/108 (1%)
Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           R+LV++DD     +L   L    Y V   + A   L  ++  ++  D+++ D+ +PD DG
Sbjct: 39  RILVIEDDHDIANVLRXDLTDAGYVVDHADSAXNGL--IKAREDHPDLILLDLGLPDFDG 96
Query: 79  FKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
             + +++     LP+I+++     ++ ++ +  GA +YL+KP    EL
Sbjct: 97  GDVVQRLRKNSALPIIVLTARDTVEEKVRLLGLGADDYLIKPFHPDEL 144

>pdb|1DC8|A Chain A, Structure Of A Transiently Phosphorylated "switch" In Bacterial Signal Transduction Length = 124

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 34/107 (31%), Positives = 47/107 (43%), Gaps = 3/107 (2%)
Query: 20  VLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGF 79
           V VVDDD     +LE+ L       T        L  L  +    D+++S + MP MDG 
Sbjct: 6   VWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAAL--ASKTPDVLLSXIRMPGMDGL 63
Query: 80  KLHEQVGLEMD-LPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKE 125
            L +Q+      LPVI+M+        +     GA +YL KP  I E
Sbjct: 64  ALLKQIKQRHPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDIDE 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 = 44.3 bits (103), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 31/108 (28%), Positives = 58/108 (53%), Gaps = 4/108 (3%)
Query: 17  GLRVLVVDDDPIWLRILEKMLRKCLYEVT-KCNRAEIALDMLRMSKNGYDIVISDVHMPD 75
           G RVL+VDD      +L+ ++ K  YEV  +      A++  +  K   DIV  D+ MP+
Sbjct: 1   GKRVLIVDDAAFMRMMLKDIITKAGYEVAGEATNGREAVEKYKELKP--DIVTMDITMPE 58
Query: 76  MDGF-KLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIR 122
           M+G   + E + ++ +  +I+ S  G    V++ +  GA ++++KP +
Sbjct: 59  MNGIDAIKEIMKIDPNAKIIVCSAMGQQAMVIEAIKAGAKDFIVKPFQ 106

>pdb|3TMY|A Chain A, Chey From Thermotoga Maritima (Mn-Iii) Length = 120

Iteration: 1
 Score = 44.3 bits (103), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 31/108 (28%), Positives = 58/108 (53%), Gaps = 4/108 (3%)
Query: 17  GLRVLVVDDDPIWLRILEKMLRKCLYEVT-KCNRAEIALDMLRMSKNGYDIVISDVHMPD 75
           G RVL+VDD      +L+ ++ K  YEV  +      A++  +  K   DIV  D+ MP+
Sbjct: 2   GKRVLIVDDAAFMRMMLKDIITKAGYEVAGEATNGREAVEKYKELKP--DIVTMDITMPE 59
Query: 76  MDGF-KLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIR 122
           M+G   + E + ++ +  +I+ S  G    V++ +  GA ++++KP +
Sbjct: 60  MNGIDAIKEIMKIDPNAKIIVCSAMGQQAMVIEAIKAGAKDFIVKPFQ 107

>pdb|2PKX|A Chain A, E.Coli Response Regulator Phop Receiver Domain Length = 121

Iteration: 1
 Score = 43.5 bits (101), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 30/109 (27%), Positives = 61/109 (55%), Gaps = 3/109 (2%)
Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           RVLVV+D+ +    L+  ++   ++V     A+ A     ++++  DI I D+ +PD DG
Sbjct: 2   RVLVVEDNALLRHHLKVQIQDAGHQVDDAEDAKEA--DYYLNEHIPDIAIVDLGLPDEDG 59
Query: 79  FKLHEQ-VGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
             L  +    ++ LP+++++     QD ++ ++ GA +Y+ KP  I+E+
Sbjct: 60  LSLIRRWRSNDVSLPILVLTARESWQDKVEVLSAGADDYVTKPFHIEEV 108

>pdb|3JTE|A Chain A, Crystal Structure Of Response Regulator Receiver Domain Protein From Clostridium Thermocellum Length = 143

Iteration: 1
 Score = 43.5 bits (101), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 31/127 (24%), Positives = 62/127 (48%), Gaps = 1/127 (0%)
Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           ++LV+DD+   L+ ++ +L     EV   + +   L +   + N  D+VI+D+ MP + G
Sbjct: 5   KILVIDDESTILQNIKFLLEIDGNEVLTASSSTEGLRIFTENCNSIDVVITDMKMPKLSG 64
Query: 79  FK-LHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQP 137
              L E   +   + VI+++  G   + +  +  GA  YL KP+  ++L     +   + 
Sbjct: 65  MDILREIKKITPHMAVIILTGHGDLDNAILAMKEGAFEYLRKPVTAQDLSIAINNAINRK 124
Query: 138 KPFEESD 144
           K   E++
Sbjct: 125 KLLMENE 131

>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 = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 31/111 (27%), Positives = 51/111 (45%), Gaps = 8/111 (7%)
Query: 20  VLVVDDDPIWLRILEKMLRK---CLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDM 76
           VL+V+D+    R L   L      ++E     R      +L  +    D++I D+ +PD 
Sbjct: 4   VLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRG-----LLEAATRKPDLIILDLGLPDG 58
Query: 77  DGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           DG +    +     +PVI++S      D +  +  GA +YL KP  I EL+
Sbjct: 59  DGIEFIRDLRQWSAVPVIVLSARSEESDKIAALDAGADDYLSKPFGIGELQ 109

>pdb|3MM4|A Chain A, Crystal Structure Of The Receiver Domain Of The Histidine Kinase Cki1 From Arabidopsis Thaliana Length = 206

Iteration: 1
 Score = 42.4 bits (98), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 35/140 (25%), Positives = 68/140 (48%), Gaps = 20/140 (14%)
Query: 12  DQFPAGLRVLVVDDDPIWLRILEKMLRK-CLYEVTKCNRAEIALDML-----------RM 59
           D+F  G RVLVVDD+ I  ++    L+K  + EV +C+  + AL ++            +
Sbjct: 56  DEFLRGKRVLVVDDNFISRKVATGKLKKMGVSEVEQCDSGKEALRLVTEGLTQREEQGSV 115
Query: 60  SKNGYDIVISDVHMPDMDGFKLHEQV-----GLEMDLPVIMMSV-DGCTQDVMKGVTHGA 113
            K  +D +  D  MP+MDG++   ++        +  P+I +S  D  +++  + +  G 
Sbjct: 116 DKLPFDYIFMDCQMPEMDGYEATREIRKVEKSYGVRTPIIAVSGHDPGSEEARETIQAGM 175
Query: 114 CNYLLKPIRIKELRNIWQHV 133
             +L K   + +L N+ + +
Sbjct: 176 DAFLDKS--LNQLANVIREI 193

>pdb|3EOD|A Chain A, Crystal Structure Of N-Terminal Domain Of E. Coli Rssb Length = 130

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 30/109 (27%), Positives = 55/109 (50%), Gaps = 7/109 (6%)
Query: 17  GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGY--DIVISDVHMP 74
           G ++L+V+D+ ++  +L+                  AL++L     G+  D++I D+ MP
Sbjct: 7   GKQILIVEDEQVFRSLLDSWFSSLGATTVLAADGVDALELL----GGFTPDLMICDIAMP 62
Query: 75  DMDGFKLHEQVGLEMD-LPVIMMSVDGCTQDVMKGVTHGACNYLLKPIR 122
            M+G KL E +    D  PV+++S      D+ K +  G  + LLKP++
Sbjct: 63  RMNGLKLLEHIRNRGDQTPVLVISATENMADIAKALRLGVEDVLLKPVK 111

>pdb|1SRR|A Chain A, Crystal Structure Of A Phosphatase Resistant Mutant Of Sporulation Response Regulator Spo0f From Bacillus Subtilis Length = 124

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 29/111 (26%), Positives = 60/111 (54%), Gaps = 3/111 (2%)
Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           ++L+VDD      +L ++  K  Y+  +      ALD++  +K   D+V+ D+ +P MDG
Sbjct: 5   KILIVDDQSGIRILLNEVFNKEGYQTFQAANGLQALDIV--TKERPDLVLLDMKIPGMDG 62
Query: 79  FKLHEQVG-LEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRN 128
            ++ +++  ++ ++ VI+M+  G    + +    GA  +  KP  I E+R+
Sbjct: 63  IEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFAKPFDIDEIRD 113

>pdb|1F51|E Chain E, A Transient Interaction Between Two Phosphorelay Proteins Trapped In A Crystal Lattice Reveals The Mechanism Of Molecular Recognition And Phosphotransfer In Singal Transduction Length = 119

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 29/111 (26%), Positives = 60/111 (54%), Gaps = 3/111 (2%)
Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           ++L+VDD      +L ++  K  Y+  +      ALD++  +K   D+V+ D+ +P MDG
Sbjct: 3   KILIVDDQSGIRILLNEVFNKEGYQTFQAANGLQALDIV--TKERPDLVLLDMKIPGMDG 60
Query: 79  FKLHEQVG-LEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRN 128
            ++ +++  ++ ++ VI+M+  G    + +    GA  +  KP  I E+R+
Sbjct: 61  IEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFAKPFDIDEIRD 111

>pdb|1M5T|A Chain A, Crystal Structure Of The Response Regulator Divk Length = 124

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 33/125 (26%), Positives = 63/125 (50%), Gaps = 10/125 (8%)
Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           +VL+V+D+ + +++   +L    YE  +      AL + R  +N  D+++ D+ +P++ G
Sbjct: 3   KVLIVEDNELNMKLFHDLLEAQGYETLQTREGLSALSIAR--ENKPDLILMDIQLPEISG 60
Query: 79  FKLHEQVGLEMDLPVIMMSVDGCTQDVMKG----VTHGACN-YLLKPIRIKE-LRNIWQH 132
            ++ + +  + DL  I   V   T   MKG    +  G C  Y+ KPI +   L  I + 
Sbjct: 61  LEVTKWLKEDDDLAHI--PVVAVTAFAMKGDEERIREGGCEAYISKPISVVHFLETIKRL 118
Query: 133 VAQQP 137
           + +QP
Sbjct: 119 LERQP 123

>pdb|3CU5|A Chain A, Crystal Structure Of A Two Component Transcriptional Regulator Arac From Clostridium Phytofermentans Isdg Length = 141

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 38/140 (27%), Positives = 62/140 (44%), Gaps = 30/140 (21%)
Query: 17  GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYD----------- 65
            LR+L+VDD        EK+ R  L  +   N   ++ D +  + +G +           
Sbjct: 2   SLRILIVDD--------EKLTRDGL--IANINWKALSFDQIDQADDGINAIQIALKHPPN 51
Query: 66  IVISDVHMPDMDGFKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIK 124
           ++++DV MP MDG +L + +  L  D  VI MS     + +   +   A  Y+ KPI   
Sbjct: 52  VLLTDVRMPRMDGIELVDNILKLYPDCSVIFMSGYSDKEYLKAAIKFRAIRYVEKPIDPS 111
Query: 125 E--------LRNIWQHVAQQ 136
           E        ++ + QH AQQ
Sbjct: 112 EIMDALKQSIQTVLQHQAQQ 131

>pdb|2JVK|A Chain A, Nmr Solution Structure Of The Hyper-Sporulation Response Regulator Spo0f Mutant L66a From Bacillus Subtilis Length = 132

Iteration: 1
 Score = 41.6 bits (96), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 29/111 (26%), Positives = 60/111 (54%), Gaps = 3/111 (2%)
Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           ++L+VDD      +L ++  K  Y+  +      ALD++  +K   D+V+ D+ +P MDG
Sbjct: 5   KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIV--TKERPDLVLLDMKIPGMDG 62
Query: 79  FKLHEQVG-LEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRN 128
            ++ +++  ++ ++ VI+M+  G    + +    GA  +  KP  I E+R+
Sbjct: 63  IEIAKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFAKPFDIDEIRD 113

>pdb|1ZES|A Chain A, Bef3- Activated Phob Receiver Domain Length = 125

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 28/111 (25%), Positives = 60/111 (54%), Gaps = 5/111 (4%)
Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           R+LVV+D+     ++  +L +  ++  +    + A++ L  ++   D+++ D  +P   G
Sbjct: 4   RILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQL--NEPWPDLILLDWMLPGGSG 61
Query: 79  FKLHEQVGLE---MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
            +  + +  E    D+PV+M++  G  +D ++G+  GA +Y+ KP   KEL
Sbjct: 62  IQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSPKEL 112

>pdb|1B00|A Chain A, Phob Receiver Domain From Escherichia Coli Length = 127

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 28/111 (25%), Positives = 60/111 (54%), Gaps = 5/111 (4%)
Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           R+LVV+D+     ++  +L +  ++  +    + A++ L  ++   D+++ D  +P   G
Sbjct: 4   RILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQL--NEPWPDLILLDWMLPGGSG 61
Query: 79  FKLHEQVGLE---MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
            +  + +  E    D+PV+M++  G  +D ++G+  GA +Y+ KP   KEL
Sbjct: 62  IQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSPKEL 112

>pdb|3Q15|C Chain C, Crystal Structure Of Raph Complexed With Spo0f Length = 126

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 29/111 (26%), Positives = 60/111 (54%), Gaps = 3/111 (2%)
Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           ++L+VDD      +L ++  K  Y+  +      ALD++  +K   D+V+ D+ +P MDG
Sbjct: 7   KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIV--TKERPDLVLLDMKIPGMDG 64
Query: 79  FKLHEQVG-LEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRN 128
            ++ +++  ++ ++ VI+M+  G    + +    GA  +  KP  I E+R+
Sbjct: 65  IEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFAKPFDIDEIRD 115

>pdb|1KGS|A Chain A, Crystal Structure At 1.50 A Of An OmprPHOB HOMOLOG FROM THERMOTOGA Maritima Length = 225

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 31/110 (28%), Positives = 56/110 (50%), Gaps = 3/110 (2%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMD 77
           +RVLVV+D+     ++ + L+K  + V  C   E            +D+VI D+ +P  D
Sbjct: 3   VRVLVVEDERDLADLITEALKKEXFTVDVCYDGEEG--XYXALNEPFDVVILDIXLPVHD 60
Query: 78  GFK-LHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
           G++ L       ++ PV+ ++     +  +KG+  GA +YL KP  ++EL
Sbjct: 61  GWEILKSXRESGVNTPVLXLTALSDVEYRVKGLNXGADDYLPKPFDLREL 110

>pdb|1DZ3|A Chain A, Domain-Swapping In The Sporulation Response Regulator Spo0a Length = 130

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 5/73 (6%)
Query: 65  DIVISDVHMPDMDGFKLHEQV--GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIR 122
           DI++ D+ MP +DG  + E++  G E    VIM++  G      K V  GA  ++LKP  
Sbjct: 50  DILLLDIIMPHLDGLAVLERIRAGFEHQPNVIMLTAFGQEDVTKKAVELGASYFILKPF- 108
Query: 123 IKELRNIWQHVAQ 135
             ++ N+  H+ Q
Sbjct: 109 --DMENLAHHIRQ 119

>pdb|1PUX|A Chain A, Nmr Solution Structure Of Bef3-Activated Spo0f, 20 Conformers Length = 124

Iteration: 1
 Score = 40.8 bits (94), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 29/111 (26%), Positives = 60/111 (54%), Gaps = 3/111 (2%)
Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           ++L+VDD      +L ++  K  Y+  +      ALD++  +K   D+V+ D+ +P MDG
Sbjct: 5   KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIV--TKERPDLVLLDMKIPGMDG 62
Query: 79  FKLHEQVG-LEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRN 128
            ++ +++  ++ ++ VI+M+  G    + +    GA  +  KP  I E+R+
Sbjct: 63  IEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFAKPFDIDEIRD 113

>pdb|1DBW|A Chain A, Crystal Structure Of Fixj-N Length = 126

Iteration: 1
 Score = 40.8 bits (94), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 29/104 (27%), Positives = 54/104 (51%), Gaps = 3/104 (2%)
Query: 20  VLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGF 79
           V +VDD+    + L  ML    + V     AE  L      +NG  ++++D+ MPDM G 
Sbjct: 6   VHIVDDEEPVRKSLAFMLTMNGFAVKMHQSAEAFLAFAPDVRNG--VLVTDLRMPDMSGV 63
Query: 80  KLHEQVG-LEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIR 122
           +L   +G L++++P I+++  G     ++ +  GA +++ KP  
Sbjct: 64  ELLRNLGDLKINIPSIVITGHGDVPMAVEAMKAGAVDFIEKPFE 107

>pdb|2JVJ|A Chain A, Nmr Solution Structure Of The Hyper-Sporulation Response Regulator Spo0f Mutant I90a From Bacillus Subtilis Length = 132

Iteration: 1
 Score = 40.0 bits (92), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 29/111 (26%), Positives = 59/111 (53%), Gaps = 3/111 (2%)
Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           ++L+VDD      +L ++  K  Y+  +      ALD++  +K   D+V+ D+ +P MDG
Sbjct: 5   KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIV--TKERPDLVLLDMKIPGMDG 62
Query: 79  FKLHEQVG-LEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRN 128
            ++ +++  ++ ++ VI+M+  G      +    GA  +  KP  I E+R+
Sbjct: 63  IEILKRMKVIDENIRVIIMTAYGELDMAQESKELGALTHFAKPFDIDEIRD 113

>pdb|3C97|A Chain A, Crystal Structure Of The Response Regulator Receiver Domain Of A Signal Transduction Histidine Kinase From Aspergillus Oryzae Length = 140

Iteration: 1
 Score = 39.7 bits (91), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 31/115 (26%), Positives = 53/115 (46%), Gaps = 5/115 (4%)
Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMD 77
           L VL+ +D+ I   +  K L KC  ++T       AL   +  +  +D++I D+ MP MD
Sbjct: 11  LSVLIAEDNDICRLVAAKALEKCTNDITVVTNGLQALQAYQNRQ--FDVIIMDIQMPVMD 68
Query: 78  GFKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGAC--NYLLKPIRIKELRNI 129
           G +   ++   E        S+   T D +     GA    Y+ KP+   +LR++
Sbjct: 69  GLEAVSEIRNYERTHNTKRASIIAITADTIDDDRPGAELDEYVSKPLNPNQLRDV 123

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	184
4dad_A	146	Putative pilus assembly-related protein; response	4e-25
3eq2_A	394	Probable two-component response regulator; adaptor	1e-24
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	1e-24
3bre_A	358	Probable two-component response regulator; protein	2e-24
3hdv_A	136	Response regulator; PSI-II, structural genomics, P	2e-24
1srr_A	124	SPO0F, sporulation response regulatory protein; as	2e-24
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	3e-24
3jte_A	143	Response regulator receiver protein; structural ge	5e-24
3hdg_A	137	Uncharacterized protein; two-component sensor acti	9e-24
1w25_A	459	Stalked-cell differentiation controlling protein;	1e-23
1w25_A	459	Stalked-cell differentiation controlling protein;	9e-16
3hv2_A	153	Response regulator/HD domain protein; PSI-2, NYSGX	2e-23
2rjn_A	154	Response regulator receiver:metal-dependent phosph	3e-23
1dc7_A	124	NTRC, nitrogen regulation protein; receiver domain	5e-23
3luf_A	259	Two-component system response regulator/ggdef doma	8e-23
3luf_A	259	Two-component system response regulator/ggdef doma	2e-20
3cfy_A	137	Putative LUXO repressor protein; structural genomi	1e-22
2qxy_A	142	Response regulator; regulation of transcription, N	2e-22
2ayx_A	254	Sensor kinase protein RCSC; two independent struct	6e-22
1yio_A	208	Response regulatory protein; transcription regulat	2e-21
3eqz_A	135	Response regulator; structural genomics, unknown f	2e-21
3i42_A	127	Response regulator receiver domain protein (CHEY-	2e-21
3cg0_A	140	Response regulator receiver modulated diguanylate	3e-21
3rqi_A	184	Response regulator protein; structural genomics, s	4e-21
3crn_A	132	Response regulator receiver domain protein, CHEY-;	5e-21
2jk1_A	139	HUPR, hydrogenase transcriptional regulatory prote	1e-20
3ilh_A	146	Two component response regulator; NYSGXRC, PSI-II,	1e-20
1qkk_A	155	DCTD, C4-dicarboxylate transport transcriptional r	2e-20
3kcn_A	151	Adenylate cyclase homolog; SGX, PSI 2, structural	2e-20
1dbw_A	126	Transcriptional regulatory protein FIXJ; doubly wo	2e-20
3h5i_A	140	Response regulator/sensory box protein/ggdef domai	4e-20
3gt7_A	154	Sensor protein; structural genomics, signal receiv	5e-20
3grc_A	140	Sensor protein, kinase; protein structure initiati	9e-20
1p6q_A	129	CHEY2; chemotaxis, signal transduction, response r	1e-19
3m6m_D	143	Sensory/regulatory protein RPFC; RPFF, REC, enoyl-	1e-19
1jbe_A	128	Chemotaxis protein CHEY; signaling protein; 1.08A	1e-19
3snk_A	135	Response regulator CHEY-like protein; P-loop conta	2e-19
3cnb_A	143	DNA-binding response regulator, MERR family; signa	2e-19
3hzh_A	157	Chemotaxis response regulator (CHEY-3); phosphatas	2e-19
3r0j_A	250	Possible two component system response transcript	2e-19
3eod_A	130	Protein HNR; response regulator, phosphoprotein, t	3e-19
2qr3_A	140	Two-component system response regulator; structura	8e-19
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	1e-18
3c3m_A	138	Response regulator receiver protein; structural ge	1e-18
1s8n_A	205	Putative antiterminator; RV1626, structural genomi	1e-18
3lte_A	132	Response regulator; structural genomics, PSI, prot	2e-18
3q9s_A	249	DNA-binding response regulator; DNA binding protei	2e-18
2qzj_A	136	Two-component response regulator; 11017X, PSI-II,	2e-18
2zay_A	147	Response regulator receiver protein; structural ge	3e-18
3f6p_A	120	Transcriptional regulatory protein YYCF; unphospho	3e-18
3lua_A	140	Response regulator receiver protein; two-component	3e-18
1i3c_A	149	Response regulator RCP1; phytochrome, signaling pr	4e-18
2rdm_A	132	Response regulator receiver protein; structural ge	5e-18
3h1g_A	129	Chemotaxis protein CHEY homolog; sulfate-bound CHE	5e-18
2qvg_A	143	Two component response regulator; NYSGXRC, PSI-2,	5e-18
3cg4_A	142	Response regulator receiver domain protein (CHEY-;	6e-18
2gwr_A	238	DNA-binding response regulator MTRA; two-component	6e-18
3c97_A	140	Signal transduction histidine kinase; structural g	9e-18
2a9o_A	120	Response regulator; essential protein, YYCF/YYCG h	1e-17
2oqr_A	230	Sensory transduction protein REGX3; response regul	1e-17
1zh2_A	121	KDP operon transcriptional regulatory protein KDPE	1e-17
1dcf_A	136	ETR1 protein; beta-alpha five sandwich, transferas	1e-17
3n53_A	140	Response regulator receiver modulated diguanylate;	2e-17
1mb3_A	124	Cell division response regulator DIVK; signal tran	2e-17
1ys7_A	233	Transcriptional regulatory protein PRRA; response	3e-17
2j48_A	119	Two-component sensor kinase; pseudo-receiver, circ	5e-17
3a10_A	116	Response regulator; phosphoacceptor, signaling pro	5e-17
3nhm_A	133	Response regulator; protein structure initiative I	8e-17
3t6k_A	136	Response regulator receiver; flavodoxin-like, stru	2e-16
2b4a_A	138	BH3024; flavodoxin-like fold, structural genomics,	3e-16
1kgs_A	225	DRRD, DNA binding response regulator D; DNA-bindin	5e-16
1k66_A	149	Phytochrome response regulator RCPB; CHEY homologu	5e-16
3heb_A	152	Response regulator receiver domain protein (CHEY);	9e-16
1xhf_A	123	DYE resistance, aerobic respiration control protei	1e-15
1zgz_A	122	Torcad operon transcriptional regulatory protein;	2e-15
3gl9_A	122	Response regulator; beta-sheet, surrounded by alph	2e-15
3cu5_A	141	Two component transcriptional regulator, ARAC FAM;	2e-15
3kto_A	136	Response regulator receiver protein; PSI-II,struct	3e-15
1mvo_A	136	PHOP response regulator; phosphate regulon, transc	3e-15
2pl1_A	121	Transcriptional regulatory protein PHOP; CHEY-like	4e-15
1k68_A	140	Phytochrome response regulator RCPA; phosphorylate	4e-15
1p2f_A	220	Response regulator; DRRB, OMPR/PHOB, transcription	8e-15
1tmy_A	120	CHEY protein, TMY; chemotaxis, phosphoryl transfer	2e-14
2jba_A	127	Phosphate regulon transcriptional regulatory PROT;	3e-14
3kht_A	144	Response regulator; PSI-II, 11023K, structural gen	6e-14
2qv0_A	143	Protein MRKE; structural genomics, transcription,	2e-13
1qo0_D	196	AMIR; binding protein, gene regulator, receptor; 2	3e-13
3mm4_A	206	Histidine kinase homolog; receiver domain, CKI1, c	1e-12
2r25_B	133	Osmosensing histidine protein kinase SLN1; alpha5-	2e-12
2gkg_A	127	Response regulator homolog; social motility, recei	4e-12
2hqr_A	223	Putative transcriptional regulator; phosporylation	3e-11
2pln_A	137	HP1043, response regulator; signaling protein; 1.8	9e-11
3kyj_B	145	CHEY6 protein, putative histidine protein kinase;	4e-10
3t8y_A	164	CHEB, chemotaxis response regulator protein-glutam	2e-09
3sy8_A	400	ROCR; TIM barrel phosphodiesterase-A, transcriptio	3e-09
1a2o_A	349	CHEB methylesterase; bacterial chemotaxis, adaptat	5e-09
2qsj_A	154	DNA-binding response regulator, LUXR family; struc	3e-08
1dz3_A	130	Stage 0 sporulation protein A; response regulator,	8e-08
3klo_A	225	Transcriptional regulator VPST; REC domain, HTH do	3e-07
3f6c_A	134	Positive transcription regulator EVGA; structural	2e-06
3b2n_A	133	Uncharacterized protein Q99UF4; structural genomic	2e-05
4e7p_A	150	Response regulator; DNA binding, cytosol, transcri	7e-05
3eul_A	152	Possible nitrate/nitrite response transcriptional	8e-04
1a04_A	215	Nitrate/nitrite response regulator protein NARL; s	8e-04

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

 Score = 93.6 bits (233), Expect = 4e-25
 Identities = 22/124 (17%), Positives = 48/124 (38%), Gaps = 2/124 (1%)

Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRM-SKNGYDIVISDVHMPDM 76
           + +LV  +D   L  L +++               A  + R    + +DI++ D    D 
Sbjct: 21  INILVASEDASRLAHLARLVGDAGRYRVTRTVGRAAQIVQRTDGLDAFDILMIDGAALDT 80

Query: 77  DGFKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ 135
                 E++  L   L  ++++ D  +Q ++  +  G  + L  P+  + L +  +  A 
Sbjct: 81  AELAAIEKLSRLHPGLTCLLVTTDASSQTLLDAMRAGVRDVLRWPLEPRALDDALKRAAA 140

Query: 136 QPKP 139
           Q   
Sbjct: 141 QCAQ 144

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

 Score = 98.0 bits (244), Expect = 1e-24
 Identities = 32/161 (19%), Positives = 67/161 (41%), Gaps = 8/161 (4%)

Query: 15  PAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMP 74
                +L++DDD +    L   L    ++V +       L +        D+VI D+ MP
Sbjct: 3   KVSATLLIIDDDEVVRESLAAYLEDSNFKVLQALNGLQGLQIFE--SEQPDLVICDLRMP 60

Query: 75  DMDGFKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL-----RN 128
            +DG +L  ++     + P+I++S  G   D ++ +  GA +YL+KP+    +     R 
Sbjct: 61  QIDGLELIRRIRQTASETPIIVLSGAGVMSDAVEALRLGAADYLIKPLEDLAVLEHSVRR 120

Query: 129 IWQHVAQQPKPFEESDDSYSVNQGNWRTSNRRKDEEEEAEK 169
                  + +     D   + N+    + N  ++++    +
Sbjct: 121 ALDRAYLRVENQRYRDKLEAANRELQASLNLLQEDQNAGRQ 161

>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 = 97.5 bits (244), Expect = 1e-24
 Identities = 26/113 (23%), Positives = 62/113 (54%), Gaps = 3/113 (2%)

Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMD 77
           + VLV++DD ++  +LE+ L     +V    R + A  +L   +  +++V+ D+ +PD++
Sbjct: 1   MNVLVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLLS--EKHFNVVLLDLLLPDVN 58

Query: 78  GFKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNI 129
           G ++ + +     +  VI+++  G  +  ++ +  GA ++L KP  ++E+   
Sbjct: 59  GLEILKWIKERSPETEVIVITGHGTIKTAVEAMKMGAYDFLTKPCMLEEIELT 111

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

 Score = 96.7 bits (241), Expect = 2e-24
 Identities = 26/132 (19%), Positives = 50/132 (37%), Gaps = 8/132 (6%)

Query: 1   MSPASSSVAVSDQFPAGLRVLVVDDDPIWLRILEKMLRK-CLYEVTKCNRAEIALDMLRM 59
            +P  S   +       + VL+VDD  +    + + L      +   C+  + A+ +   
Sbjct: 2   HNPHESKTDLGAPLDGAVMVLLVDDQAMIGEAVRRSLASEAGIDFHFCSDPQQAVAVAN- 60

Query: 60  SKNGYDIVISDVHMPDMDGF----KLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACN 115
            +    +++ D+ MP +DG               D+P+I++S              GA +
Sbjct: 61  -QIKPTVILQDLVMPGVDGLTLLAAYRGNPATR-DIPIIVLSTKEEPTVKSAAFAAGAND 118

Query: 116 YLLKPIRIKELR 127
           YL+K     EL 
Sbjct: 119 YLVKLPDAIELV 130

>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 = 91.5 bits (228), Expect = 2e-24
 Identities = 27/111 (24%), Positives = 50/111 (45%), Gaps = 3/111 (2%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
            VLVVDD+ +    L   L+    +    + AE A   L   +    ++I+D+ M    G
Sbjct: 9   LVLVVDDNAVNREALILYLKSRGIDAVGADGAEEARLYLH-YQKRIGLMITDLRMQPESG 67

Query: 79  FKLHEQVGLE--MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
             L   +       L +I++S D   ++ +  +  G  ++LLKP+ + +L 
Sbjct: 68  LDLIRTIRASERAALSIIVVSGDTDVEEAVDVMHLGVVDFLLKPVDLGKLL 118

>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 = 91.4 bits (228), Expect = 2e-24
 Identities = 29/112 (25%), Positives = 59/112 (52%), Gaps = 3/112 (2%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           ++L+VDD      +L ++  K  Y+  +      ALD++   K   D+V+ D+ +P MDG
Sbjct: 5   KILIVDDQSGIRILLNEVFNKEGYQTFQAANGLQALDIVT--KERPDLVLLDMKIPGMDG 62

Query: 79  FKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNI 129
            ++ +++  ++ ++ VI+M+  G    + +    GA  +  KP  I E+R+ 
Sbjct: 63  IEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFAKPFDIDEIRDA 114

>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 = 96.0 bits (240), Expect = 3e-24
 Identities = 28/112 (25%), Positives = 48/112 (42%), Gaps = 3/112 (2%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           RVLVVDD+      L  +L +  Y          A   ++  +  + +++ DV MPD DG
Sbjct: 2   RVLVVDDEESITSSLSAILEEEGYHPDTAKTLREAEKKIK--ELFFPVIVLDVWMPDGDG 59

Query: 79  FKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNI 129
               + +     D  VI+++  G     +K +  GA  +L KP  ++     
Sbjct: 60  VNFIDFIKENSPDSVVIVITGHGSVDTAVKAIKKGAYEFLEKPFSVERFLLT 111

>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 = 91.1 bits (227), Expect = 5e-24
 Identities = 29/113 (25%), Positives = 56/113 (49%), Gaps = 7/113 (6%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           ++LV+DD+   L+ ++ +L     EV   + +   L +   + N  D+VI+D+ MP + G
Sbjct: 5   KILVIDDESTILQNIKFLLEIDGNEVLTASSSTEGLRIFTENCNSIDVVITDMKMPKLSG 64

Query: 79  FKLHEQV-GLEMDLPVIMMSVDGCTQ---DVMKGVTHGACNYLLKPIRIKELR 127
             +  ++  +   + VI+++  G        MK    GA  YL KP+  ++L 
Sbjct: 65  MDILREIKKITPHMAVIILTGHGDLDNAILAMK---EGAFEYLRKPVTAQDLS 114

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

 Score = 89.9 bits (224), Expect = 9e-24
 Identities = 25/121 (20%), Positives = 50/121 (41%), Gaps = 3/121 (2%)

Query: 17  GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDM 76
            L++L+V+DD      L  ++     EV      E    +     +  D++I+D+ MP +
Sbjct: 7   ALKILIVEDDTDAREWLSTIISNHFPEVWSAGDGEEGERLFG--LHAPDVIITDIRMPKL 64

Query: 77  DGFKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ 135
            G ++ +++        VI++S     +  +K +  G   +L KPI    L    +    
Sbjct: 65  GGLEMLDRIKAGGAKPYVIVISAFSEMKYFIKAIELGVHLFLPKPIEPGRLMETLEDFRH 124

Query: 136 Q 136
            
Sbjct: 125 I 125

>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 = 95.6 bits (238), Expect = 1e-23
 Identities = 37/112 (33%), Positives = 58/112 (51%), Gaps = 5/112 (4%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           R+LVVDD    +R+LE  L    YEV+       AL M    ++  DI++ DV MP MDG
Sbjct: 3   RILVVDDIEANVRLLEAKLTAEYYEVSTAMDGPTALAMAA--RDLPDIILLDVMMPGMDG 60

Query: 79  FKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           F +  ++        +PV++++      D ++G+  GA ++L KPI    L 
Sbjct: 61  FTVCRKLKDDPTTRHIPVVLITALDGRGDRIQGLESGASDFLTKPIDDVMLF 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 = 73.3 bits (180), Expect = 9e-16
 Identities = 23/111 (20%), Positives = 43/111 (38%), Gaps = 9/111 (8%)

Query: 21  LVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGF- 79
           L+VDD+    + +   L      V + +  +  +     +    D+VI +    + DG  
Sbjct: 156 LIVDDNERQAQRVAAELGVEHRPVIESDPEKAKI----SAGGPVDLVIVNAAAKNFDGLR 211

Query: 80  ---KLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
               L  +      LPV+ M        ++K +  G  + L +PI  +EL 
Sbjct: 212 FTAALRSEERTR-QLPVLAMVDPDDRGRMVKALEIGVNDILSRPIDPQELS 261

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

 Score = 90.0 bits (224), Expect = 2e-23
 Identities = 31/113 (27%), Positives = 51/113 (45%), Gaps = 4/113 (3%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
            +L+VD   + L+ L+++L    Y +     A  AL +L       D+VIS  H+P MDG
Sbjct: 16  EILLVDSQEVILQRLQQLLSPLPYTLHFARDATQALQLLA--SREVDLVISAAHLPQMDG 73

Query: 79  FKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGAC-NYLLKPIRIKELRNI 129
             L  ++         I+++ D   + + K +  G    YL KP   +EL   
Sbjct: 74  PTLLARIHQQYPSTTRILLTGDPDLKLIAKAINEGEIYRYLSKPWDDQELLLA 126

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

 Score = 89.2 bits (222), Expect = 3e-23
 Identities = 29/113 (25%), Positives = 54/113 (47%), Gaps = 4/113 (3%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
            V++VDD+   L  L++++++    +        AL+ L+       +VISD+ MP+M G
Sbjct: 9   TVMLVDDEQPILNSLKRLIKRLGCNIITFTSPLDALEALK--GTSVQLVISDMRMPEMGG 66

Query: 79  FKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGAC-NYLLKPIRIKELRNI 129
               EQV     D+  +++S     Q  +  V  G    +LLKP   +++  +
Sbjct: 67  EVFLEQVAKSYPDIERVVISGYADAQATIDAVNRGKISRFLLKPWEDEDVFKV 119

>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 = 87.6 bits (218), Expect = 5e-23
 Identities = 37/115 (32%), Positives = 51/115 (44%), Gaps = 9/115 (7%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
            V VVDDD     +LE+ L       T        L  L       D+++SD+ MP MDG
Sbjct: 5   IVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAALA--SKTPDVLLSDIRMPGMDG 62

Query: 79  FKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVT---HGACNYLLKPIRIKELRNI 129
             L +Q+      LPVI+M+      D+   V+    GA +YL KP  I E   +
Sbjct: 63  LALLKQIKQRHPMLPVIIMTAHS---DLDAAVSAYQQGAFDYLPKPFDIDEAVAL 114

>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 = 90.8 bits (226), Expect = 8e-23
 Identities = 33/116 (28%), Positives = 52/116 (44%), Gaps = 6/116 (5%)

Query: 15  PAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMP 74
              + VLVVDD           LRK L +V + + A  AL  L        +V+ D +MP
Sbjct: 122 NQQIEVLVVDDSRTSRHRTMAQLRKQLLQVHEASHAREALATLEQHPA-IRLVLVDYYMP 180

Query: 75  DMDGF----KLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
           ++DG      L E+   +  L +I +SV        + +  GA ++L +P   +EL
Sbjct: 181 EIDGISLVRMLRERYSKQ-QLAIIGISVSDKRGLSARYLKQGANDFLNQPFEPEEL 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 = 84.3 bits (209), Expect = 2e-20
 Identities = 19/104 (18%), Positives = 44/104 (42%), Gaps = 3/104 (2%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           ++L+V+D     R+L + + +                  +   + Y + + D+ +PD   
Sbjct: 6   KILIVEDSMTIRRMLIQAIAQQTGLEIDAFDTLEGARHCQ--GDEYVVALVDLTLPDAPS 63

Query: 79  FKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIR 122
            +  + + LE  LPV++++ D         +  G  +Y++K  R
Sbjct: 64  GEAVKVL-LERGLPVVILTADISEDKREAWLEAGVLDYVMKDSR 106

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

 Score = 86.8 bits (216), Expect = 1e-22
 Identities = 23/110 (20%), Positives = 52/110 (47%), Gaps = 3/110 (2%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           RVL+V+D      + ++ ++   Y++        A+  +   ++   ++I D+ +PDM G
Sbjct: 6   RVLLVEDSTSLAILYKQYVKDEPYDIFHVETGRDAIQFIE--RSKPQLIILDLKLPDMSG 63

Query: 79  FKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
             + + +   ++   VI+ +  G     +  +  GA ++L KPI    L+
Sbjct: 64  EDVLDWINQNDIPTSVIIATAHGSVDLAVNLIQKGAEDFLEKPINADRLK 113

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

 Score = 86.8 bits (216), Expect = 2e-22
 Identities = 28/110 (25%), Positives = 46/110 (41%), Gaps = 4/110 (3%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
            V+VVD+  I    ++  L K  + V      + A   LR  +   D+V  DV     + 
Sbjct: 6   TVMVVDESRITFLAVKNALEKDGFNVIWAKNEQEAFTFLR--REKIDLVFVDV-FEGEES 62

Query: 79  FKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
             L  ++     D  V ++S       ++  V  GA +Y+LKP R+  L 
Sbjct: 63  LNLIRRIREEFPDTKVAVLSAYVDKDLIINSVKAGAVDYILKPFRLDYLL 112

>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 = 88.2 bits (219), Expect = 6e-22
 Identities = 43/149 (28%), Positives = 72/149 (48%), Gaps = 15/149 (10%)

Query: 2   SPASSSVAVSDQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSK 61
           + A  S   +      + +LVVDD PI  R+L   L    Y+    N    AL++L   K
Sbjct: 114 ANALPSTDKAVSDNDDMMILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVLS--K 171

Query: 62  NGYDIVISDVHMPDMDGFKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGAC------ 114
           N  DIV+SDV+MP+MDG++L +++  L + LPVI +     T + +       C      
Sbjct: 172 NHIDIVLSDVNMPNMDGYRLTQRIRQLGLTLPVIGV-----TANALAE-EKQRCLESGMD 225

Query: 115 NYLLKPIRIKELRNIWQHVAQQPKPFEES 143
           + L KP+ +  ++      A++ +   +S
Sbjct: 226 SCLSKPVTLDVIKQTLTLYAERVRKSRDS 254

>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 = 85.8 bits (213), Expect = 2e-21
 Identities = 31/113 (27%), Positives = 52/113 (46%), Gaps = 3/113 (2%)

Query: 15  PAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMP 74
            A   V VVDDD      L  +LR   +EV   + A   L+  R     +  ++ D+ MP
Sbjct: 2   TAKPTVFVVDDDMSVREGLRNLLRSAGFEVETFDCASTFLEHRR--PEQHGCLVLDMRMP 59

Query: 75  DMDGFKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
            M G +L EQ+  +   +P++ ++  G     ++ +  GA  +L KP   + L
Sbjct: 60  GMSGIELQEQLTAISDGIPIVFITAHGDIPMTVRAMKAGAIEFLPKPFEEQAL 112

>3eqz_A Response regulator; structural genomics, unknown function, PSI-2, protein struct initiative; 2.15A {Colwellia psychrerythraea} Length = 135

 Score = 84.2 bits (209), Expect = 2e-21
 Identities = 29/114 (25%), Positives = 47/114 (41%), Gaps = 9/114 (7%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           RV +VDDD +   +L+ ++      V        A   L    N  DI+I D+ MPDMDG
Sbjct: 5   RVFIVDDDTLTCNLLKTIVEPIFGNVEAFQHPR-AFLTLS--LNKQDIIILDLMMPDMDG 61

Query: 79  FKLHEQV-GLEMDLPVIMMS-----VDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
            ++   +   +    +I++S     V    + +         N   KPI  + L
Sbjct: 62  IEVIRHLAEHKSPASLILISGYDSGVLHSAETLALSCGLNVINTFTKPINTEVL 115

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

 Score = 83.8 bits (208), Expect = 2e-21
 Identities = 27/115 (23%), Positives = 46/115 (40%), Gaps = 6/115 (5%)

Query: 16  AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPD 75
           +  + L+V+D        +++L    ++         AL  +     GYD V  D+++PD
Sbjct: 2   SLQQALIVEDYQAAAETFKELLEMLGFQADYVMSGTDALHAMS--TRGYDAVFIDLNLPD 59

Query: 76  MDGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
             G  L +Q+    +E     + +S      D+ K        YL KPI I  L 
Sbjct: 60  TSGLALVKQLRALPMEKTSKFVAVSGFA-KNDLGKEACELFDFYLEKPIDIASLE 113

>3cg0_A Response regulator receiver modulated diguanylate with PAS/PAC sensor; signal receiver domain, diguanylate cyclase; 2.15A {Desulfovibrio desulfuricans subsp} Length = 140

 Score = 83.8 bits (208), Expect = 3e-21
 Identities = 23/111 (20%), Positives = 43/111 (38%), Gaps = 4/111 (3%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTK-CNRAEIALDMLRMSKNGYDIVISDVHM-PDM 76
            VL+V+D  +    L   L    Y+V    +  E A+          DI + D+ +   +
Sbjct: 11  GVLIVEDGRLAAATLRIQLESLGYDVLGVFDNGEEAVRCAP--DLRPDIALVDIMLCGAL 68

Query: 77  DGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           DG +   ++    +LP+I ++     +   +        YL KP+    L 
Sbjct: 69  DGVETAARLAAGCNLPIIFITSSQDVETFQRAKRVNPFGYLAKPVAADTLH 119

>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 = 84.3 bits (209), Expect = 4e-21
 Identities = 27/128 (21%), Positives = 59/128 (46%), Gaps = 3/128 (2%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
             LV+DD+ ++   L + L +  Y V + +  + AL +    K  ++ +   +H+ +  G
Sbjct: 9   NFLVIDDNEVFAGTLARGLERRGYAVRQAHNKDEALKLAGAEK--FEFITVXLHLGNDSG 66

Query: 79  FKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQP 137
             L   +  L+ D  +++++        ++ V  GA NYL KP  ++ +    Q  A + 
Sbjct: 67  LSLIAPLCDLQPDARILVLTGYASIATAVQAVKDGADNYLAKPANVESILAALQTNASEV 126

Query: 138 KPFEESDD 145
           +  E  ++
Sbjct: 127 QAEEALEN 134

>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 = 82.9 bits (205), Expect = 5e-21
 Identities = 28/109 (25%), Positives = 55/109 (50%), Gaps = 3/109 (2%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           R+L+VDDD   L   +++L    YEV     A   L  +      +++ +  + +PDM+G
Sbjct: 5   RILIVDDDTAILDSTKQILEFEGYEVEIAATAGEGLAKIE--NEFFNLALFXIKLPDMEG 62

Query: 79  FKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
            +L E+   L   +  IM++     ++ +  +  GA  Y++KP+  ++L
Sbjct: 63  TELLEKAHKLRPGMKKIMVTGYASLENSVFSLNAGADAYIMKPVNPRDL 111

>2jk1_A HUPR, hydrogenase transcriptional regulatory protein HU; nucleotide-binding, transcription regulation; 2.10A {Rhodobacter capsulatus} PDB: 2vui_B 2vuh_B Length = 139

 Score = 82.2 bits (204), Expect = 1e-20
 Identities = 25/113 (22%), Positives = 49/113 (43%), Gaps = 5/113 (4%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
            +L+VDD+P  L  ++  L    ++V     AE A+ +L   +    ++I D  MP   G
Sbjct: 3   AILLVDDEPHSLAAMKLALEDD-FDVLTAQGAEAAIAILE--EEWVQVIICDQRMPGRTG 59

Query: 79  FKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTH-GACNYLLKPIRIKELRNI 129
                +V     +   I+++    +  +M  +   G   +L KP   ++L + 
Sbjct: 60  VDFLTEVRERWPETVRIIITGYTDSASMMAAINDAGIHQFLTKPWHPEQLLSS 112

>3ilh_A Two component response regulator; NYSGXRC, PSI-II, protein S initiative, structural genomics; 2.59A {Cytophaga hutchinsonii} Length = 146

 Score = 82.4 bits (204), Expect = 1e-20
 Identities = 25/124 (20%), Positives = 52/124 (41%), Gaps = 11/124 (8%)

Query: 17  GLRVLVVDDDPIWLRILEKMLRK--CLYEVTKCNRAEIALDMLR---MSKNGYDIVISDV 71
              VL++DDD I   +   ++R    + E+        A++ L     +     I+  D+
Sbjct: 9   IDSVLLIDDDDIVNFLNTTIIRMTHRVEEIQSVTSGNAAINKLNELYAAGRWPSIICIDI 68

Query: 72  HMPDMDGFKLHEQV-----GLEMDLPVIMMSVDGCTQDVMKGVTHGACN-YLLKPIRIKE 125
           +MP ++G++L +        ++    V ++S     +D  K       + Y+ KP+    
Sbjct: 69  NMPGINGWELIDLFKQHFQPMKNKSIVCLLSSSLDPRDQAKAEASDWVDYYVSKPLTANA 128

Query: 126 LRNI 129
           L N+
Sbjct: 129 LNNL 132

>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 = 81.8 bits (203), Expect = 2e-20
 Identities = 34/118 (28%), Positives = 57/118 (48%), Gaps = 15/118 (12%)

Query: 16  AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPD 75
           A   V ++DDD    + +++ L    + V+    A  AL  L    +   IVISD+ MP 
Sbjct: 2   AAPSVFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGLS--ADFAGIVISDIRMPG 59

Query: 76  MDGFKLHEQV-GLEMDLPVIMMSVDGCTQDV------MKGVTHGACNYLLKPIRIKEL 126
           MDG  L  ++  L+ DLP+I+++  G   D+      ++    GA +++ KP     L
Sbjct: 60  MDGLALFRKILALDPDLPMILVTGHG---DIPMAVQAIQD---GAYDFIAKPFAADRL 111

>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 = 2e-20
 Identities = 27/113 (23%), Positives = 58/113 (51%), Gaps = 4/113 (3%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           R+L+VDDD   L  L++ L    +EVT C     AL  ++   + + +++ D+ MP M+G
Sbjct: 6   RILLVDDDYSLLNTLKRNLSFD-FEVTTCESGPEALACIK-KSDPFSVIMVDMRMPGMEG 63

Query: 79  FKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHG-ACNYLLKPIRIKELRNI 129
            ++ ++   +  +   +M++ +      M+ V  G    +L KP ++ +++  
Sbjct: 64  TEVIQKARLISPNSVYLMLTGNQDLTTAMEAVNEGQVFRFLNKPCQMSDIKAA 116

>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 = 81.0 bits (201), Expect = 2e-20
 Identities = 30/115 (26%), Positives = 52/115 (45%), Gaps = 15/115 (13%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
            V +VDD+    + L  ML    + V     AE  L           ++++D+ MPDM G
Sbjct: 5   TVHIVDDEEPVRKSLAFMLTMNGFAVKMHQSAEAFLAFAP--DVRNGVLVTDLRMPDMSG 62

Query: 79  FKLHEQV-GLEMDLPVIMMSVDGCTQDV------MKGVTHGACNYLLKPIRIKEL 126
            +L   +  L++++P I+++  G   DV      MK    GA +++ KP     +
Sbjct: 63  VELLRNLGDLKINIPSIVITGHG---DVPMAVEAMK---AGAVDFIEKPFEDTVI 111

>3h5i_A Response regulator/sensory box protein/ggdef domain protein; structural genomics, transcription, PSI-2; 1.90A {Carboxydothermus hydrogenoformans z-2901} Length = 140

 Score = 80.7 bits (200), Expect = 4e-20
 Identities = 23/110 (20%), Positives = 48/110 (43%), Gaps = 2/110 (1%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMP-DMD 77
           ++L+V+D     + +  +L K  Y V      E A++ +       D+++ D+ +   MD
Sbjct: 7   KILIVEDSKFQAKTIANILNKYGYTVEIALTGEAAVEKVS-GGWYPDLILMDIELGEGMD 65

Query: 78  GFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           G +    +    +LPV+ ++       V K  +  A  Y++K    + L 
Sbjct: 66  GVQTALAIQQISELPVVFLTAHTEPAVVEKIRSVTAYGYVMKSATEQVLI 115

>3gt7_A Sensor protein; structural genomics, signal receiver domain, kinase, PSI-2, protein structure initiative; 2.30A {Syntrophus aciditrophicus SB} Length = 154

 Score = 80.8 bits (200), Expect = 5e-20
 Identities = 32/112 (28%), Positives = 60/112 (53%), Gaps = 7/112 (6%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
            +L+V+D P     L+ +L +  Y+         A+  L +++   D++ISDV MP+MDG
Sbjct: 9   EILIVEDSPTQAEHLKHILEETGYQTEHVRNGREAVRFLSLTR--PDLIISDVLMPEMDG 66

Query: 79  F----KLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
           +     L  Q  L   +PVI++++    +DV++ +  GA +++ KP +   L
Sbjct: 67  YALCRWLKGQPDLR-TIPVILLTILSDPRDVVRSLECGADDFITKPCKDVVL 117

>3grc_A Sensor protein, kinase; protein structure initiative II(PSI II), NYSGXRC, 11025B, structural genomics; 2.21A {Polaromonas SP} Length = 140

 Score = 79.9 bits (198), Expect = 9e-20
 Identities = 28/112 (25%), Positives = 50/112 (44%), Gaps = 6/112 (5%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           R+L+ +DDP   R+L  ML K  ++    + A  AL+ +   +  Y  +  D+++PD DG
Sbjct: 8   RILICEDDPDIARLLNLMLEKGGFDSDMVHSAAQALEQVA--RRPYAAMTVDLNLPDQDG 65

Query: 79  FKLHEQV---GLEMDLPVIMMSVDGCTQD-VMKGVTHGACNYLLKPIRIKEL 126
             L   +       DL ++++S +    +            +L KPI    L
Sbjct: 66  VSLIRALRRDSRTRDLAIVVVSANAREGELEFNSQPLAVSTWLEKPIDENLL 117

>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 = 79.1 bits (196), Expect = 1e-19
 Identities = 32/114 (28%), Positives = 56/114 (49%), Gaps = 6/114 (5%)

Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYE-VTKCNRAEIALDMLRMSKNGYDIVISDVHMPDM 76
           ++VL+VDD      +L   L++  ++ +T     E  + ++   +N + +VISD +MP M
Sbjct: 7   IKVLIVDDQVTSRLLLGDALQQLGFKQITAAGDGEQGMKIMA--QNPHHLVISDFNMPKM 64

Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           DG  L + V           I+++  G    V K    GA N L KP  I++++
Sbjct: 65  DGLGLLQAVRANPATKKAAFIILTAQGDRALVQKAAALGANNVLAKPFTIEKMK 118

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

 Score = 79.5 bits (197), Expect = 1e-19
 Identities = 37/146 (25%), Positives = 64/146 (43%), Gaps = 19/146 (13%)

Query: 5   SSSVAVSDQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGY 64
           S+           +R+LV DD      +L+++L K  ++V   N AE  LD +   +  Y
Sbjct: 2   SNPFLRHRARVRSMRMLVADDHEANRMVLQRLLEKAGHKVLCVNGAEQVLDAMA--EEDY 59

Query: 65  DIVISDVHMPDMDGF------KLHEQVGLEMDLPVIMMSVDGCTQDVMKG-----VTHGA 113
           D VI D+HMP M+G       ++ +  G+    PV+++     + DV           GA
Sbjct: 60  DAVIVDLHMPGMNGLDMLKQLRVMQASGMR-YTPVVVL-----SADVTPEAIRACEQAGA 113

Query: 114 CNYLLKPIRIKELRNIWQHVAQQPKP 139
             +L KP+   +L +    +A   + 
Sbjct: 114 RAFLAKPVVAAKLLDTLADLAVSTRQ 139

>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 = 79.2 bits (196), Expect = 1e-19
 Identities = 35/114 (30%), Positives = 59/114 (51%), Gaps = 6/114 (5%)

Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYE-VTKCNRAEIALDMLRMSKNGYDIVISDVHMPDM 76
           L+ LVVDD     RI+  +L++  +  V +      AL+ L+    GY  VISD +MP+M
Sbjct: 5   LKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQ--AGGYGFVISDWNMPNM 62

Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           DG +L + +        LPV+M++ +   ++++     GA  Y++KP     L 
Sbjct: 63  DGLELLKTIRAXXAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLE 116

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

 Score = 78.9 bits (195), Expect = 2e-19
 Identities = 25/110 (22%), Positives = 46/110 (41%), Gaps = 4/110 (3%)

Query: 19  RVLVVDDDPIWLRILEKMLRKC-LYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMD 77
           +V +   DP + R +   L    +Y+V      +        ++    IVI D+   D+ 
Sbjct: 16  QVALFSSDPNFKRDVATRLDALAIYDVRVSETDDFLKGPPADTR--PGIVILDLGGGDLL 73

Query: 78  GFKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
           G     +   L   +P+I +S +  ++     V   A ++L KP+  KEL
Sbjct: 74  GKPGIVEARALWATVPLIAVSDELTSEQTRVLVRMNASDWLHKPLDGKEL 123

>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 = 79.1 bits (196), Expect = 2e-19
 Identities = 26/114 (22%), Positives = 48/114 (42%), Gaps = 7/114 (6%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCL--YEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDM 76
            +L+++DD  +  +L + L       ++        A D+L       D+V+ D+ M  M
Sbjct: 10  SILIIEDDKEFADMLTQFLENLFPYAKIKIAYNPFDAGDLLH--TVKPDVVMLDLMMVGM 67

Query: 77  DGFKLHEQVGLEM---DLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           DGF +  ++       ++ VI M+      +V + V  GA     KP+    L 
Sbjct: 68  DGFSICHRIKSTPATANIIVIAMTGALTDDNVSRIVALGAETCFGKPLNFTLLE 121

>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 = 79.5 bits (196), Expect = 2e-19
 Identities = 28/112 (25%), Positives = 50/112 (44%), Gaps = 4/112 (3%)

Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEV--TKCNRAEIALDMLRMSKNGYDIVISDVHMPD 75
             VL+VDD    ++ L ++     + +  T  +  E A+   +      DIV   + MP 
Sbjct: 37  FNVLIVDDSVFTVKQLTQIFTSEGFNIIDTAADGEE-AVIKYKNHYPNIDIVTLXITMPK 95

Query: 76  MDGFKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
           MDG      +   + +  VIM+S  G  Q V   +  GA  +++KP+   ++
Sbjct: 96  MDGITCLSNIMEFDKNARVIMISALGKEQLVKDCLIKGAKTFIVKPLDRAKV 147

>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 = 81.3 bits (200), Expect = 2e-19
 Identities = 38/174 (21%), Positives = 73/174 (41%), Gaps = 3/174 (1%)

Query: 3   PASSSVAVSDQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKN 62
              ++    +      RVLVVDD+   + +L   L+   +EV        ALD  R  + 
Sbjct: 9   DLVTAGTPGENTTPEARVLVVDDEANIVELLSVSLKFQGFEVYTATNGAQALDRAR--ET 66

Query: 63  GYDIVISDVHMPDMDGFKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPI 121
             D VI DV MP MDGF +  ++    +D P + ++     QD + G+T G  +Y+ KP 
Sbjct: 67  RPDAVILDVXMPGMDGFGVLRRLRADGIDAPALFLTARDSLQDKIAGLTLGGDDYVTKPF 126

Query: 122 RIKELRNIWQHVAQQPKPFEESDDSYSVNQGNWRTSNRRKDEEEEAEKRDDTST 175
            ++E+    + + ++     +   +  +   +        +  +  +    + T
Sbjct: 127 SLEEVVARLRVILRRAGKGNKEPRNVRLTFADIELDEETHEVWKAGQPVSLSPT 180

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

 Score = 78.0 bits (193), Expect = 3e-19
 Identities = 31/118 (26%), Positives = 56/118 (47%), Gaps = 4/118 (3%)

Query: 12  DQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDV 71
            Q   G ++L+V+D+ ++  +L+                  AL++L       D++I D+
Sbjct: 2   TQPLVGKQILIVEDEQVFRSLLDSWFSSLGATTVLAADGVDALELLGGFT--PDLMICDI 59

Query: 72  HMPDMDGFKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIR-IKELR 127
            MP M+G KL E +       PV+++S      D+ K +  G  + LLKP++ +  LR
Sbjct: 60  AMPRMNGLKLLEHIRNRGDQTPVLVISATENMADIAKALRLGVEDVLLKPVKDLNRLR 117

>2qr3_A Two-component system response regulator; structural genomics, signal receiver, PSI-2, protein structu initiative; 1.80A {Bacteroides fragilis} Length = 140

 Score = 77.2 bits (191), Expect = 8e-19
 Identities = 21/117 (17%), Positives = 53/117 (45%), Gaps = 8/117 (6%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPD--- 75
            +++VDD+   L  ++ +L+    +V   +       +LR  +   ++V+ D++      
Sbjct: 5   TIIIVDDNKGVLTAVQLLLKNHFSKVITLSSPVSLSTVLR--EENPEVVLLDMNFTSGIN 62

Query: 76  --MDGFKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNI 129
              +G     ++     DLPV++ +        ++G+  GA ++++KP   ++L   
Sbjct: 63  NGNEGLFWLHEIKRQYRDLPVVLFTAYADIDLAVRGIKEGASDFVVKPWDNQKLLET 119

>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 = 80.2 bits (198), Expect = 1e-18
 Identities = 22/111 (19%), Positives = 54/111 (48%), Gaps = 6/111 (5%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVT-KCNRAEIALDMLRMSKNGYDIVISDVHMPD-M 76
            VL+++D+P+    +E ++R+  ++VT        AL+ +   +    +V++D+ + D  
Sbjct: 162 EVLIIEDEPVIAADIEALVRELGHDVTDIAATRGEALEAVT--RRTPGLVLADIQLADGS 219

Query: 77  DGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
            G    + +   MD+PVI ++     + ++ G        + KP + + ++
Sbjct: 220 SGIDAVKDILGRMDVPVIFIT--AFPERLLTGERPEPTFLITKPFQPETVK 268

>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 = 76.8 bits (190), Expect = 1e-18
 Identities = 30/111 (27%), Positives = 52/111 (46%), Gaps = 5/111 (4%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
            +LVVDD P+ + +   ML +  Y        E  L+ L  +    D+V+ D+ M  MDG
Sbjct: 5   TILVVDDSPMIVDVFVTMLERGGYRPITAFSGEECLEALNATP--PDLVLLDIMMEPMDG 62

Query: 79  FKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
           ++  E++       D+PV+M++    T +          +Y+LKP    +L
Sbjct: 63  WETLERIKTDPATRDIPVLMLTAKPLTPEEANEYGSYIEDYILKPTTHHQL 113

>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 = 78.2 bits (193), Expect = 1e-18
 Identities = 30/116 (25%), Positives = 54/116 (46%), Gaps = 3/116 (2%)

Query: 15  PAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGY-DIVISDVHM 73
               RVL+ +D+ +    L +MLR+  YE+     A    + + +++    D+VI DV M
Sbjct: 11  AVPRRVLIAEDEALIRMDLAEMLREEGYEIVGE--AGDGQEAVELAELHKPDLVIMDVKM 68

Query: 74  PDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNI 129
           P  DG     ++  +   P+++++       V +    GA  YL+KP  I +L   
Sbjct: 69  PRRDGIDAASEIASKRIAPIVVLTAFSQRDLVERARDAGAMAYLVKPFSISDLIPA 124

>3lte_A Response regulator; structural genomics, PSI, protein structure initiative, NYSG YORK structural genomix research consortium, nysgxrc; 2.00A {Bermanella marisrubri} Length = 132

 Score = 76.1 bits (188), Expect = 2e-18
 Identities = 29/110 (26%), Positives = 49/110 (44%), Gaps = 4/110 (3%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           R+LVVDDD      +E++L++  ++V   +    A   L        I+  D+ MP +DG
Sbjct: 8   RILVVDDDQAMAAAIERVLKRDHWQVEIAHNGFDAGIKLS--TFEPAIMTLDLSMPKLDG 65

Query: 79  FKLHEQV--GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
             +   +      + P I++        + + VT GA +YL KP     L
Sbjct: 66  LDVIRSLRQNKVANQPKILVVSGLDKAKLQQAVTEGADDYLEKPFDNDAL 115

>3q9s_A DNA-binding response regulator; DNA binding protein; 2.40A {Deinococcus radiodurans} Length = 249

 Score = 78.8 bits (195), Expect = 2e-18
 Identities = 31/126 (24%), Positives = 59/126 (46%), Gaps = 2/126 (1%)

Query: 1   MSPASSSVAVSDQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMS 60
              AS +           R+LV++DD     +L   L    Y V   + A   L   R  
Sbjct: 21  SHMASMTGGQQMGRMNEQRILVIEDDHDIANVLRMDLTDAGYVVDHADSAMNGLIKAR-- 78

Query: 61  KNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKP 120
           ++  D+++ D+ +PD DG  + +++     LP+I+++     ++ ++ +  GA +YL+KP
Sbjct: 79  EDHPDLILLDLGLPDFDGGDVVQRLRKNSALPIIVLTARDTVEEKVRLLGLGADDYLIKP 138

Query: 121 IRIKEL 126
               EL
Sbjct: 139 FHPDEL 144

>2qzj_A Two-component response regulator; 11017X, PSI-II, structural genomics; 2.89A {Clostridium difficile} Length = 136

 Score = 76.0 bits (188), Expect = 2e-18
 Identities = 23/108 (21%), Positives = 53/108 (49%), Gaps = 2/108 (1%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           ++L++D D    + L+  L +    +      E A+  +    N YD++  ++ + D DG
Sbjct: 6   KILIIDGDKDNCQKLKGFLEEKGISIDLAYNCEEAIGKIF--SNKYDLIFLEIILSDGDG 63

Query: 79  FKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
           + L +++      P++ M+     Q ++  +  G  +YL+KP+ ++ L
Sbjct: 64  WTLCKKIRNVTTCPIVYMTYINEDQSILNALNSGGDDYLIKPLNLEIL 111

>2zay_A Response regulator receiver protein; structural genomics, NYSGXRC, target 11006U, protein structure initiative; 2.00A {Desulfuromonas acetoxidans} Length = 147

 Score = 76.1 bits (188), Expect = 3e-18
 Identities = 22/112 (19%), Positives = 49/112 (43%), Gaps = 7/112 (6%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           R+++VD     L      L +  +++ +C  A  A+ +    K    ++I++ +MP + G
Sbjct: 10  RIMLVDTQLPALAASISALSQEGFDIIQCGNAIEAVPVAV--KTHPHLIITEANMPKISG 67

Query: 79  F----KLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
                 L +       +PVI +S     ++  + +  G  +++ KP+    L
Sbjct: 68  MDLFNSLKKNPQTA-SIPVIALSGRATAKEEAQLLDMGFIDFIAKPVNAIRL 118

>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 = 75.1 bits (186), Expect = 3e-18
 Identities = 35/108 (32%), Positives = 62/108 (57%), Gaps = 2/108 (1%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           ++LVVDD+     ILE  LRK  YEV   +    A++M+   +   D+++ D+ +P+ DG
Sbjct: 4   KILVVDDEKPIADILEFNLRKEGYEVHCAHDGNEAVEMVE--ELQPDLILLDIMLPNKDG 61

Query: 79  FKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
            ++  +V  + D+P+IM++      D + G+  GA +Y+ KP   +EL
Sbjct: 62  VEVCREVRKKYDMPIIMLTAKDSEIDKVIGLEIGADDYVTKPFSTREL 109

>3lua_A Response regulator receiver protein; two-component signal transduction system, histidine kinase, phosphorelay, receiver domain, nysgxrc; 2.40A {Clostridium thermocellum} Length = 140

 Score = 75.8 bits (187), Expect = 3e-18
 Identities = 17/113 (15%), Positives = 41/113 (36%), Gaps = 6/113 (5%)

Query: 19  RVLVVDDDPIWLRILEKMLRKC-LYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMP-DM 76
            VL++D         + +      Y+  +    +    + +   +   ++I D+  P + 
Sbjct: 6   TVLLIDYFEYEREKTKIIFDNIGEYDFIEVENLKKFYSIFK-DLDSITLIIMDIAFPVEK 64

Query: 77  DGFKLHEQVGLEM---DLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
           +G ++   +       + PVI+ +           +     +Y+LKP   K L
Sbjct: 65  EGLEVLSAIRNNSRTANTPVIIATKSDNPGYRHAALKFKVSDYILKPYPTKRL 117

>1i3c_A Response regulator RCP1; phytochrome, signaling protein; 1.90A {Synechocystis SP} SCOP: c.23.1.1 PDB: 1jlk_A Length = 149

 Score = 75.8 bits (187), Expect = 4e-18
 Identities = 24/147 (16%), Positives = 59/147 (40%), Gaps = 19/147 (12%)

Query: 11  SDQFPAGLRVLVVDDDPIWLRILEKMLRKC--LYEVTKCNRAEIALDMLRMSKNGY---- 64
           SD+      +L+V+D     R+++++L+     +E+        A+  L+          
Sbjct: 2   SDESNPPKVILLVEDSKADSRLVQEVLKTSTIDHELIILRDGLAAMAFLQQQGEYENSPR 61

Query: 65  -DIVISDVHMPDMDGF----KLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLK 119
            ++++ D+++P  DG     ++ +   L+  +PV++++      DV+         YL K
Sbjct: 62  PNLILLDLNLPKKDGREVLAEIKQNPDLK-RIPVVVLTTSHNEDDVIASYELHVNCYLTK 120

Query: 120 PI-------RIKELRNIWQHVAQQPKP 139
                     ++ + + W      P  
Sbjct: 121 SRNLKDLFKMVQGIESFWLETVTLPAA 147

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

 Score = 74.9 bits (185), Expect = 5e-18
 Identities = 27/113 (23%), Positives = 50/113 (44%), Gaps = 7/113 (6%)

Query: 17  GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPD- 75
            + +L+ DD+ I L   E  L    + VT  +    A++ML+ S    D V++D+     
Sbjct: 5   AVTILLADDEAILLLDFESTLTDAGFLVTAVSSGAKAIEMLK-SGAAIDGVVTDIRFCQP 63

Query: 76  MDGFKLHEQVGLEM--DLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
            DG+++      E+  ++P++ +S     +    GV       L KP    +L
Sbjct: 64  PDGWQVARVA-REIDPNMPIVYISGHAALEWASNGVPDSI--ILEKPFTSAQL 113

>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 = 74.8 bits (185), Expect = 5e-18
 Identities = 32/115 (27%), Positives = 61/115 (53%), Gaps = 5/115 (4%)

Query: 16  AGLRVLVVDDDPIWLRILEKMLRKCLYE-VTKCNRAEIALDMLRMSKNGYDIVISDVHMP 74
             +++LVVDD     RI++  L +  YE V +      A + L  +     ++I+D +MP
Sbjct: 4   GSMKLLVVDDSSTMRRIIKNTLSRLGYEDVLEAEHGVEAWEKLD-ANADTKVLITDWNMP 62

Query: 75  DMDGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
           +M+G  L ++V       ++P+IM++ +G   +V+  +  G  NY++KP   + L
Sbjct: 63  EMNGLDLVKKVRSDSRFKEIPIIMITAEGGKAEVITALKAGVNNYIVKPFTPQVL 117

>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 = 5e-18
 Identities = 25/133 (18%), Positives = 61/133 (45%), Gaps = 18/133 (13%)

Query: 17  GLRVLVVDDDPIWLRILEKMLRKC--LYEVTKCNRAEIALDMLR----MSKNGYDIVISD 70
            + +L ++DD + ++ +E++  K   L ++        ALDML      +K    +++ D
Sbjct: 7   KVDILYLEDDEVDIQSVERVFHKISSLIKIEIAKSGNQALDMLYGRNKENKIHPKLILLD 66

Query: 71  VHMPDMDGF----KLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPI----- 121
           +++P M+G     +L +      D+ V +++    ++D +   +     +L+KP+     
Sbjct: 67  INIPKMNGIEFLKELRDDSSFT-DIEVFVLTAAYTSKDKLAFESLNIRGHLIKPLDYGEA 125

Query: 122 --RIKELRNIWQH 132
                 L+++  H
Sbjct: 126 IKLFWILQSMEGH 138

>3cg4_A Response regulator receiver domain protein (CHEY-; structural genomics, unknown function; HET: MSE; 1.61A {Methanospirillum hungatei jf-1} Length = 142

 Score = 75.3 bits (186), Expect = 6e-18
 Identities = 25/111 (22%), Positives = 51/111 (45%), Gaps = 5/111 (4%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
            V++VDDD      ++ +L    + +   +     +D+L+  K    +V+ D+ MP MDG
Sbjct: 9   DVMIVDDDAHVRIAVKTILSDAGFHIISADSGGQCIDLLK--KGFSGVVLLDIMMPGMDG 66

Query: 79  FKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
           +     +    LE  + ++M++        M G+     +Y+ KP   ++L
Sbjct: 67  WDTIRAILDNSLEQGIAIVMLTAKNAPDAKMIGLQEYVVDYITKPFDNEDL 117

>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 = 77.2 bits (191), Expect = 6e-18
 Identities = 33/108 (30%), Positives = 59/108 (54%), Gaps = 2/108 (1%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           R+LVVDDD     +L  +LR   ++         AL  +R  +   D+V+ D+ +P M+G
Sbjct: 7   RILVVDDDASLAEMLTIVLRGEGFDTAVIGDGTQALTAVR--ELRPDLVLLDLMLPGMNG 64

Query: 79  FKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
             +   +  +  +P++M++    T DV+ G+  GA +Y++KP + KEL
Sbjct: 65  IDVCRVLRADSGVPIVMLTAKTDTVDVVLGLESGADDYIMKPFKPKEL 112

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

 Score = 74.5 bits (184), Expect = 9e-18
 Identities = 31/140 (22%), Positives = 58/140 (41%), Gaps = 15/140 (10%)

Query: 8   VAVSDQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIV 67
           +++       L VL+ +D+ I   +  K L KC  ++T       AL   +     +D++
Sbjct: 1   MSLEPSQIMPLSVLIAEDNDICRLVAAKALEKCTNDITVVTNGLQALQAYQ--NRQFDVI 58

Query: 68  ISDVHMPDMDGF------KLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGA-CN-YLLK 119
           I D+ MP MDG       + +E+        +I +     T D +     GA  + Y+ K
Sbjct: 59  IMDIQMPVMDGLEAVSEIRNYERTHNTKRASIIAI-----TADTIDDDRPGAELDEYVSK 113

Query: 120 PIRIKELRNIWQHVAQQPKP 139
           P+   +LR++      +   
Sbjct: 114 PLNPNQLRDVVLTCHSEGAE 133

>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 = 74.0 bits (183), Expect = 1e-17
 Identities = 30/108 (27%), Positives = 56/108 (51%), Gaps = 2/108 (1%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           ++L+VDD+     I++  + K  YEV        AL+         DI+I D+ +P++DG
Sbjct: 3   KILIVDDEKPISDIIKFNMTKEGYEVVTAFNGREALEQFE--AEQPDIIILDLMLPEIDG 60

Query: 79  FKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
            ++ + +     +P++M+S      D + G+  GA +Y+ KP   +EL
Sbjct: 61  LEVAKTIRKTSSVPILMLSAKDSEFDKVIGLELGADDYVTKPFSNREL 108

>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 = 76.4 bits (189), Expect = 1e-17
 Identities = 34/108 (31%), Positives = 54/108 (50%), Gaps = 2/108 (1%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
            VL+V+D+      L  +LRK  +E T       AL      + G DIV+ D+ +P M G
Sbjct: 6   SVLIVEDEESLADPLAFLLRKEGFEATVVTDGPAALAEFD--RAGADIVLLDLMLPGMSG 63

Query: 79  FKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
             + +Q+     +PVIM++      D + G+  GA +Y+ KP   +EL
Sbjct: 64  TDVCKQLRARSSVPVIMVTARDSEIDKVVGLELGADDYVTKPYSAREL 111

>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 = 73.6 bits (182), Expect = 1e-17
 Identities = 30/108 (27%), Positives = 47/108 (43%), Gaps = 2/108 (1%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
            VL+V+D+    R L   L      V +    +  L          D++I D+ +PD DG
Sbjct: 3   NVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEAA--TRKPDLIILDLGLPDGDG 60

Query: 79  FKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
            +    +     +PVI++S      D +  +  GA +YL KP  I EL
Sbjct: 61  IEFIRDLRQWSAVPVIVLSARSEESDKIAALDAGADDYLSKPFGIGEL 108

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

 Score = 74.1 bits (183), Expect = 1e-17
 Identities = 27/139 (19%), Positives = 59/139 (42%), Gaps = 22/139 (15%)

Query: 16  AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPD 75
            GL+VLV+D++ +   + + +L     EVT  +  E  L ++    + + +V  DV MP 
Sbjct: 6   TGLKVLVMDENGVSRMVTKGLLVHLGCEVTTVSSNEECLRVVS---HEHKVVFMDVCMPG 62

Query: 76  MDGFKL------HEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGAC------NYLLKPIRI 123
           ++ +++                 ++ +     + +  K  T   C        LLKP+ +
Sbjct: 63  VENYQIALRIHEKFTKQRHQRPLLVAL-----SGNTDKS-TKEKCMSFGLDGVLLKPVSL 116

Query: 124 KELRNIWQHVAQQPKPFEE 142
             +R++   +  +P+   E
Sbjct: 117 DNIRDVLSDLL-EPRVLYE 134

>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 = 73.7 bits (182), Expect = 2e-17
 Identities = 26/112 (23%), Positives = 52/112 (46%), Gaps = 8/112 (7%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           ++L++D        L+  L    Y V +    + AL+ +    +  D+VI D+ +   + 
Sbjct: 5   KILIIDQQDFSRIELKNFLDS-EYLVIESKNEKEALEQID--HHHPDLVILDMDIIGENS 61

Query: 79  F----KLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
                KL    GL+ ++P+I++      + ++ G+  GA +YL KP    +L
Sbjct: 62  PNLCLKLKRSKGLK-NVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDL 112

>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 = 72.9 bits (180), Expect = 2e-17
 Identities = 32/129 (24%), Positives = 59/129 (45%), Gaps = 18/129 (13%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           +VL+V+D+ + +++   +L    YE  +      AL + R  +N  D+++ D+ +P++ G
Sbjct: 3   KVLIVEDNELNMKLFHDLLEAQGYETLQTREGLSALSIAR--ENKPDLILMDIQLPEISG 60

Query: 79  F----KLHEQVGLEMDLPVIMMSVDGCTQDVMKG-----VTHGACNYLLKPIRIKELRN- 128
                 L E   L   +PV+ +     T   MKG        G   Y+ KPI +      
Sbjct: 61  LEVTKWLKEDDDLA-HIPVVAV-----TAFAMKGDEERIREGGCEAYISKPISVVHFLET 114

Query: 129 IWQHVAQQP 137
           I + + +QP
Sbjct: 115 IKRLLERQP 123

>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 = 75.6 bits (187), Expect = 3e-17
 Identities = 39/116 (33%), Positives = 59/116 (50%), Gaps = 3/116 (2%)

Query: 12  DQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDV 71
           D      RVLVVDDD   L  LE+ LR   +EV        AL      +N  D ++ D+
Sbjct: 2   DTGVTSPRVLVVDDDSDVLASLERGLRLSGFEVATAVDGAEALRSAT--ENRPDAIVLDI 59

Query: 72  HMPDMDGFKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
           +MP +DG  +   +  ++ D+PV ++S      D + G+  GA +YL+KP  + EL
Sbjct: 60  NMPVLDGVSVVTALRAMDNDVPVCVLSARSSVDDRVAGLEAGADDYLVKPFVLAEL 115

>2j48_A Two-component sensor kinase; pseudo-receiver, circadian clock, transferase, response regulator, histidine protein kinase; NMR {Synechococcus elongatus} Length = 119

 Score = 72.1 bits (178), Expect = 5e-17
 Identities = 20/112 (17%), Positives = 43/112 (38%), Gaps = 10/112 (8%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
            +L+++++     ++ +ML    ++V        ALD L + +    +++     PD   
Sbjct: 3   HILLLEEEDEAATVVCEMLTAAGFKVIWLVDGSTALDQLDLLQ--PIVILMAWPPPDQSC 60

Query: 79  F----KLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
                 L E        P+++   +     V   +T  A   L KP+  + L
Sbjct: 61  LLLLQHLREHQADP-HPPLVLFLGEP---PVDPLLTAQASAILSKPLDPQLL 108

>3a10_A Response regulator; phosphoacceptor, signaling protein; HET: MSE PG4; 1.63A {Thermotoga maritima} PDB: 3a0r_B* 3a0u_A* Length = 116

 Score = 71.7 bits (177), Expect = 5e-17
 Identities = 30/109 (27%), Positives = 53/109 (48%), Gaps = 5/109 (4%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           R+LVVDD+P    +L++ L++  YE+      E AL         YD+VI D+ MP + G
Sbjct: 3   RILVVDDEPNIRELLKEELQEEGYEIDTAENGEEALKKFF--SGNYDLVILDIEMPGISG 60

Query: 79  FKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
            ++  ++   + D  +I+++     +  M      A  Y++K     EL
Sbjct: 61  LEVAGEIRKKKKDAKIILLTAYSHYRSDMSSW--AADEYVVKSFNFDEL 107

>3nhm_A Response regulator; protein structure initiative II(PSI II), NYSGXRC, structural genomics; 2.19A {Myxococcus xanthus} Length = 133

 Score = 71.9 bits (177), Expect = 8e-17
 Identities = 27/112 (24%), Positives = 45/112 (40%), Gaps = 7/112 (6%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           +VL+V++       L  +L    ++ T        L       +  D++ISDV+M  MDG
Sbjct: 6   KVLIVENSWTMRETLRLLLSG-EFDCTTAADGASGLQQAL--AHPPDVLISDVNMDGMDG 62

Query: 79  FKLHEQVGLEM---DLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           + L      E     +PVI +S      +           YL+KP++   L 
Sbjct: 63  YALCGHFRSEPTLKHIPVIFVSGYAPRTEG-PADQPVPDAYLVKPVKPPVLI 113

>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 = 71.0 bits (175), Expect = 2e-16
 Identities = 40/111 (36%), Positives = 59/111 (53%), Gaps = 5/111 (4%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
            +L+VDDD     +LE +LR   YEV +    E AL  +   KN  D +I DV +P +DG
Sbjct: 6   TLLIVDDDDTVAEMLELVLRGAGYEVRRAASGEEALQQIY--KNLPDALICDVLLPGIDG 63

Query: 79  FKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
           + L ++V    L   LP++M++  G     + G   GA +YL KP   +EL
Sbjct: 64  YTLCKRVRQHPLTKTLPILMLTAQGDISAKIAGFEAGANDYLAKPFEPQEL 114

>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 = 70.7 bits (174), Expect = 3e-16
 Identities = 24/109 (22%), Positives = 46/109 (42%), Gaps = 5/109 (4%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           RV +V+D+P    +++  L +   EVT                +  D++I    + D+  
Sbjct: 17  RVTLVEDEPSHATLIQYHLNQLGAEVTVHPSGSAFFQHRS-QLSTCDLLIVSDQLVDLSI 75

Query: 79  FKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
           F L + V        V++++      ++++   H   +YL KP  I EL
Sbjct: 76  FSLLDIVKEQTKQPSVLILTTGR--HELIESSEHNL-SYLQKPFAISEL 121

>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 = 72.1 bits (178), Expect = 5e-16
 Identities = 32/109 (29%), Positives = 61/109 (55%), Gaps = 3/109 (2%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           RVLVV+D+     ++ + L+K ++ V  C   E  + M       +D+VI D+ +P  DG
Sbjct: 4   RVLVVEDERDLADLITEALKKEMFTVDVCYDGEEGMYMAL--NEPFDVVILDIMLPVHDG 61

Query: 79  FKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
           +++ + +    ++ PV+M++     +  +KG+  GA +YL KP  ++EL
Sbjct: 62  WEILKSMRESGVNTPVLMLTALSDVEYRVKGLNMGADDYLPKPFDLREL 110

>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 = 70.4 bits (173), Expect = 5e-16
 Identities = 24/142 (16%), Positives = 61/142 (42%), Gaps = 22/142 (15%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLY--EVTKCNRAEIALDMLRMSKNGY--------DIVI 68
            +LVV+D        +++L++      + +C   + ALD L  + +           +++
Sbjct: 8   PLLVVEDSDEDFSTFQRLLQREGVVNPIYRCITGDQALDFLYQTGSYCNPDIAPRPAVIL 67

Query: 69  SDVHMPDMDGF----KLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPI--- 121
            D+++P  DG     ++ +   L   +PV++M+     +D+    ++   +Y++KP+   
Sbjct: 68  LDLNLPGTDGREVLQEIKQDEVL-KKIPVVIMTTSSNPKDIEICYSYSISSYIVKPLEID 126

Query: 122 ----RIKELRNIWQHVAQQPKP 139
                ++     W  +   P+ 
Sbjct: 127 RLTETVQTFIKYWLDIVVLPEM 148

>3heb_A Response regulator receiver domain protein (CHEY); NYSGXRC, PSI-II, respose regulator, structure initiative, structural genomics; 2.40A {Rhodospirillum rubrum} Length = 152

 Score = 69.7 bits (171), Expect = 9e-16
 Identities = 28/142 (19%), Positives = 61/142 (42%), Gaps = 22/142 (15%)

Query: 18  LRVLVVDDDPIWLRILEKMLRKC--LYEVTKCNRAEIALDMLRMSKNGY-------DIVI 68
           + +++++DD    R++EK +R+     E+        AL+ L               +V+
Sbjct: 5   VTIVMIEDDLGHARLIEKNIRRAGVNNEIIAFTDGTSALNYLFGDDKSGRVSAGRAQLVL 64

Query: 69  SDVHMPDMDGF----KLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPI--- 121
            D+++PDM G      + E        PV++++     +++ +    GA  Y+ KP+   
Sbjct: 65  LDLNLPDMTGIDILKLVKENPHTR-RSPVVILTTTDDQREIQRCYDLGANVYITKPVNYE 123

Query: 122 ----RIKELRNIWQHVAQQPKP 139
                I++L   +  + Q P+ 
Sbjct: 124 NFANAIRQLGLFFSVM-QVPET 144

>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 = 68.2 bits (168), Expect = 1e-15
 Identities = 22/108 (20%), Positives = 53/108 (49%), Gaps = 2/108 (1%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
            +L+V+D+ +    L+ +     Y+V +         +L   +   ++VI D+++P  +G
Sbjct: 5   HILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQILS--EYDINLVIMDINLPGKNG 62

Query: 79  FKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
             L  ++  + ++ ++ ++      D + G+  GA +Y+ KP   +EL
Sbjct: 63  LLLARELREQANVALMFLTGRDNEVDKILGLEIGADDYITKPFNPREL 110

>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 = 67.9 bits (167), Expect = 2e-15
 Identities = 22/108 (20%), Positives = 55/108 (50%), Gaps = 2/108 (1%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
            +++V+D+P+    L+    +  Y V+         ++++      D+++ D+++PD +G
Sbjct: 4   HIVIVEDEPVTQARLQSYFTQEGYTVSVTASGAGLREIMQ--NQSVDLILLDINLPDENG 61

Query: 79  FKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
             L   +     + +I+++      D + G+  GA +Y+ KP+ ++EL
Sbjct: 62  LMLTRALRERSTVGIILVTGRSDRIDRIVGLEMGADDYVTKPLELREL 109

>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 = 67.9 bits (166), Expect = 2e-15
 Identities = 31/111 (27%), Positives = 59/111 (53%), Gaps = 5/111 (4%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           +VL+VDD  +  +I+   L+K  YEV +    +IAL+ L   +   D+++  + MP MDG
Sbjct: 4   KVLLVDDSAVLRKIVSFNLKKEGYEVIEAENGQIALEKLS--EFTPDLIVLXIMMPVMDG 61

Query: 79  FKLHEQVGLE---MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
           F + +++  +     +PVI+++  G  +D    ++ GA   + KP    + 
Sbjct: 62  FTVLKKLQEKEEWKRIPVIVLTAKGGEEDESLALSLGARKVMRKPFSPSQF 112

>3cu5_A Two component transcriptional regulator, ARAC FAM; structural genomics, protein structure initiative; 2.60A {Clostridium phytofermentans isdg} Length = 141

 Score = 68.3 bits (168), Expect = 2e-15
 Identities = 32/126 (25%), Positives = 57/126 (45%), Gaps = 12/126 (9%)

Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRA---EIALDMLRMSKNGYDIVISDVHMP 74
           LR+L+VDD+ +    L   +        + ++A     A+ +    K+  +++++DV MP
Sbjct: 3   LRILIVDDEKLTRDGLIANINWKALSFDQIDQADDGINAIQIAL--KHPPNVLLTDVRMP 60

Query: 75  DMDGFKLHEQV-GLEMDLPVIMMSVDGCTQD---VMKGVTHGACNYLLKPIRIKELRNIW 130
            MDG +L + +  L  D  VI MS      D   +   +   A  Y+ KPI   E+ +  
Sbjct: 61  RMDGIELVDNILKLYPDCSVIFMS---GYSDKEYLKAAIKFRAIRYVEKPIDPSEIMDAL 117

Query: 131 QHVAQQ 136
           +   Q 
Sbjct: 118 KQSIQT 123

>3kto_A Response regulator receiver protein; PSI-II,structural genomics, protein structure initiative; 1.98A {Pseudoalteromonas atlantica T6C} Length = 136

 Score = 68.0 bits (167), Expect = 3e-15
 Identities = 23/116 (19%), Positives = 41/116 (35%), Gaps = 17/116 (14%)

Query: 20  VLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDM--D 77
           + +VD        L K+L      +     AE  +       +    +I + H+ D    
Sbjct: 9   IYLVDHQKDARAALSKLLSPLDVTIQCFASAESFMRQQI--SDDAIGMIIEAHLEDKKDS 66

Query: 78  GFKLHEQV-GLEMDLPVIMMSVDGCTQDV------MKGVTHGACNYLLKPIRIKEL 126
           G +L E +      LP I+M+      D+      M+     A +++ KP     L
Sbjct: 67  GIELLETLVKRGFHLPTIVMASSS---DIPTAVRAMRA---SAADFIEKPFIEHVL 116

>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 = 67.9 bits (167), Expect = 3e-15
 Identities = 30/112 (26%), Positives = 58/112 (51%), Gaps = 9/112 (8%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           ++LVVDD+   + +L+  L +  Y+V   +  E AL          D+++ DV +P +DG
Sbjct: 5   KILVVDDEESIVTLLQYNLERSGYDVITASDGEEALKKAE--TEKPDLIVLDVMLPKLDG 62

Query: 79  F----KLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
                +L +Q   ++  P++M++      D + G+  GA +Y+ KP   +E+
Sbjct: 63  IEVCKQLRQQ---KLMFPILMLTAKDEEFDKVLGLELGADDYMTKPFSPREV 111

>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 Length = 121

 Score = 67.1 bits (165), Expect = 4e-15
 Identities = 31/109 (28%), Positives = 59/109 (54%), Gaps = 3/109 (2%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           RVLVV+D+ +    L+  ++   ++V     A+ A   L    +  DI I D+ +PD DG
Sbjct: 2   RVLVVEDNALLRHHLKVQIQDAGHQVDDAEDAKEADYYLNE--HIPDIAIVDLGLPDEDG 59

Query: 79  FKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
             L  +    ++ LP+++++     QD ++ ++ GA +Y+ KP  I+E+
Sbjct: 60  LSLIRRWRSNDVSLPILVLTARESWQDKVEVLSAGADDYVTKPFHIEEV 108

>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 = 67.6 bits (165), Expect = 4e-15
 Identities = 24/137 (17%), Positives = 56/137 (40%), Gaps = 19/137 (13%)

Query: 19  RVLVVDDDPIWLRILEKMLRKC--LYEVTKCNRAEIALDMLRMSKNGY------DIVISD 70
           ++ +V+D+   +R++++ L      +EV        A+  LR  +  Y      D+++  
Sbjct: 4   KIFLVEDNKADIRLIQEALANSTVPHEVVTVRDGMEAMAYLR-QEGEYANASRPDLILLX 62

Query: 71  VHMPDMDGFKLHEQVGLE---MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPI------ 121
           +++P  DG ++  ++  +     +PV+++S      D+          Y+ K        
Sbjct: 63  LNLPKKDGREVLAEIKSDPTLKRIPVVVLSTSINEDDIFHSYDLHVNCYITKSANLSQLF 122

Query: 122 -RIKELRNIWQHVAQQP 137
             +K +   W   A  P
Sbjct: 123 QIVKGIEEFWLSTATLP 139

>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 = 68.6 bits (169), Expect = 8e-15
 Identities = 28/109 (25%), Positives = 55/109 (50%), Gaps = 6/109 (5%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           ++ VVDDD   L+ + + L++ L  V      E  L+     +  + +V+ DV +PD  G
Sbjct: 4   KIAVVDDDKNILKKVSEKLQQ-LGRVKTFLTGEDFLND----EEAFHVVVLDVMLPDYSG 58

Query: 79  FKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
           +++   +     +  VI++++    + V+KG   GA +Y+ KP   + L
Sbjct: 59  YEICRMIKETRPETWVILLTLLSDDESVLKGFEAGADDYVTKPFNPEIL 107

>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 = 65.6 bits (161), Expect = 2e-14
 Identities = 33/120 (27%), Positives = 62/120 (51%), Gaps = 6/120 (5%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEV--TKCNRAEIALDMLRMSKNGYDIVISDVHMPDM 76
           RVL+VDD      +L+ ++ K  YEV     N  E A++  +  K   DIV  D+ MP+M
Sbjct: 4   RVLIVDDAAFMRMMLKDIITKAGYEVAGEATNGRE-AVEKYKELK--PDIVTMDITMPEM 60

Query: 77  DGFK-LHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ 135
           +G   + E + ++ +  +I+ S  G    V++ +  GA ++++KP +   +      V++
Sbjct: 61  NGIDAIKEIMKIDPNAKIIVCSAMGQQAMVIEAIKAGAKDFIVKPFQPSRVVEALNKVSK 120

>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 = 65.2 bits (160), Expect = 3e-14
 Identities = 25/111 (22%), Positives = 57/111 (51%), Gaps = 5/111 (4%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           R+LVV+D+     ++  +L +  ++  +    + A++ L   +   D+++    +P   G
Sbjct: 4   RILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLN--EPWPDLILLAWMLPGGSG 61

Query: 79  FKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
            +  + +    +  D+PV+M++  G  +D ++G+  GA + + KP   KEL
Sbjct: 62  IQFIKHLRRESMTRDIPVVMLTARGEEEDRVRGLETGADDCITKPFSPKEL 112

>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 = 64.6 bits (158), Expect = 6e-14
 Identities = 23/118 (19%), Positives = 53/118 (44%), Gaps = 19/118 (16%)

Query: 16  AGLRVLVVDDDPIWLRILEKMLRKCLY--EVTKCNRAEIALDMLRMSKNGYDIVISDVHM 73
              RVLVV+D+P  + ++ ++L +     ++   +    AL  ++  +  YD++I D+ +
Sbjct: 4   RSKRVLVVEDNPDDIALIRRVLDRKDIHCQLEFVDNGAKALYQVQ--QAKYDLIILDIGL 61

Query: 74  PDMDGF----KLHEQVGLEMDLPVIMMSVDGCTQDVMKG-----VTHGACNYLLKPIR 122
           P  +GF     + +    +   P++++     T +V        +  GA + + K   
Sbjct: 62  PIANGFEVMSAVRKPGANQ-HTPIVIL-----TDNVSDDRAKQCMAAGASSVVDKSSN 113

>2qv0_A Protein MRKE; structural genomics, transcription, PSI-2, protein structure initiative; 2.40A {Klebsiella pneumoniae} Length = 143

 Score = 63.4 bits (155), Expect = 2e-13
 Identities = 22/123 (17%), Positives = 48/123 (39%), Gaps = 27/123 (21%)

Query: 18  LRVLVVDDDPIWLRILEKMLRKC--LYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPD 75
           ++V++V+D+ +  + L  ++     +  V   +     L  L+   N  D +  D+++P 
Sbjct: 10  MKVIIVEDEFLAQQELSWLINTHSQMEIVGSFDDGLDVLKFLQ--HNKVDAIFLDINIPS 67

Query: 76  MDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVT-----------HGACNYLLKPIRIK 124
           +DG  L + +      P I+             +T             A +Y+LKP +  
Sbjct: 68  LDGVLLAQNISQFAHKPFIVF------------ITAWKEHAVEAFELEAFDYILKPYQES 115

Query: 125 ELR 127
            + 
Sbjct: 116 RII 118

>1qo0_D AMIR; binding protein, gene regulator, receptor; 2.25A {Pseudomonas aeruginosa} SCOP: c.23.1.3 Length = 196

 Score = 63.9 bits (155), Expect = 3e-13
 Identities = 17/165 (10%), Positives = 40/165 (24%), Gaps = 17/165 (10%)

Query: 17  GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDM 76
            L+VLV++        L   L +    V +C     A D+        D+V + +     
Sbjct: 12  ELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDV------PVDVVFTSIFQNRH 65

Query: 77  DGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRN-----IWQ 131
                           ++ +        + + +       + +P+    +          
Sbjct: 66  HDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRI 125

Query: 132 HVAQQPKPFEESDDSYSVNQGNWRTS------NRRKDEEEEAEKR 170
                    +       +               R   +E EA + 
Sbjct: 126 SEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHGWDEREAHQH 170

>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 = 62.9 bits (153), Expect = 1e-12
 Identities = 34/160 (21%), Positives = 63/160 (39%), Gaps = 34/160 (21%)

Query: 2   SPASSSVAVSDQFPAGLRVLVVDDDPIWLRILEKMLRKC-LYEVTKCNRAEIALDMLRMS 60
               +S    D+F  G RVLVVDD+ I  ++    L+K  + EV +C+  + AL ++   
Sbjct: 46  DEQETSKPSDDEFLRGKRVLVVDDNFISRKVATGKLKKMGVSEVEQCDSGKEALRLVTEG 105

Query: 61  KNG-----------YDIVISDVHMPDMDGF-------KLHEQVGLEMDLPVIMMSVDGCT 102
                         +D +  D  MP+MDG+       K+ +  G+    P+I +     +
Sbjct: 106 LTQREEQGSVDKLPFDYIFMDCQMPEMDGYEATREIRKVEKSYGVR--TPIIAV-----S 158

Query: 103 QDVMKGVTHGAC------NYLLKPIRIKELRNIWQHVAQQ 136
                              +L K +   +L N+ + +  +
Sbjct: 159 GHDPGSEEARETIQAGMDAFLDKSLN--QLANVIREIESK 196

>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 = 60.2 bits (147), Expect = 2e-12
 Identities = 25/126 (19%), Positives = 54/126 (42%), Gaps = 20/126 (15%)

Query: 17  GLRVLVVDDDPIWLRILEKMLRKC-LYEVTKCNRAEIALDMLRMSK---NGYDIVISDVH 72
            +++LVV+D+ +   ++++ML    +  +      + A D ++        Y+++  DV 
Sbjct: 2   SVKILVVEDNHVNQEVIKRMLNLEGIENIELACDGQEAFDKVKELTSKGENYNMIFMDVQ 61

Query: 73  MPDMDGF----KLHEQVGLEMDLPVIMMSVDGCTQDVMKG-----VTHGACNYLLKPIRI 123
           MP +DG      +   +G     P++ +     T           +  G   +L KPI+ 
Sbjct: 62  MPKVDGLLSTKMIRRDLGY--TSPIVAL-----TAFADDSNIKECLESGMNGFLSKPIKR 114

Query: 124 KELRNI 129
            +L+ I
Sbjct: 115 PKLKTI 120

>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 Length = 127

 Score = 59.4 bits (145), Expect = 4e-12
 Identities = 17/112 (15%), Positives = 49/112 (43%), Gaps = 7/112 (6%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHM-PDMD 77
           ++L+V+ D      L   L    + V +    + +++ +R  ++  D+V+  V +    +
Sbjct: 7   KILIVESDTALSATLRSALEGRGFTVDETTDGKGSVEQIR--RDRPDLVVLAVDLSAGQN 64

Query: 78  GFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
           G+ +  ++       ++P++++          + +   A  Y+ KP+   +L
Sbjct: 65  GYLICGKLKKDDDLKNVPIVIIGNPD-GFAQHRKLKAHADEYVAKPVDADQL 115

>2hqr_A Putative transcriptional regulator; phosporylation-independent response regulator, H. pylori, SY dimer, signaling protein; NMR {Helicobacter pylori} Length = 223

 Score = 59.0 bits (144), Expect = 3e-11
 Identities = 18/103 (17%), Positives = 43/103 (41%), Gaps = 7/103 (6%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           RVL+++ + +    +EK L    +        E    ++      YD+V+    + D + 
Sbjct: 2   RVLLIEKNSVLGGEIEKGLNVKGFMADVTESLEDGEYLMD--IRNYDLVM----VSDKNA 55

Query: 79  FKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKP 120
                ++      + V++ S +  +++ +     GA +Y+ KP
Sbjct: 56  LSFVSRIKEKHSSIVVLVSSDNPTSEEEVHAFEQGADDYIAKP 98

>2pln_A HP1043, response regulator; signaling protein; 1.80A {Helicobacter pylori} PDB: 2hqo_A Length = 137

 Score = 56.0 bits (136), Expect = 9e-11
 Identities = 18/103 (17%), Positives = 44/103 (42%), Gaps = 7/103 (6%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           RVL+++ + +    +EK L    +        E    ++ +    YD+V+    + D + 
Sbjct: 20  RVLLIEKNSVLGGEIEKGLNVKGFMADVTESLEDGEYLMDI--RNYDLVM----VSDKNA 73

Query: 79  FKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKP 120
                ++      + V++ S +  +++ +     GA +Y+ KP
Sbjct: 74  LSFVSRIKEKHSSIVVLVSSDNPTSEEEVHAFEQGADDYIAKP 116

>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 = 54.5 bits (132), Expect = 4e-10
 Identities = 23/109 (21%), Positives = 43/109 (39%), Gaps = 9/109 (8%)

Query: 18  LRVLVVDDDPIWLRILEKMLRKC--LYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPD 75
             V++VDD  +    +   ++       V +    + ALD L  ++   D+++ D+ MP 
Sbjct: 14  YNVMIVDDAAMMRLYIASFIKTLPDFKVVAQAANGQEALDKLA-AQPNVDLILLDIEMPV 72

Query: 76  MDGFKLHEQVGLEMDLPVIMMSVDGCTQD----VMKGVTHGACNYLLKP 120
           MDG +      L+    + M+S             +    GA   + KP
Sbjct: 73  MDGMEFLRHAKLKTRAKICMLSS--VAVSGSPHAARARELGADGVVAKP 119

>3t8y_A CHEB, chemotaxis response regulator protein-glutamate methylesterase; CHEA, hydrolase; 1.90A {Thermotoga maritima} Length = 164

 Score = 52.7 bits (127), Expect = 2e-09
 Identities = 24/106 (22%), Positives = 50/106 (47%), Gaps = 6/106 (5%)

Query: 19  RVLVVDDDPIWLRILEKMLRKC--LYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDM 76
           RVLVVDD      +L+ ++     +  V        A++     K   D++  D+ MP++
Sbjct: 27  RVLVVDDSAFMRMVLKDIIDSQPDMKVVGFAKDGLEAVEKAIELK--PDVITMDIEMPNL 84

Query: 77  DGFKLHEQVGLEMDLPVIMMS--VDGCTQDVMKGVTHGACNYLLKP 120
           +G +  + +  +    VIM+S   +      ++ + +GA +++ KP
Sbjct: 85  NGIEALKLIMKKAPTRVIMVSSLTEEGAAITIEALRNGAVDFITKP 130

>3sy8_A ROCR; TIM barrel phosphodiesterase-A, transcription regulator; HET: EPE; 2.50A {Pseudomonas aeruginosa} Length = 400

 Score = 53.9 bits (130), Expect = 3e-09
 Identities = 20/95 (21%), Positives = 38/95 (40%), Gaps = 3/95 (3%)

Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYE-VTKCNRAEIALDMLRMSKNGYDIVISDVHMPDM 76
           L VLV++D+P    +    L+K +   + +    + A+ +L  S    DI I D+ M  M
Sbjct: 4   LNVLVLEDEPFQRLVAVTALKKVVPGSILEAADGKEAVAILE-SCGHVDIAICDLQMSGM 62

Query: 77  DGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTH 111
           DG        L   +  +++        + +    
Sbjct: 63  DGLAFLRHASLSGKVHSVIL-SSEVDPILRQATIS 96

>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 = 53.3 bits (129), Expect = 5e-09
 Identities = 29/108 (26%), Positives = 56/108 (51%), Gaps = 10/108 (9%)

Query: 19  RVLVVDDDPIWLRILEKMLRKC-LYEV--TKCNRAEIALDMLRMSKNGYDIVISDVHMPD 75
           RVL VDD  +  +I+ +++      E+  T  +   +A D+++      D++  DV MP 
Sbjct: 5   RVLSVDDSALMRQIMTEIINSHSDMEMVATAPD-PLVARDLIKKFN--PDVLTLDVEMPR 61

Query: 76  MDGFKLHEQVGLEMDLPVIMMS---VDGCTQDVMKGVTHGACNYLLKP 120
           MDG    E++     +PV+M+S     G ++  ++ +  GA +++ KP
Sbjct: 62  MDGLDFLEKLMRLRPMPVVMVSSLTGKG-SEVTLRALELGAIDFVTKP 108

>2qsj_A DNA-binding response regulator, LUXR family; structural genomics, PSI-2, protein structure initiative; 2.10A {Silicibacter pomeroyi dss-3} Length = 154

 Score = 49.9 bits (120), Expect = 3e-08
 Identities = 23/114 (20%), Positives = 44/114 (38%), Gaps = 10/114 (8%)

Query: 19  RVLVVDDDPIWLRILEKMLRKC--LYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDM 76
            VL+VDD  +     + +L        V        AL  L  + N  D+++ DV++PD 
Sbjct: 5   VVLIVDDHHLIRAGAKNLLEGAFSGMRVEGAETVSDALAFLE-ADNTVDLILLDVNLPDA 63

Query: 77  DGF----KLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
           +      +L           V ++S +   + +   +  GA  ++ K    + L
Sbjct: 64  EAIDGLVRLKRFDP---SNAVALISGETDHELIRAALEAGADGFIPKSADPQVL 114

>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 = 47.9 bits (115), Expect = 8e-08
 Identities = 31/113 (27%), Positives = 56/113 (49%), Gaps = 8/113 (7%)

Query: 19  RVLVVDDDPIWLRILEKML-RKCLYEV--TKCNRAEIALDMLRMSKNGYDIVISDVHMPD 75
           +V + DD+   + +L++ +  +   EV  T  N  +  L ML   +   DI++ D+ MP 
Sbjct: 4   KVCIADDNRELVSLLDEYISSQPDMEVIGTAYNGQD-CLQMLEEKRP--DILLLDIIMPH 60

Query: 76  MDGFKLHEQVGLEMDLP--VIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
           +DG  + E++    +    VIM++  G      K V  GA  ++LKP  ++ L
Sbjct: 61  LDGLAVLERIRAGFEHQPNVIMLTAFGQEDVTKKAVELGASYFILKPFDMENL 113

>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 = 47.6 bits (114), Expect = 3e-07
 Identities = 13/114 (11%), Positives = 35/114 (30%), Gaps = 7/114 (6%)

Query: 18  LRVLVVDDDPIWLRILEKMLRKCL---YEVTKCNRAEIALDMLRMSKNGYDIVISDVHMP 74
           L V ++ D  +  R+L++ L   L    E+T  +   +  +          +++ D    
Sbjct: 8   LNVRMLSDVCMQSRLLKEALESKLPLALEITPFSELWLEENKPESRS--IQMLVIDYSRI 65

Query: 75  DMDGFKLHEQVGLEM--DLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
             D    +         D   ++++     +  +    +           +  L
Sbjct: 66  SDDVLTDYSSFKHISCPDAKEVIINCPQDIEHKLLFKWNNLAGVFYIDDDMDTL 119

>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 = 44.4 bits (106), Expect = 2e-06
 Identities = 23/112 (20%), Positives = 46/112 (41%), Gaps = 6/112 (5%)

Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEV--TKCNRAEIALDMLRMSKNGYDIVISDVHMPD 75
           L  +++DD P+ +  +  +L K   E+          A+  +   K   DIVI DV +P 
Sbjct: 2   LNAIIIDDHPLAIAAIRNLLIKNDIEILAELTEGGS-AVQRVETLKP--DIVIIDVDIPG 58

Query: 76  MDGFKLHEQ-VGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
           ++G ++ E     +    +I++S              GA  ++ K   +  +
Sbjct: 59  VNGIQVLETLRKRQYSGIIIIVSAKNDHFYGKHCADAGANGFVSKKEGMNNI 110

>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 = 40.9 bits (97), Expect = 2e-05
 Identities = 20/113 (17%), Positives = 54/113 (47%), Gaps = 9/113 (7%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYE----VTKCNRAEIALDMLRMSKNGYDIVISDVHMP 74
            +++ +D  +  + + ++++  L+     +   +    A+ ++   +   ++VI D+ MP
Sbjct: 5   SLIIAEDQNMLRQAMVQLIK--LHGDFEILADTDNGLDAMKLIE--EYNPNVVILDIEMP 60

Query: 75  DMDGFKLHEQVGLEM-DLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
            M G ++  ++  +  ++ VI+++         K V +    Y+LK   I+EL
Sbjct: 61  GMTGLEVLAEIRKKHLNIKVIIVTTFKRPGYFEKAVVNDVDAYVLKERSIEEL 113

>4e7p_A Response regulator; DNA binding, cytosol, transcription regulator; 1.89A {Streptococcus pneumoniae} PDB: 4e7o_A Length = 150

 Score = 40.2 bits (95), Expect = 7e-05
 Identities = 27/113 (23%), Positives = 50/113 (44%), Gaps = 9/113 (7%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYE----VTKCNRAEIALDMLRMSKNGYDIVISDVHMP 74
           +VLV +D  +    + ++L   L      V +    + A+ +L   K   DI I DV MP
Sbjct: 22  KVLVAEDQSMLRDAMCQLLT--LQPDVESVLQAKNGQEAIQLLE--KESVDIAILDVEMP 77

Query: 75  DMDGFKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
              G ++ E +   +++  V++++         + V  G   Y+LK   I +L
Sbjct: 78  VKTGLEVLEWIRSEKLETKVVVVTTFKRAGYFERAVKAGVDAYVLKERSIADL 130

>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 = 37.1 bits (87), Expect = 8e-04
 Identities = 30/119 (25%), Positives = 56/119 (47%), Gaps = 5/119 (4%)

Query: 11  SDQFPAGLRVLVVDDDPIWLRILEKMLRKC--LYEVTKCNRAEIALDMLRMSKNGYDIVI 68
           S+  P  +RV+V DD P++   + + L     +  V + +    AL++++      D+ +
Sbjct: 9   SNPQPEKVRVVVGDDHPLFREGVVRALSLSGSVNVVGEADDGAAALELIKAHLP--DVAL 66

Query: 69  SDVHMPDMDGFKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
            D  MP MDG ++   V   E+   V+++S       V + +  GA  +LLK     E+
Sbjct: 67  LDYRMPGMDGAQVAAAVRSYELPTRVLLISAHDEPAIVYQALQQGAAGFLLKDSTRTEI 125

>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 = 37.8 bits (89), Expect = 8e-04
 Identities = 17/63 (26%), Positives = 36/63 (57%), Gaps = 1/63 (1%)

Query: 65  DIVISDVHMPDMDGFKLHEQ-VGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRI 123
           D+++ D++MP M+G +  ++     +   +++ SV    +DV+  +  GA  YLLK +  
Sbjct: 53  DLILLDLNMPGMNGLETLDKLREKSLSGRIVVFSVSNHEEDVVTALKRGADGYLLKDMEP 112

Query: 124 KEL 126
           ++L
Sbjct: 113 EDL 115

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	184
3to5_A	134	CHEY homolog; alpha(5)beta(5), chemotaxis, FLIM, p	99.95
3gl9_A	122	Response regulator; beta-sheet, surrounded by alph	99.91
3f6p_A	120	Transcriptional regulatory protein YYCF; unphospho	99.91
3t6k_A	136	Response regulator receiver; flavodoxin-like, stru	99.91
2lpm_A	123	Two-component response regulator; transcription re	99.9
2r25_B	133	Osmosensing histidine protein kinase SLN1; alpha5-	99.89
3gt7_A	154	Sensor protein; structural genomics, signal receiv	99.89
3h1g_A	129	Chemotaxis protein CHEY homolog; sulfate-bound CHE	99.89
3m6m_D	143	Sensory/regulatory protein RPFC; RPFF, REC, enoyl-	99.89
1dbw_A	126	Transcriptional regulatory protein FIXJ; doubly wo	99.89
3lua_A	140	Response regulator receiver protein; two-component	99.88
2a9o_A	120	Response regulator; essential protein, YYCF/YYCG h	99.88
3f6c_A	134	Positive transcription regulator EVGA; structural	99.88
3hdv_A	136	Response regulator; PSI-II, structural genomics, P	99.88
3r0j_A	250	Possible two component system response transcript	99.88
4e7p_A	150	Response regulator; DNA binding, cytosol, transcri	99.88
2pl1_A	121	Transcriptional regulatory protein PHOP; CHEY-like	99.87
3eod_A	130	Protein HNR; response regulator, phosphoprotein, t	99.87
3rqi_A	184	Response regulator protein; structural genomics, s	99.87
1srr_A	124	SPO0F, sporulation response regulatory protein; as	99.87
1zgz_A	122	Torcad operon transcriptional regulatory protein;	99.87
3b2n_A	133	Uncharacterized protein Q99UF4; structural genomic	99.87
1p6q_A	129	CHEY2; chemotaxis, signal transduction, response r	99.87
2qzj_A	136	Two-component response regulator; 11017X, PSI-II,	99.87
3crn_A	132	Response regulator receiver domain protein, CHEY-;	99.87
1jbe_A	128	Chemotaxis protein CHEY; signaling protein; 1.08A	99.87
3q9s_A	249	DNA-binding response regulator; DNA binding protei	99.87
1xhf_A	123	DYE resistance, aerobic respiration control protei	99.87
3kto_A	136	Response regulator receiver protein; PSI-II,struct	99.87
3eul_A	152	Possible nitrate/nitrite response transcriptional	99.87
1tmy_A	120	CHEY protein, TMY; chemotaxis, phosphoryl transfer	99.87
3grc_A	140	Sensor protein, kinase; protein structure initiati	99.87
1i3c_A	149	Response regulator RCP1; phytochrome, signaling pr	99.87
3ilh_A	146	Two component response regulator; NYSGXRC, PSI-II,	99.87
3hzh_A	157	Chemotaxis response regulator (CHEY-3); phosphatas	99.87
1mb3_A	124	Cell division response regulator DIVK; signal tran	99.87
3h5i_A	140	Response regulator/sensory box protein/ggdef domai	99.87
3jte_A	143	Response regulator receiver protein; structural ge	99.87
3lte_A	132	Response regulator; structural genomics, PSI, prot	99.86
3hv2_A	153	Response regulator/HD domain protein; PSI-2, NYSGX	99.86
3cnb_A	143	DNA-binding response regulator, MERR family; signa	99.86
3heb_A	152	Response regulator receiver domain protein (CHEY);	99.86
3mm4_A	206	Histidine kinase homolog; receiver domain, CKI1, c	99.86
3kht_A	144	Response regulator; PSI-II, 11023K, structural gen	99.86
3hdg_A	137	Uncharacterized protein; two-component sensor acti	99.86
3nhm_A	133	Response regulator; protein structure initiative I	99.86
3i42_A	127	Response regulator receiver domain protein (CHEY-	99.86
1zh2_A	121	KDP operon transcriptional regulatory protein KDPE	99.86
1mvo_A	136	PHOP response regulator; phosphate regulon, transc	99.86
1k68_A	140	Phytochrome response regulator RCPA; phosphorylate	99.86
2jba_A	127	Phosphate regulon transcriptional regulatory PROT;	99.86
1dz3_A	130	Stage 0 sporulation protein A; response regulator,	99.86
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	99.86
2qr3_A	140	Two-component system response regulator; structura	99.86
4dad_A	146	Putative pilus assembly-related protein; response	99.85
1dcf_A	136	ETR1 protein; beta-alpha five sandwich, transferas	99.85
2qxy_A	142	Response regulator; regulation of transcription, N	99.85
3snk_A	135	Response regulator CHEY-like protein; P-loop conta	99.85
1a04_A	215	Nitrate/nitrite response regulator protein NARL; s	99.85
3c3m_A	138	Response regulator receiver protein; structural ge	99.85
1k66_A	149	Phytochrome response regulator RCPB; CHEY homologu	99.85
3cg0_A	140	Response regulator receiver modulated diguanylate	99.85
3cfy_A	137	Putative LUXO repressor protein; structural genomi	99.85
3luf_A	259	Two-component system response regulator/ggdef doma	99.85
1s8n_A	205	Putative antiterminator; RV1626, structural genomi	99.85
2zay_A	147	Response regulator receiver protein; structural ge	99.84
3cz5_A	153	Two-component response regulator, LUXR family; str	99.84
1yio_A	208	Response regulatory protein; transcription regulat	99.84
1kgs_A	225	DRRD, DNA binding response regulator D; DNA-bindin	99.84
3kcn_A	151	Adenylate cyclase homolog; SGX, PSI 2, structural	99.84
3a10_A	116	Response regulator; phosphoacceptor, signaling pro	99.84
2rjn_A	154	Response regulator receiver:metal-dependent phosph	99.84
2ayx_A	254	Sensor kinase protein RCSC; two independent struct	99.83
2qvg_A	143	Two component response regulator; NYSGXRC, PSI-2,	99.83
2oqr_A	230	Sensory transduction protein REGX3; response regul	99.83
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	99.83
3n53_A	140	Response regulator receiver modulated diguanylate;	99.83
2qsj_A	154	DNA-binding response regulator, LUXR family; struc	99.83
3cg4_A	142	Response regulator receiver domain protein (CHEY-;	99.83
1qkk_A	155	DCTD, C4-dicarboxylate transport transcriptional r	99.83
2gwr_A	238	DNA-binding response regulator MTRA; two-component	99.83
3cu5_A	141	Two component transcriptional regulator, ARAC FAM;	99.83
2gkg_A	127	Response regulator homolog; social motility, recei	99.83
3eqz_A	135	Response regulator; structural genomics, unknown f	99.83
3kyj_B	145	CHEY6 protein, putative histidine protein kinase;	99.82
3c97_A	140	Signal transduction histidine kinase; structural g	99.82
1ys7_A	233	Transcriptional regulatory protein PRRA; response	99.82
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	99.82
2pln_A	137	HP1043, response regulator; signaling protein; 1.8	99.82
2rdm_A	132	Response regulator receiver protein; structural ge	99.82
2jk1_A	139	HUPR, hydrogenase transcriptional regulatory prote	99.81
3eq2_A	394	Probable two-component response regulator; adaptor	99.81
3t8y_A	164	CHEB, chemotaxis response regulator protein-glutam	99.81
3klo_A	225	Transcriptional regulator VPST; REC domain, HTH do	99.81
2j48_A	119	Two-component sensor kinase; pseudo-receiver, circ	99.81
1w25_A	459	Stalked-cell differentiation controlling protein;	99.8
3c3w_A	225	Two component transcriptional regulatory protein;	99.8
1p2f_A	220	Response regulator; DRRB, OMPR/PHOB, transcription	99.79
2qv0_A	143	Protein MRKE; structural genomics, transcription,	99.79
2hqr_A	223	Putative transcriptional regulator; phosporylation	99.78
3bre_A	358	Probable two-component response regulator; protein	99.77
2b4a_A	138	BH3024; flavodoxin-like fold, structural genomics,	99.77
1dc7_A	124	NTRC, nitrogen regulation protein; receiver domain	99.77
1qo0_D	196	AMIR; binding protein, gene regulator, receptor; 2	99.77
3sy8_A	400	ROCR; TIM barrel phosphodiesterase-A, transcriptio	99.76
1a2o_A	349	CHEB methylesterase; bacterial chemotaxis, adaptat	99.73
3luf_A	259	Two-component system response regulator/ggdef doma	99.69
2vyc_A	755	Biodegradative arginine decarboxylase; pyridoxal p	99.66
3cwo_X	237	Beta/alpha-barrel protein based on 1THF and 1TMY;	99.07
1w25_A	459	Stalked-cell differentiation controlling protein;	99.03
3q7r_A	121	Transcriptional regulatory protein; CHXR, receiver	97.76
2ayx_A	254	Sensor kinase protein RCSC; two independent struct	97.42
3n75_A	715	LDC, lysine decarboxylase, inducible; pyridoxal-5'	96.97
2yxb_A	161	Coenzyme B12-dependent mutase; alpha/beta, structu	96.29
3cwo_X	237	Beta/alpha-barrel protein based on 1THF and 1TMY;	96.27
1wv2_A	265	Thiazole moeity, thiazole biosynthesis protein THI	95.51
3q58_A	229	N-acetylmannosamine-6-phosphate 2-epimerase; TIM b	95.14
3fkq_A	373	NTRC-like two-domain protein; RER070207001320, str	94.69
3igs_A	232	N-acetylmannosamine-6-phosphate 2-epimerase 2; ene	94.39
1r8j_A	289	KAIA; circadian clock protein; 2.03A {Synechococcu	93.56
1ccw_A	137	Protein (glutamate mutase); coenzyme B12, radical	93.18
1qop_A	268	Tryptophan synthase alpha chain; lyase, carbon-oxy	91.67
2ekc_A	262	AQ_1548, tryptophan synthase alpha chain; structur	91.55
2htm_A	268	Thiazole biosynthesis protein THIG; thiamin biosyn	91.19
2l69_A	134	Rossmann 2X3 fold protein; structural genomics, no	90.8
3o63_A	243	Probable thiamine-phosphate pyrophosphorylase; thi	90.35
3ezx_A	215	MMCP 1, monomethylamine corrinoid protein 1; N ter	89.88
2i2x_B	258	MTAC, methyltransferase 1; TIM barrel and helix bu	89.15
1y80_A	210	Predicted cobalamin binding protein; corrinoid, fa	88.94
1yad_A	221	Regulatory protein TENI; TIM barrel, transcription	87.86
3lab_A	217	Putative KDPG (2-keto-3-deoxy-6-phosphogluconate)	87.69
3vnd_A	267	TSA, tryptophan synthase alpha chain; psychrophili	86.97
3qja_A	272	IGPS, indole-3-glycerol phosphate synthase; struct	85.74
3nav_A	271	Tryptophan synthase alpha chain; alpha subunit, st	85.7
2gek_A	406	Phosphatidylinositol mannosyltransferase (PIMA); G	85.34
1ujp_A	271	Tryptophan synthase alpha chain; riken structural	84.28
2xij_A	762	Methylmalonyl-COA mutase, mitochondrial; isomerase	84.13
1geq_A	248	Tryptophan synthase alpha-subunit; hyperthermophIl	83.5
1qv9_A	283	F420-dependent methylenetetrahydromethanopterin de	83.34
1req_A	727	Methylmalonyl-COA mutase; isomerase, intramolecula	83.27
1xi3_A	215	Thiamine phosphate pyrophosphorylase; structural g	81.84
1rd5_A	262	Tryptophan synthase alpha chain, chloroplast; hydr	81.47
4e38_A	232	Keto-hydroxyglutarate-aldolase/keto-deoxy-phospho	81.42
3qz6_A	261	HPCH/HPAI aldolase; structural genomics, PSI-biolo	80.61

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

Probab=99.95  E-value=2.6e-27  Score=165.58  Aligned_cols=121  Identities=25%  Similarity=0.539  Sum_probs=109.9

Q ss_pred             CCCCCeEEEEeCCHHHHHHHHHHHHhcCCe-EEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc---C
Q 029986           14 FPAGLRVLVVDDDPIWLRILEKMLRKCLYE-VTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE---M   89 (184)
Q Consensus        14 ~~~~~~Ilivdd~~~~~~~l~~~L~~~~~~-v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~---~   89 (184)
                      +.+++|||||||++..+..++.+|+..||. +..+.++.++++.+.  +..||+||+|+.||++||+++++++++.   +
T Consensus         9 m~k~~rILiVDD~~~~r~~l~~~L~~~G~~~v~~a~~g~~al~~~~--~~~~DlillD~~MP~mdG~el~~~ir~~~~~~   86 (134)
T 3to5_A            9 LNKNMKILIVDDFSTMRRIVKNLLRDLGFNNTQEADDGLTALPMLK--KGDFDFVVTDWNMPGMQGIDLLKNIRADEELK   86 (134)
T ss_dssp             CCTTCCEEEECSCHHHHHHHHHHHHHTTCCCEEEESSHHHHHHHHH--HHCCSEEEEESCCSSSCHHHHHHHHHHSTTTT
T ss_pred             hCCCCEEEEEeCCHHHHHHHHHHHHHcCCcEEEEECCHHHHHHHHH--hCCCCEEEEcCCCCCCCHHHHHHHHHhCCCCC
Confidence            446789999999999999999999999985 678999999999988  4569999999999999999999999743   5


Q ss_pred             CCCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           90 DLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        90 ~~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      ++|||++|+....+...+++++||++|+.||++.++|..++++++++
T Consensus        87 ~ipvI~lTa~~~~~~~~~~~~~Ga~~yl~KP~~~~~L~~~i~~~l~R  133 (134)
T 3to5_A           87 HLPVLMITAEAKREQIIEAAQAGVNGYIVKPFTAATLKEKLDKIFER  133 (134)
T ss_dssp             TCCEEEEESSCCHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHCC-
T ss_pred             CCeEEEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHhc
Confidence            78999999999999999999999999999999999999999988653

>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=99.91  E-value=4.8e-23  Score=140.91  Aligned_cols=116  Identities=28%  Similarity=0.453  Sum_probs=107.6

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc---CCCCEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE---MDLPVI   94 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~---~~~~iI   94 (184)
                      .+|+||||++..+..++..|+..||++..+.++.++++.+.  ...||++|+|+.||+++|++++++++..   +++|||
T Consensus         3 ~~ILivdd~~~~~~~l~~~l~~~g~~v~~~~~~~~al~~l~--~~~~dlvllD~~~p~~~g~~~~~~l~~~~~~~~~pii   80 (122)
T 3gl9_A            3 KKVLLVDDSAVLRKIVSFNLKKEGYEVIEAENGQIALEKLS--EFTPDLIVLXIMMPVMDGFTVLKKLQEKEEWKRIPVI   80 (122)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHT--TBCCSEEEECSCCSSSCHHHHHHHHHTSTTTTTSCEE
T ss_pred             ceEEEEeCCHHHHHHHHHHHHHCCcEEEEeCCHHHHHHHHH--hcCCCEEEEeccCCCCcHHHHHHHHHhcccccCCCEE
Confidence            47999999999999999999999999999999999999987  5669999999999999999999999643   578999


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      ++|+..+......+++.|+++|+.||++.++|..+++.+++
T Consensus        81 ~~s~~~~~~~~~~~~~~Ga~~~l~KP~~~~~L~~~i~~~l~  121 (122)
T 3gl9_A           81 VLTAKGGEEDESLALSLGARKVMRKPFSPSQFIEEVKHLLN  121 (122)
T ss_dssp             EEESCCSHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHHC
T ss_pred             EEecCCchHHHHHHHhcChhhhccCCCCHHHHHHHHHHHhc
Confidence            99999889999999999999999999999999999998765

>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=99.91  E-value=5.1e-23  Score=140.28  Aligned_cols=117  Identities=30%  Similarity=0.468  Sum_probs=109.0

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMS   97 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi~~   97 (184)
                      .+|+||||++..+..++..|+..||.+..+.++.++++.+.  ...||+||+|+.||+.+|+++++.++...++|+|+++
T Consensus         3 ~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~--~~~~dlii~D~~~p~~~g~~~~~~lr~~~~~~ii~~t   80 (120)
T 3f6p_A            3 KKILVVDDEKPIADILEFNLRKEGYEVHCAHDGNEAVEMVE--ELQPDLILLDIMLPNKDGVEVCREVRKKYDMPIIMLT   80 (120)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--TTCCSEEEEETTSTTTHHHHHHHHHHTTCCSCEEEEE
T ss_pred             CeEEEEECCHHHHHHHHHHHHhCCEEEEEeCCHHHHHHHHh--hCCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCEEEEE
Confidence            48999999999999999999999999999999999999987  5679999999999999999999999766789999999


Q ss_pred             ccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           98 VDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        98 ~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      +..+......+++.|+++|+.||++.++|..+++.++++
T Consensus        81 ~~~~~~~~~~~~~~ga~~~l~KP~~~~~l~~~i~~~l~~  119 (120)
T 3f6p_A           81 AKDSEIDKVIGLEIGADDYVTKPFSTRELLARVKANLRR  119 (120)
T ss_dssp             ESSCHHHHHHHHHTTCCEEEEESCCHHHHHHHHHHHHTC
T ss_pred             CCCChHHHHHHHhCCcceeEcCCCCHHHHHHHHHHHHhc
Confidence            988888889999999999999999999999999988763

>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=99.91  E-value=1.1e-22  Score=141.56  Aligned_cols=121  Identities=32%  Similarity=0.488  Sum_probs=109.5

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc---cCCCCE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL---EMDLPV   93 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~---~~~~~i   93 (184)
                      ..+|+|+||++..+..++..|+..||.+..+.++.++++.+.  ...||+||+|+.||+.+|+++++.++.   .+.+||
T Consensus         4 ~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~--~~~~dlvl~D~~lp~~~g~~~~~~lr~~~~~~~~pi   81 (136)
T 3t6k_A            4 PHTLLIVDDDDTVAEMLELVLRGAGYEVRRAASGEEALQQIY--KNLPDALICDVLLPGIDGYTLCKRVRQHPLTKTLPI   81 (136)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HSCCSEEEEESCCSSSCHHHHHHHHHHSGGGTTCCE
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHH--hCCCCEEEEeCCCCCCCHHHHHHHHHcCCCcCCccE
Confidence            468999999999999999999999999999999999999987  456999999999999999999999964   357899


Q ss_pred             EEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCC
Q 029986           94 IMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKP  139 (184)
Q Consensus        94 Ii~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~  139 (184)
                      |++++..+......+++.|+++|+.||++.++|..+++.++.+...
T Consensus        82 i~~t~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~i~~~l~~~~~  127 (136)
T 3t6k_A           82 LMLTAQGDISAKIAGFEAGANDYLAKPFEPQELVYRVKNILARTTI  127 (136)
T ss_dssp             EEEECTTCHHHHHHHHHHTCSEEEETTCCHHHHHHHHHHHHHC---
T ss_pred             EEEecCCCHHHHHHHHhcCcceEEeCCCCHHHHHHHHHHHHhccCC
Confidence            9999998888999999999999999999999999999999876543

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

Probab=99.90  E-value=6.1e-25  Score=151.20  Aligned_cols=113  Identities=27%  Similarity=0.382  Sum_probs=99.3

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEE-EECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVT-KCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIM   95 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~-~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi   95 (184)
                      .+|||||||++..+..++.+|+..||++. .+.+++++++.+.  +..||+||+|+.||+++|+++++.++. .++|||+
T Consensus         8 ~~rILiVdD~~~~~~~l~~~L~~~G~~v~~~a~~g~eAl~~~~--~~~~DlvllDi~mP~~~G~el~~~lr~-~~ipvI~   84 (123)
T 2lpm_A            8 RLRVLVVEDESMIAMLIEDTLCELGHEVAATASRMQEALDIAR--KGQFDIAIIDVNLDGEPSYPVADILAE-RNVPFIF   84 (123)
T ss_dssp             CCCEEEESSSTTTSHHHHHHHHHHCCCCCBCSCCHHHHHHHHH--HCCSSEEEECSSSSSCCSHHHHHHHHH-TCCSSCC
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHH--hCCCCEEEEecCCCCCCHHHHHHHHHc-CCCCEEE
Confidence            57999999999999999999999999875 7899999999997  456999999999999999999999975 5799999


Q ss_pred             EEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           96 MSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        96 ~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      +|++.+...   +.++|+.+|+.||++.++|..+++++.+
T Consensus        85 lTa~~~~~~---~~~~g~~~yl~KP~~~~~L~~~l~~~~~  121 (123)
T 2lpm_A           85 ATGYGSKGL---DTRYSNIPLLTKPFLDSELEAVLVQISK  121 (123)
T ss_dssp             BCTTCTTSC---CSSSCSCSCBCSSSSHHHHHHHHSTTCS
T ss_pred             EecCccHHH---HHhCCCCcEEECCCCHHHHHHHHHHHHh
Confidence            998765443   3467999999999999999998876544

>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=99.89  E-value=6.6e-22  Score=137.15  Aligned_cols=120  Identities=19%  Similarity=0.395  Sum_probs=106.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCC-eEEEECCHHHHHHHHHh---cCCCccEEEEeCCCCCCCHHHHHHHhcc--cCC
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLY-EVTKCNRAEIALDMLRM---SKNGYDIVISDVHMPDMDGFKLHEQVGL--EMD   90 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~-~v~~~~~~~~~~~~l~~---~~~~~dlvilD~~l~~~~g~~l~~~l~~--~~~   90 (184)
                      .++|+||||++..+..++..|+..|+ .+..+.++.++++.+..   ....||+||+|+.||+++|+++++.++.  .+.
T Consensus         2 ~~~ILivdD~~~~~~~l~~~L~~~g~~~v~~~~~~~~al~~~~~~~~~~~~~dlvllD~~mp~~~G~~~~~~lr~~~~~~   81 (133)
T 2r25_B            2 SVKILVVEDNHVNQEVIKRMLNLEGIENIELACDGQEAFDKVKELTSKGENYNMIFMDVQMPKVDGLLSTKMIRRDLGYT   81 (133)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHTTCCCEEEESSHHHHHHHHHHHHHHTCCCSEEEECSCCSSSCHHHHHHHHHHHSCCC
T ss_pred             CceEEEEcCCHHHHHHHHHHHHHcCCceEEEECCHHHHHHHHHHHHhcCCCCCEEEEeCCCCCCChHHHHHHHHhhcCCC
Confidence            46899999999999999999998887 58889999999998863   1146999999999999999999999974  347


Q ss_pred             CCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           91 LPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        91 ~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      +|||++|+..+......+++.|+++|+.||++.++|..+++.+...
T Consensus        82 ~~ii~lt~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~l~~~~~~  127 (133)
T 2r25_B           82 SPIVALTAFADDSNIKECLESGMNGFLSKPIKRPKLKTILTEFCAA  127 (133)
T ss_dssp             SCEEEEESCCSHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHCTT
T ss_pred             CCEEEEECCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHHh
Confidence            8999999998888899999999999999999999999999988653

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

Probab=99.89  E-value=1.1e-21  Score=139.36  Aligned_cols=121  Identities=26%  Similarity=0.422  Sum_probs=111.7

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc---CCCCE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE---MDLPV   93 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~---~~~~i   93 (184)
                      +++|+||||++..+..++..|+..||.+..+.++.++++.+.  ...||+||+|+.||+.+|+++++.++..   +.+||
T Consensus         7 ~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~--~~~~dlii~D~~l~~~~g~~~~~~lr~~~~~~~~pi   84 (154)
T 3gt7_A            7 AGEILIVEDSPTQAEHLKHILEETGYQTEHVRNGREAVRFLS--LTRPDLIISDVLMPEMDGYALCRWLKGQPDLRTIPV   84 (154)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHT--TCCCSEEEEESCCSSSCHHHHHHHHHHSTTTTTSCE
T ss_pred             CCcEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHH--hCCCCEEEEeCCCCCCCHHHHHHHHHhCCCcCCCCE
Confidence            578999999999999999999999999999999999999987  5669999999999999999999999754   57899


Q ss_pred             EEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCC
Q 029986           94 IMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKP  139 (184)
Q Consensus        94 Ii~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~  139 (184)
                      |+++...+......+++.|+++|+.||++.++|..+++.++++...
T Consensus        85 i~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~l~~~~~  130 (154)
T 3gt7_A           85 ILLTILSDPRDVVRSLECGADDFITKPCKDVVLASHVKRLLSGVKR  130 (154)
T ss_dssp             EEEECCCSHHHHHHHHHHCCSEEEESSCCHHHHHHHHHHHHHHTCC
T ss_pred             EEEECCCChHHHHHHHHCCCCEEEeCCCCHHHHHHHHHHHHHHHHh
Confidence            9999988899999999999999999999999999999999876553

>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=99.89  E-value=1.8e-21  Score=134.04  Aligned_cols=119  Identities=28%  Similarity=0.527  Sum_probs=107.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCe-EEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc---CCCC
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYE-VTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE---MDLP   92 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~-v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~---~~~~   92 (184)
                      .++|+||||++..+..++..|+..|+. +..+.++.++++.+.. ...||+||+|+.||+++|++++++++..   +.+|
T Consensus         5 ~~~iLivdd~~~~~~~l~~~L~~~g~~~v~~~~~~~~a~~~~~~-~~~~dlvi~D~~~p~~~g~~~~~~lr~~~~~~~~p   83 (129)
T 3h1g_A            5 SMKLLVVDDSSTMRRIIKNTLSRLGYEDVLEAEHGVEAWEKLDA-NADTKVLITDWNMPEMNGLDLVKKVRSDSRFKEIP   83 (129)
T ss_dssp             -CCEEEECSCHHHHHHHHHHHHHTTCCCEEEESSHHHHHHHHHH-CTTCCEEEECSCCSSSCHHHHHHHHHTSTTCTTCC
T ss_pred             CcEEEEEeCCHHHHHHHHHHHHHcCCcEEEEeCCHHHHHHHHHh-CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCCCe
Confidence            578999999999999999999999985 8899999999988763 3459999999999999999999999643   5789


Q ss_pred             EEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           93 VIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        93 iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      ||++++..+......+++.|+++|+.||++.++|..+++.++.+
T Consensus        84 ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~L~~~l~~~l~~  127 (129)
T 3h1g_A           84 IIMITAEGGKAEVITALKAGVNNYIVKPFTPQVLKEKLEVVLGT  127 (129)
T ss_dssp             EEEEESCCSHHHHHHHHHHTCCEEEESCCCHHHHHHHHHHHHCC
T ss_pred             EEEEeCCCChHHHHHHHHcCccEEEeCCCCHHHHHHHHHHHhcc
Confidence            99999998889999999999999999999999999999998764

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

Probab=99.89  E-value=8.4e-22  Score=138.36  Aligned_cols=119  Identities=30%  Similarity=0.456  Sum_probs=104.3

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-----cCC
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-----EMD   90 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-----~~~   90 (184)
                      ..++|+||||++..+..++.+|+..|+.+..+.+++++++.+.  ...||+||+|+.||+++|+++++.++.     .+.
T Consensus        13 ~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~--~~~~dlvl~D~~mp~~~g~~~~~~lr~~~~~~~~~   90 (143)
T 3m6m_D           13 RSMRMLVADDHEANRMVLQRLLEKAGHKVLCVNGAEQVLDAMA--EEDYDAVIVDLHMPGMNGLDMLKQLRVMQASGMRY   90 (143)
T ss_dssp             --CEEEEECSSHHHHHHHHHHHHC--CEEEEESSHHHHHHHHH--HSCCSEEEEESCCSSSCHHHHHHHHHHHHHTTCCC
T ss_pred             ccceEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCHHHHHHHHh--cCCCCEEEEeCCCCCCCHHHHHHHHHhchhccCCC
Confidence            4689999999999999999999999999999999999999987  456999999999999999999999963     246


Q ss_pred             CCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           91 LPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        91 ~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      +|+|+++...+.+....+++.|+++|+.||++.++|..++..+..+
T Consensus        91 ~pii~~s~~~~~~~~~~~~~~Ga~~~l~KP~~~~~L~~~l~~~~~~  136 (143)
T 3m6m_D           91 TPVVVLSADVTPEAIRACEQAGARAFLAKPVVAAKLLDTLADLAVS  136 (143)
T ss_dssp             CCEEEEESCCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHC--
T ss_pred             CeEEEEeCCCCHHHHHHHHHcChhheeeCCCCHHHHHHHHHHHHHh
Confidence            8999999988888999999999999999999999999999988654

>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=99.89  E-value=2.4e-21  Score=132.69  Aligned_cols=120  Identities=22%  Similarity=0.353  Sum_probs=109.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIM   95 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi   95 (184)
                      ..+|+|+||++..+..++..|...|+.+..+.++.++++.+.  ...||++|+|+.||+.+|+++++.++. .+.+|+|+
T Consensus         3 ~~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~--~~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~ii~   80 (126)
T 1dbw_A            3 DYTVHIVDDEEPVRKSLAFMLTMNGFAVKMHQSAEAFLAFAP--DVRNGVLVTDLRMPDMSGVELLRNLGDLKINIPSIV   80 (126)
T ss_dssp             CCEEEEEESSHHHHHHHHHHHHHTTCEEEEESCHHHHHHHGG--GCCSEEEEEECCSTTSCHHHHHHHHHHTTCCCCEEE
T ss_pred             CCEEEEEcCCHHHHHHHHHHHHhCCcEEEEeCCHHHHHHHHh--cCCCCEEEEECCCCCCCHHHHHHHHHhcCCCCCEEE
Confidence            458999999999999999999998999999999999999876  456999999999999999999999964 46889999


Q ss_pred             EEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCC
Q 029986           96 MSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPK  138 (184)
Q Consensus        96 ~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~  138 (184)
                      +++..+......+++.|+++|+.||++.++|..+++.+.++..
T Consensus        81 ~s~~~~~~~~~~~~~~ga~~~l~Kp~~~~~l~~~i~~~~~~~~  123 (126)
T 1dbw_A           81 ITGHGDVPMAVEAMKAGAVDFIEKPFEDTVIIEAIERASEHLV  123 (126)
T ss_dssp             EECTTCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHHTTCC
T ss_pred             EECCCCHHHHHHHHHhCHHHheeCCCCHHHHHHHHHHHHHhhh
Confidence            9998888899999999999999999999999999999876543

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

Probab=99.88  E-value=6.6e-22  Score=137.92  Aligned_cols=124  Identities=16%  Similarity=0.266  Sum_probs=111.1

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHh-cCCeEEEECCHHHHHHHHHhcC-CCccEEEEeCCCC-CCCHHHHHHHhcc---cC
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRK-CLYEVTKCNRAEIALDMLRMSK-NGYDIVISDVHMP-DMDGFKLHEQVGL---EM   89 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~-~~~~v~~~~~~~~~~~~l~~~~-~~~dlvilD~~l~-~~~g~~l~~~l~~---~~   89 (184)
                      ..++|+||||++..+..++.+|.. .|+.+..+.++.++++.+.  . ..||+||+|+.|| +.+|+++++.++.   .+
T Consensus         3 ~~~~ilivdd~~~~~~~l~~~L~~~~~~~v~~~~~~~~a~~~l~--~~~~~dlvi~D~~l~~~~~g~~~~~~l~~~~~~~   80 (140)
T 3lua_A            3 LDGTVLLIDYFEYEREKTKIIFDNIGEYDFIEVENLKKFYSIFK--DLDSITLIIMDIAFPVEKEGLEVLSAIRNNSRTA   80 (140)
T ss_dssp             CCCEEEEECSCHHHHHHHHHHHHHHCCCEEEEECSHHHHHTTTT--TCCCCSEEEECSCSSSHHHHHHHHHHHHHSGGGT
T ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhccCccEEEECCHHHHHHHHh--cCCCCcEEEEeCCCCCCCcHHHHHHHHHhCcccC
Confidence            356899999999999999999999 8999999999999999887  5 6799999999999 9999999999965   57


Q ss_pred             CCCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCCCC
Q 029986           90 DLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPFE  141 (184)
Q Consensus        90 ~~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~~  141 (184)
                      .+|||+++...+.....++++.|+++|+.||++.++|..+++.++++..+.+
T Consensus        81 ~~~ii~ls~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~~~~~~~~  132 (140)
T 3lua_A           81 NTPVIIATKSDNPGYRHAALKFKVSDYILKPYPTKRLENSVRSVLKICQRFR  132 (140)
T ss_dssp             TCCEEEEESCCCHHHHHHHHHSCCSEEEESSCCTTHHHHHHHHHHCC-----
T ss_pred             CCCEEEEeCCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHHHhccccC
Confidence            8999999999889999999999999999999999999999999998766544

>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=99.88  E-value=3e-21  Score=130.64  Aligned_cols=117  Identities=26%  Similarity=0.442  Sum_probs=107.6

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMS   97 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi~~   97 (184)
                      .+|+|+||++..+..++..|...|+.+..+.++.++++.+..  ..||++|+|+.||+.+|+++++.++..+.+|+|+++
T Consensus         2 ~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~~~~--~~~dlvl~D~~l~~~~g~~~~~~l~~~~~~~ii~~s   79 (120)
T 2a9o_A            2 KKILIVDDEKPISDIIKFNMTKEGYEVVTAFNGREALEQFEA--EQPDIIILDLMLPEIDGLEVAKTIRKTSSVPILMLS   79 (120)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHH--HCCSEEEECSSCSSSCHHHHHHHHHHHCCCCEEEEE
T ss_pred             ceEEEEcCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHHHh--CCCCEEEEeccCCCCCHHHHHHHHHhCCCCCEEEEe
Confidence            479999999999999999999999999999999999999873  459999999999999999999999766789999999


Q ss_pred             ccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           98 VDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        98 ~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      +..+......+++.|+++|+.||++.++|..+++.+.++
T Consensus        80 ~~~~~~~~~~~~~~g~~~~l~Kp~~~~~l~~~i~~~~~~  118 (120)
T 2a9o_A           80 AKDSEFDKVIGLELGADDYVTKPFSNRELQARVKALLRR  118 (120)
T ss_dssp             SCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHHHC
T ss_pred             cCCchHHHHHHHhCCHhheEeCCCCHHHHHHHHHHHHcc
Confidence            988888888999999999999999999999999988754

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

Probab=99.88  E-value=7.5e-22  Score=136.41  Aligned_cols=124  Identities=19%  Similarity=0.241  Sum_probs=110.4

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEE-EECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVT-KCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIM   95 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~-~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi   95 (184)
                      ++|+|+||++..+..++..|.+.|+.+. .+.++.++++.+..  ..||+||+|+.||+.+|+++++.++. .+.+|+|+
T Consensus         2 ~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~~a~~~~~~--~~~dlii~d~~l~~~~g~~~~~~l~~~~~~~~ii~   79 (134)
T 3f6c_A            2 LNAIIIDDHPLAIAAIRNLLIKNDIEILAELTEGGSAVQRVET--LKPDIVIIDVDIPGVNGIQVLETLRKRQYSGIIII   79 (134)
T ss_dssp             EEEEEECCCHHHHHHHHHHHHHTTEEEEEEESSSTTHHHHHHH--HCCSEEEEETTCSSSCHHHHHHHHHHTTCCSEEEE
T ss_pred             eEEEEEcCCHHHHHHHHHHHhhCCcEEEEEcCCHHHHHHHHHh--cCCCEEEEecCCCCCChHHHHHHHHhcCCCCeEEE
Confidence            6899999999999999999999999887 89999999999873  45999999999999999999999964 46889999


Q ss_pred             EEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCCCCCC
Q 029986           96 MSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPFEES  143 (184)
Q Consensus        96 ~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~~~~  143 (184)
                      +++..+......+++.|+++|+.||++.++|..+++.++++..+++..
T Consensus        80 ~s~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~~~~~~~~~~~  127 (134)
T 3f6c_A           80 VSAKNDHFYGKHCADAGANGFVSKKEGMNNIIAAIEAAKNGYCYFPFS  127 (134)
T ss_dssp             EECC---CTHHHHHHTTCSEEEEGGGCTHHHHHHHHHHHTTCCBCCCC
T ss_pred             EeCCCChHHHHHHHHhCCCEEEeCCCCHHHHHHHHHHHHCCCEEeCHH
Confidence            999888888999999999999999999999999999999988776543

>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=99.88  E-value=4.4e-21  Score=132.94  Aligned_cols=124  Identities=23%  Similarity=0.298  Sum_probs=109.0

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc--CCCCE
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE--MDLPV   93 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~--~~~~i   93 (184)
                      ...+|+|+||++..+..++..|...|+.+..+.+..+++..+.. ...||+||+|+.|++.+|+++++.++..  +.+|+
T Consensus         6 ~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~~~~-~~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~~i   84 (136)
T 3hdv_A            6 ARPLVLVVDDNAVNREALILYLKSRGIDAVGADGAEEARLYLHY-QKRIGLMITDLRMQPESGLDLIRTIRASERAALSI   84 (136)
T ss_dssp             -CCEEEEECSCHHHHHHHHHHHHHTTCCEEEESSHHHHHHHHHH-CTTEEEEEECSCCSSSCHHHHHHHHHTSTTTTCEE
T ss_pred             CCCeEEEECCCHHHHHHHHHHHHHcCceEEEeCCHHHHHHHHHh-CCCCcEEEEeccCCCCCHHHHHHHHHhcCCCCCCE
Confidence            35689999999999999999999999999999999999998873 2349999999999999999999999754  68899


Q ss_pred             EEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCCC
Q 029986           94 IMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPF  140 (184)
Q Consensus        94 Ii~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~  140 (184)
                      |+++...+......+++.|+++|+.||++.++|..+++++..+..+.
T Consensus        85 i~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~~~~~~~  131 (136)
T 3hdv_A           85 IVVSGDTDVEEAVDVMHLGVVDFLLKPVDLGKLLELVNKELKIGEGH  131 (136)
T ss_dssp             EEEESSCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHHC-----
T ss_pred             EEEeCCCChHHHHHHHhCCcceEEeCCCCHHHHHHHHHHHhcCchhh
Confidence            99999888889999999999999999999999999999998876544

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

Probab=99.88  E-value=2.2e-21  Score=148.31  Aligned_cols=120  Identities=31%  Similarity=0.478  Sum_probs=110.8

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc-CCCCEE
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE-MDLPVI   94 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~-~~~~iI   94 (184)
                      +.++|+||||++..+..+...|+..|+.+..+.++.++++.+..  ..||+||+|+.||+++|+++++.++.. +.+|||
T Consensus        22 ~~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~~--~~~dlvllD~~lp~~~g~~~~~~lr~~~~~~~ii   99 (250)
T 3r0j_A           22 PEARVLVVDDEANIVELLSVSLKFQGFEVYTATNGAQALDRARE--TRPDAVILDVXMPGMDGFGVLRRLRADGIDAPAL   99 (250)
T ss_dssp             SSCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHH--HCCSEEEEESCCSSSCHHHHHHHHHHTTCCCCEE
T ss_pred             CCceEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHh--CCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCCEE
Confidence            46799999999999999999999999999999999999999873  459999999999999999999999754 689999


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCC
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQP  137 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~  137 (184)
                      +++...+......+++.||++|+.||++.++|..+++.++++.
T Consensus       100 ~lt~~~~~~~~~~~~~~Ga~~yl~Kp~~~~~L~~~i~~~~~~~  142 (250)
T 3r0j_A          100 FLTARDSLQDKIAGLTLGGDDYVTKPFSLEEVVARLRVILRRA  142 (250)
T ss_dssp             EEECSTTHHHHHHHHTSTTCEEEESSCCHHHHHHHHHHHHHHH
T ss_pred             EEECCCCHHHHHHHHHcCCcEEEeCCCCHHHHHHHHHHHHHhh
Confidence            9999988899999999999999999999999999999998653

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

Probab=99.88  E-value=3.6e-21  Score=135.83  Aligned_cols=126  Identities=22%  Similarity=0.321  Sum_probs=112.5

Q ss_pred             CCCCCeEEEEeCCHHHHHHHHHHHHhcC--CeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCC
Q 029986           14 FPAGLRVLVVDDDPIWLRILEKMLRKCL--YEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMD   90 (184)
Q Consensus        14 ~~~~~~Ilivdd~~~~~~~l~~~L~~~~--~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~   90 (184)
                      ...+++|+||||++..+..+...|...+  +.+..+.++.++++.+.  ...||+||+|+.|++.+|+++++.++. .+.
T Consensus        17 ~~~m~~iLivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~al~~l~--~~~~dlii~D~~l~~~~g~~~~~~l~~~~~~   94 (150)
T 4e7p_A           17 RGSHMKVLVAEDQSMLRDAMCQLLTLQPDVESVLQAKNGQEAIQLLE--KESVDIAILDVEMPVKTGLEVLEWIRSEKLE   94 (150)
T ss_dssp             ---CEEEEEECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHHT--TSCCSEEEECSSCSSSCHHHHHHHHHHTTCS
T ss_pred             CCCccEEEEEcCCHHHHHHHHHHHHhCCCcEEEEEECCHHHHHHHhh--ccCCCEEEEeCCCCCCcHHHHHHHHHHhCCC
Confidence            3346799999999999999999999876  78899999999999987  566999999999999999999999964 468


Q ss_pred             CCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCCCC
Q 029986           91 LPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPFE  141 (184)
Q Consensus        91 ~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~~  141 (184)
                      +|||++++..+......+++.|+++|+.||++.++|..+++.++++...++
T Consensus        95 ~~ii~ls~~~~~~~~~~~~~~g~~~~l~Kp~~~~~l~~~i~~~~~~~~~~~  145 (150)
T 4e7p_A           95 TKVVVVTTFKRAGYFERAVKAGVDAYVLKERSIADLMQTLHTVLEGRKEYS  145 (150)
T ss_dssp             CEEEEEESCCCHHHHHHHHHTTCSEEEETTSCHHHHHHHHHHHHTTCCEEC
T ss_pred             CeEEEEeCCCCHHHHHHHHHCCCcEEEecCCCHHHHHHHHHHHHcCCEEcC
Confidence            999999999989999999999999999999999999999999998766443

>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=99.87  E-value=7.7e-21  Score=128.92  Aligned_cols=116  Identities=28%  Similarity=0.416  Sum_probs=106.7

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIMM   96 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi~   96 (184)
                      ++|+|+||++..+..+...|...|+.+..+.++.++++.+.  ...||++|+|+.||+.+|+++++.++. .+.+|+|++
T Consensus         1 ~~ilivdd~~~~~~~l~~~l~~~g~~v~~~~~~~~a~~~~~--~~~~dlil~D~~l~~~~g~~~~~~l~~~~~~~~ii~~   78 (121)
T 2pl1_A            1 MRVLVVEDNALLRHHLKVQIQDAGHQVDDAEDAKEADYYLN--EHIPDIAIVDLGLPDEDGLSLIRRWRSNDVSLPILVL   78 (121)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HSCCSEEEECSCCSSSCHHHHHHHHHHTTCCSCEEEE
T ss_pred             CeEEEEeCcHHHHHHHHHHHhhcCCEEEEeCCHHHHHHHHh--ccCCCEEEEecCCCCCCHHHHHHHHHhcCCCCCEEEE
Confidence            47999999999999999999999999999999999999987  356999999999999999999999964 468899999


Q ss_pred             EccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           97 SVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        97 ~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      ++..+......+++.|+++|+.||++.++|..+++.+.+
T Consensus        79 s~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~~~  117 (121)
T 2pl1_A           79 TARESWQDKVEVLSAGADDYVTKPFHIEEVMARMQALMR  117 (121)
T ss_dssp             ESCCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHHH
T ss_pred             ecCCCHHHHHHHHHcCccceEECCCCHHHHHHHHHHHHH
Confidence            998888888999999999999999999999999998765

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

Probab=99.87  E-value=4.2e-21  Score=132.06  Aligned_cols=121  Identities=25%  Similarity=0.406  Sum_probs=102.8

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEE
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVI   94 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iI   94 (184)
                      .+++|+|+||++..+..++..|...|+.+..+.++.++++.+.  ...||+||+|+.+++.+|+++++.++. .+.+|+|
T Consensus         6 ~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--~~~~dlvi~d~~l~~~~g~~~~~~l~~~~~~~~ii   83 (130)
T 3eod_A            6 VGKQILIVEDEQVFRSLLDSWFSSLGATTVLAADGVDALELLG--GFTPDLMICDIAMPRMNGLKLLEHIRNRGDQTPVL   83 (130)
T ss_dssp             TTCEEEEECSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHHHT--TCCCSEEEECCC-----CHHHHHHHHHTTCCCCEE
T ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhCCceEEEeCCHHHHHHHHh--cCCCCEEEEecCCCCCCHHHHHHHHHhcCCCCCEE
Confidence            3679999999999999999999999999999999999999986  566999999999999999999999964 4689999


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCC-CHHHHHHHHHHHHcCCC
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPI-RIKELRNIWQHVAQQPK  138 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~-~~~~l~~~l~~~~~~~~  138 (184)
                      ++++..+......+++.|+++|+.||+ +.++|..+++.+++++.
T Consensus        84 ~~t~~~~~~~~~~~~~~g~~~~l~KP~~~~~~l~~~i~~~l~~~~  128 (130)
T 3eod_A           84 VISATENMADIAKALRLGVEDVLLKPVKDLNRLREMVFACLYPSM  128 (130)
T ss_dssp             EEECCCCHHHHHHHHHHCCSEEEESCC---CHHHHHHHHHHC---
T ss_pred             EEEcCCCHHHHHHHHHcCCCEEEeCCCCcHHHHHHHHHHHhchhh
Confidence            999998888899999999999999999 89999999999987643

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

Probab=99.87  E-value=5.2e-22  Score=145.23  Aligned_cols=117  Identities=21%  Similarity=0.360  Sum_probs=108.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIM   95 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi   95 (184)
                      +++|+||||++..+..++.+|...||.+..+.++.++++.+.  ...||+||+|+.||+++|+++++.++. .+++|||+
T Consensus         7 ~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~--~~~~dlvl~D~~lp~~~g~~~~~~l~~~~~~~~ii~   84 (184)
T 3rqi_A            7 DKNFLVIDDNEVFAGTLARGLERRGYAVRQAHNKDEALKLAG--AEKFEFITVXLHLGNDSGLSLIAPLCDLQPDARILV   84 (184)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEECSHHHHHHHHT--TSCCSEEEECSEETTEESHHHHHHHHHHCTTCEEEE
T ss_pred             CCeEEEEcCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHh--hCCCCEEEEeccCCCccHHHHHHHHHhcCCCCCEEE
Confidence            568999999999999999999999999999999999999987  566999999999999999999999964 46899999


Q ss_pred             EEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           96 MSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        96 ~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      +|+..+.+....+++.||++|+.||++.++|..+++.++.
T Consensus        85 lt~~~~~~~~~~a~~~Ga~~~l~KP~~~~~L~~~i~~~~~  124 (184)
T 3rqi_A           85 LTGYASIATAVQAVKDGADNYLAKPANVESILAALQTNAS  124 (184)
T ss_dssp             EESSCCHHHHHHHHHHTCSEEEESSCCHHHHHHHTSTTHH
T ss_pred             EeCCCCHHHHHHHHHhCHHHheeCCCCHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999998876654

>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=99.87  E-value=4.2e-21  Score=131.03  Aligned_cols=117  Identities=24%  Similarity=0.396  Sum_probs=107.3

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIMM   96 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi~   96 (184)
                      .+|+|+||++..+..++..|...|+.+..+.++.++++.+..  ..||++|+|+.||+.+|+++++.++. .+.+|+|++
T Consensus         4 ~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~~~~--~~~dlvl~D~~l~~~~g~~~~~~l~~~~~~~~ii~~   81 (124)
T 1srr_A            4 EKILIVDDQSGIRILLNEVFNKEGYQTFQAANGLQALDIVTK--ERPDLVLLDMKIPGMDGIEILKRMKVIDENIRVIIM   81 (124)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHHH--HCCSEEEEESCCTTCCHHHHHHHHHHHCTTCEEEEE
T ss_pred             ceEEEEeCCHHHHHHHHHHHHHCCcEEEEeCCHHHHHHHHhc--cCCCEEEEecCCCCCCHHHHHHHHHHhCCCCCEEEE
Confidence            589999999999999999999989999999999999999873  45999999999999999999999964 478999999


Q ss_pred             EccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           97 SVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        97 ~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      ++..+......+++.|+++|+.||++.++|..+++.+.++
T Consensus        82 s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~~~  121 (124)
T 1srr_A           82 TAYGELDMIQESKELGALTHFAKPFDIDEIRDAVKKYLPL  121 (124)
T ss_dssp             ESSCCHHHHHHHHHHTCCCEEESSCCHHHHHHHHHHHSCC
T ss_pred             EccCchHHHHHHHhcChHhhccCCCCHHHHHHHHHHHhcc
Confidence            9988888889999999999999999999999999987654

>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=99.87  E-value=7.3e-21  Score=129.35  Aligned_cols=116  Identities=19%  Similarity=0.377  Sum_probs=106.9

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMS   97 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi~~   97 (184)
                      .+|+|+||++..+..++..|...|+.+..+.++.++++.+.  ...||++|+|+.||+.+|+++++.++..+.+|+|+++
T Consensus         3 ~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~--~~~~dlvi~d~~l~~~~g~~~~~~l~~~~~~~ii~~s   80 (122)
T 1zgz_A            3 HHIVIVEDEPVTQARLQSYFTQEGYTVSVTASGAGLREIMQ--NQSVDLILLDINLPDENGLMLTRALRERSTVGIILVT   80 (122)
T ss_dssp             CEEEEECSSHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HSCCSEEEEESCCSSSCHHHHHHHHHTTCCCEEEEEE
T ss_pred             cEEEEEECCHHHHHHHHHHHHHCCCeEEEecCHHHHHHHHh--cCCCCEEEEeCCCCCCChHHHHHHHHhcCCCCEEEEE
Confidence            48999999999999999999988999999999999999887  3559999999999999999999999776789999999


Q ss_pred             ccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           98 VDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        98 ~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      +..+......+++.|+++|+.||++.++|...++.+.+
T Consensus        81 ~~~~~~~~~~~~~~ga~~~l~Kp~~~~~l~~~i~~~~~  118 (122)
T 1zgz_A           81 GRSDRIDRIVGLEMGADDYVTKPLELRELVVRVKNLLW  118 (122)
T ss_dssp             SSCCHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHHH
T ss_pred             CCCChhhHHHHHHhCHHHHccCCCCHHHHHHHHHHHHH
Confidence            98888888999999999999999999999999988765

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

Probab=99.87  E-value=3.8e-21  Score=133.10  Aligned_cols=122  Identities=17%  Similarity=0.272  Sum_probs=106.0

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcC--CeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCL--YEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVI   94 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~--~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iI   94 (184)
                      ++|+|+||++..+..++..|+..+  +.+..+.++.++++.+..  ..||++|+|+.||+.+|+++++.++. .+.+|||
T Consensus         4 ~~Ilivdd~~~~~~~l~~~l~~~~~~~~v~~~~~~~~al~~~~~--~~~dlvilD~~lp~~~g~~~~~~l~~~~~~~~ii   81 (133)
T 3b2n_A            4 TSLIIAEDQNMLRQAMVQLIKLHGDFEILADTDNGLDAMKLIEE--YNPNVVILDIEMPGMTGLEVLAEIRKKHLNIKVI   81 (133)
T ss_dssp             EEEEEECSCHHHHHHHHHHHHHHSSEEEEEEESCHHHHHHHHHH--HCCSEEEECSSCSSSCHHHHHHHHHHTTCSCEEE
T ss_pred             eEEEEECCCHHHHHHHHHHHhhCCCcEEEEEcCCHHHHHHHHhh--cCCCEEEEecCCCCCCHHHHHHHHHHHCCCCcEE
Confidence            589999999999999999999876  567789999999999873  45999999999999999999999964 4689999


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCCCC
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPFE  141 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~~  141 (184)
                      ++++..+.....++++.|+++|+.||++.++|..+++.+.++..++.
T Consensus        82 ~ls~~~~~~~~~~~~~~ga~~~l~Kp~~~~~L~~~i~~~~~~~~~~~  128 (133)
T 3b2n_A           82 IVTTFKRPGYFEKAVVNDVDAYVLKERSIEELVETINKVNNGEKEGH  128 (133)
T ss_dssp             EEESCCCHHHHHHHHHTTCSEEEETTSCHHHHHHHHHHHHC------
T ss_pred             EEecCCCHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHcCCCccC
Confidence            99998888899999999999999999999999999999988765544

>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=99.87  E-value=4.9e-21  Score=131.44  Aligned_cols=119  Identities=28%  Similarity=0.426  Sum_probs=107.7

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCC-eEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc---CCC
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLY-EVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE---MDL   91 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~-~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~---~~~   91 (184)
                      ..++|+|+||++..+..++..|...|+ .+..+.++.++++.+.  ...||++|+|+.||+.+|+++++.++..   +.+
T Consensus         5 ~~~~ilivdd~~~~~~~l~~~L~~~g~~~v~~~~~~~~a~~~~~--~~~~dlvl~D~~l~~~~g~~~~~~l~~~~~~~~~   82 (129)
T 1p6q_A            5 EKIKVLIVDDQVTSRLLLGDALQQLGFKQITAAGDGEQGMKIMA--QNPHHLVISDFNMPKMDGLGLLQAVRANPATKKA   82 (129)
T ss_dssp             SCCCEEEECSSHHHHHHHHHHHHTTTCSCEECCSSHHHHHHHHH--TSCCSEEEECSSSCSSCHHHHHHHHTTCTTSTTC
T ss_pred             ccCeEEEEcCCHHHHHHHHHHHHHCCCcEEEecCCHHHHHHHHH--cCCCCEEEEeCCCCCCCHHHHHHHHhcCccccCC
Confidence            356899999999999999999998888 7888999999999987  4569999999999999999999999753   578


Q ss_pred             CEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           92 PVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        92 ~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      |+|++++..+......+++.|+++|+.||++.++|..+++.+.+.
T Consensus        83 ~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~~~  127 (129)
T 1p6q_A           83 AFIILTAQGDRALVQKAAALGANNVLAKPFTIEKMKAAIEAVFGA  127 (129)
T ss_dssp             EEEECCSCCCHHHHHHHHHHTCSCEECCCSSHHHHHHHHHHHHHC
T ss_pred             CEEEEeCCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHHHh
Confidence            999999888888889999999999999999999999999988753

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

Probab=99.87  E-value=4.1e-21  Score=133.61  Aligned_cols=118  Identities=19%  Similarity=0.365  Sum_probs=108.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMM   96 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi~   96 (184)
                      .++|+|+||++..+..+...|...|+.+..+.++.++++.+.  ...||++|+|+.||+.+|+++++.++....+|+|++
T Consensus         4 ~~~Ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~--~~~~dlvllD~~l~~~~g~~l~~~l~~~~~~~ii~l   81 (136)
T 2qzj_A            4 QTKILIIDGDKDNCQKLKGFLEEKGISIDLAYNCEEAIGKIF--SNKYDLIFLEIILSDGDGWTLCKKIRNVTTCPIVYM   81 (136)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHH--HCCCSEEEEESEETTEEHHHHHHHHHTTCCCCEEEE
T ss_pred             CCeEEEEcCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHH--hcCCCEEEEeCCCCCCCHHHHHHHHccCCCCCEEEE
Confidence            468999999999999999999988999999999999999987  356999999999999999999999976558899999


Q ss_pred             EccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           97 SVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        97 ~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      +...+......+++.|+++|+.||++.++|..+++.+.++
T Consensus        82 s~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~l~~~~~~  121 (136)
T 2qzj_A           82 TYINEDQSILNALNSGGDDYLIKPLNLEILYAKVKAILRR  121 (136)
T ss_dssp             ESCCCHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHHHH
T ss_pred             EcCCCHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHHH
Confidence            9988888899999999999999999999999999887653

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

Probab=99.87  E-value=5.1e-21  Score=132.27  Aligned_cols=118  Identities=23%  Similarity=0.356  Sum_probs=108.1

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIM   95 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi   95 (184)
                      .++|+|+||++..+..++..|+..|+.+..+.++.++++.+.  ...||++|+|+.||+.+|+++++.++. .+.+|+|+
T Consensus         3 ~~~Ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~--~~~~dlvl~D~~l~~~~g~~~~~~l~~~~~~~~ii~   80 (132)
T 3crn_A            3 LKRILIVDDDTAILDSTKQILEFEGYEVEIAATAGEGLAKIE--NEFFNLALFXIKLPDMEGTELLEKAHKLRPGMKKIM   80 (132)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HSCCSEEEECSBCSSSBHHHHHHHHHHHCTTSEEEE
T ss_pred             ccEEEEEeCCHHHHHHHHHHHHHCCceEEEeCCHHHHHHHHh--cCCCCEEEEecCCCCCchHHHHHHHHhhCCCCcEEE
Confidence            358999999999999999999988999999999999999987  356999999999999999999999964 46889999


Q ss_pred             EEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           96 MSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        96 ~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      +++..+......+++.|+++|+.||++.++|..+++.++++
T Consensus        81 ~s~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~i~~~~~~  121 (132)
T 3crn_A           81 VTGYASLENSVFSLNAGADAYIMKPVNPRDLLEKIKEKLDE  121 (132)
T ss_dssp             EESCCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHHHH
T ss_pred             EeccccHHHHHHHHhccchhhccCCCCHHHHHHHHHHHHhc
Confidence            99988888899999999999999999999999999988764

>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=99.87  E-value=1.3e-20  Score=129.20  Aligned_cols=118  Identities=30%  Similarity=0.530  Sum_probs=107.4

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCC-eEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc---cCCC
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLY-EVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL---EMDL   91 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~-~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~---~~~~   91 (184)
                      +.++|+|+||++..+..++..|...|+ .+..+.++.++++.+.  ...||++|+|+.||+.+|+++++.++.   .+.+
T Consensus         3 ~~~~ilivdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~--~~~~dlvi~D~~l~~~~g~~l~~~l~~~~~~~~~   80 (128)
T 1jbe_A            3 KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQ--AGGYGFVISDWNMPNMDGLELLKTIRAXXAMSAL   80 (128)
T ss_dssp             TTCCEEEECSCHHHHHHHHHHHHHTTCCCEEEESSHHHHHHHHT--TCCCCEEEEESCCSSSCHHHHHHHHHC--CCTTC
T ss_pred             CccEEEEECCCHHHHHHHHHHHHHcCCcEEEeeCCHHHHHHHHH--hcCCCEEEEeCCCCCCCHHHHHHHHHhhcccCCC
Confidence            457899999999999999999998888 7889999999999886  456999999999999999999999975   3578


Q ss_pred             CEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           92 PVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        92 ~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      |+|++++..+......+++.|+++|+.||++.++|..+++.+.+
T Consensus        81 ~ii~~s~~~~~~~~~~~~~~ga~~~l~KP~~~~~l~~~i~~~~~  124 (128)
T 1jbe_A           81 PVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFE  124 (128)
T ss_dssp             CEEEEESSCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHHH
T ss_pred             cEEEEecCccHHHHHHHHHhCcCceeecCCCHHHHHHHHHHHHH
Confidence            99999998888899999999999999999999999999988765

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

Probab=99.87  E-value=3.1e-21  Score=147.72  Aligned_cols=122  Identities=25%  Similarity=0.360  Sum_probs=113.4

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMM   96 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi~   96 (184)
                      .++|+||||++..+..+...|...|+.+..+.++.++++.+.  ...||+||+|+.||+.+|+++++.++..+.+|||++
T Consensus        37 ~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~--~~~~DlvllD~~lp~~~G~~l~~~lr~~~~~~iI~l  114 (249)
T 3q9s_A           37 EQRILVIEDDHDIANVLRMDLTDAGYVVDHADSAMNGLIKAR--EDHPDLILLDLGLPDFDGGDVVQRLRKNSALPIIVL  114 (249)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHH--HSCCSEEEEECCSCHHHHHHHHHHHHTTCCCCEEEE
T ss_pred             CCEEEEEECCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHh--cCCCCEEEEcCCCCCCCHHHHHHHHHcCCCCCEEEE
Confidence            468999999999999999999999999999999999999987  456999999999999999999999987788999999


Q ss_pred             EccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCCC
Q 029986           97 SVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPF  140 (184)
Q Consensus        97 ~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~  140 (184)
                      +...+......+++.||++|+.||++.++|..+++.++++....
T Consensus       115 t~~~~~~~~~~a~~~Ga~~yl~Kp~~~~~L~~~i~~~l~~~~~~  158 (249)
T 3q9s_A          115 TARDTVEEKVRLLGLGADDYLIKPFHPDELLARVKVQLRQRTSE  158 (249)
T ss_dssp             ESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHHCCCCSC
T ss_pred             ECCCCHHHHHHHHHCCCcEEEECCCCHHHHHHHHHHHHhhcccC
Confidence            99999999999999999999999999999999999999876543

>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=99.87  E-value=8.6e-21  Score=129.16  Aligned_cols=116  Identities=19%  Similarity=0.361  Sum_probs=106.9

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMS   97 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi~~   97 (184)
                      .+|+|+||++..+..++..|...|+.+..+.++.++++.+.  ...||++|+|+.||+.+|+++++.++..+.+|+|+++
T Consensus         4 ~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~~~--~~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~ii~~s   81 (123)
T 1xhf_A            4 PHILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQILS--EYDINLVIMDINLPGKNGLLLARELREQANVALMFLT   81 (123)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHH--HSCCSEEEECSSCSSSCHHHHHHHHHHHCCCEEEEEE
T ss_pred             ceEEEEeCCHHHHHHHHHHHhhCCcEEEEeCCHHHHHHHHh--cCCCCEEEEcCCCCCCCHHHHHHHHHhCCCCcEEEEE
Confidence            47999999999999999999988999999999999999987  3569999999999999999999999766789999999


Q ss_pred             ccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           98 VDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        98 ~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      +..+......+++.|+++|+.||++.++|..+++.+.+
T Consensus        82 ~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~~  119 (123)
T 1xhf_A           82 GRDNEVDKILGLEIGADDYITKPFNPRELTIRARNLLS  119 (123)
T ss_dssp             SCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHHH
T ss_pred             CCCChHHHHHHHhcCcceEEeCCCCHHHHHHHHHHHHH
Confidence            98888888999999999999999999999999988765

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

Probab=99.87  E-value=8.1e-22  Score=137.02  Aligned_cols=123  Identities=19%  Similarity=0.171  Sum_probs=110.4

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCC--CCHHHHHHHhcc-cCCCC
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPD--MDGFKLHEQVGL-EMDLP   92 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~--~~g~~l~~~l~~-~~~~~   92 (184)
                      ..++|+|+||++..+..++..|+..||.+..+.++.++++.+.  ...||+||+|+.||+  .+|+++++.++. .+.+|
T Consensus         5 ~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--~~~~dlvi~D~~l~~~~~~g~~~~~~l~~~~~~~~   82 (136)
T 3kto_A            5 HHPIIYLVDHQKDARAALSKLLSPLDVTIQCFASAESFMRQQI--SDDAIGMIIEAHLEDKKDSGIELLETLVKRGFHLP   82 (136)
T ss_dssp             --CEEEEECSCHHHHHHHHHHHTTSSSEEEEESSHHHHTTSCC--CTTEEEEEEETTGGGBTTHHHHHHHHHHHTTCCCC
T ss_pred             CCCeEEEEcCCHHHHHHHHHHHHHCCcEEEEeCCHHHHHHHHh--ccCCCEEEEeCcCCCCCccHHHHHHHHHhCCCCCC
Confidence            3568999999999999999999999999999999999998876  566999999999999  999999999964 46899


Q ss_pred             EEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCCC
Q 029986           93 VIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPF  140 (184)
Q Consensus        93 iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~  140 (184)
                      ||+++...+.....++++.|+++|+.||++.++|..+++.+..+....
T Consensus        83 ii~~s~~~~~~~~~~~~~~ga~~~l~KP~~~~~l~~~i~~~~~~~~~~  130 (136)
T 3kto_A           83 TIVMASSSDIPTAVRAMRASAADFIEKPFIEHVLVHDVQQIINGAKEG  130 (136)
T ss_dssp             EEEEESSCCHHHHHHHHHTTCSEEEESSBCHHHHHHHHHHHHHHHC--
T ss_pred             EEEEEcCCCHHHHHHHHHcChHHheeCCCCHHHHHHHHHHHHhccCCC
Confidence            999999998899999999999999999999999999999998765543

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

Probab=99.87  E-value=7.8e-21  Score=134.30  Aligned_cols=129  Identities=24%  Similarity=0.334  Sum_probs=109.7

Q ss_pred             cCCCCCeEEEEeCCHHHHHHHHHHHHhcCCe--EEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cC
Q 029986           13 QFPAGLRVLVVDDDPIWLRILEKMLRKCLYE--VTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EM   89 (184)
Q Consensus        13 ~~~~~~~Ilivdd~~~~~~~l~~~L~~~~~~--v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~   89 (184)
                      ..+.+.+|+|+||++..++.++..|...|+.  +..+.++.++++.+..  ..||+||+|+.|++.+|+++++.++. .+
T Consensus        11 ~~~~~~~iLivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~a~~~l~~--~~~dlii~d~~l~~~~g~~~~~~l~~~~~   88 (152)
T 3eul_A           11 PQPEKVRVVVGDDHPLFREGVVRALSLSGSVNVVGEADDGAAALELIKA--HLPDVALLDYRMPGMDGAQVAAAVRSYEL   88 (152)
T ss_dssp             ---CCEEEEEECSSHHHHHHHHHHHHHHSSEEEEEEESSHHHHHHHHHH--HCCSEEEEETTCSSSCHHHHHHHHHHTTC
T ss_pred             CCCceEEEEEEcCCHHHHHHHHHHHhhCCCeEEEEEeCCHHHHHHHHHh--cCCCEEEEeCCCCCCCHHHHHHHHHhcCC
Confidence            3345679999999999999999999988743  5689999999999874  45999999999999999999999964 46


Q ss_pred             CCCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCCCCCC
Q 029986           90 DLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPFEES  143 (184)
Q Consensus        90 ~~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~~~~  143 (184)
                      .+|||++++..+......+++.|+++|+.||++.++|..+++.++++...+++.
T Consensus        89 ~~~ii~~s~~~~~~~~~~~~~~g~~~~l~Kp~~~~~l~~~i~~~~~~~~~~~~~  142 (152)
T 3eul_A           89 PTRVLLISAHDEPAIVYQALQQGAAGFLLKDSTRTEIVKAVLDCAKGRDVVAPS  142 (152)
T ss_dssp             SCEEEEEESCCCHHHHHHHHHTTCSEEEETTCCHHHHHHHHHHHHHCC------
T ss_pred             CCeEEEEEccCCHHHHHHHHHcCCCEEEecCCCHHHHHHHHHHHHcCCeeeCHH
Confidence            889999999988899999999999999999999999999999999988776654

>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=99.87  E-value=6.9e-21  Score=129.11  Aligned_cols=116  Identities=25%  Similarity=0.427  Sum_probs=105.0

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCe-EEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYE-VTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVI   94 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~-v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iI   94 (184)
                      +++|+|+||++..+..++..|+..|+. +..+.++.++++.+..  ..||++|+|+.||+.+|+++++.++. .+.+|+|
T Consensus         2 ~~~ilivdd~~~~~~~l~~~l~~~g~~vv~~~~~~~~a~~~~~~--~~~dlil~D~~l~~~~g~~~~~~l~~~~~~~~ii   79 (120)
T 1tmy_A            2 GKRVLIVDDAAFMRMMLKDIITKAGYEVAGEATNGREAVEKYKE--LKPDIVTMDITMPEMNGIDAIKEIMKIDPNAKII   79 (120)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHHH--HCCSEEEEECSCGGGCHHHHHHHHHHHCTTCCEE
T ss_pred             CceEEEEcCcHHHHHHHHHHHhhcCcEEEEEECCHHHHHHHHHh--cCCCEEEEeCCCCCCcHHHHHHHHHhhCCCCeEE
Confidence            468999999999999999999988998 5689999999999874  45999999999999999999999964 4689999


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHH
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVA  134 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~  134 (184)
                      ++++..+......+++.|+++|+.||++.++|..+++.+.
T Consensus        80 ~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~  119 (120)
T 1tmy_A           80 VCSAMGQQAMVIEAIKAGAKDFIVKPFQPSRVVEALNKVS  119 (120)
T ss_dssp             EEECTTCHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHC
T ss_pred             EEeCCCCHHHHHHHHHhCcceeEeCCCCHHHHHHHHHHHh
Confidence            9999888888999999999999999999999999988763

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

Probab=99.87  E-value=1.7e-21  Score=135.70  Aligned_cols=123  Identities=23%  Similarity=0.338  Sum_probs=109.1

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc---cCCCC
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL---EMDLP   92 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~---~~~~~   92 (184)
                      ..++|+|+||++..+..+...|...|+.+..+.++.++++.+.  ...||+||+|+.|++.+|+++++.++.   .+.+|
T Consensus         5 ~~~~iLivdd~~~~~~~l~~~l~~~g~~v~~~~~~~~a~~~l~--~~~~dlvi~d~~l~~~~g~~~~~~l~~~~~~~~~~   82 (140)
T 3grc_A            5 PRPRILICEDDPDIARLLNLMLEKGGFDSDMVHSAAQALEQVA--RRPYAAMTVDLNLPDQDGVSLIRALRRDSRTRDLA   82 (140)
T ss_dssp             CCSEEEEECSCHHHHHHHHHHHHHTTCEEEEECSHHHHHHHHH--HSCCSEEEECSCCSSSCHHHHHHHHHTSGGGTTCE
T ss_pred             CCCCEEEEcCCHHHHHHHHHHHHHCCCeEEEECCHHHHHHHHH--hCCCCEEEEeCCCCCCCHHHHHHHHHhCcccCCCC
Confidence            4578999999999999999999999999999999999999987  456999999999999999999999964   46899


Q ss_pred             EEEEEccCChHHHH-HHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCCC
Q 029986           93 VIMMSVDGCTQDVM-KGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPF  140 (184)
Q Consensus        93 iIi~~~~~~~~~~~-~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~  140 (184)
                      ||++++..+..... .+++.|+++|+.||++.++|..+++.++++....
T Consensus        83 ii~~s~~~~~~~~~~~~~~~g~~~~l~kP~~~~~l~~~i~~~l~~~~~~  131 (140)
T 3grc_A           83 IVVVSANAREGELEFNSQPLAVSTWLEKPIDENLLILSLHRAIDNMAEG  131 (140)
T ss_dssp             EEEECTTHHHHHHHHCCTTTCCCEEECSSCCHHHHHHHHHHHHHHHC--
T ss_pred             EEEEecCCChHHHHHHhhhcCCCEEEeCCCCHHHHHHHHHHHHHhcCCC
Confidence            99998876666666 8899999999999999999999999998765543

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

Probab=99.87  E-value=1.4e-20  Score=132.80  Aligned_cols=120  Identities=18%  Similarity=0.324  Sum_probs=106.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCC--eEEEECCHHHHHHHHHhc-----CCCccEEEEeCCCCCCCHHHHHHHhccc
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLY--EVTKCNRAEIALDMLRMS-----KNGYDIVISDVHMPDMDGFKLHEQVGLE   88 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~--~v~~~~~~~~~~~~l~~~-----~~~~dlvilD~~l~~~~g~~l~~~l~~~   88 (184)
                      ..++|+||||++..+..++..|+..|+  .+..+.++.++++.+...     ...||+||+|+.||+.+|+++++.++..
T Consensus         7 ~~~~ILivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~al~~l~~~~~~~~~~~~dlillD~~lp~~~g~~l~~~l~~~   86 (149)
T 1i3c_A            7 PPKVILLVEDSKADSRLVQEVLKTSTIDHELIILRDGLAAMAFLQQQGEYENSPRPNLILLDLNLPKKDGREVLAEIKQN   86 (149)
T ss_dssp             CCEEEEEECCCHHHHHHHHHHHHSCCSCEEEEEECSHHHHHHHHTTCGGGTTCCCCSEEEECSCCSSSCHHHHHHHHHHC
T ss_pred             CCCeEEEEECCHHHHHHHHHHHHhcCCCccEEEeCCHHHHHHHHHhccccccCCCCCEEEEeCCCCCCcHHHHHHHHHhC
Confidence            357899999999999999999998776  788999999999988631     1469999999999999999999999754


Q ss_pred             ---CCCCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           89 ---MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        89 ---~~~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                         +.+|||++++..+.....++++.|+++|+.||++.++|..+++.+.+
T Consensus        87 ~~~~~~piiils~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~i~~~~~  136 (149)
T 1i3c_A           87 PDLKRIPVVVLTTSHNEDDVIASYELHVNCYLTKSRNLKDLFKMVQGIES  136 (149)
T ss_dssp             TTTTTSCEEEEESCCCHHHHHHHHHTTCSEEEECCSSHHHHHHHHHHHHH
T ss_pred             cCcCCCeEEEEECCCChHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHH
Confidence               57899999998888889999999999999999999999999998865

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

Probab=99.87  E-value=9.7e-21  Score=132.36  Aligned_cols=125  Identities=21%  Similarity=0.275  Sum_probs=110.2

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCC--eEEEECCHHHHHHHHHhc---CCCccEEEEeCCCCCCCHHHHHHHhcc---
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLY--EVTKCNRAEIALDMLRMS---KNGYDIVISDVHMPDMDGFKLHEQVGL---   87 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~--~v~~~~~~~~~~~~l~~~---~~~~dlvilD~~l~~~~g~~l~~~l~~---   87 (184)
                      +.++|+||||++..+..+...|...|+  .+..+.++.++++.+...   ...||+||+|+.||+.+|+++++.++.   
T Consensus         8 ~~~~iLivdd~~~~~~~l~~~l~~~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~dlvi~D~~l~~~~g~~~~~~l~~~~~   87 (146)
T 3ilh_A            8 KIDSVLLIDDDDIVNFLNTTIIRMTHRVEEIQSVTSGNAAINKLNELYAAGRWPSIICIDINMPGINGWELIDLFKQHFQ   87 (146)
T ss_dssp             CEEEEEEECSCHHHHHHHHHHHHTTCCEEEEEEESSHHHHHHHHHHHHTSSCCCSEEEEESSCSSSCHHHHHHHHHHHCG
T ss_pred             ccceEEEEeCCHHHHHHHHHHHHhcCCCeeeeecCCHHHHHHHHHHhhccCCCCCEEEEcCCCCCCCHHHHHHHHHHhhh
Confidence            467899999999999999999999998  899999999999998731   156999999999999999999999965   


Q ss_pred             --cCCCCEEEEEccCChHHHHHHHHcC-CCceEeCCCCHHHHHHHHHHHHcCCCCC
Q 029986           88 --EMDLPVIMMSVDGCTQDVMKGVTHG-ACNYLLKPIRIKELRNIWQHVAQQPKPF  140 (184)
Q Consensus        88 --~~~~~iIi~~~~~~~~~~~~a~~~g-a~~~l~kP~~~~~l~~~l~~~~~~~~~~  140 (184)
                        .+.+|+|++++..+......++..| +++|+.||++.++|..+++....+..+.
T Consensus        88 ~~~~~~~ii~~t~~~~~~~~~~~~~~g~~~~~l~KP~~~~~L~~~i~~~~~~~~~~  143 (146)
T 3ilh_A           88 PMKNKSIVCLLSSSLDPRDQAKAEASDWVDYYVSKPLTANALNNLYNKVLNEGHHH  143 (146)
T ss_dssp             GGTTTCEEEEECSSCCHHHHHHHHHCSSCCEEECSSCCHHHHHHHHHHHHCC----
T ss_pred             hccCCCeEEEEeCCCChHHHHHHHhcCCcceeeeCCCCHHHHHHHHHHHHHhccCC
Confidence              4688999999988889999999999 9999999999999999999998876543

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

Probab=99.87  E-value=7e-21  Score=135.53  Aligned_cols=120  Identities=23%  Similarity=0.298  Sum_probs=108.6

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEE-EECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCE
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVT-KCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPV   93 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~-~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~i   93 (184)
                      ..++|+||||++..+..+...|+..|+.+. .+.++.++++.+......||+||+|+.|++.+|+++++.++. .+.+||
T Consensus        35 ~~~~Ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~~al~~l~~~~~~~dliilD~~l~~~~g~~~~~~lr~~~~~~~i  114 (157)
T 3hzh_A           35 IPFNVLIVDDSVFTVKQLTQIFTSEGFNIIDTAADGEEAVIKYKNHYPNIDIVTLXITMPKMDGITCLSNIMEFDKNARV  114 (157)
T ss_dssp             EECEEEEECSCHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHHHHGGGCCEEEECSSCSSSCHHHHHHHHHHHCTTCCE
T ss_pred             CceEEEEEeCCHHHHHHHHHHHHhCCCeEEEEECCHHHHHHHHHhcCCCCCEEEEeccCCCccHHHHHHHHHhhCCCCcE
Confidence            357999999999999999999999999988 999999999999743225899999999999999999999964 468999


Q ss_pred             EEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           94 IMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        94 Ii~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      |+++...+......+++.|+++|+.||++.++|..+++.++.
T Consensus       115 i~ls~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~l~  156 (157)
T 3hzh_A          115 IMISALGKEQLVKDCLIKGAKTFIVKPLDRAKVLQRVMSVFV  156 (157)
T ss_dssp             EEEESCCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHTTC
T ss_pred             EEEeccCcHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHhc
Confidence            999999889999999999999999999999999999988754

>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=99.87  E-value=6.3e-21  Score=129.90  Aligned_cols=117  Identities=20%  Similarity=0.404  Sum_probs=101.4

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc---CCCCEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE---MDLPVI   94 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~---~~~~iI   94 (184)
                      .+|+|+||++..+..++..|+..|+.+..+.++.+++..+..  ..||++|+|+.||+.+|+++++.++..   +.+|+|
T Consensus         2 ~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~a~~~~~~--~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~~~ii   79 (124)
T 1mb3_A            2 KKVLIVEDNELNMKLFHDLLEAQGYETLQTREGLSALSIARE--NKPDLILMDIQLPEISGLEVTKWLKEDDDLAHIPVV   79 (124)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHHHHH--HCCSEEEEESBCSSSBHHHHHHHHHHSTTTTTSCEE
T ss_pred             cEEEEEcCCHHHHHHHHHHHHHcCcEEEEeCCHHHHHHHHhc--CCCCEEEEeCCCCCCCHHHHHHHHHcCccccCCcEE
Confidence            479999999999999999999999999999999999998873  459999999999999999999999653   578999


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      ++++.........+++.|+++|+.||++.++|..+++.+..+
T Consensus        80 ~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~~~  121 (124)
T 1mb3_A           80 AVTAFAMKGDEERIREGGCEAYISKPISVVHFLETIKRLLER  121 (124)
T ss_dssp             EEC------CHHHHHHHTCSEEECSSCCHHHHHHHHHHHHSC
T ss_pred             EEECCCCHHHHHHHHhCCCCEEEeCCCCHHHHHHHHHHHHhc
Confidence            999887778888999999999999999999999999988764

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

Probab=99.87  E-value=3.7e-21  Score=134.32  Aligned_cols=119  Identities=20%  Similarity=0.273  Sum_probs=108.4

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCC-CCHHHHHHHhcccCCCCEEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPD-MDGFKLHEQVGLEMDLPVIM   95 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~-~~g~~l~~~l~~~~~~~iIi   95 (184)
                      +++|+||||++..+..++..|...|+.+..+.++.++++.+.. ...||+||+|+.||+ .+|+++++.++..+.+|+|+
T Consensus         5 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~~-~~~~dlvi~D~~l~~~~~g~~~~~~l~~~~~~~ii~   83 (140)
T 3h5i_A            5 DKKILIVEDSKFQAKTIANILNKYGYTVEIALTGEAAVEKVSG-GWYPDLILMDIELGEGMDGVQTALAIQQISELPVVF   83 (140)
T ss_dssp             -CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHT-TCCCSEEEEESSCSSSCCHHHHHHHHHHHCCCCEEE
T ss_pred             CcEEEEEeCCHHHHHHHHHHHHHcCCEEEEecChHHHHHHHhc-CCCCCEEEEeccCCCCCCHHHHHHHHHhCCCCCEEE
Confidence            5689999999999999999999999999999999999999873 256999999999985 99999999997778999999


Q ss_pred             EEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           96 MSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        96 ~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      +++..+......+++.|+++|+.||++.++|..+++.++++
T Consensus        84 ls~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~l~~  124 (140)
T 3h5i_A           84 LTAHTEPAVVEKIRSVTAYGYVMKSATEQVLITIVEMALRL  124 (140)
T ss_dssp             EESSSSCCCCGGGGGSCEEEEEETTCCHHHHHHHHHHHHHH
T ss_pred             EECCCCHHHHHHHHhCCCcEEEeCCCCHHHHHHHHHHHHHH
Confidence            99988888888999999999999999999999999988764

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

Probab=99.87  E-value=2.2e-20  Score=130.43  Aligned_cols=122  Identities=23%  Similarity=0.398  Sum_probs=110.8

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIM   95 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi   95 (184)
                      .++|+|+||++..+..++..|...|+.+..+.++.++++.+......||+||+|+.+++.+|+++++.++. .+.+|||+
T Consensus         3 ~~~ilivdd~~~~~~~l~~~l~~~g~~v~~~~~~~~a~~~~~~~~~~~dlvi~d~~l~~~~g~~~~~~l~~~~~~~~ii~   82 (143)
T 3jte_A            3 LAKILVIDDESTILQNIKFLLEIDGNEVLTASSSTEGLRIFTENCNSIDVVITDMKMPKLSGMDILREIKKITPHMAVII   82 (143)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHHTTTTCCEEEEESCCSSSCHHHHHHHHHHHCTTCEEEE
T ss_pred             CCEEEEEcCCHHHHHHHHHHHHhCCceEEEeCCHHHHHHHHHhCCCCCCEEEEeCCCCCCcHHHHHHHHHHhCCCCeEEE
Confidence            46899999999999999999999999999999999999998743356999999999999999999999964 46899999


Q ss_pred             EEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCC
Q 029986           96 MSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPK  138 (184)
Q Consensus        96 ~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~  138 (184)
                      +++..+......+++.|+++|+.||++.++|..+++.++++..
T Consensus        83 ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~l~~~~~~~~  125 (143)
T 3jte_A           83 LTGHGDLDNAILAMKEGAFEYLRKPVTAQDLSIAINNAINRKK  125 (143)
T ss_dssp             EECTTCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHHHHHH
T ss_pred             EECCCCHHHHHHHHHhCcceeEeCCCCHHHHHHHHHHHHHHHH
Confidence            9998888889999999999999999999999999999877543

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

Probab=99.86  E-value=1.7e-20  Score=129.23  Aligned_cols=122  Identities=24%  Similarity=0.313  Sum_probs=102.4

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccC--CCCE
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEM--DLPV   93 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~--~~~i   93 (184)
                      ..++|+|+||++..+..++..|.+.|+.+..+.++.++++.+.  ...||+||+|+.+++.+|+++++.++...  ..++
T Consensus         5 ~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--~~~~dlii~d~~l~~~~g~~~~~~l~~~~~~~~~~   82 (132)
T 3lte_A            5 QSKRILVVDDDQAMAAAIERVLKRDHWQVEIAHNGFDAGIKLS--TFEPAIMTLDLSMPKLDGLDVIRSLRQNKVANQPK   82 (132)
T ss_dssp             --CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HTCCSEEEEESCBTTBCHHHHHHHHHTTTCSSCCE
T ss_pred             CCccEEEEECCHHHHHHHHHHHHHCCcEEEEeCCHHHHHHHHH--hcCCCEEEEecCCCCCCHHHHHHHHHhcCccCCCe
Confidence            4678999999999999999999999999999999999999987  45699999999999999999999997543  3455


Q ss_pred             EEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCC
Q 029986           94 IMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKP  139 (184)
Q Consensus        94 Ii~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~  139 (184)
                      |++++.........+++.|+++|+.||++.++|..+++....+..+
T Consensus        83 ii~~~~~~~~~~~~~~~~g~~~~l~kP~~~~~l~~~i~~~~~~~~~  128 (132)
T 3lte_A           83 ILVVSGLDKAKLQQAVTEGADDYLEKPFDNDALLDRIHDLVNEGHH  128 (132)
T ss_dssp             EEEECCSCSHHHHHHHHHTCCEEECSSCCHHHHHHHHHHHHC----
T ss_pred             EEEEeCCChHHHHHHHHhChHHHhhCCCCHHHHHHHHHHHcCCCCC
Confidence            5555555555788999999999999999999999999998876554

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

Probab=99.86  E-value=1.5e-20  Score=133.03  Aligned_cols=120  Identities=26%  Similarity=0.363  Sum_probs=110.2

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCE
Q 029986           15 PAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPV   93 (184)
Q Consensus        15 ~~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~i   93 (184)
                      ...++|+||||++..+..+...|...|+.+..+.++.++++.+.  ...||+||+|+.|++.+|+++++.++. .+.+||
T Consensus        12 ~~~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--~~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~i   89 (153)
T 3hv2_A           12 TRRPEILLVDSQEVILQRLQQLLSPLPYTLHFARDATQALQLLA--SREVDLVISAAHLPQMDGPTLLARIHQQYPSTTR   89 (153)
T ss_dssp             CSCCEEEEECSCHHHHHHHHHHHTTSSCEEEEESSHHHHHHHHH--HSCCSEEEEESCCSSSCHHHHHHHHHHHCTTSEE
T ss_pred             cCCceEEEECCCHHHHHHHHHHhcccCcEEEEECCHHHHHHHHH--cCCCCEEEEeCCCCcCcHHHHHHHHHhHCCCCeE
Confidence            34678999999999999999999999999999999999999987  456999999999999999999999964 468999


Q ss_pred             EEEEccCChHHHHHHHHcC-CCceEeCCCCHHHHHHHHHHHHcC
Q 029986           94 IMMSVDGCTQDVMKGVTHG-ACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        94 Ii~~~~~~~~~~~~a~~~g-a~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      |+++...+......+++.| +++|+.||++.++|..+++.++++
T Consensus        90 i~~s~~~~~~~~~~~~~~g~~~~~l~KP~~~~~l~~~i~~~l~~  133 (153)
T 3hv2_A           90 ILLTGDPDLKLIAKAINEGEIYRYLSKPWDDQELLLALRQALEH  133 (153)
T ss_dssp             EEECCCCCHHHHHHHHHTTCCSEEECSSCCHHHHHHHHHHHHHH
T ss_pred             EEEECCCCHHHHHHHHhCCCcceEEeCCCCHHHHHHHHHHHHHH
Confidence            9999998889999999999 999999999999999999988764

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

Probab=99.86  E-value=2.2e-20  Score=130.12  Aligned_cols=123  Identities=24%  Similarity=0.345  Sum_probs=110.0

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHh-cCCe-EEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc---cCC
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRK-CLYE-VTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL---EMD   90 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~-~~~~-v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~---~~~   90 (184)
                      ..++|+|+||++..+..+...|.. .|+. +..+.++.++++.+.  ...||+||+|+.+++.+|+++++.++.   .+.
T Consensus         7 ~~~~iLivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~a~~~l~--~~~~dlii~d~~l~~~~g~~~~~~l~~~~~~~~   84 (143)
T 3cnb_A            7 NDFSILIIEDDKEFADMLTQFLENLFPYAKIKIAYNPFDAGDLLH--TVKPDVVMLDLMMVGMDGFSICHRIKSTPATAN   84 (143)
T ss_dssp             --CEEEEECSCHHHHHHHHHHHHHHCTTCEEEEECSHHHHHHHHH--HTCCSEEEEETTCTTSCHHHHHHHHHTSTTTTT
T ss_pred             CCceEEEEECCHHHHHHHHHHHHhccCccEEEEECCHHHHHHHHH--hcCCCEEEEecccCCCcHHHHHHHHHhCccccC
Confidence            467999999999999999999998 8998 999999999999987  355999999999999999999999965   468


Q ss_pred             CCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCCC
Q 029986           91 LPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPF  140 (184)
Q Consensus        91 ~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~  140 (184)
                      +|||++++..+......+++.|+++|+.||++.++|..+++.++++....
T Consensus        85 ~~ii~~s~~~~~~~~~~~~~~g~~~~l~kP~~~~~l~~~i~~~~~~~~~~  134 (143)
T 3cnb_A           85 IIVIAMTGALTDDNVSRIVALGAETCFGKPLNFTLLEKTIKQLVEQKKAT  134 (143)
T ss_dssp             SEEEEEESSCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHHHTTC--
T ss_pred             CcEEEEeCCCCHHHHHHHHhcCCcEEEeCCCCHHHHHHHHHHHHHhhccc
Confidence            89999999888888899999999999999999999999999998876543

>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=99.86  E-value=1.9e-20  Score=132.32  Aligned_cols=121  Identities=21%  Similarity=0.376  Sum_probs=108.4

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCC--eEEEECCHHHHHHHHHh-------cCCCccEEEEeCCCCCCCHHHHHHHhc
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLY--EVTKCNRAEIALDMLRM-------SKNGYDIVISDVHMPDMDGFKLHEQVG   86 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~--~v~~~~~~~~~~~~l~~-------~~~~~dlvilD~~l~~~~g~~l~~~l~   86 (184)
                      ..++|+||||++..+..+...|...|+  .+..+.++.++++.+..       ....||+||+|+.||+.+|+++++.++
T Consensus         3 ~~~~ILivddd~~~~~~l~~~L~~~g~~~~v~~~~~~~~al~~l~~~~~~~~~~~~~~dliilD~~l~~~~g~~~~~~lr   82 (152)
T 3heb_A            3 LSVTIVMIEDDLGHARLIEKNIRRAGVNNEIIAFTDGTSALNYLFGDDKSGRVSAGRAQLVLLDLNLPDMTGIDILKLVK   82 (152)
T ss_dssp             --CEEEEECCCHHHHHHHHHHHHHTTCCCCEEEESSHHHHHHHHHCTTSSSGGGTTCBEEEEECSBCSSSBHHHHHHHHH
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHhCCCcceEEEeCCHHHHHHHHhccccccccccCCCCEEEEeCCCCCCcHHHHHHHHH
Confidence            357999999999999999999999988  89999999999999851       245699999999999999999999997


Q ss_pred             c---cCCCCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           87 L---EMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        87 ~---~~~~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      .   .+.+|||++++..+......+++.|+++|+.||++.++|..+++.+.+.
T Consensus        83 ~~~~~~~~pii~~t~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~~~  135 (152)
T 3heb_A           83 ENPHTRRSPVVILTTTDDQREIQRCYDLGANVYITKPVNYENFANAIRQLGLF  135 (152)
T ss_dssp             HSTTTTTSCEEEEESCCCHHHHHHHHHTTCSEEEECCSSHHHHHHHHHHHHHH
T ss_pred             hcccccCCCEEEEecCCCHHHHHHHHHCCCcEEEeCCCCHHHHHHHHHHHHHH
Confidence            5   3688999999998888999999999999999999999999999998654

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

Probab=99.86  E-value=7.4e-21  Score=141.67  Aligned_cols=122  Identities=26%  Similarity=0.449  Sum_probs=105.9

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHhcCC-eEEEECCHHHHHHHHHhc-----------CCCccEEEEeCCCCCCCHHHHH
Q 029986           15 PAGLRVLVVDDDPIWLRILEKMLRKCLY-EVTKCNRAEIALDMLRMS-----------KNGYDIVISDVHMPDMDGFKLH   82 (184)
Q Consensus        15 ~~~~~Ilivdd~~~~~~~l~~~L~~~~~-~v~~~~~~~~~~~~l~~~-----------~~~~dlvilD~~l~~~~g~~l~   82 (184)
                      ..+++|+||||++..+..+..+|+..|+ .+..+.++.++++.+...           ...||+||+|+.||+++|++++
T Consensus        59 ~~~~~ILiVdDd~~~~~~l~~~L~~~g~~~v~~a~~~~eal~~l~~~~~~~~~~~~~~~~~~dlillD~~lp~~~G~el~  138 (206)
T 3mm4_A           59 LRGKRVLVVDDNFISRKVATGKLKKMGVSEVEQCDSGKEALRLVTEGLTQREEQGSVDKLPFDYIFMDCQMPEMDGYEAT  138 (206)
T ss_dssp             TTTCEEEEECSCHHHHHHHHHHHHHTTCSEEEEESSHHHHHHHHHHHHHHHHHHTCSSCCSCSEEEEESCCSSSCHHHHH
T ss_pred             cCCCEEEEEeCCHHHHHHHHHHHHHcCCCeeeeeCCHHHHHHHHHhhcccccccccccCCCCCEEEEcCCCCCCCHHHHH
Confidence            3467999999999999999999999998 899999999999998742           1369999999999999999999


Q ss_pred             HHhccc-----CCCCEEEEEccC-ChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCC
Q 029986           83 EQVGLE-----MDLPVIMMSVDG-CTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPK  138 (184)
Q Consensus        83 ~~l~~~-----~~~~iIi~~~~~-~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~  138 (184)
                      +.++..     +.+|||+++... .......+++.|+++|+.||++  +|..+++.++++..
T Consensus       139 ~~lr~~~~~~~~~~piI~ls~~~~~~~~~~~~~~~Ga~~~l~KP~~--~L~~~i~~~l~~~~  198 (206)
T 3mm4_A          139 REIRKVEKSYGVRTPIIAVSGHDPGSEEARETIQAGMDAFLDKSLN--QLANVIREIESKRH  198 (206)
T ss_dssp             HHHHHHHHTTTCCCCEEEEESSCCCHHHHHHHHHHTCSEEEETTCT--THHHHHHHHC----
T ss_pred             HHHHhhhhhcCCCCcEEEEECCCCcHHHHHHHHhCCCCEEEcCcHH--HHHHHHHHHHhhhH
Confidence            999753     789999999887 6688889999999999999998  89999998876543

>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=99.86  E-value=1.7e-20  Score=131.28  Aligned_cols=118  Identities=19%  Similarity=0.331  Sum_probs=108.9

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCe--EEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc---cCCC
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYE--VTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL---EMDL   91 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~--v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~---~~~~   91 (184)
                      +++|+||||++..+..++..|...|+.  +..+.++.++++.+.  ...||+||+|+.|++.+|+++++.++.   .+.+
T Consensus         5 ~~~ILivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~a~~~l~--~~~~dlii~D~~l~~~~g~~~~~~lr~~~~~~~~   82 (144)
T 3kht_A            5 SKRVLVVEDNPDDIALIRRVLDRKDIHCQLEFVDNGAKALYQVQ--QAKYDLIILDIGLPIANGFEVMSAVRKPGANQHT   82 (144)
T ss_dssp             CEEEEEECCCHHHHHHHHHHHHHTTCCEEEEEESSHHHHHHHHT--TCCCSEEEECTTCGGGCHHHHHHHHHSSSTTTTC
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHhcCCCeeEEEECCHHHHHHHhh--cCCCCEEEEeCCCCCCCHHHHHHHHHhcccccCC
Confidence            568999999999999999999998876  889999999999987  566999999999999999999999975   4689


Q ss_pred             CEEEEEccCChHHHHHHHHcCCCceEeCCC-CHHHHHHHHHHHHcC
Q 029986           92 PVIMMSVDGCTQDVMKGVTHGACNYLLKPI-RIKELRNIWQHVAQQ  136 (184)
Q Consensus        92 ~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~-~~~~l~~~l~~~~~~  136 (184)
                      |||++++..+......+++.|+++|+.||+ +.++|..+++.++++
T Consensus        83 pii~~s~~~~~~~~~~~~~~ga~~~l~Kp~~~~~~l~~~i~~~l~~  128 (144)
T 3kht_A           83 PIVILTDNVSDDRAKQCMAAGASSVVDKSSNNVTDFYGRIYAIFSY  128 (144)
T ss_dssp             CEEEEETTCCHHHHHHHHHTTCSEEEECCTTSHHHHHHHHHHHHHH
T ss_pred             CEEEEeCCCCHHHHHHHHHcCCCEEEECCCCcHHHHHHHHHHHHHH
Confidence            999999998899999999999999999999 999999999988764

>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=99.86  E-value=5.3e-21  Score=132.69  Aligned_cols=120  Identities=21%  Similarity=0.337  Sum_probs=110.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIM   95 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi   95 (184)
                      .++|+|+||++..+..++..|...++.+..+.++.++++.+..  ..||+||+|+.+++.+|+++++.++. .+.+|||+
T Consensus         7 ~~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~a~~~l~~--~~~dlvi~d~~l~~~~g~~~~~~l~~~~~~~~ii~   84 (137)
T 3hdg_A            7 ALKILIVEDDTDAREWLSTIISNHFPEVWSAGDGEEGERLFGL--HAPDVIITDIRMPKLGGLEMLDRIKAGGAKPYVIV   84 (137)
T ss_dssp             CCCEEEECSCHHHHHHHHHHHHTTCSCEEEESSHHHHHHHHHH--HCCSEEEECSSCSSSCHHHHHHHHHHTTCCCEEEE
T ss_pred             ccEEEEEeCCHHHHHHHHHHHHhcCcEEEEECCHHHHHHHHhc--cCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCcEEE
Confidence            5799999999999999999999989999999999999999874  45999999999999999999999964 46889999


Q ss_pred             EEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCC
Q 029986           96 MSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPK  138 (184)
Q Consensus        96 ~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~  138 (184)
                      ++...+......+++.|+++|+.||++.++|..+++.++++..
T Consensus        85 ~s~~~~~~~~~~~~~~g~~~~l~kP~~~~~l~~~i~~~~~~~~  127 (137)
T 3hdg_A           85 ISAFSEMKYFIKAIELGVHLFLPKPIEPGRLMETLEDFRHIKL  127 (137)
T ss_dssp             CCCCCCHHHHHHHHHHCCSEECCSSCCHHHHHHHHHHHHHHHH
T ss_pred             EecCcChHHHHHHHhCCcceeEcCCCCHHHHHHHHHHHHHHHh
Confidence            9998888899999999999999999999999999999987643

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

Probab=99.86  E-value=5.7e-21  Score=131.76  Aligned_cols=121  Identities=22%  Similarity=0.270  Sum_probs=102.8

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc---CCCC
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE---MDLP   92 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~---~~~~   92 (184)
                      ..++|+|+||++..+..++..|+ .|+.+..+.++.++++.+.  ...||+||+|+.|++.+|+++++.++..   +.+|
T Consensus         3 ~~~~ilivdd~~~~~~~l~~~l~-~~~~v~~~~~~~~a~~~l~--~~~~dlvi~d~~l~~~~g~~~~~~l~~~~~~~~~p   79 (133)
T 3nhm_A            3 LKPKVLIVENSWTMRETLRLLLS-GEFDCTTAADGASGLQQAL--AHPPDVLISDVNMDGMDGYALCGHFRSEPTLKHIP   79 (133)
T ss_dssp             --CEEEEECSCHHHHHHHHHHHT-TTSEEEEESSHHHHHHHHH--HSCCSEEEECSSCSSSCHHHHHHHHHHSTTTTTCC
T ss_pred             CCCEEEEEcCCHHHHHHHHHHHh-CCcEEEEECCHHHHHHHHh--cCCCCEEEEeCCCCCCCHHHHHHHHHhCCccCCCC
Confidence            35689999999999999999999 7899999999999999987  4569999999999999999999999753   4789


Q ss_pred             EEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCCC
Q 029986           93 VIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPF  140 (184)
Q Consensus        93 iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~  140 (184)
                      ||++++..+... ..+++.|+++|+.||++.++|..+++.++++....
T Consensus        80 ii~~s~~~~~~~-~~~~~~g~~~~l~KP~~~~~l~~~i~~~l~~~~~~  126 (133)
T 3nhm_A           80 VIFVSGYAPRTE-GPADQPVPDAYLVKPVKPPVLIAQLHALLARAEAE  126 (133)
T ss_dssp             EEEEESCCC------TTSCCCSEEEESSCCHHHHHHHHHHHHHHHC--
T ss_pred             EEEEeCCCcHhH-HHHhhcCCceEEeccCCHHHHHHHHHHHHhhhccc
Confidence            999998776666 88999999999999999999999999998765543

>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=99.86  E-value=4.4e-21  Score=131.46  Aligned_cols=118  Identities=24%  Similarity=0.262  Sum_probs=104.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc---cCCCCE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL---EMDLPV   93 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~---~~~~~i   93 (184)
                      .++|+|+||++..+..+...|+..|+.+..+.++.++++.+.  ...||+||+|+.|++.+|+++++.++.   .+.+|+
T Consensus         3 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--~~~~dlii~D~~l~~~~g~~~~~~l~~~~~~~~~~i   80 (127)
T 3i42_A            3 LQQALIVEDYQAAAETFKELLEMLGFQADYVMSGTDALHAMS--TRGYDAVFIDLNLPDTSGLALVKQLRALPMEKTSKF   80 (127)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHHHTTEEEEEESSHHHHHHHHH--HSCCSEEEEESBCSSSBHHHHHHHHHHSCCSSCCEE
T ss_pred             cceEEEEcCCHHHHHHHHHHHHHcCCCEEEECCHHHHHHHHH--hcCCCEEEEeCCCCCCCHHHHHHHHHhhhccCCCCE
Confidence            468999999999999999999999999999999999999987  455999999999999999999999965   467899


Q ss_pred             EEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCC
Q 029986           94 IMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQP  137 (184)
Q Consensus        94 Ii~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~  137 (184)
                      |++++..+... ..++..|+++|+.||++.++|.++++...++.
T Consensus        81 i~~s~~~~~~~-~~~~~~g~~~~l~KP~~~~~L~~~i~~~~~~~  123 (127)
T 3i42_A           81 VAVSGFAKNDL-GKEACELFDFYLEKPIDIASLEPILQSIEGHH  123 (127)
T ss_dssp             EEEECC-CTTC-CHHHHHHCSEEEESSCCHHHHHHHHHHHC---
T ss_pred             EEEECCcchhH-HHHHHHhhHHheeCCCCHHHHHHHHHHhhccC
Confidence            99998877777 88899999999999999999999999876543

>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=99.86  E-value=8.2e-21  Score=128.68  Aligned_cols=117  Identities=26%  Similarity=0.344  Sum_probs=107.1

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMS   97 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi~~   97 (184)
                      ++|+|+||++..+..++..|...|+.+..+.++.+++..+..  ..||++|+|+.||+.+|+++++.++..+.+|+|+++
T Consensus         2 ~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~~--~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~ii~~s   79 (121)
T 1zh2_A            2 TNVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEAAT--RKPDLIILDLGLPDGDGIEFIRDLRQWSAVPVIVLS   79 (121)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHHH--HCCSEEEEESEETTEEHHHHHHHHHTTCCCCEEEEE
T ss_pred             cEEEEEeCCHHHHHHHHHHHhcCCCEEEEeCCHHHHHHHHhc--CCCCEEEEeCCCCCCcHHHHHHHHHhCCCCcEEEEE
Confidence            589999999999999999999889999999999999988763  459999999999999999999999866789999999


Q ss_pred             ccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           98 VDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        98 ~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      +..+......+++.|+++|+.||++.++|...++.+.++
T Consensus        80 ~~~~~~~~~~~~~~g~~~~l~Kp~~~~~l~~~i~~~~~~  118 (121)
T 1zh2_A           80 ARSEESDKIAALDAGADDYLSKPFGIGELQARLRVALRR  118 (121)
T ss_dssp             SCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHhcCCCeEEeCCcCHHHHHHHHHHHHHh
Confidence            988888889999999999999999999999999887653

>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=99.86  E-value=2e-20  Score=129.46  Aligned_cols=120  Identities=24%  Similarity=0.455  Sum_probs=108.3

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc-CCCCEEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE-MDLPVIM   95 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~-~~~~iIi   95 (184)
                      +.+|+|+||++..+..+...|...|+.+..+.++.++++.+..  ..||++|+|+.||+.+|+++++.++.. +.+|+|+
T Consensus         3 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~~~~--~~~dlvl~D~~l~~~~g~~~~~~l~~~~~~~~ii~   80 (136)
T 1mvo_A            3 NKKILVVDDEESIVTLLQYNLERSGYDVITASDGEEALKKAET--EKPDLIVLDVMLPKLDGIEVCKQLRQQKLMFPILM   80 (136)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHH--HCCSEEEEESSCSSSCHHHHHHHHHHTTCCCCEEE
T ss_pred             CCEEEEEECCHHHHHHHHHHHHHCCcEEEEecCHHHHHHHHhh--cCCCEEEEecCCCCCCHHHHHHHHHcCCCCCCEEE
Confidence            4589999999999999999999999999999999999998873  459999999999999999999999654 6789999


Q ss_pred             EEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCC
Q 029986           96 MSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPK  138 (184)
Q Consensus        96 ~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~  138 (184)
                      +++..+......+++.|+++|+.||++.++|..+++.+.++..
T Consensus        81 ~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~~~~~  123 (136)
T 1mvo_A           81 LTAKDEEFDKVLGLELGADDYMTKPFSPREVNARVKAILRRSE  123 (136)
T ss_dssp             EECTTCCCCHHHHHHTTCCEEEESSCCHHHHHHHHHHHHHTC-
T ss_pred             EECCCCHHHHHHHHhCCCCEEEECCCCHHHHHHHHHHHHHhhc
Confidence            9988888888899999999999999999999999999887543

>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=99.86  E-value=3.5e-20  Score=128.38  Aligned_cols=120  Identities=18%  Similarity=0.337  Sum_probs=108.4

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCC--eEEEECCHHHHHHHHHhc-----CCCccEEEEeCCCCCCCHHHHHHHhccc-
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLY--EVTKCNRAEIALDMLRMS-----KNGYDIVISDVHMPDMDGFKLHEQVGLE-   88 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~--~v~~~~~~~~~~~~l~~~-----~~~~dlvilD~~l~~~~g~~l~~~l~~~-   88 (184)
                      +++|+|+||++..+..+...|+..|+  .+..+.++.++++.+...     ...||+||+|+.|++.+|+++++.++.. 
T Consensus         2 ~~~ilivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~dlvi~d~~~~~~~g~~~~~~l~~~~   81 (140)
T 1k68_A            2 HKKIFLVEDNKADIRLIQEALANSTVPHEVVTVRDGMEAMAYLRQEGEYANASRPDLILLXLNLPKKDGREVLAEIKSDP   81 (140)
T ss_dssp             CCEEEEECCCHHHHHHHHHHHHTCSSCCEEEEECSHHHHHHHHTTCGGGGSCCCCSEEEECSSCSSSCHHHHHHHHHHST
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCCceEEEECCHHHHHHHHHcccccccCCCCcEEEEecCCCcccHHHHHHHHHcCc
Confidence            56899999999999999999999888  899999999999998731     0569999999999999999999999754 


Q ss_pred             --CCCCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           89 --MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        89 --~~~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                        +.+|+|++++..+......+++.|+++|+.||++.++|..+++.+.+.
T Consensus        82 ~~~~~pii~ls~~~~~~~~~~~~~~g~~~~l~kP~~~~~l~~~i~~~~~~  131 (140)
T 1k68_A           82 TLKRIPVVVLSTSINEDDIFHSYDLHVNCYITKSANLSQLFQIVKGIEEF  131 (140)
T ss_dssp             TGGGSCEEEEESCCCHHHHHHHHHTTCSEEEECCSSHHHHHHHHHHHHHH
T ss_pred             ccccccEEEEecCCcHHHHHHHHHhchhheecCCCCHHHHHHHHHHHHHH
Confidence              578999999988888999999999999999999999999999988764

>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=99.86  E-value=3.6e-21  Score=131.66  Aligned_cols=119  Identities=23%  Similarity=0.370  Sum_probs=108.0

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc---CCCCEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE---MDLPVI   94 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~---~~~~iI   94 (184)
                      ++|+|+||++..+..++..|...|+.+..+.++.++++.+.  ...||++|+|+.||+.+|+++++.++..   +++|+|
T Consensus         3 ~~ilivdd~~~~~~~l~~~l~~~g~~v~~~~~~~~a~~~~~--~~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~~~ii   80 (127)
T 2jba_A            3 RRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLN--EPWPDLILLAWMLPGGSGIQFIKHLRRESMTRDIPVV   80 (127)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEECSHHHHHTTCS--SSCCSEEEEESEETTEEHHHHHHHHHTSTTTTTSCEE
T ss_pred             cEEEEEcCCHHHHHHHHHHHHHCCceEEEeCCHHHHHHHHh--ccCCCEEEEecCCCCCCHHHHHHHHHhCcccCCCCEE
Confidence            58999999999999999999998999999999999998876  4569999999999999999999999653   578999


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCC
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPK  138 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~  138 (184)
                      ++++..+......+++.|+++|+.||++.++|...++.+.++..
T Consensus        81 ~~s~~~~~~~~~~~~~~ga~~~l~Kp~~~~~l~~~i~~~~~~~~  124 (127)
T 2jba_A           81 MLTARGEEEDRVRGLETGADDCITKPFSPKELVARIKAVMRRIS  124 (127)
T ss_dssp             EEEETTHHHHHHTTCCCSCSEEEEESCCHHHHHHHHHHHHHCCC
T ss_pred             EEeCCCCHHHHHHHHhcCCCeEEeCCCCHHHHHHHHHHHHhccc
Confidence            99988878888899999999999999999999999999887543

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

Probab=99.86  E-value=1.3e-20  Score=129.68  Aligned_cols=119  Identities=26%  Similarity=0.416  Sum_probs=106.0

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhc-CCeEE-EECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc--cCCCCE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKC-LYEVT-KCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL--EMDLPV   93 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~-~~~v~-~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~--~~~~~i   93 (184)
                      ++|+|+||++..+..++..|... |+.+. .+.++.++++.+..  ..||++|+|+.||+.+|+++++.++.  .+..|+
T Consensus         3 ~~ilivdd~~~~~~~l~~~l~~~~~~~~~~~~~~~~~a~~~~~~--~~~dlvllD~~l~~~~g~~~~~~l~~~~~~~~~i   80 (130)
T 1dz3_A            3 IKVCIADDNRELVSLLDEYISSQPDMEVIGTAYNGQDCLQMLEE--KRPDILLLDIIMPHLDGLAVLERIRAGFEHQPNV   80 (130)
T ss_dssp             EEEEEECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHHHH--HCCSEEEEESCCSSSCHHHHHHHHHHHCSSCCEE
T ss_pred             eEEEEEcCCHHHHHHHHHHHHhCCCceEEEEeCCHHHHHHHHhc--CCCCEEEEecCCCCCCHHHHHHHHHhcCCCCCcE
Confidence            58999999999999999999987 78765 79999999999873  45999999999999999999999975  356789


Q ss_pred             EEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCC
Q 029986           94 IMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPK  138 (184)
Q Consensus        94 Ii~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~  138 (184)
                      |++++..+......+++.|+++|+.||++.++|..+++.+.++..
T Consensus        81 i~ls~~~~~~~~~~~~~~ga~~~l~KP~~~~~l~~~i~~~~~~~~  125 (130)
T 1dz3_A           81 IMLTAFGQEDVTKKAVELGASYFILKPFDMENLAHHIRQVYGKTT  125 (130)
T ss_dssp             EEEEETTCHHHHHHHHHTTCEEEEECSSCCTTHHHHHHHHHHCC-
T ss_pred             EEEecCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHhcCCC
Confidence            999998888899999999999999999999999999999876543

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

Probab=99.86  E-value=2e-21  Score=151.92  Aligned_cols=118  Identities=18%  Similarity=0.305  Sum_probs=106.7

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEE-EECCHHHHHHHHHhcCCCccEEEEeCCCC-CCCHHHHHHHhcccCCCCEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVT-KCNRAEIALDMLRMSKNGYDIVISDVHMP-DMDGFKLHEQVGLEMDLPVI   94 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~-~~~~~~~~~~~l~~~~~~~dlvilD~~l~-~~~g~~l~~~l~~~~~~~iI   94 (184)
                      ..+|+++||++..+..++.+|+..||.+. .+.++.++++.+.  ...||+||+|+.|| +++|+++++.++..+++|||
T Consensus       160 ~~rILvVdD~~~~~~~l~~~L~~~g~~v~~~a~~g~eAl~~~~--~~~~dlvl~D~~MPd~mdG~e~~~~ir~~~~~piI  237 (286)
T 3n0r_A          160 ATEVLIIEDEPVIAADIEALVRELGHDVTDIAATRGEALEAVT--RRTPGLVLADIQLADGSSGIDAVKDILGRMDVPVI  237 (286)
T ss_dssp             CCEEEEECCSHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHH--HCCCSEEEEESCCTTSCCTTTTTHHHHHHTTCCEE
T ss_pred             CCcEEEEcCCHHHHHHHHHHhhccCceEEEEeCCHHHHHHHHH--hCCCCEEEEcCCCCCCCCHHHHHHHHHhcCCCCEE
Confidence            35799999999999999999999999999 9999999999997  45699999999999 79999999999766699999


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCC
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPK  138 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~  138 (184)
                      ++|+..  +....++++|+++|+.||++.++|..+++.++.+..
T Consensus       238 ~lT~~~--~~~~~~~~~G~~~~l~KP~~~~~L~~~i~~~l~~~~  279 (286)
T 3n0r_A          238 FITAFP--ERLLTGERPEPTFLITKPFQPETVKAAIGQALFFHP  279 (286)
T ss_dssp             EEESCG--GGGCCSSSCCCSSEEESSCCHHHHHHHHHHHHHHSC
T ss_pred             EEeCCH--HHHHHHHhCCCcEEEeCCCCHHHHHHHHHHHHHhCC
Confidence            999864  456678999999999999999999999999987544

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

Probab=99.86  E-value=3.2e-20  Score=128.95  Aligned_cols=123  Identities=20%  Similarity=0.313  Sum_probs=109.1

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCC-----CCCHHHHHHHhcc-cCC
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMP-----DMDGFKLHEQVGL-EMD   90 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~-----~~~g~~l~~~l~~-~~~   90 (184)
                      .++|+|+||++..+..+...|...|+.+..+.++.++++.+.  ...||+||+|+.++     +.+|+++++.++. .+.
T Consensus         3 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--~~~~dlvi~d~~~~~~~~~~~~g~~~~~~l~~~~~~   80 (140)
T 2qr3_A            3 LGTIIIVDDNKGVLTAVQLLLKNHFSKVITLSSPVSLSTVLR--EENPEVVLLDMNFTSGINNGNEGLFWLHEIKRQYRD   80 (140)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHTTTSSEEEEECCHHHHHHHHH--HSCEEEEEEETTTTC-----CCHHHHHHHHHHHCTT
T ss_pred             CceEEEEeCCHHHHHHHHHHHHhCCcEEEEeCCHHHHHHHHH--cCCCCEEEEeCCcCCCCCCCccHHHHHHHHHhhCcC
Confidence            468999999999999999999999999999999999999987  35599999999999     9999999999964 468


Q ss_pred             CCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCCCC
Q 029986           91 LPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPFE  141 (184)
Q Consensus        91 ~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~~  141 (184)
                      +|||+++...+......+++.|+++|+.||++.++|..+++.++++.....
T Consensus        81 ~~ii~ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~l~~~~~~~~~~~  131 (140)
T 2qr3_A           81 LPVVLFTAYADIDLAVRGIKEGASDFVVKPWDNQKLLETLLNAASQAKDGK  131 (140)
T ss_dssp             CCEEEEEEGGGHHHHHHHHHTTCCEEEEESCCHHHHHHHHHHHHTCC----
T ss_pred             CCEEEEECCCCHHHHHHHHHcCchheeeCCCCHHHHHHHHHHHHHhccccc
Confidence            999999998888888999999999999999999999999999988765544

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

Probab=99.85  E-value=7.5e-21  Score=133.43  Aligned_cols=124  Identities=19%  Similarity=0.288  Sum_probs=110.3

Q ss_pred             CCCCCeEEEEeCCHHHHHHHHHHHHhcC-CeEEEECCHHHHHHHHHhcC-CCccEEEEeCCCCCCCHHHHHHHhcc-cCC
Q 029986           14 FPAGLRVLVVDDDPIWLRILEKMLRKCL-YEVTKCNRAEIALDMLRMSK-NGYDIVISDVHMPDMDGFKLHEQVGL-EMD   90 (184)
Q Consensus        14 ~~~~~~Ilivdd~~~~~~~l~~~L~~~~-~~v~~~~~~~~~~~~l~~~~-~~~dlvilD~~l~~~~g~~l~~~l~~-~~~   90 (184)
                      ...+.+|+||||++..+..+..+|...| |.+..+.++.+++..+.. . ..||+||+|+.|++.+|+++++.++. .+.
T Consensus        17 ~~~~~~ilivdd~~~~~~~l~~~L~~~g~~~v~~~~~~~~~~~~~~~-~~~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~   95 (146)
T 4dad_A           17 FQGMINILVASEDASRLAHLARLVGDAGRYRVTRTVGRAAQIVQRTD-GLDAFDILMIDGAALDTAELAAIEKLSRLHPG   95 (146)
T ss_dssp             CGGGCEEEEECSCHHHHHHHHHHHHHHCSCEEEEECCCHHHHTTCHH-HHTTCSEEEEECTTCCHHHHHHHHHHHHHCTT
T ss_pred             cCCCCeEEEEeCCHHHHHHHHHHHhhCCCeEEEEeCCHHHHHHHHHh-cCCCCCEEEEeCCCCCccHHHHHHHHHHhCCC
Confidence            3346799999999999999999999988 999999998888776642 2 56999999999999999999999964 468


Q ss_pred             CCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCC
Q 029986           91 LPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPK  138 (184)
Q Consensus        91 ~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~  138 (184)
                      +|||+++...+......+++.|+++|+.||++.++|..+++.++++..
T Consensus        96 ~~ii~lt~~~~~~~~~~~~~~ga~~~l~Kp~~~~~L~~~i~~~~~~~~  143 (146)
T 4dad_A           96 LTCLLVTTDASSQTLLDAMRAGVRDVLRWPLEPRALDDALKRAAAQCA  143 (146)
T ss_dssp             CEEEEEESCCCHHHHHHHHTTTEEEEEESSCCHHHHHHHHHHHHHTCC
T ss_pred             CcEEEEeCCCCHHHHHHHHHhCCceeEcCCCCHHHHHHHHHHHHhhhc
Confidence            999999999889999999999999999999999999999999988654

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

Probab=99.85  E-value=4e-20  Score=128.19  Aligned_cols=121  Identities=21%  Similarity=0.329  Sum_probs=105.4

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cC----C
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EM----D   90 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~----~   90 (184)
                      .+++|+|+||++..+..++..|+..|+.+..+.++.++++.+.  .. +|++|+|+.||+.+|+++++.++. .+    .
T Consensus         6 ~~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~~~--~~-~dlvllD~~lp~~~g~~~~~~l~~~~~~~~~~   82 (136)
T 1dcf_A            6 TGLKVLVMDENGVSRMVTKGLLVHLGCEVTTVSSNEECLRVVS--HE-HKVVFMDVCMPGVENYQIALRIHEKFTKQRHQ   82 (136)
T ss_dssp             TTCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHCC--TT-CSEEEEECCSSTTTTTHHHHHHHHHHC-CCSC
T ss_pred             CCCeEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCHHHHHHHHh--cc-CCEEEEeCCCCCCcHHHHHHHHHHhhhhccCC
Confidence            3679999999999999999999999999999999999998875  33 499999999999999999999962 22    2


Q ss_pred             C-CEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCC
Q 029986           91 L-PVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKP  139 (184)
Q Consensus        91 ~-~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~  139 (184)
                      . +||++++..+......+++.|+++|+.||++.++|..+++.+.++...
T Consensus        83 ~~~ii~~s~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~l~~~~~~~~~  132 (136)
T 1dcf_A           83 RPLLVALSGNTDKSTKEKCMSFGLDGVLLKPVSLDNIRDVLSDLLEPRVL  132 (136)
T ss_dssp             CCEEEEEESCCSHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHHSCCCC
T ss_pred             CceEEEEeCCCCHHHHHHHHHcCCCeEEECCCCHHHHHHHHHHHhchhhh
Confidence            3 477788888888888999999999999999999999999999876543

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

Probab=99.85  E-value=3.1e-20  Score=129.57  Aligned_cols=122  Identities=23%  Similarity=0.314  Sum_probs=109.1

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEE
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVI   94 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iI   94 (184)
                      ..++|+|+||++..+..+...|...|+.+..+.++.++++.+.  ...||+||+|+ +++.+|+++++.++. .+.+|+|
T Consensus         3 ~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--~~~~dlvi~d~-~~~~~g~~~~~~l~~~~~~~pii   79 (142)
T 2qxy_A            3 LTPTVMVVDESRITFLAVKNALEKDGFNVIWAKNEQEAFTFLR--REKIDLVFVDV-FEGEESLNLIRRIREEFPDTKVA   79 (142)
T ss_dssp             CCCEEEEECSCHHHHHHHHHHHGGGTCEEEEESSHHHHHHHHT--TSCCSEEEEEC-TTTHHHHHHHHHHHHHCTTCEEE
T ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhCCCEEEEECCHHHHHHHHh--ccCCCEEEEeC-CCCCcHHHHHHHHHHHCCCCCEE
Confidence            3568999999999999999999999999999999999999987  56799999999 999999999999964 4679999


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCCC
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPF  140 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~  140 (184)
                      +++...+......+++.|+++|+.||++.++|..+++.++++....
T Consensus        80 ~ls~~~~~~~~~~~~~~g~~~~l~kP~~~~~l~~~i~~~~~~~~~~  125 (142)
T 2qxy_A           80 VLSAYVDKDLIINSVKAGAVDYILKPFRLDYLLERVKKIISSTPRV  125 (142)
T ss_dssp             EEESCCCHHHHHHHHHHTCSCEEESSCCHHHHHHHHHHHHHC----
T ss_pred             EEECCCCHHHHHHHHHCCcceeEeCCCCHHHHHHHHHHHHhhcccc
Confidence            9999888888999999999999999999999999999998865543

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

Probab=99.85  E-value=1.1e-21  Score=136.16  Aligned_cols=119  Identities=21%  Similarity=0.172  Sum_probs=107.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcC-CeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc-CCCCE
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCL-YEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE-MDLPV   93 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~-~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~-~~~~i   93 (184)
                      ...+|+|+||++..+..++..|+..| |.+..+.++.++++.+.  ...||+||+|+.||+.+|+++++.++.. +.+|+
T Consensus        13 ~~~~ilivdd~~~~~~~l~~~L~~~g~~~v~~~~~~~~a~~~l~--~~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~i   90 (135)
T 3snk_A           13 KRKQVALFSSDPNFKRDVATRLDALAIYDVRVSETDDFLKGPPA--DTRPGIVILDLGGGDLLGKPGIVEARALWATVPL   90 (135)
T ss_dssp             CCEEEEEECSCHHHHHHHHHHHHHTSSEEEEEECGGGGGGCCCT--TCCCSEEEEEEETTGGGGSTTHHHHHGGGTTCCE
T ss_pred             CCcEEEEEcCCHHHHHHHHHHHhhcCCeEEEEeccHHHHHHHHh--ccCCCEEEEeCCCCCchHHHHHHHHHhhCCCCcE
Confidence            45689999999999999999999999 99999999999998876  5679999999999999999999999644 58999


Q ss_pred             EEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           94 IMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        94 Ii~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      |++++..+......+++.|+++|+.||++.++|..+++.++++
T Consensus        91 i~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~L~~~i~~~~~~  133 (135)
T 3snk_A           91 IAVSDELTSEQTRVLVRMNASDWLHKPLDGKELLNAVTFHDTG  133 (135)
T ss_dssp             EEEESCCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHTC--
T ss_pred             EEEeCCCCHHHHHHHHHcCcHhhccCCCCHHHHHHHHHHHhcc
Confidence            9999999899999999999999999999999999999887653

>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=99.85  E-value=3.1e-20  Score=138.52  Aligned_cols=125  Identities=20%  Similarity=0.382  Sum_probs=111.6

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhc-CCeE-EEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCC
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKC-LYEV-TKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLP   92 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~-~~~v-~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~   92 (184)
                      ..++|+||||++..+..+...|+.. ++.+ ..+.++.++++.+..  ..||+||+|+.||+.+|+++++.++. .+.+|
T Consensus         4 ~~~~ilivdd~~~~~~~l~~~L~~~~~~~vv~~~~~~~~al~~~~~--~~~dlvllD~~lp~~~g~~~~~~lr~~~~~~~   81 (215)
T 1a04_A            4 EPATILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAES--LDPDLILLDLNMPGMNGLETLDKLREKSLSGR   81 (215)
T ss_dssp             CCEEEEEECSCHHHHHHHHHHHTTCTTEEEEEEESSHHHHHHHHHH--HCCSEEEEETTSTTSCHHHHHHHHHHSCCCSE
T ss_pred             CceEEEEECCCHHHHHHHHHHHhcCCCcEEEEEeCCHHHHHHHHHh--cCCCEEEEeCCCCCCcHHHHHHHHHHhCCCCc
Confidence            3568999999999999999999986 4777 689999999999873  45999999999999999999999964 46889


Q ss_pred             EEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCCCCC
Q 029986           93 VIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPFEE  142 (184)
Q Consensus        93 iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~~~  142 (184)
                      ||+++...+......+++.|+++|+.||++.++|..+++.+.++...+.+
T Consensus        82 ii~ls~~~~~~~~~~~~~~Ga~~~l~Kp~~~~~L~~~i~~~~~~~~~~~~  131 (215)
T 1a04_A           82 IVVFSVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALHQAAAGEMVLSE  131 (215)
T ss_dssp             EEEEECCCCHHHHHHHHHTTCSEEEETTCCHHHHHHHHHHHHHSCCCCCT
T ss_pred             EEEEECCCCHHHHHHHHHcCCcEEEeCCCCHHHHHHHHHHHHcCCeecCH
Confidence            99999998899999999999999999999999999999999987665543

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

Probab=99.85  E-value=4.7e-20  Score=128.34  Aligned_cols=119  Identities=27%  Similarity=0.437  Sum_probs=104.1

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc---CCCCEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE---MDLPVI   94 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~---~~~~iI   94 (184)
                      ++|+|+||++..+..++..|...|+.+..+.++.++++.+.  ...||+||+|+.||+.+|+++++.++..   +.+|||
T Consensus         4 ~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~--~~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~~~ii   81 (138)
T 3c3m_A            4 YTILVVDDSPMIVDVFVTMLERGGYRPITAFSGEECLEALN--ATPPDLVLLDIMMEPMDGWETLERIKTDPATRDIPVL   81 (138)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HSCCSEEEEESCCSSSCHHHHHHHHHHSTTTTTSCEE
T ss_pred             ceEEEEeCCHHHHHHHHHHHHHcCceEEEeCCHHHHHHHHh--ccCCCEEEEeCCCCCCCHHHHHHHHHcCcccCCCCEE
Confidence            58999999999999999999999999999999999999987  3559999999999999999999999653   478999


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCC
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPK  138 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~  138 (184)
                      ++++.........++..|+++|+.||++.++|..+++.+..+..
T Consensus        82 ~ls~~~~~~~~~~~~~~~~~~~l~KP~~~~~L~~~i~~~~~~~~  125 (138)
T 3c3m_A           82 MLTAKPLTPEEANEYGSYIEDYILKPTTHHQLYEAIEHVLARRH  125 (138)
T ss_dssp             EEESSCCCHHHHHHTTTTCSEEEECCCHHHHHHHHHHHHHSCC-
T ss_pred             EEECCCChHHHHHHhhcCHhheEeCCCCHHHHHHHHHHHHHHhh
Confidence            99987665555566677789999999999999999999887544

>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=99.85  E-value=6.6e-20  Score=128.37  Aligned_cols=121  Identities=21%  Similarity=0.395  Sum_probs=109.0

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCC--eEEEECCHHHHHHHHHhcC--------CCccEEEEeCCCCCCCHHHHHHHh
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLY--EVTKCNRAEIALDMLRMSK--------NGYDIVISDVHMPDMDGFKLHEQV   85 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~--~v~~~~~~~~~~~~l~~~~--------~~~dlvilD~~l~~~~g~~l~~~l   85 (184)
                      .+++|+|+||++..+..++..|...|+  .+..+.++.++++.+....        ..||+||+|+.|++.+|+++++.+
T Consensus         5 ~~~~iLivdd~~~~~~~l~~~L~~~g~~~~v~~~~~~~~al~~l~~~~~~~~~~~~~~~dlvi~D~~l~~~~g~~~~~~l   84 (149)
T 1k66_A            5 ATQPLLVVEDSDEDFSTFQRLLQREGVVNPIYRCITGDQALDFLYQTGSYCNPDIAPRPAVILLDLNLPGTDGREVLQEI   84 (149)
T ss_dssp             TTSCEEEECCCHHHHHHHHHHHHHTTBCSCEEEECSHHHHHHHHHTCCSSSCGGGCCCCSEEEECSCCSSSCHHHHHHHH
T ss_pred             CCccEEEEECCHHHHHHHHHHHHHcCCCceEEEECCHHHHHHHHHhcccccCcccCCCCcEEEEECCCCCCCHHHHHHHH
Confidence            356899999999999999999999888  8999999999999987310        569999999999999999999999


Q ss_pred             ccc---CCCCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           86 GLE---MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        86 ~~~---~~~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      +..   +.+|+|++++..+......+++.|+++|+.||++.++|..+++.+.+.
T Consensus        85 ~~~~~~~~~~ii~~t~~~~~~~~~~~~~~g~~~~l~kP~~~~~l~~~i~~~~~~  138 (149)
T 1k66_A           85 KQDEVLKKIPVVIMTTSSNPKDIEICYSYSISSYIVKPLEIDRLTETVQTFIKY  138 (149)
T ss_dssp             TTSTTGGGSCEEEEESCCCHHHHHHHHHTTCSEEEECCSSHHHHHHHHHHHHHH
T ss_pred             HhCcccCCCeEEEEeCCCCHHHHHHHHHCCCCEEEeCCCCHHHHHHHHHHHHHH
Confidence            754   578999999988888999999999999999999999999999988763

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

Probab=99.85  E-value=2e-20  Score=129.97  Aligned_cols=121  Identities=20%  Similarity=0.268  Sum_probs=109.7

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEE-EECCHHHHHHHHHhcCCCccEEEEeCCCC-CCCHHHHHHHhcccCCCCE
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVT-KCNRAEIALDMLRMSKNGYDIVISDVHMP-DMDGFKLHEQVGLEMDLPV   93 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~-~~~~~~~~~~~l~~~~~~~dlvilD~~l~-~~~g~~l~~~l~~~~~~~i   93 (184)
                      ..++|+|+||++..+..+...|+..|+.+. .+.++.++++.+..  ..||+||+|+.++ +.+|+++++.++..+.+||
T Consensus         8 ~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~~a~~~~~~--~~~dlii~d~~~~~~~~g~~~~~~l~~~~~~~i   85 (140)
T 3cg0_A            8 DLPGVLIVEDGRLAAATLRIQLESLGYDVLGVFDNGEEAVRCAPD--LRPDIALVDIMLCGALDGVETAARLAAGCNLPI   85 (140)
T ss_dssp             CCCEEEEECCBHHHHHHHHHHHHHHTCEEEEEESSHHHHHHHHHH--HCCSEEEEESSCCSSSCHHHHHHHHHHHSCCCE
T ss_pred             CCceEEEEECCHHHHHHHHHHHHHCCCeeEEEECCHHHHHHHHHh--CCCCEEEEecCCCCCCCHHHHHHHHHhCCCCCE
Confidence            357999999999999999999999999998 59999999999874  4599999999998 7999999999965588999


Q ss_pred             EEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCC
Q 029986           94 IMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPK  138 (184)
Q Consensus        94 Ii~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~  138 (184)
                      |++++..+......+++.|+++|+.||++.++|..+++.++++..
T Consensus        86 i~ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~~~~~~  130 (140)
T 3cg0_A           86 IFITSSQDVETFQRAKRVNPFGYLAKPVAADTLHRSIEMAIHKKK  130 (140)
T ss_dssp             EEEECCCCHHHHHHHHTTCCSEEEEESCCHHHHHHHHHHHHHHHH
T ss_pred             EEEecCCCHHHHHHHHhcCCCEEEeCCCCHHHHHHHHHHHHhccc
Confidence            999998888888999999999999999999999999999887543

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

Probab=99.85  E-value=2.6e-20  Score=129.70  Aligned_cols=117  Identities=20%  Similarity=0.368  Sum_probs=106.8

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIMM   96 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi~   96 (184)
                      .+|+|+||++..+..++..|...|+.+..+.++.++++.+..  ..||++|+|+.||+.+|+++++.++. .+.+|+|++
T Consensus         5 ~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~~--~~~dlvllD~~l~~~~g~~l~~~l~~~~~~~~ii~l   82 (137)
T 3cfy_A            5 PRVLLVEDSTSLAILYKQYVKDEPYDIFHVETGRDAIQFIER--SKPQLIILDLKLPDMSGEDVLDWINQNDIPTSVIIA   82 (137)
T ss_dssp             CEEEEECSCTTHHHHHHHHTTTSSSEEEEESSHHHHHHHHHH--HCCSEEEECSBCSSSBHHHHHHHHHHTTCCCEEEEE
T ss_pred             ceEEEEeCCHHHHHHHHHHHHhcCceEEEeCCHHHHHHHHHh--cCCCEEEEecCCCCCCHHHHHHHHHhcCCCCCEEEE
Confidence            379999999999999999999889999999999999999873  45999999999999999999999964 467899999


Q ss_pred             EccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           97 SVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        97 ~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      +...+......+++.|+++|+.||++.++|..+++.++++
T Consensus        83 s~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~i~~~~~~  122 (137)
T 3cfy_A           83 TAHGSVDLAVNLIQKGAEDFLEKPINADRLKTSVALHLKR  122 (137)
T ss_dssp             ESSCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHHHH
T ss_pred             EecCcHHHHHHHHHCCccEEEeCCCCHHHHHHHHHHHHHH
Confidence            9988888899999999999999999999999999888754

>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=99.85  E-value=3.4e-20  Score=142.86  Aligned_cols=120  Identities=28%  Similarity=0.337  Sum_probs=107.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc---CCCC
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE---MDLP   92 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~---~~~~   92 (184)
                      ..++|+||||++..+..+...|...|+.+..+.++.++++.+.. ...||+||+|+.||+++|++++++++..   ..+|
T Consensus       123 ~~~~ILivDD~~~~~~~l~~~L~~~~~~v~~a~~~~eal~~l~~-~~~~dlvllD~~mP~~dG~~l~~~lr~~~~~~~~~  201 (259)
T 3luf_A          123 QQIEVLVVDDSRTSRHRTMAQLRKQLLQVHEASHAREALATLEQ-HPAIRLVLVDYYMPEIDGISLVRMLRERYSKQQLA  201 (259)
T ss_dssp             TTCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHHH-CTTEEEEEECSCCSSSCHHHHHHHHHHHCCTTTSE
T ss_pred             CCCcEEEEeCCHHHHHHHHHHHHHcCcEEEEeCCHHHHHHHHhc-CCCCCEEEEcCCCCCCCHHHHHHHHHhccCCCCCe
Confidence            35799999999999999999999999999999999999999863 2348999999999999999999999753   2578


Q ss_pred             EEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           93 VIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        93 iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      ||+++...+.....++++.||++|+.||++.++|..+++.+++.
T Consensus       202 ii~~s~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~i~~~l~~  245 (259)
T 3luf_A          202 IIGISVSDKRGLSARYLKQGANDFLNQPFEPEELQCRVSHNLEA  245 (259)
T ss_dssp             EEEEECSSSSSHHHHHHHTTCSEEEESSCCHHHHHHHHHHHHHH
T ss_pred             EEEEEccCCHHHHHHHHhcChhheEcCCCCHHHHHHHHHHHHHh
Confidence            99999988888999999999999999999999999999888654

>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=99.85  E-value=2.4e-20  Score=138.25  Aligned_cols=118  Identities=25%  Similarity=0.408  Sum_probs=107.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEE-EECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVT-KCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIM   95 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~-~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi   95 (184)
                      ..+|+||||++..+..+...|...||.+. .+.++.++++.+..  ..||+||+|+.||+.+|+++++.++.....|||+
T Consensus        13 ~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~~al~~~~~--~~~dlvi~D~~~p~~~g~~~~~~l~~~~~~pii~   90 (205)
T 1s8n_A           13 PRRVLIAEDEALIRMDLAEMLREEGYEIVGEAGDGQEAVELAEL--HKPDLVIMDVKMPRRDGIDAASEIASKRIAPIVV   90 (205)
T ss_dssp             CCEEEEECSSHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHHH--HCCSEEEEESSCSSSCHHHHHHHHHHTTCSCEEE
T ss_pred             CccEEEEECCHHHHHHHHHHHHHCCCEEEEEeCCHHHHHHHHhh--cCCCEEEEeCCCCCCChHHHHHHHHhcCCCCEEE
Confidence            46899999999999999999999999987 89999999999873  4599999999999999999999997655569999


Q ss_pred             EEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           96 MSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        96 ~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      +++..+......+++.|+++|+.||++.++|..+++.++++
T Consensus        91 lt~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~i~~~~~~  131 (205)
T 1s8n_A           91 LTAFSQRDLVERARDAGAMAYLVKPFSISDLIPAIELAVSR  131 (205)
T ss_dssp             EEEGGGHHHHHTTGGGSCEEEEEESCCHHHHHHHHHHHHHH
T ss_pred             EecCCCHHHHHHHHhcCCcEEEeCCCCHHHHHHHHHHHHHH
Confidence            99988888889999999999999999999999999988764

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

Probab=99.84  E-value=3.5e-20  Score=129.97  Aligned_cols=119  Identities=18%  Similarity=0.307  Sum_probs=109.0

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc---cCCCC
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL---EMDLP   92 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~---~~~~~   92 (184)
                      ..++|+|+||++..+..+...|...|+.+..+.++.++++.+..  ..||+||+|+.+++.+|+++++.++.   .+.+|
T Consensus         7 ~~~~iLivd~~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~~--~~~dlii~d~~l~~~~g~~~~~~l~~~~~~~~~p   84 (147)
T 2zay_A            7 KWWRIMLVDTQLPALAASISALSQEGFDIIQCGNAIEAVPVAVK--THPHLIITEANMPKISGMDLFNSLKKNPQTASIP   84 (147)
T ss_dssp             -CEEEEEECTTGGGGHHHHHHHHHHTEEEEEESSHHHHHHHHHH--HCCSEEEEESCCSSSCHHHHHHHHHTSTTTTTSC
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCHHHHHHHHHc--CCCCEEEEcCCCCCCCHHHHHHHHHcCcccCCCC
Confidence            46789999999999999999999999999999999999999874  45999999999999999999999975   46899


Q ss_pred             EEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           93 VIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        93 iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      ||+++...+......+++.|+++|+.||++.++|..+++.++++
T Consensus        85 ii~ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~L~~~i~~~~~~  128 (147)
T 2zay_A           85 VIALSGRATAKEEAQLLDMGFIDFIAKPVNAIRLSARIKRVLKL  128 (147)
T ss_dssp             EEEEESSCCHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHHHH
T ss_pred             EEEEeCCCCHHHHHHHHhCCCCEEEeCCCCHHHHHHHHHHHHHH
Confidence            99999988888899999999999999999999999999988764

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

Probab=99.84  E-value=8.6e-20  Score=129.03  Aligned_cols=123  Identities=20%  Similarity=0.331  Sum_probs=111.4

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHh-cCCeEE-EECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRK-CLYEVT-KCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPV   93 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~-~~~~v~-~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~i   93 (184)
                      +++|+|+||++..+..+...|.. .|+.+. .+.++.++++.+.  ...||+||+|+.+++.+|+++++.++. .+.+||
T Consensus         5 ~~~ILivdd~~~~~~~l~~~L~~~~~~~v~~~~~~~~~a~~~l~--~~~~dlii~D~~l~~~~g~~~~~~l~~~~~~~~i   82 (153)
T 3cz5_A            5 TARIMLVDDHPIVREGYRRLIERRPGYAVVAEAADAGEAYRLYR--ETTPDIVVMDLTLPGPGGIEATRHIRQWDGAARI   82 (153)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHTTSTTEEEEEEESSHHHHHHHHH--TTCCSEEEECSCCSSSCHHHHHHHHHHHCTTCCE
T ss_pred             ccEEEEECCcHHHHHHHHHHHhhCCCcEEEEEeCCHHHHHHHHh--cCCCCEEEEecCCCCCCHHHHHHHHHHhCCCCeE
Confidence            56899999999999999999998 689887 8999999999987  556999999999999999999999964 468999


Q ss_pred             EEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCCCC
Q 029986           94 IMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPFE  141 (184)
Q Consensus        94 Ii~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~~  141 (184)
                      |+++...+......+++.|+++|+.||++.++|..+++.+.++...+.
T Consensus        83 i~ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~L~~~i~~~~~~~~~~~  130 (153)
T 3cz5_A           83 LIFTMHQGSAFALKAFEAGASGYVTKSSDPAELVQAIEAILAGRRAMS  130 (153)
T ss_dssp             EEEESCCSHHHHHHHHHTTCSEEEETTSCTTHHHHHHHHHTTTCCEEC
T ss_pred             EEEECCCCHHHHHHHHHCCCcEEEecCCCHHHHHHHHHHHHhCCccCC
Confidence            999998888899999999999999999999999999999988766544

>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=99.84  E-value=3.1e-20  Score=137.80  Aligned_cols=118  Identities=26%  Similarity=0.387  Sum_probs=108.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIM   95 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi   95 (184)
                      ..+|+||||++..+..+...|...|+.+..+.++.++++.+.  ...||+||+|+.||+.+|+++++.++. .+.+|||+
T Consensus         4 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~--~~~~dlvl~D~~lp~~~g~~~~~~l~~~~~~~~ii~   81 (208)
T 1yio_A            4 KPTVFVVDDDMSVREGLRNLLRSAGFEVETFDCASTFLEHRR--PEQHGCLVLDMRMPGMSGIELQEQLTAISDGIPIVF   81 (208)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHCC--TTSCEEEEEESCCSSSCHHHHHHHHHHTTCCCCEEE
T ss_pred             CCEEEEEcCCHHHHHHHHHHHHhCCceEEEcCCHHHHHHhhh--ccCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCCEEE
Confidence            458999999999999999999998999999999999999876  566999999999999999999999964 46899999


Q ss_pred             EEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           96 MSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        96 ~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      +++..+......+++.|+++|+.||++.++|..+++.++++
T Consensus        82 ls~~~~~~~~~~a~~~Ga~~~l~Kp~~~~~L~~~i~~~~~~  122 (208)
T 1yio_A           82 ITAHGDIPMTVRAMKAGAIEFLPKPFEEQALLDAIEQGLQL  122 (208)
T ss_dssp             EESCTTSCCCHHHHHTTEEEEEESSCCHHHHHHHHHHHHHH
T ss_pred             EeCCCCHHHHHHHHHCCCcEEEeCCCCHHHHHHHHHHHHhh
Confidence            99988888899999999999999999999999999988764

>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=99.84  E-value=4.2e-20  Score=138.53  Aligned_cols=122  Identities=26%  Similarity=0.461  Sum_probs=111.1

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIM   95 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi   95 (184)
                      +++|+|+||++..+..+...|...|+.+..+.++.++++.+.  ...||++|+|+.||+.+|+++++.++. .+++|||+
T Consensus         2 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~~~--~~~~dlvllD~~l~~~~g~~~~~~lr~~~~~~~ii~   79 (225)
T 1kgs_A            2 NVRVLVVEDERDLADLITEALKKEMFTVDVCYDGEEGMYMAL--NEPFDVVILDIMLPVHDGWEILKSMRESGVNTPVLM   79 (225)
T ss_dssp             CCEEEEECSSHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HSCCSEEEEESCCSSSCHHHHHHHHHHTTCCCCEEE
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh--cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCCEEE
Confidence            468999999999999999999999999999999999999987  456999999999999999999999964 46899999


Q ss_pred             EEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCCC
Q 029986           96 MSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPF  140 (184)
Q Consensus        96 ~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~  140 (184)
                      +++..+......+++.|+++|+.||++.++|..+++.+.++....
T Consensus        80 ls~~~~~~~~~~~~~~ga~~~l~Kp~~~~~l~~~i~~~~~~~~~~  124 (225)
T 1kgs_A           80 LTALSDVEYRVKGLNMGADDYLPKPFDLRELIARVRALIRRKSES  124 (225)
T ss_dssp             EESSCHHHHHHHTCCCCCSEEEESSCCHHHHHHHHHHHHHHHCCS
T ss_pred             EeCCCCHHHHHHHHhCCccEEEeCCCCHHHHHHHHHHHHhhcccc
Confidence            999888888899999999999999999999999999998765443

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

Probab=99.84  E-value=9.3e-20  Score=128.68  Aligned_cols=119  Identities=25%  Similarity=0.439  Sum_probs=107.1

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEE
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVI   94 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iI   94 (184)
                      .+++|+||||++..+..+...|+. |+.+..+.++.++++.+... ..||+||+|+.|++.+|+++++.++. .+.+|||
T Consensus         3 ~~~~ILivdd~~~~~~~l~~~L~~-~~~v~~~~~~~~a~~~l~~~-~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~ii   80 (151)
T 3kcn_A            3 LNERILLVDDDYSLLNTLKRNLSF-DFEVTTCESGPEALACIKKS-DPFSVIMVDMRMPGMEGTEVIQKARLISPNSVYL   80 (151)
T ss_dssp             CCCEEEEECSCHHHHHHHHHHHTT-TSEEEEESSHHHHHHHHHHS-CCCSEEEEESCCSSSCHHHHHHHHHHHCSSCEEE
T ss_pred             CCCeEEEEeCCHHHHHHHHHHhcc-CceEEEeCCHHHHHHHHHcC-CCCCEEEEeCCCCCCcHHHHHHHHHhcCCCcEEE
Confidence            357899999999999999999976 89999999999999998742 23599999999999999999999964 4789999


Q ss_pred             EEEccCChHHHHHHHHcC-CCceEeCCCCHHHHHHHHHHHHcC
Q 029986           95 MMSVDGCTQDVMKGVTHG-ACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~g-a~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      ++++..+......++..| +++|+.||++.++|..+++.++++
T Consensus        81 ~~s~~~~~~~~~~~~~~g~~~~~l~KP~~~~~L~~~i~~~l~~  123 (151)
T 3kcn_A           81 MLTGNQDLTTAMEAVNEGQVFRFLNKPCQMSDIKAAINAGIKQ  123 (151)
T ss_dssp             EEECGGGHHHHHHHHHHTCCSEEEESSCCHHHHHHHHHHHHHH
T ss_pred             EEECCCCHHHHHHHHHcCCeeEEEcCCCCHHHHHHHHHHHHHH
Confidence            999988888899999999 999999999999999999988764

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

Probab=99.84  E-value=6.4e-20  Score=123.56  Aligned_cols=113  Identities=26%  Similarity=0.445  Sum_probs=100.6

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIMM   96 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi~   96 (184)
                      ++|+|+||++..+..++..|...|+.+..+.++.++++.+.  ...||++|+|+.||+.+|+++++.++. .+.+|+|++
T Consensus         2 ~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~~~--~~~~dlvl~D~~l~~~~g~~~~~~l~~~~~~~~ii~~   79 (116)
T 3a10_A            2 KRILVVDDEPNIRELLKEELQEEGYEIDTAENGEEALKKFF--SGNYDLVILDIEMPGISGLEVAGEIRKKKKDAKIILL   79 (116)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HSCCSEEEECSCCSSSCHHHHHHHHHHHCTTCCEEEE
T ss_pred             cEEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHh--cCCCCEEEEECCCCCCCHHHHHHHHHccCCCCeEEEE
Confidence            47999999999999999999999999999999999999987  356999999999999999999999964 467899999


Q ss_pred             EccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHH
Q 029986           97 SVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVA  134 (184)
Q Consensus        97 ~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~  134 (184)
                      ++..+..  ..+++.|+++|+.||++.++|..+++.++
T Consensus        80 s~~~~~~--~~~~~~g~~~~l~Kp~~~~~l~~~i~~~~  115 (116)
T 3a10_A           80 TAYSHYR--SDMSSWAADEYVVKSFNFDELKEKVKKLL  115 (116)
T ss_dssp             ESCGGGG--GCGGGGGSSEEEECCSSTHHHHHHHHHHT
T ss_pred             ECCcchH--HHHHhccccceEECCCCHHHHHHHHHHHh
Confidence            8765444  67888999999999999999999988764

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

Probab=99.84  E-value=2.2e-19  Score=127.02  Aligned_cols=119  Identities=25%  Similarity=0.370  Sum_probs=108.7

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEE
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVI   94 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iI   94 (184)
                      .+++|+||||++..+..+...|...|+.+..+.++.++++.+.  ...||+||+|+.+++.+|+++++.++. .+.+|||
T Consensus         6 ~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--~~~~dlvi~d~~l~~~~g~~~~~~l~~~~~~~~ii   83 (154)
T 2rjn_A            6 KNYTVMLVDDEQPILNSLKRLIKRLGCNIITFTSPLDALEALK--GTSVQLVISDMRMPEMGGEVFLEQVAKSYPDIERV   83 (154)
T ss_dssp             SCCEEEEECSCHHHHHHHHHHHHTTTCEEEEESCHHHHHHHHT--TSCCSEEEEESSCSSSCHHHHHHHHHHHCTTSEEE
T ss_pred             CCCeEEEEcCCHHHHHHHHHHHHHcCCeEEEeCCHHHHHHHHh--cCCCCEEEEecCCCCCCHHHHHHHHHHhCCCCcEE
Confidence            3678999999999999999999999999999999999999987  456999999999999999999999964 4689999


Q ss_pred             EEEccCChHHHHHHHHcC-CCceEeCCCCHHHHHHHHHHHHcC
Q 029986           95 MMSVDGCTQDVMKGVTHG-ACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~g-a~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      +++...+......++..| +++|+.||++.++|..+++.++++
T Consensus        84 ~ls~~~~~~~~~~~~~~g~~~~~l~kP~~~~~L~~~i~~~~~~  126 (154)
T 2rjn_A           84 VISGYADAQATIDAVNRGKISRFLLKPWEDEDVFKVVEKGLQL  126 (154)
T ss_dssp             EEECGGGHHHHHHHHHTTCCSEEEESSCCHHHHHHHHHHHHHH
T ss_pred             EEecCCCHHHHHHHHhccchheeeeCCCCHHHHHHHHHHHHHH
Confidence            999888888888999998 999999999999999999988764

>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=99.83  E-value=1.3e-19  Score=139.16  Aligned_cols=118  Identities=32%  Similarity=0.537  Sum_probs=108.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEE
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVI   94 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iI   94 (184)
                      .+++|+||||++..+..+...|+..||.+..+.++.++++.+.  ...||+||+|+.||+++|+++++.++. .+.+|||
T Consensus       128 ~~~~ILivdd~~~~~~~l~~~L~~~g~~v~~a~~~~eal~~l~--~~~~dlvl~D~~mp~~~G~~l~~~ir~~~~~~piI  205 (254)
T 2ayx_A          128 DDMMILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVLS--KNHIDIVLSDVNMPNMDGYRLTQRIRQLGLTLPVI  205 (254)
T ss_dssp             CCCEEEEEESSHHHHHHHHHHHHHHTSEEEEECCSHHHHHHHH--HSCCSEEEEEESSCSSCCHHHHHHHHHHHCCSCEE
T ss_pred             CCCEEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHH--hCCCCEEEEcCCCCCCCHHHHHHHHHhcCCCCcEE
Confidence            3679999999999999999999999999999999999999987  355999999999999999999999964 4689999


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      ++++....+....+++.|+++|+.||++.++|..+++.+.+
T Consensus       206 ~lt~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~~~  246 (254)
T 2ayx_A          206 GVTANALAEEKQRCLESGMDSCLSKPVTLDVIKQTLTLYAE  246 (254)
T ss_dssp             EEESSTTSHHHHHHHHCCCEEEEESSCCHHHHHHHHHHHHH
T ss_pred             EEECCCCHHHHHHHHHcCCceEEECCCCHHHHHHHHHHHHH
Confidence            99998888899999999999999999999999999988765

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

Probab=99.83  E-value=2.6e-19  Score=124.82  Aligned_cols=122  Identities=18%  Similarity=0.320  Sum_probs=107.4

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCC--eEEEECCHHHHHHHHHhc----CCCccEEEEeCCCCCCCHHHHHHHhccc-
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLY--EVTKCNRAEIALDMLRMS----KNGYDIVISDVHMPDMDGFKLHEQVGLE-   88 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~--~v~~~~~~~~~~~~l~~~----~~~~dlvilD~~l~~~~g~~l~~~l~~~-   88 (184)
                      ..++|+|+||++..+..+...|...|+  .+..+.++.++++.+...    ...||+||+|+.+++.+|+++++.++.. 
T Consensus         6 ~~~~ILivdd~~~~~~~l~~~L~~~g~~~~v~~~~~~~~a~~~l~~~~~~~~~~~dlii~D~~l~~~~g~~~~~~l~~~~   85 (143)
T 2qvg_A            6 DKVDILYLEDDEVDIQSVERVFHKISSLIKIEIAKSGNQALDMLYGRNKENKIHPKLILLDINIPKMNGIEFLKELRDDS   85 (143)
T ss_dssp             -CCSEEEECCCHHHHHHHHHHHHHHCTTCCEEEESSHHHHHHHHHTCTTCCCCCCSEEEEETTCTTSCHHHHHHHHTTSG
T ss_pred             CCCeEEEEeCCHHHHHHHHHHHHHhCCCceEEEECCHHHHHHHHHhcccccCCCCCEEEEecCCCCCCHHHHHHHHHcCc
Confidence            356899999999999999999998887  899999999999998731    1569999999999999999999999754 


Q ss_pred             --CCCCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCC
Q 029986           89 --MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQP  137 (184)
Q Consensus        89 --~~~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~  137 (184)
                        +.+|+|+++...+......+++.|+++|+.||++.++|..++.......
T Consensus        86 ~~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~kP~~~~~L~~~~~~~~~~~  136 (143)
T 2qvg_A           86 SFTDIEVFVLTAAYTSKDKLAFESLNIRGHLIKPLDYGEAIKLFWILQSME  136 (143)
T ss_dssp             GGTTCEEEEEESCCCHHHHHHHTTTTCCEEEESSCCHHHHHHHHHHHHHC-
T ss_pred             cccCCcEEEEeCCCCHHHHHHHHhcCCCeEEECCCCHHHHHHHHHHHHHhh
Confidence              6889999999888888999999999999999999999999887765543

>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=99.83  E-value=9.2e-20  Score=137.21  Aligned_cols=120  Identities=29%  Similarity=0.408  Sum_probs=110.5

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMM   96 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi~   96 (184)
                      .++|+||||++..+..+...|...|+.+..+.++.++++.+..  ..||++|+|+.||+.+|+++++.++..+.+|||++
T Consensus         4 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~~--~~~dlvllD~~l~~~~g~~~~~~l~~~~~~~ii~l   81 (230)
T 2oqr_A            4 ATSVLIVEDEESLADPLAFLLRKEGFEATVVTDGPAALAEFDR--AGADIVLLDLMLPGMSGTDVCKQLRARSSVPVIMV   81 (230)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEECSHHHHHHHHHH--HCCSEEEEESSCSSSCHHHHHHHHHHHCSCSEEEE
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHhc--cCCCEEEEECCCCCCCHHHHHHHHHcCCCCCEEEE
Confidence            3689999999999999999999989999999999999999873  45999999999999999999999976688999999


Q ss_pred             EccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCC
Q 029986           97 SVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPK  138 (184)
Q Consensus        97 ~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~  138 (184)
                      ++..+......+++.|+++|+.||++.++|..+++.++++..
T Consensus        82 t~~~~~~~~~~~~~~ga~~~l~Kp~~~~~l~~~i~~~~~~~~  123 (230)
T 2oqr_A           82 TARDSEIDKVVGLELGADDYVTKPYSARELIARIRAVLRRGG  123 (230)
T ss_dssp             ECCHHHHHHHHHHHHCCSCCCCSSCCHHHHHHHHHHHHTTTT
T ss_pred             eCCCcHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHhhcc
Confidence            988777888899999999999999999999999999988754

>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=99.83  E-value=2.5e-20  Score=150.40  Aligned_cols=117  Identities=25%  Similarity=0.372  Sum_probs=108.7

Q ss_pred             eEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEEEE
Q 029986           19 RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIMMS   97 (184)
Q Consensus        19 ~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi~~   97 (184)
                      +|+||||++..+..++.+|+..||.+..+.++.++++.+.  ...||+||+|+.||+++|+++++.++. .+.+|||++|
T Consensus         2 ~ILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~eal~~l~--~~~~DlvllDi~mP~~dG~ell~~lr~~~~~~pvI~lT   79 (368)
T 3dzd_A            2 RVLVVDDEESITSSLSAILEEEGYHPDTAKTLREAEKKIK--ELFFPVIVLDVWMPDGDGVNFIDFIKENSPDSVVIVIT   79 (368)
T ss_dssp             EEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HBCCSEEEEESEETTEETTTHHHHHHHHCTTCEEEEEE
T ss_pred             EEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHH--hCCCCEEEEeCCCCCCCHHHHHHHHHhhCCCCeEEEEe
Confidence            7999999999999999999999999999999999999987  456999999999999999999999964 4789999999


Q ss_pred             ccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCC
Q 029986           98 VDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQP  137 (184)
Q Consensus        98 ~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~  137 (184)
                      +..+.+...++++.||++|+.||++.++|..+++.++.+.
T Consensus        80 ~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~i~~~l~~~  119 (368)
T 3dzd_A           80 GHGSVDTAVKAIKKGAYEFLEKPFSVERFLLTIKHAFEEY  119 (368)
T ss_dssp             CSSCCHHHHHHHHHTCCEEEESSCCHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHhcCcceEEeCCCCHHHHHHHHHHHHHHh
Confidence            9998999999999999999999999999999999887643

>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=99.83  E-value=2e-20  Score=130.31  Aligned_cols=120  Identities=19%  Similarity=0.287  Sum_probs=99.5

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc---CCCCE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE---MDLPV   93 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~---~~~~i   93 (184)
                      .++|+|+||++..+..+..+|+.. +.+..+.++.++++.+..  ..||+||+|+.|++.+|+++++.++..   +.+|+
T Consensus         3 ~~~iLivdd~~~~~~~l~~~l~~~-~~v~~~~~~~~a~~~~~~--~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~~~i   79 (140)
T 3n53_A            3 LKKILIIDQQDFSRIELKNFLDSE-YLVIESKNEKEALEQIDH--HHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPL   79 (140)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHTTT-SEEEEESSHHHHHHHHHH--HCCSEEEEETTC------CHHHHHHTSTTCTTCCE
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHhc-ceEEEeCCHHHHHHHHhc--CCCCEEEEeCCCCCCcHHHHHHHHHcCcccCCCCE
Confidence            468999999999999999999987 999999999999999874  459999999999999999999999654   68899


Q ss_pred             EEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCC
Q 029986           94 IMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKP  139 (184)
Q Consensus        94 Ii~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~  139 (184)
                      |+++...+.+...++++.|+++|+.||++.++|..+++.++++..+
T Consensus        80 i~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~~~~~~  125 (140)
T 3n53_A           80 ILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNY  125 (140)
T ss_dssp             EEEECC----CTTTTTTCCCSEEEESSCCHHHHHHHHHHHHHHHHH
T ss_pred             EEEecCCCHHHHHHHHhcCCCeeeeCCCCHHHHHHHHHHHHhhHHH
Confidence            9999988888888999999999999999999999999999876543

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

Probab=99.83  E-value=9.8e-20  Score=128.77  Aligned_cols=124  Identities=18%  Similarity=0.177  Sum_probs=102.1

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhc-CC-eEEEECCHHHHHHHHHhcC-CCccEEEEeCCCCCCCHHHHHHHhcc-cCCCC
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKC-LY-EVTKCNRAEIALDMLRMSK-NGYDIVISDVHMPDMDGFKLHEQVGL-EMDLP   92 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~-~~-~v~~~~~~~~~~~~l~~~~-~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~   92 (184)
                      .++|+|+||++..+..+...|... |+ .+..+.++.++++.+.  . ..||+||+|+.+++.+|+++++.++. .+.+|
T Consensus         3 ~~~iLivdd~~~~~~~l~~~L~~~~g~~~v~~~~~~~~a~~~l~--~~~~~dlvi~d~~l~~~~g~~~~~~l~~~~~~~~   80 (154)
T 2qsj_A            3 LTVVLIVDDHHLIRAGAKNLLEGAFSGMRVEGAETVSDALAFLE--ADNTVDLILLDVNLPDAEAIDGLVRLKRFDPSNA   80 (154)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHHHHCTTEEEEEESSHHHHHHHHH--TTCCCSEEEECC------CHHHHHHHHHHCTTSE
T ss_pred             ccEEEEEcCCHHHHHHHHHHHHhCCCceEEEEecCHHHHHHHHh--ccCCCCEEEEeCCCCCCchHHHHHHHHHhCCCCe
Confidence            468999999999999999999987 77 6889999999999987  4 66999999999999999999999964 46889


Q ss_pred             EEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCCCCC
Q 029986           93 VIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPFEE  142 (184)
Q Consensus        93 iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~~~  142 (184)
                      ||+++...+......+++.|+++|+.||++.++|..+++.+.++...+++
T Consensus        81 ii~ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~L~~~l~~~~~~~~~~~~  130 (154)
T 2qsj_A           81 VALISGETDHELIRAALEAGADGFIPKSADPQVLIHAVSLILEGEIFLPR  130 (154)
T ss_dssp             EEEC-----CHHHHHHHHTTCCBBCCTTSCHHHHHHHHHHHHTTCCBCCG
T ss_pred             EEEEeCCCCHHHHHHHHHccCCEEEeCCCCHHHHHHHHHHHHcCCEEcCH
Confidence            99999888888899999999999999999999999999999988776554

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

Probab=99.83  E-value=4.6e-20  Score=128.56  Aligned_cols=119  Identities=20%  Similarity=0.339  Sum_probs=108.7

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc---cCCCC
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL---EMDLP   92 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~---~~~~~   92 (184)
                      ..++|+|+||++..+..+...|...|+.+..+.++.++++.+.  ...||+||+|+.+++.+|+++++.++.   .+.+|
T Consensus         6 ~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--~~~~dlii~d~~l~~~~g~~~~~~l~~~~~~~~~p   83 (142)
T 3cg4_A            6 HKGDVMIVDDDAHVRIAVKTILSDAGFHIISADSGGQCIDLLK--KGFSGVVLLDIMMPGMDGWDTIRAILDNSLEQGIA   83 (142)
T ss_dssp             CCCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--TCCCEEEEEESCCSSSCHHHHHHHHHHTTCCTTEE
T ss_pred             CCCeEEEEcCCHHHHHHHHHHHHHCCeEEEEeCCHHHHHHHHH--hcCCCEEEEeCCCCCCCHHHHHHHHHhhcccCCCC
Confidence            4678999999999999999999999999999999999999987  556999999999999999999999965   46789


Q ss_pred             EEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           93 VIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        93 iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      ||+++...+......+++.|+++|+.||++.++|..+++.++++
T Consensus        84 ii~~s~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~~~~  127 (142)
T 3cg4_A           84 IVMLTAKNAPDAKMIGLQEYVVDYITKPFDNEDLIEKTTFFMGF  127 (142)
T ss_dssp             EEEEECTTCCCCSSTTGGGGEEEEEESSCCHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCHHHHHHHHhcCccEEEeCCCCHHHHHHHHHHHHHH
Confidence            99999888778888899999999999999999999999988764

>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=99.83  E-value=1.9e-19  Score=127.56  Aligned_cols=119  Identities=27%  Similarity=0.421  Sum_probs=107.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEE
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVI   94 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iI   94 (184)
                      .+++|+|+||++..+..+...|...|+.+..+.++.++++.+.  ...||+||+|+.+++.+|+++++.++. .+.+|||
T Consensus         2 ~~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--~~~~dliild~~l~~~~g~~~~~~l~~~~~~~pii   79 (155)
T 1qkk_A            2 AAPSVFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGLS--ADFAGIVISDIRMPGMDGLALFRKILALDPDLPMI   79 (155)
T ss_dssp             --CEEEEECSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHTCC--TTCCSEEEEESCCSSSCHHHHHHHHHHHCTTSCEE
T ss_pred             CCCEEEEEeCCHHHHHHHHHHHHHcCcEEEEECCHHHHHHHHH--hCCCCEEEEeCCCCCCCHHHHHHHHHhhCCCCCEE
Confidence            3568999999999999999999999999999999999999876  456999999999999999999999964 4689999


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      +++...+......+++.|+++|+.||++.++|..+++.+..+
T Consensus        80 ~ls~~~~~~~~~~~~~~g~~~~l~kP~~~~~L~~~i~~~~~~  121 (155)
T 1qkk_A           80 LVTGHGDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRAEEK  121 (155)
T ss_dssp             EEECGGGHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHHHH
T ss_pred             EEECCCChHHHHHHHhcCCCeEEeCCCCHHHHHHHHHHHHHH
Confidence            999988888889999999999999999999999999988764

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

Probab=99.83  E-value=1e-19  Score=137.99  Aligned_cols=120  Identities=28%  Similarity=0.438  Sum_probs=110.7

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMS   97 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi~~   97 (184)
                      ++|+||||++..+..+...|+..|+.+..+.++.++++.+..  ..||+||+|+.||+.+|+++++.++..+.+|||+++
T Consensus         6 ~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~~--~~~dlvilD~~l~~~~g~~~~~~lr~~~~~~ii~lt   83 (238)
T 2gwr_A            6 QRILVVDDDASLAEMLTIVLRGEGFDTAVIGDGTQALTAVRE--LRPDLVLLDLMLPGMNGIDVCRVLRADSGVPIVMLT   83 (238)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEECCGGGHHHHHHH--HCCSEEEEESSCSSSCHHHHHHHHHTTCCCCEEEEE
T ss_pred             CeEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHh--CCCCEEEEeCCCCCCCHHHHHHHHHhCCCCcEEEEe
Confidence            589999999999999999999989999999999999999873  459999999999999999999999766689999999


Q ss_pred             ccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCC
Q 029986           98 VDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKP  139 (184)
Q Consensus        98 ~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~  139 (184)
                      ...+......+++.|+++|+.||++.++|..+++.++++...
T Consensus        84 ~~~~~~~~~~~~~~Ga~~~l~Kp~~~~~L~~~i~~~~~~~~~  125 (238)
T 2gwr_A           84 AKTDTVDVVLGLESGADDYIMKPFKPKELVARVRARLRRNDD  125 (238)
T ss_dssp             ETTCCSCHHHHHHTTCCEEEEESCCHHHHHHHHHHHCCCCSS
T ss_pred             CCCCHHHHHHHHHCCCCEEEeCCCCHHHHHHHHHHHHhhccc
Confidence            988888889999999999999999999999999999887644

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

Probab=99.83  E-value=9.1e-20  Score=127.51  Aligned_cols=116  Identities=25%  Similarity=0.340  Sum_probs=98.0

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHh--cCCeEE-EECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRK--CLYEVT-KCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPV   93 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~--~~~~v~-~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~i   93 (184)
                      ++|+|+||++..+..+...|..  .|+.+. .+.++.++++.+.  ...||++|+|+.||+.+|+++++.++. .+.+|+
T Consensus         3 ~~ILivdd~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~al~~~~--~~~~dlvllD~~lp~~~g~~l~~~l~~~~~~~~i   80 (141)
T 3cu5_A            3 LRILIVDDEKLTRDGLIANINWKALSFDQIDQADDGINAIQIAL--KHPPNVLLTDVRMPRMDGIELVDNILKLYPDCSV   80 (141)
T ss_dssp             CEEEEECSCHHHHHHHHHHCCGGGSCCSEEEEESSHHHHHHHHT--TSCCSEEEEESCCSSSCHHHHHHHHHHHCTTCEE
T ss_pred             ceEEEEeCCHHHHHHHHHHHHHccCCcEEeeecccHHHHHHHHh--cCCCCEEEEeCCCCCCCHHHHHHHHHhhCCCCcE
Confidence            5899999999999999999974  477766 8999999999886  456999999999999999999999964 468899


Q ss_pred             EEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           94 IMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        94 Ii~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      |++++..+......+++.|+++|+.||++.++|..+++.+.+
T Consensus        81 i~ls~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~i~~~~~  122 (141)
T 3cu5_A           81 IFMSGYSDKEYLKAAIKFRAIRYVEKPIDPSEIMDALKQSIQ  122 (141)
T ss_dssp             EEECCSTTTCCC------CCCEEECSSCCHHHHHHHHHHHHH
T ss_pred             EEEeCCCcHHHHHHHHhCCccEEEeCCCCHHHHHHHHHHHHH
Confidence            999988877888899999999999999999999999988765

>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=99.83  E-value=2e-19  Score=122.47  Aligned_cols=116  Identities=15%  Similarity=0.266  Sum_probs=105.7

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCC-CCCHHHHHHHhccc---CCCCE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMP-DMDGFKLHEQVGLE---MDLPV   93 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~-~~~g~~l~~~l~~~---~~~~i   93 (184)
                      ++|+|+||++..+..+...|...|+.+..+.++.++++.+..  ..||++|+|+.++ +.+|+++++.++..   +.+|+
T Consensus         6 ~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~~~~--~~~dlvi~d~~~~~~~~g~~~~~~l~~~~~~~~~~i   83 (127)
T 2gkg_A            6 KKILIVESDTALSATLRSALEGRGFTVDETTDGKGSVEQIRR--DRPDLVVLAVDLSAGQNGYLICGKLKKDDDLKNVPI   83 (127)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHHTCEEEEECCHHHHHHHHHH--HCCSEEEEESBCGGGCBHHHHHHHHHHSTTTTTSCE
T ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCceEEEecCHHHHHHHHHh--cCCCEEEEeCCCCCCCCHHHHHHHHhcCccccCCCE
Confidence            589999999999999999999999999999999999999874  4599999999999 99999999999654   68899


Q ss_pred             EEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           94 IMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        94 Ii~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      |++ +..+......+++.|+++|+.||++.++|...++.+++.
T Consensus        84 i~~-~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~~~~  125 (127)
T 2gkg_A           84 VII-GNPDGFAQHRKLKAHADEYVAKPVDADQLVERAGALIGF  125 (127)
T ss_dssp             EEE-ECGGGHHHHHHSTTCCSEEEESSCCHHHHHHHHHHHHCC
T ss_pred             EEE-ecCCchhHHHHHHhCcchheeCCCCHHHHHHHHHHHHcC
Confidence            999 777778888999999999999999999999999988763

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

Probab=99.83  E-value=3.9e-20  Score=127.64  Aligned_cols=122  Identities=21%  Similarity=0.299  Sum_probs=105.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIM   95 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi   95 (184)
                      .++|+|+||++..+..++..|+..++.+..+.+.++++..+.  .. ||+||+|+.|++.+|+++++.++. .+.+|+|+
T Consensus         3 ~~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~--~~-~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~ii~   79 (135)
T 3eqz_A            3 LNRVFIVDDDTLTCNLLKTIVEPIFGNVEAFQHPRAFLTLSL--NK-QDIIILDLMMPDMDGIEVIRHLAEHKSPASLIL   79 (135)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHTTTCSCEEEESCHHHHTTSCC--CT-TEEEEEECCTTTTHHHHHHHHHHHTTCCCEEEE
T ss_pred             cceEEEEeCCHHHHHHHHHHHHhhcceeeeecCHHHHHHhhc--cC-CCEEEEeCCCCCCCHHHHHHHHHhCCCCCCEEE
Confidence            468999999999999999999988889999999999988765  45 999999999999999999999964 46889999


Q ss_pred             EEccCCh-----HHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCCCC
Q 029986           96 MSVDGCT-----QDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPFE  141 (184)
Q Consensus        96 ~~~~~~~-----~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~~  141 (184)
                      +++..+.     .....+++.|+++|+.||++.++|..+++.+..+....+
T Consensus        80 ~s~~~~~~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~l~~~~~~~~~~~  130 (135)
T 3eqz_A           80 ISGYDSGVLHSAETLALSCGLNVINTFTKPINTEVLTCFLTSLSNRQAEGH  130 (135)
T ss_dssp             EESSCHHHHHHHHHHHHHTTCEEEEEEESSCCHHHHHHHHHHHSCCC----
T ss_pred             EEeccchhHHHHHHHHHHcCCCcceeeCCCCCHHHHHHHHHHHHhhccccc
Confidence            9887664     566678999999999999999999999999987765443

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

Probab=99.82  E-value=6.4e-20  Score=128.58  Aligned_cols=120  Identities=21%  Similarity=0.324  Sum_probs=98.8

Q ss_pred             CCCCCeEEEEeCCHHHHHHHHHHHHhc-CCeE-EEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCC
Q 029986           14 FPAGLRVLVVDDDPIWLRILEKMLRKC-LYEV-TKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDL   91 (184)
Q Consensus        14 ~~~~~~Ilivdd~~~~~~~l~~~L~~~-~~~v-~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~   91 (184)
                      .+++.+|+|+||++..+..++.+|+.. |+.+ ..+.++.++++.+... ..||+||+|+.||+.+|+++++.++.....
T Consensus        10 ~~~~~~vlivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~al~~l~~~-~~~dlvilD~~l~~~~g~~~~~~lr~~~~~   88 (145)
T 3kyj_B           10 HGSPYNVMIVDDAAMMRLYIASFIKTLPDFKVVAQAANGQEALDKLAAQ-PNVDLILLDIEMPVMDGMEFLRHAKLKTRA   88 (145)
T ss_dssp             -CCSEEEEEECSCHHHHHHHHHHHTTCTTEEEEEEESSHHHHHHHHHHC-TTCCEEEECTTSCCCTTCHHHHHHHHHCCC
T ss_pred             CCCCCeEEEEcCCHHHHHHHHHHHHhCCCceEEEEECCHHHHHHHHhcC-CCCCEEEEeCCCCCCCHHHHHHHHHhcCCC
Confidence            344568999999999999999999987 8875 4899999999998732 269999999999999999999999766668


Q ss_pred             CEEEEEc--cCChHHHHHHHHcCCCceEeCCCC----------HHHHHHHHHHHH
Q 029986           92 PVIMMSV--DGCTQDVMKGVTHGACNYLLKPIR----------IKELRNIWQHVA  134 (184)
Q Consensus        92 ~iIi~~~--~~~~~~~~~a~~~ga~~~l~kP~~----------~~~l~~~l~~~~  134 (184)
                      |+++++.  ..+......+++.|+++|+.||++          ..++.++++.++
T Consensus        89 ~iiil~~~~~~~~~~~~~~~~~ga~~~l~KP~~~~~l~~~i~~~~~l~~~i~~~~  143 (145)
T 3kyj_B           89 KICMLSSVAVSGSPHAARARELGADGVVAKPSGTVSHDLEEKTGGELARTMRTLM  143 (145)
T ss_dssp             EEC-CBSSCSTTSSHHHHHHHTTCSCCCBCCCSCC------CTTHHHHHHHHHHH
T ss_pred             CeEEEEEeccCChHHHHHHHhCCCCEEEeCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            8888886  455667789999999999999998          455565555554

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

Probab=99.82  E-value=1.7e-19  Score=125.71  Aligned_cols=121  Identities=23%  Similarity=0.376  Sum_probs=100.1

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc------cCC
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL------EMD   90 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~------~~~   90 (184)
                      .++|+|+||++..+..+...|...|+.+..+.++.++++.+.  ...||++|+|+.||+.+|+++++.++.      .+.
T Consensus        10 ~~~iLivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~al~~l~--~~~~dlvllD~~lp~~~g~~~~~~l~~~~~~~~~~~   87 (140)
T 3c97_A           10 PLSVLIAEDNDICRLVAAKALEKCTNDITVVTNGLQALQAYQ--NRQFDVIIMDIQMPVMDGLEAVSEIRNYERTHNTKR   87 (140)
T ss_dssp             CCEEEEECCCHHHHHHHHHHHTTTCSEEEEESSHHHHHHHHH--HSCCSEEEECTTCCSSCHHHHHHHHHHHHHHHTCCC
T ss_pred             CceEEEEcCCHHHHHHHHHHHHHcCCceEEECCHHHHHHHHh--cCCCCEEEEeCCCCCCcHHHHHHHHHhhhhhcCCCc
Confidence            358999999999999999999988999999999999999987  355999999999999999999999964      257


Q ss_pred             CCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCCCCC
Q 029986           91 LPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPFEE  142 (184)
Q Consensus        91 ~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~~~  142 (184)
                      +|+++++.........   +.|+++|+.||++.++|..+++.+..+..+++.
T Consensus        88 ~~ii~~s~~~~~~~~~---~~g~~~~l~KP~~~~~L~~~i~~~~~~~~~~~~  136 (140)
T 3c97_A           88 ASIIAITADTIDDDRP---GAELDEYVSKPLNPNQLRDVVLTCHSEGAEGHH  136 (140)
T ss_dssp             CCCEEEESSCCSCCCC---CSSCSEEEESSCCHHHHHHHHHHHHC-------
T ss_pred             eEEEEEeCccchhHHH---hCChhheEeCCCCHHHHHHHHHHHhCCCCCCcc
Confidence            8899988755443332   789999999999999999999999887665543

>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=99.82  E-value=1.2e-19  Score=136.73  Aligned_cols=120  Identities=32%  Similarity=0.447  Sum_probs=109.8

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIM   95 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi   95 (184)
                      .++|+|+||++..+..+...|...|+.+..+.++.++++.+.  ...||++|+|+.||+.+|+++++.++. .+.+|||+
T Consensus         7 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~~~--~~~~dlvllD~~l~~~~g~~~~~~l~~~~~~~~ii~   84 (233)
T 1ys7_A            7 SPRVLVVDDDSDVLASLERGLRLSGFEVATAVDGAEALRSAT--ENRPDAIVLDINMPVLDGVSVVTALRAMDNDVPVCV   84 (233)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HSCCSEEEEESSCSSSCHHHHHHHHHHTTCCCCEEE
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHhCCCEEEEECCHHHHHHHHH--hCCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCCEEE
Confidence            468999999999999999999999999999999999999987  356999999999999999999999964 46899999


Q ss_pred             EEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCC
Q 029986           96 MSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPK  138 (184)
Q Consensus        96 ~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~  138 (184)
                      ++...+......+++.|+++|+.||++.++|..+++.++++..
T Consensus        85 lt~~~~~~~~~~~~~~ga~~~l~Kp~~~~~L~~~i~~~~~~~~  127 (233)
T 1ys7_A           85 LSARSSVDDRVAGLEAGADDYLVKPFVLAELVARVKALLRRRG  127 (233)
T ss_dssp             EECCCTTTCCCTTTTTTCSEEEESSCCHHHHHHHHHHHHHHHH
T ss_pred             EEcCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHhhcc
Confidence            9998888888899999999999999999999999999887643

>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=99.82  E-value=3e-19  Score=145.02  Aligned_cols=116  Identities=22%  Similarity=0.455  Sum_probs=107.5

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIMM   96 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi~   96 (184)
                      ++|+||||++..+..++..|...||.+..+.++.++++.+.  ...||+||+|+.||+++|+++++.++. .+++|||++
T Consensus         1 m~ILIVDDd~~~~~~l~~~L~~~g~~v~~a~~~~eal~~l~--~~~~DlvllD~~mp~~dG~ell~~lr~~~~~~pvIvl   78 (387)
T 1ny5_A            1 MNVLVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLLS--EKHFNVVLLDLLLPDVNGLEILKWIKERSPETEVIVI   78 (387)
T ss_dssp             CEEEEECCCHHHHHHHHHHHHHHTCEEEEESSHHHHHHHHH--HSCCSEEEEESBCSSSBHHHHHHHHHHHCTTSEEEEE
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHH--hCCCCEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEE
Confidence            57999999999999999999988999999999999999987  456999999999999999999999964 478999999


Q ss_pred             EccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           97 SVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        97 ~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      |...+.+...++++.||++|+.||++.++|..+++.++.
T Consensus        79 T~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~l~  117 (387)
T 1ny5_A           79 TGHGTIKTAVEAMKMGAYDFLTKPCMLEEIELTINKAIE  117 (387)
T ss_dssp             EETTCHHHHHHHHTTTCCEEEEESCCHHHHHHHHHHHHH
T ss_pred             eCCCCHHHHHHHHhcCceEEecCCCCHHHHHHHHHHHHH
Confidence            999989999999999999999999999999998888765

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

Probab=99.82  E-value=9.2e-19  Score=121.39  Aligned_cols=119  Identities=18%  Similarity=0.246  Sum_probs=105.9

Q ss_pred             ccCCCCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccC-C
Q 029986           12 DQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEM-D   90 (184)
Q Consensus        12 ~~~~~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~-~   90 (184)
                      .....+.+|+|+||++..+..+...|...|+.+..+.++.++++.+.  ...||++|    +++.+|+++++.++..+ .
T Consensus        13 ~~~~~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~--~~~~dlvi----~~~~~g~~~~~~l~~~~~~   86 (137)
T 2pln_A           13 LVPRGSMRVLLIEKNSVLGGEIEKGLNVKGFMADVTESLEDGEYLMD--IRNYDLVM----VSDKNALSFVSRIKEKHSS   86 (137)
T ss_dssp             --CTTCSEEEEECSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHHHH--HSCCSEEE----ECSTTHHHHHHHHHHHSTT
T ss_pred             ccCCCCCeEEEEeCCHHHHHHHHHHHHHcCcEEEEeCCHHHHHHHHH--cCCCCEEE----EcCccHHHHHHHHHhcCCC
Confidence            44445779999999999999999999999999999999999999987  35699999    88999999999996547 7


Q ss_pred             CCEEEEEccCChHHHHHHHHcCCCceEeCCC-CHHHHHHHHHHHHcC
Q 029986           91 LPVIMMSVDGCTQDVMKGVTHGACNYLLKPI-RIKELRNIWQHVAQQ  136 (184)
Q Consensus        91 ~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~-~~~~l~~~l~~~~~~  136 (184)
                      +|||+++...+......+++.|+++|+.||+ +.++|..+++.++++
T Consensus        87 ~~ii~ls~~~~~~~~~~~~~~g~~~~l~kP~~~~~~l~~~i~~~~~~  133 (137)
T 2pln_A           87 IVVLVSSDNPTSEEEVHAFEQGADDYIAKPYRSIKALVARIEARLRF  133 (137)
T ss_dssp             SEEEEEESSCCHHHHHHHHHTTCSEEEESSCSCHHHHHHHHHHHTC-
T ss_pred             ccEEEEeCCCCHHHHHHHHHcCCceeeeCCCCCHHHHHHHHHHHHhh
Confidence            9999999988888999999999999999999 999999999988764

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

Probab=99.82  E-value=1.2e-18  Score=119.70  Aligned_cols=121  Identities=21%  Similarity=0.329  Sum_probs=105.4

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCC-CccEEEEeCCCCC-CCHHHHHHHhcc-cCCCCE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKN-GYDIVISDVHMPD-MDGFKLHEQVGL-EMDLPV   93 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~-~~dlvilD~~l~~-~~g~~l~~~l~~-~~~~~i   93 (184)
                      +++|+|+||++..+..+...|...|+.+..+.++.++++.+.  .. .||++|+|+.+++ .+|+++++.++. .+.+|+
T Consensus         5 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--~~~~~dlvi~d~~l~~~~~g~~~~~~l~~~~~~~~i   82 (132)
T 2rdm_A            5 AVTILLADDEAILLLDFESTLTDAGFLVTAVSSGAKAIEMLK--SGAAIDGVVTDIRFCQPPDGWQVARVAREIDPNMPI   82 (132)
T ss_dssp             SCEEEEECSSHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--TTCCCCEEEEESCCSSSSCHHHHHHHHHHHCTTCCE
T ss_pred             CceEEEEcCcHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHH--cCCCCCEEEEeeeCCCCCCHHHHHHHHHhcCCCCCE
Confidence            568999999999999999999998999999999999999987  44 6999999999997 999999999964 468999


Q ss_pred             EEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCCCC
Q 029986           94 IMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPFE  141 (184)
Q Consensus        94 Ii~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~~  141 (184)
                      |+++...+......++..|  +|+.||++.++|..+++.+..+....+
T Consensus        83 i~~s~~~~~~~~~~~~~~~--~~l~kP~~~~~l~~~i~~~~~~~~~~~  128 (132)
T 2rdm_A           83 VYISGHAALEWASNGVPDS--IILEKPFTSAQLITAVSQLLNAREGHH  128 (132)
T ss_dssp             EEEESSCCTTHHHHSCTTC--EEEESSCCHHHHHHHHHHHHHTTC---
T ss_pred             EEEeCCccHHHHHhhcCCc--ceEeCCCCHHHHHHHHHHHHhcCCCCC
Confidence            9999888777777776665  799999999999999999988765443

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

Probab=99.81  E-value=7.1e-19  Score=122.36  Aligned_cols=115  Identities=23%  Similarity=0.344  Sum_probs=102.4

Q ss_pred             eEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEEEE
Q 029986           19 RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIMMS   97 (184)
Q Consensus        19 ~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi~~   97 (184)
                      +|+|+||++..+..++..|... +.+..+.++.++++.+.  ...||++|+|+.||+.+|+++++.++. .+.+|+|+++
T Consensus         3 ~Ilivdd~~~~~~~l~~~l~~~-~~v~~~~~~~~a~~~~~--~~~~dlvl~D~~lp~~~g~~~~~~l~~~~~~~~ii~~s   79 (139)
T 2jk1_A            3 AILLVDDEPHSLAAMKLALEDD-FDVLTAQGAEAAIAILE--EEWVQVIICDQRMPGRTGVDFLTEVRERWPETVRIIIT   79 (139)
T ss_dssp             EEEEECSSHHHHHHHHHHHTTT-SCEEEESSHHHHHHHHH--HSCEEEEEEESCCSSSCHHHHHHHHHHHCTTSEEEEEE
T ss_pred             eEEEEcCCHHHHHHHHHHhhcC-ceEEEcCCHHHHHHHHh--cCCCCEEEEeCCCCCCcHHHHHHHHHHhCCCCcEEEEe
Confidence            7999999999999999999875 88999999999999987  345999999999999999999999964 4678999999


Q ss_pred             ccCChHHHHHHHHc-CCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           98 VDGCTQDVMKGVTH-GACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        98 ~~~~~~~~~~a~~~-ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      +..+......++.. |+++|+.||++.++|..+++.+.++
T Consensus        80 ~~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~i~~~~~~  119 (139)
T 2jk1_A           80 GYTDSASMMAAINDAGIHQFLTKPWHPEQLLSSARNAARM  119 (139)
T ss_dssp             SCTTCHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHHHH
T ss_pred             CCCChHHHHHHHHhhchhhhccCCCCHHHHHHHHHHHHHH
Confidence            88877788888876 5999999999999999999988653

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

Probab=99.81  E-value=1.6e-19  Score=146.61  Aligned_cols=117  Identities=25%  Similarity=0.481  Sum_probs=103.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIM   95 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi   95 (184)
                      +++|+||||++..+..++.+|+..|+.+..+.++.++++.+.  ...||+||+|+.||+++|++++++++. .+++|||+
T Consensus         5 ~~~iLivdD~~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~~--~~~~dlvllD~~mp~~~G~~~~~~lr~~~~~~pii~   82 (394)
T 3eq2_A            5 SATLLIIDDDEVVRESLAAYLEDSNFKVLQALNGLQGLQIFE--SEQPDLVICDLRMPQIDGLELIRRIRQTASETPIIV   82 (394)
T ss_dssp             EEEEEEECSCHHHHHHHHHHHHHTTEEEEECSSHHHHHHHHH--HSCCSEEEECCCSSSSCTHHHHHHHHHTTCCCCEEE
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHhCCCEEEEECCHHHHHHHHh--hCCCCEEEEcCCCCCCCHHHHHHHHHhhCCCCcEEE
Confidence            468999999999999999999999999999999999999987  456999999999999999999999964 46899999


Q ss_pred             EEccCChHHHHHHHHcCCCceEeCCC-CHHHHHHHHHHHHc
Q 029986           96 MSVDGCTQDVMKGVTHGACNYLLKPI-RIKELRNIWQHVAQ  135 (184)
Q Consensus        96 ~~~~~~~~~~~~a~~~ga~~~l~kP~-~~~~l~~~l~~~~~  135 (184)
                      +|+..+.+...++++.|+++|+.||+ ..+.|..+++.+++
T Consensus        83 lt~~~~~~~~~~a~~~ga~~yl~KP~~~~~~l~~~i~~~~~  123 (394)
T 3eq2_A           83 LSGAGVMSDAVEALRLGAADYLIKPLEDLAVLEHSVRRALD  123 (394)
T ss_dssp             C---CHHHHHHHHHHHTCSEECCSSCSCTHHHHHHHHHHHH
T ss_pred             EEcCCCHHHHHHHHhcChhhEEECCCChHHHHHHHHHHHHh
Confidence            99988889999999999999999999 67888888777664

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

Probab=99.81  E-value=7.9e-19  Score=125.87  Aligned_cols=119  Identities=21%  Similarity=0.258  Sum_probs=101.3

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcC-C-eEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCL-Y-EVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVI   94 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~-~-~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iI   94 (184)
                      .++|+||||++..+..++..|...+ + .+..+.++.++++.+..  ..||+||+|+.|++.+|+++++.++.....|+|
T Consensus        25 ~~~ILivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~al~~l~~--~~~dlvilD~~l~~~~g~~l~~~lr~~~~~~ii  102 (164)
T 3t8y_A           25 VIRVLVVDDSAFMRMVLKDIIDSQPDMKVVGFAKDGLEAVEKAIE--LKPDVITMDIEMPNLNGIEALKLIMKKAPTRVI  102 (164)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHHHH--HCCSEEEECSSCSSSCHHHHHHHHHHHSCCEEE
T ss_pred             ccEEEEEcCCHHHHHHHHHHHhcCCCeEEEEecCCHHHHHHHhcc--CCCCEEEEeCCCCCCCHHHHHHHHHhcCCceEE
Confidence            5689999999999999999999874 3 35579999999999874  459999999999999999999999765558999


Q ss_pred             EEEccCChH--HHHHHHHcCCCceEeCCCC---------HHHHHHHHHHHHcCC
Q 029986           95 MMSVDGCTQ--DVMKGVTHGACNYLLKPIR---------IKELRNIWQHVAQQP  137 (184)
Q Consensus        95 i~~~~~~~~--~~~~a~~~ga~~~l~kP~~---------~~~l~~~l~~~~~~~  137 (184)
                      +++...+..  ....+++.|+++|+.||++         .+++...++.++...
T Consensus       103 ~~s~~~~~~~~~~~~~~~~ga~~~l~KP~~~~~l~~r~~~~~l~~~i~~~~~~~  156 (164)
T 3t8y_A          103 MVSSLTEEGAAITIEALRNGAVDFITKPHGSISLTFRQVAPELLEKIRQAMNVD  156 (164)
T ss_dssp             EEESSCCTTCHHHHHHHHTTCCEEEECSSSSSCGGGGGGHHHHHHHHHHHTTSC
T ss_pred             EEecCCccchHHHHHHHHcCcCEEEeCCCCHHHHHHHhhhHHHHHHHHHHhCCC
Confidence            998866543  6778999999999999999         678888888776643

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

Probab=99.81  E-value=3.8e-20  Score=139.28  Aligned_cols=124  Identities=9%  Similarity=-0.034  Sum_probs=105.5

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHh-cCCeEEE-ECCHHHHHH-HHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc--cCC
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRK-CLYEVTK-CNRAEIALD-MLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL--EMD   90 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~-~~~~v~~-~~~~~~~~~-~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~--~~~   90 (184)
                      ..++|+||||++..+..++.+|+. .|+.+.. +.++.++.. .+.  ...||+||+|+.||+++|+++++.++.  .++
T Consensus         6 ~~~~IlivdD~~~~~~~l~~~L~~~~~~~v~~~~~~~~~~~~~~~~--~~~~dlvllD~~mp~~~G~~~~~~lr~~~~~~   83 (225)
T 3klo_A            6 NKLNVRMLSDVCMQSRLLKEALESKLPLALEITPFSELWLEENKPE--SRSIQMLVIDYSRISDDVLTDYSSFKHISCPD   83 (225)
T ss_dssp             SSEEEEEESCCSHHHHHHHHHHHHHSSEEEEEECGGGHHHHTTCSG--GGGCCEEEEEGGGCCHHHHHHHHHHHHHHCTT
T ss_pred             CceEEEEEcCcHHHHHHHHHHHhhCCCceEEEEeCCcHHHHHHHhh--ccCCCEEEEeCCCCCCCHHHHHHHHHHhhCCC
Confidence            467999999999999999999985 5887754 344444443 343  456999999999999999999999975  578


Q ss_pred             CCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCCCC
Q 029986           91 LPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPFE  141 (184)
Q Consensus        91 ~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~~  141 (184)
                      +|||++|+..+......+++.||++|+.||++.++|..+++.++++..+++
T Consensus        84 ~~ii~lt~~~~~~~~~~~~~~Ga~~~l~Kp~~~~~L~~~i~~~~~~~~~~~  134 (225)
T 3klo_A           84 AKEVIINCPQDIEHKLLFKWNNLAGVFYIDDDMDTLIKGMSKILQDEMWLT  134 (225)
T ss_dssp             CEEEEEEECTTCCHHHHTTSTTEEEEEETTCCHHHHHHHHHHHHTTCCBCC
T ss_pred             CcEEEEECCcchhHHHHHHHhCCCEEEecCCCHHHHHHHHHHHHCCCEeeC
Confidence            999999998888888899999999999999999999999999998876554

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

Probab=99.81  E-value=4.6e-19  Score=118.97  Aligned_cols=113  Identities=17%  Similarity=0.167  Sum_probs=101.2

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc---CCCCEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE---MDLPVI   94 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~---~~~~iI   94 (184)
                      .+|+|+|+++..+..+...|...|+.+..+.+..++++.+..  ..||++|+|+.+++.+|+++++.++..   +.+|+|
T Consensus         2 ~~iliv~~~~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~l~~--~~~dlii~d~~~~~~~~~~~~~~l~~~~~~~~~~ii   79 (119)
T 2j48_A            2 GHILLLEEEDEAATVVCEMLTAAGFKVIWLVDGSTALDQLDL--LQPIVILMAWPPPDQSCLLLLQHLREHQADPHPPLV   79 (119)
T ss_dssp             CEEEEECCCHHHHHHHHHHHHHTTCEEEEESCHHHHHHHHHH--HCCSEEEEECSTTCCTHHHHHHHHHHTCCCSSCCCE
T ss_pred             CEEEEEeCCHHHHHHHHHHHHhCCcEEEEecCHHHHHHHHHh--cCCCEEEEecCCCCCCHHHHHHHHHhccccCCCCEE
Confidence            589999999999999999999999999999999999999874  459999999999999999999999654   678999


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      +++......   .++..|+++|+.||++.++|...++.+..
T Consensus        80 ~~~~~~~~~---~~~~~g~~~~l~kp~~~~~l~~~l~~~~~  117 (119)
T 2j48_A           80 LFLGEPPVD---PLLTAQASAILSKPLDPQLLLTTLQGLCP  117 (119)
T ss_dssp             EEESSCCSS---HHHHHHCSEECSSCSTTHHHHHHHHTTCC
T ss_pred             EEeCCCCch---hhhhcCHHHhccCCCCHHHHHHHHHHHhc
Confidence            998776555   88999999999999999999998887644

>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=99.80  E-value=7e-19  Score=145.23  Aligned_cols=116  Identities=32%  Similarity=0.466  Sum_probs=106.4

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc---CCCCEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE---MDLPVI   94 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~---~~~~iI   94 (184)
                      .+|+||||++..+..+...|...|+.+..+.++.++++.+..  ..||+||+|+.||+++|+++++.++..   +++|||
T Consensus         2 ~~iLivdD~~~~~~~l~~~L~~~~~~v~~a~~~~~al~~~~~--~~~dlvllD~~mp~~~G~~~~~~l~~~~~~~~~pii   79 (459)
T 1w25_A            2 ARILVVDDIEANVRLLEAKLTAEYYEVSTAMDGPTALAMAAR--DLPDIILLDVMMPGMDGFTVCRKLKDDPTTRHIPVV   79 (459)
T ss_dssp             CEEEEECSSTTHHHHHHHHHHHTTCEEEEESSHHHHHHHHHH--HCCSEEEEESCCSSSCHHHHHHHHHHSTTTTTSCEE
T ss_pred             CeEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHhc--CCCCEEEEcCCCCCCCHHHHHHHHhcCcccCCCCEE
Confidence            479999999999999999999989999999999999999873  459999999999999999999999753   478999


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      ++|+..+......+++.||++|+.||++.++|..+++.+.+
T Consensus        80 ~lt~~~~~~~~~~a~~~Ga~~~l~KP~~~~~l~~~i~~~~~  120 (459)
T 1w25_A           80 LITALDGRGDRIQGLESGASDFLTKPIDDVMLFARVRSLTR  120 (459)
T ss_dssp             EEECSSCHHHHHHHHHHTCCEEEESSCCHHHHHHHHHHHHH
T ss_pred             EEECCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHH
Confidence            99999989999999999999999999999999998887754

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

Probab=99.80  E-value=5.5e-20  Score=138.53  Aligned_cols=121  Identities=21%  Similarity=0.320  Sum_probs=108.9

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcC-Ce-EEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCL-YE-VTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVI   94 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~-~~-v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iI   94 (184)
                      ++|+||||++..+..+...|...| +. +..+.++.++++.+..  ..||+||+|+.||+.+|+++++.++. .+.+|||
T Consensus         2 ~~ILivdd~~~~~~~l~~~L~~~~~~~vv~~~~~~~~al~~l~~--~~~dlvllD~~lp~~~g~~~~~~lr~~~~~~~ii   79 (225)
T 3c3w_A            2 VKVFLVDDHEVVRRGLVDLLGADPELDVVGEAGSVAEAMARVPA--ARPDVAVLDVRLPDGNGIELCRDLLSRMPDLRCL   79 (225)
T ss_dssp             EEEEEECSCHHHHHHHHHHHHTCTTEEEEEEESSHHHHHHHHHH--HCCSEEEECSEETTEEHHHHHHHHHHHCTTCEEE
T ss_pred             cEEEEEcCCHHHHHHHHHHHhcCCCcEEEEEECCHHHHHHHHhh--cCCCEEEEeCCCCCCCHHHHHHHHHHhCCCCcEE
Confidence            689999999999999999999876 77 4579999999999873  45999999999999999999999964 4789999


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCCC
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPF  140 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~  140 (184)
                      ++++..+......+++.|+++|+.||++.++|..+++.+.++...+
T Consensus        80 ~lt~~~~~~~~~~~~~~Ga~~~l~Kp~~~~~L~~~i~~~~~~~~~~  125 (225)
T 3c3w_A           80 ILTSYTSDEAMLDAILAGASGYVVKDIKGMELARAVKDVGAGRSLL  125 (225)
T ss_dssp             EGGGSSSHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHHGGGS
T ss_pred             EEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHcCCeee
Confidence            9999888899999999999999999999999999999998875544

>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=99.79  E-value=1e-18  Score=130.65  Aligned_cols=116  Identities=24%  Similarity=0.356  Sum_probs=106.3

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc-CCCCEEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE-MDLPVIMM   96 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~-~~~~iIi~   96 (184)
                      ++|+|+||++..+..+...|...| .+..+.++.++++.+    ..||++|+|+.||+.+|+++++.++.. +.+|||++
T Consensus         3 ~~ilivdd~~~~~~~l~~~L~~~~-~v~~~~~~~~al~~~----~~~dlvllD~~lp~~~g~~~~~~lr~~~~~~~ii~l   77 (220)
T 1p2f_A            3 WKIAVVDDDKNILKKVSEKLQQLG-RVKTFLTGEDFLNDE----EAFHVVVLDVMLPDYSGYEICRMIKETRPETWVILL   77 (220)
T ss_dssp             EEEEEECSCHHHHHHHHHHHTTTE-EEEEESSHHHHHHCC----SCCSEEEEESBCSSSBHHHHHHHHHHHCTTSEEEEE
T ss_pred             ceEEEEeCCHHHHHHHHHHHHhCC-CEEEECCHHHHHHhc----CCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCcEEEE
Confidence            589999999999999999999888 888999999998765    459999999999999999999999754 78999999


Q ss_pred             EccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCC
Q 029986           97 SVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPK  138 (184)
Q Consensus        97 ~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~  138 (184)
                      +...+......+++.|+++|+.||++.++|..+++.++++..
T Consensus        78 t~~~~~~~~~~~~~~ga~~~l~Kp~~~~~L~~~i~~~~~~~~  119 (220)
T 1p2f_A           78 TLLSDDESVLKGFEAGADDYVTKPFNPEILLARVKRFLEREK  119 (220)
T ss_dssp             ESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHHHHCC
T ss_pred             EcCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHHcccc
Confidence            999888899999999999999999999999999999987643

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

Probab=99.79  E-value=6.4e-18  Score=117.83  Aligned_cols=117  Identities=19%  Similarity=0.344  Sum_probs=99.8

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhc-CCe-EEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccC-CCC
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKC-LYE-VTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEM-DLP   92 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~-~~~-v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~-~~~   92 (184)
                      ..++|+|+||++..+..+...|... ++. +..+.++.++++.+..  ..||+||+|+.+++.+|+++++.++... ..|
T Consensus         8 ~~~~iLivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~al~~l~~--~~~dlvi~d~~l~~~~g~~~~~~l~~~~~~~~   85 (143)
T 2qv0_A            8 EKMKVIIVEDEFLAQQELSWLINTHSQMEIVGSFDDGLDVLKFLQH--NKVDAIFLDINIPSLDGVLLAQNISQFAHKPF   85 (143)
T ss_dssp             --CEEEEECSCHHHHHHHHHHHHHHSCCEEEEEESCHHHHHHHHHH--CCCSEEEECSSCSSSCHHHHHHHHTTSTTCCE
T ss_pred             CceEEEEEcCCHHHHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHh--CCCCEEEEecCCCCCCHHHHHHHHHccCCCce
Confidence            3579999999999999999999876 787 4589999999999873  4599999999999999999999997554 556


Q ss_pred             EEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           93 VIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        93 iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      ||+++..  .+....+++.|+++|+.||++.++|..+++.+.++
T Consensus        86 ii~~s~~--~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~~~  127 (143)
T 2qv0_A           86 IVFITAW--KEHAVEAFELEAFDYILKPYQESRIINMLQKLTTA  127 (143)
T ss_dssp             EEEEESC--CTTHHHHHHTTCSEEEESSCCHHHHHHHHHHHHHH
T ss_pred             EEEEeCC--HHHHHHHHhCCcceEEeCCCCHHHHHHHHHHHHHH
Confidence            7878765  34677899999999999999999999999988753

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

Probab=99.78  E-value=3.7e-18  Score=127.88  Aligned_cols=114  Identities=18%  Similarity=0.269  Sum_probs=105.6

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccC-CCCEEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEM-DLPVIMM   96 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~-~~~iIi~   96 (184)
                      |+|+||||++..+..+...|...|+.+..+.++.++++.+.  ...||++|    ||+.+|+++++.++..+ ++|||++
T Consensus         1 m~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~--~~~~dlvi----lp~~~g~~~~~~lr~~~~~~~ii~l   74 (223)
T 2hqr_A            1 MRVLLIEKNSVLGGEIEKGLNVKGFMADVTESLEDGEYLMD--IRNYDLVM----VSDKNALSFVSRIKEKHSSIVVLVS   74 (223)
T ss_dssp             CCEEEECSCHHHHHHHHHHHGGGTCCEEEESSHHHHHHHHT--TSCCSEEE----ECCTTHHHHHHHHHHHCTTSEEEEE
T ss_pred             CEEEEEcCCHHHHHHHHHHHHHCCcEEEEECCHHHHHHHHh--cCCCCEEE----eCCCCHHHHHHHHHhCCCCCcEEEE
Confidence            57999999999999999999999999999999999999987  55699999    89999999999996556 8999999


Q ss_pred             EccCChHHHHHHHHcCCCceEeCCC-CHHHHHHHHHHHHcCC
Q 029986           97 SVDGCTQDVMKGVTHGACNYLLKPI-RIKELRNIWQHVAQQP  137 (184)
Q Consensus        97 ~~~~~~~~~~~a~~~ga~~~l~kP~-~~~~l~~~l~~~~~~~  137 (184)
                      ++..+......+++.||++|+.||+ +.++|..+++.++++.
T Consensus        75 t~~~~~~~~~~~~~~Ga~~~l~Kp~~~~~~L~~~i~~~~~~~  116 (223)
T 2hqr_A           75 SDNPTSEEEVHAFEQGADDYIAKPYRSIKALVARIEARLRFW  116 (223)
T ss_dssp             ESSCCHHHHHHHHHHTCSEEEETTCSCTHHHHHHHHHHTSSC
T ss_pred             ECCCCHHHHHHHHHcCCCEEEECCCCCHHHHHHHHHHHhccc
Confidence            9998899999999999999999999 9999999999998875

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

Probab=99.77  E-value=2.4e-18  Score=137.62  Aligned_cols=115  Identities=22%  Similarity=0.296  Sum_probs=103.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHh-cCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc---CCCC
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRK-CLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE---MDLP   92 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~-~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~---~~~~   92 (184)
                      ..+|+||||++..+..++..|.. .|+.+..+.++.++++.+..  ..||+||+|+.||+++|+++++.++..   +.+|
T Consensus        18 ~~~ilivdD~~~~~~~l~~~l~~~~~~~v~~~~~~~~al~~~~~--~~~dlvl~D~~mp~~~G~~~~~~l~~~~~~~~~~   95 (358)
T 3bre_A           18 AVMVLLVDDQAMIGEAVRRSLASEAGIDFHFCSDPQQAVAVANQ--IKPTVILQDLVMPGVDGLTLLAAYRGNPATRDIP   95 (358)
T ss_dssp             CEEEEEECSCTTHHHHHHTTSSSCTTEEEEEECCHHHHHHHHHH--HCCSEEEEESBCSSSBHHHHHHHHTTSTTTTTSC
T ss_pred             CceEEEEECCHHHHHHHHHHHHhccCcEEEEeCCHHHHHHHHHh--CCCCEEEEeCCCCCCCHHHHHHHHhcCcccCCCc
Confidence            35799999999999999999974 58999999999999999873  459999999999999999999999753   4789


Q ss_pred             EEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHH
Q 029986           93 VIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHV  133 (184)
Q Consensus        93 iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~  133 (184)
                      ||++|+..+......+++.|+++|+.||++.++|..++..+
T Consensus        96 ii~~s~~~~~~~~~~a~~~Ga~~~l~Kp~~~~~l~~~v~~~  136 (358)
T 3bre_A           96 IIVLSTKEEPTVKSAAFAAGANDYLVKLPDAIELVARIRYH  136 (358)
T ss_dssp             EEEEESSCCHHHHHHHHHTTCSEEEESCCCHHHHHHHHHHH
T ss_pred             EEEEeCCCCHHHHHHHHhcChheEeeccCCHHHHHHHHHHH
Confidence            99999998899999999999999999999999998888765

>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=99.77  E-value=2.7e-18  Score=119.13  Aligned_cols=116  Identities=21%  Similarity=0.236  Sum_probs=99.9

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcC-CCccEEEEeCCCCCCCHHHHHHHhcc-cCCCC
Q 029986           15 PAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSK-NGYDIVISDVHMPDMDGFKLHEQVGL-EMDLP   92 (184)
Q Consensus        15 ~~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~-~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~   92 (184)
                      ++..+|+|+||++..+..++..|+..|+.+..+.++.++++.+.  . ..||++|+|+.|++.+|+++++.++. .+.+|
T Consensus        13 ~~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~--~~~~~dlvilD~~l~~~~g~~~~~~l~~~~~~~~   90 (138)
T 2b4a_A           13 MQPFRVTLVEDEPSHATLIQYHLNQLGAEVTVHPSGSAFFQHRS--QLSTCDLLIVSDQLVDLSIFSLLDIVKEQTKQPS   90 (138)
T ss_dssp             -CCCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHTGG--GGGSCSEEEEETTCTTSCHHHHHHHHTTSSSCCE
T ss_pred             CCCCeEEEECCCHHHHHHHHHHHHHcCCEEEEeCCHHHHHHHHH--hCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCCCC
Confidence            34679999999999999999999999999999999999999886  4 46999999999999999999999965 36889


Q ss_pred             EEEEE-ccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           93 VIMMS-VDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        93 iIi~~-~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      +|+++ ...+... ..++   +++|+.||++.++|..+++.++++
T Consensus        91 ii~ls~~~~~~~~-~~~~---~~~~l~KP~~~~~L~~~i~~~~~~  131 (138)
T 2b4a_A           91 VLILTTGRHELIE-SSEH---NLSYLQKPFAISELRAAIDYHKPS  131 (138)
T ss_dssp             EEEEESCC--CCC-CSSS---CEEEEESSCCHHHHHHHHHHTCCC
T ss_pred             EEEEECCCCCHHH-HHHH---HHheeeCCCCHHHHHHHHHHHHHh
Confidence            99998 7665555 5555   999999999999999999987654

>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=99.77  E-value=3e-20  Score=126.26  Aligned_cols=118  Identities=30%  Similarity=0.409  Sum_probs=105.8

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIM   95 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi   95 (184)
                      ..+|+|+||++..+..+...|...|+.+..+.++.++++.+.  ...||++|+|+.+++.+|+++++.++. .+.+|+|+
T Consensus         3 ~~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~--~~~~dlvi~d~~~~~~~g~~~~~~l~~~~~~~~ii~   80 (124)
T 1dc7_A            3 RGIVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAALA--SKTPDVLLSDIRMPGMDGLALLKQIKQRHPMLPVII   80 (124)
T ss_dssp             CCCCEEECSSSSHHHHHHHHHTTTTCCCEECCCTTHHHHHSS--SCCCSCEEECSCSSHHHHCSTHHHHHHHCTTSCCCC
T ss_pred             ccEEEEEeCCHHHHHHHHHHHHhCCcEEEEeCCHHHHHHHHh--cCCCCEEEEeeecCCCCHHHHHHHHHhhCCCCCEEE
Confidence            347999999999999999999988999999999999999876  456999999999999999999999964 46889999


Q ss_pred             EEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           96 MSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        96 ~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      +++..+......+++.|+++|+.||++.++|..+++.+.++
T Consensus        81 ~s~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~~~~  121 (124)
T 1dc7_A           81 MTAHSDLDAAVSAYQQGAFDYLPKPFDIDEAVALVERAISH  121 (124)
T ss_dssp             BCCSTTSTTTTSSCTTCCCCCBCSSCCHHHHHHHHHHHHHH
T ss_pred             EecCCCHHHHHHHHhcCcceEeeCCCCHHHHHHHHHHHHHh
Confidence            99887778888999999999999999999999999988764

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

Probab=99.77  E-value=1.4e-18  Score=127.78  Aligned_cols=114  Identities=11%  Similarity=0.079  Sum_probs=100.5

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc-CCCCEE
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE-MDLPVI   94 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~-~~~~iI   94 (184)
                      .+++|+||||++..+..+...|...||.+..+.++.+++      ...||+||+|+.||+++|+ +++.++.. +++|+|
T Consensus        11 ~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al------~~~~dlvl~D~~mp~~~g~-l~~~~~~~~~~~~ii   83 (196)
T 1qo0_D           11 RELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAF------DVPVDVVFTSIFQNRHHDE-IAALLAAGTPRTTLV   83 (196)
T ss_dssp             GGCEEEEESCTTHHHHHHHHHHHHHTCEEEEECSCCSSC------SSCCSEEEEECCSSTHHHH-HHHHHHHSCTTCEEE
T ss_pred             cCCeEEEEcCChhHHHHHHHHHHHcCCeEEEecCchhhC------CCCCCEEEEeCCCCccchH-HHHHHhccCCCCCEE
Confidence            367999999999999999999998899988887766544      2459999999999999998 88888755 789999


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      ++++..+.+....+++.|+++|+.||++.++|..+++.+..+
T Consensus        84 ~lt~~~~~~~~~~a~~~ga~~~l~KP~~~~~L~~~l~~~~~~  125 (196)
T 1qo0_D           84 ALVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRI  125 (196)
T ss_dssp             EEECCCSHHHHHHHHHHTCSEEEESSCCGGGHHHHHHHHHHH
T ss_pred             EEEcCCChHHHHHHHHcCCCeeEecCcCHHHHHHHHHHHHHH
Confidence            999998899999999999999999999999999999877653

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

Probab=99.76  E-value=2.1e-18  Score=140.46  Aligned_cols=121  Identities=21%  Similarity=0.279  Sum_probs=102.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHh-cCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccC-CCCEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRK-CLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEM-DLPVI   94 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~-~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~-~~~iI   94 (184)
                      .++|+||||++..+..++..|+. .++.+..+.++.++++.+... ..||+||+|+.||+++|+++++.++... ..+||
T Consensus         3 ~~~ILivDD~~~~~~~l~~~L~~~~~~~v~~a~~g~eal~~l~~~-~~~DlvllDi~mP~~dG~ell~~l~~~~~~~~ii   81 (400)
T 3sy8_A            3 DLNVLVLEDEPFQRLVAVTALKKVVPGSILEAADGKEAVAILESC-GHVDIAICDLQMSGMDGLAFLRHASLSGKVHSVI   81 (400)
T ss_dssp             CEEEEEECSSHHHHHHHHHHHHHHCSEEEEEESSHHHHHHHHHHH-SCEEEEEECSSCSSSCHHHHHHHHHHHTCEEEEE
T ss_pred             CceEEEEcCCHHHHHHHHHHHHhcCCcEEEEecCHHHHHHHHhhC-CCCCEEEEeCCCCCCCHHHHHHHHHhcCCCceEE
Confidence            36899999999999999999998 578899999999999998731 3599999999999999999999997554 44555


Q ss_pred             EEEccCCh-----HHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCC
Q 029986           95 MMSVDGCT-----QDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPK  138 (184)
Q Consensus        95 i~~~~~~~-----~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~  138 (184)
                      +++.....     ....++++.|+++|+.||++.++|..+++.+.....
T Consensus        82 ~~s~~~~~~~~~~~~~~~a~~~ga~~yl~KP~~~~~L~~~i~~~~~~~~  130 (400)
T 3sy8_A           82 LSSEVDPILRQATISMIECLGLNFLGDLGKPFSLERITALLTRYNARRQ  130 (400)
T ss_dssp             ESCCCCGGGHHHHHHHHHTTTCEEEEECCSSCCHHHHHHHHHHHHHHTT
T ss_pred             EEcCchHHHHHHHHHHHHHcCCeeccCcCCCcCHHHHHHHHHHHHHhhh
Confidence            55555444     456788999999999999999999999999876543

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

Probab=99.73  E-value=6.7e-17  Score=129.47  Aligned_cols=119  Identities=24%  Similarity=0.370  Sum_probs=102.4

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhc-CCe-EEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKC-LYE-VTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVI   94 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~-~~~-v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iI   94 (184)
                      .++|+||||++..++.++..|+.. +++ +..+.++.++++.+..  ..||++++|+.||+++|+++++.++....+|||
T Consensus         3 ~~rVLIVDD~~~~r~~L~~~L~~~~g~~vv~~a~~~~eAl~~l~~--~~pDlVllDi~mp~~dGlell~~l~~~~p~pVI   80 (349)
T 1a2o_A            3 KIRVLSVDDSALMRQIMTEIINSHSDMEMVATAPDPLVARDLIKK--FNPDVLTLDVEMPRMDGLDFLEKLMRLRPMPVV   80 (349)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHHHH--HCCSEEEEECCCSSSCHHHHHHHHHHSSCCCEE
T ss_pred             CCEEEEEECCHHHHHHHHHHHhcCCCcEEEEEeCCHHHHHHHHhc--cCCCEEEEECCCCCCCHHHHHHHHHhcCCCcEE
Confidence            468999999999999999999986 888 5699999999999873  459999999999999999999999755459999


Q ss_pred             EEEccCCh--HHHHHHHHcCCCceEeCCCCH---------HHHHHHHHHHHcCC
Q 029986           95 MMSVDGCT--QDVMKGVTHGACNYLLKPIRI---------KELRNIWQHVAQQP  137 (184)
Q Consensus        95 i~~~~~~~--~~~~~a~~~ga~~~l~kP~~~---------~~l~~~l~~~~~~~  137 (184)
                      ++++..+.  +...++++.|+++|+.||++.         ++|...++.+.+..
T Consensus        81 vlS~~~~~~~~~~~~al~~Ga~d~l~KP~~~~~~~l~~~~~~L~~~I~~~~~~~  134 (349)
T 1a2o_A           81 MVSSLTGKGSEVTLRALELGAIDFVTKPQLGIREGMLAYSEMIAEKVRTAARAR  134 (349)
T ss_dssp             EEECCTHHHHHHHHHHHHHTCCEEEECSSSSCSSCHHHHHHHHHHHHHHHHHCC
T ss_pred             EEECCCcccHHHHHHHHhCCceEEEECCCCccchhHHHHHHHHHHHHHHHHhhh
Confidence            99876654  347889999999999999983         78888888776643

>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=99.69  E-value=6e-17  Score=124.62  Aligned_cols=102  Identities=18%  Similarity=0.262  Sum_probs=85.2

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhc-CCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKC-LYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMM   96 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~-~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi~   96 (184)
                      .+|+||||++..++.+...|... |+.+..+.. .++...+.  ...||+||+|+.||+++|++++++++. ..+|||++
T Consensus         5 ~~ILiVdD~~~~~~~l~~~L~~~~~~~v~~~~~-~~~~~~~~--~~~~dlvllD~~mP~~~G~~~~~~lr~-~~~pvi~l   80 (259)
T 3luf_A            5 QKILIVEDSMTIRRMLIQAIAQQTGLEIDAFDT-LEGARHCQ--GDEYVVALVDLTLPDAPSGEAVKVLLE-RGLPVVIL   80 (259)
T ss_dssp             CEEEEECCCHHHHHHHHHHHHHHHCCEEEEESS-TGGGTTCC--TTTEEEEEEESCBTTBTTSHHHHHHHH-TTCCEEEE
T ss_pred             CeEEEEECCHHHHHHHHHHHHhcCCeEEEEeCh-HHHHHHhh--cCCCcEEEEeCCCCCCCHHHHHHHHHh-CCCCEEEE
Confidence            48999999999999999999764 787765544 44444433  456999999999999999999999975 36899999


Q ss_pred             EccCChHHHHHHHHcCCCceEeCCCCH
Q 029986           97 SVDGCTQDVMKGVTHGACNYLLKPIRI  123 (184)
Q Consensus        97 ~~~~~~~~~~~a~~~ga~~~l~kP~~~  123 (184)
                      |+..+.+....++++||++|+.||...
T Consensus        81 t~~~~~~~~~~a~~~Ga~dyl~Kp~~~  107 (259)
T 3luf_A           81 TADISEDKREAWLEAGVLDYVMKDSRH  107 (259)
T ss_dssp             ECC-CHHHHHHHHHTTCCEEEECSSHH
T ss_pred             EccCCHHHHHHHHHCCCcEEEeCCchh
Confidence            999999999999999999999999743

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

Probab=99.66  E-value=1.6e-16  Score=138.51  Aligned_cols=117  Identities=12%  Similarity=0.120  Sum_probs=103.6

Q ss_pred             CeEEEEeCCH-HH-------HHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCC-CccEEEEeCCCCC----CCHHHHHHH
Q 029986           18 LRVLVVDDDP-IW-------LRILEKMLRKCLYEVTKCNRAEIALDMLRMSKN-GYDIVISDVHMPD----MDGFKLHEQ   84 (184)
Q Consensus        18 ~~Ilivdd~~-~~-------~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~-~~dlvilD~~l~~----~~g~~l~~~   84 (184)
                      |+||||||++ ..       ++.|+..|+..||+|..+.++++++..+.  .. .||+||+|+.||+    ++|++++++
T Consensus         1 m~ILiVdDd~~~~~~~~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~~~--~~~~~d~vilDi~lp~~~~~~~G~~ll~~   78 (755)
T 2vyc_A            1 MKVLIVESEFLHQDTWVGNAVERLADALSQQNVTVIKSTSFDDGFAILS--SNEAIDCLMFSYQMEHPDEHQNVRQLIGK   78 (755)
T ss_dssp             CEEEEECCTTSTTSHHHHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHT--TTCCCSEEEEECCCCSHHHHHHHHHHHHH
T ss_pred             CeEEEEeCCccccccccHHHHHHHHHHHHhCCCEEEEECCHHHHHHHHh--cCCCCcEEEEeCCCCcccccccHHHHHHH
Confidence            4899999999 88       99999999999999999999999999986  34 4999999999999    999999999


Q ss_pred             hccc-CCCCEEEEEccCC-hHHHHHHHHcCCCceEeCCCCHHH-HHHHHHHHHcC
Q 029986           85 VGLE-MDLPVIMMSVDGC-TQDVMKGVTHGACNYLLKPIRIKE-LRNIWQHVAQQ  136 (184)
Q Consensus        85 l~~~-~~~~iIi~~~~~~-~~~~~~a~~~ga~~~l~kP~~~~~-l~~~l~~~~~~  136 (184)
                      +++. +.+||+++|...+ .+.....+..|++||+.||++..+ +...++.++++
T Consensus        79 iR~~~~~iPIi~lTa~~~~~~d~~~~l~~gaddyi~kpf~~~efl~~ri~a~~rr  133 (755)
T 2vyc_A           79 LHERQQNVPVFLLGDREKALAAMDRDLLELVDEFAWILEDTADFIAGRAVAAMTR  133 (755)
T ss_dssp             HHHHSTTCCEEEEECHHHHHHTCSHHHHHHCSEEEETTTSCHHHHHHHHHHHHHH
T ss_pred             HHHhCCCCCEEEEecCCcchhhccHhHhhcCCceEeCCCCCHHHHHHHHHHHHHH
Confidence            9755 5899999998765 566778899999999999999999 77777777654

>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=99.07  E-value=1e-10  Score=87.65  Aligned_cols=92  Identities=18%  Similarity=0.264  Sum_probs=74.1

Q ss_pred             CeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc-CCCCEEEEEccCChHHHHHHHHcCCCceEeCC
Q 029986           42 YEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE-MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKP  120 (184)
Q Consensus        42 ~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~-~~~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP  120 (184)
                      +.|..+.++.++++.+..  ..||++|+|+.||+++|+++++.++.. +..++++++.....+....+++.|+++|+.||
T Consensus         6 ~~v~~~~~~~~a~~~~~~--~~~dlvl~D~~~p~~~g~~~~~~l~~~~~~~~i~vi~~~~~~~~~~~~~~~Ga~~~l~kp   83 (237)
T 3cwo_X            6 LIVDDATNGREAVEKYKE--LKPDIVTMDITMPEMNGIDAIKEIMKIDPNAKIIVCSAMGQQAMVIEAIKAGAKDFIVNT   83 (237)
T ss_dssp             EEEECCCSSSTTHHHHHH--HCCSCEEEECCSTTSSHHHHHHHHHHHSSSCCEEEECCSSTHHHHHHHHHTTCCEEEESH
T ss_pred             EEEEECCCHHHHHHHHHh--cCCCEEEEeCCCCCCCHHHHHHHHHHhCCCCCEEEEECCCCHHHHHHHHHCCHHheEeCC
Confidence            455567788888888873  459999999999999999999998643 45667777666667888899999999999999


Q ss_pred             --CCHHHHHHHHHHHHc
Q 029986          121 --IRIKELRNIWQHVAQ  135 (184)
Q Consensus       121 --~~~~~l~~~l~~~~~  135 (184)
                        ++..++...+.....
T Consensus        84 ~~~~~~~l~~~i~~~~~  100 (237)
T 3cwo_X           84 AAVENPSLITQIAQTFG  100 (237)
T ss_dssp             HHHHCTHHHHHHHHHHT
T ss_pred             cccChHHHHHHHHHHhC
Confidence              666777777776654

>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=99.03  E-value=1.7e-08  Score=83.00  Aligned_cols=115  Identities=24%  Similarity=0.254  Sum_probs=94.0

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc---CCCCE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE---MDLPV   93 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~---~~~~i   93 (184)
                      ..+|++++|+......+...|... +.+....+..++.. ..  ...||++++|..||+++|+++++.++..   ...|+
T Consensus       152 ~~~ilivdd~~~~~~~i~~~L~~~-~~~~~~~~~~~~~~-~~--~~~~dlil~D~~mp~~dG~~~~~~ir~~~~~~~~pi  227 (459)
T 1w25_A          152 GGRVLIVDDNERQAQRVAAELGVE-HRPVIESDPEKAKI-SA--GGPVDLVIVNAAAKNFDGLRFTAALRSEERTRQLPV  227 (459)
T ss_dssp             SCEEEEECSCHHHHHHHHHHHTTT-SEEEEECCHHHHHH-HH--HSSCSEEEEETTCSSSCHHHHHHHHHTSGGGTTCCE
T ss_pred             CCeEEEECCchhhHHHHHHHHhcc-cceeeccCHHHHhh-hc--cCCCCEEEEecCCCCCcHHHHHHHHHhCccccCCcE
Confidence            458999999999888888888653 56666777777753 23  3458999999999999999999998643   47899


Q ss_pred             EEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           94 IMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        94 Ii~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      ++++..........+++.|+++|+.||+...++...+..+..
T Consensus       228 i~lt~~~~~~~~~~~l~~Ga~d~~~kp~~~~~l~~~v~~~~~  269 (459)
T 1w25_A          228 LAMVDPDDRGRMVKALEIGVNDILSRPIDPQELSARVKTQIQ  269 (459)
T ss_dssp             EEEECTTCHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHHH
T ss_pred             EEEcCCCchHHHHHHHhccccccccCCCCHHHHHHHHHHHHH
Confidence            999988888888899999999999999999988776665543

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

Probab=97.76  E-value=0.00034  Score=44.96  Aligned_cols=106  Identities=15%  Similarity=0.090  Sum_probs=79.3

Q ss_pred             eEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEEEEc
Q 029986           19 RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMSV   98 (184)
Q Consensus        19 ~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi~~~   98 (184)
                      .|++|..|-.....+++++....|.+......        ......|+|+|+..+-..+-+    .-+.....-+|++-+
T Consensus        14 ~iL~VtEd~~ls~QlKel~~~~eY~~~is~~~--------~~e~~AdlIfCEYlLLPe~if----S~k~~~~~dliVLfD   81 (121)
T 3q7r_A           14 HVLLVSEHWDLFFQTKELLNPEEYRCTIGQQY--------KQELSADLVVCEYSLLPREIR----SPKSLEGSFVLVLLD   81 (121)
T ss_dssp             EEEEECSCHHHHHHHHHHSCTTTEEEEEESSC--------CCCTTEEEEEEEGGGSCTTCC----CCTTCCSCEEEEEES
T ss_pred             EEEEEecCchhhHHHHHhcCCcceeEEecccc--------CCcccceeEEEeeecChHHhc----CCCCCCcccEEEEeh
Confidence            58899999999999999987777887766532        124457999999865433210    001112445788888


Q ss_pred             cCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCC
Q 029986           99 DGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQP  137 (184)
Q Consensus        99 ~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~  137 (184)
                      .-+++...+.++.||. |+.+|++..-+..+++..+++.
T Consensus        82 ~F~EEa~v~vLd~Ga~-yLlrPIT~kvldAvIraFLrqh  119 (121)
T 3q7r_A           82 FFDEETSVDLLDRGFW-YLIRPITPRILKSAISLFLSQH  119 (121)
T ss_dssp             SCCHHHHHHHHHTTCE-EEESCCCHHHHHHHHHHHHHHC
T ss_pred             hhchHHHHHHHhCCce-eEeccCcHHHHHHHHHHHHhcc
Confidence            8888999999999999 9999999999999999888753

>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=97.42  E-value=0.00044  Score=52.26  Aligned_cols=97  Identities=13%  Similarity=0.085  Sum_probs=69.1

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEE
Q 029986           15 PAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVI   94 (184)
Q Consensus        15 ~~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iI   94 (184)
                      ..+.+|+|++|++..+..+...|...|+++..+.+         .....+|++++|..++...+.           ..++
T Consensus         9 l~~~~vlvv~d~~~~~~~l~~~L~~~g~~v~~~~~---------~~~~~~~~ii~d~~~~~~~~~-----------~~~i   68 (254)
T 2ayx_A            9 LSGKRCWLAVRNASLCQFLETSLQRSGIVVTTYEG---------QEPTPEDVLITDEVVSKKWQG-----------RAVV   68 (254)
T ss_dssp             TTTEEEEEECCCHHHHHHHHHHHTTTTEEEEECSS---------CCCCTTCEEEEESSCSCCCCS-----------SEEE
T ss_pred             cCCCEEEEEcCCHHHHHHHHHHHHHCCCEEEEecC---------CCCCcCcEEEEcCCCcccccc-----------ceEE
Confidence            35679999999999999999999999999987764         113568999999998875431           1244


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      .++.... +.   ....+...++.+|....++...+..+..
T Consensus        69 ~~~~~~~-~~---~~~~~~~~~~~~~~~~~~l~~~l~~~~~  105 (254)
T 2ayx_A           69 TFCRRHI-GI---PLEKAPGEWVHSVAAPHELPALLARIYL  105 (254)
T ss_dssp             EECSSCC-CS---CCTTSTTEEEECSSCCSHHHHHHHHHHT
T ss_pred             EEecccC-CC---cccccCCceeccccchHHHHHHHHHHhh
Confidence            4433211 10   0123445789999998899888887764

>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=96.97  E-value=0.0013  Score=57.07  Aligned_cols=91  Identities=16%  Similarity=0.184  Sum_probs=67.7

Q ss_pred             HHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEEEEccCChHHH-H
Q 029986           29 WLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIMMSVDGCTQDV-M  106 (184)
Q Consensus        29 ~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi~~~~~~~~~~-~  106 (184)
                      ....|...|++.|++|..+.+.++++..+.. +...++|++|+.++   +.+++++++. ..++||.+++........ .
T Consensus        18 ~i~~L~~~Le~~g~~V~~a~s~~Da~~~i~~-~~~i~avIld~d~~---~~~ll~~Ir~~~~~iPVFl~~~~~~~~~~~~   93 (715)
T 3n75_A           18 PIRELHRALERLNFQIVYPNDRDDLLKLIEN-NARLCGVIFDWDKY---NLELCEEISKMNENLPLYAFANTYSTLDVSL   93 (715)
T ss_dssp             HHHHHHHHHHHTTCEEECCSSHHHHHHHHHH-CTTEEEEEEEHHHH---HHHHHHHHHHHCTTCEEEEECCTTCCCCGGG
T ss_pred             HHHHHHHHHHHCCcEEEEeCCHHHHHHHHHh-CCCceEEEEecccc---HHHHHHHHHHhCCCCCEEEEecCCcccccch
Confidence            3445668888889999999999999999974 45589999999775   6789999964 469999999876432222 2


Q ss_pred             HHHHcCCCceEeCCCCHH
Q 029986          107 KGVTHGACNYLLKPIRIK  124 (184)
Q Consensus       107 ~a~~~ga~~~l~kP~~~~  124 (184)
                      +. -.++++|+.+.....
T Consensus        94 ~~-~~~~~~~~~~~~~~~  110 (715)
T 3n75_A           94 ND-LRLQISFFEYALGAA  110 (715)
T ss_dssp             TT-SCCEEEEECCCTTCH
T ss_pred             hh-hhccCeEEEeCCCCH
Confidence            22 346788888766433

>2yxb_A Coenzyme B12-dependent mutase; alpha/beta, structural genomics, NPPSFA, national project on structural and functional analyses; 1.80A {Aeropyrum pernix}

Probab=96.29  E-value=0.16  Score=35.54  Aligned_cols=116  Identities=16%  Similarity=0.136  Sum_probs=76.5

Q ss_pred             CCeEEEE----eCCHHHHHHHHHHHHhcCCeEEEE---CCHHHHHHHHHhcCCCccEEEEeCCCCCC--CHHHHHHHhcc
Q 029986           17 GLRVLVV----DDDPIWLRILEKMLRKCLYEVTKC---NRAEIALDMLRMSKNGYDIVISDVHMPDM--DGFKLHEQVGL   87 (184)
Q Consensus        17 ~~~Iliv----dd~~~~~~~l~~~L~~~~~~v~~~---~~~~~~~~~l~~~~~~~dlvilD~~l~~~--~g~~l~~~l~~   87 (184)
                      ..+|++.    |.+..-...+..+|+..||+|...   -..++..+.+.  +..||+|.+-..+...  .--++++.++.
T Consensus        18 ~~~vlla~~~gd~HdiG~~~va~~l~~~G~eVi~lG~~~p~e~lv~aa~--~~~~diV~lS~~~~~~~~~~~~~i~~L~~   95 (161)
T 2yxb_A           18 RYKVLVAKMGLDGHDRGAKVVARALRDAGFEVVYTGLRQTPEQVAMAAV--QEDVDVIGVSILNGAHLHLMKRLMAKLRE   95 (161)
T ss_dssp             SCEEEEEEESSSSCCHHHHHHHHHHHHTTCEEECCCSBCCHHHHHHHHH--HTTCSEEEEEESSSCHHHHHHHHHHHHHH
T ss_pred             CCEEEEEeCCCCccHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHH--hcCCCEEEEEeechhhHHHHHHHHHHHHh
Confidence            4478887    778888888999999999998743   35777787776  4569999998765531  12335555644


Q ss_pred             c--CCCCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           88 E--MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        88 ~--~~~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      .  .+++|++ ...........+.+.|++.++..-.+..+....+..++.
T Consensus        96 ~g~~~i~v~v-GG~~~~~~~~~l~~~G~d~v~~~~~~~~~~~~~~~~~~~  144 (161)
T 2yxb_A           96 LGADDIPVVL-GGTIPIPDLEPLRSLGIREIFLPGTSLGEIIEKVRKLAE  144 (161)
T ss_dssp             TTCTTSCEEE-EECCCHHHHHHHHHTTCCEEECTTCCHHHHHHHHHHHHH
T ss_pred             cCCCCCEEEE-eCCCchhcHHHHHHCCCcEEECCCCCHHHHHHHHHHHHH
Confidence            3  2456554 444444444456789999767655555566666666554

>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=96.27  E-value=0.039  Score=40.27  Aligned_cols=82  Identities=16%  Similarity=0.204  Sum_probs=59.9

Q ss_pred             CHHHHHHHHHhcCCCccEEEEeC-CCCCCCH--HHHHHHhcccCCCCEEEEEccCChHHHHHHHHcCCCceE------eC
Q 029986           49 RAEIALDMLRMSKNGYDIVISDV-HMPDMDG--FKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYL------LK  119 (184)
Q Consensus        49 ~~~~~~~~l~~~~~~~dlvilD~-~l~~~~g--~~l~~~l~~~~~~~iIi~~~~~~~~~~~~a~~~ga~~~l------~k  119 (184)
                      +..+....+... ..+++++.++ ..+.++|  .+.+++++...+.|+|.++.....+...++++.|+++++      .+
T Consensus       131 ~~~~~i~~~~~~-~~~~vli~~~~~~g~~~g~~~~~i~~~~~~~~~Pvia~~g~~~~~~~~~~~~~G~~~~~vg~a~~~~  209 (237)
T 3cwo_X          131 LLRDWVVEVEKR-GAGEILLTSIDRDGTKSGYDTEMIRFVRPLTTLPIIASGGAGKMEHFLEAFLAGADAALAASVFHFR  209 (237)
T ss_dssp             EHHHHHHHHHHH-TCSEEEEEETTTTTCCSCCCHHHHHHHGGGCCSCEEEESCCCSHHHHHHHHHHTCSEEEESHHHHTT
T ss_pred             CHHHHHHHHhhc-CCCeEEEEecCCCCccccccHHHHHHHHHhcCCCEEecCCCCCHHHHHHHHHcCcHHHhhhHHHHcC
Confidence            344555554422 2356888886 5555555  456777766668999999988889999999999999985      78


Q ss_pred             CCCHHHHHHHHH
Q 029986          120 PIRIKELRNIWQ  131 (184)
Q Consensus       120 P~~~~~l~~~l~  131 (184)
                      |++..++.+.+.
T Consensus       210 ~~~~~~~~~~l~  221 (237)
T 3cwo_X          210 EIDVRELKEYLK  221 (237)
T ss_dssp             SSCHHHHHHHHH
T ss_pred             CCCHHHHHHHHH
Confidence            989888877644

>1wv2_A Thiazole moeity, thiazole biosynthesis protein THIG; structural genomics, protein structure initiative, PSI; 2.90A {Pseudomonas aeruginosa} SCOP: c.1.31.1

Probab=95.51  E-value=0.13  Score=38.90  Aligned_cols=97  Identities=15%  Similarity=0.040  Sum_probs=65.3

Q ss_pred             HHHHHHhcCCeEE--EECCHHHHHHHHHhcCCCccEEEEeCCCCCC-----CHHHHHHHhcccCCCCEEEEEccCChHHH
Q 029986           33 LEKMLRKCLYEVT--KCNRAEIALDMLRMSKNGYDIVISDVHMPDM-----DGFKLHEQVGLEMDLPVIMMSVDGCTQDV  105 (184)
Q Consensus        33 l~~~L~~~~~~v~--~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~-----~g~~l~~~l~~~~~~~iIi~~~~~~~~~~  105 (184)
                      ..+.|.+.|+.+.  ...+...+..+..   .++++| +.+..|-+     ...++++.+....++|||.=..-.+++.+
T Consensus       127 aa~~L~~~Gf~Vlpy~~dd~~~akrl~~---~G~~aV-mPlg~pIGsG~Gi~~~~lI~~I~e~~~vPVI~eGGI~TPsDA  202 (265)
T 1wv2_A          127 AAEQLVKDGFDVMVYTSDDPIIARQLAE---IGCIAV-MPLAGLIGSGLGICNPYNLRIILEEAKVPVLVDAGVGTASDA  202 (265)
T ss_dssp             HHHHHHTTTCEEEEEECSCHHHHHHHHH---SCCSEE-EECSSSTTCCCCCSCHHHHHHHHHHCSSCBEEESCCCSHHHH
T ss_pred             HHHHHHHCCCEEEEEeCCCHHHHHHHHH---hCCCEE-EeCCccCCCCCCcCCHHHHHHHHhcCCCCEEEeCCCCCHHHH
Confidence            4456667799877  4455655555543   457888 54443321     23678888877788999987777889999


Q ss_pred             HHHHHcCCCceE-----eCCCCHHHHHHHHHHH
Q 029986          106 MKGVTHGACNYL-----LKPIRIKELRNIWQHV  133 (184)
Q Consensus       106 ~~a~~~ga~~~l-----~kP~~~~~l~~~l~~~  133 (184)
                      ..+++.|+++.+     .+--++..+...+...
T Consensus       203 a~AmeLGAdgVlVgSAI~~a~dP~~ma~af~~A  235 (265)
T 1wv2_A          203 AIAMELGCEAVLMNTAIAHAKDPVMMAEAMKHA  235 (265)
T ss_dssp             HHHHHHTCSEEEESHHHHTSSSHHHHHHHHHHH
T ss_pred             HHHHHcCCCEEEEChHHhCCCCHHHHHHHHHHH
Confidence            999999999987     4433445555444443

>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=95.14  E-value=0.3  Score=36.22  Aligned_cols=97  Identities=13%  Similarity=0.191  Sum_probs=65.8

Q ss_pred             CeEEEEeC----CHHHHHHHHHHHHhcCCeE-EEECCHHHHHHHHHhcCCCccEEEEeCC------CCCCCHHHHHHHhc
Q 029986           18 LRVLVVDD----DPIWLRILEKMLRKCLYEV-TKCNRAEIALDMLRMSKNGYDIVISDVH------MPDMDGFKLHEQVG   86 (184)
Q Consensus        18 ~~Ilivdd----~~~~~~~l~~~L~~~~~~v-~~~~~~~~~~~~l~~~~~~~dlvilD~~------l~~~~g~~l~~~l~   86 (184)
                      ..+++++-    ++.....+...+++.|..+ ..+++.+++.....   .++|+|.+...      .....++++++++.
T Consensus       102 ad~I~l~~~~~~~p~~l~~~i~~~~~~g~~v~~~v~t~eea~~a~~---~Gad~Ig~~~~g~t~~~~~~~~~~~li~~l~  178 (229)
T 3q58_A          102 ADIIAFDASFRSRPVDIDSLLTRIRLHGLLAMADCSTVNEGISCHQ---KGIEFIGTTLSGYTGPITPVEPDLAMVTQLS  178 (229)
T ss_dssp             CSEEEEECCSSCCSSCHHHHHHHHHHTTCEEEEECSSHHHHHHHHH---TTCSEEECTTTTSSSSCCCSSCCHHHHHHHH
T ss_pred             CCEEEECccccCChHHHHHHHHHHHHCCCEEEEecCCHHHHHHHHh---CCCCEEEecCccCCCCCcCCCCCHHHHHHHH
Confidence            34555543    3334444555556656654 46778888877654   56898865322      12345678888886


Q ss_pred             ccCCCCEEEEEccCChHHHHHHHHcCCCceEe
Q 029986           87 LEMDLPVIMMSVDGCTQDVMKGVTHGACNYLL  118 (184)
Q Consensus        87 ~~~~~~iIi~~~~~~~~~~~~a~~~ga~~~l~  118 (184)
                      .. ++|+|.-..-.+.+.+.+++..||++++.
T Consensus       179 ~~-~ipvIA~GGI~t~~d~~~~~~~GadgV~V  209 (229)
T 3q58_A          179 HA-GCRVIAEGRYNTPALAANAIEHGAWAVTV  209 (229)
T ss_dssp             TT-TCCEEEESSCCSHHHHHHHHHTTCSEEEE
T ss_pred             Hc-CCCEEEECCCCCHHHHHHHHHcCCCEEEE
Confidence            55 88999887777889999999999999975

>3fkq_A NTRC-like two-domain protein; RER070207001320, structural GE joint center for structural genomics, JCSG, protein structu initiative, PSI-2; HET: ATP 2PE; 2.10A {Eubacterium rectale}

Probab=94.69  E-value=0.083  Score=42.05  Aligned_cols=57  Identities=18%  Similarity=0.269  Sum_probs=49.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhc---CCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCC
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKC---LYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPD   75 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~---~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~   75 (184)
                      .++++|+|.|+.+.+.|..++.+.   .+++..|++.+.+.+..+.  ..+|++++|-.+..
T Consensus        21 ~i~l~i~d~d~~Y~~~l~~y~~~~~~~~~~v~~ft~~e~~~~~~~~--~~~dilli~e~~~~   80 (373)
T 3fkq_A           21 KIKVALLDKDKEYLDRLTGVFNTKYADKLEVYSFTDEKNAIESVKE--YRIDVLIAEEDFNI   80 (373)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHHHHTTTTEEEEEESCHHHHHHHHHH--HTCSEEEEETTCCC
T ss_pred             eEEEEEEeCCHHHHHHHHHHHhhccCCceEEEEECCHHHHHHHHhc--CCCCEEEEcchhhh
Confidence            468999999999999999999754   6899999999999999874  46899999987654

>3igs_A N-acetylmannosamine-6-phosphate 2-epimerase 2; energy metabolism, sugars, csgid, carbohydrate metabolism, isomerase; HET: MSE 16G; 1.50A {Salmonella enterica subsp} SCOP: c.1.2.0

Probab=94.39  E-value=0.57  Score=34.79  Aligned_cols=88  Identities=16%  Similarity=0.182  Sum_probs=61.0

Q ss_pred             HHHHHHHHHHHHhcCCeE-EEECCHHHHHHHHHhcCCCccEEEEeCC-C-----CCCCHHHHHHHhcccCCCCEEEEEcc
Q 029986           27 PIWLRILEKMLRKCLYEV-TKCNRAEIALDMLRMSKNGYDIVISDVH-M-----PDMDGFKLHEQVGLEMDLPVIMMSVD   99 (184)
Q Consensus        27 ~~~~~~l~~~L~~~~~~v-~~~~~~~~~~~~l~~~~~~~dlvilD~~-l-----~~~~g~~l~~~l~~~~~~~iIi~~~~   99 (184)
                      +.....+...+.+.|..+ ..+.+.+++.....   .++|+|.+... .     ....+++++++++.. ++|+|.-..-
T Consensus       115 p~~l~~~i~~~~~~g~~v~~~v~t~eea~~a~~---~Gad~Ig~~~~g~t~~~~~~~~~~~~i~~l~~~-~ipvIA~GGI  190 (232)
T 3igs_A          115 PVAVEALLARIHHHHLLTMADCSSVDDGLACQR---LGADIIGTTMSGYTTPDTPEEPDLPLVKALHDA-GCRVIAEGRY  190 (232)
T ss_dssp             SSCHHHHHHHHHHTTCEEEEECCSHHHHHHHHH---TTCSEEECTTTTSSSSSCCSSCCHHHHHHHHHT-TCCEEEESCC
T ss_pred             HHHHHHHHHHHHHCCCEEEEeCCCHHHHHHHHh---CCCCEEEEcCccCCCCCCCCCCCHHHHHHHHhc-CCcEEEECCC
Confidence            334444555556656654 46778888877654   56898865322 1     223467888888655 8899888777


Q ss_pred             CChHHHHHHHHcCCCceEe
Q 029986          100 GCTQDVMKGVTHGACNYLL  118 (184)
Q Consensus       100 ~~~~~~~~a~~~ga~~~l~  118 (184)
                      .+.+.+.++++.|+++++.
T Consensus       191 ~t~~d~~~~~~~GadgV~V  209 (232)
T 3igs_A          191 NSPALAAEAIRYGAWAVTV  209 (232)
T ss_dssp             CSHHHHHHHHHTTCSEEEE
T ss_pred             CCHHHHHHHHHcCCCEEEE
Confidence            7789999999999999974

>1r8j_A KAIA; circadian clock protein; 2.03A {Synechococcus elongatus pcc 7942} SCOP: a.186.1.1 c.23.1.5 PDB: 1m2e_A 1m2f_A

Probab=93.56  E-value=1.2  Score=33.65  Aligned_cols=85  Identities=13%  Similarity=0.196  Sum_probs=67.1

Q ss_pred             cCCCCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCC
Q 029986           13 QFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDL   91 (184)
Q Consensus        13 ~~~~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~   91 (184)
                      -+.+.+.|.+.-.++...+.+...|....|.+..+.+.++.++.+.......|++++..-  +.+...+..++.. ..-.
T Consensus         5 ~~~~~LsI~~~~~s~~l~~~~~~~L~~dRY~l~~~~s~~~f~~~le~~~e~iDcLvle~~--~~~~~~~~~~L~~~g~lL   82 (289)
T 1r8j_A            5 IVLSQIAICIWVESTAILQDCQRALSADRYQLQVCESGEMLLEYAQTHRDQIDCLILVAA--NPSFRAVVQQLCFEGVVV   82 (289)
T ss_dssp             -CCCCEEEEEECCCHHHHHHHHHHTCSTTEEEEEECSHHHHHHHHHHSTTSCSEEEEETT--STTHHHHHHHHHHTTCCC
T ss_pred             ccccceeEEEEeCCHHHHHHHHHhcccCceEEEEcCcHHHHHHHHHhccccCCEEEEEeC--CCccHHHHHHHHHcCccc
Confidence            345678899999999999999999988889999999999999999766677999999761  2345567777753 3467


Q ss_pred             CEEEEEcc
Q 029986           92 PVIMMSVD   99 (184)
Q Consensus        92 ~iIi~~~~   99 (184)
                      |+|++...
T Consensus        83 P~vil~~~   90 (289)
T 1r8j_A           83 PAIVVGDR   90 (289)
T ss_dssp             CEEEESCC
T ss_pred             cEEEeccC
Confidence            99988553

>1ccw_A Protein (glutamate mutase); coenzyme B12, radical reaction, TIM-barrel rossman-fold, isomerase; HET: CNC TAR; 1.60A {Clostridium cochlearium} SCOP: c.23.6.1 PDB: 1cb7_A* 1b1a_A 1i9c_A* 1be1_A 1fmf_A 1id8_A*

Probab=93.18  E-value=1.3  Score=29.90  Aligned_cols=106  Identities=7%  Similarity=-0.048  Sum_probs=67.9

Q ss_pred             CCHHHHHHHHHHHHhcCCeEE---EECCHHHHHHHHHhcCCCccEEEEeCCCCCCC--HHHHHHHhccc-C-CCCEEEEE
Q 029986           25 DDPIWLRILEKMLRKCLYEVT---KCNRAEIALDMLRMSKNGYDIVISDVHMPDMD--GFKLHEQVGLE-M-DLPVIMMS   97 (184)
Q Consensus        25 d~~~~~~~l~~~L~~~~~~v~---~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~--g~~l~~~l~~~-~-~~~iIi~~   97 (184)
                      -+..-...+..+|+..||+|.   ..-..++..+.+.  +..||+|.+...+....  .-++++.++.. . +++|+ +.
T Consensus        15 ~HdiG~~~v~~~l~~~G~~Vi~lG~~~p~e~~v~~a~--~~~~d~v~lS~~~~~~~~~~~~~i~~l~~~g~~~i~v~-vG   91 (137)
T 1ccw_A           15 CHAVGNKILDHAFTNAGFNVVNIGVLSPQELFIKAAI--ETKADAILVSSLYGQGEIDCKGLRQKCDEAGLEGILLY-VG   91 (137)
T ss_dssp             CCCHHHHHHHHHHHHTTCEEEEEEEEECHHHHHHHHH--HHTCSEEEEEECSSTHHHHHTTHHHHHHHTTCTTCEEE-EE
T ss_pred             hhHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHH--hcCCCEEEEEecCcCcHHHHHHHHHHHHhcCCCCCEEE-EE
Confidence            455566678888999999877   4556888888877  34599999988764321  12345555432 2 45554 44


Q ss_pred             ccC---ChH---HHHHHHHcCCCceEeCCCCHHHHHHHHHHH
Q 029986           98 VDG---CTQ---DVMKGVTHGACNYLLKPIRIKELRNIWQHV  133 (184)
Q Consensus        98 ~~~---~~~---~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~  133 (184)
                      ...   ..+   ....+.+.|++.|+..--+..++...+...
T Consensus        92 G~~~~~~~~~~~~~~~~~~~G~d~~~~~g~~~~~~~~~l~~~  133 (137)
T 1ccw_A           92 GNIVVGKQHWPDVEKRFKDMGYDRVYAPGTPPEVGIADLKKD  133 (137)
T ss_dssp             ESCSSSSCCHHHHHHHHHHTTCSEECCTTCCHHHHHHHHHHH
T ss_pred             CCCcCchHhhhhhHHHHHHCCCCEEECCCCCHHHHHHHHHHH
Confidence            432   111   134578899999887666777776665544

>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=91.67  E-value=0.73  Score=34.87  Aligned_cols=76  Identities=16%  Similarity=0.208  Sum_probs=53.2

Q ss_pred             CCCccEEEEeCCCCC--CC--------------------HHHHHHHhccc-CCCCEEEEEcc------CChHHHHHHHHc
Q 029986           61 KNGYDIVISDVHMPD--MD--------------------GFKLHEQVGLE-MDLPVIMMSVD------GCTQDVMKGVTH  111 (184)
Q Consensus        61 ~~~~dlvilD~~l~~--~~--------------------g~~l~~~l~~~-~~~~iIi~~~~------~~~~~~~~a~~~  111 (184)
                      +.+.|+|-+++-..+  .|                    ++++++.++.. .++|+++++..      ....++..+.++
T Consensus        42 ~~GaD~ieig~P~sdp~~DG~~i~~a~~~al~~G~~~~~~~~~v~~ir~~~~~~Pv~lm~y~n~v~~~g~~~~~~~~~~a  121 (268)
T 1qop_A           42 DAGADALELGVPFSDPLADGPTIQNANLRAFAAGVTPAQCFEMLAIIREKHPTIPIGLLMYANLVFNNGIDAFYARCEQV  121 (268)
T ss_dssp             HTTCSSEEEECCCSCCTTCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCSSSCEEEEECHHHHHTTCHHHHHHHHHHH
T ss_pred             HCCCCEEEECCCCCCccCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCEEEEEcccHHHHhhHHHHHHHHHHc
Confidence            355888888874432  12                    45667788766 68898887522      114677789999


Q ss_pred             CCCceEeCCCCHHHHHHHHHHHHcC
Q 029986          112 GACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus       112 ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      |+++++...+..+++...+..+.+.
T Consensus       122 Gadgii~~d~~~e~~~~~~~~~~~~  146 (268)
T 1qop_A          122 GVDSVLVADVPVEESAPFRQAALRH  146 (268)
T ss_dssp             TCCEEEETTCCGGGCHHHHHHHHHT
T ss_pred             CCCEEEEcCCCHHHHHHHHHHHHHc
Confidence            9999999888877777777766554

>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=91.55  E-value=0.95  Score=34.15  Aligned_cols=88  Identities=19%  Similarity=0.274  Sum_probs=57.8

Q ss_pred             CHHHHHHHHHh-cCCCccEEEEeCCCCC--C--------------------CHHHHHHHhcccC-CCCEEEEEccC----
Q 029986           49 RAEIALDMLRM-SKNGYDIVISDVHMPD--M--------------------DGFKLHEQVGLEM-DLPVIMMSVDG----  100 (184)
Q Consensus        49 ~~~~~~~~l~~-~~~~~dlvilD~~l~~--~--------------------~g~~l~~~l~~~~-~~~iIi~~~~~----  100 (184)
                      +.+..++.++. .+.+.|+|-+++-..+  .                    +.+++++.++... ++|+++++...    
T Consensus        29 ~~~~~~~~~~~l~~~G~D~IElG~P~sdP~adgp~i~~a~~~al~~G~~~~~~~~~v~~ir~~~~~~Pi~~m~y~n~v~~  108 (262)
T 2ekc_A           29 DYETSLKAFKEVLKNGTDILEIGFPFSDPVADGPTIQVAHEVALKNGIRFEDVLELSETLRKEFPDIPFLLMTYYNPIFR  108 (262)
T ss_dssp             CHHHHHHHHHHHHHTTCSEEEEECCCSCCTTSCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTSCEEEECCHHHHHH
T ss_pred             ChHHHHHHHHHHHHcCCCEEEECCCCCCcccccHHHHHHHHHHHHcCCCHHHHHHHHHHHHhhcCCCCEEEEecCcHHHH
Confidence            44444444432 2456898888775433  1                    2345677776554 89998874221    


Q ss_pred             --ChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986          101 --CTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus       101 --~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                        .......+.++|+++++.-.+..+++...+..+.+.
T Consensus       109 ~g~~~f~~~~~~aG~dgvii~dl~~ee~~~~~~~~~~~  146 (262)
T 2ekc_A          109 IGLEKFCRLSREKGIDGFIVPDLPPEEAEELKAVMKKY  146 (262)
T ss_dssp             HCHHHHHHHHHHTTCCEEECTTCCHHHHHHHHHHHHHT
T ss_pred             hhHHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHHHc
Confidence              135567789999999999888888887777776554

>2htm_A Thiazole biosynthesis protein THIG; thiamin biosynthesis, THIG, thermus thermophilus HB8, structural genomics, NPPSFA; 2.30A {Thermus thermophilus}

Probab=91.19  E-value=0.46  Score=36.04  Aligned_cols=96  Identities=15%  Similarity=0.064  Sum_probs=61.4

Q ss_pred             HHHHHhcCCeEE--EECCHHHHHHHHHhcCCCccEEEEeCCCCCCCH-----HHHHHHhcc-cCC-CCEEEEEccCChHH
Q 029986           34 EKMLRKCLYEVT--KCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG-----FKLHEQVGL-EMD-LPVIMMSVDGCTQD  104 (184)
Q Consensus        34 ~~~L~~~~~~v~--~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g-----~~l~~~l~~-~~~-~~iIi~~~~~~~~~  104 (184)
                      .+.|.+.||.+.  ...+...+..+..   .++++| +.+.-|-++|     .++++.+.. ..+ +|||+=..-.+++.
T Consensus       117 a~~L~k~Gf~Vlpy~~~D~~~ak~l~~---~G~~aV-mPlg~pIGsG~Gi~~~~~L~~i~~~~~~~vPVI~~GGI~tpsD  192 (268)
T 2htm_A          117 AERLIEEDFLVLPYMGPDLVLAKRLAA---LGTATV-MPLAAPIGSGWGVRTRALLELFAREKASLPPVVVDAGLGLPSH  192 (268)
T ss_dssp             HHHHHHTTCEECCEECSCHHHHHHHHH---HTCSCB-EEBSSSTTTCCCSTTHHHHHHHHHTTTTSSCBEEESCCCSHHH
T ss_pred             HHHHHHCCCEEeeccCCCHHHHHHHHh---cCCCEE-EecCccCcCCcccCCHHHHHHHHHhcCCCCeEEEeCCCCCHHH
Confidence            345556688866  3456655554433   347777 6654432222     456777765 567 99998777788899


Q ss_pred             HHHHHHcCCCceE-----eCCCCHHHHHHHHHHH
Q 029986          105 VMKGVTHGACNYL-----LKPIRIKELRNIWQHV  133 (184)
Q Consensus       105 ~~~a~~~ga~~~l-----~kP~~~~~l~~~l~~~  133 (184)
                      +..+++.|+++.+     .|--++..+.+.+..+
T Consensus       193 Aa~AmeLGAdgVlVgSAI~~a~dP~~ma~af~~A  226 (268)
T 2htm_A          193 AAEVMELGLDAVLVNTAIAEAQDPPAMAEAFRLA  226 (268)
T ss_dssp             HHHHHHTTCCEEEESHHHHTSSSHHHHHHHHHHH
T ss_pred             HHHHHHcCCCEEEEChHHhCCCCHHHHHHHHHHH
Confidence            9999999999986     4533445554444443

>2l69_A Rossmann 2X3 fold protein; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Artificial gene}

Probab=90.80  E-value=2  Score=27.06  Aligned_cols=113  Identities=12%  Similarity=0.195  Sum_probs=62.6

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHH----HHHHHhcccCCCCE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGF----KLHEQVGLEMDLPV   93 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~----~l~~~l~~~~~~~i   93 (184)
                      +-|++..-+......++.+++..|+.+..+.+.++.-+.+..--..+..-|+-....+..+.    .+.+.+..  .+ +
T Consensus         3 ivivvfstdeetlrkfkdiikkngfkvrtvrspqelkdsieelvkkynativvvvvddkewaekairfvkslga--qv-l   79 (134)
T 2l69_A            3 IVIVVFSTDEETLRKFKDIIKKNGFKVRTVRSPQELKDSIEELVKKYNATIVVVVVDDKEWAEKAIRFVKSLGA--QV-L   79 (134)
T ss_dssp             EEEEECCCCHHHHHHHHHHHHHTTCEEEEECSHHHHHHHHHHHTTCCCCEEEEEECSSHHHHHHHHHHHHHHCC--CC-E
T ss_pred             EEEEEEeCCHHHHHHHHHHHHhcCceEEEecCHHHHHHHHHHHHHHhCCeEEEEEEccHHHHHHHHHHHHhcCC--eE-E
Confidence            33555667777888899999999999999999988877765322234333332233344432    34444432  23 3


Q ss_pred             EEEEccCCh---HHHHHHHHcCCCceEeCC-CCHHHHHHHHHHHHcC
Q 029986           94 IMMSVDGCT---QDVMKGVTHGACNYLLKP-IRIKELRNIWQHVAQQ  136 (184)
Q Consensus        94 Ii~~~~~~~---~~~~~a~~~ga~~~l~kP-~~~~~l~~~l~~~~~~  136 (184)
                      |++..+..-   +.......-|..   ++. -+++.+...+.++.+.
T Consensus        80 iiiydqdqnrleefsrevrrrgfe---vrtvtspddfkkslerlire  123 (134)
T 2l69_A           80 IIIYDQDQNRLEEFSREVRRRGFE---VRTVTSPDDFKKSLERLIRE  123 (134)
T ss_dssp             EEEECSCHHHHHHHHHHHHHTTCC---EEEESSHHHHHHHHHHHHHH
T ss_pred             EEEEeCchhHHHHHHHHHHhcCce---EEEecChHHHHHHHHHHHHH
Confidence            333333221   222333444432   222 2456777777776654

>3o63_A Probable thiamine-phosphate pyrophosphorylase; thiamin biosynthesis, TIM barrel, transferase; 2.35A {Mycobacterium tuberculosis}

Probab=90.35  E-value=3.9  Score=30.48  Aligned_cols=85  Identities=11%  Similarity=0.027  Sum_probs=57.8

Q ss_pred             EEECCHHHHHHHHHhcCCCccEEEEeCCCCC-------CCHHHHHHHhccc--CCCCEEEEEccCChHHHHHHHHcCCCc
Q 029986           45 TKCNRAEIALDMLRMSKNGYDIVISDVHMPD-------MDGFKLHEQVGLE--MDLPVIMMSVDGCTQDVMKGVTHGACN  115 (184)
Q Consensus        45 ~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~-------~~g~~l~~~l~~~--~~~~iIi~~~~~~~~~~~~a~~~ga~~  115 (184)
                      .++.+.+++.....   .++|.|.+.-..+.       .-|++.++++...  .++|++.+..- +.+.+..++.+|+++
T Consensus       140 ~S~ht~~Ea~~A~~---~GaDyI~vgpvf~T~tK~~~~~~gl~~l~~~~~~~~~~iPvvAiGGI-~~~ni~~~~~aGa~g  215 (243)
T 3o63_A          140 RSTHDPDQVAAAAA---GDADYFCVGPCWPTPTKPGRAAPGLGLVRVAAELGGDDKPWFAIGGI-NAQRLPAVLDAGARR  215 (243)
T ss_dssp             EEECSHHHHHHHHH---SSCSEEEECCSSCCCC-----CCCHHHHHHHHTC---CCCEEEESSC-CTTTHHHHHHTTCCC
T ss_pred             EeCCCHHHHHHHhh---CCCCEEEEcCccCCCCCCCcchhhHHHHHHHHHhccCCCCEEEecCC-CHHHHHHHHHcCCCE
Confidence            36788888777654   45899999664443       2367788888544  47899998665 677888999999999


Q ss_pred             eEe-----CCCCHHHHHHHHHHH
Q 029986          116 YLL-----KPIRIKELRNIWQHV  133 (184)
Q Consensus       116 ~l~-----kP~~~~~l~~~l~~~  133 (184)
                      +..     +.-++.+-.+.+...
T Consensus       216 vav~sai~~a~dp~~a~~~l~~~  238 (243)
T 3o63_A          216 IVVVRAITSADDPRAAAEQLRSA  238 (243)
T ss_dssp             EEESHHHHTCSSHHHHHHHHHHH
T ss_pred             EEEeHHHhCCCCHHHHHHHHHHH
Confidence            864     444444444444433

>3ezx_A MMCP 1, monomethylamine corrinoid protein 1; N terminal all helical bundle C terminal rossmann fold, cobalt, metal-binding; HET: HCB; 2.56A {Methanosarcina barkeri}

Probab=89.88  E-value=2.3  Score=31.06  Aligned_cols=97  Identities=14%  Similarity=0.059  Sum_probs=63.9

Q ss_pred             CCeEEEE----eCCHHHHHHHHHHHHhcCCeEEEEC---CHHHHHHHHHhcCCCccEEEE--eCCCCC-CC-HHHHHHHh
Q 029986           17 GLRVLVV----DDDPIWLRILEKMLRKCLYEVTKCN---RAEIALDMLRMSKNGYDIVIS--DVHMPD-MD-GFKLHEQV   85 (184)
Q Consensus        17 ~~~Iliv----dd~~~~~~~l~~~L~~~~~~v~~~~---~~~~~~~~l~~~~~~~dlvil--D~~l~~-~~-g~~l~~~l   85 (184)
                      .-+|++.    |-+..=...+..+|+..||+|....   ..++..+.+.  +..||+|.+  ...+.. .. --++++.+
T Consensus        92 ~~~vll~~v~gd~HdiG~~iv~~~l~~~G~~Vi~LG~~vp~e~iv~~~~--~~~~d~v~l~~S~l~~~~~~~~~~~i~~l  169 (215)
T 3ezx_A           92 AGLAITFVAEGDIHDIGHRLVTTMLGANGFQIVDLGVDVLNENVVEEAA--KHKGEKVLLVGSALMTTSMLGQKDLMDRL  169 (215)
T ss_dssp             CCEEEEEECTTCCCCHHHHHHHHHHHHTSCEEEECCSSCCHHHHHHHHH--HTTTSCEEEEEECSSHHHHTHHHHHHHHH
T ss_pred             CCeEEEEeCCCChhHHHHHHHHHHHHHCCCeEEEcCCCCCHHHHHHHHH--HcCCCEEEEEchhcccCcHHHHHHHHHHH
Confidence            4477777    6677788888999999999987543   4677777776  456999999  876653 12 23456666


Q ss_pred             ccc-C--CCCEEEEEccCChHHHHHHHHcCCCceEe
Q 029986           86 GLE-M--DLPVIMMSVDGCTQDVMKGVTHGACNYLL  118 (184)
Q Consensus        86 ~~~-~--~~~iIi~~~~~~~~~~~~a~~~ga~~~l~  118 (184)
                      +.. .  ++||++=...-+.+.   +-+.||+.|-.
T Consensus       170 ~~~~~~~~v~v~vGG~~~~~~~---a~~iGad~~~~  202 (215)
T 3ezx_A          170 NEEKLRDSVKCMFGGAPVSDKW---IEEIGADATAE  202 (215)
T ss_dssp             HHTTCGGGSEEEEESSSCCHHH---HHHHTCCBCCS
T ss_pred             HHcCCCCCCEEEEECCCCCHHH---HHHhCCeEEEC
Confidence            543 2  566655444444433   34569987754

>2i2x_B MTAC, methyltransferase 1; TIM barrel and helix bundle (MTAB), rossman fold and helix B (MTAC); HET: B13; 2.50A {Methanosarcina barkeri}

Probab=89.15  E-value=5.7  Score=29.74  Aligned_cols=111  Identities=14%  Similarity=0.033  Sum_probs=70.4

Q ss_pred             CCeEEEE----eCCHHHHHHHHHHHHhcCCeEEEE---CCHHHHHHHHHhcCCCccEEEEeCCCCCC-C-HHHHHHHhcc
Q 029986           17 GLRVLVV----DDDPIWLRILEKMLRKCLYEVTKC---NRAEIALDMLRMSKNGYDIVISDVHMPDM-D-GFKLHEQVGL   87 (184)
Q Consensus        17 ~~~Iliv----dd~~~~~~~l~~~L~~~~~~v~~~---~~~~~~~~~l~~~~~~~dlvilD~~l~~~-~-g~~l~~~l~~   87 (184)
                      .-+|++.    |-+..-...+..+|+..||+|...   -..++..+.+.  ...||+|.+...++.. . --++++.++.
T Consensus       123 ~~~vlla~~~gd~HdiG~~iva~~L~~~G~~Vi~LG~~vp~e~l~~~~~--~~~~d~V~lS~l~~~~~~~~~~~i~~l~~  200 (258)
T 2i2x_B          123 KGTVVCHVAEGDVHDIGKNIVTALLRANGYNVVDLGRDVPAEEVLAAVQ--KEKPIMLTGTALMTTTMYAFKEVNDMLLE  200 (258)
T ss_dssp             SCEEEEEECTTCCCCHHHHHHHHHHHHTTCEEEEEEEECCSHHHHHHHH--HHCCSEEEEECCCTTTTTHHHHHHHHHHT
T ss_pred             CCeEEEEeCCCCccHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHH--HcCCCEEEEEeeccCCHHHHHHHHHHHHh
Confidence            4477777    566777888889999999987532   35666767766  3459999998876642 2 3346667754


Q ss_pred             c-CCCCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           88 E-MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        88 ~-~~~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      . +.+||++=....+.+.   +-..|++.|....   .+....+..+..
T Consensus       201 ~~~~~~v~vGG~~~~~~~---~~~igad~~~~da---~~av~~~~~l~~  243 (258)
T 2i2x_B          201 NGIKIPFACGGGAVNQDF---VSQFALGVYGEEA---ADAPKIADAIIA  243 (258)
T ss_dssp             TTCCCCEEEESTTCCHHH---HHTSTTEEECSST---THHHHHHHHHHT
T ss_pred             cCCCCcEEEECccCCHHH---HHHcCCeEEECCH---HHHHHHHHHHHc
Confidence            3 4566665443333333   2377887665533   445555555554

>1y80_A Predicted cobalamin binding protein; corrinoid, factor IIIM, methyl transferase, structural genomics, PSI, protein structure initiative; HET: B1M; 1.70A {Moorella thermoacetica}

Probab=88.94  E-value=3.4  Score=29.76  Aligned_cols=97  Identities=14%  Similarity=0.015  Sum_probs=62.7

Q ss_pred             CCeEEEE----eCCHHHHHHHHHHHHhcCCeEEEEC---CHHHHHHHHHhcCCCccEEEEeCCCCCCC--HHHHHHHhcc
Q 029986           17 GLRVLVV----DDDPIWLRILEKMLRKCLYEVTKCN---RAEIALDMLRMSKNGYDIVISDVHMPDMD--GFKLHEQVGL   87 (184)
Q Consensus        17 ~~~Iliv----dd~~~~~~~l~~~L~~~~~~v~~~~---~~~~~~~~l~~~~~~~dlvilD~~l~~~~--g~~l~~~l~~   87 (184)
                      .-+|++.    |-+..-...+..+|+..||++....   ..++..+.+.  ...||+|.+...++..-  --++++.++.
T Consensus        88 ~~~vll~~~~gd~H~iG~~~va~~l~~~G~~v~~LG~~vp~~~l~~~~~--~~~~d~v~lS~~~~~~~~~~~~~i~~l~~  165 (210)
T 1y80_A           88 VGKIVLGTVKGDLHDIGKNLVAMMLESGGFTVYNLGVDIEPGKFVEAVK--KYQPDIVGMSALLTTTMMNMKSTIDALIA  165 (210)
T ss_dssp             CCEEEEEEBTTCCCCHHHHHHHHHHHHTTCEEEECCSSBCHHHHHHHHH--HHCCSEEEEECCSGGGTHHHHHHHHHHHH
T ss_pred             CCEEEEEeCCCcccHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHH--HcCCCEEEEeccccccHHHHHHHHHHHHh
Confidence            3468777    6677788889999999999988544   4566677665  34599999988765421  2345556653


Q ss_pred             c---CCCCEEEEEccCChHHHHHHHHcCCCceEe
Q 029986           88 E---MDLPVIMMSVDGCTQDVMKGVTHGACNYLL  118 (184)
Q Consensus        88 ~---~~~~iIi~~~~~~~~~~~~a~~~ga~~~l~  118 (184)
                      .   +++||++=....+.+..   ...|++.|..
T Consensus       166 ~~~~~~~~v~vGG~~~~~~~~---~~~gad~~~~  196 (210)
T 1y80_A          166 AGLRDRVKVIVGGAPLSQDFA---DEIGADGYAP  196 (210)
T ss_dssp             TTCGGGCEEEEESTTCCHHHH---HHHTCSEECS
T ss_pred             cCCCCCCeEEEECCCCCHHHH---HHcCCeEEEC
Confidence            2   24666655444333332   4568886654

>1yad_A Regulatory protein TENI; TIM barrel, transcription; 2.10A {Bacillus subtilis} PDB: 3qh2_A*

Probab=87.86  E-value=4.4  Score=29.30  Aligned_cols=68  Identities=16%  Similarity=0.156  Sum_probs=48.3

Q ss_pred             EECCHHHHHHHHHhcCCCccEEEEeCCCCC-------CCHHHHHHHhcccCCCCEEEEEccCChHHHHHHHHcCCCceE
Q 029986           46 KCNRAEIALDMLRMSKNGYDIVISDVHMPD-------MDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYL  117 (184)
Q Consensus        46 ~~~~~~~~~~~l~~~~~~~dlvilD~~l~~-------~~g~~l~~~l~~~~~~~iIi~~~~~~~~~~~~a~~~ga~~~l  117 (184)
                      .+.+.+++.....   .+.|.|+++...+.       ..+++.++.++...++|++....- +.+.+..+++.|++++.
T Consensus       116 sv~t~~~~~~a~~---~gaD~i~~~~~f~~~~~~g~~~~~~~~l~~~~~~~~~pvia~GGI-~~~nv~~~~~~Ga~gv~  190 (221)
T 1yad_A          116 SVHSLEEAVQAEK---EDADYVLFGHVFETDCKKGLEGRGVSLLSDIKQRISIPVIAIGGM-TPDRLRDVKQAGADGIA  190 (221)
T ss_dssp             EECSHHHHHHHHH---TTCSEEEEECCC----------CHHHHHHHHHHHCCSCEEEESSC-CGGGHHHHHHTTCSEEE
T ss_pred             EcCCHHHHHHHHh---CCCCEEEECCccccCCCCCCCCCCHHHHHHHHHhCCCCEEEECCC-CHHHHHHHHHcCCCEEE
Confidence            5677777766654   45899999764432       235777887754457898887655 78888999999999875

>3vnd_A TSA, tryptophan synthase alpha chain; psychrophilic enzyme, cold adaptation; HET: PE8; 2.60A {Shewanella frigidimarina}

Probab=86.97  E-value=0.82  Score=34.74  Aligned_cols=58  Identities=14%  Similarity=0.216  Sum_probs=42.9

Q ss_pred             HHHHHHhccc-CCCCEEEEEccC------ChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           79 FKLHEQVGLE-MDLPVIMMSVDG------CTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        79 ~~l~~~l~~~-~~~~iIi~~~~~------~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      +++++.++.. .++|+++++-..      ...+..++.++|+++.+...+..++.......+.+.
T Consensus        83 ~~~v~~ir~~~~~~Pivlm~Y~npv~~~g~e~f~~~~~~aGvdgvii~Dlp~ee~~~~~~~~~~~  147 (267)
T 3vnd_A           83 FDIITKVRAQHPDMPIGLLLYANLVFANGIDEFYTKAQAAGVDSVLIADVPVEESAPFSKAAKAH  147 (267)
T ss_dssp             HHHHHHHHHHCTTCCEEEEECHHHHHHHCHHHHHHHHHHHTCCEEEETTSCGGGCHHHHHHHHHT
T ss_pred             HHHHHHHHhcCCCCCEEEEecCcHHHHhhHHHHHHHHHHcCCCEEEeCCCCHhhHHHHHHHHHHc
Confidence            6677777755 688998885322      245788899999999999888888777766666553

>3qja_A IGPS, indole-3-glycerol phosphate synthase; structural genomics, T structural genomics consortium, TBSGC, lyase; 1.29A {Mycobacterium tuberculosis} PDB: 3t40_A* 3t44_A* 3t55_A* 3t78_A* 4fb7_A*

Probab=85.74  E-value=9.8  Score=28.79  Aligned_cols=87  Identities=13%  Similarity=-0.029  Sum_probs=57.2

Q ss_pred             HHHHHHHHHHhcCCeE-EEECCHHHHHHHHHhcCCCccEEEEeCCCCC--CCHHHHHHHhccc-C-CCCEEEEEccCChH
Q 029986           29 WLRILEKMLRKCLYEV-TKCNRAEIALDMLRMSKNGYDIVISDVHMPD--MDGFKLHEQVGLE-M-DLPVIMMSVDGCTQ  103 (184)
Q Consensus        29 ~~~~l~~~L~~~~~~v-~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~--~~g~~l~~~l~~~-~-~~~iIi~~~~~~~~  103 (184)
                      ....+.......|..+ ..+++.+++.....   .++|+|-+.-.-..  .-+++.+.++... + ++|+|..+.-.+.+
T Consensus       150 ~l~~l~~~a~~lGl~~lvev~t~ee~~~A~~---~Gad~IGv~~r~l~~~~~dl~~~~~l~~~v~~~~pvVaegGI~t~e  226 (272)
T 3qja_A          150 VLVSMLDRTESLGMTALVEVHTEQEADRALK---AGAKVIGVNARDLMTLDVDRDCFARIAPGLPSSVIRIAESGVRGTA  226 (272)
T ss_dssp             HHHHHHHHHHHTTCEEEEEESSHHHHHHHHH---HTCSEEEEESBCTTTCCBCTTHHHHHGGGSCTTSEEEEESCCCSHH
T ss_pred             HHHHHHHHHHHCCCcEEEEcCCHHHHHHHHH---CCCCEEEECCCcccccccCHHHHHHHHHhCcccCEEEEECCCCCHH
Confidence            3444455556667754 46788888766654   35888888632111  1134556666433 3 67888877777789


Q ss_pred             HHHHHHHcCCCceEe
Q 029986          104 DVMKGVTHGACNYLL  118 (184)
Q Consensus       104 ~~~~a~~~ga~~~l~  118 (184)
                      .+..+.+.|++++++
T Consensus       227 dv~~l~~~GadgvlV  241 (272)
T 3qja_A          227 DLLAYAGAGADAVLV  241 (272)
T ss_dssp             HHHHHHHTTCSEEEE
T ss_pred             HHHHHHHcCCCEEEE
Confidence            999999999999985

>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=85.70  E-value=1.2  Score=33.95  Aligned_cols=58  Identities=14%  Similarity=0.179  Sum_probs=42.3

Q ss_pred             HHHHHHHhccc-CCCCEEEEEc------cCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           78 GFKLHEQVGLE-MDLPVIMMSV------DGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        78 g~~l~~~l~~~-~~~~iIi~~~------~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      .+++++.++.. .++|+++++-      +.......++.++|+++.+.-.+..++.......+.+
T Consensus        84 ~~~~v~~~r~~~~~~Pivlm~Y~n~v~~~g~~~f~~~~~~aGvdGvIipDlp~ee~~~~~~~~~~  148 (271)
T 3nav_A           84 CFELIAQIRARNPETPIGLLMYANLVYARGIDDFYQRCQKAGVDSVLIADVPTNESQPFVAAAEK  148 (271)
T ss_dssp             HHHHHHHHHHHCTTSCEEEEECHHHHHHTCHHHHHHHHHHHTCCEEEETTSCGGGCHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCCCEEEEecCcHHHHHhHHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHH
Confidence            35677777755 6899998862      2234568889999999999887877776666665544

>2gek_A Phosphatidylinositol mannosyltransferase (PIMA); GT4 glycosyltransferase, rossmann fold, complex; HET: GDP; 2.40A {Mycobacterium smegmatis} PDB: 2gej_A*

Probab=85.34  E-value=4.5  Score=31.40  Aligned_cols=108  Identities=10%  Similarity=0.052  Sum_probs=68.5

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEE--ECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTK--CNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVI   94 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~--~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iI   94 (184)
                      ..++.|+.+.+.  ..+...+++..-.+..  .-+..+..+++..    .|++++-....++-|..+++.+.  ..+|+|
T Consensus       240 ~~~l~i~G~~~~--~~l~~~~~~~~~~v~~~g~~~~~~~~~~~~~----adv~v~ps~~~e~~~~~~~Ea~a--~G~PvI  311 (406)
T 2gek_A          240 DVEILIVGRGDE--DELREQAGDLAGHLRFLGQVDDATKASAMRS----ADVYCAPHLGGESFGIVLVEAMA--AGTAVV  311 (406)
T ss_dssp             TCEEEEESCSCH--HHHHHHTGGGGGGEEECCSCCHHHHHHHHHH----SSEEEECCCSCCSSCHHHHHHHH--HTCEEE
T ss_pred             CeEEEEEcCCcH--HHHHHHHHhccCcEEEEecCCHHHHHHHHHH----CCEEEecCCCCCCCchHHHHHHH--cCCCEE
Confidence            567777777665  5555555443112222  2234455666552    58888764324444666777664  356776


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      ...    .....+.+..|..+++..|-+.+++.+.+..++..
T Consensus       312 ~~~----~~~~~e~i~~~~~g~~~~~~d~~~l~~~i~~l~~~  349 (406)
T 2gek_A          312 ASD----LDAFRRVLADGDAGRLVPVDDADGMAAALIGILED  349 (406)
T ss_dssp             ECC----CHHHHHHHTTTTSSEECCTTCHHHHHHHHHHHHHC
T ss_pred             Eec----CCcHHHHhcCCCceEEeCCCCHHHHHHHHHHHHcC
Confidence            532    24556777888899999999999999999988763

>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=84.28  E-value=1.6  Score=33.18  Aligned_cols=86  Identities=15%  Similarity=0.092  Sum_probs=55.3

Q ss_pred             CHHHHHHHHHh-cCCCccEEEEeCCCCCC----------------------CHHHHHHHhcccCCCCEEEEEcc------
Q 029986           49 RAEIALDMLRM-SKNGYDIVISDVHMPDM----------------------DGFKLHEQVGLEMDLPVIMMSVD------   99 (184)
Q Consensus        49 ~~~~~~~~l~~-~~~~~dlvilD~~l~~~----------------------~g~~l~~~l~~~~~~~iIi~~~~------   99 (184)
                      +.+...+.++. .+. .|+|.+++-..+-                      +.+++++.++...++|+++++-.      
T Consensus        28 ~~~~~~~~~~~l~~~-aD~IElG~PfsdP~adGp~Iq~a~~~Al~~G~~~~~~~~~v~~ir~~~~~Pii~m~y~n~v~~~  106 (271)
T 1ujp_A           28 SREGFLQAVEEVLPY-ADLLEIGLPYSDPLGDGPVIQRASELALRKGMSVQGALELVREVRALTEKPLFLMTYLNPVLAW  106 (271)
T ss_dssp             CHHHHHHHHHHHGGG-CSSEEEECCCCC----CHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCCSCEEEECCHHHHHHH
T ss_pred             ChHHHHHHHHHHHhc-CCEEEECCCCCCcccccHHHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCEEEEecCcHHHHh
Confidence            44444444432 244 8998888754321                      13566777776678999997421      


Q ss_pred             CChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986          100 GCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus       100 ~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      .....+..+.++|+++++.-.+..+++......+.+
T Consensus       107 g~~~f~~~~~~aG~dGviv~Dl~~ee~~~~~~~~~~  142 (271)
T 1ujp_A          107 GPERFFGLFKQAGATGVILPDLPPDEDPGLVRLAQE  142 (271)
T ss_dssp             CHHHHHHHHHHHTCCEEECTTCCGGGCHHHHHHHHH
T ss_pred             hHHHHHHHHHHcCCCEEEecCCCHHHHHHHHHHHHH
Confidence            224556778999999999887777766666655543

>2xij_A Methylmalonyl-COA mutase, mitochondrial; isomerase, organic aciduria, vitamin B12; HET: B12 5AD BTB; 1.95A {Homo sapiens} PDB: 2xiq_A* 3bic_A

Probab=84.13  E-value=13  Score=32.50  Aligned_cols=116  Identities=11%  Similarity=-0.081  Sum_probs=71.6

Q ss_pred             CCeEEEEe----CCHHHHHHHHHHHHhcCCeEEEEC---CHHHHHHHHHhcCCCccEEEEeCCCCCC--CHHHHHHHhcc
Q 029986           17 GLRVLVVD----DDPIWLRILEKMLRKCLYEVTKCN---RAEIALDMLRMSKNGYDIVISDVHMPDM--DGFKLHEQVGL   87 (184)
Q Consensus        17 ~~~Ilivd----d~~~~~~~l~~~L~~~~~~v~~~~---~~~~~~~~l~~~~~~~dlvilD~~l~~~--~g~~l~~~l~~   87 (184)
                      ..+|++..    .+..-...+..+|...||+|....   ..++..+...  +..+|+|.+-..+..-  ..-++++.|+.
T Consensus       604 r~kVvlatvg~D~HdiG~~iVa~~l~~~GfeVi~lG~~v~~eeiv~aA~--e~~adiVglSsl~~~~~~~~~~vi~~Lr~  681 (762)
T 2xij_A          604 RPRLLVAKMGQDGHDRGAKVIATGFADLGFDVDIGPLFQTPREVAQQAV--DADVHAVGVSTLAAGHKTLVPELIKELNS  681 (762)
T ss_dssp             CCEEEEECCSSCCCCHHHHHHHHHHHHTTCEEEECCTTCCHHHHHHHHH--HTTCSEEEEEECSSCHHHHHHHHHHHHHH
T ss_pred             CCEEEEEecCcchhhHHHHHHHHHHHhCCeEEeeCCCCCCHHHHHHHHH--HcCCCEEEEeeecHHHHHHHHHHHHHHHh
Confidence            34677653    555666778888999999997543   4677777776  4568999987665431  23445666653


Q ss_pred             c-CCCCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHH
Q 029986           88 E-MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVA  134 (184)
Q Consensus        88 ~-~~~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~  134 (184)
                      . ..-..|++....-......+.+.|+++|+..--+..+....+...+
T Consensus       682 ~G~~dv~VivGG~~P~~d~~~l~~~GaD~~f~pgtd~~e~~~~i~~~l  729 (762)
T 2xij_A          682 LGRPDILVMCGGVIPPQDYEFLFEVGVSNVFGPGTRIPKAAVQVLDDI  729 (762)
T ss_dssp             TTCTTSEEEEEESCCGGGHHHHHHHTCCEEECTTCCHHHHHHHHHHHH
T ss_pred             cCCCCCEEEEeCCCCcccHHHHHhCCCCEEeCCCCCHHHHHHHHHHHH
Confidence            3 2122344443122223445678999999986656666655555544

>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=83.50  E-value=5.3  Score=29.35  Aligned_cols=56  Identities=9%  Similarity=0.147  Sum_probs=38.4

Q ss_pred             HHHHHHHhcccCCCCEEEEEccCC------hHHHHHHHHcCCCceEeCCCCHHHHHHHHHHH
Q 029986           78 GFKLHEQVGLEMDLPVIMMSVDGC------TQDVMKGVTHGACNYLLKPIRIKELRNIWQHV  133 (184)
Q Consensus        78 g~~l~~~l~~~~~~~iIi~~~~~~------~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~  133 (184)
                      +.++++.+++..+.||.+++....      ...+..++++|++..+......++....++.+
T Consensus        68 ~~~~i~~i~~~~~~pv~~~~~~~~~~~~~~~~~~~~~~~~Gad~v~~~~~~~~~~~~~~~~~  129 (248)
T 1geq_A           68 AFWIVKEFRRHSSTPIVLMTYYNPIYRAGVRNFLAEAKASGVDGILVVDLPVFHAKEFTEIA  129 (248)
T ss_dssp             HHHHHHHHHTTCCCCEEEEECHHHHHHHCHHHHHHHHHHHTCCEEEETTCCGGGHHHHHHHH
T ss_pred             HHHHHHHHHhhCCCCEEEEeccchhhhcCHHHHHHHHHHCCCCEEEECCCChhhHHHHHHHH
Confidence            467788887655788887763222      46778899999999988766655554444443

>1qv9_A F420-dependent methylenetetrahydromethanopterin dehydrogenase; monomer: alpha/beta domain, helix bundle, trimer of dimers, oxidoreductase; HET: MSE; 1.54A {Methanopyrus kandleri} SCOP: c.127.1.1 PDB: 1u6i_A 1u6j_A 1u6k_A* 3iqe_A* 3iqf_A* 3iqz_A*

Probab=83.34  E-value=2.5  Score=31.54  Aligned_cols=60  Identities=12%  Similarity=0.148  Sum_probs=45.3

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEEEEccCChHHHHHHHHcCCCceEeCCC
Q 029986           61 KNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPI  121 (184)
Q Consensus        61 ~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~  121 (184)
                      .+.||++|+=.-.+..-|-.-.+.+-+..++|.|++++..... ..++++..-.+|+.-+.
T Consensus        62 ~~~pDfvI~isPN~a~PGP~~ARE~l~~~~iP~IvI~D~p~~K-~kd~l~~~g~GYIivk~  121 (283)
T 1qv9_A           62 DFEPDFIVYGGPNPAAPGPSKAREMLADSEYPAVIIGDAPGLK-VKDEMEEQGLGYILVKP  121 (283)
T ss_dssp             HHCCSEEEEECSCTTSHHHHHHHHHHHTSSSCEEEEEEGGGGG-GHHHHHHTTCEEEEETT
T ss_pred             hcCCCEEEEECCCCCCCCchHHHHHHHhCCCCEEEEcCCcchh-hHHHHHhcCCcEEEEec
Confidence            5679999997766777787777776555789999998765544 66888888888886554

>1req_A Methylmalonyl-COA mutase; isomerase, intramolecular transferase; HET: B12 DCA; 2.00A {Propionibacterium freudenreichii subspshermanii} SCOP: c.1.19.1 c.23.6.1 PDB: 2req_A* 3req_A* 4req_A* 6req_A* 7req_A* 5req_A* 1e1c_A*

Probab=83.27  E-value=15  Score=31.99  Aligned_cols=116  Identities=12%  Similarity=-0.048  Sum_probs=72.2

Q ss_pred             CCeEEEE----eCCHHHHHHHHHHHHhcCCeEEEEC---CHHHHHHHHHhcCCCccEEEEeCCCCCC--CHHHHHHHhcc
Q 029986           17 GLRVLVV----DDDPIWLRILEKMLRKCLYEVTKCN---RAEIALDMLRMSKNGYDIVISDVHMPDM--DGFKLHEQVGL   87 (184)
Q Consensus        17 ~~~Iliv----dd~~~~~~~l~~~L~~~~~~v~~~~---~~~~~~~~l~~~~~~~dlvilD~~l~~~--~g~~l~~~l~~   87 (184)
                      ..+|++.    |.+..-...+..+|+..||+|....   ..++..+...  +..+|+|.+-..+..-  ..-++++.|+.
T Consensus       596 r~kVvlatvg~D~HdiG~~iVa~~l~~~GfeVi~lG~~v~~eeiv~aA~--e~~adiVglSsl~~~~~~~~~~vi~~L~~  673 (727)
T 1req_A          596 RPRILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQTPEETARQAV--EADVHVVGVSSLAGGHLTLVPALRKELDK  673 (727)
T ss_dssp             CCEEEEECBTTCCCCHHHHHHHHHHHHHTCEEEECCTTBCHHHHHHHHH--HTTCSEEEEEECSSCHHHHHHHHHHHHHH
T ss_pred             CCEEEEEeCCcchhHHHHHHHHHHHHhCCeEEEeCCCCCCHHHHHHHHH--HcCCCEEEEeeecHhHHHHHHHHHHHHHh
Confidence            3467766    4566667778888999999997543   4677777776  4569999997765431  23445666654


Q ss_pred             c-CCCCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHH
Q 029986           88 E-MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVA  134 (184)
Q Consensus        88 ~-~~~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~  134 (184)
                      . ..-..|++....-......+.+.|+++|+..-.+..++...+...+
T Consensus       674 ~G~~~i~VivGG~~p~~d~~~l~~~GaD~~f~~gt~~~e~a~~l~~~l  721 (727)
T 1req_A          674 LGRPDILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLVKKL  721 (727)
T ss_dssp             TTCTTSEEEEEESCCGGGHHHHHHTTEEEEECTTCCHHHHHHHHHHHH
T ss_pred             cCCCCCEEEEcCCCccccHHHHHhCCCCEEEcCCccHHHHHHHHHHHH
Confidence            3 2123444443222333445688999999986666666655554443

>1xi3_A Thiamine phosphate pyrophosphorylase; structural genomics, southeast collaboratory for structural genomics, hyperthermophIle; 1.70A {Pyrococcus furiosus} SCOP: c.1.3.1

Probab=81.84  E-value=8.5  Score=27.35  Aligned_cols=68  Identities=15%  Similarity=0.190  Sum_probs=47.0

Q ss_pred             EECCHHHHHHHHHhcCCCccEEEEeCCCCC-------CCHHHHHHHhcccCCCCEEEEEccCChHHHHHHHHcCCCceE
Q 029986           46 KCNRAEIALDMLRMSKNGYDIVISDVHMPD-------MDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYL  117 (184)
Q Consensus        46 ~~~~~~~~~~~l~~~~~~~dlvilD~~l~~-------~~g~~l~~~l~~~~~~~iIi~~~~~~~~~~~~a~~~ga~~~l  117 (184)
                      .+.+..++.....   .++|.++++...+.       ..+++.++.++...++|+++...-. .+.+..+++.|++++.
T Consensus       114 ~~~t~~e~~~~~~---~g~d~i~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~pvia~GGI~-~~nv~~~~~~Ga~gv~  188 (215)
T 1xi3_A          114 SVYSLEEALEAEK---KGADYLGAGSVFPTKTKEDARVIGLEGLRKIVESVKIPVVAIGGIN-KDNAREVLKTGVDGIA  188 (215)
T ss_dssp             EESSHHHHHHHHH---HTCSEEEEECSSCC----CCCCCHHHHHHHHHHHCSSCEEEESSCC-TTTHHHHHTTTCSEEE
T ss_pred             ecCCHHHHHHHHh---cCCCEEEEcCCccCCCCCCCCCcCHHHHHHHHHhCCCCEEEECCcC-HHHHHHHHHcCCCEEE
Confidence            4567777655433   34899998764443       3477888887654578887765443 7777788899999885

>1rd5_A Tryptophan synthase alpha chain, chloroplast; hydroxamic acid, diboa, dimboa, indole, indole-glycerol-PHOS lyase; 2.02A {Zea mays} SCOP: c.1.2.4 PDB: 1tjr_A

Probab=81.47  E-value=2.3  Score=31.78  Aligned_cols=57  Identities=14%  Similarity=0.261  Sum_probs=37.9

Q ss_pred             HHHHHHHhcccCCCCEEEEEccCChH---HHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           78 GFKLHEQVGLEMDLPVIMMSVDGCTQ---DVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        78 g~~l~~~l~~~~~~~iIi~~~~~~~~---~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      ++++++.++...++|++++. +.+..   ....+.++|+++++......+++.+.+..+.+
T Consensus        82 ~~~~i~~ir~~~~~Pv~~m~-~~~~~~~~~~~~a~~aGadgv~v~d~~~~~~~~~~~~~~~  141 (262)
T 1rd5_A           82 VLEMLREVTPELSCPVVLLS-YYKPIMFRSLAKMKEAGVHGLIVPDLPYVAAHSLWSEAKN  141 (262)
T ss_dssp             HHHHHHHHGGGCSSCEEEEC-CSHHHHSCCTHHHHHTTCCEEECTTCBTTTHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCCEEEEe-cCcHHHHHHHHHHHHcCCCEEEEcCCChhhHHHHHHHHHH
Confidence            56778888766788988764 22221   12348899999999876666666666665543

>4e38_A Keto-hydroxyglutarate-aldolase/keto-deoxy-phospho aldolase; lyase; 1.64A {Vibrionales bacterium swat-3}

Probab=81.42  E-value=6.7  Score=29.02  Aligned_cols=97  Identities=11%  Similarity=0.055  Sum_probs=61.8

Q ss_pred             HHHHHHhcCC-eEEEECCHHHHHHHHHh-cCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEEEEccCChHHHHHHHH
Q 029986           33 LEKMLRKCLY-EVTKCNRAEIALDMLRM-SKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVT  110 (184)
Q Consensus        33 l~~~L~~~~~-~v~~~~~~~~~~~~l~~-~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi~~~~~~~~~~~~a~~  110 (184)
                      +.+.|.+.+. -|....+.+++..+.+. ...+..++=+  .+...++.+.++.+++...-.++-..+-.+.+.+..+.+
T Consensus        27 ~~~~l~~~~vv~Vir~~~~~~a~~~a~al~~gGi~~iEv--t~~t~~a~e~I~~l~~~~~~~~iGaGTVlt~~~a~~Ai~  104 (232)
T 4e38_A           27 INNQLKALKVIPVIAIDNAEDIIPLGKVLAENGLPAAEI--TFRSDAAVEAIRLLRQAQPEMLIGAGTILNGEQALAAKE  104 (232)
T ss_dssp             HHHHHHHHCEEEEECCSSGGGHHHHHHHHHHTTCCEEEE--ETTSTTHHHHHHHHHHHCTTCEEEEECCCSHHHHHHHHH
T ss_pred             HHHHHHhCCEEEEEEcCCHHHHHHHHHHHHHCCCCEEEE--eCCCCCHHHHHHHHHHhCCCCEEeECCcCCHHHHHHHHH
Confidence            3445555453 45555666666666542 2445665544  445667889999886543234555555566888999999


Q ss_pred             cCCCceEeCCCCHHHHHHHHHH
Q 029986          111 HGACNYLLKPIRIKELRNIWQH  132 (184)
Q Consensus       111 ~ga~~~l~kP~~~~~l~~~l~~  132 (184)
                      +||+ |+..|....++.+..+.
T Consensus       105 AGA~-fIvsP~~~~~vi~~~~~  125 (232)
T 4e38_A          105 AGAT-FVVSPGFNPNTVRACQE  125 (232)
T ss_dssp             HTCS-EEECSSCCHHHHHHHHH
T ss_pred             cCCC-EEEeCCCCHHHHHHHHH
Confidence            9998 77778776777666554

>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=80.61  E-value=16  Score=27.39  Aligned_cols=81  Identities=12%  Similarity=0.145  Sum_probs=53.0

Q ss_pred             HHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc--cCCCCEEEEEccCChHHHHHHHHcCCCceEe-CCCCHHHHH
Q 029986           51 EIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL--EMDLPVIMMSVDGCTQDVMKGVTHGACNYLL-KPIRIKELR  127 (184)
Q Consensus        51 ~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~--~~~~~iIi~~~~~~~~~~~~a~~~ga~~~l~-kP~~~~~l~  127 (184)
                      ....+.+.  ..++|.|++|++-.-.+.-++...++.  ....++++=....+...+..+++.|+++.++ |--+.+++.
T Consensus        27 p~~~e~a~--~~g~D~vilDlEhav~~~~k~~~~l~a~~~~~~~~~VRVn~~~~~di~~~ld~G~~gI~lP~v~saed~~  104 (261)
T 3qz6_A           27 PDIVRIYA--EAGLDYFIVDCEHAAYTFREINHLVSVAKNAGVSVLVRIPQVDRAHVQRLLDIGAEGFMIPGVQSAETMR  104 (261)
T ss_dssp             TTHHHHHH--HTTCSEEEEESSSSCCCHHHHHHHHHHHHHHTCEEEEECSSCCHHHHHHHHHHTCCEEEETTCCSHHHHH
T ss_pred             HHHHHHHh--cCCcCEEEEeccCCCCCHHHHHHHHHHHhhcCCeEEEEeCCCCHHHHHHHHhcCCCEEEECCcCCHHHHH
Confidence            44444444  356999999998877776666555532  1234444434445567888999999998765 334677887


Q ss_pred             HHHHHH
Q 029986          128 NIWQHV  133 (184)
Q Consensus       128 ~~l~~~  133 (184)
                      .....+
T Consensus       105 ~~~~~~  110 (261)
T 3qz6_A          105 ETVRLA  110 (261)
T ss_dssp             HHHHHH
T ss_pred             HHHHHh
Confidence            777665

---

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	184
d1dz3a_	123	c.23.1.1 (A:) Sporulation response regulator Spo0A	1e-24
d1dcfa_	134	c.23.1.2 (A:) Receiver domain of the ethylene rece	2e-23
d1u0sy_	118	c.23.1.1 (Y:) CheY protein {Thermotoga maritima [T	5e-23
d1peya_	119	c.23.1.1 (A:) Sporulation response regulator Spo0F	9e-23
d2a9pa1	117	c.23.1.1 (A:2-118) DNA-binding response regulator	1e-22
d1a04a2	138	c.23.1.1 (A:5-142) Nitrate/nitrite response regula	2e-22
d1k68a_	140	c.23.1.1 (A:) Response regulator for cyanobacteria	3e-21
d1zesa1	121	c.23.1.1 (A:3-123) PhoB receiver domain {Escherich	3e-21
d1jbea_	128	c.23.1.1 (A:) CheY protein {Escherichia coli [TaxI	1e-20
d2r25b1	128	c.23.1.1 (B:1087-1214) Response regulator Sin1 {Ba	2e-20
d1xhfa1	121	c.23.1.1 (A:2-122) Aerobic respiration control pro	2e-20
d1i3ca_	144	c.23.1.1 (A:) Response regulator for cyanobacteria	2e-20
d2b4aa1	118	c.23.1.1 (A:2-119) Hypothetical protein BH3024 {Ba	4e-20
d1zgza1	120	c.23.1.1 (A:2-121) TorCAD operon transcriptional r	5e-20
d2ayxa1	133	c.23.1.1 (A:817-949) Sensor kinase protein RcsC, C	1e-19
d1zh2a1	119	c.23.1.1 (A:2-120) Transcriptional regulatory prot	2e-19
d1a2oa1	140	c.23.1.1 (A:1-140) Methylesterase CheB, N-terminal	2e-19
d1krwa_	123	c.23.1.1 (A:) NTRC receiver domain {Salmonella typ	2e-19
d1s8na_	190	c.23.1.1 (A:) Probable two-component system transc	3e-19
d1mb3a_	123	c.23.1.1 (A:) Cell division response regulator Div	3e-19
d1p6qa_	129	c.23.1.1 (A:) CheY protein {Sinorhizobium meliloti	2e-18
d1dbwa_	123	c.23.1.1 (A:) Transcriptional regulatory protein F	3e-18
d1yioa2	128	c.23.1.1 (A:3-130) Response regulatory protein Sty	5e-18
d1qkka_	140	c.23.1.1 (A:) Transcriptional regulatory protein D	6e-18
d1ny5a1	137	c.23.1.1 (A:1-137) Transcriptional activator sigm5	9e-18
d1kgsa2	122	c.23.1.1 (A:2-123) PhoB receiver domain {Thermotog	1e-17
d1mvoa_	121	c.23.1.1 (A:) PhoP receiver domain {Bacillus subti	2e-17
d1k66a_	149	c.23.1.1 (A:) Response regulator for cyanobacteria	6e-17
d1ys7a2	121	c.23.1.1 (A:7-127) Transcriptional regulatory prot	7e-17
d2pl1a1	119	c.23.1.1 (A:1-119) PhoP receiver domain {Escherich	2e-16
d1w25a1	139	c.23.1.1 (A:2-140) Response regulator PleD, receiv	5e-16
d1w25a2	153	c.23.1.1 (A:141-293) Response regulator PleD, rece	1e-15
d1qo0d_	189	c.23.1.3 (D:) Positive regulator of the amidase op	2e-15
d1p2fa2	120	c.23.1.1 (A:1-120) Response regulator DrrB {Thermo	4e-15

>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 = 90.6 bits (225), Expect = 1e-24
 Identities = 30/120 (25%), Positives = 58/120 (48%), Gaps = 6/120 (5%)

Query: 18  LRVLVVDDDPIWLRILEKMLRK--CLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPD 75
           ++V + DD+   + +L++ +     +  +      +  L ML   +   DI++ D+ MP 
Sbjct: 2   IKVCIADDNRELVSLLDEYISSQPDMEVIGTAYNGQDCLQMLE--EKRPDILLLDIIMPH 59

Query: 76  MDGFKLHEQV--GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHV 133
           +DG  + E++  G E    VIM++  G      K V  GA  ++LKP  ++ L +  + V
Sbjct: 60  LDGLAVLERIRAGFEHQPNVIMLTAFGQEDVTKKAVELGASYFILKPFDMENLAHHIRQV 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 = 87.7 bits (217), Expect = 2e-23
 Identities = 27/132 (20%), Positives = 62/132 (46%), Gaps = 9/132 (6%)

Query: 16  AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPD 75
            GL+VLV+D++ +   + + +L     EVT  +  E     LR+  + + +V  DV MP 
Sbjct: 6   TGLKVLVMDENGVSRMVTKGLLVHLGCEVTTVSSNEEC---LRVVSHEHKVVFMDVCMPG 62

Query: 76  MDGFKLHEQVGLEM------DLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNI 129
           ++ +++  ++  +          ++ +S +       K ++ G    LLKP+ +  +R++
Sbjct: 63  VENYQIALRIHEKFTKQRHQRPLLVALSGNTDKSTKEKCMSFGLDGVLLKPVSLDNIRDV 122

Query: 130 WQHVAQQPKPFE 141
              + +    +E
Sbjct: 123 LSDLLEPRVLYE 134

>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 = 86.5 bits (214), Expect = 5e-23
 Identities = 30/120 (25%), Positives = 60/120 (50%), Gaps = 4/120 (3%)

Query: 17  GLRVLVVDDDPIWLRILEKMLRKCLYE-VTKCNRAEIALDMLRMSKNGYDIVISDVHMPD 75
           G RVL+VDD      +L+ ++ K  YE   +      A++  +  K   DIV  D+ MP+
Sbjct: 1   GKRVLIVDDAAFMRMMLKDIITKAGYEVAGEATNGREAVEKYKELK--PDIVTMDITMPE 58

Query: 76  MDGFKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVA 134
           M+G    +++  ++ +  +I+ S  G    V++ +  GA ++++KP +   +      V+
Sbjct: 59  MNGIDAIKEIMKIDPNAKIIVCSAMGQQAMVIEAIKAGAKDFIVKPFQPSRVVEALNKVS 118

>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 = 85.8 bits (212), Expect = 9e-23
 Identities = 29/111 (26%), Positives = 59/111 (53%), Gaps = 3/111 (2%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           ++L+VDD      +L ++  K  Y+  +      ALD++   K   D+V+ D+ +P MDG
Sbjct: 3   KILIVDDQSGIRILLNEVFNKEGYQTFQAANGLQALDIVT--KERPDLVLLDMKIPGMDG 60

Query: 79  FKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRN 128
            ++ +++  ++ ++ VI+M+  G    + +    GA  +  KP  I E+R+
Sbjct: 61  IEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFAKPFDIDEIRD 111

>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 = 85.8 bits (212), Expect = 1e-22
 Identities = 30/115 (26%), Positives = 59/115 (51%), Gaps = 2/115 (1%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           ++L+VDD+     I++  + K  YEV        AL+         DI+I D+ +P++DG
Sbjct: 2   KILIVDDEKPISDIIKFNMTKEGYEVVTAFNGREALEQFE--AEQPDIIILDLMLPEIDG 59

Query: 79  FKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHV 133
            ++ + +     +P++M+S      D + G+  GA +Y+ KP   +EL+   + +
Sbjct: 60  LEVAKTIRKTSSVPILMLSAKDSEFDKVIGLELGADDYVTKPFSNRELQARVKAL 114

>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 = 85.3 bits (211), Expect = 2e-22
 Identities = 25/129 (19%), Positives = 61/129 (47%), Gaps = 5/129 (3%)

Query: 18  LRVLVVDDDPIWLRILEKMLRKC--LYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPD 75
             +L++DD P+    +++++     +  V + +  E  +++        D+++ D++MP 
Sbjct: 3   ATILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAE--SLDPDLILLDLNMPG 60

Query: 76  MDGFKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVA 134
           M+G +  +++    +   +++ SV    +DV+  +  GA  YLLK +  ++L       A
Sbjct: 61  MNGLETLDKLREKSLSGRIVVFSVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALHQAA 120

Query: 135 QQPKPFEES 143
                  E+
Sbjct: 121 AGEMVLSEA 129

>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 = 82.8 bits (204), Expect = 3e-21
 Identities = 25/139 (17%), Positives = 58/139 (41%), Gaps = 17/139 (12%)

Query: 16  AGLRVLVVDDDPIWLRILEKMLRK--CLYEVTKCNRAEIALDMLRM-----SKNGYDIVI 68
           A  ++ +V+D+   +R++++ L      +EV        A+  LR      + +  D+++
Sbjct: 1   AHKKIFLVEDNKADIRLIQEALANSTVPHEVVTVRDGMEAMAYLRQEGEYANASRPDLIL 60

Query: 69  SDVHMPDMDGFKLHEQVGLEM---DLPVIMMSVDGCTQDVMKGVTHGACNYLLKPI---- 121
            D+++P  DG ++  ++  +     +PV+++S      D+          Y+ K      
Sbjct: 61  LDLNLPKKDGREVLAEIKSDPTLKRIPVVVLSTSINEDDIFHSYDLHVNCYITKSANLSQ 120

Query: 122 ---RIKELRNIWQHVAQQP 137
               +K +   W   A  P
Sbjct: 121 LFQIVKGIEEFWLSTATLP 139

>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 = 82.3 bits (203), Expect = 3e-21
 Identities = 27/112 (24%), Positives = 59/112 (52%), Gaps = 5/112 (4%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           R+LVV+D+     ++  +L +  ++  +    + A++ L   +   D+++ D  +P   G
Sbjct: 2   RILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLN--EPWPDLILLDWMLPGGSG 59

Query: 79  FKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
            +  + +    +  D+PV+M++  G  +D ++G+  GA +Y+ KP   KEL 
Sbjct: 60  IQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSPKELV 111

>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 = 80.0 bits (197), Expect = 2e-20
 Identities = 25/117 (21%), Positives = 56/117 (47%), Gaps = 6/117 (5%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYE-VTKCNRAEIALDMLRM---SKNGYDIVISDVHMP 74
           ++LVV+D+ +   ++++ML     E +      + A D ++        Y+++  DV MP
Sbjct: 3   KILVVEDNHVNQEVIKRMLNLEGIENIELACDGQEAFDKVKELTSKGENYNMIFMDVQMP 62

Query: 75  DMDGFKLHEQV--GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNI 129
            +DG    + +   L    P++ ++      ++ + +  G   +L KPI+  +L+ I
Sbjct: 63  KVDGLLSTKMIRRDLGYTSPIVALTAFADDSNIKECLESGMNGFLSKPIKRPKLKTI 119

>d1xhfa1 c.23.1.1 (A:2-122) Aerobic respiration control protein ArcA, N-terminal domain {Escherichia coli [TaxId: 562]} Length = 121

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Aerobic respiration control protein ArcA, N-terminal domain
species: Escherichia coli [TaxId: 562]

 Score = 80.1 bits (197), Expect = 2e-20
 Identities = 22/115 (19%), Positives = 56/115 (48%), Gaps = 2/115 (1%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
            +L+V+D+ +    L+ +     Y+V +         +L   +   ++VI D+++P  +G
Sbjct: 4   HILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQILS--EYDINLVIMDINLPGKNG 61

Query: 79  FKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHV 133
             L  ++  + ++ ++ ++      D + G+  GA +Y+ KP   +EL    +++
Sbjct: 62  LLLARELREQANVALMFLTGRDNEVDKILGLEIGADDYITKPFNPRELTIRARNL 116

>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 = 80.5 bits (198), Expect = 2e-20
 Identities = 21/136 (15%), Positives = 55/136 (40%), Gaps = 17/136 (12%)

Query: 19  RVLVVDDDPIWLRILEKMLRK--CLYEVTKCNRAEIALDMLRMSKNG-----YDIVISDV 71
            +L+V+D     R+++++L+     +E+        A+  L+           ++++ D+
Sbjct: 5   VILLVEDSKADSRLVQEVLKTSTIDHELIILRDGLAAMAFLQQQGEYENSPRPNLILLDL 64

Query: 72  HMPDMDGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPI------- 121
           ++P  DG ++  ++        +PV++++      DV+         YL K         
Sbjct: 65  NLPKKDGREVLAEIKQNPDLKRIPVVVLTTSHNEDDVIASYELHVNCYLTKSRNLKDLFK 124

Query: 122 RIKELRNIWQHVAQQP 137
            ++ + + W      P
Sbjct: 125 MVQGIESFWLETVTLP 140

>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 = 79.2 bits (195), Expect = 4e-20
 Identities = 25/111 (22%), Positives = 47/111 (42%), Gaps = 5/111 (4%)

Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMD 77
            RV +V+D+P    +++  L +   EVT                +  D++I    + D+ 
Sbjct: 3   FRVTLVEDEPSHATLIQYHLNQLGAEVTVHPSGSAFFQHRS-QLSTCDLLIVSDQLVDLS 61

Query: 78  GFKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
            F L + V        V++++      ++++   H   +YL KP  I ELR
Sbjct: 62  IFSLLDIVKEQTKQPSVLILT--TGRHELIESSEHNL-SYLQKPFAISELR 109

>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 = 78.9 bits (194), Expect = 5e-20
 Identities = 22/109 (20%), Positives = 55/109 (50%), Gaps = 2/109 (1%)

Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMD 77
             +++V+D+P+    L+    +  Y V+         ++++      D+++ D+++PD +
Sbjct: 2   HHIVIVEDEPVTQARLQSYFTQEGYTVSVTASGAGLREIMQ--NQSVDLILLDINLPDEN 59

Query: 78  GFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
           G  L   +     + +I+++      D + G+  GA +Y+ KP+ ++EL
Sbjct: 60  GLMLTRALRERSTVGIILVTGRSDRIDRIVGLEMGADDYVTKPLELREL 108

>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 = 78.6 bits (193), Expect = 1e-19
 Identities = 42/136 (30%), Positives = 74/136 (54%), Gaps = 5/136 (3%)

Query: 9   AVSDQFPAGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVI 68
           AVSD     + +LVVDD PI  R+L   L    Y+    N    AL++L  +    DIV+
Sbjct: 2   AVSD--NDDMMILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVLSKNH--IDIVL 57

Query: 69  SDVHMPDMDGFKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           SDV+MP+MDG++L +++  L + LPVI ++ +   ++  + +  G  + L KP+ +  ++
Sbjct: 58  SDVNMPNMDGYRLTQRIRQLGLTLPVIGVTANALAEEKQRCLESGMDSCLSKPVTLDVIK 117

Query: 128 NIWQHVAQQPKPFEES 143
                 A++ +   +S
Sbjct: 118 QTLTLYAERVRKSRDS 133

>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 = 77.4 bits (190), Expect = 2e-19
 Identities = 30/109 (27%), Positives = 48/109 (44%), Gaps = 2/109 (1%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
            VL+V+D+    R L   L      V +    +  L          D++I D+ +PD DG
Sbjct: 2   NVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEAA--TRKPDLIILDLGLPDGDG 59

Query: 79  FKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
            +    +     +PVI++S      D +  +  GA +YL KP  I EL+
Sbjct: 60  IEFIRDLRQWSAVPVIVLSARSEESDKIAALDAGADDYLSKPFGIGELQ 108

>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 = 77.7 bits (191), Expect = 2e-19
 Identities = 28/108 (25%), Positives = 55/108 (50%), Gaps = 6/108 (5%)

Query: 18  LRVLVVDDDPIWLRILEKMLRKC--LYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPD 75
           +RVL VDD  +  +I+ +++     +  V       +A D+++  K   D++  DV MP 
Sbjct: 4   IRVLSVDDSALMRQIMTEIINSHSDMEMVATAPDPLVARDLIK--KFNPDVLTLDVEMPR 61

Query: 76  MDGFKLHEQVGLEMDLPVIMMSV--DGCTQDVMKGVTHGACNYLLKPI 121
           MDG    E++     +PV+M+S      ++  ++ +  GA +++ KP 
Sbjct: 62  MDGLDFLEKLMRLRPMPVVMVSSLTGKGSEVTLRALELGAIDFVTKPQ 109

>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 = 77.5 bits (190), Expect = 2e-19
 Identities = 35/119 (29%), Positives = 49/119 (41%), Gaps = 3/119 (2%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
            V VVDDD     +LE+ L       T        L  L       D+++SD+ MP MDG
Sbjct: 5   IVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAALA--SKTPDVLLSDIRMPGMDG 62

Query: 79  FKLHEQVGLEM-DLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ 136
             L +Q+      LPVI+M+        +     GA +YL KP  I E   + +     
Sbjct: 63  LALLKQIKQRHPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDIDEAVALVERAISH 121

>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 = 78.7 bits (193), Expect = 3e-19
 Identities = 32/165 (19%), Positives = 69/165 (41%), Gaps = 3/165 (1%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTK-CNRAEIALDMLRMSKNGYDIVISDVHMPDMD 77
           RVL+ +D+ +    L +MLR+  YE+       + A+++  + K   D+VI DV MP  D
Sbjct: 5   RVLIAEDEALIRMDLAEMLREEGYEIVGEAGDGQEAVELAELHK--PDLVIMDVKMPRRD 62

Query: 78  GFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQP 137
           G     ++  +   P+++++       V +    GA  YL+KP  I +L    +    + 
Sbjct: 63  GIDAASEIASKRIAPIVVLTAFSQRDLVERARDAGAMAYLVKPFSISDLIPAIELAVSRF 122

Query: 138 KPFEESDDSYSVNQGNWRTSNRRKDEEEEAEKRDDTSTLKKPRFL 182
           +     +   +       T    +  +   + +   +     +++
Sbjct: 123 REITALEGEVATLSERLETRKLVERAKGLLQTKHGMTEPDAFKWI 167

>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 = 77.0 bits (189), Expect = 3e-19
 Identities = 26/123 (21%), Positives = 59/123 (47%), Gaps = 6/123 (4%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           +VL+V+D+ + +++   +L    YE  +      AL + R  +N  D+++ D+ +P++ G
Sbjct: 3   KVLIVEDNELNMKLFHDLLEAQGYETLQTREGLSALSIAR--ENKPDLILMDIQLPEISG 60

Query: 79  FKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRN-IWQHVA 134
            ++ + +        +PV+ ++      D  +    G   Y+ KPI +      I + + 
Sbjct: 61  LEVTKWLKEDDDLAHIPVVAVTAFAMKGDEERIREGGCEAYISKPISVVHFLETIKRLLE 120

Query: 135 QQP 137
           +QP
Sbjct: 121 RQP 123

>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 = 75.0 bits (184), Expect = 2e-18
 Identities = 32/114 (28%), Positives = 56/114 (49%), Gaps = 6/114 (5%)

Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYE-VTKCNRAEIALDMLRMSKNGYDIVISDVHMPDM 76
           ++VL+VDD      +L   L++  ++ +T     E  + ++   +N + +VISD +MP M
Sbjct: 7   IKVLIVDDQVTSRLLLGDALQQLGFKQITAAGDGEQGMKIMA--QNPHHLVISDFNMPKM 64

Query: 77  DGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           DG  L + V           I+++  G    V K    GA N L KP  I++++
Sbjct: 65  DGLGLLQAVRANPATKKAAFIILTAQGDRALVQKAAALGANNVLAKPFTIEKMK 118

>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 = 74.3 bits (182), Expect = 3e-18
 Identities = 26/120 (21%), Positives = 54/120 (45%), Gaps = 3/120 (2%)

Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMD 77
             V +VDD+    + L  ML    + V     AE  L           ++++D+ MPDM 
Sbjct: 4   YTVHIVDDEEPVRKSLAFMLTMNGFAVKMHQSAEAFLAFAP--DVRNGVLVTDLRMPDMS 61

Query: 78  GFKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ 136
           G +L   +  L++++P I+++  G     ++ +  GA +++ KP     +    +  ++ 
Sbjct: 62  GVELLRNLGDLKINIPSIVITGHGDVPMAVEAMKAGAVDFIEKPFEDTVIIEAIERASEH 121

>d1yioa2 c.23.1.1 (A:3-130) Response regulatory protein StyR, N-terminal domain {Pseudomonas fluorescens [TaxId: 294]} Length = 128

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulatory protein StyR, N-terminal domain
species: Pseudomonas fluorescens [TaxId: 294]

 Score = 73.9 bits (181), Expect = 5e-18
 Identities = 30/111 (27%), Positives = 52/111 (46%), Gaps = 3/111 (2%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
            V VVDDD      L  +LR   +EV   + A   L+  R     +  ++ D+ MP M G
Sbjct: 4   TVFVVDDDMSVREGLRNLLRSAGFEVETFDCASTFLEHRR--PEQHGCLVLDMRMPGMSG 61

Query: 79  FKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRN 128
            +L EQ+  +   +P++ ++  G     ++ +  GA  +L KP   + L +
Sbjct: 62  IELQEQLTAISDGIPIVFITAHGDIPMTVRAMKAGAIEFLPKPFEEQALLD 112

>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 = 73.9 bits (181), Expect = 6e-18
 Identities = 33/124 (26%), Positives = 60/124 (48%), Gaps = 3/124 (2%)

Query: 20  VLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGF 79
           V ++DDD    + +++ L    + V+    A  AL  L    +   IVISD+ MP MDG 
Sbjct: 3   VFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGLSA--DFAGIVISDIRMPGMDGL 60

Query: 80  KLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPK 138
            L  ++  L+ DLP+I+++  G     ++ +  GA +++ KP     L    +   ++ +
Sbjct: 61  ALFRKILALDPDLPMILVTGHGDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRAEEKRR 120

Query: 139 PFEE 142
              E
Sbjct: 121 LVME 124

>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 = 73.5 bits (180), Expect = 9e-18
 Identities = 24/127 (18%), Positives = 54/127 (42%), Gaps = 1/127 (0%)

Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMD 77
           + VLV++DD ++  +LE+ L     +V    R + A  +L        + +  +      
Sbjct: 1   MNVLVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLLSEKHFNVVL-LDLLLPDVNG 59

Query: 78  GFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQP 137
              L        +  VI+++  G  +  ++ +  GA ++L KP  ++E+        +  
Sbjct: 60  LEILKWIKERSPETEVIVITGHGTIKTAVEAMKMGAYDFLTKPCMLEEIELTINKAIEHR 119

Query: 138 KPFEESD 144
           K  +E++
Sbjct: 120 KLRKENE 126

>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 = 72.5 bits (177), Expect = 1e-17
 Identities = 32/119 (26%), Positives = 65/119 (54%), Gaps = 3/119 (2%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           RVLVV+D+     ++ + L+K ++ V  C   E  + M       +D+VI D+ +P  DG
Sbjct: 3   RVLVVEDERDLADLITEALKKEMFTVDVCYDGEEGMYMAL--NEPFDVVILDIMLPVHDG 60

Query: 79  FKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ 136
           +++ + +    ++ PV+M++     +  +KG+  GA +YL KP  ++EL    + + ++
Sbjct: 61  WEILKSMRESGVNTPVLMLTALSDVEYRVKGLNMGADDYLPKPFDLRELIARVRALIRR 119

>d1mvoa_ c.23.1.1 (A:) PhoP receiver domain {Bacillus subtilis [TaxId: 1423]} Length = 121

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: PhoP receiver domain
species: Bacillus subtilis [TaxId: 1423]

 Score = 72.4 bits (177), Expect = 2e-17
 Identities = 29/110 (26%), Positives = 59/110 (53%), Gaps = 3/110 (2%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           ++LVVDD+   + +L+  L +  Y+V   +  E AL          D+++ DV +P +DG
Sbjct: 4   KILVVDDEESIVTLLQYNLERSGYDVITASDGEEALKK--AETEKPDLIVLDVMLPKLDG 61

Query: 79  FKLHEQVGLE-MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
            ++ +Q+  + +  P++M++      D + G+  GA +Y+ KP   +E+ 
Sbjct: 62  IEVCKQLRQQKLMFPILMLTAKDEEFDKVLGLELGADDYMTKPFSPREVN 111

>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 = 71.8 bits (175), Expect = 6e-17
 Identities = 25/140 (17%), Positives = 64/140 (45%), Gaps = 20/140 (14%)

Query: 19  RVLVVDDDPIWLRILEKMLRK--CLYEVTKCNRAEIALDMLRMSKNG--------YDIVI 68
            +LVV+D        +++L++   +  + +C   + ALD L  + +           +++
Sbjct: 8   PLLVVEDSDEDFSTFQRLLQREGVVNPIYRCITGDQALDFLYQTGSYCNPDIAPRPAVIL 67

Query: 69  SDVHMPDMDGFKLHEQV---GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKE 125
            D+++P  DG ++ +++    +   +PV++M+     +D+    ++   +Y++KP+ I  
Sbjct: 68  LDLNLPGTDGREVLQEIKQDEVLKKIPVVIMTTSSNPKDIEICYSYSISSYIVKPLEIDR 127

Query: 126 LRNI-------WQHVAQQPK 138
           L          W  +   P+
Sbjct: 128 LTETVQTFIKYWLDIVVLPE 147

>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 = 70.8 bits (173), Expect = 7e-17
 Identities = 38/109 (34%), Positives = 58/109 (53%), Gaps = 3/109 (2%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           RVLVVDDD   L  LE+ LR   +EV        AL      +N  D ++ D++MP +DG
Sbjct: 3   RVLVVDDDSDVLASLERGLRLSGFEVATAVDGAEALRSAT--ENRPDAIVLDINMPVLDG 60

Query: 79  FKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKEL 126
             +   +  ++ D+PV ++S      D + G+  GA +YL+KP  + EL
Sbjct: 61  VSVVTALRAMDNDVPVCVLSARSSVDDRVAGLEAGADDYLVKPFVLAEL 109

>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 = 69.4 bits (169), Expect = 2e-16
 Identities = 30/111 (27%), Positives = 60/111 (54%), Gaps = 3/111 (2%)

Query: 18  LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMD 77
           +RVLVV+D+ +    L+  ++   ++V     A+ A   L   ++  DI I D+ +PD D
Sbjct: 1   MRVLVVEDNALLRHHLKVQIQDAGHQVDDAEDAKEADYYLN--EHIPDIAIVDLGLPDED 58

Query: 78  GF-KLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
           G   +      ++ LP+++++     QD ++ ++ GA +Y+ KP  I+E+ 
Sbjct: 59  GLSLIRRWRSNDVSLPILVLTARESWQDKVEVLSAGADDYVTKPFHIEEVM 109

>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 = 68.7 bits (167), Expect = 5e-16
 Identities = 29/125 (23%), Positives = 52/125 (41%), Gaps = 1/125 (0%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPD-MD 77
           R+LVVDD    +R+LE  L    YEV+       AL M         ++   +   D   
Sbjct: 3   RILVVDDIEANVRLLEAKLTAEYYEVSTAMDGPTALAMAARDLPDIILLDVMMPGMDGFT 62

Query: 78  GFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQP 137
             +  +       +PV++++      D ++G+  GA ++L KPI    L    + + +  
Sbjct: 63  VCRKLKDDPTTRHIPVVLITALDGRGDRIQGLESGASDFLTKPIDDVMLFARVRSLTRFK 122

Query: 138 KPFEE 142
              +E
Sbjct: 123 LVIDE 127

>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 = 68.6 bits (167), Expect = 1e-15
 Identities = 23/114 (20%), Positives = 42/114 (36%), Gaps = 7/114 (6%)

Query: 17  GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMP-- 74
           G RVL+VDD+    + +   L      V + +  +  +     +    D+VI +      
Sbjct: 13  GGRVLIVDDNERQAQRVAAELGVEHRPVIESDPEKAKI----SAGGPVDLVIVNAAAKNF 68

Query: 75  -DMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELR 127
             +              LPV+ M        ++K +  G  + L +PI  +EL 
Sbjct: 69  DGLRFTAALRSEERTRQLPVLAMVDPDDRGRMVKALEIGVNDILSRPIDPQELS 122

>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 = 68.5 bits (166), Expect = 2e-15
 Identities = 16/158 (10%), Positives = 41/158 (25%), Gaps = 6/158 (3%)

Query: 17  GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDM 76
            L+VLV++        L   L +    V +C     A D+        D+V + +     
Sbjct: 11  ELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDVP------VDVVFTSIFQNRH 64

Query: 77  DGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ 136
                           ++ +        + + +       + +P+    +  +     + 
Sbjct: 65  HDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRI 124

Query: 137 PKPFEESDDSYSVNQGNWRTSNRRKDEEEEAEKRDDTS 174
            +   +        Q       R    +    +R    
Sbjct: 125 SEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHGWD 162

>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 = 66.2 bits (161), Expect = 4e-15
 Identities = 29/121 (23%), Positives = 59/121 (48%), Gaps = 6/121 (4%)

Query: 19  RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDG 78
           ++ VVDDD   L+ + + L++ L  V      E  L+     +  + +V+ DV +PD  G
Sbjct: 4   KIAVVDDDKNILKKVSEKLQQ-LGRVKTFLTGEDFLND----EEAFHVVVLDVMLPDYSG 58

Query: 79  FKLHEQV-GLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQP 137
           +++   +     +  VI++++    + V+KG   GA +Y+ KP   + L    +   ++ 
Sbjct: 59  YEICRMIKETRPETWVILLTLLSDDESVLKGFEAGADDYVTKPFNPEILLARVKRFLERE 118

Query: 138 K 138
           K
Sbjct: 119 K 119

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	184
d2pl1a1	119	PhoP receiver domain {Escherichia coli [TaxId: 562	99.95
d2a9pa1	117	DNA-binding response regulator MicA, N-terminal do	99.95
d1dbwa_	123	Transcriptional regulatory protein FixJ, receiver	99.95
d1zh2a1	119	Transcriptional regulatory protein KdpE, N-termina	99.95
d1kgsa2	122	PhoB receiver domain {Thermotoga maritima [TaxId:	99.95
d1peya_	119	Sporulation response regulator Spo0F {Bacillus sub	99.95
d1xhfa1	121	Aerobic respiration control protein ArcA, N-termin	99.95
d1zgza1	120	TorCAD operon transcriptional regulator TorD, N-te	99.95
d1zesa1	121	PhoB receiver domain {Escherichia coli [TaxId: 562	99.94
d1a04a2	138	Nitrate/nitrite response regulator (NarL), receive	99.94
d1ny5a1	137	Transcriptional activator sigm54 (NtrC1), N-termin	99.94
d1ys7a2	121	Transcriptional regulatory protein PrrA, N-termina	99.94
d1mvoa_	121	PhoP receiver domain {Bacillus subtilis [TaxId: 14	99.94
d1u0sy_	118	CheY protein {Thermotoga maritima [TaxId: 2336]}	99.94
d1qkka_	140	Transcriptional regulatory protein DctD, receiver	99.94
d1p6qa_	129	CheY protein {Sinorhizobium meliloti, CheY2 [TaxId	99.94
d1s8na_	190	Probable two-component system transcriptional regu	99.94
d1krwa_	123	NTRC receiver domain {Salmonella typhimurium [TaxI	99.94
d1mb3a_	123	Cell division response regulator DivK {Caulobacter	99.94
d2ayxa1	133	Sensor kinase protein RcsC, C-terminal domain {Esc	99.94
d1jbea_	128	CheY protein {Escherichia coli [TaxId: 562]}	99.94
d2r25b1	128	Response regulator Sin1 {Baker's yeast (Saccharomy	99.93
d1w25a1	139	Response regulator PleD, receiver domain {Caulobac	99.93
d1dz3a_	123	Sporulation response regulator Spo0A {Bacillus ste	99.93
d1dcfa_	134	Receiver domain of the ethylene receptor {Thale cr	99.93
d1yioa2	128	Response regulatory protein StyR, N-terminal domai	99.93
d1p2fa2	120	Response regulator DrrB {Thermotoga maritima [TaxI	99.93
d1i3ca_	144	Response regulator for cyanobacterial phytochrome	99.92
d1k68a_	140	Response regulator for cyanobacterial phytochrome	99.92
d1k66a_	149	Response regulator for cyanobacterial phytochrome	99.92
d1w25a2	153	Response regulator PleD, receiver domain {Caulobac	99.91
d2b4aa1	118	Hypothetical protein BH3024 {Bacillus halodurans [	99.89
d1a2oa1	140	Methylesterase CheB, N-terminal domain {Salmonella	99.88
d1qo0d_	189	Positive regulator of the amidase operon AmiR {Pse	99.86
d1ccwa_	137	Glutamate mutase, small subunit {Clostridium cochl	95.86
d1r8ja2	135	N-terminal domain of the circadian clock protein K	95.17
d1dxea_	253	2-dehydro-3-deoxy-galactarate aldolase {Escherichi	94.47
d1xrsb1	160	D-lysine 5,6-aminomutase beta subunit KamE, C-term	92.58
d7reqa2	168	Methylmalonyl-CoA mutase alpha subunit, C-terminal	92.38
d1qpoa1	169	Quinolinic acid phosphoribosyltransferase (Nicotin	92.19
d1o4ua1	170	Quinolinic acid phosphoribosyltransferase (Nicotin	92.02
d1izca_	299	Macrophomate synthase {Macrophoma commelinae [TaxI	91.39
d1xi3a_	206	Thiamin phosphate synthase {Archaeon (Pyrococcus f	89.64
d1mxsa_	216	KDPG aldolase {Pseudomonas putida [TaxId: 303]}	88.68
d1xm3a_	251	Thiazole biosynthesis protein ThiG {Bacillus subti	88.47
d1wa3a1	202	KDPG aldolase {Thermotoga maritima [TaxId: 2336]}	88.3
d1id1a_	153	Rck domain from putative potassium channel Kch {Es	88.28
d1u6ka1	282	F420-dependent methylenetetrahydromethanopterin de	86.39
d1vhca_	212	Hypothetical protein HI0047 {Haemophilus influenza	85.78
d1wbha1	213	KDPG aldolase {Escherichia coli [TaxId: 562]}	85.55
d7reqb2	163	Methylmalonyl-CoA mutase beta subunit, C-terminal	83.06
d1ws6a1	171	Methyltransferase TTHA0928 {Thermus thermophilus [	82.43
d1qapa1	167	Quinolinic acid phosphoribosyltransferase (Nicotin	82.39

>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=99.95  E-value=1.3e-27  Score=162.28  Aligned_cols=116  Identities=28%  Similarity=0.416  Sum_probs=109.4

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIMM   96 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi~   96 (184)
                      |||+||||++..+..++..|+..||+|..+.+++++++.+.  +..||+||+|+.||+++|++++++++. .+.+|+|++
T Consensus         1 mrILvVDDd~~~~~~l~~~L~~~G~~v~~a~~g~eal~~l~--~~~~dliilD~~mP~~~G~e~~~~i~~~~~~~pvi~l   78 (119)
T d2pl1a1           1 MRVLVVEDNALLRHHLKVQIQDAGHQVDDAEDAKEADYYLN--EHIPDIAIVDLGLPDEDGLSLIRRWRSNDVSLPILVL   78 (119)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HSCCSEEEECSCCSSSCHHHHHHHHHHTTCCSCEEEE
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHH--hcccceeehhccCCCchhHHHHHHHHhcCcccceEee
Confidence            68999999999999999999999999999999999999998  456999999999999999999999965 468999999


Q ss_pred             EccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           97 SVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        97 ~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      |+..+.+...+++++||++|+.||++.++|..+++.+++
T Consensus        79 t~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~v~~~lr  117 (119)
T d2pl1a1          79 TARESWQDKVEVLSAGADDYVTKPFHIEEVMARMQALMR  117 (119)
T ss_dssp             ESCCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHHH
T ss_pred             eccCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHHc
Confidence            999999999999999999999999999999999998875

>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=99.95  E-value=2.7e-27  Score=160.34  Aligned_cols=115  Identities=26%  Similarity=0.452  Sum_probs=109.5

Q ss_pred             eEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEEEEc
Q 029986           19 RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMSV   98 (184)
Q Consensus        19 ~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi~~~   98 (184)
                      |||||||++..+..++.+|+..||++..+.+++++++.+..  ..||+||+|+.||+++|++++++++..+++|||++++
T Consensus         2 rILiVdDd~~~~~~l~~~L~~~g~~v~~a~~~~eal~~~~~--~~~dlillD~~mp~~~G~~~~~~i~~~~~~pvI~lt~   79 (117)
T d2a9pa1           2 KILIVDDEKPISDIIKFNMTKEGYEVVTAFNGREALEQFEA--EQPDIIILDLMLPEIDGLEVAKTIRKTSSVPILMLSA   79 (117)
T ss_dssp             EEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHH--HCCSEEEECSSCSSSCHHHHHHHHHTTCCCCEEEEES
T ss_pred             EEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHh--cCCCEEEeccccCCCCccHHHHHHHhCCCCCEEEEec
Confidence            79999999999999999999999999999999999999984  5699999999999999999999998778899999999


Q ss_pred             cCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           99 DGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        99 ~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      ..+......++++||++|+.||++.++|..+++.+++
T Consensus        80 ~~~~~~~~~a~~~Ga~d~l~KP~~~~~L~~~i~~~lr  116 (117)
T d2a9pa1          80 KDSEFDKVIGLELGADDYVTKPFSNRELQARVKALLR  116 (117)
T ss_dssp             CCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHhC
Confidence            9999999999999999999999999999999998875

>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=99.95  E-value=7.4e-27  Score=159.46  Aligned_cols=118  Identities=22%  Similarity=0.371  Sum_probs=110.7

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIM   95 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi   95 (184)
                      .++|+||||++..+..++.+|+..||.+..+++++++++.+.  +..||++|+|+.||+++|++++++++. .+++|+|+
T Consensus         3 ~~~ILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~~--~~~~dlvi~D~~mp~~~G~e~~~~lr~~~~~~~iI~   80 (123)
T d1dbwa_           3 DYTVHIVDDEEPVRKSLAFMLTMNGFAVKMHQSAEAFLAFAP--DVRNGVLVTDLRMPDMSGVELLRNLGDLKINIPSIV   80 (123)
T ss_dssp             CCEEEEEESSHHHHHHHHHHHHHTTCEEEEESCHHHHHHHGG--GCCSEEEEEECCSTTSCHHHHHHHHHHTTCCCCEEE
T ss_pred             CCEEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh--hcCCcEEEEeccCccccchHHHHHHHhcCCCCeEEE
Confidence            468999999999999999999999999999999999999987  566999999999999999999999964 57899999


Q ss_pred             EEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           96 MSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        96 ~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      +|+..+.+...++++.||++|+.||++.++|..+++++.++
T Consensus        81 lt~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~i~~a~e~  121 (123)
T d1dbwa_          81 ITGHGDVPMAVEAMKAGAVDFIEKPFEDTVIIEAIERASEH  121 (123)
T ss_dssp             EECTTCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHHTT
T ss_pred             EEeeCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHh
Confidence            99999999999999999999999999999999999988764

>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=99.95  E-value=2e-27  Score=161.47  Aligned_cols=116  Identities=26%  Similarity=0.350  Sum_probs=109.9

Q ss_pred             eEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEEEEc
Q 029986           19 RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMSV   98 (184)
Q Consensus        19 ~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi~~~   98 (184)
                      +||||||++..++.++.+|+..||++..+.+++++++.+..  ..||+||+|+.||+++|+++++.+++.+..|+|++++
T Consensus         2 nILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~eal~~l~~--~~~dliilD~~mP~~~G~e~~~~ir~~~~~piI~lt~   79 (119)
T d1zh2a1           2 NVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEAAT--RKPDLIILDLGLPDGDGIEFIRDLRQWSAVPVIVLSA   79 (119)
T ss_dssp             EEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHHH--HCCSEEEEESEETTEEHHHHHHHHHTTCCCCEEEEES
T ss_pred             EEEEEECCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHHh--cCCCEEEeccccCCCCCchHHHHHHhccCCcEEEEec
Confidence            69999999999999999999999999999999999999984  4599999999999999999999998888899999999


Q ss_pred             cCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           99 DGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        99 ~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      ..+.+....+++.||++|+.||++.++|..+++.++++
T Consensus        80 ~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~lrr  117 (119)
T d1zh2a1          80 RSEESDKIAALDAGADDYLSKPFGIGELQARLRVALRR  117 (119)
T ss_dssp             CCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHHhh
Confidence            99999999999999999999999999999999998763

>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=99.95  E-value=2.7e-27  Score=161.42  Aligned_cols=118  Identities=27%  Similarity=0.490  Sum_probs=110.5

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc-CCCCEEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE-MDLPVIM   95 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~-~~~~iIi   95 (184)
                      ++|||||||++..++.++.+|+..||++..+.+++++++.+.  ...||+||+|+.||+++|++++++++.. +.+|||+
T Consensus         1 nirILiVdDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~l~--~~~~dlillD~~mp~~~g~~~~~~lr~~~~~~piI~   78 (122)
T d1kgsa2           1 NVRVLVVEDERDLADLITEALKKEMFTVDVCYDGEEGMYMAL--NEPFDVVILDIMLPVHDGWEILKSMRESGVNTPVLM   78 (122)
T ss_dssp             CCEEEEECSSHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HSCCSEEEEESCCSSSCHHHHHHHHHHTTCCCCEEE
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHHCCCEEEEEcchHHHHHHHH--hhCccccccccccccchhHHHHHHHHhcCCCCcEEE
Confidence            579999999999999999999999999999999999999998  4569999999999999999999999744 6889999


Q ss_pred             EEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           96 MSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        96 ~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      +|+..+.....++++.||++|+.||++.++|..+++.++++
T Consensus        79 lt~~~~~~~~~~~~~~Ga~~yl~KP~~~~~L~~~i~~~l~r  119 (122)
T d1kgsa2          79 LTALSDVEYRVKGLNMGADDYLPKPFDLRELIARVRALIRR  119 (122)
T ss_dssp             EESSCHHHHHHHTCCCCCSEEEESSCCHHHHHHHHHHHHHH
T ss_pred             EcCCCCHHHHHHHHHcCCceeecCCCCHHHHHHHHHHHHHH
Confidence            99999899999999999999999999999999999988764

>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=99.95  E-value=1e-26  Score=157.85  Aligned_cols=116  Identities=24%  Similarity=0.404  Sum_probs=108.1

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIMM   96 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi~   96 (184)
                      -|||||||++..+..++..|+..||++..+.++.++++.+..  ..||+||+|+.||+++|++++++++. .+++|||++
T Consensus         2 krILvVDD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~~~~--~~~dlillD~~mP~~~G~el~~~lr~~~~~~pvi~l   79 (119)
T d1peya_           2 EKILIVDDQSGIRILLNEVFNKEGYQTFQAANGLQALDIVTK--ERPDLVLLDMKIPGMDGIEILKRMKVIDENIRVIIM   79 (119)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHH--HCCSEEEEESCCTTCCHHHHHHHHHHHCTTCEEEEE
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHcCCEEEEeCCHHHHHHHHHh--CCCCEEEEeccCCCCCHHHHHHHHHHhCCCCcEEEE
Confidence            489999999999999999999999999999999999999984  46999999999999999999999964 468999999


Q ss_pred             EccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           97 SVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        97 ~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      |+..+.+...+++++||++|+.||++.++|..++++++.
T Consensus        80 t~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~v~~~L~  118 (119)
T d1peya_          80 TAYGELDMIQESKELGALTHFAKPFDIDEIRDAVKKYLP  118 (119)
T ss_dssp             ESSCCHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHSC
T ss_pred             ecCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHCC
Confidence            999999999999999999999999999999999988753

>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=99.95  E-value=9.8e-27  Score=158.40  Aligned_cols=115  Identities=19%  Similarity=0.371  Sum_probs=109.9

Q ss_pred             eEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEEEEc
Q 029986           19 RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMSV   98 (184)
Q Consensus        19 ~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi~~~   98 (184)
                      |||||||++..++.++.+|+..||++..+.+++++++.+.  ...||+||+|+.||+.+|+++++.++..+++|+|++|+
T Consensus         4 ~ILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~l~--~~~~dlii~D~~mp~~~G~~~~~~~r~~~~~pii~lt~   81 (121)
T d1xhfa1           4 HILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQILS--EYDINLVIMDINLPGKNGLLLARELREQANVALMFLTG   81 (121)
T ss_dssp             EEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHH--HSCCSEEEECSSCSSSCHHHHHHHHHHHCCCEEEEEES
T ss_pred             EEEEEECCHHHHHHHHHHHHHCCCEEEEECChHHHHHHHH--hcCCCEEEeecccCCccCcHHHHHHHhcCCCcEEEEEC
Confidence            8999999999999999999999999999999999999998  45699999999999999999999998888999999999


Q ss_pred             cCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           99 DGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        99 ~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      ..+.....+++++||++|+.||++.++|..+++.+++
T Consensus        82 ~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~v~~~l~  118 (121)
T d1xhfa1          82 RDNEVDKILGLEIGADDYITKPFNPRELTIRARNLLS  118 (121)
T ss_dssp             CCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHh
Confidence            9999999999999999999999999999999998876

>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=99.95  E-value=1.4e-26  Score=157.35  Aligned_cols=116  Identities=19%  Similarity=0.377  Sum_probs=109.8

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMS   97 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi~~   97 (184)
                      +|||||||++..++.++.+|+..||++..+.+++++++.+.  +..||+|++|+.||+++|+++++.++...+.|||++|
T Consensus         2 ~rILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~~a~~~~~--~~~~dliilD~~mp~~~g~~~~~~~~~~~~~piI~lt   79 (120)
T d1zgza1           2 HHIVIVEDEPVTQARLQSYFTQEGYTVSVTASGAGLREIMQ--NQSVDLILLDINLPDENGLMLTRALRERSTVGIILVT   79 (120)
T ss_dssp             CEEEEECSSHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HSCCSEEEEESCCSSSCHHHHHHHHHTTCCCEEEEEE
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHH--hcCCCEEeeehhhccchhHHHHHHHhccCCCeEEEEE
Confidence            58999999999999999999999999999999999999998  4569999999999999999999999877889999999


Q ss_pred             ccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           98 VDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        98 ~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      +..+......++++||++|+.||++.++|..+++.+++
T Consensus        80 ~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~lr  117 (120)
T d1zgza1          80 GRSDRIDRIVGLEMGADDYVTKPLELRELVVRVKNLLW  117 (120)
T ss_dssp             SSCCHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHc
Confidence            99999999999999999999999999999999998875

>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=99.94  E-value=1.9e-26  Score=156.92  Aligned_cols=116  Identities=25%  Similarity=0.431  Sum_probs=108.7

Q ss_pred             eEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc---CCCCEEE
Q 029986           19 RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE---MDLPVIM   95 (184)
Q Consensus        19 ~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~---~~~~iIi   95 (184)
                      |||||||++..++.+..+|+..||++..+.+++++++.+.  +..||+||+|+.||+++|++++++++..   +++|||+
T Consensus         2 kILiVDD~~~~~~~l~~~L~~~g~~v~~a~~~~~al~~l~--~~~~dlil~D~~mp~~~G~~l~~~lr~~~~~~~~pvi~   79 (121)
T d1zesa1           2 RILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLN--EPWPDLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVM   79 (121)
T ss_dssp             EEEEECSCHHHHHHHHHHHHHTTCEEEEECSHHHHHHHSS--SSCCSEEEECSSCTTSCHHHHHHHHHHSTTTTTSCEEE
T ss_pred             EEEEEeCCHHHHHHHHHHHHHCCCEEEEECChHHHHHHHH--ccCCCEEEeecCCCCCCHHHHHHHHHhCccCCCCeEEE
Confidence            7999999999999999999999999999999999999987  5679999999999999999999999643   4789999


Q ss_pred             EEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           96 MSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        96 ~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      +|+..+.....++++.|+++|+.||++.++|..+++.++++
T Consensus        80 lt~~~~~~~~~~~~~~G~~d~l~KP~~~~~L~~~v~~~lrR  120 (121)
T d1zesa1          80 LTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRR  120 (121)
T ss_dssp             EESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHHHT
T ss_pred             EECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHcC
Confidence            99999999999999999999999999999999999988763

>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=99.94  E-value=2.1e-26  Score=160.22  Aligned_cols=125  Identities=20%  Similarity=0.381  Sum_probs=113.7

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcC--CeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCL--YEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPV   93 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~--~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~i   93 (184)
                      ++||+||||++..++.++.+|+..+  +.+..+.++.++++.+..  ..||++|+|+.||+++|++++++++. .+..|+
T Consensus         2 Pi~VLiVDD~~~~r~~l~~~L~~~~~~~~v~~a~~~~~al~~~~~--~~~DlvllD~~mP~~~G~el~~~ir~~~~~~~v   79 (138)
T d1a04a2           2 PATILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAES--LDPDLILLDLNMPGMNGLETLDKLREKSLSGRI   79 (138)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHTTCTTEEEEEEESSHHHHHHHHHH--HCCSEEEEETTSTTSCHHHHHHHHHHSCCCSEE
T ss_pred             CCEEEEECCCHHHHHHHHHHHHhCCCcEEEEEECCHHHHHHHHHh--cCCCEEEEecCCCCCCHHHHHHHHHhhCCCCCE
Confidence            6799999999999999999998765  567789999999999874  46999999999999999999999964 478999


Q ss_pred             EEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCCCCCCC
Q 029986           94 IMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPKPFEES  143 (184)
Q Consensus        94 Ii~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~~~~~~  143 (184)
                      |++|...+.+...+++++||++|+.||++.++|.++++++.++..++++.
T Consensus        80 ivlt~~~~~~~~~~a~~~Ga~~yl~Kp~~~~~L~~~i~~v~~g~~~~~~~  129 (138)
T d1a04a2          80 VVFSVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALHQAAAGEMVLSEA  129 (138)
T ss_dssp             EEEECCCCHHHHHHHHHTTCSEEEETTCCHHHHHHHHHHHHHSCCCCCTT
T ss_pred             EEEEEECCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHHCCCCcCCHH
Confidence            99999999999999999999999999999999999999999988776543

>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=99.94  E-value=1.4e-26  Score=160.92  Aligned_cols=117  Identities=22%  Similarity=0.456  Sum_probs=109.7

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhc-ccCCCCEEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVG-LEMDLPVIMM   96 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~-~~~~~~iIi~   96 (184)
                      ||||||||++..+..++.+|+..||++..+.+++++++.+.  ...||+||+|+.||+++|++++++++ ..+++|||++
T Consensus         1 mkILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~eAl~~l~--~~~~dlvilD~~mp~~~G~e~~~~lr~~~~~~piI~l   78 (137)
T d1ny5a1           1 MNVLVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLLS--EKHFNVVLLDLLLPDVNGLEILKWIKERSPETEVIVI   78 (137)
T ss_dssp             CEEEEECCCHHHHHHHHHHHHHHTCEEEEESSHHHHHHHHH--HSCCSEEEEESBCSSSBHHHHHHHHHHHCTTSEEEEE
T ss_pred             CEEEEEecCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHhh--ccccccchHHHhhhhhhHHHHHHHHHHhCCCCCEEEE
Confidence            68999999999999999999999999999999999999998  45699999999999999999999996 4578999999


Q ss_pred             EccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           97 SVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        97 ~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      |+..+.+...+++++||+||+.||+..++|..++++++++
T Consensus        79 T~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~l~~  118 (137)
T d1ny5a1          79 TGHGTIKTAVEAMKMGAYDFLTKPCMLEEIELTINKAIEH  118 (137)
T ss_dssp             EETTCHHHHHHHHTTTCCEEEEESCCHHHHHHHHHHHHHH
T ss_pred             ECCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999987653

>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=99.94  E-value=4.3e-27  Score=160.19  Aligned_cols=116  Identities=33%  Similarity=0.473  Sum_probs=109.0

Q ss_pred             eEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEEEE
Q 029986           19 RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIMMS   97 (184)
Q Consensus        19 ~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi~~   97 (184)
                      |||||||++..++.++..|+..||+|..+.++.++++.+.  +..||+||+|+.||+++|+++++++++ .+++|||++|
T Consensus         3 kILiVDD~~~~~~~l~~~L~~~g~~v~~a~~~~eal~~~~--~~~~dlvl~D~~mP~~~G~el~~~ir~~~~~~piI~lt   80 (121)
T d1ys7a2           3 RVLVVDDDSDVLASLERGLRLSGFEVATAVDGAEALRSAT--ENRPDAIVLDINMPVLDGVSVVTALRAMDNDVPVCVLS   80 (121)
T ss_dssp             EEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HSCCSEEEEESSCSSSCHHHHHHHHHHTTCCCCEEEEE
T ss_pred             EEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHH--hCCCCEEEEEeeccCcccHHHHHHHHhcCCCCEEEEEE
Confidence            7999999999999999999999999999999999999998  456999999999999999999999974 4689999999


Q ss_pred             ccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           98 VDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        98 ~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      +..+.+...+++++||++|+.||++.++|..+++.++++
T Consensus        81 ~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~l~r  119 (121)
T d1ys7a2          81 ARSSVDDRVAGLEAGADDYLVKPFVLAELVARVKALLRR  119 (121)
T ss_dssp             CCCTTTCCCTTTTTTCSEEEESSCCHHHHHHHHHHHHHH
T ss_pred             eeCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHc
Confidence            999999999999999999999999999999999988763

>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=99.94  E-value=2.7e-26  Score=156.24  Aligned_cols=117  Identities=25%  Similarity=0.460  Sum_probs=108.6

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIMM   96 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi~   96 (184)
                      -|||||||++..++.++.+|+..||+|..+.+++++++.+..  ..||+||+|+.||+++|++++++++. .+..|||++
T Consensus         3 krILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~l~~--~~~dlillD~~mp~~~G~~~~~~~r~~~~~~~ii~l   80 (121)
T d1mvoa_           3 KKILVVDDEESIVTLLQYNLERSGYDVITASDGEEALKKAET--EKPDLIVLDVMLPKLDGIEVCKQLRQQKLMFPILML   80 (121)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHH--HCCSEEEEESSCSSSCHHHHHHHHHHTTCCCCEEEE
T ss_pred             CCEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHhc--ccccEEEecccccCCCCchhhhhhhccCCCCEEEEE
Confidence            379999999999999999999999999999999999999984  56999999999999999999999964 467899999


Q ss_pred             EccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           97 SVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        97 ~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      ++....+....+++.||++|+.||++.++|...++.++++
T Consensus        81 t~~~~~~~~~~~~~~Ga~~yl~KP~~~~~L~~~i~~~lrR  120 (121)
T d1mvoa_          81 TAKDEEFDKVLGLELGADDYMTKPFSPREVNARVKAILRR  120 (121)
T ss_dssp             ECTTCCCCHHHHHHTTCCEEEESSCCHHHHHHHHHHHHHT
T ss_pred             EeeCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHcc
Confidence            9988888899999999999999999999999999998764

>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=99.94  E-value=3.1e-26  Score=155.21  Aligned_cols=115  Identities=26%  Similarity=0.456  Sum_probs=106.4

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEE-EECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhc-ccCCCCEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVT-KCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVG-LEMDLPVI   94 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~-~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~-~~~~~~iI   94 (184)
                      |.|||||||++..++.++.+|+..||++. .++++.++++.++.  ..||+||+|+.||+.+|++++++++ ..+++|||
T Consensus         1 GkrILivDD~~~~~~~l~~~L~~~g~~v~~~a~~~~~al~~~~~--~~~dliilD~~mp~~~G~e~~~~ir~~~~~~pvi   78 (118)
T d1u0sy_           1 GKRVLIVDDAAFMRMMLKDIITKAGYEVAGEATNGREAVEKYKE--LKPDIVTMDITMPEMNGIDAIKEIMKIDPNAKII   78 (118)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHHH--HCCSEEEEECSCGGGCHHHHHHHHHHHCTTCCEE
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHHcCCceEEEECCHHHHHHHHHh--ccCCEEEEecCCCCCCHHHHHHHHHHhCCCCcEE
Confidence            46899999999999999999999999876 68999999999984  5599999999999999999999996 45789999


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHH
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHV  133 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~  133 (184)
                      ++|+..+.+...++++.||++|+.||++.++|.++++++
T Consensus        79 ~ls~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~l~~v  117 (118)
T d1u0sy_          79 VCSAMGQQAMVIEAIKAGAKDFIVKPFQPSRVVEALNKV  117 (118)
T ss_dssp             EEECTTCHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHH
T ss_pred             EEEccCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHh
Confidence            999999999999999999999999999999999999875

>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=99.94  E-value=3.6e-26  Score=159.33  Aligned_cols=116  Identities=27%  Similarity=0.430  Sum_probs=109.2

Q ss_pred             eEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEEEE
Q 029986           19 RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIMMS   97 (184)
Q Consensus        19 ~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi~~   97 (184)
                      +|+||||++..+..++.+|+..||.+..+.++.++++.+.  ...||+||+|+.||+++|++++++++. .+++|||++|
T Consensus         2 ~ILiVDDd~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~--~~~~dlil~D~~mP~~~G~el~~~lr~~~~~~pvI~lT   79 (140)
T d1qkka_           2 SVFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGLS--ADFAGIVISDIRMPGMDGLALFRKILALDPDLPMILVT   79 (140)
T ss_dssp             EEEEECSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHTCC--TTCCSEEEEESCCSSSCHHHHHHHHHHHCTTSCEEEEE
T ss_pred             EEEEEECCHHHHHHHHHHHHHCCCEEEEeCChHHHHHHHh--ccCcchHHHhhccCCCCHHHHHHHHHHhCCCCcEEEEE
Confidence            6999999999999999999999999999999999999987  567999999999999999999999964 5789999999


Q ss_pred             ccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           98 VDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        98 ~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      +..+.+...+|++.||+||+.||++.++|..+++.++++
T Consensus        80 ~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~~~~  118 (140)
T d1qkka_          80 GHGDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRAEEK  118 (140)
T ss_dssp             CGGGHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHcCCCEeecCCCCHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999988764

>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=99.94  E-value=4.8e-26  Score=156.61  Aligned_cols=120  Identities=28%  Similarity=0.423  Sum_probs=110.0

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHhcCC-eEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc---CC
Q 029986           15 PAGLRVLVVDDDPIWLRILEKMLRKCLY-EVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE---MD   90 (184)
Q Consensus        15 ~~~~~Ilivdd~~~~~~~l~~~L~~~~~-~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~---~~   90 (184)
                      .+.+|||||||++..+..++..|+..|| ++..+.+++++++.+.  +..||+||+|++||+++|+++++.++..   .+
T Consensus         4 ~~~~kILiVDD~~~~~~~l~~~L~~~g~~~v~~a~~~~~al~~l~--~~~~dlii~D~~mP~~~G~el~~~lr~~~~~~~   81 (129)
T d1p6qa_           4 AEKIKVLIVDDQVTSRLLLGDALQQLGFKQITAAGDGEQGMKIMA--QNPHHLVISDFNMPKMDGLGLLQAVRANPATKK   81 (129)
T ss_dssp             SSCCCEEEECSSHHHHHHHHHHHHTTTCSCEECCSSHHHHHHHHH--TSCCSEEEECSSSCSSCHHHHHHHHTTCTTSTT
T ss_pred             CCCCEEEEEECCHHHHHHHHHHHHHCCCeEEEEECCHHHHHHHHH--hCCCCeEEeeeecCCCChHHHHHHHHhCcccCC
Confidence            3568999999999999999999999998 4778899999999998  5679999999999999999999999753   47


Q ss_pred             CCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           91 LPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        91 ~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      +|+|++|+..+.+...++++.|+++|+.||++.++|..++++++..
T Consensus        82 ~pii~lt~~~~~~~~~~a~~~G~~~~l~KP~~~~~L~~~i~~vl~~  127 (129)
T d1p6qa_          82 AAFIILTAQGDRALVQKAAALGANNVLAKPFTIEKMKAAIEAVFGA  127 (129)
T ss_dssp             CEEEECCSCCCHHHHHHHHHHTCSCEECCCSSHHHHHHHHHHHHHC
T ss_pred             CeEEEEEecCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHh
Confidence            8999999998899999999999999999999999999999998764

>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=99.94  E-value=1.4e-26  Score=169.24  Aligned_cols=119  Identities=25%  Similarity=0.380  Sum_probs=110.5

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEE-EECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVT-KCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIM   95 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~-~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi   95 (184)
                      ++||+||||++..+..++.+|+..||++. .++++.++++.+.  ...||+||+|++||++||++++++++..+++|||+
T Consensus         3 p~kILiVDD~~~~r~~l~~~L~~~g~~vv~~a~~g~eal~~~~--~~~pDlvllDi~mP~~dG~e~~~~ir~~~~~pIi~   80 (190)
T d1s8na_           3 PRRVLIAEDEALIRMDLAEMLREEGYEIVGEAGDGQEAVELAE--LHKPDLVIMDVKMPRRDGIDAASEIASKRIAPIVV   80 (190)
T ss_dssp             CCEEEEECSSHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHH--HHCCSEEEEESSCSSSCHHHHHHHHHHTTCSCEEE
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHh--cCCCCEEEEeccccCcchHHHHHHHHhcCCCCEEE
Confidence            57999999999999999999999999865 7999999999998  45699999999999999999999998778899999


Q ss_pred             EEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCC
Q 029986           96 MSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQP  137 (184)
Q Consensus        96 ~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~  137 (184)
                      +|+..+.++...|+++||+||++||++.++|..+++.++.+.
T Consensus        81 lTa~~~~~~~~~al~~Ga~~yl~KP~~~~~L~~~i~~~~~~~  122 (190)
T d1s8na_          81 LTAFSQRDLVERARDAGAMAYLVKPFSISDLIPAIELAVSRF  122 (190)
T ss_dssp             EEEGGGHHHHHTTGGGSCEEEEEESCCHHHHHHHHHHHHHHH
T ss_pred             EeCCCCHHHHHHHHHcCCCEeccCCCCHHHHHHHHHHHHHhh
Confidence            999999999999999999999999999999999998877643

>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=99.94  E-value=8.6e-27  Score=159.13  Aligned_cols=116  Identities=30%  Similarity=0.429  Sum_probs=109.3

Q ss_pred             eEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhc-ccCCCCEEEEE
Q 029986           19 RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVG-LEMDLPVIMMS   97 (184)
Q Consensus        19 ~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~-~~~~~~iIi~~   97 (184)
                      +||||||++..+..++..|+..||++..+.++.++++.+.  +..||+||+|+.||+++|++++++++ ..+.+|||++|
T Consensus         5 ~ILIVDDd~~~~~~l~~~L~~~g~~v~~a~~~~~a~~~l~--~~~~dlii~D~~mp~~~G~el~~~l~~~~~~~piI~~t   82 (123)
T d1krwa_           5 IVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAALA--SKTPDVLLSDIRMPGMDGLALLKQIKQRHPMLPVIIMT   82 (123)
T ss_dssp             EEEEESSSHHHHHHHHHHHHHTTCEEEEESSSHHHHHHHT--TCCCSEEEECCSSSSSTTHHHHHHHHHHSSSCCEEESC
T ss_pred             EEEEEECCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHH--hCCCCEEEehhhcCCchHHHHHHHHHHhCCCCeEEEEe
Confidence            6999999999999999999999999999999999999987  56799999999999999999999995 45789999999


Q ss_pred             ccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           98 VDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        98 ~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      +..+.+...++++.|+++|+.||++.++|..++++++++
T Consensus        83 ~~~~~~~~~~a~~~Ga~dyl~KP~~~~eL~~~i~~~l~~  121 (123)
T d1krwa_          83 AHSDLDAAVSAYQQGAFDYLPKPFDIDEAVALVERAISH  121 (123)
T ss_dssp             CCSCHHHHHHHHHHTEEEECSSCCHHHHHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHcCCCeEEeCcCCHHHHHHHHHHHHHc
Confidence            999999999999999999999999999999999988764

>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=99.94  E-value=4.6e-26  Score=155.48  Aligned_cols=117  Identities=20%  Similarity=0.404  Sum_probs=103.2

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc---CCCCEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE---MDLPVI   94 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~---~~~~iI   94 (184)
                      .|||||||++..++.++.+|+..||++..+.++.++++.+..  ..||+||+|+.||+++|++++++++..   .++|+|
T Consensus         2 krILiVDD~~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~~~--~~~dlil~D~~mp~~dG~el~~~ir~~~~~~~iPii   79 (123)
T d1mb3a_           2 KKVLIVEDNELNMKLFHDLLEAQGYETLQTREGLSALSIARE--NKPDLILMDIQLPEISGLEVTKWLKEDDDLAHIPVV   79 (123)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHHHHH--HCCSEEEEESBCSSSBHHHHHHHHHHSTTTTTSCEE
T ss_pred             ceEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHh--CCCCEEEEEeccCCCcHHHHHHHHHhCCCcCCCCeE
Confidence            379999999999999999999999999999999999999984  569999999999999999999999744   478999


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      ++|+.........++++|+++|+.||++..+|..+++.++++
T Consensus        80 ~lt~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~i~~~l~r  121 (123)
T d1mb3a_          80 AVTAFAMKGDEERIREGGCEAYISKPISVVHFLETIKRLLER  121 (123)
T ss_dssp             EEC------CHHHHHHHTCSEEECSSCCHHHHHHHHHHHHSC
T ss_pred             EEEEecCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHHhC
Confidence            999888888888999999999999999999999999999874

>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=99.94  E-value=5e-26  Score=157.29  Aligned_cols=119  Identities=32%  Similarity=0.537  Sum_probs=110.7

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEE
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVI   94 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iI   94 (184)
                      ++++||||||++..++.++.+|+..||.+..+.++.++++.+.  ...||+||+|+.||+++|+++++++++ .+.+||+
T Consensus         7 ~~~~ILiVDD~~~~~~~l~~~L~~~g~~v~~a~~g~ea~~~~~--~~~~dlillD~~mP~~dG~el~~~ir~~~~~~pii   84 (133)
T d2ayxa1           7 DDMMILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVLS--KNHIDIVLSDVNMPNMDGYRLTQRIRQLGLTLPVI   84 (133)
T ss_dssp             CCCEEEEEESSHHHHHHHHHHHHHHTSEEEEECCSHHHHHHHH--HSCCSEEEEEESSCSSCCHHHHHHHHHHHCCSCEE
T ss_pred             CCCEEEEEECCHHHHHHHHHHHHHcCCEEEEECcHHHHHHHHh--ccCceEEEEeccCCCCCHHHHHHHHHHhCCCCCEE
Confidence            4789999999999999999999999999999999999999998  456999999999999999999999974 4688999


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      ++|.....+...++++.|+++|+.||++.++|.++++.++++
T Consensus        85 ~lt~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~~~r  126 (133)
T d2ayxa1          85 GVTANALAEEKQRCLESGMDSCLSKPVTLDVIKQTLTLYAER  126 (133)
T ss_dssp             EEESSTTSHHHHHHHHCCCEEEEESSCCHHHHHHHHHHHHHH
T ss_pred             EEeccCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999887653

>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=99.93  E-value=3.1e-25  Score=152.28  Aligned_cols=118  Identities=20%  Similarity=0.418  Sum_probs=107.2

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCe-EEEECCHHHHHHHHHh---cCCCccEEEEeCCCCCCCHHHHHHHhccc--CCC
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYE-VTKCNRAEIALDMLRM---SKNGYDIVISDVHMPDMDGFKLHEQVGLE--MDL   91 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~-v~~~~~~~~~~~~l~~---~~~~~dlvilD~~l~~~~g~~l~~~l~~~--~~~   91 (184)
                      +|||||||++..++.++.+|+..|+. +..+.+++++++.++.   ....||+||+|+.||+++|+++++++++.  ...
T Consensus         2 irVLvVDD~~~~~~~l~~~L~~~g~~~v~~a~~g~eAl~~l~~~~~~~~~~dlillD~~mP~~dG~el~~~ir~~~~~~~   81 (128)
T d2r25b1           2 VKILVVEDNHVNQEVIKRMLNLEGIENIELACDGQEAFDKVKELTSKGENYNMIFMDVQMPKVDGLLSTKMIRRDLGYTS   81 (128)
T ss_dssp             SCEEEECSCHHHHHHHHHHHHHTTCCCEEEESSHHHHHHHHHHHHHHTCCCSEEEECSCCSSSCHHHHHHHHHHHSCCCS
T ss_pred             eEEEEEeCCHHHHHHHHHHHHHcCCeEEEEEcChHHHHHHHHhhhhccCCCCEEEEEeCCCCCCHHHHHHHHHHccCCCC
Confidence            68999999999999999999999985 7889999999998853   24569999999999999999999999643  468


Q ss_pred             CEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           92 PVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        92 ~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      |||++|+..+.+...+++++|+++|+.||++.++|.++++++..
T Consensus        82 piI~lT~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~~~  125 (128)
T d2r25b1          82 PIVALTAFADDSNIKECLESGMNGFLSKPIKRPKLKTILTEFCA  125 (128)
T ss_dssp             CEEEEESCCSHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHCT
T ss_pred             eEEEEECCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999998765

>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=99.93  E-value=2.4e-25  Score=154.96  Aligned_cols=116  Identities=32%  Similarity=0.478  Sum_probs=108.1

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc---CCCCEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE---MDLPVI   94 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~---~~~~iI   94 (184)
                      .|||||||++..++.++.+|+..||+|..+.++.++++.+.  ...||+||+|+.||+.+|+++++.++..   .++|||
T Consensus         2 arILiVDD~~~~~~~l~~~L~~~g~~v~~a~~~~eal~~~~--~~~~dlil~D~~~p~~~G~~~~~~ir~~~~~~~~piI   79 (139)
T d1w25a1           2 ARILVVDDIEANVRLLEAKLTAEYYEVSTAMDGPTALAMAA--RDLPDIILLDVMMPGMDGFTVCRKLKDDPTTRHIPVV   79 (139)
T ss_dssp             CEEEEECSSTTHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--HHCCSEEEEESCCSSSCHHHHHHHHHHSTTTTTSCEE
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCEEEEEccchhhhhhhh--cccceeeeeeccccCCCchHHHHHhhhcccccCCCEE
Confidence            38999999999999999999999999999999999999998  4569999999999999999999999643   478999


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      ++|+..+.....+++++||+||+.||++..+|...++.+++
T Consensus        80 ~lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~lr  120 (139)
T d1w25a1          80 LITALDGRGDRIQGLESGASDFLTKPIDDVMLFARVRSLTR  120 (139)
T ss_dssp             EEECSSCHHHHHHHHHHTCCEEEESSCCHHHHHHHHHHHHH
T ss_pred             EEEcCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999988775

>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=99.93  E-value=1.9e-25  Score=152.39  Aligned_cols=118  Identities=25%  Similarity=0.409  Sum_probs=104.7

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcC-Ce-EEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc-C-CCC
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCL-YE-VTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE-M-DLP   92 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~-~~-v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~-~-~~~   92 (184)
                      .+||+||||++..++.++.+|+..| +. +..+.+++++++.+..  ..||+||+|+.||++||+++++++++. + ..|
T Consensus         1 sirILivDD~~~~~~~l~~~L~~~~~~~~v~~a~~g~~al~~~~~--~~~dlillD~~mP~~dG~e~~~~ir~~~~~~~~   78 (123)
T d1dz3a_           1 SIKVCIADDNRELVSLLDEYISSQPDMEVIGTAYNGQDCLQMLEE--KRPDILLLDIIMPHLDGLAVLERIRAGFEHQPN   78 (123)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHHHH--HCCSEEEEESCCSSSCHHHHHHHHHHHCSSCCE
T ss_pred             CcEEEEEeCCHHHHHHHHHHHHhCCCcEEEEEECCHHHHHHHHHh--cCCCEEEEcCCCCCCCHHHHHHHHHhcCCCCCe
Confidence            3799999999999999999999775 44 5689999999999984  559999999999999999999999753 3 346


Q ss_pred             EEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           93 VIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        93 iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      ||++|+....+...++++.||++|+.||++.++|.+++++++++
T Consensus        79 ii~~t~~~~~~~~~~a~~~Ga~~~l~KP~~~~~L~~~i~~v~~k  122 (123)
T d1dz3a_          79 VIMLTAFGQEDVTKKAVELGASYFILKPFDMENLAHHIRQVYGK  122 (123)
T ss_dssp             EEEEEETTCHHHHHHHHHTTCEEEEECSSCCTTHHHHHHHHHHC
T ss_pred             EEEEECcCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHcc
Confidence            88899998899999999999999999999999999999988763

>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=99.93  E-value=7.7e-25  Score=151.44  Aligned_cols=120  Identities=21%  Similarity=0.344  Sum_probs=108.2

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc------C
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE------M   89 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~------~   89 (184)
                      .++|||||||++..+..++.+|+..|+++..+.++.++++.+.   ..||+||+|+.||+++|+++++++++.      .
T Consensus         6 ~g~rILvVDD~~~~~~~l~~~L~~~G~~v~~a~~g~eal~~l~---~~~dlillD~~mP~~dG~el~~~ir~~~~~~~~~   82 (134)
T d1dcfa_           6 TGLKVLVMDENGVSRMVTKGLLVHLGCEVTTVSSNEECLRVVS---HEHKVVFMDVCMPGVENYQIALRIHEKFTKQRHQ   82 (134)
T ss_dssp             TTCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHCC---TTCSEEEEECCSSTTTTTHHHHHHHHHHC-CCSC
T ss_pred             CCCEEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHhh---cCCCeEEEEeccCCCchHHHHHHHHHhcccccCC
Confidence            4889999999999999999999999999999999999998764   459999999999999999999999631      3


Q ss_pred             CCCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCC
Q 029986           90 DLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPK  138 (184)
Q Consensus        90 ~~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~  138 (184)
                      .+|||++|+....+...+++++|+++|+.||++.++|.++++.+++.+.
T Consensus        83 ~~~ii~lT~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~l~~r~  131 (134)
T d1dcfa_          83 RPLLVALSGNTDKSTKEKCMSFGLDGVLLKPVSLDNIRDVLSDLLEPRV  131 (134)
T ss_dssp             CCEEEEEESCCSHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHHSCCC
T ss_pred             CCeEEEEeCCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHhhhhh
Confidence            4678889988888899999999999999999999999999999987543

>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=99.93  E-value=2.5e-25  Score=152.75  Aligned_cols=115  Identities=27%  Similarity=0.412  Sum_probs=107.8

Q ss_pred             eEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEEEE
Q 029986           19 RVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIMMS   97 (184)
Q Consensus        19 ~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi~~   97 (184)
                      +||||||++..++.+..+|+..||.+..+.+++++++.+.  ...||+||+|+.||+++|++++++++. .+..||+++|
T Consensus         4 ~ILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~~--~~~~dliilD~~mp~~~G~~~~~~i~~~~~~~~ii~lt   81 (128)
T d1yioa2           4 TVFVVDDDMSVREGLRNLLRSAGFEVETFDCASTFLEHRR--PEQHGCLVLDMRMPGMSGIELQEQLTAISDGIPIVFIT   81 (128)
T ss_dssp             EEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHCC--TTSCEEEEEESCCSSSCHHHHHHHHHHTTCCCCEEEEE
T ss_pred             EEEEEECCHHHHHHHHHHHHHcCCCccccccHHHHHHHHH--hcCCCEeehhhhcccchhHHHHHHHHhhCCCCeEEEEE
Confidence            8999999999999999999999999999999999999986  567999999999999999999999964 4678999999


Q ss_pred             ccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           98 VDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        98 ~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      +..+.+...++++.||++|+.||++.++|..+++++++
T Consensus        82 ~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~l~  119 (128)
T d1yioa2          82 AHGDIPMTVRAMKAGAIEFLPKPFEEQALLDAIEQGLQ  119 (128)
T ss_dssp             SCTTSCCCHHHHHTTEEEEEESSCCHHHHHHHHHHHHH
T ss_pred             EECCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHH
Confidence            99888899999999999999999999999999988775

>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=99.93  E-value=4e-25  Score=150.11  Aligned_cols=116  Identities=24%  Similarity=0.363  Sum_probs=104.6

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEEEE
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVIMM   96 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iIi~   96 (184)
                      .||+||||++..++.++..|+..|+ +..+.++.+++..    ...||+||+|+.||+++|++++++++. .+.+|||++
T Consensus         3 ~kILiVDDd~~~~~~l~~~L~~~g~-v~~~~~~~~al~~----~~~~dlillD~~mP~~~G~~~~~~lr~~~~~~~ii~i   77 (120)
T d1p2fa2           3 WKIAVVDDDKNILKKVSEKLQQLGR-VKTFLTGEDFLND----EEAFHVVVLDVMLPDYSGYEICRMIKETRPETWVILL   77 (120)
T ss_dssp             EEEEEECSCHHHHHHHHHHHTTTEE-EEEESSHHHHHHC----CSCCSEEEEESBCSSSBHHHHHHHHHHHCTTSEEEEE
T ss_pred             CEEEEEECCHHHHHHHHHHHHhCCE-EEEECCHHHHHhc----CCCCCEEEEeCcccccchhHHHHHHhhcCCCCcEEEE
Confidence            5899999999999999999998885 7788999888752    456999999999999999999999974 478999999


Q ss_pred             EccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcCCC
Q 029986           97 SVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQPK  138 (184)
Q Consensus        97 ~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~~~  138 (184)
                      |...+.+...++++.||++|+.||++.++|..++++++++.+
T Consensus        78 t~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~l~r~r  119 (120)
T d1p2fa2          78 TLLSDDESVLKGFEAGADDYVTKPFNPEILLARVKRFLEREK  119 (120)
T ss_dssp             ESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHHHHCC
T ss_pred             ecCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHcc
Confidence            999999999999999999999999999999999999887543

>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=99.92  E-value=3.1e-24  Score=150.12  Aligned_cols=119  Identities=18%  Similarity=0.321  Sum_probs=106.5

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcC--CeEEEECCHHHHHHHHHhc-----CCCccEEEEeCCCCCCCHHHHHHHhccc-
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCL--YEVTKCNRAEIALDMLRMS-----KNGYDIVISDVHMPDMDGFKLHEQVGLE-   88 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~--~~v~~~~~~~~~~~~l~~~-----~~~~dlvilD~~l~~~~g~~l~~~l~~~-   88 (184)
                      +.+||||||++..+..++.+|+..|  +++..+.++.+|++++...     ...||+||+|+.||+++|++++++++.. 
T Consensus         3 pk~ILiVdD~~~~~~~l~~~L~~~g~~~~v~~a~~g~~Al~~l~~~~~~~~~~~pdlIllD~~mP~~~G~el~~~ir~~~   82 (144)
T d1i3ca_           3 PKVILLVEDSKADSRLVQEVLKTSTIDHELIILRDGLAAMAFLQQQGEYENSPRPNLILLDLNLPKKDGREVLAEIKQNP   82 (144)
T ss_dssp             CEEEEEECCCHHHHHHHHHHHHSCCSCEEEEEECSHHHHHHHHTTCGGGTTCCCCSEEEECSCCSSSCHHHHHHHHHHCT
T ss_pred             CCEEEEEECCHHHHHHHHHHHHHcCCCeEEEEECCHHHHHHHHHhchhhhccCCCCEEEEECccccccchHHHHHHHhCc
Confidence            3489999999999999999998765  5788999999999998631     2359999999999999999999999754 


Q ss_pred             --CCCCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           89 --MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        89 --~~~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                        .++|||++|+..+.+...+++++||++|+.||++.++|..+++.+..
T Consensus        83 ~~~~iPvi~lT~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~i~~l~~  131 (144)
T d1i3ca_          83 DLKRIPVVVLTTSHNEDDVIASYELHVNCYLTKSRNLKDLFKMVQGIES  131 (144)
T ss_dssp             TTTTSCEEEEESCCCHHHHHHHHHTTCSEEEECCSSHHHHHHHHHHHHH
T ss_pred             ccCCCeEEEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHH
Confidence              37899999999999999999999999999999999999999988765

>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=99.92  E-value=2.8e-24  Score=149.64  Aligned_cols=118  Identities=19%  Similarity=0.362  Sum_probs=106.3

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcC--CeEEEECCHHHHHHHHHh-----cCCCccEEEEeCCCCCCCHHHHHHHhcccC-
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCL--YEVTKCNRAEIALDMLRM-----SKNGYDIVISDVHMPDMDGFKLHEQVGLEM-   89 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~--~~v~~~~~~~~~~~~l~~-----~~~~~dlvilD~~l~~~~g~~l~~~l~~~~-   89 (184)
                      .|||||||++..+..++.+|++.|  +++..+.++.++++.+..     ....||+||+|++||+++|++++++++..+ 
T Consensus         3 krILiVDD~~~~~~~l~~~L~~~g~~~~v~~a~~g~eAl~~l~~~~~~~~~~~pdlillD~~mP~~dG~el~~~ir~~~~   82 (140)
T d1k68a_           3 KKIFLVEDNKADIRLIQEALANSTVPHEVVTVRDGMEAMAYLRQEGEYANASRPDLILLDLNLPKKDGREVLAEIKSDPT   82 (140)
T ss_dssp             CEEEEECCCHHHHHHHHHHHHTCSSCCEEEEECSHHHHHHHHTTCGGGGSCCCCSEEEECSSCSSSCHHHHHHHHHHSTT
T ss_pred             CcEEEEECCHHHHHHHHHHHHHcCCCeEEEEECCHHHHHHHHHHhHHhhccCCCCEEEEeeccccccChHHHHHHHhCcc
Confidence            489999999999999999999765  689999999999999853     124589999999999999999999997543 


Q ss_pred             --CCCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           90 --DLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        90 --~~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                        ++|||++|+..+.+...+++++||++|+.||++.++|..+++.+.+
T Consensus        83 ~~~iPvI~ls~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~i~~i~~  130 (140)
T d1k68a_          83 LKRIPVVVLSTSINEDDIFHSYDLHVNCYITKSANLSQLFQIVKGIEE  130 (140)
T ss_dssp             GGGSCEEEEESCCCHHHHHHHHHTTCSEEEECCSSHHHHHHHHHHHHH
T ss_pred             cCCCcEEEEeCCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHH
Confidence              6899999999999999999999999999999999999999988754

>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=99.92  E-value=3.3e-24  Score=150.80  Aligned_cols=118  Identities=20%  Similarity=0.408  Sum_probs=107.5

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCC--eEEEECCHHHHHHHHHhc--------CCCccEEEEeCCCCCCCHHHHHHHhcc
Q 029986           18 LRVLVVDDDPIWLRILEKMLRKCLY--EVTKCNRAEIALDMLRMS--------KNGYDIVISDVHMPDMDGFKLHEQVGL   87 (184)
Q Consensus        18 ~~Ilivdd~~~~~~~l~~~L~~~~~--~v~~~~~~~~~~~~l~~~--------~~~~dlvilD~~l~~~~g~~l~~~l~~   87 (184)
                      -+||||||++..+..++.+|++.|+  .+..+.++.++++++...        ...||+||+|++||+++|+++++++++
T Consensus         7 ~~ILiVDD~~~~~~~l~~~L~~~g~~~~v~~a~~g~eAl~~l~~~~~~~~~~~~~~pdlillD~~mP~~~G~el~~~ir~   86 (149)
T d1k66a_           7 QPLLVVEDSDEDFSTFQRLLQREGVVNPIYRCITGDQALDFLYQTGSYCNPDIAPRPAVILLDLNLPGTDGREVLQEIKQ   86 (149)
T ss_dssp             SCEEEECCCHHHHHHHHHHHHHTTBCSCEEEECSHHHHHHHHHTCCSSSCGGGCCCCSEEEECSCCSSSCHHHHHHHHTT
T ss_pred             CcEEEEECCHHHHHHHHHHHHHcCCceEEEEECChHHHHHHHHhhccccccccccCCCeEEccccccCCCcHHHHHHHHh
Confidence            3699999999999999999999887  788999999999999732        235999999999999999999999975


Q ss_pred             c---CCCCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           88 E---MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        88 ~---~~~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      .   .++|||++|+..+.+...+++++||++|+.||++..+|.+.++.+++
T Consensus        87 ~~~~~~ipiI~lT~~~~~~~~~~~~~~Ga~~~l~KP~~~~~L~~~i~~~l~  137 (149)
T d1k66a_          87 DEVLKKIPVVIMTTSSNPKDIEICYSYSISSYIVKPLEIDRLTETVQTFIK  137 (149)
T ss_dssp             STTGGGSCEEEEESCCCHHHHHHHHHTTCSEEEECCSSHHHHHHHHHHHHH
T ss_pred             ccccCCCeEEEEeCCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHH
Confidence            4   37899999999999999999999999999999999999999998876

>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=99.91  E-value=7.8e-24  Score=149.45  Aligned_cols=117  Identities=23%  Similarity=0.271  Sum_probs=102.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc---CCCC
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE---MDLP   92 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~---~~~~   92 (184)
                      .+.|||||||++..++.+...|...||.+..  ++.++...+.  ...||+||+|+.||+++|+++++.++..   +++|
T Consensus        12 ~~~rILiVDD~~~~~~~l~~~L~~~g~~v~~--~~~~~~~~~~--~~~~DlillD~~mP~~dG~el~~~ir~~~~~~~iP   87 (153)
T d1w25a2          12 LGGRVLIVDDNERQAQRVAAELGVEHRPVIE--SDPEKAKISA--GGPVDLVIVNAAAKNFDGLRFTAALRSEERTRQLP   87 (153)
T ss_dssp             CSCEEEEECSCHHHHHHHHHHHTTTSEEEEE--CCHHHHHHHH--HSSCSEEEEETTCSSSCHHHHHHHHHTSGGGTTCC
T ss_pred             CCCeEEEEeCCHHHHHHHHHHHHHCCCEEEE--ccHHHHHHHh--cCCCCEEEEECccccccchHHHHHHHhccccccce
Confidence            3669999999999999999999999988754  3466666665  4569999999999999999999999643   5899


Q ss_pred             EEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           93 VIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        93 iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      ||++|+..+.....++++.||++|+.||++..+|...++..++.
T Consensus        88 iI~lt~~~~~~~~~~a~~~Ga~d~l~KP~~~~~L~~~i~~~l~~  131 (153)
T d1w25a2          88 VLAMVDPDDRGRMVKALEIGVNDILSRPIDPQELSARVKTQIQR  131 (153)
T ss_dssp             EEEEECTTCHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHHHH
T ss_pred             eEEeecCCCHHHHHHHHhcCcceEEECCCCHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999887764

>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=99.89  E-value=2.8e-23  Score=140.41  Aligned_cols=112  Identities=22%  Similarity=0.324  Sum_probs=96.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc-CCCCEEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE-MDLPVIM   95 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~-~~~~iIi   95 (184)
                      ++||+||||++..++.++.+|+..||++..+.++.++++.+.. ...||+||+|+.||+++|++++++++.. +++|||+
T Consensus         2 p~rILvVdDd~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~~-~~~~dliilD~~lp~~~G~el~~~ir~~~~~~pii~   80 (118)
T d2b4aa1           2 PFRVTLVEDEPSHATLIQYHLNQLGAEVTVHPSGSAFFQHRSQ-LSTCDLLIVSDQLVDLSIFSLLDIVKEQTKQPSVLI   80 (118)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHTGGG-GGSCSEEEEETTCTTSCHHHHHHHHTTSSSCCEEEE
T ss_pred             CCEEEEEECCHHHHHHHHHHHHhcCCCeEEECCHHHHHHHHHh-cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCcEEE
Confidence            5799999999999999999999999999999999999987643 2459999999999999999999999744 6899999


Q ss_pred             EEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHH
Q 029986           96 MSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQH  132 (184)
Q Consensus        96 ~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~  132 (184)
                      +|+..+  ....+...|+ ||+.||++.++|..+++.
T Consensus        81 lt~~~~--~~~~~~~~~~-dyl~KP~~~~eL~~~i~~  114 (118)
T d2b4aa1          81 LTTGRH--ELIESSEHNL-SYLQKPFAISELRAAIDY  114 (118)
T ss_dssp             EESCC----CCCCSSSCE-EEEESSCCHHHHHHHHHH
T ss_pred             EECCcc--HHHHHhhcCC-CEEECCCCHHHHHHHHHH
Confidence            987543  3345666676 899999999999888875

>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=99.88  E-value=3.3e-22  Score=139.00  Aligned_cols=104  Identities=26%  Similarity=0.427  Sum_probs=87.1

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcC--CeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCC-CE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCL--YEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDL-PV   93 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~--~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~-~i   93 (184)
                      .+||+||||++..++.++.+|++.|  +.|..+.++.++++.+.  +..||+||+|+.||++||+++++.++..... ++
T Consensus         3 kirVLiVDD~~~~r~~l~~~L~~~g~~~~v~~a~~g~~al~~~~--~~~pDlvllDi~MP~~dG~e~~~~ir~~~~~~~i   80 (140)
T d1a2oa1           3 KIRVLSVDDSALMRQIMTEIINSHSDMEMVATAPDPLVARDLIK--KFNPDVLTLDVEMPRMDGLDFLEKLMRLRPMPVV   80 (140)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHHH--HHCCSEEEEECCCSSSCHHHHHHHHHHSSCCCEE
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHhCCCeEEEEEECCHHHHHHHHH--hcCCCEEEEcCCCCCCCHHHHHHHHHHhCCCCcE
Confidence            4699999999999999999999887  46778999999999997  4569999999999999999999999765544 45


Q ss_pred             EEEEccC-ChHHHHHHHHcCCCceEeCCCC
Q 029986           94 IMMSVDG-CTQDVMKGVTHGACNYLLKPIR  122 (184)
Q Consensus        94 Ii~~~~~-~~~~~~~a~~~ga~~~l~kP~~  122 (184)
                      ++++... ..+...++++.||++|+.||+.
T Consensus        81 ~i~~~~~~~~~~~~~al~~Ga~~yl~KP~~  110 (140)
T d1a2oa1          81 MVSSLTGKGSEVTLRALELGAIDFVTKPQL  110 (140)
T ss_dssp             EEECCTHHHHHHHHHHHHHTCCEEEECSSS
T ss_pred             EEEEecCCChHHHHHHHHcCCCEEEECCCC
Confidence            4544332 2356778999999999999963

>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=99.86  E-value=5.8e-22  Score=144.10  Aligned_cols=114  Identities=11%  Similarity=0.059  Sum_probs=103.0

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEE
Q 029986           16 AGLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIM   95 (184)
Q Consensus        16 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi   95 (184)
                      .+++||||||++..+..|...|+..||+|..+.++.+++.      ..||+||+|+.||+.+|..+.+..+..+.+|||+
T Consensus        10 ~~~~iLvvdd~~~~~~~l~~~L~~~G~~v~~~~~~~~al~------~~~Dlvl~D~~mp~~~~~~~~~~~~~~p~~pvI~   83 (189)
T d1qo0d_          10 RELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFD------VPVDVVFTSIFQNRHHDEIAALLAAGTPRTTLVA   83 (189)
T ss_dssp             GGCEEEEESCTTHHHHHHHHHHHHHTCEEEEECSCCSSCS------SCCSEEEEECCSSTHHHHHHHHHHHSCTTCEEEE
T ss_pred             cCCEEEEEeCCHHHHHHHHHHHHHcCCcceecCCHHHhcc------CCCCEEEEcCCCCCcHHHHHHHHHHcCCCCCEEE
Confidence            4679999999999999999999999999999998887762      4599999999999988877776666778999999


Q ss_pred             EEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           96 MSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        96 ~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      +|++.+.++..++++.||++|+.||++.++|..+++.+..
T Consensus        84 lta~~~~~~~~~al~~Ga~~yL~KP~~~~~L~~~i~~~~~  123 (189)
T d1qo0d_          84 LVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARR  123 (189)
T ss_dssp             EECCCSHHHHHHHHHHTCSEEEESSCCGGGHHHHHHHHHH
T ss_pred             EeccchHHHHHHHHHcCCcEEEEecchhhHHHHHHhhccc
Confidence            9999999999999999999999999999999999987754

>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=95.86  E-value=0.045  Score=35.75  Aligned_cols=110  Identities=7%  Similarity=-0.057  Sum_probs=74.5

Q ss_pred             eCCHHHHHHHHHHHHhcCCeEEE---ECCHHHHHHHHHhcCCCccEEEEeCCCCCCC--HHHHHHHhccc--CCCCEEEE
Q 029986           24 DDDPIWLRILEKMLRKCLYEVTK---CNRAEIALDMLRMSKNGYDIVISDVHMPDMD--GFKLHEQVGLE--MDLPVIMM   96 (184)
Q Consensus        24 dd~~~~~~~l~~~L~~~~~~v~~---~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~--g~~l~~~l~~~--~~~~iIi~   96 (184)
                      |-+..-...+..+|+..||+|..   ....++..+.+.  +..||+|.+...+....  .-++++.++..  .++||++=
T Consensus        14 D~H~lG~~mva~~l~~~G~~V~~LG~~~p~e~iv~a~~--~~~~d~v~lS~~~~~~~~~~~~~~~~l~~~~~~~i~iivG   91 (137)
T d1ccwa_          14 DCHAVGNKILDHAFTNAGFNVVNIGVLSPQELFIKAAI--ETKADAILVSSLYGQGEIDCKGLRQKCDEAGLEGILLYVG   91 (137)
T ss_dssp             CCCCHHHHHHHHHHHHTTCEEEEEEEEECHHHHHHHHH--HHTCSEEEEEECSSTHHHHHTTHHHHHHHTTCTTCEEEEE
T ss_pred             ChhHHHHHHHHHHHHHCCCeEEecccccCHHHHHHHHH--hcCCCEEEEeeccccchHHHHHHHHHHHHhccCCCEEEEe
Confidence            45666777888999999998873   456888888887  45599999998877532  12244455433  35565433


Q ss_pred             EccC-----ChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           97 SVDG-----CTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        97 ~~~~-----~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      ....     .+....+..+.|++..+...-+.+++.+.+++-++
T Consensus        92 G~~~~~~~~~~~~~~~l~~~Gv~~if~~~t~~~~~~~~l~~~l~  135 (137)
T d1ccwa_          92 GNIVVGKQHWPDVEKRFKDMGYDRVYAPGTPPEVGIADLKKDLN  135 (137)
T ss_dssp             ESCSSSSCCHHHHHHHHHHTTCSEECCTTCCHHHHHHHHHHHHT
T ss_pred             CCcCCCccccHHHHHHHHHcCCCEEECCCCCHHHHHHHHHHHhC
Confidence            2211     23455566788999888888888888888877654

>d1r8ja2 c.23.1.5 (A:1-135) N-terminal domain of the circadian clock protein KaiA {Synechococcus elongatus [TaxId: 32046]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: N-terminal domain of the circadian clock protein KaiA
domain: N-terminal domain of the circadian clock protein KaiA
species: Synechococcus elongatus [TaxId: 32046]

Probab=95.17  E-value=0.18  Score=32.57  Aligned_cols=80  Identities=15%  Similarity=0.240  Sum_probs=62.8

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhccc-CCCCEEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLE-MDLPVIM   95 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~-~~~~iIi   95 (184)
                      .+.|.+.-.++...+.++..|....|.+..+.+.++.++++...+...|++++--.  +.+...+..++... --.|+|+
T Consensus         4 ~LtI~l~l~s~~L~q~~~q~L~~dRY~l~~~~s~~ef~~~le~~~e~iDcLVl~~~--~~~l~~l~~qL~~~GlLlPaVi   81 (135)
T d1r8ja2           4 QIAICIWVESTAILQDCQRALSADRYQLQVCESGEMLLEYAQTHRDQIDCLILVAA--NPSFRAVVQQLCFEGVVVPAIV   81 (135)
T ss_dssp             CEEEEEECCCHHHHHHHHHHTCSTTEEEEEECSHHHHHHHHHHSTTSCSEEEEETT--STTHHHHHHHHHHTTCCCCEEE
T ss_pred             eEEEEEEeCCHHHHHHHHHhcCCCceEEEEcCCHHHHHHHHHhCcccCCEEEEEec--CCccHHHHHHHHhcCccccEEE
Confidence            45688888999999999999988889999999999999999877777999986222  23445566777543 4679888


Q ss_pred             EEc
Q 029986           96 MSV   98 (184)
Q Consensus        96 ~~~   98 (184)
                      +..
T Consensus        82 v~~   84 (135)
T d1r8ja2          82 VGD   84 (135)
T ss_dssp             ESC
T ss_pred             Eec
Confidence            854

>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=94.47  E-value=0.39  Score=34.40  Aligned_cols=98  Identities=12%  Similarity=0.050  Sum_probs=64.5

Q ss_pred             HHHHHHhcCCe--EEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc--cCCCCEEEEEccCChHHHHHH
Q 029986           33 LEKMLRKCLYE--VTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL--EMDLPVIMMSVDGCTQDVMKG  108 (184)
Q Consensus        33 l~~~L~~~~~~--v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~--~~~~~iIi~~~~~~~~~~~~a  108 (184)
                      +++.|++-...  ++.........+.+.  ..++|.|++|.+....+--++...++.  ...++.++=....++..+.++
T Consensus         7 lk~~l~~g~~~~G~~~~~~~p~~~ei~a--~~G~Dfv~iD~EHg~~~~~~~~~~i~a~~~~g~~~~VRvp~~~~~~i~~~   84 (253)
T d1dxea_           7 FKAALAAKQVQIGCWSALSNPISTEVLG--LAGFDWLVLDGEHAPNDISTFIPQLMALKGSASAPVVRVPTNEPVIIKRL   84 (253)
T ss_dssp             HHHHHHTTCCEEEEEECSCSHHHHHHHT--TSCCSEEEEESSSSSCCHHHHHHHHHHTTTCSSEEEEECSSSCHHHHHHH
T ss_pred             HHHHHHCCCCEEEEEecCCCHHHHHHHH--cCCCCEEEEecccCCCChhHHHHHHHHHhccCCCceecCCCCCHHHHHHH
Confidence            55666653222  222233344555554  567999999999888887776666642  234444444556778999999


Q ss_pred             HHcCCCceEeCCC-CHHHHHHHHHH
Q 029986          109 VTHGACNYLLKPI-RIKELRNIWQH  132 (184)
Q Consensus       109 ~~~ga~~~l~kP~-~~~~l~~~l~~  132 (184)
                      ++.||.+.+..-+ +.++..++++.
T Consensus        85 LD~Ga~GIivP~v~s~eea~~~v~~  109 (253)
T d1dxea_          85 LDIGFYNFLIPFVETKEEAELAVAS  109 (253)
T ss_dssp             HHTTCCEEEESCCCSHHHHHHHHHT
T ss_pred             HhcCccEEEecccCCHHHHHHHHHh
Confidence            9999999998666 45566665554

>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=92.58  E-value=0.46  Score=31.53  Aligned_cols=108  Identities=9%  Similarity=-0.036  Sum_probs=70.7

Q ss_pred             eCCHHHHHHHHHHHHhcC---------CeEEEE---CCHHHHHHHHHhcCCCccEEEEeCCCCCCCH-H----HHHHHhc
Q 029986           24 DDDPIWLRILEKMLRKCL---------YEVTKC---NRAEIALDMLRMSKNGYDIVISDVHMPDMDG-F----KLHEQVG   86 (184)
Q Consensus        24 dd~~~~~~~l~~~L~~~~---------~~v~~~---~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g-~----~l~~~l~   86 (184)
                      |-+..=...+..+|+..|         |+|...   -..++..+.+.  +..||+|-+...|....+ .    ++++.++
T Consensus        30 D~HdiG~~iv~~~l~~~G~~~~~~~~~~eVi~LG~~vp~e~~v~~a~--e~~~d~VglS~l~t~~~~h~~~~~~~i~~l~  107 (160)
T d1xrsb1          30 DAHTVGIDAIMNMKGYAGHYGLERYEMIDAYNLGSQVANEDFIKKAV--ELEADVLLVSQTVTQKNVHIQNMTHLIELLE  107 (160)
T ss_dssp             CCCCHHHHHHHSTTCBTTBCCGGGCTTEEEEECCSSBCHHHHHHHHH--HTTCSEEEEECCCCTTSHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHcCCcccccccceEEEeCCCCCCHHHHHHHHH--hcCCCEEEEeecccccchhHHHHHHHHHHHH
Confidence            556667777888888878         777643   36778888877  566999999988876543 2    3445554


Q ss_pred             ccC--CCCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHc
Q 029986           87 LEM--DLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQ  135 (184)
Q Consensus        87 ~~~--~~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~  135 (184)
                      ...  +.+.|++....-..  ..+.+.|++.|+..-.+..++...+...+.
T Consensus       108 ~~g~~d~v~vivGG~~~~~--~~a~~~GaD~~f~~g~~a~~~a~~l~~~l~  156 (160)
T d1xrsb1         108 AEGLRDRFVLLCGGPRINN--EIAKELGYDAGFGPGRFADDVATFAVKTLN  156 (160)
T ss_dssp             HTTCGGGSEEEEECTTCCH--HHHHTTTCSEEECTTCCHHHHHHHHHHHHH
T ss_pred             HcCCCCceEEEEcCCCCCH--HHHHHcCCCEEcCCCCCHHHHHHHHHHHHH
Confidence            332  22445555433222  245688999999877777777776665543

>d7reqa2 c.23.6.1 (A:561-728) Methylmalonyl-CoA mutase alpha subunit, C-terminal domain {Propionibacterium freudenreichii, subsp. shermanii [TaxId: 1744]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: Cobalamin (vitamin B12)-binding domain
family: Cobalamin (vitamin B12)-binding domain
domain: Methylmalonyl-CoA mutase alpha subunit, C-terminal domain
species: Propionibacterium freudenreichii, subsp. shermanii [TaxId: 1744]

Probab=92.38  E-value=0.62  Score=31.15  Aligned_cols=104  Identities=11%  Similarity=-0.053  Sum_probs=65.5

Q ss_pred             CCeEEEEe----CCHHHHHHHHHHHHhcCCeEEEE---CCHHHHHHHHHhcCCCccEEEEeCCCCCC--CHHHHHHHhcc
Q 029986           17 GLRVLVVD----DDPIWLRILEKMLRKCLYEVTKC---NRAEIALDMLRMSKNGYDIVISDVHMPDM--DGFKLHEQVGL   87 (184)
Q Consensus        17 ~~~Ilivd----d~~~~~~~l~~~L~~~~~~v~~~---~~~~~~~~~l~~~~~~~dlvilD~~l~~~--~g~~l~~~l~~   87 (184)
                      ..||++.-    -+..-...+..+|+..||+|...   .+.++..+...  +..+|+|.+...+...  .--++++.|+.
T Consensus        37 ~pkVlla~~g~D~Hd~G~~~va~~l~~~G~eVi~lg~~~~~e~iv~aa~--~~~advI~iSs~~~~~~~~~~~l~~~L~~  114 (168)
T d7reqa2          37 RPRILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQTPEETARQAV--EADVHVVGVSSLAGGHLTLVPALRKELDK  114 (168)
T ss_dssp             CCEEEEECBTTCCCCHHHHHHHHHHHHTTCEEEECCTTBCHHHHHHHHH--HHTCSEEEEEECSSCHHHHHHHHHHHHHH
T ss_pred             CCeEEEEeCCccHHHHHHHHHHHHHHhCCcceecCCCcCcHHHHHHHHH--ccCCCEEEEecCcccchHHHHHHHHHHHh
Confidence            34777763    46667788899999999998753   36788888877  4459999997654431  12234455544


Q ss_pred             cC-CCCEEEEEccCChHHHHHHHHcCCCceEeCCCC
Q 029986           88 EM-DLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIR  122 (184)
Q Consensus        88 ~~-~~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~  122 (184)
                      .. .-..|++...-.........+.|+++.+..--+
T Consensus       115 ~g~~~v~VivGG~ip~~d~~~l~~~Gv~~iF~pgt~  150 (168)
T d7reqa2         115 LGRPDILITVGGVIPEQDFDELRKDGAVEIYTPGTV  150 (168)
T ss_dssp             TTCTTSEEEEEESCCGGGHHHHHHHTEEEEECTTCC
T ss_pred             cCCCCeEEEEeCCCCHHHHHHHHhCCCCEEECcCCC
Confidence            32 222334444333455566788999987754333

>d1qpoa1 c.1.17.1 (A:117-285) Quinolinic acid phosphoribosyltransferase (Nicotinate-nucleotide pyrophosphorylase, NadC), C-terminal domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Nicotinate/Quinolinate PRTase C-terminal domain-like
family: NadC C-terminal domain-like
domain: Quinolinic acid phosphoribosyltransferase (Nicotinate-nucleotide pyrophosphorylase, NadC), C-terminal domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=92.19  E-value=0.25  Score=33.25  Aligned_cols=93  Identities=11%  Similarity=-0.033  Sum_probs=60.6

Q ss_pred             EEEEeCCHHHHHHHHHHHHhc-----C-CeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCCE
Q 029986           20 VLVVDDDPIWLRILEKMLRKC-----L-YEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPV   93 (184)
Q Consensus        20 Ilivdd~~~~~~~l~~~L~~~-----~-~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~i   93 (184)
                      |+|-|.+-.....+...++..     . --...+.+.+++.+.+.   .++|+|++|-.-| .+--+.++.++...+..+
T Consensus        53 ilikdNHi~~~g~i~~~i~~~k~~~~~~~I~VEv~s~~q~~~a~~---~~~diImLDN~sp-~~~k~~v~~~~~~~~~i~  128 (169)
T d1qpoa1          53 ALIKDNHVAAAGSVVDALRAVRNAAPDLPCEVEVDSLEQLDAVLP---EKPELILLDNFAV-WQTQTAVQRRDSRAPTVM  128 (169)
T ss_dssp             EEECHHHHHHHSSHHHHHHHHHHHCTTSCEEEEESSHHHHHHHGG---GCCSEEEEETCCH-HHHHHHHHHHHHHCTTCE
T ss_pred             EEeehhHHhHhcchhhhhhhhhhhcCCCceEEEeccHHHhhhhhh---cCCcEEEecCcCh-HhHHHHHHHhhccCCeeE
Confidence            777777777666666555432     1 23457889999988875   4589999994322 222234444443344456


Q ss_pred             EEEEccCChHHHHHHHHcCCCce
Q 029986           94 IMMSVDGCTQDVMKGVTHGACNY  116 (184)
Q Consensus        94 Ii~~~~~~~~~~~~a~~~ga~~~  116 (184)
                      +-.+..-+.+.+......|+|-.
T Consensus       129 lEaSGgI~~~ni~~ya~~GvD~I  151 (169)
T d1qpoa1         129 LESSGGLSLQTAATYAETGVDYL  151 (169)
T ss_dssp             EEEESSCCTTTHHHHHHTTCSEE
T ss_pred             EEEeCCCCHHHHHHHHHcCCCEE
Confidence            66777777888888888998843

>d1o4ua1 c.1.17.1 (A:104-273) Quinolinic acid phosphoribosyltransferase (Nicotinate-nucleotide pyrophosphorylase, NadC), C-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Nicotinate/Quinolinate PRTase C-terminal domain-like
family: NadC C-terminal domain-like
domain: Quinolinic acid phosphoribosyltransferase (Nicotinate-nucleotide pyrophosphorylase, NadC), C-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=92.02  E-value=0.14  Score=34.62  Aligned_cols=94  Identities=15%  Similarity=0.057  Sum_probs=61.2

Q ss_pred             eEEEEeCCHHHHHHHHHHHHhc----C---CeEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCC
Q 029986           19 RVLVVDDDPIWLRILEKMLRKC----L---YEVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDL   91 (184)
Q Consensus        19 ~Ilivdd~~~~~~~l~~~L~~~----~---~~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~   91 (184)
                      .|+|-|.+-.....+...++..    .   .....+.+.+++.+.+.   .++|+|++|-.-| .+--++.+.++...+-
T Consensus        50 ~ilikdNHi~~~g~~~~~~~~~~~~~~~~~~I~VEv~~~~e~~~a~~---~g~d~i~LDn~~p-e~~k~~~~~lk~~~~~  125 (170)
T d1o4ua1          50 CVMIKDNHLKMYGSAERAVQEVRKIIPFTTKIEVEVENLEDALRAVE---AGADIVMLDNLSP-EEVKDISRRIKDINPN  125 (170)
T ss_dssp             CEEECHHHHHHHSSHHHHHHHHHTTSCTTSCEEEEESSHHHHHHHHH---TTCSEEEEESCCH-HHHHHHHHHHHHHCTT
T ss_pred             ceEEcccHHHHhccHHHHHHHHHhhCCCCceEEEEeCcHHHHHHHHh---cCccEEEEcCcCh-hhHhHHHHHHHhhCCc
Confidence            3777777777666666666532    2   13457889999998875   4589999994322 2223344555443444


Q ss_pred             CEEEEEccCChHHHHHHHHcCCCceE
Q 029986           92 PVIMMSVDGCTQDVMKGVTHGACNYL  117 (184)
Q Consensus        92 ~iIi~~~~~~~~~~~~a~~~ga~~~l  117 (184)
                      ..+-.+..-+.+.+....+.|+| ||
T Consensus       126 i~lEaSGGI~~~ni~~~a~~GVD-~I  150 (170)
T d1o4ua1         126 VIVEVSGGITEENVSLYDFETVD-VI  150 (170)
T ss_dssp             SEEEEEECCCTTTGGGGCCTTCC-EE
T ss_pred             EEEEEECCCCHHHHHHHHHcCCC-EE
Confidence            56666777777777777788888 54

>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=91.39  E-value=1.9  Score=31.48  Aligned_cols=104  Identities=13%  Similarity=0.149  Sum_probs=66.1

Q ss_pred             HHHHHHHHHHhcC-CeEE-EEC-CHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhc---cc--CCCCEEEEEccC
Q 029986           29 WLRILEKMLRKCL-YEVT-KCN-RAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVG---LE--MDLPVIMMSVDG  100 (184)
Q Consensus        29 ~~~~l~~~L~~~~-~~v~-~~~-~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~---~~--~~~~iIi~~~~~  100 (184)
                      .++.|+..+.+.+ ..+. ++. ......+.+.  ..++|-|++|.+....+--++...++   ..  ..++.++=....
T Consensus        27 ~r~~l~~~~~~~~~~~~G~~~~~~s~~~~e~~a--~~g~D~v~iD~EHg~~~~~~~~~~i~a~~~~~~~~~~~iVRvp~~  104 (299)
T d1izca_          27 LRQALKDAMADPSKTLMGVAHGIPSTFVTKVLA--ATKPDFVWIDVEHGMFNRLELHDAIHAAQHHSEGRSLVIVRVPKH  104 (299)
T ss_dssp             HHHHHHHHHHCGGGCEEEEEECSCCHHHHHHHH--HTCCSEEEEETTTSCCCHHHHHHHHHHHHHHTTTCSEEEEECCTT
T ss_pred             HHHHHHHHhhccCCceeeeeccCCCHHHHHHHH--cCCCCEEEEcCCCCCCCHHHHHHHHHHHHHhCCCCCCeEEeCCCC
Confidence            5777777776532 2222 222 2234444544  45699999999988777655554442   21  223334334556


Q ss_pred             ChHHHHHHHHcCCCceEeCCC-CHHHHHHHHHHHH
Q 029986          101 CTQDVMKGVTHGACNYLLKPI-RIKELRNIWQHVA  134 (184)
Q Consensus       101 ~~~~~~~a~~~ga~~~l~kP~-~~~~l~~~l~~~~  134 (184)
                      +...+.++++.||.+.+..-+ +.++..++++...
T Consensus       105 ~~~~I~~~LD~Ga~GIivP~V~s~eea~~~v~~~r  139 (299)
T d1izca_         105 DEVSLSTALDAGAAGIVIPHVETVEEVREFVKEMY  139 (299)
T ss_dssp             CHHHHHHHHHHTCSEEEETTCCCHHHHHHHHHHHS
T ss_pred             ChHHHHHHHHhCcCeeeccccccHHHHHHHHHhhh
Confidence            678899999999999988555 5677888887764

>d1xi3a_ c.1.3.1 (A:) Thiamin phosphate synthase {Archaeon (Pyrococcus furiosus) [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Thiamin phosphate synthase
family: Thiamin phosphate synthase
domain: Thiamin phosphate synthase
species: Archaeon (Pyrococcus furiosus) [TaxId: 2261]

Probab=89.64  E-value=2.1  Score=29.16  Aligned_cols=71  Identities=14%  Similarity=0.129  Sum_probs=53.3

Q ss_pred             eEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCC-------CHHHHHHHhcccCCCCEEEEEccCChHHHHHHHHcCCCc
Q 029986           43 EVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDM-------DGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACN  115 (184)
Q Consensus        43 ~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~-------~g~~l~~~l~~~~~~~iIi~~~~~~~~~~~~a~~~ga~~  115 (184)
                      -...+++.+++.....   .++|.+.+.-..+..       -|++.++++.....+||+.+.. -+.+....+++.|+++
T Consensus       102 ig~s~h~~~e~~~a~~---~g~DYi~~gpvf~T~tk~~~~~~g~~~l~~~~~~~~~Pv~AiGG-I~~~ni~~~~~~Ga~g  177 (206)
T d1xi3a_         102 IGASVYSLEEALEAEK---KGADYLGAGSVFPTKTKEDARVIGLEGLRKIVESVKIPVVAIGG-INKDNAREVLKTGVDG  177 (206)
T ss_dssp             EEEEESSHHHHHHHHH---HTCSEEEEECSSCC----CCCCCHHHHHHHHHHHCSSCEEEESS-CCTTTHHHHHTTTCSE
T ss_pred             cccccCCHHHHHHHHh---cCCCEEEeccccccccccccccccHHHHHHHHHhcCCCEEEECC-CCHHHHHHHHHhCCCE
Confidence            4457888888776654   358999998755432       3888888886667899999866 3567788899999999


Q ss_pred             eE
Q 029986          116 YL  117 (184)
Q Consensus       116 ~l  117 (184)
                      +.
T Consensus       178 vA  179 (206)
T d1xi3a_         178 IA  179 (206)
T ss_dssp             EE
T ss_pred             EE
Confidence            84

>d1mxsa_ c.1.10.1 (A:) KDPG aldolase {Pseudomonas putida [TaxId: 303]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Aldolase
family: Class I aldolase
domain: KDPG aldolase
species: Pseudomonas putida [TaxId: 303]

Probab=88.68  E-value=1.5  Score=30.39  Aligned_cols=99  Identities=12%  Similarity=0.085  Sum_probs=64.2

Q ss_pred             HHHHHHHHHhcC-CeEEEECCHHHHHHHHHh-cCCCccEEEEeCCCCCCCHHHHHHHhccc-CCCCEEEEEccCChHHHH
Q 029986           30 LRILEKMLRKCL-YEVTKCNRAEIALDMLRM-SKNGYDIVISDVHMPDMDGFKLHEQVGLE-MDLPVIMMSVDGCTQDVM  106 (184)
Q Consensus        30 ~~~l~~~L~~~~-~~v~~~~~~~~~~~~l~~-~~~~~dlvilD~~l~~~~g~~l~~~l~~~-~~~~iIi~~~~~~~~~~~  106 (184)
                      ...+...|+... .-+....+.+++...... .+.+..  .+.+.+...++++.++.++.. ++ -.|-..+=.+.+.+.
T Consensus         7 ~~~i~~~l~~~~iipvl~~~~~~~a~~~~~al~~~Gi~--~iEitl~~p~a~~~i~~l~~~~p~-~~vGaGTV~~~~~~~   83 (216)
T d1mxsa_           7 AARIDAICEKARILPVITIAREEDILPLADALAAGGIR--TLEVTLRSQHGLKAIQVLREQRPE-LCVGAGTVLDRSMFA   83 (216)
T ss_dssp             HHHHHHHHHHHSEEEEECCSCGGGHHHHHHHHHHTTCC--EEEEESSSTHHHHHHHHHHHHCTT-SEEEEECCCSHHHHH
T ss_pred             HHHHHHHHHhCCEEEEEECCCHHHHHHHHHHHHHCCCC--EEEEeCCChhHHHHHHHHHHhCCC-cceeeeeeecHHHHH
Confidence            445566666543 234445555555555432 133455  455566667788899988644 55 345556666788999


Q ss_pred             HHHHcCCCceEeCCCCHHHHHHHHHH
Q 029986          107 KGVTHGACNYLLKPIRIKELRNIWQH  132 (184)
Q Consensus       107 ~a~~~ga~~~l~kP~~~~~l~~~l~~  132 (184)
                      .+.++||+ |++.|....++.+....
T Consensus        84 ~a~~aGa~-FivsP~~~~~v~~~a~~  108 (216)
T d1mxsa_          84 AVEAAGAQ-FVVTPGITEDILEAGVD  108 (216)
T ss_dssp             HHHHHTCS-SEECSSCCHHHHHHHHH
T ss_pred             HHHhCCCC-EEECCCCcHHHHHHHHh
Confidence            99999996 88889988888765543

>d1xm3a_ c.1.31.1 (A:) Thiazole biosynthesis protein ThiG {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: ThiG-like
family: ThiG-like
domain: Thiazole biosynthesis protein ThiG
species: Bacillus subtilis [TaxId: 1423]

Probab=88.47  E-value=2.1  Score=30.22  Aligned_cols=97  Identities=15%  Similarity=0.063  Sum_probs=63.1

Q ss_pred             HHHHHhcCCeEEEEC--CHHHHHHHHHhcCCCccEEEEeCCCCCCCH-----HHHHHHhcccCCCCEEEEEccCChHHHH
Q 029986           34 EKMLRKCLYEVTKCN--RAEIALDMLRMSKNGYDIVISDVHMPDMDG-----FKLHEQVGLEMDLPVIMMSVDGCTQDVM  106 (184)
Q Consensus        34 ~~~L~~~~~~v~~~~--~~~~~~~~l~~~~~~~dlvilD~~l~~~~g-----~~l~~~l~~~~~~~iIi~~~~~~~~~~~  106 (184)
                      .+.|-+.||.|..+.  |..-|.++....   +. .++-+.-|-++|     -..++.+....++|||+=+.-..+..+.
T Consensus       118 ae~Lv~eGF~VlpY~~~D~v~ak~Le~~G---c~-avMPlgsPIGSg~Gl~n~~~l~~i~~~~~vPvIvDAGIG~pSdAa  193 (251)
T d1xm3a_         118 SEQLLEEGFIVLPYTSDDVVLARKLEELG---VH-AIMPGASPIGSGQGILNPLNLSFIIEQAKVPVIVDAGIGSPKDAA  193 (251)
T ss_dssp             HHHHHHTTCCEEEEECSCHHHHHHHHHHT---CS-CBEECSSSTTCCCCCSCHHHHHHHHHHCSSCBEEESCCCSHHHHH
T ss_pred             HHHHHhCCcEEEEecCCCHHHHHHHHHcC---Ch-hHHHhhhhhhcCCCcCChHHHHHHHhcCCccEEEecCCCCHHHHH
Confidence            456667789887443  455555554422   22 345555554433     3456666666889999998889999999


Q ss_pred             HHHHcCCCceEe-----CCCCHHHHHHHHHHHH
Q 029986          107 KGVTHGACNYLL-----KPIRIKELRNIWQHVA  134 (184)
Q Consensus       107 ~a~~~ga~~~l~-----kP~~~~~l~~~l~~~~  134 (184)
                      .+++.|+++.++     +--++-.+.+++....
T Consensus       194 ~AMElG~daVLvNTAIA~a~dPv~MA~A~~~Av  226 (251)
T d1xm3a_         194 YAMELGADGVLLNTAVSGADDPVKMARAMKLAV  226 (251)
T ss_dssp             HHHHTTCSEEEESHHHHTSSSHHHHHHHHHHHH
T ss_pred             HHHHccCCEEEechhhhcCCCHHHHHHHHHHHH
Confidence            999999999984     3334555555555443

>d1wa3a1 c.1.10.1 (A:2-203) KDPG aldolase {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Aldolase
family: Class I aldolase
domain: KDPG aldolase
species: Thermotoga maritima [TaxId: 2336]

Probab=88.30  E-value=2  Score=29.38  Aligned_cols=96  Identities=16%  Similarity=0.203  Sum_probs=59.3

Q ss_pred             HHHHHhcCC-eEEEECCHHHHHHHHHh-cCCCccEEEEeCCCCCCCHHHHHHHhccc-CCCCEEEEEccCChHHHHHHHH
Q 029986           34 EKMLRKCLY-EVTKCNRAEIALDMLRM-SKNGYDIVISDVHMPDMDGFKLHEQVGLE-MDLPVIMMSVDGCTQDVMKGVT  110 (184)
Q Consensus        34 ~~~L~~~~~-~v~~~~~~~~~~~~l~~-~~~~~dlvilD~~l~~~~g~~l~~~l~~~-~~~~iIi~~~~~~~~~~~~a~~  110 (184)
                      .+.|++.+. -+....+.+++...... .+.+..  ++.+.|-..++++.++.++.. ..--+|-..+=.+.+.+..+.+
T Consensus         3 ~~~l~~~~iipvlr~~~~~~a~~~~~al~~~Gi~--~iEitlr~p~a~~~i~~l~~~~~~~~~vGaGTV~~~~~~~~a~~   80 (202)
T d1wa3a1           3 EELFKKHKIVAVLRANSVEEAKEKALAVFEGGVH--LIEITFTVPDADTVIKELSFLKEKGAIIGAGTVTSVEQCRKAVE   80 (202)
T ss_dssp             HHHHHHHCEEEEECCSSHHHHHHHHHHHHHTTCC--EEEEETTSTTHHHHHHHTHHHHHTTCEEEEESCCSHHHHHHHHH
T ss_pred             HHHHHhCCEEEEEECCCHHHHHHHHHHHHHcCCC--EEEEecCCccHHHHHHHHHHhcCCCcEEEecccccHHHHHHHHh
Confidence            445555443 34455566666665542 133445  455566677888888887532 1222444445566788899999


Q ss_pred             cCCCceEeCCCCHHHHHHHHHH
Q 029986          111 HGACNYLLKPIRIKELRNIWQH  132 (184)
Q Consensus       111 ~ga~~~l~kP~~~~~l~~~l~~  132 (184)
                      +||+ |++.|....++.+....
T Consensus        81 aGa~-fivsP~~~~~v~~~~~~  101 (202)
T d1wa3a1          81 SGAE-FIVSPHLDEEISQFCKE  101 (202)
T ss_dssp             HTCS-EEECSSCCHHHHHHHHH
T ss_pred             hccc-EEeCCCCcHHHHHHHHh
Confidence            9998 77788877777665543

>d1id1a_ c.2.1.9 (A:) Rck domain from putative potassium channel Kch {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Potassium channel NAD-binding domain
domain: Rck domain from putative potassium channel Kch
species: Escherichia coli [TaxId: 562]

Probab=88.28  E-value=1.7  Score=27.82  Aligned_cols=112  Identities=12%  Similarity=-0.053  Sum_probs=59.8

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeEEEEC-CHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcc-cCCCCEE
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEVTKCN-RAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGL-EMDLPVI   94 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v~~~~-~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~-~~~~~iI   94 (184)
                      +..|.++|.++.........+...|+.+..-. .-.+.++...  -...+.+++-..-. ..-...+..++. .+..+++
T Consensus        26 ~~~v~vId~d~~~~~~~~~~~~~~~~~vi~Gd~~d~~~L~~a~--i~~a~~vi~~~~~d-~~n~~~~~~~r~~~~~~~ii  102 (153)
T d1id1a_          26 GQNVTVISNLPEDDIKQLEQRLGDNADVIPGDSNDSSVLKKAG--IDRCRAILALSDND-ADNAFVVLSAKDMSSDVKTV  102 (153)
T ss_dssp             TCCEEEEECCCHHHHHHHHHHHCTTCEEEESCTTSHHHHHHHT--TTTCSEEEECSSCH-HHHHHHHHHHHHHTSSSCEE
T ss_pred             CCCEEEEeccchhHHHHHHHhhcCCcEEEEccCcchHHHHHhc--cccCCEEEEccccH-HHHHHHHHHHHHhCCCCceE
Confidence            45688888877655444444544566665322 1233444443  33478888754311 112223333343 4677777


Q ss_pred             EEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHHHHHcC
Q 029986           95 MMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQHVAQQ  136 (184)
Q Consensus        95 i~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~~~~~~  136 (184)
                      +.+  .+++.......+|++.. .-|.  ....+.+...+.+
T Consensus       103 a~~--~~~~~~~~l~~~Gad~v-i~p~--~~~~~~l~~~l~~  139 (153)
T d1id1a_         103 LAV--SDSKNLNKIKMVHPDII-LSPQ--LFGSEILARVLNG  139 (153)
T ss_dssp             EEC--SSGGGHHHHHTTCCSEE-ECHH--HHHHHHHHHHHTT
T ss_pred             EEE--cCHHHHHHHHHCCCCEE-ECHH--HHHHHHHHHHhCc
Confidence            665  34566666778899754 4452  3334455555443

>d1u6ka1 c.127.1.1 (A:2-283) F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) {Archaeon Methanopyrus kandleri [TaxId: 2320]}

class: Alpha and beta proteins (a/b)
fold: F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
superfamily: F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
family: F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
domain: F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)
species: Archaeon Methanopyrus kandleri [TaxId: 2320]

Probab=86.39  E-value=0.9  Score=32.03  Aligned_cols=60  Identities=12%  Similarity=0.148  Sum_probs=45.1

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHhcccCCCCEEEEEccCChHHHHHHHHcCCCceEeCCC
Q 029986           61 KNGYDIVISDVHMPDMDGFKLHEQVGLEMDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPI  121 (184)
Q Consensus        61 ~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~  121 (184)
                      .+.||.+|+=.-.+..-|-.-.+.+-+..++|.|+++...... ..++++..-.+|+.-|.
T Consensus        61 ~~~pDf~i~isPN~a~PGP~~ARE~l~~~giP~ivI~D~p~~k-~~d~~~~~gfGYIi~k~  120 (282)
T d1u6ka1          61 DFEPDFIVYGGPNPAAPGPSKAREMLADSEYPAVIIGDAPGLK-VKDEMEEQGLGYILVKP  120 (282)
T ss_dssp             HHCCSEEEEECSCTTSHHHHHHHHHHHTSSSCEEEEEEGGGGG-GHHHHHHTTCEEEEETT
T ss_pred             hcCCCEEEEECCCCCCCCcHHHHHHHHhcCCCEEEEcCCcchh-hHHHHHhcCCcEEEEec
Confidence            5779999987666666777767766555689999998766444 67888888888886554

>d1vhca_ c.1.10.1 (A:) Hypothetical protein HI0047 {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Aldolase
family: Class I aldolase
domain: Hypothetical protein HI0047
species: Haemophilus influenzae [TaxId: 727]

Probab=85.78  E-value=1.7  Score=30.07  Aligned_cols=97  Identities=15%  Similarity=0.177  Sum_probs=61.5

Q ss_pred             HHHHHHHhcCC-eEEEECCHHHHHHHHHh-cCCCccEEEEeCCCCCCCHHHHHHHhccc-CCCCEEEEEccCChHHHHHH
Q 029986           32 ILEKMLRKCLY-EVTKCNRAEIALDMLRM-SKNGYDIVISDVHMPDMDGFKLHEQVGLE-MDLPVIMMSVDGCTQDVMKG  108 (184)
Q Consensus        32 ~l~~~L~~~~~-~v~~~~~~~~~~~~l~~-~~~~~dlvilD~~l~~~~g~~l~~~l~~~-~~~~iIi~~~~~~~~~~~~a  108 (184)
                      .+.+.|++.+. -+....+.+++....+. .+.+..  .+.+.|...+.++.++.+++. ++ -++-..+=.+.+.+..+
T Consensus         6 ~~~~~l~~~~iipvlr~~~~~~~~~~~~al~~~Gi~--~iEitl~~~~a~~~I~~l~~~~p~-~~vGaGTV~~~~~~~~a   82 (212)
T d1vhca_           6 QIIEKLRELKIVPVIALDNADDILPLADTLAKNGLS--VAEITFRSEAAADAIRLLRANRPD-FLIAAGTVLTAEQVVLA   82 (212)
T ss_dssp             HHHHHHHHHCEEEEECCSSGGGHHHHHHHHHHTTCC--EEEEETTSTTHHHHHHHHHHHCTT-CEEEEESCCSHHHHHHH
T ss_pred             HHHHHHHHCCEEEEEeCCCHHHHHHHHHHHHHCCCC--EEEEeCCChhHHHHHHHHHhcCCC-ceEeeeecccHHHHHHH
Confidence            34444554443 34444455555544431 133444  556666677889999988643 44 35555666678899999


Q ss_pred             HHcCCCceEeCCCCHHHHHHHHHH
Q 029986          109 VTHGACNYLLKPIRIKELRNIWQH  132 (184)
Q Consensus       109 ~~~ga~~~l~kP~~~~~l~~~l~~  132 (184)
                      .++||+ |++.|....++.+..+.
T Consensus        83 ~~aGa~-FivSP~~~~~v~~~a~~  105 (212)
T d1vhca_          83 KSSGAD-FVVTPGLNPKIVKLCQD  105 (212)
T ss_dssp             HHHTCS-EEECSSCCHHHHHHHHH
T ss_pred             HhhCCc-EEECCCCCHHHHHHHHh
Confidence            999998 88888877777666553

>d1wbha1 c.1.10.1 (A:1-213) KDPG aldolase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Aldolase
family: Class I aldolase
domain: KDPG aldolase
species: Escherichia coli [TaxId: 562]

Probab=85.55  E-value=1.4  Score=30.61  Aligned_cols=62  Identities=11%  Similarity=0.071  Sum_probs=38.7

Q ss_pred             EEeCCCCCCCHHHHHHHhccc-CCCCEEEEEccCChHHHHHHHHcCCCceEeCCCCHHHHHHHHH
Q 029986           68 ISDVHMPDMDGFKLHEQVGLE-MDLPVIMMSVDGCTQDVMKGVTHGACNYLLKPIRIKELRNIWQ  131 (184)
Q Consensus        68 ilD~~l~~~~g~~l~~~l~~~-~~~~iIi~~~~~~~~~~~~a~~~ga~~~l~kP~~~~~l~~~l~  131 (184)
                      .+.+.|...+.++.++.+++. +++ ++-..+=.+.+.+..+.++||+ |++.|....++.+...
T Consensus        43 ~iEitl~tp~a~~~I~~l~~~~p~~-~vGaGTV~~~~~~~~a~~aGa~-FivSP~~~~~v~~~a~  105 (213)
T d1wbha1          43 VLNVTLRTECAVDAIRAIAKEVPEA-IVGAGTVLNPQQLAEVTEAGAQ-FAISPGLTEPLLKAAT  105 (213)
T ss_dssp             EEEEESCSTTHHHHHHHHHHHCTTS-EEEEESCCSHHHHHHHHHHTCS-CEEESSCCHHHHHHHH
T ss_pred             EEEEeCCChhHHHHHHHHHHHCCCC-eeeccccccHHHHHHHHHCCCc-EEECCCCCHHHHHHHH
Confidence            444444455677777777543 443 4455555667777788888887 6666776666655444

>d7reqb2 c.23.6.1 (B:476-638) Methylmalonyl-CoA mutase beta subunit, C-terminal domain {Propionibacterium freudenreichii, subsp. shermanii [TaxId: 1744]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: Cobalamin (vitamin B12)-binding domain
family: Cobalamin (vitamin B12)-binding domain
domain: Methylmalonyl-CoA mutase beta subunit, C-terminal domain
species: Propionibacterium freudenreichii, subsp. shermanii [TaxId: 1744]

Probab=83.06  E-value=1.2  Score=29.43  Aligned_cols=101  Identities=5%  Similarity=-0.050  Sum_probs=57.4

Q ss_pred             HHHHHHHHHHhcCCeEEE--ECCHHHHHHHHHhcCCCccEEEEeCCCCCC--CHHHHHHHhcccCCCCEEEEEcc-CChH
Q 029986           29 WLRILEKMLRKCLYEVTK--CNRAEIALDMLRMSKNGYDIVISDVHMPDM--DGFKLHEQVGLEMDLPVIMMSVD-GCTQ  103 (184)
Q Consensus        29 ~~~~l~~~L~~~~~~v~~--~~~~~~~~~~l~~~~~~~dlvilD~~l~~~--~g~~l~~~l~~~~~~~iIi~~~~-~~~~  103 (184)
                      ...-...+|..-|+++..  .-+..++.+....  ..+|++.+-.....-  -.-++++.|+... ..++++... ....
T Consensus        52 ra~f~~n~f~~gGfev~~~~~~~~~e~v~aa~~--~~a~vvvicssd~~y~~~~~~~~~aLk~ag-~~~~vlaGg~~~~~  128 (163)
T d7reqb2          52 REGFSSPVWHIAGIDTPQVEGGTTAEIVEAFKK--SGAQVADLCSSAKVYAQQGLEVAKALKAAG-AKALYLSGAFKEFG  128 (163)
T ss_dssp             HHHHHHHHHHHTTCBCCEEESCCHHHHHHHHHH--HTCSEEEEECCHHHHHHHHHHHHHHHHHTT-CSEEEEESCGGGGG
T ss_pred             HHHHHHHHHHccCeeeccCCCCCcHHHHHHHHh--CCCCEEEEecCccchHHHHHHHHHHHHhcc-cceeEEEecCCCcc
Confidence            444466778877887653  2245666666653  347777664321111  1224566665432 344444433 3334


Q ss_pred             HHHHHHHcCCCceEeCCCCHHHHHHHHHH
Q 029986          104 DVMKGVTHGACNYLLKPIRIKELRNIWQH  132 (184)
Q Consensus       104 ~~~~a~~~ga~~~l~kP~~~~~l~~~l~~  132 (184)
                      ....+.+.|+++|+..-.+.-+..+.+..
T Consensus       129 d~~~l~~aGVd~~i~~G~d~~~~l~~l~~  157 (163)
T d7reqb2         129 DDAAEAEKLIDGRLFMGMDVVDTLSSTLD  157 (163)
T ss_dssp             GGHHHHHHHCCEEECTTCCHHHHHHHHHH
T ss_pred             cHHHHHhCCCCeEecCCCcHHHHHHHHHH
Confidence            45567789999999888776666554443

>d1ws6a1 c.66.1.46 (A:15-185) Methyltransferase TTHA0928 {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: YhhF-like
domain: Methyltransferase TTHA0928
species: Thermus thermophilus [TaxId: 274]

Probab=82.43  E-value=2.7  Score=27.67  Aligned_cols=55  Identities=16%  Similarity=0.280  Sum_probs=40.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCeE-EEECCHHHHHHHHHhcCCCccEEEEeC
Q 029986           17 GLRVLVVDDDPIWLRILEKMLRKCLYEV-TKCNRAEIALDMLRMSKNGYDIVISDV   71 (184)
Q Consensus        17 ~~~Ilivdd~~~~~~~l~~~L~~~~~~v-~~~~~~~~~~~~l~~~~~~~dlvilD~   71 (184)
                      +.++..+|-++...+.++.-++..+... ....+....+.........+|+||+|-
T Consensus        63 ga~vv~vD~~~~a~~~~~~N~~~~~~~~~v~~~~~d~~~~~~~~~~~~fD~If~DP  118 (171)
T d1ws6a1          63 GWEAVLVEKDPEAVRLLKENVRRTGLGARVVALPVEVFLPEAKAQGERFTVAFMAP  118 (171)
T ss_dssp             TCEEEEECCCHHHHHHHHHHHHHHTCCCEEECSCHHHHHHHHHHTTCCEEEEEECC
T ss_pred             cchhhhcccCHHHHhhhhHHHHhhccccceeeeehhcccccccccCCccceeEEcc
Confidence            3478889999999999998888766542 345566666555544445699999984

>d1qapa1 c.1.17.1 (A:130-296) Quinolinic acid phosphoribosyltransferase (Nicotinate-nucleotide pyrophosphorylase, NadC), C-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Nicotinate/Quinolinate PRTase C-terminal domain-like
family: NadC C-terminal domain-like
domain: Quinolinic acid phosphoribosyltransferase (Nicotinate-nucleotide pyrophosphorylase, NadC), C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=82.39  E-value=4.9  Score=26.49  Aligned_cols=91  Identities=14%  Similarity=0.120  Sum_probs=57.4

Q ss_pred             eEEEEeCCHHHHHHHHHHHHhc-----CC-eEEEECCHHHHHHHHHhcCCCccEEEEeCCCCCCCHHHHHHHhcccCCCC
Q 029986           19 RVLVVDDDPIWLRILEKMLRKC-----LY-EVTKCNRAEIALDMLRMSKNGYDIVISDVHMPDMDGFKLHEQVGLEMDLP   92 (184)
Q Consensus        19 ~Ilivdd~~~~~~~l~~~L~~~-----~~-~v~~~~~~~~~~~~l~~~~~~~dlvilD~~l~~~~g~~l~~~l~~~~~~~   92 (184)
                      .|||=|.+-.....+...+...     .. ....+.+.+++.+.+.   .++|+|++|-.-|    -++.+.++....-.
T Consensus        52 ~iLIkdNHi~~~~~~~~~~~~~~~~~~~~~IeVEv~~~~~~~~a~~---~g~diImLDN~~p----e~~~~av~~i~~~~  124 (167)
T d1qapa1          52 AFLIKENHIIASGSVRQAVEKAFWLHPDVPVEVEVENLDELDDALK---AGADIIMLDNFNT----DQMREAVKRVNGQA  124 (167)
T ss_dssp             CEEECHHHHHHHSSHHHHHHHHHHHSTTSCEEEEESSHHHHHHHHH---TTCSEEEESSCCH----HHHHHHHHTTCTTC
T ss_pred             eeEechhhHhhhhhhhhhhHHHhhcCCCceEEEecCcHHHHHHHHh---cCCcEEEecCCCH----HHHHHHHHhcCCce
Confidence            3777777766555555555431     22 3357889999988875   4589999995323    23333333222223


Q ss_pred             EEEEEccCChHHHHHHHHcCCCceE
Q 029986           93 VIMMSVDGCTQDVMKGVTHGACNYL  117 (184)
Q Consensus        93 iIi~~~~~~~~~~~~a~~~ga~~~l  117 (184)
                      .+-.+..-+.+.+.+....|+| ||
T Consensus       125 ~lEaSGgI~~~ni~~ya~~GVD-~I  148 (167)
T d1qapa1         125 RLEVSGNVTAETLREFAETGVD-FI  148 (167)
T ss_dssp             CEEECCCSCHHHHHHHHHTTCS-EE
T ss_pred             EEEEeCCCCHHHHHHHHHcCCC-EE
Confidence            3445677778888888889988 55